Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 137 of 206
Found at i:41893491 original size:18 final size:18
Alignment explanation
Indices: 41893470--41893504 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41893460 TGGCTTCTTG
* *
41893470 CCCTTACTACTTTTCTCA
1 CCCTTACAACTTCTCTCA
41893488 CCCTTACAACTTCTCTC
1 CCCTTACAACTTCTCTC
41893505 TTCCACGTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.43, G:0.00, T:0.40
Consensus pattern (18 bp):
CCCTTACAACTTCTCTCA
Found at i:41899567 original size:13 final size:13
Alignment explanation
Indices: 41899549--41899595 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
41899539 GGTTGGTTTG
41899549 ATTAACTGATTCT
1 ATTAACTGATTCT
41899562 ATTAACTGATT-T
1 ATTAACTGATTCT
** *
41899574 GACCAATTGATTCT
1 -ATTAACTGATTCT
41899588 ATTAACTG
1 ATTAACTG
41899596 TTTATTTAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
12 1 0.04
13 24 0.92
14 1 0.04
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (13 bp):
ATTAACTGATTCT
Found at i:41900111 original size:31 final size:31
Alignment explanation
Indices: 41900075--41900141 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
41900065 AGAAATAGAT
* * *
41900075 ACATGTGGCAAATGGAGCAATTTTTTAGCAA
1 ACATGTCGCAAAAGGAGCAAATTTTTAGCAA
* *
41900106 GCATGTCGCAAAAGGAGTAAATTTTTAGCAA
1 ACATGTCGCAAAAGGAGCAAATTTTTAGCAA
41900137 ACATG
1 ACATG
41900142 GTCAGATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (31 bp):
ACATGTCGCAAAAGGAGCAAATTTTTAGCAA
Found at i:41901896 original size:17 final size:17
Alignment explanation
Indices: 41901861--41901898 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
41901851 TTAAACTTAT
41901861 AAAATAAAATATGTAATA
1 AAAATAAAATATG-AATA
41901879 AAAATAAACATATG-ATA
1 AAAATAAA-ATATGAATA
41901896 AAA
1 AAA
41901899 GTGTGGTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 8 0.42
19 5 0.26
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (17 bp):
AAAATAAAATATGAATA
Found at i:41903736 original size:259 final size:259
Alignment explanation
Indices: 41903277--41903796 Score: 848
Period size: 259 Copynumber: 2.0 Consensus size: 259
41903267 ATATTTTAGC
* *
41903277 TTAATTTGCATTGATCTTTGAATTGTTGAAATACAACTGAGTTTATTACTTAGGTTACAGTTTTG
1 TTAATTTGCATTGATCTTTGAATTGTTAAAATACAACTGAGTTTATTACTCAGGTTACAGTTTTG
* ** *
41903342 TTTTTCGTGCGCAGATTAGGTTAATACGTGATCCTGAATAACAACATCAGCATCCAGGCATAATT
66 TTTTTCATAAGCAGATTAGGTTAATACGTGATCCTGAATAACAACATCAGCATCCAGGCATAATC
* *
41903407 TGGGACTCAATAAAGTTGGTGAAATTATTGTGTTAGTTAATTGGCATGCACCTAGTGGAGTCCTT
131 TAGGACTCAATAAAGTTGGTGAAATTATTGTGTTAGTTAATTGGCAAGCACCTAGTGGAGTCCTT
*
41903472 TATATTTTTCTATATTGTGATGTTGAGTAGAATTTGTTAATGACATGTAATTATGTTTTGCAAG
196 TATATTTTTCTATATTGTGATGTTAAGTAGAATTTGTTAATGACATGTAATTATGTTTTGCAAG
*
41903536 TTAATTTGCATTGATCTTTGAATTGTTAAAATACAACTGAGTTTATTACTCATGTTAC-GATTTT
1 TTAATTTGCATTGATCTTTGAATTGTTAAAATACAACTGAGTTTATTACTCAGGTTACAG-TTTT
* * *
41903600 G-TTTTCTATAAGCA-AGTTAGGTTAATAGGTGATCCTGGATATCAACATCAGCATCCAGGCATA
65 GTTTTTC-ATAAGCAGA-TTAGGTTAATACGTGATCCTGAATAACAACATCAGCATCCAGGCATA
* *
41903663 ATCTAGGACTCAATAAAGTTGGTGAAATTATTGTGTTAGTTAATTGGCAAGTACTTAGTGGAGTC
128 ATCTAGGACTCAATAAAGTTGGTGAAATTATTGTGTTAGTTAATTGGCAAGCACCTAGTGGAGTC
*
41903728 CTTTATATTTTTCTATATTGTGATGTTAAGTAGAATTTGTTAATGGCATGTAATTATGTTTTGCA
193 CTTTATATTTTTCTATATTGTGATGTTAAGTAGAATTTGTTAATGACATGTAATTATGTTTTGCA
41903793 AG
258 AG
41903795 TT
1 TT
41903797 TTATAGTTAG
Statistics
Matches: 242, Mismatches: 16, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
258 7 0.03
259 235 0.97
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (259 bp):
TTAATTTGCATTGATCTTTGAATTGTTAAAATACAACTGAGTTTATTACTCAGGTTACAGTTTTG
TTTTTCATAAGCAGATTAGGTTAATACGTGATCCTGAATAACAACATCAGCATCCAGGCATAATC
TAGGACTCAATAAAGTTGGTGAAATTATTGTGTTAGTTAATTGGCAAGCACCTAGTGGAGTCCTT
TATATTTTTCTATATTGTGATGTTAAGTAGAATTTGTTAATGACATGTAATTATGTTTTGCAAG
Found at i:41910211 original size:17 final size:17
Alignment explanation
Indices: 41910191--41910223 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
41910181 AATTAGAAAA
41910191 AAATTAAACCTCCAAAG
1 AAATTAAACCTCCAAAG
41910208 AAATTAAACCTCCAAA
1 AAATTAAACCTCCAAA
41910224 TATGGCTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.24, G:0.03, T:0.18
Consensus pattern (17 bp):
AAATTAAACCTCCAAAG
Found at i:41911234 original size:14 final size:14
Alignment explanation
Indices: 41911215--41911241 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41911205 ATCATGAAGG
41911215 TAAAAACACTTAAA
1 TAAAAACACTTAAA
41911229 TAAAAACACTTAA
1 TAAAAACACTTAA
41911242 GCAAGTTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.15, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAAAACACTTAAA
Found at i:41945774 original size:20 final size:19
Alignment explanation
Indices: 41945715--41945774 Score: 52
Period size: 20 Copynumber: 3.2 Consensus size: 19
41945705 TTTTTTTAAT
* *
41945715 AAATTCAAAAAATA-AGAA
1 AAATGCAAAAAATATAAAA
* *
41945733 AAATG-AAAAAATAATTAGA
1 AAATGCAAAAAAT-ATAAAA
41945752 AAATAGCAAAAAATATAAAA
1 AAAT-GCAAAAAATATAAAA
41945772 AAA
1 AAA
41945775 GTTAGAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
17 7 0.22
18 5 0.16
19 5 0.16
20 8 0.25
21 7 0.22
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (19 bp):
AAATGCAAAAAATATAAAA
Found at i:41945801 original size:29 final size:28
Alignment explanation
Indices: 41945731--41945786 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 28
41945721 AAAAAATAAG
41945731 AAAAATGAAAAAATAATTAGAAAATAGCA
1 AAAAAT-AAAAAATAATTAGAAAATAGCA
41945760 AAAAATATAAAAA-AAGTTAGAAAATAG
1 AAAAATA-AAAAATAA-TTAGAAAATAG
41945787 GAAAGTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.18
Consensus pattern (28 bp):
AAAAATAAAAAATAATTAGAAAATAGCA
Found at i:41945973 original size:27 final size:28
Alignment explanation
Indices: 41945906--41945973 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
41945896 ATAACTTAAT
* **
41945906 TCACAAATTGGTACTTAAATTTTTTTTG
1 TCACAAGTTGGTACTTAAACATTTTTTG
*
41945934 TCACAAG-TAGTACTTAAACCATTTTTT-
1 TCACAAGTTGGTACTTAAA-CATTTTTTG
41945961 TC-CAAGTTGGTAC
1 TCACAAGTTGGTAC
41945974 CTCTATTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
26 4 0.12
27 17 0.52
28 12 0.36
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (28 bp):
TCACAAGTTGGTACTTAAACATTTTTTG
Found at i:41946075 original size:30 final size:30
Alignment explanation
Indices: 41946008--41946085 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
41945998 TGTTTTAAAA
41946008 AAATTAGTACTTAAACTATATATTTTTCTC
1 AAATTAGTACTTAAACTATATATTTTTCTC
** * * *
41946038 ATTTTAGTACTTAAA-TATATTTTTTTGTT
1 AAATTAGTACTTAAACTATATATTTTTCTC
*
41946067 AGAATTAGTACCTAAACTA
1 A-AATTAGTACTTAAACTA
41946086 GTTTCTTTTC
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 12 0.32
30 24 0.63
31 2 0.05
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.47
Consensus pattern (30 bp):
AAATTAGTACTTAAACTATATATTTTTCTC
Found at i:41947280 original size:2 final size:2
Alignment explanation
Indices: 41947270--41947318 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
41947260 TTTCAAAAAA
* * *
41947270 AT AT GT AT AT AT AT AT AT AT AT AT AC A- AT ACT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
41947312 AT AT AT A
1 AT AT AT A
41947319 CAAAAATAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:41953934 original size:14 final size:14
Alignment explanation
Indices: 41953915--41953941 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41953905 AACACATAAT
41953915 CATATAGAGCTCAC
1 CATATAGAGCTCAC
41953929 CATATAGAGCTCA
1 CATATAGAGCTCA
41953942 GATGTAACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (14 bp):
CATATAGAGCTCAC
Found at i:41977332 original size:50 final size:50
Alignment explanation
Indices: 41977224--41977470 Score: 221
Period size: 50 Copynumber: 4.8 Consensus size: 50
41977214 ATTTGGGTAA
* * *
41977224 AGAGATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGAAACTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CG--A-TATG
* *
41977280 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATG
* *
41977330 AGAGGTCCC-TCGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATG
1 AGAGGTCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACCGATATG
** * * * * *
41977380 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATT-G-ACAGTACAGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-ATATG
* ** * * *
41977429 AAACATCCCATGTAAGACCATATCTGGGATATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
41977471 TGTTATTATC
Statistics
Matches: 164, Mismatches: 22, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
48 2 0.01
49 39 0.24
50 79 0.48
51 3 0.02
53 1 0.01
55 1 0.01
56 39 0.24
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATG
Found at i:41988147 original size:59 final size:60
Alignment explanation
Indices: 41988037--41988151 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 60
41988027 CGAAAAAAAA
41988037 TTCGAATTTCGAGTTAAACGAATTGAGTTATTCGAGTTATTCGAATCAACTCGAATTTTTTT
1 TTCGAATTTCGAGTTAAACGAATTGAGTTATTCGA--TATTCGAATCAACTCGAATTTTTTT
* *
41988099 TTCGAATTTCGAGTTCGAATCGAGTTGAGTT-TTCGA-ATTCGAAT-AACTCGAAT
1 TTCGAATTTCGAGTT--AAACGAATTGAGTTATTCGATATTCGAATCAACTCGAAT
41988152 AATTCGAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
59 9 0.18
60 8 0.16
62 15 0.31
63 5 0.10
64 12 0.24
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (60 bp):
TTCGAATTTCGAGTTAAACGAATTGAGTTATTCGATATTCGAATCAACTCGAATTTTTTT
Found at i:41988163 original size:9 final size:9
Alignment explanation
Indices: 41988134--41988170 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
41988124 TGAGTTTTCG
41988134 AATTCGAAT
1 AATTCGAAT
*
41988143 AACTCGAAT
1 AATTCGAAT
41988152 AATTCGAAT
1 AATTCGAAT
*
41988161 AATTAGAAT
1 AATTCGAAT
41988170 A
1 A
41988171 TCAAAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:41988418 original size:30 final size:31
Alignment explanation
Indices: 41988384--41988443 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
41988374 AAACCTTTTA
*
41988384 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
41988414 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
41988444 TCTCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:41989214 original size:10 final size:10
Alignment explanation
Indices: 41989201--41989226 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
41989191 CTCGAAAATT
41989201 TTCGATTCAA
1 TTCGATTCAA
41989211 TTCGATTCAA
1 TTCGATTCAA
41989221 TTCGAT
1 TTCGAT
41989227 CGAATGCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (10 bp):
TTCGATTCAA
Found at i:41993373 original size:27 final size:27
Alignment explanation
Indices: 41993343--41993420 Score: 138
Period size: 27 Copynumber: 2.9 Consensus size: 27
41993333 GTTATAACAG
41993343 TCATTTTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
* *
41993370 TCATTTTATCCTATAGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
41993397 TCATTTTACCCTATGGGGGTATTT
1 TCATTTTACCCTATGGGGGTATTT
41993421 TGGTGCAGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.44
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGA
Found at i:41995861 original size:21 final size:21
Alignment explanation
Indices: 41995833--41995878 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
41995823 CTAATAAGAT
41995833 AAAA-TTATAAT-AAAAACTTC
1 AAAATTTATAATCAAAAAC-TC
* *
41995853 AAAATTTATTATCAAACACTC
1 AAAATTTATAATCAAAAACTC
41995874 AAAAT
1 AAAAT
41995879 CTGCATGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 4 0.18
21 13 0.59
22 5 0.23
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAATTTATAATCAAAAACTC
Found at i:41996271 original size:21 final size:21
Alignment explanation
Indices: 41996247--41996287 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41996237 CATTTTGTTT
*
41996247 GTGTTTGTGTTAATTTGCTTG
1 GTGTTTGTGTTAATTAGCTTG
* *
41996268 GTGTTTTTTTTAATTAGCTT
1 GTGTTTGTGTTAATTAGCTT
41996288 TCTTCACTAG
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:0.12, C:0.05, G:0.22, T:0.61
Consensus pattern (21 bp):
GTGTTTGTGTTAATTAGCTTG
Found at i:41996390 original size:17 final size:18
Alignment explanation
Indices: 41996352--41996390 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
41996342 ATTATTGCTC
*
41996352 TTATGTGTATTGTATTGC
1 TTATGTGTATTGTATTGA
41996370 TTATGTGTATT-TATTGA
1 TTATGTGTATTGTATTGA
41996387 TTAT
1 TTAT
41996391 TTGTCGTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.21, C:0.03, G:0.18, T:0.59
Consensus pattern (18 bp):
TTATGTGTATTGTATTGA
Found at i:41998254 original size:19 final size:19
Alignment explanation
Indices: 41998230--41998276 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
41998220 AACGTCTCTT
*
41998230 TTTGCATT-CATTTCATACA
1 TTTGCATTACATTACAT-CA
41998249 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
41998268 TATGCATTA
1 TTTGCATTA
41998277 AAGTCCACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:42001023 original size:23 final size:26
Alignment explanation
Indices: 42000997--42001046 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 26
42000987 ACGGCAATAG
42000997 AGGACAAAAAA-AAAA-AAA-AACAA
1 AGGACAAAAAACAAAACAAAGAACAA
42001020 AGGACAAAAAACAAAACAAAGAACAA
1 AGGACAAAAAACAAAACAAAGAACAA
42001046 A
1 A
42001047 ACTAAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 11 0.46
24 4 0.17
25 3 0.12
26 6 0.25
ACGTcount: A:0.78, C:0.12, G:0.10, T:0.00
Consensus pattern (26 bp):
AGGACAAAAAACAAAACAAAGAACAA
Found at i:42001030 original size:19 final size:19
Alignment explanation
Indices: 42001006--42001047 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
42000996 GAGGACAAAA
*
42001006 AAAAAAAAAAACAAAGGAC
1 AAAAAAAAAAACAAAGAAC
*
42001025 AAAAAACAAAACAAAGAAC
1 AAAAAAAAAAACAAAGAAC
42001044 AAAA
1 AAAA
42001048 CTAAAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.81, C:0.12, G:0.07, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAACAAAGAAC
Found at i:42001529 original size:51 final size:52
Alignment explanation
Indices: 42001414--42001550 Score: 188
Period size: 52 Copynumber: 2.7 Consensus size: 52
42001404 AAGGAGAAGG
* *
42001414 GACCAAGGTAAAAACCCGCAAAGGGCGCTTTAAGTCCTAAAAAAAAAGAGGC
1 GACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAAAAGAGGC
* *
42001466 GACCAAGGTGAAAACCCGCAAAGGGCGCTTTGATTCCTAAAAAAAAGGAGAG-
1 GACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAAAAGAG-GC
** *
42001518 G-CCAAGGTGAAAACCCAAAAAGGGCGCCTTGAG
1 GACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAG
42001551 AACAAAGGGG
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
51 28 0.37
52 47 0.62
53 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.26, T:0.12
Consensus pattern (52 bp):
GACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAAAAGAGGC
Found at i:42002486 original size:46 final size:47
Alignment explanation
Indices: 42002418--42002529 Score: 118
Period size: 51 Copynumber: 2.3 Consensus size: 47
42002408 CATTATGGCG
* *
42002418 AATCTTTTTTTACCTGGCGTTGCAGT-AGATTAAAGCTGAAGGCAACA
1 AATC-TTTTTTCCCTAGCGTTGCAGTAAGATTAAAGCTGAAGGCAACA
* * * *
42002465 AATCTTTTTTCCCTAGTGTTGCAGTGGAACAGATTAAAGCTGAAGGTAGCG
1 AATCTTTTTTCCCTAGCGTTGCAGT---A-AGATTAAAGCTGAAGGCAACA
42002516 AATCTTTTTTCCCT
1 AATCTTTTTTCCCT
42002530 GGCTGTAACA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
46 18 0.33
47 4 0.07
51 32 0.59
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (47 bp):
AATCTTTTTTCCCTAGCGTTGCAGTAAGATTAAAGCTGAAGGCAACA
Found at i:42004002 original size:27 final size:27
Alignment explanation
Indices: 42003964--42004015 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
42003954 TGCAAAAAGA
* *
42003964 GGTTACTAAGTGCTGATTCCCCCAAGG
1 GGTTACTAAGTGCTGAATCCACCAAGG
42003991 GGTTACTAAGTGCTGAATCCACCAA
1 GGTTACTAAGTGCTGAATCCACCAA
42004016 ATAACGGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (27 bp):
GGTTACTAAGTGCTGAATCCACCAAGG
Found at i:42014116 original size:51 final size:51
Alignment explanation
Indices: 42014022--42014349 Score: 444
Period size: 51 Copynumber: 6.5 Consensus size: 51
42014012 GGGTGTTACA
* * *
42014022 CTGGCGTTGGAGTGGAACAGATTAAAGCTGTAGGCAGCAAATCTTATTTCC
1 CTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCC
* * * * *
42014073 CTGGTGTCGCAGTGAAATAGATTAAAGCTGAAGGCAACGAATCTTATTTCC
1 CTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCC
* * *
42014124 TTGGCGTTACAGTGGAACAAATTAAAGCTGAAGGCAGCGAAT-TT-TTTCC
1 CTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCC
* * * *
42014173 TTGGCGTTGTAGTGGAAAAGATCAAAGCTGAAGGCAGCGAATCTTATTTCC
1 CTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCC
* ** * *
42014224 CTAGTTTTGCATTGGAACAGATTAAAGCTTAAGGCAGCGAATCTTATTTCC
1 CTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCC
* *
42014275 CTGGCATTGCAGTGGAACAGATTAAAGCTTAAGGCAGCGAATCTTATTTCC
1 CTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCC
42014326 CTGGCGTTGCAGTGGAACAGATTA
1 CTGGCGTTGCAGTGGAACAGATTA
42014350 TGGCTACAAA
Statistics
Matches: 240, Mismatches: 35, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
49 42 0.17
50 4 0.02
51 194 0.81
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.28
Consensus pattern (51 bp):
CTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATTTCC
Found at i:42014299 original size:151 final size:153
Alignment explanation
Indices: 42014022--42014347 Score: 458
Period size: 151 Copynumber: 2.1 Consensus size: 153
42014012 GGGTGTTACA
* * * *
42014022 CTGGCGTTGGAGTGGAACAGATTAAAGCTGTAGGCAGCAAATCTTATTTCCCTGGTGTCGCAGTG
1 CTGGCGTTGCAGTGGAACAGATCAAAGCTGAAGGCAGCAAATCTTATTTCCCTAGTGTCGCAGTG
* * *
42014087 AAATAGATTAAAGCTGAAGGCAACGAATCTTATTTCCTTGGCGTTACAGTGGAACAAATTAAAGC
66 AAACAGATTAAAGCTGAAGGCAACGAATCTTATTTCCCTGGCATTACAGTGGAACAAATTAAAGC
42014152 TGAAGGCAGCGAAT-TT-TTTCC
131 TGAAGGCAGCGAATCTTATTTCC
* * * * * * *
42014173 TTGGCGTTGTAGTGGAAAAGATCAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGTTTTGCATTG
1 CTGGCGTTGCAGTGGAACAGATCAAAGCTGAAGGCAGCAAATCTTATTTCCCTAGTGTCGCAGTG
* * * * *
42014238 GAACAGATTAAAGCTTAAGGCAGCGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGC
66 AAACAGATTAAAGCTGAAGGCAACGAATCTTATTTCCCTGGCATTACAGTGGAACAAATTAAAGC
*
42014303 TTAAGGCAGCGAATCTTATTTCC
131 TGAAGGCAGCGAATCTTATTTCC
42014326 CTGGCGTTGCAGTGGAACAGAT
1 CTGGCGTTGCAGTGGAACAGAT
42014348 TATGGCTACA
Statistics
Matches: 151, Mismatches: 22, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
151 125 0.83
152 2 0.01
153 24 0.16
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.28
Consensus pattern (153 bp):
CTGGCGTTGCAGTGGAACAGATCAAAGCTGAAGGCAGCAAATCTTATTTCCCTAGTGTCGCAGTG
AAACAGATTAAAGCTGAAGGCAACGAATCTTATTTCCCTGGCATTACAGTGGAACAAATTAAAGC
TGAAGGCAGCGAATCTTATTTCC
Found at i:42014513 original size:194 final size:194
Alignment explanation
Indices: 42014262--42014634 Score: 570
Period size: 194 Copynumber: 1.9 Consensus size: 194
42014252 TTAAGGCAGC
* *
42014262 GAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTTAAGGCAGCGAATCTTATTTCCC
1 GAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTGAAGCCAGCGAATCTTATTTCCC
* ** * * *
42014327 T-GGCGTTGCAGTGGAACAGATTATGGCTACAAATTATGGTGGATCTTATCTTTCTGAAGTTGCA
66 TAGG-ATTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTGAAGTTGCA
*
42014391 GTGGAGCAGATTGAAGCCACC-ATCCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAG
130 GTGAAGCAGATTGAAGCCACCAATCC-TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAG
42014455 T
194 T
* * * *
42014456 GAATCTTATTTCTCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGCCAGTGAATCTTTTTTCCC
1 GAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTGAAGCCAGCGAATCTTATTTCCC
* * *
42014521 TAGGATTGTAGTGGAATATATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTGAAGTTGCAG
66 TAGGATTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTGAAGTTGCAG
42014586 TGAAGCAGATTGAAGCCACCAATCCTATCTCCCTGAAGTTGCAGTGGAG
131 TGAAGCAGATTGAAGCCACCAATCCTATCTCCCTGAAGTTGCAGTGGAG
42014635 TGGATTAAAA
Statistics
Matches: 161, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
194 155 0.96
195 6 0.04
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (194 bp):
GAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTGAAGCCAGCGAATCTTATTTCCC
TAGGATTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGAATCTTATCTTCCTGAAGTTGCAG
TGAAGCAGATTGAAGCCACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAGT
Found at i:42014534 original size:51 final size:51
Alignment explanation
Indices: 42014445--42014548 Score: 129
Period size: 51 Copynumber: 2.0 Consensus size: 51
42014435 GTGGAGCAGA
* *
42014445 CTGAAGACAGTGAATCTTATTTCTCTGGCGTTGCAGTGGAACAGATTAAAG
1 CTGAAGACAGTGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAG
* * * * *
42014496 CTGAAGCCAGTGAATCTTTTTTCCCTAGG-ATTGTAGTGGAATATATTAAAG
1 CTGAAGACAGTGAATCTTATTTCCCT-GGCATTGCAGTGGAACAGATTAAAG
42014547 CT
1 CT
42014549 ACAAATTATG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 43 0.96
52 2 0.04
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (51 bp):
CTGAAGACAGTGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAG
Found at i:42015590 original size:16 final size:17
Alignment explanation
Indices: 42015555--42015590 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
42015545 GGGATCTGAG
*
42015555 TTTGATTTTTTTTCTCT
1 TTTGATTATTTTTCTCT
42015572 TTTGATTATTTTTCT-T
1 TTTGATTATTTTTCTCT
42015588 TTT
1 TTT
42015591 CGTTTCCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.08, C:0.08, G:0.06, T:0.78
Consensus pattern (17 bp):
TTTGATTATTTTTCTCT
Found at i:42016704 original size:21 final size:21
Alignment explanation
Indices: 42016680--42016720 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
42016670 CATTTTGTTT
*
42016680 GTGTTTGTGTTAATTTGCTTG
1 GTGTTTGTGTTAATTAGCTTG
* *
42016701 GTGTTTTTTTTAATTAGCTT
1 GTGTTTGTGTTAATTAGCTT
42016721 TCTTCACTAG
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:0.12, C:0.05, G:0.22, T:0.61
Consensus pattern (21 bp):
GTGTTTGTGTTAATTAGCTTG
Found at i:42016823 original size:17 final size:18
Alignment explanation
Indices: 42016785--42016823 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
42016775 ATTATTACTC
*
42016785 TTATGTGTATTGTATTGC
1 TTATGTGTATTGTATTGA
42016803 TTATGTGTATT-TATTGA
1 TTATGTGTATTGTATTGA
42016820 TTAT
1 TTAT
42016824 TTGACCTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.21, C:0.03, G:0.18, T:0.59
Consensus pattern (18 bp):
TTATGTGTATTGTATTGA
Found at i:42019038 original size:18 final size:18
Alignment explanation
Indices: 42019012--42019051 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
42019002 ATTTCGTTCC
*
42019012 ATATCATTTGTCACTTCA
1 ATATAATTTGTCACTTCA
*
42019030 ATATAATTTGTCATTTCA
1 ATATAATTTGTCACTTCA
42019048 ATAT
1 ATAT
42019052 CATTATCTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.47
Consensus pattern (18 bp):
ATATAATTTGTCACTTCA
Found at i:42023229 original size:43 final size:43
Alignment explanation
Indices: 42023181--42023489 Score: 397
Period size: 43 Copynumber: 7.2 Consensus size: 43
42023171 TTATAGAAAT
* *
42023181 AAACGCCGCTAAAGGTCGTGTTCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCAC
* ** *
42023224 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCACTTTTTTCAA
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCAC
* * *
42023267 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCACTTTTTTCGA-
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGC-TTTTCCCAC
* *
42023310 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTTTCGA-
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGC-TTTTCCCAC
* **
42023353 AAACGCCGCTAAAGGCTATGTTCTTTAGCGGCGCTTTTCCCGT
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCAC
* *
42023396 AAACGCCGTTAAAGGCCATGTTCTTTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCAC
* * * *
42023439 AAACGTCGTTAAAGGTCATGTGCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCAC
*
42023482 AAATGCCG
1 AAACGCCG
42023490 TCATTGTTTG
Statistics
Matches: 240, Mismatches: 24, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
42 5 0.02
43 229 0.95
44 6 0.03
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCAC
Found at i:42023290 original size:86 final size:86
Alignment explanation
Indices: 42023181--42023489 Score: 440
Period size: 86 Copynumber: 3.6 Consensus size: 86
42023171 TTATAGAAAT
* *
42023181 AAACGCCGCTAAAGGTCGTGTTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGGCCATGTT
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGGCCATGTT
*
42023246 CTTTAGCGGCACTTTTTTCAA
66 CTTTAGCGGCGCTTTTTTCAA
* * *
42023267 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCACTTTTTTCGA-AAACGCCGCTAAAGGCCATGT
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGC-TTTTCCCACAAACGCCGCTAAAGGCCATGT
*
42023331 TCTTTAGCGGCGCTTTTTTCGA
65 TCTTTAGCGGCGCTTTTTTCAA
* ** *
42023353 AAACGCCGCTAAAGGCTATGTTCTTTAGCGGCGCTTTTCCCGTAAACGCCGTTAAAGGCCATGTT
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGGCCATGTT
* *
42023418 CTTTAGCGGCGCTTTTCTCAC
66 CTTTAGCGGCGCTTTTTTCAA
* * * * *
42023439 AAACGTCGTTAAAGGTCATGTGCTTTAGCGGCGCTTTTCCCACAAATGCCG
1 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCACAAACGCCG
42023490 TCATTGTTTG
Statistics
Matches: 197, Mismatches: 24, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
85 5 0.03
86 186 0.94
87 6 0.03
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (86 bp):
AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGGCCATGTT
CTTTAGCGGCGCTTTTTTCAA
Found at i:42024184 original size:17 final size:17
Alignment explanation
Indices: 42024162--42024221 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
42024152 ATATATTTTA
42024162 AAATTATTAAGTTATGT
1 AAATTATTAAGTTATGT
** *
42024179 AAATTATGCGAGTTGT-T
1 AAATTAT-TAAGTTATGT
*
42024196 AAGTTATTAAGTTATGT
1 AAATTATTAAGTTATGT
*
42024213 AAGTTATTA
1 AAATTATTA
42024222 TGTGAATTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
16 5 0.15
17 24 0.71
18 5 0.15
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.45
Consensus pattern (17 bp):
AAATTATTAAGTTATGT
Found at i:42024207 original size:34 final size:36
Alignment explanation
Indices: 42024165--42024248 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 36
42024155 TATTTTAAAA
* *
42024165 TTATTAAGTTATGTAA-ATTATGCGAGTTGT-TAAG
1 TTATTAAGTTATGTAATATTATGCGAATTATATAAG
*
42024199 TTATTAAGTTATGTAAGTTATTATGTGAATTATATAAG
1 TTATTAAGTTATGTAA--TATTATGCGAATTATATAAG
42024237 TTATTAAGTTAT
1 TTATTAAGTTAT
42024249 ATGGTATGAC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
34 16 0.37
37 11 0.26
38 16 0.37
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.48
Consensus pattern (36 bp):
TTATTAAGTTATGTAATATTATGCGAATTATATAAG
Found at i:42024244 original size:46 final size:46
Alignment explanation
Indices: 42024189--42024345 Score: 145
Period size: 46 Copynumber: 3.3 Consensus size: 46
42024179 AAATTATGCG
*
42024189 AGTTGTTAAGTTATTAAGTTATGTAAGTTATTATGTGAATTATATA
1 AGTTATTAAGTTATTAAGTTATGTAAGTTATTATGTGAATTATATA
* * * * * *
42024235 AGTTATTAAGTTA-TATGGTATGACATATATATATGTATTATGTAAATTATGTG
1 AGTTATTAAGTTATTA-AGT-T---ATGTA-A-GT-TATTATGTGAATTATATA
* * *
42024288 AGTTGTTAAGTTGTTCAGTTATGTAAGTTATTATGTGAATTATATA
1 AGTTATTAAGTTATTAAGTTATGTAAGTTATTATGTGAATTATATA
42024334 AGTTATTAAGTT
1 AGTTATTAAGTT
42024346 GGACATTTTT
Statistics
Matches: 85, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
45 2 0.02
46 40 0.47
47 2 0.02
48 1 0.01
49 4 0.05
50 4 0.05
51 1 0.01
52 2 0.02
53 28 0.33
54 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (46 bp):
AGTTATTAAGTTATTAAGTTATGTAAGTTATTATGTGAATTATATA
Found at i:42024248 original size:8 final size:8
Alignment explanation
Indices: 42024165--42024221 Score: 51
Period size: 9 Copynumber: 6.8 Consensus size: 8
42024155 TATTTTAAAA
42024165 TTATTAAG
1 TTATTAAG
*
42024173 TTATGTAAA
1 TTAT-TAAG
**
42024182 TTATGCGAG
1 TTAT-TAAG
*
42024191 TTGTTAAG
1 TTATTAAG
42024199 TTATTAAG
1 TTATTAAG
42024207 TTATGTAAG
1 TTAT-TAAG
42024216 TTATTA
1 TTATTA
42024222 TGTGAATTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
8 19 0.49
9 20 0.51
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (8 bp):
TTATTAAG
Found at i:42024250 original size:17 final size:17
Alignment explanation
Indices: 42024195--42024250 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
42024185 TGCGAGTTGT
*
42024195 TAAGTTATTAAGTTATG
1 TAAGTTATTAAGTTATA
*
42024212 TAAGTTATTATGTGAATTATA
1 TAAGTTATTA----AGTTATA
42024233 TAAGTTATTAAGTTATA
1 TAAGTTATTAAGTTATA
42024250 T
1 T
42024251 GGTATGACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
17 17 0.53
21 15 0.47
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (17 bp):
TAAGTTATTAAGTTATA
Found at i:42024984 original size:21 final size:21
Alignment explanation
Indices: 42024960--42025006 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
42024950 TTAACTATTT
* *
42024960 AAATTAGTTAATGATATTGTA
1 AAATTAGATAATGAAATTGTA
* *
42024981 AAATTAGATGATTAAATTGTA
1 AAATTAGATAATGAAATTGTA
42025002 AAATT
1 AAATT
42025007 TCAAATTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (21 bp):
AAATTAGATAATGAAATTGTA
Found at i:42027786 original size:97 final size:97
Alignment explanation
Indices: 42027607--42028004 Score: 415
Period size: 97 Copynumber: 3.9 Consensus size: 97
42027597 TAATTTTATT
* * * * **
42027607 TTTTTATAAATTGATTTATTTTTTGCAGCGTTTTTCATAAAAACGCCACAAAA-AAAATTTCATT
1 TTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCAGAAAAACGCCACAAAATATTATTTCATT
42027671 TTGAACAAAATGACGCCGTTTTGCTATTTTGG
66 TTGAACAAAATGACGCCGTTTTGCTATTTTGG
42027703 TTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCAGAAAAACGCCACAAAATATTATTTCATT
1 TTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCAGAAAAACGCCACAAAATATTATTTCATT
*
42027768 TTGAACAAAATGACGCCGTTTTGCTATGCTAAAAAATT-T
66 TTGAACAAAATGACGCCGTTTTGCTAT--T------TTGG
** * *** *** *** * * *
42027807 TAATTTTATTTTTTTATAAATTGATTTATTTTTTGCAACGTTTTTCATAAAAACGCCACAAAAAA
1 T--TTTTATTAATTGAT---TT-A-TTATTTGCGGC-GTTTTTCAGAAAAAC--GCCACAAAATA
42027872 TT-TTTCATTTTGAACAAAATGACGCCGTTTTGCTATTTTGG
56 TTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATTTTGG
42027913 TTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCAGAAAAACGCCACAAAATATTATTTCATT
1 TTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCAGAAAAACGCCACAAAATATTATTTCATT
42027978 TTGAACAAAATGACGCCGTTTTGCTAT
66 TTGAACAAAATGACGCCGTTTTGCTAT
42028005 GCTAAAAATT
Statistics
Matches: 243, Mismatches: 38, Indels: 41
0.75 0.12 0.13
Matches are distributed among these distances:
96 61 0.25
97 70 0.29
98 7 0.03
99 9 0.04
100 1 0.00
101 2 0.01
104 12 0.05
105 4 0.02
106 12 0.05
109 2 0.01
110 1 0.00
111 9 0.04
112 7 0.03
113 34 0.14
114 12 0.05
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (97 bp):
TTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCAGAAAAACGCCACAAAATATTATTTCATT
TTGAACAAAATGACGCCGTTTTGCTATTTTGG
Found at i:42027820 original size:210 final size:210
Alignment explanation
Indices: 42027458--42028057 Score: 1112
Period size: 210 Copynumber: 2.9 Consensus size: 210
42027448 AAATTTTTTT
*
42027458 ATTTTGAACAAAATGACGCCGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGTG
1 ATTTTGAACAAAATGACGCCGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCG
* *
42027523 TTTTTCATAAAAACGCCGCAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCT
66 TTTTTCAGAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCT
42027588 AAAAAATTTTAATTTTATTTTTTTATAAATTGATTTATTTTTTGCAGCGTTTTTCATAAAAACGC
131 AAAAAATTTTAATTTTATTTTTTTATAAATTGATTTATTTTTTGCAGCGTTTTTCATAAAAACGC
42027653 CACAAAAAAAATTTC
196 CACAAAAAAAATTTC
42027668 ATTTTGAACAAAATGACGCCGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCG
1 ATTTTGAACAAAATGACGCCGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCG
42027733 TTTTTCAGAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCT
66 TTTTTCAGAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCT
*
42027798 AAAAAATTTTAATTTTATTTTTTTATAAATTGATTTATTTTTTGCAACGTTTTTCATAAAAACGC
131 AAAAAATTTTAATTTTATTTTTTTATAAATTGATTTATTTTTTGCAGCGTTTTTCATAAAAACGC
**
42027863 CACAAAAAATTTTTC
196 CACAAAAAAAATTTC
42027878 ATTTTGAACAAAATGACGCCGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCG
1 ATTTTGAACAAAATGACGCCGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCG
42027943 TTTTTCAGAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCT
66 TTTTTCAGAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCT
* * *
42028008 AAAAATTTTTTATTTTATTTTTTTATAAATTGATTTA-TTTTTGCGGCGTT
131 AAAAAATTTTAATTTTATTTTTTTATAAATTGATTTATTTTTTGCAGCGTT
42028058 CTTAAACACA
Statistics
Matches: 380, Mismatches: 10, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
209 11 0.03
210 369 0.97
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (210 bp):
ATTTTGAACAAAATGACGCCGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCG
TTTTTCAGAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCT
AAAAAATTTTAATTTTATTTTTTTATAAATTGATTTATTTTTTGCAGCGTTTTTCATAAAAACGC
CACAAAAAAAATTTC
Found at i:42028235 original size:97 final size:97
Alignment explanation
Indices: 42028082--42028458 Score: 515
Period size: 96 Copynumber: 3.7 Consensus size: 97
42028072 TTGCTTACCT
* *
42028082 TTTGCGGCGTTTTCCATAAAAACGCCACAAAAT-TTTTTTCATTTTGAACAAAATGACGCCGTTT
1 TTTGCGGCGTTTTTCATAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTT
42028146 TGCTATTTTGGTTTTTATTAATTGATTTATTA
66 TGCTATTTTGGTTTTTATTAATTGATTTATTA
42028178 TTTGCGGCGTTTTTCATAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTT
1 TTTGCGGCGTTTTTCATAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTT
** *
42028243 TGCTATGCTAAAAGTTTTTTATTTTATTTTTTTATAAATTGATTTATTT
66 TGCTA---T-----TTTGGT-TTTTA------T-T-AATTGATTTATTA
* *
42028292 TTTGCGGCGTTTTTCATAAAAACGCCACAAAAAATT-TTTCATTTTGAACAAAATGATGCCGTTT
1 TTTGCGGCGTTTTTCATAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTT
42028356 TGCTATTTTGGTTTTTATTAATTGATTTATTA
66 TGCTATTTTGGTTTTTATTAATTGATTTATTA
*
42028388 TTTGCGGCGTTTTTCATAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGAAGCCGTTT
1 TTTGCGGCGTTTTTCATAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTT
42028453 TGCTAT
66 TGCTAT
42028459 GCTAAAAATT
Statistics
Matches: 250, Mismatches: 12, Indels: 37
0.84 0.04 0.12
Matches are distributed among these distances:
96 79 0.32
97 69 0.28
98 1 0.00
100 1 0.00
104 5 0.02
105 8 0.03
106 5 0.02
110 1 0.00
112 1 0.00
113 33 0.13
114 47 0.19
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (97 bp):
TTTGCGGCGTTTTTCATAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTT
TGCTATTTTGGTTTTTATTAATTGATTTATTA
Found at i:42028281 original size:244 final size:245
Alignment explanation
Indices: 42027845--42028302 Score: 864
Period size: 244 Copynumber: 1.9 Consensus size: 245
42027835 TTTTTTGCAA
*
42027845 CGTTTTTCATAAAAACGCCACAAAAAATTTTTCATTTTGAACAAAATGACGCCGTTTTGCTATTT
1 CGTTTTCCATAAAAACGCCACAAAAAATTTTTCATTTTGAACAAAATGACGCCGTTTTGCTATTT
42027910 TGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCAGAAAAACGCCACAAAATATTATTTC
66 TGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCAGAAAAACGCCACAAAATATTATTTC
42027975 ATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTTATAAATTG
131 ATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTTATAAATTG
42028040 ATTTA-TTTTTGCGGCGTTCTTAAACACAGCTATTGCTTACCTTTTGCGG
196 ATTTATTTTTTGCGGCGTTCTTAAACACAGCTATTGCTTACCTTTTGCGG
**
42028089 CGTTTTCCATAAAAACGCCACAAAATTTTTTTCATTTTGAACAAAATGACGCCGTTTTGCTATTT
1 CGTTTTCCATAAAAACGCCACAAAAAATTTTTCATTTTGAACAAAATGACGCCGTTTTGCTATTT
*
42028154 TGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCACAAAATATTATTTC
66 TGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCAGAAAAACGCCACAAAATATTATTTC
*
42028219 ATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAGTTTTTTATTTTATTTTTTTATAAATTG
131 ATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTTATAAATTG
42028284 ATTTATTTTTTGCGGCGTT
196 ATTTATTTTTTGCGGCGTT
42028303 TTTCATAAAA
Statistics
Matches: 208, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
244 195 0.94
245 13 0.06
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (245 bp):
CGTTTTCCATAAAAACGCCACAAAAAATTTTTCATTTTGAACAAAATGACGCCGTTTTGCTATTT
TGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCAGAAAAACGCCACAAAATATTATTTC
ATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTTATAAATTG
ATTTATTTTTTGCGGCGTTCTTAAACACAGCTATTGCTTACCTTTTGCGG
Found at i:42028443 original size:210 final size:208
Alignment explanation
Indices: 42028081--42028524 Score: 800
Period size: 210 Copynumber: 2.1 Consensus size: 208
42028071 ATTGCTTACC
* **
42028081 TTTTGCGGCGTTTTCCATAAAAACGCCACAAAATTTTTTTCATTTTGAACAAAATGACGCCGTTT
1 TTTTGCGGCGTTTTTCATAAAAACGCCACAAAAAATTTTTCATTTTGAACAAAATGACGCCGTTT
42028146 TGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCACAAAAT
66 TGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCACAAAAT
* *
42028211 ATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAGTTTTTTATTTTATTTTTTT
131 ATTATTTCATTTTGAACAAAATGAAGCCGTTTTGCTATGCTAAAAATTTTTTATTTTA-TTTTTT
42028276 ATAAATTGATTTATT
195 ATAAATTGATTTA-T
*
42028291 TTTTGCGGCGTTTTTCATAAAAACGCCACAAAAAATTTTTCATTTTGAACAAAATGATGCCGTTT
1 TTTTGCGGCGTTTTTCATAAAAACGCCACAAAAAATTTTTCATTTTGAACAAAATGACGCCGTTT
42028356 TGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCACAAAAT
66 TGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCACAAAAT
42028421 ATTATTTCATTTTGAACAAAATGAAGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTA
131 ATTATTTCATTTTGAACAAAATGAAGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTA
42028486 TAAATTGATTTAT
196 TAAATTGATTTAT
*
42028499 TTTTGCGGCGTTTTT-AAAAAAACGCC
1 TTTTGCGGCGTTTTTCATAAAAACGCC
42028525 GCTATTGCTT
Statistics
Matches: 227, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
207 10 0.04
208 16 0.07
209 19 0.08
210 182 0.80
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.45
Consensus pattern (208 bp):
TTTTGCGGCGTTTTTCATAAAAACGCCACAAAAAATTTTTCATTTTGAACAAAATGACGCCGTTT
TGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCACAAAAT
ATTATTTCATTTTGAACAAAATGAAGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATTTTTTA
TAAATTGATTTAT
Found at i:42028481 original size:454 final size:455
Alignment explanation
Indices: 42027622--42029140 Score: 2673
Period size: 454 Copynumber: 3.3 Consensus size: 455
42027612 ATAAATTGAT
* * * ***
42027622 TTATTTTTTGCAGCGTTTTTCATAAAAACGCCACAAAAAAAATTTCATTTTGAACAAAATGACGC
1 TTATCTTTTGCGGCGTTTTCCATAAAAACGCCACAAAAATTTTTTCATTTTGAACAAAATGACGC
*
42027687 CGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCAGAAAAACGCCAC
66 CGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCAC
* *
42027752 AAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAAATTTTAATTTTATT
131 AAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATT
**
42027817 TTTTTATAAATTGATTTATTTTTTGCAACGTTTTTCATAAAAACGCCACAAAAAATTTTTCATTT
196 TTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTCATAAAAACGCCACAAAAAATTTTTCATTT
42027882 TGAACAAAATGACGCCGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTT
261 TGAACAAAATGACGCCGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTT
*
42027947 TCAGAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAA
326 TCATAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAA
* * *
42028012 ATTTTTTATTTTATTTTTTTATAAATTGATTTATTTTTGCGGCGTTCTT-AAACACAGCTATTGC
391 ATTTTTTATTTTATTTTTTTATAAATTGATTTATTTTTGCGGCGTTTTTAAAACGCCGCTATTGC
* *
42028076 TTACCTTTTGCGGCGTTTTCCATAAAAACGCCACAAAATTTTTTTCATTTTGAACAAAATGACGC
1 TTATCTTTTGCGGCGTTTTCCATAAAAACGCCACAAAAATTTTTTCATTTTGAACAAAATGACGC
42028141 CGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCAC
66 CGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCAC
*
42028206 AAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAGTTTTTTATTTTATT
131 AAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATT
42028271 TTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTCATAAAAACGCCACAAAAAATTTTTCATTT
196 TTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTCATAAAAACGCCACAAAAAATTTTTCATTT
*
42028336 TGAACAAAATGATGCCGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTT
261 TGAACAAAATGACGCCGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTT
*
42028401 TCATAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGAAGCCGTTTTGCTATGCTAAAA
326 TCATAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAA
42028466 ATTTTTTATTTTA-TTTTTTATAAATTGATTTATTTTTGCGGCGTTTTTAAAAAAACGCCGCTAT
391 ATTTTTTATTTTATTTTTTTATAAATTGATTTATTTTTGCGGCGTTTTT---AAAACGCCGCTAT
42028530 TGC
453 TGC
* *
42028533 TTATCTTTTGCGGCGTTTTCCATAAAAATGCCACAAAATTTTTTTCATTTTGAACAAAATGACGC
1 TTATCTTTTGCGGCGTTTTCCATAAAAACGCCACAAAAATTTTTTCATTTTGAACAAAATGACGC
*
42028598 CGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCGC
66 CGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCAC
42028663 AAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATT
131 AAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATT
*
42028728 TTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTCATAAAAAACGCCACAAAAATTTTTTCATT
196 TTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTCAT-AAAAACGCCACAAAAAATTTTTCATT
42028793 TTGAACAAAATGACGCCGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTT
260 TTGAACAAAATGACGCCGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTT
*
42028858 TTCATAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCCAAA
325 TTCATAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAA
* **
42028923 AAATTTTTATTTTATTTTTTTATAAATTGATTTATTTTTATGGCGTTTTTATAAAAAACGCCGCT
390 AATTTTTTATTTTATTTTTTTATAAATTGATTTATTTTTGCGGCG-TTTT-T--AAAACGCCGCT
42028988 ATTGC
451 ATTGC
* * *
42028993 TTATTTTTTGCGGCGTTTTTCATAAAAACGCCACAAAAATTTTTTCATTTTGAACAAAATTACGC
1 TTATCTTTTGCGGCGTTTTCCATAAAAACGCCACAAAAATTTTTTCATTTTGAACAAAATGACGC
42029058 CGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCAC
66 CGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCAC
42029123 AAAATATTATTTCATTTT
131 AAAATATTATTTCATTTT
42029141 AACTTATTTA
Statistics
Matches: 1020, Mismatches: 37, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
453 34 0.03
454 386 0.38
457 242 0.24
458 165 0.16
459 28 0.03
460 164 0.16
461 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.45
Consensus pattern (455 bp):
TTATCTTTTGCGGCGTTTTCCATAAAAACGCCACAAAAATTTTTTCATTTTGAACAAAATGACGC
CGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCAC
AAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATT
TTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTCATAAAAACGCCACAAAAAATTTTTCATTT
TGAACAAAATGACGCCGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTT
TCATAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAA
ATTTTTTATTTTATTTTTTTATAAATTGATTTATTTTTGCGGCGTTTTTAAAACGCCGCTATTGC
Found at i:42028609 original size:247 final size:251
Alignment explanation
Indices: 42028286--42028775 Score: 880
Period size: 247 Copynumber: 2.0 Consensus size: 251
42028276 ATAAATTGAT
* * *
42028286 TTATTTTTTGCGGCGTTTTTCATAAAAACGCCACAAAAAATTTTTCATTTTGAACAAAATGATGC
1 TTATCTTTTGCGGCGTTTTCCATAAAAACGCCACAAAAAATTTTTCATTTTGAACAAAATGACGC
42028351 CGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCAC
66 CGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCAC
42028416 AAAATATTATTTCATTTTGAACAAAATGAAGCCGTTTTGCTATGCTAAAAATTTTTTATTTTA-T
131 AAAATATTATTTCATTTTGAACAAAATGAAGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATT
42028480 TTTTTATAAATTGATTTA-TTTTTGCGGCGTTTTT-A-AAAAAACGCCGCTATTGC
196 TTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTCATAAAAAACGCCGCTATTGC
* **
42028533 TTATCTTTTGCGGCGTTTTCCATAAAAATGCCACAAAATTTTTTTCATTTTGAACAAAATGACGC
1 TTATCTTTTGCGGCGTTTTCCATAAAAACGCCACAAAAAATTTTTCATTTTGAACAAAATGACGC
*
42028598 CGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCGC
66 CGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCAC
*
42028663 AAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATT
131 AAAATATTATTTCATTTTGAACAAAATGAAGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATT
42028728 TTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTCATAAAAAACGCC
196 TTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTCATAAAAAACGCC
42028776 ACAAAAATTT
Statistics
Matches: 231, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
247 185 0.80
248 19 0.08
249 16 0.07
250 1 0.00
251 10 0.04
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (251 bp):
TTATCTTTTGCGGCGTTTTCCATAAAAACGCCACAAAAAATTTTTCATTTTGAACAAAATGACGC
CGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCAC
AAAATATTATTTCATTTTGAACAAAATGAAGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATT
TTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTCATAAAAAACGCCGCTATTGC
Found at i:42028704 original size:97 final size:97
Alignment explanation
Indices: 42028539--42028916 Score: 348
Period size: 97 Copynumber: 3.7 Consensus size: 97
42028529 TTGCTTATCT
* * *
42028539 TTTGCGGCGTTTTCCATAAAAATGCCACAAAAT-TTTTTTCATTTTGAACAAAATGACGCCGTTT
1 TTTGCGGCGTTTTTCATAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTT
42028603 TGCTATTTTGGTTTTTATTAATTGATTTATTA
66 TGCTATTTTGGTTTTTATTAATTGATTTATTA
*
42028635 TTTGCGGCGTTTTTCATAAAAACGCCGCAAAATATTATTTCATTTTGAACAAAATGACGCCGTTT
1 TTTGCGGCGTTTTTCATAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTT
** ** *
42028700 TGCTATGCTAAAAATTTTTTATTTTATTTTTTTATAAATTGATTTA
66 TGCTA---T-----TTTGGT-TTTTATTAATTGAT---TT-A-TTA
*** ** * * *** * * * **
42028746 TTTTTTGCGGCGTTT-TTCATAAAAAACGCCACA-AAAATTTTTTCATTTTGAACAAAATGACGC
1 TTTGCGGC-GTTTTTCAT-AAAAACGCCACAAAATATTA-TT--TCATTTTGAACAAAATGACGC
42028809 CGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTA
61 CGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTA
42028846 TTTGCGGCGTTTTTCATAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTT
1 TTTGCGGCGTTTTTCATAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTT
42028911 TGCTAT
66 TGCTAT
42028917 GCCAAAAAAT
Statistics
Matches: 217, Mismatches: 43, Indels: 43
0.72 0.14 0.14
Matches are distributed among these distances:
96 30 0.14
97 67 0.31
99 14 0.06
100 12 0.06
101 1 0.00
102 2 0.01
105 15 0.07
106 15 0.07
109 2 0.01
110 1 0.00
111 12 0.06
112 15 0.07
114 31 0.14
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (97 bp):
TTTGCGGCGTTTTTCATAAAAACGCCACAAAATATTATTTCATTTTGAACAAAATGACGCCGTTT
TGCTATTTTGGTTTTTATTAATTGATTTATTA
Found at i:42028781 original size:115 final size:113
Alignment explanation
Indices: 42028614--42028819 Score: 358
Period size: 114 Copynumber: 1.8 Consensus size: 113
42028604 GCTATTTTGG
* *
42028614 TTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCGCAAAATATTATTTCATT
1 TTTTTATAAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCACAAAA-ATTATTTCATT
42028679 TTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATT
65 TTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATT
* *
42028728 TTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTCATAAAAAACGCCACAAAAATTTTTTCATT
1 TTTTTATAAATTGATTTATTATTTGCGGCGTTTTTCAT-AAAAACGCCACAAAAATTATTTCATT
42028793 TTGAACAAAATGACGCCGTTTTGCTAT
65 TTGAACAAAATGACGCCGTTTTGCTAT
42028820 TTTGGTTTTT
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
114 73 0.84
115 14 0.16
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (113 bp):
TTTTTATAAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCACAAAAATTATTTCATTT
TGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATT
Found at i:42028803 original size:211 final size:211
Alignment explanation
Indices: 42028533--42028984 Score: 804
Period size: 211 Copynumber: 2.2 Consensus size: 211
42028523 CCGCTATTGC
* * * *
42028533 TTATCTTTTGCGGCGTTTTCCAT-AAAAATGCCACAAAATTTTTTTCATTTTGAACAAAATGACG
1 TTATTTTTTGCGGCGTTTTTCATAAAAAACGCCACAAAAATTTTTTCATTTTGAACAAAATGACG
*
42028597 CCGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCG
66 CCGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCA
* *
42028662 CAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTAT
131 CAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCCAAAAAATTTTTATTTTAT
42028727 TTTTTTATAAATTGAT
196 TTTTTTATAAATTGAT
42028743 TTATTTTTTGCGGCGTTTTTCATAAAAAACGCCACAAAAATTTTTTCATTTTGAACAAAATGACG
1 TTATTTTTTGCGGCGTTTTTCATAAAAAACGCCACAAAAATTTTTTCATTTTGAACAAAATGACG
42028808 CCGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCA
66 CCGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCA
42028873 CAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCCAAAAAATTTTTATTTTAT
131 CAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCCAAAAAATTTTTATTTTAT
42028938 TTTTTTATAAATTGAT
196 TTTTTTATAAATTGAT
42028954 TTATTTTTAT--GGCGTTTTT-ATAAAAAACGCC
1 TTATTTTT-TGCGGCGTTTTTCATAAAAAACGCC
42028985 GCTATTGCTT
Statistics
Matches: 233, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
209 12 0.05
210 30 0.13
211 190 0.82
212 1 0.00
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.45
Consensus pattern (211 bp):
TTATTTTTTGCGGCGTTTTTCATAAAAAACGCCACAAAAATTTTTTCATTTTGAACAAAATGACG
CCGTTTTGCTATTTTGGTTTTTATTAATTGATTTATTATTTGCGGCGTTTTTCATAAAAACGCCA
CAAAATATTATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCCAAAAAATTTTTATTTTAT
TTTTTTATAAATTGAT
Found at i:42029467 original size:22 final size:21
Alignment explanation
Indices: 42029424--42029525 Score: 66
Period size: 22 Copynumber: 4.7 Consensus size: 21
42029414 CCTTAACTCG
*
42029424 ACCCCTGAATCCCTAAACCTTAA
1 ACCCCT-AA-CCCTTAACCTTAA
* *
42029447 ATCCCTAACTCTTAACTCTT-A
1 ACCCCTAACCCTTAAC-CTTAA
* *
42029468 ACCCCTAA-CATCTAACCCCTAA
1 ACCCCTAACCCT-TAA-CCTTAA
*
42029490 ACCCCTAACCCCTAAACCTTAA
1 ACCCCTAA-CCCTTAACCTTAA
*
42029512 ATCCC-AACCCTTAA
1 ACCCCTAACCCTTAA
42029526 ACCATAATCC
Statistics
Matches: 61, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
20 7 0.11
21 21 0.34
22 24 0.39
23 7 0.11
24 2 0.03
ACGTcount: A:0.34, C:0.41, G:0.01, T:0.24
Consensus pattern (21 bp):
ACCCCTAACCCTTAACCTTAA
Found at i:42029476 original size:7 final size:7
Alignment explanation
Indices: 42029466--42029504 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
42029456 TCTTAACTCT
42029466 TAACCCC
1 TAACCCC
**
42029473 TAACATC
1 TAACCCC
42029480 TAACCCC
1 TAACCCC
42029487 TAAACCCC
1 T-AACCCC
42029495 TAACCCC
1 TAACCCC
42029502 TAA
1 TAA
42029505 ACCTTAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.36, C:0.46, G:0.00, T:0.18
Consensus pattern (7 bp):
TAACCCC
Found at i:42029499 original size:15 final size:15
Alignment explanation
Indices: 42029466--42029507 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
42029456 TCTTAACTCT
**
42029466 TAACCCCT-AACATC
1 TAACCCCTAAACCCC
42029480 TAACCCCTAAACCCC
1 TAACCCCTAAACCCC
42029495 TAACCCCTAAACC
1 TAACCCCTAAACC
42029508 TTAAATCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.17
Consensus pattern (15 bp):
TAACCCCTAAACCCC
Found at i:42029526 original size:21 final size:22
Alignment explanation
Indices: 42029434--42029539 Score: 67
Period size: 21 Copynumber: 5.0 Consensus size: 22
42029424 ACCCCTGAAT
*
42029434 CCCTAAACCTTAAATCCCTAA-
1 CCCTAAACCATAAATCCCTAAC
* * * *
42029455 CTCTTAACTC-TTAACCCCTAAC
1 CCCTAAAC-CATAAATCCCTAAC
** * * *
42029477 ATCTAACCCCTAAACCCCTAAC
1 CCCTAAACCATAAATCCCTAAC
*
42029499 CCCTAAACCTTAAATCCC-AAC
1 CCCTAAACCATAAATCCCTAAC
*
42029520 CCTTAAACCAT-AATCCCTAA
1 CCCTAAACCATAAATCCCTAA
42029540 TTCATAATCC
Statistics
Matches: 66, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
20 6 0.09
21 30 0.45
22 30 0.45
ACGTcount: A:0.36, C:0.41, G:0.00, T:0.24
Consensus pattern (22 bp):
CCCTAAACCATAAATCCCTAAC
Found at i:42029545 original size:14 final size:14
Alignment explanation
Indices: 42029527--42029568 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
42029517 AACCCTTAAA
42029527 CCATAATCCCTAAT
1 CCATAATCCCTAAT
*
42029541 TCATAATCCCTAAAT
1 CCATAATCCCT-AAT
*
42029556 CCATACTCCCTAA
1 CCATAATCCCTAA
42029569 CCTTAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.29
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:42030300 original size:114 final size:114
Alignment explanation
Indices: 42030108--42030589 Score: 793
Period size: 114 Copynumber: 4.2 Consensus size: 114
42030098 TATTTTTAAT
* *
42030108 GGCGCTTTCCCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTTCTTAAAAACGCTGCTA
1 GGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTA
* *
42030173 AATTCCCGAAAGCTCAGAAAACGTCGTCGTTGGGCTTAGGTTTTTTTGC
66 AATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGC
* * *
42030222 GGCGCTTTCCAAAAAACGCCGCTAAAGTCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCACTA
1 GGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTA
42030287 AATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGC
66 AATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGC
*
42030336 GGCGCTTTCCCAAAAACGCCGCTAAAGCCTTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTA
1 GGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTA
* * * *
42030401 AATGCCCGAAAGCTCAGAAAGCGGTGTCGTTTGGCTTAGGTTTTTTTGC
66 AATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGC
* * *
42030450 GGCGCTCTCCCAAAAACGCTGCTAAAGCCCTGAGCATTAGCGACGCTTTCTTAAAAACGCCGCTA
1 GGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTA
* *
42030515 AATCCCCGAAAGCTCACAAAACGGCGTCGTTGGACTTAGGTTTTTTTGC
66 AATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGC
* *
42030564 GGCGCTTTCTCAGAAACGCCGCTAAA
1 GGCGCTTTCCCAAAAACGCCGCTAAA
42030590 TCCCCGAAAG
Statistics
Matches: 339, Mismatches: 29, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 339 1.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (114 bp):
GGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTA
AATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGC
Found at i:42030582 original size:73 final size:72
Alignment explanation
Indices: 42030493--42030660 Score: 273
Period size: 73 Copynumber: 2.3 Consensus size: 72
42030483 GCATTAGCGA
*
42030493 CGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGACTTAGGTTT
1 CGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGACTTAGG-TT
42030558 TTTTGCGG
65 TTTTGCGG
* *** *
42030566 CGCTTTCTCAGAAACGCCGCTAAATCCCCGAAAGCTCGGGAAACGGCGTCGTTGGGCTTAGGTTT
1 CGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGACTTAGGTTT
42030631 TTTGCGG
66 TTTGCGG
42030638 CGCTTTCTCAAAAACGCCGCTAA
1 CGCTTTCTCAAAAACGCCGCTAA
42030661 TGCTTATTCT
Statistics
Matches: 88, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
72 32 0.36
73 56 0.64
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (72 bp):
CGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGACTTAGGTTT
TTTGCGG
Found at i:42032067 original size:51 final size:51
Alignment explanation
Indices: 42032005--42032179 Score: 219
Period size: 51 Copynumber: 3.5 Consensus size: 51
42031995 GGTCATTACA
* * * *
42032005 TGTTTAATGTTGTCCTAGATTTTTCTCAGTTAATGTTTTTTAATAATTAGT
1 TGTTTAATGTTGTCCAAGATTTTGCTCAATTAATGTTGTTTAATAATTAGT
* * * *
42032056 TATTTAATGTTGTCCAAGATTTTGCTCAATTAATGTTGTTTAGTCATTTGT
1 TGTTTAATGTTGTCCAAGATTTTGCTCAATTAATGTTGTTTAATAATTAGT
* * *
42032107 TGTTT-ATGTTGTCCAAGATTTTGCCCAATTGATGTTGTTTAATTATTA-T
1 TGTTTAATGTTGTCCAAGATTTTGCTCAATTAATGTTGTTTAATAATTAGT
*
42032156 CTGTTTAATGTTGTCCAAGGTTTT
1 -TGTTTAATGTTGTCCAAGATTTT
42032180 TCACCATTGA
Statistics
Matches: 107, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
49 1 0.01
50 43 0.40
51 63 0.59
ACGTcount: A:0.22, C:0.10, G:0.16, T:0.52
Consensus pattern (51 bp):
TGTTTAATGTTGTCCAAGATTTTGCTCAATTAATGTTGTTTAATAATTAGT
Found at i:42032189 original size:51 final size:49
Alignment explanation
Indices: 42032005--42032211 Score: 182
Period size: 51 Copynumber: 4.1 Consensus size: 49
42031995 GGTCATTACA
* * * * *
42032005 TGTTTAATGTTGTCCTAGATTTTTCTCAGTTAATGTTTTTTAATAATTAGT
1 TGTTTAATGTTGTCCAAGATTTTGCCCA-TTAATGTTGTTTAATTATTA-T
* * * * *
42032056 TATTTAATGTTGTCCAAGATTTTGCTCAATTAATGTTGTTTAGTCATTTGT
1 TGTTTAATGTTGTCCAAGATTTTGC-CCATTAATGTTGTTTAATTA-TTAT
*
42032107 TGTTT-ATGTTGTCCAAGATTTTGCCCAATTGATGTTGTTTAATTATTAT
1 TGTTTAATGTTGTCCAAGATTTTGCCC-ATTAATGTTGTTTAATTATTAT
* * * * * *
42032156 CTGTTTAATGTTGTCCAAGGTTTTTCACCATTGATGCTATTTTATTATTAAT
1 -TGTTTAATGTTGTCCAAGATTTTGC-CCATTAATGTTGTTTAATTATT-AT
42032208 TGTT
1 TGTT
42032212 CGATCTTGTC
Statistics
Matches: 129, Mismatches: 20, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
49 4 0.03
50 39 0.30
51 79 0.61
52 7 0.05
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.52
Consensus pattern (49 bp):
TGTTTAATGTTGTCCAAGATTTTGCCCATTAATGTTGTTTAATTATTAT
Found at i:42032211 original size:101 final size:102
Alignment explanation
Indices: 42031996--42032179 Score: 221
Period size: 101 Copynumber: 1.8 Consensus size: 102
42031986 GTTAGGTTCG
* * * * *
42031996 GTCATTACA-TGTTTAATGTTGTCCTAGATTTTTCTCAGTTAATGTTTTTTAATAATTAGTTATT
1 GTCATTA-ATTGTTTAATGTTGTCCAAGATTTTGCCCAATTAATGTTGTTTAATAATTAGTTATT
*
42032060 TAATGTTGTCCAAGATTTTGCTCAATTAATGTTGTTTA
65 TAATGTTGTCCAAGATTTTGCACAATTAATGTTGTTTA
** * * *
42032098 GTCATTTGTTGTTT-ATGTTGTCCAAGATTTTGCCCAATTGATGTTGTTTAATTATTA-TCTGTT
1 GTCATTAATTGTTTAATGTTGTCCAAGATTTTGCCCAATTAATGTTGTTTAATAATTAGT-TATT
*
42032161 TAATGTTGTCCAAGGTTTT
65 TAATGTTGTCCAAGATTTT
42032180 TCACCATTGA
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
100 1 0.01
101 57 0.83
102 11 0.16
ACGTcount: A:0.23, C:0.10, G:0.16, T:0.51
Consensus pattern (102 bp):
GTCATTAATTGTTTAATGTTGTCCAAGATTTTGCCCAATTAATGTTGTTTAATAATTAGTTATTT
AATGTTGTCCAAGATTTTGCACAATTAATGTTGTTTA
Found at i:42033792 original size:12 final size:12
Alignment explanation
Indices: 42033774--42033803 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
42033764 TATCGCAAAG
42033774 AAAATAGAAATA
1 AAAATAGAAATA
*
42033786 GAAATAGAAATA
1 AAAATAGAAATA
42033798 AAAATA
1 AAAATA
42033804 AAGAATACAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (12 bp):
AAAATAGAAATA
Found at i:42038871 original size:51 final size:51
Alignment explanation
Indices: 42038792--42038898 Score: 160
Period size: 51 Copynumber: 2.1 Consensus size: 51
42038782 AGGCCAACTG
*
42038792 CACACGCCCGTGTGTGATAGCTCCAGTCCCCACACGCACATGTCACTTACC
1 CACACGCCCGTGTGTGATAGCTCCAGTCCCCACACACACATGTCACTTACC
* * * * *
42038843 CACACGCCTGTGTGTGATAGCTCTAGTCCCCACACACCCGTGTCACTTTCC
1 CACACGCCCGTGTGTGATAGCTCCAGTCCCCACACACACATGTCACTTACC
42038894 CACAC
1 CACAC
42038899 ACCCATGTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.21, C:0.41, G:0.17, T:0.21
Consensus pattern (51 bp):
CACACGCCCGTGTGTGATAGCTCCAGTCCCCACACACACATGTCACTTACC
Found at i:42056265 original size:11 final size:11
Alignment explanation
Indices: 42056251--42056291 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
42056241 AACAAATCGT
42056251 AAAAAAATTCA
1 AAAAAAATTCA
42056262 AAAAAAA-TCATA
1 AAAAAAATTC--A
42056274 AAAAAAATTCA
1 AAAAAAATTCA
42056285 AAAAAAA
1 AAAAAAA
42056292 GGTAGTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 2 0.07
11 15 0.56
12 8 0.30
13 2 0.07
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:42056280 original size:12 final size:12
Alignment explanation
Indices: 42056238--42056291 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
42056228 CTGTAGTAAG
* *
42056238 TAAAACAAATCG
1 TAAAAAAAATCA
*
42056250 TAAAAAAATTC-
1 TAAAAAAAATCA
42056261 -AAAAAAAATCA
1 TAAAAAAAATCA
42056272 TAAAAAAAATTCA
1 TAAAAAAAA-TCA
42056285 -AAAAAAA
1 TAAAAAAA
42056292 GGTAGTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 9 0.25
12 24 0.67
13 3 0.08
ACGTcount: A:0.72, C:0.09, G:0.02, T:0.17
Consensus pattern (12 bp):
TAAAAAAAATCA
Found at i:42063996 original size:24 final size:23
Alignment explanation
Indices: 42063953--42064000 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
42063943 AGGAATAAGA
42063953 AGGAGAGGAAGATGACGAGGATG
1 AGGAGAGGAAGATGACGAGGATG
* *
42063976 AGGAGATGGACGATGAGGAGGATG
1 AGGAGA-GGAAGATGACGAGGATG
42064000 A
1 A
42064001 TTGATTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.38, C:0.04, G:0.48, T:0.10
Consensus pattern (23 bp):
AGGAGAGGAAGATGACGAGGATG
Found at i:42067745 original size:34 final size:35
Alignment explanation
Indices: 42067701--42067767 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
42067691 CAGTAAAATG
*
42067701 TTTTCCGTAAAATTA-TTTCTGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTTCTGGAAAATATTTTAC
*
42067735 TTTTCTGTAAAATGATTTTCTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTTCTGGAAAATATTTT
42067768 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 13 0.43
35 17 0.57
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.49
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTTCTGGAAAATATTTTAC
Found at i:42067768 original size:14 final size:15
Alignment explanation
Indices: 42067735--42067771 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
42067725 AATATTTTAC
*
42067735 TTTTCTGTAAAATGA
1 TTTTCTGGAAAATGA
42067750 TTTTCTGGAAAAT-A
1 TTTTCTGGAAAATGA
42067764 TTTTCTGG
1 TTTTCTGG
42067772 TGTTTGGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49
Consensus pattern (15 bp):
TTTTCTGGAAAATGA
Found at i:42067826 original size:32 final size:31
Alignment explanation
Indices: 42067751--42067832 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 31
42067741 GTAAAATGAT
* * *
42067751 TTTCTGGAAAATATTTTCTGGTGTTTGGTAAA
1 TTTCT-GAAAATATTTTCTGCTGTTTGGCAGA
* *
42067783 TCTGTGTAAAATATTTTCTGCTGTTTGGCAGA
1 TTTCTG-AAAATATTTTCTGCTGTTTGGCAGA
42067815 TTTCCTGAAAATATTTTC
1 TTT-CTGAAAATATTTTC
42067833 CGGAAAAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
31 1 0.02
32 38 0.93
33 2 0.05
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.46
Consensus pattern (31 bp):
TTTCTGAAAATATTTTCTGCTGTTTGGCAGA
Found at i:42070364 original size:25 final size:25
Alignment explanation
Indices: 42070328--42070376 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
42070318 ATGTTTGCTG
42070328 CTTAGAAGAGAATGGAAAATGTCTA
1 CTTAGAAGAGAATGGAAAATGTCTA
42070353 CTTAG-AGAAGAATGGAAAATGTCT
1 CTTAGAAG-AGAATGGAAAATGTCT
42070377 TACCAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.43, C:0.08, G:0.24, T:0.24
Consensus pattern (25 bp):
CTTAGAAGAGAATGGAAAATGTCTA
Found at i:42070875 original size:20 final size:20
Alignment explanation
Indices: 42070761--42070875 Score: 99
Period size: 20 Copynumber: 5.8 Consensus size: 20
42070751 TTGTACGGGA
** *
42070761 TTTGCACTTCGGTGCTTCTA
1 TTTGCACTTCGGTGCCCCTG
* *
42070781 TTTGCACTTTGGTGCCTCT-
1 TTTGCACTTCGGTGCCCCTG
*
42070800 TTATACACTTCGGTGCCCCTG
1 TT-TGCACTTCGGTGCCCCTG
* *
42070821 TTTGCACTACGGTTCCCCTG
1 TTTGCACTTCGGTGCCCCTG
*
42070841 TTTGCACATT-TGTGCCCCTG
1 TTTGCAC-TTCGGTGCCCCTG
**
42070861 TCAGCACTTCGGTGC
1 TTTGCACTTCGGTGC
42070876 TTCTGTTATG
Statistics
Matches: 77, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.05
20 70 0.91
21 3 0.04
ACGTcount: A:0.10, C:0.30, G:0.21, T:0.38
Consensus pattern (20 bp):
TTTGCACTTCGGTGCCCCTG
Found at i:42074882 original size:38 final size:37
Alignment explanation
Indices: 42074829--42074903 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
42074819 GGTTTAACCT
*
42074829 TACAACCTCTCTTAAGACTTATACCCCAAAATCTTAAGA
1 TACAACCTCCCTTAAGACTTATA-CCC-AAATCTTAAGA
** *
42074868 TACAA-CTCCCTTAAGGTTTCTACCCAAATCTTAAGA
1 TACAACCTCCCTTAAGACTTATACCCAAATCTTAAGA
42074904 ATAAACCCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 11 0.34
37 3 0.09
38 13 0.41
39 5 0.16
ACGTcount: A:0.36, C:0.28, G:0.07, T:0.29
Consensus pattern (37 bp):
TACAACCTCCCTTAAGACTTATACCCAAATCTTAAGA
Found at i:42077037 original size:21 final size:20
Alignment explanation
Indices: 42076999--42077037 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
42076989 AGCGAAACTA
*
42076999 CCCTCCATATCGCGACATGG
1 CCCTCCATATCGCAACATGG
*
42077019 CCCTCCTATGTCGCAACAT
1 CCCTCC-ATATCGCAACAT
42077038 ACCCCCTGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.21, C:0.41, G:0.15, T:0.23
Consensus pattern (20 bp):
CCCTCCATATCGCAACATGG
Found at i:42077758 original size:20 final size:21
Alignment explanation
Indices: 42077725--42077782 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
42077715 ACATCATAGA
42077725 TGCATAACAGGGGCACCGAA-G
1 TGCA-AACAGGGGCACCGAATG
* *
42077746 TGCAAACAAGGGCA-CAAATG
1 TGCAAACAGGGGCACCGAATG
42077766 TGCAAACAGGGGCACCG
1 TGCAAACAGGGGCACCG
42077783 TAGCACGAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 3 0.10
20 23 0.74
21 5 0.16
ACGTcount: A:0.36, C:0.24, G:0.31, T:0.09
Consensus pattern (21 bp):
TGCAAACAGGGGCACCGAATG
Found at i:42077809 original size:40 final size:40
Alignment explanation
Indices: 42077725--42077811 Score: 97
Period size: 40 Copynumber: 2.1 Consensus size: 40
42077715 ACATCATAGA
**
42077725 TGCATAACAGGGGCACCGAAGTGCAAACAAGGGCACAAATG
1 TGCA-AACAGGGGCACCGAAGCACAAACAAGGGCACAAATG
* *
42077766 TGCAAACAGGGGCACCGTAGCACGAAC-AGGGACACCAAA-G
1 TGCAAACAGGGGCACCGAAGCACAAACAAGGG-CA-CAAATG
42077806 TGCAAA
1 TGCAAA
42077812 TCTCATACAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
39 4 0.10
40 28 0.70
41 8 0.20
ACGTcount: A:0.39, C:0.24, G:0.29, T:0.08
Consensus pattern (40 bp):
TGCAAACAGGGGCACCGAAGCACAAACAAGGGCACAAATG
Found at i:42081029 original size:43 final size:43
Alignment explanation
Indices: 42080968--42081055 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
42080958 TTTGCATCAG
*
42080968 AACACAACCTAAACCACAAAGAGACGTATCACTGAACACAATA
1 AACACAACCTAAACCACAAAGAGACATATCACTGAACACAATA
42081011 AACACAACCTAAACCACAAAGAGACATATCACTGAACACAATA
1 AACACAACCTAAACCACAAAGAGACATATCACTGAACACAATA
42081054 AA
1 AA
42081056 TTCTTTCTCG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.53, C:0.27, G:0.08, T:0.11
Consensus pattern (43 bp):
AACACAACCTAAACCACAAAGAGACATATCACTGAACACAATA
Found at i:42084947 original size:28 final size:28
Alignment explanation
Indices: 42084915--42084988 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
42084905 ACAATGAGGT
** *
42084915 CCTTAGCCCAATTTAGTAGT-AGTGTTGG
1 CCTTAGCCCAATACAGTA-TCAGTGTGGG
*
42084943 CCTTAACCCAATACAGTATCAGTGTGGG
1 CCTTAGCCCAATACAGTATCAGTGTGGG
42084971 CCTTAGCCCAATACAGTA
1 CCTTAGCCCAATACAGTA
42084989 AGATTACAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.03
28 39 0.98
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (28 bp):
CCTTAGCCCAATACAGTATCAGTGTGGG
Found at i:42085391 original size:27 final size:27
Alignment explanation
Indices: 42085361--42085998 Score: 762
Period size: 27 Copynumber: 23.2 Consensus size: 27
42085351 GGTATAAAAA
* * *
42085361 TCATTTTACCCTAT-GGGGGTCTTTCGG
1 TCATTTTACCCT-TCGAGGGTATTTCAG
*
42085388 TCATTTTACCCTTCGAGGGTATTTTAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
42085415 TCATTTTACCCTTCGAGGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* *
42085442 TCATTTTACCTTTCGAGGGTATTTTGAGGGTATTTTGG
1 TCATTTTACCCTTCGAGGGTA-TTT-----CA-----G
* *
42085480 TCATTTTACCTTTTGAGGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
42085507 TCATTTTACCCTTCGAGGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* * *
42085534 TCATTTTACCCTTTGGGGGTATTTCAA
1 TCATTTTACCCTTCGAGGGTATTTCAG
*
42085561 TCATTTTACCCTTC-AGGGGTATTTCGG
1 TCATTTTACCCTTCGA-GGGTATTTCAG
*
42085588 TCATTTTACCCTTCGAGGGTATTTTAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* * *
42085615 TCATTTTACCTTTTGAGGGTATTTCAA
1 TCATTTTACCCTTCGAGGGTATTTCAG
**
42085642 TCATTTTACCCTTCGAGGGTATTTGGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
*
42085669 TCATTTTACCCTTCGAGGGTATTTTAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* *
42085696 TAATTTTACCCTTC-AGGGGTATTTCGG
1 TCATTTTACCCTTCGA-GGGTATTTCAG
** *
42085723 TCATTTTACCCTTTAAGGGTATTTTAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* *
42085750 TCATTTTACCTTTTGAGGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
*
42085777 TCATTTTACCCTTC-AGGGGTATTTCGG
1 TCATTTTACCCTTCGA-GGGTATTTCAG
42085804 TCATTTTACCCTTCGAGGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* * * *
42085831 TTATTTTATCTTTCGAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* *
42085858 TCATTTTACCCTTCAAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* *
42085885 TCATTTTACCCTTCGAGTGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* *
42085912 TCATTTTACCCTTCGAGTGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
*
42085939 TCATTTTACCCTTCAAGGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
*
42085966 TCATTTTACCCTTCGAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
42085993 TCATTT
1 TCATTT
42085999 GCCCATAACT
Statistics
Matches: 533, Mismatches: 60, Indels: 36
0.85 0.10 0.06
Matches are distributed among these distances:
26 3 0.01
27 498 0.93
28 6 0.01
32 1 0.00
33 1 0.00
37 3 0.01
38 21 0.04
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (27 bp):
TCATTTTACCCTTCGAGGGTATTTCAG
Found at i:42085472 original size:38 final size:38
Alignment explanation
Indices: 42085429--42085503 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
42085419 TTTACCCTTC
42085429 GAGGGTATTTCAGTCATTTTACCTTTCGAGGGTATTTT
1 GAGGGTATTTCAGTCATTTTACCTTTCGAGGGTATTTT
** *
42085467 GAGGGTATTTTGGTCATTTTACCTTTTGAGGGTATTT
1 GAGGGTATTTCAGTCATTTTACCTTTCGAGGGTATTT
42085504 CAGTCATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.17, C:0.11, G:0.25, T:0.47
Consensus pattern (38 bp):
GAGGGTATTTCAGTCATTTTACCTTTCGAGGGTATTTT
Found at i:42085506 original size:65 final size:65
Alignment explanation
Indices: 42085402--42085530 Score: 222
Period size: 65 Copynumber: 2.0 Consensus size: 65
42085392 TTTACCCTTC
*
42085402 GAGGGTATTTTAGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCTTTCGAGGGTATTTT
1 GAGGGTATTTTAGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTT
* * *
42085467 GAGGGTATTTTGGTCATTTTACCTTTTGAGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTT
1 GAGGGTATTTTAGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTT
42085531 CAGTCATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.18, C:0.15, G:0.22, T:0.45
Consensus pattern (65 bp):
GAGGGTATTTTAGTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTT
Found at i:42094797 original size:2 final size:2
Alignment explanation
Indices: 42094790--42094834 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
42094780 AATAGAGCTT
42094790 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
42094832 TC T
1 TC T
42094835 TTTTATTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:42096732 original size:28 final size:28
Alignment explanation
Indices: 42096701--42096754 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
42096691 CAGTAACAGT
*
42096701 ATAGTGTGAGCCTTAGCCCAATACAGAA
1 ATAGTGTGAGCCTAAGCCCAATACAGAA
* *
42096729 ATAGTGTGGGCCTAAGCCCGATACAG
1 ATAGTGTGAGCCTAAGCCCAATACAG
42096755 TATCAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.20
Consensus pattern (28 bp):
ATAGTGTGAGCCTAAGCCCAATACAGAA
Found at i:42096996 original size:32 final size:32
Alignment explanation
Indices: 42096946--42097023 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
42096936 AAATGGCTAC
* *
42096946 AAGCCATCAATAATGGTAATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
*
42096978 AAGCCATCAGTAACGGTAATATGATCGGTACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
42097010 AAGCCATCAGTAAC
1 AAGCCATCAGTAAC
42097024 ATCGTAGTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAACGGTAATATGATCGGCACA
Found at i:42097289 original size:27 final size:27
Alignment explanation
Indices: 42097266--42097404 Score: 179
Period size: 27 Copynumber: 5.1 Consensus size: 27
42097256 TCGAGGGTCG
42097266 TTACGGTCATTTTACCCTACAGGGGTA
1 TTACGGTCATTTTACCCTACAGGGGTA
* *
42097293 TTACAGTCATTTTACCTTACAGGGGTA
1 TTACGGTCATTTTACCCTACAGGGGTA
**
42097320 TTACGGTCATTTTACCCTATGGGGGTA
1 TTACGGTCATTTTACCCTACAGGGGTA
* * **
42097347 TTACAGTCATTTTATCCTATGGGGGTA
1 TTACGGTCATTTTACCCTACAGGGGTA
* **
42097374 TTACGGTCATTTTATCCTATGGGGGTA
1 TTACGGTCATTTTACCCTACAGGGGTA
42097401 TTAC
1 TTAC
42097405 AGTTATTATA
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 103 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (27 bp):
TTACGGTCATTTTACCCTACAGGGGTA
Found at i:42097326 original size:54 final size:54
Alignment explanation
Indices: 42097266--42097417 Score: 225
Period size: 54 Copynumber: 2.8 Consensus size: 54
42097256 TCGAGGGTCG
**
42097266 TTACGGTCATTTTACCCTACAGGGGTATTACAGTCATTTTACCTTACAGGGGTA
1 TTACGGTCATTTTACCCTATGGGGGTATTACAGTCATTTTACCTTACAGGGGTA
**
42097320 TTACGGTCATTTTACCCTATGGGGGTATTACAGTCATTTTATCC-TATGGGGGTA
1 TTACGGTCATTTTACCCTATGGGGGTATTACAGTCATTTTA-CCTTACAGGGGTA
* * *
42097374 TTACGGTCATTTTATCCTATGGGGGTATTACAGTTATTATACCT
1 TTACGGTCATTTTACCCTATGGGGGTATTACAGTCATTTTACCT
42097418 ATTTTAGGGT
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
53 2 0.02
54 85 0.96
55 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (54 bp):
TTACGGTCATTTTACCCTATGGGGGTATTACAGTCATTTTACCTTACAGGGGTA
Found at i:42102692 original size:25 final size:25
Alignment explanation
Indices: 42102663--42102747 Score: 98
Period size: 25 Copynumber: 3.1 Consensus size: 25
42102653 AAAATATTTG
42102663 AAATATTTTAATATAATTTAATATAA
1 AAATATTTTAATATAATTTAATAT-A
*
42102689 AATATTTTATTTTAAAATATAATTTAAAATA
1 AA-A---TATTTT--AATATAATTTAATATA
42102720 AAATATTTTAATATAATTTAATATA
1 AAATATTTTAATATAATTTAATATA
42102745 AAA
1 AAA
42102748 ATAATTATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
25 18 0.35
26 2 0.04
27 7 0.14
30 7 0.14
31 3 0.06
32 14 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATATTTTAATATAATTTAATATA
Found at i:42102704 original size:15 final size:15
Alignment explanation
Indices: 42102666--42102708 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
42102656 ATATTTGAAA
* *
42102666 TATTTTAATATAATT
1 TATTTTAAAATATTT
* *
42102681 TAATATAAAATATTT
1 TATTTTAAAATATTT
42102696 TATTTTAAAATAT
1 TATTTTAAAATAT
42102709 AATTTAAAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTTAAAATATTT
Found at i:42102758 original size:32 final size:31
Alignment explanation
Indices: 42102665--42102758 Score: 108
Period size: 27 Copynumber: 3.2 Consensus size: 31
42102655 AATATTTGAA
42102665 ATATTTTAATATAATTTAATATAAAAT-ATT
1 ATATTTTAATATAATTTAATATAAAATAATT
* * * *
42102695 TTATTTT-A-A-AATATAATTTAAAATAA-A
1 ATATTTTAATATAATTTAATATAAAATAATT
42102722 ATATTTTAATATAATTTAATATAAAAATAATT
1 ATATTTTAATATAATTTAATAT-AAAATAATT
42102754 ATATT
1 ATATT
42102759 AAGAATGTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
27 19 0.38
28 3 0.06
29 2 0.04
30 14 0.28
31 7 0.14
32 5 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
ATATTTTAATATAATTTAATATAAAATAATT
Found at i:42102786 original size:35 final size:35
Alignment explanation
Indices: 42102747--42102816 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
42102737 TTAATATAAA
* * *
42102747 AATAATTATATTAAGAATGTTATTAAATTA-TATTT
1 AATAATAATATTAA-AATATGATTAAATTATTATTT
42102782 AATAATAATATTAAAATATGATTAAATTATTATTT
1 AATAATAATATTAAAATATGATTAAATTATTATTT
42102817 TTTATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 13 0.42
35 18 0.58
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (35 bp):
AATAATAATATTAAAATATGATTAAATTATTATTT
Found at i:42102793 original size:23 final size:22
Alignment explanation
Indices: 42102750--42102806 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
42102740 ATATAAAAAT
**
42102750 AATTATATTAAGAATGTTATTA
1 AATTATATTAAGAATAATATTA
*
42102772 AATTATATTTAATAATAATATTA
1 AATTATA-TTAAGAATAATATTA
*
42102795 AAATATGATTAA
1 AATTAT-ATTAA
42102807 ATTATTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 7 0.24
23 21 0.72
24 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (22 bp):
AATTATATTAAGAATAATATTA
Found at i:42105231 original size:21 final size:21
Alignment explanation
Indices: 42105206--42105247 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
42105196 TATAACTTTC
42105206 TTTTTATTTACCAAAATATAT
1 TTTTTATTTACCAAAATATAT
42105227 TTTTTATTTACCAAAATATAT
1 TTTTTATTTACCAAAATATAT
42105248 CAAAAAAAAC
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:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTTATTTACCAAAATATAT
Found at i:42105377 original size:27 final size:27
Alignment explanation
Indices: 42105300--42105384 Score: 116
Period size: 27 Copynumber: 3.1 Consensus size: 27
42105290 CGTTGGTCAC
* *
42105300 GCCAAAGCCATTGGTGGCACCAAAGGT
1 GCCAAAGCCATTGGCGGCACCAATGGT
* *
42105327 GCCAAAACTATTGGCGGCACCAATGGT
1 GCCAAAGCCATTGGCGGCACCAATGGT
* *
42105354 GCCAATGCCATTGGCGGCACCAATGTT
1 GCCAAAGCCATTGGCGGCACCAATGGT
42105381 GCCA
1 GCCA
42105385 TACTGATTGG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18
Consensus pattern (27 bp):
GCCAAAGCCATTGGCGGCACCAATGGT
Found at i:42105393 original size:27 final size:26
Alignment explanation
Indices: 42105309--42105400 Score: 98
Period size: 27 Copynumber: 3.4 Consensus size: 26
42105299 CGCCAAAGCC
* *
42105309 ATTGGTGGCACCAAAGGTGCCAAAACT-
1 ATTGGCGGCACCAATGGTGCC--AACTG
42105336 ATTGGCGGCACCAATGGTGCCAA-TG
1 ATTGGCGGCACCAATGGTGCCAACTG
*
42105361 CCATTGGCGGCACCAATGTTGCCATACTG
1 --ATTGGCGGCACCAATGGTGCCA-ACTG
42105390 ATTGGCGGCAC
1 ATTGGCGGCAC
42105401 TACTCGTATT
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
24 1 0.02
25 2 0.04
27 51 0.89
28 1 0.02
29 2 0.04
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.21
Consensus pattern (26 bp):
ATTGGCGGCACCAATGGTGCCAACTG
Found at i:42105564 original size:19 final size:21
Alignment explanation
Indices: 42105526--42105564 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
42105516 AATAATTGAT
*
42105526 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
42105547 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
42105565 TTGTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:42106519 original size:18 final size:18
Alignment explanation
Indices: 42106496--42106540 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
42106486 TTGACATGGT
*
42106496 TGGTGGTGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
42106514 TGGTGGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
42106532 TGGTGGCGA
1 TGGTGGCGA
42106541 TCATTGGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.29, C:0.04, G:0.51, T:0.16
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:42114654 original size:4 final size:4
Alignment explanation
Indices: 42114638--42114764 Score: 77
Period size: 4 Copynumber: 31.0 Consensus size: 4
42114628 CTCCTTTCCT
*
42114638 TTTC TTTC CTTC TTTC TTTC TTT- TTTC TTCTCC TTTCC TTT- TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C TTTC T-TTC
* * *
42114684 -TTC TTTC TTTC TTTT TTTC TCTTC -TCC TTTCC TTTTC TTTC CTTC -TT-
1 TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTT-C -TTTC TTTC TTTC TTTC
* *
42114731 TTTC TTTC TTTCC TCTCC TTCC TTTC TTTC TTTC
1 TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC
42114765 CCTCTCCTTC
Statistics
Matches: 100, Mismatches: 9, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
3 13 0.13
4 64 0.64
5 16 0.16
6 7 0.07
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:42114696 original size:45 final size:45
Alignment explanation
Indices: 42114629--42114765 Score: 144
Period size: 45 Copynumber: 3.2 Consensus size: 45
42114619 NNNNNNNNTC
* * *
42114629 TCCTTTCCTT-TTCTTTCCTTCTTTCTTTCT-TTTTTCTTCTCCTT
1 TCCTTTCCTTCTTCTTTCTTTCTTTCTTTCTCTTCTCCTT-TCCTT
* *
42114673 TCCTTTTCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTT
1 TCCTTTCCTTCTTCTTTCTTTCTTTCTTTCTCTTCTCCTTTCCTT
* * *
42114718 TTCTTTCCTTCTT-TTTCTTTCTTTC-CTCTCCT-TCCTTT-CTT
1 TCCTTTCCTTCTTCTTTCTTTCTTTCTTTCTCTTCTCCTTTCCTT
42114759 T-CTTTCC
1 TCCTTTCC
42114766 CTCTCCTTCT
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
40 6 0.07
41 4 0.05
42 6 0.07
43 5 0.06
44 20 0.25
45 34 0.42
46 6 0.07
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (45 bp):
TCCTTTCCTTCTTCTTTCTTTCTTTCTTTCTCTTCTCCTTTCCTT
Found at i:42114718 original size:40 final size:42
Alignment explanation
Indices: 42114627--42114760 Score: 182
Period size: 40 Copynumber: 3.5 Consensus size: 42
42114617 NNNNNNNNNN
42114627 TCTCCTTTCCTTTTCTTTCCTTCTTTCTTTC--TTTTT-TCT
1 TCTCCTTTCCTTTTCTTTCCTTCTTTCTTTCTTTTTTTCTCT
42114666 TCTCCTTTCCTTTTC-TT-CTTCTTTCTTTCTTTTTTTCTCT
1 TCTCCTTTCCTTTTCTTTCCTTCTTTCTTTCTTTTTTTCTCT
*
42114706 TCTCCTTTCCTTTTCTTTCCTTC-TT-TTTCTTTCTTTC-C-
1 TCTCCTTTCCTTTTCTTTCCTTCTTTCTTTCTTTTTTTCTCT
42114744 TCTCC-TTCC-TTTCTTTC
1 TCTCCTTTCCTTTTCTTTC
42114761 TTTCCCTCTC
Statistics
Matches: 89, Mismatches: 1, Indels: 13
0.86 0.01 0.13
Matches are distributed among these distances:
36 8 0.09
37 16 0.18
38 7 0.08
39 21 0.24
40 29 0.33
41 4 0.04
42 4 0.04
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (42 bp):
TCTCCTTTCCTTTTCTTTCCTTCTTTCTTTCTTTTTTTCTCT
Found at i:42114731 original size:18 final size:18
Alignment explanation
Indices: 42114631--42114760 Score: 79
Period size: 18 Copynumber: 6.8 Consensus size: 18
42114621 NNNNNNTCTC
42114631 CTTTCCTTTTCTTTCCTT
1 CTTTCCTTTTCTTTCCTT
* * *
42114649 CTTTCTTTCTTTTTTCTTCTC
1 CTTTCCTT-TTCTTTC--CTT
*
42114670 CTTTCCTTTTCTTCTTCTTT
1 CTTTCCTTTTC-T-TTCCTT
42114690 CTTT-CTTTT-TTTCTCTTCT
1 CTTTCCTTTTCTTTC-C-T-T
42114709 CCTTTCCTTTTCTTTCCTT
1 -CTTTCCTTTTCTTTCCTT
*
42114728 CTTT-TTCTTTCTTTCCTCT
1 CTTTCCT-TTTCTTTCCT-T
*
42114747 CCTTCC-TTTCTTTC
1 CTTTCCTTTTCTTTC
42114761 TTTCCCTCTC
Statistics
Matches: 87, Mismatches: 11, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
16 3 0.03
17 2 0.02
18 30 0.34
19 17 0.20
20 12 0.14
21 16 0.18
22 7 0.08
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (18 bp):
CTTTCCTTTTCTTTCCTT
Found at i:42114775 original size:18 final size:18
Alignment explanation
Indices: 42114717--42114775 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
42114707 CTCCTTTCCT
* **
42114717 TTTCTTTCCTTCTTTTTC
1 TTTCTTTCCCTCTCCTTC
42114735 TTTCTTTCCTCTCCTTCCTTTC
1 TTTCTTTCC-CT-C-TCC-TTC
42114757 TTTCTTTCCCTCTCCTTC
1 TTTCTTTCCCTCTCCTTC
42114775 T
1 T
42114776 GCCCCCCCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
18 13 0.38
19 4 0.12
20 2 0.06
21 3 0.09
22 12 0.35
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTCTTTCCCTCTCCTTC
Found at i:42114933 original size:18 final size:17
Alignment explanation
Indices: 42114900--42114933 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42114890 TTTTTGTCTA
*
42114900 GTTTTTTTTATTTTTTT
1 GTTTTTTTTATATTTTT
42114917 GTTTTTTTATATATTTT
1 GTTTTTTT-TATATTTT
42114934 GGTAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (17 bp):
GTTTTTTTTATATTTTT
Found at i:42115222 original size:13 final size:13
Alignment explanation
Indices: 42115204--42115228 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42115194 TTTAAGGTTT
42115204 TTTAGAGTTTTTG
1 TTTAGAGTTTTTG
42115217 TTTAGAGTTTTT
1 TTTAGAGTTTTT
42115229 TAGGGTTTTT
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:0.00, G:0.20, T:0.64
Consensus pattern (13 bp):
TTTAGAGTTTTTG
Found at i:42115226 original size:23 final size:24
Alignment explanation
Indices: 42115200--42115265 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
42115190 GATTTTTAAG
42115200 GTTTTTTAGAGTTTTT-GTTTAGA
1 GTTTTTTAGAGTTTTTAGTTTAGA
* * *
42115223 GTTTTTTAGGGTTTTTATTTTAGG
1 GTTTTTTAGAGTTTTTAGTTTAGA
*
42115247 GTTTTTTTAGATTTTTTAG
1 G-TTTTTTAGAGTTTTTAG
42115266 ATTTTTAACT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 15 0.43
24 6 0.17
25 14 0.40
ACGTcount: A:0.15, C:0.00, G:0.21, T:0.64
Consensus pattern (24 bp):
GTTTTTTAGAGTTTTTAGTTTAGA
Found at i:42115238 original size:24 final size:23
Alignment explanation
Indices: 42115200--42115262 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
42115190 GATTTTTAAG
42115200 GTTTTTTAGAGTTTT-TGTTTAGA
1 GTTTTTTAGAGTTTTAT-TTTAGA
* *
42115223 GTTTTTTAGGGTTTTTATTTTAGG
1 GTTTTTTAGAG-TTTTATTTTAGA
*
42115247 GTTTTTTTAGATTTTT
1 G-TTTTTTAGAGTTTT
42115263 TAGATTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
23 10 0.30
24 14 0.42
25 9 0.27
ACGTcount: A:0.14, C:0.00, G:0.21, T:0.65
Consensus pattern (23 bp):
GTTTTTTAGAGTTTTATTTTAGA
Found at i:42115253 original size:15 final size:14
Alignment explanation
Indices: 42115226--42115252 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42115216 GTTTAGAGTT
42115226 TTTTAGGGTTTTTA
1 TTTTAGGGTTTTTA
42115240 TTTTAGGGTTTTT
1 TTTTAGGGTTTTT
42115253 TTAGATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.00, G:0.22, T:0.67
Consensus pattern (14 bp):
TTTTAGGGTTTTTA
Found at i:42115311 original size:18 final size:18
Alignment explanation
Indices: 42115250--42115311 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 18
42115240 TTTTAGGGTT
*
42115250 TTTTTAGATTTTTTA-GA
1 TTTTTAGATTTTTTATAA
42115267 TTTTTA-ACTCTTTTTATATA
1 TTTTTAGA-T-TTTTTATA-A
*
42115287 TTCTTTAGGTTTTTTATAA
1 TT-TTTAGATTTTTTATAA
42115306 TTTTTA
1 TTTTTA
42115312 TAATTGTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
16 1 0.03
17 7 0.19
18 10 0.27
19 3 0.08
20 11 0.30
21 5 0.14
ACGTcount: A:0.23, C:0.05, G:0.06, T:0.66
Consensus pattern (18 bp):
TTTTTAGATTTTTTATAA
Found at i:42115355 original size:20 final size:20
Alignment explanation
Indices: 42115332--42115379 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
42115322 AAATATATAA
*
42115332 ATTTTGAAATTTTTATAAA-T
1 ATTTTGAAA-TTTTAAAAATT
42115352 ATTTTG-AATTTTAAAAATT
1 ATTTTGAAATTTTAAAAATT
42115371 ATTTTGAAA
1 ATTTTGAAA
42115380 ATTGTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 8 0.32
19 9 0.36
20 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (20 bp):
ATTTTGAAATTTTAAAAATT
Found at i:42118017 original size:40 final size:40
Alignment explanation
Indices: 42117945--42118053 Score: 137
Period size: 40 Copynumber: 2.7 Consensus size: 40
42117935 TGTCCCTGTT
* * * * *
42117945 TGCACATTAGTGTCCCTATTTGTACTTTGGTACCCTTAAA
1 TGCACATTTGTGCCCCTATTTGAACTTCGGTACCCCTAAA
*
42117985 TGCACATTTGTGCCCCTGTTTGAACTTCGGTACCCCTAAA
1 TGCACATTTGTGCCCCTATTTGAACTTCGGTACCCCTAAA
* * *
42118025 TGCACATTTGTGCTCCTTTTTGCACTTCG
1 TGCACATTTGTGCCCCTATTTGAACTTCG
42118054 ATGCCCCTGA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.39
Consensus pattern (40 bp):
TGCACATTTGTGCCCCTATTTGAACTTCGGTACCCCTAAA
Found at i:42125276 original size:33 final size:33
Alignment explanation
Indices: 42125239--42125309 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
42125229 CTGATTTAGT
42125239 CTTCTCCTCATCTCCCTCTAGTCCTGTTGTGGC
1 CTTCTCCTCATCTCCCTCTAGTCCTGTTGTGGC
* *
42125272 CTTCTCCTTATCTCCCTCTAGTCCTTTTGTGGC
1 CTTCTCCTCATCTCCCTCTAGTCCTGTTGTGGC
42125305 CTTCT
1 CTTCT
42125310 TCATAGTGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.06, C:0.38, G:0.13, T:0.44
Consensus pattern (33 bp):
CTTCTCCTCATCTCCCTCTAGTCCTGTTGTGGC
Found at i:42127688 original size:36 final size:36
Alignment explanation
Indices: 42127643--42127738 Score: 149
Period size: 36 Copynumber: 2.7 Consensus size: 36
42127633 AATTATCACT
* *
42127643 CTTA-AATATCACAACTATATCATTAGGCCGAATCA
1 CTTATAATATCACAAGTATATCAATAGGCCGAATCA
* *
42127678 CTTATAATATCACAAGTATATTAATATGCCGAATCA
1 CTTATAATATCACAAGTATATCAATAGGCCGAATCA
42127714 CTTATAATATCACAAGTATATCAAT
1 CTTATAATATCACAAGTATATCAAT
42127739 TCAAATATAC
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 4 0.07
36 51 0.93
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (36 bp):
CTTATAATATCACAAGTATATCAATAGGCCGAATCA
Found at i:42128030 original size:43 final size:43
Alignment explanation
Indices: 42127933--42128060 Score: 120
Period size: 43 Copynumber: 3.0 Consensus size: 43
42127923 TCATATATCA
* * *
42127933 ATGCC-ACTGTCCCAGACAGGGTCTTACAC--AAA-TCAAATACG
1 ATGCCAAC-GTCCCAGAAATGGTCTTACACGAAAACACAAAT-CG
* * * *
42127974 ATGCCGATGTCCCAGAAATTGTCTTACACGTAAACACAAATCG
1 ATGCCAACGTCCCAGAAATGGTCTTACACGAAAACACAAATCG
** *
42128017 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACATATCG
1 ATGCCAACGTCCCAGAAATGGTCTTACACGAAAACACAAATCG
42128060 A
1 A
42128061 AAATCCTATG
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 23 0.32
42 1 0.01
43 42 0.59
44 5 0.07
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.20
Consensus pattern (43 bp):
ATGCCAACGTCCCAGAAATGGTCTTACACGAAAACACAAATCG
Found at i:42130410 original size:12 final size:13
Alignment explanation
Indices: 42130393--42130422 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
42130383 TCCTCATTTT
42130393 TTCTTCATCTC-C
1 TTCTTCATCTCTC
42130405 TTCTTCATCTCTC
1 TTCTTCATCTCTC
42130418 TTCTT
1 TTCTT
42130423 TCAAAATCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.07, C:0.37, G:0.00, T:0.57
Consensus pattern (13 bp):
TTCTTCATCTCTC
Found at i:42131492 original size:27 final size:27
Alignment explanation
Indices: 42131417--42131495 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
42131407 ATGGAGGAAG
* * *
42131417 TACTGTTATTGGTGGCTCTACCACAAA
1 TACTATTACTGGTGGCTCTGCCACAAA
**
42131444 TACTATTACTGGTGGCTCTGCCACACT
1 TACTATTACTGGTGGCTCTGCCACAAA
*
42131471 TACTATTACTGGTGGCTTTGCCACA
1 TACTATTACTGGTGGCTCTGCCACA
42131496 TATATTGCAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (27 bp):
TACTATTACTGGTGGCTCTGCCACAAA
Found at i:42133204 original size:43 final size:43
Alignment explanation
Indices: 42133100--42133226 Score: 127
Period size: 43 Copynumber: 3.0 Consensus size: 43
42133090 TCGTATATCA
* * *
42133100 ATGCC-ACTGTCCCAGACAGGGTCTTCCACG--AA-TCAAATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGAAAACACAAAT-CG
* * * *
42133141 ATGCCGATGTCCCAGACATGGTCTTACAGGTAAACACAAATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAAACACAAATCG
* *
42133184 ATGCCAACGTCCCAGGCATGGTCTTACACGAAAACACATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAAACACAAATCG
42133227 TAAATCCTAT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 24 0.34
42 1 0.01
43 41 0.58
44 5 0.07
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGAAAACACAAATCG
Found at i:42134396 original size:48 final size:48
Alignment explanation
Indices: 42134333--42134437 Score: 149
Period size: 48 Copynumber: 2.2 Consensus size: 48
42134323 ATTAACAACT
* * *
42134333 AAACAAGA-ATTTTTCTGCTACATTAATACAACAAACAACAGTCCTTA
1 AAACAACATATTTTTCTACTAAATTAATACAACAAACAACAGTCCTTA
* * *
42134380 AAATAACATATTTTTCTACTAAATTAATACACCAAACATCAGTCCTTA
1 AAACAACATATTTTTCTACTAAATTAATACAACAAACAACAGTCCTTA
42134428 AAACAACATA
1 AAACAACATA
42134438 AATACACCAC
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
47 6 0.12
48 44 0.88
ACGTcount: A:0.47, C:0.21, G:0.04, T:0.29
Consensus pattern (48 bp):
AAACAACATATTTTTCTACTAAATTAATACAACAAACAACAGTCCTTA
Found at i:42144231 original size:19 final size:19
Alignment explanation
Indices: 42144207--42144338 Score: 201
Period size: 19 Copynumber: 6.8 Consensus size: 19
42144197 AATTTTTTAG
*
42144207 GATATGCAATCTTATATAT
1 GATATGCAATCTTAGATAT
*
42144226 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
42144245 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
42144264 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
42144285 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
42144304 GATGTATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
42144323 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
42144339 AGATATGATT
Statistics
Matches: 102, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
19 83 0.81
21 19 0.19
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:42144274 original size:59 final size:57
Alignment explanation
Indices: 42144207--42144345 Score: 201
Period size: 59 Copynumber: 2.4 Consensus size: 57
42144197 AATTTTTTAG
* *
42144207 GATATGCAATCTTATATATGATATGCAATCCTAGATATGATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATAT
* * *
42144264 GATATATGCAATCTTAGATATGATATGCAATCTTAGATATGATGTATAATCTTAGATAT
1 G--ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATAT
42144323 GATATGCAATCTTAGA-A-GATATG
1 GATATGCAATCTTAGATATGATATG
42144346 ATTTTGTAAT
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
55 6 0.08
56 1 0.01
57 16 0.21
59 52 0.69
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (57 bp):
GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATAT
Done.