Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008647.1 Hibiscus syriacus cultivar Beakdansim tig00111634_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1422586
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1263991 original size:20 final size:20
Alignment explanation
Indices: 1263968--1264043 Score: 134
Period size: 20 Copynumber: 3.8 Consensus size: 20
1263958 ATTCGCATTG
*
1263968 CATTTCGCATTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
*
1263988 CATTTCGCGTTGTGATTTTC
1 CATTTCGCGTTGCGATTTTC
1264008 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
1264028 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1264044 AGTTGAAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.45
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:1264058 original size:21 final size:21
Alignment explanation
Indices: 1264032--1264077 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1264022 ATTTTCCATT
1264032 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
1264053 TCGCGTTGCGGTAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
1264074 TCGC
1 TCGC
1264078 AACGCGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.28
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:1264103 original size:41 final size:41
Alignment explanation
Indices: 1264053--1264149 Score: 140
Period size: 41 Copynumber: 2.4 Consensus size: 41
1264043 TAGTTGAAAA
1264053 TCGCGTTGCGGTAGTTGAAAATCGCAACGCGATTTTCCATT
1 TCGCGTTGCGGTAGTTGAAAATCGCAACGCGATTTTCCATT
* *** *
1264094 TCGCATTGCGGTAGTTGAAAATCGCGTTGCGCTTTTCCATT
1 TCGCGTTGCGGTAGTTGAAAATCGCAACGCGATTTTCCATT
*
1264135 TCGCGTTGCGATAGT
1 TCGCGTTGCGGTAGT
1264150 CTACAGTTGT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.34
Consensus pattern (41 bp):
TCGCGTTGCGGTAGTTGAAAATCGCAACGCGATTTTCCATT
Found at i:1264168 original size:17 final size:17
Alignment explanation
Indices: 1264146--1264180 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1264136 CGCGTTGCGA
1264146 TAGTCTACAGTTGTCGT
1 TAGTCTACAGTTGTCGT
1264163 TAGTCTACAGTTGTCGT
1 TAGTCTACAGTTGTCGT
1264180 T
1 T
1264181 GCGATAGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (17 bp):
TAGTCTACAGTTGTCGT
Found at i:1264188 original size:22 final size:22
Alignment explanation
Indices: 1264138--1264207 Score: 105
Period size: 22 Copynumber: 3.4 Consensus size: 22
1264128 TTCCATTTCG
1264138 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1264160 CG-T----TAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1264177 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1264199 CGTTGCGAT
1 CGTTGCGAT
1264208 TTTCCAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
17 16 0.37
18 1 0.02
21 1 0.02
22 25 0.58
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:1264231 original size:13 final size:13
Alignment explanation
Indices: 1264213--1264238 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1264203 GCGATTTTCC
1264213 AAATTCGTTGTGA
1 AAATTCGTTGTGA
1264226 AAATTCGTTGTGA
1 AAATTCGTTGTGA
1264239 TAGTTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
AAATTCGTTGTGA
Found at i:1264330 original size:6 final size:6
Alignment explanation
Indices: 1264319--1264379 Score: 108
Period size: 6 Copynumber: 10.5 Consensus size: 6
1264309 GACACGTATT
1264319 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1264367 ACCA-G ACC-CG ACC
1 ACCACG ACCACG ACC
1264380 CGAGACGGAC
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
5 8 0.15
6 46 0.85
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1264882 original size:6 final size:6
Alignment explanation
Indices: 1264862--1264898 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
1264852 GTCCGTCTCG
1264862 GGTCG- GGTC-T GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1264899 AATACGTGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 8 0.27
6 22 0.73
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:1265036 original size:22 final size:22
Alignment explanation
Indices: 1264962--1265036 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
1264952 TTTTTTTTTA
*
1264962 ACTATCGCAACAACAACTGTAG
1 ACTATCGCAACGACAACTGTAG
* *
1264984 ACTATCGCAACG--AA-TTTGG
1 ACTATCGCAACGACAACTGTAG
**
1265003 AAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGACAACTGTAG
1265025 ACTATCGCAACG
1 ACTATCGCAACG
1265037 CGAAATGGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
19 13 0.32
20 2 0.05
21 2 0.05
22 24 0.59
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (22 bp):
ACTATCGCAACGACAACTGTAG
Found at i:1265070 original size:41 final size:41
Alignment explanation
Indices: 1265025--1265121 Score: 149
Period size: 41 Copynumber: 2.4 Consensus size: 41
1265015 ACAACTGTAG
***
1265025 ACTATCGCAACGCGAAATGGAAAACCGCGTTGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAACCGCAACGCGATTTTCA
* *
1265066 ACTATCGCAACGCCAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAACCGCAACGCGATTTTCA
1265107 ACTATCGCAACGCGA
1 ACTATCGCAACGCGA
1265122 TTTTCAACTA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAACCGCAACGCGATTTTCA
Found at i:1265115 original size:21 final size:21
Alignment explanation
Indices: 1265056--1265142 Score: 104
Period size: 21 Copynumber: 4.2 Consensus size: 21
1265046 AAACCGCGTT
1265056 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
* ** ** *
1265077 GCCAAATGGAA-AATCGCAAC
1 GCGATTTTCAACTATCGCAAC
1265097 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
*
1265118 GCGATTTTCAACTATCGCAAT
1 GCGATTTTCAACTATCGCAAC
1265139 GCGA
1 GCGA
1265143 AATGCAACGC
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 14 0.27
21 38 0.73
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (21 bp):
GCGATTTTCAACTATCGCAAC
Found at i:1265313 original size:2 final size:2
Alignment explanation
Indices: 1265306--1265384 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
1265296 AAGCTCAACC
1265306 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1265348 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1265385 TCGGGGTGGA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1265474 original size:15 final size:15
Alignment explanation
Indices: 1265456--1265484 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1265446 AACCGGACCG
1265456 AACCGAATTAATCAT
1 AACCGAATTAATCAT
1265471 AACCGAATTAATCA
1 AACCGAATTAATCA
1265485 AACTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.24
Consensus pattern (15 bp):
AACCGAATTAATCAT
Found at i:1265910 original size:179 final size:183
Alignment explanation
Indices: 1265627--1265991 Score: 589
Period size: 179 Copynumber: 2.0 Consensus size: 183
1265617 AAATTAAATG
*
1265627 TTTTTAATTAAAAAAAAGCTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
1 TTTTTAATTAAAAAAAAGCTTACAATTAATTTAAATAATATATAATTAT-AAATAAAAATTTCAG
1265692 ATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT-GTATCTTAAATTATTAAT
65 ATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAG-ATCTTAAATTATTAAT
* *
1265756 TGGGTTTTAAATGGGTTGGGCTTAGCCCATATGTTATATATAATATATTTAATAT
129 TGGATTTTAAATGGGTTGGGCTGAGCCCATATGTTATATATAATATATTTAATAT
** *
1265811 TTTTTAATTAAAAAAACATTTTACAATTAATTTAAATAATATATAATTAT-AA-AAAAA-TT-AT
1 TTTTTAATTAAAAAAA-AGCTTACAATTAATTTAAATAATATATAATTATAAATAAAAATTTCAG
*
1265872 AT-AATTTTTTAATTAGTTAATATTGATTTAGGTTTAAAAGTTATTAGATCTTAAATTATTAATT
65 ATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAGATCTTAAATTATTAATT
*
1265936 GGATTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATTTAATAT
130 GGATTTTAAATGGGTTGGGCTGAGCCCATATGTTATATATAATATATTTAATAT
1265990 TT
1 TT
1265992 AAAATTTAAT
Statistics
Matches: 171, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
179 112 0.65
180 4 0.02
181 2 0.01
182 5 0.03
183 2 0.01
184 16 0.09
185 30 0.18
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (183 bp):
TTTTTAATTAAAAAAAAGCTTACAATTAATTTAAATAATATATAATTATAAATAAAAATTTCAGA
TAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAGATCTTAAATTATTAATTG
GATTTTAAATGGGTTGGGCTGAGCCCATATGTTATATATAATATATTTAATAT
Found at i:1275350 original size:6 final size:6
Alignment explanation
Indices: 1275339--1275364 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1275329 GGAACTAACC
1275339 GAATTT GAATTT GAATTT GAATTT GA
1 GAATTT GAATTT GAATTT GAATTT GA
1275365 GACTGCACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (6 bp):
GAATTT
Found at i:1277375 original size:81 final size:81
Alignment explanation
Indices: 1277262--1277682 Score: 647
Period size: 81 Copynumber: 5.2 Consensus size: 81
1277252 AAGCATTTAG
* * * * *
1277262 TCTTTTACCCAAAGGCATTCAACCTTTCATCTAACTTGCATGATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGC
*
1277327 ACAGCTAGTCAATTAA
66 ACAGCTAGACAATTAA
* *
1277343 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATCGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGC
1277408 ACAGCTAGACAATTAA
66 ACAGCTAGACAATTAA
* * *
1277424 TCTTTTACTCAAAGGTATTTAACATTTTATCTAACTAGCATAATTGTA-ACCTTTCTGTCAAATG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTG-ACACCTTTCTGTCAAATG
1277488 CACAGCTAGACAATTAA
65 CACAGCTAGACAATTAA
*
1277505 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAA-TTGGCATAATTGACACATTTCTGTCAAATG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTT-GCATAATTGACACCTTTCTGTCAAATG
*
1277569 --CA-CTAGGCAATTAA
65 CACAGCTAGACAATTAA
1277583 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAAC-TGACATAATTGACACCTTTCTGTCAAATG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTG-CATAATTGACACCTTTCTGTCAAATG
*
1277647 CACAGCTAGTCAATTAA
65 CACAGCTAGACAATTAA
1277664 TCTTTTACTCAAAGGTATT
1 TCTTTTACTCAAAGGTATT
1277683 CACTCTCCCT
Statistics
Matches: 313, Mismatches: 19, Indels: 16
0.90 0.05 0.05
Matches are distributed among these distances:
77 1 0.00
78 71 0.23
79 2 0.01
80 4 0.01
81 234 0.75
82 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATGC
ACAGCTAGACAATTAA
Found at i:1282927 original size:15 final size:15
Alignment explanation
Indices: 1282907--1282935 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1282897 CTGGAGGGTA
1282907 GTATCGATACCAAGG
1 GTATCGATACCAAGG
1282922 GTATCGATACCAAG
1 GTATCGATACCAAG
1282936 AGTACCTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (15 bp):
GTATCGATACCAAGG
Found at i:1294251 original size:19 final size:19
Alignment explanation
Indices: 1294229--1294271 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1294219 TAAACACATG
*
1294229 TATGAGTT-ATATATGTTTA
1 TATGAGTTGATACATG-TTA
*
1294248 TATGATTTGATACATGTTA
1 TATGAGTTGATACATGTTA
1294267 TATGA
1 TATGA
1294272 TTCATGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (19 bp):
TATGAGTTGATACATGTTA
Found at i:1294357 original size:19 final size:19
Alignment explanation
Indices: 1294333--1294378 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1294323 TCATATGTAC
1294333 ATGATTATGTGATGAAATT
1 ATGATTATGTGATGAAATT
1294352 ATGATTATGTGATGAAATT
1 ATGATTATGTGATGAAATT
1294371 ATGATTAT
1 ATGATTAT
1294379 ATGAAGGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (19 bp):
ATGATTATGTGATGAAATT
Found at i:1296387 original size:81 final size:81
Alignment explanation
Indices: 1296254--1296673 Score: 513
Period size: 81 Copynumber: 5.2 Consensus size: 81
1296244 AAACGTTTAG
* ** * * * * *
1296254 TCTTTTACCCAAAGACATTTAATCTTTCATTTAATTTG-CATGATTAACACATTTCTATCAAATG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAA-CTGACATAATTGACACATTTCTATCAAATG
*
1296318 CACAACTAGGTAATTAA
65 CACAACTAGGCAATTAA
* * * *
1296335 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGATACATTTATGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACATTTCTATCAAATGC
* *
1296400 ACATC-ATGCAATTAA
66 ACAACTAGGCAATTAA
* * * *
1296415 TCTTTTACTCAAAGATATTTAACCTTTCATCTAACTGACATAATTGATACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACATTTCTATCAAATGC
*
1296480 ATC-GCTAGGCAATTAA
66 A-CAACTAGGCAATTAA
* *
1296496 TATTTTACTCAAATGTATTTAACCTTTCATCTAACTGACATAATTGACACATTTCTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACATTTCTATCAAATGC
* *
1296561 ACAGCTAGACAATTAA
66 ACAACTAGGCAATTAA
* * * * *
1296577 TCTTTTACTCAAAGGTATTTAACATTTTATTTAACTGACATAATTGACACCTTTATATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACATTTCTATCAAATGC
*
1296642 ACAACTAGACAATTAA
66 ACAACTAGGCAATTAA
* *
1296658 TTTTTTCCTCAAAGGT
1 TCTTTTACTCAAAGGT
1296674 GTTCATTCTC
Statistics
Matches: 298, Mismatches: 37, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
80 74 0.25
81 224 0.75
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.38
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACATTTCTATCAAATGC
ACAACTAGGCAATTAA
Found at i:1296519 original size:161 final size:162
Alignment explanation
Indices: 1296254--1296673 Score: 551
Period size: 161 Copynumber: 2.6 Consensus size: 162
1296244 AAACGTTTAG
* * * * * * *
1296254 TCTTTTACCCAAAGACATTTAATCTTTCATTTAATTTG-CATGATTAACACATTTCTATCAAATG
1 TCTTTTACTCAAAGATATTTAACCTTTCATTTAA-CTGACATAATTGACACCTTTCTATCAAATG
* * * *
1296318 CACAACTAGGTAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGAT
65 CACAACTAGGCAATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGAC
* *
1296383 ACATTTATGTCAAATGCACATC-ATG-CAATTAA
130 ACATTTATATCAAATGCACAGCTA-GACAATTAA
* * *
1296415 TCTTTTACTCAAAGATATTTAACCTTTCATCTAACTGACATAATTGATACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGATATTTAACCTTTCATTTAACTGACATAATTGACACCTTTCTATCAAATGC
* *
1296480 ATC-GCTAGGCAATTAATATTTTACTCAAATGTATTTAACCTTTCATCTAACTGACATAATTGAC
66 A-CAACTAGGCAATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGAC
*
1296544 ACATTTCTATCAAATGCACAGCTAGACAATTAA
130 ACATTTATATCAAATGCACAGCTAGACAATTAA
* * * *
1296577 TCTTTTACTCAAAGGTATTTAACATTTTATTTAACTGACATAATTGACACCTTTATATCAAATGC
1 TCTTTTACTCAAAGATATTTAACCTTTCATTTAACTGACATAATTGACACCTTTCTATCAAATGC
* * *
1296642 ACAACTAGACAATTAATTTTTTCCTCAAAGGT
66 ACAACTAGGCAATTAATATTTTACTCAAAGGT
1296674 GTTCATTCTC
Statistics
Matches: 223, Mismatches: 31, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
160 2 0.01
161 129 0.58
162 92 0.41
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.38
Consensus pattern (162 bp):
TCTTTTACTCAAAGATATTTAACCTTTCATTTAACTGACATAATTGACACCTTTCTATCAAATGC
ACAACTAGGCAATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACA
CATTTATATCAAATGCACAGCTAGACAATTAA
Found at i:1305039 original size:6 final size:6
Alignment explanation
Indices: 1305028--1305353 Score: 624
Period size: 6 Copynumber: 55.0 Consensus size: 6
1305018 TGGTACTACC
1305028 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1305076 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1305124 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1305172 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1305220 GTATAT GTATAT G--TAT GTATAT GTATAT GTATAT GTATAT G--TAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1305264 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1305312 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1305354 AGTACAGAGT
Statistics
Matches: 316, Mismatches: 0, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
4 8 0.03
6 308 0.97
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
GTATAT
Found at i:1305574 original size:2 final size:2
Alignment explanation
Indices: 1305567--1305608 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1305557 AAGTGTTTAA
1305567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1305609 TATTTAAGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1305834 original size:14 final size:14
Alignment explanation
Indices: 1305815--1305856 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
1305805 CGTTCGTGAA
1305815 CGTTCAGTTATGTT
1 CGTTCAGTTATGTT
1305829 CGTTCAGTTATGTT
1 CGTTCAGTTATGTT
*
1305843 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
1305857 TAACCCAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.14, C:0.14, G:0.19, T:0.52
Consensus pattern (14 bp):
CGTTCAGTTATGTT
Found at i:1307473 original size:42 final size:42
Alignment explanation
Indices: 1307409--1307492 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
1307399 TTAATTAATT
* *
1307409 TGAGTATTCTTTATTTATGTTTAAAATTAATTATATTTTAAA
1 TGAGTATTCTTTATTTAGGTTTAAAATTAATTAGATTTTAAA
1307451 TGAGTATTCTTTATTTAGGTTTAAAATTAATTAGATTTTAAA
1 TGAGTATTCTTTATTTAGGTTTAAAATTAATTAGATTTTAAA
1307493 ATATTAATGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (42 bp):
TGAGTATTCTTTATTTAGGTTTAAAATTAATTAGATTTTAAA
Found at i:1307579 original size:14 final size:14
Alignment explanation
Indices: 1307557--1307586 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1307547 GAGACTGAGC
*
1307557 TGAATATAAATGAA
1 TGAACATAAATGAA
1307571 TGAACATAAATGAA
1 TGAACATAAATGAA
1307585 TG
1 TG
1307587 GATTATCCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.27
Consensus pattern (14 bp):
TGAACATAAATGAA
Found at i:1307672 original size:40 final size:41
Alignment explanation
Indices: 1307619--1307698 Score: 108
Period size: 40 Copynumber: 1.9 Consensus size: 41
1307609 GACGGGTCAT
*
1307619 TTGTTCGTATTCGTTCCTTTAAT-TAAATGAACATAAAATA
1 TTGTTCATATTCGTTCCTTTAATATAAATGAACATAAAATA
* *
1307659 TTGTTCATGTTCGTTCGTTTAATAAATAAATGAACATAAA
1 TTGTTCATATTCGTTCCTTTAAT--ATAAATGAACATAAA
1307699 TGAACTTTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 20 0.59
43 14 0.41
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (41 bp):
TTGTTCATATTCGTTCCTTTAATATAAATGAACATAAAATA
Found at i:1309835 original size:28 final size:28
Alignment explanation
Indices: 1309768--1309907 Score: 163
Period size: 29 Copynumber: 4.9 Consensus size: 28
1309758 ATCACCTTTA
* * *
1309768 TTAAAAATAATTACCAAAATATCACCGTT
1 TTAAAAATAATTCCCAAAATGTCA-CATT
* *
1309797 TTACAAATAATTCCCAAAATGTCATATT
1 TTAAAAATAATTCCCAAAATGTCACATT
*
1309825 TTAAAAATAATTACCAAAATGTCACATTT
1 TTAAAAATAATTCCCAAAATGTCACA-TT
* **
1309854 TTCAAAATAATTCCCAAAATGTCATTTT
1 TTAAAAATAATTCCCAAAATGTCACATT
*
1309882 TTCAAAAATAATTCCCAAAATATCAC
1 TT-AAAAATAATTCCCAAAATGTCAC
1309908 TGAGTCGGGT
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
28 29 0.31
29 65 0.69
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.34
Consensus pattern (28 bp):
TTAAAAATAATTCCCAAAATGTCACATT
Found at i:1309862 original size:57 final size:57
Alignment explanation
Indices: 1309768--1309907 Score: 210
Period size: 57 Copynumber: 2.4 Consensus size: 57
1309758 ATCACCTTTA
*
1309768 TTAAAAATAATTACCAAAATATCACCGTTTTACAAATAATTCCCAAAATGTCATATT
1 TTAAAAATAATTACCAAAATATCACAGTTTTACAAATAATTCCCAAAATGTCATATT
* * *
1309825 TTAAAAATAATTACCAAAATGTCACA-TTTTTCAAAATAATTCCCAAAATGTCATTTT
1 TTAAAAATAATTACCAAAATATCACAGTTTTAC-AAATAATTCCCAAAATGTCATATT
*
1309882 TTCAAAAATAATTCCCAAAATATCAC
1 TT-AAAAATAATTACCAAAATATCAC
1309908 TGAGTCGGGT
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
56 5 0.07
57 49 0.65
58 21 0.28
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.34
Consensus pattern (57 bp):
TTAAAAATAATTACCAAAATATCACAGTTTTACAAATAATTCCCAAAATGTCATATT
Found at i:1316763 original size:28 final size:29
Alignment explanation
Indices: 1316652--1316843 Score: 200
Period size: 29 Copynumber: 6.8 Consensus size: 29
1316642 ACCTTTATTA
* * * *
1316652 AAAATAATTACCAATATATCACTATTTT-
1 AAAATAATTCCCAAAATGTCACTTTTTTC
* *
1316680 ACAAATAATTCCCAAAATTTCA-TTATTTTA
1 A-AAATAATTCCCAAAATGTCACTT-TTTTC
* * *
1316710 AAAATAATT-AC-GAATGTCACTGTTTT-
1 AAAATAATTCCCAAAATGTCACTTTTTTC
*
1316736 AAAA-AATTCCAAAAATGTCACTTTTTT-
1 AAAATAATTCCCAAAATGTCACTTTTTTC
* * *
1316763 TAAATAATTCCCAAAATTTCACCTTTTTC
1 AAAATAATTCCCAAAATGTCACTTTTTTC
1316792 AAAATAATTCCCAAAATGTCACTTTTTTC
1 AAAATAATTCCCAAAATGTCACTTTTTTC
1316821 AAAATAATTCCCAAAATGTCACT
1 AAAATAATTCCCAAAATGTCACT
1316844 GGGTCGGGTC
Statistics
Matches: 137, Mismatches: 19, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
25 4 0.03
26 4 0.03
27 26 0.19
28 24 0.18
29 78 0.57
30 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAATAATTCCCAAAATGTCACTTTTTTC
Found at i:1316776 original size:82 final size:86
Alignment explanation
Indices: 1316682--1316843 Score: 226
Period size: 82 Copynumber: 1.9 Consensus size: 86
1316672 ACTATTTTAC
* *
1316682 AAATAATTCCCAAAATTTCA-TTATTTTAAAAATAATT-AC-GAATGTCACTGTTTT-AAAA-AA
1 AAATAATTCCCAAAATTTCACCT-TTTTAAAAATAATTCACAAAATGTCACTGTTTTCAAAATAA
1316742 TTCCAAAAATGTCACTTTTTTT
65 TTCCAAAAATGTCACTTTTTTT
* * *
1316764 AAATAATTCCCAAAATTTCACCTTTTTCAAAATAATTCCCAAAATGTCACTTTTTTCAAAATAAT
1 AAATAATTCCCAAAATTTCACCTTTTTAAAAATAATTCACAAAATGTCACTGTTTTCAAAATAAT
*
1316829 TCCCAAAATGTCACT
66 TCCAAAAATGTCACT
1316844 GGGTCGGGTC
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
82 33 0.48
83 2 0.03
84 13 0.19
85 4 0.06
86 17 0.25
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.38
Consensus pattern (86 bp):
AAATAATTCCCAAAATTTCACCTTTTTAAAAATAATTCACAAAATGTCACTGTTTTCAAAATAAT
TCCAAAAATGTCACTTTTTTT
Found at i:1316867 original size:17 final size:18
Alignment explanation
Indices: 1316844--1316890 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
1316834 AAATGTCACT
1316844 GGGTCGGGTCAGGTCAAC
1 GGGTCGGGTCAGGTCAAC
**
1316862 -GGTCGGGTTGGGTCAAC
1 GGGTCGGGTCAGGTCAAC
1316879 GGGTCGGGTCAG
1 GGGTCGGGTCAG
1316891 ACCGGTCAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.13, C:0.19, G:0.49, T:0.19
Consensus pattern (18 bp):
GGGTCGGGTCAGGTCAAC
Found at i:1317908 original size:18 final size:18
Alignment explanation
Indices: 1317852--1317915 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
1317842 CACATATATC
*
1317852 ATCATTATTAACATCAAT
1 ATCATTATCAACATCAAT
* ** **
1317870 ATCTTTATCATGATCTCT
1 ATCATTATCAACATCAAT
1317888 ATCATTATCAACATCAAT
1 ATCATTATCAACATCAAT
1317906 ATCATTATCA
1 ATCATTATCA
1317916 TGTAATACAT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.38, C:0.20, G:0.02, T:0.41
Consensus pattern (18 bp):
ATCATTATCAACATCAAT
Found at i:1318089 original size:29 final size:30
Alignment explanation
Indices: 1318056--1318117 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
1318046 TGTATACTTT
* *
1318056 TGATATATTTTGTAGGCCC-TATACAATAC
1 TGATATATTTTATAAGCCCATATACAATAC
* *
1318085 TGATATCTTTTATAAGCCCATGTACAATAC
1 TGATATATTTTATAAGCCCATATACAATAC
1318115 TGA
1 TGA
1318118 GAACTCAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (30 bp):
TGATATATTTTATAAGCCCATATACAATAC
Found at i:1318270 original size:21 final size:22
Alignment explanation
Indices: 1318244--1318294 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
1318234 GACCTATCAT
1318244 CTCGAAGGATGTCATTTGTG-C
1 CTCGAAGGATGTCATTTGTGTC
* *
1318265 CTCGAATGATGTTATTTGTGTC
1 CTCGAAGGATGTCATTTGTGTC
1318287 C-CGAAGGA
1 CTCGAAGGA
1318295 CCTGTAGAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (22 bp):
CTCGAAGGATGTCATTTGTGTC
Found at i:1318480 original size:33 final size:33
Alignment explanation
Indices: 1318433--1318500 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
1318423 ATCATGTAGC
1318433 TTGTATAACATTCTTGTATGATCTCATAGATCA
1 TTGTATAACATTCTTGTATGATCTCATAGATCA
* *
1318466 TTGTGTAACATTCTTGTATGATCTCATATATCA
1 TTGTATAACATTCTTGTATGATCTCATAGATCA
1318499 TT
1 TT
1318501 TTTTATACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.46
Consensus pattern (33 bp):
TTGTATAACATTCTTGTATGATCTCATAGATCA
Found at i:1319503 original size:22 final size:20
Alignment explanation
Indices: 1319457--1319505 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
1319447 AATGTTGACC
1319457 GTTGACCAGCTTTGACCACT
1 GTTGACCAGCTTTGACCACT
* **
1319477 ATTGACCAGAACTTTGACCGGT
1 GTTGACCAG--CTTTGACCACT
1319499 GTTGACC
1 GTTGACC
1319506 GGACATTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 8 0.35
22 15 0.65
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (20 bp):
GTTGACCAGCTTTGACCACT
Found at i:1322002 original size:12 final size:12
Alignment explanation
Indices: 1321987--1322056 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
1321977 GATACATTAC
1321987 CTGAATTCTGTT
1 CTGAATTCTGTT
*
1321999 CTGAATTCTGAT
1 CTGAATTCTGTT
* *
1322011 CTGGATTTTGTT
1 CTGAATTCTGTT
*
1322023 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
1322035 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1322047 TTGATTTCTG
1 CTGAATTCTG
1322057 ATATCTCCAT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:1322022 original size:24 final size:24
Alignment explanation
Indices: 1321987--1322058 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
1321977 GATACATTAC
1321987 CTGAATTCTGTTCTGAATTCTGAT
1 CTGAATTCTGTTCTGAATTCTGAT
* *
1322011 CTGGATTTTGTTCTG-ATATCTGAT
1 CTGAATTCTGTTCTGAAT-TCTGAT
* *
1322035 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTCTGAATTCTGAT
1322059 ATCTCCATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
23 2 0.05
24 37 0.93
25 1 0.03
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.50
Consensus pattern (24 bp):
CTGAATTCTGTTCTGAATTCTGAT
Found at i:1324092 original size:10 final size:10
Alignment explanation
Indices: 1324079--1324113 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
1324069 GACCAGCTTC
1324079 GACCACTGTT
1 GACCACTGTT
1324089 GACCAGCT-TT
1 GACCA-CTGTT
1324099 GACCACTGTT
1 GACCACTGTT
1324109 GACCA
1 GACCA
1324114 GAACTTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 19 0.83
11 2 0.09
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (10 bp):
GACCACTGTT
Found at i:1324123 original size:22 final size:20
Alignment explanation
Indices: 1324067--1324136 Score: 97
Period size: 20 Copynumber: 3.4 Consensus size: 20
1324057 ATGTTGACTA
*
1324067 TTGACCAGCTTCGACCACTG
1 TTGACCAGCTTTGACCACTG
1324087 TTGACCAGCTTTGACCACTG
1 TTGACCAGCTTTGACCACTG
1324107 TTGACCAGAACTTTGACCGAC-G
1 TTGACCAG--CTTTGACC-ACTG
1324129 TTGACCAG
1 TTGACCAG
1324137 GCATTAAACG
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
20 27 0.59
22 17 0.37
23 2 0.04
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (20 bp):
TTGACCAGCTTTGACCACTG
Found at i:1326642 original size:12 final size:12
Alignment explanation
Indices: 1326622--1326691 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
1326612 GATACATTAC
*
1326622 CTGAATTCTGTT
1 CTGATTTCTGTT
*
1326634 CTGATTTCTGAT
1 CTGATTTCTGTT
1326646 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
*
1326658 CTGATATCTGATT
1 CTGATTTCTG-TT
* *
1326671 -TGAATTCTATT
1 CTGATTTCTGTT
*
1326682 TTGATTTCTG
1 CTGATTTCTG
1326692 ATATCTCCGT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
11 4 0.09
12 37 0.82
13 4 0.09
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.51
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:1326653 original size:24 final size:24
Alignment explanation
Indices: 1326622--1326693 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
1326612 GATACATTAC
1326622 CTGAATTCTGTTCTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* *
1326646 CTGGATTCTGTTCTGATATCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* * *
1326670 TTGAATTCTATTTTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
1326694 ATCTCCGTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.18, C:0.14, G:0.17, T:0.51
Consensus pattern (24 bp):
CTGAATTCTGTTCTGATTTCTGAT
Found at i:1326860 original size:2 final size:2
Alignment explanation
Indices: 1326853--1326889 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1326843 GATGGGGGTG
1326853 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1326890 TTTTAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1328254 original size:9 final size:9
Alignment explanation
Indices: 1328242--1328285 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
1328232 TAAATAGCAA
*
1328242 AAATTTCAT
1 AAATTCCAT
* *
1328251 AAATTTCAG
1 AAATTCCAT
1328260 AAATTCCAT
1 AAATTCCAT
1328269 AAATTCCAT
1 AAATTCCAT
1328278 AAATTCCA
1 AAATTCCA
1328286 GTACTGAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.34
Consensus pattern (9 bp):
AAATTCCAT
Found at i:1330837 original size:3 final size:3
Alignment explanation
Indices: 1330831--1330862 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1330821 ATTTTTTCAT
1330831 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1330863 TTTTTTAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1333691 original size:17 final size:16
Alignment explanation
Indices: 1333669--1333702 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1333659 TAAAAACAGT
1333669 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
1333686 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
1333702 A
1 A
1333703 TCCTCACATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:1343451 original size:17 final size:16
Alignment explanation
Indices: 1343429--1343462 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1343419 TAAAAATAGT
1343429 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
1343446 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
1343462 A
1 A
1343463 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:1362510 original size:1 final size:1
Alignment explanation
Indices: 1362504--1362578 Score: 60
Period size: 1 Copynumber: 75.0 Consensus size: 1
1362494 ATGCTTGAAG
* * * * * * * **
1362504 AAAAAAAAAAGAAAAAAGAAAAGAAAAAGAAAAAAAAGAAAAGAAAAAAAAAGAAAAGGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
1362569 AAAGAAAAAA
1 AAAAAAAAAA
1362579 GAGGGGTCAA
Statistics
Matches: 56, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (1 bp):
A
Found at i:1362517 original size:11 final size:11
Alignment explanation
Indices: 1362501--1362578 Score: 88
Period size: 11 Copynumber: 6.8 Consensus size: 11
1362491 ATTATGCTTG
1362501 AAGAAAAAAAA
1 AAGAAAAAAAA
1362512 AAGAAAAAAGAA
1 AAGAAAAAA-AA
1362524 AAGAAAAAGAAA
1 AAGAAAAA-AAA
1362536 AA-AAAGAAAAGA
1 AAGAAA-AAAA-A
1362548 AA-AAAAAAGAA
1 AAGAAAAAA-AA
*
1362559 AAGGAAAAAAA
1 AAGAAAAAAAA
1362570 AAGAAAAAA
1 AAGAAAAAA
1362579 GAGGGGTCAA
Statistics
Matches: 59, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
11 30 0.51
12 28 0.47
13 1 0.02
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:1362518 original size:5 final size:5
Alignment explanation
Indices: 1362501--1362576 Score: 79
Period size: 5 Copynumber: 15.4 Consensus size: 5
1362491 ATTATGCTTG
1362501 AAGAA AA-AA AA-AA GAA-AA AAGAA AAGAAA AAGAA AA-AA AAGAA AAGAA
1 AAGAA AAGAA AAGAA -AAGAA AAGAA AAG-AA AAGAA AAGAA AAGAA AAGAA
* *
1362549 AAAAA AAGAA AAGGAA AAAAA AAGAA AA
1 AAGAA AAGAA AA-GAA AAGAA AAGAA AA
1362577 AAGAGGGGTC
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
4 12 0.19
5 40 0.65
6 10 0.16
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:1362540 original size:15 final size:15
Alignment explanation
Indices: 1362501--1362577 Score: 88
Period size: 15 Copynumber: 5.1 Consensus size: 15
1362491 ATTATGCTTG
1362501 AAGAAAAAAAA-AAGA
1 AAGAAAAAAAAGAA-A
*
1362516 AA-AAAGAAAAGAAA
1 AAGAAAAAAAAGAAA
1362530 AAGAAAAAAAAG-AA
1 AAGAAAAAAAAGAAA
1362544 AAGAAAAAAAAAGAAA
1 AAG-AAAAAAAAGAAA
*
1362560 AGGAAAAAAAAAGAAA
1 AAG-AAAAAAAAGAAA
1362576 AA
1 AA
1362578 AGAGGGGTCA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
14 15 0.28
15 21 0.39
16 18 0.33
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAGAAA
Found at i:1363620 original size:52 final size:52
Alignment explanation
Indices: 1363560--1363773 Score: 378
Period size: 52 Copynumber: 4.1 Consensus size: 52
1363550 GGAAAAGCAT
1363560 CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
1 CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
1363612 CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GA
1 CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
*
1363663 TCATAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
1 -CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
*
1363716 CAGAACATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-
1 CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGA
1363768 CAGAAC
1 CAGAAC
1363774 CAATCATTGA
Statistics
Matches: 156, Mismatches: 3, Indels: 6
0.95 0.02 0.04
Matches are distributed among these distances:
51 2 0.01
52 148 0.95
53 6 0.04
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.37
Consensus pattern (52 bp):
CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
Found at i:1363861 original size:83 final size:83
Alignment explanation
Indices: 1363722--1363933 Score: 354
Period size: 83 Copynumber: 2.6 Consensus size: 83
1363712 TGGACAGAAC
*
1363722 ATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1363787 TGGAAGATGAATTTGCTA
66 TGGAAGATGAATTTGCTA
* *
1363805 ATAGCATCTTCTGGAAGTTTTCTTTGAGTTATCTGATCTGG-TTGGACAGAATCAATCATTGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCATTGAAT
*
1363869 TTGGAAGATGAATTTGTTA
65 TTGGAAGATGAATTTGCTA
* *
1363888 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGTTTTGG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1363934 TAAGAACTAC
Statistics
Matches: 120, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
82 4 0.03
83 112 0.93
84 4 0.03
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.41
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
TGGAAGATGAATTTGCTA
Found at i:1364768 original size:118 final size:118
Alignment explanation
Indices: 1364526--1365320 Score: 1230
Period size: 114 Copynumber: 6.9 Consensus size: 118
1364516 GCAAAGATTC
* * * * **
1364526 AAATTTATCATTTGAAGGATCA-GCTTTTCCAG-TTAGAGTTCATAATGAGAAGAACTCGTCATC
1 AAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCATC
*
1364589 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
66 TGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
*
1364642 AAATTCATCACTTGATGGATCATTCTTTTCCATAGAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCATC
*
1364707 TGAAGAAGGAAGATAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
66 TGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
1364760 AAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATC
1 AAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCATC
1364821 TGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
66 TGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
1364874 AAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATC
1 AAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCATC
1364935 TGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
66 TGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
1364988 AAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCATC
* *
1365053 TGAAGAAGGAAGATAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
66 TGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
* * * *
1365106 GAATTCATCAAATTGATGGATCA-TCGTTTCCAGAGGAAGAGTTCACAATGAGAAGAACTCGTCA
1 AAATTCATC-ACTTGATGGATCATTCTTTTCCAGA-GAAGAGTTCATAATGAGAAGAACTCGTCA
* * *
1365170 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
64 TCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
* * * *
1365225 GAATTCATCATTTGATGGATCGA--CATTACCAG-GTAA-AGTTCATAATGAGAAGAA--C-TCA
1 AAATTCATCACTTGATGGATC-ATTCTTTTCCAGAG-AAGAGTTCATAATGAGAAGAACTCGTCA
1365283 TCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACT
64 TCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACT
1365321 CATCAAGAGC
Statistics
Matches: 643, Mismatches: 26, Indels: 23
0.93 0.04 0.03
Matches are distributed among these distances:
113 39 0.06
114 210 0.33
115 18 0.03
116 37 0.06
117 28 0.04
118 209 0.33
119 102 0.16
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (118 bp):
AAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCATC
TGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
Found at i:1365054 original size:232 final size:230
Alignment explanation
Indices: 1364526--1365320 Score: 1199
Period size: 232 Copynumber: 3.4 Consensus size: 230
1364516 GCAAAGATTC
* * * * **
1364526 AAATTTATCATTTGAAGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCGTCATCTG
1 AAATTCATCACTTGATGGATCATCTTTTCCAGGAAGAGTTCATAATGAGAAGAA--C-TCATCTG
*
1364591 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTG
63 AAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTG
* *
1364656 ATGGATCATTCTTTTCCATAGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAT
128 ATGGATCATTCTTTTCCAGAGAAGAGTTCATAATGAGAAGAAC-CGTCATCTGAAGAAGGAAGAA
1364721 AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
192 AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
1364760 AAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAG-GTTCATAATGAGAAGAACTCATCTGA
1 AAATTCATCACTTGATGGATCA-TCTTTTCCAG-GAAGAGTTCATAATGAGAAGAACTCATCTGA
1364824 AGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGA
64 AGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGA
1364889 TGGATCATTCTTTTCCAGAGAAG-GTTCATAATGAGAAGAA-C-TCATCTGAAGAAGGAAGAAAA
129 TGGATCATTCTTTTCCAGAGAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAAGAAAA
1364951 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
194 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
1364988 AAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AAATTCATCACTTGATGGATCA-TCTTTTCCAG-GAAGAGTTCATAATGAGAAGAA--C-TCATC
* * * *
1365053 TGAAGAAGGAAGATAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAAA
61 TGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATC-AC
* *
1365118 TTGATGGATCA-TCGTTTCCAGAGGAAGAGTTCACAATGAGAAGAACTCGTCATCTGAAGAAGGA
125 TTGATGGATCATTCTTTTCCAGA-GAAGAGTTCATAATGAGAAGAAC-CGTCATCTGAAGAAGGA
* * *
1365182 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
188 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
* * * *
1365225 GAATTCATCATTTGATGGATCGA-CATTACCAGGTAA-AGTTCATAATGAGAAGAACTCATCTGA
1 AAATTCATCACTTGATGGATC-ATCTTTTCCAGG-AAGAGTTCATAATGAGAAGAACTCATCTGA
1365288 AGAAGGAAGAAAAAGTTCATAATGAGAAGAACT
64 AGAAGGAAGAAAAAGTTCATAATGAGAAGAACT
1365321 CATCAAGAGC
Statistics
Matches: 524, Mismatches: 23, Indels: 30
0.91 0.04 0.05
Matches are distributed among these distances:
228 95 0.18
229 18 0.03
231 18 0.03
232 208 0.40
233 18 0.03
234 35 0.07
235 45 0.09
236 12 0.02
237 74 0.14
238 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (230 bp):
AAATTCATCACTTGATGGATCATCTTTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATG
GATCATTCTTTTCCAGAGAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAAGAAAAAG
TTCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
Found at i:1367592 original size:16 final size:16
Alignment explanation
Indices: 1367556--1367593 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1367546 TGAATTTCCA
1367556 AAAATAAATTGAATCT
1 AAAATAAATTGAATCT
*
1367572 CAAATAAATTGAA-CTT
1 AAAATAAATTGAATC-T
1367588 AAAATA
1 AAAATA
1367594 GATAGAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (16 bp):
AAAATAAATTGAATCT
Found at i:1367924 original size:1 final size:1
Alignment explanation
Indices: 1367914--1367981 Score: 73
Period size: 1 Copynumber: 68.0 Consensus size: 1
1367904 TTGACCCCTC
* ** * * * *
1367914 TTTTTCTTTTTTTTCCTTTTCTTTTTTTTTCTTTTCTTTTTTTTTTTTTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1367979 TTT
1 TTT
1367982 CTTCAAGCAT
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (1 bp):
T
Found at i:1367932 original size:10 final size:9
Alignment explanation
Indices: 1367914--1367984 Score: 85
Period size: 8 Copynumber: 7.9 Consensus size: 9
1367904 TTGACCCCTC
1367914 TTTTTCTTT
1 TTTTTCTTT
1367923 TTTTTCCTTT
1 TTTTT-CTTT
*
1367933 TCTTTTTTTT
1 T-TTTTCTTT
1367943 TCTTTTC-TT
1 T-TTTTCTTT
1367952 TTTTT-TTT
1 TTTTTCTTT
1367960 TTTTT-TTT
1 TTTTTCTTT
1367968 TTTTTCTTT
1 TTTTTCTTT
1367977 TTTTTCTT
1 TTTTTCTT
1367985 CAAGCATAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
8 19 0.34
9 19 0.34
10 14 0.25
11 4 0.07
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:1367935 original size:15 final size:13
Alignment explanation
Indices: 1367914--1367981 Score: 86
Period size: 13 Copynumber: 5.1 Consensus size: 13
1367904 TTGACCCCTC
1367914 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
1367927 TCCTTTTCTTTTTTT
1 T--TTTTCTTTTTTT
1367942 TTCTTT-TCTTTTTT
1 TT-TTTCT-TTTTTT
1367956 TTTTT-TTTTTTT
1 TTTTTCTTTTTTT
1367968 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
1367981 T
1 T
1367982 CTTCAAGCAT
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
12 11 0.22
13 15 0.30
14 11 0.22
15 13 0.26
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:1380758 original size:3 final size:3
Alignment explanation
Indices: 1380750--1380860 Score: 190
Period size: 3 Copynumber: 37.7 Consensus size: 3
1380740 TTAATATATT
1380750 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1380797 TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1380845 -AT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
1380861 TGGATAAAAA
Statistics
Matches: 102, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
2 3 0.03
3 99 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1381438 original size:21 final size:21
Alignment explanation
Indices: 1381408--1381466 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1381398 GATGAACTAT
**
1381408 CACATTAGCACCGTGGACCGC
1 CACATTAGCACCGTAAACCGC
* * *
1381429 CACGTTAGCACCATAAACTGC
1 CACATTAGCACCGTAAACCGC
1381450 CACATTAGCACCGTAAA
1 CACATTAGCACCGTAAA
1381467 GGTCAACAAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.32, C:0.34, G:0.17, T:0.17
Consensus pattern (21 bp):
CACATTAGCACCGTAAACCGC
Found at i:1388400 original size:29 final size:28
Alignment explanation
Indices: 1388358--1388417 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 28
1388348 TTCACCTAAC
*
1388358 TAAATTGATGTAAGCAATGACATCAAAAT
1 TAAATCGATGTAAGCAATGACATC-AAAT
1388387 TAAATCGATGTAAGCAATGACATCAAAT
1 TAAATCGATGTAAGCAATGACATCAAAT
1388415 TAA
1 TAA
1388418 TTTAGGTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 7 0.23
29 23 0.77
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (28 bp):
TAAATCGATGTAAGCAATGACATCAAAT
Found at i:1398063 original size:10 final size:10
Alignment explanation
Indices: 1398035--1398082 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
1398025 TGAAAATCGG
*
1398035 TTTGACCTGT
1 TTTGACCGGT
1398045 TTTGAACCGGT
1 TTTG-ACCGGT
1398056 TTTGACCGG-
1 TTTGACCGGT
*
1398065 TTTGACCGAT
1 TTTGACCGGT
*
1398075 TTCGACCG
1 TTTGACCG
1398083 ATTCGAACCG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 8 0.24
10 16 0.48
11 9 0.27
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.38
Consensus pattern (10 bp):
TTTGACCGGT
Found at i:1398081 original size:19 final size:20
Alignment explanation
Indices: 1398045--1398092 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
1398035 TTTGACCTGT
* *
1398045 TTTGAACCGGTTTTGACCGG
1 TTTGAACCGATTTCGACCGG
*
1398065 TTTG-ACCGATTTCGACCGA
1 TTTGAACCGATTTCGACCGG
*
1398084 TTCGAACCG
1 TTTGAACCG
1398093 GTCTGACCCG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (20 bp):
TTTGAACCGATTTCGACCGG
Found at i:1398111 original size:19 final size:19
Alignment explanation
Indices: 1398097--1398141 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1398087 GAACCGGTCT
1398097 GACCCGACCCGACCGACCC
1 GACCCGACCCGACCGACCC
*
1398116 GACCCGACCCGATCGA-CC
1 GACCCGACCCGACCGACCC
1398134 GACCCGAC
1 GACCCGAC
1398142 TGTTGTCCCG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.22, C:0.53, G:0.22, T:0.02
Consensus pattern (19 bp):
GACCCGACCCGACCGACCC
Found at i:1398132 original size:14 final size:15
Alignment explanation
Indices: 1398097--1398141 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 15
1398087 GAACCGGTCT
1398097 GACCCGACCCGA-CC
1 GACCCGACCCGACCC
1398111 GACCCGACCCGACCC
1 GACCCGACCCGACCC
*
1398126 GA-TCGA-CCGACCC
1 GACCCGACCCGACCC
1398139 GAC
1 GAC
1398142 TGTTGTCCCG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 9 0.32
14 15 0.54
15 4 0.14
ACGTcount: A:0.22, C:0.53, G:0.22, T:0.02
Consensus pattern (15 bp):
GACCCGACCCGACCC
Found at i:1398141 original size:9 final size:9
Alignment explanation
Indices: 1398100--1398137 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1398090 CCGGTCTGAC
1398100 CCGACCCGA
1 CCGACCCGA
1398109 CCGACCCGA
1 CCGACCCGA
1398118 CCCGACCCGA
1 -CCGACCCGA
*
1398128 TCGA-CCGA
1 CCGACCCGA
1398136 CC
1 CC
1398138 CGACTGTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 5 0.19
9 12 0.46
10 9 0.35
ACGTcount: A:0.21, C:0.55, G:0.21, T:0.03
Consensus pattern (9 bp):
CCGACCCGA
Found at i:1398159 original size:5 final size:5
Alignment explanation
Indices: 1398097--1398141 Score: 60
Period size: 5 Copynumber: 9.6 Consensus size: 5
1398087 GAACCGGTCT
*
1398097 GACCC GACCC GA-CC GACCC GACCC GACCC GA-TC GA-CC GACCC GAC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GAC
1398142 TGTTGTCCCG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
4 10 0.28
5 26 0.72
ACGTcount: A:0.22, C:0.53, G:0.22, T:0.02
Consensus pattern (5 bp):
GACCC
Found at i:1402545 original size:29 final size:28
Alignment explanation
Indices: 1402499--1402558 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 28
1402489 TTCACCTAAC
*
1402499 TAAATTGATGTAAGCAATGACATCAAAAT
1 TAAATTGATGTAAACAATGACATC-AAAT
1402528 TAAATTGATGTAAACAATGACATCAAAT
1 TAAATTGATGTAAACAATGACATCAAAT
1402556 TAA
1 TAA
1402559 TTTAGGTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 7 0.23
29 23 0.77
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (28 bp):
TAAATTGATGTAAACAATGACATCAAAT
Found at i:1404823 original size:14 final size:14
Alignment explanation
Indices: 1404804--1404830 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1404794 TACTATATAA
1404804 ATAAAAATATTAAT
1 ATAAAAATATTAAT
1404818 ATAAAAATATTAA
1 ATAAAAATATTAA
1404831 ATATTGTTTT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAAAATATTAAT
Found at i:1408798 original size:22 final size:21
Alignment explanation
Indices: 1408748--1408798 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1408738 CAAAGATAAT
* * *
1408748 AAATTATCCCATTAATATATG
1 AAATGATCCCATTAACAAATG
*
1408769 AAAAGATCCCATTAACAAATGG
1 AAATGATCCCATTAACAAAT-G
1408791 AAATGATC
1 AAATGATC
1408799 TGTATAGTAC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (21 bp):
AAATGATCCCATTAACAAATG
Found at i:1419402 original size:51 final size:51
Alignment explanation
Indices: 1419326--1419439 Score: 210
Period size: 51 Copynumber: 2.2 Consensus size: 51
1419316 ACCTTCCTTC
*
1419326 TCTTCAACCAGTATAACAGTGTCTTCAGATTTCACCGTCATGACTTAGATA
1 TCTTCAACCAGTATAACAGTGTCTTCAGATTTCACCGTCAAGACTTAGATA
*
1419377 TCTTCAACCAGTATAACAGTGTCTTCAGATTTCACTGTCAAGACTTAGATA
1 TCTTCAACCAGTATAACAGTGTCTTCAGATTTCACCGTCAAGACTTAGATA
1419428 TCTTCAACCAGT
1 TCTTCAACCAGT
1419440 TTTATCTGTA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (51 bp):
TCTTCAACCAGTATAACAGTGTCTTCAGATTTCACCGTCAAGACTTAGATA
Done.