Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006607.1 Hibiscus syriacus cultivar Beakdansim tig00016212_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: 1995858
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1470538 original size:40 final size:40
Alignment explanation
Indices: 1470494--1470626 Score: 162
Period size: 40 Copynumber: 3.3 Consensus size: 40
1470484 TTGGCTATCT
* *
1470494 CGTTGCGAATTTAACTTCTGTGTTACGATTTACAAATTCA
1 CGTTGCGAATTTGACTTCTGTGTTACGATTTACAAATTCG
* * *
1470534 CGTTGCGAATTTGACTTTTGTGTTGCGAATTTGAC-TA-TCG
1 CGTTGCGAATTTGACTTCTGTGTTACG-ATTT-ACAAATTCG
* * *
1470574 CGTTGCGAATTTGACTTCTATGTTTCGATTTACAGATTCG
1 CGTTGCGAATTTGACTTCTGTGTTACGATTTACAAATTCG
1470614 CGTTGCGAATTTG
1 CGTTGCGAATTTG
1470627 GAAAATCACA
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.03
39 5 0.06
40 66 0.82
41 5 0.06
42 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (40 bp):
CGTTGCGAATTTGACTTCTGTGTTACGATTTACAAATTCG
Found at i:1470552 original size:80 final size:80
Alignment explanation
Indices: 1470455--1470626 Score: 272
Period size: 80 Copynumber: 2.1 Consensus size: 80
1470445 GACTTTTTCT
* * * *
1470455 GTTGCGAATTTGACTTTTTTGTTGCGAATTTGGCTATCTCGTTGCGAATTTAACTTCTGTGTTAC
1 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTAACTTCTATGTTAC
1470520 GATTTACAAATTCAC
66 GATTTACAAATTCAC
* *
1470535 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTATGTTTC
1 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTAACTTCTATGTTAC
* *
1470600 GATTTACAGATTCGC
66 GATTTACAAATTCAC
1470615 GTTGCGAATTTG
1 GTTGCGAATTTG
1470627 GAAAATCACA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 84 1.00
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.43
Consensus pattern (80 bp):
GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTAACTTCTATGTTAC
GATTTACAAATTCAC
Found at i:1471412 original size:27 final size:27
Alignment explanation
Indices: 1471368--1471435 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
1471358 TGGTACTTCT
* *
1471368 CATTTGTGTAATGCTTTTCTTTGTTGC
1 CATTGGTGTTATGCTTTTCTTTGTTGC
*
1471395 CATTGGTGTTATGTTTTTCTTTGTTGC
1 CATTGGTGTTATGCTTTTCTTTGTTGC
1471422 CATTGGTGTTATGC
1 CATTGGTGTTATGC
1471436 ATAAACAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.10, C:0.13, G:0.22, T:0.54
Consensus pattern (27 bp):
CATTGGTGTTATGCTTTTCTTTGTTGC
Found at i:1488314 original size:22 final size:21
Alignment explanation
Indices: 1488289--1488360 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 21
1488279 AACTTTTTCG
1488289 GTCAATGGTATGACCGGTCAAA
1 GTCAATGGT-TGACCGGTCAAA
*
1488311 GTCAACGGTCTGACCGGTCAACA
1 GTCAATGGT-TGACCGGTCAA-A
* *
1488334 GTCTATGGGTTGACTCGGTCAAG
1 GTCAAT-GGTTGAC-CGGTCAAA
1488357 GTCA
1 GTCA
1488361 CCAGGTTCAC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
22 19 0.46
23 12 0.29
24 10 0.24
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (21 bp):
GTCAATGGTTGACCGGTCAAA
Found at i:1490527 original size:234 final size:239
Alignment explanation
Indices: 1490233--1490690 Score: 881
Period size: 234 Copynumber: 1.9 Consensus size: 239
1490223 GTAATCCAGT
1490233 AAAATCACATAAACGTGCAATGAAATAAACCATATAATATTCCTCCACTTGTACACCATATATAG
1 AAAATCACATAAACGTGCAATGAAATAAACCATATAATATTCCTCCACTTGTACACCATATATAG
1490298 TTCCATGATTAACCCAATGGAATGCCTTGGGG-ATGTGAGCCTA-CCAAGGTCACCTTAGGTCTG
66 TTCCATGATTAACCCAATGGAATGCCTTGGGGCATGTGAGCCTACCCAAGGTCACCTTAGGTCTG
1490361 GAAGGATTTACCAGCTTGATCAGAGTTGTA-CTCCATACTCC-ACCTACCCAGATAATATCCCAA
131 GAAGGATTTACCAGCTTGATCAGAGTTGTACCTCCATACTCCAACCTACCCAGATAATATCCCAA
1490424 T-AAACAGTTCGAGTATAACCAGTGAAAAAAAATAGTCATAAAG
196 TAAAACAGTTCGAGTATAACCAGTGAAAAAAAATAGTCATAAAG
1490467 AAAATCACATAAACGTGCAATGAAATAAACCATATAATATTCCTCCACTTGTACACCATATATAG
1 AAAATCACATAAACGTGCAATGAAATAAACCATATAATATTCCTCCACTTGTACACCATATATAG
1490532 TTCCATGATTAACCCAATGGAATGCCTTGGGGCATGTGAGCCTACCCAAGGTCACCTTAGGTCTG
66 TTCCATGATTAACCCAATGGAATGCCTTGGGGCATGTGAGCCTACCCAAGGTCACCTTAGGTCTG
1490597 GAAGGATTTACCAGCTTGATCAGAGTTGTACCTCCATACTCCAACCTACCCAGATAATATCCCAA
131 GAAGGATTTACCAGCTTGATCAGAGTTGTACCTCCATACTCCAACCTACCCAGATAATATCCCAA
1490662 TAAAACAGTTCGAGTATAACCAGTGAAAA
196 TAAAACAGTTCGAGTATAACCAGTGAAAA
1490691 TAGGAAACCA
Statistics
Matches: 219, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
234 97 0.44
235 11 0.05
236 50 0.23
237 11 0.05
238 23 0.11
239 27 0.12
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (239 bp):
AAAATCACATAAACGTGCAATGAAATAAACCATATAATATTCCTCCACTTGTACACCATATATAG
TTCCATGATTAACCCAATGGAATGCCTTGGGGCATGTGAGCCTACCCAAGGTCACCTTAGGTCTG
GAAGGATTTACCAGCTTGATCAGAGTTGTACCTCCATACTCCAACCTACCCAGATAATATCCCAA
TAAAACAGTTCGAGTATAACCAGTGAAAAAAAATAGTCATAAAG
Found at i:1497997 original size:108 final size:109
Alignment explanation
Indices: 1497804--1498417 Score: 409
Period size: 108 Copynumber: 5.5 Consensus size: 109
1497794 CACCTTTTTA
* * * ****
1497804 AAGCTGATGGGGCCTTAGAAATCCGACGATAATAAAATAGGTTAATTACTTGATTTGTTATCAA-
1 AAGCTAATGGAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGAAACATTATCAAC
* ** * *
1497868 TATTATCAACATATTAGGTAGCACCTAAAATGTTACCAAAGTTT
66 CATTATCAACATAACAAGTAGCGCCTAAAATGTTACCAAAGTTT
* *
1497912 AAGCTAATGGAGCCTTAGAAATCCGATGATAACAAAATAGGTTAATTACTGGAAACATTATCAAC
1 AAGCTAATGGAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGAAACATTATCAAC
* * * *
1497977 CATAAT-AACATAACAAGTAGCGCTCATTTAACGTAATAGGTACCGCATGTTT
66 CATTATCAACATAACAAGTAGCGC-C---TAA---AAT-GTTACC-AAAGTTT
* * * * ****
1498029 AAAGCTGAA-GGGGCCTTGGAAATCTGACAATAACAAAATAGGTTAATTACTTGATTTGTTATC-
1 -AAGCT-AATGGAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGAAACATTATCA
** ** * *
1498092 AGTATTATCAACATATTAGGTAACGCCTAAAATGTTACCAAAGTTT
64 ACCATTATCAACATAACAAGTAGCGCCTAAAATGTTACCAAAGTTT
* * * * *
1498138 AAGCTGATGAAGCCTTAGAAATCCAACGATAACAAAATAGGTTAATTAATCGAAACATTATCAAC
1 AAGCTAATGGAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGAAACATTATCAAC
* * * * **
1498203 CATCAT-AACATAACAAGTAACGCTTATTTAATGTAATAGGTAGCGC-TTGTTT
66 CATTATCAACATAACAAGTAGCGC----CTAA---AAT-GTTA-C-CAAAGTTT
* ** ***
1498255 AAAGCTGATGG-GCCTTAGAAATCAAACGATAACAAAATAGGTTAATTACTT-AATTTGTTATCA
1 -AAGCTAATGGAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGAA-ACATTATCA
* ** * * * *
1498318 A-TATTATCAACATATTAGGTAGCGCCTAAAATGTTACTATACACTTA
64 ACCATTATCAACATAACAAGTAGCGCCTAAAATGTTACCA-A-AGTTT
* * *
1498365 AAGATGATGGAGCCTTAGAAATCTGACGATAACAAAATAGGTTAATTACTTGA
1 AAGCTAATGGAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGA
1498418 TTTGTTATCA
Statistics
Matches: 389, Mismatches: 84, Indels: 63
0.73 0.16 0.12
Matches are distributed among these distances:
107 1 0.00
108 130 0.33
109 27 0.07
110 48 0.12
111 4 0.01
112 6 0.02
113 3 0.01
114 3 0.01
115 6 0.02
116 14 0.04
117 73 0.19
118 72 0.19
119 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (109 bp):
AAGCTAATGGAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTGAAACATTATCAAC
CATTATCAACATAACAAGTAGCGCCTAAAATGTTACCAAAGTTT
Found at i:1498123 original size:226 final size:226
Alignment explanation
Indices: 1497727--1498414 Score: 1009
Period size: 226 Copynumber: 3.0 Consensus size: 226
1497717 ACATAACTGA
* ** * *
1497727 TTAATTATTGGAAACATTATCAACCATAATAACATATTAGGTAGCGCTTATGTAACGTAATAGGT
1 TTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAACGTAATAGGT
* * * * * * *
1497792 ATCACCTTTTTAAAGCTGATGGGGCCTTAGAAATCCGACGATAATAAAATAGGTTAATTACTTGA
66 ACCGCATGTTTAAAGCTGAAGGGGCCTTAGAAATCAGACGATAACAAAATAGGTTAATTACTTGA
* *
1497857 TTTGTTATCAATATTATCAACATATTAGGTAGCACCTAAAATGTTACCAAAGTTTAAGCTAATGG
131 TTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCTGATGG
*
1497922 AGCCTTAGAAATCCGATGATAACAAAATAGG
196 AGCCTTAGAAATCCGACGATAACAAAATAGG
*
1497953 TTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTCATTTAACGTAATAGGT
1 TTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAACGTAATAGGT
* * *
1498018 ACCGCATGTTTAAAGCTGAAGGGGCCTTGGAAATCTGACAATAACAAAATAGGTTAATTACTTGA
66 ACCGCATGTTTAAAGCTGAAGGGGCCTTAGAAATCAGACGATAACAAAATAGGTTAATTACTTGA
* * *
1498083 TTTGTTATCAGTATTATCAACATATTAGGTAACGCCTAAAATGTTACCAAAGTTTAAGCTGATGA
131 TTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCTGATGG
*
1498148 AGCCTTAGAAATCCAACGATAACAAAATAGG
196 AGCCTTAGAAATCCGACGATAACAAAATAGG
* * * * *
1498179 TTAATTAATCGAAACATTATCAACCATCATAACATAACAAGTAACGCTTATTTAATGTAATAGGT
1 TTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAACGTAATAGGT
* * * * *
1498244 AGCGCTTGTTTAAAGCTG-ATGGGCCTTAGAAATCAAACGATAACAAAATAGGTTAATTACTTAA
66 ACCGCATGTTTAAAGCTGAAGGGGCCTTAGAAATCAGACGATAACAAAATAGGTTAATTACTTGA
* * * *
1498308 TTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACTATACACTTAAAGATGAT
131 TTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCA-A-AGTTTAAGCTGAT
*
1498373 GGAGCCTTAGAAATCTGACGATAACAAAATAGG
194 GGAGCCTTAGAAATCCGACGATAACAAAATAGG
1498406 TTAATTACT
1 TTAATTACT
1498415 TGATTTGTTA
Statistics
Matches: 414, Mismatches: 46, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
225 86 0.21
226 280 0.68
227 48 0.12
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (226 bp):
TTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAACGTAATAGGT
ACCGCATGTTTAAAGCTGAAGGGGCCTTAGAAATCAGACGATAACAAAATAGGTTAATTACTTGA
TTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCTGATGG
AGCCTTAGAAATCCGACGATAACAAAATAGG
Found at i:1498961 original size:199 final size:199
Alignment explanation
Indices: 1498602--1499049 Score: 650
Period size: 199 Copynumber: 2.3 Consensus size: 199
1498592 AGATCGAAAT
* *
1498602 TATCGATACCTATACAAAAAGTATC-AAAACTTTATGTTTACGCCTATTATCATTAAACTGGTAG
1 TATCGATACCTATACAAAGAGTATCGATAA-TTTATGTTTACGCCTATTATCATTAAACTGGTAG
* * * * *
1498666 ATTTTTACCGTTTACATTGTAAATTTACCTGTTACTTTAATGTAATAGGTTTCGAAATTATAAGT
65 ATTTTTACCGTTCACATTGTAAATTTACCTGATACTTTAAAGTAATAGATTTCAAAATTATAAGT
* * * ** *
1498731 ATCAATACTTGTGATACGTGTATCAATACTTTTTGAGTGGATGTTATTTGAGAAGCATA-TGGAC
130 ATCAATACTTGTGATACATGTATCAATACTTTGTGAGTGCAAATT-GTTGAGAAGCATATTGGAC
1498795 TAAAAC
194 TAAAAC
1498801 TATCGATACCTATACAAAGAGTATCGATAATTTATGTTTACGCCTATTATCATTAAACTGGTAGA
1 TATCGATACCTATACAAAGAGTATCGATAATTTATGTTTACGCCTATTATCATTAAACTGGTAGA
* *
1498866 TTTTTACGGTTCACATTGTAAATTTACCT-ATAGCTTTAAAGTAATCGATTTCAAAATTATAAGT
66 TTTTTACCGTTCACATTGTAAATTTACCTGATA-CTTTAAAGTAATAGATTTCAAAATTATAAGT
* * * *
1498930 ATCGATACTTGTTATACATGTATCGATACTTTGTGCGTGCAAATTGTTGAGAAGCATATTGGACT
130 ATCAATACTTGTGATACATGTATCAATACTTTGTGAGTGCAAATTGTTGAGAAGCATATTGGACT
*
1498995 AAAAG
195 AAAAC
* *
1499000 TATCGATACCTATACAAAGATTATCGATACTTTATGTTTACGCCTATTAT
1 TATCGATACCTATACAAAGAGTATCGATAATTTATGTTTACGCCTATTAT
1499050 TAGGTACCGA
Statistics
Matches: 224, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
198 14 0.06
199 207 0.92
200 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (199 bp):
TATCGATACCTATACAAAGAGTATCGATAATTTATGTTTACGCCTATTATCATTAAACTGGTAGA
TTTTTACCGTTCACATTGTAAATTTACCTGATACTTTAAAGTAATAGATTTCAAAATTATAAGTA
TCAATACTTGTGATACATGTATCAATACTTTGTGAGTGCAAATTGTTGAGAAGCATATTGGACTA
AAAC
Found at i:1501704 original size:20 final size:20
Alignment explanation
Indices: 1501676--1501745 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
1501666 GTATCGATAC
* * *
1501676 TACTGTTCACACAGTATCGA
1 TACTATTCATACAATATCGA
*
1501696 TACTATTCATACAATATCGG
1 TACTATTCATACAATATCGA
* *
1501716 TACTTTTCATACAATA-CAA
1 TACTATTCATACAATATCGA
1501735 TACTATTCATA
1 TACTATTCATA
1501746 AAAAAAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 11 0.26
20 31 0.74
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (20 bp):
TACTATTCATACAATATCGA
Found at i:1504475 original size:21 final size:21
Alignment explanation
Indices: 1504443--1504493 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1504433 TTAGCATCGA
* *
1504443 TACTATTTATGGTATCAGTAC
1 TACTATTCATGGTATCAATAC
*
1504464 TACTGTTCATGGTATCAATAC
1 TACTATTCATGGTATCAATAC
1504485 TACTATTCA
1 TACTATTCA
1504494 CACAATATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
TACTATTCATGGTATCAATAC
Found at i:1504510 original size:20 final size:20
Alignment explanation
Indices: 1504485--1504552 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
1504475 GTATCAATAC
*
1504485 TACTATTCACACAATATCGA
1 TACTATTCATACAATATCGA
* * *
1504505 TACTATTTATACAGTATCGG
1 TACTATTCATACAATATCGA
* *
1504525 TACTTTTCATACAATA-CAA
1 TACTATTCATACAATATCGA
1504544 TACTATTCA
1 TACTATTCA
1504553 AAAAAAAATT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 9 0.24
20 29 0.76
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.37
Consensus pattern (20 bp):
TACTATTCATACAATATCGA
Found at i:1507213 original size:21 final size:21
Alignment explanation
Indices: 1507187--1507241 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
1507177 GGCTTGATAA
1507187 TATCGATACTATTGTTCATGG
1 TATCGATACTATTGTTCATGG
*
1507208 TATCGATACTACTGTTCATGG
1 TATCGATACTATTGTTCATGG
1507229 TATCGATACTATT
1 TATCGATACTATT
1507242 CATGCAGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.42
Consensus pattern (21 bp):
TATCGATACTATTGTTCATGG
Found at i:1507253 original size:20 final size:18
Alignment explanation
Indices: 1507187--1507262 Score: 71
Period size: 21 Copynumber: 3.7 Consensus size: 18
1507177 GGCTTGATAA
1507187 TATCGATACTATTGTTCATGG
1 TATCGATACTA---TTCATGG
1507208 TATCGATACTACTGTTCATGG
1 TATCGATACTA---TTCATGG
1507229 TATCGATACTATTCATGCAG
1 TATCGATACTATTCATG--G
1507249 TATCGATACATATT
1 TATCGATAC-TATT
1507263 TTGCATTATG
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
18 6 0.12
20 10 0.20
21 35 0.69
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (18 bp):
TATCGATACTATTCATGG
Found at i:1507336 original size:20 final size:20
Alignment explanation
Indices: 1507311--1507380 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
1507301 GTATCGATAC
* *
1507311 TACTATTCACACAGTATCAA
1 TACTATTCATACAATATCAA
* **
1507331 TACTATTTATACAATATCGG
1 TACTATTCATACAATATCAA
*
1507351 TACTTTTCATACAATA-CAA
1 TACTATTCATACAATATCAA
1507370 TACTATTCATA
1 TACTATTCATA
1507381 AAAAAATTTT
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 11 0.28
20 29 0.73
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (20 bp):
TACTATTCATACAATATCAA
Found at i:1510058 original size:21 final size:21
Alignment explanation
Indices: 1510032--1510113 Score: 96
Period size: 21 Copynumber: 3.9 Consensus size: 21
1510022 GGCTTGATAA
*
1510032 TATCGATACTATTGTTCATGG
1 TATCGATACTATTGTGCATGG
*
1510053 TATCGATACTACTGTGCATGG
1 TATCGATACTATTGTGCATGG
*
1510074 TATCGATACTATTCATGCA--G
1 TATCGATACTATT-GTGCATGG
*
1510094 TATCGATACCTATTTTGCAT
1 TATCGATA-CTATTGTGCAT
1510114 TATGGATTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
20 13 0.25
21 36 0.68
22 4 0.08
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (21 bp):
TATCGATACTATTGTGCATGG
Found at i:1510181 original size:20 final size:20
Alignment explanation
Indices: 1510156--1510225 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
1510146 GTATCGATAC
* *
1510156 TACTATTCACACAGTATCAA
1 TACTATTCATACAATATCAA
*
1510176 TACTATTCATACAATATCAG
1 TACTATTCATACAATATCAA
*
1510196 TACTTTTCATACAATAT-AA
1 TACTATTCATACAATATCAA
1510215 TACTATTCATA
1 TACTATTCATA
1510226 AAAAATTTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 11 0.25
20 33 0.75
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (20 bp):
TACTATTCATACAATATCAA
Found at i:1512420 original size:46 final size:46
Alignment explanation
Indices: 1512353--1512523 Score: 270
Period size: 46 Copynumber: 3.7 Consensus size: 46
1512343 TTAGTAATTA
* * *
1512353 TTCATTCATTTCATTTATGGCATCCTTACATGCCTTAATGCATCCT
1 TTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCAT
* * *
1512399 TTCATGCATTTCATTTATGGCATCATTTCACGCCTAAATGCATCAT
1 TTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCAT
1512445 TTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCAT
1 TTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCAT
* *
1512491 TTCATGCATTTCATTTTTGGAATCCTTTCATGC
1 TTCATGCATTTCATTTATGGCATCCTTTCATGC
1512524 ATTTCATTTA
Statistics
Matches: 114, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 114 1.00
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (46 bp):
TTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCAT
Found at i:1512534 original size:118 final size:118
Alignment explanation
Indices: 1512394--1512641 Score: 334
Period size: 118 Copynumber: 2.1 Consensus size: 118
1512384 GCCTTAATGC
*
1512394 ATCCTTTCATGCATTTCATTTATGGCATCATTTCACGCCTAAATGCATCATTTCATGCATTTCAT
1 ATCCTTTCATGCATTTCATTTATGGCATCATTTCACGCCTAAATGCATCATTTCATGCATTTAAT
** * * *
1512459 TTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTTTGGA
66 TTATGGCATCCTTTCATGAATTAATGAATCATTTCATGCATCTCATTTATGGA
* * * * * *
1512512 ATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTTATGCGTTTAAT
1 ATCCTTTCATGCATTTCATTTATGGCATCATTTCACGCCTAAATGCATCATTTCATGCATTTAAT
* * * * *
1512577 TTATGGCATCTTTTCATGAATTAATTAATCCTTTCATTCATCTCATTTATGGC
66 TTATGGCATCCTTTCATGAATTAATGAATCATTTCATGCATCTCATTTATGGA
*
1512630 ATCATTTCATGC
1 ATCCTTTCATGC
1512642 CTTAATCCAT
Statistics
Matches: 112, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
118 112 1.00
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.45
Consensus pattern (118 bp):
ATCCTTTCATGCATTTCATTTATGGCATCATTTCACGCCTAAATGCATCATTTCATGCATTTAAT
TTATGGCATCCTTTCATGAATTAATGAATCATTTCATGCATCTCATTTATGGA
Found at i:1512539 original size:164 final size:164
Alignment explanation
Indices: 1512353--1512670 Score: 474
Period size: 164 Copynumber: 1.9 Consensus size: 164
1512343 TTAGTAATTA
* *
1512353 TTCATTCATTTCATTTATGGCATCCTTACATGCCTTAATGCATCCTTTCATGCATTTCATTTATG
1 TTCATGCATTTCATTTATGGCATCCTTACATGCCTTAATGCATCCTTTCATGCATTTAATTTATG
** * * *
1512418 GCATCATTTCACGCCTAAATGCATCATTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAA
66 GCATCATTTCACGAATAAATGAATCATTTCATGCATCTCATTTATGGCATCATTTCATGCCTTAA
*
1512483 TGCATCATTTCATGCATTTCATTTTTGGAATCCT
131 TCCATCATTTCATGCATTTCATTTTTGGAATCCT
* * *
1512517 TTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTTATGCGTTTAATTTATG
1 TTCATGCATTTCATTTATGGCATCCTTACATGCCTTAATGCATCCTTTCATGCATTTAATTTATG
* * * * * *
1512582 GCATCTTTTCATGAATTAATTAATCCTTTCATTCATCTCATTTATGGCATCATTTCATGCCTTAA
66 GCATCATTTCACGAATAAATGAATCATTTCATGCATCTCATTTATGGCATCATTTCATGCCTTAA
*
1512647 TCCATCCTTTCATGCATTTCATTT
131 TCCATCATTTCATGCATTTCATTT
1512671 ACGACATCCT
Statistics
Matches: 136, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
164 136 1.00
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.45
Consensus pattern (164 bp):
TTCATGCATTTCATTTATGGCATCCTTACATGCCTTAATGCATCCTTTCATGCATTTAATTTATG
GCATCATTTCACGAATAAATGAATCATTTCATGCATCTCATTTATGGCATCATTTCATGCCTTAA
TCCATCATTTCATGCATTTCATTTTTGGAATCCT
Found at i:1512562 original size:46 final size:46
Alignment explanation
Indices: 1512512--1512858 Score: 451
Period size: 46 Copynumber: 7.5 Consensus size: 46
1512502 CATTTTTGGA
*
1512512 ATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAATGC
* * * * ** **
1512558 ATCCTTTTATGCGTTTAATTTATGGCATCTTTTCATGAATTAATTA
1 ATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAATGC
* * *
1512604 ATCCTTTCATTCATCTCATTTATGGCATCATTTCATGCCTTAATCC
1 ATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAATGC
* * * *
1512650 ATCCTTTCATGCATTTCATTTACGACATCCTTTTATGCCTTAATGC
1 ATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAATGC
* * * * *
1512696 ATACTTTCATGTATTTTATTTTTGGTATCATTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAATGC
* * *
1512742 ATCCTTTCATGCATTTCATTTACGACATCATTTCATGCCTTAATAC
1 ATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAATGC
* * *
1512788 ATCATTTCATGCATTTCATTTATGGCATCCTTTCATACCTTAATGC
1 ATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAATGC
1512834 ATCCTTTCATGCATTTCATTTATGG
1 ATCCTTTCATGCATTTCATTTATGG
1512859 ATTCGTTTTA
Statistics
Matches: 252, Mismatches: 49, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 252 1.00
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.46
Consensus pattern (46 bp):
ATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAATGC
Found at i:1512608 original size:138 final size:136
Alignment explanation
Indices: 1512466--1512858 Score: 329
Period size: 138 Copynumber: 2.8 Consensus size: 136
1512456 CATTTATGGC
*
1512466 ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTTTGGAATCCTTTCATGCATTTCAT
1 ATCCTTTCATGCCTT-ATGCATCATTTCATGCATTTCATTTTT-CAATCCTTTCATGCATTTCAT
* * *
1512531 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTTATGCGTTTAATTTATGGCATCTTTTCATGA
64 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTAATTTATGGCATCATTTCATGA
*
1512596 ATTAATTA
129 ATTAATGA
* ** *
1512604 ATCCTTTCATTCATCTCATTTATGGCATCATTTCATGC----C-TTAATCCATCCTTTCATGCAT
1 ATCCTTTCA-T--GC-C--TTAT-GCATCATTTCATGCATTTCATTTTTCAATCCTTTCATGCAT
* * * * * * * *
1512664 TTCATTTACGACATCCTTTTATGCCTTAATGCATACTTTCATGTATTTTATTTTTGGTATCATTT
59 TTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTAATTTATGGCATCATTT
** *
1512729 CATGCCTTAATGC
124 CATGAATTAATGA
* * * * *
1512742 ATCCTTTCATGCATTTCATTTACGACATCATTTCATGC-CTT-A--ATAC-ATCATTTCATGCAT
1 ATCCTTTCATGC----C--TTATG-CATCATTTCATGCATTTCATTTTTCAATCCTTTCATGCAT
* *
1512802 TTCATTTATGGCATCCTTTCATACCTTAATGCATCCTTTCATGCATTTCATTTATGG
59 TTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTAATTTATGG
1512859 ATTCGTTTTA
Statistics
Matches: 207, Mismatches: 33, Indels: 30
0.77 0.12 0.11
Matches are distributed among these distances:
135 1 0.00
137 2 0.01
138 177 0.86
139 6 0.03
140 1 0.00
141 1 0.00
142 1 0.00
143 2 0.01
144 16 0.08
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.46
Consensus pattern (136 bp):
ATCCTTTCATGCCTTATGCATCATTTCATGCATTTCATTTTTCAATCCTTTCATGCATTTCATTT
ATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTAATTTATGGCATCATTTCATGAAT
TAATGA
Found at i:1512751 original size:20 final size:20
Alignment explanation
Indices: 1512726--1512845 Score: 69
Period size: 20 Copynumber: 5.4 Consensus size: 20
1512716 TTTGGTATCA
1512726 TTTCATGCCTTAATGCATCC
1 TTTCATGCCTTAATGCATCC
* * *
1512746 TTTCATGCATTTCATTTACGACATCA
1 TTTCATGC----C-TTAATG-CATCC
* *
1512772 TTTCATGCCTTAATACATCA
1 TTTCATGCCTTAATGCATCC
*
1512792 TTTCATGCATTTCATTTATGGCATCC
1 TTTCATGC----C-TTAAT-GCATCC
*
1512818 TTTCATACCTTAATGCATCC
1 TTTCATGCCTTAATGCATCC
1512838 TTTCATGC
1 TTTCATGC
1512846 ATTTCATTTA
Statistics
Matches: 76, Mismatches: 12, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
20 34 0.45
21 7 0.09
22 2 0.03
24 2 0.03
25 8 0.11
26 23 0.30
ACGTcount: A:0.23, C:0.26, G:0.08, T:0.42
Consensus pattern (20 bp):
TTTCATGCCTTAATGCATCC
Found at i:1513168 original size:13 final size:13
Alignment explanation
Indices: 1513150--1513176 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1513140 TGAAACGTAC
1513150 AATATCAAATGTT
1 AATATCAAATGTT
1513163 AATATCAAATGTT
1 AATATCAAATGTT
1513176 A
1 A
1513177 GTATATTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (13 bp):
AATATCAAATGTT
Found at i:1513342 original size:42 final size:41
Alignment explanation
Indices: 1513295--1513387 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 41
1513285 CCCAACCATG
* * *
1513295 GTATCGATACTTCTATACTATGGTACTGATACCTTTCTCTTA
1 GTATCGATACTACTACACTATGGTACTGATA-CATTCTCTTA
* * *
1513337 GTATCGATACTACTACACTATTGTATTGATACATTCTTTTA
1 GTATCGATACTACTACACTATGGTACTGATACATTCTCTTA
1513378 GTATCGATAC
1 GTATCGATAC
1513388 CATTTGACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
41 18 0.40
42 27 0.60
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (41 bp):
GTATCGATACTACTACACTATGGTACTGATACATTCTCTTA
Found at i:1515297 original size:2 final size:2
Alignment explanation
Indices: 1515290--1515352 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1515280 CCAGAAAAGC
1515290 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
1515332 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1515353 TCTGATAGTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1517397 original size:46 final size:44
Alignment explanation
Indices: 1517329--1517464 Score: 148
Period size: 46 Copynumber: 3.0 Consensus size: 44
1517319 TTAATATATC
* *
1517329 GTTATATATTTTTATTTGTGGCATCATTTCATACCAATTATGCACT
1 GTTATATA-TTTCATTTATGGCATC-TTTCATACCAATTATGCACT
***
1517375 GTTATATATATTCATTTATGGCATTCTTTCATACCAATTATGTGTT
1 GTTATATAT-TTCATTTATGGCA-TCTTTCATACCAATTATGCACT
* *
1517421 GTTATACATTTCCATTTATGGCATCTTTTCATAACAATTA-GCAC
1 GTTATATATTT-CATTTATGGCATC-TTTCATACCAATTATGCAC
1517465 GGGTAAGCAA
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
45 6 0.08
46 68 0.89
47 2 0.03
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.46
Consensus pattern (44 bp):
GTTATATATTTCATTTATGGCATCTTTCATACCAATTATGCACT
Found at i:1518021 original size:46 final size:46
Alignment explanation
Indices: 1517969--1518395 Score: 622
Period size: 46 Copynumber: 9.3 Consensus size: 46
1517959 TTACTCGTTA
*
1517969 ATTTCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * * * *
1518015 ATTTCATTTATGG-AGTCATCTCATGCCTTCATGTATTCTTTCATGC
1 ATTTCATTTATGGCA-TCCTTTCATGCCTTAATGCATCCTTTCATGC
1518061 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * * *
1518107 ATTTCATTCATCGCATCCTTTCATACCTTAATGCATCTTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
1518153 ATTTCATTTATGGCACCCTTTCATGCCTTAATGCATCCTTTCATAC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
1518199 ATTTCATTTATTGCATCCTTTCATGCCTTAATGCATCATTTGATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
1518245 ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCATTTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* **
1518291 ATTTGATTTATGGCATCCTTTCATGCCTTAACACATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
1518337 ATTTCATTTATGGCATCCTTTCATGCCTTAATGAATCATTTCACGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1518383 ATTTCATTTATGG
1 ATTTCATTTATGG
1518396 ATTCATTTTA
Statistics
Matches: 340, Mismatches: 39, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
45 1 0.00
46 338 0.99
47 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.44
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:1518843 original size:22 final size:22
Alignment explanation
Indices: 1518817--1518894 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
1518807 TACCCCAACC
1518817 ATGGTATCGATACTTCTATACT
1 ATGGTATCGATACTTCTATACT
* *
1518839 ATGGTACCGATACCTT-TCT-CT
1 ATGGTATCGATA-CTTCTATACT
* * *
1518860 -TAGTATCGATACTACTACACT
1 ATGGTATCGATACTTCTATACT
1518881 ATGGTATCGATACT
1 ATGGTATCGATACT
1518895 CTCTTTTAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
19 2 0.05
20 10 0.23
21 4 0.09
22 25 0.57
23 3 0.07
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (22 bp):
ATGGTATCGATACTTCTATACT
Found at i:1518867 original size:42 final size:41
Alignment explanation
Indices: 1518820--1518912 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 41
1518810 CCCAACCATG
* * *
1518820 GTATCGATACTTCTATACTATGGTACCGATACCTTTCTCTTA
1 GTATCGATACTACTACACTATGGTACCGATA-CTCTCTCTTA
* *
1518862 GTATCGATACTACTACACTATGGTATCGATACTCTCTTTTA
1 GTATCGATACTACTACACTATGGTACCGATACTCTCTCTTA
1518903 GTATCGATAC
1 GTATCGATAC
1518913 CATTTTGACA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 18 0.39
42 28 0.61
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.39
Consensus pattern (41 bp):
GTATCGATACTACTACACTATGGTACCGATACTCTCTCTTA
Found at i:1519797 original size:20 final size:20
Alignment explanation
Indices: 1519772--1519859 Score: 97
Period size: 20 Copynumber: 4.4 Consensus size: 20
1519762 ATATCGATAC
*
1519772 TTTGTCAGATTTTAACCAGT
1 TTTGTCAAATTTTAACCAGT
*
1519792 TTTGTCAAATTTTTACTCA-T
1 TTTGTCAAATTTTAAC-CAGT
* * *
1519812 TTTGTCAAATTTCAATCGGT
1 TTTGTCAAATTTTAACCAGT
* *
1519832 TTTGTTAAATTTTAACCGGT
1 TTTGTCAAATTTTAACCAGT
1519852 TTTGTCAA
1 TTTGTCAA
1519860 TTTCCAATCG
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
19 1 0.02
20 53 0.95
21 2 0.04
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (20 bp):
TTTGTCAAATTTTAACCAGT
Found at i:1519834 original size:40 final size:40
Alignment explanation
Indices: 1519772--1519882 Score: 118
Period size: 40 Copynumber: 2.8 Consensus size: 40
1519762 ATATCGATAC
* * * * *
1519772 TTTGTCAGATTTTAACCAGTTTTGTCAAATTTTTACTC-AT
1 TTTGTCAAATTTCAATCGGTTTTGTCAAATTTTAAC-CGAT
* *
1519812 TTTGTCAAATTTCAATCGGTTTTGTTAAATTTTAACCGGT
1 TTTGTCAAATTTCAATCGGTTTTGTCAAATTTTAACCGAT
*
1519852 TTTGTC-AATTTCCAATCGCTTTTGTCAAATT
1 TTTGTCAAATTT-CAATCGGTTTTGTCAAATT
1519883 CGTTACATGT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
39 6 0.10
40 54 0.90
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.49
Consensus pattern (40 bp):
TTTGTCAAATTTCAATCGGTTTTGTCAAATTTTAACCGAT
Found at i:1519874 original size:20 final size:19
Alignment explanation
Indices: 1519811--1519879 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 19
1519801 TTTTTACTCA
1519811 TTTTGTCAAATTTCAATCGG
1 TTTTGTC-AATTTCAATCGG
* * *
1519831 TTTTGTTAAATTTTAACCGG
1 TTTTG-TCAATTTCAATCGG
*
1519851 TTTTGTCAATTTCCAATCGC
1 TTTTGTCAATTT-CAATCGG
1519871 TTTTGTCAA
1 TTTTGTCAA
1519880 ATTCGTTACA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 6 0.15
20 33 0.82
21 1 0.03
ACGTcount: A:0.23, C:0.16, G:0.13, T:0.48
Consensus pattern (19 bp):
TTTTGTCAATTTCAATCGG
Found at i:1520403 original size:200 final size:198
Alignment explanation
Indices: 1519942--1520416 Score: 578
Period size: 199 Copynumber: 2.4 Consensus size: 198
1519932 GTATTTATGT
* * * * * * *
1519942 CTATTATCAATATACTGATAGACTTTCACCGTTTACATTGTAAATTTACCTACAACTTTAAAGTA
1 CTATTATCATTAAACCGGTAGACTTTTACCGTTTACATTGTAAATTTACCTA-TAGTTTAAAGTA
*
1520007 ATAGGTTTCAAAATTCCGCATATCGATACTTAATACATGTGTATAAATACTTTGTTCGTACAAAT
65 ATAGGTTTCAAAATTCCGCATATCGATACTTAATACATGTGTATAAATACTTTGTTCATACAAAT
*
1520072 TGTTGAGAAGCATACTGGACTAAAAGTATCAATACCTATACAAAACGAATCAATACTTGATGGTT
130 TGTTGAGAAGCATACTGGAATAAAAGTATCAATACCTATACAAAACGAATCAATACTTGATGGTT
1520137 ACGC
195 ACGC
* * *
1520141 CTATTATCATTAAACCAGTAGACTTTTACCATTTACATTGTAAATTTACCCATAGCTTTAAAGTA
1 CTATTATCATTAAACCGGTAGACTTTTACCGTTTACATTGTAAATTTACCTATAG-TTTAAAGTA
* ** * ** *
1520206 ATCGGTTTCAAAATTCCGTGTATCGATACTTTATACATGTGTATTGATACTTTTTTGCATACAAA
65 ATAGGTTTCAAAATTCCGCATATCGATACTTAATACATGTGTATAAATACTTTGTT-CATACAAA
* * * * * * * *
1520271 TTATTTTAGATGCATAC-GAGAATAAAAGTATCGATACTCTATA-ATAA-GTATCGATACTTTAT
129 TT-GTTGAGAAGCATACTG-GAATAAAAGTATCAATAC-CTATACAAAACGAATCAATACTTGAT
*
1520333 GTTTACGC
191 GGTTACGC
* * * *
1520341 CTATTATCATTAAACCGGTAGATTTTTACCGTTTATATTGTAAATTTACTTATTAGTTTAAAGAA
1 CTATTATCATTAAACCGGTAGACTTTTACCGTTTACATTGTAAATTTACCTA-TAGTTTAAAGTA
1520406 ATAGGTTTCAA
65 ATAGGTTTCAA
1520417 TATTATAAGT
Statistics
Matches: 234, Mismatches: 36, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
198 1 0.00
199 102 0.44
200 93 0.40
201 33 0.14
202 5 0.02
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37
Consensus pattern (198 bp):
CTATTATCATTAAACCGGTAGACTTTTACCGTTTACATTGTAAATTTACCTATAGTTTAAAGTAA
TAGGTTTCAAAATTCCGCATATCGATACTTAATACATGTGTATAAATACTTTGTTCATACAAATT
GTTGAGAAGCATACTGGAATAAAAGTATCAATACCTATACAAAACGAATCAATACTTGATGGTTA
CGC
Found at i:1520457 original size:200 final size:199
Alignment explanation
Indices: 1519960--1520506 Score: 547
Period size: 200 Copynumber: 2.7 Consensus size: 199
1519950 AATATACTGA
* * * * * * *
1519960 TAGACTTTCACCGTTTACATTGTAAATTTACCTACAACTTTAAAGTAATAGGTTTCAAAATTCCG
1 TAGACTTTTACCATTTACATTGTAAATTTACCCATAGCTTTAAAGAAATAGGTTTCAAAATTAC-
* * ** * *
1520025 CA-TATCGATACTTAATACATGTGTATAAATACTTTGT-TCGTACAAATT-GTTGAGAAGCATAC
65 AAGTATCGATACTTTATACA-GTGTATCGATACTTTGTGT-GTACAAATTATTTGAGATGCATAC
* *
1520087 TGGACTAAAAGTATCAATACCTATACAAAACGAATCAATACTTGATGGTTACGCCTATTATCATT
128 TGGAATAAAAGTATCGATACCTATACAAAACGAATCAATACTTGATGGTTACGCCTATTATCATT
1520152 AAACCAG
193 AAACCAG
* * * *
1520159 TAGACTTTTACCATTTACATTGTAAATTTACCCATAGCTTTAAAGTAATCGGTTTCAAAATTCCG
1 TAGACTTTTACCATTTACATTGTAAATTTACCCATAGCTTTAAAGAAATAGGTTTCAAAATTACA
* * * *
1520224 TGTATCGATACTTTATACATGTGTATTGATACTTT-TTTGCATACAAATTATTTTAGATGCATAC
66 AGTATCGATACTTTATACA-GTGTATCGATACTTTGTGTG--TACAAATTATTTGAGATGCATAC
* * * * *
1520288 -GAGAATAAAAGTATCGATACTCTATA-ATAA-GTATCGATACTTTATGTTTACGCCTATTATCA
128 TG-GAATAAAAGTATCGATAC-CTATACAAAACGAATCAATACTTGATGGTTACGCCTATTATCA
*
1520350 TTAAACCGG
191 TTAAACCAG
* * * ** * *
1520359 TAGATTTTTACCGTTTATATTGTAAATTTACTTATTAG-TTTAAAGAAATAGGTTTCAATATTAT
1 TAGACTTTTACCATTTACATTGTAAATTTACCCA-TAGCTTTAAAGAAATAGGTTTCAAAATTAC
* * * *
1520423 AAGTATTGATACGTGTTATGAC-G-GTATCGATACTTTGTGTGTGCAAATTGTTTGAGATGTATA
65 AAGTATCGATAC-T-TTAT-ACAGTGTATCGATACTTTGTGTGTACAAATTATTTGAGATGCATA
1520486 CTGGAATAATAAGTATCGATA
127 CTGGAATAA-AAGTATCGATA
1520507 TGTTATGTTT
Statistics
Matches: 293, Mismatches: 41, Indels: 27
0.81 0.11 0.07
Matches are distributed among these distances:
198 2 0.01
199 114 0.39
200 128 0.44
201 38 0.13
202 9 0.03
203 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (199 bp):
TAGACTTTTACCATTTACATTGTAAATTTACCCATAGCTTTAAAGAAATAGGTTTCAAAATTACA
AGTATCGATACTTTATACAGTGTATCGATACTTTGTGTGTACAAATTATTTGAGATGCATACTGG
AATAAAAGTATCGATACCTATACAAAACGAATCAATACTTGATGGTTACGCCTATTATCATTAAA
CCAG
Found at i:1522011 original size:6 final size:6
Alignment explanation
Indices: 1522000--1522036 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
1521990 ATATTGGAGC
* *
1522000 TCAAAT TGAAAT TCAAAT TGAAAT TCAAAT TCAAAT T
1 TCAAAT TCAAAT TCAAAT TCAAAT TCAAAT TCAAAT T
1522037 TGCACAAGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (6 bp):
TCAAAT
Found at i:1522015 original size:12 final size:12
Alignment explanation
Indices: 1522000--1522036 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
1521990 ATATTGGAGC
1522000 TCAAATTGAAAT
1 TCAAATTGAAAT
1522012 TCAAATTGAAAT
1 TCAAATTGAAAT
*
1522024 TCAAATTCAAAT
1 TCAAATTGAAAT
1522036 T
1 T
1522037 TGCACAAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (12 bp):
TCAAATTGAAAT
Found at i:1522373 original size:15 final size:15
Alignment explanation
Indices: 1522349--1522378 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1522339 TAAACTAAAC
1522349 ATACAAAACAATGTT
1 ATACAAAACAATGTT
*
1522364 ATACATAACAATGTT
1 ATACAAAACAATGTT
1522379 CTAATAGTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (15 bp):
ATACAAAACAATGTT
Found at i:1524577 original size:18 final size:18
Alignment explanation
Indices: 1524551--1524614 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
1524541 AATCCCTTAC
*
1524551 TTGATAAGAAGATCTTGG
1 TTGAGAAGAAGATCTTGG
* *
1524569 TTGAGAAGATGAACTTGG
1 TTGAGAAGAAGATCTTGG
* *
1524587 TTGAGAAGAAGGTTTTGG
1 TTGAGAAGAAGATCTTGG
1524605 TTGAGAAGAA
1 TTGAGAAGAA
1524615 CTGCGTATCG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.34, C:0.03, G:0.33, T:0.30
Consensus pattern (18 bp):
TTGAGAAGAAGATCTTGG
Found at i:1525108 original size:45 final size:45
Alignment explanation
Indices: 1525044--1525143 Score: 166
Period size: 45 Copynumber: 2.2 Consensus size: 45
1525034 AATTGTGTTG
1525044 AAAGTATCGATGTTGTTTAGATCGAAAGTATCGATACCTATACAA
1 AAAGTATCGATGTTGTTTAGATCGAAAGTATCGATACCTATACAA
* *
1525089 AAAGTATC-AGTGTTGTTTAGATTGAAAGTATTGATACCTATACAA
1 AAAGTATCGA-TGTTGTTTAGATCGAAAGTATCGATACCTATACAA
1525134 AAAGTATCGA
1 AAAGTATCGA
1525144 AACTTTATGT
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
44 1 0.02
45 49 0.96
46 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (45 bp):
AAAGTATCGATGTTGTTTAGATCGAAAGTATCGATACCTATACAA
Found at i:1525488 original size:200 final size:200
Alignment explanation
Indices: 1525113--1525655 Score: 749
Period size: 200 Copynumber: 2.7 Consensus size: 200
1525103 GTTTAGATTG
* * * *
1525113 AAAGTATTGATACCTATACAAAAAGTATCGAA-ACTTTATGTTTATGGCTATTATCATTAAACC-
1 AAAGTATCGATACCTATACAAAGAGTATC-AATACTTTATGTTTACGCCTATTATCATTAAACCG
* *
1525176 AGTAGATTTTTATCGTTTACATTGTAAATTTACCTGTTACTTTAAAGCAATAGGTTTC-AAATTT
65 A-TAGATTTTTATCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAA-TT
* * ** * * *
1525240 GTAAGTATCAATACTTGTGTTACGTGTATCAAAACTTTTTGTGTGCATGTTATTTGAGAAGCATA
128 ATAAGTATCGATACTTGTAATACATGTATCAAAACTTTCTGCGTGCATGTTATTTGAGAAGCATA
1525305 TTGGACTA
193 TTGGACTA
*
1525313 ATAGTATCGATACCTATACAAAGAGTATCAATACTTTATGTTTACGCCTATTATCATTAAACCGA
1 AAAGTATCGATACCTATACAAAGAGTATCAATACTTTATGTTTACGCCTATTATCATTAAACCGA
* *
1525378 TAGATTTTTA-CTGTTTACATTGTAAATTTACCTATTACTTCAATGTAATAGGTTTCGAAATTAT
66 TAGATTTTTATC-GTTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTAT
* *
1525442 AAGTATCGATACTTGTAATACATGTAT-AGATACTTTCTGCGTGCATGTTGTTTGAGAAGCATAT
130 AAGTATCGATACTTGTAATACATGTATCA-AAACTTTCTGCGTGCATGTTATTTGAGAAGCATAT
1525506 TGGACTA
194 TGGACTA
* * * * *
1525513 AAAGTATCGATGCCTACACAAAGAGTATCGATACTTTATGTTTACGCCTATTATCATTAATCCGG
1 AAAGTATCGATACCTATACAAAGAGTATCAATACTTTATGTTTACGCCTATTATCATTAAACCGA
* *
1525578 TAGATTTTTATCGTTTACATTGTAAATTTACCTA-TAGCTTTAAACTAATCA-GTTTCGAAGTTA
66 TAGATTTTTATCGTTTACATTGTAAATTTACCTATTA-CTTTAAAGTAAT-AGGTTTCGAAATTA
1525641 TAAGTATCGATACTT
129 TAAGTATCGATACTT
1525656 TCTGCATGCA
Statistics
Matches: 307, Mismatches: 28, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
199 6 0.02
200 295 0.96
201 6 0.02
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (200 bp):
AAAGTATCGATACCTATACAAAGAGTATCAATACTTTATGTTTACGCCTATTATCATTAAACCGA
TAGATTTTTATCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATA
AGTATCGATACTTGTAATACATGTATCAAAACTTTCTGCGTGCATGTTATTTGAGAAGCATATTG
GACTA
Found at i:1530096 original size:20 final size:21
Alignment explanation
Indices: 1530073--1530125 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
1530063 ATTGAAACCA
*
1530073 ATTTTGTCAAATTT-CAATTG
1 ATTTTGTCAAATTTCCAATCG
1530093 ATTTTGTC-AATTTCCAATCG
1 ATTTTGTCAAATTTCCAATCG
1530113 ATTTTGTCAAATT
1 ATTTTGTCAAATT
1530126 CGTTACCTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 5 0.17
20 21 0.70
21 4 0.13
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.49
Consensus pattern (21 bp):
ATTTTGTCAAATTTCCAATCG
Found at i:1533031 original size:23 final size:23
Alignment explanation
Indices: 1533005--1533051 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1532995 AACCGCATCA
*
1533005 AAAGACAAAAGAAAACGTGTCAT
1 AAAGACAAAAGAAAACATGTCAT
* *
1533028 AAAGGCAGAAGAAAACATGTCAT
1 AAAGACAAAAGAAAACATGTCAT
1533051 A
1 A
1533052 CATGCAAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.55, C:0.13, G:0.19, T:0.13
Consensus pattern (23 bp):
AAAGACAAAAGAAAACATGTCAT
Found at i:1539386 original size:40 final size:40
Alignment explanation
Indices: 1539331--1539412 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
1539321 TACTAACATA
1539331 ATGGTAACGACGGGTTTTACTATGGGGTTACTCTTCCTGT
1 ATGGTAACGACGGGTTTTACTATGGGGTTACTCTTCCTGT
1539371 ATGGTAACGACGGGTTTTACTATGGGGTTACTCTTCCTGT
1 ATGGTAACGACGGGTTTTACTATGGGGTTACTCTTCCTGT
1539411 AT
1 AT
1539413 TTGAGTCAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.38
Consensus pattern (40 bp):
ATGGTAACGACGGGTTTTACTATGGGGTTACTCTTCCTGT
Found at i:1542578 original size:49 final size:49
Alignment explanation
Indices: 1542483--1542737 Score: 289
Period size: 49 Copynumber: 5.2 Consensus size: 49
1542473 GTTCAATCGG
* ** *
1542483 CATAAAAAGTGCCATTAATGAAAGTTAAATGCATAACGGTGTATTTCGA
1 CATAAAAGGTGCCACCAATGAAAGTTAAATGCATAACGGTGCATTTCGA
* * * * *
1542532 CATATAAGGTGCTACCAATGAAAGTTAAATTCATAACAGTGCATTTCAA
1 CATAAAAGGTGCCACCAATGAAAGTTAAATGCATAACGGTGCATTTCGA
* * * * *
1542581 CATAAAATGTGTCACTAATGAAAGTTAAATGCATAACGGTACATTTCGG
1 CATAAAAGGTGCCACCAATGAAAGTTAAATGCATAACGGTGCATTTCGA
* * * *
1542630 CATAAAAGGTGCCACTC-ATAAAAGTTAAATGCATAATGGTGTATTTCAA
1 CATAAAAGGTGCCAC-CAATGAAAGTTAAATGCATAACGGTGCATTTCGA
* * * *
1542679 CAT-AAAGGTGCCACTAATGAAAGTTAAATGCATAATGCTTCATTTCGA
1 CATAAAAGGTGCCACCAATGAAAGTTAAATGCATAACGGTGCATTTCGA
1542727 CATAAAAGGTG
1 CATAAAAGGTG
1542738 TCAGTCATGG
Statistics
Matches: 169, Mismatches: 34, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
48 41 0.24
49 128 0.76
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (49 bp):
CATAAAAGGTGCCACCAATGAAAGTTAAATGCATAACGGTGCATTTCGA
Found at i:1542731 original size:97 final size:98
Alignment explanation
Indices: 1542483--1542737 Score: 336
Period size: 98 Copynumber: 2.6 Consensus size: 98
1542473 GTTCAATCGG
* * * *
1542483 CATAAAAAGTGCCATTAATGAAAGTTAAATGCATAACGGTGT-ATTTCGACATATAAGGTGCTAC
1 CATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGT-TCATTTCGACATAAAAGGTGCCAC
* *
1542547 CAATGAAAGTTAAATTCATAACAGTGCATTTCAA
65 CAATAAAAGTTAAATGCATAACAGTGCATTTCAA
* * * *
1542581 CATAAAATGTGTCACTAATGAAAGTTAAATGCATAACGGTACATTTCGGCATAAAAGGTGCCACT
1 CATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTTCATTTCGACATAAAAGGTGCCAC-
** *
1542646 C-ATAAAAGTTAAATGCATAATGGTGTATTTCAA
65 CAATAAAAGTTAAATGCATAACAGTGCATTTCAA
* *
1542679 CAT-AAAGGTGCCACTAATGAAAGTTAAATGCATAATGCTTCATTTCGACATAAAAGGTG
1 CATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTTCATTTCGACATAAAAGGTG
1542738 TCAGTCATGG
Statistics
Matches: 137, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
97 50 0.36
98 86 0.63
99 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (98 bp):
CATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTTCATTTCGACATAAAAGGTGCCACC
AATAAAAGTTAAATGCATAACAGTGCATTTCAA
Found at i:1544154 original size:49 final size:49
Alignment explanation
Indices: 1544090--1544593 Score: 704
Period size: 49 Copynumber: 10.3 Consensus size: 49
1544080 TTGTTCAATT
* * *
1544090 GGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAATGATGCATTTC
1 GGCATAAAAGGTGCCACTAATAAAAGTTAAATGCATAACGGTGCATTTC
* * * *
1544139 AGTATAAAAGCTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTC
1 GGCATAAAAGGTGCCACTAATAAAAGTTAAATGCATAACGGTGCATTTC
* * *
1544188 GACATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTTT
1 GGCATAAAAGGTGCCACTAATAAAAGTTAAATGCATAACGGTGCA-TTTC
* * *
1544238 GGCATAAAAGGTTCCACTAATGAAAGTTAAATGCATAACGGTGTATTTC
1 GGCATAAAAGGTGCCACTAATAAAAGTTAAATGCATAACGGTGCATTTC
* ** *
1544287 GACATAAAAGGTGCCACCCATAAAAGTTAAATGCATAACGGTGCATTTT
1 GGCATAAAAGGTGCCACTAATAAAAGTTAAATGCATAACGGTGCATTTC
* * * *
1544336 GGCATAAAAGATGTCACTCATAAAAGTTAAATGCATAACAGTGCATTTC
1 GGCATAAAAGGTGCCACTAATAAAAGTTAAATGCATAACGGTGCATTTC
* *
1544385 GGCATAAAAGGTGCCACTCATAAAAGTTAAATGCATAACGGTGCATTTT
1 GGCATAAAAGGTGCCACTAATAAAAGTTAAATGCATAACGGTGCATTTC
* * * *
1544434 GGCATAAAAGATGTCACTCATAAAAGTTAAATGCATAACAGTGCATTTC
1 GGCATAAAAGGTGCCACTAATAAAAGTTAAATGCATAACGGTGCATTTC
*
1544483 GGCATAAAAGGTGCCACTCATAAAAGTTAAATGCATAACGGTGCATTTC
1 GGCATAAAAGGTGCCACTAATAAAAGTTAAATGCATAACGGTGCATTTC
* * *
1544532 GGCAT-AAAGGTGCTAGTAATGAAAGTTAAATGCATAACGGTGCATTTC
1 GGCATAAAAGGTGCCACTAATAAAAGTTAAATGCATAACGGTGCATTTC
*
1544580 AGCATAAAAGGTGC
1 GGCATAAAAGGTGC
1544594 ACTCATGATA
Statistics
Matches: 410, Mismatches: 43, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
48 43 0.10
49 322 0.79
50 45 0.11
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (49 bp):
GGCATAAAAGGTGCCACTAATAAAAGTTAAATGCATAACGGTGCATTTC
Found at i:1546044 original size:49 final size:49
Alignment explanation
Indices: 1545947--1546256 Score: 360
Period size: 49 Copynumber: 6.4 Consensus size: 49
1545937 TTGTTCAATT
* * * *
1545947 GGCATAAAAAGTGCCACAAATGAAAGTTAAAT-CATAACGGTGCATTTC
1 GGCATAAAAGGTGCCACTAATAAAAGTTAAATGCATAACAGTGCATTTC
* ** *
1545995 GGCATAAAAGGTGCTACTAACGAATGTTAAATGCATAACAGTGCATTTC
1 GGCATAAAAGGTGCCACTAATAAAAGTTAAATGCATAACAGTGCATTTC
* * * *
1546044 GGCCTAAAAGGTGCCACCCAA-AAAAGTTAAATGCATAA-ATATGTATTTC
1 GGCATAAAAGGTGCCA-CTAATAAAAGTTAAATGCATAACA-GTGCATTTC
* * * *
1546093 GACATAAAAGGTGTCACTCATAAAAGTTAAATGCATAAC-GATGCATTTT
1 GGCATAAAAGGTGCCACTAATAAAAGTTAAATGCATAACAG-TGCATTTC
* *
1546142 GGCATAAAAGGTGCCACTCATAAAAGTTAAATGCATAACAATGCATTTC
1 GGCATAAAAGGTGCCACTAATAAAAGTTAAATGCATAACAGTGCATTTC
* * * *
1546191 GGCAT-AAAGGTGCCACTAATGAAAGTTAAATGTATAACGGTGCATGTC
1 GGCATAAAAGGTGCCACTAATAAAAGTTAAATGCATAACAGTGCATTTC
1546239 GGCATAAAAGGTGCCACT
1 GGCATAAAAGGTGCCACT
1546257 CATGGTATTC
Statistics
Matches: 223, Mismatches: 31, Indels: 15
0.83 0.12 0.06
Matches are distributed among these distances:
48 72 0.32
49 148 0.66
50 3 0.01
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (49 bp):
GGCATAAAAGGTGCCACTAATAAAAGTTAAATGCATAACAGTGCATTTC
Found at i:1546251 original size:97 final size:98
Alignment explanation
Indices: 1545947--1546259 Score: 398
Period size: 98 Copynumber: 3.2 Consensus size: 98
1545937 TTGTTCAATT
* ** * ** *
1545947 GGCATAAAAAGTGCCACAAATGAAAGTTAAAT-CATAACGGTGCATTTCGGCATAAAAGGTGCTA
1 GGCATAAAAGGTGCCACTCATAAAAGTTAAATGCATAACAATGCATTTCGGCATAAAAGGTGCCA
* * *
1546011 CTAACGAATGTTAAATGCATAACAGTGCATTTC
66 CTAATGAAAGTTAAATGCATAACGGTGCATTTC
* * * * * *
1546044 GGCCTAAAAGGTGCCACCCAAAAAAGTTAAATGCATAA-ATATGTATTTCGACATAAAAGGTGTC
1 GGCATAAAAGGTGCCACTCATAAAAGTTAAATGCATAACA-ATGCATTTCGGCATAAAAGGTGCC
* * * *
1546108 ACTCATAAAAGTTAAATGCATAACGATGCATTTT
65 ACTAATGAAAGTTAAATGCATAACGGTGCATTTC
1546142 GGCATAAAAGGTGCCACTCATAAAAGTTAAATGCATAACAATGCATTTCGGCAT-AAAGGTGCCA
1 GGCATAAAAGGTGCCACTCATAAAAGTTAAATGCATAACAATGCATTTCGGCATAAAAGGTGCCA
* *
1546206 CTAATGAAAGTTAAATGTATAACGGTGCATGTC
66 CTAATGAAAGTTAAATGCATAACGGTGCATTTC
1546239 GGCATAAAAGGTGCCACTCAT
1 GGCATAAAAGGTGCCACTCAT
1546260 GGTATTCATA
Statistics
Matches: 182, Mismatches: 31, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
97 83 0.46
98 98 0.54
99 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (98 bp):
GGCATAAAAGGTGCCACTCATAAAAGTTAAATGCATAACAATGCATTTCGGCATAAAAGGTGCCA
CTAATGAAAGTTAAATGCATAACGGTGCATTTC
Found at i:1551863 original size:3 final size:3
Alignment explanation
Indices: 1551855--1551896 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
1551845 CTAAGTCTCG
1551855 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TATC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC TTC TT
1551897 GTACTAGGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1553122 original size:49 final size:49
Alignment explanation
Indices: 1552996--1553380 Score: 459
Period size: 49 Copynumber: 7.9 Consensus size: 49
1552986 TGTTCAATCA
*
1552996 GCATAAAAGGTGCCACTAATGAAAGTTAAATGTATATA-GGTGCATTTCG
1 GCATAAAAGGTGCCACTAATGAAAGTTAAATGCATA-ACGGTGCATTTCG
*
1553045 ACATAAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCG
1 GCAT-AAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCG
* * * *
1553095 GTATAAAAGGTGTCACTAATGAAAGTTAAATGCATAACGGTGCAATTCA
1 GCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCG
* * * ** *
1553144 GCATAAAAAGTGCCACTAATGATAGTTAAATGCAAAACAATGCATTTCA
1 GCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCG
* * * * *
1553193 ACATAAAAGGTTCCACTAATAAAAGTTAATTGCATAACGGTGTATTTCG
1 GCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCG
* * *
1553242 GCTTAAAAGGTGTCACTCATGAAAGTTAAATGCATAACGGTGCATTTCG
1 GCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCG
* ** * * * * *
1553291 GCATAAAAGGTGTCACTTGTAAAAGTTAAATGCATAGCGTTGTATTTAG
1 GCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCG
* * *
1553340 ACAT-AAAGATGCCAATAATGAAAGTTAAATGCATAACGGTG
1 GCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTG
1553381 AATGACCATT
Statistics
Matches: 283, Mismatches: 51, Indels: 5
0.83 0.15 0.01
Matches are distributed among these distances:
48 29 0.10
49 210 0.74
50 44 0.16
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (49 bp):
GCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCG
Found at i:1557179 original size:18 final size:18
Alignment explanation
Indices: 1557156--1557196 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1557146 TAGTTTGATT
*
1557156 AATGAAATAACATTGTTC
1 AATGAAATAACATTATTC
* *
1557174 AATGAACTAACTTTATTC
1 AATGAAATAACATTATTC
1557192 AATGA
1 AATGA
1557197 GCTAAATGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (18 bp):
AATGAAATAACATTATTC
Found at i:1559310 original size:15 final size:14
Alignment explanation
Indices: 1559292--1559343 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
1559282 CCCTCTTTAA
1559292 TTTTTTTTTCTTTTC
1 TTTTTTTTT-TTTTC
**
1559307 TTTTTTCGATTTTTC
1 TTTTTT-TTTTTTTC
*
1559322 TTTTTATTTTTTTGC
1 TTTTT-TTTTTTTTC
1559337 TTTTTTT
1 TTTTTTT
1559344 ACTAACTCGG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
14 2 0.07
15 26 0.87
16 2 0.07
ACGTcount: A:0.04, C:0.10, G:0.04, T:0.83
Consensus pattern (14 bp):
TTTTTTTTTTTTTC
Found at i:1560939 original size:18 final size:18
Alignment explanation
Indices: 1560897--1560942 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1560887 TAGTTTGATT
*
1560897 AATGAAATAACATTATTC
1 AATGAACTAACATTATTC
*
1560915 AATGAACTAACTTTATTC
1 AATGAACTAACATTATTC
1560933 AATGAACTAA
1 AATGAACTAA
1560943 ATGCATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (18 bp):
AATGAACTAACATTATTC
Found at i:1561018 original size:17 final size:17
Alignment explanation
Indices: 1560998--1561039 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1560988 ACTACTTCCC
1560998 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
*
1561015 TAAAT-ACAATTCATGCT
1 TAAATGA-AATACATGCT
*
1561032 TTAATGAA
1 TAAATGAA
1561040 CAACATACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 1 0.05
17 19 0.90
18 1 0.05
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:1562934 original size:22 final size:22
Alignment explanation
Indices: 1562906--1562950 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1562896 CACTAGTTAT
*
1562906 TATATATGATTTTTATTATGAG
1 TATATATGATGTTTATTATGAG
1562928 TATATATGATGTTTATTATGAG
1 TATATATGATGTTTATTATGAG
1562950 T
1 T
1562951 CTTACTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (22 bp):
TATATATGATGTTTATTATGAG
Found at i:1563250 original size:61 final size:61
Alignment explanation
Indices: 1563125--1563252 Score: 168
Period size: 61 Copynumber: 2.1 Consensus size: 61
1563115 AAGGACACTA
* * * *
1563125 AGTGCATGTTGTGGGCACAATCTTATGTGTCATATCCAGGTTAGCACTAGAGTTTAAACCT
1 AGTGCATGTGGTGGGAACAATCTTATGTGTCATATCCAGATTAGCACTAGAGTGTAAACCT
* * * *
1563186 AGTGTATGTGGTGGGAACGATCTTATGTGTCATATCC-GAATTAGCACTAGAGTGTAAGCTT
1 AGTGCATGTGGTGGGAACAATCTTATGTGTCATATCCAG-ATTAGCACTAGAGTGTAAACCT
1563247 AGTGCA
1 AGTGCA
1563253 CGTTTAGCAC
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 1 0.02
61 56 0.98
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.32
Consensus pattern (61 bp):
AGTGCATGTGGTGGGAACAATCTTATGTGTCATATCCAGATTAGCACTAGAGTGTAAACCT
Found at i:1573201 original size:12 final size:12
Alignment explanation
Indices: 1573169--1573201 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1573159 CTTGTTATTA
1573169 TATATATGAATT
1 TATATATGAATT
1573181 T-TATCATGAATT
1 TATAT-ATGAATT
1573193 TATATATGA
1 TATATATGA
1573202 TGTTTATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.16
12 13 0.68
13 3 0.16
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.48
Consensus pattern (12 bp):
TATATATGAATT
Found at i:1573215 original size:24 final size:24
Alignment explanation
Indices: 1573169--1573215 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1573159 CTTGTTATTA
*
1573169 TATATATGAATTTTATCATGAATT
1 TATATATGAATTTTATCACGAATT
*
1573193 TATATATG-ATGTTTATTACGAAT
1 TATATATGAAT-TTTATCACGAAT
1573216 ATTACTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (24 bp):
TATATATGAATTTTATCACGAATT
Found at i:1576252 original size:47 final size:47
Alignment explanation
Indices: 1576197--1576342 Score: 199
Period size: 47 Copynumber: 3.2 Consensus size: 47
1576187 CCATAAGCTC
*
1576197 GCTTATTTTACCAAAATACTTACCATTTAAATTCCATAAGTTCGTAA
1 GCTTATTTTACCAAAATACTTACCATTTAAATTCCATAAGCTCGTAA
**
1576244 GCTTATTTTACCAAAATACTTACCATTTAAATTCTGTAAGCTCGTAA
1 GCTTATTTTACCAAAATACTTACCATTTAAATTCCATAAGCTCGTAA
* * * * *
1576291 GCTTATTTAACCCATATACTTGCCA-TT-AA-TCCAAAAGCTCGTAA
1 GCTTATTTTACCAAAATACTTACCATTTAAATTCCATAAGCTCGTAA
1576335 GCTTATTT
1 GCTTATTT
1576343 GTATGCTTAC
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
44 20 0.22
45 2 0.02
46 2 0.02
47 65 0.73
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.38
Consensus pattern (47 bp):
GCTTATTTTACCAAAATACTTACCATTTAAATTCCATAAGCTCGTAA
Found at i:1576573 original size:59 final size:58
Alignment explanation
Indices: 1576443--1576579 Score: 157
Period size: 59 Copynumber: 2.3 Consensus size: 58
1576433 ATAAGCACCG
* * * **
1576443 TAGTGCTATCCCGAATATGACATATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTC
1 TAGTG-TATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTC
* ** * *
1576502 AAGTACAGTCCCGAATATGACACATAAGGTTGTGCCCACCATATACACTAGGTATCCTT
1 TAGTGTA-TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTC
1576561 TAGTGTATTCCCGAATATG
1 TAGTGTA-TCCCGAATATG
1576580 CAGCCTGCTG
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
58 1 0.02
59 62 0.98
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (58 bp):
TAGTGTATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTC
Found at i:1583537 original size:47 final size:46
Alignment explanation
Indices: 1583467--1583637 Score: 258
Period size: 47 Copynumber: 3.7 Consensus size: 46
1583457 TATAAAATCC
*
1583467 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1583512 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1583559 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1583606 CTTGCCA-TTAA-TCCAAAAGCTCGTAAGCTTAT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTAT
1583638 CTGTATGCTT
Statistics
Matches: 119, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
44 20 0.17
45 12 0.10
46 2 0.02
47 85 0.71
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1583840 original size:59 final size:59
Alignment explanation
Indices: 1583748--1583876 Score: 179
Period size: 59 Copynumber: 2.2 Consensus size: 59
1583738 CGTAGTGCTA
* **
1583748 TCCCGAATATGACACATAAGGTCTTGCCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCTTGCCCACCATATACACTAGGTATCCTTAAGTACAG
* ** *
1583807 TCCCGAATATGACACATAAGGT-TGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCT-TGCCCACCATATACACTAGGTATCCTTAAGTACAG
1583866 TCCCGAATATG
1 TCCCGAATATG
1583877 CAGCCTGCTG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 1 0.02
59 61 0.98
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCTTGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:1592007 original size:33 final size:33
Alignment explanation
Indices: 1591954--1592056 Score: 152
Period size: 33 Copynumber: 3.1 Consensus size: 33
1591944 CATAATGAAC
* * *
1591954 ATATCATAGCATGAACTTTCATGGCAAGAACTT
1 ATATAATAACATGAACTTTCATGACAAGAACTT
* * *
1591987 ATATAATAACATGAAATTTCATGATAATAACTT
1 ATATAATAACATGAACTTTCATGACAAGAACTT
1592020 ATATAATAACATGAACTTTCATGACAAGAACTT
1 ATATAATAACATGAACTTTCATGACAAGAACTT
1592053 ATAT
1 ATAT
1592057 CATATATTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.33
Consensus pattern (33 bp):
ATATAATAACATGAACTTTCATGACAAGAACTT
Found at i:1592691 original size:25 final size:25
Alignment explanation
Indices: 1592641--1592705 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
1592631 TTACACAAGA
1592641 GAAATTTAACACATAATTCCAACACT
1 GAAA-TTAACACATAATTCCAACACT
* * *
1592667 -AAACTTAGCACATAATTTCACCACT
1 GAAA-TTAACACATAATTCCAACACT
1592692 GAAATTAACACATA
1 GAAATTAACACATA
1592706 TTATATCAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 30 0.91
26 3 0.09
ACGTcount: A:0.46, C:0.23, G:0.05, T:0.26
Consensus pattern (25 bp):
GAAATTAACACATAATTCCAACACT
Found at i:1592768 original size:26 final size:26
Alignment explanation
Indices: 1592739--1592811 Score: 128
Period size: 26 Copynumber: 2.8 Consensus size: 26
1592729 ACTTCCATCG
*
1592739 GTGAAATTTATCATGCATTTAAACCA
1 GTGAAATTTAACATGCATTTAAACCA
1592765 GTGAAATTTAACATGCATTTAAACCA
1 GTGAAATTTAACATGCATTTAAACCA
*
1592791 GTGAAATTTAACATGTATTTA
1 GTGAAATTTAACATGCATTTA
1592812 TACAAGTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (26 bp):
GTGAAATTTAACATGCATTTAAACCA
Found at i:1592775 original size:15 final size:15
Alignment explanation
Indices: 1592755--1592801 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
1592745 TTTATCATGC
1592755 ATTTAAACCAGTGAA
1 ATTTAAACCAGTGAA
*
1592770 ATTT-AA-CA-TG-C
1 ATTTAAACCAGTGAA
1592781 ATTTAAACCAGTGAA
1 ATTTAAACCAGTGAA
1592796 ATTTAA
1 ATTTAA
1592802 CATGTATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
11 4 0.15
12 4 0.15
13 4 0.15
14 4 0.15
15 10 0.38
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (15 bp):
ATTTAAACCAGTGAA
Found at i:1592890 original size:25 final size:24
Alignment explanation
Indices: 1592837--1592890 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1592827 CACATAATTC
*
1592837 CACCATTAAAGTTATCACAAATCA
1 CACCATTAAACTTATCACAAATCA
* * *
1592861 TACCATTTAACTTATCACAAACTTA
1 CACCATTAAACTTATCACAAA-TCA
1592886 CACCA
1 CACCA
1592891 GTGAAATTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.43, C:0.28, G:0.02, T:0.28
Consensus pattern (24 bp):
CACCATTAAACTTATCACAAATCA
Found at i:1593038 original size:126 final size:126
Alignment explanation
Indices: 1592761--1593041 Score: 381
Period size: 126 Copynumber: 2.2 Consensus size: 126
1592751 ATGCATTTAA
*
1592761 ACCAGTGAAATTTAACATGCATTTAAACCAGTGAAATTTAACATGTATTTATACAAGTAAAAATA
1 ACCAGTGAAATTTAACATGCATTTACACCAGTGAAATTTAACATGTATTTATACAAGTAAAAATA
* * *
1592826 ACACATAATTCCACCATTAAAGTTATCACAAATCATACCATTTAACTTATCACAAACTTAC
66 ACACATAATTCCACCACTAAAGTTATCACAAATCATACCAATGAACTTATCACAAACTTAC
* *
1592887 ACCAGTGAAATTTAACATGCATTTACACCATTGAAATTTAA-ATTGTA-TT-TGC-AGTAATGAA
1 ACCAGTGAAATTTAACATGCATTTACACCAGTGAAATTTAACA-TGTATTTATACAAGTAA--AA
* * * * * *
1592948 TGTAACACATAATTTCACCACTAAAGTTATTACAAATCATACCAATGAACTTATCATATACTTAT
63 -ATAACACATAATTCCACCACTAAAGTTATCACAAATCATACCAATGAACTTATCACAAACTTAC
*
1593013 ACCAGTGAAATTTAACATGAATTTACACC
1 ACCAGTGAAATTTAACATGCATTTACACC
1593042 GGCAAAAGTA
Statistics
Matches: 138, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
123 5 0.04
124 2 0.01
125 5 0.04
126 126 0.91
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (126 bp):
ACCAGTGAAATTTAACATGCATTTACACCAGTGAAATTTAACATGTATTTATACAAGTAAAAATA
ACACATAATTCCACCACTAAAGTTATCACAAATCATACCAATGAACTTATCACAAACTTAC
Found at i:1595487 original size:2 final size:2
Alignment explanation
Indices: 1595480--1595509 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1595470 AGTTAAATCT
1595480 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
1595510 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1595514 original size:2 final size:2
Alignment explanation
Indices: 1595509--1595538 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1595499 ATATATATAT
*
1595509 AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1595539 GGTTGAACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1598516 original size:15 final size:15
Alignment explanation
Indices: 1598431--1598517 Score: 50
Period size: 15 Copynumber: 5.4 Consensus size: 15
1598421 ATCATAGCAT
1598431 GAACTTTCATTG-CAA
1 GAACTTTCA-TGACAA
* *
1598446 GAACTTATAACATAACAT
1 GAACTT-T--CATGACAA
*
1598464 GAACTTTCTTGACAA
1 GAACTTTCATGACAA
* *
1598479 GAACTTATATCATAACAT
1 GAAC-T-T-TCATGACAA
*
1598497 TAACTTTCATGACAA
1 GAACTTTCATGACAA
1598512 GAACTT
1 GAACTT
1598518 ATATAATATA
Statistics
Matches: 53, Mismatches: 12, Indels: 14
0.67 0.15 0.18
Matches are distributed among these distances:
15 27 0.51
16 3 0.06
17 4 0.08
18 19 0.36
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.32
Consensus pattern (15 bp):
GAACTTTCATGACAA
Found at i:1598521 original size:33 final size:33
Alignment explanation
Indices: 1598419--1598521 Score: 154
Period size: 33 Copynumber: 3.1 Consensus size: 33
1598409 CATAATGAAC
*
1598419 ATATCATAGCATGAACTTTCATTG-CAAGAACTT
1 ATATCATAACATGAACTTTCA-TGACAAGAACTT
* *
1598452 ATAACATAACATGAACTTTCTTGACAAGAACTT
1 ATATCATAACATGAACTTTCATGACAAGAACTT
*
1598485 ATATCATAACATTAACTTTCATGACAAGAACTT
1 ATATCATAACATGAACTTTCATGACAAGAACTT
1598518 ATAT
1 ATAT
1598522 AATATACTTA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 2 0.03
33 61 0.97
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (33 bp):
ATATCATAACATGAACTTTCATGACAAGAACTT
Found at i:1600697 original size:78 final size:78
Alignment explanation
Indices: 1600562--1600757 Score: 214
Period size: 78 Copynumber: 2.5 Consensus size: 78
1600552 ACCATTTTCC
* * * * **
1600562 GCAGGCTCC-TCGACTTTGTGCTCAGAGTAAGTCCTTACCGAAGGTTCCTCAGCTTTGTGCTTAG
1 GCAGGCTCCTTTG-CTTTGTGCTCAGGGTAAGTCCTTACTGAAGGCTCCTCAGCTTTGTGCACAG
* *
1600626 GGTAAGTCCTTACT
65 GATAAGACCTTACT
* * * *
1600640 GCAGGCTCCTTTGCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCCTCTGTTTTGTGCACATG
1 GCAGGCTCCTTTGCTTTGTGCTCAGGGTAAGTCCTTACTGAAGGCTCCTCAGCTTTGTGCACAGG
1600705 ATAAGACCTTACT
66 ATAAGACCTTACT
* * ** * *
1600718 ACAGGCTCCTCTATTTTGTGCACAGGGTAAGCCCTTACTG
1 GCAGGCTCCTTTGCTTTGTGCTCAGGGTAAGTCCTTACTG
1600758 GTTGTATATA
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 97 0.98
79 2 0.02
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (78 bp):
GCAGGCTCCTTTGCTTTGTGCTCAGGGTAAGTCCTTACTGAAGGCTCCTCAGCTTTGTGCACAGG
ATAAGACCTTACT
Found at i:1600756 original size:39 final size:39
Alignment explanation
Indices: 1600563--1600756 Score: 194
Period size: 39 Copynumber: 5.0 Consensus size: 39
1600553 CCATTTTCCG
* * *
1600563 CAGGCTCCTCGACTTTGTGCTCAGAGTAAGTCCTTACCGA
1 CAGGCTCCTCTACTTTGTGCTCAGGGTAAGTCCTTA-CTA
* * *
1600603 -AGGTTCCTC-AGCTTTGTGCTTAGGGTAAGTCCTTACTG
1 CAGGCTCCTCTA-CTTTGTGCTCAGGGTAAGTCCTTACTA
* * *
1600641 CAGGCTCCTTTGCTTTGTGCTCAGGGTAAGTCCTTACTG
1 CAGGCTCCTCTACTTTGTGCTCAGGGTAAGTCCTTACTA
** * * * *
1600680 CAGGCTCCTCTGTTTTGTGCACATGATAAGACCTTACTA
1 CAGGCTCCTCTACTTTGTGCTCAGGGTAAGTCCTTACTA
* * *
1600719 CAGGCTCCTCTATTTTGTGCACAGGGTAAGCCCTTACT
1 CAGGCTCCTCTACTTTGTGCTCAGGGTAAGTCCTTACT
1600757 GGTTGTATAT
Statistics
Matches: 131, Mismatches: 20, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
38 2 0.02
39 129 0.98
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (39 bp):
CAGGCTCCTCTACTTTGTGCTCAGGGTAAGTCCTTACTA
Found at i:1605284 original size:16 final size:17
Alignment explanation
Indices: 1605249--1605282 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1605239 ATATTTCAAA
1605249 TTAATAATTTTCTCTCT
1 TTAATAATTTTCTCTCT
1605266 TTAAT-ATTTTC-CTCT
1 TTAATAATTTTCTCTCT
1605281 TT
1 TT
1605283 TAGAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 6 0.35
17 5 0.29
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.62
Consensus pattern (17 bp):
TTAATAATTTTCTCTCT
Found at i:1606599 original size:39 final size:39
Alignment explanation
Indices: 1606418--1606601 Score: 138
Period size: 39 Copynumber: 4.7 Consensus size: 39
1606408 AGTTTTCTCA
* * * * * **
1606418 GCTTTGTGCTCACGGTAAATCCTTACCGAAGGTTCCTAA
1 GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCCTCT
* * * *
1606457 ACTTTGTGCTCAGGGGAAGTCCTTACTACAGGCTCCTTT
1 GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCCTCT
* * * *
1606496 GATTTATGCTCAGGGTAAGTCCTT-CTTGTAGGATCCTCT
1 GCTTTGTGCTCAGGGTAAGTCCTTAC-TGCAGGCTCCTCT
* * * * **
1606535 GCTTTGTTCACATGATAAGAGCTTACTGCAGGCTCCTCT
1 GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCCTCT
*
1606574 GCTTTGTGCAT-AGGGTAAGCCCTTACTG
1 GCTTTGTGC-TCAGGGTAAGTCCTTACTG
1606602 GGTGTACAAG
Statistics
Matches: 108, Mismatches: 34, Indels: 6
0.73 0.23 0.04
Matches are distributed among these distances:
38 1 0.01
39 106 0.98
40 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.34
Consensus pattern (39 bp):
GCTTTGTGCTCAGGGTAAGTCCTTACTGCAGGCTCCTCT
Found at i:1606971 original size:37 final size:38
Alignment explanation
Indices: 1606915--1606986 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 38
1606905 GTATTACAAC
* * *
1606915 TATTTTGTTCTGTAAATGTTTTATAC-GTTTTCTGTGG
1 TATTTTGATATGTAAATGTTTTATACAATTTTCTGTGG
*
1606952 TATTTTGATATGTATATGTTTTATACAATTTTCTG
1 TATTTTGATATGTAAATGTTTTATACAATTTTCTG
1606987 ATATATGGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 23 0.77
38 7 0.23
ACGTcount: A:0.21, C:0.07, G:0.15, T:0.57
Consensus pattern (38 bp):
TATTTTGATATGTAAATGTTTTATACAATTTTCTGTGG
Found at i:1607259 original size:20 final size:20
Alignment explanation
Indices: 1607236--1607273 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1607226 AATAATCACA
*
1607236 TAAAACCATAATATAATATT
1 TAAAAACATAATATAATATT
*
1607256 TAAAAACATAATTTAATA
1 TAAAAACATAATATAATA
1607274 ATGTGCTATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAACATAATATAATATT
Found at i:1625407 original size:123 final size:122
Alignment explanation
Indices: 1625107--1625449 Score: 341
Period size: 123 Copynumber: 2.7 Consensus size: 122
1625097 ACTTAGCACG
* * * ** * * *
1625107 TAATTCTACCACTAAAATTAACACATGTTATATCAATAAACTTATCACATACTTACATCAGTGAA
1 TAATTCCACCACTAAAGTTATCACAAATCATA-CAATAAA-ATATCACATACTTACATAAGTGAA
* * * * ** * *
1625172 ATTTAACATGCATTTACATCAATGAAGTTTAAATTGTATTTATGTCAGTGGAAGTAACACA
64 ATTTAACATGCATTTACACCAGTAAAATTTAAATTGTA--TATACCAGTGAAAATAACACA
* * *
1625233 TAATTCCACCAATAAAGTTATCACAAATCATACAAAAGAACATATCACATACCTACATAAGTGAA
1 TAATTCCACCACTAAAGTTATCACAAATCATACAATA-AA-ATATCACATACTTACATAAGTGAA
*
1625298 ATTTAACATGCATTTACACCAGTAAAATTTAACA-TGTA-ATACCAGTGAAAATATCACA
64 ATTTAACATGCATTTACACCAGTAAAATTTAA-ATTGTATATACCAGTGAAAATAACACA
* * *
1625356 TAATTCCACCACTAAAGTTATCACAAATCATACCAATAAAGTCATCGCATACTTACACCAA-TGA
1 TAATTCCACCACTAAAGTTATCACAAATCATA-CAATAAAAT-ATCACATACTTACA-TAAGTGA
* *
1625420 AATTTAATATGTATTTACACCAGTGAAAAT
63 AATTTAACATGCATTTACACCAGT-AAAAT
1625450 AACACATATC
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
122 1 0.01
123 85 0.46
124 11 0.06
125 4 0.02
126 81 0.44
127 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.30
Consensus pattern (122 bp):
TAATTCCACCACTAAAGTTATCACAAATCATACAATAAAATATCACATACTTACATAAGTGAAAT
TTAACATGCATTTACACCAGTAAAATTTAAATTGTATATACCAGTGAAAATAACACA
Found at i:1625496 original size:3 final size:3
Alignment explanation
Indices: 1625488--1625555 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
1625478 TTTTTATCCA
1625488 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1625536 TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
1625556 AATATATATT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1625567 original size:11 final size:11
Alignment explanation
Indices: 1625551--1625582 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
1625541 TTATTATTAT
1625551 TATTAAATATA
1 TATTAAATATA
1625562 TATTAAATATA
1 TATTAAATATA
1625573 TATATAAATA
1 TAT-TAAATA
1625583 ATTAATTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAATATA
Found at i:1638411 original size:9 final size:9
Alignment explanation
Indices: 1638399--1638472 Score: 69
Period size: 9 Copynumber: 7.9 Consensus size: 9
1638389 GAAAAAAGAA
1638399 AAAAGAAAG
1 AAAAGAAAG
1638408 AAAAGAAAG
1 AAAAGAAAG
*
1638417 AAAATAGAA-
1 AAAAGA-AAG
1638426 AAAAGAAAG
1 AAAAGAAAG
*
1638435 AAAAGAAAA
1 AAAAGAAAG
1638444 AAATAGAAAATG
1 AAA-AG-AAA-G
*
1638456 AAAAAAAAG
1 AAAAGAAAG
*
1638465 AGAAGAAA
1 AAAAGAAA
1638473 AAGAAAAAGG
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
8 2 0.04
9 37 0.70
10 7 0.13
11 4 0.08
12 3 0.06
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:1638427 original size:26 final size:27
Alignment explanation
Indices: 1638387--1638480 Score: 131
Period size: 27 Copynumber: 3.6 Consensus size: 27
1638377 ATTATGCTTG
*
1638387 AAGAAAAAAGAAAAAAGAAAGAAAAGA
1 AAGAAAATAGAAAAAAGAAAGAAAAGA
1638414 AAGAAAATAGAAAAAAGAAAGAAAAGA
1 AAGAAAATAGAAAAAAGAAAGAAAAGA
* *
1638441 AA-AAAATAG-AAAATGAAAAAAAAGA
1 AAGAAAATAGAAAAAAGAAAGAAAAGA
1638466 GAAGAAAA-AGAAAAA
1 -AAGAAAATAGAAAAA
1638481 GGGGATCAAG
Statistics
Matches: 61, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
25 14 0.23
26 11 0.18
27 36 0.59
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (27 bp):
AAGAAAATAGAAAAAAGAAAGAAAAGA
Found at i:1638818 original size:16 final size:16
Alignment explanation
Indices: 1638797--1638836 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1638787 ATACAATTCT
*
1638797 ATTTATTTCAAG-TTCA
1 ATTTATTT-AAGAGTCA
1638813 ATTTATTTAAGAGTCA
1 ATTTATTTAAGAGTCA
1638829 ATTTATTT
1 ATTTATTT
1638837 TTGGAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.14
16 19 0.86
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (16 bp):
ATTTATTTAAGAGTCA
Found at i:1639909 original size:82 final size:82
Alignment explanation
Indices: 1639634--1639925 Score: 539
Period size: 84 Copynumber: 3.5 Consensus size: 82
1639624 TATAATGTGC
1639634 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACTAATCATTGA
1 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC-AATCATTGA
* *
1639699 ATTTAGAAGATGAATGTG
65 GTTTAGAAGATGAATTTG
1639717 CTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTG
1 -TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-CAATCATTG
1639782 AGTTTAGAAGATGAATTTG
64 AGTTTAGAAGATGAATTTG
1639801 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAG
1 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAG
1639866 TTTAGAAGATGAATTTG
66 TTTAGAAGATGAATTTG
1639883 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1639926 ATTCAGTAGG
Statistics
Matches: 205, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
82 71 0.35
83 54 0.26
84 79 0.39
85 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (82 bp):
TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCATTGAG
TTTAGAAGATGAATTTG
Found at i:1640857 original size:113 final size:112
Alignment explanation
Indices: 1640660--1641219 Score: 827
Period size: 113 Copynumber: 5.0 Consensus size: 112
1640650 GATTCAAATC
*
1640660 CATCACTTGATGGATCAACATTGCCAGA-TAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCA-TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
1640724 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATT
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
1640772 CATCATTGGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATT-GATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1640837 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
* *** *
1640885 CATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCA-TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* ** *
1640950 AGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTAATCTGAATT
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
* * *** *
1640998 CATCACTGGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCA-TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
***
1641063 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
* * *
1641111 CATCAATTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATC-ATTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
**
1641176 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACC-TTTGTTTGA
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGA
1641220 TGCTATCACA
Statistics
Matches: 416, Mismatches: 28, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
111 2 0.00
112 31 0.07
113 380 0.91
114 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (112 bp):
CATCATTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
Found at i:1641539 original size:3 final size:3
Alignment explanation
Indices: 1641531--1641599 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
1641521 TTTTTATCCG
1641531 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1641579 TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
1641600 ATATATATAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1643888 original size:26 final size:26
Alignment explanation
Indices: 1643858--1643909 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1643848 CTTTCCTGTT
1643858 TGGCCCATCTCTCGCTGAATTTTCTG
1 TGGCCCATCTCTCGCTGAATTTTCTG
* *
1643884 TGGCCCATTTCTCGCTGAGTTTTCTG
1 TGGCCCATCTCTCGCTGAATTTTCTG
1643910 AGGCTTGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.10, C:0.29, G:0.21, T:0.40
Consensus pattern (26 bp):
TGGCCCATCTCTCGCTGAATTTTCTG
Found at i:1657003 original size:6 final size:6
Alignment explanation
Indices: 1656992--1657026 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
1656982 CTAAGTAGCG
1656992 AAAATT AAAATT AAAATT AAAATT AAAATTT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAA-TT AAAA
1657027 ATTCAATTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:1657140 original size:4 final size:4
Alignment explanation
Indices: 1657124--1657251 Score: 60
Period size: 4 Copynumber: 32.2 Consensus size: 4
1657114 GAAAAAAGAT
*
1657124 ATAA ATAA TATAA ATAA ATAA ATAA ATCAT ATGGAA A-AA ATAA A-AA
1 ATAA ATAA -ATAA ATAA ATAA ATAA AT-AA AT--AA ATAA ATAA ATAA
* * *
1657170 AT-G TTAA ATAA AGT-A AT-A ATAA A-AA ATAA GA-AGA AGTAA AAAA
1 ATAA ATAA ATAA A-TAA ATAA ATAA ATAA ATAA -ATA-A A-TAA ATAA
*
1657213 ATAG A-AA ATAA ATAA ATAA A-ATA A-AA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATA-A ATAA ATAA ATAA ATAA A
1657252 ACATACTAAG
Statistics
Matches: 97, Mismatches: 11, Indels: 32
0.69 0.08 0.23
Matches are distributed among these distances:
3 19 0.20
4 63 0.65
5 12 0.12
6 3 0.03
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:1657224 original size:15 final size:15
Alignment explanation
Indices: 1657190--1657239 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 15
1657180 AAGTAATAAT
1657190 AAAAAATAAGAAGAAGTA
1 AAAAAAT-AGAA-AA-TA
1657208 AAAAAATAGAAAATA
1 AAAAAATAGAAAATA
*
1657223 AATAAAT--AAAATA
1 AAAAAATAGAAAATA
1657236 AAAA
1 AAAA
1657240 TAAATAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 9 0.30
15 8 0.27
16 2 0.07
17 4 0.13
18 7 0.23
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (15 bp):
AAAAAATAGAAAATA
Found at i:1657228 original size:19 final size:19
Alignment explanation
Indices: 1657192--1657252 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
1657182 GTAATAATAA
* * *
1657192 AAAATAAGAAGAAGTAAA-
1 AAAATAAAAATAAATAAAT
1657210 AAAATAGAAAATAAATAAAT
1 AAAATA-AAAATAAATAAAT
1657230 AAAATAAAAATAAATAAAT
1 AAAATAAAAATAAATAAAT
1657249 AAAA
1 AAAA
1657253 CATACTAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.16
19 26 0.68
20 6 0.16
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (19 bp):
AAAATAAAAATAAATAAAT
Found at i:1657240 original size:15 final size:14
Alignment explanation
Indices: 1657222--1657252 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
1657212 AATAGAAAAT
1657222 AAATAAATAAAATAA
1 AAATAAAT-AAATAA
1657237 AAATAAATAAATAA
1 AAATAAATAAATAA
1657251 AA
1 AA
1657253 CATACTAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAAATAAATAA
Found at i:1659636 original size:14 final size:15
Alignment explanation
Indices: 1659608--1659637 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1659598 TTTAAAAAAT
1659608 AAATAAAATTATTAA
1 AAATAAAATTATTAA
1659623 AAATAAAA-TATTAA
1 AAATAAAATTATTAA
1659637 A
1 A
1659638 CTAAGTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATAAAATTATTAA
Found at i:1666172 original size:55 final size:55
Alignment explanation
Indices: 1666109--1666283 Score: 197
Period size: 55 Copynumber: 3.1 Consensus size: 55
1666099 TATGTGACGA
* *
1666109 TGGTGCTACTAACAGTTGCGTTATACTTAGAACATGTCTGACGTCTCTGTGATGG
1 TGGTGCTACTAACAGATGCGTTATACTTAGAACATGTCTGACGTCTGTGTGATGG
* * * * * * *
1666164 TGGTGCTACTAGCAGGTGCATTATACTCATAACACGTGTATGATGTCTGTGTGATGG
1 TGGTGCTACTAACAGATGCGTTATACTTAGAACA--TGTCTGACGTCTGTGTGATGG
* * * * *
1666221 TGGCGCTACTAACAGATGCGTTATACTTAGCACATGTCTAACGTATGTGTGAAGG
1 TGGTGCTACTAACAGATGCGTTATACTTAGAACATGTCTGACGTCTGTGTGATGG
*
1666276 TGTTGCTA
1 TGGTGCTA
1666284 TTAGCAACTG
Statistics
Matches: 96, Mismatches: 22, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
55 51 0.53
57 45 0.47
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.33
Consensus pattern (55 bp):
TGGTGCTACTAACAGATGCGTTATACTTAGAACATGTCTGACGTCTGTGTGATGG
Found at i:1666372 original size:100 final size:100
Alignment explanation
Indices: 1666195--1666383 Score: 245
Period size: 100 Copynumber: 1.9 Consensus size: 100
1666185 TATACTCATA
* * *
1666195 ACACGTGTATGATGTCTGTGTGATGGTGGCGCTACTAACAGATGCGTTATACTTAGCACATGTCT
1 ACACGTGTATGATGTCTGAGTGACGGTGGCGCTACTAACAGATGCATTATACTTAGCACATGTCT
* *
1666260 AACGTATGTGTGAAGGTGTTGCTATTAGCAACTGC
66 AACGTATATGTGAAGGTGGTGCTATTAGCAACTGC
* * * **
1666295 ACACGTGTCTGATGTCTGAGTGACGTTGGTGCTACTAACA-ACTGCATTATACTTAGCATGTGTC
1 ACACGTGTATGATGTCTGAGTGACGGTGGCGCTACTAACAGA-TGCATTATACTTAGCACATGTC
* * *
1666359 TGACGTTTATGTGACGGTGGTGCTA
65 TAACGTATATGTGAAGGTGGTGCTA
1666384 CAAGCAGCTG
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
99 1 0.01
100 74 0.99
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (100 bp):
ACACGTGTATGATGTCTGAGTGACGGTGGCGCTACTAACAGATGCATTATACTTAGCACATGTCT
AACGTATATGTGAAGGTGGTGCTATTAGCAACTGC
Found at i:1666429 original size:57 final size:56
Alignment explanation
Indices: 1666296--1666485 Score: 224
Period size: 57 Copynumber: 3.4 Consensus size: 56
1666286 AGCAACTGCA
* * * * *
1666296 CACGTGTCTGATGTCTGAGTGACGTTGGTGCTACTAA-CAACTGCATTATACT-TAG
1 CACGTGTCTGACGTCTGTGTGACGATGGTGCTAC-AAGCAGCTGCAATATACTATAG
* * * * *
1666351 CATGTGTCTGACGTTTATGTGACGGTGGTGCTACAAGCAGCTGCAATATATTGATAG
1 CACGTGTCTGACGTCTGTGTGACGATGGTGCTACAAGCAGCTGCAATATACT-ATAG
* *
1666408 CACGTGTTTGACGTCTGTGTGACGATGGTGCTACAAGCAGCTGGAAT-TACTCATAG
1 CACGTGTCTGACGTCTGTGTGACGATGGTGCTACAAGCAGCTGCAATATACT-ATAG
1666464 CACGTGTCTGACGTCTGTGTGA
1 CACGTGTCTGACGTCTGTGTGA
1666486 ATGTGGCGCT
Statistics
Matches: 114, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
54 2 0.02
55 40 0.35
56 28 0.25
57 44 0.39
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (56 bp):
CACGTGTCTGACGTCTGTGTGACGATGGTGCTACAAGCAGCTGCAATATACTATAG
Found at i:1666667 original size:62 final size:62
Alignment explanation
Indices: 1666572--1666691 Score: 159
Period size: 62 Copynumber: 1.9 Consensus size: 62
1666562 CGTGTATGAT
* * * * * * *
1666572 GTCTGTGTGACGGTGGTGTTATAAGCAGATGCAATATACTAATAGCACGTGTCTGACGCGAC
1 GTCTATGTGACGGCGGTGCTACAAGAAGATGCAATATACAAATAACACGTGTCTGACGCGAC
* *
1666634 GTCTATGTGACGGCGGTGCTACAAGAAGTTGCAATATACAAATAACATGTGTCTGACG
1 GTCTATGTGACGGCGGTGCTACAAGAAGATGCAATATACAAATAACACGTGTCTGACG
1666692 TCTATGTGAC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 49 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (62 bp):
GTCTATGTGACGGCGGTGCTACAAGAAGATGCAATATACAAATAACACGTGTCTGACGCGAC
Found at i:1672693 original size:28 final size:28
Alignment explanation
Indices: 1672660--1672724 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
1672650 CGATCGGGTC
*
1672660 ACCGGTCGGGTCGGGTCAGATCGG-TCAA
1 ACCGGTCGGATC-GGTCAGATCGGTTCAA
** *
1672688 ACCGGTTTAGATCGGTCAGATCGGTTCGA
1 ACCGG-TCGGATCGGTCAGATCGGTTCAA
1672717 ACCGGTCG
1 ACCGGTCG
1672725 AAACCGGTCA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.18, C:0.25, G:0.35, T:0.22
Consensus pattern (28 bp):
ACCGGTCGGATCGGTCAGATCGGTTCAA
Found at i:1687427 original size:29 final size:29
Alignment explanation
Indices: 1687388--1687448 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
1687378 TATGAAATGA
*
1687388 AAAAAGTGAATATTATATGCTATAAAACG
1 AAAAAGTGAATACTATATGCTATAAAACG
* *
1687417 AAAAAGTGAATACTATATGCTATGAAATG
1 AAAAAGTGAATACTATATGCTATAAAACG
1687446 AAA
1 AAA
1687449 GTGAATGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (29 bp):
AAAAAGTGAATACTATATGCTATAAAACG
Found at i:1687463 original size:27 final size:27
Alignment explanation
Indices: 1687419--1687508 Score: 69
Period size: 27 Copynumber: 3.3 Consensus size: 27
1687409 ATAAAACGAA
*
1687419 AAAGTGAAT-ACTATATGCTATGAAATG
1 AAAGTGAATGA-TACATGCTATGAAATG
**
1687446 AAAGTGAATGATACATGCTACAAAATG
1 AAAGTGAATGATACATGCTATGAAATG
* **
1687473 AATTTAATGAATGATACATATTATGAAAT-
1 AA---AGTGAATGATACATGCTATGAAATG
1687502 AAA-TGAA
1 AAAGTGAA
1687509 GTGAATGCAT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
25 4 0.08
26 1 0.02
27 24 0.47
28 1 0.02
29 2 0.04
30 19 0.37
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.29
Consensus pattern (27 bp):
AAAGTGAATGATACATGCTATGAAATG
Found at i:1700458 original size:24 final size:24
Alignment explanation
Indices: 1700431--1700479 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1700421 GTAGACGATG
1700431 AAGAAGCACTGCAGTTGCTTGCTC
1 AAGAAGCACTGCAGTTGCTTGCTC
1700455 AAGAAGCACTGCAGTTGCTTGCTC
1 AAGAAGCACTGCAGTTGCTTGCTC
1700479 A
1 A
1700480 CACCTTGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (24 bp):
AAGAAGCACTGCAGTTGCTTGCTC
Found at i:1705323 original size:54 final size:53
Alignment explanation
Indices: 1705265--1705545 Score: 337
Period size: 54 Copynumber: 5.2 Consensus size: 53
1705255 GGTGCACAAG
* *
1705265 TAGTGCCGATACGGTCATTCATAAACATATTATGAAGTTCGTGGGTTGCACACT
1 TAGTGTCGATACGGTCATTCATAAACACATTATGAA-TTCGTGGGTTGCACACT
* ** *
1705319 TAGTGCCGATACATTCATTCATAAACACATTATGAATTCCATGGGTTGCACACT
1 TAGTGTCGATACGGTCATTCATAAACACATTATGAATT-CGTGGGTTGCACACT
* * * *
1705373 TAGTGTCGATACGGTCGTTCATAAACACATTAAGAATTTTGTGGGTTGCGCACT
1 TAGTGTCGATACGGTCATTCATAAACACATTATGAA-TTCGTGGGTTGCACACT
* * * * **
1705427 TAGTGTCGATACGATTATTCATAAAGACATTATGAAGTCCGTTAGTTGCACACT
1 TAGTGTCGATACGGTCATTCATAAACACATTATGAA-TTCGTGGGTTGCACACT
** *
1705481 TAGTGTCGATTGGGTCGTTCATAAACACATTATGAATTCTGTGGGTTGCACACT
1 TAGTGTCGATACGGTCATTCATAAACACATTATGAATTC-GTGGGTTGCACACT
*
1705535 TAGTGGCGATA
1 TAGTGTCGATA
1705546 GTACACATAG
Statistics
Matches: 190, Mismatches: 34, Indels: 6
0.83 0.15 0.03
Matches are distributed among these distances:
53 4 0.02
54 184 0.97
55 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (53 bp):
TAGTGTCGATACGGTCATTCATAAACACATTATGAATTCGTGGGTTGCACACT
Found at i:1705427 original size:108 final size:108
Alignment explanation
Indices: 1705265--1705545 Score: 393
Period size: 108 Copynumber: 2.6 Consensus size: 108
1705255 GGTGCACAAG
* * * * *
1705265 TAGTGCCGATACGGTCATTCATAAACATATTATGAAGTTCGTGGGTTGCACACTTAGTGCCGATA
1 TAGTGTCGATACGGTCGTTCATAAACACATTATGAATTTTGTGGGTTGCACACTTAGTGCCGATA
* *
1705330 C-ATTCATTCATAAACACATTATGAATTCCATGGGTTGCACACT
66 CGATT-ATTCATAAACACATTATGAAGTCCATGAGTTGCACACT
* * *
1705373 TAGTGTCGATACGGTCGTTCATAAACACATTAAGAATTTTGTGGGTTGCGCACTTAGTGTCGATA
1 TAGTGTCGATACGGTCGTTCATAAACACATTATGAATTTTGTGGGTTGCACACTTAGTGCCGATA
* * *
1705438 CGATTATTCATAAAGACATTATGAAGTCCGTTAGTTGCACACT
66 CGATTATTCATAAACACATTATGAAGTCCATGAGTTGCACACT
** * *
1705481 TAGTGTCGATTGGGTCGTTCATAAACACATTATGAATTCTGTGGGTTGCACACTTAGTGGCGATA
1 TAGTGTCGATACGGTCGTTCATAAACACATTATGAATTTTGTGGGTTGCACACTTAGTGCCGATA
1705546 GTACACATAG
Statistics
Matches: 153, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
108 150 0.98
109 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (108 bp):
TAGTGTCGATACGGTCGTTCATAAACACATTATGAATTTTGTGGGTTGCACACTTAGTGCCGATA
CGATTATTCATAAACACATTATGAAGTCCATGAGTTGCACACT
Found at i:1707471 original size:16 final size:16
Alignment explanation
Indices: 1707450--1707487 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
1707440 ATTATTATAA
1707450 GCAAATTCCTCTAAAG
1 GCAAATTCCTCTAAAG
1707466 GCAAATTCCTCTAAAG
1 GCAAATTCCTCTAAAG
1707482 GCAAAT
1 GCAAAT
1707488 ACCTTTCCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (16 bp):
GCAAATTCCTCTAAAG
Found at i:1712768 original size:55 final size:55
Alignment explanation
Indices: 1712678--1713049 Score: 453
Period size: 55 Copynumber: 6.8 Consensus size: 55
1712668 GTACAACAGA
** * * * * *
1712678 CACTATGTGTATAAATCCATGGAAGTCATCCTGAGTTGATGAATAACCGTACAGG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCATACATG
* * * * *
1712733 CACTATGTGTGCAAATCCATGAAATTTATCATGAGTTGATGAATAATCATACAGG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCATACATG
* * *
1712788 AACTATGTGTGCAAATCCACGGAATCCATCACGAGTTGATGAATAACCATACATG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCATACATG
* ** * *
1712843 CACTATGTGTGTAAATCCACAAAATTAATCATGAGTTGATGAATAACCATACATA
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCATACATG
*
1712898 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAAT-ACCTGTACATG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACC-ATACATG
* * *
1712953 CACTATGTGTGCAAATCCATGGAATTCATCATTAGTTGATGAATAACCGTACATG
1 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCATACATG
* * * *
1713008 CA-TGATATGTG-TAACCCACGTAATTCATCATGAGTTGATGAA
1 CACT-ATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAA
1713050 CTTCTGTATA
Statistics
Matches: 276, Mismatches: 38, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
54 30 0.11
55 243 0.88
56 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (55 bp):
CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCATACATG
Found at i:1713892 original size:321 final size:320
Alignment explanation
Indices: 1713310--1713954 Score: 1024
Period size: 321 Copynumber: 2.0 Consensus size: 320
1713300 ATCATCGGAC
* *
1713310 ATCACCAAGCAAGTGTCACCTCGTCAGTAACAGTACTGCATTTATGTTTACTTTTGATGTAGTTA
1 ATCACCAAGCAAGTGTCACCTCGTCAATAACAGTACTGCATTTATGTCTACTTTTGATGTAGTTA
* * * * * * *
1713375 GTTGACATGTAATAGATTTAGTAAAAATGCTCTGAAAAGCATTTTATTTAAACTATTGTTAAATG
66 GCTGACATGTAATAGATTTAGTAAAAACGCTCTAAAAAGCAATTTAGTTAAACTAATGTAAAATG
* * *
1713440 ATGAATTGTGAACATTTCTTTTTGTTATCTATTTAAGTTTAATGCATGTTTTATTATTAGTTTAA
131 ATGAAGTGTGAACATTTCTCTTTGTTATCTATTTAAGTTTAATGCATGTTTTATTATTAGTATAA
** * *
1713505 AAATGTTTTATAAAAAGAAACAAAATTTTATGGGTTTAGGAATGAGGAACTATTTTAAAAGTGAT
196 AAATGTTTTATAAAAAGAAACAAAATTTTACAGGTTTAAGAATGAGGAACTATTTAAAAAGTGAT
* * *
1713570 GTGACATATGTATCTTGTGTACGGAAAGGTATAC-GGGAGATGGGTGTTACATTTATTGGAT
261 GTGACATATGTATCTCGTGTACAGAAAGGTATACAAGG-GATGGGTGTTACATTTATTGG-T
* *
1713631 ATCACCAAGCAAGTTTCACCTCGTCAATAACAGTA-TGACATTTATGTCTATTTTTGATGTAGTT
1 ATCACCAAGCAAGTGTCACCTCGTCAATAACAGTACTG-CATTTATGTCTACTTTTGATGTAGTT
* *
1713695 AGCTGTCATGTAATAGATTTAGTAAAAACGCTCTAAAAAGCAATTTAGTTAACCTAATGTAAAAT
65 AGCTGACATGTAATAGATTTAGTAAAAACGCTCTAAAAAGCAATTTAGTTAAACTAATGTAAAAT
*
1713760 GATTAAGTGTGAACATTTCTCTTTGTTATCTATTTAAGTTTAATGCATGTTTTATTATTAGTATA
130 GATGAAGTGTGAACATTTCTCTTTGTTATCTATTTAAGTTTAATGCATGTTTTATTATTAGTATA
*
1713825 CAAATGTTTTATAAAAAGAAACAAAATTTTACAGGTTTAAGAATGAGGAACTATTTAAAAAGTGA
195 AAAATGTTTTATAAAAAGAAACAAAATTTTACAGGTTTAAGAATGAGGAACTATTTAAAAAGTGA
1713890 TGTGACATATGTATCTCGTGTACAGAAAGGTATACAAGGGATGGGTGTTACATTTATTGGT
260 TGTGACATATGTATCTCGTGTACAGAAAGGTATACAAGGGATGGGTGTTACATTTATTGGT
1713951 ATCA
1 ATCA
1713955 AAGCTACAGG
Statistics
Matches: 297, Mismatches: 25, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
320 7 0.02
321 288 0.97
322 2 0.01
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (320 bp):
ATCACCAAGCAAGTGTCACCTCGTCAATAACAGTACTGCATTTATGTCTACTTTTGATGTAGTTA
GCTGACATGTAATAGATTTAGTAAAAACGCTCTAAAAAGCAATTTAGTTAAACTAATGTAAAATG
ATGAAGTGTGAACATTTCTCTTTGTTATCTATTTAAGTTTAATGCATGTTTTATTATTAGTATAA
AAATGTTTTATAAAAAGAAACAAAATTTTACAGGTTTAAGAATGAGGAACTATTTAAAAAGTGAT
GTGACATATGTATCTCGTGTACAGAAAGGTATACAAGGGATGGGTGTTACATTTATTGGT
Found at i:1720034 original size:55 final size:55
Alignment explanation
Indices: 1719938--1720447 Score: 532
Period size: 55 Copynumber: 9.3 Consensus size: 55
1719928 CTATGTGTAC
* * * * *
1719938 TACAGGTACTATGTGTACAAATCCATGGAATTCATCGTGAGTTGATGAATAACCA
1 TACAGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCA
* *
1719993 TACATGCACTATGTATGCAAATCCACGAAATTCATCATGAGTTGATGAATAA-CA
1 TACAGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCA
* * *
1720047 TACATGCACTATGTGTGCAAATCCAC-AGAATTCATCATGAGTTAATGAATAACCG
1 TACAGGCACTATGTGTGCAAATCCACGA-AATTCATCATGAGTTGATGAATAACCA
*
1720102 TACAGGCACTATGTGTGCAAATCTACGAAATTCATCATGAGTTGATGAATAAACCA
1 TACAGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAAT-AACCA
** * * *
1720158 TACAAACACTATGTGTGCAAATTCACGGAATTCATCATGAGTTGATGAATAACCG
1 TACAGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCA
* * * **
1720213 TACAAGCACTATGTGTGTAAATCCACGGAATTCATCATGAGTTGATGAATAACTG
1 TACAGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCA
* * * * *
1720268 TATAGGCACTATGAT-TGTAGATCC-CCAGAATTCAACATGAGTTGATGAATAACCA
1 TACAGGCACTATG-TGTGCAAATCCACGA-AATTCATCATGAGTTGATGAATAACCA
* * *
1720323 TACAGGAACTATGTGTGTAAATCTGCA-G-AATTCATCAAT-AGTTGATGAATAACTA
1 TACAGGCACTATGTGTGCAAATC--CACGAAATTCATC-ATGAGTTGATGAATAACCA
* * * * * * * * * *
1720378 TAGAGGCACTGTGTGTCCATA-CCACGGAATTCATTATGAATTAATGAATTACCG
1 TACAGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCA
* *
1720432 TATAGGCACTACGTGT
1 TACAGGCACTATGTGT
1720448 TCATCTTAAT
Statistics
Matches: 388, Mismatches: 53, Indels: 29
0.83 0.11 0.06
Matches are distributed among these distances:
52 2 0.01
53 4 0.01
54 84 0.22
55 244 0.63
56 53 0.14
57 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.28
Consensus pattern (55 bp):
TACAGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCA
Found at i:1720136 original size:109 final size:110
Alignment explanation
Indices: 1719938--1720447 Score: 591
Period size: 109 Copynumber: 4.6 Consensus size: 110
1719928 CTATGTGTAC
* * * * * *
1719938 TACAGGTACTATGTGTACAAATCCATGGAATTCATCGTGAGTTGATGAATAACCATACATGCACT
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGCACT
*
1720003 ATGTATGCAAATCCACGAAATTCATCATGAGTTGATGAATAAC-A
66 ATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACTA
* * *
1720047 TACATGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTAATGAATAACCGTACAGGCACT
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGCACT
* *
1720112 ATGTGTGCAAATCTACGAAATTCATCATGAGTTGATGAATAAACCA
66 ATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAAT-AACTA
** * *
1720158 TACAAACACTATGTGTGCAAATTCACGGAATTCATCATGAGTTGATGAATAACCGTACAAGCACT
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGCACT
* * *
1720223 ATGTGTGTAAATCCACGGAATTCATCATGAGTTGATGAATAACTG
66 ATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACTA
* * * * * * * *
1720268 TATAGGCACTATGAT-TGTAGATCCCCAGAATTCAACATGAGTTGATGAATAACCATACAGGAAC
1 TACAGGCACTATG-TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGCAC
*
1720332 TATGTGTGTAAATCTGCA-G-AATTCATCAAT-AGTTGATGAATAACTA
65 TATGTGTGCAAATC--CACGAAATTCATC-ATGAGTTGATGAATAACTA
* * * * * * * * *
1720378 TAGAGGCACTGTGTGTCCATA-CCACGGAATTCATTATGAATTAATGAATTACCGTATAGGCACT
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGCACT
*
1720442 ACGTGT
66 ATGTGT
1720448 TCATCTTAAT
Statistics
Matches: 343, Mismatches: 51, Indels: 14
0.84 0.12 0.03
Matches are distributed among these distances:
109 133 0.39
110 107 0.31
111 101 0.29
112 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.28
Consensus pattern (110 bp):
TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACAGGCACT
ATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACTA
Found at i:1721649 original size:54 final size:54
Alignment explanation
Indices: 1721578--1721920 Score: 404
Period size: 54 Copynumber: 6.4 Consensus size: 54
1721568 TTCTTTGAGC
* ** *
1721578 TGCACACATAGTACCGATACGGTCATTCATAAACATATTATGAATTCTGTGGGT
1 TGCACACTTAGTGTCGATACGGTCATTCATAAACACATTATGAATTCTGTGGGT
* * *
1721632 TGCACACTTGGTGCCGATACGG-CTGTTCATAAACACATTATGAATTCCT-TGGGT
1 TGCACACTTAGTGTCGATACGGTC-ATTCATAAACACATTATGAATT-CTGTGGGT
* * *
1721686 TGTACACTTAGTGTCGATACGGTCATTCATAAACACATTATGAATTATATGGGT
1 TGCACACTTAGTGTCGATACGGTCATTCATAAACACATTATGAATTCTGTGGGT
* * ** *
1721740 TGCACATTTATTGTCGATACGGTCGCTCATAAACACATTATGAATTCCGTGGGT
1 TGCACACTTAGTGTCGATACGGTCATTCATAAACACATTATGAATTCTGTGGGT
** * *
1721794 TGCACACTTAGTGTCGATACAATCATTTATAAACACATTACGAATTTCT-TGGGT
1 TGCACACTTAGTGTCGATACGGTCATTCATAAACACATTATGAA-TTCTGTGGGT
* * * *
1721848 TGCACACTTAGTGTTGATACGTTCGTTCATAAACACATTATGAATTCCGTGGGT
1 TGCACACTTAGTGTCGATACGGTCATTCATAAACACATTATGAATTCTGTGGGT
* * *
1721902 TGAAAAATTAGTGTCGATA
1 TGCACACTTAGTGTCGATA
1721921 GTACACATAG
Statistics
Matches: 245, Mismatches: 38, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
53 5 0.02
54 234 0.96
55 6 0.02
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (54 bp):
TGCACACTTAGTGTCGATACGGTCATTCATAAACACATTATGAATTCTGTGGGT
Found at i:1721859 original size:162 final size:162
Alignment explanation
Indices: 1721592--1721893 Score: 446
Period size: 162 Copynumber: 1.9 Consensus size: 162
1721582 CACATAGTAC
* * * * *
1721592 CGATACGGTCATTCATAAACATATTATGAATTCTGTGGGTTGCACACTTGGTGCCGATACGGCTG
1 CGATACGGTCACTCATAAACACATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACAGCTG
* *
1721657 TTCATAAACACATTATGAATTCCTTGGGTTGTACACTTAGTGTCGATACGGTCATTCATAAACAC
66 TTCATAAACACATTACGAATTCCTTGGGTTGCACACTTAGTGTCGATACGGTCATTCATAAACAC
1721722 ATTATGAATTATATGGGTTGCACATTTATTGT
131 ATTATGAATTATATGGGTTGCACATTTATTGT
* * *
1721754 CGATACGGTCGCTCATAAACACATTATGAATTCCGTGGGTTGCACACTTAGTGTCGATACAATCA
1 CGATACGGTCACTCATAAACACATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATAC-AGC-
* * * *
1721819 T-TT-ATAAACACATTACGAATTTCTTGGGTTGCACACTTAGTGTTGATACGTTCGTTCATAAAC
64 TGTTCATAAACACATTACGAATTCCTTGGGTTGCACACTTAGTGTCGATACGGTCATTCATAAAC
1721882 ACATTATGAATT
129 ACATTATGAATT
1721894 CCGTGGGTTG
Statistics
Matches: 124, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
162 120 0.97
163 3 0.02
164 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (162 bp):
CGATACGGTCACTCATAAACACATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACAGCTG
TTCATAAACACATTACGAATTCCTTGGGTTGCACACTTAGTGTCGATACGGTCATTCATAAACAC
ATTATGAATTATATGGGTTGCACATTTATTGT
Found at i:1727015 original size:77 final size:76
Alignment explanation
Indices: 1726929--1727088 Score: 173
Period size: 77 Copynumber: 2.1 Consensus size: 76
1726919 TTAATTATCC
* ** * *
1726929 TAAAT-ATAG-TAAGTAAACATTAAAAGAATGTAATTTTGATTACAACTCTTTGAATGGATATTT
1 TAAATAATAGTTAAATAAACATT-AAAGAATGTAATTCAGATTACAAATATTT-AATGGATATTT
1726992 AATTCGGAAT-AAT
64 AA-TCGGAATGAAT
* * * *
1727005 TAAATAATAGTTTAAATAAACGTTAAAGAGTGTAATTCAGATTATAAATATTTAATGTATATTTA
1 TAAATAATAG-TTAAATAAACATTAAAGAATGTAATTCAGATTACAAATATTTAATGGATATTTA
*
1727070 ATCTGAATGAAT
65 ATCGGAATGAAT
1727082 TAAATAA
1 TAAATAA
1727089 GAATTTAATT
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
76 11 0.16
77 26 0.37
78 23 0.33
79 10 0.14
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.38
Consensus pattern (76 bp):
TAAATAATAGTTAAATAAACATTAAAGAATGTAATTCAGATTACAAATATTTAATGGATATTTAA
TCGGAATGAAT
Found at i:1727039 original size:78 final size:78
Alignment explanation
Indices: 1726942--1727088 Score: 181
Period size: 78 Copynumber: 1.9 Consensus size: 78
1726932 ATATAGTAAG
** * *
1726942 TAAACATTAAAAGAATGTAATTTTGATTACAACTCTTTGAATGGATATTTAATTCGGAAT-AATT
1 TAAACATTAAAAGAATGTAATTCAGATTACAAATATTT-AATGGATATTTAA-TCGGAATGAATT
1727006 AAATAATAGTTTAAA
64 AAATAATAGTTTAAA
* * * * *
1727021 TAAACGTT-AAAGAGTGTAATTCAGATTATAAATATTTAATGTATATTTAATCTGAATGAATTAA
1 TAAACATTAAAAGAATGTAATTCAGATTACAAATATTTAATGGATATTTAATCGGAATGAATTAA
1727085 ATAA
66 ATAA
1727089 GAATTTAATT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
76 6 0.10
77 22 0.38
78 23 0.40
79 7 0.12
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (78 bp):
TAAACATTAAAAGAATGTAATTCAGATTACAAATATTTAATGGATATTTAATCGGAATGAATTAA
ATAATAGTTTAAA
Found at i:1735267 original size:30 final size:30
Alignment explanation
Indices: 1735211--1735268 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1735201 GATTTATTTA
* *
1735211 GTGACCAAATTATAAATTTGGTAAAGTTTG
1 GTGACCAAAGTATAAATTTGGAAAAGTTTG
1735241 GTGACCAAAGTATAAACTTT-GAAAAGTT
1 GTGACCAAAGTATAAA-TTTGGAAAAGTT
1735269 CAAGAACCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.33
Consensus pattern (30 bp):
GTGACCAAAGTATAAATTTGGAAAAGTTTG
Found at i:1736435 original size:24 final size:24
Alignment explanation
Indices: 1736408--1736455 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1736398 ACATGACATG
1736408 GTACATAGATGTTTTATACATCAT
1 GTACATAGATGTTTTATACATCAT
1736432 GTACATAGATGTTTTATACATCAT
1 GTACATAGATGTTTTATACATCAT
1736456 TTGAAAGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCAT
Found at i:1737164 original size:2 final size:2
Alignment explanation
Indices: 1737157--1737185 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1737147 TTTTATGAAT
1737157 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1737186 TGTTAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1737228 original size:7 final size:7
Alignment explanation
Indices: 1737216--1737281 Score: 78
Period size: 7 Copynumber: 9.4 Consensus size: 7
1737206 TGCATCGATA
1737216 CACTGTT
1 CACTGTT
1737223 CACTGTT
1 CACTGTT
1737230 CACTGTT
1 CACTGTT
* *
1737237 CACGGTA
1 CACTGTT
*
1737244 CATTGTT
1 CACTGTT
1737251 CACTGTT
1 CACTGTT
* *
1737258 CACGGTA
1 CACTGTT
*
1737265 CATTGTT
1 CACTGTT
1737272 CACTGTT
1 CACTGTT
1737279 CAC
1 CAC
1737282 GGTACTATTC
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.38
Consensus pattern (7 bp):
CACTGTT
Found at i:1737252 original size:21 final size:21
Alignment explanation
Indices: 1737226--1737286 Score: 122
Period size: 21 Copynumber: 2.9 Consensus size: 21
1737216 CACTGTTCAC
1737226 TGTTCACTGTTCACGGTACAT
1 TGTTCACTGTTCACGGTACAT
1737247 TGTTCACTGTTCACGGTACAT
1 TGTTCACTGTTCACGGTACAT
1737268 TGTTCACTGTTCACGGTAC
1 TGTTCACTGTTCACGGTAC
1737287 TATTCAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.38
Consensus pattern (21 bp):
TGTTCACTGTTCACGGTACAT
Found at i:1748828 original size:20 final size:20
Alignment explanation
Indices: 1748805--1748881 Score: 93
Period size: 21 Copynumber: 3.6 Consensus size: 20
1748795 ACCCCGTGGA
1748805 GGGTATCGGTACCCTCAAGG
1 GGGTATCGGTACCCTCAAGG
1748825 GGGTATCGGTACCCACTCAAAGG
1 GGGTATCGGTA-CC-CTC-AAGG
1748848 GGGTATCGGTACCCATGCAA-G
1 GGGTATCGGTACCC-T-CAAGG
*
1748869 GGGTATCGATACC
1 GGGTATCGGTACC
1748882 TAGCTCAGAA
Statistics
Matches: 51, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
20 11 0.22
21 16 0.31
22 8 0.16
23 16 0.31
ACGTcount: A:0.23, C:0.25, G:0.32, T:0.19
Consensus pattern (20 bp):
GGGTATCGGTACCCTCAAGG
Found at i:1748851 original size:23 final size:22
Alignment explanation
Indices: 1748805--1748881 Score: 99
Period size: 23 Copynumber: 3.6 Consensus size: 22
1748795 ACCCCGTGGA
1748805 GGGTATCGGTA-CC-CTCAAGG
1 GGGTATCGGTACCCACTCAAGG
1748825 GGGTATCGGTACCCACTCAAAGG
1 GGGTATCGGTACCCACTC-AAGG
1748848 GGGTATCGGTACCCA-TGCAA-G
1 GGGTATCGGTACCCACT-CAAGG
*
1748869 GGGTATCGATACC
1 GGGTATCGGTACC
1748882 TAGCTCAGAA
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
20 11 0.21
21 15 0.29
22 6 0.12
23 20 0.38
ACGTcount: A:0.23, C:0.25, G:0.32, T:0.19
Consensus pattern (22 bp):
GGGTATCGGTACCCACTCAAGG
Done.