Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008094.1 Hibiscus syriacus cultivar Beakdansim tig00110610_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: 9952466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 43
Found at i:1231367 original size:41 final size:40
Alignment explanation
Indices: 1231311--1231404 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
1231301 CGATAGTCAG
* * *
1231311 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTGTGATTTACGTAATCGCATTGCGATTTACCT
* * *
1231351 AATTCGCATTGTGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGTGATTTACGTAATCGCATTGCGATTTACCT
1231392 ATTCGCATTGTGA
1 ATTCGCATTGTGA
1231405 ATTAGGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 13 0.28
41 34 0.72
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.41
Consensus pattern (40 bp):
ATTCGCATTGTGATTTACGTAATCGCATTGCGATTTACCT
Found at i:1231427 original size:21 final size:21
Alignment explanation
Indices: 1231403--1231446 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1231393 TTCGCATTGT
1231403 GAATTAGGAAAATCGCAACGC
1 GAATTAGGAAAATCGCAACGC
* * *
1231424 GAATTTGGGAAATCGCAATGC
1 GAATTAGGAAAATCGCAACGC
1231445 GA
1 GA
1231447 TAGTCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.18
Consensus pattern (21 bp):
GAATTAGGAAAATCGCAACGC
Found at i:1240856 original size:13 final size:13
Alignment explanation
Indices: 1240838--1240863 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1240828 TTGTTCTCAT
1240838 TGGTGGATTTGAA
1 TGGTGGATTTGAA
1240851 TGGTGGATTTGAA
1 TGGTGGATTTGAA
1240864 GGTAATATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.38, T:0.38
Consensus pattern (13 bp):
TGGTGGATTTGAA
Found at i:1242188 original size:20 final size:20
Alignment explanation
Indices: 1242150--1242188 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1242140 GGTTGTTTCT
*
1242150 AGCTGTTGGGGATGATTTTG
1 AGCTGTTGGGAATGATTTTG
1242170 AGCTGTTTGGGAATG-TTTT
1 AGCTG-TTGGGAATGATTTT
1242189 CTCTGCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.15, C:0.05, G:0.36, T:0.44
Consensus pattern (20 bp):
AGCTGTTGGGAATGATTTTG
Found at i:1243251 original size:18 final size:18
Alignment explanation
Indices: 1243228--1243266 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1243218 AATGCAAAAC
1243228 GAGTATCCAAATCATTCT
1 GAGTATCCAAATCATTCT
1243246 GAGTATCCAAATCATTCT
1 GAGTATCCAAATCATTCT
1243264 GAG
1 GAG
1243267 GGTCCAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (18 bp):
GAGTATCCAAATCATTCT
Found at i:1243272 original size:18 final size:18
Alignment explanation
Indices: 1243232--1243274 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1243222 CAAAACGAGT
*
1243232 ATCCAAATCATTCTGAGT
1 ATCCAAATCATTCTGAGG
1243250 ATCCAAATCATTCTGAGG
1 ATCCAAATCATTCTGAGG
*
1243268 GTCCAAA
1 ATCCAAA
1243275 ATAGGGAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (18 bp):
ATCCAAATCATTCTGAGG
Found at i:1243664 original size:15 final size:12
Alignment explanation
Indices: 1243630--1243669 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1243620 CACATATTGT
1243630 AAAGAAGAAGAAA
1 AAAG-AGAAGAAA
1243643 AAAGAGAAGAAA
1 AAAGAGAAGAAA
* *
1243655 AATGAGGAGAAA
1 AAAGAGAAGAAA
1243667 AAA
1 AAA
1243670 AAACGCTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (12 bp):
AAAGAGAAGAAA
Found at i:1245713 original size:3 final size:3
Alignment explanation
Indices: 1245700--1245731 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1245690 TTTACTCAAA
*
1245700 TCT TGT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1245732 GTCGGTTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.31, G:0.03, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:1254822 original size:28 final size:30
Alignment explanation
Indices: 1254764--1254821 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
1254754 TTCCAACTCA
1254764 AAGAGATAAAATATAATTAATCATAGAAAAT
1 AAGAGATAAAATATAATTAATCATA-AAAAT
*
1254795 AAGAGGATCAAATATAATT-ATC-TAAAA
1 AAGA-GATAAAATATAATTAATCATAAAA
1254822 TTTGGAATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 3 0.12
30 2 0.08
31 7 0.28
32 13 0.52
ACGTcount: A:0.59, C:0.05, G:0.10, T:0.26
Consensus pattern (30 bp):
AAGAGATAAAATATAATTAATCATAAAAAT
Found at i:1261812 original size:29 final size:28
Alignment explanation
Indices: 1261752--1261809 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
1261742 GGTAGGGTTA
*
1261752 GGTTTTTTTTAAGTTTGATATTCGGGTC
1 GGTTTTTTTTAAGTGTGATATTCGGGTC
*
1261780 GGTTTTTTTTAAGTGTGATATTTGGGTC
1 GGTTTTTTTTAAGTGTGATATTCGGGTC
1261808 GG
1 GG
1261810 GTTCGGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.14, C:0.05, G:0.29, T:0.52
Consensus pattern (28 bp):
GGTTTTTTTTAAGTGTGATATTCGGGTC
Found at i:1263305 original size:27 final size:27
Alignment explanation
Indices: 1263269--1263330 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
1263259 TACATTTCTT
1263269 AAATTTTAAATATATATCGTTAAAATA
1 AAATTTTAAATATATATCGTTAAAATA
1263296 AAATTTTAAATATATATCGTTAAAATA
1 AAATTTTAAATATATATCGTTAAAATA
1263323 AAATTTTA
1 AAATTTTA
1263331 CATCTATCGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (27 bp):
AAATTTTAAATATATATCGTTAAAATA
Found at i:1263348 original size:27 final size:26
Alignment explanation
Indices: 1263269--1263349 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 26
1263259 TACATTTCTT
*
1263269 AAATTTTAAATATATATCGTTAAAATA
1 AAATTTT-AACATATATCGTTAAAATA
*
1263296 AAATTTTAAATATATATCGTTAAAATA
1 AAATTTT-AACATATATCGTTAAAATA
*
1263323 AAATTTT-ACATCTATCGTATATAAATA
1 AAATTTTAACATATATCGT-TA-AAATA
1263350 TTAAATTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
25 9 0.18
26 2 0.04
27 39 0.78
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (26 bp):
AAATTTTAACATATATCGTTAAAATA
Found at i:1268613 original size:11 final size:10
Alignment explanation
Indices: 1268578--1268614 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
1268568 ACTAATTGCT
1268578 TCTAACC-AC
1 TCTAACCAAC
1268587 TCT-ACCAAC
1 TCTAACCAAC
1268596 TCTAACCAAC
1 TCTAACCAAC
1268606 TGCTAACCA
1 T-CTAACCA
1268615 CCTGCACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 3 0.12
9 8 0.32
10 7 0.28
11 7 0.28
ACGTcount: A:0.35, C:0.41, G:0.03, T:0.22
Consensus pattern (10 bp):
TCTAACCAAC
Found at i:1271960 original size:17 final size:17
Alignment explanation
Indices: 1271940--1271973 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1271930 AATTTCAGCT
1271940 AATTAATTGATTT-TAAA
1 AATTAATT-ATTTGTAAA
1271957 AATTAATTATTTGTAAA
1 AATTAATTATTTGTAAA
1271974 TTGATATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
AATTAATTATTTGTAAA
Found at i:1273171 original size:6 final size:6
Alignment explanation
Indices: 1273162--1273189 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1273152 AAACACGTCC
1273162 ATTTTA ATTTTA ATTTTA ATTTTA ATTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTT
1273190 GTATCTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTTA
Found at i:1278297 original size:87 final size:87
Alignment explanation
Indices: 1278151--1278400 Score: 464
Period size: 87 Copynumber: 2.9 Consensus size: 87
1278141 TATGTTATAT
**
1278151 TATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1278216 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
1278238 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1278303 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* *
1278325 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1278390 AGCGCTTATAT
66 AGCGCTTATAT
1278401 TGACCTATTT
Statistics
Matches: 159, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 159 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (87 bp):
TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:1282124 original size:120 final size:119
Alignment explanation
Indices: 1281912--1282157 Score: 420
Period size: 120 Copynumber: 2.1 Consensus size: 119
1281902 TTTTTCTTCC
*
1281912 ATTCTGGACATAAAGTACCGACACAATATTAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTA
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTA
1281977 ATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
66 ATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
*
1282031 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATT-AAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
* * * * *
1282096 CATAAAACCGGTATATTTATACTGGTTATATTTCAAAATTATCTATTACATTATA
65 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
1282151 ATTCTGG
1 ATTCTGG
1282158 GTTCCGATGT
Statistics
Matches: 119, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
119 29 0.24
120 90 0.76
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (119 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTA
ATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
Found at i:1282339 original size:183 final size:183
Alignment explanation
Indices: 1282031--1282523 Score: 873
Period size: 183 Copynumber: 2.7 Consensus size: 183
1282021 GTACATTATA
*
1282031 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
*
1282096 CATAAAACCGGTATATTTATACTGGTTATATT-TCAAAATTATCTATTACATTATAATTCTGGGT
66 CATAAAACCGGTATATTTATACCGGTTATATTAT-AAAATTATCTATTACATTATAATTCTGGGT
1282160 TCCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
130 TCCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
*
1282214 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTATACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1282279 CATAAAACCGGTATATTTATACCGGTTATATTATAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTATAAAATTATCTATTACATTATAATTCTGGGTT
1282344 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
* *
1282397 ATTCTGGACATAAAGTACCAACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* * * *
1282462 AATAAAACTGGTAT-TCTTATACCGGTTATATTACAAAATTATCTAGTACATTATAATTCTGG
66 CATAAAACCGGTATAT-TTATACCGGTTATATTATAAAATTATCTATTACATTATAATTCTGG
1282524 ACATAAAGTA
Statistics
Matches: 298, Mismatches: 10, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
182 1 0.00
183 296 0.99
184 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (183 bp):
ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
CATAAAACCGGTATATTTATACCGGTTATATTATAAAATTATCTATTACATTATAATTCTGGGTT
CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
Found at i:1282524 original size:303 final size:303
Alignment explanation
Indices: 1282214--1282822 Score: 1114
Period size: 303 Copynumber: 2.0 Consensus size: 303
1282204 TTTTTCTTCC
* *
1282214 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTATACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1282279 CATAAAACCGGTATATTTATACCGGTTATATTAT-AAAATTATCTATTACATTATAATTCTGGGT
66 CATAAAACCGGTATATTTATACCGGTTATATT-TCAAAATTATCTATTACATTATAATTCTGGGT
1282343 TCCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACAT
130 TCCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACAT
*
1282408 AAAGTACCAACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACTGG
195 AAAGTACCAACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGG
*
1282473 TAT-TCTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
260 TATAT-TTATACCGATTATATTACAAAATTATCTAGTACATTATA
1282517 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1282582 CATAAAACCGGTATATTTATACCGGTTATATTTCAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTTCAAAATTATCTATTACATTATAATTCTGGGTT
1282647 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATA
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATA
* * *
1282712 AAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
196 AAGTACCAACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGT
*
1282777 ATATTTATACCGATTATATTACAAAATTATCTATTACATTATA
261 ATATTTATACCGATTATATTACAAAATTATCTAGTACATTATA
1282820 ATT
1 ATT
1282823 ATGGGTTCTG
Statistics
Matches: 296, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
302 1 0.00
303 294 0.99
304 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (303 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
CATAAAACCGGTATATTTATACCGGTTATATTTCAAAATTATCTATTACATTATAATTCTGGGTT
CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATA
AAGTACCAACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGT
ATATTTATACCGATTATATTACAAAATTATCTAGTACATTATA
Found at i:1282610 original size:120 final size:120
Alignment explanation
Indices: 1282397--1282643 Score: 415
Period size: 120 Copynumber: 2.1 Consensus size: 120
1282387 TTTTTCTTCC
*
1282397 ATTCTGGACATAAAGTACCAACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCAACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
*
1282462 AATAAAACTGGTATTCTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
66 AATAAAACCGGTATTCTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
* *
1282517 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCAACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
* * *
1282582 CATAAAACCGGTATAT-TTATACCGGTTATATTTCAAAATTATCTATTACATTATA
66 AATAAAACCGGTAT-TCTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
1282637 ATTCTGG
1 ATTCTGG
1282644 GTTCCGATGT
Statistics
Matches: 119, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
120 118 0.99
121 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (120 bp):
ATTCTGGACATAAAGTACCAACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
AATAAAACCGGTATTCTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
Found at i:1282657 original size:486 final size:486
Alignment explanation
Indices: 1281747--1282922 Score: 2169
Period size: 486 Copynumber: 2.4 Consensus size: 486
1281737 TTAAAATTAG
* *
1281747 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACTGATATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1281812 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
1281877 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
1281942 -AAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
196 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
1282006 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTC
261 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTC
*
1282071 GATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACTGGTTATATTTCAAAATT
326 GATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTATATTTCAAAATT
1282136 ATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGAC
391 ATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGAC
1282201 ACATTTTTCTTCCATTCTGGACATAAAGTAC
456 ACATTTTTCTTCCATTCTGGACATAAAGTAC
*
1282232 CGACACAATATTAAAAAGTGTCGATATAGGTTGTATACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
1282297 ATACCGGTTATATTATAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
*
1282362 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCAACACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
* *
1282427 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACTGGTATTCTTATACCGGTTATA
196 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
1282492 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTC
261 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTC
1282557 GATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTATATTTCAAAATT
326 GATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTATATTTCAAAATT
1282622 ATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGAC
391 ATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGAC
1282687 ACATTTTTCTTCCATTCTGGACATAAAGTAC
456 ACATTTTTCTTCCATTCTGGACATAAAGTAC
1282718 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
* * * * *
1282783 ATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTTCTGATGTTTTTTCAA--T
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATG---TGTAAATGT
* *
1282846 CGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCCATTCTTGACATAAAGTACCGACACAAT
128 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAAT
1282911 ATTAAAAAGTGT
193 ATTAAAAAGTGT
1282923 GAAAACTTTG
Statistics
Matches: 669, Mismatches: 18, Indels: 6
0.97 0.03 0.01
Matches are distributed among these distances:
485 190 0.28
486 400 0.60
487 75 0.11
489 4 0.01
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (486 bp):
CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTC
GATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTATATTTCAAAATT
ATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGAC
ACATTTTTCTTCCATTCTGGACATAAAGTAC
Found at i:1282830 original size:183 final size:182
Alignment explanation
Indices: 1282517--1282922 Score: 688
Period size: 183 Copynumber: 2.2 Consensus size: 182
1282507 GTACATTATA
*
1282517 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* * *
1282582 CATAAAACCGGTATATTTATACCGGTTATATTTCAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTT
*
1282647 CCGATG-TGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
131 CCGATGTTGTAAA--TCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
1282700 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1282765 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTT
66 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTT
* * *
1282830 CTGATGTTTTTTCAATCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
131 CCGATG--TTGTAAATCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
*
1282884 ATTCTTGACATAAAGTACCGACACAATATTAAAAAGTGT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
1282923 GAAAACTTTG
Statistics
Matches: 211, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
183 131 0.62
184 76 0.36
186 4 0.02
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (182 bp):
ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTT
CCGATGTTGTAAATCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
Found at i:1284137 original size:6 final size:6
Alignment explanation
Indices: 1284130--1284181 Score: 68
Period size: 6 Copynumber: 8.7 Consensus size: 6
1284120 GTTTGGATCA
* * * *
1284130 TCATCA TCATCA TCATCG TCATCG TCATCT TCATCG TCATCT TCATCG
1 TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG
1284178 TCAT
1 TCAT
1284182 TGACCGCTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.21, C:0.33, G:0.08, T:0.38
Consensus pattern (6 bp):
TCATCG
Found at i:1284143 original size:12 final size:12
Alignment explanation
Indices: 1284130--1284181 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
1284120 GTTTGGATCA
* *
1284130 TCATCATCATCA
1 TCATCTTCATCG
*
1284142 TCATCGTCATCG
1 TCATCTTCATCG
1284154 TCATCTTCATCG
1 TCATCTTCATCG
1284166 TCATCTTCATCG
1 TCATCTTCATCG
1284178 TCAT
1 TCAT
1284182 TGACCGCTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.21, C:0.33, G:0.08, T:0.38
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:1285965 original size:200 final size:200
Alignment explanation
Indices: 1285622--1286385 Score: 1271
Period size: 200 Copynumber: 3.8 Consensus size: 200
1285612 AACATTAAAC
* * *
1285622 AGTGTCGATACA-TATTATATACCA-ATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATT
1 AGTGTCGATACATTATT-TAGA-CATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATT
* * *
1285685 GCAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATA
64 GAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATA
1285750 TGGATCGACACTTTATGGTTGCACCATGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAA
129 TGGATCGACACTTTATGGTTGCACCATGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAA
1285815 CTACAAA
194 CTACAAA
* * * *
1285822 AGTGTCGACACATTATTTAGGCCTATTCTCTCATAAAACCGGTATACTTGTACGGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1285887 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* * *
1285952 GATCGATACTTTATTGTTGCACCATATTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCATGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
1286017 ACAAA
196 ACAAA
*
1286022 AGTGTCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACGGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
1286087 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* * * *
1286152 GATCGACACTTTATTGTTGCACCCTGTTTGTCATTCATTCTTGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCATGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
1286217 ACAAA
196 ACAAA
*
1286222 AGTGTCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* * **
1286287 AAAACTACCTATTACATTATACTTTTGGGTTTCGATGTTTATATGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
1286352 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
131 GATCGACACTTTATGGTTGCACCATGTTTGCCAT
1286386 ATTGTAAATT
Statistics
Matches: 532, Mismatches: 30, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
199 1 0.00
200 527 0.99
201 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
AGTGTCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATGGTTGCACCATGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:1286628 original size:18 final size:18
Alignment explanation
Indices: 1286605--1286665 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
1286595 TCTCATTCAT
*
1286605 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
1286623 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
1286642 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
1286661 AATTA
1 AATTA
1286666 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:1286641 original size:19 final size:19
Alignment explanation
Indices: 1286617--1286665 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1286607 TTATATTCAC
1286617 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
1286636 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1286655 ATACAAAATTA
1 ATACAAAATTA
1286666 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1288494 original size:33 final size:33
Alignment explanation
Indices: 1288457--1288522 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1288447 CATCTTAATA
*
1288457 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* * *
1288490 TCACCCCTCAACACCTCTACTTTTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1288523 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1288664 original size:33 final size:33
Alignment explanation
Indices: 1288604--1288669 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
1288594 GACTTTAATA
*
1288604 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* * * *
1288637 TCACTCCTCAACACCTCTACTTTTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1288670 CCATCTATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.23, C:0.45, G:0.00, T:0.32
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1288718 original size:147 final size:147
Alignment explanation
Indices: 1288451--1288744 Score: 561
Period size: 147 Copynumber: 2.0 Consensus size: 147
1288441 CGTCACCATC
1288451 TTAATATCACCCCTTAACACCCCAACTTCTTTCACCACTTCACCCCTCAACACCTCTACTTTTTT
1 TTAATATCACCCCTTAACACCCCAACTTCTTTCACCACTTCACCCCTCAACACCTCTACTTTTTT
1288516 CACCACTCCATCTATTTTTCCTTCCACTACCCCCTTATGCCTCTCAAGTGTATCTTCAACTCTCT
66 CACCACTCCATCTATTTTTCCTTCCACTACCCCCTTATGCCTCTCAAGTGTATCTTCAACTCTCT
*
1288581 CAAGTTTCTCTTCGACT
131 CAAGTTTCTATTCGACT
*
1288598 TTAATATCACCCCTTAACACCCCAACTTCTTTCACCACTTCACTCCTCAACACCTCTACTTTTTT
1 TTAATATCACCCCTTAACACCCCAACTTCTTTCACCACTTCACCCCTCAACACCTCTACTTTTTT
*
1288663 CACCACTCCATCTATTTTTCCTTCCACTACCCCCTTATGCCTCTCAAGTGTATCTTCGACTCTCT
66 CACCACTCCATCTATTTTTCCTTCCACTACCCCCTTATGCCTCTCAAGTGTATCTTCAACTCTCT
1288728 CAAGTTTCTATTCGACT
131 CAAGTTTCTATTCGACT
1288745 CTATCAAGTT
Statistics
Matches: 144, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
147 144 1.00
ACGTcount: A:0.21, C:0.39, G:0.04, T:0.36
Consensus pattern (147 bp):
TTAATATCACCCCTTAACACCCCAACTTCTTTCACCACTTCACCCCTCAACACCTCTACTTTTTT
CACCACTCCATCTATTTTTCCTTCCACTACCCCCTTATGCCTCTCAAGTGTATCTTCAACTCTCT
CAAGTTTCTATTCGACT
Found at i:1288728 original size:21 final size:21
Alignment explanation
Indices: 1288703--1288767 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
1288693 CCCCTTATGC
* *
1288703 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
1288724 CTCTCAAGTTTCTATTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
1288745 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1288766 CT
1 CT
1288768 TGATTGTCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.18, C:0.29, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1291202 original size:20 final size:18
Alignment explanation
Indices: 1291156--1291202 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 18
1291146 TCCGGTAACA
1291156 TTTTACCGGTTTTATTAT
1 TTTTACCGGTTTTATTAT
1291174 TTTGATACCGGTTTTATCATAT
1 TTT--TACCGGTTTTAT--TAT
1291196 TTTTACC
1 TTTTACC
1291203 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.12
20 16 0.64
22 6 0.24
ACGTcount: A:0.19, C:0.15, G:0.11, T:0.55
Consensus pattern (18 bp):
TTTTACCGGTTTTATTAT
Found at i:1291384 original size:182 final size:177
Alignment explanation
Indices: 1290947--1291415 Score: 636
Period size: 176 Copynumber: 2.6 Consensus size: 177
1290937 CGTACTTACG
* * *
1290947 AAAGTATCAACACTTTCAATATATCCGGTATCGTTTTATCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAAT-TATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * *
1291012 TATCATATTTTTGCCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAG
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTATAAAGTATCGACACATTAG
*
1291077 GTGCTAAAACTGATTCTCTTTAAATTCACAAAGTGTCGATCTTTATAT
130 GTGCTAAAACTGATTCTCTTTAAATTCACAAAGTGTCGATCCTTATAT
* *
1291125 AAAGTATCGACACTTTCAA-TATCCGGTAACATTTTACCGGTTTTATTATTTTGATACCGGTTTT
1 AAAGTATCGACACTTTCAATTATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTTT
* *
1291189 ATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTATAAAGTATCGACACTTTATA
66 ATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTATAAAGTATCGACAC-AT-TA
* * * *
1291254 GGAT-TTAAAACTGCTTCTCTTTTAAATTTACGAAGTGTCGATCCTTATATT
129 GG-TGCTAAAACTGATTCTC-TTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * **
1291305 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAAT-TATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
1291370 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTTA
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTA
1291416 ATTTGGATCG
Statistics
Matches: 256, Mismatches: 28, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
176 95 0.37
177 1 0.00
178 35 0.14
179 27 0.11
180 18 0.07
182 80 0.31
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (177 bp):
AAAGTATCGACACTTTCAATTATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTTT
ATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTATAAAGTATCGACACATTAGG
TGCTAAAACTGATTCTCTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:1292317 original size:5 final size:5
Alignment explanation
Indices: 1292307--1292340 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
1292297 ATTTAATCAC
*
1292307 AATTT AATTT AATTT AATTT AA-TA AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT
1292341 TTAAATTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 23 0.88
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
AATTT
Found at i:1292347 original size:13 final size:14
Alignment explanation
Indices: 1292307--1292340 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1292297 ATTTAATCAC
*
1292307 AATTTAATTTAATTT
1 AATTTAA-TAAATTT
1292322 AATTTAATAAATTT
1 AATTTAATAAATTT
1292336 AATTT
1 AATTT
1292341 TTAAATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATTTAATAAATTT
Found at i:1293415 original size:14 final size:14
Alignment explanation
Indices: 1293393--1293435 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1293383 TTGTCTATAT
* *
1293393 GCAGAGATTCTTTC
1 GCAGGGATTATTTC
*
1293407 GCAGGGATTATTTT
1 GCAGGGATTATTTC
1293421 GCAGGGATTAATTTC
1 GCAGGGATT-ATTTC
1293436 CATTACAGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (14 bp):
GCAGGGATTATTTC
Found at i:1294106 original size:17 final size:18
Alignment explanation
Indices: 1294084--1294125 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
1294074 TATTTAATTG
1294084 AATTAAAATAATG-ATTA
1 AATTAAAATAATGTATTA
*
1294101 AATTAATATAATGTATTA
1 AATTAAAATAATGTATTA
1294119 ATATTAA
1 A-ATTAA
1294126 GAGAAAATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.55
18 5 0.23
19 5 0.23
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (18 bp):
AATTAAAATAATGTATTA
Found at i:1294414 original size:16 final size:18
Alignment explanation
Indices: 1294376--1294416 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1294366 GGGAAAATCG
*
1294376 CGCAATACGATACTGACT
1 CGCAATGCGATACTGACT
1294394 CGCAATGCGATACT-A-T
1 CGCAATGCGATACTGACT
1294410 CGCAATG
1 CGCAATG
1294417 TAATACAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 1 0.05
18 13 0.59
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.22
Consensus pattern (18 bp):
CGCAATGCGATACTGACT
Found at i:1294988 original size:20 final size:19
Alignment explanation
Indices: 1294963--1295014 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1294953 GAGAATGAAA
1294963 ATCGCAACGCGGAAATAACT
1 ATCGCAACGC-GAAATAACT
**
1294983 ATCGCAACGCGAAATAAAA
1 ATCGCAACGCGAAATAACT
1295002 ATCGC-ACGCGAAA
1 ATCGCAACGCGAAA
1295015 CCAAAATCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 8 0.27
19 12 0.40
20 10 0.33
ACGTcount: A:0.44, C:0.25, G:0.19, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATAACT
Found at i:1295012 original size:18 final size:19
Alignment explanation
Indices: 1294960--1295025 Score: 80
Period size: 18 Copynumber: 3.5 Consensus size: 19
1294950 TTCGAGAATG
1294960 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
1294980 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
1294999 AAAATCGC-ACGCGAAACC
1 AAAATCGCAACGCGAAATA
1295017 AAAATCGCA
1 AAAATCGCA
1295026 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
18 16 0.41
19 12 0.31
20 11 0.28
ACGTcount: A:0.47, C:0.26, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1295042 original size:18 final size:19
Alignment explanation
Indices: 1295021--1295070 Score: 75
Period size: 18 Copynumber: 2.7 Consensus size: 19
1295011 GAAACCAAAA
*
1295021 TCGCATTGCGATTTTCA-T
1 TCGCGTTGCGATTTTCATT
*
1295039 TCGCGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1295058 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1295071 CTCTCGTCGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1295111 original size:14 final size:14
Alignment explanation
Indices: 1295061--1295120 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 14
1295051 TTTCATTTCG
1295061 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
1295075 CGTCGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
1295094 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1295108 CGTTGCGATTCTC
1 CGTTGCGATTCTC
1295121 ATTATCTCGT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
14 23 0.62
16 2 0.05
17 2 0.05
19 10 0.27
ACGTcount: A:0.10, C:0.28, G:0.23, T:0.38
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1295123 original size:33 final size:33
Alignment explanation
Indices: 1295042--1295137 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 33
1295032 TTTTCATTCG
* *
1295042 CGTTGTGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTCTCATTTCGCGTTGCGATTCTCT
* **
1295075 CGTCGCGATAGTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTCTCATTTCGCGTTGCGATTCTCT
* *
1295108 CGTTGCGATTCTCATTATCTCGTTGTGATT
1 CGTTGCGATTCTCATT-TCGCGTTGCGATT
1295138 TTCATTTCAA
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 42 0.79
34 11 0.21
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTCTCATTTCGCGTTGCGATTCTCT
Found at i:1295130 original size:20 final size:20
Alignment explanation
Indices: 1295105--1295143 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1295095 GTTGCGATTC
1295105 TCTCGTTGCGATTCTCATTA
1 TCTCGTTGCGATTCTCATTA
* *
1295125 TCTCGTTGTGATTTTCATT
1 TCTCGTTGCGATTCTCATT
1295144 TCAACCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.21, G:0.15, T:0.51
Consensus pattern (20 bp):
TCTCGTTGCGATTCTCATTA
Found at i:1296949 original size:93 final size:87
Alignment explanation
Indices: 1296794--1296967 Score: 249
Period size: 93 Copynumber: 1.9 Consensus size: 87
1296784 TAGATTGCTT
*
1296794 AGTAAATTTATTTGGTTGCTGCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTTG
1 AGTAAATTTATTCGGTTGCTGCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTTG
*
1296859 TCTTTTTGTTTGTCTTTTGGTGA
66 TCTTTGT-TTTGTCTTTTGGTGA
* * *
1296882 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAATTTAGT
1 AGTAAATTTATTCGGTTGCTG-CAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1296947 ATTTGTCTTTGTTTTGTCTTT
61 ATTTGTCTTTGTTTTGTCTTT
1296968 GGTTGAAAGT
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
88 20 0.26
89 13 0.17
91 3 0.04
92 11 0.14
93 29 0.38
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (87 bp):
AGTAAATTTATTCGGTTGCTGCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTTG
TCTTTGTTTTGTCTTTTGGTGA
Found at i:1297265 original size:21 final size:21
Alignment explanation
Indices: 1297241--1297391 Score: 58
Period size: 21 Copynumber: 7.2 Consensus size: 21
1297231 TCATTCCTCG
1297241 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** *
1297262 AGAGGCCACTGTCATCC-CTCA
1 AGAGTCCCCTCCCA-CCGTTCA
* * * *
1297283 AGAGTCCACTCCTATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
* ** *
1297304 AGAGGCCCCTATCATTCC--TCG
1 AGAGTCCCCTCCCA--CCGTTCA
1297325 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1297346 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1297367 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1297388 AGAG
1 AGAG
1297392 CCCGATTCAC
Statistics
Matches: 86, Mismatches: 37, Indels: 15
0.62 0.27 0.11
Matches are distributed among these distances:
19 2 0.02
20 2 0.02
21 78 0.91
22 3 0.03
23 1 0.01
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1297265 original size:42 final size:42
Alignment explanation
Indices: 1297189--1297391 Score: 203
Period size: 42 Copynumber: 4.8 Consensus size: 42
1297179 GACTCGCCTG
* * * * * * *
1297189 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1297231 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * * * * * *
1297273 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1297315 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
1297357 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1297392 CCCGATTCAC
Statistics
Matches: 132, Mismatches: 27, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
41 4 0.03
42 126 0.95
43 2 0.02
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1297370 original size:84 final size:84
Alignment explanation
Indices: 1297186--1297361 Score: 352
Period size: 84 Copynumber: 2.1 Consensus size: 84
1297176 CCCGACTCGC
1297186 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1297251 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
1297270 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1297335 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
1297354 CTGTCATC
1 CTGTCATC
1297362 GTTGAAGAGG
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 92 1.00
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:1297391 original size:84 final size:84
Alignment explanation
Indices: 1297186--1297391 Score: 297
Period size: 84 Copynumber: 2.5 Consensus size: 84
1297176 CCCGACTCGC
* * * *
1297186 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1297251 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * *
1297270 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1297335 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** *
1297354 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
1297392 CCCGATTCAC
Statistics
Matches: 114, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
84 110 0.96
85 4 0.04
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:1298744 original size:13 final size:14
Alignment explanation
Indices: 1298713--1298748 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1298703 TTTGATTATT
1298713 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
1298727 GTGATTTGT-AAAG
1 TTGATTTGTAAAAG
1298740 TTGATTTGT
1 TTGATTTGT
1298749 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1298951 original size:33 final size:32
Alignment explanation
Indices: 1298909--1299032 Score: 157
Period size: 33 Copynumber: 3.9 Consensus size: 32
1298899 ATTAAATTCG
1298909 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1298942 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
1298975 CGTTGCGATTTTCATTTCGCA-TGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1299007 C-TTGCGA-TTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1299033 AGTAATTTCC
Statistics
Matches: 80, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
30 15 0.19
31 11 0.14
32 4 0.05
33 47 0.59
35 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1298968 original size:19 final size:19
Alignment explanation
Indices: 1298905--1298968 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
1298895 CGAAATTAAA
*
1298905 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1298924 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
1298940 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1298957 TTCGCATTGCGA
1 TTCGCATTGCGA
1298969 AATTAGCGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
14 6 0.17
16 6 0.17
17 6 0.17
19 17 0.49
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:1298987 original size:66 final size:63
Alignment explanation
Indices: 1298902--1299031 Score: 206
Period size: 66 Copynumber: 2.0 Consensus size: 63
1298892 ACGCGAAATT
*
1298902 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCA-TGCGATTCCCTC-TTGCGA-TTTCATTTCGCATTGC
1298967 G
63 G
* *
1298968 AAATTAGCGTTGCGATTTTCATTTCGCATGTGATTCTCTCTTGCGATTTCATTTCGCATTGCG
1 AAATTAGCGTTGCGATTTTCATTTCGCATGCGATTCCCTCTTGCGATTTCATTTCGCATTGCG
1299031 A
1 A
1299032 TAGTAATTTC
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
63 18 0.30
64 6 0.10
65 10 0.16
66 27 0.44
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (63 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATGCGATTCCCTCTTGCGATTTCATTTCGCATTGCG
Found at i:1301537 original size:23 final size:24
Alignment explanation
Indices: 1301487--1301539 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
1301477 CTGAAACATC
*
1301487 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
1301511 ATCAAAGTCCGGGTA-TGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1301534 ATCAAA
1 ATCAAA
1301540 TTTCAAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.21
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1302336 original size:20 final size:21
Alignment explanation
Indices: 1302311--1302362 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1302301 TTTTCCTAAT
*
1302311 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
1302331 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1302352 TCGCAATGCGA
1 TCGCAATGCGA
1302363 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1302384 original size:20 final size:20
Alignment explanation
Indices: 1302351--1302429 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
1302341 AATTTGGAAA
* *
1302351 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
1302371 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
1302392 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
1302412 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
1302430 AATCGCAATC
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 30 0.62
21 14 0.29
22 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:1302437 original size:19 final size:19
Alignment explanation
Indices: 1302390--1302437 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
1302380 AGATAATACA
1302390 AAATCGCAACGAGATTCTG
1 AAATCGCAACGAGATTCTG
**
1302409 ACTTTCGCAACGAGATTCTG
1 A-AATCGCAACGAGATTCTG
1302429 AAATCGCAA
1 AAATCGCAA
1302438 TCATCTTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (19 bp):
AAATCGCAACGAGATTCTG
Found at i:1302723 original size:20 final size:20
Alignment explanation
Indices: 1302648--1302715 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
1302638 CAACGGGGAA
1302648 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
1302668 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
1302688 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1302708 ATCGCAAC
1 ATCGCAAC
1302716 TAGAAAATCG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:1302727 original size:34 final size:34
Alignment explanation
Indices: 1302632--1302735 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 34
1302622 ATTCATTTGA
** *
1302632 CTATCGCAACGGGGAAATCGCAACGCGAAAATGG
1 CTATCGCAACAAGAAAATCGCAACGCGAAAATGG
1302666 CTATCGCAATTCGAAATGAAAAATCGCAACGCGAAAATGG
1 CTATCGCAA--C--AA-G-AAAATCGCAACGCGAAAATGG
* *
1302706 CTATCGCAACTAGAAAATCGCAATGCGAAA
1 CTATCGCAACAAGAAAATCGCAACGCGAAA
1302736 TGAAAATTGC
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
34 25 0.42
35 1 0.02
36 2 0.03
38 1 0.02
39 1 0.02
40 29 0.49
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.15
Consensus pattern (34 bp):
CTATCGCAACAAGAAAATCGCAACGCGAAAATGG
Found at i:1302944 original size:14 final size:14
Alignment explanation
Indices: 1302925--1302961 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1302915 CATCAATTAA
1302925 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1302939 ACAAATCATCTTTT
1 ACAAATCAACATTT
1302953 ACAAATCAA
1 ACAAATCAA
1302962 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1304869 original size:19 final size:19
Alignment explanation
Indices: 1304845--1304905 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 19
1304835 AAATCACGAC
1304845 AAAATCGCAATGCGAAAAG
1 AAAATCGCAATGCGAAAAG
*
1304864 AAAATCGCAA--CG---AC
1 AAAATCGCAATGCGAAAAG
*
1304878 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAAAG
1304897 -AAATCGCAA
1 AAAATCGCAA
1304906 CGACAAAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 11
0.71 0.06 0.23
Matches are distributed among these distances:
14 11 0.32
16 2 0.06
17 2 0.06
18 9 0.26
19 10 0.29
ACGTcount: A:0.51, C:0.20, G:0.18, T:0.11
Consensus pattern (19 bp):
AAAATCGCAATGCGAAAAG
Found at i:1304881 original size:14 final size:14
Alignment explanation
Indices: 1304864--1304921 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1304854 ATGCGAAAAG
1304864 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1304878 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1304894 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1304910 AAAATCGCAACG
1 AAAATCGCAACG
1304922 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1304906 original size:32 final size:33
Alignment explanation
Indices: 1304818--1304926 Score: 172
Period size: 32 Copynumber: 3.4 Consensus size: 33
1304808 GGAAATGGCT
1304818 ATCGCAATGCGAAATGAAAAT--C-ACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1304848 ATCGCAATGCGAAAAGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1304881 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1304913 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1304927 CACAAATCAC
Statistics
Matches: 73, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
30 20 0.27
32 30 0.41
33 23 0.32
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1304974 original size:14 final size:14
Alignment explanation
Indices: 1304955--1305012 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1304945 TTTCATTTCA
1304955 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1304969 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1304985 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1305001 CGTTGCGATTTT
1 CGTTGCGATTTT
1305013 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1305019 original size:33 final size:33
Alignment explanation
Indices: 1304942--1305028 Score: 140
Period size: 32 Copynumber: 2.7 Consensus size: 33
1304932 ATCACATTGT
* *
1304942 GATTTTCATTTCACGTTGCGATTTTGTCGTTGC
1 GATTTTCATTTCGCATTGCGATTTTGTCGTTGC
1304975 GA-TTTCATTTCGCATTGCGATTTTGTCGTTGC
1 GATTTTCATTTCGCATTGCGATTTTGTCGTTGC
*
1305007 GATTTTCATTTCGCATTACGAT
1 GATTTTCATTTCGCATTGCGAT
1305029 AGCCATTTCC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 30 0.60
33 20 0.40
ACGTcount: A:0.15, C:0.18, G:0.20, T:0.47
Consensus pattern (33 bp):
GATTTTCATTTCGCATTGCGATTTTGTCGTTGC
Found at i:1305558 original size:18 final size:18
Alignment explanation
Indices: 1305532--1305576 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1305522 GTCGATCAGA
1305532 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGTGAGG
*
1305550 TGATAGCTCTGGGTGAGG
1 TGATGGCTCTGGGTGAGG
1305568 TGATGGCTC
1 TGATGGCTC
1305577 CCGAAGTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.44, T:0.29
Consensus pattern (18 bp):
TGATGGCTCTGGGTGAGG
Found at i:1306699 original size:24 final size:24
Alignment explanation
Indices: 1306671--1306724 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1306661 CTACAAAAAA
*
1306671 CAAAAAATACTA-AGTTAGATATAC
1 CAAAAAATAC-ACAGTGAGATATAC
* *
1306695 CAAAAACTACACTGTGAGATATAC
1 CAAAAAATACACAGTGAGATATAC
1306719 CAAAAA
1 CAAAAA
1306725 CAATAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.54, C:0.17, G:0.09, T:0.20
Consensus pattern (24 bp):
CAAAAAATACACAGTGAGATATAC
Found at i:1306895 original size:19 final size:20
Alignment explanation
Indices: 1306863--1306919 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
1306853 AATAGTTTCT
**
1306863 GAAAATGAAAATCGCAA-AC
1 GAAAATGACTATCGCAACAC
*
1306882 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACAC
**
1306902 GAATTTGACTATCGCAAC
1 GAAAATGACTATCGCAAC
1306920 GAGAGAATCG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
GAAAATGACTATCGCAACAC
Found at i:1307439 original size:19 final size:20
Alignment explanation
Indices: 1307408--1307445 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1307398 ATTATGTATT
1307408 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
1307428 ATCGCG-TGCGAAAGTCAG
1 ATCGCGTTGCGAAAGTCAG
1307446 TATCTCGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.29, C:0.21, G:0.32, T:0.18
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:1307491 original size:20 final size:20
Alignment explanation
Indices: 1307466--1307519 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1307456 GATTTTGTAT
1307466 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1307486 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1307506 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1307520 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1307630 original size:21 final size:21
Alignment explanation
Indices: 1307590--1307630 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1307580 ACTGTAGACC
** *
1307590 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
1307611 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
1307631 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:1316625 original size:20 final size:19
Alignment explanation
Indices: 1316602--1316643 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1316592 GAAACCAGTT
1316602 TGAACCAGTTTCAACCGGTC
1 TGAACCAGTTT-AACCGGTC
* *
1316622 TGAACCGGTTTGACCGGTC
1 TGAACCAGTTTAACCGGTC
1316641 TGA
1 TGA
1316644 CCCGACCCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (19 bp):
TGAACCAGTTTAACCGGTC
Found at i:1323791 original size:10 final size:9
Alignment explanation
Indices: 1323770--1323836 Score: 71
Period size: 9 Copynumber: 7.1 Consensus size: 9
1323760 GGCTGGAAAT
1323770 CGGTTTGAC
1 CGGTTTGAC
1323779 CGGTTTCGAC
1 CGGTTT-GAC
*
1323789 CGGTTAGAAC
1 CGGTTTG-AC
1323799 CGGTTTGAC
1 CGGTTTGAC
*
1323808 CGGTCTGAAC
1 CGGTTTG-AC
*
1323818 AGGTTTGAC
1 CGGTTTGAC
*
1323827 CGGTCTGAC
1 CGGTTTGAC
1323836 C
1 C
1323837 CGACCCGACT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
9 25 0.52
10 23 0.48
ACGTcount: A:0.16, C:0.25, G:0.31, T:0.27
Consensus pattern (9 bp):
CGGTTTGAC
Found at i:1323808 original size:19 final size:19
Alignment explanation
Indices: 1323777--1323834 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
1323767 AATCGGTTTG
1323777 ACCGGTTTCGACCGGT-TAGA
1 ACCGGTTT-GACCGGTCT-GA
1323797 ACCGGTTTGACCGGTCTGA
1 ACCGGTTTGACCGGTCTGA
*
1323816 ACAGGTTTGACCGGTCTGA
1 ACCGGTTTGACCGGTCTGA
1323835 CCCGACCCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 27 0.75
20 9 0.25
ACGTcount: A:0.19, C:0.24, G:0.31, T:0.26
Consensus pattern (19 bp):
ACCGGTTTGACCGGTCTGA
Found at i:1323848 original size:14 final size:14
Alignment explanation
Indices: 1323831--1323859 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1323821 TTTGACCGGT
1323831 CTGACCCGACCCGA
1 CTGACCCGACCCGA
1323845 CTGACCCGACCCGA
1 CTGACCCGACCCGA
1323859 C
1 C
1323860 CGTTGACCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.52, G:0.21, T:0.07
Consensus pattern (14 bp):
CTGACCCGACCCGA
Found at i:1325454 original size:3 final size:3
Alignment explanation
Indices: 1325446--1325500 Score: 67
Period size: 3 Copynumber: 17.7 Consensus size: 3
1325436 CTACAAAATG
*
1325446 TAA TAA TAA TAA T-A TAA TAG TAA TAA TAA TAA TAA TAA TAAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA T-AA
1325492 TAAA TAA TA
1 T-AA TAA TA
1325501 TTTTTTGTAG
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 35 0.73
4 11 0.23
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1328693 original size:24 final size:24
Alignment explanation
Indices: 1328666--1328721 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1328656 AAACTTTAAG
1328666 GTGGAAAAGAACAATGGAGAGTGA
1 GTGGAAAAGAACAATGGAGAGTGA
* *
1328690 GTGGAAAATAACAATGGTGAGTGA
1 GTGGAAAAGAACAATGGAGAGTGA
*
1328714 GTAGAAAA
1 GTGGAAAA
1328722 ACTTAACATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.46, C:0.04, G:0.34, T:0.16
Consensus pattern (24 bp):
GTGGAAAAGAACAATGGAGAGTGA
Found at i:1330391 original size:13 final size:13
Alignment explanation
Indices: 1330373--1330397 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1330363 CTTTTGTTAT
1330373 TCTTTCTTATTCC
1 TCTTTCTTATTCC
1330386 TCTTTCTTATTC
1 TCTTTCTTATTC
1330398 TTTGGAGTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (13 bp):
TCTTTCTTATTCC
Found at i:1330483 original size:231 final size:231
Alignment explanation
Indices: 1330050--1330511 Score: 826
Period size: 231 Copynumber: 2.0 Consensus size: 231
1330040 GAAGTGCTTG
1330050 ACATTCTCTTCATCTTCATCTACCTCTTCACCTGAGTCTTGATTACTCTCATTGTGAACTTGAAG
1 ACATTCTCTTCATCTTCATCTACCTCTTCACCTGAGTCTTGATTACTCTCATTGTGAACTTGAAG
1330115 GTGATTCATATCCCCTTCTTTTTGTTATTCTTTTCTTATTCCTCTTTCTATTCTTTTGGAGTCTC
66 GTGATTCATATCCCCTTCTTTTTGTTATTCTTTTCTTATTCCTCTTTCTATTCTTTTGGAGTCTC
1330180 ATCTCATGGTGTAGAGAACTAATGAGCTCATCAAGAGTGAGCAACTCCAAATCATTGGCTTCTTC
131 ATCTCATGGTGTAGAGAACTAATGAGCTCATCAAGAGTGAGCAACTCCAAATCATTGGCTTCTTC
*
1330245 AATGGCAGTGACCTTTCCTTCCCAAGATATTGGCAA
196 AATGGCAGTGACCTTTCCTTCCCAAGACATTGGCAA
1330281 ACATTCTCTTCATCTTCATCTACCTCTTCACCTGAGTCTTGATTACTCTCATTGGTGAACTTGAA
1 ACATTCTCTTCATCTTCATCTACCTCTTCACCTGAGTCTTGATTACTCTCATT-GTGAACTTGAA
1330346 GGTGATTCA-ATCCCCTTC-TTTTGTTATTC-TTTCTTATTCCTCTTTCTTATTC-TTTGGAGTC
65 GGTGATTCATATCCCCTTCTTTTTGTTATTCTTTTCTTATTCCTCTTTC-TATTCTTTTGGAGTC
1330407 TCATCTCATGGGTGAGTAGAGAACTAATGAGCTCATCAAGAGTGAGCAACTCCAAATCATTGGCT
129 TCATCTCAT-GGT--GTAGAGAACTAATGAGCTCATCAAGAGTGAGCAACTCCAAATCATTGGCT
*
1330472 TCTTC-ATGGCAGTGGCCTTTCCTTCCCAAGACATTGGCAA
191 TCTTCAATGGCAGTGACCTTTCCTTCCCAAGACATTGGCAA
1330512 GGGAGAGAAC
Statistics
Matches: 224, Mismatches: 2, Indels: 10
0.95 0.01 0.04
Matches are distributed among these distances:
229 35 0.16
230 19 0.08
231 95 0.42
232 75 0.33
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (231 bp):
ACATTCTCTTCATCTTCATCTACCTCTTCACCTGAGTCTTGATTACTCTCATTGTGAACTTGAAG
GTGATTCATATCCCCTTCTTTTTGTTATTCTTTTCTTATTCCTCTTTCTATTCTTTTGGAGTCTC
ATCTCATGGTGTAGAGAACTAATGAGCTCATCAAGAGTGAGCAACTCCAAATCATTGGCTTCTTC
AATGGCAGTGACCTTTCCTTCCCAAGACATTGGCAA
Found at i:1336586 original size:3 final size:3
Alignment explanation
Indices: 1336580--1336649 Score: 106
Period size: 3 Copynumber: 23.7 Consensus size: 3
1336570 GAAGAGAAAA
* * *
1336580 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA- GAA GAA GAA GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1336627 GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GA
1336650 AGAAGAAGAA
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
2 2 0.03
3 63 0.97
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:1336654 original size:3 final size:3
Alignment explanation
Indices: 1336648--1336677 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1336638 GGAGGAGGAG
1336648 GAA GAA GAA GAA GAA GAA GAAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA G-AA GAA GAA GA
1336678 GACTGACCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1338908 original size:23 final size:23
Alignment explanation
Indices: 1338882--1338933 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
1338872 AAAAATCAGA
* *
1338882 GTTTACTAACATATTTATTTAGT
1 GTTTACTAACATATTCATTTAGC
**
1338905 GTTTGTTAACATATTCATTTAGC
1 GTTTACTAACATATTCATTTAGC
1338928 GTTTAC
1 GTTTAC
1338934 GAATTTATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.50
Consensus pattern (23 bp):
GTTTACTAACATATTCATTTAGC
Found at i:1346498 original size:16 final size:16
Alignment explanation
Indices: 1346479--1346511 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1346469 CAAATTTTAG
1346479 CCAAACC-AAAAGTAAC
1 CCAAACCGAAAA-TAAC
1346495 CCAAACCGAAAATAAC
1 CCAAACCGAAAATAAC
1346511 C
1 C
1346512 TGAATCGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.55, C:0.33, G:0.06, T:0.06
Consensus pattern (16 bp):
CCAAACCGAAAATAAC
Found at i:1346760 original size:60 final size:61
Alignment explanation
Indices: 1346688--1346803 Score: 141
Period size: 60 Copynumber: 1.9 Consensus size: 61
1346678 TGTCCCTAAT
1346688 CTATGACCATTATT-TCAAATTAGTCC-CTACAA-TTTTAAACATTTCA-ATTTCATCCTTAAA
1 CTATGACCATTATTCT-AAATTAGTCCTC-A-AACTTTTAAACATTTCATATTTCATCCTTAAA
* * * *
1346748 CTATGACTATTATTCTAAATTCGTCCTCAAACTTTTGAACATTTCATTTTTCATCC
1 CTATGACCATTATTCTAAATTAGTCCTCAAACTTTTAAACATTTCATATTTCATCC
1346804 ACAAGTTATG
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
59 2 0.04
60 36 0.75
61 10 0.21
ACGTcount: A:0.31, C:0.22, G:0.04, T:0.42
Consensus pattern (61 bp):
CTATGACCATTATTCTAAATTAGTCCTCAAACTTTTAAACATTTCATATTTCATCCTTAAA
Found at i:1347152 original size:60 final size:60
Alignment explanation
Indices: 1346999--1347174 Score: 164
Period size: 60 Copynumber: 3.0 Consensus size: 60
1346989 GAATTCGATG
* * * * * *
1346999 ATGAAAT-ATAAATATCTAAAAGTTTAGGGA-TCAATTTAGAATAAGATTCATAGTTT-GGG
1 ATGAAATCA-AAATATTTAAAAGTTTAAGGACT-AATTTAGAATGAGAGTCATAGTTTAAGA
* * * * *
1347058 ATGAAATTC-GAATGTTCAAAATTTTAATGACTAATTTAGAATGAGAGTCATAGTTTAAGA
1 ATGAAA-TCAAAATATTTAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTAAGA
* *
1347118 ATGAAATCAAAATATTTAAAAGTTTAAGGACTAATTT-GAAATGATAGTCAGAGTTTA
1 ATGAAATCAAAATATTTAAAAGTTTAAGGACTAATTTAG-AATGAGAGTCATAGTTTA
1347175 GGGACATATT
Statistics
Matches: 93, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
59 45 0.48
60 48 0.52
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (60 bp):
ATGAAATCAAAATATTTAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTAAGA
Found at i:1348991 original size:29 final size:29
Alignment explanation
Indices: 1348895--1348980 Score: 154
Period size: 29 Copynumber: 3.0 Consensus size: 29
1348885 CCCCGTCCTA
*
1348895 ATTCTACATAGGATTAATTCCCTATTCTG
1 ATTCTACATGGGATTAATTCCCTATTCTG
1348924 ATTCTACATGGGATTAATTCCCTATTCTG
1 ATTCTACATGGGATTAATTCCCTATTCTG
*
1348953 ATTCTACATGGGATTAATTCCCTGTTCT
1 ATTCTACATGGGATTAATTCCCTATTCT
1348981 ATTTTTACAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (29 bp):
ATTCTACATGGGATTAATTCCCTATTCTG
Found at i:1351200 original size:31 final size:30
Alignment explanation
Indices: 1351165--1351251 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
1351155 TCAATAAAGT
1351165 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
1351196 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
1351227 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
1351252 TATTATCAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:1351227 original size:20 final size:20
Alignment explanation
Indices: 1351160--1351227 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
1351150 TTTCGTCAAT
*
1351160 AAAG-TTTAAAAAATTA-TA
1 AAAGATTTATAAAATTATTA
* * *
1351178 AAATACTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
1351199 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
1351218 ATAA-ATTTAT
1 A-AAGATTTAT
1351228 CTAAATACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.08
19 15 0.38
20 15 0.38
21 6 0.15
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:1354413 original size:13 final size:13
Alignment explanation
Indices: 1354395--1354442 Score: 87
Period size: 13 Copynumber: 3.7 Consensus size: 13
1354385 TGCGTCATAA
1354395 ATTTATGACGCGC
1 ATTTATGACGCGC
*
1354408 ATTTATGACACGC
1 ATTTATGACGCGC
1354421 ATTTATGACGCGC
1 ATTTATGACGCGC
1354434 ATTTATGAC
1 ATTTATGAC
1354443 TTACATTGCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:1354524 original size:84 final size:85
Alignment explanation
Indices: 1354421--1354585 Score: 278
Period size: 84 Copynumber: 2.0 Consensus size: 85
1354411 TATGACACGC
* * *
1354421 ATTTATGACGCGCATTTATGACTTACATTGCGCGTCATTG-AAGCCCCGTCATAAATGAAGATGA
1 ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAACCCCCGTCATAAATGAAAATGA
*
1354485 CACACATTTGTGTGTCATAA
66 CACACATTCGTGTGTCATAA
*
1354505 ATTTATGACACGCATTTATGACTTACATTGCGTGTCATTGAAACCCCCGTCATAAATGAAAATGA
1 ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAACCCCCGTCATAAATGAAAATGA
1354570 CACACATTCGTGTGTC
66 CACACATTCGTGTGTC
1354586 GTGATTGTAT
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
84 38 0.51
85 37 0.49
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (85 bp):
ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAACCCCCGTCATAAATGAAAATGA
CACACATTCGTGTGTCATAA
Found at i:1365657 original size:23 final size:23
Alignment explanation
Indices: 1365627--1365670 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1365617 TTTTCACTTC
1365627 TAGCTCCTTGCCTTTAGATTGCT
1 TAGCTCCTTGCCTTTAGATTGCT
1365650 TAGCTCCTTGCCTTTAGATTG
1 TAGCTCCTTGCCTTTAGATTG
1365671 TTTTCCGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (23 bp):
TAGCTCCTTGCCTTTAGATTGCT
Found at i:1368517 original size:32 final size:32
Alignment explanation
Indices: 1368451--1368517 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
1368441 GTTGTGCACA
* * *
1368451 TCATCTTCAATCTCTTACATAACACACTCGTT
1 TCATCTTCAATCTCTTACACAACAAACTCCTT
*
1368483 TCATCTTCAATCTCTTACACAATAAACTCCTT
1 TCATCTTCAATCTCTTACACAACAAACTCCTT
1368515 TCA
1 TCA
1368518 CCAAACCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.30, C:0.31, G:0.01, T:0.37
Consensus pattern (32 bp):
TCATCTTCAATCTCTTACACAACAAACTCCTT
Found at i:1369925 original size:17 final size:16
Alignment explanation
Indices: 1369896--1369945 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1369886 TTTTAACTTC
*
1369896 TAAATTTTAAAAAATT
1 TAAATTTTTAAAAATT
1369912 TAATATTTTT-AAAATT
1 TAA-ATTTTTAAAAATT
*
1369928 CAAATTTGTTAAAAATT
1 TAAATTT-TTAAAAATT
1369945 T
1 T
1369946 CTAAAAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 4 0.14
16 13 0.46
17 11 0.39
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
TAAATTTTTAAAAATT
Found at i:1369933 original size:32 final size:33
Alignment explanation
Indices: 1369883--1369945 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1369873 TGTTTGATAT
*
1369883 TATTTTTAACTTCTAAATTT-TAAAAAATTTAA
1 TATTTTTAAATTCTAAATTTGTAAAAAATTTAA
*
1369915 TATTTTTAAAATTC-AAATTTGTTAAAAATTT
1 TATTTTT-AAATTCTAAATTTGTAAAAAATTT
1369946 CTAAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.51
Consensus pattern (33 bp):
TATTTTTAAATTCTAAATTTGTAAAAAATTTAA
Found at i:1369979 original size:78 final size:78
Alignment explanation
Indices: 1369848--1369999 Score: 277
Period size: 78 Copynumber: 1.9 Consensus size: 78
1369838 CCTTTTTTTC
* *
1369848 TTCAAATTTGTTAAAAATTTCTAAATGTTTGATATTATTTTTAACTTCTAAATTTTAAAAAATTT
1 TTCAAATTTGTTAAAAATTTCTAAAAGTTTGATATTATTTTTAACTTCGAAATTTTAAAAAATTT
1369913 AATATTTTTAAAA
66 AATATTTTTAAAA
*
1369926 TTCAAATTTGTTAAAAATTTCTAAAAGTTTGATATTATTTTTAACTTCGAAATTTTAAAAATTTT
1 TTCAAATTTGTTAAAAATTTCTAAAAGTTTGATATTATTTTTAACTTCGAAATTTTAAAAAATTT
1369991 AATATTTTT
66 AATATTTTT
1370000 CTTATTTTAT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 71 1.00
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (78 bp):
TTCAAATTTGTTAAAAATTTCTAAAAGTTTGATATTATTTTTAACTTCGAAATTTTAAAAAATTT
AATATTTTTAAAA
Found at i:1370053 original size:17 final size:17
Alignment explanation
Indices: 1370031--1370069 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1370021 AATATCAATG
1370031 AAATTTTAACAATTATA
1 AAATTTTAACAATTATA
* * *
1370048 AAATTTTTATAATTTTA
1 AAATTTTAACAATTATA
1370065 AAATT
1 AAATT
1370070 CTACACTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATTTTAACAATTATA
Found at i:1375581 original size:18 final size:20
Alignment explanation
Indices: 1375558--1375596 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
1375548 GAGAATTGTG
1375558 TAAAAAATAT-ATAT-TATT
1 TAAAAAATATCATATATATT
1375576 TAAAAAATATCATATATATT
1 TAAAAAATATCATATATATT
1375596 T
1 T
1375597 TGGCGTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 4 0.21
20 5 0.26
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAAAAATATCATATATATT
Found at i:1375834 original size:20 final size:20
Alignment explanation
Indices: 1375811--1375881 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
1375801 GTTTCCAGAT
*
1375811 TCGCAACGCGACTCTGACTA
1 TCGCAACGCGAATCTGACTA
** * *
1375831 TCGCATTGCGAATATGTA-AA
1 TCGCAACGCGAATCTG-ACTA
*
1375851 TTGCAACGCGAATCTGACTA
1 TCGCAACGCGAATCTGACTA
*
1375871 TCGCAATGCGA
1 TCGCAACGCGA
1375882 TTTACATAGC
Statistics
Matches: 37, Mismatches: 12, Indels: 4
0.70 0.23 0.08
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGAATCTGACTA
Found at i:1376086 original size:22 final size:21
Alignment explanation
Indices: 1376061--1376126 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
1376051 GGCGACATCC
1376061 GTCCACATCTCCGACGAAATCA
1 GTCC-CATCTCCGACGAAATCA
*
1376083 GTCCCCATCTCCGACGATATCA
1 GT-CCCATCTCCGACGAAATCA
* *
1376105 ATCTCCATCTCCGGCGAAATCA
1 GTC-CCATCTCCGACGAAATCA
1376127 TTCACGGTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 35 0.92
23 2 0.05
ACGTcount: A:0.27, C:0.38, G:0.14, T:0.21
Consensus pattern (21 bp):
GTCCCATCTCCGACGAAATCA
Found at i:1376536 original size:20 final size:20
Alignment explanation
Indices: 1376463--1376553 Score: 94
Period size: 20 Copynumber: 4.6 Consensus size: 20
1376453 GCGATTCTGT
1376463 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
* ** **
1376482 CCTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
**
1376502 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
1376522 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
1376542 TGTTGCGATTTT
1 CGTTGCGATTTT
1376554 AAGTTTCAGA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 11 0.18
20 50 0.82
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:1376560 original size:20 final size:20
Alignment explanation
Indices: 1376517--1376560 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1376507 CGATAGTCAT
* *
1376517 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
1376537 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
1376557 TTTC
1 TTTC
1376561 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:1378456 original size:20 final size:20
Alignment explanation
Indices: 1378431--1378534 Score: 105
Period size: 20 Copynumber: 5.5 Consensus size: 20
1378421 AATAGTTTAT
*
1378431 TATCGCAATGCGAAAATGAC
1 TATCGCAACGCGAAAATGAC
*
1378451 TATCGCAACACGAAAATGAC
1 TATCGCAACGCGAAAATGAC
1378471 TATCGCAA--C-AACAA--A-
1 TATCGCAACGCGAA-AATGAC
*
1378486 -ATCGCTACGCGAAAATGAC
1 TATCGCAACGCGAAAATGAC
* *
1378505 TATGGCAATGCGAAAATGAC
1 TATCGCAACGCGAAAATGAC
1378525 TATCGCAACG
1 TATCGCAACG
1378535 AAAGAATCGC
Statistics
Matches: 68, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
14 6 0.09
16 4 0.06
17 4 0.06
18 4 0.06
20 50 0.74
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.17
Consensus pattern (20 bp):
TATCGCAACGCGAAAATGAC
Found at i:1378543 original size:54 final size:54
Alignment explanation
Indices: 1378432--1378553 Score: 165
Period size: 54 Copynumber: 2.3 Consensus size: 54
1378422 ATAGTTTATT
*
1378432 ATCGCAATGCGAAAATGACTATCGCAACACGAAAATGACTATCGCAACAACAAA
1 ATCGCAACGCGAAAATGACTATCGCAACACGAAAATGACTATCGCAACAACAAA
* * ** *
1378486 ATCGCTACGCGAAAATGACTATGGCAATGCGAAAATGACTATCGCAACGAA-AGA
1 ATCGCAACGCGAAAATGACTATCGCAACACGAAAATGACTATCGCAAC-AACAAA
*
1378540 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
1378554 TGAAAATCGC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
54 57 0.97
55 2 0.03
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (54 bp):
ATCGCAACGCGAAAATGACTATCGCAACACGAAAATGACTATCGCAACAACAAA
Found at i:1378622 original size:20 final size:20
Alignment explanation
Indices: 1378577--1378625 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1378567 GCGATTCTCT
1378577 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
** **
1378597 TATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
1378617 CGTTGCGAT
1 CGTTGCGAT
1378626 TTTAAGTTTC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1379206 original size:42 final size:42
Alignment explanation
Indices: 1379136--1379227 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
1379126 TCCCATATCG
* *
1379136 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACCA
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAACA
* ** *
1379178 TTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAACA
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAACA
*
1379220 TTCTAGAG
1 TTCAAGAG
1379228 CCCGATTCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 40 0.95
43 2 0.05
ACGTcount: A:0.25, C:0.36, G:0.17, T:0.22
Consensus pattern (42 bp):
TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAACA
Found at i:1380618 original size:14 final size:14
Alignment explanation
Indices: 1380599--1380634 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1380589 ATTATTTAAT
1380599 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1380613 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1380627 TGATTTGT
1 TGATTTGT
1380635 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1380887 original size:33 final size:33
Alignment explanation
Indices: 1380831--1380914 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
1380821 CTAATTTCGT
1380831 GTTGCGATTTTCATTTTCGCATTGCAATTCACTC
1 GTTGCGATTTTCA-TTTCGCATTGCAATTCACTC
*
1380865 GTTGCGATTTTCATTTCGCATTGCAATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCAATTCACTC
**
1380898 GTTGCGATAGTCATTTC
1 GTTGCGATTTTCATTTC
1380915 CGCGTTGCGA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 34 0.72
34 13 0.28
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.44
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCATTGCAATTCACTC
Found at i:1380922 original size:20 final size:20
Alignment explanation
Indices: 1380897--1380990 Score: 145
Period size: 20 Copynumber: 4.7 Consensus size: 20
1380887 GCAATTCTCT
1380897 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1380917 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
1380937 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
1380957 TGTTGCGATAGGCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
1380977 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
1380991 AATGAATGTC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 65 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1383426 original size:24 final size:24
Alignment explanation
Indices: 1383392--1383445 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1383382 CTAAAAATTC
1383392 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1383416 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1383440 ATCAAA
1 ATCAAA
1383446 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1383459 original size:24 final size:24
Alignment explanation
Indices: 1383392--1383459 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1383382 CTAAAAATTC
* * *
1383392 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1383416 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1383440 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1383460 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1384316 original size:20 final size:20
Alignment explanation
Indices: 1384288--1384334 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1384278 AAATTCAGTA
* *
1384288 TTGCAATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
1384308 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
1384328 TTGCGAT
1 TTGCGAT
1384335 TTACGTATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:1384344 original size:20 final size:20
Alignment explanation
Indices: 1384321--1384454 Score: 187
Period size: 20 Copynumber: 6.7 Consensus size: 20
1384311 CGATAGTCAG
*
1384321 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1384341 ATTCGCATTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
1384361 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1384381 ATTCGCATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
* * **
1384401 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
1384422 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1384442 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1384455 ATTAGGAAAA
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
20 84 0.84
21 16 0.16
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1384496 original size:21 final size:21
Alignment explanation
Indices: 1384450--1384496 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1384440 GTATTCGCAT
1384450 TGCGAATTAGGAAAATCACAA
1 TGCGAATTAGGAAAATCACAA
* * **
1384471 CGCGAATTTGGAAAATTGCAA
1 TGCGAATTAGGAAAATCACAA
1384492 TGCGA
1 TGCGA
1384497 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (21 bp):
TGCGAATTAGGAAAATCACAA
Found at i:1394515 original size:23 final size:23
Alignment explanation
Indices: 1394479--1394525 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1394469 AGTCTATATG
1394479 TATGACACACTTTCATCTGTCTT
1 TATGACACACTTTCATCTGTCTT
* * *
1394502 TATGACATATTTTCTTCTGTCTT
1 TATGACACACTTTCATCTGTCTT
1394525 T
1 T
1394526 TCACATGTTT
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:0.19, C:0.21, G:0.09, T:0.51
Consensus pattern (23 bp):
TATGACACACTTTCATCTGTCTT
Found at i:1394538 original size:23 final size:23
Alignment explanation
Indices: 1394489--1394536 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1394479 TATGACACAC
*
1394489 TTTCATCTGTCTTTATGACATAT
1 TTTCATCTGTCTTTATCACATAT
* *
1394512 TTTCTTCTGTCTTT-TCACATGT
1 TTTCATCTGTCTTTATCACATAT
1394534 TTT
1 TTT
1394537 TCGGTCATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.15, C:0.19, G:0.08, T:0.58
Consensus pattern (23 bp):
TTTCATCTGTCTTTATCACATAT
Found at i:1399425 original size:17 final size:17
Alignment explanation
Indices: 1399403--1399435 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1399393 ATGACCAATA
1399403 TTAAATCAAAT-ATAATC
1 TTAAAT-AAATCATAATC
1399420 TTAAATAAATCATAAT
1 TTAAATAAATCATAAT
1399436 TTATCAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAATAAATCATAATC
Found at i:1401263 original size:30 final size:28
Alignment explanation
Indices: 1401229--1401284 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
1401219 TCGATCAACG
1401229 ACTCAATAAAAAAACTATACAATTCAAAAT
1 ACTCAAT--AAAAACTATACAATTCAAAAT
**
1401259 ACTCAATAGCAACTATACAATTCAAA
1 ACTCAATAAAAACTATACAATTCAAA
1401285 GACTCAAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.71
30 7 0.29
ACGTcount: A:0.55, C:0.20, G:0.02, T:0.23
Consensus pattern (28 bp):
ACTCAATAAAAACTATACAATTCAAAAT
Found at i:1401517 original size:20 final size:19
Alignment explanation
Indices: 1401492--1401539 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
1401482 TTTATTTTTA
1401492 TTTTTTATTATTAATTAAAT
1 TTTTTTATTATT-ATTAAAT
*
1401512 TTTTTTATTATTATTAATT
1 TTTTTTATTATTATTAAAT
1401531 TTTGTTTAT
1 TTT-TTTAT
1401540 AGGTTACAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTTTATTATTATTAAAT
Found at i:1402025 original size:14 final size:15
Alignment explanation
Indices: 1401988--1402043 Score: 69
Period size: 16 Copynumber: 3.7 Consensus size: 15
1401978 CTGGGAGAAA
1401988 AAAAAAGAAAAAACG
1 AAAAAAGAAAAAACG
1402003 AAAAGAAGAAAAAAC-
1 AAAA-AAGAAAAAACG
* *
1402018 AACAAAGAAAAAAGG
1 AAAAAAGAAAAAACG
1402033 AAAGAAAGAAA
1 AAA-AAAGAAA
1402044 GGCTTTACCT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 9 0.26
15 9 0.26
16 17 0.49
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAACG
Found at i:1410363 original size:24 final size:23
Alignment explanation
Indices: 1410310--1410381 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 23
1410300 ATACGTTACT
* *
1410310 TGAATTATGTTTTGATTCTGATC
1 TGAATTCTGTTTTGATTCTGATA
* *
1410333 TGGATTCTGTTATGATATCTGATA
1 TGAATTCTGTTTTGAT-TCTGATA
1410357 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTTTGA-TTCTGATA
1410381 T
1 T
1410382 CTCCGTTTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 13 0.32
24 27 0.66
25 1 0.02
ACGTcount: A:0.22, C:0.08, G:0.18, T:0.51
Consensus pattern (23 bp):
TGAATTCTGTTTTGATTCTGATA
Done.