Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003806.1 Hibiscus syriacus cultivar Beakdansim tig00008146_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: 1419252
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1262327 original size:21 final size:22
Alignment explanation
Indices: 1262286--1262338 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
1262276 ATTTGTCTCA
* *
1262286 AAGGACCACACTTATATGTCCCT
1 AAGGACCACAC-TAAATGTCCCG
1262309 AAGGACCACA-TAAATGTCCCG
1 AAGGACCACACTAAATGTCCCG
*
1262330 AATGACCAC
1 AAGGACCAC
1262339 TCCTTAAGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 17 0.63
23 10 0.37
ACGTcount: A:0.36, C:0.30, G:0.15, T:0.19
Consensus pattern (22 bp):
AAGGACCACACTAAATGTCCCG
Found at i:1262370 original size:21 final size:21
Alignment explanation
Indices: 1262344--1262437 Score: 82
Period size: 21 Copynumber: 4.5 Consensus size: 21
1262334 ACCACTCCTT
*
1262344 AAGGATCACATATATATTCCA
1 AAGGATCACATATATATTCCG
* *
1262365 AAGGATCA-ATATGTGTTCCG
1 AAGGATCACATATATATTCCG
* * * *
1262385 AAGAATCGCATATATGTTCCC
1 AAGGATCACATATATATTCCG
* * *
1262406 AATGATTACATATATATCCCG
1 AAGGATCACATATATATTCCG
*
1262427 AAGGACCACAT
1 AAGGATCACAT
1262438 TGAACCCTCG
Statistics
Matches: 55, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 15 0.27
21 40 0.73
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (21 bp):
AAGGATCACATATATATTCCG
Found at i:1263527 original size:13 final size:13
Alignment explanation
Indices: 1263509--1263552 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
1263499 GTCATAAATC
*
1263509 TATGACGCGCATT
1 TATGACGTGCATT
* *
1263522 TATGACATACATT
1 TATGACGTGCATT
1263535 TATGACGTGCATT
1 TATGACGTGCATT
1263548 TATGA
1 TATGA
1263553 TGCGAATTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (13 bp):
TATGACGTGCATT
Found at i:1263538 original size:26 final size:26
Alignment explanation
Indices: 1263482--1263552 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
1263472 TGAAATTTTG
* *
1263482 ATGACGCGCAATTCTGTGTCATAAATCT
1 ATGACGCGC-ATT-TATGACATAAATCT
* *
1263510 ATGACGCGCATTTATGACATACATTT
1 ATGACGCGCATTTATGACATAAATCT
*
1263536 ATGACGTGCATTTATGA
1 ATGACGCGCATTTATGA
1263553 TGCGAATTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
26 26 0.68
27 3 0.08
28 9 0.24
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (26 bp):
ATGACGCGCATTTATGACATAAATCT
Found at i:1274161 original size:105 final size:105
Alignment explanation
Indices: 1273979--1274188 Score: 402
Period size: 105 Copynumber: 2.0 Consensus size: 105
1273969 GAGGCATAAT
1273979 ATGACATGTAACAATGAATTCATGAAACATACACTTCTATCATTCCATTATGACATTACAAATTG
1 ATGACATGTAACAATGAATTCATGAAACATACACTTCTATCATTCCATTATGACATTACAAATTG
*
1274044 TATATATTTACTAAACTATAACATATATAATTATGAAGTG
66 TATATATTTACTAAACTATAACATATATAATTATAAAGTG
1274084 ATGACATGTAACAATGAATTCATGAAACATACACTTCTATCATTCCATTATGACATTACAAATTG
1 ATGACATGTAACAATGAATTCATGAAACATACACTTCTATCATTCCATTATGACATTACAAATTG
*
1274149 TATATATTTACTAAACTATAACATGTATAATTATAAAGTG
66 TATATATTTACTAAACTATAACATATATAATTATAAAGTG
1274189 CACAATTGAA
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 103 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (105 bp):
ATGACATGTAACAATGAATTCATGAAACATACACTTCTATCATTCCATTATGACATTACAAATTG
TATATATTTACTAAACTATAACATATATAATTATAAAGTG
Found at i:1274439 original size:21 final size:21
Alignment explanation
Indices: 1274413--1274492 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
1274403 ACCACTCCTT
*
1274413 AAGGATCACATATATATTCCA
1 AAGGATCAAATATATATTCCA
* * *
1274434 AAGGATCAAATATGTGTTCCG
1 AAGGATCAAATATATATTCCA
* ** * *
1274455 AAGAATCGCATATATCTTCCC
1 AAGGATCAAATATATATTCCA
*
1274476 AAGGATTAAATATATAT
1 AAGGATCAAATATATAT
1274493 CCTGAAAGAC
Statistics
Matches: 44, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (21 bp):
AAGGATCAAATATATATTCCA
Found at i:1283291 original size:22 final size:22
Alignment explanation
Indices: 1283259--1283320 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 22
1283249 GTGAGATCTG
* **
1283259 TGTCCCAAAGGACATATGTATA
1 TGTCCCGAAGGACATATCCATA
1283281 TGTCCCGAAGGACCACTATCCATA
1 TGTCCCGAAGGA-CA-TATCCATA
* *
1283305 TGTTCCGAAGAACATA
1 TGTCCCGAAGGACATA
1283321 GGTAACCTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 13 0.39
23 4 0.12
24 16 0.48
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (22 bp):
TGTCCCGAAGGACATATCCATA
Found at i:1283336 original size:31 final size:31
Alignment explanation
Indices: 1283299--1283388 Score: 144
Period size: 31 Copynumber: 2.9 Consensus size: 31
1283289 AGGACCACTA
* *
1283299 TCCATATGTTCCGAAGAACATAGGTAACCTG
1 TCCATATGTCCCGAAGGACATAGGTAACCTG
* *
1283330 TCCATATATCCCGAAGGACATAGGTAAACTG
1 TCCATATGTCCCGAAGGACATAGGTAACCTG
1283361 TCCATATGTCCCGAAGGACATAGGTAAC
1 TCCATATGTCCCGAAGGACATAGGTAAC
1283389 TCTCGACTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (31 bp):
TCCATATGTCCCGAAGGACATAGGTAACCTG
Found at i:1286741 original size:31 final size:31
Alignment explanation
Indices: 1286696--1286785 Score: 144
Period size: 31 Copynumber: 2.9 Consensus size: 31
1286686 AGGACCACTA
* *
1286696 TCCATATGTTCCGAAGAACATAGGTAACCTG
1 TCCATATGTCCCGAAGGACATAGGTAACCTG
* *
1286727 TCCATATATCCCGAAGGACATAGGTAAACTG
1 TCCATATGTCCCGAAGGACATAGGTAACCTG
1286758 TCCATATGTCCCGAAGGACATAGGTAAC
1 TCCATATGTCCCGAAGGACATAGGTAAC
1286786 TCTCGACTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (31 bp):
TCCATATGTCCCGAAGGACATAGGTAACCTG
Found at i:1315831 original size:101 final size:101
Alignment explanation
Indices: 1315656--1315859 Score: 390
Period size: 101 Copynumber: 2.0 Consensus size: 101
1315646 AAGGGCAAGG
1315656 AAAAAGTTAAAGAATAGCGGACTACAATAAGGCATAATAATGAGACATACCAGGTGAGTGCATTT
1 AAAAAGTTAAAGAATAGCGGACTACAATAAGGCATAATAATGAGACATACCAGGTGAGTGCATTT
1315721 ATTATGTATTTATATGATACAAGGACGACTTGCGAT
66 ATTATGTATTTATATGATACAAGGACGACTTGCGAT
*
1315757 AAAAAGTTAAAGAATAGCGGACTACAATAAGGCATAATAATGAGGCATACCAGGTGAGTGCATTT
1 AAAAAGTTAAAGAATAGCGGACTACAATAAGGCATAATAATGAGACATACCAGGTGAGTGCATTT
*
1315822 ATTATGTATTTATATGATACGAGGACGACTTGCGAT
66 ATTATGTATTTATATGATACAAGGACGACTTGCGAT
1315858 AA
1 AA
1315860 GTCAACCTCG
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (101 bp):
AAAAAGTTAAAGAATAGCGGACTACAATAAGGCATAATAATGAGACATACCAGGTGAGTGCATTT
ATTATGTATTTATATGATACAAGGACGACTTGCGAT
Found at i:1316626 original size:17 final size:17
Alignment explanation
Indices: 1316604--1316642 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1316594 TGAATCAAAT
1316604 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1316621 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1316638 -AATTA
1 TAATTA
1316643 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:1331734 original size:21 final size:21
Alignment explanation
Indices: 1331692--1331734 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1331682 AGTTATTAAT
* * *
1331692 TATTATCGTTGTTAGTATATA
1 TATTATCATTATTAGTACATA
*
1331713 TATTATCATTATTAGTCCATA
1 TATTATCATTATTAGTACATA
1331734 T
1 T
1331735 TATCATCAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.51
Consensus pattern (21 bp):
TATTATCATTATTAGTACATA
Found at i:1332842 original size:22 final size:22
Alignment explanation
Indices: 1332816--1332857 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1332806 CTCTTGGGTT
1332816 TTATTTGGATGAGTTTAGAGGG
1 TTATTTGGATGAGTTTAGAGGG
* * *
1332838 TTATTTTGTTGGGTTTAGAG
1 TTATTTGGATGAGTTTAGAG
1332858 TTAGGGTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (22 bp):
TTATTTGGATGAGTTTAGAGGG
Found at i:1333317 original size:14 final size:14
Alignment explanation
Indices: 1333300--1333326 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1333290 ATATTAAATA
1333300 ATAAATATAATTAT
1 ATAAATATAATTAT
1333314 ATAAATATAATTA
1 ATAAATATAATTA
1333327 AAAAATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAAATATAATTAT
Found at i:1333416 original size:20 final size:19
Alignment explanation
Indices: 1333393--1333439 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1333383 TCCCGATTTT
* *
1333393 ATTATTTTATTATTATAATA
1 ATTATTTTATTAATA-AAAA
1333413 ATTATTATTATTAATAAAAA
1 ATTATT-TTATTAATAAAAA
1333433 ATTATTT
1 ATTATTT
1333440 ACAAACAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 15 0.62
21 8 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTATTTTATTAATAAAAA
Found at i:1333419 original size:15 final size:16
Alignment explanation
Indices: 1333399--1333429 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1333389 TTTTATTATT
1333399 TTATTATTA-TAATAA
1 TTATTATTATTAATAA
1333414 TTATTATTATTAATAA
1 TTATTATTATTAATAA
1333430 AAAATTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATTATTATTAATAA
Found at i:1333861 original size:25 final size:26
Alignment explanation
Indices: 1333816--1333873 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 26
1333806 TCACCTGCAA
* *
1333816 AGAAAAAAAAAGAGGAGACAGAGAGT
1 AGAAAAAAAAAGAGGAAACAGAGAGC
*
1333842 AGAAAAAAGAAG-GGAAACAGAGAGC
1 AGAAAAAAAAAGAGGAAACAGAGAGC
1333867 AGAAAAA
1 AGAAAAA
1333874 CAGAGAGCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 18 0.62
26 11 0.38
ACGTcount: A:0.64, C:0.05, G:0.29, T:0.02
Consensus pattern (26 bp):
AGAAAAAAAAAGAGGAAACAGAGAGC
Found at i:1333895 original size:17 final size:15
Alignment explanation
Indices: 1333856--1333895 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
1333846 AAAAGAAGGG
1333856 AAACAGAGAGCAGAA
1 AAACAGAGAGCAGAA
1333871 AAACAGAGAGCAGAA
1 AAACAGAGAGCAGAA
*
1333886 AAACGGAGAG
1 AAACAGAGAG
1333896 GAGACGGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.57, C:0.12, G:0.30, T:0.00
Consensus pattern (15 bp):
AAACAGAGAGCAGAA
Found at i:1335140 original size:8 final size:7
Alignment explanation
Indices: 1335116--1335157 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
1335106 TTTTCATACA
1335116 TGCA-TT
1 TGCATTT
1335122 TGCATTT
1 TGCATTT
1335129 TGCATCTT
1 TGCAT-TT
1335137 TGCATTT
1 TGCATTT
* *
1335144 TTCATTG
1 TGCATTT
1335151 TGCATTT
1 TGCATTT
1335158 ATACTCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:1335140 original size:15 final size:14
Alignment explanation
Indices: 1335116--1335157 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
1335106 TTTTCATACA
1335116 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
1335129 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
1335144 TTCATTGTGCATTT
1 TGCATTTTGCATTT
1335158 ATACTCTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:1335228 original size:14 final size:14
Alignment explanation
Indices: 1335188--1335253 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 14
1335178 GTACTATACA
1335188 ATTTGCAT-TGTTAC
1 ATTTGCATAT-TTAC
**
1335202 ATTCACATATTTAC
1 ATTTGCATATTTAC
* *
1335216 ATTTGCATTTTTAT
1 ATTTGCATATTTAC
*
1335230 GTTTG--TATTTAC
1 ATTTGCATATTTAC
1335242 ATTTGCATATTT
1 ATTTGCATATTT
1335254 CCATAATTAC
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
12 9 0.23
14 29 0.74
15 1 0.03
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.55
Consensus pattern (14 bp):
ATTTGCATATTTAC
Found at i:1339838 original size:114 final size:113
Alignment explanation
Indices: 1339638--1339978 Score: 549
Period size: 114 Copynumber: 3.0 Consensus size: 113
1339628 GTGCCACGTT
*
1339638 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTTTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
*
1339703 ATTTGGTATGAACTCCAAAACCAATCAGTGGATTTGAAAGATGAATTTG
66 ATTTGGTATGAAC-CCAAAACCAATCATTGGATTTGAAAGATGAATTTG
1339752 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* *
1339817 ATTTGGTATGAACCCTAAAACCAATCATTTGATTTAAAAGATGAATTTG
66 ATTTGGTATGAACCC-AAAACCAATCATTGGATTTGAAAGATGAATTTG
*
1339866 CTCATAGTAGAAATAAGGAGACTCC-ATACCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
1 CTCATAGTAGAAATAAGGAGAC-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
* * * * *
1339930 GGTTCGGTAGGAATCCCAGAACCAATCATTGGAATTGAAAGATGAATTT
65 GATTTGGTATGAA-CCCAAAACCAATCATTGGATTTGAAAGATGAATTT
1339979 CATGATCGTC
Statistics
Matches: 212, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
113 2 0.01
114 205 0.97
115 5 0.02
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (113 bp):
CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
ATTTGGTATGAACCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
Found at i:1342619 original size:22 final size:22
Alignment explanation
Indices: 1342588--1342642 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1342578 ATCTACACTC
* *
1342588 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAAATTCCCTT
* *
1342610 TTTAAAGATGACAAATTCTCTT
1 TTCAAAGATGACAAATTCCCTT
1342632 TTCAAAGATGA
1 TTCAAAGATGA
1342643 AAGCTTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAAATTCCCTT
Found at i:1343240 original size:113 final size:113
Alignment explanation
Indices: 1343042--1343718 Score: 937
Period size: 113 Copynumber: 6.0 Consensus size: 113
1343032 TTAGCAAAGT
* * * *
1343042 TCAAATCCATCATTCGATTGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
1343107 AGAATGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
1343155 TCAAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
1343220 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
** * * * * *
1343267 TTGAATTCATCATTCGATGGATCATCATTACCAG-GTAGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTCGATGGATCAGCATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
* * *
1343331 AAGAAGGAAGAAGAGGTTCATAATGAGAAGAGCTTGTTTAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * *
1343380 TCAAATCCATTACTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGA
1 TCAAATCCATCACTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1343445 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-GC
** ** * * * ** *
1343493 TTGAATTTATCATTCGATGGATCAGCATTGCCAGGGCGAGTTCATAATAAGAAGAACTCATCTGA
1 TCAAATCCATCACTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* **
1343558 AGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAATTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * *
1343606 TCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
1343671 AGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
1343719 ATGATTCTAT
Statistics
Matches: 498, Mismatches: 61, Indels: 10
0.88 0.11 0.02
Matches are distributed among these distances:
111 1 0.00
112 102 0.20
113 390 0.78
114 5 0.01
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCACTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:1343445 original size:225 final size:225
Alignment explanation
Indices: 1343049--1343715 Score: 1030
Period size: 225 Copynumber: 3.0 Consensus size: 225
1343039 AGTTCAAATC
* * * * *
1343049 CATCATTCGATTGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGA
1 CATCATTCGATGGATCAACATTACCAG-GAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1343114 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCA
65 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCA
1343179 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
130 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* *
1343244 AGAAGAATTTGTTCAACCTTT-GTTTGAATT
195 AGAAGAACTTGTTCAACCTTTCGCTTGAATT
* *
1343274 CATCATTCGATGGATCATCATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACATTACCAGG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* * * *
1343339 AGAAGAGGTTCATAATGAGAAGAGCTTGTTTAACCTTTTGCTCAAATCCATTACTTGATGGATCA
65 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCA
* *
1343404 GCATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATG
130 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
1343469 AGAAGAACTTGTTCAACTTTTCGCTTGAATT
195 AGAAGAACTTGTTCAACCTTTCGCTTGAATT
* * * * *
1343500 TATCATTCGATGGATCAGCATTGCCAGGGCGAGTTCATAATAAGAAGAACTCATCTGAAGAAAGA
1 CATCATTCGATGGATCAACATTACCA-GGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* ** * *
1343565 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAAATTTTTGCTCGAATTCATCACTCGATGGATCA
65 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCA
* * *
1343630 ACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATG
130 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
1343695 AGAAGAACTTGTTCAATCTTT
195 AGAAGAACTTGTTCAACCTTT
1343716 TGCATGATTC
Statistics
Matches: 402, Mismatches: 37, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
224 1 0.00
225 200 0.50
226 199 0.50
227 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (225 bp):
CATCATTCGATGGATCAACATTACCAGGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAA
GAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAG
CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACCTTTCGCTTGAATT
Found at i:1343627 original size:226 final size:225
Alignment explanation
Indices: 1343049--1343731 Score: 1044
Period size: 226 Copynumber: 3.0 Consensus size: 225
1343039 AGTTCAAATC
* * * * * * *
1343049 CATCATTCGATTGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGA
1 CATCATTCGATGGATCAGCATTACCAGGGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1343114 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCA
66 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCA
1343179 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
131 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * *
1343244 AGAAGAATTTGTTCAACCTTTGTTTGAATT
196 AGAAGAACTTGTTCAACTTTTGCTTGAATT
* * *
1343274 CATCATTCGATGGATCATCATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAGCATTACCAGGGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* * * *
1343339 AGAAGAGGTTCATAATGAGAAGAGCTTGTTTAACCTTTTGCTCAAATCCATTACTTGATGGATCA
66 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCA
* *
1343404 GCATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATG
131 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
1343469 AGAAGAACTTGTTCAACTTTTCGCTTGAATT
196 AGAAGAACTTGTTCAACTTTT-GCTTGAATT
* * * *
1343500 TATCATTCGATGGATCAGCATTGCCAGGGCGAGTTCATAATAAGAAGAACTCATCTGAAGAAAGA
1 CATCATTCGATGGATCAGCATTACCAGGGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* ** * *
1343565 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAAATTTTTGCTCGAATTCATCACTCGATGGATCA
66 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCA
* * *
1343630 ACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATG
131 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
1343695 AGAAGAACTTGTTCAATCTTTTGCATG-ATT
196 AGAAGAACTTGTTCAA-CTTTTGCTTGAATT
1343725 CTATCAT
1 C-ATCAT
1343732 AGAAGGAGAT
Statistics
Matches: 415, Mismatches: 40, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
225 203 0.49
226 207 0.50
227 5 0.01
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (225 bp):
CATCATTCGATGGATCAGCATTACCAGGGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCA
GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACTTTTGCTTGAATT
Found at i:1344051 original size:8 final size:8
Alignment explanation
Indices: 1344038--1344082 Score: 63
Period size: 8 Copynumber: 5.4 Consensus size: 8
1344028 TTTTATCCCG
1344038 ATTTTATT
1 ATTTTATT
1344046 ATTTTATT
1 ATTTTATT
1344054 ATTTTATT
1 ATTTTATT
*
1344062 ATTATAATT
1 ATT-TTATT
1344071 ATTATTATT
1 ATT-TTATT
1344080 ATT
1 ATT
1344083 ATTACTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
8 19 0.56
9 15 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
ATTTTATT
Found at i:1344101 original size:3 final size:3
Alignment explanation
Indices: 1344041--1344086 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
1344031 TATCCCGATT
*
1344041 TTA TTA TT- TTA TTA TT- TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1344087 CTAAAAACTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1344509 original size:26 final size:26
Alignment explanation
Indices: 1344480--1344557 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
1344470 TCACCTGCAA
* *
1344480 AGAAAAAAAAAGAGGAGACAGAGAGT
1 AGAAAAAAGAAGAGGAGACAGAGAGC
* *
1344506 AGAAAAAAGAAG-GGAAACAGAGAAC
1 AGAAAAAAGAAGAGGAGACAGAGAGC
* * *
1344531 AGAAAAACGGAGAGGAGACGGAGAGC
1 AGAAAAAAGAAGAGGAGACAGAGAGC
1344557 A
1 A
1344558 ACCCAAAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
25 20 0.48
26 22 0.52
ACGTcount: A:0.58, C:0.08, G:0.33, T:0.01
Consensus pattern (26 bp):
AGAAAAAAGAAGAGGAGACAGAGAGC
Found at i:1344525 original size:25 final size:26
Alignment explanation
Indices: 1344480--1344537 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
1344470 TCACCTGCAA
* **
1344480 AGAAAAAAAAAGAGGAGACAGAGAGT
1 AGAAAAAAAAAGAGGAAACAGAGAAC
*
1344506 AGAAAAAAGAAG-GGAAACAGAGAAC
1 AGAAAAAAAAAGAGGAAACAGAGAAC
1344531 AGAAAAA
1 AGAAAAA
1344538 CGGAGAGGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 17 0.61
26 11 0.39
ACGTcount: A:0.66, C:0.05, G:0.28, T:0.02
Consensus pattern (26 bp):
AGAAAAAAAAAGAGGAAACAGAGAAC
Found at i:1350771 original size:64 final size:65
Alignment explanation
Indices: 1350648--1350783 Score: 193
Period size: 64 Copynumber: 2.1 Consensus size: 65
1350638 TACACCCATT
* ** **
1350648 TCGAATGCATTTTGTGTACCGATGCATATTCCATGCATCGATGCACTCTTGAATATTTTG-AACA
1 TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCACTCCAGAATATTTTGAAACA
** *
1350712 TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCACTCCAGGCTCTTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCACTCCAGAATATTTTGAAACA
1350777 TCGAATG
1 TCGAATG
1350784 TAATTAGTGC
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
64 52 0.83
65 11 0.17
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCACTCCAGAATATTTTGAAACA
Found at i:1356619 original size:23 final size:23
Alignment explanation
Indices: 1356589--1356668 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 23
1356579 ACACTAGACA
1356589 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCATCCCTTGAAT
* *
1356612 GTGCATCGAT--A-CGCCATGAAG
1 GTGCATCGATGCATC-CCTTGAAT
* *
1356633 GTGCACCGATGCATTCCTTGAAT
1 GTGCATCGATGCATCCCTTGAAT
1356656 GTGCATCGATGCA
1 GTGCATCGATGCA
1356669 CTCTGCTATG
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
20 1 0.02
21 16 0.35
23 29 0.63
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (23 bp):
GTGCATCGATGCATCCCTTGAAT
Found at i:1359403 original size:64 final size:65
Alignment explanation
Indices: 1359327--1359482 Score: 224
Period size: 64 Copynumber: 2.4 Consensus size: 65
1359317 CACACCCATT
* *
1359327 TCGAATGTATTTTGTGTACCGATGCACATGCCATGCATCGATGCACTCTTGAATCTTTTG-AACA
1 TCGAATGTATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCTAGAATCTTTTGAAACA
* * **
1359391 TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCGATGCAGTCTAGGCTCTTTTGAAACA
1 TCGAATGTATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCTAGAATCTTTTGAAACA
* * *
1359456 TCGAATGTAATTAGTGCACCGATGCAC
1 TCGAATGTATTTTGTGTACCGATGCAC
1359483 CCCTAGTGTG
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
64 54 0.67
65 27 0.33
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (65 bp):
TCGAATGTATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCTAGAATCTTTTGAAACA
Found at i:1365043 original size:33 final size:33
Alignment explanation
Indices: 1365006--1365110 Score: 156
Period size: 33 Copynumber: 3.2 Consensus size: 33
1364996 CTTGCGTAAA
* * * * *
1365006 CTTCTTCTTTCTTCTTATGGGATCTTAATTCAT
1 CTTCTTCATTCTTCTTCTGGAATATTGATTCAT
1365039 CTTCTTCATTCTTCTTCTGGAATATTGATTCAT
1 CTTCTTCATTCTTCTTCTGGAATATTGATTCAT
*
1365072 CTTCTTCATTCTTTTTCTGGAATATTGATTCAT
1 CTTCTTCATTCTTCTTCTGGAATATTGATTCAT
1365105 CTTCTT
1 CTTCTT
1365111 TCTTCTGGGA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.16, C:0.21, G:0.09, T:0.54
Consensus pattern (33 bp):
CTTCTTCATTCTTCTTCTGGAATATTGATTCAT
Found at i:1366834 original size:4 final size:4
Alignment explanation
Indices: 1366821--1366850 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1366811 GATTATAAGA
1366821 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1366851 GCATAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1367924 original size:11 final size:11
Alignment explanation
Indices: 1367910--1367950 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
1367900 TTACAATTCA
1367910 TTTATCTT-TT
1 TTTATCTTATT
1367920 CTTTATCTTATT
1 -TTTATCTTATT
*
1367932 TTAATCTTATT
1 TTTATCTTATT
1367943 TTTATCTT
1 TTTATCTT
1367951 GTTTCCAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 25 0.93
12 2 0.07
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTATCTTATT
Found at i:1368288 original size:12 final size:11
Alignment explanation
Indices: 1368272--1368336 Score: 58
Period size: 12 Copynumber: 5.5 Consensus size: 11
1368262 TATTTTTTTC
1368272 AAAAAACAAAA
1 AAAAAACAAAA
*
1368283 CAAAAAAAAAAA
1 -AAAAAACAAAA
1368295 AAAAAAGCCAAAA
1 AAAAAA--CAAAA
*
1368308 AAAAAGCCAAAA
1 AAAAA-ACAAAA
*
1368320 AAAAAGCCAAAA
1 AAAAA-ACAAAA
1368332 AAAAA
1 AAAAA
1368337 GCCAAAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
11 6 0.13
12 32 0.68
13 9 0.19
ACGTcount: A:0.83, C:0.12, G:0.05, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:1368311 original size:24 final size:24
Alignment explanation
Indices: 1368278--1368336 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
1368268 TTTCAAAAAA
1368278 CAAAACAAAAAAAAAAAAAAAAAGC
1 CAAAA-AAAAAAAAAAAAAAAAAGC
***
1368303 CAAAAAAAAAGCCAAAAAAAAAGC
1 CAAAAAAAAAAAAAAAAAAAAAGC
1368327 CAAAAAAAAA
1 CAAAAAAAAA
1368337 GCCAAAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.81, C:0.14, G:0.05, T:0.00
Consensus pattern (24 bp):
CAAAAAAAAAAAAAAAAAAAAAGC
Found at i:1368337 original size:12 final size:12
Alignment explanation
Indices: 1368292--1368343 Score: 104
Period size: 12 Copynumber: 4.3 Consensus size: 12
1368282 ACAAAAAAAA
1368292 AAAAAAAAAGCC
1 AAAAAAAAAGCC
1368304 AAAAAAAAAGCC
1 AAAAAAAAAGCC
1368316 AAAAAAAAAGCC
1 AAAAAAAAAGCC
1368328 AAAAAAAAAGCC
1 AAAAAAAAAGCC
1368340 AAAA
1 AAAA
1368344 TTTCAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.77, C:0.15, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGCC
Found at i:1372611 original size:22 final size:22
Alignment explanation
Indices: 1372586--1372627 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1372576 CAATTCATTT
1372586 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
1372608 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
1372628 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:1376949 original size:17 final size:17
Alignment explanation
Indices: 1376904--1376953 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
1376894 ACCCGGCCCG
* * *
1376904 TTGACCAACATTGACCG
1 TTGACCAGCGTTGACCA
*
1376921 TTGATC-GCGTTGACCA
1 TTGACCAGCGTTGACCA
1376937 TTGACCAGCGTTGACCA
1 TTGACCAGCGTTGACCA
1376954 CCGTTGACCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (17 bp):
TTGACCAGCGTTGACCA
Found at i:1379237 original size:24 final size:24
Alignment explanation
Indices: 1379180--1379287 Score: 121
Period size: 24 Copynumber: 4.5 Consensus size: 24
1379170 TAATGTTTTA
* * *
1379180 TCTGATTTCTGATTTGAATTTTAT
1 TCTGATTTCTGATCTGAATTCTGT
*
1379204 T-TGATTTCTGATCTGAATTTTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
1379227 TCTGATTTCTGATCTGGACTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
1379251 TCTGATATCTGATATGAATTCTGCT
1 TCTGATTTCTGATCTGAATTCTG-T
1379276 T-TGATTTCTGAT
1 TCTGATTTCTGAT
1379288 ATCTCCGTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
23 21 0.29
24 49 0.68
25 2 0.03
ACGTcount: A:0.19, C:0.13, G:0.17, T:0.52
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:1379242 original size:12 final size:12
Alignment explanation
Indices: 1379179--1379287 Score: 73
Period size: 12 Copynumber: 9.2 Consensus size: 12
1379169 TTAATGTTTT
1379179 ATCTGATTTCTG
1 ATCTGATTTCTG
*
1379191 ATTTGAATTT-T-
1 ATCTG-ATTTCTG
*
1379202 ATTTGATTTCTG
1 ATCTGATTTCTG
1379214 ATCTGAATTT-TG
1 ATCTG-ATTTCTG
*
1379226 TTCTGATTTCTG
1 ATCTGATTTCTG
*
1379238 ATCTGGA-CTCTG
1 ATCT-GATTTCTG
* *
1379250 TTCTGATATCTG
1 ATCTGATTTCTG
* *
1379262 ATATGAATTCTG
1 ATCTGATTTCTG
* *
1379274 CTTTGATTTCTG
1 ATCTGATTTCTG
1379286 AT
1 AT
1379288 ATCTCCGTTT
Statistics
Matches: 75, Mismatches: 15, Indels: 14
0.72 0.14 0.13
Matches are distributed among these distances:
10 4 0.05
11 12 0.16
12 49 0.65
13 10 0.13
ACGTcount: A:0.19, C:0.13, G:0.17, T:0.51
Consensus pattern (12 bp):
ATCTGATTTCTG
Found at i:1380679 original size:42 final size:41
Alignment explanation
Indices: 1380576--1380684 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 41
1380566 GCTAGCATTG
* * **
1380576 ATGCACTTCGATAAGAAACGAAGGAGACAAGAGAAGTGACTC
1 ATGCACTTCGA-AAGAAATGAAGGAAACAAGAGAAACGACTC
*
1380618 ATGCA-TTCTAATAGAAAATGAAGGAAACAAGAGAAACGACTC
1 ATGCACTTCGAA-AG-AAATGAAGGAAACAAGAGAAACGACTC
1380660 ATGCACTTCGACAAGAAATG-AGGAA
1 ATGCACTTCGA-AAGAAATGAAGGAA
1380685 GAGTGTTCAG
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
40 1 0.02
41 11 0.19
42 38 0.67
43 6 0.11
44 1 0.02
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.16
Consensus pattern (41 bp):
ATGCACTTCGAAAGAAATGAAGGAAACAAGAGAAACGACTC
Found at i:1388535 original size:20 final size:20
Alignment explanation
Indices: 1388498--1388535 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1388488 CTTTAGATGT
*
1388498 TTGAATTAATAAATTTTAAG
1 TTGAATTAATAAACTTTAAG
*
1388518 TTGAATTAATAACCTTTA
1 TTGAATTAATAAACTTTA
1388536 CATTCATTCA
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:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (20 bp):
TTGAATTAATAAACTTTAAG
Found at i:1388566 original size:27 final size:27
Alignment explanation
Indices: 1388535--1388717 Score: 143
Period size: 27 Copynumber: 6.4 Consensus size: 27
1388525 AATAACCTTT
1388535 ACATTCATTCAATTATTGATATTAATC
1 ACATTCATTCAATTATTGATATTAATC
*
1388562 ACATTAATTCAACTT-TTGATATTAATC
1 ACATTCATTCAA-TTATTGATATTAATC
* ** *
1388589 ACATTCATTAAAATATAGCGTCAACAAATATTCATC
1 ACATTCATT-CAAT-TA---T----TGATATTAATC
* * *
1388625 ATATTAATTCAAATATTGATATTAATC
1 ACATTCATTCAATTATTGATATTAATC
* *
1388652 ACATTCATTCAAATATTGATATTAATT
1 ACATTCATTCAATTATTGATATTAATC
* * * *
1388679 ACATTAATTCAACTATTGACATTAATA
1 ACATTCATTCAATTATTGATATTAATC
1388706 ACATTCATTCAA
1 ACATTCATTCAA
1388718 ATATAGCGTC
Statistics
Matches: 124, Mismatches: 21, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
27 98 0.79
28 5 0.04
31 1 0.01
32 1 0.01
34 2 0.02
35 2 0.02
36 15 0.12
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.40
Consensus pattern (27 bp):
ACATTCATTCAATTATTGATATTAATC
Found at i:1388636 original size:63 final size:63
Alignment explanation
Indices: 1388553--1388753 Score: 231
Period size: 63 Copynumber: 3.3 Consensus size: 63
1388543 TCAATTATTG
* *
1388553 ATATTAATCACATTAATTCAACTTTTGATATTAATCACATTCATTAAAATATAGCGTCAACAA
1 ATATTAATCACATTAATTCAACTATTGATATTAATCACATTCATTCAAATATAGCGTCAACAA
* * * *
1388616 ATATTCATCATATTAATTCAAATATTGATATTAATCACATTCATTCAAATAT----T-----G
1 ATATTAATCACATTAATTCAACTATTGATATTAATCACATTCATTCAAATATAGCGTCAACAA
* * *
1388670 ATATTAATTACATTAATTCAACTATTGACATTAATAACATTCATTCAAATATAGCGTCAACAA
1 ATATTAATCACATTAATTCAACTATTGATATTAATCACATTCATTCAAATATAGCGTCAACAA
** *
1388733 ATATCCATCATATTAATTCAA
1 ATATTAATCACATTAATTCAA
1388754 AAAAATAGAT
Statistics
Matches: 112, Mismatches: 17, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
54 46 0.41
58 1 0.01
59 1 0.01
63 64 0.57
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.38
Consensus pattern (63 bp):
ATATTAATCACATTAATTCAACTATTGATATTAATCACATTCATTCAAATATAGCGTCAACAA
Found at i:1388742 original size:117 final size:117
Alignment explanation
Indices: 1388535--1388754 Score: 377
Period size: 117 Copynumber: 1.9 Consensus size: 117
1388525 AATAACCTTT
* * * *
1388535 ACATTCATTCAATTATTGATATTAATCACATTAATTCAACTTTTGATATTAATCACATTCATTAA
1 ACATTCATTCAAATATTGATATTAATCACATTAATTCAACTATTGACATTAATAACATTCATTAA
*
1388600 AATATAGCGTCAACAAATATTCATCATATTAATTCAAATATTGATATTAATC
66 AATATAGCGTCAACAAATATCCATCATATTAATTCAAATATTGATATTAATC
* *
1388652 ACATTCATTCAAATATTGATATTAATTACATTAATTCAACTATTGACATTAATAACATTCATTCA
1 ACATTCATTCAAATATTGATATTAATCACATTAATTCAACTATTGACATTAATAACATTCATTAA
1388717 AATATAGCGTCAACAAATATCCATCATATTAATTCAAA
66 AATATAGCGTCAACAAATATCCATCATATTAATTCAAA
1388755 AAAATAGATA
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 96 1.00
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.38
Consensus pattern (117 bp):
ACATTCATTCAAATATTGATATTAATCACATTAATTCAACTATTGACATTAATAACATTCATTAA
AATATAGCGTCAACAAATATCCATCATATTAATTCAAATATTGATATTAATC
Found at i:1391612 original size:31 final size:31
Alignment explanation
Indices: 1391561--1391652 Score: 93
Period size: 33 Copynumber: 3.0 Consensus size: 31
1391551 CAAAATTATA
1391561 ATAAATATTATTA-AAT--TTTTTAATAAAAT
1 ATAAATA-TATTACAATAGTTTTTAATAAAAT
* *
1391590 ATAAATATATTACCAATATTTTTTATTATAAAT
1 ATAAATATATTA-CAATAGTTTTTAATA-AAAT
*
1391623 GTAAATATATTAACAATAGTTTTT-ATAAAA
1 ATAAATATATT-ACAATAGTTTTTAATAAAA
1391653 CTAATGCTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
28 5 0.09
29 7 0.13
30 3 0.06
31 3 0.06
32 10 0.19
33 24 0.45
34 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (31 bp):
ATAAATATATTACAATAGTTTTTAATAAAAT
Found at i:1391646 original size:34 final size:32
Alignment explanation
Indices: 1391575--1391652 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 32
1391565 ATATTATTAA
*
1391575 ATTTTTTAATAAAATATAAATATATTACCAAT
1 ATTTTTTAATAAAATATAAATATATTAACAAT
* *
1391607 ATTTTTTATTATAAATGTAAATATATTAACAAT
1 ATTTTTTAATA-AAATATAAATATATTAACAAT
*
1391640 AGTTTTT-ATAAAA
1 ATTTTTTAATAAAA
1391653 CTAATGCTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
31 3 0.08
32 12 0.30
33 25 0.62
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (32 bp):
ATTTTTTAATAAAATATAAATATATTAACAAT
Found at i:1391840 original size:37 final size:38
Alignment explanation
Indices: 1391781--1391884 Score: 140
Period size: 37 Copynumber: 2.8 Consensus size: 38
1391771 TTCAACAACC
* *
1391781 AACCACCAACCTACCCA-GGTTATTAATGGATAATTAAT
1 AACCACCAACATA-CTAGGGTTATTAATGGATAATTAAT
*
1391819 AACCA-CAACATACTCGGGTTATTAATGGATAATTAAT
1 AACCACCAACATACTAGGGTTATTAATGGATAATTAAT
* *
1391856 AACCACCAACTTACTAGGTTTATTAATGG
1 AACCACCAACATACTAGGGTTATTAATGG
1391885 TATCAATATT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
36 1 0.02
37 32 0.55
38 25 0.43
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.29
Consensus pattern (38 bp):
AACCACCAACATACTAGGGTTATTAATGGATAATTAAT
Found at i:1391932 original size:22 final size:21
Alignment explanation
Indices: 1391889--1391932 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1391879 TAATGGTATC
*
1391889 AATATTTTTTTCATTATAATA
1 AATATTTTTTTCATCATAATA
* *
1391910 AATATTATTTTTCGTCATTATA
1 AATATT-TTTTTCATCATAATA
1391932 A
1 A
1391933 TAAAAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (21 bp):
AATATTTTTTTCATCATAATA
Found at i:1392159 original size:25 final size:25
Alignment explanation
Indices: 1392131--1392190 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
1392121 TAATGGTGCC
*
1392131 ATTATTTTTTGTCATTATAATAAAT
1 ATTATTTTTCGTCATTATAATAAAT
1392156 ATTATTTTTCGTCATTATAATAAAT
1 ATTATTTTTCGTCATTATAATAAAT
1392181 ATTATTTTTC
1 ATTATTTTTC
1392191 TACTACAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (25 bp):
ATTATTTTTCGTCATTATAATAAAT
Found at i:1396067 original size:3 final size:3
Alignment explanation
Indices: 1396059--1396083 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1396049 TAATCCCAAC
1396059 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
1396084 GAGTGTTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1397206 original size:2 final size:2
Alignment explanation
Indices: 1397199--1397231 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1397189 TAGATGTTAC
1397199 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1397232 ATAGTGCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1398013 original size:28 final size:28
Alignment explanation
Indices: 1397973--1398087 Score: 144
Period size: 28 Copynumber: 4.1 Consensus size: 28
1397963 TGGTTCGCTG
1397973 GAATGTTTATGAGGGAATTAGAATCTGT
1 GAATGTTTATGAGGGAATTAGAATCTGT
** * **
1398001 GAATGTTTATGA-GGTTTTTGGTTC-GCT
1 GAATGTTTATGAGGGAATTAGAATCTG-T
1398028 GGAATGTTTATGAGGGAATTAGAATCTGT
1 -GAATGTTTATGAGGGAATTAGAATCTGT
*
1398057 GAATGTTTATGAGGGAATTGGAATCTGT
1 GAATGTTTATGAGGGAATTAGAATCTGT
1398085 GAA
1 GAA
1398088 GAAATTGAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.01
27 8 0.11
28 54 0.75
29 8 0.11
30 1 0.01
ACGTcount: A:0.28, C:0.04, G:0.30, T:0.37
Consensus pattern (28 bp):
GAATGTTTATGAGGGAATTAGAATCTGT
Found at i:1398024 original size:56 final size:56
Alignment explanation
Indices: 1397957--1398070 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
1397947 ACACTTAGGT
1397957 GGTTTTTGGTTCGCTGGAATGTTTATGAGGGAATTAGAATCTGTGAATGTTTATGA
1 GGTTTTTGGTTCGCTGGAATGTTTATGAGGGAATTAGAATCTGTGAATGTTTATGA
1398013 GGTTTTTGGTTCGCTGGAATGTTTATGAGGGAATTAGAATCTGTGAATGTTTATGA
1 GGTTTTTGGTTCGCTGGAATGTTTATGAGGGAATTAGAATCTGTGAATGTTTATGA
1398069 GG
1 GG
1398071 GAATTGGAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.23, C:0.05, G:0.32, T:0.40
Consensus pattern (56 bp):
GGTTTTTGGTTCGCTGGAATGTTTATGAGGGAATTAGAATCTGTGAATGTTTATGA
Found at i:1398113 original size:18 final size:18
Alignment explanation
Indices: 1398072--1398114 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1398062 TTTATGAGGG
* *
1398072 AATTGGAATCTGTGAAGA
1 AATTGAAATCTGTCAAGA
*
1398090 AATTGAAATCTGTCAGGA
1 AATTGAAATCTGTCAAGA
*
1398108 ATTTGAA
1 AATTGAA
1398115 TTCAATTTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (18 bp):
AATTGAAATCTGTCAAGA
Found at i:1398536 original size:205 final size:206
Alignment explanation
Indices: 1398183--1398584 Score: 752
Period size: 205 Copynumber: 2.0 Consensus size: 206
1398173 ATGTTTGGTC
*
1398183 ATGTCAGATGAATTTGATTTCAGTAATGTAAAATGACAGAATTGTCCTTCTTATTTTTTTGCTTT
1 ATGTCAGATGAATTTGATTTCAGTAATGTAAAATGACAGAATTGCCCTTCTTATTTTTTTGCTTT
*
1398248 ATTTTAGTTTGTTTTACAACTTACATGTAGTAATATATTATAAAAAATTAAAAAATATTAATTTT
66 ATTTTAGATTGTTTTACAACTTACATGTAGTAATATATTATAAAAAATTAAAAAATATTAATTTT
1398313 TTATTTTATTGATTGATTATTCATTTCAATAAATTATAAAAATCATTTTTATTCAATAAAAACAT
131 TTATTTTATTGATTGATTATTCATTTCAATAAATTATAAAAATCATTTTTATTCAATAAAAACAT
1398378 TGTTCGCAGTT
196 TGTTCGCAGTT
*
1398389 ATGTCAGATGGATTTGATTTCAGTAATGTAAAATGACAGAATTGCCCTTCTTATTTTTTTGCTTT
1 ATGTCAGATGAATTTGATTTCAGTAATGTAAAATGACAGAATTGCCCTTCTTATTTTTTTGCTTT
*
1398454 ATTTTA-ATTGTTTTACAACTTACATGTAGTAATATATTATAAAAAATTAAAAATTATTAATTTT
66 ATTTTAGATTGTTTTACAACTTACATGTAGTAATATATTATAAAAAATTAAAAAATATTAATTTT
*
1398518 TTATTTTATTGATTGATTATTCATTTCAATAAATTATAAAAATCATTTTTATTCAATAAAAATAT
131 TTATTTTATTGATTGATTATTCATTTCAATAAATTATAAAAATCATTTTTATTCAATAAAAACAT
1398583 TG
196 TG
1398585 ACTTAATTGA
Statistics
Matches: 191, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
205 122 0.64
206 69 0.36
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (206 bp):
ATGTCAGATGAATTTGATTTCAGTAATGTAAAATGACAGAATTGCCCTTCTTATTTTTTTGCTTT
ATTTTAGATTGTTTTACAACTTACATGTAGTAATATATTATAAAAAATTAAAAAATATTAATTTT
TTATTTTATTGATTGATTATTCATTTCAATAAATTATAAAAATCATTTTTATTCAATAAAAACAT
TGTTCGCAGTT
Found at i:1398770 original size:32 final size:33
Alignment explanation
Indices: 1398693--1398782 Score: 92
Period size: 38 Copynumber: 2.6 Consensus size: 33
1398683 TTTTCACCCT
*
1398693 AAACCCGAACTCGACCCAAATATCACACTTAAAAA
1 AAACCCG-ACTCGACCCGAATATCACACTT-AAAA
*
1398728 AACCTGACCCGGCTCGACCCGAATATCACACTT-AAA
1 AA----ACCCGACTCGACCCGAATATCACACTTAAAA
*
1398764 AAACCCGACTTGACCCGAA
1 AAACCCGACTCGACCCGAA
1398783 AAAAATAAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
32 15 0.32
35 2 0.04
36 5 0.11
38 20 0.43
39 5 0.11
ACGTcount: A:0.40, C:0.34, G:0.11, T:0.14
Consensus pattern (33 bp):
AAACCCGACTCGACCCGAATATCACACTTAAAA
Found at i:1400227 original size:43 final size:43
Alignment explanation
Indices: 1400165--1400251 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
1400155 TATTTATTCT
* * *
1400165 CTCATATTTTCTTATGTCATGAGTTCTAGATTCACTAGGAGCA
1 CTCATATTTTCTTAGGTCATGAATTCTAGACTCACTAGGAGCA
1400208 CTCATATTTTCTTAGGTCATGAATTCTAGACTCACTAGGAGCA
1 CTCATATTTTCTTAGGTCATGAATTCTAGACTCACTAGGAGCA
1400251 C
1 C
1400252 ACTTTGCTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (43 bp):
CTCATATTTTCTTAGGTCATGAATTCTAGACTCACTAGGAGCA
Found at i:1400601 original size:20 final size:20
Alignment explanation
Indices: 1400576--1400625 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1400566 CTGAACAAGT
1400576 AGTATCGATATTGTTCTTAC
1 AGTATCGATATTGTTCTTAC
1400596 AGTATCGATATTGTTCTTAC
1 AGTATCGATATTGTTCTTAC
1400616 AGTATCGATA
1 AGTATCGATA
1400626 CTAATTGAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (20 bp):
AGTATCGATATTGTTCTTAC
Found at i:1403852 original size:37 final size:37
Alignment explanation
Indices: 1403811--1403884 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
1403801 CATTGTTAGG
* *
1403811 AATTTATAATGAAAAACATACACAACGAAATCAACAT
1 AATTTATAATGAAAAACAAACACAACAAAATCAACAT
* *
1403848 AATTTATAGTGAAAAACAAACACAATAAAATCAACAT
1 AATTTATAATGAAAAACAAACACAACAAAATCAACAT
1403885 GAAATACGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.58, C:0.15, G:0.05, T:0.22
Consensus pattern (37 bp):
AATTTATAATGAAAAACAAACACAACAAAATCAACAT
Found at i:1405938 original size:59 final size:59
Alignment explanation
Indices: 1405849--1405993 Score: 177
Period size: 59 Copynumber: 2.4 Consensus size: 59
1405839 ATTGGTTTCT
* *
1405849 AAACTTTTAA-ATATTCTAATTTCATCCCTAAACTATGA-CTATTATTCTAAACTAGTCCTC
1 AAACTTTTAACAT-TT-TAATTTCATCCCTAAACTATGACCT-TCATTCTAAACTAGTCCCC
* *
1405909 AAACTTTTAACATTTTAATTTCATCCCTAAACTATGACCTTCATTCTAAATTATTCCCC
1 AAACTTTTAACATTTTAATTTCATCCCTAAACTATGACCTTCATTCTAAACTAGTCCCC
**
1405968 AAACTTTTTGAACATTCCAATTTCAT
1 AAAC-TTTT-AACATTTTAATTTCAT
1405994 TCTAAATTAT
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
59 41 0.55
60 18 0.24
61 16 0.21
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.41
Consensus pattern (59 bp):
AAACTTTTAACATTTTAATTTCATCCCTAAACTATGACCTTCATTCTAAACTAGTCCCC
Found at i:1406193 original size:60 final size:59
Alignment explanation
Indices: 1406119--1406274 Score: 183
Period size: 59 Copynumber: 2.6 Consensus size: 59
1406109 TATTTGGATG
* *
1406119 AATTT-GGAGATGAAATTGGAATATTCAAAAGTTTGGAG-ACTAATTTAGAAAGAGGGTCAT
1 AATTTAGG-GATGAAATTGGAATATTCAAAAGTTT-AAGTACTAATTTAG-AAGAGAGTCAT
* * *
1406179 AGTTTAGGGATGAAATTAGAATGA-TCAAAAGTTTAAGTACTAATTTAGATGAGAGTCAT
1 AATTTAGGGATGAAATTGGAAT-ATTCAAAAGTTTAAGTACTAATTTAGAAGAGAGTCAT
* * *
1406238 AATTTAGGGATGAAATTGAAATATTTAAAATTTTAAG
1 AATTTAGGGATGAAATTGGAATATTCAAAAGTTTAAG
1406275 GACCGATTTA
Statistics
Matches: 82, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
58 1 0.01
59 41 0.50
60 37 0.45
61 3 0.04
ACGTcount: A:0.42, C:0.04, G:0.22, T:0.33
Consensus pattern (59 bp):
AATTTAGGGATGAAATTGGAATATTCAAAAGTTTAAGTACTAATTTAGAAGAGAGTCAT
Found at i:1409407 original size:12 final size:11
Alignment explanation
Indices: 1409390--1409435 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 11
1409380 TAATCCCCAA
1409390 ATTAAAAATTAT
1 ATTAAAAA-TAT
1409402 ATT-AAAA-AT
1 ATTAAAAATAT
*
1409411 ATTAAAAACACT
1 ATTAAAAATA-T
1409423 ATTAAAAATAT
1 ATTAAAAATAT
1409434 AT
1 AT
1409436 CACAAATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
9 5 0.17
10 4 0.13
11 8 0.27
12 13 0.43
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (11 bp):
ATTAAAAATAT
Found at i:1409842 original size:23 final size:23
Alignment explanation
Indices: 1409780--1409857 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
1409770 TTGTAGAAAC
*
1409780 AGAGTTTTCCGGCTCTGGTAAAT
1 AGAGTTTTTCGGCTCTGGTAAAT
* *
1409803 TGAG-CTTTCTGGCTCTGGTAAAT
1 AGAGTTTTTC-GGCTCTGGTAAAT
* *
1409826 AGAGTTTTTCGGTTCTGATAAAT
1 AGAGTTTTTCGGCTCTGGTAAAT
*
1409849 ACAGTTTTT
1 AGAGTTTTT
1409858 TATTCTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
22 3 0.07
23 38 0.84
24 4 0.09
ACGTcount: A:0.22, C:0.14, G:0.23, T:0.41
Consensus pattern (23 bp):
AGAGTTTTTCGGCTCTGGTAAAT
Found at i:1413953 original size:22 final size:23
Alignment explanation
Indices: 1413906--1413954 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1413896 GTTTTCCGAC
*
1413906 TCTAGTAAACAAAGTTTTTCTGT
1 TCTAGTAAACAAAGTTTTTCTAT
**
1413929 TCTAGTAAACATGGTTTTT-TAT
1 TCTAGTAAACAAAGTTTTTCTAT
1413951 TCTA
1 TCTA
1413955 AAATTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (23 bp):
TCTAGTAAACAAAGTTTTTCTAT
Found at i:1415046 original size:16 final size:18
Alignment explanation
Indices: 1415021--1415062 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
1415011 TTATTTAAAA
1415021 AATATATTAATTTT-TTT-
1 AATAT-TTAATTTTATTTG
1415038 AATATTTAATTTTATTTG
1 AATATTTAATTTTATTTG
1415056 AATATTT
1 AATATTT
1415063 GAGTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
AATATTTAATTTTATTTG
Found at i:1416579 original size:60 final size:59
Alignment explanation
Indices: 1416505--1416880 Score: 297
Period size: 60 Copynumber: 6.3 Consensus size: 59
1416495 CAAGTGAATA
* *
1416505 TTTGTAACTTTTAATAATCGATGGACTTAATAAAGCAACACCCTATAGTTGAAAGATTAT
1 TTTGTAACTTTTAATAGTCGA-GGACTTAATAAAGCAACACCCTATAGTTGAAAGATCAT
** * * * *
1416565 TTTACAACTTTTAATAGTCAGAGAACTTAACAAAGCAACGCCCTATAG-TCAAAGGATCAT
1 TTTGTAACTTTTAATAGTC-GAGGACTTAATAAAGCAACACCCTATAGTTGAAA-GATCAT
* * * * * * * *
1416625 TTTGCAACTTTTAATAGTCAAATGACTTAACAAAACAATACCCTATAG-TCAGAGGATCAT
1 TTTGTAACTTTTAATAGTC-GAGGACTTAATAAAGCAACACCCTATAGTTGA-AAGATCAT
* ** * *
1416685 TTTGTAACTTTTAATAGTTGAGAGACTTAATAAAGCAACGTCCTATAGTTGTAGGATCAT
1 TTTGTAACTTTTAATAGTCGAG-GACTTAATAAAGCAACACCCTATAGTTGAAAGATCAT
* ** * * ** * * *
1416745 TTTGTAACTTTTAATAATCGATAAACTCAATAAAGTAATTCTCTATAATTGAATGATCAT
1 TTTGTAACTTTTAATAGTCGA-GGACTTAATAAAGCAACACCCTATAGTTGAAAGATCAT
* ** ** * * * *
1416805 TTTGTAACTTTTAATAGTCGAGAGACTCAATAAAATAACTTCTTATAATTAAAAGATTAT
1 TTTGTAACTTTTAATAGTCGAG-GACTTAATAAAGCAACACCCTATAGTTGAAAGATCAT
*
1416865 TTTATAACTTTTAATA
1 TTTGTAACTTTTAATA
1416881 ATTAAATAAC
Statistics
Matches: 257, Mismatches: 52, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
59 5 0.02
60 248 0.96
61 4 0.02
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (59 bp):
TTTGTAACTTTTAATAGTCGAGGACTTAATAAAGCAACACCCTATAGTTGAAAGATCAT
Found at i:1416893 original size:60 final size:59
Alignment explanation
Indices: 1416739--1416917 Score: 184
Period size: 60 Copynumber: 3.0 Consensus size: 59
1416729 ATAGTTGTAG
* * * *
1416739 GATCATTTTGTAACTTTTAATAA-TCGATAAACTCAATAAAGTAATTCTCTATAATTGAAT
1 GATCATTTTGTAACTTTTAATAATTAGAT-AACTCAATAAAATAATTCT-TATAATTAAAA
* * *
1416799 GATCATTTTGTAACTTTTAATAGTCGAGA-GACTCAATAAAATAACTTCTTATAATTAAAA
1 GATCATTTTGTAACTTTTAATAAT-TAGATAACTCAATAAAATAA-TTCTTATAATTAAAA
* * * * *
1416859 GATTATTTTATAACTTTTAATAATTAAATAACTCAACAAAA-AATCTCTTATAATCAAAA
1 GATCATTTTGTAACTTTTAATAATTAGATAACTCAATAAAATAAT-TCTTATAATTAAAA
1416918 TACTATTTAT
Statistics
Matches: 99, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
58 1 0.01
59 17 0.17
60 75 0.76
61 4 0.04
62 2 0.02
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.38
Consensus pattern (59 bp):
GATCATTTTGTAACTTTTAATAATTAGATAACTCAATAAAATAATTCTTATAATTAAAA
Done.