Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008926.1 Hibiscus syriacus cultivar Beakdansim tig00112231_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: 4069050
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 20
Found at i:1476572 original size:42 final size:42
Alignment explanation
Indices: 1476482--1476582 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
1476472 TGGTGGGAGA
*** * * **
1476482 GACCTCTTGAAATTTGACAGGGGCCTCTTGAACGGTGGGAGG
1 GACCTCTTGAACGATGAGAGGGGCCTCTTGAACGATGAAAGG
1476524 GACCTCTTGAACGATGAGAGGGGCCTCTTGAACGATAGAAAGG
1 GACCTCTTGAACGATGAGAGGGGCCTCTTGAACGAT-GAAAGG
*
1476567 G-CCTCTTGAATGATGA
1 GACCTCTTGAACGATGA
1476583 TAGGTGAATC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
42 45 0.90
43 5 0.10
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.23
Consensus pattern (42 bp):
GACCTCTTGAACGATGAGAGGGGCCTCTTGAACGATGAAAGG
Found at i:1476968 original size:42 final size:43
Alignment explanation
Indices: 1476876--1476971 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 43
1476866 GTAGAGCGGC
**
1476876 TACCTCATCACGTAAAGTAGATACCTCACCACGTAAAGCACCA
1 TACCTCATCACGTAAAACAGATACCTCACCACGTAAAGCACCA
** ** * *
1476919 T-TGTCATCACGTAAAACATCTACCTTACCACGTAAAG-ACCG
1 TACCTCATCACGTAAAACAGATACCTCACCACGTAAAGCACCA
1476960 TACCTCATCACG
1 TACCTCATCACG
1476972 CCATGCACCA
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
41 4 0.10
42 37 0.88
43 1 0.02
ACGTcount: A:0.34, C:0.32, G:0.11, T:0.22
Consensus pattern (43 bp):
TACCTCATCACGTAAAACAGATACCTCACCACGTAAAGCACCA
Found at i:1476971 original size:21 final size:22
Alignment explanation
Indices: 1476876--1477058 Score: 82
Period size: 21 Copynumber: 8.7 Consensus size: 22
1476866 GTAGAGCGGC
*
1476876 TACCTCATCACGTAAAGTA--G
1 TACCTCATCACGTAAAGCACCG
* *
1476896 ATACCTCACCACGTAAAGCACCA
1 -TACCTCATCACGTAAAGCACCG
** * *
1476919 T-TGTCATCACGTAAAACATC-
1 TACCTCATCACGTAAAGCACCG
* *
1476939 TACCTTACCACGTAAAG-ACCG
1 TACCTCATCACGTAAAGCACCG
** * *
1476960 TACCTCATCACGCCATGCACCA
1 TACCTCATCACGTAAAGCACCG
** * *
1476982 T-TTTCGTCACGTAAAGTACCG
1 TACCTCATCACGTAAAGCACCG
**
1477003 -ACCTCATCAC-TCAAATTACCG
1 TACCTCATCACGT-AAAGCACCG
*
1477024 -ACCTCATCAC-TCAAAGCACTG
1 TACCTCATCACGT-AAAGCACCG
1477045 -ACCTCATCACGTAA
1 TACCTCATCACGTAA
1477059 CTCCCCTAAC
Statistics
Matches: 119, Mismatches: 35, Indels: 16
0.70 0.21 0.09
Matches are distributed among these distances:
20 4 0.03
21 109 0.92
22 6 0.05
ACGTcount: A:0.33, C:0.34, G:0.11, T:0.22
Consensus pattern (22 bp):
TACCTCATCACGTAAAGCACCG
Found at i:1479036 original size:22 final size:22
Alignment explanation
Indices: 1479006--1479085 Score: 124
Period size: 22 Copynumber: 3.6 Consensus size: 22
1478996 GATGGAGATA
1479006 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* * *
1479028 GACGTATTTCGCTGGAGACGGG
1 GACGGATTTCGCCGGAGATGGG
1479050 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1479072 GACGGATGTCGCCG
1 GACGGATTTCGCCG
1479086 TAGAGAGTGA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.17, C:0.20, G:0.44, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1488330 original size:17 final size:18
Alignment explanation
Indices: 1488308--1488351 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
1488298 CGGGTCGGGT
1488308 ATATATATTTAA-ATTAA
1 ATATATATTTAATATTAA
* *
1488325 ATATATA-TAAATATTAT
1 ATATATATTTAATATTAA
1488342 ATATATATTT
1 ATATATATTT
1488352 TTAATTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 3 0.14
17 18 0.82
18 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATATTTAATATTAA
Found at i:1488517 original size:30 final size:30
Alignment explanation
Indices: 1488462--1488532 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
1488452 ACTAAACCCG
** *
1488462 TCCCCGTTTAACATAAATGGGTTTTCTCCA
1 TCCCCGTTTAACATAAACAGGTTTTCCCCA
* * *
1488492 TCCCCGTTTAGCATAAACAGTTTTTCCCCG
1 TCCCCGTTTAACATAAACAGGTTTTCCCCA
*
1488522 TCCTCGTTTAA
1 TCCCCGTTTAA
1488533 TTCGGTTTTC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.21, C:0.30, G:0.13, T:0.37
Consensus pattern (30 bp):
TCCCCGTTTAACATAAACAGGTTTTCCCCA
Found at i:1491410 original size:44 final size:44
Alignment explanation
Indices: 1491361--1491461 Score: 139
Period size: 44 Copynumber: 2.3 Consensus size: 44
1491351 ATACCATGAT
** *
1491361 CGGTATCGATACTACTTTACATAGTAGTATCGATACTCCCTGGA
1 CGGTATCGATACTACACTACAAAGTAGTATCGATACTCCCTGGA
* *
1491405 CGGTATCAATACTACACTACAAAGTAGTATCGATACTCCCTGGC
1 CGGTATCGATACTACACTACAAAGTAGTATCGATACTCCCTGGA
**
1491449 CAATATCGATACT
1 CGGTATCGATACT
1491462 GTTGGATTGA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29
Consensus pattern (44 bp):
CGGTATCGATACTACACTACAAAGTAGTATCGATACTCCCTGGA
Found at i:1497283 original size:21 final size:21
Alignment explanation
Indices: 1497234--1497289 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
1497224 CTACTCTTGC
1497234 TAGGTATCGATACTACTAGCA
1 TAGGTATCGATACTACTAGCA
* *
1497255 TA-GTATCGATATTACT-TCAA
1 TAGGTATCGATACTACTAGC-A
1497275 TAGGTATCGATACTA
1 TAGGTATCGATACTA
1497290 TTCTTAAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 16 0.53
21 13 0.43
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (21 bp):
TAGGTATCGATACTACTAGCA
Found at i:1499227 original size:18 final size:18
Alignment explanation
Indices: 1499206--1499246 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1499196 GATTTGGTTA
*
1499206 TTTGAATATTTG-GTTGTT
1 TTTGAATACTTGTG-TGTT
1499224 TTTGAATACTTGTGTGTT
1 TTTGAATACTTGTGTGTT
1499242 TTTGA
1 TTTGA
1499247 TTGATTATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.17, C:0.02, G:0.22, T:0.59
Consensus pattern (18 bp):
TTTGAATACTTGTGTGTT
Found at i:1500072 original size:44 final size:44
Alignment explanation
Indices: 1500023--1500120 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
1500013 CCATGATCGA
** * * *
1500023 TATCGATACTACTTTACATAGTAGTATCGATACTCCCTGG-ACGG
1 TATCGATACTACACTACAAAGTAGTATCGATACTCCATGGCA-AG
1500067 TATCGATACTACACTACAAAGTAGTATCGATACTCCATGGCAAG
1 TATCGATACTACACTACAAAGTAGTATCGATACTCCATGGCAAG
1500111 TATCGATACT
1 TATCGATACT
1500121 GTTGGATTGC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 47 0.98
45 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (44 bp):
TATCGATACTACACTACAAAGTAGTATCGATACTCCATGGCAAG
Found at i:1501182 original size:3 final size:3
Alignment explanation
Indices: 1501174--1501202 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1501164 TACTTATTTG
1501174 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1501203 GTTAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1501476 original size:44 final size:44
Alignment explanation
Indices: 1501428--1501518 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 44
1501418 GGAAACATTG
1501428 ATCCACCACCTTCTGTGATGAAATCGAACAAAGTGATGATGATA
1 ATCCACCACCTTCTGTGATGAAATCGAACAAAGTGATGATGATA
* * *
1501472 ATCCACCTCTTTCTGTGATGAAATCGAACAAAGTGATGATGCTA
1 ATCCACCACCTTCTGTGATGAAATCGAACAAAGTGATGATGATA
1501516 ATC
1 ATC
1501519 TAACTCCTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (44 bp):
ATCCACCACCTTCTGTGATGAAATCGAACAAAGTGATGATGATA
Found at i:1501533 original size:44 final size:44
Alignment explanation
Indices: 1501436--1501533 Score: 151
Period size: 44 Copynumber: 2.2 Consensus size: 44
1501426 TGATCCACCA
*
1501436 CCTTCTGTGATGAAATCGAACAAAGTGATGATGATAATCCACCT
1 CCTTCTGTGATGAAATCGAACAAAGTGATGATGATAATCCAACT
* * *
1501480 CTTTCTGTGATGAAATCGAACAAAGTGATGATGCTAATCTAACT
1 CCTTCTGTGATGAAATCGAACAAAGTGATGATGATAATCCAACT
*
1501524 CCTTATGTGA
1 CCTTCTGTGA
1501534 AGGACGAGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (44 bp):
CCTTCTGTGATGAAATCGAACAAAGTGATGATGATAATCCAACT
Found at i:1501794 original size:117 final size:117
Alignment explanation
Indices: 1501637--1502019 Score: 464
Period size: 117 Copynumber: 3.3 Consensus size: 117
1501627 GTACTGATGT
* * * * * * * *
1501637 TGATCCAACTTCTTGTGTGATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATCATGAACTTC
1 TGATCCACCTCCTTTTGTGATGGATTTGAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* *
1501702 TTCTCCCTCATCGGATGAGTTCTTCTCATTATAAACTCTCCACTGGAAATGT
66 TTCTCCCTCATCGGATGAGTTCTTCTCATTATAAACTCTCCATTGGAAATGA
1501754 TGATCCACCTCCTTTTGTGATGGATTTGAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
1 TGATCCACCTCCTTTTGTGATGGATTTGAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* * * * *
1501819 TTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACCCCTCTATTGGAAATGA
66 TTCTCCCTCATCGGATGAGTTCTTCTCATTAT-AAACTCTCCATTGGAAATGA
* * * * *
1501872 AGACCCACCTCCTTTTGTGATGGATTT-ACATAAAAGATCGAACAAGTTCTTCTCATTATGAACT
1 TGATCCACCTCCTTTTGTGATGGATTTGA-A-CAAAGGTTGAACAAGTTCTTCTCATTATGAACT
* * * * * *
1501936 TCTTCTTCCTCCTCAGATGATTTCTTCTCATTATGAACTCCTCCTTTGGAAATGA
64 TCTTCTCCCTCATCGGATGAGTTCTTCTCATTATAAACT-CTCCATTGGAAATGA
* *
1501991 TGATCCACCTCCTTCT-TGATGGACTTGAA
1 TGATCCACCTCCTTTTGTGATGGATTTGAA
1502020 TCTACAAAAA
Statistics
Matches: 226, Mismatches: 35, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
117 88 0.39
118 53 0.23
119 85 0.38
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (117 bp):
TGATCCACCTCCTTTTGTGATGGATTTGAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
TTCTCCCTCATCGGATGAGTTCTTCTCATTATAAACTCTCCATTGGAAATGA
Found at i:1501961 original size:119 final size:118
Alignment explanation
Indices: 1501675--1502019 Score: 455
Period size: 119 Copynumber: 2.9 Consensus size: 118
1501665 AGCTAAGGTT
* * *
1501675 GAACAAGTTCTTCTCATCATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT-AAACT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACCC
* * * * * *
1501739 CTCCACTGGAAATGTTGATCCACCTCCTTTTGTGATGGATTTGAACAAAGGTT
66 CTCTATTGGAAATGATGATCCACCTCCTTTTGTGATGGATTTGAAAAAAGATC
* *
1501792 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGAACCC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACCC
* *
1501857 CTCTATTGGAAATGAAGACCCACCTCCTTTTGTGATGGATTT-ACATAAAAGATC
66 CTCTATTGGAAATGATGATCCACCTCCTTTTGTGATGGATTTGA-A-AAAAGATC
* * * * *
1501911 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCCTCAGATGATTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACCC
* *
1501976 CTCCT-TTGGAAATGATGATCCACCTCCTTCT-TGATGGACTTGAA
66 CT-CTATTGGAAATGATGATCCACCTCCTTTTGTGATGGATTTGAA
1502020 TCTACAAAAA
Statistics
Matches: 199, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
117 57 0.29
118 51 0.26
119 89 0.45
120 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (118 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACCC
CTCTATTGGAAATGATGATCCACCTCCTTTTGTGATGGATTTGAAAAAAGATC
Found at i:1503308 original size:24 final size:24
Alignment explanation
Indices: 1503276--1503325 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1503266 TAGAATCTTG
1503276 TTACCTCAATATGATATGGGTTTT
1 TTACCTCAATATGATATGGGTTTT
1503300 TTACCTCAATATGATATGGGTTTT
1 TTACCTCAATATGATATGGGTTTT
1503324 TT
1 TT
1503326 CCATGCCCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (24 bp):
TTACCTCAATATGATATGGGTTTT
Found at i:1504546 original size:4 final size:4
Alignment explanation
Indices: 1504537--1504576 Score: 55
Period size: 4 Copynumber: 9.8 Consensus size: 4
1504527 TTTCTTCTTT
1504537 TTTA TTTA TTTA TTTA TTTA TTT- TTTA TTTTA TTTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA -TTTA TTT
1504577 TTTTTCATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 3 0.09
4 22 0.65
5 9 0.26
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (4 bp):
TTTA
Found at i:1504570 original size:20 final size:19
Alignment explanation
Indices: 1504534--1504592 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 19
1504524 AATTTTCTTC
1504534 TTTTTTATTTA-TTTATTTA
1 TTTTTT-TTTATTTTATTTA
1504553 TTTATTTTTTATTTTATTTTA
1 TTT-TTTTTTATTTTA-TTTA
*
1504574 TTTTTTTTCATTTTCATTT
1 TTTTTTTTTATTTT-ATTT
1504593 TCATTTTCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
19 7 0.20
20 20 0.57
21 8 0.23
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTTTTTATTTTATTTA
Found at i:1504579 original size:12 final size:11
Alignment explanation
Indices: 1504534--1504586 Score: 65
Period size: 10 Copynumber: 4.9 Consensus size: 11
1504524 AATTTTCTTC
1504534 TTTTTTATTTA
1 TTTTTTATTTA
1504545 TTTATTTATTTA
1 TTT-TTTATTTA
1504557 TTTTTTATTT-
1 TTTTTTATTTA
*
1504567 TATTTTATTT-
1 TTTTTTATTTA
*
1504577 TTTTTCATTT
1 TTTTTTATTT
1504587 TCATTTTCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
10 17 0.45
11 10 0.26
12 11 0.29
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTATTTA
Found at i:1504593 original size:12 final size:12
Alignment explanation
Indices: 1504558--1504618 Score: 76
Period size: 12 Copynumber: 5.3 Consensus size: 12
1504548 ATTTATTTAT
*
1504558 TTTTTATTTT-A
1 TTTTCATTTTCA
1504569 TTTT-ATTTT--
1 TTTTCATTTTCA
1504578 TTTTCATTTTCA
1 TTTTCATTTTCA
1504590 TTTTCATTTTCA
1 TTTTCATTTTCA
1504602 TTTTCATTTTTCA
1 TTTTCA-TTTTCA
1504615 TTTT
1 TTTT
1504619 TCTTCATTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.09
10 10 0.22
11 4 0.09
12 18 0.39
13 10 0.22
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTCATTTTCA
Found at i:1504601 original size:18 final size:18
Alignment explanation
Indices: 1504558--1504618 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
1504548 ATTTATTTAT
*
1504558 TTTTTATTTT-ATTTT-A
1 TTTTCATTTTCATTTTCA
1504574 TTTT--TTTTCATTTTCA
1 TTTTCATTTTCATTTTCA
1504590 TTTTCATTTTCATTTTCA
1 TTTTCATTTTCATTTTCA
1504608 TTTTTCATTTT
1 -TTTTCATTTT
1504619 TCTTCATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.10
15 5 0.12
16 9 0.22
18 12 0.30
19 10 0.25
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTCATTTTCATTTTCA
Found at i:1506797 original size:23 final size:22
Alignment explanation
Indices: 1506730--1506877 Score: 142
Period size: 23 Copynumber: 6.7 Consensus size: 22
1506720 CGTAATTTGC
* * *
1506730 ACCGAAGTTCCACAT-GATTAT
1 ACCGAAGTGCCACATAGGTTGT
*
1506751 CCCGAAG-GACCACATAGGTTGT
1 ACCGAAGTG-CCACATAGGTTGT
1506773 ACCGAAGTGCCACATAGGGTTGT
1 ACCGAAGTGCCACATA-GGTTGT
1506796 ACCGAAGTGCCACATAGGGTTGT
1 ACCGAAGTGCCACATA-GGTTGT
** *
1506819 ACTAAAGTGCCACATA-TTTGT
1 ACCGAAGTGCCACATAGGTTGT
* * *
1506840 CCCAAAG-GACCACATAGGTTGC
1 ACCGAAGTG-CCACATAGGTTGT
1506862 ACCGAAGTGCCACATA
1 ACCGAAGTGCCACATA
1506878 TTTGTCCCAG
Statistics
Matches: 106, Mismatches: 14, Indels: 13
0.80 0.11 0.10
Matches are distributed among these distances:
20 1 0.01
21 28 0.26
22 32 0.30
23 45 0.42
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (22 bp):
ACCGAAGTGCCACATAGGTTGT
Found at i:1506846 original size:21 final size:22
Alignment explanation
Indices: 1506760--1506920 Score: 111
Period size: 21 Copynumber: 7.4 Consensus size: 22
1506750 TCCCGAAGGA
* *
1506760 CCACATAGGTTGTACCGAAGTG
1 CCACATAGGTTGTCCCAAAGTG
* *
1506782 CCACATAGGGTTGTACCGAAGTG
1 CCACATA-GGTTGTCCCAAAGTG
* *
1506805 CCACATAGGGTTGTACTAAAGTG
1 CCACATA-GGTTGTCCCAAAGTG
*
1506828 CCACATA-TTTGTCCCAAAG-G
1 CCACATAGGTTGTCCCAAAGTG
*
1506848 ACCACATAGGTTG-CACCGAAGTG
1 -CCACATAGGTTGTC-CCAAAGTG
* *
1506871 CCACATA-TTTGTCCCAGAG-G
1 CCACATAGGTTGTCCCAAAGTG
* *
1506891 ACCACATA-ATTGTCCCGAAG-G
1 -CCACATAGGTTGTCCCAAAGTG
1506912 ACCACATAG
1 -CCACATAG
1506921 ACCCTCGACT
Statistics
Matches: 118, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
20 2 0.02
21 49 0.42
22 23 0.19
23 44 0.37
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (22 bp):
CCACATAGGTTGTCCCAAAGTG
Found at i:1506872 original size:43 final size:43
Alignment explanation
Indices: 1506726--1506898 Score: 188
Period size: 43 Copynumber: 4.0 Consensus size: 43
1506716 AACTCGTAAT
* * *
1506726 TTGCACCGAAGTTCCACATGA-TTATCCCGAAGGACCACATAGG
1 TTGCACCGAAGTGCCACAT-ATTTGTCCCAAAGGACCACATAGG
* * * *
1506769 TTGTACCGAAGTGCCACATAGGGTTGTACCGAAGTG-CCACATAGGG
1 TTGCACCGAAGTGCCACATA--TTTGTCCCAAAG-GACCACATA-GG
* **
1506815 TTGTACTAAAGTGCCACATATTTGTCCCAAAGGACCACATAGG
1 TTGCACCGAAGTGCCACATATTTGTCCCAAAGGACCACATAGG
*
1506858 TTGCACCGAAGTGCCACATATTTGTCCCAGAGGACCACATA
1 TTGCACCGAAGTGCCACATATTTGTCCCAAAGGACCACATA
1506899 ATTGTCCCGA
Statistics
Matches: 111, Mismatches: 13, Indels: 12
0.82 0.10 0.09
Matches are distributed among these distances:
42 1 0.01
43 57 0.51
44 16 0.14
45 16 0.14
46 21 0.19
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (43 bp):
TTGCACCGAAGTGCCACATATTTGTCCCAAAGGACCACATAGG
Found at i:1507497 original size:55 final size:55
Alignment explanation
Indices: 1507413--1507555 Score: 241
Period size: 55 Copynumber: 2.6 Consensus size: 55
1507403 TCATACTTAG
1507413 GGGTATCGATACACTCCTCAGTGTACCGATACATAAATAACACTCGATGTTTTGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACATAAATAACACTCGATGTTTTGA
* * ** *
1507468 GGGTATTGATACACTCCTCAATGTACCGATACATAAATGTCATTCGATGTTTTGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACATAAATAACACTCGATGTTTTGA
1507523 GGGTATCGATACACTCCTCAGTGTACCGATACA
1 GGGTATCGATACACTCCTCAGTGTACCGATACA
1507556 CACTCATATA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 81 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (55 bp):
GGGTATCGATACACTCCTCAGTGTACCGATACATAAATAACACTCGATGTTTTGA
Found at i:1522765 original size:21 final size:21
Alignment explanation
Indices: 1522736--1522819 Score: 91
Period size: 21 Copynumber: 4.0 Consensus size: 21
1522726 TCAGATAGGG
*
1522736 TTGTACCGAAGTACCACATAT
1 TTGTCCCGAAGTACCACATAT
*
1522757 TTGTCCCGAA-TGACCACATAAG
1 TTGTCCCGAAGT-ACCACAT-AT
*
1522779 TTG-CACCGAAGTTCCACATAT
1 TTGTC-CCGAAGTACCACATAT
*
1522800 TTGTCCCGAAGGACCACATA
1 TTGTCCCGAAGTACCACATA
1522820 GACCCTCGAC
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.02
21 34 0.65
22 16 0.31
23 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGTACCACATAT
Found at i:1522790 original size:43 final size:43
Alignment explanation
Indices: 1522735--1522819 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
1522725 GTCAGATAGG
* *
1522735 GTTGTACCGAAGTACCACATATTTGTCCCGAATGACCACATAA
1 GTTGCACCGAAGTACCACATATTTGTCCCGAAGGACCACATAA
*
1522778 GTTGCACCGAAGTTCCACATATTTGTCCCGAAGGACCACATA
1 GTTGCACCGAAGTACCACATATTTGTCCCGAAGGACCACATA
1522820 GACCCTCGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.25
Consensus pattern (43 bp):
GTTGCACCGAAGTACCACATATTTGTCCCGAAGGACCACATAA
Found at i:1523401 original size:55 final size:55
Alignment explanation
Indices: 1523336--1523480 Score: 218
Period size: 55 Copynumber: 2.6 Consensus size: 55
1523326 TCATACTAGG
*
1523336 GGGTATCGATACACTCCTCAATGTACCGATACACAAATAACACTCGATGTTTTGA
1 GGGTATCGATACACTCCTCAATGTACCGATACACAAATAACACTCAATGTTTTGA
* * ** *
1523391 GGGTATCGATACACTCCTTAGTGTACCGATACACAAATTGCATTCAATGTTTTGA
1 GGGTATCGATACACTCCTCAATGTACCGATACACAAATAACACTCAATGTTTTGA
* *
1523446 AGGTATCGATACACTTCTCAATGTACCGATACACA
1 GGGTATCGATACACTCCTCAATGTACCGATACACA
1523481 CTCATACAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 80 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (55 bp):
GGGTATCGATACACTCCTCAATGTACCGATACACAAATAACACTCAATGTTTTGA
Found at i:1525959 original size:14 final size:14
Alignment explanation
Indices: 1525940--1525976 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1525930 TGAAAAATGC
*
1525940 AAATGCCAATGTGA
1 AAATGCAAATGTGA
*
1525954 AAATGCAAATGTGC
1 AAATGCAAATGTGA
1525968 AAATGCAAA
1 AAATGCAAA
1525977 ATGAAAACGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.14, G:0.19, T:0.19
Consensus pattern (14 bp):
AAATGCAAATGTGA
Found at i:1530615 original size:108 final size:108
Alignment explanation
Indices: 1530462--1530750 Score: 357
Period size: 108 Copynumber: 2.7 Consensus size: 108
1530452 CTCATATTCG
* * * * *
1530462 ATTCGACCTTGTGGTGACCCGATCCGAGGTATGATCTACAATATTATGGTCCGGACTCTACTAAC
1 ATTCGACCTTATGGTGACCCGATCCGGGGTATGATCCACATTATTATGGTCCGGACTCTGCTAAC
* *
1530527 TC-CTAACCATTT-TTATTATTTTTATTAATTTGTTTGATTTATT
66 -CACTAACCATTTATT-TTATTTTTATTAATTTGTTTAAATTATT
* * * * *
1530570 ATTTGACCTTATGGTGACCCGATCTGGGGTATGATCCACTTTATTATGGTTCGGACTCTGTTAAC
1 ATTCGACCTTATGGTGACCCGATCCGGGGTATGATCCACATTATTATGGTCCGGACTCTGCTAAC
**
1530635 CACTAACTGTTTATTTTATTTTTATTAATTTGTTTAAATTATT
66 CACTAACCATTTATTTTATTTTTATTAATTTGTTTAAATTATT
* * * * *
1530678 ATTCGATCTTATGGTGACCCAATTCGGGGGTACGATCCACATTATTATGGTCTGGACTCTGCTAA
1 ATTCGACCTTATGGTGACCCGA-TCCGGGGTATGATCCACATTATTATGGTCCGGACTCTGCTAA
*
1530743 CCATTAAC
65 CCACTAAC
1530751 AACTAACATT
Statistics
Matches: 154, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
107 1 0.01
108 108 0.70
109 45 0.29
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (108 bp):
ATTCGACCTTATGGTGACCCGATCCGGGGTATGATCCACATTATTATGGTCCGGACTCTGCTAAC
CACTAACCATTTATTTTATTTTTATTAATTTGTTTAAATTATT
Found at i:1530840 original size:33 final size:31
Alignment explanation
Indices: 1530751--1530854 Score: 145
Period size: 32 Copynumber: 3.2 Consensus size: 31
1530741 AACCATTAAC
1530751 AACTAACATTCTAACTTTTATTTTATTGTTCA
1 AACTAAC-TTCTAACTTTTATTTTATTGTTCA
*
1530783 AACTAATATTCTAACTTTTATTTTATTGTTCA
1 AACTAA-CTTCTAACTTTTATTTTATTGTTCA
* *
1530815 TACTAACTTACTAACATTTTATTTTATTGCTCA
1 AACTAACTT-CTAAC-TTTTATTTTATTGTTCA
1530848 AACTAAC
1 AACTAAC
1530855 CCGCCAATTT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
31 2 0.03
32 40 0.62
33 22 0.34
ACGTcount: A:0.33, C:0.16, G:0.03, T:0.48
Consensus pattern (31 bp):
AACTAACTTCTAACTTTTATTTTATTGTTCA
Found at i:1532849 original size:16 final size:18
Alignment explanation
Indices: 1532821--1532854 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1532811 GTTATAAAAG
1532821 CATGTTAGGGTAG-ATAT
1 CATGTTAGGGTAGTATAT
1532838 CATGTT-GGGTAGTATAT
1 CATGTTAGGGTAGTATAT
1532855 TTTCCTTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.38
Consensus pattern (18 bp):
CATGTTAGGGTAGTATAT
Found at i:1534757 original size:85 final size:85
Alignment explanation
Indices: 1534601--1534759 Score: 189
Period size: 85 Copynumber: 1.9 Consensus size: 85
1534591 CGCATTGATA
* * * * * *
1534601 ACACGCATTTATGACGCGCATTGAGCGTCATTGAAGCCCCCGTCATAAATGAAGATGGTACACAT
1 ACACGCATATATGACGCACATTGAGCGTCATTGAAGCACACATCATAAATAAAGATGGTACACAT
1534666 TTGTGTGTCATAAATTTATG
66 TTGTGTGTCATAAATTTATG
* * *
1534686 ACACGCATATATGACTCACATTGCGTGTCATTGAAGCACACATCATTAAA-AAAGAT-G-ACACA
1 ACACGCATATATGACGCACATTGAGCGTCATTGAAGCACACATCA-TAAATAAAGATGGTACACA
1534748 CTTTCGTGTGTC
65 -TTT-GTGTGTC
1534760 GTGATTGTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
83 5 0.08
84 4 0.06
85 49 0.79
86 4 0.06
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (85 bp):
ACACGCATATATGACGCACATTGAGCGTCATTGAAGCACACATCATAAATAAAGATGGTACACAT
TTGTGTGTCATAAATTTATG
Found at i:1542422 original size:233 final size:232
Alignment explanation
Indices: 1542007--1542539 Score: 760
Period size: 233 Copynumber: 2.3 Consensus size: 232
1541997 TTTATAAGTT
* ** * * * * *
1542007 AAAAAATGAAAAAAATTTATCATTTAAATTTGAAAACTGAAATTTTTTATAAGTAAGAAAAGTTT
1 AAAAAATGAGAAAGGTTTCTCATCTAAATCTGAAAATTGAAA-TTTTTAAAAGTAAGAAAAGTTT
* * *
1542072 CTTACCTAGTAAATTATTTCCAAAATTGGTAAGTCTTTCGGGCCATCAGTAAGTCTTTCGAGCAT
65 CTTACCTAGTAAACTATTTCCAAAATTGATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* *
1542137 AATGCTTAAATCCTTCAGGTCATCTATAAATCTTTCGAGTAAGATGATAAGTCCTTCAGGCCATC
130 AATGCTTAAATCCTTCAGGTCATATATAAATCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATC
* * *
1542202 CATAAGACCTTCGGATATGATGTTTTCATATGTTTTTC
195 CATAAGACCTTCGGATAGGATGTTTTCACATATTTTTC
*
1542240 AAAAAATGAGAAAGGTTTCTTATCTAAATCTGAAAATTGAAATTTTTAAAATGTAAGAAAAGTTT
1 AAAAAATGAGAAAGGTTTCTCATCTAAATCTGAAAATTGAAATTTTTAAAA-GTAAGAAAAGTTT
*
1542305 CTTACCTAGTAAACTATTTCCAAAATTGATAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCAT
65 CTTACCTAGTAAACTATTTCCAAAATTGATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* * * * **
1542370 GATGCTTAAATCCTTCAGGTCATATCTAAGTCTTTCGAGCAAGATTATAAGTCCTTTGGGCCATC
130 AATGCTTAAATCCTTCAGGTCATATATAAATCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATC
* *
1542435 CATAAGACCTTCGGGTAGGATGTTTTCACATATTTTTT
195 CATAAGACCTTCGGATAGGATGTTTTCACATATTTTTC
* * * * *
1542473 GAAAAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAATGAGAAAGGTTT
1 AAAAAATGAGAAAGGTTTCTCATCTAAATCTGAAAATTGAAATTTTT-AAAAGTAAGAAAAGTTT
1542538 CT
65 CT
1542540 CATTTAAATA
Statistics
Matches: 266, Mismatches: 32, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
232 8 0.03
233 254 0.95
234 4 0.02
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (232 bp):
AAAAAATGAGAAAGGTTTCTCATCTAAATCTGAAAATTGAAATTTTTAAAAGTAAGAAAAGTTTC
TTACCTAGTAAACTATTTCCAAAATTGATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATA
ATGCTTAAATCCTTCAGGTCATATATAAATCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCC
ATAAGACCTTCGGATAGGATGTTTTCACATATTTTTC
Found at i:1542536 original size:47 final size:47
Alignment explanation
Indices: 1542468--1542571 Score: 181
Period size: 47 Copynumber: 2.2 Consensus size: 47
1542458 TTTCACATAT
* *
1542468 TTTTTGAAAAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAA
1 TTTTTGAAAAATGAGAAAGGTTTCTCATTTAAATATGAAAATTAAAA
1542515 TTTTTGAAAAATGAGAAAGGTTTCTCATTTAAATATGAAAATTAAAA
1 TTTTTGAAAAATGAGAAAGGTTTCTCATTTAAATATGAAAATTAAAA
*
1542562 TTTTTTAAAA
1 TTTTTGAAAA
1542572 GTAAGAAAAG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.38
Consensus pattern (47 bp):
TTTTTGAAAAATGAGAAAGGTTTCTCATTTAAATATGAAAATTAAAA
Found at i:1542702 original size:39 final size:40
Alignment explanation
Indices: 1542605--1542703 Score: 103
Period size: 39 Copynumber: 2.5 Consensus size: 40
1542595 AAACTATTTC
* *
1542605 CAAAATTGGTAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAA
1 CAAAA-TGATAAGTCCTTCAGGCCATCA-TAAGCCTTTCGAA
* * **
1542647 C-AGATGAGTAAATCCTTCAGGTTATC-TAAGCCTTTCGAA
1 CAAAATGA-TAAGTCCTTCAGGCCATCATAAGCCTTTCGAA
1542686 CAAAATGATAAGTCCTTC
1 CAAAATGATAAGTCCTTC
1542704 GGGCAGGATG
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
39 22 0.47
40 7 0.15
41 17 0.36
42 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.29
Consensus pattern (40 bp):
CAAAATGATAAGTCCTTCAGGCCATCATAAGCCTTTCGAA
Found at i:1543379 original size:133 final size:134
Alignment explanation
Indices: 1543085--1543595 Score: 557
Period size: 134 Copynumber: 3.8 Consensus size: 134
1543075 AATTCAATTT
* * ** * * * *
1543085 AATCTTCCCTGAAG-GACAGTGGAATGAATCAACATTTCCATATTTGATTTTCCCTCCAGAAGCA
1 AATCTTCCCT-AAGTAACAGTAGAATGAATCAACATCCCCAAATCTAATTTTCCCTCAAGAAG-A
* * * **
1543149 A-TGGAATAAATCTCTCTATTTCAAGATTTGATATTCCCTGAGTAACAGAAGAACAAGTCTGCCT
64 AGTGGAACAAATCTCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAAGTCTGCCT
*
1543213 CAATTC
129 CGATTC
* ** *
1543219 AATCTTCCCTGAGTAACAGCGGAATGAATTAACATCCCCAAATCTAATTTTCCCTCAAGAAGAAG
1 AATCTTCCCTAAGTAACAGTAGAATGAATCAACATCCCCAAATCTAATTTTCCCTCAAGAAGAAG
* * * * * *
1543284 TGGAACAGATAC-CTCTCTTTC-AGATTTGATATTCCATGTGTAATAGTGGAATAAGTTTGTCTC
66 TGGAACAAAT-CTCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAAGTCTGCCTC
1543347 GATTC
130 GATTC
* * * * *
1543352 AATCTTCCCTAAAG-AACAGTACAATGAATCAACGA-CCACATATTTGATTTTCCCTCAAGAAGA
1 AATCTTCCCT-AAGTAACAGTAGAATGAATCAAC-ATCCCCAAATCTAATTTTCCCTCAAGAAGA
* *
1543415 AGCGGAACATATCTCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAAGTCTGCCT
64 AGTGGAACAAATCTCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAAGTCTGCCT
1543480 CGATTC
129 CGATTC
* * *
1543486 AATCTTCCCTGAGTAATAGTAGAATGAATCAACATCCCCAAATCTAATTTTTCCCTCGAGAAGAA
1 AATCTTCCCTAAGTAACAGTAGAATGAATCAACATCCCCAAATCTAA-TTTTCCCTCAAGAAGAA
* * * * * * *
1543551 GCGAAACATACCTCTCTATTTCAATATTTGATCTTCCCTGAGTAA
65 GTGGAACAAATCTCTCTCTTTCAAGATTTGATATTCCCTGAGTAA
1543596 CAATCAATGT
Statistics
Matches: 316, Mismatches: 51, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
132 1 0.00
133 113 0.36
134 145 0.46
135 57 0.18
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (134 bp):
AATCTTCCCTAAGTAACAGTAGAATGAATCAACATCCCCAAATCTAATTTTCCCTCAAGAAGAAG
TGGAACAAATCTCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAAGTCTGCCTCG
ATTC
Found at i:1544069 original size:3 final size:3
Alignment explanation
Indices: 1544063--1544104 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
1544053 ATTATTATTA
*
1544063 TTG TTG TTG TT- TTG TTG TTG TTG TTG TTG TTA TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1544105 AATACCCTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.02, C:0.00, G:0.29, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:1546406 original size:2 final size:2
Alignment explanation
Indices: 1546399--1546423 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1546389 AAACATAGGG
1546399 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1546424 TTAATGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1547200 original size:24 final size:24
Alignment explanation
Indices: 1547161--1547206 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
1547151 GAACCCTAAC
1547161 GGGTTTGGGCCTCAAA-CGGGTCT
1 GGGTTTGGGCCTCAAACCGGGTCT
1547184 GGGTCTTGGG-CTGCAAACCGGGT
1 GGGT-TTGGGCCT-CAAACCGGGT
1547207 TATGGTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
24 9 0.45
25 5 0.25
ACGTcount: A:0.13, C:0.22, G:0.41, T:0.24
Consensus pattern (24 bp):
GGGTTTGGGCCTCAAACCGGGTCT
Found at i:1547701 original size:109 final size:111
Alignment explanation
Indices: 1547560--1547833 Score: 297
Period size: 114 Copynumber: 2.5 Consensus size: 111
1547550 CTCATATTTG
** * * *
1547560 ATTCAACCTTGTGGTGA-CCGATCCGGGATACGATCCTTATTATTATGGTCTGGATTCTATTAAC
1 ATTCAACCTTGTGGTGACCCGATCCGGG-TACGATCCACATTATTATGGTCTGAACTATATTAA-
* *
1547624 TC-CTAAC-CGTT-TTTTA-TTATTTTTATTAATTTGTTTGATTTATT
64 TCACTAACTCGTTATTTTATTTACTTTTATTAATTTGTTTGAATTATT
* * *
1547668 ATTTAACCTTGTGGTGACCCGATCCGGTGTACGATCCACATTATTATGGTTTGAACTATGTTAAT
1 ATTCAACCTTGTGGTGACCCGATCCGG-GTACGATCCACATTATTATGGTCTGAACTATATTAAT
** *
1547733 CACTAACTTTTTTATTTTATTTTACTTTTATTAATTTTTTTGAATTATT
65 CACTAAC-TCGTTATTTTA-TTTACTTTTATTAATTTGTTTGAATTATT
* * * * *
1547782 ATTCGACCTTGTGGTGACTCGATCCGGGGTAAGATCTACATTATTATAGTCT
1 ATTCAACCTTGTGGTGACCCGATCC-GGGTACGATCCACATTATTATGGTCT
1547834 ACACTCTACT
Statistics
Matches: 137, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
108 18 0.13
109 42 0.31
110 1 0.01
111 2 0.01
112 5 0.04
114 67 0.49
115 2 0.01
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (111 bp):
ATTCAACCTTGTGGTGACCCGATCCGGGTACGATCCACATTATTATGGTCTGAACTATATTAATC
ACTAACTCGTTATTTTATTTACTTTTATTAATTTGTTTGAATTATT
Found at i:1547896 original size:32 final size:32
Alignment explanation
Indices: 1547855--1547977 Score: 203
Period size: 32 Copynumber: 3.8 Consensus size: 32
1547845 ACCATTAACA
1547855 ACTAACATTCTAACTTTTATTTTATTGTTCAC
1 ACTAACATTCTAACTTTTATTTTATTGTTCAC
1547887 ACTAACATTCTAACTTTTATTTTATTGTTCAC
1 ACTAACATTCTAACTTTTATTTTATTGTTCAC
*
1547919 ACTAACATTCTAACTTTTATTTTATTGTTCAT
1 ACTAACATTCTAACTTTTATTTTATTGTTCAC
*
1547951 ATTAAC-TTACTAACATTTTATTTTATT
1 ACTAACATT-CTAAC-TTTTATTTTATT
1547978 ACCCAAATTA
Statistics
Matches: 87, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
31 2 0.02
32 73 0.84
33 12 0.14
ACGTcount: A:0.29, C:0.16, G:0.02, T:0.52
Consensus pattern (32 bp):
ACTAACATTCTAACTTTTATTTTATTGTTCAC
Found at i:1548132 original size:4 final size:4
Alignment explanation
Indices: 1548123--1548147 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1548113 GTAATATTCC
1548123 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
1548148 CCAACACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:1548238 original size:29 final size:28
Alignment explanation
Indices: 1548183--1548238 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1548173 ATTTTTTTGT
* *
1548183 TCCTTTAATTTCCTACATTTTATTTTAG
1 TCCTTTAATTTCCAACATCTTATTTTAG
1548211 TCCTTTAATATTCCAACA-CTTACTTTTA
1 TCCTTTAAT-TTCCAACATCTTA-TTTTA
1548239 TGTGTTCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.25, C:0.21, G:0.02, T:0.52
Consensus pattern (28 bp):
TCCTTTAATTTCCAACATCTTATTTTAG
Found at i:1549407 original size:3 final size:3
Alignment explanation
Indices: 1549399--1549423 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1549389 TATTTATTTT
1549399 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
1549424 TAAAAAATGA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1551632 original size:16 final size:14
Alignment explanation
Indices: 1551600--1551696 Score: 82
Period size: 15 Copynumber: 7.0 Consensus size: 14
1551590 TTTGAATTTG
1551600 TATAATTTTTATAT
1 TATAATTTTTATAT
1551614 TATGAATTTTTATATT
1 TAT-AATTTTTATA-T
1551630 TATAATCTTTTATAT
1 TATAAT-TTTTATAT
1551645 TAT-A--TTT-T-T
1 TATAATTTTTATAT
*
1551654 TATAATCTTT-TAT
1 TATAATTTTTATAT
1551667 TATGAATTTTTATAT
1 TAT-AATTTTTATAT
1551682 TA-AATATTATTATAT
1 TATAAT-TT-TTATAT
1551697 ACACGAAAAT
Statistics
Matches: 71, Mismatches: 1, Indels: 21
0.76 0.01 0.23
Matches are distributed among these distances:
9 4 0.06
10 2 0.03
11 3 0.04
12 4 0.06
13 7 0.10
14 12 0.17
15 28 0.39
16 11 0.15
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (14 bp):
TATAATTTTTATAT
Found at i:1551654 original size:30 final size:30
Alignment explanation
Indices: 1551565--1551657 Score: 109
Period size: 30 Copynumber: 3.1 Consensus size: 30
1551555 TAAATATTAA
* * **
1551565 ATATTTATAATCTTTTCTATTTTAATTTGA
1 ATATTTATAATCTTTTATATTATAATTTTT
1551595 AT-TTGTATAAT-TTTTATATTATGAATTTTT
1 ATATT-TATAATCTTTTATATTAT-AATTTTT
*
1551625 ATATTTATAATCTTTTATATTATATTTTTT
1 ATATTTATAATCTTTTATATTATAATTTTT
1551655 ATA
1 ATA
1551658 ATCTTTTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
29 11 0.20
30 30 0.56
31 13 0.24
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (30 bp):
ATATTTATAATCTTTTATATTATAATTTTT
Found at i:1551675 original size:24 final size:24
Alignment explanation
Indices: 1551628--1551677 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1551618 AATTTTTATA
*
1551628 TTTATAATCTTTTATATTATATTT
1 TTTATAATCTTTTATATGATATTT
1551652 TTTATAATCTTTTATTATGA-ATTT
1 TTTATAATCTTTTA-TATGATATTT
1551676 TT
1 TT
1551678 ATATTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTATAATCTTTTATATGATATTT
Found at i:1553033 original size:39 final size:41
Alignment explanation
Indices: 1552951--1553036 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 41
1552941 TATTAATAAA
*
1552951 TAATAAATAATAAAAATAGTAAATTAACTAATCTATTGTTTT
1 TAATAAATAATAAAAATAGTAAATTAACTAA-CTATTGATTT
*
1552993 TAATAAATAATAAAATATTA-TTAATTAA-TAA-TATT-ATTT
1 TAATAAATAATAAAA-A-TAGTAAATTAACTAACTATTGATTT
1553032 TAATA
1 TAATA
1553037 CAAACAAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
39 8 0.20
40 4 0.10
42 18 0.45
43 8 0.20
44 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (41 bp):
TAATAAATAATAAAAATAGTAAATTAACTAACTATTGATTT
Found at i:1554835 original size:18 final size:17
Alignment explanation
Indices: 1554781--1554829 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1554771 TTGGACTCCT
* *
1554781 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
1554799 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
1554817 AGTGCATTCGATG
1 AGTGCA-TCGATG
1554830 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:1554914 original size:64 final size:64
Alignment explanation
Indices: 1554801--1555010 Score: 205
Period size: 64 Copynumber: 3.2 Consensus size: 64
1554791 TGCACTAAGA
* * *
1554801 GTGCATCGATGCATGAAGTGCATTCGATGTTTGAA--AAAT-AGCCTGGTGCATCGATGCATGGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAG---AGTGCATCGATGCATGGA
1554863 TT
63 TT
* * **
1554865 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAGAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
* * * *
1554929 GTGCATCGGTGCATGGAATGCATTCAATGTTTCAACTT-ATTCATTGA-TGCATCGATGCATGGT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAA-TTAAATCA--GAGTGCATCGATGCATGG-
1554992 ATT
62 ATT
*
1554995 GATGCATCGGTGCATG
1 G-TGCATCGATGCATG
1555011 CCTTTGAAAA
Statistics
Matches: 124, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
64 83 0.67
65 17 0.14
66 8 0.06
67 16 0.13
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
Found at i:1554931 original size:19 final size:19
Alignment explanation
Indices: 1554907--1554945 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1554897 TAATTAAATC
1554907 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1554926 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1554945 A
1 A
1554946 ATGCATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1554997 original size:21 final size:21
Alignment explanation
Indices: 1554971--1555010 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1554961 CAACTTATTC
1554971 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
1554992 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
1555011 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:1557586 original size:24 final size:23
Alignment explanation
Indices: 1557515--1557594 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 23
1557505 CATGATCTTG
*
1557515 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* *
1557538 TGCATCGGTG--CA-TCATGCGGA
1 TGCATCGATGCACATTCAAG-GGA
1557559 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
1557583 TGCATCGATGCA
1 TGCATCGATGCA
1557595 TTGTTAAGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.09
21 13 0.28
23 11 0.23
24 17 0.36
25 2 0.04
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.23
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:1557607 original size:44 final size:44
Alignment explanation
Indices: 1557514--1557609 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 44
1557504 GCATGATCTT
* *
1557514 GTGCATCGATGCACATTCAAGGCATGCATCGGTGCATCATGCGGA
1 GTGCATCGATGCACATTCAAGGCATGCATCGATGCAT-ATGCGAA
* **
1557559 -TGCATCGATGCACATTCAAAGGGATGCATCGATGCAT-TGTTAA
1 GTGCATCGATGCACATTC-AAGGCATGCATCGATGCATATGCGAA
1557602 GTGCATCG
1 GTGCATCG
1557610 GTACATTAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
43 3 0.07
44 24 0.55
45 17 0.39
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (44 bp):
GTGCATCGATGCACATTCAAGGCATGCATCGATGCATATGCGAA
Found at i:1563516 original size:64 final size:64
Alignment explanation
Indices: 1563403--1563603 Score: 196
Period size: 64 Copynumber: 3.1 Consensus size: 64
1563393 TTCACTAAGA
* * *
1563403 GTGCATCGATGCATGAAGTGCATTCGATGTTTGAA--AAAT-AGCCTGGTGCATCGATGCATGGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAG---AGTGCATCGATGCATGGA
1563465 TT
63 TT
* * * **
1563467 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAGAGTGCATCAATGCATGGAGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
* * *
1563531 GTGCATCGGTGCATGGAATGCATTCGATGTTTCAACTT-ATTCATTGA-TGCATCGATGCATGGT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAA-TTAAATCA--GAGTGCATCGATGCATGG-
1563594 ATT
62 ATT
1563597 GATGCAT
1 G-TGCAT
1563604 GGTATTGATG
Statistics
Matches: 114, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
64 83 0.73
65 16 0.14
66 8 0.07
67 7 0.06
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
Found at i:1563533 original size:19 final size:19
Alignment explanation
Indices: 1563509--1563547 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1563499 TAATTAAATC
1563509 AGAGTGCATCAATGCATGG
1 AGAGTGCATCAATGCATGG
**
1563528 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCAATGCATGG
1563547 A
1 A
1563548 ATGCATTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.15, G:0.36, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCAATGCATGG
Found at i:1563602 original size:13 final size:13
Alignment explanation
Indices: 1563584--1563616 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
1563574 TTGATGCATC
1563584 GATGCATGGTATT
1 GATGCATGGTATT
1563597 GATGCATGGTATT
1 GATGCATGGTATT
1563610 GATGCAT
1 GATGCAT
1563617 CGGTGCATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.09, G:0.30, T:0.36
Consensus pattern (13 bp):
GATGCATGGTATT
Found at i:1563953 original size:43 final size:43
Alignment explanation
Indices: 1563875--1564046 Score: 136
Period size: 43 Copynumber: 4.0 Consensus size: 43
1563865 GTTTTTAACA
* * * * *
1563875 ATTTTTGGAACAAACGCCGCAAAAAAG-CGATATCTATAGCGGC
1 ATTTTTTGAACAAACACCAC-AAAAGGTCGAGATCTATAGCGGC
* * * *
1563918 ATTTTTTGGAACAAACATCGCAAAAGGT-TAGATCTATAGTGGC
1 ATTTTTT-GAACAAACACCACAAAAGGTCGAGATCTATAGCGGC
*
1563961 ATTTTTTGAACAAACGCCACAAAAGGTCGAGATCTATAGCGGC
1 ATTTTTTGAACAAACACCACAAAAGGTCGAGATCTATAGCGGC
* * ** * *
1564004 GTTTGTATCTAGAAAC-GCAGCAAAAGGTC-AGATCTATAGCGGC
1 ATTT-TTTGAACAAACACCA-CAAAAGGTCGAGATCTATAGCGGC
1564047 GTTTGTATCT
Statistics
Matches: 106, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
42 17 0.16
43 62 0.58
44 27 0.25
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (43 bp):
ATTTTTTGAACAAACACCACAAAAGGTCGAGATCTATAGCGGC
Found at i:1563972 original size:42 final size:44
Alignment explanation
Indices: 1563876--1564003 Score: 145
Period size: 43 Copynumber: 3.0 Consensus size: 44
1563866 TTTTTAACAA
* * * *
1563876 TTTTTGGAACAAACGCCGCAAAAAAG-CGATATCTATAGCGGCAT
1 TTTTTGGAACAAACACCAC-AAAAGGTCGAGATCTATAGCGGCAT
* * * *
1563920 TTTTTGGAACAAACATCGCAAAAGGT-TAGATCTATAGTGGCAT
1 TTTTTGGAACAAACACCACAAAAGGTCGAGATCTATAGCGGCAT
*
1563963 TTTTT-GAACAAACGCCACAAAAGGTCGAGATCTATAGCGGC
1 TTTTTGGAACAAACACCACAAAAGGTCGAGATCTATAGCGGC
1564004 GTTTGTATCT
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
42 17 0.24
43 37 0.52
44 17 0.24
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (44 bp):
TTTTTGGAACAAACACCACAAAAGGTCGAGATCTATAGCGGCAT
Found at i:1564047 original size:43 final size:44
Alignment explanation
Indices: 1563937--1564086 Score: 168
Period size: 43 Copynumber: 3.5 Consensus size: 44
1563927 AACAAACATC
* * *
1563937 GCAAAAGGTTAGATCTATAGTGGCATTT-T-T-TGAACAAACGCCA
1 GCAAAAGGTCAGATCTATAGCGGCGTTTGTATCT-AA-AAACGCCA
*
1563980 -CAAAAGGTCGAGATCTATAGCGGCGTTTGTATCTAGAAACG-CA
1 GCAAAAGGTC-AGATCTATAGCGGCGTTTGTATCTAAAAACGCCA
*
1564023 GCAAAAGGTCAGATCTATAGCGGCGTTTGTATCTAAAAACGTC-
1 GCAAAAGGTCAGATCTATAGCGGCGTTTGTATCTAAAAACGCCA
**
1564066 GCAAAATTTCAGATCTATAGC
1 GCAAAAGGTCAGATCTATAGC
1564087 TGCATTTTTT
Statistics
Matches: 94, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
42 8 0.09
43 67 0.71
44 16 0.17
45 2 0.02
46 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (44 bp):
GCAAAAGGTCAGATCTATAGCGGCGTTTGTATCTAAAAACGCCA
Found at i:1566840 original size:22 final size:21
Alignment explanation
Indices: 1566815--1566867 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
1566805 AGATTAAAAT
1566815 CATATCCAGTAGAATCAAACAA
1 CATATCCAGTAGAATC-AACAA
* *
1566837 CATAAGCCA-TAGAATCAAGAA
1 CAT-ATCCAGTAGAATCAACAA
*
1566858 CATATACAGT
1 CATATCCAGT
1566868 TCATCTAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
20 3 0.12
21 8 0.32
22 10 0.40
23 4 0.16
ACGTcount: A:0.49, C:0.21, G:0.11, T:0.19
Consensus pattern (21 bp):
CATATCCAGTAGAATCAACAA
Found at i:1567612 original size:41 final size:41
Alignment explanation
Indices: 1567556--1567715 Score: 146
Period size: 41 Copynumber: 3.9 Consensus size: 41
1567546 ATAGATGGAC
*
1567556 CTATTGCGGAGTTTGTATAAAAACGCCGCTAAAGTACTACT
1 CTATTGCGGTGTTTGTATAAAAACGCCGCTAAAGTACTACT
* * * * *
1567597 TTATTTCGGTGTTTGTGGA-AAAAACGCCACTACA-TATGTAC-
1 CTATTGCGGTGTTTGT--ATAAAAACGCCGCTAAAGTA-CTACT
* * *
1567638 CTATTGCAGTGTTTATATAAAAACACCGCTAAAGTACTACT
1 CTATTGCGGTGTTTGTATAAAAACGCCGCTAAAGTACTACT
* * * *
1567679 CTATTACGGCGTTTGTTTAAGAAATGCCGCTAAAGTA
1 CTATTGCGGTGTTTGTATAA-AAACGCCGCTAAAGTA
1567716 TCATTTTATG
Statistics
Matches: 91, Mismatches: 21, Indels: 13
0.73 0.17 0.10
Matches are distributed among these distances:
39 1 0.01
40 15 0.16
41 44 0.48
42 30 0.33
43 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (41 bp):
CTATTGCGGTGTTTGTATAAAAACGCCGCTAAAGTACTACT
Found at i:1567658 original size:82 final size:82
Alignment explanation
Indices: 1567503--1567694 Score: 235
Period size: 82 Copynumber: 2.4 Consensus size: 82
1567493 TAAAAATATT
* * * * * * *
1567503 GCTAAAGTACTAATATGTTATGGCGTTTGT--AAACAACGCCACTATAGATGGACCTATTGCGGA
1 GCTAAAGTACTACTCTATTACGGCGTTTGTGGAAAAAACGCCACTACAGATGGACCTATTGCAGA
* *
1567566 GTTTGTATAAAAACGCC
66 GTTTATATAAAAACACC
* * * * * *
1567583 GCTAAAGTACTACTTTATTTCGGTGTTTGTGGAAAAAACGCCACTACATATGTACCTATTGCAGT
1 GCTAAAGTACTACTCTATTACGGCGTTTGTGGAAAAAACGCCACTACAGATGGACCTATTGCAGA
1567648 GTTTATATAAAAACACC
66 GTTTATATAAAAACACC
1567665 GCTAAAGTACTACTCTATTACGGCGTTTGT
1 GCTAAAGTACTACTCTATTACGGCGTTTGT
1567695 TTAAGAAATG
Statistics
Matches: 93, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
80 24 0.26
82 69 0.74
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (82 bp):
GCTAAAGTACTACTCTATTACGGCGTTTGTGGAAAAAACGCCACTACAGATGGACCTATTGCAGA
GTTTATATAAAAACACC
Found at i:1572951 original size:38 final size:39
Alignment explanation
Indices: 1572893--1573324 Score: 287
Period size: 38 Copynumber: 11.5 Consensus size: 39
1572883 AAGAAAGACA
*
1572893 ATCTCAAGTGAGATAAAATTTATGTTTCCAGTGAAAACT
1 ATCTCAAGTGAGATAAAATTTATGTTTCGAGTGAAAACT
* * ** *
1572932 ATCTCAAGCGAGAT-GAATTT-TGTTTTTA-AGAAAGACT
1 ATCTCAAGTGAGATAAAATTTATGTTTCGAGTGAAA-ACT
* * *
1572969 ATCTTAAGTGAGATAAAATTTCTGTTTCGAGTGAAAATT
1 ATCTCAAGTGAGATAAAATTTATGTTTCGAGTGAAAACT
* * ** * * * *
1573008 GTCTCAAGCGAGA-CGAAGTT-TGTTT-TA-AGAAGAACA
1 ATCTCAAGTGAGATAAAATTTATGTTTCGAGTGAA-AACT
* * *
1573044 ATCACAAGTGAGATAAAATTTCTTGTTTCGAGTG-AAACC
1 ATCTCAAGTGAGATAAAATTT-ATGTTTCGAGTGAAAACT
* ** * *
1573083 ATCTCAAGTGAGATGAAA--TAT-TTTTAAG-AAAAACA
1 ATCTCAAGTGAGATAAAATTTATGTTTCGAGTGAAAACT
1573118 ATCTCAAGTGAGATAAAATTTATGTTTCGAGTG-AAACT
1 ATCTCAAGTGAGATAAAATTTATGTTTCGAGTGAAAACT
* * * * *
1573156 ATCTCAAGCGAGATGAAA-TT-TGTTT-TA-AGAAAACA
1 ATCTCAAGTGAGATAAAATTTATGTTTCGAGTGAAAACT
*
1573191 ATCTTAAGTGAGATAAAATTTATGTTTCGAGT-AAAACT
1 ATCTCAAGTGAGATAAAATTTATGTTTCGAGTGAAAACT
* * * *
1573229 ATCTCAAGCGAGATAAAATTTTTGCTTCAAGTG-AAACT
1 ATCTCAAGTGAGATAAAATTTATGTTTCGAGTGAAAACT
** * * ** * *
1573267 ATCTCAACCCGAGAT-GAATCT-TGTTTTAAG-AAAAACA
1 ATCTCAA-GTGAGATAAAATTTATGTTTCGAGTGAAAACT
1573304 ATCTCAAGTGAGATAAAATTT
1 ATCTCAAGTGAGATAAAATTT
1573325 TGTATTAAAG
Statistics
Matches: 299, Mismatches: 70, Indels: 50
0.71 0.17 0.12
Matches are distributed among these distances:
34 1 0.00
35 49 0.16
36 30 0.10
37 63 0.21
38 88 0.29
39 61 0.20
40 6 0.02
41 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (39 bp):
ATCTCAAGTGAGATAAAATTTATGTTTCGAGTGAAAACT
Found at i:1573032 original size:151 final size:150
Alignment explanation
Indices: 1572776--1573242 Score: 579
Period size: 151 Copynumber: 3.1 Consensus size: 150
1572766 ATTTAATGGG
* * * * * * * *
1572776 AAACTTTCTCAAGCGAGAAGAAATTTG-CTTTAAGAAAAAAAAACTTGAGTGAAATGAAATTTCT
1 AAACTATCTCAAGCGAGATG-AATTTGTTTTTAAGAAAAACAATCTTAAGTGAGATAAAATTTC-
* * * * *
1572840 TGTTTTGAGTAAAAACTATCTCAAGAGAGACAAAGTATGTTTTAAGAAAGACAATCTCAAGTGAG
64 TGTTTCGAGTGAAAACTATCTCAAGCGAGACGAAGTTTGTTTTAAGAAAGACAATCTCAAGTGAG
*
1572905 ATAAAATTTATGTTTCCAGTGA
129 ATAAAATTTATGTTTCGAGTGA
* *
1572927 AAACTATCTCAAGCGAGATGAATTTTGTTTTTAAGAAAGACTATCTTAAGTGAGATAAAATTTCT
1 AAACTATCTCAAGCGAGATGAA-TTTGTTTTTAAGAAAAACAATCTTAAGTGAGATAAAATTTCT
* * *
1572992 GTTTCGAGTGAAAATTGTCTCAAGCGAGACGAAGTTTGTTTTAAG-AAGAACAATCACAAGTGAG
65 GTTTCGAGTGAAAACTATCTCAAGCGAGACGAAGTTTGTTTTAAGAAAG-ACAATCTCAAGTGAG
*
1573056 ATAAAATTTCTTGTTTCGAGTG-
129 ATAAAATTT-ATGTTTCGAGTGA
* * * * * *
1573078 AAACCATCTCAAGTGAGATGAA-ATATTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTATG
1 AAACTATCTCAAGCGAGATGAATTTGTTTTTAAGAAAAACAATCTTAAGTGAGATAAAATTTCTG
* * *
1573142 TTTCGAGTG-AAACTATCTCAAGCGAGATGAAATTTGTTTTAAGAAA-ACAATCTTAAGTGAGAT
66 TTTCGAGTGAAAACTATCTCAAGCGAGACGAAGTTTGTTTTAAGAAAGACAATCTCAAGTGAGAT
1573205 AAAATTTATGTTTCGAGT-A
131 AAAATTTATGTTTCGAGTGA
1573224 AAACTATCTCAAGCGAGAT
1 AAACTATCTCAAGCGAGAT
1573243 AAAATTTTTG
Statistics
Matches: 273, Mismatches: 37, Indels: 17
0.83 0.11 0.05
Matches are distributed among these distances:
146 27 0.10
147 22 0.08
148 30 0.11
149 47 0.17
150 5 0.02
151 104 0.38
152 38 0.14
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (150 bp):
AAACTATCTCAAGCGAGATGAATTTGTTTTTAAGAAAAACAATCTTAAGTGAGATAAAATTTCTG
TTTCGAGTGAAAACTATCTCAAGCGAGACGAAGTTTGTTTTAAGAAAGACAATCTCAAGTGAGAT
AAAATTTATGTTTCGAGTGA
Found at i:1573174 original size:73 final size:73
Alignment explanation
Indices: 1572775--1573251 Score: 496
Period size: 76 Copynumber: 6.4 Consensus size: 73
1572765 TATTTAATGG
* * * * ** * *
1572775 GAAACTTTCTCAAGCGAGAAGAAAT-TTGCTTTAAGAAAAAAAAACTTGAGTGAAATGAAATTTC
1 GAAACTATCTCAAGCGAGATGAAATATT--TTTAAGAAAAACAATCTCAAGTGAGATAAAATTT-
* *
1572839 TTGTTTTGAGT
63 ATGTTTCGAGT
* * * *
1572850 AAAAACTATCTCAAGAGAGA-CAAAGTATGTTTTAAGAAAGACAATCTCAAGTGAGATAAAATTT
1 -GAAACTATCTCAAGCGAGATGAAA-TAT-TTTTAAGAAAAACAATCTCAAGTGAGATAAAATTT
*
1572914 ATGTTTCCAGT
63 ATGTTTCGAGT
* * * * *
1572925 GAAAACTATCTCAAGCGAGATGAATTTTGTTTTTAAGAAAGACTATCTTAAGTGAGATAAAATTT
1 G-AAACTATCTCAAGCGAGATGAA--ATATTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTT
*
1572990 CTGTTTCGAGT
63 ATGTTTCGAGT
* * * * * * *
1573001 GAAAATTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAGAACAATCACAAGTGAGATAAAATTTC
1 G-AAACTATCTCAAGCGAGATGAAATAT-TTTTAAGAAAAACAATCTCAAGTGAGATAAAATTT-
*
1573066 TTGTTTCGAGT
63 ATGTTTCGAGT
* *
1573077 GAAACCATCTCAAGTGAGATGAAATATTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTATG
1 GAAACTATCTCAAGCGAGATGAAATATTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTATG
1573142 TTTCGAGT
66 TTTCGAGT
* *
1573150 GAAACTATCTCAAGCGAGATGAAATTTGTTTTAAG-AAAACAATCTTAAGTGAGATAAAATTTAT
1 GAAACTATCTCAAGCGAGATGAAATAT-TTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTAT
1573214 GTTTCGAGT
65 GTTTCGAGT
*
1573223 AAAACTATCTCAAGCGAGAT-AAA-ATTTTT
1 GAAACTATCTCAAGCGAGATGAAATATTTTT
1573252 GCTTCAAGTG
Statistics
Matches: 341, Mismatches: 50, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
70 4 0.01
71 1 0.00
72 3 0.01
73 90 0.26
74 42 0.12
75 77 0.23
76 120 0.35
77 3 0.01
78 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (73 bp):
GAAACTATCTCAAGCGAGATGAAATATTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTATG
TTTCGAGT
Found at i:1573356 original size:112 final size:111
Alignment explanation
Indices: 1572875--1573334 Score: 362
Period size: 111 Copynumber: 4.1 Consensus size: 111
1572865 AGAGACAAAG
* * * * *
1572875 TATGTTTTAAG-AAAGACAATCTCAAGTGAGATAAAATTTATGTTTCCAGTGAAAACTATCTCAA
1 TATGTTTAAAGTAAA-ACTATCTCAAGCGAGATAAAATTTATGCTTCAAGTG-AAACTATCTCAA
* * * *
1572939 GCGAGATGAATTTTGTTTTTAAGAAAGACTATCTTAAGTGAGATAAAATT
64 CCGAGATGAAATTTG-TTTTAAGAAA-ACAATCTCAAGTGAGATAAAATT
* ** * * ** * * * * * *
1572989 TCTGTTTCGAGTGAAAATTGTCTCAAGCGAGA-CGAAGTT-TGTTTTAAG-AAGAACAATCACAA
1 TATGTTTAAAGT-AAAACTATCTCAAGCGAGATAAAATTTATGCTTCAAGTGA-AACTATCTCAA
** * ** * * *
1573051 GTGAGATAAAATTTCTTGTTTCGAGTGAAACCATCTCAAGTGAGATGAAA--
64 CCGAGATGAAA--T-TTGTTTTAAG-AAAACAATCTCAAGTGAGATAAAATT
* * * * * * *
1573101 TAT-TTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTATGTTTCGAGTGAAACTATCTCAAGC
1 TATGTTTAAAGTAAAACTATCTCAAGCGAGATAAAATTTATGCTTCAAGTGAAACTATCTCAACC
*
1573165 GAGATGAAATTTGTTTTAAGAAAACAATCTTAAGTGAGATAAAATT
66 GAGATGAAATTTGTTTTAAGAAAACAATCTCAAGTGAGATAAAATT
** *
1573211 TATGTTTCGAGTAAAACTATCTCAAGCGAGATAAAATTTTTGCTTCAAGTGAAACTATCTCAACC
1 TATGTTTAAAGTAAAACTATCTCAAGCGAGATAAAATTTATGCTTCAAGTGAAACTATCTCAA-C
1573276 CGAGATG-AATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATT
65 CGAGATGAAAT-TTGTTTTAAG-AAAACAATCTCAAGTGAGATAAAATT
1573324 T-TGTATTAAAG
1 TATGT-TTAAAG
1573335 GAGGTTGTCT
Statistics
Matches: 269, Mismatches: 60, Indels: 35
0.74 0.16 0.10
Matches are distributed among these distances:
108 20 0.07
109 8 0.03
110 19 0.07
111 64 0.24
112 64 0.24
113 38 0.14
114 36 0.13
115 17 0.06
116 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (111 bp):
TATGTTTAAAGTAAAACTATCTCAAGCGAGATAAAATTTATGCTTCAAGTGAAACTATCTCAACC
GAGATGAAATTTGTTTTAAGAAAACAATCTCAAGTGAGATAAAATT
Found at i:1575625 original size:52 final size:52
Alignment explanation
Indices: 1575567--1575673 Score: 160
Period size: 52 Copynumber: 2.1 Consensus size: 52
1575557 ACACTAATGC
* * *
1575567 AATGATGAAAAGATGCATATGTAAATGCAAAGATTCAAAAATGGGAATGCAA
1 AATGATGAAAAGATGCACATGCAAATGCAAAGATGCAAAAATGGGAATGCAA
* * *
1575619 AATGATGAAAAGATGCACATGCAAATGCAAATATGCAAAAATGTGAGTGCAA
1 AATGATGAAAAGATGCACATGCAAATGCAAAGATGCAAAAATGGGAATGCAA
1575671 AAT
1 AAT
1575674 ACGAGATGCA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.50, C:0.09, G:0.21, T:0.21
Consensus pattern (52 bp):
AATGATGAAAAGATGCACATGCAAATGCAAAGATGCAAAAATGGGAATGCAA
Found at i:1578394 original size:138 final size:138
Alignment explanation
Indices: 1578131--1578405 Score: 509
Period size: 138 Copynumber: 2.0 Consensus size: 138
1578121 TAAAAAGTAA
1578131 AAATAGCAGTTTTGGTCCCTACAAGTGACCAAACTATAAAAAGGCGCTAAAATAATAGGGTTTCA
1 AAATAGCAGTTTTGGTCCCTACAAGTGACCAAACTATAAAAAGGCGCTAAAATAATAGGGTTTCA
1578196 AATGTGATTTTACCCTTAACTTATTCTATATAAATAACAACTTGTTATTTTTCCCCAAAAAT-AA
66 AATGTGATTTTACCCTTAACTTATTC-ATATAAATAACAACTTGTTATTTTTCCCCAAAAATAAA
1578260 AAGAAAAAC
130 AAGAAAAAC
1578269 AAATAGCAGTTTTGGTCCCTACAAGTGACCAAACTATAAAAAGGCGCTAAAATAATAGGGTTTCA
1 AAATAGCAGTTTTGGTCCCTACAAGTGACCAAACTATAAAAAGGCGCTAAAATAATAGGGTTTCA
1578334 AATGTGATTTTACCCTTAACTTATTC-TATAAATAACAACCTTGTTATTTTTCCCCAAAAAATAA
66 AATGTGATTTTACCCTTAACTTATTCATATAAATAACAA-CTTGTTATTTTTCCCC-AAAAATAA
1578398 AAAGAAAA
129 AAAGAAAA
1578406 CTTAAAAGCT
Statistics
Matches: 134, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
136 12 0.09
137 16 0.12
138 97 0.72
139 9 0.07
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (138 bp):
AAATAGCAGTTTTGGTCCCTACAAGTGACCAAACTATAAAAAGGCGCTAAAATAATAGGGTTTCA
AATGTGATTTTACCCTTAACTTATTCATATAAATAACAACTTGTTATTTTTCCCCAAAAATAAAA
AGAAAAAC
Found at i:1579498 original size:21 final size:21
Alignment explanation
Indices: 1579455--1579503 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1579445 AAAACAACGA
**
1579455 AGGGATCAATCATTTCTTTCG
1 AGGGATCAATCATTTCTCCCG
1579476 AGGGATCAATCATTT-TCCCCG
1 AGGGATCAATCATTTCT-CCCG
1579497 AGGGATC
1 AGGGATC
1579504 GATCCTTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (21 bp):
AGGGATCAATCATTTCTCCCG
Found at i:1584830 original size:24 final size:24
Alignment explanation
Indices: 1584797--1584854 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
1584787 AAAATGGCAC
*
1584797 TGTTGAGAATGACTTATTACTCCT
1 TGTTGGGAATGACTTATTACTCCT
*
1584821 TGTTGGGAATGAGTTATTACTCCT
1 TGTTGGGAATGACTTATTACTCCT
*
1584845 TATTGGGAAT
1 TGTTGGGAAT
1584855 CTTTGTAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.41
Consensus pattern (24 bp):
TGTTGGGAATGACTTATTACTCCT
Found at i:1592523 original size:51 final size:51
Alignment explanation
Indices: 1592447--1592551 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
1592437 GTCACCTGTC
1592447 TTTGTTCTTTTATGAAGTTCAAAATTATTTCTTTACTTAAAACATTGTAAA
1 TTTGTTCTTTTATGAAGTTCAAAATTATTTCTTTACTTAAAACATTGTAAA
1592498 TTTGTTCTTTTATGAAGTTCAAAATTATTTCTTTACTTAAAACATTGTAAA
1 TTTGTTCTTTTATGAAGTTCAAAATTATTTCTTTACTTAAAACATTGTAAA
1592549 TTT
1 TTT
1592552 AGTCCTCTAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.50
Consensus pattern (51 bp):
TTTGTTCTTTTATGAAGTTCAAAATTATTTCTTTACTTAAAACATTGTAAA
Found at i:1592549 original size:27 final size:27
Alignment explanation
Indices: 1592468--1592550 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 27
1592458 ATGAAGTTCA
1592468 AAATTATTTCTTTACTTAAAACATTGT
1 AAATTATTTCTTTACTTAAAACATTGT
* * **
1592495 AAATT-TGTTC-TT--TTATGAA-GTTCA
1 AAATTAT-TTCTTTACTTA-AAACATTGT
1592519 AAATTATTTCTTTACTTAAAACATTGT
1 AAATTATTTCTTTACTTAAAACATTGT
1592546 AAATT
1 AAATT
1592551 TAGTCCTCTA
Statistics
Matches: 41, Mismatches: 8, Indels: 14
0.65 0.13 0.22
Matches are distributed among these distances:
24 13 0.32
25 5 0.12
26 5 0.12
27 18 0.44
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (27 bp):
AAATTATTTCTTTACTTAAAACATTGT
Found at i:1596211 original size:31 final size:31
Alignment explanation
Indices: 1596175--1596237 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
1596165 TGATAATATG
1596175 TTGTCTTTTGTTGAAATCAAGGTCTGGTTGT
1 TTGTCTTTTGTTGAAATCAAGGTCTGGTTGT
*
1596206 TTGTCTTTTGTTGAGATCAAGGTCTGGTTGT
1 TTGTCTTTTGTTGAAATCAAGGTCTGGTTGT
1596237 T
1 T
1596238 AGCATATGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.14, C:0.10, G:0.27, T:0.49
Consensus pattern (31 bp):
TTGTCTTTTGTTGAAATCAAGGTCTGGTTGT
Found at i:1598657 original size:42 final size:41
Alignment explanation
Indices: 1598591--1598915 Score: 344
Period size: 42 Copynumber: 7.7 Consensus size: 41
1598581 TAATTAGCGG
*
1598591 CGTTTGTTCCAAAAACGCCGCTATAGATCCTACCTTTTGCGA
1 CGTTT-TTCCAAAAACGCCGCTATAGATCCAACCTTTTGCGA
* * * * *
1598633 CATTTTCTCCAAAAACACTGCTATAGATCTAACCTTTTGCGG
1 CGTTTT-TCCAAAAACGCCGCTATAGATCCAACCTTTTGCGA
* *
1598675 CGTTTTCTCCAAAAACGCCGCTATAGATCTCGACCTATTGCGA
1 CGTTTT-TCCAAAAACGCCGCTATAGATC-CAACCTTTTGCGA
* *
1598718 CATTTGTTCCAAAAACGCCGCTATAGATCCAACCTTTTGCTA
1 CGTTT-TTCCAAAAACGCCGCTATAGATCCAACCTTTTGCGA
* *
1598760 CGTTTGTACCAAAAACGCCGCTATAGATCCAACCTTTTACGA
1 CGTTT-TTCCAAAAACGCCGCTATAGATCCAACCTTTTGCGA
* *
1598802 CGTTTGTTCCAAAAACGCCGCTATAGATCTCAACCTATTGCGG
1 CGTTT-TTCCAAAAACGCCGCTATAGATC-CAACCTTTTGCGA
* *** * * ** *
1598845 TGTTTGTGAAAAAAACACCGCCATAGATCTGACCTTTTGCGG
1 CGTTT-TTCCAAAAACGCCGCTATAGATCCAACCTTTTGCGA
*
1598887 CATTTTCTCCAAAAACGCCGCTATAGATC
1 CGTTTT-TCCAAAAACGCCGCTATAGATC
1598916 TCGACCTATT
Statistics
Matches: 237, Mismatches: 41, Indels: 10
0.82 0.14 0.03
Matches are distributed among these distances:
41 2 0.01
42 166 0.70
43 68 0.29
44 1 0.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (41 bp):
CGTTTTTCCAAAAACGCCGCTATAGATCCAACCTTTTGCGA
Found at i:1598752 original size:85 final size:84
Alignment explanation
Indices: 1598587--1598915 Score: 412
Period size: 85 Copynumber: 3.9 Consensus size: 84
1598577 ACGTTAATTA
* * *
1598587 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCCTACCTTTTGCGACATTTTCTCCAAAAACACT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCCGACCTTTTGCGACATTTTCTCCAAAAACGCC
*
1598652 GCTATAGATCTAACCTTTT
66 GCTATAGATCCAACCTTTT
*
1598671 GCGGCGTTT-TCTCCAAAAACGCCGCTATAGATCTCGACCTATTGCGACATTTGT-TCCAAAAAC
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATC-CGACCTTTTGCGACATTT-TCTCCAAAAAC
1598734 GCCGCTATAGATCCAACCTTTT
63 GCCGCTATAGATCCAACCTTTT
** * * * *
1598756 GCTACGTTTGTACCAAAAACGCCGCTATAGATCCAACCTTTTACGACGTTTGT-TCCAAAAACGC
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCCGACCTTTTGCGACATTT-TCTCCAAAAACGC
*
1598820 CGCTATAGATCTCAACCTATT
65 CGCTATAGATC-CAACCTTTT
* *** * * * *
1598841 GCGGTGTTTGTGAAAAAAACACCGCCATAGATCTGACCTTTTGCGGCATTTTCTCCAAAAACGCC
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCCGACCTTTTGCGACATTTTCTCCAAAAACGCC
1598906 GCTATAGATC
66 GCTATAGATC
1598916 TCGACCTATT
Statistics
Matches: 213, Mismatches: 26, Indels: 11
0.85 0.10 0.04
Matches are distributed among these distances:
83 1 0.00
84 70 0.33
85 140 0.66
86 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (84 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCCGACCTTTTGCGACATTTTCTCCAAAAACGCC
GCTATAGATCCAACCTTTT
Found at i:1598819 original size:127 final size:127
Alignment explanation
Indices: 1598593--1598915 Score: 425
Period size: 127 Copynumber: 2.5 Consensus size: 127
1598583 ATTAGCGGCG
* * *
1598593 TTTGTTCCAAAAACGCCGCTATAGATCCTACCTTTTGCGACATTTTCTCCAAAAACACTGCTATA
1 TTTGTTCCAAAAACGCCGCTATAGATCCAACCTTTTGCGACATTTTCTCCAAAAACGCCGCTATA
* * * *
1598658 GATCTAACCTTTTGCGGCGTTTTCTCCAAAAACGCCGCTATAGATCTCGACCTATTGCGACA
66 GATCCAACCTTTTACGACGTTTTCTCCAAAAACGCCGCTATAGATCTCAACCTATTGCGACA
* * *
1598720 TTTGTTCCAAAAACGCCGCTATAGATCCAACCTTTTGCTACGTTTGT-ACCAAAAACGCCGCTAT
1 TTTGTTCCAAAAACGCCGCTATAGATCCAACCTTTTGCGACATTT-TCTCCAAAAACGCCGCTAT
***
1598784 AGATCCAACCTTTTACGACGTTTGT-TCCAAAAACGCCGCTATAGATCTCAACCTATTGCGGTG
65 AGATCCAACCTTTTACGACGTTT-TCTCCAAAAACGCCGCTATAGATCTCAACCTATTGCGACA
*** * * ** *
1598847 TTTGTGAAAAAAACACCGCCATAGATCTGACCTTTTGCGGCATTTTCTCCAAAAACGCCGCTATA
1 TTTGTTCCAAAAACGCCGCTATAGATCCAACCTTTTGCGACATTTTCTCCAAAAACGCCGCTATA
1598912 GATC
66 GATC
1598916 TCGACCTATT
Statistics
Matches: 169, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
126 1 0.01
127 166 0.98
128 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (127 bp):
TTTGTTCCAAAAACGCCGCTATAGATCCAACCTTTTGCGACATTTTCTCCAAAAACGCCGCTATA
GATCCAACCTTTTACGACGTTTTCTCCAAAAACGCCGCTATAGATCTCAACCTATTGCGACA
Found at i:1606123 original size:6 final size:6
Alignment explanation
Indices: 1606062--1606120 Score: 82
Period size: 6 Copynumber: 9.8 Consensus size: 6
1606052 AGACACGTAT
* * *
1606062 GACCAC GACCAC GACCAC GACCAC GACCTC AACCAC GACCAC GACCAT
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
*
1606110 GACCAT GACCA
1 GACCAC GACCA
1606121 TGAGCCAAGA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.34, C:0.46, G:0.15, T:0.05
Consensus pattern (6 bp):
GACCAC
Found at i:1608345 original size:14 final size:14
Alignment explanation
Indices: 1608312--1608367 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
1608302 TGACTGGATC
**
1608312 GAGTCAACTCGGACT
1 GAGTCAACTC-GTTT
1608327 GAGTCAACTCGTTT
1 GAGTCAACTCGTTT
* *
1608341 GAGTCAAATCATTT
1 GAGTCAACTCGTTT
*
1608355 GAGTCATCTCGTT
1 GAGTCAACTCGTT
1608368 AACTTTGACC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
14 24 0.71
15 10 0.29
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (14 bp):
GAGTCAACTCGTTT
Found at i:1611083 original size:31 final size:32
Alignment explanation
Indices: 1611045--1611129 Score: 106
Period size: 32 Copynumber: 2.7 Consensus size: 32
1611035 TAAGACGACC
*
1611045 CTTGGGTAGGCTCTGAGGCCCCGAG-ATCTTT
1 CTTGGGTAGGCTCTGAGGCCCCGAGTACCTTT
1611076 CTTGGGTAGGC-CTTGCA-GCCCCGAGTACCTTT
1 CTTGGGTAGGCTC-TG-AGGCCCCGAGTACCTTT
1611108 CTTGGGTAGGCTCTCG-GGCCCC
1 CTTGGGTAGGCTCT-GAGGCCCC
1611130 AAGGCATTCC
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
30 1 0.02
31 21 0.45
32 23 0.49
33 2 0.04
ACGTcount: A:0.11, C:0.31, G:0.32, T:0.27
Consensus pattern (32 bp):
CTTGGGTAGGCTCTGAGGCCCCGAGTACCTTT
Found at i:1611113 original size:32 final size:32
Alignment explanation
Indices: 1611045--1611118 Score: 100
Period size: 31 Copynumber: 2.3 Consensus size: 32
1611035 TAAGACGACC
*
1611045 CTTGGGTAGG-CTCTGAGGCCCCGAGATCTTT
1 CTTGGGTAGGCCTCTGAGGCCCCGAGACCTTT
1611076 CTTGGGTAGGCCT-TGCA-GCCCCGAGTACCTTT
1 CTTGGGTAGGCCTCTG-AGGCCCCGAG-ACCTTT
1611108 CTTGGGTAGGC
1 CTTGGGTAGGC
1611119 TCTCGGGCCC
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
31 20 0.51
32 19 0.49
ACGTcount: A:0.12, C:0.27, G:0.32, T:0.28
Consensus pattern (32 bp):
CTTGGGTAGGCCTCTGAGGCCCCGAGACCTTT
Found at i:1611952 original size:30 final size:31
Alignment explanation
Indices: 1611903--1611963 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
1611893 TTTGATTTAG
1611903 GGAAGATGATAAGGGTTAGGTATCTTGGTTT
1 GGAAGATGATAAGGGTTAGGTATCTTGGTTT
*
1611934 GGAAGATGATAA-GGTTAGGTGTCTTGGTTT
1 GGAAGATGATAAGGGTTAGGTATCTTGGTTT
1611964 AATAGTGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 17 0.59
31 12 0.41
ACGTcount: A:0.25, C:0.03, G:0.36, T:0.36
Consensus pattern (31 bp):
GGAAGATGATAAGGGTTAGGTATCTTGGTTT
Found at i:1617500 original size:80 final size:80
Alignment explanation
Indices: 1617359--1617521 Score: 191
Period size: 80 Copynumber: 2.0 Consensus size: 80
1617349 GGAAGATTTA
* * *** * * *
1617359 ATCGAGGCAGATTTGTTTCACTGCTCCTCAAGGAAGATCAAATATGGGAAAGGGATTTGCTCCGT
1 ATCGAGGCAGATTTGTTCCACTACTCCTCAAGGAAGATCAAATATAAAAAAAGGATATGCTCCGC
* *
1617424 TGTTCTTTAGGGTAG
66 TATTCTTCAGGGTAG
* * * * *
1617439 ATCGAGGTAGATTTGTTCCACTACTCCTCAGGGAAGATCAAATCTAAAAAAATGATATGCTCTGC
1 ATCGAGGCAGATTTGTTCCACTACTCCTCAAGGAAGATCAAATATAAAAAAAGGATATGCTCCGC
1617504 TATTCTTCAGGGTAG
66 TATTCTTCAGGGTAG
1617519 ATC
1 ATC
1617522 AAATAGGGAA
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (80 bp):
ATCGAGGCAGATTTGTTCCACTACTCCTCAAGGAAGATCAAATATAAAAAAAGGATATGCTCCGC
TATTCTTCAGGGTAG
Found at i:1618907 original size:8 final size:7
Alignment explanation
Indices: 1618859--1618932 Score: 55
Period size: 7 Copynumber: 10.4 Consensus size: 7
1618849 CTTTTATTTA
1618859 TTTTCTT
1 TTTTCTT
1618866 TTTTCTT
1 TTTTCTT
1618873 TTCTCTCATT
1 TT-T-TC-TT
*
1618883 TTTCCTT
1 TTTTCTT
*
1618890 TTTTCCT
1 TTTTCTT
1618897 TTTTC--
1 TTTTCTT
*
1618902 TATT-TT
1 TTTTCTT
1618908 TTTTCTT
1 TTTTCTT
*
1618915 TCTCTCTT
1 T-TTTCTT
1618923 TTTTCTT
1 TTTTCTT
1618930 TTT
1 TTT
1618933 AAGGCGAAGT
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
5 3 0.06
6 3 0.06
7 32 0.60
8 8 0.15
9 3 0.06
10 4 0.08
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTCTT
Found at i:1618908 original size:17 final size:17
Alignment explanation
Indices: 1618888--1618926 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1618878 TCATTTTTCC
*
1618888 TTTTTTCCTTTTTCTAT
1 TTTTTTCCTTTCTCTAT
* *
1618905 TTTTTTTCTTTCTCTCT
1 TTTTTTCCTTTCTCTAT
1618922 TTTTT
1 TTTTT
1618927 CTTTTTAAGG
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:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTCCTTTCTCTAT
Found at i:1618908 original size:24 final size:24
Alignment explanation
Indices: 1618853--1618909 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
1618843 ACCCCCCTTT
*
1618853 TATTTATTTTCTTTTTTCTTTTCTC
1 TATTT-TTTCCTTTTTTCTTTTCTC
1618878 TCA-TTTTTCCTTTTTTCCTTTT-TC
1 T-ATTTTTTCCTTTTTT-CTTTTCTC
1618902 TATTTTTT
1 TATTTTTT
1618910 TTCTTTCTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 1 0.04
24 18 0.64
25 8 0.29
26 1 0.04
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (24 bp):
TATTTTTTCCTTTTTTCTTTTCTC
Found at i:1628627 original size:23 final size:23
Alignment explanation
Indices: 1628591--1628644 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
1628581 TTGTAGAAAA
*
1628591 AGAGTTTTTTGGCTCTGGTAAAC
1 AGAGTTTTTCGGCTCTGGTAAAC
* *
1628614 ATAGTTTTTCGGCTCTGGTAAAT
1 AGAGTTTTTCGGCTCTGGTAAAC
1628637 AGAGTTTT
1 AGAGTTTT
1628645 CCAACTGGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.22, C:0.11, G:0.24, T:0.43
Consensus pattern (23 bp):
AGAGTTTTTCGGCTCTGGTAAAC
Found at i:1632483 original size:21 final size:22
Alignment explanation
Indices: 1632440--1632484 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1632430 TTCACATAGT
1632440 CTTATATTTCATTATCATATGA
1 CTTATATTTCATTATCATATGA
* *
1632462 CTTATATTT-ATTCTCCTATGA
1 CTTATATTTCATTATCATATGA
1632483 CT
1 CT
1632485 CTTCATAGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (22 bp):
CTTATATTTCATTATCATATGA
Found at i:1633011 original size:19 final size:19
Alignment explanation
Indices: 1632987--1633033 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
1632977 CTTTAACATG
1632987 TGCATCGATGCACTACCCA
1 TGCATCGATGCACTACCCA
1633006 TGCATCGATGCACTACCCA
1 TGCATCGATGCACTACCCA
1633025 TGCATCGAT
1 TGCATCGAT
1633034 ACACAAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (19 bp):
TGCATCGATGCACTACCCA
Found at i:1635810 original size:22 final size:23
Alignment explanation
Indices: 1635746--1635846 Score: 95
Period size: 23 Copynumber: 4.5 Consensus size: 23
1635736 TACCATGTAG
*
1635746 AAACAGAGTTTTCTGAA-TCTGGT
1 AAACAGAGTTTTC-CAACTCTGGT
* *
1635769 AAACAGAGTTTTCTAGCTCTGGT
1 AAACAGAGTTTTCCAACTCTGGT
1635792 AAA-AGTA-TTTTCCAACTCTGGT
1 AAACAG-AGTTTTCCAACTCTGGT
* *
1635814 AAACAGAGTTTTTCGA-T-TGGT
1 AAACAGAGTTTTCCAACTCTGGT
*
1635835 AAACAGGGTTTT
1 AAACAGAGTTTT
1635847 TGATTCTGAA
Statistics
Matches: 67, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
21 15 0.22
22 21 0.31
23 31 0.46
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.36
Consensus pattern (23 bp):
AAACAGAGTTTTCCAACTCTGGT
Found at i:1635851 original size:20 final size:21
Alignment explanation
Indices: 1635810--1635851 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1635800 TTTCCAACTC
1635810 TGGTAAACAGAGTTTTTCGAT
1 TGGTAAACAGAGTTTTTCGAT
*
1635831 TGGTAAACAGGGTTTTT-GAT
1 TGGTAAACAGAGTTTTTCGAT
1635851 T
1 T
1635852 CTGAAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.40
Consensus pattern (21 bp):
TGGTAAACAGAGTTTTTCGAT
Found at i:1640228 original size:30 final size:30
Alignment explanation
Indices: 1640176--1640374 Score: 206
Period size: 30 Copynumber: 6.7 Consensus size: 30
1640166 ATTTAATGAT
* * *
1640176 TTAAGGGACTAAAATAGCAAAAATAGGAAC
1 TTAAAGGACTAAAATAGTAAAAATAGAAAC
* *
1640206 TTAAAGAACTAGAATAGTAAAAATAGAAAC
1 TTAAAGGACTAAAATAGTAAAAATAGAAAC
* ** *
1640236 TTAAGGGACTAAAATAGTAAAAA-AGGCAT
1 TTAAAGGACTAAAATAGTAAAAATAGAAAC
* *
1640265 TTAAAGGACTAAAATAGTAAAAACAAAAAC
1 TTAAAGGACTAAAATAGTAAAAATAGAAAC
* * * * *
1640295 TTAAGGGACTAATATAGCAAAAATAGACAT
1 TTAAAGGACTAAAATAGTAAAAATAGAAAC
* *
1640325 TTAAAGGACTAAAATAGGAAAAATAAAAAC
1 TTAAAGGACTAAAATAGTAAAAATAGAAAC
*
1640355 TTAAGGGACT-AAATAG-AAAA
1 TTAAAGGACTAAAATAGTAAAA
1640375 TAAAAATAAT
Statistics
Matches: 138, Mismatches: 30, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
28 4 0.03
29 31 0.22
30 103 0.75
ACGTcount: A:0.57, C:0.08, G:0.16, T:0.19
Consensus pattern (30 bp):
TTAAAGGACTAAAATAGTAAAAATAGAAAC
Found at i:1640248 original size:60 final size:60
Alignment explanation
Indices: 1640176--1640374 Score: 280
Period size: 60 Copynumber: 3.4 Consensus size: 60
1640166 ATTTAATGAT
* * * *
1640176 TTAAGGGACTAAAATAGCAAAAATAGGAACTTAAAGAACTAGAATAGTAAAAATAGAAAC
1 TTAAGGGACTAAAATAGCAAAAATAGGAATTTAAAGGACTAAAATAGTAAAAATAAAAAC
* * *
1640236 TTAAGGGACTAAAATAGTAAAAA-AGGCATTTAAAGGACTAAAATAGTAAAAACAAAAAC
1 TTAAGGGACTAAAATAGCAAAAATAGGAATTTAAAGGACTAAAATAGTAAAAATAAAAAC
* *
1640295 TTAAGGGACTAATATAGCAAAAATA-GACATTTAAAGGACTAAAATAGGAAAAATAAAAAC
1 TTAAGGGACTAAAATAGCAAAAATAGGA-ATTTAAAGGACTAAAATAGTAAAAATAAAAAC
1640355 TTAAGGGACT-AAATAG-AAAA
1 TTAAGGGACTAAAATAGCAAAA
1640375 TAAAAATAAT
Statistics
Matches: 124, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
58 4 0.03
59 57 0.46
60 63 0.51
ACGTcount: A:0.57, C:0.08, G:0.16, T:0.19
Consensus pattern (60 bp):
TTAAGGGACTAAAATAGCAAAAATAGGAATTTAAAGGACTAAAATAGTAAAAATAAAAAC
Found at i:1640279 original size:89 final size:89
Alignment explanation
Indices: 1640174--1640347 Score: 224
Period size: 89 Copynumber: 2.0 Consensus size: 89
1640164 TCATTTAATG
* * ** *
1640174 ATTTAAGGGACTAAAATAGCAAAAATAGGAACTTAAAGAACTAGA-ATAGTAAAAATAGAAACTT
1 ATTTAAAGGACTAAAATAGCAAAAACAAAAACTTAAAGAACTA-ATATAGCAAAAATAGAAACTT
* *
1640238 AAGGGACTAAAATAGTAAAAAAGGC
65 AAAGGACTAAAATAGGAAAAAAGGC
* * * * *
1640263 ATTTAAAGGACTAAAATAGTAAAAACAAAAACTTAAGGGACTAATATAGCAAAAATAGACATTTA
1 ATTTAAAGGACTAAAATAGCAAAAACAAAAACTTAAAGAACTAATATAGCAAAAATAGAAACTTA
1640328 AAGGACTAAAATAGGAAAAA
66 AAGGACTAAAATAGGAAAAA
1640348 TAAAAACTTA
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
88 1 0.01
89 71 0.99
ACGTcount: A:0.56, C:0.08, G:0.16, T:0.20
Consensus pattern (89 bp):
ATTTAAAGGACTAAAATAGCAAAAACAAAAACTTAAAGAACTAATATAGCAAAAATAGAAACTTA
AAGGACTAAAATAGGAAAAAAGGC
Found at i:1640369 original size:89 final size:88
Alignment explanation
Indices: 1640176--1640374 Score: 213
Period size: 89 Copynumber: 2.2 Consensus size: 88
1640166 ATTTAATGAT
* ** * *
1640176 TTAAGGGACTAAAATAGCAAAAATAGGAACTTAAAGAACTAGAATAGTAAAAATAGAAACTTAAG
1 TTAAGGGACTAAAATAG-AAAAACAAAAACTTAAAGAACTAGAATAGCAAAAATAGAAACTTAAA
* *** *
1640241 GGACTAAAATAGTAAAAAAGGCAT
65 GGACTAAAATAGGAAAAAAAAAAC
* * * * *
1640265 TTAAAGGACTAAAATAGTAAAAACAAAAACTTAAGGGACTA-ATATAGCAAAAATAGACATTTAA
1 TTAAGGGACTAAAATAG-AAAAACAAAAACTTAAAGAACTAGA-ATAGCAAAAATAGAAACTTAA
1640329 AGGACTAAAATAGGAAAAATAAAAAC
64 AGGACTAAAATAGGAAAAA-AAAAAC
1640355 TTAAGGGACT-AAATAGAAAA
1 TTAAGGGACTAAAATAGAAAA
1640375 TAAAAATAAT
Statistics
Matches: 91, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
88 5 0.05
89 75 0.82
90 11 0.12
ACGTcount: A:0.57, C:0.08, G:0.16, T:0.19
Consensus pattern (88 bp):
TTAAGGGACTAAAATAGAAAAACAAAAACTTAAAGAACTAGAATAGCAAAAATAGAAACTTAAAG
GACTAAAATAGGAAAAAAAAAAC
Found at i:1641444 original size:12 final size:13
Alignment explanation
Indices: 1641422--1641457 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
1641412 TATAAATTAG
1641422 TTAATTAATAATA
1 TTAATTAATAATA
1641435 TTAA-TAATAATA
1 TTAATTAATAATA
1641447 -TAATTAATAAT
1 TTAATTAATAAT
1641458 TTTTTCGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.14
12 15 0.68
13 4 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAATTAATAATA
Found at i:1642091 original size:130 final size:130
Alignment explanation
Indices: 1641650--1642129 Score: 495
Period size: 130 Copynumber: 3.7 Consensus size: 130
1641640 TTGGTCGTCT
* * * ** *
1641650 AAGGGTGACATGGCTCCTACGTGATGAGG-AGATCTGGTCGGTGGATGACACAACTCATACGTGA
1 AAGGGTGACACGGCTCCTACATGATGAGGAAG-TCTGGTCGGGGGATGACACAGTTCCTACGTGA
* * * *
1641714 TGAAGA-GTTCTGGCCATCTTTAGGAAGGGTGATAACACGGTTCCTACACGATGAGGACGGCTGG
65 TGAGGACG-ACTGGCCATCTTTAGGAA---TGATAACACGGTTCCTACATGATGAGGACGACTGG
1641778 TTATC
126 TTATC
* * * * *
1641783 TAGTGGTGACACGGCTTCTACATTATGAGGAGGTCTAGTCGGGGGATGACACAGTTCCTACGTGA
1 AAG-GGTGACACGGCTCCTACATGATGAGGAAGTCTGGTCGGGGGATGACACAGTTCCTACGTGA
* * ** *
1641848 TGATGG-CGACTGGCCATCTTTAGGGATGATAACA-GGTTCCTACGTGATGAGGATAACTAGTTA
65 TGA-GGACGACTGGCCATCTTTAGGAATGATAACACGGTTCCTACATGATGAGGACGACTGGTTA
1641911 TC
129 TC
* * * * * * * ** *
1641913 AGGGGTGACACGACTCTTACATGATAAGGAGGTCTGGTCAGGGAATGACATGGTTCCTATGTGAT
1 AAGGGTGACACGGCTCCTACATGATGAGGAAGTCTGGTCGGGGGATGACACAGTTCCTACGTGAT
* * *
1641978 GAGGACGACAT-GCCATCTTTAGGAATAATAACACGGGTCCTAAATGATGAGGACGACTGGTTAT
66 GAGGACGAC-TGGCCATCTTTAGGAATGATAACACGGTTCCTACATGATGAGGACGACTGGTTAT
1642042 C
130 C
* * * **
1642043 AAGGGTGACATGGCTCCTACGTGATGAGGAAGTCTGGTCGGGGGATGACACGGTTTTTACGTGAT
1 AAGGGTGACACGGCTCCTACATGATGAGGAAGTCTGGTCGGGGGATGACACAGTTCCTACGTGAT
1642108 GAGGACGACAT-GCCATCTTTAG
66 GAGGACGAC-TGGCCATCTTTAG
1642130 AGATTTTGGT
Statistics
Matches: 286, Mismatches: 54, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
128 2 0.01
129 77 0.27
130 126 0.44
131 8 0.03
133 2 0.01
134 68 0.24
135 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (130 bp):
AAGGGTGACACGGCTCCTACATGATGAGGAAGTCTGGTCGGGGGATGACACAGTTCCTACGTGAT
GAGGACGACTGGCCATCTTTAGGAATGATAACACGGTTCCTACATGATGAGGACGACTGGTTATC
Found at i:1642337 original size:66 final size:68
Alignment explanation
Indices: 1642267--1642418 Score: 202
Period size: 68 Copynumber: 2.3 Consensus size: 68
1642257 GTCATTTAAG
*
1642267 AGAAAATGTCTCAAGAGAGACTAAAC-CCGTTT-CAAAGGAAACAAACTCAAAG-TTTTTTTTAT
1 AGAAAATGTCTCAAGAGAGACAAAACTCCGTTTCCAAA-GAAACAAACTCAAAGATTTTTTTTAT
1642329 CAAA
65 CAAA
* ** * *
1642333 AGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTTTTTTC
1 AGAAAATGTCTCAAGAGAGACAAAACTCCGTTTCCAAAGAAACAAACTCAAAGATTTTTTTTATC
1642398 AAA
66 AAA
* *
1642401 ATAAACTGTCTCAAGAGA
1 AGAAAATGTCTCAAGAGA
1642419 CAAAATTTGT
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
66 24 0.32
67 18 0.24
68 33 0.44
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.28
Consensus pattern (68 bp):
AGAAAATGTCTCAAGAGAGACAAAACTCCGTTTCCAAAGAAACAAACTCAAAGATTTTTTTTATC
AAA
Found at i:1642400 original size:68 final size:67
Alignment explanation
Indices: 1642267--1642430 Score: 203
Period size: 66 Copynumber: 2.5 Consensus size: 67
1642257 GTCATTTAAG
* **
1642267 AGAAAATGTCTCAAGAGAGACTAAAC-CCGTTTCAAAGGAAACAAACTCAAAGTTTTTTTTATCA
1 AGAAAATGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACAAACTCAAAGTTTTTTTTATCA
1642331 AA
66 AA
* * *
1642333 AGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCCAAA-GAAACAGACTCAAAGATTTTTTTTTT
1 AGAAAATGTCTCAAGAGAGACAAAACTTTGTTT-CAAAGGAAACAAACTCAAAG-TTTTTTTTAT
1642397 CAAA
64 CAAA
* *
1642401 ATAAACTGTCTC-A-AGAGACAAAA-TTTGTTT
1 AGAAAATGTCTCAAGAGAGACAAAACTTTGTTT
1642431 TTAAGAAACC
Statistics
Matches: 87, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
65 7 0.08
66 34 0.39
67 19 0.22
68 27 0.31
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (67 bp):
AGAAAATGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACAAACTCAAAGTTTTTTTTATCA
AA
Found at i:1642598 original size:32 final size:32
Alignment explanation
Indices: 1642557--1642619 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
1642547 TTCACATCAG
*
1642557 GATGTTGAATCCCCAAAGATGTCCCAACATTT
1 GATGTTGAATCCCCAAAGATGCCCCAACATTT
* *
1642589 GATGTTGAATCTCCAAAGATGCCCCACCATT
1 GATGTTGAATCCCCAAAGATGCCCCAACATT
1642620 CATCATTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (32 bp):
GATGTTGAATCCCCAAAGATGCCCCAACATTT
Found at i:1645922 original size:13 final size:13
Alignment explanation
Indices: 1645904--1645946 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
1645894 CATAACAAAT
*
1645904 AAAATGCATATGC
1 AAAATGCAGATGC
1645917 AAAATGCAAGATGC
1 AAAATGC-AGATGC
1645931 -AAATGCAGATGC
1 AAAATGCAGATGC
1645943 AAAA
1 AAAA
1645947 ATACAAGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 6 0.22
13 16 0.59
14 5 0.19
ACGTcount: A:0.51, C:0.14, G:0.19, T:0.16
Consensus pattern (13 bp):
AAAATGCAGATGC
Found at i:1645942 original size:26 final size:27
Alignment explanation
Indices: 1645905--1645955 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
1645895 ATAACAAATA
* *
1645905 AAATGCATATGC-AAAATGCAAGATGC
1 AAATGCAGATGCAAAAATACAAGATGC
1645931 AAATGCAGATGCAAAAATACAAGAT
1 AAATGCAGATGCAAAAATACAAGAT
1645956 AGTCCACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.51, C:0.14, G:0.18, T:0.18
Consensus pattern (27 bp):
AAATGCAGATGCAAAAATACAAGATGC
Found at i:1647198 original size:18 final size:18
Alignment explanation
Indices: 1647175--1647215 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1647165 ATGACTTTTT
1647175 ATTTTGGAAAATTGGCAG
1 ATTTTGGAAAATTGGCAG
** *
1647193 ATTTTGGATTATTGGCGG
1 ATTTTGGAAAATTGGCAG
1647211 ATTTT
1 ATTTT
1647216 AGATTAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.05, G:0.27, T:0.44
Consensus pattern (18 bp):
ATTTTGGAAAATTGGCAG
Found at i:1647220 original size:18 final size:18
Alignment explanation
Indices: 1647185--1647221 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1647175 ATTTTGGAAA
*
1647185 ATTGGCAGATTTTGGATT
1 ATTGGCAGATTTTAGATT
*
1647203 ATTGGCGGATTTTAGATT
1 ATTGGCAGATTTTAGATT
1647221 A
1 A
1647222 ATTTGAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.05, G:0.27, T:0.43
Consensus pattern (18 bp):
ATTGGCAGATTTTAGATT
Found at i:1648205 original size:30 final size:29
Alignment explanation
Indices: 1648164--1648366 Score: 167
Period size: 30 Copynumber: 6.8 Consensus size: 29
1648154 ATTCAATGAT
*
1648164 TTAAGGGACTAAAATAGCAAAAACATGAAA
1 TTAAAGGACTAAAATAGCAAAAACA-GAAA
* *
1648194 TTAAAGAACTAAAATAGCAAAAGCAGAAA
1 TTAAAGGACTAAAATAGCAAAAACAGAAA
* ** * *
1648223 CTTAAGGGACTAAAATAATAAAAATAGACAT
1 -TTAAAGGACTAAAATAGCAAAAACAGA-AA
* *
1648254 TTAAAGGACTAAAATAGTAAAAAAACAAAAA
1 TTAAAGGACTAAAATAG--CAAAAACAGAAA
* * *
1648285 CTTAAGGGACTAAAATAGCAAAAATAGACAT
1 -TTAAAGGACTAAAATAGCAAAAACAGA-AA
* *
1648316 TTAAAGGACTAAAATAGCAAAGAATATAAA
1 TTAAAGGACTAAAATAGCAAA-AACAGAAA
*
1648346 CTTAAGGGACT-AAATAG-AAAA
1 -TTAAAGGACTAAAATAGCAAAA
1648367 TAAAAATAAT
Statistics
Matches: 140, Mismatches: 25, Indels: 18
0.77 0.14 0.10
Matches are distributed among these distances:
28 1 0.01
29 7 0.05
30 92 0.66
31 17 0.12
32 23 0.16
ACGTcount: A:0.58, C:0.09, G:0.14, T:0.18
Consensus pattern (29 bp):
TTAAAGGACTAAAATAGCAAAAACAGAAA
Found at i:1648308 original size:62 final size:60
Alignment explanation
Indices: 1648164--1648366 Score: 250
Period size: 62 Copynumber: 3.4 Consensus size: 60
1648154 ATTCAATGAT
* * * * * *
1648164 TTAAGGGACTAAAATAGCAAAAACATGA-AATTAAAGAACTAAAATAGCAAAAGCAGAAAC
1 TTAAGGGACTAAAATAGCAAAAATA-GACATTTAAAGGACTAAAATAGAAAAAACAAAAAC
**
1648224 TTAAGGGACTAAAATAATAAAAATAGACATTTAAAGGACTAAAATAGTAAAAAAACAAAAAC
1 TTAAGGGACTAAAATAGCAAAAATAGACATTTAAAGGACTAAAATAG--AAAAAACAAAAAC
* * *
1648286 TTAAGGGACTAAAATAGCAAAAATAGACATTTAAAGGACTAAAATAGCAAAGAATATAAAC
1 TTAAGGGACTAAAATAGCAAAAATAGACATTTAAAGGACTAAAATAG-AAAAAACAAAAAC
1648347 TTAAGGGACT-AAATAG-AAAA
1 TTAAGGGACTAAAATAGCAAAA
1648367 TAAAAATAAT
Statistics
Matches: 126, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
59 6 0.05
60 45 0.36
61 20 0.16
62 55 0.44
ACGTcount: A:0.58, C:0.09, G:0.14, T:0.18
Consensus pattern (60 bp):
TTAAGGGACTAAAATAGCAAAAATAGACATTTAAAGGACTAAAATAGAAAAAACAAAAAC
Found at i:1648325 original size:92 final size:90
Alignment explanation
Indices: 1648162--1648366 Score: 216
Period size: 92 Copynumber: 2.3 Consensus size: 90
1648152 TCATTCAATG
* * * *
1648162 ATTTAAGGGACTAAAATAGCAAAAACATGAAATTAAAGAACTAAAATAGCAAAAGCAGAAACTTA
1 ATTTAAAGGACTAAAATAGAAAAAACATAAAATTAAAGAACTAAAATAGCAAAAACAGAAACTTA
*
1648227 AGGGACTAAAATAATAAAAATAGAC
66 AAGGACTAAAATAATAAAAATAGAC
* * * * *
1648252 ATTTAAAGGACTAAAATAGTAAAAAAACA-AAAACTTAAGGGACTAAAATAGCAAAAATAGACAT
1 ATTTAAAGGACTAAAATAG--AAAAAACATAAAA-TTAAAGAACTAAAATAGCAAAAACAGAAAC
** * *
1648316 TTAAAGGACTAAAATAGCAAAGAATATAA
63 TTAAAGGACTAAAATAATAAA-AATAGAC
* *
1648345 ACTTAAGGGACT-AAATAGAAAA
1 ATTTAAAGGACTAAAATAGAAAA
1648367 TAAAAATAAT
Statistics
Matches: 95, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
90 22 0.23
91 3 0.03
92 55 0.58
93 15 0.16
ACGTcount: A:0.58, C:0.09, G:0.14, T:0.19
Consensus pattern (90 bp):
ATTTAAAGGACTAAAATAGAAAAAACATAAAATTAAAGAACTAAAATAGCAAAAACAGAAACTTA
AAGGACTAAAATAATAAAAATAGAC
Found at i:1649855 original size:20 final size:20
Alignment explanation
Indices: 1649830--1649869 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1649820 TGGGTTATGT
1649830 TGTTGGGCTAGTGTATTGGG
1 TGTTGGGCTAGTGTATTGGG
* *
1649850 TGTTGGGTTGGTGTATTGGG
1 TGTTGGGCTAGTGTATTGGG
1649870 GCTAATTGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.07, C:0.03, G:0.47, T:0.42
Consensus pattern (20 bp):
TGTTGGGCTAGTGTATTGGG
Found at i:1650894 original size:39 final size:39
Alignment explanation
Indices: 1650840--1650931 Score: 175
Period size: 39 Copynumber: 2.4 Consensus size: 39
1650830 TGAATTACTG
1650840 CATAAATTTGGTTTTGTGCACTTGGGCATTACACATGTC
1 CATAAATTTGGTTTTGTGCACTTGGGCATTACACATGTC
*
1650879 CATAAATTTGGTTTTGTGTACTTGGGCATTACACATGTC
1 CATAAATTTGGTTTTGTGCACTTGGGCATTACACATGTC
1650918 CATAAATTTGGTTT
1 CATAAATTTGGTTT
1650932 CCCGCATTTA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (39 bp):
CATAAATTTGGTTTTGTGCACTTGGGCATTACACATGTC
Found at i:1652547 original size:23 final size:23
Alignment explanation
Indices: 1652520--1652573 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
1652510 AAAAGGAAGA
*
1652520 AAAACAACGTAAAAGAACATAAC
1 AAAACAAAGTAAAAGAACATAAC
1652543 AAAACAAAGTAAAAGAACATAAC
1 AAAACAAAGTAAAAGAACATAAC
1652566 AAAACAAA
1 AAAACAAA
1652574 AAACCAACAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.70, C:0.15, G:0.07, T:0.07
Consensus pattern (23 bp):
AAAACAAAGTAAAAGAACATAAC
Found at i:1659834 original size:14 final size:15
Alignment explanation
Indices: 1659815--1659843 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1659805 ATTAATTATT
1659815 TTATTTTT-ATAATA
1 TTATTTTTAATAATA
1659829 TTATTTTTAATAATA
1 TTATTTTTAATAATA
1659844 ATCAGTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTTTTAATAATA
Found at i:1660170 original size:20 final size:20
Alignment explanation
Indices: 1660123--1660203 Score: 58
Period size: 20 Copynumber: 4.0 Consensus size: 20
1660113 AACCCTAACT
*
1660123 CTAATTGCCAA-ATTGAGTACC
1 CTAATT-CCAACATT-AGAACC
* *
1660144 ATAATTCCCACATTAGAACC
1 CTAATTCCAACATTAGAACC
*
1660164 CTAATTCTAACAATT-GAACC
1 CTAATTCCAAC-ATTAGAACC
* * *
1660184 CTAATTTCTATATTAGAACC
1 CTAATTCCAACATTAGAACC
1660204 GTATTTACCA
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
19 3 0.06
20 33 0.70
21 11 0.23
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.31
Consensus pattern (20 bp):
CTAATTCCAACATTAGAACC
Found at i:1660786 original size:21 final size:21
Alignment explanation
Indices: 1660760--1660806 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1660750 TGGTTAGTTA
1660760 AAAAATTAAAAGGTCAATTTG
1 AAAAATTAAAAGGTCAATTTG
* *
1660781 AAAAATTAAATGGTCAATTTT
1 AAAAATTAAAAGGTCAATTTG
1660802 AAAAA
1 AAAAA
1660807 AAAAAATGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.55, C:0.04, G:0.11, T:0.30
Consensus pattern (21 bp):
AAAAATTAAAAGGTCAATTTG
Found at i:1660813 original size:22 final size:21
Alignment explanation
Indices: 1660757--1660814 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
1660747 AAATGGTTAG
1660757 TTAAAAAATTAAAA-GGTCAAT
1 TTAAAAAA-TAAAATGGTCAAT
* *
1660778 TTGAAAAATTAAATGGTCAATT
1 TTAAAAAATAAAATGGTCAA-T
*
1660800 TTAAAAAAAAAAATG
1 TTAAAAAATAAAATG
1660815 AGCATATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 4 0.13
21 13 0.43
22 13 0.43
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.29
Consensus pattern (21 bp):
TTAAAAAATAAAATGGTCAAT
Found at i:1662381 original size:51 final size:50
Alignment explanation
Indices: 1662288--1662384 Score: 122
Period size: 51 Copynumber: 1.9 Consensus size: 50
1662278 ATATTACAAC
* * * **
1662288 ATATTTTTTAAAAATACGGTTTTTGAAAATATATATGGTATATATATTAG
1 ATATTTTTTAAAAATACAGTTTTTAAAAACATATATAATATATATATTAG
* *
1662338 ATATTTTTTAAAATATATAGTTTTTAAAAACATATTTAATATATATA
1 ATATTTTTTAAAA-ATACAGTTTTTAAAAACATATATAATATATATA
1662385 ATTATTGAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
50 13 0.33
51 26 0.67
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.47
Consensus pattern (50 bp):
ATATTTTTTAAAAATACAGTTTTTAAAAACATATATAATATATATATTAG
Found at i:1662399 original size:28 final size:28
Alignment explanation
Indices: 1662344--1662399 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1662334 TTAGATATTT
* *
1662344 TTTAAAATATATAGTTTTTAAAAACATA
1 TTTAAAATATATAATTATTAAAAACATA
* * *
1662372 TTTAATATATATAATTATTGAAATCATA
1 TTTAAAATATATAATTATTAAAAACATA
1662400 AGGTTTTTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (28 bp):
TTTAAAATATATAATTATTAAAAACATA
Found at i:1662469 original size:22 final size:20
Alignment explanation
Indices: 1662419--1662467 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1662409 AAAATACAAC
1662419 ATATAT-TATATAGTTTTTA
1 ATATATATATATAGTTTTTA
1662438 A-A-A-ATATATAGTTTTTA
1 ATATATATATATAGTTTTTA
1662455 ATATATATATATA
1 ATATATATATATA
1662468 TATATAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 15 0.58
18 2 0.08
19 2 0.08
20 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
ATATATATATATAGTTTTTA
Found at i:1662469 original size:46 final size:43
Alignment explanation
Indices: 1662326--1662480 Score: 118
Period size: 46 Copynumber: 3.4 Consensus size: 43
1662316 ATATATATGG
* *
1662326 TATATATATTAGATATTTTTTAAAATATATAGTTTTTAAAAACA
1 TATATATATTATATA-TTTTTAAAATATATAGTTTTTAAATACA
* * *
1662370 TATTTA-ATATATATAATTATTGAAATCATA-AGGTTTTTGAAAATACA
1 TATATATAT-TATAT-ATTTTTAAAAT-ATATA-GTTTTT--AAATACA
* *
1662417 -ACATATATTATATAGTTTTTAAAAATATATAGTTTTTAATATATA
1 TATATATATTATATA-TTTTT-AAAATATATAGTTTTTAA-ATACA
1662462 TATATATATATAGTATATT
1 TATATATAT-TA-TATATT
1662481 ATTGTTATTA
Statistics
Matches: 86, Mismatches: 11, Indels: 25
0.70 0.09 0.20
Matches are distributed among these distances:
43 2 0.02
44 20 0.23
45 15 0.17
46 28 0.33
47 17 0.20
48 4 0.05
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.47
Consensus pattern (43 bp):
TATATATATTATATATTTTTAAAATATATAGTTTTTAAATACA
Found at i:1663202 original size:21 final size:21
Alignment explanation
Indices: 1663175--1663221 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1663165 AGTTTTGAGT
*
1663175 GAAAACCATAAAAAAGAGAAAA
1 GAAACCCA-AAAAAAGAGAAAA
* *
1663197 GAAACCCAAAAAGAGAGAGAA
1 GAAACCCAAAAAAAGAGAAAA
1663218 GAAA
1 GAAA
1663222 ACGGAGAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.68, C:0.11, G:0.19, T:0.02
Consensus pattern (21 bp):
GAAACCCAAAAAAAGAGAAAA
Done.