Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001111.1 Hibiscus syriacus cultivar Beakdansim tig00002193_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: 3891333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 17
Found at i:1549868 original size:18 final size:18
Alignment explanation
Indices: 1549832--1549877 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
1549822 AATAAAAAAT
* *
1549832 ATAATGAATTGTGATAATG
1 ATAATG-ATAGTGACAATG
1549851 ATAATGATAGTGACAATG
1 ATAATGATAGTGACAATG
1549869 ATAATGATA
1 ATAATGATA
1549878 ATGATGTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.46, C:0.02, G:0.20, T:0.33
Consensus pattern (18 bp):
ATAATGATAGTGACAATG
Found at i:1549888 original size:18 final size:18
Alignment explanation
Indices: 1549843--1549946 Score: 88
Period size: 18 Copynumber: 5.9 Consensus size: 18
1549833 TAATGAATTG
* *
1549843 TGATAATGATAATGATAG
1 TGATGATGATAATGATAA
**
1549861 TGACAATGATAATGATAA
1 TGATGATGATAATGATAA
* *
1549879 TGATGTTGATAATGATAT
1 TGATGATGATAATGATAA
*
1549897 TGATGATGAT--T-ATGA
1 TGATGATGATAATGATAA
* *
1549912 TGATAATGATAATGATGA
1 TGATGATGATAATGATAA
* *
1549930 TGATGTTGATAAGGATA
1 TGATGATGATAATGATA
1549947 TATATATGTG
Statistics
Matches: 69, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
15 11 0.16
16 1 0.01
17 1 0.01
18 56 0.81
ACGTcount: A:0.40, C:0.01, G:0.23, T:0.36
Consensus pattern (18 bp):
TGATGATGATAATGATAA
Found at i:1557335 original size:41 final size:40
Alignment explanation
Indices: 1557283--1557361 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 40
1557273 ATTATCAACA
* *
1557283 TTTGTTGGCCACCGTTTTCCTTTCCA-TGACTTTTCAACAAT
1 TTTGTTAGCCACCATTTTCCTTT-CATTGAC-TTTCAACAAT
1557324 TTTGTTAGCCACCATTTTCCTTTCATTGACTTTCAACA
1 TTTGTTAGCCACCATTTTCCTTTCATTGACTTTCAACA
1557362 GGACGTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
40 10 0.29
41 25 0.71
ACGTcount: A:0.19, C:0.27, G:0.10, T:0.44
Consensus pattern (40 bp):
TTTGTTAGCCACCATTTTCCTTTCATTGACTTTCAACAAT
Found at i:1559465 original size:23 final size:23
Alignment explanation
Indices: 1559435--1559537 Score: 98
Period size: 23 Copynumber: 4.5 Consensus size: 23
1559425 GAGTCGAGGG
*
1559435 TTCTACGTGGTCCTTCGGGATAA
1 TTCTACGTGGTCCTTCGGGACAA
* *
1559458 TTCTACGTGGTCCTTCAGGACAT
1 TTCTACGTGGTCCTTCGGGACAA
* *
1559481 TTCTATGTGGTCCTTCGAGACAA
1 TTCTACGTGGTCCTTCGGGACAA
* * * ** *
1559504 TACTATGTGATCCTTCTAGACAT
1 TTCTACGTGGTCCTTCGGGACAA
*
1559527 TTCTATGTGGT
1 TTCTACGTGGT
1559538 ATTTCGGTGC
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 67 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAA
Found at i:1559491 original size:46 final size:46
Alignment explanation
Indices: 1559435--1559537 Score: 136
Period size: 46 Copynumber: 2.2 Consensus size: 46
1559425 GAGTCGAGGG
* * * * *
1559435 TTCTACGTGGTCCTTCGGGATAATTCTACGTGGTCCTTC-AGGACAT
1 TTCTATGTGGTCCTTCGAGACAATACTACGTGATCCTTCTA-GACAT
*
1559481 TTCTATGTGGTCCTTCGAGACAATACTATGTGATCCTTCTAGACAT
1 TTCTATGTGGTCCTTCGAGACAATACTACGTGATCCTTCTAGACAT
1559527 TTCTATGTGGT
1 TTCTATGTGGT
1559538 ATTTCGGTGC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
46 49 0.98
47 1 0.02
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (46 bp):
TTCTATGTGGTCCTTCGAGACAATACTACGTGATCCTTCTAGACAT
Found at i:1559667 original size:6 final size:6
Alignment explanation
Indices: 1559656--1559724 Score: 66
Period size: 6 Copynumber: 11.5 Consensus size: 6
1559646 ATATAAACTG
* * ** *
1559656 TGATAA TGATAA TGATAG TGACAA TGATAA TGATGT TGATAA TGATAT
1 TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA
* * *
1559704 TGATGA TGATGA TGATGA TGA
1 TGATAA TGATAA TGATAA TGA
1559725 GGATATATAT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.35
Consensus pattern (6 bp):
TGATAA
Found at i:1559681 original size:18 final size:17
Alignment explanation
Indices: 1559654--1559724 Score: 79
Period size: 18 Copynumber: 4.0 Consensus size: 17
1559644 ATATATAAAC
1559654 TGTGATAATGATAATGA
1 TGTGATAATGATAATGA
*
1559671 TAGTGACAATGATAATGA
1 T-GTGATAATGATAATGA
*
1559689 TGTTGATAATGATATTGA
1 TG-TGATAATGATAATGA
* *
1559707 TGATGATGATGATGATGA
1 TG-TGATAATGATAATGA
1559725 GGATATATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
17 2 0.04
18 43 0.96
ACGTcount: A:0.38, C:0.01, G:0.25, T:0.35
Consensus pattern (17 bp):
TGTGATAATGATAATGA
Found at i:1562980 original size:37 final size:37
Alignment explanation
Indices: 1562855--1563017 Score: 152
Period size: 37 Copynumber: 4.4 Consensus size: 37
1562845 ATTATAAAAG
* * *
1562855 AGTTTCTCTTGAAACAAA--ATTGATCTCACTTGAGATT
1 AGTTTCTCTTGAAACAAAGTTTTG-TCTCTCTTGAGA-C
* * ** * *
1562892 ATTTTCCCTAAAAAC-AAGTTTTATCTCACTTGAGAC
1 AGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGAC
* * *
1562928 AATTTATCTTAAAACAAAGTTTTGTCTCTCTTGAGAC
1 AGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGAC
* * *
1562965 AGTGTCTCTTGAAACAAAATTTTGTCTCTATTGAGAC
1 AGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGAC
1563002 AGTTTCTCTTGAAACA
1 AGTTTCTCTTGAAACA
1563018 TCAAAACATT
Statistics
Matches: 103, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
36 13 0.13
37 88 0.85
38 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (37 bp):
AGTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGAC
Found at i:1563064 original size:21 final size:21
Alignment explanation
Indices: 1563040--1563137 Score: 78
Period size: 21 Copynumber: 5.2 Consensus size: 21
1563030 GATTGTTTCC
1563040 CTTGAAACATATTTTGTCTCT
1 CTTGAAACATATTTTGTCTCT
* *
1563061 CTTG--AGAT-TGTT-TC-C-
1 CTTGAAACATATTTTGTCTCT
1563076 CTTGAAACATATTTTGTCTCT
1 CTTGAAACATATTTTGTCTCT
1563097 CTT-AAGACA-A--TT-TC-C-
1 CTTGAA-ACATATTTTGTCTCT
1563112 CTTGAAACATATTTTGTCTCT
1 CTTGAAACATATTTTGTCTCT
1563133 CTTGA
1 CTTGA
1563138 GACAGTTTCC
Statistics
Matches: 59, Mismatches: 4, Indels: 28
0.65 0.04 0.31
Matches are distributed among these distances:
15 10 0.17
16 5 0.08
17 7 0.12
18 10 0.17
19 7 0.12
20 5 0.08
21 15 0.25
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.45
Consensus pattern (21 bp):
CTTGAAACATATTTTGTCTCT
Found at i:1563073 original size:36 final size:36
Alignment explanation
Indices: 1563034--1563217 Score: 273
Period size: 36 Copynumber: 5.1 Consensus size: 36
1563024 CATTGAGATT
**
1563034 GTTTCCCTTGAAACATATTTTGTCTCTCTTGAGATT
1 GTTTCCCTTGAAACATATTTTGTCTCTCTTGAGACA
*
1563070 GTTTCCCTTGAAACATATTTTGTCTCTCTTAAGACA
1 GTTTCCCTTGAAACATATTTTGTCTCTCTTGAGACA
*
1563106 ATTTCCCTTGAAACATATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACATATTTTGTCTCTCTTGAGACA
*
1563142 GTTTCCCTTCAAACATATTTT-TCTCTCTTGAGACA
1 GTTTCCCTTGAAACATATTTTGTCTCTCTTGAGACA
* * *
1563177 GTTTACCTTGAAGCATATTTTGTCT-TGCTTGAGACC
1 GTTTCCCTTGAAACATATTTTGTCTCT-CTTGAGACA
1563213 GTTTC
1 GTTTC
1563218 TTTTAAAACA
Statistics
Matches: 134, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
35 33 0.25
36 101 0.75
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (36 bp):
GTTTCCCTTGAAACATATTTTGTCTCTCTTGAGACA
Found at i:1563227 original size:71 final size:72
Alignment explanation
Indices: 1563034--1563227 Score: 266
Period size: 71 Copynumber: 2.7 Consensus size: 72
1563024 CATTGAGATT
** *
1563034 GTTTCCCTTGAAACATATTTTGTCTCTCTTGAGATTGTTTCCCTTGAAACATATTTTGTCTCTCT
1 GTTTCCCTTGAAACATATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACATATTTTGTCTCTCT
1563099 TAAGACA
66 TAAGACA
* *
1563106 ATTTCCCTTGAAACATATTTTGTCTCTCTTGAGACAGTTTCCCTTCAAACATATTTT-TCTCTCT
1 GTTTCCCTTGAAACATATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACATATTTTGTCTCTCT
*
1563170 TGAGACA
66 TAAGACA
* * * **
1563177 GTTTACCTTGAAGCATATTTTGTCT-TGCTTGAGACCGTTTCTTTTAAAACA
1 GTTTCCCTTGAAACATATTTTGTCTCT-CTTGAGACAGTTTCCCTTAAAACA
1563228 AATTATACCT
Statistics
Matches: 109, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
70 1 0.01
71 55 0.50
72 53 0.49
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.43
Consensus pattern (72 bp):
GTTTCCCTTGAAACATATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACATATTTTGTCTCTCT
TAAGACA
Found at i:1563551 original size:138 final size:133
Alignment explanation
Indices: 1563273--1563554 Score: 298
Period size: 133 Copynumber: 2.1 Consensus size: 133
1563263 GTAGGAAACT
* * * * * * *
1563273 TGTCATCCACCGACCAAATCTCCTCATCACGTAGGAACCGCGTCACCCTTGGATATCAGTCGTCT
1 TGTCATCCACCGACCAAATCTCCTCATCACGTAAGAACCACATCACCCTTAGATACCAGCCGTCC
** * * * * *
1563338 TCATCAGGTAGGAACTATGTTATCATTATCCTTAAAGATGGTCAGTAGTCCTCATCGCGTAGGAA
66 TCATCACATAGGAACTATGTTATCATTATCCCTAAAGATGGCCAGTAGTCCTCATCACATAAGAA
1563403 CCG
131 CCG
* * * * *
1563406 TGTCATCCATCGACTAGATCTCCTCATCACGTAAGAGCCACATCACCCTTAGATAACCAGCCTTC
1 TGTCATCCACCGACCAAATCTCCTCATCACGTAAGAACCACATCACCCTTAGAT-ACCAGCCGTC
*
1563471 CTCATCACATAGGAA-TCATGTTATCACCATTTATCCCTAAATATGGCCAGTCA-TCCTCATCAC
65 CTCATCACATAGGAACT-ATGTTAT---CA-TTATCCCTAAAGATGGCCAGT-AGTCCTCATCAC
*
1563534 ATAAGAATCG
124 ATAAGAACCG
1563544 TGTCATCCACC
1 TGTCATCCACC
1563555 CTTAGATAGT
Statistics
Matches: 120, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
133 47 0.39
134 26 0.22
137 2 0.02
138 44 0.37
139 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.27
Consensus pattern (133 bp):
TGTCATCCACCGACCAAATCTCCTCATCACGTAAGAACCACATCACCCTTAGATACCAGCCGTCC
TCATCACATAGGAACTATGTTATCATTATCCCTAAAGATGGCCAGTAGTCCTCATCACATAAGAA
CCG
Found at i:1567654 original size:20 final size:19
Alignment explanation
Indices: 1567606--1567656 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1567596 AAATAATCAA
* *
1567606 CAAATTCGCAACGCGATCT
1 CAAATTCGCAATGCGAACT
1567625 CAAATTCGCAATGCGAACT
1 CAAATTCGCAATGCGAACT
*
1567644 CCAATTTCGCAAT
1 -CAAATTCGCAAT
1567657 ACAATTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (19 bp):
CAAATTCGCAATGCGAACT
Found at i:1567828 original size:26 final size:26
Alignment explanation
Indices: 1567790--1567839 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1567780 CGCGTTTATT
* * * *
1567790 TTCGTAACGCGAATTTTATTTTCGAA
1 TTCGAAACACGAATATTAATTTCGAA
1567816 TTCGAAACACGAATATTAATTTCG
1 TTCGAAACACGAATATTAATTTCG
1567840 TAAAAAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (26 bp):
TTCGAAACACGAATATTAATTTCGAA
Found at i:1568716 original size:19 final size:19
Alignment explanation
Indices: 1568692--1568735 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1568682 AGATACCATG
*
1568692 GAAGAGTTGAGGAGGGCAA
1 GAAGAGCTGAGGAGGGCAA
1568711 GAAGAGCTGAGGAGGGCAA
1 GAAGAGCTGAGGAGGGCAA
1568730 GAAGAG
1 GAAGAG
1568736 AGGAAATTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.39, C:0.07, G:0.48, T:0.07
Consensus pattern (19 bp):
GAAGAGCTGAGGAGGGCAA
Found at i:1569027 original size:19 final size:20
Alignment explanation
Indices: 1569005--1569042 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1568995 ATATTCTTGT
1569005 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
1569024 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
1569043 CGAGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:1570677 original size:28 final size:29
Alignment explanation
Indices: 1570632--1570693 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
1570622 TTTTCGATCT
* * *
1570632 TTTTTAGCATATAGTAATGTTT-TGGTCA
1 TTTTTAGCACATAATAATGTTTCCGGTCA
*
1570660 TTTTTAGCACCTAATAATGTTTCCGGTCA
1 TTTTTAGCACATAATAATGTTTCCGGTCA
1570689 TTTTT
1 TTTTT
1570694 TTAAAAATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 19 0.66
29 10 0.34
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.50
Consensus pattern (29 bp):
TTTTTAGCACATAATAATGTTTCCGGTCA
Found at i:1571104 original size:21 final size:21
Alignment explanation
Indices: 1571053--1571105 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1571043 ATTATGACTA
1571053 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
1571074 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
1571095 TCGCAATGCGA
1 TCGCAATGCGA
1571106 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1571138 original size:21 final size:20
Alignment explanation
Indices: 1571095--1571146 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1571085 TTTTCCCAAT
*
1571095 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
1571115 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
*
1571136 TCGCAACGCGA
1 TCGCAATGCGA
1571147 TACTGACTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:1571161 original size:20 final size:20
Alignment explanation
Indices: 1571136--1571208 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1571126 ATTTGGAAAA
1571136 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* * *
1571156 TCGCAACTCGATACTTAATT
1 TCGCAACGCGATACTGACTT
* *
1571176 TCGCAACTCAATACTGACTT
1 TCGCAACGCGATACTGACTT
*
1571196 TCGCAACGAGATA
1 TCGCAACGCGATA
1571209 ATACATAATC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:1571423 original size:22 final size:22
Alignment explanation
Indices: 1571395--1571438 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1571385 CACTCTCTCA
1571395 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1571417 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1571439 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1571739 original size:20 final size:20
Alignment explanation
Indices: 1571700--1571758 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
1571690 TTTATTCTCT
* **
1571700 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
1571720 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* * *
1571740 TGTTTCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
1571759 AGAAACTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.19, G:0.20, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:1573104 original size:18 final size:18
Alignment explanation
Indices: 1573079--1573123 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1573069 ACTTCGGGAT
1573079 CCATCACCTCACCCAGAG
1 CCATCACCTCACCCAGAG
*
1573097 CTATCACCTCACCCAGAG
1 CCATCACCTCACCCAGAG
1573115 CCATCACCT
1 CCATCACCT
1573124 GATCGACCCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.27, C:0.49, G:0.09, T:0.16
Consensus pattern (18 bp):
CCATCACCTCACCCAGAG
Found at i:1573711 original size:19 final size:20
Alignment explanation
Indices: 1573657--1573723 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
1573647 TAGTTTACTT
* *
1573657 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
* *
1573677 TCGTAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1573697 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1573716 TCGCAACG
1 TCGCAACG
1573724 ACAAAATCGG
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 14 0.38
20 23 0.62
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1573750 original size:19 final size:19
Alignment explanation
Indices: 1573696--1573778 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
1573686 GGAAATGGCT
1573696 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1573715 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
1573729 ATCGGAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1573748 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1573767 ATCGCAATGCGA
1 ATCGCAATGCGA
1573779 TTTGTGTTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
14 9 0.17
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 38 0.72
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1573790 original size:19 final size:19
Alignment explanation
Indices: 1573785--1573909 Score: 71
Period size: 20 Copynumber: 6.7 Consensus size: 19
1573775 GCGATTTGTG
*
1573785 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
1573804 TTTCGCATTGCGA-TTT--
1 TTTCGCATTGCGATTTTCA
*
1573820 TGTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
* ***
1573837 TTTCGTATTGCGATAGCCA
1 TTTCGCATTGCGATTTTCA
* **
1573856 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCATTGCGATTTTCA
* **
1573876 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCATTGCGATTTTCA
*
1573896 TTTTCGCGTTGCGA
1 -TTTCGCATTGCGA
1573910 AAGTAAGTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
14 6 0.07
15 3 0.03
16 4 0.04
17 4 0.04
18 3 0.03
19 24 0.27
20 43 0.48
21 3 0.03
ACGTcount: A:0.14, C:0.22, G:0.23, T:0.42
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:1573869 original size:20 final size:20
Alignment explanation
Indices: 1573844--1573909 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
1573834 TCATTTCGTA
*
1573844 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGTCATTTCCGCG
1573864 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGCG
*
1573884 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTCCGCG
1573904 TTGCGA
1 TTGCGA
1573910 AAGTAAGTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCG
Found at i:1573920 original size:20 final size:19
Alignment explanation
Indices: 1573855--1573935 Score: 81
Period size: 20 Copynumber: 4.1 Consensus size: 19
1573845 TGCGATAGCC
* *
1573855 ATTTCCGCGTTGCGATAGTC
1 ATTT-CGCGTTGCGAAAGTA
*
1573875 ATTTCCGCGTTGCGATAGTCA
1 ATTT-CGCGTTGCGAAAGT-A
*
1573896 TTTTCGCGTTGCGAAAGTA
1 ATTTCGCGTTGCGAAAGTA
*
1573915 AGTTTCGTGTTGCGAAAGTA
1 A-TTTCGCGTTGCGAAAGTA
1573935 A
1 A
1573936 ACTATTCTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
19 1 0.02
20 50 0.93
21 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (19 bp):
ATTTCGCGTTGCGAAAGTA
Found at i:1573927 original size:40 final size:39
Alignment explanation
Indices: 1573836--1573929 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 39
1573826 TGCGATTTTC
* * *
1573836 ATTTCGTATTGCGATAGCCATTTCCGCGTTGCGATAGTC
1 ATTTCGTGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
* * *
1573875 ATTTCCGCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTA
1 ATTT-CGTGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
1573915 AGTTTCGTGTTGCGA
1 A-TTTCGTGTTGCGA
1573930 AAGTAAACTA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
39 4 0.09
40 39 0.85
41 3 0.07
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (39 bp):
ATTTCGTGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
Found at i:1574308 original size:21 final size:20
Alignment explanation
Indices: 1574282--1574350 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
1574272 CTGTCATTCC
1574282 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
1574303 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
1574324 TCAAGAGTCCCCCCCACCGT
1 TCAAGAGTCCCCTCCATCGT
1574344 TCAAGAG
1 TCAAGAG
1574351 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:1574362 original size:41 final size:42
Alignment explanation
Indices: 1574272--1574362 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 42
1574262 CCCGACTCAC
* * *
1574272 CTGTCATTCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
1574314 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
1574355 CTGTCATC
1 CTGTCATC
1574363 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 23 0.53
42 20 0.47
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:1575799 original size:14 final size:14
Alignment explanation
Indices: 1575765--1575803 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1575755 TTGATTGTTT
1575765 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1575779 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
1575793 TGTTGATTTGT
1 AATTGATTTGT
1575804 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1575964 original size:19 final size:19
Alignment explanation
Indices: 1575940--1576007 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
1575930 ATCGCAACGA
1575940 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1575959 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1575978 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1575992 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1576008 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1576057 original size:20 final size:20
Alignment explanation
Indices: 1576041--1576087 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1576031 TCATTTCACA
*
1576041 TTGCGATAGCCATTTTCGCG
1 TTGCGATAACCATTTTCGCG
1576061 TTGCGATAACCATTTTCGCG
1 TTGCGATAACCATTTTCGCG
1576081 TTGCGAT
1 TTGCGAT
1576088 TTCCCCGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAACCATTTTCGCG
Found at i:1576326 original size:20 final size:20
Alignment explanation
Indices: 1576301--1576372 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
1576291 TTGAAGATGA
*
1576301 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGTATCTCG
* *
1576321 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGTATCTCG
** * *
1576342 TTGCGATAGTCAGTATCCCA
1 TTGCGATTTTCAGTATCTCG
1576362 TTGCGATTTTC
1 TTGCGATTTTC
1576373 CAAATTCGCA
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 25 0.62
21 15 0.38
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.43
Consensus pattern (20 bp):
TTGCGATTTTCAGTATCTCG
Found at i:1576386 original size:21 final size:20
Alignment explanation
Indices: 1576360--1576408 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1576350 GTCAGTATCC
*
1576360 CATTGCGATTTTCCAAATTCG
1 CATTGCGA-TTTACAAATTCG
**
1576381 CATTGCGATTTACTTATTCG
1 CATTGCGATTTACAAATTCG
1576401 CATTGCGA
1 CATTGCGA
1576409 ATTAGGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (20 bp):
CATTGCGATTTACAAATTCG
Found at i:1577425 original size:12 final size:12
Alignment explanation
Indices: 1577408--1577432 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1577398 ATATAATCCT
1577408 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1577420 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1577432 G
1 G
1577433 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1579783 original size:19 final size:19
Alignment explanation
Indices: 1579761--1579885 Score: 82
Period size: 19 Copynumber: 7.4 Consensus size: 19
1579751 GAAAATTACT
*
1579761 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1579780 ATCGCAA--CG--A-GATA
1 ATCGCAATGCGAAATGAAA
1579794 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1579813 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
1579827 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1579846 ATCGCAA--C--AA-GGGA
1 ATCGCAATGCGAAATGAAA
*
1579860 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1579879 ATCGCAA
1 ATCGCAA
1579886 CCCGAATTTA
Statistics
Matches: 80, Mismatches: 11, Indels: 30
0.66 0.09 0.25
Matches are distributed among these distances:
14 29 0.36
15 4 0.05
16 4 0.05
17 4 0.05
18 4 0.05
19 35 0.44
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1579798 original size:14 final size:14
Alignment explanation
Indices: 1579776--1579833 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
1579766 AATGCGAAAT
1579776 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
1579790 GATAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
1579808 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
*
1579823 GAGAATCGCAA
1 GAAAATCGCAA
1579834 TGTGAAATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:1579808 original size:33 final size:33
Alignment explanation
Indices: 1579761--1579886 Score: 198
Period size: 33 Copynumber: 3.8 Consensus size: 33
1579751 GAAAATTACT
* *
1579761 ATCGTAATGCGAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1579794 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1579827 ATCGCAATGTGAAATGAAAATCGCAACAAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1579860 ATCGCAAAGCGAAATGAAAATCGCAAC
1 ATCGCAATGCGAAATGAAAATCGCAAC
1579887 CCGAATTTAG
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 86 1.00
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1579916 original size:19 final size:19
Alignment explanation
Indices: 1579892--1579963 Score: 75
Period size: 19 Copynumber: 4.1 Consensus size: 19
1579882 GCAACCCGAA
*
1579892 TTTAGTTTCGTGTTGCGAT
1 TTTAGTTTCGCGTTGCGAT
1579911 TTTAGTTTCGCGTTGCGAT
1 TTTAGTTTCGCGTTGCGAT
1579930 TTT-G--T--CGTTGCGAT
1 TTTAGTTTCGCGTTGCGAT
*
1579944 TTTCA-TTTCGCATTGCGAT
1 TTT-AGTTTCGCGTTGCGAT
1579963 T
1 T
1579964 CTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
14 12 0.27
16 1 0.02
17 1 0.02
18 1 0.02
19 30 0.67
ACGTcount: A:0.11, C:0.15, G:0.24, T:0.50
Consensus pattern (19 bp):
TTTAGTTTCGCGTTGCGAT
Found at i:1579945 original size:33 final size:33
Alignment explanation
Indices: 1579903--1580028 Score: 191
Period size: 33 Copynumber: 3.8 Consensus size: 33
1579893 TTAGTTTCGT
* * *
1579903 GTTGCGATTTT-AGTTTCGCGTTGCGATTTTGTC
1 GTTGCGATTTTCA-TTTCGCATTGCGATTATATC
* *
1579936 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTATATC
1579969 GTTGCGATTTTCATTTCGCATTGCGATTATATC
1 GTTGCGATTTTCATTTCGCATTGCGATTATATC
1580002 GTTGCGATTTTCATTTCGCATTGCGAT
1 GTTGCGATTTTCATTTCGCATTGCGAT
1580029 AGTAATTTTT
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
33 86 0.99
34 1 0.01
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.46
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCATTGCGATTATATC
Found at i:1579994 original size:19 final size:19
Alignment explanation
Indices: 1579937--1580028 Score: 96
Period size: 19 Copynumber: 5.4 Consensus size: 19
1579927 GATTTTGTCG
1579937 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1579956 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1579970 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1579989 TTGCGA--TT-ATATCG--
1 TTGCGATTTTCATTTCGCA
1580003 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1580022 TTGCGAT
1 TTGCGAT
1580029 AGTAATTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 12 0.20
16 14 0.24
17 14 0.24
19 19 0.32
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1580154 original size:14 final size:14
Alignment explanation
Indices: 1580135--1580171 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1580125 CATCAATTAA
1580135 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1580149 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1580163 ACAAATCAA
1 ACAAATCAA
1580172 TTAAACAATC
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:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1581549 original size:21 final size:20
Alignment explanation
Indices: 1581525--1581585 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
1581515 GTGAATCGGG
*
1581525 CTCTTGAATGGTGAGAGGGAC
1 CTCTTGAACGGTGAGAGGG-C
* * *
1581546 CTCTTTAACGATGACAGTGGC
1 CTCTTGAACGGTGAGAG-GGC
*
1581567 CTCTTGAACGGTGGGAGGG
1 CTCTTGAACGGTGAGAGGG
1581586 GACTCTCGAG
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.18, G:0.36, T:0.25
Consensus pattern (20 bp):
CTCTTGAACGGTGAGAGGGC
Found at i:1581610 original size:42 final size:42
Alignment explanation
Indices: 1581564--1581643 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
1581554 CGATGACAGT
* * *
1581564 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
1581606 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
1581644 CAAGCGATTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:1581986 original size:91 final size:90
Alignment explanation
Indices: 1581808--1581992 Score: 273
Period size: 91 Copynumber: 2.0 Consensus size: 90
1581798 ATTTCAAACT
* *
1581808 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGAAAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
*
1581873 TGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
1581901 TTCAACCAAAAGAAAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGAAAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
1581965 GTATTGGCAGTAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
1581992 T
1 T
1581993 AAGCAATCTA
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
91 40 0.47
93 18 0.21
95 27 0.32
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (90 bp):
TTCAACCAAAAGAAAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:1583705 original size:20 final size:19
Alignment explanation
Indices: 1583678--1583799 Score: 102
Period size: 20 Copynumber: 6.8 Consensus size: 19
1583668 TCTTTTGGTT
1583678 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1583697 GATAATGAAAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1583718 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1583737 G--A-G--AATCGCAATGC
1 GAAATGAAAATCGCAACGA
1583751 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1583770 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
1583784 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1583800 TGCGCAATGC
Statistics
Matches: 81, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
14 20 0.25
16 4 0.05
17 4 0.05
19 21 0.26
20 30 0.37
21 2 0.02
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1583746 original size:14 final size:14
Alignment explanation
Indices: 1583727--1583782 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
1583717 GGAAATGACT
1583727 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
1583741 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
1583760 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1583774 ATCGCAACG
1 ATCGCAACG
1583783 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1583764 original size:33 final size:33
Alignment explanation
Indices: 1583678--1583799 Score: 154
Period size: 33 Copynumber: 3.5 Consensus size: 33
1583668 TCTTTTGGTT
1583678 GAAATGAAAATCGCAACGAGATAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAG---A-G--AATCGCAACGC
** *
1583717 GGAAATGACTATCGCAACGAGAGAATCGCAATGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1583751 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1583784 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1583800 TGCGCAATGC
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
33 46 0.61
34 10 0.13
36 1 0.01
37 1 0.01
40 18 0.24
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1584430 original size:20 final size:20
Alignment explanation
Indices: 1584378--1584489 Score: 118
Period size: 20 Copynumber: 5.5 Consensus size: 20
1584368 GCTATGTAAA
* *
1584378 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
1584398 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
1584418 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
* * *
1584439 TCGCATTGGGATTTACTTAA
1 TCGCATTGCGATTTACGTAT
*
1584459 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
*
1584479 TTGCATTGCGA
1 TCGCATTGCGA
1584490 ATTATGAAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
19 3 0.04
20 56 0.74
21 17 0.22
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:1584510 original size:21 final size:21
Alignment explanation
Indices: 1584486--1584545 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
1584476 TATTTGCATT
*
1584486 GCGAATTATGAAAATTGCAAC
1 GCGAATTACGAAAATTGCAAC
* * *
1584507 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATTGCAAC
* *
1584527 GCGAATTAGGAAAACTGCA
1 GCGAATTACGAAAATTGCA
1584546 TTGCGATAGT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATTGCAAC
Found at i:1584625 original size:20 final size:20
Alignment explanation
Indices: 1584602--1584682 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 20
1584592 ATTTACTTAT
1584602 TCGCATTGCGAATTGGAAAA
1 TCGCATTGCGAATTGGAAAA
**
1584622 TCGCAACGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
* *
1584643 TCGCATTGCG-ATTGTCATAA
1 TCGCATTGCGAATTG-GAAAA
*
1584663 TCGCGTTGCGAATCTGGAAA
1 TCGCATTGCGAAT-TGGAAA
1584683 CTGATTTGCG
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
19 4 0.08
20 20 0.42
21 22 0.46
22 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:1587703 original size:14 final size:14
Alignment explanation
Indices: 1587684--1587716 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1587674 TATTTTATAA
*
1587684 TAATATGAAAATTT
1 TAATATAAAAATTT
1587698 TAATATAAAAATTT
1 TAATATAAAAATTT
1587712 TAATA
1 TAATA
1587717 ATTATTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
TAATATAAAAATTT
Found at i:1592999 original size:6 final size:6
Alignment explanation
Indices: 1592988--1593012 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1592978 GATATGTATT
1592988 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
1593013 GCCGAGCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1603535 original size:18 final size:18
Alignment explanation
Indices: 1603512--1603551 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1603502 CGCCCTAATT
1603512 CGTAAAATATAACAGGCA
1 CGTAAAATATAACAGGCA
1603530 CGTAAAATATAACAGGCA
1 CGTAAAATATAACAGGCA
1603548 CGTA
1 CGTA
1603552 TCGTGATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.17
Consensus pattern (18 bp):
CGTAAAATATAACAGGCA
Found at i:1605189 original size:3 final size:3
Alignment explanation
Indices: 1605181--1605209 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1605171 AAAGAAAATA
1605181 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1605210 ACTTAATATA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1605259 original size:27 final size:27
Alignment explanation
Indices: 1605213--1605342 Score: 75
Period size: 26 Copynumber: 5.1 Consensus size: 27
1605203 ATAATAAACT
* *
1605213 TAATATA-TATATATTAAAAAACTATA
1 TAATATATTATATTTTCAAAAACTATA
*
1605239 TAATATATTATATTTTCAAAATC-ATA
1 TAATATATTATATTTTCAAAAACTATA
* *
1605265 TAATATGTT-TA----AAAAAACTATA
1 TAATATATTATATTTTCAAAAACTATA
* *
1605287 T-ATATTACATATGTTTTTCAAAAACTATA
1 TAATA-TA-TTAT-ATTTTCAAAAACTATA
*
1605316 T-ATAT-TATATGTTTTC-AAAACTATA
1 TAATATAT-TATATTTTCAAAAACTATA
1605341 TA
1 TA
1605343 TATGTTTTTA
Statistics
Matches: 80, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
21 8 0.10
22 5 0.06
23 1 0.01
24 1 0.01
25 12 0.15
26 23 0.29
27 15 0.19
28 1 0.01
29 14 0.17
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (27 bp):
TAATATATTATATTTTCAAAAACTATA
Found at i:1605317 original size:29 final size:26
Alignment explanation
Indices: 1605262--1605345 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 26
1605252 TTTCAAAATC
* **
1605262 ATATAATATGTTTAAAAAAACTATAT
1 ATATTATATGTTTTCAAAAACTATAT
1605288 ATATTACATATGTTTTTCAAAAACTATAT
1 ATATT--ATATG-TTTTCAAAAACTATAT
1605317 ATATTATATGTTTTC-AAAACTATAT
1 ATATTATATGTTTTCAAAAACTATAT
1605342 ATAT
1 ATAT
1605346 GTTTTTAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
25 14 0.27
26 9 0.17
27 5 0.10
28 5 0.10
29 19 0.37
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (26 bp):
ATATTATATGTTTTCAAAAACTATAT
Found at i:1605361 original size:46 final size:46
Alignment explanation
Indices: 1605292--1605424 Score: 134
Period size: 46 Copynumber: 2.9 Consensus size: 46
1605282 CTATATATAT
*
1605292 TACATATGTTTTTCAAAAACTATATATATTATATGTTTTCAAAACTA
1 TACATATGTTTTTCAAAAACTATATATATTATAT-TTTTCAAAACCA
* *
1605339 TATATATGTTTTT-AAAAACTATA-CTA-TATA-TTTTCAAAAACCA
1 TACATATGTTTTTCAAAAACTATATATATTATATTTTTC-AAAACCA
* *
1605382 TACATTATTTTTTTGACAAAAC--TATATATTATATATTTTCAAA
1 TACA-TATGTTTTTCA-AAAACTATATATATTATAT-TTTTCAAA
1605425 TATTCTATAT
Statistics
Matches: 72, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
42 5 0.07
43 9 0.12
44 14 0.19
45 5 0.07
46 19 0.26
47 15 0.21
48 5 0.07
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.45
Consensus pattern (46 bp):
TACATATGTTTTTCAAAAACTATATATATTATATTTTTCAAAACCA
Found at i:1605372 original size:22 final size:22
Alignment explanation
Indices: 1605241--1605420 Score: 105
Period size: 21 Copynumber: 7.7 Consensus size: 22
1605231 AAACTATATA
* *
1605241 ATATATTATATTTTCAAAATC-
1 ATATATTATATTTTTAAAAACT
* * **
1605262 ATATAATATGTTTAAAAAAACTAT
1 ATATATTATATTTTTAAAAAC--T
1605286 ATATATTACATATGTTTTTCAAAAACTAT
1 ATATATT--ATA--TTTTT-AAAAAC--T
*
1605315 ATATATTATATGTTTTCAAAACT
1 ATATATTATAT-TTTTAAAAACT
*
1605338 ATATA-TATGTTTTTAAAAACT
1 ATATATTATATTTTTAAAAACT
* *
1605359 ATACTA-TATATTTTCAAAAACC
1 ATA-TATTATATTTTTAAAAACT
* *
1605381 ATACATTATTTTTTTGACAAAACT
1 ATATATTATATTTTT-A-AAAACT
1605405 ATATATTATATATTTT
1 ATATATTATAT-TTTT
1605421 CAAATATTCT
Statistics
Matches: 124, Mismatches: 21, Indels: 24
0.73 0.12 0.14
Matches are distributed among these distances:
21 30 0.24
22 29 0.23
23 7 0.06
24 20 0.16
25 10 0.08
26 6 0.05
27 3 0.02
28 3 0.02
29 16 0.13
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.46
Consensus pattern (22 bp):
ATATATTATATTTTTAAAAACT
Found at i:1606211 original size:50 final size:51
Alignment explanation
Indices: 1606113--1606231 Score: 134
Period size: 50 Copynumber: 2.4 Consensus size: 51
1606103 GGGTGACTTC
* * * * **
1606113 TTCGTCGTGAAGTCG-AGTCCAAGTTGAATGTTCTTCTGAGCTGGATATCA
1 TTCGTTGTGAAGTTGAAATCCAACTTGAATGTTCTTCTGAGCTCAATATCA
* *
1606163 TTCGTTGTGAAGTTGAAATCCAACTTGAATGTTCTTC-GAGTTCAATATCT
1 TTCGTTGTGAAGTTGAAATCCAACTTGAATGTTCTTCTGAGCTCAATATCA
* *
1606213 TTCATTGCGAAGTTGAAAT
1 TTCGTTGTGAAGTTGAAAT
1606232 TGACCCTGAC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 39 0.67
51 19 0.33
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (51 bp):
TTCGTTGTGAAGTTGAAATCCAACTTGAATGTTCTTCTGAGCTCAATATCA
Found at i:1607706 original size:17 final size:18
Alignment explanation
Indices: 1607672--1607708 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1607662 TTTAAGATTT
1607672 TATATTCGATTCAAAATTA
1 TATATTCGATTC-AAATTA
1607691 TATATTCGATTC-AATTA
1 TATATTCGATTCAAATTA
1607708 T
1 T
1607709 TTAAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATTCGATTCAAATTA
Found at i:1614440 original size:12 final size:12
Alignment explanation
Indices: 1614423--1614447 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1614413 CTTTCAAACT
1614423 TAGTTTTCAAAA
1 TAGTTTTCAAAA
1614435 TAGTTTTCAAAA
1 TAGTTTTCAAAA
1614447 T
1 T
1614448 TGCCCGTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TAGTTTTCAAAA
Found at i:1621446 original size:21 final size:21
Alignment explanation
Indices: 1621420--1621461 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1621410 CCAGAATGGG
*
1621420 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1621441 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1621462 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1621593 original size:19 final size:19
Alignment explanation
Indices: 1621569--1621634 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 19
1621559 AGCCTCGGGG
*
1621569 TACTGTTCAAACAGTGATT
1 TACTGTTCAAACAGTAATT
*
1621588 TACTGTTCAAAGAGTAATT
1 TACTGTTCAAACAGTAATT
* *
1621607 TACTGTTCAAATAGTAAAT
1 TACTGTTCAAACAGTAATT
*
1621626 TACTATTCA
1 TACTGTTCA
1621635 TAAAAACATT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (19 bp):
TACTGTTCAAACAGTAATT
Found at i:1624257 original size:21 final size:21
Alignment explanation
Indices: 1624231--1624272 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1624221 CTAGAATGGG
*
1624231 GGGAATCGGTACACCTTCATA
1 GGGAATCGATACACCTTCATA
*
1624252 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACACCTTCATA
1624273 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACACCTTCATA
Found at i:1624414 original size:29 final size:31
Alignment explanation
Indices: 1624380--1624439 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1624370 AAATTTTGAA
*
1624380 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1624409 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1624440 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1626811 original size:12 final size:12
Alignment explanation
Indices: 1626794--1626818 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1626784 TTGGGGATGT
1626794 TTACTGTTTAAA
1 TTACTGTTTAAA
1626806 TTACTGTTTAAA
1 TTACTGTTTAAA
1626818 T
1 T
1626819 AGTAAATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TTACTGTTTAAA
Found at i:1626931 original size:29 final size:31
Alignment explanation
Indices: 1626899--1626958 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1626889 AAATTTTGAA
*
1626899 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1626928 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1626959 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1628817 original size:24 final size:24
Alignment explanation
Indices: 1628776--1628839 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
1628766 ATGGCCTGTG
* **
1628776 CTTTTGCAGTAGGCGAAGCTTGCT-
1 CTTTTGCAGCAGATGAAGCTTG-TA
1628800 CTTTTGCAGCAGATGAAGCTTGTA
1 CTTTTGCAGCAGATGAAGCTTGTA
*
1628824 CTTTTGTAGCAGATGA
1 CTTTTGCAGCAGATGA
1628840 GTCCCCTTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (24 bp):
CTTTTGCAGCAGATGAAGCTTGTA
Found at i:1631479 original size:18 final size:17
Alignment explanation
Indices: 1631455--1631501 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
1631445 GATAAGTTAG
1631455 TAAAATAGAAATAAAAA
1 TAAAATAGAAATAAAAA
* *
1631472 TCAAAATAGTAATGAAAA
1 T-AAAATAGAAATAAAAA
*
1631490 TAAAATAAAAAT
1 TAAAATAGAAAT
1631502 TCCTACCCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.21
Consensus pattern (17 bp):
TAAAATAGAAATAAAAA
Found at i:1633758 original size:2 final size:2
Alignment explanation
Indices: 1633714--1633739 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1633704 AATAAGCTTA
1633714 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1633740 TAAAAACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1633762 original size:12 final size:13
Alignment explanation
Indices: 1633712--1633763 Score: 54
Period size: 12 Copynumber: 4.1 Consensus size: 13
1633702 ATAATAAGCT
1633712 TAATATATATATA
1 TAATATATATATA
1633725 T-ATATATATATA
1 TAATATATATATA
* * *
1633737 TATTAAAAACTATA
1 TAATATATA-TATA
1633751 TAATATAT-TATA
1 TAATATATATATA
1633763 T
1 T
1633764 TTTTCAAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
12 17 0.55
13 5 0.16
14 9 0.29
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATATATATATA
Found at i:1633772 original size:27 final size:28
Alignment explanation
Indices: 1633716--1633783 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 28
1633706 TAAGCTTAAT
1633716 ATATATATATATATATATATATATTAAAA
1 ATATATA-ATATATATATATATATTAAAA
* *
1633745 ACTATATAATATAT-TATAT-TTTTCAAA
1 A-TATATAATATATATATATATATTAAAA
1633772 ATCATATAATAT
1 AT-ATATAATAT
1633784 GTTTTCAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 1 0.03
27 16 0.46
28 5 0.14
29 7 0.20
30 6 0.17
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (28 bp):
ATATATAATATATATATATATATTAAAA
Found at i:1633783 original size:20 final size:20
Alignment explanation
Indices: 1633752--1633804 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1633742 AAAACTATAT
*
1633752 AATATATTATAT-TTTTCAA
1 AATATATAATATGTTTTCAA
1633771 AATCATATAATATGTTTTCAA
1 AAT-ATATAATATGTTTTCAA
*
1633792 TATATATATATAT
1 AATATATA-ATAT
1633805 ATATTACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 3 0.10
20 13 0.45
21 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (20 bp):
AATATATAATATGTTTTCAA
Found at i:1633788 original size:22 final size:20
Alignment explanation
Indices: 1633752--1633806 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
1633742 AAAACTATAT
*
1633752 AATATATTATAT-TTTTCAA
1 AATATATAATATATTTTCAA
*
1633771 AATCATATAATATGTTTTCAA
1 AAT-ATATAATATATTTTCAA
*
1633792 TATATATATATATAT
1 AATATATA-ATATAT
1633807 ATTACATATG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 3 0.10
20 13 0.43
21 14 0.47
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (20 bp):
AATATATAATATATTTTCAA
Found at i:1633833 original size:27 final size:26
Alignment explanation
Indices: 1633802--1633882 Score: 80
Period size: 25 Copynumber: 3.2 Consensus size: 26
1633792 TATATATATA
1633802 TATATATTACATATGGTTTTCAAAAAC
1 TATATATTA-ATATGGTTTTCAAAAAC
1633829 TATATATATTAA-AT-GTTTTC-AAAAC
1 --TATATATTAATATGGTTTTCAAAAAC
* * *
1633854 TATATAATAATATGATTTT-AAAAGC
1 TATATATTAATATGGTTTTCAAAAAC
1633879 TATA
1 TATA
1633883 CTATATATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
23 9 0.20
24 2 0.04
25 17 0.37
26 6 0.13
27 2 0.04
28 1 0.02
29 9 0.20
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.42
Consensus pattern (26 bp):
TATATATTAATATGGTTTTCAAAAAC
Found at i:1635507 original size:64 final size:63
Alignment explanation
Indices: 1635299--1635507 Score: 228
Period size: 65 Copynumber: 3.2 Consensus size: 63
1635289 TTTCAAAGTG
* **
1635299 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATT
1 ATGCATCGATGCACCAA-CCATGCATCGATGCACTCA-GG--TATTTTGAAACATCGAATGCATT
1635362 TC
62 TC
*
1635364 ATGCATCGATGCA-CATACTATGCATCGATGCACTCAGAGT-TTTATGAAAACATCGAATGCATT
1 ATGCATCGATGCACCA-ACCATGCATCGATGCACTCAG-GTATTT-TG-AAACATCGAATGCATT
*
1635427 TG
62 TC
* * * *
1635429 ATTCATCGATGCACCAGCCATGCATCAATGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCACCAACCATGCATCGATGCACTCAGG-TATTTTGAAACATCGAATGCATTTC
1635493 ATGCATCGATGCACC
1 ATGCATCGATGCACC
1635508 TAGTGTATAC
Statistics
Matches: 124, Mismatches: 11, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 50 0.40
65 65 0.52
66 5 0.04
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (63 bp):
ATGCATCGATGCACCAACCATGCATCGATGCACTCAGGTATTTTGAAACATCGAATGCATTTC
Found at i:1641272 original size:21 final size:21
Alignment explanation
Indices: 1641243--1641282 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1641233 TACATCCCTT
* *
1641243 TGAATGTGCATAGATACACCA
1 TGAAGGTGCACAGATACACCA
*
1641264 TGAAGGTGCACCGATACAC
1 TGAAGGTGCACAGATACAC
1641283 GCCTTGAATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.20
Consensus pattern (21 bp):
TGAAGGTGCACAGATACACCA
Found at i:1641295 original size:23 final size:22
Alignment explanation
Indices: 1641204--1641301 Score: 87
Period size: 23 Copynumber: 4.5 Consensus size: 22
1641194 TTTGTGCTTA
*
1641204 GTGCATCGATACA--CTT-AACA
1 GTGCATCGATACACCCTTGAA-T
1641224 GTGCATCGATACATCCCTTTGAAT
1 GTGCATCGATACA-CCC-TTGAAT
* * *
1641248 GTGCATAGATACA-CCATGAAG
1 GTGCATCGATACACCCTTGAAT
*
1641269 GTGCACCGATACACGCCTTGAAT
1 GTGCATCGATACAC-CCTTGAAT
1641292 GTGCATCGAT
1 GTGCATCGAT
1641302 GCACAAGGCC
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
20 13 0.21
21 15 0.24
22 2 0.03
23 16 0.26
24 14 0.23
25 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (22 bp):
GTGCATCGATACACCCTTGAAT
Found at i:1647613 original size:21 final size:19
Alignment explanation
Indices: 1647580--1647621 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 19
1647570 AGTTTATTTT
1647580 CATTTTTCAATTTTGAAACAA
1 CATTTTTCAATTTT-AAA-AA
1647601 CATTTTT-ATATTTTAAAAA
1 CATTTTTCA-ATTTTAAAAA
1647620 CA
1 CA
1647622 ATTTCTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.20
20 4 0.20
21 12 0.60
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.45
Consensus pattern (19 bp):
CATTTTTCAATTTTAAAAA
Found at i:1651995 original size:65 final size:59
Alignment explanation
Indices: 1651926--1652077 Score: 159
Period size: 56 Copynumber: 2.5 Consensus size: 59
1651916 GAATAAATTG
* *
1651926 AACATCGAATGCATTTCATGCATCGATGCATATACTATGCATCGATGCACTCAGGGT-TTTATGA
1 AACATCGAATGCATTTCATGCATCGATGC----AC-ATACATCGATGCACTCAGGCTATTT-T-A
1651990 A
59 A
* *
1651991 AACATCGAATGCATTTGATGCA-CCA-GC-CATACATCGATGCACTCAGGCTATTTTAA
1 AACATCGAATGCATTTCATGCATCGATGCACATACATCGATGCACTCAGGCTATTTTAA
* *
1652047 AACATCGAATGCATTTTATGTATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
1652078 TCTTAGCGCA
Statistics
Matches: 76, Mismatches: 7, Indels: 14
0.78 0.07 0.14
Matches are distributed among these distances:
56 22 0.29
57 22 0.29
58 6 0.08
59 1 0.01
63 2 0.03
64 2 0.03
65 21 0.28
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.30
Consensus pattern (59 bp):
AACATCGAATGCATTTCATGCATCGATGCACATACATCGATGCACTCAGGCTATTTTAA
Found at i:1652003 original size:56 final size:55
Alignment explanation
Indices: 1651943--1652060 Score: 132
Period size: 57 Copynumber: 2.1 Consensus size: 55
1651933 AATGCATTTC
* * * *
1651943 ATGCATCGATGCA-TATACTATGCATCGATGCACTCAGGGT-TTTATGAAAACATCGA
1 ATGCATCGATGCACCA-ACCATACATCGATGCACTCAGGCTATTT-T-AAAACATCGA
* *
1651999 ATGCATTTGATGCACCAGCCATACATCGATGCACTCAGGCTATTTTAAAACATCGA
1 ATGCA-TCGATGCACCAACCATACATCGATGCACTCAGGCTATTTTAAAACATCGA
1652055 ATGCAT
1 ATGCAT
1652061 TTTATGTATC
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
55 1 0.02
56 20 0.38
57 28 0.53
58 4 0.08
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (55 bp):
ATGCATCGATGCACCAACCATACATCGATGCACTCAGGCTATTTTAAAACATCGA
Found at i:1653816 original size:54 final size:54
Alignment explanation
Indices: 1653755--1653866 Score: 206
Period size: 54 Copynumber: 2.1 Consensus size: 54
1653745 ACACTTTGAA
*
1653755 CATACATGAGATAACAAATAACATGTAATCATTTATGCTCAATACTCATGCATG
1 CATACATGAGATAACAAATAACATGTAATCATTCATGCTCAATACTCATGCATG
*
1653809 CATACATGAGATAACATATAACATGTAATCATTCATGCTCAATACTCATGCATG
1 CATACATGAGATAACAAATAACATGTAATCATTCATGCTCAATACTCATGCATG
1653863 CATA
1 CATA
1653867 GAACAAAATA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (54 bp):
CATACATGAGATAACAAATAACATGTAATCATTCATGCTCAATACTCATGCATG
Found at i:1654323 original size:20 final size:21
Alignment explanation
Indices: 1654294--1654337 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
1654284 TAAATCATTT
**
1654294 TTTTTCAAAACTGTATTTTGA
1 TTTTTCAAAACTCAATTTTGA
*
1654315 TTTTT-AAAATTCAATTTTGA
1 TTTTTCAAAACTCAATTTTGA
1654335 TTT
1 TTT
1654338 CAGAAGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTTTCAAAACTCAATTTTGA
Found at i:1666260 original size:57 final size:57
Alignment explanation
Indices: 1666101--1666466 Score: 435
Period size: 57 Copynumber: 6.6 Consensus size: 57
1666091 AAATTCACCT
* * * * * * * *
1666101 ACTTATTATGAATTTCTTA--TGTTT-CACATATAGTTCCCATACGGATATTCACAC
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAC
* *
1666155 ACTTAGTATGAATTTCCTAG---TTTGCACACATAGTGCCCATAC-AGAAATTCATAC
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGA-AAATTCATAC
1666209 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAC
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAC
*
1666266 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAA
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAC
* * * * * *
1666323 ACTAATTATGAATTTCTTAACTTTTTGCACACCATGTTCCCATACG-AAATTCATAC
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAC
* * * * *
1666379 ACTTAGTATGAATTTCTTATCTTTTTGCACCCAAATTG-CCATACGGAAATTCATAA
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAC
* * *
1666435 ACTAATTATGAATTTCTTAACTTTTTGCACAC
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACAC
1666467 TCAGTTCATT
Statistics
Matches: 274, Mismatches: 30, Indels: 14
0.86 0.09 0.04
Matches are distributed among these distances:
53 3 0.01
54 60 0.22
55 7 0.03
56 76 0.28
57 127 0.46
58 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (57 bp):
ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAC
Found at i:1666333 original size:114 final size:113
Alignment explanation
Indices: 1666105--1666466 Score: 479
Period size: 114 Copynumber: 3.2 Consensus size: 113
1666095 TCACCTACTT
* * * * *
1666105 ATTATGAATTTCTT-A-TGTTT-CACATATAGTTCCCATACGGATATTCACACACTTAGTATGAA
1 ATTATGAATTTCTTAACTTTTTGCACACAAAGTTCCCATAC-GAAATTCATACACTTAGTATGAA
* * * *
1666167 TTTCCTAG---TTTGCACACATAGTGCCCATAC-AGAAATTCATACACTT
65 TTTCTTAGCTTTTTGCACACAAAGTGCCCATACGA-AAATTCATAAACTA
* * *
1666213 AGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATACACTTAGTATGAA
1 ATTATGAATTTCTTAACTTTTTGCACACAAAGTTCCCATACG-AAATTCATACACTTAGTATGAA
1666278 TTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAAACTA
65 TTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAAACTA
* *
1666327 ATTATGAATTTCTTAACTTTTTGCACACCATGTTCCCATACGAAATTCATACACTTAGTATGAAT
1 ATTATGAATTTCTTAACTTTTTGCACACAAAGTTCCCATACGAAATTCATACACTTAGTATGAAT
* * * *
1666392 TTCTTATCTTTTTGCACCCAAATTG-CCATACGGAAATTCATAAACTA
66 TTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAAACTA
1666439 ATTATGAATTTCTTAACTTTTTGCACAC
1 ATTATGAATTTCTTAACTTTTTGCACAC
1666467 TCAGTTCATT
Statistics
Matches: 225, Mismatches: 21, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
108 13 0.06
110 5 0.02
111 42 0.19
112 49 0.22
113 45 0.20
114 70 0.31
115 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (113 bp):
ATTATGAATTTCTTAACTTTTTGCACACAAAGTTCCCATACGAAATTCATACACTTAGTATGAAT
TTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAAACTA
Found at i:1671613 original size:57 final size:57
Alignment explanation
Indices: 1671448--1671816 Score: 401
Period size: 57 Copynumber: 6.6 Consensus size: 57
1671438 AAATTCGCCT
* * * * * * *
1671448 ACTTATTATGAATTTCCTA--TGTTTGCACATATAGTTCCCATACA-AAATTTCACAC
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACAGAAA-TTCATAC
* *
1671503 ACTTAGTATGAATTTCTTAG---TTTGCACATATAGTGCCCATACAGAAATTCATAC
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACAGAAATTCATAC
* * *
1671557 ACTTAGTATGAATTTCTTAGCATTTTGTACACAAAGTGCCTATACAGAAATTCATAC
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACAGAAATTCATAC
* * * *
1671614 ACTT-GTTATGAATTTCTTATCTTTTTGCGCACAAAGTGCCCATACTGAAATTCATAA
1 ACTTAG-TATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACAGAAATTCATAC
* * * * *
1671671 ACTAATTATGAATTTCTTAACTTTTTGCACACCAAGTGCCCATACGGAAATTCATAC
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACAGAAATTCATAC
* * * * * *
1671728 ACTTAGTATGAATTTCTTCGTTTTTTGTACATAAAGTGCCCATACGGAAATTCATAA
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACAGAAATTCATAC
* * *
1671785 ACTAATTATGAATTTCTTAACTTTTTGCACAC
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACAC
1671817 TCAGTGCCAT
Statistics
Matches: 269, Mismatches: 38, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
54 48 0.18
55 20 0.07
56 1 0.00
57 200 0.74
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (57 bp):
ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACAGAAATTCATAC
Found at i:1672215 original size:19 final size:21
Alignment explanation
Indices: 1672163--1672216 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
1672153 TACTCCTACC
*
1672163 ATGGTATTGATACTATTATACT
1 ATGGTATTGATACTACTATA-T
* *
1672185 ATAGTATCGATACT-CTAT-T
1 ATGGTATTGATACTACTATAT
1672204 ATGGTATTGATAC
1 ATGGTATTGATAC
1672217 CATTTTTGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 12 0.44
21 3 0.11
22 12 0.44
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (21 bp):
ATGGTATTGATACTACTATAT
Found at i:1672324 original size:17 final size:14
Alignment explanation
Indices: 1672291--1672318 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1672281 AGTATCAATG
1672291 CTTCCCAACTAATT
1 CTTCCCAACTAATT
1672305 CTTCCCAACTAATT
1 CTTCCCAACTAATT
1672319 ATTCTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.00, T:0.36
Consensus pattern (14 bp):
CTTCCCAACTAATT
Found at i:1684568 original size:29 final size:29
Alignment explanation
Indices: 1684536--1684592 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1684526 ATCTACTCTT
1684536 TGTTGCCTAGCATCCTCATTGGGTGAACA
1 TGTTGCCTAGCATCCTCATTGGGTGAACA
*
1684565 TGTTGTCTAGCATCCTCATTGGGTGAAC
1 TGTTGCCTAGCATCCTCATTGGGTGAAC
1684593 CACCAAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (29 bp):
TGTTGCCTAGCATCCTCATTGGGTGAACA
Found at i:1688810 original size:21 final size:20
Alignment explanation
Indices: 1688784--1688838 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 20
1688774 AGATGAACTA
1688784 TGGCTTTGTAAAAGTGTAGCT
1 TGGCTTTGTAAAAGTGTAG-T
*
1688805 TGGCTTTGCAAAAGTGTAGT
1 TGGCTTTGTAAAAGTGTAGT
1688825 TGGGCTTTGTAAAA
1 T-GGCTTTGTAAAA
1688839 ATTTCATTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.25, C:0.09, G:0.29, T:0.36
Consensus pattern (20 bp):
TGGCTTTGTAAAAGTGTAGT
Found at i:1688910 original size:21 final size:20
Alignment explanation
Indices: 1688885--1688923 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1688875 CATCAAGGTC
*
1688885 TTTGTTGAGGCCATGAAATCT
1 TTTGTCGAGGCCAT-AAATCT
1688906 TTTGTCGAGGCCATAAAT
1 TTTGTCGAGGCCATAAAT
1688924 TCCTACAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (20 bp):
TTTGTCGAGGCCATAAATCT
Found at i:1698928 original size:312 final size:314
Alignment explanation
Indices: 1698325--1698948 Score: 1022
Period size: 312 Copynumber: 2.0 Consensus size: 314
1698315 GGCTCCACAT
* * *
1698325 TAGGCTGAGTATTAGGTGGATTTTGGTTCACTTCATTACTCCCACTTTGTACAGGAGTAACACGC
1 TAGGCCGAGCATTAGGTGGATTTTGGTTCACCTCATTACTCCCACTTTGTACAGGAGTAACACGC
*
1698390 TCAGCTACCCTAATAGAACTCTTGATGATCTAACATCTAAACACATTCAAAATCATCTAACATTA
66 TCAACTACCCTAATAGAACTCTTGATGATCTAACATCTAAACACATTCAAAATCATCTAACATTA
*
1698455 GTATGAAGTAACTTTAAAAAATAATAAGCATCATAGCATATATACAATTATCAGTAAAACTTTAA
131 GTAAGAAGTAACTTTAAAAAATAATAAGCATCATAGCATATATACAATTATCAGTAAAACTTTAA
*
1698520 CATCCTAATGGCATGTTCTCAATCTCAATTTAATTTAAACTCAATCCATGTCCAGAAACGACTAA
196 CATCCTAATGGCATGTTCTCAATCTCAATTTAATTTAAACTCAATCCATGTCCAAAAACGACTAA
* *
1698585 ACGTGTAGCTCTGATATCAATAAATTAACACCTACGACCCTTATACTTATTCAA
261 ACGTGTAGCTCTGATATCAAAAAATTAACACCTACGACCCTTAAACTTATTCAA
*
1698639 TAGGCCGAGCATTAGGTGGATTTTGGTTCACCTCATTACTCCCACTTTGTATAGGAGTAACACGC
1 TAGGCCGAGCATTAGGTGGATTTTGGTTCACCTCATTACTCCCACTTTGTACAGGAGTAACACGC
* * *
1698704 TCAATTTCCCTAGTAG-ACTCTTGATGATCTAACATCTAAACACATTCAAAATCATCTAACATTA
66 TCAACTACCCTAATAGAACTCTTGATGATCTAACATCTAAACACATTCAAAATCATCTAACATTA
* *
1698768 GTAAG-AGTAACTTTAATAAATAATAAGCATCATAGCATATATACAATTATCAGTAAAA-TGTTG
131 GTAAGAAGTAACTTTAAAAAATAATAAGCATCATAGCATATATACAATTATCAGTAAAACT-TTA
* * * *
1698831 ACATCCTAATGGTATGTTCTCCATCTCAATTTAATTTAAACTCAATTCATGTCCAAAAATGACTA
195 ACATCCTAATGGCATGTTCTCAATCTCAATTTAATTTAAACTCAATCCATGTCCAAAAACGACTA
**
1698896 AAC-TGTAGCTCTGATATCAAAAAATGTAACACCTACGATGCTTAAACTTATTC
260 AACGTGTAGCTCTGATATCAAAAAAT-TAACACCTACGACCCTTAAACTTATTC
1698949 TTATAAGGTT
Statistics
Matches: 288, Mismatches: 20, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
311 22 0.08
312 141 0.49
313 52 0.18
314 73 0.25
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (314 bp):
TAGGCCGAGCATTAGGTGGATTTTGGTTCACCTCATTACTCCCACTTTGTACAGGAGTAACACGC
TCAACTACCCTAATAGAACTCTTGATGATCTAACATCTAAACACATTCAAAATCATCTAACATTA
GTAAGAAGTAACTTTAAAAAATAATAAGCATCATAGCATATATACAATTATCAGTAAAACTTTAA
CATCCTAATGGCATGTTCTCAATCTCAATTTAATTTAAACTCAATCCATGTCCAAAAACGACTAA
ACGTGTAGCTCTGATATCAAAAAATTAACACCTACGACCCTTAAACTTATTCAA
Found at i:1701655 original size:15 final size:15
Alignment explanation
Indices: 1701635--1701671 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1701625 AGGTTGGGCT
1701635 GGAGGTGCTAGTGAG
1 GGAGGTGCTAGTGAG
*
1701650 GGAGGTGTTAGTGAG
1 GGAGGTGCTAGTGAG
1701665 GGAGGTG
1 GGAGGTG
1701672 GTACAACTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.19, C:0.03, G:0.57, T:0.22
Consensus pattern (15 bp):
GGAGGTGCTAGTGAG
Found at i:1704131 original size:20 final size:20
Alignment explanation
Indices: 1704103--1704161 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
1704093 GAAAAATCCT
*
1704103 ACCCTGAGGTTTTACAAATG
1 ACCCAGAGGTTTTACAAATG
*
1704123 ACCCGGAGGTTTTACAAATG
1 ACCCAGAGGTTTTACAAATG
1704143 ACCCAGAGGTTTTACAAAT
1 ACCCAGAGGTTTTACAAAT
1704162 CCGGAGGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (20 bp):
ACCCAGAGGTTTTACAAATG
Found at i:1704279 original size:19 final size:20
Alignment explanation
Indices: 1704255--1704295 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1704245 AGTTTTGCAG
1704255 ATGACCC-GATGG-TTTACAA
1 ATGACCCGGA-GGTTTTACAA
1704274 ATGACCCGGAGGTTTTACAA
1 ATGACCCGGAGGTTTTACAA
1704294 AT
1 AT
1704296 CCGGAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (20 bp):
ATGACCCGGAGGTTTTACAA
Found at i:1704403 original size:20 final size:20
Alignment explanation
Indices: 1704378--1704428 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1704368 ATGCTACCCT
*
1704378 GAGGTTTTACAGGTGACACG
1 GAGGTTTTACAGATGACACG
*
1704398 GAGGTTTTACAGATGACCCG
1 GAGGTTTTACAGATGACACG
1704418 GAGGTTTTACA
1 GAGGTTTTACA
1704429 AATCTAGAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.27
Consensus pattern (20 bp):
GAGGTTTTACAGATGACACG
Found at i:1704448 original size:136 final size:136
Alignment explanation
Indices: 1703988--1704547 Score: 822
Period size: 135 Copynumber: 4.1 Consensus size: 136
1703978 AAAACATCCT
* * * * *
1703988 ACCCTGAGGTTTTATAGATGACCCAGAGGTTTTACAAATCCGGATGATTTAATTTTTTAGAACAT
1 ACCCGGAGGTTTTACAAATGACCCAGAGGTTTTACAAATCCGGAGGATTTAATTTTCTAGAACAT
* *
1704053 TAAATGAGAAACTTTGAAAATCGATTTCTTATTTTCATGCGAAAA-ATCCTACCCTGAGGTTTTA
66 TAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTA
*
1704117 CAAATG
131 CAGATG
1704123 ACCCGGAGGTTTTACAAATGACCCAGAGGTTTTACAAATCCGGAGGATTTAATTTTCTAGAACAT
1 ACCCGGAGGTTTTACAAATGACCCAGAGGTTTTACAAATCCGGAGGATTTAATTTTCTAGAACAT
* * * *
1704188 TAAATGAGAAGCTTTGAAAATCGCTTTCT-ATTTTCATGCGAAAACATCCAACCCTGAAGTTTTG
66 TAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTA
1704252 CAGATG
131 CAGATG
* *
1704258 ACCC-GATGG-TTTACAAATGACCCGGAGGTTTTACAAATCCGGAGGATTTAATTTTCTGGAACA
1 ACCCGGA-GGTTTTACAAATGACCCAGAGGTTTTACAAATCCGGAGGATTTAATTTTCTAGAACA
*
1704321 TTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCGAAAACATGCTACCCTGAGGTTTT
65 TTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTT
*
1704386 ACAGGTG
130 ACAGATG
* * * ** *
1704393 ACACGGAGGTTTTACAGATGACCCGGAGGTTTTACAAATCTAGAGGATTTTATTTTCTAGAACAT
1 ACCCGGAGGTTTTACAAATGACCCAGAGGTTTTACAAATCCGGAGGATTTAATTTTCTAGAACAT
* * ** *
1704458 TAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTATGCGAAAGCATAATACCATGAGGTTTTA
66 TAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTA
1704523 CAGATG
131 CAGATG
* *
1704529 ACCCAGAGGATTTACAAAT
1 ACCCGGAGGTTTTACAAAT
1704548 TCATGAGAAA
Statistics
Matches: 385, Mismatches: 35, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
134 98 0.25
135 155 0.40
136 132 0.34
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (136 bp):
ACCCGGAGGTTTTACAAATGACCCAGAGGTTTTACAAATCCGGAGGATTTAATTTTCTAGAACAT
TAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTTA
CAGATG
Found at i:1707305 original size:15 final size:14
Alignment explanation
Indices: 1707264--1707311 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 14
1707254 ATATTTATCT
1707264 ATAATAATAATATA
1 ATAATAATAATATA
1707278 ATAATAA-AA-ATA
1 ATAATAATAATATA
*
1707290 ATAGTAATATATATA
1 ATAATAATA-ATATA
*
1707305 ATTATAA
1 ATAATAA
1707312 AAATGAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 9 0.32
13 3 0.11
14 8 0.29
15 8 0.29
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
ATAATAATAATATA
Found at i:1713914 original size:60 final size:60
Alignment explanation
Indices: 1713863--1714005 Score: 277
Period size: 60 Copynumber: 2.4 Consensus size: 60
1713853 GATGATGTTA
*
1713863 CTCCTTCATGTTGAGGAGATCTAATAGTCTTTAGAGAAATTACTGTAGAAGACAACATTG
1 CTCCTTCATGTTGACGAGATCTAATAGTCTTTAGAGAAATTACTGTAGAAGACAACATTG
1713923 CTCCTTCATGTTGACGAGATCTAATAGTCTTTAGAGAAATTACTGTAGAAGACAACATTG
1 CTCCTTCATGTTGACGAGATCTAATAGTCTTTAGAGAAATTACTGTAGAAGACAACATTG
1713983 CTCCTTCATGTTGACGAGATCTA
1 CTCCTTCATGTTGACGAGATCTA
1714006 GTTGTATTTT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 82 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (60 bp):
CTCCTTCATGTTGACGAGATCTAATAGTCTTTAGAGAAATTACTGTAGAAGACAACATTG
Found at i:1716970 original size:81 final size:81
Alignment explanation
Indices: 1716857--1717268 Score: 572
Period size: 81 Copynumber: 5.1 Consensus size: 81
1716847 AAGCATTTAG
* * * * * * *
1716857 TCTTTTACCCAAAGGAATTTAGCCTTTCATCTAACTTGCATGATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
*
1716922 ACAGCTAGGCATTTAA
66 ACAGCTAGGCAATTAA
* * *
1716938 TCTTTAACTCAAAGGCATTTATCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
*
1717003 ACAACTAGGCAATTAA
66 ACAGCTAGGCAATTAA
* * * *
1717019 TCTTTTACTCAAAGGCATTTAACCTTTCATTTAACTGGCCTAATTGACACTTTTATGTCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
*
1717084 ACAGCTAGGAAATTAA
66 ACAGCTAGGCAATTAA
*
1717100 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
* *
1717165 ATAGCTAGGAAATTAA
66 ACAGCTAGGCAATTAA
* * * *
1717181 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGACATAATTAACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
* * **
1717246 ATAACTAAACAATTAA
66 ACAGCTAGGCAATTAA
1717262 TCTTTTA
1 TCTTTTA
1717269 TTTAAAACAT
Statistics
Matches: 299, Mismatches: 32, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 299 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (81 bp):
TCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
ACAGCTAGGCAATTAA
Found at i:1721312 original size:27 final size:27
Alignment explanation
Indices: 1721278--1721373 Score: 156
Period size: 27 Copynumber: 3.6 Consensus size: 27
1721268 ATATTGAATA
*
1721278 GATAAGGATAATGAAAAGACAATGAAG
1 GATAAGGATAATGAAAAGACAATTAAG
*
1721305 GATAAGGATAATGTAAAGACAATTAAG
1 GATAAGGATAATGAAAAGACAATTAAG
* *
1721332 GATAAGGATAATGTAAAGAAAATTAAG
1 GATAAGGATAATGAAAAGACAATTAAG
1721359 GATAAGGATAATGAA
1 GATAAGGATAATGAA
1721374 TGTAATAGGA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 65 1.00
ACGTcount: A:0.54, C:0.02, G:0.24, T:0.20
Consensus pattern (27 bp):
GATAAGGATAATGAAAAGACAATTAAG
Found at i:1725236 original size:198 final size:201
Alignment explanation
Indices: 1724846--1725241 Score: 681
Period size: 198 Copynumber: 2.0 Consensus size: 201
1724836 TTGGTTCATT
* * *
1724846 TGTATCGTGGAACACAAGAAAATTTAAATAGACGATTAAAGGGGGGAAAATCTAAAGAGTAATAG
1 TGTATCGTGGAACACAAGAAAATTTAAACAGACGATTAAAGGGGGAAAAAACTAAAGAGTAATAG
1724911 AGGAAAAATCATATATTTCAGAGACTAATCTGAATTTCAGTTTTACTTTCACCACCTCTGAGAAT
66 AGGAAAAATCATATATTTCAGAGACTAATCTGAATTTCAGTTTTACTTTCACCACCTCTGAGAAT
* * *
1724976 GGGATCCACAATGGTCTGCCATTAAAGTCGTCATCAACCTCTTTCCTTATGGCAATCTCTATCTC
131 GGGATCCACAATGGCCTGCCATTAAAGTCGTCATCAACCTCTTTCCTTATGACAACCTCTATCTC
1725041 CGTATA
196 CGTATA
*
1725047 TGTATCGTGGAACACAAGAAAATTTTAACAGACGATTAAA-GGGGAAAAAACTAAAGAGTAATAG
1 TGTATCGTGGAACACAAGAAAATTTAAACAGACGATTAAAGGGGGAAAAAACTAAAGAGTAATAG
* *
1725111 AGGAAAAATCATAT-TTTCAGAGACTAATCTGAATTTCAGTTTTACTTTCACCACTTCTGCGAA-
66 AGGAAAAATCATATATTTCAGAGACTAATCTGAATTTCAGTTTTACTTTCACCACCTCTGAGAAT
*
1725174 GGGATCCACAATGGCCTGCCATTAAAGTCGTCATCAACCTCTTTTCTTATGACAACCTCTATCTC
131 GGGATCCACAATGGCCTGCCATTAAAGTCGTCATCAACCTCTTTCCTTATGACAACCTCTATCTC
1725239 CGT
196 CGT
1725242 CACCTCAAGT
Statistics
Matches: 185, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
198 64 0.35
199 47 0.25
200 36 0.19
201 38 0.21
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (201 bp):
TGTATCGTGGAACACAAGAAAATTTAAACAGACGATTAAAGGGGGAAAAAACTAAAGAGTAATAG
AGGAAAAATCATATATTTCAGAGACTAATCTGAATTTCAGTTTTACTTTCACCACCTCTGAGAAT
GGGATCCACAATGGCCTGCCATTAAAGTCGTCATCAACCTCTTTCCTTATGACAACCTCTATCTC
CGTATA
Found at i:1726562 original size:3 final size:3
Alignment explanation
Indices: 1726548--1726622 Score: 80
Period size: 3 Copynumber: 25.0 Consensus size: 3
1726538 ATATATATAT
* ** * *
1726548 ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A GGA AAA ATA TATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
*
1726596 TTA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1726623 TATATATAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
2 1 0.02
3 57 0.95
4 2 0.03
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1733669 original size:21 final size:21
Alignment explanation
Indices: 1733643--1733682 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1733633 CCCCCTTTGA
*
1733643 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1733664 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1733683 CTGGGGTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1737289 original size:19 final size:19
Alignment explanation
Indices: 1737275--1737318 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1737265 AAAATAAGTT
1737275 AATAA-AAAAATAATAATA
1 AATAATAAAAATAATAATA
*
1737293 AATAATAAAAATAACAATA
1 AATAATAAAAATAATAATA
1737312 AATAATA
1 AATAATA
1737319 TATATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (19 bp):
AATAATAAAAATAATAATA
Found at i:1737297 original size:10 final size:10
Alignment explanation
Indices: 1737282--1737318 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
1737272 GTTAATAAAA
1737282 AAATAATAAT
1 AAATAATAAT
1737292 AAATAATAA-
1 AAATAATAAT
*
1737301 AAATAACAAT
1 AAATAATAAT
1737311 AAATAATA
1 AAATAATA
1737319 TATATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (10 bp):
AAATAATAAT
Found at i:1737420 original size:25 final size:27
Alignment explanation
Indices: 1737354--1737437 Score: 95
Period size: 27 Copynumber: 3.2 Consensus size: 27
1737344 AGAAACATAT
*
1737354 AATATATAATTTCA-AAATGCTTTT-AAA
1 AATATATAATAT-ATAAATG-TTTTCAAA
1737381 AATATATAATATATAAATGTTTTCAAA
1 AATATATAATATATAAATGTTTTCAAA
* *
1737408 ATTATATATTATAT-AA-GTTTTCAAA
1 AATATATAATATATAAATGTTTTCAAA
1737433 AATAT
1 AATAT
1737438 TAAAAACTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
25 13 0.25
26 7 0.14
27 31 0.61
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.43
Consensus pattern (27 bp):
AATATATAATATATAAATGTTTTCAAA
Found at i:1737474 original size:12 final size:12
Alignment explanation
Indices: 1737457--1737488 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1737447 TATAATATAT
1737457 AAATATTTTCAA
1 AAATATTTTCAA
1737469 AAATATTTTCAA
1 AAATATTTTCAA
*
1737481 AACTATTT
1 AAATATTT
1737489 AATATATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (12 bp):
AAATATTTTCAA
Found at i:1737474 original size:37 final size:37
Alignment explanation
Indices: 1737395--1737721 Score: 246
Period size: 37 Copynumber: 8.9 Consensus size: 37
1737385 TATAATATAT
* * * * *
1737395 AAATGTTTTCAAAATTATATATTATATAA-GTTTTCA
1 AAATATTTTAAAAACTATATAATATATAATATTTTCA
*
1737431 AAA-ATATTAAAAACTATATAATATATAAATATTTTCAA
1 AAATATTTTAAAAACTATATAATATAT-AATATTTTC-A
* * * *
1737469 AAATATTTTCAAAACTATTTAATATAT-TTGTTTTCA
1 AAATATTTTAAAAACTATATAATATATAATATTTTCA
* * *
1737505 CAAATGTTTTCAAAAACTATATATTATAT-ATA-TTTAA
1 -AAATATTTT-AAAAACTATATAATATATAATATTTTCA
*
1737542 AAATGTTTTAAAAAACTATAT-AT-TAT-ATATTTTCA
1 AAATATTTT-AAAAACTATATAATATATAATATTTTCA
*
1737577 AAATGATTTTAAAAACTATATATTATAT-ATATTTTCA
1 AAAT-ATTTTAAAAACTATATAATATATAATATTTTCA
* *
1737614 AAATGTTTTTAAAAACTATATAATATATGAATGTTTTCA
1 AAAT-ATTTTAAAAACTATATAATATAT-AATATTTTCA
** * * *
1737653 AAACGTTTTCAAAACTATAT-AT-TATATTTTTTTCAA
1 AAATATTTTAAAAACTATATAATATATAATATTTTC-A
* * *
1737689 AAACATTTTCAAAAAATAT-TATTATATACATAT
1 AAATATTTT-AAAAACTATATAATATATA-ATAT
1737722 ATATATACAC
Statistics
Matches: 237, Mismatches: 37, Indels: 31
0.78 0.12 0.10
Matches are distributed among these distances:
34 6 0.03
35 45 0.19
36 44 0.19
37 71 0.30
38 38 0.16
39 33 0.14
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (37 bp):
AAATATTTTAAAAACTATATAATATATAATATTTTCA
Found at i:1737562 original size:146 final size:145
Alignment explanation
Indices: 1737395--1737716 Score: 379
Period size: 146 Copynumber: 2.2 Consensus size: 145
1737385 TATAATATAT
*
1737395 AAATGTTTTCAAAATTATATATTATATA-AGTTTTCAAAA-ATATTAAAAACTATATAATATATA
1 AAATGTTTTCAAAA-AATATATTATATATA-TTTTCAAAAGATATTAAAAACTATAT-AT-TATA
* * * *
1737458 AATATTTTCAAAAAT-ATTTTCAAAACTATTTAATATAT-TTGTTTTCACAAATGTTTTCAAAAA
62 AATATTTTC-AAAATGATTTTAAAAACTATATAATATATAATGTTTTCA-AAACGTTTTC-AAAA
1737521 CTATATATTATATATATTT-AA
124 CTATATATTATATATATTTCAA
* *
1737542 AAATGTTTT-AAAAAACTATA-TATTATATATTTTCAAAATGATTTTAAAAACTATATATTATAT
1 AAATGTTTTCAAAAAA-TATATTA-TATATATTTTCAAAA-GATATTAAAAACTATATATTATAA
*
1737605 ATATTTTCAAAATGTTTTTAAAAACTATATAATATATGAATGTTTTCAAAACGTTTTCAAAACTA
63 ATATTTTCAAAATGATTTTAAAAACTATATAATATAT-AATGTTTTCAAAACGTTTTCAAAACTA
* *
1737670 TATATTATATTTTTTTCAA
127 TATATTATATATATTTCAA
**
1737689 AAACATTTTCAAAAAATATTATTATATA
1 AAATGTTTTCAAAAAATA-TATTATATA
1737717 CATATATATA
Statistics
Matches: 151, Mismatches: 12, Indels: 23
0.81 0.06 0.12
Matches are distributed among these distances:
145 8 0.05
146 74 0.49
147 32 0.21
148 35 0.23
149 2 0.01
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (145 bp):
AAATGTTTTCAAAAAATATATTATATATATTTTCAAAAGATATTAAAAACTATATATTATAAATA
TTTTCAAAATGATTTTAAAAACTATATAATATATAATGTTTTCAAAACGTTTTCAAAACTATATA
TTATATATATTTCAA
Found at i:1737716 original size:2 final size:2
Alignment explanation
Indices: 1737711--1737776 Score: 73
Period size: 2 Copynumber: 34.0 Consensus size: 2
1737701 AAAATATTAT
* * * * *
1737711 TA TA TA CA TA TA TA TA TA CA CA TA -A TA -A AA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1737751 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1737777 AACAAAATAG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
1 2 0.04
2 53 0.96
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (2 bp):
TA
Found at i:1739558 original size:60 final size:60
Alignment explanation
Indices: 1739421--1739546 Score: 157
Period size: 60 Copynumber: 2.1 Consensus size: 60
1739411 AACATAATGA
* * * * * *
1739421 ATAGTCGAATGACCATTTTATAACTTTTAATAGTCGAGAGACTTAACAAAGCAATATTCT
1 ATAGTCAAAGGACCATTTTGTAACTTTTAATAATCGAGAGACTCAACAAAGCAATATCCT
*
1739481 ATAGTCAAAGGACCATTTTGTAACTTTTAATAATCGA-ATGACTCACCAAAGC-ATCATCCT
1 ATAGTCAAAGGACCATTTTGTAACTTTTAATAATCGAGA-GACTCAACAAAGCAAT-ATCCT
1739541 ATAGTC
1 ATAGTC
1739547 GGGGGACCAT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 3 0.05
60 54 0.95
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (60 bp):
ATAGTCAAAGGACCATTTTGTAACTTTTAATAATCGAGAGACTCAACAAAGCAATATCCT
Found at i:1744685 original size:21 final size:21
Alignment explanation
Indices: 1744651--1744690 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1744641 TAAAGCATCC
*
1744651 AATAATAACATTTTCGGTAGA
1 AATAATAACATTTTAGGTAGA
**
1744672 AATAATAATGTTTTAGGTA
1 AATAATAACATTTTAGGTA
1744691 ATTTTTTACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (21 bp):
AATAATAACATTTTAGGTAGA
Found at i:1746324 original size:21 final size:21
Alignment explanation
Indices: 1746287--1746326 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1746277 AAAATTGTGT
*
1746287 ATCGATGCACTATTACAGTGC
1 ATCGATGCACTACTACAGTGC
*
1746308 ATCGATGCACTGCTACAGT
1 ATCGATGCACTACTACAGT
1746327 AATTTCAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (21 bp):
ATCGATGCACTACTACAGTGC
Found at i:1746893 original size:40 final size:40
Alignment explanation
Indices: 1746849--1746958 Score: 166
Period size: 40 Copynumber: 2.8 Consensus size: 40
1746839 ACCGTAGTGC
* * *
1746849 TACACATAAGGTCGTGCCCACCATGTACACCGAAGTGTAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAATGTAT
* * *
1746889 TACACATAAGGTCATGCCCACCATATACATCTAAATTTAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAATGTAT
1746929 TACACATAAGGTCATGCCCACCATATACAC
1 TACACATAAGGTCATGCCCACCATATACAC
1746959 TTAGTGCCTT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.25
Consensus pattern (40 bp):
TACACATAAGGTCATGCCCACCATATACACCGAAATGTAT
Found at i:1748597 original size:46 final size:45
Alignment explanation
Indices: 1748499--1748604 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 45
1748489 GTGCACTAAG
** * *
1748499 AGTGCATTAATGCATAAAATGCATTCGATGTTTCAAAATAGCCAG
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCCAC
* *
1748544 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ACCCTC
1 AGTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AAATACCCAC
*
1748590 AGTGCATCGGTGCAT
1 AGTGCATCGATGCAT
1748605 GGTATGTGCA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 27 0.52
46 22 0.42
47 3 0.06
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (45 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCCAC
Found at i:1749120 original size:2 final size:2
Alignment explanation
Indices: 1749113--1749138 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1749103 ACCAATTGAT
1749113 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1749139 GCTTAAGCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.