Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_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: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 55
Found at i:1556819 original size:15 final size:15
Alignment explanation
Indices: 1556765--1556820 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
1556755 CAGTGAAGAG
*
1556765 GATGACGATGACGAT
1 GATGACGATGAGGAT
* * *
1556780 GAAGACGAAGAGGAC
1 GATGACGATGAGGAT
**
1556795 GATGTTGATGAGGAT
1 GATGACGATGAGGAT
1556810 GATGACGATGA
1 GATGACGATGA
1556821 AGAAGCAATG
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.36, C:0.09, G:0.38, T:0.18
Consensus pattern (15 bp):
GATGACGATGAGGAT
Found at i:1558507 original size:2 final size:2
Alignment explanation
Indices: 1558500--1558526 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1558490 GTATATGTAC
1558500 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1558527 ACCCAGATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1565891 original size:2 final size:2
Alignment explanation
Indices: 1565884--1565914 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1565874 CTAATACCTA
1565884 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1565915 ATAAACTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1568326 original size:21 final size:22
Alignment explanation
Indices: 1568300--1568342 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1568290 ATAATCTCTT
* *
1568300 GCATGTC-TGAACCTACAACAA
1 GCATGTCATCAACATACAACAA
1568321 GCATGTCATCAACATACAACAA
1 GCATGTCATCAACATACAACAA
1568343 TAAAATAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.19
Consensus pattern (22 bp):
GCATGTCATCAACATACAACAA
Found at i:1571798 original size:15 final size:15
Alignment explanation
Indices: 1571778--1571809 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1571768 CCCCTATTTT
1571778 TGAAAACAATTAAGC
1 TGAAAACAATTAAGC
*
1571793 TGAAAACAATTTAGC
1 TGAAAACAATTAAGC
1571808 TG
1 TG
1571810 GCCCTCCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (15 bp):
TGAAAACAATTAAGC
Found at i:1573431 original size:19 final size:19
Alignment explanation
Indices: 1573409--1573452 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1573399 CCCGTCCCTG
1573409 TCCCCGAAATGAATCCCCA
1 TCCCCGAAATGAATCCCCA
* *
1573428 TCCCCAAAATGAATCCTCA
1 TCCCCGAAATGAATCCCCA
1573447 TCCCCG
1 TCCCCG
1573453 CCCCGTTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.30, C:0.43, G:0.09, T:0.18
Consensus pattern (19 bp):
TCCCCGAAATGAATCCCCA
Found at i:1576775 original size:2 final size:2
Alignment explanation
Indices: 1576768--1576805 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1576758 ATACGTAATT
1576768 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1576806 AAAGCTGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1577113 original size:51 final size:51
Alignment explanation
Indices: 1577053--1577209 Score: 137
Period size: 50 Copynumber: 3.1 Consensus size: 51
1577043 TTAACAGTAA
* *
1577053 AGCGCG-CCCCTTGCGCCGCGCTATACGATGATTTGGTGCCACGTAGGGTAT
1 AGCGCGACCCCTTGCGCCGCGCTATACGATGATATGATGCCACGT-GGGTAT
* * * ** * *
1577104 AGCGCGCCCCCTT-CACCGCGCTATACGGTGAGCTGACGCCAGGTGGGTAT
1 AGCGCGACCCCTTGCGCCGCGCTATACGATGATATGATGCCACGTGGGTAT
* *
1577154 AGCGCGACCCC-TGCAG-CGCGCTATAC-ATGTATAT-CTGACACGTGGGGTAT
1 AGCGCGACCCCTTGC-GCCGCGCTATACGATG-ATATGATGCCACGT-GGGTAT
1577204 AGCGCG
1 AGCGCG
1577210 GTGCAGGGGG
Statistics
Matches: 85, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
49 8 0.09
50 41 0.48
51 30 0.35
52 6 0.07
ACGTcount: A:0.18, C:0.31, G:0.31, T:0.20
Consensus pattern (51 bp):
AGCGCGACCCCTTGCGCCGCGCTATACGATGATATGATGCCACGTGGGTAT
Found at i:1577165 original size:50 final size:50
Alignment explanation
Indices: 1577053--1577179 Score: 139
Period size: 51 Copynumber: 2.5 Consensus size: 50
1577043 TTAACAGTAA
* ** **
1577053 AGCGCGCCCCTTGCGCCGCGCTATACGATGATTTGGTGCCACGTAGGGTAT
1 AGCGCGCCCCTT-CACCGCGCTATACGATGAGCTGACGCCACGTAGGGTAT
* *
1577104 AGCGCGCCCCCTTCACCGCGCTATACGGTGAGCTGACGCCAGGT-GGGTAT
1 AGCGCG-CCCCTTCACCGCGCTATACGATGAGCTGACGCCACGTAGGGTAT
* *
1577154 AGCGCGACCCCTGCAGCGCGCTATAC
1 AGCGCG-CCCCTTCACCGCGCTATAC
1577180 ATGTATATCT
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
50 29 0.45
51 30 0.46
52 6 0.09
ACGTcount: A:0.17, C:0.34, G:0.31, T:0.19
Consensus pattern (50 bp):
AGCGCGCCCCTTCACCGCGCTATACGATGAGCTGACGCCACGTAGGGTAT
Found at i:1577263 original size:23 final size:20
Alignment explanation
Indices: 1577229--1577272 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 20
1577219 GCGCGCTATA
*
1577229 CCCTTAATTACCGACCCATCCT
1 CCCTTAAATACC--CCCATCCT
1577251 CCCTATAAATACCCCCATCCT
1 CCCT-TAAATACCCCCATCCT
1577272 C
1 C
1577273 AATCACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 4 0.20
23 7 0.35
ACGTcount: A:0.25, C:0.48, G:0.02, T:0.25
Consensus pattern (20 bp):
CCCTTAAATACCCCCATCCT
Found at i:1581373 original size:21 final size:21
Alignment explanation
Indices: 1581347--1581386 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1581337 CAGAACCCCA
*
1581347 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1581368 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1581387 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1593058 original size:47 final size:49
Alignment explanation
Indices: 1592956--1593071 Score: 146
Period size: 47 Copynumber: 2.4 Consensus size: 49
1592946 CAAAACGTGG
** *
1592956 TACCTGCCCCGCGCTATATAAAATTATGTCAAGAGTAAAGGTATGTCGCGG
1 TACCTGCCCCGCGCTATATAAAATTATGTC-A-AGTAAAGGTATAACGCGA
*
1593007 TACCTGCCTCGCGCTATATAAAATTATG-C-AGTAAAGGTATAACGCGA
1 TACCTGCCCCGCGCTATATAAAATTATGTCAAGTAAAGGTATAACGCGA
**
1593054 TACCTGATCCGCGCTATA
1 TACCTGCCCCGCGCTATA
1593072 CCCCTACGTG
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
47 30 0.52
50 1 0.02
51 27 0.47
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (49 bp):
TACCTGCCCCGCGCTATATAAAATTATGTCAAGTAAAGGTATAACGCGA
Found at i:1593158 original size:50 final size:51
Alignment explanation
Indices: 1593083--1593210 Score: 195
Period size: 51 Copynumber: 2.5 Consensus size: 51
1593073 CCCTACGTGG
* * * **
1593083 CGTATAGCGCGCTTCAGGGGCCGCGCTATACC-CACGTGGCGCCAGCTCAC
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATACCTCACGTGGCGCCAAATCAC
*
1593133 CGTATAGCGCGGTGCAGGGGGCGCGCTATACCTCACGTGGCGCCAAATCAT
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATACCTCACGTGGCGCCAAATCAC
1593184 CGTATAGCGCGGTGCAGGGGGCGCGCT
1 CGTATAGCGCGGTGCAGGGGGCGCGCT
1593211 TTACTGCTAA
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 29 0.41
51 42 0.59
ACGTcount: A:0.16, C:0.32, G:0.35, T:0.16
Consensus pattern (51 bp):
CGTATAGCGCGGTGCAGGGGGCGCGCTATACCTCACGTGGCGCCAAATCAC
Found at i:1612190 original size:50 final size:51
Alignment explanation
Indices: 1612122--1612260 Score: 158
Period size: 50 Copynumber: 2.8 Consensus size: 51
1612112 AACTCAATAG
* * * *
1612122 AAATCAGGATGGGGATAATGCCCTCCGAAGAGGATCCCAGTTAGAAACA-A
1 AAATTAGGATGGGGATAATGCCCTCCAAAGAGGATCCCAGTCAAAAACATA
* * * *
1612172 AAATTAGGATGTGAATAATGTCCTCCAAAAAGGATCCCAGTCAAAAACATA
1 AAATTAGGATGGGGATAATGCCCTCCAAAGAGGATCCCAGTCAAAAACATA
* *
1612223 AAA-TAGGGTGGGGAT-ATAGCCATCCAAAGAGGATCCCA
1 AAATTAGGATGGGGATAAT-GCCCTCCAAAGAGGATCCCA
1612261 AGCCGAAACA
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
49 2 0.03
50 67 0.92
51 4 0.05
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (51 bp):
AAATTAGGATGGGGATAATGCCCTCCAAAGAGGATCCCAGTCAAAAACATA
Found at i:1613373 original size:14 final size:14
Alignment explanation
Indices: 1613354--1613391 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
1613344 AAAATGAATT
1613354 ACATTTTCCAGAAA
1 ACATTTTCCAGAAA
1613368 ACATTTTCCAGAAA
1 ACATTTTCCAGAAA
1613382 ACATTTTCCA
1 ACATTTTCCA
1613392 ATGTTTGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.39, C:0.24, G:0.05, T:0.32
Consensus pattern (14 bp):
ACATTTTCCAGAAA
Found at i:1620255 original size:22 final size:22
Alignment explanation
Indices: 1620212--1620255 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1620202 AAATTTACAT
*
1620212 TCACATAAAATAAAATAAATTG
1 TCACATAAAATAAAACAAATTG
* * *
1620234 TCACTTAAAATAACACACATTG
1 TCACATAAAATAAAACAAATTG
1620256 CATCGTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (22 bp):
TCACATAAAATAAAACAAATTG
Found at i:1621820 original size:12 final size:12
Alignment explanation
Indices: 1621803--1621844 Score: 84
Period size: 12 Copynumber: 3.5 Consensus size: 12
1621793 TTCCTCCTTT
1621803 TTTCCTTTCTGA
1 TTTCCTTTCTGA
1621815 TTTCCTTTCTGA
1 TTTCCTTTCTGA
1621827 TTTCCTTTCTGA
1 TTTCCTTTCTGA
1621839 TTTCCT
1 TTTCCT
1621845 CTGTTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.07, C:0.26, G:0.07, T:0.60
Consensus pattern (12 bp):
TTTCCTTTCTGA
Found at i:1622383 original size:3 final size:3
Alignment explanation
Indices: 1622364--1622413 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
1622354 ATGTAAAATG
*
1622364 TAA TAT TAA TAA T-A TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
1622409 -AA TAA
1 TAA TAA
1622414 CGATAAAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.83
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1622756 original size:43 final size:43
Alignment explanation
Indices: 1622700--1623024 Score: 207
Period size: 43 Copynumber: 7.5 Consensus size: 43
1622690 TTAGGTGATA
* *
1622700 ACACGGTTCCTACGTGATGAGGACGGCTGATTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
* ** *
1622743 ACACGGCTCCTACGTGATGAGGA-GATCTGG---TCTGGGGAATG
1 ACACGGCTCCTACGTGATGAGGACG-GCTGGTTATCTATGG-TTG
* * * * ** * *
1622784 GCACGGCTCATACGTGATGAAGA-GTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGACG-GCTGGTTATCT-ATGGT--TG
* *
1622830 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCCATGGTTG
1 ACACGGCTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
* *** ** *
1622873 ACACGACTCCTACGTGATGAGGATATCTGG---TCTGGGGATG
1 ACACGGCTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
* * ** ** * *
1622913 ACACGGTTCCTATGTGATGAGGACTACTGGCCATCTTAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGACGGCTGGTTATC-TATGGT--TG
* *
1622959 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCCATGGTTG
1 ACACGGCTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
*
1623002 ACACGACTCCTACGTGATGAGGA
1 ACACGGCTCCTACGTGATGAGGA
1623025 GATCTGGTCT
Statistics
Matches: 214, Mismatches: 53, Indels: 30
0.72 0.18 0.10
Matches are distributed among these distances:
40 35 0.16
41 28 0.13
42 1 0.00
43 75 0.35
44 6 0.03
45 10 0.05
46 58 0.27
47 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (43 bp):
ACACGGCTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
Found at i:1622930 original size:40 final size:41
Alignment explanation
Indices: 1622700--1623064 Score: 182
Period size: 43 Copynumber: 8.6 Consensus size: 41
1622690 TTAGGTGATA
*** * ** *
1622700 ACACGGTTCCTACGTGATGAGGACGGCTGATTATCTATGGTTG
1 ACACGGTTCCTACGTGATGAGGATATCTG--GATCTGGGGATG
* *
1622743 ACACGGCTCCTACGTGATGAGGAGATCTGG-TCTGGGGAATG
1 ACACGGTTCCTACGTGATGAGGATATCTGGATCTGGGG-ATG
* * * * * *
1622784 GCACGGCTCATACGTGATGAAGAGT-TCTGGCCATCTAAAGGTGATA
1 ACACGGTTCCTACGTGATGAGGA-TATCTGG--ATCT---GGGGATG
*** *** *
1622830 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCCATGGTTG
1 ACACGGTTCCTACGTGATGAGGATATCTGG--ATCTGGGGATG
**
1622873 ACACGACTCCTACGTGATGAGGATATCTGG-TCTGGGGATG
1 ACACGGTTCCTACGTGATGAGGATATCTGGATCTGGGGATG
* * *
1622913 ACACGGTTCCTATGTGATGAGGACTA-CTGGCCATCTTAAGGTGATA
1 ACACGGTTCCTACGTGATGAGGA-TATCTGG--ATC-T--GGGGATG
*** *** *
1622959 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCCATGGTTG
1 ACACGGTTCCTACGTGATGAGGATATCTGG--ATCTGGGGATG
** *
1623002 ACACGACTCCTACGTGATGAGGAGATCTGG-TCTGGGGATG
1 ACACGGTTCCTACGTGATGAGGATATCTGGATCTGGGGATG
*
1623042 ACACGGTTCCTATGTGATGAGGA
1 ACACGGTTCCTACGTGATGAGGA
1623065 CTACTGGCCA
Statistics
Matches: 240, Mismatches: 65, Indels: 37
0.70 0.19 0.11
Matches are distributed among these distances:
40 61 0.25
41 29 0.12
43 81 0.34
44 4 0.02
46 62 0.26
47 3 0.01
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.26
Consensus pattern (41 bp):
ACACGGTTCCTACGTGATGAGGATATCTGGATCTGGGGATG
Found at i:1622988 original size:129 final size:129
Alignment explanation
Indices: 1622620--1623079 Score: 672
Period size: 129 Copynumber: 3.6 Consensus size: 129
1622610 GTGACAAGGT
* * * * * * *
1622620 TCCTACATAATGAGGAAATCTGATC-GAGGGATGACAC-TTCTCCTACGTGATGAAGAGTTCTTG
1 TCCTACGTGATGAGGAGATCTGGTCTG-GGGATGACACGGT-TCCTACGTGATGAAGACTAC-TG
* * *
1622683 GCCATCTTTAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGATTATCTATGGTTGACACG
63 GCCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCCATGGTTGACACG
*
1622748 GC
128 AC
* * * * *
1622750 TCCTACGTGATGAGGAGATCTGGTCTGGGGAATGGCACGGCTCATACGTGATGAAGAGTTCTGGC
1 TCCTACGTGATGAGGAGATCTGGTCTGGGG-ATGACACGGTTCCTACGTGATGAAGACTACTGGC
*
1622815 CATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCCATGGTTGACACGAC
65 CATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCCATGGTTGACACGAC
* * *
1622880 TCCTACGTGATGAGGATATCTGGTCTGGGGATGACACGGTTCCTATGTGATGAGGACTACTGGCC
1 TCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGTTCCTACGTGATGAAGACTACTGGCC
1622945 ATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCCATGGTTGACACGAC
66 ATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCCATGGTTGACACGAC
* *
1623009 TCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGTTCCTATGTGATGAGGACTACTGGCC
1 TCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGTTCCTACGTGATGAAGACTACTGGCC
1623074 ATCTTA
66 ATCTTA
1623080 GGAATAATGG
Statistics
Matches: 304, Mismatches: 23, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
129 161 0.53
130 117 0.38
131 26 0.09
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (129 bp):
TCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGTTCCTACGTGATGAAGACTACTGGCC
ATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCCATGGTTGACACGAC
Found at i:1623394 original size:35 final size:36
Alignment explanation
Indices: 1623343--1623422 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 36
1623333 TGAGACAAAA
* * * *
1623343 TTTGTTTTTAAGGGAAAC-GTTCTCAAAGATGTTTA-T
1 TTTG-TTTCAAGGGAAACAGAT-TCAAAGATGGTAATT
1623379 TTTGTTTCAAGGGAAACAGATTCAAAGATGGTAATT
1 TTTGTTTCAAGGGAAACAGATTCAAAGATGGTAATT
1623415 TTTGTTTC
1 TTTGTTTC
1623423 CAAAGAAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 23 0.61
36 15 0.39
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACAGATTCAAAGATGGTAATT
Found at i:1623431 original size:36 final size:35
Alignment explanation
Indices: 1623364--1623443 Score: 90
Period size: 36 Copynumber: 2.3 Consensus size: 35
1623354 GGGAAACGTT
* * * *
1623364 CTCAAAGATGTTTATTTTGTTTCAAGGGAAACAGA
1 CTCAAAGATGGTAATTTTGTTTCAAGAGAAACAAA
*
1623399 TTCAAAGATGGTAATTTTTGTTTCCAA-AGAAACAAA
1 CTCAAAGATGGTAA-TTTTGTTT-CAAGAGAAACAAA
1623435 CTCAAAGAT
1 CTCAAAGAT
1623444 TTTTCTCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
35 11 0.30
36 23 0.62
37 3 0.08
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (35 bp):
CTCAAAGATGGTAATTTTGTTTCAAGAGAAACAAA
Found at i:1623867 original size:40 final size:40
Alignment explanation
Indices: 1623818--1623897 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
1623808 GTTTTAATAA
*
1623818 AAACAATCTCCAAGGTGGGTAGTTTT-AAAAGAAATTGTCT
1 AAACAATCTCAAAGGTGGGTA-TTTTCAAAAGAAATTGTCT
* * *
1623858 AAACGATCTCAAATGTGGGTATTTTCAAAAGAAGTTGTCT
1 AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
1623898 CGAGAGACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (40 bp):
AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
Found at i:1624277 original size:36 final size:35
Alignment explanation
Indices: 1624193--1624296 Score: 129
Period size: 36 Copynumber: 3.0 Consensus size: 35
1624183 GAGAAAATGA
* * *
1624193 TGTCTCAAGCGAGACGAAATTTGCTTTT-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTGAGAAAT
* **
1624227 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTT-GAGAAAT
*
1624263 TGTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTGAGAAA
1624297 CGATCTCAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 23 0.40
35 6 0.10
36 29 0.50
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.34
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTGAGAAAT
Found at i:1624304 original size:35 final size:32
Alignment explanation
Indices: 1624194--1624323 Score: 109
Period size: 35 Copynumber: 3.8 Consensus size: 32
1624184 AGAAAATGAT
*
1624194 GTCTCAAGCGAGACGAAATTTGCTTTT-AGATATA
1 GTCTCAAGCGAGAC-AAATTTGTTTTTGAGA-A-A
**
1624228 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAA
1 GTCTCAAGCGAGAC-AAATTTGTTTTT-GAGAAA
1624262 TTGTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAA
1 --GTCTCAAGCGAGACAAA-TTTGTTTTTGAGAAA
* *
1624297 CGATCTCAAGTGAGATCAACTTTGTTT
1 -G-TCTCAAGCGAGA-CAAATTTGTTT
1624324 AATGTGAAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
34 25 0.31
35 28 0.35
36 27 0.34
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (32 bp):
GTCTCAAGCGAGACAAATTTGTTTTTGAGAAA
Found at i:1624492 original size:105 final size:100
Alignment explanation
Indices: 1624263--1624495 Score: 272
Period size: 105 Copynumber: 2.3 Consensus size: 100
1624253 TTAGAGAAAT
*
1624263 TGTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAACGATCTCAAGTGAGATCAACTTTGTTTAATG
1 TGTCTCAAGCGAGACAAAGTTTG-TTTTGAGAAACAATCTCAAGTGAGATCAACTTTGTTTAATG
* *
1624328 TGAAACAAATCCGAAATTTGGATCTCAAAGGGAAAA
65 TGAAACAAATCCAAAATTTGGATCTCAAAGGAAAAA
* * * * *
1624364 GGTCTCAAGCGAGATAAAATTTGTTTTGAAAGAAACAA-CAATCTAAGGTGAGATTAATTTTGTT
1 TGTCTCAAGCGAGACAAAGTTTGTTTTG--AGAAACAATC--TC-AA-GTGAGATCAACTTTG-T
* * *
1624428 TTAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAA
59 TTAATGTGAAACAAATCCAAAATTTGGATCTCAAAGGAAAAA
*
1624469 TGTCTCAAGCGAGACGAAGTTTGTTTT
1 TGTCTCAAGCGAGACAAAGTTTGTTTT
1624496 AAGAGAATTT
Statistics
Matches: 110, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
100 5 0.05
101 21 0.19
102 7 0.06
103 2 0.02
104 2 0.02
105 68 0.62
106 5 0.05
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (100 bp):
TGTCTCAAGCGAGACAAAGTTTGTTTTGAGAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATCCAAAATTTGGATCTCAAAGGAAAAA
Found at i:1624509 original size:36 final size:36
Alignment explanation
Indices: 1624469--1624605 Score: 170
Period size: 36 Copynumber: 3.8 Consensus size: 36
1624459 AAAGGAAAAA
* * *
1624469 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
* * **
1624505 TGTCTCAAACGAGACAAAATTTGTTTTTAGA-AAGC
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
*
1624540 TGTCTCAAGCGAGACAAAATTTGCTTTGAA-AGAAAT
1 TGTCTCAAGCGAGACAAAATTTG-TTTTAAGAGAAAT
1624576 TGTCTCAAGCGAGACAAAAATTTGTTTTAA
1 TGTCTCAAGCGAGAC-AAAATTTGTTTTAA
1624606 AATTCTCAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
35 25 0.29
36 53 0.62
37 8 0.09
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
Found at i:1624579 original size:71 final size:72
Alignment explanation
Indices: 1624469--1624603 Score: 202
Period size: 71 Copynumber: 1.9 Consensus size: 72
1624459 AAAGGAAAAA
* * * *
1624469 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATTTGTCTCAAACGAGAC-AAAATTTGTTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTTT
1624533 AGAAAGC
66 AGAAAGC
*
1624540 TGTCTCAAGCGAGACAAAATTTGCTTTGAA-AGAAATTGTCTCAAGCGAGACAAAAATTTGTTTT
1 TGTCTCAAGCGAGACAAAATTTG-TTTGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTT
1624604 AAAATTCTCA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
71 40 0.70
72 17 0.30
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (72 bp):
TGTCTCAAGCGAGACAAAATTTGTTTGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTTT
AGAAAGC
Found at i:1626214 original size:12 final size:11
Alignment explanation
Indices: 1626186--1626227 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
1626176 CCTCTTTTTG
*
1626186 TTCTTTGCTTT
1 TTCTTTGATTT
1626197 TTCTTTGATTT
1 TTCTTTGATTT
1626208 TTGCTTTGATTT
1 TT-CTTTGATTT
1626220 TCTCTTTG
1 T-TCTTTG
1626228 CTCTTTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 12 0.43
12 15 0.54
13 1 0.04
ACGTcount: A:0.05, C:0.14, G:0.12, T:0.69
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:1626245 original size:11 final size:12
Alignment explanation
Indices: 1626181--1626227 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
1626171 TTTGTCCTCT
1626181 TTTTGTTCTTTG-
1 TTTT-TTCTTTGA
*
1626193 CTTTTTCTTTGA
1 TTTTTTCTTTGA
*
1626205 TTTTTGCTTTGA
1 TTTTTTCTTTGA
*
1626217 TTTTCTCTTTG
1 TTTTTTCTTTG
1626228 CTCTTTGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
11 7 0.24
12 22 0.76
ACGTcount: A:0.04, C:0.13, G:0.13, T:0.70
Consensus pattern (12 bp):
TTTTTTCTTTGA
Found at i:1626256 original size:30 final size:31
Alignment explanation
Indices: 1626198--1626258 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
1626188 CTTTGCTTTT
**
1626198 TCTTTGATTTTTGCTTTGATTTTCTCTTTGC
1 TCTTTGATTTTTGCTTTGATTTGATCTTTGC
* *
1626229 TCTTTG-TTTTTTCTTTGGTTTGATCTTTGC
1 TCTTTGATTTTTGCTTTGATTTGATCTTTGC
1626259 ACTCTGCGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.05, C:0.15, G:0.15, T:0.66
Consensus pattern (31 bp):
TCTTTGATTTTTGCTTTGATTTGATCTTTGC
Found at i:1626910 original size:20 final size:20
Alignment explanation
Indices: 1626829--1626903 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
1626819 AAATACAGTG
*
1626829 TTTCAAGGT-GGAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
* *
1626848 TTTCAAGGTCACAAAGAGAGGGAATG
1 TTTCAAGGT--CGAA-A-A--GAATA
1626874 TTTCAAGGTCGAAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
1626894 TTTCAAGGTC
1 TTTCAAGGTC
1626904 TCAAAGAGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 9 0.20
20 14 0.32
22 2 0.05
23 2 0.05
24 4 0.09
26 13 0.30
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (20 bp):
TTTCAAGGTCGAAAAGAATA
Found at i:1626917 original size:26 final size:26
Alignment explanation
Indices: 1626839--1626918 Score: 73
Period size: 26 Copynumber: 3.3 Consensus size: 26
1626829 TTTCAAGGTG
*
1626839 GAAAGAATATTTCAAGGTCACAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
** *
1626865 GAGGGAATGTTTCAAGG--TC---GA
1 GAAAGAATATTTCAAGGTCTCAAAGA
1626886 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
*
1626911 GATAGAAT
1 GAAAGAAT
1626919 GTCAAAAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 13 0.32
21 2 0.05
22 2 0.05
24 1 0.03
25 2 0.05
26 20 0.50
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.23
Consensus pattern (26 bp):
GAAAGAATATTTCAAGGTCTCAAAGA
Found at i:1626919 original size:46 final size:45
Alignment explanation
Indices: 1626827--1626920 Score: 143
Period size: 46 Copynumber: 2.1 Consensus size: 45
1626817 ATAAATACAG
* *
1626827 TGTTTCAAGGTGGAAAGAATATTTCAAGGTCACAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCACAAAGAGAGAGAA
* *
1626872 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGTCACAAAGAGAGAGAA
1626918 TGT
1 TGT
1626921 CAAAAATTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 11 0.25
46 33 0.75
ACGTcount: A:0.39, C:0.10, G:0.26, T:0.26
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCACAAAGAGAGAGAA
Found at i:1630940 original size:22 final size:22
Alignment explanation
Indices: 1630897--1630940 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1630887 AAATTTACAT
*
1630897 TCACATAAAATAAAATAAATTG
1 TCACATAAAATAAAACAAATTG
* * *
1630919 TCACTTAAAATAACACACATTG
1 TCACATAAAATAAAACAAATTG
1630941 CATCGTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (22 bp):
TCACATAAAATAAAACAAATTG
Found at i:1632404 original size:12 final size:12
Alignment explanation
Indices: 1632382--1632421 Score: 66
Period size: 11 Copynumber: 3.5 Consensus size: 12
1632372 TTCCTCCTTT
1632382 TTTCC-TTCTGA
1 TTTCCTTTCTGA
1632393 TTTCCTTTCTGA
1 TTTCCTTTCTGA
1632405 -TTCCTTTCTGA
1 TTTCCTTTCTGA
1632416 TTTCCT
1 TTTCCT
1632422 CTGTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.07, C:0.28, G:0.07, T:0.57
Consensus pattern (12 bp):
TTTCCTTTCTGA
Found at i:1632959 original size:3 final size:3
Alignment explanation
Indices: 1632940--1632989 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
1632930 ATGTAAAATG
*
1632940 TAA TAT TAA TAA T-A TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
1632985 -AA TAA
1 TAA TAA
1632990 CGATAAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.83
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1634203 original size:56 final size:56
Alignment explanation
Indices: 1634137--1634252 Score: 171
Period size: 56 Copynumber: 2.1 Consensus size: 56
1634127 GGTAAACTTT
* *
1634137 TCATTCAATTTCAAGCATG-ATATAAACCTCCTAACATTAAATTCATGCTATTCCAA
1 TCATTCAATTTCAAACAGGAAT-TAAACCTCCTAACATTAAATTCATGCTATTCCAA
* * *
1634193 TCATTCAATTTCAAACAGGAATTCAACTTCCTAACATTAAATTCATGCTATTTCAA
1 TCATTCAATTTCAAACAGGAATTAAACCTCCTAACATTAAATTCATGCTATTCCAA
1634249 TCAT
1 TCAT
1634253 CACAACATCA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
56 52 0.96
57 2 0.04
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.35
Consensus pattern (56 bp):
TCATTCAATTTCAAACAGGAATTAAACCTCCTAACATTAAATTCATGCTATTCCAA
Found at i:1639491 original size:27 final size:27
Alignment explanation
Indices: 1639435--1639499 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
1639425 CTTTCATATA
*
1639435 AAACTAAATGATATTTTCTTTTTCCCAT
1 AAACTAAATGATA-TCTCTTTTTCCCAT
*
1639463 AAACTAAATGATA-CTGTTTTTCCCTAT
1 AAACTAAATGATATCTCTTTTTCCC-AT
*
1639490 AAACTGAATG
1 AAACTAAATG
1639500 CACTCTTGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.27
27 11 0.33
28 13 0.39
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (27 bp):
AAACTAAATGATATCTCTTTTTCCCAT
Found at i:1639752 original size:17 final size:17
Alignment explanation
Indices: 1639730--1639765 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1639720 TTTTTTCGGA
1639730 TAAAAAAATC-AGTTTTT
1 TAAAAAAATCGA-TTTTT
1639747 TAAAAAAATCGATTTTT
1 TAAAAAAATCGATTTTT
1639764 TA
1 TA
1639766 TCTGGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.94
18 1 0.06
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (17 bp):
TAAAAAAATCGATTTTT
Found at i:1639803 original size:27 final size:26
Alignment explanation
Indices: 1639747--1639828 Score: 89
Period size: 24 Copynumber: 3.2 Consensus size: 26
1639737 ATCAGTTTTT
*
1639747 TAAAAAAATCGATTTTTTATCTGG-A
1 TAAAAAAATCGATTTTTTATCCGGTA
*
1639772 T-AAAAAATCGATTTTTTATCCGGTT
1 TAAAAAAATCGATTTTTTATCCGGTA
* * *
1639797 TCAAAAAAACCGGTTTTTAATCCGGTA
1 T-AAAAAAATCGATTTTTTATCCGGTA
1639824 -AAAAA
1 TAAAAA
1639829 CCGGTCGTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
24 21 0.44
25 7 0.15
27 20 0.42
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (26 bp):
TAAAAAAATCGATTTTTTATCCGGTA
Found at i:1640101 original size:21 final size:21
Alignment explanation
Indices: 1640071--1640144 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
1640061 TAGTATATTT
1640071 TTTTATTTTTATAATTGAGTC
1 TTTTATTTTTATAATTGAGTC
* * * *
1640092 TTTTAGTTTTTTTATTTTA-TT
1 TTTTA-TTTTTATAATTGAGTC
1640113 TTTTATTTTTATAATTGAGTC
1 TTTTATTTTTATAATTGAGTC
1640134 TTTTAATTTTT
1 TTTT-ATTTTT
1640145 TTTATTTTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
20 10 0.24
21 16 0.38
22 16 0.38
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (21 bp):
TTTTATTTTTATAATTGAGTC
Found at i:1640160 original size:43 final size:43
Alignment explanation
Indices: 1640051--1640161 Score: 170
Period size: 43 Copynumber: 2.6 Consensus size: 43
1640041 TATAGGGCTC
* * *
1640051 TAATTTATTTTAGTATATTTTTTTATTTTTATAATTGAGTCTTT
1 TAATTTTTTTTATTTTA-TTTTTTATTTTTATAATTGAGTCTTT
*
1640095 T-AGTTTTTTTATTTTATTTTTTATTTTTATAATTGAGTCTTT
1 TAATTTTTTTTATTTTATTTTTTATTTTTATAATTGAGTCTTT
1640137 TAATTTTTTTTATTTTATTTTTTAT
1 TAATTTTTTTTATTTTATTTTTTAT
1640162 AATTGAGGTC
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
42 27 0.44
43 33 0.54
44 1 0.02
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (43 bp):
TAATTTTTTTTATTTTATTTTTTATTTTTATAATTGAGTCTTT
Found at i:1640164 original size:37 final size:37
Alignment explanation
Indices: 1640071--1640183 Score: 140
Period size: 37 Copynumber: 2.9 Consensus size: 37
1640061 TAGTATATTT
*
1640071 TTTTA-TTTTTATAATTGAGTCTTTTAGTTTTTTTATTTTA
1 TTTTATTTTTTATAATTGAGTCTTTTA---ATTTT-TTTTA
*
1640111 TTTTTTATTTTTATAATTGAGTCTTTTAATTTTTTTTA
1 TTTTAT-TTTTTATAATTGAGTCTTTTAATTTTTTTTA
1640149 TTTTATTTTTTATAATTGAGGTC-TTTAATTTTTTT
1 TTTTATTTTTTATAATTGA-GTCTTTTAATTTTTTT
1640184 AATCATATTT
Statistics
Matches: 67, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
37 25 0.37
38 13 0.19
39 4 0.06
40 4 0.06
42 21 0.31
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (37 bp):
TTTTATTTTTTATAATTGAGTCTTTTAATTTTTTTTA
Found at i:1640196 original size:43 final size:42
Alignment explanation
Indices: 1640051--1640207 Score: 175
Period size: 42 Copynumber: 3.8 Consensus size: 42
1640041 TATAGGGCTC
*
1640051 TAATTTATTTTAGTATATTTTTTTATTTTTATAATTGAGTCTTT
1 TAATTT-TTTTA-TATATTTTTATATTTTTATAATTGAGTCTTT
* *
1640095 TAGTTTTTTTATTTTATTTTT-TATTTTTATAATTGAGTCTTT
1 TAATTTTTTTA-TATATTTTTATATTTTTATAATTGAGTCTTT
1640137 TAA-TTTTTT-T-TA-TTTTAT-TTTTTATAATTGAGGTC-TT
1 TAATTTTTTTATATATTTTTATATTTTTATAATTGA-GTCTTT
*
1640174 TAATTTTTTTAATCATATTTTTATATCTTTATAA
1 TAATTTTTTT-AT-ATATTTTTATATTTTTATAA
1640208 GTAAGGTACT
Statistics
Matches: 99, Mismatches: 5, Indels: 18
0.81 0.04 0.15
Matches are distributed among these distances:
37 22 0.22
38 12 0.12
39 1 0.01
40 1 0.01
41 6 0.06
42 25 0.25
43 19 0.19
44 13 0.13
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (42 bp):
TAATTTTTTTATATATTTTTATATTTTTATAATTGAGTCTTT
Found at i:1640374 original size:159 final size:161
Alignment explanation
Indices: 1640115--1640438 Score: 478
Period size: 159 Copynumber: 2.0 Consensus size: 161
1640105 ATTTTATTTT
* **
1640115 TTATTTTTATAATTGAGTCTTTTAATTTTTTTTATTTTATTTTTTATAATTGAGGTCTTTAATTT
1 TTATTTTTATAATTGAGTCTTTTAATTTTCTTTA---TATTTTAGATAATTGAGGTCTTTAATTT
*
1640180 TTTTAATCATATTTTTATATCTTTATAAGTAAGGTACTT-ATTTTTTAAAATCTAATTCTTTTAC
63 TTTTAATCATATTTTTATATCTTTATAAGTAAGGTACTTAATTTTTT-AAATCTAACTCTTTTAC
*
1640244 ATTTATAATTGATGACGATCTTAAGTTTTTTAATC
127 ATTTATAATTGATGACGATCTTAAGTTTTTGAATC
1640279 TTATTTTTATAATTGAGTCTTTTAATTTTCTTTA-ATTTTAGATAATTGAGGTCTTT-ATTTTTT
1 TTATTTTTATAATTGAGTCTTTTAATTTTCTTTATATTTTAGATAATTGAGGTCTTTAATTTTTT
* * *
1640342 ATAATCTTATTTTT-TATCTTTAT-AGTTAAGGTATTTAATTTTTTAAATCTCACTCTTTTACAT
66 -TAATCATATTTTTATATCTTTATAAG-TAAGGTACTTAATTTTTTAAATCTAACTCTTTTACAT
*
1640405 TTATAATTGATGAGGATCTTAAGTTTTTGAATC
129 TTATAATTGATGACGATCTTAAGTTTTTGAATC
1640438 T
1 T
1640439 CATTGTATAC
Statistics
Matches: 148, Mismatches: 9, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
158 2 0.01
159 74 0.50
160 39 0.26
164 33 0.22
ACGTcount: A:0.27, C:0.07, G:0.08, T:0.57
Consensus pattern (161 bp):
TTATTTTTATAATTGAGTCTTTTAATTTTCTTTATATTTTAGATAATTGAGGTCTTTAATTTTTT
TAATCATATTTTTATATCTTTATAAGTAAGGTACTTAATTTTTTAAATCTAACTCTTTTACATTT
ATAATTGATGACGATCTTAAGTTTTTGAATC
Found at i:1640401 original size:44 final size:43
Alignment explanation
Indices: 1640327--1640409 Score: 98
Period size: 44 Copynumber: 1.9 Consensus size: 43
1640317 TAGATAATTG
* * *
1640327 AGGTCTTTATTTTTTATAATCTTATTTTTTATC-TTTATAGTTA
1 AGGTATTTATTTTTTATAATCTCATCTTTTA-CATTTATAGTTA
1640370 AGGTATTTAATTTTTTA-AATCTCACTCTTTTACATTTATA
1 AGGTATTT-ATTTTTTATAATCTCA-TCTTTTACATTTATA
1640410 ATTGATGAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
43 14 0.41
44 20 0.59
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.58
Consensus pattern (43 bp):
AGGTATTTATTTTTTATAATCTCATCTTTTACATTTATAGTTA
Found at i:1640495 original size:159 final size:157
Alignment explanation
Indices: 1640171--1640481 Score: 364
Period size: 159 Copynumber: 1.9 Consensus size: 157
1640161 TAATTGAGGT
*
1640171 CTTTAATTTTTTTAATCATATTTTTATATCTTTATAAGTAAGGTACTTATTTTTTAAAATCTAAT
1 CTTT-ATTTTTTTAATCATATTTTTATATCTTTATAAGTAAGGTACTTATTTTTTAAAATCTAAC
* **
1640236 TCTTTTACATTTATAATTGATGACGATCTTAAGTTTTTTAATCTTATTTTTATAATTGAGTCTTT
65 TCTTTTACATTTATAATTGATGACGATCTTAAGTTTTTGAATCTTATTTTTATAATTGAGTCTAC
* * *
1640301 TAATTTTCTTTAATTTTAGATAATTGAGG
130 TAATTTTCTTAAATCTTAGATAATTCA-G
* *
1640330 TCTTTATTTTTTATAATCTTATTTTT-TATCTTTAT-AGTTAAGGTATTTAATTTTTT-AAATCT
1 -CTTTATTTTTT-TAATCATATTTTTATATCTTTATAAG-TAAGGTACTT-ATTTTTTAAAATCT
* *
1640392 CACTCTTTTACATTTATAATTGATGAGGATCTTAAGTTTTTGAATCTCATTGTATACTTTTATAA
62 AACTCTTTTACATTTATAATTGATGACGATCTTAAGTTTTTGAA--TC--T-TAT--TTTTATAA
1640457 TTGAG-CTACTAA-TTT-TTAAATCTTA
120 TTGAGTCTACTAATTTTCTTAAATCTTA
1640482 CTTTTCACAT
Statistics
Matches: 131, Mismatches: 10, Indels: 17
0.83 0.06 0.11
Matches are distributed among these distances:
158 2 0.02
159 71 0.54
160 23 0.18
161 2 0.02
163 9 0.07
164 6 0.05
165 5 0.04
166 13 0.10
ACGTcount: A:0.29, C:0.09, G:0.08, T:0.54
Consensus pattern (157 bp):
CTTTATTTTTTTAATCATATTTTTATATCTTTATAAGTAAGGTACTTATTTTTTAAAATCTAACT
CTTTTACATTTATAATTGATGACGATCTTAAGTTTTTGAATCTTATTTTTATAATTGAGTCTACT
AATTTTCTTAAATCTTAGATAATTCAG
Found at i:1640516 original size:84 final size:86
Alignment explanation
Indices: 1640381--1640543 Score: 206
Period size: 84 Copynumber: 1.9 Consensus size: 86
1640371 GGTATTTAAT
* *
1640381 TTTTTAAATCTCACTCTTTTACATTTATAATTGATGAGGATCTTAAGTTTTTGAATCTCATTGTA
1 TTTTTAAATCTCACTCTTTCACATTTATAA-T-ATGAAGATCTTAAGTTTTTGAATCTCATTGTA
1640446 TACTTTTATAATTGAGCTACTAA
64 TACTTTTATAATTGAGCTACTAA
* * * * * *
1640469 TTTTTAAATCTTACT-TTTCACATTTATAA-A-GAAGACTCTTAATTTTTTTAATCTTATTTTTT
1 TTTTTAAATCTCACTCTTTCACATTTATAATATGAAGA-TCTTAAGTTTTTGAATCTCATTGTAT
1640531 ACTTTTATAATTG
65 ACTTTTATAATTG
1640544 GGTCCTATAA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
83 4 0.06
84 35 0.53
87 13 0.20
88 14 0.21
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.52
Consensus pattern (86 bp):
TTTTTAAATCTCACTCTTTCACATTTATAATATGAAGATCTTAAGTTTTTGAATCTCATTGTATA
CTTTTATAATTGAGCTACTAA
Found at i:1640601 original size:43 final size:43
Alignment explanation
Indices: 1640504--1640602 Score: 105
Period size: 42 Copynumber: 2.3 Consensus size: 43
1640494 ATAAAGAAGA
* ** *
1640504 CTCTTAATTTTTTTAATCTTATTTTTTACTTTTATAATTGGGT
1 CTCTTAATTTTTTCAATCTTATTTTTTACTAATATAATTGAGT
*
1640547 C-CTATAATTTTTTCAAT-TCTA-TTTTTACTAATATAATTTAGT
1 CTCT-TAATTTTTTCAATCT-TATTTTTTACTAATATAATTGAGT
1640589 CTCTTAAGTTTTTT
1 CTCTTAA-TTTTTT
1640603 ATTCTCGCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
42 24 0.51
43 23 0.49
ACGTcount: A:0.24, C:0.11, G:0.05, T:0.60
Consensus pattern (43 bp):
CTCTTAATTTTTTCAATCTTATTTTTTACTAATATAATTGAGT
Found at i:1642433 original size:32 final size:32
Alignment explanation
Indices: 1642396--1642477 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 32
1642386 CATTAAAATA
1642396 ATTTAATATTCAAATTATAATATATATATTAT
1 ATTTAATATTCAAATTATAATATATATATTAT
1642428 ATTTAATGA-T---A--A-AA-ATATATATTAT
1 ATTTAAT-ATTCAAATTATAATATATATATTAT
1642453 ATTTAATATTCAAATTATAAT-TATA
1 ATTTAATATTCAAATTATAATATATA
1642478 AGTTGTGACT
Statistics
Matches: 41, Mismatches: 0, Indels: 19
0.68 0.00 0.32
Matches are distributed among these distances:
24 1 0.02
25 19 0.46
26 2 0.05
27 1 0.02
28 1 0.02
29 1 0.02
30 1 0.02
31 6 0.15
32 8 0.20
33 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (32 bp):
ATTTAATATTCAAATTATAATATATATATTAT
Found at i:1647370 original size:44 final size:44
Alignment explanation
Indices: 1647298--1647633 Score: 380
Period size: 44 Copynumber: 7.9 Consensus size: 44
1647288 TGATCATCCT
1647298 TGAATGTGTTATATATATAACATTTGTTGCTGTGAGTCTTTGTCGA
1 TGAATGTG-T-TATATATAACATTTGTTGCTGTGAGTCTTTGTCGA
** * *
1647344 TGAATGTGTTATATATGGCATTTGTTGCTGTGAATCCTTGTCGA
1 TGAATGTGTTATATATAACATTTGTTGCTGTGAGTCTTTGTCGA
1647388 TGAATGTGTTATAT-T---A---GTTGCTGTG-GATCTTTGTCGA
1 TGAATGTGTTATATATAACATTTGTTGCTGTGAG-TCTTTGTCGA
* * * *
1647425 CGAATGTGTTATATATAACATTAGTTACTGTTAGTCTTTGTCGA
1 TGAATGTGTTATATATAACATTTGTTGCTGTGAGTCTTTGTCGA
* *
1647469 TGAATGTGTTATATATAACATTTGTAGCTGTAAGTCTTTGTCGA
1 TGAATGTGTTATATATAACATTTGTTGCTGTGAGTCTTTGTCGA
** *
1647513 TGAATGTGTTATAT-T---A---GTTGCAATGAATCTTTGTCGA
1 TGAATGTGTTATATATAACATTTGTTGCTGTGAGTCTTTGTCGA
* * *
1647550 TGAATGTGTTATATATAACATTAGTTGCTGTGAGTTTTTTTCGA
1 TGAATGTGTTATATATAACATTTGTTGCTGTGAGTCTTTGTCGA
*
1647594 TGAA-GTGTTATATATAACATTTGTAGCTGTGAGTCTTTGT
1 TGAATGTGTTATATATAACATTTGTTGCTGTGAGTCTTTGT
1647634 TGGACAGCTC
Statistics
Matches: 246, Mismatches: 28, Indels: 35
0.80 0.09 0.11
Matches are distributed among these distances:
37 61 0.25
38 2 0.01
40 2 0.01
41 2 0.01
43 34 0.14
44 135 0.55
45 2 0.01
46 8 0.03
ACGTcount: A:0.24, C:0.09, G:0.22, T:0.45
Consensus pattern (44 bp):
TGAATGTGTTATATATAACATTTGTTGCTGTGAGTCTTTGTCGA
Found at i:1647422 original size:37 final size:37
Alignment explanation
Indices: 1647367--1647563 Score: 171
Period size: 37 Copynumber: 4.9 Consensus size: 37
1647357 TATGGCATTT
*
1647367 GTTGCTGTGAATCCTTGTCGATGAATGTGTTATATTA
1 GTTGCTGTGAATCTTTGTCGATGAATGTGTTATATTA
* *
1647404 GTTGCTGTGGATCTTTGTCGACGAATGTGTTATATATAACATTA
1 GTTGCTGTGAATCTTTGTCGATGAATGTG---T-TAT---ATTA
* * *
1647448 GTTACTGTTAGTCTTTGTCGATGAATGTGTTATATATAACA
1 GTTGCTGTGAATCTTTGTCGATGAATGTGTTATAT-T---A
*
1647489 TTTG-TAGCTGTAAGTCTTTGTCGATGAATGTGTTATATTA
1 GTTGCT-G-TG-AA-TCTTTGTCGATGAATGTGTTATATTA
**
1647529 GTTGCAATGAATCTTTGTCGATGAATGTGTTATAT
1 GTTGCTGTGAATCTTTGTCGATGAATGTGTTATAT
1647564 ATAACATTAG
Statistics
Matches: 129, Mismatches: 15, Indels: 32
0.73 0.09 0.18
Matches are distributed among these distances:
37 52 0.40
38 3 0.02
39 2 0.02
40 9 0.07
41 8 0.06
42 1 0.01
43 2 0.02
44 52 0.40
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.44
Consensus pattern (37 bp):
GTTGCTGTGAATCTTTGTCGATGAATGTGTTATATTA
Found at i:1647466 original size:81 final size:81
Alignment explanation
Indices: 1647323--1647482 Score: 232
Period size: 81 Copynumber: 2.0 Consensus size: 81
1647313 TATAACATTT
* ** * *
1647323 GTTGCTGTGAGTCTTTGTCGATGAATGTGTTATATATGGCATTTGTTGCTGTGAATCCTTGTCGA
1 GTTGCTGTGAGTCTTTGTCGACGAATGTGTTATATATAACATTAGTTACTGTGAATCCTTGTCGA
1647388 TGAATGTGTTATATTA
66 TGAATGTGTTATATTA
* * *
1647404 GTTGCTGTG-GATCTTTGTCGACGAATGTGTTATATATAACATTAGTTACTGTTAGTCTTTGTCG
1 GTTGCTGTGAG-TCTTTGTCGACGAATGTGTTATATATAACATTAGTTACTGTGAATCCTTGTCG
1647468 ATGAATGTGTTATAT
65 ATGAATGTGTTATAT
1647483 ATAACATTTG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
80 1 0.01
81 69 0.99
ACGTcount: A:0.21, C:0.10, G:0.24, T:0.44
Consensus pattern (81 bp):
GTTGCTGTGAGTCTTTGTCGACGAATGTGTTATATATAACATTAGTTACTGTGAATCCTTGTCGA
TGAATGTGTTATATTA
Found at i:1647523 original size:125 final size:125
Alignment explanation
Indices: 1647299--1647633 Score: 503
Period size: 125 Copynumber: 2.7 Consensus size: 125
1647289 GATCATCCTT
* **
1647299 GAATGTGTTATATATATAACATTTGTTGCTGTGAGTCTTTGTCGATGAATGTGTTATATATGGCA
1 GAATGTG-T-TATATATAACATTAGTTGCTGTGAGTCTTTGTCGATGAATGTGTTATATATAACA
* * ** *
1647364 TTTGTTGCTGTGAA-TCCTTGTCGATGAATGTGTTATATTAGTTGCTGTGGATCTTTGTCGAC
64 TTTGTAGCTGT-AAGTCTTTGTCGATGAATGTGTTATATTAGTTGCAATGAATCTTTGTCGAC
* *
1647426 GAATGTGTTATATATAACATTAGTTACTGTTAGTCTTTGTCGATGAATGTGTTATATATAACATT
1 GAATGTGTTATATATAACATTAGTTGCTGTGAGTCTTTGTCGATGAATGTGTTATATATAACATT
*
1647491 TGTAGCTGTAAGTCTTTGTCGATGAATGTGTTATATTAGTTGCAATGAATCTTTGTCGAT
66 TGTAGCTGTAAGTCTTTGTCGATGAATGTGTTATATTAGTTGCAATGAATCTTTGTCGAC
* *
1647551 GAATGTGTTATATATAACATTAGTTGCTGTGAGTTTTTTTCGATGAA-GTGTTATATATAACATT
1 GAATGTGTTATATATAACATTAGTTGCTGTGAGTCTTTGTCGATGAATGTGTTATATATAACATT
*
1647615 TGTAGCTGTGAGTCTTTGT
66 TGTAGCTGTAAGTCTTTGT
1647634 TGGACAGCTC
Statistics
Matches: 191, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
124 37 0.19
125 146 0.76
126 1 0.01
127 7 0.04
ACGTcount: A:0.24, C:0.09, G:0.22, T:0.44
Consensus pattern (125 bp):
GAATGTGTTATATATAACATTAGTTGCTGTGAGTCTTTGTCGATGAATGTGTTATATATAACATT
TGTAGCTGTAAGTCTTTGTCGATGAATGTGTTATATTAGTTGCAATGAATCTTTGTCGAC
Found at i:1652422 original size:31 final size:32
Alignment explanation
Indices: 1652369--1652447 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 32
1652359 CAGTTACGTT
* * *
1652369 GGGATCATATTACAAACAGACTAAATGTT-AG
1 GGGACCATATTGCAAGCAGACTAAATGTTGAG
* *
1652400 GGGACCATATTGCAAGCGGACTAAATGTTGGG
1 GGGACCATATTGCAAGCAGACTAAATGTTGAG
*
1652432 GGGACTATATTGCAAG
1 GGGACCATATTGCAAG
1652448 TTTTAAAAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 25 0.61
32 16 0.39
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (32 bp):
GGGACCATATTGCAAGCAGACTAAATGTTGAG
Found at i:1653386 original size:31 final size:31
Alignment explanation
Indices: 1653350--1653416 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
1653340 TTACAATACA
* *
1653350 TCCCCCAACATTTAGTTCGTTTATAATATGG
1 TCCCCCAACATTTAGTCCGTTTACAATATGG
* *
1653381 TCCCCCAACATTTTGTCCGTTTGCAATATGG
1 TCCCCCAACATTTAGTCCGTTTACAATATGG
1653412 TCCCC
1 TCCCC
1653417 AATGTAACTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.21, C:0.30, G:0.13, T:0.36
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCCGTTTACAATATGG
Found at i:1655803 original size:36 final size:36
Alignment explanation
Indices: 1655756--1655832 Score: 154
Period size: 36 Copynumber: 2.1 Consensus size: 36
1655746 AGGCTATGTA
1655756 ATTTCAACCTAAGATCTTGTAACGTATACATTTCTC
1 ATTTCAACCTAAGATCTTGTAACGTATACATTTCTC
1655792 ATTTCAACCTAAGATCTTGTAACGTATACATTTCTC
1 ATTTCAACCTAAGATCTTGTAACGTATACATTTCTC
1655828 ATTTC
1 ATTTC
1655833 CTTATGTCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (36 bp):
ATTTCAACCTAAGATCTTGTAACGTATACATTTCTC
Found at i:1674918 original size:17 final size:18
Alignment explanation
Indices: 1674896--1674929 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1674886 AATAAAAACA
*
1674896 TAAAAATTG-AAAATATC
1 TAAAAAATGCAAAATATC
1674913 TAAAAAATGCAAAATAT
1 TAAAAAATGCAAAATAT
1674930 GGAACAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (18 bp):
TAAAAAATGCAAAATATC
Found at i:1684112 original size:16 final size:17
Alignment explanation
Indices: 1684091--1684124 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1684081 AATCATACAG
1684091 AATTT-AAAATTTCTGA
1 AATTTAAAAATTTCTGA
1684107 AATTTAAAAATTTCTGA
1 AATTTAAAAATTTCTGA
1684124 A
1 A
1684125 TGTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (17 bp):
AATTTAAAAATTTCTGA
Found at i:1684304 original size:28 final size:27
Alignment explanation
Indices: 1684252--1684304 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
1684242 AAAAATGCAA
* *
1684252 ATTATATTTTTTTTCCTGAATTTATCT
1 ATTAAATTTTTTTTCCTGAAATTATCT
1684279 ATTAAATTTTGTTTTCCCT-AAATTAT
1 ATTAAATTTT-TTTT-CCTGAAATTAT
1684305 AATTTATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 9 0.41
28 10 0.45
29 3 0.14
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.58
Consensus pattern (27 bp):
ATTAAATTTTTTTTCCTGAAATTATCT
Found at i:1687497 original size:21 final size:21
Alignment explanation
Indices: 1687473--1687530 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
1687463 ATGTTGATAT
*
1687473 TGATCAGCATAATGCAACTGA
1 TGATCAACATAATGCAACTGA
*
1687494 TGATCAACATAATGCAATTGA
1 TGATCAACATAATGCAACTGA
1687515 TGATCAACATAATGCA
1 TGATCAACATAATGCA
1687531 TGTGATGGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (21 bp):
TGATCAACATAATGCAACTGA
Found at i:1687536 original size:21 final size:20
Alignment explanation
Indices: 1687473--1687537 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 20
1687463 ATGTTGATAT
* *
1687473 TGATCAGCATAATGCAACTGA
1 TGATCAACATAATGC-ATTGA
1687494 TGATCAACATAATGCAATTGA
1 TGATCAACATAATGC-ATTGA
1687515 TGATCAACATAATGCATGTGA
1 TGATCAACATAATGCAT-TGA
1687536 TG
1 TG
1687538 GTGGTAATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
20 2 0.05
21 39 0.95
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (20 bp):
TGATCAACATAATGCATTGA
Found at i:1693526 original size:2 final size:2
Alignment explanation
Indices: 1693519--1693569 Score: 77
Period size: 2 Copynumber: 25.5 Consensus size: 2
1693509 ATGGATTGTT
*
1693519 TA TA TA TA -A TA TGA TA TA TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1693561 TA TA TA TA T
1 TA TA TA TA T
1693570 TTAGTATTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 42 0.93
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1697519 original size:199 final size:199
Alignment explanation
Indices: 1697179--1697577 Score: 712
Period size: 199 Copynumber: 2.0 Consensus size: 199
1697169 TTTACAAAGT
*
1697179 TGAATGAAGCCTCCTTTATATAGGAGTTGAGTTCTAAAGGTCCTAAATAACTAAAGAATAAAATA
1 TGAATGAAGCCTCCTTTATATAGGAGCTGAGTTCTAAAGGTCCTAAATAACTAAAGAATAAAATA
*
1697244 ATAATAAACTAACATATCTTAACTCTAATTCCTAATAAAATAATAACAATTAAAAATATTGTTTT
66 ATAATAAACTAACATATCTTAACTCTAATTCCTAATAAAATAATAACAACTAAAAATATTGTTTT
* *
1697309 AACCCAACCTTAATTCCTAATAAAATAATAAATCTGATCCTAAAAGATAATTCTTCATCCTATAT
131 AACCCAACCTTAATTCCTAATAAAATAATAAATATGATCCTAAAAGACAATTCTTCATCCTATAT
1697374 TAAA
196 TAAA
1697378 TGAATGAAGCCTCCTTTATATAGG-GACTGAGTTCTAAAGGTCCTAAATAA-TAAAGAATAAAAT
1 TGAATGAAGCCTCCTTTATATAGGAG-CTGAGTTCTAAAGGTCCTAAATAACTAAAGAATAAAAT
*
1697441 AATAATAAACTAAGCATTTCTTAACTCTAATTCCTAATAAAATAATAACAACTAAAAATATTGTT
65 AATAATAAACTAA-CATATCTTAACTCTAATTCCTAATAAAATAATAACAACTAAAAATATTGTT
*
1697506 TTAACCCAACCTTAATTCCTAATAAAATAATAAATATGATCCTAAAAGACAATTCTTCATCTTAT
129 TTAACCCAACCTTAATTCCTAATAAAATAATAAATATGATCCTAAAAGACAATTCTTCATCCTAT
1697571 ATTAAA
194 ATTAAA
1697577 T
1 T
1697578 TATATTACAA
Statistics
Matches: 192, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
198 27 0.14
199 165 0.86
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (199 bp):
TGAATGAAGCCTCCTTTATATAGGAGCTGAGTTCTAAAGGTCCTAAATAACTAAAGAATAAAATA
ATAATAAACTAACATATCTTAACTCTAATTCCTAATAAAATAATAACAACTAAAAATATTGTTTT
AACCCAACCTTAATTCCTAATAAAATAATAAATATGATCCTAAAAGACAATTCTTCATCCTATAT
TAAA
Found at i:1701877 original size:17 final size:18
Alignment explanation
Indices: 1701834--1701874 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1701824 AATTTATATT
1701834 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
1701851 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
1701869 ATTAAA
1 AGTAAA
1701875 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:1703767 original size:31 final size:29
Alignment explanation
Indices: 1703731--1703815 Score: 116
Period size: 29 Copynumber: 2.8 Consensus size: 29
1703721 CAAAATAAGG
*
1703731 GAAACAATCTCAAAGGTTTTGTGTTTCAAGA
1 GAAACAATTTCAAAGGTTTT-T-TTTCAAGA
*
1703762 GAAACATTTTCAAAGGTTTTTTTTCAAGA
1 GAAACAATTTCAAAGGTTTTTTTTCAAGA
*
1703791 GAAACAATTTTAAAGGTTTCTTTTT
1 GAAACAATTTCAAAGGTTT-TTTTT
1703816 GTGTTTCAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
29 25 0.51
30 6 0.12
31 18 0.37
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (29 bp):
GAAACAATTTCAAAGGTTTTTTTTCAAGA
Found at i:1703860 original size:36 final size:36
Alignment explanation
Indices: 1703820--1703907 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 36
1703810 CTTTTTGTGT
**
1703820 TTCAAGAGAAATTGTCTCAAGGGAGGTAAAATATGC
1 TTCAAGAGAAATTGTCTCAAGGGAGACAAAATATGC
* * *
1703856 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGT
1 TTCAAGAGAAATTGTCTCAAGGGAGACAAAATATGC
*
1703892 TTCAAGGGAAACTTGT
1 TTCAAGAGAAA-TTGT
1703908 GAAGTTGAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 41 0.93
37 3 0.07
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (36 bp):
TTCAAGAGAAATTGTCTCAAGGGAGACAAAATATGC
Found at i:1704553 original size:32 final size:32
Alignment explanation
Indices: 1704517--1704606 Score: 137
Period size: 32 Copynumber: 2.8 Consensus size: 32
1704507 ATTCCCAAAT
*
1704517 ATGCCCCAATATTCGATGTTGAATCTAAAAAA
1 ATGCCCCAACATTCGATGTTGAATCTAAAAAA
* *
1704549 ATGCCCCAACATTTGATGTTAAATCTAAAAAA
1 ATGCCCCAACATTCGATGTTGAATCTAAAAAA
1704581 ATGCCCCAACA-TCTGATGTTGAATCT
1 ATGCCCCAACATTC-GATGTTGAATCT
1704607 TCAAAGATGC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
31 1 0.02
32 51 0.98
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (32 bp):
ATGCCCCAACATTCGATGTTGAATCTAAAAAA
Found at i:1705657 original size:69 final size:69
Alignment explanation
Indices: 1705541--1705678 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
1705531 TGTCTCTCTC
* *
1705541 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGAAAATGATTATGCTTGATCAATC
1705606 TCAT
66 TCAT
*
1705610 TTGATGCTCTATGATCTTCGAGTGAAGTGATTTAGTGATTCGAAAATGATTATGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGAAAATGATTATGCTTGATCAATC
1705675 TCAT
66 TCAT
1705679 AGTTTGAATC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGAAAATGATTATGCTTGATCAATC
TCAT
Found at i:1705766 original size:12 final size:12
Alignment explanation
Indices: 1705751--1705804 Score: 65
Period size: 12 Copynumber: 4.4 Consensus size: 12
1705741 TTTTCTTCAA
1705751 TTTTCCT-TTGTT
1 TTTTCCTCTT-TT
*
1705763 TTTTTCTCTTTT
1 TTTTCCTCTTTT
*
1705775 TATTTTCTCTTTT
1 T-TTTCCTCTTTT
1705788 TTTTCCTCTTTT
1 TTTTCCTCTTTT
1705800 TTTTC
1 TTTTC
1705805 TGATTGAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
12 24 0.63
13 14 0.37
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTCCTCTTTT
Found at i:1705780 original size:13 final size:13
Alignment explanation
Indices: 1705750--1705800 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
1705740 TTTTTCTTCA
1705750 ATTTTC-CTTTGTT
1 ATTTTCTCTTT-TT
*
1705763 TTTTTCTCTTTTT
1 ATTTTCTCTTTTT
1705776 ATTTTCTCTTTTT
1 ATTTTCTCTTTTT
*
1705789 -TTTCCTCTTTTT
1 ATTTTCTCTTTTT
1705801 TTTCTGATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.32
13 19 0.56
14 4 0.12
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (13 bp):
ATTTTCTCTTTTT
Found at i:1705801 original size:13 final size:12
Alignment explanation
Indices: 1705761--1705803 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
1705751 TTTTCCTTTG
1705761 TTTTTTTCTCTT
1 TTTTTTTCTCTT
1705773 TTTATTTTCTCTT
1 TTT-TTTTCTCTT
*
1705786 TTTTTTCCTCTT
1 TTTTTTTCTCTT
1705798 TTTTTT
1 TTTTTT
1705804 CTGATTGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 17 0.59
13 12 0.41
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTTTCTCTT
Found at i:1709008 original size:29 final size:29
Alignment explanation
Indices: 1708966--1709040 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
1708956 AACCCAACCA
***
1708966 TAGGTCGCCATGCACTCCCAGCGACCTCT
1 TAGGTCGCCATGCACTCCCAGCGACCAAG
* *
1708995 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAG
*
1709024 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
1709041 GGGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.39, G:0.27, T:0.16
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAG
Found at i:1709046 original size:29 final size:29
Alignment explanation
Indices: 1708967--1709054 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
1708957 ACCCAACCAT
* * ****
1708967 AGGTCGCCATGCACTCCCAGCGACCTCTT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
1708996 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
1709025 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
1709054 A
1 A
1709055 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.36, G:0.31, T:0.12
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:1709302 original size:29 final size:29
Alignment explanation
Indices: 1709269--1709353 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
1709259 AGCAGGGGAT
* * **
1709269 GTCGCCGCGAGTGCATGGCGACCTCCTTG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
* *
1709298 GTCGCCGGGCGTGCATGGCGACCTAGGAG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
*
1709327 GTCGCTGGGAGTGCATGGCGACCTACG
1 GTCGCCGGGAGTGCATGGCGACCTACG
1709354 GCCACTGTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.13, C:0.29, G:0.40, T:0.18
Consensus pattern (29 bp):
GTCGCCGGGAGTGCATGGCGACCTACGAG
Found at i:1710815 original size:53 final size:53
Alignment explanation
Indices: 1710735--1710942 Score: 309
Period size: 53 Copynumber: 4.0 Consensus size: 53
1710725 AAAGTGCAAT
*
1710735 AATTAACACATACTTACACCAATGTAAGTATGTACATCTCTCAATATCTTAAC
1 AATTAACACATACTTACACCGATGTAAGTATGTACATCTCTCAATATCTTAAC
*
1710788 AATTAACACATACTTACACCGATGTAAGTATGTACATCTTTCAATATCTTATA-
1 AATTAACACATACTTACACCGATGTAAGTATGTACATCTCTCAATATCTTA-AC
* *
1710841 AATTAACACATACTTACACATG-TGTAAGTATGT--ATCTCTCAATATCTTAGC
1 AATTAACACATACTTACAC-CGATGTAAGTATGTACATCTCTCAATATCTTAAC
*
1710892 AATTAACACATACTTACACC-AGTGTAAGTATGTACATATCTCAATATCTTA
1 AATTAACACATACTTACACCGA-TGTAAGTATGTACATCTCTCAATATCTTA
1710943 TTACCTAACA
Statistics
Matches: 141, Mismatches: 7, Indels: 14
0.87 0.04 0.09
Matches are distributed among these distances:
51 45 0.32
53 94 0.67
54 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (53 bp):
AATTAACACATACTTACACCGATGTAAGTATGTACATCTCTCAATATCTTAAC
Found at i:1710918 original size:104 final size:105
Alignment explanation
Indices: 1710735--1710943 Score: 334
Period size: 104 Copynumber: 2.0 Consensus size: 105
1710725 AAAGTGCAAT
1710735 AATTAACACATACTTACACCAATGTAAGTATGTACATCTCTCAATATCTTAACAATTAACACATA
1 AATTAACACATACTTACACCAATGTAAGTATGTA-ATCTCTCAATATCTTAACAATTAACACATA
* *
1710800 CTTACACCGATGTAAGTATGTACATCTTTCAATATCTTATA
65 CTTACACCGATGTAAGTATGTACATATCTCAATATCTTATA
* *
1710841 AATTAACACATACTTACA-CATGTGTAAGTATGT-ATCTCTCAATATCTTAGCAATTAACACATA
1 AATTAACACATACTTACACCA-ATGTAAGTATGTAATCTCTCAATATCTTAACAATTAACACATA
1710904 CTTACACC-AGTGTAAGTATGTACATATCTCAATATCTTAT
65 CTTACACCGA-TGTAAGTATGTACATATCTCAATATCTTAT
1710944 TACCTAACAA
Statistics
Matches: 97, Mismatches: 4, Indels: 6
0.91 0.04 0.06
Matches are distributed among these distances:
103 1 0.01
104 65 0.67
105 2 0.02
106 29 0.30
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (105 bp):
AATTAACACATACTTACACCAATGTAAGTATGTAATCTCTCAATATCTTAACAATTAACACATAC
TTACACCGATGTAAGTATGTACATATCTCAATATCTTATA
Found at i:1711050 original size:2 final size:2
Alignment explanation
Indices: 1711043--1711085 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1711033 ATTTTATTGA
1711043 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
1711085 A
1 A
1711086 ATTAGAGAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1714145 original size:28 final size:28
Alignment explanation
Indices: 1714113--1714168 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1714103 TATCGTTGTG
1714113 ACTCATGATTTCGTTTAACATACAAAAT
1 ACTCATGATTTCGTTTAACATACAAAAT
1714141 ACTCATGATTTCGTTTAACATACAAAAT
1 ACTCATGATTTCGTTTAACATACAAAAT
1714169 TAGAATTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (28 bp):
ACTCATGATTTCGTTTAACATACAAAAT
Found at i:1718442 original size:111 final size:111
Alignment explanation
Indices: 1718243--1718464 Score: 376
Period size: 111 Copynumber: 2.0 Consensus size: 111
1718233 TGGAAATCAT
*
1718243 ATATCTCTACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * *
1718308 TATTTAGTTGATTTATTATATGCATGATTCTTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTATATGCATGATTATTAGATTAAGAATTAA
1718354 ATATCTCGACACTTTGCTGATACTG-TAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTA
1 ATATCTCGACACTTTGCTGATAC-GATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTA
1718418 ATAATTAGTTGATTCATT-TAATGCATGATTATTAGATTAAGAATTAA
65 ATAATTAGTTGATTCATTAT-ATGCATGATTATTAGATTAAGAATTAA
1718465 TTTTTGTAAT
Statistics
Matches: 105, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
110 1 0.01
111 103 0.98
112 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTATATGCATGATTATTAGATTAAGAATTAA
Found at i:1720331 original size:15 final size:15
Alignment explanation
Indices: 1720311--1720348 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1720301 TGCTCAGGAC
1720311 GACGATGATGACGAT
1 GACGATGATGACGAT
*
1720326 GACGATGGTGACGAT
1 GACGATGATGACGAT
1720341 GACGATGA
1 GACGATGA
1720349 CAGCGAGGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.32, C:0.13, G:0.37, T:0.18
Consensus pattern (15 bp):
GACGATGATGACGAT
Found at i:1725083 original size:15 final size:15
Alignment explanation
Indices: 1725065--1725110 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
1725055 TGTATCTGTT
1725065 CTTCTAGTATATGTA
1 CTTCTAGTATATGTA
* * *
1725080 CTTCTAGCATCTATA
1 CTTCTAGTATATGTA
*
1725095 CTACTAGTATATGTA
1 CTTCTAGTATATGTA
1725110 C
1 C
1725111 CCCTGATATC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (15 bp):
CTTCTAGTATATGTA
Found at i:1726519 original size:32 final size:32
Alignment explanation
Indices: 1726449--1726535 Score: 88
Period size: 32 Copynumber: 2.7 Consensus size: 32
1726439 TCGGTTCGGA
* * * *
1726449 TCAATATTAGATCGATTGACTTTTTGGTCAGGT
1 TCAATATTGGATCGGTTGA-TTTTGGGTCAGAT
1726482 T-AATATTGGATCGGTTAGATTTTGGGTC-GAT
1 TCAATATTGGATCGGTT-GATTTTGGGTCAGAT
* *
1726513 TCAATATCGGATTGGTTGATTTT
1 TCAATATTGGATCGGTTGATTTT
1726536 CGAAACGGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
31 9 0.20
32 34 0.74
33 3 0.07
ACGTcount: A:0.23, C:0.09, G:0.24, T:0.44
Consensus pattern (32 bp):
TCAATATTGGATCGGTTGATTTTGGGTCAGAT
Found at i:1733758 original size:99 final size:99
Alignment explanation
Indices: 1733585--1733783 Score: 353
Period size: 99 Copynumber: 2.0 Consensus size: 99
1733575 ACTCAACATT
*
1733585 AATTATTGGAGACCATTTTAAAAATTATATATATAATAATTAAATATTTTAGCATTTCTAGTGTA
1 AATTAATGGAGACCATTTTAAAAATTATATATATAATAATTAAATATTTTAGCATTTCTAGTGTA
*
1733650 ACGTACTAATCCAGTACGACCTGTAGATCGATGG
66 ACGTACTAATCCAGTACGACCCGTAGATCGATGG
* *
1733684 AATTAATGGGGACCATTTTAAAAATTATATATATAATAATTAAATATTTTAGTATTTCTAGTGTA
1 AATTAATGGAGACCATTTTAAAAATTATATATATAATAATTAAATATTTTAGCATTTCTAGTGTA
*
1733749 ACGTCCTAATCCAGTACGACCCGTAGATCGATGG
66 ACGTACTAATCCAGTACGACCCGTAGATCGATGG
1733783 A
1 A
1733784 TCAAGGCATC
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
99 95 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36
Consensus pattern (99 bp):
AATTAATGGAGACCATTTTAAAAATTATATATATAATAATTAAATATTTTAGCATTTCTAGTGTA
ACGTACTAATCCAGTACGACCCGTAGATCGATGG
Found at i:1734840 original size:19 final size:19
Alignment explanation
Indices: 1734793--1734841 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
1734783 TATGGAAAAA
**
1734793 TAGTATCGAAACCCCTCCT
1 TAGTATCGAAACCCAACCT
*
1734812 TCAGGTATCGAAACCGAACCT
1 T-A-GTATCGAAACCCAACCT
1734833 TAGTATCGA
1 TAGTATCGA
1734842 TACTCAATGC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 8 0.32
20 2 0.08
21 15 0.60
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (19 bp):
TAGTATCGAAACCCAACCT
Found at i:1737032 original size:25 final size:25
Alignment explanation
Indices: 1737004--1737052 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1736994 CTGAAAAAGA
1737004 AAAACGAAAGAATTTGGAGCTAATG
1 AAAACGAAAGAATTTGGAGCTAATG
*
1737029 AAAACGAAGGAATTTGGAGCTAAT
1 AAAACGAAAGAATTTGGAGCTAAT
1737053 TTTTTACGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.08, G:0.24, T:0.20
Consensus pattern (25 bp):
AAAACGAAAGAATTTGGAGCTAATG
Found at i:1739587 original size:17 final size:16
Alignment explanation
Indices: 1739565--1739597 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
1739555 CATCTTTTTC
1739565 ATCTCTTCTCTCCTCTT
1 ATCTCTTCT-TCCTCTT
1739582 ATCTCTTCTTCCTCTT
1 ATCTCTTCTTCCTCTT
1739598 CAAGCTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.55
Consensus pattern (16 bp):
ATCTCTTCTTCCTCTT
Found at i:1740531 original size:14 final size:14
Alignment explanation
Indices: 1740512--1740540 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1740502 AGCGTAGTTC
1740512 ATGGTGGGGTTCGA
1 ATGGTGGGGTTCGA
1740526 ATGGTGGGGTTCGA
1 ATGGTGGGGTTCGA
1740540 A
1 A
1740541 CAAACCATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.07, G:0.48, T:0.28
Consensus pattern (14 bp):
ATGGTGGGGTTCGA
Found at i:1742125 original size:18 final size:18
Alignment explanation
Indices: 1742104--1742152 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 18
1742094 GCTAAATTTG
1742104 GTATCGATACTAAGG-CCA
1 GTATCGATACT-AGGTCCA
1742122 GTATCGATACCCTAGGTCCA
1 GTATCGATA--CTAGGTCCA
1742142 GTATCGATACT
1 GTATCGATACT
1742153 GAAAGCTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 11 0.39
19 3 0.11
20 14 0.50
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (18 bp):
GTATCGATACTAGGTCCA
Found at i:1747687 original size:31 final size:31
Alignment explanation
Indices: 1747619--1747724 Score: 106
Period size: 31 Copynumber: 3.4 Consensus size: 31
1747609 GGCGCCTGAG
* **
1747619 AGCCTACCCAAGAAAGATTCTC-AGGGCCACGG
1 AGCCTACCCAAGAAA-AATCTCGA-GGCCACAA
* *
1747651 GGCCTACCCAAGAAAAATCTTGAGGCCACAA
1 AGCCTACCCAAGAAAAATCTCGAGGCCACAA
* * * *
1747682 AGCCTACCCAAGAAATATCTCGGGGCCGCAG
1 AGCCTACCCAAGAAAAATCTCGAGGCCACAA
1747713 AGCCTACCCAAG
1 AGCCTACCCAAG
1747725 GGTCACCTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
31 47 0.76
32 15 0.24
ACGTcount: A:0.33, C:0.32, G:0.23, T:0.12
Consensus pattern (31 bp):
AGCCTACCCAAGAAAAATCTCGAGGCCACAA
Found at i:1748559 original size:2 final size:2
Alignment explanation
Indices: 1748552--1748578 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1748542 GAACGATACA
1748552 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1748579 AGATCATTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1749612 original size:23 final size:24
Alignment explanation
Indices: 1749581--1749625 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1749571 TTTGTCAAAG
*
1749581 TCAACAGTCAACGGGTTGACTCGA
1 TCAACAGTCAACGAGTTGACTCGA
1749605 TCAA-AGTCAACGAGTTGACTC
1 TCAACAGTCAACGAGTTGACTC
1749626 AGTGAGTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (24 bp):
TCAACAGTCAACGAGTTGACTCGA
Found at i:1749634 original size:13 final size:13
Alignment explanation
Indices: 1749616--1749643 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1749606 CAAAGTCAAC
1749616 GAGTTGACTCAGT
1 GAGTTGACTCAGT
1749629 GAGTTGACTCAGT
1 GAGTTGACTCAGT
1749642 GA
1 GA
1749644 CTGAACCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.14, G:0.32, T:0.29
Consensus pattern (13 bp):
GAGTTGACTCAGT
Found at i:1758299 original size:23 final size:23
Alignment explanation
Indices: 1758273--1758357 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
1758263 TTAGTGCAGA
*
1758273 GGGAATCGATACCCCCTTTGAAG
1 GGGAACCGATACCCCCTTTGAAG
*
1758296 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCCTTTGAAG
* * *
1758319 GGGAACCGATTCCCCC-CTGTAG
1 GGGAACCGATACCCCCTTTGAAG
**
1758341 GGGAATAGATACCCCCT
1 GGGAACCGATACCCCCT
1758358 AGGGTTCTGG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
22 17 0.31
23 37 0.69
ACGTcount: A:0.24, C:0.31, G:0.26, T:0.20
Consensus pattern (23 bp):
GGGAACCGATACCCCCTTTGAAG
Found at i:1758334 original size:24 final size:23
Alignment explanation
Indices: 1758273--1758334 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
1758263 TTAGTGCAGA
* *
1758273 GGGAATCGATACCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
1758296 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
1758319 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
1758335 CTGTAGGGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.19
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:1759755 original size:18 final size:17
Alignment explanation
Indices: 1759725--1759772 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 17
1759715 ATGACCCAGA
1759725 ACAGCACGAGGAACAAGC
1 ACAGCA-GAGGAACAAGC
1759743 ACTAGCAGAGGAACAAGC
1 AC-AGCAGAGGAACAAGC
1759761 ACAGCCAGAGGA
1 ACAG-CAGAGGA
1759773 TCAAATGCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 2 0.07
18 22 0.79
19 4 0.14
ACGTcount: A:0.44, C:0.25, G:0.29, T:0.02
Consensus pattern (17 bp):
ACAGCAGAGGAACAAGC
Found at i:1762831 original size:18 final size:18
Alignment explanation
Indices: 1762808--1762851 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1762798 GAATTTGTGA
1762808 TTTTTTTTACCTTTTCTC
1 TTTTTTTTACCTTTTCTC
**
1762826 TTTTTTTGGCCTTTTCTC
1 TTTTTTTTACCTTTTCTC
1762844 TTTTTTTT
1 TTTTTTTT
1762852 TTTACCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (18 bp):
TTTTTTTTACCTTTTCTC
Found at i:1762850 original size:21 final size:20
Alignment explanation
Indices: 1762808--1762874 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 20
1762798 GAATTTGTGA
1762808 TTTTTTTT-ACC-TTTTC-T
1 TTTTTTTTGACCTTTTTCTT
* *
1762825 CTTTTTTTGGCCTTTTCTCTT
1 TTTTTTTTGACCTTTT-TCTT
*
1762846 TTTTTTTTTACCTTTTTCTT
1 TTTTTTTTGACCTTTTTCTT
*
1762866 TTCTTTTTG
1 TTTTTTTTG
1762875 TTGAAAATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
17 7 0.18
18 2 0.05
19 3 0.08
20 13 0.33
21 14 0.36
ACGTcount: A:0.03, C:0.18, G:0.04, T:0.75
Consensus pattern (20 bp):
TTTTTTTTGACCTTTTTCTT
Found at i:1762867 original size:18 final size:18
Alignment explanation
Indices: 1762808--1762873 Score: 62
Period size: 18 Copynumber: 3.4 Consensus size: 18
1762798 GAATTTGTGA
1762808 TTTTTTTTACC-TTTTCT
1 TTTTTTTTACCTTTTTCT
**
1762825 CTTTTTTTGGCCTTTTCTCTTT
1 -TTTTTTTTACCTTTT-TC--T
1762847 TTTTTTTTACCTTTTTCT
1 TTTTTTTTACCTTTTTCT
1762865 TTTCTTTTT
1 TTT-TTTTT
1762874 GTTGAAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
18 13 0.33
19 8 0.21
20 4 0.10
21 13 0.33
22 1 0.03
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (18 bp):
TTTTTTTTACCTTTTTCT
Found at i:1767339 original size:22 final size:22
Alignment explanation
Indices: 1767287--1767339 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
1767277 TTTTCAGCTA
*
1767287 TTTACATTCATTCCTTTTTCATT
1 TTTACATTCATT-CTTTTTAATT
1767310 TTCT-CATTCATT-TTATTTAATT
1 TT-TACATTCATTCTT-TTTAATT
1767332 TTTACATT
1 TTTACATT
1767340 AACAACCCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 12 0.46
23 10 0.38
24 1 0.04
ACGTcount: A:0.21, C:0.17, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTACATTCATTCTTTTTAATT
Found at i:1770282 original size:20 final size:21
Alignment explanation
Indices: 1770249--1770287 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1770239 TTTGTTTTCG
*
1770249 TTTATTTGATTTATTTTTAGC
1 TTTATTTGACTTATTTTTAGC
1770270 TTTATTT-ACTTATTTTTA
1 TTTATTTGACTTATTTTTA
1770288 TCTAGTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTATTTGACTTATTTTTAGC
Found at i:1772024 original size:11 final size:11
Alignment explanation
Indices: 1772003--1772034 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1771993 CATGATCCAC
1772003 AAAAAAG-AAA
1 AAAAAAGAAAA
1772013 AAAAAAGAAAA
1 AAAAAAGAAAA
1772024 AAAAAAGAAAA
1 AAAAAAGAAAA
1772035 GCAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:1772040 original size:11 final size:10
Alignment explanation
Indices: 1772003--1772034 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
1771993 CATGATCCAC
1772003 AAAAAAGAAA
1 AAAAAAGAAA
1772013 AAAAAAGAAAA
1 AAAAAAG-AAA
1772024 AAAAAAGAAA
1 AAAAAAGAAA
1772034 A
1 A
1772035 GCAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:1775393 original size:31 final size:31
Alignment explanation
Indices: 1775269--1775393 Score: 137
Period size: 31 Copynumber: 4.0 Consensus size: 31
1775259 GTTGAGGGTA
**
1775269 TACCTATGTTCTACGGAACATATGGACAAAAT
1 TACCTATGTTCTACGGAACATATGGAC-AGTT
* *
1775301 TACCTATG-TCTTTC-GAGACATATGGACAGTA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
*
1775332 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
* * *
1775363 TACCTAGGTTCTTCGGAACCTATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
1775394 GCCGAGGATC
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
31 54 0.69
32 24 0.31
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTT
Found at i:1780271 original size:31 final size:31
Alignment explanation
Indices: 1780182--1780308 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
1780172 AGAGTTGAGG
1780182 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* *
1780213 GAATTACCTATG-TCTTTC-GAGACATATGGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
* *
1780245 GTATACCTATGTTCTAAGGAATATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * *
1780276 GTTTACCTAGGTTCTTCGGAACCTATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
1780307 GT
1 GT
1780309 TTCCGAGGAT
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
31 52 0.66
32 27 0.34
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:1781162 original size:24 final size:24
Alignment explanation
Indices: 1781117--1781162 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1781107 TTCTCATTGC
*
1781117 GTAGAACTATAATTTGCCATAATT
1 GTAGAACTATAATTTGACATAATT
* *
1781141 GTAGAACTATATTTTGATATAA
1 GTAGAACTATAATTTGACATAA
1781163 CAATTTATGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (24 bp):
GTAGAACTATAATTTGACATAATT
Found at i:1782931 original size:17 final size:17
Alignment explanation
Indices: 1782900--1782933 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1782890 TTAAAGAAAT
**
1782900 AAGAAAAAGGTGAAGAA
1 AAGAAAAAGAAGAAGAA
1782917 AAGAAAAAGAAGAAGAA
1 AAGAAAAAGAAGAAGAA
1782934 GAAAGTGGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (17 bp):
AAGAAAAAGAAGAAGAA
Found at i:1786021 original size:22 final size:23
Alignment explanation
Indices: 1785995--1786037 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
1785985 GTTTTCAAAT
1785995 ATTTACTT-TT-ATTATTATTTTC
1 ATTTACTTGTTCATT-TTATTTTC
1786017 ATTTACTTGTTCATTTTATTT
1 ATTTACTTGTTCATTTTATTT
1786038 AGTTTTTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 8 0.42
24 3 0.16
ACGTcount: A:0.21, C:0.09, G:0.02, T:0.67
Consensus pattern (23 bp):
ATTTACTTGTTCATTTTATTTTC
Found at i:1786998 original size:2 final size:2
Alignment explanation
Indices: 1786987--1787029 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1786977 CATCGAAACT
1786987 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1787028 TA
1 TA
1787030 CAACAAAAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1787691 original size:21 final size:21
Alignment explanation
Indices: 1787665--1787708 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1787655 CTTTTCATAA
*
1787665 GTAAAGAAAAGAAAATAGATT
1 GTAAAGAAAAGAAAAGAGATT
1787686 GTAAAGAAAAGAAAAGAGATT
1 GTAAAGAAAAGAAAAGAGATT
1787707 GT
1 GT
1787709 CGATCTCAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.23, T:0.18
Consensus pattern (21 bp):
GTAAAGAAAAGAAAAGAGATT
Found at i:1791151 original size:119 final size:119
Alignment explanation
Indices: 1791000--1791228 Score: 406
Period size: 119 Copynumber: 1.9 Consensus size: 119
1790990 TAATTTTTCC
1791000 TACCCTCATTACTCATCTTCTTAATTTGAATAACCTAAAAATATCAATATGGTTAATAGTTAATA
1 TACCCTCATTACTCATCTTCTTAATTTGAATAACCTAAAAATATCAATATGGTTAATAGTTAATA
*
1791065 AA-AATAATAATTTAATCAACATGCACATAAAAATGTCAATATAGTAATTTTCAT
66 AACAA-AATAATTTAATCAACATGCACATAAAAATATCAATATAGTAATTTTCAT
* *
1791119 TACCCTTATTACTCATCTTTTTAATTTGAATAACCTAAAAATATCAATATGGTTAATAGTTAATA
1 TACCCTCATTACTCATCTTCTTAATTTGAATAACCTAAAAATATCAATATGGTTAATAGTTAATA
*
1791184 AACAAAATAATTTAATCAACATGCACCTAAAAATATCAATATAGT
66 AACAAAATAATTTAATCAACATGCACATAAAAATATCAATATAGT
1791229 TAATATTTAA
Statistics
Matches: 105, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
119 103 0.98
120 2 0.02
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (119 bp):
TACCCTCATTACTCATCTTCTTAATTTGAATAACCTAAAAATATCAATATGGTTAATAGTTAATA
AACAAAATAATTTAATCAACATGCACATAAAAATATCAATATAGTAATTTTCAT
Found at i:1791221 original size:57 final size:57
Alignment explanation
Indices: 1791151--1791265 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
1791141 AATTTGAATA
* *
1791151 ACCTAAAAATATCAATATGGTTAATAGTTAATAAACAAAATAATTTAATCAACATGC
1 ACCTAAAAATATCAATATAGTTAATAGTTAACAAACAAAATAATTTAATCAACATGC
*
1791208 ACCTAAAAATATCAATATAGTTAATATTTAACAAACAAAATAATTTAATCAACATGC
1 ACCTAAAAATATCAATATAGTTAATAGTTAACAAACAAAATAATTTAATCAACATGC
1791265 A
1 A
1791266 ATAAAATAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.52, C:0.13, G:0.05, T:0.30
Consensus pattern (57 bp):
ACCTAAAAATATCAATATAGTTAATAGTTAACAAACAAAATAATTTAATCAACATGC
Found at i:1796306 original size:12 final size:13
Alignment explanation
Indices: 1796262--1796309 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 13
1796252 TAATATTATT
*
1796262 TAATAATAATA-A
1 TAATAATAACATA
* *
1796274 TAATAACAATATA
1 TAATAATAACATA
1796287 TAATAATAACATA
1 TAATAATAACATA
1796300 T-ATAATAACA
1 TAATAATAACA
1796310 ACGGACAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
12 19 0.59
13 13 0.41
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (13 bp):
TAATAATAACATA
Found at i:1796307 original size:3 final size:3
Alignment explanation
Indices: 1796262--1796295 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
1796252 TAATATTATT
*
1796262 TAA TAA TAA TAA TAA TAA CAA TATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
1796296 CATATATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1796599 original size:42 final size:42
Alignment explanation
Indices: 1796538--1796629 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
1796528 GGATGGCCTT
* *
1796538 AAGGACTT-ATCATCTTGCTCAAAAGACTAACAAATGACCCA
1 AAGGATTTAATCATCATGCTCAAAAGACTAACAAATGACCCA
* * *
1796579 AAGGATTTAATCATCATGCTCGAAAGACTAACAGATGACCCG
1 AAGGATTTAATCATCATGCTCAAAAGACTAACAAATGACCCA
1796621 AAGGATTTA
1 AAGGATTTA
1796630 CAAATTCGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 7 0.16
42 38 0.84
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (42 bp):
AAGGATTTAATCATCATGCTCAAAAGACTAACAAATGACCCA
Found at i:1796960 original size:249 final size:247
Alignment explanation
Indices: 1796501--1797227 Score: 1124
Period size: 244 Copynumber: 2.9 Consensus size: 247
1796491 CAATAAAGAG
*
1796501 TGTAAACATCCTACCCAAAGGTTTGACGGATGGCCTTAAGGACTTATCATCTTGCTCAAAAGACT
1 TGTAAACATCCTACCCAAAGGTTTGACGGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACT
* *
1796566 AACAAATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTAACAGATGACCCGAAGGATTTAC
66 AACAAATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTAACAAATGACCCGAAGGATTTAC
* *
1796631 AAATTCGTGGGAAATAATTTACT-GGATAAGAAACTTCTTACTTTTAAAAAATTTCATTTTTTAG
131 AAATTCGT-GGAAATAATTTACTAGG-TAAGAAACTTCTTACTTTTCAAAAATTTCATTTTCTA-
* *
1796695 AACATTAAACGAGAAACTTTGAAAATTGCTTTCTCATTTTCATGCGAAAATCATA
193 AAGATTAAATGAGAAACTTTGAAAATTGCTTTCTCATTTTCATGCGAAAATCATA
* *
1796750 TGTAAACATCCTACCCAAAGGTTTGATGGATGGCCCTAAGGACTTATCATCTTGATCAAAAGACT
1 TGTAAACATCCTACCCAAAGGTTTGACGGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACT
* *
1796815 AACATATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTGACAAATGACCCGAAGGATTTAC
66 AACAAATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTAACAAATGACCCGAAGGATTTAC
1796880 AAATTCGTGGAAATAATTTACTAGGTAAGAAACTTCTTACTTTTCAAAAATTTCATTTTCTAAAG
131 AAATTCGTGGAAATAATTTACTAGGTAAGAAACTTCTTACTTTTCAAAAATTTCATTTTCTAAA-
1796945 GGATTAAATGAGAAACTTTGAAAA-T-C---CTCATTTTCATGCGAAAATCATA
195 -GATTAAATGAGAAACTTTGAAAATTGCTTTCTCATTTTCATGCGAAAATCATA
* * *
1796994 TGTAAACATCTTACCCAAAGGTTTGACGGGTGGCCCTAAGAACTTATCATCTTGCTCAAAAGACT
1 TGTAAACATCCTACCCAAAGGTTTGACGGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACT
* * * * *
1797059 AACAGATGACCCGAATGATTTAAGCATCATGCTTGAAAGACTAACAAATGACCCGAAGGTTTTAC
66 AACAAATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTAACAAATGACCCGAAGGATTTAC
*
1797124 AAATTTGTGGAAATAATTTACTAGGTAAGAAACTTCTTACTTTTCAAAAATTTCATTTTCTAAAA
131 AAATTCGTGGAAATAATTTACTAGGTAAGAAACTTCTTACTTTTCAAAAATTTCATTTTCT--AA
* * * * *
1797189 AGATTAAATGATAAAATTTGAAAATCGTTTTCTTATTTT
194 AGATTAAATGAGAAACTTTGAAAATTGCTTTCTCATTTT
1797228 TCGAAACAAC
Statistics
Matches: 440, Mismatches: 28, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
244 223 0.51
246 3 0.01
247 3 0.01
248 50 0.11
249 161 0.37
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (247 bp):
TGTAAACATCCTACCCAAAGGTTTGACGGATGGCCCTAAGGACTTATCATCTTGCTCAAAAGACT
AACAAATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTAACAAATGACCCGAAGGATTTAC
AAATTCGTGGAAATAATTTACTAGGTAAGAAACTTCTTACTTTTCAAAAATTTCATTTTCTAAAG
ATTAAATGAGAAACTTTGAAAATTGCTTTCTCATTTTCATGCGAAAATCATA
Found at i:1797456 original size:20 final size:20
Alignment explanation
Indices: 1797411--1797456 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
1797401 ATATCAATGT
1797411 AATGCATGATTTTTTTATGC
1 AATGCATGATTTTTTTATGC
1797431 AA---ATGATGTTTTTTATG-
1 AATGCATGAT-TTTTTTATGC
1797448 AATGCATGA
1 AATGCATGA
1797457 ATGTATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
17 7 0.32
18 9 0.41
20 6 0.27
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (20 bp):
AATGCATGATTTTTTTATGC
Found at i:1799145 original size:20 final size:22
Alignment explanation
Indices: 1799101--1799145 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1799091 ATGATCAATC
* *
1799101 CTTCTGACTGAGGTATATGCAT
1 CTTCTGAATGAAGTATATGCAT
1799123 CTTCTGAATGAAGTA-AT-CAT
1 CTTCTGAATGAAGTATATGCAT
1799143 CTT
1 CTT
1799146 TCTCTTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 13 0.62
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (22 bp):
CTTCTGAATGAAGTATATGCAT
Done.