Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 4 of 93
Found at i:1707629 original size:23 final size:23
Alignment explanation
Indices: 1707595--1707644 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1707585 AGAAGAGAGT
*
1707595 TTTTATTTTGTTTGGGTTTTTTC
1 TTTTATTCTGTTTGGGTTTTTTC
*
1707618 TTTTATTCTGTTTGGGTTTTTTT
1 TTTTATTCTGTTTGGGTTTTTTC
1707641 TTTT
1 TTTT
1707645 TTTTTTACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.04, C:0.04, G:0.16, T:0.76
Consensus pattern (23 bp):
TTTTATTCTGTTTGGGTTTTTTC
Found at i:1707862 original size:21 final size:19
Alignment explanation
Indices: 1707836--1707883 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
1707826 TGATTGATTT
1707836 TTTTTTTTTTTTACATTTATA
1 TTTTTTTTTTTTA-ATTT-TA
1707857 TTTTTTATTTTTTAATTTTA
1 TTTTTT-TTTTTTAATTTTA
*
1707877 GTTTTTT
1 TTTTTTT
1707884 AATATTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 1 0.04
20 7 0.28
21 10 0.40
22 7 0.28
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTTTTTTTTTAATTTTA
Found at i:1707884 original size:21 final size:22
Alignment explanation
Indices: 1707835--1707884 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
1707825 ATGATTGATT
*
1707835 TTTTTTTTTTTTTACATTTATA
1 TTTTTTATTTTTTACATTTATA
1707857 TTTTTTATTTTTTA-ATTT-TA
1 TTTTTTATTTTTTACATTTATA
1707877 GTTTTTTA
1 -TTTTTTA
1707885 ATATTTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 11 0.42
22 13 0.50
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTTTATTTTTTACATTTATA
Found at i:1713059 original size:9 final size:9
Alignment explanation
Indices: 1713047--1713108 Score: 58
Period size: 9 Copynumber: 7.2 Consensus size: 9
1713037 TACCTCTTCC
1713047 TCCTCATCA
1 TCCTCATCA
* *
1713056 TCCTCGTCG
1 TCCTCATCA
*
1713065 TCGTCATCA
1 TCCTCATCA
1713074 TCCTCATCA
1 TCCTCATCA
1713083 TCCTC-T-A
1 TCCTCATCA
* *
1713090 -CCCCATCT
1 TCCTCATCA
1713098 TCCTCATCA
1 TCCTCATCA
1713107 TC
1 TC
1713109 ACTATCCTCA
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
6 3 0.08
7 2 0.05
8 1 0.03
9 34 0.85
ACGTcount: A:0.16, C:0.45, G:0.05, T:0.34
Consensus pattern (9 bp):
TCCTCATCA
Found at i:1713060 original size:18 final size:18
Alignment explanation
Indices: 1713039--1713078 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1713029 TCATTATCTA
*
1713039 CCTCTTCCTCCTCATCAT
1 CCTCGTCCTCCTCATCAT
* *
1713057 CCTCGTCGTCGTCATCAT
1 CCTCGTCCTCCTCATCAT
1713075 CCTC
1 CCTC
1713079 ATCATCCTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.47, G:0.07, T:0.35
Consensus pattern (18 bp):
CCTCGTCCTCCTCATCAT
Found at i:1713442 original size:15 final size:15
Alignment explanation
Indices: 1713422--1713459 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1713412 CCCAGGATCA
1713422 TCTTCATCGTCCTCC
1 TCTTCATCGTCCTCC
*
1713437 TCTTCATCTTCCTCC
1 TCTTCATCGTCCTCC
*
1713452 TCATCATC
1 TCTTCATC
1713460 CGACTCCGGC
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:0.11, C:0.45, G:0.03, T:0.42
Consensus pattern (15 bp):
TCTTCATCGTCCTCC
Found at i:1738254 original size:18 final size:18
Alignment explanation
Indices: 1738227--1738277 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
1738217 CCAGTTACCA
* *
1738227 CCACCACCACCAGCACCC
1 CCACCCCCACCACCACCC
*
1738245 CCACCCCCACCCCCACCC
1 CCACCCCCACCACCACCC
*
1738263 CCACCCGCACCACCA
1 CCACCCCCACCACCA
1738278 ACGTCAAAGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.24, C:0.73, G:0.04, T:0.00
Consensus pattern (18 bp):
CCACCCCCACCACCACCC
Found at i:1738255 original size:12 final size:12
Alignment explanation
Indices: 1738240--1738273 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1738230 CCACCACCAG
1738240 CACCCCCACCCC
1 CACCCCCACCCC
1738252 CACCCCCACCCC
1 CACCCCCACCCC
*
1738264 CACCCGCACC
1 CACCCCCACC
1738274 ACCAACGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.79, G:0.03, T:0.00
Consensus pattern (12 bp):
CACCCCCACCCC
Found at i:1741773 original size:14 final size:14
Alignment explanation
Indices: 1741754--1741791 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
1741744 TTTATATAAT
*
1741754 TAAAACGATACGAA
1 TAAAACGATAAGAA
1741768 TAAAACGATAAGAA
1 TAAAACGATAAGAA
*
1741782 TGAAACGATA
1 TAAAACGATA
1741792 TAATTGATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.58, C:0.11, G:0.16, T:0.16
Consensus pattern (14 bp):
TAAAACGATAAGAA
Found at i:1746731 original size:25 final size:26
Alignment explanation
Indices: 1746703--1746754 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
1746693 AATAAAAGTT
* *
1746703 ATTCACAAGATGTTAATT-AAATAAA
1 ATTCACAAAATGTTAATTGAAAAAAA
1746728 ATTCACAAAATGTTAATTGAAAAAAA
1 ATTCACAAAATGTTAATTGAAAAAAA
1746754 A
1 A
1746755 AAAAAAATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.29
Consensus pattern (26 bp):
ATTCACAAAATGTTAATTGAAAAAAA
Found at i:1752789 original size:9 final size:9
Alignment explanation
Indices: 1752777--1752801 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1752767 GAAGCACTAA
1752777 CAGCAGCAC
1 CAGCAGCAC
1752786 CAGCAGCAC
1 CAGCAGCAC
1752795 CAGCAGC
1 CAGCAGC
1752802 TAACATTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.44, G:0.24, T:0.00
Consensus pattern (9 bp):
CAGCAGCAC
Found at i:1753631 original size:20 final size:19
Alignment explanation
Indices: 1753603--1753644 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1753593 TTATATTGCT
*
1753603 AAAAAATACCTGATTTAGG
1 AAAAAATACCTAATTTAGG
*
1753622 AAAAATATACCTAATTTATG
1 AAAAA-ATACCTAATTTAGG
1753642 AAA
1 AAA
1753645 CAGGCCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (19 bp):
AAAAAATACCTAATTTAGG
Found at i:1767200 original size:2 final size:2
Alignment explanation
Indices: 1767193--1767233 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1767183 TTAAAAGCAA
1767193 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1767234 AAGGCAACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1768161 original size:18 final size:18
Alignment explanation
Indices: 1768131--1768178 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1768121 CCAAAGCCCT
*
1768131 AGAAAGAAA-AAAAGCAAA
1 AGAAAAAAAGAAAAG-AAA
1768149 A-AAAAAAAGAAAAGAAA
1 AGAAAAAAAGAAAAGAAA
*
1768166 AGAAAAGAAGAAA
1 AGAAAAAAAGAAA
1768179 TACCAGCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (18 bp):
AGAAAAAAAGAAAAGAAA
Found at i:1768178 original size:13 final size:13
Alignment explanation
Indices: 1768133--1768166 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1768123 AAAGCCCTAG
1768133 AAAGAAAAAAAGCA
1 AAAGAAAAAAAG-A
1768147 AAA-AAAAAAAGA
1 AAAGAAAAAAAGA
1768159 AAAGAAAA
1 AAAGAAAA
1768167 GAAAAGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 12 0.63
14 3 0.16
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAGA
Found at i:1782950 original size:3 final size:3
Alignment explanation
Indices: 1782942--1783018 Score: 50
Period size: 3 Copynumber: 23.7 Consensus size: 3
1782932 TTTCCTTGCA
*
1782942 TCT TCT TC- TCT TC- TCT TCT TGGCT TCT TCT TCT TCT ATCTT TCT GGCT
1 TCT TCT TCT TCT TCT TCT TCT T--CT TCT TCT TCT TCT -TC-T TCT -TCT
*
1782990 TCT TCT TCT CTCTT TCT GGCT TCT TCT TC
1 TCT TCT TCT -TC-T TCT -TCT TCT TCT TC
1783019 CTCCTCTTTC
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
2 4 0.07
3 39 0.65
4 12 0.20
5 5 0.08
ACGTcount: A:0.01, C:0.32, G:0.08, T:0.58
Consensus pattern (3 bp):
TCT
Found at i:1782969 original size:24 final size:23
Alignment explanation
Indices: 1782942--1783018 Score: 106
Period size: 24 Copynumber: 3.3 Consensus size: 23
1782932 TTTCCTTGCA
1782942 TCTTCTTCTCT-TCTCTTCTTGGCT
1 TCTTCTTCTCTATCT-TTC-TGGCT
1782966 TCTTCTTCTTCTATCTTTCTGGCT
1 TCTTCTTC-TCTATCTTTCTGGCT
1782990 TCTTCTTCTC--TCTTTCTGGCT
1 TCTTCTTCTCTATCTTTCTGGCT
1783011 TCTTCTTC
1 TCTTCTTC
1783019 CTCCTCTTTC
Statistics
Matches: 51, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
21 19 0.37
23 2 0.04
24 21 0.41
25 6 0.12
26 3 0.06
ACGTcount: A:0.01, C:0.32, G:0.08, T:0.58
Consensus pattern (23 bp):
TCTTCTTCTCTATCTTTCTGGCT
Found at i:1783017 original size:21 final size:21
Alignment explanation
Indices: 1782899--1783029 Score: 106
Period size: 21 Copynumber: 5.9 Consensus size: 21
1782889 TTCTTTGCCT
* *
1782899 TTCTTCTTC-CTGTCTTCGGGC
1 TTCTTCTTCTCTCT-TTCTGGC
*
1782920 TTC-TCTT-TGCTCTTTCCTTGC
1 TTCTTCTTCT-CTCTTT-CTGGC
*
1782941 ATCTTCTTCTCTTCTCTTCTTGGC
1 TTCTTCTTCTC-TCT-TTC-TGGC
1782965 TTCTTCTTCTTCTATCTTTCTGGC
1 TTCTTCTTC-TC--TCTTTCTGGC
1782989 TTCTTCTTCTCTCTTTCTGGC
1 TTCTTCTTCTCTCTTTCTGGC
1783010 TTCTTCTTCCTCCTCTTTCT
1 TTCTTCTT-CT-CTCTTTCT
1783030 TCCTGGCTTC
Statistics
Matches: 91, Mismatches: 7, Indels: 22
0.76 0.06 0.18
Matches are distributed among these distances:
20 6 0.07
21 29 0.32
22 7 0.08
23 15 0.16
24 26 0.29
25 5 0.05
26 3 0.03
ACGTcount: A:0.02, C:0.34, G:0.09, T:0.56
Consensus pattern (21 bp):
TTCTTCTTCTCTCTTTCTGGC
Found at i:1783039 original size:24 final size:24
Alignment explanation
Indices: 1782949--1783045 Score: 88
Period size: 24 Copynumber: 4.0 Consensus size: 24
1782939 GCATCTTCTT
* *
1782949 CTCTTCTCTTCTTGGCTTCTTCTTC
1 CTCTT-TCTTCCTGGCTTCTTCCTC
* * * *
1782974 TTCTATCTTTCTGGCTTCTTCTTC
1 CTCTTTCTTCCTGGCTTCTTCCTC
** *
1782998 TCTCTTTCTGGCT-TCTTCTTCCTC
1 -CTCTTTCTTCCTGGCTTCTTCCTC
1783022 CTCTTTCTTCCTGGCTTCTTCCTC
1 CTCTTTCTTCCTGGCTTCTTCCTC
1783046 TTGCTCTCTT
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
23 10 0.18
24 36 0.63
25 11 0.19
ACGTcount: A:0.01, C:0.36, G:0.08, T:0.55
Consensus pattern (24 bp):
CTCTTTCTTCCTGGCTTCTTCCTC
Found at i:1783044 original size:21 final size:21
Alignment explanation
Indices: 1782943--1783047 Score: 59
Period size: 21 Copynumber: 4.6 Consensus size: 21
1782933 TTCCTTGCAT
*
1782943 CTTCTT-CTCTTCTCTTCTTGG
1 CTTCTTCCTCTT-TCTTCCTGG
* *
1782964 CTTCTTCTTCTTCTATCTTTCTGG
1 CTTCTTC--C-TCTTTCTTCCTGG
* * *
1782988 CTTCTTCTTCTCTCTTTCTGG
1 CTTCTTCCTCTTTCTTCCTGG
1783009 CTTCTTCTTCCTCCTCTTTCTTCCTGG
1 ---CTTC-T--TCCTCTTTCTTCCTGG
1783036 CTTCTTCCTCTT
1 CTTCTTCCTCTT
1783048 GCTCTCTTTC
Statistics
Matches: 66, Mismatches: 8, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
21 25 0.38
23 1 0.02
24 23 0.35
25 4 0.06
27 13 0.20
ACGTcount: A:0.01, C:0.35, G:0.08, T:0.56
Consensus pattern (21 bp):
CTTCTTCCTCTTTCTTCCTGG
Found at i:1797634 original size:20 final size:20
Alignment explanation
Indices: 1797609--1797648 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1797599 AGTAAAAGGG
1797609 GACAGCTGTTCTATACCTTA
1 GACAGCTGTTCTATACCTTA
1797629 GACAGCTGTTCTATACCTTA
1 GACAGCTGTTCTATACCTTA
1797649 ATAGAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (20 bp):
GACAGCTGTTCTATACCTTA
Found at i:1822196 original size:22 final size:22
Alignment explanation
Indices: 1822168--1822212 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1822158 ACAGATGAGG
**
1822168 GGTAGGAATTGTTGCCACCCTT
1 GGTAGGAATTGGAGCCACCCTT
*
1822190 GGTAGGAGTTGGAGCCACCCTT
1 GGTAGGAATTGGAGCCACCCTT
1822212 G
1 G
1822213 TAACTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.22, G:0.33, T:0.27
Consensus pattern (22 bp):
GGTAGGAATTGGAGCCACCCTT
Found at i:1824365 original size:19 final size:19
Alignment explanation
Indices: 1824341--1824388 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1824331 TAATCGAGTC
1824341 ATGTATATATATAATT-TTG
1 ATGTATATATAT-ATTATTG
*
1824360 ATGTATAAATATATTATTG
1 ATGTATATATATATTATTG
*
1824379 ATTTATATAT
1 ATGTATATAT
1824389 CGAGTAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (19 bp):
ATGTATATATATATTATTG
Found at i:1836799 original size:40 final size:38
Alignment explanation
Indices: 1836743--1836848 Score: 133
Period size: 38 Copynumber: 2.7 Consensus size: 38
1836733 AGTAAAAATT
* *
1836743 TTTTAAAACAATAAAAAAATAAACATGTGATATTAAAAAA
1 TTTTAAAA-AATAAAAAAATAAACATGTGACACT-AAAAA
1836783 TTTTAAAAAAT-AAAAAATAAACATGTGACACTAAAAA
1 TTTTAAAAAATAAAAAAATAAACATGTGACACTAAAAA
* *
1836820 TTTTGAAAAAAAAAACAAAAAAAACATGT
1 TTTT-AAAAAATAAA-AAAATAAACATGT
1836849 AAAGTAAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
37 9 0.15
38 25 0.42
39 5 0.08
40 20 0.34
ACGTcount: A:0.63, C:0.07, G:0.06, T:0.25
Consensus pattern (38 bp):
TTTTAAAAAATAAAAAAATAAACATGTGACACTAAAAA
Found at i:1840098 original size:13 final size:13
Alignment explanation
Indices: 1840080--1840106 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1840070 ACTTTAGCCT
1840080 TGTTGGGATTGAA
1 TGTTGGGATTGAA
1840093 TGTTGGGATTGAA
1 TGTTGGGATTGAA
1840106 T
1 T
1840107 ATACACCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (13 bp):
TGTTGGGATTGAA
Found at i:1844329 original size:2 final size:2
Alignment explanation
Indices: 1844322--1844371 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1844312 AATTAATTTA
1844322 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
1844364 AT AT AT AT
1 AT AT AT AT
1844372 NNNNNNNNNN
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1844399 original size:2 final size:2
Alignment explanation
Indices: 1844392--1844442 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1844382 NNNNNNNNNN
1844392 TA TA 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 TA TA
1844434 TA TA TA TA T
1 TA TA TA TA T
1844443 CTTTCCTAGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1846908 original size:118 final size:118
Alignment explanation
Indices: 1846700--1846938 Score: 444
Period size: 118 Copynumber: 2.0 Consensus size: 118
1846690 ATTTCATGGC
*
1846700 TAACCTTTCCATATGATAGTAGTAAATATTATGGGCGAGAAATGAATAGATTAGGTGGTTTGGTC
1 TAACCTTTCCATATGATAGTAGTAAATATTATAGGCGAGAAATGAATAGATTAGGTGGTTTGGTC
1846765 TGTCATATCTAAAAACCAAATGAATCAAATATTTTTAGAAAATCGACCAAACA
66 TGTCATATCTAAAAACCAAATGAATCAAATATTTTTAGAAAATCGACCAAACA
*
1846818 TAACCTTTTCATAT-ATTAGTAGTAAATATTATAGGCGAGAAATGAATAGATTAGGTGGTTTGGT
1 TAACCTTTCCATATGA-TAGTAGTAAATATTATAGGCGAGAAATGAATAGATTAGGTGGTTTGGT
1846882 CTGTCATATCTAAAAACCAAATGAATCAAATATTTTTAGAAAATCGACCAAACA
65 CTGTCATATCTAAAAACCAAATGAATCAAATATTTTTAGAAAATCGACCAAACA
1846936 TAA
1 TAA
1846939 AGGAAGATCA
Statistics
Matches: 118, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
117 1 0.01
118 117 0.99
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (118 bp):
TAACCTTTCCATATGATAGTAGTAAATATTATAGGCGAGAAATGAATAGATTAGGTGGTTTGGTC
TGTCATATCTAAAAACCAAATGAATCAAATATTTTTAGAAAATCGACCAAACA
Found at i:1847581 original size:23 final size:23
Alignment explanation
Indices: 1847536--1847581 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1847526 TAAAGCTTAT
* *
1847536 TATAAGTTATAGTAATATTTATG
1 TATAAATTATAGTAATATATATG
1847559 TATAAATTATA-TATATATATATG
1 TATAAATTATAGTA-ATATATATG
1847582 GTATTTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (23 bp):
TATAAATTATAGTAATATATATG
Found at i:1849766 original size:15 final size:15
Alignment explanation
Indices: 1849748--1849783 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
1849738 ATCCACCATT
1849748 ATCTTTCTTACCAAC
1 ATCTTTCTTACCAAC
1849763 ATCTTTCTTACCAAC
1 ATCTTTCTTACCAAC
1849778 ATCTTT
1 ATCTTT
1849784 ATCTCCTCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (15 bp):
ATCTTTCTTACCAAC
Found at i:1852193 original size:14 final size:14
Alignment explanation
Indices: 1852174--1852290 Score: 53
Period size: 14 Copynumber: 8.1 Consensus size: 14
1852164 TAATGTTATA
1852174 ATTAAAATAAAAAT
1 ATTAAAATAAAAAT
1852188 ATTAAAAT-AAAAT
1 ATTAAAATAAAAAT
* *
1852201 GTATAATATAAAAA-
1 AT-TAAAATAAAAAT
* *
1852215 ATTATATTAAAGAA-
1 ATTAAAATAAA-AAT
*
1852229 ATAAAAAT-AAAAT
1 ATTAAAATAAAAAT
*
1852242 ATATAAGATTAATAAGAT
1 AT-TAA-AATAA-AA-AT
*
1852260 ATAAAAATAAAATAT
1 ATTAAAATAAAA-AT
* * *
1852275 ATGATATTAAAAAT
1 ATTAAAATAAAAAT
1852289 AT
1 AT
1852291 ATTTAAGAGT
Statistics
Matches: 77, Mismatches: 17, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
12 2 0.03
13 16 0.21
14 27 0.35
15 19 0.25
16 5 0.06
17 4 0.05
18 4 0.05
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (14 bp):
ATTAAAATAAAAAT
Found at i:1852290 original size:29 final size:29
Alignment explanation
Indices: 1852218--1852291 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 29
1852208 ATAAAAAATT
1852218 ATATTAAAGAA-ATAAAAATAAAATATATA
1 ATATTAAA-AATATAAAAATAAAATATATA
* *
1852247 AGATTAATAAGATATAAAAATAAAATATATG
1 ATATTAA-AA-ATATAAAAATAAAATATATA
1852278 ATATTAAAAATATA
1 ATATTAAAAATATA
1852292 TTTAAGAGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 12 0.31
30 4 0.10
31 23 0.59
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (29 bp):
ATATTAAAAATATAAAAATAAAATATATA
Found at i:1870902 original size:5 final size:5
Alignment explanation
Indices: 1870892--1870916 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1870882 AATAACGTCC
1870892 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
1870917 TATTCATGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1877772 original size:29 final size:28
Alignment explanation
Indices: 1877707--1877772 Score: 64
Period size: 29 Copynumber: 2.3 Consensus size: 28
1877697 GTTTTTAATA
*
1877707 AAAAAAAAGAATAAAAATTTGTTGGGATAT
1 AAAAAAAAGAATAAAAATTTATT--GATAT
*
1877737 -AAGAAAAGAATAGAAAATTTATT-ATAT
1 AAAAAAAAGAATA-AAAATTTATTGATAT
1877764 GAAAAAAAA
1 -AAAAAAAA
1877773 ATTTAAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
27 4 0.13
29 17 0.57
30 9 0.30
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (28 bp):
AAAAAAAAGAATAAAAATTTATTGATAT
Found at i:1877966 original size:5 final size:5
Alignment explanation
Indices: 1877948--1877981 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
1877938 AATTACGCAA
*
1877948 AAAAG AAAAAG AAACG AAAAG AAAAG AAAAG AAA
1 AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1877982 GGATCATCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1878732 original size:3 final size:3
Alignment explanation
Indices: 1878724--1878752 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1878714 TTAGTCTTTT
1878724 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1878753 TTTCTTTTTG
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1897082 original size:10 final size:10
Alignment explanation
Indices: 1897069--1897093 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1897059 TCAAACTGGC
1897069 ATTTTGATGA
1 ATTTTGATGA
1897079 ATTTTGATGA
1 ATTTTGATGA
1897089 ATTTT
1 ATTTT
1897094 TTAATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (10 bp):
ATTTTGATGA
Found at i:1901891 original size:2 final size:2
Alignment explanation
Indices: 1901884--1901925 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1901874 NNNNNNNNNN
1901884 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
1901926 TACTATTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1902086 original size:21 final size:21
Alignment explanation
Indices: 1902060--1902101 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1902050 CTTAAAACAT
1902060 GATGGGGTACTCAATAATTAC
1 GATGGGGTACTCAATAATTAC
1902081 GATGGGGTACTCAATAATTAC
1 GATGGGGTACTCAATAATTAC
1902102 TTACATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (21 bp):
GATGGGGTACTCAATAATTAC
Found at i:1906688 original size:15 final size:15
Alignment explanation
Indices: 1906679--1906725 Score: 71
Period size: 14 Copynumber: 3.3 Consensus size: 15
1906669 TTATTAATTT
1906679 TTTAAATATTAATAA
1 TTTAAATATTAATAA
*
1906694 TTTATA-ATTAATAA
1 TTTAAATATTAATAA
1906708 TTTAAATATTAAT-A
1 TTTAAATATTAATAA
1906722 TTTA
1 TTTA
1906726 TTTAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 18 0.62
15 11 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTAAATATTAATAA
Found at i:1906704 original size:29 final size:28
Alignment explanation
Indices: 1906666--1906779 Score: 89
Period size: 29 Copynumber: 4.2 Consensus size: 28
1906656 ATGACATTTT
1906666 ATTT-TATTAATTTTTTAAATATTAATA
1 ATTTATATTAATTTTTTAAATATTAATA
**
1906693 ATTTATAATTAATAATTTAAATATTAAT-
1 ATTTAT-ATTAATTTTTTAAATATTAATA
*
1906721 ATTTAT-TTAA----TTAAATATTATTA
1 ATTTATATTAATTTTTTAAATATTAATA
* * * *
1906744 TTATTATTTTTATTTTTAAAATATTAATA
1 AT-TTATATTAATTTTTTAAATATTAATA
*
1906773 TTTTATA
1 ATTTATA
1906780 ATTNNNNNNN
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
22 11 0.16
23 1 0.01
24 4 0.06
25 3 0.04
26 4 0.06
27 4 0.06
28 11 0.16
29 32 0.46
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
ATTTATATTAATTTTTTAAATATTAATA
Found at i:1907268 original size:19 final size:20
Alignment explanation
Indices: 1907240--1907312 Score: 69
Period size: 22 Copynumber: 3.5 Consensus size: 20
1907230 TAATTTATTT
1907240 TATTAATAATTTATAATTTAAA
1 TATTAAT-A-TTATAATTTAAA
*
1907262 TATTAATATT-TTATTTATAA
1 TATTAATATTATAATTTA-AA
*
1907282 T-TTAATATTAATATTTTAAAA
1 TATTAATATT-ATAATTT-AAA
1907303 TATTAATATT
1 TATTAATATT
1907313 TTATTAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
19 14 0.33
20 5 0.12
21 8 0.19
22 16 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTAATATTATAATTTAAA
Found at i:1907294 original size:25 final size:26
Alignment explanation
Indices: 1907248--1907299 Score: 97
Period size: 25 Copynumber: 2.0 Consensus size: 26
1907238 TTTATTAATA
1907248 ATTTATAATTTAAATATTAATATTTT
1 ATTTATAATTTAAATATTAATATTTT
1907274 ATTTATAATTT-AATATTAATATTTT
1 ATTTATAATTTAAATATTAATATTTT
1907299 A
1 A
1907300 AAATATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
ATTTATAATTTAAATATTAATATTTT
Found at i:1907306 original size:16 final size:16
Alignment explanation
Indices: 1907285--1907315 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1907275 TTTATAATTT
1907285 AATATTAATATTTTAA
1 AATATTAATATTTTAA
1907301 AATATTAATATTTTA
1 AATATTAATATTTTA
1907316 TTAAAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATATTAATATTTTAA
Found at i:1907321 original size:19 final size:20
Alignment explanation
Indices: 1907240--1907321 Score: 71
Period size: 19 Copynumber: 4.0 Consensus size: 20
1907230 TAATTTATTT
*
1907240 TATTAATAATTTATAATTTAAA
1 TATTAAT-ATTTAT-ATTAAAA
*
1907262 TATTAATATTT-TATTTATAA
1 TATTAATATTTATA-TTAAAA
*
1907282 T-TTAATATTAATATTTTAAAA
1 TATTAATATT--TATATTAAAA
1907303 TATTAATATTT-TATTAAAA
1 TATTAATATTTATATTAAAA
1907322 ATTGAAATCA
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
19 16 0.32
20 7 0.14
21 11 0.22
22 16 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTAATATTTATATTAAAA
Found at i:1911333 original size:23 final size:23
Alignment explanation
Indices: 1911300--1911428 Score: 109
Period size: 23 Copynumber: 5.7 Consensus size: 23
1911290 ACAATGCTTA
*
1911300 AGTCACACAATGCCTTACTAACT
1 AGTCACGCAATGCCTTACTAACT
* * *
1911323 AGTCACGCAATACATTACTAACA
1 AGTCACGCAATGCCTTACTAACT
* *
1911346 AATCACACAATGCC-TA-TCAACT
1 AGTCACGCAATGCCTTACT-AACT
* * *
1911368 AATCACGTAATGTCTTACTAACT
1 AGTCACGCAATGCCTTACTAACT
* * *
1911391 AGTCACGTAATGTCTTACTAACA
1 AGTCACGCAATGCCTTACTAACT
**
1911414 AGTCGTGCAATGCCT
1 AGTCACGCAATGCCT
1911429 ATCAATTAGT
Statistics
Matches: 85, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
21 1 0.01
22 16 0.19
23 67 0.79
24 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.27
Consensus pattern (23 bp):
AGTCACGCAATGCCTTACTAACT
Found at i:1911528 original size:22 final size:22
Alignment explanation
Indices: 1911502--1911556 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1911492 GTCCAAAGTC
*
1911502 AATCACGCAATA-TCTAAAAATT
1 AATCACGCAATACT-TAAAAACT
1911524 AATCACGCAATACTTAAAAACT
1 AATCACGCAATACTTAAAAACT
*
1911546 AGTCACGCAAT
1 AATCACGCAAT
1911557 GTCCAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.47, C:0.22, G:0.07, T:0.24
Consensus pattern (22 bp):
AATCACGCAATACTTAAAAACT
Found at i:1911564 original size:22 final size:22
Alignment explanation
Indices: 1911474--1911609 Score: 73
Period size: 22 Copynumber: 6.3 Consensus size: 22
1911464 CACAATACTT
* *
1911474 AAAAACTAGTCACGTAATGTCC
1 AAAAACTAATCACGCAATGTCC
** * *
1911496 AAAGTC-AATCACGCAATATCT
1 AAAAACTAATCACGCAATGTCC
* * *
1911517 AAAAATTAATCACGCAAT-ACTT
1 AAAAACTAATCACGCAATGTC-C
*
1911539 AAAAACTAGTCACGCAATGTCC
1 AAAAACTAATCACGCAATGTCC
* * * *
1911561 AAAATC-AATAACGCATTG-CAT
1 AAAAACTAATCACGCAATGTC-C
* * *
1911582 AAAAACTAGTCATGCAATGCCC
1 AAAAACTAATCACGCAATGTCC
1911604 AAAAAC
1 AAAAAC
1911610 ATCAAAACTA
Statistics
Matches: 83, Mismatches: 25, Indels: 12
0.69 0.21 0.10
Matches are distributed among these distances:
20 1 0.01
21 29 0.35
22 51 0.61
23 2 0.02
ACGTcount: A:0.46, C:0.23, G:0.10, T:0.21
Consensus pattern (22 bp):
AAAAACTAATCACGCAATGTCC
Found at i:1911565 original size:43 final size:43
Alignment explanation
Indices: 1911504--1911607 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 43
1911494 CCAAAGTCAA
* * * * *
1911504 TCACGCAATATCTAAAAATTAATCACGCAATACTTAAAAACTAG
1 TCACGCAATGTC-CAAAATCAATAACGCAATACATAAAAACTAG
* *
1911548 TCACGCAATGTCCAAAATCAATAACGCATTGCATAAAAACTAG
1 TCACGCAATGTCCAAAATCAATAACGCAATACATAAAAACTAG
* *
1911591 TCATGCAATGCCCAAAA
1 TCACGCAATGTCCAAAA
1911608 ACATCAAAAC
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
43 40 0.78
44 11 0.22
ACGTcount: A:0.45, C:0.23, G:0.10, T:0.22
Consensus pattern (43 bp):
TCACGCAATGTCCAAAATCAATAACGCAATACATAAAAACTAG
Found at i:1911608 original size:65 final size:65
Alignment explanation
Indices: 1911474--1911609 Score: 159
Period size: 65 Copynumber: 2.1 Consensus size: 65
1911464 CACAATACTT
* * * * **
1911474 AAAAACTAGTCACGTAATGTCCAAAGTCAATCACGCAATATCTAAAAATTAATCACGCAATACTT
1 AAAAACTAGTCACGCAATGTCCAAAATCAATAACGCAATATCTAAAAACTAATCACGCAATACCC
* * *
1911539 AAAAACTAGTCACGCAATGTCCAAAATCAATAACGC-AT-TGCATAAAAACTAGTCATGCAATGC
1 AAAAACTAGTCACGCAATGTCCAAAATCAATAACGCAATAT-C-TAAAAACTAATCACGCAATAC
1911602 CC
64 CC
1911604 AAAAAC
1 AAAAAC
1911610 ATCAAAACTA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
63 1 0.02
64 3 0.05
65 56 0.93
ACGTcount: A:0.46, C:0.23, G:0.10, T:0.21
Consensus pattern (65 bp):
AAAAACTAGTCACGCAATGTCCAAAATCAATAACGCAATATCTAAAAACTAATCACGCAATACCC
Found at i:1915366 original size:13 final size:13
Alignment explanation
Indices: 1915308--1915379 Score: 56
Period size: 13 Copynumber: 5.2 Consensus size: 13
1915298 CTTTTTATTT
1915308 TTAATTAATACAAAA
1 TTAATT-ATA-AAAA
1915323 TTAATTA-AAATAA
1 TTAATTATAAA-AA
** *
1915336 TATAAAAATATAATA
1 T-TAATTATA-AAAA
1915351 TTAATTATAAAAA
1 TTAATTATAAAAA
*
1915364 TTAATTAAAAAAA
1 TTAATTATAAAAA
1915377 TTA
1 TTA
1915380 TCTTTTTATT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
12 2 0.04
13 22 0.48
14 11 0.24
15 9 0.20
16 2 0.04
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAATTATAAAAA
Found at i:1915374 original size:11 final size:10
Alignment explanation
Indices: 1915310--1915374 Score: 51
Period size: 11 Copynumber: 6.2 Consensus size: 10
1915300 TTTTATTTTT
1915310 AATTAATACAA
1 AATTAATA-AA
*
1915321 AATTAATTAA
1 AATTAATAAA
*
1915331 AATAATATAAA
1 AATTA-ATAAA
**
1915342 AATATAATATT
1 AAT-TAATAAA
1915353 AATT-ATAAA
1 AATTAATAAA
1915362 AATTAATTAAA
1 AATTAA-TAAA
1915373 AA
1 AA
1915375 AATTATCTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
9 7 0.17
10 8 0.19
11 26 0.62
12 1 0.02
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (10 bp):
AATTAATAAA
Found at i:1919086 original size:32 final size:32
Alignment explanation
Indices: 1919049--1919109 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
1919039 CTGTTCCAAT
* *
1919049 TTACATTAATTATAACGTCATATATCATGGGG
1 TTACATCAATTATAACATCATATATCATGGGG
*
1919081 TTACATCAATTATTACATCATATATCATG
1 TTACATCAATTATAACATCATATATCATG
1919110 TAAATAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (32 bp):
TTACATCAATTATAACATCATATATCATGGGG
Found at i:1924918 original size:6 final size:6
Alignment explanation
Indices: 1924909--1924943 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1924899 ATATATATAT
*
1924909 AGAGAG AGAGAC AGAGAC AGAGAC AGAGAC AGAGA
1 AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGAGA
1924944 GAGATAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.51, C:0.11, G:0.37, T:0.00
Consensus pattern (6 bp):
AGAGAC
Found at i:1928493 original size:2 final size:2
Alignment explanation
Indices: 1928486--1928526 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1928476 CTGAGAACAG
*
1928486 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1928527 CACAGTTACG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1934870 original size:18 final size:18
Alignment explanation
Indices: 1934844--1934882 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1934834 GGTCAGTCCA
1934844 TTTTTAAAAAAAAT-ATT
1 TTTTTAAAAAAAATCATT
1934861 TTTTTGAAAAAAAATCATT
1 TTTTT-AAAAAAAATCATT
1934880 TTT
1 TTT
1934883 ATAATTTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
TTTTTAAAAAAAATCATT
Found at i:1934985 original size:14 final size:14
Alignment explanation
Indices: 1934958--1935006 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1934948 ATAAAAACAT
1934958 ATTACAAACAAATAA
1 ATTAC-AACAAATAA
*
1934973 ATTACACCAAATATA
1 ATTACAACAAATA-A
*
1934988 AATA-AACAAATAA
1 ATTACAACAAATAA
1935001 ATTACA
1 ATTACA
1935007 TAAATAAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
13 4 0.14
14 15 0.54
15 9 0.32
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.22
Consensus pattern (14 bp):
ATTACAACAAATAA
Found at i:1935316 original size:22 final size:22
Alignment explanation
Indices: 1935290--1935359 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
1935280 CAATACCATT
1935290 AATAATTAAATTATTAATTTTA
1 AATAATTAAATTATTAATTTTA
* *
1935312 TATAATTAAATATATAAAATTATTA
1 AATAATTAAAT-TAT-TAATT-TTA
1935337 AATTAATTAAAATTATTAATTTT
1 AA-TAATT-AAATTATTAATTTT
1935360 TTTTATCCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 10 0.26
23 3 0.08
24 6 0.15
25 8 0.21
26 8 0.21
27 4 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAATTAAATTATTAATTTTA
Found at i:1935339 original size:8 final size:8
Alignment explanation
Indices: 1935294--1935355 Score: 56
Period size: 8 Copynumber: 7.6 Consensus size: 8
1935284 ACCATTAATA
1935294 ATTAAATT
1 ATTAAATT
1935302 ATT-AATT
1 ATTAAATT
* *
1935309 -TTATATA
1 ATTAAATT
1935316 ATTAAATAT
1 ATTAAAT-T
*
1935325 ATAAAATT
1 ATTAAATT
1935333 ATTAAATT
1 ATTAAATT
1935341 AATTAAAATT
1 -ATT-AAATT
1935351 ATTAA
1 ATTAA
1935356 TTTTTTTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
6 2 0.05
7 6 0.14
8 18 0.42
9 12 0.28
10 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
ATTAAATT
Found at i:1940518 original size:12 final size:12
Alignment explanation
Indices: 1940497--1940533 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
1940487 TTAATGCATT
*
1940497 AAAAAA-GAAAG
1 AAAAAAGGAAAA
1940508 AAAAAAGGAAAA
1 AAAAAAGGAAAA
1940520 AAAAAA-GAAAA
1 AAAAAAGGAAAA
1940531 AAA
1 AAA
1940534 GAAGTCTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAGGAAAA
Found at i:1948784 original size:6 final size:6
Alignment explanation
Indices: 1948751--1948800 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
1948741 ACAGTGCCCT
* * *
1948751 CTCCAC C-CGCAC CCCCAC CTTCAT CTCCAC CTCCAC CTCCAC CTCCAC
1 CTCCAC CTC-CAC CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC
1948799 CT
1 CT
1948801 TCTCCCAGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
5 1 0.03
6 35 0.95
7 1 0.03
ACGTcount: A:0.16, C:0.64, G:0.02, T:0.18
Consensus pattern (6 bp):
CTCCAC
Found at i:1959706 original size:3 final size:3
Alignment explanation
Indices: 1959681--1959746 Score: 51
Period size: 3 Copynumber: 22.0 Consensus size: 3
1959671 TGCCTTTCTT
* * * * * * *
1959681 TGA TGA TGT TGA TGA GGA CGA TGA TGA TGG TGA AGA TGA TGA AGA AGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
* *
1959729 AGA TGA TGA TGA GGA TGA
1 TGA TGA TGA TGA TGA TGA
1959747 AGCAACGCCA
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.36, C:0.02, G:0.38, T:0.24
Consensus pattern (3 bp):
TGA
Found at i:1959708 original size:15 final size:15
Alignment explanation
Indices: 1959685--1959743 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
1959675 TTTCTTTGAT
* *
1959685 GATGTTGATGAGGAC
1 GATGATGATGAGGAA
1959700 GATGATGATG-GTGAA
1 GATGATGATGAG-GAA
* *
1959715 GATGATGAAGAAGAA
1 GATGATGATGAGGAA
1959730 GATGATGATGAGGA
1 GATGATGATGAGGA
1959744 TGAAGCAACG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 1 0.03
15 35 0.97
ACGTcount: A:0.37, C:0.02, G:0.39, T:0.22
Consensus pattern (15 bp):
GATGATGATGAGGAA
Found at i:1962375 original size:36 final size:36
Alignment explanation
Indices: 1962309--1962377 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
1962299 TCGTCCTCGA
* * *
1962309 CATGAGCTTTAGCATATATGTCTTCTTCCTTCTTCC
1 CATGAGCTTCAGCATATATGTCATCCTCCTTCTTCC
*
1962345 CATGAGCTTCGGCATAT-TGGTCATCCTCCTTCT
1 CATGAGCTTCAGCATATAT-GTCATCCTCCTTCT
1962378 CTACATAAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 1 0.04
36 27 0.96
ACGTcount: A:0.16, C:0.29, G:0.14, T:0.41
Consensus pattern (36 bp):
CATGAGCTTCAGCATATATGTCATCCTCCTTCTTCC
Found at i:1965738 original size:38 final size:38
Alignment explanation
Indices: 1965687--1965763 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
1965677 TCAAAGCAGA
1965687 TAACTTCAATAATAAAACCTTGTTCAATTCCCAAATGG
1 TAACTTCAATAATAAAACCTTGTTCAATTCCCAAATGG
1965725 TAACTTCAATAATAAAACCTTGTTCAATTCCCAAATGG
1 TAACTTCAATAATAAAACCTTGTTCAATTCCCAAATGG
1965763 T
1 T
1965764 GTCTTTCAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (38 bp):
TAACTTCAATAATAAAACCTTGTTCAATTCCCAAATGG
Found at i:1983176 original size:8 final size:8
Alignment explanation
Indices: 1983163--1983190 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1983153 ATGGGTTTTG
1983163 TTTTTTAA
1 TTTTTTAA
1983171 TTTTTTAA
1 TTTTTTAA
1983179 TTTTTTAA
1 TTTTTTAA
1983187 TTTT
1 TTTT
1983191 CGATTGAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTAA
Found at i:1985319 original size:48 final size:48
Alignment explanation
Indices: 1985246--1985341 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
1985236 CATATCCCTC
* * *
1985246 CAAAATAATATGAATGCCCACACATGTGATACAAGAAAAATGGTAAAT
1 CAAAATAACATGAATGCCCACACATGTGAAACAAGAAAAATGGCAAAT
*
1985294 CAAAATAACATGAATGCCCATACATGTGAAACAAGAAAAATGGCAAAT
1 CAAAATAACATGAATGCCCACACATGTGAAACAAGAAAAATGGCAAAT
1985342 TAAAGTTACT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.51, C:0.16, G:0.15, T:0.19
Consensus pattern (48 bp):
CAAAATAACATGAATGCCCACACATGTGAAACAAGAAAAATGGCAAAT
Found at i:1986272 original size:2 final size:2
Alignment explanation
Indices: 1986265--1986293 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1986255 GTACTCTACT
1986265 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1986294 GAGAAAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1986391 original size:21 final size:20
Alignment explanation
Indices: 1986361--1986402 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1986351 AAAGAGAAAA
1986361 AGAAAACAAAAAAACATAAGT
1 AGAAAAC-AAAAAACATAAGT
* *
1986382 AGAAATCAAAAAACATGAGT
1 AGAAAACAAAAAACATAAGT
1986402 A
1 A
1986403 AAAGGTTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.67, C:0.10, G:0.12, T:0.12
Consensus pattern (20 bp):
AGAAAACAAAAAACATAAGT
Found at i:1987524 original size:1 final size:1
Alignment explanation
Indices: 1987518--1987551 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
1987508 GAGTGATTAC
* *
1987518 AAAAAAAAAAAAAAAAAAAAAAGAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1987552 CAAGTCACTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:1987607 original size:10 final size:10
Alignment explanation
Indices: 1987566--1987612 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
1987556 TCACTGCTGC
* *
1987566 AAAGAGCAAC
1 AAAGAGAAAG
1987576 AAAGAGAAAG
1 AAAGAGAAAG
*
1987586 AAA-AGGAGAG
1 AAAGA-GAAAG
1987596 AAAGAGAAAG
1 AAAGAGAAAG
1987606 AAAGAGA
1 AAAGAGA
1987613 CGACAGACAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 1 0.03
10 29 0.94
11 1 0.03
ACGTcount: A:0.66, C:0.04, G:0.30, T:0.00
Consensus pattern (10 bp):
AAAGAGAAAG
Found at i:1991941 original size:2 final size:2
Alignment explanation
Indices: 1991928--1991959 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1991918 GAAAAGGAAA
*
1991928 AT AT AT AC 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
1991960 TAGCTGATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1993642 original size:21 final size:21
Alignment explanation
Indices: 1993616--1993655 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1993606 GCATCAACAC
1993616 CAACAACAACAACAACAGCTA
1 CAACAACAACAACAACAGCTA
* *
1993637 CAACAACAACCACACCAGC
1 CAACAACAACAACAACAGC
1993656 AGGCAAAAGA
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:0.53, C:0.40, G:0.05, T:0.03
Consensus pattern (21 bp):
CAACAACAACAACAACAGCTA
Found at i:1995353 original size:25 final size:25
Alignment explanation
Indices: 1995305--1995358 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
1995295 TTATATTAGT
1995305 TATCCAAGTCGCTTTAAAAAAAAAAGA
1 TATCCAAGTC-CTTTAAAAAAAAAA-A
**
1995332 TATCCAAGT-CTTTAAATGAAAAAA
1 TATCCAAGTCCTTTAAAAAAAAAAA
1995356 TAT
1 TAT
1995359 ATACTAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.16
25 12 0.48
27 9 0.36
ACGTcount: A:0.50, C:0.13, G:0.09, T:0.28
Consensus pattern (25 bp):
TATCCAAGTCCTTTAAAAAAAAAAA
Found at i:2005295 original size:81 final size:82
Alignment explanation
Indices: 2005160--2005326 Score: 309
Period size: 81 Copynumber: 2.0 Consensus size: 82
2005150 ACTTCTCATA
* *
2005160 TATATTAGATAATTCATCATTTCCTTCATTCTTGATCCTTTTATTTTGTTAGCAAAGGGGGTAAA
1 TATATTAGATAATTCATCATTTCCTTCATCCTTGATCCTTTTATTTTGTTAGCAAAGGGGGAAAA
2005225 A-AAGCTTGTTATAGGC
66 AGAAGCTTGTTATAGGC
2005241 TATATTAGATAATTCATCATTTCCTTCATCCTTGATCCTTTTATTTTGTTAGCAAAGGGGGAAAA
1 TATATTAGATAATTCATCATTTCCTTCATCCTTGATCCTTTTATTTTGTTAGCAAAGGGGGAAAA
2005306 AGAAGCTTGTTATAGGC
66 AGAAGCTTGTTATAGGC
2005323 TATA
1 TATA
2005327 ACTACATGTC
Statistics
Matches: 83, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
81 64 0.77
82 19 0.23
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (82 bp):
TATATTAGATAATTCATCATTTCCTTCATCCTTGATCCTTTTATTTTGTTAGCAAAGGGGGAAAA
AGAAGCTTGTTATAGGC
Found at i:2018032 original size:4 final size:4
Alignment explanation
Indices: 2018023--2018052 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
2018013 GGTCTAGGGA
2018023 ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
2018053 GTGGTTCGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (4 bp):
ATAG
Found at i:2020413 original size:85 final size:87
Alignment explanation
Indices: 2020249--2020422 Score: 255
Period size: 85 Copynumber: 2.0 Consensus size: 87
2020239 CTATGGGAAG
* *
2020249 CTATCAAATGTAACTACCATACTAGTTAGAAGAATTGTTAGAGATCAACAAAATGAAGGAAATCA
1 CTATCAAATATAACAACCATACTAGTTAGAAGAATTGTTAGAGATCAACAAAATGAAGGAAATCA
*
2020314 AAACAAGACTAATAAGTGAACT
66 AAACAAGACCAATAAGTGAACT
* *
2020336 CTATCAAATATAACAACCCATACTAGTTAGAAGAATTGTTA-A-A-GAACACAATGAAGGAAATC
1 CTATCAAATATAACAA-CCATACTAGTTAGAAGAATTGTTAGAGATCAACAAAATGAAGGAAATC
* *
2020398 AAAGCAAGACCAATAAGTGAGCT
65 AAAACAAGACCAATAAGTGAACT
2020421 CT
1 CT
2020423 CATAGACTAG
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
85 39 0.49
86 1 0.01
87 15 0.19
88 24 0.30
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.22
Consensus pattern (87 bp):
CTATCAAATATAACAACCATACTAGTTAGAAGAATTGTTAGAGATCAACAAAATGAAGGAAATCA
AAACAAGACCAATAAGTGAACT
Found at i:2024403 original size:2 final size:2
Alignment explanation
Indices: 2024389--2024425 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
2024379 ATTGCTTACC
2024389 CT CT CT C- CAT CT CT CT CT CT CT CT CT CT CT CT C- CT CT
1 CT CT CT CT C-T CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2024426 TTGGCCAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.06
2 29 0.91
3 1 0.03
ACGTcount: A:0.03, C:0.51, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:2024480 original size:2 final size:2
Alignment explanation
Indices: 2024466--2024502 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
2024456 ATTGCTTACC
2024466 CT CT CT C- CAT CT CT CT CT CT CT CT CT CT CT CT C- CT CT
1 CT CT CT CT C-T CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2024503 TTGGCCAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.06
2 29 0.91
3 1 0.03
ACGTcount: A:0.03, C:0.51, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:2024499 original size:77 final size:76
Alignment explanation
Indices: 2024372--2024524 Score: 297
Period size: 77 Copynumber: 2.0 Consensus size: 76
2024362 ACATACAGTA
2024372 ATGCCAAATTGCTTACCCTCTCTCCATCTCTCTCTCTCTCTCTCTCTCTCCTCTTTGGCCAATAT
1 ATGCCAAATTGCTTACCCTCTCTCCATCTCTCTCTCTCTCTCTCTCTCTCCTCTTTGGCCAATAT
2024437 TAATAGGTATT
66 TAATAGGTATT
2024448 NATGCCAAATTGCTTACCCTCTCTCCATCTCTCTCTCTCTCTCTCTCTCTCCTCTTTGGCCAATA
1 -ATGCCAAATTGCTTACCCTCTCTCCATCTCTCTCTCTCTCTCTCTCTCTCCTCTTTGGCCAATA
2024513 TTAATAGGTATT
65 TTAATAGGTATT
2024525 TTCTGTGGAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.17, C:0.34, G:0.08, T:0.41
Consensus pattern (76 bp):
ATGCCAAATTGCTTACCCTCTCTCCATCTCTCTCTCTCTCTCTCTCTCTCCTCTTTGGCCAATAT
TAATAGGTATT
Found at i:2042482 original size:2 final size:2
Alignment explanation
Indices: 2042475--2042504 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2042465 AATTGAAGTA
*
2042475 AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2042505 GGAAAGACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2042509 original size:12 final size:12
Alignment explanation
Indices: 2042475--2042511 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
2042465 AATTGAAGTA
*
2042475 AGAGAGAGAGAG
1 AGAGAGAGAAAG
2042487 AGAGAGAGAAAG
1 AGAGAGAGAAAG
*
2042499 AGAGAGGGAAAG
1 AGAGAGAGAAAG
2042511 A
1 A
2042512 CAAGTTGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (12 bp):
AGAGAGAGAAAG
Found at i:2051678 original size:30 final size:30
Alignment explanation
Indices: 2051644--2051715 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
2051634 TACGTTTAAT
*
2051644 TAAGTTTTTATATTTTTATTTTGAGTCAAA
1 TAAGTTTTTATATTTTTATTTTAAGTCAAA
*
2051674 TAAGTCTTTATATTTTTATTTTAAGTCAAA
1 TAAGTTTTTATATTTTTATTTTAAGTCAAA
*
2051704 CAAGTTTTTATA
1 TAAGTTTTTATA
2051716 ATTAATAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.32, C:0.06, G:0.08, T:0.54
Consensus pattern (30 bp):
TAAGTTTTTATATTTTTATTTTAAGTCAAA
Found at i:2060456 original size:46 final size:46
Alignment explanation
Indices: 2060383--2060483 Score: 130
Period size: 46 Copynumber: 2.2 Consensus size: 46
2060373 CTTTAAAGCC
* *
2060383 CAAACAAAGCAGGCCTAAGTTCTAAGCCCAACCAAAACGAATAGGGG
1 CAAA-AAAGCAGGCCTAAGTTCCAAGCCCAACCAAAACGAATAGCGG
* * * *
2060430 CAAAAAAGCTGGCCTCAGTTCCAAGCCCAATCTAAACGAATAGCGG
1 CAAAAAAGCAGGCCTAAGTTCCAAGCCCAACCAAAACGAATAGCGG
*
2060476 TAAAAAAG
1 CAAAAAAG
2060484 TAATAGGGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
46 43 0.91
47 4 0.09
ACGTcount: A:0.43, C:0.25, G:0.20, T:0.13
Consensus pattern (46 bp):
CAAAAAAGCAGGCCTAAGTTCCAAGCCCAACCAAAACGAATAGCGG
Found at i:2070669 original size:12 final size:12
Alignment explanation
Indices: 2070652--2070685 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2070642 CTTTCCCCTC
2070652 TCTCTCTCTCTG
1 TCTCTCTCTCTG
*
2070664 TCTCTCTCTCTT
1 TCTCTCTCTCTG
*
2070676 TCTGTCTCTC
1 TCTCTCTCTC
2070686 CATGCTAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.41, G:0.06, T:0.53
Consensus pattern (12 bp):
TCTCTCTCTCTG
Found at i:2070670 original size:16 final size:16
Alignment explanation
Indices: 2070649--2070685 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
2070639 TCCCTTTCCC
2070649 CTCTCTCTCTCTCTGT
1 CTCTCTCTCTCTCTGT
*
2070665 CTCTCTCTCTTTCTGT
1 CTCTCTCTCTCTCTGT
2070681 CTCTC
1 CTCTC
2070686 CATGCTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.00, C:0.43, G:0.05, T:0.51
Consensus pattern (16 bp):
CTCTCTCTCTCTCTGT
Found at i:2075995 original size:21 final size:21
Alignment explanation
Indices: 2075971--2076034 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
2075961 ATTGTGAAGG
2075971 AAGGGTTCGAGACGGCGGAGA
1 AAGGGTTCGAGACGGCGGAGA
* * *
2075992 AAGGGATC-ATTACGGTGGAGA
1 AAGGGTTCGA-GACGGCGGAGA
2076013 AAGGGTT-GAAGACGGCGGAGA
1 AAGGGTTCG-AGACGGCGGAGA
2076034 A
1 A
2076035 GGAGATCGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.33, C:0.11, G:0.44, T:0.12
Consensus pattern (21 bp):
AAGGGTTCGAGACGGCGGAGA
Found at i:2086732 original size:217 final size:218
Alignment explanation
Indices: 2086357--2086794 Score: 648
Period size: 217 Copynumber: 2.0 Consensus size: 218
2086347 TTACACTTTT
* *
2086357 TTTTCAGAATTTAAGGTTGCACGGGATTAGATTTAAGTTCCAGCACATGACATTTGGTATTGGAG
1 TTTTCAGAATTTAAGATTGCACGGGATTAAATTTAAGTTCCAGCACATGACATTTGGTATTGGAG
* ** * *
2086422 CAAACAAAATTTAAGATTGCATGAGGTTGGGCTTAAGTTCCAACACGTGACATTTGGTATCAAAG
66 AAAACAAAATTTAAGATTGCACAAGGATGGGCTTAAGTTCCAACACGTGACATTTGGAATCAAAG
* *
2086487 CAAATTCGGATTTTCACTAATGTGGGGGTCCCATATGAGAGATAT-AAGGGTTAAGGTTGACTCG
131 CAAATTCGGATTTTCACTAATGTGGGGGTCCCATATGAGAGATATAAAAGGTCAAGGTTGACTCG
* * *
2086551 GATTAGTGTAAGAGTTTTTCTCC
196 GACTAGTATAAGAGTCTTTCTCC
* *
2086574 TTTTCAGAATTTAAGATTGCACGAGG-TTAAATTTAAGTTCTAGCACGTGACATTTGGTATTGGA
1 TTTTCAGAATTTAAGATTGCACG-GGATTAAATTTAAGTTCCAGCACATGACATTTGGTATTGGA
* * * *
2086638 GAAAATAGAATTTAAGATTGCACAAGGATGGGCTTAAGTTCTAGCACGTGACA-TTGAGAATCAA
65 GAAAACAAAATTTAAGATTGCACAAGGATGGGCTTAAGTTCCAACACGTGACATTTG-GAATCAA
* * *
2086702 AGCAAATTCGGATTTTCACTTATGTGGGGGTCCGATATGAGAGATATAAAAGGTCAAGGTTGATT
129 AGCAAATTCGGATTTTCACTAATGTGGGGGTCCCATATGAGAGATATAAAAGGTCAAGGTTGACT
2086767 CGGACTAGTATAAGAGTCTTTCTCC
194 CGGACTAGTATAAGAGTCTTTCTCC
2086792 TTT
1 TTT
2086795 ACGGGGTAAA
Statistics
Matches: 197, Mismatches: 21, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
216 3 0.02
217 153 0.78
218 41 0.21
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (218 bp):
TTTTCAGAATTTAAGATTGCACGGGATTAAATTTAAGTTCCAGCACATGACATTTGGTATTGGAG
AAAACAAAATTTAAGATTGCACAAGGATGGGCTTAAGTTCCAACACGTGACATTTGGAATCAAAG
CAAATTCGGATTTTCACTAATGTGGGGGTCCCATATGAGAGATATAAAAGGTCAAGGTTGACTCG
GACTAGTATAAGAGTCTTTCTCC
Found at i:2087076 original size:65 final size:64
Alignment explanation
Indices: 2086997--2087218 Score: 259
Period size: 65 Copynumber: 3.4 Consensus size: 64
2086987 AGATTAGGTT
* * *
2086997 TTAAGTTTCAGCACATGACATTTGGTATCTAAACAGACAAAGTTTAAGGTTGCATAAAGTTAGGC
1 TTAAGTTCCAACACATGACATTTGGTATCTAAACAGACAAAGTTTAAGGTT-CATAAGGTTAGGC
* *
2087062 TTAAGTTCCAGCACATGACATTTGGTATCTAAACAAACAAAGTTTAAGGTCTCATAAGGTTAGGC
1 TTAAGTTCCAACACATGACATTTGGTATCTAAACAGACAAAGTTTAAGGT-TCATAAGGTTAGGC
** * *** *
2087127 TTAAGTTCCAACATGTGACATTTGATATC-AGAGTTGACAAA-TTTAAGGTTACATAAGGTTGGG
1 TTAAGTTCCAACACATGACATTTGGTATCTA-AACAGACAAAGTTTAAGGTT-CATAAGGTTAGG
*
2087190 T
64 C
* *
2087191 TTAAGTTCCAACACGTGACATTTAGTAT
1 TTAAGTTCCAACACATGACATTTGGTAT
2087219 TAGAGCAGAC
Statistics
Matches: 138, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
63 1 0.01
64 45 0.33
65 91 0.66
66 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (64 bp):
TTAAGTTCCAACACATGACATTTGGTATCTAAACAGACAAAGTTTAAGGTTCATAAGGTTAGGC
Found at i:2087547 original size:35 final size:35
Alignment explanation
Indices: 2087494--2087562 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
2087484 ATTTTCAGAA
* * *
2087494 TTTAAGACCGTACAAGGTTTGGCTTAAGTTCTGAG
1 TTTAAGACCGCACAAGGTTAGACTTAAGTTCTGAG
* *
2087529 TTTAAGATCGCACGAGGTTAGACTTAAGTTCTGA
1 TTTAAGACCGCACAAGGTTAGACTTAAGTTCTGA
2087563 CCCACAACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (35 bp):
TTTAAGACCGCACAAGGTTAGACTTAAGTTCTGAG
Found at i:2093823 original size:5 final size:5
Alignment explanation
Indices: 2093815--2093925 Score: 50
Period size: 5 Copynumber: 22.4 Consensus size: 5
2093805 TAATATTATA
* * * * * * *
2093815 TATTT TATTT TAATT TCTTT TA-CT TATAT TATATA AATTT TAATTT T-TTA
1 TATTT TATTT TATTT TATTT TATTT TATTT TAT-TT TATTT T-ATTT TATTT
* * * * *
2093865 TATTT TATTT TATTT T-TTT AATTTT TATAT TA-TA TATTT TATTT TAATA
1 TATTT TATTT TATTT TATTT TA-TTT TATTT TATTT TATTT TATTT TATTT
*
2093914 TCTTT TATTT TA
1 TATTT TATTT TA
2093926 ATTATAATAT
Statistics
Matches: 74, Mismatches: 25, Indels: 14
0.65 0.22 0.12
Matches are distributed among these distances:
4 11 0.15
5 52 0.70
6 11 0.15
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (5 bp):
TATTT
Found at i:2093871 original size:15 final size:14
Alignment explanation
Indices: 2093851--2093928 Score: 65
Period size: 15 Copynumber: 5.6 Consensus size: 14
2093841 TATTATATAA
2093851 ATTTTAATTTTTTAT
1 ATTTTAATTTTTT-T
2093866 ATTTT-ATTTTATTT
1 ATTTTAATTTT-TTT
*
2093880 -TTTTAATTTTTAT
1 ATTTTAATTTTTTT
* *
2093893 ATTAT-A-TATTTT
1 ATTTTAATTTTTTT
*
2093905 ATTTTAATATCTTTT
1 ATTTTAAT-TTTTTT
2093920 ATTTTAATT
1 ATTTTAATT
2093929 ATAATATTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
12 8 0.16
13 8 0.16
14 15 0.29
15 20 0.39
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (14 bp):
ATTTTAATTTTTTT
Found at i:2093925 original size:34 final size:33
Alignment explanation
Indices: 2093863--2093936 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 33
2093853 TTTAATTTTT
*
2093863 TATATTTTATTTTATTTTTTTAATTTTTATATTA
1 TATATTTTATTTTATTCTTTTAATTTTTA-ATTA
2093897 TATATTTTATTTTAATATCTTTT-A-TTTTAATTA
1 TATATTTTATTTT-AT-TCTTTTAATTTTTAATTA
2093930 TAATATT
1 T-ATATT
2093937 ATAAAATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
33 5 0.14
34 23 0.64
35 3 0.08
36 5 0.14
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (33 bp):
TATATTTTATTTTATTCTTTTAATTTTTAATTA
Found at i:2113129 original size:44 final size:44
Alignment explanation
Indices: 2113066--2113153 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
2113056 AAGAGACAAT
2113066 GAAAGCAGACAGAAGCAACTAAAAAACTATTTCAAGTGCATCTA
1 GAAAGCAGACAGAAGCAACTAAAAAACTATTTCAAGTGCATCTA
*
2113110 GAAAGCAGACAGAAGCAACTAAAAAACTATTTCGAGTGCATCTA
1 GAAAGCAGACAGAAGCAACTAAAAAACTATTTCAAGTGCATCTA
2113154 ATGAGTAGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.47, C:0.18, G:0.17, T:0.18
Consensus pattern (44 bp):
GAAAGCAGACAGAAGCAACTAAAAAACTATTTCAAGTGCATCTA
Found at i:2118216 original size:26 final size:27
Alignment explanation
Indices: 2118185--2118236 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
2118175 AAATATTTAT
*
2118185 TTAATTTAA-AATAAAAATATAAAAAC
1 TTAATTTAACAATAAAAAGATAAAAAC
2118211 TTAATTTAATCAATAAAAAGATAAAA
1 TTAATTTAA-CAATAAAAAGATAAAA
2118237 TTTTATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 9 0.39
28 14 0.61
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (27 bp):
TTAATTTAACAATAAAAAGATAAAAAC
Found at i:2122587 original size:32 final size:33
Alignment explanation
Indices: 2122550--2122614 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
2122540 GATTTTTAAA
2122550 TAAAATGTAAAATGAAT-AAAATATATATGATT
1 TAAAATGTAAAATGAATAAAAATATATATGATT
* * * *
2122582 TAAAATTTTAATTTAATAAAAATATATATGATT
1 TAAAATGTAAAATGAATAAAAATATATATGATT
2122615 CAAATCCTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (33 bp):
TAAAATGTAAAATGAATAAAAATATATATGATT
Found at i:2151116 original size:16 final size:17
Alignment explanation
Indices: 2151097--2151129 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2151087 AAAAACAAAG
*
2151097 AGAAGAATG-AAAGAGA
1 AGAAGAAAGTAAAGAGA
2151113 AGAAGAAAGTAAAGAGA
1 AGAAGAAAGTAAAGAGA
2151130 CATGGGATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.64, C:0.00, G:0.30, T:0.06
Consensus pattern (17 bp):
AGAAGAAAGTAAAGAGA
Found at i:2151127 original size:12 final size:13
Alignment explanation
Indices: 2151093--2151121 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2151083 AAGCAAAAAC
2151093 AAAGAGAAGAATG
1 AAAGAGAAGAATG
2151106 AAAGAGAAGAA-G
1 AAAGAGAAGAATG
2151118 AAAG
1 AAAG
2151122 TAAAGAGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (13 bp):
AAAGAGAAGAATG
Found at i:2170812 original size:26 final size:25
Alignment explanation
Indices: 2170765--2170818 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
2170755 GTATCATTTT
* * *
2170765 TAATTAATAAATTATATTTTTAAAA
1 TAATTAAAAAAATATATATTTAAAA
2170790 TAATTAAAAAAATATTATATTTAAAA
1 TAATTAAAAAAATA-TATATTTAAAA
2170816 TAA
1 TAA
2170819 ATAATTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TAATTAAAAAAATATATATTTAAAA
Found at i:2171177 original size:14 final size:14
Alignment explanation
Indices: 2171166--2171195 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2171156 CATCATATGA
2171166 ATAAATAAATATAT
1 ATAAATAAATATAT
*
2171180 ATATATAAATATAT
1 ATAAATAAATATAT
2171194 AT
1 AT
2171196 GCTTGATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAAATAAATATAT
Found at i:2178495 original size:34 final size:34
Alignment explanation
Indices: 2178457--2178546 Score: 144
Period size: 34 Copynumber: 2.6 Consensus size: 34
2178447 GGCTGCCATC
* * *
2178457 ATTTCAGTTTTCTATAGCATTAGAGGTTGTTTTT
1 ATTTCAGTTTTCTATAGCATTACAGGCTGTCTTT
*
2178491 ATTTCAGTTTTCTATAGCATTACTGGCTGTCTTT
1 ATTTCAGTTTTCTATAGCATTACAGGCTGTCTTT
2178525 ATTTCAGTTTTCTATAGCATTA
1 ATTTCAGTTTTCTATAGCATTA
2178547 TTTGGTTTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 52 1.00
ACGTcount: A:0.21, C:0.13, G:0.14, T:0.51
Consensus pattern (34 bp):
ATTTCAGTTTTCTATAGCATTACAGGCTGTCTTT
Found at i:2187625 original size:2 final size:2
Alignment explanation
Indices: 2187618--2187644 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2187608 TTCATTTTTG
2187618 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
2187645 AAAGGAGNCC
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:2204940 original size:36 final size:36
Alignment explanation
Indices: 2204893--2204965 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
2204883 TGATTTAGCA
*
2204893 GCCAATGTGCTTCCAGCAATGAGCAACCCTAAAGCT
1 GCCAATGTGCTTCCAGCAATGAGCAACACTAAAGCT
2204929 GCCAATGTGCTTCCAGCAATGAGCAACACTAAAGCT
1 GCCAATGTGCTTCCAGCAATGAGCAACACTAAAGCT
2204965 G
1 G
2204966 TCTATACAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.19
Consensus pattern (36 bp):
GCCAATGTGCTTCCAGCAATGAGCAACACTAAAGCT
Found at i:2217068 original size:23 final size:22
Alignment explanation
Indices: 2217017--2217068 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
2217007 TGTTACCTTC
2217017 TTTTT-TTTTAATGATTTTTCT
1 TTTTTCTTTTAATGATTTTTCT
* * *
2217038 TTGGTTCTTTTAATTATTTCTTGT
1 TT-TTTCTTTTAATGATTT-TTCT
2217062 TTTTTCT
1 TTTTTCT
2217069 GCAGATTCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 2 0.08
22 2 0.08
23 15 0.62
24 5 0.21
ACGTcount: A:0.12, C:0.08, G:0.08, T:0.73
Consensus pattern (22 bp):
TTTTTCTTTTAATGATTTTTCT
Found at i:2221766 original size:28 final size:28
Alignment explanation
Indices: 2221677--2221770 Score: 84
Period size: 28 Copynumber: 3.4 Consensus size: 28
2221667 AGTTCGTAAA
* * * *
2221677 TAATAATAATA-TTTTAGATATTAAAATA
1 TAATAATAATATTTTTAAATA-TGACATG
* *
2221705 TAATAA-AATATTTTTAAATATGATATT
1 TAATAATAATATTTTTAAATATGACATG
* * *
2221732 TAGTAATAATATTTTTTAATATGACGTG
1 TAATAATAATATTTTTAAATATGACATG
2221760 TAATAATAATA
1 TAATAATAATA
2221771 CTATTTTTTC
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
27 13 0.24
28 41 0.76
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (28 bp):
TAATAATAATATTTTTAAATATGACATG
Found at i:2221785 original size:32 final size:28
Alignment explanation
Indices: 2221703--2221796 Score: 84
Period size: 31 Copynumber: 3.2 Consensus size: 28
2221693 GATATTAAAA
* *
2221703 TATAATAA-AATATTTTTAAATAT-GATA
1 TATAATAATAATATTTTTTAATATAG-TG
* *
2221730 TTTAGTAATAATATTTTTTAATATGACGTG
1 TATAATAATAATATTTTTTAATAT-A-GTG
*
2221760 TAATAATAATACTATTTTTTCAATATAGTG
1 T-ATAATAATAATATTTTTT-AATATAGTG
2221790 TATAATA
1 TATAATA
2221797 TGTTTTTATA
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
27 6 0.11
28 14 0.26
29 6 0.11
30 6 0.11
31 17 0.31
32 5 0.09
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (28 bp):
TATAATAATAATATTTTTTAATATAGTG
Found at i:2228619 original size:20 final size:21
Alignment explanation
Indices: 2228575--2228620 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
2228565 ATTCAATTTA
*
2228575 TTTAATAAATGTATTAGTGATCG
1 TTTAATAAATGGATTA--GATCG
2228598 TTTAATAAATGGATTA-ATCG
1 TTTAATAAATGGATTAGATCG
2228618 TTT
1 TTT
2228621 TATATCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
23 15 0.68
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (21 bp):
TTTAATAAATGGATTAGATCG
Found at i:2232187 original size:2 final size:2
Alignment explanation
Indices: 2232180--2232205 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2232170 TTAAGTCAAC
2232180 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
2232206 GTGTGTGTAC
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:2240223 original size:8 final size:8
Alignment explanation
Indices: 2240196--2240241 Score: 51
Period size: 7 Copynumber: 5.9 Consensus size: 8
2240186 ATAGCATCTA
2240196 TTTTTACAT
1 TTTTTA-AT
*
2240205 ATTTTAAT
1 TTTTTAAT
2240213 TTTTT-AT
1 TTTTTAAT
2240220 TTTTTAAT
1 TTTTTAAT
*
2240228 TTATT-AT
1 TTTTTAAT
2240235 TTTTTAA
1 TTTTTAA
2240242 CTAATTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
7 13 0.42
8 13 0.42
9 5 0.16
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTTTAAT
Found at i:2240224 original size:15 final size:15
Alignment explanation
Indices: 2240206--2240241 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
2240196 TTTTTACATA
*
2240206 TTTTAATTTTTTATT
1 TTTTAATTTATTATT
2240221 TTTTAATTTATTATT
1 TTTTAATTTATTATT
2240236 TTTTAA
1 TTTTAA
2240242 CTAATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTAATTTATTATT
Found at i:2240278 original size:18 final size:18
Alignment explanation
Indices: 2240225--2240279 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
2240215 TTTATTTTTT
*
2240225 AATTTATTATTT-TTTAACT
1 AATTT-TTATTTATTTAA-A
* *
2240244 AATTTTTATGTA-ATAAA
1 AATTTTTATTTATTTAAA
2240261 AATTTTTATTTATTTAAA
1 AATTTTTATTTATTTAAA
2240279 A
1 A
2240280 TAAAAATTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
17 11 0.38
18 13 0.45
19 5 0.17
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
AATTTTTATTTATTTAAA
Found at i:2240279 original size:17 final size:16
Alignment explanation
Indices: 2240213--2240280 Score: 50
Period size: 17 Copynumber: 4.1 Consensus size: 16
2240203 ATATTTTAAT
2240213 TTTTTATTTTTT--AA
1 TTTTTATTTTTTAAAA
2240227 TTTATTATTTTTTAACTAA
1 TTT-TTATTTTTTAA--AA
** *
2240246 TTTTTATGTAATAAAAA
1 TTTTTAT-TTTTTAAAA
2240263 TTTTTATTTATTTAAAA
1 TTTTTATTT-TTTAAAA
2240280 T
1 T
2240281 AAAAATTTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
14 3 0.07
15 9 0.22
16 1 0.02
17 15 0.37
18 4 0.10
19 9 0.22
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (16 bp):
TTTTTATTTTTTAAAA
Found at i:2240524 original size:18 final size:18
Alignment explanation
Indices: 2240501--2240536 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2240491 ATGAGAATTC
2240501 TATTTATT-TTATTTTATT
1 TATTTATTATT-TTTTATT
2240519 TATTTATTATTTTTTATT
1 TATTTATTATTTTTTATT
2240537 GTTTATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TATTTATTATTTTTTATT
Found at i:2240998 original size:37 final size:37
Alignment explanation
Indices: 2240957--2241035 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 37
2240947 CGCCGGCATC
* **
2240957 CTTCTCTCTCTT-CTTCTTCTTCTTTTTTTCTTTTTCT
1 CTTCTCTCTCTTGCTTCTT-TTCCTTCCTTCTTTTTCT
2240994 CTTCTCTCTCTTGGCTTCTTTTCCTTCCTTCTTTTTCT
1 CTTCTCTCTCTT-GCTTCTTTTCCTTCCTTCTTTTTCT
2241032 -TTCT
1 CTTCT
2241036 TTTTCTCCCT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 16 0.43
38 15 0.41
39 6 0.16
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.66
Consensus pattern (37 bp):
CTTCTCTCTCTTGCTTCTTTTCCTTCCTTCTTTTTCT
Found at i:2241045 original size:102 final size:106
Alignment explanation
Indices: 2240921--2241149 Score: 272
Period size: 102 Copynumber: 2.2 Consensus size: 106
2240911 AAGCTGATTT
* * * * *
2240921 TTTTTCTTTCTTTACTTCTCCCTAGCCGCCGGCATCC-TTCTCTCTCTTCTTCTTCTTCTTTT-T
1 TTTTTCTTTCTTT--TTCTCCCTAACCGCAGGCACCCTTTCTCTCTCTT-TT-TCCTCCTTTTCT
2240984 TTCTTTTTCTCTTCTCTCTCTTGGCTT-CT-TTTC-C-TTCCTTC
62 TTCTTTTTCTCTTCTCTCTCTTGGCTTCCTCTTTCTCTTTCCTTC
* *
2241025 TTTTTCTTTCTTTTTCTCCCTAACCGCAGGCCCCCTTTTTCTCTCTTTTTCCTCCTTTTCTTTCT
1 TTTTTCTTTCTTTTTCTCCCTAACCGCAGGCACCCTTTCTCTCTCTTTTTCCTCCTTTTCTTTCT
* * * *
2241090 TTTTTTCTTTTCTTTCTTGGCTTCCTCTTTCTCTTTTTCTTC
66 TTTTCTCTTCTCTCTCTTGGCTTCCTCTTTCTC-TTTCCTTC
2241132 TTTTTCTTTCTTTTTCTC
1 TTTTTCTTTCTTTTTCTC
2241150 TTCTCTCTCT
Statistics
Matches: 107, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
101 8 0.07
102 45 0.42
103 12 0.11
104 17 0.16
105 1 0.01
107 24 0.22
ACGTcount: A:0.03, C:0.32, G:0.05, T:0.60
Consensus pattern (106 bp):
TTTTTCTTTCTTTTTCTCCCTAACCGCAGGCACCCTTTCTCTCTCTTTTTCCTCCTTTTCTTTCT
TTTTCTCTTCTCTCTCTTGGCTTCCTCTTTCTCTTTCCTTC
Found at i:2241091 original size:9 final size:9
Alignment explanation
Indices: 2241079--2241145 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
2241069 CTTTTTCCTC
2241079 CTTTTCTTT
1 CTTTTCTTT
2241088 CTTTT-TTT
1 CTTTTCTTT
2241096 CTTTTCTTT
1 CTTTTCTTT
** *
2241105 CTTGGCTTC
1 CTTTTCTTT
*
2241114 CTCTTTCTCT
1 CT-TTTCTTT
2241124 -TTTTC-TT
1 CTTTTCTTT
2241131 CTTTTTCTTT
1 C-TTTTCTTT
2241141 CTTTT
1 CTTTT
2241146 TCTCTTCTCT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
7 1 0.02
8 12 0.27
9 26 0.58
10 6 0.13
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.73
Consensus pattern (9 bp):
CTTTTCTTT
Found at i:2241133 original size:15 final size:16
Alignment explanation
Indices: 2241093--2241160 Score: 52
Period size: 15 Copynumber: 4.4 Consensus size: 16
2241083 TCTTTCTTTT
2241093 TTTCTT-TTCTTTCT-
1 TTTCTTCTTCTTTCTC
** *
2241107 TGGCTTCCTCTTTCTC
1 TTTCTTCTTCTTTCTC
*
2241123 TTT-TTCTTCTTTTTC
1 TTTCTTCTTCTTTCTC
*
2241138 TTTCTTTTTCTCTTCTC
1 TTTCTTCTTCT-TTCTC
*
2241155 TCTCTT
1 TTTCTT
2241161 GGCTTCTCGC
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
14 4 0.10
15 20 0.50
16 7 0.17
17 9 0.22
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTCTTCTTCTTTCTC
Found at i:2241138 original size:53 final size:53
Alignment explanation
Indices: 2241066--2241166 Score: 157
Period size: 53 Copynumber: 1.9 Consensus size: 53
2241056 CCCCTTTTTC
* * *
2241066 TCTCTTTTTCCTCCTTTTCTTTCTTTTTTTCTTTTCTTTCTTGGCTTCCTCTT
1 TCTCTTTTTCCTCCTTTTCTTTCTTTTTCTCTTCTCTCTCTTGGCTTCCTCTT
* *
2241119 TCTCTTTTTCTTCTTTTTCTTTCTTTTTCTCTTCTCTCTCTTGGCTTC
1 TCTCTTTTTCCTCCTTTTCTTTCTTTTTCTCTTCTCTCTCTTGGCTTC
2241167 TCGCCCTTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.00, C:0.29, G:0.04, T:0.67
Consensus pattern (53 bp):
TCTCTTTTTCCTCCTTTTCTTTCTTTTTCTCTTCTCTCTCTTGGCTTCCTCTT
Found at i:2241139 original size:21 final size:21
Alignment explanation
Indices: 2241059--2241153 Score: 65
Period size: 21 Copynumber: 4.5 Consensus size: 21
2241049 CGCAGGCCCC
* *
2241059 CTTTTTCTCTCTTTTTCCTCCT
1 CTTTTTCT-TCTTTTTCTTTCT
*
2241081 TTTCTTTCTT-TTTTTCTTT-T
1 CTT-TTTCTTCTTTTTCTTTCT
**
2241101 C--TTTCTTGGCTTCCTCTTTCT
1 CTTTTTCTT--CTTTTTCTTTCT
2241122 CTTTTTCTTCTTTTTCTTTCT
1 CTTTTTCTTCTTTTTCTTTCT
2241143 -TTTTCTCTTCT
1 CTTTT-TCTTCT
2241154 CTCTCTTGGC
Statistics
Matches: 57, Mismatches: 8, Indels: 17
0.70 0.10 0.21
Matches are distributed among these distances:
17 6 0.11
20 12 0.21
21 25 0.44
22 3 0.05
23 11 0.19
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (21 bp):
CTTTTTCTTCTTTTTCTTTCT
Found at i:2241160 original size:21 final size:21
Alignment explanation
Indices: 2241114--2241160 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2241104 TCTTGGCTTC
*
2241114 CTCTTTCTCTTTTTCTTCTTT
1 CTCTTTCTCTTTTTCTTCTCT
*
2241135 TTCTTTCT-TTTTCTCTTCTCT
1 CTCTTTCTCTTTT-TCTTCTCT
2241156 CTCTT
1 CTCTT
2241161 GGCTTCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (21 bp):
CTCTTTCTCTTTTTCTTCTCT
Done.