Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold181
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: 2212501
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 130279 characters in sequence are not A, C, G, or T
File 5 of 6
Found at i:1515799 original size:10 final size:10
Alignment explanation
Indices: 1515786--1515831 Score: 67
Period size: 10 Copynumber: 4.7 Consensus size: 10
1515776 AAAAAATTTG
1515786 AAAAAAAATC
1 AAAAAAAATC
1515796 AAAAAAAATC
1 AAAAAAAATC
1515806 -AAAAAAATC
1 AAAAAAAATC
* *
1515815 AAAAAAATTG
1 AAAAAAAATC
1515825 AAAAAAA
1 AAAAAAA
1515832 GAAAAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
9 9 0.27
10 24 0.73
ACGTcount: A:0.80, C:0.07, G:0.02, T:0.11
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:1515809 original size:19 final size:19
Alignment explanation
Indices: 1515787--1515831 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1515777 AAAAATTTGA
1515787 AAAAAAATCAAAAAAAATC
1 AAAAAAATCAAAAAAAATC
* *
1515806 AAAAAAATCAAAAAAATTG
1 AAAAAAATCAAAAAAAATC
1515825 AAAAAAA
1 AAAAAAA
1515832 GAAAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.80, C:0.07, G:0.02, T:0.11
Consensus pattern (19 bp):
AAAAAAATCAAAAAAAATC
Found at i:1534956 original size:23 final size:23
Alignment explanation
Indices: 1534928--1535018 Score: 110
Period size: 23 Copynumber: 4.0 Consensus size: 23
1534918 GGGTTTGTTA
**
1534928 CGAAATGGTAATGTGATTTGGTT
1 CGAAATGGTAATACGATTTGGTT
* *
1534951 CAAAATGGTAATACGATTTGGTA
1 CGAAATGGTAATACGATTTGGTT
* ***
1534974 CGAATTGGTAAGGTGATTTGGTT
1 CGAAATGGTAATACGATTTGGTT
1534997 CGAAATGGTAATACGATTTGGT
1 CGAAATGGTAATACGATTTGGT
1535019 ACCGGAAAGA
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.30, C:0.07, G:0.29, T:0.35
Consensus pattern (23 bp):
CGAAATGGTAATACGATTTGGTT
Found at i:1534983 original size:46 final size:46
Alignment explanation
Indices: 1534921--1535020 Score: 164
Period size: 46 Copynumber: 2.2 Consensus size: 46
1534911 CGGTTTTGGG
* *
1534921 TTTGTTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAAGGTGATTTGGTTCAAAATGGTAATACGA
* *
1534967 TTTGGTACGAATTGGTAAGGTGATTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAAGGTGATTTGGTTCAAAATGGTAATACGA
1535013 TTTGGTAC
1 TTTGGTAC
1535021 CGGAAAGACG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.29, C:0.07, G:0.27, T:0.37
Consensus pattern (46 bp):
TTTGGTACGAAATGGTAAGGTGATTTGGTTCAAAATGGTAATACGA
Found at i:1536732 original size:17 final size:17
Alignment explanation
Indices: 1536710--1536742 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1536700 GTTAATGCAC
*
1536710 ATTGTCGTTGCATTTTT
1 ATTGTCATTGCATTTTT
1536727 ATTGTCATTGCATTTT
1 ATTGTCATTGCATTTT
1536743 AATGTTACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (17 bp):
ATTGTCATTGCATTTTT
Found at i:1542199 original size:25 final size:26
Alignment explanation
Indices: 1542171--1542220 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
1542161 AAGAGGATAG
1542171 TTTAAAGAACATAAAA-GAAAAAAAA
1 TTTAAAGAACATAAAACGAAAAAAAA
** *
1542196 TTTAAATTACTTAAAACGAAAAAAA
1 TTTAAAGAACATAAAACGAAAAAAA
1542221 TATGGGGATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.22
Consensus pattern (26 bp):
TTTAAAGAACATAAAACGAAAAAAAA
Found at i:1543161 original size:101 final size:102
Alignment explanation
Indices: 1543040--1543224 Score: 302
Period size: 101 Copynumber: 1.8 Consensus size: 102
1543030 AAAGTGATGG
*
1543040 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAAAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACC-AAATGATAATGGTCACATGTGTAGT
1543103 ACTATGTGCAGGCTACTATGCGTACCGGAGAGTTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGAGAGTTTCGA
* * * *
1543141 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATGGTAATTGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAAATGATAATGGTCACATGTGTAGTA
1543206 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
1543225 TGAACCGAGC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
100 5 0.06
101 39 0.51
102 33 0.43
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAAATGATAATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGAGAGTTTCGA
Found at i:1543170 original size:51 final size:49
Alignment explanation
Indices: 1543039--1543233 Score: 198
Period size: 51 Copynumber: 3.9 Consensus size: 49
1543029 GAAAGTGATG
* * * *
1543039 GTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACC-AAAATGATAG
1 GTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAGAGT-AT-T
* * *
1543089 GTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAGAGT-TT
1 GTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAGAGTATT
* *
1543138 CGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGA-ATGGTAATT
1 -G-TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAGA--GT-ATT
* *
1543191 GTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCGAG
1 GTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAG
1543234 CATCATTGAT
Statistics
Matches: 120, Mismatches: 16, Indels: 16
0.79 0.11 0.11
Matches are distributed among these distances:
49 1 0.01
50 40 0.33
51 73 0.61
52 4 0.03
53 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30
Consensus pattern (49 bp):
GTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAGAGTATT
Found at i:1554493 original size:21 final size:19
Alignment explanation
Indices: 1554443--1554485 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1554433 GATCTAAATG
1554443 AATAAATTCAATTCAATTC
1 AATAAATTCAATTCAATTC
*
1554462 AATAATTATTCTATTCAATTC
1 AATAA--ATTCAATTCAATTC
1554483 AAT
1 AAT
1554486 CCAAATTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
21 16 0.76
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (19 bp):
AATAAATTCAATTCAATTC
Found at i:1569410 original size:64 final size:64
Alignment explanation
Indices: 1569283--1569411 Score: 177
Period size: 64 Copynumber: 2.0 Consensus size: 64
1569273 ACAGCATTCT
* * * * * * *
1569283 GATCAGTATTGATCCTGCATGTGTTGCGGATATACCGTAGCTCTTTGTGAGCATCTTGTTATAG
1 GATCAGTATTGATCCTGCATATATTGCGGACATACCGCAGCTCTTTATGAGCATCCTGATATAG
* *
1569347 GATCGGTATTGATCCTGCATATATTGCGGACATACCGCAGCTCTTTATGAGCGTCCTGATATAG
1 GATCAGTATTGATCCTGCATATATTGCGGACATACCGCAGCTCTTTATGAGCATCCTGATATAG
1569411 G
1 G
1569412 CTCTTTGAGA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (64 bp):
GATCAGTATTGATCCTGCATATATTGCGGACATACCGCAGCTCTTTATGAGCATCCTGATATAG
Found at i:1569423 original size:25 final size:25
Alignment explanation
Indices: 1569386--1569433 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1569376 ACATACCGCA
1569386 GCTCTTTATGAGCGTCCTGATATAG
1 GCTCTTTATGAGCGTCCTGATATAG
*
1569411 GCTCTTTGA-GAGCTTCCTGATAT
1 GCTCTTT-ATGAGCGTCCTGATAT
1569434 GACTCGCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.38
Consensus pattern (25 bp):
GCTCTTTATGAGCGTCCTGATATAG
Found at i:1571365 original size:27 final size:27
Alignment explanation
Indices: 1571334--1571395 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
1571324 GTGCTCACTC
1571334 GAGCTGTGAAAATGGGCCTACTCACAG
1 GAGCTGTGAAAATGGGCCTACTCACAG
* * *
1571361 GAGCTATGAAAATGGGCCTGCTCACAT
1 GAGCTGTGAAAATGGGCCTACTCACAG
1571388 GAGCTGTG
1 GAGCTGTG
1571396 GGTCAAAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (27 bp):
GAGCTGTGAAAATGGGCCTACTCACAG
Found at i:1574285 original size:27 final size:27
Alignment explanation
Indices: 1574254--1574314 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
1574244 TCTTCTCCTA
*
1574254 AGGGTATAACAGTCATTTTACCCTGTG
1 AGGGTATAACAGTCATTTTACCCTATG
* ** * *
1574281 GGGGTATTTCGGTCATTTTATCCTATG
1 AGGGTATAACAGTCATTTTACCCTATG
1574308 AGGGTAT
1 AGGGTAT
1574315 TTTAGAGCAG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (27 bp):
AGGGTATAACAGTCATTTTACCCTATG
Found at i:1574315 original size:27 final size:27
Alignment explanation
Indices: 1574265--1574316 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1574255 GGGTATAACA
* *
1574265 GTCATTTTACCCTGTGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
*
1574292 GTCATTTTATCCTATGAGGGTATTT
1 GTCATTTTACCCTATGAGGGTATTT
1574317 TAGAGCAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.15, C:0.15, G:0.25, T:0.44
Consensus pattern (27 bp):
GTCATTTTACCCTATGAGGGTATTTCG
Found at i:1576239 original size:26 final size:26
Alignment explanation
Indices: 1576210--1576295 Score: 102
Period size: 26 Copynumber: 3.3 Consensus size: 26
1576200 CCCCAATTTT
*
1576210 CTAGGCCCACTGGCTATCCCTA-TTCG
1 CTAGGCCCACTGGCTAT-CCTAGCTCG
* * *
1576236 CTAGGCCCATTGGCGATCTTAGCTCG
1 CTAGGCCCACTGGCTATCCTAGCTCG
* *
1576262 CTAGGCCTACTGGTTATCCTAGCTCG
1 CTAGGCCCACTGGCTATCCTAGCTCG
1576288 CTAGGCCC
1 CTAGGCCC
1576296 CAAACTCTTA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
25 3 0.06
26 46 0.94
ACGTcount: A:0.15, C:0.35, G:0.23, T:0.27
Consensus pattern (26 bp):
CTAGGCCCACTGGCTATCCTAGCTCG
Found at i:1578129 original size:27 final size:27
Alignment explanation
Indices: 1578076--1578130 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1578066 AACACTAAAT
* *
1578076 GGATAGGATGTGTGGAGAATACTGAAG
1 GGATAGGATGTATGGAGAATACAGAAG
*
1578103 GGATAGGATGTATGGTGAACT-CAGAAG
1 GGATAGGATGTATGGAGAA-TACAGAAG
1578130 G
1 G
1578131 AACATTAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.33, C:0.05, G:0.40, T:0.22
Consensus pattern (27 bp):
GGATAGGATGTATGGAGAATACAGAAG
Found at i:1581033 original size:149 final size:150
Alignment explanation
Indices: 1580762--1581061 Score: 494
Period size: 149 Copynumber: 2.0 Consensus size: 150
1580752 TAAAAATATC
* * *
1580762 AAAGAAGCATTAAATGATGAATATTTGATATTGTCTATGCAAGAAGAGTTAAATCAATTTGAGAG
1 AAAGAAGCATTAAATGATGAATATTGGATATTGGCTATGCAAGAAGAGTTAAATCAATATGAGAG
*
1580827 AAGTAAAGTATGGACCATAGTTGAAAGATCTAGTGACAAATCTACTATAGGTACTAAGTGGGTTT
66 AAGTAAAGTATGGACCATAGTTGAAAGATCTAGTGAAAAATCTACTATAGGTACTAAGTGGGTTT
1580892 TTACCAATAAGCTAGATGAG
131 TTACCAATAAGCTAGATGAG
* * *
1580912 AAAGAAGCATTGAATGATGAATATTGGA-ATTGGCTATGTAAGTAGAGTTAAATCAATATGAGAG
1 AAAGAAGCATTAAATGATGAATATTGGATATTGGCTATGCAAGAAGAGTTAAATCAATATGAGAG
* *
1580976 AAGTAAAGTATGGACTATAGTTGAAAGATCTAGTGAAAAATCTACTGTAGGTACTAAGTGGGTTT
66 AAGTAAAGTATGGACCATAGTTGAAAGATCTAGTGAAAAATCTACTATAGGTACTAAGTGGGTTT
**
1581041 TTAGGAATAAGCTAGATGAG
131 TTACCAATAAGCTAGATGAG
1581061 A
1 A
1581062 GTGGTAACAT
Statistics
Matches: 139, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
149 113 0.81
150 26 0.19
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (150 bp):
AAAGAAGCATTAAATGATGAATATTGGATATTGGCTATGCAAGAAGAGTTAAATCAATATGAGAG
AAGTAAAGTATGGACCATAGTTGAAAGATCTAGTGAAAAATCTACTATAGGTACTAAGTGGGTTT
TTACCAATAAGCTAGATGAG
Found at i:1589609 original size:21 final size:21
Alignment explanation
Indices: 1589583--1589645 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
1589573 TTGGTATTTG
1589583 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
1589604 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
1589625 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
1589646 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:1594698 original size:19 final size:19
Alignment explanation
Indices: 1594677--1594713 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1594667 TTTTCAATTT
1594677 TTTTG-ATTTTTTTTTCGA
1 TTTTGAATTTTTTTTTCGA
1594695 TTTTGAATTTTTTTTTCGA
1 TTTTGAATTTTTTTTTCGA
1594714 ACTCTCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.14, C:0.05, G:0.11, T:0.70
Consensus pattern (19 bp):
TTTTGAATTTTTTTTTCGA
Found at i:1596858 original size:10 final size:10
Alignment explanation
Indices: 1596843--1596891 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
1596833 ACGAGCTCAA
1596843 TGAGCTGAAT
1 TGAGCTGAAT
1596853 TGAGCTCGAA-
1 TGAGCT-GAAT
*
1596863 TGAGCTGACT
1 TGAGCTGAAT
* *
1596873 TGAGCTCAAG
1 TGAGCTGAAT
1596883 TGAGCTGAA
1 TGAGCTGAA
1596892 CCAAGGACGT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 27 0.84
11 3 0.09
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (10 bp):
TGAGCTGAAT
Found at i:1596864 original size:20 final size:19
Alignment explanation
Indices: 1596835--1596891 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 19
1596825 AGCTAATAAC
1596835 GAGCTCAATGAGCTGAATT
1 GAGCTCAATGAGCTGAATT
*
1596854 GAGCTCGAATGAGCTGACTT
1 GAGCTC-AATGAGCTGAATT
1596874 GAGCTCAAGTGAGCTGAA
1 GAGCTCAA-TGAGCTGAA
1596892 CCAAGGACGT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 8 0.24
20 26 0.76
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.23
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:1599774 original size:12 final size:12
Alignment explanation
Indices: 1599757--1599856 Score: 86
Period size: 12 Copynumber: 8.8 Consensus size: 12
1599747 ACTTTCCTCT
*
1599757 TTTTCTTCTTCA
1 TTTTCTTTTTCA
1599769 TTTTCTTTTTC-
1 TTTTCTTTTTCA
1599780 TTTTC--TTTCA
1 TTTTCTTTTTCA
* *
1599790 ATTTCTCTTTCA
1 TTTTCTTTTTCA
* *
1599802 TTCTCTTTTTCT
1 TTTTCTTTTTCA
1599814 TTTTCTTTTTC-
1 TTTTCTTTTTCA
1599825 TTTTC-TTTT-A
1 TTTTCTTTTTCA
*
1599835 ATTTCTTTTTCAA
1 TTTTCTTTTTC-A
*
1599848 TGTTCTTTT
1 TTTTCTTTT
1599857 CTCGCTCACA
Statistics
Matches: 71, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
9 4 0.06
10 12 0.17
11 14 0.20
12 33 0.46
13 8 0.11
ACGTcount: A:0.08, C:0.19, G:0.01, T:0.72
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:1599828 original size:45 final size:45
Alignment explanation
Indices: 1599760--1599846 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
1599750 TTCCTCTTTT
1599760 TCTTCTTCATTTTCTTTTTCTTTTCTTTCAATTTCTCTTTCATTC
1 TCTTCTTCATTTTCTTTTTCTTTTCTTTCAATTTCTCTTTCATTC
* * * *
1599805 TCTTTTTCTTTTTCTTTTTCTTTTCTTTTAATTTCTTTTTCA
1 TCTTCTTCATTTTCTTTTTCTTTTCTTTCAATTTCTCTTTCA
1599847 ATGTTCTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (45 bp):
TCTTCTTCATTTTCTTTTTCTTTTCTTTCAATTTCTCTTTCATTC
Found at i:1599845 original size:6 final size:6
Alignment explanation
Indices: 1599754--1599833 Score: 69
Period size: 6 Copynumber: 14.0 Consensus size: 6
1599744 CTTACTTTCC
* * ** *
1599754 TCTTTT TCTTCT TCATTT TCTTTT TC-TTT TC--TT TCAATT TCTCTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
* *
1599799 TCATTC TCTTTT TCTTTT TCTTTT TC-TTT TCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
1599834 AATTTCTTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
4 4 0.07
5 10 0.17
6 46 0.77
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (6 bp):
TCTTTT
Found at i:1599857 original size:45 final size:43
Alignment explanation
Indices: 1599758--1599858 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 43
1599748 CTTTCCTCTT
*
1599758 TTTCTTCTTCATTTTCTTTTTCTTTTCTTTCAATTTCTCTTTCA
1 TTTCTT-TTCTTTTTCTTTTTCTTTTCTTTCAATTTCTCTTTCA
* *
1599802 TTCTCTTTTTCTTTTTCTTTTTCTTTTCTTTTAATTTCTTTTTCAA
1 TT-TC-TTTTCTTTTTCTTTTTCTTTTCTTTCAATTTCTCTTTC-A
1599848 TGTTCTTTTCT
1 T-TTCTTTTCT
1599859 CGCTCACATT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
44 2 0.04
45 41 0.82
46 6 0.12
47 1 0.02
ACGTcount: A:0.08, C:0.20, G:0.01, T:0.71
Consensus pattern (43 bp):
TTTCTTTTCTTTTTCTTTTTCTTTTCTTTCAATTTCTCTTTCA
Found at i:1602403 original size:20 final size:20
Alignment explanation
Indices: 1602380--1602489 Score: 161
Period size: 20 Copynumber: 5.5 Consensus size: 20
1602370 TAACGAGCCT
* * *
1602380 AATGAGCTTAATTAAGCTCG
1 AATGAGCTGACTTGAGCTCG
1602400 AATGAGCTGACTTCG-GCTCG
1 AATGAGCTGACTT-GAGCTCG
1602420 AATGAGCTGACTTGAGCTCG
1 AATGAGCTGACTTGAGCTCG
1602440 AATGAGCTGACTTGAGCTCG
1 AATGAGCTGACTTGAGCTCG
1602460 AATGAGCTGACTTGAGCTC-
1 AATGAGCTGACTTGAGCTCG
1602479 AAGTGAGCTGA
1 AA-TGAGCTGA
1602490 ACCAAGGATG
Statistics
Matches: 84, Mismatches: 3, Indels: 6
0.90 0.03 0.06
Matches are distributed among these distances:
19 3 0.04
20 81 0.96
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (20 bp):
AATGAGCTGACTTGAGCTCG
Found at i:1602407 original size:10 final size:10
Alignment explanation
Indices: 1602394--1602467 Score: 57
Period size: 10 Copynumber: 7.4 Consensus size: 10
1602384 AGCTTAATTA
1602394 AGCTCGAATG
1 AGCTCGAATG
*
1602404 AGCT-GACTTCG
1 AGCTCGA-AT-G
1602415 -GCTCGAATG
1 AGCTCGAATG
*
1602424 AGCT-GACTTG
1 AGCTCGA-ATG
1602434 AGCTCGAATG
1 AGCTCGAATG
*
1602444 AGCT-GACTTG
1 AGCTCGA-ATG
1602454 AGCTCGAATG
1 AGCTCGAATG
1602464 AGCT
1 AGCT
1602468 GACTTGAGCT
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
9 7 0.14
10 36 0.72
11 7 0.14
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (10 bp):
AGCTCGAATG
Found at i:1602475 original size:10 final size:10
Alignment explanation
Indices: 1602422--1602477 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
1602412 TCGGCTCGAA
1602422 TGAGCTGACT
1 TGAGCTGACT
*
1602432 TGAGCTCGA-A
1 TGAGCT-GACT
1602442 TGAGCTGACT
1 TGAGCTGACT
*
1602452 TGAGCTCGA-A
1 TGAGCT-GACT
1602462 TGAGCTGACT
1 TGAGCTGACT
1602472 TGAGCT
1 TGAGCT
1602478 CAAGTGAGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 4 0.11
10 30 0.79
11 4 0.11
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (10 bp):
TGAGCTGACT
Found at i:1604031 original size:35 final size:35
Alignment explanation
Indices: 1603965--1604032 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
1603955 TTTAACATAG
* * *
1603965 TGGCATGCTTAACATGCGAATCAAAATCAGAATTA
1 TGGCACGCTTAACATGCAAATCAAAAGCAGAATTA
* * *
1604000 TGGCACGCTTAATATGCAAATCACAGGCAGAAT
1 TGGCACGCTTAACATGCAAATCAAAAGCAGAAT
1604033 GGTAGCATAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (35 bp):
TGGCACGCTTAACATGCAAATCAAAAGCAGAATTA
Found at i:1616098 original size:29 final size:29
Alignment explanation
Indices: 1616056--1616147 Score: 148
Period size: 29 Copynumber: 3.2 Consensus size: 29
1616046 TATCGACAAT
* **
1616056 CATCAAATATGAAAAGGGATGGTGACGAC
1 CATCGAATATGAAAAGGGATGGTTTCGAC
*
1616085 CATCGAATATGAAAAGGGATGGTTTCAAC
1 CATCGAATATGAAAAGGGATGGTTTCGAC
1616114 CATCGAATATGAAAAGGGATGGTTTCGAC
1 CATCGAATATGAAAAGGGATGGTTTCGAC
1616143 CATCG
1 CATCG
1616148 TTTAGCACAC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (29 bp):
CATCGAATATGAAAAGGGATGGTTTCGAC
Found at i:1630322 original size:29 final size:29
Alignment explanation
Indices: 1630273--1630339 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
1630263 ATTGACAAAT
* *
1630273 GAAAAGGGATAGCTTCAGCTATCGAA-TAC
1 GAAAAGGGATAACTTCAGCTA-CCAACTAC
** *
1630302 GAAAAGGGATAACTTTGGCTACCAACTAT
1 GAAAAGGGATAACTTCAGCTACCAACTAC
1630331 GAAAAGGGA
1 GAAAAGGGA
1630340 AGGTGACGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.09
29 29 0.91
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.19
Consensus pattern (29 bp):
GAAAAGGGATAACTTCAGCTACCAACTAC
Found at i:1630388 original size:30 final size:30
Alignment explanation
Indices: 1630271--1630506 Score: 133
Period size: 30 Copynumber: 7.9 Consensus size: 30
1630261 TCATTGACAA
* *
1630271 ATGAAAAGGGATAGCTTCAGCTATCGAA-T
1 ATGAAAAGGGATGGCTTCAGCTATCAAACT
* ** ** *
1630300 ACGAAAAGGGATAACTTTGGCTA-CCAACT
1 ATGAAAAGGGATGGCTTCAGCTATCAAACT
* * *
1630329 ATGAAAAGGGAAGG--TGACGACCATCAAACT
1 ATGAAAAGGGATGGCTTCA-G-CTATCAAACT
* *
1630359 ACGAAAAGGGATGGCTTCAGCTATTAAACT
1 ATGAAAAGGGATGGCTTCAGCTATCAAACT
* * * * *
1630389 ATGAAAAGGGTTAGCTTCGGCTATCAGATT
1 ATGAAAAGGGATGGCTTCAGCTATCAAACT
* * * *
1630419 ATGAAAAGGGATGG--TGACGACCATTAAATT
1 ATGAAAAGGGATGGCTTCA-G-CTATCAAACT
* * * *
1630449 ATGAAAAGGGATAGCTTCGGCTGTCGAACT
1 ATGAAAAGGGATGGCTTCAGCTATCAAACT
** *
1630479 ATGAAAAGGGATAACTTCAGTTATCAAA
1 ATGAAAAGGGATGGCTTCAGCTATCAAA
1630507 TTACAAAAAA
Statistics
Matches: 152, Mismatches: 45, Indels: 19
0.70 0.21 0.09
Matches are distributed among these distances:
27 1 0.01
28 5 0.03
29 33 0.22
30 108 0.71
31 2 0.01
32 3 0.02
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23
Consensus pattern (30 bp):
ATGAAAAGGGATGGCTTCAGCTATCAAACT
Found at i:1630509 original size:60 final size:60
Alignment explanation
Indices: 1630271--1630506 Score: 178
Period size: 60 Copynumber: 4.0 Consensus size: 60
1630261 TCATTGACAA
* ** *
1630271 ATGAAAAGGGATAGCTTCAGCTATCGAA-TACGAAAAGGGATAACTTTGGCTA-CCAACT
1 ATGAAAAGGGATAGCTTCGGCTATCGAACTACGAAAAGGGATAACTTCAGCTATCAAACT
* * * * * ** *
1630329 ATGAAAAGGGA-AGGTGACGACCATCAAACTACGAAAAGGGATGGCTTCAGCTATTAAACT
1 ATGAAAAGGGATAGCT-TCGGCTATCGAACTACGAAAAGGGATAACTTCAGCTATCAAACT
* * * ** * * * *
1630389 ATGAAAAGGGTTAGCTTCGGCTATC-AGATTATGAAAAGGGAT--GGTGACGACCATTAAATT
1 ATGAAAAGGGATAGCTTCGGCTATCGA-ACTACGAAAAGGGATAACTTCA-G-CTATCAAACT
* * *
1630449 ATGAAAAGGGATAGCTTCGGCTGTCGAACTATGAAAAGGGATAACTTCAGTTATCAAA
1 ATGAAAAGGGATAGCTTCGGCTATCGAACTACGAAAAGGGATAACTTCAGCTATCAAA
1630507 TTACAAAAAA
Statistics
Matches: 135, Mismatches: 33, Indels: 18
0.73 0.18 0.10
Matches are distributed among these distances:
57 3 0.02
58 20 0.15
59 22 0.16
60 83 0.61
61 5 0.04
62 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23
Consensus pattern (60 bp):
ATGAAAAGGGATAGCTTCGGCTATCGAACTACGAAAAGGGATAACTTCAGCTATCAAACT
Found at i:1630522 original size:90 final size:90
Alignment explanation
Indices: 1630271--1630509 Score: 302
Period size: 90 Copynumber: 2.7 Consensus size: 90
1630261 TCATTGACAA
* * * *
1630271 ATGAAAAGGGATAGCTTCAGCTATCGAA-TACGAAAAGGGATAACTTTGGCTA-CCAACTATGAA
1 ATGAAAAGGGATAGCTTCAGCTATCGAACTATGAAAAGGGATAACTTCGGCTATCAAATTATGAA
*
1630334 AAGGGAAGGTGACGACCATCAAACT
66 AAGGGATGGTGACGACCATCAAACT
* * ** * * *
1630359 ACGAAAAGGGATGGCTTCAGCTATTAAACTATGAAAAGGGTTAGCTTCGGCTATCAGATTATGAA
1 ATGAAAAGGGATAGCTTCAGCTATCGAACTATGAAAAGGGATAACTTCGGCTATCAAATTATGAA
* *
1630424 AAGGGATGGTGACGACCATTAAATT
66 AAGGGATGGTGACGACCATCAAACT
* * * *
1630449 ATGAAAAGGGATAGCTTCGGCTGTCGAACTATGAAAAGGGATAACTTCAGTTATCAAATTA
1 ATGAAAAGGGATAGCTTCAGCTATCGAACTATGAAAAGGGATAACTTCGGCTATCAAATTA
1630510 CAAAAAAGGA
Statistics
Matches: 124, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
88 24 0.19
89 20 0.16
90 80 0.65
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (90 bp):
ATGAAAAGGGATAGCTTCAGCTATCGAACTATGAAAAGGGATAACTTCGGCTATCAAATTATGAA
AAGGGATGGTGACGACCATCAAACT
Found at i:1635643 original size:24 final size:23
Alignment explanation
Indices: 1635603--1635647 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1635593 TTTCTTTGAT
*
1635603 AAATTATTTTGATATAACAAATAA
1 AAATTATTTTGAAATAA-AAATAA
*
1635627 AAATTATTTTTAAATAAAAAT
1 AAATTATTTTGAAATAAAAAT
1635648 TTCTTTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATTATTTTGAAATAAAAATAA
Found at i:1644037 original size:20 final size:20
Alignment explanation
Indices: 1644012--1644051 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1644002 ATATGCCCGC
1644012 TAGGAAGAGCAGAAAAACTA
1 TAGGAAGAGCAGAAAAACTA
1644032 TAGGAAGAGCAGAAAAACTA
1 TAGGAAGAGCAGAAAAACTA
1644052 ACGTGCAAGA
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:0.55, C:0.10, G:0.25, T:0.10
Consensus pattern (20 bp):
TAGGAAGAGCAGAAAAACTA
Found at i:1650013 original size:25 final size:26
Alignment explanation
Indices: 1649982--1650042 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
1649972 TTAATATGTG
1649982 ATTATATTATGATTA-TAT-CAATAT
1 ATTATATTATGATTAGTATGCAATAT
*
1650006 A-TATATATATG-TTAGTATGCAATTT
1 ATTATAT-TATGATTAGTATGCAATAT
*
1650031 ATTGTATTATGA
1 ATTATATTATGA
1650043 AATGACGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
23 8 0.27
24 8 0.27
25 10 0.33
26 4 0.13
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (26 bp):
ATTATATTATGATTAGTATGCAATAT
Found at i:1650169 original size:25 final size:25
Alignment explanation
Indices: 1650141--1650234 Score: 86
Period size: 25 Copynumber: 3.8 Consensus size: 25
1650131 TTATCAATTC
1650141 TCAGCTCG-AGAGAGCTTACCAATAT
1 TCAGCTCGTA-AGAGCTTACCAATAT
* * *
1650166 TCAGCTTGTATGAGCTTACCGATAT
1 TCAGCTCGTAAGAGCTTACCAATAT
* *
1650191 TCAGCTTGTATGAGCTTACC-AT-T
1 TCAGCTCGTAAGAGCTTACCAATAT
* *
1650214 TACAACTCGTAAGAGCATACC
1 T-CAGCTCGTAAGAGCTTACC
1650235 GATTCAGAGC
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.03
24 17 0.28
25 40 0.67
26 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (25 bp):
TCAGCTCGTAAGAGCTTACCAATAT
Found at i:1650254 original size:25 final size:24
Alignment explanation
Indices: 1650164--1650258 Score: 72
Period size: 25 Copynumber: 3.9 Consensus size: 24
1650154 GCTTACCAAT
* *
1650164 ATTC-AGCTTGTATGAGCTTACCG
1 ATTCAAGCTCGTATGAGCATACCG
* *
1650187 ATATTC-AGCTTGTATGAGCTTACC-
1 --ATTCAAGCTCGTATGAGCATACCG
*
1650211 ATTTACAA-CTCGTAAGAGCATACCG
1 A-TT-CAAGCTCGTATGAGCATACCG
1650236 ATTCAGAGCTCGTATGAGCATAC
1 ATTCA-AGCTCGTATGAGCATAC
1650259 ATGTACAGGA
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
22 1 0.02
23 4 0.07
24 17 0.28
25 38 0.63
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (24 bp):
ATTCAAGCTCGTATGAGCATACCG
Found at i:1655030 original size:20 final size:20
Alignment explanation
Indices: 1655005--1655053 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1654995 TGAGTTATTT
*
1655005 AAGTAAGCAAGTAAGTGAAC
1 AAGTAAGCAAGTAAGTAAAC
*
1655025 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
1655045 AA-TAAGCAA
1 AAGTAAGCAA
1655054 AGACCATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.55, C:0.06, G:0.24, T:0.14
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:1662487 original size:18 final size:18
Alignment explanation
Indices: 1662464--1662501 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1662454 GACATAATGT
1662464 TATGGTTGACTATCGTAC
1 TATGGTTGACTATCGTAC
1662482 TATGGTTGACTATCGTAC
1 TATGGTTGACTATCGTAC
1662500 TA
1 TA
1662502 AAGGTGTACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (18 bp):
TATGGTTGACTATCGTAC
Found at i:1666309 original size:21 final size:21
Alignment explanation
Indices: 1666283--1666344 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
1666273 CTTGTACAAG
1666283 ATTGCACTTTGGTGCCTCTGT
1 ATTGCACTTTGGTGCCTCTGT
* *
1666304 ATTGCACTCTGGTGCCTCTAT
1 ATTGCACTTTGGTGCCTCTGT
* * *
1666325 ATTGCTCTTCGATGCCTCTG
1 ATTGCACTTTGGTGCCTCTG
1666345 CCTGCACTTC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.11, C:0.27, G:0.21, T:0.40
Consensus pattern (21 bp):
ATTGCACTTTGGTGCCTCTGT
Found at i:1684510 original size:16 final size:16
Alignment explanation
Indices: 1684489--1684521 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1684479 AAGAAAGATT
1684489 GAAAATTATGAATAAA
1 GAAAATTATGAATAAA
1684505 GAAAATTATGAATAAA
1 GAAAATTATGAATAAA
1684521 G
1 G
1684522 GACGTTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (16 bp):
GAAAATTATGAATAAA
Found at i:1688159 original size:15 final size:15
Alignment explanation
Indices: 1688139--1688169 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1688129 TCTCTTTGTC
1688139 TTTTTATTTGTCCTT
1 TTTTTATTTGTCCTT
*
1688154 TTTTTATTTTTCCTT
1 TTTTTATTTGTCCTT
1688169 T
1 T
1688170 CTCCCTCACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTTTATTTGTCCTT
Found at i:1698685 original size:27 final size:27
Alignment explanation
Indices: 1698329--1698675 Score: 435
Period size: 27 Copynumber: 12.9 Consensus size: 27
1698319 AAAATGACTA
* *
1698329 AAATACCCTCGATGGGTAAAATAACCG
1 AAATACCCTCGAAGGGTAAAATTACCG
*
1698356 AAATACCCTCGAAGGGTAAAATTATCG
1 AAATACCCTCGAAGGGTAAAATTACCG
* * *
1698383 AAATACCCTCAAAGAGTAAAATTACCA
1 AAATACCCTCGAAGGGTAAAATTACCG
* * *
1698410 AAATACCCTCGAAGGGTTAAATTATCA
1 AAATACCCTCGAAGGGTAAAATTACCG
* *
1698437 AAATACCCTCAAAGGGAAAAATTACCG
1 AAATACCCTCGAAGGGTAAAATTACCG
*
1698464 AAATACCCTCGAAGGGTAAAATTACCA
1 AAATACCCTCGAAGGGTAAAATTACCG
* * * *
1698491 AAATACCCTCAAAGGGTTAAATCACTG
1 AAATACCCTCGAAGGGTAAAATTACCG
* * * *
1698518 AAATACCCTCAAAAGGAAAAATTACTG
1 AAATACCCTCGAAGGGTAAAATTACCG
*
1698545 AAATACCCTTGAAGGGTAAAATTACCG
1 AAATACCCTCGAAGGGTAAAATTACCG
* * *
1698572 AAACA-CCTTGAAGGGTAAAATTACTG
1 AAATACCCTCGAAGGGTAAAATTACCG
**
1698598 AAATACCCTCGAAGGGTAAAATTACTA
1 AAATACCCTCGAAGGGTAAAATTACCG
* *
1698625 AAATACCCTCGAAGGATAAAATTACCA
1 AAATACCCTCGAAGGGTAAAATTACCG
1698652 AAATACCCTCGAAGGGTAAAATTA
1 AAATACCCTCGAAGGGTAAAATTA
1698676 TTTAAATACC
Statistics
Matches: 278, Mismatches: 41, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
26 24 0.09
27 254 0.91
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (27 bp):
AAATACCCTCGAAGGGTAAAATTACCG
Found at i:1702984 original size:17 final size:17
Alignment explanation
Indices: 1702962--1702995 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1702952 ATTTGCATTA
1702962 GGGATCATAGCATTTAG
1 GGGATCATAGCATTTAG
*
1702979 GGGATCATTGCATTTAG
1 GGGATCATAGCATTTAG
1702996 TTTAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.32
Consensus pattern (17 bp):
GGGATCATAGCATTTAG
Found at i:1703509 original size:4 final size:4
Alignment explanation
Indices: 1703502--1703526 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1703492 TGGTGATTAG
1703502 TTGT TTGT TTGT TTGT TTGT TTGT T
1 TTGT TTGT TTGT TTGT TTGT TTGT T
1703527 GGCTTAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (4 bp):
TTGT
Found at i:1705585 original size:20 final size:20
Alignment explanation
Indices: 1705502--1705587 Score: 111
Period size: 20 Copynumber: 4.3 Consensus size: 20
1705492 ATCAAATGTC
*
1705502 ATTTCCATTTC-GATAACCA
1 ATTTCCATTTCATATAACCA
* *
1705521 ATTTCCATTTCATATATCAA
1 ATTTCCATTTCATATAACCA
* *
1705541 ATTCCCATTTCATATATCCA
1 ATTTCCATTTCATATAACCA
1705561 ATTTCCATTTCATATAACCA
1 ATTTCCATTTCATATAACCA
*
1705581 CTTTCCA
1 ATTTCCA
1705588 CCTAATGAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 11 0.19
20 47 0.81
ACGTcount: A:0.31, C:0.27, G:0.01, T:0.41
Consensus pattern (20 bp):
ATTTCCATTTCATATAACCA
Found at i:1714499 original size:17 final size:18
Alignment explanation
Indices: 1714463--1714504 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1714453 TGTTTGCTAA
* *
1714463 TTTTATATTTTATTTCAT
1 TTTTATATTTTATGTAAT
1714481 TTTTAT-TTTTATGTAAT
1 TTTTATATTTTATGTAAT
*
1714498 TTATATA
1 TTTTATA
1714505 ATATAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTATATTTTATGTAAT
Found at i:1719546 original size:18 final size:18
Alignment explanation
Indices: 1719498--1719553 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
1719488 AAAACTACTC
*
1719498 AAAATTCAAAAAATATAT
1 AAAATTCAAAAAATATAA
* *
1719516 ATAATATCTAAAATATATAA
1 AAAAT-TC-AAAAAATATAA
1719536 AAAATTCAAAAAAATATA
1 AAAATTC-AAAAAATATA
1719554 CAAATTTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 4 0.13
19 13 0.43
20 13 0.43
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATTCAAAAAATATAA
Found at i:1719558 original size:18 final size:17
Alignment explanation
Indices: 1719498--1719559 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 17
1719488 AAAACTACTC
1719498 AAAATTCAAAAAATATAT
1 AAAATTCAAAAAA-ATAT
* * *
1719516 ATAATATCTAAAATATATAA
1 AAAAT-TC-AAAA-AAATAT
1719536 AAAATTCAAAAAAATAT
1 AAAATTCAAAAAAATAT
1719553 ACAAATT
1 A-AAATT
1719560 TATTAAGTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
17 5 0.15
18 13 0.38
19 4 0.12
20 11 0.32
21 1 0.03
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATTCAAAAAAATAT
Found at i:1724676 original size:16 final size:16
Alignment explanation
Indices: 1724655--1724691 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1724645 TTGGTTCGCT
1724655 GTAATGGAATAGAAGC
1 GTAATGGAATAGAAGC
*
1724671 GTAATGGAATAGAGGC
1 GTAATGGAATAGAAGC
1724687 GTAAT
1 GTAAT
1724692 AGGTAATTCT
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:0.41, C:0.05, G:0.32, T:0.22
Consensus pattern (16 bp):
GTAATGGAATAGAAGC
Found at i:1724760 original size:44 final size:46
Alignment explanation
Indices: 1724671--1724761 Score: 132
Period size: 44 Copynumber: 2.0 Consensus size: 46
1724661 GAATAGAAGC
* * *
1724671 GTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAAT
1 GTAATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTAGTTGAAT
*
1724717 GTAATGAAATAGATGCGTAAT-GGT-ATTCTTGTGTTTAGTTGAAT
1 GTAATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTAGTTGAAT
1724761 G
1 G
1724762 GAATAGAGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 19 0.46
45 3 0.07
46 19 0.46
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.40
Consensus pattern (46 bp):
GTAATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTAGTTGAAT
Found at i:1724767 original size:39 final size:41
Alignment explanation
Indices: 1724673--1724778 Score: 117
Period size: 44 Copynumber: 2.5 Consensus size: 41
1724663 ATAGAAGCGT
* *
1724673 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTAGTTG
*
1724714 AATGTAATGAAATAGATGCGTAAT-GGT-ATTCTTGTGTTTAGTTG
1 AATG----G-AATAGAGGCGTAATAGGTAATTCTTGTGTTTAGTTG
*
1724758 AATGGAATAGAGGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
1724779 TACAAGGAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
39 12 0.22
40 2 0.04
41 4 0.07
44 19 0.35
45 4 0.07
46 13 0.24
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.37
Consensus pattern (41 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTAGTTG
Found at i:1724864 original size:26 final size:28
Alignment explanation
Indices: 1724834--1724897 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
1724824 TAATACTATA
* *
1724834 AAATATAATTTGA-AATAAT-TATTATT
1 AAATATAATTTAATAATAATATATAATT
1724860 AAATATAATTTAATAATAATATATAATT
1 AAATATAATTTAATAATAATATATAATT
* *
1724888 TAATAAAATT
1 AAATATAATT
1724898 CTTATTCTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 12 0.38
27 6 0.19
28 14 0.44
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
AAATATAATTTAATAATAATATATAATT
Found at i:1724976 original size:32 final size:32
Alignment explanation
Indices: 1724940--1725003 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
1724930 TATATAATAC
*
1724940 TATAAAATATAATTTAAATAATTATTATTAAA
1 TATAAAATATAATATAAATAATTATTATTAAA
** ** *
1724972 TATAATTTATAATATACTTTATTATTATTAAA
1 TATAAAATATAATATAAATAATTATTATTAAA
1725004 CTGCAATACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
TATAAAATATAATATAAATAATTATTATTAAA
Found at i:1731599 original size:17 final size:17
Alignment explanation
Indices: 1731577--1731615 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1731567 TGATTCAGCT
*
1731577 GTGTGAGGCACATGGTC
1 GTGTGAGGCACACGGTC
1731594 GTGTGAGGCACACGGTC
1 GTGTGAGGCACACGGTC
1731611 GTGTG
1 GTGTG
1731616 TCATCTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.15, C:0.18, G:0.44, T:0.23
Consensus pattern (17 bp):
GTGTGAGGCACACGGTC
Found at i:1731954 original size:15 final size:16
Alignment explanation
Indices: 1731934--1731963 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1731924 ATGATGTGAT
1731934 TATAATATT-AAATGA
1 TATAATATTCAAATGA
1731949 TATAATATTCAAATG
1 TATAATATTCAAATG
1731964 TTCCTGATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (16 bp):
TATAATATTCAAATGA
Found at i:1735321 original size:24 final size:26
Alignment explanation
Indices: 1735266--1735319 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
1735256 ATAATTTCAC
*
1735266 TTTTTCACTATCTCAATTCCATTGAA
1 TTTTTCACTATCTCAATTCCAATGAA
*
1735292 TTTTTCAC-ATC-CCATTCCAAT-AA
1 TTTTTCACTATCTCAATTCCAATGAA
1735315 TTTTT
1 TTTTT
1735320 TCGGTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 7 0.27
24 8 0.31
25 3 0.12
26 8 0.31
ACGTcount: A:0.26, C:0.24, G:0.02, T:0.48
Consensus pattern (26 bp):
TTTTTCACTATCTCAATTCCAATGAA
Found at i:1739837 original size:19 final size:20
Alignment explanation
Indices: 1739813--1739851 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1739803 CTCACATGAC
*
1739813 AAAGTG-AAAATTGATTTTT
1 AAAGTGAAAAAGTGATTTTT
1739832 AAAGTGAAAAAGTGATTTTT
1 AAAGTGAAAAAGTGATTTTT
1739852 GTGGCCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.18, T:0.38
Consensus pattern (20 bp):
AAAGTGAAAAAGTGATTTTT
Found at i:1739948 original size:47 final size:47
Alignment explanation
Indices: 1739897--1740053 Score: 224
Period size: 47 Copynumber: 3.3 Consensus size: 47
1739887 AAGGAGGAAG
* * * *
1739897 AAGTGGCAGTTTATCTGCGAAAGTGGTGGCTTGTCCACAGTATGATA
1 AAGTGGCAGTTTATCTGCAAAAGTGGTGGCTTGTCCACAGTTTTATT
* *
1739944 AAGTGACAGTTTATCTGCAAAAGTGGTGGTTTGTCCACAGTTTTATT
1 AAGTGGCAGTTTATCTGCAAAAGTGGTGGCTTGTCCACAGTTTTATT
* * * *
1739991 AAGTGGTAGCTTATTTGCAAAAGTGGTGGCTTGTCCACAATTTTATT
1 AAGTGGCAGTTTATCTGCAAAAGTGGTGGCTTGTCCACAGTTTTATT
1740038 AAGTGGCAGTTTATCT
1 AAGTGGCAGTTTATCT
1740054 ACATTACTGT
Statistics
Matches: 95, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 95 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (47 bp):
AAGTGGCAGTTTATCTGCAAAAGTGGTGGCTTGTCCACAGTTTTATT
Found at i:1748398 original size:207 final size:207
Alignment explanation
Indices: 1748043--1748454 Score: 788
Period size: 207 Copynumber: 2.0 Consensus size: 207
1748033 CTGGAACTTA
*
1748043 TGCGTTAAATTGCTGTGTTGGTCCTCATGATTTCTATTGATTGTAAATCTAGTCTTCTAGGTACT
1 TGCGTTAAAATGCTGTGTTGGTCCTCATGATTTCTATTGATTGTAAATCTAGTCTTCTAGGTACT
* *
1748108 GGATCCTCGATTTAATTATTTTTTTAATTTTATTTTCTTTATTACTTATTAATCGTCAGGCTTTG
66 GGATCCTCAATTTAATTATTTTTTTAATTTTATTTTCTTTATTACTTATTAATCGTAAGGCTTTG
*
1748173 TTTAAATATTAATGTTTTGTTGATTTATAATAAATTTTAAATATTAGGATTAACATTGTTTTCAA
131 TTTAAATATTAATGTTTTGTTGATTTATAATAAATTTTAAATATTAGGATTAACAATGTTTTCAA
1748238 ACATCTTTTTTC
196 ACATCTTTTTTC
1748250 TGCGTTAAAATGCTGTGTTGGTCCTCATGATTTCTATTGATTGTAAATCTAGTCTTCTAGGTACT
1 TGCGTTAAAATGCTGTGTTGGTCCTCATGATTTCTATTGATTGTAAATCTAGTCTTCTAGGTACT
1748315 GGATCCTCAATTTAATTATTTTTTTAATTTTATTTTCTTTATTACTTATTAATCGTAAGGCTTTG
66 GGATCCTCAATTTAATTATTTTTTTAATTTTATTTTCTTTATTACTTATTAATCGTAAGGCTTTG
1748380 TTTAAATATTAATGTTTTGTTGATTTATAATAAATTTTAAATATTAGGATTAACAATGTTTTCAA
131 TTTAAATATTAATGTTTTGTTGATTTATAATAAATTTTAAATATTAGGATTAACAATGTTTTCAA
1748445 ACATCTTTTT
196 ACATCTTTTT
1748455 ATTATTATAA
Statistics
Matches: 201, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
207 201 1.00
ACGTcount: A:0.27, C:0.11, G:0.12, T:0.50
Consensus pattern (207 bp):
TGCGTTAAAATGCTGTGTTGGTCCTCATGATTTCTATTGATTGTAAATCTAGTCTTCTAGGTACT
GGATCCTCAATTTAATTATTTTTTTAATTTTATTTTCTTTATTACTTATTAATCGTAAGGCTTTG
TTTAAATATTAATGTTTTGTTGATTTATAATAAATTTTAAATATTAGGATTAACAATGTTTTCAA
ACATCTTTTTTC
Found at i:1748918 original size:13 final size:14
Alignment explanation
Indices: 1748900--1748929 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1748890 GTATTAAGAC
1748900 TTTTATATG-GTTA
1 TTTTATATGTGTTA
1748913 TTTTATATGTGTTA
1 TTTTATATGTGTTA
1748927 TTT
1 TTT
1748930 AAGGTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.20, C:0.00, G:0.13, T:0.67
Consensus pattern (14 bp):
TTTTATATGTGTTA
Found at i:1750961 original size:19 final size:19
Alignment explanation
Indices: 1750937--1750974 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1750927 GTGCCTACAG
1750937 TGGAGGAATATACAACTTT
1 TGGAGGAATATACAACTTT
*
1750956 TGGAGGAGTATACAACTTT
1 TGGAGGAATATACAACTTT
1750975 ACTGCACTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (19 bp):
TGGAGGAATATACAACTTT
Found at i:1761168 original size:44 final size:43
Alignment explanation
Indices: 1761070--1761750 Score: 275
Period size: 44 Copynumber: 15.7 Consensus size: 43
1761060 CAAAGATGGT
** * * *
1761070 GGATCTTATCTCCCTGAGATTACAGCAGAGCAGATT-GAAGCT
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATCA
* * *
1761112 GGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA
1 GG--ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT-CA
* * * * * ***
1761158 GGATCTTATCTCTCTGCGGTTACAGTAGAGTAGA-TCGCATCA
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATCA
* ** **
1761200 GG-TCTTATCTCCCTGAGATTACAATGGAATAGACCGAAGAATTTCA
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-AA--TCA
* * * * *
1761246 -GATCTTATCTCCTTGAGATTACAGCGGAGCAGATT-GAAGCT
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATCA
* * *
1761287 GGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA
1 GG--ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT-CA
* * * * * ***
1761333 GGATCTTATCTCTCTGCGGTTACAGTAGAGTAGA-TCGCATCA
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATCA
* * * ** *
1761375 GG-TCTTATCTCACTAAGGTTACAGTGGAATAGACTGAAGAATTTCA
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-AA--TCA
* * * * * *
1761421 -GATCTTATATCCCTGAGATTACAGCGAAGCAGATT-GAAGCT
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATCA
* * *
1761462 GGTAATCCTATCTCCCTGAGATTACAGTGCAGCAGATTAAAATAAA
1 GG--ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT-CA
* * * * * *** *
1761508 AGATCTTATCTCTCTGA-AGTGACAGTAGAGTAGA-TCGCATTA
1 GGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATCA
* ** **
1761550 GG-TCTTATCTCCCAGAGATTACAGTGGAATAGACCGAAGAATTTCA
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-AA--TCA
* * * * *
1761596 -GATCTTATCTCCTTGAGATTACAGCGGAGCAGATT-GAAGCT
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATCA
* * *
1761637 GGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA
1 GG--ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT-CA
* * ***
1761683 GTATCTTATCT--CTGA-AGTTACAGTAGAGCAGA-TCGTATCA
1 GGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATCA
*
1761723 GG-TCTTATCTCCTTGAGATTACAGTGGA
1 GGATCTTATCTCCCTGAGATTACAGTGGA
1761751 ATAGACCGAA
Statistics
Matches: 458, Mismatches: 138, Indels: 87
0.67 0.20 0.13
Matches are distributed among these distances:
39 8 0.02
40 2 0.00
41 94 0.21
42 32 0.07
43 16 0.03
44 205 0.45
45 12 0.03
46 89 0.19
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (43 bp):
GGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATCA
Found at i:1761362 original size:175 final size:175
Alignment explanation
Indices: 1761071--1761774 Score: 1169
Period size: 175 Copynumber: 4.0 Consensus size: 175
1761061 AAAGATGGTG
*
1761071 GATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCTGGTAATCCTATCTCCCTGAGATTA
1 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTGGTAATCCTATCTCCCTGAGATTA
**
1761136 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGCGGTTACAGTAGAGTAGATCGCATCAG
66 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
*
1761201 GTCTTATCTCCCTGAGATTACAATGGAATAGACCGAAGAATTTCA
131 GTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCA
*
1761246 GATCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGCTGGTAATCCTATCTCCCTGAGATTA
1 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTGGTAATCCTATCTCCCTGAGATTA
**
1761311 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGCGGTTACAGTAGAGTAGATCGCATCAG
66 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
* * * *
1761376 GTCTTATCTCACTAAGGTTACAGTGGAATAGACTGAAGAATTTCA
131 GTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCA
* *
1761421 GATCTTATATCCCTGAGATTACAGCGAAGCAGATTGAAGCTGGTAATCCTATCTCCCTGAGATTA
1 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTGGTAATCCTATCTCCCTGAGATTA
* * * * *
1761486 CAGTGCAGCAGATTAAAATAAAAGATCTTATCTCTCTGAAGTGACAGTAGAGTAGATCGCATTAG
66 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
*
1761551 GTCTTATCTCCCAGAGATTACAGTGGAATAGACCGAAGAATTTCA
131 GTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCA
*
1761596 GATCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGCTGGTAATCCTATCTCCCTGAGATTA
1 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTGGTAATCCTATCTCCCTGAGATTA
* * *
1761661 CAGTGGAGCGGATTAAAATAAAGTATCTTA--TCTCTGAAGTTACAGTAGAGCAGATCGTATCAG
66 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
* *
1761724 GTCTTATCTCCTTGAGATTACAGTGGAATAGACCGAAGAATTACA
131 GTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCA
1761769 GATCTT
1 GATCTT
1761775 GCCTCCCTAA
Statistics
Matches: 493, Mismatches: 36, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
173 77 0.16
175 416 0.84
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (175 bp):
GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTGGTAATCCTATCTCCCTGAGATTA
CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
GTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCA
Found at i:1780658 original size:16 final size:16
Alignment explanation
Indices: 1780634--1780671 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1780624 TTTGGTTCGC
* *
1780634 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
1780650 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
1780666 TGTAAT
1 TGTAAT
1780672 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:1780755 original size:39 final size:43
Alignment explanation
Indices: 1780650--1780759 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
1780640 GGATTAGAGG
1780650 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
1780695 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
1780735 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
1780760 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:1780926 original size:18 final size:17
Alignment explanation
Indices: 1780905--1780939 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1780895 TTATTATTAA
*
1780905 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
1780923 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
1780940 TCTNNNNNNN
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:1797855 original size:12 final size:12
Alignment explanation
Indices: 1797833--1797862 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
1797823 AAATAATCAA
1797833 AATTAATAAAATT
1 AATT-ATAAAATT
1797846 AATTATAAAATT
1 AATTATAAAATT
1797858 AATTA
1 AATTA
1797863 AATTTCAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AATTATAAAATT
Found at i:1812541 original size:25 final size:25
Alignment explanation
Indices: 1812513--1812575 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
1812503 AAGTGTTTTT
*
1812513 AGTATAGT-CTATCTATAGCAGTCTC
1 AGTATA-TACTATCTACAGCAGTCTC
*
1812538 AGTATATACTATCTACAGCAGTTTC
1 AGTATATACTATCTACAGCAGTCTC
* *
1812563 AGGATATATTATC
1 AGTATATACTATC
1812576 AAGGACAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 1 0.03
25 32 0.97
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (25 bp):
AGTATATACTATCTACAGCAGTCTC
Found at i:1812951 original size:19 final size:17
Alignment explanation
Indices: 1812907--1812954 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 17
1812897 TCTTGTTCGT
1812907 TTTCAAAATATTATTCA
1 TTTCAAAATATTATTCA
1812924 TTT-ACAAATCATTATTCAA
1 TTTCA-AAAT-ATTATTC-A
1812943 TTTCAAAATATT
1 TTTCAAAATATT
1812955 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
17 7 0.26
18 10 0.37
19 8 0.30
20 1 0.04
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTCAAAATATTATTCA
Found at i:1826714 original size:49 final size:49
Alignment explanation
Indices: 1826642--1826739 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
1826632 CCAAAATACT
1826642 CGTGTAATAAAATTTAAAAGAATATCCATTTGTTTAAGATTTATAAAGA
1 CGTGTAATAAAATTTAAAAGAATATCCATTTGTTTAAGATTTATAAAGA
1826691 CGTGTAATAAAATTTAAAAGAATATCCATTTGTTTAAGATTTATAAAGA
1 CGTGTAATAAAATTTAAAAGAATATCCATTTGTTTAAGATTTATAAAGA
1826740 AATCGCGGCC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (49 bp):
CGTGTAATAAAATTTAAAAGAATATCCATTTGTTTAAGATTTATAAAGA
Found at i:1827865 original size:19 final size:19
Alignment explanation
Indices: 1827841--1827894 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
1827831 AATCATATCT
1827841 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
1827860 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
1827879 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
1827895 CTTGTAGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:1827890 original size:38 final size:40
Alignment explanation
Indices: 1827818--1827894 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
1827808 AAATTAAATC
1827818 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTACAAAATCATA--TTCTAAGATTGCATATCATA
*
1827860 TCTAAGATTAC-ATATCATA-TCTAAGATTGCATATC
1 TCTAAGATTACAAAATCATATTCTAAGATTGCATATC
1827895 CTTGTAGATA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 16 0.47
41 7 0.21
42 11 0.32
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (40 bp):
TCTAAGATTACAAAATCATATTCTAAGATTGCATATCATA
Found at i:1828501 original size:45 final size:45
Alignment explanation
Indices: 1828414--1828578 Score: 151
Period size: 45 Copynumber: 3.8 Consensus size: 45
1828404 TTGTTTATTT
* * * * **
1828414 AGTCTGCCCCACTACAATTTCAGGGGGATAAGACTTGATTTCTTG
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGATTTCTTG
*
1828459 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGCTTTCTTG
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGATTTCTTG
* ** * * * *
1828504 GGTCTATTCTACTGCAACTTCAAGGAGATAAGACCC-AATGC--G
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGATTTCTTG
* *
1828546 A-TCTGCT-CTCTGCAACTTCAGAGAGATAAGACC
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACC
1828579 TGTGATTTTA
Statistics
Matches: 98, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
40 22 0.22
41 4 0.04
42 1 0.01
44 2 0.02
45 69 0.70
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (45 bp):
AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGATTTCTTG
Found at i:1828750 original size:44 final size:44
Alignment explanation
Indices: 1828652--1828751 Score: 157
Period size: 44 Copynumber: 2.3 Consensus size: 44
1828642 ACTATAACTT
* *
1828652 CAGGGAGATAAGATTCACCATCTTCAACCTATTCCACTGCTGAC
1 CAGGGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTGAC
*
1828696 CAGGGAGATAGGACTT-ACAATCTTCAACCTATTCCACTGCTGTC
1 CAGGGAGATAGGA-TTCACAATCTTCAACCTATTCCACTGCTGAC
1828740 CAGGGAGATAGG
1 CAGGGAGATAGG
1828752 GCTAGGGTCA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
44 50 0.96
45 2 0.04
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (44 bp):
CAGGGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTGAC
Found at i:1828870 original size:88 final size:88
Alignment explanation
Indices: 1828762--1829709 Score: 1628
Period size: 88 Copynumber: 10.8 Consensus size: 88
1828752 GCTAGGGTCA
1828762 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
* *
1828827 CCAGGGAGGCAAGACTGGTGTCT
66 CCAAGGAGGCAAGACAGGTGTCT
*
1828850 TCGATCTGTTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1828915 CCAAGGAGGCAAGACAGGTGTCT
66 CCAAGGAGGCAAGACAGGTGTCT
1828938 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1829003 CCAAGGAGGCAAGACAGGTGTCT
66 CCAAGGAGGCAAGACAGGTGTCT
1829026 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1829091 CCAAGGAGGCAAGACAGGTGTCT
66 CCAAGGAGGCAAGACAGGTGTCT
1829114 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1829179 CCAAGGAGGCAAGACAGGTGTCT
66 CCAAGGAGGCAAGACAGGTGTCT
1829202 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1829267 CCAAGGAGGCAAGACAGGTGTCT
66 CCAAGGAGGCAAGACAGGTGTCT
1829290 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1829355 CCAAGGAGGCAAGACAGGTGTCT
66 CCAAGGAGGCAAGACAGGTGTCT
* * * *
1829378 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATTTGCAATTTTTAACCTGCTCTGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
* * *
1829443 CCAAGGAGGCAAGGCTGGTGTAT
66 CCAAGGAGGCAAGACAGGTGTCT
* * *
1829466 TTGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCAATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
* * *
1829531 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAAGGAGGCAAGACAGGTGTCT
* * *
1829554 TCAATCTGCTTCGCTATCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
* *
1829619 CCAGGGAGGCAAGGCTA-GTGTCT
66 CCAAGGAGGCAAGAC-AGGTGTCT
* * ** ** *
1829642 TCGATCTGCTTCACTTTCGGCACAGGAAGACAAGATCTGCTATTTTTAACCTGCTCCGCTACAAC
1 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1829707 CCA
66 CCA
1829710 TGTGTGAATG
Statistics
Matches: 831, Mismatches: 28, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
88 831 1.00
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
CCAAGGAGGCAAGACAGGTGTCT
Found at i:1829497 original size:44 final size:44
Alignment explanation
Indices: 1829449--1829587 Score: 118
Period size: 44 Copynumber: 3.2 Consensus size: 44
1829439 CAACCCAAGG
*
1829449 AGGCAAGGCTGGTGTATTTGATCTGCTTCGCTGTCGGTGCAGGA
1 AGGCAAGGCTGGTGTATTTAATCTGCTTCGCTGTCGGTGCAGGA
* *** * * * **** *
1829493 AGGCAAGATCTGCAATTTTTAACCTGCTCCGCTG-CAACCCAGGG
1 AGGCAAG-GCTGGTGTATTTAATCTGCTTCGCTGTCGGTGCAGGA
* * *
1829537 AGGCAAGGCTGGTGTCTTCAATCTGCTTCGCTATCGGTGCAGGA
1 AGGCAAGGCTGGTGTATTTAATCTGCTTCGCTGTCGGTGCAGGA
1829581 AGGCAAG
1 AGGCAAG
1829588 ATCTGCTATT
Statistics
Matches: 66, Mismatches: 27, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
43 17 0.26
44 31 0.47
45 18 0.27
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25
Consensus pattern (44 bp):
AGGCAAGGCTGGTGTATTTAATCTGCTTCGCTGTCGGTGCAGGA
Found at i:1830843 original size:14 final size:15
Alignment explanation
Indices: 1830820--1830852 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1830810 ATCGACGCTT
1830820 TTCCAAATAAGG-CC
1 TTCCAAATAAGGTCC
*
1830834 TTCCACATAAGGTCC
1 TTCCAAATAAGGTCC
1830849 TTCC
1 TTCC
1830853 CAGCTTGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (15 bp):
TTCCAAATAAGGTCC
Found at i:1836222 original size:23 final size:22
Alignment explanation
Indices: 1836179--1836236 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1836169 AAAAGGTATC
* *
1836179 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
1836200 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
1836223 TGCATATCATATCT
1 TACAAATCATATCT
1836237 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:1839243 original size:88 final size:87
Alignment explanation
Indices: 1839150--1839309 Score: 212
Period size: 88 Copynumber: 1.8 Consensus size: 87
1839140 CTTATCTGGA
* * *** * * *
1839150 TACTTAAACTTTTAACATGTATCAAAAAGGTCTTCAAACCTTTTAAAAGAAAAGCAATTAAGCTC
1 TACTTAAACTTTCAAAATGTATCAAAAAAACCCTCAAACCTTTTAAAA-AAAAGCAAATAAGCCC
1839215 CTACTTTTTTTGCACTAATTGGG
65 CTACTTTTTTTGCACTAATTGGG
* * *
1839238 TACTTAAACTTTCAAAATGTATCAAAAAAACCCTCAAACTTTTTCAAAAAAGGCAAATAAGCCCC
1 TACTTAAACTTTCAAAATGTATCAAAAAAACCCTCAAACCTTTTAAAAAAAAGCAAATAAGCCCC
1839303 TACTTTT
66 TACTTTT
1839310 ATTAAAAATT
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
87 21 0.34
88 40 0.66
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (87 bp):
TACTTAAACTTTCAAAATGTATCAAAAAAACCCTCAAACCTTTTAAAAAAAAGCAAATAAGCCCC
TACTTTTTTTGCACTAATTGGG
Found at i:1839476 original size:19 final size:20
Alignment explanation
Indices: 1839431--1839488 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
1839421 AATATCAACA
*
1839431 TCGTAAAAACTATATAAAAAT
1 TCGTAAAAAAT-TATAAAAAT
* **
1839452 TTGTAAAATTTTATAAAAA-
1 TCGTAAAAAATTATAAAAAT
1839471 TCGTAAAAAATTATAAAA
1 TCGTAAAAAATTATAAAA
1839489 TATATAGAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 15 0.48
20 8 0.26
21 8 0.26
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
TCGTAAAAAATTATAAAAAT
Found at i:1839499 original size:28 final size:28
Alignment explanation
Indices: 1839442--1839515 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
1839432 CGTAAAAACT
* * *
1839442 ATATAAAAATTTGTAAAATTTTATAAAA
1 ATATAAAAAATTATAAAATTATATAAAA
* *
1839470 ATCGTAAAAAATTATAAAA-TATATAGAA
1 AT-ATAAAAAATTATAAAATTATATAAAA
1839498 ATATAAAAAAATTATAAA
1 ATAT-AAAAAATTATAAA
1839516 GTCGTAAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
27 1 0.03
28 24 0.63
29 13 0.34
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (28 bp):
ATATAAAAAATTATAAAATTATATAAAA
Found at i:1839580 original size:8 final size:9
Alignment explanation
Indices: 1839553--1839637 Score: 57
Period size: 10 Copynumber: 9.2 Consensus size: 9
1839543 TTATAAAAAA
1839553 TTATAATTT
1 TTATAATTT
1839562 TTAATAATTT
1 TT-ATAATTT
1839572 TTA-AATTT
1 TTATAATTT
**
1839580 TTATTAAAAT
1 TTA-TAATTT
1839590 TTATTAATTT
1 TTA-TAATTT
* **
1839600 TTCTAAAAT
1 TTATAATTT
*
1839609 TTATTATTT
1 TTATAATTT
*
1839618 TT-TATTTT
1 TTATAATTT
1839626 TCTATAATTT
1 T-TATAATTT
1839636 TT
1 TT
1839638 TTTCTAAATT
Statistics
Matches: 57, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
8 13 0.23
9 16 0.28
10 28 0.49
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (9 bp):
TTATAATTT
Found at i:1839581 original size:19 final size:19
Alignment explanation
Indices: 1839559--1839620 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 19
1839549 AAAATTATAA
1839559 TTTTTAATAATTT-TTAAATT
1 TTTTTAA-AATTTATT-AATT
1839579 TTTATTAAAATTTATTAATT
1 TTT-TTAAAATTTATTAATT
*
1839599 TTTCTAAAATTTATT-ATT
1 TTTTTAAAATTTATTAATT
1839617 TTTT
1 TTTT
1839621 ATTTTTCTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 6 0.16
19 11 0.29
20 15 0.39
21 6 0.16
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTTAAAATTTATTAATT
Found at i:1839619 original size:18 final size:19
Alignment explanation
Indices: 1839584--1839619 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1839574 AAATTTTTAT
1839584 TAAAATTTATTAATTTTTC
1 TAAAATTTATTAATTTTTC
1839603 TAAAATTTATT-ATTTTT
1 TAAAATTTATTAATTTTT
1839620 TATTTTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TAAAATTTATTAATTTTTC
Found at i:1839819 original size:89 final size:88
Alignment explanation
Indices: 1839659--1839878 Score: 241
Period size: 89 Copynumber: 2.5 Consensus size: 88
1839649 TAATAAGAGT
* * * **
1839659 AGGGGCTTAATTG-TATTTTCGAAAATTTTGGAGGGTCTTTTTTATGCATTTTGAAAGTTTAAGT
1 AGGGGCTTAATTGCTATTTTTGAAAAATTT-GAGGG-CTTTTTTATACATTTTGAAAGTACAAGT
*
1839723 ACCCAATTGAGTG-AAAGAAAA-AG
64 ACCCAATTGAGTGTAAAAAAAACAG
* * *
1839746 CAGGGGCTTAATTGCTTTTTTTGAAGAAGTTTGAGGGCATTTTTTATATATTTTGAAAGTACAAG
1 -AGGGGCTTAATTGCTATTTTTGAA-AAATTTGAGGGC-TTTTTTATACATTTTGAAAGTACAAG
* *
1839811 TGCTCAATTGAGTGTAAAAAAAACAG
63 TACCCAATTGAGTGTAAAAAAAACAG
*
1839837 AGGGGCTTAAATT-CTATTTTTGAAAAAATTTGAGAGCTTTTT
1 AGGGGCTT-AATTGCTATTTTTG-AAAAATTTGAGGGCTTTTT
1839879 ACAACATTAA
Statistics
Matches: 112, Mismatches: 13, Indels: 13
0.81 0.09 0.09
Matches are distributed among these distances:
88 14 0.12
89 52 0.46
90 38 0.34
91 8 0.07
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (88 bp):
AGGGGCTTAATTGCTATTTTTGAAAAATTTGAGGGCTTTTTTATACATTTTGAAAGTACAAGTAC
CCAATTGAGTGTAAAAAAAACAG
Found at i:1840641 original size:29 final size:27
Alignment explanation
Indices: 1840577--1840641 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
1840567 TTTTAGAAAG
* * *
1840577 AAAATATATAAAAATTTTATAAAATTT
1 AAAATATATAAAAAATTTATAAAAATC
1840604 ATAAA-ATATAAAAGAATTTATAAATAATC
1 A-AAATATATAAAA-AATTTATAAA-AATC
1840633 AAAATATAT
1 AAAATATAT
1840642 GTATATAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 9 0.29
28 15 0.48
29 7 0.23
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (27 bp):
AAAATATATAAAAAATTTATAAAAATC
Found at i:1842457 original size:14 final size:14
Alignment explanation
Indices: 1842429--1842457 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1842419 GCTTAGTGGC
1842429 TTTTGACTTGATTT
1 TTTTGACTTGATTT
1842443 TTTTG-CTTGATTT
1 TTTTGACTTGATTT
1842456 TT
1 TT
1842458 AAGCAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.10, C:0.07, G:0.14, T:0.69
Consensus pattern (14 bp):
TTTTGACTTGATTT
Found at i:1846695 original size:96 final size:95
Alignment explanation
Indices: 1846567--1846763 Score: 308
Period size: 96 Copynumber: 2.1 Consensus size: 95
1846557 TGACCAAATG
* *
1846567 AAAT-GAGGAATACGATTGAGCTATCACCTTTTGTGTAGTGTTATTGGTGTAGTTCAAAAGATCA
1 AAATAGAGGAATACGATTGAGCTATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATCA
1846631 TAAGGGTTTCCAATG-CGCAATTAAATATCC
66 TAAGGGTTTCCAATGTC-CAATTAAATATCC
* **
1846661 AAATAGAGAGAATATGATTGAGCTATCATTTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATC
1 AAATAGAG-GAATACGATTGAGCTATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATC
1846726 ATAAGGGTTTCCAATGTCCAATTAAATATCC
65 ATAAGGGTTTCCAATGTCCAATTAAATATCC
*
1846757 AACTAGA
1 AAATAGA
1846764 AAAGAAAGTA
Statistics
Matches: 94, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
94 4 0.04
95 3 0.03
96 86 0.91
97 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.34
Consensus pattern (95 bp):
AAATAGAGGAATACGATTGAGCTATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATCA
TAAGGGTTTCCAATGTCCAATTAAATATCC
Found at i:1849841 original size:21 final size:20
Alignment explanation
Indices: 1849817--1849886 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 20
1849807 TGTTTTAAAA
*
1849817 AAAATAATGTATGATAAATTT
1 AAAATAATGTATAAT-AATTT
*
1849838 AAAA-CATGTCAATAATAATTT
1 AAAATAATGT--ATAATAATTT
*
1849859 AAAATAATAGTATATTACATTTT
1 AAAATAAT-GTATAATA-A-TTT
1849882 AAAAT
1 AAAAT
1849887 TATATTAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
20 4 0.10
21 18 0.46
22 7 0.18
23 10 0.26
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (20 bp):
AAAATAATGTATAATAATTT
Found at i:1849905 original size:23 final size:22
Alignment explanation
Indices: 1849848--1849907 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
1849838 AAAACATGTC
1849848 AATAATAATTTAAAATAATAGT
1 AATAATAATTTAAAATAATAGT
* * *
1849870 -ATATTACATTTTAAAATTATATT
1 AATAATA-A-TTTAAAATAATAGT
1849893 AATAATAAGTTTAAA
1 AATAATAA-TTTAAA
1849908 GGTAATGTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 5 0.17
22 1 0.03
23 19 0.63
24 5 0.17
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (22 bp):
AATAATAATTTAAAATAATAGT
Found at i:1850113 original size:5 final size:6
Alignment explanation
Indices: 1850094--1850150 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
1850084 TTCAAAAAAC
* *
1850094 AAATAA AAATAA AAATAA AACACTAC AAATAG AAAT-A AAATGAA AAATAA
1 AAATAA AAATAA AAATAA AA-A-TAA AAATAA AAATAA AAAT-AA AAATAA
*
1850144 AGATAA A
1 AAATAA A
1850151 CTAAATTGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
5 4 0.09
6 28 0.65
7 7 0.16
8 4 0.09
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:1851679 original size:128 final size:128
Alignment explanation
Indices: 1851526--1851766 Score: 376
Period size: 128 Copynumber: 1.9 Consensus size: 128
1851516 ACTTTAGGGG
* * * *
1851526 GATAAGACCTGCTTACTCAGTCTGCTCCACTACAA-CTTCAGGGAGATAAGACTTGATGTGATCC
1 GATAAGACCTACTTACTCAGGCTGCTCCACTACAACCTT-AGGGAGATAAGACCTGATGCGATCC
* *
1851590 ACTCTACTACAACTTTAGAGAGATAAGATCTATTACTTTAATCTGCTCCACTACTGCTTAAGGA
65 ACTCTACTACAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACTGCTTAAGGA
* * *
1851654 GATAAGATCTACTTACTCAGGCTGCTCCACTGCAACCTTAGGGAGATAAGACCTGATGCGATCTA
1 GATAAGACCTACTTACTCAGGCTGCTCCACTACAACCTTAGGGAGATAAGACCTGATGCGATCCA
*
1851719 CTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCC
66 CTCTACTACAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCC
1851767 TCTGCAACTT
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
128 99 0.97
129 3 0.03
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (128 bp):
GATAAGACCTACTTACTCAGGCTGCTCCACTACAACCTTAGGGAGATAAGACCTGATGCGATCCA
CTCTACTACAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACTGCTTAAGGA
Found at i:1851816 original size:44 final size:44
Alignment explanation
Indices: 1851425--1851834 Score: 197
Period size: 44 Copynumber: 9.5 Consensus size: 44
1851415 CACTCCACTA
* * * *
1851425 CAACGTCAAGGAGATAGGAT-TATCGACTTCAATCTGCTC-CCTTG
1 CAACTTCAGGGAGATAAGATCTAT-GACTTCAATCTGCTCTAC-TG
* * * *
1851469 CAACCTCAGGGAGATAAGAT-T-TGCCATCTTCGATCTGCCCCACTG
1 CAACTTCAGGGAGATAAGATCTATG--A-CTTCAATCTGCTCTACTG
* * * * * * * *
1851514 CAACTTTAGGGGGATAAGACCTGCTTAC-TCAGTCTGCTCCACTA
1 CAACTTCAGGGAGATAAGATCT-ATGACTTCAATCTGCTCTACTG
* ** *
1851558 CAACTTCAGGGAGATAAGA-CT-TGA-TGT-GATCCACTCTACTA
1 CAACTTCAGGGAGATAAGATCTATGACT-TCAATCTGCTCTACTG
* * * * * *
1851599 CAACTTTAGAGAGATAAGATCTATTACTTTAATCTGCTCCACTA
1 CAACTTCAGGGAGATAAGATCTATGACTTCAATCTGCTCTACTG
** * * ** *
1851643 CTGCTT-AAGGAGATAAGATCTACTTAC-TCAGGCTGCTCCACTG
1 CAACTTCAGGGAGATAAGATCTA-TGACTTCAATCTGCTCTACTG
* * * *
1851686 CAACCTT-AGGGAGATAAGA-C-CTGA-TGCGATCTACTCTACTG
1 CAA-CTTCAGGGAGATAAGATCTATGACTTCAATCTGCTCTACTG
* * * *
1851727 CAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCT-CTG
1 CAACTTCAGGGAGATAAGATCTATGACTTCAATCTGCT-CTACTG
* *
1851771 CAACTTCAGGGAGATAGGAT-TATCGGCTTCAATCTGCTCTACTG
1 CAACTTCAGGGAGATAAGATCTAT-GACTTCAATCTGCTCTACTG
* *
1851815 CAACCTCAGGGTGATAAGAT
1 CAACTTCAGGGAGATAAGAT
1851835 GATAGAGGGT
Statistics
Matches: 277, Mismatches: 66, Indels: 46
0.71 0.17 0.12
Matches are distributed among these distances:
40 3 0.01
41 54 0.19
42 5 0.02
43 41 0.15
44 138 0.50
45 32 0.12
46 3 0.01
48 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
CAACTTCAGGGAGATAAGATCTATGACTTCAATCTGCTCTACTG
Found at i:1853511 original size:217 final size:218
Alignment explanation
Indices: 1853135--1853532 Score: 654
Period size: 217 Copynumber: 1.8 Consensus size: 218
1853125 ACTCGTATCG
* * * *
1853135 TAAGATTTGTCATCTTCGATCTGTCCGACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTC
1 TAAGATTTGCCATCTTCGATCTGTCCCACTACAACTTCAAGGGGATAAGACCTGCTTACTCAGTC
* *
1853200 TGCTCCGCTGCAACCTCAGGGAGATAAGACCTGATGCGATCCACACTACTGCAACTTCAGAGAGG
66 TGCTCCGCTGCAACCTCAGGGAGATAAGACCTAATGCGATCCACACTACTGCAACTTCAGAGAGA
* * *
1853265 TAAGATTTATTACTTTAAACCGCTCCACTACAACTTTAGAGAGATAGGATTATCGGCTTCAATCT
131 TAAGATCTATTACTTTAAACCACTCCACTACAACTTCAGAGAGATAGGATTATCGGCTTCAATCT
1853330 GCTCCACTGGAACCTTAGGGAGA
196 GCTCCACTGGAACCTTAGGGAGA
*
1853353 TAAGATTTGCCATCTTCGATCTGTCCCACTACAACTTCAAGGGGATAAG-CCTGCTTCCTCAGTC
1 TAAGATTTGCCATCTTCGATCTGTCCCACTACAACTTCAAGGGGATAAGACCTGCTTACTCAGTC
* * *
1853417 TGCTCTGCTGCAACCTCAGGGAGATAAGACCTAATGCGATCCACTCTACTGTAACTTCAGAGAGA
66 TGCTCCGCTGCAACCTCAGGGAGATAAGACCTAATGCGATCCACACTACTGCAACTTCAGAGAGA
* *
1853482 TAAGATCTATTACTTTAATCCACTCCACTACAACTTCAGGGAGATAGGATT
131 TAAGATCTATTACTTTAAACCACTCCACTACAACTTCAGAGAGATAGGATT
1853533 TGTGCCTTAA
Statistics
Matches: 165, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
217 120 0.73
218 45 0.27
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (218 bp):
TAAGATTTGCCATCTTCGATCTGTCCCACTACAACTTCAAGGGGATAAGACCTGCTTACTCAGTC
TGCTCCGCTGCAACCTCAGGGAGATAAGACCTAATGCGATCCACACTACTGCAACTTCAGAGAGA
TAAGATCTATTACTTTAAACCACTCCACTACAACTTCAGAGAGATAGGATTATCGGCTTCAATCT
GCTCCACTGGAACCTTAGGGAGA
Found at i:1853658 original size:129 final size:129
Alignment explanation
Indices: 1853519--1853773 Score: 411
Period size: 129 Copynumber: 2.0 Consensus size: 129
1853509 CTACAACTTC
* * *
1853519 AGGGAGATAGGATTTGTGCCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGACATCTTCG
1 AGGGAGATAGGACTTGTGCCTTAAACCTGCTTCCTTACACTTGAAGATAAGATTCGACATCCTCG
*
1853584 ATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCTACCCTATTCCACTGCTGACT
66 ATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCTAACCTATTCCACTGCTGACT
* * * *
1853648 AGGGATATAGGACTTGTGGCTTAAACCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCCTCG
1 AGGGAGATAGGACTTGTGCCTTAAACCTGCTTCCTTACACTTGAAGATAAGATTCGACATCCTCG
* * *
1853713 ATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTTCTAACCTATTCCACTGCTG
66 ATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCTAACCTATTCCACTGCTG
1853774 GTCAGGGAGC
Statistics
Matches: 115, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
129 115 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.32
Consensus pattern (129 bp):
AGGGAGATAGGACTTGTGCCTTAAACCTGCTTCCTTACACTTGAAGATAAGATTCGACATCCTCG
ATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCTAACCTATTCCACTGCTGACT
Found at i:1853806 original size:44 final size:44
Alignment explanation
Indices: 1853757--1853879 Score: 201
Period size: 44 Copynumber: 2.8 Consensus size: 44
1853747 GTAATTTTCT
**
1853757 AACCTATTCCACTGCTGGTCAGGGAGCTAGGTTTTGCAATCTTC
1 AACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTGCAATCTTC
* *
1853801 AACCTATTCCACTGTTGGTTAGGGAGCTAGGACTTGCAATCTTC
1 AACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTGCAATCTTC
*
1853845 TACCTATTCCACTGCTGGTCAGGGAGCTAGGACTT
1 AACCTATTCCACTGCTGGTCAGGGAGCTAGGACTT
1853880 ATGATTTCAC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 72 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (44 bp):
AACCTATTCCACTGCTGGTCAGGGAGCTAGGACTTGCAATCTTC
Found at i:1855144 original size:22 final size:23
Alignment explanation
Indices: 1855119--1855162 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1855109 TTAGCCTCTC
1855119 CATTTTTA-CTTTTTCATTTTTT
1 CATTTTTATCTTTTTCATTTTTT
*
1855141 CATTTTTATTTTTTTCATTTTT
1 CATTTTTATCTTTTTCATTTTT
1855163 CTTTTTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (23 bp):
CATTTTTATCTTTTTCATTTTTT
Found at i:1855146 original size:15 final size:15
Alignment explanation
Indices: 1855119--1855169 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
1855109 TTAGCCTCTC
*
1855119 CATTTTTAC-TTTTT
1 CATTTTTTCATTTTT
1855133 CATTTTTTCATTTTT
1 CATTTTTTCATTTTT
1855148 -ATTTTTTTCATTTTT
1 CA-TTTTTTCATTTTT
1855163 C-TTTTTT
1 CATTTTTT
1855170 TTGACTCGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 15 0.45
15 18 0.55
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (15 bp):
CATTTTTTCATTTTT
Found at i:1855170 original size:15 final size:15
Alignment explanation
Indices: 1855128--1855170 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
1855118 CCATTTTTAC
*
1855128 TTTTTCATTTTTTCA
1 TTTTTCTTTTTTTCA
*
1855143 TTTTTATTTTTTTCA
1 TTTTTCTTTTTTTCA
1855158 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
1855171 TGACTCGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTCTTTTTTTCA
Found at i:1860567 original size:20 final size:20
Alignment explanation
Indices: 1860542--1860584 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1860532 AATGCGAGTG
1860542 TTTGGGCCGGGGTTAGGTGA
1 TTTGGGCCGGGGTTAGGTGA
1860562 TTTGGGCCGGGGTTAGGTGA
1 TTTGGGCCGGGGTTAGGTGA
1860582 TTT
1 TTT
1860585 TTATTTTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.09, C:0.09, G:0.47, T:0.35
Consensus pattern (20 bp):
TTTGGGCCGGGGTTAGGTGA
Found at i:1868755 original size:24 final size:22
Alignment explanation
Indices: 1868707--1868747 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1868697 AGGTGGTGCA
1868707 AAAGGAGAGGAGGAGAGAGAAG
1 AAAGGAGAGGAGGAGAGAGAAG
1868729 AAAGGAGAGGA-GAG-GAGAA
1 AAAGGAGAGGAGGAGAGAGAA
1868748 TGATGAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 3 0.16
22 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (22 bp):
AAAGGAGAGGAGGAGAGAGAAG
Found at i:1869263 original size:18 final size:18
Alignment explanation
Indices: 1869240--1869278 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1869230 TTCAGGTATG
1869240 ACCACTCTTTGATCATTA
1 ACCACTCTTTGATCATTA
1869258 ACCACTCTTTGATCATTA
1 ACCACTCTTTGATCATTA
1869276 ACC
1 ACC
1869279 CAATTTCTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.31, G:0.05, T:0.36
Consensus pattern (18 bp):
ACCACTCTTTGATCATTA
Found at i:1894648 original size:27 final size:27
Alignment explanation
Indices: 1894618--1895076 Score: 260
Period size: 27 Copynumber: 17.2 Consensus size: 27
1894608 TCGATATCTG
* *
1894618 GACCGAAATACCCCGAAATGGTAAAAT
1 GACCGAAATACCCCGATAGGGTAAAAT
* *
1894645 GACCGAAATATCCTCGA-AAGGTAAAAT
1 GACCGAAATA-CCCCGATAGGGTAAAAT
*
1894672 GACCGAAATACCCTCGAT-GGGTAAGAT
1 GACCGAAATACCC-CGATAGGGTAAAAT
* ** *
1894699 GACTGAAATGTCCCTATAGGGTAAAAT
1 GACCGAAATACCCCGATAGGGTAAAAT
* *
1894726 GACCAAAATACCCCCG-TAGGGTAGAAT
1 GACCGAAATA-CCCCGATAGGGTAAAAT
* *
1894753 -ACCAAAATACCCCCATAGGGTAAAAT
1 GACCGAAATACCCCGATAGGGTAAAAT
* * *
1894779 GATCGTAATACCCCTATAGGGTAAAAT
1 GACCGAAATACCCCGATAGGGTAAAAT
* ** **
1894806 GA-CTATAATGTCGTG-TAGGGTAAAAT
1 GACCGA-AATACCCCGATAGGGTAAAAT
* * **
1894832 GACCGTAATGCCCTTAT-GGGTAAAAT
1 GACCGAAATACCCCGATAGGGTAAAAT
* * * *
1894858 GATCGTAATGCCCTTG-TAGGGTAAAAT
1 GACCGAAATACCC-CGATAGGGTAAAAT
* * *
1894885 GATCGTAATGCCCCTG-TAGGGTAAAAT
1 GACCGAAATACCCC-GATAGGGTAAAAT
* **
1894912 GACCGTAATACCCCTCTAGGGTAAAAT
1 GACCGAAATACCCCGATAGGGTAAAAT
* * ** * *
1894939 GACTGTAAT-GTCCTATCGGGTAAAAT
1 GACCGAAATACCCCGATAGGGTAAAAT
* * **
1894965 GACCGTAATGCCCTTATA-GGTAAAAT
1 GACCGAAATACCCCGATAGGGTAAAAT
*
1894991 GACC-ATAATGCCCCTG-TAGGGTAAAAT
1 GACCGA-AATACCCC-GATAGGGTAAAAT
* * * *
1895018 GACCGTAATGCCCCTATAAGGTAAAAT
1 GACCGAAATACCCCGATAGGGTAAAAT
*** * *
1895045 GACATTAATGCCCCTATAGGGTAAAAT
1 GACCGAAATACCCCGATAGGGTAAAAT
1895072 GACCG
1 GACCG
1895077 TAATGCCCTG
Statistics
Matches: 351, Mismatches: 61, Indels: 40
0.78 0.13 0.09
Matches are distributed among these distances:
25 4 0.01
26 108 0.31
27 231 0.66
28 8 0.02
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (27 bp):
GACCGAAATACCCCGATAGGGTAAAAT
Found at i:1894825 original size:53 final size:52
Alignment explanation
Indices: 1894768--1895095 Score: 367
Period size: 53 Copynumber: 6.2 Consensus size: 52
1894758 AATACCCCCA
* ** * *
1894768 TAGGGTAAAATGATCGTAATACCCCTATAGGGTAAAATGACTATAATGTCGTG
1 TAGGGTAAAATGA-CGTAATGCCCCTATAGGGTAAAATGACCGTAATGCCCTG
* *
1894821 TAGGGTAAAATGACCGTAATGCCCTTAT-GGGTAAAATGATCGTAATGCCCTTG
1 TAGGGTAAAATGA-CGTAATGCCCCTATAGGGTAAAATGACCGTAATGCCC-TG
* * *
1894874 TAGGGTAAAATGATCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTC
1 TAGGGTAAAATGA-CGTAATGCCCCTATAGGGTAAAATGACCGTAAT-GCCCTG
* *
1894928 TAGGGTAAAATGACTGTAATG-TCCTATCGGGTAAAATGACCGTAATGCCCT-
1 TAGGGTAAAATGAC-GTAATGCCCCTATAGGGTAAAATGACCGTAATGCCCTG
* * * *
1894979 TATAGGTAAAATGACCATAATGCCCCTGTAGGGTAAAATGACCGTAATGCCCCTA
1 TA-GGGTAAAATGA-CGTAATGCCCCTATAGGGTAAAATGACCGTAATG-CCCTG
* *
1895034 TAAGGTAAAATGACATTAATGCCCCTATAGGGTAAAATGACCGTAATGCCCTGG
1 TAGGGTAAAATGAC-GTAATGCCCCTATAGGGTAAAATGACCGTAATGCCCT-G
1895088 T-GGGTAAA
1 TAGGGTAAA
1895096 TTACTATTTT
Statistics
Matches: 237, Mismatches: 27, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
51 2 0.01
52 36 0.15
53 110 0.46
54 84 0.35
55 5 0.02
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (52 bp):
TAGGGTAAAATGACGTAATGCCCCTATAGGGTAAAATGACCGTAATGCCCTG
Found at i:1895080 original size:27 final size:27
Alignment explanation
Indices: 1894664--1895084 Score: 422
Period size: 27 Copynumber: 15.8 Consensus size: 27
1894654 ATCCTCGAAA
* * *
1894664 GGTAAAATGACCGAAATACCCTCGAT-G
1 GGTAAAATGACCGTAATGCCC-CTATAG
* * * *
1894691 GGTAAGATGACTGAAATGTCCCTATAG
1 GGTAAAATGACCGTAATGCCCCTATAG
** * **
1894718 GGTAAAATGACCAAAATACCCCCGTAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* ** * *
1894745 GGTAGAAT-ACCAAAATACCCCCATAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* *
1894771 GGTAAAATGATCGTAATACCCCTATAG
1 GGTAAAATGACCGTAATGCCCCTATAG
** * * *
1894798 GGTAAAATGACTATAATG-TCGTGTAG
1 GGTAAAATGACCGTAATGCCCCTATAG
*
1894824 GGTAAAATGACCGTAATGCCCTTAT-G
1 GGTAAAATGACCGTAATGCCCCTATAG
* * *
1894850 GGTAAAATGATCGTAATGCCCTTGTAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* *
1894877 GGTAAAATGATCGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* *
1894904 GGTAAAATGACCGTAATACCCCTCTAG
1 GGTAAAATGACCGTAATGCCCCTATAG
* * *
1894931 GGTAAAATGACTGTAATG-TCCTATCG
1 GGTAAAATGACCGTAATGCCCCTATAG
*
1894957 GGTAAAATGACCGTAATGCCCTTATA-
1 GGTAAAATGACCGTAATGCCCCTATAG
* *
1894983 GGTAAAATGACCATAATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTATAG
*
1895010 GGTAAAATGACCGTAATGCCCCTATAA
1 GGTAAAATGACCGTAATGCCCCTATAG
**
1895037 GGTAAAATGACATTAATGCCCCTATAG
1 GGTAAAATGACCGTAATGCCCCTATAG
1895064 GGTAAAATGACCGTAATGCCC
1 GGTAAAATGACCGTAATGCCC
1895085 TGGTGGGTAA
Statistics
Matches: 331, Mismatches: 57, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
26 117 0.35
27 214 0.65
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (27 bp):
GGTAAAATGACCGTAATGCCCCTATAG
Found at i:1895110 original size:133 final size:132
Alignment explanation
Indices: 1894690--1895095 Score: 494
Period size: 133 Copynumber: 3.1 Consensus size: 132
1894680 TACCCTCGAT
* * * * * * *
1894690 GGGTAAGATGACTGAAATGTCCC-TATAGGGTAAAATGACCAAAATACCCCCGTAGGGTAGAAT-
1 GGGTAAAATGACCGTAATG-CCCTTATA-GGTAAAATGACCATAATGCCCCTGTAGGGTAAAATG
** * * *
1894753 ACCAAAATACCCCCATAGGGTAAAATGATCGTAATACCCCTATAGGGTAAAATGACTATAATGTC
64 ACCGTAATGCCCCTATAGGGTAAAATGA-CGTAATACCCCTATAGGGTAAAATGACTGTAATGTC
*
1894818 GTGTA
128 CTGTA
* * * * *
1894823 GGGTAAAATGACCGTAATGCCCTTATGGGTAAAATGATCGTAATGCCCTTGTAGGGTAAAATGAT
1 GGGTAAAATGACCGTAATGCCCTTATAGGTAAAATGACCATAATGCCCCTGTAGGGTAAAATGAC
* *
1894888 CGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTCTAGGGTAAAATGACTGTAATGTCCT
66 CGTAATGCCCCTATAGGGTAAAATGA-CGTAATACCCCTATAGGGTAAAATGACTGTAATGTCCT
* *
1894953 ATC
130 GTA
1894956 GGGTAAAATGACCGTAATGCCCTTATAGGTAAAATGACCATAATGCCCCTGTAGGGTAAAATGAC
1 GGGTAAAATGACCGTAATGCCCTTATAGGTAAAATGACCATAATGCCCCTGTAGGGTAAAATGAC
* * * * *
1895021 CGTAATGCCCCTATAAGGTAAAATGACATTAATGCCCCTATAGGGTAAAATGACCGTAATGCCCT
66 CGTAATGCCCCTATAGGGTAAAATGAC-GTAATACCCCTATAGGGTAAAATGACTGTAATGTCCT
1895086 GGT-
130 -GTA
1895089 GGGTAAA
1 GGGTAAA
1895096 TTACTATTTT
Statistics
Matches: 233, Mismatches: 36, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
132 32 0.14
133 200 0.86
134 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Consensus pattern (132 bp):
GGGTAAAATGACCGTAATGCCCTTATAGGTAAAATGACCATAATGCCCCTGTAGGGTAAAATGAC
CGTAATGCCCCTATAGGGTAAAATGACGTAATACCCCTATAGGGTAAAATGACTGTAATGTCCTG
TA
Found at i:1895307 original size:27 final size:27
Alignment explanation
Indices: 1895266--1895329 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
1895256 ATGGAGGAAG
*
1895266 TACTG-TACTGGTGGCTCT-GCCACA-A
1 TACTGTTACTGATGGCT-TGGCCACATA
1895291 TCACTGTTACTGATGGCTTGGCCACATA
1 T-ACTGTTACTGATGGCTTGGCCACATA
*
1895319 TACTATTACTG
1 TACTGTTACTG
1895330 GCAGCTTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 1 0.03
26 5 0.15
27 25 0.76
28 2 0.06
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (27 bp):
TACTGTTACTGATGGCTTGGCCACATA
Found at i:1895414 original size:32 final size:32
Alignment explanation
Indices: 1895378--1895578 Score: 208
Period size: 32 Copynumber: 6.2 Consensus size: 32
1895368 CTATACTTCC
* *
1895378 GATGGCTTTGTGTCGATCATATTACTATTACT
1 GATGGCTTTGTGCCGATCATATTACTGTTACT
** *
1895410 GATGGCTTTGTGTTGATCATAGTACTGTTACT
1 GATGGCTTTGTGCCGATCATATTACTGTTACT
* *
1895442 GATGGCTTTGTGCCTATTATATTTCACTGTTACT
1 GATGGCTTTGTGCCGATCATA-TT-ACTGTTACT
* * * **
1895476 GATGGCTGTGTGCCGGTCATGTTACCATTACT
1 GATGGCTTTGTGCCGATCATATTACTGTTACT
* * *
1895508 GATGGCTATGTGCCGATCATATCACTGCTACT
1 GATGGCTTTGTGCCGATCATATTACTGTTACT
*
1895540 GATGGCTTTGTG-CGAATCACATTACTG-TACT
1 GATGGCTTTGTGCCG-ATCATATTACTGTTACT
*
1895571 TATGGCTT
1 GATGGCTT
1895579 GTAGCCATTC
Statistics
Matches: 140, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
31 13 0.09
32 99 0.71
33 3 0.02
34 25 0.18
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.40
Consensus pattern (32 bp):
GATGGCTTTGTGCCGATCATATTACTGTTACT
Found at i:1896971 original size:3 final size:3
Alignment explanation
Indices: 1896965--1897031 Score: 125
Period size: 3 Copynumber: 22.3 Consensus size: 3
1896955 TTTAATCAAT
*
1896965 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1897013 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
1897032 CATCGATATC
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1904283 original size:128 final size:128
Alignment explanation
Indices: 1904055--1905923 Score: 2642
Period size: 128 Copynumber: 14.7 Consensus size: 128
1904045 TCGCTGAAAT
* * * *
1904055 CACAAGTCCTATATCCCTGACCAACAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGATCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * * *
1904120 CAGTAGCGGAGCAGATCGAA-AGCGGTAAACCTTATCTTCGAGAGTAAGGAAGCATATTTAAGC
66 CAGTAGCGGAGCAGATCGAAGA-CGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
* *
1904183 CACAAGTCCTATATCCCTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGATCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
*
1904248 CAGTAGCGGAGCAGATCGAA-AGTGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
66 CAGTAGCGGAGCAGATCGAAGA-CGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
* *
1904311 CACAAGTTCTATGTCCCT-AGTCAGCAGTGCAATAGGTTGGAAATTACAGATCTTGTCTCCCTAA
1 CACAAGTCCTATGTCCCTGA-TCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAA
* * * * *
1904375 GCAGTAGCGGAGCAGATCGAACATGGC-GA----ATC-T---GAGTAAGGAAGTAGATTTAAGA
65 GCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
* *
1904430 CACAAGTCCTATGTCCCTGGTCAACAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGATCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
*
1904495 CAGTAGCGGAGCAGATCGAAGACGACAAAT-TGTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
66 CAGTAGCGGAGCAGATCGAAGACGGCAAATCT-TATCTTCAAGAGTAAGGAAGCAGATTTAAGC
* * *
1904558 CACAAGTCCTATATCCCTAACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGATCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * *
1904623 AAGTAGCAGAGCAGATTGAA-AGCGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
66 CAGTAGCGGAGCAGATCGAAGA-CGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
* * * *
1904686 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGATTGGAAATTACAAATCTTGTCTCCCTGAG
1 CACAAGTCCTATGTCCCTGATCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* *
1904751 CAGTAGCGGAGCAGATCGAAGACGACGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
66 CAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
* *
1904814 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAAATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGATCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * ** ** *
1904879 CAGTAACGGAGCAGATTGAAGACGGTGAATCTTATCTTCAAGTTTAAGGAAGTAGATTTAAGC
66 CAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
* * * * *
1904942 CACAAGTCCTATCTCTCT-AGTCAGCAGTAGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTGA
1 CACAAGTCCTATGTCCCTGA-TCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAA
1905006 GCAGTAGCGGAGCAGATCGAA-AGCGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
65 GCAGTAGCGGAGCAGATCGAAGA-CGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
* * * *
1905070 CACAAGTCCTATGTCCCTAACCAGCAGTGGAATAGGTGGGAAATTACAGATCTTGTCTCTCTAAG
1 CACAAGTCCTATGTCCCTGATCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
*
1905135 AAGTAGCGGAGCAGATCGAA-AGCGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
66 CAGTAGCGGAGCAGATCGAAGA-CGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
* *
1905198 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTGAG
1 CACAAGTCCTATGTCCCTGATCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* ** * * *
1905263 TAGTAGTAGAGCAGATCGAAGACGACGAATCTTATATTCAAGAGTAAGGAAGCAGATTTAAGC
66 CAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
* * *
1905326 CACAAGTCCTATGTCCCTGGTCAACAGTGGAATAGGTTGGAAATTACAAATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGATCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * * * * ** *
1905391 CAGTAACGGAGCAGATTGAAAACGACGAATCTTATCTTCAAGTTTAAGGAAGTAGATTTAAGC
66 CAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
* * * * * *
1905454 CACAAATCCTATCTCTCTGGTCAGCAGTAGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGATCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * * *
1905519 CAGTAGCGGAGCAGATCGAAGACGGCGAATCCTATCTTCAAAAGTAAGGAAGCAGTTTTAAGC
66 CAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
*
1905582 CACAAGTCCTATGTCCCT-AGTCAGCAGTGGAATAGGTTGAAAATTACAGATCTTGTCTCCCTAA
1 CACAAGTCCTATGTCCCTGA-TCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAA
* *
1905646 TCAGTAGCGGAGCAGATCGAAGATGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
65 GCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
* * *
1905710 CACAAGTCCTATATCCCTTG-TCAGCAGTGGAGTAGGTTAGAAATTACAGATCTTGTCTCCCTAA
1 CACAAGTCCTATGTCCC-TGATCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAA
* * * * *
1905774 GCAGTAGCGGAGCAGATTGAAGACGGCGAATCTTATCTCCAAGTGTAAGGAAGTAGATTTAAGC
65 GCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
* * * *
1905838 CACAAGTCCTATCTCCCTGGTCAGCAGTAGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGATCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
*
1905903 CAGTAGCGGAGCAGATTGAAG
66 CAGTAGCGGAGCAGATCGAAG
1905924 CCAGTAATCT
Statistics
Matches: 1572, Mismatches: 146, Indels: 46
0.89 0.08 0.03
Matches are distributed among these distances:
119 103 0.07
120 1 0.00
122 1 0.00
123 3 0.00
124 3 0.00
125 1 0.00
127 6 0.00
128 1448 0.92
129 6 0.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (128 bp):
CACAAGTCCTATGTCCCTGATCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
CAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGC
Found at i:1905942 original size:43 final size:43
Alignment explanation
Indices: 1905895--1905986 Score: 98
Period size: 44 Copynumber: 2.1 Consensus size: 43
1905885 AGATCTTGTC
* * *
1905895 TCCCTAAGCAGT-AGCGGAGC-AGATTGAAGCCAGTAATCTTATT
1 TCCCTAAG-AGTAAACGGAGCGA-ATTAAAGCCAGTAATCCTATT
* *
1905938 TCCCTGAGATTACAACGGAGCGAATTAAAGCCAGTAATCCTATT
1 TCCCTAAGAGTA-AACGGAGCGAATTAAAGCCAGTAATCCTATT
1905982 TCCCT
1 TCCCT
1905987 GAGATTACAC
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
42 2 0.05
43 7 0.17
44 31 0.76
45 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (43 bp):
TCCCTAAGAGTAAACGGAGCGAATTAAAGCCAGTAATCCTATT
Found at i:1906003 original size:44 final size:44
Alignment explanation
Indices: 1905921--1906010 Score: 137
Period size: 44 Copynumber: 2.0 Consensus size: 44
1905911 GAGCAGATTG
* *
1905921 AAGCCAGTAATCTTATTTCCCTGAGATTACAACGGAGCGAATTA
1 AAGCCAGTAATCCTATTTCCCTGAGATTACAACAGAGCGAATTA
*
1905965 AAGCCAGTAATCCTATTTCCCTGAGATTAC-ACTAGAGCGGATTA
1 AAGCCAGTAATCCTATTTCCCTGAGATTACAAC-AGAGCGAATTA
1906009 AA
1 AA
1906011 ATAAAGGTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
43 2 0.05
44 40 0.95
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (44 bp):
AAGCCAGTAATCCTATTTCCCTGAGATTACAACAGAGCGAATTA
Found at i:1906164 original size:44 final size:44
Alignment explanation
Indices: 1906103--1906406 Score: 251
Period size: 44 Copynumber: 7.0 Consensus size: 44
1906093 GAAGAATTTC
* * * *
1906103 AAATCTTATCTCACTGAGGTTACAGTGGAGCAGATTGAAGCAAG
1 AAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAG
*
1906147 AAATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCCAG
1 AAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAG
* * * * * * ***
1906191 TAATCCTATTTCCCTAAGATTACA-CTAGAGCGGATT-AAAATA-
1 AAATCTTATCTCCCTGAGATTACAGC-GGAGCAGATTGAAGCCAG
* * ** * * * *
1906233 AAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATCGCA-TCAG
1 AA--ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAG
* ** * *
1906278 --GTCTTATCTTTCTAAGGTTACAGCGGAGCAGATTGAAGCCAG
1 AAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAG
* *
1906320 AAATCTTATCTCCCTGAGGTTACAGCGGAGTAGATTGAAGCCAG
1 AAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAG
* * *
1906364 AAATCTTATCTCCCTGAGATTACAGCAGAACAGATTAAAGCCA
1 AAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCA
1906407 CATTGGTGAA
Statistics
Matches: 203, Mismatches: 48, Indels: 18
0.75 0.18 0.07
Matches are distributed among these distances:
41 27 0.13
42 4 0.02
43 4 0.02
44 167 0.82
45 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (44 bp):
AAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAG
Found at i:1906543 original size:50 final size:51
Alignment explanation
Indices: 1906480--1906633 Score: 152
Period size: 50 Copynumber: 3.1 Consensus size: 51
1906470 CCACGTGATA
** * *
1906480 CAGTGAAGCAGATTAAAGCCAC-ATCGGTGAATCTTGCTTCCCCGACATTG
1 CAGTGAAAAAGATTAAAGCTACAATCGGTGAATCTTGCTTCCCAGACATTG
* * * * * *
1906530 CAGTTAAAAAGATTAAAGCTACAAT-AGCGAATCTTACTTCCCAGGCAGTG
1 CAGTGAAAAAGATTAAAGCTACAATCGGTGAATCTTGCTTCCCAGACATTG
* * * * *
1906580 TAGTGAAATAGATTAAAGCTACGA-CGGTAAATCTTGTTTCCCAGACATTG
1 CAGTGAAAAAGATTAAAGCTACAATCGGTGAATCTTGCTTCCCAGACATTG
1906630 CAGT
1 CAGT
1906634 CAGACAGAAG
Statistics
Matches: 80, Mismatches: 22, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
50 78 0.98
51 2 0.03
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (51 bp):
CAGTGAAAAAGATTAAAGCTACAATCGGTGAATCTTGCTTCCCAGACATTG
Found at i:1908359 original size:3 final size:3
Alignment explanation
Indices: 1908353--1909028 Score: 1352
Period size: 3 Copynumber: 225.3 Consensus size: 3
1908343 TTTAATCAAT
1908353 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1908401 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1908449 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1908497 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1908545 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1908593 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1908641 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1908689 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1908737 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1908785 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1908833 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1908881 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1908929 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1908977 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1909025 TTA T
1 TTA T
1909029 CATTGTATAA
Statistics
Matches: 673, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 673 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1909437 original size:16 final size:17
Alignment explanation
Indices: 1909412--1909445 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1909402 ATATAGTTCA
1909412 TAATAAATTATT-TTTT
1 TAATAAATTATTGTTTT
*
1909428 TAATATATTATTGTTTT
1 TAATAAATTATTGTTTT
1909445 T
1 T
1909446 GTATATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TAATAAATTATTGTTTT
Found at i:1913047 original size:51 final size:51
Alignment explanation
Indices: 1912992--1913123 Score: 153
Period size: 50 Copynumber: 2.6 Consensus size: 51
1912982 CCGATACACG
* * *
1912992 TAGTAGGCTGCACATAGTACTACACACGTGATCGAAACTATTC-GGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGAACCAAAC-ATTCTGGTACGCA
* * * *
1913043 TAGTAGCCTACACATAGTACTACACA--TGCAACCTATCATTCTGGTACGCG
1 TAGTAGCCTGCACATAGTACTACACACGTG-AACCAAACATTCTGGTACGCA
*
1913093 TAGTAGCCTGCACATAGTATTACACACGTGA
1 TAGTAGCCTGCACATAGTACTACACACGTGA
1913124 CCATCACTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
49 6 0.09
50 35 0.51
51 25 0.37
52 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGAACCAAACATTCTGGTACGCA
Done.