Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008424.1 Hibiscus syriacus cultivar Beakdansim tig00111207_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4198033
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 16
Found at i:1758800 original size:24 final size:22
Alignment explanation
Indices: 1758757--1758800 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
1758747 TGAGTCTGTT
*
1758757 TCCCATGAAACAAAGTTTTGTC
1 TCCCATGAAACAAAATTTTGTC
*
1758779 TCCCTTGAAACACAAATATTTG
1 TCCCATGAAACA-AAAT-TTTG
1758801 AGTATGTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
23 3 0.17
24 4 0.22
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (22 bp):
TCCCATGAAACAAAATTTTGTC
Found at i:1759241 original size:134 final size:132
Alignment explanation
Indices: 1758901--1759254 Score: 362
Period size: 134 Copynumber: 2.7 Consensus size: 132
1758891 TAGAAACTAA
* * * * *
1758901 GTCATCCCCCGACCAAACCTCCTCATCACGTATGA-GCGATATCAACCTTAGATAACCAGCCTTC
1 GTCATCCCCCGACCAAATCTCCTCATCACGTAGGATCCG-CATC-ACCTTAGATAACCAGACTTC
* * * ** *
1758965 CTCATCACGTAAGAACCGTGT-T-ATCATCCGTAAAGATGGTTAACAATCCTCATCACGTAGGAA
64 CTCATCACGTAGGAACCGTGTATCATCATCCCTAAAGATAGCCAACAATCCTCATCACATAGGAA
*
1759028 CTAT
129 CCAT
* *
1759032 GTCATCCCCCGACCAAATCTCCTCACCACGTAGGAGTCGCGC--CACCCCTAGATAACCA-ATCA
1 GTCATCCCCCGACCAAATCTCCTCATCACGTAGGA-TC-CGCATCA-CCTTAGATAACCAGA-C-
** * * *
1759094 TT-CTTGTCGCGTAGGAACCGTGTTATCATCATCCCTAAAGATAGCCAGCCATCCTCATCACATA
61 TTCCTCATCACGTAGGAACCGTG-TATCATCATCCCTAAAGATAGCCAACAATCCTCATCACATA
*
1759158 GGAACCGT
125 GGAACCAT
* * *
1759166 GTCATCCACCGACCAGATCTCCTCATCACGTAGGATCCGCATCACTCTTAGATAGCCAGACTTCC
1 GTCATCCCCCGACCAAATCTCCTCATCACGTAGGATCCGCATCAC-CTTAGATAACCAGACTTCC
1759231 TCATCACGTAGGAACCGTGCTATC
65 TCATCACGTAGGAACCGTG-TATC
1759255 TCCTAATTTT
Statistics
Matches: 180, Mismatches: 29, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
130 1 0.01
131 62 0.34
132 6 0.03
133 6 0.03
134 104 0.58
135 1 0.01
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.23
Consensus pattern (132 bp):
GTCATCCCCCGACCAAATCTCCTCATCACGTAGGATCCGCATCACCTTAGATAACCAGACTTCCT
CATCACGTAGGAACCGTGTATCATCATCCCTAAAGATAGCCAACAATCCTCATCACATAGGAACC
AT
Found at i:1762362 original size:24 final size:22
Alignment explanation
Indices: 1762334--1762394 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
1762324 AAATCAAGAA
1762334 TTTTTCAAATAAAAGTCATAATTG
1 TTTTTCAAATAAAA-T-ATAATTG
* *
1762358 TTTTTTAAATAATATATAATTG
1 TTTTTCAAATAAAATATAATTG
1762380 TTTTTCATAA-AAAAT
1 TTTTTCA-AATAAAAT
1762395 GGTTATGCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 17 0.53
23 3 0.09
24 12 0.38
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (22 bp):
TTTTTCAAATAAAATATAATTG
Found at i:1764640 original size:37 final size:37
Alignment explanation
Indices: 1764591--1764673 Score: 159
Period size: 37 Copynumber: 2.3 Consensus size: 37
1764581 AACACTCCCC
1764591 TTACC-ATAATCATTCTCTTCAATCTTCTCATCCTCG
1 TTACCAATAATCATTCTCTTCAATCTTCTCATCCTCG
1764627 TTACCAATAATCATTCTCTTCAATCTTCTCATCCTCG
1 TTACCAATAATCATTCTCTTCAATCTTCTCATCCTCG
1764664 TTACCAATAA
1 TTACCAATAA
1764674 CCTTCAAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 5 0.11
37 41 0.89
ACGTcount: A:0.27, C:0.31, G:0.02, T:0.40
Consensus pattern (37 bp):
TTACCAATAATCATTCTCTTCAATCTTCTCATCCTCG
Found at i:1764915 original size:3 final size:3
Alignment explanation
Indices: 1764907--1764973 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
1764897 TTAATATGAG
1764907 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1764955 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
1764974 ACATATATTC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1765470 original size:22 final size:21
Alignment explanation
Indices: 1765427--1765493 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
1765417 ACATTTGATT
* *
1765427 AAAGGACTTAGCC-ATTCGATG
1 AAAGGACTTAACCTTTTC-ATG
*
1765448 AAAAGGGCTTAACCTTTTCATG
1 -AAAGGACTTAACCTTTTCATG
* *
1765470 AAAGGATTTAATCTTTTCAT-
1 AAAGGACTTAACCTTTTCATG
1765490 AAAG
1 AAAG
1765494 AGCATTGTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 4 0.11
21 17 0.45
22 14 0.37
23 3 0.08
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (21 bp):
AAAGGACTTAACCTTTTCATG
Found at i:1766152 original size:13 final size:13
Alignment explanation
Indices: 1766136--1766161 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1766126 TAGGACCTTA
1766136 AATATTAATGGGC
1 AATATTAATGGGC
1766149 AATATTAATGGGC
1 AATATTAATGGGC
1766162 TTTAGTCACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
AATATTAATGGGC
Found at i:1768237 original size:21 final size:21
Alignment explanation
Indices: 1768213--1768308 Score: 93
Period size: 21 Copynumber: 4.5 Consensus size: 21
1768203 GGGTTAAGAC
* *
1768213 CTTTTAATGAAATGACTTAAA
1 CTTTTCATGAAAGGACTTAAA
* * * *
1768234 CTTTTTATTAAAGAACTTAAT
1 CTTTTCATGAAAGGACTTAAA
* *
1768255 CTTTTGATGAAAAGGGCTTAAA
1 CTTTTCATG-AAAGGACTTAAA
* *
1768277 CTTTTCATGAAAGGATTTAAT
1 CTTTTCATGAAAGGACTTAAA
1768298 CTTTTCATGAA
1 CTTTTCATGAA
1768309 GAGAATTGTT
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
21 43 0.72
22 17 0.28
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.41
Consensus pattern (21 bp):
CTTTTCATGAAAGGACTTAAA
Found at i:1769497 original size:27 final size:28
Alignment explanation
Indices: 1769455--1769516 Score: 99
Period size: 27 Copynumber: 2.2 Consensus size: 28
1769445 AAAGAACTAT
*
1769455 ATACCCTTGAACTGTAAAATAA-CCAAA
1 ATACCCCTGAACTGTAAAATAACCCAAA
*
1769482 ATACCCCTGAAGTGTAAAATAACCCAAA
1 ATACCCCTGAACTGTAAAATAACCCAAA
1769510 ATACCCC
1 ATACCCC
1769517 CAAGCCCTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 20 0.62
28 12 0.38
ACGTcount: A:0.45, C:0.27, G:0.08, T:0.19
Consensus pattern (28 bp):
ATACCCCTGAACTGTAAAATAACCCAAA
Found at i:1770629 original size:32 final size:32
Alignment explanation
Indices: 1770608--1770684 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
1770598 GTAGGCTTTG
1770608 AGGCCCCAAGGTATTTCCTTGGATAAGCTCTA
1 AGGCCCCAAGGTATTTCCTTGGATAAGCTCTA
* * *
1770640 AGGCTCCAAGGTATTAT-CTTAGG-TTAGCTCTT
1 AGGCCCCAAGGTATT-TCCTT-GGATAAGCTCTA
*
1770672 AGGCCACAAGGTA
1 AGGCCCCAAGGTA
1770685 CACTTTTGGG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
32 35 0.92
33 3 0.08
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (32 bp):
AGGCCCCAAGGTATTTCCTTGGATAAGCTCTA
Found at i:1772188 original size:2 final size:2
Alignment explanation
Indices: 1772183--1772212 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1772173 ACACACACAC
1772183 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1772213 GAGTGTGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1772288 original size:13 final size:15
Alignment explanation
Indices: 1772259--1772292 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
1772249 TTATATATTA
1772259 TATATTATATGTTCT
1 TATATTATATGTTCT
1772274 TATATT-TAT-TTCT
1 TATATTATATGTTCT
1772287 TATATT
1 TATATT
1772293 GCAAGGTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 3 0.16
15 6 0.32
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (15 bp):
TATATTATATGTTCT
Found at i:1776649 original size:22 final size:22
Alignment explanation
Indices: 1776611--1776655 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1776601 TCTTTAATTA
*
1776611 ATTTATTTAATTATTTTCTTTT
1 ATTTATTTAATTATTTTATTTT
*
1776633 ATTTATTT-TTTATTTTTATTTT
1 ATTTATTTAATTA-TTTTATTTT
1776655 A
1 A
1776656 AAAACAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (22 bp):
ATTTATTTAATTATTTTATTTT
Found at i:1777724 original size:25 final size:25
Alignment explanation
Indices: 1777695--1777744 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1777685 TGAAAATAAG
1777695 TTAGATAAATTAACTAAAGTAGTTA
1 TTAGATAAATTAACTAAAGTAGTTA
* *
1777720 TTAGATAAATTAATTGAAGTAGTTA
1 TTAGATAAATTAACTAAAGTAGTTA
1777745 ATTCACTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.02, G:0.14, T:0.38
Consensus pattern (25 bp):
TTAGATAAATTAACTAAAGTAGTTA
Found at i:1781345 original size:65 final size:65
Alignment explanation
Indices: 1781191--1781370 Score: 192
Period size: 65 Copynumber: 2.8 Consensus size: 65
1781181 TTGGACCCTT
* * * * *
1781191 AGTGCATCGGTGCACT-AAGAGTGCAGCGATGCATGAAGTGCATTCGATG-TTTCAAAATAGCCT
1 AGTGCATCGATGCA-TGAAGAATGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCC
*
1781254 G
65 A
* *
1781255 AGTGCATCGATGCATG--GTATTTGCATCGATGCATCAAATGCATTCGATGTTTTCATTAAA-A-
1 AGTGCATCGATGCATGAAG-A-ATGCATCGATGCATGAAATGCATTCGATGTTTTCA--AAATAG
1781316 CCCA
62 CCCA
*
1781320 AGTGCATCGATGCATGAAGAATGCATCGATGCATGAACTGCATTCGATGTT
1 AGTGCATCGATGCATGAAGAATGCATCGATGCATGAAATGCATTCGATGTT
1781371 CAATTTAATT
Statistics
Matches: 98, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 38 0.39
65 51 0.52
66 2 0.02
67 4 0.04
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (65 bp):
AGTGCATCGATGCATGAAGAATGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCCA
Found at i:1781390 original size:65 final size:65
Alignment explanation
Indices: 1781192--1781400 Score: 184
Period size: 65 Copynumber: 3.2 Consensus size: 65
1781182 TGGACCCTTA
* * * * *
1781192 GTGCATCGGTGCACT-AAGAGTGCAGCGATGCATGAAGTGCATTCGATGTTTCAA--AATAGCC-
1 GTGCATCGATGCA-TGAAGAATGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAT-CCCA
1781253 TG
64 TG
* * *
1781255 AGTGCATCGATGCATG--GTATTTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATTAAAAC
1 -GTGCATCGATGCATGAAG-A-ATGCATCGATGCATGAAATGCATTCGATG-TTTCAATT-AATC
*
1781317 CCA-A
61 CCATG
* *
1781321 GTGCATCGATGCATGAAGAATGCATCGATGCATGAACTGCATTCGATG-TTCAATTTAATTCCAT
1 GTGCATCGATGCATGAAGAATGCATCGATGCATGAAATGCATTCGATGTTTCAA-TTAATCCCAT
1781385 G
65 G
1781386 GTGCATCGATGCATG
1 GTGCATCGATGCATG
1781401 GATTGGTACA
Statistics
Matches: 118, Mismatches: 14, Indels: 25
0.75 0.09 0.16
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 44 0.37
65 62 0.53
66 3 0.03
67 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.29
Consensus pattern (65 bp):
GTGCATCGATGCATGAAGAATGCATCGATGCATGAAATGCATTCGATGTTTCAATTAATCCCATG
Found at i:1790020 original size:65 final size:65
Alignment explanation
Indices: 1789866--1790045 Score: 188
Period size: 65 Copynumber: 2.8 Consensus size: 65
1789856 TTGGACCCTT
* * * *
1789866 AGTGCATCAGTGCAC-TAAGAGTTCATCGATGCATGAAGTGCATTCGATG-TTTCAAAATAGCCT
1 AGTGCATCAATGCACGGAA-AGTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCT
1789929 G
65 G
* ** *
1789930 AGTGCATCAATGCACGGTATTTGCATCGATGCATAAAATGCATTCGATGTTTTCATTAAA-A-CC
1 AGTGCATCAATGCACGGAAAGTGCATCGATGCATGAAATGCATTCGATGTTTTCA--AAATAGCC
1789993 TG
64 TG
* * * * *
1789995 AGTGCATCGATGCATGGAAAGTGCATCGATTCATGAACTACATTCGATGTT
1 AGTGCATCAATGCACGGAAAGTGCATCGATGCATGAAATGCATTCGATGTT
1790046 CAATTAATTC
Statistics
Matches: 95, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
64 39 0.41
65 52 0.55
66 1 0.01
67 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (65 bp):
AGTGCATCAATGCACGGAAAGTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCTG
Found at i:1793583 original size:75 final size:75
Alignment explanation
Indices: 1793495--1793657 Score: 177
Period size: 76 Copynumber: 2.2 Consensus size: 75
1793485 AAACTCAACC
* * *
1793495 TTAGGATAATATTTTAAACATTATAT-TTTATCTTTT-TATTTTAGTTTAAATAGGTTTTTGTAT
1 TTAGGATATTATTTT-AACATTATATCTTTAT-TTTTGTATTTTAGTTGAAATAGGTTTTAGTAT
*
1793558 TTTAATTAAGTT
64 TTTAATTAAGAT
* * * * *
1793570 TTAGGATATTATTTTTATATTTTATCTTTGTTTTTGGTATTTTAGTTGAAATAGGTTTTAGTGTT
1 TTAGGATATTATTTTAACATTATATCTTTATTTTT-GTATTTTAGTTGAAATAGGTTTTAGTATT
* *
1793635 TTGATTAGGAT
65 TTAATTAAGAT
*
1793646 TTAGAATATTAT
1 TTAGGATATTAT
1793658 ATTATTTTTA
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
74 11 0.15
75 18 0.25
76 44 0.60
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (75 bp):
TTAGGATATTATTTTAACATTATATCTTTATTTTTGTATTTTAGTTGAAATAGGTTTTAGTATTT
TAATTAAGAT
Found at i:1794324 original size:22 final size:21
Alignment explanation
Indices: 1794298--1794338 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1794288 ATCTCTTTAA
1794298 TTTATTTATTTAATTATTTTCT
1 TTTATTTATTT-ATTATTTTCT
*
1794320 TTTATTTATTTTTTATTTT
1 TTTATTTATTTATTATTTT
1794339 AAAAATAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTATTTATTTATTATTTTCT
Found at i:1794325 original size:18 final size:16
Alignment explanation
Indices: 1794298--1794339 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1794288 ATCTCTTTAA
1794298 TTTA-TTTATTTAATTAT
1 TTTATTTTATTT-ATT-T
*
1794315 TTTCTTTTATTTATTT
1 TTTATTTTATTTATTT
1794331 TTTATTTTA
1 TTTATTTTA
1794340 AAAATAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 9 0.41
17 6 0.27
18 7 0.32
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTTTATTTATTT
Found at i:1799077 original size:3 final size:3
Alignment explanation
Indices: 1799071--1799102 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1799061 AACTATTATT
1799071 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1799103 ATGGGACGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1799486 original size:87 final size:82
Alignment explanation
Indices: 1799228--1799510 Score: 311
Period size: 82 Copynumber: 3.4 Consensus size: 82
1799218 GGTAAATCTA
* * * * * *
1799228 CTCCACTCTTC-TTTAAGAGGAGATCAGACTTGATCTGTTCCACTTTTCTGGGTAGTT-AGATCT
1 CTCCACTATTCATTT-AGGGGAGATCAGACTTGATCTGTGCCTCTTTTCTGGGTA-TTCAAATCA
1799291 ATTTTGGAAGACGTGTCTG
64 ATTTTGGAAGACGTGTCTG
*
1799310 CTCCACTATTCATTTAGGGGAGATCAGACTTGATCTGTGCCTTTTTTCT-GGTATTCAAATCAAT
1 CTCCACTATTCATTTAGGGGAGATCAGACTTGATCTGTGCCTCTTTTCTGGGTATTCAAATCAAT
* *
1799374 TTTAGAAGAAGTGTCTG
66 TTTGGAAGACGTGTCTG
* * *
1799391 CTCTACTATTCATTTAGGGGAGGGGAGATTAGACTTGATTTGTGCCTCTTTTCTGGGTATTCAAA
1 CTCCACTATTCATTT-----AGGGGAGATCAGACTTGATCTGTGCCTCTTTTCTGGGTATTCAAA
**
1799456 TCAATTTTGGAAGACGTGTCAA
61 TCAATTTTGGAAGACGTGTCTG
* * * * *
1799478 ATCCACTATTCATTCAAGGGAGACCATACTTGA
1 CTCCACTATTCATTTAGGGGAGATCAGACTTGA
1799511 GAAATCTTTG
Statistics
Matches: 169, Mismatches: 24, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
80 2 0.01
81 39 0.23
82 54 0.32
83 3 0.02
86 31 0.18
87 40 0.24
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Consensus pattern (82 bp):
CTCCACTATTCATTTAGGGGAGATCAGACTTGATCTGTGCCTCTTTTCTGGGTATTCAAATCAAT
TTTGGAAGACGTGTCTG
Found at i:1799699 original size:89 final size:89
Alignment explanation
Indices: 1799588--1800250 Score: 634
Period size: 89 Copynumber: 7.4 Consensus size: 89
1799578 ATGAATTTGA
* * * * * ** * *
1799588 TCCACTACTTTTCTGGGGAGATCAGACTCAAAATTGATTTGATTCGCTGTTTTTTCAGGAATATC
1 TCCACTACTCTTCCGTGGAGATCAGACTCAAGATTGATTTGATTCACTACTTTTTCAGGAAGACC
* *
1799653 AAATCTGAAATAAAAATAATATGT
66 AAATCTGAAATAAGAAGAATATGT
* * * *
1799677 TCCACTACTCTTTCGTGGAGATCAGACTCGAGATGGATTTGATTCACTACTATTTC-GTGAAGAC
1 TCCACTACTCTTCCGTGGAGATCAGACTCAAGATTGATTTGATTCACTACTTTTTCAG-GAAGAC
*
1799741 CAAATCTGAAATAAGAAGAATTTGT
65 CAAATCTGAAATAAGAAGAATATGT
** * * * *
1799766 TCCACTACTCTTCCGTGTTGATCAGACT-AGAGATTGATTTGATTCATTTCTTTTTCAGAAAGAA
1 TCCACTACTCTTCCGTGGAGATCAGACTCA-AGATTGATTTGATTCACTACTTTTTCAGGAAGAC
*
1799830 CAAATCTGACATAAGAAGAATATGT
65 CAAATCTGAAATAAGAAGAATATGT
* * ** * * * * * **
1799855 TACACTACTTTTTTGTGGAGATTATACTCAATATGGATTTGATTCACTACTCTTTCATAAAGACC
1 TCCACTACTCTTCCGTGGAGATCAGACTCAAGATTGATTTGATTCACTACTTTTTCAGGAAGACC
*
1799920 AAATCTGAAATAAGAAGAATCTGT
66 AAATCTGAAATAAGAAGAATATGT
* * * * * * ** *
1799944 TCCACAACTCTACCGTGGTGATTAGACTCGAGATTGATTTGAGTCGTTGCTTTTTCAGGAAGACC
1 TCCACTACTCTTCCGTGGAGATCAGACTCAAGATTGATTTGATTCACTACTTTTTCAGGAAGACC
* * * **
1800009 AAATCTGACATAACAAGAATCTAC
66 AAATCTGAAATAAGAAGAATATGT
* * * * *
1800033 TCCACTATTCTTCCATGGTGATCAGACTCTAGATTGATTTGATTCACTACTCTTTC-GTGAAGAC
1 TCCACTACTCTTCCGTGGAGATCAGACTCAAGATTGATTTGATTCACTACTTTTTCAG-GAAGAC
1800097 CAAATCT-AACATAAGAAGAATATGT
65 CAAATCTGAA-ATAAGAAGAATATGT
* * * * * * * *
1800122 TCCACTACTCTTCCGGGGAGATCAGACTCGAGATTGATTTGCTTCGCTACTCTTTCGGGAAGGCT
1 TCCACTACTCTTCCGTGGAGATCAGACTCAAGATTGATTTGATTCACTACTTTTTCAGGAAGACC
* *
1800187 AAATCTAAAATAAGAAGAAT-TTT
66 AAATCTGAAATAAGAAGAATATGT
* * **
1800210 CTCCACTACTCTTCCATGGTGATCAGACTCTGGATTGATTT
1 -TCCACTACTCTTCCGTGGAGATCAGACTCAAGATTGATTT
1800251 AGCATCCCTC
Statistics
Matches: 467, Mismatches: 98, Indels: 18
0.80 0.17 0.03
Matches are distributed among these distances:
88 5 0.01
89 457 0.98
90 5 0.01
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (89 bp):
TCCACTACTCTTCCGTGGAGATCAGACTCAAGATTGATTTGATTCACTACTTTTTCAGGAAGACC
AAATCTGAAATAAGAAGAATATGT
Found at i:1800069 original size:267 final size:266
Alignment explanation
Indices: 1799590--1800250 Score: 707
Period size: 267 Copynumber: 2.5 Consensus size: 266
1799580 GAATTTGATC
* * * * * ** * * * *
1799590 CACTACTTTTCTGGGGAGATCAGACTCAAAATTGATTTGATTCGCTGTTTTTTCAGGAATATCAA
1 CACTACTCTTCCGGGGAGATCAGACTCAAGATGGATTTGATTCACTACTCTTTCAGAAAGACCAA
* * * * * *
1799655 ATCTGAAATAAAAATAATATGTTCCACTACTCTTTCGTGGAGATCAGACTCGAGATGGATTTGAT
66 ATCTGAAATAAGAAGAAT-TGTTCCACTACTCTTCCGTGGTGATCAGACTCGAGATTGATTTGAG
* * ** * *
1799720 TCACTACTATTTCGTGAAGACCAAATCTGAAATAAGAAGAATTTGTTCCACTACTCTTCCGTGTT
130 TCACTACTATTTCGTGAAGACCAAATCTGAAATAACAAGAATCTACTCCACTACTCTTCCATGGT
* * * *
1799785 GATCAGACTAGAGATTGATTTGATTCATTTCTTTTTCAG-AAAGAACAAATCTGACATAAGAAGA
195 GATCAGACTAGAGATTGATTTGATTCACTACTCTTTC-GTAAAGAACAAATCTAACATAAGAAGA
1799849 ATATGTTA
259 ATATGTTA
* ** * * * * *
1799857 CACTACTTTTTTGTGGAGATTATACTCAATATGGATTTGATTCACTACTCTTTCATAAAGACCAA
1 CACTACTCTTCCGGGGAGATCAGACTCAAGATGGATTTGATTCACTACTCTTTCAGAAAGACCAA
* * *
1799922 ATCTGAAATAAGAAGAATCTGTTCCACAACTCTACCGTGGTGATTAGACTCGAGATTGATTTGAG
66 ATCTGAAATAAGAAGAAT-TGTTCCACTACTCTTCCGTGGTGATCAGACTCGAGATTGATTTGAG
** * * * *
1799987 TCGTTGCTTTTTCAG-GAAGACCAAATCTGACATAACAAGAATCTACTCCACTATTCTTCCATGG
130 TCACTACTATTTC-GTGAAGACCAAATCTGAAATAACAAGAATCTACTCCACTACTCTTCCATGG
** * *
1800051 TGATCAGACTCTAGATTGATTTGATTCACTACTCTTTCGTGAAGACCAAATCTAACATAAGAAGA
194 TGATCAGACTAGAGATTGATTTGATTCACTACTCTTTCGTAAAGAACAAATCTAACATAAGAAGA
*
1800116 ATATGTTC
259 ATATGTTA
* * * * * * * *
1800124 CACTACTCTTCCGGGGAGATCAGACTCGAGATTGATTTGCTTCGCTACTCTTTCGGGAAGGCTAA
1 CACTACTCTTCCGGGGAGATCAGACTCAAGATGGATTTGATTCACTACTCTTTCAGAAAGACCAA
* * *
1800189 ATCTAAAATAAGAAGAATTTTCTCCACTACTCTTCCATGGTGATCAGACTCTG-GATTGATTT
66 ATCTGAAATAAGAAGAATTGT-TCCACTACTCTTCCGTGGTGATCAGACTC-GAGATTGATTT
1800251 AGCATCCCTC
Statistics
Matches: 323, Mismatches: 67, Indels: 8
0.81 0.17 0.02
Matches are distributed among these distances:
266 3 0.01
267 318 0.98
268 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (266 bp):
CACTACTCTTCCGGGGAGATCAGACTCAAGATGGATTTGATTCACTACTCTTTCAGAAAGACCAA
ATCTGAAATAAGAAGAATTGTTCCACTACTCTTCCGTGGTGATCAGACTCGAGATTGATTTGAGT
CACTACTATTTCGTGAAGACCAAATCTGAAATAACAAGAATCTACTCCACTACTCTTCCATGGTG
ATCAGACTAGAGATTGATTTGATTCACTACTCTTTCGTAAAGAACAAATCTAACATAAGAAGAAT
ATGTTA
Found at i:1800216 original size:178 final size:178
Alignment explanation
Indices: 1799588--1800250 Score: 722
Period size: 178 Copynumber: 3.7 Consensus size: 178
1799578 ATGAATTTGA
* * * * * *
1799588 TCCACTACTTTTCTGGGGAGATCAGACTCAAAATTGATTTGATTCGCTGTTTTTTCAGGAATA-T
1 TCCACTACTCTTCCGGGGAGATCAGACTCGAGATTGATTTGATTCGCTGCTTTTTCAGGAAGACT
* * * * *
1799652 CAAATCTGAAATAAAAATAATATGTTCCACTACTCTTTCGTGGAGATCAGACTCGAGATGGATTT
66 -AAATCTGAAATAAGAAGAATATGTTCCACTACTCTTCCATGGAGATCAGACTCTAGATGGATTT
* *
1799717 GATTCACTACTATTTCGTGAAGACCAAATCTGAAATAAGAAGAATTTGT
130 GATTCACTACTCTTTCGTGAAGACCAAATCTGAAATAAGAAGAATATGT
* ** * ** * *
1799766 TCCACTACTCTTCCGTGTTGATCAGACTAGAGATTGATTTGATTCATTTCTTTTTCAGAAAGAAC
1 TCCACTACTCTTCCGGGGAGATCAGACTCGAGATTGATTTGATTCGCTGCTTTTTCAGGAAG-AC
* * * *** * * * *
1799831 -AAATCTGACATAAGAAGAATATGTTACACTACTTTTTTGTGGAGATTATACTCAATATGGATTT
65 TAAATCTGAAATAAGAAGAATATGTTCCACTACTCTTCCATGGAGATCAGACTCTAGATGGATTT
* * *
1799895 GATTCACTACTCTTTCATAAAGACCAAATCTGAAATAAGAAGAATCTGT
130 GATTCACTACTCTTTCGTGAAGACCAAATCTGAAATAAGAAGAATATGT
* * * * * * * *
1799944 TCCACAACTCTACCGTGGTGATTAGACTCGAGATTGATTTGAGTCGTTGCTTTTTCAGGAAGACC
1 TCCACTACTCTTCCGGGGAGATCAGACTCGAGATTGATTTGATTCGCTGCTTTTTCAGGAAGACT
* * * ** * * *
1800009 AAATCTGACATAACAAGAATCTACTCCACTATTCTTCCATGGTGATCAGACTCTAGATTGATTTG
66 AAATCTGAAATAAGAAGAATATGTTCCACTACTCTTCCATGGAGATCAGACTCTAGATGGATTTG
1800074 ATTCACTACTCTTTCGTGAAGACCAAATCT-AACATAAGAAGAATATGT
131 ATTCACTACTCTTTCGTGAAGACCAAATCTGAA-ATAAGAAGAATATGT
* * * * *
1800122 TCCACTACTCTTCCGGGGAGATCAGACTCGAGATTGATTTGCTTCGCTACTCTTTCGGGAAGGCT
1 TCCACTACTCTTCCGGGGAGATCAGACTCGAGATTGATTTGATTCGCTGCTTTTTCAGGAAGACT
* * * * *
1800187 AAATCTAAAATAAGAAGAAT-TTTCTCCACTACTCTTCCATGGTGATCAGACTCTGGATTGATTT
66 AAATCTGAAATAAGAAGAATATGT-TCCACTACTCTTCCATGGAGATCAGACTCTAGATGGATTT
1800251 AGCATCCCTC
Statistics
Matches: 404, Mismatches: 76, Indels: 10
0.82 0.16 0.02
Matches are distributed among these distances:
177 5 0.01
178 398 0.99
179 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (178 bp):
TCCACTACTCTTCCGGGGAGATCAGACTCGAGATTGATTTGATTCGCTGCTTTTTCAGGAAGACT
AAATCTGAAATAAGAAGAATATGTTCCACTACTCTTCCATGGAGATCAGACTCTAGATGGATTTG
ATTCACTACTCTTTCGTGAAGACCAAATCTGAAATAAGAAGAATATGT
Found at i:1803561 original size:20 final size:20
Alignment explanation
Indices: 1803506--1803565 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 20
1803496 TATATATACC
*
1803506 GGTAAGGGGTATCAATACCAT
1 GGTAA-GGGTATCGATACCAT
* *
1803527 AGTAGGGTAGTATCGATACCAT
1 GGTAAGG--GTATCGATACCAT
1803549 GGTAAGGGTATCGATAC
1 GGTAAGGGTATCGATAC
1803566 TAGACAGCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 12 0.38
21 3 0.09
22 17 0.53
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (20 bp):
GGTAAGGGTATCGATACCAT
Found at i:1803624 original size:94 final size:94
Alignment explanation
Indices: 1803436--1803661 Score: 235
Period size: 94 Copynumber: 2.4 Consensus size: 94
1803426 ATACCAATGA
* * * * *
1803436 GGTAGCATCGATACCATGATAAGGGGTATCGATTCCAAGAAACATCAAATCTAATTTTGGTATAT
1 GGTAGTATCGATACCATGGTAA-GGGTATCGA-TACTAGAAACATCAAACCTAATTTTGGTATAT
1803501 ATACCGGTAAGGGGTATCAATACCATAGTAG
64 ATACCGGTAAGGGGTATCAATACCATAGTAG
* *
1803532 GGTAGTATCGATACCATGGTAAGGGTATCGATACTAGACAGCATCAAACCTATTTTTGGTATCGA
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACTAGA-AACATCAAACCTAATTTTGGTAT--A
* * *
1803597 TAT-GC-G-AAGGGGTATCAGTACCATAGTAT
63 TATACCGGTAAGGGGTATCAATACCATAGTAG
* * * * *
1803626 AGAAGTATCGGTACTATGGT-AGTAGTATCGATACTA
1 GGTAGTATCGATACCATGGTAAG-GGTATCGATACTA
1803662 TGTAGCCAAA
Statistics
Matches: 111, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
93 2 0.02
94 54 0.49
95 30 0.27
96 21 0.19
97 4 0.04
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (94 bp):
GGTAGTATCGATACCATGGTAAGGGTATCGATACTAGAAACATCAAACCTAATTTTGGTATATAT
ACCGGTAAGGGGTATCAATACCATAGTAG
Found at i:1804601 original size:80 final size:80
Alignment explanation
Indices: 1804462--1804939 Score: 647
Period size: 80 Copynumber: 6.0 Consensus size: 80
1804452 GTGTCTTTGA
* * * * * **
1804462 GGCCTAACTCTGCATATGGTAGAAATGTGTCAATTATGCCAGTTAGAAGAATGGTTAAGTATTGT
1 GGCCTAACTGTGCAT-TGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
1804527 TGAGTAAAAGAATAAT
65 TGAGTAAAAGAATAAT
* * *
1804543 GGCCTAACTGTGCATTGGCAGAAAGATGTAAATTATGCCAGTTAGATGAACGGATAAGTACCGTT
1 GGCCTAACTGTGCATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTT
1804608 GAGTAAAAGAATAAT
66 GAGTAAAAGAATAAT
* * * *
1804623 GGCCTAACTG-GCATTGACAGAAAGGTGCCAATTATGCCAATTAGATGAACGGTTAAGTACCTTT
1 GGCCTAACTGTGCATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTT
*
1804687 GAGTAAAACAATAAT
66 GAGTAAAAGAATAAT
* *
1804702 GGCCTAATTGTGCATTGGCAGAAAGGTGTCAATTATG-CAGTTAGATGAATGGTTAAGTACCGTT
1 GGCCTAACTGTGCATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTT
*
1804766 GAGTGAAAGAATAAT
66 GAGTAAAAGAATAAT
* * * *
1804781 GGCCTAATTATGCATTGGCAGAAAGGTGTCAATTATGTCAGTTAGATGAACGGTTAAGTACCATT
1 GGCCTAACTGTGCATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTT
* *
1804846 GCGTAAAACAATAAT
66 GAGTAAAAGAATAAT
* * * * * *
1804861 GGCCTAACTCTGCATTGGCAGAAAAGTGTCAATTATGCTAGTTAGACGAAC-GTTAAGCACTGTT
1 GGCCTAACTGTGCATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTT
*
1804925 GAGTAAGAGAATAAT
66 GAGTAAAAGAATAAT
1804940 TTTTTTTAAT
Statistics
Matches: 351, Mismatches: 44, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
79 165 0.47
80 172 0.49
81 14 0.04
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (80 bp):
GGCCTAACTGTGCATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTT
GAGTAAAAGAATAAT
Found at i:1804796 original size:159 final size:156
Alignment explanation
Indices: 1804482--1804939 Score: 621
Period size: 159 Copynumber: 2.9 Consensus size: 156
1804472 TGCATATGGT
* * * * *
1804482 AGAAATGTGTCAATTATGCCAGTTAGAAGAATGGTTAAGTA-TTGTTGAGTAAAAGAATAATGGC
1 AGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCT-TTGAGTAAAACAATAATGGC
* * *
1804546 CTAACTGTGCATTGGCAGAAAGATGTAAATTATGCCAGTTAGATGAACGGATAAGTACCGTTGAG
65 CTAACTGTGCATTGGCAGAAAGGTGTCAATTATG-CAGTTAGATGAA-GGTTAAGTACCGTTGAG
1804611 TAAAAGAATAATGGCCTAACTGGCATTGAC
128 T-AAAGAATAATGGCCTAACTGGCATTGAC
* *
1804641 AGAAAGGTGCCAATTATGCCAATTAGATGAACGGTTAAGTACCTTTGAGTAAAACAATAATGGCC
1 AGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCTTTGAGTAAAACAATAATGGCC
*
1804706 TAATTGTGCATTGGCAGAAAGGTGTCAATTATGCAGTTAGATGAATGGTTAAGTACCGTTGAGTG
66 TAACTGTGCATTGGCAGAAAGGTGTCAATTATGCAGTTAGATGAA-GGTTAAGTACCGTTGAGT-
* * *
1804771 AAAGAATAATGGCCTAATTATGCATTGGC
129 AAAGAATAATGGCCTAACT-GGCATTGAC
* * *
1804800 AGAAAGGTGTCAATTATGTCAGTTAGATGAACGGTTAAGTACCATTGCGTAAAACAATAATGGCC
1 AGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCTTTGAGTAAAACAATAATGGCC
* * * * * *
1804865 TAACTCTGCATTGGCAGAAAAGTGTCAATTATGCTAGTTAGACGAACGTTAAGCACTGTTGAGTA
66 TAACTGTGCATTGGCAGAAAGGTGTCAATTATGC-AGTTAGATGAAGGTTAAGTACCGTTGAGTA
1804930 AGAGAATAAT
130 A-AGAATAAT
1804940 TTTTTTTAAT
Statistics
Matches: 267, Mismatches: 28, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
158 49 0.18
159 207 0.78
160 11 0.04
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (156 bp):
AGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCTTTGAGTAAAACAATAATGGCC
TAACTGTGCATTGGCAGAAAGGTGTCAATTATGCAGTTAGATGAAGGTTAAGTACCGTTGAGTAA
AGAATAATGGCCTAACTGGCATTGAC
Found at i:1809881 original size:20 final size:20
Alignment explanation
Indices: 1809856--1809898 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1809846 TCTAAGAGCC
* *
1809856 CATTTAGGATCATTTAGATG
1 CATTTAGGAGCATATAGATG
*
1809876 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
1809896 CAT
1 CAT
1809899 GAGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:1818122 original size:15 final size:14
Alignment explanation
Indices: 1818091--1818131 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
1818081 CTCCCTTTCT
*
1818091 AAAAAAACGAAAGA
1 AAAAAAAAGAAAGA
*
1818105 AAAGAAAAGAAAGAA
1 AAAAAAAAGAAAG-A
1818120 AAAAAAAAGAAA
1 AAAAAAAAGAAA
1818132 ACAATGTGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAGA
Found at i:1818783 original size:27 final size:27
Alignment explanation
Indices: 1818744--1818798 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1818734 TATTTTCACG
1818744 GGATCTCTAATCATGACCGAGAAATCC
1 GGATCTCTAATCATGACCGAGAAATCC
*
1818771 GGATCTCTGATCATGACCGAGAAATCC
1 GGATCTCTAATCATGACCGAGAAATCC
1818798 G
1 G
1818799 CCTGGATCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (27 bp):
GGATCTCTAATCATGACCGAGAAATCC
Found at i:1820334 original size:20 final size:20
Alignment explanation
Indices: 1820277--1820335 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 20
1820267 ATATCGATCC
* *
1820277 AGTAAGGGGTATTGATACCCT
1 AGTAA-GGGTATCGATACCAT
1820298 AGT-AGGGTAGAATCGATACCAT
1 AGTAAGGGT---ATCGATACCAT
1820320 AGTAAGGGTATCGATA
1 AGTAAGGGTATCGATA
1820336 ACAAGCAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
19 4 0.12
20 8 0.25
21 3 0.09
22 12 0.38
23 5 0.16
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (20 bp):
AGTAAGGGTATCGATACCAT
Found at i:1821374 original size:80 final size:80
Alignment explanation
Indices: 1821253--1821632 Score: 443
Period size: 80 Copynumber: 4.8 Consensus size: 80
1821243 ATTGTTTATA
* * * * ** *
1821253 TGGTATAAAAGTGTCAATTATGCCAATTTGATGAACGGTTAAGTACCTTTGAGTAAAAGAATAAT
1 TGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAATAGTTAAGTACCGTTGAGTAAAAGAATAAT
* *
1821318 GGCCTAATTGTGCAG
66 GGCCTAACTGTGCAT
1821333 TGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAATAGTTAAAG-ACCGTTGAGTAAAAGAATAA
1 TGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAATAGTT-AAGTACCGTTGAGTAAAAGAATAA
1821397 TGGCCTAACTGTGCAT
65 TGGCCTAACTGTGCAT
* * * * * *
1821413 TGGCAAAAATGTGTCAATTATGCAAGTTAGATGAATGGTTAAGTACCGATGAGTAAAAGAATAAT
1 TGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAATAGTTAAGTACCGTTGAGTAAAAGAATAAT
1821478 GGCCTAACTGTGCAT
66 GGCCTAACTGTGCAT
* * * *
1821493 TGGTAGAAAGGTTTCAATTATACCAGTTAGATG-A-A--T-AGTACCATTGAGTAAAAAAATAAT
1 TGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAATAGTTAAGTACCGTTGAGTAAAAGAATAAT
* * *
1821553 GGCCTAAATGAGAAT
66 GGCCTAACTGTGCAT
* ** * *
1821568 TGGTAGAAAGGTGTCAATTATGCCAGTTAGA-CAA-ACGTTAAACACTGTTGAGTAAGAGAATAA
1 TGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAATA-GTTAAGTACCGTTGAGTAAAAGAATAA
1821631 TG
65 TG
1821633 AAATTTCAAT
Statistics
Matches: 256, Mismatches: 37, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
75 64 0.25
76 1 0.00
78 1 0.00
79 23 0.09
80 164 0.64
81 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (80 bp):
TGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAATAGTTAAGTACCGTTGAGTAAAAGAATAAT
GGCCTAACTGTGCAT
Found at i:1827009 original size:23 final size:23
Alignment explanation
Indices: 1826979--1827048 Score: 97
Period size: 23 Copynumber: 3.0 Consensus size: 23
1826969 TCTCCGACGT
1826979 TTCAGAATCGAGCTCTTCGCCGC
1 TTCAGAATCGAGCTCTTCGCCGC
*
1827002 TTCAGAATCGAGCTC-TCTGTCGC
1 TTCAGAATCGAGCTCTTC-GCCGC
* *
1827025 TTCAGAATCGAGTTCTCCGCCGC
1 TTCAGAATCGAGCTCTTCGCCGC
1827048 T
1 T
1827049 CAATATTGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 2 0.05
23 38 0.93
24 1 0.02
ACGTcount: A:0.17, C:0.33, G:0.21, T:0.29
Consensus pattern (23 bp):
TTCAGAATCGAGCTCTTCGCCGC
Found at i:1828995 original size:18 final size:18
Alignment explanation
Indices: 1828974--1829041 Score: 61
Period size: 23 Copynumber: 3.6 Consensus size: 18
1828964 ATTTTTTTAT
1828974 TTTTTTCTTTTCTATCTC
1 TTTTTTCTTTTCTATCTC
1828992 TTTTATTTTTTCTTTTCTATCTC
1 -----TTTTTTCTTTTCTATCTC
1829015 TTTTCTT-TTTT-TA-CTC
1 TTTT-TTCTTTTCTATCTC
1829031 TTTTTTCTTTT
1 TTTTTTCTTTT
1829042 TTCAATAGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
15 2 0.05
16 11 0.26
17 2 0.05
18 8 0.19
19 2 0.05
23 18 0.42
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTTCTTTTCTATCTC
Found at i:1828995 original size:24 final size:24
Alignment explanation
Indices: 1828968--1829026 Score: 102
Period size: 23 Copynumber: 2.5 Consensus size: 24
1828958 TTTTTTATTT
1828968 TTTTATTTTTTTCTTTTCTATCTC
1 TTTTATTTTTTTCTTTTCTATCTC
1828992 TTTTA-TTTTTTCTTTTCTATCTC
1 TTTTATTTTTTTCTTTTCTATCTC
*
1829015 TTTTCTTTTTTT
1 TTTTATTTTTTT
1829027 ACTCTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 22 0.67
24 11 0.33
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTATTTTTTTCTTTTCTATCTC
Found at i:1829041 original size:16 final size:17
Alignment explanation
Indices: 1828997--1829042 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
1828987 ATCTCTTTTA
1828997 TTTTTTCTTTTCTATCTC
1 TTTTTTCTTTT-TATCTC
1829015 TTTTCTT-TTTTTA-CTC
1 TTTT-TTCTTTTTATCTC
1829031 TTTTTTCTTTTT
1 TTTTTTCTTTTT
1829043 TCAATAGAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.08
16 12 0.46
17 2 0.08
18 8 0.31
19 2 0.08
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTCTTTTTATCTC
Found at i:1829646 original size:35 final size:35
Alignment explanation
Indices: 1829583--1829672 Score: 100
Period size: 35 Copynumber: 2.6 Consensus size: 35
1829573 TTGAACCCCA
*
1829583 TTTCA-TTTTCTATTTCTATTTTTATTTTTTCATT
1 TTTCATTTTTCTATTTCTATTTCTATTTTTTCATT
1829617 TTTCATTTTTC-ATTTTCCTATTTCT-TTTTTTCATT
1 TTTCATTTTTCTA-TTT-CTATTTCTATTTTTTCATT
*
1829652 TTTC-TTTTGT-TTTTTCTATTT
1 TTTCATTTT-TCTATTTCTATTT
1829673 TCTTATATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
33 6 0.12
34 13 0.27
35 23 0.47
36 7 0.14
ACGTcount: A:0.11, C:0.13, G:0.01, T:0.74
Consensus pattern (35 bp):
TTTCATTTTTCTATTTCTATTTCTATTTTTTCATT
Found at i:1829655 original size:7 final size:7
Alignment explanation
Indices: 1829583--1829659 Score: 58
Period size: 7 Copynumber: 11.3 Consensus size: 7
1829573 TTGAACCCCA
1829583 TTTCA-T
1 TTTCATT
*
1829589 TTTC-TA
1 TTTCATT
1829595 TTTCTATT
1 TTTC-ATT
1829603 TTT-ATTT
1 TTTCA-TT
1829610 TTTCATT
1 TTTCATT
1829617 TTTCATT
1 TTTCATT
1829624 TTTCATT
1 TTTCATT
*
1829631 TTCCTATT
1 TTTC-ATT
1829639 TCTT--TT
1 T-TTCATT
1829645 TTTCATT
1 TTTCATT
1829652 TTTC-TT
1 TTTCATT
1829658 TT
1 TT
1829660 GTTTTTTCTA
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
5 2 0.03
6 16 0.28
7 30 0.52
8 9 0.16
9 1 0.02
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTCATT
Found at i:1829683 original size:19 final size:20
Alignment explanation
Indices: 1829642--1829689 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1829632 TCCTATTTCT
* *
1829642 TTTTTTC-ATTTTTCTTTTG
1 TTTTTTCTATTTTTCTTATA
1829661 TTTTTTCTA-TTTTCTTATA
1 TTTTTTCTATTTTTCTTATA
1829680 TTTTCTTCTA
1 TTTT-TTCTA
1829690 GCATAATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.75
Consensus pattern (20 bp):
TTTTTTCTATTTTTCTTATA
Found at i:1830045 original size:20 final size:20
Alignment explanation
Indices: 1830020--1830060 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1830010 TAAAAATTTG
1830020 GAGGACTAAATTGAATAAGA
1 GAGGACTAAATTGAATAAGA
1830040 GAGGACTAAATTGAATAAGA
1 GAGGACTAAATTGAATAAGA
1830060 G
1 G
1830061 GGTAAAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.05, G:0.27, T:0.20
Consensus pattern (20 bp):
GAGGACTAAATTGAATAAGA
Found at i:1838074 original size:18 final size:18
Alignment explanation
Indices: 1838051--1838089 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1838041 TGTTCGAAAT
1838051 GATTGAAATAAATAATAA
1 GATTGAAATAAATAATAA
* * *
1838069 GATTGAATTTAATAGTAA
1 GATTGAAATAAATAATAA
1838087 GAT
1 GAT
1838090 CGGACGGAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.33
Consensus pattern (18 bp):
GATTGAAATAAATAATAA
Found at i:1839676 original size:63 final size:63
Alignment explanation
Indices: 1839574--1839697 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
1839564 CTAATATGAC
* * * *
1839574 TCTTAGGTAGGCTCTATGACCCTGAGATCATTCTCGGGTAGGCCCTGCA-GCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCATGACCCCGAAATCATTCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* * * *
1839637 TCTTAGGTAGGCCCCATGGCCCCGAAATC-TATCTTGGGTATGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCATGACCCCGAAATCAT-TCTCGGGTAGGCCCTCAGGCCCTAAGATGT
1839698 TCCCTTAAGT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 3 0.06
63 48 0.94
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.28
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCATGACCCCGAAATCATTCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:1844897 original size:13 final size:13
Alignment explanation
Indices: 1844879--1844904 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1844869 CATGCTTCTA
1844879 CTTCGGTTGTTTG
1 CTTCGGTTGTTTG
1844892 CTTCGGTTGTTTG
1 CTTCGGTTGTTTG
1844905 GAATCGTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.31, T:0.54
Consensus pattern (13 bp):
CTTCGGTTGTTTG
Found at i:1852080 original size:20 final size:21
Alignment explanation
Indices: 1852055--1852100 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1852045 GATTTATCAA
1852055 ATACCAAAAAGGG-AG-TATCG
1 ATACC-AAAAGGGAAGATATCG
1852075 ATACC-AAAGGGAAGATATCG
1 ATACCAAAAGGGAAGATATCG
1852095 ATACCA
1 ATACCA
1852101 TAGTATAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 6 0.26
19 2 0.09
20 15 0.65
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (21 bp):
ATACCAAAAGGGAAGATATCG
Found at i:1852085 original size:18 final size:20
Alignment explanation
Indices: 1852062--1852100 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1852052 CAAATACCAA
1852062 AAAGGG-AG-TATCGATACC
1 AAAGGGAAGATATCGATACC
1852080 AAAGGGAAGATATCGATACC
1 AAAGGGAAGATATCGATACC
1852100 A
1 A
1852101 TAGTATAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 2 0.11
20 11 0.58
ACGTcount: A:0.44, C:0.15, G:0.26, T:0.15
Consensus pattern (20 bp):
AAAGGGAAGATATCGATACC
Found at i:1852618 original size:54 final size:55
Alignment explanation
Indices: 1852483--1852629 Score: 215
Period size: 55 Copynumber: 2.7 Consensus size: 55
1852473 TGCAAAAAGA
* *
1852483 TAAGAAATTCATACTAAGTGTATGAATTTCTGTATAGGCACTATATGTGCAAAAC
1 TAAGAAATTCATACTAAGTGTATGAATTTCTGTATGGGCACTAGATGTGCAAAAC
* * *
1852538 TAATAAATTCATACTAAGTGTATGAATTTCTGTATGGGCACTAGGTGTGC-GAAC
1 TAAGAAATTCATACTAAGTGTATGAATTTCTGTATGGGCACTAGATGTGCAAAAC
* * *
1852592 TAAGAAATTCATACAAAGTGTCTGAATTTCCGTATGGG
1 TAAGAAATTCATACTAAGTGTATGAATTTCTGTATGGG
1852630 AAATATACGT
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
54 37 0.45
55 46 0.55
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.33
Consensus pattern (55 bp):
TAAGAAATTCATACTAAGTGTATGAATTTCTGTATGGGCACTAGATGTGCAAAAC
Found at i:1852674 original size:109 final size:109
Alignment explanation
Indices: 1852483--1852681 Score: 249
Period size: 109 Copynumber: 1.8 Consensus size: 109
1852473 TGCAAAAAGA
* * * * * * *
1852483 TAAGAAATTCATACTAAGTGTATGAATTTCTGTATAGGCACTATATGTGCAAAACTAATAAATTC
1 TAAGAAATTCATACAAAGTGTATGAATTTCCGTATAGGAAATATACGTACAAAACTAAGAAATTC
* *
1852548 ATACTAAGTGTATGAATTTCTGTATGGGCACTAGGTGTGCGAAC
66 ATAATAAGTGTATGAATTTCCGTATGGGCACTAGGTGTGCGAAC
* * *
1852592 TAAGAAATTCATACAAAGTGTCTGAATTTCCGTATGGGAAATATACGTACAAATA-TAAGAAGTT
1 TAAGAAATTCATACAAAGTGTATGAATTTCCGTATAGGAAATATACGTACAAA-ACTAAGAAATT
*
1852656 CATAATAAGTAG-GTGAATTTCCGTAT
65 CATAATAAGT-GTATGAATTTCCGTAT
1852682 TGGTAGTGGG
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
109 73 0.97
110 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (109 bp):
TAAGAAATTCATACAAAGTGTATGAATTTCCGTATAGGAAATATACGTACAAAACTAAGAAATTC
ATAATAAGTGTATGAATTTCCGTATGGGCACTAGGTGTGCGAAC
Found at i:1853317 original size:68 final size:68
Alignment explanation
Indices: 1852842--1853302 Score: 694
Period size: 68 Copynumber: 6.8 Consensus size: 68
1852832 AAAGATTAAT
* * * *
1852842 GGCCTAGTTGTGCATTTGACAGAAACGTGTC-ATTAATGCCAATTAGACGAAAGGCTAAGTGCCT
1 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATT-ATGCCAGTTAGATGAAAGGCTAAGTGCCT
1852906 TTGA
65 TTGA
* * * * * * *
1852910 GGCCTAGCTGTGCATTGGACATAAATGTGTC-ATTAATACCAGTTAGATGAAAGGATAAATTCCT
1 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATT-ATGCCAGTTAGATGAAAGGCTAAGTGCCT
1852974 TTGA
65 TTGA
* *
1852978 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTACGCCAGTTAGATGAAAAGCTAAGTGCCTT
1 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1853043 TGA
66 TGA
* *
1853046 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATACCAGTTAGATGAAAGGCTAAGTGTCTT
1 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
*
1853111 TAA
66 TGA
* * * *
1853114 GGCCTAGTTGTGCATTTAATAGAAAGGTGTCAATTATTCCAGTTAGATGAAAGGCTAAGTGCCTT
1 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1853179 TGA
66 TGA
*
1853182 GGCCTA-CTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1853246 TGA
66 TGA
1853249 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
1 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
1853303 TTAAATACAT
Statistics
Matches: 355, Mismatches: 36, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
67 62 0.17
68 290 0.82
69 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (68 bp):
GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
TGA
Found at i:1853709 original size:25 final size:25
Alignment explanation
Indices: 1853635--1853709 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 25
1853625 TCTCAGTATG
1853635 AAAGGATGCCATAATTGAAATGCAT
1 AAAGGATGCCATAATTGAAATGCAT
* * ** * *
1853660 -ATGGGTG-CATTCTCGACATG---
1 AAAGGATGCCATAATTGAAATGCAT
1853680 AAAGGATGCCATAATTGAAATGCAT
1 AAAGGATGCCATAATTGAAATGCAT
1853705 AAAGG
1 AAAGG
1853710 TGCATTTTAA
Statistics
Matches: 33, Mismatches: 12, Indels: 10
0.60 0.22 0.18
Matches are distributed among these distances:
21 5 0.15
22 9 0.27
23 9 0.27
24 5 0.15
25 5 0.15
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (25 bp):
AAAGGATGCCATAATTGAAATGCAT
Found at i:1853732 original size:45 final size:45
Alignment explanation
Indices: 1853369--1853715 Score: 426
Period size: 45 Copynumber: 7.7 Consensus size: 45
1853359 GGCAACAAAT
* * * *
1853369 GATGCCATAATTGAAAGGCATATGGGTGCATTCTTGGCAAGAAAG
1 GATGCCATAATTGAAATGCATATGGGTGCATTCTCGACATGAAAG
* *
1853414 GATGCCATAATTGAAATGCATATGAGTGCATTATCGACATGAAAG
1 GATGCCATAATTGAAATGCATATGGGTGCATTCTCGACATGAAAG
* * * * *
1853459 GATGCCATAATTGTAATGCATATGGGAGTATTATCGACACGAAAG
1 GATGCCATAATTGAAATGCATATGGGTGCATTCTCGACATGAAAG
* * * * *
1853504 GATACCATAATTGAAATGAATATGGGTGCATTATTGCCATGAAAG
1 GATGCCATAATTGAAATGCATATGGGTGCATTCTCGACATGAAAG
** * * * *
1853549 GATGTTATAATTGAAATGCACATGGGTGTATTCTCGGCATAAAAG
1 GATGCCATAATTGAAATGCATATGGGTGCATTCTCGACATGAAAG
* * * *
1853594 GATGTCATGATTGAAATACATATGGGTGCATTCTC-AGTATGAAAG
1 GATGCCATAATTGAAATGCATATGGGTGCATTCTCGA-CATGAAAG
1853639 GATGCCATAATTGAAATGCATATGGGTGCATTCTCGACATGAAAG
1 GATGCCATAATTGAAATGCATATGGGTGCATTCTCGACATGAAAG
**
1853684 GATGCCATAATTGAAATGCATAAAGGTGCATT
1 GATGCCATAATTGAAATGCATATGGGTGCATT
1853716 TTAAGCATGA
Statistics
Matches: 257, Mismatches: 43, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
45 256 1.00
46 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (45 bp):
GATGCCATAATTGAAATGCATATGGGTGCATTCTCGACATGAAAG
Found at i:1857537 original size:20 final size:20
Alignment explanation
Indices: 1857512--1857562 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
1857502 ATGCAATCAA
*
1857512 TATCGATACCAAAGGG-GGAG
1 TATCGATACCAAAGGGAAG-G
1857532 TATCGATACCAAAGGGAAGG
1 TATCGATACCAAAGGGAAGG
1857552 TATCGATACCA
1 TATCGATACCA
1857563 TTGCAAAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (20 bp):
TATCGATACCAAAGGGAAGG
Found at i:1857597 original size:19 final size:19
Alignment explanation
Indices: 1857573--1857609 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1857563 TTGCAAAACT
*
1857573 GGTATCGGTACCATAATAG
1 GGTATCAGTACCATAATAG
1857592 GGTATCAGTACCATAATA
1 GGTATCAGTACCATAATA
1857610 TAGTAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (19 bp):
GGTATCAGTACCATAATAG
Found at i:1858191 original size:45 final size:45
Alignment explanation
Indices: 1858127--1858524 Score: 566
Period size: 45 Copynumber: 8.9 Consensus size: 45
1858117 TATAAAAGGG
** * *
1858127 ATGAAAGGATGCTC-TAATTGAAATGTGTATGGGTGTATTATCGAC
1 ATGAAAGGATGC-CATAATTGAAATGCATATGGGTGCATTATCGGC
* * *
1858172 ATGAATGGATGCCATAATTGAAATGCATATGAGTGCATTCTCGGC
1 ATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGGC
* *
1858217 ATGAAAGGATTCCATAATTGAAATGCATATGGGTACATTATCGGC
1 ATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGGC
1858262 ATGAAAGGATGCCA-AATTGAAATGCATATGGGTGCATTATCGGC
1 ATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGGC
* * *
1858306 ATGAAAGGATGCCATAATTGAAATACATATGGGTGCATTATTGGA
1 ATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGGC
* * * **
1858351 ATGATAGGATGCCATAATTGAAATGCATATGGGTACATTCTCAAC
1 ATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGGC
* *
1858396 ATGAAAGGATGCCATAATTGAAATGCATATGGATGCATTCTCGGC
1 ATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGGC
*
1858441 ATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTCTCGGC
1 ATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGGC
* * *
1858486 ATAAAAAGATGCCATAATTGAAATGCATATAGGTGCATT
1 ATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATT
1858525 TTAAGCATGA
Statistics
Matches: 317, Mismatches: 34, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
44 44 0.14
45 273 0.86
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (45 bp):
ATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGGC
Found at i:1876801 original size:17 final size:18
Alignment explanation
Indices: 1876779--1876819 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1876769 AAATTCCATA
1876779 ATACCAAAAT-GGTATCG
1 ATACCAAAATGGGTATCG
*
1876796 ATACCAAAGTGGGTATCG
1 ATACCAAAATGGGTATCG
*
1876814 GTACCA
1 ATACCA
1876820 TAGAAGAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (18 bp):
ATACCAAAATGGGTATCG
Found at i:1890238 original size:20 final size:19
Alignment explanation
Indices: 1890214--1890251 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1890204 TTCTTCTTGT
1890214 TCTTCTT-TT-CTTTATCA
1 TCTTCTTCTTCCTTTATCA
1890231 TCTTCTTCTTCCTTTATCA
1 TCTTCTTCTTCCTTTATCA
1890250 TC
1 TC
1890252 AACTCATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 2 0.11
19 10 0.53
ACGTcount: A:0.11, C:0.29, G:0.00, T:0.61
Consensus pattern (19 bp):
TCTTCTTCTTCCTTTATCA
Found at i:1892964 original size:5 final size:5
Alignment explanation
Indices: 1892954--1893018 Score: 53
Period size: 5 Copynumber: 12.8 Consensus size: 5
1892944 AACGGTCAAC
* * *
1892954 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGT-T GGTATG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGT-CG GGTCG
*
1893001 GGTC- GGTCA GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC
1893019 AAACCGGTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
4 7 0.14
5 35 0.71
6 3 0.06
7 4 0.08
ACGTcount: A:0.06, C:0.18, G:0.52, T:0.23
Consensus pattern (5 bp):
GGTCG
Found at i:1892969 original size:17 final size:17
Alignment explanation
Indices: 1892947--1892984 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1892937 CACGGTCAAC
1892947 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1892964 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1892981 GGTC
1 GGTC
1892985 GGGTTGGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:1892988 original size:22 final size:23
Alignment explanation
Indices: 1892940--1892988 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
1892930 TAACGGTCAC
1892940 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC-ACGGTCGGGTCG
*
1892964 GGTCAACGGTC-GGGTCGGGTCG
1 GGTCAACGGTCACGGTCGGGTCG
1892986 GGT
1 GGT
1892989 TGGTATGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 13 0.54
24 11 0.46
ACGTcount: A:0.12, C:0.22, G:0.47, T:0.18
Consensus pattern (23 bp):
GGTCAACGGTCACGGTCGGGTCG
Found at i:1900239 original size:29 final size:29
Alignment explanation
Indices: 1900188--1900243 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1900178 GTCGGGTCAG
* *
1900188 ACCGGTCAAACCGATTCAGACCGGTTTGA
1 ACCGGTCAAACCGAGTCAAACCGGTTTGA
1900217 ACCGGTCAAAACCG-GTCAAACCGGTTT
1 ACCGGTC-AAACCGAGTCAAACCGGTTT
1900244 TCAGCCACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.20
Consensus pattern (29 bp):
ACCGGTCAAACCGAGTCAAACCGGTTTGA
Found at i:1901336 original size:20 final size:20
Alignment explanation
Indices: 1901313--1901362 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1901303 ACTTTTAATG
1901313 GACTTTGAATTATTTTTGAA
1 GACTTTGAATTATTTTTGAA
1901333 GACTTTGAATTATTTTTGAA
1 GACTTTGAATTATTTTTGAA
*
1901353 AACTTTGAAT
1 GACTTTGAAT
1901363 AAATTCAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (20 bp):
GACTTTGAATTATTTTTGAA
Found at i:1904101 original size:35 final size:36
Alignment explanation
Indices: 1904054--1904121 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
1904044 ATTTAGAAGT
1904054 TGGTGATAATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGACTA
* *
1904089 TGGTGATGATATAGGTGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
1904122 AATAGTAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.28, C:0.03, G:0.37, T:0.32
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGACTA
Found at i:1904116 original size:11 final size:11
Alignment explanation
Indices: 1904071--1904119 Score: 55
Period size: 11 Copynumber: 4.2 Consensus size: 11
1904061 AATATAGGCG
1904071 TGATATGGTGA
1 TGATATGGTGA
1904082 TGGACTATGGTGA
1 T-GA-TATGGTGA
1904095 TGATATAGGTG-
1 TGATAT-GGTGA
1904106 TGATAATGGTGA
1 TGAT-ATGGTGA
1904118 TG
1 TG
1904120 GAAATAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 12 0.36
12 12 0.36
13 9 0.27
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.35
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:1907949 original size:15 final size:16
Alignment explanation
Indices: 1907898--1907950 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
1907888 CGATAGTGAA
1907898 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
1907915 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
1907932 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
1907947 ATAA
1 ATAA
1907951 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:1916705 original size:13 final size:13
Alignment explanation
Indices: 1916687--1916711 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1916677 ACTGTAAGAT
1916687 TTATTAGTATTAC
1 TTATTAGTATTAC
1916700 TTATTAGTATTA
1 TTATTAGTATTA
1916712 GGTATTTGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (13 bp):
TTATTAGTATTAC
Found at i:1919421 original size:18 final size:17
Alignment explanation
Indices: 1919398--1919435 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1919388 CTTTCAATTC
1919398 TTTTATTATT-TTTTATTA
1 TTTTATT-TTATTTTA-TA
1919416 TTTTATTTTATTTTATA
1 TTTTATTTTATTTTATA
1919433 TTT
1 TTT
1919436 ATTGTATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTATTTTATTTTATA
Found at i:1922279 original size:37 final size:34
Alignment explanation
Indices: 1922233--1922378 Score: 107
Period size: 37 Copynumber: 4.0 Consensus size: 34
1922223 TAAGAGATAT
*
1922233 AGAAAAAACACAAAAAAAAAAAAGTAAAAACAGAAA
1 AGAAAAAACA-AAAAAAAAAAAAG-AAAAAAAGAAA
**
1922269 AGAGAAAAACAAAAGAAAAAGAAAAGAAAAGGAGAAA
1 AGA-AAAAACAAAA-AAAAA-AAAAGAAAAAAAGAAA
1922306 AGAAAAAA-AATAAAAAATAAAAAGAAAGAAAAAGAAA
1 AGAAAAAACAA-AAAAAA-AAAAAG-AA-AAAAAGAAA
* * * * *
1922343 A-AAGAGAGAAAAAAGAATAAAAGAAGAAGAAGAAA
1 AGAAAAAACAAAAAA-AAAAAAAGAA-AAAAAGAAA
1922378 A
1 A
1922379 TAGACAGATC
Statistics
Matches: 93, Mismatches: 8, Indels: 19
0.77 0.07 0.16
Matches are distributed among these distances:
35 23 0.25
36 29 0.31
37 36 0.39
38 5 0.05
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.03
Consensus pattern (34 bp):
AGAAAAAACAAAAAAAAAAAAAGAAAAAAAGAAA
Found at i:1922296 original size:22 final size:22
Alignment explanation
Indices: 1922271--1922344 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
1922261 AACAGAAAAG
1922271 AGAAAAACAAAAGAAAAAGAAA
1 AGAAAAACAAAAGAAAAAGAAA
*
1922293 AGAAAAGGAGAAAAGAAAAA-AAA
1 AGAAAA--ACAAAAGAAAAAGAAA
* *
1922316 TA-AAAAATAAAA-AGAAAGAAAA
1 -AGAAAAACAAAAGAAAAAG-AAA
1922338 AGAAAAA
1 AGAAAAA
1922345 AGAGAGAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
20 4 0.09
21 6 0.14
22 14 0.33
23 7 0.16
24 12 0.28
ACGTcount: A:0.81, C:0.01, G:0.15, T:0.03
Consensus pattern (22 bp):
AGAAAAACAAAAGAAAAAGAAA
Found at i:1922310 original size:35 final size:33
Alignment explanation
Indices: 1922236--1922378 Score: 103
Period size: 32 Copynumber: 4.1 Consensus size: 33
1922226 GAGATATAGA
**
1922236 AAAAACACAAAAAAAAAAAAGTAAAAACAGAAAAG
1 AAAAA-ACAAAAAAAAAAAAG-AAAAGGAGAAAAG
1922271 AGAAAAACAAAAGAAAAAGAAAAGAAAAGGAGAAAAG
1 A-AAAAAC-AAA-AAAAA-AAAAGAAAAGGAGAAAAG
*
1922308 AAAAAAAATAAAAAATAAAAAG-AAA-GA-AAAAG
1 AAAAAACA-AAAAAA-AAAAAGAAAAGGAGAAAAG
* * * * *
1922340 AAAAAAGAGAGAAAAAAGAATAAAAGAAGAAGAAG
1 AAAAAACA-AAAAAAAAAAAGAAAAGGAGAA-AAG
1922375 AAAA
1 AAAA
1922379 TAGACAGATC
Statistics
Matches: 89, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
31 4 0.04
32 20 0.22
33 3 0.03
34 5 0.06
35 20 0.22
36 15 0.17
37 17 0.19
38 5 0.06
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (33 bp):
AAAAAACAAAAAAAAAAAAGAAAAGGAGAAAAG
Found at i:1922320 original size:9 final size:9
Alignment explanation
Indices: 1922244--1922370 Score: 68
Period size: 9 Copynumber: 13.8 Consensus size: 9
1922234 GAAAAAACAC
1922244 AAAA-AAAA
1 AAAAGAAAA
*
1922252 AAAAGTAAA
1 AAAAGAAAA
*
1922261 AACAG--AA
1 AAAAGAAAA
*
1922268 AAGAGAAAA
1 AAAAGAAAA
* *
1922277 ACAA-AAGA
1 AAAAGAAAA
1922285 AAAAGAAAA
1 AAAAGAAAA
1922294 GAAAAGGAGAAA
1 -AAAA-GA-AAA
1922306 AGAAA-AAAA
1 A-AAAGAAAA
1922315 ATAAA-AAATA
1 A-AAAGAAA-A
1922325 AAAAGAAAGA
1 AAAAGAAA-A
1922335 AAAAGAAAA
1 AAAAGAAAA
* *
1922344 AAGAGAGAA
1 AAAAGAAAA
1922353 AAAAGAATAA
1 AAAAGAA-AA
1922363 AAGAAGAA
1 AA-AAGAA
1922371 GAAGAAAATA
Statistics
Matches: 93, Mismatches: 14, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
7 6 0.06
8 10 0.11
9 40 0.43
10 23 0.25
11 8 0.09
12 6 0.06
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.03
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:1922345 original size:17 final size:16
Alignment explanation
Indices: 1922244--1922378 Score: 105
Period size: 17 Copynumber: 8.1 Consensus size: 16
1922234 GAAAAAACAC
*
1922244 AAAAAAA-AAAAAG-T
1 AAAAAAAGAAAAAGAA
*
1922258 AAAAACAGAAAAGAGAA
1 AAAAAAAGAAAA-AGAA
1922275 AAACAAAAGAAAAAGAA
1 AAA-AAAAGAAAAAGAA
*
1922292 AAGAAAAGGAGAAAAGAA
1 AA-AAAAAGA-AAAAGAA
*
1922310 AAAAAATA-AAAAATAA
1 AAAAAA-AGAAAAAGAA
*
1922326 AAAGAAAGAAAAAGAA
1 AAAAAAAGAAAAAGAA
*
1922342 AAAAGAGAGAAAAAAGAA
1 AAAA-AAAG-AAAAAGAA
* *
1922360 TAAAAGAAGAAGAAGAA
1 -AAAAAAAGAAAAAGAA
1922377 AA
1 AA
1922379 TAGACAGATC
Statistics
Matches: 97, Mismatches: 13, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
14 6 0.06
15 5 0.05
16 25 0.26
17 29 0.30
18 28 0.29
19 4 0.04
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.03
Consensus pattern (16 bp):
AAAAAAAGAAAAAGAA
Found at i:1922353 original size:67 final size:65
Alignment explanation
Indices: 1922244--1922378 Score: 150
Period size: 67 Copynumber: 2.0 Consensus size: 65
1922234 GAAAAAACAC
* * *
1922244 AAAAAAAAAAAAGTAAAAACAGAAAAGAGAAAAACAAAAGAAAAAGAAAAGAAAAGGAGAA-AAG
1 AAAAAAAAAAAAATAAAAAAAGAAAAGAGAAAAACAAAAGAAAAA-AAAAGAAAAGAAGAAGAAG
1922308 A
65 A
* * *
1922309 AAAAAAATAAAAAATAAAAAGAAAGAAAA-AGAAAAA-AGAGAGAAAAAAGAATAAAAGAAGAAG
1 AAAAAAA-AAAAAAT-AAAA-AAAGAAAAGAGAAAAACA-AAAGAAAAAAAAAGAAAAGAAGAAG
1922372 AAGA
62 AAGA
1922376 AAA
1 AAA
1922379 TAGACAGATC
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
65 7 0.12
66 19 0.32
67 26 0.44
68 7 0.12
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.03
Consensus pattern (65 bp):
AAAAAAAAAAAAATAAAAAAAGAAAAGAGAAAAACAAAAGAAAAAAAAAGAAAAGAAGAAGAAGA
Found at i:1922355 original size:40 final size:40
Alignment explanation
Indices: 1922246--1922373 Score: 116
Period size: 39 Copynumber: 3.0 Consensus size: 40
1922236 AAAAACACAA
*
1922246 AAAAAAAAAAGTAAAAACAGAAAAGAGAAA-AACAAAAGAAAAAG
1 AAAAGAAAAAG-AAAAA-AGAAAA-A-AAATAA-AAAAGAAAAAG
* * *
1922290 AAAAGAAAAGGAGAAAAGAAAAAAAATAAAAAATAAAAAG
1 AAAAGAAAAAGAAAAAAGAAAAAAAATAAAAAAGAAAAAG
* *
1922330 -AAAGAAAAAGAAAAAAGAGAGAAAAAAGAATAAAAGAAGAAG
1 AAAAGAAAAAGAAAAAAGA-A-AAAAAATAA-AAAAGAAAAAG
1922372 AA
1 AA
1922374 GAAAATAGAC
Statistics
Matches: 70, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
39 16 0.23
40 14 0.20
41 11 0.16
42 15 0.21
43 5 0.07
44 9 0.13
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.03
Consensus pattern (40 bp):
AAAAGAAAAAGAAAAAAGAAAAAAAATAAAAAAGAAAAAG
Found at i:1922357 original size:74 final size:76
Alignment explanation
Indices: 1922233--1922373 Score: 173
Period size: 73 Copynumber: 1.9 Consensus size: 76
1922223 TAAGAGATAT
* * * *
1922233 AGAAAAAACACAAAAAAAAAAAAGTAAAAACAGAAAAGAGAAAAACAAAAG-A-AAAAGAA-AAG
1 AGAAAAAAAACAAAAAAAAAAAAGAAAAAAAAGAAAAAAGAAAAACAAAAGAATAAAAGAAGAAG
1922295 AAAAGGAGAAA
66 AAAAGGAGAAA
* * *
1922306 AGAAAAAAAATAAAAAATAAAAAGAAAGAAAAAGAAAAAAGAGAGAA-AAAAGAATAAAAGAAGA
1 AGAAAAAAAACAAAAAAAAAAAAGAAA-AAAAAGAAAAAAGA-AAAACAAAAGAATAAAAGAAGA
1922370 AGAA
64 AGAA
1922374 GAAAATAGAC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
73 23 0.41
74 17 0.30
75 4 0.07
76 7 0.12
77 5 0.09
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.03
Consensus pattern (76 bp):
AGAAAAAAAACAAAAAAAAAAAAGAAAAAAAAGAAAAAAGAAAAACAAAAGAATAAAAGAAGAAG
AAAAGGAGAAA
Found at i:1924110 original size:4 final size:4
Alignment explanation
Indices: 1924095--1924744 Score: 1223
Period size: 4 Copynumber: 162.5 Consensus size: 4
1924085 TTCATTTAAG
*
1924095 TACA TTCA TACA TACA TACA TACA T--A TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* *
1924141 TACA TACA TACA TACA TACA TATA TATA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
1924189 TACA TACA TACA TACA TATA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1924237 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1924285 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1924333 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1924381 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1924429 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1924477 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1924525 TACA TACA TACA TACA TACA TGCACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA T--ACA TACA TACA TACA TACA TACA TACA
1924575 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1924623 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
1924671 TACA TACA TACA TACA TACA TACA TATA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1924719 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
1924745 TATAATTCTT
Statistics
Matches: 634, Mismatches: 8, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
2 2 0.00
4 628 0.99
6 4 0.01
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:1924992 original size:55 final size:55
Alignment explanation
Indices: 1924916--1925342 Score: 477
Period size: 55 Copynumber: 7.8 Consensus size: 55
1924906 GTGTTTTTTT
**
1924916 AACTAAGTCTGATTTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAAGA
1 AACTAAGTCTGA-TTTTCAGAAGTTTCTTGATGATTTTCAAATGAGCTTTTAAAGA
* * * * * *
1924972 AATTAATTCTAATTTTCAGAAGTTTCTTGATGATTTTTAAATGATCTTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGCTTTTAAAGA
* * *
1925027 AATTATGTCTGATTTCCAGAAGTTTCTTGATGATTTTCAAATGAGCTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGCTTTTAAAGA
* * * *
1925082 AACTAAGTCTGATTTTCAGAAGTTTGTTGACGATTTTCAAATTAGTTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGCTTTTAAAGA
* *
1925137 AACTAAGTTTGATTTTTAGAAGTTTCTTGATGATTTTCAAATGA--TTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGCTTTTAAAGA
* * * * * *
1925190 AACTAAGTCTGATTTTTAAAAGTTTCTTAATGATTTTTAAAAGAACTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGCTTTTAAAGA
* * * * ** * * *
1925245 AATTAAGCCTAATTTTTAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAAAAAAA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGCTTT--TAAAGA
** *
1925300 AACTAAGTCTGATTTTCAGGGGTTTCTCGATG-TTTTCAAATGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGA
1925343 ATTTGAAAGG
Statistics
Matches: 318, Mismatches: 49, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
53 51 0.16
54 9 0.03
55 249 0.78
56 9 0.03
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (55 bp):
AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGCTTTTAAAGA
Found at i:1925305 original size:163 final size:163
Alignment explanation
Indices: 1924929--1925370 Score: 458
Period size: 163 Copynumber: 2.7 Consensus size: 163
1924919 TAAGTCTGAT
* * * * * * *
1924929 TTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTT-TAAAGAAATTAATTCTAATTTTCAGAA
1 TTTTCAGAAGTTTCTTGACGATTTTCAAATGA-ATTTAAAAAAAAACTAAGTCTGATTTTCAGAA
* * * ** * *
1924993 GTTTCTTGATGATTTTTAAATGATCTTTCAAAGAAATTATGTCTGATTTCCAGAAGTTTCTTGAT
65 GTTTCTTGATGATTTTCAAATGAT-TTT-AAAGAAACTAAGTCTGATTTTTAAAAGTTTCTTAAT
* * * *
1925058 GATTTTCAAATGAGCTTTTAAAGAAACTAAGTCTGA
128 GATTTTCAAAAGAACTTTTAAAGAAACTAAGCCTAA
* * * ** * * *
1925094 TTTTCAGAAGTTTGTTGACGATTTTCAAATTAGTTTTTAAAGAAACTAAGTTTGATTTTTAGAAG
1 TTTTCAGAAGTTTCTTGACGATTTTCAAATGAATTTAAAAAAAAACTAAGTCTGATTTTCAGAAG
1925159 TTTCTTGATGATTTTCAAATGATTTTAAAGAAACTAAGTCTGATTTTTAAAAGTTTCTTAATGAT
66 TTTCTTGATGATTTTCAAATGATTTTAAAGAAACTAAGTCTGATTTTTAAAAGTTTCTTAATGAT
* *
1925224 TTTTAAAAGAACTTTTAAAGAAATTAAGCCTAA
131 TTTCAAAAGAACTTTTAAAGAAACTAAGCCTAA
* ** * **
1925257 TTTTTAGGGGTTTCTTGATG-TTTTCAAATGAATTTGAAAAAAAAACTAAGTCTGATTTTCAGGG
1 TTTTCAGAAGTTTCTTGACGATTTTCAAATGAATTT-AAAAAAAAACTAAGTCTGATTTTCAGAA
* * * * * *
1925321 GTTTCTCGATG-TTTTCAAATGAATTTGAAAGGAGCTAAGCCTAATTTTTA
65 GTTTCTTGATGATTTTCAAATG-ATTTTAAAGAAACTAAGTCTGATTTTTA
1925371 GGGGTTCTTT
Statistics
Matches: 232, Mismatches: 42, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
162 23 0.10
163 129 0.56
164 6 0.03
165 74 0.32
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (163 bp):
TTTTCAGAAGTTTCTTGACGATTTTCAAATGAATTTAAAAAAAAACTAAGTCTGATTTTCAGAAG
TTTCTTGATGATTTTCAAATGATTTTAAAGAAACTAAGTCTGATTTTTAAAAGTTTCTTAATGAT
TTTCAAAAGAACTTTTAAAGAAACTAAGCCTAA
Found at i:1925314 original size:218 final size:220
Alignment explanation
Indices: 1924916--1925318 Score: 553
Period size: 218 Copynumber: 1.8 Consensus size: 220
1924906 GTGTTTTTTT
* *
1924916 AACTAAGTCTGATTTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAAGAAATTAATTC
1 AACTAAGTCTGATTTTTCAGAAGTTTCTTGACAATTTTCAAATGA-CTTTTAAAGAAACTAAGTC
* * * * * * *
1924981 TAATTTTCAGAAGTTTCTTGATGATTTTTAAATGATCTTTCAAAGAAATTATGTCTGATTTCCAG
65 TAATTTTCAAAAGTTTCTTAATGATTTTTAAAAGAACTTTCAAAGAAATTAAGCCTAATTTCCAG
* * *
1925046 AAGTTTCTTGATGATTTTCAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTGTTG
130 AAGTTTCTTGATGATTTTCAAATGAGATTTAAAAAAAACTAAGTCTGATTTTCAGAAGTTTGTTG
1925111 ACGATTTTCAAATTAGTTTTTAAAGA
195 ACGATTTTCAAATTAGTTTTTAAAGA
* **
1925137 AACTAAGTTTGATTTTT-AGAAGTTTCTTGATGATTTTCAAATGA-TTTTAAAGAAACTAAGTCT
1 AACTAAGTCTGATTTTTCAGAAGTTTCTTGACAATTTTCAAATGACTTTTAAAGAAACTAAGTCT
* * * ** *
1925200 GATTTTTAAAAGTTTCTTAATGATTTTTAAAAGAACTTTTAAAGAAATTAAGCCTAATTTTTAGG
66 AATTTTCAAAAGTTTCTTAATGATTTTTAAAAGAACTTTCAAAGAAATTAAGCCTAATTTCCAGA
*
1925265 GGTTTCTTGATG-TTTTCAAATGA-ATTTGAAAAAAAAACTAAGTCTGATTTTCAG
131 AGTTTCTTGATGATTTTCAAATGAGATTT--AAAAAAAACTAAGTCTGATTTTCAG
1925319 GGGTTTCTCG
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
216 3 0.02
217 11 0.07
218 103 0.65
220 25 0.16
221 16 0.10
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.42
Consensus pattern (220 bp):
AACTAAGTCTGATTTTTCAGAAGTTTCTTGACAATTTTCAAATGACTTTTAAAGAAACTAAGTCT
AATTTTCAAAAGTTTCTTAATGATTTTTAAAAGAACTTTCAAAGAAATTAAGCCTAATTTCCAGA
AGTTTCTTGATGATTTTCAAATGAGATTTAAAAAAAACTAAGTCTGATTTTCAGAAGTTTGTTGA
CGATTTTCAAATTAGTTTTTAAAGA
Found at i:1925640 original size:37 final size:36
Alignment explanation
Indices: 1925599--1925799 Score: 152
Period size: 36 Copynumber: 5.4 Consensus size: 36
1925589 GTTTTGCTCG
1925599 AAACAAAATTTTATCTCACTCGAGATTGTTTTTCTTA
1 AAAC-AAATTTTATCTCACTCGAGATTGTTTTTCTTA
* * * * ** **
1925636 AAACAAACTTTGTCTCACTTGAGACTGTTTCACTCG
1 AAACAAATTTTATCTCACTCGAGATTGTTTTTCTTA
* *
1925672 AAACAAAATTTTATCTTACTCGAGATTATTTTTCTTA
1 AAAC-AAATTTTATCTCACTCGAGATTGTTTTTCTTA
* ** * * ** *
1925709 AAACAAACTTCGTCTCGCTTGAGACAGTTTTTACTCA
1 AAACAAATTTTATCTCACTCGAGATTGTTTTT-CTTA
* *
1925746 AAACAATAAATTTTATCTCACTAGGGATTG-TTTTCTTA
1 AAAC---AAATTTTATCTCACTCGAGATTGTTTTTCTTA
*
1925784 AAACAAATTTCATCTC
1 AAACAAATTTTATCTC
1925800 GTTTGAGAAA
Statistics
Matches: 121, Mismatches: 38, Indels: 12
0.71 0.22 0.07
Matches are distributed among these distances:
35 11 0.09
36 47 0.39
37 37 0.31
38 7 0.06
39 4 0.03
40 15 0.12
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTATCTCACTCGAGATTGTTTTTCTTA
Found at i:1925665 original size:36 final size:36
Alignment explanation
Indices: 1925574--1925751 Score: 131
Period size: 37 Copynumber: 4.9 Consensus size: 36
1925564 AGAGATCTTC
* * * * *
1925574 GTCTCGCTTGAGACAGTTTTGCTCGAAACAAAATTTT
1 GTCTCACTTGAGACTGTTTTTCTCAAAAC-AAACTTT
* * * *
1925611 ATCTCACTCGAGATTGTTTTTCTTAAAACAAACTTT
1 GTCTCACTTGAGACTGTTTTTCTCAAAACAAACTTT
** * *
1925647 GTCTCACTTGAGACTGTTTCACTCGAAACAAAATTTT
1 GTCTCACTTGAGACTGTTTTTCTCAAAAC-AAACTTT
* * * * * * *
1925684 ATCTTACTCGAGATTATTTTTCTTAAAACAAACTTC
1 GTCTCACTTGAGACTGTTTTTCTCAAAACAAACTTT
* *
1925720 GTCTCGCTTGAGACAGTTTTTACTCAAAACAA
1 GTCTCACTTGAGACTGTTTTT-CTCAAAACAA
1925752 TAAATTTTAT
Statistics
Matches: 103, Mismatches: 36, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
36 47 0.46
37 56 0.54
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (36 bp):
GTCTCACTTGAGACTGTTTTTCTCAAAACAAACTTT
Found at i:1925693 original size:73 final size:73
Alignment explanation
Indices: 1925570--1925813 Score: 328
Period size: 73 Copynumber: 3.3 Consensus size: 73
1925560 CTTGAGAGAT
*
1925570 CTTCGTCTCGCTTGAGACAGTTTTGCTCGAAACAAAATTTTATCTCACTCGAGATTGTTTTTCTT
1 CTTCGTCTCGCTTGAGACAGTTTTACTCGAAACAAAATTTTATCTCACTCGAGATTGTTTTTCTT
1925635 AAAACAAA
66 AAAACAAA
* * * * * *
1925643 CTTTGTCTCACTTGAGACTGTTTCACTCGAAACAAAATTTTATCTTACTCGAGATTATTTTTCTT
1 CTTCGTCTCGCTTGAGACAGTTTTACTCGAAACAAAATTTTATCTCACTCGAGATTGTTTTTCTT
1925708 AAAACAAA
66 AAAACAAA
* * *
1925716 CTTCGTCTCGCTTGAGACAGTTTTTACTCAAAACAATAAATTTTATCTCACTAGGGATTG-TTTT
1 CTTCGTCTCGCTTGAGACAG-TTTTACTCGAAAC-A-AAATTTTATCTCACTCGAGATTGTTTTT
1925780 CTTAAAACAAA
63 CTTAAAACAAA
* * * *
1925791 TTTCATCTCGTTTGAGAAAGTTT
1 CTTCGTCTCGCTTGAGACAGTTT
1925814 CCCTTGAAAT
Statistics
Matches: 148, Mismatches: 20, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
73 83 0.56
74 14 0.09
75 32 0.22
76 19 0.13
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (73 bp):
CTTCGTCTCGCTTGAGACAGTTTTACTCGAAACAAAATTTTATCTCACTCGAGATTGTTTTTCTT
AAAACAAA
Found at i:1926483 original size:139 final size:139
Alignment explanation
Indices: 1926233--1926863 Score: 774
Period size: 139 Copynumber: 4.6 Consensus size: 139
1926223 GGTAAACCAG
* **
1926233 TCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCTTATGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
* * *
1926298 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTTATCACATATGGAGTTGAATCAGCAACACCTCA
66 ATGAGAAGAACTTGTTCAACATTAGCTCGAATCATCACATATGGAGTTGAATCAGCAACACCTCA
* *
1926363 CTCAAGGAA
131 CTCGAGGGA
* * * * * *
1926372 TCAACATTTCAAATAGAGAGTTCATAATGAGAAGAATTCATCCGATGAAGGAGAAGAAGCTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
* * * *
1926437 ATGAGAAGAGCTTGTTCGACATTAGCTCGAATCATCGCATATGGAGTTGAATCAGCAACAACTCA
66 ATGAGAAGAACTTGTTCAACATTAGCTCGAATCATCACATATGGAGTTGAATCAGCAACACCTCA
*
1926502 CTTGAGGGA
131 CTCGAGGGA
*
1926511 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCGT
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAT-GAGGGAGAAGAAGTTCAT
* * * * * ** **
1926576 AATGAGAAGAGCTTGTTTGACCCATCA-CTC-AATTCA-CGACAT-T----TCGAATCAGTGATG
65 AATGAGAAGAACTTG-TTCA-ACATTAGCTCGAA-TCATC-ACATATGGAGTTGAATCAGCAACA
*
1926633 CTTCACTCGAGGGA
126 CCTCACTCGAGGGA
* *
1926647 TCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
* * * *
1926712 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCGTCACATATGGAGTTGAATCAGCAACATCTCA
66 ATGAGAAGAACTTGTTCAACATTAGCTCGAATCATCACATATGGAGTTGAATCAGCAACACCTCA
1926777 CTCGAGGGA
131 CTCGAGGGA
* * * * * * *
1926786 TCAACCTTTTCAGTGGAGAGTTCATAATGATAATAACTCATCCGATAAGGAAAAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
1926851 ATGAGAAGAACTT
66 ATGAGAAGAACTT
1926864 TAGCTTGCTT
Statistics
Matches: 414, Mismatches: 65, Indels: 26
0.82 0.13 0.05
Matches are distributed among these distances:
133 3 0.01
134 12 0.03
135 34 0.08
136 64 0.15
139 252 0.61
140 34 0.08
141 11 0.03
142 4 0.01
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.25
Consensus pattern (139 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACATTAGCTCGAATCATCACATATGGAGTTGAATCAGCAACACCTCA
CTCGAGGGA
Found at i:1926728 original size:275 final size:276
Alignment explanation
Indices: 1926233--1926863 Score: 817
Period size: 275 Copynumber: 2.3 Consensus size: 276
1926223 GGTAAACCAG
**
1926233 TCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCTTAT-GAGGGAGAAGAAGTTCAT
1 TCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCAT
* * * *
1926297 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTTATCACATATGGAGTTGAATCAGCAACACCTC
66 AATGAGAAGAACTTGTTCAACCTCAGCTCAATTCATCACATAT---GTCGAATCAGCAACACCTC
* *
1926362 ACTCAAGGAATCAACATTTCAAATAGAGAGTTCATAATGAGAAGAATTCATCCGATGAAGGAGAA
128 ACTCAAGGAATCAACATTTCAAATAGAGAGTTCATAATGAGAAGAACTCATCCAATGAAGGAGAA
* * *
1926427 GAAGCTCATAATGAGAAGAGCTTGTTCGACATTAGCTCGAATCATCGCATATGGAGTTGAATCAG
193 GAAGCTCATAATGAGAAGAACTTGTTCAACATTAGCTCGAATCATCACATATGGAGTTGAATCAG
*
1926492 CAACAACTCACTTGAGGGA
258 CAACAACTCACTCGAGGGA
* *
1926511 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCGT
1 TCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCAT
* * * ** ** *
1926576 AATGAGAAGAGCTTGTTTGACCCATCA-CTCAATTCA-CGACAT-T-TCGAATCAGTGATGCTTC
66 AATGAGAAGAACTTG-TTCAACC-TCAGCTCAATTCATC-ACATATGTCGAATCAGCAACACCTC
* * * * *
1926637 ACTCGAGGGATCAACATTTCCAGT-GAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGA
128 ACTCAAGGAATCAACATTTCAAATAG-AGAGTTCATAATGAGAAGAACTCATCCAATGAAGGAGA
* * * *
1926701 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCGTCACATATGGAGTTGAATCA
192 AGAAGCTCATAATGAGAAGAACTTGTTCAACATTAGCTCGAATCATCACATATGGAGTTGAATCA
*
1926766 GCAACATCTCACTCGAGGGA
257 GCAACAACTCACTCGAGGGA
* * * * *
1926786 TCAACCTTTTCAGTGGAGAGTTCATAATGATAATAACTCATCCGATA-AGGAAAAAGAAGTTCAT
1 TCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCAT
1926850 AATGAGAAGAACTT
66 AATGAGAAGAACTT
1926864 TAGCTTGCTT
Statistics
Matches: 308, Mismatches: 40, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
274 28 0.09
275 186 0.60
278 43 0.14
279 33 0.11
280 16 0.05
281 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.25
Consensus pattern (276 bp):
TCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTCAGCTCAATTCATCACATATGTCGAATCAGCAACACCTCACT
CAAGGAATCAACATTTCAAATAGAGAGTTCATAATGAGAAGAACTCATCCAATGAAGGAGAAGAA
GCTCATAATGAGAAGAACTTGTTCAACATTAGCTCGAATCATCACATATGGAGTTGAATCAGCAA
CAACTCACTCGAGGGA
Found at i:1935361 original size:19 final size:19
Alignment explanation
Indices: 1935300--1935368 Score: 68
Period size: 19 Copynumber: 3.4 Consensus size: 19
1935290 TTTTATAATT
1935300 TAATCTTTAAATTTATTATA
1 TAAT-TTTAAATTTATTATA
*
1935320 T-TTATTTAATATTTTATTTATA
1 TAAT-TTTAA-A-TTTA-TTATA
*
1935342 TAGTTTTAAATTTATTATA
1 TAATTTTAAATTTATTATA
1935361 TAATTTTA
1 TAATTTTA
1935369 TACGAGTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
19 18 0.44
20 6 0.15
21 5 0.12
22 11 0.27
23 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (19 bp):
TAATTTTAAATTTATTATA
Found at i:1958938 original size:44 final size:45
Alignment explanation
Indices: 1958877--1958969 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 45
1958867 AAGAAATAAA
* *
1958877 AAAATAAAAAGAGAAAAATAAAAAAAAGGAAAAA-AAGGAAAAATG
1 AAAAGAAAAAGAGAAAAATAAAAAAAA-GAAAAATAAGAAAAAATG
* * *
1958922 AAAAGAAAAA-AGAAAAATGAAGAAAAGAAAAATGAGAAAAAATG
1 AAAAGAAAAAGAGAAAAATAAAAAAAAGAAAAATAAGAAAAAATG
1958966 AAAA
1 AAAA
1958970 ATGATGAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
43 6 0.14
44 27 0.64
45 9 0.21
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.06
Consensus pattern (45 bp):
AAAAGAAAAAGAGAAAAATAAAAAAAAGAAAAATAAGAAAAAATG
Found at i:1958993 original size:62 final size:58
Alignment explanation
Indices: 1958862--1959002 Score: 160
Period size: 62 Copynumber: 2.4 Consensus size: 58
1958852 ATATTTCGCT
* *
1958862 TGAAGAAGAAATAA-AAAAATAAAAAGAGAAAAATAAAAAAAAGGAAAAAAAGGAAAAA
1 TGAA-AAGAAAAAAGAAAAATAAAAAGAGAAAAATAAAAAAAAGGAAAAAAAGAAAAAA
* * *
1958920 TGAAAAGAAAAAAGAAAAATGAAGAAA-AGAAAAATGAGAAAAAATGAAAAATGATGAAAAAA
1 TGAAAAGAAAAAAGAAAAAT-AA-AAAGAGAAAAAT-AAAAAAAAGGAAAAA--AAGAAAAAA
*
1958982 TGAAAAGAAAAAAGGAAAATA
1 TGAAAAGAAAAAAGAAAAATA
1959003 GAAATTAGGA
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
57 8 0.11
58 10 0.14
59 10 0.14
60 16 0.23
61 1 0.01
62 26 0.37
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (58 bp):
TGAAAAGAAAAAAGAAAAATAAAAAGAGAAAAATAAAAAAAAGGAAAAAAAGAAAAAA
Found at i:1959005 original size:15 final size:15
Alignment explanation
Indices: 1958877--1959022 Score: 81
Period size: 15 Copynumber: 9.8 Consensus size: 15
1958867 AAGAAATAAA
* *
1958877 AAAATA-AAAAGAGA
1 AAAATAGAAAAAAGG
*
1958891 AAAATAAAAAAAAGG
1 AAAATAGAAAAAAGG
* * *
1958906 AAAAAAAGGAAAAATG
1 -AAAATAGAAAAAAGG
*
1958922 -AAA-AGAAAAAAGA
1 AAAATAGAAAAAAGG
*
1958935 AAAAT-GAAGAAAAGA
1 AAAATAGAA-AAAAGG
*
1958950 AAAATGAGAAAAAATGA
1 AAAAT-AGAAAAAA-GG
*
1958967 AAAATGATGAAAAAATG
1 AAAAT-A-GAAAAAAGG
1958984 -AAA-AGAAAAAAGG
1 AAAATAGAAAAAAGG
**
1958997 AAAATAGAAATTAGG
1 AAAATAGAAAAAAGG
1959012 AAAAT-GAAAAA
1 AAAATAGAAAAA
1959023 GAAAAAATGA
Statistics
Matches: 105, Mismatches: 16, Indels: 22
0.73 0.11 0.15
Matches are distributed among these distances:
13 15 0.14
14 23 0.22
15 30 0.29
16 18 0.17
17 12 0.11
18 7 0.07
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (15 bp):
AAAATAGAAAAAAGG
Found at i:1959016 original size:62 final size:59
Alignment explanation
Indices: 1958877--1959067 Score: 166
Period size: 62 Copynumber: 3.2 Consensus size: 59
1958867 AAGAAATAAA
* * * *
1958877 AAAATAAAAAGAGAAAAAT-AA-AAAAAAGGAAAAA-AAGGAAAAATGAAAAGAAAAAAGA
1 AAAATAGAAATAGAAAAATGAAGAAAAAATGAAAAAGAA--AAAAATGAAAAGAAAAAAGG
1958935 AAAATGAAGAAA-AGAAAAATG-AGAAAAAATGAAAAATGATGAAAAAATGAAAAGAAAAAAGG
1 AAAAT--AGAAATAGAAAAATGAAGAAAAAATGAAAAA-GA--AAAAAATGAAAAGAAAAAAGG
* *
1958997 AAAATAGAAATTAGGAAAATGAAAAAGAAAAAATGAAAAAGAAAAAAATG--ATGAAAAAA-G
1 AAAATAGAAA-TAGAAAAATG---AAGAAAAAATGAAAAAGAAAAAAATGAAAAGAAAAAAGG
1959057 AAAA-AGAAATA
1 AAAATAGAAATA
1959068 AAAGGGGGTT
Statistics
Matches: 114, Mismatches: 5, Indels: 28
0.78 0.03 0.19
Matches are distributed among these distances:
58 7 0.06
59 14 0.12
60 26 0.23
61 8 0.07
62 33 0.29
63 8 0.07
64 1 0.01
65 2 0.02
66 15 0.13
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (59 bp):
AAAATAGAAATAGAAAAATGAAGAAAAAATGAAAAAGAAAAAAATGAAAAGAAAAAAGG
Found at i:1959042 original size:15 final size:15
Alignment explanation
Indices: 1958874--1959047 Score: 95
Period size: 14 Copynumber: 11.7 Consensus size: 15
1958864 AAGAAGAAAT
1958874 AAAAAAAT-AAAAAG
1 AAAAAAATGAAAAAG
*
1958888 AGAAAAAT-AAAAA-
1 AAAAAAATGAAAAAG
**
1958901 AAAGGAA--AAAAAG
1 AAAAAAATGAAAAAG
*
1958914 -GAAAAATG-AAAAG
1 AAAAAAATGAAAAAG
1958927 -AAAAAA-GAAAAATG
1 AAAAAAATGAAAAA-G
*
1958941 AAGAAAA-GAAAAATG
1 AAAAAAATGAAAAA-G
1958956 AGAAAAAATGAAAAATG
1 A-AAAAAATGAAAAA-G
1958973 ATGAAAAAATG-AAAAG
1 A--AAAAAATGAAAAAG
*
1958989 -AAAAAAGGAAAATAG
1 AAAAAAATGAAAA-AG
1959004 AAATTAGGAAAATGAAAAAG
1 -AA--A--AAAATGAAAAAG
1959024 -AAAAAATGAAAAAG
1 AAAAAAATGAAAAAG
1959038 AAAAAAATGA
1 AAAAAAATGA
1959048 TGAAAAAAGA
Statistics
Matches: 130, Mismatches: 12, Indels: 35
0.73 0.07 0.20
Matches are distributed among these distances:
12 9 0.07
13 25 0.19
14 28 0.22
15 25 0.19
16 7 0.05
17 14 0.11
18 10 0.08
19 1 0.01
20 2 0.02
21 9 0.07
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.09
Consensus pattern (15 bp):
AAAAAAATGAAAAAG
Found at i:1959061 original size:7 final size:7
Alignment explanation
Indices: 1958875--1959043 Score: 80
Period size: 7 Copynumber: 22.9 Consensus size: 7
1958865 AGAAGAAATA
*
1958875 AAAAAAT
1 AAAAAAG
1958882 AAAAAGAG
1 AAAAA-AG
*
1958890 AAAAATAA
1 AAAAA-AG
1958898 AAAAAAGG
1 AAAAAA-G
1958906 AAAAAAAGG
1 -AAAAAA-G
*
1958915 AAAAATG
1 AAAAAAG
1958922 --AAAAG
1 AAAAAAG
1958927 AAAAAAG
1 AAAAAAG
*
1958934 AAAAATG
1 AAAAAAG
1958941 AAGAAAAG
1 AA-AAAAG
1958949 AAAAATGAG
1 AAAAA--AG
1958958 AAAAAATG
1 AAAAAA-G
1958966 AAAAATGATG
1 AAAAA--A-G
1958976 AAAAAATG
1 AAAAAA-G
1958984 --AAAAG
1 AAAAAAG
1958989 AAAAAAGG
1 AAAAAA-G
*
1958997 AAAATAG
1 AAAAAAG
**
1959004 AAATTAG
1 AAAAAAG
* *
1959011 GAAAATG
1 AAAAAAG
1959018 -AAAAAG
1 AAAAAAG
1959024 AAAAAATG
1 AAAAAA-G
1959032 -AAAAAG
1 AAAAAAG
1959038 AAAAAA
1 AAAAAA
1959044 ATGATGAAAA
Statistics
Matches: 130, Mismatches: 15, Indels: 34
0.73 0.08 0.19
Matches are distributed among these distances:
5 5 0.04
6 10 0.08
7 53 0.41
8 39 0.30
9 15 0.12
10 8 0.06
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (7 bp):
AAAAAAG
Found at i:1960742 original size:55 final size:55
Alignment explanation
Indices: 1960397--1960741 Score: 446
Period size: 55 Copynumber: 6.3 Consensus size: 55
1960387 TTTATGAAGA
* * * *
1960397 TCGAGTCCTATACTCTTTGATA-GAATAGGGAGCAGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGA-AGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
* * *
1960452 TCGAGTTCTATACTCTCTGAAGGAATAAAGAGCGGATCCATTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
* *
1960507 TCGAGTTCTATACTCTCTGAAGGAAAAGAGAGCGAACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
* *
1960562 TCGAGTTCTATAATCTCTGTAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
* * *
1960617 TTGAGTTCTATACTCTCTTAAGGAATAGAGAGCGGACTCGTTT-TATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT-TGAAGATTGT
* * * ** *
1960672 TCGAGTTCTATACTCCCTGAATGAATAG-GAAGCAGACATGTTTGTCGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAG-AGCGGACCCGTTTGTTGAAGATTGT
1960727 TCGAG-TCTTATACTC
1 TCGAGTTC-TATACTC
1960742 CTTGAAATAA
Statistics
Matches: 256, Mismatches: 29, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
54 5 0.02
55 250 0.98
56 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (55 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
Found at i:1963212 original size:27 final size:28
Alignment explanation
Indices: 1963177--1963232 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
1963167 CTATTGGGAA
1963177 TTACTTGGCTTTGTCCTCGCATA-CAAT
1 TTACTTGGCTTTGTCCTCGCATACCAAT
*
1963204 TTACTTGGCTTTGTCCTTGCATACCAAT
1 TTACTTGGCTTTGTCCTCGCATACCAAT
1963232 T
1 T
1963233 GCTTGGTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.18, C:0.25, G:0.14, T:0.43
Consensus pattern (28 bp):
TTACTTGGCTTTGTCCTCGCATACCAAT
Found at i:1963237 original size:27 final size:26
Alignment explanation
Indices: 1963175--1963238 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 26
1963165 TGCTATTGGG
1963175 AATTACTTGGCTTTGTCCTCGCATAC
1 AATTACTTGGCTTTGTCCTCGCATAC
*
1963201 AATTTACTTGGCTTTGTCCTTGCATACC
1 AA-TTACTTGGCTTTGTCCTCGCATA-C
*
1963229 AATTGCTTGG
1 AATTACTTGG
1963239 TGTTGCATGC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 2 0.06
27 29 0.85
28 3 0.09
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (26 bp):
AATTACTTGGCTTTGTCCTCGCATAC
Found at i:1969862 original size:13 final size:13
Alignment explanation
Indices: 1969844--1969868 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1969834 TTTAATATTT
1969844 AACTCTAAGTTTA
1 AACTCTAAGTTTA
1969857 AACTCTAAGTTT
1 AACTCTAAGTTT
1969869 CCTCATGGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
AACTCTAAGTTTA
Found at i:1988601 original size:16 final size:17
Alignment explanation
Indices: 1988580--1988613 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1988570 GTGTGCGCCC
1988580 ACGTGCA-TACGTGTGT
1 ACGTGCACTACGTGTGT
1988596 ACGTGCACTACGTGTGT
1 ACGTGCACTACGTGTGT
1988613 A
1 A
1988614 AAAAAGGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (17 bp):
ACGTGCACTACGTGTGT
Found at i:1989623 original size:17 final size:18
Alignment explanation
Indices: 1989586--1989623 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1989576 AGCAAGATAA
1989586 CTAAATACATAATTTAGT
1 CTAAATACATAATTTAGT
1989604 CTAAATA-ATAACTTTA-T
1 CTAAATACATAA-TTTAGT
1989621 CTA
1 CTA
1989624 TTTTAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (18 bp):
CTAAATACATAATTTAGT
Found at i:1990986 original size:19 final size:19
Alignment explanation
Indices: 1990959--1991002 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1990949 ATAGAGTGTT
*
1990959 ATGTATATAAAATCATAGG
1 ATGTTTATAAAATCATAGG
1990978 ATGTTTATAAAATCATAGG
1 ATGTTTATAAAATCATAGG
1990997 ATGTTT
1 ATGTTT
1991003 TTTCTAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.39
Consensus pattern (19 bp):
ATGTTTATAAAATCATAGG
Found at i:1991592 original size:6 final size:6
Alignment explanation
Indices: 1991581--1991605 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1991571 GACACGTATT
1991581 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
1991606 GACGAGACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1992122 original size:6 final size:6
Alignment explanation
Indices: 1992106--1992137 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1992096 TCTCGTCTAG
1992106 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1992138 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:1992277 original size:22 final size:22
Alignment explanation
Indices: 1992249--1992301 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
1992239 AATTTGGAAA
1992249 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
1992271 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
1992293 ATCGCAACG
1 ATCGCAACG
1992302 CGAAATGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:1992318 original size:20 final size:20
Alignment explanation
Indices: 1992293--1992365 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
1992283 ACTGTAGACT
1992293 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
1992313 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
1992334 ATCGCAACGCGAAGTGGAAA
1 ATCGCAACGCGAAATGGAAA
*
1992354 AGCGCAACGCGA
1 ATCGCAACGCGA
1992366 TTTTCAACTA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.37, C:0.25, G:0.25, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1992339 original size:21 final size:21
Alignment explanation
Indices: 1992313--1992386 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
1992303 GAAATGGAAA
1992313 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
1992334 ATCGCAACGCGAAGTGGAA-A
1 ATCGCAACGCGATTTTCAACT
*
1992354 AGCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
1992375 ATCGCAACGCGA
1 ATCGCAACGCGA
1992387 ATTTGCGATA
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:1992339 original size:41 final size:41
Alignment explanation
Indices: 1992290--1992387 Score: 178
Period size: 41 Copynumber: 2.4 Consensus size: 41
1992280 ACAACTGTAG
*
1992290 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCA
*
1992331 ACTATCGCAACGCGAAGTGGAAAAGCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCA
1992372 ACTATCGCAACGCGAA
1 ACTATCGCAACGCGAA
1992388 TTTGCGATAG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAAGCGCAACGCGATTTTCA
Found at i:1994918 original size:7 final size:7
Alignment explanation
Indices: 1994906--1994930 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1994896 TCATAATTTT
1994906 AAAATAA
1 AAAATAA
1994913 AAAATAA
1 AAAATAA
1994920 AAAATAA
1 AAAATAA
1994927 AAAA
1 AAAA
1994931 AAATCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:1994932 original size:16 final size:16
Alignment explanation
Indices: 1994911--1994975 Score: 76
Period size: 16 Copynumber: 4.0 Consensus size: 16
1994901 ATTTTAAAAT
1994911 AAAAAATAAAAAATAAA
1 AAAAAATAAAAAAT-AA
* *
1994928 AAAAAATCAAAAATCA
1 AAAAAATAAAAAATAA
* *
1994944 AAAAAATCAAAAATCA
1 AAAAAATAAAAAATAA
*
1994960 AAAAAATAAATAATAA
1 AAAAAATAAAAAATAA
1994976 TTATAATTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
16 30 0.70
17 13 0.30
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAAAATAAAAAATAA
Found at i:1994939 original size:7 final size:7
Alignment explanation
Indices: 1994929--1994963 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
1994919 AAAAATAAAA
1994929 AAAAATC
1 AAAAATC
1994936 AAAAATC
1 AAAAATC
1994943 AAAAAAATC
1 --AAAAATC
1994952 AAAAATC
1 AAAAATC
1994959 AAAAA
1 AAAAA
1994964 AATAAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 19 0.73
9 7 0.27
ACGTcount: A:0.77, C:0.11, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAATC
Found at i:1994981 original size:6 final size:6
Alignment explanation
Indices: 1994972--1995001 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1994962 AAAATAAATA
1994972 ATAATT ATAATT ATAATT ATAATT ATAATT
1 ATAATT ATAATT ATAATT ATAATT ATAATT
1995002 TTCTTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:2001180 original size:23 final size:23
Alignment explanation
Indices: 2001154--2001232 Score: 140
Period size: 23 Copynumber: 3.4 Consensus size: 23
2001144 CCTTCCATAC
*
2001154 AATGCTTCATACGGTGCCATTTT
1 AATGCTTGATACGGTGCCATTTT
*
2001177 AATGCTTGATACGGGGCCATTTT
1 AATGCTTGATACGGTGCCATTTT
2001200 AATGCTTGATACGGTGCCATTTT
1 AATGCTTGATACGGTGCCATTTT
2001223 AATGCTTGAT
1 AATGCTTGAT
2001233 TGATAGCTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.38
Consensus pattern (23 bp):
AATGCTTGATACGGTGCCATTTT
Found at i:2004413 original size:35 final size:35
Alignment explanation
Indices: 2004374--2004447 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
2004364 AGGTACCACA
* *
2004374 TCTCTTATTTCATTGTGTCCTTTTCTCCACAAACC
1 TCTCTTATTCCATTGTGTCCTTTGCTCCACAAACC
*
2004409 TCTCTTATTCCATTGTGTCCTTTGCTCTACAAACC
1 TCTCTTATTCCATTGTGTCCTTTGCTCCACAAACC
2004444 TCTC
1 TCTC
2004448 ATTTTGAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.16, C:0.32, G:0.07, T:0.45
Consensus pattern (35 bp):
TCTCTTATTCCATTGTGTCCTTTGCTCCACAAACC
Found at i:2007018 original size:49 final size:49
Alignment explanation
Indices: 2006964--2007221 Score: 372
Period size: 49 Copynumber: 5.2 Consensus size: 49
2006954 TTTTGACAAC
* * *
2006964 AAAGGTGCTACTAAAGAAAGTTAAATGCATAACGGTGCATTTCTGCATA
1 AAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCAGCATA
* *
2007013 AAAGGTGCCACTAATGAAAGTTAAATGCATAACAGTACATTTCAGCATA
1 AAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCAGCATA
* *
2007062 AAAGGTGCCACTAATGAAAGTTAAATGCATAACAGTGCATTTCGGCATA
1 AAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCAGCATA
* * * **
2007111 AAAGGTGCCATTAATGAAAGTTAAATGTATAATGGTGCATTTTGGCATA
1 AAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCAGCATA
* * *
2007160 AAATGTGTCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCAACATA
1 AAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCA-TTTCAGCATA
2007210 AAAGGTGCCACT
1 AAAGGTGCCACT
2007222 CATGGTATTC
Statistics
Matches: 186, Mismatches: 22, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
49 169 0.91
50 17 0.09
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (49 bp):
AAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCAGCATA
Found at i:2011645 original size:18 final size:18
Alignment explanation
Indices: 2011622--2011664 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2011612 CTTTAGATTA
*
2011622 TTTATTTAATTAGTT-TCT
1 TTTATTTAATT-CTTATCT
2011640 TTTATTTAATTCTTATCT
1 TTTATTTAATTCTTATCT
2011658 TTTATTT
1 TTTATTT
2011665 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTATTTAATTCTTATCT
Found at i:2011755 original size:15 final size:16
Alignment explanation
Indices: 2011735--2011764 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2011725 ATTTCCCTTT
2011735 TTTTATC-TTATTTTG
1 TTTTATCTTTATTTTG
2011750 TTTTATCTTTATTTT
1 TTTTATCTTTATTTT
2011765 CCCACTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTATCTTTATTTTG
Found at i:2011784 original size:38 final size:38
Alignment explanation
Indices: 2011731--2011803 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
2011721 TTATATTTCC
* * *
2011731 CTTTTTTTATCTTATTTTGTTTTA-TCTTTATTTTCCCA
1 CTTTTTTAATCTTATTTTATTTAACT-TTTATTTTCCCA
*
2011769 CTTTTTTAATTTTATTTTATTTAACTTTTATTTTC
1 CTTTTTTAATCTTATTTTATTTAACTTTTATTTTC
2011804 TCTTTTAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
38 29 0.97
39 1 0.03
ACGTcount: A:0.16, C:0.12, G:0.01, T:0.70
Consensus pattern (38 bp):
CTTTTTTAATCTTATTTTATTTAACTTTTATTTTCCCA
Found at i:2011799 original size:16 final size:15
Alignment explanation
Indices: 2011773--2011802 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2011763 TTCCCACTTT
2011773 TTTAATTTTATTTTA
1 TTTAATTTTATTTTA
2011788 TTTAACTTTTATTTT
1 TTTAA-TTTTATTTT
2011803 CTCTTTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTAATTTTATTTTA
Found at i:2011828 original size:19 final size:19
Alignment explanation
Indices: 2011772--2011828 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
2011762 TTTCCCACTT
2011772 TTTTAA-TTTTA-TTT-TA
1 TTTTAACTTTTATTTTATA
* *
2011788 -TTTAACTTTTATTTTCTC
1 TTTTAACTTTTATTTTATA
2011806 TTTTAACATTTT-TTTTATA
1 TTTTAAC-TTTTATTTTATA
2011825 TTTT
1 TTTT
2011829 TTTATTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 5 0.15
16 5 0.15
17 3 0.09
18 1 0.03
19 15 0.45
20 4 0.12
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTAACTTTTATTTTATA
Found at i:2021192 original size:139 final size:139
Alignment explanation
Indices: 2020951--2021286 Score: 448
Period size: 139 Copynumber: 2.4 Consensus size: 139
2020941 GAACAGTCAT
* * * * * * * **
2020951 AATGGAACCTCGAGCATAAGCGAGCATCAAATAAAAAATTCTCCTAAATTAAAACACT-AGTTAT
1 AATGGAACCTCGAGTAAAAGTGAGGACCAAATTAAAAATTCTCCTAAATTTAAGGACTAAGTTAT
*
2021015 GAATTAAACCTAAAATGGAGGCTCTAATTATTAACCTAGTCAATTTTAACAAATTATTTGATTCG
66 GAATTAAACCTAAAATGGAGGCTCTAATTATTAACCTAGACAATTTTAACAAATTATTTGATTCG
*
2021080 AATTATTAA
131 AATAATTAA
*
2021089 AATGGAACCTCGAGTAAAAGTGAGGACCAAATTAAAAATTC-CACTAAATTTAAGGGCTAAGTT-
1 AATGGAACCTCGAGTAAAAGTGAGGACCAAATTAAAAATTCTC-CTAAATTTAAGGACTAAGTTA
* * *
2021152 TGAAATTAAACCTAAAATGGAGGCTCTAATTATTATCCTAGACAATTTTAACCAATTATTTGGTT
65 TG-AATTAAACCTAAAATGGAGGCTCTAATTATTAACCTAGACAATTTTAACAAATTATTTGATT
*
2021217 TGAATAATTAA
129 CGAATAATTAA
* *
2021228 AATGGAACATCGAGCT-AGAGTGAGGACCAAATTAAAAA-TCTCCTAAATTTAAGGACTAA
1 AATGGAACCTCGAG-TAAAAGTGAGGACCAAATTAAAAATTCTCCTAAATTTAAGGACTAA
2021287 AATTAAAGAA
Statistics
Matches: 174, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
137 1 0.01
138 66 0.38
139 106 0.61
140 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.29
Consensus pattern (139 bp):
AATGGAACCTCGAGTAAAAGTGAGGACCAAATTAAAAATTCTCCTAAATTTAAGGACTAAGTTAT
GAATTAAACCTAAAATGGAGGCTCTAATTATTAACCTAGACAATTTTAACAAATTATTTGATTCG
AATAATTAA
Found at i:2021665 original size:23 final size:23
Alignment explanation
Indices: 2021602--2021671 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
2021592 AATCTAAATG
* * *
2021602 AACACAAACAAACGAAAATAAACG
1 AACATAAACAAAC-AACATAAACA
**
2021626 AACATAATA-AATGAACATAAACA
1 AACATAA-ACAAACAACATAAACA
*
2021649 AACATAAACAAACAACACAAACA
1 AACATAAACAAACAACATAAACA
2021672 CAAAAAAACG
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
22 1 0.03
23 26 0.72
24 8 0.22
25 1 0.03
ACGTcount: A:0.67, C:0.20, G:0.04, T:0.09
Consensus pattern (23 bp):
AACATAAACAAACAACATAAACA
Found at i:2021945 original size:14 final size:14
Alignment explanation
Indices: 2021925--2021985 Score: 76
Period size: 14 Copynumber: 4.6 Consensus size: 14
2021915 TCCCTTTGTT
2021925 CGAACATAAATGAA
1 CGAACATAAATGAA
*
2021939 AGAACATAAATGAA
1 CGAACATAAATGAA
*
2021953 CGAAGATAAAT---
1 CGAACATAAATGAA
2021964 -GAACATAAATGAA
1 CGAACATAAATGAA
2021977 CGAACATAA
1 CGAACATAA
2021986 GCGAACATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 9 0.23
14 30 0.77
ACGTcount: A:0.59, C:0.11, G:0.15, T:0.15
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:2021953 original size:24 final size:24
Alignment explanation
Indices: 2021932--2022004 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
2021922 GTTCGAACAT
2021932 AAATGAAA-GAACATAAATGAACGA
1 AAAT-AAATGAACATAAATGAACGA
*
2021956 AGATAAATGAACATAAATGAACGA
1 AAATAAATGAACATAAATGAACGA
* **
2021980 ACATAAGCGAACATATAATCGAACG
1 AAATAAATGAACATA-AAT-GAACG
2022005 TTCACGAACG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 3 0.07
24 31 0.74
25 3 0.07
26 5 0.12
ACGTcount: A:0.56, C:0.12, G:0.16, T:0.15
Consensus pattern (24 bp):
AAATAAATGAACATAAATGAACGA
Done.