Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007782.1 Hibiscus syriacus cultivar Beakdansim tig00110065_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: 3900615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 19
Found at i:1741588 original size:28 final size:27
Alignment explanation
Indices: 1741549--1741636 Score: 106
Period size: 28 Copynumber: 3.2 Consensus size: 27
1741539 CGAACCCTCC
*
1741549 TTTTTCATTTTTCTTTTCATTTTTTCTT
1 TTTTTCCTTTTT-TTTTCATTTTTTCTT
**
1741577 TTTTTCCTTTTTTTTCTTTTTTTTTCTT
1 TTTTTCCTTTTTTTT-TCATTTTTTCTT
*
1741605 TTTTTTC-TTTTTTTTCATTTTTTCATT
1 TTTTTCCTTTTTTTTTCATTTTTTC-TT
1741632 TTTTT
1 TTTTT
1741637 TATTTTTTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
26 8 0.15
27 17 0.33
28 27 0.52
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (27 bp):
TTTTTCCTTTTTTTTTCATTTTTTCTT
Found at i:1741641 original size:9 final size:9
Alignment explanation
Indices: 1741568--1741644 Score: 102
Period size: 9 Copynumber: 8.4 Consensus size: 9
1741558 TTTCTTTTCA
1741568 TTTTTTCTT
1 TTTTTTCTT
*
1741577 TTTTTCCTT
1 TTTTTTCTT
1741586 TTTTTTCTTT
1 TTTTTTC-TT
1741596 TTTTTTCTT
1 TTTTTTCTT
1741605 TTTTTTCTT
1 TTTTTTCTT
*
1741614 TTTTTTC-A
1 TTTTTTCTT
1741622 TTTTTTCATT
1 TTTTTTC-TT
*
1741632 TTTTTTATT
1 TTTTTTCTT
1741641 TTTT
1 TTTT
1741645 ATTTTTCACT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
8 7 0.12
9 38 0.63
10 15 0.25
ACGTcount: A:0.04, C:0.10, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:1741658 original size:31 final size:29
Alignment explanation
Indices: 1741575--1741666 Score: 53
Period size: 29 Copynumber: 3.1 Consensus size: 29
1741565 TCATTTTTTC
* ** ***
1741575 TTTTTTTCCTTTTTTTTCTTTTTTTTTCT
1 TTTTTTTTCTTTTTTTTCACTTTTTCATT
* ***
1741604 TTTT-TTTCTTTTTTTTCATTTTTTCATTT
1 TTTTTTTTCTTTTTTTTCA-CTTTTTCATT
1741633 TTTTTATTT-TTTATTTTTCACTTTTTCATT
1 TTTTT-TTTCTTT-TTTTTCACTTTTTCATT
1741663 TTTT
1 TTTT
1741667 CATTCATTCT
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
28 12 0.24
29 15 0.30
30 13 0.26
31 10 0.20
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.83
Consensus pattern (29 bp):
TTTTTTTTCTTTTTTTTCACTTTTTCATT
Found at i:1741658 original size:39 final size:36
Alignment explanation
Indices: 1741569--1741670 Score: 116
Period size: 36 Copynumber: 2.7 Consensus size: 36
1741559 TTCTTTTCAT
* * * *
1741569 TTTTTCTTTTTTTCCTTTTTTTTCTTTTTTTTTCTTT
1 TTTTTCTTTTTTTTC-ATTTTTTCATTTTTTTTATTT
1741606 TTTTTCTTTTTTTTCATTTTTTCATTTTTTTTATTT
1 TTTTTCTTTTTTTTCATTTTTTCATTTTTTTTATTT
1741642 TTTATT-TTTCACTTTTTCATTTTTTCATT
1 TTT-TTCTTT---TTTTTCATTTTTTCATT
1741671 CATTCTCTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
36 24 0.42
37 16 0.28
39 17 0.30
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (36 bp):
TTTTTCTTTTTTTTCATTTTTTCATTTTTTTTATTT
Found at i:1741666 original size:1 final size:1
Alignment explanation
Indices: 1741568--1741650 Score: 58
Period size: 1 Copynumber: 83.0 Consensus size: 1
1741558 TTTCTTTTCA
* ** * * * ** **
1741568 TTTTTTCTTTTTTTCCTTTTTTTTCTTTTTTTTTCTTTTTTTTCTTTTTTTTCATTTTTTCATTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
1741633 TTTTTATTTTTTATTTTT
1 TTTTTTTTTTTTTTTTTT
1741651 CACTTTTTCA
Statistics
Matches: 62, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:1745208 original size:14 final size:14
Alignment explanation
Indices: 1745189--1745215 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1745179 AAATGAATGT
1745189 AAAGAATGAAGAAC
1 AAAGAATGAAGAAC
1745203 AAAGAATGAAGAA
1 AAAGAATGAAGAA
1745216 TGAAAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.04, G:0.22, T:0.07
Consensus pattern (14 bp):
AAAGAATGAAGAAC
Found at i:1756302 original size:11 final size:11
Alignment explanation
Indices: 1756303--1756332 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1756293 TCCGGTCTCC
1756303 CTCCCTCCGGT
1 CTCCCTCCGGT
1756314 CTCCCTCCGGT
1 CTCCCTCCGGT
1756325 CTCCCTCC
1 CTCCCTCC
1756333 CTCCCTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.60, G:0.13, T:0.27
Consensus pattern (11 bp):
CTCCCTCCGGT
Found at i:1756305 original size:15 final size:15
Alignment explanation
Indices: 1756285--1756336 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
1756275 CCTACCCTGT
1756285 TCCCTCCCTCCGGTC
1 TCCCTCCCTCCGGTC
1756300 TCCCTCCCTCCGG--
1 TCCCTCCCTCCGGTC
1756313 T--CTCCCTCCGGTC
1 TCCCTCCCTCCGGTC
1756326 TCCCTCCCTCC
1 TCCCTCCCTCC
1756337 CTTTCTCCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 10 0.30
13 2 0.06
15 21 0.64
ACGTcount: A:0.00, C:0.62, G:0.12, T:0.27
Consensus pattern (15 bp):
TCCCTCCCTCCGGTC
Found at i:1756350 original size:23 final size:23
Alignment explanation
Indices: 1756318--1756390 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
1756308 TCCGGTCTCC
*
1756318 CTCCGGTCTCCCTCCCTCCCTTT
1 CTCCAGTCTCCCTCCCTCCCTTT
*
1756341 CTCCATTCTCCCTCCCTCCCTTT
1 CTCCAGTCTCCCTCCCTCCCTTT
*
1756364 CTCCAGTCTCCCTACCTCCCTTT
1 CTCCAGTCTCCCTCCCTCCCTTT
1756387 CTCC
1 CTCC
1756391 CTCCCTCTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.04, C:0.56, G:0.04, T:0.36
Consensus pattern (23 bp):
CTCCAGTCTCCCTCCCTCCCTTT
Found at i:1769184 original size:25 final size:25
Alignment explanation
Indices: 1769155--1769204 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1769145 ACTAAACAAG
*
1769155 TCATAGTCCAGTAAATCTCATAAAA
1 TCATAATCCAGTAAATCTCATAAAA
*
1769180 TCATAATGCAGTAAATCTCATAAAA
1 TCATAATCCAGTAAATCTCATAAAA
1769205 GAGTTAACCT
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:0.18, G:0.08, T:0.28
Consensus pattern (25 bp):
TCATAATCCAGTAAATCTCATAAAA
Found at i:1773468 original size:135 final size:135
Alignment explanation
Indices: 1773212--1773471 Score: 321
Period size: 135 Copynumber: 1.9 Consensus size: 135
1773202 TTGATCGTTA
1773212 ACTTTGACCAAAAAGTCAAAATTTTCGAAAAGACATATTTTATGTTTTTGGACGTCTTGAGTTCG
1 ACTTTGACCAAAAAGTCAAAATTTTCGAAAAGACATATTTTATGTTTTTGGACGTCTTGAGTTCG
** * * * * *
1773277 AATCCGAAGTCCGTTTTTCGAAATTCGAATATGAAAGCCTCGAAATCGTCAGTCAAACCCGTTGA
66 AATCCGAAGTCCGTTTGGCCAAATTCAAATATGAAAACCTCCAAATCGTCAATCAAACCCGTTGA
1773342 CTTTG
131 CTTTG
* * * *
1773347 ACTTTGACCAAAAAGTCAACATTTTTGAAAAGTCATATTTTATG-TTTTGTGATGATC-TGAGTT
1 ACTTTGACCAAAAAGTCAAAATTTTCGAAAAGACATATTTTATGTTTTTG-GACG-TCTTGAGTT
* * * *
1773410 CGATTCC-ATAGTTCGTTTGGCCAAATTCAAACTCT-AAAACCTCCAAATTGTCAATCAAACCC
64 CGAATCCGA-AGTCCGTTTGGCCAAATTCAAA-TATGAAAACCTCCAAATCGTCAATCAAACCC
1773472 AAAAAATGGA
Statistics
Matches: 106, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
134 6 0.06
135 96 0.91
136 4 0.04
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Consensus pattern (135 bp):
ACTTTGACCAAAAAGTCAAAATTTTCGAAAAGACATATTTTATGTTTTTGGACGTCTTGAGTTCG
AATCCGAAGTCCGTTTGGCCAAATTCAAATATGAAAACCTCCAAATCGTCAATCAAACCCGTTGA
CTTTG
Found at i:1774083 original size:31 final size:31
Alignment explanation
Indices: 1774048--1774140 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
1774038 GTGACTCTTA
* *
1774048 GGTAGGCTCTGCGACCTTGGGATCATTCTCG
1 GGTAGGCTCTGCGACCCTGAGATCATTCTCG
1774079 GGTAGGCTCTGCGACCCTGAGATCATTCTCG
1 GGTAGGCTCTGCGACCCTGAGATCATTCTCG
1774110 GGTAGGCTCTGCGACCCTGAGATCATTCTCG
1 GGTAGGCTCTGCGACCCTGAGATCATTCTCG
1774141 AGTAACGACC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.15, C:0.28, G:0.30, T:0.27
Consensus pattern (31 bp):
GGTAGGCTCTGCGACCCTGAGATCATTCTCG
Found at i:1774291 original size:25 final size:25
Alignment explanation
Indices: 1774239--1774291 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1774229 AGGTTAACTC
* * * *
1774239 TTTTATGAGATTTATTGCAGTATGA
1 TTTTATGAGATTTACTGAACTATCA
1774264 TTTTATGAGATTTACTGAACTATCA
1 TTTTATGAGATTTACTGAACTATCA
1774289 TTT
1 TTT
1774292 GATTAGTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49
Consensus pattern (25 bp):
TTTTATGAGATTTACTGAACTATCA
Found at i:1776870 original size:44 final size:40
Alignment explanation
Indices: 1776822--1776907 Score: 109
Period size: 40 Copynumber: 2.0 Consensus size: 40
1776812 ATGTTTTGAC
1776822 ATATAGTGGCGTTTGTGAATATAAAACGCCGCTATTGACTACGT
1 ATATAGTGGCGTTT-T-AA-A-AAAACGCCGCTATTGACTACGT
* * *
1776866 ATATAGTGGCGTTTTCAAAAAACGCCGGTATTGACTATGT
1 ATATAGTGGCGTTTTAAAAAAACGCCGCTATTGACTACGT
1776906 AT
1 AT
1776908 TTGGCGTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
40 22 0.56
41 1 0.03
42 1 0.03
43 1 0.03
44 14 0.36
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (40 bp):
ATATAGTGGCGTTTTAAAAAAACGCCGCTATTGACTACGT
Found at i:1777033 original size:21 final size:21
Alignment explanation
Indices: 1777008--1777069 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
1776998 ATTATCCAAT
*
1777008 AAACTTGACATCCATAATAAC
1 AAACTTGAAATCCATAATAAC
* * *
1777029 AAACTTAAAATCCATAACAAG
1 AAACTTGAAATCCATAATAAC
* *
1777050 AAAATTGAAATCCACAATAA
1 AAACTTGAAATCCATAATAA
1777070 TAAATCAAAG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.55, C:0.19, G:0.05, T:0.21
Consensus pattern (21 bp):
AAACTTGAAATCCATAATAAC
Found at i:1780279 original size:85 final size:83
Alignment explanation
Indices: 1780190--1780711 Score: 386
Period size: 81 Copynumber: 6.3 Consensus size: 83
1780180 AAAAACACCG
* * *
1780190 CTAAAGAATGATTATTTAGCGGCGTTTGTGCTTAAAACACCATT-AAGATATAGTATTTAGCGGC
1 CTAAAGTATGAGTATTTAGCGGCGTTTGTGCTTAAAACACCATTAAAG-TATAGTATTTGGCGGC
*
1780254 GTTTATTATATAAAAGTGCCA
65 GTTTATGAT-TAAAA-TGCCA
* * * *
1780275 CTAAAGTACGAGTATTTAGCGGTGTTTGTGCTTAAAACACCACTAAAGTACAAGTATTTGGCGGC
1 CTAAAGTATGAGTATTTAGCGGCGTTTGTGCTTAAAACACCATTAAAGTA-TAGTATTTGGCGGC
* *
1780340 GTTTGTGCTTAAAATGCCA
65 GTTTATGATTAAAATGCCA
* *
1780359 CTAAAGTATGAGTATTTAGTGGCGTTTGTGCTTAAAACGCCATTAAAGTATGAGTATTTGGCGGC
1 CTAAAGTATGAGTATTTAGCGGCGTTTGTGCTTAAAACACCATTAAAGTAT-AGTATTTGGCGGC
* *
1780424 G-TTAT-A--CAAACGCCA
65 GTTTATGATTAAAATGCCA
* * * * * * * * *
1780439 CTAAAGGACGAGTATTTGGCGGCATTCGT--ATACAAACGCCACTAAAGTAT-GATATTTAGCGG
1 CTAAAGTATGAGTATTTAGCGGCGTTTGTGCTTA-AAACACCATTAAAGTATAG-TATTTGGCGG
**
1780501 CGTTCGT-A-TACAAATGCCA
64 CGTTTATGATTA-AAATGCCA
* * * * * * * * * **
1780520 CTAAAGTACGAGTATTTAGTGGCATTTGTGGTTAAAACGCCACTAATGTACAATATTCAGCGGCG
1 CTAAAGTATGAGTATTTAGCGGCGTTTGTGCTTAAAACACCATTAAAGTATAGTATTTGGCGGCG
*
1780585 TTTAT-ATAAAAATGCCA
66 TTTATGATTAAAATGCCA
* * * * * * * * ** * *
1780602 CTAAAGTACGTGTCTTTAGTGGTGTTTATAC-AAAAATGCCACTAAAGTATAGTATTTAGCGGCG
1 CTAAAGTATGAGTATTTAGCGGCGTTTGTGCTTAAAACACCATTAAAGTATAGTATTTGGCGGCG
* *
1780666 TTTAT-ATAAAAACGCCA
66 TTTATGATTAAAATGCCA
* * * *
1780683 CTAAAATACGAGTATTTACCGGCATTTGT
1 CTAAAGTATGAGTATTTAGCGGCGTTTGT
1780712 TCAAAAAATT
Statistics
Matches: 358, Mismatches: 67, Indels: 28
0.79 0.15 0.06
Matches are distributed among these distances:
77 1 0.00
78 13 0.04
79 19 0.05
80 30 0.08
81 96 0.27
82 62 0.17
83 6 0.02
84 64 0.18
85 46 0.13
86 21 0.06
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (83 bp):
CTAAAGTATGAGTATTTAGCGGCGTTTGTGCTTAAAACACCATTAAAGTATAGTATTTGGCGGCG
TTTATGATTAAAATGCCA
Found at i:1780325 original size:42 final size:42
Alignment explanation
Indices: 1780202--1780711 Score: 386
Period size: 42 Copynumber: 12.4 Consensus size: 42
1780192 AAAGAATGAT
* * *
1780202 TATTTAGCGGCGTTTGTGCTTAAAACACCA-TTAAGATA-TAG
1 TATTTAGCGGCGTTTGTGCTTAAAACGCCACTAAAG-TACGAG
* ** *
1780243 TATTTAGCGGCGTTTATTATATAAAAGTGCCACTAAAGTACGAG
1 TATTTAGCGGCGTTTGTGCT-TAAAA-CGCCACTAAAGTACGAG
* * *
1780287 TATTTAGCGGTGTTTGTGCTTAAAACACCACTAAAGTACAAG
1 TATTTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACGAG
* * *
1780329 TATTTGGCGGCGTTTGTGCTTAAAATGCCACTAAAGTATGAG
1 TATTTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACGAG
* * *
1780371 TATTTAGTGGCGTTTGTGCTTAAAACGCCATTAAAGTATGAG
1 TATTTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACGAG
* * * *
1780413 TATTTGGCGGCG-TTATAC---AAACGCCACTAAAGGACGAG
1 TATTTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACGAG
* * * * *
1780451 TATTTGGCGGCATTCGT--ATACAAACGCCACTAAAGTATGA-
1 TATTTAGCGGCGTTTGTGCTTA-AAACGCCACTAAAGTACGAG
* * *
1780491 TATTTAGCGGCGTTCGT--ATACAAATGCCACTAAAGTACGAG
1 TATTTAGCGGCGTTTGTGCTTA-AAACGCCACTAAAGTACGAG
* * * * *
1780532 TATTTAGTGGCATTTGTGGTTAAAACGCCACTAATGTAC-AA
1 TATTTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACGAG
* * * * * *
1780573 TATTCAGCGGCGTTTAT-ATAAAAATGCCACTAAAGTACGTG
1 TATTTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACGAG
* * * * * * * *
1780614 TCTTTAGTGGTGTTTATAC-AAAAATGCCACTAAAGTA-TAG
1 TATTTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACGAG
* * * *
1780654 TATTTAGCGGCGTTTAT-ATAAAAACGCCACTAAAATACGAG
1 TATTTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACGAG
* *
1780695 TATTTACCGGCATTTGT
1 TATTTAGCGGCGTTTGT
1780712 TCAAAAAATT
Statistics
Matches: 379, Mismatches: 74, Indels: 32
0.78 0.15 0.07
Matches are distributed among these distances:
38 28 0.07
39 2 0.01
40 84 0.22
41 113 0.30
42 118 0.31
43 12 0.03
44 22 0.06
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (42 bp):
TATTTAGCGGCGTTTGTGCTTAAAACGCCACTAAAGTACGAG
Found at i:1780695 original size:163 final size:161
Alignment explanation
Indices: 1780156--1780711 Score: 523
Period size: 163 Copynumber: 3.4 Consensus size: 161
1780146 GTTAAATGTG
* * * * * * *
1780156 GTATA-TATATAGCGACGTTTGTATAAAAACACCGCTAAAGA-ATGATTATTTAGCGGCGTTTGT
1 GTATAGTATTTAGCGGCGTTTGTATAAAAACGCCACTAAA-ATACGAGTATTTAGCGGCATTTGT
* *
1780219 GCTTAAAACACCATTAAGATATAGTATTTAGCGGCGTTTATTATATAAAAGTGCCACTAAAGTAC
65 GCTTAAAACGCCATTAAG-TACAGTATTTAGCGGCGTTTA-TATA-AAAA-TGCCACTAAAGTAC
* * *
1780284 GAGTATTTAGCGGTGTTTGTGCTTAAAACACCACTAAA
126 GAGTATTTAGCGGTGTTTATAC--AAAACGCCACTAAA
* * * * * * * * *
1780322 GTACAAGTATTTGGCGGCGTTTGTGCTTAAAATGCCACTAAAGTATGAGTATTTAGTGGCGTTTG
1 GTA-TAGTATTTAGCGGCGTTTGT-ATAAAAACGCCACTAAAATACGAGTATTTAGCGGCATTTG
* * * * *
1780387 TGCTTAAAACGCCATTAAAGTATGAGTATTTGGCGGCG--T-TATACAAACGCCACTAAAGGACG
64 TGCTTAAAACGCCATT-AAGTA-CAGTATTTAGCGGCGTTTATATAAAAATGCCACTAAAGTACG
* **
1780449 AGTATTTGGCGGCATTCGTATAC-AAACGCCACTAAA
127 AGTATTTAGCGGTGTT--TATACAAAACGCCACTAAA
* * * * *
1780485 GTAT-GATATTTAGCGGCGTTCGTATACAAATGCCACTAAAGTACGAGTATTTAGTGGCATTTGT
1 GTATAG-TATTTAGCGGCGTTTGTATAAAAACGCCACTAAAATACGAGTATTTAGCGGCATTTGT
* * * * *
1780549 GGTTAAAACGCCACTAATGTACAATATTCAGCGGCGTTTATATAAAAATGCCACTAAAGTACGTG
65 GCTTAAAACGCCATTAA-GTACAGTATTTAGCGGCGTTTATATAAAAATGCCACTAAAGTACGAG
* * *
1780614 TCTTTAGTGGTGTTTATACAAAAATGCCACTAAA
129 TATTTAGCGGTGTTTATAC-AAAACGCCACTAAA
* *
1780648 GTATAGTATTTAGCGGCGTTTATATAAAAACGCCACTAAAATACGAGTATTTACCGGCATTTGT
1 GTATAGTATTTAGCGGCGTTTGTATAAAAACGCCACTAAAATACGAGTATTTAGCGGCATTTGT
1780712 TCAAAAAATT
Statistics
Matches: 319, Mismatches: 55, Indels: 35
0.78 0.13 0.09
Matches are distributed among these distances:
160 13 0.04
161 58 0.18
162 16 0.05
163 112 0.35
164 27 0.08
165 3 0.01
166 10 0.03
167 1 0.00
168 15 0.05
169 48 0.15
170 16 0.05
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (161 bp):
GTATAGTATTTAGCGGCGTTTGTATAAAAACGCCACTAAAATACGAGTATTTAGCGGCATTTGTG
CTTAAAACGCCATTAAGTACAGTATTTAGCGGCGTTTATATAAAAATGCCACTAAAGTACGAGTA
TTTAGCGGTGTTTATACAAAACGCCACTAAA
Found at i:1787274 original size:40 final size:44
Alignment explanation
Indices: 1787227--1787353 Score: 147
Period size: 44 Copynumber: 3.0 Consensus size: 44
1787217 CTTATTGGTT
*
1787227 AATAAATGGTAA-ACA-T-G-AAAATAAGTTTACGAGCTTATGA
1 AATAAATGGTAAGACATTGGTAAAATAAGCTTACGAGCTTATGA
* *
1787267 AATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 AATAAATGGTAAG-ACATTGGTAAAATAAGCTTACGAGCTTATGA
* * *
1787312 AATAAATGGT-AGTATATTGGTAGAATAAGCTTACAAGCTTAT
1 AATAAATGGTAAG-ACATTGGTAAAATAAGCTTACGAGCTTAT
1787354 AGGATAAATG
Statistics
Matches: 77, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
40 12 0.16
42 2 0.03
43 1 0.01
44 31 0.40
45 31 0.40
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.31
Consensus pattern (44 bp):
AATAAATGGTAAGACATTGGTAAAATAAGCTTACGAGCTTATGA
Found at i:1787294 original size:45 final size:44
Alignment explanation
Indices: 1787244--1787353 Score: 175
Period size: 45 Copynumber: 2.5 Consensus size: 44
1787234 GGTAAACATG
*
1787244 AAAATAAGTTTACGAGCTTATGAAATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGAAATAAATGGT-AGTATATTGGT
*
1787289 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGAAATAAATGGTAGTATATTGGT
* *
1787333 AGAATAAGCTTACAAGCTTAT
1 AAAATAAGCTTACGAGCTTAT
1787354 AGGATAAATG
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 30 0.49
45 31 0.51
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (44 bp):
AAAATAAGCTTACGAGCTTATGAAATAAATGGTAGTATATTGGT
Found at i:1787341 original size:44 final size:45
Alignment explanation
Indices: 1787244--1787368 Score: 182
Period size: 44 Copynumber: 2.8 Consensus size: 45
1787234 GGTAAACATG
* *
1787244 AAAATAAGTTTACGAGCTTATGAAATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
1787289 AAAATAAGCTTACGAGCTTATGGAATAAATGGT-AGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* * *
1787333 AGAATAAGCTTACAAGCTTATAGG-ATAAATGATAAG
1 AAAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAG
1787369 AAATTTTTAT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
44 38 0.52
45 35 0.48
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.30
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
Found at i:1789340 original size:18 final size:18
Alignment explanation
Indices: 1789294--1789336 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1789284 TCTTCTTATT
*
1789294 TTTACTTTAATTGCTTTTA
1 TTTA-TTTAATCGCTTTTA
1789313 TTTATTTAATCGCTTTTA
1 TTTATTTAATCGCTTTTA
1789331 -TTATTT
1 TTTATTT
1789337 TAATATCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCGCTTTTA
Found at i:1789346 original size:18 final size:18
Alignment explanation
Indices: 1789294--1789347 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
1789284 TCTTCTTATT
*
1789294 TTTACTTTAATTGCTTTTA
1 TTTA-TTTAATAGCTTTTA
*
1789313 TTTATTTAATCGCTTTTA
1 TTTATTTAATAGCTTTTA
*
1789331 -TTATTTTAATATCTTTT
1 TTTA-TTTAATAGCTTTT
1789348 TACCAAACCC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.10
18 24 0.77
19 4 0.13
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.65
Consensus pattern (18 bp):
TTTATTTAATAGCTTTTA
Found at i:1795404 original size:13 final size:13
Alignment explanation
Indices: 1795388--1795412 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1795378 TTCTGTTAAA
1795388 TTTTTATTTTTAC
1 TTTTTATTTTTAC
1795401 TTTTTATTTTTA
1 TTTTTATTTTTA
1795413 TTCGATCAAG
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:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATTTTTAC
Found at i:1800046 original size:18 final size:18
Alignment explanation
Indices: 1800000--1800042 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1799990 TCTTCTTATT
*
1800000 TTTACTTTAATTGCTTTTA
1 TTTA-TTTAATCGCTTTTA
1800019 TTTATTTAATCGCTTTTA
1 TTTATTTAATCGCTTTTA
1800037 -TTATTT
1 TTTATTT
1800043 TAATATCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCGCTTTTA
Found at i:1800052 original size:18 final size:18
Alignment explanation
Indices: 1800000--1800053 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
1799990 TCTTCTTATT
*
1800000 TTTACTTTAATTGCTTTTA
1 TTTA-TTTAATAGCTTTTA
*
1800019 TTTATTTAATCGCTTTTA
1 TTTATTTAATAGCTTTTA
*
1800037 -TTATTTTAATATCTTTT
1 TTTA-TTTAATAGCTTTT
1800054 TTCAAAATCC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.10
18 24 0.77
19 4 0.13
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.65
Consensus pattern (18 bp):
TTTATTTAATAGCTTTTA
Found at i:1805539 original size:15 final size:15
Alignment explanation
Indices: 1805519--1805571 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
1805509 ATATTTAGTT
*
1805519 GGGCGGGCGGATGTG
1 GGGCGGGTGGATGTG
* *
1805534 GGGCGGGTGAATGCG
1 GGGCGGGTGGATGTG
1805549 GGGCGGGTGGATGTG
1 GGGCGGGTGGATGTG
1805564 GGGCGGGT
1 GGGCGGGT
1805572 AATGTCTCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.08, C:0.11, G:0.66, T:0.15
Consensus pattern (15 bp):
GGGCGGGTGGATGTG
Found at i:1805555 original size:30 final size:29
Alignment explanation
Indices: 1805519--1805575 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
1805509 ATATTTAGTT
1805519 GGGCGGGCGGATGTGGGGCGGGTGAATGCG
1 GGGCGGGCGGATGTGGGGCGGGT-AATGCG
*
1805549 GGGCGGGTGGATGTGGGGCGGGTAATG
1 GGGCGGGCGGATGTGGGGCGGGTAATG
1805576 TCTCAAACCC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.11, C:0.11, G:0.63, T:0.16
Consensus pattern (29 bp):
GGGCGGGCGGATGTGGGGCGGGTAATGCG
Found at i:1815464 original size:19 final size:20
Alignment explanation
Indices: 1815418--1815467 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1815408 AAACTATTTT
*
1815418 TGGGTATTGATACTAAGCCC
1 TGGGTATCGATACTAAGCCC
* *
1815438 TCGGTATCGATACT-AGCTC
1 TGGGTATCGATACTAAGCCC
1815457 TGGGTATCGAT
1 TGGGTATCGAT
1815468 GCTACCGAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (20 bp):
TGGGTATCGATACTAAGCCC
Found at i:1817693 original size:22 final size:22
Alignment explanation
Indices: 1817668--1817709 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1817658 AGAAATAAGT
*
1817668 GGATGATGATGGTCTTGATGAA
1 GGATGATGATAGTCTTGATGAA
* *
1817690 GGATGTTGATAGTGTTGATG
1 GGATGATGATAGTCTTGATG
1817710 TTGAAATGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.02, G:0.38, T:0.36
Consensus pattern (22 bp):
GGATGATGATAGTCTTGATGAA
Found at i:1818905 original size:18 final size:18
Alignment explanation
Indices: 1818866--1818909 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
1818856 TATGTGAACT
1818866 TATATAATGTGTATAAGA
1 TATATAATGTGTATAAGA
1818884 TATA-AATGTGTACTATAG-
1 TATATAATGTGTA-TA-AGA
1818902 TATATAAT
1 TATATAAT
1818910 AATAATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 8 0.35
18 10 0.43
19 5 0.22
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (18 bp):
TATATAATGTGTATAAGA
Found at i:1818906 original size:20 final size:18
Alignment explanation
Indices: 1818866--1818908 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
1818856 TATGTGAACT
1818866 TATAT-AATGTGTATAAG
1 TATATAAATGTGTATAAG
1818883 -ATATAAATGTGTACTATAG
1 TATATAAATGTGTA-TA-AG
1818902 TATATAA
1 TATATAA
1818909 TAATAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.18
17 8 0.36
18 2 0.09
19 2 0.09
20 6 0.27
ACGTcount: A:0.44, C:0.02, G:0.14, T:0.40
Consensus pattern (18 bp):
TATATAAATGTGTATAAG
Found at i:1826467 original size:23 final size:23
Alignment explanation
Indices: 1826407--1826458 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
1826397 CTCTACACCA
*
1826407 TCTACTGATCCAAATGCCCCCTGC
1 TCTA-TGATCCAAATGCCCCATGC
*
1826431 TCTATGATCCAAATTCCCCATGC
1 TCTATGATCCAAATGCCCCATGC
1826454 TCTAT
1 TCTAT
1826459 AGTCTAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.23, C:0.37, G:0.10, T:0.31
Consensus pattern (23 bp):
TCTATGATCCAAATGCCCCATGC
Found at i:1830755 original size:17 final size:17
Alignment explanation
Indices: 1830742--1830805 Score: 76
Period size: 17 Copynumber: 3.7 Consensus size: 17
1830732 GCTAGTTTGT
1830742 TCAATGAACTAGTTTAA
1 TCAATGAACTAGTTTAA
* *
1830759 TGAATGAACTAGTGTAA
1 TCAATGAACTAGTTTAA
*
1830776 TCAATGAACTAACG-TTAT
1 TCAATGAACT-A-GTTTAA
1830794 TCAATGAACTAG
1 TCAATGAACTAG
1830806 ATGCATGAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
16 1 0.03
17 25 0.62
18 13 0.32
19 1 0.03
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (17 bp):
TCAATGAACTAGTTTAA
Found at i:1830881 original size:17 final size:17
Alignment explanation
Indices: 1830827--1830883 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
1830817 AGTAGCTTAC
*
1830827 TAAATGATCTAAATGCA
1 TAAATGATCTAAATGCT
* *
1830844 TAAATGATCT-ACTTCT
1 TAAATGATCTAAATGCT
*
1830860 CTAAATGATCTAAAAGCT
1 -TAAATGATCTAAATGCT
1830878 TAAATG
1 TAAATG
1830884 CAATGCATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
16 3 0.09
17 26 0.81
18 3 0.09
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (17 bp):
TAAATGATCTAAATGCT
Found at i:1834422 original size:3 final size:3
Alignment explanation
Indices: 1834414--1834438 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1834404 ATGCTCTAAC
1834414 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
1834439 GAATGGCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1845554 original size:17 final size:17
Alignment explanation
Indices: 1845514--1845579 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
1845504 GCTAGTTTGT
*
1845514 TCAATAAACTAGTTTAA
1 TCAATGAACTAGTTTAA
** *
1845531 TTGATGAACTAGTATAA
1 TCAATGAACTAGTTTAA
* * *
1845548 TCAATGAATTGACTTTAT
1 TCAATGAACT-AGTTTAA
1845566 TCAATGAACTAGTT
1 TCAATGAACTAGTT
1845580 GCATGAATGA
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
17 23 0.64
18 13 0.36
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (17 bp):
TCAATGAACTAGTTTAA
Found at i:1847182 original size:28 final size:28
Alignment explanation
Indices: 1847141--1847201 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
1847131 CATATTTTTA
1847141 TTTTTTATAATTTTAATATTATTCAT-AT
1 TTTTTTATAATTTTAATATT-TTCATCAT
** * *
1847169 TTTTTTATTTTTTTTATATTTTTATCAT
1 TTTTTTATAATTTTAATATTTTCATCAT
1847197 TTTTT
1 TTTTT
1847202 AAACTGTAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 4 0.14
28 24 0.86
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (28 bp):
TTTTTTATAATTTTAATATTTTCATCAT
Found at i:1847199 original size:17 final size:16
Alignment explanation
Indices: 1847132--1847200 Score: 50
Period size: 17 Copynumber: 4.0 Consensus size: 16
1847122 TCATTTTCTC
1847132 ATATTTTTAT-TTTTT
1 ATATTTTTATATTTTT
*
1847147 ATAATTTTAATATTATTCAT
1 AT-ATTTTTATATT-TT--T
* *
1847167 ATTTTTTTATTTTTTTT
1 ATATTTTTA-TATTTTT
1847184 ATATTTTTATCATTTTT
1 ATATTTTTAT-ATTTTT
1847201 TAAACTGTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
15 2 0.05
16 8 0.20
17 16 0.39
18 2 0.05
19 7 0.17
20 6 0.15
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
ATATTTTTATATTTTT
Found at i:1847373 original size:27 final size:27
Alignment explanation
Indices: 1847337--1847423 Score: 71
Period size: 27 Copynumber: 3.4 Consensus size: 27
1847327 TATGAAAGTA
*
1847337 TTTAATTTTTAATATTTTATAATTACT
1 TTTAAATTTTAATATTTTATAATTACT
*
1847364 TTTAAATTTTAA-A-TTTA-AA-TA-A
1 TTTAAATTTTAATATTTTATAATTACT
*
1847386 TTTATAATTTCTATTATTTTAT-ATT-CT
1 TTTA-AATTT-TAATATTTTATAATTACT
1847413 TTTGAAATTTT
1 TTT-AAATTTT
1847424 TAAAATATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 17
0.70 0.06 0.25
Matches are distributed among these distances:
22 4 0.08
23 7 0.15
24 4 0.08
25 5 0.10
26 7 0.15
27 20 0.42
28 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (27 bp):
TTTAAATTTTAATATTTTATAATTACT
Found at i:1847482 original size:17 final size:17
Alignment explanation
Indices: 1847444--1847482 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1847434 TATTTTTATT
1847444 TTTTTAACATTTAATAA
1 TTTTTAACATTTAATAA
*
1847461 ATTTTAACATTTTAAT-A
1 TTTTTAACA-TTTAATAA
1847478 TTTTT
1 TTTTT
1847483 TTGTTTAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTTAACATTTAATAA
Found at i:1847483 original size:18 final size:17
Alignment explanation
Indices: 1847443--1847483 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
1847433 TTATTTTTAT
1847443 TTTTTTAACATTTAATA
1 TTTTTTAACATTTAATA
**
1847460 AATTTTAACATTTTAATA
1 TTTTTTAACA-TTTAATA
1847478 TTTTTT
1 TTTTTT
1847484 TGTTTAAAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTTTAACATTTAATA
Found at i:1853889 original size:2 final size:2
Alignment explanation
Indices: 1853882--1853920 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1853872 GTTCCCATCA
1853882 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1853921 CTCCGAAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1855910 original size:13 final size:13
Alignment explanation
Indices: 1855892--1855925 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
1855882 CATAACCCGA
1855892 GTTGACCCGACCC
1 GTTGACCCGACCC
1855905 GTTGACCCGACCC
1 GTTGACCCGACCC
1855918 GTTGACCC
1 GTTGACCC
1855926 ATTGACCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.15, C:0.44, G:0.24, T:0.18
Consensus pattern (13 bp):
GTTGACCCGACCC
Found at i:1859269 original size:55 final size:55
Alignment explanation
Indices: 1859198--1859467 Score: 343
Period size: 55 Copynumber: 4.9 Consensus size: 55
1859188 CTTCGGAAAA
* * * *
1859198 CGTGTCCGCTCTCTATTCTTTCAGAGAGTATAAGACTCAAACAATCTTCAATAAT
1 CGTGTCTGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
* * *
1859253 CGTGTCTGCTCCCTATTCCTTCAAAGAGTATAAGACTCGAACAATCTTCAACGAT
1 CGTGTCTGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
*
1859308 CGTGTCTGCTCCCTATT-TCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAGT
1 CGTGTCTGCTCCCTATTCT-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
*
1859363 CGTGTCTACTCCCTATT-TCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
1 CGTGTCTGCTCCCTATTCT-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
* * *
1859418 CGGGT-TCGCTCCCTCTTTCTTTCAG-GCAGTAT-AGAACTCGAATAATCTTC
1 CGTGTCT-GCTCCCT-ATTCTTTCAGAG-AGTATAAG-ACTCGAACAATCTTC
1859468 TTACGGGGTT
Statistics
Matches: 192, Mismatches: 17, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
54 1 0.01
55 164 0.85
56 26 0.14
57 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (55 bp):
CGTGTCTGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT
Found at i:1859531 original size:54 final size:54
Alignment explanation
Indices: 1859397--1860109 Score: 892
Period size: 54 Copynumber: 13.3 Consensus size: 54
1859387 AGAGTATAAG
** * * * *
1859397 ACTCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTTCAGGCAGTATAGA
1 ACTCGAA-AATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGA
* *
1859453 ACTCGAATAATCTTCTT---ACGGGGTTCACTCCCTCTTTCTCTAGGAAGTATGGA
1 ACTCGAA-AATCTTCTTCAAAC-GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1859506 ACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * *
1859560 ACTC-AAACATCTT-TTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGA
1 ACTCGAAA-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * * *
1859613 ACTCG--GAT-ATCTTCACACGGGTTCGCTCCCTCTTTCTCTAGGAAGTATGGA
1 ACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * * *
1859664 ACTTGGAAATCTTCTTCAAACGGGTTCGCTTCCTCTTTCTCTAGGGAGTATAGA
1 ACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * *
1859718 ACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGA
1 ACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* *
1859772 ACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* *
1859826 ACTCGTACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * * * *
1859880 ACTCGGATATTTTCTTCAAACGGGTTCGCTTCCTCTTTCTCTAGGGAGTATAGA
1 ACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* * * * * **
1859934 ACTCGGACATCTTCTTCAAACTGGTTCGCTCCCTCTTTCTTTAAGGAGTATAAA
1 ACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
* ** *
1859988 ACTCGTACCTCTTCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAGGGAGTATGAA
1 ACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGA
*
1860042 ACTCGAACAA---TCTTCAAACGGGTTCGCTCCCTTTTTCTCTAGGGAGTATGGA
1 ACTCGAA-AATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1860094 ACTCGAAAATCTTCTT
1 ACTCGAAAATCTTCTT
1860110 TTGCTTCACT
Statistics
Matches: 587, Mismatches: 54, Indels: 34
0.87 0.08 0.05
Matches are distributed among these distances:
50 1 0.00
51 43 0.07
52 54 0.09
53 66 0.11
54 407 0.69
55 2 0.00
56 14 0.02
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (54 bp):
ACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
Found at i:1860571 original size:36 final size:36
Alignment explanation
Indices: 1860481--1860601 Score: 100
Period size: 36 Copynumber: 3.3 Consensus size: 36
1860471 ACTCTTATGA
* * * *
1860481 GAAGGCTTAAAATGGATTTCCTTCACGACTCTTT-GAT
1 GAAGGCTTAAGACGG-TTTGCTTCACTACTCTTTAG-T
* ** * * * *
1860518 GAAGACACAAGATGGTTTGCTTCATTATTCTTTGGT
1 GAAGGCTTAAGACGGTTTGCTTCACTACTCTTTAGT
* *
1860554 GCATGCTTAAGACGGTTTGCTTCACTACTCTTTAGT
1 GAAGGCTTAAGACGGTTTGCTTCACTACTCTTTAGT
1860590 GAAGGCTTAAGA
1 GAAGGCTTAAGA
1860602 TTGACTTTGC
Statistics
Matches: 64, Mismatches: 19, Indels: 3
0.74 0.22 0.03
Matches are distributed among these distances:
36 52 0.81
37 12 0.19
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (36 bp):
GAAGGCTTAAGACGGTTTGCTTCACTACTCTTTAGT
Found at i:1866383 original size:46 final size:47
Alignment explanation
Indices: 1866308--1866430 Score: 176
Period size: 47 Copynumber: 2.6 Consensus size: 47
1866298 CACAAAAAGA
* * * *
1866308 AAACCTAATCGCATGATATCTAATTCGCATGC-TTGTTCGAGAAAAT
1 AAACATAACCGCATGATTTCTAGTTCGCATGCTTTGTTCGAGAAAAT
*
1866354 AAACATAACCGCGTGATTTCTAGTTCGCATGCTTTGTTCGAGAAAAT
1 AAACATAACCGCATGATTTCTAGTTCGCATGCTTTGTTCGAGAAAAT
* *
1866401 ATACCTAACCGCATGATTTCTAGTTCGCAT
1 AAACATAACCGCATGATTTCTAGTTCGCAT
1866431 ACATTTATTC
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
46 27 0.40
47 41 0.60
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (47 bp):
AAACATAACCGCATGATTTCTAGTTCGCATGCTTTGTTCGAGAAAAT
Found at i:1871501 original size:43 final size:43
Alignment explanation
Indices: 1871440--1871817 Score: 580
Period size: 43 Copynumber: 8.8 Consensus size: 43
1871430 TTAATTATCG
*
1871440 TTACAGTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
*
1871483 TTACAGTTCCCCCAGGTCCCTTTACTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* *
1871526 TTACAGTTCCCCTAGGTCCCTTTGCTGTGTACAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1871569 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
*
1871612 TTATAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1871655 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* **
1871698 TTACAGTCCCCCCAGGTTTCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* * **
1871741 TTACAGTT-TCCCAGGTTCCTTTATTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* * * * *
1871783 TTATAGTTTCCACAGG-CTCTTTTGCTATGTGCAAG
1 TTACAGTTCCCCCAGGTC-CCTTTGCTGTGTGCAAG
1871818 TATAAGACCT
Statistics
Matches: 308, Mismatches: 25, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
42 37 0.12
43 271 0.88
ACGTcount: A:0.17, C:0.27, G:0.24, T:0.31
Consensus pattern (43 bp):
TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:1873917 original size:17 final size:18
Alignment explanation
Indices: 1873897--1873933 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1873887 TTTATTTGAG
1873897 TTTAAAAT-TTAATGGAT
1 TTTAAAATATTAATGGAT
1873914 TTTAAAATATTAATGGAT
1 TTTAAAATATTAATGGAT
1873932 TT
1 TT
1873934 AATGTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTTAAAATATTAATGGAT
Found at i:1875555 original size:20 final size:21
Alignment explanation
Indices: 1875530--1875622 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
1875520 TTTTCCCAAT
*
1875530 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1875550 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1875571 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1875591 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1875612 TCGCAATGCGA
1 TCGCAATGCGA
1875623 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1875575 original size:41 final size:41
Alignment explanation
Indices: 1875530--1875622 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1875520 TTTTCCCAAT
1875530 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1875571 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1875612 TCGCAATGCGA
1 TCGCAATGCGA
1875623 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1875635 original size:41 final size:41
Alignment explanation
Indices: 1875549--1875683 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
1875539 GAATAAGTAA
** *
1875549 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
1875590 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * * *
1875631 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTGACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
1875672 TTCGCAACGCGA
1 ATCGCAACGCGA
1875684 TTCTGACTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 5 0.06
41 73 0.91
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:1875701 original size:20 final size:20
Alignment explanation
Indices: 1875653--1875705 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1875643 TAATACAAAA
* *
1875653 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
1875673 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
1875693 TCGCAACGCGATT
1 TCGCAACGCGATT
1875706 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:1876278 original size:19 final size:19
Alignment explanation
Indices: 1876218--1876298 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
1876208 TTCGAGAATG
1876218 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
1876238 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
1876254 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
1876271 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1876290 AAAATCGCA
1 AAAATCGCA
1876299 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 1 0.02
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1876316 original size:19 final size:19
Alignment explanation
Indices: 1876294--1876478 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
1876284 GAAACCAAAA
*
1876294 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1876313 TCGCGTTACGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1876332 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1876351 TCGCTGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1876371 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1876387 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1876404 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1876418 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1876437 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1876457 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1876477 TC
1 TC
1876479 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 58 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1876375 original size:39 final size:38
Alignment explanation
Indices: 1876294--1876383 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
1876284 GAAACCAAAA
*
1876294 TCGCATTGCGATTTTCATTTCGCGTTACGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTACGATTTTCATT
* *
1876332 TCGCGTTGCGATTTTTATTTCGCTGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTACGATTTTCATT
1876371 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1876384 GTCTGGTCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 21 0.44
39 27 0.56
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTACGATTTTCATT
Found at i:1876403 original size:33 final size:33
Alignment explanation
Indices: 1876366--1876453 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
1876356 GTTGCGATTT
* *
1876366 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
1876399 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1876432 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
1876454 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:1876455 original size:20 final size:20
Alignment explanation
Indices: 1876421--1876478 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1876411 GCGATTCTCT
**
1876421 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
1876441 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
1876461 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1876479 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:1878320 original size:42 final size:41
Alignment explanation
Indices: 1878260--1878351 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
1878250 GCCCGACTCG
* * *
1878260 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCC-CTCCCACCGTTCAAGAGGCC
* *
1878302 CCTATCATTCCTCGAGAGTCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCCTCCCACCGTTCAAGAGGCC
* *
1878343 ACTGTCATC
1 CCTATCATC
1878352 GTTGAAGCGT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 23 0.55
42 19 0.45
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (41 bp):
CCTATCATCCCTCAAGAGTCCCTCCCACCGTTCAAGAGGCC
Found at i:1878873 original size:45 final size:45
Alignment explanation
Indices: 1878820--1878909 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
1878810 AATAATTAGG
1878820 AACTTAAGGAAAATAAAAGAAATACACGGTATACAATTATGTCGA
1 AACTTAAGGAAAATAAAAGAAATACACGGTATACAATTATGTCGA
1878865 AACTTAAGGAAAATAAAAGAAATACACGGTATACAATTATGTCGA
1 AACTTAAGGAAAATAAAAGAAATACACGGTATACAATTATGTCGA
1878910 CGTCTTTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.22
Consensus pattern (45 bp):
AACTTAAGGAAAATAAAAGAAATACACGGTATACAATTATGTCGA
Found at i:1879790 original size:14 final size:14
Alignment explanation
Indices: 1879771--1879806 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1879761 ATTGTTTAAT
1879771 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1879785 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1879799 TGATTTGT
1 TGATTTGT
1879807 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1879966 original size:20 final size:20
Alignment explanation
Indices: 1879913--1879966 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1879903 AAAAAGTACT
* *
1879913 ATCGCAATGCG-AAATGAAA
1 ATCGCAACGCGAAAATAAAA
*
1879932 ATCGCAAACGAGAAAATAAAA
1 ATCGC-AACGCGAAAATAAAA
1879953 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1879967 TTTCCACAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 5 0.17
20 12 0.41
21 12 0.41
ACGTcount: A:0.52, C:0.19, G:0.19, T:0.11
Consensus pattern (20 bp):
ATCGCAACGCGAAAATAAAA
Found at i:1880019 original size:33 final size:32
Alignment explanation
Indices: 1879977--1880103 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
1879967 TTTCCACAAG
1879977 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
1880010 CGTTGCGATTTTCATTTCGCATTGAGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1880043 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1880076 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1880104 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1880081 original size:66 final size:66
Alignment explanation
Indices: 1879975--1880099 Score: 241
Period size: 66 Copynumber: 1.9 Consensus size: 66
1879965 AATTTCCACA
1879975 AGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGAGAAAT
1 AGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGAGAAAT
1880040 T
66 T
*
1880041 AGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTG
1 AGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTG
1880100 CGATAGTAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGAGAAAT
T
Found at i:1880111 original size:19 final size:20
Alignment explanation
Indices: 1880089--1880130 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1880079 TGCGATTTTC
*
1880089 ATTT-CGCATTGCGATAGTA
1 ATTTCCGCATTGCGATAGAA
*
1880108 ATTTCCGCGTTGCGATAGAA
1 ATTTCCGCATTGCGATAGAA
1880128 ATT
1 ATT
1880131 AAGATGATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGAA
Found at i:1882608 original size:24 final size:24
Alignment explanation
Indices: 1882574--1882627 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1882564 CTGAAACATC
* *
1882574 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
1882598 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
1882622 ATCAAA
1 ATCAAA
1882628 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:1883707 original size:20 final size:20
Alignment explanation
Indices: 1883682--1883739 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
1883672 ATTCATTTGA
*
1883682 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
1883702 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
1883722 TTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
1883740 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:1883782 original size:14 final size:14
Alignment explanation
Indices: 1883763--1883816 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1883753 GAAAATCGCA
1883763 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
1883777 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
1883794 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
1883810 TTGCGAT
1 TTGCGAT
1883817 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:1883782 original size:33 final size:33
Alignment explanation
Indices: 1883745--1883815 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
1883735 AAAATCGCAA
1883745 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
1883778 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1883811 TGCGA
1 TGCGA
1883816 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:1883824 original size:33 final size:33
Alignment explanation
Indices: 1883758--1883827 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
1883748 GAAATGAAAA
***
1883758 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1883791 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1883824 TCGC
1 TCGC
1883828 GTTGTGATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:1885857 original size:20 final size:19
Alignment explanation
Indices: 1885822--1885888 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
1885812 GAAACTTAAA
1885822 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1885841 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* * **
1885861 ATCGTAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1885880 ATCGCAACG
1 ATCGCAACG
1885889 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1885896 original size:14 final size:14
Alignment explanation
Indices: 1885877--1885934 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1885867 ATGCGAAATG
1885877 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1885891 AAAATCGCAACGTGAA
1 AAAATCGCAAC--GAC
1885907 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1885923 AAAATCGCAACG
1 AAAATCGCAACG
1885935 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 22 0.58
16 6 0.16
18 10 0.26
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1885918 original size:32 final size:33
Alignment explanation
Indices: 1885869--1885939 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 33
1885859 CTATCGTAAT
1885869 GCGAAATGAAAATCGCAACGACAAAATCGCAAC
1 GCGAAATGAAAATCGCAACGACAAAATCGCAAC
*
1885902 GTGAAATG-AAATCGCAACGACAAAATCGCAAC
1 GCGAAATGAAAATCGCAACGACAAAATCGCAAC
1885934 GCGAAA
1 GCGAAA
1885940 CACAAATCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 29 0.81
33 7 0.19
ACGTcount: A:0.48, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
GCGAAATGAAAATCGCAACGACAAAATCGCAAC
Found at i:1885991 original size:14 final size:14
Alignment explanation
Indices: 1885968--1886025 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
1885958 TTTCATTTCG
*
1885968 CGTTGTGATTTTTT
1 CGTTGCGATTTTTT
1885982 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TTT
* *
1885998 CGCATTGCAATTTTGT
1 CG--TTGCGATTTTTT
1886014 CGTTGCGATTTT
1 CGTTGCGATTTT
1886026 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.53
16 9 0.25
18 8 0.22
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.52
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:1886032 original size:33 final size:33
Alignment explanation
Indices: 1885951--1886038 Score: 133
Period size: 32 Copynumber: 2.7 Consensus size: 33
1885941 ACAAATCACA
* ** *
1885951 TTGCGATTTTCATTTCGCGTTGTGATTTTTTCG
1 TTGCGATTTTCATTTCGCATTGCAATTTTGTCG
1885984 TTGCGA-TTTCATTTCGCATTGCAATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCAATTTTGTCG
1886016 TTGCGATTTTCATTTCGCATTGC
1 TTGCGATTTTCATTTCGCATTGC
1886039 GATAGCCATT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 28 0.56
33 22 0.44
ACGTcount: A:0.12, C:0.18, G:0.19, T:0.50
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCAATTTTGTCG
Found at i:1886048 original size:19 final size:20
Alignment explanation
Indices: 1886026--1886069 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1886016 TTGCGATTTT
1886026 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
1886045 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
1886065 CATTT
1 CATTT
1886070 TCATGTTGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:1886077 original size:20 final size:20
Alignment explanation
Indices: 1886035--1886080 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1886025 TCATTTCGCA
*
1886035 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCACG
* * *
1886055 TTGCGATAGTCATTTTCATG
1 TTGCGATAGCCATTTCCACG
1886075 TTGCGA
1 TTGCGA
1886081 AAGTAAACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCACG
Found at i:1886587 original size:18 final size:18
Alignment explanation
Indices: 1886561--1886605 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1886551 GTCGATCAGA
*
1886561 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1886579 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1886597 TGATGGCTC
1 TGATGGCTC
1886606 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1887950 original size:20 final size:20
Alignment explanation
Indices: 1887925--1887962 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1887915 AATAGTTTCT
1887925 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1887945 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1887963 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1888482 original size:20 final size:20
Alignment explanation
Indices: 1888457--1888550 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1888447 GATTATGTAT
1888457 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1888477 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
1888497 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
1888518 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1888538 TATCGCATTGCGA
1 TATCGCGTTGCGA
1888551 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1888522 original size:41 final size:41
Alignment explanation
Indices: 1888477--1888554 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
1888467 CGAAAGTCAG
* * *
1888477 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
1888518 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
1888555 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:1888551 original size:20 final size:20
Alignment explanation
Indices: 1888437--1888551 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1888427 CGCTTTGAAA
*
1888437 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
1888458 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
1888478 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
1888498 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1888519 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1888539 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1888552 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1888570 original size:41 final size:41
Alignment explanation
Indices: 1888477--1888572 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
1888467 CGAAAGTCAG
* * * ** *
1888477 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
* *
1888518 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
1888560 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
1888573 TTACTTATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:1888707 original size:19 final size:19
Alignment explanation
Indices: 1888683--1888719 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1888673 CGATAATGGA
*
1888683 GATCGCGTTGCGAATTTGC
1 GATCGCATTGCGAATTTGC
*
1888702 GATCGCATTGCGATTTTG
1 GATCGCATTGCGAATTTG
1888720 TTGGTCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.19, G:0.30, T:0.35
Consensus pattern (19 bp):
GATCGCATTGCGAATTTGC
Found at i:1899523 original size:35 final size:35
Alignment explanation
Indices: 1899481--1899552 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 35
1899471 TAAAAAATAA
* * *
1899481 ATTTATGGACCCTACTTTTAATTTAGTTTATTAAT
1 ATTTATGGACCATACTTTTAATTTAATATATTAAT
** *
1899516 ATTTATGGGTCATGCTTTTAATTTAATATATTAAT
1 ATTTATGGACCATACTTTTAATTTAATATATTAAT
1899551 AT
1 AT
1899553 AATTTTTAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (35 bp):
ATTTATGGACCATACTTTTAATTTAATATATTAAT
Found at i:1900325 original size:7 final size:7
Alignment explanation
Indices: 1900313--1900398 Score: 163
Period size: 7 Copynumber: 12.3 Consensus size: 7
1900303 ATCCAAGTGA
1900313 AGTGAAG
1 AGTGAAG
1900320 AGTGAAG
1 AGTGAAG
1900327 AGTGAAG
1 AGTGAAG
1900334 AGTGAAG
1 AGTGAAG
1900341 AGTGAAG
1 AGTGAAG
1900348 AGTGAAG
1 AGTGAAG
1900355 AGTGAAG
1 AGTGAAG
1900362 AGTGAAG
1 AGTGAAG
1900369 AGTGAAG
1 AGTGAAG
1900376 AGTGAAG
1 AGTGAAG
*
1900383 AGCGAAG
1 AGTGAAG
1900390 AGTGAAG
1 AGTGAAG
1900397 AG
1 AG
1900399 AGACAGAAAG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 77 1.00
ACGTcount: A:0.43, C:0.01, G:0.43, T:0.13
Consensus pattern (7 bp):
AGTGAAG
Found at i:1901302 original size:21 final size:21
Alignment explanation
Indices: 1901254--1901305 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1901244 ATATGTAAAG
*
1901254 TAATATCCTATATTAATTATA
1 TAATATTCTATATTAATTATA
1901275 TAATATTCTATATTAATTATA
1 TAATATTCTATATTAATTATA
1901296 TAATATTCTA
1 TAATATTCTA
1901306 CATCAAATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATATTCTATATTAATTATA
Found at i:1901558 original size:19 final size:19
Alignment explanation
Indices: 1901524--1901560 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1901514 TTTTTAGTAT
1901524 TTTATTTTTAATATATTTA
1 TTTATTTTTAATATATTTA
1901543 TTTATATTTTAA-ATATTT
1 TTTAT-TTTTAATATATTT
1901561 GAATTAACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATTTTTAATATATTTA
Found at i:1904277 original size:2 final size:2
Alignment explanation
Indices: 1904266--1904303 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1904256 TATCTTATTT
1904266 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1904304 TATGTTAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1906235 original size:21 final size:21
Alignment explanation
Indices: 1906187--1906236 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1906177 TTAACATAAC
1906187 AATAAATCGTTAAATACATCA
1 AATAAATCGTTAAATACATCA
* * * *
1906208 AACAAATTGTTAAATACTTCT
1 AATAAATCGTTAAATACATCA
1906229 AATAAATC
1 AATAAATC
1906237 ATAAAAATAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.50, C:0.14, G:0.04, T:0.32
Consensus pattern (21 bp):
AATAAATCGTTAAATACATCA
Found at i:1909253 original size:20 final size:19
Alignment explanation
Indices: 1909221--1909259 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1909211 TGATGAAAAT
*
1909221 TATAAAAAAAATATTAATA
1 TATAAAAAAAATAATAATA
*
1909240 TATAAAAACCAATAATAATA
1 TATAAAAA-AAATAATAATA
1909260 AATTTTGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (19 bp):
TATAAAAAAAATAATAATA
Found at i:1909457 original size:36 final size:36
Alignment explanation
Indices: 1909409--1909480 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
1909399 AGCCAAAGAA
*
1909409 AAATGGTGAAATTACATCATTAATCCTTAAGTTTCT
1 AAATGGTAAAATTACATCATTAATCCTTAAGTTTCT
1909445 AAATGGTAAAATTACATCATTAATCCTTAAGTTTCT
1 AAATGGTAAAATTACATCATTAATCCTTAAGTTTCT
1909481 TAGATTTTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.39
Consensus pattern (36 bp):
AAATGGTAAAATTACATCATTAATCCTTAAGTTTCT
Found at i:1916890 original size:31 final size:30
Alignment explanation
Indices: 1916855--1916941 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 30
1916845 TAAATAAAGT
1916855 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* * *
1916886 TTAAAAGATTATAAATTTATTAATAAATTTA
1 TTAAAAAATTATAAA-ATATTATTAAATTTA
* *
1916917 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
1916942 TATTATTGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
30 1 0.02
31 42 0.91
32 3 0.07
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:1923616 original size:24 final size:24
Alignment explanation
Indices: 1923584--1923629 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1923574 TGTTCCTCAC
*
1923584 TGCTTCCTCATCTCTCTTCTTCGA
1 TGCTTCCTCATCCCTCTTCTTCGA
*
1923608 TGCTTCCTCGTCCCTCTTCTTC
1 TGCTTCCTCATCCCTCTTCTTC
1923630 TCCACCCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.04, C:0.41, G:0.09, T:0.46
Consensus pattern (24 bp):
TGCTTCCTCATCCCTCTTCTTCGA
Found at i:1931532 original size:17 final size:17
Alignment explanation
Indices: 1931510--1931548 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1931500 AGAAACATCA
* *
1931510 TTTGATCTAAAAATTGG
1 TTTGATCCAAAAATGGG
*
1931527 TTTGATCCGAAAATGGG
1 TTTGATCCAAAAATGGG
1931544 TTTGA
1 TTTGA
1931549 GACTGCCCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (17 bp):
TTTGATCCAAAAATGGG
Found at i:1932713 original size:24 final size:24
Alignment explanation
Indices: 1932661--1932713 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
1932651 CGCTCGTGAA
*
1932661 CGTTCGGTTATGTTCATTTATGTT
1 CGTTTGGTTATGTTCATTTATGTT
*
1932685 CGTTTGGTTATGTTCGTTTATGTT
1 CGTTTGGTTATGTTCATTTATGTT
1932709 CGTTT
1 CGTTT
1932714 ATGTTCATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.09, C:0.11, G:0.23, T:0.57
Consensus pattern (24 bp):
CGTTTGGTTATGTTCATTTATGTT
Found at i:1932728 original size:24 final size:23
Alignment explanation
Indices: 1932661--1932732 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
1932651 CGCTCGTGAA
*
1932661 CGTTCGGTTATGTTCATTTATGTT
1 CGTTTGGTTA-GTTCATTTATGTT
*
1932685 CGTTTGGTTATGTTCGTTTATGTT
1 CGTTTGGTTA-GTTCATTTATGTT
*
1932709 CGTTTATGTTCA-TTCATTTATGTT
1 CGTTT-GGTT-AGTTCATTTATGTT
1932733 TAACCTAATC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 38 0.90
25 3 0.07
26 1 0.02
ACGTcount: A:0.12, C:0.11, G:0.19, T:0.57
Consensus pattern (23 bp):
CGTTTGGTTAGTTCATTTATGTT
Found at i:1932730 original size:34 final size:34
Alignment explanation
Indices: 1932662--1932732 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
1932652 GCTCGTGAAC
* **
1932662 GTTCGGTTATGTTCATTTATGTTCGTTTGGTTAT
1 GTTCGGTTATGTTCATTTATGTTCATTCAGTTAT
* * *
1932696 GTTCGTTTATGTTCGTTTATGTTCATTCATTTAT
1 GTTCGGTTATGTTCATTTATGTTCATTCAGTTAT
1932730 GTT
1 GTT
1932733 TAACCTAATC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.13, C:0.10, G:0.20, T:0.58
Consensus pattern (34 bp):
GTTCGGTTATGTTCATTTATGTTCATTCAGTTAT
Found at i:1933671 original size:16 final size:16
Alignment explanation
Indices: 1933646--1933718 Score: 78
Period size: 16 Copynumber: 4.7 Consensus size: 16
1933636 CCAACGTTTA
* *
1933646 TGTTCGTTTATGTTCT
1 TGTTCATTTATGTTCG
*
1933662 TGTTTATTTATGTTCG
1 TGTTCATTTATGTTCG
* *
1933678 TGTTCGTTTATGATCG
1 TGTTCATTTATGTTCG
*
1933694 TGTTCATTTATGCTCG
1 TGTTCATTTATGTTCG
1933710 T-TT-ATTTAT
1 TGTTCATTTAT
1933719 TAAATGAACG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 6 0.12
15 2 0.04
16 41 0.84
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.59
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:1933687 original size:32 final size:32
Alignment explanation
Indices: 1933646--1933710 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1933636 CCAACGTTTA
* * * *
1933646 TGTTCGTTTATGTTCTTGTTTATTTATGTTCG
1 TGTTCGTTTATGATCGTGTTCATTTATGCTCG
1933678 TGTTCGTTTATGATCGTGTTCATTTATGCTCG
1 TGTTCGTTTATGATCGTGTTCATTTATGCTCG
1933710 T
1 T
1933711 TTATTTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.11, C:0.12, G:0.20, T:0.57
Consensus pattern (32 bp):
TGTTCGTTTATGATCGTGTTCATTTATGCTCG
Found at i:1937210 original size:24 final size:24
Alignment explanation
Indices: 1937183--1937242 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
1937173 AATATATATT
*
1937183 AATTAGGATTTTTAAT-TTGTTAGG
1 AATTAGGATTTTGAATGTT-TTAGG
* *
1937207 AATTAAGAGTTTGAATGTTTTAGG
1 AATTAGGATTTTGAATGTTTTAGG
* *
1937231 AGTTAGTATTTT
1 AATTAGGATTTT
1937243 ATTTTCATTA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (24 bp):
AATTAGGATTTTGAATGTTTTAGG
Found at i:1939683 original size:20 final size:20
Alignment explanation
Indices: 1939643--1939683 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1939633 TTGGGCCTGT
* * *
1939643 TAGTATCGATACTGGCTTTA
1 TAGTATCGACACTGACCTTA
1939663 TAGTATCGACACTGACCTTA
1 TAGTATCGACACTGACCTTA
1939683 T
1 T
1939684 TATTGATACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (20 bp):
TAGTATCGACACTGACCTTA
Found at i:1951948 original size:103 final size:103
Alignment explanation
Indices: 1951742--1951946 Score: 290
Period size: 103 Copynumber: 2.0 Consensus size: 103
1951732 TCACGAGATG
* *
1951742 ACTCTACCTGACTAGCTCGGGGGTGGAAGGTATGCTCCCTTTCACCTAGAGTGTGGGATAGTAGG
1 ACTCTACCTGACTAGCTCGGGGGTGAAAGGTATGCTCCCTTTCACCTAGAGTGTGGAATAGTAGG
*
1951807 TGTGATAGGTTGACTCCCCTCGAAGCAGTGTTAAAAAA
66 TGTGATAGGCTGACTCCCCTCGAAGCAGTGTTAAAAAA
* * *
1951845 ACTCTATCTGACTAGCTCGGGGGTGAAAGGTATGCTCCCTTTCACTTAGAGTGTGGAATGGTA-G
1 ACTCTACCTGACTAGCTCGGGGGTGAAAGGTATGCTCCCTTTCACCTAGAGTGTGGAATAGTAGG
* * * *
1951909 TGTTAT-GAGCTGACTCTCCTTGAAGTA-TGTTAAAAAA
66 TGTGATAG-GCTGACTCCCCTCGAAGCAGTGTTAAAAAA
1951946 A
1 A
1951947 AAGTTAAAGT
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
101 12 0.13
102 21 0.23
103 58 0.64
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (103 bp):
ACTCTACCTGACTAGCTCGGGGGTGAAAGGTATGCTCCCTTTCACCTAGAGTGTGGAATAGTAGG
TGTGATAGGCTGACTCCCCTCGAAGCAGTGTTAAAAAA
Found at i:1957155 original size:14 final size:14
Alignment explanation
Indices: 1957131--1957166 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1957121 TCATTTACAT
1957131 ATGAG-AGAATAAG
1 ATGAGAAGAATAAG
1957144 ATGAGAAGAATAAG
1 ATGAGAAGAATAAG
1957158 ATGAGAAGA
1 ATGAGAAGA
1957167 GAAATACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.56, C:0.00, G:0.31, T:0.14
Consensus pattern (14 bp):
ATGAGAAGAATAAG
Found at i:1960932 original size:44 final size:45
Alignment explanation
Indices: 1960884--1960969 Score: 138
Period size: 44 Copynumber: 1.9 Consensus size: 45
1960874 GTAACCATGC
* * *
1960884 AAATAAGCTTATGAGCTTATGGAAT-AATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTAATGGAATAAATGGTAAGTAAATTGGTA
1960928 AAATAAGCTTACGAGCTAATGGAATAAATGGTAAGTAAATTG
1 AAATAAGCTTACGAGCTAATGGAATAAATGGTAAGTAAATTG
1960970 ATAAGAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 23 0.61
45 15 0.39
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTAATGGAATAAATGGTAAGTAAATTGGTA
Found at i:1973968 original size:113 final size:113
Alignment explanation
Indices: 1973570--1974282 Score: 1089
Period size: 112 Copynumber: 6.3 Consensus size: 113
1973560 AACTTTCAAC
* *
1973570 AAAGTATCGATACATTTTTATAAAAAGAATCGACT-CTTTCAACATATCAGGTAAATTTTACCGG
1 AAAGTATCGATTCATTTTTATAAAAAGGATCGA-TACTTTCAACATATCAGGTAAATTTTACCGG
1973634 TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
65 TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* *
1973683 AAAGTATCGA-TCATTTTTATAAAAATGATCGATACTTTCAACATATTAGGTAAATTTTACCGGT
1 AAAGTATCGATTCATTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
* * * *
1973747 TTTGTCATAATGAAAATGTTTTTGTCATATTTTTACATGTTTTATTGT
66 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * *
1973795 AAAGTATC-AATCATTTTTATAAAAAGGATCGATACTTTCAACATATTAGGTACATTTTACCGGT
1 AAAGTATCGATTCATTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
*
1973859 TTTATCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
66 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* *
1973907 AAATTATCGATTC-TTTTTATAAAAAAGGATCGATACTTTCAACATATCAGGTACATTTTACCGG
1 AAAGTATCGATTCATTTTTAT-AAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGG
**
1973971 TTTTGTCATAATGAAACTAATTTTGTCATATTTTTACCTGTTATATTGT
65 TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * *
1974020 AAAGCATCGA-TCATTTTTATAAAAAAGATCGATACTTTCAACATATTAGGTAAATTTTACCGGT
1 AAAGTATCGATTCATTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
* * *
1974084 TTTGTCATAATGAAATTGATTTTGTCATACTTTTACCTGTTATATTGT
66 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * * *
1974132 AAAGTATCGATACATTTTTATAAAAATGATCGATACTTTCAACATATCCGGTAAATTTTACCGTT
1 AAAGTATCGATTCATTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
*
1974197 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACATGTTATATTGT
66 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* *
1974245 AAAGTATCGATAT-ATTTTT-TATAAAGTATCGATACTTT
1 AAAGTATCGAT-TCATTTTTATAAAAAGGATCGATACTTT
1974283 ATAAGCGCTA
Statistics
Matches: 550, Mismatches: 43, Indels: 15
0.90 0.07 0.02
Matches are distributed among these distances:
111 2 0.00
112 322 0.59
113 226 0.41
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (113 bp):
AAAGTATCGATTCATTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
Found at i:1974003 original size:225 final size:225
Alignment explanation
Indices: 1973570--1974282 Score: 1112
Period size: 225 Copynumber: 3.2 Consensus size: 225
1973560 AACTTTCAAC
* * *
1973570 AAAGTATCGATACATTTTTATAAAAAGAATCGACT-CTTTCAACATATCAGGTAAATTTTACCGG
1 AAAGTATCAAT-CATTTTTATAAAAAGGATCGA-TACTTTCAACATATTAGGTAAATTTTACCGG
1973634 TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGA-TCATT
64 TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATTCATT
* *
1973698 TTTATAAAAATGATCGATACTTTCAACATATTAGGTAAATTTTACCGGTTTTGTCATAATGAAAA
129 TTTATAAAAATGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAAC
* *
1973763 TGTTTTTGTCATATTTTTACATGTTTTATTGT
194 TGATTTTGTCATATTTTTACATGTTATATTGT
*
1973795 AAAGTATCAATCATTTTTATAAAAAGGATCGATACTTTCAACATATTAGGTACATTTTACCGGTT
1 AAAGTATCAATCATTTTTATAAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCGGTT
* *
1973860 TTATCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAATTATCGATTC-TTTT
66 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATTCATTTT
* *
1973924 TATAAAAAAGGATCGATACTTTCAACATATCAGGTACATTTTACCGGTTTTGTCATAATGAAACT
131 TAT-AAAAATGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACT
* *
1973989 AATTTTGTCATATTTTTACCTGTTATATTGT
195 GATTTTGTCATATTTTTACATGTTATATTGT
* * *
1974020 AAAGCATCGATCATTTTTATAAAAAAGATCGATACTTTCAACATATTAGGTAAATTTTACCGGTT
1 AAAGTATCAATCATTTTTATAAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCGGTT
* * * *
1974085 TTGTCATAATGAAATTGATTTTGTCATACTTTTACCTGTTATATTGTAAAGTATCGATACATTTT
66 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATTCATTTT
* *
1974150 TATAAAAATGATCGATACTTTCAACATATCCGGTAAATTTTACCGTTTTTGTCATAATGAAACTG
131 TATAAAAATGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTG
*
1974215 GTTTTGTCATATTTTTACATGTTATATTGT
196 ATTTTGTCATATTTTTACATGTTATATTGT
* *
1974245 AAAGTATCGATAT-ATTTTT-TATAAAGTATCGATACTTT
1 AAAGTATC-A-ATCATTTTTATAAAAAGGATCGATACTTT
1974283 ATAAGCGCTA
Statistics
Matches: 446, Mismatches: 36, Indels: 12
0.90 0.07 0.02
Matches are distributed among these distances:
223 1 0.00
224 111 0.25
225 319 0.72
226 13 0.03
227 2 0.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (225 bp):
AAAGTATCAATCATTTTTATAAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCGGTT
TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATTCATTTT
TATAAAAATGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTG
ATTTTGTCATATTTTTACATGTTATATTGT
Found at i:1974655 original size:87 final size:87
Alignment explanation
Indices: 1974509--1974770 Score: 418
Period size: 87 Copynumber: 3.0 Consensus size: 87
1974499 ACAAATTAAA
* * * * *
1974509 TAATTAACATATTTTATTATATAAGCGCTACTTATTACGTTATATAAGCGCTACCTAATATGCTA
1 TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTATATAAACGGTACCTAATATGTTA
*
1974574 TTGTGCTTGATAATATTTTCGG
66 TTGTGTTTGATAATATTTTCGG
1974596 TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTATATAAACGGTACCTAATATGTTA
1 TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTATATAAACGGTACCTAATATGTTA
* *
1974661 TTGTGTTTAATAAT-GTTTCTGG
66 TTGTGTTTGATAATATTTTC-GG
*
1974683 TAATTAACTTATTTTATTATATAAGCGCTACCTATTACATTATATAAACGGTACCTAATATGTTA
1 TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTATATAAACGGTACCTAATATGTTA
*
1974748 TTATGTTTGATAATATTTTCGG
66 TTGTGTTTGATAATATTTTCGG
1974770 T
1 T
1974771 TAAATGATAT
Statistics
Matches: 161, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
86 4 0.02
87 153 0.95
88 4 0.02
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.44
Consensus pattern (87 bp):
TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTATATAAACGGTACCTAATATGTTA
TTGTGTTTGATAATATTTTCGG
Found at i:1974661 original size:23 final size:23
Alignment explanation
Indices: 1974611--1974655 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1974601 AACATATTTT
* *
1974611 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAACGCTACCTAATAC
*
1974634 ATTATATAAACGGTACCTAATA
1 ATTATATAAACGCTACCTAATA
1974656 TGTTATTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAACGCTACCTAATAC
Found at i:1974748 original size:23 final size:23
Alignment explanation
Indices: 1974698--1974742 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1974688 AACTTATTTT
* *
1974698 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAACGCTACCTAATAC
*
1974721 ATTATATAAACGGTACCTAATA
1 ATTATATAAACGCTACCTAATA
1974743 TGTTATTATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAACGCTACCTAATAC
Found at i:1987738 original size:21 final size:20
Alignment explanation
Indices: 1987695--1987740 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1987685 TTTCCAATTT
* *
1987695 TTATATTTTAATATTTTATA
1 TTATATTTTAATATTTAAAA
*
1987715 TTATTTTTTATATATTTAAAA
1 TTATATTTTA-ATATTTAAAA
1987736 TTATA
1 TTATA
1987741 AAAATAATGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATATTTTAATATTTAAAA
Found at i:1988565 original size:153 final size:156
Alignment explanation
Indices: 1988325--1988634 Score: 599
Period size: 153 Copynumber: 2.0 Consensus size: 156
1988315 TTTTAGTTTT
1988325 TTCAATTTACTCACTGAACTTTATAGATTGAATATTTTTTGTCATCCACTGTTAAATAATTAACG
1 TTCAATTTACTCACTGAACTTTATAGATTGAATATTTTTTGTCATCCACTGTTAAATAATTAACG
1988390 ACATTATGACATGGTCGTATTTAAATCAAAATGAATTCATTTTAGTCTAGATTTTTTTTTCTTTC
66 ACATTATGACATGGTCGTATTTAAATCAAAATGAATTCATTTTAGTCTAGATTTTTTTTTCTTTC
1988455 ACGAATTCGAAATGATG-TGTTTTGG
131 ACGAATTCGAAATGATGTTGTTTTGG
1988480 TTCAATTTACTCACTGAAC-TT-TAGATTGAATATTTTTTGTCATCCACTGTTAAATAATTAACG
1 TTCAATTTACTCACTGAACTTTATAGATTGAATATTTTTTGTCATCCACTGTTAAATAATTAACG
1988543 ACATTATGACATGGTCGTATTTAAATCAAAATGAATTCATTTTAGTCTAGATTTTTTTTTCTTTC
66 ACATTATGACATGGTCGTATTTAAATCAAAATGAATTCATTTTAGTCTAGATTTTTTTTTCTTTC
1988608 ACGAATTCGAAATGATGTTGTTTTGG
131 ACGAATTCGAAATGATGTTGTTTTGG
1988634 T
1 T
1988635 GTAAGTTGTC
Statistics
Matches: 154, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
153 124 0.81
154 11 0.07
155 19 0.12
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (156 bp):
TTCAATTTACTCACTGAACTTTATAGATTGAATATTTTTTGTCATCCACTGTTAAATAATTAACG
ACATTATGACATGGTCGTATTTAAATCAAAATGAATTCATTTTAGTCTAGATTTTTTTTTCTTTC
ACGAATTCGAAATGATGTTGTTTTGG
Found at i:1990176 original size:2 final size:2
Alignment explanation
Indices: 1990169--1990199 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1990159 AAATTTTTAA
1990169 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1990200 AAGATTTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1991341 original size:42 final size:42
Alignment explanation
Indices: 1991295--1991409 Score: 203
Period size: 42 Copynumber: 2.7 Consensus size: 42
1991285 AGCAACACAT
1991295 TATAATCAAAGAACCATTTTATAACTTTTAAACAAAAAACCC
1 TATAATCAAAGAACCATTTTATAACTTTTAAACAAAAAACCC
1991337 TATAATCAAAGAACCATTTTATAACTTTTAAACAAAAAACCC
1 TATAATCAAAGAACCATTTTATAACTTTTAAACAAAAAACCC
* * *
1991379 TATAATCAAAGAATCATTTTGTAATTTTTAA
1 TATAATCAAAGAACCATTTTATAACTTTTAA
1991410 TAGCCAGAAG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.48, C:0.16, G:0.03, T:0.33
Consensus pattern (42 bp):
TATAATCAAAGAACCATTTTATAACTTTTAAACAAAAAACCC
Found at i:1992650 original size:21 final size:20
Alignment explanation
Indices: 1992631--1992673 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1992621 AGGTAAAAAT
1992631 ATGA-AAAACCGGTATCAAA
1 ATGATAAAACCGGTATCAAA
1992650 ATGATAAAACCGGTA--AAA
1 ATGATAAAACCGGTATCAAA
1992668 ATGATA
1 ATGATA
1992674 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.39
19 4 0.17
20 10 0.43
ACGTcount: A:0.53, C:0.12, G:0.16, T:0.19
Consensus pattern (20 bp):
ATGATAAAACCGGTATCAAA
Found at i:1992660 original size:20 final size:18
Alignment explanation
Indices: 1992626--1992673 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
1992616 ATAACAGGTA
1992626 AAAATATGA-AAAACCGGT
1 AAAA-ATGATAAAACCGGT
1992644 ATCAAAATGATAAAACCGGT
1 A--AAAATGATAAAACCGGT
1992664 AAAAATGATA
1 AAAAATGATA
1992674 CCGGATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 10 0.37
19 4 0.15
20 13 0.48
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (18 bp):
AAAAATGATAAAACCGGT
Found at i:1994924 original size:21 final size:21
Alignment explanation
Indices: 1994877--1994941 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1994867 AAGACAATCA
* *
1994877 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
1994899 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
1994919 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
1994940 AG
1 AG
1994942 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:1995017 original size:33 final size:33
Alignment explanation
Indices: 1994975--1995040 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1994965 AAATAGATGG
*
1994975 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
1995008 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1995041 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1997430 original size:18 final size:18
Alignment explanation
Indices: 1997409--1997476 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
1997399 AGCGGTCACA
1997409 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
1997427 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
1997448 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
1997469 GAAGATGA
1 GAAGATGA
1997477 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Done.