Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009267.1 Hibiscus syriacus cultivar Beakdansim tig00112925_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: 1725308
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:1514474 original size:14 final size:16
Alignment explanation
Indices: 1514454--1514527 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
1514444 TGAAAATCGC
1514454 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
1514469 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
1514486 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
1514505 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
1514521 -TTGCGAT
1 ATTGCGAT
1514528 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:1514491 original size:19 final size:19
Alignment explanation
Indices: 1514450--1514517 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
1514440 GAAATGAAAA
1514450 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1514466 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1514483 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1514502 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1514518 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1516573 original size:20 final size:19
Alignment explanation
Indices: 1516538--1516593 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1516528 AAAACTTAAA
1516538 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1516557 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* *
1516577 ATCGCAATGTGAAATGA
1 ATCGCAACGCGAAATGA
1516594 AAATCGCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1516612 original size:14 final size:14
Alignment explanation
Indices: 1516593--1516650 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1516583 ATGTGAAATG
*
1516593 AAAATCGCAATGAC
1 AAAATCGCAACGAC
*
1516607 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1516623 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1516639 AAAATCGCAACG
1 AAAATCGCAACG
1516651 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 21 0.57
16 7 0.19
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1516640 original size:32 final size:33
Alignment explanation
Indices: 1516577--1516655 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
1516567 GGAAATGGCT
* * *
1516577 ATCGCAATGTGAAATGAAAATCGCAATGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1516610 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1516642 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1516656 CACAAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 29 0.67
33 14 0.33
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1516684 original size:19 final size:18
Alignment explanation
Indices: 1516662--1516756 Score: 82
Period size: 19 Copynumber: 5.7 Consensus size: 18
1516652 GAAACACAAA
1516662 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
*
1516681 TCGCGTTGCGATTT--TT
1 TCGCATTGCGATTTCATT
*
1516697 T-G--TTGTGATTTCATT
1 TCGCATTGCGATTTCATT
*
1516712 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
1516728 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
1516745 TCGCATTGCGAT
1 TCGCATTGCGAT
1516757 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 5, Indels: 21
0.70 0.06 0.24
Matches are distributed among these distances:
13 8 0.13
14 6 0.10
15 7 0.11
16 8 0.13
17 4 0.07
18 12 0.20
19 16 0.26
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:1516710 original size:31 final size:33
Alignment explanation
Indices: 1516667--1516756 Score: 139
Period size: 31 Copynumber: 2.8 Consensus size: 33
1516657 ACAAATCGCA
* *
1516667 TTGCGATTTTCATTTCGCGTTGCGATTTT-TTG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
1516699 TTGTGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1516731 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1516757 AGCCATTTCC
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
31 21 0.40
32 12 0.23
33 19 0.37
ACGTcount: A:0.12, C:0.17, G:0.21, T:0.50
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1516775 original size:20 final size:19
Alignment explanation
Indices: 1516741--1516795 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1516731 TTGCGATTTT
*
1516741 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1516760 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1516780 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1516796 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1517303 original size:18 final size:18
Alignment explanation
Indices: 1517277--1517321 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1517267 GTCGATCAGA
*
1517277 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1517295 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1517313 TGATGGCTC
1 TGATGGCTC
1517322 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:1518651 original size:20 final size:20
Alignment explanation
Indices: 1518626--1518663 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1518616 AATAGTTTCT
1518626 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1518646 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1518664 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:1518950 original size:22 final size:22
Alignment explanation
Indices: 1518925--1518968 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1518915 GATTTAGATA
1518925 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1518947 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1518969 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1519242 original size:20 final size:20
Alignment explanation
Indices: 1519136--1519250 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
1519126 CGCTTTGAAA
*
1519136 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
1519157 ATCGCGTTGCGAAAGTCTGT
1 ATCGCATTGCGATAGTCAGT
* * *
1519177 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
1519197 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1519218 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1519238 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1519251 TTTCCCAATT
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
19 2 0.03
20 48 0.65
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1519268 original size:21 final size:21
Alignment explanation
Indices: 1519239--1519331 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
1519229 ATAGTCAGTA
1519239 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1519260 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1519280 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1519301 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1519321 TCGCATTGCGA
1 TCGCATTGCGA
1519332 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:1519269 original size:41 final size:41
Alignment explanation
Indices: 1519178--1519312 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
1519168 AAAGTCTGTA
* * * ** *
1519178 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
1519218 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
1519260 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
1519301 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1519313 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:1519313 original size:41 final size:41
Alignment explanation
Indices: 1519239--1519331 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1519229 ATAGTCAGTA
1519239 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1519280 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1519321 TCGCATTGCGA
1 TCGCATTGCGA
1519332 ATTGGGAAAA
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:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1522056 original size:130 final size:127
Alignment explanation
Indices: 1521922--1522200 Score: 292
Period size: 127 Copynumber: 2.2 Consensus size: 127
1521912 AAGACTACAT
*
1521922 AACAAGTTAATTTCAGTGAGTTACCCTAGATGTTAATATTAAATGCTTTCTTTGACGAC-ATACA
1 AACAAGTTAATTTCAGTGAATT-CCCT--ATGTTAATATTAAATGCTTTCTTTGACGACGA-ACA
* *
1521986 TACATCTCAGAGTCCAAAAGAGATATAATATCCAAATTCAAAATTATGTCGA-AATTAGGACTGC
62 TACATCTCAGAGTCCAAAAAAGATATAACATCCAAATTCAAAATTATGTC-ATAATTAGGACTGC
1522050 AA
126 AA
* * ** * * * *
1522052 AACAAGTTAATTTCAGTGAATTGCCTTTGTTAATATTGTATGTTTTCTTTGATGACGAACGTACC
1 AACAAGTTAATTTCAGTGAATTCCCTATGTTAATATTAAATGCTTTCTTTGACGACGAACATACA
** * * * * * * *
1522117 TCTCAGAGTTTAAAAAAGTTGTAACATCCAAATTCAACATTGTGTCATAGTTAGGATTGCAT
66 TCTCAGAGTCCAAAAAAGATATAACATCCAAATTCAAAATTATGTCATAATTAGGACTGCAA
* * *
1522179 GACAAGTTAATTTTAATGAATT
1 AACAAGTTAATTTCAGTGAATT
1522201 ACCTTTGATA
Statistics
Matches: 124, Mismatches: 23, Indels: 7
0.81 0.15 0.05
Matches are distributed among these distances:
126 1 0.01
127 98 0.79
128 1 0.01
129 3 0.02
130 21 0.17
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (127 bp):
AACAAGTTAATTTCAGTGAATTCCCTATGTTAATATTAAATGCTTTCTTTGACGACGAACATACA
TCTCAGAGTCCAAAAAAGATATAACATCCAAATTCAAAATTATGTCATAATTAGGACTGCAA
Found at i:1522280 original size:130 final size:127
Alignment explanation
Indices: 1521922--1522507 Score: 341
Period size: 130 Copynumber: 4.6 Consensus size: 127
1521912 AAGACTACAT
* * * ** * *
1521922 AACAAGTTAATTTCAGTGAGTTACCCTAGATGTTAATATTAAATGCTTTCTTTGACGAC-ATACA
1 AACAAGTTAATTTCAATGAATTA-CCT--TTGTTAATATTGGATGCTTACTTTGATGACGA-ACA
* * ** * * * *
1521986 TACATCTCAGAGTCCAAAAGAGATATAATATCCAAATTCAAAATTATGTCGAAATTAGGACTGCA
62 TACCTCTCAAAGTTTAAAAAAGGTGTAACATCCAAATTCAAAATTATGTCGAAATTAGGACTGCA
1522051 A
127 A
* * * * * *
1522052 AACAAGTTAATTTCAGTGAATTGCCTTTGTTAATATTGTATGTTTTCTTTGATGACGAACGTACC
1 AACAAGTTAATTTCAATGAATTACCTTTGTTAATATTGGATGCTTACTTTGATGACGAACATACC
* * * * * * *
1522117 TCTCAGAGTTTAAAAAAGTTGTAACATCCAAATTCAACATTGTGTC-ATAGTTAGGATTGCAT
66 TCTCAAAGTTTAAAAAAGGTGTAACATCCAAATTCAAAATTATGTCGA-AATTAGGACTGCAA
* * * *
1522179 GACAAGTTAATTTTAATGAATTACCTTTGATATGAATATTGGATGCTTACTTTGATGATGTACAT
1 AACAAGTTAATTTCAATGAATTACCTTTG-T-T-AATATTGGATGCTTACTTTGATGACGAACAT
* *** *** * * * ** *
1522244 ACCTCAT-AAAGTTTGAAGTGGGTGTAACATCCAAATTCTGTAGTGTGTTGCGATCAGGACTGCA
63 ACCTC-TCAAAGTTTAAAAAAGGTGTAACATCCAAATTCAAAATTATGTCGAAATTAGGACTGCA
*
1522308 T
127 A
* * * ** * * *
1522309 AACAAGTTAATTTCAGTGAGTTACTTTTGATGTGAATATCAGATGCTTTCTTTGATAAC-ATACG
1 AACAAGTTAATTTCAATGAATTACCTTTG-T-T-AATATTGGATGCTTACTTTGATGACGA-ACA
* * * * *
1522373 TAACTCTC-AGGGTTAAAAAA---GTAACATCCAAATTCAGTAA-TATGTC-ATAATTAGAACTA
62 TACCTCTCAAAGTTTAAAAAAGGTGTAACATCCAAATTCA-AAATTATGTCGA-AATTAGGACT-
1522432 G-AA
124 GCAA
* * * *
1522435 AACAAGTTAATATCAATGAATTGCCTTTGATGTTATTATTGGATGCTTGCTTTGATGAC-ATACA
1 AACAAGTTAATTTCAATGAATTACC-TT--TGTTAATATTGGATGCTTACTTTGATGACGA-ACA
1522499 TACCTCTCA
62 TACCTCTCA
1522508 GATGTTGAAG
Statistics
Matches: 352, Mismatches: 88, Indels: 35
0.74 0.19 0.07
Matches are distributed among these distances:
126 79 0.22
127 109 0.31
128 3 0.01
129 13 0.04
130 147 0.42
131 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (127 bp):
AACAAGTTAATTTCAATGAATTACCTTTGTTAATATTGGATGCTTACTTTGATGACGAACATACC
TCTCAAAGTTTAAAAAAGGTGTAACATCCAAATTCAAAATTATGTCGAAATTAGGACTGCAA
Found at i:1522464 original size:256 final size:255
Alignment explanation
Indices: 1522042--1522536 Score: 581
Period size: 256 Copynumber: 1.9 Consensus size: 255
1522032 TGTCGAAATT
* * * *
1522042 AGGACTGCAAAACAAGTTAATTTCAGTGAATTGCCTTTGTTAATATTGTATGTTTTCTTTGATGA
1 AGGACTGCAAAACAAGTTAATTTCAGTGAATTACCTTTGTTAATATAGTATGCTTTCTTTGATAA
* * * * * *
1522107 CGAACGTACCTCTCAGAGTTTAAAAAAGTTGTAACATCCAAATTCAACATTGTGTCATAGTTAGG
66 CGAACGTAACTCTCAGAGGTTAAAAAA--TGTAACATCCAAATTCAACAATATGTCATAATTAGA
* ** * *
1522172 ATTGCATGACAAGTTAATTTTAATGAATTACCTTTGATATGAATATTGGATGCTTACTTTGATGA
129 ATAGCAAAACAAGTTAATATCAATGAATTACCTTTGATATGAATATTGGATGCTTACTTTGATGA
** *
1522237 TGTACATACCTCATAA-A-GTTTGAAGTGGGTGTAACATCCAAATTCTGTAGTGTGTTGCGATC
194 CATACATACCTC-TAAGATG-TTGAAGTGGGTCTAACATCCAAATTCTGTAGTGTGTTGCGATC
* * *
1522299 AGGACTGCATAACAAGTTAATTTCAGTGAGTTACTTTTGATGTGAATATCAG-ATGCTTTCTTTG
1 AGGACTGCAAAACAAGTTAATTTCAGTGAATTACCTTTG-T-T-AATAT-AGTATGCTTTCTTTG
**
1522363 ATAAC-ATACGTAACTCTCAG-GGTTAAAAAA-GTAACATCCAAATTCAGTAATATGTCATAATT
62 ATAACGA-ACGTAACTCTCAGAGGTTAAAAAATGTAACATCCAAATTCAACAATATGTCATAATT
* * * * *
1522425 AGAACTAG-AAAACAAGTTAATATCAATGAATTGCCTTTGATGTTATTATTGGATGCTTGCTTTG
126 AGAA-TAGCAAAACAAGTTAATATCAATGAATTACCTTTGATATGAATATTGGATGCTTACTTTG
* *
1522489 ATGACATACATACCTCTCAGATGTTGAAGTGGGTCTAACATCTAAATT
190 ATGACATACATACCTCTAAGATGTTGAAGTGGGTCTAACATCCAAATT
1522537 TTGCAATGTG
Statistics
Matches: 200, Mismatches: 30, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
255 2 0.01
256 115 0.57
257 38 0.19
258 1 0.00
259 11 0.05
260 32 0.16
261 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.36
Consensus pattern (255 bp):
AGGACTGCAAAACAAGTTAATTTCAGTGAATTACCTTTGTTAATATAGTATGCTTTCTTTGATAA
CGAACGTAACTCTCAGAGGTTAAAAAATGTAACATCCAAATTCAACAATATGTCATAATTAGAAT
AGCAAAACAAGTTAATATCAATGAATTACCTTTGATATGAATATTGGATGCTTACTTTGATGACA
TACATACCTCTAAGATGTTGAAGTGGGTCTAACATCCAAATTCTGTAGTGTGTTGCGATC
Found at i:1525971 original size:20 final size:20
Alignment explanation
Indices: 1525942--1525993 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1525932 ACTTAAGGGA
1525942 TGTACCGATACCCTGTAGAG
1 TGTACCGATACCCTGTAGAG
*
1525962 TGTACTGATACCCTGTAGAG
1 TGTACCGATACCCTGTAGAG
1525982 TGTACCGATACC
1 TGTACCGATACC
1525994 TATGTTAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (20 bp):
TGTACCGATACCCTGTAGAG
Found at i:1527144 original size:32 final size:31
Alignment explanation
Indices: 1527072--1527191 Score: 127
Period size: 32 Copynumber: 3.9 Consensus size: 31
1527062 GAGTCGAGGG
* * * *
1527072 TTACCTATGTCTTTCGAGACATATGGATAGT
1 TTACCTATGTCCTTCGGGACATATGGACAGA
1527103 TTACCTATGTCCTTCGGGACATATGGACACGA
1 TTACCTATGTCCTTCGGGACATATGGACA-GA
**
1527135 TTACCTATGTCCTTTAGGACATATGGAC--A
1 TTACCTATGTCCTTCGGGACATATGGACAGA
* **
1527164 TCTACCTATGTTCTTCGAAACATATGGA
1 T-TACCTATGTCCTTCGGGACATATGGA
1527192 TAGGTCCTTC
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
29 2 0.03
30 21 0.28
31 26 0.34
32 27 0.36
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (31 bp):
TTACCTATGTCCTTCGGGACATATGGACAGA
Found at i:1529098 original size:20 final size:20
Alignment explanation
Indices: 1529068--1529190 Score: 142
Period size: 20 Copynumber: 6.0 Consensus size: 20
1529058 TAAATTGTAG
*
1529068 CACATAAGTCAAATTCGCAA
1 CACAGAAGTCAAATTCGCAA
*
1529088 CATAGAAGTCAAATTCGCAA
1 CACAGAAGTCAAATTCGCAA
*
1529108 CACAGAAGTCAAAATCGCAA
1 CACAGAAGTCAAATTCGCAA
*
1529128 AACAGAAGTCAAATTCGCAA
1 CACAGAAGTCAAATTCGCAA
*
1529148 CAC-GAAATTTCAAATTCGCAA
1 CACAG-AA-GTCAAATTCGCAA
*
1529169 CAC-GAAATTTCAAATTCGCAA
1 CACAG-AA-GTCAAATTCGCAA
1529190 C
1 C
1529191 CCGAATTTAT
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
19 1 0.01
20 58 0.62
21 34 0.37
ACGTcount: A:0.46, C:0.24, G:0.12, T:0.19
Consensus pattern (20 bp):
CACAGAAGTCAAATTCGCAA
Found at i:1529162 original size:21 final size:21
Alignment explanation
Indices: 1529136--1529195 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
1529126 AAAACAGAAG
1529136 TCAAATTCGCAACACGAAATT
1 TCAAATTCGCAACACGAAATT
1529157 TCAAATTCGCAACACGAAATT
1 TCAAATTCGCAACACGAAATT
*
1529178 TCAAATTCGCAACCCGAA
1 TCAAATTCGCAACACGAA
1529196 TTTATTTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.42, C:0.27, G:0.10, T:0.22
Consensus pattern (21 bp):
TCAAATTCGCAACACGAAATT
Found at i:1529264 original size:40 final size:40
Alignment explanation
Indices: 1529208--1529310 Score: 107
Period size: 40 Copynumber: 2.6 Consensus size: 40
1529198 TATTTTTCAT
** * *
1529208 ACACAAATTTCCTTTTCGCAACAATATTTTCTAAATCGCA
1 ACACAAATTTTATTTTCGCAACAAGATTTTCGAAATCGCA
* * ** * *
1529248 ACACGAATTTTGTTTTCGCAACTCGATTTTCGAATTCGTA
1 ACACAAATTTTATTTTCGCAACAAGATTTTCGAAATCGCA
*
1529288 ACACAAATTTTAATTTCGCAACA
1 ACACAAATTTTATTTTCGCAACA
1529311 GCTTTTATTT
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (40 bp):
ACACAAATTTTATTTTCGCAACAAGATTTTCGAAATCGCA
Found at i:1529266 original size:20 final size:20
Alignment explanation
Indices: 1529243--1529310 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
1529233 ATTTTCTAAA
*
1529243 TCGCAACACGAATTTTGTTT
1 TCGCAACACGAATTTTGATT
* *
1529263 TCGCAACTCG-ATTTTCGAAT
1 TCGCAACACGAATTTT-GATT
* * *
1529283 TCGTAACACAAATTTTAATT
1 TCGCAACACGAATTTTGATT
1529303 TCGCAACA
1 TCGCAACA
1529311 GCTTTTATTT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
19 5 0.14
20 27 0.73
21 5 0.14
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (20 bp):
TCGCAACACGAATTTTGATT
Found at i:1529486 original size:14 final size:15
Alignment explanation
Indices: 1529467--1529504 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1529457 TCACCATCTC
1529467 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
1529481 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1529497 TAATTTTT
1 TAATTTTT
1529505 CAATGATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1530117 original size:12 final size:12
Alignment explanation
Indices: 1530096--1530129 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1530086 ACCACATTTC
*
1530096 CAATACCAAACA
1 CAATATCAAACA
1530108 CAATATCAAACA
1 CAATATCAAACA
*
1530120 CAATCTCAAA
1 CAATATCAAA
1530130 ACCCACAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1530467 original size:3 final size:3
Alignment explanation
Indices: 1530459--1530483 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1530449 ATATAACCCT
1530459 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
1530484 TCCCCGGAGA
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:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1532579 original size:18 final size:18
Alignment explanation
Indices: 1532556--1532591 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1532546 AAGCAAAAGG
*
1532556 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1532574 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1532592 CAACCGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1532910 original size:20 final size:20
Alignment explanation
Indices: 1532868--1532921 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
1532858 CGATTTTTGC
* * **
1532868 TTGCGAATTTGATTTTCGCG
1 TTGCAAATTTGACTTTCAAG
*
1532888 TTGTAAATTTGACTTTCAAG
1 TTGCAAATTTGACTTTCAAG
*
1532908 TTGCGAATTTGACT
1 TTGCAAATTTGACT
1532922 ATCGCAACGC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.44
Consensus pattern (20 bp):
TTGCAAATTTGACTTTCAAG
Found at i:1533025 original size:17 final size:17
Alignment explanation
Indices: 1533003--1533040 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1532993 TGCAGATTGA
*
1533003 AATTAAACAAAAAAATC
1 AATTAAACAAAAAAAAC
1533020 AATTAAACAAAAAAAAC
1 AATTAAACAAAAAAAAC
1533037 AATT
1 AATT
1533041 CTTATTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.18
Consensus pattern (17 bp):
AATTAAACAAAAAAAAC
Found at i:1534453 original size:21 final size:21
Alignment explanation
Indices: 1534429--1534526 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 21
1534419 GCGAATCGGG
*
1534429 CTCTTGAATGGTGAGAGGGGC
1 CTCTTGAATGATGAGAGGGGC
*
1534450 CTCTTGAATGATGAGAGAGGC
1 CTCTTGAATGATGAGAGGGGC
*
1534471 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAATGATGAGAGGGGC
* *
1534492 CTCTTGAACGA-CATGAGGGGC
1 CTCTTGAATGATGA-GAGGGGC
* *
1534513 ATCTTGAATAATGA
1 CTCTTGAATGATGA
1534527 CAGGTGAATC
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
20 1 0.02
21 64 0.97
22 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.34, T:0.23
Consensus pattern (21 bp):
CTCTTGAATGATGAGAGGGGC
Found at i:1534942 original size:21 final size:21
Alignment explanation
Indices: 1534918--1534967 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1534908 ACCATTGTCG
* * *
1534918 TCACGTAAAGTATTGACCTCA
1 TCACGTAAAGCACTGACCACA
**
1534939 TCACACAAAGCACTGACCACA
1 TCACGTAAAGCACTGACCACA
1534960 TCACGTAA
1 TCACGTAA
1534968 CTCCACTAAC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.30, G:0.12, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCACTGACCACA
Found at i:1535162 original size:42 final size:42
Alignment explanation
Indices: 1535081--1535176 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
1535071 TGTGATGGTA
* * * * * *
1535081 TAGGTGATGGCTCTCGTTGTGGAGGTGTATAATCGGCTCGAT
1 TAGGTGATGGCTCTAGGTGTCGAGCTGTAGAATCAGCTCGAT
1535123 TAGGTGATGGCTCTAGGTGTCGAGCTGTAGAATCAGCTCGAT
1 TAGGTGATGGCTCTAGGTGTCGAGCTGTAGAATCAGCTCGAT
* *
1535165 CAAGTGATGGCT
1 TAGGTGATGGCT
1535177 ATCGAAGTGG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.20, C:0.16, G:0.34, T:0.30
Consensus pattern (42 bp):
TAGGTGATGGCTCTAGGTGTCGAGCTGTAGAATCAGCTCGAT
Found at i:1536638 original size:20 final size:20
Alignment explanation
Indices: 1536615--1536667 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1536605 AAACTTAAAT
*
1536615 TCGCAACACGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
1536635 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
1536655 TCGCAACGCGAAA
1 TCGCAACGCGAAA
1536668 CCAAAATCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.49, C:0.23, G:0.19, T:0.09
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:1536675 original size:19 final size:20
Alignment explanation
Indices: 1536615--1536675 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
1536605 AAACTTAAAT
* **
1536615 TCGCAACACGAAAATGAAAA
1 TCGCAACGCGAAAACCAAAA
**
1536635 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAACCAAAA
1536655 TCGCAACGCG-AAACCAAAA
1 TCGCAACGCGAAAACCAAAA
1536674 TC
1 TC
1536676 ACGTTGCGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
19 9 0.24
20 29 0.76
ACGTcount: A:0.49, C:0.25, G:0.16, T:0.10
Consensus pattern (20 bp):
TCGCAACGCGAAAACCAAAA
Found at i:1536709 original size:20 final size:20
Alignment explanation
Indices: 1536684--1536722 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1536674 TCACGTTGCG
1536684 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
1536704 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
1536723 AAGTTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:1536729 original size:20 final size:20
Alignment explanation
Indices: 1536686--1536729 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1536676 ACGTTGCGAT
* *
1536686 TTTCGTGTTGCGAATTTCAT
1 TTTCGTGTTGCGAATTTAAG
1536706 TTTCGTGTTGCGAATTTAAG
1 TTTCGTGTTGCGAATTTAAG
1536726 TTTC
1 TTTC
1536730 AAAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAG
Found at i:1537074 original size:22 final size:22
Alignment explanation
Indices: 1537049--1537103 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1537039 ATAGAGGGGG
*
1537049 GTCGCCGGATATGGGGACGGAT
1 GTCGCCGGAGATGGGGACGGAT
* *
1537071 GTCGCTGGAGATGGGGATGGAT
1 GTCGCCGGAGATGGGGACGGAT
1537093 GTCGCCGGAGA
1 GTCGCCGGAGA
1537104 GAGTGAGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.18, C:0.16, G:0.47, T:0.18
Consensus pattern (22 bp):
GTCGCCGGAGATGGGGACGGAT
Found at i:1537251 original size:20 final size:20
Alignment explanation
Indices: 1537226--1537295 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
1537216 TAAAATTCGC
1537226 GTTGCGATTTTGACTTCTGT
1 GTTGCGATTTTGACTTCTGT
1537246 GTTGCGATTTTGACTTCTGT
1 GTTGCGATTTTGACTTCTGT
* * *
1537266 GTTACGAATTTGACTTCTAT
1 GTTGCGATTTTGACTTCTGT
*
1537286 GTTGGGATTT
1 GTTGCGATTT
1537296 ACATATTCGC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.14, C:0.13, G:0.24, T:0.49
Consensus pattern (20 bp):
GTTGCGATTTTGACTTCTGT
Found at i:1537314 original size:40 final size:39
Alignment explanation
Indices: 1537219--1537317 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 39
1537209 TCGAAAATAA
* * **
1537219 AATTCGCGTTGCGATTTTGACTTCTGTGTTGCGATTTTG
1 AATTCGCGTTGCGAATTTGACTTCTATGTTGCGATTTAC
* * * *
1537258 ACTTCTGTGTTACGAATTTGACTTCTATGTTGGGATTTAC
1 AATTC-GCGTTGCGAATTTGACTTCTATGTTGCGATTTAC
1537298 ATATTCGCGTTGCGAATTTG
1 A-ATTCGCGTTGCGAATTTG
1537318 GAACCTGTGT
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
39 4 0.09
40 40 0.85
41 3 0.06
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.44
Consensus pattern (39 bp):
AATTCGCGTTGCGAATTTGACTTCTATGTTGCGATTTAC
Found at i:1537902 original size:3 final size:3
Alignment explanation
Indices: 1537894--1537918 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1537884 CATGATAGTA
1537894 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1537919 GAAATTAAAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1541139 original size:21 final size:21
Alignment explanation
Indices: 1541109--1541149 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1541099 AAATGTTAAA
* *
1541109 AAATATTAATGTTTTAGGTAG
1 AAATAATAATATTTTAGGTAG
1541130 AAATAATAATATTTTAGGTA
1 AAATAATAATATTTTAGGTA
1541150 ATATTTTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (21 bp):
AAATAATAATATTTTAGGTAG
Found at i:1544466 original size:15 final size:16
Alignment explanation
Indices: 1544426--1544470 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
1544416 TAAATTTAAT
1544426 AAATATCATA-TA-AA
1 AAATATCATATTATAA
1544440 AATATATCATATTATAA
1 AA-ATATCATATTATAA
1544457 AAATAT-ATATTATA
1 AAATATCATATTATA
1544471 CATAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 2 0.07
15 16 0.57
16 6 0.21
17 4 0.14
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATATCATATTATAA
Found at i:1545511 original size:22 final size:22
Alignment explanation
Indices: 1545483--1545528 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1545473 TTATATGTAA
1545483 GAATAATATCATTTTAAGACAT
1 GAATAATATCATTTTAAGACAT
1545505 GAATAATATCATTTTAAGACAT
1 GAATAATATCATTTTAAGACAT
1545527 GA
1 GA
1545529 CAAACCTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.35
Consensus pattern (22 bp):
GAATAATATCATTTTAAGACAT
Found at i:1549066 original size:21 final size:21
Alignment explanation
Indices: 1549040--1549080 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1549030 AGGGCAGGCG
*
1549040 TTGCACGCATTATCGGAGCAC
1 TTGCACACATTATCGGAGCAC
*
1549061 TTGCACACATTATTGGAGCA
1 TTGCACACATTATCGGAGCA
1549081 TGCATCGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (21 bp):
TTGCACACATTATCGGAGCAC
Found at i:1552297 original size:16 final size:17
Alignment explanation
Indices: 1552268--1552302 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1552258 TAATATTTAA
*
1552268 ATTAAAATTTTAATTTT
1 ATTAAAATTTTAATATT
1552285 ATTAAAA-TTTAATATT
1 ATTAAAATTTTAATATT
1552301 AT
1 AT
1552303 CTCATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTAAAATTTTAATATT
Found at i:1554393 original size:25 final size:24
Alignment explanation
Indices: 1554365--1554431 Score: 88
Period size: 22 Copynumber: 2.9 Consensus size: 24
1554355 GTTACCAGAA
1554365 TTGTTAGTAGTAGTTAGGCTTGAGT
1 TTGTTAGTAGTA-TTAGGCTTGAGT
1554390 TTGTTAGTA--ATTAGGCTTGAGT
1 TTGTTAGTAGTATTAGGCTTGAGT
*
1554412 TTGTTAGCAGTA--AGGCTTGA
1 TTGTTAGTAGTATTAGGCTTGA
1554432 CTGTTAGCTA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
22 28 0.72
23 1 0.03
24 1 0.03
25 9 0.23
ACGTcount: A:0.22, C:0.06, G:0.30, T:0.42
Consensus pattern (24 bp):
TTGTTAGTAGTATTAGGCTTGAGT
Found at i:1554397 original size:22 final size:22
Alignment explanation
Indices: 1554372--1554431 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
1554362 GAATTGTTAG
1554372 TAGTAGTTAGGCTTGAGTTTGT
1 TAGTAGTTAGGCTTGAGTTTGT
*
1554394 TAGTAATTAGGCTTGAGTTTGT
1 TAGTAGTTAGGCTTGAGTTTGT
* *
1554416 TAGCAGTAAGGCTTGA
1 TAGTAGTTAGGCTTGA
1554432 CTGTTAGCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.23, C:0.07, G:0.30, T:0.40
Consensus pattern (22 bp):
TAGTAGTTAGGCTTGAGTTTGT
Found at i:1559404 original size:3 final size:3
Alignment explanation
Indices: 1559396--1559468 Score: 76
Period size: 3 Copynumber: 23.7 Consensus size: 3
1559386 ACACAAAATG
* * *
1559396 TAA TAA TAA TTAA TAA TAA TAA -AA GGAA CAA TAA TAA TAA TAA TAC
1 TAA TAA TAA -TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
*
1559442 TAA TAA TAA TTAA AAA TAA TAA TAA TA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TA
1559469 TATATTTTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.03
3 50 0.83
4 8 0.13
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:1559468 original size:31 final size:30
Alignment explanation
Indices: 1559396--1559468 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 30
1559386 ACACAAAATG
*
1559396 TAATAATAATTAATAATAATAAAAGGAACAA
1 TAATAATAA-TAATAATAATAAAAGGAAAAA
* **
1559427 TAATAATAATAATACTAATAATAATTAAAAA
1 TAATAATAATAATAATAATAA-AAGGAAAAA
1559458 TAATAATAATA
1 TAATAATAATA
1559469 TATATTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 11 0.30
31 26 0.70
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (30 bp):
TAATAATAATAATAATAATAAAAGGAAAAA
Found at i:1559959 original size:131 final size:131
Alignment explanation
Indices: 1559667--1560018 Score: 402
Period size: 131 Copynumber: 2.7 Consensus size: 131
1559657 TCGTCTAAGA
* * * *
1559667 GTGACACGACTCCTATGTGATGAGGAGATCTATTCGGTGGATGACACAGTTCTTACGTGATGAGG
1 GTGACGCGACTCCTACGTGATGAGGAGATCTATT-GGGGGATGACACAGTTCCTACGTGATGAGG
** * * * *
1559732 ACAACTGGCCATATTTTGGGATGATAATAACACAATTCCTACGCGATGAGGACAACTGGTTATCT
65 ACGGCTAGCCATCTTTAGGGATG--AATAACACAATTCCTACACGATGAGGACAACTGGTTATCT
1559797 AGGG
128 AGGG
* *
1559801 GTGACGCGACTACTACGTGATGAGGAGATCTAATTGGGGGATGACACAGTTCCTATGTGATGAGG
1 GTGACGCGACTCCTACGTGATGAGGAGATCT-ATTGGGGGATGACACAGTTCCTACGTGATGAGG
* * ***
1559866 ACGGTTAGCCATCTTTAGGGATG-ATAACACAATTCCTACATGATGAGGATGGCTGGTTATCTAG
65 ACGGCTAGCCATCTTTAGGGATGAATAACACAATTCCTACACGATGAGGACAACTGGTTATCTAG
1559930 GG
130 GG
* * * * * * **
1559932 GTGACGCGACTCCTACCTGAGGAGGAGATTTGGTCGGTGGG-TGACACGGTTCCTACACGATGAG
1 GTGACGCGACTCCTACGTGATGAGGAGATCT-ATTGG-GGGATGACACAGTTCCTACGTGATGAG
*
1559996 GATGGCTAGCCATCTTTAGGGAT
64 GACGGCTAGCCATCTTTAGGGAT
1560019 TTATTTTAAG
Statistics
Matches: 186, Mismatches: 30, Indels: 7
0.83 0.13 0.03
Matches are distributed among these distances:
131 108 0.58
132 3 0.02
134 72 0.39
135 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (131 bp):
GTGACGCGACTCCTACGTGATGAGGAGATCTATTGGGGGATGACACAGTTCCTACGTGATGAGGA
CGGCTAGCCATCTTTAGGGATGAATAACACAATTCCTACACGATGAGGACAACTGGTTATCTAGG
G
Found at i:1560137 original size:65 final size:65
Alignment explanation
Indices: 1560031--1560157 Score: 200
Period size: 65 Copynumber: 2.0 Consensus size: 65
1560021 ATTTTAAGAC
* *
1560031 TGTCTCAAGAGAGAGAAAATTCGTTTCAAAGGAAATAATCTCAAAGATGATGTATAAAGAGAAAT
1 TGTCTCAAGAGAGACAAAATTCGTTTCAAAGGAAACAATCTCAAAGATGATGTATAAAGAGAAAT
* * * *
1560096 TGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGATGTTTCAAGAGA
1 TGTCTCAAGAGAGACAAAATTCGTTTCAAAGGAAACAATCTCAAAGATGATGTATAAAGAGA
1560158 CCACCGTACC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (65 bp):
TGTCTCAAGAGAGACAAAATTCGTTTCAAAGGAAACAATCTCAAAGATGATGTATAAAGAGAAAT
Found at i:1560421 original size:30 final size:30
Alignment explanation
Indices: 1560387--1560452 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
1560377 TAAAAATGGG
*
1560387 TTTGGTGATTTGGTTTACTGTTGCTGATGA
1 TTTGGTGATTTGGTTTACTGTTGCTGACGA
1560417 TTTGGTGATTTGGTTTACTGTTGCTGACGA
1 TTTGGTGATTTGGTTTACTGTTGCTGACGA
1560447 TTTGGT
1 TTTGGT
1560453 TTGATGTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.12, C:0.08, G:0.30, T:0.50
Consensus pattern (30 bp):
TTTGGTGATTTGGTTTACTGTTGCTGACGA
Found at i:1560845 original size:3 final size:3
Alignment explanation
Indices: 1560837--1560896 Score: 68
Period size: 3 Copynumber: 19.7 Consensus size: 3
1560827 ACACAAAATG
* *
1560837 TAA TAA TAA TTAA TAA TAA TAA -AG TAA TAA TAA TAA TAA TAA CAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1560882 TTAA AAA TAA TAA TA
1 -TAA TAA TAA TAA TA
1560897 TATTTTTTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 1 0.02
3 42 0.88
4 5 0.10
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1561313 original size:134 final size:131
Alignment explanation
Indices: 1561109--1561444 Score: 363
Period size: 131 Copynumber: 2.5 Consensus size: 131
1561099 CGAATCCTAT
* * ** * * *
1561109 GTGATGAGGAGATCT-ATTCAGTGGATGACACAATTCCTACGTGATGAGGACGACTGGCCATATT
1 GTGATGAGGAGATCTGATT-GGGGGATGACACGGTTCCTACGTGATGAGGACGGCTAGCCATCTT
* * * * *
1561173 TTGGGATGATAATAACACGATTCTTACGCGATGAGGACGACTGGTTATCTAGGGGTGACGCGGCT
65 TAGGGATGATAA-AACA-G-TTCCTACACGATGAGGACGACTGGTTATCTAGGGATGACGCAGCT
1561238 AC-TAC
127 -CTTAC
* *
1561243 GTGATGAGGAGATCTGATTGGGGGATGACACGGTTCCTATGTGATGAGGACGGTTAGCCATCTTT
1 GTGATGAGGAGATCTGATTGGGGGATGACACGGTTCCTACGTGATGAGGACGGCTAGCCATCTTT
* *
1561308 AGGGATGATAACACAGTTCCTACATGATGAGGACGACTGGTTATCTAGGGATGACGCAGCTCTTA
66 AGGGATGATAAAACAGTTCCTACACGATGAGGACGACTGGTTATCTAGGGATGACGCAGCTCTTA
1561373 C
131 C
* * * * * * ** * *
1561374 CTAAGGAGGAGATTTGGTCGGTGGG-TGACACGGTTCCTACACGATGAGAATGGCTAGCCATCTT
1 GTGATGAGGAGATCTGATTGG-GGGATGACACGGTTCCTACGTGATGAGGACGGCTAGCCATCTT
1561438 TAGGGAT
65 TAGGGAT
1561445 TTGTTTCAAG
Statistics
Matches: 171, Mismatches: 28, Indels: 9
0.82 0.13 0.04
Matches are distributed among these distances:
130 1 0.01
131 98 0.57
132 4 0.02
133 3 0.02
134 62 0.36
135 3 0.02
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (131 bp):
GTGATGAGGAGATCTGATTGGGGGATGACACGGTTCCTACGTGATGAGGACGGCTAGCCATCTTT
AGGGATGATAAAACAGTTCCTACACGATGAGGACGACTGGTTATCTAGGGATGACGCAGCTCTTA
C
Found at i:1561585 original size:55 final size:55
Alignment explanation
Indices: 1561518--1561624 Score: 144
Period size: 55 Copynumber: 1.9 Consensus size: 55
1561508 GTTTAAAGAG
* * * **
1561518 AAACTGTCTCAAGAGAGACAAAA-TTCGTTTTAAGGGAAATGATCTCAAAGATGAT
1 AAACTGTCTCAAGAAAGACAAAACTT-GTTTCAAGGAAAACAATCTCAAAGATGAT
*
1561573 AAACTGTCTCAAGAAATACAAAACTTGTTTCAAGGAAAACAATCTCAAAGAT
1 AAACTGTCTCAAGAAAGACAAAACTTGTTTCAAGGAAAACAATCTCAAAGAT
1561625 AATCAATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
55 43 0.96
56 2 0.04
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (55 bp):
AAACTGTCTCAAGAAAGACAAAACTTGTTTCAAGGAAAACAATCTCAAAGATGAT
Found at i:1561606 original size:21 final size:20
Alignment explanation
Indices: 1561573--1561614 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
1561563 CAAAGATGAT
1561573 AAACTGTCTCAA-GAAATACA
1 AAACTGTCTCAAGGAAA-ACA
*
1561593 AAACTTGTTTCAAGGAAAACA
1 AAAC-TGTCTCAAGGAAAACA
1561614 A
1 A
1561615 TCTCAAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (20 bp):
AAACTGTCTCAAGGAAAACA
Found at i:1562989 original size:15 final size:15
Alignment explanation
Indices: 1562966--1563027 Score: 79
Period size: 15 Copynumber: 4.1 Consensus size: 15
1562956 TCTTGTCATA
*
1562966 TTTTTTTCTTTGCTC
1 TTTTTTTCTTTGCTT
* *
1562981 TTCTTTTCTTTTCTT
1 TTTTTTTCTTTGCTT
*
1562996 TTTTTTTCTTTTTCTT
1 TTTTTTTC-TTTGCTT
1563012 TTTTTTTCTTTGCTT
1 TTTTTTTCTTTGCTT
1563027 T
1 T
1563028 GATGTGATCT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
15 26 0.63
16 15 0.37
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (15 bp):
TTTTTTTCTTTGCTT
Found at i:1562991 original size:5 final size:5
Alignment explanation
Indices: 1562969--1563027 Score: 64
Period size: 5 Copynumber: 11.6 Consensus size: 5
1562959 TGTCATATTT
* * * *
1562969 TTTTC TTTGC TCTTC TTTTC TTTTC TTTTT TTTTC TTTTTC TTTTT TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC
*
1563020 TTTGC TTT
1 TTTTC TTT
1563028 GATGTGATCT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
5 39 0.89
6 5 0.11
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:1569636 original size:21 final size:23
Alignment explanation
Indices: 1569597--1569639 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
1569587 GAGGCTATTT
*
1569597 TTTAAATAGTAATTTAAATAAAA
1 TTTAAATAGTAATTCAAATAAAA
1569620 TTTAAA-A-TAATTCAAATAAA
1 TTTAAATAGTAATTCAAATAAA
1569640 TAAATTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 1 0.05
23 6 0.32
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (23 bp):
TTTAAATAGTAATTCAAATAAAA
Found at i:1571367 original size:66 final size:65
Alignment explanation
Indices: 1571243--1571394 Score: 186
Period size: 66 Copynumber: 2.3 Consensus size: 65
1571233 GCACTAAGAG
* *
1571243 TGCATGAAATGCATTCGATG--TTTCAAACAAGCCAGAGTGCATCGATGCATGTCTTGTGCATCG
1 TGCAT-AAATGCATTCGATGTTTTTCAAACAAACCAGAGTGCATCGATGCATGTCATGTGCATCG
1571306 A
65 A
** *
1571307 TGCATCAAATGCATTCGATGTTTTTCATAA-AAACTTGAGTGCATTGATGCATGGT-ATGTGCAT
1 TGCAT-AAATGCATTCGATGTTTTTCA-AACAAACCAGAGTGCATCGATGCAT-GTCATGTGCAT
1571370 CGA
63 CGA
1571373 TGCATATAATGCATTCGATGTT
1 TGCATA-AATGCATTCGATGTT
1571395 CAATTTATTC
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
64 19 0.25
65 1 0.01
66 53 0.69
67 4 0.05
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (65 bp):
TGCATAAATGCATTCGATGTTTTTCAAACAAACCAGAGTGCATCGATGCATGTCATGTGCATCGA
Found at i:1574181 original size:44 final size:42
Alignment explanation
Indices: 1574066--1574188 Score: 117
Period size: 44 Copynumber: 2.8 Consensus size: 42
1574056 AAAACCCGAC
* *
1574066 GGATGCATCGATGCA-TGGCTT-TGTGCATCGATGCACATTCAA
1 GGATGCATCGATGCACT-G-TTATGTGTATCGATGCACATACAA
* *
1574108 GGAGTGCATCGGTGCATCT-TGATGATGTATCGATGCACATACAAA
1 GGA-TGCATCGATGCA-CTGTTATG-TGTATCGATGCACATAC-AA
*
1574153 GGGATGCATCGATGCACTGTTAAGTGTATCGATGCA
1 -GGATGCATCGATGCACTGTTATGTGTATCGATGCA
1574189 TTAAGCACAA
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
42 4 0.06
43 13 0.20
44 29 0.44
45 17 0.26
46 3 0.05
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (42 bp):
GGATGCATCGATGCACTGTTATGTGTATCGATGCACATACAA
Found at i:1579962 original size:45 final size:46
Alignment explanation
Indices: 1579892--1579999 Score: 139
Period size: 45 Copynumber: 2.4 Consensus size: 46
1579882 CGGTGCACTA
* * * *
1579892 AGAGTACATCGATGCATGAAGTGCATTCGATG-TTTCA-AACAAGCC
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAA-AAACC
1579937 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAACC
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAACC
* *
1579983 TGAGTGAATCGATGCAT
1 AGAGTGCATCGATGCAT
1580000 GGTATGTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
45 29 0.53
46 24 0.44
47 2 0.04
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (46 bp):
AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAACC
Found at i:1579994 original size:46 final size:45
Alignment explanation
Indices: 1579899--1579999 Score: 132
Period size: 46 Copynumber: 2.2 Consensus size: 45
1579889 CTAAGAGTAC
* * * *
1579899 ATCGATGCATGAAGTGCATTCGATGTTTCAAACAAGCCAGAGTGC
1 ATCGATGCATCAAATGCATTCGATGTTTCAAACAAACCAGAGTGA
*
1579944 ATCGATGCATCAAATGCATTCGATGTTTTCATAA-AAACCTGAGTGA
1 ATCGATGCATCAAATGCATTCGATG-TTTCA-AACAAACCAGAGTGA
1579990 ATCGATGCAT
1 ATCGATGCAT
1580000 GGTATGTGCA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
45 23 0.47
46 24 0.49
47 2 0.04
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (45 bp):
ATCGATGCATCAAATGCATTCGATGTTTCAAACAAACCAGAGTGA
Found at i:1582037 original size:14 final size:14
Alignment explanation
Indices: 1582018--1582044 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1582008 ATCCCTTATT
1582018 ATTATTTATATTTA
1 ATTATTTATATTTA
1582032 ATTATTTATATTT
1 ATTATTTATATTT
1582045 TTATATATTT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTATTTATATTTA
Found at i:1582231 original size:16 final size:16
Alignment explanation
Indices: 1582201--1582276 Score: 59
Period size: 15 Copynumber: 4.9 Consensus size: 16
1582191 TTAAGTACTA
*
1582201 TTTTTTATTTGTTTGGT
1 TTTTTTATTTATTT-GT
1582218 TTTTTTA-TTATTTGT
1 TTTTTTATTTATTTGT
*** *
1582233 TTTACGAATTATTT-T
1 TTTTTTATTTATTTGT
* *
1582248 TTCTTTATTTCTTT-T
1 TTTTTTATTTATTTGT
1582263 TTTTTTATTTATTT
1 TTTTTTATTTATTT
1582277 ATTCTAATTT
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
15 28 0.61
16 11 0.24
17 7 0.15
ACGTcount: A:0.13, C:0.04, G:0.07, T:0.76
Consensus pattern (16 bp):
TTTTTTATTTATTTGT
Found at i:1582263 original size:42 final size:42
Alignment explanation
Indices: 1582171--1582277 Score: 110
Period size: 43 Copynumber: 2.5 Consensus size: 42
1582161 TATTTTTTCC
* * *
1582171 TTCTTTTTTTCTTATTTTATTTAAGTACTATTTTTTATTTGT
1 TTCTTTTTTTATTATTTTATTTAAGAACTATTTTTTATTTAT
* * * *
1582213 TTGGTTTTTTTATTATTTGT-TTTACGAATTATTTTTTCTTTAT
1 TT-CTTTTTTTATTATTT-TATTTAAGAACTATTTTTTATTTAT
*
1582256 TTCTTTTTTTTTTA-TTTATTTA
1 TTCTTTTTTTATTATTTTATTTA
1582278 TTCTAATTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
40 1 0.02
41 6 0.11
42 12 0.23
43 33 0.62
44 1 0.02
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.73
Consensus pattern (42 bp):
TTCTTTTTTTATTATTTTATTTAAGAACTATTTTTTATTTAT
Found at i:1582374 original size:28 final size:27
Alignment explanation
Indices: 1582343--1582400 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
1582333 TTTATTTGTT
1582343 TTTA-CCTAGTACTTTATATTTATATATA
1 TTTATCCTA-TACTTTATATTTATAT-TA
* * *
1582371 TTTATTCTATATTTTATATTTGTATTA
1 TTTATCCTATACTTTATATTTATATTA
1582398 TTT
1 TTT
1582401 TTTATTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 5 0.19
28 18 0.69
29 3 0.12
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (27 bp):
TTTATCCTATACTTTATATTTATATTA
Found at i:1582534 original size:22 final size:22
Alignment explanation
Indices: 1582506--1582642 Score: 93
Period size: 22 Copynumber: 6.6 Consensus size: 22
1582496 ATGTCCTTCC
1582506 TTATTTTTATTTTTATTTCATT
1 TTATTTTTATTTTTATTTCATT
* * *
1582528 CTA--TTT-TGTTTA-CTCATT
1 TTATTTTTATTTTTATTTCATT
1582546 TTACTTGTTT-TATTTTATTT-ATT
1 TTA-TT-TTTAT-TTTTATTTCATT
*
1582569 TT-TTTTT-TATTT-TTT-ATT
1 TTATTTTTATTTTTATTTCATT
1582587 TTA-TTTTA-TTTTATCTT-ATCT
1 TTATTTTTATTTTTAT-TTCAT-T
*
1582608 TTATTTTTATTTTTATTTTATT
1 TTATTTTTATTTTTATTTCATT
1582630 TTATTTTTATTTT
1 TTATTTTTATTTT
1582643 GTTTATTTAT
Statistics
Matches: 93, Mismatches: 8, Indels: 28
0.72 0.06 0.22
Matches are distributed among these distances:
18 22 0.24
19 9 0.10
20 11 0.12
21 6 0.06
22 27 0.29
23 17 0.18
24 1 0.01
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (22 bp):
TTATTTTTATTTTTATTTCATT
Found at i:1582563 original size:5 final size:5
Alignment explanation
Indices: 1582553--1582655 Score: 101
Period size: 5 Copynumber: 20.8 Consensus size: 5
1582543 ATTTTACTTG
1582553 TTTTA TTTTA -TTTA TTTT- TTTT- TTATT- TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA
* *
1582600 TCTTA TCTTTA TTTTTA TTTTTA TTTTA TTTTA TTTTTA TTTT- GTTTA
1 TTTTA T-TTTA -TTTTA -TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA
1582648 -TTTA TTTT
1 TTTTA TTTT
1582656 TTTATGTGTC
Statistics
Matches: 87, Mismatches: 3, Indels: 16
0.82 0.03 0.15
Matches are distributed among these distances:
4 19 0.22
5 49 0.56
6 18 0.21
7 1 0.01
ACGTcount: A:0.17, C:0.02, G:0.01, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:1582575 original size:28 final size:26
Alignment explanation
Indices: 1582543--1582655 Score: 106
Period size: 28 Copynumber: 4.2 Consensus size: 26
1582533 TTGTTTACTC
1582543 ATTTTACTTGTTTTATTTTATTTATTTTT
1 ATTTTA-TT-TTTTATTTTATTTA-TTTT
*
1582572 TTTTTATTTTTTATTTTATTTTATTTT
1 ATTTTATTTTTTATTTTA-TTTATTTT
* *
1582599 ATCTTATCTTTATT-TTTATTTTTATTTT
1 ATTTTAT-TTT-TTATTT-TATTTATTTT
*
1582627 ATTTTA-TTTTTATTTTGTTTA-TTT
1 ATTTTATTTTTTATTTTATTTATTTT
1582651 ATTTT
1 ATTTT
1582656 TTTATGTGTC
Statistics
Matches: 73, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
24 8 0.11
25 7 0.10
26 6 0.08
27 19 0.26
28 25 0.34
29 8 0.11
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.79
Consensus pattern (26 bp):
ATTTTATTTTTTATTTTATTTATTTT
Found at i:1582577 original size:11 final size:11
Alignment explanation
Indices: 1582558--1582658 Score: 94
Period size: 11 Copynumber: 8.5 Consensus size: 11
1582548 ACTTGTTTTA
*
1582558 TTTTATTTATT
1 TTTTTTTTATT
1582569 TTTTTTTTATT
1 TTTTTTTTATT
1582580 TTTTATTTTATTT
1 TTTT-TTTTA-TT
1582593 TATTTTATCTTATCT
1 T-TTTT-T-TTAT-T
*
1582608 TTATTTTTATT
1 TTTTTTTTATT
*
1582619 TTTATTTTATT
1 TTTTTTTTATT
*
1582630 TTATTTTTATT
1 TTTTTTTTATT
1582641 TTGTTTATTTATT
1 TT-TTT-TTTATT
1582654 TTTTT
1 TTTTT
1582659 ATGTGTCTAT
Statistics
Matches: 75, Mismatches: 7, Indels: 15
0.77 0.07 0.15
Matches are distributed among these distances:
11 35 0.47
12 14 0.19
13 13 0.17
14 8 0.11
15 5 0.07
ACGTcount: A:0.16, C:0.02, G:0.01, T:0.81
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:1582581 original size:6 final size:6
Alignment explanation
Indices: 1582563--1582656 Score: 87
Period size: 6 Copynumber: 16.5 Consensus size: 6
1582553 TTTTATTTTA
* *
1582563 TTTATT TTT-TT TTTATT TTT-TAT TTTA-T TTTA-T TTTA-T CTTATC
1 TTTATT TTTATT TTTATT TTTAT-T TTTATT TTTATT TTTATT TTTATT
1582607 TTTATT TTTATT TTTA-T TTTA-T TTTATT TTTATT TTGT-TT ATTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TT-TATT -TTTATT
1582654 TTT
1 TTT
1582657 TTATGTGTCT
Statistics
Matches: 76, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
5 30 0.39
6 41 0.54
7 5 0.07
ACGTcount: A:0.16, C:0.02, G:0.01, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:1582611 original size:33 final size:32
Alignment explanation
Indices: 1582553--1582655 Score: 120
Period size: 33 Copynumber: 3.1 Consensus size: 32
1582543 ATTTTACTTG
*
1582553 TTTTATTTTA-TTTATTTTTTTTTTATTTTTTA
1 TTTTATTTTATTTTA-TTTTATTTTATTTTTTA
*
1582585 TTTTATTTTATTTTATCTTATCTTTA-TTTTTA
1 TTTTATTTTATTTTATTTTAT-TTTATTTTTTA
*
1582617 TTTTTATTTTATTTTATTTTTATTTTGTTTATTTA
1 -TTTTATTTTATTTTA-TTTTATTTTATTT-TTTA
1582652 TTTT
1 TTTT
1582656 TTTATGTGTC
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
32 20 0.33
33 26 0.43
34 11 0.18
35 4 0.07
ACGTcount: A:0.17, C:0.02, G:0.01, T:0.81
Consensus pattern (32 bp):
TTTTATTTTATTTTATTTTATTTTATTTTTTA
Found at i:1582658 original size:22 final size:23
Alignment explanation
Indices: 1582553--1582658 Score: 85
Period size: 23 Copynumber: 4.5 Consensus size: 23
1582543 ATTTTACTTG
*
1582553 TTTTATTTTATTTATTTTTTTT-
1 TTTTATTTTTTTTATTTTTTTTA
1582575 TTATT-TTTTATTTTATTTTATTTTA
1 TT-TTATTTT-TTTTATTTT-TTTTA
* * *
1582600 TCTTATCTTTATTT-TTATTTTTA
1 TTTTAT-TTTTTTTATTTTTTTTA
*
1582623 TTTTATTTTATTTTTATTTTGTTTA
1 TTTTA-TTT-TTTTTATTTTTTTTA
1582648 -TTTATTTTTTT
1 TTTTATTTTTTT
1582659 ATGTGTCTAT
Statistics
Matches: 67, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
22 10 0.15
23 24 0.36
24 18 0.27
25 12 0.18
26 3 0.04
ACGTcount: A:0.16, C:0.02, G:0.01, T:0.81
Consensus pattern (23 bp):
TTTTATTTTTTTTATTTTTTTTA
Found at i:1582659 original size:27 final size:25
Alignment explanation
Indices: 1582563--1582660 Score: 80
Period size: 27 Copynumber: 4.0 Consensus size: 25
1582553 TTTTATTTTA
*
1582563 TTTATTTTTTT-TTTATTTTTTA-T
1 TTTATTTTTTTATTTTTTTTTTATT
* * *
1582586 TTTATTTTATTTTATCTTATCTTTATT
1 TTTA-TTT-TTTTATTTTTTTTTTATT
*
1582613 TTTA--TTTTTA-TTTTATTTTATT
1 TTTATTTTTTTATTTTTTTTTTATT
1582635 TTTATTTTGTTTATTTATTTTTTTAT
1 TTTATTTT-TTTATTT-TTTTTTTAT
1582661 GTGTCTATTT
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
22 12 0.21
23 9 0.16
24 6 0.11
25 8 0.14
26 9 0.16
27 13 0.23
ACGTcount: A:0.16, C:0.02, G:0.01, T:0.81
Consensus pattern (25 bp):
TTTATTTTTTTATTTTTTTTTTATT
Found at i:1582669 original size:20 final size:19
Alignment explanation
Indices: 1582553--1582670 Score: 55
Period size: 20 Copynumber: 5.9 Consensus size: 19
1582543 ATTTTACTTG
* * *
1582553 TTTTATTTTATTTATTTTTT
1 TTTTATTTTGTCTA-TTTAT
1582573 TTTTATTTT-T-TATTT-T
1 TTTTATTTTGTCTATTTAT
*
1582589 ATTTTATTTTATCTTATCTTTAT
1 -TTTTATTTTGTC-TA--TTTAT
* *
1582612 TTTTATTTTTATTTTATTTTAT
1 TTTTA-TTTT-GTCTA-TTTAT
*
1582634 TTTTATTTTGTTTATTTAT
1 TTTTATTTTGTCTATTTAT
1582653 TTTT-TTATGTGTCTATTT
1 TTTTATT-T-TGTCTATTT
1582671 GTCTTTTTCT
Statistics
Matches: 82, Mismatches: 5, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
16 1 0.01
17 12 0.15
18 5 0.06
19 11 0.13
20 23 0.28
21 4 0.05
22 18 0.22
23 7 0.09
24 1 0.01
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (19 bp):
TTTTATTTTGTCTATTTAT
Found at i:1590642 original size:23 final size:22
Alignment explanation
Indices: 1590607--1590655 Score: 89
Period size: 23 Copynumber: 2.2 Consensus size: 22
1590597 GGAATGGATA
1590607 CCCCATTGAAGGGGAACCGATT
1 CCCCATTGAAGGGGAACCGATT
1590629 CCCCATTTGAAGGGGAACCGATT
1 CCCCA-TTGAAGGGGAACCGATT
1590652 CCCC
1 CCCC
1590656 CTAGGGGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.18
Consensus pattern (22 bp):
CCCCATTGAAGGGGAACCGATT
Found at i:1590677 original size:20 final size:19
Alignment explanation
Indices: 1590639--1590681 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1590629 CCCCATTTGA
*
1590639 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATCCCCCCT
*
1590658 AGGGGAATCGATACCCCCCT
1 AGGGGAACCGAT-CCCCCCT
1590678 -GGGG
1 AGGGG
1590682 TTCTGGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.21, C:0.33, G:0.33, T:0.14
Consensus pattern (19 bp):
AGGGGAACCGATCCCCCCT
Found at i:1594338 original size:128 final size:127
Alignment explanation
Indices: 1594052--1594338 Score: 326
Period size: 128 Copynumber: 2.2 Consensus size: 127
1594042 AAAATATTAA
* * * * *
1594052 ATGCTTTCTTTGATGACATACATACCTCTCAGAGTCCAAAAGAGATGTAATATCCAAATTCAAGA
1 ATGCTTACTTTGATGACGTACATA-CTCTCAGAGTCCAAAAAAGATGTAACATCCAAATTCAACA
* *
1594117 TTATGTCAGAAATTAGGACTGCAAAACAAGTTAATTTCAGTGAATTGCCTTTGTTAATATTGT
65 TTATGTCAGAAATTAGGACTGCAAAACAAGTTAATTTCAGTGAATTACCTTTGTTAATATTGG
* * * ** *
1594180 ATGCTTGCTTTGATGACGAACGTACCTCTCAGAGTTTAAAAAAGTTGTAACATCCAAATTCAACA
1 ATGCTTACTTTGATGACGTACATA-CTCTCAGAGTCCAAAAAAGATGTAACATCCAAATTCAACA
* * * * ** *
1594245 TTGTGTCA-TAGTTAGGATTGCATGACAAGTTAATTTTAGTGAATTACCTTTGATGTTAATATTG
65 TTATGTCAGAAATTAGGACTGCAAAACAAGTTAATTTCAGTGAATTACC-TT--TGTTAATATTG
1594309 G
127 G
*
1594310 ATGCTTACTTTGATGATGTACATA-TCTCA
1 ATGCTTACTTTGATGACGTACATACTCTCA
1594339 TAAAGCTTGA
Statistics
Matches: 133, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
127 33 0.25
128 69 0.52
130 31 0.23
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (127 bp):
ATGCTTACTTTGATGACGTACATACTCTCAGAGTCCAAAAAAGATGTAACATCCAAATTCAACAT
TATGTCAGAAATTAGGACTGCAAAACAAGTTAATTTCAGTGAATTACCTTTGTTAATATTGG
Found at i:1594360 original size:130 final size:128
Alignment explanation
Indices: 1594052--1594598 Score: 317
Period size: 128 Copynumber: 4.2 Consensus size: 128
1594042 AAAATATTAA
* * * * * *
1594052 ATGCTTTCTTTGATGAC-ATACATACCTCTCAGAG-TCCAAAAGAGATGTAATATCCAAATTCAA
1 ATGCTTACTTTGATGACGA-ACATACCTCTCAAAGCT-TAAAAAAGGTGTAACATCCAAATTCAA
* * *
1594115 GATTATGTCAGAAATTAGGACTGCAAAACAAGTTAATTTCAGTGAATTGCCTTTGTTAATATTGT
64 CATTATGTCAGAAATTAGGACTGCAAAACAAGTTAATTTCAGTGAATTACCTTTGTTAATATTGG
* * * * *
1594180 ATGCTTGCTTTGATGACGAACGTACCTCTCAGAGTTTAAAAAAGTTGTAACATCCAAATTCAACA
1 ATGCTTACTTTGATGACGAACATACCTCTCAAAGCTTAAAAAAGGTGTAACATCCAAATTCAACA
* * * * ** *
1594245 TTGTGTCA-TAGTTAGGATTGCATGACAAGTTAATTTTAGTGAATTACCTTTGATGTTAATATTG
66 TTATGTCAGAAATTAGGACTGCAAAACAAGTTAATTTCAGTGAATTACC-TT--TGTTAATATTG
1594309 G
128 G
* * * * *** ****
1594310 ATGCTTACTTTGATGATGTACATATCTCAT-AAAGCTTGAAGTGGGTGTAACATCCAAATTTTGT
1 ATGCTTACTTTGATGACGAACATACCTC-TCAAAGCTTAAAAAAGGTGTAACATCCAAATTCAAC
*** * * * * * *
1594374 AGCGTGTTACG--ATCAGGACTGCATAACAAGTTAATTTCAGTGAGTTACTTTTAATGTGAATAT
65 ATTATGTCA-GAAATTAGGACTGCAAAACAAGTTAATTTCAGTGAATTAC-CTT--TGTTAATAT
*
1594437 CGG
126 TGG
* * ** * ** ** *
1594440 ATGCTTTCTTTGATAAC-ATATGTACCTCTC-AGGGATAAAAAA-AAGTAACATCCAAATTCAAT
1 ATGCTTACTTTGATGACGA-ACATACCTCTCAAAGCTTAAAAAAGGTGTAACATCCAAATTCAAC
* * * * * * * *
1594502 AATATATCA-TAATTAGAACTAG-AAAACAATTTAATTTCAATGAATTGCCTTTGATGTTATTAT
65 ATTATGTCAGAAATTAGGACT-GCAAAACAAGTTAATTTCAGTGAATTACC-TT--TGTTAATAT
1594565 TGG
126 TGG
*
1594568 ATGCTTGCTTTGATGAC-ATACATACCTCTCA
1 ATGCTTACTTTGATGACGA-ACATACCTCTCA
1594599 GATGTTGAAG
Statistics
Matches: 318, Mismatches: 85, Indels: 31
0.73 0.20 0.07
Matches are distributed among these distances:
127 33 0.10
128 148 0.47
129 9 0.03
130 127 0.40
131 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (128 bp):
ATGCTTACTTTGATGACGAACATACCTCTCAAAGCTTAAAAAAGGTGTAACATCCAAATTCAACA
TTATGTCAGAAATTAGGACTGCAAAACAAGTTAATTTCAGTGAATTACCTTTGTTAATATTGG
Found at i:1598250 original size:2 final size:2
Alignment explanation
Indices: 1598239--1598273 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1598229 CCACTTTTGA
1598239 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1598274 TGTTTGTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1598426 original size:2 final size:2
Alignment explanation
Indices: 1598419--1598450 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1598409 TTTTCACCAA
1598419 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1598451 TTGTTTGTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1602135 original size:21 final size:21
Alignment explanation
Indices: 1602111--1602245 Score: 145
Period size: 21 Copynumber: 6.6 Consensus size: 21
1602101 TATCACAAAT
1602111 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
1602132 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
1602153 T--CGTTGCGATAGTTAAAAAA
1 TCGCGTTGCGATAGTT-GAAAA
*
1602173 TCGCGTTGCGATAGTTAAAAAA
1 TCGCGTTGCGATAGTT-GAAAA
* * ** **
1602195 T--CGTTGCAAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
1602213 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
1602234 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1602246 TTTCCATTTC
Statistics
Matches: 95, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
18 2 0.02
19 15 0.16
20 21 0.22
21 37 0.39
22 20 0.21
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:1602219 original size:20 final size:20
Alignment explanation
Indices: 1602196--1602265 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
1602186 GTTAAAAAAT
*
1602196 CGTTGCAATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* ** **
1602216 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGAT-TTTCCATTTCG
1602237 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
*
1602257 CGTTACGAT
1 CGTTGCGAT
1602266 AGTCTACAGT
Statistics
Matches: 37, Mismatches: 12, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
20 22 0.59
21 15 0.41
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:1602253 original size:41 final size:39
Alignment explanation
Indices: 1602132--1602268 Score: 157
Period size: 41 Copynumber: 3.4 Consensus size: 39
1602122 TAGTTGAAAA
*** **
1602132 TCGCGTTGCGATAGTTGAAAATCGTTGCGATAGTTAAAAAA
1 TCGCGTTGCGATAGTTGAAAATCGTTGCGAT--TTTCCATT
* *
1602173 TCGCGTTGCGATAGTTAAAAAATCGTTGCAATTTTCCATT
1 TCGCGTTGCGATAGTT-GAAAATCGTTGCGATTTTCCATT
1602213 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAAT--CGTTGCGATTTTCCATT
*
1602254 TCGCGTTACGATAGT
1 TCGCGTTGCGATAGT
1602269 CTACAGTTGT
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
39 5 0.06
40 19 0.23
41 46 0.55
42 13 0.16
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (39 bp):
TCGCGTTGCGATAGTTGAAAATCGTTGCGATTTTCCATT
Found at i:1602294 original size:22 final size:22
Alignment explanation
Indices: 1602257--1602308 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
1602247 TTCCATTTCG
* *
1602257 CGTTACGATAGTCTACAGTTGT
1 CGTTGCGAAAGTCTACAGTTGT
*
1602279 TGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGAAAGTCTACAGTTGT
1602301 CGTTGCGA
1 CGTTGCGA
1602309 TTTTCCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (22 bp):
CGTTGCGAAAGTCTACAGTTGT
Found at i:1602457 original size:5 final size:6
Alignment explanation
Indices: 1602407--1602454 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
1602397 GACACGTATT
1602407 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1602452 ACC
1 ACC
1602455 CGAGACGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.36
6 27 0.64
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1603109 original size:19 final size:19
Alignment explanation
Indices: 1603085--1603131 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1603075 CAACGAATTT
*
1603085 TCGCAATGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
1603104 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
1603123 TCGCAACGA
1 TCGCAACGA
1603132 CAACTGTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:1603190 original size:21 final size:21
Alignment explanation
Indices: 1603164--1603217 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
1603154 GAACTGGAAA
1603164 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
1603185 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
1603206 ATCGCAACGCGA
1 ATCGCAACGCGA
1603218 AATGGAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:1603217 original size:62 final size:62
Alignment explanation
Indices: 1603143--1603343 Score: 240
Period size: 62 Copynumber: 3.4 Consensus size: 62
1603133 AACTGTAGAC
* *
1603143 TATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAAC
1 TATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAAA
** * * *** *
1603205 TATCGCAACGCGAAATGGAAAAT--C-A---G--TTGAAAATCTCGCAACGC-AAACTGAAA
1 TATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAAA
*
1603258 AATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAAA
1 TATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAAA
1603320 TATCGCAACGCGAAATGGAAAATC
1 TATCGCAACGCGAAATGGAAAATC
1603344 AGTTATCGCA
Statistics
Matches: 110, Mismatches: 20, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
53 26 0.24
54 14 0.13
55 1 0.01
56 2 0.02
59 2 0.02
60 1 0.01
61 14 0.13
62 50 0.45
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (62 bp):
TATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAAA
Found at i:1603265 original size:20 final size:20
Alignment explanation
Indices: 1603240--1603290 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
1603230 GTTGAAAATC
1603240 TCGCAACGC-AAACTGAAAAA
1 TCGCAACGCGAAA-TGAAAAA
*
1603260 TCGCAACGCGAAATGGAAAA
1 TCGCAACGCGAAATGAAAAA
1603280 TCGCAACGCGA
1 TCGCAACGCGA
1603291 TTTTCAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.43, C:0.25, G:0.22, T:0.10
Consensus pattern (20 bp):
TCGCAACGCGAAATGAAAAA
Found at i:1603283 original size:115 final size:109
Alignment explanation
Indices: 1603144--1603421 Score: 394
Period size: 115 Copynumber: 2.5 Consensus size: 109
1603134 ACTGTAGACT
* *
1603144 ATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAACTATC
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAAATATC
1603209 GCAACGCGAAATGGAAAATCAGTTGAAAATCTCGCAACGCAAACTGAAAA
66 GCAACGCGAAATGGAAAATCAGTT----A--TCGCAACGCAAACTGAAAA
1603259 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAAATATC
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAAATATC
* *
1603324 GCAACGCGAAATGGAAAATCAGTTATCGCAACGCGAACTGGAAA
66 GCAACGCGAAATGGAAAATCAGTTATCGCAACGCAAACTGAAAA
** ** * * *
1603368 ATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAATTATCGCAATGCGA
1 ATCGCAACGCGAAATGGAA-AATCGCAACGCGATTTTCAACTATCGCAACGCGA
1603422 AATGCAACGC
Statistics
Matches: 151, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
109 32 0.21
110 31 0.21
111 1 0.01
115 87 0.58
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (109 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAAATATC
GCAACGCGAAATGGAAAATCAGTTATCGCAACGCAAACTGAAAA
Found at i:1603305 original size:21 final size:21
Alignment explanation
Indices: 1603279--1603421 Score: 117
Period size: 21 Copynumber: 6.6 Consensus size: 21
1603269 GAAATGGAAA
1603279 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
1603300 ATCGCAACGCGATTTTCAAAT
1 ATCGCAACGCGATTTTCAACT
** **
1603321 ATCGCAACGCGAAATGGAAAATCAGTT
1 ATCGCAACGCG--AT----TTTCAACT
** ** *
1603348 ATCGCAACGCGAACTGGAA-A
1 ATCGCAACGCGATTTTCAACT
1603368 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
1603389 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
*
1603410 ATCGCAATGCGA
1 ATCGCAACGCGA
1603422 AATGCAACGC
Statistics
Matches: 96, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
20 15 0.16
21 63 0.66
23 2 0.02
25 1 0.01
27 15 0.16
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:1603381 original size:89 final size:89
Alignment explanation
Indices: 1603259--1603425 Score: 307
Period size: 89 Copynumber: 1.9 Consensus size: 89
1603249 AAACTGAAAA
1603259 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAAATATC
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAAATATC
1603324 GCAACGCGAAATGGAAAATCAGTT
66 GCAACGCGAAATGGAAAATCAGTT
* *
1603348 ATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAATTATC
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAAATATC
*
1603413 GCAATGCGAAATG
66 GCAACGCGAAATG
1603426 CAACGCGAAT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 75 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.22
Consensus pattern (89 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAAATATC
GCAACGCGAAATGGAAAATCAGTT
Found at i:1604808 original size:3 final size:3
Alignment explanation
Indices: 1604800--1604824 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1604790 CATGATAGTA
1604800 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1604825 GAAATTAAAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1608144 original size:3 final size:3
Alignment explanation
Indices: 1608136--1608179 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
1608126 AAATATTTAT
1608136 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
1608180 TTCAAATGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1611471 original size:20 final size:20
Alignment explanation
Indices: 1611448--1611502 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
1611438 TGGAATATTC
*
1611448 TGGAGATGTGTGGAACCTTG
1 TGGAGATGTGTGGAACCTTA
*
1611468 TGGAG-TAGTGTGGATCCTTA
1 TGGAGAT-GTGTGGAACCTTA
1611488 TGGAAGA-GTGTGGAA
1 TGG-AGATGTGTGGAA
1611503 GAATATGGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 1 0.03
20 26 0.90
21 2 0.07
ACGTcount: A:0.24, C:0.07, G:0.40, T:0.29
Consensus pattern (20 bp):
TGGAGATGTGTGGAACCTTA
Found at i:1612797 original size:25 final size:25
Alignment explanation
Indices: 1612763--1612821 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 25
1612753 CTTTGGATTA
*
1612763 TCTCATTTGCTATGATTTTCCATGG
1 TCTCTTTTGCTATGATTTTCCATGG
*
1612788 TCTCTTTTGCTATGATTTTCCATTG
1 TCTCTTTTGCTATGATTTTCCATGG
1612813 TCTCATTTT
1 TCTC-TTTT
1612822 TCTCTCTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 27 0.87
26 4 0.13
ACGTcount: A:0.14, C:0.20, G:0.12, T:0.54
Consensus pattern (25 bp):
TCTCTTTTGCTATGATTTTCCATGG
Found at i:1620927 original size:8 final size:8
Alignment explanation
Indices: 1620913--1620942 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1620903 TATGAAGAAA
1620913 TATAATAT
1 TATAATAT
*
1620921 CATAATAT
1 TATAATAT
1620929 TATAATAT
1 TATAATAT
1620937 TATAAT
1 TATAAT
1620943 TAAATTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (8 bp):
TATAATAT
Found at i:1626217 original size:24 final size:24
Alignment explanation
Indices: 1626190--1626301 Score: 188
Period size: 24 Copynumber: 4.7 Consensus size: 24
1626180 TTATATTATA
*
1626190 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
1626214 ATACTTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
*
1626238 ATACTTGACCTGGATTCTGATCGA
1 ATACTTGACCTGGATTCTGATCGG
* *
1626262 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTCTGATCGG
1626286 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
1626302 ATGTTATGAT
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 83 1.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:1627377 original size:21 final size:23
Alignment explanation
Indices: 1627337--1627381 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
1627327 GGAGGTTATT
*
1627337 TTTTAAATAGTAATTTAAATAAA
1 TTTTAAATAGTAATTCAAATAAA
1627360 TTTTAAA-A-TAATTCAAATAAA
1 TTTTAAATAGTAATTCAAATAAA
1627381 T
1 T
1627382 AAATTTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
22 1 0.05
23 7 0.33
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TTTTAAATAGTAATTCAAATAAA
Found at i:1628550 original size:16 final size:17
Alignment explanation
Indices: 1628520--1628569 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 17
1628510 AAAAAATACA
*
1628520 ATATT-CCCAGTAATC-
1 ATATTCCCCGGTAATCT
1628535 ATATTCCCCGGTAATCTT
1 ATATTCCCCGGTAATC-T
*
1628553 TTATTCCCCGGTAATCT
1 ATATTCCCCGGTAATCT
1628570 TTTATTCCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 5 0.17
16 9 0.30
17 1 0.03
18 15 0.50
ACGTcount: A:0.24, C:0.28, G:0.10, T:0.38
Consensus pattern (17 bp):
ATATTCCCCGGTAATCT
Found at i:1628616 original size:20 final size:19
Alignment explanation
Indices: 1628536--1628610 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 19
1628526 CCAGTAATCA
1628536 TATTCC-CCGGTAATCTTT
1 TATTCCTCCGGTAATCTTT
1628554 TATTCC-CCGGTAATCTTT
1 TATTCCTCCGGTAATCTTT
*
1628572 TATTCCTCCCGATAATCTTT
1 TATTCCT-CCGGTAATCTTT
1628592 TATTCCTCCTGGTAATCTT
1 TATTCCTCC-GGTAATCTT
1628611 ACATTCTGTG
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
18 24 0.46
19 2 0.04
20 26 0.50
ACGTcount: A:0.17, C:0.28, G:0.09, T:0.45
Consensus pattern (19 bp):
TATTCCTCCGGTAATCTTT
Found at i:1635152 original size:2 final size:2
Alignment explanation
Indices: 1635145--1635178 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1635135 CATAAAAGCA
1635145 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1635179 TGAGCTTACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1636391 original size:8 final size:8
Alignment explanation
Indices: 1636374--1636404 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
1636364 AATTGGGGAT
1636374 TAAA-TTG
1 TAAAGTTG
1636381 TAAAGTTG
1 TAAAGTTG
1636389 TAAAGTTG
1 TAAAGTTG
1636397 TAAAGTTG
1 TAAAGTTG
1636405 GCAGACCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.17
8 19 0.83
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.39
Consensus pattern (8 bp):
TAAAGTTG
Found at i:1639542 original size:24 final size:24
Alignment explanation
Indices: 1639515--1639626 Score: 179
Period size: 24 Copynumber: 4.7 Consensus size: 24
1639505 TTATATTATA
*
1639515 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
1639539 ATACTTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
* *
1639563 ATACCTGACCTGGATTCTGATCGA
1 ATACTTGACCTGGATTCTGATCGG
* *
1639587 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTCTGATCGG
1639611 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
1639627 ATGTTATGAT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 81 1.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.34
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:1640742 original size:21 final size:23
Alignment explanation
Indices: 1640702--1640746 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
1640692 GGAGGCTATT
*
1640702 TTTTAAATAGTAATTTAAATAAA
1 TTTTAAATAGTAATTCAAATAAA
1640725 TTTTAAA-A-TAATTCAAATAAA
1 TTTTAAATAGTAATTCAAATAAA
1640746 T
1 T
1640747 AAATTTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
22 1 0.05
23 7 0.33
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TTTTAAATAGTAATTCAAATAAA
Found at i:1644613 original size:21 final size:21
Alignment explanation
Indices: 1644532--1644613 Score: 87
Period size: 21 Copynumber: 4.0 Consensus size: 21
1644522 GCAGAACCCC
* *
1644532 AGGGGGGTATCGATTCCCT-G
1 AGGGGGGAATCGATTCCCTCA
* *
1644552 TGGGGGGAATCGGTTCCCTTCA
1 AGGGGGGAATCGATTCCC-TCA
* *
1644574 A-AGGGGAATCGGTTCCCTCA
1 AGGGGGGAATCGATTCCCTCA
1644594 AGGGGGGAATCGATTCCCTC
1 AGGGGGGAATCGATTCCCTC
1644614 TGCACCAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
20 19 0.37
21 32 0.63
ACGTcount: A:0.18, C:0.23, G:0.35, T:0.23
Consensus pattern (21 bp):
AGGGGGGAATCGATTCCCTCA
Found at i:1651295 original size:16 final size:17
Alignment explanation
Indices: 1651265--1651334 Score: 63
Period size: 18 Copynumber: 4.0 Consensus size: 17
1651255 AAAAAATACA
*
1651265 ATATT-CCCAGTAATC-
1 ATATTCCCCGGTAATCT
1651280 ATATTCCCCGGTAATCTT
1 ATATTCCCCGGTAATC-T
*
1651298 TTATTCCCCGGTAATCTT
1 ATATTCCCCGGTAATC-T
*
1651316 TTATTCCTCCTGGTAATCT
1 ATATTCC-CC-GGTAATCT
1651335 TACATTCTGT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
15 5 0.10
16 9 0.19
18 24 0.50
19 3 0.06
20 7 0.15
ACGTcount: A:0.21, C:0.27, G:0.10, T:0.41
Consensus pattern (17 bp):
ATATTCCCCGGTAATCT
Found at i:1651341 original size:20 final size:18
Alignment explanation
Indices: 1651281--1651335 Score: 92
Period size: 18 Copynumber: 2.9 Consensus size: 18
1651271 CCAGTAATCA
1651281 TATTCCCCGGTAATCTTT
1 TATTCCCCGGTAATCTTT
1651299 TATTCCCCGGTAATCTTT
1 TATTCCCCGGTAATCTTT
1651317 TATTCCTCCTGGTAATCTT
1 TATTCC-CC-GGTAATCTT
1651336 ACATTCTGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 24 0.69
19 2 0.06
20 9 0.26
ACGTcount: A:0.16, C:0.27, G:0.11, T:0.45
Consensus pattern (18 bp):
TATTCCCCGGTAATCTTT
Found at i:1652726 original size:16 final size:15
Alignment explanation
Indices: 1652705--1652736 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1652695 TAATATAAAA
1652705 CCTAAACTAAACTAAT
1 CCTAAACTAAAC-AAT
1652721 CCTAAACTAAACAAT
1 CCTAAACTAAACAAT
1652736 C
1 C
1652737 ATTCAGCCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (15 bp):
CCTAAACTAAACAAT
Found at i:1653802 original size:53 final size:53
Alignment explanation
Indices: 1653710--1653964 Score: 316
Period size: 53 Copynumber: 4.8 Consensus size: 53
1653700 ATGATGAGTC
* *
1653710 CGCTCCCTCTTG-TTCAGGGATTAAGGAACTCGAACAATCTTATAAAAACGGGTT
1 CGCTCCCTCTTGCTTCAGGGAGT-A-GAACTCGAACAATCTTCTAAAAACGGGTT
* * **** *
1653764 CGCTCCCTATTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCTTATGGGTT
1 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTAAAAACGGGTT
* * * ****
1653817 CACTCCCTCTTGCTTCAAGGG-GTAAAACTTGAACAATCTTCTGCCTACGGGTT
1 CGCTCCCTCTTGCTTC-AGGGAGTAGAACTCGAACAATCTTCTAAAAACGGGTT
1653870 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTAAAAACGGGTT
1 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTAAAAACGGGTT
*
1653923 CGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCT
1 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT
1653965 GGTGTGATTC
Statistics
Matches: 174, Mismatches: 24, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
52 4 0.02
53 145 0.83
54 16 0.09
55 9 0.05
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (53 bp):
CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTAAAAACGGGTT
Found at i:1654073 original size:13 final size:13
Alignment explanation
Indices: 1654055--1654079 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1654045 TGCTCGAAAG
1654055 ACTTACTGATGGC
1 ACTTACTGATGGC
1654068 ACTTACTGATGG
1 ACTTACTGATGG
1654080 GTTTGCTTCA
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:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:1654179 original size:42 final size:42
Alignment explanation
Indices: 1654120--1654202 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
1654110 ATAAATTACC
* * *
1654120 CTAAGGATTTAATCATCATGCTTGAAAGACTTACTGATGGCA
1 CTAAGAATTTAAACATCATGCTCGAAAGACTTACTGATGGCA
*
1654162 CTAAGAATTTAAACATCATGCTCGAAAGACTTATTGATGGC
1 CTAAGAATTTAAACATCATGCTCGAAAGACTTACTGATGGC
1654203 CCGAAGGACT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (42 bp):
CTAAGAATTTAAACATCATGCTCGAAAGACTTACTGATGGCA
Found at i:1664492 original size:131 final size:130
Alignment explanation
Indices: 1664253--1664577 Score: 451
Period size: 131 Copynumber: 2.5 Consensus size: 130
1664243 TATAGTATCA
* * *
1664253 ATACTTGTACATTTA-AGCCTATTTTTATTAT-ACTGGTAGAAATGTTTACCGTGTATATTGTTA
1 ATACTTGGACATTTACA-CCTATTTTCATTATAAC--GTAGAAATGTTTACCGTGTACATTGTTA
* * *
1664316 ATTTACCTATTATTTTAAAGTAATAAGTTTCGAAATTATACGTATCGATATTTTATATATGAGTA
63 ATTTACCTATTATTTTAAAGTAATAAGCTTCGAAATTATACGTATCGATACTTTATATATAAGTA
1664381 CT-G
128 -TAG
* *
1664384 ATACTTGGACATTTACACCTATTTTCATTATAACAGTAGAAACGTTTACCGTGTACATTTTTAAT
1 ATACTTGGACATTTACACCTATTTTCATTATAAC-GTAGAAATGTTTACCGTGTACATTGTTAAT
* *
1664449 TTACCTATTATTTTAAAGTAATAGGCTTCGAAATTATTA-GTATCGATACTTTGTATATAAGTAT
65 TTACCTATTATTTTAAAGTAATAAGCTTCGAAATTA-TACGTATCGATACTTTATATATAAGTAT
1664513 AG
129 AG
* *
1664515 ATACTTGGACATTTACGCCTATTTTCATTATATCGATAGAAATGTTTACCGTGTACATTGTTA
1 ATACTTGGACATTTACACCTATTTTCATTATAACG-TAGAAATGTTTACCGTGTACATTGTTA
1664578 TAGGTTTCAA
Statistics
Matches: 174, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
130 2 0.01
131 167 0.96
132 5 0.03
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (130 bp):
ATACTTGGACATTTACACCTATTTTCATTATAACGTAGAAATGTTTACCGTGTACATTGTTAATT
TACCTATTATTTTAAAGTAATAAGCTTCGAAATTATACGTATCGATACTTTATATATAAGTATAG
Found at i:1664950 original size:198 final size:199
Alignment explanation
Indices: 1664577--1665859 Score: 1753
Period size: 198 Copynumber: 6.5 Consensus size: 199
1664567 GTACATTGTT
** * * *
1664577 ATAGGTTTC-AAACTTATAAGTATCGATACTTTATATATGTGTATTGATACCTTTTACGTGCAAA
1 ATAGGTTTCGAAA-TTCCAAGTATCGATACTTTATATATGTGTATCGATACATTTTGCGTGCAAA
* * ** * *
1664641 TTATTTGAAAAGTGTAATGGAATAAACGTA-TCGATACCTATATAAAAGTATCGATACTTGGTAT
65 TTGTTTGAGAAGCATACTGGAATAAAAGTATTC-ATACCTATATAAAAGTATCGATACTTGGTAT
* * *
1664705 TTACGCCTATTAACAATATA-CCGATAGACTTTTACCG-TTATATTGTTAATTTACCTATTACTT
129 TTACGCCTATTATCATTATATCCG-TAGACTTTTACCGTTTACATTGTTAATTTACCTATTACTT
1664768 TAAAGTA
193 TAAAGTA
* *
1664775 ATAGGTTTCGAAATTCCAAGTATCGATGCTTTATATATGTGTATCGATACATTTTGTGTGCAAAT
1 ATAGGTTTCGAAATTCCAAGTATCGATACTTTATATATGTGTATCGATACATTTTGCGTGCAAAT
* *
1664840 TGTTTGAGAAGCATACTAGAATAAAAGTATTCATACCTATATAAAATTATCGATACTTGGTATTT
66 TGTTTGAGAAGCATACTGGAATAAAAGTATTCATACCTATATAAAAGTATCGATACTTGGTATTT
* *
1664905 ACGCCTATTATCATTATA-CCATAGACTTTTACCATTTACATTGTTAATTTACCTATTACTTTAA
131 ACGCCTATTATCATTATATCCGTAGACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAA
1664969 AGTA
196 AGTA
* * * * *
1664973 ATAAGTTTCGAAATTTCAAGTATAGATACTTTATATATGTGTATCGATATATTTTGTGTGCAAAT
1 ATAGGTTTCGAAATTCCAAGTATCGATACTTTATATATGTGTATCGATACATTTTGCGTGCAAAT
* **
1665038 TGTTTGAGAAACATACTTAAATAAAAGTATTCATACCTATATAAAAGTATCGATACTTGGTATTT
66 TGTTTGAGAAGCATACTGGAATAAAAGTATTCATACCTATATAAAAGTATCGATACTTGGTATTT
* * *
1665103 ACGCCTATTATCATTATATCGGTAGACTTTTACCG-TTATATTGTTAATTTACTTATTACTTTAA
131 ACGCCTATTATCATTATATCCGTAGACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAA
1665167 AGTA
196 AGTA
* * * * * * *
1665171 ATAAGTTTCGAAATTTCAAGTATTGATATTTTATATATATGTATCAATACATTTTGCATGCAAAT
1 ATAGGTTTCGAAATTCCAAGTATCGATACTTTATATATGTGTATCGATACATTTTGCGTGCAAAT
* * * * * * *
1665236 TGTTTAAGAAACATACTGAAATAAAAATATTCATACCTATATAAACGTATTGATACTTGATATTT
66 TGTTTGAGAAGCATACTGGAATAAAAGTATTCATACCTATATAAAAGTATCGATACTTGGTATTT
* * *
1665301 ACGCATATTATCATTATATCGGTAGACTTTTACCGTTTGCATTGTTAATTTACCTATTACTTTAA
131 ACGCCTATTATCATTATATCCGTAGACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAA
1665366 AGTA
196 AGTA
* ** * **
1665370 ATAGGTTTCAAAATTTGAAGTATCGATACTTTATATATGTGTATCGATATATTTTGTTTGCAAAT
1 ATAGGTTTCGAAATTCCAAGTATCGATACTTTATATATGTGTATCGATACATTTTGCGTGCAAAT
* *
1665435 TGTTTGAGAAGTATACTGGAATAAAAGTA-TCAATACCTATATAAAAGTATCAATACTTGGTATT
66 TGTTTGAGAAGCATACTGGAATAAAAGTATTC-ATACCTATATAAAAGTATCGATACTTGGTATT
*
1665499 TACGCCTATTATCATTATA-CCGGTAGACTTTTACTGTTTACATTGTTAATTTACCTATTACTTT
130 TACGCCTATTATCATTATATCC-GTAGACTTTTACCGTTTACATTGTTAATTTACCTATTACTTT
1665563 AAAGTA
194 AAAGTA
* **
1665569 ATAGGTTTTGAAATTCCAAGTATCGATA-TTT-TATACATGTATCGATACATTTTGCGTGCAAAT
1 ATAGGTTTCGAAATTCCAAGTATCGATACTTTATATATGTGTATCGATACATTTTGCGTGCAAAT
* * *
1665632 TATTTGAGAAGCATAATGGAATAGAAGTATTCATACCTATATAAAGAGTATCGATACTTGGTATT
66 TGTTTGAGAAGCATACTGGAATAAAAGTATTCATACCTATATAAA-AGTATCGATACTTGGTATT
* *
1665697 TACGCCTATTATCATTATATCGGTAGACTTTTACCGTTTACATTGTTAATTTACCTATTAATTTA
130 TACGCCTATTATCATTATATCCGTAGACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTA
1665762 AAGTA
195 AAGTA
* * ** * *
1665767 ATAGATTTCGAAATTCCAATTATCGATACTTT-T-TACATGTATCAATACATTTTGCGTGCAATT
1 ATAGGTTTCGAAATTCCAAGTATCGATACTTTATATATGTGTATCGATACATTTTGCGTGCAAAT
* ** *
1665830 TGTTTGACAAATATATTGGAATAAAAGTAT
66 TGTTTGAGAAGCATACTGGAATAAAAGTAT
1665860 CTACACCGGC
Statistics
Matches: 972, Mismatches: 102, Indels: 22
0.89 0.09 0.02
Matches are distributed among these distances:
197 77 0.08
198 647 0.67
199 248 0.26
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (199 bp):
ATAGGTTTCGAAATTCCAAGTATCGATACTTTATATATGTGTATCGATACATTTTGCGTGCAAAT
TGTTTGAGAAGCATACTGGAATAAAAGTATTCATACCTATATAAAAGTATCGATACTTGGTATTT
ACGCCTATTATCATTATATCCGTAGACTTTTACCGTTTACATTGTTAATTTACCTATTACTTTAA
AGTA
Found at i:1666583 original size:17 final size:17
Alignment explanation
Indices: 1666527--1666583 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
1666517 TTTTTCATTG
*
1666527 AAAAACCGAACCGAACC
1 AAAACCCGAACCGAACC
1666544 GAAAAACCCGAACCGTTAA--
1 --AAAACCCGAACCG--AACC
1666563 AAAACCCGAACCGAACC
1 AAAACCCGAACCGAACC
1666580 AAAA
1 AAAA
1666584 AAACCGGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
15 2 0.06
17 17 0.52
19 12 0.36
21 2 0.06
ACGTcount: A:0.53, C:0.32, G:0.12, T:0.04
Consensus pattern (17 bp):
AAAACCCGAACCGAACC
Found at i:1667848 original size:177 final size:177
Alignment explanation
Indices: 1667542--1667869 Score: 485
Period size: 177 Copynumber: 1.9 Consensus size: 177
1667532 ATTGAAACGA
* * * * *
1667542 TTTTGTCAAATTTCAACCTATTATATTGTCATGTATCGATACATATGTCTAAGATATCGATACTT
1 TTTTATCAAATTTAAACATATTATATTGTCACGTATCAATACATATGTCTAAGATATCGATACTT
* * * * ** **
1667607 TATAGGCGTTATTATTGCAATTCTTTTAAATTCGTAAAGTACCGATACTTTAGTACTTATACTTA
66 TATAGCCGTTATTATTACAATTCTTTTAAATTCCTAAAGTACCAATACTAGAGTACACATACTTA
1667672 TAAAAGTATCGATACAAATTTTGACCATTCCGGTAGCTCTTTACCGG
131 TAAAAGTATCGATACAAATTTTGACCATTCCGGTAGCTCTTTACCGG
* * *
1667719 TTTTATCAAATTTAAACATGTTATATTGTCACGTATCAATACATGTGTCTAAGATATTGATACTT
1 TTTTATCAAATTTAAACATATTATATTGTCACGTATCAATACATATGTCTAAGATATCGATACTT
* *
1667784 TATAGCCGTTATTATTACAATTCTTTTACATTCCTAAAGTACCAATACTAGGGTACACATACTTA
66 TATAGCCGTTATTATTACAATTCTTTTAAATTCCTAAAGTACCAATACTAGAGTACACATACTTA
*
1667849 TAAACGTATCGATACAAATTT
131 TAAAAGTATCGATACAAATTT
1667870 CAACAATTTC
Statistics
Matches: 132, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
177 132 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (177 bp):
TTTTATCAAATTTAAACATATTATATTGTCACGTATCAATACATATGTCTAAGATATCGATACTT
TATAGCCGTTATTATTACAATTCTTTTAAATTCCTAAAGTACCAATACTAGAGTACACATACTTA
TAAAAGTATCGATACAAATTTTGACCATTCCGGTAGCTCTTTACCGG
Found at i:1668062 original size:198 final size:198
Alignment explanation
Indices: 1667719--1668077 Score: 511
Period size: 198 Copynumber: 1.8 Consensus size: 198
1667709 TCTTTACCGG
**
1667719 TTTTATCAAATTTAAACATGTTATATTGTCACGTATCAATACATGTGTCTAAGATATTGATACTT
1 TTTTATCAAATTTAAACATGTTATATTGTCACGTATCAATACATGTGTCTAAGATATCAATACTT
** * *
1667784 TATAGCCGTTATTATTACAATTCTTTTACATTCCTAAAGTACCAATACTAGGGTACACATACTTA
66 TATAGCCACTATTATTACAATTCTTTTAAATTCCTAAAGTACCAATACTAGGGTACACATAATTA
1667849 TAAACGTATCGATACAAATTTCAACAATTTCGATAGATCTTTAACCTTTTTTTTCAAATTAAAAT
131 TAAACGTATCGATACAAATTTCAACAATTTCGATAGATCTTTAACCTTTTTTTTCAAATTAAAAT
1667914 CAA
196 CAA
* * * * * * *
1667917 TTTTGTCAAATTTCAATATGTTATATTGTCATGTATCGATACATGTGTGTAAGGTATCAATACTT
1 TTTTATCAAATTTAAACATGTTATATTGTCACGTATCAATACATGTGTCTAAGATATCAATACTT
** * * * ** ** *
1667982 TATAGCCACTATTATTGTAATTTTTTTAAATTCCTACATTACTGATACTTTGGTACATATAATTA
66 TATAGCCACTATTATTACAATTCTTTTAAATTCCTAAAGTACCAATACTAGGGTACACATAATTA
1668047 TAAACGTATCGATACAAATTTCAACAATTTC
131 TAAACGTATCGATACAAATTTCAACAATTTC
1668078 ATTAGCTCTT
Statistics
Matches: 138, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
198 138 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (198 bp):
TTTTATCAAATTTAAACATGTTATATTGTCACGTATCAATACATGTGTCTAAGATATCAATACTT
TATAGCCACTATTATTACAATTCTTTTAAATTCCTAAAGTACCAATACTAGGGTACACATAATTA
TAAACGTATCGATACAAATTTCAACAATTTCGATAGATCTTTAACCTTTTTTTTCAAATTAAAAT
CAA
Done.