Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008290.1 Hibiscus syriacus cultivar Beakdansim tig00110954_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: 1890093
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1311383 original size:22 final size:22
Alignment explanation
Indices: 1311337--1311383 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
1311327 ATTATTATTT
*
1311337 TTATTATTATTATTAATATATA
1 TTATTATTATTATTAATATAAA
1311359 TTATTATTATTATATAA-ATAAA
1 TTATTATTATTAT-TAATATAAA
1311381 TTA
1 TTA
1311384 CAAAACTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATTATTATTATTAATATAAA
Found at i:1313228 original size:16 final size:17
Alignment explanation
Indices: 1313188--1313228 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1313178 TTCTAAATAA
*
1313188 ATAATATCTTATAAATT
1 ATAATTTCTTATAAATT
1313205 ATATATTTCTTA-AAATT
1 ATA-ATTTCTTATAAATT
1313222 ATAATTT
1 ATAATTT
1313229 GAAATAACCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 11 0.50
18 7 0.32
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
ATAATTTCTTATAAATT
Found at i:1316001 original size:21 final size:21
Alignment explanation
Indices: 1315983--1316087 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
1315973 ATGAAGCAAG
1315983 GGAAGCAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* * *
1316004 AGAAGCA-ACCAGAGCAGCAGT
1 GGAAGCAGA-GAGAGCAGCAGC
* *
1316025 GGAAGCAGAGAAAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* * *
1316046 GGCAGCACAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* * * *
1316067 GGCATCACAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
1316088 ATATCAGCAT
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
20 1 0.01
21 68 0.97
22 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.36, T:0.02
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:1316748 original size:43 final size:43
Alignment explanation
Indices: 1316487--1316749 Score: 230
Period size: 43 Copynumber: 6.2 Consensus size: 43
1316477 ACCTGTACCA
* * * * **
1316487 GCGTTTTTA-GCAGAAACGCCGCAAAACATCAATACCTGCTGCG
1 GCGTTTTTATG-ACAAACGCCGCTAAATATCAACACCTATTGCG
* ** * * *
1316530 GCGTTTGTAAAAAAAACGCCGCTAAACATCATA-ACCTATTACG
1 GCGTTTTTATGACAAACGCCGCTAAATATCA-ACACCTATTGCG
* * * * * *
1316573 ACGTTTGTCTGAAAAACGCTGCTAAATATTAACACCTATTGCG
1 GCGTTTTTATGACAAACGCCGCTAAATATCAACACCTATTGCG
* * * * *
1316616 ACGTTTTTATGACAAAC-ACACTAAATATCGACACCTATTGTG
1 GCGTTTTTATGACAAACGCCGCTAAATATCAACACCTATTGCG
* * *
1316658 GCATTTTTAT-A-AAATGCCACTAAATATCAACACCTATTGCG
1 GCGTTTTTATGACAAACGCCGCTAAATATCAACACCTATTGCG
*
1316699 GCGTTTTTATGACAAACGCCGCTAAATATCAACACCTATTACG
1 GCGTTTTTATGACAAACGCCGCTAAATATCAACACCTATTGCG
1316742 GCGTTTTT
1 GCGTTTTT
1316750 TGTGAAAAAA
Statistics
Matches: 180, Mismatches: 34, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
40 3 0.02
41 32 0.18
42 29 0.16
43 115 0.64
44 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (43 bp):
GCGTTTTTATGACAAACGCCGCTAAATATCAACACCTATTGCG
Found at i:1318182 original size:2 final size:2
Alignment explanation
Indices: 1318175--1318201 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1318165 TCCGGTTTAT
1318175 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 T
1318202 TAAATGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1318456 original size:2 final size:2
Alignment explanation
Indices: 1318449--1318481 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1318439 ATTTTAGAAT
1318449 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1318482 AAAATAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1324537 original size:88 final size:88
Alignment explanation
Indices: 1324387--1324571 Score: 352
Period size: 88 Copynumber: 2.1 Consensus size: 88
1324377 TTAAGGTTTA
1324387 AGAAGTTGAGGTTACATCAAACAAGATGAACCTGTTTCGACCTATGCCTATCAATAGGGTGAGAG
1 AGAAGTTGAGGTTACATCAAACAAGATGAACCTGTTTCGACCTATGCCTATCAATAGGGTGAGAG
1324452 TTAGTCTTGAGTCAAGTCAATTT
66 TTAGTCTTGAGTCAAGTCAATTT
*
1324475 GGAAGTTGAGGTTACATCAAACAAGATGAACCTGTTTCGACCTATGCCTATCAATAGGGTGAGAG
1 AGAAGTTGAGGTTACATCAAACAAGATGAACCTGTTTCGACCTATGCCTATCAATAGGGTGAGAG
1324540 TTAGTCTTGAGTCAAGTCAATTT
66 TTAGTCTTGAGTCAAGTCAATTT
*
1324563 AAAAGTTGA
1 AGAAGTTGA
1324572 ATTGGTTTCA
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 94 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (88 bp):
AGAAGTTGAGGTTACATCAAACAAGATGAACCTGTTTCGACCTATGCCTATCAATAGGGTGAGAG
TTAGTCTTGAGTCAAGTCAATTT
Found at i:1326814 original size:32 final size:32
Alignment explanation
Indices: 1326767--1326847 Score: 101
Period size: 32 Copynumber: 2.6 Consensus size: 32
1326757 TTAGCTCGTG
* * *
1326767 AGTTTTTGAG-TCGAGTTAAGCTTACTTTTAA
1 AGTTTTAGAGTTCGAGTCAAGATTACTTTTAA
*
1326798 AGTTTTAGAGTTCGAGTCGAGATTACTTTTAA
1 AGTTTTAGAGTTCGAGTCAAGATTACTTTTAA
* *
1326830 AGTTTTCGAGTTCAAGTC
1 AGTTTTAGAGTTCGAGTC
1326848 GAGCTCAGCA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 9 0.21
32 34 0.79
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (32 bp):
AGTTTTAGAGTTCGAGTCAAGATTACTTTTAA
Found at i:1326848 original size:32 final size:32
Alignment explanation
Indices: 1326788--1326850 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1326778 CGAGTTAAGC
*
1326788 TTACTTTTAAAGTTTTAGAGTTCGAGTCGAGA
1 TTACTTTTAAAGTTTTAGAGTTCAAGTCGAGA
*
1326820 TTACTTTTAAAGTTTTCGAGTTCAAGTCGAG
1 TTACTTTTAAAGTTTTAGAGTTCAAGTCGAG
1326851 CTCAGCAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (32 bp):
TTACTTTTAAAGTTTTAGAGTTCAAGTCGAGA
Found at i:1330711 original size:19 final size:19
Alignment explanation
Indices: 1330687--1330740 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1330677 AAAATGTTTA
1330687 AAAGTATCGATACTTATAG
1 AAAGTATCGATACTTATAG
*
1330706 AAAGTATCGAAACTTTTATAG
1 AAAGTATCGATAC--TTATAG
*
1330727 -GAGTATCGATACTT
1 AAAGTATCGATACTT
1330741 TCAGTCTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.07
19 12 0.40
20 10 0.33
21 6 0.20
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (19 bp):
AAAGTATCGATACTTATAG
Found at i:1356822 original size:19 final size:18
Alignment explanation
Indices: 1356798--1356837 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1356788 TTATCAATAA
1356798 AAAATATAAATAAAATTTT
1 AAAATAT-AATAAAATTTT
* *
1356817 AAAATATATTATAATTTT
1 AAAATATAATAAAATTTT
1356835 AAA
1 AAA
1356838 TTTTTCAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATATAATAAAATTTT
Found at i:1359718 original size:9 final size:9
Alignment explanation
Indices: 1359693--1359729 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
1359683 TCGTTACTAC
1359693 CATCGTTGT
1 CATCGTTGT
* *
1359702 TATTGTTGT
1 CATCGTTGT
1359711 CATCGTTGT
1 CATCGTTGT
1359720 CATCGTTGT
1 CATCGTTGT
1359729 C
1 C
1359730 GTTGCTACCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.49
Consensus pattern (9 bp):
CATCGTTGT
Found at i:1360177 original size:22 final size:23
Alignment explanation
Indices: 1360141--1360189 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
1360131 CATATAATTA
**
1360141 TAAATTAGTTTAAAATTCAAAGG
1 TAAATTAGTTTAAAATAAAAAGG
1360164 TAAATTA-TTTAAAATAAAAAGG
1 TAAATTAGTTTAAAATAAAAAGG
1360186 TAAA
1 TAAA
1360190 CTATACTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (23 bp):
TAAATTAGTTTAAAATAAAAAGG
Found at i:1361546 original size:31 final size:31
Alignment explanation
Indices: 1361511--1361577 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1361501 GGTTTAAAAA
*
1361511 AAGATATAGCCA-TTCTTGTTTTTATTTAATT
1 AAGATATAGCCACTT-TCGTTTTTATTTAATT
* *
1361542 AAGATATGGTCACTTTCGTTTTTATTTAATT
1 AAGATATAGCCACTTTCGTTTTTATTTAATT
1361573 AAGAT
1 AAGAT
1361578 GAGATCATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (31 bp):
AAGATATAGCCACTTTCGTTTTTATTTAATT
Found at i:1361779 original size:32 final size:32
Alignment explanation
Indices: 1361709--1361780 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
1361699 AAATTTTAAC
1361709 ATAAAAT-AAACATTTTTAAATGAAAATAAAA
1 ATAAAATAAAACATTTTTAAATGAAAATAAAA
* * *
1361740 ATAAAAATAAAATATTTTTAAAT-TAAGTAAATA
1 AT-AAAATAAAACATTTTTAAATGAAAATAAA-A
1361773 ATAAAATA
1 ATAAAATA
1361781 TATTTAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 2 0.06
32 17 0.49
33 16 0.46
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (32 bp):
ATAAAATAAAACATTTTTAAATGAAAATAAAA
Found at i:1361803 original size:25 final size:27
Alignment explanation
Indices: 1361741--1361802 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
1361731 AAAATAAAAA
*
1361741 TAAA-AATAAAATATTTTTAAATTAAG
1 TAAATAATAAAATATATTTAAATTAAG
1361767 TAAATAATAAAATATATTT-AA-TAAG
1 TAAATAATAAAATATATTTAAATTAAG
*
1361792 TTAAT-ATAAAA
1 TAAATAATAAAA
1361803 AATTAAGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 6 0.18
25 8 0.24
26 6 0.18
27 13 0.39
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (27 bp):
TAAATAATAAAATATATTTAAATTAAG
Found at i:1372536 original size:64 final size:64
Alignment explanation
Indices: 1372452--1372597 Score: 188
Period size: 64 Copynumber: 2.3 Consensus size: 64
1372442 CATTCATAAG
* * *
1372452 TGCATCGATGCATTCC-TTTAAAAGAAGAACATCGAATGCCTTTGATGCATCGATGCA-TAGCTA
1 TGCATCGATGCA-TCCTTTTAAAAGAAGAACATCGAATGCATTTGATGCACCGATGCACAAG-TA
1372515 A
64 A
* * * *
1372516 TGCATCGATGCATCCTTTTAAAATAATAACATCGAATGCATTTTATGCACCGATGCACAAGTAG
1 TGCATCGATGCATCCTTTTAAAAGAAGAACATCGAATGCATTTGATGCACCGATGCACAAGTAA
1372580 TGCATCGATGCATACCTT
1 TGCATCGATGCAT-CCTT
1372598 CATTGAAAGA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
63 3 0.04
64 63 0.88
65 6 0.08
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATCCTTTTAAAAGAAGAACATCGAATGCATTTGATGCACCGATGCACAAGTAA
Found at i:1373307 original size:30 final size:30
Alignment explanation
Indices: 1373271--1373334 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1373261 AAGGAACATA
* *
1373271 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
1373301 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
1373331 TGGA
1 TGGA
1373335 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:1376316 original size:21 final size:22
Alignment explanation
Indices: 1376285--1376329 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1376275 ATTATATTTT
*
1376285 TATATTTTTAATAAT-TAAATAA
1 TATATTTTTAACAATATAAA-AA
1376307 TATA-TTTTAACAATATAAAAA
1 TATATTTTTAACAATATAAAAA
1376328 TA
1 TA
1376330 AAAATTCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TATATTTTTAACAATATAAAAA
Found at i:1376732 original size:21 final size:20
Alignment explanation
Indices: 1376646--1376803 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
1376636 AAATGACCAA
**
1376646 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1376665 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1376685 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1376705 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
1376726 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1376747 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1376767 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
1376788 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1376804 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1376796 original size:20 final size:20
Alignment explanation
Indices: 1376771--1377081 Score: 79
Period size: 20 Copynumber: 15.5 Consensus size: 20
1376761 GATTTTCAAT
* *
1376771 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
1376791 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
1376811 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1376831 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
1376851 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
1376871 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1376891 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
1376911 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
1376932 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1376952 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
1376972 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1376992 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
1377012 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
1377032 AATCGCAACGATAATC-CGTA
1 AATCGCAACGCGAA-CACATA
* *
1377052 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
1377072 AATCGCAACG
1 AATCGCAACG
1377082 ATAATCCGTA
Statistics
Matches: 244, Mismatches: 38, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
19 3 0.01
20 224 0.92
21 16 0.07
22 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:1376816 original size:40 final size:40
Alignment explanation
Indices: 1376771--1377160 Score: 439
Period size: 40 Copynumber: 9.7 Consensus size: 40
1376761 GATTTTCAAT
* ** * * *
1376771 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAAC-CGTA
* *
1376811 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
** * * *
1376851 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
1376891 TATCGCAACGCGTATCCGTAAATCGCAACGA-TAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGT-A
* *
1376932 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
1376972 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
1377012 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
1377052 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * *
1377092 AATCGCAACGAGAATCTGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * * *
1377132 AATCGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGTATCCGTAAATCGCAAC
1377161 ACTGAAATTT
Statistics
Matches: 312, Mismatches: 33, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
39 4 0.01
40 272 0.87
41 34 0.11
42 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
Found at i:1377088 original size:20 final size:19
Alignment explanation
Indices: 1376809--1377160 Score: 398
Period size: 20 Copynumber: 17.6 Consensus size: 19
1376799 CGCGAACACA
1376809 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
1376829 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
**
1376849 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACG-GTATCCG
*
1376869 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
1376889 TATATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
* * *
1376909 TAAATCGCAACGATAATACA
1 TAAATCGCAACGGT-ATCCG
1376929 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACG-GTATCCG
1376950 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
1376970 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
1376990 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
1377010 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
1377030 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
1377050 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
1377070 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
1377090 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
1377110 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
1377130 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
1377150 TAAATCACAAC
1 TAAATCGCAAC
1377161 ACTGAAATTT
Statistics
Matches: 290, Mismatches: 33, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.01
20 270 0.93
21 16 0.06
22 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (19 bp):
TAAATCGCAACGGTATCCG
Found at i:1377405 original size:14 final size:14
Alignment explanation
Indices: 1377386--1377412 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1377376 TTTTGGAGGG
1377386 TCATGGGATAATGT
1 TCATGGGATAATGT
1377400 TCATGGGATAATG
1 TCATGGGATAATG
1377413 AACATGTTGA
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:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (14 bp):
TCATGGGATAATGT
Found at i:1377468 original size:12 final size:12
Alignment explanation
Indices: 1377451--1377475 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1377441 ATATAATCCT
1377451 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1377463 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1377475 G
1 G
1377476 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1379771 original size:19 final size:19
Alignment explanation
Indices: 1379749--1380022 Score: 345
Period size: 19 Copynumber: 15.4 Consensus size: 19
1379739 CGGAAAATAC
*
1379749 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1379768 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1379782 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1379802 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1379816 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1379835 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1379854 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
1379868 AATCGTAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1379887 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1379906 AATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
1379925 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1379944 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1379963 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1379977 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1379996 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1380015 AATCGCAA
1 AATCGCAA
1380023 CGAGATAATC
Statistics
Matches: 224, Mismatches: 10, Indels: 42
0.81 0.04 0.15
Matches are distributed among these distances:
14 39 0.17
15 2 0.01
16 11 0.05
17 10 0.04
18 3 0.01
19 146 0.65
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1379921 original size:13 final size:13
Alignment explanation
Indices: 1379816--1379963 Score: 53
Period size: 13 Copynumber: 11.6 Consensus size: 13
1379806 GCAACGAGAG
*
1379816 AATCGCAATGCGA
1 AATCGAAATGCGA
*
1379829 AAT-GAAAAT-CGC
1 AATCG-AAATGCGA
*
1379841 AATGCGAAATG-AA
1 AAT-CGAAATGCGA
* * *
1379854 AATCGCAACGAGA
1 AATCGAAATGCGA
*
1379867 GAATCGTAATGCGA
1 -AATCGAAATGCGA
*
1379881 AAT-GAAAAT-CGC
1 AATCG-AAATGCGA
*
1379893 AATGCGAAATG-AA
1 AAT-CGAAATGCGA
*
1379906 AATCGCAATGCGA
1 AATCGAAATGCGA
* *
1379919 AATGGAAAT-CGC
1 AATCGAAATGCGA
*
1379931 AATGCGAAATG-AA
1 AAT-CGAAATGCGA
*
1379944 AATCGCAATGCGA
1 AATCGAAATGCGA
1379957 AAT-GAAA
1 AATCGAAA
1379964 ATCGCAACGA
Statistics
Matches: 96, Mismatches: 25, Indels: 29
0.64 0.17 0.19
Matches are distributed among these distances:
12 37 0.39
13 47 0.49
14 12 0.12
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.16
Consensus pattern (13 bp):
AATCGAAATGCGA
Found at i:1379951 original size:109 final size:105
Alignment explanation
Indices: 1379777--1380044 Score: 450
Period size: 109 Copynumber: 2.5 Consensus size: 105
1379767 AAATCCCAAC
1379777 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGA-GAATCGCAATGCGAAATGAAAATCGC
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAATGAAAATCGC
* *
1379841 AATGCGAAATGAAAATCGCAACGAGAGAATCGTAATGCGAA
65 AATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
1379882 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGAT-G-AATCGCAATGCGAAATGAAAAT
1379947 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
62 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1379991 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAT-AATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAAT
1380045 TATAAACGCA
Statistics
Matches: 154, Mismatches: 4, Indels: 11
0.91 0.02 0.07
Matches are distributed among these distances:
104 32 0.21
105 16 0.10
106 4 0.03
107 5 0.03
108 1 0.01
109 96 0.62
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.15
Consensus pattern (105 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAATGAAAATCGCA
ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:1380060 original size:52 final size:52
Alignment explanation
Indices: 1379777--1380044 Score: 446
Period size: 52 Copynumber: 5.0 Consensus size: 52
1379767 AAATCCCAAC
1379777 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1379830 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGTAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1379882 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA--G-AATCGCAATGCGAA
*
1379939 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1379991 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1380043 AT
1 AT
1380045 TATAAACGCA
Statistics
Matches: 205, Mismatches: 5, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
52 133 0.65
53 17 0.08
54 4 0.02
55 5 0.02
56 1 0.00
57 45 0.22
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1380060 original size:71 final size:70
Alignment explanation
Indices: 1379749--1380044 Score: 331
Period size: 71 Copynumber: 4.2 Consensus size: 70
1379739 CGGAAAATAC
* *
1379749 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
1379809 ACGAGA
65 ACGAGA
* * *
1379815 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-TAATGC
1 -AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-C
* *
1379879 GAAATGA-A
62 GCAACGAGA
*
1379887 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
* *
1379952 TGCGA
66 CGAGA
* * *
1379957 AAT-GAAAAT-CGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCG
1 AATCG-CAATGCGAAATG-AA-AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCG
1380020 CAACGAGA
63 CAACGAGA
1380028 TAATCGCAATGCGAAAT
1 -AATCGCAATGCGAAAT
1380045 TATAAACGCA
Statistics
Matches: 191, Mismatches: 22, Indels: 26
0.80 0.09 0.11
Matches are distributed among these distances:
67 25 0.13
69 14 0.07
70 15 0.08
71 98 0.51
72 27 0.14
73 12 0.06
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (70 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
CGAGA
Found at i:1380140 original size:19 final size:18
Alignment explanation
Indices: 1380051--1380132 Score: 100
Period size: 19 Copynumber: 4.6 Consensus size: 18
1380041 AAATTATAAA
1380051 CGCATTGCGATTTCATTT
1 CGCATTGCGATTTCATTT
1380069 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGA-TTTCATTT
*
1380089 CGCATTGCGA-TTC-TCT
1 CGCATTGCGATTTCATTT
1380105 CG--TTGCGATTTTCATTT
1 CGCATTGCGA-TTTCATTT
1380122 CGCATTGCGAT
1 CGCATTGCGAT
1380133 AGTCATTTTG
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
14 6 0.11
16 7 0.13
17 7 0.13
18 1 0.02
19 26 0.47
20 8 0.15
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.43
Consensus pattern (18 bp):
CGCATTGCGATTTCATTT
Found at i:1380254 original size:13 final size:14
Alignment explanation
Indices: 1380238--1380272 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1380228 CATCAATTAC
1380238 ACAAATCA-CTTTT
1 ACAAATCATCTTTT
1380251 ACAAATCATCTTTT
1 ACAAATCATCTTTT
1380265 ACAAATCA
1 ACAAATCA
1380273 ATTAAACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (14 bp):
ACAAATCATCTTTT
Found at i:1382237 original size:14 final size:14
Alignment explanation
Indices: 1382218--1382274 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1382208 GCGAAATGAA
*
1382218 AATCGCAACGACAG
1 AATCGCAACGAAAG
1382232 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1382249 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1382265 AATCGCAACG
1 AATCGCAACG
1382275 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1382245 original size:33 final size:33
Alignment explanation
Indices: 1382199--1382291 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1382189 GCGAAACCAA
*
1382199 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1382232 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1382265 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1382292 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1382256 original size:19 final size:19
Alignment explanation
Indices: 1382162--1382296 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1382152 TAGTTTACTT
* *
1382162 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1382182 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1382201 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1382220 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1382234 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1382253 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1382267 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1382286 TCGCAATGCGA
1 TCGCAACGCGA
1382297 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1382314 original size:19 final size:19
Alignment explanation
Indices: 1382292--1382420 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1382282 AAAATCGCAA
1382292 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1382311 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1382325 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1382344 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1382358 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1382377 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1382396 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1382416 TGCGA
1 TGCGA
1382421 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1382334 original size:33 final size:33
Alignment explanation
Indices: 1382292--1382383 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1382282 AAAATCGCAA
1382292 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1382325 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1382358 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1382384 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1382772 original size:181 final size:186
Alignment explanation
Indices: 1382464--1382839 Score: 708
Period size: 181 Copynumber: 2.0 Consensus size: 186
1382454 TTGAATGGAT
1382464 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1382529 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1382594 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1382649 AAATTTACTTTCAACCAAAAGAC-AAACAAAGAC-AA-A-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1382710 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
1382775 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1382831 AAATTTACT
1 AAATTTACT
1382840 AAGCAATCTA
Statistics
Matches: 189, Mismatches: 1, Indels: 5
0.97 0.01 0.03
Matches are distributed among these distances:
181 92 0.49
182 62 0.33
183 2 0.01
184 10 0.05
185 23 0.12
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1384564 original size:14 final size:14
Alignment explanation
Indices: 1384545--1384667 Score: 102
Period size: 14 Copynumber: 7.7 Consensus size: 14
1384535 TTGAAATGAA
1384545 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1384559 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1384576 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
1384592 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1384609 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1384625 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1384644 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1384658 AATCGCAACG
1 AATCGCAACG
1384668 CGAAATGAAA
Statistics
Matches: 92, Mismatches: 2, Indels: 30
0.74 0.02 0.24
Matches are distributed among these distances:
14 36 0.39
15 1 0.01
16 14 0.15
17 14 0.15
18 1 0.01
19 26 0.28
ACGTcount: A:0.41, C:0.24, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1384582 original size:33 final size:33
Alignment explanation
Indices: 1384537--1384686 Score: 264
Period size: 33 Copynumber: 4.5 Consensus size: 33
1384527 TCTTTTGGTT
1384537 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1384570 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1384603 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1384636 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1384669 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
1384687 CGAAATGAAA
Statistics
Matches: 113, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 113 1.00
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1384583 original size:19 final size:18
Alignment explanation
Indices: 1384544--1384708 Score: 137
Period size: 19 Copynumber: 9.8 Consensus size: 18
1384534 GTTGAAATGA
1384544 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1384559 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1384576 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
1384592 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1384609 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1384625 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1384642 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1384658 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1384675 AAAATCGCAACGCGAAATG
1 -AAATCGCAACGCGAGATG
*
1384694 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1384709 TTTTGGTTTC
Statistics
Matches: 126, Mismatches: 4, Indels: 36
0.76 0.02 0.22
Matches are distributed among these distances:
14 32 0.25
16 21 0.17
17 18 0.14
19 55 0.44
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1384648 original size:52 final size:52
Alignment explanation
Indices: 1384537--1384708 Score: 182
Period size: 52 Copynumber: 3.4 Consensus size: 52
1384527 TCTTTTGGTT
* * *
1384537 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAGATGACAATCGCAA--C
1 GAAATGAAAATCGCAACGCGAGAATCGCAACGCGAAATGAAAATCGCAACGC
* *
1384587 G--A-GAGAATCGCAACGCGAG-AT-GACAATCGC-AACGA-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAGAATCG-CAA-CGCGAA--ATGAAAATCGCAACGC
*
1384636 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAGAATCGCAACGCGAAATGAAAATCGCAACGC
*
1384688 GAAATGAAAATCGCAATGCGA
1 GAAATGAAAATCGCAACGCGA
1384709 TTTTGGTTTC
Statistics
Matches: 100, Mismatches: 9, Indels: 24
0.75 0.07 0.18
Matches are distributed among these distances:
45 1 0.01
46 6 0.06
47 28 0.28
48 2 0.02
49 2 0.02
50 1 0.01
51 2 0.02
52 50 0.50
53 7 0.07
54 1 0.01
ACGTcount: A:0.44, C:0.22, G:0.25, T:0.10
Consensus pattern (52 bp):
GAAATGAAAATCGCAACGCGAGAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:1384739 original size:14 final size:14
Alignment explanation
Indices: 1384720--1384776 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1384710 TTTGGTTTCG
1384720 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1384734 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1384753 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1384767 CGTTGCGATT
1 CGTTGCGATT
1384777 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1384752 original size:33 final size:33
Alignment explanation
Indices: 1384704--1384784 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
1384694 AAAATCGCAA
**
1384704 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1384737 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1384770 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
1384785 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1384787 original size:21 final size:21
Alignment explanation
Indices: 1384761--1384836 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1384751 CGCGTTGCGA
1384761 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1384782 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1384802 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
1384823 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1384837 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1384817 original size:41 final size:41
Alignment explanation
Indices: 1384760--1384837 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1384750 TCGCGTTGCG
*
1384760 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
1384801 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1384838 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:1384958 original size:33 final size:33
Alignment explanation
Indices: 1384916--1384986 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1384906 AATACTAACT
*
1384916 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1384949 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1384982 TGAAA
1 TGAAA
1384987 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1385219 original size:22 final size:22
Alignment explanation
Indices: 1385167--1385221 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1385157 TGGTTGTGAG
**
1385167 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1385189 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1385211 GGATTTCTTCG
1 GGATTTCTTCG
1385222 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1385392 original size:20 final size:20
Alignment explanation
Indices: 1385367--1385559 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
1385357 CTTTAAATAT
1385367 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1385387 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1385409 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1385428 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1385448 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1385468 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1385488 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1385508 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1385528 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1385548 CGCGTTGCGATT
1 CGCGTTGCGATT
1385560 ATTGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1385554 original size:60 final size:60
Alignment explanation
Indices: 1385367--1385559 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1385357 CTTTAAATAT
**
1385367 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1385428 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1385488 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1385548 CGCGTTGCGATT
1 CGCGTTGCGATT
1385560 ATTGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1388768 original size:15 final size:15
Alignment explanation
Indices: 1388727--1388769 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1388717 TGGCACCGAA
*
1388727 AGCTGAGAAGAAACC
1 AGCTGAGAAGAAGCC
*
1388742 AGCGGAGAAGAAGCC
1 AGCTGAGAAGAAGCC
*
1388757 AGCTGAGGAGAAG
1 AGCTGAGAAGAAG
1388770 AAGACCGTCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.37, T:0.05
Consensus pattern (15 bp):
AGCTGAGAAGAAGCC
Found at i:1391211 original size:14 final size:14
Alignment explanation
Indices: 1391194--1391220 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1391184 AATTAAATTA
1391194 TTAGAATTTATTTC
1 TTAGAATTTATTTC
1391208 TTAGAATTTATTT
1 TTAGAATTTATTT
1391221 AAATAGTTTT
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:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (14 bp):
TTAGAATTTATTTC
Found at i:1394565 original size:83 final size:82
Alignment explanation
Indices: 1394468--1394904 Score: 424
Period size: 83 Copynumber: 5.3 Consensus size: 82
1394458 CATGTCATAG
* * * *
1394468 TGTTTTCCATTATTATTTAGAGAATATATTCCATGTCATAGCGTTTTC-TCCCATCTGAAATGAA
1 TGTTTTCCATTATTATTCAGAGAATATCTTCCATGTCATAGTG-TTTCATCCCATCTAAAATGAA
**
1394532 AGGTGAATTCCAGGAGAAA
65 AGGTGCGTTCCAGG-GAAA
* * * *
1394551 TGTTTTCCATTATTATTCAGAGAATCTCTAT-CATGTTATAGTGTTCCATCCCATCCAAAATGAA
1 TGTTTTCCATTATTATTCAGAGAATATCT-TCCATGTCATAGTGTTTCATCCCATCTAAAATGAA
** ** *
1394615 AAATTTGTTCCAGGGAAG
65 AGGTGCGTTCCAGGGAAA
* * * * *
1394633 TATTTTCCATTATTATTCAGAGAAT-TTTTGCCATGTCATAGTGTTCCATTCCAT-TCGAAATGA
1 TGTTTTCCATTATTATTCAGAGAATATCTT-CCATGTCATAGTGTTTCATCCCATCT-AAAATGA
* *
1394696 AAGGGGCGTTCTAGGGGAAA
64 AAGGTGCGTTCCA-GGGAAA
* * * *
1394716 TGTTTTTCA-TATTATTCAGAGAATATCTACCATGTCATAATG-TTCTATCCCATCCAAAATGAA
1 TGTTTTCCATTATTATTCAGAGAATATCTTCCATGTCATAGTGTTTC-ATCCCATCTAAAATGAA
*
1394779 AGGTGC-ATCCTAGGGAAA
65 AGGTGCGTTCC-AGGGAAA
*
1394797 GTGTTTTCCATTATTATTCAGAGAATCTCTAT-CATGTCATAGTGTTTCATCCCAT-TAAAAATG
1 -TGTTTTCCATTATTATTCAGAGAATATCT-TCCATGTCATAGTGTTTCATCCCATCT-AAAATG
1394860 AAAGGTGCGTTCCAGGGGAAA
63 AAAGGTGCGTTCCA-GGGAAA
** *
1394881 CATTTTCCATTATTATTTAGAGAA
1 TGTTTTCCATTATTATTCAGAGAA
1394905 AATTTACAGT
Statistics
Matches: 289, Mismatches: 48, Indels: 34
0.78 0.13 0.09
Matches are distributed among these distances:
80 1 0.00
81 12 0.04
82 118 0.41
83 145 0.50
84 13 0.04
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (82 bp):
TGTTTTCCATTATTATTCAGAGAATATCTTCCATGTCATAGTGTTTCATCCCATCTAAAATGAAA
GGTGCGTTCCAGGGAAA
Found at i:1394806 original size:165 final size:163
Alignment explanation
Indices: 1394466--1394904 Score: 519
Period size: 165 Copynumber: 2.7 Consensus size: 163
1394456 GTCATGTCAT
* * *
1394466 AGTGTTTTCCATTATTATTTAGAGAATATATTCCATGTCATAGCGTTTTC-TCCCA-TCTGAAAT
1 AGTGTTTTCCATTATTATTCAGAGAAT-TTTTCCATGTCATAGTG-TTTCATCCCATTC-GAAAT
** * * * * *
1394529 GAAAGGTGAATTCCAGGAGAAATGTTTTCCATTATTATTCAGAGAATCTCTATCATGTTATAGTG
63 GAAAGGTGCGTTCCAGGGGAAATGTTTTCCATTATTATTCAGAGAATATCTACCATGTCATAATG
** *
1394594 TTCCATCCCATCCAAAATGAAAAATTTGTTCCAGGGA
128 TTCCATCCCATCCAAAATG-AAAAGGTGATCCAGGGA
* * *
1394631 AGTATTTTCCATTATTATTCAGAGAATTTTTGCCATGTCATAGTGTTCCATTCCATTCGAAATGA
1 AGTGTTTTCCATTATTATTCAGAGAATTTTT-CCATGTCATAGTGTTTCATCCCATTCGAAATGA
* * *
1394696 AAGGGGCGTTCTAGGGGAAATGTTTTTCA-TATTATTCAGAGAATATCTACCATGTCATAATGTT
65 AAGGTGCGTTCCAGGGGAAATGTTTTCCATTATTATTCAGAGAATATCTACCATGTCATAATGTT
*
1394760 CTATCCCATCCAAAATG-AAAGGTGCATCCTAGGGAA
130 CCATCCCATCCAAAATGAAAAGGTG-ATCC-AGGG-A
* **
1394796 AGTGTTTTCCATTATTATTCAGAGAATCTCTAT-CATGTCATAGTGTTTCATCCCATTAAAAATG
1 AGTGTTTTCCATTATTATTCAGAGAAT-T-TTTCCATGTCATAGTGTTTCATCCCATTCGAAATG
** *
1394860 AAAGGTGCGTTCCAGGGGAAACATTTTCCATTATTATTTAGAGAA
64 AAAGGTGCGTTCCAGGGGAAATGTTTTCCATTATTATTCAGAGAA
1394905 AATTTACAGT
Statistics
Matches: 233, Mismatches: 32, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
162 5 0.02
163 3 0.01
164 57 0.24
165 150 0.64
166 16 0.07
167 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (163 bp):
AGTGTTTTCCATTATTATTCAGAGAATTTTTCCATGTCATAGTGTTTCATCCCATTCGAAATGAA
AGGTGCGTTCCAGGGGAAATGTTTTCCATTATTATTCAGAGAATATCTACCATGTCATAATGTTC
CATCCCATCCAAAATGAAAAGGTGATCCAGGGA
Found at i:1395835 original size:18 final size:18
Alignment explanation
Indices: 1395808--1395880 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
1395798 ACTGAATATT
1395808 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1395826 TGTCCTGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
1395845 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
1395864 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1395881 GTTTGTCTCG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 31 0.66
19 2 0.04
20 14 0.30
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1395855 original size:38 final size:38
Alignment explanation
Indices: 1395807--1395900 Score: 127
Period size: 38 Copynumber: 2.5 Consensus size: 38
1395797 CACTGAATAT
* *
1395807 TTGTCCCGAAGGACCACTATGTCCTGAAGGACCACTGA
1 TTGTTCCGAAGGACCACTATGTCCCGAAGGACCACTGA
* *
1395845 TTGTTCCGAAGAACCACTATGTCCCGAAGGACCACTGT
1 TTGTTCCGAAGGACCACTATGTCCCGAAGGACCACTGA
*
1395883 TTG-TCTCGAATGACCACT
1 TTGTTC-CGAAGGACCACT
1395901 GATAATCCCT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
37 2 0.04
38 47 0.96
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (38 bp):
TTGTTCCGAAGGACCACTATGTCCCGAAGGACCACTGA
Found at i:1395860 original size:20 final size:20
Alignment explanation
Indices: 1395807--1395903 Score: 89
Period size: 18 Copynumber: 5.0 Consensus size: 20
1395797 CACTGAATAT
*
1395807 TTGTCCCGAAGGACCACT-A
1 TTGTTCCGAAGGACCACTGA
1395826 -TG-TCCTGAAGGACCACTGA
1 TTGTTCC-GAAGGACCACTGA
*
1395845 TTGTTCCGAAGAACCACT-A
1 TTGTTCCGAAGGACCACTGA
* *
1395864 -TGTCCCGAAGGACCACTGT
1 TTGTTCCGAAGGACCACTGA
*
1395883 TTG-TCTCGAATGACCACTGA
1 TTGTTC-CGAAGGACCACTGA
1395903 T
1 T
1395904 AATCCCTCGA
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
17 2 0.03
18 28 0.44
19 3 0.05
20 27 0.43
21 3 0.05
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (20 bp):
TTGTTCCGAAGGACCACTGA
Found at i:1396321 original size:21 final size:21
Alignment explanation
Indices: 1396297--1396336 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1396287 AAATCTAAAT
**
1396297 ATCATATATTTTTCATATATA
1 ATCATATATACTTCATATATA
1396318 ATCATATATACTTCATATA
1 ATCATATATACTTCATATA
1396337 GTACATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (21 bp):
ATCATATATACTTCATATATA
Found at i:1402639 original size:23 final size:23
Alignment explanation
Indices: 1402613--1402662 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
1402603 GTAAATGAGG
1402613 AGGTTAACCCCTAATCTGAGTGA
1 AGGTTAACCCCTAATCTGAGTGA
1402636 AGGTTAACCCCTAATCTGAGTGA
1 AGGTTAACCCCTAATCTGAGTGA
1402659 AGGT
1 AGGT
1402663 CACTCTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (23 bp):
AGGTTAACCCCTAATCTGAGTGA
Found at i:1404482 original size:22 final size:22
Alignment explanation
Indices: 1404434--1404494 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
1404424 GGGTCTACGC
1404434 GGTCCTTCGGGACATATACACA
1 GGTCCTTCGGGACATATACACA
* * * *
1404456 AGTCCTTCGGGATATATGCATA
1 GGTCCTTCGGGACATATACACA
* *
1404478 GGTCCTACGTGACATAT
1 GGTCCTTCGGGACATAT
1404495 TTCACATGCC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (22 bp):
GGTCCTTCGGGACATATACACA
Found at i:1404945 original size:14 final size:14
Alignment explanation
Indices: 1404926--1404961 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
1404916 ATGAGAATTT
1404926 AGATAAATTAATGG
1 AGATAAATTAATGG
1404940 AGATAAATTAATGG
1 AGATAAATTAATGG
1404954 AGATAAAT
1 AGATAAAT
1404962 AAATAATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (14 bp):
AGATAAATTAATGG
Found at i:1405280 original size:7 final size:7
Alignment explanation
Indices: 1405268--1405292 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1405258 GAAGTATATG
1405268 GATATAA
1 GATATAA
1405275 GATATAA
1 GATATAA
1405282 GATATAA
1 GATATAA
1405289 GATA
1 GATA
1405293 GATGACTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (7 bp):
GATATAA
Found at i:1405325 original size:35 final size:35
Alignment explanation
Indices: 1405244--1405325 Score: 84
Period size: 35 Copynumber: 2.4 Consensus size: 35
1405234 AGTCTATAGG
1405244 TTATATGA-TAA-ATAGAAGTATATGGATATAAGA
1 TTATATGATTAAGATAGAAGTATATGGATATAAGA
* *
1405277 -TATAAGATATAAGATAGATG-ACTAT-GATATAGAGA
1 TTATATGAT-TAAGATAGAAGTA-TATGGATATA-AGA
1405312 TTATATGATTAAGA
1 TTATATGATTAAGA
1405326 ATTGTAAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
32 6 0.15
34 10 0.25
35 17 0.43
36 7 0.17
ACGTcount: A:0.48, C:0.01, G:0.18, T:0.33
Consensus pattern (35 bp):
TTATATGATTAAGATAGAAGTATATGGATATAAGA
Found at i:1406777 original size:2 final size:2
Alignment explanation
Indices: 1406770--1406804 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1406760 GTTGGTTTAT
1406770 TA 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 T
1406805 GCAAAGCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1411942 original size:2 final size:2
Alignment explanation
Indices: 1411935--1411966 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
1411925 ATTGAAAATA
1411935 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
1411967 AAGAAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1414920 original size:16 final size:16
Alignment explanation
Indices: 1414896--1414928 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1414886 AAGTAGAAAC
1414896 GAGTCTGAGCATTCAT
1 GAGTCTGAGCATTCAT
*
1414912 GAGTTTGAGCATTCAT
1 GAGTCTGAGCATTCAT
1414928 G
1 G
1414929 GCAGGGGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.33
Consensus pattern (16 bp):
GAGTCTGAGCATTCAT
Found at i:1417466 original size:22 final size:22
Alignment explanation
Indices: 1417433--1417476 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1417423 TGTATGATAG
1417433 AGATCTATGGAGCCATATGAAA
1 AGATCTATGGAGCCATATGAAA
**
1417455 AGAT-TATAGGAGTTATATGAAA
1 AGATCTAT-GGAGCCATATGAAA
1417477 TTGAATTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (22 bp):
AGATCTATGGAGCCATATGAAA
Found at i:1417739 original size:16 final size:17
Alignment explanation
Indices: 1417708--1417741 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1417698 GAAAATGATT
*
1417708 TATGTGTTTATATGTAA
1 TATGTGATTATATGTAA
1417725 TATGTGATT-TATGTAA
1 TATGTGATTATATGTAA
1417741 T
1 T
1417742 CATTAGTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (17 bp):
TATGTGATTATATGTAA
Found at i:1418114 original size:30 final size:31
Alignment explanation
Indices: 1418047--1418134 Score: 115
Period size: 31 Copynumber: 2.9 Consensus size: 31
1418037 TAGTCGAGGG
* * *
1418047 TTACCTATGTCTTTCGAGACATATGGATAAT
1 TTACCTATGTCCTTCGGGACATATGGACAAT
*
1418078 TTACCTATGTCCTTAGGGACATATGGACAA-
1 TTACCTATGTCCTTCGGGACATATGGACAAT
* *
1418108 TTACCTATGTTCTTCGGAACATATGGA
1 TTACCTATGTCCTTCGGGACATATGGA
1418135 TAGTGGTCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 24 0.48
31 26 0.52
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (31 bp):
TTACCTATGTCCTTCGGGACATATGGACAAT
Found at i:1423939 original size:16 final size:17
Alignment explanation
Indices: 1423906--1423950 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
1423896 ACAAATATTT
1423906 TAAAAAAATGAAATTGAA
1 TAAAAAAAT-AAATTGAA
1423924 TAAAAAAATAAA-TGAA
1 TAAAAAAATAAATTGAA
*
1423940 GAAAAAAATAA
1 TAAAAAAATAA
1423951 TATATATACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 14 0.54
17 3 0.12
18 9 0.35
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (17 bp):
TAAAAAAATAAATTGAA
Found at i:1424057 original size:13 final size:13
Alignment explanation
Indices: 1424041--1424100 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
1424031 CATAATGAAA
*
1424041 ATAAATAAATAGT
1 ATAAATAAATAAT
1424054 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
1424068 A-AAATAAAATAA-
1 ATAAAT-AAATAAT
*
1424080 ATATATAAA-AAT
1 ATAAATAAATAAT
1424092 ATAAA-AAAT
1 ATAAATAAAT
1424101 GTATGTATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
11 5 0.12
12 8 0.20
13 20 0.50
14 7 0.17
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.27
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:1424072 original size:22 final size:22
Alignment explanation
Indices: 1424038--1424082 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1424028 AAACATAATG
**
1424038 AAAATAAATAAATAGTATAAAT
1 AAAATAAATAAATAAAATAAAT
1424060 AAAAT-AATAAAATAAAATAAAT
1 AAAATAAAT-AAATAAAATAAAT
1424082 A
1 A
1424083 TATAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAATAAATAAATAAAATAAAT
Found at i:1424072 original size:26 final size:26
Alignment explanation
Indices: 1424043--1424150 Score: 66
Period size: 26 Copynumber: 4.1 Consensus size: 26
1424033 TAATGAAAAT
1424043 AAATAAATAGTATAAATAAAATAATA
1 AAATAAATAGTATAAATAAAATAATA
* *
1424069 AAATAAAATA-AATATATAAAA-ATATA
1 AAAT-AAATAGTATAAATAAAATA-ATA
*
1424095 AAA-AATGTATGTAT-AATAAAATAA-A
1 AAATAA-ATA-GTATAAATAAAATAATA
*
1424120 ATACTAAATAGTA-ACAATAATAATAAATA
1 A-AATAAATAGTATA-AATAA-AAT-AATA
1424149 AA
1 AA
1424151 TGAAAAATAA
Statistics
Matches: 62, Mismatches: 7, Indels: 24
0.67 0.08 0.26
Matches are distributed among these distances:
24 2 0.03
25 8 0.13
26 34 0.55
27 13 0.21
28 3 0.05
29 2 0.03
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (26 bp):
AAATAAATAGTATAAATAAAATAATA
Found at i:1424232 original size:2 final size:2
Alignment explanation
Indices: 1424225--1424251 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1424215 TAGAGTAAGA
1424225 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1424252 ATGTTAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1424320 original size:8 final size:8
Alignment explanation
Indices: 1424307--1424449 Score: 53
Period size: 8 Copynumber: 16.9 Consensus size: 8
1424297 TAGATAAAAA
1424307 ATAATAAT
1 ATAATAAT
1424315 ATAATATAT
1 ATAATA-AT
1424324 ATATATATAT
1 ATA-ATA-AT
1424334 ATAATAAT
1 ATAATAAT
* *
1424342 AGAAAAAT
1 ATAATAAT
1424350 A-ATATAAT
1 ATA-ATAAT
* *
1424358 ATAACACAA
1 ATAATA-AT
* *
1424367 AGAAAAAT
1 ATAATAAT
* *
1424375 GAAAAAAAATT
1 --ATAATAA-T
1424386 ATAATAA-
1 ATAATAAT
1424393 ATAAATAA-
1 AT-AATAAT
1424401 ATAA-AAT
1 ATAATAAT
*
1424408 ATAATTAT
1 ATAATAAT
1424416 AT-ATATAT
1 ATAATA-AT
1424424 ATAATATAT
1 ATAATA-AT
1424433 ATATATATAT
1 ATA-ATA-AT
1424443 ATAATAA
1 ATAATAA
1424450 GGGTTAAATT
Statistics
Matches: 108, Mismatches: 13, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
6 2 0.02
7 11 0.10
8 39 0.36
9 31 0.29
10 24 0.22
11 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (8 bp):
ATAATAAT
Found at i:1424420 original size:2 final size:2
Alignment explanation
Indices: 1424413--1424445 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1424403 AAAATATAAT
1424413 TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1424446 ATAAGGGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1424881 original size:37 final size:37
Alignment explanation
Indices: 1424840--1424932 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
1424830 ATGCTTGTGG
* * *
1424840 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
* ** *
1424877 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
*
1424914 ATCATATTTTTAGGAGTTT
1 ATCCTATTTTTAGGAGTTT
1424933 GAATCCTAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
Found at i:1430610 original size:64 final size:65
Alignment explanation
Indices: 1430494--1430618 Score: 184
Period size: 64 Copynumber: 1.9 Consensus size: 65
1430484 GAATGCATTT
*
1430494 CATGCATCGATGCACTCAGAGTTTTATGAAATCATCGAATGAATTTGATGCATCGATGCACCAGC
1 CATGCATCGATGCACTCAGAGTTTTATGAAATCATCGAATGAATTTCATGCATCGATGCACCAGC
* *
1430559 CATGCATCGATGCACTCTG-GCTATTT-TGAAA-CATCGAATGCATTTCATGCATCGATGCAC
1 CATGCATCGATGCACTCAGAG-T-TTTATGAAATCATCGAATGAATTTCATGCATCGATGCAC
1430619 TCTTAGTGCA
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
64 28 0.51
65 24 0.44
66 3 0.05
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (65 bp):
CATGCATCGATGCACTCAGAGTTTTATGAAATCATCGAATGAATTTCATGCATCGATGCACCAGC
Found at i:1430710 original size:13 final size:13
Alignment explanation
Indices: 1430692--1430716 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1430682 CCGATGCACC
1430692 TTGAATTTTACAT
1 TTGAATTTTACAT
1430705 TTGAATTTTACA
1 TTGAATTTTACA
1430717 CATGTCGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
TTGAATTTTACAT
Found at i:1431318 original size:29 final size:28
Alignment explanation
Indices: 1431286--1431343 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
1431276 GGATGTTTAA
1431286 ATTTGATGGTTGT-TGGATGTTTTGAACTT
1 ATTTG-TGGTTGTATGGAT-TTTTGAACTT
* *
1431315 ATTTGTTGTTTTATGGATTTTTGAACTT
1 ATTTGTGGTTGTATGGATTTTTGAACTT
1431343 A
1 A
1431344 ATATTTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.55
Consensus pattern (28 bp):
ATTTGTGGTTGTATGGATTTTTGAACTT
Found at i:1432118 original size:46 final size:45
Alignment explanation
Indices: 1432049--1432168 Score: 154
Period size: 45 Copynumber: 2.6 Consensus size: 45
1432039 TAAATTGAAT
*
1432049 ATCGAATGTATTTCATGCATCGATGCACTCAGAG-T-TTTACGAAAAC
1 ATCGAATGCATTTCATGCATCGATGCACTCAG-GCTATTT-CG-AAAC
* * * *
1432095 ATCGAATGCATTTGATGCCTCGATGCACTCTGGCTATTTTGAAAC
1 ATCGAATGCATTTCATGCATCGATGCACTCAGGCTATTTCGAAAC
1432140 ATCGAATGCATTTCATGCATCGATGCACT
1 ATCGAATGCATTTCATGCATCGATGCACT
1432169 AAGGGTCCAA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
45 32 0.49
46 30 0.46
47 3 0.05
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (45 bp):
ATCGAATGCATTTCATGCATCGATGCACTCAGGCTATTTCGAAAC
Found at i:1438712 original size:2 final size:2
Alignment explanation
Indices: 1438705--1438753 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
1438695 ATATTAAATA
1438705 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1438747 AT CT AT A
1 AT AT AT A
1438754 CTTGCACGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1440689 original size:64 final size:65
Alignment explanation
Indices: 1440589--1440715 Score: 213
Period size: 63 Copynumber: 2.0 Consensus size: 65
1440579 TATAAATTAA
1440589 ATATCTATAATATAATATTAAAATGAATATTTAATTTATTTAAAAAATTAATATTAAAATTAATA
1 ATATCTATAATATAATATTAAAATGAATATTTAATTTATTT-AAAAATTAATATTAAAATTAATA
1440654 T
65 T
* *
1440655 ATATCTAT-ATATATTATT-AAATTAATATTTAATTTATTTAAAAATTAATATTAAAATTAAT
1 ATATCTATAATATAATATTAAAATGAATATTTAATTTATTTAAAAATTAATATTAAAATTAAT
1440716 CAATATAATA
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
63 22 0.37
64 20 0.34
65 9 0.15
66 8 0.14
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (65 bp):
ATATCTATAATATAATATTAAAATGAATATTTAATTTATTTAAAAATTAATATTAAAATTAATAT
Found at i:1442137 original size:112 final size:112
Alignment explanation
Indices: 1441922--1442606 Score: 1099
Period size: 112 Copynumber: 6.1 Consensus size: 112
1441912 TTTTCGGTTT
* *
1441922 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
1441986 GGTCTATAAATGAAAAAACAGGTAAAACGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
1442033 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1442098 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1442145 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAAAGAC-AAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
* * *
1442209 TGGTCTATAAATGACAAAACAAGTAAAGCGCTACCAGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1442257 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGG-CAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1442321 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
1442368 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAAGAAAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
1442433 GGTTTATAAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * ** *
1442480 GTATCGATATTTTATAAAAATGTATTAATCCATAACAATATAACAGGTAAACAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
1442545 GGTCTATAAATGACAAAACAGCTCAAA-CGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGT-AAAGCGCTACCGGATATATTGAAA
*
1442592 GTGTCGATATTTTAT
1 GTGTCGATACTTTAT
1442607 TATAAGTATA
Statistics
Matches: 534, Mismatches: 35, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
110 9 0.02
111 143 0.27
112 370 0.69
113 12 0.02
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:1442322 original size:223 final size:222
Alignment explanation
Indices: 1441922--1442606 Score: 1086
Period size: 223 Copynumber: 3.1 Consensus size: 222
1441912 TTTTCGGTTT
* * * *
1441922 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAAGAC-AAACT
* *
1441986 GGTCTATAAATGAAAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
65 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
* *
1442051 AATATATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAACCGGTCTATAAATGACAAAA
130 AATGTATCGATCCATAACAATATAACAGG-AAAAAAATGACAAAACCGGTCTATAAATGACAAAA
1442116 CAGGTAAAGCGCTACCGGATATATTGAAA
194 CAGGTAAAGCGCTACCGGATATATTGAAA
1442145 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAAAGACAAACT
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAAAGACAAACT
* *
1442210 GGTCTATAAATGACAAAACAAGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTATAAA
65 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
*
1442275 AATGTATCGATCCATAACAATATAACAGGCAAAAAATGACAAAACCGGTCTATAAATGACAAAAC
130 AATGTATCGATCCATAACAATATAACAGGAAAAAAATGACAAAACCGGTCTATAAATGACAAAAC
1442340 AGGTAAAGCGCTACCGGATATATTGAAA
195 AGGTAAAGCGCTACCGGATATATTGAAA
* *
1442368 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAAGAAAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAAGACAAACT-
* * * *
1442433 GGTTTATAAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAAAGTATCGATATTTTATAAA
65 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
** *
1442498 AATGTATTAATCCATAACAATATAACAGGTAAACAAATGACAAAACCGGTCTATAAATGACAAAA
130 AATGTATCGATCCATAACAATATAACAGG-AAAAAAATGACAAAACCGGTCTATAAATGACAAAA
* * *
1442563 CAGCTCAAA-CGCTACCGGATATGTTGATA
194 CAGGT-AAAGCGCTACCGGATATATTGAAA
*
1442592 GTGTCGATATTTTAT
1 GTGTCGATACTTTAT
1442607 TATAAGTATA
Statistics
Matches: 430, Mismatches: 27, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
222 14 0.03
223 242 0.56
224 162 0.38
225 12 0.03
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (222 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAAGACAAACTG
GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
ATGTATCGATCCATAACAATATAACAGGAAAAAAATGACAAAACCGGTCTATAAATGACAAAACA
GGTAAAGCGCTACCGGATATATTGAAA
Found at i:1442551 original size:335 final size:335
Alignment explanation
Indices: 1441922--1442606 Score: 1124
Period size: 335 Copynumber: 2.0 Consensus size: 335
1441912 TTTTCGGTTT
* *
1441922 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGCAAAAAATGACAAAACCG
1441987 GTCTATAAATGAAAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
66 GTCTATAAATGAAAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
* *
1442052 ATATATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAACCGGTCTATAAATGACAAAAC
131 ATATATCGATCCATAACAATATAACAGGTAAAAAAAAGAAAAAACCGGTCTATAAATGACAAAAC
* *
1442117 AGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACA
196 AGGTAAAGCGCTACCGGATATATTGAAAGTATCGATACTTTATAAAAATGTATCAATCCATAACA
*
1442182 ATATAACAGGTAAAAAAAAAGACAAACTGGTCTATAAATGACAAAACAAG-T-AAAGCGCTACCA
261 ATATAACAGGTAAAAAAAAAGACAAACCGGTCTATAAATGACAAAAC-AGCTCAAA-CGCTACCA
1442245 GATATATTGAAA
324 GATATATTGAAA
*
1442257 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGCAAAAAATGACAAAACCG
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGCAAAAAATGACAAAACCG
* *
1442322 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
66 GTCTATAAATGAAAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
* * *
1442387 ATGTATCGATCCATAACAATATAACAGGTAAAAAAAAGAAAAAATCGGTTTATAAATGACAAAAC
131 ATATATCGATCCATAACAATATAACAGGTAAAAAAAAGAAAAAACCGGTCTATAAATGACAAAAC
* * *
1442452 AGGTAAAGCGCTATCGGATATATTGAAAGTATCGATATTTTATAAAAATGTATTAATCCATAACA
196 AGGTAAAGCGCTACCGGATATATTGAAAGTATCGATACTTTATAAAAATGTATCAATCCATAACA
* * *
1442517 ATATAACAGGT-AAACAAATGACAAAACCGGTCTATAAATGACAAAACAGCTCAAACGCTACCGG
261 ATATAACAGGTAAAAAAAAAGAC-AAACCGGTCTATAAATGACAAAACAGCTCAAACGCTACCAG
* *
1442581 ATATGTTGATA
325 ATATATTGAAA
*
1442592 GTGTCGATATTTTAT
1 GTGTCGATACTTTAT
1442607 TATAAGTATA
Statistics
Matches: 325, Mismatches: 22, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
334 11 0.03
335 311 0.96
336 3 0.01
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (335 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGCAAAAAATGACAAAACCG
GTCTATAAATGAAAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
ATATATCGATCCATAACAATATAACAGGTAAAAAAAAGAAAAAACCGGTCTATAAATGACAAAAC
AGGTAAAGCGCTACCGGATATATTGAAAGTATCGATACTTTATAAAAATGTATCAATCCATAACA
ATATAACAGGTAAAAAAAAAGACAAACCGGTCTATAAATGACAAAACAGCTCAAACGCTACCAGA
TATATTGAAA
Found at i:1442797 original size:182 final size:181
Alignment explanation
Indices: 1442483--1442925 Score: 649
Period size: 182 Copynumber: 2.4 Consensus size: 181
1442473 ATTGAAAGTA
*
1442483 TCGATATTTTATAAAAATGTATTAATCCATAACAATATAACAGGTAAACAA-ATGACAAAACCGG
1 TCGATACTTTATAAAAATGTATTAATCCATAACAATATAACA-GTAAA-AATATGACAAAACCGG
** * * *
1442547 TCTATAAATGACAAAACAGCTCAAACGCTACCGGATATGTTGATAGTGTCGATATTTTATTATAA
64 TCTCGAAATGACAAAACAGCTCAAAAGCTACCGGATATGTTGAAAGTGTCGATACTTTATTATAA
* * *
1442612 GTATAGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGTACTAATAAAATG
129 GTATAGACACTTTTGGAATTTAAAAGAAAAAAAGTTATAGCACCAATAAAATG
*
1442665 TCGATACTTTATAAAAATGTATTAATCCATAACAATATAACAGTTAAAAATATGACAAAACCAGT
1 TCGATACTTTATAAAAATGTATTAATCCATAACAATATAACAG-TAAAAATATGACAAAACCGGT
* *
1442730 CTCGAAATGACAAAATC-GGT-AAAGAGCTACCGTATATGTTGAAAGTGTCGATACTTTATTATA
65 CTCGAAATGACAAAA-CAGCTCAAA-AGCTACCGGATATGTTGAAAGTGTCGATACTTTATTATA
* * *
1442793 AGTATCGACACTTTTGGAATTTAAAAGAAAAAAAGTTATAGCGCCAATAAAGTG
128 AGTATAGACACTTTTGGAATTTAAAAGAAAAAAAGTTATAGCACCAATAAAATG
** *
1442847 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAATCGGT
1 TCGATACTTTATAAAAATGTATTAATCCATAACAATATAAC-AGTAAAAATATGACAAAACCGGT
1442912 CTCGAAATGACAAA
65 CTCGAAATGACAAA
1442926 GCCGATAGTA
Statistics
Matches: 237, Mismatches: 19, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
181 6 0.03
182 228 0.96
183 3 0.01
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.28
Consensus pattern (181 bp):
TCGATACTTTATAAAAATGTATTAATCCATAACAATATAACAGTAAAAATATGACAAAACCGGTC
TCGAAATGACAAAACAGCTCAAAAGCTACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGT
ATAGACACTTTTGGAATTTAAAAGAAAAAAAGTTATAGCACCAATAAAATG
Found at i:1443508 original size:23 final size:23
Alignment explanation
Indices: 1443479--1443526 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1443469 AAATAAGTCA
*
1443479 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
*
1443502 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
1443525 AT
1 AT
1443527 TGTATTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:1447961 original size:15 final size:15
Alignment explanation
Indices: 1447941--1447978 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1447931 GCCCAAAGCT
1447941 GAGAAGAAGCCAGCC
1 GAGAAGAAGCCAGCC
*
1447956 GAGAAGAAGCCGGCC
1 GAGAAGAAGCCAGCC
*
1447971 GAGGAGAA
1 GAGAAGAA
1447979 AAAGACAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.39, C:0.21, G:0.39, T:0.00
Consensus pattern (15 bp):
GAGAAGAAGCCAGCC
Found at i:1448551 original size:30 final size:30
Alignment explanation
Indices: 1448483--1448557 Score: 125
Period size: 29 Copynumber: 2.5 Consensus size: 30
1448473 CAGTCCCGGG
1448483 GGTAGGTCGCCATGCACGCCCAGCGACCTA
1 GGTAGGTCGCCATGCACGCCCAGCGACCTA
**
1448513 -CCAGGTCGCCATGCACGCCCAGCGACCTA
1 GGTAGGTCGCCATGCACGCCCAGCGACCTA
1448542 GGTAGGTCGCCATGCA
1 GGTAGGTCGCCATGCA
1448558 ATCCATGCAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 27 0.68
30 13 0.32
ACGTcount: A:0.20, C:0.37, G:0.29, T:0.13
Consensus pattern (30 bp):
GGTAGGTCGCCATGCACGCCCAGCGACCTA
Found at i:1448799 original size:42 final size:42
Alignment explanation
Indices: 1448752--1448834 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
1448742 ATGTCGGCAT
*
1448752 GGCAACGTGGCATGGGTCTGGGCGAGGTTGGAGTCTCTGCAC
1 GGCAACGTGGCATGGGTCTGGGCAAGGTTGGAGTCTCTGCAC
1448794 GGCAACGTGGCATGGGTCTGGGCAAGGTTGGAGTCTCTGCA
1 GGCAACGTGGCATGGGTCTGGGCAAGGTTGGAGTCTCTGCA
1448835 TGGCTGTGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.16, C:0.20, G:0.42, T:0.22
Consensus pattern (42 bp):
GGCAACGTGGCATGGGTCTGGGCAAGGTTGGAGTCTCTGCAC
Found at i:1448905 original size:29 final size:28
Alignment explanation
Indices: 1448863--1448941 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 28
1448853 TGCAACGTGG
*
1448863 GTAGGTCGCTAGGGAATCCCAGCGACATT
1 GTAGGTCGCCAGGG-ATCCCAGCGACATT
1448892 GTAGGTCGCCAGGGTATCCCAGCGACATT
1 GTAGGTCGCCAGGG-ATCCCAGCGACATT
*
1448921 GTAGGTTGCCAAGGGATCCCA
1 GTAGGTCGCC-AGGGATCCCA
1448942 ACAACCTATG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 42 0.91
30 4 0.09
ACGTcount: A:0.23, C:0.25, G:0.32, T:0.20
Consensus pattern (28 bp):
GTAGGTCGCCAGGGATCCCAGCGACATT
Found at i:1449395 original size:28 final size:27
Alignment explanation
Indices: 1449356--1449408 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
1449346 ATATTAAAAA
1449356 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
1449384 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
1449409 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:1449414 original size:27 final size:29
Alignment explanation
Indices: 1449355--1449419 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
1449345 TATATTAAAA
1449355 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
1449384 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
1449410 AAATAGTTAA
1 AAATAATTAA
1449420 GTTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:1449558 original size:18 final size:18
Alignment explanation
Indices: 1449535--1449589 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
1449525 AATAATTATT
1449535 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
1449553 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
1449565 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
1449582 TAAATTAG
1 TAAATTAG
1449590 GGTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:1449642 original size:21 final size:21
Alignment explanation
Indices: 1449617--1449656 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1449607 GTTAATTAGT
1449617 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
1449638 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
1449657 CATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:1449885 original size:29 final size:30
Alignment explanation
Indices: 1449852--1449936 Score: 131
Period size: 30 Copynumber: 2.9 Consensus size: 30
1449842 TAGTAGTAAA
1449852 TTATAATTAAA-AATCA-TTTATTAGTTAAT-
1 TTAT-ATTAAAGAAT-AGTTTATTAGTTAATG
1449881 TTATATTAAAGAATAGTTTATTAGTTAATG
1 TTATATTAAAGAATAGTTTATTAGTTAATG
1449911 TTATATTAAAGAATAGTTTATTAGTT
1 TTATATTAAAGAATAGTTTATTAGTT
1449937 GTTTAAGGGA
Statistics
Matches: 53, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
28 7 0.13
29 20 0.38
30 26 0.49
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.48
Consensus pattern (30 bp):
TTATATTAAAGAATAGTTTATTAGTTAATG
Found at i:1449917 original size:30 final size:29
Alignment explanation
Indices: 1449834--1449936 Score: 129
Period size: 30 Copynumber: 3.4 Consensus size: 29
1449824 ATTAGTTAAT
* *
1449834 TAGTTTTTTAGTAGTAAATTATAATTAAA-AA
1 TAGTTTATTAGT--TAATTTAT-ATTAAAGAA
1449865 TCA-TTTATTAGTTAATTTATATTAAAGAA
1 T-AGTTTATTAGTTAATTTATATTAAAGAA
1449894 TAGTTTATTAGTTAATGTTATATTAAAGAA
1 TAGTTTATTAGTTAAT-TTATATTAAAGAA
1449924 TAGTTTATTAGTT
1 TAGTTTATTAGTT
1449937 GTTTAAGGGA
Statistics
Matches: 66, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
28 7 0.11
29 23 0.35
30 26 0.39
31 9 0.14
32 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.11, T:0.49
Consensus pattern (29 bp):
TAGTTTATTAGTTAATTTATATTAAAGAA
Found at i:1449932 original size:15 final size:15
Alignment explanation
Indices: 1449884--1449933 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1449874 AGTTAATTTA
1449884 TATTAAAGAATAGTT
1 TATTAAAGAATAGTT
***
1449899 TATTAGTTAAT-GTT
1 TATTAAAGAATAGTT
1449913 ATATTAAAGAATAGTT
1 -TATTAAAGAATAGTT
1449929 TATTA
1 TATTA
1449934 GTTGTTTAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 3 0.11
15 21 0.78
16 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (15 bp):
TATTAAAGAATAGTT
Found at i:1452272 original size:14 final size:14
Alignment explanation
Indices: 1452253--1452345 Score: 84
Period size: 14 Copynumber: 6.6 Consensus size: 14
1452243 TTCAAGTAGT
1452253 AAATCATTACTATC
1 AAATCATTACTATC
1452267 AAATCATTAC--T-
1 AAATCATTACTATC
*
1452278 AAATCATTAATATC
1 AAATCATTACTATC
* *
1452292 AAATCATTAATATA
1 AAATCATTACTATC
* *
1452306 ATAATAATTATTATTAC
1 A-AATCATTACTA-T-C
*
1452323 TAATCATTACTATC
1 AAATCATTACTATC
1452337 AAATCATTA
1 AAATCATTA
1452346 AAAATTAATA
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
11 9 0.14
12 1 0.02
13 1 0.02
14 33 0.52
15 10 0.16
16 10 0.16
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:1452280 original size:25 final size:25
Alignment explanation
Indices: 1452252--1452345 Score: 92
Period size: 25 Copynumber: 4.0 Consensus size: 25
1452242 GTTCAAGTAG
1452252 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTACTATCAAATCATTAC
* *
1452277 TAAATCATTAATATCAAATCATTAA
1 TAAATCATTACTATCAAATCATTAC
* * *
1452302 TATAAT-AATA--AT--TATTATTAC
1 TA-AATCATTACTATCAAATCATTAC
1452323 T-AATCATTACTATCAAATCATTA
1 TAAATCATTACTATCAAATCATTA
1452346 AAAATTAATA
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.06
20 3 0.06
21 7 0.13
22 2 0.04
23 2 0.04
24 6 0.11
25 28 0.52
26 3 0.06
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (25 bp):
TAAATCATTACTATCAAATCATTAC
Found at i:1452377 original size:49 final size:49
Alignment explanation
Indices: 1452272--1452552 Score: 300
Period size: 60 Copynumber: 5.3 Consensus size: 49
1452262 CTATCAAATC
* *
1452272 ATTACTAAATCATTAATATCAAATCATT-AATA-TAATAATAA-TT-ATT
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1452318 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
1452367 ATTACTAATCATTACTAAATCATTACTATCAAATAATTAAAAATTAATAATGATTTCATT
1 ATTACTAATCATTACT--ATCA--A--ATC-----ATTAAAAATTAATAATAATTTCATT
1452427 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAAT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC------A-T--T
1452485 CATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 -ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1452536 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
1452553 AATCATTAAT
Statistics
Matches: 205, Mismatches: 4, Indels: 49
0.79 0.02 0.19
Matches are distributed among these distances:
45 20 0.10
46 9 0.04
47 9 0.04
48 2 0.01
49 51 0.25
50 6 0.03
51 5 0.02
53 2 0.01
54 4 0.02
55 4 0.02
56 2 0.01
58 5 0.02
59 6 0.03
60 80 0.39
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
Found at i:1452449 original size:109 final size:108
Alignment explanation
Indices: 1452268--1452830 Score: 680
Period size: 109 Copynumber: 5.1 Consensus size: 108
1452258 ATTACTATCA
* *
1452268 AATCATTACTAAATCATTAATATCAAATCATT-AATA-TAATAATAA-TT-ATTATTACTAATCA
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
1452329 TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
66 TTACTAT-AAATCATTAAAAATTAATAATAATTTCATTATTACT
* *
1452373 AATCATTACTAAATCATTACTATCAAATAATTAAAAATTAATAATGATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
1452438 TTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
66 TTACTAT-AAATCATTAAAAATTAATAATAATTTCATTATTACT
1452482 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
* * * * * *
1452547 TTAC--TAAATCATT-AATATCAAATCATTAA-AT-ATTAATAAT
66 TTACTATAAATCATTAAAAAT-TAAT-AATAATTTCATTATTACT
*
1452587 AATTTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTA
1 AA--TCATTACTA--AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTA
* ** * *
1452652 ATCATTAC--TAAATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAAT
62 ATCATTACTATAAATCATTA--AAA--ATTA--AT--AATAATT--TCATTATTACT
* *
1452707 GATTTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTA
1 -A-ATCATTACTA--AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTA
1452772 ATCATTACTATTAAATCATTAAAAATTAATAATAATTTCATTATTACT
62 ATCATTACTA-TAAATCATTAAAAATTAATAATAATTTCATTATTACT
1452820 AATCATTACTA
1 AATCATTACTA
1452831 TCAAATCATT
Statistics
Matches: 403, Mismatches: 28, Indels: 48
0.84 0.06 0.10
Matches are distributed among these distances:
105 43 0.11
106 15 0.04
107 21 0.05
108 2 0.00
109 192 0.48
111 8 0.02
112 3 0.01
113 8 0.02
114 2 0.00
115 8 0.02
116 3 0.01
117 2 0.00
119 4 0.01
120 78 0.19
121 4 0.01
123 10 0.02
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (108 bp):
AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
TTACTATAAATCATTAAAAATTAATAATAATTTCATTATTACT
Found at i:1452497 original size:60 final size:60
Alignment explanation
Indices: 1452427--1452732 Score: 419
Period size: 60 Copynumber: 5.1 Consensus size: 60
1452417 TGATTTCATT
1452427 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1452486 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* *
1452546 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* * * * * * *
1452606 ATTACTATCAAATCATTA--A--AAATTAATAATAATT--TCATTATTACTAATCATTACTAAAT
1 ATTAC--T-AAATCATTACTATCAAATCATTAAAAATTAATAATAATT--TCATTATTACT-AAT
1452665 C
60 C
*
1452666 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATGATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1452726 ATTACTA
1 ATTACTA
1452733 TCAAATCATT
Statistics
Matches: 217, Mismatches: 17, Indels: 25
0.84 0.07 0.10
Matches are distributed among these distances:
57 15 0.07
58 1 0.00
59 27 0.12
60 136 0.63
61 22 0.10
62 1 0.00
63 15 0.07
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:1452503 original size:169 final size:168
Alignment explanation
Indices: 1452318--1452883 Score: 813
Period size: 169 Copynumber: 3.4 Consensus size: 168
1452308 AATAATTATT
1452318 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
* *
1452383 AAATCATTACTATCAAATAATTAAAAATTAATAATGATTTCATTATTACTAATCATTACTATCAA
66 AAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATCAA
1452448 ATCATTAAAAATTAATAATAATTTCATTATTACTAATC
131 ATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1452486 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
* *
1452551 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTATCA
65 TAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATCA
1452616 AATCATTAAAAATTAATAATAATTTCATTATTACTAATC
130 AATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* * * * * *
1452655 ATTACTAAATCATTAC--T-AAATCATTACTATCAAATCATTAAAAATTAATAATGATT--TCAT
1 ATTACT-AATCATTACTATCAAATCATTA--A--AAATTAATAATAATT--TCATTATTACTAAT
*
1452715 TATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTA
59 CATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTA
*
1452779 CTATTAAATCATTAAAAATTAATAATAATTTC------A-T--T-
124 CTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* * *
1452814 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATAATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1452879 AAATC
66 AAATC
1452884 TTATAAATAC
Statistics
Matches: 363, Mismatches: 22, Indels: 36
0.86 0.05 0.09
Matches are distributed among these distances:
155 6 0.02
157 20 0.06
158 13 0.04
159 7 0.02
160 2 0.01
161 9 0.02
162 1 0.00
163 1 0.00
166 9 0.02
167 1 0.00
168 7 0.02
169 260 0.72
170 21 0.06
172 6 0.02
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (168 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
AAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATCAA
ATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:1452659 original size:49 final size:49
Alignment explanation
Indices: 1452546--1452661 Score: 205
Period size: 49 Copynumber: 2.3 Consensus size: 49
1452536 ATTACTAATC
* *
1452546 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1452596 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1452645 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
1452662 AATCATTACT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
49 58 0.91
50 6 0.09
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
Found at i:1452682 original size:71 final size:70
Alignment explanation
Indices: 1452596--1452732 Score: 256
Period size: 71 Copynumber: 1.9 Consensus size: 70
1452586 TAATTTCATT
1452596 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1452661 AAATC
66 AAATC
*
1452666 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATGATTTCATTATTACTAATCATTAC
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1452731 TA
65 TA
1452733 TCAAATCATT
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
70 6 0.09
71 59 0.91
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.40
Consensus pattern (70 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
AAATC
Found at i:1452693 original size:49 final size:49
Alignment explanation
Indices: 1452591--1452743 Score: 111
Period size: 49 Copynumber: 3.1 Consensus size: 49
1452581 AATAATAATT
* *
1452591 TCATTATTACTAATCATTACTATCAAATCATTA--AAA--ATTAATAAT-AATT
1 TCATTATTACTAATCATTAC--T-AAATCATTACTAAATCATTACT-ATCAA-A
1452640 TCATTATTACTAATCATTACTAAATCATTACTAAATCATTACTATCAAA
1 TCATTATTACTAATCATTACTAAATCATTACTAAATCATTACTATCAAA
** * * * * ** *
1452689 TCATTAAAAATTAATAATGATTTCATTATTACT-AATCATTACTATCAAA
1 TCATT-ATTACTAATCATTACTAAATCATTACTAAATCATTACTATCAAA
1452738 TCATTA
1 TCATTA
1452744 AAAATTAATA
Statistics
Matches: 87, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
46 9 0.10
47 1 0.01
48 4 0.05
49 48 0.55
50 25 0.29
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.41
Consensus pattern (49 bp):
TCATTATTACTAATCATTACTAAATCATTACTAAATCATTACTATCAAA
Found at i:1452693 original size:98 final size:97
Alignment explanation
Indices: 1452566--1452892 Score: 290
Period size: 98 Copynumber: 3.2 Consensus size: 97
1452556 CATTAATATC
*
1452566 AAATCA-T-TAAATATTAATAATAATTTCATTATTACTAATCATTACTATCAAATCATTAAAAAT
1 AAATCATTATAAATATTAATAATAATATCATTATTACTAATCATTACTATCAAATCATTAAAAAT
1452629 TAATAATAATTTCATTATTACTAATCATTACT
66 TAATAATAATTTCATTATTACTAATCATTACT
* *
1452661 AAATCATTACTAAATCATTACT-ATCAA-ATCATTAAAAATTAATAATGATTTCATTATTACTAA
1 AAATCATTA-TAAAT-ATTAATAAT-AATATCATT----ATTACT-A--A--TC---ATTACT-A
1452724 TCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATT
50 TCA---------AATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC---T
* *
1452784 AAATCATTA-AAA-ATTAATAATAATTTCATTATTACTAATCATTACTATCAAATCATTAAATAT
1 AAATCATTATAAATATTAATAATAATATCATTATTACTAATCATTACTATCAAATCATTAAAAAT
* *
1452847 TAATAATAATTTCATCATTACTAATAATTACT
66 TAATAATAATTTCATTATTACTAATCATTACT
1452879 AAATC-TTATAAATA
1 AAATCATTATAAATA
1452893 CATAGAAATT
Statistics
Matches: 189, Mismatches: 9, Indels: 67
0.71 0.03 0.25
Matches are distributed among these distances:
94 3 0.02
95 15 0.08
96 2 0.01
98 53 0.28
99 7 0.04
102 5 0.03
103 1 0.01
105 1 0.01
107 6 0.03
108 6 0.03
110 6 0.03
111 6 0.03
113 1 0.01
115 1 0.01
116 5 0.03
119 7 0.04
120 51 0.27
121 3 0.02
123 10 0.05
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (97 bp):
AAATCATTATAAATATTAATAATAATATCATTATTACTAATCATTACTATCAAATCATTAAAAAT
TAATAATAATTTCATTATTACTAATCATTACT
Found at i:1452694 original size:14 final size:11
Alignment explanation
Indices: 1452645--1452683 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
1452635 TAATTTCATT
1452645 ATTACT-AATC
1 ATTACTAAATC
1452655 ATTACTAAATC
1 ATTACTAAATC
1452666 ATTACTAAATC
1 ATTACTAAATC
1452677 ATTACTA
1 ATTACTA
1452684 TCAAATCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 6 0.21
11 22 0.79
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTACTAAATC
Found at i:1452744 original size:49 final size:49
Alignment explanation
Indices: 1452666--1452879 Score: 374
Period size: 49 Copynumber: 4.3 Consensus size: 49
1452656 TTACTAAATC
*
1452666 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATGATTTCATT
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1452716 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
1452765 ATTACTAATCATTACTATTAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* *
1452814 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATC
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
1452863 ATTACTAATAATTACTA
1 ATTACTAATCATTACTA
1452880 AATCTTATAA
Statistics
Matches: 158, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
49 152 0.96
50 6 0.04
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
Found at i:1452765 original size:71 final size:69
Alignment explanation
Indices: 1452596--1452753 Score: 212
Period size: 71 Copynumber: 2.2 Consensus size: 69
1452586 TAATTTCATT
* *
1452596 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1 ATTAC-AAACATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1452661 AAATC
65 AAATC
* *
1452666 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATGATTTCATTATTACTAATCATTAC
1 ATTAC-AAA-CATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
1452731 TATCAAATC
64 --T-AAATC
1452740 ATTA-AAA-ATTAATA
1 ATTACAAACATTAATA
1452754 ATAATTTCAT
Statistics
Matches: 81, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
70 14 0.17
71 54 0.67
72 3 0.04
73 1 0.01
74 9 0.11
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.39
Consensus pattern (69 bp):
ATTACAAACATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTA
AATC
Found at i:1455981 original size:28 final size:28
Alignment explanation
Indices: 1455950--1456003 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1455940 ATAATCTAAT
*
1455950 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
1455978 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
1456004 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:1456010 original size:28 final size:28
Alignment explanation
Indices: 1455946--1456010 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
1455936 TTATATAATC
*
1455946 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
1455974 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
1456002 TAATTTATA
1 TAATATATA
1456011 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:1456013 original size:21 final size:21
Alignment explanation
Indices: 1455980--1456028 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1455970 TTAATATAAT
1455980 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1456001 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1456022 ATTAACT
1 A-TAACT
1456029 AAATTTCTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1456771 original size:29 final size:29
Alignment explanation
Indices: 1456677--1456803 Score: 101
Period size: 29 Copynumber: 4.2 Consensus size: 29
1456667 GCGTGGATGG
* * * *
1456677 CGACCTATAAGGTCGCTGGGCGTACATGG
1 CGACCTACAAGGTCGCTGGGAGTGCATGA
* * * *
1456706 CGACCTACCATCTTGGTCGCTGGGATTGCTTGG
1 CGACCTA-CA---AGGTCGCTGGGAGTGCATGA
1456739 CGACCTACAAGGTCGCTGGGAGTGCATGA
1 CGACCTACAAGGTCGCTGGGAGTGCATGA
*** * *
1456768 CGACCTTGTAGGTCGCTTGGAGTGCTTGA
1 CGACCTACAAGGTCGCTGGGAGTGCATGA
1456797 CGACCTA
1 CGACCTA
1456804 TGGTTGGGTT
Statistics
Matches: 78, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
29 53 0.68
30 1 0.01
32 2 0.03
33 22 0.28
ACGTcount: A:0.18, C:0.25, G:0.32, T:0.24
Consensus pattern (29 bp):
CGACCTACAAGGTCGCTGGGAGTGCATGA
Found at i:1467027 original size:21 final size:20
Alignment explanation
Indices: 1467003--1467053 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1466993 ATAAAAGGAA
1467003 ATTTTTTAAAAAGATATTTAT
1 ATTTTTTAAAAAGA-ATTTAT
*
1467024 A-TTTTTAAAAATAATTTAT
1 ATTTTTTAAAAAGAATTTAT
1467043 ACTATTTTTAA
1 A-T-TTTTTAA
1467054 CATTTTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 7 0.27
20 11 0.42
21 1 0.04
22 7 0.27
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTTTTAAAAAGAATTTAT
Found at i:1467028 original size:20 final size:19
Alignment explanation
Indices: 1467005--1467043 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1466995 AAAAGGAAAT
1467005 TTTTTAAAAAGATATTTATA
1 TTTTTAAAAAGA-ATTTATA
*
1467025 TTTTTAAAAATAATTTATA
1 TTTTTAAAAAGAATTTATA
1467044 CTATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TTTTTAAAAAGAATTTATA
Found at i:1467033 original size:19 final size:20
Alignment explanation
Indices: 1467005--1467043 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1466995 AAAAGGAAAT
1467005 TTTTTAAAAAGAT-ATTTATA
1 TTTTTAAAAA-ATAATTTATA
1467025 TTTTT-AAAAATAATTTATA
1 TTTTTAAAAAATAATTTATA
1467044 CTATTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 11 0.61
20 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TTTTTAAAAAATAATTTATA
Found at i:1479548 original size:20 final size:20
Alignment explanation
Indices: 1479523--1479575 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1479513 GACCAACAAA
1479523 TTCGCAACGCGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
* **
1479543 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ACTCCAAT
1479563 TTCGCAACGCGAA
1 TTCGCAACGCGAA
1479576 TCTGTAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Done.