Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008933.1 Hibiscus syriacus cultivar Beakdansim tig00112249_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: 2862162
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 14
Found at i:1481114 original size:54 final size:54
Alignment explanation
Indices: 1480942--1481480 Score: 682
Period size: 54 Copynumber: 9.9 Consensus size: 54
1480932 TCGTGCCTGT
* * * ** * * * *
1480942 ACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACATCGTGCCTAT
1 ACGGTTATTCATCCACTTAGGATGAATTCCGT-GAAATGCACACTTAGTGCCGAA
* ** * **
1480997 ATGGTTATTCATAAACTTATGATGAATTCCGTGGATTTGCACACTTAGTGCCGAA
1 ACGGTTATTCATCCACTTAGGATGAATTCCGT-GAAATGCACACTTAGTGCCGAA
** * * * *
1481052 ACAATTATTCATCCACTTAGAATGAATTTCATGAAATGTACACTTAGTGCCGAA
1 ACGGTTATTCATCCACTTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* * ** *
1481106 ACGTTTATTCATCCGCTTAGGATGAATTATGTGAAATGCACACTTAGTACCGAA
1 ACGGTTATTCATCCACTTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* * * * *
1481160 ATGGTTATTCATCCACTTAGGATGAATTCCATGAAATGCATACTTAGTGTCAAA
1 ACGGTTATTCATCCACTTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
*
1481214 ATGGTTATTCATCCACTTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
1 ACGGTTATTCATCCACTTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* **
1481268 ACAGTTATTCATCCACTTAGGATGAATTCCGTGAAATGCACACTTAGTATCGAA
1 ACGGTTATTCATCCACTTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
*
1481322 ACAGTTATTCATCCACTTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
1 ACGGTTATTCATCCACTTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* *
1481376 ACGGTTATTCATCCACTTAGGATGAATTTCGTGAAATGCACACTTAGTGTCGAA
1 ACGGTTATTCATCCACTTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
* * * *
1481430 ACGATTATTCATCCACTTAGGATGAATTTCATAAAATGCACACTTAGTGCC
1 ACGGTTATTCATCCACTTAGGATGAATTCCGTGAAATGCACACTTAGTGCC
1481481 TATTTGGTAA
Statistics
Matches: 429, Mismatches: 55, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
54 358 0.83
55 71 0.17
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (54 bp):
ACGGTTATTCATCCACTTAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
Found at i:1481257 original size:27 final size:27
Alignment explanation
Indices: 1481227--1481368 Score: 89
Period size: 27 Copynumber: 5.3 Consensus size: 27
1481217 GTTATTCATC
1481227 CACTTAGGATGAATTCCGTGAAATGCA
1 CACTTAGGATGAATTCCGTGAAATGCA
** * * * *
1481254 CACTTAGTGCCGAA-ACAGT--TATTCA
1 CACTTAG-GATGAATTCCGTGAAATGCA
1481279 TCCACTTAGGATGAATTCCGTGAAATGCA
1 --CACTTAGGATGAATTCCGTGAAATGCA
* * * * *
1481308 CACTTAGTATCGAA-ACAGT--TATTCA
1 CACTTAGGAT-GAATTCCGTGAAATGCA
1481333 TCCACTTAGGATGAATTCCGTGAAATGCA
1 --CACTTAGGATGAATTCCGTGAAATGCA
1481362 CACTTAG
1 CACTTAG
1481369 TGCCGAAACG
Statistics
Matches: 81, Mismatches: 22, Indels: 24
0.64 0.17 0.19
Matches are distributed among these distances:
25 8 0.10
26 7 0.09
27 51 0.63
28 7 0.09
29 8 0.10
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.28
Consensus pattern (27 bp):
CACTTAGGATGAATTCCGTGAAATGCA
Found at i:1481968 original size:95 final size:95
Alignment explanation
Indices: 1481837--1482025 Score: 326
Period size: 95 Copynumber: 2.0 Consensus size: 95
1481827 CGATACTTTT
* *
1481837 ATACTATGGTACTGATACCCCCTTCCGGTATTGATACCAAATTTAGGTTCGATGTT-TCCTGGTA
1 ATACTATGGTACTGATACCCCCTTCCGGTATCGATACCAAATTTAGATTCGATGTTGT-CTGGTA
1481901 TCGATACCCTTACCATGGTATCGATACTACA
65 TCGATACCCTTACCATGGTATCGATACTACA
* *
1481932 ATACTATGGTACTGATACCCCCTTCTGGTATCGATACCAAATTTAGATTCGATGTTGTTTGGTAT
1 ATACTATGGTACTGATACCCCCTTCCGGTATCGATACCAAATTTAGATTCGATGTTGTCTGGTAT
1481997 CGATACCCTTACCATGGTATCGATACTAC
66 CGATACCCTTACCATGGTATCGATACTAC
1482026 CTCATTGGTA
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
95 88 0.99
96 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.34
Consensus pattern (95 bp):
ATACTATGGTACTGATACCCCCTTCCGGTATCGATACCAAATTTAGATTCGATGTTGTCTGGTAT
CGATACCCTTACCATGGTATCGATACTACA
Found at i:1483461 original size:11 final size:11
Alignment explanation
Indices: 1483447--1483471 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1483437 AACCTGCCGT
1483447 AAATATGCCAA
1 AAATATGCCAA
1483458 AAATATGCCAA
1 AAATATGCCAA
1483469 AAA
1 AAA
1483472 CACTAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (11 bp):
AAATATGCCAA
Found at i:1487622 original size:2 final size:2
Alignment explanation
Indices: 1487615--1487646 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1487605 TACAAAATTA
1487615 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
1487647 TGTGTTGGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1488917 original size:31 final size:27
Alignment explanation
Indices: 1488881--1488939 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 27
1488871 TTATTATCGC
1488881 AATAATTATCTTATAATATATCTATAAATTT
1 AATAATTAT-TTATAAT-TAT-TA-AAATTT
1488912 AATAATTATTTATAATTATTAAAATTT
1 AATAATTATTTATAATTATTAAAATTT
1488939 A
1 A
1488940 GTGATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 7 0.25
28 2 0.07
29 3 0.11
30 7 0.25
31 9 0.32
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.49
Consensus pattern (27 bp):
AATAATTATTTATAATTATTAAAATTT
Found at i:1491831 original size:50 final size:50
Alignment explanation
Indices: 1491738--1491838 Score: 121
Period size: 50 Copynumber: 2.0 Consensus size: 50
1491728 TCGATTGTTT
* * *
1491738 TCGTATTCTATATAGATTCAAATATGATAAAACTATACGATATTTCATTA
1 TCGTATTCGATATAGATTCAAATATGATAAAACTATACAATATTCCATTA
* * * * * *
1491788 TCGTCTTCGATATATATTCAAATATGGTAAAATTGTATAATATTCCATTA
1 TCGTATTCGATATAGATTCAAATATGATAAAACTATACAATATTCCATTA
1491838 T
1 T
1491839 TGGACGCATA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.42
Consensus pattern (50 bp):
TCGTATTCGATATAGATTCAAATATGATAAAACTATACAATATTCCATTA
Found at i:1492934 original size:100 final size:92
Alignment explanation
Indices: 1492878--1493097 Score: 273
Period size: 90 Copynumber: 2.4 Consensus size: 92
1492868 GAATTTCATT
* *
1492878 TTTCGCAACGCTAATTAACGATATAGGTAAACACAATTATTCACAACTCAGTTTTCAAATTCGCA
1 TTTCGCAACGCTAATTAACGATATAGGTAAACACAACTATTCACAACTCAGTTTTCAAATTCACA
* **
1492943 ACGCGAATTTCGATTTCGCAACTCGAA
66 ACGCGAATTTCAAAATCGCAACTCGAA
* * * * *
1492970 TTTCGCAACGCTAATTACCGATATATGTTAACACAACTATTCACAACTCAGTTTTTAAATT--CG
1 TTTCGCAACGCTAATTAACGATATAGGTAAACACAACTATTCACAACTCAGTTTTCAAATTCACA
** * * *
1493033 TGGCGATTTTCAAATTCGTAACTCGAA
66 ACGCGAATTTCAAAATCGCAACTCGAA
* *
1493060 TTTCGCAACTCTAATTACCGATATAGGTAAACACAACT
1 TTTCGCAACGCTAATTAACGATATAGGTAAACACAACT
1493098 CAGTTTTTAA
Statistics
Matches: 113, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
90 57 0.50
92 56 0.50
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.31
Consensus pattern (92 bp):
TTTCGCAACGCTAATTAACGATATAGGTAAACACAACTATTCACAACTCAGTTTTCAAATTCACA
ACGCGAATTTCAAAATCGCAACTCGAA
Found at i:1492953 original size:20 final size:20
Alignment explanation
Indices: 1492930--1492973 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1492920 ACAACTCAGT
1492930 TTTCAAATTCGCAACGCGAA
1 TTTCAAATTCGCAACGCGAA
* * *
1492950 TTTCGATTTCGCAACTCGAA
1 TTTCAAATTCGCAACGCGAA
1492970 TTTC
1 TTTC
1492974 GCAACGCTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (20 bp):
TTTCAAATTCGCAACGCGAA
Found at i:1492974 original size:20 final size:20
Alignment explanation
Indices: 1492937--1492974 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1492927 AGTTTTCAAA
1492937 TTCGCAACGCGAATTTCGAT
1 TTCGCAACGCGAATTTCGAT
*
1492957 TTCGCAACTCGAATTTCG
1 TTCGCAACGCGAATTTCG
1492975 CAACGCTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (20 bp):
TTCGCAACGCGAATTTCGAT
Found at i:1493093 original size:90 final size:91
Alignment explanation
Indices: 1492878--1493097 Score: 316
Period size: 92 Copynumber: 2.4 Consensus size: 91
1492868 GAATTTCATT
* *
1492878 TTTCGCAACGCTAATTAACGATATAGGTAAACACAATTATTCACAACTCAGTTTTCAAATTCGCA
1 TTTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCACAACTCAGTTTTCAAATTCG-A
* *
1492943 ACGCGAATTTCGATTTCGCAACTCGAA
65 ACGCGAATTTCAAATTCGCAACTCGAA
* * * *
1492970 TTTCGCAACGCTAATTACCGATATATGTTAACACAACTATTCACAACTCAGTTTTTAAATTCG-T
1 TTTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCACAACTCAGTTTTCAAATTCGAA
* * *
1493034 GGCGATTTTCAAATTCGTAACTCGAA
66 CGCGAATTTCAAATTCGCAACTCGAA
*
1493060 TTTCGCAACTCTAATTACCGATATAGGTAAACACAACT
1 TTTCGCAACGCTAATTACCGATATAGGTAAACACAACT
1493098 CAGTTTTTAA
Statistics
Matches: 114, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
90 56 0.49
92 58 0.51
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.31
Consensus pattern (91 bp):
TTTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCACAACTCAGTTTTCAAATTCGAA
CGCGAATTTCAAATTCGCAACTCGAA
Found at i:1493318 original size:85 final size:85
Alignment explanation
Indices: 1493223--1493386 Score: 283
Period size: 85 Copynumber: 1.9 Consensus size: 85
1493213 GCGAATAGTT
* *
1493223 GTGTTTACCTATATTGGTAATTATTGTTGCGAAATCCGCGTTGCGATTTTAGAGAATCGCGTTGC
1 GTGTTTACCTATATCGGTAATTATCGTTGCGAAATCCGCGTTGCGATTTTAGAGAATCGCGTTGC
1493288 GAATTTGAAAACTGAGTTGC
66 GAATTTGAAAACTGAGTTGC
* * *
1493308 GTGTTTACCTATATCGGTAATTATCGTTGCGAAATTCGCGTTGCGATTTTGGAGAATCGCTTTGC
1 GTGTTTACCTATATCGGTAATTATCGTTGCGAAATCCGCGTTGCGATTTTAGAGAATCGCGTTGC
1493373 GAATTTGAAAACTG
66 GAATTTGAAAACTG
1493387 TGCTGCGAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 74 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (85 bp):
GTGTTTACCTATATCGGTAATTATCGTTGCGAAATCCGCGTTGCGATTTTAGAGAATCGCGTTGC
GAATTTGAAAACTGAGTTGC
Found at i:1497661 original size:259 final size:253
Alignment explanation
Indices: 1497354--1497910 Score: 587
Period size: 257 Copynumber: 2.2 Consensus size: 253
1497344 CTTATTTATA
*
1497354 TATTGAAGAAAAAT-ATTTTTTT-TTATTTC---T-GG-TCGGGTCGGATTTCTAATTCATATAT
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGCTCGGGTCGGATTTCTAATTCATATAT
** * * *
1497412 TCGGGCCGGGTTGGGTCGGGTGAAA-TTT-TATT-T-TGGTCGGATTAATTTTTTTAAGTGTGAT
66 TAAGGCCAGG-T---T-GGGTGAAACTTTATATTATCTGGTCGGATCAATTTTTTTAAATGTGAT
*
1497473 ATTCGAGTCGGGTCGAATTCGGATTTAGGGT-AAAAATACCT-T-A-CTCAAAAATATAT-ATTT
126 ATTC---T--GGTCG-----GG-TTTAGGGTGAAAAATACCTATCACCTAAAAAATATATAATTT
* *
1497533 TACTTTATATATTTAGGAATAATTATAATAATA-T-CT-T-TCTATATATAATTTTTTTCAATTA
180 TAC-CT-TATATTTAGGAATAATTATAATAATACTCCTCTCTCTATATAT-ATTTTTTCCAATTA
*
1497594 AGTTACTGTTTT
242 AGTCACTGTTTT
*
1497606 TATTTAATAAAAATAATTTTTTTATTATTTCGGGTCGGCTCGGGTCGGATTTCTAATTCATATAT
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGCTCGGGTCGGATTTCTAATTCATATAT
* * **
1497671 TAAGGTCAGGTTGGGTGAAACTTTATTTTGATCTGGTCGGATCGGTTTTTTTAAATGTGATATTC
66 TAAGGCCAGGTTGGGTGAAACTTTATATT-ATCTGGTCGGATCAATTTTTTTAAATGTGATATTC
1497736 TGGTCGGGTTTAGGGTGAAAAATACCTGATCCGACCTAAAAAATATATAATTTTACCTTATATTT
130 TGGTCGGGTTTAGGGTGAAAAATACCT-AT-C-ACCTAAAAAATATATAATTTTACCTTATATTT
* * *
1497801 AGGAATAATTATAATAATACTCCTCTCTCTCTCTATATTTTTTCCAATTAAGTCATTGTTTT
192 AGGAATAATTATAATAATACTCCTCTCTCTATATATATTTTTTCCAATTAAGTCACTGTTTT
* *
1497863 TATTGAATAAAAATAGTTTTTTTATTATTTCGGGTCGGGTCGGGTCGG
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGCTCGGGTCGG
1497911 GTGAAACTTT
Statistics
Matches: 260, Mismatches: 21, Indels: 43
0.80 0.06 0.13
Matches are distributed among these distances:
248 8 0.03
249 12 0.05
251 1 0.00
252 12 0.05
253 8 0.03
254 47 0.18
255 18 0.07
256 13 0.05
257 70 0.27
258 11 0.04
259 60 0.23
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.44
Consensus pattern (253 bp):
TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGCTCGGGTCGGATTTCTAATTCATATAT
TAAGGCCAGGTTGGGTGAAACTTTATATTATCTGGTCGGATCAATTTTTTTAAATGTGATATTCT
GGTCGGGTTTAGGGTGAAAAATACCTATCACCTAAAAAATATATAATTTTACCTTATATTTAGGA
ATAATTATAATAATACTCCTCTCTCTATATATATTTTTTCCAATTAAGTCACTGTTTT
Found at i:1498333 original size:18 final size:18
Alignment explanation
Indices: 1498310--1498346 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1498300 TTAATTCCTG
1498310 ACAGATTCCAATTCCTTC
1 ACAGATTCCAATTCCTTC
*
1498328 ACAGATTCTAATTCCTTC
1 ACAGATTCCAATTCCTTC
1498346 A
1 A
1498347 TAAACATTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (18 bp):
ACAGATTCCAATTCCTTC
Found at i:1499585 original size:2 final size:2
Alignment explanation
Indices: 1499578--1499602 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1499568 TATTGGTATC
1499578 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 A
1499603 CTCTTAGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1499805 original size:20 final size:20
Alignment explanation
Indices: 1499780--1499837 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
1499770 AACACGCTGG
1499780 GCATCCGAGGCCATCCGAAA
1 GCATCCGAGGCCATCCGAAA
*
1499800 GCATCCGAGGCCATCCGAGA
1 GCATCCGAGGCCATCCGAAA
1499820 GCATCCGAGGCCATCCGA
1 GCATCCGAGGCCATCCGA
1499838 CCGAGGCCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.26, C:0.36, G:0.28, T:0.10
Consensus pattern (20 bp):
GCATCCGAGGCCATCCGAAA
Found at i:1499843 original size:14 final size:14
Alignment explanation
Indices: 1499824--1499856 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1499814 CCGAGAGCAT
1499824 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
1499838 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
1499852 GCGAG
1 CCGAG
1499857 CTATGCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.39, G:0.33, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:1499852 original size:10 final size:10
Alignment explanation
Indices: 1499781--1499837 Score: 73
Period size: 10 Copynumber: 5.7 Consensus size: 10
1499771 ACACGCTGGG
1499781 CATCCGAGGC
1 CATCCGAGGC
*
1499791 CATCCGAAAG-
1 CATCCG-AGGC
1499801 CATCCGAGGC
1 CATCCGAGGC
1499811 CATCCGAGAG-
1 CATCCGAG-GC
1499821 CATCCGAGGC
1 CATCCGAGGC
1499831 CATCCGA
1 CATCCGA
1499838 CCGAGGCCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 3 0.07
10 35 0.85
11 3 0.07
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:1499979 original size:33 final size:32
Alignment explanation
Indices: 1499922--1500004 Score: 114
Period size: 33 Copynumber: 2.6 Consensus size: 32
1499912 GCGACCTACC
*
1499922 CTCGCTCGGTTG-CTCGGATTCCCTCGCATAG
1 CTCGCTCGGTTGCCTCGGATGCCCTCGCATAG
1499953 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTG-CCTCGGATGCCCTCGCATAG
* *
1499986 CTCGTTCGGATGGCCTCGG
1 CTCGCTCGG-TTGCCTCGG
1500005 TCGGATGGCC
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
31 12 0.26
33 32 0.70
34 2 0.04
ACGTcount: A:0.08, C:0.36, G:0.29, T:0.27
Consensus pattern (32 bp):
CTCGCTCGGTTGCCTCGGATGCCCTCGCATAG
Found at i:1500008 original size:14 final size:14
Alignment explanation
Indices: 1499986--1500052 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
1499976 CCTCGCATAG
*
1499986 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
1500000 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
1500014 CTCGGATGCTTTCGGATGGC
1 CTC-G--G---TCGGATGGC
1500034 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
1500048 CTCGG
1 CTCGG
1500053 ATGCCCAGCG
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
14 30 0.65
15 1 0.02
17 2 0.04
19 1 0.02
20 12 0.26
ACGTcount: A:0.07, C:0.28, G:0.39, T:0.25
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:1500033 original size:34 final size:34
Alignment explanation
Indices: 1499990--1500056 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
1499980 GCATAGCTCG
1499990 TTCGGATGGCCTCGGTCGGATGGCCTCGGATGCT
1 TTCGGATGGCCTCGGTCGGATGGCCTCGGATGCT
1500024 TTCGGATGGCCTCGGTCGGATGGCCTCGGATGC
1 TTCGGATGGCCTCGGTCGGATGGCCTCGGATGC
1500057 CCAGCGTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.09, C:0.27, G:0.39, T:0.25
Consensus pattern (34 bp):
TTCGGATGGCCTCGGTCGGATGGCCTCGGATGCT
Found at i:1500110 original size:29 final size:29
Alignment explanation
Indices: 1500068--1500143 Score: 143
Period size: 29 Copynumber: 2.6 Consensus size: 29
1500058 CAGCGTGTTG
1500068 GGGCGTGCATGGCGACCTGGTAGGTCGCT
1 GGGCGTGCATGGCGACCTGGTAGGTCGCT
1500097 GGGCGTGCATGGCGACCTGGTAGGTCGCT
1 GGGCGTGCATGGCGACCTGGTAGGTCGCT
*
1500126 GGGCGTGCATGACGACCT
1 GGGCGTGCATGGCGACCT
1500144 ATATGGGGAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.12, C:0.25, G:0.43, T:0.20
Consensus pattern (29 bp):
GGGCGTGCATGGCGACCTGGTAGGTCGCT
Found at i:1504557 original size:43 final size:42
Alignment explanation
Indices: 1504467--1504557 Score: 94
Period size: 42 Copynumber: 2.1 Consensus size: 42
1504457 TTCAATTTTA
** * *
1504467 TTTTTATCTTTATAATTTAGGCCCATAATTTTGTAATCCTAC
1 TTTTTATCTCCATAATTGAGGCCCATAATTTTGTAATCCCAC
* * *
1504509 GTTTTATCTCCATAATTGAGGGCCTTAGATTTT-TCAATCCCAC
1 TTTTTATCTCCATAATTGAGGCCCATA-ATTTTGT-AATCCCAC
1504552 TTTTTA
1 TTTTTA
1504558 CGTTTATAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
42 22 0.56
43 17 0.44
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.47
Consensus pattern (42 bp):
TTTTTATCTCCATAATTGAGGCCCATAATTTTGTAATCCCAC
Found at i:1504567 original size:43 final size:41
Alignment explanation
Indices: 1504520--1504630 Score: 102
Period size: 43 Copynumber: 2.7 Consensus size: 41
1504510 TTTTATCTCC
* * *
1504520 ATAATTGAGG-GCCTTAGATTTTTCAATCCCACTTTTTACGTTT
1 ATAATTGAGGACCCTAAG-TTTTTCAATCCC-CTTTGTAC-TTT
**
1504563 ATAATTGATTACCCTAAGTTTTTCAATCCCCTTTGTACTTT
1 ATAATTGAGGACCCTAAGTTTTTCAATCCCCTTTGTACTTT
* *
1504604 ATAACTGA-GACTCCTAA-TTTTTTAATC
1 ATAATTGAGGAC-CCTAAGTTTTTCAATC
1504631 TCACTTTTCA
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
40 11 0.19
41 15 0.26
42 7 0.12
43 20 0.34
44 5 0.09
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.44
Consensus pattern (41 bp):
ATAATTGAGGACCCTAAGTTTTTCAATCCCCTTTGTACTTT
Found at i:1504620 original size:41 final size:42
Alignment explanation
Indices: 1504537--1504637 Score: 118
Period size: 41 Copynumber: 2.4 Consensus size: 42
1504527 AGGGCCTTAG
* * *
1504537 ATTTTTCAATCCCACTTTTTACGTTTATAATTGATTACCCTA
1 ATTTTTCAATCCCACTTTGTACGTTTATAACTGATGACCCTA
1504579 AGTTTTTCAATCCC-CTTTGTAC-TTTATAACTGA-GACTCCTA
1 A-TTTTTCAATCCCACTTTGTACGTTTATAACTGATGAC-CCTA
* *
1504620 ATTTTTTAATCTCACTTT
1 ATTTTTCAATCCCACTTT
1504638 TCACATTTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
40 12 0.24
41 19 0.37
42 8 0.16
43 12 0.24
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.48
Consensus pattern (42 bp):
ATTTTTCAATCCCACTTTGTACGTTTATAACTGATGACCCTA
Found at i:1508468 original size:22 final size:22
Alignment explanation
Indices: 1508438--1508494 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
1508428 CCCTCGGCAT
*
1508438 TGATACAAAAGTGTGTTTGCAC
1 TGATACAAAAGTGTGTTCGCAC
*
1508460 TGGTACAAAAGTGTGTTCGCAC
1 TGATACAAAAGTGTGTTCGCAC
*
1508482 TGATACTAAAGTG
1 TGATACAAAAGTG
1508495 CCTTAACACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (22 bp):
TGATACAAAAGTGTGTTCGCAC
Found at i:1510672 original size:2 final size:2
Alignment explanation
Indices: 1510655--1510703 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
1510645 ATGATAACCT
1510655 TA TA T- TA TA T- TA TA TA 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 TA TA TA TA
1510695 TA TA TA TA T
1 TA TA TA TA T
1510704 TGTAAAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1511461 original size:19 final size:19
Alignment explanation
Indices: 1511437--1511482 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1511427 AAATCATTTA
1511437 ATTCGGTTAACCGAACTTT
1 ATTCGGTTAACCGAACTTT
1511456 ATTCGGTTAACCGAACTTT
1 ATTCGGTTAACCGAACTTT
1511475 ATTCGGTT
1 ATTCGGTT
1511483 CGATTAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (19 bp):
ATTCGGTTAACCGAACTTT
Found at i:1511489 original size:24 final size:22
Alignment explanation
Indices: 1511442--1511489 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 22
1511432 ATTTAATTCG
1511442 GTTAACCGAACTTTATTCG---
1 GTTAACCGAACTTTATTCGTTC
1511461 GTTAACCGAACTTTATTCGGTTC
1 GTTAACCGAACTTTATTC-GTTC
1511484 GATTAA
1 G-TTAA
1511490 TATATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 18 0.75
20 1 0.04
23 1 0.04
24 4 0.17
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (22 bp):
GTTAACCGAACTTTATTCGTTC
Found at i:1511734 original size:30 final size:30
Alignment explanation
Indices: 1511700--1511770 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
1511690 TAATGGTGAG
1511700 GTATTAAAATGAAACAAAACTAAATG-TTAA
1 GTATTAAAATGAAACAAAA-TAAATGTTTAA
*** *
1511730 GTATTATTTTGAAATAAAATAAATGTTTAA
1 GTATTAAAATGAAACAAAATAAATGTTTAA
* *
1511760 ATACTAAAATG
1 GTATTAAAATG
1511771 GATTAAAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
29 6 0.19
30 25 0.81
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.34
Consensus pattern (30 bp):
GTATTAAAATGAAACAAAATAAATGTTTAA
Found at i:1515295 original size:2 final size:2
Alignment explanation
Indices: 1515290--1515320 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1515280 TTGTTCTGTA
1515290 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1515321 CACCTTGCGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1521459 original size:30 final size:30
Alignment explanation
Indices: 1521424--1521486 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
1521414 TGTAAATTTA
1521424 ATATATT-TTAAATATTTACATTATAATATT
1 ATATATTATTAAATATTTA-ATTATAATATT
* *
1521454 ATATATTATTATATATTTAATTTTAATATT
1 ATATATTATTAAATATTTAATTATAATATT
1521484 ATA
1 ATA
1521487 CTTTAAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (30 bp):
ATATATTATTAAATATTTAATTATAATATT
Found at i:1522640 original size:17 final size:17
Alignment explanation
Indices: 1522602--1522641 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1522592 AAAGTTAGAC
1522602 ATCA-TTTTAAATAATT
1 ATCATTTTTAAATAATT
1522618 AT-ATTTTTACAATAA-T
1 ATCATTTTTA-AATAATT
1522634 ATCATTTT
1 ATCATTTT
1522642 CACCTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.05
16 10 0.48
17 10 0.48
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (17 bp):
ATCATTTTTAAATAATT
Found at i:1523104 original size:43 final size:44
Alignment explanation
Indices: 1523008--1523118 Score: 161
Period size: 44 Copynumber: 2.5 Consensus size: 44
1522998 GTTGGCCACT
* * *
1523008 TGCACAACTTGTCAACTTGCCAACCAAGGATGAATTATCCTATG
1 TGCACAAGTTGGCAACTTGCCAACCAAGGATGAATTATCCCATG
* *
1523052 TGCTCAAGTTGGCAACTTGCTAACCAAGGATGAA-TATCCCATG
1 TGCACAAGTTGGCAACTTGCCAACCAAGGATGAATTATCCCATG
*
1523095 TGCACAAGTTGGCTACTTGCCAAC
1 TGCACAAGTTGGCAACTTGCCAAC
1523119 TTGTCAACTT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
43 29 0.49
44 30 0.51
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (44 bp):
TGCACAAGTTGGCAACTTGCCAACCAAGGATGAATTATCCCATG
Found at i:1526879 original size:79 final size:72
Alignment explanation
Indices: 1526825--1526958 Score: 223
Period size: 72 Copynumber: 1.9 Consensus size: 72
1526815 TTGTTCTTGA
* * *
1526825 TTCTTGTGGGCATCACTGGAACAAATTTTTGATTTAGTTTTCTTGTTTCTTGATTACTTTATCAA
1 TTCTTGTAGGCATCACTGGAACAAATTTTTGATTGAGTTTTCTTGTTTCTTGATTACTTTACCAA
1526890 GGTATTG
66 GGTATTG
* *
1526897 TTCTTGTAGGCATCACTGGAACAAGTTTTTGATTGAGTTTTCTTGTTTCTTGATTAATTTAC
1 TTCTTGTAGGCATCACTGGAACAAATTTTTGATTGAGTTTTCTTGTTTCTTGATTACTTTAC
1526959 TTTTTTTTCC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 57 1.00
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.49
Consensus pattern (72 bp):
TTCTTGTAGGCATCACTGGAACAAATTTTTGATTGAGTTTTCTTGTTTCTTGATTACTTTACCAA
GGTATTG
Found at i:1531480 original size:45 final size:46
Alignment explanation
Indices: 1531410--1531501 Score: 168
Period size: 45 Copynumber: 2.0 Consensus size: 46
1531400 AAATGTTCTT
*
1531410 TCATAAGATAGAAACTTTTGTCAACAATGTCTGATTAAGTAAATAA
1 TCATAAGATAGAAACTTATGTCAACAATGTCTGATTAAGTAAATAA
1531456 TCATAAGATAG-AACTTATGTCAACAATGTCTGATTAAGTAAATAA
1 TCATAAGATAGAAACTTATGTCAACAATGTCTGATTAAGTAAATAA
1531501 T
1 T
1531502 TTTTCGTAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 34 0.76
46 11 0.24
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (46 bp):
TCATAAGATAGAAACTTATGTCAACAATGTCTGATTAAGTAAATAA
Found at i:1536722 original size:266 final size:266
Alignment explanation
Indices: 1536248--1536782 Score: 1070
Period size: 266 Copynumber: 2.0 Consensus size: 266
1536238 TTTGATCACT
1536248 TTTAACTATAATATTACTTTAAAATGTCGTTAGAATGGTGCTAGAGACATAAGTTATGATTTTGG
1 TTTAACTATAATATTACTTTAAAATGTCGTTAGAATGGTGCTAGAGACATAAGTTATGATTTTGG
1536313 AGTAGTTGTAGAATTTAGAAGTTACAATCTTTGCTTACATTTGATTAAGAAACTTGGAGTTTCAA
66 AGTAGTTGTAGAATTTAGAAGTTACAATCTTTGCTTACATTTGATTAAGAAACTTGGAGTTTCAA
1536378 TAGGTTATTTGGGGCCTTACATGCATAAGTAATTGCGTTTACATTTTTATGAGAAAATGGGTAGT
131 TAGGTTATTTGGGGCCTTACATGCATAAGTAATTGCGTTTACATTTTTATGAGAAAATGGGTAGT
1536443 AGTTTCTGTTTCATATCTGATGGATTTTAGAAGGAATATCATGAGTGAAGTCTGTGTTCATTTCA
196 AGTTTCTGTTTCATATCTGATGGATTTTAGAAGGAATATCATGAGTGAAGTCTGTGTTCATTTCA
1536508 AAATTG
261 AAATTG
1536514 TTTAACTATAATATTACTTTAAAATGTCGTTAGAATGGTGCTAGAGACATAAGTTATGATTTTGG
1 TTTAACTATAATATTACTTTAAAATGTCGTTAGAATGGTGCTAGAGACATAAGTTATGATTTTGG
1536579 AGTAGTTGTAGAATTTAGAAGTTACAATCTTTGCTTACATTTGATTAAGAAACTTGGAGTTTCAA
66 AGTAGTTGTAGAATTTAGAAGTTACAATCTTTGCTTACATTTGATTAAGAAACTTGGAGTTTCAA
1536644 TAGGTTATTTGGGGCCTTACATGCATAAGTAATTGCGTTTACATTTTTATGAGAAAATGGGTAGT
131 TAGGTTATTTGGGGCCTTACATGCATAAGTAATTGCGTTTACATTTTTATGAGAAAATGGGTAGT
1536709 AGTTTCTGTTTCATATCTGATGGATTTTAGAAGGAATATCATGAGTGAAGTCTGTGTTCATTTCA
196 AGTTTCTGTTTCATATCTGATGGATTTTAGAAGGAATATCATGAGTGAAGTCTGTGTTCATTTCA
1536774 AAATTG
261 AAATTG
1536780 TTT
1 TTT
1536783 TTATACAAAT
Statistics
Matches: 269, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
266 269 1.00
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.40
Consensus pattern (266 bp):
TTTAACTATAATATTACTTTAAAATGTCGTTAGAATGGTGCTAGAGACATAAGTTATGATTTTGG
AGTAGTTGTAGAATTTAGAAGTTACAATCTTTGCTTACATTTGATTAAGAAACTTGGAGTTTCAA
TAGGTTATTTGGGGCCTTACATGCATAAGTAATTGCGTTTACATTTTTATGAGAAAATGGGTAGT
AGTTTCTGTTTCATATCTGATGGATTTTAGAAGGAATATCATGAGTGAAGTCTGTGTTCATTTCA
AAATTG
Found at i:1539713 original size:215 final size:215
Alignment explanation
Indices: 1539342--1539767 Score: 843
Period size: 215 Copynumber: 2.0 Consensus size: 215
1539332 AAGTAGTAAG
1539342 TAACTTGGGGTATATCATAGTTTAAGAAAATGAATTTTTAAGGTTATCGAAACCCAATCATCAGG
1 TAACTTGGGGTATATCATAGTTTAAGAAAATGAATTTTTAAGGTTATCGAAACCCAATCATCAGG
1539407 ATCGATATCAGTGATTTTAAAATATTTTTTAGTACCAAAACCGTCATTTAATATAGAAATAGAGT
66 ATCGATATCAGTGATTTTAAAATATTTTTTAGTACCAAAACCGTCATTTAATATAGAAATAGAGT
1539472 GCCTGGTATCGAAACGAGACCCTTAGTATCGATATTGAGCTTTGAATTTCAAAATTTTGCATTTT
131 GCCTGGTATCGAAACGAGACCCTTAGTATCGATATTGAGCTTTGAATTTCAAAATTTTGCATTTT
1539537 AATCCTTAATTCATAATTCA
196 AATCCTTAATTCATAATTCA
1539557 TAACTTGGGGTATATCATAGTTTAAGAAAATGAATTTTTAAGGTTATCGAAACCCAATCATCAGG
1 TAACTTGGGGTATATCATAGTTTAAGAAAATGAATTTTTAAGGTTATCGAAACCCAATCATCAGG
1539622 ATCGATATCAGTGATTTTAAAATATTTTTTAGTACCAAAACCGTCATTTAATATAGAAATAGAGT
66 ATCGATATCAGTGATTTTAAAATATTTTTTAGTACCAAAACCGTCATTTAATATAGAAATAGAGT
*
1539687 GTCTGGTATCGAAACGAGACCCTTAGTATCGATATTGAGCTTTGAATTTCAAAATTTTGCATTTT
131 GCCTGGTATCGAAACGAGACCCTTAGTATCGATATTGAGCTTTGAATTTCAAAATTTTGCATTTT
1539752 AATCCTTAATTCATAA
196 AATCCTTAATTCATAA
1539768 CTTTTTCATA
Statistics
Matches: 210, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
215 210 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (215 bp):
TAACTTGGGGTATATCATAGTTTAAGAAAATGAATTTTTAAGGTTATCGAAACCCAATCATCAGG
ATCGATATCAGTGATTTTAAAATATTTTTTAGTACCAAAACCGTCATTTAATATAGAAATAGAGT
GCCTGGTATCGAAACGAGACCCTTAGTATCGATATTGAGCTTTGAATTTCAAAATTTTGCATTTT
AATCCTTAATTCATAATTCA
Found at i:1543602 original size:21 final size:21
Alignment explanation
Indices: 1543576--1543691 Score: 132
Period size: 21 Copynumber: 5.6 Consensus size: 21
1543566 GTTTCCAGAT
*
1543576 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
1543597 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
1543618 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
1543638 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
1543659 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
1543680 TCGCAATGCGAA
1 TCGCAATGCGAA
1543692 TATGTAAATC
Statistics
Matches: 82, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
20 17 0.21
21 65 0.79
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:1543643 original size:62 final size:62
Alignment explanation
Indices: 1543576--1543702 Score: 220
Period size: 62 Copynumber: 2.0 Consensus size: 62
1543566 GTTTCCAGAT
*
1543576 TCGCAACGCGA-ACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAA
1 TCGCAACGCGATA-GTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAA
*
1543638 TCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAA
1 TCGCAACGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAA
1543700 TCG
1 TCG
1543703 ACTATCGCAT
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
62 61 0.98
63 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (62 bp):
TCGCAACGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAA
Found at i:1543718 original size:27 final size:27
Alignment explanation
Indices: 1543675--1543729 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
1543665 TGCGAACTTG
*
1543675 GACTATCGCAATGCGAATATGTAAATC
1 GACTATCGCAATACGAATATGTAAATC
*
1543702 GACTATCGCATTACGAATATGTAAATC
1 GACTATCGCAATACGAATATGTAAATC
1543729 G
1 G
1543730 CAATGGGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (27 bp):
GACTATCGCAATACGAATATGTAAATC
Found at i:1543842 original size:21 final size:21
Alignment explanation
Indices: 1543727--1543834 Score: 82
Period size: 21 Copynumber: 5.2 Consensus size: 21
1543717 AATATGTAAA
* *
1543727 TCGCAATGGGATAG-TCGAAGT
1 TCGCATTGCGATAGTTC-AAGT
* *
1543748 TCGCGTTGCGATAGTACAAGT
1 TCGCATTGCGATAGTTCAAGT
* *
1543769 TCGCATTGCGATAG-TCGACT
1 TCGCATTGCGATAGTTCAAGT
1543789 ATCGCATTGCGAT--TTACATA-T
1 -TCGCATTGCGATAGTT-CA-AGT
*
1543810 TCGCATTACGATAGTTCAAGT
1 TCGCATTGCGATAGTTCAAGT
1543831 TCGC
1 TCGC
1543835 GTTTCGATTT
Statistics
Matches: 69, Mismatches: 10, Indels: 16
0.73 0.11 0.17
Matches are distributed among these distances:
20 16 0.23
21 49 0.71
22 4 0.06
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (21 bp):
TCGCATTGCGATAGTTCAAGT
Found at i:1543843 original size:41 final size:40
Alignment explanation
Indices: 1543736--1543845 Score: 114
Period size: 41 Copynumber: 2.6 Consensus size: 40
1543726 ATCGCAATGG
* *
1543736 GATAGTCGAAGTTCGCGTTGCGATAGTACAAGTTCGCATTGC
1 GATAGTC-AAGTTCGCGTTGCGAT-TTACAAGTTCGCATTAC
* * *
1543778 GATAGTCGACTATCGCATTGCGATTTACATA-TTCGCATTAC
1 GATAGTCAAGT-TCGCGTTGCGATTTACA-AGTTCGCATTAC
*
1543819 GATAGTTCAAGTTCGCGTTTCGATTTA
1 GATAG-TCAAGTTCGCGTTGCGATTTA
1543846 TTCCAAATTC
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
41 33 0.59
42 23 0.41
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (40 bp):
GATAGTCAAGTTCGCGTTGCGATTTACAAGTTCGCATTAC
Found at i:1544149 original size:21 final size:21
Alignment explanation
Indices: 1544123--1544164 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1544113 GAGCATTACC
1544123 AACACTTGTTTCCAATACAAT
1 AACACTTGTTTCCAATACAAT
1544144 AACACTTGTTTCCAATACAAT
1 AACACTTGTTTCCAATACAAT
1544165 GTGATTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (21 bp):
AACACTTGTTTCCAATACAAT
Found at i:1544640 original size:21 final size:21
Alignment explanation
Indices: 1544616--1544714 Score: 123
Period size: 21 Copynumber: 4.8 Consensus size: 21
1544606 TGCGATTTTG
*
1544616 GACTATCGCAACGCGAACTTC
1 GACTATCGCAATGCGAACTTC
1544637 GACTATCGCAATGCGAA-TAT-
1 GACTATCGCAATGCGAACT-TC
*
1544657 GTA-AATCGCAATGCGAACTTC
1 G-ACTATCGCAATGCGAACTTC
*
1544678 GACTATCGCAATACGAACTTC
1 GACTATCGCAATGCGAACTTC
*
1544699 GACTATCGCATTGCGA
1 GACTATCGCAATGCGA
1544715 TTTCGAAGTT
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
20 17 0.25
21 50 0.75
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.23
Consensus pattern (21 bp):
GACTATCGCAATGCGAACTTC
Found at i:1544727 original size:20 final size:21
Alignment explanation
Indices: 1544704--1544755 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1544694 ACTTCGACTA
*
1544704 TCGCATTGCGAT-TTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
1544724 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
1544745 TCGCGTTGCGA
1 TCGCATTGCGA
1544756 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:1548590 original size:3 final size:3
Alignment explanation
Indices: 1548584--1548623 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
1548574 TATGTAACAT
1548584 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1548624 TTTATAATCC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1548962 original size:55 final size:56
Alignment explanation
Indices: 1548866--1549691 Score: 616
Period size: 55 Copynumber: 15.3 Consensus size: 56
1548856 TCGCTCCTGA
* * ** *
1548866 AGTATGGAACTCGAACAGTCTTCTGCCAAT-GGGTTCGTTCCCTCTTTCTTTCAGGG
1 AGTATAGAACTCGAACAATCTTC-AACAATCGGGTTCGCTCCCTCTTTCTTTCAGGG
* * * * * * * *
1548922 AGTATAGAACTCAAAC-ATCTTCAACACTCGTGTTTGTTCCCT-ATTCCTTCAGAG
1 AGTATAGAACTCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTTCAGGG
* ** ** * * *
1548976 AGTATA-AGACTTGAACAATCTTCAACAATCATG-TCTTTTCCCTATTCCTTT-AGAG
1 AGTATAGA-ACTCGAACAATCTTCAACAATCGGGTTC-GCTCCCTCTTTCTTTCAGGG
* ** * * *
1549031 AGTATA-AGACTCGAACAATCTTCAACTATC-ATTTCTGCTCCCT-ATTCCTTCAGAG
1 AGTATAGA-ACTCGAACAATCTTCAACAATCGGGTTC-GCTCCCTCTTTCTTTCAGGG
** * *
1549086 AGTAT-GAGACTCGAACAATCTTCTTC-TTACGGGTTCGCTCCCTCTTTC-TTCAGAG
1 AGTATAGA-ACTCGAACAATCTTCAACAAT-CGGGTTCGCTCCCTCTTTCTTTCAGGG
* *** * * *
1549141 AGTATAGAACTCGAA-TATCTTTTTCAAACGGGTTTGCTCCCTCTTTCTCT-AGGG
1 AGTATAGAACTCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTTCAGGG
* * ** * * *
1549195 AGTATAAAACTCGGAC-ATCTTCTTCAAACGGGTTTGCTTCCTCTTTCTTT-A-GG
1 AGTATAGAACTCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTTCAGGG
*
1549248 ATGTATAGAACTCGAACAATCTTC-A-AA-CGGGTTCGCT--CTCTCTCTTT-AGGG
1 A-GTATAGAACTCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTTCAGGG
* ** * * *
1549299 AGTATGGAACTCGAAC-ATCTTCTTC-TTACGAGTTCGCTCCCTCTTTCTCT-AGGG
1 AGTATAGAACTCGAACAATCTTCAACAAT-CGGGTTCGCTCCCTCTTTCTTTCAGGG
** *
1549353 AGTATAGAACTC-AGAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTC-TTCAGGG
1 AGTATAGAACTCGA-ACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTTCAGGG
* *
1549407 AGTATAGAACTCGAA-AATCTTC-A-AA-CGGGTTCGCTCCTTCTTTC-TTCAAGG
1 AGTATAGAACTCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTTCAGGG
*
1549458 AGTATAAAACTCGAACAATCTTCTGAA-AAT-GGGTTCGCTCCCTCTTTC-TTCAGGG
1 AGTATAGAACTCGAACAATCTTC--AACAATCGGGTTCGCTCCCTCTTTCTTTCAGGG
*
1549513 AGTATAGAACTCGAACAATCTTCTGAA-AAT-GGGTTCGCTCCCTTTTTC-TTCAGGG
1 AGTATAGAACTCGAACAATCTTC--AACAATCGGGTTCGCTCCCTCTTTCTTTCAGGG
1549568 AGTATAGAACTCGAACAATCTTCTGAA-AAT-GGGTTCGCTCCCTCTTTC-TTCAGGG
1 AGTATAGAACTCGAACAATCTTC--AACAATCGGGTTCGCTCCCTCTTTCTTTCAGGG
* *
1549623 AGTATAGAACTCAAACAATCTTC-A-AA-CGGGTTTGCTCCCTC--TCTTT-AGGG
1 AGTATAGAACTCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTTCAGGG
1549673 AGTATAGAACTCGAACAAT
1 AGTATAGAACTCGAACAAT
1549692 AATCTTCCTA
Statistics
Matches: 659, Mismatches: 75, Indels: 78
0.81 0.09 0.10
Matches are distributed among these distances:
49 6 0.01
50 48 0.07
51 43 0.07
52 43 0.07
53 8 0.01
54 192 0.29
55 293 0.44
56 26 0.04
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.33
Consensus pattern (56 bp):
AGTATAGAACTCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTTCAGGG
Found at i:1549141 original size:110 final size:110
Alignment explanation
Indices: 1548866--1549691 Score: 692
Period size: 110 Copynumber: 7.7 Consensus size: 110
1548856 TCGCTCCTGA
* * * * * * *
1548866 AGTATGGAACTCGAACAGTCTTCTGCCAATGGGTTCGTTCCCTCTTTCTTTCAGGGAGTATAGAA
1 AGTATAGAACTCGAACAATCTTCTTCAAACGGGTTCGCTCCCTCTTTC-TTCAGAGAGTATAGAA
* * * * * * * *
1548931 CTCAAAC-ATCTTCAACACTCGTGTTTGTTCCCTATTCCTTCAGAG
65 CTCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTCAGGG
* ** * ** ** * * *
1548976 AGTATA-AGACTTGAACAATCTTCAACAATCATG-TCTTTTCCCTATTCCTTTAGAGAGTATA-A
1 AGTATAGA-ACTCGAACAATCTTCTTCAAACGGGTTC-GCTCCCTCTTTCTTCAGAGAGTATAGA
* ** * * *
1549038 GACTCGAACAATCTTCAACTATC-ATTTCTGCTCCCTATTCCTTCAGAG
64 -ACTCGAACAATCTTCAACAATCGGGTTC-GCTCCCTCTTTCTTCAGGG
**
1549086 AGTAT-GAGACTCGAACAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGAGAGTATAGAA
1 AGTATAGA-ACTCGAACAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGAGAGTATAGAA
* *** * *
1549150 CTCGAA-TATCTTTTTCAAACGGGTTTGCTCCCTCTTTC-TCTAGGG
65 CTCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTC-AGGG
* * * * *
1549195 AGTATAAAACTCGGAC-ATCTTCTTCAAACGGGTTTGCTTCCTCTTTCTTTAG-GATGTATAGAA
1 AGTATAGAACTCGAACAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGAGA-GTATAGAA
* *
1549258 CTCGAACAATCTTC-A-AA-CGGGTTCGCT--CTCTCTCTTTAGGG
65 CTCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTCAGGG
* ** * *
1549299 AGTATGGAACTCGAAC-ATCTTCTTCTTACGAGTTCGCTCCCTCTTTC-TCTAGGGAGTATAGAA
1 AGTATAGAACTCGAACAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGAGAGTATAGAA
** *
1549362 CTC-AGAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGG
65 CTCGA-ACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTCAGGG
* *
1549407 AGTATAGAACTCGAA-AA---TCTTCAAACGGGTTCGCTCCTTCTTTCTTCA-AGGAGTATAAAA
1 AGTATAGAACTCGAACAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGA-GAGTATAGAA
1549467 CTCGAACAATCTTCTGAA-AAT-GGGTTCGCTCCCTCTTTCTTCAGGG
65 CTCGAACAATCTTC--AACAATCGGGTTCGCTCCCTCTTTCTTCAGGG
** * * *
1549513 AGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAAC
1 AGTATAGAACTCGAACAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGAGAGTATAGAAC
1549578 TCGAACAATCTTCTGAA-AAT-GGGTTCGCTCCCTCTTTCTTCAGGG
66 TCGAACAATCTTC--AACAATCGGGTTCGCTCCCTCTTTCTTCAGGG
* * * *
1549623 AGTATAGAACTCAAACAA---TCTTCAAACGGGTTTGCTCCCTC--TCTTTAGGGAGTATAGAAC
1 AGTATAGAACTCGAACAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGAGAGTATAGAAC
1549683 TCGAACAAT
66 TCGAACAAT
1549692 AATCTTCCTA
Statistics
Matches: 586, Mismatches: 96, Indels: 73
0.78 0.13 0.10
Matches are distributed among these distances:
103 8 0.01
104 64 0.11
105 70 0.12
106 68 0.12
107 26 0.04
108 75 0.13
109 61 0.10
110 211 0.36
111 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.33
Consensus pattern (110 bp):
AGTATAGAACTCGAACAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGAGAGTATAGAAC
TCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTTTCTTCAGGG
Found at i:1549183 original size:54 final size:54
Alignment explanation
Indices: 1549067--1549687 Score: 666
Period size: 55 Copynumber: 11.6 Consensus size: 54
1549057 TATCATTTCT
* * * **
1549067 GCTCCCTATTCCTTCAGAGAGTAT-GAGACTCGAACAATCTTCTTCTTACGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATAGA-ACTCGAA-AATCTTCTTCAAACGGGTTC
* * * *
1549122 GCTCCCTCTTTCTTCAGAGAGTATAGAACTCGAATATCTTTTTCAAACGGGTTT
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGGGTTC
* * * *
1549176 GCTCCCTCTTTC-TCTAGGGAGTATAAAACTCGGACATCTTCTTCAAACGGGTTT
1 GCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAAAATCTTCTTCAAACGGGTTC
* *
1549230 GCTTCCTCTTTCTTTA-GGATGTATAGAACTCGAACAA---TCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTCAGGGA-GTATAGAACTCGAA-AATCTTCTTCAAACGGGTTC
* * * * ** *
1549282 GCT--CTCTCTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCTTACGAGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGGGTTC
*
1549334 GCTCCCTCTTTC-TCTAGGGAGTATAGAACTC-AGACATCTTCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGA-AAATCTTCTTCAAACGGGTTC
1549388 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAA---TCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGGGTTC
* * * ** *
1549439 GCTCCTTCTTTCTTCAAGGAGTATAAAACTCGAACAATCTTCTGAAAATGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-AATCTTCTTCAAACGGGTTC
** *
1549494 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-AATCTTCTTCAAACGGGTTC
* ** *
1549549 GCTCCCTTTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-AATCTTCTTCAAACGGGTTC
* *
1549604 GCTCCCTCTTTCTTCAGGGAGTATAGAACTC--AAA-CAATCTTCAAACGGGTTT
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATC-TTCTTCAAACGGGTTC
*
1549656 GCTCCCTC--TCTTTAGGGAGTATAGAACTCGAA
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA
1549688 CAATAATCTT
Statistics
Matches: 496, Mismatches: 48, Indels: 47
0.84 0.08 0.08
Matches are distributed among these distances:
49 1 0.00
50 43 0.09
51 50 0.10
52 56 0.11
53 8 0.02
54 154 0.31
55 182 0.37
56 2 0.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (54 bp):
GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGGGTTC
Found at i:1549336 original size:212 final size:209
Alignment explanation
Indices: 1549078--1549691 Score: 765
Period size: 212 Copynumber: 2.9 Consensus size: 209
1549068 CTCCCTATTC
* *
1549078 CTTCAGAGAGTATGAGACTCGAACAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGAGAG
1 CTTCAGGGAGTATGA-ACTCGAACAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGGAG
* * * *
1549143 TATAGAACTCGAATATCTTTTTCAAACGGGTTTGCTCCCTCTTTC-TCTAGGGAGTATAAAACTC
65 TATAGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTC
*
1549207 GGACATCTTCTTCAAACGGGTTTGCTTCCTCTTTCTTTAGGATGTATAGAACTCGAACAATCTTC
129 -GACA--ATCTTCAAACGGGTTTGC-TCCTCTTTCTTTAGGA-GTATAGAACTCGAACAATCTTC
1549272 -AAACGGGTTCGCT-CTCTCT
189 AAAACGGGTTCGCTCCTCTCT
* *
1549291 CTTTAGGGAGTATGGAACTCGAAC-ATCTTCTTCTTACGAGTTCGCTCCCTCTTTC-TCTAGGGA
1 CTTCAGGGAGTAT-GAACTCGAACAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTC-AGGGA
*
1549354 GTATAGAACTC-AGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACT
64 GTATAGAACTCGA-AAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACT
* * * *
1549418 CGAAAATCTTCAAACGGGTTCGCTCCTTCTTTCTTCAAGGAGTATAAAACTCGAACAATCTTCTG
128 CGACAATCTTCAAACGGGTTTGCTCC-TCTTTCTT-TAGGAGTATAGAACTCGAACAATCTTC--
* *
1549483 AAAATGGGTTCGCTCCCTCTTT
189 AAAACGGGTTCGCT-CCTCTCT
**** * *
1549505 CTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGCTCCCTTTTTCTTCAGGGAG
1 CTTCAGGGAGTAT-GAACTCGAACAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGGAG
** *
1549570 TATAGAACTCGAACAATCTTCTGAAAATGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTC
65 TATAGAACTCGAA-AATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTC
* *
1549635 AAACAATCTTCAAACGGGTTTGCTCC-CTCTCTTTAGGGAGTATAGAACTCGAACAAT
129 -GACAATCTTCAAACGGGTTTGCTCCTCTTTCTTTA-GGAGTATAGAACTCGAACAAT
1549692 AATCTTCCTA
Statistics
Matches: 350, Mismatches: 34, Indels: 32
0.84 0.08 0.08
Matches are distributed among these distances:
208 3 0.01
209 45 0.13
210 4 0.01
211 6 0.02
212 102 0.29
213 21 0.06
214 30 0.09
215 67 0.19
216 50 0.14
217 22 0.06
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.33
Consensus pattern (209 bp):
CTTCAGGGAGTATGAACTCGAACAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTTCAGGGAGT
ATAGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGA
CAATCTTCAAACGGGTTTGCTCCTCTTTCTTTAGGAGTATAGAACTCGAACAATCTTCAAAACGG
GTTCGCTCCTCTCT
Found at i:1549735 original size:52 final size:52
Alignment explanation
Indices: 1549677--1550008 Score: 592
Period size: 52 Copynumber: 6.4 Consensus size: 52
1549667 TTAGGGAGTA
* *
1549677 TAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAATTTTCTTCAGGGAC
1 TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
1549729 TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
1 TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
* * *
1549781 TAGAACTCGAAAAATAATCTTCTTACGGGTCTGCCCAATTTTCTTCAAGGAC
1 TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
1549833 TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
1 TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
1549885 TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
1 TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
* **
1549937 TAGAACTCGAACAATAATCTTCCTACGAGAATGCCCAATTTTCTTCAGGGAC
1 TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
1549989 TAGAACTCGAACAATAATCT
1 TAGAACTCGAACAATAATCT
1550009 CCAACGATCG
Statistics
Matches: 269, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 269 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (52 bp):
TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
Found at i:1550074 original size:55 final size:55
Alignment explanation
Indices: 1550004--1550393 Score: 626
Period size: 55 Copynumber: 7.1 Consensus size: 55
1549994 CTCGAACAAT
*
1550004 AATCTCCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
1550059 AATCTTCAACAATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
1550114 AATCTTCAACGATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
1550167 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
*
1550222 AATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CAC
1 AATCTTCAACGATCGCGTCTG-CCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
1550276 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1550331 AATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTG-CCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1550387 AATCTTC
1 AATCTTC
1550394 TTTTGCTTCA
Statistics
Matches: 306, Mismatches: 23, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
53 74 0.24
54 26 0.08
55 139 0.45
56 67 0.22
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (55 bp):
AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
Found at i:1550212 original size:108 final size:111
Alignment explanation
Indices: 1550001--1550393 Score: 681
Period size: 109 Copynumber: 3.6 Consensus size: 111
1549991 GAACTCGAAC
*
1550001 AATAATCTCCAACGATCGCGTCTG-CCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
1 AATAATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
* *
1550065 CAACAATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCG
66 CATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
* * *
1550111 AACAATCTTCAACGATCGTGTCTG-CCCCCTATTTCTTCAGAGAGTATAAGA-TC-CACAATCTT
1 AATAATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
1550173 CATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
66 CATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
*
1550219 AATAATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CACAATCTT
1 AATAATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
1550282 CATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
66 CATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
1550328 AATAATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
1 AATAATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
1550393 C
66 C
1550394 TTTTGCTTCA
Statistics
Matches: 271, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
108 74 0.27
109 138 0.51
110 50 0.18
111 9 0.03
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.29
Consensus pattern (111 bp):
AATAATCTTCAACGATCGCGTCTGCCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
CATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
Found at i:1551694 original size:11 final size:11
Alignment explanation
Indices: 1551678--1551725 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
1551668 CCCCCTTTTA
*
1551678 TTTTTTTGTTT
1 TTTTTTTCTTT
*
1551689 TTTTTTTTTTT
1 TTTTTTTCTTT
1551700 TTTTTCTTCTTT
1 TTTTT-TTCTTT
*
1551712 TTTTCTTCTTT
1 TTTTTTTCTTT
1551723 TTT
1 TTT
1551726 CCATTTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
11 24 0.73
12 9 0.27
ACGTcount: A:0.00, C:0.08, G:0.02, T:0.90
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:1551717 original size:8 final size:8
Alignment explanation
Indices: 1551673--1551781 Score: 66
Period size: 8 Copynumber: 13.5 Consensus size: 8
1551663 TTGAACCCCC
*
1551673 TTTTATTT
1 TTTTCTTT
*
1551681 TTTTGTTT
1 TTTTCTTT
1551689 TTTT-TTT
1 TTTTCTTT
1551696 TTTT-TTT
1 TTTTCTTT
1551703 TTCTTCTTT
1 TT-TTCTTT
1551712 TTTTCTTCTT
1 TTTTC-T-TT
*
1551722 TTTTCCATT
1 TTTT-CTTT
*
1551731 TTTTCTAT
1 TTTTCTTT
1551739 TTTTC--T
1 TTTTCTTT
* *
1551745 ATTTCATT
1 TTTTCTTT
1551753 TTTTCATTT
1 TTTTC-TTT
*
1551762 TTTTC-AT
1 TTTTCTTT
1551769 TTTTCATTT
1 TTTTC-TTT
1551778 TTTT
1 TTTT
1551782 TATCTTTAAG
Statistics
Matches: 82, Mismatches: 9, Indels: 19
0.75 0.08 0.17
Matches are distributed among these distances:
6 5 0.06
7 18 0.22
8 28 0.34
9 24 0.29
10 6 0.07
11 1 0.01
ACGTcount: A:0.07, C:0.11, G:0.01, T:0.81
Consensus pattern (8 bp):
TTTTCTTT
Found at i:1551742 original size:1 final size:1
Alignment explanation
Indices: 1551673--1551725 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
1551663 TTGAACCCCC
* * * * * *
1551673 TTTTATTTTTTTGTTTTTTTTTTTTTTTTTTTCTTCTTTTTTTCTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1551726 CCATTTTTTC
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.02, C:0.08, G:0.02, T:0.89
Consensus pattern (1 bp):
T
Found at i:1551752 original size:22 final size:24
Alignment explanation
Indices: 1551727--1551780 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1551717 TTCTTTTTTC
1551727 CATTTTTTC-TATTTTTC-TATTT
1 CATTTTTTCATATTTTTCATATTT
* *
1551749 CATTTTTTCATTTTTTTCATTTTT
1 CATTTTTTCATATTTTTCATATTT
1551773 CATTTTTT
1 CATTTTTT
1551781 TTATCTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 9 0.32
23 7 0.25
24 12 0.43
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (24 bp):
CATTTTTTCATATTTTTCATATTT
Found at i:1551755 original size:30 final size:29
Alignment explanation
Indices: 1551721--1551777 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
1551711 TTTTTCTTCT
1551721 TTTTTCCA-TTTTTTCTATTTTTCTATTTCA
1 TTTTTCCATTTTTTTC-ATTTTTC-ATTTCA
*
1551751 TTTTTTCATTTTTTTCATTTTTCATTT
1 TTTTTCCATTTTTTTCATTTTTCATTT
1551778 TTTTTATCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 4 0.16
30 14 0.56
31 7 0.28
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (29 bp):
TTTTTCCATTTTTTTCATTTTTCATTTCA
Found at i:1551782 original size:17 final size:17
Alignment explanation
Indices: 1551700--1551781 Score: 67
Period size: 19 Copynumber: 4.4 Consensus size: 17
1551690 TTTTTTTTTT
* *
1551700 TTTTTCTTCTTTTTTTCT
1 TTTTT-TTCATTTTTTCA
1551718 TCTTTTTTCCATTTTTTCTA
1 T-TTTTTT-CATTTTTTC-A
1551738 TTTTTCTATTTCATTTTTTCA
1 --TTT-T-TTTCATTTTTTCA
1551759 TTTTTTTCA-TTTTTCA
1 TTTTTTTCATTTTTTCA
1551775 TTTTTTT
1 TTTTTTT
1551782 TATCTTTAAG
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
16 14 0.25
17 5 0.09
18 4 0.07
19 15 0.27
21 3 0.05
22 11 0.20
23 3 0.05
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTTTCATTTTTTCA
Found at i:1560344 original size:3 final size:3
Alignment explanation
Indices: 1560338--1560369 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1560328 TATGTAACAT
1560338 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1560370 TATATATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1562021 original size:69 final size:69
Alignment explanation
Indices: 1561937--1562066 Score: 233
Period size: 69 Copynumber: 1.9 Consensus size: 69
1561927 AGAATTGTCT
* *
1561937 TTATACTAAAATTTTACGATACTCAGTTTAGATGAATTAATAAACTAGATATCAATGATTATAAA
1 TTATAATAAAATTTTACGATACTCAATTTAGATGAATTAATAAACTAGATATCAATGATTATAAA
1562002 AAGA
66 AAGA
*
1562006 TTATAATAAAATTTTACGATATTCAATTTAGATGAATTAATAAACTAGATATCAATGATTA
1 TTATAATAAAATTTTACGATACTCAATTTAGATGAATTAATAAACTAGATATCAATGATTA
1562067 ACTATTGGAC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.37
Consensus pattern (69 bp):
TTATAATAAAATTTTACGATACTCAATTTAGATGAATTAATAAACTAGATATCAATGATTATAAA
AAGA
Found at i:1565418 original size:14 final size:14
Alignment explanation
Indices: 1565381--1565421 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
1565371 ATTAAATTAC
*
1565381 ATTACATTAATATTT
1 ATTA-ATTAAGATTT
1565396 ATT-ATTAAGATTT
1 ATTAATTAAGATTT
1565409 ATTAATTAAGATT
1 ATTAATTAAGATT
1565422 AGATATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 12 0.50
14 9 0.38
15 3 0.12
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (14 bp):
ATTAATTAAGATTT
Found at i:1569310 original size:27 final size:27
Alignment explanation
Indices: 1569280--1569334 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1569270 GAAGTAAGGT
1569280 TATGAACATGAAATAAAATCAATCAAA
1 TATGAACATGAAATAAAATCAATCAAA
*
1569307 TATGAACATGAAATGAAATCAATCAAA
1 TATGAACATGAAATAAAATCAATCAAA
1569334 T
1 T
1569335 GCAAAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.56, C:0.11, G:0.09, T:0.24
Consensus pattern (27 bp):
TATGAACATGAAATAAAATCAATCAAA
Found at i:1573992 original size:60 final size:60
Alignment explanation
Indices: 1573822--1573978 Score: 278
Period size: 60 Copynumber: 2.6 Consensus size: 60
1573812 TAGAATGTTG
* *
1573822 TTTTATTGAGTTTCCTGACTATTAAAAGTTACAAAATAGTCATATGACTATAAGACATTA
1 TTTTATTGAGTTACTTGACTATTAAAAGTTACAAAATAGTCATATGACTATAAGACATTA
*
1573882 TTTTATTGAGTTACTTGGCTATTAAAAGTTACAAAATAGTCATATGACTATAAGACATTA
1 TTTTATTGAGTTACTTGACTATTAAAAGTTACAAAATAGTCATATGACTATAAGACATTA
*
1573942 TTTTATTGAGTTACTTAACTATTAAAAGTTACAAAAT
1 TTTTATTGAGTTACTTGACTATTAAAAGTTACAAAAT
1573979 TATCACGCAA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 92 1.00
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.39
Consensus pattern (60 bp):
TTTTATTGAGTTACTTGACTATTAAAAGTTACAAAATAGTCATATGACTATAAGACATTA
Found at i:1576309 original size:2 final size:2
Alignment explanation
Indices: 1576304--1576329 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1576294 AAAATAAAAA
1576304 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
1576330 TTTCTTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1577827 original size:3 final size:3
Alignment explanation
Indices: 1577819--1577847 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1577809 AATGTTCGTG
1577819 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1577848 AACCCTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1578027 original size:13 final size:13
Alignment explanation
Indices: 1578009--1578033 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1577999 ATAGTTGAAC
1578009 AGTCTTCATATGA
1 AGTCTTCATATGA
1578022 AGTCTTCATATG
1 AGTCTTCATATG
1578034 CGCGTTTGTA
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
AGTCTTCATATGA
Found at i:1585851 original size:15 final size:16
Alignment explanation
Indices: 1585825--1585867 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1585815 TTTATATATA
*
1585825 TAATAATATTAATTATT
1 TAAT-ATATTAATAATT
1585842 TAAT-TATTAATAATT
1 TAATATATTAATAATT
*
1585857 TTATATATTAA
1 TAATATATTAA
1585868 ATTAAACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 13 0.57
16 6 0.26
17 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATATATTAATAATT
Found at i:1585865 original size:24 final size:24
Alignment explanation
Indices: 1585825--1585871 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1585815 TTTATATATA
*
1585825 TAATAATATTAATTATTTAATTAT
1 TAATAATATTAATTATTAAATTAT
*
1585849 TAATAAT-TTTATATATTAAATTA
1 TAATAATATTAAT-TATTAAATTA
1585872 AACTAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TAATAATATTAATTATTAAATTAT
Found at i:1587205 original size:3 final size:3
Alignment explanation
Indices: 1587197--1587222 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1587187 CATCAATCTA
1587197 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
1587223 ATCATCATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:1590914 original size:21 final size:20
Alignment explanation
Indices: 1590829--1590985 Score: 75
Period size: 21 Copynumber: 7.8 Consensus size: 20
1590819 ATGACCAACA
** *
1590829 AAAATCGCAACGCGA-AATA
1 AAAATCGCAACGCGATTTTC
***
1590848 AAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATTTTC
* ** *
1590868 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTTTC
*
1590888 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * *
1590909 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* **
1590930 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-C
* * * *
1590951 AGAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTC
1590971 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1590986 ACACATAAAT
Statistics
Matches: 102, Mismatches: 30, Indels: 11
0.71 0.21 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:1590978 original size:20 final size:20
Alignment explanation
Indices: 1590953--1591146 Score: 78
Period size: 20 Copynumber: 9.7 Consensus size: 20
1590943 GATTTTCCAG
* *
1590953 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
1590973 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
1590993 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1591013 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
1591033 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * * *
1591053 AATTGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1591073 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
1591093 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
1591114 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
1591134 AATCGCAACGCGA
1 AATCGCAACGCGA
1591147 TATTTAAAGC
Statistics
Matches: 147, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.02
20 128 0.87
21 15 0.10
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:1591000 original size:40 final size:40
Alignment explanation
Indices: 1590953--1591145 Score: 138
Period size: 40 Copynumber: 4.8 Consensus size: 40
1590943 GATTTTCCAG
*
1590953 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAAC-CATA
* * * * * *
1590993 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAACCATA
* * * * * * *
1591033 AATCGCAACGCGTATCCGTAAATTGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAACCATA
* * * * * *
1591073 TATCGCAACGCGTATCCGTAAATCGCAACG-ATAATACATAA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTAA-CCAT-A
* * *
1591114 AATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AATCGCAACGCGAATACGAAAATCGCAACGCG
1591146 ATATTTAAAG
Statistics
Matches: 130, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
39 2 0.02
40 96 0.74
41 32 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGAATACGAAAATCGCAACGCGTAACCATA
Found at i:1591036 original size:60 final size:60
Alignment explanation
Indices: 1590953--1591145 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
1590943 GATTTTCCAG
* ** *
1590953 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
* * * * *
1591013 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATC-CGTAAATTGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTA
* ** *
1591073 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT-AAATCGCAACGCGTATCCGTA
1591134 AATCGCAACGCG
1 AATCGCAACGCG
1591146 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
59 1 0.01
60 78 0.70
61 32 0.29
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
Found at i:1591565 original size:33 final size:33
Alignment explanation
Indices: 1591526--1591595 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
1591516 TCACTTAGAT
1591526 TTCATTTCGCGTTACGATTCTCTCGTTGCGATA
1 TTCATTTCGCGTTACGATTCTCTCGTTGCGATA
* * *
1591559 TTCATTTCGCGTTGCTATTCTCTCGTTGCGATT
1 TTCATTTCGCGTTACGATTCTCTCGTTGCGATA
1591592 TTCA
1 TTCA
1591596 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.46
Consensus pattern (33 bp):
TTCATTTCGCGTTACGATTCTCTCGTTGCGATA
Found at i:1591732 original size:41 final size:41
Alignment explanation
Indices: 1591674--1591751 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1591664 TTGCAGAAGA
*
1591674 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
1591715 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1591752 CGCAACGCGA
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:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:1591748 original size:21 final size:21
Alignment explanation
Indices: 1591675--1591750 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1591665 TGCAGAAGAG
*
1591675 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
1591696 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
1591716 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
1591737 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1591751 TCGCAACGCG
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:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:1592650 original size:14 final size:14
Alignment explanation
Indices: 1592631--1592666 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1592621 ATTGTTTAAT
1592631 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1592645 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1592659 TGATTTGT
1 TGATTTGT
1592667 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1592830 original size:19 final size:20
Alignment explanation
Indices: 1592806--1592852 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1592796 ACAACGAGAG
* *
1592806 AATCGCAATGC-GAAATTAA
1 AATCGCAATACGGAAATGAA
1592825 AATCGCAATACGGAAATGAA
1 AATCGCAATACGGAAATGAA
1592845 AATCGCAA
1 AATCGCAA
1592853 CGAGAGAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (20 bp):
AATCGCAATACGGAAATGAA
Found at i:1592846 original size:20 final size:19
Alignment explanation
Indices: 1592774--1592852 Score: 69
Period size: 19 Copynumber: 4.4 Consensus size: 19
1592764 AAAAATGACT
*
1592774 ATCGCAATGCGAAATGAAA
1 ATCGCAATACGAAATGAAA
* *
1592793 ATCAC-A-ACG--A-GAGA
1 ATCGCAATACGAAATGAAA
* *
1592807 ATCGCAATGCGAAATTAAA
1 ATCGCAATACGAAATGAAA
1592826 ATCGCAATACGGAAATGAAA
1 ATCGCAATAC-GAAATGAAA
1592846 ATCGCAA
1 ATCGCAA
1592853 CGAGAGAATC
Statistics
Matches: 45, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
14 7 0.16
15 2 0.04
16 2 0.04
17 2 0.04
18 2 0.04
19 15 0.33
20 15 0.33
ACGTcount: A:0.48, C:0.18, G:0.19, T:0.15
Consensus pattern (19 bp):
ATCGCAATACGAAATGAAA
Found at i:1592919 original size:33 final size:33
Alignment explanation
Indices: 1592867--1593029 Score: 145
Period size: 33 Copynumber: 4.8 Consensus size: 33
1592857 AGAATCGCAA
*
1592867 TGCGATTTT-AATTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
* *
1592899 TGCGATTTTCATTTCGCATTGCAATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
1592937 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
1592970 TGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
1593004 TGCGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
1593030 TTCATTTCCG
Statistics
Matches: 104, Mismatches: 14, Indels: 25
0.73 0.10 0.17
Matches are distributed among these distances:
31 4 0.04
32 15 0.14
33 36 0.35
34 18 0.17
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1592925 original size:19 final size:19
Alignment explanation
Indices: 1592861--1593082 Score: 216
Period size: 19 Copynumber: 12.7 Consensus size: 19
1592851 AACGAGAGAA
* *
1592861 TCGCAATGCGATTTT-AAT
1 TCGCATTGCGATTTTCATT
*
1592879 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1592895 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1592912 TCGCATTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1592931 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1592947 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1592964 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1592983 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
1593000 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1593017 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1593036 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
1593054 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1593070 TCGCATTGCGATT
1 TCGCATTGCGATT
1593083 CTCTCGTTGC
Statistics
Matches: 169, Mismatches: 12, Indels: 45
0.75 0.05 0.20
Matches are distributed among these distances:
14 29 0.17
16 22 0.13
17 18 0.11
18 14 0.08
19 60 0.36
20 26 0.15
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1592934 original size:52 final size:53
Alignment explanation
Indices: 1592861--1593082 Score: 362
Period size: 53 Copynumber: 4.2 Consensus size: 53
1592851 AACGAGAGAA
* *
1592861 TCGCAATGCGATTTT-AATT-CGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
1592912 TCGCATTGCAATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1592964 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
* *
1593017 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGTTGCGATTTTCATT
1593070 TCGCATTGCGATT
1 TCGCATTGCGATT
1593083 CTCTCGTTGC
Statistics
Matches: 162, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
51 13 0.08
52 54 0.33
53 94 0.58
54 1 0.01
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (53 bp):
TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1593021 original size:86 final size:84
Alignment explanation
Indices: 1592917--1593096 Score: 233
Period size: 86 Copynumber: 2.1 Consensus size: 84
1592907 TCATTTCGCA
*
1592917 TTGCAATTTTCATTTCGCATTGCGA-TTC-TCT-CG-TTGCGATTTTCATTTCGCATTGCGATTT
1 TTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGATTGCGATTTTCA--T-G--TTGCGATTT
1592978 TCATTTCCGCATTGCGATTCTCTCG
61 TCATTT-CGCATTGCGATTCTCTCG
* *
1593003 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATCTCCG-ATTGCGATTTTCATGTTGCGATTTTCA
1593068 TTTCGCATTGCGATTCTCTCG
64 TTTCGCATTGCGATTCTCTCG
1593089 TTGCGATT
1 TTGCGATT
1593097 GTAATTTCCG
Statistics
Matches: 85, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
86 50 0.59
87 14 0.16
88 3 0.04
89 3 0.04
90 3 0.04
92 12 0.14
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (84 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGATTGCGATTTTCATGTTGCGATTTTCATT
TCGCATTGCGATTCTCTCG
Found at i:1593080 original size:33 final size:34
Alignment explanation
Indices: 1592898--1593096 Score: 176
Period size: 33 Copynumber: 5.7 Consensus size: 34
1592888 GATTCTCTCG
*
1592898 TTGCGATTTTCATTTCGCATTGCAATTTTCATTTCGCA
1 TTGCGATTTTCA--TCG--TTGCGATTTTCATTTCGCA
*
1592936 TTGCGATTCTC-TCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
* * * *
1592969 TTGCGATTTTCAT--TTCCGCA-TTGCGATTCTCTCG
1 TTGCGATTTTCATCGTTGCG-ATTTTC-ATT-TCGCA
1593003 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCA--TCG--TTGCGATTTTCATTT-CGCA
*
1593042 TTGCGATTTTCAT-GTTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
*
1593075 TTGCGATTCTC-TCGTTGCGATT
1 TTGCGATTTTCATCGTTGCGATT
1593097 GTAATTTCCG
Statistics
Matches: 134, Mismatches: 14, Indels: 31
0.75 0.08 0.17
Matches are distributed among these distances:
32 8 0.06
33 54 0.40
34 30 0.22
35 3 0.02
36 2 0.01
37 1 0.01
38 11 0.08
39 18 0.13
40 7 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (34 bp):
TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
Found at i:1593111 original size:53 final size:53
Alignment explanation
Indices: 1592897--1593115 Score: 227
Period size: 53 Copynumber: 4.2 Consensus size: 53
1592887 CGATTCTCTC
* * *
1592897 GTTGCGATTTTCATTTCGCATTGCAATTTTCA-TTTCGCATTGCGA-TTCTC-T
1 GTTGCGATTTTCATTTCGCATTGCGATTTTCAGTTCCGCATTGCAATTTC-CAT
* *
1592948 CGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGA-TTCTC-T
1 -GTTGCGATTTTCATTTCGCATTGCGATTTTCAGTTCCGCATTGCAATTTC-CAT
* * *
1593001 CGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 -GTTGCGATTTTCATTTCGCATTGCGATTTTCAGTTCCGCATTGCAATTTCCAT
* * * *
1593055 GTTGGGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCG-ATTGTAATTTCCGT
1 GTTGCGATTTTCATTTCGCATTGCGATT-T-TCAGTTCCGCATTGCAATTTCCAT
1593108 GTTGCGAT
1 GTTGCGAT
1593116 AGTCAAATGC
Statistics
Matches: 151, Mismatches: 11, Indels: 9
0.88 0.06 0.05
Matches are distributed among these distances:
52 31 0.21
53 110 0.73
54 8 0.05
55 2 0.01
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (53 bp):
GTTGCGATTTTCATTTCGCATTGCGATTTTCAGTTCCGCATTGCAATTTCCAT
Found at i:1595607 original size:24 final size:24
Alignment explanation
Indices: 1595573--1595619 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1595563 CTGAAACATC
1595573 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1595597 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1595620 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1596340 original size:20 final size:20
Alignment explanation
Indices: 1596312--1596540 Score: 237
Period size: 20 Copynumber: 11.4 Consensus size: 20
1596302 AAATTTCAGT
* * *
1596312 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1596332 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1596352 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1596372 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1596392 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1596412 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1596432 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1596452 GTTGCGATTTACGGATAT-AC
1 GTTGCGATTTACGGAT-TCGC
*
1596472 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1596492 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* ** *
1596512 GTTGCGATTTTCATATTCGT
1 GTTGCGATTTACGGATTCGC
1596532 GTTGCGATT
1 GTTGCGATT
1596541 CTGGAAAATC
Statistics
Matches: 180, Mismatches: 25, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
20 179 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1596513 original size:60 final size:60
Alignment explanation
Indices: 1596312--1596521 Score: 262
Period size: 60 Copynumber: 3.5 Consensus size: 60
1596302 AAATTTCAGT
* * * * * *
1596312 GTTGTGATTTACAGATTCTCGTTGCGATTTACGGAT-TATCGTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGCGTTGCGATTTACGGATATA-CGTTGCGATTTACGGATACGC
** ** *
1596372 GTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGCGTTGCGATTTACGGATATACGTTGCGATTTACGGATACGC
* *
1596432 ATTGCGATTTACGGATACGCGTTGCGATTTACGGATATACGTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGCGTTGCGATTTACGGATATACGTTGCGATTTACGGATACGC
*
1596492 GTTGCGATTTATGTG-TTCGCGTTGCGATTT
1 GTTGCGATTTACG-GATTCGCGTTGCGATTT
1596522 TCATATTCGT
Statistics
Matches: 129, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
60 128 0.99
61 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (60 bp):
GTTGCGATTTACGGATTCGCGTTGCGATTTACGGATATACGTTGCGATTTACGGATACGC
Found at i:1597096 original size:13 final size:13
Alignment explanation
Indices: 1597066--1597098 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1597056 CAAACCCTAA
1597066 TTATTATTTTATTG
1 TTATT-TTTTATTG
1597080 -TATTTTTTATTG
1 TTATTTTTTATTG
1597092 TTATTTT
1 TTATTTT
1597099 GATGTTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (13 bp):
TTATTTTTTATTG
Found at i:1597305 original size:31 final size:31
Alignment explanation
Indices: 1597255--1597340 Score: 127
Period size: 31 Copynumber: 2.7 Consensus size: 31
1597245 TACCAATGAG
*
1597255 CTTAACGAGCAGCGAGTCGAGAAACAAATTTT
1 CTTAACAAGCA-CGAGTCGAGAAACAAATTTT
* *
1597287 CTTGACAAGCACGAGTCGAGCAACAAATTTT
1 CTTAACAAGCACGAGTCGAGAAACAAATTTT
*
1597318 CTTAACGAGCACGAGTCGAGAAA
1 CTTAACAAGCACGAGTCGAGAAA
1597341 AATTTTAACG
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 39 0.81
32 9 0.19
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (31 bp):
CTTAACAAGCACGAGTCGAGAAACAAATTTT
Found at i:1597527 original size:32 final size:32
Alignment explanation
Indices: 1597465--1597527 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
1597455 TGCACCATAT
* *
1597465 ATCCCCAAACTATGATTCTCATTTCCAATTAC
1 ATCCCCAAACTATGACTCTCATTTCAAATTAC
*
1597497 ATCCTCAAACTATGACTCTCA-TTCTAAATTA
1 ATCCCCAAACTATGACTCTCATTTC-AAATTA
1597528 GTCCTTGAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 3 0.11
32 24 0.89
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (32 bp):
ATCCCCAAACTATGACTCTCATTTCAAATTAC
Found at i:1597580 original size:59 final size:60
Alignment explanation
Indices: 1597487--1597599 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 60
1597477 TGATTCTCAT
* * *
1597487 TTCCAATTACATCCTCAAACTATGACTCTCATTCTAAATTAGTCCTTGAACTTTTGAACA
1 TTCCAATTACATCCTCAAACTATGAATCTCATTCTAAATTAGTCCATAAACTTTTGAACA
* *
1597547 TTCCAATTTCATCC-CAAACTATGAATCTCATTCTAAATTGGTCCATAAACTTT
1 TTCCAATTACATCCTCAAACTATGAATCTCATTCTAAATTAGTCCATAAACTTT
1597600 CAGATCTTCC
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 35 0.73
60 13 0.27
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (60 bp):
TTCCAATTACATCCTCAAACTATGAATCTCATTCTAAATTAGTCCATAAACTTTTGAACA
Found at i:1597889 original size:60 final size:60
Alignment explanation
Indices: 1597763--1597916 Score: 163
Period size: 60 Copynumber: 2.6 Consensus size: 60
1597753 AAAATATAAA
* * * * * * *
1597763 AAAATTTTGGGGACCAATTTAGAATGAAGATCACAGTTT-GGGATGAAAATGAAATGTTT
1 AAAAGTTTAGGGACCAATTTAAAATGAAGGTCATATTTTAAGGATGAAAATGAAATGTTT
* **
1597822 AATAGTTT-GAGGACTGATTTAAAATGATA-GTCATATTTTAAGGAT-AAAATTGAAATGTTT
1 AAAAGTTTAG-GGACCAATTTAAAATGA-AGGTCATATTTTAAGGATGAAAA-TGAAATGTTT
1597882 AAAAGTTTAGGGACCAATTTAAAATGAAGGTCATA
1 AAAAGTTTAGGGACCAATTTAAAATGAAGGTCATA
1597917 CATTGGGGAC
Statistics
Matches: 77, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
58 1 0.01
59 32 0.42
60 43 0.56
61 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (60 bp):
AAAAGTTTAGGGACCAATTTAAAATGAAGGTCATATTTTAAGGATGAAAATGAAATGTTT
Found at i:1598094 original size:26 final size:27
Alignment explanation
Indices: 1598055--1598105 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
1598045 GTTCGTACAA
*
1598055 TAAATATTTTATATAA-AAATATATTTG
1 TAAATATTTAATATAATAAAT-TATTTG
1598082 TAAATA-TTAATATAATAAATTATT
1 TAAATATTTAATATAATAAATTATT
1598106 ATAAATGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
TAAATATTTAATATAATAAATTATTTG
Found at i:1601105 original size:20 final size:20
Alignment explanation
Indices: 1601082--1601168 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
1601072 CACAGAATGT
1601082 AAGATTACCAGT-AGGAATAA
1 AAGATTACCAGTGA-GAATAA
* *
1601102 AAGATTACCAGTGTGAACAA
1 AAGATTACCAGTGAGAATAA
* *
1601122 AAGATTATCAGTGGGAATAA
1 AAGATTACCAGTGAGAATAA
*
1601142 AAGATTACCAATGAGAATAA
1 AAGATTACCAGTGAGAATAA
1601162 AAGATTA
1 AAGATTA
1601169 TCAGAGAATA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.49, C:0.09, G:0.20, T:0.22
Consensus pattern (20 bp):
AAGATTACCAGTGAGAATAA
Found at i:1601139 original size:40 final size:40
Alignment explanation
Indices: 1601082--1601172 Score: 137
Period size: 40 Copynumber: 2.3 Consensus size: 40
1601072 CACAGAATGT
* * *
1601082 AAGATTACCAGTAGGAATAAAAGATTACCAGTGTGAACAA
1 AAGATTATCAGTAGGAATAAAAGATTACCAATGAGAACAA
* *
1601122 AAGATTATCAGTGGGAATAAAAGATTACCAATGAGAATAA
1 AAGATTATCAGTAGGAATAAAAGATTACCAATGAGAACAA
1601162 AAGATTATCAG
1 AAGATTATCAG
1601173 AGAATATGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.48, C:0.10, G:0.20, T:0.22
Consensus pattern (40 bp):
AAGATTATCAGTAGGAATAAAAGATTACCAATGAGAACAA
Found at i:1601828 original size:16 final size:18
Alignment explanation
Indices: 1601786--1601830 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
1601776 TCACGGAATG
1601786 TAAGATTACCAGTAGGAA
1 TAAGATTACCAGTAGGAA
1601804 TAAAAGATTACCAG-A-GAA
1 T--AAGATTACCAGTAGGAA
1601822 TAAGATTAC
1 TAAGATTAC
1601831 TGGAATTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 5 0.20
19 1 0.04
20 11 0.44
ACGTcount: A:0.49, C:0.11, G:0.18, T:0.22
Consensus pattern (18 bp):
TAAGATTACCAGTAGGAA
Found at i:1602000 original size:37 final size:36
Alignment explanation
Indices: 1601959--1602031 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
1601949 TTTTTTTAAC
*
1601959 AAATTGAAAAATATTTATAT-ATTTTCTTTAAAAAATT
1 AAATTCAAAAA-ATTTATATAATTTT-TTTAAAAAATT
* *
1601996 AAATTCATAAAATTTATATAATTTTTTTACAAAATT
1 AAATTCAAAAAATTTATATAATTTTTTTAAAAAATT
1602032 GAAAATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 18 0.56
37 14 0.44
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (36 bp):
AAATTCAAAAAATTTATATAATTTTTTTAAAAAATT
Found at i:1602042 original size:36 final size:34
Alignment explanation
Indices: 1601949--1602043 Score: 92
Period size: 36 Copynumber: 2.8 Consensus size: 34
1601939 TATATATTTG
1601949 TTTTTTTAACAAATTGAAAA-AT---ATTTATATA
1 TTTTTTTAA-AAATTGAAAATATAAAATTTATATA
*
1601980 TTTTCTTTAAAAAATT-AAATTCATAAAATTTATATAA
1 TTTT-TTT-AAAAATTGAAAAT-ATAAAATTTATAT-A
1602017 TTTTTTTACAAAATTGAAAATATAAAA
1 TTTTTTTA-AAAATTGAAAATATAAAA
1602044 AGGTTTAATG
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
31 7 0.13
32 8 0.15
33 4 0.08
35 1 0.02
36 23 0.44
37 9 0.17
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.45
Consensus pattern (34 bp):
TTTTTTTAAAAATTGAAAATATAAAATTTATATA
Found at i:1609792 original size:166 final size:166
Alignment explanation
Indices: 1609518--1609853 Score: 672
Period size: 166 Copynumber: 2.0 Consensus size: 166
1609508 GGGGTGGTTT
1609518 GTTGTTTTTAGCTATGAAACTCACCAATTTGAAGTTTCTTGCATTTTGAACTGTTTATTCTGTGA
1 GTTGTTTTTAGCTATGAAACTCACCAATTTGAAGTTTCTTGCATTTTGAACTGTTTATTCTGTGA
1609583 TTTTCCATAGGTAATGACTTGCAGGCCTAGATTAGATCTTTTCATTAATCTCGCCGCACTTCGAA
66 TTTTCCATAGGTAATGACTTGCAGGCCTAGATTAGATCTTTTCATTAATCTCGCCGCACTTCGAA
1609648 AGCTCGACAACATGCTTCTGGTGAGAACTTACAATA
131 AGCTCGACAACATGCTTCTGGTGAGAACTTACAATA
1609684 GTTGTTTTTAGCTATGAAACTCACCAATTTGAAGTTTCTTGCATTTTGAACTGTTTATTCTGTGA
1 GTTGTTTTTAGCTATGAAACTCACCAATTTGAAGTTTCTTGCATTTTGAACTGTTTATTCTGTGA
1609749 TTTTCCATAGGTAATGACTTGCAGGCCTAGATTAGATCTTTTCATTAATCTCGCCGCACTTCGAA
66 TTTTCCATAGGTAATGACTTGCAGGCCTAGATTAGATCTTTTCATTAATCTCGCCGCACTTCGAA
1609814 AGCTCGACAACATGCTTCTGGTGAGAACTTACAATA
131 AGCTCGACAACATGCTTCTGGTGAGAACTTACAATA
1609850 GTTG
1 GTTG
1609854 ATTTATAATT
Statistics
Matches: 170, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
166 170 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (166 bp):
GTTGTTTTTAGCTATGAAACTCACCAATTTGAAGTTTCTTGCATTTTGAACTGTTTATTCTGTGA
TTTTCCATAGGTAATGACTTGCAGGCCTAGATTAGATCTTTTCATTAATCTCGCCGCACTTCGAA
AGCTCGACAACATGCTTCTGGTGAGAACTTACAATA
Found at i:1612290 original size:15 final size:15
Alignment explanation
Indices: 1612266--1612296 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1612256 ATTGGAATGA
1612266 CGAGGCTGTTGCTGC
1 CGAGGCTGTTGCTGC
*
1612281 CGAGGTTGTTGCTGC
1 CGAGGCTGTTGCTGC
1612296 C
1 C
1612297 AAGTCTGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.06, C:0.26, G:0.39, T:0.29
Consensus pattern (15 bp):
CGAGGCTGTTGCTGC
Found at i:1618297 original size:127 final size:126
Alignment explanation
Indices: 1618098--1618338 Score: 362
Period size: 127 Copynumber: 1.9 Consensus size: 126
1618088 TATTTATATA
* *
1618098 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATAATTTAATTAGGATCTGACATGTGTTAG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATAATTTAATCAGGATCTGACATGTGTTAA
*
1618163 CACATGATCATGACACGTGTCATTGGTGA-ACATGTTACCACCTAATTATTTATATATGCT
66 CACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
1618223 ATCAA-TTGGTCCT-AATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAA-T-A--ATTTAATCAGGATCTGACATGTG
* * * *
1618286 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
62 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
1618339 GAAGAAAATT
Statistics
Matches: 104, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
123 21 0.20
124 9 0.09
125 6 0.06
127 51 0.49
128 17 0.16
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (126 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATAATTTAATCAGGATCTGACATGTGTTAA
CACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:1618812 original size:16 final size:18
Alignment explanation
Indices: 1618791--1618824 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1618781 ATTTCTTATT
1618791 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
1618807 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
1618825 TACATTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:1618966 original size:21 final size:21
Alignment explanation
Indices: 1618942--1618984 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1618932 TATTACCTTA
1618942 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
1618963 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
1618984 A
1 A
1618985 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:1619002 original size:35 final size:35
Alignment explanation
Indices: 1618953--1619038 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 35
1618943 ATTGAAGTAT
** * *
1618953 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
1618988 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* *
1619023 TTTATAATGAAATTGA
1 TTTAGAATAAAATTGA
1619039 TGACTGTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.37, C:0.01, G:0.20, T:0.42
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:1620251 original size:50 final size:49
Alignment explanation
Indices: 1620192--1620291 Score: 173
Period size: 50 Copynumber: 2.0 Consensus size: 49
1620182 AGTTTAGTCT
*
1620192 TCATACTCTTGGTTTTGAATTTCATACAGATAACAACATTGGATCATTTG
1 TCATACTCTTGGTTTTGAATTTCATACAGATAACAAC-GTGGATCATTTG
*
1620242 TCATACTCTTGGTTTTGAATTTCATACAGGTAACAACGTGGATCATTTG
1 TCATACTCTTGGTTTTGAATTTCATACAGATAACAACGTGGATCATTTG
1620291 T
1 T
1620292 GTATGTATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 12 0.25
50 36 0.75
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (49 bp):
TCATACTCTTGGTTTTGAATTTCATACAGATAACAACGTGGATCATTTG
Found at i:1625458 original size:19 final size:19
Alignment explanation
Indices: 1625434--1625475 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
1625424 TTTTCTCTCT
1625434 TTTTCTTGACTACTCTTTA
1 TTTTCTTGACTACTCTTTA
*
1625453 TTTTCTTGATTACTCTTTA
1 TTTTCTTGACTACTCTTTA
1625472 TTTT
1 TTTT
1625476 TCAGCGACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.14, C:0.17, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTTCTTGACTACTCTTTA
Found at i:1625751 original size:50 final size:49
Alignment explanation
Indices: 1625676--1625775 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 49
1625666 AGTTTAGTCT
1625676 TCATACTCTTGGTTTTGAATTTCATACAGGTAACAACGTTGGATCATTTG
1 TCATACTCTTGGTTTTGAATTTCATACAGGTAACAACG-TGGATCATTTG
1625726 TCATACTCTTGGTTTTGAATTTCATACAGGTAACAACGTGGATCATTTG
1 TCATACTCTTGGTTTTGAATTTCATACAGGTAACAACGTGGATCATTTG
1625775 T
1 T
1625776 GTATGTATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 12 0.24
50 38 0.76
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (49 bp):
TCATACTCTTGGTTTTGAATTTCATACAGGTAACAACGTGGATCATTTG
Found at i:1628250 original size:19 final size:21
Alignment explanation
Indices: 1628206--1628251 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
1628196 TAAATTAAAT
1628206 TAATTTAAATTATTATAATAC
1 TAATTTAAATTATTATAATAC
* *
1628227 T-ATTTAAA-TATTTTTATA-
1 TAATTTAAATTATTATAATAC
1628245 TAATTTA
1 TAATTTA
1628252 TTCTTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 1 0.05
19 13 0.59
20 7 0.32
21 1 0.05
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TAATTTAAATTATTATAATAC
Found at i:1628288 original size:55 final size:60
Alignment explanation
Indices: 1628179--1628292 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 60
1628169 TAATTTTAAA
1628179 TTATATTAATATATTCTTAAATTAAATTAATTTAAATTATTATAATACTATTTAAATATTT
1 TTATATTAATATATTCTTAAATTAAATTAATTTAAATTATTATAATA-TATTTAAATATTT
*
1628240 TTATA-TAATTTATTCTTAAATTAAATTAA-TTAAATTA-TATAAT-T-TTTAAATAT
1 TTATATTAATATATTCTTAAATTAAATTAATTTAAATTATTATAATATATTTAAATAT
1628293 AATAAAGATT
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
55 9 0.17
56 1 0.02
58 6 0.12
59 8 0.15
60 23 0.44
61 5 0.10
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (60 bp):
TTATATTAATATATTCTTAAATTAAATTAATTTAAATTATTATAATATATTTAAATATTT
Found at i:1630448 original size:13 final size:13
Alignment explanation
Indices: 1630430--1630454 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1630420 TAATATTAAT
1630430 ATTTAAATTATAA
1 ATTTAAATTATAA
1630443 ATTTAAATTATA
1 ATTTAAATTATA
1630455 TTAATATATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTAAATTATAA
Found at i:1633671 original size:50 final size:48
Alignment explanation
Indices: 1633596--1633694 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 48
1633586 AGTTTAGTCT
1633596 TCATACTCTTGGTTTTGAATTTCATACAGGTAACAACGTTGGATCATTTG
1 TCATACTCTTGGTTTTGAATTTCATACAGGTAAC-ACG-TGGATCATTTG
1633646 TCATACTCTTGGTTTTGAATTTCATACAGGTAACACGTGGATCATTTG
1 TCATACTCTTGGTTTTGAATTTCATACAGGTAACACGTGGATCATTTG
1633694 T
1 T
1633695 GTATGTATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 12 0.24
49 3 0.06
50 34 0.69
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.40
Consensus pattern (48 bp):
TCATACTCTTGGTTTTGAATTTCATACAGGTAACACGTGGATCATTTG
Found at i:1634869 original size:19 final size:19
Alignment explanation
Indices: 1634845--1634886 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1634835 TTTTCTCTCT
1634845 TTTTCTTGATTACTCTTTA
1 TTTTCTTGATTACTCTTTA
1634864 TTTTCTTGATTACTCTTTA
1 TTTTCTTGATTACTCTTTA
1634883 TTTT
1 TTTT
1634887 TCAGCGACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTCTTGATTACTCTTTA
Found at i:1644300 original size:21 final size:23
Alignment explanation
Indices: 1644266--1644309 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
1644256 ATTTCCAATC
*
1644266 ATATTCTATAAAATTATATTAAT
1 ATATTCTATAAAATTAAATTAAT
1644289 ATATTCT-T-AAATTAAATTAAT
1 ATATTCTATAAAATTAAATTAAT
1644310 TTGGACTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 1 0.05
23 7 0.35
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATTCTATAAAATTAAATTAAT
Found at i:1657945 original size:244 final size:244
Alignment explanation
Indices: 1657516--1657960 Score: 782
Period size: 244 Copynumber: 1.8 Consensus size: 244
1657506 GACATCCATT
1657516 TATAGTGTCTAGAATAAGTCATGTTGAGGGGTGAAGTGAAATTAAAAATGTGGTCGGTGATTGGC
1 TATAGTGTCTAGAATAAGTCATGTTGAGGGGTGAAGTGAAATTAAAAATGTGGTCGGTGATTGGC
* * *
1657581 GGAAAAAGTAGGGGTGTGCAAATCCGGGTATCCGAAGTGTTGGGTACTCTAATCTTAGGTAATTG
66 GGAAAAAGTAGGGGTGTGCAAATCCGGGTACCCGAAGTGTCGGGTACTCGAATCTTAGGTAATTG
* * * **
1657646 ATTTCTTGACCTGTTTCTTGACCCAAATGTTGCGAGTACCCAGTAATCGGGTACCCGGATTTTGC
131 ATTTCTCGACCCGTGTCCCGACCCAAATGTTGCGAGTACCCAGTAATCGGGTACCCGGATTTTGC
1657711 GGGTACCTGAAAATTGATTTTTTTTGGGTATGTGGTGTTTGAATATAGG
196 GGGTACCTGAAAATTGATTTTTTTTGGGTATGTGGTGTTTGAATATAGG
1657760 TATAGTGTCTAGAATAAGTCATGTTGAGGGGTGAAGTGAAATTAAAAATGTGGTCGGTGATTGGC
1 TATAGTGTCTAGAATAAGTCATGTTGAGGGGTGAAGTGAAATTAAAAATGTGGTCGGTGATTGGC
* *
1657825 GTAAAAAGTAGGGGTGTGCAAATCCGGGTACCCGAAGTGTCGGGTACTCGGATCTTAGGTAATTG
66 GGAAAAAGTAGGGGTGTGCAAATCCGGGTACCCGAAGTGTCGGGTACTCGAATCTTAGGTAATTG
* *
1657890 ATTTCTCGACCCGTGTCCCGACCCATATGTTGCGAGTACCCAGTAATTGGGTACCCGGATTTTGC
131 ATTTCTCGACCCGTGTCCCGACCCAAATGTTGCGAGTACCCAGTAATCGGGTACCCGGATTTTGC
1657955 GGGTAC
196 GGGTAC
1657961 TTGTATTTTG
Statistics
Matches: 189, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
244 189 1.00
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.31
Consensus pattern (244 bp):
TATAGTGTCTAGAATAAGTCATGTTGAGGGGTGAAGTGAAATTAAAAATGTGGTCGGTGATTGGC
GGAAAAAGTAGGGGTGTGCAAATCCGGGTACCCGAAGTGTCGGGTACTCGAATCTTAGGTAATTG
ATTTCTCGACCCGTGTCCCGACCCAAATGTTGCGAGTACCCAGTAATCGGGTACCCGGATTTTGC
GGGTACCTGAAAATTGATTTTTTTTGGGTATGTGGTGTTTGAATATAGG
Found at i:1666786 original size:20 final size:19
Alignment explanation
Indices: 1666775--1666826 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
1666765 ACTAGCCTTA
*
1666775 CAGTATCGATACCCACTCTT
1 CAGTATCGATA-CTACTCTT
1666795 CAGTATCGATACTCACTCTT
1 CAGTATCGATACT-ACTCTT
1666815 CAGTATCGATAC
1 CAGTATCGATAC
1666827 CGAAATGACA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.31
Consensus pattern (19 bp):
CAGTATCGATACTACTCTT
Found at i:1670257 original size:2 final size:2
Alignment explanation
Indices: 1670250--1670275 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1670240 CCCTTCAATT
1670250 TA 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
1670276 AATAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1675652 original size:30 final size:30
Alignment explanation
Indices: 1675616--1675676 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
1675606 ATAAAATTAG
* *
1675616 TAGCGCCTAATAATGTTTTC-GATCATTTTT
1 TAGCGCCTAATAATATTTCCAG-TCATTTTT
1675646 TAGCGCCTAATAATATTTCCAGTCATTTTT
1 TAGCGCCTAATAATATTTCCAGTCATTTTT
1675676 T
1 T
1675677 TTGAAAATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.46
Consensus pattern (30 bp):
TAGCGCCTAATAATATTTCCAGTCATTTTT
Done.