Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008314.1 Hibiscus syriacus cultivar Beakdansim tig00111008_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: 2414839
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:1891511 original size:19 final size:19
Alignment explanation
Indices: 1891489--1891619 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
1891479 GGAAATTACT
*
1891489 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1891508 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1891522 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1891541 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1891555 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1891574 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
1891588 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1891607 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1891620 TTTAATTTCG
Statistics
Matches: 83, Mismatches: 14, Indels: 30
0.65 0.11 0.24
Matches are distributed among these distances:
14 27 0.33
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 38 0.46
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1891536 original size:33 final size:33
Alignment explanation
Indices: 1891489--1891615 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
1891479 GGAAATTACT
*
1891489 ATCGTAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1891522 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1891554 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1891588 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1891616 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1891600 original size:66 final size:66
Alignment explanation
Indices: 1891494--1891622 Score: 240
Period size: 66 Copynumber: 2.0 Consensus size: 66
1891484 TTACTATCGT
*
1891494 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTCG
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCG
1891559 C
66 C
*
1891560 AATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1891623 AATTTCGCGT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (66 bp):
AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCG
C
Found at i:1891817 original size:14 final size:14
Alignment explanation
Indices: 1891798--1891834 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1891788 CATCAATTAA
1891798 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1891812 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1891826 ACAAATCAA
1 ACAAATCAA
1891835 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1893258 original size:21 final size:21
Alignment explanation
Indices: 1893192--1893258 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1893182 GTGAATCGGG
*
1893192 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1893212 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1893234 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1893255 CTCT
1 CTCT
1893259 CGAGGAATCA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1893277 original size:42 final size:42
Alignment explanation
Indices: 1893231--1893314 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
1893221 CGATGACAGT
* * *
1893231 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATCATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATCATAGG
* * * *
1893273 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATCATAGG
1893315 CGAGTCGGGC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATCATAGG
Found at i:1895274 original size:33 final size:33
Alignment explanation
Indices: 1895217--1895315 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
1895207 ACGAGATAAT
*
1895217 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
1895251 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
1895284 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
1895316 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1895309 original size:19 final size:19
Alignment explanation
Indices: 1895192--1895376 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
1895182 TATTTTGGTT
*
1895192 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1895211 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1895231 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1895249 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1895265 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
1895283 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1895298 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
1895318 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1895337 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1895356 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1895375 GA
1 GA
1895377 TTTTGGTTTC
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 62 0.45
20 45 0.33
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1895330 original size:39 final size:38
Alignment explanation
Indices: 1895287--1895376 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
1895277 GCGACCAGAC
1895287 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
1895326 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
1895364 AATCGCAATGCGA
1 AATCGCAACGCGA
1895377 TTTTGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 22 0.45
39 27 0.55
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:1895394 original size:19 final size:19
Alignment explanation
Indices: 1895372--1895438 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
1895362 AAAATCGCAA
* *
1895372 TGCGATTTTGGTTTCTCGT
1 TGCGATTTTGATTTCGCGT
*
1895391 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
1895410 TGCGATAGTT-ATTTCCGCGT
1 TGCGAT-TTTGATTT-CGCGT
1895430 TGCGATTTT
1 TGCGATTTT
1895439 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 28 0.68
20 13 0.32
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:1895982 original size:20 final size:20
Alignment explanation
Indices: 1895957--1896008 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1895947 CGCTATGTAA
*
1895957 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
1895977 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
1895997 ATCTCGTTGCGA
1 ATCGCGTTGCGA
1896009 TTTTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:1896063 original size:20 final size:20
Alignment explanation
Indices: 1896019--1896111 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1896009 TTTTTTATTA
* **
1896019 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
1896040 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
1896060 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
1896081 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
1896101 TCGCATTGCGA
1 TCGCATTGCGA
1896112 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:1896064 original size:41 final size:41
Alignment explanation
Indices: 1896001--1896111 Score: 188
Period size: 41 Copynumber: 2.7 Consensus size: 41
1895991 GTAAGTATCT
*
1896001 CGTTGCGATTT-TTTATTATCGCATTGCGATTTTCCCAATTCG
1 CGTTGCGATTTACTTA-T-TCGCATTGCGATTTTCCCAATTCG
1896043 CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
1 CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
1896084 CGTTGCGATTTACTTATTCGCATTGCGA
1 CGTTGCGATTTACTTATTCGCATTGCGA
1896112 ATTGGGAAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
41 52 0.78
42 12 0.18
43 3 0.04
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (41 bp):
CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
Found at i:1914499 original size:15 final size:16
Alignment explanation
Indices: 1914457--1914499 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
1914447 AGTGACAACC
1914457 ATTATTATTTTCTATA
1 ATTATTATTTTCTATA
1914473 ATTATATATTTT-TAT-
1 ATTAT-TATTTTCTATA
1914488 ATTCATTATTTT
1 ATT-ATTATTTT
1914500 AATTTATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 9 0.36
16 10 0.40
17 6 0.24
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTATTATTTTCTATA
Found at i:1922420 original size:37 final size:37
Alignment explanation
Indices: 1922344--1922420 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
1922334 TTTTTATATT
*
1922344 TTTAATTTTGTAAAAAAATATATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATATATATAAATATTATCAA
* * *
1922381 TTTAATTTTTTAAAGAAA-ATATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAATATATATAAATATTAT-CAA
1922418 TTT
1 TTT
1922421 GTAATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 14 0.40
37 21 0.60
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAATATATATAAATATTATCAA
Found at i:1922428 original size:17 final size:17
Alignment explanation
Indices: 1922406--1922451 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
1922396 AAAATATATA
1922406 AATATTTTACAATTTGT
1 AATATTTTACAATTTGT
1922423 AATATTTTACAATTTGT
1 AATATTTTACAATTTGT
*
1922440 AATATTATACAA
1 AATATTTTACAA
1922452 ATATATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (17 bp):
AATATTTTACAATTTGT
Found at i:1922792 original size:30 final size:32
Alignment explanation
Indices: 1922734--1922794 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
1922724 TAAGGTAATA
*
1922734 TATATGTTTAGTAATTAAATTATTATTTTTAT
1 TATATGTTTAATAATTAAATTATTATTTTTAT
*
1922766 TATAT-TTTAATATTTAAATT-TTATTTTTA
1 TATATGTTTAATAATTAAATTATTATTTTTA
1922795 AAAAATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 9 0.33
31 13 0.48
32 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (32 bp):
TATATGTTTAATAATTAAATTATTATTTTTAT
Found at i:1925852 original size:35 final size:35
Alignment explanation
Indices: 1925779--1925853 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
1925769 CGTCACTAAC
**
1925779 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
1925814 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
1925849 AGTAA
1 AGTAA
1925854 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:1925991 original size:23 final size:24
Alignment explanation
Indices: 1925931--1926021 Score: 105
Period size: 24 Copynumber: 3.8 Consensus size: 24
1925921 CATAATTCAA
*
1925931 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
*
1925955 GT-AATGTATCAGATCAGAATCCAT
1 GTCAA-GTATCAGATCAGAATCCAG
*
1925979 GTCAA-TATCAGATAAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
1926002 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
1926022 TCAAGTCGGA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
23 22 0.39
24 32 0.57
25 2 0.04
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:1926001 original size:47 final size:48
Alignment explanation
Indices: 1925931--1926021 Score: 121
Period size: 47 Copynumber: 1.9 Consensus size: 48
1925921 CATAATTCAA
* * * *
1925931 GTCAAGTATCATATCAGAATCCAGGTAATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATAAGAATCCAGGTAAGGTATCAGAACAGAATCCAT
* *
1925979 GTCAA-TATCAGATAAGAATCCAGGTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATAAGAATCCAGGTAAGGTATCAGAACAGAAT
1926022 TCAAGTCGGA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
47 32 0.86
48 5 0.14
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.25
Consensus pattern (48 bp):
GTCAAGTATCAGATAAGAATCCAGGTAAGGTATCAGAACAGAATCCAT
Found at i:1928557 original size:18 final size:18
Alignment explanation
Indices: 1928536--1928581 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
1928526 GTCGGGTAAA
1928536 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
*
1928554 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
1928572 CGGGTCGGGT
1 CGGGTCGGGT
1928582 TGTGACCGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.11, C:0.20, G:0.52, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:1928570 original size:26 final size:27
Alignment explanation
Indices: 1928511--1928571 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
1928501 CGGTCAACGA
*
1928511 TCAACGGGTCAACGGGTCGGGTAAACGGG
1 TCAACGGGTAAACGGGTCGGGT--ACGGG
1928540 T---CGGGTAAACGGGTCGGGT-CGGG
1 TCAACGGGTAAACGGGTCGGGTACGGG
1928563 TCAACGGGT
1 TCAACGGGT
1928572 CGGGTCGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
23 5 0.18
26 22 0.79
29 1 0.04
ACGTcount: A:0.20, C:0.20, G:0.44, T:0.16
Consensus pattern (27 bp):
TCAACGGGTAAACGGGTCGGGTACGGG
Found at i:1928577 original size:13 final size:13
Alignment explanation
Indices: 1928515--1928558 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
1928505 CAACGATCAA
*
1928515 CGGGTCAACGGGT
1 CGGGTAAACGGGT
1928528 CGGGTAAACGGGT
1 CGGGTAAACGGGT
1928541 CGGGTAAACGGGT
1 CGGGTAAACGGGT
1928554 CGGGT
1 CGGGT
1928559 CGGGTCAACG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.18, C:0.18, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTAAACGGGT
Found at i:1933350 original size:62 final size:62
Alignment explanation
Indices: 1933269--1933393 Score: 223
Period size: 62 Copynumber: 2.0 Consensus size: 62
1933259 ATCAAGTGGG
* *
1933269 CTTAATTCATCTAATAAAGTAAATACTCTTTATTTATTTTGACCACTACATATCGTTGTCGT
1 CTTAATTCATCTAATAAAGTAAATACTCCTTATTTATTTTGACCACTACAGATCGTTGTCGT
*
1933331 CTTAGTTCATCTAATAAAGTAAATACTCCTTATTTATTTTGACCACTACAGATCGTTGTCGT
1 CTTAATTCATCTAATAAAGTAAATACTCCTTATTTATTTTGACCACTACAGATCGTTGTCGT
1933393 C
1 C
1933394 GAAGGTCAGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.42
Consensus pattern (62 bp):
CTTAATTCATCTAATAAAGTAAATACTCCTTATTTATTTTGACCACTACAGATCGTTGTCGT
Found at i:1940073 original size:5 final size:5
Alignment explanation
Indices: 1940031--1940057 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1940021 AAAACCGAAA
1940031 AACCG AACCG AACCG AACCG AACCG AA
1 AACCG AACCG AACCG AACCG AACCG AA
1940058 AAACCCGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.44, C:0.37, G:0.19, T:0.00
Consensus pattern (5 bp):
AACCG
Found at i:1940079 original size:19 final size:19
Alignment explanation
Indices: 1940043--1940079 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1940033 CCGAACCGAA
*
1940043 CCGAACCGAACCGAAAAAC
1 CCGAACCGAACCAAAAAAC
1940062 CCGAACCGAACCAAAAAA
1 CCGAACCGAACCAAAAAA
1940080 ACCGGTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.35, G:0.14, T:0.00
Consensus pattern (19 bp):
CCGAACCGAACCAAAAAAC
Found at i:1941018 original size:24 final size:24
Alignment explanation
Indices: 1940991--1941036 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1940981 GACTAGACAT
*
1940991 TTTGCCAATGTTGGCAGGATAATC
1 TTTGCCAATGGTGGCAGGATAATC
***
1941015 TTTGGTGATGGTGGCAGGATAA
1 TTTGCCAATGGTGGCAGGATAA
1941037 CCATTTATGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.24, C:0.11, G:0.33, T:0.33
Consensus pattern (24 bp):
TTTGCCAATGGTGGCAGGATAATC
Found at i:1941715 original size:30 final size:30
Alignment explanation
Indices: 1941694--1941760 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
1941684 TACTTGAATT
*
1941694 TGAATTACTGGAATTTGAATTACTGAAAAA
1 TGAATTACTGAAATTTGAATTACTGAAAAA
*
1941724 TGAATTACTGAAATTTGAATT-CTGGAAAA
1 TGAATTACTGAAATTTGAATTACTGAAAAA
1941753 TGAATTAC
1 TGAATTAC
1941761 ATTTCTGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 15 0.43
30 20 0.57
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.34
Consensus pattern (30 bp):
TGAATTACTGAAATTTGAATTACTGAAAAA
Found at i:1941739 original size:45 final size:44
Alignment explanation
Indices: 1941672--1941760 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 44
1941662 ATTAAATTTT
**
1941672 TGAAAAATAAATTACTTGAATTTGAATTACTGGAATTTGAATTAC
1 TGAAAAATAAATTACTTGAATTTGAATT-CTGGAAAATGAATTAC
*
1941717 TGAAAAATGAATTAC-TGAAATTTGAATTCTGGAAAATGAATTAC
1 TGAAAAATAAATTACTTG-AATTTGAATTCTGGAAAATGAATTAC
1941761 ATTTCTGGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
44 16 0.40
45 24 0.60
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.35
Consensus pattern (44 bp):
TGAAAAATAAATTACTTGAATTTGAATTCTGGAAAATGAATTAC
Found at i:1941751 original size:15 final size:15
Alignment explanation
Indices: 1941681--1941744 Score: 85
Period size: 15 Copynumber: 4.3 Consensus size: 15
1941671 TTGAAAAATA
1941681 AATTACTTG-AATTTG
1 AATTAC-TGAAATTTG
*
1941696 AATTACTGGAATTTG
1 AATTACTGAAATTTG
**
1941711 AATTACTGAAAAATG
1 AATTACTGAAATTTG
1941726 AATTACTGAAATTTG
1 AATTACTGAAATTTG
1941741 AATT
1 AATT
1941745 CTGGAAAATG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
14 2 0.05
15 41 0.95
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (15 bp):
AATTACTGAAATTTG
Found at i:1941781 original size:14 final size:14
Alignment explanation
Indices: 1941762--1941793 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1941752 ATGAATTACA
1941762 TTTCTGGAAAACGT
1 TTTCTGGAAAACGT
*
1941776 TTTCTGGAAAATGT
1 TTTCTGGAAAACGT
1941790 TTTC
1 TTTC
1941794 CGTAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (14 bp):
TTTCTGGAAAACGT
Found at i:1941978 original size:21 final size:21
Alignment explanation
Indices: 1941934--1942004 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 21
1941924 CAATAAATAA
* *
1941934 TATTATTTATCATAAAACTTATT
1 TATTATTTA-AATAATA-TTATT
1941957 TATTATTTAAAATAAT-TTATT
1 TATTATTT-AAATAATATTATT
1941978 TATTA-TTAAATAATATT-TT
1 TATTATTTAAATAATATTATT
*
1941997 TATAATTT
1 TATTATTT
1942005 TATTAATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
19 13 0.31
20 6 0.14
21 10 0.24
23 12 0.29
24 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTATTTAAATAATATTATT
Found at i:1941994 original size:17 final size:19
Alignment explanation
Indices: 1941952--1941999 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
1941942 ATCATAAAAC
1941952 TTATTTATTATTTAAAATAA
1 TTATTTATTA-TTAAAATAA
1941972 TTTATTTATTATT-AAATAA
1 -TTATTTATTATTAAAATAA
1941991 -TATTT-TTAT
1 TTATTTATTAT
1942000 AATTTTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 4 0.15
17 5 0.19
19 6 0.22
20 2 0.07
21 10 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATTTATTATTAAAATAA
Found at i:1942186 original size:19 final size:20
Alignment explanation
Indices: 1942134--1942186 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
1942124 TTAAATATCT
1942134 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
1942153 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
1942174 TTATTAAATATAT
1 TTATTAAATATAT
1942187 AAAAATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:1942199 original size:28 final size:27
Alignment explanation
Indices: 1942143--1942221 Score: 79
Period size: 31 Copynumber: 2.7 Consensus size: 27
1942133 TTTATTAAAA
1942143 TATTATTTAAATATATAAATAATATTAT
1 TATTA-TTAAATATATAAATAATATTAT
*
1942171 TCATTATTAAATATATAAAAATTTATATTAT
1 T-ATTATTAAATATAT--AAA-TAATATTAT
*
1942202 ATATTATTAAA-ATAAAAATA
1 -TATTATTAAATATATAAATA
1942222 TAATATCTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
27 1 0.02
28 14 0.33
29 4 0.09
30 6 0.14
31 17 0.40
32 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (27 bp):
TATTATTAAATATATAAATAATATTAT
Found at i:1942208 original size:31 final size:31
Alignment explanation
Indices: 1942142--1942316 Score: 91
Period size: 28 Copynumber: 5.6 Consensus size: 31
1942132 CTTTATTAAA
*
1942142 ATATTATTTAAATATAT--AAA-TAATATTAT
1 ATATTA-TTAAATATATAAAAATTTATATTAT
1942171 -TCATTATTAAATATATAAAAATTTATATTAT
1 AT-ATTATTAAATATATAAAAATTTATATTAT
*
1942202 ATATTATT-AA-A-ATAAAAATATAATATCT-T
1 ATATTATTAAATATATAAAAAT-TTATAT-TAT
* * *
1942231 ATATTATTATAATA-ATATAATTGATTATTTTAT
1 ATATTATTA-AATATATAAAAAT--TTATATTAT
* * *
1942264 ATAATATTAAAAATAT-AATATTATATTATTAT
1 ATATTATTAAATATATAAAAATT-TA-TATTAT
* *
1942296 AAATATTAATAAATAAATAAA
1 --ATATTATTAAATATATAAA
1942317 TAAATAATAT
Statistics
Matches: 112, Mismatches: 16, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
28 19 0.17
29 19 0.17
30 7 0.06
31 18 0.16
32 19 0.17
33 16 0.14
34 12 0.11
35 2 0.02
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.46
Consensus pattern (31 bp):
ATATTATTAAATATATAAAAATTTATATTAT
Found at i:1942215 original size:60 final size:61
Alignment explanation
Indices: 1942142--1942295 Score: 158
Period size: 60 Copynumber: 2.5 Consensus size: 61
1942132 CTTTATTAAA
*
1942142 ATATTATTTAAATATATAA-ATAATATTATTCATTATTA-AATATATAAAAAT-TTATATTAT
1 ATATTATTAAAATATATAATATAATATTATT-ATTATTATAATA-ATAAAAATATTATATTAT
* * * *
1942202 ATATTATTAAAATA-AAAATATAATATCT-TATATTATTATAATAATATAATTGATTATTTTAT
1 ATATTATTAAAATATATAATATAATAT-TAT-TATTATTATAATAATAAAAAT-ATTATATTAT
* *
1942264 ATAATATTAAAA-ATATAATATTATATTATTAT
1 ATATTATTAAAATATATAATATAATATTATTAT
1942296 AAATATTAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
59 3 0.04
60 34 0.44
61 11 0.14
62 30 0.38
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (61 bp):
ATATTATTAAAATATATAATATAATATTATTATTATTATAATAATAAAAATATTATATTAT
Found at i:1942288 original size:22 final size:23
Alignment explanation
Indices: 1942263--1942306 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1942253 GATTATTTTA
1942263 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
1942285 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
1942307 AATAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:1942790 original size:2 final size:2
Alignment explanation
Indices: 1942783--1942814 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1942773 TTTATTTCGT
1942783 TA 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
1942815 AAGATTTGAA
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):
TA
Found at i:1947214 original size:22 final size:20
Alignment explanation
Indices: 1947189--1947228 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
1947179 ATAATATTTA
1947189 TACTATTAACGTATTAAATAAT
1 TACTATTAA-GT-TTAAATAAT
*
1947211 TACTTTTAAGTTTAAATA
1 TACTATTAAGTTTAAATA
1947229 TGATTATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 2 0.12
22 8 0.47
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (20 bp):
TACTATTAAGTTTAAATAAT
Found at i:1949474 original size:23 final size:23
Alignment explanation
Indices: 1949447--1949496 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1949437 ATAAGTCTAT
* *
1949447 ATTAAAAAAATAGTTATTTTTAC
1 ATTAAAAAAATAATTAATTTTAC
* *
1949470 ATTAAAAAATTAATTAATTTTAT
1 ATTAAAAAAATAATTAATTTTAC
1949493 ATTA
1 ATTA
1949497 TATTAATTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTAAAAAAATAATTAATTTTAC
Found at i:1953088 original size:114 final size:114
Alignment explanation
Indices: 1952888--1953115 Score: 420
Period size: 114 Copynumber: 2.0 Consensus size: 114
1952878 TATTATTATG
1952888 GGGTAATTAATTAATAAAACTGTAGCACAATGTTCGCTATATTAATTGGTTCGACGTTTTAGTGT
1 GGGTAATTAATTAATAAAACTGTAGCACAATGTTCGCTATATTAATTGGTTCGACGTTTTAGTGT
1952953 GACTAAAATTATACTATAACAACTAGCGGGATTAGTTTAAGTAGTAATT
66 GACTAAAATTATACTATAACAACTAGCGGGATTAGTTTAAGTAGTAATT
* * *
1953002 GGGTAATTAATTAATAAAACTTTAGTATAATGTTCGCTATATTAATTGGTTCGACGTTTTAGTGT
1 GGGTAATTAATTAATAAAACTGTAGCACAATGTTCGCTATATTAATTGGTTCGACGTTTTAGTGT
*
1953067 GACTAAAATTATACTATAACAACTAGCGGGGTTAGTTTAAGTAGTAATT
66 GACTAAAATTATACTATAACAACTAGCGGGATTAGTTTAAGTAGTAATT
1953116 AACATGATAT
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 110 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (114 bp):
GGGTAATTAATTAATAAAACTGTAGCACAATGTTCGCTATATTAATTGGTTCGACGTTTTAGTGT
GACTAAAATTATACTATAACAACTAGCGGGATTAGTTTAAGTAGTAATT
Found at i:1955602 original size:24 final size:24
Alignment explanation
Indices: 1955557--1955602 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1955547 TGAAGTAAAG
* *
1955557 TTTAATAAGTAAATTTGTAATTTA
1 TTTAATAAATAAATTTGAAATTTA
1955581 TTTAATAAATAAAATTT-AAATT
1 TTTAATAAAT-AAATTTGAAATT
1955603 AAATCAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
TTTAATAAATAAATTTGAAATTTA
Found at i:1957423 original size:2 final size:2
Alignment explanation
Indices: 1957416--1957468 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1957406 AATGCTACAG
1957416 TA TA TA TA TA TA 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
1957458 TA TA TA TA TA T
1 TA TA TA TA TA T
1957469 GATTAAAGTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1963546 original size:16 final size:18
Alignment explanation
Indices: 1963525--1963561 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
1963515 AAGATGTAGT
1963525 TTAGGTT-TAGTTTA-AA
1 TTAGGTTATAGTTTATAA
*
1963541 TTAGGTTATATTTTATAA
1 TTAGGTTATAGTTTATAA
1963559 TTA
1 TTA
1963562 TAGGGTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 6 0.33
18 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (18 bp):
TTAGGTTATAGTTTATAA
Found at i:1975217 original size:18 final size:17
Alignment explanation
Indices: 1975190--1975322 Score: 69
Period size: 18 Copynumber: 8.2 Consensus size: 17
1975180 AAGAAGAAAT
1975190 AAAA-GAGAAAAAATGAG
1 AAAATGAGAAAAAA-GAG
1975207 AAAATGAGAAAAAAGA-
1 AAAATGAGAAAAAAGAG
*
1975223 AAAATGATGGAAAAAA-CG
1 AAAATGA--GAAAAAAGAG
1975241 AAAA-G-GAAAAAA-A-
1 AAAATGAGAAAAAAGAG
*
1975254 AGAA-GA-AAAAAATG-G
1 AAAATGAGAAAAAA-GAG
*
1975269 AAAAGGGAAGAAAAAATGA-
1 AAAA-TG-AGAAAAAA-GAG
1975288 AAAAT--GAAAAAAGAG
1 AAAATGAGAAAAAAGAG
1975303 AAAAATGA-AAAAAAGAG
1 -AAAATGAGAAAAAAGAG
1975320 AAA
1 AAA
1975323 TAAAAGGAGG
Statistics
Matches: 94, Mismatches: 5, Indels: 35
0.70 0.04 0.26
Matches are distributed among these distances:
13 10 0.11
14 9 0.10
15 10 0.11
16 15 0.16
17 17 0.18
18 21 0.22
19 12 0.13
ACGTcount: A:0.72, C:0.01, G:0.21, T:0.06
Consensus pattern (17 bp):
AAAATGAGAAAAAAGAG
Found at i:1975289 original size:28 final size:28
Alignment explanation
Indices: 1975195--1975291 Score: 80
Period size: 28 Copynumber: 3.6 Consensus size: 28
1975185 GAAATAAAAG
*
1975195 AGAAAAA-ATG-AGAAAATGAGAAAA--A
1 AGAAAAAGATGAAAAAAATG-GAAAAGGA
* *
1975220 AGAAAAATGATGGAAAAAA-CGAAAAGGA
1 AGAAAAA-GATGAAAAAAATGGAAAAGGA
* *
1975248 AAAAAAAGAAGAAAAAAATGGAAAAGGGA
1 AGAAAAAGATGAAAAAAATGGAAAA-GGA
1975277 AGAAAAA-ATGAAAAA
1 AGAAAAAGATGAAAAA
1975292 TGAAAAAAGA
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
25 7 0.12
26 5 0.09
27 12 0.21
28 24 0.42
29 9 0.16
ACGTcount: A:0.71, C:0.01, G:0.22, T:0.06
Consensus pattern (28 bp):
AGAAAAAGATGAAAAAAATGGAAAAGGA
Found at i:1975299 original size:62 final size:64
Alignment explanation
Indices: 1975192--1975321 Score: 146
Period size: 63 Copynumber: 2.0 Consensus size: 64
1975182 GAAGAAATAA
*
1975192 AAGAGAAAAAATGAGAAAATGAGAAAAAAGAAAAATGATGGAAAAA-ACG-AAAAGGAAAAAAA-
1 AAGAGAAAAAATGAGAAAAGGAGAAAAAAGAAAAATGA--GAAAAAGA-GAAAAAGGAAAAAAAG
1975254 AG
63 AG
*
1975256 AAGA-AAAAAATG-GAAAAGGGAAGAAAAAATGAAAAATGA-AAAAAGAGAAAAATGAAAAAAAG
1 AAGAGAAAAAATGAGAAAA-GG-AGAAAAAA-GAAAAATGAGAAAAAGAGAAAAAGGAAAAAAAG
1975318 AG
63 AG
1975320 AA
1 AA
1975322 ATAAAAGGAG
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
62 11 0.19
63 22 0.38
64 16 0.28
65 9 0.16
ACGTcount: A:0.72, C:0.01, G:0.22, T:0.06
Consensus pattern (64 bp):
AAGAGAAAAAATGAGAAAAGGAGAAAAAAGAAAAATGAGAAAAAGAGAAAAAGGAAAAAAAGAG
Found at i:1975317 original size:17 final size:16
Alignment explanation
Indices: 1975286--1975322 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 16
1975276 AAGAAAAAAT
1975286 GAAAAATGAAAAAAGA
1 GAAAAATGAAAAAAGA
1975302 GAAAAATGAAAAAAAGA
1 GAAAAATG-AAAAAAGA
1975319 GAAA
1 GAAA
1975323 TAAAAGGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (16 bp):
GAAAAATGAAAAAAGA
Found at i:1975322 original size:61 final size:59
Alignment explanation
Indices: 1975185--1975327 Score: 141
Period size: 62 Copynumber: 2.3 Consensus size: 59
1975175 GCTTGAAGAA
*
1975185 GAAATAAAAGAG-AAAAAATGAGAAAATGAGAAAAAAGAAAAATGATGGAAAAAACGAAAAG
1 GAAA-AAAAGAGAAAAAAATGAGAAAAGGAGAAAAAAGAAAAATGA--GAAAAAACGAAAAG
1975246 GAAAAAAAAGAAGAAAAAAATG-GAAAAGGGAAGAAAAAATGAAAAATGA-AAAAAGA-GAAAAA
1 G-AAAAAAAG-AGAAAAAAATGAGAAAA-GG-AGAAAAAA-GAAAAATGAGAAAAA-ACG-AAAA
*
1975308 T
59 G
1975309 GAAAAAAAGAGAAATAAAA
1 GAAAAAAAGAGAAA-AAAA
1975328 GGAGGGTTCA
Statistics
Matches: 71, Mismatches: 2, Indels: 17
0.79 0.02 0.19
Matches are distributed among these distances:
61 11 0.15
62 28 0.39
63 15 0.21
64 8 0.11
65 9 0.13
ACGTcount: A:0.72, C:0.01, G:0.20, T:0.07
Consensus pattern (59 bp):
GAAAAAAAGAGAAAAAAATGAGAAAAGGAGAAAAAAGAAAAATGAGAAAAAACGAAAAG
Found at i:1976706 original size:51 final size:51
Alignment explanation
Indices: 1976641--1977101 Score: 751
Period size: 51 Copynumber: 9.0 Consensus size: 51
1976631 AAGCAAATTC
*
1976641 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCAGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
*
1976692 GTTCGTTGAAGATTGAGTCATATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1976743 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1976794 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1976845 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
*
1976896 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATTAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
* *
1976947 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACTA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
* * **
1976998 GTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCT
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
** * * * *
1977049 GTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAAGAGAGAGCGGAC
1 GTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1977102 CCGTTTTATT
Statistics
Matches: 389, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
51 357 0.92
54 2 0.01
55 30 0.08
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (51 bp):
GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
Found at i:1977098 original size:55 final size:55
Alignment explanation
Indices: 1976712--1977208 Score: 244
Period size: 51 Copynumber: 9.5 Consensus size: 55
1976702 GATTGAGTCA
* * ** ** *
1976712 TATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-GAGTCC
1 TATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTGTTCGAGTTC
* * ** ** *
1976763 TATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-GAGTCC
1 TATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTGTTCGAGTTC
* * ** ** *
1976814 TATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-GAGTCC
1 TATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTGTTCGAGTTC
* * ** ** *
1976865 TATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-GAGTCC
1 TATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTGTTCGAGTTC
** * ** ** *
1976916 TATACTCTCTGAATTAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-GAGTCC
1 TATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTGTTCGAGTTC
* ** *
1976967 TATACTCTCTGAAAGAATAGGGAGCGGA-CTAGTTCGTTGAAGA---TT-GAGTCC
1 TATACTCTCTGAAAGAATAGAGAGCGGACCT-GTTTATTGAAGATTGTTCGAGTTC
* * *
1977018 TATACTCCCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTTTTCGAGTTC
1 TATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTGTTCGAGTTC
* * * * **
1977073 TATACTCTCTGAAGGAAGAGAGAGCGGACCCGTTTTATTAAAGATTGTTC-AAATC
1 TATACTCTCTGAAAGAATAGAGAGCGGACCTG-TTTATTGAAGATTGTTCGAGTTC
* *
1977128 TTATACTCTCTGAATGAATAGAGAGCAGACAC-GTTT-TATGAAGATTGTTCGAG-TC
1 -TATACTCTCTGAAAGAATAGAGAGCGGAC-CTGTTTAT-TGAAGATTGTTCGAGTTC
* *
1977183 TTATACT-TCCTGAAGGAATAGGGAGC
1 -TATACTCT-CTGAAAGAATAGAGAGC
1977209 AGGCTCGTCA
Statistics
Matches: 409, Mismatches: 25, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
51 286 0.70
52 2 0.00
54 4 0.01
55 73 0.18
56 43 0.11
57 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.29
Consensus pattern (55 bp):
TATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTGTTCGAGTTC
Found at i:1977209 original size:55 final size:55
Alignment explanation
Indices: 1977012--1977210 Score: 208
Period size: 55 Copynumber: 3.6 Consensus size: 55
1977002 GTTGAAGATT
* * * * * *
1977012 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACC-TGTTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCGT-TTTATTGAAGATTGTTC
* * *
1977067 GAGT-TCTATACTCTCTGAAGGAAGAGAGAGCGGACCCGTTTTATTAAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGA-CCGTTTTATTGAAGATTGTTC
* * *
1977123 AAATCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA-TGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
*
1977178 GAGTCTTATACT-TCCTGAAGGAATAGGGAGCAG
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGCAG
1977211 GCTCGTCATT
Statistics
Matches: 121, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
54 1 0.01
55 67 0.55
56 51 0.42
57 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (55 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCGTTTTATTGAAGATTGTTC
Found at i:1977225 original size:55 final size:55
Alignment explanation
Indices: 1977073--1977234 Score: 166
Period size: 55 Copynumber: 2.9 Consensus size: 55
1977063 TTTCGAGTTC
* * * * *
1977073 TATACTCTCTGAAGGAAGAGAGAGCGGACCCGTTTTATTAAAGATTGTTCAAATCT
1 TATACTCTCTGAAGGAATAGAGAGCAGACACGTATTA-TGAAGATTGTTCAAATCT
* * * *
1977129 TATACTCTCTGAATGAATAGAGAGCAGACACGTTTTATGAAGATTGTTCGAGTCT
1 TATACTCTCTGAAGGAATAGAGAGCAGACACGTATTATGAAGATTGTTCAAATCT
* * * *
1977184 TATACT-TCCTGAAGGAATAGGGAGCAGGCTCGTCATT-TGAAGATTTTTCAA
1 TATACTCT-CTGAAGGAATAGAGAGCAGACACGT-ATTATGAAGATTGTTCAA
1977235 GTATTTATCC
Statistics
Matches: 90, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
54 1 0.01
55 54 0.60
56 35 0.39
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (55 bp):
TATACTCTCTGAAGGAATAGAGAGCAGACACGTATTATGAAGATTGTTCAAATCT
Found at i:1978433 original size:16 final size:18
Alignment explanation
Indices: 1978412--1978448 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
1978402 AAGATGTAGT
1978412 TTAGGTT-TAGTTTA-AA
1 TTAGGTTATAGTTTATAA
*
1978428 TTAGGTTATATTTTATAA
1 TTAGGTTATAGTTTATAA
1978446 TTA
1 TTA
1978449 TAGGGTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 6 0.33
18 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (18 bp):
TTAGGTTATAGTTTATAA
Found at i:1993919 original size:2 final size:2
Alignment explanation
Indices: 1993901--1993951 Score: 66
Period size: 2 Copynumber: 24.5 Consensus size: 2
1993891 GCTCTGTATG
* *
1993901 AT AT AT GT AT AT CAT AT AT GAA AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT -AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
1993945 AT AT AT A
1 AT AT AT A
1993952 GTTATAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 40 0.93
3 3 0.07
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2005725 original size:38 final size:38
Alignment explanation
Indices: 2005674--2005747 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
2005664 GTCGCTTTCA
*
2005674 TCAAATTAAGATTTAGACTAATTACTCTTTATGTTATT
1 TCAAATTAAGATTTAGACTAATTAATCTTTATGTTATT
*
2005712 TCAAATTACGATTTAGACTAATTAATCTTTATGTTA
1 TCAAATTAAGATTTAGACTAATTAATCTTTATGTTA
2005748 CGATAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (38 bp):
TCAAATTAAGATTTAGACTAATTAATCTTTATGTTATT
Found at i:2012511 original size:93 final size:94
Alignment explanation
Indices: 2012352--2012541 Score: 319
Period size: 93 Copynumber: 2.0 Consensus size: 94
2012342 TCTGAAGCTT
*
2012352 CTTATGCATTTATGCTGTTGGTTTTCCTTGTTTCGTGTTTCCGCTTGTCTCAGCGGAAATTGTAA
1 CTTATGCATTTATGCTGTTGGTTTTCCTTGTTTCGTGTTTCCGCTTGTCTCAGCGGAAACTGTAA
* *
2012417 AAAG-TGTCTAGTGTTCATGTGTTTGCTA
66 AAAGTTGTCAAGTGTTCATGTGCTTGCTA
* *
2012445 CTTATGCATTTATGCTGTTGGTTTTCCTTGTTTCGTGTTTCCTCTTGTCTCAGCGGCAACTGTAA
1 CTTATGCATTTATGCTGTTGGTTTTCCTTGTTTCGTGTTTCCGCTTGTCTCAGCGGAAACTGTAA
2012510 AAAGTTTGTCAAGTGTTCATGTGCTTGCTA
66 AAAG-TTGTCAAGTGTTCATGTGCTTGCTA
2012540 CT
1 CT
2012542 CGAAACATAG
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
93 66 0.73
95 24 0.27
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.45
Consensus pattern (94 bp):
CTTATGCATTTATGCTGTTGGTTTTCCTTGTTTCGTGTTTCCGCTTGTCTCAGCGGAAACTGTAA
AAAGTTGTCAAGTGTTCATGTGCTTGCTA
Found at i:2013995 original size:23 final size:23
Alignment explanation
Indices: 2013969--2014013 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2013959 TAAATTATTG
2013969 TATATAGAAGAT-ATAATAAATAT
1 TATATAGAAGATAATAA-AAATAT
* *
2013992 TATATCGTAGATAATAAAAATA
1 TATATAGAAGATAATAAAAATA
2014014 ATTTGTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (23 bp):
TATATAGAAGATAATAAAAATAT
Found at i:2014216 original size:15 final size:15
Alignment explanation
Indices: 2014196--2014226 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2014186 CAACAAATAG
2014196 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
2014211 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
2014226 A
1 A
2014227 TTTAAAATTT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:2014538 original size:33 final size:33
Alignment explanation
Indices: 2014475--2014539 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
2014465 TCCTTCTTTT
* *
2014475 CTTCAGTTGCTCTTATAAATCATTCTCTCTCTC
1 CTTCAGTTGATCTTATAAATCATCCTCTCTCTC
*
2014508 CTTCAGTTGATCTTATAATTC-TCCTACTCTCT
1 CTTCAGTTGATCTTATAAATCATCCT-CTCTCT
2014540 TCCATCCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 3 0.11
33 25 0.89
ACGTcount: A:0.18, C:0.29, G:0.06, T:0.46
Consensus pattern (33 bp):
CTTCAGTTGATCTTATAAATCATCCTCTCTCTC
Found at i:2022575 original size:42 final size:42
Alignment explanation
Indices: 2022527--2022608 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
2022517 TTAATAATGT
* * *
2022527 TTTTAATATGTTAGTTTGATTTATTTATGAATTGTTACTTGA
1 TTTTAATATGTTAATTTAATATATTTATGAATTGTTACTTGA
*
2022569 TTTTAATATGTTAATTTAATATATTTATGGATTGTTACTT
1 TTTTAATATGTTAATTTAATATATTTATGAATTGTTACTT
2022609 TAAAGTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.57
Consensus pattern (42 bp):
TTTTAATATGTTAATTTAATATATTTATGAATTGTTACTTGA
Found at i:2032337 original size:21 final size:20
Alignment explanation
Indices: 2032304--2032345 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
2032294 TAATACTACT
2032304 TTATATTTTATTTTAGTTAA
1 TTATATTTTATTTTAGTTAA
*
2032324 TTATATTCTTATTTTATTTAA
1 TTATATT-TTATTTTAGTTAA
2032345 T
1 T
2032346 AAAAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TTATATTTTATTTTAGTTAA
Found at i:2032896 original size:36 final size:36
Alignment explanation
Indices: 2032856--2032928 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
2032846 TGAAACATGT
2032856 TAAACATCTTTCTAGAAATAAAAGTGGAATTTCGTG
1 TAAACATCTTTCTAGAAATAAAAGTGGAATTTCGTG
*
2032892 TAAACATCTTTCTAGAAATAAAGGTGGAATTTCGTG
1 TAAACATCTTTCTAGAAATAAAAGTGGAATTTCGTG
2032928 T
1 T
2032929 GTTCTTTTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (36 bp):
TAAACATCTTTCTAGAAATAAAAGTGGAATTTCGTG
Found at i:2034752 original size:30 final size:30
Alignment explanation
Indices: 2034718--2034775 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
2034708 ACACTATACA
*
2034718 TAACACGCATACACGAATCTAAATCAACAT
1 TAACAAGCATACACGAATCTAAATCAACAT
*
2034748 TAACAAGCATACACGTATCTAAATCAAC
1 TAACAAGCATACACGAATCTAAATCAAC
2034776 TTTTTTACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.47, C:0.26, G:0.07, T:0.21
Consensus pattern (30 bp):
TAACAAGCATACACGAATCTAAATCAACAT
Found at i:2042762 original size:20 final size:20
Alignment explanation
Indices: 2042737--2042797 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
2042727 TTTTGGTGCA
*
2042737 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
2042757 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
*
2042778 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATACCCCC
2042798 CCACAGGGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:2044814 original size:17 final size:17
Alignment explanation
Indices: 2044781--2044814 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2044771 TTGAATATTT
* *
2044781 TGGATTGTTTGATTTTG
1 TGGATTGTTAGACTTTG
2044798 TGGATTGTTAGACTTTG
1 TGGATTGTTAGACTTTG
2044815 GATTTGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.29, T:0.53
Consensus pattern (17 bp):
TGGATTGTTAGACTTTG
Found at i:2047649 original size:31 final size:31
Alignment explanation
Indices: 2047611--2047683 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
2047601 AATTTTTAAA
2047611 ATTATAAAATAAATATTAAAATTTTAATTTT
1 ATTATAAAATAAATATTAAAATTTTAATTTT
2047642 ATTATAAAATAAATATTAAAATTTTAATTTT
1 ATTATAAAATAAATATTAAAATTTTAATTTT
2047673 ATTATAAAATA
1 ATTATAAAATA
2047684 GGTATAATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
ATTATAAAATAAATATTAAAATTTTAATTTT
Found at i:2047651 original size:19 final size:19
Alignment explanation
Indices: 2047627--2047682 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
2047617 AAATAAATAT
2047627 TAAAATTTTAATTTTATTA
1 TAAAATTTTAATTTTATTA
*
2047646 TAAAA---TAA--ATA-T-
1 TAAAATTTTAATTTTATTA
2047658 TAAAATTTTAATTTTATTA
1 TAAAATTTTAATTTTATTA
2047677 TAAAAT
1 TAAAAT
2047683 AGGTATAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 14
0.64 0.05 0.32
Matches are distributed among these distances:
12 5 0.18
13 1 0.04
14 2 0.07
15 3 0.11
16 3 0.11
17 2 0.07
18 1 0.04
19 11 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAAATTTTAATTTTATTA
Found at i:2047836 original size:21 final size:23
Alignment explanation
Indices: 2047802--2047847 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
2047792 ACTTTTTACT
2047802 AATAATTTTATAAAA-ATA-AAA
1 AATAATTTTATAAAATATATAAA
2047823 AATAAGTTTT-TAAAATATATAAA
1 AATAA-TTTTATAAAATATATAAA
2047846 AA
1 AA
2047848 ATTAAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 10 0.45
22 7 0.32
23 5 0.23
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
AATAATTTTATAAAATATATAAA
Found at i:2052193 original size:35 final size:34
Alignment explanation
Indices: 2052108--2052194 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
2052098 ATTTGGTATT
*
2052108 TAAATATAACAAACTTACAATAAGAATTAAATGG
1 TAAATATAACAAAATTACAATAAGAATTAAATGG
* *
2052142 TAAATGATAACCAAATTACAATAACTGATGTTAAATGG
1 TAAAT-ATAACAAAATTACAATAA--GA-ATTAAATGG
2052180 T-AATA-AACAAAATTA
1 TAAATATAACAAAATTA
2052195 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 25 0.56
36 1 0.02
37 5 0.11
38 9 0.20
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (34 bp):
TAAATATAACAAAATTACAATAAGAATTAAATGG
Found at i:2052428 original size:9 final size:9
Alignment explanation
Indices: 2052410--2052459 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
2052400 CTCGCTATCA
*
2052410 TCGTCGTCG
1 TCGTCATCG
2052419 TCGTCATCG
1 TCGTCATCG
* *
2052428 TCGTCACCA
1 TCGTCATCG
2052437 TCGTCA---
1 TCGTCATCG
2052443 TCGTCATCG
1 TCGTCATCG
2052452 TCGTCATC
1 TCGTCATC
2052460 CTGAGCAGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
6 6 0.17
9 29 0.83
ACGTcount: A:0.12, C:0.36, G:0.20, T:0.32
Consensus pattern (9 bp):
TCGTCATCG
Found at i:2052430 original size:12 final size:12
Alignment explanation
Indices: 2052413--2052456 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
2052403 GCTATCATCG
2052413 TCGTCGTCGTCA
1 TCGTCGTCGTCA
**
2052425 TCGTCGTCACCA
1 TCGTCGTCGTCA
*
2052437 TCGTCATCGTCA
1 TCGTCGTCGTCA
2052449 TCGTCGTC
1 TCGTCGTC
2052457 ATCCTGAGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.11, C:0.36, G:0.20, T:0.32
Consensus pattern (12 bp):
TCGTCGTCGTCA
Found at i:2054453 original size:111 final size:111
Alignment explanation
Indices: 2054314--2054646 Score: 585
Period size: 111 Copynumber: 3.0 Consensus size: 111
2054304 ATTACAAAAA
*
2054314 TTAATTCTTAATATAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
2054379 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTCGAGATAT
* *
2054425 TTAATTCATAATCTAATAATCATACATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
** *
2054490 AATTAAAACGTTAAAATGTTATTGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTCGAGATAT
* *
2054536 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTATTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
2054601 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTCGAGATAT
2054647 ATGATTTCCA
Statistics
Matches: 208, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 208 1.00
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTCGAGATAT
Found at i:2054957 original size:49 final size:49
Alignment explanation
Indices: 2054904--2055027 Score: 167
Period size: 49 Copynumber: 2.5 Consensus size: 49
2054894 AGATACTCAG
* *
2054904 GTATAGCGCAGATCAGGGGCGCGCTATACCCACGTGGCGCCAGATCACC
1 GTATAGCGCGGATCAGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
* ** *
2054953 GTATATCGCGGGGCAGGGGCGCGCTATACCCACGTGGCGCCAAATCAGC
1 GTATAGCGCGGATCAGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
* *
2055002 GTATAGTGCGGTTCAGGAGGCGCGCT
1 GTATAGCGCGGATCAGG-GGCGCGCT
2055028 TTACTGTTAC
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
49 56 0.88
50 8 0.12
ACGTcount: A:0.20, C:0.29, G:0.35, T:0.16
Consensus pattern (49 bp):
GTATAGCGCGGATCAGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
Found at i:2056793 original size:67 final size:67
Alignment explanation
Indices: 2056693--2056882 Score: 213
Period size: 67 Copynumber: 2.8 Consensus size: 67
2056683 AATCATTATG
* *
2056693 TAACTCATGATCGCTAACCAATATGTAACTTTTGAAAGATTAGTGTCAAAAAAAATATTATGCAA
1 TAACTCATG-TCACTAACCATTATGTAACTTTTGAAAGATTAGTGTCAAAAAAAATATTATGCAA
2056758 TAT
65 TAT
* * * * *
2056761 TAACTCATGTCACTAACCGTTATGCAACTTTTGAAAGA--CGTGTCCAAAAAAAGTATTATGCAG
1 TAACTCATGTCACTAACCATTATGTAACTTTTGAAAGATTAGTGT-CAAAAAAAATATTATGCAA
*
2056824 TTT
65 TAT
* * * * * *
2056827 TATCTCATGGTCACTAATCATTATGTAACTTTTAAAATATTAGTTTCCAAAAAAAT
1 TAACTCAT-GTCACTAACCATTATGTAACTTTTGAAAGATTAGTGTCAAAAAAAAT
2056883 CATTTTAATG
Statistics
Matches: 100, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
65 4 0.04
66 26 0.26
67 50 0.50
68 17 0.17
69 3 0.03
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (67 bp):
TAACTCATGTCACTAACCATTATGTAACTTTTGAAAGATTAGTGTCAAAAAAAATATTATGCAAT
AT
Found at i:2060198 original size:19 final size:21
Alignment explanation
Indices: 2060169--2060207 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2060159 AGTTTCAGAG
2060169 AGTGAAATCAG-ATCCAAGAA
1 AGTGAAATCAGAATCCAAGAA
2060189 AGTG-AATCAGAATCCAAGA
1 AGTGAAATCAGAATCCAAGA
2060208 GATGGAGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.49, C:0.15, G:0.21, T:0.15
Consensus pattern (21 bp):
AGTGAAATCAGAATCCAAGAA
Found at i:2062321 original size:18 final size:20
Alignment explanation
Indices: 2062281--2062337 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
2062271 AGAAGTTAAA
* * *
2062281 AAAATAAATAAAATTTTAATT
1 AAAATAAGTAATA-TTTATTT
2062302 AAAA-AA-TAATATTTATTT
1 AAAATAAGTAATATTTATTT
*
2062320 AAAATAAGTTATATTTAT
1 AAAATAAGTAATATTTAT
2062338 ATATTCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 10 0.32
19 6 0.19
20 11 0.35
21 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
AAAATAAGTAATATTTATTT
Found at i:2070331 original size:2 final size:2
Alignment explanation
Indices: 2070324--2070351 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2070314 ATTAATAAAA
2070324 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
2070352 TAAAAATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2077281 original size:21 final size:21
Alignment explanation
Indices: 2077251--2077295 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2077241 CCTTTCGACT
* *
2077251 AAAGGACTTATCATTTTGATG
1 AAAGGACTTAACATTTTAATG
* *
2077272 AAAGGGCTTAACCTTTTAATG
1 AAAGGACTTAACATTTTAATG
2077293 AAA
1 AAA
2077296 AGATTTAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (21 bp):
AAAGGACTTAACATTTTAATG
Found at i:2078306 original size:17 final size:17
Alignment explanation
Indices: 2078284--2078320 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
2078274 CATGATCAAT
2078284 AATAACATCTTTTTAAC
1 AATAACATCTTTTTAAC
2078301 AATAACATCTTTTTAAC
1 AATAACATCTTTTTAAC
2078318 AAT
1 AAT
2078321 GCGCATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAACATCTTTTTAAC
Found at i:2082833 original size:15 final size:15
Alignment explanation
Indices: 2082813--2082843 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2082803 GCTACCTAAA
2082813 ATAAATATTTTCGAT
1 ATAAATATTTTCGAT
2082828 ATAAATATTTTCGAT
1 ATAAATATTTTCGAT
2082843 A
1 A
2082844 GAAAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (15 bp):
ATAAATATTTTCGAT
Found at i:2082919 original size:14 final size:15
Alignment explanation
Indices: 2082900--2082934 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
2082890 AAAAATATTA
2082900 ATATT-TTTAATAAT
1 ATATTCTTTAATAAT
2082914 ATATTTCTTTAATAAT
1 ATA-TTCTTTAATAAT
2082930 ATATT
1 ATATT
2082935 AGACTATCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.16
15 4 0.21
16 12 0.63
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATTCTTTAATAAT
Found at i:2090721 original size:112 final size:115
Alignment explanation
Indices: 2090524--2090757 Score: 429
Period size: 112 Copynumber: 2.1 Consensus size: 115
2090514 CAACAGCGGC
2090524 TATGCAGGTAAGGACACATTAAATGCTTGCTGAACTTCAAGTTCTTGGATTAAATATGACTAACT
1 TATGCAGGTAAGGACACATTAAATGCTTGCTGAACTTCAAGTTCTTGGATTAAATATGACTAACT
2090589 TGACTCGACCAACTCCTCTAAGACTCTTTGC-A-A-TGGTAAATATTGTG
66 TGACTCGACCAACTCCTCTAAGACTCTTTGCAAGACTGGTAAATATTGTG
*
2090636 TATGCAGGTAAGGACACATTAAATGCTTGCTGAACTTCAAGTTCTTGGATTAAATATGACTATCT
1 TATGCAGGTAAGGACACATTAAATGCTTGCTGAACTTCAAGTTCTTGGATTAAATATGACTAACT
2090701 TGACTCGACCAACTCCTCTAAGACTCTTTGCAATGACTGGTAAATATTGTG
66 TGACTCGACCAACTCCTCTAAGACTCTTTGCAA-GACTGGTAAATATTGTG
2090752 TATGCA
1 TATGCA
2090758 ACGAAAAATC
Statistics
Matches: 117, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
112 95 0.81
113 1 0.01
115 1 0.01
116 20 0.17
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (115 bp):
TATGCAGGTAAGGACACATTAAATGCTTGCTGAACTTCAAGTTCTTGGATTAAATATGACTAACT
TGACTCGACCAACTCCTCTAAGACTCTTTGCAAGACTGGTAAATATTGTG
Found at i:2091634 original size:2 final size:2
Alignment explanation
Indices: 2091629--2091657 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2091619 TTTTTTCATA
2091629 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2091658 TAGACACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2092252 original size:20 final size:20
Alignment explanation
Indices: 2092207--2092248 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2092197 ATTAGGTCAC
*
2092207 TAATAATAAAAATAAATAAA
1 TAATAAGAAAAATAAATAAA
*
2092227 TTATAAGAAAAATAAA-AAA
1 TAATAAGAAAAATAAATAAA
2092246 TAA
1 TAA
2092249 ATAAACTTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (20 bp):
TAATAAGAAAAATAAATAAA
Found at i:2095849 original size:15 final size:16
Alignment explanation
Indices: 2095824--2095856 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2095814 AAATAATCAT
2095824 ATATAATTATAAAAAA
1 ATATAATTATAAAAAA
*
2095840 ATAT-ATTATAACAAA
1 ATATAATTATAAAAAA
2095855 AT
1 AT
2095857 TACCTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATAATTATAAAAAA
Found at i:2097971 original size:20 final size:20
Alignment explanation
Indices: 2097926--2097977 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2097916 ACTTAAAATG
2097926 TTTTATTTTTA-AAAATAAT
1 TTTTATTTTTATAAAATAAT
** * *
2097945 TAATATTATTATAAAATTAT
1 TTTTATTTTTATAAAATAAT
2097965 TTTTATTTTTATA
1 TTTTATTTTTATA
2097978 TGATTTTTAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATTTTTATAAAATAAT
Found at i:2099518 original size:4 final size:4
Alignment explanation
Indices: 2099509--2099619 Score: 55
Period size: 4 Copynumber: 26.0 Consensus size: 4
2099499 AATGTTAGGA
** * *
2099509 AAAT AAAT AAAT AAAT AAAT ATTT AAAT AAAT CAAAG AAA- AAA- ACAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT
* * * *
2099556 AAGAAT GAAAAT AAAA ATAAT AAAT CAAAA AGAAG AAAT AAGAT AAAT AGAT
1 -A-AAT --AAAT AAAT A-AAT AAAT -AAAT A-AAT AAAT AA-AT AAAT AAAT
2099608 AAAT AAAT AAAT
1 AAAT AAAT AAAT
2099620 CAATTGGGAA
Statistics
Matches: 84, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
3 5 0.06
4 55 0.65
5 17 0.20
6 5 0.06
7 2 0.02
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:2099765 original size:22 final size:22
Alignment explanation
Indices: 2099723--2099766 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2099713 ATCAAAAGGA
*
2099723 AAAAATAAGATAAAGAATAAAT
1 AAAAATAAGATAAAAAATAAAT
*
2099745 AAAAATTAGA-AAAAAATTAAAT
1 AAAAATAAGATAAAAAA-TAAAT
2099767 CAAGGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (22 bp):
AAAAATAAGATAAAAAATAAAT
Found at i:2103075 original size:106 final size:106
Alignment explanation
Indices: 2102890--2103318 Score: 669
Period size: 106 Copynumber: 4.0 Consensus size: 106
2102880 TGTATTGTTC
* * * * * *
2102890 CGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTATGGAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
2102955 ACCAGTCGTCCCTTCGTTTTGAAGTTGAACTTGTGTTGTCT
66 ACCAGTCGTCCATTCGTTGTGAAGTTGAACTTGTGTTGTCT
** *
2102996 CGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
2103061 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
66 ACCAGTCGTCCATTCGTTGTGAAGTTGAACTTGTGTTGTCT
**
2103102 CGAGTCCAATGCCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
2103167 ACCAGTCGTTCATTCATTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGTCGTCCATTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
2103208 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
**
2103273 ACCAACCGTCCATTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGTCGTCCATTCGTTGTGAAGTTGAACTTGTGTTGTCT
2103314 CGAGT
1 CGAGT
2103319 GGCGCGATAT
Statistics
Matches: 296, Mismatches: 27, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 296 1.00
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.36
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGTCGTCCATTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:2104029 original size:37 final size:37
Alignment explanation
Indices: 2103947--2104031 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 37
2103937 GTTTCATGAG
* * * * **
2103947 AAACGGTCTCAAGGGAGACAAAATTTTGTTTTAAGAA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
2103984 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAA-AA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
*
2104020 GAAATTGTCTCA
1 -AAACTGTCTCA
2104032 TGGGGAGATG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 2 0.05
37 38 0.95
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (37 bp):
AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
Found at i:2104232 original size:36 final size:38
Alignment explanation
Indices: 2104178--2104254 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 38
2104168 GAAACAATTT
* *
2104178 CAAAGGTTTTTTTCCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTTGTTTCCAAGGGAAACTGTCTCAAGAGACA
2104216 CAAA-GTTTGTTT-CAAGGGAAACTGTCTCAAGAGACA
1 CAAAGGTTTGTTTCCAAGGGAAACTGTCTCAAGAGACA
2104252 CAA
1 CAA
2104255 TGGTGAGCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 26 0.70
37 7 0.19
38 4 0.11
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (38 bp):
CAAAGGTTTGTTTCCAAGGGAAACTGTCTCAAGAGACA
Found at i:2105894 original size:21 final size:21
Alignment explanation
Indices: 2105847--2105894 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
2105837 TGATTTTTGC
*
2105847 TTCTTTTATTTTTTGTTCTTG
1 TTCTTTTATTTTTTGTTATTG
*
2105868 TT-TTTTCTTTTTTGCTTATT-
1 TTCTTTTATTTTTTG-TTATTG
2105888 TTCTTTT
1 TTCTTTT
2105895 TTGTTCTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.04, C:0.10, G:0.06, T:0.79
Consensus pattern (21 bp):
TTCTTTTATTTTTTGTTATTG
Found at i:2111720 original size:84 final size:82
Alignment explanation
Indices: 2111565--2111818 Score: 239
Period size: 80 Copynumber: 3.1 Consensus size: 82
2111555 ACTCGACAAT
* * * * * *
2111565 TTTGTTGACAGATAGCCTCTCTTC-CCTTGAGCTATGTTGTAAATGATGGTGCCTTTGAGGTGAG
1 TTTGTTGACAGATAACC-CT-TCCACCTTAAGTTATGTTGCAAATGAT-GTGCCTTTGAGCTGAG
*
2111629 TGTAATCGAGCTCGAAGGTC
63 TGTAATCGAGCTCGAAGATC
* *
2111649 TTTGGTTGGCAGATGACCCTTCTCGA-CTTAAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAG
1 TTT-GTTGACAGATAACCCTTC-C-ACCTTAAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAG
* * *
2111713 TGGAATCGAACTCTAAGATC
63 TGTAATCGAGCTCGAAGATC
* * * *
2111733 --T-TTGACAGATAACCCTTCCATCCTTGAGTTATGTTGCAAATGATGTACCCTCGAAGCTGAGT
1 TTTGTTGACAGATAACCCTTCCA-CCTTAAGTTATGTTGCAAATGATGTGCCTTTG-AGCTGAGT
* *
2111795 GTAGTCGAGCTCGAAGTTC
64 GTAATCGAGCTCGAAGATC
2111814 TTTGT
1 TTTGT
2111819 GTTTCAAGAG
Statistics
Matches: 137, Mismatches: 23, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
78 1 0.01
79 1 0.01
80 42 0.31
81 22 0.16
82 1 0.01
83 2 0.01
84 38 0.28
85 30 0.22
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (82 bp):
TTTGTTGACAGATAACCCTTCCACCTTAAGTTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGT
AATCGAGCTCGAAGATC
Found at i:2111889 original size:34 final size:35
Alignment explanation
Indices: 2111814--2111901 Score: 135
Period size: 36 Copynumber: 2.5 Consensus size: 35
2111804 CTCGAAGTTC
2111814 TTTGTGTTTCAAGAGAAACATTTTCAAAGGTTTTTT
1 TTTGTGTTTCAAGAGAAACATTTTCAAAGG-TTTTT
*
2111850 TTTGTGTTTCAAGAGAAACGA-TTTGAAAGG-TTTT
1 TTTGTGTTTCAAGAGAAAC-ATTTTCAAAGGTTTTT
2111884 TTTGTGTTTCAAGAGAAA
1 TTTGTGTTTCAAGAGAAA
2111902 TTGTCTCCAG
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
34 22 0.44
36 27 0.54
37 1 0.02
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (35 bp):
TTTGTGTTTCAAGAGAAACATTTTCAAAGGTTTTT
Found at i:2112043 original size:36 final size:37
Alignment explanation
Indices: 2111955--2112093 Score: 183
Period size: 37 Copynumber: 3.8 Consensus size: 37
2111945 CAAAGATTGG
* *
2111955 TGTTTCAAGAGAAACTGACTCAAGAGAGATAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
*
2111992 TGTTTTAAG-GAAAACTGTCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAACTT
2112028 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
* * * * *
2112065 AGTTCCAAAAGAAATTGTCTCAAGGGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA
2112094 TGGAATTTGT
Statistics
Matches: 90, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
36 34 0.38
37 56 0.62
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
Found at i:2112084 original size:73 final size:73
Alignment explanation
Indices: 2111955--2112113 Score: 196
Period size: 73 Copynumber: 2.2 Consensus size: 73
2111945 CAAAGATTGG
* * ** *
2111955 TGTTTCAAGAGAAACTGACTCAAGAGAGATAAAACTTTGTTTTAAGGAAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGACTCAAGAGAGACAAAACTTAGTTCAAAAGAAAACTGTCTCAAGAGAG
2112020 ACAAAATT
66 ACAAAATT
* * *
2112028 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAG-AAATTGTCTCAAGGGA
1 TGTTTCAAGAGAAACTGACTCAAGAGAGACAAAACTTAGTT-CAAAAGAAAACTGTCTCAAGAGA
***
2112092 GATGGAATT
65 GACAAAATT
2112101 TGTTTCAAG-GAAA
1 TGTTTCAAGAGAAA
2112114 ACATATTCAA
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
72 4 0.05
73 67 0.91
74 3 0.04
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.26
Consensus pattern (73 bp):
TGTTTCAAGAGAAACTGACTCAAGAGAGACAAAACTTAGTTCAAAAGAAAACTGTCTCAAGAGAG
ACAAAATT
Found at i:2112194 original size:56 final size:56
Alignment explanation
Indices: 2112128--2112320 Score: 190
Period size: 56 Copynumber: 3.2 Consensus size: 56
2112118 ATTCAAAGAT
*
2112128 TTTGTTTCAAGAGAGACAAAATTTTGTTTCAAGTGAAACTGTCTCAAGAGAGAAAA
1 TTTGTTTCAAGAGAGACAAAATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGAAAA
* * * * *
2112184 TTTGTTTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA
1 TTTGTTTCAAGAGAGACAAAATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGA--AAA
* * *
2112242 TTTGTTTCAAG-GAAAACATATTCACAGATTTTGTTTAAAGGGAAACTGTCTCAAGAGAGACAAA
1 TTTGTTTCAAGAG-AGAC--A---A-A-ATTTTGTTTCAAGAGAAACTGTCTCAAGAGAG--AAA
2112306 A
56 A
2112307 TTTGTTTCAAGAGA
1 TTTGTTTCAAGAGA
2112321 AACTGTCTCA
Statistics
Matches: 110, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
56 47 0.43
57 1 0.01
58 17 0.15
60 1 0.01
63 1 0.01
64 1 0.01
65 40 0.36
66 1 0.01
67 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.28
Consensus pattern (56 bp):
TTTGTTTCAAGAGAGACAAAATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGAAAA
Found at i:2112195 original size:19 final size:19
Alignment explanation
Indices: 2112128--2112199 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 19
2112118 ATTCAAAGAT
2112128 TTTGTTTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAG--AAAA
*
2112149 TTTTGTTTC-A-AGTG-AAA
1 -TTTGTTTCAAGAGAGAAAA
* *
2112166 -CTGTCTCAAGAGAGAAAA
1 TTTGTTTCAAGAGAGAAAA
2112184 TTTGTTTCAAGAGAGA
1 TTTGTTTCAAGAGAGA
2112200 CAAAACTTAG
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
15 5 0.12
16 1 0.03
17 6 0.15
18 3 0.08
19 13 0.32
20 3 0.08
21 1 0.03
22 8 0.20
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.32
Consensus pattern (19 bp):
TTTGTTTCAAGAGAGAAAA
Found at i:2112323 original size:36 final size:36
Alignment explanation
Indices: 2112271--2112342 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
2112261 ATTCACAGAT
*
2112271 TTTGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTAAAGAGAAACTGTCTCAAGAGAGACAAAA
*
2112307 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTAAAGAGAAACTGTCTCAAGAGAGACAAAA
2112343 CTATGTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (36 bp):
TTTGTTTAAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:2112369 original size:37 final size:35
Alignment explanation
Indices: 2112273--2112350 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 35
2112263 TCACAGATTT
* *
2112273 TGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTT-AAGAGAAACTGTCTCAAGAGAGACAAAATA
2112309 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTA
1 TGTTT-AAGAGAAACTGTCTCAAGAGAGACAAAA-TA
2112346 TGTTT
1 TGTTT
2112351 TGAGTAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 32 0.84
37 6 0.16
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.27
Consensus pattern (35 bp):
TGTTTAAGAGAAACTGTCTCAAGAGAGACAAAATA
Found at i:2118707 original size:45 final size:45
Alignment explanation
Indices: 2118651--2119191 Score: 875
Period size: 45 Copynumber: 12.0 Consensus size: 45
2118641 CCGTAAGACT
* *
2118651 TTCAGTGCATGATGTTTTTAAAACCTTCGGGTCATCTGTAAGTCC
1 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
*
2118696 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCC
1 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
*
2118741 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCC
1 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
* *
2118786 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCA
1 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
* * *
2118831 TTTAGTGCATGATGTTTTCAAAAACCTTTGGGTCATCTGTAAACCC
1 TTCAGTGCATGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCC
* * *
2118877 TTTAGTGCATGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCA
1 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
* *
2118922 TTCAGTGCATGATTTTTTCAAAAACCTTCGGATCATCTGTAAGCCC
1 TTCAGTGCATGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCC
*
2118968 TTCAGTGCATGATGTTTTCAAAACCTTTGGGTCATCTGTAAGCCC
1 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
*
2119013 TTCAGTGCATGATGTTTTCAAAACCTTTGGGTCATCTGTAAGCCC
1 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
* *
2119058 TTCAGTGCATGATGTTTTCAAAACCTTTGGGTCATCTGTAAGCCT
1 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
2119103 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
1 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
* * *
2119148 TTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCATTTGTGAGCC
1 TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCC
2119192 TTCCGAGCAA
Statistics
Matches: 470, Mismatches: 24, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
45 388 0.83
46 82 0.17
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (45 bp):
TTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCC
Found at i:2119393 original size:3 final size:3
Alignment explanation
Indices: 2119387--2119434 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
2119377 ATAGTTTTTT
** * * *
2119387 TTA TTA TTA AAA TTA TTA TTA TTT TTA TTA ATA TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2119435 AATAATAATA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:2119416 original size:21 final size:21
Alignment explanation
Indices: 2119390--2119430 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2119380 GTTTTTTTTA
*
2119390 TTATTAAAATTATTATTATTT
1 TTATTAAAATTAATATTATTT
*
2119411 TTATTAATATTAATATTATT
1 TTATTAAAATTAATATTATT
2119431 ATTAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATTAAAATTAATATTATTT
Found at i:2122075 original size:2 final size:2
Alignment explanation
Indices: 2122068--2122104 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2122058 TAATAAAAGC
2122068 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2122105 TTGTATTTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2131595 original size:354 final size:354
Alignment explanation
Indices: 2130939--2131631 Score: 1260
Period size: 354 Copynumber: 2.0 Consensus size: 354
2130929 GTCACTTGAG
* *
2130939 GATTATCTTCTTTTCATTTTATTTATCTTTTATTTATTGTTTTTACCATTTTTCATTGTCTTGAC
1 GATTATATTCTTTTCATTTTATTTATCTTTTATTTATTGTTTTTACCATTTTTCATTGCCTTGAC
*
2131004 ATTTCATCATTTTCAACACTAAACATCTATTCTTGCCACTGCATTTCCATTTGCTACACCATCAC
66 ATTTCATCATTTCCAACACTAAACATCTATTCTTGCCACTGCATTTCCATTTGCTACACCATCAC
*
2131069 ACCATCAATCCACATTCACCAGCATACACATATCCATTGTCGTGACATTTGTATATATCAAGACT
131 ACCATCAATCCACATTCACCAGCATACACATATCCATTGCCGTGACATTTGTATATATCAAGACT
2131134 AACTATACTTAGATAGAATAGTACATAAAATTTACCCAATATCCTTCCAATCCCTGTGGAGACGA
196 AACTATACTTAGATAGAATAGTACATAAAATTTACCCAATATCCTTCCAATCCCTGTGGAGACGA
2131199 TACTCACTCATCACTTTATTACTTGAGCGATTGTGTATACTTGCACATTATTTGCGTATATTTTA
261 TACTCACTCATCACTTTATTACTTGAGCGATTGTGTATACTTGCACATTATTTGCGTATATTTTA
2131264 TAGTACTCACAACACGAGAACAAGTATTT
326 TAGTACTCACAACACGAGAACAAGTATTT
*
2131293 GATTATATTCTTTTTATTTTATTTATCTTTTATTTATTGTTTTTACCATTTTTCATTGCCTTGAC
1 GATTATATTCTTTTCATTTTATTTATCTTTTATTTATTGTTTTTACCATTTTTCATTGCCTTGAC
* * * * *
2131358 ATTTCATCATTTCCAACATTGAATATCTGTTCTTGTCACTGCATTTCCATTTGCTACACCATCAC
66 ATTTCATCATTTCCAACACTAAACATCTATTCTTGCCACTGCATTTCCATTTGCTACACCATCAC
*
2131423 ACCATCAATCCACATTCACCAGCATACACATATTCATTGCCGTGACATTTGTATATATCAAGACT
131 ACCATCAATCCACATTCACCAGCATACACATATCCATTGCCGTGACATTTGTATATATCAAGACT
* * *
2131488 AACTATACTTAGATAGAATAGTGCATAAACTTTACTCAATATCCTTCCAATCCCTGTGGAGACGA
196 AACTATACTTAGATAGAATAGTACATAAAATTTACCCAATATCCTTCCAATCCCTGTGGAGACGA
2131553 TACTCACTCATCACTTTATTACTTGAGCGATTGTGTATACTTGCACATTATTTGCGTATATTTTA
261 TACTCACTCATCACTTTATTACTTGAGCGATTGTGTATACTTGCACATTATTTGCGTATATTTTA
2131618 TAGTACTCACAACA
326 TAGTACTCACAACA
2131632 TGCCTGTTAT
Statistics
Matches: 325, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
354 325 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.40
Consensus pattern (354 bp):
GATTATATTCTTTTCATTTTATTTATCTTTTATTTATTGTTTTTACCATTTTTCATTGCCTTGAC
ATTTCATCATTTCCAACACTAAACATCTATTCTTGCCACTGCATTTCCATTTGCTACACCATCAC
ACCATCAATCCACATTCACCAGCATACACATATCCATTGCCGTGACATTTGTATATATCAAGACT
AACTATACTTAGATAGAATAGTACATAAAATTTACCCAATATCCTTCCAATCCCTGTGGAGACGA
TACTCACTCATCACTTTATTACTTGAGCGATTGTGTATACTTGCACATTATTTGCGTATATTTTA
TAGTACTCACAACACGAGAACAAGTATTT
Found at i:2133277 original size:16 final size:15
Alignment explanation
Indices: 2133206--2133289 Score: 61
Period size: 15 Copynumber: 5.7 Consensus size: 15
2133196 AGAGGCTGTT
2133206 TTTAT-TTTTAATCTA
1 TTTATATTTTAAT-TA
*
2133221 TTT-TATTTTAGTTA
1 TTTATATTTTAATTA
* **
2133235 -TTAT-TTTAAAAAA
1 TTTATATTTTAATTA
*
2133248 TTTATATATTAATTA
1 TTTATATTTTAATTA
2133263 TTTATATTTTCAATT-
1 TTTATATTTT-AATTA
2133278 TATTATATTTTA
1 T-TTATATTTTA
2133290 TTTAATAAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
13 7 0.13
14 8 0.15
15 25 0.47
16 13 0.25
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (15 bp):
TTTATATTTTAATTA
Found at i:2133416 original size:23 final size:25
Alignment explanation
Indices: 2133358--2133416 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 25
2133348 AATTTTCAAA
2133358 TTGATCTCTTAATTTAAAAAAAATAT
1 TTGATCTCTT-ATTTAAAAAAAATAT
* **
2133384 TT-ATCCCTTA-TT-AAAAAGGTAT
1 TTGATCTCTTATTTAAAAAAAATAT
2133406 TTGATCTCTTA
1 TTGATCTCTTA
2133417 ATTTTTAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
22 10 0.36
23 9 0.32
24 1 0.04
25 6 0.21
26 2 0.07
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (25 bp):
TTGATCTCTTATTTAAAAAAAATAT
Found at i:2133987 original size:2 final size:2
Alignment explanation
Indices: 2133980--2134021 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2133970 AAAATAGTTC
2133980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2134022 TGCTTTTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2134732 original size:31 final size:31
Alignment explanation
Indices: 2134697--2134761 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
2134687 ATAAAATGCT
2134697 AAAT-ATAAAAATAATAAACAAAACAAGGGAA
1 AAATAATAAAAA-AATAAACAAAACAAGGGAA
* * * *
2134728 AAATAATAATAAAATAAATAACATAAGGGAA
1 AAATAATAAAAAAATAAACAAAACAAGGGAA
2134759 AAA
1 AAA
2134762 ATGTTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 23 0.79
32 6 0.21
ACGTcount: A:0.71, C:0.05, G:0.09, T:0.15
Consensus pattern (31 bp):
AAATAATAAAAAAATAAACAAAACAAGGGAA
Found at i:2135128 original size:3 final size:3
Alignment explanation
Indices: 2135113--2135151 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
2135103 ATAAGAAATA
*
2135113 AAT AAT TAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2135152 CGTATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2136563 original size:26 final size:26
Alignment explanation
Indices: 2136513--2136563 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
2136503 AGGTACAATA
* * * *
2136513 CCCTTTGTTGTGAATTTGTGTATGGC
1 CCCTTCGTTGTGAAGTTGAGCATGGC
2136539 CCCTTCGTTGTGAAGTTGAGCATGG
1 CCCTTCGTTGTGAAGTTGAGCATGG
2136564 GAATTAGATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.14, C:0.18, G:0.29, T:0.39
Consensus pattern (26 bp):
CCCTTCGTTGTGAAGTTGAGCATGGC
Found at i:2136757 original size:106 final size:106
Alignment explanation
Indices: 2136617--2137155 Score: 810
Period size: 106 Copynumber: 5.0 Consensus size: 106
2136607 GTACTGTTCT
* * * *
2136617 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTTTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAA
* * *
2136682 CCAGCCGTCCCTTTGTTGTGAAGTTGAACTTATATTGTCTC
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
*
2136723 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAA
2136788 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* *
2136829 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAA
* *
2136894 CCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* * * *
2136935 GAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTG-TTTGTTGACA
*
2137000 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* * * *
2137042 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTTGCTCTAAATGAAACT-GAAAAGTGGTTTATT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC----TGAAACTGGGAAA-TTGTTTGTT
* *
2137106 GACAACCAGCCGTCCCTTCGTCGTGAAGTTAAACTTGTGTTGTCTC
61 GACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
2137152 GAGT
1 GAGT
2137156 GGCGCGATAT
Statistics
Matches: 398, Mismatches: 29, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
106 249 0.63
107 87 0.22
110 55 0.14
111 7 0.02
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
Found at i:2138068 original size:31 final size:32
Alignment explanation
Indices: 2138012--2138089 Score: 99
Period size: 31 Copynumber: 2.5 Consensus size: 32
2138002 AAAAAAACAT
*
2138012 AAGAATGAAAATAAAAATAATAAATCAAAAGG
1 AAGAAAGAAAATAAAAATAATAAATCAAAAGG
* *
2138044 AAGAAAGAAAATAAATA-AATAAATCAAATGG
1 AAGAAAGAAAATAAAAATAATAAATCAAAAGG
2138075 AA-AATA-AAAATAAAA
1 AAGAA-AGAAAATAAAA
2138090 TCAAAATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 10 0.24
31 16 0.39
32 15 0.37
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (32 bp):
AAGAAAGAAAATAAAAATAATAAATCAAAAGG
Found at i:2138096 original size:24 final size:24
Alignment explanation
Indices: 2138050--2138094 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
2138040 AAGGAAGAAA
2138050 GAAAATAAATAAATAAATCAAATG
1 GAAAATAAATAAATAAATCAAATG
2138074 GAAAAT-AA-AAATAAAATCAAA
1 GAAAATAAATAAAT-AAATCAAA
2138095 ATATATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 10 0.50
24 6 0.30
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.18
Consensus pattern (24 bp):
GAAAATAAATAAATAAATCAAATG
Found at i:2138160 original size:21 final size:19
Alignment explanation
Indices: 2138131--2138191 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 19
2138121 AGAAAAATGT
2138131 AAAAATAAATAAAAAGAATA
1 AAAAATAAAT-AAAAGAATA
*
2138151 AAAGAATAAATCAAAAGGA-A
1 AAA-AATAAAT-AAAAGAATA
2138171 AAAAATAACAT-AAAGAATA
1 AAAAATAA-ATAAAAGAATA
2138190 AA
1 AA
2138192 TAAAAATTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
18 5 0.14
19 8 0.23
20 9 0.26
21 13 0.37
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.13
Consensus pattern (19 bp):
AAAAATAAATAAAAGAATA
Found at i:2138189 original size:31 final size:32
Alignment explanation
Indices: 2138151--2138230 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 32
2138141 AAAAAGAATA
* *
2138151 AAAGAATAAATCAAAA-GGAAAAAAATAACAT
1 AAAGAATAAATCAAAATAGAAAAAAATAAAAT
*
2138182 AAAGAATAAATAAAAATTAGAAAAAAATAAAAT
1 AAAGAATAAATCAAAA-TAGAAAAAAATAAAAT
* * *
2138215 CAAGAAAAAAACAAAA
1 AAAGAATAAATCAAAA
2138231 CAAAACAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 15 0.38
33 25 0.62
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.12
Consensus pattern (32 bp):
AAAGAATAAATCAAAATAGAAAAAAATAAAAT
Found at i:2138211 original size:52 final size:52
Alignment explanation
Indices: 2138102--2138217 Score: 128
Period size: 52 Copynumber: 2.2 Consensus size: 52
2138092 AAAATATATT
** *
2138102 AAATAAATCAAAAGAAAGAAGAAAAATGTAAAAATAAATAAAAAGAATAAAA
1 AAATAAATCAAAAGAAAGAAGAAAAACATAAAAATAAATAAAAAGAAGAAAA
* * **
2138154 GAATAAATCAAAAGGAAA-AA-AATAACATAAAGAATAAATAAAAATTAGAAAA
1 AAATAAATCAAAA-GAAAGAAGAAAAACATAAA-AATAAATAAAAAGAAGAAAA
2138206 AAATAAAATCAA
1 AAAT-AAATCAA
2138218 GAAAAAAACA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
51 8 0.15
52 34 0.64
53 11 0.21
ACGTcount: A:0.73, C:0.03, G:0.09, T:0.15
Consensus pattern (52 bp):
AAATAAATCAAAAGAAAGAAGAAAAACATAAAAATAAATAAAAAGAAGAAAA
Found at i:2138220 original size:17 final size:16
Alignment explanation
Indices: 2138168--2138230 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
2138158 AAATCAAAAG
*
2138168 GAAAAAAATAACATAA
1 GAAAAAAATAAAATAA
* *
2138184 -AGAATAAATAAAAATTA
1 GA-AAAAAAT-AAAATAA
2138201 GAAAAAAATAAAATCAA
1 GAAAAAAATAAAAT-AA
*
2138218 GAAAAAAACAAAA
1 GAAAAAAATAAAA
2138231 CAAAACAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
15 1 0.03
16 11 0.30
17 24 0.65
18 1 0.03
ACGTcount: A:0.76, C:0.05, G:0.06, T:0.13
Consensus pattern (16 bp):
GAAAAAAATAAAATAA
Done.