Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008245.1 Hibiscus syriacus cultivar Beakdansim tig00110895_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: 6601124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 33
Found at i:1942354 original size:54 final size:54
Alignment explanation
Indices: 1942230--1942616 Score: 439
Period size: 54 Copynumber: 7.2 Consensus size: 54
1942220 TGCACCCGTA
* * * * *** *
1942230 GTGCCAATACAGTAATTCACAAACTCATTATGAATTACACGGGGTTGCACAC-TT
1 GTGCCAATACAGAAATTCATAAACTTATTATGAATTTC-TTAGGTTGCACACACT
** *
1942284 AGTGCCAATATGGAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACACT
1 -GTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACT
* * *
1942339 GTGCCAATACAGAAATTCATAAACTCATCATGAATTTCTTAAGTTGCACACA-T
1 GTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACT
* * *
1942392 AGTGCCTATAC-GAAAATTCATAAACTTATTATGAATTTCTTAGGTTACACACACA
1 -GTGCCAATACAG-AAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACT
* *
1942447 GTGCCAATACAAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACA-T
1 GTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACT
* *
1942500 AGAGCCAATAC-GAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACA
1 -GTGCCAATACAG-AAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACT
** *
1942555 GTGCCAATATGGAAATTCAT--ACTTATTATGAATTTTTTAGGTTGCACACACAT
1 GTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACAC-T
1942608 -TGCCAATAC
1 GTGCCAATAC
1942617 GGTAATTGCA
Statistics
Matches: 289, Mismatches: 33, Indels: 23
0.84 0.10 0.07
Matches are distributed among these distances:
52 38 0.13
53 2 0.01
54 214 0.74
55 35 0.12
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (54 bp):
GTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACT
Found at i:1942428 original size:108 final size:108
Alignment explanation
Indices: 1942229--1942617 Score: 530
Period size: 108 Copynumber: 3.6 Consensus size: 108
1942219 TTGCACCCGT
* * * **** *
1942229 AGTGCCAATACAGTAATTCACAAACTCATTATGAATTACACGGGGTTGCACACTTAGTGCCAATA
1 AGTGCCAATACAGAAATTCATAAACTCATTATGAATTTC-TTAAGTTGCACACATAGTGCCAATA
* * *
1942294 TGGAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACAC
65 CGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACAC
* * *
1942338 TGTGCCAATACAGAAATTCATAAACTCATCATGAATTTCTTAAGTTGCACACATAGTGCCTATAC
1 AGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATAC
*
1942403 GAAAATTCATAAACTTATTATGAATTTCTTAGGTTACACACAC
66 GAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACAC
* * *
1942446 AGTGCCAATACAAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACATAGAGCCAATAC
1 AGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATAC
1942511 GAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACAC
66 GAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACAC
** * * * * *
1942554 AGTGCCAATATGGAAATTCAT--ACTTATTATGAATTTTTTAGGTTGCACACACATTGCCAATAC
1 AGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATAC
1942617 G
66 G
1942618 GTAATTGCAA
Statistics
Matches: 250, Mismatches: 30, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
106 38 0.15
108 178 0.71
109 34 0.14
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.32
Consensus pattern (108 bp):
AGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATAC
GAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACAC
Found at i:1943591 original size:6 final size:6
Alignment explanation
Indices: 1943564--1943624 Score: 59
Period size: 6 Copynumber: 10.2 Consensus size: 6
1943554 TATATATACA
* ** * * * *
1943564 TATCAT CATCAT TATCGC TATCAT TATCAT TATCAA CATCAC TATTAT
1 TATCAT TATCAT TATCAT TATCAT TATCAT TATCAT TATCAT TATCAT
1943612 TATCAT TATCAT T
1 TATCAT TATCAT T
1943625 CACTATTCAT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (6 bp):
TATCAT
Found at i:1944012 original size:39 final size:41
Alignment explanation
Indices: 1943958--1944074 Score: 139
Period size: 39 Copynumber: 2.8 Consensus size: 41
1943948 TTTTCAGATT
1943958 TTCACGTAGTTCAGTATCACATAGCTTATATCACA-CTT-G
1 TTCACGTAGTTCAGTATCACATAGCTTATATCACAGCTTAG
* * *
1943997 TTCACGTAGTTCAGTATCACATAGTTTATATTACATGTTTACAAG
1 TTCACGTAGTTCAGTATCACATAGCTTATATCACA-GCTT---AG
* *
1944042 TTCAAGTAGTTCGGTATCACATAGCTTATATCA
1 TTCACGTAGTTCAGTATCACATAGCTTATATCA
1944075 TTTTATCATG
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
39 33 0.51
41 2 0.03
45 30 0.46
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (41 bp):
TTCACGTAGTTCAGTATCACATAGCTTATATCACAGCTTAG
Found at i:1944696 original size:19 final size:20
Alignment explanation
Indices: 1944672--1944711 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1944662 GGAATTCATT
1944672 CTTAAAAATT-ATATTGATA
1 CTTAAAAATTGATATTGATA
* *
1944691 CTTAAACATTGGTATTGATA
1 CTTAAAAATTGATATTGATA
1944711 C
1 C
1944712 CCCTAGTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (20 bp):
CTTAAAAATTGATATTGATA
Found at i:1949459 original size:31 final size:31
Alignment explanation
Indices: 1949422--1949500 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 31
1949412 GAATGACCAT
*
1949422 TATCCATATCTCCCGAAGGACATAGGT-AAC
1 TATCCATATGTCCCGAAGGACATAGGTAAAC
* *
1949452 ATGTCCATATGTCCCAAAGGACATAGGTAAAC
1 -TATCCATATGTCCCGAAGGACATAGGTAAAC
1949484 TATCCATATGTCCCGAA
1 TATCCATATGTCCCGAA
1949501 AAACATGGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 39 0.93
32 3 0.07
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.24
Consensus pattern (31 bp):
TATCCATATGTCCCGAAGGACATAGGTAAAC
Found at i:1949512 original size:31 final size:32
Alignment explanation
Indices: 1949422--1949512 Score: 107
Period size: 31 Copynumber: 2.9 Consensus size: 32
1949412 GAATGACCAT
* *
1949422 TATCCATATCTCCCGAAGGACATAGGT-AACA
1 TATCCATATGTCCCGAAAGACATAGGTAAACA
*
1949453 TGTCCATATGTCCC-AAAGGACATAGGTAAAC-
1 TATCCATATGTCCCGAAA-GACATAGGTAAACA
* *
1949484 TATCCATATGTCCCGAAAAACATGGGTAA
1 TATCCATATGTCCCGAAAGACATAGGTAA
1949513 CCCTCGACTC
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
30 2 0.04
31 43 0.84
32 6 0.12
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (32 bp):
TATCCATATGTCCCGAAAGACATAGGTAAACA
Found at i:1952931 original size:14 final size:14
Alignment explanation
Indices: 1952912--1952938 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1952902 ATGTCATTGT
1952912 TAATATATTATTTA
1 TAATATATTATTTA
1952926 TAATATATTATTT
1 TAATATATTATTT
1952939 TATTTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATATATTATTTA
Found at i:1953491 original size:20 final size:23
Alignment explanation
Indices: 1953466--1953511 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1953456 ATTTTTATAT
1953466 TATAAA-T-AATAAAA-ATGAAC
1 TATAAATTAAATAAAAGATGAAC
*
1953486 TATAAATTAAATAAAAGATTAAC
1 TATAAATTAAATAAAAGATGAAC
1953509 TAT
1 TAT
1953512 TTAATTCACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 1 0.05
22 7 0.32
23 8 0.36
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.30
Consensus pattern (23 bp):
TATAAATTAAATAAAAGATGAAC
Found at i:1953534 original size:21 final size:21
Alignment explanation
Indices: 1953509--1953549 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1953499 AAAGATTAAC
1953509 TATTTAATTCACAAAATCACA
1 TATTTAATTCACAAAATCACA
*
1953530 TATTTAATTCACATAATCAC
1 TATTTAATTCACAAAATCAC
1953550 CATGTATCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.37
Consensus pattern (21 bp):
TATTTAATTCACAAAATCACA
Found at i:1954680 original size:157 final size:158
Alignment explanation
Indices: 1954394--1954711 Score: 602
Period size: 157 Copynumber: 2.0 Consensus size: 158
1954384 AGTCCTACTC
1954394 ATGTTATGTTTTCTTTGAATATACTTTTACAGTAGATGATCAAATCTTGATGTTTCATACTTTAG
1 ATGTTATGTTTTCTTTGAATATACTTTTACAGTAGATGATCAAATCTTGATGTTTCATACTTTAG
1954459 CTAGTTTCGATAGAATTTTTCCACTTTGCATTTCAATATCTAAATCAATTTCTAGGTCTAGAAGA
66 CTAGTTTCGATAGAATTTTTCCACTTTGCATTTCAATATCTAAATCAATTTCTAGGTCTAGAAGA
1954524 TAA-TTTTACTAGTAGCAGCATATAAAA
131 TAAGTTTTACTAGTAGCAGCATATAAAA
1954551 ATGTTATGTTTTCTTTGAATATACTTTTACAGTAGATGATCAAATCTTGATGTTTCATACTTTAG
1 ATGTTATGTTTTCTTTGAATATACTTTTACAGTAGATGATCAAATCTTGATGTTTCATACTTTAG
1954616 CTAGTTTCGATAGAATTTTTCCACTTTGCATTTCAATATCTAAATCAATTTCTAGGTCTAGAAGA
66 CTAGTTTCGATAGAATTTTTCCACTTTGCATTTCAATATCTAAATCAATTTCTAGGTCTAGAAGA
1954681 TAATTGGTTTTACTAGTAGCAGCATATAAAA
131 TAA---GTTTTACTAGTAGCAGCATATAAAA
1954712 TGATTGATTA
Statistics
Matches: 157, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
157 133 0.85
161 24 0.15
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (158 bp):
ATGTTATGTTTTCTTTGAATATACTTTTACAGTAGATGATCAAATCTTGATGTTTCATACTTTAG
CTAGTTTCGATAGAATTTTTCCACTTTGCATTTCAATATCTAAATCAATTTCTAGGTCTAGAAGA
TAAGTTTTACTAGTAGCAGCATATAAAA
Found at i:1958251 original size:20 final size:20
Alignment explanation
Indices: 1958215--1958266 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1958205 AATATAAGAA
*
1958215 TTTATGGTTTAAAGTTTAAGG
1 TTTAGGGTTT-AAGTTTAAGG
*
1958236 TTTAGGGTTTAAGTTTAATG
1 TTTAGGGTTTAAGTTTAAGG
*
1958256 TTTAGAGTTTA
1 TTTAGGGTTTA
1958267 TGATTTTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (20 bp):
TTTAGGGTTTAAGTTTAAGG
Found at i:1962151 original size:18 final size:18
Alignment explanation
Indices: 1962128--1962166 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1962118 AATTATAAAA
1962128 ATTATAAAATGATTTTTT
1 ATTATAAAATGATTTTTT
** *
1962146 ATTATAGGATGTTTTTTT
1 ATTATAAAATGATTTTTT
1962164 ATT
1 ATT
1962167 GAGTTTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (18 bp):
ATTATAAAATGATTTTTT
Found at i:1962357 original size:31 final size:31
Alignment explanation
Indices: 1962314--1962375 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
1962304 CAAACGACTA
*
1962314 TCATATCCCAATCAACATGTTAATTTATAAT
1 TCATATCCCAATCAACATGTTAACTTATAAT
*
1962345 TCATATCTCAATCAACATGTTAACTTATAAT
1 TCATATCCCAATCAACATGTTAACTTATAAT
1962376 ACAAACGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (31 bp):
TCATATCCCAATCAACATGTTAACTTATAAT
Found at i:1963487 original size:20 final size:22
Alignment explanation
Indices: 1963439--1963496 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
1963429 GCATGGGTAG
1963439 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
*
1963463 TGCATCGATGCACTG-T-AGCA
1 TGCATCGATGCACTGTTAAGAA
1963483 TGCATCGATGCACT
1 TGCATCGATGCACT
1963497 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1964727 original size:31 final size:31
Alignment explanation
Indices: 1964689--1964753 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1964679 AGAGTCGAGG
1964689 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTATGTTC-TTCGAGACATATGGACA
* *
1964720 GTTTACCTATGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTTCGAGACATATGGACA
1964751 GTT
1 GTT
1964754 GCCGAGGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGAGACATATGGACA
Found at i:1964807 original size:29 final size:30
Alignment explanation
Indices: 1964739--1964810 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
1964729 TGTTCTTCGG
* *
1964739 GACCTATGGACAGTTGCCGAGGTTCTTTAT
1 GACCTATGGATAGTTGCCGAGGGTCTTTAT
* *
1964769 GACCTATGGATAGTTGTCG-GGGTCTTTGT
1 GACCTATGGATAGTTGCCGAGGGTCTTTAT
*
1964798 GACCTCTGGATAG
1 GACCTATGGATAG
1964811 GTCATTCGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.18, C:0.18, G:0.31, T:0.33
Consensus pattern (30 bp):
GACCTATGGATAGTTGCCGAGGGTCTTTAT
Found at i:1967166 original size:2 final size:2
Alignment explanation
Indices: 1967159--1967183 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1967149 ATACCGTCAT
1967159 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 T
1967184 TATTTCATGG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1967582 original size:31 final size:31
Alignment explanation
Indices: 1967546--1967605 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1967536 AACTTAAAAG
* *
1967546 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
1967577 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
1967606 CATACAGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1968116 original size:20 final size:20
Alignment explanation
Indices: 1968068--1968129 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
1968058 AACTTAAATC
*
1968068 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
1968088 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
1968106 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
1968125 AAAAT
1 AAAAT
1968130 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:1968209 original size:63 final size:63
Alignment explanation
Indices: 1968124--1968271 Score: 264
Period size: 63 Copynumber: 2.4 Consensus size: 63
1968114 TTATATGATA
1968124 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAATTAATAT
1 TAAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAATTAATAT
1968188 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAATTAATAT
*
1968251 TAAAATTAAAAT-TA-AATATAA
1 TAAAATTAATATCTATAATATAA
1968272 AACCTCTTTG
Statistics
Matches: 83, Mismatches: 1, Indels: 3
0.95 0.01 0.03
Matches are distributed among these distances:
61 7 0.08
62 2 0.02
63 67 0.81
64 7 0.08
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (63 bp):
TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAATTAATAT
Found at i:1970671 original size:21 final size:22
Alignment explanation
Indices: 1970626--1970671 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
1970616 TATATTTGTT
1970626 TTATTATTTATATCGTATTTAAA
1 TTATTATTTATATCGTA-TTAAA
1970649 TTATT-TTCTATATCGTA-TAAA
1 TTATTATT-TATATCGTATTAAA
1970670 TT
1 TT
1970672 TTAAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 6 0.27
22 2 0.09
23 14 0.64
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.57
Consensus pattern (22 bp):
TTATTATTTATATCGTATTAAA
Found at i:1975150 original size:20 final size:20
Alignment explanation
Indices: 1975116--1975180 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
1975106 AATTCGAATT
1975116 ACGATTTTCCAAATTCGCAAC
1 ACGATTTT-CAAATTCGCAAC
* *
1975137 GCGATTTTCAAATTTGCAAC
1 ACGATTTTCAAATTCGCAAC
* *
1975157 ATGATTTTCAAATTCGCATC
1 ACGATTTTCAAATTCGCAAC
1975177 ACGA
1 ACGA
1975181 ATCTGTAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
20 30 0.81
21 7 0.19
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (20 bp):
ACGATTTTCAAATTCGCAAC
Found at i:1975419 original size:22 final size:22
Alignment explanation
Indices: 1975394--1975440 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1975384 GGCGACATCT
1975394 GTCCCCATCTCCGACGAAATCC
1 GTCCCCATCTCCGACGAAATCC
*
1975416 GTCCCCATCTCCGGCGAAATCC
1 GTCCCCATCTCCGACGAAATCC
1975438 GTC
1 GTC
1975441 TGTCTCTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.45, G:0.17, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCC
Found at i:1977977 original size:21 final size:21
Alignment explanation
Indices: 1977947--1978050 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
1977937 GATTCACCTG
* *
1977947 TCATCATTCAAGAGGCCTCTCA
1 TCATCCTTCAAGAGGCCCCT-A
*
1977969 T-ATCGTTCAAGAGGCCCCTA
1 TCATCCTTCAAGAGGCCCCTA
* * *
1977989 TCATCCTTCAAGAGACTCCTC
1 TCATCCTTCAAGAGGCCCCTA
* *
1978010 CCA-CTATTCAAGAGGCCCCTA
1 TCATC-CTTCAAGAGGCCCCTA
* *
1978031 TCATCATTCAAGAGGTCCCT
1 TCATCCTTCAAGAGGCCCCT
1978051 TCCACCGTTC
Statistics
Matches: 66, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
20 3 0.05
21 61 0.92
22 2 0.03
ACGTcount: A:0.26, C:0.34, G:0.14, T:0.26
Consensus pattern (21 bp):
TCATCCTTCAAGAGGCCCCTA
Found at i:1978062 original size:42 final size:41
Alignment explanation
Indices: 1977947--1978065 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 41
1977937 GATTCACCTG
* *
1977947 TCATCATTCAAGAGG-CCTCTCATATCGTTCAAGAGGCCCCTA
1 TCATCATTCAAGAGGCCCT-TC-CACCGTTCAAGAGGCCCCTA
* * * **
1977989 TCATCCTTCAAGAGACTCCTCCCACTATTCAAGAGGCCCCTA
1 TCATCATTCAAGAGGC-CCTTCCACCGTTCAAGAGGCCCCTA
1978031 TCATCATTCAAGAGGTCCCTTCCACCGTTCAAGAG
1 TCATCATTCAAGAGG-CCCTTCCACCGTTCAAGAG
1978066 CCCGATTCAC
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
42 57 0.92
43 2 0.03
44 3 0.05
ACGTcount: A:0.26, C:0.34, G:0.15, T:0.25
Consensus pattern (41 bp):
TCATCATTCAAGAGGCCCTTCCACCGTTCAAGAGGCCCCTA
Found at i:1988010 original size:64 final size:64
Alignment explanation
Indices: 1987932--1988100 Score: 266
Period size: 64 Copynumber: 2.6 Consensus size: 64
1987922 TGGGGTACAC
1987932 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
1 TTTTTTT-CTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
* * * ***
1987997 TTTTTTTCTTGTTTAACTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTA
1 TTTTTTTCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
*
1988061 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTTTTTCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1988101 GTTTTAAATT
Statistics
Matches: 96, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
64 89 0.93
65 7 0.07
ACGTcount: A:0.27, C:0.03, G:0.17, T:0.54
Consensus pattern (64 bp):
TTTTTTTCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
Found at i:1988191 original size:20 final size:20
Alignment explanation
Indices: 1988162--1988263 Score: 114
Period size: 20 Copynumber: 5.1 Consensus size: 20
1988152 GTACACTTTT
* *
1988162 GCAACACGAAAATCAAATTC
1 GCAACGCGAAAGTCAAATTC
1988182 GCAACGCGAAAGTCAAATTC
1 GCAACGCGAAAGTCAAATTC
**** *
1988202 GCATTATGATAGTCAAATTC
1 GCAACGCGAAAGTCAAATTC
* *
1988222 GCAACGTGATAGTCAAATTC
1 GCAACGCGAAAGTCAAATTC
*
1988242 GCAATGCGAAAGTCAAATTC
1 GCAACGCGAAAGTCAAATTC
1988262 GC
1 GC
1988264 GTTGCGATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
GCAACGCGAAAGTCAAATTC
Found at i:1988236 original size:40 final size:40
Alignment explanation
Indices: 1988162--1988263 Score: 132
Period size: 40 Copynumber: 2.5 Consensus size: 40
1988152 GTACACTTTT
* *
1988162 GCAACACGAAAATCAAATTCGCAACGCGAAAGTCAAATTC
1 GCAATACGAAAGTCAAATTCGCAACGCGAAAGTCAAATTC
* * * * *
1988202 GCATTATGATAGTCAAATTCGCAACGTGATAGTCAAATTC
1 GCAATACGAAAGTCAAATTCGCAACGCGAAAGTCAAATTC
*
1988242 GCAATGCGAAAGTCAAATTCGC
1 GCAATACGAAAGTCAAATTCGC
1988264 GTTGCGATTT
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.22
Consensus pattern (40 bp):
GCAATACGAAAGTCAAATTCGCAACGCGAAAGTCAAATTC
Found at i:1988601 original size:18 final size:18
Alignment explanation
Indices: 1988578--1988613 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1988568 AAGCCAATTG
*
1988578 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1988596 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1988614 CCTTTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1991152 original size:35 final size:35
Alignment explanation
Indices: 1991074--1991153 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
1991064 TTTTAATTAC
*
1991074 AACAAACTTACAATAAGTATTAAATGGTAAATGAT
1 AACAAAATTACAATAAGTATTAAATGGTAAATGAT
*
1991109 AACCAAATTACAATAACTGATATTAAATGGT-AAT-A-
1 AACAAAATTACAATAA--G-TATTAAATGGTAAATGAT
1991144 AACAAAATTA
1 AACAAAATTA
1991154 ACTGAAATAC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
35 23 0.59
36 1 0.03
37 4 0.10
38 11 0.28
ACGTcount: A:0.54, C:0.10, G:0.09, T:0.28
Consensus pattern (35 bp):
AACAAAATTACAATAAGTATTAAATGGTAAATGAT
Found at i:2013158 original size:46 final size:46
Alignment explanation
Indices: 2013100--2013196 Score: 126
Period size: 46 Copynumber: 2.1 Consensus size: 46
2013090 GAATTTGAGG
*** **
2013100 TTTC-AATCGAGTTAAGTTTAAGATT-TTTTTTTTCATTTCGAGCCT
1 TTTCGAATCGAGTTAAGTTT-AGATTCGAGTTTTTCATCACGAGCCT
2013145 TTTCGAATCGAGTTAAGTTTAGATTCGAGTTTTTCATCACGAGCCT
1 TTTCGAATCGAGTTAAGTTTAGATTCGAGTTTTTCATCACGAGCCT
2013191 TTTCGA
1 TTTCGA
2013197 GTTATCACTT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 9 0.20
46 36 0.80
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.45
Consensus pattern (46 bp):
TTTCGAATCGAGTTAAGTTTAGATTCGAGTTTTTCATCACGAGCCT
Found at i:2015796 original size:28 final size:28
Alignment explanation
Indices: 2015756--2015820 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
2015746 CTAAATTTAG
2015756 TTCTTGAAATATTATGTTGGTAAGTCAA
1 TTCTTGAAATATTATGTTGGTAAGTCAA
* * *
2015784 TTCTTTAAATATTATGTTGGTGAGTCAG
1 TTCTTGAAATATTATGTTGGTAAGTCAA
*
2015812 TGCTTGAAA
1 TTCTTGAAA
2015821 GCAATGACGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (28 bp):
TTCTTGAAATATTATGTTGGTAAGTCAA
Found at i:2018335 original size:30 final size:30
Alignment explanation
Indices: 2018298--2018359 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
2018288 CAAGTGTTGG
* * *
2018298 TCAAAATTGGTAGCCATTAAAGAATTTAATT
1 TCAAATTTGGTA-CCACTAAAGAATTCAATT
*
2018329 TCAAATTTGTTACCACTAAAGAATTCAATT
1 TCAAATTTGGTACCACTAAAGAATTCAATT
2018359 T
1 T
2018360 GTAAGTTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (30 bp):
TCAAATTTGGTACCACTAAAGAATTCAATT
Found at i:2020359 original size:41 final size:41
Alignment explanation
Indices: 2020314--2020439 Score: 113
Period size: 41 Copynumber: 3.1 Consensus size: 41
2020304 TTTTGAAATT
2020314 AAGTGACCAATTTAAGAAGAATTAAAAAGTTCAAGGATTTA
1 AAGTGACCAATTTAAGAAGAATTAAAAAGTTCAAGGATTTA
** * * * *
2020355 AAGTGA--AATATTCTTGTATTGGATTAAATAG-T-AAAGA--T-
1 AAGTGACCAAT-TT-AAG-A-AGAATTAAAAAGTTCAAGGATTTA
2020393 AAGTGACCAATTTAAGAAGAATTAAAAAGTTCAAGGATTTA
1 AAGTGACCAATTTAAGAAGAATTAAAAAGTTCAAGGATTTA
2020434 AAGTGA
1 AAGTGA
2020440 AATATTCTTG
Statistics
Matches: 62, Mismatches: 12, Indels: 22
0.65 0.12 0.23
Matches are distributed among these distances:
36 9 0.15
37 2 0.03
38 11 0.18
39 6 0.10
40 6 0.10
41 17 0.27
42 2 0.03
43 9 0.15
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (41 bp):
AAGTGACCAATTTAAGAAGAATTAAAAAGTTCAAGGATTTA
Found at i:2020444 original size:79 final size:79
Alignment explanation
Indices: 2020313--2020471 Score: 318
Period size: 79 Copynumber: 2.0 Consensus size: 79
2020303 TTTTTGAAAT
2020313 TAAGTGACCAATTTAAGAAGAATTAAAAAGTTCAAGGATTTAAAGTGAAATATTCTTGTATTGGA
1 TAAGTGACCAATTTAAGAAGAATTAAAAAGTTCAAGGATTTAAAGTGAAATATTCTTGTATTGGA
2020378 TTAAATAGTAAAGA
66 TTAAATAGTAAAGA
2020392 TAAGTGACCAATTTAAGAAGAATTAAAAAGTTCAAGGATTTAAAGTGAAATATTCTTGTATTGGA
1 TAAGTGACCAATTTAAGAAGAATTAAAAAGTTCAAGGATTTAAAGTGAAATATTCTTGTATTGGA
2020457 TTAAATAGTAAAGA
66 TTAAATAGTAAAGA
2020471 T
1 T
2020472 GGAAAGAATG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (79 bp):
TAAGTGACCAATTTAAGAAGAATTAAAAAGTTCAAGGATTTAAAGTGAAATATTCTTGTATTGGA
TTAAATAGTAAAGA
Found at i:2022852 original size:25 final size:25
Alignment explanation
Indices: 2022824--2022885 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 25
2022814 AAGAAAGCGT
2022824 AATAAAAAAATAAAGAA-AATAAATG
1 AATAAAAAAATAAAGAATAA-AAATG
2022849 AAT---AAAATAAA-AATAAAAATG
1 AATAAAAAAATAAAGAATAAAAATG
*
2022870 AAGAAAAAAATAAAGA
1 AATAAAAAAATAAAGA
2022886 CAAGAAAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
21 9 0.29
22 10 0.32
24 8 0.26
25 4 0.13
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (25 bp):
AATAAAAAAATAAAGAATAAAAATG
Found at i:2022946 original size:2 final size:2
Alignment explanation
Indices: 2022941--2022967 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2022931 AGTAAAAAAC
2022941 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2022968 CGAAATAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2023075 original size:2 final size:2
Alignment explanation
Indices: 2023070--2023096 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2023060 AAAAAAAGTA
2023070 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2023097 ATAGAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2023175 original size:2 final size:2
Alignment explanation
Indices: 2023170--2023228 Score: 95
Period size: 2 Copynumber: 30.5 Consensus size: 2
2023160 ATAAAAAATA
2023170 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
*
2023211 AA AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT A
2023229 AAAATGAGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2024427 original size:96 final size:95
Alignment explanation
Indices: 2024254--2024517 Score: 325
Period size: 96 Copynumber: 2.7 Consensus size: 95
2024244 AAATTATAAT
* *
2024254 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTA-AATCAATTGGTTAAACGGCCCAACTTT
1 ATTATA-ATATACAATAAAGCTTGAGTTGTCCCTCTAGAA-CAATTGGTTAAACGCCCCAGCTTT
**
2024318 ATGGATAAGATTCATTTAAGCCTGATAAAGGTG
64 ATGGATAAGATTCAGCT-AGCCTGATAAAGGTG
* *
2024351 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCCCAGCTTTAT
1 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAACAATTGGTTAAACGCCCCAGCTTTAT
*
2024416 GGATAATATTCAGCTAGCCTGATAAAGGTG
66 GGATAAGATTCAGCTAGCCTGATAAAGGTG
* * * * * * *
2024446 ATTATAATAT-CTATACAATGATATTAAGCTATCCCTCTAGAAAAATTGGTTAAACGCCCCGGCT
1 ATTATAATATACAATA-AA-G--CTTGAGTTGTCCCTCTAGAACAATTGGTTAAACGCCCCAGCT
2024510 TTATGGAT
62 TTATGGAT
2024518 TCAACTAGCC
Statistics
Matches: 146, Mismatches: 16, Indels: 9
0.85 0.09 0.05
Matches are distributed among these distances:
94 4 0.03
95 27 0.18
96 66 0.45
97 7 0.05
98 42 0.29
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Consensus pattern (95 bp):
ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAACAATTGGTTAAACGCCCCAGCTTTAT
GGATAAGATTCAGCTAGCCTGATAAAGGTG
Found at i:2026844 original size:84 final size:84
Alignment explanation
Indices: 2026700--2027077 Score: 504
Period size: 84 Copynumber: 4.5 Consensus size: 84
2026690 AACTCGATAA
* * * * * *
2026700 TTGGCATATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATGATGAGCCTTCGAGTTGAGTGTAAT
1 TTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
*
2026765 CGAACTCGAAGGTCTTTGG
66 CGAACTCGAAGGTCTTTTG
* * * *
2026784 TTGGCAGATAGCCCTTCTCGCCTTAAGCTATACTGCAAATGATGTGCCTTTGAGCCGAGTGTAAT
1 TTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
2026849 CGAACTCGAAGGTCTTTTG
66 CGAACTCGAAGGTCTTTTG
* * * * * *
2026868 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
2026933 CGAACTCGAAGGTCTTTTG
66 CGAACTCGAAGGTCTTTTG
* * * ** *
2026952 TTGGCTGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCTTTGAGCTGAGTGTAGT
1 TTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
*
2027017 CGAACTCGATGGTCTTTTG
66 CGAACTCGAAGGTCTTTTG
* * * *
2027036 TTAGCAGATAGCCCTTATCGACTTGAGCTATGCTGCAAATGA
1 TTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGA
2027078 ACACGATATC
Statistics
Matches: 260, Mismatches: 34, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
84 260 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (84 bp):
TTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
CGAACTCGAAGGTCTTTTG
Found at i:2027431 original size:124 final size:123
Alignment explanation
Indices: 2027096--2027421 Score: 415
Period size: 124 Copynumber: 2.6 Consensus size: 123
2027086 TCATTCTTCG
* * * ** * *
2027096 TGAATTTGAAATCGTGGAGGGCCCATTCGTAATGAAGTTGAGCCTTGAA-TTGGATATCTTTCAT
1 TGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTT-AACTTGAATATCCTTCAT
* * *
2027160 CGTGAAGTTGAAATCCAACCTGAAGATGAATATTACTGGTGAGTACGATTTCCTTCATCG
65 CGTGAAGTTGAAAT-CAACCTGAAGATGAATATTACTGGTGAGCACGATTCCCTTCATCA
** *
2027220 TGAAGTTGAAACTATGGATGGCCTC-TTCATTGTGAAGTTGAGCCTTAACTTGAATATCCTTCAT
1 TGAAGTTGAAACCGTGGATGGCC-CATTCGTTGTGAAGTTGAGCCTTAACTTGAATATCCTTCAT
* * * *
2027284 CGTGAAGTTGGAATCCAAGCTGAAGATGAATGTTA-TCGGTGAGCACGATTCCCTTCGTCA
65 CGTGAAGTTGAAAT-CAACCTGAAGATGAATATTACT-GGTGAGCACGATTCCCTTCATCA
**
2027344 TGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTAACTTGAATATCCTTCGCC
1 TGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTAACTTGAATATCCTTCATC
2027409 GTGAAGTTGAAAT
66 GTGAAGTTGAAAT
2027422 TGGCTCTGAA
Statistics
Matches: 175, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
123 4 0.02
124 170 0.97
125 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (123 bp):
TGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTAACTTGAATATCCTTCATC
GTGAAGTTGAAATCAACCTGAAGATGAATATTACTGGTGAGCACGATTCCCTTCATCA
Found at i:2029278 original size:96 final size:95
Alignment explanation
Indices: 2029063--2029326 Score: 341
Period size: 96 Copynumber: 2.7 Consensus size: 95
2029053 GGCTAGTTGA
* ** * * * *
2029063 ATCCATAAAGCCGGGGCGTTTAACCAATTTTTCTAGAGGGATAGCTTAATATCATTGTATAG-AT
1 ATCCATAAAGCTGGGGCGTTTAACCAATTGATCTAGAGGGATAAC-TCA-AGC-TT-TATTGTAT
*
2029127 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
62 ATTATAATCACCTTTATCAGGCTAGATGAATATT
* * *
2029161 ATCCATAAAGCTGGGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCTGGGGCGTTTAACCAATTGATCTAGAGGGATAACTCAAGCTTTATTGTATATTA
*
2029226 TAATCACCTTTATCAGGCTTAGATGAATCTT
66 TAATCACCTTTATCAGGC-TAGATGAATATT
* *
2029257 ATCCATAAAGTTGGGGCGTTTAACCAATTGATTTAGAGGGATAACTCAAGCTTTATTGTATATAT
1 ATCCATAAAGCTGGGGCGTTTAACCAATTGATCTAGAGGGATAACTCAAGCTTTATTGTATAT-T
2029322 ATAAT
65 ATAAT
2029327 ATTATAATTT
Statistics
Matches: 147, Mismatches: 16, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
94 4 0.03
95 26 0.18
96 70 0.48
97 8 0.05
98 39 0.27
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (95 bp):
ATCCATAAAGCTGGGGCGTTTAACCAATTGATCTAGAGGGATAACTCAAGCTTTATTGTATATTA
TAATCACCTTTATCAGGCTAGATGAATATT
Found at i:2033317 original size:13 final size:13
Alignment explanation
Indices: 2033286--2033370 Score: 50
Period size: 13 Copynumber: 6.5 Consensus size: 13
2033276 AAGAAAGCGC
2033286 AATAAAA-AAATA
1 AATAAAATAAATA
* *
2033298 AAGAAAATAAATG
1 AATAAAATAAATA
2033311 AATAAAAT-AA-A
1 AATAAAATAAATA
* *
2033322 AATAAAAAGGAAAAA
1 AAT-AAAA-TAAATA
* *
2033337 AATAAAGACAAGAAA
1 AATAAA-ATAA-ATA
*
2033352 AATGAAATAAATA
1 AATAAAATAAATA
2033365 AATAAA
1 AATAAA
2033371 TGAAGTATAG
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
11 3 0.05
12 12 0.21
13 18 0.32
14 10 0.18
15 13 0.23
ACGTcount: A:0.76, C:0.01, G:0.08, T:0.14
Consensus pattern (13 bp):
AATAAAATAAATA
Found at i:2033368 original size:43 final size:42
Alignment explanation
Indices: 2033289--2033370 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 42
2033279 AAAGCGCAAT
*
2033289 AAAAAAATAAAGAAAATAAATGAATAAAATAAAAATAAAAAGG
1 AAAAAAATAAAGAAAAAAAATGAATAAAAT-AAAATAAAAAGG
2033332 AAAAAAATAAAGACAAGAAAAATGAA-ATAAAT-AAATAAA
1 AAAAAAATAAAGA-AA-AAAAATGAATA-AAATAAAATAAA
2033371 TGAAGTATAG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
43 20 0.57
44 3 0.09
45 12 0.34
ACGTcount: A:0.77, C:0.01, G:0.09, T:0.13
Consensus pattern (42 bp):
AAAAAAATAAAGAAAAAAAATGAATAAAATAAAATAAAAAGG
Found at i:2033580 original size:16 final size:16
Alignment explanation
Indices: 2033559--2033599 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
2033549 AAAAAGTAGT
2033559 AATAATAAATAAAGGA
1 AATAATAAATAAAGGA
2033575 AATAAT--ATAAAGGA
1 AATAATAAATAAAGGA
2033589 AA-AA-AAATAAA
1 AATAATAAATAAA
2033600 AAAGAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 2 0.09
14 15 0.65
16 6 0.26
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (16 bp):
AATAATAAATAAAGGA
Found at i:2033586 original size:14 final size:14
Alignment explanation
Indices: 2033562--2033613 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
2033552 AAGTAGTAAT
2033562 AATAA-ATAAAGGA
1 AATAATATAAAGGA
2033575 AATAATATAAAGGAAA
1 AATAATATAAAGG--A
* * *
2033591 AAAAATAAAAAAGA
1 AATAATATAAAGGA
2033605 AATAATATA
1 AATAATATA
2033614 TATATATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 5 0.16
14 15 0.48
16 11 0.35
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (14 bp):
AATAATATAAAGGA
Found at i:2033614 original size:2 final size:2
Alignment explanation
Indices: 2033609--2033648 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2033599 AAAAGAAATA
* *
2033609 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT GT 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
2033649 TAAAATATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2037839 original size:12 final size:12
Alignment explanation
Indices: 2037822--2037846 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2037812 ATATAAAGTG
2037822 ATAAAGTTCGGT
1 ATAAAGTTCGGT
2037834 ATAAAGTTCGGT
1 ATAAAGTTCGGT
2037846 A
1 A
2037847 AATAATCGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (12 bp):
ATAAAGTTCGGT
Found at i:2040286 original size:22 final size:22
Alignment explanation
Indices: 2040256--2040299 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2040246 TACCTAATGC
2040256 CTTACTAAGTGAAAACTTAGCA
1 CTTACTAAGTGAAAACTTAGCA
*
2040278 CTTATTAAGTGAAAACTTAGCA
1 CTTACTAAGTGAAAACTTAGCA
2040300 TGTGATTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (22 bp):
CTTACTAAGTGAAAACTTAGCA
Found at i:2042065 original size:31 final size:31
Alignment explanation
Indices: 2042023--2042086 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
2042013 TTGTCTACCA
2042023 TAGAGGCAGAGTAGGTGATAGTTTCAGAGGC
1 TAGAGGCAGAGTAGGTGATAGTTTCAGAGGC
*
2042054 TAGAGGTAGAGTAGGTGATAGTTTCAGAGGC
1 TAGAGGCAGAGTAGGTGATAGTTTCAGAGGC
2042085 TA
1 TA
2042087 TGAAGGAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.30, C:0.08, G:0.38, T:0.25
Consensus pattern (31 bp):
TAGAGGCAGAGTAGGTGATAGTTTCAGAGGC
Found at i:2043657 original size:2 final size:2
Alignment explanation
Indices: 2043650--2043696 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
2043640 TCCACCTAGT
* *
2043650 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA AA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2043691 TT TA TA
1 TA TA TA
2043697 ACCTAAATGG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2052561 original size:2 final size:2
Alignment explanation
Indices: 2052554--2052585 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2052544 ATTTTACATG
2052554 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
2052586 TGTTTTATTT
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:2054824 original size:83 final size:81
Alignment explanation
Indices: 2054686--2054839 Score: 245
Period size: 83 Copynumber: 1.9 Consensus size: 81
2054676 AAAAGTGCCC
* * * *
2054686 ATATTTTAAATTTAAAATATATTATTATGTTTAAATTTAGATATTAAAAGAGTTTTGGTTGGAGT
1 ATATTTTAAATTTAAAAGATATTATTATATTTAAATTTAGATATTAAAAGAGTTTTCGTTAGAGT
*
2054751 TAAACTCTCAAGTTCA
66 AAAACTCTCAAGTTCA
2054767 ATATTTTAAATTTAAAAGATATTATTATCTATTTAAATTTAGATATTAAAAGAGTTTTCGTTAGA
1 ATATTTTAAATTTAAAAGATATTATTA--TATTTAAATTTAGATATTAAAAGAGTTTTCGTTAGA
2054832 GTAAAACT
64 GTAAAACT
2054840 ATCTCGAAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
81 26 0.39
83 40 0.61
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (81 bp):
ATATTTTAAATTTAAAAGATATTATTATATTTAAATTTAGATATTAAAAGAGTTTTCGTTAGAGT
AAAACTCTCAAGTTCA
Found at i:2056423 original size:24 final size:24
Alignment explanation
Indices: 2056387--2056469 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
2056377 GAGATTTCAA
* *
2056387 AAATCA-AAGCAGAATTCATATCAT
1 AAATCAGAA-CAGAATTCAGATCAG
* *
2056411 ATATCAGAACAGAATCCAGATCAG
1 AAATCAGAACAGAATTCAGATCAG
* * *
2056435 AAATCAGATCAAAATTCAGATAAG
1 AAATCAGAACAGAATTCAGATCAG
2056459 AAATCAGAACA
1 AAATCAGAACA
2056470 TATTTCAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 46 0.96
25 2 0.04
ACGTcount: A:0.52, C:0.17, G:0.12, T:0.19
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAGATCAG
Found at i:2058960 original size:22 final size:23
Alignment explanation
Indices: 2058928--2058976 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
2058918 CCACCTTCTG
*
2058928 CAAATATTTACA-AAACTAACACC
1 CAAATATTTACACAAA-TAAAACC
2058951 CAAAT-TTTACACAAATAAAACC
1 CAAATATTTACACAAATAAAACC
2058973 CAAA
1 CAAA
2058977 CAGAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.20
Consensus pattern (23 bp):
CAAATATTTACACAAATAAAACC
Found at i:2061241 original size:18 final size:18
Alignment explanation
Indices: 2061209--2061300 Score: 130
Period size: 18 Copynumber: 4.9 Consensus size: 18
2061199 ACTGAATATT
*
2061209 TGTCCCGAAGAACCACTA
1 TGTCCCGAAGGACCACTA
* *
2061227 TTTCCCAAAGGACCACTGATA
1 TGTCCCGAAGGACCAC---TA
2061248 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
2061266 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
2061284 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
2061301 GATAATCCCT
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
18 50 0.76
21 16 0.24
ACGTcount: A:0.29, C:0.33, G:0.20, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:2061255 original size:39 final size:36
Alignment explanation
Indices: 2061209--2061300 Score: 130
Period size: 39 Copynumber: 2.5 Consensus size: 36
2061199 ACTGAATATT
* *
2061209 TGTCCCGAAGAACCACTATTTCCCAAAGGACCACTGATA
1 TGTCCCGAAGGACCACTATGTCCCAAAGGACCAC---TA
*
2061248 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTATGTCCCAAAGGACCACTA
2061284 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
2061301 GATAATCCCT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
36 19 0.38
39 31 0.62
ACGTcount: A:0.29, C:0.33, G:0.20, T:0.18
Consensus pattern (36 bp):
TGTCCCGAAGGACCACTATGTCCCAAAGGACCACTA
Found at i:2066284 original size:18 final size:18
Alignment explanation
Indices: 2066253--2066287 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2066243 ACTGAATATT
*
2066253 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
2066271 TGTCCTGAAGGACCACT
1 TGTCCCGAAGGACCACT
2066288 GATAATCCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:2069612 original size:18 final size:18
Alignment explanation
Indices: 2069581--2069615 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2069571 ACTGAATATT
*
2069581 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
2069599 TGTCCTGAAGGACCACT
1 TGTCCCGAAGGACCACT
2069616 GATAATCCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:2077149 original size:94 final size:94
Alignment explanation
Indices: 2076988--2077175 Score: 376
Period size: 94 Copynumber: 2.0 Consensus size: 94
2076978 TAGATATTAA
2076988 AATTGACGAACCACAACAATTTAACTAATCTTCGCTTTGCCCATAAAAATTTATTGTTCCTCCAC
1 AATTGACGAACCACAACAATTTAACTAATCTTCGCTTTGCCCATAAAAATTTATTGTTCCTCCAC
2077053 GTCCTATCCAGGGTAGGGATGGCAAACGG
66 GTCCTATCCAGGGTAGGGATGGCAAACGG
2077082 AATTGACGAACCACAACAATTTAACTAATCTTCGCTTTGCCCATAAAAATTTATTGTTCCTCCAC
1 AATTGACGAACCACAACAATTTAACTAATCTTCGCTTTGCCCATAAAAATTTATTGTTCCTCCAC
2077147 GTCCTATCCAGGGTAGGGATGGCAAACGG
66 GTCCTATCCAGGGTAGGGATGGCAAACGG
2077176 GCGGATCGGG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (94 bp):
AATTGACGAACCACAACAATTTAACTAATCTTCGCTTTGCCCATAAAAATTTATTGTTCCTCCAC
GTCCTATCCAGGGTAGGGATGGCAAACGG
Found at i:2078634 original size:15 final size:15
Alignment explanation
Indices: 2078614--2078662 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
2078604 TATTTAGCTA
2078614 GGCGGGCGGATGTGG
1 GGCGGGCGGATGTGG
*
2078629 GGCGGGTGGATGTGG
1 GGCGGGCGGATGTGG
* *
2078644 GGCAGGCGGATGCGG
1 GGCGGGCGGATGTGG
2078659 GGCG
1 GGCG
2078663 AGTAAGGTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.08, C:0.14, G:0.65, T:0.12
Consensus pattern (15 bp):
GGCGGGCGGATGTGG
Found at i:2083908 original size:16 final size:16
Alignment explanation
Indices: 2083887--2083919 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2083877 TTTGAGGTGA
2083887 AGTTAAAATTCATTTT
1 AGTTAAAATTCATTTT
*
2083903 AGTTAAAATTTATTTT
1 AGTTAAAATTCATTTT
2083919 A
1 A
2083920 ATTTAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (16 bp):
AGTTAAAATTCATTTT
Found at i:2084769 original size:31 final size:31
Alignment explanation
Indices: 2084718--2084792 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
2084708 TCAAAAATAG
* * *
2084718 AAAATCGGTCGCTAATGTTATTGATATGTAAC
1 AAAAT-GGTCACTAACGTTATCGATATGTAAC
*
2084750 AAAATGGTCACTAACGTTATCGATTTGTAAC
1 AAAATGGTCACTAACGTTATCGATATGTAAC
*
2084781 AAAATAGTCACT
1 AAAATGGTCACT
2084793 CTATTGTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
31 33 0.87
32 5 0.13
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (31 bp):
AAAATGGTCACTAACGTTATCGATATGTAAC
Found at i:2090871 original size:64 final size:65
Alignment explanation
Indices: 2090751--2090896 Score: 149
Period size: 64 Copynumber: 2.3 Consensus size: 65
2090741 ATGGACAGGA
** *
2090751 AGTGCATCGATGCACCC-ATTAAAAATGGAAACATCGAATGCCATTAGTGCATCGATGCATA-AG
1 AGTGCATCGATGCACCCGATTAAAAATACAAACATCGAATGCCATTAGTGCACCGATGCATAGA-
*
2090814 G
65 C
* * * *
2090815 AGTGCATCGATGCACCCGCTT-AAAATACAAATATCGAATAG-GATTTA-TGCACCGATGTATAG
1 AGTGCATCGATGCACCCGATTAAAAATACAAACATCGAAT-GCCA-TTAGTGCACCGATGCATAG
2090877 AC
64 AC
*
2090879 AGTGTATCGATGCACCCG
1 AGTGCATCGATGCACCCG
2090897 TCAAGGGATG
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
64 62 0.90
65 7 0.10
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (65 bp):
AGTGCATCGATGCACCCGATTAAAAATACAAACATCGAATGCCATTAGTGCACCGATGCATAGAC
Found at i:2091566 original size:27 final size:27
Alignment explanation
Indices: 2091536--2091597 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
2091526 GTGGTCCTTC
*
2091536 GGGACAAATATAGTACATAGGTCTTTT
1 GGGACAAATATAGTACATAGGTATTTT
2091563 GGGACAAATATAGTACATAGGTATTTT
1 GGGACAAATATAGTACATAGGTATTTT
2091590 GGGACAAA
1 GGGACAAA
2091598 ATTTCATAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (27 bp):
GGGACAAATATAGTACATAGGTATTTT
Found at i:2092956 original size:2 final size:2
Alignment explanation
Indices: 2092949--2092981 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2092939 TAGTCACTAT
2092949 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 T
2092982 GGGTTAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2093141 original size:24 final size:23
Alignment explanation
Indices: 2093098--2093179 Score: 62
Period size: 24 Copynumber: 3.5 Consensus size: 23
2093088 AATTATGTTA
* *
2093098 TTTAATTA-TATTACTT-TATAT
1 TTTAATTATTAATAATTATATAT
2093119 TTTAATTATTAATAATTAGTATAT
1 TTTAATTATTAATAATTA-TATAT
* *
2093143 TATATAATTAATTAGTATTTATAT-T
1 T-T-TAATT-ATTAATAATTATATAT
2093168 TTTAGATTATTA
1 TTTA-ATTATTA
2093180 TTTTACATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
21 8 0.16
22 6 0.12
23 6 0.12
24 10 0.20
25 3 0.06
26 8 0.16
27 9 0.18
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTAATTATTAATAATTATATAT
Found at i:2093156 original size:20 final size:19
Alignment explanation
Indices: 2093123--2093166 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
2093113 TTATATTTTA
2093123 ATTAT-TAATAATTAGTAT
1 ATTATATAATAATTAGTAT
2093141 ATTATATAATTAATTAGTAT
1 ATTATATAA-TAATTAGTAT
2093161 -TTATAT
1 ATTATAT
2093167 TTTTAGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.21
19 9 0.38
20 10 0.42
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (19 bp):
ATTATATAATAATTAGTAT
Found at i:2099417 original size:22 final size:22
Alignment explanation
Indices: 2099389--2099437 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
2099379 ATTCTGCAAG
2099389 GATGATAGATTCTCTTTTCAAA
1 GATGATAGATTCTCTTTTCAAA
2099411 GATGATAGATTCTCTTTTCAAA
1 GATGATAGATTCTCTTTTCAAA
2099433 GATGA
1 GATGA
2099438 AAGCTTTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (22 bp):
GATGATAGATTCTCTTTTCAAA
Found at i:2100144 original size:20 final size:20
Alignment explanation
Indices: 2100119--2100162 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
2100109 TCTAGAAAAT
2100119 TAAAGCCTCCGGGTAATTTG
1 TAAAGCCTCCGGGTAATTTG
*
2100139 TAAAGCCTTCGGGTAATTTG
1 TAAAGCCTCCGGGTAATTTG
2100159 TAAA
1 TAAA
2100163 TTCTTTGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (20 bp):
TAAAGCCTCCGGGTAATTTG
Found at i:2100408 original size:45 final size:45
Alignment explanation
Indices: 2100359--2100513 Score: 131
Period size: 45 Copynumber: 3.4 Consensus size: 45
2100349 AAATTTAGTT
2100359 TTCACGGAAGAGTAGTGGAACAGATTTTTCAGCAAAGTATCAAAC
1 TTCACGGAAGAGTAGTGGAACAGATTTTTCAGCAAAGTATCAAAC
** ** **
2100404 TTCACGGAAGAGTAGT-GAAGCAGA--AATCAAG-AATAAAATTC-AGT
1 TTCACGGAAGAGTAGTGGAA-CAGATTTTTC-AGCAA-AGTA-TCAAAC
* * *
2100448 TTCCACGGAAGAGTAGTGGAACGGATTTTTCAACAAAGTATGAGAAC
1 TT-CACGGAAGAGTAGTGGAACAGATTTTTCAGCAAAGTATCA-AAC
*
2100495 TTCACAGAAGAGTAGTGGA
1 TTCACGGAAGAGTAGTGGA
2100514 GTAATCCAAG
Statistics
Matches: 83, Mismatches: 16, Indels: 21
0.69 0.13 0.17
Matches are distributed among these distances:
43 4 0.05
44 10 0.12
45 40 0.48
46 22 0.27
47 7 0.08
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (45 bp):
TTCACGGAAGAGTAGTGGAACAGATTTTTCAGCAAAGTATCAAAC
Found at i:2100410 original size:90 final size:90
Alignment explanation
Indices: 2100308--2100511 Score: 336
Period size: 90 Copynumber: 2.3 Consensus size: 90
2100298 TCAATCATTT
* *
2100308 TCAAACTTCACGGAAGAGTAGTGAAGCAGAAAGCAAGAATAAAATTTAGTTTTCACGGAAGAGTA
1 TCAAACTTCACGGAAGAGTAGTGAAGCAGAAAGCAAGAATAAAATTCAGTTTCCACGGAAGAGTA
*
2100373 GTGGAACAGATTTTTCAGCAAAGTA
66 GTGGAACAGATTTTTCAACAAAGTA
*
2100398 TCAAACTTCACGGAAGAGTAGTGAAGCAGAAATCAAGAATAAAATTCAGTTTCCACGGAAGAGTA
1 TCAAACTTCACGGAAGAGTAGTGAAGCAGAAAGCAAGAATAAAATTCAGTTTCCACGGAAGAGTA
*
2100463 GTGGAACGGATTTTTCAACAAAGTA
66 GTGGAACAGATTTTTCAACAAAGTA
* *
2100488 TGAGAACTTCACAGAAGAGTAGTG
1 TCA-AACTTCACGGAAGAGTAGTG
2100512 GAGTAATCCA
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
90 87 0.82
91 19 0.18
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.23
Consensus pattern (90 bp):
TCAAACTTCACGGAAGAGTAGTGAAGCAGAAAGCAAGAATAAAATTCAGTTTCCACGGAAGAGTA
GTGGAACAGATTTTTCAACAAAGTA
Found at i:2100972 original size:16 final size:16
Alignment explanation
Indices: 2100916--2100975 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
2100906 CCAAGTGATG
*
2100916 ATTATTTATATATGTT
1 ATTATTTATATATATT
* *
2100932 ATTATATATATATA-A
1 ATTATTTATATATATT
* *
2100947 ATAATATTATAAATATT
1 ATTAT-TTATATATATT
2100964 ATTATTTATATA
1 ATTATTTATATA
2100976 GCCCGAAGGC
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
15 4 0.12
16 25 0.76
17 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTATTTATATATATT
Found at i:2102295 original size:20 final size:19
Alignment explanation
Indices: 2102262--2102305 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
2102252 TTATATTTTA
2102262 ATTAT-TAATAATTAGTAT
1 ATTATATAATAATTAGTAT
2102280 ATTATATAATTAATTAGTAT
1 ATTATATAA-TAATTAGTAT
2102300 -TTATAT
1 ATTATAT
2102306 TTTTAGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.21
19 9 0.38
20 10 0.42
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (19 bp):
ATTATATAATAATTAGTAT
Found at i:2103941 original size:121 final size:121
Alignment explanation
Indices: 2103742--2103962 Score: 347
Period size: 121 Copynumber: 1.8 Consensus size: 121
2103732 TCTGTACACA
*
2103742 TTTTAATTTCACTTTAGTACCCCACCATTAAAAATTTAACGCATTTAGTACTTAAACTATCATAT
1 TTTTAATTTCACTTTAGTACCCCACCATTAAAAATTTAACGCATTTAGTACATAAACTATCATAT
*
2103807 TTGGTCTATTTTAGCACTTAAACTTTTAATTTTTTAAAATCATATCTAACTTTTAG
66 TTGGTCTATTTTAGCACCTAAACTTTTAATTTTTTAAAATCATATCTAACTTTTAG
* * *
2103863 TTTTCATTTCACTTTAGTACCCTACCATT-AAAATCTTAACGCGTTTAGTACATAAACTATCA-A
1 TTTTAATTTCACTTTAGTACCCCACCATTAAAAAT-TTAACGCATTTAGTACATAAACTATCATA
* *
2103926 TTTTGGTCTGTTTTAGTACCTAAACTTTTAATTTTTT
65 -TTTGGTCTATTTTAGCACCTAAACTTTTAATTTTTT
2103963 CTAAACTTAA
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
120 6 0.07
121 85 0.93
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (121 bp):
TTTTAATTTCACTTTAGTACCCCACCATTAAAAATTTAACGCATTTAGTACATAAACTATCATAT
TTGGTCTATTTTAGCACCTAAACTTTTAATTTTTTAAAATCATATCTAACTTTTAG
Found at i:2104891 original size:22 final size:22
Alignment explanation
Indices: 2104866--2104937 Score: 92
Period size: 22 Copynumber: 3.2 Consensus size: 22
2104856 ACCACAGACA
2104866 CACATGGGCGCACACACACAAG
1 CACATGGGCGCACACACACAAG
* *
2104888 CACACGCGCGCGCACACACGCACA-
1 CACATG-G-GCGCACACACACA-AG
2104912 CACATGGGCGCACACACACAAG
1 CACATGGGCGCACACACACAAG
2104934 CACA
1 CACA
2104938 CACGCGCGCG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
21 1 0.02
22 21 0.50
23 2 0.05
24 17 0.40
25 1 0.02
ACGTcount: A:0.35, C:0.42, G:0.21, T:0.03
Consensus pattern (22 bp):
CACATGGGCGCACACACACAAG
Found at i:2104891 original size:24 final size:24
Alignment explanation
Indices: 2104850--2104980 Score: 106
Period size: 24 Copynumber: 5.3 Consensus size: 24
2104840 TTTTACTTTT
* *
2104850 ACACACACCACAGACACACATGGGCGC
1 ACACACA-CA-AG-CACACACGCGCGC
*
2104877 ACACACACAAGCACACGCGCGCGC
1 ACACACACAAGCACACACGCGCGC
* * *
2104901 ACACACGC-A-CACACATGGGCGC
1 ACACACACAAGCACACACGCGCGC
2104923 ACACACACAAGCACACACGCGCGC
1 ACACACACAAGCACACACGCGCGC
* * *
2104947 GCACACATGCACA-CACACAAGCGCAC
1 ACACACA--CA-AGCACACACGCGCGC
2104973 ACACACAC
1 ACACACAC
2104981 GTACACGCGC
Statistics
Matches: 85, Mismatches: 14, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
22 17 0.20
23 2 0.02
24 35 0.41
25 2 0.02
26 21 0.25
27 8 0.09
ACGTcount: A:0.37, C:0.44, G:0.18, T:0.02
Consensus pattern (24 bp):
ACACACACAAGCACACACGCGCGC
Found at i:2104902 original size:12 final size:12
Alignment explanation
Indices: 2104888--2104976 Score: 52
Period size: 12 Copynumber: 7.4 Consensus size: 12
2104878 CACACACAAG
*
2104888 CACACGCGCGCG
1 CACACGCGCGCA
* *
2104900 CACACACGCACA
1 CACACGCGCGCA
* *
2104912 CACATGGGCGCA
1 CACACGCGCGCA
* **
2104924 CACACACAAGCA
1 CACACGCGCGCA
*
2104936 CACACGCGCGCG
1 CACACGCGCGCA
** *
2104948 CACACATGCACA
1 CACACGCGCGCA
**
2104960 CACACAAGCGCA
1 CACACGCGCGCA
2104972 CACAC
1 CACAC
2104977 ACACGTACAC
Statistics
Matches: 55, Mismatches: 22, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
12 55 1.00
ACGTcount: A:0.34, C:0.45, G:0.19, T:0.02
Consensus pattern (12 bp):
CACACGCGCGCA
Found at i:2104940 original size:48 final size:46
Alignment explanation
Indices: 2104863--2104990 Score: 184
Period size: 48 Copynumber: 2.7 Consensus size: 46
2104853 CACACCACAG
2104863 ACACACATGGGCGCACACACACAAGCACACGCGCGCGCACACACGC
1 ACACACATGGGCGCACACACACAAGCACACGCGCGCGCACACACGC
*
2104909 ACACACATGGGCGCACACACACAAGCACACACGCGCGCGCACACATGC
1 ACACACATGGGCGCACACACACAAG--CACACGCGCGCGCACACACGC
*** * *
2104957 ACACACACAAGCGCACACACACACGTACACGCGC
1 ACACACATGGGCGCACACACACAAGCACACGCGC
2104991 ACACGCACGC
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
46 33 0.45
48 41 0.55
ACGTcount: A:0.34, C:0.43, G:0.20, T:0.03
Consensus pattern (46 bp):
ACACACATGGGCGCACACACACAAGCACACGCGCGCGCACACACGC
Found at i:2104944 original size:22 final size:22
Alignment explanation
Indices: 2104873--2104962 Score: 85
Period size: 22 Copynumber: 4.0 Consensus size: 22
2104863 ACACACATGG
*
2104873 GCGCACACACACAAGCACACGC
1 GCGCACACACACAAGCACACAC
*
2104895 GCGCGCACACAC--GCACACAC
1 GCGCACACACACAAGCACACAC
2104915 ATGGGCGCACACACACAAGCACACAC
1 ----GCGCACACACACAAGCACACAC
* * *
2104941 GCGCGCGCACACATGCACACAC
1 GCGCACACACACAAGCACACAC
2104963 ACAAGCGCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.12
22 30 0.54
24 11 0.20
26 8 0.14
ACGTcount: A:0.33, C:0.44, G:0.20, T:0.02
Consensus pattern (22 bp):
GCGCACACACACAAGCACACAC
Found at i:2104970 original size:22 final size:22
Alignment explanation
Indices: 2104926--2104975 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
2104916 TGGGCGCACA
* **
2104926 CACACAAGCACACACGCGCGCG
1 CACACAAGCACACACACAAGCG
*
2104948 CACACATGCACACACACAAGCG
1 CACACAAGCACACACACAAGCG
2104970 CACACA
1 CACACA
2104976 CACACGTACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.44, G:0.16, T:0.02
Consensus pattern (22 bp):
CACACAAGCACACACACAAGCG
Found at i:2104997 original size:6 final size:6
Alignment explanation
Indices: 2104936--2105033 Score: 61
Period size: 6 Copynumber: 15.0 Consensus size: 6
2104926 CACACAAGCA
* * * * *
2104936 CACACG CGCGCG CACACATG CACACA CACAAGCG CACACA CACACG TACACGCG
1 CACACG CACACG CACAC--G CACACG CAC-A-CG CACACG CACACG --CACACG
* *
2104990 CACACG CACGCG CACATGCG CACACG CACACG CACATG CACACG
1 CACACG CACACG CACA--CG CACACG CACACG CACACG CACACG
2105034 TTAACACACA
Statistics
Matches: 70, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
6 47 0.67
7 2 0.03
8 21 0.30
ACGTcount: A:0.32, C:0.45, G:0.19, T:0.04
Consensus pattern (6 bp):
CACACG
Found at i:2105025 original size:12 final size:12
Alignment explanation
Indices: 2104936--2105033 Score: 61
Period size: 14 Copynumber: 7.5 Consensus size: 12
2104926 CACACAAGCA
* *
2104936 CACACGCGCGCG
1 CACACGCACACG
*
2104948 CACACATGCACACA
1 CACAC--GCACACG
*
2104962 CACAAGCGCACACA
1 CAC-A-CGCACACG
*
2104976 CACACGTACACGCG
1 CACACG--CACACG
*
2104990 CACACGCACGCG
1 CACACGCACACG
2105002 CACATGCGCACACG
1 CACA--CGCACACG
*
2105016 CACACGCACATG
1 CACACGCACACG
2105028 CACACG
1 CACACG
2105034 TTAACACACA
Statistics
Matches: 71, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
12 30 0.42
13 1 0.01
14 38 0.54
15 1 0.01
16 1 0.01
ACGTcount: A:0.32, C:0.45, G:0.19, T:0.04
Consensus pattern (12 bp):
CACACGCACACG
Found at i:2105026 original size:20 final size:20
Alignment explanation
Indices: 2104945--2105028 Score: 96
Period size: 20 Copynumber: 4.1 Consensus size: 20
2104935 ACACACGCGC
* *
2104945 GCGCACACATGCACACACACAA
1 GCGCACAC--GCACACGCACAT
* * *
2104967 GCGCACACACACACGTACAC
1 GCGCACACGCACACGCACAT
*
2104987 GCGCACACGCACGCGCACAT
1 GCGCACACGCACACGCACAT
2105007 GCGCACACGCACACGCACAT
1 GCGCACACGCACACGCACAT
2105027 GC
1 GC
2105029 ACACGTTAAC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 45 0.85
22 8 0.15
ACGTcount: A:0.32, C:0.44, G:0.19, T:0.05
Consensus pattern (20 bp):
GCGCACACGCACACGCACAT
Found at i:2105564 original size:186 final size:186
Alignment explanation
Indices: 2105237--2105628 Score: 671
Period size: 186 Copynumber: 2.1 Consensus size: 186
2105227 TTTTCTAATT
* * *
2105237 TATATAA-AAATTAAATATTTTATAATTCAAAAAAACAGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
2105301 ATTATAAAATAAAAAAATTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAAAATTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
*
2105366 TTGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
131 TTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
*
2105422 TATATAATATATTTAATATTTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
** *
2105487 ATTATAAAATAAAAATTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAAAATTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
2105552 TTTG-ATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
131 -TTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
* *
2105608 GATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
2105629 AAAATTTTAT
Statistics
Matches: 195, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
185 7 0.04
186 185 0.95
187 3 0.02
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (186 bp):
TATATAATATATTTAATATTTTATAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
ATTATAAAATAAAAAAATTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
TTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
Found at i:2108522 original size:22 final size:22
Alignment explanation
Indices: 2108497--2108539 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2108487 CATAACTTTT
2108497 TATTTTGATTAAATTTAATATA
1 TATTTTGATTAAATTTAATATA
*
2108519 TATTTTTATTAAATTTAATAT
1 TATTTTGATTAAATTTAATAT
2108540 GTTATTGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TATTTTGATTAAATTTAATATA
Found at i:2110443 original size:3 final size:3
Alignment explanation
Indices: 2110432--2110469 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
2110422 ATCTTCTTAA
*
2110432 AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2110470 CTTCATAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:2111482 original size:19 final size:19
Alignment explanation
Indices: 2111460--2111499 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2111450 TTTGAACATT
*
2111460 TTGTTTTTTATAATAATAA
1 TTGTATTTTATAATAATAA
* *
2111479 TTGTATTTTATCATTATAA
1 TTGTATTTTATAATAATAA
2111498 TT
1 TT
2111500 AAATATATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
TTGTATTTTATAATAATAA
Found at i:2111876 original size:136 final size:136
Alignment explanation
Indices: 2111621--2111881 Score: 416
Period size: 136 Copynumber: 1.9 Consensus size: 136
2111611 GTTACAAAAC
* * *
2111621 TTGTTACTATATAACATTTTTGCACCAAAAACTAGGGAGAAATATTTCTGATAGTATAAGTTTTC
1 TTGTTACTATATAACATTTTTGCACCAAAAAATAGGGAGAAATAGTTATGATAGTATAAGTTTTC
*
2111686 ATAATGATTAAAATATATAACTACAAAAATAATTAATTACAAAAAACTTAAA-TTTATTAATACA
66 ATAATGATTAAAATATATAACTACAAAAATAATTAATTACAAAAAACATAAATTTTATTAATACA
2111750 ATATAT
131 ATATAT
* * *
2111756 TTGTTACTATATAACATTTTTGACACTAAAAAATAGGGAGAAATGGTTATGATAGTATAATTTTT
1 TTGTTACTATATAACATTTTTG-CACCAAAAAATAGGGAGAAATAGTTATGATAGTATAAGTTTT
* * *
2111821 CATAATGATTAAAATATATAAGTACAAAAATAATTTATTACAAAAAACATGAATTTTATTA
65 CATAATGATTAAAATATATAACTACAAAAATAATTAATTACAAAAAACATAAATTTTATTA
2111882 TTTGATGTGA
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
135 22 0.19
136 85 0.75
137 7 0.06
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.37
Consensus pattern (136 bp):
TTGTTACTATATAACATTTTTGCACCAAAAAATAGGGAGAAATAGTTATGATAGTATAAGTTTTC
ATAATGATTAAAATATATAACTACAAAAATAATTAATTACAAAAAACATAAATTTTATTAATACA
ATATAT
Found at i:2112419 original size:180 final size:178
Alignment explanation
Indices: 2111998--2112442 Score: 447
Period size: 181 Copynumber: 2.5 Consensus size: 178
2111988 TAATATATGC
* * * * *
2111998 TATCACTATAGTTAAAATTTATAACTACAAATATAATTTGTCACAAAAA-CGTGAATATTATTAT
1 TATCACTATAATTAAAATATATAACTACAAACATAATTTGTCACAAAAATC-TGAATCTCATTAT
* * * **
2112062 TTTTTGTGACAATATTTTTTGTAATAATTATTAACACTTATAGTTACAAAATTTGTCACTATATG
65 TTGTTGTGACAAT-TTTTTTGTAACAATAATTAACACTTATAGTTACAAAACATGTCACTATATG
* * *
2112127 ACTTTTTTGGCGCAAAAATAATATAGAGGGAAATATTTGTGACACTATATTT
129 ACTTTTTTGACGCAAAAAT-ATAGAGAGGG-AATATTTGTGACACTACATTT
* * * ** * *
2112179 TGTCACTATAATTAAAATATATAACGAAAAACATTGTTTTTTACTAAAAAAT-TGAATCTCATTA
1 TATCACTATAATTAAAATATATAACTACAAACATAATTTGTCAC--AAAAATCTGAATCTCATTA
* *
2112243 TTTGTTGTGATAATTTTTTTGTAACAATAATTATA-GCTTATAGTTACAAAACATGTCACTATAT
64 TTTGTTGTGACAATTTTTTTGTAACAATAATTA-ACACTTATAGTTACAAAACATGTCACTATAT
* * *
2112307 GATTTTGTTTTTGTAC-CAAAAAT-TGGAGA-TG-ATCATTTGTGACTA-TACATTT
128 GA--CT-TTTTTG-ACGCAAAAATATAGAGAGGGAAT-ATTTGTGAC-ACTACATTT
* * * *
2112359 TATCACTATAATTAAAATATATAATTACAAAGAAAATTTGTCACAACAAATCTAAATCTCATTAT
1 TATCACTATAATTAAAATATATAACTACAAACATAATTTGTCACAA-AAATCTGAATCTCATTAT
2112424 TTGTTGTGACAATTTTTTT
65 TTGTTGTGACAATTTTTTT
2112443 TCTGTTCTAA
Statistics
Matches: 215, Mismatches: 37, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
178 2 0.01
179 6 0.03
180 79 0.37
181 81 0.38
182 27 0.13
183 6 0.03
184 13 0.06
185 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (178 bp):
TATCACTATAATTAAAATATATAACTACAAACATAATTTGTCACAAAAATCTGAATCTCATTATT
TGTTGTGACAATTTTTTTGTAACAATAATTAACACTTATAGTTACAAAACATGTCACTATATGAC
TTTTTTGACGCAAAAATATAGAGAGGGAATATTTGTGACACTACATTT
Found at i:2114803 original size:60 final size:60
Alignment explanation
Indices: 2114700--2114860 Score: 261
Period size: 60 Copynumber: 2.7 Consensus size: 60
2114690 TTTGAGTGAT
* * *
2114700 TTTTGGGGATGTTATTGAAATGT-TCAAAGTTTGGATACCAATATAGAATGAGGGTCATA
1 TTTTGGGGATGTTATTGAAATGTATAAAATTTTGGAGACCAATATAGAATGAGGGTCATA
*
2114759 TTTTGGGGATGTTATTGAAATGTATAAAATTTTGGAGACCAATATAGGATGAGGGTCATA
1 TTTTGGGGATGTTATTGAAATGTATAAAATTTTGGAGACCAATATAGAATGAGGGTCATA
* *
2114819 TTTTGGAGATGTTATTGAAATGTATACAATTTTGGAGACCAA
1 TTTTGGGGATGTTATTGAAATGTATAAAATTTTGGAGACCAA
2114861 ATTAAAATGA
Statistics
Matches: 95, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
59 23 0.24
60 72 0.76
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (60 bp):
TTTTGGGGATGTTATTGAAATGTATAAAATTTTGGAGACCAATATAGAATGAGGGTCATA
Found at i:2115569 original size:10 final size:9
Alignment explanation
Indices: 2115538--2115579 Score: 52
Period size: 8 Copynumber: 4.8 Consensus size: 9
2115528 CATAGTATTA
*
2115538 AATAAAAAT
1 AATAGAAAT
2115547 AATAGAAA-
1 AATAGAAAT
2115555 AATAGAAAT
1 AATAGAAAT
2115564 ATATAGAAAT
1 A-ATAGAAAT
2115574 -ATAGAA
1 AATAGAA
2115580 CAAAATATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 14 0.47
9 8 0.27
10 8 0.27
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (9 bp):
AATAGAAAT
Found at i:2115571 original size:18 final size:17
Alignment explanation
Indices: 2115537--2115579 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
2115527 ACATAGTATT
*
2115537 AAATAAAAATAATAGAA
1 AAATAGAAATAATAGAA
2115554 AAATAGAAATATATAGAA
1 AAATAGAAATA-ATAGAA
*
2115572 ATATAGAA
1 AAATAGAA
2115580 CAAAATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (17 bp):
AAATAGAAATAATAGAA
Found at i:2115756 original size:2 final size:2
Alignment explanation
Indices: 2115749--2115816 Score: 106
Period size: 2 Copynumber: 35.0 Consensus size: 2
2115739 GTATACTTAA
2115749 AT AT AT AT AT AT AT AT AT AT AT AT -T 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
2115790 AT AT AT AT AT AT AT ACT A- AT AT -T AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
2115817 TAATAAAATA
Statistics
Matches: 62, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.05
2 57 0.92
3 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2117292 original size:106 final size:106
Alignment explanation
Indices: 2117153--2117356 Score: 329
Period size: 106 Copynumber: 1.9 Consensus size: 106
2117143 TTCTGGAACT
**
2117153 GGAAATTGTTTTGTTGACAGTCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAGT
1 GGAAATTGTTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT-GAGT
*
2117218 CCAATGCCCTTCAATGTGAAGTTGAAATTGGCTCCAAAATTG
65 CCAATACCCTTCAATGTGAAGTTGAAATTGGCTCCAAAATTG
*
2117260 GGAAATTG-TTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAGTC
1 GGAAATTGTTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTGAGTC
* **
2117324 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CAATACCCTTCAATGTGAAGTTGAAATTGGCTC
2117357 TAGCTAAAAC
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
105 34 0.38
106 48 0.53
107 8 0.09
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.34
Consensus pattern (106 bp):
GGAAATTGTTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTGAGTC
CAATACCCTTCAATGTGAAGTTGAAATTGGCTCCAAAATTG
Found at i:2117832 original size:65 final size:67
Alignment explanation
Indices: 2117726--2117853 Score: 179
Period size: 65 Copynumber: 1.9 Consensus size: 67
2117716 TGAGAACGGC
* *
2117726 CTCAAGGGAGACAAAATTTTGTTTTAAGGGAAATAAACTCAAA-GATTTGTATTTCAAGAGAAAT
1 CTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAACAAACTCAAAGGATTTGTATTTCAAGAGAAAT
2117790 TGT
65 TGT
* * * *
2117793 CTCAAGGGAGACGAAA-TTGTTTCAAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAA
1 CTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAACTCAAAGGATTTGTATTTCAAGAGAA
2117854 CATTTTCAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
65 22 0.41
66 17 0.31
67 15 0.28
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (67 bp):
CTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAACTCAAAGGATTTGTATTTCAAGAGAAATT
GT
Found at i:2117898 original size:32 final size:32
Alignment explanation
Indices: 2117810--2117918 Score: 150
Period size: 31 Copynumber: 3.4 Consensus size: 32
2117800 GAGACGAAAT
* *
2117810 TGTTTCAAGGGAAACAATCTCAAAGG-TTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTG
*
2117841 TGTTTCAAGAG-AACATTTTCAAAGGTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTG
*
2117872 TGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTT
1 TGTTTCAAGAGAAACAATTTCAAAGG-TT-TTTG
2117906 TGTTTCAAGAGAA
1 TGTTTCAAGAGAA
2117919 CTGTATCAAG
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
30 12 0.17
31 26 0.38
32 13 0.19
33 2 0.03
34 16 0.23
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (32 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTG
Found at i:2118069 original size:36 final size:35
Alignment explanation
Indices: 2117960--2118072 Score: 120
Period size: 36 Copynumber: 3.1 Consensus size: 35
2117950 CAAGGATTGA
* *
2117960 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAATTT
1 TGTTTCAAGAGAAACAGTCTCAAGAGAGACAAA-TT
* * * *
2117996 TATTTTAAGA-AAACATTCTTAAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACAGTC-TCAAGAGAGAC-AAATT
*
2118032 TGTTTCAAGAGAAACCGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGAGAAACAGTCTCAAGAGAGAC-AAATT
2118068 TGTTT
1 TGTTT
2118073 AATGTAAAAC
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
35 6 0.10
36 47 0.76
37 9 0.15
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (35 bp):
TGTTTCAAGAGAAACAGTCTCAAGAGAGACAAATT
Found at i:2118175 original size:35 final size:35
Alignment explanation
Indices: 2118136--2118210 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 35
2118126 TGTTTCAATA
*
2118136 GAAACTGTCTCAAAG-GAGACAAAATT-TGTTCAAGG
1 GAAACTATCT-AAAGAGAGACAAAATTAT-TTCAAGG
*
2118171 GAAACTATCTTAAGAGAGACAAAATTCATTTCAAGG
1 GAAACTATCTAAAGAGAGACAAAATT-ATTTCAAGG
2118207 GAAA
1 GAAA
2118211 TGTTTTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
34 3 0.09
35 20 0.57
36 11 0.31
37 1 0.03
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (35 bp):
GAAACTATCTAAAGAGAGACAAAATTATTTCAAGG
Found at i:2118233 original size:100 final size:99
Alignment explanation
Indices: 2118099--2118376 Score: 441
Period size: 100 Copynumber: 2.8 Consensus size: 99
2118089 AAAGATTTTG
* * * *
2118099 TTTCAAGGGAATTGTTTTCAAAGTTTATGTTTCAATAGAAACTGTCTCAAAGGAGACAAAA-TTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
*
2118163 GTTCAAGGGAAACTATCTTAAGAGAGACAAAATTCA
66 GTTCAAGGGAAACTATCTCAAGAGAGAC--AATTCA
*
2118199 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
*
2118264 GTTTCAAGGGAAACTATCTCAAGAGAGACAATTTA
66 G-TTCAAGGGAAACTATCTCAAGAGAGACAATTCA
*
2118299 TTTCAAGGGAAATGCTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
2118364 GTTCCAAGGGAAA
66 GTT-CAAGGGAAA
2118377 TGTTTTCAAT
Statistics
Matches: 166, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
99 2 0.01
100 134 0.81
101 4 0.02
102 26 0.16
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (99 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
GTTCAAGGGAAACTATCTCAAGAGAGACAATTCA
Found at i:2118284 original size:37 final size:37
Alignment explanation
Indices: 2118226--2118464 Score: 155
Period size: 37 Copynumber: 7.0 Consensus size: 37
2118216 TCAATGTTTA
* *
2118226 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* *
2118263 TGTTTCAAGGGAAACTATCTCAAGAGAGAC--AA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* * *
2118297 TATTTCAAGGGAAA-TGCTTTCAA---TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGGGAGACAAAATTT
*
2118325 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* * *
2118363 TGTTCCAAGGGAAA-TGTTTTCAA---TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGGGAGACAAAATTT
*
2118391 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* *
2118429 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
2118465 CATTTCAAGG
Statistics
Matches: 154, Mismatches: 23, Indels: 50
0.68 0.10 0.22
Matches are distributed among these distances:
28 5 0.03
29 34 0.22
30 4 0.03
31 1 0.01
32 2 0.01
33 1 0.01
34 21 0.14
35 2 0.01
36 2 0.01
37 76 0.49
38 6 0.04
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:2118397 original size:66 final size:65
Alignment explanation
Indices: 2118263--2118442 Score: 276
Period size: 66 Copynumber: 2.8 Consensus size: 65
2118253 GACAAAATTT
* * *
2118263 TGTTTCAAGGGAAACTATCTCAAGAGAGAC--AATTTAT-TTCAAGGGAAATGCTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT-TGTTCAAGGGAAATGCTTTCAATGTTT
2118325 A
65 A
*
2118326 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTT-CAAGGGAAATGCTTTCAATGTTT
2118391 A
65 A
2118392 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG-TTCAAGGGAAA
2118443 CTATCTCAAG
Statistics
Matches: 108, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
63 27 0.25
64 1 0.01
65 7 0.06
66 71 0.66
67 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCAAGGGAAATGCTTTCAATGTTTA
Found at i:2118504 original size:166 final size:165
Alignment explanation
Indices: 2118171--2118543 Score: 581
Period size: 166 Copynumber: 2.2 Consensus size: 165
2118161 TTGTTCAAGG
* * *
2118171 GAAACTATCTTAAGAGAGACAAAATTCAT-TTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
1 GAAACTGTCTCAAGAGAGACAAAATT-TTGTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
* *
2118235 AGAAATTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAATTTAT
65 AGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAATTCAT
*
2118300 TTCAAGGGAAATGCTTTCAATGTTTATGTTTCAAGA
130 TTCAAGGGAAATGCTTTCAATGTTTATGTTTAAAGA
*
2118336 GAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
1 GAAACTGTCTCAAGAGAGACAAAATTTTGTT-CAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
2118401 AGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTC
65 AGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAC--AATTC
*
2118466 ATTTCAA-GGAAATGTTTTCAATGTTTA-GTTTAAAGA
128 ATTTCAAGGGAAATGCTTTCAATGTTTATGTTTAAAGA
* *
2118502 GAAACTGTCTCAAGTGAGACAAAACTTTCTGTTCGAGGGAAA
1 GAAACTGTCTCAAGAGAGACAAAA-TTT-TGTTCAAGGGAAA
2118544 CTATCTCAAG
Statistics
Matches: 192, Mismatches: 10, Indels: 10
0.91 0.05 0.05
Matches are distributed among these distances:
164 1 0.01
165 25 0.13
166 121 0.63
167 30 0.16
168 15 0.08
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (165 bp):
GAAACTGTCTCAAGAGAGACAAAATTTTGTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGA
GAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAATTCATT
TCAAGGGAAATGCTTTCAATGTTTATGTTTAAAGA
Found at i:2118543 original size:101 final size:103
Alignment explanation
Indices: 2118326--2118563 Score: 333
Period size: 101 Copynumber: 2.3 Consensus size: 103
2118316 TCAATGTTTA
* * * *
2118326 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTATGTTCCAAGGGAAATGTTTTCAATGTTT
*
2118391 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 ATGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAATTT
2118429 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT-TT-CAA-GGAAATGTTTTCAATGTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT-ATGTTCCAAGGGAAATGTTTTCAATGTT
*
2118491 TA-GTTTAAAGAGAAACTGTCTCAAGTGAGACAAAACTTT
65 TATGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT
* * *
2118530 CTG-TTCGAGGGAAACTATCTCAAGCGAGATAAAA
1 -TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
2118564 ATCTTGTTTT
Statistics
Matches: 123, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
100 31 0.25
101 51 0.41
102 5 0.04
103 35 0.28
104 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (103 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTATGTTCCAAGGGAAATGTTTTCAATGTTT
ATGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:2123924 original size:18 final size:19
Alignment explanation
Indices: 2123884--2123922 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2123874 ACATAGTATT
2123884 AAATAA-AAATAATAAGAA
1 AAATAAGAAATAATAAGAA
2123902 AAATAAGAAAT-ATATAGAA
1 AAATAAGAAATAATA-AGAA
2123921 AA
1 AA
2123923 TATAGAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (19 bp):
AAATAAGAAATAATAAGAA
Found at i:2123936 original size:12 final size:13
Alignment explanation
Indices: 2123919--2123951 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2123909 AAATATATAG
*
2123919 AAAATATAGAAC-
1 AAAATATAAAACA
2123931 AAAATATAAAACA
1 AAAATATAAAACA
2123944 AAAATATA
1 AAAATATA
2123952 CGTAGTAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (13 bp):
AAAATATAAAACA
Found at i:2125968 original size:181 final size:184
Alignment explanation
Indices: 2125661--2126032 Score: 723
Period size: 181 Copynumber: 2.0 Consensus size: 184
2125651 TTTATTGGGC
2125661 TCATTGAGTTTATTGCTTTCGTGACTTCATCATAGTTGAAACCCATGTTCAGGACCTCATTCATG
1 TCATTGAGTTTATTGCTTTCGTGACTTCATCATAGTTGAAACCCATGTTCAGGACCTCATTCATG
2125726 CTCGTCGTGATACTCGGTGTGATCGCCATTGTGATTGTGTCATCTGTCTCTACTGTTTCGCTCGT
66 CTCGTCGTGATACTCGGTGTGATCGCCATTGTGATTGTGTCATCTGTCTCTACTGTTTCGCTCGT
2125791 AAACAAA-TCTCAAAGTAAGTCTTTGTTGAA-TCTAAATGAAACTCTTGTCATA
131 AAACAAATTCTCAAAGTAAGTCTTTGTTGAATTCTAAATGAAACTCTTGTCATA
2125843 TC-TTGAGTTTATTGCTTTCGTGACTTCATCATAGTTGAAACCCATGTTCAGGACCTCATTCATG
1 TCATTGAGTTTATTGCTTTCGTGACTTCATCATAGTTGAAACCCATGTTCAGGACCTCATTCATG
2125907 CTCGTCGTGATACTCGGTGTGATCGCCATTGTGATTGTGTCATCTGTCTCTACTGTTTCGCTCGT
66 CTCGTCGTGATACTCGGTGTGATCGCCATTGTGATTGTGTCATCTGTCTCTACTGTTTCGCTCGT
2125972 AAACAAATTCTCAAAGTAAGTCTTTGTTGAATTCTAAATGAAACTCTTGTCATA
131 AAACAAATTCTCAAAGTAAGTCTTTGTTGAATTCTAAATGAAACTCTTGTCATA
2126026 TCATTGA
1 TCATTGA
2126033 ACCCCTCGTC
Statistics
Matches: 187, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
181 134 0.72
182 25 0.13
183 24 0.13
184 4 0.02
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (184 bp):
TCATTGAGTTTATTGCTTTCGTGACTTCATCATAGTTGAAACCCATGTTCAGGACCTCATTCATG
CTCGTCGTGATACTCGGTGTGATCGCCATTGTGATTGTGTCATCTGTCTCTACTGTTTCGCTCGT
AAACAAATTCTCAAAGTAAGTCTTTGTTGAATTCTAAATGAAACTCTTGTCATA
Found at i:2134445 original size:14 final size:14
Alignment explanation
Indices: 2134426--2134455 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2134416 TTAGTTGATT
2134426 GTGAGAAAGAACAA
1 GTGAGAAAGAACAA
2134440 GTGAGAAAGAACAA
1 GTGAGAAAGAACAA
2134454 GT
1 GT
2134456 AAACAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.30, T:0.10
Consensus pattern (14 bp):
GTGAGAAAGAACAA
Found at i:2137438 original size:15 final size:15
Alignment explanation
Indices: 2137414--2137454 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
2137404 ACCTAATCTT
*
2137414 CATTTCATAAACATA
1 CATTTGATAAACATA
2137429 CATTTGATAAACATA
1 CATTTGATAAACATA
2137444 CATTTGCATAA
1 CATTTG-ATAA
2137455 CTTATTGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (15 bp):
CATTTGATAAACATA
Found at i:2141143 original size:14 final size:14
Alignment explanation
Indices: 2141124--2141159 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
2141114 CATCACTATT
2141124 CCTTCCTCCGGCGG
1 CCTTCCTCCGGCGG
2141138 CCTTCCTCCGGCGG
1 CCTTCCTCCGGCGG
2141152 CCTTCCTC
1 CCTTCCTC
2141160 GATGGTTACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.00, C:0.53, G:0.22, T:0.25
Consensus pattern (14 bp):
CCTTCCTCCGGCGG
Found at i:2143831 original size:29 final size:30
Alignment explanation
Indices: 2143798--2143874 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
2143788 AAATGAACAC
*
2143798 TTTAAGTTTTTATTTTGACCAAAAA-AT-AA
1 TTTAAGTATTTATTTTGA-CAAAAATATAAA
* * *
2143827 TTTAAATATTTAATTTGATAAAAATATAAA
1 TTTAAGTATTTATTTTGACAAAAATATAAA
*
2143857 TTTAAGTACTTATTTTGA
1 TTTAAGTATTTATTTTGA
2143875 AATTGAAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 5 0.13
29 17 0.44
30 17 0.44
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (30 bp):
TTTAAGTATTTATTTTGACAAAAATATAAA
Found at i:2164049 original size:14 final size:14
Alignment explanation
Indices: 2164030--2164085 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
2164020 CGTTCGTGAA
2164030 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
2164044 CGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
2164057 --TT-GTTTATGTT
1 CGTTCGATTATGTT
2164068 CGTTCGATTATGTT
1 CGTTCGATTATGTT
2164082 CGTT
1 CGTT
2164086 TATGTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 3 0.09
13 3 0.09
14 23 0.66
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:2164064 original size:24 final size:24
Alignment explanation
Indices: 2164037--2164106 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
2164027 GAACGTTCGA
*
2164037 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGATTATGTTTGT
*
2164061 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTTGT
*
2164085 TTATGTTCATTC-ATTTATGTTT
1 TTATGTTCGTTCGA-TTATGTTT
2164107 AACTCAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTTGT
Found at i:2164848 original size:10 final size:10
Alignment explanation
Indices: 2164833--2164904 Score: 55
Period size: 10 Copynumber: 7.4 Consensus size: 10
2164823 TCTCCAACGG
2164833 TTATGTTCGT
1 TTATGTTCGT
2164843 TTATGTTCGT
1 TTATGTTCGT
*
2164853 GTTCAT-TTATGT
1 -TT-ATGTT-CGT
**
2164865 TCGTGTTCGT
1 TTATGTTCGT
2164875 TTATGTTCG-
1 TTATGTTCGT
2164884 ---TGTTCGT
1 TTATGTTCGT
2164891 TTATGTTCGT
1 TTATGTTCGT
2164901 TTAT
1 TTAT
2164905 TTATTAAATG
Statistics
Matches: 48, Mismatches: 6, Indels: 16
0.69 0.09 0.23
Matches are distributed among these distances:
6 6 0.12
10 31 0.65
11 7 0.15
12 4 0.08
ACGTcount: A:0.10, C:0.11, G:0.21, T:0.58
Consensus pattern (10 bp):
TTATGTTCGT
Found at i:2164861 original size:16 final size:16
Alignment explanation
Indices: 2164836--2164900 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
2164826 CCAACGGTTA
2164836 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
2164852 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
2164868 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2164884 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2164900 T
1 T
2164901 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:2165272 original size:22 final size:23
Alignment explanation
Indices: 2165223--2165265 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
2165213 TGTATGATTA
2165223 TAATTTAGTTGAAAATATAATTG
1 TAATTTAGTTGAAAATATAATTG
*
2165246 TAATTTA-TTTAAAATATAAT
1 TAATTTAGTTGAAAATATAAT
2165266 ATTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (23 bp):
TAATTTAGTTGAAAATATAATTG
Found at i:2165279 original size:22 final size:22
Alignment explanation
Indices: 2165234--2165280 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2165224 AATTTAGTTG
* *
2165234 AAAATATAATTGTAATTTATTT
1 AAAATATAATTGTAATTAAATT
2165256 AAAATATAATAT-TAATTAAATT
1 AAAATATAAT-TGTAATTAAATT
2165278 AAA
1 AAA
2165281 TTTTTAATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAATATAATTGTAATTAAATT
Found at i:2173711 original size:15 final size:15
Alignment explanation
Indices: 2173691--2173736 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
2173681 TGAGACATTA
2173691 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
2173706 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
* *
2173721 CCTGCCCCACATCCG
1 CCCGCCCCGCATCCG
2173736 C
1 C
2173737 TCACCCAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.09, C:0.65, G:0.17, T:0.09
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Done.