Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007823.1 Hibiscus syriacus cultivar Beakdansim tig00110160_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: 6287495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 33
Found at i:1942474 original size:43 final size:42
Alignment explanation
Indices: 1942420--1942511 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 42
1942410 TATAAACCAT
*
1942420 ATTATATTAATATAAGTTAATATTAATATTAATTATATTAATA-TTA
1 ATTATAAT-ATATAA-TT-ATATTAATATTAATTATA--AATAGTTA
*
1942466 ATTATAATATATAATTATTTTAATATTAATTATAAATAGTTA
1 ATTATAATATATAATTATATTAATATTAATTATAAATAGTTA
1942508 ATTA
1 ATTA
1942512 ATAAAAATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
41 4 0.09
42 7 0.16
43 17 0.40
44 2 0.05
45 6 0.14
46 7 0.16
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (42 bp):
ATTATAATATATAATTATATTAATATTAATTATAAATAGTTA
Found at i:1942489 original size:28 final size:27
Alignment explanation
Indices: 1942443--1942511 Score: 102
Period size: 28 Copynumber: 2.4 Consensus size: 27
1942433 AAGTTAATAT
1942443 TAATATTAATTATATTAATATTAATTA
1 TAATATTAATTATATTAATATTAATTA
*
1942470 TAATATATAATTATTTTAATATTAATTA
1 TAATAT-TAATTATATTAATATTAATTA
1942498 TAAATAGTTAATTA
1 T-AATA-TTAATTA
1942512 ATAAAAATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
27 6 0.16
28 21 0.55
29 10 0.26
30 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
TAATATTAATTATATTAATATTAATTA
Found at i:1942521 original size:28 final size:27
Alignment explanation
Indices: 1942418--1942521 Score: 79
Period size: 28 Copynumber: 3.8 Consensus size: 27
1942408 ATTATAAACC
* *
1942418 ATATTATATTA-ATATAAGTTAA-TATTA
1 ATATTA-ATTATATAAAAATTAATTA-TA
* *
1942445 ATATTAATTATATTAATATTAATTATA
1 ATATTAATTATATAAAAATTAATTATA
* * *
1942472 ATATATAATTATTTTAATATTAATTATAA
1 ATAT-TAATTATATAAAAATTAATTAT-A
1942501 ATAGTTAATTA-ATAAAAATTA
1 ATA-TTAATTATATAAAAATTA
1942522 TATAGGGATG
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
26 4 0.06
27 19 0.30
28 30 0.47
29 10 0.16
30 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
ATATTAATTATATAAAAATTAATTATA
Found at i:1942776 original size:18 final size:19
Alignment explanation
Indices: 1942755--1942799 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
1942745 TCTCTCTCTC
*
1942755 TCTCTCTAACTCTCTG-TT
1 TCTCTCTAACTCTCTGCCT
* *
1942773 TCTCTCAAATTCTCTGCCT
1 TCTCTCTAACTCTCTGCCT
1942792 TCTCTCTA
1 TCTCTCTA
1942800 GAACTTCATC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.13, C:0.36, G:0.04, T:0.47
Consensus pattern (19 bp):
TCTCTCTAACTCTCTGCCT
Found at i:1943268 original size:6 final size:6
Alignment explanation
Indices: 1943257--1943370 Score: 81
Period size: 6 Copynumber: 19.2 Consensus size: 6
1943247 CTAAATCAAC
* * *
1943257 ACCCAA ACCCAA ACCTAA ACCCAA ACCCAA ACTCAA ACCCAA ACCCGA
1 ACCCAA ACCCAA ACCCAA ACCCAA ACCCAA ACCCAA ACCCAA ACCCAA
* * * * * *
1943305 ACTCGAA A--CGA ATCCAA ACCCAA ATCCAAA ACCTAA ACCC-G ACCCAA
1 AC-CCAA ACCCAA ACCCAA ACCCAA A-CCCAA ACCCAA ACCCAA ACCCAA
* * *
1943352 ATCTAA ACCCGA ACCCAA A
1 ACCCAA ACCCAA ACCCAA A
1943371 ACTTGAACCC
Statistics
Matches: 81, Mismatches: 22, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
4 2 0.02
5 4 0.05
6 67 0.83
7 8 0.10
ACGTcount: A:0.47, C:0.41, G:0.04, T:0.07
Consensus pattern (6 bp):
ACCCAA
Found at i:1943280 original size:18 final size:18
Alignment explanation
Indices: 1943257--1943413 Score: 80
Period size: 18 Copynumber: 9.1 Consensus size: 18
1943247 CTAAATCAAC
1943257 ACCCAAACCCAAACCTAA
1 ACCCAAACCCAAACCTAA
1943275 ACCCAAACCCAAA-CTCAA
1 ACCCAAACCCAAACCT-AA
*
1943293 ACCCAAACCCGAA-CT--
1 ACCCAAACCCAAACCTAA
* * *
1943308 --CGAAA-CGAATCC-AA
1 ACCCAAACCCAAACCTAA
*
1943322 ACCCAAATCCAAAACCTAA
1 ACCCAAA-CCCAAACCTAA
* *
1943341 ACCC-GACCCAAATCTAA
1 ACCCAAACCCAAACCTAA
* * *
1943358 ACCCGAACCCAAAACTTGA
1 ACCCAAACCC-AAACCTAA
* * *
1943377 ACCCTAACCCTAACCCAA
1 ACCCAAACCCAAACCTAA
** *
1943395 ATTCAAACCTAAACCTAA
1 ACCCAAACCCAAACCTAA
1943413 A
1 A
1943414 AAACCATAAC
Statistics
Matches: 102, Mismatches: 26, Indels: 22
0.68 0.17 0.15
Matches are distributed among these distances:
12 2 0.02
13 5 0.05
16 4 0.04
17 15 0.15
18 56 0.55
19 20 0.20
ACGTcount: A:0.46, C:0.39, G:0.04, T:0.10
Consensus pattern (18 bp):
ACCCAAACCCAAACCTAA
Found at i:1943359 original size:17 final size:18
Alignment explanation
Indices: 1943337--1943370 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1943327 AATCCAAAAC
1943337 CTAAACCCG-ACCCAAAT
1 CTAAACCCGAACCCAAAT
1943354 CTAAACCCGAACCCAAA
1 CTAAACCCGAACCCAAA
1943371 ACTTGAACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.44, C:0.41, G:0.06, T:0.09
Consensus pattern (18 bp):
CTAAACCCGAACCCAAAT
Found at i:1943862 original size:120 final size:119
Alignment explanation
Indices: 1943646--1944022 Score: 592
Period size: 120 Copynumber: 3.2 Consensus size: 119
1943636 AAATATACTG
* * *
1943646 TAATTTGTAGTTAATGTTGATTTGTTTCCTCTGTAGTCCTTGTTTGTGTTGTTGGTTGTTTATTT
1 TAATTTGTAGCTAATGTTGATTTGTTTCCTCTGTAGTCCTTGTTTGTGTTGTTGGTTGTTCATTC
* * *
1943711 GGATTACTTGTATAAGGTTGTTAGCTGCCTTTATTTAGTATTTAAATAAACTATT
66 GGATTGCTTGTATAAGGTTGTTAGCTACCTTTATTTAGGATTTAAATAAACT-TT
* * * * * *
1943766 TAATTTATAGTTATTGTTGATTTATTACCTCTGTAGTCCTTGTATGTGTTGTTGGTTGTTCATTC
1 TAATTTGTAGCTAATGTTGATTTGTTTCCTCTGTAGTCCTTGTTTGTGTTGTTGGTTGTTCATTC
*
1943831 GGATTGCTTGTATAAGGTTGTTAGCTTCCTTTATTTAGGATTTAAATAAACTGTT
66 GGATTGCTTGTATAAGGTTGTTAGCTACCTTTATTTAGGATTTAAATAAACT-TT
*
1943886 TAATTTGTAGCTAATGTTGATTTGTTTCCTCTGTAGTCCTTGTTTGTATTGTTGGTTGTTCATTC
1 TAATTTGTAGCTAATGTTGATTTGTTTCCTCTGTAGTCCTTGTTTGTGTTGTTGGTTGTTCATTC
*
1943951 GGATTGCTTGTATAAGGTTGTTAGCTACCTTTATTTAGGATTTAAATAAACTGT
66 GGATTGCTTGTATAAGGTTGTTAGCTACCTTTATTTAGGATTTAAATAAACTTT
*
1944005 TAATTTGTAGCTATTGTT
1 TAATTTGTAGCTAATGTT
1944023 TAATTTTTAC
Statistics
Matches: 236, Mismatches: 21, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
119 18 0.08
120 218 0.92
ACGTcount: A:0.20, C:0.10, G:0.19, T:0.51
Consensus pattern (119 bp):
TAATTTGTAGCTAATGTTGATTTGTTTCCTCTGTAGTCCTTGTTTGTGTTGTTGGTTGTTCATTC
GGATTGCTTGTATAAGGTTGTTAGCTACCTTTATTTAGGATTTAAATAAACTTT
Found at i:1946558 original size:10 final size:10
Alignment explanation
Indices: 1946554--1946589 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1946544 CTGCCTTTTG
*
1946554 TTGCCTGCTA
1 TTGCCTGTTA
*
1946564 TTGCCTGTTG
1 TTGCCTGTTA
1946574 TTGCCTGTTA
1 TTGCCTGTTA
1946584 TTGCCT
1 TTGCCT
1946590 TGTAATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.06, C:0.25, G:0.22, T:0.47
Consensus pattern (10 bp):
TTGCCTGTTA
Found at i:1946559 original size:30 final size:30
Alignment explanation
Indices: 1946525--1946589 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
1946515 TGCCTGCAGC
* * *
1946525 TGCCTGCTGTTACCTGTTGCTGCCTTTTGT
1 TGCCTGCTATTACCTGTTGCTGCCTGTTAT
* *
1946555 TGCCTGCTATTGCCTGTTGTTGCCTGTTAT
1 TGCCTGCTATTACCTGTTGCTGCCTGTTAT
1946585 TGCCT
1 TGCCT
1946590 TGTAATTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.05, C:0.26, G:0.23, T:0.46
Consensus pattern (30 bp):
TGCCTGCTATTACCTGTTGCTGCCTGTTAT
Found at i:1946568 original size:20 final size:20
Alignment explanation
Indices: 1946545--1946590 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1946535 TACCTGTTGC
1946545 TGCCTTTTGTTGCCTGCTAT
1 TGCCTTTTGTTGCCTGCTAT
* *
1946565 TGCCTGTTGTTGCCTGTTAT
1 TGCCTTTTGTTGCCTGCTAT
1946585 TGCCTT
1 TGCCTT
1946591 GTAATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.04, C:0.24, G:0.22, T:0.50
Consensus pattern (20 bp):
TGCCTTTTGTTGCCTGCTAT
Found at i:1947169 original size:23 final size:24
Alignment explanation
Indices: 1947142--1947191 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
1947132 TTATTTTTTC
1947142 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
*
1947165 TTTATATAAATTAAATTATATTAA
1 TTTATATAAATTAAACTATATTAA
1947189 TTT
1 TTT
1947192 TCCTTTTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:1947262 original size:13 final size:14
Alignment explanation
Indices: 1947228--1947260 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
1947218 TCTAATTTAC
1947228 ATATAAATAATTTT
1 ATATAAATAATTTT
1947242 AT-TAAATAATTTT
1 ATATAAATAATTTT
1947255 ATATAA
1 ATATAA
1947261 TAGGTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATAAATAATTTT
Found at i:1947484 original size:15 final size:16
Alignment explanation
Indices: 1947464--1947516 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
1947454 TGTCATGTTA
1947464 AAAACAAGACAGGTT-
1 AAAACAAGACAGGTTG
* *
1947479 AAAACAGGTCAGGTTG
1 AAAACAAGACAGGTTG
* * *
1947495 AAAATAGGCCAGGTTG
1 AAAACAAGACAGGTTG
1947511 AAAACA
1 AAAACA
1947517 TGTCGGGTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 13 0.41
16 19 0.59
ACGTcount: A:0.47, C:0.13, G:0.25, T:0.15
Consensus pattern (16 bp):
AAAACAAGACAGGTTG
Found at i:1947498 original size:16 final size:16
Alignment explanation
Indices: 1947473--1947516 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
1947463 AAAAACAAGA
*
1947473 CAGGTT-AAAACAGGT
1 CAGGTTGAAAACAGGC
*
1947488 CAGGTTGAAAATAGGC
1 CAGGTTGAAAACAGGC
1947504 CAGGTTGAAAACA
1 CAGGTTGAAAACA
1947517 TGTCGGGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 6 0.24
16 19 0.76
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.18
Consensus pattern (16 bp):
CAGGTTGAAAACAGGC
Found at i:1953844 original size:12 final size:12
Alignment explanation
Indices: 1953829--1953858 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1953819 GATTTTTTGA
1953829 AAGTAGGAAATG
1 AAGTAGGAAATG
1953841 AAGTAGGAAATG
1 AAGTAGGAAATG
1953853 AAGTAG
1 AAGTAG
1953859 AAGCTTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (12 bp):
AAGTAGGAAATG
Found at i:1954031 original size:14 final size:14
Alignment explanation
Indices: 1954012--1954074 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
1954002 CCTTGTTGCA
1954012 TTTGCATCTCGCAT
1 TTTGCATCTCGCAT
*
1954026 TTTGCA-CTCCCAT
1 TTTGCATCTCGCAT
*
1954039 TTTCGCATCTTTGCA-
1 TTT-GCATC-TCGCAT
*
1954054 TTTGCATGT-GCAT
1 TTTGCATCTCGCAT
1954067 CTTTGCAT
1 -TTTGCAT
1954075 TTGCATGTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
12 3 0.08
13 10 0.25
14 20 0.50
15 4 0.10
16 3 0.08
ACGTcount: A:0.14, C:0.27, G:0.14, T:0.44
Consensus pattern (14 bp):
TTTGCATCTCGCAT
Found at i:1954068 original size:20 final size:20
Alignment explanation
Indices: 1954043--1954095 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
1954033 TCCCATTTTC
1954043 GCATCTTTGCATTTGCATGT
1 GCATCTTTGCATTTGCATGT
1954063 GCATCTTTGCATTTGCATGT
1 GCATCTTTGCATTTGCATGT
1954083 GCATCTTTGCATT
1 GCATCTTTGCATT
1954096 AGTATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (20 bp):
GCATCTTTGCATTTGCATGT
Found at i:1956064 original size:19 final size:19
Alignment explanation
Indices: 1956026--1956065 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1956016 TGAATAATTG
* *
1956026 AATCAAATATAATATTTTA
1 AATCAAATATAAAATCTTA
1956045 AATCAAATATAAAATCTTA
1 AATCAAATATAAAATCTTA
1956064 AA
1 AA
1956066 ATTACTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATCAAATATAAAATCTTA
Found at i:1956496 original size:16 final size:15
Alignment explanation
Indices: 1956454--1956496 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
1956444 CAAGCATTCA
1956454 AAACACAAAATATCC
1 AAACACAAAATATCC
*
1956469 AAACAACCAAATATCC
1 AAAC-ACAAAATATCC
1956485 AAACACATAAAT
1 AAACACA-AAAT
1956497 CCATCAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.60, C:0.26, G:0.00, T:0.14
Consensus pattern (15 bp):
AAACACAAAATATCC
Found at i:1958460 original size:21 final size:20
Alignment explanation
Indices: 1958436--1958491 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 20
1958426 ACATTCAAGG
*
1958436 AGTATCGGTACTATT-AAGAA
1 AGTATCGATACTATTGAAG-A
1958456 CAGTATCGATACCTATTGAAGA
1 -AGTATCGATA-CTATTGAAGA
1958478 AGTATCGATACTAT
1 AGTATCGATACTAT
1958492 GCTAGTAGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 4 0.12
21 19 0.59
22 6 0.19
23 3 0.09
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (20 bp):
AGTATCGATACTATTGAAGA
Found at i:1964327 original size:19 final size:19
Alignment explanation
Indices: 1964289--1964328 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1964279 TGAATAATTG
* * *
1964289 AATCGAATATAATATTTTA
1 AATCAAATATAAAATCTTA
1964308 AATCAAATATAAAATCTTA
1 AATCAAATATAAAATCTTA
1964327 AA
1 AA
1964329 ATTACTTAAC
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:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (19 bp):
AATCAAATATAAAATCTTA
Found at i:1965302 original size:36 final size:36
Alignment explanation
Indices: 1965255--1966087 Score: 194
Period size: 38 Copynumber: 22.0 Consensus size: 36
1965245 ATTTAATACG
* *
1965255 AAGATTTATCTCAATTGAGATGGTTTTTCTTAAAAC
1 AAGATTTATCTCACTTGAGATAGTTTTTCTTAAAAC
* ** *
1965291 AAGATTCATCTCACTTGAGATAGTTTCACTCAAAAC
1 AAGATTTATCTCACTTGAGATAGTTTTTCTTAAAAC
*
1965327 -AGAATATTAGTCTCACTTGAGATTA-TCTTTCTTAAAAC
1 AAG-AT-TTA-TCTCACTTGAGA-TAGTTTTTCTTAAAAC
* * ** * **
1965365 AAGATTTACCTCGCTTGAGATAGTTTCACTCGAAATTG
1 AAGATTTATCTCACTTGAGATAGTTTTTCT-TAAA-AC
* * ** *
1965403 AAGATTCATTTCACTCAAGATTGTTTTTCTTAAAAC
1 AAGATTTATCTCACTTGAGATAGTTTTTCTTAAAAC
* * ** * *
1965439 AAG------CTCGCTGGAGATAGTTTCACTCAAAATTG
1 AAGATTTATCTCACTTGAGATAGTTTTTCTTAAAA--C
** *
1965471 AAGATTTATCTCACTTGATATTGTTTGAGATAGTTTCACTCAAAAC
1 AAGATTTATCTCAC----------TTGAGATAGTTTTTCTTAAAAC
* * ** *
1965517 TGAAGATTCATTTCACTCAAGATTGTTTTTCTTAAAAC
1 --AAGATTTATCTCACTTGAGATAGTTTTTCTTAAAAC
* * * ** * *
1965555 AAGATTCATCTCGCTGGAGATAGTTTCACTCGAAACAG
1 AAGATTTATCTCACTTGAGATAGTTTTTCT-TAAA-AC
* *
1965593 AAGATTTATCTCACTTGAGATTGTTTAAGATAGTTTCACTCGAAATAC
1 AAGATTTATCTCACTTGAGA-----T-AG-T--TTT-TCT-TAAA-AC
* * ** * *
1965641 AAGATTCATTTCACTCAATATTGTTTTT-TTAAAAC
1 AAGATTTATCTCACTTGAGATAGTTTTTCTTAAAAC
* * ** * *
1965676 AAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAG
1 AAGATTTATCTCACTTGAGATAGTTTTTCT-TAAA-AC
*
1965714 AAGA-TTAGTCTCACTTGAGATTGTTTTTCTTAAAAC
1 AAGATTTA-TCTCACTTGAGATAGTTTTTCTTAAAAC
* * ** ** **
1965750 AATATTTTACCTCGTTTGAGATAGTTTCACTCGAAAC
1 AAGA-TTTATCTCACTTGAGATAGTTTTTCTTAAAAC
* ** *
1965787 ATA-ATATTCATTTCACTCAAGATTGTTTTTCTTAAAAC
1 A-AGAT-TT-ATCTCACTTGAGATAGTTTTTCTTAAAAC
* ** *
1965825 AAGATTTGTCTCACTTGAGATAGTTTCACTCAAAAC
1 AAGATTTATCTCACTTGAGATAGTTTTTCTTAAAAC
* * * *
1965861 AAAAGATTAATTTCACTTGATATTGTTTTTCTTAAAAC
1 --AAGATTTATCTCACTTGAGATAGTTTTTCTTAAAAC
* * * * * **
1965899 AATATTTGTCTCGCTTGAGACATTTTTTACTCGAAAC
1 AAGATTTATCTCACTTGAGATAGTTTTT-CTTAAAAC
* ** * **
1965936 AAGATATTTCATTTCACTCAATATTTTTTTTCTTAAAAC
1 AAG--ATTT-ATCTCACTTGAGATAGTTTTTCTTAAAAC
* ** ** ** *
1965975 AAGATTCATCTTGCTTGAGATAGTTTCACTCGAAGC
1 AAGATTTATCTCACTTGAGATAGTTTTTCTTAAAAC
* * ** ** *
1966011 AAAAATTTTATCTCGCAGGAGATAGTTTCACTTGAAAC
1 -AAGA-TTTATCTCACTTGAGATAGTTTTTCTTAAAAC
*
1966049 AAGAAGTTTATCTCACTTGAGATTGTTTTTCTTAAAAC
1 AAG-A-TTTATCTCACTTGAGATAGTTTTTCTTAAAAC
1966087 A
1 A
1966088 GACTACACCT
Statistics
Matches: 559, Mismatches: 179, Indels: 116
0.65 0.21 0.14
Matches are distributed among these distances:
30 18 0.03
32 3 0.01
35 26 0.05
36 137 0.25
37 66 0.12
38 211 0.38
39 20 0.04
40 13 0.02
41 1 0.00
42 1 0.00
43 2 0.00
44 2 0.00
45 1 0.00
47 2 0.00
48 56 0.10
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.38
Consensus pattern (36 bp):
AAGATTTATCTCACTTGAGATAGTTTTTCTTAAAAC
Found at i:1965417 original size:74 final size:74
Alignment explanation
Indices: 1965271--1966008 Score: 474
Period size: 74 Copynumber: 9.7 Consensus size: 74
1965261 TATCTCAATT
* * * * *
1965271 GAGATGGTTTTTCTTAAAACAAGATTCATCTCACTTGAGATAGTTTCACTCAAAACAGAATATT-
1 GAGATTGTTTTTCTTAAAACAAGATTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTC
* *
1965335 AGTCTCACTT
66 A-TTTCACTC
* * * **
1965345 GAGATTATCTTTCTTAAAACAAGATTTACCTCGCTTGAGATAGTTTCACTCGAAATTGAAGATTC
1 GAGATTGTTTTTCTTAAAACAAGATTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTC
1965410 ATTTCACTC
66 ATTTCACTC
* * * ** *
1965419 AAGATTGTTTTTCTTAAAACAAG------CTCGCTGGAGATAGTTTCACTCAAAATTGAAGATTT
1 GAGATTGTTTTTCTTAAAACAAGATTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTC
* *
1965478 ATCTCACTT
66 ATTTCACTC
* * * * * ** * ** *
1965487 GATATTGTTTGAGATAGTTTCACTCAAAACTGAAGATTCATTTCACTCAAGATTGTTTTTCT-TA
1 GAGATTG--T----T--TTT--CTTAAAAC--AAGATTTATCTCGCTTGAGATAGTTTCACTCGA
* * * *
1965551 AA-ACAAGATTCATCTCGCTG
54 AACAGAAGATTCATTTCACTC
* ** * * *
1965571 GAGATAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGATTGTTTAAGATAGTTTCACTCGA
1 GAGATTGTTTTTCT-TAAA-ACAAGATTTATCT--C----GCTTG----AGATAGTTTCACTCGA
* *
1965636 AATACAAGATTCATTTCACTC
54 AACAGAAGATTCATTTCACTC
* * *
1965657 AATATTGTTTTT-TTAAAACAAGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATT-
1 GAGATTGTTTTTCTTAAAACAAGATTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTC
* *
1965720 AGTCTCACTT
66 A-TTTCACTC
* * * * *
1965730 GAGATTGTTTTTCTTAAAACAATATTTTACCTCGTTTGAGATAGTTTCACTCGAAACATAATATT
1 GAGATTGTTTTTCTTAAAACAAGA-TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATT
1965795 CATTTCACTC
65 CATTTCACTC
* * * * * *
1965805 AAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGATAGTTTCACTCAAAACAAAAGATTA
1 GAGATTGTTTTTCTTAAAACAAGATTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTC
*
1965870 ATTTCACTT
66 ATTTCACTC
* * * * * * *
1965879 GATATTGTTTTTCTTAAAACAATATTTGTCTCGCTTGAGACATTTTTTACTCGAAACAAGATA-T
1 GAGATTGTTTTTCTTAAAACAAGATTTATCTCGCTTGAGATA-GTTTCACTCGAAAC-AGA-AGA
1965943 TTCATTTCACTC
63 TTCATTTCACTC
* * * * *
1965955 AATATTTTTTTTCTTAAAACAAGATTCATCTTGCTTGAGATAGTTTCACTCGAA
1 GAGATTGTTTTTCTTAAAACAAGATTTATCTCGCTTGAGATAGTTTCACTCGAA
1966009 GCAAAAATTT
Statistics
Matches: 514, Mismatches: 110, Indels: 79
0.73 0.16 0.11
Matches are distributed among these distances:
68 45 0.09
70 1 0.00
72 1 0.00
73 41 0.08
74 180 0.35
75 88 0.17
76 54 0.11
77 5 0.01
78 8 0.02
80 4 0.01
81 1 0.00
82 1 0.00
83 11 0.02
84 31 0.06
85 7 0.01
86 36 0.07
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (74 bp):
GAGATTGTTTTTCTTAAAACAAGATTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTC
ATTTCACTC
Found at i:1965542 original size:48 final size:48
Alignment explanation
Indices: 1965449--1965544 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
1965439 AAGCTCGCTG
* * ** *
1965449 GAGATAGTTTCACTCAAAATTGAAGATTTATCTCACTTGATATTGTTT
1 GAGATAGTTTCACTCAAAACTGAAGATTCATCTCACTCAAGATTGTTT
*
1965497 GAGATAGTTTCACTCAAAACTGAAGATTCATTTCACTCAAGATTGTTT
1 GAGATAGTTTCACTCAAAACTGAAGATTCATCTCACTCAAGATTGTTT
1965545 TTCTTAAAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (48 bp):
GAGATAGTTTCACTCAAAACTGAAGATTCATCTCACTCAAGATTGTTT
Found at i:1965664 original size:48 final size:48
Alignment explanation
Indices: 1965572--1965666 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
1965562 ATCTCGCTGG
* * **
1965572 AGATAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGATTGTTTA
1 AGATAGTTTCACTCGAAACACAAGATTCATCTCACTCAAGATTGTTTA
* * *
1965620 AGATAGTTTCACTCGAAATACAAGATTCATTTCACTCAATATTGTTT
1 AGATAGTTTCACTCGAAACACAAGATTCATCTCACTCAAGATTGTTT
1965667 TTTTAAAACA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.37
Consensus pattern (48 bp):
AGATAGTTTCACTCGAAACACAAGATTCATCTCACTCAAGATTGTTTA
Found at i:1965732 original size:121 final size:122
Alignment explanation
Indices: 1965382--1965739 Score: 538
Period size: 122 Copynumber: 3.0 Consensus size: 122
1965372 ACCTCGCTTG
**
1965382 AGATAGTTTCACTCGAAATTGAAGATTCATTTCACTCAAGATTGTTTTTCTTAAAACAAG-----
1 AGATAGTTTCACTCGAAATACAAGATTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTCA
* ** * *
1965442 -CTCGCTGGAGATAGTTTCACTCAAAATTGAAGATTTATCTCACTTGATATTGTTTG
66 TCTCGCTGGAGATAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGATTGTTTA
1965498 AGATAGTTTCACTC-AAA-ACTGAAGATTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATT
1 AGATAGTTTCACTCGAAATAC--AAGATTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATT
1965561 CATCTCGCTGGAGATAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGATTGTTTA
64 CATCTCGCTGGAGATAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGATTGTTTA
*
1965620 AGATAGTTTCACTCGAAATACAAGATTCATTTCACTCAATATTGTTTTT-TTAAAACAAGATTCA
1 AGATAGTTTCACTCGAAATACAAGATTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTCA
*
1965684 TCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTAGTCTCACTTGAGATTGTTT
66 TCTCGCTGGAGATAGTTTCACTCGAAACAGAAGATTTA-TCTCACTTGAGATTGTTT
1965740 TTCTTAAAAC
Statistics
Matches: 222, Mismatches: 9, Indels: 17
0.90 0.04 0.07
Matches are distributed among these distances:
115 3 0.01
116 53 0.24
120 3 0.01
121 66 0.30
122 92 0.41
123 3 0.01
124 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (122 bp):
AGATAGTTTCACTCGAAATACAAGATTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTCA
TCTCGCTGGAGATAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGATTGTTTA
Found at i:1965889 original size:149 final size:147
Alignment explanation
Indices: 1965615--1966014 Score: 552
Period size: 149 Copynumber: 2.7 Consensus size: 147
1965605 ACTTGAGATT
* * *
1965615 GTTTAAGATAGTTTCACTCGAAATACAAGATTCATTTCACTCAATATTGTTTTT-TTAAAACAAG
1 GTTTGAGATAGTTTCACTCGAAACA-AATATTCATTTCACTCAATATTGTTTTTCTTAAAACAAG
* *
1965679 ATTCATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTAGTCTCACTTGAGATTGTTTTTCT
65 ATTCATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTAATCTCACTTGAGATTGTTTTTCT
1965744 TAAAACAATATTT-TACCTC
130 TAAAACAATATTTGT--CTC
*
1965763 GTTTGAGATAGTTTCACTCGAAACATAATATTCATTTCACTCAAGATTGTTTTTCTTAAAACAAG
1 GTTTGAGATAGTTTCACTCGAAACA-AATATTCATTTCACTCAATATTGTTTTTCTTAAAACAAG
** * * * *
1965828 ATTTGTCTCACTTGAGATAGTTTCACTCAAAACAAAAGATTAATTTCACTTGATATTGTTTTTCT
65 ATTCATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTAATCTCACTTGAGATTGTTTTTCT
1965893 TAAAACAATATTTGTCTC
130 TAAAACAATATTTGTCTC
* * * * *
1965911 GCTTGAGACATTTTTTACTCGAAACAAGATATTTCATTTCACTCAATATTTTTTTTCTTAAAACA
1 GTTTGAGATA-GTTTCACTCGAAACAA-ATA-TTCATTTCACTCAATATTGTTTTTCTTAAAACA
* *
1965976 AGATTCATCTTGCTTGAGATAGTTTCACTCGAAGCAAAA
63 AGATTCATCTCGCTTGAGATAGTTTCACTCGAAACAAAA
1966015 ATTTTATCTC
Statistics
Matches: 222, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
148 61 0.27
149 96 0.43
150 65 0.29
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.39
Consensus pattern (147 bp):
GTTTGAGATAGTTTCACTCGAAACAAATATTCATTTCACTCAATATTGTTTTTCTTAAAACAAGA
TTCATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTAATCTCACTTGAGATTGTTTTTCTT
AAAACAATATTTGTCTC
Found at i:1966343 original size:93 final size:92
Alignment explanation
Indices: 1966162--1966366 Score: 248
Period size: 93 Copynumber: 2.2 Consensus size: 92
1966152 AACCTTACAT
* * * *
1966162 GAGGGACCAAAATTTCCAATAGAGAATTCATGAGAAGAACTTATTAAACCTTGGCTCGATTCACG
1 GAGGGACCAACATTTCCAATAGAGAAATCATAAGAAAAACTTATTAAACCTTGGCTCGATTCACG
*
1966227 ACATTGTAAATCAGCGACACCTCACTC
66 ACATTGTAAATCAGCAACACCTCACTC
* * * * **
1966254 GAGGGACCATCATTTTCAATAGAGAAATCATAATGAAAAACTTGTTCAACCTTTTCTCGATTCAC
1 GAGGGACCAACATTTCCAATAGAGAAATCATAA-GAAAAACTTATTAAACCTTGGCTCGATTCAC
* * * * *
1966319 GATATTTTGAATTAGCAACTCCTCACTC
65 GACATTGTAAATCAGCAACACCTCACTC
*
1966347 GAGGGATCAACATTTCCAAT
1 GAGGGACCAACATTTCCAAT
1966367 GGAAAGACCA
Statistics
Matches: 93, Mismatches: 19, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
92 28 0.30
93 65 0.70
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.28
Consensus pattern (92 bp):
GAGGGACCAACATTTCCAATAGAGAAATCATAAGAAAAACTTATTAAACCTTGGCTCGATTCACG
ACATTGTAAATCAGCAACACCTCACTC
Found at i:1970119 original size:225 final size:225
Alignment explanation
Indices: 1969728--1970177 Score: 873
Period size: 225 Copynumber: 2.0 Consensus size: 225
1969718 CTAATAACAG
*
1969728 AAACGTATAAAAAATAGAAGTCATGGAGATTACTACGAAGGCATTAAAAGGAGACAGATATGCTA
1 AAACGTATAAAAAATAGAAGTCATGGAGATTACTACGAAGGCATTAAAAGGAGACAGAGATGCTA
1969793 CACCCTATGGTTGTGACCCACACTACTCGACTACCCTGGTCTTAAGTCTCCATACTTTTCTATCA
66 CACCCTATGGTTGTGACCCACACTACTCGACTACCCTGGTCTTAAGTCTCCATACTTTTCTATCA
1969858 GAGGTCATGTCCTCGGTAAGGGCTAATTCCTTCAGATCAGATCTCAAGCAGTCTACCCACTTCCT
131 GAGGTCATGTCCTCGGTAAGGGCTAATTCCTTCAGATCAGATCTCAAGCAGTCTACCCACTTCCT
1969923 CCTTGGTCGTCCTCTCTTTCTGGCACCGTC
196 CCTTGGTCGTCCTCTCTTTCTGGCACCGTC
*
1969953 AAACGTATAAAAAGTAGAAGTCATGGAGATTACTACGAAGGCATTAAAAGGAGACAGAGATGCTA
1 AAACGTATAAAAAATAGAAGTCATGGAGATTACTACGAAGGCATTAAAAGGAGACAGAGATGCTA
1970018 CACCCTATGGTTGTGACCCACACTACTCGACTACCCTGGTCTTAAGTCTCCATACTTTTCTATCA
66 CACCCTATGGTTGTGACCCACACTACTCGACTACCCTGGTCTTAAGTCTCCATACTTTTCTATCA
*
1970083 GAGGTCATGTCCTCGGTAAGGGCTAATTCCTTCAGATCAGATCTCAAGCAGTCTACTCACTTCCT
131 GAGGTCATGTCCTCGGTAAGGGCTAATTCCTTCAGATCAGATCTCAAGCAGTCTACCCACTTCCT
1970148 CCTTGGTCGTCCTCTCTTTCTGGCACCGTC
196 CCTTGGTCGTCCTCTCTTTCTGGCACCGTC
1970178 GAGTGTAATT
Statistics
Matches: 222, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
225 222 1.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (225 bp):
AAACGTATAAAAAATAGAAGTCATGGAGATTACTACGAAGGCATTAAAAGGAGACAGAGATGCTA
CACCCTATGGTTGTGACCCACACTACTCGACTACCCTGGTCTTAAGTCTCCATACTTTTCTATCA
GAGGTCATGTCCTCGGTAAGGGCTAATTCCTTCAGATCAGATCTCAAGCAGTCTACCCACTTCCT
CCTTGGTCGTCCTCTCTTTCTGGCACCGTC
Found at i:1978565 original size:20 final size:19
Alignment explanation
Indices: 1978525--1978589 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 19
1978515 GGGTTTCTAG
* *
1978525 TTTTTTGGGAA-TTTAGTT
1 TTTTTTAGGAATTTTAGGT
*
1978543 TTTTTTTGGAATTTTGAGGT
1 TTTTTTAGGAATTTT-AGGT
* *
1978563 TTTTTAAGGAATTTTAGAAT
1 TTTTTTAGGAATTTTAG-GT
1978583 TTTTTTA
1 TTTTTTA
1978590 AAAAATTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
18 10 0.26
19 5 0.13
20 23 0.61
ACGTcount: A:0.22, C:0.00, G:0.18, T:0.60
Consensus pattern (19 bp):
TTTTTTAGGAATTTTAGGT
Found at i:1979312 original size:16 final size:16
Alignment explanation
Indices: 1979291--1979324 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1979281 ATTTACAAAG
* *
1979291 ATTTAAATTAAATTAA
1 ATTTAAATAAAAATAA
1979307 ATTTAAATAAAAATAA
1 ATTTAAATAAAAATAA
1979323 AT
1 AT
1979325 AAACTTCTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTTAAATAAAAATAA
Found at i:1982999 original size:14 final size:14
Alignment explanation
Indices: 1982982--1983045 Score: 55
Period size: 14 Copynumber: 4.9 Consensus size: 14
1982972 TTCATTTATG
1982982 TTCGTTTATGTTCA
1 TTCGTTTATGTTCA
* *
1982996 TTCGTTTATTTTCG
1 TTCGTTTATGTTCA
*
1983010 TTTGTTTA---T-A
1 TTCGTTTATGTTCA
* *
1983020 TTCATTTATGTTCG
1 TTCGTTTATGTTCA
1983034 TTCGTTTATGTT
1 TTCGTTTATGTT
1983046 TAGGTTAATC
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
10 6 0.16
11 1 0.03
13 1 0.03
14 30 0.79
ACGTcount: A:0.12, C:0.11, G:0.14, T:0.62
Consensus pattern (14 bp):
TTCGTTTATGTTCA
Found at i:1983011 original size:24 final size:24
Alignment explanation
Indices: 1982948--1983035 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
1982938 GACTCATTCG
* **
1982948 TTCATTTACGTTCGTGAATGTTCA
1 TTCATTTATGTTCGTTTATGTTCA
1982972 TTCATTTATGTTCGTTTATGTTCA
1 TTCATTTATGTTCGTTTATGTTCA
* * * *
1982996 TTCGTTTATTTTCGTTTGT-TTATA
1 TTCATTTATGTTCGTTTATGTT-CA
1983020 TTCATTTATGTTCGTT
1 TTCATTTATGTTCGTT
1983036 CGTTTATGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 2 0.04
24 52 0.96
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.58
Consensus pattern (24 bp):
TTCATTTATGTTCGTTTATGTTCA
Found at i:1983413 original size:20 final size:19
Alignment explanation
Indices: 1983375--1983422 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
1983365 CATTTATGTT
1983375 AGTTTGTTTTGTTCATTTA
1 AGTTTGTTTTGTTCATTTA
*
1983394 AGTTTGTTTGTGTTCGTTTA
1 AGTTTGTTT-TGTTCATTTA
*
1983414 TGTTTGTTT
1 AGTTTGTTT
1983423 ACATTCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.10, C:0.04, G:0.21, T:0.65
Consensus pattern (19 bp):
AGTTTGTTTTGTTCATTTA
Found at i:1983433 original size:20 final size:20
Alignment explanation
Indices: 1983386--1983434 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
1983376 GTTTGTTTTG
* ***
1983386 TTCATTTAAGTTTGTTTGTG
1 TTCATTTATGTTTGTTTACA
*
1983406 TTCGTTTATGTTTGTTTACA
1 TTCATTTATGTTTGTTTACA
1983426 TTCATTTAT
1 TTCATTTAT
1983435 TGTGTTTGTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.08, G:0.14, T:0.61
Consensus pattern (20 bp):
TTCATTTATGTTTGTTTACA
Found at i:1983488 original size:24 final size:23
Alignment explanation
Indices: 1983430--1983495 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
1983420 TTTACATTCA
1983430 TTTATTGTGTTTGTTTATGTTAG
1 TTTATTGTGTTTGTTTATGTTAG
* *
1983453 TTTACATT-TGTTCGTTTATGTTTG
1 TTT--ATTGTGTTTGTTTATGTTAG
1983477 TTTATTTGTGTTTGTTTAT
1 TTTA-TTGTGTTTGTTTAT
1983496 CATTTAAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
22 1 0.03
23 5 0.14
24 27 0.75
25 3 0.08
ACGTcount: A:0.12, C:0.03, G:0.18, T:0.67
Consensus pattern (23 bp):
TTTATTGTGTTTGTTTATGTTAG
Found at i:1988883 original size:32 final size:30
Alignment explanation
Indices: 1988847--1988910 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
1988837 TATATCATGT
*
1988847 ATTATTTAATTATAAATAATATT-AATTTTTAC
1 ATTATTT-A-TATAAAT-ATATTAAAATTTTAC
*
1988879 ATTATTTATCTAAATATATTAAAATTTTAC
1 ATTATTTATATAAATATATTAAAATTTTAC
1988909 AT
1 AT
1988911 CAACATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 5 0.17
30 16 0.55
31 1 0.03
32 7 0.24
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (30 bp):
ATTATTTATATAAATATATTAAAATTTTAC
Found at i:1993722 original size:20 final size:20
Alignment explanation
Indices: 1993681--1993723 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1993671 TAAAATTTTA
*
1993681 TAAGTTTAAATTCATCCCTT
1 TAAGTTTAAATTCATCACTT
*
1993701 TAAGTTTAAATTCATCATTT
1 TAAGTTTAAATTCATCACTT
1993721 TAA
1 TAA
1993724 CATAAAATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.47
Consensus pattern (20 bp):
TAAGTTTAAATTCATCACTT
Found at i:1995055 original size:15 final size:16
Alignment explanation
Indices: 1995037--1995070 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1995027 TTATAAAATA
1995037 TATATTTATTATA-AT
1 TATATTTATTATATAT
*
1995052 TATATTTTTTATATAT
1 TATATTTATTATATAT
1995068 TAT
1 TAT
1995071 TATAGTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATATTTATTATATAT
Found at i:1995273 original size:20 final size:20
Alignment explanation
Indices: 1995248--1995287 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1995238 TGATGCTTAC
1995248 TCCTTATGCTTATAAATATA
1 TCCTTATGCTTATAAATATA
1995268 TCCTTATGCTTATAAATATA
1 TCCTTATGCTTATAAATATA
1995288 AGTGTTGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (20 bp):
TCCTTATGCTTATAAATATA
Found at i:2005038 original size:19 final size:20
Alignment explanation
Indices: 2005014--2005070 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
2005004 TTTTGGTGCA
*
2005014 GAGGGAATCGATACCCC-AT
1 GAGGGAATCGATACCCCAAC
* *
2005033 GAGGGAACCGATTCCCCCAAC
1 GAGGGAATCGA-TACCCCAAC
*
2005054 AAGGGAATCGATACCCC
1 GAGGGAATCGATACCCC
2005071 CCTGGGGTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 10 0.33
20 10 0.33
21 10 0.33
ACGTcount: A:0.32, C:0.32, G:0.25, T:0.12
Consensus pattern (20 bp):
GAGGGAATCGATACCCCAAC
Found at i:2007549 original size:13 final size:13
Alignment explanation
Indices: 2007531--2007563 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
2007521 TTTCTAAGTA
2007531 TATTCGATATAAT
1 TATTCGATATAAT
2007544 TATTCGATATAAT
1 TATTCGATATAAT
2007557 TATTCGA
1 TATTCGA
2007564 ATATCATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (13 bp):
TATTCGATATAAT
Found at i:2022660 original size:17 final size:16
Alignment explanation
Indices: 2022638--2022671 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2022628 TAAAGACAGT
2022638 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
2022655 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
2022671 A
1 A
2022672 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:2023190 original size:24 final size:24
Alignment explanation
Indices: 2023146--2023195 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2023136 ATAAAGAACC
*
2023146 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
2023170 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
2023194 AA
1 AA
2023196 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:2032905 original size:17 final size:16
Alignment explanation
Indices: 2032883--2032916 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2032873 TAAAGACAGT
2032883 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
2032900 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
2032916 A
1 A
2032917 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:2033417 original size:23 final size:23
Alignment explanation
Indices: 2033391--2033439 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2033381 ATAAAGAACC
*
2033391 AAAATAAA-CTTAAATATACCATT
1 AAAATAAAGCTTAAACA-ACCATT
*
2033414 AAAATAAAGTTTAAACAACCATT
1 AAAATAAAGCTTAAACAACCATT
2033437 AAA
1 AAA
2033440 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAAGCTTAAACAACCATT
Found at i:2042554 original size:17 final size:20
Alignment explanation
Indices: 2042532--2042571 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2042522 CGGTCTAATT
2042532 TTTATTTA-G-AA-TTGATA
1 TTTATTTACGAAATTTGATA
2042549 TTTATTTACGAAATTTGATA
1 TTTATTTACGAAATTTGATA
2042569 TTT
1 TTT
2042572 TTATTTGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
19 2 0.10
20 9 0.45
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.55
Consensus pattern (20 bp):
TTTATTTACGAAATTTGATA
Found at i:2044342 original size:13 final size:13
Alignment explanation
Indices: 2044324--2044348 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2044314 AGGTGAGTGA
2044324 ATATGATTATAGT
1 ATATGATTATAGT
2044337 ATATGATTATAG
1 ATATGATTATAG
2044349 GAAATTAGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (13 bp):
ATATGATTATAGT
Found at i:2045576 original size:23 final size:23
Alignment explanation
Indices: 2045548--2045631 Score: 143
Period size: 23 Copynumber: 3.7 Consensus size: 23
2045538 TCGGGACATT
2045548 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
2045571 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
*
2045594 TATGTGACACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
2045617 TATGTGGTC-CTTCGG
1 TATGTGG-CACTTCGG
2045632 GACAATTTTG
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
23 57 0.98
24 1 0.02
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.29
Consensus pattern (23 bp):
TATGTGGCACTTCGGTGCAAACC
Found at i:2046301 original size:16 final size:17
Alignment explanation
Indices: 2046274--2046307 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2046264 ATTTTAATTC
2046274 TTTTGTAAAAGTAAATG
1 TTTTGTAAAAGTAAATG
*
2046291 TTTTG-AAAAGTTAATG
1 TTTTGTAAAAGTAAATG
2046307 T
1 T
2046308 GACACCTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (17 bp):
TTTTGTAAAAGTAAATG
Found at i:2050738 original size:21 final size:21
Alignment explanation
Indices: 2050712--2050776 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
2050702 TCTCCAACCA
2050712 AACTAATTCGGTGGCCGACCG
1 AACTAATTCGGTGGCCGACCG
2050733 AACTAATTCGGTGGCCGACCG
1 AACTAATTCGGTGGCCGACCG
* *
2050754 AAATAATTCGGTGACCGACCG
1 AACTAATTCGGTGGCCGACCG
2050775 AA
1 AA
2050777 TTAACCGAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.18
Consensus pattern (21 bp):
AACTAATTCGGTGGCCGACCG
Found at i:2054599 original size:55 final size:55
Alignment explanation
Indices: 2054515--2054625 Score: 168
Period size: 55 Copynumber: 2.0 Consensus size: 55
2054505 ACAACTCAAA
* * *
2054515 TTGAGATAATAATACAATTCTCTTCCTTTACTGTTATACCTTTTCTTCTTTATGT
1 TTGAGATAATAATACAATTATCTCCCTTTACTGTTATACCTCTTCTTCTTTATGT
* * *
2054570 TTGAGATAATAATACAATTATCTCCCTTTATTGTTTTATCTCTTCTTCTTTATGT
1 TTGAGATAATAATACAATTATCTCCCTTTACTGTTATACCTCTTCTTCTTTATGT
2054625 T
1 T
2054626 CTTATTGTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.23, C:0.17, G:0.07, T:0.52
Consensus pattern (55 bp):
TTGAGATAATAATACAATTATCTCCCTTTACTGTTATACCTCTTCTTCTTTATGT
Found at i:2066667 original size:20 final size:20
Alignment explanation
Indices: 2066573--2066941 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
2066563 GATTTTCCAT
* ** *
2066573 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
2066593 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
2066613 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2066633 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
2066653 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
2066673 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2066693 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2066713 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
2066733 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2066753 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2066773 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2066793 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2066813 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
2066833 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2066853 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2066873 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2066893 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2066913 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2066933 AATCACAAC
1 AATCGCAAC
2066942 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2067654 original size:24 final size:24
Alignment explanation
Indices: 2067615--2067661 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2067605 AAATTTGGTC
2067615 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2067639 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2067662 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:2067852 original size:12 final size:12
Alignment explanation
Indices: 2067835--2067859 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2067825 ATATAATCCT
2067835 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2067847 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2067859 G
1 G
2067860 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2070181 original size:19 final size:19
Alignment explanation
Indices: 2070159--2070483 Score: 396
Period size: 19 Copynumber: 18.4 Consensus size: 19
2070149 CGGAAAATAC
*
2070159 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2070178 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
2070192 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
2070212 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2070226 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2070245 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
2070263 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2070277 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2070296 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2070315 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
2070329 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2070348 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
2070367 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
2070386 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2070405 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2070424 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
2070438 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2070457 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2070476 AATCGCAA
1 AATCGCAA
2070484 CGAGATAATC
Statistics
Matches: 267, Mismatches: 12, Indels: 54
0.80 0.04 0.16
Matches are distributed among these distances:
13 1 0.00
14 49 0.18
15 2 0.01
16 15 0.06
17 10 0.04
18 13 0.05
19 164 0.61
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2070443 original size:109 final size:104
Alignment explanation
Indices: 2070187--2070505 Score: 532
Period size: 109 Copynumber: 3.0 Consensus size: 104
2070177 AAATCCCAAC
2070187 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
* *
2070252 ATGCGAAA-TGAAATCGCAACGAGAGAATCGCAATGCGAA
65 ATGCGAAATTAAAATCGCAACGAGAAAATCGCAATGCGAA
2070291 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
2070356 TGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
66 TGCGAAATTAAAATCGC-A-ACG--A-GAAAATCGCAATGCGAA
*
2070400 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
* *
2070465 TGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
66 TGCGAAATTAAAATCGCAACGAGAAAATCGCAATGCGAA
2070504 AT
1 AT
2070506 TATAAACGCA
Statistics
Matches: 204, Mismatches: 5, Indels: 12
0.92 0.02 0.05
Matches are distributed among these distances:
103 56 0.27
104 42 0.21
105 2 0.01
106 3 0.01
107 3 0.01
108 2 0.01
109 96 0.47
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (104 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATTAAAATCGCAACGAGAAAATCGCAATGCGAA
Found at i:2070521 original size:52 final size:52
Alignment explanation
Indices: 2070187--2070505 Score: 541
Period size: 52 Copynumber: 6.0 Consensus size: 52
2070177 AAATCCCAAC
2070187 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
2070240 ATGAAAATCGCAATGCGAAATG-AAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
2070291 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
2070343 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAA
*
2070400 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
2070452 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
2070504 AT
1 AT
2070506 TATAAACGCA
Statistics
Matches: 253, Mismatches: 7, Indels: 13
0.93 0.03 0.05
Matches are distributed among these distances:
51 51 0.20
52 131 0.52
53 18 0.07
54 3 0.01
55 3 0.01
56 2 0.01
57 45 0.18
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:2070621 original size:19 final size:19
Alignment explanation
Indices: 2070512--2070613 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
2070502 AAATTATAAA
2070512 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2070531 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
2070551 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
2070567 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2070584 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2070603 CGCATTGCGAT
1 CGCATTGCGAT
2070614 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:2070739 original size:14 final size:14
Alignment explanation
Indices: 2070720--2070756 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2070710 CATCAATTAC
2070720 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2070734 ACAAATCATCTTTT
1 ACAAATCAACTTTT
2070748 ACAAATCAA
1 ACAAATCAA
2070757 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:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2070803 original size:36 final size:37
Alignment explanation
Indices: 2070737--2070806 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
2070727 AACTTTTACA
*
2070737 AATCATCTTTTACAAATCAATTAAACAATCAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAATTG
2070774 AATCAACTTTTACAAATC-ATTAAACAATCAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAA
2070807 ACAATCAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 15 0.47
37 17 0.53
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.30
Consensus pattern (37 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAATTG
Found at i:2072650 original size:19 final size:19
Alignment explanation
Indices: 2072610--2072744 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
2072600 TAGTTTACTT
* *
2072610 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
2072630 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
2072649 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2072668 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
2072682 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2072701 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
2072715 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2072734 TCGCAATGCGA
1 TCGCAACGCGA
2072745 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2072685 original size:14 final size:14
Alignment explanation
Indices: 2072666--2072722 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2072656 GCGAAATGAA
*
2072666 AATCGCAACGACAG
1 AATCGCAACGAAAG
2072680 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
2072697 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
2072713 AATCGCAACG
1 AATCGCAACG
2072723 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2072689 original size:33 final size:33
Alignment explanation
Indices: 2072647--2072739 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
2072637 GCGAAACCAA
*
2072647 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2072680 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2072713 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2072740 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:2072736 original size:52 final size:54
Alignment explanation
Indices: 2072610--2072744 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 54
2072600 TAGTTTACTT
*
2072610 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
2072668 TCGCAA-CGACA-G--AATCGCAACGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
2072715 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
2072745 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.08
50 6 0.09
52 37 0.56
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:2072762 original size:19 final size:19
Alignment explanation
Indices: 2072740--2072868 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2072730 AAAATCGCAA
2072740 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2072759 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
2072773 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2072792 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2072806 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2072825 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
2072844 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
2072864 TGCGA
1 TGCGA
2072869 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2072782 original size:33 final size:33
Alignment explanation
Indices: 2072740--2072831 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2072730 AAAATCGCAA
2072740 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
2072773 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
2072806 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
2072832 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:2073202 original size:92 final size:93
Alignment explanation
Indices: 2072912--2073290 Score: 735
Period size: 92 Copynumber: 4.1 Consensus size: 93
2072902 TTGAATGGAT
2072912 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2072977 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2073005 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2073070 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2073098 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
2073162 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2073190 AAATTTACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
2073254 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
2073282 AAATTTACT
1 AAATTTACT
2073291 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
91 10 0.04
92 142 0.50
93 132 0.46
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:2075013 original size:14 final size:14
Alignment explanation
Indices: 2074994--2075083 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
2074984 TTGAAATGAA
2074994 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2075008 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
2075025 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
2075041 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2075060 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2075074 AATCGCAACG
1 AATCGCAACG
2075084 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2075031 original size:33 final size:33
Alignment explanation
Indices: 2074986--2075100 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
2074976 TCTTTTGGTT
2074986 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
2075019 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2075052 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2075085 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2075101 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2075032 original size:19 final size:18
Alignment explanation
Indices: 2074993--2075105 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
2074983 GTTGAAATGA
2074993 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
2075008 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
2075025 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
2075041 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
2075058 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
2075074 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
2075091 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
2075106 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:2075136 original size:14 final size:14
Alignment explanation
Indices: 2075117--2075171 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2075107 TTTGGTTTCG
2075117 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2075131 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
2075150 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2075164 CGTTGCGA
1 CGTTGCGA
2075172 CAGTCATCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2075187 original size:33 final size:33
Alignment explanation
Indices: 2075114--2075192 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
2075104 GATTTTGGTT
** *
2075114 TCGCGTTGCGATTCTCTCGTTGCGATTTCCATT
1 TCGCGTTGCGATTCTCTCGTTGCGAAGTCCATC
2075147 TCGCGTTGCGATTCTCTCGTTGCGACAGT-CATC
1 TCGCGTTGCGATTCTCTCGTTGCGA-AGTCCATC
*
2075180 TCTCGTTGCGATT
1 TCGCGTTGCGATT
2075193 TTCATTTATC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 40 0.98
34 1 0.02
ACGTcount: A:0.10, C:0.28, G:0.23, T:0.39
Consensus pattern (33 bp):
TCGCGTTGCGATTCTCTCGTTGCGAAGTCCATC
Found at i:2075197 original size:19 final size:19
Alignment explanation
Indices: 2075126--2075211 Score: 56
Period size: 19 Copynumber: 4.7 Consensus size: 19
2075116 GCGTTGCGAT
*
2075126 TCTCTCGTTGCGATTTCCA
1 TCTCTCGTTGCGATTTTCA
* *
2075145 TTTCGCGTTGCGA---T--
1 TCTCTCGTTGCGATTTTCA
***
2075159 TCTCTCGTTGCGACAGTCA
1 TCTCTCGTTGCGATTTTCA
2075178 TCTCTCGTTGCGATTTTCA
1 TCTCTCGTTGCGATTTTCA
*
2075197 TTTATCTCGTTGCGA
1 --TCTCTCGTTGCGA
2075212 CTCTTCTGCA
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
14 11 0.22
17 1 0.02
19 27 0.53
21 12 0.24
ACGTcount: A:0.12, C:0.27, G:0.20, T:0.42
Consensus pattern (19 bp):
TCTCTCGTTGCGATTTTCA
Found at i:2075333 original size:33 final size:33
Alignment explanation
Indices: 2075291--2075361 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2075281 AATACTAACT
*
2075291 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
2075324 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
2075357 TGAAA
1 TGAAA
2075362 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:2075594 original size:22 final size:22
Alignment explanation
Indices: 2075542--2075596 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2075532 TGGTTGTGAG
**
2075542 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
2075564 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
2075586 GGATTTCTTCG
1 GGATTTCTTCG
2075597 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:2075767 original size:20 final size:20
Alignment explanation
Indices: 2075742--2075935 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
2075732 CTTTAAATAT
2075742 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2075762 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
2075784 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2075803 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
2075823 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
2075843 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2075863 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2075883 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
2075903 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
2075923 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2075936 TTGGAAAATC
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2075929 original size:60 final size:60
Alignment explanation
Indices: 2075742--2075935 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
2075732 CTTTAAATAT
**
2075742 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
2075803 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
2075863 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
2075923 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2075936 TTGGAAAATC
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:2076016 original size:20 final size:20
Alignment explanation
Indices: 2075991--2076042 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2075981 AAGAATCGCG
*
2075991 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
2076011 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
2076031 TTGCGATTCTGG
1 TTGCGATTCTGG
2076043 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:2078766 original size:11 final size:12
Alignment explanation
Indices: 2078745--2078770 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2078735 CTTATAATTT
2078745 TTTTAAAAAAAA
1 TTTTAAAAAAAA
2078757 TTTTAAAAAAAA
1 TTTTAAAAAAAA
2078769 TT
1 TT
2078771 AAAATTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TTTTAAAAAAAA
Found at i:2081119 original size:16 final size:16
Alignment explanation
Indices: 2081098--2081130 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2081088 TTAATGGGGT
2081098 CCAGAAGCTGAGGTTG
1 CCAGAAGCTGAGGTTG
2081114 CCAGAAGCTGAGGTTG
1 CCAGAAGCTGAGGTTG
2081130 C
1 C
2081131 TTTTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.36, T:0.18
Consensus pattern (16 bp):
CCAGAAGCTGAGGTTG
Found at i:2084524 original size:33 final size:33
Alignment explanation
Indices: 2084479--2084562 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
2084469 TAATACTTAC
2084479 TTTATTTTTGTTAATTTGGTTGAATTTTTT-TAAA
1 TTTA-TTTTGTTAATTT-GTTGAATTTTTTGTAAA
* *
2084513 TTTATTTTGTTAATATTGTTGGATTTTTTGTTAA
1 TTTATTTTGTTAAT-TTGTTGAATTTTTTGTAAA
* *
2084547 TGTATTTGGTTAATTT
1 TTTATTTTGTTAATTT
2084563 TGTTTATTAC
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
33 23 0.52
34 21 0.48
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.64
Consensus pattern (33 bp):
TTTATTTTGTTAATTTGTTGAATTTTTTGTAAA
Found at i:2084566 original size:34 final size:33
Alignment explanation
Indices: 2084488--2084566 Score: 95
Period size: 34 Copynumber: 2.4 Consensus size: 33
2084478 CTTTATTTTT
* * *
2084488 GTTAATTTGGTTGAATTTTTTTAAATTTATTTT
1 GTTAATTTTGTTGAATTTTTTTAAATGTATTTG
* * *
2084521 GTTAATATTGTTGGATTTTTTGTTAATGTATTTG
1 GTTAATTTTGTTGAATTTTTT-TAAATGTATTTG
2084555 GTTAATTTTGTT
1 GTTAATTTTGTT
2084567 TATTACCATT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 18 0.47
34 20 0.53
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (33 bp):
GTTAATTTTGTTGAATTTTTTTAAATGTATTTG
Found at i:2085157 original size:20 final size:20
Alignment explanation
Indices: 2085132--2085178 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
2085122 CATTTGGTTA
2085132 TTTTCCCCTGAGTTAGATTC
1 TTTTCCCCTGAGTTAGATTC
2085152 TTTTCCCCTGAGTTAGATTC
1 TTTTCCCCTGAGTTAGATTC
*
2085172 CTTTCCC
1 TTTTCCC
2085179 AATAAGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.13, C:0.30, G:0.13, T:0.45
Consensus pattern (20 bp):
TTTTCCCCTGAGTTAGATTC
Found at i:2087743 original size:11 final size:11
Alignment explanation
Indices: 2087727--2087765 Score: 51
Period size: 11 Copynumber: 3.3 Consensus size: 11
2087717 TTTATCTTTT
2087727 AAATTTTATAA
1 AAATTTTATAA
2087738 AAATTTTATATA
1 AAATTTTATA-A
2087750 TAAATTTTATTAA
1 -AAATTTTA-TAA
2087763 AAA
1 AAA
2087766 GTATATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 10 0.40
12 4 0.16
13 9 0.36
14 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AAATTTTATAA
Found at i:2087749 original size:13 final size:13
Alignment explanation
Indices: 2087733--2087765 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2087723 TTTTAAATTT
2087733 TATAAAAATTTTA
1 TATAAAAATTTTA
*
2087746 TATATAAATTTTA
1 TATAAAAATTTTA
2087759 T-TAAAAA
1 TATAAAAA
2087766 GTATATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TATAAAAATTTTA
Found at i:2092626 original size:31 final size:31
Alignment explanation
Indices: 2092584--2092644 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
2092574 AAATCTAATG
*
2092584 TAGGAGATAATGCTTTTAATGTAACACAATC
1 TAGGAGATAATGCTTTTAATCTAACACAATC
* *
2092615 TAGGAGTTAATGCTTTTAATCTAACGCAAT
1 TAGGAGATAATGCTTTTAATCTAACACAAT
2092645 GTAATCTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (31 bp):
TAGGAGATAATGCTTTTAATCTAACACAATC
Found at i:2093069 original size:20 final size:20
Alignment explanation
Indices: 2093041--2093079 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2093031 TACTGAACAT
2093041 CACTCCACCACTTTGATTTC
1 CACTCCACCACTTTGATTTC
*
2093061 CACTTCACCACTTTGATTT
1 CACTCCACCACTTTGATTT
2093080 TTTACATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.36, G:0.05, T:0.38
Consensus pattern (20 bp):
CACTCCACCACTTTGATTTC
Found at i:2094062 original size:23 final size:23
Alignment explanation
Indices: 2094032--2094075 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2094022 AAAGTTATAC
* *
2094032 TAAAATATTAATTTAAAAAATAT
1 TAAAATATAAAGTTAAAAAATAT
2094055 TAAAATATAAAGTTAAAAAAT
1 TAAAATATAAAGTTAAAAAAT
2094076 TACCTTGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
TAAAATATAAAGTTAAAAAATAT
Found at i:2096050 original size:19 final size:19
Alignment explanation
Indices: 2096026--2096066 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
2096016 ATCCCCTCTC
2096026 TTGTTAACCAAATTAGTAT
1 TTGTTAACCAAATTAGTAT
2096045 TTGTTAACCAAATTAGTAT
1 TTGTTAACCAAATTAGTAT
2096064 TTG
1 TTG
2096067 CCTTGGAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (19 bp):
TTGTTAACCAAATTAGTAT
Found at i:2111412 original size:81 final size:79
Alignment explanation
Indices: 2111252--2111414 Score: 177
Period size: 81 Copynumber: 2.0 Consensus size: 79
2111242 ATAATTTTAT
* * * * * *
2111252 TGACAATAGCCCTTCTTGCCTTGAGCTATGTTGTAAATGATGCCTTAGAGTGAGCATAGTCGAAC
1 TGACAATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGCCTCAAAGTGAGCATAATCGAAC
*
2111317 TCGAAGGTCTTTTGG
66 TCGAAGG-CATTTGG
* **
2111332 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATTGCCCTCAAAGCTGAGTGTAATC
1 TGACA-ATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGA-TG-CCTCAAAG-TGAGCATAATC
2111397 GAACTCG-AGG-ATTTGG
62 GAACTCGAAGGCATTTGG
2111413 TG
1 TG
2111415 TTTCAAGAGA
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
80 5 0.07
81 38 0.55
82 2 0.03
83 9 0.13
84 15 0.22
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (79 bp):
TGACAATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGCCTCAAAGTGAGCATAATCGAAC
TCGAAGGCATTTGG
Found at i:2111510 original size:36 final size:36
Alignment explanation
Indices: 2111458--2111567 Score: 125
Period size: 36 Copynumber: 3.1 Consensus size: 36
2111448 AGTTTTTAAG
*
2111458 GAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
1 GAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGA
* ** * *
2111494 GAAACTGTCTCAAGAGAGACAAAA--ACTTCCAAAA
1 GAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGA
* * *
2111528 GAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGG
1 GAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGA
2111564 GAAA
1 GAAA
2111568 TAGATTCAAA
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
34 27 0.46
36 32 0.54
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGA
Found at i:2111531 original size:34 final size:35
Alignment explanation
Indices: 2111458--2111552 Score: 102
Period size: 34 Copynumber: 2.7 Consensus size: 35
2111448 AGTTTTTAAG
* ** * *
2111458 GAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
1 GAAAATGTCTCAAGAGAGACAAAA-TACTTCCAAAA
*
2111494 GAAACTGTCTCAAGAGAGACAAAA-ACTTCCAAAA
1 GAAAATGTCTCAAGAGAGACAAAATACTTCCAAAA
* *
2111528 GAAAATGTCTCAAGGGAGACGAAAT
1 GAAAATGTCTCAAGAGAGACAAAAT
2111553 TTGTTTCAAG
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
34 27 0.54
36 23 0.46
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (35 bp):
GAAAATGTCTCAAGAGAGACAAAATACTTCCAAAA
Found at i:2111731 original size:20 final size:19
Alignment explanation
Indices: 2111706--2111748 Score: 77
Period size: 20 Copynumber: 2.2 Consensus size: 19
2111696 TGTCTCAATG
2111706 GAGACAAAATTTGTTTCAGA
1 GAGACAAAATTTGTTTCA-A
2111726 GAGACAAAATTTGTTTCAA
1 GAGACAAAATTTGTTTCAA
2111745 GAGA
1 GAGA
2111749 AACAATCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (19 bp):
GAGACAAAATTTGTTTCAA
Found at i:2111753 original size:21 final size:20
Alignment explanation
Indices: 2111709--2111753 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
2111699 CTCAATGGAG
*
2111709 ACAAAATTTGTTTCAGAGAG
1 ACAAAATTTGTTTCAGAGAA
2111729 ACAAAATTTGTTTCAAGAGAA
1 ACAAAATTTGTTTC-AGAGAA
2111750 ACAA
1 ACAA
2111754 TCTTGACTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.27
Consensus pattern (20 bp):
ACAAAATTTGTTTCAGAGAA
Found at i:2111949 original size:72 final size:72
Alignment explanation
Indices: 2111743--2111950 Score: 230
Period size: 72 Copynumber: 2.9 Consensus size: 72
2111733 AATTTGTTTC
* * * *
2111743 AAGAGAAACAATCTTGACTGAAATAAATCTTCTTTCGAGTGAAAACGGTCTCTACAG-AGACAAA
1 AAGAAAAACAAACTTGAGTGAAATAAATCTTCTTTCGAGT-AAAACAGTCTC-A-AGTAGACAAA
*
2111807 -TCTGGTTTT
63 GTCTGATTTT
* * *
2111816 AAGAAAAACAATCTTGAG-G-AATAAATCTTCTTTCGAGTAAAACAGTCTCAGGTGAGTCAAAGT
1 AAGAAAAACAAACTTGAGTGAAATAAATCTTCTTTCGAGTAAAACAGTCTCAAGT-AGACAAAGT
2111879 CT-ATTTT
65 CTGATTTT
* *
2111886 AA-ACAAAGCAAACTTGAGTGAAATAAATCTTCTTTCGAGTAAAATAGTCTCAAGTAAGACAAAG
1 AAGA-AAAACAAACTTGAGTGAAATAAATCTTCTTTCGAGTAAAACAGTCTCAAGT-AGACAAAG
2111950 T
64 T
2111951 ATCTTTAAGA
Statistics
Matches: 117, Mismatches: 12, Indels: 13
0.82 0.08 0.09
Matches are distributed among these distances:
68 1 0.01
69 2 0.02
70 34 0.29
71 23 0.20
72 41 0.35
73 16 0.14
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (72 bp):
AAGAAAAACAAACTTGAGTGAAATAAATCTTCTTTCGAGTAAAACAGTCTCAAGTAGACAAAGTC
TGATTTT
Found at i:2115710 original size:190 final size:191
Alignment explanation
Indices: 2115375--2115757 Score: 693
Period size: 190 Copynumber: 2.0 Consensus size: 191
2115365 ATATGAAGTT
2115375 CATTAGTCTGTTCTTGAGTTCATCAGCAATGGTTTCCAATTTCATCTATTGTTTGCCATTGATGT
1 CATTAGTCTGTTCTTGAGTTCATCAGCAATGGTTTCCAATTTCATCTATTGTTTGCCATTGATGT
*
2115440 CTTCGAAGGGACTCCCAGATCAGTAACCTCATCTTGCCCCTGCAACCTAACCAGTCAGTTCTTCA
66 CTTCGAAGGGACTCCAAGATCAGTAACCTCATCTTGCCCCTGCAACCTAACCAGTCAGTTCTTCA
2115505 AAGATAGACTTTTATTATGCTTGATGTAGACCCAGTTCATTCTGAGCCCTTTATAATGCAG
131 AAGATAGACTTTTATTATGCTTGATGTAGACCCAGTTCATTCTGAGCCCTTTATAATGCAG
*
2115566 CATTAGTCTG-T-TTGAGTTCATCAGCAATGGTTTCCAATTTCATCTATTGTTTTGCCATTGCTG
1 CATTAGTCTGTTCTTGAGTTCATCAGCAATGGTTTCCAATTTCATCTATTG-TTTGCCATTGATG
2115629 TCTTCGAAGGGAC-CCAAGATCAGTAACCTTCATCTTGCCCCTGCAA-CTCAACCAGTCAGTTCT
65 TCTTCGAAGGGACTCCAAGATCAGTAACC-TCATCTTGCCCCTGCAACCT-AACCAGTCAGTTCT
2115692 TCAAAGATAGACTTTTATTATGCTTGATGTAGACCCAGTTCATTCTGAGCCCTTTATAATGCAG
128 TCAAAGATAGACTTTTATTATGCTTGATGTAGACCCAGTTCATTCTGAGCCCTTTATAATGCAG
2115756 CA
1 CA
2115758 GAGCAATATA
Statistics
Matches: 187, Mismatches: 2, Indels: 7
0.95 0.01 0.04
Matches are distributed among these distances:
189 54 0.29
190 123 0.66
191 10 0.05
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (191 bp):
CATTAGTCTGTTCTTGAGTTCATCAGCAATGGTTTCCAATTTCATCTATTGTTTGCCATTGATGT
CTTCGAAGGGACTCCAAGATCAGTAACCTCATCTTGCCCCTGCAACCTAACCAGTCAGTTCTTCA
AAGATAGACTTTTATTATGCTTGATGTAGACCCAGTTCATTCTGAGCCCTTTATAATGCAG
Found at i:2117054 original size:9 final size:9
Alignment explanation
Indices: 2117040--2117107 Score: 50
Period size: 9 Copynumber: 7.7 Consensus size: 9
2117030 GACGAAAAGA
2117040 AAAATAAAT
1 AAAATAAAT
2117049 AAAATAAA-
1 AAAATAAAT
* *
2117057 GACATAAA-
1 AAAATAAAT
2117065 AAAATAAAT
1 AAAATAAAT
* **
2117074 AAAGTCCAT
1 AAAATAAAT
*
2117083 AAAAGCAAAT
1 AAAA-TAAAT
*
2117093 GAAATAAAT
1 AAAATAAAT
2117102 AAAATA
1 AAAATA
2117108 CTAGAAAATA
Statistics
Matches: 43, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
8 12 0.28
9 26 0.60
10 5 0.12
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (9 bp):
AAAATAAAT
Found at i:2117066 original size:29 final size:29
Alignment explanation
Indices: 2116960--2117076 Score: 80
Period size: 29 Copynumber: 4.1 Consensus size: 29
2116950 AAATAAAACG
* * *
2116960 AATAAAAGAAAGACAAAGAAAAGAATAAT-
1 AATAAAATAAAGACATA-AAAAGAAAAATA
* * * * *
2116989 AATAAATTAACG--ATAATAAGTAAATTA
1 AATAAAATAAAGACATAAAAAGAAAAATA
* **
2117016 AATAAAAATAAAGAGACGAAAAGAAAAATA
1 AAT-AAAATAAAGACATAAAAAGAAAAATA
2117046 AATAAAATAAAGACATAAAAA-AATAAATA
1 AATAAAATAAAGACATAAAAAGAA-AAATA
2117075 AA
1 AA
2117077 GTCCATAAAA
Statistics
Matches: 65, Mismatches: 18, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
26 7 0.11
27 5 0.08
28 9 0.14
29 31 0.48
30 13 0.20
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.16
Consensus pattern (29 bp):
AATAAAATAAAGACATAAAAAGAAAAATA
Found at i:2117295 original size:38 final size:41
Alignment explanation
Indices: 2117234--2117323 Score: 116
Period size: 40 Copynumber: 2.2 Consensus size: 41
2117224 TGATAATATG
2117234 TATATATATAAAATAAATAAAAACATA-AA-AAAATAGTAA-A
1 TATATATAT-AAATAAATAAAAACATATAATAAAA-AGTAACA
* *
2117274 TATATATATAAATTAAT-AAAACATATAATAAAAATTAACA
1 TATATATATAAATAAATAAAAACATATAATAAAAAGTAACA
2117314 TATATATATA
1 TATATATATA
2117324 TTGTGTGTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
38 8 0.18
39 13 0.29
40 24 0.53
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.31
Consensus pattern (41 bp):
TATATATATAAATAAATAAAAACATATAATAAAAAGTAACA
Found at i:2117800 original size:66 final size:65
Alignment explanation
Indices: 2117708--2117830 Score: 228
Period size: 66 Copynumber: 1.9 Consensus size: 65
2117698 CTAATGCAAG
*
2117708 AGACTCCTTGCTCGTTATTGCACGTTTGTTGTTGTGGTTGTTGCTTTAAAATATATAGTGGAACT
1 AGACTCCTTGCTCGTTATTGCACGTTTGTTGTTGTGGTTGTTGCTTTAAAAGATATAGTGGAACT
2117773 AGACTCCTTGCTCGGTTATTGCACGTTTGTTGTTGTGGTTGTTGCTTTAAAAGATATA
1 AGACTCCTTGCTC-GTTATTGCACGTTTGTTGTTGTGGTTGTTGCTTTAAAAGATATA
2117831 ATGGTGAGAG
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
65 13 0.23
66 43 0.77
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.43
Consensus pattern (65 bp):
AGACTCCTTGCTCGTTATTGCACGTTTGTTGTTGTGGTTGTTGCTTTAAAAGATATAGTGGAACT
Found at i:2119850 original size:24 final size:26
Alignment explanation
Indices: 2119823--2119881 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 26
2119813 AGAAAAATCT
*
2119823 AAATATTTATA-AT-ATTAATGGCTA
1 AAATATTTATAGATAAATAATGGCTA
*
2119847 AAATATTTTTTTAGATAAATAATGGCTA
1 AAATA--TTTATAGATAAATAATGGCTA
2119875 AAATATT
1 AAATATT
2119882 GACATGTGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 5 0.17
26 7 0.24
27 2 0.07
28 15 0.52
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.42
Consensus pattern (26 bp):
AAATATTTATAGATAAATAATGGCTA
Found at i:2120385 original size:28 final size:29
Alignment explanation
Indices: 2120348--2120403 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
2120338 GTTTTTTAGT
2120348 TTCTTAATCTGCTTGA-TTTTTTGGCGAC
1 TTCTTAATCTGCTTGATTTTTTTGGCGAC
* * *
2120376 TTCTTTATCTGTTTTATTTTTTTGGCGA
1 TTCTTAATCTGCTTGATTTTTTTGGCGA
2120404 TTGTTCAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.12, C:0.14, G:0.16, T:0.57
Consensus pattern (29 bp):
TTCTTAATCTGCTTGATTTTTTTGGCGAC
Found at i:2120611 original size:2 final size:2
Alignment explanation
Indices: 2120606--2120647 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2120596 GAAAAAATGT
2120606 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
2120648 ATTGTTTGAA
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):
TA
Found at i:2123233 original size:20 final size:20
Alignment explanation
Indices: 2123210--2123276 Score: 125
Period size: 20 Copynumber: 3.4 Consensus size: 20
2123200 GTTTCCAAAT
2123210 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
2123230 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
*
2123250 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATATGTAAA
2123270 TCGCAAC
1 TCGCAAC
2123277 ACAGAAGTCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:2123234 original size:40 final size:41
Alignment explanation
Indices: 2123203--2123337 Score: 120
Period size: 40 Copynumber: 3.3 Consensus size: 41
2123193 CAACCTAGTT
2123203 TCCAAATTCGCAACGCGAATATGTAAATCGCAACGCGAATA
1 TCCAAATTCGCAACGCGAATATGTAAATCGCAACGCGAATA
** * * *
2123244 TGTAAA-TCGCAACGCGAATTTGTAAATCGCAACACAGAA-G
1 TCCAAATTCGCAACGCGAATATGTAAATCGCAACGC-GAATA
* * *
2123284 TCAAAATTCGCAACACAGAA-GT-TAAATTCGCAACGCG-ATA
1 TCCAAATTCGCAACGC-GAATATGTAAA-TCGCAACGCGAATA
2123324 GT-CAAATTCGCAAC
1 -TCCAAATTCGCAAC
2123338 ACTGAAGTCA
Statistics
Matches: 76, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
39 1 0.01
40 47 0.62
41 25 0.33
42 3 0.04
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (41 bp):
TCCAAATTCGCAACGCGAATATGTAAATCGCAACGCGAATA
Found at i:2123290 original size:20 final size:20
Alignment explanation
Indices: 2123270--2123456 Score: 188
Period size: 20 Copynumber: 9.3 Consensus size: 20
2123260 AATTTGTAAA
2123270 TCGCAACACAGAAGTCAAAAT
1 TCGCAACACAGAAGTC-AAAT
*
2123291 TCGCAACACAGAAGTTAAAT
1 TCGCAACACAGAAGTCAAAT
*
2123311 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
2123331 TCGCAACACTGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
2123351 TCGCAACACATAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
***
2123371 TCGCAA-TGTGATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
2123391 TCGCAACGCA-AA-TCTGTAAA-
1 TCGCAACACAGAAGTC---AAAT
2123411 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
2123431 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
2123451 TCGCAA
1 TCGCAA
2123457 AGCGCGTTTA
Statistics
Matches: 140, Mismatches: 15, Indels: 23
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.01
19 9 0.06
20 105 0.75
21 22 0.16
22 2 0.01
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.20
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:2123310 original size:60 final size:60
Alignment explanation
Indices: 2123246--2123456 Score: 254
Period size: 60 Copynumber: 3.5 Consensus size: 60
2123236 CGCGAATATG
*
2123246 TAAA-TCGCAACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAAATTCGCAACACAGAAGT
1 TAAATTCGCAACGCG-A-TAGTCAAATTCGCAACACAGAAGTC-AAATTCGCAACACAGAAGT
* *
2123306 TAAATTCGCAACGCGATAGTCAAATTCGCAACACTGAAGTCAAATTCGCAACACATAAGT
1 TAAATTCGCAACGCGATAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACACAGAAGT
* * * *
2123366 CAAATTCGCAATGTGATAGTCAAATTCGCAACGCA-AA-TCTGTAAA-TCGCAACACAGAAGT
1 TAAATTCGCAACGCGATAGTCAAATTCGCAACACAGAAGTC---AAATTCGCAACACAGAAGT
*
2123426 CAAATTCGCAACGCGATAGTCAAATTCGCAA
1 TAAATTCGCAACGCGATAGTCAAATTCGCAA
2123457 AGCGCGTTTA
Statistics
Matches: 134, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
58 2 0.01
59 5 0.04
60 99 0.74
61 28 0.21
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (60 bp):
TAAATTCGCAACGCGATAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACACAGAAGT
Found at i:2123335 original size:81 final size:79
Alignment explanation
Indices: 2123226--2123456 Score: 233
Period size: 80 Copynumber: 2.9 Consensus size: 79
2123216 CGCGAATATG
*
2123226 TAAATCGCAACGCGAATATGTAAATCGCAACGC-GAATTTGT-AAA-TCGCAACACAGAAGTCAA
1 TAAATCGCAACGCGAATATGTAAATCGCAACACTGAA---GTCAAATTCGCAACACAGAAGTC-A
2123288 AATTCGCAACACAGAAGT
62 AATTCGCAACACAGAAGT
*
2123306 TAAATTCGCAACGCG-ATA-GTCAAATTCGCAACACTGAAGTCAAATTCGCAACACATAAGTCAA
1 TAAA-TCGCAACGCGAATATGT-AAA-TCGCAACACTGAAGTCAAATTCGCAACACAGAAGTCAA
***
2123369 ATTCGCAA-TGTGATAGT
63 ATTCGCAACACAGA-AGT
* * * * *
2123386 CAAATTCGCAACGCAAATCTGTAAATCGCAACACAGAAGTCAAATTCGCAACGC-GATAGTCAAA
1 TAAA-TCGCAACGCGAATATGTAAATCGCAACACTGAAGTCAAATTCGCAACACAGA-AGTCAAA
2123450 TTCGCAA
64 TTCGCAA
2123457 AGCGCGTTTA
Statistics
Matches: 130, Mismatches: 11, Indels: 20
0.81 0.07 0.12
Matches are distributed among these distances:
79 7 0.05
80 80 0.62
81 38 0.29
82 5 0.04
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (79 bp):
TAAATCGCAACGCGAATATGTAAATCGCAACACTGAAGTCAAATTCGCAACACAGAAGTCAAATT
CGCAACACAGAAGT
Found at i:2123641 original size:22 final size:22
Alignment explanation
Indices: 2123616--2123666 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
2123606 CTATGGCGAC
2123616 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
2123638 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
*
2123660 ATACGTC
1 ATCCGTC
2123667 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:2125858 original size:63 final size:63
Alignment explanation
Indices: 2125753--2125910 Score: 156
Period size: 63 Copynumber: 2.5 Consensus size: 63
2125743 AGGGGAGTTA
* *
2125753 CGTGATGAGGTCGGTACTTTGCGTCATGAGGTCGATACTTTACGTGAAGACAATGGTGCATGG
1 CGTGATGAGGTCGGTACTTTACGTCATGAGGTCGATACTTTACGCGAAGACAATGGTGCATGG
** * ** * ** **
2125816 CGTGATGAGGTACGGT-CTTTACGTGGTGAGGTGGATGTTTTACGCGATGACAATGGTGTGTTA
1 CGTGATGAGGT-CGGTACTTTACGTCATGAGGTCGATACTTTACGCGAAGACAATGGTGCATGG
*** *
2125879 CGTGATGAGGTATCTACTTTACGTGATGAGGT
1 CGTGATGAGGTCGGTACTTTACGTCATGAGGT
2125911 AGCCGCTCTA
Statistics
Matches: 77, Mismatches: 16, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
62 1 0.01
63 72 0.94
64 4 0.05
ACGTcount: A:0.21, C:0.13, G:0.34, T:0.32
Consensus pattern (63 bp):
CGTGATGAGGTCGGTACTTTACGTCATGAGGTCGATACTTTACGCGAAGACAATGGTGCATGG
Found at i:2125922 original size:21 final size:21
Alignment explanation
Indices: 2125877--2125925 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2125867 AATGGTGTGT
* * *
2125877 TACGTGATGAGGTATCTACTT
1 TACGTGATGAGGTAGCCACTC
*
2125898 TACGTGATGAGGTAGCCGCTC
1 TACGTGATGAGGTAGCCACTC
2125919 TACGTGA
1 TACGTGA
2125926 GATTGTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (21 bp):
TACGTGATGAGGTAGCCACTC
Found at i:2126273 original size:20 final size:21
Alignment explanation
Indices: 2126208--2126279 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 21
2126198 CACCTGTCAT
*
2126208 CGTTCAAGTGGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
** *
2126229 CGTTCAAGAGGCCCCTGTCAT
1 CGTTCAAGAGGCCCCTCCCAC
* *
2126250 CGTTCATG-GGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
2126270 CGTTCAAGAG
1 CGTTCAAGAG
2126280 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 15 0.38
21 25 0.62
ACGTcount: A:0.17, C:0.39, G:0.22, T:0.22
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCCCAC
Found at i:2126274 original size:41 final size:42
Alignment explanation
Indices: 2126200--2126279 Score: 135
Period size: 41 Copynumber: 1.9 Consensus size: 42
2126190 GCCCGATTCA
2126200 CCTGTCATCGTTCAAGTGGCCCCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGTGGCCCCTCCCACCGTTCAAGAGGCC
* *
2126242 CCTGTCATCGTTCATG-GGTCCCTCCCACCGTTCAAGAG
1 CCTGTCATCGTTCAAGTGGCCCCTCCCACCGTTCAAGAG
2126280 CCCGATTCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 21 0.58
42 15 0.42
ACGTcount: A:0.16, C:0.39, G:0.21, T:0.24
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGTGGCCCCTCCCACCGTTCAAGAGGCC
Found at i:2127665 original size:14 final size:14
Alignment explanation
Indices: 2127623--2127676 Score: 72
Period size: 14 Copynumber: 3.9 Consensus size: 14
2127613 GCTTGTTTAA
*
2127623 TTGATTTGTAAAAG
1 TTGATTTGTAAAAT
2127637 TTGATTTGTAAAAT
1 TTGATTTGTAAAAT
**
2127651 TTGATTTGTTTAAT
1 TTGATTTGTAAAAT
*
2127665 TTGATGTGTAAA
1 TTGATTTGTAAA
2127677 TAAGAATTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (14 bp):
TTGATTTGTAAAAT
Found at i:2127711 original size:80 final size:78
Alignment explanation
Indices: 2127573--2127725 Score: 261
Period size: 80 Copynumber: 1.9 Consensus size: 78
2127563 ACATTGAAAG
2127573 TTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTAAAAGT
1 TTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTAAAAGT
2127638 TGATTTGTAAAAT
66 TGATTTGTAAAAT
* * *
2127651 TTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTTTTTAATTGATTTGTAAAA
1 TTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA-TTTTTTGCTTGTTTAATTGATTTGTAAAA
2127716 GTTGATTTGT
64 GTTGATTTGT
2127726 TGTTTTAAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
78 13 0.19
79 19 0.27
80 38 0.54
ACGTcount: A:0.29, C:0.01, G:0.17, T:0.52
Consensus pattern (78 bp):
TTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTAAAAGT
TGATTTGTAAAAT
Found at i:2128108 original size:18 final size:18
Alignment explanation
Indices: 2128085--2128120 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2128075 AAGCCGGTTA
2128085 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
2128103 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
2128121 CCTTTTGCTT
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:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:2130549 original size:25 final size:25
Alignment explanation
Indices: 2130521--2130584 Score: 110
Period size: 25 Copynumber: 2.5 Consensus size: 25
2130511 GAAAGTTTAT
2130521 TGGGATTTGGATTAGGAAAAGGTTG
1 TGGGATTTGGATTAGGAAAAGGTTG
2130546 TGGGATTTGGATTAGGAAAAGGTTG
1 TGGGATTTGGATTAGGAAAAGGTTG
*
2130571 TGGGTTTTGAGATT
1 TGGGATTTG-GATT
2130585 GTGTTTGATA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 33 0.89
26 4 0.11
ACGTcount: A:0.25, C:0.00, G:0.39, T:0.36
Consensus pattern (25 bp):
TGGGATTTGGATTAGGAAAAGGTTG
Found at i:2130597 original size:12 final size:12
Alignment explanation
Indices: 2130576--2130609 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2130566 GGTTGTGGGT
*
2130576 TTTGAGATTGTG
1 TTTGATATTGTG
2130588 TTTGATATTGTG
1 TTTGATATTGTG
*
2130600 TTTGGTATTG
1 TTTGATATTG
2130610 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Done.