Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006908.1 Hibiscus syriacus cultivar Beakdansim tig00017651_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: 118476
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:6591 original size:89 final size:89
Alignment explanation
Indices: 6422--6674 Score: 284
Period size: 89 Copynumber: 2.8 Consensus size: 89
6412 AATAGAAATA
* * * *
6422 TTTTTAACTTAAAATAAAATATTGAGGGTTAAAATACTCTTAAAAAAAGAATAAAAGACAAAATG
1 TTTTT-ACCTAAAATAAAATATTGATGGCTAAAATATTCTTAAAAAAAGAATAAAAGACAAAATG
*
6487 ATTATTTTGACAAATATTATGGGTT
65 ATTATTTTGACAAATATTATGGGTG
* *
6512 TTTTTACCATAAAATGAAATATTGATGGCTAAAATATTC-TAGAAAAAA-AATAAGAGA-AAAAG
1 TTTTTACC-TAAAATAAAATATTGATGGCTAAAATATTCTTA-AAAAAAGAATAAAAGACAAAA-
6574 TGATTATTTTGACAAATATTATGGGTG
63 TGATTATTTTGACAAATATTATGGGTG
* * *
6601 TTTTTACTCTAAAATAAAATGTT-ATGAGCTAAAATATT-TCAAAAAAATAGAATAGGAA-ACAA
1 TTTTTAC-CTAAAATAAAATATTGATG-GCTAAAATATTCT-TAAAAAA-AGAATA-AAAGACAA
*
6663 AATGATAATTTT
61 AATGATTATTTT
6675 AGTAAACGTT
Statistics
Matches: 139, Mismatches: 13, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
88 7 0.05
89 73 0.53
90 40 0.29
91 14 0.10
92 5 0.04
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.34
Consensus pattern (89 bp):
TTTTTACCTAAAATAAAATATTGATGGCTAAAATATTCTTAAAAAAAGAATAAAAGACAAAATGA
TTATTTTGACAAATATTATGGGTG
Found at i:11843 original size:30 final size:30
Alignment explanation
Indices: 11757--11822 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
11747 TCCTAATGGA
*
11757 CTAAATAAAAAAGCCATTATCTTTATTGGG
1 CTAAATCAAAAAGCCATTATCTTTATTGGG
11787 CTAAATCAAAAAGCCATTATCTTTATTGGG
1 CTAAATCAAAAAGCCATTATCTTTATTGGG
11817 CTAAAT
1 CTAAAT
11823 GATGTAAGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (30 bp):
CTAAATCAAAAAGCCATTATCTTTATTGGG
Found at i:15207 original size:34 final size:34
Alignment explanation
Indices: 15169--15236 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
15159 ATTTCATATG
15169 TTAGATTGCTTTTCTG-TTTTTCAATTTAATTCAT
1 TTAGATTGCTTTTCTGTTTTTTC-ATTTAATTCAT
* *
15203 TTAGATTTCTTTTTTGTTTTTTCATTTAATTCAT
1 TTAGATTGCTTTTCTGTTTTTTCATTTAATTCAT
15237 ATGTTGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 25 0.81
35 6 0.19
ACGTcount: A:0.19, C:0.10, G:0.07, T:0.63
Consensus pattern (34 bp):
TTAGATTGCTTTTCTGTTTTTTCATTTAATTCAT
Found at i:28097 original size:20 final size:20
Alignment explanation
Indices: 28074--28147 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
28064 GATTCTGACT
* *
28074 ATCGCATTGCGATTACGTAA
1 ATCGCAATGCGAATACGTAA
28094 ATCGCAATGCGAATACGTAA
1 ATCGCAATGCGAATACGTAA
* *
28114 ATCGTAATGCGAATATGTAA
1 ATCGCAATGCGAATACGTAA
*
28134 ATCGCAACGCGAAT
1 ATCGCAATGCGAAT
28148 CTGACTATCG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGAATACGTAA
Found at i:28099 original size:40 final size:40
Alignment explanation
Indices: 28055--28167 Score: 122
Period size: 40 Copynumber: 2.8 Consensus size: 40
28045 GTTTCCAGAT
*
28055 TCGCAACGCGATTCTGACTATCGCATTGCGATTACGTAAA
1 TCGCAACGCGATTCTGACTATCGCAATGCGATTACGTAAA
* * * * * *
28095 TCGCAATGCGAATAC-GTA-AATCGTAATGCGAATATGTAAA
1 TCGCAACGCG-ATTCTG-ACTATCGCAATGCGATTACGTAAA
*
28135 TCGCAACGCGAATCTGACTATCGCAATGCGATT
1 TCGCAACGCGATTCTGACTATCGCAATGCGATT
28168 TTCATAGCGC
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
39 3 0.05
40 49 0.88
41 4 0.07
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (40 bp):
TCGCAACGCGATTCTGACTATCGCAATGCGATTACGTAAA
Found at i:28371 original size:22 final size:22
Alignment explanation
Indices: 28346--28409 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
28336 CGACATCCGT
28346 CCCCATCTCCGACGAAATCAGG
1 CCCCATCTCCGACGAAATCAGG
* *
28368 CCCCATCTCCGACGATATCAGT
1 CCCCATCTCCGACGAAATCAGG
* *
28390 CTCCATCTCCGGCGAAATCA
1 CCCCATCTCCGACGAAATCA
28410 TTCACGGTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.19
Consensus pattern (22 bp):
CCCCATCTCCGACGAAATCAGG
Found at i:28822 original size:20 final size:20
Alignment explanation
Indices: 28746--28815 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
28736 CGATTCTGTC
*
28746 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
**
28765 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
28785 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
28805 GTTGCGATTTT
1 GTTGCGATTTT
28816 AAGTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 11 0.24
20 34 0.76
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:30720 original size:20 final size:20
Alignment explanation
Indices: 30692--30743 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
30682 AGAATAGTTT
30692 ACTATCGCAATGCAAAAATG
1 ACTATCGCAATGCAAAAATG
* * *
30712 ACTAACGCAACGCGAAAATG
1 ACTATCGCAATGCAAAAATG
30732 ACTATCGCAATG
1 ACTATCGCAATG
30744 AGAGAATCGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (20 bp):
ACTATCGCAATGCAAAAATG
Found at i:30826 original size:20 final size:20
Alignment explanation
Indices: 30803--30874 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
30793 AAAATGACTA
**
30803 TCGCATTGCGATAGTCAAAT
1 TCGCATTGCGATAGTCATTT
30823 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
*
30843 TCGCGTTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
30863 TCGCATTGCGAT
1 TCGCATTGCGAT
30875 TTTAAGTTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATAGTCATTT
Found at i:31449 original size:21 final size:21
Alignment explanation
Indices: 31358--31462 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
31348 GACTCACCTG
*
31358 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
31380 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
31400 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
31421 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
31442 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
31463 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:31455 original size:42 final size:42
Alignment explanation
Indices: 31355--31465 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
31345 CCCGACTCAC
* * * *
31355 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
31397 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
31439 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
31466 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:32795 original size:14 final size:14
Alignment explanation
Indices: 32776--32811 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
32766 ATTGTCTAAT
32776 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
32790 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
32804 TGATTTGT
1 TGATTTGT
32812 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:32967 original size:33 final size:33
Alignment explanation
Indices: 32917--33012 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
32907 AAAACAGACT
* **
32917 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
32951 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
32984 ATCACAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
33013 TGAAACTAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:33089 original size:33 final size:33
Alignment explanation
Indices: 33029--33122 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
33019 TAAATTCGCG
33029 TTGCGATTTTCATTTTCACATTGCGATTCACTCA
1 TTGCGATTTTCA-TTTCACATTGCGATTCACTCA
* * *
33063 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCACATTGCGATTCACTCA
** *
33096 TTGCGATAGTCATTTCCACGTTGCGAT
1 TTGCGATTTTCATTT-CACATTGCGAT
33123 AGTCAATTCC
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
33 31 0.60
34 21 0.40
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (33 bp):
TTGCGATTTTCATTTCACATTGCGATTCACTCA
Found at i:33153 original size:20 final size:20
Alignment explanation
Indices: 33094--33163 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
33084 GCGATTCTCT
*
33094 CGTTGCGATAGTCATTTCCA
1 CGTTGCGATAGTCATTTCCG
*
33114 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
33134 CGTTGCCATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
33154 TGTTTCGATA
1 CGTTGCGATA
33164 AGTGATAACA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:35628 original size:24 final size:24
Alignment explanation
Indices: 35577--35628 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
35567 ATCCGAGTAT
** *
35577 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
* *
35601 TGACCAAGATCAAATTTTGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
35625 TGAC
1 TGAC
35629 TAGTACTCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:36469 original size:20 final size:20
Alignment explanation
Indices: 36444--36510 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
36434 AAATTCAGTA
36444 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
*
36464 TTGCGATAGTCAAAATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
36484 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCTCG
36504 TTGCGAT
1 TTGCGAT
36511 TTACATATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:36520 original size:20 final size:20
Alignment explanation
Indices: 36497--36590 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
36487 CGATAGTCAG
*
36497 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACAT
*
36517 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACAT
* *
36537 ATTCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACAT
*
36558 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACAT
36578 ATTCGCATTGCGA
1 ATTCGCATTGCGA
36591 ATTAGGTAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 48 0.75
21 16 0.25
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACAT
Found at i:36573 original size:41 final size:40
Alignment explanation
Indices: 36497--36590 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 40
36487 CGATAGTCAG
* * *
36497 ATTCGCGTTGCGATTTACATATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACAAATTCGCATTGCGATTTACAT
* *
36537 ATTCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGA-TTTACAAATTCGCATTGCGATTTACAT
36578 ATTCGCATTGCGA
1 ATTCGCATTGCGA
36591 ATTAGGTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 12 0.25
41 36 0.75
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACAAATTCGCATTGCGATTTACAT
Found at i:36611 original size:21 final size:21
Alignment explanation
Indices: 36587--36627 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
36577 TATTCGCATT
*
36587 GCGAATTAGGTAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
*
36608 GCGAATTTGGAAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
36628 TGTGATAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:37028 original size:50 final size:50
Alignment explanation
Indices: 36971--37077 Score: 126
Period size: 50 Copynumber: 2.1 Consensus size: 50
36961 AGAAAAGCGC
* * * *
36971 CCCCCTGCACCGCGCTATATC-CTGATTTGGCACCACGTGGGTATAACGCG
1 CCCCCTGCACCGCGATATA-CGCTGATCTGGCACAACGTGGGTATAACGCA
* * * *
37021 CCCCCTGCCCCGCGATATACGGTGATCTGGCGCAACGTGGGTATAGCGCA
1 CCCCCTGCACCGCGATATACGCTGATCTGGCACAACGTGGGTATAACGCA
37071 CCCCCTG
1 CCCCCTG
37078 ATCTGCGCTA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 1 0.02
50 47 0.98
ACGTcount: A:0.17, C:0.37, G:0.26, T:0.20
Consensus pattern (50 bp):
CCCCCTGCACCGCGATATACGCTGATCTGGCACAACGTGGGTATAACGCA
Found at i:40767 original size:35 final size:34
Alignment explanation
Indices: 40682--40768 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
40672 ATTTGATATT
*
40682 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
40716 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
40754 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
40769 ACTAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:41002 original size:9 final size:9
Alignment explanation
Indices: 40987--41042 Score: 58
Period size: 9 Copynumber: 6.2 Consensus size: 9
40977 GCTGTCATCA
*
40987 TCATCGTCA
1 TCATCGTCG
*
40996 TCGTCGTCG
1 TCATCGTCG
* *
41005 TCACCATCG
1 TCATCGTCG
41014 TCATCGTCG
1 TCATCGTCG
*
41023 TCATCGTCA
1 TCATCGTCG
*
41032 TCTTCGTCG
1 TCATCGTCG
41041 TC
1 TC
41043 CTGAGCAGGT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.12, C:0.36, G:0.18, T:0.34
Consensus pattern (9 bp):
TCATCGTCG
Found at i:41027 original size:15 final size:15
Alignment explanation
Indices: 40984--41039 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
40974 CTCGCTGTCA
*
40984 TCATCATCGTCATCG
1 TCATCGTCGTCATCG
* **
40999 TCGTCGTCACCATCG
1 TCATCGTCGTCATCG
41014 TCATCGTCGTCATCG
1 TCATCGTCGTCATCG
*
41029 TCATCTTCGTC
1 TCATCGTCGTC
41040 GTCCTGAGCA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.14, C:0.36, G:0.16, T:0.34
Consensus pattern (15 bp):
TCATCGTCGTCATCG
Found at i:43269 original size:12 final size:10
Alignment explanation
Indices: 43255--43295 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
43245 ACCTTAAAAA
*
43255 GAGAGTATTT
1 GAGAGAATTT
43265 GAGAGAAATTT
1 GAGAG-AATTT
43276 -AGAGAATTT
1 GAGAGAATTT
43285 GAGAGAATTT
1 GAGAGAATTT
43295 G
1 G
43296 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:43470 original size:50 final size:49
Alignment explanation
Indices: 43416--43541 Score: 198
Period size: 50 Copynumber: 2.5 Consensus size: 49
43406 AGATATCCAG
*
43416 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAGATCACC
1 GTATATCGCGG-TCAGGGGGCGCGCTATACCCACGTGGCGCCAGATCACC
* *
43466 GTATATCGCTGGGCAGGGGGCGCGCTATACCCACGTGGCGCCAGATCACT
1 GTATATCGC-GGTCAGGGGGCGCGCTATACCCACGTGGCGCCAGATCACC
43516 GTATATCGCGGTGCAGGGGGCGCGCT
1 GTATATCGCGGT-CAGGGGGCGCGCT
43542 TTCCTGCTAA
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
49 2 0.03
50 66 0.94
51 2 0.03
ACGTcount: A:0.17, C:0.29, G:0.37, T:0.17
Consensus pattern (49 bp):
GTATATCGCGGTCAGGGGGCGCGCTATACCCACGTGGCGCCAGATCACC
Found at i:47673 original size:31 final size:31
Alignment explanation
Indices: 47635--47699 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
47625 AGAGTCGAGG
*
47635 GTTTACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTAAGTTCTAAGGAACATATGGACA
** * *
47666 GTTTACCTAAGTTCTTCGGGACCTATGGACA
1 GTTTACCTAAGTTCTAAGGAACATATGGACA
47697 GTT
1 GTT
47700 ACCGAGGATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (31 bp):
GTTTACCTAAGTTCTAAGGAACATATGGACA
Found at i:47755 original size:30 final size:30
Alignment explanation
Indices: 47685--47757 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
47675 AGTTCTTCGG
* * *
47685 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTCTAT
47715 GACCTCTGGATAGTTACCGAGGATCTCTAT
1 GACCTCTGGATAGTTACCGAGGATCTCTAT
47745 GACCTCTGGATAG
1 GACCTCTGGATAG
47758 GTCCTTCAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.29
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTCTAT
Found at i:49584 original size:26 final size:26
Alignment explanation
Indices: 49544--49601 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
49534 TCATTTTTCT
49544 AATTAATAAATATTC-CAAAAATTTAA
1 AATTAATAAATATTCTCAAAAATTT-A
* *
49570 AATTAATATAA-ATTCTGAAAACTTTA
1 AATTAATA-AATATTCTCAAAAATTTA
49596 AATTAA
1 AATTAA
49602 AAAAAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 19 0.68
27 9 0.32
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (26 bp):
AATTAATAAATATTCTCAAAAATTTA
Found at i:49894 original size:137 final size:145
Alignment explanation
Indices: 49654--49945 Score: 467
Period size: 148 Copynumber: 2.1 Consensus size: 145
49644 CTATATCACT
* * *
49654 AAAATGTATTGAGATATGATTTGCATCCAATCGCAGCAGCATCTCTAATTAGCACAAATAATTAA
1 AAAATATATTGAGATATGATTTGCATCAAATCGCAGCAGCATCTCTAATTAACACAAATAATTAA
49719 TTAATAAATTTAAATATATAATAATTATATAAATATTATTTTAATAAAAAAATATAACATTATTT
66 TT-ATAAA-TTAAATATATAATAATTATATAAATATTATTTTAAT-AAAAAATATAACATTATTT
49784 TTAAATAATTATTTATAA
128 TTAAATAATTATTTATAA
49802 AAAATATATTGAGATATGATTTGCATCAAATCGCAGCAGCATCTCTAATTAACACAAATAATTAA
1 AAAATATATTGAGATATGATTTGCATCAAATCGCAGCAGCATCTCTAATTAACACAAATAATTAA
49867 -T-T-AA-TAAAT-T-T-A-AA-TATATAAATATTATTTTAATAAAAAATATAACATTATTTTTA
66 TTATAAATTAAATATATAATAATTATATAAATATTATTTTAATAAAAAATATAACATTATTTTTA
49923 AATAATTATTTATAA
131 AATAATTATTTATAA
49938 AAAATATA
1 AAAATATA
49946 ATAACTTTTT
Statistics
Matches: 141, Mismatches: 3, Indels: 12
0.90 0.02 0.08
Matches are distributed among these distances:
136 45 0.32
137 20 0.14
138 2 0.01
139 1 0.01
140 1 0.01
141 1 0.01
142 5 0.04
144 2 0.01
145 1 0.01
147 1 0.01
148 62 0.44
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (145 bp):
AAAATATATTGAGATATGATTTGCATCAAATCGCAGCAGCATCTCTAATTAACACAAATAATTAA
TTATAAATTAAATATATAATAATTATATAAATATTATTTTAATAAAAAATATAACATTATTTTTA
AATAATTATTTATAA
Found at i:49949 original size:22 final size:21
Alignment explanation
Indices: 49923--49983 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
49913 ATTATTTTTA
49923 AATAATTATTTATAA-AAAATAT
1 AATAATT-TTTA-AATAAAATAT
49945 AATAACTTTTTAAATAAAATAT
1 AATAA-TTTTTAAATAAAATAT
* **
49967 ATTAATTTAAAAATAAA
1 AATAATTTTTAAATAAA
49984 TTTTTTATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 12 0.35
22 20 0.59
23 2 0.06
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
AATAATTTTTAAATAAAATAT
Found at i:49955 original size:34 final size:37
Alignment explanation
Indices: 49885--49961 Score: 101
Period size: 34 Copynumber: 2.2 Consensus size: 37
49875 TTTAAATATA
*
49885 TAAAT-ATTATTTTAATAAAAAATATAACATTATTTT
1 TAAATAATTATTTTAATAAAAAATATAACATAATTTT
49921 TAAATAATTA-TTT-ATAAAAAATAT-A-ATAACTTTT
1 TAAATAATTATTTTAATAAAAAATATAACATAA-TTTT
49955 TAAATAA
1 TAAATAA
49962 AATATATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
33 3 0.08
34 12 0.32
35 11 0.29
36 8 0.21
37 4 0.11
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (37 bp):
TAAATAATTATTTTAATAAAAAATATAACATAATTTT
Found at i:50613 original size:14 final size:14
Alignment explanation
Indices: 50595--50640 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
50585 TAATAATAAT
50595 AATAAAATAAGATA
1 AATAAAATAAGATA
*
50609 GAT-AAATAAAGATA
1 AATAAAAT-AAGATA
*
50623 AATAAAA-AAGAAA
1 AATAAAATAAGATA
50636 AATAA
1 AATAA
50641 TACAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 14 0.52
14 10 0.37
15 3 0.11
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (14 bp):
AATAAAATAAGATA
Found at i:52564 original size:106 final size:106
Alignment explanation
Indices: 52374--52847 Score: 759
Period size: 106 Copynumber: 4.5 Consensus size: 106
52364 GTATTGTTCG
* * * * * *
52374 GAGTCCAACATCCTCCGCCGTGAAGTTGAAATTGGCTCAGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
52439 CCAGCCGTCCCTTCACTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTC
* *
52480 AAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAGATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
52545 ACAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTC
66 CCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTC
* * * *
52586 GAGTCCAATATCATTCGCTGTGAAGTTGAGATTGGCTCTGAAATTAGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
52651 CCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTC
66 CCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTC
*
52692 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAGATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
52757 CCAGCCGCCCCTTCGCTGAGAAATTGAGCTTGTGTTGTCTC
66 CCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTC
52798 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
52848 GCCCCTTCAT
Statistics
Matches: 337, Mismatches: 31, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 337 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTC
Found at i:56105 original size:16 final size:16
Alignment explanation
Indices: 56084--56127 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
56074 AATAAAAGTC
56084 TTACCCCACATGATGT
1 TTACCCCACATGATGT
56100 TTACCCCACATGATGT
1 TTACCCCACATGATGT
56116 TTACCCCACATG
1 TTACCCCACATG
56128 CTTTAATTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.25, C:0.34, G:0.11, T:0.30
Consensus pattern (16 bp):
TTACCCCACATGATGT
Found at i:57116 original size:15 final size:13
Alignment explanation
Indices: 57059--57108 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
57049 AATTGGTTGG
57059 ATAATAGAAAAAA
1 ATAATAGAAAAAA
* *
57072 ATAAT--AAATAT
1 ATAATAGAAAAAA
57083 AT-ATATGAAAAAA
1 ATAATA-GAAAAAA
57096 ATAATAGAAAAAA
1 ATAATAGAAAAAA
57109 TATTAATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
10 2 0.07
11 6 0.21
13 18 0.62
14 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (13 bp):
ATAATAGAAAAAA
Found at i:62815 original size:2 final size:2
Alignment explanation
Indices: 62808--62833 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
62798 ACTAAAGAAT
62808 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
62834 GGTCTGTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:70201 original size:2 final size:2
Alignment explanation
Indices: 70194--70233 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
70184 TCAATTTGTA
70194 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
70234 TATGATTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72304 original size:21 final size:21
Alignment explanation
Indices: 72280--72324 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
72270 CTTAATTATC
* *
72280 TATTTTTAATAAATTTAGATA
1 TATTTTTAATAAATTCAAATA
*
72301 TATTTTTCATAAATTCAAATA
1 TATTTTTAATAAATTCAAATA
72322 TAT
1 TAT
72325 AATATATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (21 bp):
TATTTTTAATAAATTCAAATA
Found at i:78731 original size:21 final size:21
Alignment explanation
Indices: 78707--78749 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
78697 GTGACGTGCC
78707 TTTATTTGAAATACTTATTTT
1 TTTATTTGAAATACTTATTTT
78728 TTTATTTGAAATACTTATTTT
1 TTTATTTGAAATACTTATTTT
78749 T
1 T
78750 ATAACTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.63
Consensus pattern (21 bp):
TTTATTTGAAATACTTATTTT
Found at i:79350 original size:33 final size:33
Alignment explanation
Indices: 79313--79384 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
79303 AATTTGATGG
*
79313 ATTTGACCATTCATAGGTAAATTTAATAGAGTT
1 ATTTGACCATTCATAGGTAAATTTAATAGAATT
*
79346 ATTTGACCATTCTTAGGTAAATTTAATAGAATT
1 ATTTGACCATTCATAGGTAAATTTAATAGAATT
79379 ATTTGA
1 ATTTGA
79385 GTTTGGTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (33 bp):
ATTTGACCATTCATAGGTAAATTTAATAGAATT
Found at i:79734 original size:2 final size:2
Alignment explanation
Indices: 79727--79759 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
79717 ATATCTCTTT
79727 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
79760 TAATTTGGGA
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:82179 original size:60 final size:58
Alignment explanation
Indices: 82072--82232 Score: 157
Period size: 60 Copynumber: 2.7 Consensus size: 58
82062 GTTATTGGAT
* * * * * * **
82072 TGTTCAAAAGTTT-GGGACTATTTATAAA-GAGGGTCATAGTTTGGGGATGAATTTGTCA
1 TGTTCAAAAGTTTAAGAACAATTTA-AAATGA-GGTCATAGTTTAGGGATAAAATTGAAA
82130 TGTTCAAAAG-TTATAGAACCAATTTAAAATGAGAGTCATAGTTTAGGGATAAAATTGAAA
1 TGTTCAAAAGTTTA-AGAA-CAATTTAAAATGAG-GTCATAGTTTAGGGATAAAATTGAAA
* *
82190 TGTTTAAAAGTTTAAGAATAATTTAAAATGAGGTTCATAGTTT
1 TGTTCAAAAGTTTAAGAACAATTTAAAATGAGG-TCATAGTTT
82233 GAGTATGTGT
Statistics
Matches: 86, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
57 2 0.02
58 11 0.13
59 28 0.33
60 42 0.49
61 3 0.03
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (58 bp):
TGTTCAAAAGTTTAAGAACAATTTAAAATGAGGTCATAGTTTAGGGATAAAATTGAAA
Found at i:87249 original size:15 final size:14
Alignment explanation
Indices: 87228--87285 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
87218 ATTGATTTTC
*
87228 TGGAAATTGAATTA
1 TGGAAAATGAATTA
87242 TGGAAAATGAATTA
1 TGGAAAATGAATTA
* *
87256 CT-GAAATTTGAATTC
1 -TGGAAA-ATGAATTA
87271 TGGAAAATGAATTA
1 TGGAAAATGAATTA
87285 T
1 T
87286 ATTTCTGGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
14 25 0.69
15 11 0.31
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.34
Consensus pattern (14 bp):
TGGAAAATGAATTA
Found at i:87274 original size:29 final size:28
Alignment explanation
Indices: 87230--87284 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
87220 TGATTTTCTG
87230 GAAATTGAATTATGGAAAATGAATTACT
1 GAAATTGAATTATGGAAAATGAATTACT
*
87258 GAAATTTGAATTCTGGAAAATGAATTA
1 GAAA-TTGAATTATGGAAAATGAATTA
87285 TATTTCTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.45, C:0.04, G:0.18, T:0.33
Consensus pattern (28 bp):
GAAATTGAATTATGGAAAATGAATTACT
Found at i:87326 original size:14 final size:14
Alignment explanation
Indices: 87287--87326 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
87277 ATGAATTATA
* *
87287 TTTCTGGAAAACGT
1 TTTCCGGAAAATGT
87301 TTTCCGGAAAATGT
1 TTTCCGGAAAATGT
*
87315 TTTCCGTAAAAT
1 TTTCCGGAAAAT
87327 AAATTACATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (14 bp):
TTTCCGGAAAATGT
Found at i:87523 original size:27 final size:27
Alignment explanation
Indices: 87476--87527 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
87466 ATCATAAAAC
87476 ATAATATTATTTTTTTAAAATATTAAA
1 ATAATATTATTTTTTTAAAATATTAAA
87503 ATAAT-TTATTTATTATT-AAATATTA
1 ATAATATTATTT-TT-TTAAAATATTA
87528 TTTTTGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 6 0.26
27 15 0.65
28 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
ATAATATTATTTTTTTAAAATATTAAA
Found at i:87885 original size:20 final size:20
Alignment explanation
Indices: 87860--87973 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 20
87850 AATTGGGAAA
*
87860 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
87880 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * * *
87900 ATCGCAATGCAATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
87921 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
87941 TTCACAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
87961 TTCGCAACGCGAT
1 ATCGCAACGCGAT
87974 TTACATAGCG
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
19 2 0.03
20 61 0.79
21 12 0.16
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:87904 original size:61 final size:61
Alignment explanation
Indices: 87839--87972 Score: 137
Period size: 61 Copynumber: 2.2 Consensus size: 61
87829 GAATAAGTAA
** * * * * *
87839 ATCGCAACGCGAAT-TGGGAAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATAT-ACAAAATCGCAACGAGATACTGACTATCACAACGCGATACTGACT
* * *
87900 ATCGCAATGC-AATAATACAAAATCGCAACGAGATACTGACTTTCACAACGCGATTCTGACT
1 ATCGCAACGCGAAT-ATACAAAATCGCAACGAGATACTGACTATCACAACGCGATACTGACT
*
87961 TTCGCAACGCGA
1 ATCGCAACGCGA
87973 TTTACATAGC
Statistics
Matches: 58, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
60 3 0.05
61 53 0.91
62 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (61 bp):
ATCGCAACGCGAATATACAAAATCGCAACGAGATACTGACTATCACAACGCGATACTGACT
Found at i:88530 original size:19 final size:19
Alignment explanation
Indices: 88492--88558 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
88482 TTCGAGAATG
88492 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
88512 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
88531 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
88550 AAAATCGCA
1 AAAATCGCA
88559 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:88576 original size:19 final size:19
Alignment explanation
Indices: 88554--88699 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
88544 GAAACCAAAA
*
88554 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
88573 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
88587 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
88606 TGGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
88625 TTGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
** **
88639 TCTAGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
88658 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
88678 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
88698 TC
1 TC
88700 AACCAAAAGA
Statistics
Matches: 100, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
14 18 0.18
16 5 0.05
17 6 0.06
19 40 0.40
20 30 0.30
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:88637 original size:52 final size:53
Alignment explanation
Indices: 88559--88691 Score: 180
Period size: 52 Copynumber: 2.5 Consensus size: 53
88549 CAAAATCGCA
* * ** *
88559 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTT-GGCG
1 TTGCGATTTTCATTTTGCGTTGCGATTCTCTAGTTGCGATAGTCATTTCCGCG
88611 TTGCGATTTTCATTTTGCGTTGCGATTCTCTAGTTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTTTGCGTTGCGATTCTCTAGTTGCGATAGTCATTTCCGCG
*
88664 TTGCGATTCTCATTATCT-CGTTGCGATT
1 TTGCGATTTTCATT-T-TGCGTTGCGATT
88692 TTCATTTCAA
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
52 44 0.61
53 16 0.22
54 11 0.15
55 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (53 bp):
TTGCGATTTTCATTTTGCGTTGCGATTCTCTAGTTGCGATAGTCATTTCCGCG
Found at i:88670 original size:34 final size:33
Alignment explanation
Indices: 88610--88674 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
88600 TTCATTTGGC
** *
88610 GTTGCGATTTTCATTTTGCGTTGCGATTCTCTA
1 GTTGCGATAGTCATTTCGCGTTGCGATTCTCTA
88643 GTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 GTTGCGATAGTCATTT-CGCGTTGCGATTCTC
88675 ATTATCTCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 14 0.50
34 14 0.50
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.43
Consensus pattern (33 bp):
GTTGCGATAGTCATTTCGCGTTGCGATTCTCTA
Found at i:90523 original size:17 final size:17
Alignment explanation
Indices: 90501--90533 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
90491 GTTGCTGCCA
90501 ATTCTTCTAA-ACTGTGT
1 ATTCTT-TAACACTGTGT
90518 ATTCTTTAACACTGTG
1 ATTCTTTAACACTGTG
90534 AAGTTAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (17 bp):
ATTCTTTAACACTGTGT
Found at i:90868 original size:42 final size:42
Alignment explanation
Indices: 90792--90880 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
90782 GACTCGCCTG
* * * *
90792 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
* * *
90834 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
90876 TCATC
1 TCATC
90881 GTTGAAGAGG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
Found at i:92287 original size:14 final size:14
Alignment explanation
Indices: 92267--92303 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
92257 GATTGTTTAA
92267 TTGATTTGTAAAA-
1 TTGATTTGTAAAAG
92280 TGTGATTTGTAAAAG
1 T-TGATTTGTAAAAG
92295 TTGATTTGT
1 TTGATTTGT
92304 TTAATTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:92447 original size:14 final size:14
Alignment explanation
Indices: 92428--92465 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
92418 GCGAAATGAA
92428 AATCGCAACGAGAG
1 AATCGCAACGAGAG
92442 AATCGCAACGAGAG
1 AATCGCAACGAGAG
92456 AATCGCAACG
1 AATCGCAACG
92466 CGAAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.42, C:0.24, G:0.26, T:0.08
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:92498 original size:19 final size:19
Alignment explanation
Indices: 92476--92606 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
92466 CGAAATTAAA
*
92476 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
92495 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
92511 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
92528 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
92542 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
92561 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
92577 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
92594 TTCGCATTGCGAT
1 TTCGCATTGCGAT
92607 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 23 0.27
16 13 0.15
17 13 0.15
19 35 0.42
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:92522 original size:33 final size:32
Alignment explanation
Indices: 92480--92606 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
92470 ATTAAATTCG
92480 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
92513 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
92546 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
92579 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
92607 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:92543 original size:66 final size:66
Alignment explanation
Indices: 92473--92605 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
92463 ACGCGAAATT
*
92473 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
92538 G
66 G
*
92539 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
92604 G
66 G
92605 A
1 A
92606 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:94931 original size:12 final size:12
Alignment explanation
Indices: 94898--94933 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
94888 TCTTCGGGGA
*
94898 CTTTTTCTTATT
1 CTTTTTCTTCTT
94910 CTTTTTCTTCTT
1 CTTTTTCTTCTT
94922 CTTTTTCTTCTT
1 CTTTTTCTTCTT
94934 TAGGATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:95140 original size:24 final size:24
Alignment explanation
Indices: 95106--95159 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
95096 CTGAAACATC
*
95106 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
95130 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
95154 ATCAAA
1 ATCAAA
95160 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:95969 original size:20 final size:21
Alignment explanation
Indices: 95944--95995 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
95934 TTTTCCTAAT
*
95944 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
95964 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
95985 TCGCAATGCGA
1 TCGCAATGCGA
95996 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:96069 original size:20 final size:20
Alignment explanation
Indices: 95980--96071 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
95970 TGCGAATTTG
* *
95980 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
96000 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
96020 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
96041 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
96061 GAAAATCGCAA
1 GAAAATCGCAA
96072 TTATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:96380 original size:20 final size:20
Alignment explanation
Indices: 96288--96372 Score: 91
Period size: 20 Copynumber: 4.2 Consensus size: 20
96278 CGGGGAAATT
96288 GCAACGCGAAAATGGCTATC
1 GCAACGCGAAAATGGCTATC
*
96308 GCAACGCGAAACTGGCTATC
1 GCAACGCGAAAATGGCTATC
** *** *
96328 GCAATTCG-AAATGAAAAATT
1 GCAACGCGAAAATG-GCTATC
96348 GCAACGCGAAAATGGCTATC
1 GCAACGCGAAAATGGCTATC
96368 GCAAC
1 GCAAC
96373 TAGAAAATCG
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
19 4 0.08
20 40 0.82
21 5 0.10
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
GCAACGCGAAAATGGCTATC
Found at i:96595 original size:14 final size:14
Alignment explanation
Indices: 96576--96612 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
96566 CATTAATTAA
96576 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
96590 ACAAATCATCTTTT
1 ACAAATCAACATTT
96604 ACAAATCAA
1 ACAAATCAA
96613 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:98080 original size:21 final size:20
Alignment explanation
Indices: 98056--98115 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
98046 AACGGTGAGG
98056 GGGGACTCTTGAGGGA-GGATA
1 GGGGACTCTTGAGGGATGG--A
* **
98077 GGGGCCTCTTGAACGATTGGA
1 GGGGACTCTTGAGGGA-TGGA
98098 GGGGACTCTTGAGGGATG
1 GGGGACTCTTGAGGGATG
98116 ACAGGTGAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
23 2 0.06
ACGTcount: A:0.20, C:0.13, G:0.45, T:0.22
Consensus pattern (20 bp):
GGGGACTCTTGAGGGATGGA
Found at i:98505 original size:20 final size:19
Alignment explanation
Indices: 98482--98582 Score: 77
Period size: 20 Copynumber: 5.5 Consensus size: 19
98472 GAAACTTAAA
*
98482 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGAAT
**
98502 ATCGCAACGCGGAAATGGTT
1 ATCGCAACGC-GAAATGAAT
* *
98522 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAT
*
98541 ATCGCAA--CGACA--AA-
1 ATCGCAACGCGAAATGAAT
* *
98555 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAT
98574 ATCGCAACG
1 ATCGCAACG
98583 ACAAAATCGC
Statistics
Matches: 66, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
14 7 0.11
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 21 0.32
20 25 0.38
21 1 0.02
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAT
Found at i:98557 original size:14 final size:14
Alignment explanation
Indices: 98538--98594 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
98528 ATGCGAAATG
98538 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
98552 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
98571 AAAATCGCAACGAC
1 AAAATCGCAACGAC
98585 AAAATCGCAA
1 AAAATCGCAA
98595 TGCGAAATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.51, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:98614 original size:32 final size:33
Alignment explanation
Indices: 98522--98633 Score: 181
Period size: 33 Copynumber: 3.4 Consensus size: 33
98512 GGAAATGGTT
98522 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
98555 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
98588 ATCGCAATGCGAAATG-AAATCTCAACGATAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
98620 ATCGTAACGCGAAA
1 ATCGCAATGCGAAA
98634 CACAAATCGC
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 26 0.35
33 49 0.65
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:98641 original size:65 final size:66
Alignment explanation
Indices: 98522--98644 Score: 178
Period size: 65 Copynumber: 1.9 Consensus size: 66
98512 GGAAATGGTT
* *
98522 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
98587 A
66 A
* * *
98588 ATCGCAATGCGAAATG-AAATCTCAACGATAAAATCGTAACGCGAAA-CACAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCA-AAATCGCA
98645 TTGCGATTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
64 1 0.02
65 34 0.67
66 16 0.31
ACGTcount: A:0.47, C:0.22, G:0.17, T:0.14
Consensus pattern (66 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
A
Found at i:98662 original size:19 final size:19
Alignment explanation
Indices: 98640--98736 Score: 72
Period size: 19 Copynumber: 5.6 Consensus size: 19
98630 GAAACACAAA
98640 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
98659 TCGCGTTGCGATTTTGC---
1 TCGCATTGCGATTTT-CATT
*
98676 -CG--TTGCGATTTCCATT
1 TCGCATTGCGATTTTCATT
* *
98692 TCGCATTGC-AATTT--TG
1 TCGCATTGCGATTTTCATT
98708 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
98725 TCGCATTGCGAT
1 TCGCATTGCGAT
98737 AGCCATTTCC
Statistics
Matches: 59, Mismatches: 7, Indels: 24
0.66 0.08 0.27
Matches are distributed among these distances:
13 1 0.02
14 13 0.22
15 4 0.07
16 6 0.10
17 6 0.10
18 3 0.05
19 25 0.42
20 1 0.02
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:98692 original size:33 final size:33
Alignment explanation
Indices: 98645--98736 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
98635 ACAAATCGCA
*
98645 TTGCGATTTTCATTTCGCGTTGCGATTTTGCCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGCCG
* * *
98678 TTGCGATTTCCATTTCGCATTGCAATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGCCG
98711 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
98737 AGCCATTTCC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGCCG
Found at i:98755 original size:20 final size:19
Alignment explanation
Indices: 98721--98775 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
98711 TTGCGATTTT
*
98721 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
98740 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
98760 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
98776 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:100669 original size:20 final size:20
Alignment explanation
Indices: 100621--100679 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
100611 AATAGTTTCT
** *
100621 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
100641 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
100661 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
100680 AGAGGATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:100950 original size:22 final size:22
Alignment explanation
Indices: 100923--100966 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
100913 GATGGAGATA
100923 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
100945 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
100967 TGAGAGAGTG
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:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:101240 original size:20 final size:20
Alignment explanation
Indices: 101134--101268 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
101124 CGCTTTGAAA
*
101134 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
101155 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
101175 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
101195 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
101216 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
101236 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
*
101256 ATTGCATTGCGAT
1 ATCGCATTGCGAT
101269 TTTCCCAATT
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
19 5 0.05
20 65 0.68
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:101240 original size:61 final size:61
Alignment explanation
Indices: 101137--101271 Score: 182
Period size: 61 Copynumber: 2.2 Consensus size: 61
101127 TTTGAAAATC
* * * *
101137 GCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCT
1 GCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTAT-T
* * * *
101199 -CGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATT
1 GCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATT
101259 GCATTGCGATTTT
1 GCATTGCGATTTT
101272 CCCAATTCGC
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
60 1 0.02
61 62 0.98
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (61 bp):
GCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATT
Found at i:101287 original size:61 final size:61
Alignment explanation
Indices: 101154--101289 Score: 150
Period size: 61 Copynumber: 2.2 Consensus size: 61
101144 GATTATGTAT
* * * * ** *
101154 TATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCTCATTGCGATTTTCCAA
* * *
101215 TATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTAT-TGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCT-CATTGCGATTTT-CCAA
101277 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
101290 TTACTTATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
60 1 0.02
61 59 0.95
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCTCATTGCGATTTTCCAA
Found at i:101811 original size:21 final size:20
Alignment explanation
Indices: 101765--101831 Score: 52
Period size: 21 Copynumber: 3.4 Consensus size: 20
101755 TTTTGTTATA
*
101765 ATATTAAAATATTATATTAT
1 ATATTAAAATATTATATAAT
101785 ATTATTAGAAATATTA-ATAAAT
1 A-TATTA-AAATATTATAT-AAT
*
101807 ATATTTTAAATATT-T-TAAT
1 ATA-TTAAAATATTATATAAT
101826 A-ATTAA
1 ATATTAA
101832 TATTTTGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
17 3 0.08
18 1 0.03
19 4 0.10
20 2 0.05
21 16 0.41
22 13 0.33
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (20 bp):
ATATTAAAATATTATATAAT
Found at i:108148 original size:2 final size:2
Alignment explanation
Indices: 108143--108176 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
108133 ATAATTTACC
108143 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
108177 GAAAAGAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:108877 original size:17 final size:18
Alignment explanation
Indices: 108851--108884 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
108841 AAACAAGTAT
*
108851 AGATATAATA-TTATTTA
1 AGATAAAATATTTATTTA
108868 AGATAAAATATTTATTT
1 AGATAAAATATTTATTT
108885 GATCACTCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
AGATAAAATATTTATTTA
Found at i:109386 original size:12 final size:12
Alignment explanation
Indices: 109371--109414 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
109361 AACAGAAGGA
109371 AAACCAGAAATC
1 AAACCAGAAATC
* *
109383 AAACAAGAAATT
1 AAACCAGAAATC
**
109395 AAACCAGAAGCC
1 AAACCAGAAATC
109407 AAACCAGA
1 AAACCAGA
109415 GTCTAAAGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.59, C:0.23, G:0.11, T:0.07
Consensus pattern (12 bp):
AAACCAGAAATC
Done.