Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006722.1 Hibiscus syriacus cultivar Beakdansim tig00016836_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: 136976
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:8061 original size:24 final size:24
Alignment explanation
Indices: 8034--8079 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
8024 CATTTAATAG
8034 TTTAA-TATTTTTATTATTATTTAA
1 TTTAATTA-TTTTATTATTATTTAA
* *
8058 TTTACTTATTTTCTTATTATTT
1 TTTAATTATTTTATTATTATTT
8080 TTTGCAGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTAATTATTTTATTATTATTTAA
Found at i:8230 original size:24 final size:23
Alignment explanation
Indices: 8203--8248 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
8193 ATTTTTATTT
* *
8203 TTTTTATTTTTTTATTAATTTATA
1 TTTTAATTTTTATATT-ATTTATA
8227 TTTTAATTTTTATATTATTTAT
1 TTTTAATTTTTATATTATTTAT
8249 TTAATTAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTAATTTTTATATTATTTATA
Found at i:16555 original size:23 final size:22
Alignment explanation
Indices: 16520--16562 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
16510 TGTTCCTAAA
*
16520 AAATGAATCTTTACTATGTATG
1 AAATGAATATTTACTATGTATG
16542 AAATAGAATATTTACTATGTA
1 AAAT-GAATATTTACTATGTA
16563 AGTCACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.40
Consensus pattern (22 bp):
AAATGAATATTTACTATGTATG
Found at i:22281 original size:15 final size:17
Alignment explanation
Indices: 22256--22289 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
22246 TAAAGGTCCT
22256 AAATAACTAATAAA-TA
1 AAATAACTAATAAACTA
22272 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
22288 AA
1 AA
22290 CATATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:23791 original size:33 final size:33
Alignment explanation
Indices: 23725--23796 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
23715 TTGTTTGTTT
* *
23725 ATTGCTCAAGATTTTTCGATGAGTCGTTGGTTG
1 ATTGCTCAAGATTTTTCGATGAGTCATTAGTTG
* *
23758 ATTGCTCGAGATTTTTGGATGAG-CTATTAGTTG
1 ATTGCTCAAGATTTTTCGATGAGTC-ATTAGTTG
23791 ATTGCT
1 ATTGCT
23797 TCATATTATG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 1 0.03
33 33 0.97
ACGTcount: A:0.19, C:0.11, G:0.26, T:0.43
Consensus pattern (33 bp):
ATTGCTCAAGATTTTTCGATGAGTCATTAGTTG
Found at i:25527 original size:15 final size:15
Alignment explanation
Indices: 25491--25534 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
25481 ACATATATAT
25491 ACATATATCATCATCA
1 ACAT-TATCATCATCA
*
25507 GCATTATCATCATCA
1 ACATTATCATCATCA
* *
25522 ATATTATTATCAT
1 ACATTATCATCAT
25535 TGTCCCTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 21 0.88
16 3 0.12
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (15 bp):
ACATTATCATCATCA
Found at i:25800 original size:21 final size:22
Alignment explanation
Indices: 25765--25808 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
25755 CACTGAAGCT
25765 CCACATAGAATGTCCCAAAGGA
1 CCACATAGAATGTCCCAAAGGA
*
25787 CCACATAG-ATGTCCCGAAGGA
1 CCACATAGAATGTCCCAAAGGA
25808 C
1 C
25809 AGCGTAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.36, C:0.30, G:0.20, T:0.14
Consensus pattern (22 bp):
CCACATAGAATGTCCCAAAGGA
Found at i:25816 original size:21 final size:21
Alignment explanation
Indices: 25774--25839 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 21
25764 TCCACATAGA
* *
25774 ATGTCCCAAAGGACCA-CATAG
1 ATGTCCCGAAGGA-CAGCGTAG
25795 ATGTCCCGAAGGACAGCGTAG
1 ATGTCCCGAAGGACAGCGTAG
* *
25816 AAATGTCCCGAAAGACCGCGTAG
1 --ATGTCCCGAAGGACAGCGTAG
25839 A
1 A
25840 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
20 2 0.05
21 17 0.45
23 19 0.50
ACGTcount: A:0.35, C:0.26, G:0.26, T:0.14
Consensus pattern (21 bp):
ATGTCCCGAAGGACAGCGTAG
Found at i:25825 original size:23 final size:23
Alignment explanation
Indices: 25795--25840 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
25785 GACCACATAG
*
25795 ATGTCCCGAAGGACAGCGTAGAA
1 ATGTCCCGAAAGACAGCGTAGAA
*
25818 ATGTCCCGAAAGACCGCGTAGAA
1 ATGTCCCGAAAGACAGCGTAGAA
25841 CCCTCGACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.24, G:0.28, T:0.13
Consensus pattern (23 bp):
ATGTCCCGAAAGACAGCGTAGAA
Found at i:31886 original size:28 final size:28
Alignment explanation
Indices: 31846--31900 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
31836 ATTACTTGAA
*
31846 ATATCATCCTATCGGCAGCAGAGATATG
1 ATATCATCCTATCAGCAGCAGAGATATG
* *
31874 ATATCATCCTATCAGTAGCATAGATAT
1 ATATCATCCTATCAGCAGCAGAGATAT
31901 ACAAGCATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (28 bp):
ATATCATCCTATCAGCAGCAGAGATATG
Found at i:36285 original size:13 final size:13
Alignment explanation
Indices: 36285--36363 Score: 80
Period size: 13 Copynumber: 6.3 Consensus size: 13
36275 CCGTTGACCC
36285 GACCCGACCCGTT
1 GACCCGACCCGTT
*
36298 TACCCGACCCGTT
1 GACCCGACCCGTT
36311 GACCCGA-CC--T
1 GACCCGACCCGTT
36321 GACCCGTTGACCC---
1 GACCC---GACCCGTT
36334 GACCCGACCCGTT
1 GACCCGACCCGTT
36347 GACCCGACCCGTT
1 GACCCGACCCGTT
36360 GACC
1 GACC
36364 GTTGACCGGA
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
10 11 0.19
12 2 0.04
13 42 0.74
14 2 0.04
ACGTcount: A:0.16, C:0.47, G:0.22, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:36286 original size:18 final size:18
Alignment explanation
Indices: 36263--36357 Score: 137
Period size: 18 Copynumber: 5.6 Consensus size: 18
36253 ACCGGTCACA
36263 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
36281 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
36298 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
36312 ACCCGACCTGACCCGTTG
1 ACCCGACCCGACCCGTTG
36330 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
36348 ACCCGACCCG
1 ACCCGACCCG
36358 TTGACCGTTG
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
13 12 0.18
18 56 0.82
ACGTcount: A:0.17, C:0.49, G:0.21, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:36306 original size:31 final size:31
Alignment explanation
Indices: 36267--36363 Score: 128
Period size: 31 Copynumber: 3.1 Consensus size: 31
36257 GTCACAACCC
36267 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* *
36298 TACCCGACCCGTTGACCCGACCTGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
36329 GACCCGACCC---GACCCGTTGACCCGACCCGTT
1 GACCCGACCCGTTGACCC---GACCCGACCCGTT
36360 GACC
1 GACC
36364 GTTGACCGGA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
28 5 0.08
31 54 0.92
ACGTcount: A:0.16, C:0.47, G:0.22, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:36334 original size:49 final size:49
Alignment explanation
Indices: 36263--36363 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 49
36253 ACCGGTCACA
*
36263 ACCCGACCCGACCCGTTGACCCGACCCGACCCGTTTACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGACCCGTTGACCCGACCCGTTG
*
36312 ACCCGACCTGACCCGTTGACCCGACCCGACCCGTTGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGACCCGTTGACCCGACCCGTTG
36361 ACC
1 ACC
36364 GTTGACCGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.17, C:0.49, G:0.21, T:0.14
Consensus pattern (49 bp):
ACCCGACCCGACCCGTTGACCCGACCCGACCCGTTGACCCGACCCGTTG
Found at i:37708 original size:18 final size:18
Alignment explanation
Indices: 37682--37717 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
37672 TCGAAATGAC
*
37682 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
37700 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
37718 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:38852 original size:48 final size:48
Alignment explanation
Indices: 38800--38931 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 48
38790 AATATTTTAC
*
38800 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
38848 CTGA-TATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
38896 CTG-TTACTT-GACCTGATTTCTGATATGATACTTGAC
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTTGAC
38932 CTGATTTATA
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
47 5 0.07
48 60 0.87
49 3 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:38938 original size:24 final size:24
Alignment explanation
Indices: 38817--38931 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
38807 TCGATTTGAT
38817 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
38841 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
38865 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
38889 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
38912 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
38932 CTGATTTATA
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:38948 original size:24 final size:24
Alignment explanation
Indices: 38868--38940 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
38858 ACATGGATTC
* * *
38868 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
38892 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
38916 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
38940 T
1 T
38941 ATTTTGATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:41056 original size:13 final size:13
Alignment explanation
Indices: 41056--41134 Score: 80
Period size: 13 Copynumber: 6.3 Consensus size: 13
41046 CCGTTGACCC
41056 GACCCGACCCGTT
1 GACCCGACCCGTT
*
41069 TACCCGACCCGTT
1 GACCCGACCCGTT
41082 GACCCGA-CC--T
1 GACCCGACCCGTT
41092 GACCCGTTGACCC---
1 GACCC---GACCCGTT
41105 GACCCGACCCGTT
1 GACCCGACCCGTT
41118 GACCCGACCCGTT
1 GACCCGACCCGTT
41131 GACC
1 GACC
41135 GTTGACCGGA
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
10 11 0.19
12 2 0.04
13 42 0.74
14 2 0.04
ACGTcount: A:0.16, C:0.47, G:0.22, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:41057 original size:18 final size:18
Alignment explanation
Indices: 41034--41128 Score: 137
Period size: 18 Copynumber: 5.6 Consensus size: 18
41024 ACCGGTCACA
41034 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
41052 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
41069 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
41083 ACCCGACCTGACCCGTTG
1 ACCCGACCCGACCCGTTG
41101 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
41119 ACCCGACCCG
1 ACCCGACCCG
41129 TTGACCGTTG
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
13 12 0.18
18 56 0.82
ACGTcount: A:0.17, C:0.49, G:0.21, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:41077 original size:31 final size:31
Alignment explanation
Indices: 41038--41134 Score: 128
Period size: 31 Copynumber: 3.1 Consensus size: 31
41028 GTCACAACCC
41038 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* *
41069 TACCCGACCCGTTGACCCGACCTGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
41100 GACCCGACCC---GACCCGTTGACCCGACCCGTT
1 GACCCGACCCGTTGACCC---GACCCGACCCGTT
41131 GACC
1 GACC
41135 GTTGACCGGA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
28 5 0.08
31 54 0.92
ACGTcount: A:0.16, C:0.47, G:0.22, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:41105 original size:49 final size:49
Alignment explanation
Indices: 41034--41134 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 49
41024 ACCGGTCACA
*
41034 ACCCGACCCGACCCGTTGACCCGACCCGACCCGTTTACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGACCCGTTGACCCGACCCGTTG
*
41083 ACCCGACCTGACCCGTTGACCCGACCCGACCCGTTGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCGACCCGTTGACCCGACCCGTTG
41132 ACC
1 ACC
41135 GTTGACCGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.17, C:0.49, G:0.21, T:0.14
Consensus pattern (49 bp):
ACCCGACCCGACCCGTTGACCCGACCCGACCCGTTGACCCGACCCGTTG
Found at i:42465 original size:18 final size:18
Alignment explanation
Indices: 42439--42474 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42429 TCGAAATGAC
*
42439 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
42457 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
42475 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:43611 original size:48 final size:48
Alignment explanation
Indices: 43559--43690 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 48
43549 AATATTTTAC
*
43559 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
43607 CTGA-TATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
43655 CTG-TTACTT-GACCTGATTTCTGATATGATACTTGAC
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTTGAC
43691 CTGATTTATA
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
47 5 0.07
48 60 0.87
49 3 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:43697 original size:24 final size:24
Alignment explanation
Indices: 43576--43690 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
43566 TCGATTTGAT
43576 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
43600 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
43624 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
43648 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
43671 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
43691 CTGATTTATA
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:43707 original size:24 final size:24
Alignment explanation
Indices: 43627--43699 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
43617 ACATGGATTC
* * *
43627 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
43651 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
43675 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
43699 T
1 T
43700 ATTTTGATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:45821 original size:26 final size:28
Alignment explanation
Indices: 45778--45830 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
45768 ATTGATTAGA
*
45778 TAATCATTTTAGTCTTTA-TTATTAATAT
1 TAATCATTTTACTCTTTAGTTA-TAATAT
45806 TAAT-ATTTTACT-TTTAGTTATAATA
1 TAATCATTTTACTCTTTAGTTATAATA
45831 ATTTTTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 9 0.39
27 10 0.43
28 4 0.17
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.57
Consensus pattern (28 bp):
TAATCATTTTACTCTTTAGTTATAATAT
Found at i:50675 original size:28 final size:28
Alignment explanation
Indices: 50643--50700 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
50633 ATGTAGCTAA
* *
50643 ATCCTGAGCCTTATTTAATTTAAGGTTC
1 ATCCTGAGCCATATTCAATTTAAGGTTC
50671 ATCCTGAGCCATATTCAATTTAAGGTTC
1 ATCCTGAGCCATATTCAATTTAAGGTTC
50699 AT
1 AT
50701 TGTCGACATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (28 bp):
ATCCTGAGCCATATTCAATTTAAGGTTC
Found at i:51811 original size:16 final size:16
Alignment explanation
Indices: 51788--51831 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
51778 AGCTCATTGT
51788 TATT-TAAAATTTAT-
1 TATTATAAAATTTATA
51802 TATTAATAAAA-TTATA
1 TATT-ATAAAATTTATA
51818 TATTATAAAATTTA
1 TATTATAAAATTTA
51832 ATTTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTATAAAATTTATA
Found at i:52671 original size:2 final size:2
Alignment explanation
Indices: 52664--52721 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
52654 ATATGAAGAA
52664 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52706 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
52722 GGTTAGAGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53229 original size:14 final size:14
Alignment explanation
Indices: 53210--53279 Score: 68
Period size: 14 Copynumber: 4.7 Consensus size: 14
53200 TTGTATCAAC
53210 TTATTAAATTATTA
1 TTATTAAATTATTA
*
53224 TTATTAAATCATTA
1 TTATTAAATTATTA
*
53238 GTAGTTAAAATTTAATTA
1 TTA-TT-AAA-TT-ATTA
* *
53256 TGATTAAATCATTA
1 TTATTAAATTATTA
53270 TTATTAAATT
1 TTATTAAATT
53280 TTACTAAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
14 27 0.61
15 3 0.07
16 6 0.14
17 3 0.07
18 5 0.11
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (14 bp):
TTATTAAATTATTA
Found at i:53262 original size:32 final size:31
Alignment explanation
Indices: 53220--53282 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
53210 TTATTAAATT
*
53220 ATTATTATTAAATCATTAGTAGTTAAAATTTA
1 ATTATGATTAAATCATTAGTA-TTAAAATTTA
* *
53252 ATTATGATTAAATCATTATTATTAAATTTTA
1 ATTATGATTAAATCATTAGTATTAAAATTTA
53283 CTAAATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 9 0.32
32 19 0.68
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (31 bp):
ATTATGATTAAATCATTAGTATTAAAATTTA
Found at i:56880 original size:30 final size:30
Alignment explanation
Indices: 56846--56905 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
56836 GGAAACTGTG
*
56846 TTGAAGACGCCGAGCCCTCCAAGTTTGAAT
1 TTGAAGACGCCGAGACCTCCAAGTTTGAAT
* * *
56876 TTGAATATGCCGAGACCTCCATGTTTGAAT
1 TTGAAGACGCCGAGACCTCCAAGTTTGAAT
56906 GCAAATTATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (30 bp):
TTGAAGACGCCGAGACCTCCAAGTTTGAAT
Found at i:57496 original size:35 final size:35
Alignment explanation
Indices: 57450--57528 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
57440 ACACAGTCAA
57450 CAATTACATTCTAAATCC-CAAATTCCAAAATACTT
1 CAATTACATTCTAAA-CCTCAAATTCCAAAATACTT
*
57485 CAATTACATTCTAAACCTCAAATTCCAAAATATTT
1 CAATTACATTCTAAACCTCAAATTCCAAAATACTT
*
57520 TAATTACAT
1 CAATTACAT
57529 GCCCAACCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
34 2 0.05
35 39 0.95
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (35 bp):
CAATTACATTCTAAACCTCAAATTCCAAAATACTT
Found at i:57543 original size:35 final size:35
Alignment explanation
Indices: 57450--57544 Score: 95
Period size: 35 Copynumber: 2.7 Consensus size: 35
57440 ACACAGTCAA
* *
57450 CAATTACATTCTAAATCC-CAAATTCCAAAATACTT
1 CAATTACATCCCAAA-CCTCAAATTCCAAAATACTT
* * *
57485 CAATTACATTCTAAACCTCAAATTCCAAAATATTT
1 CAATTACATCCCAAACCTCAAATTCCAAAATACTT
* *
57520 TAATTACATGCCCAACCCT-AAATTC
1 CAATTACAT-CCCAAACCTCAAATTC
57545 ATAAATCCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
34 2 0.04
35 45 0.85
36 6 0.11
ACGTcount: A:0.41, C:0.26, G:0.01, T:0.32
Consensus pattern (35 bp):
CAATTACATCCCAAACCTCAAATTCCAAAATACTT
Found at i:58304 original size:91 final size:91
Alignment explanation
Indices: 58203--58386 Score: 350
Period size: 91 Copynumber: 2.0 Consensus size: 91
58193 ATATTATAAT
58203 ATGATAAATATTTATAATTAAATTTAAATAGAAACTCGAAAATTCAATTCAATTTGACTTGATTT
1 ATGATAAATATTTATAATTAAATTTAAATAGAAACTCGAAAATTCAATTCAATTTGACTTGATTT
*
58268 AAATTTTATAAGCTCAAATCGAAAAA
66 AAATTTTATAAACTCAAATCGAAAAA
58294 ATGATAAATATTTATAATTAAATTTAAATAGAAACTCGAAAATTCAATTCAATTTGACTTGATTT
1 ATGATAAATATTTATAATTAAATTTAAATAGAAACTCGAAAATTCAATTCAATTTGACTTGATTT
*
58359 CAATTTTATAAACTCAAATCGAAAAA
66 AAATTTTATAAACTCAAATCGAAAAA
58385 AT
1 AT
58387 TTTGAGTCAA
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.36
Consensus pattern (91 bp):
ATGATAAATATTTATAATTAAATTTAAATAGAAACTCGAAAATTCAATTCAATTTGACTTGATTT
AAATTTTATAAACTCAAATCGAAAAA
Found at i:58630 original size:35 final size:35
Alignment explanation
Indices: 58589--58668 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
58579 TGGGGTTGGT
58589 ATATAATT-AAAGTATTTTGGAATTTGA-GGTTTAGA
1 ATATAATTGAAA-TATTTTGG-ATTTGAGGGTTTAGA
* *
58624 ATATAATTGAAATATTTTGGATTTTAGGGTTTATA
1 ATATAATTGAAATATTTTGGATTTGAGGGTTTAGA
*
58659 ATGTAATTGA
1 ATATAATTGA
58669 TTACTGTGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
34 5 0.12
35 32 0.80
36 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (35 bp):
ATATAATTGAAATATTTTGGATTTGAGGGTTTAGA
Found at i:59540 original size:64 final size:66
Alignment explanation
Indices: 59464--59619 Score: 189
Period size: 65 Copynumber: 2.4 Consensus size: 66
59454 TTGAGGGTGC
* *
59464 ATCGATGCATAAAA-CACATTCGATGTTTTAA-AATAGCA-AGGGTGCATCGATGCATAGCT-TG
1 ATCGGTGCATAAAAGCACATTCGATGTTTTAATAATA-CATAGAGTGCATCGATGCATAG-TATG
59525 TGA
64 TGA
*
59528 ATCGGTGCATAAAATCA-ATTCGATGTTTTAATAATACATAGAGTGCATCGATGCATAGTATGTG
1 ATCGGTGCATAAAAGCACATTCGATGTTTTAATAATACATAGAGTGCATCGATGCATAGTATGTG
*
59592 C
66 A
* * *
59593 ATCTGTACACAAAAGC-CATTCGATGTT
1 ATCGGTGCATAAAAGCACATTCGATGTT
59620 CAATTAAAAC
Statistics
Matches: 80, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
64 30 0.38
65 50 0.62
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (66 bp):
ATCGGTGCATAAAAGCACATTCGATGTTTTAATAATACATAGAGTGCATCGATGCATAGTATGTG
A
Found at i:62190 original size:21 final size:21
Alignment explanation
Indices: 62166--62228 Score: 56
Period size: 24 Copynumber: 2.9 Consensus size: 21
62156 CAGTGCATCG
62166 TCATGATGTATCGATGCACAT
1 TCATGATGTATCGATGCACAT
* *
62187 TCATAGGGATGCATCGATGCACCT
1 TCAT---GATGTATCGATGCACAT
*
62211 TCAT-AGTATATCGATGCA
1 TCATGA-TGTATCGATGCA
62229 TTATGCACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 1 0.03
21 14 0.41
24 19 0.56
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (21 bp):
TCATGATGTATCGATGCACAT
Found at i:62202 original size:24 final size:24
Alignment explanation
Indices: 62170--62216 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
62160 GCATCGTCAT
*
62170 GATGTATCGATGCACATTCATAGG
1 GATGCATCGATGCACATTCATAGG
*
62194 GATGCATCGATGCACCTTCATAG
1 GATGCATCGATGCACATTCATAG
62217 TATATCGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (24 bp):
GATGCATCGATGCACATTCATAGG
Found at i:67583 original size:65 final size:64
Alignment explanation
Indices: 67448--67584 Score: 165
Period size: 64 Copynumber: 2.1 Consensus size: 64
67438 TACATTGAGG
* * *
67448 GTGCATCGATGCATAAAACACATTCGATGTTTTAAAATAGTCGGGGTGCATCGATGCATAGCTT
1 GTGCATCGATGCATAAAACACATTCGATGTTTTAAAATAATCAGAGTGCATCGATGCATAGCTT
*
67512 GTGCATC-AGTGCATAAAATCA-ATTCGATGTTTTAACAATACAT-AGAGTGCATTGATGCATAG
1 GTGCATCGA-TGCATAAAA-CACATTCGATGTTTTAA-AATA-ATCAGAGTGCATCGATGCATAG
67574 -TAT
62 CT-T
67577 GTGCATCG
1 GTGCATCG
67585 GTACACAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
63 1 0.02
64 31 0.49
65 30 0.48
66 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAAAACACATTCGATGTTTTAAAATAATCAGAGTGCATCGATGCATAGCTT
Found at i:69564 original size:24 final size:24
Alignment explanation
Indices: 69537--69583 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
69527 CACCACAGCT
*
69537 CGTATAAATTGCATCGAAGTGCCG
1 CGTATAAATTGCACCGAAGTGCCG
69561 CGTATAAATTGCACCGAAGTGCC
1 CGTATAAATTGCACCGAAGTGCC
69584 ACATAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (24 bp):
CGTATAAATTGCACCGAAGTGCCG
Found at i:69593 original size:24 final size:24
Alignment explanation
Indices: 69542--69593 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
69532 CAGCTCGTAT
* * * *
69542 AAATTGCATCGAAGTGCCGCGTAT
1 AAATTGCACCGAAGTGCCACATAG
69566 AAATTGCACCGAAGTGCCACATAG
1 AAATTGCACCGAAGTGCCACATAG
69590 AAAT
1 AAAT
69594 GTCCCGAAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
AAATTGCACCGAAGTGCCACATAG
Found at i:69612 original size:23 final size:23
Alignment explanation
Indices: 69574--69675 Score: 89
Period size: 23 Copynumber: 4.4 Consensus size: 23
69564 ATAAATTGCA
69574 CCGAAGTG-CCACATAGAAATGTC
1 CCGAAG-GACCACATAGAAATGTC
* * *
69597 CCGAAGGACCATATAGTATTGTC
1 CCGAAGGACCACATAGAAATGTC
* * * *
69620 CCAAAGGACCGCGTAAAAATGTC
1 CCGAAGGACCACATAGAAATGTC
* *
69643 CCGAATGACCACATAGAATTGTC
1 CCGAAGGACCACATAGAAATGTC
* *
69666 CTGAATGACC
1 CCGAAGGACC
69676 GCGTAGAACC
Statistics
Matches: 61, Mismatches: 17, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
22 1 0.02
23 60 0.98
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (23 bp):
CCGAAGGACCACATAGAAATGTC
Found at i:69643 original size:46 final size:46
Alignment explanation
Indices: 69590--69680 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
69580 TGCCACATAG
* *
69590 AAATGTCCCGAAGGACCATATAGTATTGTCCCAAAGGACCGCGTAA
1 AAATGTCCCGAAGGACCACATAGAATTGTCCCAAAGGACCGCGTAA
* ** *
69636 AAATGTCCCGAATGACCACATAGAATTGTCCTGAATGACCGCGTA
1 AAATGTCCCGAAGGACCACATAGAATTGTCCCAAAGGACCGCGTA
69681 GAACCCTCGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (46 bp):
AAATGTCCCGAAGGACCACATAGAATTGTCCCAAAGGACCGCGTAA
Found at i:75665 original size:3 final size:3
Alignment explanation
Indices: 75645--75714 Score: 122
Period size: 3 Copynumber: 23.3 Consensus size: 3
75635 AAAATCCAGG
* *
75645 ATA ATG ATA ATT ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
75693 ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
75715 AGAGAGATTT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:76773 original size:25 final size:25
Alignment explanation
Indices: 76742--76795 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
76732 CCCGAACCCG
*
76742 AAAATATTTTATATATAATTAATAT
1 AAAATATTATATATATAATTAATAT
76767 AAAATATTATATATATAATTAATAT
1 AAAATATTATATATATAATTAATAT
76792 AAAA
1 AAAA
76796 AATATAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AAAATATTATATATATAATTAATAT
Found at i:84404 original size:3 final size:3
Alignment explanation
Indices: 84398--84475 Score: 93
Period size: 3 Copynumber: 25.3 Consensus size: 3
84388 TTTATTTTTT
* **
84398 TAA TAA TAA TATA TAA TAA TAA TAA TAA TAA TAC TTT TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
84444 TAA TAC TAA TATT TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA T
84476 TTTTAAAAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
3 59 0.92
4 5 0.08
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:84480 original size:22 final size:22
Alignment explanation
Indices: 84398--84487 Score: 126
Period size: 22 Copynumber: 4.0 Consensus size: 22
84388 TTTATTTTTT
*
84398 TAATAATAATATATAATAATAA
1 TAATAATAATATTTAATAATAA
84420 TAATAATAATACTTTTAATAATAA
1 TAATAATAATA--TTTAATAATAA
*
84444 TAATACTAATATTTAATAATAA
1 TAATAATAATATTTAATAATAA
* *
84466 TAATAATAATTTTTAAAAATAA
1 TAATAATAATATTTAATAATAA
84488 AATGAAAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
22 41 0.67
24 20 0.33
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TAATAATAATATTTAATAATAA
Found at i:93711 original size:21 final size:21
Alignment explanation
Indices: 93671--93711 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
93661 TGAATTTCTA
* *
93671 TCTTACAAAACTGAATCATCT
1 TCTTAAAAAACTGAACCATCT
*
93692 TCTTAAAAAACTGGACCATC
1 TCTTAAAAAACTGAACCATC
93712 ATCTGGAAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.29
Consensus pattern (21 bp):
TCTTAAAAAACTGAACCATCT
Found at i:98917 original size:19 final size:19
Alignment explanation
Indices: 98893--98936 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
98883 GCCCATATGT
98893 CTTGCCAAAACCGAATGAA
1 CTTGCCAAAACCGAATGAA
*
98912 CTTGCC-ACACCGAATGAA
1 CTTGCCAAAACCGAATGAA
98930 CTTGCCA
1 CTTGCCA
98937 TTTCCAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (19 bp):
CTTGCCAAAACCGAATGAA
Found at i:110183 original size:17 final size:17
Alignment explanation
Indices: 110156--110200 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
110146 TCTGCACAAG
110156 AGAATGTGTCTGCTTTGA
1 AGAA-GTGTCTGCTTTGA
110174 AGAAGTGTCTGCTTTGA
1 AGAAGTGTCTGCTTTGA
110191 AGAAGTGTCT
1 AGAAGTGTCT
110201 TCTCTGCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 23 0.85
18 4 0.15
ACGTcount: A:0.24, C:0.11, G:0.29, T:0.36
Consensus pattern (17 bp):
AGAAGTGTCTGCTTTGA
Found at i:112884 original size:3 final size:3
Alignment explanation
Indices: 112876--112911 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
112866 ATGCATATTA
112876 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
112912 TAAAACTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:135103 original size:26 final size:25
Alignment explanation
Indices: 135055--135103 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
135045 ATTTATATAC
* *
135055 TTTTTAATAAAATTTATATATAATT
1 TTTTTAATAAAATTTAAAGATAATT
*
135080 TTTTTTATAAAATTTAAAAGATAA
1 TTTTTAATAAAATTT-AAAGATAA
135104 ATGGGTAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TTTTTAATAAAATTTAAAGATAATT
Done.