Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019387.1 Corchorus olitorius cultivar O-4 contig19420, 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: 118126
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:4096 original size:12 final size:12
Alignment explanation
Indices: 4079--4103 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4069 AATACTTAAT
4079 AAATAATAATAA
1 AAATAATAATAA
4091 AAATAATAATAA
1 AAATAATAATAA
4103 A
1 A
4104 TATTACAACT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAATAATAA
Found at i:4097 original size:19 final size:19
Alignment explanation
Indices: 4075--4127 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
4065 AATGAATACT
4075 TAATAAATAATAATAAAAA
1 TAATAAATAATAATAAAAA
* * *
4094 TAAT-AATAAATATTACAAC
1 TAATAAAT-AATAATAAAAA
*
4113 TATTAAATAATAATA
1 TAATAAATAATAATA
4128 CCACCTGATG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 3 0.11
19 21 0.78
20 3 0.11
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (19 bp):
TAATAAATAATAATAAAAA
Found at i:22096 original size:40 final size:37
Alignment explanation
Indices: 22037--22113 Score: 102
Period size: 37 Copynumber: 2.0 Consensus size: 37
22027 AAACATTATA
22037 GTGAATAGTGACTGGGGGGGGGACAAAAAGCCAACCCCTC
1 GTGAATAGTGACT--GGGGGGGAC-AAAAGCCAACCCCTC
*
22077 GTGAATAGTGA-TAGTGGGGGACAAAAGCCAACCCCTC
1 GTGAATAGTGACT-GGGGGGGACAAAAGCCAACCCCTC
22114 CCCTCTCCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
37 15 0.43
38 8 0.23
39 1 0.03
40 11 0.31
ACGTcount: A:0.31, C:0.22, G:0.32, T:0.14
Consensus pattern (37 bp):
GTGAATAGTGACTGGGGGGGACAAAAGCCAACCCCTC
Found at i:23038 original size:14 final size:14
Alignment explanation
Indices: 23019--23049 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
23009 AAAATCTTAT
23019 ATTTTTTATAATTA
1 ATTTTTTATAATTA
23033 ATTTTTTATAATTA
1 ATTTTTTATAATTA
23047 ATT
1 ATT
23050 AAGTTTAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTTTTATAATTA
Found at i:24036 original size:26 final size:26
Alignment explanation
Indices: 24007--24056 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
23997 GTTTCTCTGG
24007 TGTTTTAGTTTATATTGCTAAATAAA
1 TGTTTTAGTTTATATTGCTAAATAAA
24033 TGTTTTAGTTTATATTGCTAAATA
1 TGTTTTAGTTTATATTGCTAAATA
24057 TTTAGTCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (26 bp):
TGTTTTAGTTTATATTGCTAAATAAA
Found at i:28313 original size:4 final size:4
Alignment explanation
Indices: 28299--28345 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
28289 TCAGACTTTT
* * *
28299 CTAA GTAA CTAA CTAA CTTAA CTAA CTAA CT-T CCAA CTAA CTAA CTA
1 CTAA CTAA CTAA CTAA C-TAA CTAA CTAA CTAA CTAA CTAA CTAA CTA
28346 TAGTATATTC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
3 1 0.03
4 30 0.86
5 4 0.11
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.28
Consensus pattern (4 bp):
CTAA
Found at i:28322 original size:13 final size:13
Alignment explanation
Indices: 28304--28344 Score: 64
Period size: 13 Copynumber: 3.0 Consensus size: 13
28294 CTTTTCTAAG
28304 TAACTAACTAACT
1 TAACTAACTAACT
28317 TAACTAACTAACT
1 TAACTAACTAACT
28330 TCCAACTAACTAACT
1 T--AACTAACTAACT
28345 ATAGTATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 14 0.54
15 12 0.46
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (13 bp):
TAACTAACTAACT
Found at i:28444 original size:17 final size:16
Alignment explanation
Indices: 28422--28455 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
28412 AAATTGCATA
*
28422 GAAAGGAAGTAGGGAAG
1 GAAAGGAAATA-GGAAG
28439 GAAAGGAAATAGGAAG
1 GAAAGGAAATAGGAAG
28455 G
1 G
28456 GAGGAAATGA
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:0.50, C:0.00, G:0.44, T:0.06
Consensus pattern (16 bp):
GAAAGGAAATAGGAAG
Found at i:39324 original size:12 final size:12
Alignment explanation
Indices: 39307--39331 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39297 CACCCTAATA
39307 TACATATCAATG
1 TACATATCAATG
39319 TACATATCAATG
1 TACATATCAATG
39331 T
1 T
39332 GTTACGTTCC
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TACATATCAATG
Found at i:39777 original size:59 final size:59
Alignment explanation
Indices: 39680--39840 Score: 243
Period size: 59 Copynumber: 2.7 Consensus size: 59
39670 AATACCCCAT
* * *
39680 CACGGTTTTAAAATTTCACCACCTCTCTGTCTACTTACCATCTGAGTCCACTGAT-GACC
1 CACGGTTTTAAAACTCCACCACCTCTCTGTCTACTTACCATCTGAATCCACTGATCG-CC
* * *
39739 CACGATTTTAAAACTCCACCACCTTTCTGTCTACTTACCATCTGAATTCACTGATCGCC
1 CACGGTTTTAAAACTCCACCACCTCTCTGTCTACTTACCATCTGAATCCACTGATCGCC
*
39798 CACGGTTTTAAAACTCCACCACCTCTCTGCCTACTTACCATCT
1 CACGGTTTTAAAACTCCACCACCTCTCTGTCTACTTACCATCT
39841 TCCCCCATCG
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
59 91 0.99
60 1 0.01
ACGTcount: A:0.24, C:0.35, G:0.09, T:0.32
Consensus pattern (59 bp):
CACGGTTTTAAAACTCCACCACCTCTCTGTCTACTTACCATCTGAATCCACTGATCGCC
Found at i:39962 original size:85 final size:84
Alignment explanation
Indices: 39799--40005 Score: 305
Period size: 85 Copynumber: 2.5 Consensus size: 84
39789 CTGATCGCCC
* *
39799 ACGGTTTTAAAACTCCACCACCTCTCTGCCTACTT---A-CCATCTTCCCCCATCGAATATTCCT
1 ACGGTTTTAAAACTCCACCACCTCTCTG-CTACTTACCATCCATCTTCCACCACCGAATATTCCT
39860 TATTATCCTAATACCCCACT
65 TATTATCCTAATACCCCACT
* *
39880 ACGGTTTTAAAACTCCACCACCTCTATGCATACTTACCATCCATCTTCGACCACCGAATATTCCT
1 ACGGTTTTAAAACTCCACCACCTCTCTGC-TACTTACCATCCATCTTCCACCACCGAATATTCCT
*
39945 TATTATCCTTATACCCCACT
65 TATTATCCTAATACCCCACT
*
39965 ACGGTTTTAAAACTCCACCACCCCTCTGTCTACTTACCATC
1 ACGGTTTTAAAACTCCACCACCTCTCTG-CTACTTACCATC
40006 TTCGCCCACT
Statistics
Matches: 113, Mismatches: 7, Indels: 8
0.88 0.05 0.06
Matches are distributed among these distances:
80 1 0.01
81 32 0.28
84 1 0.01
85 78 0.69
86 1 0.01
ACGTcount: A:0.26, C:0.37, G:0.06, T:0.31
Consensus pattern (84 bp):
ACGGTTTTAAAACTCCACCACCTCTCTGCTACTTACCATCCATCTTCCACCACCGAATATTCCTT
ATTATCCTAATACCCCACT
Found at i:40139 original size:139 final size:142
Alignment explanation
Indices: 39878--40152 Score: 421
Period size: 139 Copynumber: 1.9 Consensus size: 142
39868 TAATACCCCA
*
39878 CTACGGTTTTAAAACTCCACCACCTCTATGCATACTTACCATCCATCTTCGACCACCGAATATTC
1 CTACGGTTTTAAAACTCCACCACCTCTATGCATACTT--CATCCATCTTCCACCACCGAATATTC
* **
39943 CTTATTATCCTTATACCCCACTACGGTTTTAAAACTCCACCACCCCTCTGTCTACTTACCATCTT
64 CTTATTATCCTAATACCCCACTACGGTTTTAAAACTCCACCACCCCTCTACCTACTTACCATCTT
40008 CGCCCACTGATCGC
129 CGCCCACTGATCGC
* * *
40022 CTACGG-TTTAAAACTCCACCACCTCTCTGCCTACTT-A-CCATCTTCCCCCACCGAATATTCCT
1 CTACGGTTTTAAAACTCCACCACCTCTATGCATACTTCATCCATCTTCCACCACCGAATATTCCT
* * *
40084 TATTATCCTAATACCCCACTACGTTTTTAAAACTCCACCACCTCTTTACCTACTTACCATCTTCG
66 TATTATCCTAATACCCCACTACGGTTTTAAAACTCCACCACCCCTCTACCTACTTACCATCTTCG
40149 CCCA
131 CCCA
40153 TCGAATATTC
Statistics
Matches: 121, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
139 86 0.71
140 1 0.01
143 28 0.23
144 6 0.05
ACGTcount: A:0.24, C:0.39, G:0.06, T:0.31
Consensus pattern (142 bp):
CTACGGTTTTAAAACTCCACCACCTCTATGCATACTTCATCCATCTTCCACCACCGAATATTCCT
TATTATCCTAATACCCCACTACGGTTTTAAAACTCCACCACCCCTCTACCTACTTACCATCTTCG
CCCACTGATCGC
Found at i:40140 original size:224 final size:221
Alignment explanation
Indices: 39744--40183 Score: 693
Period size: 224 Copynumber: 2.0 Consensus size: 221
39734 TGACCCACGA
** **
39744 TTTTAAAACTCCACCACCTTTCTGTCTACTTACCATCTGAATTCACTGATCGCCCACGGTTTTAA
1 TTTTAAAACTCCACCACCCCTCTGTCTACTTACCATCTGAACCCACTGATCGCCCACGGTTTTAA
*
39809 AACTCCACCACCTCTCTGCCTACTTACCATCTTCCCCCATCGAATATTCCTTATTATCCTAATAC
66 AACTCCACCACCTCTCTGCCTACTTACCATCTTCCCCCACCGAATATTCCTTATTATCCTAATAC
*
39874 CCCACTACGGTTTTAAAACTCCACCACCTCTATGCATACTTACCATCCATCTTCGACCACCGAAT
131 CCCACTACGGTTTTAAAACTCCACCACCTCTATACATACTT---A-CCATCTTCGACCACCGAAT
*
39939 ATTCCTTATTATCCTTATACCCCACTACGG
192 ATTCCTTATTATCCTGATACCCCACTACGG
*** *
39969 TTTTAAAACTCCACCACCCCTCTGTCTACTTACCATCTTCGCCCACTGATCGCCTACGG-TTTAA
1 TTTTAAAACTCCACCACCCCTCTGTCTACTTACCATCTGAACCCACTGATCGCCCACGGTTTTAA
40033 AACTCCACCACCTCTCTGCCTACTTACCATCTTCCCCCACCGAATATTCCTTATTATCCTAATAC
66 AACTCCACCACCTCTCTGCCTACTTACCATCTTCCCCCACCGAATATTCCTTATTATCCTAATAC
* * * * *
40098 CCCACTACGTTTTTAAAACTCCACCACCTCTTTACCTACTTACCATCTTCGCCCATCGAATATTC
131 CCCACTACGGTTTTAAAACTCCACCACCTCTATACATACTTACCATCTTCGACCACCGAATATTC
40163 CTTATTATCCTGATACCCCAC
196 CTTATTATCCTGATACCCCAC
40184 CACGACTTTA
Statistics
Matches: 199, Mismatches: 16, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
220 41 0.21
221 1 0.01
224 106 0.53
225 51 0.26
ACGTcount: A:0.25, C:0.38, G:0.06, T:0.32
Consensus pattern (221 bp):
TTTTAAAACTCCACCACCCCTCTGTCTACTTACCATCTGAACCCACTGATCGCCCACGGTTTTAA
AACTCCACCACCTCTCTGCCTACTTACCATCTTCCCCCACCGAATATTCCTTATTATCCTAATAC
CCCACTACGGTTTTAAAACTCCACCACCTCTATACATACTTACCATCTTCGACCACCGAATATTC
CTTATTATCCTGATACCCCACTACGG
Found at i:40163 original size:81 final size:81
Alignment explanation
Indices: 40028--40183 Score: 267
Period size: 81 Copynumber: 1.9 Consensus size: 81
40018 TCGCCTACGG
*
40028 TTTAAAACTCCACCACCTCTCTGCCTACTTACCATCTTCCCCCACCGAATATTCCTTATTATCCT
1 TTTAAAACTCCACCACCTCTCTACCTACTTACCATCTTCCCCCACCGAATATTCCTTATTATCCT
40093 AATACCCCACTACGTT
66 AATACCCCACTACGTT
* * *
40109 TTTAAAACTCCACCACCTCTTTACCTACTTACCATCTTCGCCCATCGAATATTCCTTATTATCCT
1 TTTAAAACTCCACCACCTCTCTACCTACTTACCATCTTCCCCCACCGAATATTCCTTATTATCCT
*
40174 GATACCCCAC
66 AATACCCCAC
40184 CACGACTTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.25, C:0.38, G:0.04, T:0.33
Consensus pattern (81 bp):
TTTAAAACTCCACCACCTCTCTACCTACTTACCATCTTCCCCCACCGAATATTCCTTATTATCCT
AATACCCCACTACGTT
Found at i:40228 original size:104 final size:102
Alignment explanation
Indices: 40100--40455 Score: 463
Period size: 104 Copynumber: 3.5 Consensus size: 102
40090 CCTAATACCC
* * *
40100 CACTACGTTTTTAAAACTCCACCACCTCTTTACCTACTTACCATCTTCGCCCATCGAATATTCCT
1 CACTACGGTTTTAAAACTCCACCACCTCTCTGCCTACTTACCATCTTCGCCCATCGAATATTCCT
* * *
40165 TATTATCCTGATACCCCACCACGACTTTAAAAAATATCA
66 TATTATCCTAATACCCCACCACG-GTTTTAAAAATA-CA
* *
40204 CACTACGGTTTTAAAACTCCACCACCTCTCTGCTTACTTACCATCTTCGTCCATCGAATATTCCT
1 CACTACGGTTTTAAAACTCCACCACCTCTCTGCCTACTTACCATCTTCGCCCATCGAATATTCCT
* * *
40269 CATCATCCTAATACCCCATCACGGTTTTAAAAATACCA
66 TATTATCCTAATACCCCACCACGGTTTTAAAAATA-CA
* * * *
40307 TACTACGGTTTTAGAACTCCACCACCTCTCTGCC-ACTTACCATCTTCGCTCACCGAATATTCCT
1 CACTACGGTTTTAAAACTCCACCACCTCTCTGCCTACTTACCATCTTCGCCCATCGAATATTCCT
* * *
40371 TATTATCCTAAAACCCCACTA-GGTTTTTAAAATAC-
66 TATTATCCTAATACCCCACCACGGTTTTAAAAATACA
* *
40406 C-CCAC--TTTTAAAACTCCACTACCTCTCTGCCTACTTACCATCTTCGCCCA
1 CACTACGGTTTTAAAACTCCACCACCTCTCTGCCTACTTACCATCTTCGCCCA
40456 CCGATCGCCA
Statistics
Matches: 222, Mismatches: 29, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
96 24 0.11
97 17 0.08
98 3 0.01
100 1 0.00
101 12 0.05
102 43 0.19
103 43 0.19
104 79 0.36
ACGTcount: A:0.28, C:0.35, G:0.06, T:0.31
Consensus pattern (102 bp):
CACTACGGTTTTAAAACTCCACCACCTCTCTGCCTACTTACCATCTTCGCCCATCGAATATTCCT
TATTATCCTAATACCCCACCACGGTTTTAAAAATACA
Found at i:40603 original size:81 final size:81
Alignment explanation
Indices: 40468--40714 Score: 281
Period size: 81 Copynumber: 3.1 Consensus size: 81
40458 GATCGCCACG
* * * * * *
40468 GTTTTAAAACTCCATCACCTCTCTGTGTACTTACTATCTTCGCCCATCGAATATTCCGTATTATC
1 GTTTTAAAACTCCACCACCTCTCTGTCTACTTACCATCCTCCCCCACCGAATATTCCGTATTATC
*
40533 CTAATACTCCACTACA
66 CTAATACCCCACTACA
*
40549 GTTTTAAAACTCCACCACCTCTCTGTCTACTTACCATCCTCCCCCACCGAATATTCCTTATTATC
1 GTTTTAAAACTCCACCACCTCTCTGTCTACTTACCATCCTCCCCCACCGAATATTCCGTATTATC
*
40614 CTAATACCCCACTACG
66 CTAATACCCCACTACA
* * ** * *
40630 GTTTTAAAACTCCACAATCTCTCTACCTGCTTACCAT-CT----TACCGAATATTCC-TAATTAT
1 GTTTTAAAACTCCACCACCTCTCTGTCTACTTACCATCCTCCCCCACCGAATATTCCGT-ATTAT
* * *
40689 CCTGATACCCCACCACG
65 CCTAATACCCCACTACA
40706 GTTTTAAAA
1 GTTTTAAAA
40715 ATATCACACT
Statistics
Matches: 148, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
75 1 0.01
76 41 0.28
80 2 0.01
81 104 0.70
ACGTcount: A:0.27, C:0.34, G:0.06, T:0.33
Consensus pattern (81 bp):
GTTTTAAAACTCCACCACCTCTCTGTCTACTTACCATCCTCCCCCACCGAATATTCCGTATTATC
CTAATACCCCACTACA
Found at i:40743 original size:21 final size:22
Alignment explanation
Indices: 40693--40736 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40683 AATTATCCTG
* *
40693 ATACCCCACCACGGTTTTAAAA
1 ATACCACACTACGGTTTTAAAA
*
40715 ATATCACACTACGGTTTTAAAA
1 ATACCACACTACGGTTTTAAAA
40737 CTCCACAACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (22 bp):
ATACCACACTACGGTTTTAAAA
Found at i:40930 original size:19 final size:19
Alignment explanation
Indices: 40894--40934 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
40884 GTATTATCCT
40894 AATACCCCACTAGGTTTTGAA
1 AATACCCCAC-AGGTTTT-AA
40915 AATACCCCAC-GGTTTTAA
1 AATACCCCACAGGTTTTAA
40933 AA
1 AA
40935 CTCCAATACC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 6 0.30
21 10 0.50
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (19 bp):
AATACCCCACAGGTTTTAA
Found at i:40957 original size:99 final size:97
Alignment explanation
Indices: 40622--40964 Score: 382
Period size: 99 Copynumber: 3.5 Consensus size: 97
40612 TCCTAATACC
* * * *
40622 CCACTACGGTTTTAAAACTCCACAATCTCTCTACCTGCTTACCATCT-T-ACCGAATATTCCTAA
1 CCACTACGGTTTTAAAACTCCACAACCTCTCTGCCTACTTACCATCTGTCACTGAATATTCCT-A
*
40685 TTATCCTGATACCCCACCACGGTTTTAAAAATA
65 TTATCCTAATACCCCACCACGGTTTTAAAAATA
40718 TCACACTACGGTTTTAAAACTCCACAACCTCTCTG----CTTACCATCTTTGTC-CATCGAATAT
1 -C-CACTACGGTTTTAAAACTCCACAACCTCTCTGCCTACTTACCATC--TGTCAC-T-GAATAT
*
40778 TCCTTATCATCCTAATACCCCACCACGGTTTTAAAAATA
60 TCC-TATTATCCTAATACCCCACCACGGTTTTAAAAATA
* *
40817 CCATACTACGGTTTTAGAACTCCACCACCTCTCTGCCTACTTACCATTCTCGCTCACTGAATATT
1 CC--ACTACGGTTTTAAAACTCCACAACCTCTCTGCCTACTTACCA-TCT-G-TCACTGAATATT
* *
40882 CCGTATTATCCTAATACCCCACTA-GGTTTTGAAAATA
61 CC-TATTATCCTAATACCCCACCACGGTTTTAAAAATA
*
40919 CC-CCACGGTTTTAAAACTCCA-ATACCTCTCTGCCTACTTACCATCT
1 CCACTACGGTTTTAAAACTCCACA-ACCTCTCTGCCTACTTACCATCT
40965 TCGCCCACCG
Statistics
Matches: 213, Mismatches: 14, Indels: 37
0.81 0.05 0.14
Matches are distributed among these distances:
94 9 0.04
96 1 0.00
97 4 0.02
98 34 0.16
99 107 0.50
100 1 0.00
102 15 0.07
103 36 0.17
104 5 0.02
105 1 0.00
ACGTcount: A:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (97 bp):
CCACTACGGTTTTAAAACTCCACAACCTCTCTGCCTACTTACCATCTGTCACTGAATATTCCTAT
TATCCTAATACCCCACCACGGTTTTAAAAATA
Found at i:41015 original size:58 final size:58
Alignment explanation
Indices: 40921--41033 Score: 190
Period size: 58 Copynumber: 1.9 Consensus size: 58
40911 TGAAAATACC
*
40921 CCACGGTTTTAAAACTCCAATACCTCTCTGCCTACTTACCATCTTCGCCCACCGATCG
1 CCACGGTTTTAAAACTCCAACACCTCTCTGCCTACTTACCATCTTCGCCCACCGATCG
* **
40979 CCACGGTTTTAAAACTCCACCACCTCTCTGTGTACTTACCATCTTCGCCCACCGA
1 CCACGGTTTTAAAACTCCAACACCTCTCTGCCTACTTACCATCTTCGCCCACCGA
41034 ATATTCCGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.22, C:0.40, G:0.11, T:0.27
Consensus pattern (58 bp):
CCACGGTTTTAAAACTCCAACACCTCTCTGCCTACTTACCATCTTCGCCCACCGATCG
Found at i:41037 original size:516 final size:516
Alignment explanation
Indices: 40028--41110 Score: 1789
Period size: 516 Copynumber: 2.1 Consensus size: 516
40018 TCGCCTACGG
40028 TTTAAAACTCCACCACCTCTCTGCCTACTTACCATCTTCCCCCACCGAATATTCCTTATTATCCT
1 TTTAAAACTCCACCACCTCTCTGCCTACTTACCATCTTCCCCCACCGAATATTCCTTATTATCCT
* * * *
40093 AATACCCCACTACGTTTTTAAAACTCCACCACCTCTTTACCTACTTACCATCTTCGCCCATCGAA
66 AATACCCCACTACGGTTTTAAAACTCCACAACCTCTCTACCTACTTACCATCTT----CACCGAA
*
40158 TATTCCTTATTATCCTGATACCCCACCACGACTTTAAAAAATATCACACTACGGTTTTAAAACTC
127 TATTCCTAATTATCCTGATACCCCACCACGACTTTAAAAAATATCACACTACGGTTTTAAAACTC
* *
40223 CACCACCTCTCTGCTTACTTACCATCTTCGTCCATCGAATATTCCTCATCATCCTAATACCCCAT
192 CACAACCTCTCTG--T-CTTACCATCTTCGTCCATCGAATATTCCTCATCATCCTAATACCCCAC
40288 CACGGTTTTAAAAATACCATACTACGGTTTTAGAACTCCACCACCTCTCTGCCACTTACCATCTT
254 CACGGTTTTAAAAATACCATACTACGGTTTTAGAACTCCACCACCTCTCTGCCACTTACCATCTT
* *
40353 CGCTCACCGAATATTCCTTATTATCCTAAAACCCCACTAGGTTTTTAAAATACCCCACTTTTAAA
319 CGCTCACCGAATATTCCGTATTATCCTAAAACCCCACTAGGTTTTGAAAATACCCCACTTTTAAA
* *
40418 ACTCCACTACCTCTCTGCCTACTTACCATCTTCGCCCACCGATCGCCACGGTTTTAAAACTCCAT
384 ACTCCAATACCTCTCTGCCTACTTACCATCTTCGCCCACCGATCGCCACGGTTTTAAAACTCCAC
* *
40483 CACCTCTCTGTGTACTTACTATCTTCGCCCATCGAATATTCCGTATTATCCTAATACTCCACTAC
449 CACCTCTCTGTGTACTTACCATCTTCGCCCACCGAATATTCCGTATTATCCTAATACTCCACTAC
40548 AGT
514 AGT
* *
40551 TTTAAAACTCCACCACCTCTCTGTCTACTTACCATCCTCCCCCACCGAATATTCCTTATTATCCT
1 TTTAAAACTCCACCACCTCTCTGCCTACTTACCATCTTCCCCCACCGAATATTCCTTATTATCCT
* *
40616 AATACCCCACTACGGTTTTAAAACTCCACAATCTCTCTACCTGCTTACCATCTT-ACCGAATATT
66 AATACCCCACTACGGTTTTAAAACTCCACAACCTCTCTACCTACTTACCATCTTCACCGAATATT
* *
40680 CCTAATTATCCTGATACCCCACCACG-GTTTTAAAAATATCACACTACGGTTTTAAAACTCCACA
131 CCTAATTATCCTGATACCCCACCACGACTTTAAAAAATATCACACTACGGTTTTAAAACTCCACA
* *
40744 ACCTCTCTG-CTTACCATCTTTGTCCATCGAATATTCCTTATCATCCTAATACCCCACCACGGTT
196 ACCTCTCTGTCTTACCATCTTCGTCCATCGAATATTCCTCATCATCCTAATACCCCACCACGGTT
40808 TTAAAAATACCATACTACGGTTTTAGAACTCCACCACCTCTCTGCCTACTTACCAT-TCTCGCTC
261 TTAAAAATACCATACTACGGTTTTAGAACTCCACCACCTCTCTGCC-ACTTACCATCT-TCGCTC
* *
40872 ACTGAATATTCCGTATTATCCTAATACCCCACTAGGTTTTGAAAATACCCCACGGTTTTAAAACT
324 ACCGAATATTCCGTATTATCCTAAAACCCCACTAGGTTTTGAAAATACCCCAC--TTTTAAAACT
40937 CCAATACCTCTCTGCCTACTTACCATCTTCGCCCACCGATCGCCACGGTTTTAAAACTCCACCAC
387 CCAATACCTCTCTGCCTACTTACCATCTTCGCCCACCGATCGCCACGGTTTTAAAACTCCACCAC
* *
41002 CTCTCTGTGTACTTACCATCTTCGCCCACCGAATATTCCGTATTATCCTAATACTCCATTACGGT
452 CTCTCTGTGTACTTACCATCTTCGCCCACCGAATATTCCGTATTATCCTAATACTCCACTACAGT
* *
41067 TTTAAAACTCCACC-CCTCTCTACCTACTTACCATCTTCGCCCAC
1 TTTAAAACTCCACCACCTCTCTGCCTACTTACCATCTTCCCCCAC
41111 TGATCGCCCA
Statistics
Matches: 527, Mismatches: 29, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
513 99 0.19
514 64 0.12
515 26 0.05
516 148 0.28
517 44 0.08
518 34 0.06
523 112 0.21
ACGTcount: A:0.26, C:0.35, G:0.07, T:0.31
Consensus pattern (516 bp):
TTTAAAACTCCACCACCTCTCTGCCTACTTACCATCTTCCCCCACCGAATATTCCTTATTATCCT
AATACCCCACTACGGTTTTAAAACTCCACAACCTCTCTACCTACTTACCATCTTCACCGAATATT
CCTAATTATCCTGATACCCCACCACGACTTTAAAAAATATCACACTACGGTTTTAAAACTCCACA
ACCTCTCTGTCTTACCATCTTCGTCCATCGAATATTCCTCATCATCCTAATACCCCACCACGGTT
TTAAAAATACCATACTACGGTTTTAGAACTCCACCACCTCTCTGCCACTTACCATCTTCGCTCAC
CGAATATTCCGTATTATCCTAAAACCCCACTAGGTTTTGAAAATACCCCACTTTTAAAACTCCAA
TACCTCTCTGCCTACTTACCATCTTCGCCCACCGATCGCCACGGTTTTAAAACTCCACCACCTCT
CTGTGTACTTACCATCTTCGCCCACCGAATATTCCGTATTATCCTAATACTCCACTACAGT
Found at i:41175 original size:139 final size:137
Alignment explanation
Indices: 40923--41252 Score: 480
Period size: 139 Copynumber: 2.4 Consensus size: 137
40913 AAAATACCCC
** *
40923 ACGGTTTTAAAACTCCAATACCTCTCTGCCTACTTACCATCTTCGCCCACCGATCGCCACGGTTT
1 ACGGTTTTAAAACTCC-ACCCCTCTCT-CCTACTTACCATCTTCGCCCACCGATCGCCACGATTT
**
40988 TAAAACTCCACCACCTCTCTGTGTACTTACCATCTTCGCCCACCGAATATTCCGTATTATCCTAA
64 TAAAACTCCACCACCTCTCTGCCTACTTACCATCTTCGCCCACCGAATATTCCGTATTATCCTAA
*
41053 TACTCCATT
129 TACCCCATT
*
41062 ACGGTTTTAAAACTCCACCCCTCTCTACCTACTTACCATCTTCGCCCACTGATCGCCCACGATTT
1 ACGGTTTTAAAACTCCACCCCTCTCT-CCTACTTACCATCTTCGCCCACCGATCG-CCACGATTT
* ** *
41127 TAAAACTCCACCACCTTTCTGCCTACTTACCATCTTCGCCCATTGAATATTCCTTATTATCCTAA
64 TAAAACTCCACCACCTCTCTGCCTACTTACCATCTTCGCCCACCGAATATTCCGTATTATCCTAA
41192 TACCCCATT
129 TACCCCATT
* * * *
41201 ACGGTTTTAAAACTCTACCACCTCTCTGCTACTTATCATCTTTGCCCACCGA
1 ACGGTTTTAAAACTCCACC-CCTCTCTCCTACTTACCATCTTCGCCCACCGA
41253 ATATTCCTTA
Statistics
Matches: 172, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
138 35 0.20
139 130 0.76
140 7 0.04
ACGTcount: A:0.24, C:0.36, G:0.08, T:0.32
Consensus pattern (137 bp):
ACGGTTTTAAAACTCCACCCCTCTCTCCTACTTACCATCTTCGCCCACCGATCGCCACGATTTTA
AAACTCCACCACCTCTCTGCCTACTTACCATCTTCGCCCACCGAATATTCCGTATTATCCTAATA
CCCCATT
Found at i:53202 original size:33 final size:34
Alignment explanation
Indices: 53139--53205 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
53129 AAAATGGAAT
*
53139 TATTGAAGATTTGGGGTGGCTTTTGGGGTGATTC
1 TATTAAAGATTTGGGGTGGCTTTTGGGGTGATTC
53173 TATTAAAGATTTGGGGTGGC-TTTGGGGTGATTC
1 TATTAAAGATTTGGGGTGGCTTTTGGGGTGATTC
53206 CTGGATGTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 13 0.41
34 19 0.59
ACGTcount: A:0.16, C:0.06, G:0.37, T:0.40
Consensus pattern (34 bp):
TATTAAAGATTTGGGGTGGCTTTTGGGGTGATTC
Found at i:65552 original size:38 final size:38
Alignment explanation
Indices: 65509--65624 Score: 232
Period size: 38 Copynumber: 3.1 Consensus size: 38
65499 TCCATGATTA
65509 TATGCAAGATAATAGCCTGTTTGTTTTCCTTGATTGTT
1 TATGCAAGATAATAGCCTGTTTGTTTTCCTTGATTGTT
65547 TATGCAAGATAATAGCCTGTTTGTTTTCCTTGATTGTT
1 TATGCAAGATAATAGCCTGTTTGTTTTCCTTGATTGTT
65585 TATGCAAGATAATAGCCTGTTTGTTTTCCTTGATTGTT
1 TATGCAAGATAATAGCCTGTTTGTTTTCCTTGATTGTT
65623 TA
1 TA
65625 GGTTCTCATT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 78 1.00
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (38 bp):
TATGCAAGATAATAGCCTGTTTGTTTTCCTTGATTGTT
Found at i:69017 original size:58 final size:58
Alignment explanation
Indices: 68934--69048 Score: 221
Period size: 58 Copynumber: 2.0 Consensus size: 58
68924 AAACTTCTTG
68934 TAGTATTTGATTATACCCAATCCTCATCGATGAATGCATTTATCTTTTGCATCTTGTA
1 TAGTATTTGATTATACCCAATCCTCATCGATGAATGCATTTATCTTTTGCATCTTGTA
*
68992 TAGTATTTGATTATACCCAATCCTCATGGATGAATGCATTTATCTTTTGCATCTTGT
1 TAGTATTTGATTATACCCAATCCTCATCGATGAATGCATTTATCTTTTGCATCTTGT
69049 TTGACCATTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.43
Consensus pattern (58 bp):
TAGTATTTGATTATACCCAATCCTCATCGATGAATGCATTTATCTTTTGCATCTTGTA
Found at i:77970 original size:437 final size:435
Alignment explanation
Indices: 77117--78059 Score: 1176
Period size: 437 Copynumber: 2.1 Consensus size: 435
77107 AATTAACTGG
* * *
77117 AGTTGTAGATCATAAAATTACCTTTTAATAGACACTTGAATTACCTTAATTGGACAAATAGAACA
1 AGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATAACCTTAATCGGACAAATAGAACA
* *
77182 GAGAAAATAAAAAATGAAGCGTTAAATCGAGTAAGATAGAATTTGTAAAGAACTAAGTAGCATAA
66 AAGAAAATAAAAAATGAAACGTTAAAT--AGTAAGATAGAATTTGTAAAGAACTAAGTAG-----
* * * *
77247 AATATATAAAATAGAAAAGTATGAGAGTCATTTGATAACTAATTCAAATAAGAAATTATTTCTTA
124 ---ATATAAAATAGAAAAATATGAGAGTCATTTGATAAATAATCCAAATAAGAAAATATTTCTTA
* * *
77312 ATGGATATCTTGAAACATAAAGATTCCCTTTTGAACCCTTCATGAAACTCGTAGCTCAAATTAAC
186 ATGGAGATCTTGAAACATAAAGACTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTAAC
* * * * * *
77377 TTTTGGATTCTTCATGAAATTCGTAGATCATACAATAACCTTTTAACCGACACTTGAATAACTTT
251 TTTCGGATTCTTCAAGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTC
* * * * * *
77442 AATCGGACATGTGGATCGAAAATTATATGGTATTAAATAGACCAACAATCGAAACGACCAAATTT
316 AATCGGACATGTGGATCAAAAATTATACGATATTAAATAGACCAACAATCAAAACGACAAAATTC
* *
77507 AGGAAGCATTTTTTTGAATTAAAACATAAAAATTTG-CTTTTGAGTCCTTCATGAA
381 AGGAAACATTTTTTTGAATCAAAACATAAAAA-TTGACTTTTGAGTCCTTCATGAA
* * *
77562 AGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATAAACTTAATCAGACAAATAGAACA
1 AGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATAACCTTAATCGGACAAATAGAACA
* * * *
77627 AAGAATACTAATCAAATTTTAAACGTTAGAT-G-AAGATAGAATTTGTAAAGAACTAAGTAG-TA
66 AAGAA-AATAA--AAA-ATGAAACGTTAAATAGTAAGATAGAATTTGTAAAGAACTAAGTAGATA
* * * * * *
77689 TAGAGTAGAAAAATATGAGGGTTATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAG
127 TAAAATAGAAAAATATGAGAGTCATTTGATAAATAATCCAAATAAGAAAATATTTCTTAATGGAG
* * * * *
77754 GTCTTGAAGCATAAATACTCCCTTTTGAGCCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCG
192 ATCTTGAAACATAAAGACTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAA-TTAACTTTCG
* * *
77819 GGTTCTTTAAGAAAGTCGTAAATCATGCAATAACCTTTTAACCGACACTTCAATAACTTCAATCG
256 GATTCTTCAAGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCG
* * ** * *
77884 GATATGTGGA-CAACAAATTATACGATATTAAATTGACCGGCAATCAAAACTACAAAATTCCGGA
321 GACATGTGGATCAA-AAATTATACGATATTAAATAGACCAACAATCAAAACGACAAAATTCAGGA
* *
77948 AACATTTTTTTGAATCAAAACATTAAAATTGACTTTTGAGTTCTTCATGAA
385 AACATTTTTTTGAATCAAAACATAAAAATTGACTTTTGAGTCCTTCATGAA
* * *
77999 AATTGTAGATCATGAAATTACCTTTTAATAAACACTTGAATCACCTTAATCGGACAAATAG
1 AGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATAACCTTAATCGGACAAATAG
78060 GGGAAAAAAA
Statistics
Matches: 430, Mismatches: 61, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
436 109 0.25
437 212 0.49
445 91 0.21
446 5 0.01
448 3 0.01
449 10 0.02
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (435 bp):
AGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATAACCTTAATCGGACAAATAGAACA
AAGAAAATAAAAAATGAAACGTTAAATAGTAAGATAGAATTTGTAAAGAACTAAGTAGATATAAA
ATAGAAAAATATGAGAGTCATTTGATAAATAATCCAAATAAGAAAATATTTCTTAATGGAGATCT
TGAAACATAAAGACTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCGGATTC
TTCAAGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCAATCGGACAT
GTGGATCAAAAATTATACGATATTAAATAGACCAACAATCAAAACGACAAAATTCAGGAAACATT
TTTTTGAATCAAAACATAAAAATTGACTTTTGAGTCCTTCATGAA
Found at i:78691 original size:135 final size:133
Alignment explanation
Indices: 78412--78715 Score: 418
Period size: 135 Copynumber: 2.3 Consensus size: 133
78402 TTCGAATCTA
* *
78412 TAGTCGCCGCCCATTGATTTATTTGA---CT-ATTCGAGTCTAGATTAGTCGCCACCTATGATTC
1 TAGTCGCCTCCCATTGATTTATTTGATTTCTGATTGGAGTCTAGATTAGTCGCCACCTATGATTC
*
78473 ATTTGACTGTCGTCTATCTGATATGGACAGAAATGAATATTGATTTATTTGACTATTCGACTCCA
66 ATTTGACTGTCGTCTATCTGATATGGACAGAAATGAATATTGATTCATTTGACTATTCGACTCCA
78538 GAT
131 GAT
* * * *
78541 TAGTAGCCTCCCATTGATTTATTTGATTGTCTGATGTGGAGTGTAGATTAGTTGCTACCTATGAT
1 TAGTCGCCTCCCATTGATTTATTTGATT-TCTGAT-TGGAGTCTAGATTAGTCGCCACCTATGAT
* * * * * *
78606 TCATTTGACTGTCGTCTGTTTGATATGGATAGACATGGATATTGATTCATTTGACTATTTGACTC
64 TCATTTGACTGTCGTCTATCTGATATGGACAGAAATGAATATTGATTCATTTGACTATTCGACTC
*
78671 TAGAT
129 CAGAT
78676 TAGTCGCCTCCCATTGATTTATTTGATTCTCTGATATGGA
1 TAGTCGCCTCCCATTGATTTATTTGATT-TCTGAT-TGGA
78716 TATGGATTCA
Statistics
Matches: 152, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
129 24 0.16
133 2 0.01
134 2 0.01
135 124 0.82
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (133 bp):
TAGTCGCCTCCCATTGATTTATTTGATTTCTGATTGGAGTCTAGATTAGTCGCCACCTATGATTC
ATTTGACTGTCGTCTATCTGATATGGACAGAAATGAATATTGATTCATTTGACTATTCGACTCCA
GAT
Found at i:78806 original size:11 final size:11
Alignment explanation
Indices: 78790--78824 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
78780 TTTTTCTGTT
78790 TTTTGTTTTTG
1 TTTTGTTTTTG
*
78801 TTTTGTTTTCG
1 TTTTGTTTTTG
78812 TTTTGTTTTTG
1 TTTTGTTTTTG
78823 TT
1 TT
78825 GCGCTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:82495 original size:6 final size:6
Alignment explanation
Indices: 82455--82537 Score: 91
Period size: 6 Copynumber: 13.5 Consensus size: 6
82445 GAACGCAAAC
*
82455 AAACAA AAAAAA AAACAA ATATGTACAA AAA-AA AAACAA AAA-ACA AAAC-A
1 AAACAA AAACAA AAACAA A-A---ACAA AAACAA AAACAA AAACA-A AAACAA
82505 AAACAA AAACAA AAACAA AAACAA AAACAA AAA
1 AAACAA AAACAA AAACAA AAACAA AAACAA AAA
82538 AAGAACTTTT
Statistics
Matches: 67, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
5 11 0.16
6 49 0.73
7 1 0.01
9 1 0.01
10 5 0.07
ACGTcount: A:0.82, C:0.13, G:0.01, T:0.04
Consensus pattern (6 bp):
AAACAA
Found at i:82505 original size:23 final size:23
Alignment explanation
Indices: 82451--82537 Score: 88
Period size: 23 Copynumber: 3.6 Consensus size: 23
82441 ACCAGAACGC
*
82451 AAACAAACAAAAAA-AAAAACAA
1 AAACAAAAAAAAAACAAAAACAA
82473 ATATGTACAAAAAAAAAACAAAAA-ACA
1 A-A---ACAAAAAAAAAACAAAAACA-A
*
82500 AAACAAAACAAAAACAAAAACAA
1 AAACAAAAAAAAAACAAAAACAA
82523 AAACAAAAACAAAAA
1 AAACAAAAA-AAAAA
82538 AAGAACTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
22 1 0.02
23 27 0.50
24 6 0.11
26 13 0.24
27 7 0.13
ACGTcount: A:0.82, C:0.14, G:0.01, T:0.03
Consensus pattern (23 bp):
AAACAAAAAAAAAACAAAAACAA
Found at i:85802 original size:69 final size:69
Alignment explanation
Indices: 85726--85863 Score: 204
Period size: 69 Copynumber: 2.0 Consensus size: 69
85716 AGAATCTGAA
85726 AACAAATATCCACTTCAGCAATAAATATGTGAAAAGTTCAGTATAAGAAAGAAAGAAACAGACAT
1 AACAAATATCCACTTCAGCAATAAATATGTGAAAAGTTCAGTATAAGAAAGAAAGAAACAGACAT
85791 TTGG
66 TTGG
*** * * ** *
85795 AACAAATATTTGCTTTAGCAGTAAATATGTGAAAAGTTCAGTATTTGAAAGAAAGAAACAGATAT
1 AACAAATATCCACTTCAGCAATAAATATGTGAAAAGTTCAGTATAAGAAAGAAAGAAACAGACAT
85860 TTGG
66 TTGG
85864 GACAGCTCCA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.26
Consensus pattern (69 bp):
AACAAATATCCACTTCAGCAATAAATATGTGAAAAGTTCAGTATAAGAAAGAAAGAAACAGACAT
TTGG
Found at i:93058 original size:4 final size:4
Alignment explanation
Indices: 93049--93079 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
93039 ATAAAAATTA
93049 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
93080 AACAAGCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:96667 original size:25 final size:25
Alignment explanation
Indices: 96638--96686 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
96628 ATGTAGTTTG
*
96638 ATAATAGAGTGCTGAAATTTTATTA
1 ATAATAGAGTACTGAAATTTTATTA
*
96663 ATAATAGAGTACTGAATTTTTATT
1 ATAATAGAGTACTGAAATTTTATT
96687 TCCAATAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.43
Consensus pattern (25 bp):
ATAATAGAGTACTGAAATTTTATTA
Found at i:96756 original size:11 final size:12
Alignment explanation
Indices: 96740--96768 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
96730 TAGATCCCTG
96740 AAGAAATTGT-A
1 AAGAAATTGTAA
96751 AAGAAATTGTAA
1 AAGAAATTGTAA
96763 AAGAAA
1 AAGAAA
96769 AGAGAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.21
Consensus pattern (12 bp):
AAGAAATTGTAA
Found at i:101023 original size:45 final size:45
Alignment explanation
Indices: 100974--101063 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
100964 AATAAAAGAT
100974 ACAGAATAAAGAAAAGGCCTACTGTTTCCATTACTAGGAAATATA
1 ACAGAATAAAGAAAAGGCCTACTGTTTCCATTACTAGGAAATATA
* *
101019 ACAGAATTAAGAAAAGGCCTACTGTTTCCGTTACTAGGAAATATA
1 ACAGAATAAAGAAAAGGCCTACTGTTTCCATTACTAGGAAATATA
101064 CTCACAACTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.26
Consensus pattern (45 bp):
ACAGAATAAAGAAAAGGCCTACTGTTTCCATTACTAGGAAATATA
Found at i:102045 original size:2 final size:2
Alignment explanation
Indices: 102038--102065 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
102028 AAAATGAAAC
102038 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
102066 ATTCTAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:102992 original size:8 final size:8
Alignment explanation
Indices: 102941--102994 Score: 54
Period size: 8 Copynumber: 6.8 Consensus size: 8
102931 CCAGAAATAT
102941 ATATATAC
1 ATATATAC
* *
102949 ATATACAT
1 ATATATAC
* *
102957 ATACAAAC
1 ATATATAC
*
102965 ATACATAC
1 ATATATAC
*
102973 ATAAATAC
1 ATATATAC
102981 ATATATAC
1 ATATATAC
102989 ATATAT
1 ATATAT
102995 CACTTTCACT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (8 bp):
ATATATAC
Found at i:111577 original size:25 final size:25
Alignment explanation
Indices: 111548--111598 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
111538 GGCGTCATCG
*
111548 TGCTTATTCTATTCCATTATAATTC
1 TGCTTATTCTATTCCATAATAATTC
111573 TGCTTATTCTATTCCATAATAATTC
1 TGCTTATTCTATTCCATAATAATTC
111598 T
1 T
111599 ATTATTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.20, G:0.04, T:0.51
Consensus pattern (25 bp):
TGCTTATTCTATTCCATAATAATTC
Found at i:112639 original size:21 final size:21
Alignment explanation
Indices: 112615--112664 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
112605 GAGGAGGAGG
112615 AGGG-AAGAGGAAGAGAGAGAA
1 AGGGAAAGA-GAAGAGAGAGAA
* *
112636 AGGGAAAGAGAAGAGAGGGAG
1 AGGGAAAGAGAAGAGAGAGAA
112657 AGGGAAAG
1 AGGGAAAG
112665 GGAAAGGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (21 bp):
AGGGAAAGAGAAGAGAGAGAA
Found at i:112648 original size:27 final size:27
Alignment explanation
Indices: 112618--112670 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
112608 GAGGAGGAGG
112618 GAAGAG-GAAGAGAGAGAAAGGGAAAGA
1 GAAGAGAG-AGAGAGAGAAAGGGAAAGA
* *
112645 GAAGAGAGGGAGAGGGAAAGGGAAAG
1 GAAGAGAGAGAGAGAGAAAGGGAAAG
112671 GGATGATTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (27 bp):
GAAGAGAGAGAGAGAGAAAGGGAAAGA
Done.