Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011211.1 Corchorus capsularis cultivar CVL-1 contig11232, 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: 53186
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:125 original size:12 final size:12
Alignment explanation
Indices: 76--126 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
66 AAGACGGACG
*
76 ATCTTCTTCATC
1 ATCTTCCTCATC
*
88 ATCATCCTCAATC
1 ATCTTCCTC-ATC
* *
101 -TCTTCATCGTC
1 ATCTTCCTCATC
112 ATCTTCCTCATC
1 ATCTTCCTCATC
124 ATC
1 ATC
127 CCCCTCATCG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
11 2 0.07
12 25 0.83
13 3 0.10
ACGTcount: A:0.20, C:0.37, G:0.02, T:0.41
Consensus pattern (12 bp):
ATCTTCCTCATC
Found at i:3818 original size:23 final size:23
Alignment explanation
Indices: 3770--3819 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
3760 ATTCAGTATG
* * *
3770 CATCACTCATAAGCACATATATA
1 CATCACTCACAAGCACATAGACA
3793 CATCACTCACAAGCACATAGACA
1 CATCACTCACAAGCACATAGACA
3816 CATC
1 CATC
3820 GCAAATAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.32, G:0.06, T:0.20
Consensus pattern (23 bp):
CATCACTCACAAGCACATAGACA
Found at i:6202 original size:40 final size:41
Alignment explanation
Indices: 6064--6271 Score: 267
Period size: 41 Copynumber: 5.1 Consensus size: 41
6054 CATGTGCGTT
* *
6064 AAGCAAACACAGTCAAAGTCTTAATTCAGGGTAATTAAGAA
1 AAGCAAACACAATCAAGGTCTTAATTCAGGGTAATTAAGAA
* *
6105 AAGTAAACACAATTAAGGTCTTAATTCAGGGTAATTAAGAA
1 AAGCAAACACAATCAAGGTCTTAATTCAGGGTAATTAAGAA
*
6146 AAGCAAACACAGTCAAGGTCTTAATTCAGGGTAATTAAG-A
1 AAGCAAACACAATCAAGGTCTTAATTCAGGGTAATTAAGAA
*
6186 AAGCAAACACAATCAAGGTCTTAATTCAAGGTAATTAAG-A
1 AAGCAAACACAATCAAGGTCTTAATTCAGGGTAATTAAGAA
* * * * * * * * *
6226 GAGTAAAGACAAGCAAAGACTTGATTCAGGGTAATCAAGTA
1 AAGCAAACACAATCAAGGTCTTAATTCAGGGTAATTAAGAA
6267 AAGCA
1 AAGCA
6272 GGTAAAAGAC
Statistics
Matches: 146, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
40 69 0.47
41 77 0.53
ACGTcount: A:0.46, C:0.13, G:0.19, T:0.22
Consensus pattern (41 bp):
AAGCAAACACAATCAAGGTCTTAATTCAGGGTAATTAAGAA
Found at i:6270 original size:81 final size:81
Alignment explanation
Indices: 6064--6271 Score: 285
Period size: 81 Copynumber: 2.6 Consensus size: 81
6054 CATGTGCGTT
* *
6064 AAGCAAACACAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAATTAAGGTCTTAA
1 AAGCAAACACAGTCAAAGTCTTAATTCAGGGTAATTAAG-AAAGCAAACACAATCAAGGTCTTAA
*
6129 TTCAGGGTAATTAAGAA
65 TTCAAGGTAATTAAGAA
*
6146 AAGCAAACACAGTCAAGGTCTTAATTCAGGGTAATTAAGAAAGCAAACACAATCAAGGTCTTAAT
1 AAGCAAACACAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAGCAAACACAATCAAGGTCTTAAT
6211 TCAAGGTAATTAAG-A
66 TCAAGGTAATTAAGAA
* * * * * *
6226 GAGTAAAGACAAG-CAAAGACTTGATTCAGGGTAATCAAGTAAAGCA
1 AAGCAAACAC-AGTCAAAGTCTTAATTCAGGGTAATTAAG-AAAGCA
6272 GGTAAAAGAC
Statistics
Matches: 113, Mismatches: 11, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
80 30 0.27
81 45 0.40
82 38 0.34
ACGTcount: A:0.46, C:0.13, G:0.19, T:0.22
Consensus pattern (81 bp):
AAGCAAACACAGTCAAAGTCTTAATTCAGGGTAATTAAGAAAGCAAACACAATCAAGGTCTTAAT
TCAAGGTAATTAAGAA
Found at i:6320 original size:37 final size:37
Alignment explanation
Indices: 6083--6415 Score: 212
Period size: 37 Copynumber: 8.6 Consensus size: 37
6073 CAGTCAAAGT
* * *
6083 CTTAATTCAGGGTAATTAAG-AAAAGTAAACACAATTAAGGT
1 CTTAATTCAGGGTAATTAAGTAAAAG--CA-ATAA--AAGGA
* *
6124 CTTAATTCAGGGTAATTAAG-AAAAGCAAACACAGTCAAGGT
1 CTTAATTCAGGGTAATTAAGTAAAAGC-AATA-A---AAGGA
* *
6165 CTTAATTCAGGGTAATTAAG--AAAGCAAACACAATCAAGGT
1 CTTAATTCAGGGTAATTAAGTAAAAGC--A-ATAA--AAGGA
* * **
6205 CTTAATTCAAGGTAATTAAGAGAGTAAAGACAAGCAAA-GA
1 CTTAATTCAGGGTAATTAAG-TA--AAAG-CAATAAAAGGA
* * *
6245 CTTGATTCAGGGTAATCAAGT-AAAGCAGGTAAAA-GA
1 CTTAATTCAGGGTAATTAAGTAAAAGCA-ATAAAAGGA
*
6281 CTTAATTCAGGGTAATTAAGTAAAAGCAGTAAAAGGA
1 CTTAATTCAGGGTAATTAAGTAAAAGCAATAAAAGGA
* * * **
6318 CTTAATTTAGGATAATTAAGTAAATGCAATAAAAATA
1 CTTAATTCAGGGTAATTAAGTAAAAGCAATAAAAGGA
* *
6355 CTTAATTCAGGGTAATTAAGTAAAAGCAACAAAAGGG
1 CTTAATTCAGGGTAATTAAGTAAAAGCAATAAAAGGA
* * *
6392 CTTAATTTAGGGAAATTGAGTAAA
1 CTTAATTCAGGGTAATTAAGTAAA
6416 CTGAGCACAG
Statistics
Matches: 247, Mismatches: 31, Indels: 32
0.80 0.10 0.10
Matches are distributed among these distances:
35 2 0.01
36 34 0.14
37 90 0.36
39 3 0.01
40 51 0.21
41 56 0.23
42 3 0.01
43 2 0.01
44 1 0.00
45 4 0.02
46 1 0.00
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (37 bp):
CTTAATTCAGGGTAATTAAGTAAAAGCAATAAAAGGA
Found at i:6473 original size:37 final size:37
Alignment explanation
Indices: 6419--6918 Score: 606
Period size: 37 Copynumber: 12.9 Consensus size: 37
6409 GAGTAAACTG
*
6419 AGCACAGACTTAATTTCAAGGAAATTAAGTAAAGACA
1 AGCACAGACTTAATTTCAAGGAAATTAGGTAAAGACA
* *
6456 AGCACAAACTTAGTTTCAAGGAAATTAGGTAAACGACA
1 AGCACAGACTTAATTTCAAGGAAATTAGGTAAA-GACA
*
6494 AGCACGGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACA
1 AGCACAGACTTAATTTC----AAGGAAATTAGGTAAAGACA
6535 AGCACAGACTTAATTTCAAGGAAATTAGGTAAAGACA
1 AGCACAGACTTAATTTCAAGGAAATTAGGTAAAGACA
*
6572 AGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAAGACA
1 AGCACAGACTTAATTTC----AAGGAAATTAGGT-AAAGACA
* *
6614 AGAACATACTTAATTTCAAGGAAATTAGGTAAAAGACA
1 AGCACAGACTTAATTTCAAGGAAATTAGGT-AAAGACA
* *
6652 AGCATATACTTAATTTCAAGGAAGGAAATTAGGTAAAGACA
1 AGCACAGACTTAATTTC----AAGGAAATTAGGTAAAGACA
6693 AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAAGACA
1 AGCACAGACTTAATTTC----AAGGAAATTAGGT-AAAGACA
* *
6735 AGCACAGATTTAATTTCAAGGAAACTAGGTAAAGACA
1 AGCACAGACTTAATTTCAAGGAAATTAGGTAAAGACA
*
6772 AGCACATACTTAATTTCAAGGAAGGAAATTAGGTAAAGACA
1 AGCACAGACTTAATTTC----AAGGAAATTAGGTAAAGACA
* * *
6813 AGAACATACTTAATTTCAAGGAAATCAGGTAAAGACA
1 AGCACAGACTTAATTTCAAGGAAATTAGGTAAAGACA
*
6850 AGCACATACTTAATTTCAAGGAAATTAGGTAAAGACA
1 AGCACAGACTTAATTTCAAGGAAATTAGGTAAAGACA
* * *
6887 AGCACAGACTTAA-TTCAGGGTAATTAAGTAAA
1 AGCACAGACTTAATTTCAAGGAAATTAGGTAAA
6919 ATCAACAAAA
Statistics
Matches: 417, Mismatches: 27, Indels: 39
0.86 0.06 0.08
Matches are distributed among these distances:
36 16 0.04
37 154 0.37
38 66 0.16
41 107 0.26
42 74 0.18
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.22
Consensus pattern (37 bp):
AGCACAGACTTAATTTCAAGGAAATTAGGTAAAGACA
Found at i:6537 original size:79 final size:78
Alignment explanation
Indices: 6419--6901 Score: 639
Period size: 79 Copynumber: 6.2 Consensus size: 78
6409 GAGTAAACTG
* * *
6419 AGCACAGACTTAATTTC----AAGGAAATTAAGTAAAGACAAGCACAAACTTAGTTTCAAGGAAA
1 AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACATACTTAATTTCAAGGAAA
6480 TTAGGTAAACGACA
66 TTAGGTAAA-GACA
* *
6494 AGCACGGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAA
1 AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACATACTTAATTTCAAGGAAA
6559 TTAGGTAAAGACA
66 TTAGGTAAAGACA
* *
6572 AGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAAGACAAGAACATACTTAATTTCAAGGAA
1 AGCACAGACTTAATTTCAAGGAAGGAAATTAGGT-AAAGACAAGCACATACTTAATTTCAAGGAA
6637 ATTAGGTAAAAGACA
65 ATTAGGT-AAAGACA
* * *
6652 AGCATATACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAG
1 AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACATACTTAATTTC----AAG
6717 GAAATTAGGTAAAAGACA
62 GAAATTAGGT-AAAGACA
* *
6735 AGCACAGATTTAATTTC----AAGGAAACTAGGTAAAGACAAGCACATACTTAATTTCAAGGAAG
1 AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACATACTTAATTTC----AAG
6796 GAAATTAGGTAAAGACA
62 GAAATTAGGTAAAGACA
* * *
6813 AGAACATACTTAATTTC----AAGGAAATCAGGTAAAGACAAGCACATACTTAATTTCAAGGAAA
1 AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACATACTTAATTTCAAGGAAA
6874 TTAGGTAAAGACA
66 TTAGGTAAAGACA
6887 AGCACAGACTTAATT
1 AGCACAGACTTAATT
6902 CAGGGTAATT
Statistics
Matches: 374, Mismatches: 24, Indels: 21
0.89 0.06 0.05
Matches are distributed among these distances:
74 33 0.09
75 16 0.04
78 92 0.25
79 159 0.43
80 39 0.10
83 35 0.09
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.22
Consensus pattern (78 bp):
AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACATACTTAATTTCAAGGAAA
TTAGGTAAAGACA
Found at i:7011 original size:35 final size:35
Alignment explanation
Indices: 6857--7090 Score: 190
Period size: 35 Copynumber: 6.7 Consensus size: 35
6847 ACAAGCACAT
* * *
6857 ACTTAATTTCAAGGAAATTAGGTAAAGA-CAAGCACAG
1 ACTTAA-TTCAAGGTAATTAAGTAAA-ATC-AGCAAAG
* * *
6894 ACTTAATTCAGGGTAATTAAGTAAAATCAACAAAA
1 ACTTAATTCAAGGTAATTAAGTAAAATCAGCAAAG
* *
6929 ATTTAATTCAGGGTAATTAAGTAAAATCAGCAAAG
1 ACTTAATTCAAGGTAATTAAGTAAAATCAGCAAAG
*
6964 ACTTAATTCAAAGTAATTAAGTAAAATCAGCAAAG
1 ACTTAATTCAAGGTAATTAAGTAAAATCAGCAAAG
* * * * * *
6999 ACTTAATCCAAAGATGATTAAGCAAGATTAGACAAAG
1 ACTTAATTC-AAGGTAATTAAGTAAAATCAG-CAAAG
** ** *
7036 ACTTAACCCAAGGGGATTAAGTAAAGA--A--AATG
1 ACTTAATTCAAGGTAATTAAGTAAA-ATCAGCAAAG
*
7068 ACTTAATTCAGGGTAATTAAGTA
1 ACTTAATTCAAGGTAATTAAGTA
7091 GAGTCAAGGA
Statistics
Matches: 163, Mismatches: 30, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
32 21 0.13
35 78 0.48
36 44 0.27
37 20 0.12
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (35 bp):
ACTTAATTCAAGGTAATTAAGTAAAATCAGCAAAG
Found at i:7087 original size:32 final size:31
Alignment explanation
Indices: 7051--7153 Score: 109
Period size: 32 Copynumber: 3.3 Consensus size: 31
7041 ACCCAAGGGG
*
7051 ATTAAGTAAAGAAAATGACTTAATTCAGGGTA
1 ATTAAGTAAAGTAAA-GACTTAATTCAGGGTA
* * * **
7083 ATTAAGTAGAGTCAAGGACTTAATTCAAGACA
1 ATTAAGTAAAGT-AAAGACTTAATTCAGGGTA
*
7115 ATTAAGTCAA-TAAAGAGCTTAATTCAGGGTA
1 ATTAAGTAAAGTAAAGA-CTTAATTCAGGGTA
7146 ATTAAGTA
1 ATTAAGTA
7154 GAGTCAATAA
Statistics
Matches: 56, Mismatches: 13, Indels: 5
0.76 0.18 0.07
Matches are distributed among these distances:
30 4 0.07
31 19 0.34
32 31 0.55
33 2 0.04
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.28
Consensus pattern (31 bp):
ATTAAGTAAAGTAAAGACTTAATTCAGGGTA
Found at i:7166 original size:36 final size:36
Alignment explanation
Indices: 7068--7205 Score: 141
Period size: 36 Copynumber: 4.1 Consensus size: 36
7058 AAAGAAAATG
* *
7068 ACTTAATTCAGGGTAATTAAGTAGAGTC----AAGG
1 ACTTAATTCAGGGCAATTAAGTAGAGTCAATAAAGA
* *
7100 ACTTAATTCAAGACAA-T---TA-AGTCAATAAAGA
1 ACTTAATTCAGGGCAATTAAGTAGAGTCAATAAAGA
* *
7131 GCTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGA
1 ACTTAATTCAGGGCAATTAAGTAGAGTCAATAAAGA
* *
7167 ATTTAATTCAGGGCAATTAAGTGGAGTCAATAAAGA
1 ACTTAATTCAGGGCAATTAAGTAGAGTCAATAAAGA
7203 ACT
1 ACT
7206 CAATCTAAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 14
0.76 0.12 0.13
Matches are distributed among these distances:
27 4 0.05
28 2 0.02
31 16 0.19
32 14 0.17
35 2 0.02
36 46 0.55
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.28
Consensus pattern (36 bp):
ACTTAATTCAGGGCAATTAAGTAGAGTCAATAAAGA
Found at i:11210 original size:56 final size:57
Alignment explanation
Indices: 11136--11245 Score: 195
Period size: 56 Copynumber: 1.9 Consensus size: 57
11126 ATTGGGGTAT
* *
11136 GTTTTACTGAATTGGTGATTTTGATTCATGGATTAATTTGGATTTGGTTAATTGGGG
1 GTTTTACTAAATTGGTGATTTTGATTCATGGATTAATTTGAATTTGGTTAATTGGGG
11193 GTTTT-CTAAATTGGTGATTTTGATTCATGGATTAATTTGAATTTGGTTAATTG
1 GTTTTACTAAATTGGTGATTTTGATTCATGGATTAATTTGAATTTGGTTAATTG
11246 CTCAAAAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
56 46 0.90
57 5 0.10
ACGTcount: A:0.23, C:0.04, G:0.25, T:0.49
Consensus pattern (57 bp):
GTTTTACTAAATTGGTGATTTTGATTCATGGATTAATTTGAATTTGGTTAATTGGGG
Found at i:14435 original size:18 final size:18
Alignment explanation
Indices: 14412--14447 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
14402 GATTTTATCA
14412 AGATTAGTGCATTATGAG
1 AGATTAGTGCATTATGAG
14430 AGATTAGTGCATTATGAG
1 AGATTAGTGCATTATGAG
14448 TTTTATGGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (18 bp):
AGATTAGTGCATTATGAG
Found at i:15322 original size:5 final size:5
Alignment explanation
Indices: 15312--15336 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
15302 AATTATTCAG
15312 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
15337 TTAGTTAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:19078 original size:119 final size:119
Alignment explanation
Indices: 18859--19092 Score: 432
Period size: 119 Copynumber: 2.0 Consensus size: 119
18849 TATCTAAGGC
* *
18859 CTATGCATTGATCATTAGAGAGGAAAAGCAATAGCTTCTCCAATCTACTCGCTCACCTACAATGG
1 CTATGCATTGATCATTAGAGAGGAAAAGCAACAGCTTCTCCAATCTACTAGCTCACCTACAATGG
* *
18924 AAGCAGCTGCTTTTCATGTCAATAGCATGGCCAATGCAGTGCAACGATCTGCTT
66 AAGCAGCTGCTTTTCATGTCAATAGCACGGACAATGCAGTGCAACGATCTGCTT
18978 CTATGCATTGATCATTAGAGAGGAAAAGCAACAGCTTCTCCAATCTACTAGCTCACCTACAATGG
1 CTATGCATTGATCATTAGAGAGGAAAAGCAACAGCTTCTCCAATCTACTAGCTCACCTACAATGG
19043 AAGCAGCTGCTTTTCATGTCAATAGCACGGACAATGCAGTGCAACGATCT
66 AAGCAGCTGCTTTTCATGTCAATAGCACGGACAATGCAGTGCAACGATCT
19093 TCATTTCAAA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
119 111 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (119 bp):
CTATGCATTGATCATTAGAGAGGAAAAGCAACAGCTTCTCCAATCTACTAGCTCACCTACAATGG
AAGCAGCTGCTTTTCATGTCAATAGCACGGACAATGCAGTGCAACGATCTGCTT
Found at i:22963 original size:2 final size:2
Alignment explanation
Indices: 22956--22995 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
22946 GATCCAATGC
*
22956 AT AT AT AT -T AT AC AT AT -T AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22995 A
1 A
22996 AAAACAACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:22994 original size:9 final size:9
Alignment explanation
Indices: 22956--22995 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
22946 GATCCAATGC
22956 ATATATATT
1 ATATATATT
*
22965 ATACATATT
1 ATATATATT
22974 ATATATA-T
1 ATATATATT
*
22982 ATATATATA
1 ATATATATT
22991 ATATA
1 ATATA
22996 AAAACAACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (9 bp):
ATATATATT
Found at i:23954 original size:20 final size:21
Alignment explanation
Indices: 23918--23958 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
23908 AACTGGATTA
23918 CTAAACACCGCCCCCCTTTTG
1 CTAAACACCGCCCCCCTTTTG
* *
23939 CTAAATACCGCCCCCTTTTT
1 CTAAACACCGCCCCCCTTTT
23959 TACACTTTTG
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:0.20, C:0.44, G:0.07, T:0.29
Consensus pattern (21 bp):
CTAAACACCGCCCCCCTTTTG
Found at i:24092 original size:25 final size:25
Alignment explanation
Indices: 24030--24088 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
24020 TTCAAACCCT
*
24030 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACATCTTC
24055 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
24079 AAA-TTCATTT
1 AAACTTCATTT
24089 TTCTTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 18 0.55
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.41
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Found at i:24127 original size:26 final size:26
Alignment explanation
Indices: 24098--24165 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
24088 TTTCTTCATT
24098 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
24124 TTAATCATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
24150 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
24166 AAACTAAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:24128 original size:15 final size:15
Alignment explanation
Indices: 24098--24165 Score: 62
Period size: 15 Copynumber: 5.1 Consensus size: 15
24088 TTTCTTCATT
24098 TTAATCATAAACTAA
1 TTAATCATAAACTAA
24113 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
24124 TTAATCATAAACTAA
1 TTAATCATAAACTAA
*
24139 TT-A-GAT--ACTAA
1 TTAATCATAAACTAA
*
24150 TTAAACATAAACTAA
1 TTAATCATAAACTAA
24165 T
1 T
24166 AAACTAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
11 16 0.37
12 1 0.02
13 8 0.19
14 1 0.02
15 17 0.40
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (15 bp):
TTAATCATAAACTAA
Found at i:24236 original size:11 final size:10
Alignment explanation
Indices: 24218--24257 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
24208 CTAATTAATA
24218 TTAAAAAAAT
1 TTAAAAAAAT
24228 TTAAAAAAATT
1 TTAAAAAAA-T
*
24239 TTAAAAAATT
1 TTAAAAAAAT
24249 TTAAAAAAA
1 TTAAAAAAA
24258 GCAATGGCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TTAAAAAAAT
Found at i:24309 original size:33 final size:33
Alignment explanation
Indices: 24261--24376 Score: 146
Period size: 33 Copynumber: 3.5 Consensus size: 33
24251 AAAAAAAGCA
*
24261 ATGGCCTAGCGGCCCAAGC-TGGGCGGCATA-TCC
1 ATGG-CTAGCCGCCC-AGCGTGGGCGGCATAGTCC
* *
24294 ATTGGCTAGCTGCCCAGCGTTGGCGGCATAGTCC
1 A-TGGCTAGCCGCCCAGCGTGGGCGGCATAGTCC
* *
24328 ATGGCTAGCCGCCCAGCGTGGGCGGCATGGCCC
1 ATGGCTAGCCGCCCAGCGTGGGCGGCATAGTCC
24361 ATGGCTAGCCGCCCAG
1 ATGGCTAGCCGCCCAG
24377 GCCTTTTTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
32 3 0.04
33 64 0.86
34 7 0.09
ACGTcount: A:0.16, C:0.34, G:0.34, T:0.16
Consensus pattern (33 bp):
ATGGCTAGCCGCCCAGCGTGGGCGGCATAGTCC
Found at i:24403 original size:13 final size:12
Alignment explanation
Indices: 24385--24427 Score: 61
Period size: 12 Copynumber: 3.5 Consensus size: 12
24375 AGGCCTTTTT
24385 TTTTTTTAAATAA
1 TTTTTTTAAA-AA
24398 -TTTTTTAAAAA
1 TTTTTTTAAAAA
24409 TTTTTTTAAAAGA
1 TTTTTTTAAAA-A
24422 TTTTTT
1 TTTTTT
24428 ACCTCATTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.07
12 19 0.68
13 7 0.25
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (12 bp):
TTTTTTTAAAAA
Found at i:24592 original size:20 final size:21
Alignment explanation
Indices: 24566--24610 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
24556 CAAAAATTAT
* *
24566 AAAAAGGGGACGGTGTTTAGC
1 AAAAGGGGGACGATGTTTAGC
24587 AAAAGGGGGACGATGTTTAGC
1 AAAAGGGGGACGATGTTTAGC
24608 AAA
1 AAA
24611 CCCCCACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.09, G:0.36, T:0.18
Consensus pattern (21 bp):
AAAAGGGGGACGATGTTTAGC
Found at i:26203 original size:47 final size:47
Alignment explanation
Indices: 26126--26220 Score: 156
Period size: 47 Copynumber: 2.0 Consensus size: 47
26116 CATATTGTTC
* *
26126 GTTTAGAAAGCTGAGGCTACTTGATCAAAAAAAAGGGAGAAAAGAAA
1 GTTTAGAAAGCTGAGCCTACTTGATCAAAAAAAAAGGAGAAAAGAAA
26173 GTTTAGAAAGCTGAGCCTACTT-ATCAAAAAAAAAAGGAGAAAAGAAA
1 GTTTAGAAAGCTGAGCCTACTTGATC-AAAAAAAAAGGAGAAAAGAAA
26220 G
1 G
26221 CAACCTTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 3 0.07
47 42 0.93
ACGTcount: A:0.51, C:0.09, G:0.23, T:0.17
Consensus pattern (47 bp):
GTTTAGAAAGCTGAGCCTACTTGATCAAAAAAAAAGGAGAAAAGAAA
Found at i:26827 original size:2 final size:2
Alignment explanation
Indices: 26820--26854 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
26810 TGAAAACTAG
*
26820 TA TA TA TA AA 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 TA T
26855 CAATCTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:28702 original size:7 final size:7
Alignment explanation
Indices: 28692--28720 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
28682 TTTCATCAGA
28692 AATGCCC
1 AATGCCC
28699 AATGCCC
1 AATGCCC
28706 AATGCCC
1 AATGCCC
28713 AATGCCC
1 AATGCCC
28720 A
1 A
28721 CCCTGATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.41, G:0.14, T:0.14
Consensus pattern (7 bp):
AATGCCC
Found at i:29157 original size:7 final size:7
Alignment explanation
Indices: 29145--29170 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29135 GATTCTGCCG
29145 ATTCTGC
1 ATTCTGC
29152 ATTCTGC
1 ATTCTGC
29159 ATTCTGC
1 ATTCTGC
29166 ATTCT
1 ATTCT
29171 TCCAATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.27, G:0.12, T:0.46
Consensus pattern (7 bp):
ATTCTGC
Found at i:33997 original size:11 final size:11
Alignment explanation
Indices: 33960--34003 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
33950 TTCCTATATA
*
33960 AAATAAATTAT
1 AAATTAATTAT
33971 CAAA-TAATTAT
1 -AAATTAATTAT
33982 AAATTAATTAT
1 AAATTAATTAT
*
33993 AAATTTATTAT
1 AAATTAATTAT
34004 GAATATACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 3 0.10
11 23 0.79
12 3 0.10
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:34381 original size:41 final size:42
Alignment explanation
Indices: 34309--34392 Score: 161
Period size: 41 Copynumber: 2.0 Consensus size: 42
34299 CAAAAATTTC
34309 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
34351 ATTTCTTAACTGAA-TTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
34392 A
1 A
34393 CAGCCGCACG
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 28 0.67
42 14 0.33
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (42 bp):
ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
Found at i:39390 original size:12 final size:12
Alignment explanation
Indices: 39373--39404 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
39363 ACCTGGCAAT
*
39373 TCGTGTTTCGTG
1 TCGTGTTTCATG
39385 TCGTGTTTCATG
1 TCGTGTTTCATG
39397 TCGTGTTT
1 TCGTGTTT
39405 ACATAGGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.03, C:0.16, G:0.28, T:0.53
Consensus pattern (12 bp):
TCGTGTTTCATG
Found at i:39629 original size:10 final size:10
Alignment explanation
Indices: 39611--39646 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
39601 CAATTAACTA
39611 AATTATATAT
1 AATTATATAT
*
39621 AATTTTATAT
1 AATTATATAT
39631 ATATTATATAT
1 A-ATTATATAT
39642 AATTA
1 AATTA
39647 AAGATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
AATTATATAT
Found at i:39654 original size:31 final size:32
Alignment explanation
Indices: 39619--39678 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
39609 TAAATTATAT
*
39619 ATAATTTTATATATATTATAT-ATAATTAAAG
1 ATAATTTAATATATATTATATAATAATTAAAG
* *
39650 ATAATTTAATATATTTTTTATAATAATTA
1 ATAATTTAATATATATTATATAATAATTA
39679 TTTGGGTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (32 bp):
ATAATTTAATATATATTATATAATAATTAAAG
Found at i:39821 original size:20 final size:21
Alignment explanation
Indices: 39784--39826 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
39774 AACCCGTTAA
*
39784 TTAAAGCGTGTCACTCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
*
39805 TTAAA-CGTGTTAATCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
39825 TT
1 TT
39827 GACACGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (21 bp):
TTAAAGCGTGTCAATCGTGTC
Found at i:39884 original size:42 final size:43
Alignment explanation
Indices: 39814--39896 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
39804 CTTAAACGTG
*
39814 TTAATCGTGTCTTGACACGATTACGACACGAAACACGATAATC
1 TTAATCGTGTCTCGACACGATTACGACACGAAACACGATAATC
*
39857 TTAATCGTGTC-CGACACGATT-CAGACACGAGACACGATAA
1 TTAATCGTGTCTCGACACGATTAC-GACACGAAACACGATAA
39897 GCCAAACACG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 1 0.03
42 25 0.68
43 11 0.30
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (43 bp):
TTAATCGTGTCTCGACACGATTACGACACGAAACACGATAATC
Found at i:40786 original size:28 final size:26
Alignment explanation
Indices: 40728--40789 Score: 83
Period size: 24 Copynumber: 2.4 Consensus size: 26
40718 TAATATTGTT
*
40728 GAAGAGGTTGGTTGAGATTAAAATTA
1 GAAGAGTTTGGTTGAGATTAAAATTA
40754 G--GAGTTTGGTTGAGATTAAAATTA
1 GAAGAGTTTGGTTGAGATTAAAATTA
40778 GTCAAGAGTTTG
1 G--AAGAGTTTG
40790 TCTAAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 23 0.74
26 1 0.03
28 7 0.23
ACGTcount: A:0.34, C:0.02, G:0.31, T:0.34
Consensus pattern (26 bp):
GAAGAGTTTGGTTGAGATTAAAATTA
Found at i:43750 original size:6 final size:7
Alignment explanation
Indices: 43736--43767 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
43726 ATTGAGTTCC
43736 ATAAAAA
1 ATAAAAA
43743 AT-AAAA
1 ATAAAAA
43749 ATAAAAA
1 ATAAAAA
43756 ATAAAAA
1 ATAAAAA
43763 ATAAA
1 ATAAA
43768 GCCACTCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
ATAAAAA
Found at i:43754 original size:13 final size:14
Alignment explanation
Indices: 43736--43767 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
43726 ATTGAGTTCC
43736 ATAAAAAAT-AAAA
1 ATAAAAAATAAAAA
43749 ATAAAAAATAAAAA
1 ATAAAAAATAAAAA
43763 ATAAA
1 ATAAA
43768 GCCACTCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (14 bp):
ATAAAAAATAAAAA
Done.