Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019891.1 Corchorus olitorius cultivar O-4 contig19924, 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: 36001
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Found at i:2440 original size:16 final size:16
Alignment explanation
Indices: 2412--2446 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2402 ACACCGGTTG
2412 AATACAAACTCTCTCA
1 AATACAAACTCTCTCA
2428 AATACCAAA-TCTCTCA
1 AATA-CAAACTCTCTCA
2444 AAT
1 AAT
2447 TTTAGTGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.26
Consensus pattern (16 bp):
AATACAAACTCTCTCA
Found at i:5065 original size:75 final size:74
Alignment explanation
Indices: 4879--5092 Score: 280
Period size: 75 Copynumber: 2.9 Consensus size: 74
4869 ATTCGACATA
*
4879 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTGCTTTCCTTTTT-TATGCTTCTGGCTTAT
1 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTGCTTTCCTTTTTGT-TGTTTCTGGCTTAT
*
4943 GTGGCCAATC
65 GTAGCCAATC
* * *
4953 AAGA-T---T-C-CAGCAAGGATTGTAGCCTTAAGTGCCTTTCCTTTTTGTTGTTTCTGACTTAT
1 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTG-CTTTCCTTTTTGTTGTTTCTGGCTTAT
5012 GTAGCCAATC
65 GTAGCCAATC
* * *
5022 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTGTCTTTCCTTGTTGATGTTTCTGGCCTAT
1 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTG-CTTTCCTTTTTGTTGTTTCTGGCTTAT
5087 GTAGCC
65 GTAGCC
5093 CATTAAAAAA
Statistics
Matches: 120, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
68 22 0.18
69 37 0.31
70 3 0.03
73 2 0.02
74 5 0.04
75 51 0.43
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (74 bp):
AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTGCTTTCCTTTTTGTTGTTTCTGGCTTATG
TAGCCAATC
Found at i:5253 original size:116 final size:110
Alignment explanation
Indices: 5054--5299 Score: 366
Period size: 116 Copynumber: 2.2 Consensus size: 110
5044 TCGTAGCCAT
* *
5054 AAGTGTCTTTCCTTGTTGATGTTTCTGGCCTATGTAGCCCATTAAAAAAATCTATATGTTGACTT
1 AAGTGTCCTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTAAAAAAATCTATATGTTGACTT
*
5119 GGAGTGAGTGCACCCTTAGGAGTGCTGCACTGGTTGCACCTCCAG
66 GGAATGAGTGCACCCTTAGGAGTGCTGCACTGGTTGCACCTCCAG
* * *
5164 GAGTGTCCTTCCTTGTTGATGATTCTGGCCTATGTAGCCCAAGCCCATTAAAAAATTCTATATTT
1 AAGTGTCCTTCCTTGTTGATGATTCTGGCCTATGT------AGCCCATTAAAAAAATCTATATGT
*
5229 TGACTTGGAATGAGTGCACCCTTAGGAGTGTTGCACTGGTTGCACCTCCAG
60 TGACTTGGAATGAGTGCACCCTTAGGAGTGCTGCACTGGTTGCACCTCCAG
*
5280 AAGTGCCCTTCCTTGTTGAT
1 AAGTGTCCTTCCTTGTTGAT
5300 ACTTCTAGTC
Statistics
Matches: 121, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
110 32 0.26
116 89 0.74
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.34
Consensus pattern (110 bp):
AAGTGTCCTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTAAAAAAATCTATATGTTGACTT
GGAATGAGTGCACCCTTAGGAGTGCTGCACTGGTTGCACCTCCAG
Found at i:5795 original size:28 final size:28
Alignment explanation
Indices: 5757--5823 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
5747 CGTCAAAGGC
* *
5757 ATGTGGCATTCGCGATGTGGTATTCGCA
1 ATGTGGTATTCGCAATGTGGTATTCGCA
5785 ATGTGGTATTCGCAATGTGGTATTCGCA
1 ATGTGGTATTCGCAATGTGGTATTCGCA
* *
5813 ATATAGTATTC
1 ATGTGGTATTC
5824 CTTCTTCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.36
Consensus pattern (28 bp):
ATGTGGTATTCGCAATGTGGTATTCGCA
Found at i:5823 original size:14 final size:14
Alignment explanation
Indices: 5757--5814 Score: 98
Period size: 14 Copynumber: 4.1 Consensus size: 14
5747 CGTCAAAGGC
* *
5757 ATGTGGCATTCGCG
1 ATGTGGTATTCGCA
5771 ATGTGGTATTCGCA
1 ATGTGGTATTCGCA
5785 ATGTGGTATTCGCA
1 ATGTGGTATTCGCA
5799 ATGTGGTATTCGCA
1 ATGTGGTATTCGCA
5813 AT
1 AT
5815 ATAGTATTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 42 1.00
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.34
Consensus pattern (14 bp):
ATGTGGTATTCGCA
Found at i:5965 original size:19 final size:19
Alignment explanation
Indices: 5943--6008 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
5933 ATATGGTACC
5943 CGCGATGTGGTATGGTATT
1 CGCGATGTGGTATGGTATT
* * *
5962 CGCGACGCTAAAGGCATGGTACT
1 CGCGATG-T---GGTATGGTATT
*
5985 CGCGATATGGTATGGTATT
1 CGCGATGTGGTATGGTATT
6004 CGCGA
1 CGCGA
6009 CACTAAAGGC
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
19 20 0.56
20 1 0.03
22 1 0.03
23 14 0.39
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.27
Consensus pattern (19 bp):
CGCGATGTGGTATGGTATT
Found at i:5980 original size:23 final size:22
Alignment explanation
Indices: 5954--6020 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 22
5944 GCGATGTGGT
5954 ATGGTATTCGCGACGCTAAAGGC
1 ATGGTATTCGCGAC-CTAAAGGC
* * *
5977 ATGGTACTCGCGA--T-ATGGT
1 ATGGTATTCGCGACCTAAAGGC
5996 ATGGTATTCGCGACACTAAAGGC
1 ATGGTATTCGCGAC-CTAAAGGC
6019 AT
1 AT
6021 TTGGCGTCGA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
19 15 0.44
20 1 0.03
22 1 0.03
23 17 0.50
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (22 bp):
ATGGTATTCGCGACCTAAAGGC
Found at i:5996 original size:42 final size:42
Alignment explanation
Indices: 5935--6020 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
5925 GAGATGGCAT
* *
5935 ATGGTACCCGCGATGTGGTATGGTATTCGCGACGCTAAAGGC
1 ATGGTACCCGCGATATGGTATGGTATTCGCGACACTAAAGGC
*
5977 ATGGTACTCGCGATATGGTATGGTATTCGCGACACTAAAGGC
1 ATGGTACCCGCGATATGGTATGGTATTCGCGACACTAAAGGC
6019 AT
1 AT
6021 TTGGCGTCGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (42 bp):
ATGGTACCCGCGATATGGTATGGTATTCGCGACACTAAAGGC
Found at i:6277 original size:44 final size:43
Alignment explanation
Indices: 6169--6362 Score: 165
Period size: 44 Copynumber: 4.5 Consensus size: 43
6159 CAACTGCGAC
* * *
6169 GTCAACGACATATGGTGTTCACGAAATTATCACCCTCTTTCAATGTCAAT
1 GTCAAAGACATATGGTGTTCGC-AAACTATCACCCTC--T---T-TCAAT
*
6219 GTCAAAGGCATATGGTGTTCGCAAGACTATCACCCTCTTTCAAT
1 GTCAAAGACATATGGTGTTCGCAA-ACTATCACCCTCTTTCAAT
* *
6263 GTCAAAGACATATGGTGTT-------TGT--GCCTCTTTCAAT
1 GTCAAAGACATATGGTGTTCGCAAACTATCACCCTCTTTCAAT
*
6297 GTCAAAGGCATATGGTGTTCGCGAAACTATCACCCTCTTTCAAT
1 GTCAAAGACATATGGTGTTCGC-AAACTATCACCCTCTTTCAAT
6341 GTCAAA-AGCATATGGTGTTCGC
1 GTCAAAGA-CATATGGTGTTCGC
6363 GAAGTACCAC
Statistics
Matches: 121, Mismatches: 11, Indels: 30
0.75 0.07 0.19
Matches are distributed among these distances:
34 29 0.24
36 2 0.02
42 2 0.02
44 54 0.45
45 1 0.01
48 1 0.01
49 2 0.02
50 30 0.25
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (43 bp):
GTCAAAGACATATGGTGTTCGCAAACTATCACCCTCTTTCAAT
Found at i:6307 original size:78 final size:78
Alignment explanation
Indices: 6214--6359 Score: 260
Period size: 78 Copynumber: 1.9 Consensus size: 78
6204 TCTTTCAATG
6214 TCAATGTCAAAGGCATATGGTGTTCGC-AAGACTATCACCCTCTTTCAATGTC-AAAGACATATG
1 TCAATGTCAAAGGCATATGGTGTTCGCGAA-ACTATCACCCTCTTTCAATGTCAAAAG-CATATG
6277 GTGTTTGTGCCTCTT
64 GTGTTTGTGCCTCTT
6292 TCAATGTCAAAGGCATATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAAGCATATGGT
1 TCAATGTCAAAGGCATATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAAGCATATGGT
6357 GTT
66 GTT
6360 CGCGAAGTAC
Statistics
Matches: 66, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
78 60 0.91
79 6 0.09
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (78 bp):
TCAATGTCAAAGGCATATGGTGTTCGCGAAACTATCACCCTCTTTCAATGTCAAAAGCATATGGT
GTTTGTGCCTCTT
Found at i:6388 original size:30 final size:30
Alignment explanation
Indices: 6352--6412 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
6342 TCAAAAGCAT
*
6352 ATGGTGTTCGCGAAGTAC-CACCTCCTTCCA
1 ATGGTGTTAGCGAAGT-CTCACCTCCTTCCA
6382 ATGGTGTTAGCGAAGTCTCACCTCCTTCCA
1 ATGGTGTTAGCGAAGTCTCACCTCCTTCCA
6412 A
1 A
6413 CATCCTGAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.21, C:0.31, G:0.20, T:0.28
Consensus pattern (30 bp):
ATGGTGTTAGCGAAGTCTCACCTCCTTCCA
Found at i:6525 original size:51 final size:51
Alignment explanation
Indices: 6399--6566 Score: 185
Period size: 51 Copynumber: 3.3 Consensus size: 51
6389 TAGCGAAGTC
* ** * * *
6399 TCACCTCCTTCCAACATCCTGAAGCCTCTTGCATATGGTGTTCACAAAATA
1 TCACCTCCTTCCAATATTATGAAGTCTTTTGCATATGGTGTTCGCAAAATA
* *
6450 TCACCT-TTTCCCAATATTATGAAGTCTTTTGCATATGTTGTTCGCAAAATA
1 TCACCTCCTT-CCAATATTATGAAGTCTTTTGCATATGGTGTTCGCAAAATA
* * * * * * *
6501 TCACCTTCTTCCAATATTATGAAGTTTTTTGTATATGGCGTTGGCGAACTA
1 TCACCTCCTTCCAATATTATGAAGTCTTTTGCATATGGTGTTCGCAAAATA
6552 TCACCTCCTTCCAAT
1 TCACCTCCTTCCAAT
6567 GTCGAAGGGT
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
50 2 0.02
51 94 0.96
52 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (51 bp):
TCACCTCCTTCCAATATTATGAAGTCTTTTGCATATGGTGTTCGCAAAATA
Found at i:6640 original size:31 final size:32
Alignment explanation
Indices: 6575--6662 Score: 115
Period size: 31 Copynumber: 2.8 Consensus size: 32
6565 ATGTCGAAGG
* *
6575 GTACATCCTCTTCCATATGGTGTTATCAAGAA
1 GTACACCCTCTTCCATATGGTGTTGTCAAGAA
*
6607 GTACACCCTCTTCCATATGATGTTGT-AAGAA
1 GTACACCCTCTTCCATATGGTGTTGTCAAGAA
* * *
6638 GTACACCATTTTCCACATGGTGTTG
1 GTACACCCTCTTCCATATGGTGTTG
6663 GCAAACTATC
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 26 0.53
32 23 0.47
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (32 bp):
GTACACCCTCTTCCATATGGTGTTGTCAAGAA
Found at i:6908 original size:72 final size:72
Alignment explanation
Indices: 6817--6982 Score: 287
Period size: 72 Copynumber: 2.3 Consensus size: 72
6807 TGCTCTGTCT
*
6817 TTGGCTATAATGTTGATGGCCTAAGTCGCCTAATAATTGGCTATAAAGCCGCTGGCCTTAGTCGC
1 TTGGCTATAATGTTGATGGCCTAAGTCGCCCAATAATTGGCTATAAAGCCGCTGGCCTTAGTCGC
6882 CCAATAC
66 CCAATAC
*
6889 TTGGCTATAATGTTGATGGCCTAAGTCGCCCAGTAATTGGCTATAAAGCCGCTGGCCTTAGTCGC
1 TTGGCTATAATGTTGATGGCCTAAGTCGCCCAATAATTGGCTATAAAGCCGCTGGCCTTAGTCGC
*
6954 CCAATAT
66 CCAATAC
* *
6961 TTGGCTATAATGCTGCTGGCCT
1 TTGGCTATAATGTTGATGGCCT
6983 TTAATGCCAT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 89 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (72 bp):
TTGGCTATAATGTTGATGGCCTAAGTCGCCCAATAATTGGCTATAAAGCCGCTGGCCTTAGTCGC
CCAATAC
Found at i:6983 original size:36 final size:36
Alignment explanation
Indices: 6817--6983 Score: 208
Period size: 36 Copynumber: 4.6 Consensus size: 36
6807 TGCTCTGTCT
* * * *
6817 TTGGCTATAATGTTGATGGCCTAAGTCGCCTAATAA
1 TTGGCTATAATGCTGCTGGCCTTAGTCGCCCAATAA
* * *
6853 TTGGCTATAAAGCCGCTGGCCTTAGTCGCCCAATAC
1 TTGGCTATAATGCTGCTGGCCTTAGTCGCCCAATAA
* * * *
6889 TTGGCTATAATGTTGATGGCCTAAGTCGCCCAGTAA
1 TTGGCTATAATGCTGCTGGCCTTAGTCGCCCAATAA
* * *
6925 TTGGCTATAAAGCCGCTGGCCTTAGTCGCCCAATAT
1 TTGGCTATAATGCTGCTGGCCTTAGTCGCCCAATAA
6961 TTGGCTATAATGCTGCTGGCCTT
1 TTGGCTATAATGCTGCTGGCCTT
6984 TAATGCCATC
Statistics
Matches: 108, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 108 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (36 bp):
TTGGCTATAATGCTGCTGGCCTTAGTCGCCCAATAA
Found at i:7230 original size:46 final size:46
Alignment explanation
Indices: 7145--7416 Score: 381
Period size: 46 Copynumber: 6.0 Consensus size: 46
7135 GAGATGCATT
*
7145 TTATGTGAGCA-CC--CTTCAGAAAGAATACTCTATACGGTAGCTC
1 TTATGTGAGCACCCTTCTTCAGAAAAAATACTCTATACGGTAGCTC
* *
7188 TTATGTGAGCACCCTTCTTCAAAAAAAATACTCTATATGGTAGCTC
1 TTATGTGAGCACCCTTCTTCAGAAAAAATACTCTATACGGTAGCTC
* * **
7234 TTATGTGAGCACCCTTCTTCAGAAAGAATACTCTAGAAAGTAGCTC
1 TTATGTGAGCACCCTTCTTCAGAAAAAATACTCTATACGGTAGCTC
* *
7280 TTATGTGAGCACCCTTCTTCAGAAAGAATACTCTATACAGTAGCTC
1 TTATGTGAGCACCCTTCTTCAGAAAAAATACTCTATACGGTAGCTC
* * *
7326 TTATGTGAGCA-CATTCTTCAGAAAAAATAACTCTACATGGTAGCTC
1 TTATGTGAGCACCCTTCTTCAGAAAAAAT-ACTCTATACGGTAGCTC
* *
7372 TTATGTGAGCACCCATCTTCAGAAAAAATTCTCTATACGGTAGCT
1 TTATGTGAGCACCCTTCTTCAGAAAAAATACTCTATACGGTAGCT
7417 TCTTGCAAAG
Statistics
Matches: 204, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
43 11 0.05
44 2 0.01
45 15 0.07
46 161 0.79
47 15 0.07
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (46 bp):
TTATGTGAGCACCCTTCTTCAGAAAAAATACTCTATACGGTAGCTC
Found at i:7716 original size:12 final size:11
Alignment explanation
Indices: 7689--7761 Score: 55
Period size: 12 Copynumber: 6.7 Consensus size: 11
7679 AACCGTTTAA
7689 TAATTATATAT
1 TAATTATATAT
7700 T-ATTATATAT
1 TAATTATATAT
7710 GTAATTATATAT
1 -TAATTATATAT
7722 ATAA-TAT-TAT
1 -TAATTATATAT
* *
7732 T-TTTTTATAT
1 TAATTATATAT
* *
7742 AAAATATATATT
1 TAATTATATA-T
7754 TAATTATA
1 TAATTATA
7762 AATATTACTA
Statistics
Matches: 47, Mismatches: 9, Indels: 11
0.70 0.13 0.16
Matches are distributed among these distances:
9 3 0.06
10 15 0.32
11 10 0.21
12 19 0.40
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (11 bp):
TAATTATATAT
Found at i:8363 original size:45 final size:45
Alignment explanation
Indices: 8299--8394 Score: 142
Period size: 45 Copynumber: 2.1 Consensus size: 45
8289 CTCCAAGGCG
*
8299 TTGAACATGGGAGATACACAAA-TGAT-TTCCACCATGACAAAGACA
1 TTGAACATGAGAGATACACAAATTG-TCTT-CACCATGACAAAGACA
*
8344 TTGAACATGAGAGATACACAAATTGTCTTCACCATGACAAAGGCA
1 TTGAACATGAGAGATACACAAATTGTCTTCACCATGACAAAGACA
8389 TTGAAC
1 TTGAAC
8395 CTCTCAATAC
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
45 43 0.91
46 4 0.09
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (45 bp):
TTGAACATGAGAGATACACAAATTGTCTTCACCATGACAAAGACA
Found at i:12924 original size:41 final size:41
Alignment explanation
Indices: 12879--12975 Score: 149
Period size: 41 Copynumber: 2.4 Consensus size: 41
12869 CACATGGTTT
* *
12879 TGCAAGAGTGTAATTGCCATAAGGTATATATTGCCAAAGGG
1 TGCAAGAGGGTAATTGCCATAAGATATATATTGCCAAAGGG
* *
12920 TGCAAGAGGGTAATTGCCATAAGATATATATTTCCAGAGGG
1 TGCAAGAGGGTAATTGCCATAAGATATATATTGCCAAAGGG
*
12961 TACAAGAGGGTAATT
1 TGCAAGAGGGTAATT
12976 AATTCTTAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.35, C:0.11, G:0.27, T:0.27
Consensus pattern (41 bp):
TGCAAGAGGGTAATTGCCATAAGATATATATTGCCAAAGGG
Found at i:14997 original size:23 final size:25
Alignment explanation
Indices: 14970--15018 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
14960 CTTTGTTCAT
*
14970 ATTTT-TAA-ACTTCTTCAACCTTC
1 ATTTTCTAACACTTCTTCAAACTTC
14993 ATTTTCTAACTACTTCTTCAAACTTC
1 ATTTTCTAAC-ACTTCTTCAAACTTC
15019 TTCAACCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 3 0.14
26 14 0.64
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTTTCTAACACTTCTTCAAACTTC
Found at i:17476 original size:18 final size:18
Alignment explanation
Indices: 17453--17488 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17443 TAAATAAACC
17453 ATTTCTTTGACTTATTAT
1 ATTTCTTTGACTTATTAT
*
17471 ATTTCTTTTACTTATTAT
1 ATTTCTTTGACTTATTAT
17489 GTTTTGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.11, G:0.03, T:0.64
Consensus pattern (18 bp):
ATTTCTTTGACTTATTAT
Found at i:17703 original size:10 final size:10
Alignment explanation
Indices: 17690--17720 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
17680 ATTATACTTG
17690 TTTATGGATT
1 TTTATGGATT
17700 TTTATGGATT
1 TTTATGGATT
*
17710 TTTATGTATT
1 TTTATGGATT
17720 T
1 T
17721 GTGTATTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.16, T:0.65
Consensus pattern (10 bp):
TTTATGGATT
Found at i:21240 original size:18 final size:15
Alignment explanation
Indices: 21205--21247 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
21195 TACAACAAAA
21205 AAAAATAATTTACTC
1 AAAAATAATTTACTC
21220 AAAAATAATTTACTC
1 AAAAATAATTTACTC
*
21235 AACAAAAAATTTA
1 AA-AAATAATTTA
21248 TAAAACAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAATAATTTACTC
Found at i:21247 original size:16 final size:15
Alignment explanation
Indices: 21204--21247 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
21194 TTACAACAAA
21204 AAAAAATAATTTACTC
1 AAAAAA-AATTTACTC
*
21220 AAAAATAATTTACTC
1 AAAAAAAATTTACTC
21235 AACAAAAAATTTA
1 AA-AAAAAATTTA
21248 TAAAACAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAAAAATTTACTC
Found at i:23755 original size:21 final size:21
Alignment explanation
Indices: 23731--23796 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 21
23721 GGATTGGAGT
23731 ATTTATTTATCTTGTTGCTTA
1 ATTTATTTATCTTGTTGCTTA
* * *
23752 ATTT-TATTATTTTCTTG-TTT
1 ATTTAT-TTATCTTGTTGCTTA
* *
23772 ATTTATTTTTCTTGTTTCTTTA
1 ATTTATTTATCTTGTTGC-TTA
23794 ATT
1 ATT
23797 CAAAAAACCC
Statistics
Matches: 33, Mismatches: 8, Indels: 7
0.69 0.17 0.15
Matches are distributed among these distances:
20 14 0.42
21 14 0.42
22 5 0.15
ACGTcount: A:0.17, C:0.08, G:0.06, T:0.70
Consensus pattern (21 bp):
ATTTATTTATCTTGTTGCTTA
Found at i:23779 original size:24 final size:25
Alignment explanation
Indices: 23733--23780 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
23723 ATTGGAGTAT
*
23733 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
23758 TTATTT-TCTTGTTTATTTATTTT
1 TTATTTATCTTGTTGATTAATTTT
23781 TCTTGTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:23783 original size:17 final size:17
Alignment explanation
Indices: 23761--23793 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
23751 AATTTTATTA
23761 TTTTCTTGTTTATTTAT
1 TTTTCTTGTTTATTTAT
*
23778 TTTTCTTGTTTCTTTA
1 TTTTCTTGTTTATTTA
23794 ATTCAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTCTTGTTTATTTAT
Found at i:25498 original size:24 final size:25
Alignment explanation
Indices: 25452--25499 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
25442 ATTTGAGTAT
*
25452 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
25477 TTATTT-TCTTGTTTATTTATTTT
1 TTATTTATCTTGTTGATTAATTTT
25500 TATTGTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:25699 original size:32 final size:32
Alignment explanation
Indices: 25658--25723 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
25648 CCATCATCAA
25658 TCATCTCTTTCTTTTCTTTTCCTTGTTTTTTT
1 TCATCTCTTTCTTTTCTTTTCCTTGTTTTTTT
25690 TCATCTCTTTCTTTTCTTTTCCTTGTTTTTTT
1 TCATCTCTTTCTTTTCTTTTCCTTGTTTTTTT
25722 TC
1 TC
25724 TGTCCTTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.03, C:0.23, G:0.03, T:0.71
Consensus pattern (32 bp):
TCATCTCTTTCTTTTCTTTTCCTTGTTTTTTT
Found at i:25722 original size:18 final size:18
Alignment explanation
Indices: 25669--25724 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
25659 CATCTCTTTC
25669 TTTTCTTTTCCTTGTTTT
1 TTTTCTTTTCCTTGTTTT
* * *
25687 TTTTC--AT-C-TCTTTC
1 TTTTCTTTTCCTTGTTTT
25701 TTTTCTTTTCCTTGTTTT
1 TTTTCTTTTCCTTGTTTT
25719 TTTTCT
1 TTTTCT
25725 GTCCTTATGT
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 9 0.32
15 1 0.04
16 2 0.07
17 1 0.04
18 15 0.54
ACGTcount: A:0.02, C:0.20, G:0.04, T:0.75
Consensus pattern (18 bp):
TTTTCTTTTCCTTGTTTT
Found at i:26132 original size:29 final size:29
Alignment explanation
Indices: 26090--26147 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
26080 CAACAATCAC
26090 CGCTGCTCTCCTTCTTCTTCTTCATTTGT
1 CGCTGCTCTCCTTCTTCTTCTTCATTTGT
26119 CGCTGCTCTCCTTCTTCTTCTTCATTTGT
1 CGCTGCTCTCCTTCTTCTTCTTCATTTGT
26148 TGTTCTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.03, C:0.34, G:0.10, T:0.52
Consensus pattern (29 bp):
CGCTGCTCTCCTTCTTCTTCTTCATTTGT
Found at i:27000 original size:45 final size:45
Alignment explanation
Indices: 26936--27027 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
26926 GCGGTCTGCC
26936 GTTTTCTTCTTCTTCTTCAGAGTACTGTTTCATTTACTACAAATT
1 GTTTTCTTCTTCTTCTTCAGAGTACTGTTTCATTTACTACAAATT
26981 GTTTTCTTCTTCTTCTTCAGAGTACTGTTTCATTTACTACAAATT
1 GTTTTCTTCTTCTTCTTCAGAGTACTGTTTCATTTACTACAAATT
27026 GT
1 GT
27028 AAGTATCAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.51
Consensus pattern (45 bp):
GTTTTCTTCTTCTTCTTCAGAGTACTGTTTCATTTACTACAAATT
Found at i:35208 original size:26 final size:26
Alignment explanation
Indices: 35152--35203 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
35142 TATATATATC
**
35152 ATTAGTCATTACGTTTTTTTTTTAGGA
1 ATTAGTCATTACGTTTTTTTTCCA-GA
35179 ATTAGTCATTACGTTTTTCTTTCCA
1 ATTAGTCATTACGTTTTT-TTTCCA
35204 TATTACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.21, C:0.13, G:0.12, T:0.54
Consensus pattern (26 bp):
ATTAGTCATTACGTTTTTTTTCCAGA
Found at i:35423 original size:139 final size:141
Alignment explanation
Indices: 35052--35450 Score: 646
Period size: 143 Copynumber: 2.8 Consensus size: 141
35042 TCCAATCAGA
* * * *
35052 TTTTATTTCCATATTAAAAAAGTC-TAAA--ATAATAACAATTATTTTTACATTAAACAACTTAT
1 TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATT-TTTTTACATTAAACAACTTAT
35114 TATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTTTAGGA
65 TATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACG--TTTTTTTTAGGA
*
35179 ATTAGTCATTACGT
128 ATTAATCATTACGT
*
35193 TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATTTTTTTACGTTAAACAACTTATT
1 TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATTTTTTTACATTAAACAACTTATT
35258 ATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTAGGAATT
66 ATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTAGGAATT
35323 AATCATTACGT
131 AATCATTACGT
* *
35334 TTTT-TTTCCGTATTACAAAAGTCTTAAATGATACTGATAATTTTTTTAC-TTAAACAACTTATT
1 TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATTTTTTTACATTAAACAACTTATT
* *
35397 ATTATAATTATTAAAATTATTATTAGTTATATATATTATTAGTCACTACGTTTT
66 ATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTT
35451 CCTTTCCATA
Statistics
Matches: 245, Mismatches: 10, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
139 66 0.27
140 43 0.18
141 51 0.21
142 4 0.02
143 71 0.29
144 10 0.04
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (141 bp):
TTTTCTTTCCATATTACAAAAGTCTTAAATGATACTAATAATTTTTTTACATTAAACAACTTATT
ATTATAATTATTAAAATTATTATTAGTTATATATATCATTAGTCATTACGTTTTTTTTAGGAATT
AATCATTACGT
Found at i:35457 original size:115 final size:113
Alignment explanation
Indices: 35320--35541 Score: 306
Period size: 115 Copynumber: 1.9 Consensus size: 113
35310 TTTTTTAGGA
* * * *
35320 ATTAATCATTACGTTTTTTTTCCGTATTACAAAAGTCTT-AAATGATACTGATA-ATTTTTTTAC
1 ATTAATCACTACGTTTTCTTTCCATATTACAAAAGT-TTAAAATAATACT-A-ACATTTTTTTAC
35383 -TTAAACAACTTATTATTATAATTATTAAAATTATTATTAGTTATATATATT
63 GTTAAACAACTTATTATTATAATTATTAAAATTATTATTA-TTATATATATT
*
35434 ATTAGTCACTACGTTTTCCTTTCCATATTACAAAAGTTTAAAATAATACTAACATTTTTTTACGT
1 ATTAATCACTACGTTTT-CTTTCCATATTACAAAAGTTTAAAATAATACTAACATTTTTTTACGT
* * *
35499 TAAACATCTTCTTATTATAATTATTAAACTTATTATTATTATA
65 TAAACAACTTATTATTATAATTATTAAAATTATTATTATTATA
35542 ACAATTATTA
Statistics
Matches: 96, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
113 1 0.01
114 33 0.34
115 62 0.65
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (113 bp):
ATTAATCACTACGTTTTCTTTCCATATTACAAAAGTTTAAAATAATACTAACATTTTTTTACGTT
AAACAACTTATTATTATAATTATTAAAATTATTATTATTATATATATT
Found at i:35536 original size:15 final size:16
Alignment explanation
Indices: 35513--35560 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
35503 CATCTTCTTA
*
35513 TTATAATTATTA-AAC
1 TTATTATTATTATAAC
35528 TTATTATTATTATAAC
1 TTATTATTATTATAAC
35544 AATTATTATTAGTTATA
1 --TTATTATTA-TTATA
35561 TGATCACTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 11 0.39
16 3 0.11
18 9 0.32
19 5 0.18
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (16 bp):
TTATTATTATTATAAC
Found at i:35549 original size:18 final size:17
Alignment explanation
Indices: 35510--35560 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
35500 AAACATCTTC
* *
35510 TTATTATAATTATTAAAC
1 TTATTATTATTA-TAAAA
35528 TTATTATTATTATAACAA
1 TTATTATTATTATAA-AA
35546 TTATTATTAGTTATA
1 TTATTATTA-TTATA
35561 TGATCACTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 3 0.10
18 21 0.72
19 5 0.17
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
TTATTATTATTATAAAA
Done.