Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015247.1 Corchorus capsularis cultivar CVL-1 contig15268, 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: 89983
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:851 original size:18 final size:18
Alignment explanation
Indices: 828--892 Score: 51
Period size: 18 Copynumber: 3.3 Consensus size: 18
818 CATCGCACAA
828 GCCATCCGGCCACAACCG
1 GCCATCCGGCCACAACCG
*
846 GCCATCGCACGGGC-CAACGCATG
1 GCCAT--C-CGGCCACAAC-C--G
869 CGCCATCCGGCCACAACCG
1 -GCCATCCGGCCACAACCG
888 GCCAT
1 GCCAT
893 TCGATCCATT
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
18 10 0.27
19 1 0.03
20 5 0.14
21 10 0.27
22 5 0.14
23 1 0.03
24 5 0.14
ACGTcount: A:0.22, C:0.46, G:0.25, T:0.08
Consensus pattern (18 bp):
GCCATCCGGCCACAACCG
Found at i:855 original size:42 final size:42
Alignment explanation
Indices: 809--892 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
799 CATGGGACGC
*
809 CGCACGAGACATCGCACAAGCCATCCGGCCACAACCGGCCAT
1 CGCACGAGACAACGCACAAGCCATCCGGCCACAACCGGCCAT
* * ***
851 CGCACGGGCCAACGCATGCGCCATCCGGCCACAACCGGCCAT
1 CGCACGAGACAACGCACAAGCCATCCGGCCACAACCGGCCAT
893 TCGATCCATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.25, C:0.44, G:0.24, T:0.07
Consensus pattern (42 bp):
CGCACGAGACAACGCACAAGCCATCCGGCCACAACCGGCCAT
Found at i:4950 original size:12 final size:12
Alignment explanation
Indices: 4929--4968 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
4919 GTTGTGGCCG
*
4929 GTTGCCCCATGC
1 GTTGCTCCATGC
4941 GTTGCTCCATGC
1 GTTGCTCCATGC
*
4953 GATGCTCCATGC
1 GTTGCTCCATGC
4965 GTTG
1 GTTG
4969 GCTGGTCATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.10, C:0.33, G:0.28, T:0.30
Consensus pattern (12 bp):
GTTGCTCCATGC
Found at i:5187 original size:22 final size:22
Alignment explanation
Indices: 5161--5243 Score: 103
Period size: 22 Copynumber: 3.8 Consensus size: 22
5151 GGCGCATAAG
* *
5161 TTCTGCCCAGAACTTGTACAGC
1 TTCTGCCCAGAACTTGGACAAC
* * *
5183 GTCTGTCCAAAACTTGGACAAC
1 TTCTGCCCAGAACTTGGACAAC
* *
5205 TTCCGCCCAGAACTGGGACAAC
1 TTCTGCCCAGAACTTGGACAAC
5227 TTCTGCCCAGAACTTGG
1 TTCTGCCCAGAACTTGG
5244 TCTGTTGAAA
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.23
Consensus pattern (22 bp):
TTCTGCCCAGAACTTGGACAAC
Found at i:8033 original size:18 final size:17
Alignment explanation
Indices: 7992--8035 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
7982 CCAATTGTCC
*
7992 TATTAATTTAGTTTAAT
1 TATTAGTTTAGTTTAAT
*
8009 TAGTTAGTTTAGTTTAGTT
1 TA-TTAGTTTAGTTTA-AT
8028 TATTAGTT
1 TATTAGTT
8036 AATTGAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 18 0.78
19 3 0.13
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (17 bp):
TATTAGTTTAGTTTAAT
Found at i:8360 original size:3 final size:3
Alignment explanation
Indices: 8352--8376 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
8342 GGTTCAACGG
8352 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
8377 AAATAGTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12959 original size:22 final size:23
Alignment explanation
Indices: 12924--12974 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
12914 AGGTTACTAA
*
12924 TATCAATATATCATA-TGGAGGT
1 TATCAACATATCATAGTGGAGGT
* **
12946 TATCAACATCTCATAGTGTTGGT
1 TATCAACATATCATAGTGGAGGT
12969 TATCAA
1 TATCAA
12975 AATTCCATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (23 bp):
TATCAACATATCATAGTGGAGGT
Found at i:13011 original size:22 final size:22
Alignment explanation
Indices: 12971--13012 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12961 GTGTTGGTTA
**
12971 TCAAAATTCCATATTAAGGTCT
1 TCAAAATTCCATAGGAAGGTCT
*
12993 TCAAAATTCCTTAGGAAGGT
1 TCAAAATTCCATAGGAAGGT
13013 TAACAAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (22 bp):
TCAAAATTCCATAGGAAGGTCT
Found at i:24366 original size:20 final size:21
Alignment explanation
Indices: 24326--24366 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
24316 AATAGAGCTA
24326 TTATTTATTTATTAATTTCTT
1 TTATTTATTTATTAATTTCTT
* *
24347 TTATTTCTTT-TTATTTTCTT
1 TTATTTATTTATTAATTTCTT
24367 ATTTTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (21 bp):
TTATTTATTTATTAATTTCTT
Found at i:24940 original size:15 final size:16
Alignment explanation
Indices: 24922--24952 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
24912 GAATTCAACA
24922 TTTTCAAC-TTCAAAC
1 TTTTCAACTTTCAAAC
24937 TTTTCAACTTTCAAAC
1 TTTTCAACTTTCAAAC
24953 CGCGAGACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTTCAACTTTCAAAC
Found at i:24990 original size:23 final size:23
Alignment explanation
Indices: 24960--25004 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
24950 AACCGCGAGA
24960 CTAGAATAGAGCCGTTTAAGGGC
1 CTAGAATAGAGCCGTTTAAGGGC
**
24983 CTAGAATAGAGTTGTTTAAGGG
1 CTAGAATAGAGCCGTTTAAGGG
25005 TCGGCTACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.27
Consensus pattern (23 bp):
CTAGAATAGAGCCGTTTAAGGGC
Found at i:32775 original size:25 final size:26
Alignment explanation
Indices: 32725--32775 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
32715 TAGAAAATTA
* *
32725 AGCGGCAAGATTTGTCTTTTTTTTTC
1 AGCGGAAAAATTTGTCTTTTTTTTTC
32751 AGCGGAAAAATTTGT-TTTTTTTTTC
1 AGCGGAAAAATTTGTCTTTTTTTTTC
32776 CCTTGTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.20, C:0.12, G:0.18, T:0.51
Consensus pattern (26 bp):
AGCGGAAAAATTTGTCTTTTTTTTTC
Found at i:37006 original size:81 final size:81
Alignment explanation
Indices: 36871--37030 Score: 293
Period size: 81 Copynumber: 2.0 Consensus size: 81
36861 TACCCCTGAC
* *
36871 AATTTGTTATTGGGTGAATGTGGTGCATCTTATAGCTGGACAAAATGGTAATTTCCTTTCCAACT
1 AATTTGTTATTGGGTGAATGTGGTGCATCTTATAGCTAGACAAAAGGGTAATTTCCTTTCCAACT
36936 TTAATATATGTTATAG
66 TTAATATATGTTATAG
*
36952 AATTTGTTCTTGGGTGAATGTGGTGCATCTTATAGCTAGACAAAAGGGTAATTTCCTTTCCAACT
1 AATTTGTTATTGGGTGAATGTGGTGCATCTTATAGCTAGACAAAAGGGTAATTTCCTTTCCAACT
37017 TTAATATATGTTAT
66 TTAATATATGTTAT
37031 TCTTGAAATA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 76 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (81 bp):
AATTTGTTATTGGGTGAATGTGGTGCATCTTATAGCTAGACAAAAGGGTAATTTCCTTTCCAACT
TTAATATATGTTATAG
Found at i:38182 original size:33 final size:33
Alignment explanation
Indices: 38140--38206 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
38130 TCGCATGGGG
**
38140 CAACCGGCCACAAACGGCCATCGTATGGGGCAT
1 CAACCGGCCACAAACGGCCATCCCATGGGGCAT
*
38173 CAACCGGCCACAACCGGCCATCCCATGGGGCAT
1 CAACCGGCCACAAACGGCCATCCCATGGGGCAT
38206 C
1 C
38207 CGCGCACAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.25, C:0.39, G:0.25, T:0.10
Consensus pattern (33 bp):
CAACCGGCCACAAACGGCCATCCCATGGGGCAT
Found at i:38217 original size:30 final size:31
Alignment explanation
Indices: 38127--38218 Score: 100
Period size: 33 Copynumber: 3.0 Consensus size: 31
38117 ATCGCATGCA
* *
38127 CCATCGCATGGGGCAACCG-GCCACAAACGG
1 CCATCGCATGGGGCATCCGCGCCACAACCGG
*
38157 CCATCGTATGGGGCATCAAC-CGGCCACAACCGG
1 CCATCGCATGGGGCATC--CGC-GCCACAACCGG
*
38190 CCATCCCATGGGGCATCCGCG-CACAACCG
1 CCATCGCATGGGGCATCCGCGCCACAACCG
38219 ACCAATGGAT
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
30 23 0.44
31 2 0.04
32 2 0.04
33 25 0.48
ACGTcount: A:0.24, C:0.39, G:0.27, T:0.10
Consensus pattern (31 bp):
CCATCGCATGGGGCATCCGCGCCACAACCGG
Found at i:43928 original size:22 final size:22
Alignment explanation
Indices: 43881--43933 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
43871 TACCTTTATC
* *
43881 TTTTTCTTTTTCGTTATTCTTC
1 TTTTTATTTTTCGTTATTCTTA
*
43903 TTTTTATTTTTCGTT-TTGTTTA
1 TTTTTATTTTTCGTTATT-CTTA
43925 TTTTTATTT
1 TTTTTATTT
43934 CTTTTCTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.08, C:0.09, G:0.06, T:0.77
Consensus pattern (22 bp):
TTTTTATTTTTCGTTATTCTTA
Found at i:45452 original size:34 final size:34
Alignment explanation
Indices: 45406--45472 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
45396 TTCCCAAAAC
45406 ATCCTTTACTACCCCTCTTTTGAATGATGAACGA
1 ATCCTTTACTACCCCTCTTTTGAATGATGAACGA
*
45440 ATCCTTTCCTACCCCTCTTTTGAATGATGAACG
1 ATCCTTTACTACCCCTCTTTTGAATGATGAACG
45473 GATCTGATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (34 bp):
ATCCTTTACTACCCCTCTTTTGAATGATGAACGA
Found at i:45658 original size:2 final size:2
Alignment explanation
Indices: 45651--45677 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45641 TTTATTACTC
45651 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
45678 TCTATTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48545 original size:21 final size:21
Alignment explanation
Indices: 48520--48564 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
48510 CTTCTATTAC
*
48520 CTTTATTC-TCAATTTCACTCA
1 CTTTAATCATCAATTTCACT-A
*
48541 CTTTAATCATTAATTTCACTA
1 CTTTAATCATCAATTTCACTA
48562 CTT
1 CTT
48565 CATCACTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.49
Consensus pattern (21 bp):
CTTTAATCATCAATTTCACTA
Found at i:53555 original size:33 final size:33
Alignment explanation
Indices: 53488--53603 Score: 175
Period size: 33 Copynumber: 3.6 Consensus size: 33
53478 TTCTTTTCAC
*
53488 CCAAAACAGAATTATTTTCAATGC---CATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
53518 CCAAAACAGAATTATTTTCAATGCTATGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
*
53551 CCAAAACATAATTATTTTCAATGCTATGATCAA
1 CCAAAACAGAATTATTTTCAATGCTATGATCAA
* *
53584 CCAAAACAGATTTGTTTTCA
1 CCAAAACAGAATTATTTTCA
53604 TCACAATTAG
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
30 24 0.31
33 54 0.69
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (33 bp):
CCAAAACAGAATTATTTTCAATGCTATGATCAA
Found at i:53621 original size:66 final size:63
Alignment explanation
Indices: 53488--53626 Score: 154
Period size: 66 Copynumber: 2.2 Consensus size: 63
53478 TTCTTTTCAC
* * *
53488 CCAAAACAGAATTATTTTCAATGCCATCAACCAAAACAGAATTATTTTCAATGCTATGATCAA
1 CCAAAACAGAATTATTTTCAATGCCATCAACCAAAACAGAATTATTTTCAATACAATGAGCAA
* * * * *
53551 CCAAAACATAATTATTTTCAATGCTATGATCAACCAAAACAGATTTGTTTTC-ATCACAATTAGC
1 CCAAAACAGAATTATTTTCAATGC---CATCAACCAAAACAGAATTATTTTCAAT-ACAATGAGC
*
53615 AT
62 AA
53617 CCAAAACAGA
1 CCAAAACAGA
53627 TTTAGTGTCA
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
63 23 0.37
65 2 0.03
66 37 0.60
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (63 bp):
CCAAAACAGAATTATTTTCAATGCCATCAACCAAAACAGAATTATTTTCAATACAATGAGCAA
Found at i:56258 original size:12 final size:12
Alignment explanation
Indices: 56237--56275 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
56227 GCGTTGGCCG
*
56237 GTTGCCCCATGC
1 GTTGCTCCATGC
56249 GTTGCTCCATGC
1 GTTGCTCCATGC
*
56261 GATGCT-CATGC
1 GTTGCTCCATGC
56272 GTTG
1 GTTG
56276 GCTGGTCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.10, C:0.31, G:0.28, T:0.31
Consensus pattern (12 bp):
GTTGCTCCATGC
Found at i:58303 original size:33 final size:33
Alignment explanation
Indices: 58266--58329 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
58256 CCTAATGTGA
* * *
58266 GTGTTGTTTGCGATGACACTAAGTCTGTTTTAG
1 GTGTTGTTTGCGATGAAACAAAATCTGTTTTAG
*
58299 GTGTTGTTTGTGATGAAACAAAATCTGTTTT
1 GTGTTGTTTGCGATGAAACAAAATCTGTTTT
58330 GGATGCTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.22, C:0.09, G:0.25, T:0.44
Consensus pattern (33 bp):
GTGTTGTTTGCGATGAAACAAAATCTGTTTTAG
Found at i:65902 original size:19 final size:18
Alignment explanation
Indices: 65865--65904 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
65855 TTCTTGAAAT
*
65865 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
65883 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
65902 AAT
1 AAT
65905 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:74880 original size:41 final size:41
Alignment explanation
Indices: 74815--74983 Score: 148
Period size: 42 Copynumber: 4.0 Consensus size: 41
74805 CTATTTTTGT
* **
74815 TTAATACCATCTCTTACTGGATACCATTTTTGACCCTT-TTAC
1 TTAATACCAT-TTTTACTTAATACCATTTTTGA-CCTTCTTAC
* * *
74857 TTAACACCATTTTTAATTAATACCATTCTTT-A-CTCCTTTAC
1 TTAATACCATTTTTACTTAATACCATT-TTTGACCTTC-TTAC
*
74898 TTAATACCAATTTTTACTCTACT-CCATTTTTTGACCTTCTTAC
1 TTAATACC-ATTTTTACT-TAATACCA-TTTTTGACCTTCTTAC
* * *
74941 TCAATACCATATTTCACTTGATACCATTTTTGACCTTCTTAC
1 TTAATACCAT-TTTTACTTAATACCATTTTTGACCTTCTTAC
74983 T
1 T
74984 GATTACTTCT
Statistics
Matches: 103, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
39 2 0.02
41 25 0.24
42 47 0.46
43 26 0.25
44 3 0.03
ACGTcount: A:0.25, C:0.25, G:0.04, T:0.46
Consensus pattern (41 bp):
TTAATACCATTTTTACTTAATACCATTTTTGACCTTCTTAC
Found at i:74902 original size:25 final size:25
Alignment explanation
Indices: 74868--74916 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
74858 TAACACCATT
74868 TTTAATTAATACC-ATTCTTTACTCC
1 TTTAATTAATACCAATT-TTTACTCC
*
74893 TTTACTTAATACCAATTTTTACTC
1 TTTAATTAATACCAATTTTTACTC
74917 TACTCCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTAATTAATACCAATTTTTACTCC
Found at i:75020 original size:14 final size:13
Alignment explanation
Indices: 74979--75078 Score: 78
Period size: 14 Copynumber: 7.3 Consensus size: 13
74969 TTTGACCTTC
74979 TTACTGATTACTT
1 TTACTGATTACTT
74992 CTTACTGATTACTT
1 -TTACTGATTACTT
75006 TTATCTGATTACTTTT
1 TTA-CTGATTAC--TT
*
75022 TTACT-ACT-CTT
1 TTACTGATTACTT
** **
75033 TGCCATTTTTACTTT
1 TTAC-TGATTAC-TT
75048 TTACTGATTACTCT
1 TTACTGATTACT-T
75062 TTACTGATTACTT
1 TTACTGATTACTT
75075 TTAC
1 TTAC
75079 CTTTTTACTG
Statistics
Matches: 69, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
11 4 0.06
12 1 0.01
13 11 0.16
14 42 0.61
15 6 0.09
16 5 0.07
ACGTcount: A:0.20, C:0.19, G:0.06, T:0.55
Consensus pattern (13 bp):
TTACTGATTACTT
Found at i:75072 original size:21 final size:21
Alignment explanation
Indices: 75048--75094 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
75038 TTTTTACTTT
75048 TTACTGATTA-CTCTTTACTGA
1 TTACT-ATTACCTCTTTACTGA
* *
75069 TTACTTTTACCTTTTTACTGA
1 TTACTATTACCTCTTTACTGA
75090 TTACT
1 TTACT
75095 CTTAGCTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.53
Consensus pattern (21 bp):
TTACTATTACCTCTTTACTGA
Found at i:75382 original size:32 final size:32
Alignment explanation
Indices: 75323--75409 Score: 129
Period size: 32 Copynumber: 2.7 Consensus size: 32
75313 TTCTTAATTA
*
75323 TTAATTTACTGATTAGTCCTTTTTACTTCCTTTC
1 TTAA-TTACTGATTAAT-CTTTTTACTTCCTTTC
*
75357 TTAATTACTGATTAATCTTTTTACTTCCTTTT
1 TTAATTACTGATTAATCTTTTTACTTCCTTTC
*
75389 TTAATTACTGATTACTCTTTT
1 TTAATTACTGATTAATCTTTT
75410 ACTCTCTCCC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 35 0.70
33 11 0.22
34 4 0.08
ACGTcount: A:0.21, C:0.17, G:0.05, T:0.57
Consensus pattern (32 bp):
TTAATTACTGATTAATCTTTTTACTTCCTTTC
Found at i:75539 original size:38 final size:38
Alignment explanation
Indices: 75487--75651 Score: 285
Period size: 38 Copynumber: 4.3 Consensus size: 38
75477 TATTTCTACC
* * *
75487 TTGACTCTTGATTATCAATTTTACTGATTATTCTTACT
1 TTGACTCTTAATTATCAATTTTACTGATTACTATTACT
75525 TTGACTCTTAATTATCAATTTTACTGATTACTATTACT
1 TTGACTCTTAATTATCAATTTTACTGATTACTATTACT
*
75563 TTGACTCTTAATTATCAATTTTACTGATTACTATTATT
1 TTGACTCTTAATTATCAATTTTACTGATTACTATTACT
*
75601 TTGGCTCTTAATTATCAATTTTACTGATTACTATTACT
1 TTGACTCTTAATTATCAATTTTACTGATTACTATTACT
75639 TTGACTCTTAATT
1 TTGACTCTTAATT
75652 TTGTTGGGAT
Statistics
Matches: 120, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 120 1.00
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.52
Consensus pattern (38 bp):
TTGACTCTTAATTATCAATTTTACTGATTACTATTACT
Found at i:76326 original size:24 final size:23
Alignment explanation
Indices: 76285--76331 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
76275 ATTTATCATG
76285 AATCCATTATTATGTTATTATGCT
1 AATCCATTATTATGTTA-TATGCT
*
76309 AATCTATTATTAAT-TTATATGCT
1 AATCCATTATT-ATGTTATATGCT
76332 CTAATTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 13 0.62
25 2 0.10
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (23 bp):
AATCCATTATTATGTTATATGCT
Found at i:80397 original size:15 final size:16
Alignment explanation
Indices: 80377--80417 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
80367 TTGACGTGTC
80377 TTTTCCTTTATTT-TT
1 TTTTCCTTTATTTCTT
80392 TTTTCCTTT-TTTCTT
1 TTTTCCTTTATTTCTT
*
80407 TTTTCTTTTAT
1 TTTTCCTTTAT
80418 CTTTATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 3 0.13
15 19 0.83
16 1 0.04
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTCCTTTATTTCTT
Found at i:80407 original size:7 final size:7
Alignment explanation
Indices: 80377--80454 Score: 50
Period size: 7 Copynumber: 10.3 Consensus size: 7
80367 TTGACGTGTC
*
80377 TTTTCCT
1 TTTTTCT
80384 TTATTT-T
1 TT-TTTCT
80391 TTTTTCCT
1 TTTTT-CT
80399 TTTTTCT
1 TTTTTCT
80406 TTTTTCT
1 TTTTTCT
*
80413 TTTATCTTT
1 TTT-T-TCT
80422 ATTTTATCT
1 -TTTT-TCT
*
80431 TTTTCCT
1 TTTTTCT
*
80438 TTTATCT
1 TTTTTCT
80445 TTTTATCT
1 TTTT-TCT
80453 TT
1 TT
80455 CTTTTTCTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
6 3 0.05
7 27 0.48
8 18 0.32
9 5 0.09
10 3 0.05
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCT
Found at i:80408 original size:14 final size:14
Alignment explanation
Indices: 80377--80448 Score: 69
Period size: 14 Copynumber: 5.3 Consensus size: 14
80367 TTGACGTGTC
* *
80377 TTTTCCTTTATTTTT
1 TTTTCCTTT-TATCT
*
80392 TTTTCCTTTTTTCT
1 TTTTCCTTTTATCT
*
80406 TTTTTCTTTTATC-
1 TTTTCCTTTTATCT
*
80419 -TTT-ATTTTATCT
1 TTTTCCTTTTATCT
80431 TTTTCCTTTTATCT
1 TTTTCCTTTTATCT
80445 TTTT
1 TTTT
80449 ATCTTTCTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
11 7 0.14
12 3 0.06
13 3 0.06
14 27 0.55
15 9 0.18
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTCCTTTTATCT
Found at i:80426 original size:25 final size:24
Alignment explanation
Indices: 80398--80461 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 24
80388 TTTTTTTTCC
*
80398 TTTTTTCTTTTTTCTTTTATCTTT
1 TTTTTTCTTTTTCCTTTTATCTTT
*
80422 ATTTTATCTTTTTCCTTTTATCTTT
1 -TTTTTTCTTTTTCCTTTTATCTTT
80447 TTATCTTTCTTTTTC
1 TT-T-TTTCTTTTTC
80462 TATTATTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.06
25 23 0.68
26 9 0.26
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTTTCTTTTTCCTTTTATCTTT
Found at i:81671 original size:20 final size:20
Alignment explanation
Indices: 81646--81683 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
81636 GTCATTTGGT
*
81646 CTTTTAGCCATGTGTCACGC
1 CTTTTAGCCACGTGTCACGC
81666 CTTTTAGCCACGTGTCAC
1 CTTTTAGCCACGTGTCAC
81684 TCTCACTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.32, G:0.18, T:0.34
Consensus pattern (20 bp):
CTTTTAGCCACGTGTCACGC
Found at i:82160 original size:51 final size:54
Alignment explanation
Indices: 82071--82177 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 54
82061 AAAGGAATTG
* * **
82071 AATTTTAAAAAATATGATAAACATGTTAAAAAAACAAAAAGGATTATTTTTTTT
1 AATTTTAAAAAATATGATAAACACGTTAAAAAAACAAAAAAGATTAACTTTTTT
*
82125 AATTTT-AAAAATATGATAAACACG-T-AAAAATCAAAAAAGATTAACTTTTTT
1 AATTTTAAAAAATATGATAAACACGTTAAAAAAACAAAAAAGATTAACTTTTTT
82176 AA
1 AA
82178 CAAATTAAGA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
51 24 0.50
52 1 0.02
53 17 0.35
54 6 0.12
ACGTcount: A:0.53, C:0.06, G:0.07, T:0.35
Consensus pattern (54 bp):
AATTTTAAAAAATATGATAAACACGTTAAAAAAACAAAAAAGATTAACTTTTTT
Found at i:83807 original size:17 final size:18
Alignment explanation
Indices: 83780--83813 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
83770 GATCTCGAAG
*
83780 ATTTATTTTTTTATTTTT
1 ATTTATTTTTTAATTTTT
83798 ATTT-TTTTTTAATTTT
1 ATTTATTTTTTAATTTT
83814 CTTCCTTCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (18 bp):
ATTTATTTTTTAATTTTT
Found at i:88632 original size:24 final size:24
Alignment explanation
Indices: 88605--88652 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
88595 ATCAGCATCT
88605 GAATCTGAACTAGACAAGTCATTC
1 GAATCTGAACTAGACAAGTCATTC
88629 GAATCTGAACTAGACAAGTCATTC
1 GAATCTGAACTAGACAAGTCATTC
88653 TCCTCCTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (24 bp):
GAATCTGAACTAGACAAGTCATTC
Done.