Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011874.1 Corchorus capsularis cultivar CVL-1 contig11895, 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: 80839
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:677 original size:24 final size:23
Alignment explanation
Indices: 649--712 Score: 71
Period size: 24 Copynumber: 2.9 Consensus size: 23
639 ATTTTTTTTC
*
649 TCAATAGAATATATTCCTTTCTTT
1 TCAATAGAATATATTCCTTTC-CT
* *
673 TCAATAGAATATTTTCCATTCCT
1 TCAATAGAATATATTCCTTTCCT
696 T---TAGAATATATTCCTTT
1 TCAATAGAATATATTCCTTT
713 GAATTCAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 14 0.40
23 2 0.06
24 19 0.54
ACGTcount: A:0.30, C:0.17, G:0.05, T:0.48
Consensus pattern (23 bp):
TCAATAGAATATATTCCTTTCCT
Found at i:744 original size:3 final size:3
Alignment explanation
Indices: 736--773 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
726 TTGTCTGACA
736 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
774 TATATTCGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4407 original size:35 final size:35
Alignment explanation
Indices: 4317--4415 Score: 144
Period size: 37 Copynumber: 2.8 Consensus size: 35
4307 TTTAGTTAAA
* *
4317 ACTAGTATTATCATGTTTAGTTATTTTAATTGTCT
1 ACTAGTATTCTCATGTTTAGTTGTTTTAATTGTCT
*
4352 ACTAGTATTTTCTCATGTTTAGTTGTTTTAATTGTGT
1 ACTAGTA--TTCTCATGTTTAGTTGTTTTAATTGTCT
*
4389 ACTACTATTCTCATGTTTAGTTGTTTT
1 ACTAGTATTCTCATGTTTAGTTGTTTT
4416 TATAATTTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
35 27 0.47
37 31 0.53
ACGTcount: A:0.21, C:0.10, G:0.13, T:0.56
Consensus pattern (35 bp):
ACTAGTATTCTCATGTTTAGTTGTTTTAATTGTCT
Found at i:5269 original size:2 final size:2
Alignment explanation
Indices: 5262--5293 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5252 AGCAGGGTCC
5262 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5294 TGTGGGAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6986 original size:31 final size:31
Alignment explanation
Indices: 6919--7018 Score: 119
Period size: 31 Copynumber: 3.2 Consensus size: 31
6909 TGTGCACGTG
* * **
6919 CGTGGCATGCCACGTGCCATTTTTTGAAACA
1 CGTGGCATGCCACGTGTCACTTTTTGGTACA
*
6950 TGTGGCATGCCACGTGTCACTTTTTGGTACA
1 CGTGGCATGCCACGTGTCACTTTTTGGTACA
* * *
6981 CGTGGCGTGACATGTGTCACTTTTTGGTACA
1 CGTGGCATGCCACGTGTCACTTTTTGGTACA
*
7012 TGTGGCA
1 CGTGGCA
7019 CAACTTTTTG
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (31 bp):
CGTGGCATGCCACGTGTCACTTTTTGGTACA
Found at i:7030 original size:53 final size:53
Alignment explanation
Indices: 6968--7070 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 53
6958 GCCACGTGTC
** * *
6968 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACA
1 ACTTTTTGGTACACGTGGCGTGACACATATCACTTTTTGGTACACGTGGCACA
* * * *
7021 ACTTTTTGGTATATGTGGTGTGTCACATATCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCGTGACACATATCACTTTTTGGTACACGTGGC
7071 GTGCCACGTC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.39
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCGTGACACATATCACTTTTTGGTACACGTGGCACA
Found at i:9957 original size:53 final size:52
Alignment explanation
Indices: 9825--9974 Score: 187
Period size: 53 Copynumber: 2.8 Consensus size: 52
9815 TTATAAGTCT
* *
9825 CTAAACACAGAGGCAATTCTATATCAAAGTCCTCAAACACAAGGGTATTCATCC
1 CTAAACACAGAGGC-ATT-TACATCAAAGTCCTCAAACACAAGGGTATTCACCC
* * *
9879 CTAAACACAGATGCACCTGT-C-TCAAAAGTCCCCAAACACAAGGGTATTCACCC
1 CTAAACACAGAGGCA--TTTACATC-AAAGTCCTCAAACACAAGGGTATTCACCC
*
9932 CTAAACACAGAGGCATTTACATCAAAGTCCTCAAGCACAAGGG
1 CTAAACACAGAGGCATTTACATCAAAGTCCTCAAACACAAGGG
9975 CATCTATATT
Statistics
Matches: 82, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
51 2 0.02
52 21 0.26
53 44 0.54
54 14 0.17
55 1 0.01
ACGTcount: A:0.38, C:0.29, G:0.15, T:0.19
Consensus pattern (52 bp):
CTAAACACAGAGGCATTTACATCAAAGTCCTCAAACACAAGGGTATTCACCC
Found at i:9989 original size:30 final size:30
Alignment explanation
Indices: 9955--10030 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
9945 CATTTACATC
* * *
9955 AAAGTCCTCAAGCACAAG-GGCATCTATATT
1 AAAGTCC-CAAACACAAGAGACATCTATACT
9985 AAAGTCCCTAAACAC-AGAGACATCTATACT
1 AAAGTCCC-AAACACAAGAGACATCTATACT
10015 AAAGTCCCCAAACACA
1 AAAGT-CCCAAACACA
10031 TATAACAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 3 0.08
30 33 0.85
31 3 0.08
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.18
Consensus pattern (30 bp):
AAAGTCCCAAACACAAGAGACATCTATACT
Found at i:17712 original size:15 final size:14
Alignment explanation
Indices: 17698--17748 Score: 75
Period size: 15 Copynumber: 3.5 Consensus size: 14
17688 TCATACATAC
*
17698 CCAAAGACCAAATA
1 CCAAATACCAAATA
17712 CCAAATATCCAAATA
1 CCAAATA-CCAAATA
17727 CCAAATACCAAATA
1 CCAAATACCAAATA
17741 TCCAAATA
1 -CCAAATA
17749 TTCAAATACT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
14 13 0.38
15 21 0.62
ACGTcount: A:0.55, C:0.27, G:0.02, T:0.16
Consensus pattern (14 bp):
CCAAATACCAAATA
Found at i:17714 original size:7 final size:7
Alignment explanation
Indices: 17698--17748 Score: 75
Period size: 7 Copynumber: 7.0 Consensus size: 7
17688 TCATACATAC
*
17698 CCAAAGA
1 CCAAATA
17705 CCAAATA
1 CCAAATA
17712 CCAAATA
1 CCAAATA
17719 TCCAAATA
1 -CCAAATA
17727 CCAAATA
1 CCAAATA
17734 CCAAATA
1 CCAAATA
17741 TCCAAATA
1 -CCAAATA
17749 TTCAAATACT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
7 27 0.66
8 14 0.34
ACGTcount: A:0.55, C:0.27, G:0.02, T:0.16
Consensus pattern (7 bp):
CCAAATA
Found at i:17747 original size:22 final size:22
Alignment explanation
Indices: 17698--17757 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
17688 TCATACATAC
*
17698 CCAAAGACCAAATACCAAATAT
1 CCAAATACCAAATACCAAATAT
17720 CCAAATACCAAATACCAAATAT
1 CCAAATACCAAATACCAAATAT
*
17742 CCAAATATTCAAATAC
1 CCAAATA-CCAAATAC
17758 TCATCAGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 28 0.80
23 7 0.20
ACGTcount: A:0.53, C:0.27, G:0.02, T:0.18
Consensus pattern (22 bp):
CCAAATACCAAATACCAAATAT
Found at i:22640 original size:54 final size:53
Alignment explanation
Indices: 22573--22723 Score: 189
Period size: 53 Copynumber: 2.8 Consensus size: 53
22563 CATTTATAAG
22573 TCCCTAAACACAGAGGCAATTCTATATCAAAGTCCTCAAACACAAGAGTATTCA
1 TCCCTAAACACAGAGGC-ATTCTATATCAAAGTCCTCAAACACAAGAGTATTCA
* * * * * *
22627 TCCCTAAAAACAGAGGCA-CCTCTCTCAAAAATCCTCAAACACAAGGGTATTCA
1 TCCCTAAACACAGAGGCATTCTATATC-AAAGTCCTCAAACACAAGAGTATTCA
* * *
22680 CCCCTAAACACAGAGGCATT-TACATCAAAGTCCTCAAGCACAAG
1 TCCCTAAACACAGAGGCATTCTATATCAAAGTCCTCAAACACAAG
22724 GGCATCTATA
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
52 21 0.26
53 44 0.54
54 16 0.20
ACGTcount: A:0.40, C:0.29, G:0.12, T:0.19
Consensus pattern (53 bp):
TCCCTAAACACAGAGGCATTCTATATCAAAGTCCTCAAACACAAGAGTATTCA
Found at i:22740 original size:30 final size:30
Alignment explanation
Indices: 22706--22781 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
22696 CATTTACATC
* * *
22706 AAAGTCCTCAAGCACAAG-GGCATCTATATT
1 AAAGTCC-CAAACACAAGAGACATCTATACT
22736 AAAGTCCCTAAACAC-AGAGACATCTATACT
1 AAAGTCCC-AAACACAAGAGACATCTATACT
22766 AAAGTCCCCAAACACA
1 AAAGT-CCCAAACACA
22782 TATAACATAG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 3 0.08
30 33 0.85
31 3 0.08
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.18
Consensus pattern (30 bp):
AAAGTCCCAAACACAAGAGACATCTATACT
Found at i:22869 original size:2 final size:2
Alignment explanation
Indices: 22862--22897 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
22852 TTCCATTATT
*
22862 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22898 ATAACAAAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:24685 original size:12 final size:12
Alignment explanation
Indices: 24668--24697 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
24658 TTATTATGAT
24668 TTGATGGAAAGA
1 TTGATGGAAAGA
24680 TTGATGGAAAGA
1 TTGATGGAAAGA
*
24692 TGGATG
1 TTGATG
24698 AGTAATAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.27
Consensus pattern (12 bp):
TTGATGGAAAGA
Found at i:27251 original size:17 final size:17
Alignment explanation
Indices: 27205--27252 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
27195 TCAGATTGTA
27205 ATTTGTTTAATTTAA-G
1 ATTTGTTTAATTTAATG
* *
27221 A-TT-TTCATTTTAATG
1 ATTTGTTTAATTTAATG
27236 ATTTGTTTAATTTAATG
1 ATTTGTTTAATTTAATG
27253 CTTAATTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
14 8 0.32
15 4 0.16
16 3 0.12
17 10 0.40
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.58
Consensus pattern (17 bp):
ATTTGTTTAATTTAATG
Found at i:27269 original size:10 final size:10
Alignment explanation
Indices: 27254--27300 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
27244 AATTTAATGC
*
27254 TTAATTTGTT
1 TTAATTTGTA
27264 TTAATTTGTA
1 TTAATTTGTA
*
27274 ATAATTTAGTA
1 TTAATTT-GTA
*
27285 TTAATTAGTA
1 TTAATTTGTA
27295 TTAATT
1 TTAATT
27301 AATTTAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 24 0.75
11 8 0.25
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (10 bp):
TTAATTTGTA
Found at i:27290 original size:21 final size:20
Alignment explanation
Indices: 27255--27300 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
27245 ATTTAATGCT
* *
27255 TAATTTGTTTTAATTTGTAA
1 TAATTTGTATTAATTAGTAA
*
27275 TAATTTAGTATTAATTAGTAT
1 TAATTT-GTATTAATTAGTAA
27296 TAATT
1 TAATT
27301 AATTTAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (20 bp):
TAATTTGTATTAATTAGTAA
Found at i:31187 original size:29 final size:31
Alignment explanation
Indices: 31111--31191 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 31
31101 CGTAACACCT
* ** *
31111 CTTTTACGGCAAAACTCACCAT-GCAAAGCA
1 CTTTTACAGCAAAACTCACTTTACCAAAGCA
*
31141 CTTTTACCGCAAAACTCACTTTACCAAA-CA
1 CTTTTACAGCAAAACTCACTTTACCAAAGCA
*
31171 C-TTTACAGCAAATCTCACTTT
1 CTTTTACAGCAAAACTCACTTT
31192 GCGATAGCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 18 0.41
30 22 0.50
31 4 0.09
ACGTcount: A:0.35, C:0.31, G:0.07, T:0.27
Consensus pattern (31 bp):
CTTTTACAGCAAAACTCACTTTACCAAAGCA
Found at i:32088 original size:37 final size:37
Alignment explanation
Indices: 32035--32136 Score: 116
Period size: 37 Copynumber: 2.8 Consensus size: 37
32025 CTTTGCGATA
* *
32035 ACACTCTTCATCGCAGAGCTCTCCTTACCGCGGTAGC
1 ACACTCTTTACCGCAGAGCTCTCCTTACCGCGGTAGC
* *
32072 ACCCTCTTTACCGCAGAGCTC-CGCTTACTGCGGTAGC
1 ACACTCTTTACCGCAGAGCTCTC-CTTACCGCGGTAGC
* * * *
32109 ACATTCTTTGCGGCAGAGCTCTCATTAC
1 ACACTCTTTACCGCAGAGCTCTCCTTAC
32137 AAGGCACTGC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
36 1 0.02
37 52 0.96
38 1 0.02
ACGTcount: A:0.19, C:0.35, G:0.20, T:0.26
Consensus pattern (37 bp):
ACACTCTTTACCGCAGAGCTCTCCTTACCGCGGTAGC
Found at i:43011 original size:11 final size:11
Alignment explanation
Indices: 42993--43026 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
42983 AATTGTCTTC
42993 AAATCTTCAAA
1 AAATCTTCAAA
*
43004 ATATCTTCAAA
1 AAATCTTCAAA
43015 AAATCTTCAAA
1 AAATCTTCAAA
43026 A
1 A
43027 CACGAACTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (11 bp):
AAATCTTCAAA
Found at i:46707 original size:21 final size:20
Alignment explanation
Indices: 46668--46712 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
46658 AGAAATTAAT
* *
46668 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
46688 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
46709 TAAA
1 TAAA
46713 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:52154 original size:17 final size:17
Alignment explanation
Indices: 52132--52171 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
52122 CTTTAAAGAA
* *
52132 TTTTTTTAGTTTTGATT
1 TTTTTTTAGGTTAGATT
*
52149 TTTTTTTGGGTTAGATT
1 TTTTTTTAGGTTAGATT
52166 TTTTTT
1 TTTTTT
52172 CGCCTTAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.15, T:0.75
Consensus pattern (17 bp):
TTTTTTTAGGTTAGATT
Found at i:53417 original size:16 final size:16
Alignment explanation
Indices: 53381--53419 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
53371 ACCCGAAAAT
* *
53381 ACCCAAATCCGACATA
1 ACCCGAATCCGACAGA
53397 ACCCGAATCCGACAGA
1 ACCCGAATCCGACAGA
53413 ACCCGAA
1 ACCCGAA
53420 CCCAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.38, G:0.13, T:0.08
Consensus pattern (16 bp):
ACCCGAATCCGACAGA
Found at i:55297 original size:2 final size:2
Alignment explanation
Indices: 55290--55336 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
55280 CTTTATAGGA
* *
55290 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AC AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55331 AT AT AT
1 AT AT AT
55337 CAGTATTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:62479 original size:24 final size:24
Alignment explanation
Indices: 62420--62487 Score: 66
Period size: 27 Copynumber: 2.7 Consensus size: 24
62410 TGTTTATATG
*
62420 ATATATATATAATATATACATTATT
1 ATATATATAT-ATATATACATTATC
*
62445 ATTAGATTATATATATATCACATTA-C
1 A-TATA-TATATATATAT-ACATTATC
*
62471 ATATATATATAAATATA
1 ATATATATATATATATA
62488 TTATAAGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
23 1 0.03
24 10 0.28
25 4 0.11
26 10 0.28
27 11 0.31
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (24 bp):
ATATATATATATATATACATTATC
Found at i:62712 original size:14 final size:14
Alignment explanation
Indices: 62689--62718 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
62679 TGAGTTCATC
*
62689 CACATTTACATATA
1 CACATATACATATA
62703 CACATATACATATA
1 CACATATACATATA
62717 CA
1 CA
62719 TTAGATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (14 bp):
CACATATACATATA
Found at i:70090 original size:11 final size:11
Alignment explanation
Indices: 70074--70127 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
70064 TCTCCAAGAA
70074 ATTTCTCATCT
1 ATTTCTCATCT
70085 ATTTCT-ATTCT
1 ATTTCTCA-TCT
*
70096 GTTTTCTCATCT
1 -ATTTCTCATCT
*
70108 -TTT-TCTTCT
1 ATTTCTCATCT
70117 ATTTCTCATCT
1 ATTTCTCATCT
70128 CCTTCTTCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
9 5 0.14
10 7 0.20
11 14 0.40
12 8 0.23
13 1 0.03
ACGTcount: A:0.13, C:0.24, G:0.02, T:0.61
Consensus pattern (11 bp):
ATTTCTCATCT
Found at i:70133 original size:20 final size:20
Alignment explanation
Indices: 70098--70135 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
70088 TCTATTCTGT
**
70098 TTTCTCATCTTTTTCTTCTA
1 TTTCTCATCTCCTTCTTCTA
70118 TTTCTCATCTCCTTCTTC
1 TTTCTCATCTCCTTCTTC
70136 CTAGATAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.08, C:0.32, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTCTCATCTCCTTCTTCTA
Found at i:75099 original size:20 final size:20
Alignment explanation
Indices: 75064--75101 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
75054 TCTGTTCTGT
**
75064 TTTCTCATCTTTTTCTTCTA
1 TTTCTCATCTCCTTCTTCTA
75084 TTTCTCATCTCCTTCTTC
1 TTTCTCATCTCCTTCTTC
75102 CTAGATAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.08, C:0.32, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTCTCATCTCCTTCTTCTA
Found at i:75886 original size:30 final size:28
Alignment explanation
Indices: 75815--75892 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
75805 GAACTTACAC
*
75815 AAAACGGCCAAATAAGCCCCTGAACTCT
1 AAAAAGGCCAAATAAGCCCCTGAACTCT
**
75843 -AATTGCAGCCAAATAAGCCCCTGAACTCTTT
1 AAAAAG--GCCAAATAAGCCCCTGAACTC--T
75874 AAAAAGGCCAAATAAGCCC
1 AAAAAGGCCAAATAAGCCC
75893 TTTCTAAATG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 3 0.07
29 21 0.51
30 13 0.32
31 1 0.02
32 3 0.07
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.17
Consensus pattern (28 bp):
AAAAAGGCCAAATAAGCCCCTGAACTCT
Found at i:77056 original size:6 final size:6
Alignment explanation
Indices: 77047--77087 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
77037 CTCTTCTTCA
*
77047 TCTTTC TCTTTC TCTTTC TCTTTC T-TGT- TCTTTC T-TTTC TC
1 TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC TC
77088 ACTTTCGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
4 1 0.03
5 9 0.30
6 20 0.67
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.68
Consensus pattern (6 bp):
TCTTTC
Found at i:77777 original size:2 final size:2
Alignment explanation
Indices: 77770--77800 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
77760 TACATATCTC
77770 TA TA 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 TA TA T
77801 CACGTTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:79855 original size:39 final size:39
Alignment explanation
Indices: 79812--79890 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
79802 ACAAACCTTG
* *
79812 TATATATGAATTTAAAGATAAATAAAAATCTAAGGAAAT
1 TATATATGAACTTAAAGATAAATAAAAATATAAGGAAAT
* *
79851 TATATTTGAACTTAAAGATAAATAATAATATAAGGAAAT
1 TATATATGAACTTAAAGATAAATAAAAATATAAGGAAAT
79890 T
1 T
79891 TTGCAAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.54, C:0.03, G:0.10, T:0.33
Consensus pattern (39 bp):
TATATATGAACTTAAAGATAAATAAAAATATAAGGAAAT
Found at i:80210 original size:28 final size:26
Alignment explanation
Indices: 80179--80239 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 26
80169 TTATTTTAGA
*
80179 CAAACTCTTAACCAATTTTAATCTCAAC
1 CAAACTCTT-A-CAATTTCAATCTCAAC
80207 CAAACTC--ACAATTTCAATCTCAAC
1 CAAACTCTTACAATTTCAATCTCAAC
*
80231 CAACCTCTT
1 CAAACTCTT
80240 CAAGATTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 21 0.72
25 1 0.03
28 7 0.24
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.30
Consensus pattern (26 bp):
CAAACTCTTACAATTTCAATCTCAAC
Found at i:80345 original size:34 final size:34
Alignment explanation
Indices: 80305--80413 Score: 155
Period size: 34 Copynumber: 3.1 Consensus size: 34
80295 ATATCCACTT
*
80305 AACCCGTAATATATAATTGGAATTGGACTAAGAA
1 AACCCGTAATATATAATTGGAATTGGACTAAAAA
*
80339 AACCCGTAATATATAATTTGAATTGGACTAATAAAA
1 AACCCGTAATATATAATTGGAATTGGACT-A-AAAA
80375 TTCAACCCGTAATATATAATTGGAATTGGACTAAAAA
1 ---AACCCGTAATATATAATTGGAATTGGACTAAAAA
80412 AA
1 AA
80414 TTCAATTTGA
Statistics
Matches: 67, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
34 30 0.45
35 1 0.01
36 3 0.04
37 4 0.06
38 1 0.01
39 28 0.42
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (34 bp):
AACCCGTAATATATAATTGGAATTGGACTAAAAA
Found at i:80384 original size:39 final size:38
Alignment explanation
Indices: 80305--80418 Score: 164
Period size: 39 Copynumber: 3.1 Consensus size: 38
80295 ATATCCACTT
*
80305 AACCCGTAATATATAATTGGAATTGGACT-AAGAA---
1 AACCCGTAATATATAATTGGAATTGGACTAAAAAATTC
*
80339 AACCCGTAATATATAATTTGAATTGGACTAATAAAATTC
1 AACCCGTAATATATAATTGGAATTGGACTAA-AAAATTC
80378 AACCCGTAATATATAATTGGAATTGGACTAAAAAAATTC
1 AACCCGTAATATATAATTGGAATTGGACT-AAAAAATTC
80417 AA
1 AA
80419 TTTGATTACT
Statistics
Matches: 71, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
34 28 0.39
35 1 0.01
36 3 0.04
39 37 0.52
40 2 0.03
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (38 bp):
AACCCGTAATATATAATTGGAATTGGACTAAAAAATTC
Done.