Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008753.1 Corchorus capsularis cultivar CVL-1 contig08774, 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: 45737
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Found at i:6164 original size:2 final size:2
Alignment explanation
Indices: 6157--6181 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6147 GGGTTTTGAT
6157 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
6182 AGATTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9828 original size:21 final size:19
Alignment explanation
Indices: 9799--9837 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
9789 TGGGTTTGGG
*
9799 TTTGGCCTTTCTTTATTTATC
1 TTTGCCCTTT-TTT-TTTATC
9820 TTTGCCCTTTTTTTTTAT
1 TTTGCCCTTTTTTTTTAT
9838 TTTCTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 3 0.18
21 9 0.53
ACGTcount: A:0.08, C:0.18, G:0.08, T:0.67
Consensus pattern (19 bp):
TTTGCCCTTTTTTTTTATC
Found at i:10206 original size:33 final size:32
Alignment explanation
Indices: 10127--10233 Score: 110
Period size: 33 Copynumber: 3.3 Consensus size: 32
10117 TGTCCCAAGA
* *
10127 GGGCGGCTT-ACCGTGGCGAAGCCGCCCCACTT
1 GGGCGGCTTCACCAT-GCGAAGCCGCCCCACTG
*
10159 GGGAGGC-TCAACCATAGCGAAGCCGCCCCACTG
1 GGGCGGCTTC-ACCAT-GCGAAGCCGCCCCACTG
** *
10192 GGGCGGCTTCACCATGAAAAGGCCGCCCCATTG
1 GGGCGGCTTCACCATGCGAA-GCCGCCCCACTG
10225 GGGCGGCTT
1 GGGCGGCTT
10234 AGCCACGGCA
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
31 1 0.02
32 9 0.14
33 51 0.81
34 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.34, T:0.14
Consensus pattern (32 bp):
GGGCGGCTTCACCATGCGAAGCCGCCCCACTG
Found at i:10369 original size:32 final size:32
Alignment explanation
Indices: 10320--10404 Score: 118
Period size: 32 Copynumber: 2.7 Consensus size: 32
10310 CGCGGCGCCC
* *
10320 TGCCATGGC-AAAGCCGCCTCATGAGGGCGGCA
1 TGCCGTGGCGAAA-CCGCCCCATGAGGGCGGCA
*
10352 TGCCGTGGCGAAACCGCCCCATGAGGGCGGCT
1 TGCCGTGGCGAAACCGCCCCATGAGGGCGGCA
*
10384 TGCCGTGGCGAAGCCGCCCCA
1 TGCCGTGGCGAAACCGCCCCA
10405 GTAGGGAGGT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 45 0.94
33 3 0.06
ACGTcount: A:0.18, C:0.35, G:0.35, T:0.12
Consensus pattern (32 bp):
TGCCGTGGCGAAACCGCCCCATGAGGGCGGCA
Found at i:10437 original size:33 final size:33
Alignment explanation
Indices: 10395--10457 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
10385 GCCGTGGCGA
* *
10395 AGCCGCCCCAGTAGGGAGGTTCCGCCGTGGTTG
1 AGCCGCCCCAGTAGGGAGGCTCCACCGTGGTTG
* *
10428 AGCCTCCCCAGTGGGGAGGCTCCACCGTGG
1 AGCCGCCCCAGTAGGGAGGCTCCACCGTGG
10458 CTGAACCGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.13, C:0.33, G:0.38, T:0.16
Consensus pattern (33 bp):
AGCCGCCCCAGTAGGGAGGCTCCACCGTGGTTG
Found at i:10791 original size:55 final size:55
Alignment explanation
Indices: 10726--10832 Score: 160
Period size: 55 Copynumber: 1.9 Consensus size: 55
10716 ATTAGGCAAA
* * *
10726 CTCTCTTTTAAGTTTCGTAATTGATTGAATGTTGAATTTTTGGATTGAAAAAATC
1 CTCTCTTTTAAGTATCGTAATTGATTCAATATTGAATTTTTGGATTGAAAAAATC
* * *
10781 CTCTCTTTTAAGTATGGTAATTGATTCAATATTGATTTTTTGGATTGTAAAA
1 CTCTCTTTTAAGTATCGTAATTGATTCAATATTGAATTTTTGGATTGAAAAA
10833 GAGCGTAATC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.47
Consensus pattern (55 bp):
CTCTCTTTTAAGTATCGTAATTGATTCAATATTGAATTTTTGGATTGAAAAAATC
Found at i:11907 original size:31 final size:31
Alignment explanation
Indices: 11872--11931 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
11862 AAGTACAAGT
*
11872 TAGAAGACAAAAAATCTTGAAGGTCATAAGC
1 TAGAAGACAAAAAATCTTAAAGGTCATAAGC
11903 TAGAAGACAAAAAATCTTAAAGGTCATAA
1 TAGAAGACAAAAAATCTTAAAGGTCATAA
11932 AAGCTTAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.52, C:0.12, G:0.17, T:0.20
Consensus pattern (31 bp):
TAGAAGACAAAAAATCTTAAAGGTCATAAGC
Found at i:14410 original size:22 final size:22
Alignment explanation
Indices: 14385--14427 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
14375 CAACAAAACC
*
14385 CCTTCCCTAACAAATACAATTT
1 CCTTCCATAACAAATACAATTT
*
14407 CCTTCCATAATAAATACAATT
1 CCTTCCATAACAAATACAATT
14428 GAAATCTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.33
Consensus pattern (22 bp):
CCTTCCATAACAAATACAATTT
Found at i:15333 original size:24 final size:24
Alignment explanation
Indices: 15301--15349 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
15291 TTATATTTTT
* *
15301 AGAATTTTTACTAAGCTATCATTA
1 AGAAATTTTACTAAGCTATAATTA
15325 AGAAATTTTACTAAGCTATAATTA
1 AGAAATTTTACTAAGCTATAATTA
15349 A
1 A
15350 TATTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (24 bp):
AGAAATTTTACTAAGCTATAATTA
Found at i:18790 original size:33 final size:31
Alignment explanation
Indices: 18741--18822 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 31
18731 CTATATATCT
18741 ATCTATA-TTATTATGGTTTTTTTTTTGTACC
1 ATCTATATTTATTATGGTTTTTTTTTTG-ACC
*
18772 AATCTATATTTATTATGG-TTTTTTTTTGGCC
1 -ATCTATATTTATTATGGTTTTTTTTTTGACC
18803 ATACTATATTTATTATGGTT
1 AT-CTATATTTATTATGGTT
18823 AAGAGTAAAG
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
30 2 0.04
31 17 0.37
32 18 0.39
33 9 0.20
ACGTcount: A:0.22, C:0.09, G:0.11, T:0.59
Consensus pattern (31 bp):
ATCTATATTTATTATGGTTTTTTTTTTGACC
Found at i:18797 original size:31 final size:30
Alignment explanation
Indices: 18741--18822 Score: 112
Period size: 31 Copynumber: 2.6 Consensus size: 30
18731 CTATATATCT
18741 ATCTATA-TTATTATGGTTTTTTTTTTGTACC
1 ATCTATATTTATTATGG-TTTTTTTTTG-ACC
*
18772 AATCTATATTTATTATGGTTTTTTTTTGGCC
1 -ATCTATATTTATTATGGTTTTTTTTTGACC
18803 ATACTATATTTATTATGGTT
1 AT-CTATATTTATTATGGTT
18823 AAGAGTAAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
30 2 0.04
31 19 0.40
32 17 0.36
33 9 0.19
ACGTcount: A:0.22, C:0.09, G:0.11, T:0.59
Consensus pattern (30 bp):
ATCTATATTTATTATGGTTTTTTTTTGACC
Found at i:23729 original size:118 final size:118
Alignment explanation
Indices: 23521--23755 Score: 416
Period size: 118 Copynumber: 2.0 Consensus size: 118
23511 TTACACCAGG
* * * *
23521 TAAATTCCCAGGAAATATGGAGGAGTCACAAACGGTCTCGCTTAAAATCCAACTTCTAAGACAGA
1 TAAATTCCCAGGAAAGATGGAGGAGTCACAAACGGTCTCACTTAAAACCCAACTCCTAAGACAGA
23586 ATTTGCCTAGACATGTAATTAAAGCACAATGACAACTTCTAGTGTCAAATGGA
66 ATTTGCCTAGACATGTAATTAAAGCACAATGACAACTTCTAGTGTCAAATGGA
* *
23639 TAAATTCCCAGGAAAGATGGATGAGTCACAAACGGTCTCACTTAAAACCCAACTCCTTAGACAGA
1 TAAATTCCCAGGAAAGATGGAGGAGTCACAAACGGTCTCACTTAAAACCCAACTCCTAAGACAGA
23704 ATTTGCCTAGACATGTAATTAAAGCACAATGACAACTTCTAGTGTCAAATGG
66 ATTTGCCTAGACATGTAATTAAAGCACAATGACAACTTCTAGTGTCAAATGG
23756 GAATTAGTTA
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
118 111 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.24
Consensus pattern (118 bp):
TAAATTCCCAGGAAAGATGGAGGAGTCACAAACGGTCTCACTTAAAACCCAACTCCTAAGACAGA
ATTTGCCTAGACATGTAATTAAAGCACAATGACAACTTCTAGTGTCAAATGGA
Found at i:23872 original size:30 final size:30
Alignment explanation
Indices: 23810--24285 Score: 456
Period size: 30 Copynumber: 15.7 Consensus size: 30
23800 CATGGTGTAT
* *
23810 ATGACAACTTCTGGTGTCAATTGAATAAATC
1 ATGACAACTTCAGGTGTCAATTGCA-AAATC
** *
23841 ATGACATTTTCAAGTGTCAATTGCAAAATC
1 ATGACAACTTCAGGTGTCAATTGCAAAATC
*
23871 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCAGGTGTCAATTGCAAAATC
23901 ATGACAACTT-ATGGTGTCAATTGCAAAATC
1 ATGACAACTTCA-GGTGTCAATTGCAAAATC
**
23931 ATGACAACTTCTTGTGTCAATTGCAAAATC
1 ATGACAACTTCAGGTGTCAATTGCAAAATC
* *
23961 ATGGCAACTT-ATGGTGTCAATTACAAAATC
1 ATGACAACTTCA-GGTGTCAATTGCAAAATC
*
23991 ATGACAACTTCCA-GAGTCAATTGCAAAATC
1 ATGACAACTT-CAGGTGTCAATTGCAAAATC
*
24021 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCAGGTGTCAATTGCAAAATC
* * ** * *
24051 ATGACAACTTCTGGTGTCATTTATAAGATT
1 ATGACAACTTCAGGTGTCAATTGCAAAATC
* *
24081 ATTGACAACTTCTGGTGTCAATTGTAAAATC
1 A-TGACAACTTCAGGTGTCAATTGCAAAATC
* * * *
24112 ATGACAACTT-ATGGTGTCATTTGTAAGATT
1 ATGACAACTTCA-GGTGTCAATTGCAAAATC
* *
24142 ATTGACAACTTCTGGTGTCAATTGTAAAATC
1 A-TGACAACTTCAGGTGTCAATTGCAAAATC
* * * * * *
24173 ATGACAACTTCTGTTGTCATTTGTAAGACC
1 ATGACAACTTCAGGTGTCAATTGCAAAATC
* * * * *
24203 ATGACAACTTCTGGTGTCATTTGTAAGATT
1 ATGACAACTTCAGGTGTCAATTGCAAAATC
* * * *
24233 ATTGACAACTTCTGGTGTCAATTGTAACACC
1 A-TGACAACTTCAGGTGTCAATTGCAAAATC
* *
24264 ATTGGCAACTTCTGGTGTCAAT
1 A-TGACAACTTCAGGTGTCAAT
24286 GGAGATTTAA
Statistics
Matches: 384, Mismatches: 50, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
29 1 0.00
30 265 0.69
31 117 0.30
32 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (30 bp):
ATGACAACTTCAGGTGTCAATTGCAAAATC
Found at i:23925 original size:60 final size:60
Alignment explanation
Indices: 23810--24315 Score: 575
Period size: 60 Copynumber: 8.3 Consensus size: 60
23800 CATGGTGTAT
* ** **
23810 ATGACAACTTCTGGTGTCAATTGAATAAATCATGACATTTTCAAGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGTA-AAATCATGACAACTTCTGGTGTCAATTGCAAAATC
* *
23871 ATGACAACTTCTGGTGTCAATTGCAAAATCATGACAACTTATGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGCAAAATC
* * * * *
23931 ATGACAACTTCTTGTGTCAATTGCAAAATCATGGCAACTTATGGTGTCAATTACAAAATC
1 ATGACAACTTCTGGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGCAAAATC
** * *
23991 ATGACAACTTCCAGAGTCAATTGCAAAATCATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGCAAAATC
* * * * *
24051 ATGACAACTTCTGGTGTCATTTATAAGATTATTGACAACTTCTGGTGTCAATTGTAAAATC
1 ATGACAACTTCTGGTGTCAATTGTAAAATCA-TGACAACTTCTGGTGTCAATTGCAAAATC
* * * * *
24112 ATGACAACTTATGGTGTCATTTGTAAGATTATTGACAACTTCTGGTGTCAATTGTAAAATC
1 ATGACAACTTCTGGTGTCAATTGTAAAATCA-TGACAACTTCTGGTGTCAATTGCAAAATC
* * * * * * * *
24173 ATGACAACTTCTGTTGTCATTTGTAAGACCATGACAACTTCTGGTGTCATTTGTAAGATT
1 ATGACAACTTCTGGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGCAAAATC
* * * *
24233 ATTGACAACTTCTGGTGTCAATTGTAACACCATTGGCAACTTCTGGTGTCAA-TGGAGATTTAA-
1 A-TGACAACTTCTGGTGTCAATTGTAAAATCA-TGACAACTTCTGGTGTCAATTGCA-A---AAT
24296 C
60 C
24297 ATGACAACTTCTGGTGTCA
1 ATGACAACTTCTGGTGTCA
24316 TTTGGAGACT
Statistics
Matches: 397, Mismatches: 41, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
60 191 0.48
61 168 0.42
62 18 0.05
63 18 0.05
64 1 0.00
65 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (60 bp):
ATGACAACTTCTGGTGTCAATTGTAAAATCATGACAACTTCTGGTGTCAATTGCAAAATC
Found at i:28139 original size:12 final size:12
Alignment explanation
Indices: 28094--28171 Score: 59
Period size: 12 Copynumber: 6.2 Consensus size: 12
28084 AAGCCATAAC
28094 TAGTAGCAAAAA
1 TAGTAGCAAAAA
* * *
28106 TAGTGTGCCAAGA
1 TAGT-AGCAAAAA
28119 TCA-TAGCAAAAA
1 T-AGTAGCAAAAA
28131 TAGTAGCAAAAA
1 TAGTAGCAAAAA
* * *
28143 TAGTGTGCCATAAC
1 TAGT-AG-CAAAAA
28157 TAGTAGCAAAAA
1 TAGTAGCAAAAA
28169 TAG
1 TAG
28172 CAAAAATAAC
Statistics
Matches: 49, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
11 1 0.02
12 30 0.61
13 9 0.18
14 9 0.18
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (12 bp):
TAGTAGCAAAAA
Found at i:28423 original size:16 final size:16
Alignment explanation
Indices: 28402--28506 Score: 72
Period size: 16 Copynumber: 6.6 Consensus size: 16
28392 GAACCCGCTC
*
28402 GACCCGAGATCCGAAT
1 GACCCGAGACCCGAAT
*
28418 GACCCGCA-A-CCTAGAT
1 GACCCG-AGACCCGA-AT
* *
28434 AACCCGAGACCCAAAT
1 GACCCGAGACCCGAAT
*
28450 GACCCGTA-ACCCGAGT
1 GACCCG-AGACCCGAAT
* *
28466 GACCTGAGACCCGTAT
1 GACCCGAGACCCGAAT
* *
28482 GACCTGAAACCCGAAT
1 GACCCGAGACCCGAAT
*
28498 AACCCGAGA
1 GACCCGAGA
28507 AGTTAACTCG
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
15 5 0.07
16 59 0.86
17 5 0.07
ACGTcount: A:0.33, C:0.34, G:0.21, T:0.11
Consensus pattern (16 bp):
GACCCGAGACCCGAAT
Found at i:29402 original size:16 final size:16
Alignment explanation
Indices: 29359--29403 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
29349 ACCCAGAACT
*
29359 CGAATGACCCGAAACC
1 CGAATGACCCGAGACC
* *
29375 C-TATGGCCCGAGACC
1 CGAATGACCCGAGACC
29390 CGAATGACCCGAGA
1 CGAATGACCCGAGA
29404 AAACTGCCTG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.31, C:0.36, G:0.24, T:0.09
Consensus pattern (16 bp):
CGAATGACCCGAGACC
Found at i:32606 original size:19 final size:18
Alignment explanation
Indices: 32569--32608 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
32559 TTCTTGAGAT
*
32569 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
32587 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
32606 AAT
1 AAT
32609 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:38520 original size:3 final size:3
Alignment explanation
Indices: 38497--38559 Score: 54
Period size: 3 Copynumber: 20.3 Consensus size: 3
38487 TGCTTTTACC
* * * *
38497 ATT ATT AAT ATT ACT ACT ATT ATT ATT ACTT ATT ATTT ATT ATG ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT A-TT ATT ATT ATT
**
38544 ATT ATT GCT ATT ATT A
1 ATT ATT ATT ATT ATT A
38560 AATTTGTACA
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
3 42 0.88
4 6 0.12
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:38786 original size:12 final size:12
Alignment explanation
Indices: 38769--38796 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
38759 TCATATGTTG
38769 TTTTCTTCTCTT
1 TTTTCTTCTCTT
38781 TTTTCTTCTCTT
1 TTTTCTTCTCTT
38793 TTTT
1 TTTT
38797 TTTTGGTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTTCTCTT
Found at i:41394 original size:42 final size:41
Alignment explanation
Indices: 41348--41427 Score: 117
Period size: 41 Copynumber: 1.9 Consensus size: 41
41338 TATATATTTA
*
41348 AGAGATAATTATGGTGATTATA-TAATTAACCATATTATCCAT
1 AGAGATAATTAT-G-GATTATATTAATTAAACATATTATCCAT
*
41390 AGAGATAATTATGGATTATATTTATTAAACATATTATC
1 AGAGATAATTATGGATTATATTAATTAAACATATTATC
41428 TACATAGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
40 7 0.20
41 16 0.46
42 12 0.34
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.40
Consensus pattern (41 bp):
AGAGATAATTATGGATTATATTAATTAAACATATTATCCAT
Found at i:41427 original size:41 final size:41
Alignment explanation
Indices: 41348--41494 Score: 125
Period size: 50 Copynumber: 3.3 Consensus size: 41
41338 TATATATTTA
* *
41348 AGAGATAATTATGGTGATTATA-TAATTAACCATATTATCCAT
1 AGAGATAATTAT-G-GATTATATTTATTAAACATATTATCCAT
41390 AGAGATAATTATGGATTATATTTATTAAACATATTATCTACATAGATATT
1 AGAGATAATTATGGATTATATTTATTAAACATATTATC--C------A-T
** **
41440 AGAGATAATTATGGATTATATTTATTAGTCATATTATCTTT
1 AGAGATAATTATGGATTATATTTATTAAACATATTATCCAT
*
41481 AAAGATAATTATGG
1 AGAGATAATTATGG
41495 CAATTATCAA
Statistics
Matches: 88, Mismatches: 7, Indels: 21
0.76 0.06 0.18
Matches are distributed among these distances:
40 7 0.08
41 30 0.34
42 12 0.14
43 1 0.01
49 1 0.01
50 37 0.42
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.41
Consensus pattern (41 bp):
AGAGATAATTATGGATTATATTTATTAAACATATTATCCAT
Found at i:41487 original size:50 final size:50
Alignment explanation
Indices: 41389--41487 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 50
41379 ATATTATCCA
*
41389 TAGAGATAATTATGGATTATATTTATTAAACATATTATCTACATAGATAT
1 TAGAGATAATTATGGATTATATTTATTAAACATATTATCTACAAAGATAT
** **
41439 TAGAGATAATTATGGATTATATTTATTAGTCATATTATCTTTAAAGATA
1 TAGAGATAATTATGGATTATATTTATTAAACATATTATCTACAAAGATA
41488 ATTATGGCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.43
Consensus pattern (50 bp):
TAGAGATAATTATGGATTATATTTATTAAACATATTATCTACAAAGATAT
Found at i:44303 original size:1 final size:1
Alignment explanation
Indices: 44297--44361 Score: 67
Period size: 1 Copynumber: 65.0 Consensus size: 1
44287 AGTCACACAC
* * * * * * *
44297 AAAAAAAAAAAACAAAACAAAAAACAAAAAACAAAAAACAAAAACAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
44362 CAAATATGTT
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:44313 original size:7 final size:7
Alignment explanation
Indices: 44295--44365 Score: 89
Period size: 7 Copynumber: 10.7 Consensus size: 7
44285 TCAGTCACAC
44295 ACAAAAA
1 ACAAAAA
44302 A-AAAAA
1 ACAAAAA
44308 AC--AAA
1 ACAAAAA
44313 ACAAAAA
1 ACAAAAA
44320 ACAAAAA
1 ACAAAAA
44327 ACAAAAA
1 ACAAAAA
44334 AC-AAAA
1 ACAAAAA
44340 ACAAAAA
1 ACAAAAA
44347 A-AAAACA
1 ACAAAA-A
*
44354 AAAAAAA
1 ACAAAAA
44361 ACAAA
1 ACAAA
44366 TATGTTTACA
Statistics
Matches: 57, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
5 5 0.09
6 16 0.28
7 32 0.56
8 4 0.07
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (7 bp):
ACAAAAA
Found at i:44340 original size:27 final size:26
Alignment explanation
Indices: 44295--44365 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 26
44285 TCAGTCACAC
44295 ACAAAAAAAAAAAAC-AAAACAAAAA
1 ACAAAAAAAAAAAACAAAAACAAAAA
44320 ACAAAAAACAAAAAACAAAAACAAAAA
1 ACAAAAAA-AAAAAACAAAAACAAAAA
*
44347 AAAAACAAAAAAAAACAAA
1 ACAAA-AAAAAAAAACAAA
44366 TATGTTTACA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
25 8 0.19
26 7 0.17
27 24 0.57
28 3 0.07
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (26 bp):
ACAAAAAAAAAAAACAAAAACAAAAA
Found at i:44359 original size:32 final size:32
Alignment explanation
Indices: 44295--44358 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
44285 TCAGTCACAC
44295 ACAAAAAAAAAAAACAAAACAAAAAACAAAAA
1 ACAAAAAAAAAAAACAAAACAAAAAACAAAAA
*
44327 ACAAAAAACAAAAACAAAA-AAAAAACAAAAA
1 ACAAAAAAAAAAAACAAAACAAAAAACAAAAA
44358 A
1 A
44359 AAACAAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (32 bp):
ACAAAAAAAAAAAACAAAACAAAAAACAAAAA
Found at i:44413 original size:2 final size:2
Alignment explanation
Indices: 44406--44438 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
44396 TGTCACCCAC
44406 AT AT AT AT AT AT 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
44439 TAGATGGCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44460 original size:29 final size:27
Alignment explanation
Indices: 44442--44493 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
44432 ATAATATTAG
44442 ATGGCCTATGACACCATATATACAACA
1 ATGGCCTATGACACCATATATACAACA
* *
44469 ATGGCCTATGACGCCATATAAACAA
1 ATGGCCTATGACACCATATATACAA
44494 AAAATACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.21
Consensus pattern (27 bp):
ATGGCCTATGACACCATATATACAACA
Found at i:44665 original size:29 final size:29
Alignment explanation
Indices: 44541--44664 Score: 128
Period size: 29 Copynumber: 4.3 Consensus size: 29
44531 ACAATTACCT
* * *
44541 TGGCCTATGACGCCACTCCATATATACAAAAA
1 TGGCCTATGATGCCAC-ACATATAT--AACAA
44573 TGGCCTATGATGCCACACATATATAACAA
1 TGGCCTATGATGCCACACATATATAACAA
* * *
44602 TGGTCTATGATGCAACAC-T-TAT-GCAA
1 TGGCCTATGATGCCACACATATATAACAA
* *
44628 CGGCCTATTATGCCACACATATATAACAA
1 TGGCCTATGATGCCACACATATATAACAA
44657 TGGCCTAT
1 TGGCCTAT
44665 TTCGACAAAC
Statistics
Matches: 77, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
26 17 0.22
27 4 0.05
28 4 0.05
29 30 0.39
31 7 0.09
32 15 0.19
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.26
Consensus pattern (29 bp):
TGGCCTATGATGCCACACATATATAACAA
Found at i:44847 original size:90 final size:88
Alignment explanation
Indices: 44745--44917 Score: 276
Period size: 90 Copynumber: 1.9 Consensus size: 88
44735 ACATTTTCTT
* *
44745 TGCTGCTAATCAAAGCGAGCTCAATATCTTAATGCTCCCTCCAAGTGGCAGAAT-ATTTTTTCTC
1 TGCTGCTAATCAAAGCGAGCTCAATATCATAATGCTCCCTCCAAGTAGCAGAATCA--TTTTCTC
44809 CTTGTAGAGGTTGAAAGCACTTTGAC
64 CTTGTAGAGGTTG-AAGCACTTTGAC
* *
44835 TGCTGCTGATCAAAGCGAGCTCAATATCATAATGCTCCCTCCAAGTAGTAGAATCATTTTCTCCT
1 TGCTGCTAATCAAAGCGAGCTCAATATCATAATGCTCCCTCCAAGTAGCAGAATCATTTTCTCCT
44900 TGTAGAGGTTGAAGCACT
66 TGTAGAGGTTGAAGCACT
44918 CCCATTGAAG
Statistics
Matches: 78, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
88 7 0.09
89 20 0.26
90 50 0.64
91 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (88 bp):
TGCTGCTAATCAAAGCGAGCTCAATATCATAATGCTCCCTCCAAGTAGCAGAATCATTTTCTCCT
TGTAGAGGTTGAAGCACTTTGAC
Done.