Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018587.1 Corchorus olitorius cultivar O-4 contig18620, 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: 12423
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:871 original size:12 final size:13
Alignment explanation
Indices: 853--882 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
843 GTTTTCTTTA
853 ATTTTCTTGATTG
1 ATTTTCTTGATTG
866 -TTTTCTTGATTG
1 ATTTTCTTGATTG
878 ATTTT
1 ATTTT
883 AATTGCTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (13 bp):
ATTTTCTTGATTG
Found at i:1215 original size:15 final size:15
Alignment explanation
Indices: 1195--1231 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1185 AAACTCGTTT
**
1195 TTGAAAACCTTTTTC
1 TTGAAAACAATTTTC
1210 TTGAAAACAATTTTC
1 TTGAAAACAATTTTC
1225 TTGAAAA
1 TTGAAAA
1232 ACGTCTCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.41
Consensus pattern (15 bp):
TTGAAAACAATTTTC
Found at i:2955 original size:14 final size:14
Alignment explanation
Indices: 2936--2972 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2926 AATAAAACAT
2936 CAAAACAAACAAAA
1 CAAAACAAACAAAA
*
2950 CAAAACAAACCAAA
1 CAAAACAAACAAAA
*
2964 CAACACAAA
1 CAAAACAAA
2973 GCAACCATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.73, C:0.27, G:0.00, T:0.00
Consensus pattern (14 bp):
CAAAACAAACAAAA
Found at i:3512 original size:20 final size:20
Alignment explanation
Indices: 3487--3526 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3477 GGCAAAACGG
* *
3487 GAATAAAAGGTTGAGAACAA
1 GAATAAAAGATTGAAAACAA
3507 GAATAAAAGATTGAAAACAA
1 GAATAAAAGATTGAAAACAA
3527 CACCTTCCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.60, C:0.05, G:0.20, T:0.15
Consensus pattern (20 bp):
GAATAAAAGATTGAAAACAA
Found at i:3587 original size:67 final size:68
Alignment explanation
Indices: 3461--3593 Score: 169
Period size: 67 Copynumber: 2.0 Consensus size: 68
3451 AGGAATAACT
** * ** * *
3461 CCTTCCGATGGGGAAGGGCAAAACGGGAATAAAAGGTTGAGAACAAGAATAAAAGATTGAAAACA
1 CCTTCCGACAGGGAAGGGCAAAACGAGAATAAAACATTGAGAACAAGAACAAAACATTGAAAACA
3526 ACA
66 ACA
* * *
3529 CCTTCCGACAGGGAAGGGC-AAACGAGAATAAAACATTGAGGACATGAACAAGACATTGAAAACA
1 CCTTCCGACAGGGAAGGGCAAAACGAGAATAAAACATTGAGAACAAGAACAAAACATTGAAAACA
3593 A
66 A
3594 GAATAAAACA
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
67 38 0.69
68 17 0.31
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.13
Consensus pattern (68 bp):
CCTTCCGACAGGGAAGGGCAAAACGAGAATAAAACATTGAGAACAAGAACAAAACATTGAAAACA
ACA
Found at i:3604 original size:20 final size:20
Alignment explanation
Indices: 3548--3613 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
3538 AGGGAAGGGC
*
3548 AAACGAGAATAAAACATTGA
1 AAACAAGAATAAAACATTGA
** * * *
3568 GGACATGAACAAGACATTGA
1 AAACAAGAATAAAACATTGA
3588 AAACAAGAATAAAACATTGA
1 AAACAAGAATAAAACATTGA
3608 AAACAA
1 AAACAA
3614 CACCTCCCGA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.14
Consensus pattern (20 bp):
AAACAAGAATAAAACATTGA
Found at i:3664 original size:20 final size:20
Alignment explanation
Indices: 3641--3682 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3631 GGACAAAATT
3641 GGAATAAAACAATGAAAACA
1 GGAATAAAACAATGAAAACA
*
3661 GGAATAAAACATTGAAAACA
1 GGAATAAAACAATGAAAACA
3681 GG
1 GG
3683 GACGAAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.60, C:0.10, G:0.19, T:0.12
Consensus pattern (20 bp):
GGAATAAAACAATGAAAACA
Found at i:3697 original size:88 final size:88
Alignment explanation
Indices: 3497--3737 Score: 288
Period size: 88 Copynumber: 2.8 Consensus size: 88
3487 GAATAAAAGG
* * * * *
3497 TTGAGAACAAGAATAAAAGATTGAAAACAACACCTTCCGACAGGGAAGGGC-AAA-CGAGAATAA
1 TTGAAAACAAGAACAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAATTG-GAATAA
* ** * *
3560 AACATTGAGGACATGAACAAGACA
65 AACAATGAAAACAGGAACAAAACA
* * *
3584 TTGAAAACAAGAATAAAACATTGAAAACAACACCTCCCGACCGGGAAGGACAAAATTGGAATAAA
1 TTGAAAACAAGAACAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAATTGGAATAAA
*
3649 ACAATGAAAACAGGAATAAAACA
66 ACAATGAAAACAGGAACAAAACA
* * * **
3672 TTGAAAACAGGGACGAAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAATTGGAATAAA
1 TTGAAAACAAGAACAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAATTGGAATAAA
3737 A
66 A
3738 TATTGAAGAC
Statistics
Matches: 132, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
87 46 0.35
88 85 0.64
89 1 0.01
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (88 bp):
TTGAAAACAAGAACAAAACATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAATTGGAATAAA
ACAATGAAAACAGGAACAAAACA
Found at i:3763 original size:48 final size:48
Alignment explanation
Indices: 3687--4432 Score: 920
Period size: 48 Copynumber: 15.1 Consensus size: 48
3677 AACAGGGACG
**
3687 AAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAATTGGAATA
1 AAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* * * ** *
3735 AAATATTGAAGACAACACCTTCCGACCGGAAAGGGCAAAACATGAATG
1 AAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* * *
3783 AAATATTGAAAAGAACACCTTCCGACTGGGAAGGGCAAAACGGGAATA
1 AAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
**
3831 AAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAATAGGAATA
1 AAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* * *
3879 AAATGTTGAAAACAACACCTTCCAACCGGGAAAGGCCAAACGGGAATA
1 AAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
3927 AAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
1 AAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* ** *
3975 CAATGTTGAAAACAACACCTTCCGATTGGGAAGGGCAAAACAGGAATA
1 AAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* *
4023 AAATGTTGAAAACAACACCTTCCGACTGGGAAGGGCAAAACATGAATAAAATGTGAATG
1 AAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAAC--G--------G-GAATA
* * *
4082 AAATATTGAAAACAAGAACTTCCGACCGGGAAGGGCAAAACGGGAATA
1 AAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
*
4130 AAATGTTTAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
1 AAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* * *
4178 AAATGTTGAAAACAACATCTTTCGACCGGGAAGGGCAAAACAGGAATA
1 AAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* *
4226 CAATGTTGAAAACAACACCTTCCGACCGGGATGGGCAAAACGGGAATA
1 AAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* * **
4274 CAATGTTGAAAAC-A-ACCTTCCGACTGGGAAGGGCAAAATTGGAATA
1 AAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
* * *
4320 CAATGTTGAAAACAACACCTTCCGACTGGGAAGGGCAAAACAGGAATAAA
1 AAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAAT--A
* *
4370 ATGGGAATGAAATACTGAAAACAACACCTTCCGACCGGGAATGGAAAAACGGGAATA
1 A----AATG---T--TGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
4427 AAATGT
1 AAATGT
4433 GAATGGAATA
Statistics
Matches: 610, Mismatches: 64, Indels: 46
0.85 0.09 0.06
Matches are distributed among these distances:
46 41 0.07
47 2 0.00
48 473 0.78
49 1 0.00
50 2 0.00
53 4 0.01
54 4 0.01
57 4 0.01
58 1 0.00
59 78 0.13
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (48 bp):
AAATGTTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATA
Found at i:4120 original size:59 final size:59
Alignment explanation
Indices: 4018--4183 Score: 174
Period size: 59 Copynumber: 3.0 Consensus size: 59
4008 GGCAAAACAG
* * * *
4018 GAATAAAATGTTGAAAACAACACCTTCCGACTGGGAAGGGCAAAACATGAATAAAATGT
1 GAATAAAATATTGAAAACAACAACTTCCGACCGGGAAGGGCAAAACAGGAATAAAATGT
* * *
4077 GAATGAAATATTGAAAACAAGAACTTCCGACCGGGAAGGGCAAAACGGGAATAAAA--T
1 GAATAAAATATTGAAAACAACAACTTCCGACCGGGAAGGGCAAAACAGGAATAAAATGT
* *
4134 G-------T-TT-AAAACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAAATGT
1 GAATAAAATATTGAAAACAACAACTTCCGACCGGGAAGGGCAAAACAGGAATAAAATGT
4184 TGAAAACAAC
Statistics
Matches: 96, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
48 41 0.43
49 2 0.02
50 2 0.02
57 2 0.02
59 49 0.51
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.16
Consensus pattern (59 bp):
GAATAAAATATTGAAAACAACAACTTCCGACCGGGAAGGGCAAAACAGGAATAAAATGT
Found at i:4400 original size:59 final size:59
Alignment explanation
Indices: 4326--4489 Score: 238
Period size: 59 Copynumber: 2.8 Consensus size: 59
4316 AATACAATGT
*
4326 TGAAAACAACACCTTCCGACTGGGAAGGGCAAAACAGGAATAAAATGGGAATGAAATAC
1 TGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAATGGGAATGAAATAC
* * * * * *
4385 TGAAAACAACACCTTCCGACCGGGAATGGAAAAACGGGAATAAAATGTGAATGGAATAT
1 TGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAATGGGAATGAAATAC
* * *
4444 TGAAAACAACACCTTCCGACCAGGAAGGGCAAAATAGGAATGAAAT
1 TGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAAT
4490 AGAAAAACCA
Statistics
Matches: 92, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 92 1.00
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (59 bp):
TGAAAACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAATGGGAATGAAATAC
Found at i:5170 original size:51 final size:50
Alignment explanation
Indices: 5078--5336 Score: 218
Period size: 50 Copynumber: 5.1 Consensus size: 50
5068 AAATTTCATT
** * ** *
5078 TTTATTTACAAATTAATTTAAAGTTCAATATTTTAATTTAAAGATTTC-ATC
1 TTTATTTACAAATTTCTTAAAAGTTCAACCTTTTAA-TTAAA-ATTTCAACC
* * *
5129 TTTATTTACAAATTGCTTAAAAGGTTTCAA-CTTTCAATTAAAAGTTCAACC
1 TTTATTTACAAATTTCTTAAAA-G-TTCAACCTTTTAATTAAAATTTCAACC
* *
5180 TTCACTTACAAATTTCTTAAAAGTTCAACCTTTTAATTAAAATTTCAACC
1 TTTATTTACAAATTTCTTAAAAGTTCAACCTTTTAATTAAAATTTCAACC
** * * * *
5230 TTTATTTACAAATTTCTTAAAAGTTTGATCTTTTAATCT-AAAGTCCAATC
1 TTTATTTACAAATTTCTTAAAAGTTCAACCTTTTAAT-TAAAATTTCAACC
* * * * * * * *
5280 ATTATTTACAAACTACTTACAAGCTTCAATCTTTTAATTAAAAGTCCAACT
1 TTTATTTACAAATTTCTTAAAAG-TTCAACCTTTTAATTAAAATTTCAACC
5331 TTTATT
1 TTTATT
5337 CCACTACTAG
Statistics
Matches: 172, Mismatches: 29, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
49 5 0.03
50 84 0.49
51 72 0.42
52 6 0.03
53 5 0.03
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.43
Consensus pattern (50 bp):
TTTATTTACAAATTTCTTAAAAGTTCAACCTTTTAATTAAAATTTCAACC
Found at i:5223 original size:30 final size:30
Alignment explanation
Indices: 5166--5225 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
5156 CAACTTTCAA
*
5166 TTAAAAGTTCAACCTTCACTTACAAATTTC
1 TTAAAAGTTCAACCTTCAATTACAAATTTC
*
5196 TTAAAAGTTCAACCTTTTAATTA-AAATTTC
1 TTAAAAGTTCAACC-TTCAATTACAAATTTC
5226 AACCTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.40
Consensus pattern (30 bp):
TTAAAAGTTCAACCTTCAATTACAAATTTC
Found at i:5242 original size:20 final size:20
Alignment explanation
Indices: 5196--5245 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5186 TACAAATTTC
*
5196 TTAAAAGTTCAACCTTTTAA
1 TTAAAATTTCAACCTTTTAA
*
5216 TTAAAATTTCAACC-TTTAT
1 TTAAAATTTCAACCTTTTAA
5235 TTACAAATTTC
1 TTA-AAATTTC
5246 TTAAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.44
Consensus pattern (20 bp):
TTAAAATTTCAACCTTTTAA
Found at i:5308 original size:101 final size:101
Alignment explanation
Indices: 5083--5336 Score: 255
Period size: 101 Copynumber: 2.5 Consensus size: 101
5073 TCATTTTTAT
* * * ** *
5083 TTACAAATTAATTTAAAGTTCAATATTTTAATTTAAAGATTTC-ATCTTTATTTACAAATTGCTT
1 TTACAAACTACTTAAAAGTTCAACCTTTTAA-TTAAA-ATTTCAACCTTTATTTACAAATTGCTT
* *
5147 AAAAGGTTTCAACTTTCAATTAAAAGTTCAACCTTCAC
64 AAAAGGTTTCAACTTTCAATTAAAAGTCCAACATTCAC
* * *
5185 TTACAAATTTCTTAAAAGTTCAACCTTTTAATTAAAATTTCAACCTTTATTTACAAATTTCTTAA
1 TTACAAACTACTTAAAAGTTCAACCTTTTAATTAAAATTTCAACCTTTATTTACAAATTGCTTAA
* * * *
5250 AA-GTTTGATCTTTTAATCT-AAAGTCCAATCATT-AT
66 AAGGTTTCAACTTTCAAT-TAAAAGTCCAA-CATTCAC
* * * * *
5285 TTACAAACTACTTACAAGCTTCAATCTTTTAATTAAAAGTCCAACTTTTATT
1 TTACAAACTACTTAAAAG-TTCAACCTTTTAATTAAAATTTCAACCTTTATT
5337 CCACTACTAG
Statistics
Matches: 128, Mismatches: 20, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
100 41 0.32
101 61 0.48
102 26 0.20
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.43
Consensus pattern (101 bp):
TTACAAACTACTTAAAAGTTCAACCTTTTAATTAAAATTTCAACCTTTATTTACAAATTGCTTAA
AAGGTTTCAACTTTCAATTAAAAGTCCAACATTCAC
Found at i:5779 original size:173 final size:173
Alignment explanation
Indices: 5589--6132 Score: 899
Period size: 173 Copynumber: 3.1 Consensus size: 173
5579 AGTTTTACAA
* * * **
5589 CGACTTCTATTAGTCGTTGCGAAATCATAGTCTTTTCGCAACGACTTTTGTTAGTCGTTGCTTAA
1 CGACTTTTGTTAGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTTAGTCGTTGCTTAA
* * *
5654 TATATGTTACTAATTGATTTTCGCAACGACCTTGAAAGTCGCTACAAAAAACATGATTATTTTTG
66 TATATGTTACTAATTGATTTTCGCAGCGACCTTAAAAGTCGCTACAAAAAACATGATTACTTTTG
* *
5719 AAACGACAGATTAGGTCGTTGCGAAATCTTAAACTTTCTGCAG
131 AAACGACAGATTAAGTCGTTGCGAAATCTTAAACTTTCCGCAG
*
5762 CGACTTTTGTTAGTCGTTGCGAAATCTTAAACTTTTCGCAGCGACTTTTGTTAGTCGTTGCTTAA
1 CGACTTTTGTTAGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTTAGTCGTTGCTTAA
*
5827 TATATGTTACTAATTGATTTTCGCAGCGACCTTAAAAGTCGCTACAAAAAACATGATTACTCTTG
66 TATATGTTACTAATTGATTTTCGCAGCGACCTTAAAAGTCGCTACAAAAAACATGATTACTTTTG
5892 AAACGACAGATTAAGTCGTTGCGAAATCTTAAACTTTCCGCAG
131 AAACGACAGATTAAGTCGTTGCGAAATCTTAAACTTTCCGCAG
* ******
5935 CGACTTTTGTTAGTCGTTGCGAAATTTTAAACTTTTCGCAACGACTAACAAAAGTCGTTGCTTAA
1 CGACTTTTGTTAGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTTAGTCGTTGCTTAA
*
6000 TATATGTTACTAATTGATTTTCGTAGCGACCTTAAAAGTCGCTACAAAAAACATGATTACTTTTG
66 TATATGTTACTAATTGATTTTCGCAGCGACCTTAAAAGTCGCTACAAAAAACATGATTACTTTTG
6065 AAACGACAGATTAAGTCGTTGCGAAATCTTAAACTTTCCGCAG
131 AAACGACAGATTAAGTCGTTGCGAAATCTTAAACTTTCCGCAG
*
6108 CGACTTTTGTTAGTTGTTGCGAAAT
1 CGACTTTTGTTAGTCGTTGCGAAAT
6133 ATATGTTACT
Statistics
Matches: 348, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
173 348 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (173 bp):
CGACTTTTGTTAGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTTAGTCGTTGCTTAA
TATATGTTACTAATTGATTTTCGCAGCGACCTTAAAAGTCGCTACAAAAAACATGATTACTTTTG
AAACGACAGATTAAGTCGTTGCGAAATCTTAAACTTTCCGCAG
Found at i:5790 original size:41 final size:41
Alignment explanation
Indices: 5733--5822 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
5723 GACAGATTAG
5733 GTCGTTGCGAAATCTTAAAC-TTTCTGCAGCGACTTTTGTTA
1 GTCGTTGCGAAATCTTAAACTTTTC-GCAGCGACTTTTGTTA
5774 GTCGTTGCGAAATCTTAAACTTTTCGCAGCGACTTTTGTTA
1 GTCGTTGCGAAATCTTAAACTTTTCGCAGCGACTTTTGTTA
5815 GTCGTTGC
1 GTCGTTGC
5823 TTAATATATG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 44 0.92
42 4 0.08
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (41 bp):
GTCGTTGCGAAATCTTAAACTTTTCGCAGCGACTTTTGTTA
Found at i:5991 original size:41 final size:41
Alignment explanation
Indices: 5904--5995 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 41
5894 ACGACAGATT
* *****
5904 AAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGT
1 AAGTCGTTGCGAAATCTTAAACTTTCCGCAACGACTAACAA
* * *
5945 TAGTCGTTGCGAAATTTTAAACTTTTCGCAACGACTAACAA
1 AAGTCGTTGCGAAATCTTAAACTTTCCGCAACGACTAACAA
5986 AAGTCGTTGC
1 AAGTCGTTGC
5996 TTAATATATG
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (41 bp):
AAGTCGTTGCGAAATCTTAAACTTTCCGCAACGACTAACAA
Found at i:6151 original size:305 final size:307
Alignment explanation
Indices: 5773--6439 Score: 1110
Period size: 305 Copynumber: 2.2 Consensus size: 307
5763 GACTTTTGTT
* **
5773 AGTCGTTGCGAAATCTTAAACTTTTCGCAGCGACTTTTGTTAGTCGTTGCTTAATATATGTTACT
1 AGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTCGTTGCGAAATATATGTTACT
*
5838 AATTGATTTTCGCAGCGACCTTAAAAGTCGCTACAAAAAACATGATTACTCTTGAAACGACAGAT
66 AATTGATTTTCGCAACGACCTTAAAAGTCGCTACAAAAAACATGATTACTCTTGAAACGACAGAT
* *
5903 TAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTCGTTGCGAAATTTTAAACT
131 TAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTCATTGCGAAATCTTAAAC-
* *
5968 TTTCGC-AACGAC-TAACAAAAGTCGTTGCTTAATATATGTTACTAATTGATTTTCGTAGCGACC
195 TTTCGCTAACGACTTAACAAAAGT-GTTGCTTAATATACGTTACTAATTGATTTTCGCAGCGACC
6031 TT-AAAAGTCGCTACAAAAAACATGATTACTTTT-G-AAACGACAGATTA
259 TTGAAAA-TCGCTACAAAAAACATGATTACTTTTCGAAAACGACAGATTA
*
6078 AGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTTGTTGCGAAATATATGTTACT
1 AGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTCGTTGCGAAATATATGTTACT
* * *
6143 AATTGATTTTCGCAACGACCTTGAAAGTCGCTACAAAAAACATGATTACTTTTGAAATGACAGAT
66 AATTGATTTTCGCAACGACCTTAAAAGTCGCTACAAAAAACATGATTACTCTTGAAACGACAGAT
6208 TAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTCATTGCGAAATCTTAAACT
131 TAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTCATTGCGAAATCTTAAACT
***** *
6273 TTCGCTAACGACTTTTGTTAGGTGTTGCTTAATATACGTTACTAATTGATTTTCGCAGCGACCTT
196 TTCGCTAACGACTTAACAAAAGTGTTGCTTAATATACGTTACTAATTGATTTTCGCAGCGACCTT
6338 GAAAATCGCTACAAAAAACATGATTACTTTTCGAAAACGACAGATTA
261 GAAAATCGCTACAAAAAACATGATTACTTTTCGAAAACGACAGATTA
6385 AGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTCGTTGCGAAAT
1 AGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTCGTTGCGAAAT
6440 CTTAAACTTT
Statistics
Matches: 338, Mismatches: 19, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
304 6 0.02
305 256 0.76
306 9 0.03
307 67 0.20
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (307 bp):
AGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTCGTTGCGAAATATATGTTACT
AATTGATTTTCGCAACGACCTTAAAAGTCGCTACAAAAAACATGATTACTCTTGAAACGACAGAT
TAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTCATTGCGAAATCTTAAACT
TTCGCTAACGACTTAACAAAAGTGTTGCTTAATATACGTTACTAATTGATTTTCGCAGCGACCTT
GAAAATCGCTACAAAAAACATGATTACTTTTCGAAAACGACAGATTA
Found at i:6183 original size:132 final size:132
Alignment explanation
Indices: 5998--6264 Score: 480
Period size: 132 Copynumber: 2.0 Consensus size: 132
5988 GTCGTTGCTT
* *
5998 AATATATGTTACTAATTGATTTTCGTAGCGACCTTAAAAGTCGCTACAAAAAACATGATTACTTT
1 AATATATGTTACTAATTGATTTTCGCAACGACCTTAAAAGTCGCTACAAAAAACATGATTACTTT
**
6063 TGAAACGACAGATTAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTTGTTGC
66 TGAAACGACAGATTAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTCATTGC
6128 GA
131 GA
*
6130 AATATATGTTACTAATTGATTTTCGCAACGACCTTGAAAGTCGCTACAAAAAACATGATTACTTT
1 AATATATGTTACTAATTGATTTTCGCAACGACCTTAAAAGTCGCTACAAAAAACATGATTACTTT
*
6195 TGAAATGACAGATTAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTCATTGC
66 TGAAACGACAGATTAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTCATTGC
6260 GA
131 GA
6262 AAT
1 AAT
6265 CTTAAACTTT
Statistics
Matches: 129, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 129 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (132 bp):
AATATATGTTACTAATTGATTTTCGCAACGACCTTAAAAGTCGCTACAAAAAACATGATTACTTT
TGAAACGACAGATTAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTCATTGC
GA
Found at i:6260 original size:41 final size:41
Alignment explanation
Indices: 6210--6293 Score: 134
Period size: 41 Copynumber: 2.0 Consensus size: 41
6200 TGACAGATTA
* *
6210 AGTCGTTGCGAAATCTTAAACTTTCCGC-AGCGACTTTTGTT
1 AGTCATTGCGAAATCTTAAACTTT-CGCTAACGACTTTTGTT
6251 AGTCATTGCGAAATCTTAAACTTTCGCTAACGACTTTTGTT
1 AGTCATTGCGAAATCTTAAACTTTCGCTAACGACTTTTGTT
6292 AG
1 AG
6294 GTGTTGCTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 3 0.08
41 37 0.93
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (41 bp):
AGTCATTGCGAAATCTTAAACTTTCGCTAACGACTTTTGTT
Found at i:6262 original size:173 final size:174
Alignment explanation
Indices: 6078--6509 Score: 724
Period size: 175 Copynumber: 2.5 Consensus size: 174
6068 CGACAGATTA
* **
6078 AGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTTGTTGCGAAATATATGTTACT
1 AGTCGTTGCGAAATCTTAAACTTT-CGCAACGACTTTTGTTAGTTGTTGCTTAATATATGTTACT
* * *
6143 AATTGATTTTCGCAACGACCTTGAAAGTCGCTACAAAAAACATGATTACTTTT-G-AAATGACAG
65 AATTGATTTTCGCAGCGACCTTGAAAATCGCTACAAAAAACATGATTACTTTTCGAAAACGACAG
6206 ATTAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTT
130 ATTAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTT
* * *
6251 AGTCATTGCGAAATCTTAAACTTTCGCTAACGACTTTTGTTAGGTGTTGCTTAATATACGTTACT
1 AGTCGTTGCGAAATCTTAAACTTTCGC-AACGACTTTTGTTAGTTGTTGCTTAATATATGTTACT
6316 AATTGATTTTCGCAGCGACCTTGAAAATCGCTACAAAAAACATGATTACTTTTCGAAAACGACAG
65 AATTGATTTTCGCAGCGACCTTGAAAATCGCTACAAAAAACATGATTACTTTTCGAAAACGACAG
6381 ATTAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTT
130 ATTAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTT
* *
6426 AGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTTAGTCGTTGCTTAACATATGTTACT
1 AGTCGTTGCGAAATCTTAAAC-TTTCGCAACGACTTTTGTTAGTTGTTGCTTAATATATGTTACT
6491 AATTGATTTTCGCAGCGAC
65 AATTGATTTTCGCAGCGAC
6510 AAATTAAGTC
Statistics
Matches: 241, Mismatches: 14, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
172 3 0.01
173 106 0.44
174 1 0.00
175 125 0.52
176 6 0.02
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (174 bp):
AGTCGTTGCGAAATCTTAAACTTTCGCAACGACTTTTGTTAGTTGTTGCTTAATATATGTTACTA
ATTGATTTTCGCAGCGACCTTGAAAATCGCTACAAAAAACATGATTACTTTTCGAAAACGACAGA
TTAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTT
Found at i:6353 original size:478 final size:480
Alignment explanation
Indices: 5600--6509 Score: 1533
Period size: 478 Copynumber: 1.9 Consensus size: 480
5590 GACTTCTATT
** * **
5600 AGTCGTTGCGAAATCATAGTCTTTTCGCAACGACTTTTGTTAGTCGTTGCTTAATATATGTTACT
1 AGTCGTTGCGAAATCATAAACTTTCCGCAACGACTTTTGTTAGTCGTTGCGAAATATATGTTACT
*
5665 AATTGATTTTCGCAACGACCTTGAAAGTCGCTACAAAAAACATGATTATTTTTGAAACGACAGAT
66 AATTGATTTTCGCAACGACCTTGAAAGTCGCTACAAAAAACATGATTACTTTTGAAACGACAGAT
* * *
5730 TAGGTCGTTGCGAAATCTTAAACTTTCTGCAGCGACTTTTGTTAGTCGTTGCGAAATCTTAAACT
131 TAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTCATTGCGAAATCTTAAACT
* *
5795 TTTCGCAGCGACTTTTGTTAGTCGTTGCTTAATATATGTTACTAATTGATTTTCGCAGCGACCTT
196 TTTCGCAACGACTTTTGTTAGTCGTTGCTTAATATACGTTACTAATTGATTTTCGCAGCGACCTT
5860 AAAAGTCGCTACAAAAAACATGATTACTCTT-G-AAACGACAGATTAAGTCGTTGCGAAATCTTA
261 AAAAGTCGCTACAAAAAACATGATTACTCTTCGAAAACGACAGATTAAGTCGTTGCGAAATCTTA
*
5923 AACTTTCCGCAGCGACTTTTGTTAGTCGTTGCGAAATTTTAAACTTTTCGCAACGACTAACAAAA
326 AACTTTCCGCAGCGACTTTTGTTAGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTAACAAAA
* *
5988 GTCGTTGCTTAATATATGTTACTAATTGATTTTCGTAGCGACCTTAAAAGTCGCTACAAAAAACA
391 GTCGTTGCTTAACATATGTTACTAATTGATTTTCGCAGCGACCTTAAAAGTCGCTACAAAAAACA
6053 TGATTACTTTTGAAACGACAGATTA
456 TGATTACTTTTGAAACGACAGATTA
* * *
6078 AGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTTGTTGCGAAATATATGTTACT
1 AGTCGTTGCGAAATCATAAACTTTCCGCAACGACTTTTGTTAGTCGTTGCGAAATATATGTTACT
*
6143 AATTGATTTTCGCAACGACCTTGAAAGTCGCTACAAAAAACATGATTACTTTTGAAATGACAGAT
66 AATTGATTTTCGCAACGACCTTGAAAGTCGCTACAAAAAACATGATTACTTTTGAAACGACAGAT
6208 TAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTCATTGCGAAATCTTAAAC-
131 TAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTCATTGCGAAATCTTAAACT
6272 TTTCGCTAACGACTTTTGTTAGGT-GTTGCTTAATATACGTTACTAATTGATTTTCGCAGCGACC
196 TTTCGC-AACGACTTTTGTTA-GTCGTTGCTTAATATACGTTACTAATTGATTTTCGCAGCGACC
*
6336 TTGAAAA-TCGCTACAAAAAACATGATTACTTTTCGAAAACGACAGATTAAGTCGTTGCGAAATC
259 TT-AAAAGTCGCTACAAAAAACATGATTACTCTTCGAAAACGACAGATTAAGTCGTTGCGAAATC
****
6400 TTAAACTTTCCGCAGCGACTTTTGTTAGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTG
323 TTAAACTTTCCGCAGCGACTTTTGTTAGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTAACA
**
6465 TTAGTCGTTGCTTAACATATGTTACTAATTGATTTTCGCAGCGAC
388 AAAGTCGTTGCTTAACATATGTTACTAATTGATTTTCGCAGCGAC
6510 AAATTAAGTC
Statistics
Matches: 402, Mismatches: 25, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
477 6 0.01
478 260 0.65
479 7 0.02
480 129 0.32
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (480 bp):
AGTCGTTGCGAAATCATAAACTTTCCGCAACGACTTTTGTTAGTCGTTGCGAAATATATGTTACT
AATTGATTTTCGCAACGACCTTGAAAGTCGCTACAAAAAACATGATTACTTTTGAAACGACAGAT
TAAGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTTAGTCATTGCGAAATCTTAAACT
TTTCGCAACGACTTTTGTTAGTCGTTGCTTAATATACGTTACTAATTGATTTTCGCAGCGACCTT
AAAAGTCGCTACAAAAAACATGATTACTCTTCGAAAACGACAGATTAAGTCGTTGCGAAATCTTA
AACTTTCCGCAGCGACTTTTGTTAGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTAACAAAA
GTCGTTGCTTAACATATGTTACTAATTGATTTTCGCAGCGACCTTAAAAGTCGCTACAAAAAACA
TGATTACTTTTGAAACGACAGATTA
Found at i:6430 original size:41 final size:41
Alignment explanation
Indices: 6385--6475 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
6375 CGACAGATTA
*
6385 AGTCGTTGCGAAATCTTAAACTTTCCGCAGCGACTTTTGTT
1 AGTCGTTGCGAAATCTTAAACTTTCCGCAACGACTTTTGTT
*
6426 AGTCGTTGCGAAATCTTAAACTTTTCGCAACGACTTTTGTT
1 AGTCGTTGCGAAATCTTAAACTTTCCGCAACGACTTTTGTT
6467 AGTCGTTGC
1 AGTCGTTGC
6476 TTAACATATG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (41 bp):
AGTCGTTGCGAAATCTTAAACTTTCCGCAACGACTTTTGTT
Found at i:6527 original size:18 final size:18
Alignment explanation
Indices: 6500--6539 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
6490 TAATTGATTT
*
6500 TCGCAGCGACAAATTAAG
1 TCGCAACGACAAATTAAG
6518 TCGCAACGACAAATTAAG
1 TCGCAACGACAAATTAAG
6536 TCGC
1 TCGC
6540 TGTGAAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (18 bp):
TCGCAACGACAAATTAAG
Done.