Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020370.1 Corchorus olitorius cultivar O-4 contig20403, 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: 122934
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:54 original size:21 final size:22
Alignment explanation
Indices: 11--52 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1 GCGCGACCCG
11 ACTTTACTGCGTTTTTTTTTTA
1 ACTTTACTGCGTTTTTTTTTTA
*
33 ACTTTTCTGCGTTTTTTTTT
1 ACTTTACTGCGTTTTTTTTT
53 AAATTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.10, C:0.14, G:0.10, T:0.67
Consensus pattern (22 bp):
ACTTTACTGCGTTTTTTTTTTA
Found at i:3606 original size:30 final size:30
Alignment explanation
Indices: 3570--3629 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
3560 CCATGTGTTT
3570 TGATAAAAGTTCTTGATTGAGTGATAAAAG
1 TGATAAAAGTTCTTGATTGAGTGATAAAAG
3600 TGATAAAAGTTCTTGATTGAGTGATAAAAG
1 TGATAAAAGTTCTTGATTGAGTGATAAAAG
3630 AGATGCGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.33
Consensus pattern (30 bp):
TGATAAAAGTTCTTGATTGAGTGATAAAAG
Found at i:5814 original size:39 final size:39
Alignment explanation
Indices: 5760--5837 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
5750 AAATCATAAT
5760 TAGATCTGACAGAGAGAGCAACGAATCTGCATCCTCTGG
1 TAGATCTGACAGAGAGAGCAACGAATCTGCATCCTCTGG
** *
5799 TAGATCTGATGGAGAGAGCAGCGAATCTGCATCCTCTGG
1 TAGATCTGACAGAGAGAGCAACGAATCTGCATCCTCTGG
5838 CAACTAGTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (39 bp):
TAGATCTGACAGAGAGAGCAACGAATCTGCATCCTCTGG
Found at i:12514 original size:22 final size:23
Alignment explanation
Indices: 12480--12527 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
12470 TGCTATAAAC
12480 GAGAAAGTTTATAAGATAAAAAA
1 GAGAAAGTTTATAAGATAAAAAA
*
12503 GAGAAA-TTTATAAGATATAAAA
1 GAGAAAGTTTATAAGATAAAAAA
12525 GAG
1 GAG
12528 GAGAGTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (23 bp):
GAGAAAGTTTATAAGATAAAAAA
Found at i:12690 original size:19 final size:19
Alignment explanation
Indices: 12666--12702 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12656 CTGTTTAGCA
12666 ACTGTACAGATAAGATTAC
1 ACTGTACAGATAAGATTAC
*
12685 ACTGTACAGATTAGATTA
1 ACTGTACAGATAAGATTA
12703 GGTACTGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
ACTGTACAGATAAGATTAC
Found at i:13993 original size:20 final size:19
Alignment explanation
Indices: 13960--14002 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
13950 TAACCTTTTC
13960 TTTTTGCTAAAAAAAAGATT
1 TTTTTGCTAAAAAAAA-ATT
* * *
13980 TTTTTTCTACAAAAGAATT
1 TTTTTGCTAAAAAAAAATT
13999 TTTT
1 TTTT
14003 GTAATTAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (19 bp):
TTTTTGCTAAAAAAAAATT
Found at i:16542 original size:27 final size:28
Alignment explanation
Indices: 16504--16562 Score: 111
Period size: 27 Copynumber: 2.1 Consensus size: 28
16494 GGATTTGACC
16504 GTGGTTTATATGTTGAGGAAT-GGGGCA
1 GTGGTTTATATGTTGAGGAATGGGGGCA
16531 GTGGTTTATATGTTGAGGAATGGGGGCA
1 GTGGTTTATATGTTGAGGAATGGGGGCA
16559 GTGG
1 GTGG
16563 CTGGGTTGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 21 0.68
28 10 0.32
ACGTcount: A:0.20, C:0.03, G:0.44, T:0.32
Consensus pattern (28 bp):
GTGGTTTATATGTTGAGGAATGGGGGCA
Found at i:23593 original size:17 final size:17
Alignment explanation
Indices: 23571--23609 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
23561 CATAAATATT
* *
23571 ATAAATAATAATACAAA
1 ATAAATAACAAAACAAA
*
23588 ATAAATAACAAAACCAA
1 ATAAATAACAAAACAAA
23605 ATAAA
1 ATAAA
23610 ACAAATTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (17 bp):
ATAAATAACAAAACAAA
Found at i:25951 original size:2 final size:2
Alignment explanation
Indices: 25946--25972 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25936 ACACACACAC
25946 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
25973 CTAAATATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27599 original size:13 final size:13
Alignment explanation
Indices: 27581--27606 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27571 GAGGTCTCAT
27581 GTTCAACTCTTAC
1 GTTCAACTCTTAC
27594 GTTCAACTCTTAC
1 GTTCAACTCTTAC
27607 CGTATTCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (13 bp):
GTTCAACTCTTAC
Found at i:37960 original size:44 final size:44
Alignment explanation
Indices: 37910--38033 Score: 153
Period size: 44 Copynumber: 3.1 Consensus size: 44
37900 TTCATATACG
37910 TCAACGATCTCTTTAATACATTCATACATTAAATTAAAGTTGGT
1 TCAACGATCTCTTTAATACATTCATACATTAAATTAAAGTTGGT
*
37954 TCAACGATCTCTTTAATACATTCATACATT---CT--A------
1 TCAACGATCTCTTTAATACATTCATACATTAAATTAAAGTTGGT
*
37987 TCAACGATCTCTTTAATACATTCATGCATTAAATTAAAGTTGGT
1 TCAACGATCTCTTTAATACATTCATACATTAAATTAAAGTTGGT
38031 TCA
1 TCA
38034 CAAGTTACAC
Statistics
Matches: 66, Mismatches: 3, Indels: 22
0.73 0.03 0.24
Matches are distributed among these distances:
33 29 0.44
36 1 0.02
38 1 0.02
39 1 0.02
41 1 0.02
44 33 0.50
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.39
Consensus pattern (44 bp):
TCAACGATCTCTTTAATACATTCATACATTAAATTAAAGTTGGT
Found at i:37993 original size:33 final size:33
Alignment explanation
Indices: 37954--38016 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
37944 TAAAGTTGGT
37954 TCAACGATCTCTTTAATACATTCATACATTCTA
1 TCAACGATCTCTTTAATACATTCATACATTCTA
*
37987 TCAACGATCTCTTTAATACATTCATGCATT
1 TCAACGATCTCTTTAATACATTCATACATT
38017 AAATTAAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.40
Consensus pattern (33 bp):
TCAACGATCTCTTTAATACATTCATACATTCTA
Found at i:39794 original size:30 final size:31
Alignment explanation
Indices: 39758--39820 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
39748 ACAGATTAGC
* *
39758 ATTTACATAT-TATGTTATAAAAGGAAACAA
1 ATTTACATATATATGTTATAAAAGAAAAAAA
39788 ATTTACATATATATGTTATAAAAGAAAAAAA
1 ATTTACATATATATGTTATAAAAGAAAAAAA
39819 AT
1 AT
39821 AGAGAACGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 10 0.33
31 20 0.67
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (31 bp):
ATTTACATATATATGTTATAAAAGAAAAAAA
Found at i:42065 original size:21 final size:19
Alignment explanation
Indices: 42014--42067 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
42004 ATTAAAATGG
42014 TAAAAATA-AA-TTAATTA
1 TAAAAATAGAATTTAATTA
42031 TAAAAATATTGAATTTAATTAAA
1 TAAAAATA--GAATTTAATT--A
42054 TAAAAATAGAATTT
1 TAAAAATAGAATTT
42068 TTAGTAGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 8 0.26
20 2 0.06
21 12 0.39
23 9 0.29
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (19 bp):
TAAAAATAGAATTTAATTA
Found at i:42971 original size:23 final size:23
Alignment explanation
Indices: 42941--42986 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
42931 TTAGTCTTCT
*
42941 TCATTCAGTGCCAATCAAGGGTA
1 TCATTCAGTGCCAACCAAGGGTA
42964 TCATTCAGTGCCAACCAAGGGTA
1 TCATTCAGTGCCAACCAAGGGTA
42987 GATATGTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
TCATTCAGTGCCAACCAAGGGTA
Found at i:48494 original size:19 final size:20
Alignment explanation
Indices: 48449--48506 Score: 82
Period size: 19 Copynumber: 2.9 Consensus size: 20
48439 GCTGCTCTAA
*
48449 TAATCTCATCTGTACAGTACT
1 TAATCTCATCTGTACAGTA-G
*
48470 TAATCTAATCTGTACAGT-G
1 TAATCTCATCTGTACAGTAG
48489 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
48507 TGCTAAACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTAG
Found at i:55213 original size:45 final size:45
Alignment explanation
Indices: 55122--55218 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 45
55112 AGCAACAATT
* * ** * *
55122 AATATTAACTTTATTTTGATGAATTATTTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTAATGAATTACCTAGAGACGGAAGAGTAG
* *
55167 AATATTAGCTTTATTTTAATGAATTACCTAGAGACGGAATATTAG
1 AATATTAGCTTTATTTTAATGAATTACCTAGAGACGGAAGAGTAG
55212 AAT-TTAG
1 AATATTAG
55219 GTAATTAATG
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 4 0.09
45 40 0.91
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (45 bp):
AATATTAGCTTTATTTTAATGAATTACCTAGAGACGGAAGAGTAG
Found at i:56432 original size:78 final size:79
Alignment explanation
Indices: 56349--56499 Score: 195
Period size: 80 Copynumber: 1.9 Consensus size: 79
56339 CGTCTTCCTC
56349 ACTTATTCCCTTTTC-TT-T-T-GCATTACAATACTTACATACATATAT-ATTAATTGTCATTCA
1 ACTTATTCCCTTTTCTTTGTCTAGCATTACAATACTTACATAC-T-TATGA--AATTGTCATTCA
*
56409 CACAAGTTTATAAATACT
62 AACAAGTTTATAAATACT
* *
56427 ACTTATTCCCTTTTCTTTGTGCTAGCATTTCAATACTTACATACTTATGAACTTGTCATTCAAAC
1 ACTTATTCCCTTTTCTTTGT-CTAGCATTACAATACTTACATACTTATGAAATTGTCATTCAAAC
56492 AAGTTTAT
65 AAGTTTAT
56500 GAATGCGTAA
Statistics
Matches: 64, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
78 15 0.23
79 2 0.03
80 22 0.34
81 3 0.05
82 3 0.05
83 19 0.30
ACGTcount: A:0.30, C:0.20, G:0.06, T:0.44
Consensus pattern (79 bp):
ACTTATTCCCTTTTCTTTGTCTAGCATTACAATACTTACATACTTATGAAATTGTCATTCAAACA
AGTTTATAAATACT
Found at i:57769 original size:13 final size:13
Alignment explanation
Indices: 57751--57775 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57741 CATATATGGT
57751 ATATTATAAATAA
1 ATATTATAAATAA
57764 ATATTATAAATA
1 ATATTATAAATA
57776 CATGAAGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATTATAAATAA
Found at i:61073 original size:31 final size:31
Alignment explanation
Indices: 60976--61076 Score: 88
Period size: 31 Copynumber: 3.5 Consensus size: 31
60966 AAACTGACGC
*
60976 TAGGCCCTTATTTGAGCATTTTGGCAAACTT
1 TAGGCCCTTATTTGAGCATTTTGGCAAACAT
* * ** **
61007 TAAGCTCTTATTTGTTCAAATT---AAA-A-
1 TAGGCCCTTATTTGAGCATTTTGGCAAACAT
*
61033 GA-GCCCTTATTTGAGCATTTTGGCAAACAT
1 TAGGCCCTTATTTGAGCATTTTGGCAAACAT
61063 TAGGCCCTTATTTG
1 TAGGCCCTTATTTG
61077 TGCAATTAGC
Statistics
Matches: 50, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
25 14 0.28
26 1 0.02
28 6 0.12
29 1 0.02
30 1 0.02
31 27 0.54
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.39
Consensus pattern (31 bp):
TAGGCCCTTATTTGAGCATTTTGGCAAACAT
Found at i:62590 original size:25 final size:25
Alignment explanation
Indices: 62561--62626 Score: 114
Period size: 25 Copynumber: 2.6 Consensus size: 25
62551 AGGTATGTCA
*
62561 TTTGCTTAAATAATGAATGTCTTGC
1 TTTGCTTAAATAATGAATGCCTTGC
62586 TTTGCTTAAATAATGAATGCCTTGC
1 TTTGCTTAAATAATGAATGCCTTGC
*
62611 TTTGCTCAAATAATGA
1 TTTGCTTAAATAATGA
62627 TTTTTTTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (25 bp):
TTTGCTTAAATAATGAATGCCTTGC
Found at i:62845 original size:29 final size:29
Alignment explanation
Indices: 62803--62861 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
62793 ATGGCAGGCA
62803 AACACAATTTTGAAAAGTTGAAAAGACTT
1 AACACAATTTTGAAAAGTTGAAAAGACTT
*
62832 AACATAATTTTGAAAAGTTGAAAAGACTT
1 AACACAATTTTGAAAAGTTGAAAAGACTT
62861 A
1 A
62862 TGTAGTTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (29 bp):
AACACAATTTTGAAAAGTTGAAAAGACTT
Found at i:63424 original size:16 final size:16
Alignment explanation
Indices: 63399--63430 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
63389 TTGAAATCTT
*
63399 TTGATGATATTCTCTG
1 TTGATAATATTCTCTG
63415 TTGATAATATTCTCTG
1 TTGATAATATTCTCTG
63431 AAATATTCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (16 bp):
TTGATAATATTCTCTG
Found at i:63727 original size:28 final size:28
Alignment explanation
Indices: 63684--63748 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
63674 TTCCTTCTAA
*
63684 TTTTCTCCACTGCCTTCCG-TTCACATTC
1 TTTTCTCCACTACCTT-CGTTTCACATTC
*
63712 TTTTCTCCACTACCTTCGTTTTACATTC
1 TTTTCTCCACTACCTTCGTTTCACATTC
63740 TTTTCTCCA
1 TTTTCTCCA
63749 ACCCTTGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 2 0.06
28 32 0.94
ACGTcount: A:0.12, C:0.35, G:0.05, T:0.48
Consensus pattern (28 bp):
TTTTCTCCACTACCTTCGTTTCACATTC
Found at i:69600 original size:29 final size:30
Alignment explanation
Indices: 69544--69604 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
69534 AGTTTTTGAC
*
69544 CAAACCATTGTGATTTTTAAAAATAATTCT
1 CAAACCATTGTGAATTTTAAAAATAATTCT
*
69574 CAAACCATTGT-AATTTTAAAATTAATTCT
1 CAAACCATTGTGAATTTTAAAAATAATTCT
69603 CA
1 CA
69605 TTCTCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (30 bp):
CAAACCATTGTGAATTTTAAAAATAATTCT
Found at i:69712 original size:14 final size:14
Alignment explanation
Indices: 69693--69720 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
69683 TACTTTAAAG
69693 AAATCACCATTAGT
1 AAATCACCATTAGT
69707 AAATCACCATTAGT
1 AAATCACCATTAGT
69721 CTCGGTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (14 bp):
AAATCACCATTAGT
Found at i:73743 original size:34 final size:34
Alignment explanation
Indices: 73672--73745 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
73662 CCATGACATG
* *
73672 AAAATAACCATATATCTTTTAATATCTCAAGAAA
1 AAAAAAACCATATATCTTTTAATATCTCAACAAA
* *
73706 AAAAAAACCATATATCTTTTAATGATGT-AACAGA
1 AAAAAAACCATATATCTTTTAAT-ATCTCAACAAA
73740 AAAAAA
1 AAAAAA
73746 GGCATGCACC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 32 0.91
35 3 0.09
ACGTcount: A:0.54, C:0.12, G:0.05, T:0.28
Consensus pattern (34 bp):
AAAAAAACCATATATCTTTTAATATCTCAACAAA
Found at i:74526 original size:30 final size:29
Alignment explanation
Indices: 74453--74526 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 29
74443 AAGAATTCTC
* *
74453 TAATTTGTAAGAATTTGCTAAGTATGTTTT
1 TAATTTGT-TGAAATTGCTAAGTATGTTTT
74483 T--TTT-TTGGCAAATTGCTAAGTATGTGTTT
1 TAATTTGTT-G-AAATTGCTAAGTATGT-TTT
74512 TAATTTGTTGAAATT
1 TAATTTGTTGAAATT
74527 ATGTATTTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
27 2 0.06
28 18 0.50
29 4 0.11
30 6 0.17
31 4 0.11
32 2 0.06
ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51
Consensus pattern (29 bp):
TAATTTGTTGAAATTGCTAAGTATGTTTT
Found at i:77239 original size:21 final size:21
Alignment explanation
Indices: 77207--77246 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
77197 TTAATATCCT
*
77207 TTTGGTTTACGT-TTGTTTGA
1 TTTGGTTAACGTCTTGTTTGA
77227 TTTGAGTTAACGTCTTGTTT
1 TTTG-GTTAACGTCTTGTTT
77247 CAACTATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 7 0.41
22 6 0.35
ACGTcount: A:0.12, C:0.07, G:0.23, T:0.57
Consensus pattern (21 bp):
TTTGGTTAACGTCTTGTTTGA
Found at i:80628 original size:126 final size:128
Alignment explanation
Indices: 80473--80719 Score: 340
Period size: 126 Copynumber: 1.9 Consensus size: 128
80463 ATGAAGTGAA
* * * * * *
80473 TAAATAATAGTACATGATTTTATGGTCAATAAATG-TGTTTACATTGAAGTGGTTAAAAACCCTT
1 TAAATAATAATACATGATTTTATGATCAATAAATGCT-TTCACATTCAACTGATTAAAAACCCTT
* *
80537 GTAATT-AAAAAGAAA-GC-GGAGGAAAAAGAAATGCTGAGAAACTAATTGAGGGCCTTCTTAG
65 GCAATTAAAAAAAAAAGGCTGGAGGAAAAAGAAATGCTGAGAAACTAATTGAGGGCCTTCTTAG
80598 TAAATAAATAATACATGATTTTATGATCAATAAATGCTTTCACATTCAACTGATTAAAAACCCTT
1 TAAAT-AATAATACATGATTTTATGATCAATAAATGCTTTCACATTCAACTGATTAAAAACCCTT
* * *
80663 GCAATTACAAAAAAAAAGGCTGGAGGAGAAAGGAATGGTGAGAAACTAATTGAGGGC
65 GCAATTA-AAAAAAAAAGGCTGGAGGAAAAAGAAATGCTGAGAAACTAATTGAGGGC
80720 TTAAAGTAAT
Statistics
Matches: 105, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
125 5 0.05
126 56 0.53
127 1 0.01
128 8 0.08
129 2 0.02
130 33 0.31
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (128 bp):
TAAATAATAATACATGATTTTATGATCAATAAATGCTTTCACATTCAACTGATTAAAAACCCTTG
CAATTAAAAAAAAAAGGCTGGAGGAAAAAGAAATGCTGAGAAACTAATTGAGGGCCTTCTTAG
Found at i:91667 original size:97 final size:97
Alignment explanation
Indices: 91499--91682 Score: 262
Period size: 97 Copynumber: 1.9 Consensus size: 97
91489 TTGTCTCTGA
* * * *
91499 TTATGAACTTCTATAAGGTTTTTCTCCCAATTCAATTGATTTTGTTCTTTTGGAGGACTCTTTTA
1 TTATGAACTTCTATAAGGTTCTTCTCCCAATTCAATTGATTTTGTTCTTTTAGAGAACTCTATTA
*
91564 ATTTTGTAATATACCATCTATAACCTCTGAAT
66 AATTTGTAATATACCATCTATAACCTCTGAAT
* * * * *
91596 TTATGAACTTCTCTAAGGTTCTTCTCCTAGTTCAATTGATTTTTTTTCTTTTAGATAACTC-ATT
1 TTATGAACTTCTATAAGGTTCTTCTCCCAATTCAATTGA-TTTTGTTCTTTTAGAGAACTCTATT
91660 AAATTTGTAATATACCATCTATA
65 AAATTTGTAATATACCATCTATA
91683 GTCACTATAT
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
97 59 0.78
98 17 0.22
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.47
Consensus pattern (97 bp):
TTATGAACTTCTATAAGGTTCTTCTCCCAATTCAATTGATTTTGTTCTTTTAGAGAACTCTATTA
AATTTGTAATATACCATCTATAACCTCTGAAT
Found at i:102523 original size:2 final size:2
Alignment explanation
Indices: 102516--102557 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
102506 TTGAGACGAC
102516 AT AT AT AT AT 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 AT AT AT AT AT
102558 GCAAAAACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:108275 original size:32 final size:32
Alignment explanation
Indices: 108234--108294 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
108224 TGTAAAACTT
*
108234 TTGAATCGACTATTATA-TCCTTATTTTTCTAA
1 TTGAATCGACCATTATACT-CTTATTTTTCTAA
108266 TTGAATCGACCATTATACTCTTATTTTTC
1 TTGAATCGACCATTATACTCTTATTTTTC
108295 AAACATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (32 bp):
TTGAATCGACCATTATACTCTTATTTTTCTAA
Found at i:113992 original size:4 final size:5
Alignment explanation
Indices: 113962--113998 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
113952 CAACTTAAAG
113962 TTTTC TTTTC TTTTC TTTTC TTTTC -TTTC -TTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
113999 TTTCAAAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 8 0.26
5 23 0.74
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:118930 original size:72 final size:72
Alignment explanation
Indices: 118838--118976 Score: 233
Period size: 72 Copynumber: 1.9 Consensus size: 72
118828 AAAGACAAGC
*
118838 CAAGGTGTGAACATTGTCAAAAGATGGGGCACACAAAAGATCAATGCTATGAGATCATTGGATAT
1 CAAGGTGTGAACATTATCAAAAGATGGGGCACACAAAAGATCAATGCTATGAGATCATTGGATAT
118903 CCTGTTG
66 CCTGTTG
* * **
118910 CAAGGTGTGGACATTATCAAAAGATGGGGCACACGAAAGATCTGTGCTATGAGATCATTGGATAT
1 CAAGGTGTGAACATTATCAAAAGATGGGGCACACAAAAGATCAATGCTATGAGATCATTGGATAT
118975 CC
66 CC
118977 CGCAGGGTGG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (72 bp):
CAAGGTGTGAACATTATCAAAAGATGGGGCACACAAAAGATCAATGCTATGAGATCATTGGATAT
CCTGTTG
Done.