Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008618.1 Corchorus capsularis cultivar CVL-1 contig08639, 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: 55953
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:730 original size:6 final size:6
Alignment explanation
Indices: 719--757 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
709 AGCAGGTGAA
* *
719 CCGGAG CCGGAG CCGGAG CCGGAG CCGAAG CCGAAG CCG
1 CCGGAG CCGGAG CCGGAG CCGGAG CCGGAG CCGGAG CCG
758 AAGTTGAAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.21, C:0.36, G:0.44, T:0.00
Consensus pattern (6 bp):
CCGGAG
Found at i:4714 original size:20 final size:20
Alignment explanation
Indices: 4689--4728 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4679 TAGTAGTAGT
4689 GAGGAGGATGAGGATGAGGA
1 GAGGAGGATGAGGATGAGGA
4709 GAGGAGGATGAGGATGAGGA
1 GAGGAGGATGAGGATGAGGA
4729 TAGGGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.55, T:0.10
Consensus pattern (20 bp):
GAGGAGGATGAGGATGAGGA
Found at i:7781 original size:25 final size:24
Alignment explanation
Indices: 7747--7806 Score: 86
Period size: 25 Copynumber: 2.5 Consensus size: 24
7737 TTCAAACCCT
*
7747 AAACTTCATTTTTAACAACTTCTTC
1 AAACTTCATTTTTAACAA-ATCTTC
*
7772 AAACTTCATTTCTAACAAATCTTC
1 AAACTTCATTTTTAACAAATCTTC
7796 AAA-TTCATTTT
1 AAACTTCATTTT
7807 CCATCATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 7 0.22
24 8 0.25
25 17 0.53
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (24 bp):
AAACTTCATTTTTAACAAATCTTC
Found at i:7807 original size:24 final size:26
Alignment explanation
Indices: 7747--7807 Score: 85
Period size: 24 Copynumber: 2.5 Consensus size: 26
7737 TTCAAACCCT
*
7747 AAACTTCATTTT-TAACAACTTCTTC
1 AAACTTCATTTTCTAACAACATCTTC
7772 AAACTTCA-TTTCTAACAA-ATCTTC
1 AAACTTCATTTTCTAACAACATCTTC
7796 AAA-TTCATTTTC
1 AAACTTCATTTTC
7808 CATCATTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
23 4 0.12
24 15 0.45
25 14 0.42
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (26 bp):
AAACTTCATTTTCTAACAACATCTTC
Found at i:7844 original size:26 final size:26
Alignment explanation
Indices: 7815--7932 Score: 111
Period size: 26 Copynumber: 4.7 Consensus size: 26
7805 TTCCATCATT
7815 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
7841 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
7867 TTAAACATAAACTAA-T-AA-ACTAA
1 TTAATCATAAACTAATTAAATACTAA
* * * * * * *
7890 GTAAT-TTTAATTAACTAATTA-AAA
1 TTAATCATAAACTAATTAAATACTAA
7914 TTAATCATAAACTAATTAA
1 TTAATCATAAACTAATTAA
7933 TATTAAAAAA
Statistics
Matches: 71, Mismatches: 17, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
22 6 0.08
23 9 0.13
24 8 0.11
25 11 0.15
26 37 0.52
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:15780 original size:30 final size:30
Alignment explanation
Indices: 15744--15803 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
15734 ATAGGAGAGG
15744 ATGGAATCGCAAAGTCC-CATGAAGATGCCA
1 ATGGAATCGCAAAG-CCTCATGAAGATGCCA
*
15774 ATGGAATCGCAAAGCCTCATGGAGATGCCA
1 ATGGAATCGCAAAGCCTCATGAAGATGCCA
15804 TTAAGATGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.17
Consensus pattern (30 bp):
ATGGAATCGCAAAGCCTCATGAAGATGCCA
Found at i:22665 original size:56 final size:56
Alignment explanation
Indices: 22579--23053 Score: 265
Period size: 56 Copynumber: 8.6 Consensus size: 56
22569 ATGCAAATTA
* **
22579 GTAATCAACTTAATTCGGTGTAATTAAGTAATTTGGA-AATTAAATTAAGTCTTTTG
1 GTAATCAACTTAATTCGGTGTAATTAAGTAAATT-GATAATTAAATTAAGTAATTTG
22635 GTAATCAACTTAATTCGGTGTAATTAAGTAAATTGATAATTAAATTAAGTAATTTG
1 GTAATCAACTTAATTCGGTGTAATTAAGTAAATTGATAATTAAATTAAGTAATTTG
* * ** **
22691 GTAATCAACTTAATTCAGTGTAATTAAGTAAATTGATAATCAGCTTAA-T--TCGG
1 GTAATCAACTTAATTCGGTGTAATTAAGTAAATTGATAATTAAATTAAGTAATTTG
* * * * * * * * * * * **
22744 TGTAATTAAGTGAATT---AGTAAATAACTTAATTCGGT--GT-GATTAGGTAGA-TCA
1 -GTAATCAACTTAATTCGGTGTAATTAAGTAAATT-GATAATTAAATTAAGTA-ATTTG
* * * * * **
22796 GTAATCAACTTAATTCGGTGAAATTAGGTAAA-TCAGTAATCAACTTAA-T--TCGG
1 GTAATCAACTTAATTCGGTGTAATTAAGTAAATTGA-TAATTAAATTAAGTAATTTG
* * * * * * * * *
22849 TGTAATTAA-GTAAATC--AGTAATCAACTTAATTCGGT--GT-AATTAAGTGAA-TTG
1 -GTAATCAACTTAATTCGGTGTAATTAAGTAAATT-GATAATTAAATTAAGT-AATTTG
22901 GTAATCAACTTAATTCGGTGTAATTAAGTAAATTGGTAATTAAATTAAGAAATTAAGTAATTTG
1 GTAATCAACTTAATTCGGTGTAATTAAGTAAATT-G--A-T-AATT---AAATTAAGTAATTTG
* * *
22965 GTAATCAAATTAATTCGGTGCAATTAAGTAAATTGGTAATTAAATTAAGTAATTTG
1 GTAATCAACTTAATTCGGTGTAATTAAGTAAATTGATAATTAAATTAAGTAATTTG
* *
23021 GTAATTAACTTAGTTCGGTGTAATTAAGTAAAT
1 GTAATCAACTTAATTCGGTGTAATTAAGTAAAT
23054 CAGTAATCAA
Statistics
Matches: 307, Mismatches: 76, Indels: 72
0.67 0.17 0.16
Matches are distributed among these distances:
49 9 0.03
50 2 0.01
51 39 0.13
52 10 0.03
53 9 0.03
54 40 0.13
55 4 0.01
56 141 0.46
57 1 0.00
59 4 0.01
60 2 0.01
63 3 0.01
64 43 0.14
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (56 bp):
GTAATCAACTTAATTCGGTGTAATTAAGTAAATTGATAATTAAATTAAGTAATTTG
Found at i:22680 original size:21 final size:21
Alignment explanation
Indices: 22656--22695 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
22646 AATTCGGTGT
22656 AATTAAGTAAATTGATAATTA
1 AATTAAGTAAATTGATAATTA
* *
22677 AATTAAGTAATTTGGTAAT
1 AATTAAGTAAATTGATAAT
22696 CAACTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.40
Consensus pattern (21 bp):
AATTAAGTAAATTGATAATTA
Found at i:22703 original size:21 final size:21
Alignment explanation
Indices: 22656--22703 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
22646 AATTCGGTGT
*
22656 AATTAAGTAAATTGATAATTA
1 AATTAAGTAAATTGATAATCA
* *
22677 AATTAAGTAATTTGGTAATCA
1 AATTAAGTAAATTGATAATCA
*
22698 ACTTAA
1 AATTAA
22704 TTCAGTGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.10, T:0.38
Consensus pattern (21 bp):
AATTAAGTAAATTGATAATCA
Found at i:22899 original size:19 final size:19
Alignment explanation
Indices: 22840--23119 Score: 103
Period size: 19 Copynumber: 16.1 Consensus size: 19
22830 AGTAATCAAC
22840 TTAATTCGGTGTAATTAAG
1 TTAATTCGGTGTAATTAAG
* * * *
22859 -TAAATC--AGTAATCAAC
1 TTAATTCGGTGTAATTAAG
22875 TTAATTCGGTGTAATTAAG
1 TTAATTCGGTGTAATTAAG
* * *
22894 TGAATT--G-GTAATCAAC
1 TTAATTCGGTGTAATTAAG
22910 TTAATTCGGTGTAATTAAG
1 TTAATTCGGTGTAATTAAG
* *
22929 TAAATT--G-GTAATTAAA
1 TTAATTCGGTGTAATTAAG
*
22945 TTAA------GAAATTAAG
1 TTAATTCGGTGTAATTAAG
* * *
22958 -TAATT-TG-GTAATCAAA
1 TTAATTCGGTGTAATTAAG
*
22974 TTAATTCGGTGCAATTAAG
1 TTAATTCGGTGTAATTAAG
* *
22993 TAAATT-GGTAATTAAATTAAG
1 TTAATTCGGT--GT-AATTAAG
* *
23014 -TAATT-TG-GTAATTAAC
1 TTAATTCGGTGTAATTAAG
*
23030 TTAGTTCGGTGTAATTAAG
1 TTAATTCGGTGTAATTAAG
* * * *
23049 -TAAATC--AGTAATCAAT
1 TTAATTCGGTGTAATTAAG
23065 TTAATTCGGTGTAATTAAG
1 TTAATTCGGTGTAATTAAG
* * *
23084 TGAA-TC--AGTAATTAAC
1 TTAATTCGGTGTAATTAAG
23100 TTAATTCGGTGTAATTAAG
1 TTAATTCGGTGTAATTAAG
23119 T
1 T
23120 AAATAATCAA
Statistics
Matches: 185, Mismatches: 51, Indels: 50
0.65 0.18 0.17
Matches are distributed among these distances:
12 3 0.02
13 7 0.04
16 60 0.32
17 24 0.13
18 17 0.09
19 62 0.34
20 5 0.03
21 7 0.04
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.38
Consensus pattern (19 bp):
TTAATTCGGTGTAATTAAG
Found at i:22941 original size:16 final size:16
Alignment explanation
Indices: 22885--23007 Score: 72
Period size: 16 Copynumber: 7.5 Consensus size: 16
22875 TTAATTCGGT
*
22885 GTAATTAAGTGAATTG
1 GTAATTAAGTAAATTG
* * *
22901 GTAATCAACTTAATTCGG
1 GTAATTAAGTAAATT--G
22919 TGTAATTAAGTAAATTG
1 -GTAATTAAGTAAATTG
* *
22936 GTAATTAAATTAA---
1 GTAATTAAGTAAATTG
* *
22949 GAAATTAAGTAATTTG
1 GTAATTAAGTAAATTG
* * *
22965 GTAATCAAATTAATTCG
1 GTAATTAAGTAAATT-G
22982 GTGCAATTAAGTAAATTG
1 GT--AATTAAGTAAATTG
23000 GTAATTAA
1 GTAATTAA
23008 ATTAAGTAAT
Statistics
Matches: 78, Mismatches: 20, Indels: 18
0.67 0.17 0.16
Matches are distributed among these distances:
13 9 0.12
16 39 0.50
17 4 0.05
18 4 0.05
19 22 0.28
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.37
Consensus pattern (16 bp):
GTAATTAAGTAAATTG
Found at i:22955 original size:29 final size:29
Alignment explanation
Indices: 22922--23018 Score: 104
Period size: 29 Copynumber: 3.1 Consensus size: 29
22912 AATTCGGTGT
22922 AATTAAGTAAATTGGTAATTAAATTAAGA
1 AATTAAGTAAATTGGTAATTAAATTAAGA
* * *
22951 AATTAAGTAATTTGGTAATCAAATTAATTCGGTGC
1 AATTAAGTAAATTGGTAATTAAATTAA------GA
*
22986 AATTAAGTAAATTGGTAATTAAATTAAGT
1 AATTAAGTAAATTGGTAATTAAATTAAGA
23015 AATT
1 AATT
23019 TGGTAATTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
29 30 0.54
35 26 0.46
ACGTcount: A:0.45, C:0.03, G:0.14, T:0.37
Consensus pattern (29 bp):
AATTAAGTAAATTGGTAATTAAATTAAGA
Found at i:22960 original size:21 final size:21
Alignment explanation
Indices: 22922--22962 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
22912 AATTCGGTGT
*
22922 AATTAAGTAAATTGGTAATTA
1 AATTAAGTAAATTAGTAATTA
22943 AATTAAG-AAATTAAGTAATT
1 AATTAAGTAAATT-AGTAATT
22963 TGGTAATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (21 bp):
AATTAAGTAAATTAGTAATTA
Found at i:23011 original size:21 final size:21
Alignment explanation
Indices: 22986--23028 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
22976 AATTCGGTGC
22986 AATTAAGTAAATTGGTAATTA
1 AATTAAGTAAATTGGTAATTA
*
23007 AATTAAGTAATTTGGTAATTA
1 AATTAAGTAAATTGGTAATTA
23028 A
1 A
23029 CTTAGTTCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.40
Consensus pattern (21 bp):
AATTAAGTAAATTGGTAATTA
Found at i:23012 original size:35 final size:35
Alignment explanation
Indices: 22677--23004 Score: 382
Period size: 35 Copynumber: 9.5 Consensus size: 35
22667 TTGATAATTA
* *
22677 AATTAAGTAATTTGGTAATCAACTTAATTCAGTGT
1 AATTAAGTAAATTGGTAATCAACTTAATTCGGTGT
* *
22712 AATTAAGTAAATTGATAATCAGCTTAATTCGGTGT
1 AATTAAGTAAATTGGTAATCAACTTAATTCGGTGT
* *
22747 AATTAAGTGAATTAGTAAAT-AACTTAATTCGGTGT
1 AATTAAGTAAATTGGT-AATCAACTTAATTCGGTGT
* * * ** *
22782 GATTAGGTAGATCAGTAATCAACTTAATTCGGTGA
1 AATTAAGTAAATTGGTAATCAACTTAATTCGGTGT
* **
22817 AATTAGGTAAATCAGTAATCAACTTAATTCGGTGT
1 AATTAAGTAAATTGGTAATCAACTTAATTCGGTGT
**
22852 AATTAAGTAAATCAGTAATCAACTTAATTCGGTGT
1 AATTAAGTAAATTGGTAATCAACTTAATTCGGTGT
*
22887 AATTAAGTGAATTGGTAATCAACTTAATTCGGTGT
1 AATTAAGTAAATTGGTAATCAACTTAATTCGGTGT
* * *
22922 AATTAAGTAAATTGGTAATTAAATTAA------GA
1 AATTAAGTAAATTGGTAATCAACTTAATTCGGTGT
* * *
22951 AATTAAGTAATTTGGTAATCAAATTAATTCGGTGC
1 AATTAAGTAAATTGGTAATCAACTTAATTCGGTGT
22986 AATTAAGTAAATTGGTAAT
1 AATTAAGTAAATTGGTAAT
23005 TAAATTAAGT
Statistics
Matches: 256, Mismatches: 29, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
29 26 0.10
34 3 0.01
35 224 0.88
36 3 0.01
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (35 bp):
AATTAAGTAAATTGGTAATCAACTTAATTCGGTGT
Found at i:23046 original size:35 final size:34
Alignment explanation
Indices: 23007--23121 Score: 158
Period size: 35 Copynumber: 3.3 Consensus size: 34
22997 TTGGTAATTA
** *
23007 AATTAAGTAATTTGGTAATTAACTTAGTTCGGTGT
1 AATTAAGTAA-TCAGTAATTAACTTAATTCGGTGT
* *
23042 AATTAAGTAAATCAGTAATCAATTTAATTCGGTGT
1 AATTAAGT-AATCAGTAATTAACTTAATTCGGTGT
23077 AATTAAGTGAATCAGTAATTAACTTAATTCGGTGT
1 AATTAAGT-AATCAGTAATTAACTTAATTCGGTGT
23112 AATTAAGTAA
1 AATTAAGTAA
23122 ATAATCAAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
34 2 0.03
35 67 0.94
36 2 0.03
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (34 bp):
AATTAAGTAATCAGTAATTAACTTAATTCGGTGT
Found at i:29276 original size:78 final size:81
Alignment explanation
Indices: 29161--29321 Score: 231
Period size: 78 Copynumber: 2.0 Consensus size: 81
29151 TTATATTTAA
* *
29161 TATTTTTTTTCTAAAACCCTAAGGAACAAATATTTTAAGTTTAGGGCATACCCTTAAAA-CAAAT
1 TATTTTTTTCCTAAAACCCTAAGAAACAAATATTTTAAGTTTAGGGCATACCCTTAAAATC-AAT
29225 -TTTTTT-ATTTGGGGC
65 CTTTTTTAATTTGGGGC
* * * *
29240 TATTTTTTTCCTAAAGCCCT-AGAAATAAATATTTTAAGTTTAGGGCATATCTTTAAAATCAATC
1 TATTTTTTTCCTAAAACCCTAAGAAACAAATATTTTAAGTTTAGGGCATACCCTTAAAATCAATC
29304 TTTTTTAATTTGGGGC
66 TTTTTTAATTTGGGGC
29320 TA
1 TA
29322 AACCTTATTA
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
78 37 0.51
79 25 0.34
80 11 0.15
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.42
Consensus pattern (81 bp):
TATTTTTTTCCTAAAACCCTAAGAAACAAATATTTTAAGTTTAGGGCATACCCTTAAAATCAATC
TTTTTTAATTTGGGGC
Found at i:29984 original size:13 final size:13
Alignment explanation
Indices: 29966--29990 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29956 TTCAATGTTC
29966 TAAATATTATTTA
1 TAAATATTATTTA
29979 TAAATATTATTT
1 TAAATATTATTT
29991 GGAATTCCAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:30072 original size:353 final size:352
Alignment explanation
Indices: 29425--30109 Score: 977
Period size: 353 Copynumber: 1.9 Consensus size: 352
29415 ATTATCCGAA
* ** *
29425 CGCATTCGCGTTGGGGTTTTTGGTTTATAATTGGAGTTGAGTAATTTCAATTATAAGTAAAGTTT
1 CGCATTCGCGTT-GGGTTTTTGGTTTATAATTGAAACTGAGTAATTTCAATTATAAGTAAAATTT
* ** *
29490 TATCTTAGGTAATAGCAATTAAGTTAAATGTAAGGAAATATTGTTAGAATTCTAATGTTTGTTCA
65 TATCTTAGGTAATAGCAATTAAGTTAAATGGAAGGAAATATTGTTAGAATTCTAATGCCTATTCA
* * * *
29555 AATAATTATCTACCAGAAAAAGGATATGGAGTTTTAATTTTATTATAATTTAATGTTCTAAATAT
130 AATAATTATATACCAGAAAAAGGAAATGGAGTTTTAATTTGATTATAATTCAATGTTCTAAATAT
29620 TATTTAAAAATATTATTTGGAATTCCAAATATATAATAAATAATATATATTAGTTTTCTCCCAAC
195 TATTTAAAAATATTATTTGGAATTCCAAATATATAATAAATAATATATATTAGTTTTCTCCCAAC
* * *
29685 CAATCAACGTTGGACAAATGTGAGAGAAGAGGCAAATGCTGAGCATACGGTAGTTTGGGGATAAC
260 CAATCAACGTTGGACAAATGTGAGAGAAGAGGCAAATACTGAGCATACAGCAGTTTGGGGATAAC
29750 TTTAATAGTTAATTAGATATTTTTCCCG
325 TTTAATAGTTAATTAGATATTTTTCCCG
*
29778 CGCATTCGCGTCT-GGTTTTTCGGTTTATAATTGAAACTGAGTAATTTCAATTCTAAGTAAAATT
1 CGCATTCGCGT-TGGGTTTTT-GGTTTATAATTGAAACTGAGTAATTTCAATTATAAGTAAAATT
* * * * *
29842 TTATCTTATGTAATAGCAATTAAGTTAAATGGATGTAAATATTTTTAGAATTTTAATGCCTATTC
64 TTATCTTAGGTAATAGCAATTAAGTTAAATGGAAGGAAATATTGTTAGAATTCTAATGCCTATTC
* * * *
29907 AAATAATTATATA-CTGTGAAAATGAAATGGAGTTTTACTTTGATTATAATTCAATGTTCTAAAT
129 AAATAATTATATACCAG-AAAAAGGAAATGGAGTTTTAATTTGATTATAATTCAATGTTCTAAAT
* * *
29971 ATTATTTATAAATATTATTTGGAATTCC-AA-ATAT-A-AAATAATATATATTGGTTTTCTCTCA
193 ATTATTTAAAAATATTATTTGGAATTCCAAATATATAATAAATAATATATATTAGTTTTCTCCCA
* * *
30032 ACCAATCAACTTTGGATAAATGTTAGCATGAGATGAGGCAAATACTGAGCATACAGCAGTTTGGG
258 ACCAATCAACGTTGGACAAATG-T-G-A-GAGAAGAGGCAAATACTGAGCATACAGCAGTTTGGG
30097 GATAACTTTAATA
319 GATAACTTTAATA
30110 TAATAATAAT
Statistics
Matches: 294, Mismatches: 31, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
349 44 0.15
350 2 0.01
351 5 0.02
352 12 0.04
353 230 0.78
354 1 0.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.39
Consensus pattern (352 bp):
CGCATTCGCGTTGGGTTTTTGGTTTATAATTGAAACTGAGTAATTTCAATTATAAGTAAAATTTT
ATCTTAGGTAATAGCAATTAAGTTAAATGGAAGGAAATATTGTTAGAATTCTAATGCCTATTCAA
ATAATTATATACCAGAAAAAGGAAATGGAGTTTTAATTTGATTATAATTCAATGTTCTAAATATT
ATTTAAAAATATTATTTGGAATTCCAAATATATAATAAATAATATATATTAGTTTTCTCCCAACC
AATCAACGTTGGACAAATGTGAGAGAAGAGGCAAATACTGAGCATACAGCAGTTTGGGGATAACT
TTAATAGTTAATTAGATATTTTTCCCG
Found at i:30117 original size:3 final size:3
Alignment explanation
Indices: 30105--30203 Score: 79
Period size: 3 Copynumber: 34.0 Consensus size: 3
30095 GGGATAACTT
*
30105 TAA T-A TAA TAA TAA T-A TAA TAA T-A TAA TATA TAA T-A TAG T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
*
30146 TAA TAA TAA TAA TAA TAA TAA T-A TAG T-A TAA TATA TATA TATA TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TA-A TA-A TA-A
30193 TAA T-A TAA TAA
1 TAA TAA TAA TAA
30204 AGGTATAGAT
Statistics
Matches: 82, Mismatches: 4, Indels: 20
0.77 0.04 0.19
Matches are distributed among these distances:
2 14 0.17
3 50 0.61
4 18 0.22
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:30123 original size:5 final size:5
Alignment explanation
Indices: 30105--30202 Score: 87
Period size: 5 Copynumber: 19.0 Consensus size: 5
30095 GGGATAACTT
*
30105 TAATA TAATAA TAATA T-A-A TAATA TAATATA TAATA TAGTA TAATAA
1 TAATA TAAT-A TAATA TAATA TAATA T-A-ATA TAATA TAATA TAAT-A
*
30152 TAATAA TAATAA TAATA TAGTA TAATA T-ATA T-ATA TATATA TAATA
1 TAAT-A TAAT-A TAATA TAATA TAATA TAATA TAATA TA-ATA TAATA
30198 TAATA
1 TAATA
30203 AAGGTATAGA
Statistics
Matches: 81, Mismatches: 4, Indels: 16
0.80 0.04 0.16
Matches are distributed among these distances:
3 2 0.02
4 10 0.12
5 36 0.44
6 29 0.36
7 4 0.05
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:30123 original size:8 final size:8
Alignment explanation
Indices: 30112--30203 Score: 91
Period size: 8 Copynumber: 10.9 Consensus size: 8
30102 CTTTAATATA
30112 ATAATAAT
1 ATAATAAT
30120 ATAATAAT
1 ATAATAAT
30128 ATAAT-AT
1 ATAATAAT
30135 ATAAT-AT
1 ATAATAAT
30142 AGT-ATAAT
1 A-TAATAAT
30150 AATAATAAT
1 -ATAATAAT
30159 AATAATAAT
1 -ATAATAAT
30168 ATAGTATAAT
1 ATA--ATAAT
30178 ATATATATAT
1 ATA-ATA-AT
30188 ATATATAAT
1 ATA-ATAAT
30197 ATAATAA
1 ATAATAA
30204 AGGTATAGAT
Statistics
Matches: 77, Mismatches: 0, Indels: 14
0.85 0.00 0.15
Matches are distributed among these distances:
7 12 0.16
8 24 0.31
9 24 0.31
10 17 0.22
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (8 bp):
ATAATAAT
Found at i:30166 original size:28 final size:27
Alignment explanation
Indices: 30105--30199 Score: 119
Period size: 28 Copynumber: 3.6 Consensus size: 27
30095 GGGATAACTT
30105 TAATATAATAATA-A-TATAATAAT-A
1 TAATATAATAATATAGTATAATAATAA
30129 TAATAT-ATAATATAGTATAATAATAA
1 TAATATAATAATATAGTATAATAATAA
30155 TAATAATAATAATATAGTATAAT-ATATA
1 TAAT-ATAATAATATAGTATAATAATA-A
30183 TATATATATATAATATA
1 TA-ATATA-ATAATATA
30200 ATAAAGGTAT
Statistics
Matches: 63, Mismatches: 0, Indels: 11
0.85 0.00 0.15
Matches are distributed among these distances:
23 6 0.10
24 7 0.11
25 9 0.14
26 5 0.08
27 5 0.08
28 21 0.33
29 10 0.16
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
TAATATAATAATATAGTATAATAATAA
Found at i:30339 original size:14 final size:15
Alignment explanation
Indices: 30313--30341 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
30303 ATTATTATAA
30313 ATAAAATGAAAATAT
1 ATAAAATGAAAATAT
30328 ATAAAA-GAAAATAT
1 ATAAAATGAAAATAT
30342 TAGATTTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (15 bp):
ATAAAATGAAAATAT
Found at i:30577 original size:22 final size:23
Alignment explanation
Indices: 30552--30598 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
30542 GATAAACCCG
*
30552 TAACCCGAATGACCTAAGAA-AT
1 TAACCCGAATGACCCAAGAATAT
*
30574 TAACCCGGATGACCCAAGAATAT
1 TAACCCGAATGACCCAAGAATAT
30597 TA
1 TA
30599 TAAACTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.19
Consensus pattern (23 bp):
TAACCCGAATGACCCAAGAATAT
Found at i:31305 original size:7 final size:8
Alignment explanation
Indices: 31287--31314 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
31277 TTAATAAACG
31287 AAAATGCA
1 AAAATGCA
31295 AAAATGCA
1 AAAATGCA
31303 AAAATGCA
1 AAAATGCA
31311 AAAA
1 AAAA
31315 AGGTAGCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.68, C:0.11, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAATGCA
Found at i:31725 original size:17 final size:17
Alignment explanation
Indices: 31692--31732 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
31682 TTGATCACCG
*
31692 GTGATCTTGCATCACTA
1 GTGATCTTGCATAACTA
31709 GTGATCTTAG-ATAACTA
1 GTGATCTT-GCATAACTA
31726 GTGATCT
1 GTGATCT
31733 GGGGGTGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 21 0.95
18 1 0.05
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (17 bp):
GTGATCTTGCATAACTA
Found at i:35056 original size:26 final size:26
Alignment explanation
Indices: 35020--35098 Score: 149
Period size: 26 Copynumber: 3.0 Consensus size: 26
35010 TAAATCAACT
35020 ATGAGCAATATGAAAGTTGAAGAACA
1 ATGAGCAATATGAAAGTTGAAGAACA
35046 ATGAGCAATATGAAAGTTGAAGAACA
1 ATGAGCAATATGAAAGTTGAAGAACA
*
35072 ATGAACAATATGAAAGTTGAAGAACA
1 ATGAGCAATATGAAAGTTGAAGAACA
35098 A
1 A
35099 ATACAATCAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.52, C:0.08, G:0.22, T:0.19
Consensus pattern (26 bp):
ATGAGCAATATGAAAGTTGAAGAACA
Found at i:39316 original size:31 final size:31
Alignment explanation
Indices: 39281--39349 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
39271 AAATTACCGA
**
39281 TTGACCCCATTAAAATGATATGTTTATAGTT
1 TTGACCCCATTAAAATGATAAATTTATAGTT
39312 TTGACCCCATTAAAATGATAAATTTATAGTT
1 TTGACCCCATTAAAATGATAAATTTATAGTT
39343 TTGACCC
1 TTGACCC
39350 TACTATGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (31 bp):
TTGACCCCATTAAAATGATAAATTTATAGTT
Found at i:40636 original size:11 final size:11
Alignment explanation
Indices: 40608--40647 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
40598 GAGAAGAAAT
*
40608 AAATTTTCTCC
1 AAATTTTATCC
*
40619 AAAATTTATTCC
1 AAATTTTA-TCC
40631 AAATTTTATCC
1 AAATTTTATCC
40642 AAATTT
1 AAATTT
40648 GCTTTTATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (11 bp):
AAATTTTATCC
Found at i:40988 original size:31 final size:31
Alignment explanation
Indices: 40950--41011 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
40940 TATGTTCGAC
40950 AAATAAGGATATAATAGGCGTTTCAAAAGTT
1 AAATAAGGATATAATAGGCGTTTCAAAAGTT
* *
40981 AAATAAGGGTATAATAGGTGTTTCAAAAGTT
1 AAATAAGGATATAATAGGCGTTTCAAAAGTT
41012 TCACAAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (31 bp):
AAATAAGGATATAATAGGCGTTTCAAAAGTT
Found at i:41576 original size:29 final size:29
Alignment explanation
Indices: 41528--41585 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
41518 TAACTATCCA
*
41528 TTTTGGGACAAATTGACCCCTTAACTTTT
1 TTTTGGAACAAATTGACCCCTTAACTTTT
* *
41557 TTTTGGAACAAGTTGGCCCCTTAACTTTT
1 TTTTGGAACAAATTGACCCCTTAACTTTT
41586 AAGAATGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (29 bp):
TTTTGGAACAAATTGACCCCTTAACTTTT
Found at i:43308 original size:58 final size:58
Alignment explanation
Indices: 43218--43327 Score: 211
Period size: 58 Copynumber: 1.9 Consensus size: 58
43208 AGGAGTTTAA
43218 TTGTTAACCAACTTTATACTCCTAGCACTTTTTATTTTATTTTTAGTTTTATATTTGT
1 TTGTTAACCAACTTTATACTCCTAGCACTTTTTATTTTATTTTTAGTTTTATATTTGT
*
43276 TTGTTAACCAACTTTATACTCCTAGCATTTTTTATTTTATTTTTAGTTTTAT
1 TTGTTAACCAACTTTATACTCCTAGCACTTTTTATTTTATTTTTAGTTTTAT
43328 TTGTTGTTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.23, C:0.14, G:0.06, T:0.57
Consensus pattern (58 bp):
TTGTTAACCAACTTTATACTCCTAGCACTTTTTATTTTATTTTTAGTTTTATATTTGT
Found at i:43416 original size:14 final size:14
Alignment explanation
Indices: 43397--43440 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
43387 TAGAGTTTAA
43397 TTGATAACCAATTT
1 TTGATAACCAATTT
** **
43411 TTGATAAAAAAAAT
1 TTGATAACCAATTT
43425 TTGATAACCAATTT
1 TTGATAACCAATTT
43439 TT
1 TT
43441 ATGGCAGTTT
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (14 bp):
TTGATAACCAATTT
Found at i:50857 original size:24 final size:23
Alignment explanation
Indices: 50810--50858 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
50800 GCCACGTGGC
*
50810 AATTAAATTATTAAAAAATCGCA
1 AATTAAATTATTAAAAAATAGCA
50833 AATTATAATT-TTAAAAAATTAGCA
1 AATTA-AATTATTAAAAAA-TAGCA
50857 AA
1 AA
50859 CGGAAATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATTATTAAAAAATAGCA
Done.