Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007576.1 Corchorus capsularis cultivar CVL-1 contig07597, 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: 112751
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:813 original size:2 final size:2
Alignment explanation
Indices: 806--832 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
796 TACATTACAT
806 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
833 TGTAAGCTCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2153 original size:3 final size:3
Alignment explanation
Indices: 2147--2181 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2137 CCTCCTATGT
2147 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
2182 TTTTTCCCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:4725 original size:1 final size:1
Alignment explanation
Indices: 4719--4753 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
4709 AAGAAGAATT
4719 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4754 CTTTAGGGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:8370 original size:23 final size:23
Alignment explanation
Indices: 8300--8371 Score: 94
Period size: 23 Copynumber: 3.1 Consensus size: 23
8290 TCCTTTTCAA
8300 ATAA-ATTTATTTTTATTTATTT
1 ATAATATTTATTTTTATTTATTT
*
8322 TTAATATTTATCATTTTATTTATTT
1 ATAATATTTAT--TTTTATTTATTT
8347 AT-ATATTTATTTTGTATTTATTT
1 ATAATATTTATTTT-TATTTATTT
8370 AT
1 AT
8372 TGATAAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.14
23 17 0.39
24 8 0.18
25 13 0.30
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (23 bp):
ATAATATTTATTTTTATTTATTT
Found at i:8568 original size:30 final size:30
Alignment explanation
Indices: 8503--8569 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
8493 CGTCTGATTT
* * *
8503 TATCCTGAATTGACACAAACCGATAACGTTT
1 TATCCTCAATTGACACAAA-CGATAACGGTG
*
8534 TATCCTCAATTGACACAAGA-GGTAACGGTG
1 TATCCTCAATTGACACAA-ACGATAACGGTG
8564 TATCCT
1 TATCCT
8570 GGATTACATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 13 0.42
31 17 0.55
32 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.28
Consensus pattern (30 bp):
TATCCTCAATTGACACAAACGATAACGGTG
Found at i:10710 original size:11 final size:11
Alignment explanation
Indices: 10672--10720 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
10662 ACCGACCGAC
10672 TAATAATATATA
1 TAAT-ATATATA
* *
10684 TAATTTTTTATA
1 TAA-TATATATA
*
10696 TAATATATGTA
1 TAATATATATA
10707 TAATATATATA
1 TAATATATATA
10718 TAA
1 TAA
10721 AATGATTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
11 18 0.60
12 11 0.37
13 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (11 bp):
TAATATATATA
Found at i:10773 original size:15 final size:16
Alignment explanation
Indices: 10735--10780 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
10725 ATTTTAAATT
10735 TATATTTA-ATATAATTA
1 TATATTTATAT-TAA-TA
*
10752 TATATTTATGTTAATA
1 TATATTTATATTAATA
10768 TA-ATTTATATTAA
1 TATATTTATATTAA
10781 AAAATAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 10 0.38
16 4 0.15
17 11 0.42
18 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
TATATTTATATTAATA
Found at i:19327 original size:38 final size:38
Alignment explanation
Indices: 19140--19320 Score: 299
Period size: 38 Copynumber: 4.7 Consensus size: 38
19130 GGCTGTGCAT
19140 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
1 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
19178 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
1 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
* *
19216 AGTGGACCCGCGTCTCAGGGGGTTAAACTAATGGTAAAG
1 AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGT-AAG
*
19255 AGTGGACCCGCGCCTCAGGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGCGCCTCA-GGGGGTTAAACTGATGGTAAG
*
19294 AGTGGACCCGTGCCTCAGGGGGGTTAA
1 AGTGGACCCGCGCCTCA-GGGGGTTAA
19321 CTGTTGGCTA
Statistics
Matches: 135, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
38 71 0.53
39 48 0.36
40 16 0.12
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.19
Consensus pattern (38 bp):
AGTGGACCCGCGCCTCAGGGGGTTAAACTGATGGTAAG
Found at i:20678 original size:26 final size:24
Alignment explanation
Indices: 20636--20687 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
20626 GCATAGTAGC
*
20636 ACCAACAAATAATATTCCTCATGGCA
1 ACCAACAAATAAAATT-CT-ATGGCA
20662 ACCAACACAA-AAAATTCTATGGCA
1 ACCAACA-AATAAAATTCTATGGCA
20686 AC
1 AC
20688 ATCAGCATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 8 0.33
25 2 0.08
26 12 0.50
27 2 0.08
ACGTcount: A:0.46, C:0.27, G:0.08, T:0.19
Consensus pattern (24 bp):
ACCAACAAATAAAATTCTATGGCA
Found at i:27827 original size:41 final size:40
Alignment explanation
Indices: 27746--27832 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
27736 TGGTAAAGGA
* * *
27746 AAAAAGAGAAAAAGTGGTAAGAGTAAAAATAATATGAAGT
1 AAAAAGAGAAAAAGTAGTAAGACTAAAAATAACATGAAGT
* ** *
27786 AAAAAGAGAAAAAGTATTAAGACTAAAAAATGGCATTAAGT
1 AAAAAGAGAAAAAGTAGTAAGACT-AAAAATAACATGAAGT
27827 AAAAAG
1 AAAAAG
27833 GTCAAAAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 21 0.54
41 18 0.46
ACGTcount: A:0.61, C:0.02, G:0.20, T:0.17
Consensus pattern (40 bp):
AAAAAGAGAAAAAGTAGTAAGACTAAAAATAACATGAAGT
Found at i:27839 original size:25 final size:25
Alignment explanation
Indices: 27811--27992 Score: 119
Period size: 25 Copynumber: 7.8 Consensus size: 25
27801 ATTAAGACTA
*
27811 AAAAATGGCATTAAGTAAAAAGGTC
1 AAAAATGGTATTAAGTAAAAAGGTC
* *
27836 AAAAATGATATCAAGT-AAAA-G--
1 AAAAATGGTATTAAGTAAAAAGGTC
*
27857 ----ATGGTATTGAGTAAAAAGGTC
1 AAAAATGGTATTAAGTAAAAAGGTC
*
27878 AAAAATGGTATCAAGT-AAAA-G--
1 AAAAATGGTATTAAGTAAAAAGGTC
27899 ----ATGGTATTAAGTAAAAAGAGT-
1 AAAAATGGTATTAAGTAAAAAG-GTC
* *
27920 AAAGAATGGTATTAAGTAGAAAGAGTAA
1 AAA-AATGGTATTAAGTAAAAAG-GT-C
* *
27948 AAAAATGGTATTAGGTAAAAGGGTC
1 AAAAATGGTATTAAGTAAAAAGGTC
*
27973 AGAAATGGTATTAAGTAAAA
1 AAAAATGGTATTAAGTAAAA
27993 GGTGGTATCA
Statistics
Matches: 122, Mismatches: 16, Indels: 38
0.69 0.09 0.22
Matches are distributed among these distances:
17 20 0.16
18 8 0.07
19 1 0.01
20 1 0.01
23 2 0.02
24 8 0.07
25 41 0.34
26 22 0.18
27 16 0.13
28 3 0.02
ACGTcount: A:0.51, C:0.03, G:0.23, T:0.23
Consensus pattern (25 bp):
AAAAATGGTATTAAGTAAAAAGGTC
Found at i:27870 original size:42 final size:42
Alignment explanation
Indices: 27809--27943 Score: 191
Period size: 42 Copynumber: 3.2 Consensus size: 42
27799 GTATTAAGAC
* * *
27809 TAAAAAATGGCATTAAGTAAAAAGGTCAAAAATGATATCAAG
1 TAAAAGATGGTATTAAGTAAAAAGGTCAAAAATGGTATCAAG
*
27851 TAAAAGATGGTATTGAGTAAAAAGGTCAAAAATGGTATCAAG
1 TAAAAGATGGTATTAAGTAAAAAGGTCAAAAATGGTATCAAG
*
27893 TAAAAGATGGTATTAAGTAAAAAGAGT-AAAGAATGGTATTAAG
1 TAAAAGATGGTATTAAGTAAAAAG-GTCAAA-AATGGTATCAAG
27936 TAGAAAGA
1 TA-AAAGA
27944 GTAAAAAAAT
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
42 64 0.76
43 15 0.18
44 5 0.06
ACGTcount: A:0.52, C:0.04, G:0.21, T:0.23
Consensus pattern (42 bp):
TAAAAGATGGTATTAAGTAAAAAGGTCAAAAATGGTATCAAG
Found at i:27917 original size:18 final size:17
Alignment explanation
Indices: 27878--27914 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
27868 TAAAAAGGTC
27878 AAAA-ATGGTATCAAGT
1 AAAAGATGGTATCAAGT
*
27894 AAAAGATGGTATTAAGT
1 AAAAGATGGTATCAAGT
27911 AAAA
1 AAAA
27915 AGAGTAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.54, C:0.03, G:0.19, T:0.24
Consensus pattern (17 bp):
AAAAGATGGTATCAAGT
Found at i:27994 original size:25 final size:24
Alignment explanation
Indices: 27891--27993 Score: 116
Period size: 26 Copynumber: 4.0 Consensus size: 24
27881 AATGGTATCA
27891 AGTAAAAGATGGTATTAAGTAAAAAG
1 AGTAAAA-ATGGTATTAAGT-AAAAG
27917 AGTAAAGAATGGTATTAAGTAGAAAG
1 AGTAAA-AATGGTATTAAGTA-AAAG
*
27943 AGTAAAAAAATGGTATTAGGTAAAAG
1 AGT--AAAAATGGTATTAAGTAAAAG
* *
27969 GGTCAGAAATGGTATTAAGTAAAAG
1 AGT-AAAAATGGTATTAAGTAAAAG
27994 GTGGTATCAA
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
25 20 0.29
26 31 0.46
27 14 0.21
28 3 0.04
ACGTcount: A:0.50, C:0.01, G:0.25, T:0.23
Consensus pattern (24 bp):
AGTAAAAATGGTATTAAGTAAAAG
Found at i:28000 original size:17 final size:16
Alignment explanation
Indices: 27975--28026 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
27965 AAAGGGTCAG
27975 AAATGGTATTAAGTAA
1 AAATGGTATTAAGTAA
* * *
27991 AAGGTGGTATCAACTAA
1 AA-ATGGTATTAAGTAA
*
28008 AAATAGTATTAAGTAA
1 AAATGGTATTAAGTAA
28024 AAA
1 AAA
28027 GAGTAAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.52, C:0.04, G:0.17, T:0.27
Consensus pattern (16 bp):
AAATGGTATTAAGTAA
Found at i:28049 original size:19 final size:19
Alignment explanation
Indices: 28025--28100 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 19
28015 ATTAAGTAAA
28025 AAGAGTAAAAAAAAATGGT
1 AAGAGTAAAAAAAAATGGT
*
28044 AAGAGTAAAAATGATAAAACTAGT
1 AAGAGT-AAAA--A-AAAA-TGGT
28068 AAGAGT-AAAAAAAATGGT
1 AAGAGTAAAAAAAAATGGT
**
28086 ATTCAGTAAAAAAAA
1 A-AGAGTAAAAAAAA
28101 GAGAAAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
18 4 0.09
19 13 0.28
20 12 0.26
22 4 0.09
23 4 0.09
24 9 0.20
ACGTcount: A:0.62, C:0.03, G:0.17, T:0.18
Consensus pattern (19 bp):
AAGAGTAAAAAAAAATGGT
Found at i:44095 original size:2 final size:2
Alignment explanation
Indices: 44059--44087 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44049 TTCATATCAG
44059 AT 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 AT A
44088 ACATATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46528 original size:21 final size:24
Alignment explanation
Indices: 46499--46549 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
46489 TTTTTAACTC
46499 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
46522 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
46545 ATTAT
1 ATTAT
46550 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:46544 original size:25 final size:25
Alignment explanation
Indices: 46499--46547 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
46489 TTTTTAACTC
*
46499 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
46524 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
46548 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:47839 original size:38 final size:38
Alignment explanation
Indices: 47797--47872 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
47787 AAGAAGGATG
*
47797 GTAGCTGGCACTTCTGTGTTGACTATAGACAGCTGAAT
1 GTAGCTGGCACTTCTGTGTGGACTATAGACAGCTGAAT
** *
47835 GTAGCTGGCGTTTCTGTGTGGACTATAGACAGTTGAAT
1 GTAGCTGGCACTTCTGTGTGGACTATAGACAGCTGAAT
47873 AAGCTTACAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (38 bp):
GTAGCTGGCACTTCTGTGTGGACTATAGACAGCTGAAT
Found at i:49914 original size:523 final size:523
Alignment explanation
Indices: 48930--49977 Score: 2087
Period size: 523 Copynumber: 2.0 Consensus size: 523
48920 TCAGGCTACT
48930 TTGTGTGCAATTACTACTTTTAGCATAGATCTAGGTTATCGTATTCAAACTTCATGCATGCAAGA
1 TTGTGTGCAATTACTACTTTTAGCATAGATCTAGGTTATCGTATTCAAACTTCATGCATGCAAGA
48995 TCCATCGTTGGCAGCTCTCATCCAAAGGTTACAACAGAATACCCTTAGTAACAACAAATATACTT
66 TCCATCGTTGGCAGCTCTCATCCAAAGGTTACAACAGAATACCCTTAGTAACAACAAATATACTT
49060 ATACATTGGGGCAGCTACGCAGAAGAGGCAAACTTATGGTGGGAAATGATGCTAAGCTTCGGGCT
131 ATACATTGGGGCAGCTACGCAGAAGAGGCAAACTTATGGTGGGAAATGATGCTAAGCTTCGGGCT
49125 GACATCTTGACTCACTTTCACTCCTCACCCACTGCTGGCCATTCAGGCATGGAAGCCACACTAAA
196 GACATCTTGACTCACTTTCACTCCTCACCCACTGCTGGCCATTCAGGCATGGAAGCCACACTAAA
49190 AAGGGTTGCTAGTGTTGTCTGAAAGGACTCAAGAAAGCTGTGAAGCAATTTGTACGCGAGTGTCA
261 AAGGGTTGCTAGTGTTGTCTGAAAGGACTCAAGAAAGCTGTGAAGCAATTTGTACGCGAGTGTCA
*
49255 AATCTGCCAACAGTGTAAATCAGAAAATGTGGCTTACCCAGGGCTTTTACAACCATTACCAATCC
326 AATCTGCCAACAATGTAAATCAGAAAATGTGGCTTACCCAGGGCTTTTACAACCATTACCAATCC
49320 CAGACAAGGTATGGGTCGACATCTCAATGGACTTTATTACTGGCTTACCTAAGTGTCAAGGAAAG
391 CAGACAAGGTATGGGTCGACATCTCAATGGACTTTATTACTGGCTTACCTAAGTGTCAAGGAAAG
49385 GAAGTGATCATGGTAGTGGTAGACAGGCTTAGCAAAATGGCTCACTTTGTTGCTTTAGCTCACCC
456 GAAGTGATCATGGTAGTGGTAGACAGGCTTAGCAAAATGGCTCACTTTGTTGCTTTAGCTCACCC
49450 TTA
521 TTA
49453 TTGTGTGCAATTACTACTTTTAGCATAGATCTAGGTTATCGTATTCAAACTTCATGCATGCAAGA
1 TTGTGTGCAATTACTACTTTTAGCATAGATCTAGGTTATCGTATTCAAACTTCATGCATGCAAGA
49518 TCCATCGTTGGCAGCTCTCATCCAAAGGTTACAACAGAATACCCTTAGTAACAACAAATATACTT
66 TCCATCGTTGGCAGCTCTCATCCAAAGGTTACAACAGAATACCCTTAGTAACAACAAATATACTT
49583 ATACATTGGGGCAGCTACGCAGAAGAGGCAAACTTATGGTGGGAAATGATGCTAAGCTTCGGGCT
131 ATACATTGGGGCAGCTACGCAGAAGAGGCAAACTTATGGTGGGAAATGATGCTAAGCTTCGGGCT
49648 GACATCTTGACTCACTTTCACTCCTCACCCACTGCTGGCCATTCAGGCATGGAAGCCACACTAAA
196 GACATCTTGACTCACTTTCACTCCTCACCCACTGCTGGCCATTCAGGCATGGAAGCCACACTAAA
49713 AAGGGTTGCTAGTGTTGTCTGAAAGGACTCAAGAAAGCTGTGAAGCAATTTGTACGCGAGTGTCA
261 AAGGGTTGCTAGTGTTGTCTGAAAGGACTCAAGAAAGCTGTGAAGCAATTTGTACGCGAGTGTCA
49778 AATCTGCCAACAATGTAAATCAGAAAATGTGGCTTACCCAGGGCTTTTACAACCATTACCAATCC
326 AATCTGCCAACAATGTAAATCAGAAAATGTGGCTTACCCAGGGCTTTTACAACCATTACCAATCC
49843 CAGACAAGGTATGGGTCGACATCTCAATGGACTTTATTACTGGCTTACCTAAGTGTCAAGGAAAG
391 CAGACAAGGTATGGGTCGACATCTCAATGGACTTTATTACTGGCTTACCTAAGTGTCAAGGAAAG
49908 GAAGTGATCATGGTAGTGGTAGACAGGCTTAGCAAAATGGCTCACTTTGTTGCTTTAGCTCACCC
456 GAAGTGATCATGGTAGTGGTAGACAGGCTTAGCAAAATGGCTCACTTTGTTGCTTTAGCTCACCC
49973 TTA
521 TTA
49976 TT
1 TT
49978 CTGCTATCTC
Statistics
Matches: 524, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
523 524 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (523 bp):
TTGTGTGCAATTACTACTTTTAGCATAGATCTAGGTTATCGTATTCAAACTTCATGCATGCAAGA
TCCATCGTTGGCAGCTCTCATCCAAAGGTTACAACAGAATACCCTTAGTAACAACAAATATACTT
ATACATTGGGGCAGCTACGCAGAAGAGGCAAACTTATGGTGGGAAATGATGCTAAGCTTCGGGCT
GACATCTTGACTCACTTTCACTCCTCACCCACTGCTGGCCATTCAGGCATGGAAGCCACACTAAA
AAGGGTTGCTAGTGTTGTCTGAAAGGACTCAAGAAAGCTGTGAAGCAATTTGTACGCGAGTGTCA
AATCTGCCAACAATGTAAATCAGAAAATGTGGCTTACCCAGGGCTTTTACAACCATTACCAATCC
CAGACAAGGTATGGGTCGACATCTCAATGGACTTTATTACTGGCTTACCTAAGTGTCAAGGAAAG
GAAGTGATCATGGTAGTGGTAGACAGGCTTAGCAAAATGGCTCACTTTGTTGCTTTAGCTCACCC
TTA
Found at i:51040 original size:2 final size:2
Alignment explanation
Indices: 51033--51083 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
51023 AAGTGTTGGC
*
51033 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC 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
51075 AT AT AT AT A
1 AT AT AT AT A
51084 ATGTCTTATC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:52687 original size:3 final size:3
Alignment explanation
Indices: 52679--52713 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
52669 TTTTCAAAGA
52679 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
52714 CAACAAGAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:56417 original size:23 final size:23
Alignment explanation
Indices: 56363--56423 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
56353 AGTATTCCTA
*
56363 ATCTCAAGACACATTTGATACATT
1 ATCTCAAGACACA-CTGATACATT
*
56387 -TCTTAAGACACACTGATAC-TGT
1 ATCTCAAGACACACTGATACAT-T
56409 ATCTCAAGACACACT
1 ATCTCAAGACACACT
56424 TGTAAAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 1 0.03
22 7 0.22
23 24 0.75
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.30
Consensus pattern (23 bp):
ATCTCAAGACACACTGATACATT
Found at i:59441 original size:4 final size:4
Alignment explanation
Indices: 59432--59457 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
59422 TTATAACAAC
59432 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
59458 GGGCTCTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:66338 original size:18 final size:18
Alignment explanation
Indices: 66311--66346 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
66301 AATCTTTAGG
66311 AAAAAACTATTTAATCAT
1 AAAAAACTATTTAATCAT
*
66329 AAAAAGCTATTTAATCAT
1 AAAAAACTATTTAATCAT
66347 GACTATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.33
Consensus pattern (18 bp):
AAAAAACTATTTAATCAT
Found at i:102859 original size:33 final size:34
Alignment explanation
Indices: 102805--102903 Score: 112
Period size: 33 Copynumber: 2.9 Consensus size: 34
102795 CATGTTCTAT
* * * *
102805 CGGCCCTGGCCAAAGGGTTATAGTA-TTTGGAAAA
1 CGGCCCT-GCTAACGGGTTATAGTAGTTAGCAAAA
**
102839 CGGCCCTGCTAACGGGTTATAGTAGTTAGCTTAA
1 CGGCCCTGCTAACGGGTTATAGTAGTTAGCAAAA
*
102873 -GGCCCTGCTAACGGGTTATAATAGTTAGCAA
1 CGGCCCTGCTAACGGGTTATAGTAGTTAGCAA
102904 TATGTCGATA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
33 43 0.78
34 12 0.22
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (34 bp):
CGGCCCTGCTAACGGGTTATAGTAGTTAGCAAAA
Found at i:108457 original size:34 final size:34
Alignment explanation
Indices: 108406--108472 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
108396 CCTAAATCAA
* *
108406 CTATTAATTATAGCTAAATAAAACCACATTTTAT
1 CTATCAATTATACCTAAATAAAACCACATTTTAT
*
108440 CTATCAATTATACCTAAATCAAACCACATTTTA
1 CTATCAATTATACCTAAATAAAACCACATTTTA
108473 ACTTAATCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.43, C:0.19, G:0.01, T:0.36
Consensus pattern (34 bp):
CTATCAATTATACCTAAATAAAACCACATTTTAT
Found at i:108615 original size:84 final size:85
Alignment explanation
Indices: 108513--108688 Score: 300
Period size: 84 Copynumber: 2.1 Consensus size: 85
108503 AGAAAGATTC
* *
108513 TTTTCATTGAAAAATAGAAAATAAAAGGGAAGAAATTTTAAAGGAACAGACTATATTC-CTCATT
1 TTTTAATTGAAAAATAGAAAATAAAAGAGAAGAAATTTTAAAGGAACAGACTATATTCTCTCATT
108577 GAGTTGTAGCAATATTATTA
66 GAGTTGTAGCAATATTATTA
* *
108597 TTTTAATTGAAAAATAGAAAATAAAAGAGAAGAAATTTTAAAGGAATAGACTATATTCTTTTCAT
1 TTTTAATTGAAAAATAGAAAATAAAAGAGAAGAAATTTTAAAGGAACAGACTATATTC-TCTCAT
108662 TGAGTTGTAGCAATATTATTA
65 TGAGTTGTAGCAATATTATTA
108683 TTTTAA
1 TTTTAA
108689 ATTTAGAGTA
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
84 55 0.64
86 31 0.36
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.35
Consensus pattern (85 bp):
TTTTAATTGAAAAATAGAAAATAAAAGAGAAGAAATTTTAAAGGAACAGACTATATTCTCTCATT
GAGTTGTAGCAATATTATTA
Found at i:110420 original size:30 final size:30
Alignment explanation
Indices: 110384--110485 Score: 88
Period size: 30 Copynumber: 3.4 Consensus size: 30
110374 CTGTGTTATA
*
110384 TGTGTTTGGGGACTTTAGTATAGATGCCTC
1 TGTGTTTAGGGACTTTAGTATAGATGCCTC
* *
110414 TGTGTTTAGGGACTTTAATGT-GAATGCC-C
1 TGTGTTTAGGGACTTTAGTATAG-ATGCCTC
*
110443 TTGTGCTT-GAGGACTTTGATGTA-A-ATGCCTC
1 -TGTGTTTAG-GGACTTT-A-GTATAGATGCCTC
110474 TGTGTTTAGGGA
1 TGTGTTTAGGGA
110486 TGAATACCCT
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
29 3 0.05
30 50 0.88
31 3 0.05
32 1 0.02
ACGTcount: A:0.19, C:0.13, G:0.29, T:0.39
Consensus pattern (30 bp):
TGTGTTTAGGGACTTTAGTATAGATGCCTC
Found at i:110512 original size:52 final size:54
Alignment explanation
Indices: 110434--110565 Score: 223
Period size: 54 Copynumber: 2.5 Consensus size: 54
110424 GACTTTAATG
* * *
110434 TGAATGCCCTTGTGCTTGAGGACTTTGATGTA-AA-TGCCTCTGTGTTTAGGGA
1 TGAATACCCTTGTGTTTGAGGACTTTGATATAGAATTGCCTCTGTGTTTAGGGA
110486 TGAATACCCTTGTGTTTGAGGACTTTGATATAGAATTGCCTCTGTGTTTAGGGA
1 TGAATACCCTTGTGTTTGAGGACTTTGATATAGAATTGCCTCTGTGTTTAGGGA
110540 TGAATACCCTTGTGTTTGAGGACTTT
1 TGAATACCCTTGTGTTTGAGGACTTT
110566 AATTATTGGG
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
52 29 0.39
53 2 0.03
54 44 0.59
ACGTcount: A:0.20, C:0.14, G:0.27, T:0.39
Consensus pattern (54 bp):
TGAATACCCTTGTGTTTGAGGACTTTGATATAGAATTGCCTCTGTGTTTAGGGA
Done.