Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024063.1 Corchorus olitorius cultivar O-4 contig24096, 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: 24500
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Found at i:468 original size:3 final size:3
Alignment explanation
Indices: 460--493 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
450 GTCTTGTGTA
460 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
494 TAAAAAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:587 original size:25 final size:23
Alignment explanation
Indices: 567--706 Score: 82
Period size: 25 Copynumber: 5.7 Consensus size: 23
557 TACTACGCTC
**
567 TAGGTGAGACTCCCTTGCTACACAT
1 TAGGTGAGACTCCC-TGCTATGC-T
* * *
592 TAGGGGAGACTTCCCTACTATGCGG
1 TAGGTGAGAC-TCCCTGCTATGC-T
*
617 TACGTGAGACTCACCTGCTATGCGT
1 TAGGTGAGACTC-CCTGCTATGC-T
* *
642 TAGGGGAGACTCCCTTGCTATGCGC
1 TAGGTGAGACTCCC-TGCTATGC-T
* * *
667 TAGGTGAGACTCACCTGTTGTGCGC
1 TAGGTGAGACTC-CCTGCTATGC-T
*
692 TAGGGGAGACTCCCT
1 TAGGTGAGACTCCCT
707 CAATCTACGC
Statistics
Matches: 94, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
24 7 0.07
25 81 0.86
26 6 0.06
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.26
Consensus pattern (23 bp):
TAGGTGAGACTCCCTGCTATGCT
Found at i:610 original size:50 final size:50
Alignment explanation
Indices: 545--683 Score: 156
Period size: 50 Copynumber: 2.8 Consensus size: 50
535 TGCGTACTAA
* * * *
545 GGGAGACTGCTCTACTACGCTCTAGGTGAGACTC-CCTTGCTACACATTAG
1 GGGAGACTTCCCTACTATGCGCTAGGTGAGACTCACC-TGCTACACATTAG
* * ** *
595 GGGAGACTTCCCTACTATGCGGTACGTGAGACTCACCTGCTATGCGTTAG
1 GGGAGACTTCCCTACTATGCGCTAGGTGAGACTCACCTGCTACACATTAG
*
645 GGGAGAC-TCCCTTGCTATGCGCTAGGTGAGACTCACCTG
1 GGGAGACTTCCC-TACTATGCGCTAGGTGAGACTCACCTG
684 TTGTGCGCTA
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
49 4 0.05
50 69 0.92
51 2 0.03
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.25
Consensus pattern (50 bp):
GGGAGACTTCCCTACTATGCGCTAGGTGAGACTCACCTGCTACACATTAG
Found at i:696 original size:50 final size:50
Alignment explanation
Indices: 592--706 Score: 160
Period size: 50 Copynumber: 2.3 Consensus size: 50
582 TGCTACACAT
* *
592 TAGGGGAGACTTCCC-TACTATGCGGTACGTGAGACTCACCTGCTATGCGT
1 TAGGGGAGAC-TCCCTTACTATGCGCTACGTGAGACTCACCTGCTATGCGC
* * * *
642 TAGGGGAGACTCCCTTGCTATGCGCTAGGTGAGACTCACCTGTTGTGCGC
1 TAGGGGAGACTCCCTTACTATGCGCTACGTGAGACTCACCTGCTATGCGC
692 TAGGGGAGACTCCCT
1 TAGGGGAGACTCCCT
707 CAATCTACGC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
49 4 0.07
50 54 0.93
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.25
Consensus pattern (50 bp):
TAGGGGAGACTCCCTTACTATGCGCTACGTGAGACTCACCTGCTATGCGC
Found at i:4547 original size:50 final size:50
Alignment explanation
Indices: 4458--4830 Score: 362
Period size: 50 Copynumber: 7.4 Consensus size: 50
4448 GTTTGTCAAT
* * * *
4458 AATAAAGATTGAATTTTTTAAGTGAAAA-TTGAAGCTTTTAAGTAGTTTGTA
1 AATAAAGATTGAA-TTTTTAA-TTAAAAGATGAAACTTTTAAGTAATTTGTA
* * *
4509 AATAAAGGTTGGATTTTTAATTAAAAGATGAAACTTTTAAGTAA-TTGATG
1 AATAAAGATTGAATTTTTAATTAAAAGATGAAACTTTTAAGTAATTTG-TA
* * * * *
4559 AATAAAGATTGAATTTTTTTAAGTGAAAA-TTGAAGCTTTTTAGTAGTTTGTA
1 AATAAAGATTGAA--TTTTTAA-TTAAAAGATGAAACTTTTAAGTAATTTGTA
* * * * *
4611 AATAAAGATTGGATTTTTGATCAAAAGATGAAACTTTTAAGTAATTTATG
1 AATAAAGATTGAATTTTTAATTAAAAGATGAAACTTTTAAGTAATTTGTA
* *
4661 AATAAAGATTGAATTTTTAGTTAAAAGATGAAATTTTTAAGTAATTTGTA
1 AATAAAGATTGAATTTTTAATTAAAAGATGAAACTTTTAAGTAATTTGTA
* * * *
4711 AATAAAGATTGGATTTTTAATGAAAAGTTGAAACCTTTTAAGCAATTTGTA
1 AATAAAGATTGAATTTTTAATTAAAAGATGAAA-CTTTTAAGTAATTTGTA
* * * *
4762 AATAAA-AATGAAATCTTTAAGTTAAAATATTG-AACTTTTAATTAATTTGTA
1 AATAAAGATTG-AATTTTTAA-TTAAAAGA-TGAAACTTTTAAGTAATTTGTA
4813 AATAAAGA-TGAAATTTTT
1 AATAAAGATTG-AATTTTT
4831 GATGGGCTTA
Statistics
Matches: 264, Mismatches: 46, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
49 13 0.05
50 131 0.50
51 69 0.26
52 41 0.16
53 10 0.04
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.40
Consensus pattern (50 bp):
AATAAAGATTGAATTTTTAATTAAAAGATGAAACTTTTAAGTAATTTGTA
Found at i:4584 original size:102 final size:101
Alignment explanation
Indices: 4458--4821 Score: 459
Period size: 102 Copynumber: 3.6 Consensus size: 101
4448 GTTTGTCAAT
* *
4458 AATAAAGATTGAATTTTTTAAGTGAAAATTGAAGCTTTTAAGTAGTTTGTAAATAAAGGTTGGAT
1 AATAAAGATTGAATTTTTTAAGTGAAAATTGAAGCTTTTAAGTAATTTGTAAATAAAGATTGGAT
*
4523 TTTTAATTAAAAGATGAAACTTTTAAGTAATTGATG
66 TTTTAATCAAAAGATGAAACTTTTAAGTAATTGATG
* *
4559 AATAAAGATTGAATTTTTTTAAGTGAAAATTGAAGCTTTTTAGTAGTTTGTAAATAAAGATTGGA
1 AATAAAGATTGAA-TTTTTTAAGTGAAAATTGAAGCTTTTAAGTAATTTGTAAATAAAGATTGGA
* *
4624 TTTTTGATCAAAAGATGAAACTTTTAAGTAATTTATG
65 TTTTTAATCAAAAGATGAAACTTTTAAGTAATTGATG
* * **
4661 AATAAAGATTGAA-TTTTT-AGTTAAAAGATGAAATTTTTAAGTAATTTGTAAATAAAGATTGGA
1 AATAAAGATTGAATTTTTTAAGTGAAAA-TTGAAGCTTTTAAGTAATTTGTAAATAAAGATTGGA
* * * *
4724 TTTTTAATGAAAAGTTGAAACCTTTTAAGCAATTTG-TA
65 TTTTTAATCAAAAGATGAAA-CTTTTAAGTAA-TTGATG
* * * * *
4762 AATAAA-AATGAAATCTTTAAGTTAAAATATTGAA-CTTTTAATTAATTTGTAAATAAAGAT
1 AATAAAGATTGAATTTTTTAAG-TGAAA-ATTGAAGCTTTTAAGTAATTTGTAAATAAAGAT
4822 GAAATTTTTG
Statistics
Matches: 232, Mismatches: 23, Indels: 15
0.86 0.09 0.06
Matches are distributed among these distances:
99 7 0.03
100 58 0.25
101 34 0.15
102 124 0.53
103 8 0.03
104 1 0.00
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.40
Consensus pattern (101 bp):
AATAAAGATTGAATTTTTTAAGTGAAAATTGAAGCTTTTAAGTAATTTGTAAATAAAGATTGGAT
TTTTAATCAAAAGATGAAACTTTTAAGTAATTGATG
Found at i:4798 original size:152 final size:151
Alignment explanation
Indices: 4485--4830 Score: 389
Period size: 152 Copynumber: 2.3 Consensus size: 151
4475 TTAAGTGAAA
* * *
4485 ATTGAAGCTTTTAAGTAGTTTGTAAATAAAGGTTGGATTTTTAATTAAAAGATGAAACTTTTAAG
1 ATTGAA-CTTTTAAGTAATTTGTAAATAAAGATTGAATTTTTAATTAAAAGATGAAACTTTTAAG
* * * * *
4550 TAATTGATGAATAAAGATTGAATTTTTTTAAGTGAAAATTGAAGCTTTTTAGTAGTTTGTAAATA
65 TAATTGATAAATAAAGATTGAA-TTTTTTAAGTGAAAATTGAACCTTTTAAGCAATTTGTAAATA
* * * *
4615 AAGATTGGATTTTTGATCAAAAG
129 AAGAATGAATCTTTAATCAAAAG
* * * *
4638 A-TGAAACTTTTAAGTAATTTATGAATAAAGATTGAATTTTTAGTTAAAAGATGAAATTTTTAAG
1 ATTG-AACTTTTAAGTAATTTGTAAATAAAGATTGAATTTTTAATTAAAAGATGAAACTTTTAAG
*
4702 TAATTTG-TAAATAAAGATTGGA-TTTTTAA-TGAAAAGTTGAAACCTTTTAAGCAATTTGTAAA
65 TAA-TTGATAAATAAAGATTGAATTTTTTAAGTGAAAA-TTG-AACCTTTTAAGCAATTTGTAAA
* *
4764 TAAA-AATGAAATCTTTAAGTTAAAAT
127 TAAAGAATG-AATCTTTAA-TCAAAAG
*
4790 ATTGAACTTTTAATTAATTTGTAAATAAAGA-TGAAATTTTT
1 ATTGAACTTTTAAGTAATTTGTAAATAAAGATTG-AATTTTT
4831 GATGGGCTTA
Statistics
Matches: 163, Mismatches: 22, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
149 6 0.04
150 13 0.08
151 30 0.18
152 106 0.65
153 8 0.05
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.40
Consensus pattern (151 bp):
ATTGAACTTTTAAGTAATTTGTAAATAAAGATTGAATTTTTAATTAAAAGATGAAACTTTTAAGT
AATTGATAAATAAAGATTGAATTTTTTAAGTGAAAATTGAACCTTTTAAGCAATTTGTAAATAAA
GAATGAATCTTTAATCAAAAG
Found at i:5478 original size:46 final size:46
Alignment explanation
Indices: 5413--5862 Score: 432
Period size: 46 Copynumber: 9.7 Consensus size: 46
5403 TTTTATCTCT
* *
5413 TTCCAAAAAATGCCCCTTCCTTGTTGGAAGATCCCCGTTTTCTCTTA
1 TTCC-AAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTCTTA
* * * ** *
5460 TTCCAAAAATGTCACTTCCTAGTTGGAAGGTCCTTGTTTTTATCTCT-
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCG-TTTTCTCT-TA
* ** * *** *
5507 TTCCAAAAATGTCCCTTTATGGTTGGATGGTCTTTGTTTTTATCTCT-
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCG-TTTTCTCT-TA
*
5554 TTCCAAAAATGCCCCTTCTTGGTTGGAAGGTCCCCGTTTTCTCTTA
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTCTTA
*
5600 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTCGTTTTCTCTCT-
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTCT-TA
* * *
5646 TTCCAAAAATGTCCCTTCCTGGTTAGAAGGT-CCC-TGTT-T-TTA
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTCTTA
* * * *
5688 TTCCAAATATGCCCCTTCCTGGTCGGAAGGTCCCAGTTTTCAATATCTCA
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTC----TCTTA
** *
5738 -TCCTAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTATTTTCTTTTA
1 TTCC-AAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTCTTA
* *
5784 TTCCAAAAATGCCCCTTCCTGGTTAGAAGGTCCCCGTTTTCTTTTA
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTCTTA
* * * *
5830 TTCC-AAAATGTCCCTTCCTAGTCGAAAGGTCCC
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCC
5863 AGTTGTTTAC
Statistics
Matches: 340, Mismatches: 48, Indels: 32
0.81 0.11 0.08
Matches are distributed among these distances:
41 1 0.00
42 28 0.08
43 3 0.01
44 6 0.02
45 27 0.08
46 150 0.44
47 85 0.25
48 1 0.00
49 4 0.01
50 35 0.10
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.38
Consensus pattern (46 bp):
TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTCTTA
Found at i:5805 original size:184 final size:182
Alignment explanation
Indices: 5413--5851 Score: 553
Period size: 184 Copynumber: 2.4 Consensus size: 182
5403 TTTTATCTCT
* * *
5413 TTCCAAAAAATGCCCCTTCCTTGTTGGAAGATCCCCGTTTTCTCTTATTCCAAAAATGTCACTTC
1 TTCC-AAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTCTTATTCCAAAAATGTCCCTTC
* * * * * * ***
5478 CTAGTTGGAAGGTCCTTGTTTTTATCTCTTTCCAAAAATGTCCCTTTATGGTTGGATGGTCTTTG
65 CTAGTTAGAAGGTCCCTGTTTTTA----TTTCCAAAAATGCCCCTTCATGGTCGGAAGGTCCCAG
* * *
5543 TTTTTATCTCTTTCCAAAAATGCCCCTTCTTGGTTGGAAGGTCCCCGTTTTCTCTTA
126 TTTTTATCTCTATCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCATTTTCTCTTA
*
5600 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTCGTTTTCTCTCT-TTCCAAAAATGTCCCTTC
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTCT-TATTCCAAAAATGTCCCTTC
* * *
5664 CTGGTTAGAAGGTCCCTGTTTTTA-TTCCAAATATGCCCCTTCCTGGTCGGAAGGTCCCAGTTTT
65 CTAGTTAGAAGGTCCCTGTTTTTATTTCCAAAAATGCCCCTTCATGGTCGGAAGGTCCCAGTTTT
* *
5728 CAATATCTC-ATCCTAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTATTTTCTTTTA
130 ---TATCTCTATCC-AAAAATGCCCCTTCCTGGTTGGAAGGTCCCCATTTTCTCTTA
* *
5784 TTCCAAAAATGCCCCTTCCTGGTTAGAAGGTCCCCGTTTTCTTTTATTCC-AAAATGTCCCTTCC
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTCTTATTCCAAAAATGTCCCTTCC
5848 TAGT
66 TAGT
5852 CGAAAGGTCC
Statistics
Matches: 221, Mismatches: 25, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
181 31 0.14
183 21 0.10
184 89 0.40
186 75 0.34
187 5 0.02
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.38
Consensus pattern (182 bp):
TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCGTTTTCTCTTATTCCAAAAATGTCCCTTCC
TAGTTAGAAGGTCCCTGTTTTTATTTCCAAAAATGCCCCTTCATGGTCGGAAGGTCCCAGTTTTT
ATCTCTATCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCCATTTTCTCTTA
Found at i:5996 original size:49 final size:49
Alignment explanation
Indices: 5925--6149 Score: 285
Period size: 49 Copynumber: 4.6 Consensus size: 49
5915 TACCTTGTGC
* *
5925 TGCCCTTCTCGGTCGGAAGGTGTTGTTTTCAATGATTTCATTCCTGTTC
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGATTTCATTCCTGTTT
*
5974 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGACTTCATTCCTGTTT
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGATTTCATTCCTGTTT
* * *
6023 TGCCCTTCCCGATCGGAAGGTGTTATTTTCAATGCTTT-ATTCCTGTTT
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGATTTCATTCCTGTTT
* * * * **
6071 TGCCCTTCCTGGTCGGAAGGTATTGATTTCAATG-TTTTATTCCCATTT
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGATTTCATTCCTGTTT
** *
6119 TGCCCTT-CCGCACCGGAAGGTGTTGATTTCA
1 TGCCCTTCCCG-GTCGGAAGGTGTTGTTTTCA
6150 TTCCTGTTTT
Statistics
Matches: 156, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
47 5 0.03
48 71 0.46
49 80 0.51
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.41
Consensus pattern (49 bp):
TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGATTTCATTCCTGTTT
Found at i:6101 original size:97 final size:97
Alignment explanation
Indices: 5925--6147 Score: 288
Period size: 97 Copynumber: 2.3 Consensus size: 97
5915 TACCTTGTGC
* * *
5925 TGCCCTTCTCGGTCGGAAGGTGTTGTTTTCAATGATTTCATTCCTGTTCTGCCCTTCCCGGTCGG
1 TGCCCTTCCCGATCGGAAGGTGTTATTTTCAATGATTTCATTCCTGTTCTGCCCTTCCCGGTCGG
* * **
5990 AAGGTGTTGTTTTCAATGACTTCATTCCTGTTT
66 AAGGTATTGATTTCAATG-CTTCATTCCCATTT
* * *
6023 TGCCCTTCCCGATCGGAAGGTGTTATTTTCAATGCTTT-ATTCCTGTTTTGCCCTTCCTGGTCGG
1 TGCCCTTCCCGATCGGAAGGTGTTATTTTCAATGATTTCATTCCTGTTCTGCCCTTCCCGGTCGG
* *
6087 AAGGTATTGATTTCAATGTTTTATTCCCATTT
66 AAGGTATTGATTTCAATGCTTCATTCCCATTT
*
6119 TGCCCTT-CCGCACCGGAAGGTGTTGATTT
1 TGCCCTTCCCG-ATCGGAAGGTGTT-ATTT
6148 CATTCCTGTT
Statistics
Matches: 110, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
95 3 0.03
96 29 0.26
97 44 0.40
98 34 0.31
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.41
Consensus pattern (97 bp):
TGCCCTTCCCGATCGGAAGGTGTTATTTTCAATGATTTCATTCCTGTTCTGCCCTTCCCGGTCGG
AAGGTATTGATTTCAATGCTTCATTCCCATTT
Found at i:7521 original size:25 final size:25
Alignment explanation
Indices: 7487--7534 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
7477 TTCAGCATAT
7487 AATCGTTTCTCTCAATCATTGACGG
1 AATCGTTTCTCTCAATCATTGACGG
7512 AATCGTTTCTCTCAATCATTGAC
1 AATCGTTTCTCTCAATCATTGAC
7535 AACACTCTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (25 bp):
AATCGTTTCTCTCAATCATTGACGG
Found at i:11971 original size:9 final size:9
Alignment explanation
Indices: 11957--11994 Score: 76
Period size: 9 Copynumber: 4.2 Consensus size: 9
11947 GTTTTCTTGT
11957 ATGGGGTTG
1 ATGGGGTTG
11966 ATGGGGTTG
1 ATGGGGTTG
11975 ATGGGGTTG
1 ATGGGGTTG
11984 ATGGGGTTG
1 ATGGGGTTG
11993 AT
1 AT
11995 TAGAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.13, C:0.00, G:0.53, T:0.34
Consensus pattern (9 bp):
ATGGGGTTG
Found at i:13636 original size:15 final size:15
Alignment explanation
Indices: 13604--13633 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13594 TAAATTTCAA
13604 TAAAATAAAATATAT
1 TAAAATAAAATATAT
13619 TAAAATAAAA-ATAT
1 TAAAATAAAATATAT
13633 T
1 T
13634 TAATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATAAAATATAT
Found at i:14736 original size:14 final size:14
Alignment explanation
Indices: 14705--14747 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
14695 GTTTATGGAT
14705 TTTTTCATTTTTTC
1 TTTTTCATTTTTTC
14719 -TTTTC-TTCTTTTC
1 TTTTTCATT-TTTTC
14732 TTTTTCATTTTTTC
1 TTTTTCATTTTTTC
14746 TT
1 TT
14748 CAACTTTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 2 0.08
13 10 0.38
14 12 0.46
15 2 0.08
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTCATTTTTTC
Found at i:19232 original size:24 final size:22
Alignment explanation
Indices: 19180--19234 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
19170 AAATTTGGTT
19180 ACCCGCGCGCGTCCAAGGTTCA
1 ACCCGCGCGCGTCCAAGGTTCA
19202 ACCCGCGCGCGTCCAAGGTTCA
1 ACCCGCGCGCGTCCAAGGTTCA
19224 ACCCGCGCGCG
1 ACCCGCGCGCG
19235 GGTTATGCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.16, C:0.44, G:0.29, T:0.11
Consensus pattern (22 bp):
ACCCGCGCGCGTCCAAGGTTCA
Found at i:20591 original size:21 final size:21
Alignment explanation
Indices: 20558--20598 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20548 TCCCCATACA
*
20558 CAATACATATACATTCCAAAC
1 CAATACATATACAATCCAAAC
20579 CAAT-CATACTACAATCCAAA
1 CAATACATA-TACAATCCAAA
20599 GTAGTCTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (21 bp):
CAATACATATACAATCCAAAC
Done.