Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008825.1 Corchorus capsularis cultivar CVL-1 contig08846, 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: 40294
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4693 original size:16 final size:16
Alignment explanation
Indices: 4657--4695 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
4647 ACTCAACTAC
* *
4657 TTTGCAACTTGATTCT
1 TTTGTAACTTAATTCT
4673 TTTGTAACTTAATTCT
1 TTTGTAACTTAATTCT
4689 TTTGTAA
1 TTTGTAA
4696 TTGGTTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.54
Consensus pattern (16 bp):
TTTGTAACTTAATTCT
Found at i:5495 original size:6 final size:6
Alignment explanation
Indices: 5484--5511 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5474 TCCAGTAACC
5484 CCAACT CCAACT CCAACT CCAACT CCAA
1 CCAACT CCAACT CCAACT CCAACT CCAA
5512 ACGGCAGCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.50, G:0.00, T:0.14
Consensus pattern (6 bp):
CCAACT
Found at i:6718 original size:2 final size:2
Alignment explanation
Indices: 6711--6753 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
6701 GATGATTCAT
6711 TA TA TA TA TA GT- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6753 T
1 T
6754 TAAGAAATAG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.95
3 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7921 original size:58 final size:58
Alignment explanation
Indices: 7850--7963 Score: 194
Period size: 58 Copynumber: 2.0 Consensus size: 58
7840 TGTTTGTCAA
7850 AATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAG-GACCTAACGTTATTG
1 AATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGAG-CCTAACGTTATTG
* *
7908 AATGCTCAAATAAGGGTCCGGTCTTTTAATTTGGCCAAATAAGAGCCTAACGTTAT
1 AATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGAGCCTAACGTTAT
7964 CGAAAATGCT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
58 52 0.98
59 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (58 bp):
AATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGAGCCTAACGTTATTG
Found at i:8031 original size:31 final size:30
Alignment explanation
Indices: 7996--8160 Score: 144
Period size: 31 Copynumber: 5.5 Consensus size: 30
7986 CGTGTGTGAC
7996 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTT-GCAAACGTT
**
8027 AGGCCCTTATTTG-GCCAAATT-CAAA-GATT
1 AGGCCCTTATTTGAG-CATTTTGCAAACG-TT
*
8056 GGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTT-GCAAACGTT
** * *
8087 AGGCCCTTATTTG-GCCAAATT--AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGCAAACG-TT
* *
8116 AGGTCCTTATTTGAGTATTTTGTCAAACGTT
1 AGGCCCTTATTTGAGCATTTTG-CAAACGTT
8147 AGGCCCTTATTTGA
1 AGGCCCTTATTTGA
8161 ACAATTAGCC
Statistics
Matches: 105, Mismatches: 17, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
28 5 0.05
29 38 0.36
30 4 0.04
31 53 0.50
32 5 0.05
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (30 bp):
AGGCCCTTATTTGAGCATTTTGCAAACGTT
Found at i:8061 original size:29 final size:29
Alignment explanation
Indices: 8025--8128 Score: 104
Period size: 29 Copynumber: 3.5 Consensus size: 29
8015 TTGGCAAACG
8025 TTAGGCCCTTATTTGGCCAAATTCAAAGA
1 TTAGGCCCTTATTTGGCCAAATTCAAAGA
* **
8054 TTGGGCCCTTATTTGAG-CATTTTGGCAAACG-
1 TTAGGCCCTTATTTG-GCCAAATT--CAAA-GA
*
8085 TTAGGCCCTTATTTGGCCAAATTAAAAGA
1 TTAGGCCCTTATTTGGCCAAATTCAAAGA
* *
8114 TCAGGTCCTTATTTG
1 TTAGGCCCTTATTTG
8129 AGTATTTTGT
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
28 1 0.02
29 34 0.57
30 2 0.03
31 22 0.37
32 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (29 bp):
TTAGGCCCTTATTTGGCCAAATTCAAAGA
Found at i:8068 original size:60 final size:60
Alignment explanation
Indices: 7995--8159 Score: 276
Period size: 60 Copynumber: 2.8 Consensus size: 60
7985 ACGTGTGTGA
*
7995 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
**
8055 TGGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
* * *
8115 CAGGTCCTTATTTGAGTATTTTGTCAAACGTTAGGCCCTTATTTG
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
8160 AACAATTAGC
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 97 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
Found at i:8572 original size:14 final size:14
Alignment explanation
Indices: 8553--8581 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
8543 TTTGGTTTTA
8553 ATTAAAATTAAATT
1 ATTAAAATTAAATT
8567 ATTAAAATTAAATT
1 ATTAAAATTAAATT
8581 A
1 A
8582 ATTCCTAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTAAAATTAAATT
Found at i:11155 original size:19 final size:19
Alignment explanation
Indices: 11122--11160 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
11112 ACAATTGAAA
11122 CGTTTGGCCCTAAATCGAG
1 CGTTTGGCCCTAAATCGAG
*
11141 CGTTTAGGCCC-AAATTGAG
1 CGTTT-GGCCCTAAATCGAG
11160 C
1 C
11161 ATTTTGCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (19 bp):
CGTTTGGCCCTAAATCGAG
Found at i:14470 original size:59 final size:59
Alignment explanation
Indices: 14378--14496 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
14368 TTGTTTAGAG
14378 AGAGAGAGAGAGAGAACTCCAATGTGGACTGATACACAAAAAGTTACAACAAATATGCA
1 AGAGAGAGAGAGAGAACTCCAATGTGGACTGATACACAAAAAGTTACAACAAATATGCA
14437 AGAGAGAGAGAGAGAACTCCAATGTGGACTGATACACAAAAAGTTACAACAAATATGCA
1 AGAGAGAGAGAGAGAACTCCAATGTGGACTGATACACAAAAAGTTACAACAAATATGCA
14496 A
1 A
14497 TTCCGATTAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.48, C:0.15, G:0.22, T:0.15
Consensus pattern (59 bp):
AGAGAGAGAGAGAGAACTCCAATGTGGACTGATACACAAAAAGTTACAACAAATATGCA
Found at i:15690 original size:93 final size:93
Alignment explanation
Indices: 15585--15765 Score: 344
Period size: 93 Copynumber: 1.9 Consensus size: 93
15575 AAATAGTAAC
* *
15585 ATGTATTCTAAAGAATTATTATTTCTTACTAAAATAATTCATTTATGGTTCCATTAACTCCTCAA
1 ATGTATTCTAAAGAATTATTATTTCTTACTAAAATAATTCATTAATGGTTCCATTAACTCCCCAA
15650 AGGGAGTCAAGAATACATACATACATAT
66 AGGGAGTCAAGAATACATACATACATAT
15678 ATGTATTCTAAAGAATTATTATTTCTTACTAAAATAATTCATTAATGGTTCCATTAACTCCCCAA
1 ATGTATTCTAAAGAATTATTATTTCTTACTAAAATAATTCATTAATGGTTCCATTAACTCCCCAA
15743 AGGGAGTCAAGAATACATACATA
66 AGGGAGTCAAGAATACATACATA
15766 GATACATATA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 86 1.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.35
Consensus pattern (93 bp):
ATGTATTCTAAAGAATTATTATTTCTTACTAAAATAATTCATTAATGGTTCCATTAACTCCCCAA
AGGGAGTCAAGAATACATACATACATAT
Found at i:15778 original size:2 final size:2
Alignment explanation
Indices: 15771--15798 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15761 ACATAGATAC
15771 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
15799 TATGATACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17486 original size:157 final size:156
Alignment explanation
Indices: 17074--17479 Score: 378
Period size: 157 Copynumber: 2.6 Consensus size: 156
17064 CATTTAGGTG
* ** * * *
17074 AAATTTCATCTCAAACAGACTTAGCATGAAAAACTTGTGCTAGTTTTTCAGTTAAGGACAGTTTG
1 AAATTTCAGCTCATTCAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTG
* * * * * *
17139 AGGAGACAAACCAACTTCTCTATGTTAGAGAGTTCGGTTTCACTTGAATTTTTTCCCATAGCCTT
66 AGGTGAGAAACCAAGTTCACTATG-AAGAGAGCTCGGTTTCACTTGAATTTTTTCCCATAGCCTT
*
17204 ATGGTGATAATCTAAGTATACTGGTGGA
130 ATGGTGATAATCTAAGTACACT-GTGGA
* * * * *
17232 AAA--TCAGCTTCGTT-GGACTTAGTATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTC
1 AAATTTCAGC-TCATTCAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGAC-AGTT
* * * * * * * * * *
17294 AGGGGTG-GAAACCTAGTTCACCATCAAGGGGAGCTCGGTTTTACTTATAATTTTTTTCCATAGT
64 TGAGGTGAGAAACCAAGTTCACTATGAA-GAGAGCTCGGTTTCACTT-GAATTTTTTCCCATAGC
** *
17358 CTTAT-GTGGATCTTCTAAG-ACCCT-TGGCA
127 CTTATGGT-GATAATCTAAGTACACTGTGG-A
17387 AAATTTCAGCTCATTCAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTG
1 AAATTTCAGCTCATTCAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTG
* *
17452 AGGTGAGAAGCTC-GGTTCACTATGAAGA
66 AGGTGAGAAAC-CAAGTTCACTATGAAGA
17480 AAAGCTCAGA
Statistics
Matches: 195, Mismatches: 42, Indels: 24
0.75 0.16 0.09
Matches are distributed among these distances:
154 3 0.02
155 5 0.03
156 87 0.45
157 96 0.49
158 4 0.02
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (156 bp):
AAATTTCAGCTCATTCAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTG
AGGTGAGAAACCAAGTTCACTATGAAGAGAGCTCGGTTTCACTTGAATTTTTTCCCATAGCCTTA
TGGTGATAATCTAAGTACACTGTGGA
Found at i:17828 original size:17 final size:18
Alignment explanation
Indices: 17806--17842 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
17796 GCAGCCTATC
17806 ACCTCATACTACCT-GGT
1 ACCTCATACTACCTAGGT
17823 ACCTCATACTACCTAGGT
1 ACCTCATACTACCTAGGT
17841 AC
1 AC
17843 TATGGGGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.27, C:0.35, G:0.11, T:0.27
Consensus pattern (18 bp):
ACCTCATACTACCTAGGT
Found at i:18993 original size:45 final size:46
Alignment explanation
Indices: 18913--19003 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 46
18903 GATTACTTCT
18913 CCAGCTCATCATTAATCCTAGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCTAGGGTAGGGATCTTTTAGTAATTCCAC
* *
18959 CCAGCTCATCATTAATTC-GGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCTAGGGTAGGGATCTTTTAGTAATTCCAC
19004 GTACTACTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 26 0.60
46 17 0.40
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (46 bp):
CCAGCTCATCATTAATCCTAGGGTAGGGATCTTTTAGTAATTCCAC
Found at i:19247 original size:2 final size:2
Alignment explanation
Indices: 19202--19231 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19192 ATGTAATAAG
19202 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19232 AAGTATCCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21733 original size:2 final size:2
Alignment explanation
Indices: 21726--21759 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
21716 TATTAATTAC
21726 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
21760 TGCTATTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22630 original size:17 final size:18
Alignment explanation
Indices: 22603--22640 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
22593 CCCTCCTCAT
22603 GGTACCTAGGTACCATGA
1 GGTACCTAGGTACCATGA
*
22621 GGTA-CTAGGTAGCATGA
1 GGTACCTAGGTACCATGA
22638 GGT
1 GGT
22641 GCTGGATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.24
Consensus pattern (18 bp):
GGTACCTAGGTACCATGA
Found at i:23299 original size:156 final size:154
Alignment explanation
Indices: 23002--23355 Score: 378
Period size: 156 Copynumber: 2.3 Consensus size: 154
22992 CCTCAAACTA
* * *
23002 TCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTATGTCTAAATGAGTTGAAATTTTGCCAAG
1 TCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTAAACGAGCTG-AATTTTGCCAAG
* * * *
23067 GGACTTAGAATATCCACATAAGACTATGGGAAAAATTCTAAGTAAAACAGAGCTCCCCTTGATGG
65 AGACTTAGAATATCCACATAAGACTATGGGAAAAATTCTAAGTAAAACAGAACTCCCCTAGATAG
* * * *
23132 TGAACTAGGTTT-CTCTCCATGAGTTG
130 AGAACTAGGTTTACACCCCA--AATTG
*
23158 TCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAAGCTG-ATTTT-CCATC
1 TCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTAAACG-AGCTGAATTTTGCCA--
* * * *
23220 AGTAGACTTAGATTATCCTCATAA-AGCTATGGGAAAAATTCTAAGTAAAACCGAACT-CTCTAG
63 AG-AGACTTAGAATATCCACATAAGA-CTATGGGAAAAATTCTAAGTAAAACAGAACTCCCCTAG
* *
23283 CATAGAGAAGTTGGTTTGACACCCCAAATTG
126 -ATAGAGAACTAGGTTT-ACACCCCAAATTG
* * * *
23314 TCCTTAACTGAAAAACTTGCATAAGTTTTTCATACGAAGTCT
1 TCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCT
23356 GTTTGAGATG
Statistics
Matches: 167, Mismatches: 22, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
153 3 0.02
154 5 0.03
155 10 0.06
156 144 0.86
158 5 0.03
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (154 bp):
TCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTAAACGAGCTGAATTTTGCCAAGA
GACTTAGAATATCCACATAAGACTATGGGAAAAATTCTAAGTAAAACAGAACTCCCCTAGATAGA
GAACTAGGTTTACACCCCAAATTG
Found at i:30544 original size:12 final size:12
Alignment explanation
Indices: 30529--30553 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30519 ATCAAATTAA
30529 ATGCAAAATGCC
1 ATGCAAAATGCC
30541 ATGCAAAATGCC
1 ATGCAAAATGCC
30553 A
1 A
30554 GTTCAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.24, G:0.16, T:0.16
Consensus pattern (12 bp):
ATGCAAAATGCC
Found at i:35506 original size:156 final size:154
Alignment explanation
Indices: 35203--35553 Score: 350
Period size: 156 Copynumber: 2.3 Consensus size: 154
35193 CCTCTTACCT
* * * * *
35203 CAAACTATCCTTAAATGAAAAACTACCATAAGTTTTTCATTCTAAGTCTGAATGAGTTCAAATTT
1 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAATCTCAACGAG-TCAAATTT
* * *
35268 TGACAAGGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACGGAGCTCCCCT
65 TCACAAGGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTCCCCT
* * * * *
35333 TGATGGTGAACTAGGTTTCTCTCCC
130 AGATAGAGAACTAGGTTTCACACCC
** ** **
35358 TGAGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAATC-CAACGAAG-CTGATTT
1 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAATCTCAACG-AGTCAAATTT
* * * *
35421 TCCACCAGTAGACTTAGATTATCCTCATAA-AGCTATGGGAAAAATTCTAAGTAAAACCGAACT-
65 T-CACAAG--GACTTAGAATATCCACATAAGA-CTATGGAAAAAATTCTAAGTAAAACCGAACTC
* * * *
35484 CTCTAGCATAGAGAAGTTGGTTTGACACCC
126 CCCTAG-ATAGAGAACTAGGTTTCACACCC
* *
35514 CAAACTGTCCTTAACTGAAAAACTTGCATAAGTTTTTCAT
1 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCAT
35554 ACGAAGTCTG
Statistics
Matches: 157, Mismatches: 33, Indels: 11
0.78 0.16 0.05
Matches are distributed among these distances:
153 6 0.04
154 7 0.04
155 48 0.31
156 96 0.61
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (154 bp):
CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAATCTCAACGAGTCAAATTTT
CACAAGGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTCCCCTA
GATAGAGAACTAGGTTTCACACCC
Found at i:40068 original size:2 final size:2
Alignment explanation
Indices: 40061--40093 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
40051 GGAGGAGCAA
40061 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
40094 ATTAAGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Done.