Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024430.1 Corchorus olitorius cultivar O-4 contig24463, 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: 22747
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2312 original size:25 final size:25
Alignment explanation
Indices: 2278--2363 Score: 154
Period size: 25 Copynumber: 3.4 Consensus size: 25
2268 GAGTATCACA
2278 CCCGAGCTCGAGCTCGACACAATTT
1 CCCGAGCTCGAGCTCGACACAATTT
2303 CCCGAGCTCGAGCTCGACACAATTT
1 CCCGAGCTCGAGCTCGACACAATTT
* *
2328 TCCGAGCTCGAGCTTGACACAATTT
1 CCCGAGCTCGAGCTCGACACAATTT
2353 CCCGAGCTCGA
1 CCCGAGCTCGA
2364 TACTCGGCTC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 58 1.00
ACGTcount: A:0.23, C:0.35, G:0.21, T:0.21
Consensus pattern (25 bp):
CCCGAGCTCGAGCTCGACACAATTT
Found at i:4283 original size:181 final size:184
Alignment explanation
Indices: 3971--4339 Score: 629
Period size: 181 Copynumber: 2.0 Consensus size: 184
3961 TTGGTGGAAG
*
3971 AAGAAATGAGAAGAAAGGGGAAGAATACCTCAAGTCTCAGGCATTCAGATCCGTCGACGGTGGGC
1 AAGAAAGGAGAAGAAAGGGGAAGAATACCTCAAGTCTCAGGCATTCAGATCCGTCGACGGTGGGC
* *
4036 GAACGGAGGGGCGACTATCGTGGATTTGGAAATGAAGGAGGCGAAGGGAGAGAGTG--AAAGA-G
66 GAACGGAGGGGCGACCATCGTGGATTTGAAAATGAAGGAGGCGAAGGGAGAGAGTGAAAAAGATG
4098 AG-TTGAGAGAGCTCGAGCAAAAGAGGGAATTAGGGATTAGGTTTATGAAAATTT
131 AGATTGAGAGAGCTCGAGCAAAAGAGGGAATTAGGGATTAGGTTTA-GAAAATTT
4152 AAGAAAGGAGAAGAAAGGGGAAGAATACCTCAAGTCTCAGGCATTCAGATCCGTCGACGGTGGGC
1 AAGAAAGGAGAAGAAAGGGGAAGAATACCTCAAGTCTCAGGCATTCAGATCCGTCGACGGTGGGC
* *
4217 GAACGGAGGGGCGACCATCGTGGATTTGAAAATGAAGGAGGCGGAGGGAGATAGTGAAAAAGAGT
66 GAACGGAGGGGCGACCATCGTGGATTTGAAAATGAAGGAGGCGAAGGGAGAGAGTGAAAAAGA--
4282 TGAGACTTGAGAGAGCTCGAGCAAAAGAGGGAATTAGGGATTAGGTTTAGAAAATTT
129 TGAGA-TTGAGAGAGCTCGAGCAAAAGAGGGAATTAGGGATTAGGTTTAGAAAATTT
4339 A
1 A
4340 GGAATTTTTA
Statistics
Matches: 176, Mismatches: 5, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
181 116 0.66
183 5 0.03
186 3 0.02
187 9 0.05
188 43 0.24
ACGTcount: A:0.36, C:0.11, G:0.36, T:0.17
Consensus pattern (184 bp):
AAGAAAGGAGAAGAAAGGGGAAGAATACCTCAAGTCTCAGGCATTCAGATCCGTCGACGGTGGGC
GAACGGAGGGGCGACCATCGTGGATTTGAAAATGAAGGAGGCGAAGGGAGAGAGTGAAAAAGATG
AGATTGAGAGAGCTCGAGCAAAAGAGGGAATTAGGGATTAGGTTTAGAAAATTT
Found at i:6519 original size:20 final size:20
Alignment explanation
Indices: 6494--6532 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
6484 CATACCCCTC
6494 CATCAGACTCAACCAAACTG
1 CATCAGACTCAACCAAACTG
*
6514 CATCAGACTCAACTAAACT
1 CATCAGACTCAACCAAACT
6533 CATTCTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.33, G:0.08, T:0.18
Consensus pattern (20 bp):
CATCAGACTCAACCAAACTG
Found at i:7028 original size:21 final size:21
Alignment explanation
Indices: 7002--7042 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
6992 CTTTCGATTT
7002 GTTTGTTGGTTCATGTTATGC
1 GTTTGTTGGTTCATGTTATGC
*
7023 GTTTGTTGGTTTATGTTATG
1 GTTTGTTGGTTCATGTTATG
7043 TTTAGTATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.05, G:0.29, T:0.56
Consensus pattern (21 bp):
GTTTGTTGGTTCATGTTATGC
Found at i:9455 original size:22 final size:22
Alignment explanation
Indices: 9428--9530 Score: 62
Period size: 22 Copynumber: 4.6 Consensus size: 22
9418 ACCTCCTTGT
* *
9428 GAAATTTTGATAACCTCCCTAC
1 GAAATTTTGATAACATCACTAC
* * * *
9450 GGAATTTTAAAAACATCACTAT
1 GAAATTTTGATAACATCACTAC
* *** *
9472 GAAATTTTGATAACTTCTGAAT
1 GAAATTTTGATAACATCACTAC
* *
9494 GAAATTTTGATAACCAACACTAT
1 GAAATTTTGATAA-CATCACTAC
* *
9517 GAGATGTTGATAAC
1 GAAATTTTGATAAC
9531 CTCCATATGA
Statistics
Matches: 60, Mismatches: 20, Indels: 2
0.73 0.24 0.02
Matches are distributed among these distances:
22 45 0.75
23 15 0.25
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.33
Consensus pattern (22 bp):
GAAATTTTGATAACATCACTAC
Found at i:9548 original size:22 final size:23
Alignment explanation
Indices: 9500--9554 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
9490 GAATGAAATT
*
9500 TTGATAACCAACACTATGAGATG
1 TTGATAACCAACACTATGAGATA
** *
9523 TTGATAACCTCCA-TATGATATA
1 TTGATAACCAACACTATGAGATA
9545 TTGATAACCA
1 TTGATAACCA
9555 CGTTATGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (23 bp):
TTGATAACCAACACTATGAGATA
Found at i:9618 original size:22 final size:22
Alignment explanation
Indices: 9593--9639 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
9583 GAATTATTAG
* *
9593 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTGTGA
9615 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTGTGA
9637 TAA
1 TAA
9640 CCTTGCTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (22 bp):
TAATCACACTATGAAATTGTGA
Found at i:9739 original size:22 final size:23
Alignment explanation
Indices: 9689--9833 Score: 85
Period size: 22 Copynumber: 6.6 Consensus size: 23
9679 TGATAACTAC
*
9689 AAATTTTGATAACCTCCCT-ATG
1 AAATTTTGATAACCTCCATAATG
**
9711 ATTTTTTGATAACCT-CATAATG
1 AAATTTTGATAACCTCCATAATG
* * *
9733 AAATTTTGTTAATCTCCCT-ATG
1 AAATTTTGATAACCTCCATAATG
*
9755 AAATTTTGAT---CTACATACTATG
1 AAATTTTGATAACCTCCATA--ATG
*
9777 AAATTTTGATAACC-CTC-TTATG
1 AAATTTTGATAACCTC-CATAATG
* **
9799 AAATTTTGA-AAACTAAACT-ATG
1 AAATTTTGATAACCTCCA-TAATG
9821 AAATTTTGATAAC
1 AAATTTTGATAAC
9834 TTCCCCATAA
Statistics
Matches: 93, Mismatches: 17, Indels: 25
0.69 0.13 0.19
Matches are distributed among these distances:
19 4 0.04
21 5 0.05
22 76 0.82
23 5 0.05
24 1 0.01
25 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (23 bp):
AAATTTTGATAACCTCCATAATG
Found at i:9778 original size:44 final size:43
Alignment explanation
Indices: 9730--9833 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 43
9720 TAACCTCATA
* *
9730 ATGAAATTTTGTTAATCTCC-C-TATGAAATTTTG-ATCTACATACT
1 ATGAAATTTTGATAA-C-CCTCTTATGAAATTTTGAAACTA-A-ACT
9774 ATGAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTAAACT
1 ATGAAATTTTGATAACCCTCTTATGAAATTTTG-AAACTAAACT
9818 ATGAAATTTTGATAAC
1 ATGAAATTTTGATAAC
9834 TTCCCCATAA
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
42 2 0.04
43 2 0.04
44 45 0.83
45 1 0.02
46 4 0.07
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (43 bp):
ATGAAATTTTGATAACCCTCTTATGAAATTTTGAAACTAAACT
Found at i:9834 original size:22 final size:22
Alignment explanation
Indices: 9750--9834 Score: 86
Period size: 22 Copynumber: 3.9 Consensus size: 22
9740 GTTAATCTCC
9750 CTATGAAATTTTGAT--CTACATA
1 CTATGAAATTTTGATAACTA-A-A
***
9772 CTATGAAATTTTGATAAC-CCT
1 CTATGAAATTTTGATAACTAAA
*
9793 CTTATGAAATTTTGAAAACTAAA
1 C-TATGAAATTTTGATAACTAAA
9816 CTATGAAATTTTGATAACT
1 CTATGAAATTTTGATAACT
9835 TCCCCATAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.02
22 48 0.94
23 1 0.02
24 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (22 bp):
CTATGAAATTTTGATAACTAAA
Found at i:10029 original size:22 final size:23
Alignment explanation
Indices: 9850--10093 Score: 113
Period size: 22 Copynumber: 11.0 Consensus size: 23
9840 ATAAATACCA
* *
9850 CTATGAAATTTTGGTAATC-GCAT
1 CTATGAAATTTTGATAATCTTC-T
* * *
9873 -TTTGAAAATTTGATAA-CCTCT
1 CTATGAAATTTTGATAATCTTCT
*
9894 TTATGAAATTTTGATAATC-TCT
1 CTATGAAATTTTGATAATCTTCT
* * * **
9916 CTATAAAATTTTGTTGA-CCCCT
1 CTATGAAATTTTGATAATCTTCT
*
9938 CTATGAAATTTTGAT-ATTTTCAT
1 CTATGAAATTTTGATAATCTTC-T
* * *
9961 -TATGTAATTTGGATAACCTTGCT
1 CTATGAAATTTTGATAATCTT-CT
* ** *
9984 -T-TGAAATCTTGATAA-CAACA
1 CTATGAAATTTTGATAATCTTCT
10004 CTATGAAATTTTGATAATCTTC-
1 CTATGAAATTTTGATAATCTTCT
*
10026 CTAT-AAATTTCT-ATAATCCGATCT
1 CTATGAAATTT-TGATAAT-C-TTCT
* *
10050 CTATGAAATTTCGATAATC-ACT
1 CTATGAAATTTTGATAATCTTCT
* *
10072 CTATGAGA-TTTGATAACCTTCT
1 CTATGAAATTTTGATAATCTTCT
10094 ATCAAATTTT
Statistics
Matches: 167, Mismatches: 36, Indels: 37
0.70 0.15 0.15
Matches are distributed among these distances:
20 1 0.01
21 25 0.15
22 113 0.68
23 11 0.07
24 6 0.04
25 11 0.07
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (23 bp):
CTATGAAATTTTGATAATCTTCT
Found at i:10170 original size:22 final size:23
Alignment explanation
Indices: 10145--10204 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 23
10135 CCTTCATATG
*
10145 AAATTTTGATAATCACACTA-AA
1 AAATTTTGATAACCACACTATAA
* *
10167 AAATTTTAATAACCACACTATGA
1 AAATTTTGATAACCACACTATAA
10190 AAA-TTTGATAACCAC
1 AAATTTTGATAACCAC
10205 CCTACCTCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.48, C:0.17, G:0.05, T:0.30
Consensus pattern (23 bp):
AAATTTTGATAACCACACTATAA
Found at i:10253 original size:22 final size:22
Alignment explanation
Indices: 10215--10274 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
10205 CCTACCTCCT
*
10215 TATGAAATTTTGTTAACCACAC
1 TATGAAATTTTGATAACCACAC
* *
10237 TATGAAATTCTT-ATAACCGCGC
1 TATGAAATT-TTGATAACCACAC
*
10259 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
10275 TCCCTCTGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:10388 original size:22 final size:22
Alignment explanation
Indices: 10360--10492 Score: 137
Period size: 22 Copynumber: 6.0 Consensus size: 22
10350 TAACCTGATC
* *
10360 CTATGAAATTTTGGTAAGCACA
1 CTATGAAATTTTGATAACCACA
*
10382 CTATGAAATTTTGATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
*
10404 CCATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
* *
10426 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* *
10447 CTCATGAAATTATAATAACCATC-
1 CT-ATGAAATTTTGATAACCA-CA
*
10470 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
10492 C
1 C
10493 AGAGACAAGA
Statistics
Matches: 90, Mismatches: 16, Indels: 10
0.78 0.14 0.09
Matches are distributed among these distances:
21 4 0.04
22 83 0.92
23 3 0.03
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.34
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:10426 original size:44 final size:44
Alignment explanation
Indices: 10341--10488 Score: 174
Period size: 44 Copynumber: 3.3 Consensus size: 44
10331 CCTTCCTAAA
* * * *
10341 AAATTTTAATAACCTGATCCTATGAAATTTTGGTAAGCACACTATG
1 AAATTTTGATAACCT--TCCCATGAAATTTTGATAACCACACTATG
10387 AAATTTTGATAACCTTCCCATGAAATTTTGATAACCACACTATG
1 AAATTTTGATAACCTTCCCATGAAATTTTGATAACCACACTATG
* * * *
10431 GAATTTTGATAACC-TCCTCATGAAATTATAATAACCATC-TTATG
1 AAATTTTGATAACCTTCC-CATGAAATTTTGATAACCA-CACTATG
10475 AAATTTTGATAACC
1 AAATTTTGATAACC
10489 ACACAGAGAC
Statistics
Matches: 91, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
43 3 0.03
44 73 0.80
45 1 0.01
46 14 0.15
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (44 bp):
AAATTTTGATAACCTTCCCATGAAATTTTGATAACCACACTATG
Found at i:10686 original size:19 final size:20
Alignment explanation
Indices: 10655--10692 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
10645 TATTGAAATT
10655 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
10674 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
10693 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:12003 original size:42 final size:45
Alignment explanation
Indices: 11948--12041 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 45
11938 AGTGTATTAC
11948 CTAA-ATTCTACT-C-C-ATCTC-TAGATAAGTCATCAAAATAAAA
1 CTAATATTCTACTCCTCTATCTCTTA-ATAAGTCATCAAAATAAAA
* * *
11989 CTAATATTTTACTCCTCTATCTCTTAATAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCTATCTCTTAATAAGTCATCAAAATAAAA
12034 CTAATATT
1 CTAATATT
12042 AATTGTTGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
41 4 0.09
42 7 0.16
43 1 0.02
44 1 0.02
45 30 0.67
46 2 0.04
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.36
Consensus pattern (45 bp):
CTAATATTCTACTCCTCTATCTCTTAATAAGTCATCAAAATAAAA
Found at i:15273 original size:35 final size:35
Alignment explanation
Indices: 15233--15307 Score: 125
Period size: 35 Copynumber: 2.1 Consensus size: 35
15223 AGTTCGTTTA
*
15233 TGTTCACGAACATG-CTTGTTTATTGTTCATTTAAG
1 TGTTCACGAACA-GACTCGTTTATTGTTCATTTAAG
15268 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
15303 TGTTC
1 TGTTC
15308 GTTTATATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 1 0.03
35 37 0.97
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.44
Consensus pattern (35 bp):
TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
Found at i:15370 original size:16 final size:16
Alignment explanation
Indices: 15349--15380 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
15339 TATAATTATT
15349 TATATATTAATAATAA
1 TATATATTAATAATAA
*
15365 TATATATTATTAATAA
1 TATATATTAATAATAA
15381 AAATTATAAA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATTAATAATAA
Found at i:15375 original size:19 final size:19
Alignment explanation
Indices: 15333--15380 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
15323 GAACGTTCGT
* *
15333 TTATTATATAATTATTTATA
1 TTATTA-ATAATAATATATA
15353 -TATTAATAATAATATATA
1 TTATTAATAATAATATATA
15371 TTATTAATAA
1 TTATTAATAA
15381 AAATTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTAATAATAATATATA
Found at i:15675 original size:31 final size:33
Alignment explanation
Indices: 15639--15720 Score: 96
Period size: 35 Copynumber: 2.5 Consensus size: 33
15629 TGAACGAGTT
*
15639 TCGAACAC-CCTAAA-TTTTAAACGAGCCGAGC
1 TCGAACACACCAAAATTTTTAAACGAGCCGAGC
15670 TCGAACGAACACCAAAATTTTTAAACGAGCCGAGC
1 TCGAAC--ACACCAAAATTTTTAAACGAGCCGAGC
* * *
15705 TTGAACAAAGCAAAAT
1 TCGAACACACCAAAAT
15721 GTTCGCGAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
31 6 0.14
33 10 0.23
34 5 0.12
35 22 0.51
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.18
Consensus pattern (33 bp):
TCGAACACACCAAAATTTTTAAACGAGCCGAGC
Found at i:15681 original size:35 final size:35
Alignment explanation
Indices: 15640--15710 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 35
15630 GAACGAGTTT
*
15640 CGAACACCCTAAA-TTTTAAACGAGCCGAGCTCGAA
1 CGAACA-CCAAAATTTTTAAACGAGCCGAGCTCGAA
*
15675 CGAACACCAAAATTTTTAAACGAGCCGAGCTTGAA
1 CGAACACCAAAATTTTTAAACGAGCCGAGCTCGAA
15710 C
1 C
15711 AAAGCAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 5 0.15
35 28 0.85
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (35 bp):
CGAACACCAAAATTTTTAAACGAGCCGAGCTCGAA
Found at i:18147 original size:16 final size:16
Alignment explanation
Indices: 18120--18178 Score: 75
Period size: 16 Copynumber: 3.7 Consensus size: 16
18110 TTTGGTTGAG
18120 AGGAAA-GAAATAGGA
1 AGGAAAGGAAATAGGA
*
18135 AGGAAAGGAAATAGCA
1 AGGAAAGGAAATAGGA
*
18151 AGGGAAAGGAAATAGGG
1 A-GGAAAGGAAATAGGA
*
18168 AGGAAGGGAAA
1 AGGAAAGGAAA
18179 GGAAGTCATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 6 0.16
16 18 0.47
17 14 0.37
ACGTcount: A:0.54, C:0.02, G:0.39, T:0.05
Consensus pattern (16 bp):
AGGAAAGGAAATAGGA
Found at i:18158 original size:17 final size:16
Alignment explanation
Indices: 18120--18165 Score: 67
Period size: 17 Copynumber: 2.9 Consensus size: 16
18110 TTTGGTTGAG
*
18120 AGGAAA-GAAATAGGA
1 AGGAAAGGAAATAGCA
18135 AGGAAAGGAAATAGCA
1 AGGAAAGGAAATAGCA
18151 AGGGAAAGGAAATAG
1 A-GGAAAGGAAATAG
18166 GGAGGAAGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 13 0.46
ACGTcount: A:0.57, C:0.02, G:0.35, T:0.07
Consensus pattern (16 bp):
AGGAAAGGAAATAGCA
Done.