Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019880.1 Corchorus olitorius cultivar O-4 contig19913, 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: 36618
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Found at i:2347 original size:17 final size:17
Alignment explanation
Indices: 2306--2349 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2296 TTTTGAGGAG
*
2306 CTAATAAGGGAATGGGCT
1 CTAA-AAGGAAATGGGCT
*
2324 TTAAAAGGAAATGGGCT
1 CTAAAAGGAAATGGGCT
*
2341 CTGAAAGGA
1 CTAAAAGGA
2350 TTAAAGCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.39, C:0.09, G:0.32, T:0.20
Consensus pattern (17 bp):
CTAAAAGGAAATGGGCT
Found at i:8248 original size:28 final size:27
Alignment explanation
Indices: 8209--8288 Score: 115
Period size: 28 Copynumber: 2.9 Consensus size: 27
8199 AGCATTGGGG
*
8209 ACATCCAGGGGCATTTTGGTCATTTGC
1 ACATCAAGGGGCATTTTGGTCATTTGC
8236 ACATCAAGGGGGCATTTTGGTCATTTGC
1 ACATCAA-GGGGCATTTTGGTCATTTGC
** *
8264 ACATTTAGGGGCATTTTAGTCATTT
1 ACATCAAGGGGCATTTTGGTCATTT
8289 TAAGTTCAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 23 0.48
28 25 0.52
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.36
Consensus pattern (27 bp):
ACATCAAGGGGCATTTTGGTCATTTGC
Found at i:9902 original size:19 final size:19
Alignment explanation
Indices: 9878--9935 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
9868 TCAAGCTCTC
9878 ACCCTCTCTCCTATCATCG
1 ACCCTCTCTCCTATCATCG
*
9897 ACCCTC-AT-CT-TC-TC-
1 ACCCTCTCTCCTATCATCG
9911 ACCCTCTCTCCTATCATCG
1 ACCCTCTCTCCTATCATCG
9930 ACCCTC
1 ACCCTC
9936 ATCTTCTCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 6 0.19
15 3 0.09
16 4 0.12
17 4 0.12
18 3 0.09
19 12 0.38
ACGTcount: A:0.16, C:0.50, G:0.03, T:0.31
Consensus pattern (19 bp):
ACCCTCTCTCCTATCATCG
Found at i:9911 original size:33 final size:33
Alignment explanation
Indices: 9874--9943 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
9864 TTGATCAAGC
9874 TCTCACCCTCTCTCCTATCATCGACCCTCATCT
1 TCTCACCCTCTCTCCTATCATCGACCCTCATCT
9907 TCTCACCCTCTCTCCTATCATCGACCCTCATCT
1 TCTCACCCTCTCTCCTATCATCGACCCTCATCT
9940 TCTC
1 TCTC
9944 TCACTCAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.14, C:0.49, G:0.03, T:0.34
Consensus pattern (33 bp):
TCTCACCCTCTCTCCTATCATCGACCCTCATCT
Found at i:11793 original size:9 final size:9
Alignment explanation
Indices: 11779--11805 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
11769 AAATAGTTGC
11779 TTTGTTTTG
1 TTTGTTTTG
11788 TTTGTTTTG
1 TTTGTTTTG
11797 TTTGTTTTG
1 TTTGTTTTG
11806 ATGTTTACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (9 bp):
TTTGTTTTG
Found at i:13794 original size:16 final size:15
Alignment explanation
Indices: 13776--13811 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
13766 CAAGACATGT
13776 TTTTCAAGAAAATTG
1 TTTTCAAGAAAATTG
*
13791 TTTTCAAGAAAA-GG
1 TTTTCAAGAAAATTG
13805 TTTTCAA
1 TTTTCAA
13812 AAATAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (15 bp):
TTTTCAAGAAAATTG
Found at i:13796 original size:15 final size:14
Alignment explanation
Indices: 13776--13834 Score: 61
Period size: 13 Copynumber: 4.3 Consensus size: 14
13766 CAAGACATGT
*
13776 TTTTCAAGAAAATTG
1 TTTTCAAGAAAA-GG
13791 TTTTCAAGAAAAGG
1 TTTTCAAGAAAAGG
13805 TTTTCAA-AAATA-G
1 TTTTCAAGAAA-AGG
*
13818 ATTTCAA-AAAAGG
1 TTTTCAAGAAAAGG
13831 TTTT
1 TTTT
13835 GAGTCTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
12 1 0.03
13 17 0.44
14 9 0.23
15 12 0.31
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (14 bp):
TTTTCAAGAAAAGG
Found at i:14509 original size:11 final size:12
Alignment explanation
Indices: 14482--14525 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
14472 GCAACTAATC
14482 AAAAAAGAAATG
1 AAAAAAGAAATG
*
14494 AAAAATGAAATG
1 AAAAAAGAAATG
*
14506 AAAAAA-ATGATG
1 AAAAAAGA-AATG
14518 AAAAAAGA
1 AAAAAAGA
14526 GAAATAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 1 0.04
12 25 0.93
13 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (12 bp):
AAAAAAGAAATG
Found at i:15633 original size:69 final size:70
Alignment explanation
Indices: 15557--15708 Score: 218
Period size: 69 Copynumber: 2.2 Consensus size: 70
15547 AAGACTAAAT
* * *
15557 TCGTTTCCATACGAGTTAGTTCAAGCCTTGGTTCCATCCAAGCAGCAT-GTGCTTTTCCATAAGC
1 TCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAGCAGCATAG-GCTTTTCCACAAGC
15621 CA-AAC
65 CACAAC
* *
15626 TCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCGTCCAGGCAGCATAGGCTTTTCCACAAGCC
1 TCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAGCAGCATAGGCTTTTCCACAAGCC
**
15691 ACAGT
66 ACAAC
15696 TCGTTTCCATACG
1 TCGTTTCCATACG
15709 GTGCATTACC
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
69 59 0.80
70 15 0.20
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.30
Consensus pattern (70 bp):
TCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAGCAGCATAGGCTTTTCCACAAGCC
ACAAC
Found at i:15681 original size:174 final size:172
Alignment explanation
Indices: 15385--15706 Score: 488
Period size: 174 Copynumber: 1.9 Consensus size: 172
15375 CAAGCCAAAC
*
15385 TCGTTTCCATACGAGTTAGTTCAAGCCTTGGTTCCATTCAAGCAGCATGCTTTTCCATAAGCCAA
1 TCGTTTCCATACGAGTTAGTTCAAGCCTTGGTTCCATCCAAGCAGCATGCTTTTCCATAAGCCAA
* * * *
15450 ACTCGTTTCCATACGAGTCAGTTGAAGCCTTGATTCCACCTTAGCAACAAGGGCTTTTTCATAAG
66 ACTCGTTTCCATACGAGTCAGTTCAAACCTTGATTCCACC-TAGCAACAAGGGCTTTTCCACAAG
15515 CCA-AGTTCATTTCCATATGAATTCAGTCTTCCAAGACTAAAT
130 CCACAGTTCATTTCCATATGAATTCAGTCTTCCAAGACTAAAT
15557 TCGTTTCCATACGAGTTAGTTCAAGCCTTGGTTCCATCCAAGCAGCATGTGCTTTTCCATAAGCC
1 TCGTTTCCATACGAGTTAGTTCAAGCCTTGGTTCCATCCAAGCAGCA--TGCTTTTCCATAAGCC
* * *
15622 AAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCGTCC-AGGCAGCATA-GGCTTTTCCA
64 AAACTCGTTTCCATACGAGTCAGTTCAAACCTTGATTCC-ACCTA-GCAACA-AGGGCTTTTCCA
*
15685 CAAGCCACAGTTCGTTTCCATA
126 CAAGCCACAGTTCATTTCCATA
15707 CGGTGCATTA
Statistics
Matches: 135, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
172 46 0.34
173 1 0.01
174 72 0.53
175 16 0.12
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (172 bp):
TCGTTTCCATACGAGTTAGTTCAAGCCTTGGTTCCATCCAAGCAGCATGCTTTTCCATAAGCCAA
ACTCGTTTCCATACGAGTCAGTTCAAACCTTGATTCCACCTAGCAACAAGGGCTTTTCCACAAGC
CACAGTTCATTTCCATATGAATTCAGTCTTCCAAGACTAAAT
Found at i:15771 original size:35 final size:35
Alignment explanation
Indices: 15725--16101 Score: 556
Period size: 35 Copynumber: 10.8 Consensus size: 35
15715 TACCATCTTC
*
15725 TCAGATGACTCGATGTAGCATCTTCAAAGTTGAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
* *
15760 TCAGATGACTCGGTGTAGCATCTTCAAAGATGACT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
15795 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
* * *
15830 CCAGATGACTCGGTGTAGCATCTTCAAAGATGAAG
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
* * * *
15865 TCGGATGACTCGGTGTAACAACTCCAAAGTTGAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
* * *
15900 TCAGATGAATCAGTGTAGCATCTTCAAGGTTGAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
* * * *
15935 CCAGATGACTTGGTGTAGCATCTTCAAAGATGAAC
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
*
15970 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAC
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
*
16005 TCATATGACTCGGTGTAGCATCTTCAAAGTTGAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
* *
16040 CCAGATGACTCGGTGTAGCATCTTCAAAGATGAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
*
16075 TCGGATGACTCGGTGTAGCATCTTCAA
1 TCAGATGACTCGGTGTAGCATCTTCAA
16102 TATGGGCTCA
Statistics
Matches: 303, Mismatches: 39, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 303 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (35 bp):
TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
Found at i:16136 original size:36 final size:36
Alignment explanation
Indices: 16094--16206 Score: 119
Period size: 34 Copynumber: 3.2 Consensus size: 36
16084 TCGGTGTAGC
16094 ATCTTCAATATGGGCTCAGTGGGCTCGGTGCAGCAA
1 ATCTTCAATATGGGCTCAGTGGGCTCGGTGCAGCAA
* * * *
16130 ATCTTCAA-AT-AGATCAG-GATGACTCGGTGTAGC--
1 ATCTTCAATATGGGCTCAGTG--GGCTCGGTGCAGCAA
*
16163 ATCTTCAATATGGACTCAGTGGGCTCGGTGCAGCAA
1 ATCTTCAATATGGGCTCAGTGGGCTCGGTGCAGCAA
*
16199 ACCTTCAA
1 ATCTTCAA
16207 ATAGATTAGG
Statistics
Matches: 60, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
33 9 0.15
34 18 0.30
35 17 0.28
36 16 0.27
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (36 bp):
ATCTTCAATATGGGCTCAGTGGGCTCGGTGCAGCAA
Found at i:16161 original size:69 final size:69
Alignment explanation
Indices: 16077--16227 Score: 257
Period size: 69 Copynumber: 2.2 Consensus size: 69
16067 AGATGAATTC
* *
16077 GGATGACTCGGTGTAGCATCTTCAATATGGGCTCAGTGGGCTCGGTGCAGCAAATCTTCAAATAG
1 GGATGACTCGGTGTAGCATCTTCAATATGGACTCAGTGGGCTCGGTGCAGCAAACCTTCAAATAG
16142 ATCA
66 ATCA
16146 GGATGACTCGGTGTAGCATCTTCAATATGGACTCAGTGGGCTCGGTGCAGCAAACCTTCAAATAG
1 GGATGACTCGGTGTAGCATCTTCAATATGGACTCAGTGGGCTCGGTGCAGCAAACCTTCAAATAG
*
16211 ATTA
66 ATCA
* *
16215 GGGTGATTCGGTG
1 GGATGACTCGGTG
16228 AATTAAGTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 77 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.26
Consensus pattern (69 bp):
GGATGACTCGGTGTAGCATCTTCAATATGGACTCAGTGGGCTCGGTGCAGCAAACCTTCAAATAG
ATCA
Found at i:16227 original size:35 final size:35
Alignment explanation
Indices: 16117--16227 Score: 113
Period size: 35 Copynumber: 3.2 Consensus size: 35
16107 GCTCAGTGGG
*
16117 CTCGGTGCAGCAAATCTTCAAATAGATCAGGATGA
1 CTCGGTGCAGCAAATCTTCAAATAGATCAGGGTGA
* *
16152 CTCGGTGTAGC--ATCTTCAATATGGACTCAGTGG-G-
1 CTCGGTGCAGCAAATCTTCAA-ATAGA-TCAG-GGTGA
* *
16186 CTCGGTGCAGCAAACCTTCAAATAGATTAGGGTGA
1 CTCGGTGCAGCAAATCTTCAAATAGATCAGGGTGA
*
16221 TTCGGTG
1 CTCGGTG
16228 AATTAAGTTG
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
33 10 0.16
34 18 0.30
35 25 0.41
36 8 0.13
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (35 bp):
CTCGGTGCAGCAAATCTTCAAATAGATCAGGGTGA
Found at i:16597 original size:28 final size:27
Alignment explanation
Indices: 16558--16637 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 27
16548 AGCATTGGGG
*
16558 ACATCCAGGGGCTTTTTGGTCATTTGC
1 ACATCCAGGGGCATTTTGGTCATTTGC
16585 ACATCCAGGGGGCATTTTGGTCATTTGC
1 ACATCCA-GGGGCATTTTGGTCATTTGC
** *
16613 ACATTTAGGGGCATTTTAGTCATTT
1 ACATCCAGGGGCATTTTGGTCATTT
16638 TAAGTTCACT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 24 0.50
28 24 0.50
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (27 bp):
ACATCCAGGGGCATTTTGGTCATTTGC
Found at i:18038 original size:16 final size:16
Alignment explanation
Indices: 18017--18047 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
18007 ATAGCTCTCA
18017 ATCTCCACAGACTCCC
1 ATCTCCACAGACTCCC
18033 ATCTCCACAGACTCC
1 ATCTCCACAGACTCC
18048 ATACACACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.48, G:0.06, T:0.19
Consensus pattern (16 bp):
ATCTCCACAGACTCCC
Found at i:18276 original size:33 final size:33
Alignment explanation
Indices: 18239--18308 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
18229 TTGATCAAGC
*
18239 TCTCACCCTTTCTCCTATCATCGACCCTCATCT
1 TCTCACCCTCTCTCCTATCATCGACCCTCATCT
18272 TCTCACCCTCTCTCCTATCATCGACCCTCATCT
1 TCTCACCCTCTCTCCTATCATCGACCCTCATCT
18305 TCTC
1 TCTC
18309 TCACTTAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.14, C:0.47, G:0.03, T:0.36
Consensus pattern (33 bp):
TCTCACCCTCTCTCCTATCATCGACCCTCATCT
Found at i:18300 original size:19 final size:19
Alignment explanation
Indices: 18243--18300 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
18233 TCAAGCTCTC
*
18243 ACCCTTTCTCCTATCATCG
1 ACCCTCTCTCCTATCATCG
*
18262 ACCCTC-AT-CT-TC-TC-
1 ACCCTCTCTCCTATCATCG
18276 ACCCTCTCTCCTATCATCG
1 ACCCTCTCTCCTATCATCG
18295 ACCCTC
1 ACCCTC
18301 ATCTTCTCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
14 6 0.19
15 3 0.10
16 4 0.13
17 4 0.13
18 3 0.10
19 11 0.35
ACGTcount: A:0.16, C:0.48, G:0.03, T:0.33
Consensus pattern (19 bp):
ACCCTCTCTCCTATCATCG
Found at i:19279 original size:41 final size:40
Alignment explanation
Indices: 19234--19360 Score: 128
Period size: 41 Copynumber: 3.1 Consensus size: 40
19224 ATTCAATCGG
* **
19234 GTCCCAAATTTAGGCTGTTATTTATTCATTGATTCAATTTT
1 GTCCCTAATTTAGG-TAATATTTATTCATTGATTCAATTTT
* ** * ***
19275 GTCCCTGATCCAAGGTAATATTTATTGATTGATTCAAACAT
1 GTCCCTAAT-TTAGGTAATATTTATTCATTGATTCAATTTT
*
19316 GTCCCTAATTTAGAGTAATATTTATTTATTGATTCAATTTT
1 GTCCCTAATTTAG-GTAATATTTATTCATTGATTCAATTTT
19357 GTCC
1 GTCC
19361 TTGATTTAAG
Statistics
Matches: 67, Mismatches: 17, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
40 2 0.03
41 62 0.93
42 3 0.04
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.45
Consensus pattern (40 bp):
GTCCCTAATTTAGGTAATATTTATTCATTGATTCAATTTT
Found at i:19368 original size:41 final size:41
Alignment explanation
Indices: 19252--19370 Score: 141
Period size: 41 Copynumber: 2.9 Consensus size: 41
19242 TTTAGGCTGT
**
19252 TATTTATTCATTGATTCAATTTTGTCCCTGATCCAAGGTAA
1 TATTTATTCATTGATTCAATTTTGTCCCTGATTTAAGGTAA
* *** *
19293 TATTTATTGATTGATTCAAACATGTCCCTAATTT-AGAGTAA
1 TATTTATTCATTGATTCAATTTTGTCCCTGATTTAAG-GTAA
* *
19334 TATTTATTTATTGATTCAATTTTGTCCTTGATTTAAG
1 TATTTATTCATTGATTCAATTTTGTCCCTGATTTAAG
19371 ATTTATTTCC
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
40 2 0.03
41 59 0.94
42 2 0.03
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.47
Consensus pattern (41 bp):
TATTTATTCATTGATTCAATTTTGTCCCTGATTTAAGGTAA
Found at i:24168 original size:22 final size:22
Alignment explanation
Indices: 24139--24282 Score: 134
Period size: 22 Copynumber: 6.5 Consensus size: 22
24129 TAGATATATT
24139 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACTACCC
* *
24161 TATTAAATTTTGATAACCACCC
1 TATGAAATTTTGATAACTACCC
*
24183 TATGAAATTTTGATAATTA-CC
1 TATGAAATTTTGATAACTACCC
* *
24204 TATGAAATTGTGATAAACT-CCA
1 TATGAAATTTTGAT-AACTACCC
* * *
24226 TATGAAACTTAGATAACCTA-AC
1 TATGAAATTTTGATAA-CTACCC
* *
24248 TATGAAATTTTAATAAACCT-TCC
1 TATGAAATTTTGAT-AA-CTACCC
24271 TATGAAATTTTG
1 TATGAAATTTTG
24283 TAATCTTCTT
Statistics
Matches: 98, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
21 17 0.17
22 64 0.65
23 17 0.17
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACCC
Found at i:24243 original size:65 final size:65
Alignment explanation
Indices: 24139--24263 Score: 155
Period size: 65 Copynumber: 1.9 Consensus size: 65
24129 TAGATATATT
* * * * * * *
24139 TATGAAATTTTGATAACTACCCTATTAAATTTTGATAACC-ACCCTATGAAATTTTGATAATTAC
1 TATGAAATTGTGATAACTACCATATGAAACTTAGATAACCTA-ACTATGAAATTTTAATAATTAC
24203 C
65 C
24204 TATGAAATTGTGATAAACT-CCATATGAAACTTAGATAACCTAACTATGAAATTTTAATAA
1 TATGAAATTGTGAT-AACTACCATATGAAACTTAGATAACCTAACTATGAAATTTTAATAA
24264 ACCTTCCTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
65 46 0.90
66 5 0.10
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (65 bp):
TATGAAATTGTGATAACTACCATATGAAACTTAGATAACCTAACTATGAAATTTTAATAATTACC
Found at i:24752 original size:36 final size:34
Alignment explanation
Indices: 24712--24820 Score: 87
Period size: 36 Copynumber: 3.1 Consensus size: 34
24702 TAATTTAAAT
24712 TTATATATTATAATTATATTTTATGTATATAATTAA
1 TTATATATTATAATTATA-TTTAT-TATATAATTAA
* ** * * **
24748 TTATAAAACAAAATATATAATTATATATATAACAAA
1 TTATATATTATAAT-TATATTTAT-TATATAATTAA
**
24784 AAATATATTATAATTATA-TTA-TATATAATTAA
1 TTATATATTATAATTATATTTATTATATAATTAA
24816 TTATA
1 TTATA
24821 AAACAAATAT
Statistics
Matches: 54, Mismatches: 18, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
32 12 0.22
34 3 0.06
35 4 0.07
36 31 0.57
37 4 0.07
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (34 bp):
TTATATATTATAATTATATTTATTATATAATTAA
Found at i:24764 original size:24 final size:24
Alignment explanation
Indices: 24737--24801 Score: 80
Period size: 26 Copynumber: 2.7 Consensus size: 24
24727 ATATTTTATG
24737 TATATAATTAATTATAA-AACAAAA
1 TATATAATTAATTATAACAA-AAAA
24761 TATATAATTATATATATAACAAAAAA
1 TATATAATTA-AT-TATAACAAAAAA
*
24787 TATATTA-TAATTATA
1 TATATAATTAATTATA
24802 TTATATATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
23 4 0.11
24 12 0.32
25 4 0.11
26 15 0.41
27 2 0.05
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (24 bp):
TATATAATTAATTATAACAAAAAA
Found at i:24766 original size:26 final size:25
Alignment explanation
Indices: 24737--24806 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 25
24727 ATATTTTATG
24737 TATATAATTA-ATTATAA-AACAAAA
1 TATATAATTATATTATAACAA-AAAA
24761 TATATAATTATATATATAACAAAAAATA
1 TATATAATTATAT-TATAAC-AAAAA-A
24789 TATTATAATTATATTATA
1 TA-TATAATTATATTATA
24807 TATAATTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
24 10 0.25
25 2 0.05
26 5 0.12
27 3 0.08
28 9 0.22
29 11 0.28
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (25 bp):
TATATAATTATATTATAACAAAAAA
Found at i:24797 original size:72 final size:67
Alignment explanation
Indices: 24714--24845 Score: 210
Period size: 67 Copynumber: 1.9 Consensus size: 67
24704 ATTTAAATTT
*
24714 ATATATTATAATTATATTTTATGTATATAATTAATTATAAAACAAAATATATAATTATATATATA
1 ATATATTATAATTATA--TTA--TATATAATTAATTATAAAAC-AAATATATAAATATATATATA
24779 ACAAAAA
61 ACAAAAA
24786 ATATATTATAATTATATTATATATAATTAATTATAAAACAAATATATAAATATATATATA
1 ATATATTATAATTATATTATATATAATTAATTATAAAACAAATATATAAATATATATATA
24846 TATATATAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
67 20 0.34
68 20 0.34
70 3 0.05
72 16 0.27
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (67 bp):
ATATATTATAATTATATTATATATAATTAATTATAAAACAAATATATAAATATATATATAACAAA
AA
Found at i:26506 original size:19 final size:19
Alignment explanation
Indices: 26484--26534 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
26474 GGGCTGAAAT
26484 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
26503 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
26522 TAATT-ATTATTAA
1 TAATTAATTATTAA
26535 AAATCTCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:27415 original size:17 final size:17
Alignment explanation
Indices: 27393--27426 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27383 ATGATGTCAA
27393 TTGGAGGCAATCAGAAG
1 TTGGAGGCAATCAGAAG
*
27410 TTGGAGGCAATTAGAAG
1 TTGGAGGCAATCAGAAG
27427 GAGAAGGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21
Consensus pattern (17 bp):
TTGGAGGCAATCAGAAG
Found at i:28812 original size:13 final size:13
Alignment explanation
Indices: 28779--28831 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 13
28769 GCACCCAAAA
*
28779 CATTTAT-TAAAA
1 CATTTATATAAAG
28791 CATTT-TATAAAG
1 CATTTATATAAAG
28803 CATTTATATAAAG
1 CATTTATATAAAG
*
28816 CAGTTATA-AAA-
1 CATTTATATAAAG
28827 CATTT
1 CATTT
28832 CCTCAACGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 5 0.14
12 17 0.47
13 14 0.39
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
CATTTATATAAAG
Found at i:29044 original size:19 final size:19
Alignment explanation
Indices: 29004--29044 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
28994 AGATCATAGT
* *
29004 AAAACCAAGATAATCAATC
1 AAAACCAAGATAATAAACC
*
29023 AAAACCGAGATAATAAACC
1 AAAACCAAGATAATAAACC
29042 AAA
1 AAA
29045 TCAATCAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.61, C:0.20, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAACCAAGATAATAAACC
Found at i:33666 original size:21 final size:22
Alignment explanation
Indices: 33624--33667 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
33614 GTTCAATTTT
33624 AAGTAATGACAATTTAAAAAAA
1 AAGTAATGACAATTTAAAAAAA
33646 AAGTAAT-AGCAATTTAAAAAAA
1 AAGTAATGA-CAATTTAAAAAAA
33668 GGTTACAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.64, C:0.05, G:0.09, T:0.23
Consensus pattern (22 bp):
AAGTAATGACAATTTAAAAAAA
Found at i:34426 original size:24 final size:27
Alignment explanation
Indices: 34374--34427 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 27
34364 TATAGTATAG
**
34374 ATATATAATATAATATATATTATTTTT
1 ATATATAATATAATATATATTATCATT
34401 ATAT-TAAT-TAAT-TATATTATCATT
1 ATATATAATATAATATATATTATCATT
34425 ATA
1 ATA
34428 AATTAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 13 0.52
25 4 0.16
26 4 0.16
27 4 0.16
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (27 bp):
ATATATAATATAATATATATTATCATT
Found at i:34931 original size:15 final size:16
Alignment explanation
Indices: 34911--34940 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
34901 GATCTTCCAA
34911 TCTTAAGTT-TTTATT
1 TCTTAAGTTGTTTATT
34926 TCTTAAGTTGTTTAT
1 TCTTAAGTTGTTTAT
34941 ATTATTATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (16 bp):
TCTTAAGTTGTTTATT
Found at i:35065 original size:40 final size:41
Alignment explanation
Indices: 34978--35065 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 41
34968 ATATTATTTA
*
34978 AAAATTACCATTGACACCAGAAGTTGTCACTTTGGTAAATT
1 AAAATTACCATTGACACCAGAAGTTGTCACTCTGGTAAATT
* * *
35019 AAAATTACCTTTGACACTAGAAG-TGTCACTCTGGTATATT
1 AAAATTACCATTGACACCAGAAGTTGTCACTCTGGTAAATT
*
35059 ATAATTA
1 AAAATTA
35066 ATGTTGACCT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 21 0.50
41 21 0.50
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (41 bp):
AAAATTACCATTGACACCAGAAGTTGTCACTCTGGTAAATT
Found at i:35159 original size:56 final size:56
Alignment explanation
Indices: 35080--35231 Score: 191
Period size: 56 Copynumber: 2.7 Consensus size: 56
35070 TGACCTTGAA
* * *
35080 TTACTACAGTTAACTTATT-TTTGACACCAGAAGCTGTTATAATAAACATTACTTAT
1 TTACTAC-GGTAAATTATTCTTTGACACCAGAAGCTGTCATAATAAACATTACTTAT
* *
35136 TTACTACGGTAAATTATTCTTTGACACCGGAAGTTGTCATAATAAACATTACTTAT
1 TTACTACGGTAAATTATTCTTTGACACCAGAAGCTGTCATAATAAACATTACTTAT
* * * *
35192 TTACTATGGTAAATCA-TCTTTTGACACCCGAAGTTGTCAT
1 TTACTACGGTAAATTATTC-TTTGACACCAGAAGCTGTCAT
35232 GGTATATTCT
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
55 11 0.13
56 75 0.87
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (56 bp):
TTACTACGGTAAATTATTCTTTGACACCAGAAGCTGTCATAATAAACATTACTTAT
Done.