Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013370.1 Corchorus olitorius cultivar O-4 contig13403, 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: 36266
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:278 original size:38 final size:38
Alignment explanation
Indices: 227--302 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
217 AAGGCCCAAG
* *
227 TCAAGAAACAAACCGTA-CTCAACTCATGAAATAAACCA
1 TCAAGAAACAAACC-AAGCCCAACTCATGAAATAAACCA
* *
265 TCAAGAAATAAACCAAGCCCAAGTCATGAAATAAACCA
1 TCAAGAAACAAACCAAGCCCAACTCATGAAATAAACCA
303 AGCCCATGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.51, C:0.25, G:0.09, T:0.14
Consensus pattern (38 bp):
TCAAGAAACAAACCAAGCCCAACTCATGAAATAAACCA
Found at i:5382 original size:3 final size:3
Alignment explanation
Indices: 5374--5406 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
5364 GTTTGGCTAG
*
5374 GAA GAA GAA GAA GAA GAA GAT GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
5407 AACGTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:7718 original size:766 final size:764
Alignment explanation
Indices: 6248--7764 Score: 2752
Period size: 766 Copynumber: 2.0 Consensus size: 764
6238 AAAAAAGAAG
6248 AGAAAAATCAGAAAATAAAAAGATGCAATAAAAGTGTTTTCAAAAATGTTTTCTCAAATCATGTT
1 AGAAAAATCAGAAAATAAAAAGATGCAATAAAAGTGTTTTCAAAAATGTTTTCTCAAATCATGTT
*
6313 CTCTTATTTGATTTTCAATATTAAGAAATTAGTAAATCAAGAGATTTAAAGGTAAGAATTTTCAA
66 CTCTTATTTGATTTTCAAAATTAAGAAATTAGTAAATCAAGAGATTTAAAGGTAAGAATTTTCAA
* *
6378 AAATAACATTTTTTTAGCAACTCCAAAAGAAGATTTTGGAAAATAAAAGTTCAGGTAATTCCAAA
131 AAAGAACATTTTTTTAGCAACTCAAAAAGAAGATTTTGGAAAATAAAAGTTCAGGTAATTCCAAA
6443 AGAAGATTTTGGAAAATAAAGATACCCAAAAGAAGATTTTGGAAATTAATAAAATTGATCAAGTT
196 AGAAGATTTTGGAAAATAAAGATACCCAAAAGAAGATTTTGGAAATTAATAAAATTGATCAAGTT
*
6508 TTTAGAAAAATCAAAAATGGTAAAAAGATTTTGTCACAACATTTTCAAAACTTCCTTTTCGTAGA
261 TTTAGAAAAATCAAAAATGGTAAAAAGATTTTGTCACAACATTTTCAAAACTTCCTTTTCGAAGA
*
6573 GAAAGGATCAACAAGAGAGCAAATAGTGAAAGAGAATCGTGATAGAATTAATCGACGGTGTTCGA
326 GAAAGGATCAACAAGAGAGCAAACAGTGAAAGAGAATCGTGATAGAATTAATCGACGGTGTTCGA
*
6638 TTATATTCTTCGAATTCTCGACATCGGTTCCAAAAAATGGTTTTATTTTCTTTTTATAACCCTTT
391 TTATATTCTTCGAATTCTCGACATCGGTTCCAAAAAATGGTTTTATTTTCATTTTATAACCCTTT
*
6703 TAATAATCAAGATTAGAATTAAAAGCAACCAACTTTTCTTTTCGACCCAATAGATCAAGTTAGAC
456 TAATAATCAAGATTAGAATTAAAAGCAACCAACTTTTCTTTTCGACCAAATAGATCAAGTTAGAC
* * *
6768 TAGAGGTACTGTCACTTGATGGGCGACTCGGGGGTGCTAATCCTTCCCCCAGCGTAATCGACTCT
521 TAGAGGTACTATCACTTGACGGGCGACTCGGGGGTGCTAATCCTTCCCCCAGCGTAATCGACTCC
6833 CGAACCTAGATTTAGATTGCAAGACCGGACCATAGGTTTAGTGGGTCCATTGCCGAGCTTTGGAC
586 CGAACCTAGATTTAGATTGCAAGACCGGACCATAGGTTTAGTGGGTCCATTGCCGAGCTTTGGAC
6898 CTTACTTAGCTTAGGTAGCCTTTAGGTGACTAATCACACCTTAGAAAAAAGATTAATGGCGACTC
651 CTTACTTAGCTTAGGTAGCCTTTAGGTGACTAATCACACCTTAGAAAAAAGATTAATGGCGACTC
*
6963 CATTTCCAATGTCGTTTCGGCAAGGTTCCCCTGACCCGATTCGACAGCT
716 CATTTCCAATGTCGTTTCGGCAAGGTTCCCCAGACCCGATTCGACAGCT
7012 AGAAAAATCAGAAAATAAAAAGATGCAATAAAAGTGTTTTCAAAAATGTTTTCTCAAATCATGTT
1 AGAAAAATCAGAAAATAAAAAGATGCAATAAAAGTGTTTTCAAAAATGTTTTCTCAAATCATGTT
*
7077 CTCTTATTTGATTTTCAAAATTAAGAAATTAGTAAATCAAGAGATTTCAAGGTAA-ACATTTTCA
66 CTCTTATTTGATTTTCAAAATTAAGAAATTAGTAAATCAAGAGATTTAAAGGTAAGA-ATTTTCA
7141 AAAAGAACATTTTTTTTAGCAACTCAAAAAGAAGATTTTGGAAAATAAAAGTTCAGGTAATTCCA
130 AAAAGAACA-TTTTTTTAGCAACTCAAAAAGAAGATTTTGGAAAATAAAAGTTCAGGTAATTCCA
7206 AAAGAAGATTTTGGAAAATAAAGATACCCAAAAGAAGATTTTGGAAATTAATAAAATTGATCAAG
194 AAAGAAGATTTTGGAAAATAAAGATACCCAAAAGAAGATTTTGGAAATTAATAAAATTGATCAAG
**
7271 TTTTTAGAAAAATCAAAAATGG-AGAAAAGATTTTGTCACCGCATTTTCAAAACTTCCTTTTCGA
259 TTTTTAGAAAAATCAAAAATGGTA-AAAAGATTTTGTCACAACATTTTCAAAACTTCCTTTTCGA
7335 AGAGAAAAGGATCAACAAGAGAGCAAACAGTGAAAGAGAATCGTGATAGAATTAATCGACGGTGT
323 AGAG-AAAGGATCAACAAGAGAGCAAACAGTGAAAGAGAATCGTGATAGAATTAATCGACGGTGT
* * *
7400 TCGATTATATTCTTTGAATTCTCGATATTGGTTCCAAAAAATGGTTTTATTTTCATTTTATAACC
387 TCGATTATATTCTTCGAATTCTCGACATCGGTTCCAAAAAATGGTTTTATTTTCATTTTATAACC
* * *
7465 GTTTTATTAATCAAGATTAGAATTAAAAGCAACCAACTTTTCTTTTCGACCAAATAGATCTAGTT
452 CTTTTAATAATCAAGATTAGAATTAAAAGCAACCAACTTTTCTTTTCGACCAAATAGATCAAGTT
*
7530 AGACTAGAGGTA-TCATCACTTGACGGGCGACTCGGGGGTGCTAATCCTTCCCCGAGCGTAATCG
517 AGACTAGAGGTACT-ATCACTTGACGGGCGACTCGGGGGTGCTAATCCTTCCCCCAGCGTAATCG
7594 ACTCCCGAACCTAGATTTAGATTGCAAGACCGGACCATAGGTTTAGTGGGTCCATTGCCGAGCTT
581 ACTCCCGAACCTAGATTTAGATTGCAAGACCGGACCATAGGTTTAGTGGGTCCATTGCCGAGCTT
* *
7659 TGTACCTTACTTAGCTTAGGTAGCCTTTAGGTGACTAATCACACCTTAGAAAAAAGATTAGTGGC
646 TGGACCTTACTTAGCTTAGGTAGCCTTTAGGTGACTAATCACACCTTAGAAAAAAGATTAATGGC
*
7724 GACTCCATTTCCAATGTCGTTTCGGCAGGGTTCCCCAGACC
711 GACTCCATTTCCAATGTCGTTTCGGCAAGGTTCCCCAGACC
7765 TGAACGTTTC
Statistics
Matches: 724, Mismatches: 24, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
763 1 0.00
764 134 0.19
765 183 0.25
766 406 0.56
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (764 bp):
AGAAAAATCAGAAAATAAAAAGATGCAATAAAAGTGTTTTCAAAAATGTTTTCTCAAATCATGTT
CTCTTATTTGATTTTCAAAATTAAGAAATTAGTAAATCAAGAGATTTAAAGGTAAGAATTTTCAA
AAAGAACATTTTTTTAGCAACTCAAAAAGAAGATTTTGGAAAATAAAAGTTCAGGTAATTCCAAA
AGAAGATTTTGGAAAATAAAGATACCCAAAAGAAGATTTTGGAAATTAATAAAATTGATCAAGTT
TTTAGAAAAATCAAAAATGGTAAAAAGATTTTGTCACAACATTTTCAAAACTTCCTTTTCGAAGA
GAAAGGATCAACAAGAGAGCAAACAGTGAAAGAGAATCGTGATAGAATTAATCGACGGTGTTCGA
TTATATTCTTCGAATTCTCGACATCGGTTCCAAAAAATGGTTTTATTTTCATTTTATAACCCTTT
TAATAATCAAGATTAGAATTAAAAGCAACCAACTTTTCTTTTCGACCAAATAGATCAAGTTAGAC
TAGAGGTACTATCACTTGACGGGCGACTCGGGGGTGCTAATCCTTCCCCCAGCGTAATCGACTCC
CGAACCTAGATTTAGATTGCAAGACCGGACCATAGGTTTAGTGGGTCCATTGCCGAGCTTTGGAC
CTTACTTAGCTTAGGTAGCCTTTAGGTGACTAATCACACCTTAGAAAAAAGATTAATGGCGACTC
CATTTCCAATGTCGTTTCGGCAAGGTTCCCCAGACCCGATTCGACAGCT
Found at i:8876 original size:44 final size:43
Alignment explanation
Indices: 8810--8928 Score: 132
Period size: 44 Copynumber: 2.8 Consensus size: 43
8800 ATATCCATTG
* * **
8810 ATATATGTCATACATCCTTCATGCATTGTCCATGTCTTTGTAT
1 ATATATGTCATACATCCATCATGCATTATCCATCCCTTTGTAT
*
8853 ATATATGTTCATACATTCATCATGCATTATCCATCCCTTTGTAT
1 ATATATG-TCATACATCCATCATGCATTATCCATCCCTTTGTAT
* * ***
8897 ATATGT-TCATGCATAGGTCATGCATTATCCAT
1 ATATATGTCATACATCCATCATGCATTATCCAT
8929 TCATTACTAC
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
42 22 0.34
43 7 0.11
44 36 0.55
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (43 bp):
ATATATGTCATACATCCATCATGCATTATCCATCCCTTTGTAT
Found at i:8918 original size:42 final size:43
Alignment explanation
Indices: 8810--8928 Score: 134
Period size: 42 Copynumber: 2.8 Consensus size: 43
8800 ATATCCATTG
* * * **
8810 ATATATG-TCATACATCCTTCATGCATTGTCCATGTCTTTGTAT
1 ATATATGTTCATACATACATCATGCATTATCCATCCCTTTG-AT
*
8853 ATATATGTTCATACATTCATCATGCATTATCCATCCCTTTG-T
1 ATATATGTTCATACATACATCATGCATTATCCATCCCTTTGAT
* **
8895 ATATATGTTCATGCATAGGTCATGCATTATCCAT
1 ATATATGTTCATACATACATCATGCATTATCCAT
8929 TCATTACTAC
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
42 31 0.47
43 7 0.11
44 28 0.42
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (43 bp):
ATATATGTTCATACATACATCATGCATTATCCATCCCTTTGAT
Found at i:10105 original size:14 final size:15
Alignment explanation
Indices: 10072--10107 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
10062 CAAGACATGT
*
10072 TTTTCAAGAAAATTG
1 TTTTCAAGAAAATGG
10087 TTTTCAAGAAAA-GG
1 TTTTCAAGAAAATGG
10101 TTTTCAA
1 TTTTCAA
10108 AAATGAGTTT
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):
TTTTCAAGAAAATGG
Found at i:10512 original size:23 final size:22
Alignment explanation
Indices: 10469--10522 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
10459 GAACCCGTTA
10469 GGAAAATGCAGTAGAACCAATG
1 GGAAAATGCAGTAGAACCAATG
*
10491 GAGAAAATGCAGTA-CACGCAATG
1 G-GAAAATGCAGTAGAAC-CAATG
*
10514 GTAAAATGC
1 GGAAAATGC
10523 TATCTGAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.44, C:0.15, G:0.26, T:0.15
Consensus pattern (22 bp):
GGAAAATGCAGTAGAACCAATG
Found at i:10584 original size:24 final size:24
Alignment explanation
Indices: 10551--10597 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
10541 ACTTCATTGC
* *
10551 AATAATAGCATATGCCAAA-AAAGA
1 AATAAAAGCAAATG-CAAATAAAGA
10575 AATAAAAGCAAATGCAAATAAAG
1 AATAAAAGCAAATGCAAATAAAG
10598 GGCACAGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.62, C:0.11, G:0.13, T:0.15
Consensus pattern (24 bp):
AATAAAAGCAAATGCAAATAAAGA
Found at i:10804 original size:8 final size:9
Alignment explanation
Indices: 10783--10812 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
10773 ACTCAAAAAA
10783 AAAAAGAAT
1 AAAAAGAAT
10792 AAAAAGAAT
1 AAAAAGAAT
10801 AAAAAGAA-
1 AAAAAGAAT
10809 AAAA
1 AAAA
10813 CTCAGCCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (9 bp):
AAAAAGAAT
Found at i:13288 original size:64 final size:64
Alignment explanation
Indices: 13185--13691 Score: 533
Period size: 64 Copynumber: 7.9 Consensus size: 64
13175 TGCTAGAAAG
* * * *
13185 AATTTTCAGATGTTGATCGGAAGACAATCTTGTCGAGAAGTACACCAGAAGATGGTTTCTCAAC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTCGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* * * *
13249 AATTTTCAGAAGATGAGCGGAAGACGATCTCGCCAAGAAGTACACCAGCAGATGGTTTCTCAAC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTCGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* * * * *
13313 AGTTTTCCGATGTTGATCGGAAGATGATCTCGTCGAGAAGTACACCAGAAGATGGTTTCTCAAC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTCGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* * *
13377 AATTTTCA-AATGTTGATTC-GAAAACGATCTCATTAAGAAGTACACCAGAAGATGGTTTCTCAA
1 AATTTTCAGAA-GTTGA-TCGGAAGACGATCTCGTCAAGAAGTACACCAGAAGATGGTTTCTCAA
13440 C
64 C
* * * * ** *
13441 AGTTTTTAGATGTTGATCGGAAGATGATCTTTTCGAGAAGTACACCAGAAGATGGTTTCTCAAC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTCGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
* * * * *
13505 AATTTTCAGGAGTTGTTCAGG-AGACGACCTTGTCAAGAAATACACC-GAAAGATGGTTTCTCAA
1 AATTTTCAGAAGTTGATC-GGAAGACGATCTCGTCAAGAAGTACACCAG-AAGATGGTTTCTCAA
13568 C
64 C
* * * * *
13569 AATTTTCAGGAGTTGTTCGGAAGACGACCAT-GTCAAGAAGTACACCAGAAAATAGTTTCTCGCA
1 AATTTTCAGAAGTTGATCGGAAGACGATC-TCGTCAAGAAGTACACCAGAAGATGGTTTCT--CA
13633 A-
63 AC
** * * * *
13634 AGGTTTCAGAAGTTGATTCGGAAGACGATCTTGTTAAGACA-TGCACCAGAAGACGGTT
1 AATTTTCAGAAGTTGA-TCGGAAGACGATCTCGTCAAGA-AGTACACCAGAAGATGGTT
13692 ATTTAGAAAT
Statistics
Matches: 372, Mismatches: 57, Indels: 26
0.82 0.13 0.06
Matches are distributed among these distances:
63 6 0.02
64 311 0.84
65 20 0.05
66 34 0.09
67 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (64 bp):
AATTTTCAGAAGTTGATCGGAAGACGATCTCGTCAAGAAGTACACCAGAAGATGGTTTCTCAAC
Found at i:13348 original size:128 final size:129
Alignment explanation
Indices: 13187--13691 Score: 605
Period size: 128 Copynumber: 3.9 Consensus size: 129
13177 CTAGAAAGAA
*
13187 TTTTCAGATGTTGATCGGAAGACAATCTTGTCGAGAAGTACACCAGAAGATGGTTTCTCAACAAT
1 TTTTCAGATGTTGATCGGAAGACGATCTTGTCGAGAAGTACACCAGAAGATGGTTTCTCAACAAT
* * * *
13252 TTTCAGAAGATGA-GCGGAAGACGATCTCGCCAAGAAGTACACCAGCAGATGGTTTCTCAACAG
66 TTTCAGAAGTTGATTCGGAAGACGATCTCGTCAAGAAGTACACCAGAAGATGGTTTCTCAACAG
* * *
13315 TTTTCCGATGTTGATCGGAAGATGATCTCGTCGAGAAGTACACCAGAAGATGGTTTCTCAACAAT
1 TTTTCAGATGTTGATCGGAAGACGATCTTGTCGAGAAGTACACCAGAAGATGGTTTCTCAACAAT
* * *
13380 TTTCA-AATGTTGATTC-GAAAACGATCTCATTAAGAAGTACACCAGAAGATGGTTTCTCAACAG
66 TTTCAGAA-GTTGATTCGGAAGACGATCTCGTCAAGAAGTACACCAGAAGATGGTTTCTCAACAG
* * *
13443 TTTTTAGATGTTGATCGGAAGATGATCTTTTCGAGAAGTACACCAGAAGATGGTTTCTCAACAAT
1 TTTTCAGATGTTGATCGGAAGACGATCTTGTCGAGAAGTACACCAGAAGATGGTTTCTCAACAAT
* * * *
13508 TTTCAGGAGTTG-TTCAGG-AGACGACCTTGTCAAGAAATACACC-GAAAGATGGTTTCTCAACA
66 TTTCAGAAGTTGATTC-GGAAGACGATCTCGTCAAGAAGTACACCAG-AAGATGGTTTCTCAACA
*
13570 A
129 G
* * * * * *
13571 TTTTCAGGA-GTTGTTCGGAAGACGACCATGTCAAGAAGTACACCAGAAAATAGTTTCTCGCAA-
1 TTTTCA-GATGTTGATCGGAAGACGATCTTGTCGAGAAGTACACCAGAAGATGGTTTCT--CAAC
** * * * *
13634 AGGTTTCAGAAGTTGATTCGGAAGACGATCTTGTTAAGACA-TGCACCAGAAGACGGTT
63 AATTTTCAGAAGTTGATTCGGAAGACGATCTCGTCAAGA-AGTACACCAGAAGATGGTT
13692 ATTTAGAAAT
Statistics
Matches: 325, Mismatches: 39, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
127 6 0.02
128 264 0.81
129 19 0.06
130 34 0.10
131 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (129 bp):
TTTTCAGATGTTGATCGGAAGACGATCTTGTCGAGAAGTACACCAGAAGATGGTTTCTCAACAAT
TTTCAGAAGTTGATTCGGAAGACGATCTCGTCAAGAAGTACACCAGAAGATGGTTTCTCAACAG
Found at i:14349 original size:26 final size:25
Alignment explanation
Indices: 14308--14359 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
14298 GGCATTAGGG
*
14308 TCACCTAGGGGCATTT-TGGTCATTT
1 TCACCTAAGGGCATTTAT-GTCATTT
14333 TCACACTAAGGGCATTTATGTCATTT
1 TCAC-CTAAGGGCATTTATGTCATTT
14359 T
1 T
14360 AAGTTCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 19 0.79
27 1 0.04
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (25 bp):
TCACCTAAGGGCATTTATGTCATTT
Found at i:16746 original size:3 final size:3
Alignment explanation
Indices: 16738--16836 Score: 180
Period size: 3 Copynumber: 33.0 Consensus size: 3
16728 GTTTGGCTAG
16738 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
16786 GAA GAA GAA GAA TAA GAA GAA GAA GAA GAA GAC GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
16834 GAA
1 GAA
16837 AGCGTAATAA
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 92 1.00
ACGTcount: A:0.66, C:0.01, G:0.32, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:17677 original size:22 final size:21
Alignment explanation
Indices: 17650--17700 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
17640 TTAGAGATAG
17650 AAAAAAGATCAAAATCAAAAAA
1 AAAAAAGAT-AAAATCAAAAAA
*
17672 AAAAAAGA-AAAATCAGAAAA
1 AAAAAAGATAAAATCAAAAAA
*
17692 TAAAAAGAT
1 AAAAAAGAT
17701 GCAATAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 18 0.69
22 8 0.31
ACGTcount: A:0.76, C:0.06, G:0.08, T:0.10
Consensus pattern (21 bp):
AAAAAAGATAAAATCAAAAAA
Found at i:23053 original size:47 final size:47
Alignment explanation
Indices: 23000--23114 Score: 212
Period size: 47 Copynumber: 2.4 Consensus size: 47
22990 TGTAGATAAG
* *
23000 ATTTCCTGGATCGGGCTTAAATTATCTTTTTTATTCTTTAGCAATCA
1 ATTTCCTGGATCGGGCTTAAATTATCCTTTTTATCCTTTAGCAATCA
23047 ATTTCCTGGATCGGGCTTAAATTATCCTTTTTATCCTTTAGCAATCA
1 ATTTCCTGGATCGGGCTTAAATTATCCTTTTTATCCTTTAGCAATCA
23094 ATTTCCTGGATCGGGCTTAAA
1 ATTTCCTGGATCGGGCTTAAA
23115 CTTCACTAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 66 1.00
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (47 bp):
ATTTCCTGGATCGGGCTTAAATTATCCTTTTTATCCTTTAGCAATCA
Found at i:24201 original size:19 final size:18
Alignment explanation
Indices: 24168--24203 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
24158 TCGAGATCAT
24168 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
24186 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
24204 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:25854 original size:15 final size:15
Alignment explanation
Indices: 25830--25867 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
25820 ATGAAATCCT
25830 AAAAAGAGAAAGAAAG
1 AAAAA-AGAAAGAAAG
*
25846 ATAAAAGAAAGAAAG
1 AAAAAAGAAAGAAAG
25861 AAAAAAG
1 AAAAAAG
25868 TAAGGGTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (15 bp):
AAAAAAGAAAGAAAG
Found at i:29922 original size:11 final size:11
Alignment explanation
Indices: 29906--29953 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
29896 GAAATTCGTG
29906 TTTGAAGACCA
1 TTTGAAGACCA
**
29917 TTTGAAGATAA
1 TTTGAAGACCA
29928 TTTGAAGA-C-
1 TTTGAAGACCA
29937 -TTGAAGACCA
1 TTTGAAGACCA
29947 -TTGAAGA
1 TTTGAAGA
29954 TTTTGATGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 7 0.22
9 1 0.03
10 7 0.22
11 17 0.53
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (11 bp):
TTTGAAGACCA
Found at i:31341 original size:15 final size:15
Alignment explanation
Indices: 31311--31352 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
31301 TTACCTTGTT
31311 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
31327 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
31342 TTGTTTTCTGT
1 TTGTTTTCTGT
31353 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:31723 original size:31 final size:28
Alignment explanation
Indices: 31685--31742 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 28
31675 GCGTCGTTTT
*
31685 GAAAAAAAAAATTGTTTTGTGTTTTTGCGTC
1 GAAAAAAAAAA-TCTTTT-TG-TTTTGCGTC
31716 GAAAAAAAAAATCTTTTTGTTTTGCGT
1 GAAAAAAAAAATCTTTTTGTTTTGCGT
31743 TTTTAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 8 0.31
29 2 0.08
30 5 0.19
31 11 0.42
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (28 bp):
GAAAAAAAAAATCTTTTTGTTTTGCGTC
Found at i:31808 original size:30 final size:30
Alignment explanation
Indices: 31770--31838 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
31760 CCTGCGTCAC
31770 AAAAAAAAGAGTTTTTGCGT-TTTATAAAA
1 AAAAAAAAGAGTTTTTGCGTATTTATAAAA
**
31799 AAAATAAAAGTTTTTTTGCGTCATTTATAAAA
1 AAAA-AAAAGAGTTTTTGCGT-ATTTATAAAA
31831 AAAAAAAA
1 AAAAAAAA
31839 TTTTCTGCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 4 0.11
30 14 0.40
31 4 0.11
32 13 0.37
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.33
Consensus pattern (30 bp):
AAAAAAAAGAGTTTTTGCGTATTTATAAAA
Found at i:31842 original size:29 final size:29
Alignment explanation
Indices: 31770--31851 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 29
31760 CCTGCGTCAC
* *
31770 AAAAAAAAGAGTTTTTGCGT--TTTATAA
1 AAAAAAAAAATTTTTTGCGTCATTTATAA
31797 AAAAAATAAAAGTTTTTTTGCGTCATTTATAA
1 AAAAAA-AAAA--TTTTTTGCGTCATTTATAA
*
31829 AAAAAAAAAATTTTCTGCGTCAT
1 AAAAAAAAAATTTTTTGCGTCAT
31852 AAAAAAAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
27 6 0.13
28 3 0.06
29 12 0.26
30 9 0.19
31 4 0.09
32 13 0.28
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (29 bp):
AAAAAAAAAATTTTTTGCGTCATTTATAA
Found at i:31859 original size:29 final size:29
Alignment explanation
Indices: 31795--31859 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
31785 TGCGTTTTAT
* ** * *
31795 AAAAAAAATAAAAGTTTTTTTGCGTCATT
1 AAAAAAAAAAAAAAATTTTCTGCGTCATA
* *
31824 TATAAAAAAAAAAAATTTTCTGCGTCATA
1 AAAAAAAAAAAAAAATTTTCTGCGTCATA
31853 AAAAAAA
1 AAAAAAA
31860 TTATTCTTGT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (29 bp):
AAAAAAAAAAAAAAATTTTCTGCGTCATA
Found at i:34366 original size:22 final size:21
Alignment explanation
Indices: 34336--34378 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
34326 CCAAGTCATT
*
34336 ACCGCCCATTCACCGTGCCATC
1 ACCGCCCATGC-CCGTGCCATC
*
34358 ACCGGCCATGCCCGTGCCATC
1 ACCGCCCATGCCCGTGCCATC
34379 GCCATTCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.16, C:0.49, G:0.19, T:0.16
Consensus pattern (21 bp):
ACCGCCCATGCCCGTGCCATC
Done.