Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007245.1 Corchorus capsularis cultivar CVL-1 contig07266, 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: 28129
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:1672 original size:864 final size:862
Alignment explanation
Indices: 8--2610 Score: 4856
Period size: 860 Copynumber: 3.0 Consensus size: 862
1 AGCCATG
8 CAAAGAAATCGATTTGGGTCCTATTTTGTACCACTTGAATCCAATAGGGTTTGTAACCTGAAATT
1 CAAAGAAATCGATTTGGGTCCTATTTTGTACCACTTGAATCCAATAGGGTTTGTAACCTGAAATT
* * *
73 CTTCAAATCAAATCACAACTCATAGTAAAAGCAATCCAAGGATCCTAATTCACAATCAATTAGAG
66 CTTCAAATCAAATCACAACTCACAGCAAAAGCAATCCAAGGATCCCAATTCACAATCAATTAGAG
*
138 TTATTGCAACTAATTAGATCAATTGCACATGAAAACCCTAATCCCCAAATTTCCAAAACGAAGAA
131 TTATTGCAACTAATTAGATCAATTGCACATGAAAACCCTAATCCCCAAATTTCCAAAACTAAGAA
*
203 CCCTAGTTCCTGAAAAAACTCGATAAGAGCACAGATTTTTTTGATTTTTTTCAATATTTTTCCCA
196 CCCTAGTTCCTGAAAAAACTCGATAACAGCACAGATTTTTTTGATTTTTTTCAATATTTTTCCCA
268 GAAAGATCACACCAAAATAAGGCTAAAGCTCAAATTTCACAGCGTTCCGAGCTCAAACGAATCCA
261 GAAAGATCACACCAAAATAAGGCTAAAGCTCAAATTTCACAGCGTTCCGAGCTCAAACGAATCCA
*
333 GAACAAAAATCACAAGTTTCTGTTCGAAATTTTTTTTA--TTTTTTTTATATTTTTCGATATAAC
326 GAACAAAAATCACAAGTTTCTGGTCGAAATTTTTTTTATTTTTTTTTTATATTTTTCGATATAAC
* *
396 TACTAGTTATAAGGGACTCAAATCTGAAATTTTAAAGCAAAAAGATTTAAGATGAATCGGCTATG
391 TACTAGTTATAAGGGACTCAAATCTGAAATTTCAAAGCAAAAAGATGTAAGATGAATCGGCTATG
461 AATTTTCAAAGTTGCTGATTTTTTGAATTTTCAAGAAGGGTGGTGCGATGAGTGTGTGGGTGAAA
456 AATTTTCAAAGTTGCTGATTTTTTGAATTTTCAAGAAGGGTGGTGCGATGAGTGTGTGGGTGAAA
526 TCGATGTGATGAATGATGAGTAAAAAGATAGATTTACCGATTGAAGATGATAAACCTAAGCTCTG
521 TCGATGTGATGAATGATGAGTAAAAAGATAGATTTACCGATTGAAGATGATAAACCTAAGCTCTG
591 ATTACCAATTGATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATC
586 ATTACCAATTGATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATC
656 AACTTGAATCACCAAACTTCTAGATGAGTATGTCGACAATCTTCACTGGATAAGTCTTCCTTCGT
651 AACTTGAATCACCAAACTTCTAGATGAGTATGTCGACAATCTTCACTGGATAAGTCTTCCTTCGT
721 TCGTCAGCCTTAGACCTCCAAGTCGACCTGCACTTGAACACCTAAGATCACAAGATTCACAAACA
716 TCGTCAGCCTTAGACCTCCAAGTCGACCTGCACTTGAACACCTAAGATCACAAGATTCACAAACA
786 ACCAAGCAATCACAACCTAATTGTTTGCTAGGACTCTACAAGATGAAGAACCCTAAGTTTGCTCA
781 ACCAAGCAATCACAACCTAATTGTTTGCTAGGACTCTACAAGATGAAGAACCCTAAGTTTGCTCA
*
851 AACTAGAACAAACAAGC
846 AACTAGAACAAAGAAGC
868 CAAAGAAATCGATTTGGGTCCTATTTTGTACCACTTGAATCCAATAGGGTTTGTAACCTGAAATT
1 CAAAGAAATCGATTTGGGTCCTATTTTGTACCACTTGAATCCAATAGGGTTTGTAACCTGAAATT
933 CTTCAAATCAAATCACAACTCACAGCAAAAGCAATCCAAGGATCCCAATTCACAATCAATTAGAG
66 CTTCAAATCAAATCACAACTCACAGCAAAAGCAATCCAAGGATCCCAATTCACAATCAATTAGAG
998 TTATTGCAACTAATTAGATCAATTGCACATGAAAACCCTAATCCCCAAATTTCCCAAAACTAAGA
131 TTATTGCAACTAATTAGATCAATTGCACATGAAAACCCTAATCCCCAAATTT-CCAAAACTAAGA
1063 ACCCTAGTTCCTGAAAAAACTCGATAACAGCACAGATTTTTTTGATTTTTTTCAATATTTTTCCC
195 ACCCTAGTTCCTGAAAAAACTCGATAACAGCACAGATTTTTTTGATTTTTTTCAATATTTTTCCC
1128 AGAAAGATCACACCAAAATAAGGCTAAAGCTCAAATTTCACAGCGTTCCGAGCTCAAACGAATCC
260 AGAAAGATCACACCAAAATAAGGCTAAAGCTCAAATTTCACAGCGTTCCGAGCTCAAACGAATCC
*
1193 AGAACAAAAATCACAAGTTTCTGGTCGAAATTTTTTTTATTTTTTTTTTCATATTTTTCGTTATA
325 AGAACAAAAATCACAAGTTTCTGGTCGAAATTTTTTTTATTTTTTTTTT-ATATTTTTCGATATA
*
1258 ACTACTAGTTATAAGGGACTCAAATCTGAAATTTCAAAGCGAAAAGATGTAAGATGAATCGGCTA
389 ACTACTAGTTATAAGGGACTCAAATCTGAAATTTCAAAGCAAAAAGATGTAAGATGAATCGGCTA
1323 TGAATTTTCAAAGTTGCTGATTTTTTGAATTTTCAAGAAGGGTGGTGCGATGAGTGTGTGGGTGA
454 TGAATTTTCAAAGTTGCTGATTTTTTGAATTTTCAAGAAGGGTGGTGCGATGAGTGTGTGGGTGA
*
1388 AATCGATGTGATGAATGATGAGTAAAAATATAGATTTACCGATTGAAGATGATAAACCTAAGCTC
519 AATCGATGTGATGAATGATGAGTAAAAAGATAGATTTACCGATTGAAGATGATAAACCTAAGCTC
1453 TGATTACCAATTGATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGA
584 TGATTACCAATTGATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGA
1518 TCAACTTGAATCACCAAACTTCTAGATGAGTATGTCGACAATCTTCACTGGATAAGTCTTCCTTC
649 TCAACTTGAATCACCAAACTTCTAGATGAGTATGTCGACAATCTTCACTGGATAAGTCTTCCTTC
*
1583 GTTCGTCAGCCTTAGACCTCCAAGTCGACCTGCACTTGAACACCTAAGATCACAAGATTCATAAA
714 GTTCGTCAGCCTTAGACCTCCAAGTCGACCTGCACTTGAACACCTAAGATCACAAGATTCACAAA
1648 CAACCAAGCAATCACAACCTAATTGTTTGCTAGGACTCTACAAGATGAAGAACCCTAAGTTTGCT
779 CAACCAAGCAATCACAACCTAATTGTTTGCTAGGACTCTACAAGATGAAGAACCCTAAGTTTGCT
*
1713 CAAACTAGAAGAAAGAAGC
844 CAAACTAGAACAAAGAAGC
*
1732 CAAAGAAATCGATTTGGGTCCTACTTTGTACCACTTGAATCCAATAGGGTTTGTAACCTGAAATT
1 CAAAGAAATCGATTTGGGTCCTATTTTGTACCACTTGAATCCAATAGGGTTTGTAACCTGAAATT
*
1797 CTTCAAATCAAATCACAACTCACAGCAAAAGCAATCCAA-GAGTCGCAATTCACAATCAATTAGA
66 CTTCAAATCAAATCACAACTCACAGCAAAAGCAATCCAAGGA-TCCCAATTCACAATCAATTAGA
**
1861 GTTATTGCAACTAATTAGATCAATTGCACATGAAAACCCTAATCCCCAAATTTCTGAAACTAAGA
130 GTTATTGCAACTAATTAGATCAATTGCACATGAAAACCCTAATCCCCAAATTTCCAAAACTAAGA
* *
1926 ACCCTAGTTCCTGAAAAAAATCGATAACAGCACAGATTTTTTTGATTTTTTTCAATA-TTTTCCG
195 ACCCTAGTTCCTGAAAAAACTCGATAACAGCACAGATTTTTTTGATTTTTTTCAATATTTTTCCC
*
1990 AGAAAGATAACACCAAAATAAGGCTAAAGCTCAAATTTCACAGCGTTCCGAGCTCAAACGAATCC
260 AGAAAGATCACACCAAAATAAGGCTAAAGCTCAAATTTCACAGCGTTCCGAGCTCAAACGAATCC
* *
2055 AGAACAAAAATCACAAGTTTCTGGTCGAAA-TTTTTTTCTTTTTTTTTTATATTTTTCGATCTAA
325 AGAACAAAAATCACAAGTTTCTGGTCGAAATTTTTTTTATTTTTTTTTTATATTTTTCGATATAA
* *
2119 CTTCTAGTTATAAGGGACTCAAATCTGAAATTTCAAAGCAAAAAGATGTAAGATGAATCCGCTAT
390 CTACTAGTTATAAGGGACTCAAATCTGAAATTTCAAAGCAAAAAGATGTAAGATGAATCGGCTAT
2184 GAATTTTCAAAGTTGCTGATTTTTTGAATTTTCAAGAAGGGTGGTGCGATGAGTGTGTGGGTGAA
455 GAATTTTCAAAGTTGCTGATTTTTTGAATTTTCAAGAAGGGTGGTGCGATGAGTGTGTGGGTGAA
2249 ATCGATGTGATGAATGATGAGTAAAAAGATAGATTTACCGATTGAAGATGATAAACCTAAGCTCT
520 ATCGATGTGATGAATGATGAGTAAAAAGATAGATTTACCGATTGAAGATGATAAACCTAAGCTCT
2314 GATTACCAATTGATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGAT
585 GATTACCAATTGATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGAT
* * *
2379 CAACTTGACTCACCAAACTTCTAGATGAGTATGTCGACAATCTTCACTTGATAAATCTTCCTTCG
650 CAACTTGAATCACCAAACTTCTAGATGAGTATGTCGACAATCTTCACTGGATAAGTCTTCCTTCG
* * *
2444 TTCGTCGGCCTTAAACCTCCATGTCGACCTGCACTTGAACACCTAAGATCACAAGATTCACAAAC
715 TTCGTCAGCCTTAGACCTCCAAGTCGACCTGCACTTGAACACCTAAGATCACAAGATTCACAAAC
*
2509 AACCAAGCAATCACAACCTAATTGTTTGCTAGGACTCTACAAGATGAAGAACCCTAAGTTAGCTC
780 AACCAAGCAATCACAACCTAATTGTTTGCTAGGACTCTACAAGATGAAGAACCCTAAGTTTGCTC
2574 AAACTAGAACAAAGAAGC
845 AAACTAGAACAAAGAAGC
2592 CAAAGAAATCGATTTGGGT
1 CAAAGAAATCGATTTGGGT
2611 ATAAACCTCT
Statistics
Matches: 1701, Mismatches: 37, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
860 672 0.40
861 195 0.11
862 100 0.06
863 76 0.04
864 658 0.39
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (862 bp):
CAAAGAAATCGATTTGGGTCCTATTTTGTACCACTTGAATCCAATAGGGTTTGTAACCTGAAATT
CTTCAAATCAAATCACAACTCACAGCAAAAGCAATCCAAGGATCCCAATTCACAATCAATTAGAG
TTATTGCAACTAATTAGATCAATTGCACATGAAAACCCTAATCCCCAAATTTCCAAAACTAAGAA
CCCTAGTTCCTGAAAAAACTCGATAACAGCACAGATTTTTTTGATTTTTTTCAATATTTTTCCCA
GAAAGATCACACCAAAATAAGGCTAAAGCTCAAATTTCACAGCGTTCCGAGCTCAAACGAATCCA
GAACAAAAATCACAAGTTTCTGGTCGAAATTTTTTTTATTTTTTTTTTATATTTTTCGATATAAC
TACTAGTTATAAGGGACTCAAATCTGAAATTTCAAAGCAAAAAGATGTAAGATGAATCGGCTATG
AATTTTCAAAGTTGCTGATTTTTTGAATTTTCAAGAAGGGTGGTGCGATGAGTGTGTGGGTGAAA
TCGATGTGATGAATGATGAGTAAAAAGATAGATTTACCGATTGAAGATGATAAACCTAAGCTCTG
ATTACCAATTGATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATC
AACTTGAATCACCAAACTTCTAGATGAGTATGTCGACAATCTTCACTGGATAAGTCTTCCTTCGT
TCGTCAGCCTTAGACCTCCAAGTCGACCTGCACTTGAACACCTAAGATCACAAGATTCACAAACA
ACCAAGCAATCACAACCTAATTGTTTGCTAGGACTCTACAAGATGAAGAACCCTAAGTTTGCTCA
AACTAGAACAAAGAAGC
Found at i:4138 original size:30 final size:30
Alignment explanation
Indices: 4102--4164 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
4092 CCTCTTCAAG
* *
4102 TCCATGATAAGTTCTT-GGCGCATCTTTCCC
1 TCCATGATAAG-CCTTGGGCGCATCATTCCC
4132 TCCATGATAAGCCTTGGGCGCATCATTCCC
1 TCCATGATAAGCCTTGGGCGCATCATTCCC
4162 TCC
1 TCC
4165 CCCTTGAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 3 0.10
30 27 0.90
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.32
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCGCATCATTCCC
Found at i:6118 original size:12 final size:12
Alignment explanation
Indices: 6103--6134 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
6093 TCGCATGCGA
6103 TGGCCGGTCATG
1 TGGCCGGTCATG
*
6115 TGGCCGGACATG
1 TGGCCGGTCATG
6127 TGGCCGGT
1 TGGCCGGT
6135 GTTGCGCGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.09, C:0.25, G:0.44, T:0.22
Consensus pattern (12 bp):
TGGCCGGTCATG
Found at i:7197 original size:13 final size:13
Alignment explanation
Indices: 7179--7208 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
7169 GCCGATTGGA
7179 AGAGAAGTCGACT
1 AGAGAAGTCGACT
*
7192 AGAGAAGTCGATT
1 AGAGAAGTCGACT
7205 AGAG
1 AGAG
7209 GAAGCAAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.33, T:0.17
Consensus pattern (13 bp):
AGAGAAGTCGACT
Found at i:8978 original size:1 final size:1
Alignment explanation
Indices: 8972--8997 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
8962 TTTTCTAGTT
8972 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
8998 CTCCATTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:9816 original size:19 final size:18
Alignment explanation
Indices: 9792--9827 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
9782 AAGATTTCTT
9792 GAAGATAATTTGAAGAATA
1 GAAGATAA-TTGAAGAATA
*
9811 GAAGATTATTGAAGAAT
1 GAAGATAATTGAAGAAT
9828 TATTTCAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28
Consensus pattern (18 bp):
GAAGATAATTGAAGAATA
Found at i:9838 original size:30 final size:30
Alignment explanation
Indices: 9781--9838 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
9771 GTTCGTGTTT
* *
9781 GAAGATTTCTTGAAGATAATTTGAAGAATA
1 GAAGATTTATTGAAGATAATTTCAAGAATA
*
9811 GAAGA-TTATTGAAGAATTATTTCAAGAA
1 GAAGATTTATTGAAG-ATAATTTCAAGAA
9839 GACAGAATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.33
Consensus pattern (30 bp):
GAAGATTTATTGAAGATAATTTCAAGAATA
Found at i:12284 original size:22 final size:23
Alignment explanation
Indices: 12259--12311 Score: 63
Period size: 27 Copynumber: 2.2 Consensus size: 23
12249 CATGGATTGG
12259 AAAC-TCCAATCCATGAGAGGTT
1 AAACTTCCAATCCATGAGAGGTT
12281 AAACCTGTTTCCAATCCATGAGAGGTT
1 AAA-C---TTCCAATCCATGAGAGGTT
12308 AAAC
1 AAAC
12312 CTTTATACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
22 3 0.12
23 1 0.04
26 1 0.04
27 21 0.81
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (23 bp):
AAACTTCCAATCCATGAGAGGTT
Found at i:15836 original size:33 final size:33
Alignment explanation
Indices: 15799--15872 Score: 123
Period size: 33 Copynumber: 2.2 Consensus size: 33
15789 TACTTGTGAT
15799 GAAAATAATTCT-GTTTTGGTTGATCATAGCATG
1 GAAAATAATT-TAGTTTTGGTTGATCATAGCATG
*
15832 GAAAATAATTTAGTTTTGGTTGATCATAGCATT
1 GAAAATAATTTAGTTTTGGTTGATCATAGCATG
15865 GAAAATAA
1 GAAAATAA
15873 GACTATTTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 1 0.03
33 38 0.97
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (33 bp):
GAAAATAATTTAGTTTTGGTTGATCATAGCATG
Found at i:15882 original size:33 final size:32
Alignment explanation
Indices: 15798--15883 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 32
15788 CTACTTGTGA
*
15798 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAA-TCTATTTTGGTTGATCATAGCAT
* *
15831 GGAAAATAATTTAGTTTTGGTTGATCATAGCAT
1 TGAAAATAATCTA-TTTTGGTTGATCATAGCAT
*
15864 TGAAAATAAGACTATTTTGG
1 TGAAAATAA-TCTATTTTGG
15884 GTGAAAAGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
32 2 0.04
33 41 0.91
34 2 0.04
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.40
Consensus pattern (32 bp):
TGAAAATAATCTATTTTGGTTGATCATAGCAT
Found at i:18831 original size:8 final size:8
Alignment explanation
Indices: 18818--18851 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
18808 CACCTTCTTG
18818 AAAAATTC
1 AAAAATTC
18826 AAAAATTC
1 AAAAATTC
*
18834 AGAAACTTC
1 A-AAAATTC
18843 AAAAATTC
1 AAAAATTC
18851 A
1 A
18852 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:18941 original size:9 final size:9
Alignment explanation
Indices: 18929--18958 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
18919 TATCGAAAAT
18929 ATAAAATAA
1 ATAAAATAA
18938 ATAAAATAAA
1 ATAAAAT-AA
18948 ATAAAATAA
1 ATAAAATAA
18957 AT
1 AT
18959 TTCGACCCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
ATAAAATAA
Found at i:18958 original size:4 final size:5
Alignment explanation
Indices: 18929--18957 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
18919 TATCGAAAAT
18929 ATAAA AT-AA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
18958 TTTCGACCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:21176 original size:33 final size:32
Alignment explanation
Indices: 21139--21245 Score: 108
Period size: 33 Copynumber: 3.2 Consensus size: 32
21129 CGCCAAGCGA
* *
21139 TGGCCGGTTGTGGCCGGACATGTCCATGTCGCG
1 TGGCCGGTTGTGGCCGGGCATCTCCA-GTCGCG
**
21172 TGGCCGGTCATGGCCGGGCATCTCCGAGTCGCG
1 TGGCCGGTTGTGGCCGGGCATCTCC-AGTCGCG
* * *
21205 TGGCC-GCTGTTGGCCGGGCTTCTCCAAGTCGCA
1 TGGCCGGTTG-TGGCCGGGCATCTCC-AGTCGCG
21238 TGGCCGGT
1 TGGCCGGT
21246 CACTAGTGCT
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
32 1 0.02
33 57 0.95
34 2 0.03
ACGTcount: A:0.08, C:0.31, G:0.38, T:0.22
Consensus pattern (32 bp):
TGGCCGGTTGTGGCCGGGCATCTCCAGTCGCG
Found at i:26179 original size:33 final size:33
Alignment explanation
Indices: 26137--26245 Score: 191
Period size: 33 Copynumber: 3.3 Consensus size: 33
26127 TTCTTTTCAC
* **
26137 CCAAAACAGAATTATTTTCAATATTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
26170 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
26203 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
26236 CCAAAACAGA
1 CCAAAACAGA
26246 TTTGTTTTCA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 73 1.00
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:26273 original size:66 final size:66
Alignment explanation
Indices: 26137--26278 Score: 169
Period size: 66 Copynumber: 2.2 Consensus size: 66
26127 TTCTTTTCAC
* * * * *
26137 CCAAAACAGAATTATTTTCAATATTATGATCAACCAAAACAGAATTATTTGCAATGCTATGATCA
1 CCAAAACAGAATTATTTGCAATACTATGATCAACCAAAACAGAATTATTTGCAATACAATGAGCA
26202 A
66 A
* * * * *
26203 CCAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGATTTGTTTTC-ATCACAATTAGC
1 CCAAAACAGAATTATTTGCAATACTATGATCAACCAAAACAGAATTATTTGCAAT-ACAATGAGC
*
26267 AT
65 AA
26269 CCAAAACAGA
1 CCAAAACAGA
26279 TTTAGTATCG
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
65 2 0.03
66 62 0.97
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28
Consensus pattern (66 bp):
CCAAAACAGAATTATTTGCAATACTATGATCAACCAAAACAGAATTATTTGCAATACAATGAGCA
A
Found at i:26293 original size:33 final size:33
Alignment explanation
Indices: 26236--26375 Score: 113
Period size: 33 Copynumber: 4.2 Consensus size: 33
26226 CTATGATCAA
* ** *
26236 CCAAAACAGATTT-GTTTTCATCACAATTAGCAT
1 CCAAAACAGATTTAG-TATCATCACAAACAACAT
*
26269 CCAAAACAGATTTAGTATCGTCACAAACAACAT
1 CCAAAACAGATTTAGTATCATCACAAACAACAT
** * **
26302 TTAAAACAGATTTAGTGTCATTGCAAACAACA-
1 CCAAAACAGATTTAGTATCATCACAAACAACAT
** * *
26334 CTCAAATTAGGTTTAGTATCATCGCAAACAACAT
1 C-CAAAACAGATTTAGTATCATCACAAACAACAT
*
26368 CTAAAACA
1 CCAAAACA
26376 CTCTTTGCAA
Statistics
Matches: 83, Mismatches: 21, Indels: 6
0.75 0.19 0.05
Matches are distributed among these distances:
33 81 0.98
34 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (33 bp):
CCAAAACAGATTTAGTATCATCACAAACAACAT
Found at i:27908 original size:10 final size:10
Alignment explanation
Indices: 27876--27909 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
27866 GGTCGAAATT
27876 TTTTTTTATA
1 TTTTTTTATA
*
27886 TTATTTTAT-
1 TTTTTTTATA
27895 TTTTTTTATA
1 TTTTTTTATA
27905 TTTTT
1 TTTTT
27910 CGATATAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTTATA
Found at i:28010 original size:8 final size:8
Alignment explanation
Indices: 27982--28015 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
27972 GAATCGGCTA
27982 TGAATTTT
1 TGAATTTT
*
27990 TGAAGTTTC
1 TGAA-TTTT
27999 TGAATTTT
1 TGAATTTT
28007 TGAATTTT
1 TGAATTTT
28015 T
1 T
28016 AAGAAGGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Done.