Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008516.1 Corchorus capsularis cultivar CVL-1 contig08537, 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: 31221
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Found at i:3057 original size:33 final size:32
Alignment explanation
Indices: 3020--3143 Score: 106
Period size: 33 Copynumber: 3.7 Consensus size: 32
3010 TAGACAAAGG
* * *
3020 ATCGTGTGGCCGGTTGTGGCCGGGCATGGCCGA
1 ATCGCGTGGCCGGTTGTGGCCGGACATGTCC-A
** * * *
3053 ATCGTTTGGCCGGTTGTAGCCGGCCATGTCCTT
1 ATCGCGTGGCCGGTTGTGGCCGGACATGTCC-A
*
3086 GTCGCGTGGCCGG-TGATGGCCGGACATGTCCA
1 ATCGCGTGGCCGGTTG-TGGCCGGACATGTCCA
3118 TATCGCGTGGCCGGTCTTGTGGCCGG
1 -ATCGCGTGGCCGG--TTGTGGCCGG
3144 TGTTGCGCGG
Statistics
Matches: 73, Mismatches: 13, Indels: 8
0.78 0.14 0.09
Matches are distributed among these distances:
32 2 0.03
33 62 0.85
35 7 0.10
36 2 0.03
ACGTcount: A:0.09, C:0.27, G:0.40, T:0.25
Consensus pattern (32 bp):
ATCGCGTGGCCGGTTGTGGCCGGACATGTCCA
Found at i:5856 original size:2 final size:2
Alignment explanation
Indices: 5851--5889 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5841 TATATATATA
5851 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
5890 ATAACCTGGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:10432 original size:21 final size:20
Alignment explanation
Indices: 10393--10437 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
10383 AATTATCAAT
* *
10393 TAAAAATAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
10413 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
10434 TAAA
1 TAAA
10438 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.07, T:0.18
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:12751 original size:21 final size:20
Alignment explanation
Indices: 12725--12766 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
12715 TCTTGAAGGT
*
12725 TTGAAGTCCATTGAAGATCAA
1 TTGAAGACCATTGAAGA-CAA
*
12746 TTGAAGAGCATTGAAGACAA
1 TTGAAGACCATTGAAGACAA
12766 T
1 T
12767 AAGCAAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (20 bp):
TTGAAGACCATTGAAGACAA
Found at i:14146 original size:15 final size:15
Alignment explanation
Indices: 14126--14156 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
14116 AATAATATTA
14126 TGTTGTATGTGTGTG
1 TGTTGTATGTGTGTG
*
14141 TGTTGTGTGTGTGTG
1 TGTTGTATGTGTGTG
14156 T
1 T
14157 ATGTGTGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.03, C:0.00, G:0.42, T:0.55
Consensus pattern (15 bp):
TGTTGTATGTGTGTG
Found at i:14161 original size:8 final size:8
Alignment explanation
Indices: 14124--14166 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
14114 TAAATAATAT
14124 TATGT-TG
1 TATGTGTG
14131 TATGTGTG
1 TATGTGTG
*
14139 TGTGTTGTG
1 TATG-TGTG
*
14148 TGTGTGTG
1 TATGTGTG
14156 TATGTGTG
1 TATGTGTG
14164 TAT
1 TAT
14167 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
7 5 0.16
8 19 0.59
9 8 0.25
ACGTcount: A:0.09, C:0.00, G:0.37, T:0.53
Consensus pattern (8 bp):
TATGTGTG
Found at i:14169 original size:2 final size:2
Alignment explanation
Indices: 14164--14195 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
14154 TGTATGTGTG
*
14164 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14196 AATAACCTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14557 original size:34 final size:34
Alignment explanation
Indices: 14510--14585 Score: 116
Period size: 34 Copynumber: 2.2 Consensus size: 34
14500 TTAACATGAC
*
14510 CTTGTTGGCCCTTATTGACTAAGCTTTCCATAGTG
1 CTTGTT-GCCCTTATTGACTAAGCTTTACATAGTG
* *
14545 CTTGTTGCCCTTATTGATTAAGCTTTACATGGTG
1 CTTGTTGCCCTTATTGACTAAGCTTTACATAGTG
14579 CTTGTTG
1 CTTGTTG
14586 TCCCGATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
34 32 0.84
35 6 0.16
ACGTcount: A:0.16, C:0.20, G:0.21, T:0.43
Consensus pattern (34 bp):
CTTGTTGCCCTTATTGACTAAGCTTTACATAGTG
Found at i:17042 original size:14 final size:14
Alignment explanation
Indices: 17025--17053 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17015 ATCAAAAGAA
17025 ATATAAAAACATAC
1 ATATAAAAACATAC
17039 ATATAAAAACATAC
1 ATATAAAAACATAC
17053 A
1 A
17054 CAATAGTTCT
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:0.66, C:0.14, G:0.00, T:0.21
Consensus pattern (14 bp):
ATATAAAAACATAC
Found at i:18999 original size:27 final size:27
Alignment explanation
Indices: 18940--19000 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
18930 GGATTAGTTA
18940 TAAAG-AAAGCAAATTAATCTAAAAAC
1 TAAAGCAAAGCAAATTAATCTAAAAAC
* * *
18966 -AACGCAAAGTAAATTAAATCT-AAATC
1 TAAAGCAAAGCAAATT-AATCTAAAAAC
18992 TAAAGCAAA
1 TAAAGCAAA
19001 TTATGAAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
25 3 0.11
26 13 0.46
27 12 0.43
ACGTcount: A:0.59, C:0.13, G:0.08, T:0.20
Consensus pattern (27 bp):
TAAAGCAAAGCAAATTAATCTAAAAAC
Found at i:20368 original size:11 final size:11
Alignment explanation
Indices: 20350--20382 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
20340 AATGGTCTTC
20350 AAATCTTCAA-
1 AAATCTTCAAT
20360 AATATCTTCAAT
1 AA-ATCTTCAAT
20372 AAATCTTCAAT
1 AAATCTTCAAT
20383 CACGAACTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.10
11 17 0.81
12 2 0.10
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (11 bp):
AAATCTTCAAT
Found at i:23029 original size:123 final size:122
Alignment explanation
Indices: 22811--23431 Score: 859
Period size: 123 Copynumber: 5.0 Consensus size: 122
22801 AACGAATGGG
* *
22811 AAATGATA-ATGCCCTCAAGAGGTCCAACGCCAAAAGGCGAGCGATCAGGCAAGGCCGAGCTCGA
1 AAATGA-AGATGCCCTCAAG-GGACCAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGA
* * * * * * * *
22875 CCTTGTATCGCC-CCTGACCGGCAGGCGATCGACAAGGACCATCCCTGACCGAGTATGGG
64 CCTAGTATGGCCATC-GACCGGCAGGCGATCGGCATGAACCATCCCTGACCGAGTATAGA
* *
22934 AAATGAAGAAGCCCTCAAGGGACCGAACGCCAACCGGCGAGCGATCAGGCAAGGCCGAGCTCGAC
1 AAATGAAGATGCCCTCAAGGGACC-AACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGAC
* * *
22999 CTAGTATGGCCATCGACCGGCAGGCAATCGACATGAACCATCCCTGATCGAGTATAGA
65 CTAGTATGGCCATCGACCGGCAGGCGATCGGCATGAACCATCCCTGACCGAGTATAGA
* * * * *
23057 AAATGATGATGCCCTCAATGGGCCCAACGCCTACAGGCGAGCGATCAGGCGAGGCCGAACTCGAC
1 AAATGAAGATGCCCTCAA-GGGACCAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGAC
*
23122 CTAGTATGGCCATCGACCGGCAGGCGATCGGTATGAACCATCCCTGACCGAGTATAGA
65 CTAGTATGGCCATCGACCGGCAGGCGATCGGCATGAACCATCCCTGACCGAGTATAGA
*
23180 AAATGAAGATGCCCTCAAGGGGACCAACGCCAACAGGCAAGCGATCAGGCAAGGCCGAGCTCGAC
1 AAATGAAGATGCCCTCAA-GGGACCAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGAC
* **
23245 CTAGTATGGTCATCGACCAACAGGCGATCGGCATGAACCATCCCTGACCGAGTATAGA
65 CTAGTATGGCCATCGACCGGCAGGCGATCGGCATGAACCATCCCTGACCGAGTATAGA
*
23303 AAATGAAGATGCCCTCAAGGGTACCAACGCCAACAGGCGAGCGACCAGGCAAGGCCGAGCTCGAC
1 AAATGAAGATGCCCTCAAGGG-ACCAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGAC
** * ** * **
23368 CTAGTATCTCTATCGACCGGCAATCGATCGGCATGAACCATCCTTGACCGAGTACGGA
65 CTAGTATGGCCATCGACCGGCAGGCGATCGGCATGAACCATCCCTGACCGAGTATAGA
23426 AAATGA
1 AAATGA
23432 TAAAACCCCC
Statistics
Matches: 445, Mismatches: 48, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
122 8 0.02
123 431 0.97
124 6 0.01
ACGTcount: A:0.30, C:0.29, G:0.27, T:0.14
Consensus pattern (122 bp):
AAATGAAGATGCCCTCAAGGGACCAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGACC
TAGTATGGCCATCGACCGGCAGGCGATCGGCATGAACCATCCCTGACCGAGTATAGA
Found at i:23535 original size:246 final size:244
Alignment explanation
Indices: 22811--23539 Score: 894
Period size: 246 Copynumber: 3.0 Consensus size: 244
22801 AACGAATGGG
*
22811 AAATGATA-ATGCCCTCAAGAGGTCCAACGCCAAAAGGCGAGCGATCAGGCAAGGCCGAGCTCGA
1 AAATGA-AGATGCCCTCAAG-GGTCCAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGA
* ** * * * *
22875 CCTTGTATCGCCCCTGACCGGCAGGCGATCGACAAGGACCATCCCTGACCGAGTATGGGAAATGA
64 CCTAGTATCGCATC-GACCGGCAGGCGATCGGCATGAACCATCCCTGACCGAGTATGGAAAATGA
*
22940 AGAAGCCCTCAA-GGGACCGAACGCCAACCGGCGAGCGATCAGGCAAGGCCGAGCTCGACCTAGT
128 AGAAGCCCTCAAGGGGACC-AACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGACCTAGT
* *
23004 ATGGCCATCGACCGGCAGGCAATCGACATGAACCATCCCTGATCGAGTATAGA
192 ATGGCCATCGACCGGCAGGCGATCGACATGAACCATCCCTGACCGAGTATAGA
* * * * *
23057 AAATGATGATGCCCTCAATGGGCCCAACGCCTACAGGCGAGCGATCAGGCGAGGCCGAACTCGAC
1 AAATGAAGATGCCCTCAA-GGGTCCAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGAC
* * *
23122 CTAGTATGGCCATCGACCGGCAGGCGATCGGTATGAACCATCCCTGACCGAGTATAGAAAATGAA
65 CTAGTATCG-CATCGACCGGCAGGCGATCGGCATGAACCATCCCTGACCGAGTATGGAAAATGAA
* *
23187 GATGCCCTCAAGGGGACCAACGCCAACAGGCAAGCGATCAGGCAAGGCCGAGCTCGACCTAGTAT
129 GAAGCCCTCAAGGGGACCAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGACCTAGTAT
* ** *
23252 GGTCATCGACCAACAGGCGATCGGCATGAACCATCCCTGACCGAGTATAGA
194 GGCCATCGACCGGCAGGCGATCGACATGAACCATCCCTGACCGAGTATAGA
*
23303 AAATGAAGATGCCCTCAAGGGTACCAACGCCAACAGGCGAGCGACCAGGCAAGGCCGAGCTCGAC
1 AAATGAAGATGCCCTCAAGGGT-CCAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGAC
* ** * *
23368 CTAGTATCTCTATCGACCGGCAATCGATCGGCATGAACCATCCTTGACCGAGTACGGAAAATGAT
65 CTAGTATCGC-ATCGACCGGCAGGCGATCGGCATGAACCATCCCTGACCGAGTATGGAAAATGA-
* * * * ** * * * * *
23433 A-AAACCCCCAAGGGGTCCAACACTGACAGGCGAGTGCTCA-GCATA-GCC-ATCCTCAACCAAG
128 AGAAGCCCTCAAGGGGACCAACGCCAACAGGCGAGCGATCAGGCA-AGGCCGA-GCTCGACCTAG
* * * *
23494 TATGGCCACCGACTGGCAGGCGATCGACGAAGAATCATCCCTGACC
191 TATGGCCATCGACCGGCAGGCGATCGAC-ATGAACCATCCCTGACC
23540 AAGCATGGAA
Statistics
Matches: 413, Mismatches: 60, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
244 1 0.00
245 40 0.10
246 362 0.88
247 10 0.02
ACGTcount: A:0.30, C:0.30, G:0.27, T:0.14
Consensus pattern (244 bp):
AAATGAAGATGCCCTCAAGGGTCCAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGACC
TAGTATCGCATCGACCGGCAGGCGATCGGCATGAACCATCCCTGACCGAGTATGGAAAATGAAGA
AGCCCTCAAGGGGACCAACGCCAACAGGCGAGCGATCAGGCAAGGCCGAGCTCGACCTAGTATGG
CCATCGACCGGCAGGCGATCGACATGAACCATCCCTGACCGAGTATAGA
Found at i:23535 original size:369 final size:369
Alignment explanation
Indices: 22811--23539 Score: 916
Period size: 369 Copynumber: 2.0 Consensus size: 369
22801 AACGAATGGG
* *
22811 AAATGATAATGCCCTCAAGAGGTCCAACGCCAAAAGGCGAGCGATCAGGCAAGGCCGAGCTCGAC
1 AAATGATAATGCCCTCAAGAGGACCAACGCCAAAAGGCAAGCGATCAGGCAAGGCCGAGCTCGAC
* * ** * * *
22876 CTTGTATCGCCCCTGACCGGCAGGCGATCGACAAGGACCATCCCTGACCGAGTATGGGAAATGAA
66 CTAGTATCGCACCTGACCAACAGGCGATCGACAAGAACCATCCCTGACCGAGTATAGAAAATGAA
* *
22941 GAAGCCCTCAAGGGACCGAACGCCAACCGGCGAGCGATCAGGCAAGGCCGAGCTCGACCTAGTAT
131 GAAGCCCTCAAGGGACCGAACGCCAACAGGCGAGCGACCAGGCAAGGCCGAGCTCGACCTAGTAT
* * * * * **
23006 GGCCATCGACCGGCAGGCAATCGACATGAACCATCCCTGATCGAGTATAGAAAATGATGATGCCC
196 CGCCATCGACCGGCAAGCAATCGACATGAACCATCCCTGACCGAGTACAGAAAATGATAAAACCC
* * * * * * *
23071 TCAATGGGCCCAACGCCTACAGGCGAGCGATCAGGCGAGGCCGAACTCGACCTAGTATGGCCATC
261 CCAAGGGGCCCAACGACTACAGGCGAGCGATCAGGCGAAGCCGAACTCAACCAAGTATGGCCACC
*
23136 GACCGGCAGGCGATCGGTATGAACCATCCCTGACCGAGTATAGA
326 GACCGGCAGGCGATCGGTAAGAACCATCCCTGACCGAGTATAGA
* *
23180 AAATGA-AGATGCCCTCAAGGGGACCAACGCCAACAGGCAAGCGATCAGGCAAGGCCGAGCTCGA
1 AAATGATA-ATGCCCTCAAGAGGACCAACGCCAAAAGGCAAGCGATCAGGCAAGGCCGAGCTCGA
* * * *
23244 CCTAGTATGGTCATC-GACCAACAGGCGATCGGCATGAACCATCCCTGACCGAGTATAGAAAATG
65 CCTAGTATCG-CACCTGACCAACAGGCGATCGACAAGAACCATCCCTGACCGAGTATAGAAAATG
*
23308 AAGATGCCCTCAAGGGTACC-AACGCCAACAGGCGAGCGACCAGGCAAGGCCGAGCTCGACCTAG
129 AAGAAGCCCTCAAGGG-ACCGAACGCCAACAGGCGAGCGACCAGGCAAGGCCGAGCTCGACCTAG
* * * * * * *
23372 TATCTCTATCGACCGGCAATCGATCGGCATGAACCATCCTTGACCGAGTACGGAAAATGATAAAA
193 TATCGCCATCGACCGGCAAGCAATCGACATGAACCATCCCTGACCGAGTACAGAAAATGATAAAA
* * * *
23437 CCCCCAAGGGGTCCAAC-ACTGACAGGCGAGTGCTCA-GC-ATAGCC-ATCCTCAACCAAGTATG
258 CCCCCAAGGGGCCCAACGACT-ACAGGCGAGCGATCAGGCGA-AGCCGA-ACTCAACCAAGTATG
* *
23498 GCCACCGACTGGCAGGCGATCGACG-AAGAATCATCCCTGACC
320 GCCACCGACCGGCAGGCGATCG--GTAAGAACCATCCCTGACC
23540 AAGCATGGAA
Statistics
Matches: 306, Mismatches: 46, Indels: 16
0.83 0.12 0.04
Matches are distributed among these distances:
367 2 0.01
368 40 0.13
369 258 0.84
370 6 0.02
ACGTcount: A:0.30, C:0.30, G:0.27, T:0.14
Consensus pattern (369 bp):
AAATGATAATGCCCTCAAGAGGACCAACGCCAAAAGGCAAGCGATCAGGCAAGGCCGAGCTCGAC
CTAGTATCGCACCTGACCAACAGGCGATCGACAAGAACCATCCCTGACCGAGTATAGAAAATGAA
GAAGCCCTCAAGGGACCGAACGCCAACAGGCGAGCGACCAGGCAAGGCCGAGCTCGACCTAGTAT
CGCCATCGACCGGCAAGCAATCGACATGAACCATCCCTGACCGAGTACAGAAAATGATAAAACCC
CCAAGGGGCCCAACGACTACAGGCGAGCGATCAGGCGAAGCCGAACTCAACCAAGTATGGCCACC
GACCGGCAGGCGATCGGTAAGAACCATCCCTGACCGAGTATAGA
Found at i:23849 original size:21 final size:21
Alignment explanation
Indices: 23812--24067 Score: 227
Period size: 21 Copynumber: 12.3 Consensus size: 21
23802 CCCCCCCCCC
*
23812 CCCCAAGGAGAGGAGAATGCT
1 CCCCAAAGAGAGGAGAATGCT
* * **
23833 CTCCAAAGATAAAAGAATGCT
1 CCCCAAAGAGAGGAGAATGCT
*
23854 CCCCGAAGAGAGGAGAATGC-
1 CCCCAAAGAGAGGAGAATGCT
*
23874 CCCCAATGAGAGGAGAATGCT
1 CCCCAAAGAGAGGAGAATGCT
* * *
23895 CTCCAAAGATA--AAAATGCT
1 CCCCAAAGAGAGGAGAATGCT
*
23914 CCCCAAAGAGAGGAGAATGCC
1 CCCCAAAGAGAGGAGAATGCT
*
23935 CCCCAAAGAGAGGAGAATGTT
1 CCCCAAAGAGAGGAGAATGCT
* * *
23956 CTCCAAAGA-ATGAAAAATGCT
1 CCCCAAAGAGA-GGAGAATGCT
*
23977 CCCCAAGGAGAGGAGAATGCT
1 CCCCAAAGAGAGGAGAATGCT
** *
23998 CTTCAAAGA-ATGAAGAATGCT
1 CCCCAAAGAGA-GGAGAATGCT
* *
24019 CCCCAAGGAGAGGTGAATGC-
1 CCCCAAAGAGAGGAGAATGCT
* *
24039 CTCCCAAGGAGAGGAGAACGCT
1 C-CCCAAAGAGAGGAGAATGCT
*
24061 CGCCAAA
1 CCCCAAA
24068 TGCAAAGTGT
Statistics
Matches: 183, Mismatches: 43, Indels: 18
0.75 0.18 0.07
Matches are distributed among these distances:
19 16 0.09
20 21 0.11
21 143 0.78
22 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.26, T:0.13
Consensus pattern (21 bp):
CCCCAAAGAGAGGAGAATGCT
Found at i:24016 original size:63 final size:59
Alignment explanation
Indices: 23811--23996 Score: 273
Period size: 62 Copynumber: 3.0 Consensus size: 59
23801 CCCCCCCCCC
*
23811 CCCCCAAGGAGAGGAGAATGCTCTCCAAAGATAAAAGAATGCTCCCCGAAGAGAGGAGAATG
1 CCCCCAAAGAGAGGAGAATGCTCTCCAAAGAT-AAA-AATGCTCCCC-AAGAGAGGAGAATG
*
23873 CCCCCAATGAGAGGAGAATGCTCTCCAAAGATAAAAATGCTCCCCAAAGAGAGGAGAATG
1 CCCCCAAAGAGAGGAGAATGCTCTCCAAAGATAAAAATGCTCCCC-AAGAGAGGAGAATG
*
23933 CCCCCCAAAGAGAGGAGAATGTTCTCCAAAGAATGAAAAATGCTCCCCAAGGAGAGGAGAATG
1 -CCCCCAAAGAGAGGAGAATGCTCTCCAAAG-AT-AAAAATGCTCCCCAA-GAGAGGAGAATG
23996 C
1 C
23997 TCTTCAAAGA
Statistics
Matches: 116, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
60 24 0.21
61 31 0.27
62 36 0.31
63 25 0.22
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.12
Consensus pattern (59 bp):
CCCCCAAAGAGAGGAGAATGCTCTCCAAAGATAAAAATGCTCCCCAAGAGAGGAGAATG
Found at i:24186 original size:98 final size:96
Alignment explanation
Indices: 24080--24370 Score: 330
Period size: 98 Copynumber: 3.1 Consensus size: 96
24070 CAAAGTGTGA
* * * *
24080 GACGCTCGCCGAGCACCAAATGGAGAATGCTCCTAGAGAGCAAATGAAGAATGCCCGAGATGGTG
1 GACGCTCGCCGAGCGCGAAATGGAGAATGCTCCTCGAGAGCAAATGAAGAATGCCCGAGATGGCG
24145 AAACGAATAACGCTTACCGAACGCGAAGCGTAG
66 AAACG-ATAACGC-TACCGAACGCGAAGCGTAG
* * ** *
24178 GACGCTCGCCGAACGCGAAATGGAGAATGCTCCTCTAGAGCAGGTGAAGAATTCCCGAGATGGCG
1 GACGCTCGCCGAGCGCGAAATGGAGAATGCTCCTCGAGAGCAAATGAAGAATGCCCGAGATGGCG
*
24243 AAAC----A-G--A--TAACGCGAAGCGTAG
66 AAACGATAACGCTACCGAACGCGAAGCGTAG
* * * *
24265 GACACTCGCTGAGCGCGAAATGGAGAATGCTCCTCGAGAGCAAATGAAGAATGCCCCAGATGGCA
1 GACGCTCGCCGAGCGCGAAATGGAGAATGCTCCTCGAGAGCAAATGAAGAATGCCCGAGATGGCG
* * *
24330 AAATGGATAACGCTCGCCGATCGCGAAGCGTAG
66 AAA-CGATAACGCT-ACCGAACGCGAAGCGTAG
24363 GACGCTCG
1 GACGCTCG
24371 TCGAACGCAA
Statistics
Matches: 158, Mismatches: 24, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
87 73 0.46
89 1 0.01
92 2 0.01
93 2 0.01
98 80 0.51
ACGTcount: A:0.32, C:0.24, G:0.30, T:0.14
Consensus pattern (96 bp):
GACGCTCGCCGAGCGCGAAATGGAGAATGCTCCTCGAGAGCAAATGAAGAATGCCCGAGATGGCG
AAACGATAACGCTACCGAACGCGAAGCGTAG
Found at i:24313 original size:87 final size:87
Alignment explanation
Indices: 24164--24342 Score: 259
Period size: 87 Copynumber: 2.1 Consensus size: 87
24154 ACGCTTACCG
* * **
24164 AACGCGAAGCGTAGGACGCTCGCCGAACGCGAAATGGAGAATGCTCCTCTAGAGCAGGTGAAGAA
1 AACGCGAAGCGTAGGACACTCGCCGAACGCGAAATGGAGAATGCTCCTCGAGAGCAAATGAAGAA
* * *
24229 TTCCCGAGATGGCGAAACAGAT
66 TGCCCCAGATGGCAAAACAGAT
* *
24251 AACGCGAAGCGTAGGACACTCGCTGAGCGCGAAATGGAGAATGCTCCTCGAGAGCAAATGAAGAA
1 AACGCGAAGCGTAGGACACTCGCCGAACGCGAAATGGAGAATGCTCCTCGAGAGCAAATGAAGAA
**
24316 TGCCCCAGATGGCAAAATGGAT
66 TGCCCCAGATGGCAAAACAGAT
24338 AACGC
1 AACGC
24343 TCGCCGATCG
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.34, C:0.23, G:0.30, T:0.13
Consensus pattern (87 bp):
AACGCGAAGCGTAGGACACTCGCCGAACGCGAAATGGAGAATGCTCCTCGAGAGCAAATGAAGAA
TGCCCCAGATGGCAAAACAGAT
Found at i:24387 original size:25 final size:25
Alignment explanation
Indices: 24339--24387 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
24329 AAAATGGATA
* *
24339 ACGCTCGCCGATCGCGAAGCGTAGG
1 ACGCTCGCCGAACGCAAAGCGTAGG
* *
24364 ACGCTCGTCGAACGCAAAGTGTAG
1 ACGCTCGCCGAACGCAAAGCGTAG
24388 AACACTTACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.24, C:0.29, G:0.33, T:0.14
Consensus pattern (25 bp):
ACGCTCGCCGAACGCAAAGCGTAGG
Found at i:24955 original size:19 final size:19
Alignment explanation
Indices: 24931--24986 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
24921 CATTCAAATA
24931 TCCCAATTATTTTTACAAG
1 TCCCAATTATTTTTACAAG
* *
24950 TCCCAATTA--TTCA-AATA
1 TCCCAATTATTTTTACAA-G
24967 TCCCAATTATTTTTACAAG
1 TCCCAATTATTTTTACAAG
24986 T
1 T
24987 TCCAGAACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
16 2 0.07
17 12 0.41
19 13 0.45
20 2 0.07
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (19 bp):
TCCCAATTATTTTTACAAG
Found at i:24972 original size:17 final size:17
Alignment explanation
Indices: 24922--24977 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
24912 GATATATTTC
24922 ATTCAAATATCCCAATT
1 ATTCAAATATCCCAATT
* *
24939 ATTTTTACAA-GTCCCAATT
1 A--TTCA-AATATCCCAATT
24958 ATTCAAATATCCCAATT
1 ATTCAAATATCCCAATT
24975 ATT
1 ATT
24978 TTTACAAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 2 0.06
17 15 0.48
19 12 0.39
20 2 0.06
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.39
Consensus pattern (17 bp):
ATTCAAATATCCCAATT
Done.