Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007601.1 Corchorus capsularis cultivar CVL-1 contig07622, 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: 68965
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:641 original size:142 final size:143
Alignment explanation
Indices: 380--655 Score: 500
Period size: 142 Copynumber: 1.9 Consensus size: 143
370 AAGGAAGAAG
380 ATAGTTTTTATATTTTTATTTAATAAGGGTATTTTTGGTTTAATAATAAAATGGTAAGGATAAAT
1 ATAGTTTTTATATTTTTATTTAATAAGGGTATTTTTGGTTTAATAATAAAATGGTAAGGATAAAT
*
445 TTGACAATGAAAAATTGGACCAAAACCCACCCCTCCCAAATACCCCGATTTGGAGGGGTGGAAAA
66 TTGACAATGAAAAATTAGACCAAAACCCACCCCTCCCAAATACCCCGATTTGGAGGGGTGGAAAA
510 TGGGTGGGGTGGA
131 TGGGTGGGGTGGA
* *
523 ATAGTTTTTATGTTTTTATTTAATAAGGGTATTTTTGGTTTAATAATAACATGGTAA-GATAAAT
1 ATAGTTTTTATATTTTTATTTAATAAGGGTATTTTTGGTTTAATAATAAAATGGTAAGGATAAAT
* *
587 TTGACAATGAAAATTTAGTCCAAAACCCACCCCTCCCAAATACCCCGATTTGGAGGGGTGGAAAA
66 TTGACAATGAAAAATTAGACCAAAACCCACCCCTCCCAAATACCCCGATTTGGAGGGGTGGAAAA
652 TGGG
131 TGGG
656 GGGTTTGGAG
Statistics
Matches: 128, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
142 73 0.57
143 55 0.43
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.33
Consensus pattern (143 bp):
ATAGTTTTTATATTTTTATTTAATAAGGGTATTTTTGGTTTAATAATAAAATGGTAAGGATAAAT
TTGACAATGAAAAATTAGACCAAAACCCACCCCTCCCAAATACCCCGATTTGGAGGGGTGGAAAA
TGGGTGGGGTGGA
Found at i:3222 original size:14 final size:14
Alignment explanation
Indices: 3203--3230 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3193 GCAGCTAAAA
3203 GCAAGTCATATTGT
1 GCAAGTCATATTGT
3217 GCAAGTCATATTGT
1 GCAAGTCATATTGT
3231 TAGTTAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
GCAAGTCATATTGT
Found at i:4508 original size:32 final size:32
Alignment explanation
Indices: 4447--4508 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
4437 ATTTCAACTG
* * *
4447 ATTAAATGCAAATAAAGCCAAATTTACAAGGC
1 ATTAAATGCAAATAAAGACAAAATAACAAGGC
*
4479 ATTAAATGCAAATCAAGACAAAATAACAAG
1 ATTAAATGCAAATAAAGACAAAATAACAAG
4509 CCATCAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.55, C:0.15, G:0.11, T:0.19
Consensus pattern (32 bp):
ATTAAATGCAAATAAAGACAAAATAACAAGGC
Found at i:4805 original size:32 final size:33
Alignment explanation
Indices: 4758--4844 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 33
4748 GATGACCCGT
* **
4758 GCCGCCCCAAGAGGGCGGCTT-ACCATGGGCAG
1 GCCGCCCCAATAGGGCGGCTTCACCATGAACAG
* * *
4790 GCCGCCCCACTAGGGCGGCTTCACTATGAATAG
1 GCCGCCCCAATAGGGCGGCTTCACCATGAACAG
* *
4823 GCCGCCCCAGTGGGGCGGCTTC
1 GCCGCCCCAATAGGGCGGCTTC
4845 GCCACGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
32 19 0.41
33 27 0.59
ACGTcount: A:0.16, C:0.36, G:0.34, T:0.14
Consensus pattern (33 bp):
GCCGCCCCAATAGGGCGGCTTCACCATGAACAG
Found at i:5025 original size:32 final size:31
Alignment explanation
Indices: 4929--5083 Score: 150
Period size: 33 Copynumber: 4.8 Consensus size: 31
4919 AAATTTGCTC
4929 AAGCCGCCCCATGAGGGCGGCCTGCCTTGCGCG
1 AAGCCGCCCCATG-GGGCGGCCTGCCTTG-GCG
* ** *
4962 AAGCTGCCCCAT-GGGCGGTTTGCCGTGGCG
1 AAGCCGCCCCATGGGGCGGCCTGCCTTGGCG
* *
4992 AAGCCGCTCCATGAGGGTGGCCTGCCTTGGCG
1 AAGCCGCCCCATG-GGGCGGCCTGCCTTGGCG
* **
5024 AAGCCGCCCCAGTGGGGCGGCCTGCCCATGATG
1 AAGCCGCCCCA-TGGGGCGGCCTG-CCTTGGCG
*
5057 AAGCCGCCCCAGTGGGGAGGCTCTGCC
1 AAGCCGCCCCA-TGGGGCGGC-CTGCC
5084 GTGGTTGAGC
Statistics
Matches: 101, Mismatches: 16, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
30 13 0.13
31 12 0.12
32 33 0.33
33 40 0.40
34 3 0.03
ACGTcount: A:0.13, C:0.35, G:0.37, T:0.15
Consensus pattern (31 bp):
AAGCCGCCCCATGGGGCGGCCTGCCTTGGCG
Found at i:5147 original size:14 final size:15
Alignment explanation
Indices: 5118--5159 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
5108 GACTCAGTGT
*
5118 AAAAGTGTAAAAAGGGT
1 AAAAGTGT--AAAGGGC
5135 AAAAG-GTAAAGGGC
1 AAAAGTGTAAAGGGC
5149 AAAAGTGTAAA
1 AAAAGTGTAAA
5160 ACGTGGGGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 11 0.48
15 5 0.22
16 2 0.09
17 5 0.22
ACGTcount: A:0.55, C:0.02, G:0.29, T:0.14
Consensus pattern (15 bp):
AAAAGTGTAAAGGGC
Found at i:5559 original size:85 final size:85
Alignment explanation
Indices: 5416--5583 Score: 300
Period size: 85 Copynumber: 2.0 Consensus size: 85
5406 GGAGGAGTGG
**
5416 AAAACGGGGACATTTGGAGGGGTGGGCTGGACCCCTTCTTACCTCTCATTCTTCACAAGCCCTCC
1 AAAACGGGGACATTTGGAGGGGTGGGCTGGACCCCTTCTTACCTCTCACCCTTCACAAGCCCTCC
5481 AACCAAGCAGAAAATACCGA
66 AACCAAGCAGAAAATACCGA
*
5501 AAAACGGGGGCATTTGGAGGGGTGGGCTGGACCCCTTCTTACCTCTCACCCTTCACAAGCCCTCC
1 AAAACGGGGACATTTGGAGGGGTGGGCTGGACCCCTTCTTACCTCTCACCCTTCACAAGCCCTCC
*
5566 AACCAAGCAGACAATACC
66 AACCAAGCAGAAAATACC
5584 CTCATTGTTT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.27, C:0.32, G:0.23, T:0.19
Consensus pattern (85 bp):
AAAACGGGGACATTTGGAGGGGTGGGCTGGACCCCTTCTTACCTCTCACCCTTCACAAGCCCTCC
AACCAAGCAGAAAATACCGA
Found at i:6026 original size:14 final size:14
Alignment explanation
Indices: 6007--6034 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5997 TAAGGTATTG
6007 TATAGATGTATAGA
1 TATAGATGTATAGA
6021 TATAGATGTATAGA
1 TATAGATGTATAGA
6035 CAATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (14 bp):
TATAGATGTATAGA
Found at i:11379 original size:7 final size:7
Alignment explanation
Indices: 11367--11403 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
11357 TATACTTAAT
11367 AGAGTTG
1 AGAGTTG
11374 AGAGTTG
1 AGAGTTG
11381 AGAGTTG
1 AGAGTTG
11388 AGAGTTG
1 AGAGTTG
11395 AGAG-TG
1 AGAGTTG
11401 AGA
1 AGA
11404 ATGGGATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.32, C:0.00, G:0.43, T:0.24
Consensus pattern (7 bp):
AGAGTTG
Found at i:12956 original size:109 final size:109
Alignment explanation
Indices: 12824--13062 Score: 437
Period size: 109 Copynumber: 2.2 Consensus size: 109
12814 AAAAAAATTA
12824 TATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
12887 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
65 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
12932 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
* *
12997 AAAAATTTTAGTATATCTAAATTTTTTGGTAAAAATAAAGTAAT
66 AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
13041 TATAAAGATATTAGATTTAATT
1 TATAAAGATATTAGATTTAATT
13063 TAATTGAATA
Statistics
Matches: 127, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
108 6 0.05
109 120 0.94
110 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.11, T:0.40
Consensus pattern (109 bp):
TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
Found at i:13102 original size:109 final size:110
Alignment explanation
Indices: 12836--13096 Score: 377
Period size: 109 Copynumber: 2.3 Consensus size: 110
12826 TAAAATATTG
12836 AATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAAATTTTAATA
1 AATTTAATT-AATGAAAATAGAGTTTTTAGTAGAAT-AAA-T-TATATTAGAAAAAATTTTAATA
12901 TATCCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGATTT
62 TATCCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGATTT
*
12950 AA-TT-A--AATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAAATTTTAGTAT
1 AATTTAATTAATGAAAATAGAGTTTTTAGTAGAAT-AAA-T-TATATTAGAAAAAATTTTAATAT
*
13011 ATCTAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGATTT
63 ATCCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGATTT
* **
13059 AATTTAATTGAATAAAAATAGAGTTACTAGTAGAATAA
1 AATTTAATT-AATGAAAATAGAGTTTTTAGTAGAATAA
13097 TATATTTGAA
Statistics
Matches: 137, Mismatches: 5, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
109 104 0.76
110 2 0.01
111 1 0.01
112 1 0.01
113 4 0.03
114 25 0.18
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (110 bp):
AATTTAATTAATGAAAATAGAGTTTTTAGTAGAATAAATTATATTAGAAAAAATTTTAATATATC
CAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGATTT
Found at i:21399 original size:104 final size:104
Alignment explanation
Indices: 21219--21425 Score: 396
Period size: 104 Copynumber: 2.0 Consensus size: 104
21209 GTGAGTTTAT
21219 TTGTAATTTGTTTATTTATGTATTTAATAGGTAGGTAGTTTATTTATGGGCATAGAGATTTATTT
1 TTGTAATTTGTTTATTTATGTATTTAATAGGTAGGTAGTTTATTTATGGGCATAGAGATTTATTT
*
21284 GAATTGTAATGAGATTTCATTGGGTTTATTTGTTGGCTA
66 GAATTGTAATGAGATTTCATTGGATTTATTTGTTGGCTA
*
21323 TTGTAATTTGTTTATTTATGTATTTAATAGGTATGTAGTTTATTTATGGGCATAGAGATTTATTT
1 TTGTAATTTGTTTATTTATGTATTTAATAGGTAGGTAGTTTATTTATGGGCATAGAGATTTATTT
21388 GAATTGTAATGAGATTTCATTGGATTTATTTGTTGGCT
66 GAATTGTAATGAGATTTCATTGGATTTATTTGTTGGCT
21426 CATAGATTAG
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 101 1.00
ACGTcount: A:0.25, C:0.03, G:0.21, T:0.51
Consensus pattern (104 bp):
TTGTAATTTGTTTATTTATGTATTTAATAGGTAGGTAGTTTATTTATGGGCATAGAGATTTATTT
GAATTGTAATGAGATTTCATTGGATTTATTTGTTGGCTA
Found at i:22052 original size:40 final size:40
Alignment explanation
Indices: 21997--22077 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
21987 ACCGAGTCAA
*
21997 TTGGCGGACATGGTGTCAGACCAGTAATCTGGTTCGATTC
1 TTGGCGGACATGGTGTCAAACCAGTAATCTGGTTCGATTC
22037 TTGGCGGACATGGTGTCAAACCAGTAATCTGGTTCGATTC
1 TTGGCGGACATGGTGTCAAACCAGTAATCTGGTTCGATTC
22077 T
1 T
22078 AATAACAATG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (40 bp):
TTGGCGGACATGGTGTCAAACCAGTAATCTGGTTCGATTC
Found at i:23713 original size:16 final size:17
Alignment explanation
Indices: 23688--23725 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
23678 CAATTTTCAT
*
23688 GATTTTAGCTTCATTA-
1 GATTTCAGCTTCATTAG
23704 GATTTCAGCTTCATTAG
1 GATTTCAGCTTCATTAG
23721 GATTT
1 GATTT
23726 GTTTTATGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (17 bp):
GATTTCAGCTTCATTAG
Found at i:25702 original size:9 final size:9
Alignment explanation
Indices: 25688--25717 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
25678 AAATTCGAGA
25688 TTTTGTTTT
1 TTTTGTTTT
25697 TTTTG-TTT
1 TTTTGTTTT
25705 TTTTGTTTT
1 TTTTGTTTT
25714 TTTT
1 TTTT
25718 TTTGTGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (9 bp):
TTTTGTTTT
Found at i:25713 original size:14 final size:14
Alignment explanation
Indices: 25688--25727 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
25678 AAATTCGAGA
*
25688 TTTTGTTTTTTTTGT
1 TTTTGTGTTTTTT-T
*
25703 TTTTTTGTTTTTTT
1 TTTTGTGTTTTTTT
25717 TTTTGTGTTTT
1 TTTTGTGTTTT
25728 CAAATCACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (14 bp):
TTTTGTGTTTTTTT
Found at i:25727 original size:9 final size:8
Alignment explanation
Indices: 25688--25720 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
25678 AAATTCGAGA
25688 TTTTGTTTT
1 TTTTG-TTT
25697 TTTTGTTT
1 TTTTGTTT
25705 TTTTGTTT
1 TTTTGTTT
25713 TTTT-TTT
1 TTTTGTTT
25720 T
1 T
25721 GTGTTTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 4 0.17
8 15 0.62
9 5 0.21
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (8 bp):
TTTTGTTT
Found at i:25964 original size:56 final size:55
Alignment explanation
Indices: 25873--26042 Score: 214
Period size: 56 Copynumber: 3.0 Consensus size: 55
25863 GTGAAAGGTT
* * *
25873 TCGGGTCCGAATCCTGAGATAGGCGGGGTGAGATTATGGGAAAGGAGAGAGCTACC
1 TCGGGTTCGAATCCTGAGATAGG-GGAGTGAGATTATGGGAAAGGAGAAAGCTACC
* * *
25929 TCGGGTTCGAATCCTGGGATAGGTGGAGTGGGATTATGGGAAAGAAGAAAGCTACC
1 TCGGGTTCGAATCCTGAGATAGG-GGAGTGAGATTATGGGAAAGGAGAAAGCTACC
** * * *
25985 TCGGGTTTTAATCCTGAGATAGGCGAGATGAGATTATGCGAAAGGAGAAAACTACC
1 TCGGGTTCGAATCCTGAGATAGGGGAG-TGAGATTATGGGAAAGGAGAAAGCTACC
26041 TC
1 TC
26043 CTATTGTTTA
Statistics
Matches: 98, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
55 3 0.03
56 95 0.97
ACGTcount: A:0.29, C:0.15, G:0.35, T:0.21
Consensus pattern (55 bp):
TCGGGTTCGAATCCTGAGATAGGGGAGTGAGATTATGGGAAAGGAGAAAGCTACC
Found at i:34130 original size:16 final size:16
Alignment explanation
Indices: 34091--34131 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
34081 TTCAATTAAC
34091 TAAACTATATATATAAT
1 TAAA-TATATATATAAT
* *
34108 GATATATATATATAAT
1 TAAATATATATATAAT
34124 TAAATATA
1 TAAATATA
34132 ATTGAATATT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (16 bp):
TAAATATATATATAAT
Found at i:34300 original size:20 final size:21
Alignment explanation
Indices: 34263--34302 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
34253 TACCTGTTAA
*
34263 TTAAAGCGTGTCACTCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
*
34284 TTAAA-CGTGTTAATCGTGT
1 TTAAAGCGTGTCAATCGTGT
34303 TTTGACACGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (21 bp):
TTAAAGCGTGTCAATCGTGTC
Found at i:41436 original size:31 final size:30
Alignment explanation
Indices: 41380--41437 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
41370 ATGTTTTTCG
*
41380 ATTGTACCTTATTTTTAAAATATATTTTTA
1 ATTGTACCTTATTTTTAAAACATATTTTTA
41410 ATTGTACCCTT-TTTTTAAAAACATATTT
1 ATTGTA-CCTTATTTTT-AAAACATATTT
41438 CTAAATTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.53
Consensus pattern (30 bp):
ATTGTACCTTATTTTTAAAACATATTTTTA
Found at i:41789 original size:22 final size:21
Alignment explanation
Indices: 41761--41930 Score: 101
Period size: 22 Copynumber: 7.8 Consensus size: 21
41751 GTTAGGAAGA
*
41761 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAATG-TG
* * *
41783 TTATCAAAATTTCAAAACGAGG
1 TTATCAAAATTTCATAATG-TG
*
41805 TTATCAAAATTACATAATGTG
1 TTATCAAAATTTCATAATGTG
* * *
41826 ATTATCAGAATTTCATAGAGGGG
1 -TTATCAAAATTTCATA-ATGTG
* * * *
41849 TCAACAAAATTTTATAGA-GAG
1 TTATCAAAATTTCATA-ATGTG
* *
41870 ATTATCAAAATTTCATAAAGAGG
1 -TTATCAAAATTTCATAATG-TG
* *
41893 TTATCAAATTTTCAAAATGTG
1 TTATCAAAATTTCATAATGTG
41914 TT-TACAAAAATTTCATA
1 TTAT-C-AAAATTTCATA
41931 GTGGTATTTT
Statistics
Matches: 113, Mismatches: 28, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
20 1 0.01
21 8 0.07
22 100 0.88
23 4 0.04
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTTCATAATGTG
Found at i:41831 original size:44 final size:44
Alignment explanation
Indices: 41761--41930 Score: 168
Period size: 44 Copynumber: 3.9 Consensus size: 44
41751 GTTAGGAAGA
*
41761 TTATCAAAATTTCATAGTGTTG-TTATCAAAATTTCA-AAACGAGG
1 TTATCAAAATTTCATAATG-TGATTATCAAAATTTCATAAA-GAGG
* * * *
41805 TTATCAAAATTACATAATGTGATTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAATGTGATTATCAAAATTTCATAAAGAGG
* * * *
41849 TCAACAAAATTTTATAGA-GAGATTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATA-ATGTGATTATCAAAATTTCATAAAGAGG
* * *
41893 TTATCAAATTTTCAAAATGTGTTTA-CAAAAATTTCATA
1 TTATCAAAATTTCATAATGTGATTATC-AAAATTTCATA
41931 GTGGTATTTT
Statistics
Matches: 101, Mismatches: 20, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
43 4 0.04
44 94 0.93
45 3 0.03
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (44 bp):
TTATCAAAATTTCATAATGTGATTATCAAAATTTCATAAAGAGG
Found at i:42103 original size:22 final size:22
Alignment explanation
Indices: 42012--42239 Score: 116
Period size: 22 Copynumber: 10.6 Consensus size: 22
42002 TTATGAAGTA
* *
42012 ATCAAAATTTC--AGGAAGGAT
1 ATCAAAATTTCATAGGGAGGTT
* **
42032 ATCAAAATTTTATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* * * *
42054 TTCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
*
42076 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
42098 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
42120 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
42142 ATCAAAATCT-ATA---A--TT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
42158 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
42180 GTCAGAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* * *
42203 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGGGAG-GTT
42226 ATCAAAATTTCATA
1 ATCAAAATTTCATA
42240 ACGAGGTCAC
Statistics
Matches: 156, Mismatches: 38, Indels: 25
0.71 0.17 0.11
Matches are distributed among these distances:
16 10 0.06
17 3 0.02
18 1 0.01
20 13 0.08
21 5 0.03
22 87 0.56
23 37 0.24
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:42215 original size:23 final size:23
Alignment explanation
Indices: 42185--42235 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
42175 AAGTTGTCAG
* *
42185 AATTTTATAGGGAGGTTTATCAA
1 AATTTTATAGGAAGATTTATCAA
42208 AATTTTATAGGAAGATTTATCAA
1 AATTTTATAGGAAGATTTATCAA
42231 AATTT
1 AATTT
42236 CATAACGAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.39, C:0.04, G:0.16, T:0.41
Consensus pattern (23 bp):
AATTTTATAGGAAGATTTATCAA
Found at i:42398 original size:23 final size:22
Alignment explanation
Indices: 42326--42421 Score: 72
Period size: 22 Copynumber: 4.3 Consensus size: 22
42316 CTTTTTAAAT
* *
42326 TTTCATAACGTGGTTATCAATA
1 TTTCATAATGTGGTTATCAAAA
* * *
42348 TATCAT-ATGGAGGTTATCAACA
1 TTTCATAAT-GTGGTTATCAAAA
*
42370 TCTCATAATGTTGGTTATCAAAA
1 TTTCATAATG-TGGTTATCAAAA
*
42393 TTTCAT--TGGGAAGTTATCAAAA
1 TTTCATAATGTG--GTTATCAAAA
42415 TTTCATA
1 TTTCATA
42422 TCGAAGTCTT
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
20 1 0.02
21 3 0.05
22 38 0.64
23 17 0.29
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (22 bp):
TTTCATAATGTGGTTATCAAAA
Found at i:42409 original size:45 final size:44
Alignment explanation
Indices: 42328--42421 Score: 109
Period size: 45 Copynumber: 2.1 Consensus size: 44
42318 TTTTAAATTT
* * *
42328 TCATAACGTGGTTATCAATATATCATATGGAGGTTATCAACATC
1 TCATAACGTGGTTATCAAAATATCATATGGAAGTTATCAAAATC
* * *
42372 TCATAATGTTGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATT
1 TCATAACG-TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATC
42417 TCATA
1 TCATA
42422 TCGAAGTCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
44 8 0.19
45 34 0.81
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (44 bp):
TCATAACGTGGTTATCAAAATATCATATGGAAGTTATCAAAATC
Found at i:42427 original size:22 final size:22
Alignment explanation
Indices: 42383--42440 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
42373 CATAATGTTG
*
42383 GTTATCAAAATTTCATTGGGAA
1 GTTATCAAAATTTCATTGCGAA
42405 GTTATCAAAATTTCATAT-CGAA
1 GTTATCAAAATTTCAT-TGCGAA
42427 GTCT-TCAAAATTTC
1 GT-TATCAAAATTTC
42441 TTAGAGAGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
22 31 0.94
23 2 0.06
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (22 bp):
GTTATCAAAATTTCATTGCGAA
Found at i:42457 original size:22 final size:22
Alignment explanation
Indices: 42410--42480 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
42400 GGGAAGTTAT
*
42410 CAAAATTTCATATCGAA-GTCTT-
1 CAAAATTTCATA-AGAAGGT-TTA
*
42432 CAAAATTTC-TTAGAGAGGTTTA
1 CAAAATTTCATAAGA-AGGTTTA
42454 CAAAATTTCATAAGAAGGTTTA
1 CAAAATTTCATAAGAAGGTTTA
*
42476 AAAAA
1 CAAAA
42481 AATTATAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 2 0.05
21 4 0.10
22 31 0.76
23 4 0.10
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATAAGAAGGTTTA
Found at i:43831 original size:12 final size:12
Alignment explanation
Indices: 43814--43842 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
43804 AGGGACTCAT
43814 ATTGTGGAAGTA
1 ATTGTGGAAGTA
43826 ATTGTGGAAGTA
1 ATTGTGGAAGTA
43838 ATTGT
1 ATTGT
43843 AGTTACACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (12 bp):
ATTGTGGAAGTA
Found at i:47762 original size:12 final size:12
Alignment explanation
Indices: 47724--47762 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
47714 AAAACCCACC
* *
47724 TTTTATCTTTCT
1 TTTTTTCTTCCT
*
47736 TTATTTCTTCCT
1 TTTTTTCTTCCT
47748 TTTTTTCTTCCT
1 TTTTTTCTTCCT
47760 TTT
1 TTT
47763 CTTTTTTCTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTTCTTCCT
Found at i:49707 original size:22 final size:22
Alignment explanation
Indices: 49682--49781 Score: 105
Period size: 22 Copynumber: 4.6 Consensus size: 22
49672 TATTTTTATG
*
49682 AAATTTTGATAACTACCCTATT
1 AAATTTTGATAACTACCATATT
* *
49704 AAATTTTGATAACCACCATATG
1 AAATTTTGATAACTACCATATT
* *
49726 AAATTTTGATAATTACC-TATA
1 AAATTTTGATAACTACCATATT
* *
49747 AAATTGTGATAAACT-CCATAAT
1 AAATTTTGAT-AACTACCATATT
*
49769 AAACTTTGATAAC
1 AAATTTTGATAAC
49782 CTAACTATGA
Statistics
Matches: 64, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
21 17 0.27
22 47 0.73
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAACTACCATATT
Found at i:49756 original size:21 final size:21
Alignment explanation
Indices: 49682--49802 Score: 93
Period size: 22 Copynumber: 5.6 Consensus size: 21
49672 TATTTTTATG
*
49682 AAATTTTGATAACTACCCTATT
1 AAATTTTGATAACTA-CCTATA
* *
49704 AAATTTTGATAACCACCATATG
1 AAATTTTGATAACTACC-TATA
*
49726 AAATTTTGATAATTACCTATA
1 AAATTTTGATAACTACCTATA
*
49747 AAATTGTGATAAACT-CC-ATAA
1 AAATTTTGAT-AACTACCTAT-A
* * *
49768 TAAACTTTGATAACCTAACTATG
1 -AAATTTTGATAA-CTACCTATA
*
49791 AAATTTTAATAA
1 AAATTTTGATAA
49803 ACTTTCCTAT
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
20 2 0.03
21 19 0.24
22 55 0.70
23 1 0.01
24 2 0.03
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (21 bp):
AAATTTTGATAACTACCTATA
Found at i:49758 original size:43 final size:44
Alignment explanation
Indices: 49678--49781 Score: 131
Period size: 43 Copynumber: 2.4 Consensus size: 44
49668 TGAATATTTT
* * *
49678 TATGAAATTTTGATAACTACCCTATTAAATTTTGATAACCACCA
1 TATGAAATTTTGATAACTACCCTATAAAATTGTGATAAACACCA
* *
49722 TATGAAATTTTGATAATTA-CCTATAAAATTGTGATAAACTCCA
1 TATGAAATTTTGATAACTACCCTATAAAATTGTGATAAACACCA
*
49765 TAAT-AAACTTTGATAAC
1 T-ATGAAATTTTGATAAC
49782 CTAACTATGA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
43 32 0.62
44 20 0.38
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (44 bp):
TATGAAATTTTGATAACTACCCTATAAAATTGTGATAAACACCA
Found at i:49831 original size:20 final size:21
Alignment explanation
Indices: 49786--49879 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 21
49776 GATAACCTAA
* *
49786 CTATGAAATTTTAATAAACTTTC
1 CTATG-AATTTTGATAATC-TTC
49809 CTATGAATTTTG-TAATCTTC
1 CTATGAATTTTGATAATCTTC
*
49829 CTATGATTTTTGATAATC-T-
1 CTATGAATTTTGATAATCTTC
* *
49848 CTCTGAGATTTT-ATTAATCTCC
1 CTATGA-ATTTTGA-TAATCTTC
49870 CTAT-AATTTT
1 CTATGAATTTT
49880 TTAATACTAT
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
19 6 0.10
20 29 0.49
21 10 0.17
22 9 0.15
23 5 0.08
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (21 bp):
CTATGAATTTTGATAATCTTC
Found at i:51323 original size:22 final size:21
Alignment explanation
Indices: 51289--51329 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
51279 GTGGATTTCC
* *
51289 TCTATTTGGTACCCACTCCCCT
1 TCTATTCGATACCCA-TCCCCT
51311 TCTATTCGATACCCATCCC
1 TCTATTCGATACCCATCCC
51330 TCATTTTGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.17, C:0.41, G:0.07, T:0.34
Consensus pattern (21 bp):
TCTATTCGATACCCATCCCCT
Done.