Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014530.1 Corchorus capsularis cultivar CVL-1 contig14551, 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: 175618
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1369 original size:32 final size:32
Alignment explanation
Indices: 1328--1395 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
1318 CCCGTGGTTG
*
1328 AGCCTCCCCAGTGGGGCGGCTTCGCCACGGTA
1 AGCCTCCCCAGTGGGGCGGCTTCGCCAAGGTA
1360 AGCCTCCCCAGTGGGGCGGCTTCGCCAAGGTA
1 AGCCTCCCCAGTGGGGCGGCTTCGCCAAGGTA
1392 AGCC
1 AGCC
1396 GCCCTCTTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.15, C:0.37, G:0.34, T:0.15
Consensus pattern (32 bp):
AGCCTCCCCAGTGGGGCGGCTTCGCCAAGGTA
Found at i:13875 original size:15 final size:15
Alignment explanation
Indices: 13855--13884 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
13845 TTAGCACGTG
13855 CAGACATAAGACCTT
1 CAGACATAAGACCTT
13870 CAGACATAAGACCTT
1 CAGACATAAGACCTT
13885 ATTTATCGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (15 bp):
CAGACATAAGACCTT
Found at i:16584 original size:2 final size:2
Alignment explanation
Indices: 16575--16607 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
16565 AAAAAAACTC
16575 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16608 TGAAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:19696 original size:2 final size:2
Alignment explanation
Indices: 19691--19719 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19681 GGTGTGTGTG
19691 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19720 GATAATTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23622 original size:18 final size:17
Alignment explanation
Indices: 23594--23641 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
23584 CGGCTGCCAC
* *
23594 CCCCACTCCAACCCCAT
1 CCCCACCCCAACCCCAA
*
23611 CACCCACCCCAACTCCAA
1 C-CCCACCCCAACCCCAA
23629 CCCCAACCCCAAC
1 CCCC-ACCCCAAC
23642 TCCTTCTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.29, C:0.65, G:0.00, T:0.06
Consensus pattern (17 bp):
CCCCACCCCAACCCCAA
Found at i:23631 original size:12 final size:12
Alignment explanation
Indices: 23592--23641 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
23582 ACCGGCTGCC
*
23592 ACCCCCACTCCA
1 ACCCCAACTCCA
* * *
23604 ACCCCATCACCC
1 ACCCCAACTCCA
23616 ACCCCAACTCCA
1 ACCCCAACTCCA
*
23628 ACCCCAACCCCA
1 ACCCCAACTCCA
23640 AC
1 AC
23642 TCCTTCTCCT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.30, C:0.64, G:0.00, T:0.06
Consensus pattern (12 bp):
ACCCCAACTCCA
Found at i:25550 original size:40 final size:39
Alignment explanation
Indices: 25506--25583 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 39
25496 TCCTTCCTAA
*
25506 ATAATTAAGG-AAACAAATTAAATTCAGATTTAGTCCCCTG
1 ATAATTAAGGTAAA-AAATTAAATACAGATTTAG-CCCCTG
*
25546 ATAATTAAGGTAAAAAATTAAATACAGGTTTAGCCCCT
1 ATAATTAAGGTAAAAAATTAAATACAGATTTAGCCCCT
25584 AGTTATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
39 5 0.14
40 27 0.77
41 3 0.09
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (39 bp):
ATAATTAAGGTAAAAAATTAAATACAGATTTAGCCCCTG
Found at i:26936 original size:53 final size:53
Alignment explanation
Indices: 26864--26970 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
26854 CGGTTGTTTT
* *
26864 ATTTTATAAATTTTTTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGTGA
1 ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGTGA
26917 ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGTGA
1 ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGTGA
26970 A
1 A
26971 ATGATAATAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (53 bp):
ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGTGA
Found at i:27036 original size:16 final size:16
Alignment explanation
Indices: 27015--27049 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
27005 AGTATGTAAA
27015 AGACAAGAGAATAGAG
1 AGACAAGAGAATAGAG
* *
27031 AGACAATAGAATATAG
1 AGACAAGAGAATAGAG
27047 AGA
1 AGA
27050 AGAAGAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.06, G:0.26, T:0.11
Consensus pattern (16 bp):
AGACAAGAGAATAGAG
Found at i:38287 original size:19 final size:20
Alignment explanation
Indices: 38241--38288 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
38231 TGTGGCAAGC
*
38241 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
38263 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
38282 CACATGT
1 CACATGT
38289 CACGCCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:38296 original size:53 final size:53
Alignment explanation
Indices: 38208--38310 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
38198 GACGTGACAC
* ** *
38208 GCCACGTGTACCAAAAAGTGACATGTGGCAAGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCAAGCCACATGTACAAAAAAGTCGT
* * *
38261 GCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACAAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCAAGCCACATGTACAAAAAAGT
38311 GACACGTGGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCAAGCCACATGTACAAAAAAGTCGT
Found at i:38327 original size:31 final size:31
Alignment explanation
Indices: 38260--38368 Score: 112
Period size: 31 Copynumber: 3.5 Consensus size: 31
38250 CAAAAAGTCG
* * *
38260 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACAAAAAAGTGACACGTGGCA
* *
38291 CGCCACGTGTACAAAAAAGTGACACGTGGCA
1 TGCCACATGTACAAAAAAGTGACACGTGGCA
* *
38322 TGCCACATGTTTCAAAAAA-TGGCACGTGGCA
1 TGCCACATG-TACAAAAAAGTGACACGTGGCA
* * *
38353 TGTCACGTGCACAAAA
1 TGCCACATGTACAAAA
38369 GGATACATGC
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
30 5 0.08
31 51 0.80
32 8 0.12
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (31 bp):
TGCCACATGTACAAAAAAGTGACACGTGGCA
Found at i:39746 original size:20 final size:20
Alignment explanation
Indices: 39721--39770 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
39711 TCAAATCAAT
39721 ACGTAGCAAAACAATCCAAC
1 ACGTAGCAAAACAATCCAAC
*
39741 ACGTAGCAAAACAATTCAAC
1 ACGTAGCAAAACAATCCAAC
39761 ACGTAGCAAA
1 ACGTAGCAAA
39771 TAAAAAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.50, C:0.26, G:0.12, T:0.12
Consensus pattern (20 bp):
ACGTAGCAAAACAATCCAAC
Found at i:43263 original size:28 final size:28
Alignment explanation
Indices: 43232--43288 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 28
43222 TCAGTACTTT
43232 CTTTTCTTAAATCATGTAT-CATTTCTAA
1 CTTTTCTTAAATCATGT-TCCATTTCTAA
43260 CTTTTCTTAAATCATGTTCCATTTCTAA
1 CTTTTCTTAAATCATGTTCCATTTCTAA
43288 C
1 C
43289 GGCCTGTGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.26, C:0.21, G:0.04, T:0.49
Consensus pattern (28 bp):
CTTTTCTTAAATCATGTTCCATTTCTAA
Found at i:46256 original size:14 final size:16
Alignment explanation
Indices: 46233--46264 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
46223 TTATATATAC
46233 AAATTAATTA-ATTCA
1 AAATTAATTACATTCA
46248 AAATT-ATTACATTCA
1 AAATTAATTACATTCA
46263 AA
1 AA
46265 TCAAATTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTAATTACATTCA
Found at i:61687 original size:12 final size:12
Alignment explanation
Indices: 61631--61767 Score: 83
Period size: 12 Copynumber: 11.8 Consensus size: 12
61621 GCCCAGTAAA
61631 ATGAATAGTTGTT
1 ATGAATAG-TGTT
61644 ATGAATAGTAGTT
1 ATGAATAGT-GTT
*
61657 -TG--TGAGTG-A
1 ATGAAT-AGTGTT
*
61666 ATGAACAGTGTT
1 ATGAATAGTGTT
61678 ATGAATAGTGTT
1 ATGAATAGTGTT
* **
61690 TTGAATAGT-AA
1 ATGAATAGTGTT
61701 ATGAATAGTGTT
1 ATGAATAGTGTT
*
61713 ATGAATAGTATT
1 ATGAATAGTGTT
* *
61725 TTG--TGAGTG-A
1 ATGAAT-AGTGTT
* *
61735 ATGAACAATGTT
1 ATGAATAGTGTT
61747 ATGAATAGTGTT
1 ATGAATAGTGTT
*
61759 TTGAATAGT
1 ATGAATAGT
61768 AAAAGGTGGG
Statistics
Matches: 92, Mismatches: 21, Indels: 23
0.68 0.15 0.17
Matches are distributed among these distances:
10 7 0.08
11 21 0.23
12 53 0.58
13 11 0.12
ACGTcount: A:0.34, C:0.01, G:0.25, T:0.39
Consensus pattern (12 bp):
ATGAATAGTGTT
Found at i:61704 original size:23 final size:23
Alignment explanation
Indices: 61678--61722 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
61668 GAACAGTGTT
*
61678 ATGAATAGTGTTTTGAATAGTAA
1 ATGAATAGTGTTATGAATAGTAA
61701 ATGAATAGTGTTATGAATAGTA
1 ATGAATAGTGTTATGAATAGTA
61723 TTTTGTGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.22, T:0.38
Consensus pattern (23 bp):
ATGAATAGTGTTATGAATAGTAA
Found at i:61719 original size:69 final size:70
Alignment explanation
Indices: 61629--61770 Score: 259
Period size: 69 Copynumber: 2.0 Consensus size: 70
61619 TAGCCCAGTA
*
61629 AAATGAATAGTTGTTATGAATAGTAGTTTGTGAGTGAATGAACAGTGTTATGAATAGTGTTTTGA
1 AAATGAATAGTTGTTATGAATAGTAGTTTGTGAGTGAATGAACAATGTTATGAATAGTGTTTTGA
61694 ATAGT
66 ATAGT
*
61699 AAATGAATAG-TGTTATGAATAGTATTTTGTGAGTGAATGAACAATGTTATGAATAGTGTTTTGA
1 AAATGAATAGTTGTTATGAATAGTAGTTTGTGAGTGAATGAACAATGTTATGAATAGTGTTTTGA
61763 ATAGT
66 ATAGT
61768 AAA
1 AAA
61771 AGGTGGGGAT
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
69 60 0.86
70 10 0.14
ACGTcount: A:0.37, C:0.01, G:0.24, T:0.38
Consensus pattern (70 bp):
AAATGAATAGTTGTTATGAATAGTAGTTTGTGAGTGAATGAACAATGTTATGAATAGTGTTTTGA
ATAGT
Found at i:61761 original size:34 final size:34
Alignment explanation
Indices: 61630--61761 Score: 169
Period size: 34 Copynumber: 3.8 Consensus size: 34
61620 AGCCCAGTAA
*
61630 AATGAATAGTTGTTATGAATAGTAG-TTTGTGAGTG
1 AATGAACAG-TGTTATGAATAGT-GTTTTGTGAGTG
*
61665 AATGAACAGTGTTATGAATAGTGTTTTGAAT-AGTA
1 AATGAACAGTGTTATGAATAGTGTTTTG--TGAGTG
* *
61700 AATGAATAGTGTTATGAATAGTATTTTGTGAGTG
1 AATGAACAGTGTTATGAATAGTGTTTTGTGAGTG
*
61734 AATGAACAATGTTATGAATAGTGTTTTG
1 AATGAACAGTGTTATGAATAGTGTTTTG
61762 AATAGTAAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
33 2 0.02
34 45 0.53
35 37 0.44
36 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.39
Consensus pattern (34 bp):
AATGAACAGTGTTATGAATAGTGTTTTGTGAGTG
Found at i:62716 original size:31 final size:30
Alignment explanation
Indices: 62668--62729 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
62658 AGTTTTGAGA
* *
62668 AACTTTTGAAATGCCTATTGTAACCTTATTT
1 AACTTTTGAAATACCTA-TATAACCTTATTT
*
62699 AACTTTT-AATATACCTATATATCCTTATTT
1 AACTTTTGAA-ATACCTATATAACCTTATTT
62729 A
1 A
62730 TCTAACATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 14 0.52
31 13 0.48
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (30 bp):
AACTTTTGAAATACCTATATAACCTTATTT
Found at i:64740 original size:14 final size:14
Alignment explanation
Indices: 64721--64750 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
64711 TCTATTATCA
64721 CTTACCTTACAAAC
1 CTTACCTTACAAAC
64735 CTTACCTTACAAAC
1 CTTACCTTACAAAC
64749 CT
1 CT
64751 CACAGTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (14 bp):
CTTACCTTACAAAC
Found at i:87930 original size:2 final size:2
Alignment explanation
Indices: 87923--87947 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
87913 AATTATTATG
87923 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
87948 AAGCCATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:96172 original size:6 final size:7
Alignment explanation
Indices: 96155--96181 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
96145 AATGAGATAA
96155 AAAAAAC
1 AAAAAAC
96162 AAAAAAC
1 AAAAAAC
96169 AAAAAAC
1 AAAAAAC
96176 AAAAAA
1 AAAAAA
96182 TGACCAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:98852 original size:20 final size:21
Alignment explanation
Indices: 98827--98869 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
98817 TAATTGTGTC
*
98827 AAGACACGATTAACACG-TTT
1 AAGACACGAGTAACACGCTTT
*
98847 AAGACACGAGTGACACGCTTT
1 AAGACACGAGTAACACGCTTT
98868 AA
1 AA
98870 TTAACGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
AAGACACGAGTAACACGCTTT
Found at i:99024 original size:15 final size:15
Alignment explanation
Indices: 99004--99033 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
98994 ATACTCAATT
99004 ATCTTTAATTATATA
1 ATCTTTAATTATATA
99019 ATCTTTAATTATATA
1 ATCTTTAATTATATA
99034 TATATAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (15 bp):
ATCTTTAATTATATA
Found at i:104751 original size:24 final size:24
Alignment explanation
Indices: 104724--104769 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
104714 CTGCCCTAGT
* *
104724 GCCCCTTGCTGTATGCGGTGCTGG
1 GCCCCTTGCTGCATACGGTGCTGG
104748 GCCCCTTGCTGCATACGGTGCT
1 GCCCCTTGCTGCATACGGTGCT
104770 TATAATGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.07, C:0.33, G:0.33, T:0.28
Consensus pattern (24 bp):
GCCCCTTGCTGCATACGGTGCTGG
Found at i:104792 original size:33 final size:33
Alignment explanation
Indices: 104750--104812 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
104740 GGTGCTGGGC
104750 CCCTTGCTG-CATACGGTGCTTATAATGTTGGTG
1 CCCTTGCTGCCA-ACGGTGCTTATAATGTTGGTG
104783 CCCTTGCTGCCAACGGTGCTTATAATGTTG
1 CCCTTGCTGCCAACGGTGCTTATAATGTTG
104813 CCTACGGTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.35
Consensus pattern (33 bp):
CCCTTGCTGCCAACGGTGCTTATAATGTTGGTG
Found at i:105170 original size:18 final size:18
Alignment explanation
Indices: 105125--105172 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
105115 ATCACAAAAT
*
105125 TGAGGGACGAAGCTCGGA
1 TGAGGGAAGAAGCTCGGA
**
105143 TGAGTAAAGAAGCTCGGA
1 TGAGGGAAGAAGCTCGGA
105161 TGAGGGAAGAAG
1 TGAGGGAAGAAG
105173 AAGAAGAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.10, G:0.42, T:0.12
Consensus pattern (18 bp):
TGAGGGAAGAAGCTCGGA
Found at i:105174 original size:3 final size:3
Alignment explanation
Indices: 105166--105199 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
105156 TCGGATGAGG
*
105166 GAA GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
105200 CAAATTATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:109169 original size:21 final size:21
Alignment explanation
Indices: 109135--109194 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
109125 TTGTAGAAAC
* *
109135 GGTGGA-ATGTGTGGCGGAGGT
1 GGTGGAGATG-GTGGCGGAAGA
*
109156 GGTGGAGCTGGTGGCGGAAGA
1 GGTGGAGATGGTGGCGGAAGA
*
109177 GGTGGAGATGGTTGCGGA
1 GGTGGAGATGGTGGCGGA
109195 TGAAGTTGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.17, C:0.07, G:0.57, T:0.20
Consensus pattern (21 bp):
GGTGGAGATGGTGGCGGAAGA
Found at i:109830 original size:2 final size:2
Alignment explanation
Indices: 109823--109858 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
109813 TCTTTTGGGT
109823 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
109859 AACTTCATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:118949 original size:2 final size:2
Alignment explanation
Indices: 118944--118974 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
118934 AGTGTGTGTG
118944 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
118975 TATTTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:119523 original size:11 final size:11
Alignment explanation
Indices: 119501--119531 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
119491 TGGGTTGATG
119501 TAAAAAATATTT
1 TAAAAAA-ATTT
119513 TAAAAAAATTT
1 TAAAAAAATTT
119524 TAAAAAAA
1 TAAAAAAA
119532 GAAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAAAATTT
Found at i:119538 original size:10 final size:10
Alignment explanation
Indices: 119525--119557 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
119515 AAAAAATTTT
119525 AAAAAAAGAA
1 AAAAAAAGAA
119535 AAAAAAAGAA
1 AAAAAAAGAA
*
119545 AGAAAAAGAA
1 AAAAAAAGAA
119555 AAA
1 AAA
119558 GGCCGAACCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:119546 original size:14 final size:14
Alignment explanation
Indices: 119525--119557 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
119515 AAAAAATTTT
119525 AAAAAAAGAAAAA-
1 AAAAAAAGAAAAAG
119538 AAAAGAAAGAAAAAG
1 AAAA-AAAGAAAAAG
119553 AAAAA
1 AAAAA
119558 GGCCGAACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 10 0.56
15 4 0.22
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:119703 original size:26 final size:26
Alignment explanation
Indices: 119674--119741 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
119664 TACTTAGTTT
119674 ATTAGTTTATGTTTAATTAATATCTA
1 ATTAGTTTATGTTTAATTAATATCTA
* *
119700 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAATATCTA
*
119726 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
119742 AATTAAGGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 1 0.03
26 36 0.97
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAATATCTA
Found at i:119718 original size:15 final size:15
Alignment explanation
Indices: 119698--119741 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
119688 AATTAATATC
119698 TAATTAGTTTATTAT
1 TAATTAGTTTATTAT
119713 TAATTAG--TA-T-T
1 TAATTAGTTTATTAT
*
119724 TAATTAGTTTATGAT
1 TAATTAGTTTATTAT
119739 TAA
1 TAA
119742 AATTAAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
11 8 0.33
12 1 0.04
13 4 0.17
15 11 0.46
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (15 bp):
TAATTAGTTTATTAT
Found at i:119789 original size:24 final size:25
Alignment explanation
Indices: 119750--119809 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
119740 AAAATTAAGG
*
119750 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
119773 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
*
119798 GAAATGAAGTTT
1 AAAATGAAGTTT
119810 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 8 0.24
24 7 0.21
25 18 0.55
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:119921 original size:21 final size:21
Alignment explanation
Indices: 119880--119923 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
119870 GCAAAAGTGT
**
119880 AAAAAGGGGGCGGTATTTAGC
1 AAAAAGGGGGCGGTAAATAGC
*
119901 AAAAGGGGGGCGGTAAATAGC
1 AAAAAGGGGGCGGTAAATAGC
119922 AA
1 AA
119924 TCCAGTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.09, G:0.39, T:0.14
Consensus pattern (21 bp):
AAAAAGGGGGCGGTAAATAGC
Found at i:133469 original size:39 final size:40
Alignment explanation
Indices: 133390--133485 Score: 176
Period size: 39 Copynumber: 2.4 Consensus size: 40
133380 AAAAAAAAGT
133390 AATTGTGTCTGAATTTAGACAAGTTTTGAGTTTATGATTAG
1 AATTGTGTCTGAATTTAGACAAG-TTTGAGTTTATGATTAG
133431 AATTGTGTCTGAATTTAGACAAG-TTGAGTTTATGATTAG
1 AATTGTGTCTGAATTTAGACAAGTTTGAGTTTATGATTAG
133470 AATTGTGTCTGAATTT
1 AATTGTGTCTGAATTT
133486 TGATTTCCGT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
39 32 0.58
41 23 0.42
ACGTcount: A:0.29, C:0.05, G:0.22, T:0.44
Consensus pattern (40 bp):
AATTGTGTCTGAATTTAGACAAGTTTGAGTTTATGATTAG
Found at i:148591 original size:2 final size:2
Alignment explanation
Indices: 148582--148634 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
148572 TTGGTCAGAC
* * *
148582 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TG CA -A CA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
148621 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
148635 CACACACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:148648 original size:28 final size:28
Alignment explanation
Indices: 148586--148648 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
148576 TCAGACTATA
* **
148586 ATATATATATATATATATATATATGCAAC
1 ATAT-TATATATATATATATACACACAAC
148615 ATATTATATATATATATATACACACACAC
1 ATATTATATATATATATATACACACA-AC
148644 A-ATTA
1 ATATTA
148649 GAGCTGACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 23 0.77
29 7 0.23
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (28 bp):
ATATTATATATATATATATACACACAAC
Found at i:157398 original size:30 final size:29
Alignment explanation
Indices: 157336--157405 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
157326 ACCAAACCGT
****
157336 CAAATAAGCCCCTGAACTATTATTTCGGC
1 CAAATAAGCCCCTGAACTATTAAAAAGGC
*
157365 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
1 CAAATAAGCCCCTGAACTATT-AAAAAGGC
157395 CAAATAAGCCC
1 CAAATAAGCCC
157406 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAGGC
Found at i:167233 original size:5 final size:5
Alignment explanation
Indices: 167223--167248 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
167213 TAGACTATAG
167223 TTTAA TTTAA TTTAA TTTAA TTTAA T
1 TTTAA TTTAA TTTAA TTTAA TTTAA T
167249 GATGATGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:170095 original size:2 final size:2
Alignment explanation
Indices: 170088--170113 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
170078 ACTTATTTAA
170088 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
170114 GCTTTTAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.