Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022440.1 Corchorus olitorius cultivar O-4 contig22473, 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: 148018
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:437 original size:25 final size:24
Alignment explanation
Indices: 394--450 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
384 GTCAGCCTTG
*
394 AATTT-TTTAATATTTAATTCTTA
1 AATTTATTTAATATTTAATTATTA
* *
417 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATAT-TTAATTATTA
442 AATTTATTT
1 AATTTATTT
451 TACAATCCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.17
24 7 0.24
25 17 0.59
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (24 bp):
AATTTATTTAATATTTAATTATTA
Found at i:5026 original size:22 final size:23
Alignment explanation
Indices: 4998--5045 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
4988 GTAATTTTTG
* *
4998 AGAGAGTGAAGGAAGAAG-AAGA
1 AGAGAGTAAAAGAAGAAGAAAGA
*
5020 AGAGAGTAAAAGAGGAAGAAAGA
1 AGAGAGTAAAAGAAGAAGAAAGA
5043 AGA
1 AGA
5046 AGAAATTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.58, C:0.00, G:0.38, T:0.04
Consensus pattern (23 bp):
AGAGAGTAAAAGAAGAAGAAAGA
Found at i:5943 original size:46 final size:43
Alignment explanation
Indices: 5891--6019 Score: 114
Period size: 46 Copynumber: 3.1 Consensus size: 43
5881 GGGTGAAGTA
5891 ATAATATGAGTTTGAGGCTTGTAAATAGTGAAAAATATGTTTCGAG
1 ATAATATGAGTTTGAGGC-TGTAAATAGT-AAAAATAT-TTTCGAG
* *
5937 ATAATAT--GTTT-A----ATAAATAGT-AATATATTTT-GAG
1 ATAATATGAGTTTGAGGCTGTAAATAGTAAAAATATTTTCGAG
*
5971 ATAATATGAGTTCGAGGCTCGTAAATAGTAAAACATATATTTCGAG
1 ATAATATGAGTTTGAGGCT-GTAAATAGTAAAA-ATAT-TTTCGAG
6017 ATA
1 ATA
6020 GTTTTCTCCT
Statistics
Matches: 66, Mismatches: 5, Indels: 24
0.69 0.05 0.25
Matches are distributed among these distances:
34 10 0.15
35 3 0.05
36 9 0.14
37 1 0.02
38 8 0.12
42 8 0.12
43 3 0.05
44 8 0.12
45 3 0.05
46 13 0.20
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (43 bp):
ATAATATGAGTTTGAGGCTGTAAATAGTAAAAATATTTTCGAG
Found at i:8643 original size:13 final size:13
Alignment explanation
Indices: 8625--8655 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
8615 TATGGCAATT
*
8625 ATATAATTATATA
1 ATATAACTATATA
8638 ATATAACTATATA
1 ATATAACTATATA
8651 ATATA
1 ATATA
8656 TAGATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATAACTATATA
Found at i:8656 original size:15 final size:14
Alignment explanation
Indices: 8624--8683 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 14
8614 CTATGGCAAT
8624 TATATAATTATATAA
1 TATATAA-TATATAA
*
8639 TATA-ACTATATAA
1 TATATAATATATAA
*
8652 TATATAGATATATAT
1 TATATA-ATATATAA
8667 TATTATAATATAGTAA
1 TA-TATAATATA-TAA
8683 T
1 T
8684 CTCAAATTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
13 11 0.30
14 2 0.05
15 17 0.46
16 7 0.19
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (14 bp):
TATATAATATATAA
Found at i:10558 original size:47 final size:46
Alignment explanation
Indices: 10472--10564 Score: 141
Period size: 47 Copynumber: 2.0 Consensus size: 46
10462 TTACAAGTTC
* **
10472 GTCAAGTTCTGAGTTTTTTTTTTTTTTTGGTAATCGTCGAGTTTGA
1 GTCAAGTACTGAGTTTTTTTTTTTTTTTAATAATCGTCGAGTTTGA
*
10518 GTCAAGTACTGTAGTTTTTTTTTTTTTTTAATAATTGTCGAGTTTGA
1 GTCAAGTACTG-AGTTTTTTTTTTTTTTTAATAATCGTCGAGTTTGA
10565 ATTCAGTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 10 0.24
47 32 0.76
ACGTcount: A:0.18, C:0.08, G:0.19, T:0.55
Consensus pattern (46 bp):
GTCAAGTACTGAGTTTTTTTTTTTTTTTAATAATCGTCGAGTTTGA
Found at i:11911 original size:11 final size:11
Alignment explanation
Indices: 11895--11925 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
11885 TAGTACAACA
11895 AAAACAAAACG
1 AAAACAAAACG
11906 AAAACAAAACG
1 AAAACAAAACG
11917 AAAACAAAA
1 AAAACAAAA
11926 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.16, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAACAAAACG
Found at i:11941 original size:6 final size:6
Alignment explanation
Indices: 11895--11944 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
11885 TAGTACAACA
*
11895 AAAAC- AAAACG AAAAC- AAAACG AAAACAA AAAACAG AAAAACG AAAACG
1 AAAACG AAAACG AAAACG AAAACG AAAAC-G AAAAC-G -AAAACG AAAACG
11944 A
1 A
11945 TGCCAAACGA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 10 0.26
6 17 0.44
7 7 0.18
8 5 0.13
ACGTcount: A:0.74, C:0.16, G:0.10, T:0.00
Consensus pattern (6 bp):
AAAACG
Found at i:13976 original size:14 final size:13
Alignment explanation
Indices: 13945--13990 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
13935 GTCGGGTTTT
13945 AGTCAGTTTGTTG
1 AGTCAGTTTGTTG
*
13958 AGTCAGTTTTTTCG
1 AGTCAGTTTGTT-G
13972 AGTCAGTTAGTGTTG
1 AGTCAGTT--TGTTG
13987 AGTC
1 AGTC
13991 CGAGTCTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.39
14 9 0.32
15 5 0.18
16 3 0.11
ACGTcount: A:0.17, C:0.11, G:0.28, T:0.43
Consensus pattern (13 bp):
AGTCAGTTTGTTG
Found at i:34030 original size:31 final size:31
Alignment explanation
Indices: 33994--34068 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
33984 TTTGTGCACG
33994 TAGCATGCCACGTGTCACTTTTTGGTACACA
1 TAGCATGCCACGTGTCACTTTTTGGTACACA
** *
34025 TAGCATGATACGTGTCACTTTTTGGTACACG
1 TAGCATGCCACGTGTCACTTTTTGGTACACA
* *
34056 TGGCGTGCCACGT
1 TAGCATGCCACGT
34069 CGGACACCGT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (31 bp):
TAGCATGCCACGTGTCACTTTTTGGTACACA
Found at i:35295 original size:11 final size:12
Alignment explanation
Indices: 35268--35296 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
35258 GGATTGATTT
35268 TTTTTACTCATC
1 TTTTTACTCATC
35280 TTTTTACTCATC
1 TTTTTACTCATC
35292 TTTTT
1 TTTTT
35297 CAAATGTAAC
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:0.14, C:0.21, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTTACTCATC
Found at i:36452 original size:12 final size:12
Alignment explanation
Indices: 36435--36459 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36425 AGCTTTTGTT
36435 AAAATTTGAAGA
1 AAAATTTGAAGA
36447 AAAATTTGAAGA
1 AAAATTTGAAGA
36459 A
1 A
36460 CTACCTCGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (12 bp):
AAAATTTGAAGA
Found at i:37538 original size:31 final size:31
Alignment explanation
Indices: 37500--37573 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
37490 GGCTAATTGC
* *
37500 TCAAATAAGGGCCTAATATTTTCAAAAATGT
1 TCAAATAAGGGCCTAATATTATCAAAAATGA
* *
37531 TCAAATAAGGGCCTAATGTTATCGAAAATGA
1 TCAAATAAGGGCCTAATATTATCAAAAATGA
37562 TCAAATAAGGGC
1 TCAAATAAGGGC
37574 TCGATCTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.27
Consensus pattern (31 bp):
TCAAATAAGGGCCTAATATTATCAAAAATGA
Found at i:37744 original size:29 final size:29
Alignment explanation
Indices: 37709--37805 Score: 90
Period size: 29 Copynumber: 3.3 Consensus size: 29
37699 AACGTTAGGT
*
37709 CCTTATTTGGCCAAATTAAAGGATAAGAC
1 CCTTATTTGGCCAAATTAAAAGATAAGAC
** * *
37738 CCTTATTTGAG-CATTTTAGCAAATG-TTAGGC
1 CCTTATTTG-GCCAAATTA--AAA-GATAAGAC
*
37769 CCTTATTTGGCCAAATTAAAAGATCAGAC
1 CCTTATTTGGCCAAATTAAAAGATAAGAC
37798 CCTTATTT
1 CCTTATTT
37806 AGCATTTTAA
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
28 1 0.02
29 29 0.55
30 2 0.04
31 20 0.38
32 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (29 bp):
CCTTATTTGGCCAAATTAAAAGATAAGAC
Found at i:37773 original size:60 final size:60
Alignment explanation
Indices: 37680--37836 Score: 253
Period size: 60 Copynumber: 2.6 Consensus size: 60
37670 TATCAGGCCT
* * * *
37680 TTATTTGAGCATTTTGGCAAACGTTAGGTCCTTATTTGGCCAAATTAAAGGATAAGACCC
1 TTATTTGAGCATTTTAGCAAATGTTAGGCCCTTATTTGGCCAAATTAAAAGATAAGACCC
*
37740 TTATTTGAGCATTTTAGCAAATGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGACCC
1 TTATTTGAGCATTTTAGCAAATGTTAGGCCCTTATTTGGCCAAATTAAAAGATAAGACCC
*
37800 TTATTT-AGCATTTTAACAAATGTTAGGCCCTTATTTG
1 TTATTTGAGCATTTTAGCAAATGTTAGGCCCTTATTTG
37837 AGCAATTAGT
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
59 30 0.33
60 61 0.67
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (60 bp):
TTATTTGAGCATTTTAGCAAATGTTAGGCCCTTATTTGGCCAAATTAAAAGATAAGACCC
Found at i:37775 original size:31 final size:30
Alignment explanation
Indices: 37737--37840 Score: 108
Period size: 31 Copynumber: 3.5 Consensus size: 30
37727 AAGGATAAGA
37737 CCCTTATTTGAGCATTTTAGCAAATGTTAGG
1 CCCTTATTTGAGCATTTTA-CAAATGTTAGG
** * *
37768 CCCTTATTTG-GCCAAATTA-AAA-GATCAGA
1 CCCTTATTTGAG-CATTTTACAAATG-TTAGG
37797 CCCTTATTT-AGCATTTTAACAAATGTTAGG
1 CCCTTATTTGAGCATTTT-ACAAATGTTAGG
37827 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
37841 ATTAGTCCAA
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
28 5 0.09
29 17 0.29
30 16 0.28
31 20 0.34
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTACAAATGTTAGG
Found at i:39891 original size:21 final size:20
Alignment explanation
Indices: 39863--39903 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
39853 CCTAGGGCGG
39863 CATGCGCCCCACGACACAAC
1 CATGCGCCCCACGACACAAC
* *
39883 CATGACGCCTCACGCCACAAC
1 CATG-CGCCCCACGACACAAC
39904 TATGGCATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.29, C:0.49, G:0.15, T:0.07
Consensus pattern (20 bp):
CATGCGCCCCACGACACAAC
Found at i:40385 original size:130 final size:130
Alignment explanation
Indices: 40152--40410 Score: 518
Period size: 130 Copynumber: 2.0 Consensus size: 130
40142 TGGAGAGTCT
40152 TCTTCGAGTGACAGCATTGTTCCTTCAAGTTTTGATGGAAGTGAAGTTTCAAAAAGCGTGCCTTA
1 TCTTCGAGTGACAGCATTGTTCCTTCAAGTTTTGATGGAAGTGAAGTTTCAAAAAGCGTGCCTTA
40217 TTACTGTTGGCAAGGATAGAAGCTGGAGATGTTGATAAAGGAGTATCACTGTCTGATTTTGAGGC
66 TTACTGTTGGCAAGGATAGAAGCTGGAGATGTTGATAAAGGAGTATCACTGTCTGATTTTGAGGC
40282 TCTTCGAGTGACAGCATTGTTCCTTCAAGTTTTGATGGAAGTGAAGTTTCAAAAAGCGTGCCTTA
1 TCTTCGAGTGACAGCATTGTTCCTTCAAGTTTTGATGGAAGTGAAGTTTCAAAAAGCGTGCCTTA
40347 TTACTGTTGGCAAGGATAGAAGCTGGAGATGTTGATAAAGGAGTATCACTGTCTGATTTTGAGG
66 TTACTGTTGGCAAGGATAGAAGCTGGAGATGTTGATAAAGGAGTATCACTGTCTGATTTTGAGG
40411 GTGTATCATT
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 129 1.00
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (130 bp):
TCTTCGAGTGACAGCATTGTTCCTTCAAGTTTTGATGGAAGTGAAGTTTCAAAAAGCGTGCCTTA
TTACTGTTGGCAAGGATAGAAGCTGGAGATGTTGATAAAGGAGTATCACTGTCTGATTTTGAGGC
Found at i:40983 original size:2 final size:2
Alignment explanation
Indices: 40970--41003 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
40960 ATTTTGGACA
* *
40970 AT AT AT AA AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41004 TCATGTATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:41202 original size:19 final size:20
Alignment explanation
Indices: 41171--41209 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
41161 TAATTCAAAA
41171 TGTTTTCAAGTTGTAAGCTC
1 TGTTTTCAAGTTGTAAGCTC
41191 TGTTTT-AAGTTGTAAGCTC
1 TGTTTTCAAGTTGTAAGCTC
41210 ATTGGTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.46
Consensus pattern (20 bp):
TGTTTTCAAGTTGTAAGCTC
Found at i:51717 original size:79 final size:79
Alignment explanation
Indices: 51624--51769 Score: 215
Period size: 79 Copynumber: 1.8 Consensus size: 79
51614 AAAACATGCG
* *
51624 AATTCAAATTCCAAATTAAAAACTTTCACAGA-AATAG-ATATACCATAACTCAGAAACCCTAAT
1 AATTCAAATGCCAAATTAAAAACTTTCACAGACAA-AGAAT-TACCAAAACTCAGAAACCCTAAT
51687 CTAACCAACAAAAAAA
64 CTAACCAACAAAAAAA
* **
51703 AATTCAAATGCCAAATTAAAAACTTTCGCAGACAAAGAATTTGCAAAACTCAGAAACCCTAATCT
1 AATTCAAATGCCAAATTAAAAACTTTCACAGACAAAGAATTACCAAAACTCAGAAACCCTAATCT
51768 AA
66 AA
51770 AAAAAATACA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
79 56 0.93
80 4 0.07
ACGTcount: A:0.51, C:0.21, G:0.06, T:0.22
Consensus pattern (79 bp):
AATTCAAATGCCAAATTAAAAACTTTCACAGACAAAGAATTACCAAAACTCAGAAACCCTAATCT
AACCAACAAAAAAA
Found at i:58603 original size:55 final size:55
Alignment explanation
Indices: 58538--58660 Score: 147
Period size: 58 Copynumber: 2.2 Consensus size: 55
58528 CATGATTGGA
* * * *
58538 TTGTCAAAGTGGATTAATCATCCTACTGGGTATGGGATGACCTAATCCTCCCCAT
1 TTGTCAAAGTGGATTAATCATCATACTAGGTATAGGATGACCTAAACCTCCCCAT
* * * *
58593 TTGTCAAAGTGGTGGATTTATCATCATATTATGTATAGGATGACCTAAACCTCCTCAT
1 TTGTCAAA---GTGGATTAATCATCATACTAGGTATAGGATGACCTAAACCTCCCCAT
58651 TTGTCAAAGT
1 TTGTCAAAGT
58661 CCACCTTAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
55 10 0.18
58 47 0.82
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (55 bp):
TTGTCAAAGTGGATTAATCATCATACTAGGTATAGGATGACCTAAACCTCCCCAT
Found at i:65025 original size:14 final size:13
Alignment explanation
Indices: 64999--65038 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
64989 ACAGATATCA
*
64999 AAAAAAAAAAAAG
1 AAAAAAGAAAAAG
*
65012 AGAAGAAGAAAAAG
1 A-AAAAAGAAAAAG
65026 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
65039 CTAATGAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:80129 original size:18 final size:18
Alignment explanation
Indices: 80098--80134 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
80088 TTGATTGATC
*
80098 AAAGATAAAGCAAGATAA
1 AAAGAAAAAGCAAGATAA
*
80116 AAAGAAAAATCAAGATAA
1 AAAGAAAAAGCAAGATAA
80134 A
1 A
80135 GCAACTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.70, C:0.05, G:0.14, T:0.11
Consensus pattern (18 bp):
AAAGAAAAAGCAAGATAA
Found at i:80398 original size:13 final size:12
Alignment explanation
Indices: 80380--80410 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
80370 CCTTTTCACC
80380 ATTTTTATTTTCT
1 ATTTTTATTTT-T
80393 ATTTTTATTTTT
1 ATTTTTATTTTT
80405 ATTTTT
1 ATTTTT
80411 TGCTCGAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (12 bp):
ATTTTTATTTTT
Found at i:80411 original size:7 final size:6
Alignment explanation
Indices: 80380--80410 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
80370 CCTTTTCACC
80380 ATTTTT ATTTTCT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTT-T ATTTTT ATTTTT ATTTTT
80411 TGCTCGAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:85733 original size:3 final size:3
Alignment explanation
Indices: 85678--85713 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
85668 ATGCAAGTTT
85678 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
85714 TTTCACCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:111027 original size:17 final size:17
Alignment explanation
Indices: 111005--111037 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
110995 TGTTTAAAAT
111005 AAAAAGGAAAGAAGAAG
1 AAAAAGGAAAGAAGAAG
111022 AAAAAGGAAAGAAGAA
1 AAAAAGGAAAGAAGAA
111038 TCAATTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (17 bp):
AAAAAGGAAAGAAGAAG
Found at i:114254 original size:64 final size:63
Alignment explanation
Indices: 114179--114298 Score: 195
Period size: 64 Copynumber: 1.9 Consensus size: 63
114169 GAATTTTGCA
*
114179 CATAATAATACAAAAATCAAACCAGTAGATTATAGAAGCAAGAAACAAATGAAGAAAGAAAAGT
1 CATAATAATACAAAAATCAAACCAATAGATTATAG-AGCAAGAAACAAATGAAGAAAGAAAAGT
* * *
114243 CATAATTATACAAAAGTCAAACCAATAGATTATAGAGCAAGAAACAAGTGAAGAAA
1 CATAATAATACAAAAATCAAACCAATAGATTATAGAGCAAGAAACAAATGAAGAAA
114299 ACGCAAGCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
63 20 0.38
64 32 0.62
ACGTcount: A:0.57, C:0.12, G:0.14, T:0.17
Consensus pattern (63 bp):
CATAATAATACAAAAATCAAACCAATAGATTATAGAGCAAGAAACAAATGAAGAAAGAAAAGT
Found at i:118955 original size:39 final size:40
Alignment explanation
Indices: 118912--118987 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
118902 AGCTCAATCT
118912 TGATAA-GATCTTTCATCAATTCAAATATGGGTAAACGAA
1 TGATAATGATCTTTCATCAATTCAAATATGGGTAAACGAA
*
118951 TGATAATGATCTTTCATCAATTCATATATGGGTAAAC
1 TGATAATGATCTTTCATCAATTCAAATATGGGTAAAC
118988 TTATAAGACA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 6 0.17
40 29 0.83
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (40 bp):
TGATAATGATCTTTCATCAATTCAAATATGGGTAAACGAA
Found at i:130482 original size:29 final size:28
Alignment explanation
Indices: 130450--130520 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 28
130440 GTCAAGAACG
130450 TTTTGCCCCTTGAACTTCAAATCAGGACA
1 TTTTGCCCC-TGAACTTCAAATCAGGACA
130479 TTTTG-CCC--AACTTCAAATCAGGACA
1 TTTTGCCCCTGAACTTCAAATCAGGACA
130504 TTTTGCCCGCTGAACTT
1 TTTTGCCC-CTGAACTT
130521 TCCAAATTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
25 22 0.58
26 2 0.05
27 1 0.03
28 3 0.08
29 10 0.26
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.32
Consensus pattern (28 bp):
TTTTGCCCCTGAACTTCAAATCAGGACA
Found at i:135290 original size:2 final size:2
Alignment explanation
Indices: 135240--135273 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
135230 CTTAAAAAAA
135240 AT AT AT 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
135274 GAAATGTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:136983 original size:17 final size:17
Alignment explanation
Indices: 136937--137003 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
136927 AACCCATGTA
* *
136937 ATCTTTGATCACCGGTG
1 ATCTTAGATCACTGGTG
*
136954 ATCTTGGATCACTGGTG
1 ATCTTAGATCACTGGTG
136971 ATCTTAGATCACTAGTGGTG
1 ATCTTAGATCAC---TGGTG
*
136991 ATCCTAGATCACT
1 ATCTTAGATCACT
137004 AGTGGTGATC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
17 27 0.63
20 16 0.37
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.34
Consensus pattern (17 bp):
ATCTTAGATCACTGGTG
Found at i:136991 original size:20 final size:20
Alignment explanation
Indices: 136950--137013 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
136940 TTTGATCACC
*
136950 GGTGATCTTGGATCAC---T
1 GGTGATCTTAGATCACTAGT
136967 GGTGATCTTAGATCACTAGT
1 GGTGATCTTAGATCACTAGT
*
136987 GGTGATCCTAGATCACTAGT
1 GGTGATCTTAGATCACTAGT
137007 GGTGATC
1 GGTGATC
137014 CTATCCTAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
17 15 0.36
20 27 0.64
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (20 bp):
GGTGATCTTAGATCACTAGT
Found at i:137014 original size:20 final size:20
Alignment explanation
Indices: 136966--137016 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
136956 CTTGGATCAC
*
136966 TGGTGATCTTAGATCACTAG
1 TGGTGATCCTAGATCACTAG
136986 TGGTGATCCTAGATCACTAG
1 TGGTGATCCTAGATCACTAG
137006 TGGTGATCCTA
1 TGGTGATCCTA
137017 TCCTAACCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (20 bp):
TGGTGATCCTAGATCACTAG
Found at i:141854 original size:18 final size:18
Alignment explanation
Indices: 141831--141869 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
141821 TTTTGGAGTT
141831 ATTAATTCATAATAATAA
1 ATTAATTCATAATAATAA
141849 ATTAATTCATAATAATAA
1 ATTAATTCATAATAATAA
141867 ATT
1 ATT
141870 CTTTACAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTAATTCATAATAATAA
Done.