Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016039.1 Corchorus capsularis cultivar CVL-1 contig16060, 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: 73748
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Found at i:292 original size:1 final size:1
Alignment explanation
Indices: 286--311 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
276 ACTGATGTCC
286 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
312 AATTATCTAG
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:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:966 original size:15 final size:15
Alignment explanation
Indices: 943--976 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
933 GAGAGTGAAA
* *
943 ATGGGGAAGCTCTTG
1 ATGGAGAAGCACTTG
958 ATGGAGAAGCACTTG
1 ATGGAGAAGCACTTG
973 ATGG
1 ATGG
977 GGTCAGTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.12, G:0.38, T:0.24
Consensus pattern (15 bp):
ATGGAGAAGCACTTG
Found at i:4320 original size:57 final size:57
Alignment explanation
Indices: 4232--4343 Score: 215
Period size: 57 Copynumber: 2.0 Consensus size: 57
4222 TATGAGTTAT
*
4232 GAGCAAATCAAAGCAGTACTTTTGGATTCAGCCGGCTTCCATGGTATAATGTGACCG
1 GAGCAAATCAAAGCAGTACTTTTGGATTCAGCCGCCTTCCATGGTATAATGTGACCG
4289 GAGCAAATCAAAGCAGTACTTTTGGATTCAGCCGCCTTCCATGGTATAATGTGAC
1 GAGCAAATCAAAGCAGTACTTTTGGATTCAGCCGCCTTCCATGGTATAATGTGAC
4344 TCAACAGCTG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (57 bp):
GAGCAAATCAAAGCAGTACTTTTGGATTCAGCCGCCTTCCATGGTATAATGTGACCG
Found at i:4412 original size:155 final size:155
Alignment explanation
Indices: 4130--4546 Score: 789
Period size: 155 Copynumber: 2.7 Consensus size: 155
4120 AAGATGTATT
* *
4130 ACCGGAGCAAATCAAAGCAGTATTTTTAGATTCAGCCGGCTTCCATGGTATAATGTGACTCAACA
1 ACCGGAGCAAATCAAAGCAGTACTTTTGGATTCAGCCGGCTTCCATGGTATAATGTGACTCAACA
4195 GCTGATCTATATGCAAATGAACCATCTTATGAGTTATGAGCAAATCAAAGCAGTACTTTTGGATT
66 GCTGATCTATATGCAAATGAACCATCTTATGAGTTATGAGCAAATCAAAGCAGTACTTTTGGATT
4260 CAGCCGGCTTCCATGGTATAATGTG
131 CAGCCGGCTTCCATGGTATAATGTG
*
4285 ACCGGAGCAAATCAAAGCAGTACTTTTGGATTCAGCCGCCTTCCATGGTATAATGTGACTCAACA
1 ACCGGAGCAAATCAAAGCAGTACTTTTGGATTCAGCCGGCTTCCATGGTATAATGTGACTCAACA
*
4350 GCTGATCTATATGCAAATGAACCATCTTATGAGTTATGAGCAAATCAAAGCAGTGCTTTTGGATT
66 GCTGATCTATATGCAAATGAACCATCTTATGAGTTATGAGCAAATCAAAGCAGTACTTTTGGATT
4415 CAGCCGGCTTCCATGGTATAATGTG
131 CAGCCGGCTTCCATGGTATAATGTG
*
4440 ACCGGAGCAAATCAAAGCAGTACTTTTGGATTCAGCCGGGTTCCATGGTATAATGTGACTCAACA
1 ACCGGAGCAAATCAAAGCAGTACTTTTGGATTCAGCCGGCTTCCATGGTATAATGTGACTCAACA
4505 GCTGATCTATATGCAAATGAACCATCTTATGAGTTATGAGCA
66 GCTGATCTATATGCAAATGAACCATCTTATGAGTTATGAGCA
4547 GAGGCACTGA
Statistics
Matches: 256, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
155 256 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (155 bp):
ACCGGAGCAAATCAAAGCAGTACTTTTGGATTCAGCCGGCTTCCATGGTATAATGTGACTCAACA
GCTGATCTATATGCAAATGAACCATCTTATGAGTTATGAGCAAATCAAAGCAGTACTTTTGGATT
CAGCCGGCTTCCATGGTATAATGTG
Found at i:4475 original size:57 final size:57
Alignment explanation
Indices: 4387--4498 Score: 206
Period size: 57 Copynumber: 2.0 Consensus size: 57
4377 TATGAGTTAT
*
4387 GAGCAAATCAAAGCAGTGCTTTTGGATTCAGCCGGCTTCCATGGTATAATGTGACCG
1 GAGCAAATCAAAGCAGTACTTTTGGATTCAGCCGGCTTCCATGGTATAATGTGACCG
*
4444 GAGCAAATCAAAGCAGTACTTTTGGATTCAGCCGGGTTCCATGGTATAATGTGAC
1 GAGCAAATCAAAGCAGTACTTTTGGATTCAGCCGGCTTCCATGGTATAATGTGAC
4499 TCAACAGCTG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (57 bp):
GAGCAAATCAAAGCAGTACTTTTGGATTCAGCCGGCTTCCATGGTATAATGTGACCG
Found at i:5044 original size:24 final size:24
Alignment explanation
Indices: 5012--5060 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
5002 ATCGGGACAA
* *
5012 AGAGTTTGGGTCTTGATGGTCATG
1 AGAGTTTGGGTCCTGATAGTCATG
5036 AGAGTTTGGGTCCTGATAGTCATG
1 AGAGTTTGGGTCCTGATAGTCATG
5060 A
1 A
5061 TATTCCATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.20, C:0.10, G:0.35, T:0.35
Consensus pattern (24 bp):
AGAGTTTGGGTCCTGATAGTCATG
Found at i:9506 original size:33 final size:33
Alignment explanation
Indices: 9450--9541 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 33
9440 TTTGGATTCT
* *
9450 ATTGTTCCCACTAATATTATGCCTCAGAATGAG
1 ATTGCTCCCACTAATATTGTGCCTCAGAATGAG
* * * *
9483 ATTGCTGCCACTGATGTTGTGCCTCGGAATGAG
1 ATTGCTCCCACTAATATTGTGCCTCAGAATGAG
9516 ATTGCTCCCACTAATATTGTGCCTCA
1 ATTGCTCCCACTAATATTGTGCCTCA
9542 ACGAACACAC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (33 bp):
ATTGCTCCCACTAATATTGTGCCTCAGAATGAG
Found at i:11837 original size:40 final size:41
Alignment explanation
Indices: 11759--11842 Score: 116
Period size: 40 Copynumber: 2.0 Consensus size: 41
11749 GTCATGAAAA
* *
11759 GAGTGCATGGTTGGAGTATACAGAGTACATCAATAATACTTTTT
1 GAGTGCATGGTTGGAGGAT--A-AGTACAACAATAATACTTTTT
11803 GAGTGCATGGTTGGAGGAT-AGTACAACAATAATACTTTTT
1 GAGTGCATGGTTGGAGGATAAGTACAACAATAATACTTTTT
11843 ATGTAATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 20 0.53
44 18 0.47
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (41 bp):
GAGTGCATGGTTGGAGGATAAGTACAACAATAATACTTTTT
Found at i:16462 original size:32 final size:32
Alignment explanation
Indices: 16418--16646 Score: 168
Period size: 32 Copynumber: 7.7 Consensus size: 32
16408 GGGACTTATG
16418 AATGCCCATGTGTTT-GAGGACTTTTTGATAGA
1 AATGCCCATGTGTTTAG-GGACTTTTTGATAGA
16450 AATGCCTC-TGTGTTTAGGGAC---TT-AT-G-
1 AATGCC-CATGTGTTTAGGGACTTTTTGATAGA
16476 AATGCCCATGTGTTT-GAGGACTTTTTGATAGA
1 AATGCCCATGTGTTTAG-GGACTTTTTGATAGA
*
16508 GATGCCTC-TGTGTTTAGGGAC---TT-AT-G-
1 AATGCC-CATGTGTTTAGGGACTTTTTGATAGA
16534 AATGCCCATGTGTTT-GAGGACTTTTTGATAGA
1 AATGCCCATGTGTTTAG-GGACTTTTTGATAGA
*
16566 AATACCTC-TGTGTTTAGGGAC---TT-AT--A
1 AATGCC-CATGTGTTTAGGGACTTTTTGATAGA
* *
16592 AATACCCGTGTGTTT-GAGGACTTTTTGATAGA
1 AATGCCCATGTGTTTAG-GGACTTTTTGATAGA
16624 AATGCCTC-TGTGTTTAGGGACTT
1 AATGCC-CATGTGTTTAGGGACTT
16647 ATGAATGCCC
Statistics
Matches: 161, Mismatches: 4, Indels: 64
0.70 0.02 0.28
Matches are distributed among these distances:
25 6 0.04
26 51 0.32
27 2 0.01
28 6 0.04
29 12 0.07
30 6 0.04
31 2 0.01
32 68 0.42
33 8 0.05
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (32 bp):
AATGCCCATGTGTTTAGGGACTTTTTGATAGA
Found at i:16468 original size:58 final size:58
Alignment explanation
Indices: 16338--16674 Score: 538
Period size: 58 Copynumber: 5.8 Consensus size: 58
16328 TAAGAAAAAT
* ** *
16338 TGCCTCTGTGTTTAGGGAGTTATGAATTGCCGTTGTGTTTGAGGAC-TTTTG--AGAGA
1 TGCCTCTGTGTTTAGGGACTTATGAA-TGCCCATGTGTTTGAGGACTTTTTGATAGAAA
*
16394 TGCCTCTGTATTTAGGGACTTATGAATGCCCATGTGTTTGAGGACTTTTTGATAGAAA
1 TGCCTCTGTGTTTAGGGACTTATGAATGCCCATGTGTTTGAGGACTTTTTGATAGAAA
*
16452 TGCCTCTGTGTTTAGGGACTTATGAATGCCCATGTGTTTGAGGACTTTTTGATAGAGA
1 TGCCTCTGTGTTTAGGGACTTATGAATGCCCATGTGTTTGAGGACTTTTTGATAGAAA
16510 TGCCTCTGTGTTTAGGGACTTATGAATGCCCATGTGTTTGAGGACTTTTTGATAGAAA
1 TGCCTCTGTGTTTAGGGACTTATGAATGCCCATGTGTTTGAGGACTTTTTGATAGAAA
* * * *
16568 TACCTCTGTGTTTAGGGACTTATAAATACCCGTGTGTTTGAGGACTTTTTGATAGAAA
1 TGCCTCTGTGTTTAGGGACTTATGAATGCCCATGTGTTTGAGGACTTTTTGATAGAAA
16626 TGCCTCTGTGTTTAGGGACTTATGAATGCCC-TGGTGTTTGAGGACTTTT
1 TGCCTCTGTGTTTAGGGACTTATGAATGCCCAT-GTGTTTGAGGACTTTT
16675 AATTATTGGG
Statistics
Matches: 262, Mismatches: 15, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
55 17 0.06
56 29 0.11
57 1 0.00
58 215 0.82
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.39
Consensus pattern (58 bp):
TGCCTCTGTGTTTAGGGACTTATGAATGCCCATGTGTTTGAGGACTTTTTGATAGAAA
Found at i:24895 original size:16 final size:15
Alignment explanation
Indices: 24874--24907 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
24864 TAGAATTTGA
24874 TGGATATTTGAGTATT
1 TGGATATTTG-GTATT
24890 TGGATATTTGGTATT
1 TGGATATTTGGTATT
24905 TGG
1 TGG
24908 GTATGTAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (15 bp):
TGGATATTTGGTATT
Found at i:27317 original size:21 final size:20
Alignment explanation
Indices: 27288--27344 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
27278 TAGAGTTAGA
* *
27288 TTTAATTTACTTTGCTTTGTT
1 TTTAATTTA-ATTGCTTTCTT
*
27309 TTTAGTTTAATTGCTTTCTT
1 TTTAATTTAATTGCTTTCTT
*
27329 TTTAA-TTAATTTCTTT
1 TTTAATTTAATTGCTTT
27345 AATCCCCTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 10 0.32
20 13 0.42
21 8 0.26
ACGTcount: A:0.18, C:0.09, G:0.07, T:0.67
Consensus pattern (20 bp):
TTTAATTTAATTGCTTTCTT
Found at i:34514 original size:58 final size:58
Alignment explanation
Indices: 34424--34546 Score: 185
Period size: 58 Copynumber: 2.1 Consensus size: 58
34414 AGAAGAAGGA
*
34424 AACTTTTTGATAGAAATACCTTTGTGTTTAGGGACTTATAAATACCCAT-GTGTTTGAG
1 AACTTTTTGATAGAAATACCTCTGTGTTTAGGGACTTATAAATACCC-TGGTGTTTGAG
* * *
34482 AACTTTTTGATAGAAATGCCTCTGTGTTTAGGGACTTATGAATGCCCTGGTGTTTGAG
1 AACTTTTTGATAGAAATACCTCTGTGTTTAGGGACTTATAAATACCCTGGTGTTTGAG
*
34540 GACTTTT
1 AACTTTT
34547 AATTATTGGG
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 1 0.02
58 58 0.98
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (58 bp):
AACTTTTTGATAGAAATACCTCTGTGTTTAGGGACTTATAAATACCCTGGTGTTTGAG
Found at i:39238 original size:202 final size:203
Alignment explanation
Indices: 38883--39256 Score: 624
Period size: 202 Copynumber: 1.8 Consensus size: 203
38873 GCCACACTTG
* * * * * *
38883 TCACCTCTGATGGCCACTTAGAAAAGTCAGTTATTTATGTAATAATCCTCGATATTTGAACTTTA
1 TCACCCCTAATGGCCACCTAGAAAAGTCAGTTATTTATGCAATAATCCTCGACATTTAAACTTTA
* *
38948 TGCTTTTATGTCCCCATTATATTTCTTATAAGTCCTTCAACTTAATCTATTTTACATTAAAGACC
66 TGCTTTTAAGTCCCCATTATAATTCTTATAAGTCCTTCAACTTAATCTATTTTACATTAAAGACC
39013 TCAAACATTTATCCTTTATGCAATTTAATCCTCAAA-CTTTTATTCTTTAAATTGGGGGTTGACA
131 TCAAACATTTATCCTTTATGCAATTTAATCCTCAAACCTTTTATTCTTTAAATTGGGGGTTGACA
39077 CTTGTCAC
196 CTTGTCAC
**
39085 TCACCCCTAATGGCCACCTAGAAAAGTGGGTTATTTATGCAATAATCCTCGACATTTAAACTTTA
1 TCACCCCTAATGGCCACCTAGAAAAGTCAGTTATTTATGCAATAATCCTCGACATTTAAACTTTA
*
39150 TGCTTTTAAGTCTCCATTATAATTCTTATAAGTCCTTCAACTTAATCTATTTTACATTAAAGACC
66 TGCTTTTAAGTCCCCATTATAATTCTTATAAGTCCTTCAACTTAATCTATTTTACATTAAAGACC
* *
39215 TCAAACATTTTTCTTTTATGCAATTTAATCCTCAAACCTTTT
131 TCAAACATTTATCCTTTATGCAATTTAATCCTCAAACCTTTT
39257 GTTTTATACA
Statistics
Matches: 158, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
202 153 0.97
203 5 0.03
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (203 bp):
TCACCCCTAATGGCCACCTAGAAAAGTCAGTTATTTATGCAATAATCCTCGACATTTAAACTTTA
TGCTTTTAAGTCCCCATTATAATTCTTATAAGTCCTTCAACTTAATCTATTTTACATTAAAGACC
TCAAACATTTATCCTTTATGCAATTTAATCCTCAAACCTTTTATTCTTTAAATTGGGGGTTGACA
CTTGTCAC
Found at i:41640 original size:23 final size:23
Alignment explanation
Indices: 41614--41672 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
41604 TCTTTCATAT
41614 ATTTAGATTTCTTTTATA-TATTG
1 ATTTAGATTTCTTTTATACT-TTG
*
41637 ATTTAGATTTCCTTTATACTTTG
1 ATTTAGATTTCTTTTATACTTTG
* *
41660 TTTTAGTTTTCTT
1 ATTTAGATTTCTT
41673 AATTAGCTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 30 0.97
24 1 0.03
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.63
Consensus pattern (23 bp):
ATTTAGATTTCTTTTATACTTTG
Found at i:49616 original size:17 final size:16
Alignment explanation
Indices: 49589--49634 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
49579 CTTACCTTTA
49589 TCTTTTTATTTTTCGT
1 TCTTTTTATTTTTCGT
49605 TCTTTTTAATTTTTCGT
1 TCTTTTT-ATTTTTCGT
* *
49622 TATTTTTCTTTTT
1 TCTTTTTATTTTT
49635 TATTTTTCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.09, C:0.11, G:0.04, T:0.76
Consensus pattern (16 bp):
TCTTTTTATTTTTCGT
Found at i:60281 original size:16 final size:16
Alignment explanation
Indices: 60262--60301 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
60252 AAAAATCTGA
*
60262 AACCCGATAAAACCCG
1 AACCCGAAAAAACCCG
60278 AACCCGAAAAAACCCG
1 AACCCGAAAAAACCCG
60294 AACCCGAA
1 AACCCGAA
60302 CTTGAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.47, C:0.38, G:0.12, T:0.03
Consensus pattern (16 bp):
AACCCGAAAAAACCCG
Found at i:60537 original size:32 final size:31
Alignment explanation
Indices: 60501--60608 Score: 144
Period size: 32 Copynumber: 3.4 Consensus size: 31
60491 CCAACTCGAG
*
60501 CCCGAACCCGAATTAACCTGACCCAAAATTTA
1 CCCGAACCCGAATCAACCTGACCC-AAATTTA
*
60533 CCCGAACCTGAATCAACCTGACCCAAATTTAA
1 CCCGAACCCGAATCAACCTGACCCAAATTT-A
* * *
60565 TCCGAACCCGAATCAACCCGACCCAAATATAA
1 CCCGAACCCGAATCAACCTGACCCAAAT-TTA
60597 CCCGAACCCGAA
1 CCCGAACCCGAA
60609 AACGGCCTGA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
31 6 0.09
32 60 0.90
33 1 0.01
ACGTcount: A:0.38, C:0.37, G:0.10, T:0.15
Consensus pattern (31 bp):
CCCGAACCCGAATCAACCTGACCCAAATTTA
Found at i:60598 original size:16 final size:15
Alignment explanation
Indices: 60501--60601 Score: 58
Period size: 16 Copynumber: 6.3 Consensus size: 15
60491 CCAACTCGAG
*
60501 CCCGAACCCGAATTAA
1 CCCG-ACCCAAATTAA
* *
60517 CCTGACCCAAAATTTA
1 CCCGACCC-AAATTAA
** *
60533 CCCGAACCTGAATCAA
1 CCCG-ACCCAAATTAA
*
60549 CCTGACCCAAATTTAA
1 CCCGACCCAAA-TTAA
* * *
60565 TCCGAACCCGAATCAA
1 CCCG-ACCCAAATTAA
60581 CCCGACCCAAATATAA
1 CCCGACCCAAAT-TAA
60597 CCCGA
1 CCCGA
60602 ACCCGAAAAC
Statistics
Matches: 61, Mismatches: 19, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
15 16 0.26
16 36 0.59
17 9 0.15
ACGTcount: A:0.38, C:0.37, G:0.10, T:0.16
Consensus pattern (15 bp):
CCCGACCCAAATTAA
Found at i:63896 original size:11 final size:11
Alignment explanation
Indices: 63880--63921 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
63870 TGATCTTCAA
63880 ATCTTCAAATT
1 ATCTTCAAATT
*
63891 ATCTTCAAGA-A
1 ATCTTCAA-ATT
63902 ATCTTCAAATT
1 ATCTTCAAATT
63913 ATCTTCAAA
1 ATCTTCAAA
63922 CACGAACTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 1 0.04
11 25 0.93
12 1 0.04
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (11 bp):
ATCTTCAAATT
Found at i:63896 original size:19 final size:19
Alignment explanation
Indices: 63863--63921 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 19
63853 TTGAAATAAT
*
63863 TCTTC-AATGATCTTCAAA
1 TCTTCAAATTATCTTCAAA
63881 TCTTCAAATTATCTTCAAGAAA
1 TCTTCAAATTATCTTC---AAA
63903 TCTTCAAATTATCTTCAAA
1 TCTTCAAATTATCTTCAAA
63922 CACGAACTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 5 0.14
19 12 0.33
22 19 0.53
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.39
Consensus pattern (19 bp):
TCTTCAAATTATCTTCAAA
Found at i:63906 original size:22 final size:22
Alignment explanation
Indices: 63878--63920 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
63868 AATGATCTTC
63878 AAATCTTCAAATTATCTTCAAG
1 AAATCTTCAAATTATCTTCAAG
63900 AAATCTTCAAATTATCTTCAA
1 AAATCTTCAAATTATCTTCAA
63921 ACACGAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (22 bp):
AAATCTTCAAATTATCTTCAAG
Found at i:64693 original size:24 final size:24
Alignment explanation
Indices: 64646--64693 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
64636 TTATTAAAAT
* * * *
64646 ATATATTAATTCATAAATATATAA
1 ATATATAAATTAATAAAAAAATAA
64670 ATATATAAATTAATAAAAAAATAA
1 ATATATAAATTAATAAAAAAATAA
64694 GAAAATTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
ATATATAAATTAATAAAAAAATAA
Found at i:64989 original size:23 final size:23
Alignment explanation
Indices: 64963--65021 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
64953 TCTTTCATAT
64963 ATTTAGATTTCTTTTATA-TATTG
1 ATTTAGATTTCTTTTATACT-TTG
*
64986 ATTTAGATTTCCTTTATACTTTG
1 ATTTAGATTTCTTTTATACTTTG
* *
65009 TTTTAGTTTTCTT
1 ATTTAGATTTCTT
65022 AATTAGCTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 30 0.97
24 1 0.03
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.63
Consensus pattern (23 bp):
ATTTAGATTTCTTTTATACTTTG
Found at i:70710 original size:12 final size:12
Alignment explanation
Indices: 70693--70717 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
70683 ACATCTATCC
70693 TTTTCTTTTTAA
1 TTTTCTTTTTAA
70705 TTTTCTTTTTAA
1 TTTTCTTTTTAA
70717 T
1 T
70718 AGTTATAGGT
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:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTTAA
Done.