Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013122.1 Corchorus olitorius cultivar O-4 contig13155, 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: 111844
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4497 original size:22 final size:22
Alignment explanation
Indices: 4472--4518 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
4462 TTTTTAGTTG
*
4472 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
4494 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
4516 AGT
1 AGT
4519 TATAAGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:4575 original size:91 final size:92
Alignment explanation
Indices: 4396--4577 Score: 287
Period size: 92 Copynumber: 2.0 Consensus size: 92
4386 GCTTTTTAAT
* *
4396 TAAATTAGTAATATCGTAAAAATAAAATAGGTATAAGATATTAGATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGATATTAGATTTAATTAAATAAAAATAGA
* *
4461 GTTTTTAGTTGAGTAAAACTATAAAAG
66 GTTTTTAATTGACTAAAACTATAAAAG
* *
4488 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTTAATT-AA-AAAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAA-GATATTAGATTTAATTAAATAAAAATAG
4551 AGTTTTTAATTGACTAAAACTATAAAA
65 AGTTTTTAATTGACTAAAACTATAAAA
4578 ATTTAAACAA
Statistics
Matches: 83, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
91 33 0.40
92 34 0.41
93 16 0.19
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (92 bp):
TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGATATTAGATTTAATTAAATAAAAATAGA
GTTTTTAATTGACTAAAACTATAAAAG
Found at i:4648 original size:31 final size:31
Alignment explanation
Indices: 4613--4674 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
4603 ATATTTAAAA
*
4613 AATAAGGGTATAATAGGTGATTCAAAAGTTT
1 AATAAGGGTATAATAGGTAATTCAAAAGTTT
*
4644 AATAAGGGTATAATAGGTAATTTAAAAGTTT
1 AATAAGGGTATAATAGGTAATTCAAAAGTTT
4675 TACAAAACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.34
Consensus pattern (31 bp):
AATAAGGGTATAATAGGTAATTCAAAAGTTT
Found at i:7145 original size:23 final size:23
Alignment explanation
Indices: 7112--7164 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
7102 TGCATCAAGT
*
7112 TCACACACTTAAAGATTACAATGA
1 TCACA-ACTTAAAGATTACAAGGA
7136 TCACAACTTAAAGATTACAAGGA
1 TCACAACTTAAAGATTACAAGGA
7159 TCACAA
1 TCACAA
7165 TATCGAGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.23
Consensus pattern (23 bp):
TCACAACTTAAAGATTACAAGGA
Found at i:8549 original size:26 final size:25
Alignment explanation
Indices: 8519--8567 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
8509 TTTAAAACTT
8519 AATTTAATCAAAATATAATTTTTTAA
1 AATTTAAT-AAAATATAATTTTTTAA
* *
8545 AATTTAATTATATATAATTTTTT
1 AATTTAATAAAATATAATTTTTT
8568 TATAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
AATTTAATAAAATATAATTTTTTAA
Found at i:11688 original size:21 final size:21
Alignment explanation
Indices: 11664--11704 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11654 TCACTAAGTT
11664 CAAATCGGA-CGGTTAAACCGA
1 CAAATC-GACCGGTTAAACCGA
*
11685 CAAATCGACCGGTTCAACCG
1 CAAATCGACCGGTTAAACCG
11705 TAGACAGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.34, C:0.29, G:0.22, T:0.15
Consensus pattern (21 bp):
CAAATCGACCGGTTAAACCGA
Found at i:17011 original size:30 final size:30
Alignment explanation
Indices: 16970--17061 Score: 166
Period size: 30 Copynumber: 3.1 Consensus size: 30
16960 CATTCTTCAC
*
16970 CAGAAAACTCGTCAACACAGCTTGAAATGG
1 CAGAAAGCTCGTCAACACAGCTTGAAATGG
17000 CAGAAAGCTCGTCAACACAGCTTGAAATGG
1 CAGAAAGCTCGTCAACACAGCTTGAAATGG
*
17030 CAGAAAGCTCGTCAACACAACTTGAAATGG
1 CAGAAAGCTCGTCAACACAGCTTGAAATGG
17060 CA
1 CA
17062 TCTCTCAGTA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (30 bp):
CAGAAAGCTCGTCAACACAGCTTGAAATGG
Found at i:17915 original size:97 final size:97
Alignment explanation
Indices: 17749--17943 Score: 372
Period size: 97 Copynumber: 2.0 Consensus size: 97
17739 CTTAGCAACT
17749 TTCTGAAGTCTTATTGTTTTATAAACTCAGTGGCTGATACTTCATTGTTCATCGTTCACAAAGAT
1 TTCTGAAGTCTTATTGTTTTATAAACTCAGTGGCTGATACTTCATTGTTCATCGTTCACAAAGAT
17814 GATTGCTTACTCTACATGCTTGTTTATGTTGA
66 GATTGCTTACTCTACATGCTTGTTTATGTTGA
* *
17846 TTCTGAAGTCTTATTGTTTTATAAACTCAGTGGTTGATACTTCATTGTTCATCTTTCACAAAGAT
1 TTCTGAAGTCTTATTGTTTTATAAACTCAGTGGCTGATACTTCATTGTTCATCGTTCACAAAGAT
17911 GATTGCTTACTCTACATGCTTGTTTATGTTGA
66 GATTGCTTACTCTACATGCTTGTTTATGTTGA
17943 T
1 T
17944 ATAGTTCTTA
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 96 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.45
Consensus pattern (97 bp):
TTCTGAAGTCTTATTGTTTTATAAACTCAGTGGCTGATACTTCATTGTTCATCGTTCACAAAGAT
GATTGCTTACTCTACATGCTTGTTTATGTTGA
Found at i:19655 original size:69 final size:69
Alignment explanation
Indices: 19563--19728 Score: 314
Period size: 69 Copynumber: 2.4 Consensus size: 69
19553 CTATGAGGTT
*
19563 TGATAAGCTATGAGTTTAAAGTTTACAACACCTAATACAAGGATAGTTATCTTTACAATTTAAAC
1 TGATAAGCTAGGAGTTTAAAGTTTACAACACCTAATACAAGGATAGTTATCTTTACAATTTAAAC
19628 AAAC
66 AAAC
*
19632 TGATAAGCTAGGAGTCTAAAGTTTACAACACCTAATACAAGGATAGTTATCTTTACAATTTAAAC
1 TGATAAGCTAGGAGTTTAAAGTTTACAACACCTAATACAAGGATAGTTATCTTTACAATTTAAAC
19697 AAAC
66 AAAC
19701 TGATAAGCTAGGAGTTTAAAGTTTACAA
1 TGATAAGCTAGGAGTTTAAAGTTTACAA
19729 TTTAAACAAT
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 94 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (69 bp):
TGATAAGCTAGGAGTTTAAAGTTTACAACACCTAATACAAGGATAGTTATCTTTACAATTTAAAC
AAAC
Found at i:19758 original size:39 final size:39
Alignment explanation
Indices: 19683--19759 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
19673 GATAGTTATC
*
19683 TTTACAATTTAAACAAACTGATAAGCTAGGAGTTTAAAG
1 TTTACAATTTAAACAAACTGATAAGCTAGGAATTTAAAG
* **
19722 TTTACAATTTAAACAATCTGATAAGCTATTAATTTAAA
1 TTTACAATTTAAACAAACTGATAAGCTAGGAATTTAAA
19760 CTACGAGGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.35
Consensus pattern (39 bp):
TTTACAATTTAAACAAACTGATAAGCTAGGAATTTAAAG
Found at i:26130 original size:30 final size:30
Alignment explanation
Indices: 26051--26311 Score: 378
Period size: 30 Copynumber: 8.6 Consensus size: 30
26041 AATAGTGCAT
* * *
26051 ATGACAACTTCTGGTGTCAATTGAATAAAATT
1 ATGACAACTTCTGGTGTCAATTG--CAAGATC
* **
26083 ATGACATCTTCAAGTGTCAATTGCAAGATC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
*
26113 ATGACAACTTATGGTGTCAATTGCAAGATC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
* *
26143 ATGACAGCTTATGGTGTCAATTGCAAGATC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
* * *
26173 ATGACAGCTTCTGGTGTCATTTGCAAGACC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
*
26203 ATGACAACTTCTGGTGTCAATTGCAAGACC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
26233 ATGACAACTTCTGGTGTCAATTGCAAGATC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
*
26263 ATGACAACTTCTGGTGTCAATTGCAAGACC
1 ATGACAACTTCTGGTGTCAATTGCAAGATC
26293 ATGACAACTTCTGGTGTCA
1 ATGACAACTTCTGGTGTCA
26312 TTTAGAGAGT
Statistics
Matches: 211, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
30 191 0.91
32 20 0.09
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAATTGCAAGATC
Found at i:28238 original size:15 final size:16
Alignment explanation
Indices: 28206--28240 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28196 ATTAAAAATG
*
28206 ATTATTTAAAATATAA
1 ATTATTCAAAATATAA
28222 ATTATTCAAAA-ATAA
1 ATTATTCAAAATATAA
28237 ATTA
1 ATTA
28241 GTATTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTATTCAAAATATAA
Found at i:28665 original size:21 final size:20
Alignment explanation
Indices: 28584--28665 Score: 54
Period size: 18 Copynumber: 4.2 Consensus size: 20
28574 AATTGACCGT
*
28584 TTAT-TAATATATATAA-AA
1 TTATATAATATATATAATTA
28602 TTA-AGT-ATATATAT-ATTA
1 TTATA-TAATATATATAATTA
28620 -TATATAATATA-AT-ATTAGA
1 TTATATAATATATATAATT--A
28639 TATATATAATTATATATAATTA
1 T-TATATAA-TATATATAATTA
28661 TTATA
1 TTATA
28666 CGGTCTAAAC
Statistics
Matches: 51, Mismatches: 1, Indels: 21
0.70 0.01 0.29
Matches are distributed among these distances:
17 9 0.18
18 18 0.35
19 2 0.04
21 11 0.22
22 6 0.12
23 2 0.04
24 3 0.06
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTATATAATATATATAATTA
Found at i:30862 original size:2 final size:2
Alignment explanation
Indices: 30855--30931 Score: 55
Period size: 2 Copynumber: 42.5 Consensus size: 2
30845 CCGTTTATTA
* *
30855 AT AT AT AT A- AT A- AA AT AT AT GT -T AT AT AT AT -T A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
30892 -T AG AT AT AT AT AT AT AT CAT -T AT AT AT A- AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
30931 A
1 A
30932 ATTATTAAAC
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
1 9 0.15
2 50 0.82
3 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:30917 original size:14 final size:12
Alignment explanation
Indices: 30853--30933 Score: 64
Period size: 12 Copynumber: 7.1 Consensus size: 12
30843 GACCGTTTAT
30853 TAATATATATAA
1 TAATATATATAA
* *
30865 TAAAATATAT-G
1 TAATATATATAA
*
30876 TTATATATATTAA
1 TAATATATA-TAA
* *
30889 TATTAGATAT-A
1 TAATATATATAA
*
30900 T-ATATATATCA
1 TAATATATATAA
30911 T--TATATATAA
1 TAATATATATAA
30921 TAATATATATAA
1 TAATATATATAA
30933 T
1 T
30934 TATTAAACCG
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
10 15 0.28
11 11 0.21
12 21 0.40
13 6 0.11
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (12 bp):
TAATATATATAA
Found at i:35697 original size:45 final size:42
Alignment explanation
Indices: 35647--35738 Score: 123
Period size: 45 Copynumber: 2.1 Consensus size: 42
35637 CAACAATTAT
* *
35647 TATTAGCTTTATTTTGATAAATTATCTAGAGATAGAGGAGTAGAA
1 TATTAGCTTCATTTTGATAAATTACCTAGAGAT---GGAGTAGAA
*
35692 TATTAGCTTCATTTTGATGAATTACCTAGAGATGGAGTAGAA
1 TATTAGCTTCATTTTGATAAATTACCTAGAGATGGAGTAGAA
35734 T-TTAG
1 TATTAG
35739 GTAATGCACT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 10 0.23
45 30 0.68
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.38
Consensus pattern (42 bp):
TATTAGCTTCATTTTGATAAATTACCTAGAGATGGAGTAGAA
Found at i:44337 original size:25 final size:25
Alignment explanation
Indices: 44303--44373 Score: 133
Period size: 25 Copynumber: 2.8 Consensus size: 25
44293 TTTAATTGTA
44303 TTTGTTGGGGAAAGGGGATTAGCCT
1 TTTGTTGGGGAAAGGGGATTAGCCT
44328 TTTGTTGGGGAAAGGGGATTAGCCT
1 TTTGTTGGGGAAAGGGGATTAGCCT
*
44353 TTTGTTGGGGAAAGGGAATTA
1 TTTGTTGGGGAAAGGGGATTA
44374 ACGTTTCGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.23, C:0.06, G:0.39, T:0.32
Consensus pattern (25 bp):
TTTGTTGGGGAAAGGGGATTAGCCT
Found at i:44734 original size:2 final size:2
Alignment explanation
Indices: 44727--44756 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
44717 CCATGACATC
44727 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
44757 TAAAACTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45004 original size:69 final size:68
Alignment explanation
Indices: 44866--45045 Score: 275
Period size: 65 Copynumber: 2.7 Consensus size: 68
44856 TATATTTTAA
*
44866 ATTGATTGATTGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATGATATTAA
1 ATTGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTACT-AAATGATATTAA
44931 ATTG
65 ATTG
44935 ATTGATTGATTGATTT-AA-ATATCTTGATCCAATTAGAATCAATTAGTACT-AATGATATTAAA
1 ATTGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTACTAAATGATATTAAA
44997 TTG
66 TTG
* *
45000 ATTGATTGATTGATTTG-A-ATA--TTGATCAAATTAAAATCAATTAGTA
1 ATTGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTA
45046 TTAATGTCAT
Statistics
Matches: 107, Mismatches: 3, Indels: 8
0.91 0.03 0.07
Matches are distributed among these distances:
63 23 0.21
65 35 0.33
67 31 0.29
68 2 0.02
69 16 0.15
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (68 bp):
ATTGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTACTAAATGATATTAAA
TTG
Found at i:50952 original size:42 final size:42
Alignment explanation
Indices: 50892--50972 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
50882 CCTCTCTCCA
* * *
50892 TTTGCACAAATGAAAGGAGGGTATGAACTAATTAACATTACT
1 TTTGCACAAACGAAAGGAGGGCACGAACTAATTAACATTACT
* *
50934 TTTGCACACACGAGAGGAGGGCACGAACTAATTAACATT
1 TTTGCACAAACGAAAGGAGGGCACGAACTAATTAACATT
50973 TAATTACATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (42 bp):
TTTGCACAAACGAAAGGAGGGCACGAACTAATTAACATTACT
Found at i:52739 original size:28 final size:28
Alignment explanation
Indices: 52685--52739 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
52675 CCATATAAGT
*****
52685 ATATTTCCTTTTATTCATTTTTTTATAG
1 ATATTTCCTTTTATTCATAAGGATATAG
52713 ATATTTCCTTTTATTCATAAGGATATA
1 ATATTTCCTTTTATTCATAAGGATATA
52740 CACCATGTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.27, C:0.11, G:0.05, T:0.56
Consensus pattern (28 bp):
ATATTTCCTTTTATTCATAAGGATATAG
Found at i:58001 original size:16 final size:16
Alignment explanation
Indices: 57977--58012 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
57967 TAGGGAGTAG
*
57977 TATTTAGGAAGGGTAA
1 TATTCAGGAAGGGTAA
57993 TATTCAGGAAGGGTAA
1 TATTCAGGAAGGGTAA
58009 TATT
1 TATT
58013 ATGCTTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (16 bp):
TATTCAGGAAGGGTAA
Found at i:58053 original size:19 final size:19
Alignment explanation
Indices: 58029--58068 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
58019 CTTAGGTGTG
*
58029 TATGTCTCTTAAGTGTATA
1 TATGTCTCTCAAGTGTATA
58048 TATGTCTCTCAAGTGTATA
1 TATGTCTCTCAAGTGTATA
58067 TA
1 TA
58069 CATAGAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TATGTCTCTCAAGTGTATA
Found at i:65405 original size:4 final size:4
Alignment explanation
Indices: 65396--65422 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
65386 ACGGGGAAGT
65396 GGGA GGGA GGGA GGGA GGGA GGGA GGG
1 GGGA GGGA GGGA GGGA GGGA GGGA GGG
65423 GGGGCAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.78, T:0.00
Consensus pattern (4 bp):
GGGA
Found at i:70394 original size:14 final size:14
Alignment explanation
Indices: 70375--70402 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
70365 AAAGATCAGT
70375 GTTCTTGAGGAGCA
1 GTTCTTGAGGAGCA
70389 GTTCTTGAGGAGCA
1 GTTCTTGAGGAGCA
70403 CAAAACAATG
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:0.21, C:0.14, G:0.36, T:0.29
Consensus pattern (14 bp):
GTTCTTGAGGAGCA
Found at i:72220 original size:23 final size:22
Alignment explanation
Indices: 72180--72223 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
72170 AATCTCTCTC
*
72180 AGAGAGAGAGAGAGAGGGGAAG
1 AGAGAGAGAGAGAAAGGGGAAG
*
72202 AGAGAGATTAGAGAAAGGGGAA
1 AGAGAGA-GAGAGAAAGGGGAA
72224 AGAAAGCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.48, C:0.00, G:0.48, T:0.05
Consensus pattern (22 bp):
AGAGAGAGAGAGAAAGGGGAAG
Found at i:96510 original size:41 final size:42
Alignment explanation
Indices: 96465--96561 Score: 128
Period size: 41 Copynumber: 2.4 Consensus size: 42
96455 AAAGAAGGAA
* *
96465 TACTTCTT-TACAATTTAC-AAATCACAACCAGAATCGACAAT
1 TACTTTTTCTACAA-TTACTAAATCACAACCAGAACCGACAAT
* *
96506 TACTTTTTCTACAA-TCCTAAATCACAACCAGAACCTACAAT
1 TACTTTTTCTACAATTACTAAATCACAACCAGAACCGACAAT
96547 TACTTTTTCTACAAT
1 TACTTTTTCTACAAT
96562 CCTAAAATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
40 2 0.04
41 42 0.86
42 5 0.10
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (42 bp):
TACTTTTTCTACAATTACTAAATCACAACCAGAACCGACAAT
Found at i:96562 original size:41 final size:41
Alignment explanation
Indices: 96483--96567 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 41
96473 TACAATTTAC
*
96483 AAATCACAACCAGAATCGACAATTACTTTTTCTACAATCCT
1 AAATCACAACCAGAACCGACAATTACTTTTTCTACAATCCT
*
96524 AAATCACAACCAGAACCTACAATTACTTTTTCTACAATCCT
1 AAATCACAACCAGAACCGACAATTACTTTTTCTACAATCCT
96565 AAA
1 AAA
96568 ATTACGTTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.41, C:0.27, G:0.04, T:0.28
Consensus pattern (41 bp):
AAATCACAACCAGAACCGACAATTACTTTTTCTACAATCCT
Found at i:100323 original size:7 final size:7
Alignment explanation
Indices: 100313--100338 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
100303 AAGAAAAACA
100313 CAAAAGG
1 CAAAAGG
100320 CAAAAGG
1 CAAAAGG
100327 CAAAAGG
1 CAAAAGG
100334 CAAAA
1 CAAAA
100339 TGGATATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.15, G:0.23, T:0.00
Consensus pattern (7 bp):
CAAAAGG
Found at i:107237 original size:17 final size:17
Alignment explanation
Indices: 107210--107264 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
107200 AACCCATGTA
* *
107210 ATCTTTGATCACCAGTG
1 ATCTTAGATCACTAGTG
*
107227 ATCTT-GCATCACTGGTG
1 ATCTTAG-ATCACTAGTG
107244 ATCTTAGATCACTAGTG
1 ATCTTAGATCACTAGTG
107261 ATCT
1 ATCT
107265 GGGGGTGATC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 1 0.03
17 31 0.94
18 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (17 bp):
ATCTTAGATCACTAGTG
Found at i:110205 original size:22 final size:24
Alignment explanation
Indices: 110144--110205 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 24
110134 AGTAATCAAA
*
110144 AATCAGAATTCAGAAACCAAGATCAG
1 AATCA-AA-TCAGAAAGCAAGATCAG
110170 AATCAAATCA-AAAGCAA-ATCAG
1 AATCAAATCAGAAAGCAAGATCAG
110192 AAATC-AA-CAGAAAG
1 -AATCAAATCAGAAAG
110206 TTCGAAAAGC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 2 0.06
22 11 0.33
23 10 0.30
24 3 0.09
25 2 0.06
26 5 0.15
ACGTcount: A:0.56, C:0.18, G:0.13, T:0.13
Consensus pattern (24 bp):
AATCAAATCAGAAAGCAAGATCAG
Done.