Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008493.1 Corchorus capsularis cultivar CVL-1 contig08514, 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: 98143
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3170 original size:21 final size:21
Alignment explanation
Indices: 3146--3188 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3136 TAACGTGAGT
3146 AATAAAGACTACCAAAAATTC
1 AATAAAGACTACCAAAAATTC
3167 AATAAAGACTACCAAAAATTC
1 AATAAAGACTACCAAAAATTC
3188 A
1 A
3189 CATTCCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.19, G:0.05, T:0.19
Consensus pattern (21 bp):
AATAAAGACTACCAAAAATTC
Found at i:3212 original size:59 final size:59
Alignment explanation
Indices: 3140--3251 Score: 215
Period size: 59 Copynumber: 1.9 Consensus size: 59
3130 TGTCATTAAC
*
3140 GTGAGTAATAAAGACTACCAAAAATTCAATAAAGACTACCAAAAATTCACATTCCAAAT
1 GTGAGTAATAAAGACTACAAAAAATTCAATAAAGACTACCAAAAATTCACATTCCAAAT
3199 GTGAGTAATAAAGACTACAAAAAATTCAATAAAGACTACCAAAAATTCACATT
1 GTGAGTAATAAAGACTACAAAAAATTCAATAAAGACTACCAAAAATTCACATT
3252 TCAGCGAGAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.52, C:0.17, G:0.09, T:0.22
Consensus pattern (59 bp):
GTGAGTAATAAAGACTACAAAAAATTCAATAAAGACTACCAAAAATTCACATTCCAAAT
Found at i:3229 original size:21 final size:21
Alignment explanation
Indices: 3205--3247 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3195 AAATGTGAGT
3205 AATAAAGACTACAAAAAATTC
1 AATAAAGACTACAAAAAATTC
*
3226 AATAAAGACTACCAAAAATTC
1 AATAAAGACTACAAAAAATTC
3247 A
1 A
3248 CATTTCAGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.60, C:0.16, G:0.05, T:0.19
Consensus pattern (21 bp):
AATAAAGACTACAAAAAATTC
Found at i:13153 original size:10 final size:10
Alignment explanation
Indices: 13138--13163 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
13128 AATTTAATAT
13138 GGATATTTAC
1 GGATATTTAC
13148 GGATATTTAC
1 GGATATTTAC
13158 GGATAT
1 GGATAT
13164 ATTGAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (10 bp):
GGATATTTAC
Found at i:13653 original size:29 final size:30
Alignment explanation
Indices: 13602--13659 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
13592 TTTACATTAC
*
13602 AAATTCAGTGCTTAATACTTCAAA-AATAA
1 AAATTCAGTACTTAATACTTCAAACAATAA
*
13631 AAATTCAGTACTTAAT-TTATCAAACAATA
1 AAATTCAGTACTTAATACT-TCAAACAATA
13660 TCGAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 1 0.04
29 20 0.80
30 4 0.16
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (30 bp):
AAATTCAGTACTTAATACTTCAAACAATAA
Found at i:15527 original size:44 final size:44
Alignment explanation
Indices: 15476--15563 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
15466 AATGTTTGAC
* *
15476 TTTAGTTCGAATGATCAGGATTTAAGTTTTGATAAAATTGAAGT
1 TTTAGTTCGAATGATCAGGATTTAAGTTCTGACAAAATTGAAGT
* *
15520 TTTAGTTCTAATGATCAGGGTTTAAGTTCTGACAAAATTGAAGT
1 TTTAGTTCGAATGATCAGGATTTAAGTTCTGACAAAATTGAAGT
15564 ATCAAAAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (44 bp):
TTTAGTTCGAATGATCAGGATTTAAGTTCTGACAAAATTGAAGT
Found at i:18810 original size:13 final size:13
Alignment explanation
Indices: 18792--18817 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18782 TCCAAAAGTG
18792 TATTATAGTAACT
1 TATTATAGTAACT
18805 TATTATAGTAACT
1 TATTATAGTAACT
18818 GTCTTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TATTATAGTAACT
Found at i:23169 original size:22 final size:21
Alignment explanation
Indices: 23144--23188 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
23134 AATAAAAAAA
23144 TTTCATTTTTGTTCTTTTTCTT
1 TTTCATTTTTGTTCTTTTT-TT
*
23166 TTTCTTTTTTGTTCTTTTTTT
1 TTTCATTTTTGTTCTTTTTTT
23187 TT
1 TT
23189 GTTTTTGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.02, C:0.11, G:0.04, T:0.82
Consensus pattern (21 bp):
TTTCATTTTTGTTCTTTTTTT
Found at i:24458 original size:11 final size:11
Alignment explanation
Indices: 24442--24498 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
24432 GGGGTCGAGG
24442 AAGAAGAAGGA
1 AAGAAGAAGGA
24453 AAGAAGAAGAGA
1 AAGAAGAAG-GA
24465 AAGAAAAGAAGGGA
1 AAG--AAGAA-GGA
*
24479 AA-AAGAAAGA
1 AAGAAGAAGGA
*
24489 AAGAAAAAGG
1 AAGAAGAAGG
24499 GATGGGAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
10 4 0.11
11 19 0.50
12 5 0.13
14 9 0.24
15 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (11 bp):
AAGAAGAAGGA
Found at i:24460 original size:14 final size:14
Alignment explanation
Indices: 24441--24485 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
24431 GGGGGTCGAG
24441 GAAGAAGAAGGAAA
1 GAAGAAGAAGGAAA
24455 GAAGAAG-A-GAAA
1 GAAGAAGAAGGAAA
24467 GAA-AAGAAGGGAAA
1 GAAGAAGAA-GGAAA
24481 -AAGAA
1 GAAGAA
24486 AGAAAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
11 3 0.11
12 8 0.30
13 3 0.11
14 13 0.48
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
GAAGAAGAAGGAAA
Found at i:24497 original size:25 final size:25
Alignment explanation
Indices: 24445--24495 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
24435 GTCGAGGAAG
24445 AAGAAGGAAAGAAGAAGAGAAAGAA
1 AAGAAGGAAAGAAGAAGAGAAAGAA
24470 AAGAAGGGAAA-AAGAA-AGAAAGAA
1 AAGAA-GGAAAGAAGAAGAGAAAGAA
24494 AA
1 AA
24496 AGGGATGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 10 0.40
25 10 0.40
26 5 0.20
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (25 bp):
AAGAAGGAAAGAAGAAGAGAAAGAA
Found at i:29205 original size:893 final size:893
Alignment explanation
Indices: 27478--29589 Score: 3666
Period size: 893 Copynumber: 2.4 Consensus size: 893
27468 TTGCCTGATA
* * * * *
27478 ATTGAGTATGAAAAGTTTTTATTTAGTGTTGATTTTGTTACTTCCAAATTGATATTCTAGTTTCT
1 ATTGAGTATGAAAAATTTTTATTTAATGTTTATTTTGCTACTTCCAAATTGATATTCTAGTTTCC
* * * * * * *
27543 ATATGATTATTCTCTTCGAAGCAATTATAACAACTTGGATGAAAATGAAGTGTTGTTTTCGTATC
66 ATATGATTATTCTCTTCCAAACTATTATTATAACTTGGATGAAAATGAAGTGTTGTTTTGGTTTC
27608 TTGAGGTCTAAGCATTTCTTGGATTGACCATATCTTGTCTGTTAGCTGTAAAAATTGAGATTTCA
131 TTGAGGTCTAAGCATTTCTTGGATTGACCATATCTTGTCTGTTAGCTGTAAAAATTGAGATTTCA
* * * *
27673 TCAAGTAAAACCAGCTTTAACATTCTACAATTAGGCAAGTTTAGTTGTACAATTATAATAATTTT
196 TCAAGTAAAACCAGCTTTAACATTCTCCAATCAGGCAAGTTTAGCTGCACAATTATAATAATTTT
27738 TTGTTTGATGAGTAAGAGAATTAGTATTTAATATATATCGCAATCTTTCATAGAGTGAAAAACTC
261 TTGTTTGATGAGTAAGAGAATTAGTATTTAATATATATCGCAATCTTTCATAGAGTGAAAAACTC
27803 CTTCTATAACCACTACACTTTTGCCGTTTATGGTTTTTGTGGGGTTAATTCTGCAATTGTTGCCA
326 CTTCTATAACCACTACACTTTTGCCGTTTATGGTTTTTGTGGGGTTAATTCTGCAATTGTTGCCA
*
27868 TGGCTCTAATCTTTTATGGGTCAATTAAGATGCACTTTGACTGTCTTCACTTTATATTTTTGGAC
391 TGGCCCTAATCTTTTATGGGTCAATTAAGATGCACTTTGACTGTCTTCACTTTATATTTTTGGAC
*
27933 GACTGATTTGACATAGACGATAAAGTTAAACAAAATGGTAAGGATCACATGTTCCTACAAATTGC
456 GACTGATTTGACATAGACGATAAAGTTAAACAAAATGGTAAGGATCACATGCTCCTACAAATTGC
**
27998 CTACGATGCCATTATATTTGAACATAGGGACCTTGAAACCCAAGCGTCTGGAATAATAAAAACCA
521 CTACGATGCCATTATATTTGAACATAGGGACCTTGAAACCCAAGCGTCTAAAATAATAAAAACCA
* *
28063 AGTTCTTTCCAAGCGGTGTTTACGCAATCGTTACGGGTTTATTCTAGATTCTTTAGTTGTGCGAG
586 AGTTCTTTCCAAGCGGTGTTTACGCAATCGTTACGGGTTTATTCTAGATTCCTTAGTTCTGCGAG
*
28128 GTGATGGAGCACTCCGATCAGAACAAAAGCTATTCTAAAATATATATTTGACTATGATATCATTT
651 GTGATGGAGCACTCCGATCAGAACAAAAACTATTCTAAAATATATATTTGACTATGATATCATTT
*
28193 ATGTAAGAGAAATAGAAAATGAGAAAATAATTTCTTTTCTATGTATAAATAAATATTAATAAATT
716 ATGCAAGAGAAATAGAAAATGAGAAAATAATTTCTTTTCTATGTATAAATAAATATTAATAAATT
28258 CTTAAACACGAATTTATTTGGCTAATATTATACCTGACTCTGATATTTGGCGAAAAACATTCTAT
781 CTTAAACACGAATTTATTTGGCTAATATTATACCTGACTCTGATATTTGGCGAAAAACATTCTAT
*
28323 ATGAAGAACTTGCCTTCCAGTATTGTGGAAAAAAAAATCAATCAGATC
846 ATGAAGAACTTGCCTTCCAGTATCGTGGAAAAAAAAATCAATCAGATC
28371 ATTGAGTATGAAAAATTTTTATTTAATGTTTATTTTGCTACTTCCAAATTGATATTCTAGTTTCC
1 ATTGAGTATGAAAAATTTTTATTTAATGTTTATTTTGCTACTTCCAAATTGATATTCTAGTTTCC
* * *
28436 ATATGATTATTCTTTTCCAAACTATTATTATAACTTGGATCAAAATGAAGTATTGTTTTGGTTTC
66 ATATGATTATTCTCTTCCAAACTATTATTATAACTTGGATGAAAATGAAGTGTTGTTTTGGTTTC
* * * *
28501 TTAAGGTCTAAGAATTTCTTGGATTGACCATGTCTTGTCTGTTAGCTGTAAAAATTAAGATTTCA
131 TTGAGGTCTAAGCATTTCTTGGATTGACCATATCTTGTCTGTTAGCTGTAAAAATTGAGATTTCA
*
28566 TCAAGTAAAACCAGTTTTAACATTCTCCAATCAGGCAAGTTTAGCTGCACAATTATAATAATTTT
196 TCAAGTAAAACCAGCTTTAACATTCTCCAATCAGGCAAGTTTAGCTGCACAATTATAATAATTTT
28631 TTGTTTGATGAGTAAGAGAATTAGTATTTAATATATATCGCAATCTTTCATAGAGTGAAAAACTC
261 TTGTTTGATGAGTAAGAGAATTAGTATTTAATATATATCGCAATCTTTCATAGAGTGAAAAACTC
* *
28696 CTTCTATAACCACTACACTTTTGCCGTTTATGGTTTTTGTGGGGTTAATTCTGCATTTGTTGTCA
326 CTTCTATAACCACTACACTTTTGCCGTTTATGGTTTTTGTGGGGTTAATTCTGCAATTGTTGCCA
*
28761 TGGCCCTAATCTTTTATGGGTCAATTAAGATGCACTTTGACTGTCTTCACTTTGTATTTTTGGAC
391 TGGCCCTAATCTTTTATGGGTCAATTAAGATGCACTTTGACTGTCTTCACTTTATATTTTTGGAC
28826 GACTGATTTGACATAGACGATAAAGTTAAACAAAATGGTAAGGATCACATGCTCCTACAAATTGC
456 GACTGATTTGACATAGACGATAAAGTTAAACAAAATGGTAAGGATCACATGCTCCTACAAATTGC
*
28891 CTACGATGTCATTATATTTGAACATAGGGACCTTGAAACCCAAGCGTCTAAAATAATAAAAACCA
521 CTACGATGCCATTATATTTGAACATAGGGACCTTGAAACCCAAGCGTCTAAAATAATAAAAACCA
28956 AGTTCTTTCCAAGCGGTGTTTACGCAATCGTTACGGGTTTATTCTAGATTCCTTAGTTCTGCGAG
586 AGTTCTTTCCAAGCGGTGTTTACGCAATCGTTACGGGTTTATTCTAGATTCCTTAGTTCTGCGAG
* * * *
29021 GTGATGGAGCACTCCGATCAGGACAAAAACTATTTTATAATATATATTTGACTCTGATATCATTT
651 GTGATGGAGCACTCCGATCAGAACAAAAACTATTCTAAAATATATATTTGACTATGATATCATTT
29086 ATGCAAGAGAAATAGAAAATGAGAAAATAATTTCTTTTCTATGTATAAATAAATATTAATAAATT
716 ATGCAAGAGAAATAGAAAATGAGAAAATAATTTCTTTTCTATGTATAAATAAATATTAATAAATT
29151 CTTAAACACGAATTTATTTGGCTAATATTATACCTGACTCTGATATTTGGCGAAAAACATTCTAT
781 CTTAAACACGAATTTATTTGGCTAATATTATACCTGACTCTGATATTTGGCGAAAAACATTCTAT
* *
29216 ATGAAGAACTTGCCTTTCAGTGTCGTGGAAAAAAAAATCAATCAGATC
846 ATGAAGAACTTGCCTTCCAGTATCGTGGAAAAAAAAATCAATCAGATC
* *
29264 ATTGAGTATGAAAAATTTTTATTTATTGTTTACTTTGCTACTTCCAAATTGATATTCTAGTTTCC
1 ATTGAGTATGAAAAATTTTTATTTAATGTTTATTTTGCTACTTCCAAATTGATATTCTAGTTTCC
29329 ATATGATTATTCTCTTCCAAACTATTATTATAACTTGGATGAAAATGAAGTGTTGTTTTGGTTTC
66 ATATGATTATTCTCTTCCAAACTATTATTATAACTTGGATGAAAATGAAGTGTTGTTTTGGTTTC
** *** * * *
29394 TTGAGGTCCGAGCATCAATTGGATTGACCATTTCTTGTATGTTAGCCGTAAAAATTGAGATTTCA
131 TTGAGGTCTAAGCATTTCTTGGATTGACCATATCTTGTCTGTTAGCTGTAAAAATTGAGATTTCA
* * * *
29459 TCAAGTAAAACGAACTTTAACATTCTCTAATCAGGCAAGTTTAGCTGCACGATTATAATAATTTT
196 TCAAGTAAAACCAGCTTTAACATTCTCCAATCAGGCAAGTTTAGCTGCACAATTATAATAATTTT
* * * * *
29524 TTGTTTGATGATTAAGAGAATTAATATTTAATATACATCGCCATCCTTCATAGAGTGAAAAACTC
261 TTGTTTGATGAGTAAGAGAATTAGTATTTAATATATATCGCAATCTTTCATAGAGTGAAAAACTC
29589 C
326 C
29590 ATATATAAAT
Statistics
Matches: 1150, Mismatches: 69, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
893 1150 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.37
Consensus pattern (893 bp):
ATTGAGTATGAAAAATTTTTATTTAATGTTTATTTTGCTACTTCCAAATTGATATTCTAGTTTCC
ATATGATTATTCTCTTCCAAACTATTATTATAACTTGGATGAAAATGAAGTGTTGTTTTGGTTTC
TTGAGGTCTAAGCATTTCTTGGATTGACCATATCTTGTCTGTTAGCTGTAAAAATTGAGATTTCA
TCAAGTAAAACCAGCTTTAACATTCTCCAATCAGGCAAGTTTAGCTGCACAATTATAATAATTTT
TTGTTTGATGAGTAAGAGAATTAGTATTTAATATATATCGCAATCTTTCATAGAGTGAAAAACTC
CTTCTATAACCACTACACTTTTGCCGTTTATGGTTTTTGTGGGGTTAATTCTGCAATTGTTGCCA
TGGCCCTAATCTTTTATGGGTCAATTAAGATGCACTTTGACTGTCTTCACTTTATATTTTTGGAC
GACTGATTTGACATAGACGATAAAGTTAAACAAAATGGTAAGGATCACATGCTCCTACAAATTGC
CTACGATGCCATTATATTTGAACATAGGGACCTTGAAACCCAAGCGTCTAAAATAATAAAAACCA
AGTTCTTTCCAAGCGGTGTTTACGCAATCGTTACGGGTTTATTCTAGATTCCTTAGTTCTGCGAG
GTGATGGAGCACTCCGATCAGAACAAAAACTATTCTAAAATATATATTTGACTATGATATCATTT
ATGCAAGAGAAATAGAAAATGAGAAAATAATTTCTTTTCTATGTATAAATAAATATTAATAAATT
CTTAAACACGAATTTATTTGGCTAATATTATACCTGACTCTGATATTTGGCGAAAAACATTCTAT
ATGAAGAACTTGCCTTCCAGTATCGTGGAAAAAAAAATCAATCAGATC
Found at i:29653 original size:2 final size:2
Alignment explanation
Indices: 29648--29693 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
29638 TTTGTGTGTC
29648 TA TA TA 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 TA TA TA
29690 TA TA
1 TA TA
29694 CCAATTAAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34456 original size:20 final size:20
Alignment explanation
Indices: 34433--34475 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
34423 TACTCAAACT
*
34433 AAATTATAAAATGCCAAAAA
1 AAATTATAAAATGACAAAAA
34453 AAATTATAAAATGACAAAAA
1 AAATTATAAAATGACAAAAA
34473 AAA
1 AAA
34476 ATTCAATAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.19
Consensus pattern (20 bp):
AAATTATAAAATGACAAAAA
Found at i:34659 original size:30 final size:29
Alignment explanation
Indices: 34592--34666 Score: 104
Period size: 27 Copynumber: 2.7 Consensus size: 29
34582 TATTAATTTC
34592 AAAA-AATAATTATGACTTTTCGTCAAAA
1 AAAATAATAATTATGACTTTTCGTCAAAA
34620 AAAAT--TAATTATGACTTTTC-TCCAAAA
1 AAAATAATAATTATGACTTTTCGT-CAAAA
34647 AAAACTAATAATTATGACTT
1 AAAA-TAATAATTATGACTT
34667 ACTATATTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
26 1 0.02
27 24 0.57
28 5 0.12
30 12 0.29
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.35
Consensus pattern (29 bp):
AAAATAATAATTATGACTTTTCGTCAAAA
Found at i:37319 original size:10 final size:10
Alignment explanation
Indices: 37296--37336 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
37286 CTTAGTCTTG
37296 ATCTT-TTTC
1 ATCTTCTTTC
37305 ATCTTCTTTC
1 ATCTTCTTTC
*
37315 TTCTTCTATTC
1 ATCTTCT-TTC
37326 ATCTTCTTTC
1 ATCTTCTTTC
37336 A
1 A
37337 ATACTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 5 0.18
10 14 0.50
11 9 0.32
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (10 bp):
ATCTTCTTTC
Found at i:37975 original size:21 final size:21
Alignment explanation
Indices: 37951--37991 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
37941 AGTACAAAAA
*
37951 TATTATATACTTATA-ATATGT
1 TATTATA-AATTATATATATGT
37972 TATTATAAATTATATATATG
1 TATTATAAATTATATATATG
37992 CATATGTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (21 bp):
TATTATAAATTATATATATGT
Found at i:38435 original size:15 final size:15
Alignment explanation
Indices: 38412--38455 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
38402 ATAAAAATTA
38412 AATAT-TTTTATTTT
1 AATATATTTTATTTT
38426 AATATATTTTATTTT
1 AATATATTTTATTTT
* * *
38441 ATTAAAATTTATTTT
1 AATATATTTTATTTT
38456 TAAAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
AATATATTTTATTTT
Found at i:40278 original size:15 final size:15
Alignment explanation
Indices: 40232--40275 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
40222 TTATTTTTTA
* * *
40232 AAAATAAATTTTAAT
1 AAAATAAAATATATT
40247 AAAATAAAATATATT
1 AAAATAAAATATATT
40262 AAAATAAAA-ATATT
1 AAAATAAAATATATT
40276 TAATTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAATAAAATATATT
Found at i:41499 original size:97 final size:97
Alignment explanation
Indices: 41396--41571 Score: 264
Period size: 97 Copynumber: 1.8 Consensus size: 97
41386 TTATTATTTT
* * * *
41396 AGTATTATTTATGG-AGAATGAGGAGGAATGATTGGCTATATATATAGACGATCATTTGATTGTT
1 AGTATTATTTATGGAAG-AGGAGGAGGAATGATTGGCTATATATAAAGACAATCATTTGATGGTT
41460 TTAGCTTTCAAGATAAGAGGATTATTTACTTCA
65 TTAGCTTTCAAGATAAGAGGATTATTTACTTCA
* * *
41493 AGTATTATTTATGGAAGAGGAGGAGTAATGATTGTCTATATATAAAGATAATCATTTGATGGTTT
1 AGTATTATTTATGGAAGAGGAGGAGGAATGATTGGCTATATATAAAGACAATCATTTGATGGTTT
*
41558 TAGCTTTTAAGATA
66 TAGCTTTCAAGATA
41572 CAAGCATTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
97 68 0.97
98 2 0.03
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.39
Consensus pattern (97 bp):
AGTATTATTTATGGAAGAGGAGGAGGAATGATTGGCTATATATAAAGACAATCATTTGATGGTTT
TAGCTTTCAAGATAAGAGGATTATTTACTTCA
Found at i:57171 original size:202 final size:204
Alignment explanation
Indices: 56817--57231 Score: 667
Period size: 202 Copynumber: 2.0 Consensus size: 204
56807 AATATCAATA
*
56817 TAAAAATTATTACGCAACCAATCAAATATTGCTACGTAAAAGATTTCACAACCACAACCAAAACG
1 TAAAAATTATTACACAACCAATCAAATATTGCTACGTAAAAGATTTCACAACCACAA-CAAAAC-
*
56882 ATGTCATTGTGTAAGGGTTTTCGCAACGACATTTAATCGTTTTTAAATTATTTTGGCAACTACCT
64 A-GTCATTGCGTAAGGGTTTTCGCAACGACATTTAATCGTTTTTAAATTATTTTGGCAACTACCT
* *
56947 AGAGGTTGTTATGTAAGTGTTTTGGAAACGACT-TTTAATCATTTTTAAAAGTTATTCGTAACCA
128 AGAGGTCGTTATGTAAGTGTTTTGGAAACGA-TATTTAATCATTTTTAAAAGTTATCCGTAACCA
57011 ATTAAAAGTGGTTG
192 ATT-AAAGTGGTTG
* * * *
57025 TGAAAATTATTACACAACCAATCAAATGTTGTTACGTAAAAGATTTCACAACCA-AA-ACAAC-G
1 TAAAAATTATTACACAACCAATCAAATATTGCTACGTAAAAGATTTCACAACCACAACAAAACAG
*
57087 TCGTTGCGTAAGGGTTTTCGCAACGACATTTAATCGTTTTTAAATTATTTTGGCAACTACCTAGA
66 TCATTGCGTAAGGGTTTTCGCAACGACATTTAATCGTTTTTAAATTATTTTGGCAACTACCTAGA
*
57152 GGTCGTTATGTAAGTGTTTTGGAAACGATATTTAATCGTTTTTAAAAGTTATCCGTAACCAATTA
131 GGTCGTTATGTAAGTGTTTTGGAAACGATATTTAATCATTTTTAAAAGTTATCCGTAACCAATTA
57217 AAGTGGTTG
196 AAGTGGTTG
57226 TAAAAA
1 TAAAAA
57232 AAATTTTCGC
Statistics
Matches: 195, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
201 16 0.08
202 123 0.63
205 4 0.02
207 2 0.01
208 50 0.26
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (204 bp):
TAAAAATTATTACACAACCAATCAAATATTGCTACGTAAAAGATTTCACAACCACAACAAAACAG
TCATTGCGTAAGGGTTTTCGCAACGACATTTAATCGTTTTTAAATTATTTTGGCAACTACCTAGA
GGTCGTTATGTAAGTGTTTTGGAAACGATATTTAATCATTTTTAAAAGTTATCCGTAACCAATTA
AAGTGGTTG
Found at i:57373 original size:20 final size:20
Alignment explanation
Indices: 57348--57392 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
57338 ACAACGAATA
57348 CTTAAGTCATTGCGTTAGAT
1 CTTAAGTCATTGCGTTAGAT
* *
57368 CTTAAGTCGTTGTGTTAGAT
1 CTTAAGTCATTGCGTTAGAT
*
57388 ATTAA
1 CTTAA
57393 ACAACGGAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (20 bp):
CTTAAGTCATTGCGTTAGAT
Found at i:59592 original size:24 final size:24
Alignment explanation
Indices: 59557--59603 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
59547 TTTTTTACAC
*
59557 TTTTACACTTTGACCTTTGCCACA
1 TTTTACACTTTGACCTTAGCCACA
*
59581 TTTT-CACTTTTGCCCTTAGCCAC
1 TTTTACAC-TTTGACCTTAGCCAC
59604 GCGGAGCCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.17, C:0.32, G:0.09, T:0.43
Consensus pattern (24 bp):
TTTTACACTTTGACCTTAGCCACA
Found at i:59759 original size:33 final size:33
Alignment explanation
Indices: 59717--59844 Score: 134
Period size: 33 Copynumber: 3.9 Consensus size: 33
59707 TAGTATCGGT
* *
59717 GCCGCCCCAGGGGGGCGGTCTATCCATGGTAGG
1 GCCGCCCCAGGGGGGCGGCCTAGCCATGGTAGG
* * *
59750 GCCGCCCCAGGGAGGCGGCCTGGCCATGGTAGT
1 GCCGCCCCAGGGGGGCGGCCTAGCCATGGTAGG
* * * *
59783 GCCGCCCCAAGAGGGCGGCTTGGCCATGGCTCA--
1 GCCGCCCCAGGGGGGCGGCCTAGCCATGG-T-AGG
*
59816 GCCGCCCCAGGGGGACGGCCTAGCCATGG
1 GCCGCCCCAGGGGGGCGGCCTAGCCATGG
59845 CAAGTCGTCC
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
33 77 0.97
34 1 0.01
35 1 0.01
ACGTcount: A:0.13, C:0.34, G:0.41, T:0.12
Consensus pattern (33 bp):
GCCGCCCCAGGGGGGCGGCCTAGCCATGGTAGG
Found at i:61508 original size:25 final size:25
Alignment explanation
Indices: 61478--61529 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
61468 ATTGGAGTAT
*
61478 TTATTTATCTTG-TTGCTTAATTTTA
1 TTATTT-TCTTGTTTACTTAATTTTA
*
61503 TTATTTTCTTGTTTATTTAATTTTA
1 TTATTTTCTTGTTTACTTAATTTTA
61528 TT
1 TT
61530 GCTCTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (25 bp):
TTATTTTCTTGTTTACTTAATTTTA
Found at i:63905 original size:29 final size:27
Alignment explanation
Indices: 63863--63930 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 27
63853 TATATAATTT
* *
63863 ATTAT-TATATAT-ATCTAACATTATA
1 ATTATATATATATAATATTACATTATA
*
63888 ATTATATATATATAATA-TATATT-TA
1 ATTATATATATATAATATTACATTATA
63913 ATTATATATAT-TAATATT
1 ATTATATATATATAATATT
63931 CGGTCAGTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
24 5 0.14
25 19 0.51
26 11 0.30
27 2 0.05
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTATATATATATAATATTACATTATA
Found at i:69398 original size:9 final size:10
Alignment explanation
Indices: 69382--69407 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
69372 TTTTGGTCGA
69382 ATTTTTTTTT
1 ATTTTTTTTT
69392 ATTTTTTTTT
1 ATTTTTTTTT
69402 ATTTTT
1 ATTTTT
69408 CGATATAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:70478 original size:2 final size:2
Alignment explanation
Indices: 70471--70522 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
70461 AGCTTGTCCA
70471 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
70513 TG TG TG TG TG
1 TG TG TG TG TG
70523 GCATTGTTAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:71229 original size:24 final size:24
Alignment explanation
Indices: 71202--71248 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
71192 TTCACATTTT
71202 TTTTCTAAACATTATTTACGTGAA
1 TTTTCTAAACATTATTTACGTGAA
* ***
71226 TTTTTTTGGCATTATTTACGTGA
1 TTTTCTAAACATTATTTACGTGA
71249 TTAGAGTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.51
Consensus pattern (24 bp):
TTTTCTAAACATTATTTACGTGAA
Found at i:71873 original size:28 final size:27
Alignment explanation
Indices: 71828--71904 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 27
71818 TTTATTATCT
*
71828 CAAAAAAA-TCAATATTTTATTTTACT-
1 CAAAAAAACTCTAT-TTTTATTTTACTG
*
71854 CAACTAAAAACTCTATTTTTATTTTTCTG
1 CAA--AAAAACTCTATTTTTATTTTACTG
*
71883 TAAAAAAACTCTATTTTTATTT
1 CAAAAAAACTCTATTTTTATTT
71905 AATTAAATCT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 3 0.07
27 19 0.43
28 16 0.36
29 6 0.14
ACGTcount: A:0.39, C:0.13, G:0.01, T:0.47
Consensus pattern (27 bp):
CAAAAAAACTCTATTTTTATTTTACTG
Found at i:71911 original size:25 final size:27
Alignment explanation
Indices: 71859--71911 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
71849 TTACTCAACT
**
71859 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
71886 AAAAACTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
71911 A
1 A
71912 TCTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 16 0.67
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Found at i:72013 original size:26 final size:26
Alignment explanation
Indices: 71984--72034 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
71974 ATATTAGAAC
**
71984 TTTTAAAATATATTCTTTTACAATTTT
1 TTTTAAAA-ATAAACTTTTACAATTTT
72011 TTTTAAAAATAAACTTTTACAATT
1 TTTTAAAAATAAACTTTTACAATT
72035 ATTCTACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (26 bp):
TTTTAAAAATAAACTTTTACAATTTT
Found at i:72060 original size:29 final size:30
Alignment explanation
Indices: 72024--72087 Score: 114
Period size: 29 Copynumber: 2.2 Consensus size: 30
72014 TAAAAATAAA
72024 CTTTTACAATTATTCTACT-AAAACTCTAT
1 CTTTTACAATTATTCTACTAAAAACTCTAT
72053 CTTTTACAATTATTCTACTAAAAACTCTAT
1 CTTTTACAATTATTCTACTAAAAACTCTAT
72083 -TTTTA
1 CTTTTA
72088 TTCGATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 24 0.71
30 10 0.29
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (30 bp):
CTTTTACAATTATTCTACTAAAAACTCTAT
Found at i:72915 original size:21 final size:21
Alignment explanation
Indices: 72891--72934 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
72881 TTAAACTGGA
*
72891 TTGCTAAAT-ACCGCCCTATTT
1 TTGCT-AATCACCGCCCCATTT
*
72912 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
72933 TT
1 TT
72935 TACGCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:73159 original size:33 final size:33
Alignment explanation
Indices: 73116--73210 Score: 104
Period size: 33 Copynumber: 2.9 Consensus size: 33
73106 CCGTCCCAAG
* *
73116 AGGGCAGCTTCACCATGGGCAGACCGCCCCA-C
1 AGGGCGGCTTCACCATGGGCAGGCCGCCCCATC
***
73148 TAGGGCGGCTTCACCATGAAAAGGCCGCCCCATC
1 -AGGGCGGCTTCACCATGGGCAGGCCGCCCCATC
* *
73182 GGGGCGGCTTAACCA-GGGCAGGCCGCCCC
1 AGGGCGGCTTCACCATGGGCAGGCCGCCCC
73211 GGTGGGGGTG
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
32 11 0.22
33 39 0.76
34 1 0.02
ACGTcount: A:0.20, C:0.38, G:0.32, T:0.11
Consensus pattern (33 bp):
AGGGCGGCTTCACCATGGGCAGGCCGCCCCATC
Found at i:79928 original size:23 final size:23
Alignment explanation
Indices: 79902--79947 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
79892 TTGTGGCAAT
79902 GGTTTTGCCAAATGAATAACTAC
1 GGTTTTGCCAAATGAATAACTAC
79925 GGTTTTGCCAAATGAATAACTAC
1 GGTTTTGCCAAATGAATAACTAC
79948 TAGAAATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (23 bp):
GGTTTTGCCAAATGAATAACTAC
Found at i:87356 original size:27 final size:27
Alignment explanation
Indices: 87294--87398 Score: 131
Period size: 27 Copynumber: 3.8 Consensus size: 27
87284 TAGGGTCACC
*
87294 CAGGGGCATTTTGGTCATTTTTTTACATT
1 CAGGGGCATTTAGGTCA--TTTTTACATT
* *
87323 CGGGGGGCACTTTTGG-CATTTTTACATT
1 C-AGGGGCA-TTTAGGTCATTTTTACATT
*
87351 CAGGGGCATTTAGGTCATTTTTGCATT
1 CAGGGGCATTTAGGTCATTTTTACATT
87378 CAGGGGCATTTAGGTCATTTT
1 CAGGGGCATTTAGGTCATTTT
87399 AAGTTCACTT
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
26 5 0.07
27 38 0.55
28 11 0.16
29 1 0.01
30 8 0.12
31 6 0.09
ACGTcount: A:0.17, C:0.15, G:0.26, T:0.42
Consensus pattern (27 bp):
CAGGGGCATTTAGGTCATTTTTACATT
Found at i:96326 original size:12 final size:13
Alignment explanation
Indices: 96311--96355 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
96301 ATATACTTAT
*
96311 TTATAT-TATGTA
1 TTATATATATATA
96323 TTATATA-ATATA
1 TTATATATATATA
96335 -TATATATATAT-
1 TTATATATATATA
96346 TTATATATAT
1 TTATATATAT
96356 TGTATGTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
11 6 0.21
12 23 0.79
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
TTATATATATATA
Found at i:97468 original size:15 final size:16
Alignment explanation
Indices: 97438--97476 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
97428 CGATAGATAA
*
97438 TTTTCTTTCTTTTTCT
1 TTTTCTTTCTTCTTCT
97454 TTTTCTTTC-TCTTCT
1 TTTTCTTTCTTCTTCT
*
97469 TCTTCTTT
1 TTTTCTTT
97477 TTTATTTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCTTTCTTCTTCT
Found at i:97469 original size:21 final size:20
Alignment explanation
Indices: 97439--97478 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
97429 GATAGATAAT
*
97439 TTTCTTTCTTTTTCTTTTTC
1 TTTCTTTCTTCTTCTTTTTC
97459 TTTCTCTTCTTCTTCTTTTT
1 TTTCT-TTCTTCTTCTTTTT
97479 TATTTACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTCTTTCTTCTTCTTTTTC
Done.