Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021815.1 Corchorus olitorius cultivar O-4 contig21848, 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: 70664
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:2386 original size:68 final size:69
Alignment explanation
Indices: 2277--2413 Score: 231
Period size: 68 Copynumber: 1.9 Consensus size: 69
2267 AGATCACTAC
2277 TAATCTAAAATCACCAGTGATGCAAGATCACCGGTG-ATCAAAGATTACATGGGTTTATGGTGGT
1 TAATCTAAAATCACCAGTGATGCAAGATCACCGGTGAATCAAAGATTACATGGGTTTATGGTGGT
2341 CTAG
66 CTAG
2345 TAATCTAAAATCACCAGTGATGCAAGATCACCGGTGATCAAATCAAAGATTACATGGGTTTATGG
1 TAATCTAAAATCACCAGTGATGCAAGATCACCGGTG----AATCAAAGATTACATGGGTTTATGG
2410 TGGT
62 TGGT
2414 AATCCAGATC
Statistics
Matches: 64, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
68 36 0.56
73 28 0.44
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.28
Consensus pattern (69 bp):
TAATCTAAAATCACCAGTGATGCAAGATCACCGGTGAATCAAAGATTACATGGGTTTATGGTGGT
CTAG
Found at i:2796 original size:98 final size:95
Alignment explanation
Indices: 2642--2883 Score: 344
Period size: 98 Copynumber: 2.5 Consensus size: 95
2632 TATTATAGAA
* * *
2642 TTTTAGAAATGAAATATAAAACTAATTTCACTAAGTTTAACCCCAAATTAAATTTTTTTTAGGGT
1 TTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATT-AATTTTTTTAAGGGT
*
2707 AAATTTCAAAATTAATAATTTATTGTTATACGG
65 AAATTCCAAAATTAATAA--TATTGTTATACGG
* *
2740 TTTTAGAAATAAAATACAAAACTAATTTCACTAAATTTAGCCCCAAATTAATTTTTTTAAGGGTA
1 TTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAATTTTTTTAAGGGTA
* *
2805 AATTCCATAATTAATAATATTGTTATAGGG
66 AATTCCAAAATTAATAATATTGTTATACGG
* * *
2835 TTTTAGAAATAAAATATATAACT-AGTTCACTAAGTTTAG-CACAAATTAA
1 TTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAA
2884 AATTAAAATT
Statistics
Matches: 131, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
93 9 0.07
94 14 0.11
95 33 0.25
97 30 0.23
98 45 0.34
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (95 bp):
TTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAATTTTTTTAAGGGTA
AATTCCAAAATTAATAATATTGTTATACGG
Found at i:7099 original size:107 final size:107
Alignment explanation
Indices: 6971--7226 Score: 361
Period size: 107 Copynumber: 2.4 Consensus size: 107
6961 TAAAAATATA
** * *
6971 TTAATTTGGGGTTAAATTTAGTGACATTAGTTTTATATTTTAATTCTAAAACCCTATAATAATAA
1 TTAATTTGGGACTAAACTTAGTGACATTAGTTTTATATTTTAATTCTAAAACCCTATAACAATAA
* *
7036 ACTATTAATTTTGGAATTTACCCTTTAAATTAAATTAAAATT
66 ACTATTAATTTTGAAATTTACCCTTAAAATTAAATTAAAATT
* * * *
7078 TTAATTTGGGACTAAACTTAGTGACATTAATGTTATATTTTAATTCTAAAATCTTATAACAATAA
1 TTAATTTGGGACTAAACTTAGTGACATTAGTTTTATATTTTAATTCTAAAACCCTATAACAATAA
* *
7143 ATTATTAATTTTGAAATTTACCCTTAAAATTTAATTAAAATT
66 ACTATTAATTTTGAAATTTACCCTTAAAATTAAATTAAAATT
*
7185 TTAATTT-GGAGCTAAACTTGGTGACATTAGTAATTTATATTT
1 TTAATTTGGGA-CTAAACTTAGTGACATTAGT--TTTATATTT
7227 AATGTTTAAA
Statistics
Matches: 131, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
106 3 0.02
107 120 0.92
109 8 0.06
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (107 bp):
TTAATTTGGGACTAAACTTAGTGACATTAGTTTTATATTTTAATTCTAAAACCCTATAACAATAA
ACTATTAATTTTGAAATTTACCCTTAAAATTAAATTAAAATT
Found at i:20550 original size:29 final size:29
Alignment explanation
Indices: 20516--20582 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
20506 ATAAGTCTGA
* *
20516 GGGGCAAACAT-CCCAAAATTGAAGTTCAT
1 GGGGCAAA-ATGCCCAAAATTGAAATTCAG
*
20545 GGGGCAAAATGGCCAAAATTGAAATTCAG
1 GGGGCAAAATGCCCAAAATTGAAATTCAG
20574 GGGGCAAAA
1 GGGGCAAAA
20583 CGTCCAAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 2 0.06
29 32 0.94
ACGTcount: A:0.40, C:0.16, G:0.27, T:0.16
Consensus pattern (29 bp):
GGGGCAAAATGCCCAAAATTGAAATTCAG
Found at i:20589 original size:29 final size:29
Alignment explanation
Indices: 20528--20590 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
20518 GGCAAACATC
* * *
20528 CCAAAATTGAAGTTCATGGGGCAAAATGG
1 CCAAAATTGAAATTCAGGGGGCAAAACGG
*
20557 CCAAAATTGAAATTCAGGGGGCAAAACGT
1 CCAAAATTGAAATTCAGGGGGCAAAACGG
20586 CCAAA
1 CCAAA
20591 CGCTACAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (29 bp):
CCAAAATTGAAATTCAGGGGGCAAAACGG
Found at i:24422 original size:28 final size:28
Alignment explanation
Indices: 24382--24440 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
24372 ACAAAATTGA
24382 AAGTAAATTTC-AATTTATCCTACTCTGC
1 AAGTAAATTTCAAATTT-TCCTACTCTGC
* *
24410 AAGTACATTTCAAATTTTCTTACTCTGC
1 AAGTAAATTTCAAATTTTCCTACTCTGC
24438 AAG
1 AAG
24441 CCCAAATAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 23 0.82
29 5 0.18
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.39
Consensus pattern (28 bp):
AAGTAAATTTCAAATTTTCCTACTCTGC
Found at i:26473 original size:2 final size:2
Alignment explanation
Indices: 26468--26529 Score: 72
Period size: 2 Copynumber: 31.0 Consensus size: 2
26458 GTCTCCACAC
* * *
26468 AT AT AT AT AT AC AT AC AT AC 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 AT AT AT AT
*
26510 AT AT GT AT -T AT CAT AT AT AT
1 AT AT AT AT AT AT -AT AT AT AT
26530 GTAATTTTCA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
1 1 0.02
2 47 0.94
3 2 0.04
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:26725 original size:20 final size:20
Alignment explanation
Indices: 26688--26725 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
26678 TGAGGCTCTG
*
26688 ACTTTTGAGATGATAATATT
1 ACTTTTGAGATGACAATATT
26708 ACTTTT-AGATGACCAATA
1 ACTTTTGAGATGA-CAATA
26726 GCATTCGGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (20 bp):
ACTTTTGAGATGACAATATT
Found at i:28568 original size:39 final size:39
Alignment explanation
Indices: 28514--28595 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
28504 TTTACTTTTT
* *
28514 TTTTTGGCACCAATCTATTTTATTAGTTTAAAATCCAAC
1 TTTTTGGCACCAATCTATTTTACTAATTTAAAATCCAAC
28553 TTTTTGGCACCAATCTATTTTACTAATTTAAAATCCAAC
1 TTTTTGGCACCAATCTATTTTACTAATTTAAAATCCAAC
28592 TTTT
1 TTTT
28596 AGTATATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (39 bp):
TTTTTGGCACCAATCTATTTTACTAATTTAAAATCCAAC
Found at i:32547 original size:4 final size:4
Alignment explanation
Indices: 32530--32570 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
32520 AAACTAGTGA
* * *
32530 TTTC TTTC TCTC TTTC TTTC TTTC TTTC TTTT TTTT TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
32571 AACTTTGGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:36814 original size:62 final size:63
Alignment explanation
Indices: 36727--36849 Score: 176
Period size: 62 Copynumber: 2.0 Consensus size: 63
36717 ATTTTTGGCT
* * * *
36727 AATTGCTCAAATAAGGGTCCAATATTTGCAAAAATGTTCAAATAAGGGCCCAAAGAAAAAACA
1 AATTGCTCAAATAAGGGCCCAATATTTACAAAAATGCTCAAATAAGGACCCAAAGAAAAAACA
* * *
36790 AATT-CTCAAATCAGGGCCCAATATTTACGAAAATGCTCAAATAAGGATCCAAAGAAAAAA
1 AATTGCTCAAATAAGGGCCCAATATTTACAAAAATGCTCAAATAAGGACCCAAAGAAAAAA
36850 ATGTTCCAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
62 49 0.92
63 4 0.08
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.20
Consensus pattern (63 bp):
AATTGCTCAAATAAGGGCCCAATATTTACAAAAATGCTCAAATAAGGACCCAAAGAAAAAACA
Found at i:36829 original size:31 final size:31
Alignment explanation
Indices: 36730--36835 Score: 106
Period size: 31 Copynumber: 3.4 Consensus size: 31
36720 TTTGGCTAAT
* *
36730 TGCTCAAATAAGGGTCCAATATTTGCAAAAA
1 TGCTCAAATAAGGGCCCAATATTTACAAAAA
* *** *
36761 TGTTCAAATAAGGGCCCAA-AGAAAAAACAAA
1 TGCTCAAATAAGGGCCCAATATTTACAA-AAA
* * *
36792 TTCTCAAATCAGGGCCCAATATTTACGAAAA
1 TGCTCAAATAAGGGCCCAATATTTACAAAAA
36823 TGCTCAAATAAGG
1 TGCTCAAATAAGG
36836 ATCCAAAGAA
Statistics
Matches: 56, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
30 3 0.05
31 50 0.89
32 3 0.05
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCCAATATTTACAAAAA
Found at i:37029 original size:31 final size:31
Alignment explanation
Indices: 36953--37029 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
36943 GCACGGGTTT
* * *
36953 ATTTAAGCAATTTTTGCAACGTTGGACCCTG
1 ATTTGAGCAATTTTTGCAACATTAGACCCTG
* * *
36984 ATTTGAGTAATTTTTGTAACATTAGATCCTG
1 ATTTGAGCAATTTTTGCAACATTAGACCCTG
*
37015 ATTTGAGCATTTTTT
1 ATTTGAGCAATTTTT
37030 TTTGTAAAGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.44
Consensus pattern (31 bp):
ATTTGAGCAATTTTTGCAACATTAGACCCTG
Found at i:37060 original size:33 final size:34
Alignment explanation
Indices: 36994--37062 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
36984 ATTTGAGTAA
* *
36994 TTTTTGTAACATTAGATCCTGATTTGAGCATTTT
1 TTTTTGTAACATTAGACCCTGATTTAAGCATTTT
*
37028 TTTTTGTAA-AGTTAGGCCCTGATTTAAG-ATTTT
1 TTTTTGTAACA-TTAGACCCTGATTTAAGCATTTT
37061 TT
1 TT
37063 CTTTAGGCCC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 8 0.26
34 23 0.74
ACGTcount: A:0.23, C:0.10, G:0.16, T:0.51
Consensus pattern (34 bp):
TTTTTGTAACATTAGACCCTGATTTAAGCATTTT
Found at i:38438 original size:30 final size:31
Alignment explanation
Indices: 38402--38469 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
38392 TTTGGTTAAT
38402 TAAGTCC-AAACATTGCAAAATCGGCTCAAA
1 TAAGTCCTAAACATTGCAAAATCGGCTCAAA
* * *
38432 TAAGTCCTTAACGTTGCAAAATCGGTTCAAA
1 TAAGTCCTAAACATTGCAAAATCGGCTCAAA
38463 TAAGTCC
1 TAAGTCC
38470 CTAGAGTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 7 0.21
31 27 0.79
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (31 bp):
TAAGTCCTAAACATTGCAAAATCGGCTCAAA
Found at i:42115 original size:2 final size:2
Alignment explanation
Indices: 42108--42134 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42098 TTTGACCAAC
42108 AT 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 AT A
42135 GTCCTTGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42192 original size:52 final size:52
Alignment explanation
Indices: 42116--42224 Score: 209
Period size: 52 Copynumber: 2.1 Consensus size: 52
42106 ACATATATAT
*
42116 ATATATATATATATATATAGTCCTTGGTCTACATCTAAATGCCTAAAGAGAG
1 ATATGTATATATATATATAGTCCTTGGTCTACATCTAAATGCCTAAAGAGAG
42168 ATATGTATATATATATATAGTCCTTGGTCTACATCTAAATGCCTAAAGAGAG
1 ATATGTATATATATATATAGTCCTTGGTCTACATCTAAATGCCTAAAGAGAG
42220 ATATG
1 ATATG
42225 ACCGGAATTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (52 bp):
ATATGTATATATATATATAGTCCTTGGTCTACATCTAAATGCCTAAAGAGAG
Found at i:47895 original size:27 final size:27
Alignment explanation
Indices: 47843--47895 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
47833 GGATTATTTA
* * *
47843 TTTATTTATTGTATTTTTTCTTATTAC
1 TTTATTTATTGTATTATTCCTCATTAC
47870 TTTATTTATAT-TATTATTCCTCATTA
1 TTTATTTAT-TGTATTATTCCTCATTA
47896 AGTTGGTGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (27 bp):
TTTATTTATTGTATTATTCCTCATTAC
Found at i:49424 original size:25 final size:26
Alignment explanation
Indices: 49396--49446 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
49386 GCCATTAGAG
49396 AGGAAAAAAAGGAAGGAGAG-AGGGA
1 AGGAAAAAAAGGAAGGAGAGAAGGGA
* *
49421 AGGAAAAAATGGGAGGAGAGAAGGGA
1 AGGAAAAAAAGGAAGGAGAGAAGGGA
49447 GAGCATTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.53, C:0.00, G:0.45, T:0.02
Consensus pattern (26 bp):
AGGAAAAAAAGGAAGGAGAGAAGGGA
Found at i:52425 original size:18 final size:19
Alignment explanation
Indices: 52387--52427 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
52377 GGGTTTACAC
*
52387 ATTAAAAATATTTTTAATTA
1 ATTAAAAATA-TTTAAATTA
52407 ATTAAAAATA-TTAAATTA
1 ATTAAAAATATTTAAATTA
52425 ATT
1 ATT
52428 TAATTAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
20 10 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTAAAAATATTTAAATTA
Found at i:61279 original size:3 final size:3
Alignment explanation
Indices: 61271--61296 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
61261 TCTAAACAAA
61271 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
61297 ATGAATGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:62229 original size:52 final size:52
Alignment explanation
Indices: 62141--62244 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
62131 TGTATTGCAT
*
62141 AAGCATGGAGGTTGCAGGCTGGTTCTTCAATCATCTGCGATACATATGCAGA
1 AAGCATGGAGGTTGCAGGCCGGTTCTTCAATCATCTGCGATACATATGCAGA
* * *
62193 AAGCCTGGAGGTTGCAGGCCGGTTCTTCAATTATCTGCTATACATATGCAGA
1 AAGCATGGAGGTTGCAGGCCGGTTCTTCAATCATCTGCGATACATATGCAGA
62245 GGCCAGTTCT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (52 bp):
AAGCATGGAGGTTGCAGGCCGGTTCTTCAATCATCTGCGATACATATGCAGA
Found at i:63152 original size:70 final size:71
Alignment explanation
Indices: 63069--63210 Score: 277
Period size: 71 Copynumber: 2.0 Consensus size: 71
63059 AATTCCAATC
63069 ACCCTATTTTTCGAATGTAAAAAAA-ATTGTCAATTTATGGTGATTTACATTTGTTAAACATCAT
1 ACCCTATTTTTCGAATGTAAAAAAATATTGTCAATTTATGGTGATTTACATTTGTTAAACATCAT
63133 GATATT
66 GATATT
63139 ACCCTATTTTTCGAATGTAAAAAAATATTGTCAATTTATGGTGATTTACATTTGTTAAACATCAT
1 ACCCTATTTTTCGAATGTAAAAAAATATTGTCAATTTATGGTGATTTACATTTGTTAAACATCAT
63204 GATATT
66 GATATT
63210 A
1 A
63211 TTTTTTGCGC
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 25 0.35
71 46 0.65
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (71 bp):
ACCCTATTTTTCGAATGTAAAAAAATATTGTCAATTTATGGTGATTTACATTTGTTAAACATCAT
GATATT
Found at i:63569 original size:28 final size:28
Alignment explanation
Indices: 63529--63582 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
63519 GCCTACCAAG
63529 TGCTTAGTATTTTTACATTAAAATCTCT
1 TGCTTAGTATTTTTACATTAAAATCTCT
*
63557 TGCTTAGTATTTTTACATTATAATCT
1 TGCTTAGTATTTTTACATTAAAATCT
63583 AGCTGATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.28, C:0.13, G:0.07, T:0.52
Consensus pattern (28 bp):
TGCTTAGTATTTTTACATTAAAATCTCT
Found at i:65750 original size:31 final size:30
Alignment explanation
Indices: 65715--65791 Score: 111
Period size: 29 Copynumber: 2.6 Consensus size: 30
65705 ATACCGTACA
65715 GGTCCCTCTACTTACAAAAAAGGATCAATTT
1 GGTCCCTCTACTTACAAAAAAGG-TCAATTT
* **
65746 GGTCCCTCTAC-TATAAAAACTGTCAATTT
1 GGTCCCTCTACTTACAAAAAAGGTCAATTT
65775 GGTCCCTCTACTTACAA
1 GGTCCCTCTACTTACAA
65792 TTTGGTGTCG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
29 18 0.44
30 12 0.29
31 11 0.27
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (30 bp):
GGTCCCTCTACTTACAAAAAAGGTCAATTT
Found at i:65837 original size:31 final size:30
Alignment explanation
Indices: 65715--65835 Score: 102
Period size: 31 Copynumber: 4.0 Consensus size: 30
65705 ATACCGTACA
* ***
65715 GGTCCCTCTACTTACAAAAAAGGATCAATTT
1 GGTCCCTCTACTTATAAAATCTG-TCAATTT
*
65746 GGTCCCTCTAC-TATAAAAACTGTCAATTT
1 GGTCCCTCTACTTATAAAATCTGTCAATTT
* ** * *
65775 GGTCCCTCTACTTACAATTTGGTGTCGA-TT
1 GGTCCCTCTACTTATAAAAT-CTGTCAATTT
65805 GAGTCCCTCTACTTAATAAAATCTGTCAATT
1 G-GTCCCTCTACTT-ATAAAATCTGTCAATT
65836 GATTATATAT
Statistics
Matches: 71, Mismatches: 14, Indels: 9
0.76 0.15 0.10
Matches are distributed among these distances:
29 18 0.25
30 15 0.21
31 33 0.46
32 5 0.07
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (30 bp):
GGTCCCTCTACTTATAAAATCTGTCAATTT
Found at i:65986 original size:12 final size:12
Alignment explanation
Indices: 65962--65994 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
65952 TTGGAAGCTC
65962 ACAACAAAC-TCA
1 ACAA-AAACATCA
65974 ACAAAAACATCA
1 ACAAAAACATCA
65986 ACAAAAACA
1 ACAAAAACA
65995 GAAGCAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.67, C:0.27, G:0.00, T:0.06
Consensus pattern (12 bp):
ACAAAAACATCA
Found at i:66130 original size:29 final size:31
Alignment explanation
Indices: 66084--66160 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 31
66074 TGACACCAAA
* *
66084 TTGTAAGTAAAGGGACCAAATTGA-CAGTTT
1 TTGTAAGTAGAGGGACCAAATTGATCACTTT
* *
66114 TTGT-AGTAGGGGGACCAAATTGATCCCTTT
1 TTGTAAGTAGAGGGACCAAATTGATCACTTT
66144 TTGTAAGTAGAGGGACC
1 TTGTAAGTAGAGGGACC
66161 TATACGGTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 17 0.43
30 12 0.30
31 11 0.28
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (31 bp):
TTGTAAGTAGAGGGACCAAATTGATCACTTT
Done.