Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021472.1 Corchorus olitorius cultivar O-4 contig21505, 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: 57495
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:898 original size:45 final size:45
Alignment explanation
Indices: 849--977 Score: 240
Period size: 45 Copynumber: 2.9 Consensus size: 45
839 AGCAACAATT
*
849 AATATTAGCTTTATTTTGATGAATTATCTAGAGACGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGGAGTAG
894 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGGAGTAG
*
939 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAG
1 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAG
978 TAGAATTTAG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.37
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGGAGTAG
Found at i:8313 original size:14 final size:14
Alignment explanation
Indices: 8294--8324 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
8284 TGGCATTAAT
8294 TAAGATTATAACCA
1 TAAGATTATAACCA
8308 TAAGATTATAACCA
1 TAAGATTATAACCA
8322 TAA
1 TAA
8325 TTTTTTCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (14 bp):
TAAGATTATAACCA
Found at i:13130 original size:18 final size:18
Alignment explanation
Indices: 13107--13143 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
13097 AAAGGGTAGT
*
13107 TAAAAAAAATTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
*
13125 TAAAAAGAAGTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
13143 T
1 T
13144 GCAACTGCTT
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:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (18 bp):
TAAAAAAAAGTGTTTTCA
Found at i:14115 original size:15 final size:16
Alignment explanation
Indices: 14084--14123 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
14074 TTACTCTGCT
14084 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
14100 TTGTTTTCTA-TTTAA
1 TTGTTTTCTAGTTTAA
*
14115 TTCTTTTCT
1 TTGTTTTCT
14124 GTCAATCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.15, C:0.10, G:0.07, T:0.68
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:18298 original size:16 final size:16
Alignment explanation
Indices: 18260--18305 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
18250 AGGCCAAATC
*
18260 GACGATAAGG-AGCAA
1 GACGATAAGGAAGAAA
18275 GACGATAAGGAAGAAA
1 GACGATAAGGAAGAAA
* *
18291 GTCGATAAAGAAGAA
1 GACGATAAGGAAGAA
18306 GCCAAAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 10 0.37
16 17 0.63
ACGTcount: A:0.52, C:0.09, G:0.30, T:0.09
Consensus pattern (16 bp):
GACGATAAGGAAGAAA
Found at i:18427 original size:23 final size:23
Alignment explanation
Indices: 18393--18438 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
18383 ACTTCAAGAG
18393 AAGCAAGTGTCGACTAAAGAGGA
1 AAGCAAGTGTCGACTAAAGAGGA
*
18416 AAGCAA-TAGTCGACTAAGGAGGA
1 AAGCAAGT-GTCGACTAAAGAGGA
18439 CGCACTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.43, C:0.13, G:0.30, T:0.13
Consensus pattern (23 bp):
AAGCAAGTGTCGACTAAAGAGGA
Found at i:20089 original size:17 final size:18
Alignment explanation
Indices: 20067--20102 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20057 AAAGGGTAAT
*
20067 TAAAAA-AATTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
20084 TAAAAAGAAGTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
20102 T
1 T
20103 GATAGAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
TAAAAAGAAGTGTTTTCA
Found at i:20978 original size:19 final size:18
Alignment explanation
Indices: 20954--20989 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20944 TGAAGACTTA
20954 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
20973 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
20990 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:24178 original size:7 final size:7
Alignment explanation
Indices: 24156--24213 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
24146 CTCTTAAATT
24156 ATTAATAA
1 ATTAAT-A
*
24164 AATAATA
1 ATTAATA
24171 ATTAATA
1 ATTAATA
24178 ATTAATA
1 ATTAATA
* *
24185 AATCAT-
1 ATTAATA
*
24191 ATTATTA
1 ATTAATA
24198 AGTTAATA
1 A-TTAATA
24206 ATTAATA
1 ATTAATA
24213 A
1 A
24214 CTCTTAAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
6 3 0.08
7 26 0.65
8 11 0.28
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (7 bp):
ATTAATA
Found at i:24222 original size:35 final size:33
Alignment explanation
Indices: 24143--24222 Score: 88
Period size: 35 Copynumber: 2.4 Consensus size: 33
24133 TAGTTAATCC
24143 TAACTCTTAAATTATTAATAAAATAATAATTAA
1 TAACTCTTAAATTATTAATAAAATAATAATTAA
* ** * **
24176 TAATTAATAAATCATATTATTAAGTTAATAATTAA
1 TAACTCTTAAAT--TATTAATAAAATAATAATTAA
24211 TAACTCTTAAAT
1 TAACTCTTAAAT
24223 AACCAATAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
33 9 0.25
35 27 0.75
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.41
Consensus pattern (33 bp):
TAACTCTTAAATTATTAATAAAATAATAATTAA
Found at i:26460 original size:16 final size:17
Alignment explanation
Indices: 26441--26474 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
26431 ATTTTTTCCG
26441 TTATTTTTCTTT-TTTT
1 TTATTTTTCTTTATTTT
*
26457 TTATTTTTGTTTATTTT
1 TTATTTTTCTTTATTTT
26474 T
1 T
26475 CTTAGTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.09, C:0.03, G:0.03, T:0.85
Consensus pattern (17 bp):
TTATTTTTCTTTATTTT
Found at i:41685 original size:69 final size:71
Alignment explanation
Indices: 41550--41697 Score: 237
Period size: 69 Copynumber: 2.1 Consensus size: 71
41540 AGAGTGAAAG
*
41550 AAATTGGCTGATAAATGACTCTTTCCATCAGATTCGATCCCTTTCATCTCTTTCAACAAAATTAT
1 AAATTGGCTGATAAATGACTCTTTCAATCA-A-T-GATCCCTTTCATCTCTTTCAACAAAATTAT
41615 ACACAAAAC
63 ACACAAAAC
41624 AAATTGGCTGATAAATGACTCTTTCAATC-A-GATCCCTTTCATCTCTTTCAACAAAATTATACA
1 AAATTGGCTGATAAATGACTCTTTCAATCAATGATCCCTTTCATCTCTTTCAACAAAATTATACA
*
41687 CAAAAG
66 CAAAAC
41693 AAATT
1 AAATT
41698 TGCATAACAA
Statistics
Matches: 72, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
69 43 0.60
72 1 0.01
74 28 0.39
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.32
Consensus pattern (71 bp):
AAATTGGCTGATAAATGACTCTTTCAATCAATGATCCCTTTCATCTCTTTCAACAAAATTATACA
CAAAAC
Found at i:42925 original size:223 final size:221
Alignment explanation
Indices: 42524--43094 Score: 883
Period size: 223 Copynumber: 2.6 Consensus size: 221
42514 AATCATTTCT
*
42524 CATCATCCCCAAATTCCTTAGAGATTGACATTTTTTCTCATATACCCAAAATTGGCATTAAAACG
1 CATCATCCCCAAATTCTTTAGAGATTGACATTTTTTCTCATATACCCAAAATTGGC-TTAAAACG
* *
42589 TGCTTTAATCCATATTTTTCATCCTAGTTAATTGAATAAACCTCGG-CTATATGATTTTAGTGCC
65 TGCTTTAATCCATATTTTTCATCCTAATTAATTGAATAAACCT-GGTCTATATGATTTTAGTGAC
* * *
42653 ATCTAATAATTAAACAAAATGCAAAATTCAGCATCCCCAAACCGATATACTTTATACCCACATCA
129 ATCTAATAATTAAACAAAATGCAAAATTCAGCACCCCCAAACCGATATACTCTATACCCAAATC-
*
42718 TTTTCTCATCATCCCCAAATAATCATATG
193 GTTTCTCATCATCCCCAAATAATCATATG
* * *
42747 CATCATCCCCAAATTCTTTAGAGATTGAAATTTTTTCTCATATACCCGAAATTGGCTTTAAAAAG
1 CATCATCCCCAAATTCTTTAGAGATTGACATTTTTTCTCATATACCCAAAATTGGC-TTAAAACG
42812 TGCTTTAATCCATATTTTTCATCCTAATTAATTGAATAAACCTGGTCTATATGATTTTAGTGACA
65 TGCTTTAATCCATATTTTTCATCCTAATTAATTGAATAAACCTGGTCTATATGATTTTAGTGACA
* * ***
42877 TCTAATAATTAAACAAGATGCAAAATTCAGGACCCCCAATTTGATATACTCTATACCCAAATCGT
130 TCTAATAATTAAACAAAATGCAAAATTCAGCACCCCCAAACCGATATACTCTATACCCAAATCGT
42942 TTCTCATCATCCCCAAATAATCATATG
195 TTCTCATCATCCCCAAATAATCATATG
* * * *
42969 CACCATCCCCAAATTCTTAAGAGATTGACATTTTTTCTCATATATCCAAAATTGGCTTCAAACGT
1 CATCATCCCCAAATTCTTTAGAGATTGACATTTTTTCTCATATACCCAAAATTGGCTTAAAACGT
* *** *
43034 GTTTTAATCCATATTTTTCATCCTAATTAATTGAATAAACCCCATCTATATGAATTTAGTG
66 GCTTTAATCCATATTTTTCATCCTAATTAATTGAATAAACCTGGTCTATATGATTTTAGTG
43095 TGATCGGTCG
Statistics
Matches: 319, Mismatches: 28, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
221 63 0.20
222 81 0.25
223 175 0.55
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.35
Consensus pattern (221 bp):
CATCATCCCCAAATTCTTTAGAGATTGACATTTTTTCTCATATACCCAAAATTGGCTTAAAACGT
GCTTTAATCCATATTTTTCATCCTAATTAATTGAATAAACCTGGTCTATATGATTTTAGTGACAT
CTAATAATTAAACAAAATGCAAAATTCAGCACCCCCAAACCGATATACTCTATACCCAAATCGTT
TCTCATCATCCCCAAATAATCATATG
Found at i:44642 original size:22 final size:21
Alignment explanation
Indices: 44590--44643 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
44580 TACTTCTTGA
44590 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
44611 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
44630 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
44644 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:45930 original size:222 final size:220
Alignment explanation
Indices: 45437--45990 Score: 860
Period size: 222 Copynumber: 2.5 Consensus size: 220
45427 TGAGGCATGC
* *
45437 ACAAAATTCAGCATCCCCAAAGTGATATACTCTATACCCAAATCATTTATCATCATCCCCAAATA
1 ACAAAATTCAGCATCCCCAAAGTGATATA-TTTATACCCAAATCATTTCTCATCATCCCCAAATA
* * *
45502 ATCACTA-GCACCATCCCCAAATTCATTATAGATTGACATTTTTTCTTATATACCCAAAATTGGC
65 ATCA-TATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTCTCATATACCCAAAATTGGC
* *
45566 TTCAAACATGTTTTAATCCATATTTTTCATTCTAATTAATTGAATAAACCCCTTCTATATGATTT
129 TTCAAAAATGTTTTAATCCATATTTTTCATTCTAATTAATTGAATAAACCCCGTCTATATGATTT
* *
45631 CAGTGCCATCTAATAATTAAACATAAT
194 CAGTGCCATCTAATAATGAAACAAAAT
* * * *
45658 GCAAAATTCAGTATCCCCAAAGTAATATACTTTATACCCAAATCATTTCTCATAATCCCCAAATA
1 ACAAAATTCAGCATCCCCAAAGTGATATA-TTTATACCCAAATCATTTCTCATCATCCCCAAATA
*
45723 ATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTCTCATATATCCAAAATTGGCT
65 ATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTCTCATATACCCAAAATTGGCT
*
45788 TTAAAAAGTGTTTTAATCCATATTTTTCATTCTAATTAATTGAATAAACCCCGTCTATATGAATT
130 TCAAAAA-TGTTTTAATCCATATTTTTCATTCTAATTAATTGAATAAACCCCGTCTATATG-ATT
*
45853 T-AGTGTCATCTAATAATGAAACAAAAT
193 TCAGTGCCATCTAATAATGAAACAAAAT
* * * *
45880 ACAAAATTCAGCATCCCCATACTGATATATTATATACCTAAATAATTTCTCATCATCCCCAAATA
1 ACAAAATTCAGCATCCCCAAAGTGATATATT-TATACCCAAATCATTTCTCATCATCCCCAAATA
45945 ATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTCT
65 ATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTCT
45991 TTTATAGCCA
Statistics
Matches: 305, Mismatches: 24, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
220 2 0.01
221 124 0.41
222 175 0.57
223 4 0.01
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.35
Consensus pattern (220 bp):
ACAAAATTCAGCATCCCCAAAGTGATATATTTATACCCAAATCATTTCTCATCATCCCCAAATAA
TCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTTCTCATATACCCAAAATTGGCTT
CAAAAATGTTTTAATCCATATTTTTCATTCTAATTAATTGAATAAACCCCGTCTATATGATTTCA
GTGCCATCTAATAATGAAACAAAAT
Found at i:46109 original size:105 final size:107
Alignment explanation
Indices: 45912--46302 Score: 471
Period size: 114 Copynumber: 3.5 Consensus size: 107
45902 TGATATATTA
* *
45912 TATACCTAAATAATTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGA
1 TATACCAAAATCATTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTC-------A
* * *
45977 TTGACATTTTTTCTTTTATAGCCAAAAGTATCCCCCAACTTATAAGCTT
59 TTGACATTTTTTCTTATATACCCAAAAGTATCCCCCAACTTATAAACTT
* * *
46026 TATACCTAAATCATTTCTCTTCATCCCCAAATAATCATATGCACCATCCCCGAATTC-TTGACA-
1 TATACCAAAATCATTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCATTGACAT
46089 TTTTTCTTATATACCCAAAAGTATCCCCCAACTTATAAACTT
66 TTTTTCTTATATACCCAAAAGTATCCCCCAACTTATAAACTT
* * * *
46131 TATACCCAAATCATTTCTCGTCTTTCCCCAAATAATCATATGCACCATCCTCAAATTCTTTAGAG
1 TATACCAAAATCATTTCTCATC-ATCCCCAAATAATCATATGCACCATCCCCAAATTC-------
* * *
46196 ATTGACATTTTTTCTTATATACGCAAAAGTATCCCCAAACTGATAAACTT
58 ATTGACATTTTTTCTTATATACCCAAAAGTATCCCCCAACTTATAAACTT
* * *
46246 TATACCAAAATTATTTCTCATCATCTCCAAATAATCATATGCATCATCCCCAAATTC
1 TATACCAAAATCATTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTC
46303 CAAATGAAAT
Statistics
Matches: 246, Mismatches: 21, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
105 59 0.24
106 38 0.15
114 91 0.37
115 58 0.24
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.35
Consensus pattern (107 bp):
TATACCAAAATCATTTCTCATCATCCCCAAATAATCATATGCACCATCCCCAAATTCATTGACAT
TTTTTCTTATATACCCAAAAGTATCCCCCAACTTATAAACTT
Found at i:46300 original size:114 final size:114
Alignment explanation
Indices: 46083--46302 Score: 334
Period size: 115 Copynumber: 1.9 Consensus size: 114
46073 CCCCGAATTC
* * *
46083 TTGACATTTTTCTTATATACCCAAAAGTATCCCCCAACTTATAAACTTTATACCCAAATCATTTC
1 TTGACATTTTTCTTATATACCCAAAAGTATCCCCAAACTGATAAACTTTATACCAAAATCATTTC
* * *
46148 TCGTCTTTCCCCAAATAATCATATGCACCATCCTCAAATTCTTTAGAGA
66 TCATCTATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGA
* *
46197 TTGACATTTTTTCTTATATACGCAAAAGTATCCCCAAACTGATAAACTTTATACCAAAATTATTT
1 TTGACA-TTTTTCTTATATACCCAAAAGTATCCCCAAACTGATAAACTTTATACCAAAATCATTT
* *
46262 CTCATC-ATCTCCAAATAATCATATGCATCATCCCCAAATTC
65 CTCATCTATCCCCAAATAATCATATGCACCATCCCCAAATTC
46303 CAAATGAAAT
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
114 37 0.39
115 58 0.61
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (114 bp):
TTGACATTTTTCTTATATACCCAAAAGTATCCCCAAACTGATAAACTTTATACCAAAATCATTTC
TCATCTATCCCCAAATAATCATATGCACCATCCCCAAATTCTTTAGAGA
Found at i:46724 original size:32 final size:32
Alignment explanation
Indices: 46688--46756 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
46678 ATGGCTTATC
* * *
46688 AAATCCCTGAATCTTTTGCTTATCAAATCTCT
1 AAATCCCTAAATCTTTTGATTATCAAATCCCT
46720 AAATCCCTAAATCTTTTGATTATCAAATCCCT
1 AAATCCCTAAATCTTTTGATTATCAAATCCCT
46752 AAATC
1 AAATC
46757 TTTTCTCTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (32 bp):
AAATCCCTAAATCTTTTGATTATCAAATCCCT
Found at i:53544 original size:13 final size:15
Alignment explanation
Indices: 53534--53566 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
53524 TTAATATTAA
53534 ATAAGACTATTATAT
1 ATAAGACTATTATAT
*
53549 ATATGACTATTATAT
1 ATAAGACTATTATAT
53564 ATA
1 ATA
53567 TGAATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (15 bp):
ATAAGACTATTATAT
Found at i:53558 original size:15 final size:15
Alignment explanation
Indices: 53538--53569 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
53528 TATTAAATAA
53538 GACTATTATATATAT
1 GACTATTATATATAT
53553 GACTATTATATATAT
1 GACTATTATATATAT
53568 GA
1 GA
53570 ATATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (15 bp):
GACTATTATATATAT
Found at i:53954 original size:31 final size:30
Alignment explanation
Indices: 53883--53954 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 30
53873 GTCTATCAGC
*
53883 TTTTAATTTGTTTAATTTAAGACTTTCATT
1 TTTTAATTTGTTTAATTTAAGACTTACATT
*
53913 TTAATT-ATTTGTTTAATTTAATG-CTTAGATT
1 TT--TTAATTTGTTTAATTTAA-GACTTACATT
53944 GTTTTAATTTG
1 -TTTTAATTTG
53955 CAATAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
30 4 0.11
31 26 0.74
32 5 0.14
ACGTcount: A:0.26, C:0.04, G:0.10, T:0.60
Consensus pattern (30 bp):
TTTTAATTTGTTTAATTTAAGACTTACATT
Found at i:54433 original size:16 final size:16
Alignment explanation
Indices: 54412--54578 Score: 259
Period size: 16 Copynumber: 10.6 Consensus size: 16
54402 CTACCCGAGA
54412 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
54428 CCGAACCCG-ACATAAC
1 CCGAACCCGAAAAT-AC
*
54444 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
54460 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
54476 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
54492 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
54508 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
54524 CCGAACCTGAAAATAC
1 CCGAACCCGAAAATAC
*
54540 CCGAACCCG-AAGTAC
1 CCGAACCCGAAAATAC
*
54555 CCGAACCCG-AAGTAC
1 CCGAACCCGAAAATAC
54570 CCGAACCCG
1 CCGAACCCG
54579 CTCGAGCCCG
Statistics
Matches: 142, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
15 32 0.23
16 107 0.75
17 3 0.02
ACGTcount: A:0.40, C:0.39, G:0.15, T:0.07
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:56167 original size:35 final size:35
Alignment explanation
Indices: 56120--56199 Score: 151
Period size: 35 Copynumber: 2.3 Consensus size: 35
56110 TGCAGGACTG
*
56120 GAATTATGAATCTCTAGGGAAATCTCTAGGCATCA
1 GAATTATAAATCTCTAGGGAAATCTCTAGGCATCA
56155 GAATTATAAATCTCTAGGGAAATCTCTAGGCATCA
1 GAATTATAAATCTCTAGGGAAATCTCTAGGCATCA
56190 GAATTATAAA
1 GAATTATAAA
56200 GTAACTAGCT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (35 bp):
GAATTATAAATCTCTAGGGAAATCTCTAGGCATCA
Done.