Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016066.1 Corchorus olitorius cultivar O-4 contig16099, 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: 83461
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:7396 original size:2 final size:2
Alignment explanation
Indices: 7389--7421 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
7379 ACCAAAAGAA
7389 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
7422 ACTCACACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:9652 original size:17 final size:17
Alignment explanation
Indices: 9627--9661 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
9617 ATCTAAAAAA
* *
9627 TTAATGATTTAACGGTT
1 TTAACGATTTAACAGTT
9644 TTAACGATTTAACAGTT
1 TTAACGATTTAACAGTT
9661 T
1 T
9662 AATGGTTGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (17 bp):
TTAACGATTTAACAGTT
Found at i:9816 original size:45 final size:44
Alignment explanation
Indices: 9765--9849 Score: 152
Period size: 45 Copynumber: 1.9 Consensus size: 44
9755 CAACGTGTAA
*
9765 AATCTAACATATCTAAGATTTAACGGTTTCAACGGTTTAACCGTT
1 AATCTAACATATCTAAGATTTAACGATTT-AACGGTTTAACCGTT
9810 AATCTAACATATCTAAGATTTAACGATTTAACGGTTTAAC
1 AATCTAACATATCTAAGATTTAACGATTTAACGGTTTAAC
9850 GATTTAACGA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
44 11 0.28
45 28 0.72
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35
Consensus pattern (44 bp):
AATCTAACATATCTAAGATTTAACGATTTAACGGTTTAACCGTT
Found at i:9839 original size:8 final size:8
Alignment explanation
Indices: 9826--9861 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
9816 ACATATCTAA
9826 GATTTAAC
1 GATTTAAC
9834 GATTTAAC
1 GATTTAAC
*
9842 GGTTTAAC
1 GATTTAAC
9850 GATTTAAC
1 GATTTAAC
9858 GATT
1 GATT
9862 GGCGAATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (8 bp):
GATTTAAC
Found at i:18951 original size:13 final size:13
Alignment explanation
Indices: 18933--18977 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
18923 CTTATTTCTT
18933 TTTGATTTTGTTG
1 TTTGATTTTGTTG
18946 TTTGATTTTGTTG
1 TTTGATTTTGTTG
* *
18959 CTTTGGTCCTTGTTG
1 -TTTGAT-TTTGTTG
18974 TTTG
1 TTTG
18978 TTGTTGGCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 13 0.46
14 9 0.32
15 6 0.21
ACGTcount: A:0.04, C:0.07, G:0.24, T:0.64
Consensus pattern (13 bp):
TTTGATTTTGTTG
Found at i:24716 original size:54 final size:55
Alignment explanation
Indices: 24623--24734 Score: 190
Period size: 54 Copynumber: 2.1 Consensus size: 55
24613 TCCTCATCGA
* *
24623 TTTTGTTTTTCACTCTGGGGGACAGAGTCAAATCCTCAATGCCTCATTACTGTGT
1 TTTTGTTTTTCACCCTGGGGAACAGAGTCAAATCCTCAATGCCTCATTACTGTGT
*
24678 TTTTGTTTTTCACCCT-GGGAACAGAGTCAATTCCTCAATGCCTCATTACTGTGT
1 TTTTGTTTTTCACCCTGGGGAACAGAGTCAAATCCTCAATGCCTCATTACTGTGT
24732 TTT
1 TTT
24735 CAGGGTTGCT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
54 39 0.72
55 15 0.28
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (55 bp):
TTTTGTTTTTCACCCTGGGGAACAGAGTCAAATCCTCAATGCCTCATTACTGTGT
Found at i:25103 original size:21 final size:21
Alignment explanation
Indices: 25079--25146 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
25069 GATTAAAAAG
25079 AAAAATGATGAATGAATGTGT
1 AAAAATGATGAATGAATGTGT
* ***
25100 AAAAAT-AAGAAAT-ACAAAAG-
1 AAAAATGATG-AATGA-ATGTGT
25120 AAAAATGATGAATGAATGTGT
1 AAAAATGATGAATGAATGTGT
25141 AAAAAT
1 AAAAAT
25147 AAGAAATACT
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.59, C:0.01, G:0.18, T:0.22
Consensus pattern (21 bp):
AAAAATGATGAATGAATGTGT
Found at i:25131 original size:41 final size:41
Alignment explanation
Indices: 25074--25155 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
25064 AATATGATTA
25074 AAAAGAAAAATGATGAATGAATGTGTAAAAATAAGAAATAC
1 AAAAGAAAAATGATGAATGAATGTGTAAAAATAAGAAATAC
25115 AAAAGAAAAATGATGAATGAATGTGTAAAAATAAGAAATAC
1 AAAAGAAAAATGATGAATGAATGTGTAAAAATAAGAAATAC
25156 TTTCACTAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.61, C:0.02, G:0.17, T:0.20
Consensus pattern (41 bp):
AAAAGAAAAATGATGAATGAATGTGTAAAAATAAGAAATAC
Found at i:28780 original size:2 final size:2
Alignment explanation
Indices: 28773--28805 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
28763 CGTAAACAAG
*
28773 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28806 GGCAAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29312 original size:45 final size:42
Alignment explanation
Indices: 29251--29339 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 42
29241 ATTAATTCCT
29251 ATGTAATATATATATAATAACTAAAATACGTACATTAATTAA
1 ATGTAATATATATATAATAACTAAAATACGTACATTAATTAA
* *
29293 ATGTAATAATAATACTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAAT-AT-ATA-TATAATAACTAAAATACGTACATTAATTAA
29338 AT
1 AT
29340 TCTTAGATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
42 7 0.17
43 2 0.05
44 3 0.07
45 30 0.71
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.36
Consensus pattern (42 bp):
ATGTAATATATATATAATAACTAAAATACGTACATTAATTAA
Found at i:30400 original size:36 final size:36
Alignment explanation
Indices: 30353--30422 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
30343 GAGATTTTGG
*
30353 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAATA
30389 AGAAATATGATAACCAAAATTACAAAAAATGTAA
1 AGAAATATGATAACCAAAATTACAAAAAATGTAA
30423 GGTTATTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.23
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATTACAAAAAATGTAATA
Found at i:31189 original size:180 final size:179
Alignment explanation
Indices: 30878--31223 Score: 568
Period size: 180 Copynumber: 1.9 Consensus size: 179
30868 TTACTAATGT
*
30878 TATTAAGAATGTAAGGATTGGTAAATACAATTTTACAAACTTTTATAGCTTTTTTAGTAGATTAC
1 TATTAAGAATGTAAGGATTGGTAAATACAATTTTACAAACTTTTATAGCTTTTATAGTAGATTAC
* *
30943 TCAAGTAATTAAATTGGTAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAGGATGT
66 TCAAGTAATTAAATTGGCAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAAGATGT
*
31008 AAGATTACTTGAATCTAGATAGTACTATAATGTTTTTCGGGAAAAAAAA
131 AAGATCACTTGAATCTAGATAGTACTATAATGTTTTTCGGGAAAAAAAA
* * *
31057 TATTGAGAATGTAAGGATTGGTAAATGCAATTTTA-ATAACTTTTTTAGCTTTTATAGTAGTATT
1 TATTAAGAATGTAAGGATTGGTAAATACAATTTTACA-AACTTTTATAGCTTTTATAGTAG-ATT
* * *
31121 ACTTAAGTAATTAAATTGGCAACTTTCATTATTGATCATACAAAGTTACTAAAATTAATAAAGAT
64 ACTCAAGTAATTAAATTGGCAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAAGAT
*
31186 GTAAGATCATTTGAATCTAGATAGTACTATAATGTTTT
129 GTAAGATCACTTGAATCTAGATAGTACTATAATGTTTT
31224 CATAACTTTT
Statistics
Matches: 154, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
178 1 0.01
179 54 0.35
180 99 0.64
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.39
Consensus pattern (179 bp):
TATTAAGAATGTAAGGATTGGTAAATACAATTTTACAAACTTTTATAGCTTTTATAGTAGATTAC
TCAAGTAATTAAATTGGCAACTTTCATTATTAATCATAAAAAGTTACTAAAATTAATAAAGATGT
AAGATCACTTGAATCTAGATAGTACTATAATGTTTTTCGGGAAAAAAAA
Found at i:32961 original size:104 final size:104
Alignment explanation
Indices: 32839--33026 Score: 349
Period size: 104 Copynumber: 1.8 Consensus size: 104
32829 TTGATAATCA
* *
32839 TCTTTCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACTTTGTTCTTAATAGCCCTG
1 TCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTAATAGCCCTG
32904 TAGTTTTTTTAGTAAATTCTTTCTTCTTCTTCTTCTTTT
66 TAGTTTTTTTAGTAAATTCTTTCTTCTTCTTCTTCTTTT
*
32943 TCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATGTTTAACTTCGTTCTTAATAGCCCTG
1 TCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTAATAGCCCTG
33008 TAGTTTTTTTAGTAAATTC
66 TAGTTTTTTTAGTAAATTC
33027 AAATAAGAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 81 1.00
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (104 bp):
TCTTGCATCAGAGATCGATAACCTTCTTAATTGATTAATATTTAACTTCGTTCTTAATAGCCCTG
TAGTTTTTTTAGTAAATTCTTTCTTCTTCTTCTTCTTTT
Found at i:40386 original size:13 final size:13
Alignment explanation
Indices: 40365--40396 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40355 TGCTACATGA
40365 CCCTCCAATTTGT
1 CCCTCCAATTTGT
*
40378 CCCTTCAATTTGT
1 CCCTCCAATTTGT
40391 CCCTCC
1 CCCTCC
40397 TGACGTGTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.12, C:0.44, G:0.06, T:0.38
Consensus pattern (13 bp):
CCCTCCAATTTGT
Found at i:40549 original size:41 final size:41
Alignment explanation
Indices: 40496--40577 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
40486 TTTATAACTA
*
40496 GGGGCTAAACCTGGATTTAATTTCTTACCTTAATTATTAGG
1 GGGGCTAAACCTGGATTTAATTTATTACCTTAATTATTAGG
*
40537 GGGGCTAAACCTGGATTTAATTTATTTCCTTAATTATTAGG
1 GGGGCTAAACCTGGATTTAATTTATTACCTTAATTATTAGG
40578 AGGGTCAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (41 bp):
GGGGCTAAACCTGGATTTAATTTATTACCTTAATTATTAGG
Found at i:40594 original size:13 final size:13
Alignment explanation
Indices: 40576--40612 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
40566 TTAATTATTA
*
40576 GGAGGGTCAAGTT
1 GGAGGGTCAAATT
*
40589 GGAGGGACAAATT
1 GGAGGGTCAAATT
40602 GGAGGGTCAAA
1 GGAGGGTCAAA
40613 AAGAATTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.08, G:0.43, T:0.16
Consensus pattern (13 bp):
GGAGGGTCAAATT
Found at i:42978 original size:63 final size:62
Alignment explanation
Indices: 42806--43020 Score: 328
Period size: 62 Copynumber: 3.4 Consensus size: 62
42796 TTTAAATTTA
**
42806 ATTGACACCAGAAGTTGTCATA-TTAA--ATTATCTTGACACCAGAAGTTGTCATGAAAATT
1 ATTGACACCAGAAGTTGTCATACCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATT
42865 ATTGACACCAGAAGTTGTCATACCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATT
1 ATTGACACCAGAAGTTGTCATACCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATT
42927 ATTGACACCAGAAGATTGTCATACCAAATTATTATCTTGACACCAGAAGTTGTCATGCTGAGGAA
1 ATTGACACCAGAAG-TTGTCATACCAAATTATTATCTTGACACCAGAAGTTGTCA---TGA--AA
42992 ATT
60 ATT
*
42995 ATTGACACCAGAAGTTGTCATCCCAA
1 ATTGACACCAGAAGTTGTCATACCAA
43021 GATTGGAATT
Statistics
Matches: 144, Mismatches: 3, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
59 22 0.15
60 2 0.01
62 47 0.33
63 40 0.28
66 3 0.02
67 11 0.08
68 19 0.13
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (62 bp):
ATTGACACCAGAAGTTGTCATACCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATT
Found at i:50875 original size:53 final size:54
Alignment explanation
Indices: 50832--50934 Score: 145
Period size: 53 Copynumber: 1.9 Consensus size: 54
50822 GCATTAGGGT
* *
50832 CATCCAGGGGCATTTTAATCATTTGCAC-GTCCGGGGCATTTTGGTCATTTGCA
1 CATCCAGGGGCATTTTAATCATTTGCACAGTCAGGGGCATTTTGGTCATTGGCA
* * * *
50885 CATTCAGGGGCATTTTAGTCATTTGTACATTCAGGGGCATTTTGGTCATT
1 CATCCAGGGGCATTTTAATCATTTGCACAGTCAGGGGCATTTTGGTCATT
50935 TTAAGTTCAC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 25 0.57
54 19 0.43
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37
Consensus pattern (54 bp):
CATCCAGGGGCATTTTAATCATTTGCACAGTCAGGGGCATTTTGGTCATTGGCA
Found at i:50900 original size:27 final size:27
Alignment explanation
Indices: 50836--50935 Score: 139
Period size: 27 Copynumber: 3.7 Consensus size: 27
50826 TAGGGTCATC
* *
50836 CAGGGGCATTTTAATCATTTGCAC-GT
1 CAGGGGCATTTTAGTCATTTGCACATT
* *
50862 CCGGGGCATTTTGGTCATTTGCACATT
1 CAGGGGCATTTTAGTCATTTGCACATT
*
50889 CAGGGGCATTTTAGTCATTTGTACATT
1 CAGGGGCATTTTAGTCATTTGCACATT
*
50916 CAGGGGCATTTTGGTCATTT
1 CAGGGGCATTTTAGTCATTT
50936 TAAGTTCACT
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
26 21 0.32
27 44 0.68
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (27 bp):
CAGGGGCATTTTAGTCATTTGCACATT
Found at i:53301 original size:44 final size:44
Alignment explanation
Indices: 53252--53338 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
53242 TTTTATAGGG
53252 TTGTAAAAACTACCGGGTATTTGTAGGGTTCAGGTACCCTGGAT
1 TTGTAAAAACTACCGGGTATTTGTAGGGTTCAGGTACCCTGGAT
*
53296 TTGTAAAAACTACCGGGTATTTGTAGGGTTCGGGTACCCTGGA
1 TTGTAAAAACTACCGGGTATTTGTAGGGTTCAGGTACCCTGGA
53339 ATTTTATAGG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (44 bp):
TTGTAAAAACTACCGGGTATTTGTAGGGTTCAGGTACCCTGGAT
Found at i:57933 original size:31 final size:29
Alignment explanation
Indices: 57875--57933 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
57865 CTTGCTAAAT
* *
57875 TTGAGGCTAAACCTTTAAACTGGACCAAA
1 TTGAGGCTAAACCTTTAAAATGCACCAAA
*
57904 TTGAGTCTAAACCTTATTAAAATGCACCAA
1 TTGAGGCTAAACC-T-TTAAAATGCACCAA
57934 TTTGGGCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.48
30 1 0.04
31 12 0.48
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (29 bp):
TTGAGGCTAAACCTTTAAAATGCACCAAA
Found at i:58111 original size:31 final size:31
Alignment explanation
Indices: 58076--58154 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
58066 GCTTTTATTG
*
58076 TTTTTAGGCTCAAATTGAGCAATTTTTGAAA
1 TTTTTAGGCTCAAATTGAGCAACTTTTGAAA
* * *
58107 TTTTTAGACTGAAATTGAGTAACTTTTGAAA
1 TTTTTAGGCTCAAATTGAGCAACTTTTGAAA
**
58138 GCTTTAGGCTCAAATTG
1 TTTTTAGGCTCAAATTG
58155 GTAATTTGGC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.41
Consensus pattern (31 bp):
TTTTTAGGCTCAAATTGAGCAACTTTTGAAA
Found at i:58596 original size:12 final size:12
Alignment explanation
Indices: 58579--58608 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
58569 ATCGATACCT
58579 CGATATATCCGC
1 CGATATATCCGC
*
58591 CGATATATCCGT
1 CGATATATCCGC
58603 CGATAT
1 CGATAT
58609 CTGGATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.30
Consensus pattern (12 bp):
CGATATATCCGC
Found at i:63261 original size:32 final size:33
Alignment explanation
Indices: 63200--63264 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
63190 TATGGAATAT
*
63200 GGACTATAATTTAAGGGCATAATGATGAATTAA
1 GGACTATAATTTAAGGGCACAATGATGAATTAA
*
63233 GGACTATAGTTTAAGGGC-CAATGATGAATTAA
1 GGACTATAATTTAAGGGCACAATGATGAATTAA
63265 TCAATTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.43
33 17 0.57
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (33 bp):
GGACTATAATTTAAGGGCACAATGATGAATTAA
Found at i:64922 original size:15 final size:16
Alignment explanation
Indices: 64886--64923 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
64876 TTTTAAAAAT
*
64886 TAAAATTTTATTATGA
1 TAAAATTTTAATATGA
64902 TAAAATTTTAAT-TGA
1 TAAAATTTTAATATGA
*
64917 TGAAATT
1 TAAAATT
64924 GCGTCACCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (16 bp):
TAAAATTTTAATATGA
Found at i:72861 original size:179 final size:178
Alignment explanation
Indices: 72489--72877 Score: 469
Period size: 179 Copynumber: 2.2 Consensus size: 178
72479 TTTCCACCAT
* * *
72489 AAGCACAAATTATGTAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACTAATTCTTTG
1 AAGCAAAAATTATATAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACAAATTCTTTG
* *
72554 GAAGCATTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCA
66 AAAGCATTTTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCA
* * * * *
72619 TGGAACAACCTTTCAAGAGACACTTGAACCATCTCACTCAGACATCTG
131 TGGAACAACCTTTCAAGAGACACTTAAACCACCTCAATCAGACAACCG
* * * ** *
72667 GAGCAAAAGTTATATAATATTAAGTGGACCGTCTATTTCCCGTTAAGTGAAATAACAAATT-TTT
1 AAGCAAAAATTATATAATATTAAGTAGACCGTCTATTT-CCGTTAACCGAAACAACAAATTCTTT
72731 CGAAAGCATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGA
65 -GAAAGCATTTTTGATACCTTG-AACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGA
* * * * * * ** *
72795 TCATGGAACAATCTTTTAATAGAGACTTAAATCACCTTAATTGGATAACCG
128 TCATGGAACAACCTTTCAAGAGACACTTAAACCACCTCAATCAGACAACCG
* * *
72846 AAG-AAGAAATTATATAATGTTAAATAAACCGT
1 AAGCAA-AAATTATATAATATTAAGTAGACCGT
72878 TTAAACAAAC
Statistics
Matches: 176, Mismatches: 31, Indels: 7
0.82 0.14 0.03
Matches are distributed among these distances:
178 42 0.24
179 134 0.76
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (178 bp):
AAGCAAAAATTATATAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACAAATTCTTTG
AAAGCATTTTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCA
TGGAACAACCTTTCAAGAGACACTTAAACCACCTCAATCAGACAACCG
Found at i:74160 original size:21 final size:20
Alignment explanation
Indices: 74120--74199 Score: 66
Period size: 19 Copynumber: 4.3 Consensus size: 20
74110 CCGTTTAGTA
*
74120 ATATT-TATA-ATTAAATAT
1 ATATTATATATATAAAATAT
74138 ATATTATATATATAAAATA-
1 ATATTATATATATAAAATAT
* *
74157 ATATTAGATATATATAAT-T
1 ATATTATATATATAAAATAT
* *
74176 ACA-TATATA-ATAATATAT
1 ATATTATATATATAAAATAT
74194 A-ATTAT
1 ATATTAT
74200 TAAATGGTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
17 6 0.12
18 15 0.30
19 22 0.44
20 7 0.14
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (20 bp):
ATATTATATATATAAAATAT
Found at i:74183 original size:12 final size:11
Alignment explanation
Indices: 74125--74198 Score: 59
Period size: 10 Copynumber: 6.7 Consensus size: 11
74115 TAGTAATATT
74125 TATAATTAA-A
1 TATAATTAATA
74135 TATATATTATATA
1 TATA-ATTA-ATA
*
74148 TATAAAATAATA
1 TAT-AATTAATA
74160 T-TAGA-T-ATA
1 TATA-ATTAATA
74169 TATAATTACATA
1 TATAATTA-ATA
74181 TATAA-TAATA
1 TATAATTAATA
74191 TATAATTA
1 TATAATTA
74199 TTAAATGGTT
Statistics
Matches: 53, Mismatches: 1, Indels: 19
0.73 0.01 0.26
Matches are distributed among these distances:
9 5 0.09
10 17 0.32
11 10 0.19
12 13 0.25
13 7 0.13
14 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (11 bp):
TATAATTAATA
Found at i:78638 original size:30 final size:30
Alignment explanation
Indices: 78580--78639 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
78570 GAAATTCGTG
* *
78580 ATTGAAGATTTATTGAAGATAATTTCAAGA
1 ATTGAAGATCTATTGAAGATAATCTCAAGA
*
78610 ATTGAAGA-CTATTGAAGAATTATCTCAAGA
1 ATTGAAGATCTATTGAAG-ATAATCTCAAGA
78640 GGCAATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (30 bp):
ATTGAAGATCTATTGAAGATAATCTCAAGA
Done.