Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012981.1 Corchorus olitorius cultivar O-4 contig13014, 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: 64037
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1932 original size:11 final size:11
Alignment explanation
Indices: 1913--1949 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
1903 TAAGTGGGTT
1913 AAAAA-AAATA
1 AAAAATAAATA
1923 AAAAATAAATA
1 AAAAATAAATA
1934 AAAAATAAATA
1 AAAAATAAATA
1945 AAAAA
1 AAAAA
1950 AAACCCCTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 5 0.19
11 21 0.81
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAATAAATA
Found at i:1945 original size:15 final size:14
Alignment explanation
Indices: 1914--1952 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
1904 AAGTGGGTTA
*
1914 AAAAAAATAAAAAAT
1 AAAAAAA-AATAAAT
1929 AAATAAAAAATAAAT
1 AAA-AAAAAATAAAT
1944 AAAAAAAAA
1 AAAAAAAAA
1953 CCCCTCCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 6 0.27
15 12 0.55
16 4 0.18
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAAAAAATAAAT
Found at i:8265 original size:20 final size:21
Alignment explanation
Indices: 8240--8278 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
8230 TTAACTGTTC
8240 TCCAATTTTCAT-CTCCATTT
1 TCCAATTTTCATCCTCCATTT
*
8260 TCCAATTTTTATCCTCCAT
1 TCCAATTTTCATCCTCCAT
8279 CTCCACTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.21, C:0.31, G:0.00, T:0.49
Consensus pattern (21 bp):
TCCAATTTTCATCCTCCATTT
Found at i:8283 original size:20 final size:20
Alignment explanation
Indices: 8237--8283 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
8227 CTTTTAACTG
8237 TTCTCCAATTTTCATCTCCA
1 TTCTCCAATTTTCATCTCCA
* *
8257 TTTTCCAATTTTTATCCTCCA
1 TTCTCCAATTTTCAT-CTCCA
8278 -TCTCCA
1 TTCTCCA
8284 CTACCAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.19, C:0.34, G:0.00, T:0.47
Consensus pattern (20 bp):
TTCTCCAATTTTCATCTCCA
Found at i:11305 original size:329 final size:329
Alignment explanation
Indices: 10707--11365 Score: 1255
Period size: 329 Copynumber: 2.0 Consensus size: 329
10697 GATCCTATAA
10707 GTACAGTTTTGCATGCTACTAAACTTCAAGAGAAATGGAACTTTACTTTCAACCAGACTTCTAGA
1 GTACAGTTTTGCATGCTACTAAACTTCAAGAGAAATGGAACTTTACTTTCAACCAGACTTCTAGA
* *
10772 TCTTTACAGAGTCTCCACAGATTACCCGCATCCATGGGACATCTAGTTTTAGCAACACAACATAA
66 TCTTTACAGAGTCTCCACAGATTACCCACATCCATGGGACATCTAGTTTTAGCAACACAACAGAA
*
10837 TTTTGATTGTTTTGTTATGATGCACATCCATAGGAACAATATCACTCAACTCTATGGAGCAGTGT
131 TTTTGATTGTTTTGTTATGATGCACATCCACAGGAACAATATCACTCAACTCTATGGAGCAGTGT
*
10902 CAATGATCTGCATTGGTGATAATTGGGTGCAAGCTATTTTCTGCAGATCCTACAGAGCAACTGAT
196 CAATGATCTGCATTGGTGATAATTGGGTGCAAGCTATTTTATGCAGATCCTACAGAGCAACTGAT
*
10967 AGCAGGATGGCGATCTTACTTTTAATCAAGGAAATACTTGTGCGATTACATGAATTGAGAATTGT
261 AGCAGGATGGCGATCTTACTTTTAATCAAGGAAATACTTGTGCGATTACATGAATTGAGAATTGC
11032 AGCT
326 AGCT
*
11036 GTACAGTTTTGCATGCTACTAAACTTCAAGAGAAATGGAACTTTGCTTTCAACCAGACTTCTAGA
1 GTACAGTTTTGCATGCTACTAAACTTCAAGAGAAATGGAACTTTACTTTCAACCAGACTTCTAGA
11101 TCTTTACAGAGTCTCCACAGATTACCCACATCCATGGGACATCTAGTTTTAGCAACACAACAGAA
66 TCTTTACAGAGTCTCCACAGATTACCCACATCCATGGGACATCTAGTTTTAGCAACACAACAGAA
11166 TTTTGATTGTTTTGTTATGATGCACATCCACAGGAACAATATCACTCAACTCTATGGAGCAGTGT
131 TTTTGATTGTTTTGTTATGATGCACATCCACAGGAACAATATCACTCAACTCTATGGAGCAGTGT
11231 CAATGATCTGCATTGGTGATAATTGGGTGCAAGCTATTTTATGCAGATCCTACAGAGCAACTGAT
196 CAATGATCTGCATTGGTGATAATTGGGTGCAAGCTATTTTATGCAGATCCTACAGAGCAACTGAT
*
11296 AGCAGGATGGCGATCTTACTTTTAATCAGGGAAATACTTGTGCGATTACATGAATTGAGAATTGC
261 AGCAGGATGGCGATCTTACTTTTAATCAAGGAAATACTTGTGCGATTACATGAATTGAGAATTGC
11361 AGCT
326 AGCT
11365 G
1 G
11366 CCACAATCTG
Statistics
Matches: 323, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
329 323 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (329 bp):
GTACAGTTTTGCATGCTACTAAACTTCAAGAGAAATGGAACTTTACTTTCAACCAGACTTCTAGA
TCTTTACAGAGTCTCCACAGATTACCCACATCCATGGGACATCTAGTTTTAGCAACACAACAGAA
TTTTGATTGTTTTGTTATGATGCACATCCACAGGAACAATATCACTCAACTCTATGGAGCAGTGT
CAATGATCTGCATTGGTGATAATTGGGTGCAAGCTATTTTATGCAGATCCTACAGAGCAACTGAT
AGCAGGATGGCGATCTTACTTTTAATCAAGGAAATACTTGTGCGATTACATGAATTGAGAATTGC
AGCT
Found at i:13151 original size:9 final size:9
Alignment explanation
Indices: 13137--13163 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
13127 TAAACTTTAG
13137 GGGTAAAAT
1 GGGTAAAAT
13146 GGGTAAAAT
1 GGGTAAAAT
13155 GGGTAAAAT
1 GGGTAAAAT
13164 AAATTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (9 bp):
GGGTAAAAT
Found at i:13757 original size:29 final size:31
Alignment explanation
Indices: 13725--13782 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
13715 TTGCTTCCTA
*
13725 TTTTTCTTTTG-GCT-AAATTCTTATAATCC
1 TTTTTCTTTTGCGATAAAATTCTTATAATCC
*
13754 TTTTTTTTTTGCGATAAAATTCTTATAAT
1 TTTTTCTTTTGCGATAAAATTCTTATAAT
13783 ATAATCCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 2 0.08
31 13 0.52
ACGTcount: A:0.24, C:0.12, G:0.07, T:0.57
Consensus pattern (31 bp):
TTTTTCTTTTGCGATAAAATTCTTATAATCC
Found at i:13892 original size:22 final size:21
Alignment explanation
Indices: 13865--13922 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
13855 GAGAAAATAG
13865 AAAGAAATAAAAAAAATATTTT
1 AAAGAAATAAAAAAAATA-TTT
**
13887 AAAGAAGA-ATTAAAAATATTT
1 AAAGAA-ATAAAAAAAATATTT
*
13908 AAA-ACATAAAAAAAA
1 AAAGAAATAAAAAAAA
13923 ATCCACATAG
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 1 0.03
20 7 0.24
21 6 0.21
22 14 0.48
23 1 0.03
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (21 bp):
AAAGAAATAAAAAAAATATTT
Found at i:14074 original size:45 final size:45
Alignment explanation
Indices: 14023--14110 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
14013 CAATTTTGTA
*
14023 ACATTTGGTACTAAATTGAGCAATTTTGAAGCTTTGGTAAAAATT
1 ACATTTGGTACTAAATTGAGCAATTTTAAAGCTTTGGTAAAAATT
*
14068 ACATTTGGTACTAAATTGAGCAGTTTTAAAGCTTTGGTAAAAA
1 ACATTTGGTACTAAATTGAGCAATTTTAAAGCTTTGGTAAAAA
14111 AATGAGCATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (45 bp):
ACATTTGGTACTAAATTGAGCAATTTTAAAGCTTTGGTAAAAATT
Found at i:22939 original size:29 final size:29
Alignment explanation
Indices: 22890--22977 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 29
22880 ACGGCTTCAT
* * *
22890 CCTGGACATTGCCAAATGAACACGAACGC
1 CCTGGACATTACCACAGGAACACGAACGC
** *
22919 CCTGGACATTACCATC-GGAACACGTTCGT
1 CCTGGACATTACCA-CAGGAACACGAACGC
* *
22948 CCTGGACTTTGCCACAGGAACGACGAACGC
1 CCTGGACATTACCACAGGAAC-ACGAACGC
22978 TAGGATCTTC
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
28 1 0.02
29 39 0.87
30 5 0.11
ACGTcount: A:0.28, C:0.32, G:0.23, T:0.17
Consensus pattern (29 bp):
CCTGGACATTACCACAGGAACACGAACGC
Found at i:27864 original size:11 final size:11
Alignment explanation
Indices: 27839--27882 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
27829 CATTTTCATT
27839 TTTCTGTTTTTG
1 TTTC-GTTTTTG
*
27851 TTTCGTTTTCG
1 TTTCGTTTTTG
*
27862 TTTTGTTTTTG
1 TTTCGTTTTTG
*
27873 TTGCGTTTTT
1 TTTCGTTTTT
27883 AATTTCTTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 23 0.85
12 4 0.15
ACGTcount: A:0.00, C:0.09, G:0.18, T:0.73
Consensus pattern (11 bp):
TTTCGTTTTTG
Found at i:28494 original size:18 final size:17
Alignment explanation
Indices: 28468--28501 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
28458 TAAGAACTAT
28468 AAAAACAAGAAAGAAAG
1 AAAAACAAGAAAGAAAG
28485 AAAAACCAAGAAAGAAA
1 AAAAA-CAAGAAAGAAA
28502 CAGGCAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAACAAGAAAGAAAG
Found at i:32906 original size:18 final size:17
Alignment explanation
Indices: 32883--32916 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
32873 GTTTTGCCTG
32883 TTTCTTTCTTGGTTTTTC
1 TTTCTTTCTT-GTTTTTC
32901 TTTCTTTCTTGTTTTT
1 TTTCTTTCTTGTTTTT
32917 ATAGTTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.76
Consensus pattern (17 bp):
TTTCTTTCTTGTTTTTC
Found at i:33535 original size:22 final size:24
Alignment explanation
Indices: 33505--33556 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
33495 AGGAATTAAC
*
33505 AACGCAACAAAAAC-AAAA-CGAA
1 AACGAAACAAAAACAAAAATCGAA
33527 AACGAAACAAAAACATAAAATCGAA
1 AACGAAACAAAAACA-AAAATCGAA
33552 AACGA
1 AACGA
33557 TGCCAAACGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 13 0.50
24 4 0.15
25 9 0.35
ACGTcount: A:0.67, C:0.19, G:0.10, T:0.04
Consensus pattern (24 bp):
AACGAAACAAAAACAAAAATCGAA
Found at i:33920 original size:11 final size:11
Alignment explanation
Indices: 33896--33937 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
33886 TTGACAACGC
33896 AACAAAAACAA
1 AACAAAAACAA
* *
33907 AACGAAAACGA
1 AACAAAAACAA
33918 AACAAAAACAAA
1 AACAAAAAC-AA
33930 AACAAAAA
1 AACAAAAA
33938 ACGGAAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.79, C:0.17, G:0.05, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:33939 original size:7 final size:6
Alignment explanation
Indices: 33896--33937 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
33886 TTGACAACGC
* *
33896 AACAAA AAC-AA AACGAA AAC-GA AACAAA AACAAA AACAAA AA
1 AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AA
33938 ACGGAAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 9 0.28
6 23 0.72
ACGTcount: A:0.79, C:0.17, G:0.05, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:40529 original size:15 final size:16
Alignment explanation
Indices: 40499--40530 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
40489 TTGAGAGTGA
40499 TCAAAGCAATTTAAAT
1 TCAAAGCAATTTAAAT
40515 TCAAAGCAA-TTAAAT
1 TCAAAGCAATTTAAAT
40530 T
1 T
40531 ATAAAAACGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (16 bp):
TCAAAGCAATTTAAAT
Found at i:48747 original size:2 final size:2
Alignment explanation
Indices: 48740--48770 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
48730 TCATATAATG
*
48740 TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48771 TAATGTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:48937 original size:10 final size:10
Alignment explanation
Indices: 48878--48936 Score: 84
Period size: 10 Copynumber: 5.9 Consensus size: 10
48868 CATCTACCTC
48878 ATAAGCTCTG
1 ATAAGCTCTG
48888 ATAAGCTCTG
1 ATAAGCTCTG
48898 ATAAGCTCTG
1 ATAAGCTCTG
48908 ATAAGCTCTG
1 ATAAGCTCTG
* *
48918 AGAAGTTCT-
1 ATAAGCTCTG
48927 ACTAAGCTCT
1 A-TAAGCTCT
48937 ATTATGCTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
9 1 0.02
10 43 0.98
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (10 bp):
ATAAGCTCTG
Found at i:49277 original size:10 final size:9
Alignment explanation
Indices: 49250--49300 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 9
49240 CGAGGGTGTG
*
49250 ATAGAGCATA
1 ATAGAGC-TT
49260 ATAGAGCTT
1 ATAGAGCTT
49269 AGTAGAGCTT
1 A-TAGAGCTT
49279 ATCAGAGCTT
1 AT-AGAGCTT
49289 ATCAGAGCTT
1 AT-AGAGCTT
49299 AT
1 AT
49301 GAGGTAGATG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
9 3 0.08
10 35 0.92
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (9 bp):
ATAGAGCTT
Found at i:53181 original size:22 final size:21
Alignment explanation
Indices: 53129--53355 Score: 130
Period size: 22 Copynumber: 10.5 Consensus size: 21
53119 TTAGGAGTAC
*
53129 CAAAATTTGATAGA-AGGTTAT
1 CAAAATTTCATAGAGA-GTTAT
*
53150 C-AAATCTCATAGAGTAGTTAT
1 CAAAATTTCATAGAG-AGTTAT
*
53171 CGAAATTTCATAGAGATCAGATTAT
1 CAAAATTTCATAGAG---AG-TTAT
*
53196 CAAAATTT-ATA-AGA-CTAT
1 CAAAATTTCATAGAGAGTTAT
* *
53214 CAAAATTTTATAGTGTTA-TTAT
1 CAAAATTTCATAGAG--AGTTAT
*
53236 CAAAATTTCA-AAACGAGGTTAT
1 CAAAATTTCATAGA-GA-GTTAT
* *
53258 CAAAATTACATA-ATGTGATTAT
1 CAAAATTTCATAGA-GAG-TTAT
*
53280 CAAAATTTCATAGAGGGGTCTA-
1 CAAAATTTCATAGA-GAGT-TAT
*
53302 CAAAATTTTATAGAGAGGTTAT
1 CAAAATTTCATAGAGA-GTTAT
*
53324 CAAAATTTCATAAAGAGGTTAT
1 CAAAATTTCATAGAGA-GTTAT
*
53346 CAAATTTTCA
1 CAAAATTTCA
53356 AAATGTGAGT
Statistics
Matches: 165, Mismatches: 22, Indels: 37
0.74 0.10 0.17
Matches are distributed among these distances:
18 11 0.07
19 3 0.02
20 13 0.08
21 12 0.07
22 102 0.62
23 8 0.05
24 5 0.03
25 11 0.07
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (21 bp):
CAAAATTTCATAGAGAGTTAT
Found at i:53279 original size:44 final size:44
Alignment explanation
Indices: 53190--53376 Score: 172
Period size: 44 Copynumber: 4.3 Consensus size: 44
53180 ATAGAGATCA
* * *
53190 GATTATCAAAATTT-AT-AAGA--CTATCAAAATTTTATAGTGT
1 GATTATCAAAATTTCATAAAGAGGTTATCAAAATTTCATAATGT
* *
53230 TATTATCAAAATTTCA-AAACGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCATAAA-GAGGTTATCAAAATTTCATAATGT
* * * *
53274 GATTATCAAAATTTCATAGAGGGGTCTA-CAAAATTTTATAGA-GA
1 GATTATCAAAATTTCATAAAGAGGT-TATCAAAATTTCATA-ATGT
* * *
53318 GGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCATAAAGAGGTTATCAAAATTTCATAATGT
* *
53362 GAGTACCAAAATTTC
1 GATTATCAAAATTTC
53377 GTAGTGGTAT
Statistics
Matches: 116, Mismatches: 21, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
40 13 0.11
41 3 0.03
42 2 0.02
43 3 0.03
44 90 0.78
45 5 0.04
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (44 bp):
GATTATCAAAATTTCATAAAGAGGTTATCAAAATTTCATAATGT
Found at i:53324 original size:88 final size:88
Alignment explanation
Indices: 53214--53376 Score: 229
Period size: 88 Copynumber: 1.9 Consensus size: 88
53204 ATAAGACTAT
* ** * *
53214 CAAAATTTTATAGTGTTATTATCAAAATTTCA-AAACGAGGTTATCAAAATTACATAATGTGATT
1 CAAAATTTTATAGAGAGATTATCAAAATTTCATAAA-GAGGTTATCAAAATTACAAAATGTGAGT
*
53278 ATCAAAATTTCATAGAGGGGTCTA
65 ACCAAAATTTCATAGAGGGGTCTA
* * *
53302 CAAAATTTTATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGAGTA
1 CAAAATTTTATAGAGAGATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGAGTA
53367 CCAAAATTTC
66 CCAAAATTTC
53377 GTAGTGGTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
88 62 0.95
89 3 0.05
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (88 bp):
CAAAATTTTATAGAGAGATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGAGTA
CCAAAATTTCATAGAGGGGTCTA
Found at i:53671 original size:82 final size:84
Alignment explanation
Indices: 53546--53706 Score: 204
Period size: 82 Copynumber: 1.9 Consensus size: 84
53536 ATAGTATGTA
* *
53546 TATCAAAATTTCATAGGGAGATTAAAAAATTTTCATAATGAGG-TTATCAAAAAATTATAGGGA-
1 TATCAAAATTTCATAGGGAGATTAAAAAATTTTCATAAGGAGGTTTATCAAAAAATTATAGGAAG
53609 GTTTATCAAAATTTGTAGT
66 GTTTATCAAAATTTGTAGT
* * * * **
53628 TATCAAGATTTCATCA-GGAGGTTATCAAAATTTT-ATAGGGAGGTTTATCAAAACTTTATAGGA
1 TATCAAAATTTCAT-AGGGAGATTA-AAAAATTTTCATAAGGAGGTTTATCAAAAAATTATAGGA
53691 AGGTTTATCAAAATTT
64 AGGTTTATCAAAATTT
53707 CATAGCGAGG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
82 27 0.40
83 26 0.39
84 14 0.21
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (84 bp):
TATCAAAATTTCATAGGGAGATTAAAAAATTTTCATAAGGAGGTTTATCAAAAAATTATAGGAAG
GTTTATCAAAATTTGTAGT
Found at i:53679 original size:23 final size:22
Alignment explanation
Indices: 53461--54021 Score: 228
Period size: 22 Copynumber: 25.9 Consensus size: 22
53451 TTATGGAGTA
* *
53461 ATCAAAATTTC--AGGCAGGAT
1 ATCAAAATTTCATAGGGAGGTT
* * *
53481 ATCAAAATTTCATATGAAGATT
1 ATCAAAATTTCATAGGGAGGTT
**
53503 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* * *
53525 TTCAAAATTTCATA-GTATGTAT
1 ATCAAAATTTCATAGGGAGGT-T
*
53547 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
53569 A-AAAAATTTTCATAATGAGGTT
1 ATCAAAA-TTTCATAGGGAGGTT
* *
53591 ATCAAAAAATT-ATAGGGAGTTT
1 ATC-AAAATTTCATAGGGAGGTT
*
53613 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
*
53629 ATCAAGATTTCATCA-GGAGGTT
1 ATCAAAATTTCAT-AGGGAGGTT
*
53651 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
*
53674 ATCAAAACTTT-ATAGGAAGGTTT
1 ATCAAAA-TTTCATAGGGAGG-TT
*
53697 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
53719 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
53741 ATCAAAATTTCAGATTGA--TT
1 ATCAAAATTTCATAGGGAGGTT
* * *
53761 A-CTAACAA-TTCATATGAATGTT
1 ATC-AA-AATTTCATAGGGAGGTT
* * * ** *
53783 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
53805 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
** * **
53827 ATCAACGTCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
* * *
53850 ATCAAAATTTTATTGGGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
53872 ATCAAAATTTTATAGTGAAGTCT
1 ATCAAAATTTCATAGGGAGGT-T
*
53895 -TCAAAATTTCTTAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
53916 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * ***
53938 A-AAAAATTTTATATAAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * * *
53959 CTCGAAATTCCATA-GTATCGTT
1 ATCAAAATTTCATAGGGA-GGTT
* * * *
53981 ATTAAAATCTCATAGGAAGATT
1 ATCAAAATTTCATAGGGAGGTT
*
54003 ATCAAAATTTCATAAGGAG
1 ATCAAAATTTCATAGGGAG
54022 ATCATAAAAA
Statistics
Matches: 403, Mismatches: 107, Indels: 60
0.71 0.19 0.11
Matches are distributed among these distances:
16 8 0.02
17 4 0.01
19 3 0.01
20 27 0.07
21 34 0.08
22 262 0.65
23 58 0.14
24 7 0.02
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:54031 original size:22 final size:22
Alignment explanation
Indices: 53984--54031 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
53974 TATCGTTATT
* *
53984 AAAATCTCATAGGAAGATTATC
1 AAAATCTCATAGGAAGATCATA
*
54006 AAAATTTCATAAGG-AGATCATA
1 AAAATCTCAT-AGGAAGATCATA
54028 AAAA
1 AAAA
54032 ATAGTGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.25
Consensus pattern (22 bp):
AAAATCTCATAGGAAGATCATA
Found at i:59632 original size:11 final size:12
Alignment explanation
Indices: 59605--59631 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
59595 ATTGACATTC
59605 AAAATGTATGGA
1 AAAATGTATGGA
59617 AAAATGTATGGA
1 AAAATGTATGGA
59629 AAA
1 AAA
59632 TATGGAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (12 bp):
AAAATGTATGGA
Done.