Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011966.1 Corchorus capsularis cultivar CVL-1 contig11987, 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: 50809
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1925 original size:15 final size:16
Alignment explanation
Indices: 1890--1923 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1880 TTTTGGTACA
*
1890 TTTAAATTGGTAGTTT
1 TTTAAATTAGTAGTTT
1906 TTTAAATTAGTAGTTT
1 TTTAAATTAGTAGTTT
1922 TT
1 TT
1924 AATCTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (16 bp):
TTTAAATTAGTAGTTT
Found at i:2022 original size:25 final size:25
Alignment explanation
Indices: 1994--2045 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
1984 TTAGTATAGA
* *
1994 TATAGATATAAATTATTATTATTAT
1 TATAGATATAAATTAATATTAATAT
* *
2019 TATATATATTAATTAATATTAATAT
1 TATAGATATAAATTAATATTAATAT
2044 TA
1 TA
2046 ATTAATGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TATAGATATAAATTAATATTAATAT
Found at i:5570 original size:3 final size:3
Alignment explanation
Indices: 5564--5589 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5554 ATTATTTATG
5564 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
5590 CAAAATGAAA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6071 original size:2 final size:2
Alignment explanation
Indices: 6064--6088 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6054 ATGTTAGATG
6064 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 A
6089 ATTTGCTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15690 original size:26 final size:25
Alignment explanation
Indices: 15661--15717 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 25
15651 ATTTCTACAT
*
15661 AAATTTAGTAAC-CTCACATTCTTAGA
1 AAATTTAGAAACACT-ACATTCTTA-A
15687 AAATTTAGAAACACTACATTCTTAA
1 AAATTTAGAAACACTACATTCTTAA
15712 AAATTT
1 AAATTT
15718 CAGGTTTCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 7 0.24
26 20 0.69
27 2 0.07
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (25 bp):
AAATTTAGAAACACTACATTCTTAA
Found at i:17222 original size:30 final size:30
Alignment explanation
Indices: 17188--17247 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
17178 ACTAATTAAT
*
17188 CAATCAATCTAAACTAATTAATATATTTCC
1 CAATCAAGCTAAACTAATTAATATATTTCC
* *
17218 CAATCAAGCTAAAGTAATTAATTTATTTCC
1 CAATCAAGCTAAACTAATTAATATATTTCC
17248 TTTTGTCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.37
Consensus pattern (30 bp):
CAATCAAGCTAAACTAATTAATATATTTCC
Found at i:19054 original size:6 final size:6
Alignment explanation
Indices: 19045--19069 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19035 TGTTTGATCA
19045 AGGCAC AGGCAC AGGCAC AGGCAC A
1 AGGCAC AGGCAC AGGCAC AGGCAC A
19070 TACGGGGACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.32, T:0.00
Consensus pattern (6 bp):
AGGCAC
Found at i:27675 original size:21 final size:21
Alignment explanation
Indices: 27632--27675 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
27622 ATTAAGGGGG
*
27632 TTGCTAAATACCGCCCTAGTT
1 TTGCTAAATACCGCCCTACTT
27653 TTGCTAAATACCG-CCTCACTT
1 TTGCTAAATACCGCCCT-ACTT
27674 TT
1 TT
27676 TACACTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.23, C:0.30, G:0.11, T:0.36
Consensus pattern (21 bp):
TTGCTAAATACCGCCCTACTT
Found at i:27703 original size:14 final size:15
Alignment explanation
Indices: 27674--27717 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
27664 CGCCTCACTT
*
27674 TTTACACTTTTGCCC
1 TTTACACTTTTACCC
27689 TTTAC-CTTTTACCC
1 TTTACACTTTTACCC
27703 TTTTTACACTTTTAC
1 --TTTACACTTTTAC
27718 ACTGAGTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 8 0.32
15 5 0.20
16 5 0.20
17 7 0.28
ACGTcount: A:0.16, C:0.30, G:0.02, T:0.52
Consensus pattern (15 bp):
TTTACACTTTTACCC
Found at i:27825 original size:32 final size:32
Alignment explanation
Indices: 27745--27825 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 32
27735 GGACGGCTCA
* *
27745 GCCACGGCAGAGCCTCCCCACTGGGGCGGCTTC
1 GCCAAGGCAG-GCCGCCCCACTGGGGCGGCTTC
27778 GCGCAAGGCAGGCCGCCCCACTGGGGCGGCTTC
1 GC-CAAGGCAGGCCGCCCCACTGGGGCGGCTTC
*
27811 GCCAGGGCAGGCCGC
1 GCCAAGGCAGGCCGC
27826 TGAGGGCGGC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 12 0.27
33 25 0.57
34 7 0.16
ACGTcount: A:0.12, C:0.41, G:0.38, T:0.09
Consensus pattern (32 bp):
GCCAAGGCAGGCCGCCCCACTGGGGCGGCTTC
Found at i:27890 original size:34 final size:33
Alignment explanation
Indices: 27845--27934 Score: 128
Period size: 34 Copynumber: 2.7 Consensus size: 33
27835 CCTATTCATA
*
27845 GTGAAGGCGCCCTAGTGGGGCGGCCTGCCCAATG
1 GTGAAGCCGCCCTAGTGGGGCGGCCTGCCC-ATG
*
27879 GTGAAGCCGCCCTAGTGGGGCGACCTGCCCATG
1 GTGAAGCCGCCCTAGTGGGGCGGCCTGCCCATG
* *
27912 GT-AAGCCGTCCTATTGGGGCGGC
1 GTGAAGCCGCCCTAGTGGGGCGGC
27935 ACGGGTCATC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 18 0.35
33 5 0.10
34 28 0.55
ACGTcount: A:0.14, C:0.30, G:0.39, T:0.17
Consensus pattern (33 bp):
GTGAAGCCGCCCTAGTGGGGCGGCCTGCCCATG
Found at i:29169 original size:22 final size:23
Alignment explanation
Indices: 29106--29169 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
29096 CGATTATTAT
*
29106 ATAAACGAAGACTTAA-ATGAACA
1 ATAAACGAA-ACTGAACATGAACA
** **
29129 ATAAACGAGTCTGTTCATGAAC-
1 ATAAACGAAACTGAACATGAACA
29151 ATAAACGAAACTGAACATG
1 ATAAACGAAACTGAACATG
29170 TCTTGTTCAA
Statistics
Matches: 31, Mismatches: 9, Indels: 3
0.72 0.21 0.07
Matches are distributed among these distances:
22 17 0.55
23 14 0.45
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (23 bp):
ATAAACGAAACTGAACATGAACA
Found at i:32530 original size:28 final size:30
Alignment explanation
Indices: 32490--32548 Score: 104
Period size: 28 Copynumber: 2.0 Consensus size: 30
32480 TTAAAAAATC
32490 ATTTGCCACAGTAT-A-ATATATAGTATAT
1 ATTTGCCACAGTATAATATATATAGTATAT
32518 ATTTGCCACAGTATAATATATATAGTATAT
1 ATTTGCCACAGTATAATATATATAGTATAT
32548 A
1 A
32549 ATAAGATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 14 0.48
29 1 0.03
30 14 0.48
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (30 bp):
ATTTGCCACAGTATAATATATATAGTATAT
Found at i:32817 original size:104 final size:104
Alignment explanation
Indices: 32637--32850 Score: 401
Period size: 104 Copynumber: 2.1 Consensus size: 104
32627 CTATACTAAT
*
32637 TATAATGCGAAGTCCTGAGGTTGTGTCTCGAGTTGACTCGGATACAAACTCAGTTTTTAAAAGAT
1 TATAATGCGAAGTCCTGAGGTTGTGTCACGAGTTGACTCGGATACAAACTCAGTTTTTAAAAGAT
* *
32702 TTAAAACCACCCATTTGAAAATAAACCACCAAGGATGTA
66 TCAAAACCACCCATTTGAAAATAAACCACCAAGGATATA
32741 TATAATGCGAAGTCCTGAGGTTGTGTCACGAGTTGACTCGGATACAAACTCAGTTTTTAAAAGAT
1 TATAATGCGAAGTCCTGAGGTTGTGTCACGAGTTGACTCGGATACAAACTCAGTTTTTAAAAGAT
32806 TCAAAACCACCCATTTGAAAATAAACCACCAAGGATATA
66 TCAAAACCACCCATTTGAAAATAAACCACCAAGGATATA
32845 TATAAT
1 TATAAT
32851 AATTAATTTT
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 107 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (104 bp):
TATAATGCGAAGTCCTGAGGTTGTGTCACGAGTTGACTCGGATACAAACTCAGTTTTTAAAAGAT
TCAAAACCACCCATTTGAAAATAAACCACCAAGGATATA
Found at i:33084 original size:3 final size:3
Alignment explanation
Indices: 33076--33104 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
33066 ATTAATTTTT
33076 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
33105 TATTATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:33109 original size:3 final size:3
Alignment explanation
Indices: 33103--33131 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
33093 AATAATAATA
33103 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
33132 ATAGTAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:33877 original size:125 final size:122
Alignment explanation
Indices: 33653--33886 Score: 423
Period size: 125 Copynumber: 1.9 Consensus size: 122
33643 TTTGTTCCTA
33653 TTATATGTCATCACTTTGTTCAAACAGTTTCAACTTTGACCATTTTTAAAAAAATATATATAAAC
1 TTATATGTCATCACTTTGTTCAAACAGTTTCAACTTTGACCATTTTTAAAAAAATATATATAAAC
*
33718 CAAAATAAAATTTTAAAATAATACTCATAAACTTTTGAACACAAGTTTTTCAAATAT
66 CAAAATAAAATTTTAAAATAATACTCATAAACTTTGGAACACAAGTTTTTCAAATAT
*
33775 TTATATGTCATCACTTTGTTTAAACAGTTTCAACTTTGACCATTTTTTAAAAAAATATATATATA
1 TTATATGTCATCACTTTGTTCAAACAGTTTCAACTTTGACCA-TTTTT-AAAAAA-ATATATATA
33840 AACCAAAATAAAATTTTAAAATAATACTCATAAACTTTGGAACACAA
63 AACCAAAATAAAATTTTAAAATAATACTCATAAACTTTGGAACACAA
33887 ACTTTTTAAA
Statistics
Matches: 107, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
122 41 0.38
123 5 0.05
124 6 0.06
125 55 0.51
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.37
Consensus pattern (122 bp):
TTATATGTCATCACTTTGTTCAAACAGTTTCAACTTTGACCATTTTTAAAAAAATATATATAAAC
CAAAATAAAATTTTAAAATAATACTCATAAACTTTGGAACACAAGTTTTTCAAATAT
Found at i:34032 original size:2 final size:2
Alignment explanation
Indices: 34025--34052 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
34015 TATACTTAAT
34025 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
34053 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34193 original size:43 final size:43
Alignment explanation
Indices: 34132--34218 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
34122 TGGTTTGAAG
34132 TATGAAATTAAATATCCGTCGATATATCCGATATCTGTACCCC
1 TATGAAATTAAATATCCGTCGATATATCCGATATCTGTACCCC
*
34175 TATGAAATTAAATATCCGTCGATATATCCGATATCTGTATCCC
1 TATGAAATTAAATATCCGTCGATATATCCGATATCTGTACCCC
34218 T
1 T
34219 CGATATAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.34
Consensus pattern (43 bp):
TATGAAATTAAATATCCGTCGATATATCCGATATCTGTACCCC
Found at i:34328 original size:10 final size:10
Alignment explanation
Indices: 34315--34350 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
34305 AAATCTCGAT
34315 ATATCCGTAA
1 ATATCCGTAA
34325 ATATCCGTAA
1 ATATCCGTAA
*
34335 ATATCTGTAA
1 ATATCCGTAA
34345 ATATCC
1 ATATCC
34351 ATATTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.33
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:35472 original size:12 final size:12
Alignment explanation
Indices: 35455--35484 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
35445 CATCGATAAC
35455 TCGATATATCCA
1 TCGATATATCCA
*
35467 TCGATATATCCG
1 TCGATATATCCA
35479 TCGATA
1 TCGATA
35485 CCTGTATTAA
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:0.30, C:0.23, G:0.13, T:0.33
Consensus pattern (12 bp):
TCGATATATCCA
Found at i:37601 original size:6 final size:6
Alignment explanation
Indices: 37592--37632 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
37582 CTACAGACGA
* *
37592 CGGAGG CGGAGG CGGAGG CGGAGG CGGAGA CGGAGA CGGAG
1 CGGAGG CGGAGG CGGAGG CGGAGG CGGAGG CGGAGG CGGAG
37633 AGAGCCTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.22, C:0.17, G:0.61, T:0.00
Consensus pattern (6 bp):
CGGAGG
Found at i:39128 original size:24 final size:24
Alignment explanation
Indices: 39101--39157 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
39091 TAATTAATTG
39101 TATATTTACTTTAACATATA-TTAT
1 TATATTTA-TTTAACATATATTTAT
* **
39125 TATATTCATTTTCCATATATTTAT
1 TATATTTATTTAACATATATTTAT
39149 T-TATTTATT
1 TATATTTATT
39158 AATTATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.60
Consensus pattern (24 bp):
TATATTTATTTAACATATATTTAT
Found at i:39164 original size:21 final size:21
Alignment explanation
Indices: 39140--39189 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
39130 TCATTTTCCA
* * *
39140 TATATTTATTTATTTATTAAT
1 TATATATATATATTTAATAAT
39161 TATATATATATATTTAATAA-
1 TATATATATATATTTAATAAT
39181 TATA-ATATA
1 TATATATATA
39190 CTATCATCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 5 0.19
20 4 0.15
21 17 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATATATATATTTAATAAT
Found at i:39183 original size:18 final size:17
Alignment explanation
Indices: 39156--39189 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
39146 TATTTATTTA
*
39156 TTAATTATATATATATAT
1 TTAATAATATA-ATATAT
39174 TTAATAATATAATATA
1 TTAATAATATAATATA
39190 CTATCATCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATAATATAATATAT
Found at i:40569 original size:19 final size:20
Alignment explanation
Indices: 40526--40570 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
40516 GGCACGTCAT
*
40526 ATGTACCAAAAAGTCGTGCCAC
1 ATGTACCAAAAA--CGTGACAC
40548 ATGTACCAAAAA-GTGACAC
1 ATGTACCAAAAACGTGACAC
40567 ATGT
1 ATGT
40571 CACGCCACGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 10 0.45
22 12 0.55
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (20 bp):
ATGTACCAAAAACGTGACAC
Found at i:40584 original size:31 final size:30
Alignment explanation
Indices: 40543--40663 Score: 111
Period size: 31 Copynumber: 4.0 Consensus size: 30
40533 AAAAAGTCGT
* *
40543 GCCACATGTACCAAAAAGTGACACATGTCAC
1 GCCACGTGTACCAAAAA-TGACACATGGCAC
* *
40574 GCCACGTGTACCAAAAAGTGACACGTGGCAT
1 GCCACGTGTACCAAAAA-TGACACATGGCAC
* * * *
40605 GCCACGTGGACCAAAAATGGCACGTGGCAT
1 GCCACGTGTACCAAAAATGACACATGGCAC
* * *
40635 GCCACGTGCA-C-AAAATGATACATGTCAC
1 GCCACGTGTACCAAAAATGACACATGGCAC
40663 G
1 G
40664 TGTCATTTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
28 13 0.17
29 1 0.01
30 21 0.27
31 43 0.55
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.16
Consensus pattern (30 bp):
GCCACGTGTACCAAAAATGACACATGGCAC
Found at i:40584 original size:53 final size:53
Alignment explanation
Indices: 40491--40592 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
40481 ACGTGGCACA
* ** * *
40491 CCACGTGTACCAAAAAGTGACATGTGGCACGTCATATGTACCAAAAAGTCGTG
1 CCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGTG
* *
40544 CCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAAGT
1 CCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT
40593 GACACGTGGC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (53 bp):
CCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGTG
Found at i:40631 original size:30 final size:31
Alignment explanation
Indices: 40542--40642 Score: 141
Period size: 31 Copynumber: 3.3 Consensus size: 31
40532 CAAAAAGTCG
* * *
40542 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACGTGTACCAAAAAGTGACACGTGGCA
*
40573 CGCCACGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACGTGTACCAAAAAGTGACACGTGGCA
* *
40604 TGCCACGTGGACCAAAAA-TGGCACGTGGCA
1 TGCCACGTGTACCAAAAAGTGACACGTGGCA
40634 TGCCACGTG
1 TGCCACGTG
40643 CACAAAATGA
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
30 20 0.32
31 43 0.68
ACGTcount: A:0.32, C:0.28, G:0.25, T:0.16
Consensus pattern (31 bp):
TGCCACGTGTACCAAAAAGTGACACGTGGCA
Found at i:40917 original size:4 final size:4
Alignment explanation
Indices: 40910--40954 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
40900 ATTCATATAT
40910 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
40955 CACACATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:42015 original size:14 final size:14
Alignment explanation
Indices: 41996--42108 Score: 63
Period size: 14 Copynumber: 8.1 Consensus size: 14
41986 TTTATTTTAT
41996 AAATTCTTTTAAGA
1 AAATTCTTTTAAGA
**
42010 AAATTCAGTTAAG-
1 AAATTCTTTTAAGA
* * *
42023 AAATTTTATTTTA-T
1 AAATTCT-TTTAAGA
42037 AAATTCTTTTAAGA
1 AAATTCTTTTAAGA
**
42051 AAATTCAGTTAAG-
1 AAATTCTTTTAAGA
* * *
42064 AAATTTTATTTTA-T
1 AAATTCT-TTTAAGA
42078 AAATTCTTTTAAGAA
1 AAATTCTTTTAAG-A
**
42093 AAATTCAGTTAAGA
1 AAATTCTTTTAAGA
42107 AA
1 AA
42109 TGAAATTTTG
Statistics
Matches: 72, Mismatches: 20, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
13 18 0.25
14 43 0.60
15 11 0.15
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (14 bp):
AAATTCTTTTAAGA
Found at i:42042 original size:41 final size:41
Alignment explanation
Indices: 41985--42109 Score: 241
Period size: 41 Copynumber: 3.0 Consensus size: 41
41975 CGTGCGGCTG
41985 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
42026 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
42067 TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAG-AAAATTCAGTTAAGAAA
42109 T
1 T
42110 GAAATTTTGT
Statistics
Matches: 83, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
41 65 0.78
42 18 0.22
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (41 bp):
TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
Found at i:43038 original size:2 final size:2
Alignment explanation
Indices: 43026--43099 Score: 57
Period size: 2 Copynumber: 38.0 Consensus size: 2
43016 TTATTACTAC
** *
43026 AT AT A- AT AT AT AT AT AT AT AT AT AT AT CA- AT GC AT GCT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT -AT AT AT
* *
43068 AT -T AT AT A- AT AT AT AT AT GT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43100 TCCCAAGATT
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
1 4 0.07
2 50 0.89
3 2 0.04
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:43568 original size:2 final size:2
Alignment explanation
Indices: 43525--43552 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43515 ACAATTAATA
43525 AT AT AT 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
43553 GAAGCATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.