Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007573.1 Corchorus capsularis cultivar CVL-1 contig07594, 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: 134005
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:580 original size:32 final size:32
Alignment explanation
Indices: 543--603 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
533 AATCACTGAA
*
543 TTTACTTAATAACACTGAATTAAGTTGATCAC
1 TTTACTTAATAACACTGAATCAAGTTGATCAC
*
575 TTTACTTAATTACACTGAATCAAGTTGAT
1 TTTACTTAATAACACTGAATCAAGTTGAT
604 TACTAGTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (32 bp):
TTTACTTAATAACACTGAATCAAGTTGATCAC
Found at i:715 original size:44 final size:43
Alignment explanation
Indices: 667--1060 Score: 412
Period size: 44 Copynumber: 9.7 Consensus size: 43
657 TTACTTAACC
667 TACTTAATTACACTGAATTAAGTTGATTACCGAATTACTAAATT
1 TACTTAATTACACTGAATTAAGTTGATTACCGAATTACT-AATT
*
711 TACTTAATTACACTGAATTAAGTTGATTA-C----T--TAACT
1 TACTTAATTACACTGAATTAAGTTGATTACCGAATTACTAATT
* * *
747 TACTTAATTACACCGAATTAAGTTGATTACCGAATTACTTGATC
1 TACTTAATTACACTGAATTAAGTTGATTACCGAATTAC-TAATT
*
791 TACTTAATTACACTGAATTAAGTTGATTA-C----T--TAACT
1 TACTTAATTACACTGAATTAAGTTGATTACCGAATTACTAATT
* * *
827 TACTTAATTACACCGAATTAAGTTGATTACCGAATTACTTGATC
1 TACTTAATTACACTGAATTAAGTTGATTACCGAATTAC-TAATT
* *
871 TACTTAATTACACTGAACTAAGTTGATTA-C----T--TAACT
1 TACTTAATTACACTGAATTAAGTTGATTACCGAATTACTAATT
* * *
907 TACTTAATTACACCGAATTAAGTTGATTACCGAATTACTTGATC
1 TACTTAATTACACTGAATTAAGTTGATTACCGAATTAC-TAATT
*
951 TACTTAATTACACTGAATTAAGTTGATTA-C----T--TAACT
1 TACTTAATTACACTGAATTAAGTTGATTACCGAATTACTAATT
*
987 TACTTAATTACACTGAATTAAGTTGATTACCGAATTACTTAATC
1 TACTTAATTACACTGAATTAAGTTGATTACCGAATTAC-TAATT
1031 TACTTAATTACACTGAATTAAGTTGATTAC
1 TACTTAATTACACTGAATTAAGTTGATTAC
1061 TTAACTTACT
Statistics
Matches: 289, Mismatches: 29, Indels: 64
0.76 0.08 0.17
Matches are distributed among these distances:
36 121 0.42
37 5 0.02
39 4 0.01
41 4 0.01
43 4 0.01
44 151 0.52
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.39
Consensus pattern (43 bp):
TACTTAATTACACTGAATTAAGTTGATTACCGAATTACTAATT
Found at i:729 original size:80 final size:80
Alignment explanation
Indices: 492--1078 Score: 835
Period size: 80 Copynumber: 7.3 Consensus size: 80
482 TTTGCCATGT
** * * * * *
492 TTACTTAGTTTACTTAATTACACTGAATTAA-TCGATTACCAAATCAC-TGAATTTACTTAATAA
1 TTACTTAACTTACTTAATTACACTGAATTAAGTTGATTACCGAATTACTTG-ATCTACTTAATTA
555 CACTGAATTAAGTTGA
65 CACTGAATTAAGTTGA
* * * *
571 TCAC-T---TTACTTAATTACACTGAATCAAGTTGATTACTAGTTTCCAATTCACTTACCGATTT
1 TTACTTAACTTACTTAATTACACTGAATTAAGTTGATTAC------CGAATT-ACTT---GATCT
* *
632 ACTTAATTGCACCGAATTAAGTTGA
56 ACTTAATTACACTGAATTAAGTTGA
* ** *
657 TTACTTAACCTACTTAATTACACTGAATTAAGTTGATTACCGAATTACTAAATTTACTTAATTAC
1 TTACTTAACTTACTTAATTACACTGAATTAAGTTGATTACCGAATTACTTGATCTACTTAATTAC
722 ACTGAATTAAGTTGA
66 ACTGAATTAAGTTGA
*
737 TTACTTAACTTACTTAATTACACCGAATTAAGTTGATTACCGAATTACTTGATCTACTTAATTAC
1 TTACTTAACTTACTTAATTACACTGAATTAAGTTGATTACCGAATTACTTGATCTACTTAATTAC
802 ACTGAATTAAGTTGA
66 ACTGAATTAAGTTGA
*
817 TTACTTAACTTACTTAATTACACCGAATTAAGTTGATTACCGAATTACTTGATCTACTTAATTAC
1 TTACTTAACTTACTTAATTACACTGAATTAAGTTGATTACCGAATTACTTGATCTACTTAATTAC
*
882 ACTGAACTAAGTTGA
66 ACTGAATTAAGTTGA
*
897 TTACTTAACTTACTTAATTACACCGAATTAAGTTGATTACCGAATTACTTGATCTACTTAATTAC
1 TTACTTAACTTACTTAATTACACTGAATTAAGTTGATTACCGAATTACTTGATCTACTTAATTAC
962 ACTGAATTAAGTTGA
66 ACTGAATTAAGTTGA
*
977 TTACTTAACTTACTTAATTACACTGAATTAAGTTGATTACCGAATTACTTAATCTACTTAATTAC
1 TTACTTAACTTACTTAATTACACTGAATTAAGTTGATTACCGAATTACTTGATCTACTTAATTAC
1042 ACTGAATTAAGTTGA
66 ACTGAATTAAGTTGA
1057 TTACTTAACTTACTTAATTACA
1 TTACTTAACTTACTTAATTACA
1079 AGCACAGACG
Statistics
Matches: 467, Mismatches: 25, Indels: 31
0.89 0.05 0.06
Matches are distributed among these distances:
75 21 0.04
76 7 0.01
78 1 0.00
79 3 0.01
80 360 0.77
82 4 0.01
83 5 0.01
84 6 0.01
86 29 0.06
87 2 0.00
90 29 0.06
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (80 bp):
TTACTTAACTTACTTAATTACACTGAATTAAGTTGATTACCGAATTACTTGATCTACTTAATTAC
ACTGAATTAAGTTGA
Found at i:739 original size:19 final size:19
Alignment explanation
Indices: 717--776 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
707 AATTTACTTA
717 ATTACACTGAATTAAGTTG
1 ATTACACTGAATTAAGTTG
* * *
736 ATT--ACTTAACTT-ACTTA
1 ATTACACTGAA-TTAAGTTG
*
753 ATTACACCGAATTAAGTTG
1 ATTACACTGAATTAAGTTG
772 ATTAC
1 ATTAC
777 CGAATTACTT
Statistics
Matches: 30, Mismatches: 7, Indels: 8
0.67 0.16 0.18
Matches are distributed among these distances:
17 11 0.37
18 4 0.13
19 15 0.50
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
ATTACACTGAATTAAGTTG
Found at i:989 original size:9 final size:8
Alignment explanation
Indices: 976--1077 Score: 51
Period size: 9 Copynumber: 11.6 Consensus size: 8
966 AATTAAGTTG
976 ATTACTTA
1 ATTACTTA
984 ACTTACTTA
1 A-TTACTTA
*
993 ATTACACTGA
1 ATT--ACTTA
* *
1003 ATTAAGTTG
1 ATT-ACTTA
**
1012 ATTACCGA
1 ATTACTTA
1020 ATTACTTA
1 ATTACTTA
1028 ATCTACTTA
1 AT-TACTTA
*
1037 ATTACACTGA
1 ATT--ACTTA
* *
1047 ATTAAGTTG
1 ATT-ACTTA
1056 ATTACTTA
1 ATTACTTA
1064 ACTTACTTA
1 A-TTACTTA
1073 ATTAC
1 ATTAC
1078 AAGCACAGAC
Statistics
Matches: 69, Mismatches: 18, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
8 21 0.30
9 34 0.49
10 14 0.20
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (8 bp):
ATTACTTA
Found at i:4828 original size:12 final size:13
Alignment explanation
Indices: 4811--4839 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4801 AAAAGCTTCC
4811 CTTTCACTTTC-A
1 CTTTCACTTTCAA
4823 CTTTCACTTTCAA
1 CTTTCACTTTCAA
4836 CTTT
1 CTTT
4840 AAAAACAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.17, C:0.31, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTTCACTTTCAA
Found at i:10117 original size:12 final size:12
Alignment explanation
Indices: 10100--10130 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
10090 TGCTAAACCA
10100 ATCCTCCTCAAT
1 ATCCTCCTCAAT
*
10112 ATCCTCTTCAAT
1 ATCCTCCTCAAT
10124 ATCCTCC
1 ATCCTCC
10131 CAAACTCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (12 bp):
ATCCTCCTCAAT
Found at i:23115 original size:21 final size:21
Alignment explanation
Indices: 23067--23126 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
23057 CTTGGAGCAA
* **
23067 GAATATTTCAATCGATTCTTT
1 GAATATTACAATCGATTCTAG
**
23088 GTCTATTACAATCGATTCTAG
1 GAATATTACAATCGATTCTAG
*
23109 GAATATTCCAATCGATTC
1 GAATATTACAATCGATTC
23127 CAACATATGC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (21 bp):
GAATATTACAATCGATTCTAG
Found at i:24736 original size:27 final size:27
Alignment explanation
Indices: 24706--24826 Score: 103
Period size: 27 Copynumber: 4.7 Consensus size: 27
24696 ACAAAATTAT
*
24706 TATATTTTAATAATGACATAATTAAAA
1 TATATTTTGATAATGACATAATTAAAA
* *
24733 TATATTTTGATAAAGACA-ATTTAGAAA
1 TATATTTTGATAATGACATAATTA-AAA
* * *
24760 TATA-TTTGA-AA--A-A-AAGTACAC
1 TATATTTTGATAATGACATAATTAAAA
* * *
24781 GATATTTTAATAATGACCTAATTAAAA
1 TATATTTTGATAATGACATAATTAAAA
24808 TATATTTTGATAATGACAT
1 TATATTTTGATAATGACAT
24827 TGCAGAAATA
Statistics
Matches: 71, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
21 4 0.06
22 8 0.11
23 3 0.04
25 3 0.04
26 9 0.13
27 44 0.62
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (27 bp):
TATATTTTGATAATGACATAATTAAAA
Found at i:24890 original size:74 final size:74
Alignment explanation
Indices: 24707--24893 Score: 261
Period size: 75 Copynumber: 2.5 Consensus size: 74
24697 CAAAATTATT
*
24707 ATATTTTAATAATGACATAATTAAAATATATTTTGATAAAGACAATTTAGAAATATATTTGAAAA
1 ATATTTTAATAATGACATAATTAAAATATATTTTGATAAAGACAATTCAGAAATATATTTGAAAA
*
24772 AAAGTACACG
66 AAAG-AAACG
* *
24782 ATATTTTAATAATGACCTAATTAAAATATATTTTGATAATGAC-ATTGCAGAAATATATTTGAAA
1 ATATTTTAATAATGACATAATTAAAATATATTTTGATAAAGACAATT-CAGAAATATATTTGAAA
*
24846 AAAA-AAATG
65 AAAAGAAACG
* * *
24855 AGTTTTTTAATAATGGCATAATTAAAAAATATTTTGATA
1 A-TATTTTAATAATGACATAATTAAAATATATTTTGATA
24894 CTAGCAATCT
Statistics
Matches: 101, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
73 4 0.04
74 36 0.36
75 61 0.60
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.37
Consensus pattern (74 bp):
ATATTTTAATAATGACATAATTAAAATATATTTTGATAAAGACAATTCAGAAATATATTTGAAAA
AAAGAAACG
Found at i:27085 original size:14 final size:15
Alignment explanation
Indices: 27058--27090 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
27048 TGACTAAAAA
27058 TAATATTAATTAAAT
1 TAATATTAATTAAAT
*
27073 TAATATTCA-TAAAT
1 TAATATTAATTAAAT
27087 TAAT
1 TAAT
27091 TCTTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATATTAATTAAAT
Found at i:27302 original size:4 final size:4
Alignment explanation
Indices: 27293--27319 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
27283 TCATTGAGTA
27293 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
27320 AATATTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:28377 original size:74 final size:74
Alignment explanation
Indices: 28256--28410 Score: 301
Period size: 74 Copynumber: 2.1 Consensus size: 74
28246 ATAATCAGGA
28256 AAGTTTAATTAAAGATGTTTTTAGTGCAAGAATTACGTGTAAATATAGGATTGGAAACATGTGAA
1 AAGTTTAATTAAAGATGTTTTTAGTGCAAGAATTACGTGTAAATATAGGATTGGAAACATGTGAA
28321 AACAATGAT
66 AACAATGAT
28330 AAGTTTAATTAAAGATGTTTTTAGTGCAAGAATTACGTGTAAATATAGGATTGGAAACATGTGAA
1 AAGTTTAATTAAAGATGTTTTTAGTGCAAGAATTACGTGTAAATATAGGATTGGAAACATGTGAA
*
28395 AACGATGAT
66 AACAATGAT
28404 AAGTTTA
1 AAGTTTA
28411 TCACTGTTTG
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 80 1.00
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (74 bp):
AAGTTTAATTAAAGATGTTTTTAGTGCAAGAATTACGTGTAAATATAGGATTGGAAACATGTGAA
AACAATGAT
Found at i:33037 original size:89 final size:90
Alignment explanation
Indices: 32930--33112 Score: 323
Period size: 89 Copynumber: 2.0 Consensus size: 90
32920 GAACCAACAA
* *
32930 ATAAACCCAGTGAAATCTCATTACAATTCAAATAAATTTCTATACTCATAAATAAACTACCTACC
1 ATAAACCCAGTGAAATCTCATTACAATTCAAATAAATCTCTATACCCATAAATAAACTACCTACC
32995 TACCAAATACAT-AATAAACAAATT
66 TACCAAATACATAAATAAACAAATT
*
33019 ATAAACCCAGTGAAATCTCATTACAATTCAAATAAATCTCTATACCCATAAATAAACTACCTGCC
1 ATAAACCCAGTGAAATCTCATTACAATTCAAATAAATCTCTATACCCATAAATAAACTACCTACC
*
33084 TACCAAATATATAAATAAACAAATT
66 TACCAAATACATAAATAAACAAATT
33109 ATAA
1 ATAA
33113 TTCAAATAAA
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 73 0.82
90 16 0.18
ACGTcount: A:0.49, C:0.21, G:0.03, T:0.27
Consensus pattern (90 bp):
ATAAACCCAGTGAAATCTCATTACAATTCAAATAAATCTCTATACCCATAAATAAACTACCTACC
TACCAAATACATAAATAAACAAATT
Found at i:33122 original size:68 final size:68
Alignment explanation
Indices: 33038--33180 Score: 259
Period size: 68 Copynumber: 2.1 Consensus size: 68
33028 GTGAAATCTC
*
33038 ATTACAATTCAAATAAATCTCTATACCCATAAATAAACTACCTGCCTACCAAATATATAAATAAA
1 ATTACAATTCAAATAAATCTCTATACCCATAAATAAACTACCTACCTACCAAATATATAAATAAA
33103 CAA
66 CAA
* *
33106 ATTATAATTCAAATAAATTTCTATACCCATAAATAAACTACCTACCTACCAAATATATAAATAAA
1 ATTACAATTCAAATAAATCTCTATACCCATAAATAAACTACCTACCTACCAAATATATAAATAAA
33171 CAA
66 CAA
33174 ATTACAA
1 ATTACAA
33181 ATCATGTAAC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 71 1.00
ACGTcount: A:0.51, C:0.20, G:0.01, T:0.28
Consensus pattern (68 bp):
ATTACAATTCAAATAAATCTCTATACCCATAAATAAACTACCTACCTACCAAATATATAAATAAA
CAA
Found at i:35537 original size:3 final size:3
Alignment explanation
Indices: 35531--35572 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
35521 AAAAAAAAAA
35531 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG TAA- AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG
35573 CTTCTGTATC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 33 0.89
4 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:44371 original size:14 final size:14
Alignment explanation
Indices: 44352--44380 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
44342 ACAATTAAGA
44352 ACAAATTAAGAAAC
1 ACAAATTAAGAAAC
44366 ACAAATTAAGAAAC
1 ACAAATTAAGAAAC
44380 A
1 A
44381 ACTCACCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.14, G:0.07, T:0.14
Consensus pattern (14 bp):
ACAAATTAAGAAAC
Found at i:44498 original size:13 final size:13
Alignment explanation
Indices: 44480--44516 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
44470 GACTTCAGGG
44480 GAAAAAAAAGAAA
1 GAAAAAAAAGAAA
44493 GAAAAAAACA-AAA
1 GAAAAAAA-AGAAA
44506 -AAAAAAAAGAA
1 GAAAAAAAAGAA
44517 GGCTTGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 1 0.05
12 9 0.41
13 11 0.50
14 1 0.05
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (13 bp):
GAAAAAAAAGAAA
Found at i:57399 original size:60 final size:61
Alignment explanation
Indices: 57331--57480 Score: 214
Period size: 61 Copynumber: 2.5 Consensus size: 61
57321 GCTAATTGCT
* ** * *
57331 CAAATAAGGGTCTAACGTTTGTC-AAAATGCTAAAATAAGGGTTTCATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTAATCGAAAATGCTAAAATAAGGGCTTCATCTTTTAATTTGAC
* **
57391 CAAATAAGGGCCTAACGTTAATCGAAAATGCTTAAATAAGGGCTTGGTCTTTTAATTTGAC
1 CAAATAAGGGCCTAACGTTAATCGAAAATGCTAAAATAAGGGCTTCATCTTTTAATTTGAC
57452 CAAATAAGGGCCTAACGTT-ATCGAAAATG
1 CAAATAAGGGCCTAACGTTAATCGAAAATG
57481 GTCAAACAAG
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
60 30 0.37
61 51 0.63
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (61 bp):
CAAATAAGGGCCTAACGTTAATCGAAAATGCTAAAATAAGGGCTTCATCTTTTAATTTGAC
Found at i:60698 original size:12 final size:12
Alignment explanation
Indices: 60681--60714 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
60671 TCCTTTTGTG
*
60681 CACGTGGCATGC
1 CACGTGCCATGC
60693 CACGTGCCATGC
1 CACGTGCCATGC
60705 CACGTGCCAT
1 CACGTGCCAT
60715 TTTTTGAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.38, G:0.26, T:0.18
Consensus pattern (12 bp):
CACGTGCCATGC
Found at i:60738 original size:31 final size:31
Alignment explanation
Indices: 60700--60794 Score: 91
Period size: 31 Copynumber: 3.1 Consensus size: 31
60690 TGCCACGTGC
*
60700 CATGCCACGTGCCATTTTTTGAAACATGTGG
1 CATGCCACGTGCCACTTTTTGAAACATGTGG
* **
60731 CATGCCACGTGTCACTTTTTGGTACATGTGG
1 CATGCCACGTGCCACTTTTTGAAACATGTGG
* ** * * **
60762 CGTGATATGTGTCACTTTTTGGTACATGTGG
1 CATGCCACGTGCCACTTTTTGAAACATGTGG
60793 CA
1 CA
60795 CGACTTTTTG
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (31 bp):
CATGCCACGTGCCACTTTTTGAAACATGTGG
Found at i:60830 original size:53 final size:53
Alignment explanation
Indices: 60744--60846 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
60734 GCCACGTGTC
* ** * *
60744 ACTTTTTGGTACATGTGGCGTGATATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACATGTGGCGTGACACATATCACTTTTTGGTACACGTGGCACG
*
60797 ACTTTTTGGTACATGTGGCGTGCCACATATCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACATGTGGCGTGACACATATCACTTTTTGGTACACGTGGC
60847 GTGCCACGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.38
Consensus pattern (53 bp):
ACTTTTTGGTACATGTGGCGTGACACATATCACTTTTTGGTACACGTGGCACG
Found at i:62511 original size:27 final size:27
Alignment explanation
Indices: 62238--62575 Score: 220
Period size: 27 Copynumber: 12.4 Consensus size: 27
62228 CGCAAAACCT
* *
62238 AACTGCGGGAGCTTCAACATAAGTCCC
1 AACTGCGGGAGCTTCAGCATGAGTCCC
* * * *
62265 AACTGC-GGAGGCTTCGGCGTCAGTTCC
1 AACTGCGGGA-GCTTCAGCATGAGTCCC
* * * *
62292 AACTACGGGAACTTCAGCATAACTCCC
1 AACTGCGGGAGCTTCAGCATGAGTCCC
* * * *
62319 AACTGCGGCAGTTTCAGCATAACTCCC
1 AACTGCGGGAGCTTCAGCATGAGTCCC
*
62346 AACTGCGGGAGCTTCAGCATGAATCCC
1 AACTGCGGGAGCTTCAGCATGAGTCCC
* *
62373 AACTGCGGGAGCTGCATAGCGTGAGTCCC
1 AACTGCGGGAGCTTC--AGCATGAGTCCC
* *
62402 AACTGCGGGAGTTTCAGCATGAGCCCC
1 AACTGCGGGAGCTTCAGCATGAGTCCC
* * **
62429 AACTGCGGGAACTTTATTATGAGT-CC
1 AACTGCGGGAGCTTCAGCATGAGTCCC
* * * * *
62455 TA-T--AGGAGTTTTATAGCATGAGTCAC
1 AACTGCGGGAG-CTT-CAGCATGAGTCCC
* *
62481 AACTGCGGGATCTTCAGCGTGAGTCCC
1 AACTGCGGGAGCTTCAGCATGAGTCCC
* * *
62508 AACTACGGGAGCTGCATAGCGTGAGTCCC
1 AACTGCGGGAGCTTC--AGCATGAGTCCC
* * * *
62537 AACTACAGGAG-TTCTAACATAAGTCCC
1 AACTGCGGGAGCTTC-AGCATGAGTCCC
*
62564 AACTGCCGGAGC
1 AACTGCGGGAGC
62576 ATCTTTCTCT
Statistics
Matches: 241, Mismatches: 57, Indels: 25
0.75 0.18 0.08
Matches are distributed among these distances:
23 3 0.01
24 2 0.01
25 9 0.04
26 8 0.03
27 164 0.68
28 7 0.03
29 48 0.20
ACGTcount: A:0.26, C:0.28, G:0.25, T:0.21
Consensus pattern (27 bp):
AACTGCGGGAGCTTCAGCATGAGTCCC
Found at i:62817 original size:42 final size:38
Alignment explanation
Indices: 62758--62847 Score: 108
Period size: 38 Copynumber: 2.3 Consensus size: 38
62748 TTAGTGTTGT
* *
62758 TGTCCTTCTCGCTAACCGTAACAACAGTCTCAATTGCGGGAA
1 TGTCCTTCTCCCTAACCG-AAC-A-A-TCTCAACTGCGGGAA
* *
62800 TGTCCTTCTCCCTAACCGATCAATGTCAACTGCGGGAA
1 TGTCCTTCTCCCTAACCGAACAATCTCAACTGCGGGAA
62838 TGTCCTTCTC
1 TGTCCTTCTC
62848 TATAGCCACA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
38 23 0.52
39 1 0.02
40 1 0.02
41 2 0.05
42 17 0.39
ACGTcount: A:0.22, C:0.31, G:0.18, T:0.29
Consensus pattern (38 bp):
TGTCCTTCTCCCTAACCGAACAATCTCAACTGCGGGAA
Found at i:63800 original size:48 final size:48
Alignment explanation
Indices: 63700--63839 Score: 154
Period size: 48 Copynumber: 2.9 Consensus size: 48
63690 CACCATTTTG
* * * * ***
63700 CGGCAAAAATTAATCACAATTCTACTGCAGAAGTCAAACACCATTTTG
1 CGGCAGAAGTTAATCACAATTCTACCGCAGAAGTCAAGCACCATTCCA
* *
63748 CGGCAGAAGTTAATCACAATTCTACCGTAGTAGTCAAGCACCATTCCA
1 CGGCAGAAGTTAATCACAATTCTACCGCAGAAGTCAAGCACCATTCCA
** * * *
63796 CGGCAGAAGCCAACCACAATTTTACCGCAGAAGCCAAGCACCAT
1 CGGCAGAAGTTAATCACAATTCTACCGCAGAAGTCAAGCACCAT
63840 GCTGCCACAT
Statistics
Matches: 76, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 76 1.00
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Consensus pattern (48 bp):
CGGCAGAAGTTAATCACAATTCTACCGCAGAAGTCAAGCACCATTCCA
Found at i:72192 original size:55 final size:55
Alignment explanation
Indices: 72108--72217 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
72098 CACTACCCGT
72108 ACGCTACCCTAACCCTATTATATAATACCCTAATCCTACTTAATCGGGTCGGGTA
1 ACGCTACCCTAACCCTATTATATAATACCCTAATCCTACTTAATCGGGTCGGGTA
72163 ACGCTACCCTAACCCTATTATATAATACCCTAATCCTACTTAATCGGGTCGGGTA
1 ACGCTACCCTAACCCTATTATATAATACCCTAATCCTACTTAATCGGGTCGGGTA
72218 GTGCCGAGTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (55 bp):
ACGCTACCCTAACCCTATTATATAATACCCTAATCCTACTTAATCGGGTCGGGTA
Found at i:72472 original size:21 final size:19
Alignment explanation
Indices: 72440--72478 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
72430 CCTTCTTATC
*
72440 TTTTTTTCCCCCTTTTCTG
1 TTTTTTTCCCCCTCTTCTG
72459 TTTTTTTCTTCCCCTCTTCT
1 TTTTTTTC--CCCCTCTTCT
72479 TAGCTAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTTTTCCCCCTCTTCTG
Found at i:72751 original size:15 final size:15
Alignment explanation
Indices: 72731--72760 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
72721 TGTAACTGCT
*
72731 GCCCATTTGGCTTGA
1 GCCCATTTAGCTTGA
72746 GCCCATTTAGCTTGA
1 GCCCATTTAGCTTGA
72761 TGGTCATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.27, G:0.23, T:0.33
Consensus pattern (15 bp):
GCCCATTTAGCTTGA
Found at i:76292 original size:24 final size:22
Alignment explanation
Indices: 76260--76305 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
76250 CCGCACATAT
76260 TTATTTTTTAAAATAAAATAATAA
1 TTATTTTTT-AAATAAAA-AATAA
*
76284 TTATTTTTTTAATAAAAAATAA
1 TTATTTTTTAAATAAAAAATAA
76306 AATTTAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.24
23 7 0.33
24 9 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTATTTTTTAAATAAAAAATAA
Found at i:76302 original size:25 final size:24
Alignment explanation
Indices: 76263--76309 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
76253 CACATATTTA
76263 TTTTTTAAAATAAAATAATAATTAT
1 TTTTTTAAAATAAAATAA-AATTAT
76288 TTTTTTAATAA-AAAATAAAATT
1 TTTTTTAA-AATAAAATAAAATT
76310 TAAACATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.19
25 15 0.71
26 2 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTTTTAAAATAAAATAAAATTAT
Found at i:91892 original size:6 final size:6
Alignment explanation
Indices: 91875--91935 Score: 77
Period size: 6 Copynumber: 10.2 Consensus size: 6
91865 AGAAACTGGA
* * *
91875 GATTGG GTTTGG GATTGG AATTGG GATTGG GATTGG GATTGG GGTTGG
1 GATTGG GATTGG GATTGG GATTGG GATTGG GATTGG GATTGG GATTGG
* *
91923 GGTTGG GGTTGG G
1 GATTGG GATTGG G
91936 GTTGAGGTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.11, C:0.00, G:0.54, T:0.34
Consensus pattern (6 bp):
GATTGG
Found at i:91929 original size:18 final size:18
Alignment explanation
Indices: 91875--91939 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 18
91865 AGAAACTGGA
*
91875 GATTGGGTTTGGGATTGG
1 GATTGGGGTTGGGATTGG
* *
91893 AATTGGGATTGGGATTGG
1 GATTGGGGTTGGGATTGG
*
91911 GATTGGGGTTGGGGTTGG
1 GATTGGGGTTGGGATTGG
*
91929 GGTTGGGGTTG
1 GATTGGGGTTG
91940 AGGTTGAGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.11, C:0.00, G:0.54, T:0.35
Consensus pattern (18 bp):
GATTGGGGTTGGGATTGG
Found at i:91936 original size:12 final size:12
Alignment explanation
Indices: 91875--91945 Score: 79
Period size: 12 Copynumber: 5.9 Consensus size: 12
91865 AGAAACTGGA
*
91875 GATTGGGTTTGG
1 GATTGGGGTTGG
**
91887 GATTGGAATTGG
1 GATTGGGGTTGG
*
91899 GATTGGGATTGG
1 GATTGGGGTTGG
91911 GATTGGGGTTGG
1 GATTGGGGTTGG
*
91923 GGTTGGGGTTGG
1 GATTGGGGTTGG
* *
91935 GGTTGAGGTTG
1 GATTGGGGTTG
91946 AGTTTGTTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 53 1.00
ACGTcount: A:0.11, C:0.00, G:0.54, T:0.35
Consensus pattern (12 bp):
GATTGGGGTTGG
Found at i:91947 original size:6 final size:6
Alignment explanation
Indices: 91895--91945 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
91885 GGGATTGGAA
* * * *
91895 TTGGGA TTGGGA TTGGGA TTGGGG TTGGGG TTGGGG TTGGGG TTGAGG
1 TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG TTGGGG
91943 TTG
1 TTG
91946 AGTTTGTTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.08, C:0.00, G:0.57, T:0.35
Consensus pattern (6 bp):
TTGGGG
Found at i:93853 original size:56 final size:56
Alignment explanation
Indices: 93767--93878 Score: 174
Period size: 56 Copynumber: 2.0 Consensus size: 56
93757 TTCTTCTTCC
* *
93767 CTATAGCTAATCCTTATCTTTCCCGCAACCAAAA-TTTCTGAATGGTTCCTTAAGAT
1 CTATAACTAATCCTTAACTTTCCCGCAACCAAAATTTTC-GAATGGTTCCTTAAGAT
93823 CTATAACTAATCCTTAACTTTCCC-CTAACCAAAATTTTCGAATGGTTCCTTAAGAT
1 CTATAACTAATCCTTAACTTTCCCGC-AACCAAAATTTTCGAATGGTTCCTTAAGAT
93879 TATTTTAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
55 1 0.02
56 47 0.90
57 4 0.08
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (56 bp):
CTATAACTAATCCTTAACTTTCCCGCAACCAAAATTTTCGAATGGTTCCTTAAGAT
Found at i:95015 original size:17 final size:17
Alignment explanation
Indices: 94977--95009 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
94967 ATCATGATAC
94977 CTAGGTAGTATGAGGTA
1 CTAGGTAGTATGAGGTA
94994 CTAGGTAGTATGAGGT
1 CTAGGTAGTATGAGGT
95010 GATAGGCTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.36, T:0.30
Consensus pattern (17 bp):
CTAGGTAGTATGAGGTA
Found at i:97709 original size:35 final size:34
Alignment explanation
Indices: 97640--97708 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
97630 TCCAAGAATT
* *
97640 AGTTTTTGTTTTTCCGTTTTTTTCTAAAAAAAAA
1 AGTTTTTCTTTTTCCGTATTTTTCTAAAAAAAAA
97674 AGTTTTTCCTTTTTCCG-ATTTTTCTAAAAAAAAA
1 AGTTTTT-CTTTTTCCGTATTTTTCTAAAAAAAAA
97708 A
1 A
97709 ATTGCGATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 24 0.75
35 8 0.25
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (34 bp):
AGTTTTTCTTTTTCCGTATTTTTCTAAAAAAAAA
Found at i:101437 original size:9 final size:9
Alignment explanation
Indices: 101423--101447 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
101413 ATTTATATAG
101423 ATATAGGTT
1 ATATAGGTT
101432 ATATAGGTT
1 ATATAGGTT
101441 ATATAGG
1 ATATAGG
101448 ATTTAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (9 bp):
ATATAGGTT
Found at i:106505 original size:184 final size:183
Alignment explanation
Indices: 106133--106516 Score: 449
Period size: 184 Copynumber: 2.1 Consensus size: 183
106123 TAATTGGTTA
*
106133 AATT-AGCCAAAAATCAGTAGGTAAACCCTTGAAAATTAGGTCATATCACATGAAAATGAACCTA
1 AATTAAGCCAAAAATCAGTAGGTAAACCCTTGAAAACTAGGTCATATCACATGAAAATGAACCTA
* * * * * * *
106197 ATTTGATAAAATCACGCAATCCCTAATAGGCCGTGACCCATTTTGTAAAAATTGCAACTTGGCGG
66 ATTTAATAAAACCAAGCAACCCCTAATAGGCCGAGACCCATTTTGCAAAAATTGCAACTAGGCGG
** * * *
106262 CAAATTGGCTAGCTTGATAAATTAGGGTTTTTGTGATTTTGGCCAAATTGATT
131 CAAATTAACTAGCTTGATAAATTAGGGTTTTTGTGATTTAGGCAAAATTGATC
* *
106315 AATTAAGCCTAAAATCAGTAGGTTAAACCCTT-AAAACTAGGTTATATCACAT-AAATAT-AAGC
1 AATTAAGCCAAAAATCAGTAGG-TAAACCCTTGAAAACTAGGTCATATCACATGAAA-ATGAA-C
* * * **
106377 CTAATTTAAT-GAACCAAGCTACCCCTAAT-GAGCCGAGTCCGTTTTTTGCAAAAATTGCAACAT
63 CTAATTTAATAAAACCAAGCAACCCCTAATAG-GCCGAGACC-CATTTTGCAAAAATTGCAAC-T
* * *
106440 AGGCGGCAAATTAACTTGCTTGGTGAATTAGGGTTTTTGTGATTTAGGCAAAATT-AGTC
125 AGGCGGCAAATTAACTAGCTTGATAAATTAGGGTTTTTGTGATTTAGGCAAAATTGA-TC
106499 AATTAAGCCAAAAATCAG
1 AATTAAGCCAAAAATCAG
106517 GGGTTTAGTG
Statistics
Matches: 170, Mismatches: 24, Indels: 14
0.82 0.12 0.07
Matches are distributed among these distances:
181 1 0.01
182 30 0.18
183 64 0.38
184 75 0.44
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (183 bp):
AATTAAGCCAAAAATCAGTAGGTAAACCCTTGAAAACTAGGTCATATCACATGAAAATGAACCTA
ATTTAATAAAACCAAGCAACCCCTAATAGGCCGAGACCCATTTTGCAAAAATTGCAACTAGGCGG
CAAATTAACTAGCTTGATAAATTAGGGTTTTTGTGATTTAGGCAAAATTGATC
Found at i:114858 original size:11 final size:11
Alignment explanation
Indices: 114841--114872 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
114831 ATTGCCTTCA
114841 AATCTTCAAAT
1 AATCTTCAAAT
*
114852 TATCTTCAAAT
1 AATCTTCAAAT
114863 AATCTTCAAA
1 AATCTTCAAA
114873 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:116286 original size:21 final size:21
Alignment explanation
Indices: 116260--116301 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
116250 AGTGTCGACC
116260 CAATCA-AGCAATTCAAAGCAT
1 CAATCATAGC-ATTCAAAGCAT
*
116281 CAATCATAGCATTCATAGCAT
1 CAATCATAGCATTCAAAGCAT
116302 ATGGGTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.24
Consensus pattern (21 bp):
CAATCATAGCATTCAAAGCAT
Found at i:119237 original size:15 final size:15
Alignment explanation
Indices: 119217--119252 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
119207 GAAACAGGGG
*
119217 ATTAAAAAGAAAGCA
1 ATTAAAAAGAAAACA
119232 ATTAAAAAGAAAACA
1 ATTAAAAAGAAAACA
119247 ATTAAA
1 ATTAAA
119253 CTAAAAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.69, C:0.06, G:0.08, T:0.17
Consensus pattern (15 bp):
ATTAAAAAGAAAACA
Found at i:119286 original size:6 final size:6
Alignment explanation
Indices: 119270--119300 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
119260 CTAAGCAAAA
119270 TAAAT- TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TA
119301 CAGCAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:120684 original size:11 final size:11
Alignment explanation
Indices: 120667--120698 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
120657 ATTGCCCTCA
120667 AATCTTCAAAT
1 AATCTTCAAAT
*
120678 TATCTTCAAAT
1 AATCTTCAAAT
120689 AATCTTCAAA
1 AATCTTCAAA
120699 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:122669 original size:30 final size:31
Alignment explanation
Indices: 122633--122751 Score: 84
Period size: 30 Copynumber: 4.2 Consensus size: 31
122623 ATTCATCCCT
122633 AAACACAGAGGCAT-TTACATCAAAGTCCTC
1 AAACACAGAGGCATATTACATCAAAGTCCTC
*
122663 AAACACA-AGG-GTATT-CATC--A---CT-
1 AAACACAGAGGCATATTACATCAAAGTCCTC
* *
122685 AAACATAGAGGCAT-TTACATCCAAGTCCTC
1 AAACACAGAGGCATATTACATCAAAGTCCTC
* * *
122715 AAGCACAGAGGCATCTATAC-T-AAAGTCCCC
1 AAACACAGAGGCATAT-TACATCAAAGTCCTC
122745 AAACACA
1 AAACACA
122752 TATAACACAG
Statistics
Matches: 69, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
22 6 0.09
23 7 0.10
24 5 0.07
26 2 0.03
28 5 0.07
29 7 0.10
30 32 0.46
31 2 0.03
32 3 0.04
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.19
Consensus pattern (31 bp):
AAACACAGAGGCATATTACATCAAAGTCCTC
Found at i:122676 original size:52 final size:52
Alignment explanation
Indices: 122545--122721 Score: 214
Period size: 52 Copynumber: 3.3 Consensus size: 52
122535 CCAACAATTA
* * *
122545 AAAGTCCTCAAACACAAGGGCATTTATAAGTCCCTAAACACAGAGGCACCTCT-C-TC
1 AAAGTCCTCAAACACAAGGG--TAT-TCA-TCCCTAAACACAGAGGCA--TTTACATC
122601 AAAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCATTTACATC
1 -AAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCATTTACATC
* *
122654 AAAGTCCTCAAACACAAGGGTATTCATCACTAAACATAGAGGCATTTACATC
1 AAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCATTTACATC
* *
122706 CAAGTCCTCAAGCACA
1 AAAGTCCTCAAACACA
122722 GAGGCATCTA
Statistics
Matches: 111, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
51 2 0.02
52 65 0.59
53 20 0.18
54 2 0.02
55 2 0.02
57 20 0.18
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.20
Consensus pattern (52 bp):
AAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCATTTACATC
Found at i:126355 original size:31 final size:31
Alignment explanation
Indices: 126297--126355 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
126287 AACCCGAGAC
* *
126297 CCGAACCCAGATGAGCGAAAGCACAAATTAT
1 CCGAACCCAGATGAGCCAAAACACAAATTAT
*
126328 CCGAACCCAGATGAGCCAAAACCCAAAT
1 CCGAACCCAGATGAGCCAAAACACAAAT
126356 GACCAGAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.31, G:0.17, T:0.10
Consensus pattern (31 bp):
CCGAACCCAGATGAGCCAAAACACAAATTAT
Found at i:127320 original size:129 final size:131
Alignment explanation
Indices: 127093--127356 Score: 372
Period size: 129 Copynumber: 2.0 Consensus size: 131
127083 AACAATTCTA
* *
127093 ATATATCAAGTTTTTTAATTAAAGTAGTAAAATGGTAAACTAAAATAGTTATAAGGATATTAGAT
1 ATATATCAAGTTTTTTAATTAAAGTACT--AA--G-AAACGAAAATAGTTATAAGGATATTAGAT
* * *
127158 TTGATTAAAGAGAAATAGATTTTTTAGTTGAGTAAAATAATAAAATGGTAAAATAAAATAGTTAT
61 TTGATTAAAGAAAAATAGAGTTTTTAGTCGAGTAAAATAATAAAATGGT-AAATAAAATAGTTAT
127223 AAAGATG
125 AAAGATG
*
127230 ATATATCAAGTTTTTTAATTAAAGTACT-A-AAACGAAAATATTTAT-AGGATATTAGATTTGAT
1 ATATATCAAGTTTTTTAATTAAAGTACTAAGAAACGAAAATAGTTATAAGGATATTAGATTTGAT
* * *
127292 TAAATAAAAATATAGTTTTTAGTCGAGTAAAATAGTAAAATGGTAAATAAAATAGTTATAAAGAT
66 TAAAGAAAAATAGAGTTTTTAGTCGAGTAAAATAATAAAATGGTAAATAAAATAGTTATAAAGAT
127357 ATTAGATTAA
Statistics
Matches: 118, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
128 21 0.18
129 55 0.47
130 14 0.12
134 1 0.01
137 27 0.23
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (131 bp):
ATATATCAAGTTTTTTAATTAAAGTACTAAGAAACGAAAATAGTTATAAGGATATTAGATTTGAT
TAAAGAAAAATAGAGTTTTTAGTCGAGTAAAATAATAAAATGGTAAATAAAATAGTTATAAAGAT
G
Found at i:133041 original size:20 final size:20
Alignment explanation
Indices: 133012--133053 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
133002 AACTATTATC
*
133012 GCTCCAATTTTCTTGTTGTT
1 GCTCCAATTTTCATGTTGTT
*
133032 GCTCCCATTTTCATGTTGTT
1 GCTCCAATTTTCATGTTGTT
133052 GC
1 GC
133054 AACGTGGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.24, G:0.17, T:0.50
Consensus pattern (20 bp):
GCTCCAATTTTCATGTTGTT
Found at i:133554 original size:33 final size:32
Alignment explanation
Indices: 133517--133635 Score: 148
Period size: 32 Copynumber: 3.7 Consensus size: 32
133507 GACCGGATCG
* * *
133517 CGCCTCGCCGTATGGTGAGGGGCCTCCTTGGGA
1 CGCCTCCCCATATGGTGAGGCGCCTCC-TGGGA
*
133550 CGCCTCCCCATATGGTGAGGCCCCTCCTGGGA
1 CGCCTCCCCATATGGTGAGGCGCCTCCTGGGA
* * *
133582 CGCCTCCCCATATGGTCAGGCGCCCCCTAGGA
1 CGCCTCCCCATATGGTGAGGCGCCTCCTGGGA
* *
133614 CGCCTCGCCATATGGTTAGGCG
1 CGCCTCCCCATATGGTGAGGCG
133636 TCCCCGACAA
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
32 53 0.70
33 23 0.30
ACGTcount: A:0.13, C:0.37, G:0.31, T:0.19
Consensus pattern (32 bp):
CGCCTCCCCATATGGTGAGGCGCCTCCTGGGA
Found at i:133857 original size:17 final size:17
Alignment explanation
Indices: 133816--133857 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
133806 TAATTAAATT
133816 TTACAATTAATAGATTAA
1 TTACAATTAATA-ATTAA
133834 TTA-AATTAAT-ATTAAA
1 TTACAATTAATAATT-AA
133850 TTACAATT
1 TTACAATT
133858 TTTTTGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.14
16 5 0.23
17 11 0.50
18 3 0.14
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (17 bp):
TTACAATTAATAATTAA
Done.