Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006867.1 Corchorus capsularis cultivar CVL-1 contig06888, 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: 71835
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:10266 original size:11 final size:11
Alignment explanation
Indices: 10230--10276 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
10220 AAGACAAAAA
*
10230 AAAAACACTCTA
1 AAAAACAC-CTT
10242 AGAAAACA-CTT
1 A-AAAACACCTT
10253 AAAAACACCTT
1 AAAAACACCTT
*
10264 AAAAACACTTT
1 AAAAACACCTT
10275 AA
1 AA
10277 GAGAACTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 6 0.19
11 18 0.58
12 1 0.03
13 6 0.19
ACGTcount: A:0.57, C:0.21, G:0.02, T:0.19
Consensus pattern (11 bp):
AAAAACACCTT
Found at i:10270 original size:21 final size:23
Alignment explanation
Indices: 10230--10273 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
10220 AAGACAAAAA
10230 AAAAACACTCTAAGAAAACACTT
1 AAAAACACTCTAAGAAAACACTT
*
10253 AAAAACAC-CTTA-AAAACACTT
1 AAAAACACTCTAAGAAAACACTT
10274 TAAGAGAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 3 0.15
23 8 0.40
ACGTcount: A:0.57, C:0.23, G:0.02, T:0.18
Consensus pattern (23 bp):
AAAAACACTCTAAGAAAACACTT
Found at i:16784 original size:2 final size:2
Alignment explanation
Indices: 16772--16812 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
16762 TGATTCAAGG
16772 AT AT CAT AT AT AT 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 AT AT AT AT AT AT
16813 GTTCAAACTG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17595 original size:26 final size:26
Alignment explanation
Indices: 17559--17615 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
17549 ATTAAATATA
*
17559 AATTGGTTTCTTTTGTTTTGTAGCTT
1 AATTTGTTTCTTTTGTTTTGTAGCTT
17585 AATTTGTTTCTTTTGTTTTGTAGCTT
1 AATTTGTTTCTTTTGTTTTGTAGCTT
17611 AATTT
1 AATTT
17616 TTAATATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.14, C:0.07, G:0.16, T:0.63
Consensus pattern (26 bp):
AATTTGTTTCTTTTGTTTTGTAGCTT
Found at i:18448 original size:86 final size:86
Alignment explanation
Indices: 18337--18508 Score: 310
Period size: 87 Copynumber: 2.0 Consensus size: 86
18327 GGGGGGGGGG
*
18337 GGGGGATTACTTTAAATTAAGCTCCACTTTTCAA-GTAGATTTCCTAATTAATCACTTTAAATCC
1 GGGGGATTACTTTAAATTAAGCTCCACTTTTCAAGGTACATTTCCTAATTAATCACTTTAAATCC
18401 ATAAATATTGTGTCAAATATT
66 ATAAATATTGTGTCAAATATT
*
18422 GGGGGATTTACTTTAAATTAAGCTCCACTTTTCAAGGTACATTTCCTAATTAATTACTTTAAATC
1 GGGGGA-TTACTTTAAATTAAGCTCCACTTTTCAAGGTACATTTCCTAATTAATCACTTTAAATC
18487 CATAAATATTGTGTCAAATATT
65 CATAAATATTGTGTCAAATATT
18509 TCCCATCTTG
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
85 6 0.07
86 28 0.34
87 49 0.59
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.40
Consensus pattern (86 bp):
GGGGGATTACTTTAAATTAAGCTCCACTTTTCAAGGTACATTTCCTAATTAATCACTTTAAATCC
ATAAATATTGTGTCAAATATT
Found at i:21826 original size:15 final size:16
Alignment explanation
Indices: 21806--21838 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21796 CCTATTGAAT
*
21806 TTTTGTT-AATTTTCA
1 TTTTGTTGAAATTTCA
21821 TTTTGTTGAAATTTCA
1 TTTTGTTGAAATTTCA
21837 TT
1 TT
21839 GATTATGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.21, C:0.06, G:0.09, T:0.64
Consensus pattern (16 bp):
TTTTGTTGAAATTTCA
Found at i:24369 original size:16 final size:16
Alignment explanation
Indices: 24350--24402 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
24340 ACGCACAAAT
24350 CCGAAAAAATCAGAAC
1 CCGAAAAAATCAGAAC
*
24366 CCG-AAAAATCTGAAAC
1 CCGAAAAAATCAG-AAC
* * *
24382 CCGATAAAACCCGAAC
1 CCGAAAAAATCAGAAC
24398 CCGAA
1 CCGAA
24403 CTTGAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 8 0.27
16 16 0.53
17 6 0.20
ACGTcount: A:0.49, C:0.30, G:0.13, T:0.08
Consensus pattern (16 bp):
CCGAAAAAATCAGAAC
Found at i:24672 original size:32 final size:31
Alignment explanation
Indices: 24594--24702 Score: 121
Period size: 32 Copynumber: 3.4 Consensus size: 31
24584 GCCAAAACCC
* *
24594 AACCCGAACCCGAATTAACCTGACCAAAAATT
1 AACCCGAACCCGAATCAACCTGACC-AAATTT
* *
24626 GACCTGAACCCGAATCAACCTGACCGAAATTT
1 AACCCGAACCCGAATCAACCTGACC-AAATTT
* *
24658 AACCCAAACTCGAATCAAACC-GATCCAAATTT
1 AACCCGAACCCGAATC-AACCTGA-CCAAATTT
24690 AACCCGAACCCGA
1 AACCCGAACCCGA
24703 CTTAAACCCG
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 58 0.91
33 6 0.09
ACGTcount: A:0.40, C:0.33, G:0.11, T:0.16
Consensus pattern (31 bp):
AACCCGAACCCGAATCAACCTGACCAAATTT
Found at i:33265 original size:35 final size:36
Alignment explanation
Indices: 33196--33297 Score: 109
Period size: 36 Copynumber: 2.8 Consensus size: 36
33186 GCATCCATAC
* ** *
33196 ATTAAGTAAAATTATTCAAAAACTTAATTTCAAGG-A
1 ATTAAGTAAAATCAAACAAAGACTTAA-TTCAAGGTA
* *
33232 ATTTAGGTAAAATC-AACAAAGAGTTAATTCAAGGTA
1 A-TTAAGTAAAATCAAACAAAGACTTAATTCAAGGTA
*
33268 ATTAAGTAAAGTCAAACAAAGACTTAATTC
1 ATTAAGTAAAATCAAACAAAGACTTAATTC
33298 CATGTTCATA
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
35 17 0.31
36 27 0.50
37 10 0.19
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (36 bp):
ATTAAGTAAAATCAAACAAAGACTTAATTCAAGGTA
Found at i:33558 original size:318 final size:318
Alignment explanation
Indices: 32974--33614 Score: 1183
Period size: 318 Copynumber: 2.0 Consensus size: 318
32964 TAAATGTTTC
*
32974 TAATGCCATGTTCATATAAGATAAATAAATTGACTCCGATGATGGAATAATCGGTTGGAATTTAG
1 TAATTCCATGTTCATATAAGATAAATAAATTGACTCCGATGATGGAATAATCGGTTGGAATTTAG
*
33039 ACAGTATTTGTCTGTTTCAGTCTGAGTTTCCTAGGCTTGAAACATCTAAATGTGGGTCTTACCAG
66 ACAGTACTTGTCTGTTTCAGTCTGAGTTTCCTAGGCTTGAAACATCTAAATGTGGGTCTTACCAG
*
33104 TATGAGTGGAAAGTGCCCAAATAGTATTTCTCGTATAATCATATAGTAAAGAACTTTATCAACCA
131 TATGAGTGGAAAGTGCCCAAATAGTATTTCTAGTATAATCATATAGTAAAGAACTTTATCAACCA
*
33169 GTGTACATGCATCATACGCATCCATACATTAAGTAAAATTATTCAAAAACTTAATTTCAAGGAAT
196 GTGTACATGCATCATACGCATCCATACATTAAGTAAAATTATTCAAAAACTTAATTTCAAGGAAA
*
33234 TTAGGTAAAATCAACAAAGAGTTAATTCAAGGTAATTAAGTAAAGTCAAACAAAGACT
261 TTAGGTAAAATCAACAAAGACTTAATTCAAGGTAATTAAGTAAAGTCAAACAAAGACT
33292 TAATTCCATGTTCATATAAGATAAATAAATTGACTCCGATGATGGAATAATCGGTTGGAATTTAG
1 TAATTCCATGTTCATATAAGATAAATAAATTGACTCCGATGATGGAATAATCGGTTGGAATTTAG
*
33357 ACAGTACTTGTCTGTTTTAGTCTGAGTTTCCTAGGCTTGAAACATCTAAATGTGGGTCTTACCAG
66 ACAGTACTTGTCTGTTTCAGTCTGAGTTTCCTAGGCTTGAAACATCTAAATGTGGGTCTTACCAG
* *
33422 TATGAGTGGAAGGTGCCCAAATAGTGTTTCTAGTATAATCATATAGTAAAGAACTTTATCAACCA
131 TATGAGTGGAAAGTGCCCAAATAGTATTTCTAGTATAATCATATAGTAAAGAACTTTATCAACCA
*
33487 GTGTACATGCATCATATGCATCCATACATTAAGTAAAATTATTCAAAAACTTAATTTCAAGGAAA
196 GTGTACATGCATCATACGCATCCATACATTAAGTAAAATTATTCAAAAACTTAATTTCAAGGAAA
* *
33552 TTAGGTAAAATCAGCAAAGACTTAATTCAAGGTAATTAAGTAAAGTCAAGCAAAGACT
261 TTAGGTAAAATCAACAAAGACTTAATTCAAGGTAATTAAGTAAAGTCAAACAAAGACT
33610 TAATT
1 TAATT
33615 TCAAGGAAAC
Statistics
Matches: 312, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
318 312 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (318 bp):
TAATTCCATGTTCATATAAGATAAATAAATTGACTCCGATGATGGAATAATCGGTTGGAATTTAG
ACAGTACTTGTCTGTTTCAGTCTGAGTTTCCTAGGCTTGAAACATCTAAATGTGGGTCTTACCAG
TATGAGTGGAAAGTGCCCAAATAGTATTTCTAGTATAATCATATAGTAAAGAACTTTATCAACCA
GTGTACATGCATCATACGCATCCATACATTAAGTAAAATTATTCAAAAACTTAATTTCAAGGAAA
TTAGGTAAAATCAACAAAGACTTAATTCAAGGTAATTAAGTAAAGTCAAACAAAGACT
Found at i:33632 original size:72 final size:72
Alignment explanation
Indices: 33530--34257 Score: 553
Period size: 72 Copynumber: 9.9 Consensus size: 72
33520 TAAAATTATT
* *
33530 CAAAAACTTAATTTCAAGGAAATTAGGTAAAATCAGCAAAGACTTAATTCAAGGTAATTAAGTAA
1 CAAAGACTTAATTTCAAGGAAATTAAGTAAAATCAGCAAAGACTTAATTCAAGGTAATTAAGTAA
33595 AGTCAAG
66 AGTCAAG
* *
33602 CAAAGACTTAATTTCAAGGAAACTAAGTAAAATCGGCAAAGACTTAATTCAAGGTAATTAAGTAA
1 CAAAGACTTAATTTCAAGGAAATTAAGTAAAATCAGCAAAGACTTAATTCAAGGTAATTAAGTAA
*
33667 AGTTAAG
66 AGTCAAG
* * * *
33674 CAAAGGCTTAATTTTCAAGGAAATTAGGTAAAATCAGCAAAGACGTAACTCAAGGTAATTAAGTA
1 CAAAGACTTAA-TTTCAAGGAAATTAAGTAAAATCAGCAAAGACTTAATTCAAGGTAATTAAGTA
33739 AAGTCAAG
65 AAGTCAAG
* * *
33747 CAAAGACTTAATTTCAA-GATAATTAAGTAAACTTAGTCCAAGACTTAATTCAAGGTAATTAAGT
1 CAAAGACTTAATTTCAAGGA-AATTAAGTAAAATCAG-CAAAGACTTAATTCAAGGTAATTAAGT
*
33811 AAAATC-AG
64 AAAGTCAAG
* *
33819 CAAAGACTTAA-TTCAAGGTAATTAAGTAAAAATCAGTCAAAGACTTAATTCAAGATAATTAAGT
1 CAAAGACTTAATTTCAAGGAAATTAAGT-AAAATCAG-CAAAGACTTAATTCAAGGTAATTAAGT
*
33883 AAAATC-AG
64 AAAGTCAAG
* * * * * * *
33891 TCAAAGACTTAATTTCAAGAAAATTAGGTAAAATCAAGCAAAAAC-TCAGTCAAAGACTTAGTTT
1 -CAAAGACTTAATTTCAAGGAAATTAAGTAAAATC-AGCAAAGACTTAATTC-AAG--GTA-ATT
* *
33955 CAAGGAAA-TTAAG
60 -AAGTAAAGTCAAG
* * * * ** * * *
33968 TAAACTCAATCAACGTCTT-AATTCAAGGTAATTAAGTAAAATCAGCAAAGAGTTAATTCAAGGT
1 CAAA--GACTTAA--T-TTCAA-GGAA-AT-T--AAGTAAAATCAGCAAAGACTTAATTCAAGGT
* *
34032 ATTTAAGTAAAATCAAG
56 AATTAAGTAAAGTCAAG
* *** * *
34049 CAAAGACTTAATTTCGAGGAAATTAAGTTGGATTAGTCAAAGACTTAATTCAAGGTAATTAAATA
1 CAAAGACTTAATTTCAAGGAAATTAAGTAAAATCAG-CAAAGACTTAATTCAAGGTAATTAAGTA
* *
34114 AGGTTAA-
65 AAGTCAAG
* ** * * * ** * *
34121 TAAAGAACTTAA-TTCAAGTTAATTAAATAGAGTCAATAAAGAATTTAATTCAAGGTAATTAATT
1 CAAAG-ACTTAATTTCAAGGAAATTAAGTAAAATCAGCAAAG-ACTTAATTCAAGGTAATTAAGT
*
34185 AGAGTCAA-
64 AAAGTCAAG
* * * * * * * * *
34193 TAAAGAACTTAA-TTCAGGGTAATTAAG-AAACTCGGTAAATAACTTAATTCAAGGAAATCAAGT
1 CAAAG-ACTTAATTTCAAGGAAATTAAGTAAAATCAGCAAA-GACTTAATTCAAGGTAATTAAGT
34256 AA
64 AA
34258 GATAATAAAA
Statistics
Matches: 526, Mismatches: 99, Indels: 63
0.76 0.14 0.09
Matches are distributed among these distances:
71 46 0.09
72 230 0.44
73 155 0.29
74 15 0.03
75 3 0.01
76 10 0.02
77 10 0.02
78 4 0.01
79 4 0.01
80 9 0.02
81 14 0.03
82 3 0.01
84 10 0.02
85 13 0.02
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (72 bp):
CAAAGACTTAATTTCAAGGAAATTAAGTAAAATCAGCAAAGACTTAATTCAAGGTAATTAAGTAA
AGTCAAG
Found at i:33727 original size:108 final size:109
Alignment explanation
Indices: 33514--34257 Score: 541
Period size: 108 Copynumber: 6.8 Consensus size: 109
33504 GCATCCATAC
* ** * *
33514 ATTAAGTAAAATTATTCAAAAACTTAATTTCAAGGA-AATTAGGTAAAATCAG-CAAAGACTTAA
1 ATTAAGTAAAATCAGGCAAAGACTTAATTTCAA-GATAATTAAGTAAAATCAGTCAAAGACTTAA
* * *
33577 TTCAAGGTAATTAAGTAAAGTCAAGCAAAGACTTAATTTCAAGGAA
65 TTCAAGGAAATTAAGTAAAATCAAGCAAAGACTTAA-TTCAAGGTA
* * * * *
33623 ACTAAGTAAAATC-GGCAAAGACTTAA-TTCAAGGTAATTAAGTAAAGTTAAG-CAAAGGCTTAA
1 ATTAAGTAAAATCAGGCAAAGACTTAATTTCAAGATAATTAAGTAAA-ATCAGTCAAAGACTTAA
* * *
33685 TTTTCAAGGAAATTAGGTAAAATC-AGCAAAGACGTAACTCAAGGTA
65 --TTCAAGGAAATTAAGTAAAATCAAGCAAAGACTTAATTCAAGGTA
* * * * *
33731 ATTAAGTAAAGTCAAGCAAAGACTTAATTTCAAGATAATTAAGTAAACTTAGTCCAAGACTTAAT
1 ATTAAGTAAAATCAGGCAAAGACTTAATTTCAAGATAATTAAGTAAAATCAGTCAAAGACTTAAT
*
33796 TCAAGGTAATTAAGTAAAATC-AGCAAAGACTTAATTCAAGGTA
66 TCAAGGAAATTAAGTAAAATCAAGCAAAGACTTAATTCAAGGTA
*
33839 ATTAAGTAAAAATCAGTCAAAGACTTAA-TTCAAGATAATTAAGTAAAATCAGTCAAAGACTTAA
1 ATTAAGT-AAAATCAGGCAAAGACTTAATTTCAAGATAATTAAGTAAAATCAGTCAAAGACTTAA
* * * *
33903 TTTCAAGAAAATTAGGTAAAATCAAGCAAAAACTCAGTCAAAGACTTAGTTTCAAGGAA
65 -TTCAAGGAAATTAAGTAAAAT----C----A---AG-CAAAGACTTA-ATTCAAGGTA
* ** * * * *
33962 ATTAAGTAAACTCAATCAACGTCTTAA-TTCAAGGTAATTAAGTAAAATCAG-CAAAGAGTTAAT
1 ATTAAGTAAAATCAGGCAAAGACTTAATTTCAAGATAATTAAGTAAAATCAGTCAAAGACTTAAT
* * * *
34025 TCAAGGTATTTAAGTAAAATCAAGCAAAGACTTAATTTCGAGGAA
66 TCAAGGAAATTAAGTAAAATCAAGCAAAGACTTAA-TTCAAGGTA
*** * * * * ** * *
34070 ATTAAGTTGGATTAGTCAAAGACTTAA-TTCAAGGTAATTAAATAAGGTTAAT-AAAGAACTTAA
1 ATTAAGTAAAATCAGGCAAAGACTTAATTTCAAGATAATTAAGTAAAATCAGTCAAAG-ACTTAA
** * * * * *
34133 TTCAAGTTAATTAAATAGAGTCAA-TAAAGAATTTAATTCAAGGTA
65 TTCAAGGAAATTAAGTAAAATCAAGCAAAG-ACTTAATTCAAGGTA
* * * ** * * * * *
34178 ATTAATTAGAGTCA-ATAAAGAACTTAA-TTCAGGGTAATTAAG-AAACTCGGT-AAATAACTTA
1 ATTAAGTAAAATCAGGCAAAG-ACTTAATTTCAAGATAATTAAGTAAAATCAGTCAAA-GACTTA
*
34239 ATTCAAGGAAATCAAGTAA
64 ATTCAAGGAAATTAAGTAA
34258 GATAATAAAA
Statistics
Matches: 512, Mismatches: 94, Indels: 60
0.77 0.14 0.09
Matches are distributed among these distances:
106 1 0.00
107 45 0.09
108 220 0.43
109 104 0.20
110 46 0.09
112 1 0.00
113 1 0.00
116 1 0.00
120 17 0.03
121 12 0.02
122 49 0.10
123 15 0.03
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (109 bp):
ATTAAGTAAAATCAGGCAAAGACTTAATTTCAAGATAATTAAGTAAAATCAGTCAAAGACTTAAT
TCAAGGAAATTAAGTAAAATCAAGCAAAGACTTAATTCAAGGTA
Found at i:33821 original size:145 final size:142
Alignment explanation
Indices: 33514--34110 Score: 608
Period size: 145 Copynumber: 4.0 Consensus size: 142
33504 GCATCCATAC
* * * * *
33514 ATTAAGTAAAATTATTCAAAAACTTAATTTCAAGGAAATTAGGTAAAATCAGCAAAGACTTAATT
1 ATTAAGTAAAATCA-GCAAAGACTTAA-TTCAAGGAAATTAAGTAAAATCAGCAAAGACGTAATT
* * * * *
33579 CAAGGTAATTAAGTAAAGTCAAGCAAAGACTTAATTTCAAGGAAACTAAG-TAAAATCGGCAAAG
64 CAAGGTAATTAAGTAAAATCAAGCAAAGACTTAATTTCAA-GAAATTAAGATAAATTAGTCAAAG
33643 ACTTAATTCAAGGTA
128 ACTTAATTCAAGGTA
* * * * *
33658 ATTAAGTAAAGTTAAGCAAAGGCTTAATTTTCAAGGAAATTAGGTAAAATCAGCAAAGACGTAAC
1 ATTAAGTAAA-ATCAGCAAAGACTTAA--TTCAAGGAAATTAAGTAAAATCAGCAAAGACGTAAT
* *
33723 TCAAGGTAATTAAGTAAAGTCAAGCAAAGACTTAATTTCAAGATAATTAAG-TAAACTTAGTCCA
63 TCAAGGTAATTAAGTAAAATCAAGCAAAGACTTAATTTCAAGA-AATTAAGATAAA-TTAGTCAA
33787 AGACTTAATTCAAGGTA
126 AGACTTAATTCAAGGTA
* *
33804 ATTAAGTAAAATCAGCAAAGACTTAATTCAAGGTAATTAAGTAAAAATCAGTCAAAGACTTAATT
1 ATTAAGTAAAATCAGCAAAGACTTAATTCAAGGAAATTAAGT-AAAATCAG-CAAAGACGTAATT
* *
33869 CAAGATAATTAAGTAAAATC-AGTCAAAGACTTAATTTCAAGAAAATTAGGTAAAATCAAGCAAA
64 CAAGGTAATTAAGTAAAATCAAG-CAAAGACTTAATTTCAAG--AA--A--T----T-AAG-ATA
* * *
33933 AACTCAGTCAAAGACTTAGTTTCAAGGAA
116 AA-TTAGTCAAAGACTTA-ATTCAAGGTA
* * * * *
33962 ATTAAGTAAACTCAATCAACGTCTTAATTCAAGGTAATTAAGTAAAATCAGCAAAGA-GTTAATT
1 ATTAAGTAAAATC-AGCAAAGACTTAATTCAAGGAAATTAAGTAAAATCAGCAAAGACG-TAATT
* * * **
34026 CAAGGTATTTAAGTAAAATCAAGCAAAGACTTAATTTCGAGGAAATTAAGTTGGATTAGTCAAAG
64 CAAGGTAATTAAGTAAAATCAAGCAAAGACTTAATTTC-AAGAAATTAAGATAAATTAGTCAAAG
34091 ACTTAATTCAAGGTA
128 ACTTAATTCAAGGTA
34106 ATTAA
1 ATTAA
34111 ATAAGGTTAA
Statistics
Matches: 387, Mismatches: 41, Indels: 50
0.81 0.09 0.10
Matches are distributed among these distances:
143 14 0.04
144 44 0.11
145 162 0.42
146 33 0.09
147 4 0.01
148 2 0.01
150 1 0.00
152 1 0.00
154 2 0.01
155 3 0.01
156 2 0.01
157 61 0.16
158 32 0.08
159 26 0.07
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (142 bp):
ATTAAGTAAAATCAGCAAAGACTTAATTCAAGGAAATTAAGTAAAATCAGCAAAGACGTAATTCA
AGGTAATTAAGTAAAATCAAGCAAAGACTTAATTTCAAGAAATTAAGATAAATTAGTCAAAGACT
TAATTCAAGGTA
Found at i:33949 original size:85 final size:83
Alignment explanation
Indices: 33846--34016 Score: 220
Period size: 85 Copynumber: 2.0 Consensus size: 83
33836 GTAATTAAGT
*
33846 AAAAATCAGTCAAAGACTTA-ATTCAA-GATAATTAAGTAAAATCAGTCAAAGACTTAATTTCAA
1 AAAAATCAGTCAAAGACTTAGATTCAAGGA-AATTAAGTAAAATCAATCAAAGACTTAA-TTCAA
*
33909 GAAAATTAGGTAAAATCAAGC
64 GAAAATTAAGTAAAATC-AGC
* * * *
33930 AAAAACTCAGTCAAAGACTTAGTTTCAAGGAAATTAAGTAAACTCAATCAACGTCTTAATTCAAG
1 AAAAA-TCAGTCAAAGACTTAGATTCAAGGAAATTAAGTAAAATCAATCAAAGACTTAATTCAAG
**
33995 GTAATTAAGTAAAATCAGC
65 AAAATTAAGTAAAATCAGC
34014 AAA
1 AAA
34017 GAGTTAATTC
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
84 11 0.14
85 34 0.45
86 29 0.38
87 2 0.03
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.25
Consensus pattern (83 bp):
AAAAATCAGTCAAAGACTTAGATTCAAGGAAATTAAGTAAAATCAATCAAAGACTTAATTCAAGA
AAATTAAGTAAAATCAGC
Found at i:33964 original size:49 final size:48
Alignment explanation
Indices: 33883--33976 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 48
33873 ATAATTAAGT
*
33883 AAAATCAGTCAAAGACTTAATTTCAAGAAAATTAGGTAAAATCAAGCA
1 AAAATCAGTCAAAGACTTAATTTCAAGAAAATTAAGTAAAATCAAGCA
* * *
33931 AAAACTCAGTCAAAGACTTAGTTTCAAGGAAATTAAGTAAACTCAA
1 AAAA-TCAGTCAAAGACTTAATTTCAAGAAAATTAAGTAAAATCAA
33977 TCAACGTCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 4 0.10
49 37 0.90
ACGTcount: A:0.50, C:0.14, G:0.13, T:0.23
Consensus pattern (48 bp):
AAAATCAGTCAAAGACTTAATTTCAAGAAAATTAAGTAAAATCAAGCA
Found at i:33991 original size:122 final size:118
Alignment explanation
Indices: 33811--34052 Score: 324
Period size: 122 Copynumber: 2.0 Consensus size: 118
33801 GTAATTAAGT
* *
33811 AAAATCAGCAAAGACTTAATTCAAGGTAATTAAGTAAAAATCAGTCAAAGACTTAATTCAAGATA
1 AAAATCAGCAAAGACTTAATTCAAGGAAATTAAGTAAAAATCAATCAAAGACTTAATTCAAGATA
*
33876 ATTAAGTAAAATCAGTCAAAGACTTAATTTCAAGAAAATTAGGTAAAATCAAGCA
66 ATTAAGTAAAATCAG-CAAAGACTTAA-TTCAAGAAAATTAAGTAAAATCAAGCA
* * * *
33931 AAAACTCAGTCAAAGACTTAGTTTCAAGGAAATTAAGT-AAACTCAATCAACGTCTTAATTCAAG
1 AAAA-TCAG-CAAAGACTTA-ATTCAAGGAAATTAAGTAAAAATCAATCAAAGACTTAATTCAAG
* * ** *
33995 GTAATTAAGTAAAATCAGCAAAGAGTTAATTCAAGGTATTTAAGTAAAATCAAGCA
63 ATAATTAAGTAAAATCAGCAAAGACTTAATTCAAGAAAATTAAGTAAAATCAAGCA
34051 AA
1 AA
34053 GACTTAATTT
Statistics
Matches: 107, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
120 29 0.27
121 14 0.13
122 49 0.46
123 15 0.14
ACGTcount: A:0.49, C:0.12, G:0.13, T:0.26
Consensus pattern (118 bp):
AAAATCAGCAAAGACTTAATTCAAGGAAATTAAGTAAAAATCAATCAAAGACTTAATTCAAGATA
ATTAAGTAAAATCAGCAAAGACTTAATTCAAGAAAATTAAGTAAAATCAAGCA
Found at i:34001 original size:36 final size:36
Alignment explanation
Indices: 33940--34219 Score: 228
Period size: 36 Copynumber: 7.8 Consensus size: 36
33930 AAAAACTCAG
* * *
33940 TCAAAGACTTAGTTTCAAGGAAATTAAGTAAACTCAA
1 TCAAAGACTTA-ATTCAAGGTAATTAAGTAAAGTCAA
* * *
33977 TCAACGTCTTAATTCAAGGTAATTAAGTAAAATC-A
1 TCAAAGACTTAATTCAAGGTAATTAAGTAAAGTCAA
* * * *
34012 GCAAAGAGTTAATTCAAGGTATTTAAGTAAAATCAA
1 TCAAAGACTTAATTCAAGGTAATTAAGTAAAGTCAA
* * * ** * *
34048 GCAAAGACTTAATTTCGAGGAAATTAAGT-TGGATTAG
1 TCAAAGACTTAA-TTCAAGGTAATTAAGTAAAG-TCAA
* * *
34085 TCAAAGACTTAATTCAAGGTAATTAAATAAGGTTAA
1 TCAAAGACTTAATTCAAGGTAATTAAGTAAAGTCAA
* * *
34121 T-AAAGAACTTAATTCAAGTTAATTAAATAGAGTCAA
1 TCAAAG-ACTTAATTCAAGGTAATTAAGTAAAGTCAA
* * *
34157 T-AAAGAATTTAATTCAAGGTAATTAATTAGAGTCAA
1 TCAAAG-ACTTAATTCAAGGTAATTAAGTAAAGTCAA
*
34193 T-AAAGAACTTAATTCAGGGTAATTAAG
1 TCAAAG-ACTTAATTCAAGGTAATTAAG
34220 AAACTCGGTA
Statistics
Matches: 203, Mismatches: 35, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
35 34 0.17
36 132 0.65
37 37 0.18
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.30
Consensus pattern (36 bp):
TCAAAGACTTAATTCAAGGTAATTAAGTAAAGTCAA
Found at i:34038 original size:157 final size:157
Alignment explanation
Indices: 33775--34073 Score: 433
Period size: 157 Copynumber: 1.9 Consensus size: 157
33765 ATAATTAAGT
* * *
33775 AAACTTAGTCCAAGACTTAATTCAAGGTAATTAAGTAAAATCAGCAAAGACTTAATTCAAGGTAA
1 AAACTCAGTCAAAGACTTAATTCAAGGAAATTAAGTAAAATCAGCAAAGACTTAATTCAAGGTAA
33840 TTAAGTAAAAATCAGTCAAAGACTTAATTCAAGATAATTAAGTAAAATC-AGTCAAAGACTTAAT
66 TTAAGTAAAAATCAGTCAAAGACTTAATTCAAGATAATTAAGTAAAATCAAG-CAAAGACTTAAT
33904 TTCAAGAAAATTAGGTAAAATCAAGCAA
130 TTCAAGAAAATTAGGTAAAATCAAGCAA
* * * * *
33932 AAACTCAGTCAAAGACTTAGTTTCAAGGAAATTAAGTAAACTCAATCAACGTCTTAATTCAAGGT
1 AAACTCAGTCAAAGACTTA-ATTCAAGGAAATTAAGTAAAATC-AGCAAAGACTTAATTCAAGGT
* * *
33997 AATTAAGT-AAAATCAG-CAAAGAGTTAATTCAAGGTATTTAAGTAAAATCAAGCAAAGACTTAA
64 AATTAAGTAAAAATCAGTCAAAGACTTAATTCAAGATAATTAAGTAAAATCAAGCAAAGACTTAA
* *
34060 TTTCGAGGAAATTA
129 TTTCAAGAAAATTA
34074 AGTTGGATTA
Statistics
Matches: 126, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
157 70 0.56
158 30 0.24
159 26 0.21
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.27
Consensus pattern (157 bp):
AAACTCAGTCAAAGACTTAATTCAAGGAAATTAAGTAAAATCAGCAAAGACTTAATTCAAGGTAA
TTAAGTAAAAATCAGTCAAAGACTTAATTCAAGATAATTAAGTAAAATCAAGCAAAGACTTAATT
TCAAGAAAATTAGGTAAAATCAAGCAA
Found at i:34076 original size:194 final size:193
Alignment explanation
Indices: 33747--34102 Score: 524
Period size: 194 Copynumber: 1.8 Consensus size: 193
33737 TAAAGTCAAG
* *
33747 CAAAGACTTAATTTCAAGATAATTAAGTAAACTTAGTCCAAGACTTAATTCAAGGTAATTAAGTA
1 CAAAGACTTAATTTCAAGATAATTAAGTAAACTCAATCCAAGACTTAATTCAAGGTAATTAAGTA
33812 AAATCAGCAAAGACTTAATTCAAGGTAATTAAGTAAAAATCAGTCAAAGACTTAATTCAAGATAA
66 AAATCAGCAAAGACTTAATTCAAGGTAATTAAGTAAAAATCAGTCAAAGACTTAATTCAAGATAA
33877 TTAAGTAAAATCAGTCAAAGACTTAATTTCAAGAAAATTAGGTAAAATCAAGCAAAAACTCAGT
131 TTAAGTAAAATCAGTCAAAGACTTAA-TTCAAGAAAATTAGGTAAAATCAAGCAAAAACTCAGT
* *
33941 CAAAGACTTAGTTTCAAGGA-AATTAAGTAAACTCAAT-CAACGTCTTAATTCAAGGTAATTAAG
1 CAAAGACTTAATTTCAA-GATAATTAAGTAAACTCAATCCAA-GACTTAATTCAAGGTAATTAAG
* * *
34004 TAAAATCAGCAAAGAGTTAATTCAAGGTATTTAAGT-AAAATCAAG-CAAAGACTTAATTTCGAG
64 TAAAATCAGCAAAGACTTAATTCAAGGTAATTAAGTAAAAATC-AGTCAAAGACTTAA-TTC-AA
*** *
34067 GA-AATTAAGTTGGATTAGTCAAAGACTTAATTCAAG
126 GATAATTAAGTAAAATCAGTCAAAGACTTAATTCAAG
34103 GTAATTAAAT
Statistics
Matches: 146, Mismatches: 11, Indels: 11
0.87 0.07 0.07
Matches are distributed among these distances:
193 26 0.18
194 115 0.79
195 5 0.03
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (193 bp):
CAAAGACTTAATTTCAAGATAATTAAGTAAACTCAATCCAAGACTTAATTCAAGGTAATTAAGTA
AAATCAGCAAAGACTTAATTCAAGGTAATTAAGTAAAAATCAGTCAAAGACTTAATTCAAGATAA
TTAAGTAAAATCAGTCAAAGACTTAATTCAAGAAAATTAGGTAAAATCAAGCAAAAACTCAGT
Found at i:37376 original size:108 final size:109
Alignment explanation
Indices: 37177--37380 Score: 374
Period size: 108 Copynumber: 1.9 Consensus size: 109
37167 CGCATTTTAT
37177 TTTGCTTTTTAGATTGGATAAAATAAAAATGAGCCTTATAAATGATTAAAGTATAGTCAATAATT
1 TTTGCTTTTTAGATTGGATAAAATAAAAATGAGCCTTATAAATGATTAAAGTATAGTCAATAATT
*
37242 GGGCTCATGGGCACTTGGTTGGGCGTAGAAGGCCAATGCAAATA
66 GGGCTCATGGGCACTTGGTTGAGCGTAGAAGGCCAATGCAAATA
* *
37286 TTTGTTTTTTAGATTGGATAAAAT-GAAATGAGCCTTATAAATGATTAAAGTATAGTCAATAATT
1 TTTGCTTTTTAGATTGGATAAAATAAAAATGAGCCTTATAAATGATTAAAGTATAGTCAATAATT
37350 GGGCTCATGGGCACTTGGTTGAGCGTAGAAG
66 GGGCTCATGGGCACTTGGTTGAGCGTAGAAG
37381 CCCCTAATAT
Statistics
Matches: 92, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
108 69 0.75
109 23 0.25
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.33
Consensus pattern (109 bp):
TTTGCTTTTTAGATTGGATAAAATAAAAATGAGCCTTATAAATGATTAAAGTATAGTCAATAATT
GGGCTCATGGGCACTTGGTTGAGCGTAGAAGGCCAATGCAAATA
Found at i:42365 original size:16 final size:16
Alignment explanation
Indices: 42344--42382 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
42334 TGGCCAGGAG
42344 GGAAAGACCCGATTAA
1 GGAAAGACCCGATTAA
42360 GGAAAGACCCGATTAA
1 GGAAAGACCCGATTAA
42376 GGAAAGA
1 GGAAAGA
42383 GTCCCAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.46, C:0.15, G:0.28, T:0.10
Consensus pattern (16 bp):
GGAAAGACCCGATTAA
Found at i:46119 original size:16 final size:17
Alignment explanation
Indices: 46100--46145 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
46090 AATTCCCTGC
46100 TTTTATAATTTCA-TTG
1 TTTTATAATTTCACTTG
*
46116 TTTT-TAATTTTAACTTG
1 TTTTATAA-TTTCACTTG
46133 TTTTGATAATTTC
1 TTTT-ATAATTTC
46146 TCAAAATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.12
16 8 0.33
17 7 0.29
18 3 0.12
19 3 0.12
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.63
Consensus pattern (17 bp):
TTTTATAATTTCACTTG
Found at i:46655 original size:13 final size:15
Alignment explanation
Indices: 46635--46669 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
46625 GAGTTTGGGT
46635 TCGGGTTTT-TCGGG
1 TCGGGTTTTCTCGGG
46649 T-GGGTTTTCTCGGG
1 TCGGGTTTTCTCGGG
46663 TCGGGTT
1 TCGGGTT
46670 CATTTTGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.37
14 7 0.37
15 5 0.26
ACGTcount: A:0.00, C:0.14, G:0.43, T:0.43
Consensus pattern (15 bp):
TCGGGTTTTCTCGGG
Found at i:48092 original size:39 final size:39
Alignment explanation
Indices: 48049--48170 Score: 199
Period size: 39 Copynumber: 3.0 Consensus size: 39
48039 TTTAGTCTCG
48049 GTTCGTCCAATTTGAACATTCAAAAAAACATCAGTAATT
1 GTTCGTCCAATTTGAACATTCAAAAAAACATCAGTAATT
48088 GTTCGTCCAATTTGAACATTCAAAAAAACATCAGTAATT
1 GTTCGTCCAATTTGAACATTCAAAAAAACATCAGTAATT
*
48127 GTTCGCCCAATTTGAACATTCCAAAAAAAAAACATCAGTAATT
1 GTTCGTCCAATTTGAACATT-C---AAAAAAACATCAGTAATT
48170 G
1 G
48171 ATCAATTATA
Statistics
Matches: 78, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
39 58 0.74
40 1 0.01
43 19 0.24
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.29
Consensus pattern (39 bp):
GTTCGTCCAATTTGAACATTCAAAAAAACATCAGTAATT
Found at i:48248 original size:72 final size:72
Alignment explanation
Indices: 47968--48340 Score: 378
Period size: 72 Copynumber: 5.0 Consensus size: 72
47958 GTGCCCCTGA
*
47968 AGTCTTGGTTCGTCCAATTTGAACATTAAAAAAAAAACATCAGTAATTGATCAATTATACCCAAG
1 AGTCTCGGTTCGTCCAATTTGAACATT--AAAAAAAACATCAGTAATTGATCAATTATACCCAAG
48033 TCAATTTTT
64 TCAATTTTT
* *
48042 AGTCTCGGTTCGTCCAATTTGAACATTCAAAAAAACATCAGTAATTGTTCGTCCAATT-TGAACA
1 AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAACATCAGTAATTG---AT-CAATTAT--AC-
* ** *** *
48106 TTCAA-AAAAACATC
59 -CCAAGTCAATTTTT
* * *
48120 AGTAAT-TGTTCGCCCAATTTGAACATTCCAAAAAAAAAACATCAGTAATTGATCAATTATACCC
1 AGT-CTCGGTTCGTCCAATTTGAACATT----AAAAAAAACATCAGTAATTGATCAATTATACCC
48184 AAGTCAATTTTT
61 AAGTCAATTTTT
* *
48196 AGTCTCGGTTCGTCCAATTTGAACATTTAAAAAAACATCAGTAATTGATCAATTATATCCAAGTC
1 AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAACATCAGTAATTGATCAATTATACCCAAGTC
48261 AATATTTTTT
66 -A-A-TTTTT
* * * *
48271 TGTCTCGGTTCGTCCAATTTGAACATT-CAAAAAA-ATCAGTAATTGATCAGTTATACCCAAATC
1 AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAACATCAGTAATTGATCAATTATACCCAAGTC
48334 AATTTTT
66 AATTTTT
48341 GCAGAGATAA
Statistics
Matches: 248, Mismatches: 32, Indels: 42
0.77 0.10 0.13
Matches are distributed among these distances:
70 5 0.02
71 1 0.00
72 56 0.23
73 27 0.11
74 33 0.13
75 37 0.15
76 30 0.12
77 4 0.02
78 30 0.12
79 6 0.02
82 19 0.08
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (72 bp):
AGTCTCGGTTCGTCCAATTTGAACATTAAAAAAAACATCAGTAATTGATCAATTATACCCAAGTC
AATTTTT
Found at i:50765 original size:20 final size:20
Alignment explanation
Indices: 50740--50783 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
50730 GAGACCATGA
*
50740 GAAGGTGGCAAGTGTGTGAT
1 GAAGGTGGCAAGGGTGTGAT
50760 GAAGGTGGCAAGGGTGTGAT
1 GAAGGTGGCAAGGGTGTGAT
50780 GAAG
1 GAAG
50784 TCCATGGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.05, G:0.48, T:0.20
Consensus pattern (20 bp):
GAAGGTGGCAAGGGTGTGAT
Found at i:68784 original size:2 final size:2
Alignment explanation
Indices: 68771--68807 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
68761 TATATCCAAC
*
68771 TA TA TG TA TA TA TA TA TA TA 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 TA TA TA T
68808 TCAAAAGCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Done.