Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024358.1 Corchorus olitorius cultivar O-4 contig24391, 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: 60396
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:563 original size:27 final size:28
Alignment explanation
Indices: 508--569 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
498 TCTAAATTTT
*
508 TATTATTTTAATAATAGAATCATTAAAA
1 TATTATTTTAATAATAGAACCATTAAAA
536 TATTATTTT-ATAAT-G-ACCATTTAGAAA
1 TATTATTTTAATAATAGAACCA-TTA-AAA
563 TA-TATTT
1 TATTATTT
570 GAAAAAAGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
25 3 0.10
26 9 0.29
27 10 0.32
28 9 0.29
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (28 bp):
TATTATTTTAATAATAGAACCATTAAAA
Found at i:3101 original size:11 final size:11
Alignment explanation
Indices: 3071--3104 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3061 TTATATAAAA
**
3071 ATATATATACT
1 ATATATATTTT
3082 ATATATATTTT
1 ATATATATTTT
3093 ATATATATTTT
1 ATATATATTTT
3104 A
1 A
3105 GTATTACTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (11 bp):
ATATATATTTT
Found at i:3254 original size:22 final size:22
Alignment explanation
Indices: 3156--3394 Score: 161
Period size: 22 Copynumber: 10.7 Consensus size: 22
3146 AGATATCTCC
3156 ATGAAATTTTGATATTACA-CACT
1 ATGAAATTTTGATA--ACATCACT
* **
3179 ATGAAATTGTGATATA-ATTTTTCT
1 ATGAAATTTTGATA-ACA--TCACT
* *
3203 ATGAAATTTTGATAATC-TCTCC
1 ATGAAATTTTGATAA-CATCACT
* *
3225 ATAAAATTTTGATAACAACACT
1 ATGAAATTTTGATAACATCACT
* * *
3247 ATGGAATTTCGATAACCTCACT
1 ATGAAATTTTGATAACATCACT
* *
3269 ATGAAATTTTGTTAATC-TCCCT
1 ATGAAATTTTGATAA-CATCACT
* * *
3291 ATGAAATTTTGATAACCTCCCA
1 ATGAAATTTTGATAACATCACT
*
3313 ATGAAAATTTGATAACCATTCACT
1 ATGAAATTTTGATAA-CA-TCACT
*
3337 -T-AAATTTTAATAACCA-CACT
1 ATGAAATTTTGATAA-CATCACT
*
3357 ATGAAATTTTGATAA-AGTTACT
1 ATGAAATTTTGATAACA-TCACT
3379 ATGAAATTTTGATAAC
1 ATGAAATTTTGATAAC
3395 CTCGATGTTG
Statistics
Matches: 172, Mismatches: 29, Indels: 30
0.74 0.13 0.13
Matches are distributed among these distances:
20 5 0.03
21 4 0.02
22 128 0.74
23 17 0.10
24 18 0.10
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (22 bp):
ATGAAATTTTGATAACATCACT
Found at i:3327 original size:66 final size:67
Alignment explanation
Indices: 3201--3371 Score: 181
Period size: 66 Copynumber: 2.6 Consensus size: 67
3191 TATAATTTTT
* * *
3201 CTATGAAATTTTGATAATCTCTCC-ATAAAATTTTGATAACAACACTATGGAATTTCGATAACC-
1 CTATGAAATTTTGATAATCTC-CCTATGAAATTTTGATAACAACACAATGAAATTTCGATAACCA
3264 TCA
65 TCA
* ** *
3267 CTATGAAATTTTGTTAATCTCCCTATGAAATTTTGATAACCTCCCAATGAAAATTT-GATAACCA
1 CTATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACAACACAATG-AAATTTCGATAACCA
3331 TTCA
65 -TCA
* * * *
3335 CT-T-AAATTTTAATAACCACACTATGAAATTTTGATAA
1 CTATGAAATTTTGATAATCTCCCTATGAAATTTTGATAA
3372 AGTTACTATG
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
65 2 0.02
66 76 0.85
67 6 0.07
68 5 0.06
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (67 bp):
CTATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACAACACAATGAAATTTCGATAACCAT
CA
Found at i:4685 original size:23 final size:23
Alignment explanation
Indices: 4608--4669 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
4598 ATGTTGATAA
* *
4608 ATGAAATTGTGAT-AACATCACT
1 ATGAAATTTTGATAAACATCTCT
4630 ATGAAATTTTGATAAACATCTCT
1 ATGAAATTTTGATAAACATCTCT
*
4653 ATAAAATTTTGATAAAC
1 ATGAAATTTTGATAAAC
4670 CTCCTTATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 12 0.33
23 24 0.67
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (23 bp):
ATGAAATTTTGATAAACATCTCT
Found at i:9000 original size:19 final size:18
Alignment explanation
Indices: 8976--9014 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
8966 TTGAAGATTT
*
8976 TTGAAGATAATTTGAAGAA
1 TTGAAGACAA-TTGAAGAA
*
8995 TTGAAGACCATTGAAGAA
1 TTGAAGACAATTGAAGAA
9013 TT
1 TT
9015 ATTTCAAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAA
Found at i:10762 original size:24 final size:24
Alignment explanation
Indices: 10735--10787 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
10725 TTAATATAAA
10735 AAAAAGTTTTCTT-CTTTTTGCGAT
1 AAAAA-TTTTCTTGCTTTTTGCGAT
* *
10759 AAAAATTTTTTTGCTTTTTGCGTT
1 AAAAATTTTCTTGCTTTTTGCGAT
10783 AAAAA
1 AAAAA
10788 AAATTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.49
Consensus pattern (24 bp):
AAAAATTTTCTTGCTTTTTGCGAT
Found at i:10789 original size:27 final size:25
Alignment explanation
Indices: 10731--10798 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 25
10721 TGCGTTAATA
*
10731 TAAAAAAAAGTTTTCTTCTTTTTGCG
1 TAAAAAAAA-TTTTTTTCTTTTTGCG
*
10757 --ATAAAAATTTTTTTGCTTTTTGCG
1 TAAAAAAAATTTTTTT-CTTTTTGCG
10781 TTAAAAAAAATTATTTTT
1 -TAAAAAAAATT-TTTTT
10799 ATGTCTTTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
23 6 0.18
24 15 0.44
27 8 0.24
28 5 0.15
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (25 bp):
TAAAAAAAATTTTTTTCTTTTTGCG
Found at i:18022 original size:19 final size:18
Alignment explanation
Indices: 17998--18037 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
17988 TTGAAGATTT
*
17998 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
18017 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
18035 ATT
1 ATT
18038 ATTTCAAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:18105 original size:9 final size:9
Alignment explanation
Indices: 18091--18123 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
18081 GATTGAAGAC
18091 GAAGCCCTT
1 GAAGCCCTT
18100 GAAGCCCTT
1 GAAGCCCTT
*
18109 GAAGACCTT
1 GAAGCCCTT
18118 GAAGCC
1 GAAGCC
18124 ATGGATTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.18
Consensus pattern (9 bp):
GAAGCCCTT
Found at i:20402 original size:22 final size:21
Alignment explanation
Indices: 20346--20446 Score: 87
Period size: 22 Copynumber: 4.6 Consensus size: 21
20336 TATTTCCAAT
*
20346 AAATTTTGATAAGCTCCCTATG
1 AAATTTTGATAA-CTCACTATG
* * *
20368 -ATTTTTCTATAACTTCATTATG
1 AAATTTT-GATAAC-TCACTATG
* *
20390 AAATTTTGCTAACCTCCCTATG
1 AAATTTTGATAA-CTCACTATG
*
20412 AAATTTTGATATACACACTATG
1 AAATTTTGATA-ACTCACTATG
20434 AAATTTTGATAAC
1 AAATTTTGATAAC
20447 CACACATGGT
Statistics
Matches: 62, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
21 8 0.13
22 47 0.76
23 7 0.11
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.41
Consensus pattern (21 bp):
AAATTTTGATAACTCACTATG
Found at i:20450 original size:22 final size:22
Alignment explanation
Indices: 20386--20451 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
20376 ATAACTTCAT
* * *
20386 TATGAAATTTTGCTAACCTCCC
1 TATGAAATTTTGATAACCACAC
20408 TATGAAATTTTGATATA-CACAC
1 TATGAAATTTTGATA-ACCACAC
20430 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
20452 ATGGTGAGCA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
21 1 0.03
22 37 0.95
23 1 0.03
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:21861 original size:22 final size:22
Alignment explanation
Indices: 21791--21934 Score: 102
Period size: 22 Copynumber: 6.6 Consensus size: 22
21781 TATCAACACA
*
21791 CTATGAAATTTTGATAACC-CC
1 CTATGAAATTTTGATAACCTAC
* *
21812 CTAT-AAATTTTTGA-AAACTAAA
1 CTATGAAA-TTTTGATAACCT-AC
* *
21834 CAATGAAATTTTGATAACGTAC
1 CTATGAAATTTTGATAACCTAC
* * *
21856 TTATGAAATTTTCATAACCTCC
1 CTATGAAATTTTGATAACCTAC
*
21878 CTATGAAATTTTGATTA-CT-C
1 CTATGAAATTTTGATAACCTAC
* *
21898 CATAAT-ATAATTTTAATAACCTTC
1 C-T-ATGA-AATTTTGATAACCTAC
21922 CTATGAAATTTTG
1 CTATGAAATTTTG
21935 TTATCACACT
Statistics
Matches: 94, Mismatches: 18, Indels: 21
0.71 0.14 0.16
Matches are distributed among these distances:
20 8 0.09
21 14 0.15
22 60 0.64
23 10 0.11
24 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.39
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCTAC
Found at i:21910 original size:66 final size:65
Alignment explanation
Indices: 21791--21933 Score: 155
Period size: 66 Copynumber: 2.2 Consensus size: 65
21781 TATCAACACA
* * *
21791 CTATGAAATTTTGATAACCCCCTATAAATTTTTGAAAACTAAACAATGAAATTTTGATAACGTAC
1 CTATGAAATTTTCATAACCCCCTATAAATTTTTGAAAACTAAACAATGAAATTTTAATAACCTAC
* ** ** *
21856 TTATGAAATTTTCATAACCTCCCTATGAAA-TTTTGATTACTCCATAAT-ATAATTTTAATAACC
1 CTATGAAATTTTCATAACC-CCCTAT-AAATTTTTGAAAACTAAACAATGA-AATTTTAATAACC
*
21919 TTC
63 TAC
21922 CTATGAAATTTT
1 CTATGAAATTTT
21934 GTTATCACAC
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
65 18 0.28
66 43 0.67
67 3 0.05
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (65 bp):
CTATGAAATTTTCATAACCCCCTATAAATTTTTGAAAACTAAACAATGAAATTTTAATAACCTAC
Found at i:22145 original size:22 final size:22
Alignment explanation
Indices: 22117--22196 Score: 115
Period size: 22 Copynumber: 3.6 Consensus size: 22
22107 CTCCACACTC
22117 TGAAATTTTGATAACCTCGTTT
1 TGAAATTTTGATAACCTCGTTT
22139 TGAAATTTTGATAACCTCGTTT
1 TGAAATTTTGATAACCTCGTTT
* ** *
22161 TGATATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCTCGTTT
*
22183 TGAAATTTTAATAA
1 TGAAATTTTGATAA
22197 TTTGATCTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCGTTT
Found at i:22324 original size:29 final size:28
Alignment explanation
Indices: 22282--22336 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
22272 CCACACTATA
22282 AGATTTTGATAACCCTCCCTATGAAATAG
1 AGATTTTGATAA-CCTCCCTATGAAATAG
*
22311 AGATTTAT-ATAACCTTCCTATGAAAT
1 AGATTT-TGATAACCTCCCTATGAAAT
22337 TTTGATAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 13 0.54
29 10 0.42
30 1 0.04
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (28 bp):
AGATTTTGATAACCTCCCTATGAAATAG
Found at i:22344 original size:22 final size:22
Alignment explanation
Indices: 22069--22365 Score: 112
Period size: 22 Copynumber: 12.8 Consensus size: 22
22059 TAATAATCTC
22069 CCTATG-AATTTTCGATAA--TT
1 CCTATGAAATTTT-GATAACCTT
* *
22089 -CTATGAAATTTTGTTAACCTCCA
1 CCTATGAAATTTTGATAACCT--T
*
22112 CACTCTGAAATTTTGATAACC-T
1 C-CTATGAAATTTTGATAACCTT
* *
22134 CGTTTTGAAATTTTGATAACC-T
1 C-CTATGAAATTTTGATAACCTT
* * * *
22156 CGTTTTGATATTTTGATAACCTC
1 C-CTATGAAATTTTGATAACCTT
* **
22179 CCTATGAAATTTTAATAATTTGAT
1 CCTATGAAATTTTGATAACCT--T
22203 CTCTATGAAATTTTGATTTTGATAACCATT
1 C-CTATG-AA-----ATTTTGATAACC-TT
*
22233 -CTATGAGATTTTGATAACCTT
1 CCTATGAAATTTTGATAACCTT
* * *
22254 CTTATGAAATTTCGATAACC-A
1 CCTATGAAATTTTGATAACCTT
*
22275 CACTAT-AAGATTTTGATAACCCTC
1 C-CTATGAA-ATTTTGATAA-CCTT
*
22299 CCTATGAAATAGAGATTTATATAACCTT
1 CCTATGAAAT-----TTT-GATAACCTT
22327 CCTATGAAATTTTGATAACC-T
1 CCTATGAAATTTTGATAACCTT
*
22348 CCTTTCGAAATTTT-ATAA
1 CCTAT-GAAATTTTGATAA
22366 ATTTTGATAA
Statistics
Matches: 214, Mismatches: 32, Indels: 61
0.70 0.10 0.20
Matches are distributed among these distances:
19 9 0.04
20 6 0.03
21 15 0.07
22 107 0.50
23 12 0.06
24 4 0.02
25 22 0.10
26 2 0.01
27 1 0.00
28 21 0.10
29 4 0.02
30 1 0.00
31 9 0.04
32 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (22 bp):
CCTATGAAATTTTGATAACCTT
Found at i:22392 original size:22 final size:22
Alignment explanation
Indices: 22364--22533 Score: 79
Period size: 22 Copynumber: 7.6 Consensus size: 22
22354 GAAATTTTAT
*
22364 AAATTTTGATAATCACACTATG
1 AAATTTTGATAACCACACTATG
* ***
22386 AAATTTTGAAAACCTTTCTATG
1 AAATTTTGATAACCACACTATG
*
22408 AAATTTTGATAACTAGTC-CTATG
1 AAATTTTGATAACCA--CACTATG
*
22431 AAAATTTTG-TAACTACAC--TG
1 -AAATTTTGATAACCACACTATG
22451 -AATTTTCG-TAACCACACACTATTG
1 AAATTTT-GATAA-C-CACACTA-TG
* *
22475 AAAATTTTGATAACCTC-CATATA
1 -AAATTTTGATAACCACAC-TATG
*
22498 AAATTTTGAAAATCTC-CA-TATG
1 AAATTTTGATAA-C-CACACTATG
*
22520 AAATTGTGATAACC
1 AAATTTTGATAACC
22534 TTTCTTATGA
Statistics
Matches: 115, Mismatches: 16, Indels: 36
0.69 0.10 0.22
Matches are distributed among these distances:
18 6 0.05
19 4 0.03
20 4 0.03
21 6 0.05
22 54 0.47
23 15 0.13
24 15 0.13
25 2 0.02
26 9 0.08
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATG
Found at i:22569 original size:45 final size:44
Alignment explanation
Indices: 22475--22569 Score: 102
Period size: 45 Copynumber: 2.1 Consensus size: 44
22465 CACACTATTG
*
22475 AAAATTTTGATAACCTCCATATAAAATTTTGAAAATCTCCATAT
1 AAAATTGTGATAACCTCCATATAAAATTTTGAAAATCTCCATAT
* * * * * *
22519 GAAATTGTGATAACCTTTCTTATGAAGTTTTGATAATCT-CATTAT
1 AAAATTGTGATAACC-TCCATATAAAATTTTGAAAATCTCCA-TAT
22564 AAAATT
1 AAAATT
22570 TTAATAATCA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
44 15 0.37
45 26 0.63
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (44 bp):
AAAATTGTGATAACCTCCATATAAAATTTTGAAAATCTCCATAT
Found at i:22571 original size:22 final size:22
Alignment explanation
Indices: 22475--22578 Score: 93
Period size: 22 Copynumber: 4.7 Consensus size: 22
22465 CACACTATTG
*
22475 AAAATTTTGATAACCTCCATAT
1 AAAATTTTGATAATCTCCATAT
*
22497 AAAATTTTGAAAATCTCCATAT
1 AAAATTTTGATAATCTCCATAT
* * * * *
22519 GAAATTGTGATAACCTTTCTTAT
1 AAAATTTTGATAATC-TCCATAT
* *
22542 GAAGTTTTGATAATCT-CATTAT
1 AAAATTTTGATAATCTCCA-TAT
*
22564 AAAATTTTAATAATC
1 AAAATTTTGATAATC
22579 ACACAAATAC
Statistics
Matches: 65, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
21 1 0.02
22 47 0.72
23 17 0.26
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.40
Consensus pattern (22 bp):
AAAATTTTGATAATCTCCATAT
Found at i:22725 original size:2 final size:2
Alignment explanation
Indices: 22718--22742 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22708 AAATACCTCT
22718 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 T
22743 TACAAGAATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23344 original size:38 final size:38
Alignment explanation
Indices: 23302--23384 Score: 148
Period size: 38 Copynumber: 2.2 Consensus size: 38
23292 GAATTTAGGG
*
23302 CAATTTGATACCGCCTCACAACTTGCGAATTCCCAATT
1 CAATTTCATACCGCCTCACAACTTGCGAATTCCCAATT
*
23340 CAATTTCATACCGCCTCACAACTTGCGAATTCGCAATT
1 CAATTTCATACCGCCTCACAACTTGCGAATTCCCAATT
23378 CAATTTC
1 CAATTTC
23385 CTATCTAACA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.30
Consensus pattern (38 bp):
CAATTTCATACCGCCTCACAACTTGCGAATTCCCAATT
Found at i:24847 original size:18 final size:18
Alignment explanation
Indices: 24824--24861 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
24814 ATTCTAGTAC
24824 GTCCTAGTAAAATTAGAA
1 GTCCTAGTAAAATTAGAA
24842 GTCCTAGTAAAATTAGAA
1 GTCCTAGTAAAATTAGAA
24860 GT
1 GT
24862 GGACATGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (18 bp):
GTCCTAGTAAAATTAGAA
Found at i:25089 original size:293 final size:293
Alignment explanation
Indices: 24562--25129 Score: 994
Period size: 293 Copynumber: 1.9 Consensus size: 293
24552 GAAAAGCTTC
24562 TAGAAGTGGACATGTAAATAGAAACGGAGAGAATATCTAATAGTAACATCTAGTTTTGACTAATT
1 TAGAAGTGGACATGTAAATAGAAACGGAGAGAATATCTAATAGTAACATCTAGTTTTGACTAATT
* *
24627 TAGATTGAAGTCCCGTTGGATCCTAAATGAGGATAAATTCTGTGAATTATTTAATCCATTCACAA
66 TAGATTGAAATCCCGTTGGATCCTAAATGAGGATAAATTCTGTAAATTATTTAATCCATTCACAA
* * *
24692 ATTTTGGATCGCGACATTAAACAATTCCTTCCACTTGATCCAGAACATTAATGAAGTTGTTTCAA
131 ATTTTGGATCGAGACATTAAACAATTCCTTCCACTTGATCCAAAACATTAATGAAGCTGTTTCAA
24757 ATTTTCCAGGCAACTTCCGCAGATATGAAATTATGAACATAATAAGGAGCCCAATAAATTCTAGT
196 ATTTTCCAGGCAACTTCCGCAGATATGAAATTATGAACATAATAAGGAGCCCAATAAATTCTAGT
24822 ACGTCCTAGTAAAATTAGAAGTCCTAGTAAAAT
261 ACGTCCTAGTAAAATTAGAAGTCCTAGTAAAAT
* * * *
24855 TAGAAGTGGACATGTAAATAGAGATGGAGGGAGTATCTAATAGTAACATCTAGTTTTGACTAATT
1 TAGAAGTGGACATGTAAATAGAAACGGAGAGAATATCTAATAGTAACATCTAGTTTTGACTAATT
*
24920 TAGATTGAAATCCCGTTGGATCCTAAATGAGGATAAGTTCTGTAAATTATTTAATCCATTCACGA
66 TAGATTGAAATCCCGTTGGATCCTAAATGAGGATAAATTCTGTAAATTATTTAATCCATTCAC-A
*
24985 AA-TTTGGATCGAGACATTAAACAATTCCTTCCACTTGATCCAAAATATTAATGAAGCTGTTTCA
130 AATTTTGGATCGAGACATTAAACAATTCCTTCCACTTGATCCAAAACATTAATGAAGCTGTTTCA
* * *
25049 AATTTTTCAGGCAACTTCCGCATATATGAAATTATGAACATAGTAAGGAGCCCAATAAATTCTAG
195 AATTTTCCAGGCAACTTCCGCAGATATGAAATTATGAACATAATAAGGAGCCCAATAAATTCTAG
25114 TACGTCCTAGTAAAAT
260 TACGTCCTAGTAAAAT
25130 CTAGCCGAAA
Statistics
Matches: 260, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
293 257 0.99
294 3 0.01
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (293 bp):
TAGAAGTGGACATGTAAATAGAAACGGAGAGAATATCTAATAGTAACATCTAGTTTTGACTAATT
TAGATTGAAATCCCGTTGGATCCTAAATGAGGATAAATTCTGTAAATTATTTAATCCATTCACAA
ATTTTGGATCGAGACATTAAACAATTCCTTCCACTTGATCCAAAACATTAATGAAGCTGTTTCAA
ATTTTCCAGGCAACTTCCGCAGATATGAAATTATGAACATAATAAGGAGCCCAATAAATTCTAGT
ACGTCCTAGTAAAATTAGAAGTCCTAGTAAAAT
Found at i:34497 original size:11 final size:11
Alignment explanation
Indices: 34473--34507 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
34463 TTGACAGCGC
34473 AACAAAAACAA
1 AACAAAAACAA
* *
34484 AACGAAAACGA
1 AACAAAAACAA
34495 AACAAAAACAA
1 AACAAAAACAA
34506 AA
1 AA
34508 AAACAGAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:40846 original size:130 final size:130
Alignment explanation
Indices: 40570--40813 Score: 418
Period size: 130 Copynumber: 1.9 Consensus size: 130
40560 AGTTCTAAAG
40570 ATAGAGAAGTATATTAAACGTAAGAGTAGTAGTCTAATATCAAGAGTAGTAGTCTAGTGAGGTAA
1 ATAGAGAAGTATATTAAACGTAAGAGTAGTAGTCTAATATCAAGAGTAGTAGTCTAGTGAGGTAA
*
40635 TAATTGCTAATCAAATTAATTTTTATTAGTAATCATTAAATAAGAAATTAATATAAACAATATAG
66 TAATTGCTAATCAAATTAATTTTTATTAGTAATCATTAAATAAGAAATTAATATAAACAATATAA
*
40700 ATAGAGAAGTATATTAAACGTAAGAGTAGTAGTCTAATATTAAGAGTAGTAGTCTAGTGAGGTAA
1 ATAGAGAAGTATATTAAACGTAAGAGTAGTAGTCTAATATCAAGAGTAGTAGTCTAGTGAGGTAA
* * *
40765 TAATTGTTAATTAAATTTTAA-TTTTATTAGTAATCATTAAATAATAAAT
66 TAATTGCTAATCAAA--TTAATTTTTATTAGTAATCATTAAATAAGAAAT
40814 ATAAACAATA
Statistics
Matches: 108, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
130 77 0.71
131 27 0.25
132 4 0.04
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (130 bp):
ATAGAGAAGTATATTAAACGTAAGAGTAGTAGTCTAATATCAAGAGTAGTAGTCTAGTGAGGTAA
TAATTGCTAATCAAATTAATTTTTATTAGTAATCATTAAATAAGAAATTAATATAAACAATATAA
Found at i:41592 original size:103 final size:102
Alignment explanation
Indices: 41463--41666 Score: 295
Period size: 103 Copynumber: 2.0 Consensus size: 102
41453 ATTCTTATTG
* * * *
41463 TCCTCTGTTTCTGTATTCTTTCTGTTTGTCCTCTG-TTTTGCAGATAGTTCCAATTTGTTTTGTA
1 TCCTCTGTTTCTGTATTCTTTCTGTTTGTCCTCTGTTTTTG-AGATACTTACAATTTGTTCTGCA
* * * *
41527 TGTTTGATTTCTTGGTTTGTTTCTGCTA-TTTGTTCCTC
65 TATTTCATTCCTTGATTTGTTTCTGCTACTTT-TTCCTC
41565 TCCTCTGTTTCTGTTATTCTTTCTGTTTGTCCTCTGTTTTTGAGATACTTACAATTTGTTCTGCA
1 TCCTCTGTTTCTG-TATTCTTTCTGTTTGTCCTCTGTTTTTGAGATACTTACAATTTGTTCTGCA
41630 TATTTCATTCCTTGATTTGTTTCTGCTACTTTTTCCT
65 TATTTCATTCCTTGATTTGTTTCTGCTACTTTTTCCT
41667 GTTTTGGATA
Statistics
Matches: 91, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
102 13 0.14
103 70 0.77
104 8 0.09
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.56
Consensus pattern (102 bp):
TCCTCTGTTTCTGTATTCTTTCTGTTTGTCCTCTGTTTTTGAGATACTTACAATTTGTTCTGCAT
ATTTCATTCCTTGATTTGTTTCTGCTACTTTTTCCTC
Found at i:49693 original size:17 final size:19
Alignment explanation
Indices: 49671--49713 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
49661 TTTTAAGTAA
49671 AAATATAATATAT-ATA-T
1 AAATATAATATATAATATT
49688 AAATATAA-ATATAATATT
1 AAATATAATATATAATATT
49706 AAA-ATAAT
1 AAATATAAT
49714 TAATTGGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.17
17 15 0.65
18 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATATAATATATAATATT
Found at i:49712 original size:11 final size:11
Alignment explanation
Indices: 49671--49713 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
49661 TTTTAAGTAA
49671 AAATATAATAT
1 AAATATAATAT
*
49682 ATATATAAATAT
1 AAATAT-AATAT
49694 AAATATAATATT
1 AAATATAATA-T
49706 AAA-ATAAT
1 AAATATAAT
49714 TAATTGGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 14 0.50
12 14 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AAATATAATAT
Found at i:55554 original size:21 final size:24
Alignment explanation
Indices: 55510--55589 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 24
55500 TATCTTAGAT
*
55510 ATAATATATATTATTAAATAAATA
1 ATAATATATATTACTAAATAAATA
55534 ATAA-ATATATT-CTAAAT-AAT-
1 ATAATATATATTACTAAATAAATA
*
55554 A-AATA-ATGAGTT-CAAAATAAATAA
1 ATAATATAT-A-TTACTAAATAAAT-A
55578 ATAATATATATT
1 ATAATATATATT
55590 TAATTACTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
19 4 0.09
20 3 0.07
21 10 0.22
22 8 0.17
23 7 0.15
24 7 0.15
25 5 0.11
26 2 0.04
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (24 bp):
ATAATATATATTACTAAATAAATA
Found at i:58328 original size:14 final size:15
Alignment explanation
Indices: 58304--58332 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
58294 ATTTTCTGTT
58304 ATATCATATATAAGA
1 ATATCATATATAAGA
58319 ATAT-ATATATAAGA
1 ATATCATATATAAGA
58333 TCTTCTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.34
Consensus pattern (15 bp):
ATATCATATATAAGA
Found at i:59186 original size:14 final size:14
Alignment explanation
Indices: 59167--59200 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
59157 TTTTATAATT
59167 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
59181 ATTTTATTTTTACT
1 ATTTTATTTTTACC
59195 ATTTTA
1 ATTTTA
59201 ATTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:59248 original size:15 final size:15
Alignment explanation
Indices: 59228--59258 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
59218 GATTAACCTG
59228 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
59243 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
59258 T
1 T
59259 AATGTATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTATTTGATAGT
Done.