Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013016.1 Corchorus olitorius cultivar O-4 contig13049, 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: 70987
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:3428 original size:75 final size:76
Alignment explanation
Indices: 3336--3477 Score: 173
Period size: 76 Copynumber: 1.9 Consensus size: 76
3326 TGATGAGCTA
* * *
3336 TGACACAGCCCATCTGGGTGATTAGGCAAA-CACATGGGT-CTTCA-GACAAACCATGTGGGCAC
1 TGACACAGCCCACCTGGGTGATCAAGCAAACCACATGGGTGC-TCAGGAC-AACCATGTGGGCAC
3398 CCAGCTGGAGTCG
64 CCAGCTGGAGTCG
* ** * *
3411 TGACACTGCCCACCTGGGTTCTCAAGCAAACCACATGGGTGCTCAGGGCAACCATGTGGGCGCCC
1 TGACACAGCCCACCTGGGTGATCAAGCAAACCACATGGGTGCTCAGGACAACCATGTGGGCACCC
3476 AG
66 AG
3478 GCAGAGTCGG
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
75 24 0.43
76 29 0.52
77 3 0.05
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.18
Consensus pattern (76 bp):
TGACACAGCCCACCTGGGTGATCAAGCAAACCACATGGGTGCTCAGGACAACCATGTGGGCACCC
AGCTGGAGTCG
Found at i:13629 original size:16 final size:16
Alignment explanation
Indices: 13608--13649 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
13598 TGTGGTATGC
13608 GGAATGGAA-AGGATGG
1 GGAATGGAATA-GATGG
13624 GGAATGGAATAGATGG
1 GGAATGGAATAGATGG
*
13640 GGAATAGAAT
1 GGAATGGAAT
13650 GTAATAGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 23 0.96
17 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (16 bp):
GGAATGGAATAGATGG
Found at i:17723 original size:100 final size:100
Alignment explanation
Indices: 17550--17748 Score: 362
Period size: 100 Copynumber: 2.0 Consensus size: 100
17540 TATTCCAGCT
* *
17550 GGGACTAGGTGACCGGCCAACTTTGGGAGCAAGTTTTGGCCACAAAGGCCGGTGATTCTTGCCCA
1 GGGACTAGGTGACCAGCCAACTTTGGGAGCAAGTTTTGGCCACAAAGGCCAGTGATTCTTGCCCA
*
17615 AATTCGACTTGGATGTCCTAACTGACATGGGAAGC
66 AATTCGACTTGGATGTCCTAACTAACATGGGAAGC
*
17650 GGGACTAGGTGACCAGCCAACTTTGGGAGCAAGTTTTGGCCACAAAGGGCAGTGATTCTTGCCCA
1 GGGACTAGGTGACCAGCCAACTTTGGGAGCAAGTTTTGGCCACAAAGGCCAGTGATTCTTGCCCA
17715 AATTCGACTTGGATGTCCTAACTAACATGGGAAG
66 AATTCGACTTGGATGTCCTAACTAACATGGGAAG
17749 AGTGTCCATA
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 95 1.00
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (100 bp):
GGGACTAGGTGACCAGCCAACTTTGGGAGCAAGTTTTGGCCACAAAGGCCAGTGATTCTTGCCCA
AATTCGACTTGGATGTCCTAACTAACATGGGAAGC
Found at i:25492 original size:12 final size:14
Alignment explanation
Indices: 25461--25500 Score: 57
Period size: 12 Copynumber: 3.0 Consensus size: 14
25451 ATCGTGTCGT
*
25461 TTGAGTGTTGAGAC
1 TTGAGAGTTGAGAC
25475 TTGAGAGTTGA-A-
1 TTGAGAGTTGAGAC
25487 TTGAGAGTTGAGAC
1 TTGAGAGTTGAGAC
25501 AAAGTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 11 0.48
13 2 0.09
14 10 0.43
ACGTcount: A:0.28, C:0.05, G:0.35, T:0.33
Consensus pattern (14 bp):
TTGAGAGTTGAGAC
Found at i:28193 original size:20 final size:19
Alignment explanation
Indices: 28160--28205 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
28150 ATAATTTTAT
28160 TTTATTATTTTTAAATTAA
1 TTTATTATTTTTAAATTAA
*
28179 TTTATTGTTTATTAAATT-A
1 TTTATTATTT-TTAAATTAA
28198 -TTATTATT
1 TTTATTATT
28206 ATAAACAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.29
19 10 0.42
20 7 0.29
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTATTATTTTTAAATTAA
Found at i:38083 original size:23 final size:21
Alignment explanation
Indices: 38016--38241 Score: 185
Period size: 22 Copynumber: 10.5 Consensus size: 21
38006 AATCACACTC
* *
38016 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAACCTC-CTA
*
38038 TGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAACCTC-CTA
38060 TGAAATTTTGATAAACCTTCCTA
1 TGAAATTTTGAT-AACC-TCCTA
*
38083 TAAAATTTTGATAAACCTCCGTA
1 TGAAATTTTGAT-AACCTCC-TA
* *
38106 TAAAATTTTGATAATCTCCTTA
1 TGAAATTTTGATAACCTCC-TA
*
38128 TGAAATCTTGATAA----CTA
1 TGAAATTTTGATAACCTCCTA
*
38145 -CAAATTTTGATAACCTCGCTA
1 TGAAATTTTGATAACCTC-CTA
** *
38166 TGATTTTTTGATAACCTCATTA
1 TGAAATTTTGATAACCTC-CTA
* *
38188 TGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAACCT-CCTA
*
38210 TG-AATTTTGATAACCCTCTTA
1 TGAAATTTTGATAA-CCTCCTA
38231 TGAAATTTTGA
1 TGAAATTTTGA
38242 AAACTAAACT
Statistics
Matches: 167, Mismatches: 25, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
16 11 0.07
17 2 0.01
18 1 0.01
21 18 0.11
22 95 0.57
23 38 0.23
24 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (21 bp):
TGAAATTTTGATAACCTCCTA
Found at i:38211 original size:44 final size:44
Alignment explanation
Indices: 37838--38241 Score: 240
Period size: 44 Copynumber: 9.3 Consensus size: 44
37828 AAACTTTCTC
* *
37838 ATGAAATTTT-ATTAACCTCCCT-GGAGAATTTTGA-AGACCTCATT
1 ATGAAATTTTGA-TAATCTCCCTATGA-AATTTTGATA-ACCTCATT
* * * * * *
37882 ATGAAATTTTGTTTATTTCCCAATGAAATTTCGATAACCAACATT
1 ATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACC-TCATT
* * * * * * * *
37927 ATGAAATGTTGATAACCTCCATATGATATATTGATGACCACGTT
1 ATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCTCATT
* * * * * * * *
37971 ATGAAAATTTAAAAAGCTCCATATG-AATTGTT-AGTAATCACACT
1 ATGAAATTTTGATAATCTCCCTATGAAATT-TTGA-TAACCTCATT
* * * * **
38015 CTGAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCT
1 ATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCTCATT
* * * **
38059 ATGAAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCCGT
1 ATGAAATTTTGAT-AATCTCCCTATGAAATTTTGAT-AACCTCATT
* * *
38105 ATAAAATTTTGATAATCTCCTTATGAAATCTTGATAA---C--T
1 ATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCTCATT
* * * **
38144 A-CAAATTTTGATAACCTCGCTATGATTTTTTGATAACCTCATT
1 ATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCTCATT
*
38187 ATGAAATTTTGTTAATCTCCCTATG-AATTTTGATAACCCTC-TT
1 ATGAAATTTTGATAATCTCCCTATGAAATTTTGATAA-CCTCATT
38230 ATGAAATTTTGA
1 ATGAAATTTTGA
38242 AAACTAAACT
Statistics
Matches: 271, Mismatches: 72, Indels: 35
0.72 0.19 0.09
Matches are distributed among these distances:
38 28 0.10
39 2 0.01
41 2 0.01
43 27 0.10
44 120 0.44
45 73 0.27
46 19 0.07
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (44 bp):
ATGAAATTTTGATAATCTCCCTATGAAATTTTGATAACCTCATT
Found at i:38466 original size:22 final size:21
Alignment explanation
Indices: 38368--38622 Score: 114
Period size: 22 Copynumber: 11.9 Consensus size: 21
38358 CTCCCCAGAA
38368 ATAA-CAC-TATGAAATTTTG
1 ATAATCACTTATGAAATTTTG
* * * *
38387 GTGATCACATTTTGAAAATTTG
1 ATAATCAC-TTATGAAATTTTG
* * *
38409 ATAACCTCTCTATAAAATTTTG
1 ATAATCACT-TATGAAATTTTG
* * * *
38431 TTGACCCCTCTATGAAATTTTG
1 ATAATCACT-TATGAAATTTTG
*
38453 ATAATCACATTATGTAATTTTG
1 ATAATCAC-TTATGAAATTTTG
*
38475 ATAACCTCGCTT-TGAAATTTTG
1 ATAA--TCACTTATGAAATTTTG
*
38497 ATAA-CAACACTATGAAATTTTG
1 ATAATC-AC-TTATGAAATTTTG
* *
38519 ATAATCTTCCTAT-AAATTTTG
1 ATAATC-ACTTATGAAATTTTG
* *
38540 ATAATCCGATTTTATGAAATTTCG
1 ATAAT-C-A-CTTATGAAATTTTG
*
38564 ATAATCACTCTATGATA-TTTG
1 ATAATCACT-TATGAAATTTTG
*
38585 ATAA-C-CTTCTATTAAATTTTG
1 ATAATCAC-T-TATGAAATTTTG
* *
38606 GTACTC-CTTATGAAATT
1 ATAATCACTTATGAAATT
38623 GAGACTTTTA
Statistics
Matches: 179, Mismatches: 39, Indels: 35
0.71 0.15 0.14
Matches are distributed among these distances:
19 4 0.02
20 20 0.11
21 30 0.17
22 101 0.56
23 9 0.05
24 15 0.08
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.42
Consensus pattern (21 bp):
ATAATCACTTATGAAATTTTG
Found at i:38472 original size:44 final size:44
Alignment explanation
Indices: 38399--39043 Score: 131
Period size: 44 Copynumber: 14.3 Consensus size: 44
38389 GATCACATTT
* ** * * * * *
38399 TGAAAATTTGATAACCTCTCTATAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACAACACTATGAAATTTTGATAACCCCGCTA
* * * *
38443 TGAAATTTTGATAATC-ACATTATGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAA-CAACACTATGAAATTTTGATAACCCCGCTA
**
38487 TGAAATTTTGATAACAACACTATGAAATTTTGATAATCTTC-CTA
1 TGAAATTTTGATAACAACACTATGAAATTTTGATAA-CCCCGCTA
* *** * * * *
38531 T-AAATTTTGATAATCCGATTTTATGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAA--CAACACTATGAAATTTTGATAACCCCGCTA
* * * * * *
38576 TGATA-TTTGATAAC--CTTCTATTAAATTTTGGT-ACTCC-TTA
1 TGAAATTTTGATAACAAC-ACTATGAAATTTTGATAACCCCGCTA
* ** * * *
38616 TGAAATTGAGACTTTTATAACCTTCA-TATGAAATTTTGATAAACACACTA
1 TGAAA-T-----TTTGATAA-CAACACTATGAAATTTTGATAACCCCGCTA
** * * * * * *
38666 AAAAATTTTGATAACCACACTATGATATTTTAATAACCTCTCCA
1 TGAAATTTTGATAACAACACTATGAAATTTTGATAACCCCGCTA
* * * * * *
38710 TGAAATATT-AGTAAC--CTC-ATGAAATTTTGTTGACCACACTA
1 TGAAATTTTGA-TAACAACACTATGAAATTTTGATAACCCCGCTA
* * ***
38751 TGAAATTCTT-ATAATCTCGCTATGACATTTTGATAATCTCTTTGATAACCTTTCTA
1 TGAAATT-TTGATAA-----C-A--ACACTATGA-AA--T-TTTGATAACCCCGCTA
* * * ** ***
38807 TAAAATTGTGATAACCACACTATGAAATTTCAATAACCATACTA
1 TGAAATTTTGATAACAACACTATGAAATTTTGATAACCCCGCTA
* * *** * * *
38851 AGAAATTTTAATAACCTGATCTTATGAAATTTTGGTAACCACACTA
1 TGAAATTTTGATAACAACA-C-TATGAAATTTTGATAACCCCGCTA
** * * *
38897 TGAAATTTTGATAACCTTC-CCATGAAATTTTGATAACTTCC-ATA
1 TGAAATTTTGATAA-CAACACTATGAAATTTTGATAAC-CCCGCTA
* *
38941 TGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCC-C-A
1 TGAAATTTTGATAACAACACTATGAAATTTTGATAACC--CCGCTA
** * * *
38985 TGAAATTTTGATAACTTC-CATATGAAATTTTGGTAACCACACTA
1 TGAAATTTTGATAACAACAC-TATGAAATTTTGATAACCCCGCTA
39029 TGAAATTTTGATAAC
1 TGAAATTTTGATAAC
39044 CTCCTCATGA
Statistics
Matches: 440, Mismatches: 112, Indels: 98
0.68 0.17 0.15
Matches are distributed among these distances:
40 6 0.01
41 27 0.06
42 18 0.04
43 22 0.05
44 223 0.51
45 39 0.09
46 35 0.08
47 11 0.03
48 20 0.05
49 3 0.01
50 6 0.01
51 2 0.00
52 3 0.01
53 2 0.00
55 2 0.00
56 21 0.05
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (44 bp):
TGAAATTTTGATAACAACACTATGAAATTTTGATAACCCCGCTA
Found at i:38480 original size:66 final size:66
Alignment explanation
Indices: 38370--38524 Score: 193
Period size: 66 Copynumber: 2.3 Consensus size: 66
38360 CCCCAGAAAT
* * * * * *
38370 AACACTATGAAATTTTGGTGATCACATTTTGAAAATTTGATAACCTCTCTATAAAATTTTGTTGA
1 AACACTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCGCTATAAAATTTTGATAA
38435 C
66 C
** * * * * *
38436 CCCTCTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTTTGAAATTTTGATAA
1 AACACTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCGCTATAAAATTTTGATAA
38501 C
66 C
38502 AACACTATGAAATTTTGATAATC
1 AACACTATGAAATTTTGATAATC
38525 TTCCTATAAA
Statistics
Matches: 73, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
66 73 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (66 bp):
AACACTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCGCTATAAAATTTTGATAA
C
Found at i:38657 original size:22 final size:21
Alignment explanation
Indices: 38628--38738 Score: 52
Period size: 22 Copynumber: 5.2 Consensus size: 21
38618 AAATTGAGAC
38628 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACCTTC-TATGAAA
* **
38649 TTTTGATAAACAC-ACTAAAAAA
1 TTTTGAT-AAC-CTTCTATGAAA
** *
38671 TTTTGATAACCACACTATGATA
1 TTTTGATAACC-TTCTATGAAA
* *
38693 TTTTAATAACCTCTCCATGAAA
1 TTTTGATAACCT-TCTATGAAA
*
38715 TATT-AGTAACC-TC-ATGAAA
1 TTTTGA-TAACCTTCTATGAAA
38734 TTTTG
1 TTTTG
38739 TTGACCACAC
Statistics
Matches: 69, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
19 9 0.13
20 3 0.04
21 8 0.12
22 44 0.64
23 4 0.06
24 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (21 bp):
TTTTGATAACCTTCTATGAAA
Found at i:38773 original size:22 final size:22
Alignment explanation
Indices: 38748--38790 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
38738 GTTGACCACA
38748 CTATGAAATTCTT-ATAATCTCG
1 CTATGAAATT-TTGATAATCTCG
*
38770 CTATGACATTTTGATAATCTC
1 CTATGAAATTTTGATAATCTC
38791 TTTGATAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCTCG
Found at i:38829 original size:22 final size:22
Alignment explanation
Indices: 38804--39092 Score: 243
Period size: 22 Copynumber: 13.0 Consensus size: 22
38794 GATAACCTTT
* *
38804 CTATAAAATTGTGATAACCACA
1 CTATGAAATTTTGATAACCACA
** *
38826 CTATGAAATTTCAATAACCATA
1 CTATGAAATTTTGATAACCACA
* * **
38848 CTAAGAAATTTTAATAACCTGA
1 CTATGAAATTTTGATAACCACA
*
38870 TCTTATGAAATTTTGGTAACCACA
1 -C-TATGAAATTTTGATAACCACA
*
38894 CTATGAAATTTTGATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
*
38916 CCATGAAATTTTGATAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
*
38939 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
*
38960 CTATGAAATTTTGATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
*
38982 CCATGAAATTTTGATAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
*
39005 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
*
39026 CTATGAAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* *
39047 CTCATGAAATTATAATAACCATC-
1 CT-ATGAAATTTTGATAACCA-CA
* *
39070 TTTTGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
39092 C
1 C
39093 AGAGACAAGA
Statistics
Matches: 216, Mismatches: 34, Indels: 34
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.01
21 7 0.03
22 183 0.85
23 6 0.03
24 18 0.08
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:38972 original size:66 final size:66
Alignment explanation
Indices: 38791--39092 Score: 369
Period size: 66 Copynumber: 4.5 Consensus size: 66
38781 TGATAATCTC
* * * ** * * * *
38791 TTTGATAACCTTTC-TATAAAATTGTGATAACCACACTATGAAATTTCAATAACCATACTAAGAA
1 TTTGATAACC-TTCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAA
38855 AT
65 AT
* *
38857 TTTAATAACCTGATCTTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGA
1 TTTGATAACCT--TCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGA
38922 AAT
64 AAT
38925 TTTGATAA-CTTCCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAA
1 TTTGATAACCTT-CATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAA
38989 AT
65 AT
38991 TTTGATAA-CTTCCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACC-TCCTCATGA
1 TTTGATAACCTT-CATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCC-CATGA
39054 AAT
64 AAT
* * * * * *
39057 TATAATAACCATCTTTTGAAATTTTGATAACCACAC
1 TTTGATAACCTTCATATGAAATTTTGGTAACCACAC
39093 AGAGACAAGA
Statistics
Matches: 212, Mismatches: 18, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
65 5 0.02
66 151 0.71
67 6 0.03
68 50 0.24
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (66 bp):
TTTGATAACCTTCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAA
T
Found at i:42721 original size:19 final size:21
Alignment explanation
Indices: 42674--42729 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
42664 ATTCGAAATT
42674 TCTCTATTTGGTACCCACATCC
1 TCTCTATTTGGTACCCACA-CC
*
42696 TCTCTATTCGGTACCCAC-CC
1 TCTCTATTTGGTACCCACACC
42716 -CTCTATTTGGTACC
1 TCTCTATTTGGTACC
42730 TGTTTCCACT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 13 0.41
20 2 0.06
22 17 0.53
ACGTcount: A:0.16, C:0.38, G:0.11, T:0.36
Consensus pattern (21 bp):
TCTCTATTTGGTACCCACACC
Found at i:46762 original size:2 final size:2
Alignment explanation
Indices: 46757--46793 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
46747 TGTGTGCTAC
46757 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
46794 GTCAATTCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:50992 original size:46 final size:46
Alignment explanation
Indices: 50925--51019 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
50915 AGTAAGGTTC
50925 CTTGAATTGATTTAATTGGAGTCTCAATTGTTAACGTTTGTTTGTT
1 CTTGAATTGATTTAATTGGAGTCTCAATTGTTAACGTTTGTTTGTT
50971 CTTGAATTGATTTAATTGGAGTCTCAATTGTTAACGTTTGTTTGTT
1 CTTGAATTGATTTAATTGGAGTCTCAATTGTTAACGTTTGTTTGTT
51017 CTT
1 CTT
51020 ATTTGCGCTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.51
Consensus pattern (46 bp):
CTTGAATTGATTTAATTGGAGTCTCAATTGTTAACGTTTGTTTGTT
Found at i:52679 original size:65 final size:64
Alignment explanation
Indices: 52599--52786 Score: 321
Period size: 60 Copynumber: 3.0 Consensus size: 64
52589 TTTCCCAAAT
52599 CCGATATAAAGGAACAAGTCTGCGGTGAAGCGCTAGCTTCCGATATTTTGATTAAAACTCCTTAC
1 CCGATATAAAGGAACAAGTCTGCGG-GAAGCGCTAGCTTCCGATATTTTGATTAAAACTCCTTAC
52664 CCGATATAAAGGAACAAGTCTGC--G--GCGCTAGCTTCCGATATTTTGATTAAAACTCCTTAC
1 CCGATATAAAGGAACAAGTCTGCGGGAAGCGCTAGCTTCCGATATTTTGATTAAAACTCCTTAC
*
52724 CCGATATAAAGGAACAAGTCTGCGGCGAAGCGCTAGCTTCCAATATTTTGATTAAAACTCCTT
1 CCGATATAAAGGAACAAGTCTGCGG-GAAGCGCTAGCTTCCGATATTTTGATTAAAACTCCTT
52787 GATCTCATGC
Statistics
Matches: 117, Mismatches: 1, Indels: 10
0.91 0.01 0.08
Matches are distributed among these distances:
60 59 0.50
62 1 0.01
63 1 0.01
65 56 0.48
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (64 bp):
CCGATATAAAGGAACAAGTCTGCGGGAAGCGCTAGCTTCCGATATTTTGATTAAAACTCCTTAC
Found at i:62474 original size:6 final size:6
Alignment explanation
Indices: 62465--62498 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
62455 AAAGTGCCGG
62465 TGCCAC TGCCAC TGCCAC TGCCAC TGCCAC TGCC
1 TGCCAC TGCCAC TGCCAC TGCCAC TGCCAC TGCC
62499 GGCCGAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.15, C:0.50, G:0.18, T:0.18
Consensus pattern (6 bp):
TGCCAC
Found at i:63536 original size:36 final size:36
Alignment explanation
Indices: 63489--63593 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
63479 GGTGTTTTGA
63489 ATCCATGTCTTTAAATGACTTCTGCTATCTCTCCGT
1 ATCCATGTCTTTAAATGACTTCTGCTATCTCTCCGT
*
63525 ATCCATGTCTTTAAATGACTTCTGCTATTTCTCCGT
1 ATCCATGTCTTTAAATGACTTCTGCTATCTCTCCGT
* *
63561 ATCCATAT-TTTCAAATGACTTCTACTATCTCTC
1 ATCCATGTCTTT-AAATGACTTCTGCTATCTCTC
63594 AGTCATTAGG
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
35 3 0.05
36 61 0.95
ACGTcount: A:0.22, C:0.27, G:0.09, T:0.43
Consensus pattern (36 bp):
ATCCATGTCTTTAAATGACTTCTGCTATCTCTCCGT
Found at i:69156 original size:61 final size:60
Alignment explanation
Indices: 69075--69189 Score: 194
Period size: 61 Copynumber: 1.9 Consensus size: 60
69065 TTGAGTATTT
* *
69075 TTTTTACATATGTTATGGCCCTATTTGACCAAATTAAAAGCAATGAGGCCTAAATTGAGCA
1 TTTTTACATATGTTAGGGCCCTATTTGACCAAATTAAAAGC-ATGAGGCATAAATTGAGCA
*
69136 TTTTTGCATATGTTAGGGCCCTATTTGACCAAATTAAAAGCATGAGGCATAAAT
1 TTTTTACATATGTTAGGGCCCTATTTGACCAAATTAAAAGCATGAGGCATAAAT
69190 ACATTAGGAC
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
60 12 0.24
61 39 0.76
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (60 bp):
TTTTTACATATGTTAGGGCCCTATTTGACCAAATTAAAAGCATGAGGCATAAATTGAGCA
Done.