Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022803.1 Corchorus olitorius cultivar O-4 contig22836, 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: 18655
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:36 original size:25 final size:25
Alignment explanation
Indices: 2--61 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
1 C
2 ATATTTTAATAATAACATAATTA-AA
1 ATATTTTAATAATAACA-AATTAGAA
*
27 ATATTTTAATAATAACAATTTAGAA
1 ATATTTTAATAATAACAAATTAGAA
52 ATATATTTAA
1 ATAT-TTTAA
62 AAAAAAAGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 4 0.12
25 23 0.72
26 5 0.16
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (25 bp):
ATATTTTAATAATAACAAATTAGAA
Found at i:868 original size:22 final size:22
Alignment explanation
Indices: 728--987 Score: 135
Period size: 22 Copynumber: 11.8 Consensus size: 22
718 CTATTTTATA
* * *
728 AAATTTT-TTAACCTTCTTATG
1 AAATTTTGATAACCTCCATATG
* * * * *
749 GAATTTTGTTAATCTCCCTAAG
1 AAATTTTGATAACCTCCATATG
* *
771 GAATTTTGA-AGACCTCAATATG
1 AAATTTTGATA-ACCTCCATATG
*
793 AAATTTTGATAACATCGCA-ATG
1 AAATTTTGATAACCTC-CATATG
**
815 AAATTTTGATAACCAACACTATG
1 AAATTTTGATAACCTCCA-TATG
* *
838 AGATGTTGATAACCTCCATATG
1 AAATTTTGATAACCTCCATATG
* * *
860 ATATATTGATAACC-ACATTATG
1 AAATTTTGATAACCTCCA-TATG
* * *
882 AAAATTTAAAAACCTCCATATG
1 AAATTTTGATAACCTCCATATG
* *
904 -AATTGTT-AGTAACC-ACACTTTG
1 AAATT-TTGA-TAACCTCCA-TATG
926 AAAATTTT-ATAA--TCACACTATG
1 -AAATTTTGATAACCTC-CA-TATG
*
948 AAATTGTGATAACCTCCATATG
1 AAATTTTGATAACCTCCATATG
970 AAATTTTGATAAACCTCC
1 AAATTTTGAT-AACCTCC
988 TGATCAGACC
Statistics
Matches: 183, Mismatches: 37, Indels: 36
0.71 0.14 0.14
Matches are distributed among these distances:
21 23 0.13
22 121 0.66
23 33 0.18
24 6 0.03
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (22 bp):
AAATTTTGATAACCTCCATATG
Found at i:2874 original size:22 final size:22
Alignment explanation
Indices: 2831--3007 Score: 114
Period size: 22 Copynumber: 8.1 Consensus size: 22
2821 AATTTCGACC
* * **
2831 GATAACCTCCCAATGATTTTTT
1 GATAACCTCACTATGAAATTTT
* *
2853 GATAACCTCATTAAGAAATTTT
1 GATAACCTCACTATGAAATTTT
* * *
2875 GTTAATCTCCCTATGAAATTTT
1 GATAACCTCACTATGAAATTTT
* * *
2897 GATCAGCAT-ACCATGAAATTTT
1 GAT-AACCTCACTATGAAATTTT
* *
2919 GCTAACCCTC-TTATGAAATTTT
1 GATAA-CCTCACTATGAAATTTT
* *
2941 GA-AAACTAAACTATGAAATTTT
1 GATAACCT-CACTATGAAATTTT
2963 GATAACCTTCA-TATGAAATTTT
1 GATAACC-TCACTATGAAATTTT
* *
2985 GATATCCTC-C-CTGAAATTTT
1 GATAACCTCACTATGAAATTTT
3005 GAT
1 GAT
3008 TACTCCATAA
Statistics
Matches: 117, Mismatches: 30, Indels: 18
0.71 0.18 0.11
Matches are distributed among these distances:
20 14 0.12
21 5 0.04
22 91 0.78
23 6 0.05
24 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (22 bp):
GATAACCTCACTATGAAATTTT
Found at i:3138 original size:22 final size:22
Alignment explanation
Indices: 3089--3302 Score: 153
Period size: 22 Copynumber: 9.7 Consensus size: 22
3079 GAAATACCAC
* * * *
3089 TATGAAATTTTGGTAATCACAT
1 TATGAAATTTTGATAACCCCTT
* * *
3111 TCTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCCCTT
* *
3133 TATGAAATTTTGATAACCTCTC
1 TATGAAATTTTGATAACCCCTT
* * * *
3155 TATAAAATTTTGTTGACCCCTA
1 TATGAAATTTTGATAACCCCTT
* * *
3177 TATGAAATTTTGTTGACCCCTA
1 TATGAAATTTTGATAACCCCTT
* *
3199 TATGAAATTTTGTTGACCCCTT
1 TATGAAATTTTGATAACCCCTT
* * * *
3221 TATGAGATTTTGATAATCACAT
1 TATGAAATTTTGATAACCCCTT
* *
3243 TATGTAATTTTGATAGCCTCGC-T
1 TATGAAATTTTGATAACC-C-CTT
** *
3266 T-TGAAATTTTGATAACAACAT
1 TATGAAATTTTGATAACCCCTT
3287 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
3303 TCTTACTATA
Statistics
Matches: 157, Mismatches: 31, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
20 1 0.01
21 2 0.01
22 151 0.96
23 2 0.01
24 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCCCTT
Found at i:3359 original size:20 final size:19
Alignment explanation
Indices: 3295--3359 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 19
3285 ATTATGAAAT
*
3295 TTTGATAATCTTACTATAAA
1 TTTGATAACCTT-CTATAAA
*
3315 TTTCGATAATCAC-TCTATGAGA
1 TTT-GATAA-C-CTTCTAT-AAA
3337 TTTGATAACCTTCTATCAAA
1 TTTGATAACCTTCTAT-AAA
3357 TTT
1 TTT
3360 TGGTACTCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
19 1 0.03
20 14 0.39
21 14 0.39
22 6 0.17
23 1 0.03
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (19 bp):
TTTGATAACCTTCTATAAA
Found at i:3361 original size:21 final size:22
Alignment explanation
Indices: 3088--3361 Score: 115
Period size: 22 Copynumber: 12.6 Consensus size: 22
3078 AGAAATACCA
*
3088 CTATGAAATTTTGGTAATCACATT
1 CTATGAAATTTTGATAA-CAC-TT
*
3112 C--TGAAAATTTGATAAC-CTCT
1 CTATGAAATTTTGATAACACT-T
*
3132 TTATGAAATTTTGATAAC-CTCT
1 CTATGAAATTTTGATAACACT-T
* * * * *
3154 CTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAACACTT
* * * * *
3176 ATATGAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAACACTT
* * * *
3198 ATATGAAATTTTGTTGACCCCTT
1 CTATGAAATTTTGAT-AACACTT
* *
3221 -TATGAGATTTTGATAATCACAT
1 CTATGAAATTTTGATAA-CACTT
* * *
3243 -TATGTAATTTTGATAGC-CTCG
1 CTATGAAATTTTGATAACACT-T
* *
3264 CTTTGAAATTTTGATAACAACAT
1 CTATGAAATTTTGATAAC-ACTT
*
3287 -TATGAAATTTTGATAA-TCTT
1 CTATGAAATTTTGATAACACTT
*
3307 ACTAT-AAATTTCGATAATCAC-T
1 -CTATGAAATTTTGATAA-CACTT
*
3329 CTATGAGA-TTTGATAAC-CTT
1 CTATGAAATTTTGATAACACTT
*
3349 CTATCAAATTTTG
1 CTATGAAATTTTG
3362 GTACTCCTTA
Statistics
Matches: 195, Mismatches: 38, Indels: 37
0.72 0.14 0.14
Matches are distributed among these distances:
19 2 0.01
20 13 0.07
21 29 0.15
22 143 0.73
23 6 0.03
24 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATAACACTT
Found at i:3413 original size:22 final size:21
Alignment explanation
Indices: 3384--3523 Score: 97
Period size: 22 Copynumber: 6.4 Consensus size: 21
3374 AAATTGAGAC
3384 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* *
3405 TTTTGATAACCACACTA-AAGAA
1 TTTTGATAACCTCA-TATGA-AA
*
3427 TTTTGATAACCACACTATGAAA
1 TTTTGATAACCTCA-TATGAAA
**
3449 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCT-CATATGAAA
* *
3471 TATT-AGTAACCTCCTTATGAAA
1 TTTTGA-TAACCT-CATATGAAA
* *
3493 TTTTGTTAACCACAATATGAAA
1 TTTTGATAACCTC-ATATGAAA
*
3515 TTTTTATAA
1 TTTTGATAA
3524 TCTCTTTGAT
Statistics
Matches: 96, Mismatches: 15, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
21 9 0.09
22 85 0.89
23 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:3571 original size:22 final size:22
Alignment explanation
Indices: 3528--3741 Score: 141
Period size: 22 Copynumber: 9.6 Consensus size: 22
3518 TTATAATCTC
* * * *
3528 TTTGATAACCTCTCCATAAAAT
1 TTTGATAACCACACTATGAAAT
*
3550 TGTGATAACCACACTATGAAAT
1 TTTGATAACCACACTATGAAAT
** * *
3572 TTCAATAACCTTC-CTAAGAAAT
1 TTTGATAACC-ACACTATGAAAT
* *
3594 TTTAATCACCTGATC-CTATGAAAT
1 TTTGATAACC--A-CACTATGAAAT
*
3618 TTTGGTAACCACACTATGAAAT
1 TTTGATAACCACACTATGAAAT
*
3640 TTTGATAACTTACA-TATGAAAT
1 TTTGATAAC-CACACTATGAAAT
* * *
3662 TTTGGTACCCACACTATGGAAT
1 TTTGATAACCACACTATGAAAT
*
3684 TTTGATAACCTC-CTCATGAAAT
1 TTTGATAACCACACT-ATGAAAT
*** *
3706 TACAATAACCATC-TTATGAAAT
1 TTTGATAACCA-CACTATGAAAT
3728 TTTGATAACCACAC
1 TTTGATAACCACAC
3742 AGACAAGAAA
Statistics
Matches: 146, Mismatches: 37, Indels: 18
0.73 0.18 0.09
Matches are distributed among these distances:
21 7 0.05
22 117 0.80
23 6 0.04
24 16 0.11
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (22 bp):
TTTGATAACCACACTATGAAAT
Found at i:3580 original size:122 final size:122
Alignment explanation
Indices: 3425--3647 Score: 304
Period size: 122 Copynumber: 1.8 Consensus size: 122
3415 CACACTAAAG
* ** * *
3425 AATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATATTAGTAACC-TCCTTAT
1 AATTGTGATAACCACACTATGAAATTTCAATAACCTCCCCAAGAAATATTAATAACCATCC-TAT
* *
3489 GAAATTTTGTTAACCACAATATGAAATTTTTATAATCTCTTTGATAACCTCTCCATAA
65 GAAATTTTGGTAACCACAATATGAAATTTTGATAATCTCTTTGATAACCTCTCCATAA
* * * *
3547 AATTGTGATAACCACACTATGAAATTTCAATAACCTTCCTAAGAAATTTTAATCACCTGATCCTA
1 AATTGTGATAACCACACTATGAAATTTCAATAACCTCCCCAAGAAATATTAATAACC--ATCCTA
*
3612 TGAAATTTTGGTAACCACACTATGAAATTTTGATAA
64 TGAAATTTTGGTAACCACAATATGAAATTTTGATAA
3648 CTTACATATG
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
122 48 0.56
124 35 0.41
125 3 0.03
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (122 bp):
AATTGTGATAACCACACTATGAAATTTCAATAACCTCCCCAAGAAATATTAATAACCATCCTATG
AAATTTTGGTAACCACAATATGAAATTTTGATAATCTCTTTGATAACCTCTCCATAA
Found at i:3714 original size:66 final size:66
Alignment explanation
Indices: 3528--3741 Score: 173
Period size: 66 Copynumber: 3.2 Consensus size: 66
3518 TTATAATCTC
* * * * * * * * *
3528 TTTGATAACCTCTCCATAAAATTGTGATAACCACACTATGAAATTTCAATAACCTTCCTAAGAAA
1 TTTGATAACCACACTATGAAATTTTGATAACCACACTATGAAATTACAATAACCATCATATGAAA
3593 T
66 T
* * * *** *
3594 TTTAATCACCTGATC-CTATGAAATTTTGGTAACCACACTATGAAATTTTGATAA-CTTACATAT
1 TTTGATAACC--A-CACTATGAAATTTTGATAACCACACTATGAAATTACAATAACCAT-CATAT
3657 GAAAT
62 GAAAT
* * * * *
3662 TTTGGTACCCACACTATGGAATTTTGATAACCTC-CTCATGAAATTACAATAACCATCTTATGAA
1 TTTGATAACCACACTATGAAATTTTGATAACCACACT-ATGAAATTACAATAACCATCATATGAA
3726 AT
65 AT
3728 TTTGATAACCACAC
1 TTTGATAACCACAC
3742 AGACAAGAAA
Statistics
Matches: 116, Mismatches: 25, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
65 3 0.03
66 60 0.52
67 5 0.04
68 47 0.41
69 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (66 bp):
TTTGATAACCACACTATGAAATTTTGATAACCACACTATGAAATTACAATAACCATCATATGAAA
T
Found at i:5902 original size:22 final size:22
Alignment explanation
Indices: 5872--6275 Score: 187
Period size: 22 Copynumber: 18.0 Consensus size: 22
5862 TTTTTCTCCT
5872 ACCT-ACTATGAAATTTTGATA
1 ACCTCACTATGAAATTTTGATA
* * *
5893 ATCTCGCTAT-ATTATTTTGATA
1 ACCTCACTATGA-AATTTTGATA
* ** *
5915 ACCTCCCTAAAAAATTGTGATA
1 ACCTCACTATGAAATTTTGATA
* * *
5937 ACCTCCCTGTGAAACTTTGATA
1 ACCTCACTATGAAATTTTGATA
*
5959 ACCACACTATGAAATTTTGATA
1 ACCTCACTATGAAATTTTGATA
* * *
5981 ATCACACTATGAAATTGTGATA
1 ACCTCACTATGAAATTTTGATA
*
6003 ACCTCTA-TATGGAATTAATTTTGATG
1 ACCTC-ACTAT-G-A--AATTTTGATA
* *
6029 ACCTTTA-TATAAAATTTTGA-A
1 ACC-TCACTATGAAATTTTGATA
* ** *
6050 TCC-CACATTAATTGCGAAAGGTTGATT
1 ACCTCAC--T-A-T--GAAATTTTGATA
*** *
6077 TGGTACACTATGAAATTTGGATA
1 ACCT-CACTATGAAATTTTGATA
*
6100 ACCAT-ACTATGAACTTTTGATA
1 ACC-TCACTATGAAATTTTGATA
* * *
6122 ACCTCCCTATGGAATGTTGATA
1 ACCTCACTATGAAATTTTGATA
* * ** *
6144 ACTTCCCTACAAAATTTTGTTA
1 ACCTCACTATGAAATTTTGATA
* * *
6166 ATCTCATTATGAAATTTTGATT
1 ACCTCACTATGAAATTTTGATA
*
6188 ACCT-TCTATGAAATTTTTG-TA
1 ACCTCACTATGAAA-TTTTGATA
* *
6209 ACCACATTATGAAATTTTGATA
1 ACCTCACTATGAAATTTTGATA
* * *
6231 ACCACATTATGTAATTTTGATA
1 ACCTCACTATGAAATTTTGATA
* * *
6253 GCCACAGTATGAAATTTTGATA
1 ACCTCACTATGAAATTTTGATA
6275 A
1 A
6276 TCTGCGAAGT
Statistics
Matches: 286, Mismatches: 73, Indels: 47
0.70 0.18 0.12
Matches are distributed among these distances:
19 1 0.00
21 23 0.08
22 216 0.76
23 12 0.04
24 4 0.01
25 1 0.00
26 23 0.08
27 3 0.01
29 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.38
Consensus pattern (22 bp):
ACCTCACTATGAAATTTTGATA
Found at i:6469 original size:277 final size:279
Alignment explanation
Indices: 6133--6685 Score: 932
Period size: 277 Copynumber: 2.0 Consensus size: 279
6123 CCTCCCTATG
* *
6133 GAATGTTGATAACTTCCCTACAAAATTTTGTTAATCTCATTATGAAATTTTGATTACCTTCTATG
1 GAATGTTGATAACTTCCCTACAAAATTTTGTTAATCTCACTATGAAATTTTAATTACCTTCTATG
* *
6198 AAATTTTTGTAACCACATTATGAAATTTTGATAACCACATTATGTAATTTTGATAGCCACAGTAT
66 AAATTTTTGTAACCACATTATGAAATTTTGATAACCACATTATGAAATTTTGATAGCCACACTAT
* *
6263 GAAATTTTGATAATCTGCGAAGTTTAACTTCTTCTATAGGGTAGGGAGCAATTTATTATCCTTA-
131 GAAATTTCGATAATCTGCGAAGTTCAACTTCTTCTATAGGGTAGGGAGCAATTTATTATCCTTAG
*
6327 AGTTAGGACTTATAAAC-T-TATAGTTCAAATCCTATTGCAATTAAAAAATCTAGCATGAGAGAA
196 A-TTAGGACTTAGAAACTTATATAGTTCAAATCCTATTGCAATTAAAAAATCTAGCATGAGAGAA
6390 GTGGAAAAAATTGAAAAATT
260 GTGGAAAAAATTGAAAAATT
* *
6410 GAATGTTGATAACTTCCCTATAGAATTTTGTTAATCTCACTATGAAATTTTAATTACCTTCTATG
1 GAATGTTGATAACTTCCCTACAAAATTTTGTTAATCTCACTATGAAATTTTAATTACCTTCTATG
* *
6475 AAATTTTTGTAACTACATTATGAAATTTTGATAACCACATTATGAAATTTTGGTAGCCACACTAT
66 AAATTTTTGTAACCACATTATGAAATTTTGATAACCACATTATGAAATTTTGATAGCCACACTAT
* *
6540 GAAATTTCGATAATCTGCGAGGTTCAACTTCTTCTATAGGGTAGGGAGTAATTTATTATCCTTAG
131 GAAATTTCGATAATCTGCGAAGTTCAACTTCTTCTATAGGGTAGGGAGCAATTTATTATCCTTAG
* *
6605 ATTAGGACTTAGAAACTTATATAGTTCAAATCCTATTGCAATTTAAAAATCTAGCGTGAGAGAAG
196 ATTAGGACTTAGAAACTTATATAGTTCAAATCCTATTGCAATTAAAAAATCTAGCATGAGAGAAG
*
6670 TGGCAAAAATTGAAAA
261 TGGAAAAAATTGAAAA
6686 TTTATAATTA
Statistics
Matches: 257, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
277 196 0.76
278 2 0.01
279 59 0.23
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Consensus pattern (279 bp):
GAATGTTGATAACTTCCCTACAAAATTTTGTTAATCTCACTATGAAATTTTAATTACCTTCTATG
AAATTTTTGTAACCACATTATGAAATTTTGATAACCACATTATGAAATTTTGATAGCCACACTAT
GAAATTTCGATAATCTGCGAAGTTCAACTTCTTCTATAGGGTAGGGAGCAATTTATTATCCTTAG
ATTAGGACTTAGAAACTTATATAGTTCAAATCCTATTGCAATTAAAAAATCTAGCATGAGAGAAG
TGGAAAAAATTGAAAAATT
Found at i:6496 original size:22 final size:22
Alignment explanation
Indices: 6471--6546 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
6461 AATTACCTTC
*
6471 TATGAAATTTTTGTAACTACAT
1 TATGAAATTTTTGTAACCACAT
6493 TATGAAA-TTTTGATAACCACAT
1 TATGAAATTTTTG-TAACCACAT
* * *
6515 TATGAAATTTTGGTAGCCACAC
1 TATGAAATTTTTGTAACCACAT
6537 TATGAAATTT
1 TATGAAATTT
6547 CGATAATCTG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.10
22 39 0.81
23 4 0.08
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTTGTAACCACAT
Found at i:7088 original size:21 final size:21
Alignment explanation
Indices: 7046--7090 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
7036 GCAAAATTGT
* ***
7046 CAAAAGGGGGGCGGTGTTTAG
1 CAAAAAGGGGGCGGTAAATAG
7067 CAAAAAGGGGGCGGTAAATAG
1 CAAAAAGGGGGCGGTAAATAG
7088 CAA
1 CAA
7091 CTCCTTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.40, T:0.13
Consensus pattern (21 bp):
CAAAAAGGGGGCGGTAAATAG
Found at i:7188 original size:17 final size:17
Alignment explanation
Indices: 7166--7198 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
7156 GAGGGGTTGA
7166 TATTTT-ATTTCGTTTTC
1 TATTTTAATTT-GTTTTC
7183 TATTTTAATTTGTTTT
1 TATTTTAATTTGTTTT
7199 AAAATAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73
Consensus pattern (17 bp):
TATTTTAATTTGTTTTC
Found at i:7794 original size:3 final size:3
Alignment explanation
Indices: 7786--7821 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
7776 AGCAAGCATA
*
7786 TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TTT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
7822 TTGTCTTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:7806 original size:17 final size:17
Alignment explanation
Indices: 7784--7820 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
7774 CAAGCAAGCA
7784 TATATTATTATTATTAT
1 TATATTATTATTATTAT
*
7801 TATATTATTATTATTTT
1 TATATTATTATTATTAT
7818 TAT
1 TAT
7821 TTTGTCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATATTATTATTATTAT
Found at i:7808 original size:14 final size:14
Alignment explanation
Indices: 7789--7815 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
7779 AAGCATATAT
7789 TATTATTATTATTA
1 TATTATTATTATTA
7803 TATTATTATTATT
1 TATTATTATTATT
7816 TTTATTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:9876 original size:11 final size:11
Alignment explanation
Indices: 9833--9870 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
9823 TTCCTATATA
*
9833 AAATAAATTAT
1 AAATTAATTAT
9844 CAAA-TAATTAT
1 -AAATTAATTAT
9855 AAATTAATTAT
1 AAATTAATTAT
9866 AAATT
1 AAATT
9871 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Done.