Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011502.1 Corchorus capsularis cultivar CVL-1 contig11523, 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: 72949
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:413 original size:14 final size:14
Alignment explanation
Indices: 396--425 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
386 AATTATGGAT
396 ATAGAATCCATTAC
1 ATAGAATCCATTAC
410 ATAGAATCCATTAC
1 ATAGAATCCATTAC
424 AT
1 AT
426 TACAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (14 bp):
ATAGAATCCATTAC
Found at i:2634 original size:28 final size:28
Alignment explanation
Indices: 2590--2644 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
2580 AAGTGATTTA
2590 CTCCCTCTGTTCCTTTTTAATTGTCCCT
1 CTCCCTCTGTTCCTTTTTAATTGTCCCT
2618 CTCCCT-TGTTCCTTTTTAATTGTCCCT
1 CTCCCTCTGTTCCTTTTTAATTGTCCCT
2645 GATATTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.07, C:0.35, G:0.07, T:0.51
Consensus pattern (28 bp):
CTCCCTCTGTTCCTTTTTAATTGTCCCT
Found at i:5341 original size:18 final size:17
Alignment explanation
Indices: 5315--5348 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5305 ATGTATTGAT
5315 AAAAAAAAAGGAAAAAG
1 AAAAAAAAAGGAAAAAG
*
5332 AAAAAGAAAAGTAAAAA
1 AAAAA-AAAAGGAAAAA
5349 ACCATGTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (17 bp):
AAAAAAAAAGGAAAAAG
Found at i:7064 original size:11 final size:11
Alignment explanation
Indices: 7021--7058 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
7011 TTTCTATATA
*
7021 AAATAAATTAT
1 AAATTAATTAT
7032 CAAA-TAATTAT
1 -AAATTAATTAT
7043 AAATTAATTAT
1 AAATTAATTAT
7054 AAATT
1 AAATT
7059 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
Found at i:12314 original size:60 final size:60
Alignment explanation
Indices: 12221--12342 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 60
12211 TTAAGTGGTG
12221 ACATTTCCAAATTTGTTCAATTTGAGACTAAACCTTTAAACAGGACCAAATTGGGCCTAA
1 ACATTTCCAAATTTGTTCAATTTGAGACTAAACCTTTAAACAGGACCAAATTGGGCCTAA
*
12281 ACATTTCCAAATTTGTTCAATTTGAGGCTAAACCTTTAAACAGGACCAAATTGGGCCTAA
1 ACATTTCCAAATTTGTTCAATTTGAGACTAAACCTTTAAACAGGACCAAATTGGGCCTAA
12341 AC
1 AC
12343 GTTAACAAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (60 bp):
ACATTTCCAAATTTGTTCAATTTGAGACTAAACCTTTAAACAGGACCAAATTGGGCCTAA
Found at i:12342 original size:29 final size:29
Alignment explanation
Indices: 12248--12342 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 29
12238 CAATTTGAGA
12248 CTAAACCTTTAAACAGGACCAAATTGGGC
1 CTAAACCTTTAAACAGGACCAAATTGGGC
* *** ** *
12277 CTAAACATTTCCAAATTTGTTCAATTTGAGG-
1 CTAAACCTTT--AAACAGGACCAAATTG-GGC
12308 CTAAACCTTTAAACAGGACCAAATTGGGC
1 CTAAACCTTTAAACAGGACCAAATTGGGC
12337 CTAAAC
1 CTAAAC
12343 GTTAACAAAT
Statistics
Matches: 48, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
28 2 0.04
29 25 0.52
31 19 0.40
32 2 0.04
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (29 bp):
CTAAACCTTTAAACAGGACCAAATTGGGC
Found at i:12366 original size:60 final size:60
Alignment explanation
Indices: 12228--12367 Score: 174
Period size: 60 Copynumber: 2.3 Consensus size: 60
12218 GTGACATTTC
** * **
12228 CAAATTTGTTCAATTTGAGACTAAACCTTTAAACAGGACCAAATTGGGCCTAAACATTTC
1 CAAATTTGACCAAATTGAGACTAAACCTTTAAACAGGACCAAATTGGGCCTAAACATTAA
** * * *
12288 CAAATTTGTTCAATTTGAGGCTAAACCTTTAAACAGGACCAAATTGGGCCTAAACGTTAA
1 CAAATTTGACCAAATTGAGACTAAACCTTTAAACAGGACCAAATTGGGCCTAAACATTAA
12348 CAAA-TTGCACCAAATTGAGA
1 CAAATTTG-ACCAAATTGAGA
12368 ACAGATTTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
59 3 0.04
60 68 0.96
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (60 bp):
CAAATTTGACCAAATTGAGACTAAACCTTTAAACAGGACCAAATTGGGCCTAAACATTAA
Found at i:14218 original size:1 final size:1
Alignment explanation
Indices: 14203--14249 Score: 58
Period size: 1 Copynumber: 47.0 Consensus size: 1
14193 AATTTGTAGA
* * * *
14203 TTTTGTTTTTCTTTTTTTTTTGTTTTTTTTTTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
14250 CTATTTTAGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.02, G:0.06, T:0.91
Consensus pattern (1 bp):
T
Found at i:14225 original size:17 final size:16
Alignment explanation
Indices: 14203--14249 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
14193 AATTTGTAGA
14203 TTTTGTTTTTCTTTTTT
1 TTTTGTTTTT-TTTTTT
14220 TTTTGTTTTTTTTTTT
1 TTTTGTTTTTTTTTTT
14236 TGTTT-TTTTTTTTT
1 T-TTTGTTTTTTTTT
14250 CTATTTTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.00, C:0.02, G:0.06, T:0.91
Consensus pattern (16 bp):
TTTTGTTTTTTTTTTT
Found at i:14256 original size:14 final size:13
Alignment explanation
Indices: 14214--14249 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
14204 TTTGTTTTTC
14214 TTTTTTTTTTGTT
1 TTTTTTTTTTGTT
14227 TTTTTTTTTTGTT
1 TTTTTTTTTTGTT
14240 TTTTTTTTTT
1 TTTTTTTTTT
14250 CTATTTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (13 bp):
TTTTTTTTTTGTT
Found at i:15937 original size:30 final size:31
Alignment explanation
Indices: 15889--15946 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
15879 TCCGAGTCTG
*
15889 AAAAACCCAAACTCGAAAGAAATCCGAACCT
1 AAAAACCCAAACTCGAAAGAAACCCGAACCT
*
15920 AAAAACCCGAA-TCGAAAGAAACCCGAA
1 AAAAACCCAAACTCGAAAGAAACCCGAA
15947 AAAATCCGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.53, C:0.28, G:0.12, T:0.07
Consensus pattern (31 bp):
AAAAACCCAAACTCGAAAGAAACCCGAACCT
Found at i:15943 original size:16 final size:16
Alignment explanation
Indices: 15891--15946 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
15881 CGAGTCTGAA
*
15891 AAACCCAAACTCGAAAG
1 AAACCCGAA-TCGAAAG
* **
15908 AAATCCGAA-CCTAA-
1 AAACCCGAATCGAAAG
15922 AAACCCGAATCGAAAG
1 AAACCCGAATCGAAAG
15938 AAACCCGAA
1 AAACCCGAA
15947 AAAATCCGAG
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
14 8 0.27
15 6 0.20
16 9 0.30
17 7 0.23
ACGTcount: A:0.52, C:0.29, G:0.12, T:0.07
Consensus pattern (16 bp):
AAACCCGAATCGAAAG
Found at i:18923 original size:32 final size:32
Alignment explanation
Indices: 18877--18962 Score: 118
Period size: 32 Copynumber: 2.7 Consensus size: 32
18867 CCACCGTCAT
** * * *
18877 GCCGATGACATGGCATTGTCATGTCGGACTAA
1 GCCGATGATGTGGCATTGCCACGTCGGACCAA
18909 GCCGATGATGTGGCATTGCCACGTCGGACCAA
1 GCCGATGATGTGGCATTGCCACGTCGGACCAA
*
18941 ACCGATGATGTGGCATTGCCAC
1 GCCGATGATGTGGCATTGCCAC
18963 ATCAACGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.23, C:0.26, G:0.29, T:0.22
Consensus pattern (32 bp):
GCCGATGATGTGGCATTGCCACGTCGGACCAA
Found at i:19994 original size:22 final size:22
Alignment explanation
Indices: 19969--20545 Score: 155
Period size: 22 Copynumber: 26.6 Consensus size: 22
19959 ATGATCCCAT
19969 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* ** *
19991 TATGAAATTTTAATAACAATAC
1 TATGAAATTTTGATAACCTTCC
* * * *
20013 TATGGAATTTCGAGAACCCTT-T
1 TATGAAATTTTGATAA-CCTTCC
** *
20035 TAT--AATTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* * *
20055 TATGAAATTTGGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * * *
20077 TAAGGAATTTTGA-AGATC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
20099 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* * **
20121 AATTAAA--TTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
20142 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
20163 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * *
20186 TATGAAAATTTAAGAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
20207 ATATG-AATTGTT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* * *
20230 TCTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
20252 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
* *
20274 TATGAAATTTTAATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
20297 TATAAAATATTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
20320 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
20342 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
20359 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** *
20380 TATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * * **
20402 TATAAAATTTTGTTAATCACCC
1 TATGAAATTTTGATAACCTTCC
* * *
20424 TATGAAATTTTGATCTA-CATGC
1 TATGAAATTTTGAT-AACCTTCC
* * *
20446 TATGAATTTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* * * ***
20468 TGTGAAATTTT-AAAAACTAAAA
1 TATGAAATTTTGATAACCT-TCC
* * *
20490 TATGAAAATTTGATAGCCTTCA
1 TATGAAATTTTGATAACCTTCC
*
20512 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
20533 T-TGAAATTTTGAT
1 TATGAAATTTTGAT
20546 TACTCCATAA
Statistics
Matches: 405, Mismatches: 115, Indels: 72
0.68 0.19 0.12
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
19 4 0.01
20 31 0.08
21 26 0.06
22 269 0.66
23 60 0.15
24 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:20304 original size:23 final size:23
Alignment explanation
Indices: 20234--20335 Score: 91
Period size: 23 Copynumber: 4.5 Consensus size: 23
20224 TCACACTCTG
* * * *
20234 AAATTTTGAT-AATCACACTATG
1 AAATTTTGATAAACCTCCCTATA
* * *
20256 AAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAACCTCCCTATA
* * *
20278 AAATTTTAATAAATCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
*
20301 AAATATTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
20324 AAATTTTGATAA
1 AAATTTTGATAA
20336 CTTTCTTATG
Statistics
Matches: 64, Mismatches: 15, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
22 26 0.41
23 38 0.59
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:20356 original size:45 final size:45
Alignment explanation
Indices: 20251--20357 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 45
20241 GATAATCACA
* *
20251 CTATGAAATTGTGAT-AACCTCGCTATGAAATTTTAATAAATCTTC
1 CTATGAAATT-TGATAAACCTCCCTATAAAATTTTAATAAATCTTC
* * *
20296 CTATAAAATATTGATAAACCTCCCTATAAAATTTTGATAACT-TTC
1 CTATGAAAT-TTGATAAACCTCCCTATAAAATTTTAATAAATCTTC
*
20341 TTATGAAATCTTGATAA
1 CTATGAAAT-TTGATAA
20358 CTACAAATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
45 29 0.56
46 23 0.44
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (45 bp):
CTATGAAATTTGATAAACCTCCCTATAAAATTTTAATAAATCTTC
Found at i:20703 original size:22 final size:22
Alignment explanation
Indices: 20651--20897 Score: 157
Period size: 22 Copynumber: 11.3 Consensus size: 22
20641 AATCATATTT
*
20651 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
20673 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
20695 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * * *
20717 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* * *
20739 TGTAATTTTGATAACATCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
20761 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
*
20783 TGAAATTTTGATAATCT-TTCTA
1 TGAAATTTTGATAACCTCTT-TA
*
20805 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTTTA
* * * *
20829 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTTTA
* *
20851 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
* *
20871 TCAAATTTTGGT-A-CTCTTTA
1 TGAAATTTTGATAACCTCTTTA
20891 TGAAATT
1 TGAAATT
20898 GAGACTTTTA
Statistics
Matches: 172, Mismatches: 43, Indels: 22
0.73 0.18 0.09
Matches are distributed among these distances:
19 2 0.01
20 17 0.10
21 26 0.15
22 108 0.63
23 2 0.01
24 5 0.03
25 12 0.07
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:20933 original size:22 final size:22
Alignment explanation
Indices: 20903--20975 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
20893 AAATTGAGAC
*
20903 TTTT-ATAACCTTCATATGAAA
1 TTTTAATAACCTACATATGAAA
*
20924 TTTTAATAACC-ACACTATAAAA
1 TTTTAATAACCTACA-TATGAAA
* * **
20946 TTTTGATAACCTCCCCATGAAA
1 TTTTAATAACCTACATATGAAA
20968 TATTTAAT
1 T-TTTAAT
20976 GAAATTTTGT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
21 6 0.15
22 28 0.70
23 6 0.15
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (22 bp):
TTTTAATAACCTACATATGAAA
Found at i:21000 original size:34 final size:34
Alignment explanation
Indices: 20943--21007 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
20933 CCACACTATA
* *
20943 AAATTTTGATAACCTCCCCATGAAATATTTAATG
1 AAATTTTGATAACCACACCATGAAATATTTAATG
* * *
20977 AAATTTTGTTAACCACACTATGAAATTTTTA
1 AAATTTTGATAACCACACCATGAAATATTTA
21008 TTACCTTGCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (34 bp):
AAATTTTGATAACCACACCATGAAATATTTAATG
Found at i:21409 original size:19 final size:20
Alignment explanation
Indices: 21378--21420 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
21368 TATTGACATT
21378 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTAAAAAG
21397 TAAAATATT-AAATTCAAAAAG
1 TAAAA-ATTGAAATT-AAAAAG
21418 TAA
1 TAA
21421 TAGTAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 3 0.14
21 8 0.38
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (20 bp):
TAAAAATTGAAATTAAAAAG
Found at i:21628 original size:37 final size:36
Alignment explanation
Indices: 21552--21628 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
21542 AATTTAAGAT
*
21552 CAAAGACAAAGTAAAATTAAATACAACGATTGGAAA
1 CAAAGACAAAGCAAAATTAAATACAACGATTGGAAA
**
21588 CAAAGACAAAAGACAAAATTAAATAGGACG-TTGGAAA
1 CAAAGAC-AAAG-CAAAATTAAATACAACGATTGGAAA
21625 CAAA
1 CAAA
21629 AAGGCAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 7 0.19
37 15 0.42
38 14 0.39
ACGTcount: A:0.58, C:0.12, G:0.16, T:0.14
Consensus pattern (36 bp):
CAAAGACAAAGCAAAATTAAATACAACGATTGGAAA
Found at i:26190 original size:31 final size:31
Alignment explanation
Indices: 26146--26224 Score: 126
Period size: 31 Copynumber: 2.5 Consensus size: 31
26136 CGTTTATGTT
26146 TTTAGCCTCAAATTGGTCAACTTTTGAAAGG
1 TTTAGCCTCAAATTGGTCAACTTTTGAAAGG
26177 TTTAAG-CTCAAATTGAG-CAACTTTTGAAAGG
1 TTT-AGCCTCAAATTG-GTCAACTTTTGAAAGG
26208 TTTAGCCTCAAATTGGT
1 TTTAGCCTCAAATTGGT
26225 GGTTAAAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
30 3 0.07
31 38 0.86
32 3 0.07
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.35
Consensus pattern (31 bp):
TTTAGCCTCAAATTGGTCAACTTTTGAAAGG
Found at i:30011 original size:27 final size:27
Alignment explanation
Indices: 29981--30048 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
29971 GTCAGACTCT
* * *
29981 CATTCCAAGTTAGTCAAGACAG-TTCTC
1 CATTCAAAGCTAGTCAAAACAGTTTC-C
30008 CATTCAAAGCTAGTCAAAACAGTTTCC
1 CATTCAAAGCTAGTCAAAACAGTTTCC
30035 CATTCAAAGCTAGT
1 CATTCAAAGCTAGT
30049 TCCCTAGGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 34 0.92
28 3 0.08
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (27 bp):
CATTCAAAGCTAGTCAAAACAGTTTCC
Found at i:38206 original size:31 final size:30
Alignment explanation
Indices: 38133--38272 Score: 101
Period size: 29 Copynumber: 4.7 Consensus size: 30
38123 ACGTTTGCCA
* **
38133 AAATGCTTAAATAAGGGCCCGATCTT-TT-
1 AAATGCTCAAATAAGGGCCTAATCTTATTG
* * *
38161 AATTTGGTCAAATAAGGGCCTAACCTTATTGG
1 AA-ATGCTCAAATAAGGGCCTAATCTTATT-G
*
38193 AAATGCTCAAATAAGGGCCTGATCTT-TT-
1 AAATGCTCAAATAAGGGCCTAATCTTATTG
* * * *
38221 AATTTGAC-CAAATAAGGACCTAATGTTATCG
1 AA-ATG-CTCAAATAAGGGCCTAATCTTATTG
38252 AAAATGCTCAAATAAGGGCCT
1 -AAATGCTCAAATAAGGGCCT
38273 GGCGTCAGTT
Statistics
Matches: 85, Mismatches: 17, Indels: 17
0.71 0.14 0.14
Matches are distributed among these distances:
28 4 0.05
29 36 0.42
30 7 0.08
31 34 0.40
32 4 0.05
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (30 bp):
AAATGCTCAAATAAGGGCCTAATCTTATTG
Found at i:38272 original size:60 final size:60
Alignment explanation
Indices: 38132--38273 Score: 203
Period size: 60 Copynumber: 2.4 Consensus size: 60
38122 AACGTTTGCC
* * ** * *
38132 AAAATGCTTAAATAAGGGCCCGATCTTTTAATTTGGTCAAATAAGGGCCTAACCTTATTG
1 AAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGACCAAATAAGGACCTAACCTTATCG
* **
38192 GAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGACCAAATAAGGACCTAATGTTATCG
1 AAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGACCAAATAAGGACCTAACCTTATCG
38252 AAAATGCTCAAATAAGGGCCTG
1 AAAATGCTCAAATAAGGGCCTG
38274 GCGTCAGTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 72 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (60 bp):
AAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGACCAAATAAGGACCTAACCTTATCG
Found at i:38352 original size:31 final size:30
Alignment explanation
Indices: 38311--38478 Score: 130
Period size: 31 Copynumber: 5.6 Consensus size: 30
38301 TTTCGACGCC
*
38311 AGGCCCTTATTTGAGCATTTTGGCAAATGTT
1 AGGCCCTTATTTGAGCATTTT-GCAAACGTT
* ** * * *
38342 AGACCCTTATTTG-GCCAAATT-AAAAGGTC
1 AGGCCCTTATTTGAG-CATTTTGCAAACGTT
*
38371 GGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTT-GCAAACGTT
** * *
38402 AGGCCCTTATTTG-GCCAAATT--AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGCAAACG-TT
*
38431 AGACCCTTATTTGAGCATTTTGACAAACGTT
1 AGGCCCTTATTTGAGCATTTTG-CAAACGTT
38462 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
38479 ATAAGCCTCT
Statistics
Matches: 103, Mismatches: 24, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
28 4 0.04
29 37 0.36
30 4 0.04
31 54 0.52
32 4 0.04
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (30 bp):
AGGCCCTTATTTGAGCATTTTGCAAACGTT
Found at i:38383 original size:29 final size:29
Alignment explanation
Indices: 38345--38443 Score: 92
Period size: 29 Copynumber: 3.3 Consensus size: 29
38335 AAATGTTAGA
*
38345 CCCTTATTTGGCCAAATTAAAAGGTCGGG
1 CCCTTATTTGGCCAAATTAAAAGGTCAGG
** * * *
38374 CCCTTATTTGAG-CATTTTGGCAAACGTTAGG
1 CCCTTATTTG-GCCAAATT--AAAAGGTCAGG
* *
38405 CCCTTATTTGGCCAAATTAAAAGATCAGA
1 CCCTTATTTGGCCAAATTAAAAGGTCAGG
38434 CCCTTATTTG
1 CCCTTATTTG
38444 AGCATTTTGA
Statistics
Matches: 53, Mismatches: 13, Indels: 8
0.72 0.18 0.11
Matches are distributed among these distances:
29 30 0.57
30 2 0.04
31 21 0.40
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (29 bp):
CCCTTATTTGGCCAAATTAAAAGGTCAGG
Found at i:38409 original size:60 final size:60
Alignment explanation
Indices: 38310--38474 Score: 276
Period size: 60 Copynumber: 2.8 Consensus size: 60
38300 TTTTCGACGC
* * *
38310 CAGGCCCTTATTTGAGCATTTTGGCAAATGTTAGACCCTTATTTGGCCAAATTAAAAGGT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
*
38370 CGGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
* *
38430 CAGACCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTG
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
38475 AGCAATAAGC
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 98 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
Found at i:42781 original size:18 final size:18
Alignment explanation
Indices: 42758--42794 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
42748 AGAAGTGATG
42758 ATGAGGAAGAGCTTGAAA
1 ATGAGGAAGAGCTTGAAA
*
42776 ATGAGGAAGAGTTTGAAA
1 ATGAGGAAGAGCTTGAAA
42794 A
1 A
42795 CAGAATTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.32, T:0.19
Consensus pattern (18 bp):
ATGAGGAAGAGCTTGAAA
Found at i:43019 original size:57 final size:57
Alignment explanation
Indices: 42931--43060 Score: 260
Period size: 57 Copynumber: 2.3 Consensus size: 57
42921 ACCTGTTGCT
42931 GCAGCTTCATACACTTCCGGATTCATTGTTAAAGGAGGGATTTCTCTGGTTTAATTA
1 GCAGCTTCATACACTTCCGGATTCATTGTTAAAGGAGGGATTTCTCTGGTTTAATTA
42988 GCAGCTTCATACACTTCCGGATTCATTGTTAAAGGAGGGATTTCTCTGGTTTAATTA
1 GCAGCTTCATACACTTCCGGATTCATTGTTAAAGGAGGGATTTCTCTGGTTTAATTA
43045 GCAGCTTCATACACTT
1 GCAGCTTCATACACTT
43061 GGGATTCTTT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 73 1.00
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (57 bp):
GCAGCTTCATACACTTCCGGATTCATTGTTAAAGGAGGGATTTCTCTGGTTTAATTA
Found at i:47200 original size:31 final size:31
Alignment explanation
Indices: 47165--47243 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
47155 CATTTCTGTT
*
47165 TTTAGACTCAAATTGGTCAACTTTTGGAAGG
1 TTTAGACTCAAATTGGTCAACTTTTGAAAGG
*
47196 TTTAGACTCAAATTGAG-CAACTTTTGAAAGT
1 TTTAGACTCAAATTG-GTCAACTTTTGAAAGG
* *
47227 TTTAGGCTAAAATTGGT
1 TTTAGACTCAAATTGGT
47244 GGCTGAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 1 0.02
31 40 0.95
32 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (31 bp):
TTTAGACTCAAATTGGTCAACTTTTGAAAGG
Found at i:48835 original size:21 final size:20
Alignment explanation
Indices: 48807--48846 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
48797 CAACCGAGGG
*
48807 AGTAATTAATAATTTACTTA
1 AGTAATTAATAATTAACTTA
48827 AGTAGATTAATAATTAACTT
1 AGTA-ATTAATAATTAACTT
48847 TTGCAGGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (20 bp):
AGTAATTAATAATTAACTTA
Found at i:52372 original size:41 final size:41
Alignment explanation
Indices: 52327--52444 Score: 130
Period size: 43 Copynumber: 2.8 Consensus size: 41
52317 TGACCGGAGC
* *
52327 AACAACTTCTAGTTTCAAAGTTAATTTTAATTTACCAAGGT
1 AACAACTTCTAGTTTCAAAGGTAATTTTAATTTACCAAAGT
*
52368 AACAACTTCTGGTATT-AAAGGTAATTTTAATTCTTACCAAAGT
1 AACAACTTCTAGT-TTCAAAGGTAATTTTAA-T-TTACCAAAGT
* * * *
52411 GACAACTTCTTGTGTCAATGGTAGATTTTAATTT
1 AACAACTTCTAGTTTCAAAGGTA-ATTTTAATTT
52445 TATTTGTGTG
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
41 25 0.38
42 6 0.09
43 27 0.42
44 7 0.11
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.40
Consensus pattern (41 bp):
AACAACTTCTAGTTTCAAAGGTAATTTTAATTTACCAAAGT
Found at i:52552 original size:48 final size:47
Alignment explanation
Indices: 52453--52862 Score: 581
Period size: 47 Copynumber: 8.7 Consensus size: 47
52443 TTTATTTGTG
* * *
52453 TGACAACTTCTAGTGTCAATTAAATTCAATAAAGTAGAATTTTAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
** * *
52500 TGACAACTTCTTA-TGTCAATTATGTTTTACTAAAGTAAGATTTTACTT
1 TGACAACTTC-TAGTGTCAATTA-AATTTACTAAAGTAAAATTTTAATT
* * *
52548 TGACAAATTGTAGTGTCAATTAAAGTTACTAAAGTAAAA-TTTAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
52594 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
*
52641 TGACAACTTCTAGTGTCAATTAAATTTACTTAAGTAAAATTTTAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
* * **
52688 TGACAACTCCTGGTGTCAATTAAAATTTACTAAAACAAAATTTTAATT
1 TGACAACTTCTAGTGTCAATT-AAATTTACTAAAGTAAAATTTTAATT
**
52736 TGACAACTTCTAGTGTCAATTAAAATTTACTAAAACAAAATTTTAATT
1 TGACAACTTCTAGTGTCAATT-AAATTTACTAAAGTAAAATTTTAATT
*
52784 TGACAACTTCTAGTGTCAATTAAATTTACTTAAGTAAAATTTTAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
* *
52831 TGACAACTCCTGGTGTCAATTAAAATTTACTA
1 TGACAACTTCTAGTGTCAATT-AAATTTACTA
52863 GAGCTCTCGT
Statistics
Matches: 326, Mismatches: 31, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
46 42 0.13
47 148 0.45
48 136 0.42
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.40
Consensus pattern (47 bp):
TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
Found at i:52570 original size:95 final size:94
Alignment explanation
Indices: 52453--52862 Score: 581
Period size: 95 Copynumber: 4.3 Consensus size: 94
52443 TTTATTTGTG
* * *
52453 TGACAACTTCTAGTGTCAATTAAATTCAATAAAGTAGAATTTTAATTTGACAACTTCTTA-TGTC
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATTTGACAACTTC-TAGTGTC
** * *
52517 AATTATGTTTTACTAAAGTAAGATTTTACTT
65 AATTA-AATTTACTAAAGTAAAATTTTAATT
* * *
52548 TGACAAATTGTAGTGTCAATTAAAGTTACTAAAGTAAAA-TTTAATTTGACAACTTCTAGTGTCA
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATTTGACAACTTCTAGTGTCA
52612 ATTAAATTTACTAAAGTAAAATTTTAATT
66 ATTAAATTTACTAAAGTAAAATTTTAATT
* * *
52641 TGACAACTTCTAGTGTCAATTAAATTTACTTAAGTAAAATTTTAATTTGACAACTCCTGGTGTCA
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATTTGACAACTTCTAGTGTCA
**
52706 ATTAAAATTTACTAAAACAAAATTTTAATT
66 ATT-AAATTTACTAAAGTAAAATTTTAATT
**
52736 TGACAACTTCTAGTGTCAATTAAAATTTACTAAAACAAAATTTTAATTTGACAACTTCTAGTGTC
1 TGACAACTTCTAGTGTCAATT-AAATTTACTAAAGTAAAATTTTAATTTGACAACTTCTAGTGTC
*
52801 AATTAAATTTACTTAAGTAAAATTTTAATT
65 AATTAAATTTACTAAAGTAAAATTTTAATT
* *
52831 TGACAACTCCTGGTGTCAATTAAAATTTACTA
1 TGACAACTTCTAGTGTCAATT-AAATTTACTA
52863 GAGCTCTCGT
Statistics
Matches: 283, Mismatches: 28, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
93 58 0.20
94 52 0.18
95 131 0.46
96 42 0.15
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.40
Consensus pattern (94 bp):
TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATTTGACAACTTCTAGTGTCA
ATTAAATTTACTAAAGTAAAATTTTAATT
Found at i:52614 original size:26 final size:26
Alignment explanation
Indices: 52585--52667 Score: 63
Period size: 26 Copynumber: 3.4 Consensus size: 26
52575 ACTAAAGTAA
*
52585 AATTTAATTTGACAACTTCTAGTGTC
1 AATTAAATTTGACAACTTCTAGTGTC
**
52611 AATTAAATTT-ACTAA-----AGT-AA
1 AATTAAATTTGAC-AACTTCTAGTGTC
*
52631 AATTTTAATTTGACAACTTCTAGTGTC
1 AA-TTAAATTTGACAACTTCTAGTGTC
52658 AATTAAATTT
1 AATTAAATTT
52668 ACTTAAGTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 18
0.62 0.11 0.27
Matches are distributed among these distances:
20 2 0.05
21 12 0.29
22 2 0.05
25 2 0.05
26 21 0.51
27 2 0.05
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (26 bp):
AATTAAATTTGACAACTTCTAGTGTC
Found at i:63297 original size:122 final size:123
Alignment explanation
Indices: 63155--63386 Score: 421
Period size: 122 Copynumber: 1.9 Consensus size: 123
63145 CACATCTTAA
*
63155 TTAATTCTCTGCTTTTATAATTTCATTATTTTTAGTTTTAATTTACTTGATATCTCTCAATTTTC
1 TTAATTCTATGCTTTTATAATTTCATTATTTTTAGTTTTAATTTACTTGATATCTCTCAATTTTC
63220 CTTTTCTTGATAGAATTAATTGCAATAG-AAATTTCTTGTTACTTATTAATTCATAGG
66 CTTTTCTTGATAGAATTAATTGCAATAGAAAATTTCTTGTTACTTATTAATTCATAGG
* *
63277 TTAATTTTATGCTTTTATAATTTCATTGTTTTTAGTTTTAATTTACTTGATATCTCTCAATTTTC
1 TTAATTCTATGCTTTTATAATTTCATTATTTTTAGTTTTAATTTACTTGATATCTCTCAATTTTC
*
63342 TTTTTCTTGATAGAATTAATTGCAATAGAAAATTTCTTGTTACTT
66 CTTTTCTTGATAGAATTAATTGCAATAGAAAATTTCTTGTTACTT
63387 GTGGGTTCGA
Statistics
Matches: 105, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
122 89 0.85
123 16 0.15
ACGTcount: A:0.27, C:0.11, G:0.08, T:0.54
Consensus pattern (123 bp):
TTAATTCTATGCTTTTATAATTTCATTATTTTTAGTTTTAATTTACTTGATATCTCTCAATTTTC
CTTTTCTTGATAGAATTAATTGCAATAGAAAATTTCTTGTTACTTATTAATTCATAGG
Found at i:69145 original size:18 final size:18
Alignment explanation
Indices: 69122--69156 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
69112 AAGTGATGAA
69122 GAGGAAGAGCTTGAAAAT
1 GAGGAAGAGCTTGAAAAT
*
69140 GAGGAAGAGTTTGAAAA
1 GAGGAAGAGCTTGAAAA
69157 CAGAATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.34, T:0.17
Consensus pattern (18 bp):
GAGGAAGAGCTTGAAAAT
Found at i:70695 original size:15 final size:14
Alignment explanation
Indices: 70670--70706 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
70660 GATTCTCTCT
70670 TTATA-AGACTGTC
1 TTATATAGACTGTC
70683 TTATAGTAGACTGTC
1 TTATA-TAGACTGTC
70698 TTATATAGA
1 TTATATAGA
70707 GAGAATCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.23
14 4 0.18
15 13 0.59
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (14 bp):
TTATATAGACTGTC
Found at i:71042 original size:12 final size:13
Alignment explanation
Indices: 71010--71044 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
71000 TACCCACGGG
71010 TTTTGCCACAATC
1 TTTTGCCACAATC
71023 TGTTTGCCACAAT-
1 T-TTTGCCACAATC
71036 TTTTGCCAC
1 TTTTGCCAC
71045 GGGCTTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.38
13 2 0.10
14 11 0.52
ACGTcount: A:0.20, C:0.29, G:0.11, T:0.40
Consensus pattern (13 bp):
TTTTGCCACAATC
Done.