Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008306.1 Corchorus capsularis cultivar CVL-1 contig08327, 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: 74711
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:2282 original size:10 final size:10
Alignment explanation
Indices: 2267--2292 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2257 GCCCAATCGA
2267 TGGCCGGTTG
1 TGGCCGGTTG
2277 TGGCCGGTTG
1 TGGCCGGTTG
2287 TGGCCG
1 TGGCCG
2293 TTTGGTGTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.50, T:0.27
Consensus pattern (10 bp):
TGGCCGGTTG
Found at i:3369 original size:33 final size:33
Alignment explanation
Indices: 3329--3425 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 33
3319 AGCACTTGTG
3329 ACCGGCCACGCGACTTGGAGATGCCC-GCGCAAC
1 ACCGGCCACGCGACTTGGAGATGCCCGGC-CAAC
* *
3362 ACCGGCCATGCGACTTGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
* * **
3395 ACCGGCCACGTGACATGGCCATGCCCGGCCA
1 ACCGGCCACGCGACTTGGAGATGCCCGGCCA
3426 CGCGACATGG
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.20, C:0.39, G:0.30, T:0.11
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
Found at i:3414 original size:23 final size:23
Alignment explanation
Indices: 3387--3496 Score: 145
Period size: 23 Copynumber: 4.8 Consensus size: 23
3377 TGGAGATGCC
*
3387 CGGCCAT-CACCGGCCACGTGACAT
1 CGGCCATGC-CCGGCCACATGAC-T
**
3411 -GGCCATGCCCGGCCACGCGACAT
1 CGGCCATGCCCGGCCACATGAC-T
3434 -GGCCATGCCCGGCCACATGACT
1 CGGCCATGCCCGGCCACATGACT
3456 CGGCCATGCCCGGCCACATGACT
1 CGGCCATGCCCGGCCACATGACT
3479 CGGCCATGCCCGGCCACA
1 CGGCCATGCCCGGCCACA
3497 ACCGGCCACA
Statistics
Matches: 81, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
22 1 0.01
23 79 0.98
24 1 0.01
ACGTcount: A:0.18, C:0.44, G:0.27, T:0.11
Consensus pattern (23 bp):
CGGCCATGCCCGGCCACATGACT
Found at i:3461 original size:13 final size:13
Alignment explanation
Indices: 3443--3484 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
3433 TGGCCATGCC
3443 CGGCCACATGACT
1 CGGCCACATGACT
*
3456 CGG-C-CATG-CC
1 CGGCCACATGACT
3466 CGGCCACATGACT
1 CGGCCACATGACT
3479 CGGCCA
1 CGGCCA
3485 TGCCCGGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 4 0.17
11 5 0.21
12 5 0.21
13 10 0.42
ACGTcount: A:0.19, C:0.43, G:0.26, T:0.12
Consensus pattern (13 bp):
CGGCCACATGACT
Found at i:9020 original size:16 final size:16
Alignment explanation
Indices: 8987--9021 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
8977 GGGTTCTCTT
**
8987 GTTTAGATAGATCTGG
1 GTTTAGATAGATAAGG
9003 GTTTAGATAGATAAGG
1 GTTTAGATAGATAAGG
9019 GTT
1 GTT
9022 CCCTATTGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.31, T:0.37
Consensus pattern (16 bp):
GTTTAGATAGATAAGG
Found at i:10475 original size:10 final size:10
Alignment explanation
Indices: 10460--10523 Score: 62
Period size: 10 Copynumber: 6.5 Consensus size: 10
10450 GATCCGGTTT
10460 AAAAATATTA
1 AAAAATATTA
*
10470 AAAAAT-TAAA
1 AAAAATAT-TA
*
10480 AAAAAAATT-
1 AAAAATATTA
*
10489 -AAAATTTTA
1 AAAAATATTA
10498 AAAAATATTAA
1 AAAAATATT-A
10509 AAAAATATTA
1 AAAAATATTA
10519 AAAAA
1 AAAAA
10524 GCCACGTAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
8 6 0.14
9 1 0.02
10 25 0.58
11 11 0.26
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAAATATTA
Found at i:10492 original size:18 final size:18
Alignment explanation
Indices: 10471--10510 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
10461 AAAATATTAA
10471 AAAATTAAAAAAAAAATT
1 AAAATTAAAAAAAAAATT
** *
10489 AAAATTTTAAAAAATATT
1 AAAATTAAAAAAAAAATT
10507 AAAA
1 AAAA
10511 AAATATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATTAAAAAAAAAATT
Found at i:10499 original size:28 final size:29
Alignment explanation
Indices: 10461--10521 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
10451 ATCCGGTTTA
10461 AAAATATTAAAAAAT-TAAAAAAAAAATT
1 AAAATATTAAAAAATATAAAAAAAAAATT
* * *
10489 AAAATTTTAAAAAATATTAAAAAAATATT
1 AAAATATTAAAAAATATAAAAAAAAAATT
10518 AAAA
1 AAAA
10522 AAGCCACGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (29 bp):
AAAATATTAAAAAATATAAAAAAAAAATT
Found at i:10511 original size:11 final size:11
Alignment explanation
Indices: 10460--10523 Score: 59
Period size: 11 Copynumber: 6.4 Consensus size: 11
10450 GATCCGGTTT
10460 AAAAATATT-A
1 AAAAATATTAA
*
10470 AAAAAT-TAAA
1 AAAAATATTAA
*
10480 AAAAAAATT--
1 AAAAATATTAA
*
10489 -AAAAT-TTTA
1 AAAAATATTAA
10498 AAAAATATTAA
1 AAAAATATTAA
10509 AAAAATATTAA
1 AAAAATATTAA
10520 AAAA
1 AAAA
10524 GCCACGTAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
7 2 0.05
8 4 0.09
9 1 0.02
10 17 0.40
11 19 0.44
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAAATATTAA
Found at i:21860 original size:30 final size:31
Alignment explanation
Indices: 21825--21899 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
21815 CGGCTTGTGC
** *
21825 CCGGTCTTGTGCGATTGGC-CCATGCCATGG
1 CCGGTCTTGTGCGATTCCCTCCATGCAATGG
*
21855 CCGGTCATGTGCGA-TCCCTCCATGCAATGG
1 CCGGTCTTGTGCGATTCCCTCCATGCAATGG
*
21885 CTGGTCTTGTGCGAT
1 CCGGTCTTGTGCGAT
21900 GGCATCCTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 2 0.05
30 35 0.95
ACGTcount: A:0.12, C:0.29, G:0.31, T:0.28
Consensus pattern (31 bp):
CCGGTCTTGTGCGATTCCCTCCATGCAATGG
Found at i:28465 original size:36 final size:36
Alignment explanation
Indices: 28423--28541 Score: 133
Period size: 36 Copynumber: 3.4 Consensus size: 36
28413 TCTTTTTTAG
* *
28423 ATTAAGTTCTTTATTGATTTCACTTAGTTACCTTGA
1 ATTAAGTTCTTTATTGATCTCACTTAATTACCTTGA
*
28459 ATTAAGTTCTTTA-T--TCT-ACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGATCTCACTTAATTACCTTGA
* *
28491 ATTAAG-CCTTTTATTGACCTCACTTAATTACACTT-A
1 ATTAAGTTC-TTTATTGATCTCACTTAATTAC-CTTGA
28527 ATTAAGTTCTTTATT
1 ATTAAGTTCTTTATT
28542 TTACTTAATT
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
31 1 0.01
32 23 0.33
33 3 0.04
35 3 0.04
36 36 0.52
37 3 0.04
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.48
Consensus pattern (36 bp):
ATTAAGTTCTTTATTGATCTCACTTAATTACCTTGA
Found at i:28486 original size:32 final size:32
Alignment explanation
Indices: 28444--28556 Score: 113
Period size: 32 Copynumber: 3.4 Consensus size: 32
28434 TATTGATTTC
*
28444 ACTTAGTTACCTTGAATTAAGTTCTTTATTCT
1 ACTTAATTACCTTGAATTAAGTTCTTTATTCT
* *
28476 ACTTAATTACCCTGAATTAAG-CCTTTTATTGACCT
1 ACTTAATTACCTTGAATTAAGTTC-TTTATT---CT
*
28511 CACTTAATTACACTT-AATTAAGTTCTTTATTTT
1 -ACTTAATTAC-CTTGAATTAAGTTCTTTATTCT
*
28544 ACTTAATTTCCTT
1 ACTTAATTACCTT
28557 TCCTGAAATG
Statistics
Matches: 67, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
31 4 0.06
32 34 0.51
33 1 0.01
35 2 0.03
36 23 0.34
37 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (32 bp):
ACTTAATTACCTTGAATTAAGTTCTTTATTCT
Found at i:28606 original size:35 final size:35
Alignment explanation
Indices: 28540--28961 Score: 401
Period size: 35 Copynumber: 11.9 Consensus size: 35
28530 AAGTTCTTTA
* * *
28540 TTTTACTTAATTTCCTTTCCTGAAATGAAGCCTGTGTCT
1 TTTTACTTAATTTCC--T--TGAAATTAAGCCAGTCTCT
*
28579 TTTTACTTAATTTCCTTGAAATTAAGCCAATCT-T
1 TTTTACTTAATTTCCTTGAAATTAAGCCAGTCTCT
* *
28613 TTCTTCACTTAGTTTCCTTGAAACTAAGCCAGTC-CTT
1 TT-TT-ACTTAATTTCCTTGAAATTAAGCCAGTCTC-T
** * *
28650 TTTTACTTAATTTCCTTGAAATTAAGAAAATCTAT
1 TTTTACTTAATTTCCTTGAAATTAAGCCAGTCTCT
* * * *
28685 CTTTACCTAATTTCCTTGAAATTAAGTCAG--TAT
1 TTTTACTTAATTTCCTTGAAATTAAGCCAGTCTCT
* *
28718 TTTTACCTAATTTCCTTGAAATTAAGCCAGTCTTT
1 TTTTACTTAATTTCCTTGAAATTAAGCCAGTCTCT
* * * *
28753 TCTTTACCTAGTTTCCTTGAAACTAAGACAGTC-CTT
1 T-TTTACTTAATTTCCTTGAAATTAAGCCAGTCTC-T
* *
28789 TTTTACTGAATTTCCTTGAATTTAAGCCAGTCTACT
1 TTTTACTTAATTTCCTTGAAATTAAGCCAGTCT-CT
* * *
28825 TTTTACCTAGTTTCCTTGAAACTAAGCCAGTCT-T
1 TTTTACTTAATTTCCTTGAAATTAAGCCAGTCTCT
* *
28859 GTTTTACTTAATTTCCTTGAAATTAAGTCTGT-T-T
1 -TTTTACTTAATTTCCTTGAAATTAAGCCAGTCTCT
*
28893 TCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTAT
1 T-TTTACTTAATTTCCTTGAAATTAAGCCAGTCTCT
* * *
28929 CTTTACCTAATTTCCTTGAAATTAAGTCAGTCT
1 TTTTACTTAATTTCCTTGAAATTAAGCCAGTCT
28962 GTCTTTTAGT
Statistics
Matches: 322, Mismatches: 46, Indels: 34
0.80 0.11 0.08
Matches are distributed among these distances:
33 32 0.10
34 34 0.11
35 149 0.46
36 87 0.27
37 5 0.02
39 15 0.05
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.44
Consensus pattern (35 bp):
TTTTACTTAATTTCCTTGAAATTAAGCCAGTCTCT
Found at i:28642 original size:71 final size:70
Alignment explanation
Indices: 28555--28954 Score: 431
Period size: 71 Copynumber: 5.7 Consensus size: 70
28545 CTTAATTTCC
*
28555 TTTCC-TGAAA-TGAAGCCTGTGTCTTTTTACTTAATTTCCTTGAAATTAAGCCAATCTTTTCTT
1 TTTCCTTGAAACT-AAGCCAGT-TCTTTTTACTTAATTTCCTTGAAATTAAGCCAATCTTTTCTT
* *
28618 CACTTAG
64 TACCTAG
* ** *
28625 TTTCCTTGAAACTAAGCCAGTCCTTTTTTACTTAATTTCCTTGAAATTAAGAAAATC-TATCTTT
1 TTTCCTTGAAACTAAGCCAGTTC-TTTTTACTTAATTTCCTTGAAATTAAGCCAATCTTTTCTTT
*
28689 ACCTAA
65 ACCTAG
* * * * *
28695 TTTCCTTGAAATTAAGTCAG-TATTTTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTA
1 TTTCCTTGAAACTAAGCCAGTTCTTTTTACTTAATTTCCTTGAAATTAAGCCAATCTTTTCTTTA
28759 CCTAG
66 CCTAG
* * * * * *
28764 TTTCCTTGAAACTAAGACAGTCCTTTTTTACTGAATTTCCTTGAATTTAAGCCAGTCTACTT-TT
1 TTTCCTTGAAACTAAGCCAGTTC-TTTTTACTTAATTTCCTTGAAATTAAGCCAATCT-TTTCTT
28828 TACCTAG
64 TACCTAG
* *
28835 TTTCCTTGAAACTAAGCCAG-TCTTGTTTTACTTAATTTCCTTGAAATTAAGTC--TGTTTTCTT
1 TTTCCTTGAAACTAAGCCAGTTC-T-TTTTACTTAATTTCCTTGAAATTAAGCCAATCTTTTCTT
* *
28897 TACTTAA
64 TACCTAG
* *
28904 TTTCCTTGAAATTAAGCCAG-TCTATCTTTACCTAATTTCCTTGAAATTAAG
1 TTTCCTTGAAACTAAGCCAGTTCT-T-TTTACTTAATTTCCTTGAAATTAAG
28955 TCAGTCTGTC
Statistics
Matches: 282, Mismatches: 38, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
68 33 0.12
69 83 0.29
70 36 0.13
71 127 0.45
72 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.44
Consensus pattern (70 bp):
TTTCCTTGAAACTAAGCCAGTTCTTTTTACTTAATTTCCTTGAAATTAAGCCAATCTTTTCTTTA
CCTAG
Found at i:28772 original size:175 final size:175
Alignment explanation
Indices: 28555--28954 Score: 481
Period size: 175 Copynumber: 2.3 Consensus size: 175
28545 CTTAATTTCC
* * * * * *
28555 TTTCC-TGAAATGAAGCCTGTGTCTT-TTTACTTAATTTCCTTGAAATTAAGCCAAT-CTTTTCT
1 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGACAATCCTTTT-T
* * * *
28617 TCACTTAGTTTCCTTGAAACTAAGCCAGTCCT-TTTTTACTTAATTTCCTTGAAATTAAGAAAAT
65 T-ACTGAATTTCCTTGAAACTAAGCCAGT-CTATTTTTACCTAATTTCCTTGAAACTAAGAAAAT
28681 CTAT-CTTTACCTAATTTCCTTGAAATTAAGTCAGTATT-TTTACCTAA
128 CT-TGCTTTACCTAATTTCCTTGAAATTAAGTCAGTATTCTTTACCTAA
* * *
28728 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGACAGTCCTTTTTT
1 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGACAATCCTTTTTT
** * ** *
28793 ACTGAATTTCCTTGAATTTAAGCCAGTCTACTTTTTACCTAGTTTCCTTGAAACTAAGCCAGTCT
66 ACTGAATTTCCTTGAAACTAAGCCAGTCTA-TTTTTACCTAATTTCCTTGAAACTAAGAAAATCT
* * * * *
28858 TGTTTTACTTAATTTCCTTGAAATTAAGTCTGTTTTCTTTACTTAA
130 TGCTTTACCTAATTTCCTTGAAATTAAGTCAGTATTCTTTACCTAA
*
28904 TTTCCTTGAAATTAAGCCAGTC-TATCTTTACCTAATTTCCTTGAAATTAAG
1 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAG
28955 TCAGTCTGTC
Statistics
Matches: 193, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
173 7 0.04
174 40 0.21
175 111 0.58
176 35 0.18
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.44
Consensus pattern (175 bp):
TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAATTTCCTTGAAATTAAGACAATCCTTTTTT
ACTGAATTTCCTTGAAACTAAGCCAGTCTATTTTTACCTAATTTCCTTGAAACTAAGAAAATCTT
GCTTTACCTAATTTCCTTGAAATTAAGTCAGTATTCTTTACCTAA
Found at i:29074 original size:36 final size:36
Alignment explanation
Indices: 29053--29192 Score: 228
Period size: 36 Copynumber: 3.9 Consensus size: 36
29043 TTGATGACTC
*
29053 TACTTGATTCTTGTGAAATTAAGTCTTTGCTAATTT
1 TACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTT
*
29089 TACTTAATTCTTGTGAAATTAAGTCTTTGCCAATTT
1 TACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTT
* *
29125 TACTTAATTCTTGTGAAATTAAGTTTTTGCCAA-TT
1 TACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTT
*
29160 TACTTAATTTTTGTGAAATTAAGTCTTTGCTAA
1 TACTTAATTCTTGTGAAATTAAGTCTTTGCTAA
29193 CTTCTTTCAG
Statistics
Matches: 98, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 32 0.33
36 66 0.67
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.49
Consensus pattern (36 bp):
TACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTT
Found at i:29094 original size:72 final size:71
Alignment explanation
Indices: 28992--29188 Score: 193
Period size: 72 Copynumber: 2.7 Consensus size: 71
28982 CTAATTTCCT
* * **
28992 TGAAATTAAGCCCTTTGTCTGATTTTACTTAATCATCTTAG-G-ATTAAATCTTTGATGACTCTA
1 TGAAATTAAG-TCTTTG-CTAATTTTACTTAAT--TCTT-GTGAATTAAATCTTTGACAACTCTA
*
29055 CTTGATTCTTG
61 CTTAATTCTTG
* * * *
29066 TGAAATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAAATTAAGTCTTTGCCAATTTTACTTA
1 TGAAATTAAGTCTTTGCTAATTTTACTTAATTCTTGTG-AATTAAATCTTTGACAACTCTACTTA
29131 ATTCTTG
65 ATTCTTG
* * * *
29138 TGAAATTAAGTTTTTGCCAA-TTTACTTAATTTTTGTGAAATTAAGTCTTTG
1 TGAAATTAAGTCTTTGCTAATTTTACTTAATTCTTGTG-AATTAAATCTTTG
29189 CTAACTTCTT
Statistics
Matches: 108, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
69 1 0.01
70 5 0.05
71 30 0.28
72 57 0.53
73 5 0.05
74 10 0.09
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (71 bp):
TGAAATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAATTAAATCTTTGACAACTCTACTTAA
TTCTTG
Found at i:29212 original size:12 final size:12
Alignment explanation
Indices: 29193--29270 Score: 117
Period size: 12 Copynumber: 6.7 Consensus size: 12
29183 TCTTTGCTAA
29193 CTTC-TTTCAGT
1 CTTCTTTTCAGT
29204 CTTCTTTTCAGT
1 CTTCTTTTCAGT
*
29216 CTTCTTTCCAGT
1 CTTCTTTTCAGT
29228 CTTC-TTTCAGT
1 CTTCTTTTCAGT
29239 CTTCTTTTCAGT
1 CTTCTTTTCAGT
29251 CTTCTATTT-AGT
1 CTTCT-TTTCAGT
29263 CTTCTTTT
1 CTTCTTTT
29271 GCCTAATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
11 17 0.27
12 42 0.68
13 3 0.05
ACGTcount: A:0.09, C:0.26, G:0.08, T:0.58
Consensus pattern (12 bp):
CTTCTTTTCAGT
Found at i:29219 original size:23 final size:23
Alignment explanation
Indices: 29193--29269 Score: 113
Period size: 23 Copynumber: 3.3 Consensus size: 23
29183 TCTTTGCTAA
29193 CTTCTTTCAGTCTTCTTTTCAGT
1 CTTCTTTCAGTCTTCTTTTCAGT
29216 CTTCTTTCCAGTCTTC-TTTCAGT
1 CTTCTTT-CAGTCTTCTTTTCAGT
29239 CTTCTTTTCAGTCTTCTATTT-AGT
1 CTTC-TTTCAGTCTTCT-TTTCAGT
29263 CTTCTTT
1 CTTCTTT
29270 TGCCTAATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
23 29 0.58
24 18 0.36
25 3 0.06
ACGTcount: A:0.09, C:0.26, G:0.08, T:0.57
Consensus pattern (23 bp):
CTTCTTTCAGTCTTCTTTTCAGT
Found at i:29264 original size:35 final size:35
Alignment explanation
Indices: 29193--29269 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 35
29183 TCTTTGCTAA
29193 CTTCTTTCAGTCTTCTTTTCAGTCTTCTTTCCAGT
1 CTTCTTTCAGTCTTCTTTTCAGTCTTCTTTCCAGT
*
29228 CTTCTTTCAGTCTTCTTTTCAGTCTTCTATT-TAGT
1 CTTCTTTCAGTCTTCTTTTCAGTCTTCT-TTCCAGT
29263 CTTCTTT
1 CTTCTTT
29270 TGCCTAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
35 38 0.95
36 2 0.05
ACGTcount: A:0.09, C:0.26, G:0.08, T:0.57
Consensus pattern (35 bp):
CTTCTTTCAGTCTTCTTTTCAGTCTTCTTTCCAGT
Found at i:34596 original size:8 final size:8
Alignment explanation
Indices: 34568--34604 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
34558 GAATCGGCTA
34568 TGAATTTT
1 TGAATTTT
*
34576 TGAAGTTTC
1 TGAA-TTTT
34585 TGAATTTT
1 TGAATTTT
34593 TGAATTTT
1 TGAATTTT
34601 TGAA
1 TGAA
34605 GAAGGGTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.27, C:0.03, G:0.16, T:0.54
Consensus pattern (8 bp):
TGAATTTT
Found at i:36586 original size:28 final size:28
Alignment explanation
Indices: 36555--36623 Score: 111
Period size: 28 Copynumber: 2.5 Consensus size: 28
36545 TGACAGCTTC
* *
36555 AGCGCGTCCTTACAGCGTTGACGTCTTT
1 AGCGCGTCCGTACAACGTTGACGTCTTT
*
36583 AGCGCGTCCGTACAACGTTGATGTCTTT
1 AGCGCGTCCGTACAACGTTGACGTCTTT
36611 AGCGCGTCCGTAC
1 AGCGCGTCCGTAC
36624 TGTTTGTTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.16, C:0.29, G:0.26, T:0.29
Consensus pattern (28 bp):
AGCGCGTCCGTACAACGTTGACGTCTTT
Found at i:40584 original size:33 final size:33
Alignment explanation
Indices: 40547--40653 Score: 135
Period size: 33 Copynumber: 3.2 Consensus size: 33
40537 AGCACTAGTG
* *
40547 ACCGGCCATGCGACTTGGAGAAGTCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* * *
40580 ACCGGCCACGTGACTCGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* *
40613 ACCGGCCACGCGACATGGACATGTCCGGCC-AC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
40645 AACCGGCCA
1 -ACCGGCCA
40654 TCGCTAGGCG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 2 0.03
33 61 0.97
ACGTcount: A:0.23, C:0.38, G:0.29, T:0.09
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
Found at i:51564 original size:26 final size:25
Alignment explanation
Indices: 51520--51568 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
51510 ATGATTTAGG
* *
51520 GGTTACTAACGCCCTTTTTCTTTTGA
1 GGTTACTAACACCCATTTT-TTTTGA
*
51546 GGTTACTAACACTCATTTTTTTT
1 GGTTACTAACACCCATTTTTTTT
51569 CAAAGAGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.18, C:0.20, G:0.12, T:0.49
Consensus pattern (25 bp):
GGTTACTAACACCCATTTTTTTTGA
Found at i:56871 original size:18 final size:18
Alignment explanation
Indices: 56848--56889 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
56838 TAAACAAGGG
56848 CTAATTAATACTAATTGC
1 CTAATTAATACTAATTGC
56866 CTAATTAATACTAATTGC
1 CTAATTAATACTAATTGC
*
56884 TTAATT
1 CTAATT
56890 TTCTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (18 bp):
CTAATTAATACTAATTGC
Found at i:60704 original size:18 final size:19
Alignment explanation
Indices: 60670--60707 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
60660 GTCCTTCGTT
*
60670 ATCTCCATGGTCTCCATGC
1 ATCTCCATGGCCTCCATGC
60689 ATCTCCAT-GCCTCCATGC
1 ATCTCCATGGCCTCCATGC
60707 A
1 A
60708 GCCCATGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.18, C:0.39, G:0.13, T:0.29
Consensus pattern (19 bp):
ATCTCCATGGCCTCCATGC
Found at i:66348 original size:6 final size:6
Alignment explanation
Indices: 66337--66370 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
66327 TTGTGTTCTA
66337 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTT
66371 CTATTAGATT
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:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTGT
Found at i:73926 original size:15 final size:16
Alignment explanation
Indices: 73906--73939 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
73896 GATTGCTTTC
*
73906 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
73921 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
73937 TTA
1 TTA
73940 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Done.