Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006190.1 Corchorus capsularis cultivar CVL-1 contig06208, 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: 35100
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:1572 original size:32 final size:32
Alignment explanation
Indices: 1531--1613 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
1521 CCCTGGAACA
* * * *
1531 GCCGACCCC-TGGGGCGTCCTTGCCTAGGGCAT
1 GCCGCCCCCTTGGGGCGGCCTCGCC-ACGGCAT
1563 GCCGCCCCCTTGGGGCGGCCTCGCCACGGCAT
1 GCCGCCCCCTTGGGGCGGCCTCGCCACGGCAT
* * *
1595 GCCACCCCCCTGGAGCGGC
1 GCCGCCCCCTTGGGGCGGC
1614 ACAGCCAAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 30 0.70
33 13 0.30
ACGTcount: A:0.08, C:0.45, G:0.34, T:0.13
Consensus pattern (32 bp):
GCCGCCCCCTTGGGGCGGCCTCGCCACGGCAT
Found at i:3447 original size:156 final size:155
Alignment explanation
Indices: 3066--3448 Score: 375
Period size: 156 Copynumber: 2.5 Consensus size: 155
3056 CTTCTTACCT
* *
3066 CAAACTGTCCTTAAATGAAAAACTTGAATAAGTTTTTCATTCTAAGTCTGAATGAGCA-GAAACT
1 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAG-ATGAAACT
* * * * *
3130 TTACCAAGGGACTTAGACTATCTCCATGAGACTATGGAAAAAATTGCAAGTAAAACTGAGCTCCC
65 TCACC-AGAGACTTAGACTATCCCCATGAGACTATGGAAAAAATTGCAAGTAAAACCGACCTCCC
** * * * *
3195 CTTGATGGTGAACTAGGTTTCTCTCCC
129 CAAGATAGAGAACTAGGTTTCACACCC
** * * **
3222 TGAA-TCGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAATGAAGTTG-ATT
1 CAAACT-GTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATG-AGATGAAAC
* *
3284 TTCCACCAGTAGACTTAGATTATCCCCATGA-AGCTATGGGAAAAATT-CTAAGTAAAACCGACC
64 TT-CACCAG-AGACTTAGACTATCCCCATGAGA-CTATGGAAAAAATTGC-AAGTAAAACCGACC
* * *
3347 T-CTCAAGCATAGAGAAGTAGGTTTGACACCC
125 TCCCCAAG-ATAGAGAACTAGGTTTCACACCC
* * * **
3378 CAAACTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCATACGAAGTCTGTTTGAGATGAAACTT
1 CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGATGAAACTT
3443 CACCAG
66 CACCAG
3449 GATGACCTAC
Statistics
Matches: 181, Mismatches: 35, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
155 15 0.08
156 160 0.88
157 6 0.03
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (155 bp):
CAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGATGAAACTT
CACCAGAGACTTAGACTATCCCCATGAGACTATGGAAAAAATTGCAAGTAAAACCGACCTCCCCA
AGATAGAGAACTAGGTTTCACACCC
Found at i:7786 original size:14 final size:14
Alignment explanation
Indices: 7767--7793 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
7757 ACACTTCCAA
7767 TATGTATTTGAAGG
1 TATGTATTTGAAGG
7781 TATGTATTTGAAG
1 TATGTATTTGAAG
7794 CTAAACTCGG
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:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (14 bp):
TATGTATTTGAAGG
Found at i:9792 original size:35 final size:35
Alignment explanation
Indices: 9741--10376 Score: 707
Period size: 35 Copynumber: 18.1 Consensus size: 35
9731 CTTAATTTCC
* * *
9741 TTTCC-TGAAATTAAGCCTGTGTCTTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTCTTTTTACCTAA
* *
9775 TTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCTCTTTTTACCTAA
* * *
9810 TTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTCTCTTTTTACCTAA
* * * * *
9845 TTTTCTTGAAACTAAGCCAGACTTTTCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTCTCTT-TTTACCTAA
* *
9881 TTTCCTTGAAACTAAGCCAGT-TCTTTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTC-TTTTTACCTAA
* * *
9916 TTTCCTTCAAATTAAGCCAGTCTATCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCTCTTTTTACCTAA
*
9951 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACC-AA
1 TTTCCTTGAAATTAAGCCAGTCTCTT-TTTACCTAA
* * * *
9986 GTTCCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAGT
1 -TTTCCTTGAAATTAAGCCAGTCTCTT-TTTACCTA-A
* *
10024 TTTCCTTGAAACTAAGCCAGTCGT-TTCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTC-TCTT-TTTACCTAA
* *
10060 TTTCCTTGAAACTAAGCCAGTC-CTTTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTC-TTTTTACCTAA
* *
10095 TTTCCTTGAAATTAAGCTAGTC-CTTTTTACGTAA
1 TTTCCTTGAAATTAAGCCAGTCTCTTTTTACCTAA
*
10129 TTTCCTTGAAATTAAGCCAGTCT-TGTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTCT-TTTTACCTAA
* * *
10164 TTTCCTTGAAATTAAGTCAGTCT-TCTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTCTTTTTACCTAA
* *
10198 TTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCTCTTTTTACCTAA
* *
10233 TTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCTCTTTTTACCTAA
* * *
10268 TTTCCTTGAAATTAAGCCAATCTTTTCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTCTCTT-TTTACCTAA
* *
10304 TTTCCTTGAAACTAAGCCAGTC-CTTTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTC-TTTTTACCTAA
*
10339 TTTCCTTGAAATTAAGCCAGTC-CTTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTCTTTTTACCTAA
10373 TTTC
1 TTTC
10377 TATGAATTAA
Statistics
Matches: 536, Mismatches: 50, Indels: 32
0.87 0.08 0.05
Matches are distributed among these distances:
34 83 0.15
35 297 0.55
36 122 0.23
37 33 0.06
38 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.43
Consensus pattern (35 bp):
TTTCCTTGAAATTAAGCCAGTCTCTTTTTACCTAA
Found at i:9885 original size:106 final size:105
Alignment explanation
Indices: 9741--10376 Score: 754
Period size: 106 Copynumber: 6.0 Consensus size: 105
9731 CTTAATTTCC
* ** * * *
9741 TTTCC-TGAAATTAAGCCTGTGTCTT-TTTACTTAATTTCCTTGAAATTAAGCCAGTCTATCTTT
1 TTTCCTTGAAATTAAGCCAGACTTTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCT-TCTTT
*
9804 ACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAG
65 ACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAA
* * * *
9845 TTTTCTTGAAACTAAGCCAGACTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTTCTTTTTT
1 TTTCCTTGAAATTAAGCCAGACTTTTCTTTACCTAATTTCCTTGAAACTAAGCCAG-TCTTCTTT
* *
9910 ACTTAATTTCCTTCAAATTAAGCCAGTCTATCTTTACCTAA
65 ACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAA
* *
9951 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACC-AAGTTCCCTTGAAACTAAGCCAGTCTTTTCT
1 TTTCCTTGAAATTAAGCCAGACTTTTCTTTACCTAA-TTTCCTTGAAACTAAGCCAGTC--TTCT
* * * *
10015 TTACCTAGTTTTCCTTGAAACTAAGCCAGTCGTTTCTTTACCTAG
63 TTACCTA-ATTTCCTTGAAATTAAGCCAGTC-TATCTTTACCTAA
* * * * * *
10060 TTTCCTTGAAACTAAGCCAGTCCTTT-TTTACTTAATTTCCTTGAAATTAAGCTAGTCCTT-TTT
1 TTTCCTTGAAATTAAGCCAGACTTTTCTTTACCTAATTTCCTTGAAACTAAGCCAGT-CTTCTTT
* * *
10123 ACGTAATTTCCTTGAAATTAAGCCAGTCT-TGTTTTACTTAA
65 ACCTAATTTCCTTGAAATTAAGCCAGTCTAT-CTTTACCTAA
* * * *
10164 TTTCCTTGAAATTAAGTCAG--TCTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATCTTT
1 TTTCCTTGAAATTAAGCCAGACTTTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCT-TCTTT
10227 ACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAA
65 ACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAA
* *
10268 TTTCCTTGAAATTAAGCCA-ATCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCCTTTTT
1 TTTCCTTGAAATTAAGCCAGA-CTTTTCTTTACCTAATTTCCTTGAAACTAAGCCAGT-CTTCTT
* *
10332 TACTTAATTTCCTTGAAATTAAGCCAGTCCT-T-TTTACTTAA
64 TACCTAATTTCCTTGAAATTAAGCCAGT-CTATCTTTACCTAA
10373 TTTC
1 TTTC
10377 TATGAATTAA
Statistics
Matches: 459, Mismatches: 53, Indels: 39
0.83 0.10 0.07
Matches are distributed among these distances:
102 4 0.01
103 31 0.07
104 87 0.19
105 52 0.11
106 186 0.41
107 18 0.04
108 43 0.09
109 38 0.08
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.43
Consensus pattern (105 bp):
TTTCCTTGAAATTAAGCCAGACTTTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCTTCTTTA
CCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAA
Found at i:10405 original size:35 final size:36
Alignment explanation
Indices: 10364--10468 Score: 162
Period size: 35 Copynumber: 3.0 Consensus size: 36
10354 GCCAGTCCTT
* *
10364 TTTACTTAATTTCTATG-AATTAAGTCTTTTGCTAA
1 TTTACTTAATTTTTGTGAAATTAAGTCTTTTGCTAA
*
10399 TTTACTTAATTTTTGTGAAATTAAGT-TTTTGCCAA
1 TTTACTTAATTTTTGTGAAATTAAGTCTTTTGCTAA
10434 TTTACTTAATTTTTGTGAAATTAAGTC-TTTGCTAA
1 TTTACTTAATTTTTGTGAAATTAAGTCTTTTGCTAA
10469 CTTCTTTCAG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
35 56 0.88
36 8 0.12
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (36 bp):
TTTACTTAATTTTTGTGAAATTAAGTCTTTTGCTAA
Found at i:10448 original size:19 final size:19
Alignment explanation
Indices: 10390--10448 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
10380 GAATTAAGTC
*
10390 TTTTGCTAATTTACTTAAT
1 TTTTGCCAATTTACTTAAT
**
10409 TTTTGTGAA---A-TTAAGT
1 TTTTGCCAATTTACTTAA-T
10425 TTTTGCCAATTTACTTAAT
1 TTTTGCCAATTTACTTAAT
10444 TTTTG
1 TTTTG
10449 TGAAATTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
15 4 0.13
16 9 0.29
19 14 0.45
20 4 0.13
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.56
Consensus pattern (19 bp):
TTTTGCCAATTTACTTAAT
Found at i:10455 original size:20 final size:20
Alignment explanation
Indices: 10397--10455 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 20
10387 GTCTTTTGCT
10397 AATTTACTTAATTTTTGTGA
1 AATTTACTTAATTTTTGTGA
* **
10417 AA-TTA---AGTTTTTG-CC
1 AATTTACTTAATTTTTGTGA
10432 AATTTACTTAATTTTTGTGA
1 AATTTACTTAATTTTTGTGA
10452 AATT
1 AATT
10456 AAGTCTTTGC
Statistics
Matches: 28, Mismatches: 6, Indels: 10
0.64 0.14 0.23
Matches are distributed among these distances:
15 2 0.07
16 10 0.36
19 10 0.36
20 6 0.21
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.53
Consensus pattern (20 bp):
AATTTACTTAATTTTTGTGA
Found at i:10458 original size:175 final size:173
Alignment explanation
Indices: 9741--10376 Score: 672
Period size: 179 Copynumber: 3.6 Consensus size: 173
9731 CTTAATTTCC
** * * * *
9741 TTTCC-TGAAATTAAGCCTGTGTCTTTTTACTTAATTTCCTTGAAATTAAGCCAGTCTAT-CTTT
1 TTTCCTTGAAATTAAGCCAAT-CCTTTTTACCTAATTTCCTTGAAACTAAGCCAGTCT-TGTTTT
* * * * * *
9804 ACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAGTTTTCTTGAAACTAAGCCAGACTT
64 ACTTAATTTCCTTGAAATTAAGCCAGTCT-TCTTTACTTAATTTCCTTGAAATTAAGCCAGTC-T
* * * * * * *
9869 TTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTTCTTTTTTACTTAA
127 ATATTTACCTAATTTCCTTGAAATTAAGCCAGTCCATATTTACTTAA
* * * *
9916 TTTCCTTCAAATTAAGCCAGT-CTATCTTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTCTT
1 TTTCCTTGAAATTAAGCCAATCCT-T-TTTACCTAATTTCCTTGAAACTAAGCCAGTCTTGT-TT
* * * * * *
9980 TAC-CAAGTTCCCTTGAAACTAAGCCAGTCTTTTCTTTACCTAGTTTTCCTTGAAACTAAGCCAG
63 TACTTAA-TTTCCTTGAAATTAAGCCAGTC--TTCTTTACTTA-ATTTCCTTGAAATTAAGCCAG
* * * * * *
10044 TCGTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCCTTTTTTACTTAA
124 TC-TATATTTACCTAATTTCCTTGAAATTAAGCCAGTCCATATTTACTTAA
* * * *
10095 TTTCCTTGAAATTAAGCTAGTCCTTTTTACGTAATTTCCTTGAAATTAAGCCAGTCTTGTTTTAC
1 TTTCCTTGAAATTAAGCCAATCCTTTTTACCTAATTTCCTTGAAACTAAGCCAGTCTTGTTTTAC
* *
10160 TTAATTTCCTTGAAATTAAGTCAGTCTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATCT
66 TTAATTTCCTTGAAATTAAGCCAGTCTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATAT
* * *
10225 TTACCTAATTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAA
131 TTACCTAATTTCCTTGAAATTAAGCCAGTCCATATTTACTTAA
* *
10268 TTTCCTTGAAATTAAGCCAATCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCCTT-TTT
1 TTTCCTTGAAATTAAGCCAATC-CTT-TTTACCTAATTTCCTTGAAACTAAGCCAGT-CTTGTTT
10332 TACTTAATTTCCTTGAAATTAAGCCAGTCCTT-TTTACTTAATTTC
63 TACTTAATTTCCTTGAAATTAAGCCAGT-CTTCTTTACTTAATTTC
10377 TATGAATTAA
Statistics
Matches: 409, Mismatches: 37, Indels: 30
0.86 0.08 0.06
Matches are distributed among these distances:
173 61 0.15
174 25 0.06
175 87 0.21
176 52 0.13
177 49 0.12
178 45 0.11
179 88 0.22
180 2 0.00
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.43
Consensus pattern (173 bp):
TTTCCTTGAAATTAAGCCAATCCTTTTTACCTAATTTCCTTGAAACTAAGCCAGTCTTGTTTTAC
TTAATTTCCTTGAAATTAAGCCAGTCTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTATAT
TTACCTAATTTCCTTGAAATTAAGCCAGTCCATATTTACTTAA
Found at i:10485 original size:11 final size:11
Alignment explanation
Indices: 10469--10558 Score: 126
Period size: 11 Copynumber: 7.6 Consensus size: 11
10459 TCTTTGCTAA
10469 CTTCTTTCAGT
1 CTTCTTTCAGT
10480 CTTCTTTCAGT
1 CTTCTTTCAGT
10491 CTTCTTTTCAGT
1 CTTC-TTTCAGT
10503 CTTCTTTTTTCCAGT
1 CTTC---TTT-CAGT
10518 CTTCTTTCAGT
1 CTTCTTTCAGT
10529 CTTCTTTTCAGT
1 CTTC-TTTCAGT
10541 CTTCTTTCAGT
1 CTTCTTTCAGT
10552 CTTCTTT
1 CTTCTTT
10559 TGTCTAATTT
Statistics
Matches: 74, Mismatches: 0, Indels: 10
0.88 0.00 0.12
Matches are distributed among these distances:
11 37 0.50
12 25 0.34
14 4 0.05
15 8 0.11
ACGTcount: A:0.08, C:0.27, G:0.08, T:0.58
Consensus pattern (11 bp):
CTTCTTTCAGT
Found at i:10499 original size:23 final size:23
Alignment explanation
Indices: 10469--10559 Score: 139
Period size: 23 Copynumber: 3.8 Consensus size: 23
10459 TCTTTGCTAA
10469 CTTCTTTCAGTCTTC-TTTCAGT
1 CTTCTTTCAGTCTTCTTTTCAGT
10491 CTTCTTTTCAGTCTTCTTTTTTCCAGT
1 CTTC-TTTCAGTCTTC--TTTT-CAGT
10518 CTTCTTTCAGTCTTCTTTTCAGT
1 CTTCTTTCAGTCTTCTTTTCAGT
10541 CTTCTTTCAGTCTTCTTTT
1 CTTCTTTCAGTCTTCTTTT
10560 GTCTAATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 9
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.06
23 34 0.53
24 4 0.06
26 14 0.22
27 8 0.12
ACGTcount: A:0.08, C:0.26, G:0.08, T:0.58
Consensus pattern (23 bp):
CTTCTTTCAGTCTTCTTTTCAGT
Found at i:10517 original size:15 final size:14
Alignment explanation
Indices: 10479--10559 Score: 74
Period size: 12 Copynumber: 6.4 Consensus size: 14
10469 CTTCTTTCAG
*
10479 TCTTCTTTCAGTCT
1 TCTTTTTTCAGTCT
10493 TC--TTTTCAGTCT
1 TCTTTTTTCAGTCT
10505 TCTTTTTTCCAGTCT
1 TCTTTTTT-CAGTCT
10520 TC---TTTCAGTCT
1 TCTTTTTTCAGTCT
10531 TC--TTTTCAGTCT
1 TCTTTTTTCAGTCT
10543 TC---TTTCAGTCT
1 TCTTTTTTCAGTCT
10554 TCTTTT
1 TCTTTT
10560 GTCTAATTTC
Statistics
Matches: 59, Mismatches: 1, Indels: 14
0.80 0.01 0.19
Matches are distributed among these distances:
11 19 0.32
12 25 0.42
14 7 0.12
15 8 0.14
ACGTcount: A:0.07, C:0.26, G:0.07, T:0.59
Consensus pattern (14 bp):
TCTTTTTTCAGTCT
Found at i:10769 original size:71 final size:70
Alignment explanation
Indices: 10678--10811 Score: 182
Period size: 71 Copynumber: 1.9 Consensus size: 70
10668 TAATATTCTT
* *
10678 ACTTAATTTCCCTGAATTAAGCCTT-TTA-ACTGTTGCTTCTACTTAATTTCTATGAATTAAGTC
1 ACTTAATTTCCATGAATTAAGCCTTCTGAGACTGTT-C-TC-ACTTAATTTCTATGAATTAAGTC
10741 TTTTGACC
63 TTTTGACC
* *
10749 ACTTAATTTCGATGAATTAAGTCTTCTGAGTACTGTTCTCACTTAATTTCTATGAATTAAGTC
1 ACTTAATTTCCATGAATTAAGCCTTCTGAG-ACTGTTCTCACTTAATTTCTATGAATTAAGTC
10812 CTCAACTATG
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
71 45 0.80
72 4 0.07
73 1 0.02
74 6 0.11
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (70 bp):
ACTTAATTTCCATGAATTAAGCCTTCTGAGACTGTTCTCACTTAATTTCTATGAATTAAGTCTTT
TGACC
Found at i:17598 original size:28 final size:28
Alignment explanation
Indices: 17510--17611 Score: 140
Period size: 27 Copynumber: 3.7 Consensus size: 28
17500 AGGGTCACCT
17510 AGGGGCATTTTGGTCATTTTAATG--TTC-
1 AGGGGCATTTTGGTCATTTT--TGCATTCA
**
17537 AGGGGCATTTTGGTCATTTTCACATTCA
1 AGGGGCATTTTGGTCATTTTTGCATTCA
17565 A-GGGCATTTTGGTCATTTTTGCATTCA
1 AGGGGCATTTTGGTCATTTTTGCATTCA
17592 AGGGGCATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
17612 GAGTCCATTT
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
27 48 0.72
28 19 0.28
ACGTcount: A:0.19, C:0.14, G:0.25, T:0.43
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTTGCATTCA
Found at i:25430 original size:156 final size:155
Alignment explanation
Indices: 25129--25488 Score: 354
Period size: 156 Copynumber: 2.3 Consensus size: 155
25119 TTCTCACCTC
** * * *
25129 AAACTGTTATTAAATGAAAAACTTGCATAAGTTTTTTATTCTAAGTCTGAATGAGCAGAAACTTT
1 AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAATGA-CAGAAACTTT
* * *
25194 ACCAAGGGACTTAGACTATCTCCACGAGACTATGGAAAAAATTCCAAGTAAAACTGAGCTCCCCT
65 ACCAAGGGACTTAGACTATCCCCACGAGACTATGGAAAAAATTCCAAGTAAAACCGACCTCCCCT
* * * * *
25259 TGATGGTGAACTAGGTTTCTCTCCAT
130 AGATAGAGAACTAGGTTTCACACCAT
* **
25285 GAA-TCGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAATGA-AGTTGA-TT
1 AAACT-GTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAATGACAG-AAACTT
* * * *
25346 TTCCACCAGTGGACTTAGATTATCCCCATGA-AGCTATGGAAAAAATTCTAAGTAAAACCGACCT
64 TACCA--AG-GGACTTAGACTATCCCCACGAGA-CTATGGAAAAAATTCCAAGTAAAACCGACCT
* * * *
25410 -CTCTAGTATAGAGAAGTAGGTTTGACACCCT
125 CCCCTAG-ATAGAGAACTAGGTTTCACACCAT
* * * *
25441 AAACTGTCCTTAACTGAAAAACTATCATAAGTTTTTCATACGAAGTCT
1 AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCT
25489 GTTTGAGATG
Statistics
Matches: 166, Mismatches: 29, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
153 8 0.05
154 1 0.01
155 13 0.08
156 143 0.86
157 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (155 bp):
AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAATGACAGAAACTTTA
CCAAGGGACTTAGACTATCCCCACGAGACTATGGAAAAAATTCCAAGTAAAACCGACCTCCCCTA
GATAGAGAACTAGGTTTCACACCAT
Found at i:26455 original size:21 final size:23
Alignment explanation
Indices: 26413--26456 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
26403 ATAAGATAAA
*
26413 ATACGTAGGTTACAAAATATTTT
1 ATACGTAGGTTACAAAACATTTT
*
26436 ATAC-TAGG-TACAAAGCATTTT
1 ATACGTAGGTTACAAAACATTTT
26457 TATTTGGCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 4 0.21
23 4 0.21
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (23 bp):
ATACGTAGGTTACAAAACATTTT
Found at i:27139 original size:15 final size:15
Alignment explanation
Indices: 27119--27148 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
27109 AACCGATCAC
27119 CCGAAGTCTCTCATG
1 CCGAAGTCTCTCATG
27134 CCGAAGTCTCTCATG
1 CCGAAGTCTCTCATG
27149 TTAGCGAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.27
Consensus pattern (15 bp):
CCGAAGTCTCTCATG
Found at i:28352 original size:21 final size:25
Alignment explanation
Indices: 28313--28362 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 25
28303 GTGTTTGTAG
*
28313 AAAAAAAATAACTTCAAAC-TTTTT
1 AAAAAAAATAACTTCAAACAATTTT
28337 AAAAAAAA-AA-TT-AAACAATTTT
1 AAAAAAAATAACTTCAAACAATTTT
28359 AAAA
1 AAAA
28363 TATTTTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 4 0.17
22 10 0.42
23 2 0.08
24 8 0.33
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (25 bp):
AAAAAAAATAACTTCAAACAATTTT
Found at i:28433 original size:17 final size:19
Alignment explanation
Indices: 28402--28441 Score: 66
Period size: 17 Copynumber: 2.2 Consensus size: 19
28392 ATTTTTTTAT
28402 TTTAATAATTCTTTTAATA
1 TTTAATAATTCTTTTAATA
28421 TTTAATAA-T-TTTTAATA
1 TTTAATAATTCTTTTAATA
28438 TTTA
1 TTTA
28442 TTTATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 12 0.57
18 1 0.05
19 8 0.38
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAATAATTCTTTTAATA
Found at i:30474 original size:3 final size:3
Alignment explanation
Indices: 30466--30506 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
30456 CTAGATAAAT
30466 ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30507 TAAGTTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:30529 original size:9 final size:9
Alignment explanation
Indices: 30515--30539 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
30505 TATAAGTTTT
30515 TATATATGA
1 TATATATGA
30524 TATATATGA
1 TATATATGA
30533 TATATAT
1 TATATAT
30540 AATAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (9 bp):
TATATATGA
Found at i:32253 original size:92 final size:92
Alignment explanation
Indices: 32096--32334 Score: 460
Period size: 92 Copynumber: 2.6 Consensus size: 92
32086 CTTTGTACTA
32096 TTTGCATTATTGGAGACAATTTCTGCAGAGATTCTTCATGATAACTTTGCAGACCTTCATAATTT
1 TTTGCATTATTGGAGACAATTTCTGCAGAGATTCTTCATGATAACTTTGCAGACCTTCATAATTT
32161 GGCTTTCTCTTCATCCAATGAGTAAGC
66 GGCTTTCTCTTCATCCAATGAGTAAGC
32188 TTTGCATTATTGGAGACAATTTCTGCAGAGATTCTTCATGATAACTTTGCAGACCTTCATAATTT
1 TTTGCATTATTGGAGACAATTTCTGCAGAGATTCTTCATGATAACTTTGCAGACCTTCATAATTT
*
32253 GGCTTTCTCTTCATCCAATGAGTCAGC
66 GGCTTTCTCTTCATCCAATGAGTAAGC
*
32280 TTTGCATTATTGGAGACAATATCTGCAGAGATTCTTCATGATAACTTTGCAGACC
1 TTTGCATTATTGGAGACAATTTCTGCAGAGATTCTTCATGATAACTTTGCAGACC
32335 ATTATTTTTC
Statistics
Matches: 145, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 145 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (92 bp):
TTTGCATTATTGGAGACAATTTCTGCAGAGATTCTTCATGATAACTTTGCAGACCTTCATAATTT
GGCTTTCTCTTCATCCAATGAGTAAGC
Found at i:32349 original size:20 final size:20
Alignment explanation
Indices: 32324--32364 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
32314 TTCATGATAA
32324 CTTTGCAGACCATTATTTTT
1 CTTTGCAGACCATTATTTTT
32344 CTTTGCAGACCATTATTTTT
1 CTTTGCAGACCATTATTTTT
32364 C
1 C
32365 CCTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.22, G:0.10, T:0.49
Consensus pattern (20 bp):
CTTTGCAGACCATTATTTTT
Done.