Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013129.1 Corchorus capsularis cultivar CVL-1 contig13150, 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: 44329
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:3023 original size:15 final size:16
Alignment explanation
Indices: 2996--3037 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
2986 TTTGAAATCT
*
2996 ATAAAAACAAACA-AA
1 ATAAAATCAAACATAA
*
3011 ATTAAATCAAACATAA
1 ATAAAATCAAACATAA
*
3027 GTAAAATCAAA
1 ATAAAATCAAA
3038 ACTAAAACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.69, C:0.12, G:0.02, T:0.17
Consensus pattern (16 bp):
ATAAAATCAAACATAA
Found at i:3483 original size:15 final size:16
Alignment explanation
Indices: 3451--3484 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3441 AAAGAAGAAT
*
3451 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
3467 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
3482 TAA
1 TAA
3485 GAAAGCAATC
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:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:4799 original size:19 final size:18
Alignment explanation
Indices: 4766--4801 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4756 TTGAAATAAT
4766 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
4784 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
4802 GAAATATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:6412 original size:34 final size:32
Alignment explanation
Indices: 6374--6441 Score: 82
Period size: 34 Copynumber: 2.1 Consensus size: 32
6364 CCTAAGATGC
6374 TTAAAAATAAAATCCTAAATCTAGAAAACATAAA
1 TTAAAAATAAAATCCT-AAT-TAGAAAACATAAA
** * *
6408 TTAAACTTAAAATCCTAATTTGAAAACCTAAA
1 TTAAAAATAAAATCCTAATTAGAAAACATAAA
6440 TT
1 TT
6442 GGTTTAGGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 13 0.43
33 3 0.10
34 14 0.47
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.29
Consensus pattern (32 bp):
TTAAAAATAAAATCCTAATTAGAAAACATAAA
Found at i:11906 original size:6 final size:6
Alignment explanation
Indices: 11895--11921 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
11885 ATTAATCTGC
11895 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
11922 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:14880 original size:11 final size:12
Alignment explanation
Indices: 14864--14894 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
14854 AAGAAGCTTA
14864 AAAAAAAAG-AG
1 AAAAAAAAGAAG
14875 AAAAAAAAGAAG
1 AAAAAAAAGAAG
14887 AAAAAAAA
1 AAAAAAAA
14895 ACTTGGCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAG
Found at i:14880 original size:12 final size:13
Alignment explanation
Indices: 14863--14895 Score: 52
Period size: 11 Copynumber: 2.7 Consensus size: 13
14853 GAAGAAGCTT
14863 AAAAAAAAAG-AG
1 AAAAAAAAAGAAG
14875 -AAAAAAAAGAAG
1 AAAAAAAAAGAAG
14887 AAAAAAAAA
1 AAAAAAAAA
14896 CTTGGCCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.47
12 2 0.11
13 8 0.42
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAG
Found at i:16088 original size:57 final size:57
Alignment explanation
Indices: 16011--16176 Score: 190
Period size: 59 Copynumber: 2.9 Consensus size: 57
16001 AATCTTGTTC
* * * *
16011 TTTTCAAATCCTAATCGAGGTCTCTAATCGAGAGTTTCTTGTTTCAAATTTTGTTTCA
1 TTTT-AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAAATCTAGTTCCA
* * * ** *
16069 TTTTAAATCCTATTTGAGGTCTTTAGTCGAGAGTTT-TCAATTCCAAAGTCTAGTTCCA
1 TTTTAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCT-TGTTTCAAA-TCTAGTTCCA
*
16127 TTTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAAATC
1 TTT-TAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAAATC
16177 AAGAGTTTTC
Statistics
Matches: 87, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
56 1 0.01
57 34 0.39
58 16 0.18
59 35 0.40
60 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.42
Consensus pattern (57 bp):
TTTTAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAAATCTAGTTCCA
Found at i:16147 original size:59 final size:58
Alignment explanation
Indices: 15995--16163 Score: 173
Period size: 57 Copynumber: 2.9 Consensus size: 58
15985 CTTGTTTCAT
* * * **
15995 TTCCAGAATCTTGTT-CTTTTCAAATCCTAATCGAGGTCTCTAATCGAGAG-TTTCTTG
1 TTCCA-AATCTAGTTCCATTTCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTTCTAA
* * * * * * * *
16052 TTTCAAATTTTGTTTCATTTTAAATCCTATTTGAGGTCTTTAGTCGAGAGTTTTC-AA
1 TTCCAAATCTAGTTCCATTTCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTTCTAA
16109 TTCCAAAGTCTAGTTCCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTT
1 TTCCAAA-TCTAGTTCCATTT-CAAATCCTAATCGAGGTCTCTAGTCGAGAGTTT
16164 CTTGTTTCAA
Statistics
Matches: 90, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
56 8 0.09
57 39 0.43
58 14 0.16
59 29 0.32
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.41
Consensus pattern (58 bp):
TTCCAAATCTAGTTCCATTTCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTTCTAA
Found at i:16330 original size:18 final size:18
Alignment explanation
Indices: 16296--16330 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16286 CGAGAGTTTC
*
16296 TTGTTTCAATTCTAAATT
1 TTGTTTCAATTCCAAATT
*
16314 TTGTTTCATTTCCAAAT
1 TTGTTTCAATTCCAAAT
16331 CCTAATCGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.14, G:0.06, T:0.54
Consensus pattern (18 bp):
TTGTTTCAATTCCAAATT
Found at i:16389 original size:310 final size:296
Alignment explanation
Indices: 16183--16725 Score: 661
Period size: 302 Copynumber: 1.8 Consensus size: 296
16173 AATCAAGAGT
* ** *
16183 TTTCAATTCTAAATCTTG-TTCTTTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTGTC-G-T
1 TTTCAATTCTAAATCTTGATTCATTTCAAATCCTAATCGAGGTCTCTAGTCGAGAGTT-TCTGTT
*
16245 TC-C-AAATCTTGTTC-TTTCAAATCCTAATCGAGGTCTCTAATCGAGAGTTTCTTGTTTCAATT
65 TCACTAAATCTTGTTCATTTCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATT
* *
16307 CTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTGTC-GTTCCAAGTT
130 CTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAATCGAGAGTT-TCTGTTCCAAATT
** * *
16371 TTGTTTTGTTTGAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTTCAATTCCAAAGTCTAGTTTC
194 TTGTTTCATTTGAAATCCTACTTGAGGTCTCTAGTCGAGAGTTTTCAATTCCAAAGTCTAGTTCC
16436 AATTCCAAATCCTAATCGAGGTCTCTAGTCGAGGGTTG
259 AATTCCAAATCCTAATCGAGGTCTCTAGTCGAGGGTTG
* * *
16474 TTTCAATTCTAAATTTTGATTCATTTCCAATCCTAATCGAGGTCTCTAGTCGAGGGTTTCTTGTT
1 TTTCAATTCTAAATCTTGATTCATTTCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTC-TGTT
* * *
16539 TCAATTCTAAATTTTGTTTCATTTCCAAACCCTAATCGAGGTCTCTAGTCGAGGGTTTCTTGTTT
65 TC-A--CTAAATCTTG-TTCATTT-CAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTT
** * *
16604 CAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCAATAATTGAGGGTTTCTTGTTTC
125 CAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAATCGAGAGTTTC-TG-TTC
* * * *
16669 AATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAATCGAG-GTTTTC
188 ----C-AAATTTTGTTTCATTT-GAAATCCTACTTGAGGTCTCTAGTCGAGAGTTTTC
16726 TTGTTTCAAT
Statistics
Matches: 207, Mismatches: 24, Indels: 24
0.81 0.09 0.09
Matches are distributed among these distances:
291 19 0.09
292 33 0.16
293 1 0.00
294 3 0.01
298 1 0.00
299 7 0.03
300 3 0.01
301 5 0.02
302 88 0.43
303 1 0.00
304 3 0.01
308 1 0.00
309 19 0.09
310 23 0.11
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (296 bp):
TTTCAATTCTAAATCTTGATTCATTTCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTGTTT
CACTAAATCTTGTTCATTTCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTC
TAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAATCGAGAGTTTCTGTTCCAAATTTT
GTTTCATTTGAAATCCTACTTGAGGTCTCTAGTCGAGAGTTTTCAATTCCAAAGTCTAGTTCCAA
TTCCAAATCCTAATCGAGGTCTCTAGTCGAGGGTTG
Found at i:16606 original size:64 final size:64
Alignment explanation
Indices: 16413--16772 Score: 541
Period size: 64 Copynumber: 5.7 Consensus size: 64
16403 AGTCGAGAGT
* * * *
16413 TTTCAATTCCAAAGTCTAGTTTCAATTCCAAATCCTAATCGAGGTCTCTAGTCGAGGG----TTG
1 TTTCAATTCTAAA-TTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGGGTTTCTTG
*
16474 TTTCAATTCTAAATTTTGATTCATTTCC-AATCCTAATCGAGGTCTCTAGTCGAGGGTTTCTTG
1 TTTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGGGTTTCTTG
*
16537 TTTCAATTCTAAATTTTGTTTCATTTCCAAACCCTAATCGAGGTCTCTAGTCGAGGGTTTCTTG
1 TTTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGGGTTTCTTG
** * *
16601 TTTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCAATAATTGAGGGTTTCTTG
1 TTTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGGGTTTCTTG
* *
16665 TTTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAATCGAGGTTTTCTTG
1 TTTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGGGTTTCTTG
** *
16729 TTTCAATTCTATGTTTTGTTTCATTTTCAAATCCTAATCGAGGT
1 TTTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGT
16773 TTACAAATCA
Statistics
Matches: 275, Mismatches: 19, Indels: 7
0.91 0.06 0.02
Matches are distributed among these distances:
59 28 0.10
60 11 0.04
61 12 0.04
63 30 0.11
64 194 0.71
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.43
Consensus pattern (64 bp):
TTTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGGGTTTCTTG
Found at i:16632 original size:18 final size:18
Alignment explanation
Indices: 16598--16632 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16588 CGAGGGTTTC
*
16598 TTGTTTCAATTCTAAATT
1 TTGTTTCAATTCCAAATT
*
16616 TTGTTTCATTTCCAAAT
1 TTGTTTCAATTCCAAAT
16633 CCTAATCGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.14, G:0.06, T:0.54
Consensus pattern (18 bp):
TTGTTTCAATTCCAAATT
Found at i:16676 original size:128 final size:128
Alignment explanation
Indices: 15927--16772 Score: 683
Period size: 128 Copynumber: 6.8 Consensus size: 128
15917 AGTCAAGAGA
* * ** * * *
15927 TTTCAATTCTAAATCTTG-TTC-TTTTCAAATCCTGCTTGAGGTCTCTGGTCGAGAGTTTCTTGT
1 TTTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGGGTTTCTTGT
* * * *
15990 TTCATTTCCAGAATCTTG-TTC-TTTTCAAATCCTAATCGAGGTCTCTAATCGAGAGTTTCTTG
66 TTCAATTCTA-AATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAATCGAGAGTTTCTTG
* * * * *
16052 --T---TTC-AAATTTTGTTTCATTT-TAAATCCTATTTGAGGTCTTTAGTCGAGAG-----T-T
1 TTTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGGGTTTCTTGT
* * * * *
16104 TTCAATTCCAAAGTCTAGTTCCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTG
66 TTCAATTCTAAA-TTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAATCGAGAGTTTCTTG
* * * ** *
16168 TTTCAAATC-AAGAGTTTTCAATTCTAAATCTTGTTCTTTTCAAATCCTGCTTGAGGTCTCTAGT
1 TTTCAATTCTAA-A-TTTT---GT-T---TCAT-TTC----CAAATCCTAATCGAGGTCTCTAGT
* *
16232 CGAGAGTTGTC--G-TTC----C-AAATCTTG-TTC-TTT-CAAATCCTAATCGAGGTCTCTAAT
52 CGAGGGTT-TCTTGTTTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAAT
16286 CGAGAGTTTCTTG
116 CGAGAGTTTCTTG
*
16299 TTTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTGTC--G
1 TTTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGGGTT-TCTTG
* ** * ** * *
16362 -TTC----C-AAGTTTTGTTTTGTTT-GAAATCCTGCTTGAGGTCTCTAGTCGAGAG-----T-
65 TTTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAATCGAGAGTTTCTTG
* * * *
16413 TTTCAATTCCAAAGTCTAGTTTCAATTCCAAATCCTAATCGAGGTCTCTAGTCGAGGG----TTG
1 TTTCAATTCTAAA-TTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGGGTTTCTTG
* * *
16474 TTTCAATTCTAAATTTTGATTCATTTCC-AATCCTAATCGAGGTCTCTAGTCGAGGGTTTCTTG
65 TTTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAATCGAGAGTTTCTTG
*
16537 TTTCAATTCTAAATTTTGTTTCATTTCCAAACCCTAATCGAGGTCTCTAGTCGAGGGTTTCTTGT
1 TTTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGGGTTTCTTGT
** * *
16602 TTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCAATAATTGAGGGTTTCTTG
66 TTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAATCGAGAGTTTCTTG
* *
16665 TTTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAATCGAGGTTTTCTTGT
1 TTTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGGGTTTCTTGT
** *
16730 TTCAATTCTATGTTTTGTTTCATTTTCAAATCCTAATCGAGGT
66 TTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGT
16773 TTACAAATCA
Statistics
Matches: 601, Mismatches: 65, Indels: 107
0.78 0.08 0.14
Matches are distributed among these distances:
112 1 0.00
113 5 0.01
114 26 0.04
115 44 0.07
116 39 0.06
117 1 0.00
118 80 0.13
119 9 0.01
120 59 0.10
121 7 0.01
122 4 0.01
123 49 0.08
124 12 0.02
126 2 0.00
127 32 0.05
128 133 0.22
130 7 0.01
131 47 0.08
132 5 0.01
133 2 0.00
134 4 0.01
135 3 0.00
136 27 0.04
140 3 0.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (128 bp):
TTTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGGGTTTCTTGT
TTCAATTCTAAATTTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAATCGAGAGTTTCTTG
Found at i:16696 original size:18 final size:18
Alignment explanation
Indices: 16662--16696 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16652 TGAGGGTTTC
*
16662 TTGTTTCAATTCTAAATT
1 TTGTTTCAATTCCAAATT
*
16680 TTGTTTCATTTCCAAAT
1 TTGTTTCAATTCCAAAT
16697 CCTAATCGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.14, G:0.06, T:0.54
Consensus pattern (18 bp):
TTGTTTCAATTCCAAATT
Found at i:17296 original size:15 final size:15
Alignment explanation
Indices: 17259--17301 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
17249 ATGGCATTCT
17259 GAAGAA-AA-AAAAA
1 GAAGAAGAAGAAAAA
17272 GAAGAAGAAGAGAAAA
1 GAAGAAGAAGA-AAAA
17288 GAA-AAGAAGAAAAA
1 GAAGAAGAAGAAAAA
17302 TATATTTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.22
14 6 0.22
15 8 0.30
16 7 0.26
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAGAAAAA
Found at i:20459 original size:21 final size:20
Alignment explanation
Indices: 20418--20474 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
20408 ATTATGAGCT
* **
20418 AATTTTAATTTAAAGGTTAA
1 AATTTTAATTAAAAGACTAA
20438 AATTTTGAATTAAAAGACTAA
1 AATTTT-AATTAAAAGACTAA
*
20459 ATTATTTATATTAAAA
1 AAT-TTTA-ATTAAAA
20475 ATCAACTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.20
21 14 0.47
22 10 0.33
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (20 bp):
AATTTTAATTAAAAGACTAA
Found at i:26387 original size:12 final size:12
Alignment explanation
Indices: 26370--26401 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
26360 ACCTGGCAAT
26370 TCGTGTTTCGTG
1 TCGTGTTTCGTG
26382 TCGTGTTTCGTG
1 TCGTGTTTCGTG
26394 TCGTGTTT
1 TCGTGTTT
26402 ACATAGGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.16, G:0.31, T:0.53
Consensus pattern (12 bp):
TCGTGTTTCGTG
Found at i:26627 original size:12 final size:12
Alignment explanation
Indices: 26610--26644 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
26600 ATTAACTAAA
26610 TTATATATAATT
1 TTATATATAATT
*
26622 TTATATAT-ATA
1 TTATATATAATT
26633 TTATATATAATT
1 TTATATATAATT
26645 AAAGATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTATATATAATT
Found at i:26820 original size:20 final size:21
Alignment explanation
Indices: 26783--26825 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
26773 AACCCGTTAA
*
26783 TTAAAGCGTGTCACTCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
*
26804 TTAAA-CGTGTTAATCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
26824 TT
1 TT
26826 GACACGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (21 bp):
TTAAAGCGTGTCAATCGTGTC
Found at i:26883 original size:42 final size:43
Alignment explanation
Indices: 26813--26895 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
26803 CTTAAACGTG
**
26813 TTAATCGTGTCTTGACACGATTACGACACGAAACACGATAATC
1 TTAATCGTGTCTCAACACGATTACGACACGAAACACGATAATC
*
26856 TTAATCGTGTC-CAACACGATT-CAGACACGAGACACGATAA
1 TTAATCGTGTCTCAACACGATTAC-GACACGAAACACGATAA
26896 GCCAAACACG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 1 0.03
42 24 0.67
43 11 0.31
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (43 bp):
TTAATCGTGTCTCAACACGATTACGACACGAAACACGATAATC
Found at i:27970 original size:21 final size:21
Alignment explanation
Indices: 27931--27970 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27921 ATGATTTAGG
* *
27931 GGTTACTAACGCCCTTTTTGA
1 GGTTACTAACACCCATTTTGA
*
27952 GGTTACTAACACTCATTTT
1 GGTTACTAACACCCATTTT
27971 TTTTCAAGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (21 bp):
GGTTACTAACACCCATTTTGA
Found at i:28089 original size:3 final size:3
Alignment explanation
Indices: 28076--28113 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
28066 GAAAGTATAT
*
28076 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28114 TAAAAAACAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:28883 original size:15 final size:16
Alignment explanation
Indices: 28853--28890 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
28843 CATAAGTCTT
28853 ACATAAGATCCAAATAA
1 ACATAAGA-CCAAATAA
28870 ACATAAGA-CAAATAA
1 ACATAAGACCAAATAA
*
28885 AAATAA
1 ACATAA
28891 AATGCATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
17 8 0.40
ACGTcount: A:0.66, C:0.13, G:0.05, T:0.16
Consensus pattern (16 bp):
ACATAAGACCAAATAA
Found at i:44302 original size:30 final size:30
Alignment explanation
Indices: 44266--44328 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
44256 AAGGGGTCAA
*
44266 ATGGCCGGTTGTGGCCGGATGGCCCATGCG
1 ATGGCCGGTTGTGGCCGGATGCCCCATGCG
*
44296 ATGGCCGGTTGTGGCCGGTTGCCCCATGCG
1 ATGGCCGGTTGTGGCCGGATGCCCCATGCG
44326 ATG
1 ATG
44329 T
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.10, C:0.27, G:0.41, T:0.22
Consensus pattern (30 bp):
ATGGCCGGTTGTGGCCGGATGCCCCATGCG
Done.