Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011359.1 Corchorus olitorius cultivar O-4 contig11392, 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: 16478
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Found at i:90 original size:35 final size:38
Alignment explanation
Indices: 5--182 Score: 150
Period size: 40 Copynumber: 4.5 Consensus size: 38
1 GGAT
*
5 GATGGGATCTTTCCCTAAATTAAAACTTCTGAAAAACTT
1 GATGGGATCTTTCCCTAAA-TAAAACTTCTGAAAAACTG
*
44 GATGGGATCTTTCCCTAAA-AAAACTT-TG-AAGACTG
1 GATGGGATCTTTCCCTAAATAAAACTTCTGAAAAACTG
* *
79 GATGGGATCTTTCCCTAAATTTTAAAAAACTTTTAAAAAGAAACTG
1 GATGGGATCTTTCCCTAAA---T--AAAACTTCT--GAA-AAACTG
* *
125 GATGGGATCTTTCCCTAAATCGGAAGAC-T-TGAACAAACTT
1 GATGGGATCTTTCCCTAAAT---AAAACTTCTGAA-AAACTG
165 GATGGGATCTTTCCCTAA
1 GATGGGATCTTTCCCTAA
183 TTTTGAAATC
Statistics
Matches: 117, Mismatches: 10, Indels: 23
0.78 0.07 0.15
Matches are distributed among these distances:
35 24 0.21
36 2 0.02
37 7 0.06
39 19 0.16
40 25 0.21
41 7 0.06
42 2 0.02
43 2 0.02
44 4 0.03
45 1 0.01
46 24 0.21
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (38 bp):
GATGGGATCTTTCCCTAAATAAAACTTCTGAAAAACTG
Found at i:253 original size:42 final size:43
Alignment explanation
Indices: 81--364 Score: 346
Period size: 42 Copynumber: 6.7 Consensus size: 43
71 GAAGACTGGA
* * * * ***
81 TGGGATCTTTCCCTAAATTTTAAAAAACTTTTAAAAAGAAACTGG
1 TGGGATCTTTCCCT-AATTTT-GAAATCTTTGAAAAATACTTTGG
* ** * *
126 ATGGGATCTTTCCCTAAATCGGAAGA-C-TTGAACAA-AC-TTGA
1 -TGGGATCTTTCCCTAATTTTGAA-ATCTTTGAAAAATACTTTGG
*
167 TGGGATCTTTCCCTAATTTTGAAATCCTTGAAAAATACTTTGG
1 TGGGATCTTTCCCTAATTTTGAAATCTTTGAAAAATACTTTGG
210 TGGGATCTTTCCCTAATTTTG-AATCTTTGAAAAATACTTTGG
1 TGGGATCTTTCCCTAATTTTGAAATCTTTGAAAAATACTTTGG
*
252 TGGGTTCTTTCCCTAATTTTGAAATCTTTGAAAAATACTTTGG
1 TGGGATCTTTCCCTAATTTTGAAATCTTTGAAAAATACTTTGG
* *
295 TGGAATCATTCCCTAATTTTG-AATCTTTGAAAAATACTTTGG
1 TGGGATCTTTCCCTAATTTTGAAATCTTTGAAAAATACTTTGG
337 TGGGATCTTTCCCTAATTTTGAAATCTT
1 TGGGATCTTTCCCTAATTTTGAAATCTT
365 AATGGGATCT
Statistics
Matches: 210, Mismatches: 21, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
39 1 0.00
40 21 0.10
41 9 0.04
42 83 0.40
43 75 0.36
44 3 0.01
45 4 0.02
46 14 0.07
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (43 bp):
TGGGATCTTTCCCTAATTTTGAAATCTTTGAAAAATACTTTGG
Found at i:363 original size:85 final size:85
Alignment explanation
Indices: 167--364 Score: 360
Period size: 85 Copynumber: 2.3 Consensus size: 85
157 ACAAACTTGA
* * *
167 TGGGATCTTTCCCTAATTTTGAAATCCTTGAAAAATACTTTGGTGGGATCTTTCCCTAATTTTGA
1 TGGGATCTTTCCCTAATTTTGAAATCTTTGAAAAATACTTTGGTGGAATCATTCCCTAATTTTGA
232 ATCTTTGAAAAATACTTTGG
66 ATCTTTGAAAAATACTTTGG
*
252 TGGGTTCTTTCCCTAATTTTGAAATCTTTGAAAAATACTTTGGTGGAATCATTCCCTAATTTTGA
1 TGGGATCTTTCCCTAATTTTGAAATCTTTGAAAAATACTTTGGTGGAATCATTCCCTAATTTTGA
317 ATCTTTGAAAAATACTTTGG
66 ATCTTTGAAAAATACTTTGG
337 TGGGATCTTTCCCTAATTTTGAAATCTT
1 TGGGATCTTTCCCTAATTTTGAAATCTT
365 AATGGGATCT
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 108 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (85 bp):
TGGGATCTTTCCCTAATTTTGAAATCTTTGAAAAATACTTTGGTGGAATCATTCCCTAATTTTGA
ATCTTTGAAAAATACTTTGG
Found at i:490 original size:50 final size:49
Alignment explanation
Indices: 387--492 Score: 148
Period size: 50 Copynumber: 2.2 Consensus size: 49
377 CCCTAAATTA
387 AAAAACTTGAAGAAACTGATGGGATCTTTCCCTAAATTTGAAAAACTTG
1 AAAAACTTGAAGAAACTGATGGGATCTTTCCCTAAATTTGAAAAACTTG
436 -AAAACTTGAA-AACTACTGGATGGGATCTTTCCCTAAA-TTG-AAAACTTTG
1 AAAAACTTGAAGAA--ACT-GATGGGATCTTTCCCTAAATTTGAAAAAC-TTG
485 AAAAACTT
1 AAAAACTT
493 CTTTTCGATT
Statistics
Matches: 52, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
47 2 0.04
48 15 0.29
49 9 0.17
50 26 0.50
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (49 bp):
AAAAACTTGAAGAAACTGATGGGATCTTTCCCTAAATTTGAAAAACTTG
Found at i:1210 original size:19 final size:19
Alignment explanation
Indices: 1188--1230 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1178 AATAAGACTT
*
1188 AAATCATAAATAAAAACCC
1 AAATAATAAATAAAAACCC
* *
1207 AAATAATAAATAGAAGCCC
1 AAATAATAAATAAAAACCC
1226 AAATA
1 AAATA
1231 TGTTGTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.63, C:0.16, G:0.05, T:0.16
Consensus pattern (19 bp):
AAATAATAAATAAAAACCC
Found at i:1714 original size:85 final size:85
Alignment explanation
Indices: 1571--1740 Score: 331
Period size: 85 Copynumber: 2.0 Consensus size: 85
1561 CTTCACAAAT
*
1571 CACCCTAAATCTAAGGAACCTGCGACCTAAAGCCATCGTCGGTCCTTCTTTTTTCTTAACTTGAA
1 CACCCTAAATCTAAGGAACCTACGACCTAAAGCCATCGTCGGTCCTTCTTTTTTCTTAACTTGAA
1636 CACAGACTTAAAACAATGAA
66 CACAGACTTAAAACAATGAA
1656 CACCCTAAATCTAAGGAACCTACGACCTAAAGCCATCGTCGGTCCTTCTTTTTTCTTAACTTGAA
1 CACCCTAAATCTAAGGAACCTACGACCTAAAGCCATCGTCGGTCCTTCTTTTTTCTTAACTTGAA
1721 CACAGACTTAAAACAATGAA
66 CACAGACTTAAAACAATGAA
1741 ATCCCAATCC
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (85 bp):
CACCCTAAATCTAAGGAACCTACGACCTAAAGCCATCGTCGGTCCTTCTTTTTTCTTAACTTGAA
CACAGACTTAAAACAATGAA
Found at i:4040 original size:22 final size:21
Alignment explanation
Indices: 4012--4068 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 21
4002 TGTTATGTTA
4012 TACTAAATGCAAAAAGTGAATT
1 TACTAAATGCAAAAAGTGAA-T
*
4034 TACTAAATGCCAAAAGTGAAT
1 TACTAAATGCAAAAAGTGAAT
*
4055 GACATAAATGCAAA
1 TAC-TAAATGCAAA
4069 TGTAGAAGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 3 0.10
22 28 0.90
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.23
Consensus pattern (21 bp):
TACTAAATGCAAAAAGTGAAT
Found at i:4418 original size:63 final size:62
Alignment explanation
Indices: 4333--4493 Score: 223
Period size: 63 Copynumber: 2.6 Consensus size: 62
4323 TCCAATTCGT
* * * *
4333 TCTTAAAACTTTTTTCACGAACTGTCTTCAGAACCTATCTTCGTGAACTGTCTTAAGATTCAC
1 TCTTAAATCTTTTTT-AGGAACTGTCTTCAGAACCCATCTCCGTGAACTGTCTTAAGATTCAC
* *
4396 TCTTAATTGCTTTTTTAGGAACTGTCTTCAGAACCCATCTCCGTGAACTGTCTTCAGATTCAC
1 TCTTAAAT-CTTTTTTAGGAACTGTCTTCAGAACCCATCTCCGTGAACTGTCTTAAGATTCAC
* **
4459 TCTTAAATATCATTTAGGAACTGTCTTCAGAACCC
1 TCTTAAATCTTTTTTAGGAACTGTCTTCAGAACCC
4494 GTCTATGAGC
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
62 24 0.28
63 56 0.64
64 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.37
Consensus pattern (62 bp):
TCTTAAATCTTTTTTAGGAACTGTCTTCAGAACCCATCTCCGTGAACTGTCTTAAGATTCAC
Found at i:4582 original size:58 final size:58
Alignment explanation
Indices: 4407--4582 Score: 187
Period size: 58 Copynumber: 3.0 Consensus size: 58
4397 CTTAATTGCT
* * *
4407 TTTTTAGGAACTGTCTTCAGAACCCATCTCCGTGAACTGTCTTCAGAT-TCACTCTTAAATA
1 TTTTTAGGAACTGTCTTCAGAACCCATCT--ATGAGCTGTCTTCAG-TCTCAATCTT-AATA
* * * *
4468 TCATTTAGGAACTGTCTTCAGAACCCGTCTATGAGCAGTCTTCA-TACTCATTCTTAATA
1 T-TTTTAGGAACTGTCTTCAGAACCCATCTATGAGCTGTCTTCAGT-CTCAATCTTAATA
* *
4527 TTTTTCAGGAACTGTCTTCAG-ATCCATCTATGAGTTGTCTTCAGTCTCAATCTTAA
1 TTTTT-AGGAACTGTCTTCAGAACCCATCTATGAGCTGTCTTCAGTCTCAATCTTAA
4583 ATGGACCGCC
Statistics
Matches: 98, Mismatches: 12, Indels: 13
0.80 0.10 0.11
Matches are distributed among these distances:
58 32 0.33
59 21 0.21
60 18 0.18
61 1 0.01
62 26 0.27
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.38
Consensus pattern (58 bp):
TTTTTAGGAACTGTCTTCAGAACCCATCTATGAGCTGTCTTCAGTCTCAATCTTAATA
Found at i:4661 original size:60 final size:60
Alignment explanation
Indices: 4562--4737 Score: 212
Period size: 60 Copynumber: 2.9 Consensus size: 60
4552 ATCTATGAGT
* * * **
4562 TGTCTTCAG-TCTCAATCTTAAATGGACCGCCTTCAATCCATCTTTTAAAATCTTCAATGATC
1 TGTCTTCAGAT-TC-AT-TTAAAAGGACCGTCTTCGATCCATCTTACAAAATCTTCAATGATC
4624 TGTCTTCAGATTCATTTAAAAGGACCGTCTTCGATCCATCTTACAAAATCTTCAATGATC
1 TGTCTTCAGATTCATTTAAAAGGACCGTCTTCGATCCATCTTACAAAATCTTCAATGATC
* * *
4684 TGTCGTCAGATCCATCTAAAAGGACCGTCTTCCGATCCATCCTT-CAAAAATCTT
1 TGTCTTCAGATTCATTTAAAAGGACCGTCTT-CGATCCAT-CTTAC-AAAATCTT
4738 TCGTGATCGT
Statistics
Matches: 102, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
60 68 0.67
61 11 0.11
62 22 0.22
63 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.34
Consensus pattern (60 bp):
TGTCTTCAGATTCATTTAAAAGGACCGTCTTCGATCCATCTTACAAAATCTTCAATGATC
Found at i:5980 original size:5 final size:6
Alignment explanation
Indices: 5958--6002 Score: 54
Period size: 6 Copynumber: 7.0 Consensus size: 6
5948 CACCCTAGAG
*
5958 CTTTAT CTTTTT CTTTTT CTTTTT CTTTTGTT CTTTTT CTATTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT C-TTT-TT CTTTTT CT-TTTT
6003 TTCCTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
6 22 0.63
7 10 0.29
8 3 0.09
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (6 bp):
CTTTTT
Found at i:6615 original size:10 final size:10
Alignment explanation
Indices: 6600--6629 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
6590 TTTGGCTGAG
6600 TTTTTTCTTT
1 TTTTTTCTTT
6610 TTTTTTCTTT
1 TTTTTTCTTT
6620 TTTTTTCTTT
1 TTTTTTCTTT
6630 GAGTTGAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:7345 original size:7 final size:7
Alignment explanation
Indices: 7325--7374 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
7315 ATTCAATTTC
*
7325 TCTTTTC
1 TCTTTTT
7332 TCTTTTT
1 TCTTTTT
7339 TCTTTTT
1 TCTTTTT
*
7346 TATTCTTT
1 TCTT-TTT
7354 TCATTTTT
1 TC-TTTTT
7362 TCTTTTT
1 TCTTTTT
*
7369 TATTTT
1 TCTTTT
7375 CTAATGGGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
7 26 0.70
8 9 0.24
9 2 0.05
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (7 bp):
TCTTTTT
Found at i:7364 original size:23 final size:24
Alignment explanation
Indices: 7325--7372 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
7315 ATTCAATTTC
*
7325 TCTTTTCTCTTTTTTCTTTTTTAT
1 TCTTTTCTATTTTTTCTTTTTTAT
7349 TCTTTTC-ATTTTTTCTTTTTTAT
1 TCTTTTCTATTTTTTCTTTTTTAT
7372 T
1 T
7373 TTCTAATGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (24 bp):
TCTTTTCTATTTTTTCTTTTTTAT
Found at i:11402 original size:23 final size:21
Alignment explanation
Indices: 11358--11402 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
11348 TAGCCATTTT
*
11358 TTCTCATTTGTAAATGCTCTG
1 TTCTCATTTGTAAATGCCCTG
*
11379 TTCTCATTGCTGTTAATGCCCTG
1 TTCTCATT--TGTAAATGCCCTG
11402 T
1 T
11403 ACTGTTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
23 12 0.60
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.47
Consensus pattern (21 bp):
TTCTCATTTGTAAATGCCCTG
Found at i:12932 original size:29 final size:29
Alignment explanation
Indices: 12898--13260 Score: 318
Period size: 29 Copynumber: 12.5 Consensus size: 29
12888 GAACCCAGAG
12898 TATGCAAAAATGACCAAAATGCCCCTGGA
1 TATGCAAAAATGACCAAAATGCCCCTGGA
* ** **
12927 CATGCAAAGGTGACCAAAATGCCCCCAGA
1 TATGCAAAAATGACCAAAATGCCCCTGGA
* * *
12956 TATGCAAAAATTACCATAATGCCCCTAGA
1 TATGCAAAAATGACCAAAATGCCCCTGGA
* **
12985 TATGCAAAAATTACCCTAATGCCCCTGGA
1 TATGCAAAAATGACCAAAATGCCCCTGGA
* ** *
13014 TATGTAAAAATGACCATCATGTCCCTGGA
1 TATGCAAAAATGACCAAAATGCCCCTGGA
* *
13043 TATGCAAAAATGACCATAATGTCCCTGGA
1 TATGCAAAAATGACCAAAATGCCCCTGGA
* * * * *
13072 TCTGTAAATACGACCAAAATG-CCTTCGGA
1 TATGCAAAAATGACCAAAATGCCCCT-GGA
* * * *
13101 TGTGCAAAAACGATCAAAATGCCCCTGAA
1 TATGCAAAAATGACCAAAATGCCCCTGGA
* *
13130 TTGTGCAAAAATGACCAAAATGCCCTTGGA
1 -TATGCAAAAATGACCAAAATGCCCCTGGA
** *
13160 TATGTGAAAATGACCAAAATGCCCTTGGA
1 TATGCAAAAATGACCAAAATGCCCCTGGA
* ** * *
13189 TTTGCGTAAATGATCAAAATGCTCCC-GAA
1 TATGCAAAAATGACCAAAATGC-CCCTGGA
* *
13218 TGTGCAAAAATGACCAAAATGCCCTTGGA
1 TATGCAAAAATGACCAAAATGCCCCTGGA
* *
13247 TGTAC-AAAATGACC
1 TATGCAAAAATGACC
13261 TAAGTGCCAA
Statistics
Matches: 277, Mismatches: 52, Indels: 11
0.81 0.15 0.03
Matches are distributed among these distances:
28 14 0.05
29 233 0.84
30 30 0.11
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (29 bp):
TATGCAAAAATGACCAAAATGCCCCTGGA
Found at i:13160 original size:88 final size:87
Alignment explanation
Indices: 13045--13247 Score: 270
Period size: 88 Copynumber: 2.3 Consensus size: 87
13035 TCCCTGGATA
* *
13045 TGCAAAAATGACCATAATGTCCC-TGGATCTGT-AAATACGACCAAAATG-CCTTCGGATGTGCA
1 TGCAAAAATGACCAAAATG-CCCTTGGATATGTGAAA-ACGACCAAAATGCCCTT-GGATGTGCA
13107 AAAACGATCAAAATGC-CCCTGAATTG
63 AAAACGATCAAAATGCTCCC-GAA-TG
* * **
13133 TGCAAAAATGACCAAAATGCCCTTGGATATGTGAAAATGACCAAAATGCCCTTGGATTTGCGTAA
1 TGCAAAAATGACCAAAATGCCCTTGGATATGTGAAAACGACCAAAATGCCCTTGGATGTGCAAAA
*
13198 ATGATCAAAATGCTCCCGAATG
66 ACGATCAAAATGCTCCCGAATG
13220 TGCAAAAATGACCAAAATGCCCTTGGAT
1 TGCAAAAATGACCAAAATGCCCTTGGAT
13248 GTACAAAATG
Statistics
Matches: 104, Mismatches: 7, Indels: 9
0.87 0.06 0.08
Matches are distributed among these distances:
87 33 0.32
88 61 0.59
89 10 0.10
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (87 bp):
TGCAAAAATGACCAAAATGCCCTTGGATATGTGAAAACGACCAAAATGCCCTTGGATGTGCAAAA
ACGATCAAAATGCTCCCGAATG
Found at i:13233 original size:146 final size:146
Alignment explanation
Indices: 12898--13255 Score: 332
Period size: 146 Copynumber: 2.5 Consensus size: 146
12888 GAACCCAGAG
* * *** *** * *
12898 TATGCAAAAATGACCAAAATGCCCCTGGA-CATGCAAAGGTGACCAAAATGCCCCCAGATATGCA
1 TATGCAAAAATGACCAAAATGTCCCTGAATC-TGCAAAAACGACCAAAATGCCCTTGGATGTACA
** * * * * **
12962 AAAATTACCATAATGCCCCT-AGA-TATGCAAAAATTACCCTAATGCCCCTGGATATGTAAAAAT
65 AAAACGATCAAAATGCCCCTGA-ATTGTGCAAAAATGACCAAAATGCCCCTGGATATGTAAAAAT
**
13025 GACCATCATGTCCCTGGA
129 GACCAAAATGTCCCTGGA
* * * * *
13043 TATGCAAAAATGACCATAATGTCCCTGGATCTGTAAATACGACCAAAATG-CCTTCGGATGTGCA
1 TATGCAAAAATGACCAAAATGTCCCTGAATCTGCAAAAACGACCAAAATGCCCTT-GGATGTACA
* *
13107 AAAACGATCAAAATGCCCCTGAATTGTGCAAAAATGACCAAAATGCCCTTGGATATGTGAAAATG
65 AAAACGATCAAAATGCCCCTGAATTGTGCAAAAATGACCAAAATGCCCCTGGATATGTAAAAATG
13172 ACCAAAATG-CCCTTGGA
130 ACCAAAATGTCCC-TGGA
* ** * * *
13189 TTTGCGTAAATGATCAAAATGCTCCC-GAATGTGCAAAAATGACCAAAATGCCCTTGGATGTACA
1 TATGCAAAAATGACCAAAATG-TCCCTGAATCTGCAAAAACGACCAAAATGCCCTTGGATGTACA
13253 AAA
65 AAA
13256 TGACCTAAGT
Statistics
Matches: 173, Mismatches: 33, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
144 2 0.01
145 69 0.40
146 94 0.54
147 8 0.05
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (146 bp):
TATGCAAAAATGACCAAAATGTCCCTGAATCTGCAAAAACGACCAAAATGCCCTTGGATGTACAA
AAACGATCAAAATGCCCCTGAATTGTGCAAAAATGACCAAAATGCCCCTGGATATGTAAAAATGA
CCAAAATGTCCCTGGA
Found at i:14140 original size:91 final size:91
Alignment explanation
Indices: 13755--14565 Score: 945
Period size: 91 Copynumber: 9.0 Consensus size: 91
13745 ATCTGAAGAG
* * *
13755 GCAATAATCCT-AAACCAGGATTAAAAAATAAAGCACTGATCCT-AAACCAGGATTGAAATAAAG
1 GCAATGATCCTCAAA-CAGGATT--AAAATAAAGCAATGATCCTCAAA-CAGGATTAAAATAAAG
13818 C-AATGATCCTCAACCAGGATTAAAATAAA
62 CAAATGATCCTCAACCAGGATTAAAATAAA
* *
13847 GCAATGATCCTCAACCAGGATTAAAAT-AAGCAACGATCCTCAAACAGGATTAAAATAAAGC-AA
1 GCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAAA
13910 TGATCCTCAACCAGGATTAAAAT-AA
66 TGATCCTCAACCAGGATTAAAATAAA
* * *
13935 GCAACGATCCTCAAACAGGATTAAAATACAGCAATGATCCTCAACCAGGATTAAAAT-AAGC-AA
1 GCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAAA
* * *
13998 CGATCCTCAAACAGGATTAAAATGAA
66 TGATCCTCAACCAGGATTAAAATAAA
* * * *
14024 GCAATGATCCTCAACCAGGATTAAAATAAAACAACGATCCTCAAACAAGATTAAAATAAAGCAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAAA
*
14089 T-ATCCTCAACCAGGATTAAAAATGAA
66 TGATCCTCAACCAGGATT-AAAATAAA
* * ** * * *
14115 GTAATGATCCTCAAACAGGATTAAAATGAAGCAATGATCCTTGACCAGGAATAAAATAAAAC-AA
1 GCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAAA
* *
14179 CGATCCTCAAACAGGATTAAAATAAA
66 TGATCCTCAACCAGGATTAAAATAAA
* * * * *
14205 GCAAAT-ATCCTCAACCAGGATTAAAAATGAAGTAATGATCGTCAAACAGGATTAAAATGAAGC-
1 GC-AATGATCCTCAAACAGGATT-AAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAGCA
*
14268 ATTGATCCTCAACCAGGATTAAAATAAA
64 AATGATCCTCAACCAGGATTAAAATAAA
* * * * *
14296 ACAACGATCCTCAAACAGGATTAAAATAAAGCAAAT-ATCCTCAACCAGGATTGAAAATGAAG-T
1 GCAATGATCCTCAAACAGGATTAAAATAAAGC-AATGATCCTCAAACAGGATT-AAAATAAAGCA
*
14359 AATGATCCTCAACCAGGATTGAAAATGAA
64 AATGATCCTCAACCAGGATT-AAAATAAA
* * * *
14388 GTAATGATCCTCAAACAGGATTAAAATGAAGTAATGATCCTCAAACAGGATTAAAATAAAAC-AA
1 GCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAAA
* * *
14452 CGATCCTCAAACAGGATTCAAATAAA
66 TGATCCTCAACCAGGATTAAAATAAA
* * * * *
14478 GCAAAT-ATCCTCAACCAGGATTAAAAATGAAGTAATGATCCTCAAACAGGATTAAAATGAAG-T
1 GC-AATGATCCTCAAACAGGATT-AAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAGCA
*
14541 AATGATCCTCAAACAGGATTAAAAT
64 AATGATCCTCAACCAGGATTAAAAT
14566 GAGCAGATAA
Statistics
Matches: 624, Mismatches: 75, Indels: 41
0.84 0.10 0.06
Matches are distributed among these distances:
88 54 0.09
89 130 0.21
90 98 0.16
91 274 0.44
92 66 0.11
93 2 0.00
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (91 bp):
GCAATGATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAAACAGGATTAAAATAAAGCAAA
TGATCCTCAACCAGGATTAAAATAAA
Found at i:14150 original size:121 final size:120
Alignment explanation
Indices: 13761--14565 Score: 1102
Period size: 121 Copynumber: 6.7 Consensus size: 120
13751 AGAGGCAATA
* * * * *
13761 ATCCT-AAACCAGGATTAAAAAATAAAGCACTGATCCTAAACCAGGATTGAAATAAAGCAATGAT
1 ATCCTCAAA-CAGGATT--AAAATGAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAACGAT
* * *
13825 CCTCAACCAGGATTAAAATAAAGC-AATGATCCTCAACCAGGATTAAAAT-AAGCAACG
63 CCTCAAACAGGATTAAAATAAAGCAAAT-ATCCTCAACCAGGATTAAAATGAAGTAATG
*
13882 ATCCTCAAACAGGATTAAAATAAAGCAATGATCCTCAACCAGGATTAAAAT-AAGCAACGATCCT
1 ATCCTCAAACAGGATTAAAATGAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAACGATCCT
* * *
13946 CAAACAGGATTAAAATACAGC-AATGATCCTCAACCAGGATTAAAAT-AAGCAACG
66 CAAACAGGATTAAAATAAAGCAAAT-ATCCTCAACCAGGATTAAAATGAAGTAATG
*
14000 ATCCTCAAACAGGATTAAAATGAAGCAATGATCCTCAACCAGGATTAAAATAAAACAACGATCCT
1 ATCCTCAAACAGGATTAAAATGAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAACGATCCT
*
14065 CAAACAAGATTAAAATAAAGCAAATATCCTCAACCAGGATTAAAAATGAAGTAATG
66 CAAACAGGATTAAAATAAAGCAAATATCCTCAACCAGGATT-AAAATGAAGTAATG
** * *
14121 ATCCTCAAACAGGATTAAAATGAAGCAATGATCCTTGACCAGGAATAAAATAAAACAACGATCCT
1 ATCCTCAAACAGGATTAAAATGAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAACGATCCT
14186 CAAACAGGATTAAAATAAAGCAAATATCCTCAACCAGGATTAAAAATGAAGTAATG
66 CAAACAGGATTAAAATAAAGCAAATATCCTCAACCAGGATT-AAAATGAAGTAATG
* * *
14242 ATCGTCAAACAGGATTAAAATGAAGCATTGATCCTCAACCAGGATTAAAATAAAACAACGATCCT
1 ATCCTCAAACAGGATTAAAATGAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAACGATCCT
14307 CAAACAGGATTAAAATAAAGCAAATATCCTCAACCAGGATTGAAAATGAAGTAATG
66 CAAACAGGATTAAAATAAAGCAAATATCCTCAACCAGGATT-AAAATGAAGTAATG
* * * * * *
14363 ATCCTCAACCAGGATTGAAAATGAAGTAATGATCCTCAAACAGGATTAAAATGAAGTAATGATCC
1 ATCCTCAAACAGGATT-AAAATGAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAACGATCC
* ** * * * *
14428 TCAAACAGGATTAAAATAAAACAACGATCCTCAAACAGGATTCAAATAAAGCAAAT-
65 TCAAACAGGATTAAAATAAAGCAAATATCCTCAACCAGGATTAAAATGAAG-TAATG
* * * * * *
14484 ATCCTCAACCAGGATTAAAAATGAAGTAATGATCCTCAAACAGGATTAAAATGAAGTAATGATCC
1 ATCCTCAAACAGGATT-AAAATGAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAACGATCC
14549 TCAAACAGGATTAAAAT
65 TCAAACAGGATTAAAAT
14566 GAGCAGATAA
Statistics
Matches: 638, Mismatches: 39, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
118 114 0.18
119 79 0.12
120 8 0.01
121 352 0.55
122 85 0.13
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (120 bp):
ATCCTCAAACAGGATTAAAATGAAGCAATGATCCTCAACCAGGATTAAAATAAAGCAACGATCCT
CAAACAGGATTAAAATAAAGCAAATATCCTCAACCAGGATTAAAATGAAGTAATG
Found at i:14567 original size:30 final size:30
Alignment explanation
Indices: 13755--14565 Score: 983
Period size: 30 Copynumber: 26.9 Consensus size: 30
13745 ATCTGAAGAG
*
13755 GCAATAATCCT-AAACCAGGATTAAAAAATAAA
1 GCAATGATCCTCAAA-CAGGATT--AAAATAAA
* *
13787 GCACTGATCCT-AAACCAGGATTGAAATAAA
1 GCAATGATCCTCAAA-CAGGATTAAAATAAA
*
13817 GCAATGATCCTCAACCAGGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
13847 GCAATGATCCTCAACCAGGATTAAAAT-AA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
13876 GCAACGATCCTCAAACAGGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
13906 GCAATGATCCTCAACCAGGATTAAAAT-AA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* *
13935 GCAACGATCCTCAAACAGGATTAAAATACA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
13965 GCAATGATCCTCAACCAGGATTAAAAT-AA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* *
13994 GCAACGATCCTCAAACAGGATTAAAATGAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
14024 GCAATGATCCTCAACCAGGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* * *
14054 ACAACGATCCTCAAACAAGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* *
14084 GCAAAT-ATCCTCAACCAGGATTAAAAATGAA
1 GC-AATGATCCTCAAACAGGATT-AAAATAAA
* *
14115 GTAATGATCCTCAAACAGGATTAAAATGAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
** * *
14145 GCAATGATCCTTGACCAGGAATAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* *
14175 ACAACGATCCTCAAACAGGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* *
14205 GCAAAT-ATCCTCAACCAGGATTAAAAATGAA
1 GC-AATGATCCTCAAACAGGATT-AAAATAAA
* * *
14236 GTAATGATCGTCAAACAGGATTAAAATGAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* *
14266 GCATTGATCCTCAACCAGGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* *
14296 ACAACGATCCTCAAACAGGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* *
14326 GCAAAT-ATCCTCAACCAGGATTGAAAATGAA
1 GC-AATGATCCTCAAACAGGATT-AAAATAAA
* * *
14357 GTAATGATCCTCAACCAGGATTGAAAATGAA
1 GCAATGATCCTCAAACAGGATT-AAAATAAA
* *
14388 GTAATGATCCTCAAACAGGATTAAAATGAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
14418 GTAATGATCCTCAAACAGGATTAAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* * *
14448 ACAACGATCCTCAAACAGGATTCAAATAAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
* *
14478 GCAAAT-ATCCTCAACCAGGATTAAAAATGAA
1 GC-AATGATCCTCAAACAGGATT-AAAATAAA
* *
14509 GTAATGATCCTCAAACAGGATTAAAATGAA
1 GCAATGATCCTCAAACAGGATTAAAATAAA
*
14539 GTAATGATCCTCAAACAGGATTAAAAT
1 GCAATGATCCTCAAACAGGATTAAAAT
14566 GAGCAGATAA
Statistics
Matches: 685, Mismatches: 78, Indels: 34
0.86 0.10 0.04
Matches are distributed among these distances:
29 80 0.12
30 454 0.66
31 131 0.19
32 20 0.03
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (30 bp):
GCAATGATCCTCAAACAGGATTAAAATAAA
Found at i:14901 original size:35 final size:35
Alignment explanation
Indices: 14833--15306 Score: 401
Period size: 36 Copynumber: 13.5 Consensus size: 35
14823 CATTTTGCAG
* *
14833 TCAATTGAAATAAACTGCAGAGAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGA-AAGATCGCCCTGGA
* * * *
14869 TCTACTGAAGTAAATTGAGGAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
** * *
14904 TCAA-T-TCA-AAA-T--A-AAAGAACGCCCTCGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* *
14932 TCAACTGAAATAAACTGAAGAAAAGATTGCCCCGGA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
* *
14968 TCAATTGAAATAAACTGAAGAAAAGATCACCCTGGA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
* *
15004 TCAATTGAAATAAACTGAAGAAAGGATCGTCCTGGA
1 TCAACTGAAATAAACTGAAGAAA-GATCGCCCTGGA
* *
15040 TCAA-TTAATATAAACTGAAGAAAGGATCGCCCTAGA
1 TCAACTGAA-ATAAACTGAAGAAA-GATCGCCCTGGA
** * * *
15076 TCAACTGAAATAAACTGAA-ATGGGACCACCCTGGG
1 TCAACTGAAATAAACTGAAGA-AAGATCGCCCTGGA
* * * *
15111 TCAACTGAAATGAATTGAACAAGGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * *
15146 TCAAACTGAAATAAACTGAA-ATAGGACCACCCTGGG
1 TC-AACTGAAATAAACTGAAGA-AAGATCGCCCTGGA
* * * *
15182 TCAACTGAAATGAATTGAATAAGGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * *
15217 TCAACTGAAGTGAATTGAAGATAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGA-AAGATCGCCCTGGA
* * * *
15253 TCAATTGAAATAAACTGAATAAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
*
15288 TCAACTGAAATGAACTGAA
1 TCAACTGAAATAAACTGAA
15307 ACATCTAAAA
Statistics
Matches: 358, Mismatches: 63, Indels: 35
0.79 0.14 0.08
Matches are distributed among these distances:
28 17 0.05
29 1 0.00
30 1 0.00
31 4 0.01
32 4 0.01
34 2 0.01
35 136 0.38
36 190 0.53
37 3 0.01
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (35 bp):
TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
Found at i:14979 original size:63 final size:63
Alignment explanation
Indices: 14855--14981 Score: 157
Period size: 63 Copynumber: 2.0 Consensus size: 63
14845 AACTGCAGAG
* * * * * * *
14855 AAGATCGCCCTGGATCTACTGAAGTAAATTGAGGAAAGATCGCCCTGGATCAATTCAAAATAA
1 AAGAACGCCCTCGATCAACTGAAATAAACTGAGAAAAGATCGCCCCGGATCAATTCAAAATAA
* *
14918 AAGAACGCCCTCGATCAACTGAAATAAACTGAAGAAAAGATTGCCCCGGATCAATT-GAAATAA
1 AAGAACGCCCTCGATCAACTGAAATAAACTG-AGAAAAGATCGCCCCGGATCAATTCAAAATAA
14981 A
1 A
14982 CTGAAGAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 33 0.61
64 21 0.39
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.20
Consensus pattern (63 bp):
AAGAACGCCCTCGATCAACTGAAATAAACTGAGAAAAGATCGCCCCGGATCAATTCAAAATAA
Found at i:15161 original size:71 final size:70
Alignment explanation
Indices: 14923--15307 Score: 331
Period size: 71 Copynumber: 5.4 Consensus size: 70
14913 AATAAAAGAA
* * * *** * * * * *
14923 CGCCCTCGATCAACTGAAATAAACTGAAGAAAAGATTGCCCCGGATCAATTGAAATAAACTGAAG
1 CGCCCTGGATCAACTGAAATAAACTGAA-ATAGGACCACCCTGGGTCAACTGAAATGAATTGAA-
* *
14988 AAAAGAT
64 TAAGGAT
* * * * ** * * * *
14995 CACCCTGGATCAATTGAAATAAACTGAAGAAAGGATCGTCCTGGATCAA-TTAATATAAACTGAA
1 CGCCCTGGATCAACTGAAATAAACTGAA-ATAGGACCACCCTGGGTCAACTGAA-ATGAATTGAA
*
15059 GAAAGGAT
64 -TAAGGAT
* * *
15067 CGCCCTAGATCAACTGAAATAAACTGAAATGGGACCACCCTGGGTCAACTGAAATGAATTGAACA
1 CGCCCTGGATCAACTGAAATAAACTGAAATAGGACCACCCTGGGTCAACTGAAATGAATTGAATA
15132 AGGAT
66 AGGAT
15137 CGCCCTGGATCAAACTGAAATAAACTGAAATAGGACCACCCTGGGTCAACTGAAATGAATTGAAT
1 CGCCCTGGATC-AACTGAAATAAACTGAAATAGGACCACCCTGGGTCAACTGAAATGAATTGAAT
15202 AAGGAT
65 AAGGAT
* * * * * * * * * *
15208 CGCCCTGGATCAACTGAAGTGAATTGAAGATAAGATCGCCCTGGATCAATTGAAATAAACTGAAT
1 CGCCCTGGATCAACTGAAATAAACTGAA-ATAGGACCACCCTGGGTCAACTGAAATGAATTGAAT
* *
15273 AAAGAC
65 AAGGAT
* *
15279 CGCCCTGGGTCAACTGAAATGAACTGAAA
1 CGCCCTGGATCAACTGAAATAAACTGAAA
15308 CATCTAAAAT
Statistics
Matches: 269, Mismatches: 40, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
70 31 0.12
71 151 0.56
72 87 0.32
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.20
Consensus pattern (70 bp):
CGCCCTGGATCAACTGAAATAAACTGAAATAGGACCACCCTGGGTCAACTGAAATGAATTGAATA
AGGAT
Found at i:15187 original size:106 final size:106
Alignment explanation
Indices: 14923--15307 Score: 393
Period size: 106 Copynumber: 3.6 Consensus size: 106
14913 AATAAAAGAA
* ** * *
14923 CGCCCTCGATCAACTGAAATAAACTGAAGAAAAGATTGCCCCGGATCAATTGAAATAAACTGAAG
1 CGCCCTGGATCAACTGAAATAAACTGAAGAAAAGACCGCCCTGGATCAACTGAAATAAACTGAA-
* * * * *
14988 AAAAGATCACCCTGGATCAATTGAAATAAACTGAAGAAAGGAT
65 ATAGGATCACCCTGGATCAACTGAAATGAATTGAA-AAAGGAT
* * * * *
15031 CGTCCTGGATCAA-TTAATATAAACTGAAGAAAGGATCGCCCTAGATCAACTGAAATAAACTGAA
1 CGCCCTGGATCAACTGAA-ATAAACTGAAGAAAAGACCGCCCTGGATCAACTGAAATAAACTGAA
* * * *
15095 ATGGGACCACCCTGGGTCAACTGAAATGAATTGAACAAGGAT
65 ATAGGATCACCCTGGATCAACTGAAATGAATTGAAAAAGGAT
* * * * * *
15137 CGCCCTGGATCAAACTGAAATAAACTGAA-ATAGGACCACCCTGGGTCAACTGAAATGAATTG-A
1 CGCCCTGGATC-AACTGAAATAAACTGAAGAAAAGACCGCCCTGGATCAACTGAAATAAACTGAA
* *
15200 ATAAGGATCGCCCTGGATCAACTGAAGTGAATTGAAGATAA-GAT
65 AT-AGGATCACCCTGGATCAACTGAAATGAATTGAA-A-AAGGAT
* * * *
15244 CGCCCTGGATCAATTGAAATAAACTGAA-TAAAGACCGCCCTGGGTCAACTGAAATGAACTGAAA
1 CGCCCTGGATCAACTGAAATAAACTGAAGAAAAGACCGCCCTGGATCAACTGAAATAAACTGAAA
15308 CATCTAAAAT
Statistics
Matches: 232, Mismatches: 38, Indels: 15
0.81 0.13 0.05
Matches are distributed among these distances:
105 3 0.01
106 114 0.49
107 58 0.25
108 57 0.25
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.20
Consensus pattern (106 bp):
CGCCCTGGATCAACTGAAATAAACTGAAGAAAAGACCGCCCTGGATCAACTGAAATAAACTGAAA
TAGGATCACCCTGGATCAACTGAAATGAATTGAAAAAGGAT
Done.