Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024331.1 Corchorus olitorius cultivar O-4 contig24364, 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: 35782
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:5825 original size:22 final size:22
Alignment explanation
Indices: 5797--5839 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5787 TTTTCCGCAA
* *
5797 CAAGTCCTGGGCAGGAGTTGTC
1 CAAGTCCTGGACAGGACTTGTC
5819 CAAGTCCTGGACAGGACTTGT
1 CAAGTCCTGGACAGGACTTGT
5840 TCTGAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.23, G:0.33, T:0.23
Consensus pattern (22 bp):
CAAGTCCTGGACAGGACTTGTC
Found at i:5895 original size:21 final size:21
Alignment explanation
Indices: 5869--5911 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5859 TTCAACAGAC
*
5869 CAAGTCCTGGACAGGAGTTGT
1 CAAGTCCTGGACAGGACTTGT
*
5890 CAAGTCCTGGGCAGGACTTGT
1 CAAGTCCTGGACAGGACTTGT
5911 C
1 C
5912 CTGTTTTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.23, G:0.33, T:0.23
Consensus pattern (21 bp):
CAAGTCCTGGACAGGACTTGT
Found at i:6343 original size:37 final size:34
Alignment explanation
Indices: 6319--6382 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
6309 GAATACTTTG
*
6319 AAAATTAATGGGAACTTTCCCTAAATTGAAAACT
1 AAAATTAATGGGAACTCTCCCTAAATTGAAAACT
*
6353 AAAATTGATGGGAACTCTCCC--AATTGAAAA
1 AAAATTAATGGGAACTCTCCCTAAATTGAAAA
6383 AAAAAAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 9 0.32
34 19 0.68
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.27
Consensus pattern (34 bp):
AAAATTAATGGGAACTCTCCCTAAATTGAAAACT
Found at i:6464 original size:79 final size:76
Alignment explanation
Indices: 6313--6464 Score: 189
Period size: 81 Copynumber: 1.9 Consensus size: 76
6303 TAAATTGAAT
*
6313 ACTTTGAAAATTAATGGGAACTTTCCCTAAATTGAAAACTAAAATTGATGGGAACTCTCCCAATT
1 ACTTTGAAAATGAATGGGAACTTTCCCTAAATTGAAAACTAAAATTGATGGGAACTCTCCCAATT
6378 GAAAAAAAAAAA
66 -AAAAAAAAAAA
* * * *
6390 ACTTTGAGAAACTGAATGGGAACTTTCCCT-ATTTTAAAACTTAAAAACTTGTTGGGAACTTTCC
1 ACTTTGA-AAA-TGAATGGGAACTTTCCCTAAATTGAAAAC-T-AAAA-TTGATGGGAACTCTCC
*
6454 CAATTTAAAAA
61 CAATTAAAAAA
6465 CTAAAACCTG
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
77 7 0.11
78 11 0.17
79 18 0.28
80 9 0.14
81 19 0.30
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (76 bp):
ACTTTGAAAATGAATGGGAACTTTCCCTAAATTGAAAACTAAAATTGATGGGAACTCTCCCAATT
AAAAAAAAAAA
Found at i:6480 original size:34 final size:35
Alignment explanation
Indices: 6406--6501 Score: 122
Period size: 34 Copynumber: 2.7 Consensus size: 35
6396 AGAAACTGAA
* * * *
6406 TGGGAACTTTCCCTATTTTAAAACTTAAAAACTTGT
1 TGGGAACTTTCCCAATTTAAAAAC-TAAAAACCTGG
6442 TGGGAACTTTCCCAATTTAAAAACT-AAAACCTGG
1 TGGGAACTTTCCCAATTTAAAAACTAAAAACCTGG
*
6476 TGGGAACTTTCCCGATTTGAAAAACT
1 TGGGAACTTTCCCAATTT-AAAAACT
6502 TCAAAGACCG
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
34 24 0.44
35 8 0.15
36 22 0.41
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (35 bp):
TGGGAACTTTCCCAATTTAAAAACTAAAAACCTGG
Found at i:12436 original size:47 final size:48
Alignment explanation
Indices: 12382--13138 Score: 398
Period size: 47 Copynumber: 16.0 Consensus size: 48
12372 CATTTTACTT
* *
12382 ATTACTGCTT-TTTACTTTTTTTAGTTTAATTACTCTGAATTAAACTA
1 ATTACTGCTTCTTTACTTTTTTTAGTTTAATTACCCAGAATTAAACTA
* ** *
12429 ATTACTGCTTACTCTTTCTTTTAGTCTTTAACTTAATTACTCAGAATTAAACTA
1 ATTACTGCTT-CT-TTAC-TTT--T-TTTAGTTTAATTACCCAGAATTAAACTA
* * * *
12483 ATTATTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCATAATTAAACTA
1 ATTACTGCTT-CT-TTAC-TTT--T-TTTAGTTTAATTACCCAGAATTAAACTA
*
12537 ATTACTG---CTTTAC--TATTTAGTTTAATTACCCAGAATTAAACTA
1 ATTACTGCTTCTTTACTTTTTTTAGTTTAATTACCCAGAATTAAACTA
* * *
12580 A-CATCTTCTTCTTT--TTCTCTTTAGTTTAATTACCCAGAATTAAACTA
1 ATTA-CTGCTTCTTTACTT-TTTTTAGTTTAATTACCCAGAATTAAACTA
*** * *
12627 ACCCCTTCTTCTTTTAC--TATTTAGTTTAATTACCCAGAATTAAACTA
1 ATTACTGCTTC-TTTACTTTTTTTAGTTTAATTACCCAGAATTAAACTA
* * * *
12674 A-CATCTTCTTCTTT--TGCTCTTTAGTTTAATTACCCAGAATTAAACTA
1 ATTA-CTGCTTCTTTACT-TTTTTTAGTTTAATTACCCAGAATTAAACTA
* * *
12721 A--CCT-CTTC-TT-C-TTTTATAGTTTAAATACCCAGAATTAAACTA
1 ATTACTGCTTCTTTACTTTTTTTAGTTTAATTACCCAGAATTAAACTA
* * *
12763 ACCT-CTCCTTCTTTTAC--TATTTAGTTTAATTACCCAGAATTAAACTA
1 A-TTACTGCTTC-TTTACTTTTTTTAGTTTAATTACCCAGAATTAAACTA
* * *
12810 ACCT-CTCCTTCTTTTAC--TATTTAGTTTAATTACCCAGAATTAAACTA
1 A-TTACTGCTTC-TTTACTTTTTTTAGTTTAATTACCCAGAATTAAACTA
* ** * * *
12857 ACCT-CTTATTCTTT--TGCTCTTTAGTTTAATTACCCATAATTAAACTA
1 A-TTACTGCTTCTTTACT-TTTTTTAGTTTAATTACCCAGAATTAAACTA
* * *
12904 A-CATCTTCTTCTTTTAC--TATTTAGTTTAATTACCCAGAATTAAACTA
1 ATTA-CTGCTTC-TTTACTTTTTTTAGTTTAATTACCCAGAATTAAACTA
*** * *
12951 ACCCCTTCTTCTTTTAC--TATTTAGTTTAATTACCCAGAATTAAACTA
1 ATTACTGCTTC-TTTACTTTTTTTAGTTTAATTACCCAGAATTAAACTA
*
12998 A-CA-T-C-TCTTT-CTTTGGCTCTTTAGTTTAATTACCCAGAATTAAACTA
1 ATTACTGCTTCTTTACTTT---T-TTTAGTTTAATTACCCAGAATTAAACTA
* * * *
13045 ACCT-CTCCTTCTTTTAC--TATTTAGTTTAATTTCCCAGAATTAAACTA
1 A-TTACTGCTTC-TTTACTTTTTTTAGTTTAATTACCCAGAATTAAACTA
* * * *
13092 ACCT-CTTCTTCTTTGAC--TATTTAGTTTAATTACCCGGAATTAAACTA
1 A-TTACTGCTTCTTT-ACTTTTTTTAGTTTAATTACCCAGAATTAAACTA
13139 GTTATTGTTT
Statistics
Matches: 610, Mismatches: 47, Indels: 106
0.80 0.06 0.14
Matches are distributed among these distances:
41 1 0.00
42 32 0.05
43 35 0.06
44 7 0.01
45 7 0.01
46 16 0.03
47 403 0.66
48 9 0.01
49 5 0.01
50 6 0.01
51 6 0.01
52 3 0.00
53 2 0.00
54 78 0.13
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.45
Consensus pattern (48 bp):
ATTACTGCTTCTTTACTTTTTTTAGTTTAATTACCCAGAATTAAACTA
Found at i:12466 original size:54 final size:54
Alignment explanation
Indices: 12407--12546 Score: 201
Period size: 54 Copynumber: 2.6 Consensus size: 54
12397 TTTTTTTAGT
*
12407 TTAATTACTCTGAATTAAACTAATTACTGCTTACTCTTTCTTTTAGTCTTTAAC
1 TTAATTACTCTGAATTAAACTAATTACTGCTTACTCTTTCTTTTACTCTTTAAC
* * * **
12461 TTAATTACTCAGAATTAAACTAATTATTGTTTACTCTTTCTTTTACTCTTTAGT
1 TTAATTACTCTGAATTAAACTAATTACTGCTTACTCTTTCTTTTACTCTTTAAC
*
12515 TTAATTACCCAT-AATTAAACTAATTACTGCTT
1 TTAATTACTC-TGAATTAAACTAATTACTGCTT
12547 TACTATTTAG
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
54 75 1.00
ACGTcount: A:0.30, C:0.17, G:0.05, T:0.48
Consensus pattern (54 bp):
TTAATTACTCTGAATTAAACTAATTACTGCTTACTCTTTCTTTTACTCTTTAAC
Found at i:12669 original size:94 final size:94
Alignment explanation
Indices: 12498--13138 Score: 960
Period size: 94 Copynumber: 6.9 Consensus size: 94
12488 TGTTTACTCT
* * *
12498 TTCTTTTACTCTTTAGTTTAATTACCCATAATTAAACTAA--T-TACTGC-TTTACTATTTAGTT
1 TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTT
*
12559 TAATTACCCAGAATTAAACTAACATCTTC
66 TAATTACCCAGAATTAAACTAACCTCTTC
* *
12588 TTCTTTTTCTCTTTAGTTTAATTACCCAGAATTAAACTAACCCCTTCTTCTTTTACTATTTAGTT
1 TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTT
*
12653 TAATTACCCAGAATTAAACTAACATCTTC
66 TAATTACCCAGAATTAAACTAACCTCTTC
*
12682 TTCTTTTGCTCTTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTC-TTT--TA--TAGTT
1 TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTT
* *
12742 TAAATACCCAGAATTAAACTAACCTCTCC
66 TAATTACCCAGAATTAAACTAACCTCTTC
* *
12771 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTCCTTCTTTTACTATTTAGTT
1 TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTT
*
12836 TAATTACCCAGAATTAAACTAACCTCTTA
66 TAATTACCCAGAATTAAACTAACCTCTTC
* * *
12865 TTCTTTTGCTCTTTAGTTTAATTACCCATAATTAAACTAACATCTTCTTCTTTTACTATTTAGTT
1 TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTT
*
12930 TAATTACCCAGAATTAAACTAACCCCTTC
66 TAATTACCCAGAATTAAACTAACCTCTTC
* * ** *
12959 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACATC-TCTTTCTTTGGCTCTTTAGT
1 TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACCTCTTC-TTCTTTTACTATTTAGT
*
13023 TTAATTACCCAGAATTAAACTAACCTCTCC
65 TTAATTACCCAGAATTAAACTAACCTCTTC
* * *
13053 TTCTTTTACTATTTAGTTTAATTTCCCAGAATTAAACTAACCTCTTCTTCTTTGACTATTTAGTT
1 TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTT
*
13118 TAATTACCCGGAATTAAACTA
66 TAATTACCCAGAATTAAACTA
13139 GTTATTGTTT
Statistics
Matches: 504, Mismatches: 36, Indels: 18
0.90 0.06 0.03
Matches are distributed among these distances:
89 78 0.15
90 41 0.08
91 2 0.00
92 2 0.00
93 9 0.02
94 370 0.73
95 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (94 bp):
TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTT
TAATTACCCAGAATTAAACTAACCTCTTC
Found at i:12720 original size:141 final size:140
Alignment explanation
Indices: 12498--13138 Score: 976
Period size: 141 Copynumber: 4.6 Consensus size: 140
12488 TGTTTACTCT
* * * *
12498 TTCTTTTACTCTTTAGTTTAATTACCCATAATTAAACTAA--T-TACTGC-TTTACTATTTAGTT
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTT
*
12559 TAATTACCCAGAATTAAACTAACATCTTCTTCTTTTTCTCTTTAGTTTAATTACCCAGAATTAAA
66 TAATTACCCAGAATTAAACTAACATC-TCTTCTTTTGCTCTTTAGTTTAATTACCCAGAATTAAA
* *
12624 CTAACCCCTTC
130 CTAACCTCTCC
* * *
12635 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACATCTTCTTCTTTTGCTCTTTAGTT
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTT
* *
12700 TAATTACCCAGAATTAAACTAAC--CTCTTCTTCTT--T-TATAGTTTAAATACCCAGAATTAAA
66 TAATTACCCAGAATTAAACTAACATCTCTTCTT-TTGCTCTTTAGTTTAATTACCCAGAATTAAA
12760 CTAACCTCTCC
130 CTAACCTCTCC
*
12771 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTCCTTCTTTTACTATTTAGTT
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTT
* * *
12836 TAATTACCCAGAATTAAACTAACCTCTTATTCTTTTGCTCTTTAGTTTAATTACCCATAATTAAA
66 TAATTACCCAGAATTAAACTAACATC-TCTTCTTTTGCTCTTTAGTTTAATTACCCAGAATTAAA
* *
12901 CTAACATCTTC
130 CTAACCTCTCC
*
12912 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCCCTTCTTCTTTTACTATTTAGTT
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTT
*
12977 TAATTACCCAGAATTAAACTAACATCTCTTTCTTTGGCTCTTTAGTTTAATTACCCAGAATTAAA
66 TAATTACCCAGAATTAAACTAACATCTC-TTCTTTTGCTCTTTAGTTTAATTACCCAGAATTAAA
13042 CTAACCTCTCC
130 CTAACCTCTCC
* *
13053 TTCTTTTACTATTTAGTTTAATTTCCCAGAATTAAACTAACCTCTTCTTCTTTGACTATTTAGTT
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTT
*
13118 TAATTACCCGGAATTAAACTA
66 TAATTACCCAGAATTAAACTA
13139 GTTATTGTTT
Statistics
Matches: 460, Mismatches: 32, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
136 116 0.25
137 39 0.08
138 10 0.02
139 10 0.02
140 6 0.01
141 279 0.61
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (140 bp):
TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTATTTAGTT
TAATTACCCAGAATTAAACTAACATCTCTTCTTTTGCTCTTTAGTTTAATTACCCAGAATTAAAC
TAACCTCTCC
Found at i:13216 original size:22 final size:22
Alignment explanation
Indices: 13185--13233 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
13175 AATTGCTCTT
13185 CTTCTAATTACTCTTTC-TCCTA
1 CTTCTAATTACTCTTTCGTCC-A
*
13207 CTTCTGATTACTCTTTCGTCCA
1 CTTCTAATTACTCTTTCGTCCA
13229 CTTCT
1 CTTCT
13234 TAGCTTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.14, C:0.33, G:0.04, T:0.49
Consensus pattern (22 bp):
CTTCTAATTACTCTTTCGTCCA
Found at i:16819 original size:22 final size:22
Alignment explanation
Indices: 16794--16841 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
16784 ATTACACTAT
*
16794 TTTTGATGACC-TCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
16816 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
16838 TTTT
1 TTTT
16842 AGTAACGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (22 bp):
TTTTGATAACCTTCCTATGAAA
Found at i:16926 original size:28 final size:28
Alignment explanation
Indices: 16878--16931 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
16868 ACCTTTTTAT
* * *
16878 AATTTTTTTAACCTTCTTAAGAAATTGA
1 AATTTTGTTAACCTCCCTAAGAAATTGA
*
16906 AATTTTGTTAACCTCCCTAAGGAATT
1 AATTTTGTTAACCTCCCTAAGAAATT
16932 TTGAAGACCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (28 bp):
AATTTTGTTAACCTCCCTAAGAAATTGA
Found at i:17086 original size:22 final size:22
Alignment explanation
Indices: 17054--17113 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
17044 AAAACCTCCA
*
17054 TATGAATTGTT-AGTAATCACAC
1 TATGAAATGTTGA-TAATCACAC
*
17076 TCTGAAATGTTGATAATCACAC
1 TATGAAATGTTGATAATCACAC
17098 TATGAAAT-TGTGATAA
1 TATGAAATGT-TGATAA
17114 CCTCGCTATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 1 0.03
22 31 0.94
23 1 0.03
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (22 bp):
TATGAAATGTTGATAATCACAC
Found at i:17122 original size:22 final size:22
Alignment explanation
Indices: 17078--17262 Score: 138
Period size: 22 Copynumber: 8.3 Consensus size: 22
17068 AATCACACTC
* * * *
17078 TGAAATGTTGATAATCACACTA
1 TGAAATTTTGATAACCTCCCTA
* *
17100 TGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAACCTCCCTA
* * *
17122 TGGAATTTTTATAAACCTTCCTA
1 TGAAATTTTGAT-AACCTCCCTA
**
17145 CAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AACCTCCCTA
* **
17168 TAAAATTTTGATAACCTCATTA
1 TGAAATTTTGATAACCTCCCTA
* *
17190 TGAAATCTTGATAACCTCCCCA
1 TGAAATTTTGATAACCTCCCTA
* *
17212 TGAAATATT-AGTAACCTCCTTA
1 TGAAATTTTGA-TAACCTCCCTA
* * * *
17234 TGAAATTTTGTTGACCACACTA
1 TGAAATTTTGATAACCTCCCTA
17256 TGAAATT
1 TGAAATT
17263 CTTATAATTA
Statistics
Matches: 128, Mismatches: 32, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
21 1 0.01
22 90 0.70
23 37 0.29
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCCCTA
Found at i:17151 original size:23 final size:23
Alignment explanation
Indices: 17125--17185 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
17115 CTCGCTATGG
* *
17125 AATTTTTATAAACCTTCCTACAA
1 AATTTTGATAAACCTCCCTACAA
*
17148 AATTTTGATAAACCTCCCTATAA
1 AATTTTGATAAACCTCCCTACAA
17171 AATTTTGAT-AACCTC
1 AATTTTGATAAACCTC
17186 ATTATGAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 6 0.17
23 29 0.83
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (23 bp):
AATTTTGATAAACCTCCCTACAA
Found at i:17351 original size:22 final size:22
Alignment explanation
Indices: 17326--17535 Score: 115
Period size: 22 Copynumber: 9.5 Consensus size: 22
17316 TAAAATTGTG
*
17326 ATAACCACACTATGAAATTTCA
1 ATAACCACACTATGAAATTTTA
*** *
17348 ATAACCTTTCTAAGAAATTTTA
1 ATAACCACACTATGAAATTTTA
*
17370 ATAACCTGATC-CTATGAAATTTTG
1 ATAACC--A-CACTATGAAATTTTA
* *
17394 GTAACCACACTATGAAATTTTG
1 ATAACCACACTATGAAATTTTA
* * *
17416 ATAACCTTC-CCATGAAATTTTG
1 ATAACC-ACACTATGAAATTTTA
** *
17438 ATAACTTTCA-TATGAAATTTTG
1 ATAAC-CACACTATGAAATTTTA
* * * *
17460 GTAACCACACTATGGAATTATG
1 ATAACCACACTATGAAATTTTA
* * *
17482 ATAACCTC-CTCATAAAATTATA
1 ATAACCACACT-ATGAAATTTTA
* *
17504 ATAACCATC-TTATGAAATTTTG
1 ATAACCA-CACTATGAAATTTTA
17526 ATAACCACAC
1 ATAACCACAC
17536 AGAGACAAGA
Statistics
Matches: 146, Mismatches: 31, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
21 6 0.04
22 121 0.83
23 3 0.02
24 16 0.11
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.34
Consensus pattern (22 bp):
ATAACCACACTATGAAATTTTA
Found at i:17452 original size:44 final size:43
Alignment explanation
Indices: 17300--17530 Score: 160
Period size: 44 Copynumber: 5.2 Consensus size: 43
17290 TGATAATCTC
* * *
17300 TTTGATAACATTTCTATAAAATTGTGATAACC-ACACTATGAAAT
1 TTTGATAAC-TTTCTATGAAATTTTGATAACCTTC-CTATGAAAT
** * *
17344 TTCAATAACCTTTCTAAGAAATTTTAATAACCTGATCCTATGAAAT
1 TTTGATAA-CTTTCTATGAAATTTTGATAACCT--TCCTATGAAAT
* *** *
17390 TTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAAT
1 TTTGATAA-CTTTCTATGAAATTTTGATAACCTTCCTATGAAAT
* * *
17434 TTTGATAACTTTCATATGAAATTTTGGTAACC-ACACTATGGAAT
1 TTTGATAACTTTC-TATGAAATTTTGATAACCTTC-CTATGAAAT
* * * * * * * *
17478 TATGATAACCTCCTCATAAAATTATAATAACCATCTTATGAAAT
1 TTTGATAACTTTCT-ATGAAATTTTGATAACCTTCCTATGAAAT
17522 TTTGATAAC
1 TTTGATAAC
17531 CACACAGAGA
Statistics
Matches: 144, Mismatches: 35, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
43 4 0.03
44 103 0.72
45 2 0.01
46 34 0.24
47 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.36
Consensus pattern (43 bp):
TTTGATAACTTTCTATGAAATTTTGATAACCTTCCTATGAAAT
Found at i:17484 original size:66 final size:64
Alignment explanation
Indices: 17312--17535 Score: 234
Period size: 66 Copynumber: 3.4 Consensus size: 64
17302 TGATAACATT
* * * * * *
17312 TCTATAAAATTGTGATAACCACACTATGAAATTTCAATAACCTTTCTAAGAAATTTTAATAACCT
1 TCTATGAAATTTTGATAACCACACTATGAAATTT-GATAACCTTCCCATGAAATTTTAATAA-CT
17377 GA
64 -A
* *
17379 TCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAACT
1 T-CTATGAAATTTTGATAACCACACTATGAAA-TTTGATAACCTTCCCATGAAATTTTAATAACT
*
17444 T
64 A
* * * *
17445 TCATATGAAATTTTGGTAACCACACTATGGAATTATGATAACC-TCCTCATAAAATTATAATAAC
1 TC-TATGAAATTTTGATAACCACACTATGAAATT-TGATAACCTTCC-CATGAAATTTTAATAAC
*
17509 CA
63 TA
17511 TCTTATGAAATTTTGATAACCACAC
1 TC-TATGAAATTTTGATAACCACAC
17536 AGAGACAAGA
Statistics
Matches: 135, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
65 6 0.04
66 74 0.55
67 3 0.02
68 49 0.36
69 3 0.02
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (64 bp):
TCTATGAAATTTTGATAACCACACTATGAAATTTGATAACCTTCCCATGAAATTTTAATAACTA
Found at i:17736 original size:20 final size:20
Alignment explanation
Indices: 17698--17736 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
17688 TATTGACATT
17698 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
17718 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
17737 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:19041 original size:3 final size:3
Alignment explanation
Indices: 19027--19066 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
19017 CACGTTGGCC
* * *
19027 TCT TCT TTT TCT TCT TCT TCT TTT TCT TCT TCT TCC TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
19067 GCTTTCCAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:19047 original size:15 final size:15
Alignment explanation
Indices: 19027--19061 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
19017 CACGTTGGCC
19027 TCTTCTTTTTCTTCT
1 TCTTCTTTTTCTTCT
19042 TCTTCTTTTTCTTCT
1 TCTTCTTTTTCTTCT
19057 TCTTC
1 TCTTC
19062 CTCTTGCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
TCTTCTTTTTCTTCT
Found at i:26338 original size:2 final size:2
Alignment explanation
Indices: 26333--26364 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
26323 TCACACATGC
26333 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26365 GTGTGTTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29008 original size:30 final size:30
Alignment explanation
Indices: 28972--29054 Score: 157
Period size: 30 Copynumber: 2.8 Consensus size: 30
28962 TTAGTAAGAT
*
28972 ATTAAAATTTGAAGGTATAAGAGAAAAATC
1 ATTAAAATTTGAGGGTATAAGAGAAAAATC
29002 ATTAAAATTTGAGGGTATAAGAGAAAAATC
1 ATTAAAATTTGAGGGTATAAGAGAAAAATC
29032 ATTAAAATTTGAGGGTATAAGAG
1 ATTAAAATTTGAGGGTATAAGAG
29055 GTAAGTCAAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.49, C:0.02, G:0.20, T:0.28
Consensus pattern (30 bp):
ATTAAAATTTGAGGGTATAAGAGAAAAATC
Found at i:32698 original size:202 final size:203
Alignment explanation
Indices: 32348--32722 Score: 515
Period size: 202 Copynumber: 1.9 Consensus size: 203
32338 AAATTTTGGT
* ** * *
32348 TATGGAAAATAGTTATTATTTGATACACTGTTAGTGTAGTTTTTGGATTCCATAAACGGGTTAAA
1 TATGGAAAAGAGTTATTATTTGATACACTGCCAGTGTAGTTTTTGGATTCCACAAACGGCTTAAA
* * * * *
32413 AGGTTGACAAGTATCCTATTTCAGAATTAATTGAATTCTTAATATTTCAATCTAGTCCCTAAGTA
66 AGGTTGACAAATACCCCATTTCAGAATTAATTAAATTCTTAATATTTCAATCTAATCCCTAAGTA
* * * *
32478 GACACATGTCACCTTTCTAGACCCGTATGTGCAGTCTGCTAAACTTCACTGACGCTGGATTTGAT
131 GAAACATGTCACCTTTCTAAACCCGCACGTGCAGTCTGCTAAACTTCACTGACGCTGGATTTGAT
32543 AATAATTC
196 AATAATTC
* *
32551 TATGGAAAAGAGTTATTATTTGATACA-TCGCCAGTGTAG-TTTTGGACTT-CACAACCGGCTTG
1 TATGGAAAAGAGTTATTATTTGATACACT-GCCAGTGTAGTTTTTGGA-TTCCACAAACGGCTTA
*
32613 AAAGGTTGACAAATACCCCATTTCAGAATTAATTAAATTTTTAATATTTCAATCTAATCCCTAA-
64 AAAGGTTGACAAATACCCCATTTCAGAATTAATTAAATTCTTAATATTTCAATCTAATCCCTAAG
* * *
32677 TGGGAAACATGTCATCTTTCTAAACTCGCACGTGCAGTCTGCTAAA
129 T-AGAAACATGTCACCTTTCTAAACCCGCACGTGCAGTCTGCTAAA
32723 GAGACCCTGT
Statistics
Matches: 149, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
201 1 0.01
202 112 0.75
203 36 0.24
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (203 bp):
TATGGAAAAGAGTTATTATTTGATACACTGCCAGTGTAGTTTTTGGATTCCACAAACGGCTTAAA
AGGTTGACAAATACCCCATTTCAGAATTAATTAAATTCTTAATATTTCAATCTAATCCCTAAGTA
GAAACATGTCACCTTTCTAAACCCGCACGTGCAGTCTGCTAAACTTCACTGACGCTGGATTTGAT
AATAATTC
Found at i:35290 original size:40 final size:38
Alignment explanation
Indices: 35227--35301 Score: 105
Period size: 40 Copynumber: 1.9 Consensus size: 38
35217 AACCTCTCAA
* * *
35227 ATTGGGATTATGTGGTTCGACTTCGAATTAGTCGAAAT
1 ATTGGGATTATGTGATTCAACTTCGAACTAGTCGAAAT
35265 ATTGGGATCTAATGTGATTCAACTTCGAACTAGTCGA
1 ATTGGGAT-T-ATGTGATTCAACTTCGAACTAGTCGA
35302 TCTAATGTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 8 0.25
39 1 0.03
40 23 0.72
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (38 bp):
ATTGGGATTATGTGATTCAACTTCGAACTAGTCGAAAT
Found at i:35304 original size:30 final size:30
Alignment explanation
Indices: 35270--35331 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
35260 GAAATATTGG
*
35270 GATCTAATGTGATTCAACTTCGAACTAGTC
1 GATCTAATGTGATCCAACTTCGAACTAGTC
* *
35300 GATCTAATGTGATCCAACTTTGAATTAGTC
1 GATCTAATGTGATCCAACTTCGAACTAGTC
35330 GA
1 GA
35332 AATATTGCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (30 bp):
GATCTAATGTGATCCAACTTCGAACTAGTC
Done.