Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017853.1 Corchorus olitorius cultivar O-4 contig17886, 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: 85404
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:6114 original size:21 final size:21
Alignment explanation
Indices: 6090--6153 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
6080 TCTTTAGCTA
6090 CCGCATCAATCTCCATCTTCG
1 CCGCATCAATCTCCATCTTCG
* * ** *
6111 CCGCGTC-TTCTTTAGCTT--
1 CCGCATCAATCTCCATCTTCG
6129 CCGCATCAATCTCCATCTTCG
1 CCGCATCAATCTCCATCTTCG
6150 CCGC
1 CCGC
6154 GCCATTCGAG
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
18 6 0.20
19 7 0.23
20 7 0.23
21 10 0.33
ACGTcount: A:0.14, C:0.42, G:0.12, T:0.31
Consensus pattern (21 bp):
CCGCATCAATCTCCATCTTCG
Found at i:6133 original size:39 final size:39
Alignment explanation
Indices: 6077--6154 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
6067 CATAATGACA
6077 TCTTCTTTAGCTACCGCATCAATCTCCATCTTCGCCGCG
1 TCTTCTTTAGCTACCGCATCAATCTCCATCTTCGCCGCG
*
6116 TCTTCTTTAGCTTCCGCATCAATCTCCATCTTCGCCGCG
1 TCTTCTTTAGCTACCGCATCAATCTCCATCTTCGCCGCG
6155 CCATTCGAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.14, C:0.38, G:0.13, T:0.35
Consensus pattern (39 bp):
TCTTCTTTAGCTACCGCATCAATCTCCATCTTCGCCGCG
Found at i:24854 original size:60 final size:60
Alignment explanation
Indices: 24777--24894 Score: 218
Period size: 60 Copynumber: 2.0 Consensus size: 60
24767 GAGATTACAG
24777 AGCCTTTCACACCAAAATTAAACATGGAACCTAATTACCTAATAAACACAAGATAGCAAT
1 AGCCTTTCACACCAAAATTAAACATGGAACCTAATTACCTAATAAACACAAGATAGCAAT
**
24837 AGCCTTTCACATTAAAATTAAACATGGAACCTAATTACCTAATAAACACAAGATAGCA
1 AGCCTTTCACACCAAAATTAAACATGGAACCTAATTACCTAATAAACACAAGATAGCA
24895 TAGTAGGAGT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.47, C:0.22, G:0.08, T:0.23
Consensus pattern (60 bp):
AGCCTTTCACACCAAAATTAAACATGGAACCTAATTACCTAATAAACACAAGATAGCAAT
Found at i:25156 original size:24 final size:25
Alignment explanation
Indices: 25069--25294 Score: 104
Period size: 24 Copynumber: 9.2 Consensus size: 25
25059 TCTCCTGGCC
* *
25069 TCTTTTTCTGC-TCTCCTTTGCCTT
1 TCTTCTTCTGCTTCGCCTTTGCCTT
* *
25093 TCTTCTTCCTGTCTTCTGGCCGCTT-CTTGT
1 TCTTCTT-CTG-CTTC--GCC-TTTGCCT-T
* *
25123 TCTTCCTCTGCTTC-CCTTTGTCTT
1 TCTTCTTCTGCTTCGCCTTTGCCTT
*
25147 TCTTCTTCTGC-TCTCC-TTGCCTCT
1 TCTTCTTCTGCTTCGCCTTTGCCT-T
25171 TCTTCTTCTGCTGCTCGCCTTTGCCTT
1 TCTTCTTCTGCT--TCGCCTTTGCCTT
* * *
25198 TCTTC--CTG--TCTCC-TGGCTTCT
1 TCTTCTTCTGCTTCGCCTTTGCCT-T
*
25219 TCTTCTTCCGC-TCGCCTTTGCCTT
1 TCTTCTTCTGCTTCGCCTTTGCCTT
* * *
25243 TCTTCTTC--CTCTCTCC-TGGCTTCT
1 TCTTCTTCTGCT-TCGCCTTTGCCT-T
*
25267 TCTTCTTCAGC-TCGCCTTTGCCTT
1 TCTTCTTCTGCTTCGCCTTTGCCTT
25291 TCTT
1 TCTT
25295 TTTCCTGTCT
Statistics
Matches: 153, Mismatches: 24, Indels: 50
0.67 0.11 0.22
Matches are distributed among these distances:
20 4 0.03
21 10 0.07
22 1 0.01
23 13 0.08
24 68 0.44
25 17 0.11
26 2 0.01
27 12 0.08
28 10 0.07
29 7 0.05
30 9 0.06
ACGTcount: A:0.00, C:0.38, G:0.12, T:0.50
Consensus pattern (25 bp):
TCTTCTTCTGCTTCGCCTTTGCCTT
Found at i:25174 original size:48 final size:48
Alignment explanation
Indices: 25122--25374 Score: 250
Period size: 48 Copynumber: 5.2 Consensus size: 48
25112 CCGCTTCTTG
* * *
25122 TTCTTCCTCTGCTTC-CCTTTGTCTTTCTTCTT-CTGCTCTCCTTGCCTCTTC
1 TTCTTCTTCTGC-TCGCCTTTGCCTTTCTTCTTCCTG-TCTCC-TG--GCTTC
*
25173 TTCTTCTGCTGCTCGCCTTTGCC--T-TTCTTCCTGTCTCCTGGCTTC
1 TTCTTCTTCTGCTCGCCTTTGCCTTTCTTCTTCCTGTCTCCTGGCTTC
* *
25218 TTCTTCTTCCGCTCGCCTTTGCCTTTCTTCTTCCTCTCTCCTGGCTTC
1 TTCTTCTTCTGCTCGCCTTTGCCTTTCTTCTTCCTGTCTCCTGGCTTC
* *
25266 TTCTTCTTCAGCTCGCCTTTGCCTTTCTTTTTCCTGTCTCCTGGCTTC
1 TTCTTCTTCTGCTCGCCTTTGCCTTTCTTCTTCCTGTCTCCTGGCTTC
* * * * *
25314 TTCTTCTTTTGTTCTCC-TT-CCTTCTTCCTCTTCCTCTCTCCTCCTGGCTTC
1 TTCTTCTTCTGCTCGCCTTTGCC-T-TTCTTCTT-C-CTGT-CTCCTGGCTTC
25365 TTCTTCTTCT
1 TTCTTCTTCT
25375 TCCTCCCTCC
Statistics
Matches: 174, Mismatches: 18, Indels: 20
0.82 0.08 0.09
Matches are distributed among these distances:
45 25 0.14
46 2 0.01
47 6 0.03
48 94 0.54
49 5 0.03
50 5 0.03
51 37 0.21
ACGTcount: A:0.00, C:0.39, G:0.10, T:0.51
Consensus pattern (48 bp):
TTCTTCTTCTGCTCGCCTTTGCCTTTCTTCTTCCTGTCTCCTGGCTTC
Found at i:25268 original size:96 final size:96
Alignment explanation
Indices: 25056--25374 Score: 275
Period size: 96 Copynumber: 3.3 Consensus size: 96
25046 GCCTCTCCCT
* * *
25056 CTCTCTCCTGGC--C-TCTT-TT-TCTGCTCTCCTTTGCCTTTCTTCTTCCTGTCTTCTGGCCGC
1 CTCTCTCCTGGCTTCTTCTTCTTCTCAGCTCGCCTTTGCCTTTC-T-TTCCTGTCTCCT-G--GC
* *
25116 TTCTTGTTCTTCCTCTGCTTC-CCTTTGTCTTTCTTCTT-
61 TTCTTCTTCTT-C-C-GC-TCGCCTTTGCCTTTCTTCTTC
* * *
25154 CTGCTCTCCTTGCCTCTTCTTCTTCTGCTGCTCGCCTTTGCCTTTC-TTCCTGTCTCCTGGCTTC
1 CT-CTCTCCTGGCTTCTTCTTCTTCT-CAGCTCGCCTTTGCCTTTCTTTCCTGTCTCCTGGCTTC
25218 TTCTTCTTCCGCTCGCCTTTGCCTTTCTTCTTC
64 TTCTTCTTCCGCTCGCCTTTGCCTTTCTTCTTC
25251 CTCTCTCCTGGCTTCTTCTTC-T-TCAGCTCGCCTTTGCCTTTCTTTTTCCTGTCTCCTGGCTTC
1 CTCTCTCCTGGCTTCTTCTTCTTCTCAGCTCGCCTTTGCCTTTC--TTTCCTGTCTCCTGGCTTC
** * * *
25314 TTCTTCTTTTGTTCTCC-TT-CCTTCTTCCTCTTCC
64 TTCTTCTTCCGCTCGCCTTTGCC-T-TTCTTCTT-C
25348 TCTCTCCTCCTGGCTTCTTCTTCTTCT
1 -CTCT-CTCCTGGCTTCTTCTTCTTCT
25375 TCCTCCCTCC
Statistics
Matches: 189, Mismatches: 13, Indels: 35
0.80 0.05 0.15
Matches are distributed among these distances:
93 18 0.10
94 3 0.02
95 6 0.03
96 73 0.39
97 4 0.02
98 7 0.04
99 38 0.20
100 1 0.01
101 3 0.02
102 15 0.08
103 2 0.01
104 1 0.01
105 18 0.10
ACGTcount: A:0.00, C:0.39, G:0.11, T:0.50
Consensus pattern (96 bp):
CTCTCTCCTGGCTTCTTCTTCTTCTCAGCTCGCCTTTGCCTTTCTTTCCTGTCTCCTGGCTTCTT
CTTCTTCCGCTCGCCTTTGCCTTTCTTCTTC
Found at i:25317 original size:24 final size:24
Alignment explanation
Indices: 25197--25373 Score: 121
Period size: 24 Copynumber: 7.2 Consensus size: 24
25187 GCCTTTGCCT
25197 TTCTTCCTGTCTCCTGGCTTCTTC
1 TTCTTCCTGTCTCCTGGCTTCTTC
* * *
25221 TTCTTCC-GCTCGCCTTTGCCT-TTC
1 TTCTTCCTG-TCTCC-TGGCTTCTTC
*
25245 TTCTTCCTCTCTCCTGGCTTCTTC
1 TTCTTCCTGTCTCCTGGCTTCTTC
* * * *
25269 TTCTT-CAGCTCGCCTTTGCCT-TTC
1 TTCTTCCTG-TCTCC-TGGCTTCTTC
*
25293 TTTTTCCTGTCTCCTGGCTTCTTC
1 TTCTTCCTGTCTCCTGGCTTCTTC
* **
25317 TTCTT-TTGTTCTCCTTCCTTCTTC
1 TTCTTCCTG-TCTCCTGGCTTCTTC
* *
25341 CTCTTCCTCTCTCCTCCTGGCTTCTTC
1 TTCTT-C-CTGT-CTCCTGGCTTCTTC
25368 TTCTTC
1 TTCTTC
25374 TTCCTCCCTC
Statistics
Matches: 113, Mismatches: 27, Indels: 24
0.69 0.16 0.15
Matches are distributed among these distances:
23 12 0.11
24 72 0.64
25 10 0.09
26 2 0.02
27 17 0.15
ACGTcount: A:0.01, C:0.39, G:0.10, T:0.51
Consensus pattern (24 bp):
TTCTTCCTGTCTCCTGGCTTCTTC
Found at i:25368 original size:30 final size:30
Alignment explanation
Indices: 25334--25477 Score: 104
Period size: 30 Copynumber: 5.3 Consensus size: 30
25324 GTTCTCCTTC
25334 CTTCTTCCTCTTCCTCTCTCCTCCTGGCTT
1 CTTCTTCCTCTTCCTCTCTCCTCCTGGCTT
* * **
25364 CTTCTTCTTCTTCCTCCCTCCTCCCAGCTT
1 CTTCTTCCTCTTCCTCTCTCCTCCTGGCTT
* *
25394 CTTC-T--TCTTCCTTTCTCCTTCTGG---
1 CTTCTTCCTCTTCCTCTCTCCTCCTGGCTT
*
25418 C--C-TCCTCTTCCTCTCTCGC-CCTCGCTT
1 CTTCTTCCTCTTCCTCTCTC-CTCCTGGCTT
25445 CTTCTT-C-C-T-CTCTCT-C-CCTGGCTT
1 CTTCTTCCTCTTCCTCTCTCCTCCTGGCTT
25469 CTTCTTCCT
1 CTTCTTCCT
25478 TTCTCCTTCT
Statistics
Matches: 90, Mismatches: 13, Indels: 26
0.70 0.10 0.20
Matches are distributed among these distances:
22 2 0.02
24 29 0.32
25 2 0.02
26 6 0.07
27 16 0.18
28 1 0.01
29 3 0.03
30 31 0.34
ACGTcount: A:0.01, C:0.47, G:0.06, T:0.46
Consensus pattern (30 bp):
CTTCTTCCTCTTCCTCTCTCCTCCTGGCTT
Found at i:25383 original size:27 final size:26
Alignment explanation
Indices: 25303--25483 Score: 99
Period size: 24 Copynumber: 7.0 Consensus size: 26
25293 TTTTTCCTGT
* *
25303 CTCCTGGCTTCTTCTTCTT-TTGT-T
1 CTCCTGGCTTCTTCTTCTTCTTCTCC
** * *
25327 CTCCTTCCTTCTTCCTCTTCCTCTCTC
1 CTCCTGGCTTCTTCTTCTTCTTCTC-C
25354 CTCCTGGCTTCTTCTTCTTCTTCCTCC
1 CTCCTGGCTTCTTCTTCTTCTT-CTCC
*
25381 CTCCTCCCAGCTTCTTCTTCTTCCTT-TCTC
1 CTCCT---GGCTTCTTCTTCTT-CTTCTC-C
* * * * *
25411 CTTCTGGCCTCCTCTTCCTC-TCTCG
1 CTCCTGGCTTCTTCTTCTTCTTCTCC
* * *
25436 C-CCTCGCTTCTTCTTCCTC-TCTCT
1 CTCCTGGCTTCTTCTTCTTCTTCTCC
*
25460 C-CCTGGCTTCTTCTTCCT-TTCTCC
1 CTCCTGGCTTCTTCTTCTTCTTCTCC
25484 TTCTGGCCTC
Statistics
Matches: 122, Mismatches: 24, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
24 55 0.45
25 4 0.03
26 3 0.02
27 34 0.28
28 3 0.02
29 2 0.02
30 18 0.15
31 3 0.02
ACGTcount: A:0.01, C:0.45, G:0.07, T:0.48
Consensus pattern (26 bp):
CTCCTGGCTTCTTCTTCTTCTTCTCC
Found at i:25466 original size:48 final size:48
Alignment explanation
Indices: 25369--25553 Score: 158
Period size: 48 Copynumber: 3.8 Consensus size: 48
25359 GGCTTCTTCT
* * *
25369 TCTTCTTCCTCCCTCCTCC-CAGCTTCTTCTTCTTCCTTTCTCCTTCTGGCC
1 TCTTCTTCCTCTCTCCTCCTC-GCTTCTTCTTCCT-CTCTCTCC--CTGGCC
* *
25420 TCCTCTTCCTCTCTCGC-CCTCGCTTCTTCTTCCTCTCTCTCCCTGGCT
1 TCTTCTTCCTCTCTC-CTCCTCGCTTCTTCTTCCTCTCTCTCCCTGGCC
* * * * * **
25468 TCTTCTTCCTTTCTCCTTCTGGCCTCCTCTTCCTCTCTCTTTCTGGCC
1 TCTTCTTCCTCTCTCCTCCTCGCTTCTTCTTCCTCTCTCTCCCTGGCC
* * * * *
25516 TCTTCTTCCTCTCTCTTTCTAGCCTCCTCTTCCTCTCT
1 TCTTCTTCCTCTCTCCTCCTCGCTTCTTCTTCCTCTCT
25554 TTTTCTGGCT
Statistics
Matches: 114, Mismatches: 17, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
47 1 0.01
48 77 0.68
50 7 0.06
51 27 0.24
52 2 0.02
ACGTcount: A:0.01, C:0.46, G:0.06, T:0.46
Consensus pattern (48 bp):
TCTTCTTCCTCTCTCCTCCTCGCTTCTTCTTCCTCTCTCTCCCTGGCC
Found at i:25487 original size:72 final size:73
Alignment explanation
Indices: 25367--25531 Score: 233
Period size: 72 Copynumber: 2.2 Consensus size: 73
25357 CTGGCTTCTT
* *
25367 CTTCTTCTTCCTCCCTCCTCCCAGCTTCTTCTTCTTCCTTTCTCCTTCTGGCCTCCTCTTCCTCT
1 CTTCTTCTTCCTCTCT-CTCCCAGC-GCTTCTTCTTCCTTTCTCCTTCTGGCCTCCTCTTCCTCT
25432 CTCGCCCTCG
64 CTCGCCCTCG
*
25442 CTTCTTCTTCCTCTCTCTCCCTG-GCTTCTTCTTCCTTTCTCCTTCTGGCCTCCTCTTCCTCTCT
1 CTTCTTCTTCCTCTCTCTCCCAGCGCTTCTTCTTCCTTTCTCCTTCTGGCCTCCTCTTCCTCTCT
*** *
25506 CTTTCTGG
66 CGCCCTCG
*
25514 CCTCTTCTTCCTCTCTCT
1 CTTCTTCTTCCTCTCTCT
25532 TTCTAGCCTC
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
72 61 0.74
74 6 0.07
75 15 0.18
ACGTcount: A:0.01, C:0.47, G:0.07, T:0.46
Consensus pattern (73 bp):
CTTCTTCTTCCTCTCTCTCCCAGCGCTTCTTCTTCCTTTCTCCTTCTGGCCTCCTCTTCCTCTCT
CGCCCTCG
Found at i:25547 original size:72 final size:72
Alignment explanation
Indices: 25399--25568 Score: 214
Period size: 72 Copynumber: 2.4 Consensus size: 72
25389 AGCTTCTTCT
*
25399 TCTTCCTTTCTCCTTCTGGCCTCCTCTTCCTCTCTCGCCCTCGCTTCTTCTTCCTCTCTCTCCCT
1 TCTTCCTTTCTCCTTCTGGCCTCCTCTTCCTCTCTCGCCCTCGCCTCTTCTTCCTCTCTCTCCCT
* * *
25464 GGCTTCT
66 AGCCTCC
*** * **
25471 TCTTCCTTTCTCCTTCTGGCCTCCTCTTCCTCTCTCTTTCTGGCCTCTTCTTCCTCTCTCTTTCT
1 TCTTCCTTTCTCCTTCTGGCCTCCTCTTCCTCTCTCGCCCTCGCCTCTTCTTCCTCTCTCTCCCT
25536 AGCCTCC
66 AGCCTCC
* ** *
25543 TCTTCCTCTCTTTTTCTGGCTTCCTC
1 TCTTCCTTTCTCCTTCTGGCCTCCTC
25569 CTCTTCCTGC
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 84 1.00
ACGTcount: A:0.01, C:0.45, G:0.08, T:0.47
Consensus pattern (72 bp):
TCTTCCTTTCTCCTTCTGGCCTCCTCTTCCTCTCTCGCCCTCGCCTCTTCTTCCTCTCTCTCCCT
AGCCTCC
Found at i:25576 original size:27 final size:24
Alignment explanation
Indices: 25399--25568 Score: 178
Period size: 24 Copynumber: 7.1 Consensus size: 24
25389 AGCTTCTTCT
* *
25399 TCTTCCTTTCTCCTTCTGGCCTCC
1 TCTTCCTCTCTCTTTCTGGCCTCC
*** * * *
25423 TCTTCCTCTCTCGCCCTCGCTTCT
1 TCTTCCTCTCTCTTTCTGGCCTCC
** * *
25447 TCTTCCTCTCTCTCCCTGGCTTCT
1 TCTTCCTCTCTCTTTCTGGCCTCC
* *
25471 TCTTCCTTTCTCCTTCTGGCCTCC
1 TCTTCCTCTCTCTTTCTGGCCTCC
*
25495 TCTTCCTCTCTCTTTCTGGCCTCT
1 TCTTCCTCTCTCTTTCTGGCCTCC
*
25519 TCTTCCTCTCTCTTTCTAGCCTCC
1 TCTTCCTCTCTCTTTCTGGCCTCC
* *
25543 TCTTCCTCTCTTTTTCTGGCTTCC
1 TCTTCCTCTCTCTTTCTGGCCTCC
25567 TC
1 TC
25569 CTCTTCCTGC
Statistics
Matches: 123, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 123 1.00
ACGTcount: A:0.01, C:0.45, G:0.08, T:0.47
Consensus pattern (24 bp):
TCTTCCTCTCTCTTTCTGGCCTCC
Found at i:31684 original size:17 final size:16
Alignment explanation
Indices: 31655--31705 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
31645 CATGTAATAT
*
31655 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
31671 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
31688 TTTGATCACTAGTGATC
1 -TTGATCACTGGTGATC
31705 T
1 T
31706 GGGGGTGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 4 0.13
17 24 0.77
18 3 0.10
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:32914 original size:11 final size:11
Alignment explanation
Indices: 32900--32937 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
32890 ATTCATAACA
32900 AATTTATAATT
1 AATTTATAATT
32911 AATTTATAATT
1 AATTTATAATT
32922 -ATTTGATAATT
1 AATTT-ATAATT
*
32933 TATTT
1 AATTT
32938 TATATAGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:45045 original size:6 final size:6
Alignment explanation
Indices: 45034--45061 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
45024 GATAGTTACT
45034 TTTGAA TTTGAA TTTGAA TTTGAA TTTG
1 TTTGAA TTTGAA TTTGAA TTTGAA TTTG
45062 CTTAGTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.54
Consensus pattern (6 bp):
TTTGAA
Found at i:51207 original size:13 final size:13
Alignment explanation
Indices: 51173--51199 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
51163 CTACATAAAA
51173 TAATTAATAGTAT
1 TAATTAATAGTAT
51186 TAATTAATAGTAT
1 TAATTAATAGTAT
51199 T
1 T
51200 GCATAATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (13 bp):
TAATTAATAGTAT
Found at i:51555 original size:34 final size:35
Alignment explanation
Indices: 51506--51574 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
51496 CCAGAAAACA
*
51506 GAGAAGAAAAGAATAAA-AAATAAAAAAAAAGTTT
1 GAGAAAAAAAGAATAAACAAATAAAAAAAAAGTTT
* * *
51540 GAGAAAAAAATAATAAATCAAGTAAAAAAATAGTT
1 GAGAAAAAAAGAATAAA-CAAATAAAAAAAAAGTT
51575 GATATCAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 15 0.52
36 14 0.48
ACGTcount: A:0.68, C:0.01, G:0.13, T:0.17
Consensus pattern (35 bp):
GAGAAAAAAAGAATAAACAAATAAAAAAAAAGTTT
Found at i:52166 original size:11 final size:11
Alignment explanation
Indices: 52142--52176 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
52132 TTGACAGCGT
52142 AACAAAAACAA
1 AACAAAAACAA
* *
52153 AACGAAAACGA
1 AACAAAAACAA
52164 AACAAAAACAA
1 AACAAAAACAA
52175 AA
1 AA
52177 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:52514 original size:29 final size:30
Alignment explanation
Indices: 52461--52520 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
52451 ATTCCTCTAA
52461 TTATTCAAAATCAGAAACCATTACCCAAAAT
1 TTATTCAAAAT-AGAAACCATTACCCAAAAT
*
52492 TTATTCAAAAT-GAAATCATTACCCAAAAT
1 TTATTCAAAATAGAAACCATTACCCAAAAT
52521 GGAGCTAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 17 0.61
31 11 0.39
ACGTcount: A:0.48, C:0.20, G:0.03, T:0.28
Consensus pattern (30 bp):
TTATTCAAAATAGAAACCATTACCCAAAAT
Found at i:59312 original size:12 final size:12
Alignment explanation
Indices: 59275--59354 Score: 103
Period size: 12 Copynumber: 6.8 Consensus size: 12
59265 GGAATGTGAG
59275 TTGGTTTGTAAT
1 TTGGTTTGTAAT
*
59287 TT-GTTTGTTTAT
1 TTGGTTTG-TAAT
59299 TTGGTTTGTAAT
1 TTGGTTTGTAAT
59311 TTGGTTTGTAAT
1 TTGGTTTGTAAT
*
59323 TT-GTTTGTTTAT
1 TTGGTTTG-TAAT
59335 TTGGTTTGTAAT
1 TTGGTTTGTAAT
59347 TT-GTTTGT
1 TTGGTTTGT
59355 TTATTTGGTA
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
11 16 0.27
12 34 0.57
13 10 0.17
ACGTcount: A:0.12, C:0.00, G:0.23, T:0.65
Consensus pattern (12 bp):
TTGGTTTGTAAT
Found at i:59324 original size:24 final size:24
Alignment explanation
Indices: 59278--59363 Score: 106
Period size: 24 Copynumber: 3.6 Consensus size: 24
59268 ATGTGAGTTG
*
59278 GTTTG-TAATTT-GTTTGTTTATTT
1 GTTTGTTAATTTGGTTTG-TAATTT
59301 GGTTTG-TAATTTGGTTTGTAATTT
1 -GTTTGTTAATTTGGTTTGTAATTT
*
59325 GTTTGTTTATTTGGTTTGTAATTT
1 GTTTGTTAATTTGGTTTGTAATTT
*
59349 GTTTGTTTATTTGGT
1 GTTTGTTAATTTGGT
59364 AGGTAGGTAG
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
23 5 0.09
24 48 0.83
25 5 0.09
ACGTcount: A:0.13, C:0.00, G:0.22, T:0.65
Consensus pattern (24 bp):
GTTTGTTAATTTGGTTTGTAATTT
Found at i:59361 original size:36 final size:36
Alignment explanation
Indices: 59275--59354 Score: 153
Period size: 36 Copynumber: 2.2 Consensus size: 36
59265 GGAATGTGAG
59275 TTGGTTTGTAATTTGTTTGTTTATTTGGTTTGTAAT
1 TTGGTTTGTAATTTGTTTGTTTATTTGGTTTGTAAT
59311 TTGGTTTGTAATTTGTTTGTTTATTTGGTTTGTAAT
1 TTGGTTTGTAATTTGTTTGTTTATTTGGTTTGTAAT
59347 TT-GTTTGT
1 TTGGTTTGT
59355 TTATTTGGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 6 0.14
36 38 0.86
ACGTcount: A:0.12, C:0.00, G:0.23, T:0.65
Consensus pattern (36 bp):
TTGGTTTGTAATTTGTTTGTTTATTTGGTTTGTAAT
Found at i:59376 original size:24 final size:24
Alignment explanation
Indices: 59325--59382 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
59315 TTTGTAATTT
** * *
59325 GTTTGTTTATTTGGTTTGTAATTT
1 GTTTGTTTATTTGGTAGGTAAGTA
*
59349 GTTTGTTTATTTGGTAGGTAGGTA
1 GTTTGTTTATTTGGTAGGTAAGTA
*
59373 GTTTATTTAT
1 GTTTGTTTAT
59383 GGTATAATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (24 bp):
GTTTGTTTATTTGGTAGGTAAGTA
Found at i:64314 original size:14 final size:13
Alignment explanation
Indices: 64286--64311 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
64276 GTGTGGCACG
64286 TGAGAACCAAAAA
1 TGAGAACCAAAAA
64299 TGAGAACCAAAAA
1 TGAGAACCAAAAA
64312 ATGGGAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.15, T:0.08
Consensus pattern (13 bp):
TGAGAACCAAAAA
Found at i:70192 original size:20 final size:20
Alignment explanation
Indices: 70164--70205 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
70154 AGACAGAGAG
*
70164 TCGGGGTAATCACATTGAAC
1 TCGGAGTAATCACATTGAAC
70184 TCGGAGTAATCACATTGAAC
1 TCGGAGTAATCACATTGAAC
70204 TC
1 TC
70206 CGATTAAGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGGAGTAATCACATTGAAC
Found at i:70232 original size:58 final size:55
Alignment explanation
Indices: 70071--70243 Score: 238
Period size: 58 Copynumber: 3.0 Consensus size: 55
70061 AACTTGTATC
70071 CGGATAATCACATTGAACTCCGATTAAGACAGAGTCGGGGTAATCACATTGAACT
1 CGGATAATCACATTGAACTCCGATTAAGACAGAGTCGGGGTAATCACATTGAACT
* * * * *
70126 CCGATTAAGACAGAGTGAGCTCCGATTAAGACAGAGAGTCGGGGTAATCACATTGAACT
1 CGGA-TAA-TCACATTGAACTCCGATTAAGAC--AGAGTCGGGGTAATCACATTGAACT
70185 CGGAGTAATCACATTGAACTCCGATTAAGACAGAGTCGAGGGGTAATCACATTGAACT
1 CGGA-TAATCACATTGAACTCCGATTAAGACAGAGTC--GGGGTAATCACATTGAACT
70243 C
1 C
70244 CGATTAAGAC
Statistics
Matches: 101, Mismatches: 11, Indels: 9
0.83 0.09 0.07
Matches are distributed among these distances:
55 3 0.03
56 9 0.09
57 19 0.19
58 39 0.39
59 31 0.31
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (55 bp):
CGGATAATCACATTGAACTCCGATTAAGACAGAGTCGGGGTAATCACATTGAACT
Found at i:70240 original size:38 final size:38
Alignment explanation
Indices: 70189--70300 Score: 224
Period size: 38 Copynumber: 2.9 Consensus size: 38
70179 TGAACTCGGA
70189 GTAATCACATTGAACTCCGATTAAGACAGAGTCGAGGG
1 GTAATCACATTGAACTCCGATTAAGACAGAGTCGAGGG
70227 GTAATCACATTGAACTCCGATTAAGACAGAGTCGAGGG
1 GTAATCACATTGAACTCCGATTAAGACAGAGTCGAGGG
70265 GTAATCACATTGAACTCCGATTAAGACAGAGTCGAG
1 GTAATCACATTGAACTCCGATTAAGACAGAGTCGAG
70301 ATACATCGAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 74 1.00
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (38 bp):
GTAATCACATTGAACTCCGATTAAGACAGAGTCGAGGG
Found at i:73535 original size:3 final size:3
Alignment explanation
Indices: 73527--73555 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
73517 GCATTTGTAG
73527 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
73556 TTTTTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:78658 original size:23 final size:23
Alignment explanation
Indices: 78622--78665 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
78612 TATTAAAAGA
*
78622 TAAAAAGAAATTAAAAGAAAATC
1 TAAAAAGAAATTAAAAAAAAATC
**
78645 TAAAAAGATTTTAAAAAAAAA
1 TAAAAAGAAATTAAAAAAAAA
78666 CACAGGAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.20
Consensus pattern (23 bp):
TAAAAAGAAATTAAAAAAAAATC
Found at i:79210 original size:91 final size:91
Alignment explanation
Indices: 79012--79193 Score: 355
Period size: 91 Copynumber: 2.0 Consensus size: 91
79002 AAAAATCTTT
79012 GTGTATGAGTTTTGATGTTGTTTTACTTGAATGATTTTGAATGATCGAGTTTTGAAAGTTTGAAG
1 GTGTATGAGTTTTGATGTTGTTTTACTTGAATGATTTTGAATGATCGAGTTTTGAAAGTTTGAAG
79077 GTTGAGAGAATTTGAGAGAATTGAAA
66 GTTGAGAGAATTTGAGAGAATTGAAA
*
79103 GTGTATGAGTTTTGATGTTGTTTTACTTGAATGATTTTGAATGATTGAGTTTTGAAAGTTTGAAG
1 GTGTATGAGTTTTGATGTTGTTTTACTTGAATGATTTTGAATGATCGAGTTTTGAAAGTTTGAAG
79168 GTTGAGAGAATTTGAGAGAATTGAAA
66 GTTGAGAGAATTTGAGAGAATTGAAA
79194 AGTTTTGAAG
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.30, C:0.02, G:0.27, T:0.41
Consensus pattern (91 bp):
GTGTATGAGTTTTGATGTTGTTTTACTTGAATGATTTTGAATGATCGAGTTTTGAAAGTTTGAAG
GTTGAGAGAATTTGAGAGAATTGAAA
Found at i:84867 original size:28 final size:28
Alignment explanation
Indices: 84835--85382 Score: 364
Period size: 28 Copynumber: 19.6 Consensus size: 28
84825 TTGTCTTCGA
84835 GAGCGTACTACCTCTTCGCGATCTTTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * *
84863 GAGCGTACTACCGCTTCGCGGTCGTTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * *
84891 GAGCGTACCACCGCTTCGCGGTCTTTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * *
84919 GAGCGTACTACCGCTTCGCGCTCTCTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * *
84947 GAGCGTACTACCTCTTTGCGATCCTTGA
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * * * *
84975 GAGCGTACTACCACCTCGAGAGCTTGGAGG
1 GAGCGTACTACCTCTTCGCGATCTT--TGG
* * * ** *
85005 GGGCATTCTACCAATTCGCGAGCTTTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
*
85033 G-GCGTACTACCGCTTCGC-ACTCTTTGG
1 GAGCGTACTACCTCTTCGCGA-TCTTTGG
** * *
85060 GAGCGTACTACGCAT-TT-TTG-TCTTCGA
1 GAGCGTACTAC-C-TCTTCGCGATCTTTGG
85087 GAGCGTACTACCTCTTCGCGATCTTTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * * *
85115 GAGTGTACTACCTCTTTGCGATCCTTGA
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * * *
85143 GAGCGTCCTACCGCTTCGCGGTCGTTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
*
85171 GAGCGTACTA-CTGCTTCGCGCTCTTTGG
1 GAGCGTACTACCT-CTTCGCGATCTTTGG
* * *
85199 GAGCGTACTACCGCTTCACGCTCTTTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * * *
85227 GAGCGTACTACCACCTCGAGAGC-TTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * * *
85254 AGGGCGTACTACCAT-TTCGTGAACTTTGA
1 -GAGCGTACTACC-TCTTCGCGATCTTTGG
* * * * *
85283 G-GCGTACTATCACTTTGCGATCCTTGA
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * * *
85310 GAGCGTACTACCACCTCGGGAGC-TTGG
1 GAGCGTACTACCTCTTCGCGATCTTTGG
* * * *
85337 AGGGAGTACTACCAT-TTCGCGAACTTTGA
1 -GAGCGTACTACC-TCTTCGCGATCTTTGG
*
85366 G-GCGTACTACCACTTCG
1 GAGCGTACTACCTCTTCG
85383 AGAGCTTGGA
Statistics
Matches: 406, Mismatches: 93, Indels: 43
0.75 0.17 0.08
Matches are distributed among these distances:
25 1 0.00
26 4 0.01
27 78 0.19
28 293 0.72
29 10 0.02
30 20 0.05
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.28
Consensus pattern (28 bp):
GAGCGTACTACCTCTTCGCGATCTTTGG
Found at i:85404 original size:83 final size:83
Alignment explanation
Indices: 84949--85385 Score: 303
Period size: 83 Copynumber: 5.2 Consensus size: 83
84939 CTCTCTGGGA
* * * * *
84949 GCGTACTACCTCTTTGCGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGGGCATTCT
1 GCGTACTACCACTTCGAGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGAG--TACT
* * *
85014 ACCAATTCGCGAGCTTTGGG
64 ACCATTTCGCGAACTTTGAG
* * * * * *** * * * *
85034 GCGTACTACCGCTTCGCA-CTCTTTGGGAGCGTACTACGCA-TTTTTG-TCTTCGAGAGCGTACT
1 GCGTACTACCACTTCG-AGATCCTTGAGAGCGTACTAC-CACCTCGAGAGCTTGGAGGGAGTACT
* *
85096 ACC-TCTTCGCGATCTTTGGG
64 ACCAT-TTCGCGAACTTTGAG
* * * * * * * * * *
85116 AGTGTACTACCTCTTTGCGATCCTTGAGAGCGTCCTACCGCTTCGCG-GTCGTTGG-GAGCGTAC
1 -GCGTACTACCACTTCGAGATCCTTGAGAGCGTACTACCACCTCGAGAG-C-TTGGAGGGAGTAC
*** ** *
85179 TACTGCTTCGCGCTCTTTGGG
63 TACCATTTCGCGAACTTTGAG
* * * * *
85200 AGCGTACTACCGCTTC-ACGCTCTTTGGGAGCGTACTACCACCTCGAGAGCTTGGAGGGCGTACT
1 -GCGTACTACCACTTCGA-GATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGAGTACT
*
85264 ACCATTTCGTGAACTTTGAG
64 ACCATTTCGCGAACTTTGAG
* * * *
85284 GCGTACTATCACTTTGCGATCCTTGAGAGCGTACTACCACCTCGGGAGCTTGGAGGGAGTACTAC
1 GCGTACTACCACTTCGAGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGAGTACTAC
85349 CATTTCGCGAACTTTGAG
66 CATTTCGCGAACTTTGAG
85367 GCGTACTACCACTTCGAGA
1 GCGTACTACCACTTCGAGA
85386 GCTTGGAGGG
Statistics
Matches: 273, Mismatches: 66, Indels: 28
0.74 0.18 0.08
Matches are distributed among these distances:
82 21 0.08
83 123 0.45
84 91 0.33
85 36 0.13
86 2 0.01
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (83 bp):
GCGTACTACCACTTCGAGATCCTTGAGAGCGTACTACCACCTCGAGAGCTTGGAGGGAGTACTAC
CATTTCGCGAACTTTGAG
Done.