Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007526.1 Kokia drynarioides strain JFW-HI SEQ_122151, 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: 74447
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:2216 original size:82 final size:82
Alignment explanation
Indices: 2085--2276 Score: 258
Period size: 82 Copynumber: 2.3 Consensus size: 82
2075 TATGAGAAAA
* ** *
2085 CGCCGCTAATGCTCTGTGACCTTTAACGGTGCTTTCCCACAAACACCGCTAATGCTCTGACCTTT
1 CGCCGCTAATGCTC--TGACCTTTAGCGACGCTTTCCCACAAACACCGCTAATGCACTGACCTTT
2150 AGCGACGCTTTATCACAAG
64 AGCGACGCTTTATCACAAG
* ** *
2169 CGCCGCTAATGCTCTGACCTTTAGTGACGCTTTCCCACAAATGCCGCTAATGCACTGATCTTTAG
1 CGCCGCTAATGCTCTGACCTTTAGCGACGCTTTCCCACAAACACCGCTAATGCACTGACCTTTAG
* *
2234 CGGCGCTTTCTCACAAG
66 CGACGCTTTATCACAAG
* *
2251 CGCCACTAATGCTCTAACCTTTAGCG
1 CGCCGCTAATGCTCTGACCTTTAGCG
2277 GCGTTTTTTT
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
82 81 0.85
84 14 0.15
ACGTcount: A:0.22, C:0.32, G:0.18, T:0.28
Consensus pattern (82 bp):
CGCCGCTAATGCTCTGACCTTTAGCGACGCTTTCCCACAAACACCGCTAATGCACTGACCTTTAG
CGACGCTTTATCACAAG
Found at i:2277 original size:41 final size:41
Alignment explanation
Indices: 2082--2279 Score: 234
Period size: 41 Copynumber: 4.8 Consensus size: 41
2072 GCTTATGAGA
* *
2082 AAACGCCGCTAATGCTCTGTGACCTTTAACGGTGCTTTCCCAC
1 AAACGCCGCTAATGCTC--TGACCTTTAGCGGCGCTTTCCCAC
* * **
2125 AAACACCGCTAATGCTCTGACCTTTAGCGACGCTTTATCAC
1 AAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTCCCAC
* * *
2166 AAGCGCCGCTAATGCTCTGACCTTTAGTGACGCTTTCCCAC
1 AAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTCCCAC
* * * *
2207 AAATGCCGCTAATGCACTGATCTTTAGCGGCGCTTTCTCAC
1 AAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTCCCAC
* * *
2248 AAGCGCCACTAATGCTCTAACCTTTAGCGGCG
1 AAACGCCGCTAATGCTCTGACCTTTAGCGGCG
2280 TTTTTTTATA
Statistics
Matches: 131, Mismatches: 24, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
41 115 0.88
43 16 0.12
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.27
Consensus pattern (41 bp):
AAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTCCCAC
Found at i:2297 original size:123 final size:123
Alignment explanation
Indices: 2086--2312 Score: 267
Period size: 123 Copynumber: 1.8 Consensus size: 123
2076 ATGAGAAAAC
* * * *
2086 GCCGCTAATGCTCTGTGACCTTTAACGGTGCTTTCCCACAAACACCGCTAATGCTCTGACCTTTA
1 GCCGCTAATGCAC-GTGACCTTTAACGGCGCTTTCCCACAAACACCACTAATGCTCTAACCTTTA
*
2151 GCGACGCTTTATCACAAGCGCCGCTAATGCTCTGACCTTTAGTGACGCTTTCCCACAAAT
65 GCGACGCTTTATCACAAACGCCGCTAATGCT-TGACCTTTAGTGACGCTTTCCCACAAAT
* * * * *
2211 GCCGCTAATGCAC-TGATCTTTAGCGGCGCTTTCTCACAAGCGCCACTAATGCTCTAACCTTTAG
1 GCCGCTAATGCACGTGACCTTTAACGGCGCTTTCCCACAAACACCACTAATGCTCTAACCTTTAG
* * * * * * * *
2275 CGGCGTTTTTTTATAAATGCCGCTATTGCTTTACCTTT
66 CGACGCTTTATCACAAACGCCGCTAATGCTTGACCTTT
2313 TGCAGCGTTT
Statistics
Matches: 84, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
122 7 0.08
123 65 0.77
125 12 0.14
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.31
Consensus pattern (123 bp):
GCCGCTAATGCACGTGACCTTTAACGGCGCTTTCCCACAAACACCACTAATGCTCTAACCTTTAG
CGACGCTTTATCACAAACGCCGCTAATGCTTGACCTTTAGTGACGCTTTCCCACAAAT
Found at i:2322 original size:40 final size:40
Alignment explanation
Indices: 2252--2363 Score: 170
Period size: 40 Copynumber: 2.8 Consensus size: 40
2242 TCTCACAAGC
* * * *
2252 GCCACTAATGCTCTAACCTTTAGCGGCGTTTTTTTATAAAT
1 GCCACTATTGCT-TTACCTTTTGCAGCGTTTTTTTATAAAT
*
2293 GCCGCTATTGCTTTACCTTTTGCAGCGTTTTTTTATAAAT
1 GCCACTATTGCTTTACCTTTTGCAGCGTTTTTTTATAAAT
2333 GCCACTATTGCTTTACCTTTTGCAGCGTTTT
1 GCCACTATTGCTTTACCTTTTGCAGCGTTTT
2364 CTATACAAAC
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
40 55 0.85
41 10 0.15
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (40 bp):
GCCACTATTGCTTTACCTTTTGCAGCGTTTTTTTATAAAT
Found at i:3371 original size:18 final size:18
Alignment explanation
Indices: 3348--3389 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
3338 TCCAGGTCTC
3348 AAGCATTGACAAGCTGTA
1 AAGCATTGACAAGCTGTA
3366 AAGCATTGACAAGCTGTA
1 AAGCATTGACAAGCTGTA
3384 AAGCAT
1 AAGCAT
3390 ATGTTAAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (18 bp):
AAGCATTGACAAGCTGTA
Found at i:5472 original size:68 final size:68
Alignment explanation
Indices: 5338--5472 Score: 166
Period size: 68 Copynumber: 2.0 Consensus size: 68
5328 TTTTAATAGT
* * * * * *
5338 TTAATATTAAATTTAATTTTATACTTATTTTAATAATATTTTATTAATTTAATATTGAAGTTATT
1 TTAATATTAAATTTAATCTAATACTTATTTGAATAATATTATATTAATTTAATATTGAAATGATT
5403 ATC
66 ATC
* *
5406 TTAATATTAAATTTAATCTAATATTTATCTTGAGA-AATATTATATTAGTTTAATATT-AAATGA
1 TTAATATTAAATTTAATCTAATACTTAT-TTGA-ATAATATTATATTAATTTAATATTGAAATGA
5469 TTAT
64 TTAT
5473 GTTTAATCAT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
68 33 0.58
69 23 0.40
70 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (68 bp):
TTAATATTAAATTTAATCTAATACTTATTTGAATAATATTATATTAATTTAATATTGAAATGATT
ATC
Found at i:9937 original size:19 final size:19
Alignment explanation
Indices: 9913--9956 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
9903 TCTTTCCAAT
9913 GGAGAAACAATGGAAAAAG
1 GGAGAAACAATGGAAAAAG
9932 GGAGAAACAATGGAAAAAG
1 GGAGAAACAATGGAAAAAG
9951 GGAGAA
1 GGAGAA
9957 TGACCTTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.57, C:0.05, G:0.34, T:0.05
Consensus pattern (19 bp):
GGAGAAACAATGGAAAAAG
Found at i:11527 original size:33 final size:33
Alignment explanation
Indices: 11485--11553 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
11475 TTATTAGAAA
11485 GAAAGGGTACTTTAAGGTGAACTATAAAGAGTG
1 GAAAGGGTACTTTAAGGTGAACTATAAAGAGTG
11518 GAAAGGGTACTTTAAGGTGAACTATAAAGAGTG
1 GAAAGGGTACTTTAAGGTGAACTATAAAGAGTG
11551 GAA
1 GAA
11554 TGAGTACCTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.41, C:0.06, G:0.30, T:0.23
Consensus pattern (33 bp):
GAAAGGGTACTTTAAGGTGAACTATAAAGAGTG
Found at i:14182 original size:24 final size:24
Alignment explanation
Indices: 14154--14225 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
14144 GAGCAGGCCA
*
14154 ATTTTCACAGCTCGTGTGACCATT
1 ATTTTCACAGCTCGTGTGAGCATT
* *
14178 ATTTTCATAGTTCGTGTGAGCATT
1 ATTTTCACAGCTCGTGTGAGCATT
*
14202 ATTTTCACAGCTCATGTGAGCATT
1 ATTTTCACAGCTCGTGTGAGCATT
14226 TTTATCCCGC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.40
Consensus pattern (24 bp):
ATTTTCACAGCTCGTGTGAGCATT
Found at i:16053 original size:25 final size:24
Alignment explanation
Indices: 16018--16066 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
16008 TGAAAAAAAA
*
16018 ATTGTTTCGAAGAAATCTCGTTAT
1 ATTGTTTCGAAGAAAGCTCGTTAT
16042 ATTGTTTTCGAAGAAAGCTCGTTAT
1 ATTG-TTTCGAAGAAAGCTCGTTAT
16067 TTCGAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (24 bp):
ATTGTTTCGAAGAAAGCTCGTTAT
Found at i:17538 original size:39 final size:38
Alignment explanation
Indices: 17438--17540 Score: 111
Period size: 39 Copynumber: 2.7 Consensus size: 38
17428 AGAGTTTTAG
** *
17438 GGGTAAAAGATTGGATTATTTCAATCTGCCCCATGGTC
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTA
* *
17476 GGGTAAGAGATCT-GATGGTCTTCAATCTGCCCTC-TGGTTA
1 GGGTAAAAGAT-TGGATTG-CTTCAATCTGCCC-CATGG-TA
17516 GGGTAAAAGATTGGATTGCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAAT
17541 TTGTCGGATG
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
38 13 0.25
39 24 0.45
40 16 0.30
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (38 bp):
GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTA
Found at i:17581 original size:58 final size:58
Alignment explanation
Indices: 17489--17598 Score: 168
Period size: 58 Copynumber: 1.9 Consensus size: 58
17479 TAAGAGATCT
* *
17489 GATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATTGCTTCAATTTGTCG
1 GATGGTCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTACTTCAATTTGTCG
* *
17547 GATGGTCTTCAATTTGCCCTTTAGTT-GGGATAAAAGATTGGATTACTTCAAT
1 GATGGTCTTCAATCTGCCCTCTAGTTAGGG-TAAAAGATTGGATTACTTCAAT
17599 CTACCCCATT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
57 3 0.06
58 44 0.94
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (58 bp):
GATGGTCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTACTTCAATTTGTCG
Found at i:17620 original size:39 final size:39
Alignment explanation
Indices: 17577--17947 Score: 313
Period size: 39 Copynumber: 9.3 Consensus size: 39
17567 TTAGTTGGGA
* *
17577 TAAAAGATTGGATTACTTCAATCTACCCCATTG-TCAGGG
1 TAAAAGATTGGATTTCTTCAATCTGCCCCA-TGATCAGGG
* * *
17616 TAAAAGATTGGATTTGTTTAATCTGCCCCATGATCGGGG
1 TAAAAGATTGGATTTCTTCAATCTGCCCCATGATCAGGG
* * ** * *
17655 TAAAAGATCGGATGGTCTTCAATCTTGCCCTTTAATTAGGG
1 TAAAAGATTGGAT-TTCTTCAATC-TGCCCCATGATCAGGG
* * **
17696 TAAAAGATTGAATTTCTTCAATCTGCCTCATGATTGGGG
1 TAAAAGATTGGATTTCTTCAATCTGCCCCATGATCAGGG
* * * *
17735 TAAAAGATCGGATGGTCTTCAATCTTGTCCTC-TGATTAGGG
1 TAAAAGATTGGAT-TTCTTCAATC-TG-CCCCATGATCAGGG
* *
17776 TAAAAGATTGGATTTCTTCAATCTGCTCCATGATCGGGG
1 TAAAAGATTGGATTTCTTCAATCTGCCCCATGATCAGGG
* * *
17815 TAAAAGATCGGATGATT-TTCAATCTTGCCCTC-TGGTTAGGG
1 TAAAAGATTGGAT--TTCTTCAATC-TGCCC-CATGATCAGGG
* *
17856 TAAAAGATTGAATTTCTTCAATCTGCCCCATGATCGGGG
1 TAAAAGATTGGATTTCTTCAATCTGCCCCATGATCAGGG
* * *
17895 TAAAAGATCGGATGGTT-TTCAATCTTGCCCTC-TGGTTAGGG
1 TAAAAGATTGGAT--TTCTTCAATC-TGCCC-CATGATCAGGG
17936 TAAAAGATTGGA
1 TAAAAGATTGGA
17948 GGTTGTAACT
Statistics
Matches: 267, Mismatches: 48, Indels: 32
0.77 0.14 0.09
Matches are distributed among these distances:
38 5 0.02
39 110 0.41
40 55 0.21
41 91 0.34
42 6 0.02
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (39 bp):
TAAAAGATTGGATTTCTTCAATCTGCCCCATGATCAGGG
Found at i:17704 original size:80 final size:80
Alignment explanation
Indices: 17612--17947 Score: 537
Period size: 80 Copynumber: 4.2 Consensus size: 80
17602 CCCCATTGTC
* *
17612 AGGGTAAAAGATTGGATTTGTTTAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
* *
17677 TCTTGCCCTTTAATT
66 TCTTGCCCTCTGATT
* * *
17692 AGGGTAAAAGATTGAATTTCTTCAATCTGCCTCATGATTGGGGTAAAAGATCGGATGGTCTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
*
17757 TCTTGTCCTCTGATT
66 TCTTGCCCTCTGATT
* * *
17772 AGGGTAAAAGATTGGATTTCTTCAATCTGCTCCATGATCGGGGTAAAAGATCGGATGATTTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
*
17837 TCTTGCCCTCTGGTT
66 TCTTGCCCTCTGATT
* *
17852 AGGGTAAAAGATTGAATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTTTTCAA
1 AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
*
17917 TCTTGCCCTCTGGTT
66 TCTTGCCCTCTGATT
17932 AGGGTAAAAGATTGGA
1 AGGGTAAAAGATTGGA
17948 GGTTGTAACT
Statistics
Matches: 236, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 236 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.33
Consensus pattern (80 bp):
AGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
TCTTGCCCTCTGATT
Found at i:18189 original size:50 final size:50
Alignment explanation
Indices: 18002--18192 Score: 222
Period size: 50 Copynumber: 3.8 Consensus size: 50
17992 TCCTTGTGAC
* * * * * * *
18002 TTCAATCTTCTCCTCTACAGCTTTAAGTGAATGAGATTTGTCATTACAGC
1 TTCAATCTGCACCTCCACAGCTTTAGGTGTATGAGATTTGTCATTGCAGT
* * * * *
18052 TTCATTCTACCCCTCTACAGCTTTAGGTGTATGAGATTT-TCCATTGCGGT
1 TTCAATCTGCACCTCCACAGCTTTAGGTGTATGAGATTTGT-CATTGCAGT
*
18102 TTCAATCTGCACCTCCACAGCTTAAGGTGTATGAGATTTGTCATTGCAGT
1 TTCAATCTGCACCTCCACAGCTTTAGGTGTATGAGATTTGTCATTGCAGT
* **
18152 TTCAATCTGCACCTCCACAGCTTTAGGGGTAAAAGATTTGT
1 TTCAATCTGCACCTCCACAGCTTTAGGTGTATGAGATTTGT
18193 TGTTCTATCG
Statistics
Matches: 121, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
49 1 0.01
50 119 0.98
51 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.36
Consensus pattern (50 bp):
TTCAATCTGCACCTCCACAGCTTTAGGTGTATGAGATTTGTCATTGCAGT
Found at i:18189 original size:100 final size:100
Alignment explanation
Indices: 18002--18190 Score: 245
Period size: 100 Copynumber: 1.9 Consensus size: 100
17992 TCCTTGTGAC
* * * * *
18002 TTCAATCTTCTCCTCTACAGCTTTAAGTGAATGAGATTTGTCATTACAGCTTCATTCTACCCCTC
1 TTCAATCTGCACCTCCACAGCTTTAAGTGAATGAGATTTGTCATTACAGCTTCAATCTACACCTC
* * **
18067 TACAGCTTTAGGTGTATGAGATTTTCCATTGCGGT
66 CACAGCTTTAGGGGTAAAAGATTTTCCATTGCGGT
* * * *
18102 TTCAATCTGCACCTCCACAGC-TTAAGGTGTATGAGATTTGTCATTGCAGTTTCAATCTGCACCT
1 TTCAATCTGCACCTCCACAGCTTTAA-GTGAATGAGATTTGTCATTACAGCTTCAATCTACACCT
18166 CCACAGCTTTAGGGGTAAAAGATTT
65 CCACAGCTTTAGGGGTAAAAGATTT
18191 GTTGTTCTAT
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
99 4 0.05
100 71 0.95
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (100 bp):
TTCAATCTGCACCTCCACAGCTTTAAGTGAATGAGATTTGTCATTACAGCTTCAATCTACACCTC
CACAGCTTTAGGGGTAAAAGATTTTCCATTGCGGT
Found at i:19077 original size:20 final size:20
Alignment explanation
Indices: 19054--19144 Score: 74
Period size: 20 Copynumber: 4.9 Consensus size: 20
19044 TCGACATCCC
19054 CTTTTTCTCTTTC-TTTTCTT
1 CTTTTTCTCTTTCTTTTTC-T
19074 CTTTTTC-CTTTTCTTTTTCT
1 CTTTTTCTC-TTTCTTTTTCT
*
19094 CTTTTTCTC-TT-TTTCTCT
1 CTTTTTCTCTTTCTTTTTCT
*
19112 -TTTTTC-CTTT-TTTTCCT
1 CTTTTTCTCTTTCTTTTTCT
*
19129 -TTTTTGTCTTT-TTTTT
1 CTTTTTCTCTTTCTTTTT
19145 TGAAATTTCT
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
16 1 0.02
17 18 0.30
18 14 0.23
19 3 0.05
20 19 0.31
21 6 0.10
ACGTcount: A:0.00, C:0.22, G:0.01, T:0.77
Consensus pattern (20 bp):
CTTTTTCTCTTTCTTTTTCT
Found at i:19142 original size:9 final size:8
Alignment explanation
Indices: 19054--19143 Score: 76
Period size: 8 Copynumber: 11.0 Consensus size: 8
19044 TCGACATCCC
*
19054 CTTTTTCT
1 CTTTTTTT
19062 CTTTCTTTT
1 CTTT-TTTT
19071 CTTCTTTTT
1 CTT-TTTTT
*
19080 C--CTTTT
1 CTTTTTTT
*
19086 CTTTTTCT
1 CTTTTTTT
*
19094 CTTTTTCT
1 CTTTTTTT
*
19102 CTTTTTCT
1 CTTTTTTT
*
19110 CTTTTTTC
1 CTTTTTTT
19118 CTTTTTTT
1 CTTTTTTT
19126 CCTTTTTTGT
1 -CTTTTTT-T
19136 CTTTTTTT
1 CTTTTTTT
19144 TTGAAATTTC
Statistics
Matches: 69, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
6 5 0.07
8 37 0.54
9 25 0.36
10 2 0.03
ACGTcount: A:0.00, C:0.22, G:0.01, T:0.77
Consensus pattern (8 bp):
CTTTTTTT
Found at i:24251 original size:66 final size:67
Alignment explanation
Indices: 24150--24297 Score: 192
Period size: 66 Copynumber: 2.2 Consensus size: 67
24140 TATATTCATA
** ** *
24150 AAATAATAAAGCAAAATTAATATTATTTTACATTTATTTAT-TTATATTCATACAATAATAAATA
1 AAATAATAAAATAAAATTAATATTATTTTACATTTATTTATATT-TATAAAAACAATAATAAATA
24214 AAT
65 AAT
* *
24217 AAATAATAAAATAAAA-TAATATTATTTTATATTTATTTATATTTATAAAAATAATAATAAATAA
1 AAATAATAAAATAAAATTAATATTATTTTACATTTATTTATATTTATAAAAACAATAATAAATAA
24281 AT
66 AT
*
24283 AAATAAAAATAATAA
1 AAATAATAA-AATAA
24298 GAAAAATGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
66 50 0.70
67 21 0.30
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.40
Consensus pattern (67 bp):
AAATAATAAAATAAAATTAATATTATTTTACATTTATTTATATTTATAAAAACAATAATAAATAA
AT
Found at i:24276 original size:62 final size:67
Alignment explanation
Indices: 24150--24290 Score: 186
Period size: 62 Copynumber: 2.2 Consensus size: 67
24140 TATATTCATA
* *
24150 AAATAATAAAGCAAAATTAATATTATTTTACATTTATTTATTTATATTCATACAATAATAAATAA
1 AAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATATTCATAAAATAATAAATAA
24215 AT
66 AT
* *
24217 AAATAATAAAATAAAA-TAATATTATTTT--A--TATTTATTTATATTTATAAAAATAAT-AATA
1 AAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATATTCAT-AAAATAATAAATA
24276 AAT
65 AAT
24279 AAATAAATAAAA
1 AAAT-AATAAAA
24291 ATAATAAGAA
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
62 27 0.40
63 14 0.21
64 1 0.01
66 12 0.18
67 14 0.21
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (67 bp):
AAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATATTCATAAAATAATAAATAA
AT
Found at i:24304 original size:18 final size:18
Alignment explanation
Indices: 24263--24304 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
24253 TTATATTTAT
*
24263 AAAAATAATAATAAATAA
1 AAAAATAAAAATAAATAA
*
24281 ATAAATAAAAAT-AATAA
1 AAAAATAAAAATAAATAA
24298 GAAAAAT
1 -AAAAAT
24305 GAAATTGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (18 bp):
AAAAATAAAAATAAATAA
Found at i:24608 original size:28 final size:28
Alignment explanation
Indices: 24577--24647 Score: 117
Period size: 28 Copynumber: 2.5 Consensus size: 28
24567 AAGTAGACCG
24577 AAGCTCTACCCGAGCTATAAAC-AGTTCA
1 AAGCTCTACCCGAGCTATAAACGA-TTCA
*
24605 AAGCTCTACTCGAGCTATAAACGATTCA
1 AAGCTCTACCCGAGCTATAAACGATTCA
24633 AAGCTCTACCCGAGC
1 AAGCTCTACCCGAGC
24648 AACCATTCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 39 0.98
29 1 0.03
ACGTcount: A:0.34, C:0.30, G:0.15, T:0.21
Consensus pattern (28 bp):
AAGCTCTACCCGAGCTATAAACGATTCA
Found at i:27029 original size:62 final size:63
Alignment explanation
Indices: 26923--27040 Score: 150
Period size: 62 Copynumber: 1.9 Consensus size: 63
26913 TGATAGGCCA
* * * * *
26923 TGTAACTCACTATTTATGAATTAATGGCACACAGGCTAGGGACACGAGCGTGTGTCCATGCTT
1 TGTAACTCACTATTTAGGAAATAATGGCACACAGGCCAGAGACACGAGCATGTGTCCATGCTT
* *
26986 TGTAACTCATTATTT-GGAAATAA-GGTCACACGGGCCAGAGACACGAGCATGTGTC
1 TGTAACTCACTATTTAGGAAATAATGG-CACACAGGCCAGAGACACGAGCATGTGTC
27041 TAGGCCGTGT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
61 2 0.04
62 31 0.66
63 14 0.30
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (63 bp):
TGTAACTCACTATTTAGGAAATAATGGCACACAGGCCAGAGACACGAGCATGTGTCCATGCTT
Found at i:29279 original size:27 final size:26
Alignment explanation
Indices: 29249--29323 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 26
29239 AATCAATATT
29249 TTTAT-TTATTTAGAAGATTAGATTTAG
1 TTTATATTA-TTAGAA-ATTAGATTTAG
* *
29276 TTTATGATTATTAGGAATTAGATTTAA
1 TTTAT-ATTATTAGAAATTAGATTTAG
* *
29303 TTTCTGATTATTAGGAATTAG
1 TTTAT-ATTATTAGAAATTAG
29324 CTATTGTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 35 0.81
28 5 0.12
29 3 0.07
ACGTcount: A:0.33, C:0.01, G:0.16, T:0.49
Consensus pattern (26 bp):
TTTATATTATTAGAAATTAGATTTAG
Found at i:38379 original size:20 final size:20
Alignment explanation
Indices: 38354--38408 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
38344 TTTAAATTCA
*
38354 TTTTTAAATTTAAATTTATC
1 TTTTTAAATTTAAATTTAGC
38374 TTTTTAAATTTAAATTT-GC
1 TTTTTAAATTTAAATTTAGC
38393 --TTTAAATTTAAATTTA
1 TTTTTAAATTTAAATTTA
38409 ATCAAATTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
17 15 0.45
19 1 0.03
20 17 0.52
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTTTAAATTTAAATTTAGC
Found at i:40324 original size:29 final size:29
Alignment explanation
Indices: 40289--40480 Score: 160
Period size: 29 Copynumber: 6.5 Consensus size: 29
40279 CTAAATTATT
40289 CAAAAATTACATTTTTACCCCTAAACTTC
1 CAAAAATTACATTTTTACCCCTAAACTTC
*
40318 CAAAAA-TATCATTTTTA-CCCTCGAACTTC
1 CAAAAATTA-CATTTTTACCCCT-AAACTTC
* *
40347 CAAAAATTCCATTTTTGACCCCAAAACTTC
1 CAAAAATTACATTTTT-ACCCCTAAACTTC
* * * *
40377 TAGAAATT-CTATTTTTGACCACGAAACTTC
1 CAAAAATTAC-ATTTTT-ACCCCTAAACTTC
* * * *
40407 CAAAATTTTCATTTTTACCCCCAAACCTC
1 CAAAAATTACATTTTTACCCCTAAACTTC
* *
40436 C-AAAATTTCTATTTTTTA-CCCTAAACTTT
1 CAAAAATTAC-A-TTTTTACCCCTAAACTTC
40465 CAAAAATTACCATTTT
1 CAAAAATTA-CATTTT
40481 GCCCTCGGAT
Statistics
Matches: 133, Mismatches: 19, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
28 13 0.10
29 59 0.44
30 56 0.42
31 5 0.04
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
CAAAAATTACATTTTTACCCCTAAACTTC
Found at i:40391 original size:59 final size:57
Alignment explanation
Indices: 40289--40480 Score: 192
Period size: 59 Copynumber: 3.3 Consensus size: 57
40279 CTAAATTATT
* *
40289 CAAAAATTACATTTTTACCCCTAAACTTCCAAAAATATC-ATTTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTACCCCAAAACTTCC-AAAAT-TCTATTTTTACCCTCGAACTTC
* *
40347 CAAAAATTCCATTTTTGACCCCAAAACTTCTAGAAATTCTATTTTTGA-CCACGAAACTTC
1 CAAAAATTCCATTTTT-ACCCCAAAACTTCCA-AAATTCTATTTTT-ACCCTCG-AACTTC
* * * * * *
40407 CAAAATTTTCATTTTTACCCCCAAACCTCCAAAATTTCTATTTTTTACCCT-AAACTTT
1 CAAAAATTCCATTTTTACCCCAAAACTTCCAAAA-TTCTA-TTTTTACCCTCGAACTTC
40465 CAAAAATTACCATTTT
1 CAAAAATT-CCATTTT
40481 GCCCTCGGAT
Statistics
Matches: 111, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
58 33 0.30
59 50 0.45
60 28 0.25
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (57 bp):
CAAAAATTCCATTTTTACCCCAAAACTTCCAAAATTCTATTTTTACCCTCGAACTTC
Found at i:52058 original size:13 final size:14
Alignment explanation
Indices: 52029--52058 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
52019 TTCAGTACAT
52029 TGACATTTAACCTC
1 TGACATTTAACCTC
52043 TGACATTTAA-CTC
1 TGACATTTAACCTC
52056 TGA
1 TGA
52059 TTACATTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:52325 original size:36 final size:36
Alignment explanation
Indices: 52278--52400 Score: 176
Period size: 36 Copynumber: 3.4 Consensus size: 36
52268 GACGCGATCA
* *
52278 AACATACCCAGATATTTTCTGTCATATTGCATGAAG
1 AACATACCCACATATTTTCTGTCACATTGCATGAAG
* *
52314 AACATACCCAGATATTTTCTATCACA-TGCCATGAAG
1 AACATACCCACATATTTTCTGTCACATTG-CATGAAG
* *
52350 AACATACCTACATATTTTCTGTCACATGGCATGAAG
1 AACATACCCACATATTTTCTGTCACATTGCATGAAG
52386 AACATACCCACATAT
1 AACATACCCACATAT
52401 CCACTTTCAC
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
35 2 0.03
36 75 0.96
37 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (36 bp):
AACATACCCACATATTTTCTGTCACATTGCATGAAG
Found at i:52508 original size:23 final size:23
Alignment explanation
Indices: 52481--52582 Score: 141
Period size: 23 Copynumber: 4.4 Consensus size: 23
52471 ATCTTAATTC
*
52481 TTTAAGCACAAATCCCATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
52504 TTTAAGCATAAATCACACTAATA
1 TTTAAGCACAAATCACATTAATA
**
52527 TTTAAGCATGAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
52550 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
52573 TTTAAGCACA
1 TTTAAGCACA
52583 GATATAAGAA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:61357 original size:21 final size:24
Alignment explanation
Indices: 61333--61375 Score: 65
Period size: 21 Copynumber: 1.9 Consensus size: 24
61323 ACTCAAAAGA
61333 AAATAAAA-A-TA-TTTTATAATT
1 AAATAAAATATTATTTTTATAATT
61354 AAATAAAATATTATTTTTATAA
1 AAATAAAATATTATTTTTATAA
61376 ATATTAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 1 0.05
23 2 0.11
24 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
AAATAAAATATTATTTTTATAATT
Found at i:67958 original size:23 final size:24
Alignment explanation
Indices: 67932--68003 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 24
67922 ATAAAAATGT
67932 ATGTTTTATTATTATTATTTGA-A
1 ATGTTTTATTATTATTATTTGATA
67955 ATG-TTTAGTTATTATTATTTGATA
1 ATGTTTTA-TTATTATTATTTGATA
*
67979 AT-TAATTGTTTTATTATTATTTGAT
1 ATGT--TT-TATTATTATTATTTGAT
68004 TTTAATAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
22 4 0.10
23 17 0.40
24 3 0.07
26 17 0.40
27 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (24 bp):
ATGTTTTATTATTATTATTTGATA
Found at i:68017 original size:26 final size:26
Alignment explanation
Indices: 67963--68017 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
67953 AAATGTTTAG
**
67963 TTATTATTATTTGATAATTAATTGTT
1 TTATTATTATTTGATAATTAATAATT
*
67989 TTATTATTATTTGAT-TTTAATAATAT
1 TTATTATTATTTGATAATTAATAAT-T
68015 TTA
1 TTA
68018 CATAATTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (26 bp):
TTATTATTATTTGATAATTAATAATT
Found at i:70346 original size:6 final size:6
Alignment explanation
Indices: 70335--70361 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
70325 CTATTTAAAT
70335 CCTTCA CCTTCA CCTTCA CCTTCA CCT
1 CCTTCA CCTTCA CCTTCA CCTTCA CCT
70362 CCCCCTCCCC
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:0.15, C:0.52, G:0.00, T:0.33
Consensus pattern (6 bp):
CCTTCA
Done.