Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012465.1 Kokia drynarioides strain JFW-HI SEQ_127469, 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: 29962
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:414 original size:16 final size:16
Alignment explanation
Indices: 393--424 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
383 AAAACTTTTA
393 CCACTCCACTCCCATC
1 CCACTCCACTCCCATC
*
409 CCACTCCACTCTCATC
1 CCACTCCACTCCCATC
425 TACCCCCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.59, G:0.00, T:0.22
Consensus pattern (16 bp):
CCACTCCACTCCCATC
Found at i:638 original size:20 final size:20
Alignment explanation
Indices: 605--644 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
595 AAAACCTCTA
*
605 AAACTTTTTATTTTCCCCCT
1 AAACTTTTTATTTTCACCCT
625 AAAC-TTTTACTTTTCACCCT
1 AAACTTTTTA-TTTTCACCCT
645 TTACCCCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (20 bp):
AAACTTTTTATTTTCACCCT
Found at i:788 original size:18 final size:19
Alignment explanation
Indices: 765--808 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
755 CTATTTATAT
765 TATTGAAAATTT-TAATAA
1 TATTGAAAATTTATAATAA
* *
783 TATTGAATATTTATATTAA
1 TATTGAAAATTTATAATAA
*
802 AATTGAA
1 TATTGAA
809 TTATTAATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (19 bp):
TATTGAAAATTTATAATAA
Found at i:808 original size:19 final size:18
Alignment explanation
Indices: 766--809 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
756 TATTTATATT
* *
766 ATTGAAAATTTTAATAAT
1 ATTGAATATTTTAATAAA
*
784 ATTGAATATTTATATTAAA
1 ATTGAATATTT-TAATAAA
803 ATTGAAT
1 ATTGAAT
810 TATTAATGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (18 bp):
ATTGAATATTTTAATAAA
Found at i:3488 original size:114 final size:114
Alignment explanation
Indices: 3277--3490 Score: 286
Period size: 114 Copynumber: 1.9 Consensus size: 114
3267 ATCCGATTTG
* * * * * *
3277 TTTTGATCCACTTCTCTGTACCTCACCAAGAAGATGAGATTGGAAGTCTTACTTCACTTCACTGT
1 TTTTGACCCACTTCTCTATACCTCACCAAGAAAATGAGATTGGAAGTCTCACTCCACTCCACTGT
** *
3342 ATTCTCAGGGACGTTGAGCTCGACTTCGTTATTTTGATTCAATACACTA
66 AACCTCAGGGACGTTGAGCTCGACTTCATTATTTTGATTCAATACACTA
* * *
3391 TTTTGACCCACTTCTTTATACCTCACCAGGAAAATGAGATTTGAAGTCTCACTCCACTCCACTGT
1 TTTTGACCCACTTCTCTATACCTCACCAAGAAAATGAGATTGGAAGTCTCACTCCACTCCACTGT
* *
3456 AACCTTATGGACGTTGAGCTCTG-CTTCATTATTTT
66 AACCTCAGGGACGTTGAGCTC-GACTTCATTATTTT
3491 CATCCGATCC
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
114 84 0.99
115 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (114 bp):
TTTTGACCCACTTCTCTATACCTCACCAAGAAAATGAGATTGGAAGTCTCACTCCACTCCACTGT
AACCTCAGGGACGTTGAGCTCGACTTCATTATTTTGATTCAATACACTA
Found at i:3718 original size:188 final size:188
Alignment explanation
Indices: 3388--3945 Score: 746
Period size: 188 Copynumber: 3.0 Consensus size: 188
3378 ATTCAATACA
* * *
3388 CTATTTTGACCCACTTCTTTATACCTCACCAGGAAAATGAGATTTGAAGTCTCACTCCACTCCAC
1 CTATTTTGACCCACTTCTTTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCAC
* * * **
3453 TGTAACCTTATGGACGTTGAGCTCTGCTTCATTATTTTCATCCGA-TCCACTACAACTCAGGGAC
66 TGTAACCTTAGGGACGTTGAGCTCTGATTCATTATTTTCATCCGACT-CACTGCAACTCAGGGGT
* * *
3517 ATAGGAATTGGTGCTTCACTCCACTCTCCTGTAACCTTAGGGACATTGAGATTTGCTAC
130 ATAGGATTTGGTGCTTCACTCCACTCTCCTGTAACCTCAGGGACATTGAGATCTGCTAC
* * * * * * *
3576 TTGTTTTGACCCACTTCTTTGTACCTCACTAGGAAGATGGGAATTAAAGTCTTACTCCAATCCAC
1 CTATTTTGACCCACTTCTTTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCAC
*
3641 TGTAACCTTAGGGACGTTGAGCTCTGATTCATTATTTTCAACCGACTCACTGCAACTCAGGGGTA
66 TGTAACCTTAGGGACGTTGAGCTCTGATTCATTATTTTCATCCGACTCACTGCAACTCAGGGGTA
** * * *
3706 TAGGATTTGGTGCTTCACTCCACT-TAATTGTAACCTGAGGGACGTTAAGATCTGCTAC
131 TAGGATTTGGTGCTTCACTCCACTCT-CCTGTAACCTCAGGGACATTGAGATCTGCTAC
*
3764 CTATTTTGACCCACTTCTATGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCAC
1 CTATTTTGACCCACTTCTTTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCAC
* * * * * *
3829 TGTAACCTCAGAGACGTTGAGCTCT-ACTTCATTATTTTTATCCGACCCACTGTAACTCAGAGGT
66 TGTAACCTTAGGGACGTTGAGCTCTGA-TTCATTATTTTCATCCGACTCACTGCAACTCAGGGGT
* * *
3893 ATACGATTTGGTGCTTTACTCCACTC-CACTGTAACCTCAGAGACATTGAGATC
130 ATAGGATTTGGTGCTTCACTCCACTCTC-CTGTAACCTCAGGGACATTGAGATC
3946 CGCTTTGTTG
Statistics
Matches: 319, Mismatches: 46, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
187 2 0.01
188 316 0.99
189 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (188 bp):
CTATTTTGACCCACTTCTTTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCAC
TGTAACCTTAGGGACGTTGAGCTCTGATTCATTATTTTCATCCGACTCACTGCAACTCAGGGGTA
TAGGATTTGGTGCTTCACTCCACTCTCCTGTAACCTCAGGGACATTGAGATCTGCTAC
Found at i:3833 original size:95 final size:96
Alignment explanation
Indices: 3384--3866 Score: 336
Period size: 95 Copynumber: 5.1 Consensus size: 96
3374 TTTGATTCAA
* * * * *
3384 TACACTATTTTGACCCACTTCTTTATACCTCACCAGGAAAATGAGATTTGAAGTCTCACTCCACT
1 TACATTATTTTGACCCACTTCTATGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACT
* *
3449 CCACTGTAACCTTATGGACGTTGAGCTCTGC
66 CCACTGTAACCTTAGGGACGTTGAGATCTGC
* * * * * * * * * *
3480 TTCATTATTTTCATCCGA--TCCA-CTA-C-AACTCAGGGACATAGGAATTG--GTGCTTCACTC
1 TACATTATTTTGA-CCCACTTCTATGTACCTCAC-CAGGAAGATGGGATTTGAAGT-C-TCACTC
* *
3538 CACTCTC-CTGTAACCTTAGGGACATTGAGATTTGC
62 CACTC-CACTGTAACCTTAGGGACGTTGAGATCTGC
* * * * * * *
3573 TAC-TTGTTTTGACCCACTTCTTTGTACCTCACTAGGAAGATGGGAATTAAAGTCTTACTCCAAT
1 TACATTATTTTGACCCACTTCTATGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACT
* *
3637 CCACTGTAACCTTAGGGACGTTGAGCTCTGA
66 CCACTGTAACCTTAGGGACGTTGAGATCTGC
* * * * * * *
3668 TTCATTATTTTCAACCGAC-TC-ACTGCAACT---CAGG-GGTATAGGATTTG--GTGCTTCACT
1 TACATTATTTT-GACCCACTTCTA-TGTACCTCACCAGGAAG-ATGGGATTTGAAGT-C-TCACT
** * * *
3725 CCACTTAATTGTAACCTGAGGGACGTTAAGATCTGC
61 CCACTCCACTGTAACCTTAGGGACGTTGAGATCTGC
*
3761 TAC-CTATTTTGACCCACTTCTATGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACT
1 TACATTATTTTGACCCACTTCTATGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACT
* * * *
3825 CCACTGTAACCTCAGAGACGTTGAGCTCTAC
66 CCACTGTAACCTTAGGGACGTTGAGATCTGC
*
3856 TTCATTATTTT
1 TACATTATTTT
3867 TATCCGACCC
Statistics
Matches: 284, Mismatches: 75, Indels: 56
0.68 0.18 0.13
Matches are distributed among these distances:
91 12 0.04
92 25 0.09
93 97 0.34
94 6 0.02
95 98 0.35
96 34 0.12
97 12 0.04
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (96 bp):
TACATTATTTTGACCCACTTCTATGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACT
CCACTGTAACCTTAGGGACGTTGAGATCTGC
Found at i:3919 original size:93 final size:92
Alignment explanation
Indices: 3439--3942 Score: 274
Period size: 93 Copynumber: 5.4 Consensus size: 92
3429 ATTTGAAGTC
* * *
3439 TCACTCCACTCCACTGTAACCTTATG-GACGTTGAGCTCTGCTTCATTATTTTCATCCGATCCAC
1 TCACTCCACTCCACTGTAACCTCA-GAGACGTTGAGCTCTACTTCATTATTTTCA-CCGACCCAC
** * *
3503 TACAACTCAG-GGACATAGGAATTGGTGCT
64 TGTAACTCAGAGG-TATAGGATTTGGTGCT
* * * * * * * * * * * **
3532 TCACTCCACTCTC-CTGTAACCTTAGGGACATTGAGATTTGCTAC-TTGTTTTGACCCACTTCTT
1 TCACTCCACTC-CACTGTAACCTCAGAGACGTTGAGCTCTACTTCATTATTTTCACCGAC-CCAC
* * * * **
3595 TGTACCTCACTAGGAAGATGGGAATTAAAGT-CT
64 TGTAACTCA-GAGG--TATAGG-ATT-TGGTGCT
* * * *
3628 T-ACTCCAATCCACTGTAACCTTAGGGACGTTGAGCTCTGA-TTCATTATTTTCAACCGACTCAC
1 TCACTCCACTCCACTGTAACCTCAGAGACGTTGAGCTCT-ACTTCATTATTTTC-ACCGACCCAC
* *
3691 TGCAACTCAGGGGTATAGGATTTGGTGCT
64 TGTAACTCAGAGGTATAGGATTTGGTGCT
** * * * * * * * * * * *
3720 TCACTCCACTTAATTGTAACCTGAGGGACGTTAAGATCTGCTAC-CTATTTTGACCCACTTCTA-
1 TCACTCCACTCCACTGTAACCTCAGAGACGTTGAGCTCTACTTCATTATTTTCACCGAC--CCAC
* * * *
3783 TGTACCTCACCAGGAAGATGGGATTTGAAGT-C-
64 TGTAACTCA-GAGG--TATAGGATTTG--GTGCT
*
3815 TCACTCCACTCCACTGTAACCTCAGAGACGTTGAGCTCTACTTCATTATTTTTATCCGACCCACT
1 TCACTCCACTCCACTGTAACCTCAGAGACGTTGAGCTCTACTTCATTATTTTCA-CCGACCCACT
*
3880 GTAACTCAGAGGTATACGATTTGGTGCT
65 GTAACTCAGAGGTATAGGATTTGGTGCT
* *
3908 TTACTCCACTCCACTGTAACCTCAGAGACATTGAG
1 TCACTCCACTCCACTGTAACCTCAGAGACGTTGAG
3943 ATCCGCTTTG
Statistics
Matches: 305, Mismatches: 79, Indels: 54
0.70 0.18 0.12
Matches are distributed among these distances:
91 12 0.04
92 35 0.11
93 116 0.38
94 4 0.01
95 89 0.29
96 36 0.12
97 13 0.04
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (92 bp):
TCACTCCACTCCACTGTAACCTCAGAGACGTTGAGCTCTACTTCATTATTTTCACCGACCCACTG
TAACTCAGAGGTATAGGATTTGGTGCT
Found at i:4104 original size:49 final size:48
Alignment explanation
Indices: 4051--4335 Score: 236
Period size: 49 Copynumber: 5.8 Consensus size: 48
4041 TATAAGATTT
* * * * *
4051 GTCGTTATGGCTTCAATATTTCCCTTCACATCTCTAAGGTATAAGGTAC
1 GTCGTTGTGGCTTCAATCTTTCCCTTCACATCTTTAGGGTATAAGCT-C
* * * * *
4100 GTCGTTGCGACTTCAACCTTT-CCTTCTACATCTCTAGGGTATAAGATTC
1 GTCGTTGTGGCTTCAATCTTTCCCTTC-ACATCTTTAGGGTATAAG-CTC
* * * * *
4149 GCCGTTGTAGCTTAAATCTTTCCCTTCACATCTTTAGGGTATAAGGTTT
1 GTCGTTGTGGCTTCAATCTTTCCCTTCACATCTTTAGGGTATAA-GCTC
* *
4198 GTCGTTGTGGCTT-TAGCTTTTCCC-TCAACATCTTTAGGGTATAAGACTC
1 GTCGTTGTGGCTTCAATC-TTTCCCTTC-ACATCTTTAGGGTATAAG-CTC
* * *
4247 G-CTGTTGTGGCTTTAACCTTTCTCTTCACATCTTTAGGGTATAAGACTC
1 GTC-GTTGTGGCTTCAATCTTTCCCTTCACATCTTTAGGGTATAAG-CTC
* * * *
4296 GCCGTTGCGGCTTCAATATTTCCCTTCATATCTTCTAGGG
1 GTCGTTGTGGCTTCAATCTTTCCCTTCACATCTT-TAGGG
4336 CATATGAATC
Statistics
Matches: 194, Mismatches: 30, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
48 11 0.06
49 166 0.86
50 17 0.09
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.39
Consensus pattern (48 bp):
GTCGTTGTGGCTTCAATCTTTCCCTTCACATCTTTAGGGTATAAGCTC
Found at i:4190 original size:98 final size:98
Alignment explanation
Indices: 4041--4291 Score: 295
Period size: 98 Copynumber: 2.6 Consensus size: 98
4031 GAGACATAAT
* * * * * * *
4041 TATAAGATTTGTCGTTATGGCTTCAATATTTCCCTTCACATCTCTAAGGTATAAGGTACGTCGTT
1 TATAAGATTCGCCGTTGTGGCTTAAATCTTTCCCTTCACATCTTTAGGGTATAAGGTACGTCGTT
* *
4106 GCGACTTCAACCTTTCCTTCTACATCTCTAGGG
66 GCGACTTCAACCTTTCCCTCAACATCTCTAGGG
* **
4139 TATAAGATTCGCCGTTGTAGCTTAAATCTTTCCCTTCACATCTTTAGGGTATAAGGTTTGTCGTT
1 TATAAGATTCGCCGTTGTGGCTTAAATCTTTCCCTTCACATCTTTAGGGTATAAGGTACGTCGTT
* * * * * *
4204 GTGGCTTTAGCTTTTCCCTCAACATCTTTAGGG
66 GCGACTTCAACCTTTCCCTCAACATCTCTAGGG
* * * * *
4237 TATAAGACTCGCTGTTGTGGCTTTAACCTTTCTCTTCACATCTTTAGGGTATAAG
1 TATAAGATTCGCCGTTGTGGCTTAAATCTTTCCCTTCACATCTTTAGGGTATAAG
4292 ACTCGCCGTT
Statistics
Matches: 129, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
98 129 1.00
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (98 bp):
TATAAGATTCGCCGTTGTGGCTTAAATCTTTCCCTTCACATCTTTAGGGTATAAGGTACGTCGTT
GCGACTTCAACCTTTCCCTCAACATCTCTAGGG
Found at i:4329 original size:98 final size:97
Alignment explanation
Indices: 4069--4323 Score: 271
Period size: 98 Copynumber: 2.6 Consensus size: 97
4059 GGCTTCAATA
* * * * * *
4069 TTTCCCTTCACATCTCTAAGGTATAAGGTACGTCGTTGCGACTTCAACCTTT-CCTTCTACATCT
1 TTTCCCTTCACATCTTTAGGGTATAAGCT-CGTCGTTGCGGCTTCAA-TTTTCCCTTCAACATCT
* * *
4133 CTAGGGTATAAGATTCGCCGTTGTAGCTTAAATC
64 TTAGGGTATAAGACTCGCCGTTGTAGCTTAAACC
* * * * *
4167 TTTCCCTTCACATCTTTAGGGTATAAGGTTTGTCGTTGTGGCTTTAGCTTTTCCC-TCAACATCT
1 TTTCCCTTCACATCTTTAGGGTATAA-GCTCGTCGTTGCGGCTTCA-ATTTTCCCTTCAACATCT
* * *
4231 TTAGGGTATAAGACTCGCTGTTGTGGCTTTAACC
64 TTAGGGTATAAGACTCGCCGTTGTAGCTTAAACC
* *
4265 TTTCTCTTCACATCTTTAGGGTATAAGACTCGCCGTTGCGGCTTCAATATTTCCCTTCA
1 TTTCCCTTCACATCTTTAGGGTATAAG-CTCGTCGTTGCGGCTTCAAT-TTTCCCTTCA
4324 TATCTTCTAG
Statistics
Matches: 128, Mismatches: 23, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
97 2 0.02
98 119 0.93
99 7 0.05
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (97 bp):
TTTCCCTTCACATCTTTAGGGTATAAGCTCGTCGTTGCGGCTTCAATTTTCCCTTCAACATCTTT
AGGGTATAAGACTCGCCGTTGTAGCTTAAACC
Found at i:4978 original size:20 final size:20
Alignment explanation
Indices: 4942--4980 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4932 CCTTTTTCTT
*
4942 TTTTTCTTTCTTTTTTTTTA
1 TTTTTCTTTCTTATTTTTTA
4962 TTTTTCTATT-TTATTTTTT
1 TTTTTCT-TTCTTATTTTTT
4981 GGGTGAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTCTTTCTTATTTTTTA
Found at i:5803 original size:14 final size:14
Alignment explanation
Indices: 5784--5813 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5774 TTTTTCATTA
*
5784 TTTTCTTTGTTTTT
1 TTTTCTTTCTTTTT
5798 TTTTCTTTCTTTTT
1 TTTTCTTTCTTTTT
5812 TT
1 TT
5814 CTTGGGTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (14 bp):
TTTTCTTTCTTTTT
Found at i:9819 original size:23 final size:23
Alignment explanation
Indices: 9789--9835 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
9779 TTAAATTATG
*
9789 GGATTT-AATTAAAAAGTATAAAA
1 GGATTTAAATTAAAAAATA-AAAA
9812 GGATTTAAATTAAAAAATAAAAA
1 GGATTTAAATTAAAAAATAAAAA
9835 G
1 G
9836 AATAAAAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.28
Consensus pattern (23 bp):
GGATTTAAATTAAAAAATAAAAA
Found at i:9967 original size:59 final size:60
Alignment explanation
Indices: 9904--10023 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 60
9894 GACAAAAGGG
* ** *
9904 TTTAAATAAAAAAT-AAAA-GGGAAAATTTAAAAGAAACAAAATGGTGAAAGGATTAAATT
1 TTTAAA-AAAAAATGAAAAGGGGAAAATTTAAAAGAAACAAAATAGCAAAAGGATCAAATT
* * *
9963 TTTAAAAAAGAATGAAAAGGGGAAATTTTAAAAGAAATAAAATAGCAAAAGGATCAAATT
1 TTTAAAAAAAAATGAAAAGGGGAAAATTTAAAAGAAACAAAATAGCAAAAGGATCAAATT
10023 T
1 T
10024 AAACTAAAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 6 0.12
59 10 0.19
60 36 0.69
ACGTcount: A:0.58, C:0.03, G:0.16, T:0.23
Consensus pattern (60 bp):
TTTAAAAAAAAATGAAAAGGGGAAAATTTAAAAGAAACAAAATAGCAAAAGGATCAAATT
Found at i:11126 original size:6 final size:6
Alignment explanation
Indices: 11111--11139 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
11101 TGCTTTTGAA
11111 TTTT-T TTTTCT TTTTCT TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
11140 ACTTTGGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:13438 original size:13 final size:13
Alignment explanation
Indices: 13420--13446 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13410 TAATAAAATA
13420 AAAATTGAGGAGT
1 AAAATTGAGGAGT
13433 AAAATTGAGGAGT
1 AAAATTGAGGAGT
13446 A
1 A
13447 CTTTTTTAGA
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:0.48, C:0.00, G:0.30, T:0.22
Consensus pattern (13 bp):
AAAATTGAGGAGT
Found at i:14459 original size:41 final size:41
Alignment explanation
Indices: 14399--14504 Score: 124
Period size: 41 Copynumber: 2.6 Consensus size: 41
14389 CGCTCATAAC
* * ** *
14399 GCCGCTAAAGGTCAGAGCATTAGTGACGTTTATGA-AGAAAT
1 GCCGCTAAAGGTTAGAGCATTAGCGACACTTATGAGA-AAAA
* *
14440 GCCGCTAAAGGTTAAAGCATTAGCGACACTTCTGAGAAAAA
1 GCCGCTAAAGGTTAGAGCATTAGCGACACTTATGAGAAAAA
*
14481 GCCGCTAAAAGTTAGAGCATTAGC
1 GCCGCTAAAGGTTAGAGCATTAGC
14505 TAAAAGTTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 54 0.98
42 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.22
Consensus pattern (41 bp):
GCCGCTAAAGGTTAGAGCATTAGCGACACTTATGAGAAAAA
Found at i:15457 original size:18 final size:18
Alignment explanation
Indices: 15430--15466 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
15420 TCTTTAGAAT
*
15430 CTGCACAGGAATTTGCAC
1 CTGCAAAGGAATTTGCAC
15448 CTGCAAAGGAATTTGCAC
1 CTGCAAAGGAATTTGCAC
15466 C
1 C
15467 ATGTTAGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.22
Consensus pattern (18 bp):
CTGCAAAGGAATTTGCAC
Found at i:16032 original size:50 final size:50
Alignment explanation
Indices: 15957--16054 Score: 196
Period size: 50 Copynumber: 2.0 Consensus size: 50
15947 GACTCGTTAT
15957 AAATTTCCTGCATTATTTTGATTCTATTCTCCCTGGTTAAGGGGTATTAG
1 AAATTTCCTGCATTATTTTGATTCTATTCTCCCTGGTTAAGGGGTATTAG
16007 AAATTTCCTGCATTATTTTGATTCTATTCTCCCTGGTTAAGGGGTATT
1 AAATTTCCTGCATTATTTTGATTCTATTCTCCCTGGTTAAGGGGTATT
16055 GTTTTTCAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.45
Consensus pattern (50 bp):
AAATTTCCTGCATTATTTTGATTCTATTCTCCCTGGTTAAGGGGTATTAG
Found at i:19063 original size:43 final size:43
Alignment explanation
Indices: 19015--19174 Score: 178
Period size: 43 Copynumber: 3.7 Consensus size: 43
19005 TTTGTTATTG
* * * *
19015 GTGGGAAAAGCGTCGTTAAAGATTATGTTTTTTAGTGACGTTT
1 GTGGGAAAAACGTCGTTAAAGATCACGTTTTTTAGTGGCGTTT
* * ** *
19058 GTGGGAAAAACGTCGTTAAAAATCACGTTATTTAACGGTGTTT
1 GTGGGAAAAACGTCGTTAAAGATCACGTTTTTTAGTGGCGTTT
* * * *
19101 AT-GAAAAAAGCGTCGTCAAGGATCACGTTTTTTAGTGGCGTTT
1 GTGGGAAAAA-CGTCGTTAAAGATCACGTTTTTTAGTGGCGTTT
*
19144 GTGGGAAAAACGTCGTTAAAGATCATGTTTT
1 GTGGGAAAAACGTCGTTAAAGATCACGTTTT
19175 ATAGCGATTT
Statistics
Matches: 92, Mismatches: 23, Indels: 4
0.77 0.19 0.03
Matches are distributed among these distances:
42 6 0.07
43 80 0.87
44 6 0.07
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.34
Consensus pattern (43 bp):
GTGGGAAAAACGTCGTTAAAGATCACGTTTTTTAGTGGCGTTT
Found at i:20002 original size:21 final size:22
Alignment explanation
Indices: 19970--20018 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
19960 TTTAATAAAA
19970 TTATTAGTTTATATTTT-TATT
1 TTATTAGTTTATATTTTATATT
19991 TTATT-GTATTATATTTTATATT
1 TTATTAGT-TTATATTTTATATT
20013 TT-TTAG
1 TTATTAG
20019 AAGGGGTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.08
21 16 0.64
22 7 0.28
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.69
Consensus pattern (22 bp):
TTATTAGTTTATATTTTATATT
Found at i:22707 original size:9 final size:9
Alignment explanation
Indices: 22693--22735 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
22683 CAGTTCGATT
22693 GTTGATTCA
1 GTTGATTCA
22702 GTTGATTCA
1 GTTGATTCA
22711 GTTGATTCA
1 GTTGATTCA
* *
22720 ATCGATTCA
1 GTTGATTCA
*
22729 ATTGATT
1 GTTGATT
22736 AACGAGTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.44
Consensus pattern (9 bp):
GTTGATTCA
Found at i:24274 original size:17 final size:17
Alignment explanation
Indices: 24248--24289 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
24238 TGGGTCTTTT
* *
24248 TTTAATTTTAAATTTGA
1 TTTAAATTTAAATTTAA
24265 TTTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAA
24282 TTTAAATT
1 TTTAAATT
24290 AAAAGGTCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TTTAAATTTAAATTTAA
Found at i:24292 original size:5 final size:6
Alignment explanation
Indices: 24248--24289 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
24238 TGGGTCTTTT
* *
24248 TTTAAT TTTAAA TTT-GA TTTAAA TTTAAA TTT-AA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
24290 AAAAGGTCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
5 9 0.29
6 22 0.71
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:26163 original size:29 final size:29
Alignment explanation
Indices: 26129--26727 Score: 313
Period size: 29 Copynumber: 20.8 Consensus size: 29
26119 CTAAACTATT
26129 CAAAAATTACCATTTTACCCCCGAACTTC
1 CAAAAATTACCATTTTACCCCCGAACTTC
** *
26158 CAAAAA-T-CCAATTTTTGA-CCCTAAACCTTT
1 CAAAAATTACC-A-TTTT-ACCCCCGAA-CTTC
26188 CAAAAATTACCATTTTACCCCCGAACTTC
1 CAAAAATTACCATTTTACCCCCGAACTTC
*
26217 CAAAAA-TCCCATTTTTGA-CCCCGAACCTTC
1 CAAAAATTACCA-TTTT-ACCCCCGAA-CTTC
* *
26247 CAAAAATTATCATTTTACTCCCGAACTTC
1 CAAAAATTACCATTTTACCCCCGAACTTC
* **
26276 CAAAAA-TCCCATTTCTGA-CCCTAAACCTTC
1 CAAAAATTACCATTT-T-ACCCCCGAA-CTTC
26306 C-AAAATTACCATTTTACCCCCGAACTTC
1 CAAAAATTACCATTTTACCCCCGAACTTC
* *
26334 CAAAAA-TCCCATTTTTGA-CCCTGAACCTTC
1 CAAAAATTACCA-TTTT-ACCCCCGAA-CTTC
* *
26364 CAAAAATTACCATTTTACTCCCAAACTTC
1 CAAAAATTACCATTTTACCCCCGAACTTC
* * *
26393 CAAAAA-TCCCATTTTTGA-CTCCAAACCTTC
1 CAAAAATTACCA-TTTT-ACCCCCGAA-CTTC
*
26423 C-AAAATTA-CATTTTACTCCCGAA--T-
1 CAAAAATTACCATTTTACCCCCGAACTTC
* * ** ** **
26447 C--ACATT----TTTGACTTCGAACTTTC
1 CAAAAATTACCATTTTACCCCCGAACTTC
*
26470 CAAAAATTACCATTTTACCCTCGAACTTC
1 CAAAAATTACCATTTTACCCCCGAACTTC
* * *
26499 CAAAAA-TCCCATTTTTAACCTCGAACCTTC
1 CAAAAATTACCA-TTTTACCCCCGAA-CTTC
*
26529 C-AAAATTACCATTTTACCCTCGAACTTC
1 CAAAAATTACCATTTTACCCCCGAACTTC
* ***
26557 TAAAAA-T-CTCATTTTTGACCCGAACCTTC
1 CAAAAATTAC-CATTTTACCCCCGAA-CTTC
* **
26586 CAAAAATTACCATTTTATCCCTAAACTTC
1 CAAAAATTACCATTTTACCCCCGAACTTC
* *
26615 CAAAAA-TCCCATTTTTGA-CCCCAAACCTTC
1 CAAAAATTACCA-TTTT-ACCCCCGAA-CTTC
* * * * *
26645 TAAAAATTACCATTTTATCTCCAAACTCC
1 CAAAAATTACCATTTTACCCCCGAACTTC
* * * *
26674 CAAAAA-TCCCATTTTTAACCTCGAAACATC
1 CAAAAATTACCA-TTTTACCCCCG-AACTTC
* *
26704 CAAAAATTACTATTTTACTCCCGA
1 CAAAAATTACCATTTTACCCCCGA
26728 TTATTCGAAG
Statistics
Matches: 437, Mismatches: 80, Indels: 106
0.70 0.13 0.17
Matches are distributed among these distances:
20 8 0.02
22 1 0.00
23 5 0.01
24 1 0.00
25 5 0.01
27 4 0.01
28 62 0.14
29 195 0.45
30 137 0.31
31 17 0.04
32 2 0.00
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCCCGAACTTC
Found at i:26194 original size:30 final size:30
Alignment explanation
Indices: 26147--26427 Score: 255
Period size: 30 Copynumber: 9.6 Consensus size: 30
26137 ACCATTTTAC
*
26147 CCCCGAA-CTTCCAAAAATCCAATTTTTGA
1 CCCCGAACCTTCCAAAAATCCCATTTTTGA
** * *
26176 CCCTAAACCTTTCAAAAATTACCA-TTTT-A
1 CCCCGAACCTTCCAAAAA-TCCCATTTTTGA
26205 CCCCCGAA-CTTCCAAAAATCCCATTTTTGA
1 -CCCCGAACCTTCCAAAAATCCCATTTTTGA
**
26235 CCCCGAACCTTCCAAAAATTATCA-TTTT-A
1 CCCCGAACCTTCCAAAAA-TCCCATTTTTGA
*
26264 CTCCCGAA-CTTCCAAAAATCCCATTTCTGA
1 C-CCCGAACCTTCCAAAAATCCCATTTTTGA
** * *
26294 CCCTAAACCTTCCAAAATTACCA-TTTT-A
1 CCCCGAACCTTCCAAAAATCCCATTTTTGA
26322 CCCCCGAA-CTTCCAAAAATCCCATTTTTGA
1 -CCCCGAACCTTCCAAAAATCCCATTTTTGA
* *
26352 CCCTGAACCTTCCAAAAATTACCA-TTTT-A
1 CCCCGAACCTTCCAAAAA-TCCCATTTTTGA
*
26381 CTCCC-AAACTTCCAAAAATCCCATTTTTGA
1 C-CCCGAACCTTCCAAAAATCCCATTTTTGA
* *
26411 CTCCAAACCTTCCAAAA
1 CCCCGAACCTTCCAAAA
26428 TTACATTTTA
Statistics
Matches: 202, Mismatches: 30, Indels: 39
0.75 0.11 0.14
Matches are distributed among these distances:
28 25 0.12
29 83 0.41
30 84 0.42
31 10 0.05
ACGTcount: A:0.34, C:0.33, G:0.04, T:0.29
Consensus pattern (30 bp):
CCCCGAACCTTCCAAAAATCCCATTTTTGA
Found at i:26339 original size:58 final size:58
Alignment explanation
Indices: 26117--26727 Score: 669
Period size: 59 Copynumber: 10.6 Consensus size: 58
26107 CCCCGAAGGT
* * *
26117 CCCTAAACTATTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCAATTTTTGA
1 CCCTAAAC-CTTCCAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
*
26176 CCCTAAACCTTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
1 CCCTAAACC-TTCCAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
** * * *
26235 CCCCGAACCTTCCAAAAATTATCATTTTACTCCCGAACTTCCAAAAATCCCATTTCTGA
1 CCCTAAACCTTCC-AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
26294 CCCTAAACCTTCCAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
1 CCCTAAACCTTCCAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * *
26352 CCCTGAACCTTCCAAAAATTACCATTTTACTCCCAAACTTCCAAAAATCCCATTTTTGA
1 CCCTAAACCTTCC-AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
*
26411 CTCC-AAACCTTCCAAAATTA-CATTTTACTCCCGAA--T-C----A---CATTTTTGA
1 C-CCTAAACCTTCCAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * * *
26458 -CTTCGAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTT-A
1 CCCT-AAACCTTCC-AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * * * *
26516 ACCTCGAACCTTCCAAAATTACCATTTTACCCTCGAACTTCTAAAAATCTCATTTTTGA
1 CCCT-AAACCTTCCAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * **
26575 CCC-GAACCTTCCAAAAATTACCATTTTATCCCTAAACTTCCAAAAATCCCATTTTTGA
1 CCCTAAACCTTCC-AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * * * * * *
26633 CCCCAAACCTTCTAAAAATTACCATTTTATCTCCAAACTCCCAAAAATCCCATTTTTAA
1 CCCTAAACCTTC-CAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * * *
26692 CCTCGAAA-CATCCAAAAATTACTATTTTACTCCCGA
1 CC-CTAAACCTTCC-AAAATTACCATTTTACCCCCGA
26728 TTATTCGAAG
Statistics
Matches: 479, Mismatches: 48, Indels: 50
0.83 0.08 0.09
Matches are distributed among these distances:
45 1 0.00
47 16 0.03
48 7 0.01
49 13 0.03
50 1 0.00
51 1 0.00
52 1 0.00
54 1 0.00
55 1 0.00
56 1 0.00
57 23 0.05
58 148 0.31
59 259 0.54
60 6 0.01
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (58 bp):
CCCTAAACCTTCCAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
Done.