Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015004.1 Kokia drynarioides strain JFW-HI SEQ_130048, 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: 190203
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 243 characters in sequence are not A, C, G, or T
Found at i:1921 original size:25 final size:23
Alignment explanation
Indices: 1893--1939 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1883 TTTTATGATA
*
1893 ATTACATATTTTTTATTTCTTAAAG
1 ATTACA-AATTTTTATTT-TTAAAG
*
1918 ATTATAAATTTTTATTTTTAAA
1 ATTACAAATTTTTATTTTTAAA
1940 ATGTTATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 10 0.50
25 5 0.25
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (23 bp):
ATTACAAATTTTTATTTTTAAAG
Found at i:3301 original size:6 final size:6
Alignment explanation
Indices: 3290--3345 Score: 112
Period size: 6 Copynumber: 9.3 Consensus size: 6
3280 TGCCTCTTCA
3290 AGGCAT AGGCAT AGGCAT AGGCAT AGGCAT AGGCAT AGGCAT AGGCAT
1 AGGCAT AGGCAT AGGCAT AGGCAT AGGCAT AGGCAT AGGCAT AGGCAT
3338 AGGCAT AG
1 AGGCAT AG
3346 ATACTCTCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.34, C:0.16, G:0.34, T:0.16
Consensus pattern (6 bp):
AGGCAT
Found at i:8327 original size:17 final size:17
Alignment explanation
Indices: 8307--8366 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
8297 TCAACATGAT
8307 TAAATAATTCAATAATA
1 TAAATAATTCAATAATA
* * *
8324 TAAATAATACAAAACATG
1 TAAATAATTCAATA-ATA
*
8342 TAATTTAATTCAATAATA
1 TAA-ATAATTCAATAATA
8360 TAAATAA
1 TAAATAA
8367 CAAACATAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 15 0.45
18 10 0.30
19 8 0.24
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (17 bp):
TAAATAATTCAATAATA
Found at i:8537 original size:21 final size:19
Alignment explanation
Indices: 8487--8536 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
8477 AGTAGTTTTT
*
8487 GAAAATAAAATTTTTGAGG
1 GAAAATAAAATTTTTGAGA
*
8506 GAAGAGTAAAATTTTTGGAGA
1 GAA-AATAAAATTTTT-GAGA
8527 GAAAATAAAA
1 GAAAATAAAA
8537 AAAAAAATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 3 0.12
20 17 0.65
21 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (19 bp):
GAAAATAAAATTTTTGAGA
Found at i:23536 original size:12 final size:13
Alignment explanation
Indices: 23511--23540 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
23501 AATATAACAA
23511 TTTACATCAATTT
1 TTTACATCAATTT
23524 TTTACAT-AATTT
1 TTTACATCAATTT
23536 TTTAC
1 TTTAC
23541 CTATAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTACATCAATTT
Found at i:24449 original size:17 final size:17
Alignment explanation
Indices: 24395--24449 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
24385 TATATAATGA
*
24395 AATTA-AAAAAA-ACGT
1 AATTATAAAAAATACTT
*
24410 AATTGTAAAAAATA-TAT
1 AATTATAAAAAATACT-T
*
24427 ATTTATAAAAAATACTT
1 AATTATAAAAAATACTT
24444 AATTAT
1 AATTAT
24450 TAAATGAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 4 0.13
16 6 0.19
17 20 0.65
18 1 0.03
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (17 bp):
AATTATAAAAAATACTT
Found at i:24789 original size:13 final size:13
Alignment explanation
Indices: 24771--24796 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24761 CTTTTTCTTA
24771 TATTATATTATAT
1 TATTATATTATAT
24784 TATTATATTATAT
1 TATTATATTATAT
24797 ATACCAAAAA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATATTATAT
Found at i:41013 original size:25 final size:25
Alignment explanation
Indices: 40979--41028 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
40969 CGAAATAGTG
40979 TTTCAATACATCATGAGACAATCAC
1 TTTCAATACATCATGAGACAATCAC
41004 TTTCAATACATCATGAGACAATCAC
1 TTTCAATACATCATGAGACAATCAC
41029 ATACCTGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (25 bp):
TTTCAATACATCATGAGACAATCAC
Found at i:44908 original size:30 final size:30
Alignment explanation
Indices: 44860--44940 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 30
44850 AATCTCAAAG
** *
44860 TTTGAAAAGTAAAAGACTAAAAATACCA-A
1 TTTGAAAAGTAAGGGACTAAAAATACAATA
**
44889 TTTGAAAAGTATAGGGACTAAATTTACAATA
1 TTTGAAAAGTA-AGGGACTAAAAATACAATA
*
44920 TTTGTAAAGTACAGGGACTAA
1 TTTGAAAAGTA-AGGGACTAA
44941 TAAAAAATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 11 0.26
30 12 0.28
31 20 0.47
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.27
Consensus pattern (30 bp):
TTTGAAAAGTAAGGGACTAAAAATACAATA
Found at i:55492 original size:14 final size:15
Alignment explanation
Indices: 55454--55492 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
55444 ATAAAAAATG
*
55454 ATATGAATATGTCAC
1 ATATTAATATGTCAC
55469 ATATTAATATGTCA-
1 ATATTAATATGTCAC
*
55483 ATATTTATAT
1 ATATTAATAT
55493 AAAATAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (15 bp):
ATATTAATATGTCAC
Found at i:59933 original size:21 final size:22
Alignment explanation
Indices: 59909--59950 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
59899 TATTTTGATT
*
59909 CATTTTTAT-TTTTTTAATATG
1 CATTTTTATAATTTTTAATATG
*
59930 CATTTTTCTAATTTTTAATAT
1 CATTTTTATAATTTTTAATAT
59951 TTAATTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.64
Consensus pattern (22 bp):
CATTTTTATAATTTTTAATATG
Found at i:61261 original size:29 final size:30
Alignment explanation
Indices: 61127--61269 Score: 148
Period size: 30 Copynumber: 4.8 Consensus size: 30
61117 TCCAATCAAA
* * *
61127 AATTTTT-GAAAGTTTAGGGGTAAAATTGG
1 AATTTTTGGAAAATTTAGGAGTCAAATTGG
* *
61156 AATTTTTGGTAAATTT-GAGAGTCAAATTTG
1 AATTTTTGGAAAATTTAG-GAGTCAAATTGG
**
61186 AATTTTTGGAAAATTTAGGAGTCAAATTTT
1 AATTTTTGGAAAATTTAGGAGTCAAATTGG
* *
61216 AATTTTTGGAAAATTTAGGGGTTAAATTGG
1 AATTTTTGGAAAATTTAGGAGTCAAATTGG
* * *
61246 AA-TTTTAGAAAGTTTAGGCGTCAA
1 AATTTTTGGAAAATTTAGGAGTCAA
61270 GAAATAATTT
Statistics
Matches: 96, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
29 26 0.27
30 69 0.72
31 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.40
Consensus pattern (30 bp):
AATTTTTGGAAAATTTAGGAGTCAAATTGG
Found at i:62277 original size:3 final size:3
Alignment explanation
Indices: 62269--62294 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
62259 TTATAAAATA
62269 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
62295 ATAAAAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:63002 original size:40 final size:40
Alignment explanation
Indices: 62958--63067 Score: 105
Period size: 40 Copynumber: 2.8 Consensus size: 40
62948 CCATGGTCGA
** * *
62958 GGTAAGAGATTTGATGGTCTTCAATCTGTCTTATGGTTAG
1 GGTAAGAGATCAGATGGTCTTCAATCTGCCTTATGATTAG
* * * *
62998 GGTAAAAGATCCA-ATAGTCTTCAATTTGCCTTCTGATTAG
1 GGTAAGAGAT-CAGATGGTCTTCAATCTGCCTTATGATTAG
* * *
63038 GGAAAGAGATCAGATGATCTTCAATTTGCC
1 GGTAAGAGATCAGATGGTCTTCAATCTGCC
63068 CTCGGGTTAG
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
39 2 0.04
40 54 0.96
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (40 bp):
GGTAAGAGATCAGATGGTCTTCAATCTGCCTTATGATTAG
Found at i:63255 original size:50 final size:50
Alignment explanation
Indices: 63180--63303 Score: 167
Period size: 50 Copynumber: 2.5 Consensus size: 50
63170 TTGTGACTTT
* *
63180 AATCTGCCCCTCTACAGCTTTAGGTGAATGAGATTCGCCATTACGGCTTC
1 AATCTGCCCCTCTACAGCTTTAGGTGAATAAGATTCGCCACTACGGCTTC
* * **
63230 AATCTGCCCCTCTACAGCTTTAGGTGTATAAGATTTGCCACTGTGGCTTC
1 AATCTGCCCCTCTACAGCTTTAGGTGAATAAGATTCGCCACTACGGCTTC
***
63280 AATCTGTTACTCTACAGCTTTAGG
1 AATCTGCCCCTCTACAGCTTTAGG
63304 GGTATAGGAC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (50 bp):
AATCTGCCCCTCTACAGCTTTAGGTGAATAAGATTCGCCACTACGGCTTC
Found at i:67413 original size:21 final size:22
Alignment explanation
Indices: 67384--67426 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
67374 TATTGATTAT
*
67384 AAATAGGTTTAA-TAAAGGTTAA
1 AAATAGG-TTAATTAAAGCTTAA
67406 AAAT-GGTTAATTAAAGCTTAA
1 AAATAGGTTAATTAAAGCTTAA
67427 TGATGAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (22 bp):
AAATAGGTTAATTAAAGCTTAA
Found at i:77372 original size:79 final size:79
Alignment explanation
Indices: 77274--77432 Score: 318
Period size: 79 Copynumber: 2.0 Consensus size: 79
77264 AAAAAAATTC
77274 ATGTTATGCAAAAAATATGCACATGATTTACAAGTATACATAATAAAAAATAATACATACACAAA
1 ATGTTATGCAAAAAATATGCACATGATTTACAAGTATACATAATAAAAAATAATACATACACAAA
77339 ATACAATAAAATAA
66 ATACAATAAAATAA
77353 ATGTTATGCAAAAAATATGCACATGATTTACAAGTATACATAATAAAAAATAATACATACACAAA
1 ATGTTATGCAAAAAATATGCACATGATTTACAAGTATACATAATAAAAAATAATACATACACAAA
77418 ATACAATAAAATAA
66 ATACAATAAAATAA
77432 A
1 A
77433 ATAATATTCA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.57, C:0.11, G:0.06, T:0.25
Consensus pattern (79 bp):
ATGTTATGCAAAAAATATGCACATGATTTACAAGTATACATAATAAAAAATAATACATACACAAA
ATACAATAAAATAA
Found at i:77568 original size:29 final size:29
Alignment explanation
Indices: 77494--77690 Score: 100
Period size: 30 Copynumber: 6.6 Consensus size: 29
77484 CATTAAAATC
**
77494 GGGTCAAATTTGAATTTTTTAAAACTTT-A
1 GGGTCAAATTTGAATTTTTGGAAA-TTTGA
***
77523 TGGGTCAAATAAAAATTTTTGGAAATTTGA
1 -GGGTCAAATTTGAATTTTTGGAAATTTGA
* ****
77553 GGGTCAAATTGGAATTTCAATAAAGTTTG-
1 GGGTCAAATTTGAATTTTTGGAAA-TTTGA
* *
77582 GGATCAAATTTGATTTTTTTGGAAAATTTG-
1 GGGTCAAATTTGA-ATTTTTGG-AAATTTGA
*
77612 GTGGTTAAATTTGAATTTTTGGAAAATTT-A
1 G-GGTCAAATTTGAATTTTTGG-AAATTTGA
* * *
77642 GGGGTTAAA-TTCAATTTTTTGGAAAAATT-A
1 -GGGTCAAATTTGAA-TTTTTGG-AAATTTGA
*
77672 GGGGTTAAATTTGAATTTT
1 -GGGTCAAATTTGAATTTT
77691 AAAAAAATTT
Statistics
Matches: 133, Mismatches: 25, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
29 35 0.26
30 80 0.60
31 18 0.14
ACGTcount: A:0.34, C:0.04, G:0.20, T:0.42
Consensus pattern (29 bp):
GGGTCAAATTTGAATTTTTGGAAATTTGA
Found at i:77622 original size:31 final size:30
Alignment explanation
Indices: 77578--77690 Score: 140
Period size: 30 Copynumber: 3.7 Consensus size: 30
77568 TTCAATAAAG
* * *
77578 TTTGGGATCAAATTTGATTTTTTTGGAAAA
1 TTTGGGGTTAAATTTGAATTTTTTGGAAAA
77608 TTTGGTGGTTAAATTTGAA-TTTTTGGAAAA
1 TTTGG-GGTTAAATTTGAATTTTTTGGAAAA
*
77638 TTTAGGGGTTAAA-TTCAATTTTTTGGAAAAA
1 TTT-GGGGTTAAATTTGAATTTTTTGG-AAAA
*
77669 TTAGGGGTTAAATTTGAATTTT
1 TTTGGGGTTAAATTTGAATTTT
77691 AAAAAAATTT
Statistics
Matches: 72, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
29 4 0.06
30 42 0.58
31 26 0.36
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (30 bp):
TTTGGGGTTAAATTTGAATTTTTTGGAAAA
Found at i:77631 original size:30 final size:29
Alignment explanation
Indices: 77536--77690 Score: 134
Period size: 30 Copynumber: 5.2 Consensus size: 29
77526 GTCAAATAAA
* *
77536 AATTTTTGG-AAATTTGAGGGTCAAATTGG
1 AATTTTTGGAAAATTTG-GGGTTAAATTTG
**** * * *
77565 AATTTCAATAAAGTTTGGGATCAAATTTG
1 AATTTTTGGAAAATTTGGGGTTAAATTTG
*
77594 ATTTTTTTGGAAAATTTGGTGGTTAAATTTG
1 A-ATTTTTGGAAAATTTGG-GGTTAAATTTG
*
77625 AATTTTTGGAAAATTTAGGGGTTAAA-TTC
1 AATTTTTGGAAAATTT-GGGGTTAAATTTG
*
77654 AATTTTTTGGAAAAATTAGGGGTTAAATTTG
1 AA-TTTTTGG-AAAATTTGGGGTTAAATTTG
77685 AATTTT
1 AATTTT
77691 AAAAAAATTT
Statistics
Matches: 100, Mismatches: 19, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
29 20 0.20
30 58 0.58
31 22 0.22
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.43
Consensus pattern (29 bp):
AATTTTTGGAAAATTTGGGGTTAAATTTG
Found at i:77717 original size:60 final size:60
Alignment explanation
Indices: 77596--77719 Score: 135
Period size: 60 Copynumber: 2.1 Consensus size: 60
77586 CAAATTTGAT
* *** * * * **
77596 TTTTTTGGAAAATTTGGTGGTTAAATTTGAATTTTTGGAAAATTTAGGGGTTAAATTCAA
1 TTTTTTGGAAAATTAGGTGGTTAAATTTGAATTTTAAAAAAATTTAGAGCTAAAAAACAA
77656 TTTTTTGGAAAAATTAGG-GGTTAAATTTGAATTTTAAAAAAATTTA-AGCTCAAAAAACAA
1 TTTTTTGG-AAAATTAGGTGGTTAAATTTGAATTTTAAAAAAATTTAGAGCT-AAAAAACAA
77716 TTTT
1 TTTT
77720 AAAATAAAGC
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
59 2 0.04
60 43 0.81
61 8 0.15
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (60 bp):
TTTTTTGGAAAATTAGGTGGTTAAATTTGAATTTTAAAAAAATTTAGAGCTAAAAAACAA
Found at i:90641 original size:22 final size:23
Alignment explanation
Indices: 90616--90663 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
90606 AAACTTATTT
*
90616 AATTCATTTATGTTCA-TGAATA
1 AATTCATTTATATTCATTGAATA
*
90638 AATTCATTTATATTCATTTAATA
1 AATTCATTTATATTCATTGAATA
90661 AAT
1 AAT
90664 CGTTTAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (23 bp):
AATTCATTTATATTCATTGAATA
Found at i:90669 original size:22 final size:23
Alignment explanation
Indices: 90650--90693 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
90640 TTCATTTATA
90650 TTCATTTAATAAATCGTTTAAAG
1 TTCATTTAATAAATCGTTTAAAG
* *
90673 TTTATTTAA-AACTCGTTTAAA
1 TTCATTTAATAAATCGTTTAAA
90694 CTCAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (23 bp):
TTCATTTAATAAATCGTTTAAAG
Found at i:91324 original size:33 final size:32
Alignment explanation
Indices: 91263--91332 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 32
91253 GGAAAAACAT
*
91263 AATTTTAAATAAAACAATATAAACATAAATTTAA
1 AATTTTAAATAAAACAATACAAACATAAA--TAA
*
91297 AATTTT-AATAAATACAA-ACAAATATAAATAA
1 AATTTTAAATAAA-ACAATACAAACATAAATAA
91328 AATTT
1 AATTT
91333 AATTGGTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
31 8 0.24
33 15 0.45
34 10 0.30
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (32 bp):
AATTTTAAATAAAACAATACAAACATAAATAA
Found at i:98684 original size:14 final size:16
Alignment explanation
Indices: 98652--98685 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
98642 ATTAGTATTA
98652 TATATTTTTGTATATG
1 TATATTTTTGTATATG
98668 TATATTTTT-TA-ATG
1 TATATTTTTGTATATG
98682 TATA
1 TATA
98686 AATTACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 2 0.11
16 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (16 bp):
TATATTTTTGTATATG
Found at i:99298 original size:16 final size:16
Alignment explanation
Indices: 99277--99310 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
99267 TGGCATACAT
99277 ATATATATATATATAC
1 ATATATATATATATAC
* *
99293 ATATATGTATATCTAC
1 ATATATATATATATAC
99309 AT
1 AT
99311 GAATAAACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (16 bp):
ATATATATATATATAC
Found at i:100235 original size:23 final size:23
Alignment explanation
Indices: 100144--100335 Score: 146
Period size: 23 Copynumber: 8.3 Consensus size: 23
100134 ACGGAACAAG
* *
100144 CAGAGAGTAC-CAAAGTACT-AA
1 CAGAGAGCACACAAAGTGCTAAA
*
100165 CAGAGAGCAC-CAAAGTACT-AA
1 CAGAGAGCACACAAAGTGCTAAA
* *
100186 CAGAGAGCACA-TAAGTGCTGGGCAA
1 CAGAGAGCACACAAAGTGCT---AAA
*
100211 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
* * *
100234 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAA
* *
100257 CAGAGAGCACACAAAGTGTTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
100280 CAAAGAGCACACACAA-TGCTAATAA
1 CAGAGAGCACACA-AAGTGCT-A-AA
* *
100305 CAGAGAGCACGAGACA-TGCTAAA
1 CAGAGAGCAC-ACAAAGTGCTAAA
100328 CAGAGAGC
1 CAGAGAGC
100336 GCGCTAGTGT
Statistics
Matches: 142, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
21 36 0.25
23 66 0.46
24 4 0.03
25 28 0.20
26 8 0.06
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAA
Found at i:100287 original size:69 final size:69
Alignment explanation
Indices: 100162--100314 Score: 179
Period size: 69 Copynumber: 2.2 Consensus size: 69
100152 ACCAAAGTAC
* * *
100162 TAACAGAGAGCACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAG
1 TAACAGAGAGCACCAAAGTACTAACAGAGAGCACAAAAGTGCT--GCAACAAAGAGCACACACAA
100227 TGCT-A
64 TGCTAA
* *
100232 -AACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTG-T-TAATCAAAGAGCACACAC
1 TAACAGAGAGCAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGCAA-CAAAGAGCACACAC
100294 AATGCTAA
62 AATGCTAA
100302 TAACAGAGAGCAC
1 TAACAGAGAGCAC
100315 GAGACATGCT
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
68 2 0.03
69 29 0.41
70 12 0.17
71 23 0.32
72 5 0.07
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (69 bp):
TAACAGAGAGCACCAAAGTACTAACAGAGAGCACAAAAGTGCTGCAACAAAGAGCACACACAATG
CTAA
Found at i:105273 original size:13 final size:13
Alignment explanation
Indices: 105239--105274 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
105229 AAAGCGAACA
105239 GTTTTATAATTT-
1 GTTTTATAATTTG
105251 -TTTTAT-ATTTG
1 GTTTTATAATTTG
105262 GTTTTATAATTTG
1 GTTTTATAATTTG
105275 AATTATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 4 0.19
11 6 0.29
12 6 0.29
13 5 0.24
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (13 bp):
GTTTTATAATTTG
Found at i:105969 original size:9 final size:9
Alignment explanation
Indices: 105911--105973 Score: 54
Period size: 9 Copynumber: 6.6 Consensus size: 9
105901 AATTTTTTTT
105911 ATTTTTATAA
1 ATTTTTA-AA
*
105921 AATTTTAAA
1 ATTTTTAAA
105930 CATTTTTAAA
1 -ATTTTTAAA
*
105940 TTTTCTTCAAA
1 ATTT-TT-AAA
* *
105951 ACTTTCAAA
1 ATTTTTAAA
105960 ATTTTTAAA
1 ATTTTTAAA
105969 ATTTT
1 ATTTT
105974 ATAATATTAG
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
9 20 0.48
10 17 0.40
11 5 0.12
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:110465 original size:16 final size:17
Alignment explanation
Indices: 110444--110481 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
110434 CGGCGTCGGA
* *
110444 AAGAAATAAAG-AGTGG
1 AAGAAACAAAGAAATGG
110460 AAGAAACAAAGAAATGG
1 AAGAAACAAAGAAATGG
110477 AAGAA
1 AAGAA
110482 GAAGAAACGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.63, C:0.03, G:0.26, T:0.08
Consensus pattern (17 bp):
AAGAAACAAAGAAATGG
Found at i:115269 original size:16 final size:16
Alignment explanation
Indices: 115248--115288 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
115238 AGATGTGAAC
*
115248 AAAAAAAAAAA-AATT
1 AAAAAAAAAAAGAAAT
115263 AAAAAAAAAAAGAAAT
1 AAAAAAAAAAAGAAAT
115279 AAAATAAAAA
1 AAAA-AAAAA
115289 TATTATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.48
16 7 0.30
17 5 0.22
ACGTcount: A:0.88, C:0.00, G:0.02, T:0.10
Consensus pattern (16 bp):
AAAAAAAAAAAGAAAT
Found at i:115270 original size:17 final size:16
Alignment explanation
Indices: 115248--115288 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
115238 AGATGTGAAC
*
115248 AAAAAAAAAAAAATTA
1 AAAAAAAAAAAAAATA
*
115264 AAAAAAAAAAGAAATA
1 AAAAAAAAAAAAAATA
115280 AAATAAAAA
1 AAA-AAAAA
115289 TATTATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.88, C:0.00, G:0.02, T:0.10
Consensus pattern (16 bp):
AAAAAAAAAAAAAATA
Found at i:115354 original size:28 final size:28
Alignment explanation
Indices: 115279--115360 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 28
115269 AAAAAGAAAT
* *
115279 AAAATAAAAATA-TTATAAAAGTTGTAA
1 AAAATAAAAATATTTATAAAAATTGCAA
*
115306 AACAATTGAAAATATATTATAAAAATT-CAA
1 AA-AA-TAAAAATAT-TTATAAAAATTGCAA
115336 AAAATAAAAAATATTTATAAAAATT
1 AAAAT-AAAAATATTTATAAAAATT
115361 ATTAATATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
27 2 0.04
28 14 0.30
29 16 0.35
30 4 0.09
31 10 0.22
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (28 bp):
AAAATAAAAATATTTATAAAAATTGCAA
Found at i:115431 original size:14 final size:13
Alignment explanation
Indices: 115407--115471 Score: 52
Period size: 13 Copynumber: 5.4 Consensus size: 13
115397 TAAAAAATAA
115407 AAAAATATATTAT
1 AAAAATATATTAT
*
115420 AAAAATATTATTTT
1 AAAAATA-TATTAT
115434 AAAAA-A-A-TAT
1 AAAAATATATTAT
*
115444 -AAAATAAATTAT
1 AAAAATATATTAT
*
115456 TAAAAT-TATT-T
1 AAAAATATATTAT
115467 AAAAA
1 AAAAA
115472 CATAAAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
9 4 0.09
10 3 0.07
11 7 0.16
12 6 0.14
13 13 0.30
14 10 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAAATATATTAT
Found at i:115439 original size:37 final size:35
Alignment explanation
Indices: 115392--115478 Score: 97
Period size: 36 Copynumber: 2.5 Consensus size: 35
115382 TTTTATTAAA
* *
115392 ATTTTTAAAAAATAAAAAAATATATTATAAAAATATT
1 ATTTTAAAAAAATAAAAAAATAAATTAT-AAAA-ATT
* *
115429 ATTTTAAAAAAAT-ATAAAATAAATTATTAAAATT
1 ATTTTAAAAAAATAAAAAAATAAATTATAAAAATT
*
115463 A-TTTAAAAACATAAAA
1 ATTTTAAAAAAATAAAA
115479 TATTTAACTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
33 10 0.23
34 6 0.14
35 3 0.07
36 12 0.28
37 12 0.28
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (35 bp):
ATTTTAAAAAAATAAAAAAATAAATTATAAAAATT
Found at i:115477 original size:31 final size:30
Alignment explanation
Indices: 115384--115480 Score: 81
Period size: 31 Copynumber: 2.9 Consensus size: 30
115374 ACTTAAAATT
115384 TTATTAAAATT-TTTAAAAAATAAAA-AAA
1 TTATTAAAATTATTTAAAAAATAAAATAAA
115412 TATATTATAAAAATATTATTTTAAAAAAATATAAAATAAA
1 T-TA-T-T--AAA-ATTA-TTT--AAAAA-ATAAAATAAA
115452 TTATTAAAATTATTTAAAAACATAAAATA
1 TTATTAAAATTATTTAAAAA-ATAAAATA
115481 TTTAACTTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 21
0.72 0.01 0.27
Matches are distributed among these distances:
28 1 0.02
29 2 0.04
30 1 0.02
31 14 0.25
33 6 0.11
34 7 0.12
35 3 0.05
36 3 0.05
37 1 0.02
38 6 0.11
39 8 0.14
40 4 0.07
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (30 bp):
TTATTAAAATTATTTAAAAAATAAAATAAA
Found at i:115966 original size:28 final size:28
Alignment explanation
Indices: 115926--115989 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
115916 AATGAAAAAA
*
115926 AAAAAAAAAATTAAAATTTTAAATTAAT
1 AAAAATAAAATTAAAATTTTAAATTAAT
* * * **
115954 AAAAATAAAATTATATTTTTAATTTTTT
1 AAAAATAAAATTAAAATTTTAAATTAAT
115982 AAAAATAA
1 AAAAATAA
115990 TAAAAAATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
AAAAATAAAATTAAAATTTTAAATTAAT
Found at i:116012 original size:30 final size:32
Alignment explanation
Indices: 115971--116031 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 32
115961 AAATTATATT
*
115971 TTTAATTTTTTAAAAATA-ATA-AAAAATTAA
1 TTTAATCTTTTAAAAATATATATAAAAATTAA
*
116001 TTTAATCTTTTAAATATATATATAAAAATTA
1 TTTAATCTTTTAAAAATATATATAAAAATTA
116032 TTAAAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 16 0.59
31 3 0.11
32 8 0.30
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (32 bp):
TTTAATCTTTTAAAAATATATATAAAAATTAA
Found at i:118793 original size:157 final size:158
Alignment explanation
Indices: 118507--118827 Score: 581
Period size: 157 Copynumber: 2.0 Consensus size: 158
118497 TATGTGCTAG
*
118507 AAGCTAAGTTGCTTCTGCTTTCGAATTTTGTTTAGCCATTCAATTTATTATGGAAAATTCTTATC
1 AAGCTAAGTTGCTTCTGCTTTCGAATCTTGTTTAGCCATTCAATTTATTATGGAAAATTCTTATC
* *
118572 ATATATCTTGCGATTTTATGGTTAAATATGGTCTCTGTGGTATCATAAGTTGTAGGTCAAGATAA
66 ATATATCTTGCGATTTTATGGTTAAATATGGTCTCTATGGTATCATAAGTTGTAGCTCAAGATAA
118637 AGATGTATCACCACTATT-GTTTACCTC
131 AGATGTATCACCACTATTAGTTTACCTC
118664 AAGCTAAGTTGCTTCTGCTTTCGAATCTTGTTTAGCCATTCAATTTATTATGGAAAATTCTTATC
1 AAGCTAAGTTGCTTCTGCTTTCGAATCTTGTTTAGCCATTCAATTTATTATGGAAAATTCTTATC
*
118729 ATATATCTTGTGATTTTATGGTTAAATATGGTCTCTATGGTATCATAAGTTGTAGCTCAAGATAA
66 ATATATCTTGCGATTTTATGGTTAAATATGGTCTCTATGGTATCATAAGTTGTAGCTCAAGATAA
* *
118794 AGTTGTATCACCACTATTATTTTACCTC
131 AGATGTATCACCACTATTAGTTTACCTC
118822 AAGCTA
1 AAGCTA
118828 CTCTTGGTGG
Statistics
Matches: 157, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
157 143 0.91
158 14 0.09
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (158 bp):
AAGCTAAGTTGCTTCTGCTTTCGAATCTTGTTTAGCCATTCAATTTATTATGGAAAATTCTTATC
ATATATCTTGCGATTTTATGGTTAAATATGGTCTCTATGGTATCATAAGTTGTAGCTCAAGATAA
AGATGTATCACCACTATTAGTTTACCTC
Found at i:119738 original size:17 final size:16
Alignment explanation
Indices: 119703--119738 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
119693 TCCAAGAATT
*
119703 TTGTTTTTATCTAATG
1 TTGTTTTTATCTAAGG
119719 TTGTTTTTATCTACAGG
1 TTGTTTTTATCTA-AGG
119736 TTG
1 TTG
119739 AAAAATTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.17, C:0.08, G:0.17, T:0.58
Consensus pattern (16 bp):
TTGTTTTTATCTAAGG
Found at i:125635 original size:29 final size:30
Alignment explanation
Indices: 125598--125668 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
125588 CCCTTTTTTT
*
125598 TTATAAAAATAACCCTAAA-TTT-TGATTAA
1 TTATGAAAATAA-CCTAAATTTTCTGATTAA
*
125627 TTATGAAAATGA-CTAAATTTTCTGATTAA
1 TTATGAAAATAACCTAAATTTTCTGATTAA
*
125656 ATATGAAAATAAC
1 TTATGAAAATAAC
125669 TTGAAATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 5 0.14
28 3 0.09
29 27 0.77
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.37
Consensus pattern (30 bp):
TTATGAAAATAACCTAAATTTTCTGATTAA
Found at i:127523 original size:5 final size:5
Alignment explanation
Indices: 127513--127540 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
127503 TTGAGCCTTG
127513 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
127541 TCACAAACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:135465 original size:5 final size:5
Alignment explanation
Indices: 135455--135491 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
135445 TGAATTAGAC
*
135455 AGAAA AGAAA AGAAA AGAAA AGAAA AGGAAA GGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA A-GAAA AGAAA A
135492 TTTAATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:139039 original size:2 final size:2
Alignment explanation
Indices: 139032--139061 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
139022 GTCTGTTTAG
*
139032 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
139062 TTAACACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:149485 original size:16 final size:17
Alignment explanation
Indices: 149454--149486 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
149444 AATAATTTTT
*
149454 TTTTAAAACTTTAATAA
1 TTTTAAAACATTAATAA
149471 TTTTAAAA-ATTAATAA
1 TTTTAAAACATTAATAA
149487 ATAAACTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTTAAAACATTAATAA
Found at i:153165 original size:7 final size:7
Alignment explanation
Indices: 153149--153185 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
153139 TTAAATGACT
*
153149 ACACGTC
1 ACACGCC
153156 ACACGCC
1 ACACGCC
153163 ACACGCC
1 ACACGCC
153170 ACACGCC
1 ACACGCC
153177 ACACGCC
1 ACACGCC
153184 AC
1 AC
153186 GCTCCTCCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.30, C:0.54, G:0.14, T:0.03
Consensus pattern (7 bp):
ACACGCC
Found at i:153673 original size:31 final size:30
Alignment explanation
Indices: 153616--153720 Score: 81
Period size: 31 Copynumber: 3.5 Consensus size: 30
153606 AACTTTAAAA
*
153616 AAAAAGTGTCAAGTTTAGGTATCAAATTAGG
1 AAAAAGTGTCAAGTTTAGGTACCAAATT-GG
* *
153647 AAAACGTGTCACGTTT-GAGTACCAAATTGG
1 AAAAAGTGTCAAGTTTAG-GTACCAAATTGG
*** * **
153677 AAAAA--AAAAAGTTTAGGTACAAAATTAAA
1 AAAAAGTGTCAAGTTTAGGTACCAAATT-GG
153706 AAAAAGTGTCAAGTT
1 AAAAAGTGTCAAGTT
153721 CAAGTACAAA
Statistics
Matches: 55, Mismatches: 14, Indels: 10
0.70 0.18 0.13
Matches are distributed among these distances:
28 14 0.25
29 6 0.11
30 7 0.13
31 28 0.51
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.26
Consensus pattern (30 bp):
AAAAAGTGTCAAGTTTAGGTACCAAATTGG
Found at i:154906 original size:37 final size:36
Alignment explanation
Indices: 154854--154964 Score: 127
Period size: 37 Copynumber: 3.0 Consensus size: 36
154844 GTTAAACATA
*
154854 ATATTATTTTGATATTCTGACTCGCATGTTAAGCATGCT
1 ATATT-TTTT-ATATT-TGATTCGCATGTTAAGCATGCT
* *
154893 ATATTTTTTATATTTCGATTCTCATGTTAAGCATGCC
1 ATATTTTTTATATTT-GATTCGCATGTTAAGCATGCT
* *
154930 ATA-TTTTCAT-TTTGATTCGCATGTTAAACATGCT
1 ATATTTTTTATATTTGATTCGCATGTTAAGCATGCT
154964 A
1 A
154965 CTATGATAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
34 19 0.30
35 3 0.05
36 7 0.11
37 26 0.41
38 4 0.06
39 5 0.08
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (36 bp):
ATATTTTTTATATTTGATTCGCATGTTAAGCATGCT
Found at i:155601 original size:13 final size:14
Alignment explanation
Indices: 155583--155612 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
155573 GTTTAATTAC
155583 TTTGGACTTTGG-T
1 TTTGGACTTTGGAT
155596 TTTGGACTTTGGAT
1 TTTGGACTTTGGAT
155610 TTT
1 TTT
155613 AGATTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.10, C:0.07, G:0.27, T:0.57
Consensus pattern (14 bp):
TTTGGACTTTGGAT
Found at i:160840 original size:13 final size:13
Alignment explanation
Indices: 160818--160847 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
160808 TTGTTTATTA
*
160818 TTCATTAACATTG
1 TTCATGAACATTG
160831 TTCATGAACATTG
1 TTCATGAACATTG
160844 TTCA
1 TTCA
160848 ATTATATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (13 bp):
TTCATGAACATTG
Found at i:175406 original size:12 final size:12
Alignment explanation
Indices: 175391--175434 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
175381 GATAAAAAAT
175391 TTAAATTTTGAA
1 TTAAATTTTGAA
* *
175403 TTAAATAGTTCGAC
1 TTAAAT--TTTGAA
175417 TTAAATTTTGAA
1 TTAAATTTTGAA
175429 TTAAAT
1 TTAAAT
175435 AGTTCGAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 16 0.62
14 10 0.38
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (12 bp):
TTAAATTTTGAA
Found at i:175422 original size:14 final size:14
Alignment explanation
Indices: 175400--175441 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
175390 TTTAAATTTT
175400 GAATTAAATAGTTC
1 GAATTAAATAGTTC
* *
175414 GACTTAAAT--TTT
1 GAATTAAATAGTTC
175426 GAATTAAATAGTTC
1 GAATTAAATAGTTC
175440 GA
1 GA
175442 GTTATTTGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
12 10 0.45
14 12 0.55
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (14 bp):
GAATTAAATAGTTC
Found at i:175422 original size:26 final size:26
Alignment explanation
Indices: 175391--175441 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
175381 GATAAAAAAT
175391 TTAAATTTTGAATTAAATAGTTCGAC
1 TTAAATTTTGAATTAAATAGTTCGAC
175417 TTAAATTTTGAATTAAATAGTTCGA
1 TTAAATTTTGAATTAAATAGTTCGA
175442 GTTATTTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (26 bp):
TTAAATTTTGAATTAAATAGTTCGAC
Found at i:176696 original size:3 final size:3
Alignment explanation
Indices: 176688--176713 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
176678 ATGTTCCTTT
176688 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
176714 AAAGAGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:177206 original size:18 final size:17
Alignment explanation
Indices: 177154--177209 Score: 69
Period size: 16 Copynumber: 3.3 Consensus size: 17
177144 TATAATCAAA
*
177154 ATATTAATTTATTTTTT
1 ATATAAATTTATTTTTT
* *
177171 A-ATAAATATATTTATT
1 ATATAAATTTATTTTTT
177187 ATATAAATTTTATTTTTT
1 ATATAAA-TTTATTTTTT
177205 ATATA
1 ATATA
177210 TAAATATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
16 13 0.41
17 6 0.19
18 13 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATATAAATTTATTTTTT
Found at i:177221 original size:20 final size:21
Alignment explanation
Indices: 177181--177223 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
177171 AATAAATATA
* *
177181 TTTATTATATAAATTTTATTT
1 TTTATTATATAAATATAATTT
177202 TTTA-TATATAAATATAATTT
1 TTTATTATATAAATATAATTT
177222 TT
1 TT
177224 ATTTACGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTATTATATAAATATAATTT
Found at i:184170 original size:92 final size:92
Alignment explanation
Indices: 184059--184244 Score: 268
Period size: 92 Copynumber: 2.0 Consensus size: 92
184049 ATGTCACATT
* * * *
184059 TGGTACTTGTACTTCCATAAAATATTCAATGT-AGTACATGTACTTTGAAAATGTCCAA-TGTGG
1 TGGTACCTGTACTTCCATAAAATATCCAATGTGA-TACATATACTTTGAAAATGT-CAAGTATGG
* *
184122 TATCTGAACTATCAATATGTGTTTTCTTA
64 TACCTGAACTATCAATATGTGTTTTATTA
* *
184151 TGGTACCTGTACTTTCATAAAATATCCAATGTGATACCTATACTTTGAAAATGTCAAGTATGGTA
1 TGGTACCTGTACTTCCATAAAATATCCAATGTGATACATATACTTTGAAAATGTCAAGTATGGTA
184216 CCTGAACTATCAATATGTGTTTTATTA
66 CCTGAACTATCAATATGTGTTTTATTA
184243 TG
1 TG
184245 ATAGCTGGTG
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
91 3 0.04
92 80 0.95
93 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (92 bp):
TGGTACCTGTACTTCCATAAAATATCCAATGTGATACATATACTTTGAAAATGTCAAGTATGGTA
CCTGAACTATCAATATGTGTTTTATTA
Found at i:188184 original size:23 final size:23
Alignment explanation
Indices: 188149--188204 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
188139 AACCTTTATA
*
188149 AACCCAAGA-CCTTTAAACCTAAT
1 AACCCAA-ACCCTTTAAACCCAAT
*
188172 AACCCAAACCCTTTTAACCCAAT
1 AACCCAAACCCTTTAAACCCAAT
**
188195 AGTCCAAACC
1 AACCCAAACC
188205 AAACCAAGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.41, C:0.36, G:0.04, T:0.20
Consensus pattern (23 bp):
AACCCAAACCCTTTAAACCCAAT
Found at i:188891 original size:2 final size:2
Alignment explanation
Indices: 188884--188909 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
188874 AATGTTATGC
188884 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
188910 GTACCTTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:189742 original size:3 final size:3
Alignment explanation
Indices: 189734--189764 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
189724 TACAAATTTA
189734 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
189765 GTTTTGGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:189908 original size:2 final size:2
Alignment explanation
Indices: 189901--189927 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
189891 TTTAAAATTT
189901 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
189928 GTTTATCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.