Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013386.1 Kokia drynarioides strain JFW-HI SEQ_128409, 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: 170050
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:965 original size:19 final size:18
Alignment explanation
Indices: 925--965 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
915 GAAATTAAGG
*
925 ATTTAGAAATGATTACGA
1 ATTTAGAAATGATGACGA
*
943 ATTTAGAAATGAATGAGGA
1 ATTTAGAAATG-ATGACGA
962 ATTT
1 ATTT
966 TTTTGATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.34
Consensus pattern (18 bp):
ATTTAGAAATGATGACGA
Found at i:1170 original size:41 final size:41
Alignment explanation
Indices: 1092--1238 Score: 177
Period size: 41 Copynumber: 3.5 Consensus size: 41
1082 TTATAGGAAA
* * *
1092 AAACGCCGCTAATGCTCTGGACCTTTTGCGATATTTTTCCCAT
1 AAACGCCGCTATTGAT-T-GACCTTTAGCGATATTTTTCCCAT
* * *
1135 AAACGTCGCTATTGATTGACCTTTAACGATGTTTTTCCCAT
1 AAACGCCGCTATTGATTGACCTTTAGCGATATTTTTCCCAT
** *
1176 AAACGCCGCTATTGATTGACCTTTAGCGGCATTTTCCCCAT
1 AAACGCCGCTATTGATTGACCTTTAGCGATATTTTTCCCAT
* *
1217 AAACGCCACTATTGCTTGACCT
1 AAACGCCGCTATTGATTGACCT
1239 CTAATTTTTT
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
41 76 0.84
42 1 0.01
43 13 0.14
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (41 bp):
AAACGCCGCTATTGATTGACCTTTAGCGATATTTTTCCCAT
Found at i:1310 original size:22 final size:21
Alignment explanation
Indices: 1279--1320 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1269 TCTTAAAATT
1279 TTTAGAAATTTTATAATATTTAA
1 TTTAGAAATTTTA-AA-ATTTAA
1302 TTTA-AAATTTTAAAATTTA
1 TTTAGAAATTTTAAAATTTA
1321 TAAAAGTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 8 0.42
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTAGAAATTTTAAAATTTAA
Found at i:2801 original size:22 final size:22
Alignment explanation
Indices: 2776--2824 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
2766 CATTTCCAAG
2776 TAAT-ATTAA-AAGTATCTTATAC
1 TAATCATTAACAA-TAT-TTATAC
2798 TAATCATTAACAATATTTATAC
1 TAATCATTAACAATATTTATAC
*
2820 CAATC
1 TAATC
2825 GAATTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 14 0.58
23 8 0.33
24 2 0.08
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (22 bp):
TAATCATTAACAATATTTATAC
Found at i:3230 original size:41 final size:41
Alignment explanation
Indices: 3175--3396 Score: 184
Period size: 41 Copynumber: 5.4 Consensus size: 41
3165 ATATAAAATA
* *
3175 TAATGCTCCAACCTTTAGTAGCACTTTATC-ATAAATGCCGC
1 TAATGCTCCGACCTTTAGCAGCACTTT-TCTATAAATGCCGC
* ** * *
3216 TACTTTTCCGACCTTTAGCGGCACTTTTCTATAAATGTCGC
1 TAATGCTCCGACCTTTAGCAGCACTTTTCTATAAATGCCGC
* * *
3257 TAATGCTCCGACCTTTAGCGGCGC-TTTCACATAAA-GTCCGC
1 TAATGCTCCGACCTTTAGCAGCACTTTTC-TATAAATG-CCGC
* * * *
3298 TAATGCTCCGACCTTTAGCGGCGC-TTTCGCATAAACGCCGC
1 TAATGCTCCGACCTTTAGCAGCACTTTTC-TATAAATGCCGC
* * ** * * *
3339 TAATGCTCCGACCTTTAACGGTGC-TTTCCACAAAAGCCGC
1 TAATGCTCCGACCTTTAGCAGCACTTTTCTATAAATGCCGC
3379 TAATGCTCCGACCTTTAG
1 TAATGCTCCGACCTTTAG
3397 TGGCGCTCCG
Statistics
Matches: 158, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
40 34 0.22
41 123 0.78
42 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (41 bp):
TAATGCTCCGACCTTTAGCAGCACTTTTCTATAAATGCCGC
Found at i:3312 original size:82 final size:81
Alignment explanation
Indices: 3222--3396 Score: 255
Period size: 82 Copynumber: 2.1 Consensus size: 81
3212 CCGCTACTTT
* * * *
3222 TCCGACCTTTAGCGGCACTTTTC-TATAAATGTCGCTAATGCTCCGACCTTTAGCGGCGCTTT-C
1 TCCGACCTTTAGCGGCAC-TTTCGCATAAACGCCGCTAATGCTCCGACCTTTAACGGCGCTTTCC
3285 ACATAAAGTCCGCTAATGC
65 ACA-AAAG-CCGCTAATGC
* *
3304 TCCGACCTTTAGCGGCGCTTTCGCATAAACGCCGCTAATGCTCCGACCTTTAACGGTGCTTTCCA
1 TCCGACCTTTAGCGGCACTTTCGCATAAACGCCGCTAATGCTCCGACCTTTAACGGCGCTTTCCA
3369 CAAAAGCCGCTAATGC
66 CAAAAGCCGCTAATGC
3385 TCCGACCTTTAG
1 TCCGACCTTTAG
3397 TGGCGCTCCG
Statistics
Matches: 85, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
81 26 0.31
82 55 0.65
83 4 0.05
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (81 bp):
TCCGACCTTTAGCGGCACTTTCGCATAAACGCCGCTAATGCTCCGACCTTTAACGGCGCTTTCCA
CAAAAGCCGCTAATGC
Found at i:3389 original size:40 final size:40
Alignment explanation
Indices: 3222--3403 Score: 231
Period size: 41 Copynumber: 4.5 Consensus size: 40
3212 CCGCTACTTT
* * * * *
3222 TCCGACCTTTAGCGGCACTTTTCTATAAATGTCGCTAATGC
1 TCCGACCTTTAGCGGCGC-TTTCCACAAAAGCCGCTAATGC
3263 TCCGACCTTTAGCGGCGCTTT-CACATAAAGTCCGCTAATGC
1 TCCGACCTTTAGCGGCGCTTTCCACA-AAAG-CCGCTAATGC
* *
3304 TCCGACCTTTAGCGGCGCTTTCGCATAAACGCCGCTAATGC
1 TCCGACCTTTAGCGGCGCTTTC-CACAAAAGCCGCTAATGC
* *
3345 TCCGACCTTTAACGGTGCTTTCCACAAAAGCCGCTAATGC
1 TCCGACCTTTAGCGGCGCTTTCCACAAAAGCCGCTAATGC
*
3385 TCCGACCTTTAGTGGCGCT
1 TCCGACCTTTAGCGGCGCT
3404 CCGACCTTTA
Statistics
Matches: 123, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
39 2 0.02
40 38 0.31
41 77 0.63
42 3 0.02
43 3 0.02
ACGTcount: A:0.21, C:0.31, G:0.20, T:0.28
Consensus pattern (40 bp):
TCCGACCTTTAGCGGCGCTTTCCACAAAAGCCGCTAATGC
Found at i:3406 original size:18 final size:18
Alignment explanation
Indices: 3383--3423 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
3373 AGCCGCTAAT
*
3383 GCTCCGACCTTTAGTGGC
1 GCTCCGACCTTTAGCGGC
3401 GCTCCGACCTTTAGCGGC
1 GCTCCGACCTTTAGCGGC
3419 GCTCC
1 GCTCC
3424 TCAATAAACG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.39, G:0.27, T:0.24
Consensus pattern (18 bp):
GCTCCGACCTTTAGCGGC
Found at i:3445 original size:59 final size:58
Alignment explanation
Indices: 3343--3455 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 58
3333 CGCCGCTAAT
* * *
3343 GCTCCGACCTTTAACGGTGCTTTCCACAAAAGCCGCTAATGCTCCGACCTTTAGTGGC
1 GCTCCGACCTTTAACGGCGCTCTCAACAAAAGCCGCTAATGCTCCGACCTTTAGTGGC
* * * *
3401 GCTCCGACCTTTAGCGGCGCTCCTCAATAAACGCCGCTAATGCTCCGATCTTTAG
1 GCTCCGACCTTTAACGGCGCT-CTCAACAAAAGCCGCTAATGCTCCGACCTTTAG
3456 CGGTGCTTTG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
58 19 0.40
59 28 0.60
ACGTcount: A:0.20, C:0.34, G:0.20, T:0.26
Consensus pattern (58 bp):
GCTCCGACCTTTAACGGCGCTCTCAACAAAAGCCGCTAATGCTCCGACCTTTAGTGGC
Found at i:3458 original size:41 final size:41
Alignment explanation
Indices: 3401--3500 Score: 130
Period size: 41 Copynumber: 2.4 Consensus size: 41
3391 CTTTAGTGGC
3401 GCTCCGACCTTTAGCGGCGC-TCCTCAATAAACGCCGCTAAT
1 GCTCCGACCTTTAGCGGCGCTTCCTC-ATAAACGCCGCTAAT
* * ** *
3442 GCTCCGATCTTTAGCGGTGCTTTGTCGTAAACGCCGCTAAT
1 GCTCCGACCTTTAGCGGCGCTTCCTCATAAACGCCGCTAAT
*
3483 GCTCTGACCTTTAGCGGC
1 GCTCCGACCTTTAGCGGC
3501 ATTTTTCCTA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
41 47 0.94
42 3 0.06
ACGTcount: A:0.18, C:0.32, G:0.23, T:0.27
Consensus pattern (41 bp):
GCTCCGACCTTTAGCGGCGCTTCCTCATAAACGCCGCTAAT
Found at i:3608 original size:80 final size:82
Alignment explanation
Indices: 3469--3625 Score: 228
Period size: 80 Copynumber: 1.9 Consensus size: 82
3459 TGCTTTGTCG
*
3469 TAAACGCCGCTAATGCTCTGACCTTTAGCGGCATTTTTCCTAAAAACGCCGCTATTGCTTTACCT
1 TAAACGCCGCTAATGCTCTGACCTTTAGCGGCATTTTTCCAAAAAACGCCGCTATTGCTTTACCT
3534 TTTGCAGCGTTTATGGT
66 TTTGCAGCGTTTATGGT
* * * * * * *
3551 TAAACGTCGCTAATGCT-TTACCTTTTGCGGCGTTTTT-GAAAAAATGTCGCTATTGCTTTACCT
1 TAAACGCCGCTAATGCTCTGACCTTTAGCGGCATTTTTCCAAAAAACGCCGCTATTGCTTTACCT
3614 TTTGCAGCGTTT
66 TTTGCAGCGTTT
3626 TCTTTCCAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
80 34 0.51
81 17 0.25
82 16 0.24
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.38
Consensus pattern (82 bp):
TAAACGCCGCTAATGCTCTGACCTTTAGCGGCATTTTTCCAAAAAACGCCGCTATTGCTTTACCT
TTTGCAGCGTTTATGGT
Found at i:3626 original size:40 final size:40
Alignment explanation
Indices: 3510--3626 Score: 162
Period size: 40 Copynumber: 2.9 Consensus size: 40
3500 CATTTTTCCT
* * *
3510 AAAAACGCCGCTATTGCTTTACCTTTTGCAGCGTTTATGG
1 AAAAACGTCGCTATTGCTTTACCTTTTGCAGCGTTTTTGA
** * *
3550 TTAAACGTCGCTAATGCTTTACCTTTTGCGGCGTTTTTGA
1 AAAAACGTCGCTATTGCTTTACCTTTTGCAGCGTTTTTGA
*
3590 AAAAATGTCGCTATTGCTTTACCTTTTGCAGCGTTTT
1 AAAAACGTCGCTATTGCTTTACCTTTTGCAGCGTTTT
3627 CTTTCCAAAC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (40 bp):
AAAAACGTCGCTATTGCTTTACCTTTTGCAGCGTTTTTGA
Found at i:6242 original size:12 final size:12
Alignment explanation
Indices: 6225--6250 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6215 GGGTGTATGG
6225 GAAGAGCCTACT
1 GAAGAGCCTACT
6237 GAAGAGCCTACT
1 GAAGAGCCTACT
6249 GA
1 GA
6251 CTCGGGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.27, T:0.15
Consensus pattern (12 bp):
GAAGAGCCTACT
Found at i:8402 original size:16 final size:17
Alignment explanation
Indices: 8356--8404 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
8346 AAAATATTTA
8356 TTTTAATATTTTA-ATGT
1 TTTTAAT-TTTTATATGT
*
8373 TTTTGATTTATTATAT-T
1 TTTTAATTT-TTATATGT
8390 TTTTAATTTTTATAT
1 TTTTAATTTTTATAT
8405 AAAAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 8 0.29
17 18 0.64
18 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (17 bp):
TTTTAATTTTTATATGT
Found at i:19185 original size:15 final size:15
Alignment explanation
Indices: 19147--19185 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
19137 TTATTCGCTT
19147 TACTTCTAAAATTTG
1 TACTTCTAAAATTTG
19162 TACTT-TAAAATTTG
1 TACTTCTAAAATTTG
19176 -ACTTACTAAA
1 TACTT-CTAAA
19186 TTCAGTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.18
14 9 0.41
15 9 0.41
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (15 bp):
TACTTCTAAAATTTG
Found at i:21119 original size:31 final size:30
Alignment explanation
Indices: 21081--21196 Score: 112
Period size: 31 Copynumber: 3.8 Consensus size: 30
21071 TTGCCATTCT
*
21081 ATTTGGTACCTGAGTTTGGTTTCAAAGTTCA
1 ATTTGGTACCTGAGTTT-GTTTCAATGTTCA
* * *
21112 ATTTGGTACCT-ACGTTT-TTTTATTGTCCCA
1 ATTTGGTACCTGA-GTTTGTTTCAATGT-TCA
* *
21142 ATTTAGTACCTGAGTTTAGCTTCAATGTTCA
1 ATTTGGTACCTGAGTTT-GTTTCAATGTTCA
*
21173 GTTTGGTACCTGAGTTT-TTTCAAT
1 ATTTGGTACCTGAGTTTGTTTCAAT
21197 TTGATACTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
29 12 0.18
30 17 0.25
31 33 0.49
32 6 0.09
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.46
Consensus pattern (30 bp):
ATTTGGTACCTGAGTTTGTTTCAATGTTCA
Found at i:21199 original size:22 final size:23
Alignment explanation
Indices: 21169--21214 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
21159 AGCTTCAATG
* *
21169 TTCAGTTTGGTAC-CTGAGTTTT
1 TTCAATTTGATACTCTGAGTTTT
*
21191 TTCAATTTGATACTTTGAGTTTT
1 TTCAATTTGATACTCTGAGTTTT
21214 T
1 T
21215 CTTTGCCCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.54
Consensus pattern (23 bp):
TTCAATTTGATACTCTGAGTTTT
Found at i:21407 original size:31 final size:31
Alignment explanation
Indices: 21369--21435 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
21359 GTCTAGGTAT
21369 CAAATTGAACATTGAAA-CCAAACTCATGTAC
1 CAAATTGAACATT-AAAGCCAAACTCATGTAC
* *
21400 CAAATTGAACCTTAAAGCCAAACTGATGTAC
1 CAAATTGAACATTAAAGCCAAACTCATGTAC
21431 CAAAT
1 CAAAT
21436 GGTATATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 3 0.09
31 30 0.91
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.22
Consensus pattern (31 bp):
CAAATTGAACATTAAAGCCAAACTCATGTAC
Found at i:21660 original size:187 final size:187
Alignment explanation
Indices: 21319--21697 Score: 553
Period size: 187 Copynumber: 2.0 Consensus size: 187
21309 TTACTAGAAA
21319 ACATTTGTCAAATATTCATTGGACCACATGATATCGTTTAGTCTAGGTATCAAATTGAACATTGA
1 ACATTTGTCAAATATTCATTGGACCACATGATATCGTTTAGTCTAGGTATCAAATTGAACATTGA
* * * *
21384 AACCAAACTCATGTACCAAATTGAACCTTAAAGCCAAACTGATGTACCAAATGGTATATTAACCC
66 AACCAAACTCATGTACCAAATTAAACCTTAAAACCAAACTCATGTACCAAATGATATATTAACCC
* * *
21449 TTTGTTTGGTCTTAATTATTACCAAAGACCAACCTAGCTGATTTGGTGTGTTAATTT
131 TTTGTCTGGTATTAATTATTACCAAAGACCAACCTAGCTGATTTGGTGTGTTAATAT
* * * *
21506 ACATTTGTCAAATATTCTTTGGGCCACATGATATTGTTTAGTCTAGGTATCAAATTGAATATT-A
1 ACATTTGTCAAATATTCATTGGACCACATGATATCGTTTAGTCTAGGTATCAAATTGAACATTGA
* * * * * ***
21570 AAGTCAAATTCATGTACTAATTTAAACCTTAAAATCAAACTCATGTACCAAATGATATATTAGGT
66 AA-CCAAACTCATGTACCAAATTAAACCTTAAAACCAAACTCATGTACCAAATGATATATTAACC
* *
21635 CTTTGTCTGGTATTAATTGTTACCAAAGACCAACCTAGCTGATTTGGTGTTTTAATAT
130 CTTTGTCTGGTATTAATTATTACCAAAGACCAACCTAGCTGATTTGGTGTGTTAATAT
21693 ACATT
1 ACATT
21698 GTACTGAACC
Statistics
Matches: 170, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
186 3 0.02
187 167 0.98
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (187 bp):
ACATTTGTCAAATATTCATTGGACCACATGATATCGTTTAGTCTAGGTATCAAATTGAACATTGA
AACCAAACTCATGTACCAAATTAAACCTTAAAACCAAACTCATGTACCAAATGATATATTAACCC
TTTGTCTGGTATTAATTATTACCAAAGACCAACCTAGCTGATTTGGTGTGTTAATAT
Found at i:22288 original size:15 final size:16
Alignment explanation
Indices: 22265--22297 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
22255 TCAATTAATT
*
22265 AATTTAAAAATTA-AA
1 AATTAAAAAATTATAA
22280 AATTAAAAAATTATAA
1 AATTAAAAAATTATAA
22296 AA
1 AA
22298 ATTATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATTAAAAAATTATAA
Found at i:22302 original size:9 final size:9
Alignment explanation
Indices: 22265--22345 Score: 57
Period size: 9 Copynumber: 9.2 Consensus size: 9
22255 TCAATTAATT
22265 AATT-TAAA
1 AATTATAAA
22273 AA-T-TAAA
1 AATTATAAA
22280 AATTA-AAA
1 AATTATAAA
22288 AATTATAAA
1 AATTATAAA
22297 AATTATTAAA
1 AATTA-TAAA
*
22307 TAA--ATTAA
1 -AATTATAAA
*
22315 CATTATTAAA
1 AATTA-TAAA
22325 AATGTATAAA
1 AAT-TATAAA
*
22335 AATTACAAA
1 AATTATAAA
22344 AA
1 AA
22346 AAAATATAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
7 8 0.14
8 14 0.24
9 17 0.29
10 16 0.27
11 4 0.07
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.32
Consensus pattern (9 bp):
AATTATAAA
Found at i:22313 original size:21 final size:20
Alignment explanation
Indices: 22281--22358 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
22271 AAAATTAAAA
22281 ATTAAAAAATTATAAAAATT
1 ATTAAAAAATTATAAAAATT
*
22301 ATTAAATAAA-T-T-AACATT
1 ATTAAA-AAATTATAAAAATT
22319 ATT-AAAAATGTATAAAAATT
1 ATTAAAAAAT-TATAAAAATT
** *
22339 ACAAAAAAAAATATAAAAAT
1 A-TTAAAAAATTATAAAAAT
22359 GTTTTTGAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
16 3 0.07
17 2 0.04
18 9 0.20
19 2 0.04
20 13 0.28
21 12 0.26
22 5 0.11
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (20 bp):
ATTAAAAAATTATAAAAATT
Found at i:23260 original size:33 final size:33
Alignment explanation
Indices: 23223--23290 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
23213 TATCTGATAC
23223 TTAAATTAGATATATTTG-TGTAGAGATATGATT
1 TTAAATTAGATATA-TTGATGTAGAGATATGATT
*
23256 TTAAATTAGATATATTGATGTAGAGGTATGATT
1 TTAAATTAGATATATTGATGTAGAGATATGATT
23289 TT
1 TT
23291 TAAAAATTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
32 3 0.09
33 30 0.91
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (33 bp):
TTAAATTAGATATATTGATGTAGAGATATGATT
Found at i:28695 original size:2 final size:2
Alignment explanation
Indices: 28688--28715 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28678 ATTTATCAGT
28688 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28716 CAAGATGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30049 original size:5 final size:5
Alignment explanation
Indices: 30039--30065 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
30029 ATGTAACGAA
30039 AATAT AATAT AATAT AATAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AA
30066 ATGTGAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:30842 original size:14 final size:14
Alignment explanation
Indices: 30823--30849 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30813 CGACCTCCTT
30823 AAAATGATAAAATA
1 AAAATGATAAAATA
30837 AAAATGATAAAAT
1 AAAATGATAAAAT
30850 CAATTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (14 bp):
AAAATGATAAAATA
Found at i:37142 original size:23 final size:23
Alignment explanation
Indices: 37116--37219 Score: 118
Period size: 23 Copynumber: 4.4 Consensus size: 23
37106 AGTGTTAGGC
**
37116 AACAGAGAGCACACTCAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
37139 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACAAAGTGCTA
*
37162 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
37185 ATCAGAAAGCACACACAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
37209 TAACAGAGAGC
1 -AACAGAGAGC
37220 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
23 59 0.87
24 1 0.01
25 8 0.12
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:37207 original size:69 final size:67
Alignment explanation
Indices: 37070--37218 Score: 167
Period size: 69 Copynumber: 2.1 Consensus size: 67
37060 TATACGGAAC
* * * * *
37070 AAACAGAAAGACCAAAGTACTAATAGAGAGCACATAAGTGTTAGGCAACAGAGAGCACACTCAGT
1 AAACAGAGAGACCAAAGTACTAATAGAGAGCACAAAAGTGCTA-G-AACAGAAAGCACACACAGT
37135 GCT-
64 GCTA
*
37138 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCTA-ATCAGAAAGCACACACA
1 AAACAGAGAG-AC-CAAAGTACTAAT-AGAGAGCACA-AAAGTGCTAGAACAGAAAGCACACACA
37202 GTGCTA
62 GTGCTA
37208 ATAACAGAGAG
1 A-AACAGAGAG
37219 CGCGCTAGTG
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
68 9 0.13
69 21 0.30
70 13 0.19
71 19 0.28
72 7 0.10
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.13
Consensus pattern (67 bp):
AAACAGAGAGACCAAAGTACTAATAGAGAGCACAAAAGTGCTAGAACAGAAAGCACACACAGTGC
TA
Found at i:43761 original size:41 final size:41
Alignment explanation
Indices: 43702--43793 Score: 148
Period size: 41 Copynumber: 2.2 Consensus size: 41
43692 AAAAATCATA
* * *
43702 TTTAATACAATAATATATTTATTATATTTATGGTAGTGTTT
1 TTTAATATAATAAAATATTTATTATATTTATGGTAGTATTT
43743 TTTAATATAATAAAATATTTATTATATTTATGGTAGTATTT
1 TTTAATATAATAAAATATTTATTATATTTATGGTAGTATTT
*
43784 TCTAATATAA
1 TTTAATATAA
43794 ATACTTTTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (41 bp):
TTTAATATAATAAAATATTTATTATATTTATGGTAGTATTT
Found at i:44196 original size:3 final size:3
Alignment explanation
Indices: 44190--44220 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
44180 TAAATTGATG
44190 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
44221 AGGTTAAAAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:49430 original size:43 final size:43
Alignment explanation
Indices: 49369--49455 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
49359 TATTTCTCAC
*
49369 TTTAATGAGGTATTTATACATATGAAAATGTAACAAAAATAGA
1 TTTAATGAGGTATTTATACATATGAAAATATAACAAAAATAGA
49412 TTTAATGAGGTATTTATACATATGAAAATATAACAAAAATAGA
1 TTTAATGAGGTATTTATACATATGAAAATATAACAAAAATAGA
49455 T
1 T
49456 CTAACTCCTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (43 bp):
TTTAATGAGGTATTTATACATATGAAAATATAACAAAAATAGA
Found at i:68107 original size:22 final size:21
Alignment explanation
Indices: 68058--68108 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
68048 AATGTCAATA
*
68058 TTAAAATAAGAATTTTTTAAT
1 TTAAAATAAGAAATTTTTAAT
*
68079 TGAAAAATAAGAAATTTTTAACT
1 T-TAAAATAAGAAATTTTTAA-T
68102 TTAAAAT
1 TTAAAAT
68109 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 22 0.88
23 2 0.08
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (21 bp):
TTAAAATAAGAAATTTTTAAT
Found at i:72003 original size:62 final size:61
Alignment explanation
Indices: 71883--72006 Score: 149
Period size: 61 Copynumber: 2.0 Consensus size: 61
71873 TATATTTTCT
* * * * *
71883 TAAATATCGAACAAAACTTACTCTAAAAAATGTTAACAAACTTTCGAATTTAAACAAATAA
1 TAAATATCAAACAAAACTTACTCTAAAAAATATAAACAAACTTCCGAACTTAAACAAATAA
* * * * *
71944 TAAATATCAAATAAAATTTACTCTCAAAAATATCAAACAAACTTCCGGACTTGAACAAATAA
1 TAAATATCAAACAAAACTTACTCTAAAAAATAT-AAACAAACTTCCGAACTTAAACAAATAA
72006 T
1 T
72007 TAGCCATCAA
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
61 28 0.54
62 24 0.46
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (61 bp):
TAAATATCAAACAAAACTTACTCTAAAAAATATAAACAAACTTCCGAACTTAAACAAATAA
Found at i:80936 original size:210 final size:210
Alignment explanation
Indices: 80574--81076 Score: 598
Period size: 210 Copynumber: 2.4 Consensus size: 210
80564 CTGTGACATT
** *
80574 ATCATTTGGCCCAGAATGATTAAGTTGTCATCAAGTCTATTACTGCTACAATTTATCCAAACCCA
1 ATCATTTGGCCCAGAATGATTAAGCCGTCATCAAGTCTATTACTGCTACAATTTATCCTAACCCA
* * * * ** * * *
80639 AAGGCTAAAAAGCACTTCTTCGAGATGCAGTTGATCGATCCCCATCCCAATTAAAAGCTTCTCAG
66 TAGGTTGAAAAGCACTTCTTCGAAACACAGTTGATCGATCCCCATCCCAAATAAAAGCCTCTAAG
**
80704 CTTCAGAAAACTAACCTTTTTCAAACAATGCTGTAACCAAAGCT-TCAAAAGCTTTAAAATCAGG
131 CTTCAGAAAACTAACCTTTTTCAAACAATGCTCCAACCAAAG-TATCAAAAGCTTTAAAATCAGG
* * * *
80768 CCAGTATCCTAATGTA
195 CCAGAAACCCAATCTA
* *
80784 ATCATTTGGCCCAGAATGATTAAGCCCTCATAAAGTCTATTACTGCTACAATTTATCCTAACCCA
1 ATCATTTGGCCCAGAATGATTAAGCCGTCATCAAGTCTATTACTGCTACAATTTATCCTAACCCA
*
80849 TAGGTTGAAAAGCACTTCTTC-ATAACACAGTTGATCGATCCCCAT-TCAAGATAAAAGCCTCTA
66 TAGGTTGAAAAGCACTTCTTCGA-AACACAGTTGATCGATCCCCATCCCAA-ATAAAAGCCTCTA
** * * * * * *
80912 AGCTTGTGAAAGCTTACTTTTTTCAAGCAATGCTCCAACCAATGTATCATAAGCTTTAAAATCAG
129 AGCTTCAGAAAACTAACCTTTTTCAAACAATGCTCCAACCAAAGTATCAAAAGCTTTAAAATCAG
* *
80977 GCCAGAAACCCGATCTG
194 GCCAGAAACCCAATCTA
* ** * * ** *
80994 ATCATTTGACCCAGAATGATTAAGCCGTCATCAAGTCTATTACAACTATAGTACATCCTAACCCC
1 ATCATTTGGCCCAGAATGATTAAGCCGTCATCAAGTCTATTACTGCTACAATTTATCCTAACCCA
*
81059 TAGGTTGAAAAGCTCTTC
66 TAGGTTGAAAAGCACTTC
81077 GTCTTGACAT
Statistics
Matches: 248, Mismatches: 42, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
209 5 0.02
210 243 0.98
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (210 bp):
ATCATTTGGCCCAGAATGATTAAGCCGTCATCAAGTCTATTACTGCTACAATTTATCCTAACCCA
TAGGTTGAAAAGCACTTCTTCGAAACACAGTTGATCGATCCCCATCCCAAATAAAAGCCTCTAAG
CTTCAGAAAACTAACCTTTTTCAAACAATGCTCCAACCAAAGTATCAAAAGCTTTAAAATCAGGC
CAGAAACCCAATCTA
Found at i:86509 original size:30 final size:30
Alignment explanation
Indices: 86473--86544 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
86463 AAAAATCAGT
86473 TTAATTATATTATGTTACAA-AAATATTATA
1 TTAATTATATTATGTTA-AATAAATATTATA
*
86503 TTAATTATA-TATGTTAAATAATTATTATA
1 TTAATTATATTATGTTAAATAAATATTATA
*
86532 TATATTTATATTA
1 T-TAATTATATTA
86545 AATCACTAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
28 2 0.05
29 17 0.46
30 16 0.43
31 2 0.05
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (30 bp):
TTAATTATATTATGTTAAATAAATATTATA
Found at i:86726 original size:39 final size:39
Alignment explanation
Indices: 86649--86736 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 39
86639 AAAAATCATA
* * **
86649 TTTAATACAATAAAATATTTATTATATTTGTTTTTGTTT
1 TTTAATATAATAAAATATTTATTATATTTGGTAGTGTTT
86688 TTTAATATAAT-AAA-ATTTATTATATTTATGGTAGTGTTT
1 TTTAATATAATAAAATATTTATTATA-TT-TGGTAGTGTTT
*
86727 TCTAATATAA
1 TTTAATATAA
86737 ATACTTTTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
37 10 0.24
38 5 0.12
39 27 0.64
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (39 bp):
TTTAATATAATAAAATATTTATTATATTTGGTAGTGTTT
Found at i:86827 original size:15 final size:16
Alignment explanation
Indices: 86807--86837 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
86797 TTTAGTGTAT
86807 TATATTTTT-AATAAA
1 TATATTTTTAAATAAA
86822 TATATTTTTAAATAAA
1 TATATTTTTAAATAAA
86838 AACCAATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATATTTTTAAATAAA
Found at i:89430 original size:21 final size:21
Alignment explanation
Indices: 89405--89447 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
89395 CCTCTTAAAT
89405 ACATTCATCAAATAATATACA
1 ACATTCATCAAATAATATACA
*
89426 ACATTCATCGAATAATATACA
1 ACATTCATCAAATAATATACA
89447 A
1 A
89448 GTCATTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.51, C:0.19, G:0.02, T:0.28
Consensus pattern (21 bp):
ACATTCATCAAATAATATACA
Found at i:89891 original size:12 final size:12
Alignment explanation
Indices: 89876--89905 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
89866 AACAAGTTCA
*
89876 TTTATTGGCTCG
1 TTTATTGACTCG
89888 TTTATTGACTCG
1 TTTATTGACTCG
89900 TTTATT
1 TTTATT
89906 TATTAATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.57
Consensus pattern (12 bp):
TTTATTGACTCG
Found at i:90043 original size:23 final size:23
Alignment explanation
Indices: 89999--90044 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
89989 ATATTGTTCG
* *
89999 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
90022 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
90045 CAAACAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:91665 original size:17 final size:18
Alignment explanation
Indices: 91638--91671 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
91628 CTTAGTCCGT
91638 ATTTTTGTTAAAAAATTA
1 ATTTTTGTTAAAAAATTA
*
91656 ATTTTT-TTAAGAAATT
1 ATTTTTGTTAAAAAATT
91672 GATAATCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATTTTTGTTAAAAAATTA
Found at i:96922 original size:15 final size:15
Alignment explanation
Indices: 96902--96931 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
96892 GAATATTAAA
*
96902 AATATTTTTTATATT
1 AATATTTTATATATT
96917 AATATTTTATATATT
1 AATATTTTATATATT
96932 TCTATAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
AATATTTTATATATT
Found at i:97952 original size:6 final size:6
Alignment explanation
Indices: 97941--97973 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
97931 GAGAAAGTGG
97941 AAATAA AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAA
97974 CAACAGAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:98222 original size:12 final size:12
Alignment explanation
Indices: 98207--98235 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
98197 ACGAAGACTT
98207 CGAGGAAGAAGA
1 CGAGGAAGAAGA
98219 CGAGGAAGAAGA
1 CGAGGAAGAAGA
98231 -GAGGA
1 CGAGGA
98236 GGAGAGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.48, C:0.07, G:0.45, T:0.00
Consensus pattern (12 bp):
CGAGGAAGAAGA
Found at i:98407 original size:24 final size:24
Alignment explanation
Indices: 98379--98448 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
98369 AACGGCGAAG
*
98379 GAGGAAGTGGAGGAGGAAGAAGAT
1 GAGGAAGTGGAGGAGGAAGAAGAA
* *
98403 GAGGAAGAT-GAGGAAGAGGAAGAA
1 GAGGAAG-TGGAGGAGGAAGAAGAA
*
98427 GAGGAAAGTGAGAGAAGGAAGA
1 GAGG-AAGTG-GAGGAGGAAGA
98449 GAAAGATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
24 24 0.67
25 4 0.11
26 8 0.22
ACGTcount: A:0.47, C:0.00, G:0.47, T:0.06
Consensus pattern (24 bp):
GAGGAAGTGGAGGAGGAAGAAGAA
Found at i:98421 original size:15 final size:15
Alignment explanation
Indices: 98388--98432 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
98378 GGAGGAAGTG
* * *
98388 GAGGAGGAAGAAGAT
1 GAGGAAGAAGAGGAA
*
98403 GAGGAAGATGAGGAA
1 GAGGAAGAAGAGGAA
98418 GAGGAAGAAGAGGAA
1 GAGGAAGAAGAGGAA
98433 AGTGAGAGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.47, T:0.04
Consensus pattern (15 bp):
GAGGAAGAAGAGGAA
Found at i:98910 original size:6 final size:6
Alignment explanation
Indices: 98888--98923 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
98878 TCTCCTTTAG
*
98888 CTGTCA CTGTCTC CTGTCA CTGTCA CTGTCA CTGTC
1 CTGTCA CTGTC-A CTGTCA CTGTCA CTGTCA CTGTC
98924 TCATTCTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.11, C:0.36, G:0.17, T:0.36
Consensus pattern (6 bp):
CTGTCA
Found at i:100216 original size:16 final size:16
Alignment explanation
Indices: 100195--100229 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
100185 GTGTTTTATG
100195 GTTTTTGGGCAAGAGT
1 GTTTTTGGGCAAGAGT
100211 GTTTTTGGGCAAGAGT
1 GTTTTTGGGCAAGAGT
100227 GTT
1 GTT
100230 CTGGATTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.17, C:0.06, G:0.37, T:0.40
Consensus pattern (16 bp):
GTTTTTGGGCAAGAGT
Found at i:107246 original size:20 final size:22
Alignment explanation
Indices: 107210--107253 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
107200 AATGTTGAAT
107210 ATCAAATTTAACTAAAAAA-AA
1 ATCAAATTTAACTAAAAAATAA
107231 ATCAAA-TTAA-TAAAAAAATAA
1 ATCAAATTTAACT-AAAAAATAA
107252 AT
1 AT
107254 GTTAAAGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 1 0.05
20 10 0.48
21 10 0.48
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (22 bp):
ATCAAATTTAACTAAAAAATAA
Found at i:107253 original size:21 final size:21
Alignment explanation
Indices: 107210--107248 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
107200 AATGTTGAAT
107210 ATCAAATTTAACTAAAAAAAA
1 ATCAAATTTAACTAAAAAAAA
107231 ATCAAA-TTAA-TAAAAAAA
1 ATCAAATTTAACTAAAAAAA
107249 TAAATGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 4 0.22
21 6 0.33
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (21 bp):
ATCAAATTTAACTAAAAAAAA
Found at i:116920 original size:22 final size:22
Alignment explanation
Indices: 116895--116938 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
116885 GGCTGTCAAA
116895 ATAAAATAAAAATAAAACCTAT
1 ATAAAATAAAAATAAAACCTAT
116917 ATAAAATAAAAATAAAACCTAT
1 ATAAAATAAAAATAAAACCTAT
116939 TGACATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (22 bp):
ATAAAATAAAAATAAAACCTAT
Found at i:117370 original size:22 final size:21
Alignment explanation
Indices: 117309--117358 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
117299 CTAAATTTTC
*
117309 AAAATTCAAAAAGTATAAAGATT
1 AAAATTGAAAAA-T-TAAAGATT
*
117332 AAAATTGAAGAATTAAAGATT
1 AAAATTGAAAAATTAAAGATT
117353 AAAATT
1 AAAATT
117359 AATCAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 14 0.56
22 1 0.04
23 10 0.40
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.28
Consensus pattern (21 bp):
AAAATTGAAAAATTAAAGATT
Found at i:119850 original size:32 final size:32
Alignment explanation
Indices: 119809--119871 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
119799 AATAAATAAT
*
119809 TTTAGTCAAAATAAAATTAAGAAAATAACAAA
1 TTTAGTCAAAACAAAATTAAGAAAATAACAAA
*
119841 TTTAGTCAAAACAAAATTAATAAAATAACAA
1 TTTAGTCAAAACAAAATTAAGAAAATAACAA
119872 CTTTGAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.25
Consensus pattern (32 bp):
TTTAGTCAAAACAAAATTAAGAAAATAACAAA
Found at i:130445 original size:32 final size:33
Alignment explanation
Indices: 130385--130456 Score: 103
Period size: 32 Copynumber: 2.2 Consensus size: 33
130375 TTATTCACTT
*
130385 AAAATAAATAATTTTAGTCAAAATAAAATTAAG
1 AAAATAAATAATTTTAGTCAAAACAAAATTAAG
*
130418 AAAATAACA-AATTTT-GTCAAAACAAAATTAAT
1 AAAATAA-ATAATTTTAGTCAAAACAAAATTAAG
130450 AAAATAA
1 AAAATAA
130457 TAACTTTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 22 0.61
33 13 0.36
34 1 0.03
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (33 bp):
AAAATAAATAATTTTAGTCAAAACAAAATTAAG
Found at i:132100 original size:14 final size:14
Alignment explanation
Indices: 132081--132108 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
132071 TGCAAGTTAA
132081 TATGAACTATGAAG
1 TATGAACTATGAAG
132095 TATGAACTATGAAG
1 TATGAACTATGAAG
132109 CTGTGAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (14 bp):
TATGAACTATGAAG
Found at i:133085 original size:3 final size:3
Alignment explanation
Indices: 133071--133113 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
133061 CAACTCTAAC
*
133071 ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
133114 TTGAGTAGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:135506 original size:29 final size:29
Alignment explanation
Indices: 135463--135836 Score: 353
Period size: 29 Copynumber: 12.8 Consensus size: 29
135453 TGGAGGTCCG
* *
135463 TAAACTTTCCAAAAATTTCGTTTTTACCCC
1 TAAAC-TTCCAAAAATTCCATTTTTACCCC
* *
135493 TAAACTTCCAAAAATGCCATTTTTAACCC
1 TAAACTTCCAAAAATTCCATTTTTACCCC
* *
135522 TAAAACTTCCAAAAATTTCATTTTTACCCT
1 T-AAACTTCCAAAAATTCCATTTTTACCCC
* *
135552 TAAACTTCCAAAAATCCCATTTTTGACCTC
1 TAAACTTCCAAAAATTCCATTTTT-ACCCC
* * **
135582 AAAACTTTCAAAAATTTTATTTTTACCCAC
1 TAAACTTCCAAAAATTCCATTTTTACCC-C
* *
135612 -AAACTTCCAAAAATCCCATTTTTAACCCT
1 TAAACTTCCAAAAATTCCATTTTT-ACCCC
* * * *
135641 TGAACTTCCAAAAATCCCATTTTGACCTC
1 TAAACTTCCAAAAATTCCATTTTTACCCC
*
135670 GAAACTTCCAAAAA-TCC-TATTTTA-CCC
1 TAAACTTCCAAAAATTCCAT-TTTTACCCC
* * * * *
135697 TCGAATTTCCAAAAAATCCAATTTTAACCC
1 T-AAACTTCCAAAAATTCCATTTTTACCCC
* *
135727 AAAAATTCCAAAAATTCCATTTTTACCCC
1 TAAACTTCCAAAAATTCCATTTTTACCCC
*
135756 TAAACTTCCAAAAATGCCATTTTTACCCC
1 TAAACTTCCAAAAATTCCATTTTTACCCC
* * * *
135785 GAAACTTCCAAAAATGCCATTTTTGCCCT
1 TAAACTTCCAAAAATTCCATTTTTACCCC
*
135814 TGAACTTCC-AAAATCTCCATTTT
1 TAAACTTCCAAAAAT-TCCATTTT
135837 CAACCTCAAA
Statistics
Matches: 282, Mismatches: 51, Indels: 23
0.79 0.14 0.06
Matches are distributed among these distances:
27 3 0.01
28 22 0.08
29 176 0.62
30 81 0.29
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
TAAACTTCCAAAAATTCCATTTTTACCCC
Found at i:135557 original size:59 final size:59
Alignment explanation
Indices: 135464--135836 Score: 373
Period size: 59 Copynumber: 6.4 Consensus size: 59
135454 GGAGGTCCGT
* * * *
135464 AAACTTTCCAAAAATTTCGTTTTTACCCCTAAACTTCCAAAAATGCCATTTTTAACCCTA
1 AAAC-TTCCAAAAATTCCATTTTTACCCCGAAACTTCCAAAAATCCCATTTTTAACCCTA
* ** *
135524 AAACTTCCAAAAATTTCATTTTTACCCTTAAACTTCCAAAAATCCCATTTTTGA-CCTCA
1 AAACTTCCAAAAATTCCATTTTTACCCCGAAACTTCCAAAAATCCCATTTTTAACCCT-A
* ** *
135583 AAACTTTCAAAAATTTTATTTTTACCCAC-AAACTTCCAAAAATCCCATTTTTAACCCTT
1 AAACTTCCAAAAATTCCATTTTTACCC-CGAAACTTCCAAAAATCCCATTTTTAACCCTA
* * * * * *
135642 GAACTTCCAAAAATCCCATTTTGACCTCGAAACTTCCAAAAATCCTA-TTTT-ACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCGAAACTTCCAAAAATCCCATTTTTAACCCTA
* * * * * * * * *
135699 GAATTTCCAAAAAATCCAATTTTAACCCAAAAATTCCAAAAATTCCATTTTTACCCCT-
1 AAACTTCCAAAAATTCCATTTTTACCCCGAAACTTCCAAAAATCCCATTTTTAACCCTA
* * * *
135757 AAACTTCCAAAAATGCCATTTTTACCCCGAAACTTCCAAAAATGCCATTTTT-GCCCTT
1 AAACTTCCAAAAATTCCATTTTTACCCCGAAACTTCCAAAAATCCCATTTTTAACCCTA
*
135815 GAACTTCC-AAAATCTCCATTTT
1 AAACTTCCAAAAAT-TCCATTTT
135837 CAACCTCAAA
Statistics
Matches: 263, Mismatches: 42, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
57 50 0.19
58 69 0.26
59 137 0.52
60 7 0.03
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCCGAAACTTCCAAAAATCCCATTTTTAACCCTA
Found at i:139106 original size:40 final size:40
Alignment explanation
Indices: 139053--139128 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
139043 ACCAACTCAA
139053 TCAATGACTTAATAAATAGTATAGATATTGATCATGATAC
1 TCAATGACTTAATAAATAGTATAGATATTGATCATGATAC
* *
139093 TCAATGGCTTAATAAATAGTATAGATGTTGATCATG
1 TCAATGACTTAATAAATAGTATAGATATTGATCATG
139129 CATATTAACG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (40 bp):
TCAATGACTTAATAAATAGTATAGATATTGATCATGATAC
Found at i:140107 original size:22 final size:23
Alignment explanation
Indices: 140079--140122 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
140069 CTCATTTTTA
140079 TCAAAA-TAAATCCAAAAACAAC
1 TCAAAATTAAATCCAAAAACAAC
**
140101 TCAAAATTAAATTGAAAAACAA
1 TCAAAATTAAATCCAAAAACAA
140123 AAAATAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.64, C:0.16, G:0.02, T:0.18
Consensus pattern (23 bp):
TCAAAATTAAATCCAAAAACAAC
Found at i:144348 original size:28 final size:28
Alignment explanation
Indices: 144311--144382 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
144301 TTTAACTTGG
* *
144311 ACCTTGAACCCTAAATTTTAAACTTTAA
1 ACCTTGAACCCTAAACTTTAAACCTTAA
* *
144339 ACCTTCAACCCTAAACTTTAAACCTTGA
1 ACCTTGAACCCTAAACTTTAAACCTTAA
*
144367 ACCTTGAATCCTAAAC
1 ACCTTGAACCCTAAAC
144383 CCAAAATCCT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.38, C:0.28, G:0.04, T:0.31
Consensus pattern (28 bp):
ACCTTGAACCCTAAACTTTAAACCTTAA
Found at i:144353 original size:21 final size:21
Alignment explanation
Indices: 144329--144369 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
144319 CCCTAAATTT
144329 TAAACTTTAAACCTTCAACCC
1 TAAACTTTAAACCTTCAACCC
*
144350 TAAACTTTAAACCTTGAACC
1 TAAACTTTAAACCTTCAACC
144370 TTGAATCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.29, G:0.02, T:0.29
Consensus pattern (21 bp):
TAAACTTTAAACCTTCAACCC
Found at i:144390 original size:14 final size:14
Alignment explanation
Indices: 144373--144453 Score: 56
Period size: 14 Copynumber: 5.8 Consensus size: 14
144363 TTGAACCTTG
144373 AATCCTAAACCCAA
1 AATCCTAAACCCAA
* **
144387 AATCCTAAATCGTA
1 AATCCTAAACCCAA
* *
144401 AATCCTGAATCCAA
1 AATCCTAAACCCAA
* * *
144415 AATCCAAAATCCTA
1 AATCCTAAACCCAA
144429 AA-CTCTAAACCCAA
1 AATC-CTAAACCCAA
* *
144443 TACCCTAAACC
1 AATCCTAAACC
144454 TTAGACCTTA
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
13 1 0.02
14 50 0.96
15 1 0.02
ACGTcount: A:0.46, C:0.32, G:0.02, T:0.20
Consensus pattern (14 bp):
AATCCTAAACCCAA
Found at i:144402 original size:7 final size:7
Alignment explanation
Indices: 144373--144430 Score: 62
Period size: 7 Copynumber: 8.3 Consensus size: 7
144363 TTGAACCTTG
144373 AATCCTA
1 AATCCTA
* *
144380 AACCCAA
1 AATCCTA
144387 AATCCTA
1 AATCCTA
*
144394 AATCGTA
1 AATCCTA
*
144401 AATCCTG
1 AATCCTA
*
144408 AATCCAA
1 AATCCTA
*
144415 AATCCAA
1 AATCCTA
144422 AATCCTA
1 AATCCTA
144429 AA
1 AA
144431 CTCTAAACCC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.48, C:0.28, G:0.03, T:0.21
Consensus pattern (7 bp):
AATCCTA
Found at i:144520 original size:35 final size:35
Alignment explanation
Indices: 144444--144523 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 35
144434 TAAACCCAAT
* *
144444 ACCCTAAACCTTAGACCTTAAATCCTAGACCATGG
1 ACCCTAAACCTAAGACCCTAAATCCTAGACCATGG
* * * *
144479 ATCCTAAACCTAAGACCCTATAA-CTTGGACCTTGG
1 ACCCTAAACCTAAGACCCTA-AATCCTAGACCATGG
144514 ACCCTAAACC
1 ACCCTAAACC
144524 CTAGATCCAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
35 35 0.95
36 2 0.05
ACGTcount: A:0.34, C:0.33, G:0.11, T:0.23
Consensus pattern (35 bp):
ACCCTAAACCTAAGACCCTAAATCCTAGACCATGG
Found at i:144580 original size:7 final size:7
Alignment explanation
Indices: 144529--144613 Score: 59
Period size: 7 Copynumber: 12.1 Consensus size: 7
144519 AAACCCTAGA
144529 TCCAAGG
1 TCCAAGG
144536 -CTCAAGG
1 TC-CAAGG
*
144543 TCCAAAG
1 TCCAAGG
144550 T-CAATGG
1 TCCAA-GG
*
144557 TCCAGGG
1 TCCAAGG
* *
144564 TCTAACG
1 TCCAAGG
*
144571 TCCATGG
1 TCCAAGG
144578 TCCAAGG
1 TCCAAGG
144585 TCC-AGG
1 TCCAAGG
*
144591 ATCCAAAG
1 -TCCAAGG
144599 TCCAAGG
1 TCCAAGG
*
144606 TCGAAGG
1 TCCAAGG
144613 T
1 T
144614 TTAGGGTTTA
Statistics
Matches: 59, Mismatches: 13, Indels: 12
0.70 0.15 0.14
Matches are distributed among these distances:
6 7 0.12
7 47 0.80
8 5 0.08
ACGTcount: A:0.28, C:0.26, G:0.27, T:0.19
Consensus pattern (7 bp):
TCCAAGG
Found at i:144586 original size:28 final size:28
Alignment explanation
Indices: 144542--144613 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
144532 AAGGCTCAAG
* * * *
144542 GTCCAAAGT-CAATGGTCCAGGGTCTAAC
1 GTCCAAGGTCCAA-GGTCCAGGATCCAAA
*
144570 GTCCATGGTCCAAGGTCCAGGATCCAAA
1 GTCCAAGGTCCAAGGTCCAGGATCCAAA
*
144598 GTCCAAGGTCGAAGGT
1 GTCCAAGGTCCAAGGT
144614 TTAGGGTTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 33 0.92
29 3 0.08
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.19
Consensus pattern (28 bp):
GTCCAAGGTCCAAGGTCCAGGATCCAAA
Found at i:158643 original size:17 final size:18
Alignment explanation
Indices: 158621--158655 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
158611 TATGCATTTG
*
158621 TTATATTTTCATA-CATA
1 TTATATATTCATATCATA
158638 TTATATATTCATATCATA
1 TTATATATTCATATCATA
158656 CACTCATTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATATATTCATATCATA
Done.