Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold734
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: 82603
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:8320 original size:18 final size:18
Alignment explanation
Indices: 8299--8354 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
8289 TATTAACTTC
* * *
8299 AAATTTTATTTTGTATTT
1 AAATTTTAATTTATATTA
*
8317 AAATTTAAATTTATATTA
1 AAATTTTAATTTATATTA
8335 AAATTTTTAATATTA-ATTA
1 AAA-TTTTAAT-TTATATTA
8354 A
1 A
8355 TAATAAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 17 0.55
19 11 0.35
20 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
AAATTTTAATTTATATTA
Found at i:8428 original size:97 final size:95
Alignment explanation
Indices: 8317--8502 Score: 277
Period size: 97 Copynumber: 1.9 Consensus size: 95
8307 TTTTGTATTT
* * *
8317 AAATTTAAATTTATATTAAAATTTTTAATATTAATTAATAAT-AAATATATATTAAAAATAAAAA
1 AAATTCAAATTTATATTAAAATTTTTAAAAATAATTAATAATAAAATATATATT---AA-AAAAA
8381 AATTATTCAAACTTAACTC-AAATTACTCCAGCC
62 AATTATTCAAACTTAACTCAAAATTACTCCAGCC
8414 AAATTCAAATTTATATTAAAATTTTTAAAAATAATTAATAATAAAATATATATTAAAAAAAAATT
1 AAATTCAAATTTATATTAAAATTTTTAAAAATAATTAATAATAAAATATATATTAAAAAAAAATT
* *
8479 ATTCAAGCTTACCTCAAAATTACT
66 ATTCAAACTTAACTCAAAATTACT
8503 TTGAGCCAAA
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
94 22 0.27
95 10 0.12
97 39 0.48
98 11 0.13
ACGTcount: A:0.53, C:0.09, G:0.01, T:0.38
Consensus pattern (95 bp):
AAATTCAAATTTATATTAAAATTTTTAAAAATAATTAATAATAAAATATATATTAAAAAAAAATT
ATTCAAACTTAACTCAAAATTACTCCAGCC
Found at i:11139 original size:5 final size:5
Alignment explanation
Indices: 11132--11172 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
11122 CCCCCCTTTT
* * *
11132 CCTTT CCTTT CCTTT CCTTC CCTTC CCTTC CCTTC CCTTC C
1 CCTTC CCTTC CCTTC CCTTC CCTTC CCTTC CCTTC CCTTC C
11173 TCCATGAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (5 bp):
CCTTC
Found at i:11149 original size:15 final size:15
Alignment explanation
Indices: 11129--11172 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
11119 AAACCCCCCT
* *
11129 TTTCCTTTCCTTTCC
1 TTTCCTTCCCTTCCC
11144 TTTCCTTCCCTTCCC
1 TTTCCTTCCCTTCCC
*
11159 TTCCCTTCCCTTCC
1 TTTCCTTCCCTTCC
11173 TCCATGAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTCCTTCCCTTCCC
Found at i:16556 original size:17 final size:17
Alignment explanation
Indices: 16534--16567 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16524 TTGACCTTTG
16534 AGTTTGAGATATTGGGT
1 AGTTTGAGATATTGGGT
16551 AGTTTGAGATATTGGGT
1 AGTTTGAGATATTGGGT
16568 CCTAATGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (17 bp):
AGTTTGAGATATTGGGT
Found at i:24719 original size:19 final size:18
Alignment explanation
Indices: 24690--24727 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
24680 TAAAAAATAA
24690 TTATTGTGTTGTAATTAT
1 TTATTGTGTTGTAATTAT
*
24708 TTATTGGTGTTGTTATTAT
1 TTATT-GTGTTGTAATTAT
24727 T
1 T
24728 GAAAGCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.63
Consensus pattern (18 bp):
TTATTGTGTTGTAATTAT
Found at i:25492 original size:20 final size:20
Alignment explanation
Indices: 25467--25530 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
25457 GTTTGAAGCA
25467 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCATC
25487 ATGTATCGAT---A--CA--
1 ATGTATCGATACAATTCATC
25500 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCATC
25520 ATGTATCGATA
1 ATGTATCGATA
25531 TGCCATGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.27
15 2 0.05
16 1 0.03
17 1 0.03
18 2 0.05
20 21 0.57
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATTCATC
Found at i:25505 original size:13 final size:13
Alignment explanation
Indices: 25465--25514 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 13
25455 CCGTTTGAAG
25465 CAATGTATCGATA
1 CAATGTATCGATA
25478 CAA--T-TC-AT-
1 CAATGTATCGATA
25486 C-ATGTATCGATA
1 CAATGTATCGATA
25498 CAATGTATCGATA
1 CAATGTATCGATA
25511 CAAT
1 CAAT
25515 TCATCATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.10
10 4 0.13
11 3 0.10
12 1 0.03
13 18 0.58
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:25507 original size:33 final size:34
Alignment explanation
Indices: 25463--25548 Score: 147
Period size: 33 Copynumber: 2.5 Consensus size: 34
25453 AGCCGTTTGA
25463 AGCAATGTATCGATACAATTCATCATGTATCGAT
1 AGCAATGTATCGATACAATTCATCATGTATCGAT
25497 A-CAATGTATCGATACAATTCATCATGTATCGAT
1 AGCAATGTATCGATACAATTCATCATGTATCGAT
*
25530 ATGCCATGTATCGATACAA
1 A-GCAATGTATCGATACAA
25549 ACAGTGGTAG
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
33 33 0.67
34 1 0.02
35 15 0.31
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (34 bp):
AGCAATGTATCGATACAATTCATCATGTATCGAT
Found at i:25627 original size:19 final size:19
Alignment explanation
Indices: 25581--25632 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
25571 CAGTTTCATA
**
25581 TATCGATACAATTGTGCATG
1 TATCGATACAA-TGAACATG
* *
25601 CATTGATACAATGAACATG
1 TATCGATACAATGAACATG
25620 TATCGATACAATG
1 TATCGATACAATG
25633 TATCGATACA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (19 bp):
TATCGATACAATGAACATG
Found at i:25635 original size:13 final size:13
Alignment explanation
Indices: 25617--25643 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25607 TACAATGAAC
25617 ATGTATCGATACA
1 ATGTATCGATACA
25630 ATGTATCGATACA
1 ATGTATCGATACA
25643 A
1 A
25644 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:26624 original size:33 final size:33
Alignment explanation
Indices: 26558--26624 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
26548 AAGTGCACTA
* * * *
26558 AAGTGCTCATCCATGCGTTGCTAGAGTGTAGTG
1 AAGTGCTCATCCATGCGATGCGAAAGTGAAGTG
* *
26591 AAGTGCTCATTCATGTGATGCGAAAGTGAAGTG
1 AAGTGCTCATCCATGCGATGCGAAAGTGAAGTG
26624 A
1 A
26625 TCAACTCTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (33 bp):
AAGTGCTCATCCATGCGATGCGAAAGTGAAGTG
Found at i:27974 original size:19 final size:21
Alignment explanation
Indices: 27929--27975 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
27919 AACGTTTTTG
27929 TTGATGATTTTGATGAAAAAA
1 TTGATGATTTTGATGAAAAAA
** *
27950 GAGATG-TTTTGATG-TAAAA
1 TTGATGATTTTGATGAAAAAA
27969 TTGATGA
1 TTGATGA
27976 AAATTTAAGA
Statistics
Matches: 20, Mismatches: 5, Indels: 3
0.71 0.18 0.11
Matches are distributed among these distances:
19 8 0.40
20 8 0.40
21 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (21 bp):
TTGATGATTTTGATGAAAAAA
Found at i:27980 original size:10 final size:10
Alignment explanation
Indices: 27958--28008 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
27948 AAGAGATGTT
27958 TTGATGTAAAA
1 TTGATG-AAAA
27969 TTGATGAAAA
1 TTGATGAAAA
* *
27979 TTTAAGAAAA
1 TTGATGAAAA
27989 TTTGA-GAAAAA
1 -TTGATG-AAAA
28000 TTGATGAAA
1 TTGATGAAA
28009 TATCGTTAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
10 20 0.59
11 14 0.41
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (10 bp):
TTGATGAAAA
Found at i:37775 original size:36 final size:34
Alignment explanation
Indices: 37696--37788 Score: 111
Period size: 36 Copynumber: 2.7 Consensus size: 34
37686 CAATACCACC
*
37696 TTTCAAGGCTAAGATAGAAA---TCTCCTTATCT
1 TTTCAAGGCTAAGATAGAAACTCTCTCCCTATCT
*
37727 TTTCACGAGCTAAGATAGAAACTCTCTCCCTATCTT
1 TTTCAAG-GCTAAGATAGAAACTCTCTCCCTATC-T
*
37763 TTTCAAAGGCTAAGATAGAACCTCTC
1 TTTC-AAGGCTAAGATAGAAACTCTC
37789 AATCACTTAG
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
31 6 0.12
32 13 0.25
35 9 0.17
36 22 0.42
37 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (34 bp):
TTTCAAGGCTAAGATAGAAACTCTCTCCCTATCT
Found at i:38244 original size:20 final size:20
Alignment explanation
Indices: 38219--38256 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
38209 GTTAGGCTCA
38219 ATGTATCGATACAATTCACC
1 ATGTATCGATACAATTCACC
38239 ATGTATCGATACAATTCA
1 ATGTATCGATACAATTCA
38257 TTATATATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:38265 original size:20 final size:20
Alignment explanation
Indices: 38222--38268 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
38212 AGGCTCAATG
*
38222 TATCGATACAATTCACCATG
1 TATCGATACAATTCACCATA
**
38242 TATCGATACAATTCATTATA
1 TATCGATACAATTCACCATA
38262 TATCGAT
1 TATCGAT
38269 GTAATGTATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (20 bp):
TATCGATACAATTCACCATA
Found at i:38517 original size:20 final size:21
Alignment explanation
Indices: 38492--38532 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
38482 GATACTTTGA
38492 ATTATTTTTA-CTTGAAAAAC
1 ATTATTTTTAGCTTGAAAAAC
38512 ATTATTTTTATGCTTGAAAAA
1 ATTATTTTTA-GCTTGAAAAA
38533 AATCTATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (21 bp):
ATTATTTTTAGCTTGAAAAAC
Found at i:40167 original size:19 final size:19
Alignment explanation
Indices: 40143--40190 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
40133 ACTAAAGCAA
40143 TGTATCGATATATTAAAAT
1 TGTATCGATATATTAAAAT
40162 TGTATCGATATATTAAAAT
1 TGTATCGATATATTAAAAT
40181 TGTATCGATA
1 TGTATCGATA
40191 CAATGTATCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (19 bp):
TGTATCGATATATTAAAAT
Found at i:40203 original size:32 final size:32
Alignment explanation
Indices: 40162--40227 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 32
40152 ATATTAAAAT
40162 TGTATCGATAT-ATTAAAATTGTATCGATACAA
1 TGTATCGATATAATT-AAATTGTATCGATACAA
**
40194 TGTATCGATATAAATTTGATTGTATCGATACAA
1 TGTATCGATAT-AATTAAATTGTATCGATACAA
40227 T
1 T
40228 CTGAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 11 0.37
33 16 0.53
34 3 0.10
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (32 bp):
TGTATCGATATAATTAAATTGTATCGATACAA
Found at i:41332 original size:13 final size:13
Alignment explanation
Indices: 41311--41340 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41301 ACAATTCTTC
*
41311 ATGTGTCGATACA
1 ATGTATCGATACA
41324 ATGTATCGATACA
1 ATGTATCGATACA
41337 ATGT
1 ATGT
41341 CCCATGTATC
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:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:41332 original size:33 final size:33
Alignment explanation
Indices: 41290--41356 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
41280 CATTGGGCAT
* *
41290 AATGTATCGATACAAT-TCTTCATGTGTCGATAC
1 AATGTATCGATACAATGTC-CCATGTATCGATAC
41323 AATGTATCGATACAATGTCCCATGTATCGATAC
1 AATGTATCGATACAATGTCCCATGTATCGATAC
41356 A
1 A
41357 TTTCACTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (33 bp):
AATGTATCGATACAATGTCCCATGTATCGATAC
Found at i:42330 original size:25 final size:25
Alignment explanation
Indices: 42296--42347 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
42286 CAAAAACAAG
42296 TAAAAATAAATATGACTACTCCTAT
1 TAAAAATAAATATGACTACTCCTAT
42321 TAAAAATAAATATGACTACTCCTAT
1 TAAAAATAAATATGACTACTCCTAT
42346 TA
1 TA
42348 CAAAGACCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (25 bp):
TAAAAATAAATATGACTACTCCTAT
Found at i:45410 original size:16 final size:16
Alignment explanation
Indices: 45381--45420 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
45371 GAGTTTTATC
*
45381 AAAATTTCTTCTATTA
1 AAAATTTTTTCTATTA
*
45397 AAACTTTTTTCTATTA
1 AAAATTTTTTCTATTA
45413 AAAATTTT
1 AAAATTTT
45421 GAAAGCCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAATTTTTTCTATTA
Found at i:48057 original size:24 final size:22
Alignment explanation
Indices: 48029--48074 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
48019 TTTCATCATT
48029 TAGTTTAGAGAGAGTTTTCTTTTC
1 TAGTTTAGAGA-A-TTTTCTTTTC
* *
48053 TAGTTTCGATAATTTTCTTTTC
1 TAGTTTAGAGAATTTTCTTTTC
48075 AAGAATTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 1 0.05
24 9 0.45
ACGTcount: A:0.20, C:0.11, G:0.15, T:0.54
Consensus pattern (22 bp):
TAGTTTAGAGAATTTTCTTTTC
Found at i:48533 original size:3 final size:3
Alignment explanation
Indices: 48525--48555 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
48515 CAAGTCAAGT
*
48525 TCA TCA TCA TCA TCA TCA TCA TCA TCT TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
48556 TATCTTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (3 bp):
TCA
Found at i:50205 original size:20 final size:20
Alignment explanation
Indices: 50159--50211 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
50149 GTTGGACATA
* **
50159 ATGTATCGATACAATTTTTC
1 ATGTATCGATACAATGTCCC
*
50179 ATATATCGATACAATGTCCC
1 ATGTATCGATACAATGTCCC
*
50199 ATGTATCAATACA
1 ATGTATCGATACA
50212 TTTCACTTAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATGTCCC
Found at i:50282 original size:19 final size:20
Alignment explanation
Indices: 50240--50292 Score: 90
Period size: 19 Copynumber: 2.7 Consensus size: 20
50230 CTGCCAGTTT
*
50240 CATGTATCAATACAATTGAG
1 CATGTATCGATACAATTGAG
50260 CATGTATCGATACAATT-AG
1 CATGTATCGATACAATTGAG
50279 CATGTATCGATACA
1 CATGTATCGATACA
50293 TTGTATCGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:53207 original size:21 final size:21
Alignment explanation
Indices: 53186--53237 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
53176 ATTTAATTCA
*
53186 TCATTTTCTTCTTGCAACTCATT
1 TCATTTTCTT-TTCCAACTCA-T
53209 TC-TTTTCTTTTCCAACTCAT
1 TCATTTTCTTTTCCAACTCAT
*
53229 TTATTTTCT
1 TCATTTTCT
53238 CCTCTAGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 2 0.08
21 15 0.58
22 7 0.27
23 2 0.08
ACGTcount: A:0.15, C:0.25, G:0.02, T:0.58
Consensus pattern (21 bp):
TCATTTTCTTTTCCAACTCAT
Found at i:54884 original size:36 final size:32
Alignment explanation
Indices: 54801--54884 Score: 89
Period size: 36 Copynumber: 2.5 Consensus size: 32
54791 CTTTCAAGAT
* **
54801 TAAGATAGAAATCTCTCTATCTTTTCACGGGC
1 TAAGATAGAACTCTCTCTATCTTTTCAAAGGC
*
54833 TAAGATAGGATCTCTCTCCCTATCTTTTTCAAAGGC
1 TAAGATA-GAACTCTCT--CTATC-TTTTCAAAGGC
54869 TAAGATAGAAC-CTCTC
1 TAAGATAGAACTCTCTC
54885 AATCACTTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
32 8 0.19
33 7 0.16
34 4 0.09
35 8 0.19
36 16 0.37
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (32 bp):
TAAGATAGAACTCTCTCTATCTTTTCAAAGGC
Found at i:55362 original size:20 final size:20
Alignment explanation
Indices: 55315--55369 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
55305 GTTGGGCTCA
*
55315 ATGTATCAATACAATTCACC
1 ATGTATCGATACAATTCACC
*
55335 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCACC
*
55355 ATGTATCGTTACAAT
1 ATGTATCGATACAAT
55370 GTATCGATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:55470 original size:32 final size:33
Alignment explanation
Indices: 55429--55490 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
55419 TATTTCAAGG
55429 TGTATCGATA-TCAAG-AACATGTATCGATATAA
1 TGTATCGATACT-AAGCAACATGTATCGATATAA
*
55461 TGTATCGATACTAAGCAATATGTATCGATA
1 TGTATCGATACTAAGCAACATGTATCGATA
55491 CATCTAGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (33 bp):
TGTATCGATACTAAGCAACATGTATCGATATAA
Found at i:55489 original size:33 final size:32
Alignment explanation
Indices: 55429--55490 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
55419 TATTTCAAGG
55429 TGTATCGATATCAAGAACATGTATCGATATAA
1 TGTATCGATATCAAGAACATGTATCGATATAA
*
55461 TGTATCGATA-CTAAGCAATATGTATCGATA
1 TGTATCGATATC-AAG-AACATGTATCGATA
55491 CATCTAGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 1 0.04
32 13 0.48
33 13 0.48
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (32 bp):
TGTATCGATATCAAGAACATGTATCGATATAA
Found at i:64870 original size:52 final size:52
Alignment explanation
Indices: 64792--64919 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
64782 CGAAATATGA
*
64792 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
64844 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
64896 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
64920 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 21 0.28
52 48 0.65
53 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:64946 original size:13 final size:13
Alignment explanation
Indices: 64928--64952 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64918 CAAAGATCAG
64928 TGTATCGATACAA
1 TGTATCGATACAA
64941 TGTATCGATACA
1 TGTATCGATACA
64953 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:65030 original size:33 final size:33
Alignment explanation
Indices: 64993--65059 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
64983 AGTAGCTTAA
64993 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
65026 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
65059 A
1 A
65060 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:65033 original size:13 final size:13
Alignment explanation
Indices: 65015--65039 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65005 CAAAAAAATA
65015 TGTATCGATACAT
1 TGTATCGATACAT
65028 TGTATCGATACA
1 TGTATCGATACA
65040 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:65972 original size:49 final size:49
Alignment explanation
Indices: 65851--66710 Score: 1113
Period size: 49 Copynumber: 17.9 Consensus size: 49
65841 TTGGGTTTTA
* *
65851 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
*
65900 -AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* *
65948 AAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* * *
65997 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* * *
66046 AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* * *
66095 AAGGTGCCAATATGCTGATTCAAGACTAGCTATATTGGACTT----A--
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* * *
66138 AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* * *
66187 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* * * *
66236 AAAGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* * * *
66285 AAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* *
66334 AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G
* *
66384 AAAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--
1 --AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
*
66429 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G
*
66479 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--
1 --AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
*
66524 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G
*
66574 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--
1 --AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
*
66619 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* *
66668 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
66711 GAAGGGTTGC
Statistics
Matches: 709, Mismatches: 68, Indels: 68
0.84 0.08 0.08
Matches are distributed among these distances:
43 156 0.22
45 1 0.00
47 4 0.01
48 50 0.07
49 379 0.53
50 1 0.00
52 118 0.17
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
Found at i:66048 original size:98 final size:93
Alignment explanation
Indices: 65850--66715 Score: 1283
Period size: 98 Copynumber: 9.1 Consensus size: 93
65840 ATTGGGTTTT
* * * *
65850 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGT-GAGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
*
65914 TGATTCAAGGCCAGCTACATTGGACTTAAA
66 TGATTCAAGGCCAGCTATATTGGACTT--A
*
65944 GATGAAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATA
1 -A--AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATA
66009 TGCTGATTCAAGGCCAGCTATATTGGACTTA
63 TGCTGATTCAAGGCCAGCTATATTGGACTTA
66040 ATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAA
1 A-----AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAA
* *
66105 TATGCTGATTCAAGACTAGCTATATTGGACTT-
61 TATGCTGATTCAAGGCCAGCTATATTGGACTTA
66137 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
66202 TGATTCAAGGCCAGCTATATTGGACTTA
66 TGATTCAAGGCCAGCTATATTGGACTTA
* *
66230 ATGGTGAAAGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAGTGCCAA
1 A-----AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAA
66295 TATGCTGATTCAAGGCCAGCTATATTGGACTTA
61 TATGCTGATTCAAGGCCAGCTATATTGGACTTA
66328 ATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGC
1 A-----AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGC
*
66393 CGATATGCTGATTCAAGGCCAGCTATATTGGACTT-
58 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
*
66428 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAATA
66493 TGCTGATTCAAGGCCAGCTATATTGGACTT-
63 TGCTGATTCAAGGCCAGCTATATTGGACTTA
*
66523 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAATA
66588 TGCTGATTCAAGGCCAGCTATATTGGACTT-
63 TGCTGATTCAAGGCCAGCTATATTGGACTTA
* *
66618 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
*
66683 TGATTCAAGGCCAGCTATATTGGGCTTA
66 TGATTCAAGGCCAGCTATATTGGACTTA
*
66711 GAAGG
1 AAAGG
66716 GTTGCCACCG
Statistics
Matches: 734, Mismatches: 21, Indels: 34
0.93 0.03 0.04
Matches are distributed among these distances:
92 130 0.18
93 5 0.01
95 238 0.32
96 1 0.00
97 46 0.06
98 272 0.37
100 1 0.00
101 41 0.06
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (93 bp):
AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTTA
Found at i:66173 original size:190 final size:186
Alignment explanation
Indices: 65848--66715 Score: 1305
Period size: 190 Copynumber: 4.5 Consensus size: 186
65838 TCATTGGGTT
* * *
65848 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGT-GAGGTGCCAATGT
1 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATAT
* *
65912 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGAGTCAAGGCCAG
66 GCTGATTCAAGGCCAGCTATATTGGACTT----A-GAAGGTGCCAATGTGCTGAGTCAAGGCCAG
65977 CTACATTGGACTTAAAGAT-AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
126 CTACATTGGACTTAAAGATGAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
*
66037 TTAATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 TT-A-----AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
* *
66102 CAATATGCTGATTCAAGACTAGCTATATTGGACTTA-AAGGTGCCAATGTGCTGAGTCAAGGCCA
60 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAGAAGGTGCCAATGTGCTGAGTCAAGGCCA
66166 GCTACATTGGACTTAAAGAT-AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
125 GCTACATTGGACTTAAAGATGAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* * *
66227 TTAATGGTGAAAGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAGTGC
1 TT-A-----AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
66292 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATGTGCTGAGTCAA
60 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-A----GAAGGTGCCAATGTGCTGAGTCAA
*
66357 GGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATT
120 GGCCAGCTACATTGGACTTAAAGAT-G-AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATT
66422 GGAC
183 GGAC
66426 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAA
1 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAA
*
66491 TATGCTGATTCAAGGCCAGCTATATTGGACTTA-AAGGTGCCAATGTGCTGATTCAAGGCCAGCT
63 TATGCTGATTCAAGGCCAGCTATATTGGACTTAGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCT
66555 ACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
128 ACATTGGACTTAAAGAT-G-AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
*
66616 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATAT
1 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATAT
*
66681 GCTGATTCAAGGCCAGCTATATTGGGCTTAGAAGG
66 GCTGATTCAAGGCCAGCTATATTGGACTTAGAAGG
66716 GTTGCCACCG
Statistics
Matches: 639, Mismatches: 20, Indels: 41
0.91 0.03 0.06
Matches are distributed among these distances:
187 42 0.07
188 4 0.01
189 2 0.00
190 326 0.51
191 1 0.00
192 1 0.00
193 46 0.07
195 47 0.07
196 127 0.20
198 1 0.00
199 42 0.07
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (186 bp):
TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATAT
GCTGATTCAAGGCCAGCTATATTGGACTTAGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACA
TTGGACTTAAAGATGAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
Found at i:66754 original size:33 final size:33
Alignment explanation
Indices: 66710--66848 Score: 201
Period size: 33 Copynumber: 4.2 Consensus size: 33
66700 TATTGGGCTT
66710 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
66743 AGAATGGTTGCCACCAACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* * *
66775 GGAAAGGTTGCCACTGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
66808 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAG
*
66841 GGAAGGGT
1 AGAAGGGT
66849 GAAAGATGCC
Statistics
Matches: 94, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
32 29 0.31
33 42 0.45
34 23 0.24
ACGTcount: A:0.18, C:0.17, G:0.37, T:0.29
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:66794 original size:65 final size:66
Alignment explanation
Indices: 66715--66844 Score: 226
Period size: 65 Copynumber: 2.0 Consensus size: 66
66705 GGCTTAGAAG
*
66715 GGTTGCCACCGACTTGTGTGGGCTTTAGAGAATGG-TTGCCACCAACTTGTGTGGGCTTTGGGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCAACTTGTGTGGGCTTTGGGAA
66779 A
66 A
* *
66780 GGTTGCCACTGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCGACTTGTGTGGGCTTTGGGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCAACTTGTGTGGGCTTTGGGAA
66845 GGGTGAAAGA
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
65 33 0.54
66 28 0.46
ACGTcount: A:0.17, C:0.18, G:0.35, T:0.30
Consensus pattern (66 bp):
GGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCAACTTGTGTGGGCTTTGGGAA
A
Found at i:66892 original size:33 final size:33
Alignment explanation
Indices: 66850--67478 Score: 851
Period size: 33 Copynumber: 18.8 Consensus size: 33
66840 GGGAAGGGTG
* * * *
66850 AAAGA-TGCCACGAAGTTGTGGACTTAAAAAGA
1 AAAGAGTGCCACGCAGTTGTGGGCTTAGAAGGA
* *
66882 ACAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGGAAA
1 A-AAGAGTGCCACGCAGTTGTGGGC-TT-AGAAGG--A
*
66919 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGCAGTTGTGGGCTTAGAAGG-A
*
66953 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGCAGTTGTGGGCTTAGAAGG-A
66987 AAAGAGTGCCACAG-AGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCAC-GCAGTTGTGGGCTTAGAAGG-A
* *
67021 AAAGAGTGCCACGTAGCTGTGGGCTTTA-AAGGA
1 AAAGAGTGCCACGCAGTTGTGGGC-TTAGAAGGA
* *
67054 AAAGAGTGCCACGTAGCTGTGGGCTTTA-AAGGA
1 AAAGAGTGCCACGCAGTTGTGGGC-TTAGAAGGA
67087 AAAGAGTGCCACGCAGTTGTGGGCTTAGAAGGA
1 AAAGAGTGCCACGCAGTTGTGGGCTTAGAAGGA
* *
67120 AAAAAGTGCCACGTAGTTGTGGGCTTTA-AAGGA
1 AAAGAGTGCCACGCAGTTGTGGGC-TTAGAAGGA
67153 AAAGAGTGCCACGCAGTTGTGGGCTTTA-AAGGA
1 AAAGAGTGCCACGCAGTTGTGGGC-TTAGAAGGA
67186 AAAGAGTGCCACGCAGTTGTGGGCTTAGAAGGA
1 AAAGAGTGCCACGCAGTTGTGGGCTTAGAAGGA
67219 AAAGAGTGCCACGCAGTTGTGGGCTTAGAAGGA
1 AAAGAGTGCCACGCAGTTGTGGGCTTAGAAGGA
*
67252 AAAGAGTGCCACGTAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGCAGTTGTGGGCTTAGAAGG-A
* *
67286 AAAGAGGGCCACGGAGTTGTGGGCTTAGAAGGA
1 AAAGAGTGCCACGCAGTTGTGGGCTTAGAAGGA
67319 AAAGAGTGCCACGCAGTTGTGGGCTTAGAAGGA
1 AAAGAGTGCCACGCAGTTGTGGGCTTAGAAGGA
67352 AAAGAGTGCCACGCAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGCAGTTGTGGGCTTAGAAGG-A
* *
67386 AAAGAGGGCCACGGAGTTGTGGGCTTAGAAGGA
1 AAAGAGTGCCACGCAGTTGTGGGCTTAGAAGGA
*
67419 AAAGAGTGCCACGTAGTTGTGGGCTTTA-AAGGAA
1 AAAGAGTGCCACGCAGTTGTGGGC-TTAGAAGG-A
* *
67453 AAAGGGTGCCACGGAGTTGTGGGCTT
1 AAAGAGTGCCACGCAGTTGTGGGCTT
67479 TAAGAAGGTA
Statistics
Matches: 558, Mismatches: 22, Indels: 33
0.91 0.04 0.05
Matches are distributed among these distances:
32 7 0.01
33 325 0.58
34 186 0.33
35 14 0.03
36 5 0.01
37 21 0.04
ACGTcount: A:0.32, C:0.14, G:0.35, T:0.19
Consensus pattern (33 bp):
AAAGAGTGCCACGCAGTTGTGGGCTTAGAAGGA
Found at i:67119 original size:100 final size:100
Alignment explanation
Indices: 66850--67481 Score: 879
Period size: 100 Copynumber: 6.3 Consensus size: 100
66840 GGGAAGGGTG
* * * * * *
66850 AAAGA-TGCCACGAAGTTGTGGACTTAAAAAGAACAAG-GTGCCACGGAGTTGTGGGCTTTAAAA
1 AAAGAGTGCCACGCAGTTGTGGGCTTTAAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AGA
*
66913 AGGAAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
64 AGG--AAAAGAGTGCCACGTAGTTGTGGGCTTAGAAGG-A
* *
66953 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAGAA
1 AAAGAGTGCCACGCAGTTGTGGGCTTTA-AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAA
*
67017 GGAAAAAGAGTGCCACGTAGCTGTGGGCTTTA-AAGGA
65 GG-AAAAGAGTGCCACGTAGTTGTGGGC-TTAGAAGGA
* * *
67054 AAAGAGTGCCACGTAGCTGTGGGCTTTAAAGG-AAAAGAGTGCCACGCAGTTGTGGGCTTAGAAG
1 AAAGAGTGCCACGCAGTTGTGGGCTTTAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAG
*
67118 GAAAAAAGTGCCACGTAGTTGTGGGCTTTA-AAGGA
66 GAAAAGAGTGCCACGTAGTTGTGGGC-TTAGAAGGA
*
67153 AAAGAGTGCCACGCAGTTGTGGGCTTTAAAGG-AAAAGAGTGCCACGCAGTTGTGGGCTTAGAAG
1 AAAGAGTGCCACGCAGTTGTGGGCTTTAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAG
*
67217 GAAAAGAGTGCCACGCAGTTGTGGGCTTAGAAGGA
66 GAAAAGAGTGCCACGTAGTTGTGGGCTTAGAAGGA
* *
67252 AAAGAGTGCCACGTAGTTGTGGGC-TTAGAAGGAAAAAGAGGGCCACGGAGTTGTGGGCTTAGAA
1 AAAGAGTGCCACGCAGTTGTGGGCTTTA-AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAA
*
67316 GGAAAAGAGTGCCACGCAGTTGTGGGCTTAGAAGGA
65 GGAAAAGAGTGCCACGTAGTTGTGGGCTTAGAAGGA
*
67352 AAAGAGTGCCACGCAGTTGTGGGC-TTAGAAGGAAAAAGAGGGCCACGGAGTTGTGGGCTTAGAA
1 AAAGAGTGCCACGCAGTTGTGGGCTTTA-AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAA
67416 GGAAAAGAGTGCCACGTAGTTGTGGGCTTTA-AAGGAA
65 GGAAAAGAGTGCCACGTAGTTGTGGGC-TTAGAAGG-A
* *
67453 AAAGGGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGAGTGCCACGCAGTTGTGGGCTTTAA
67482 GAAGGTATTT
Statistics
Matches: 492, Mismatches: 26, Indels: 24
0.91 0.05 0.04
Matches are distributed among these distances:
98 6 0.01
99 150 0.30
100 189 0.38
101 54 0.11
102 34 0.07
103 15 0.03
104 26 0.05
105 18 0.04
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.19
Consensus pattern (100 bp):
AAAGAGTGCCACGCAGTTGTGGGCTTTAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAG
GAAAAGAGTGCCACGTAGTTGTGGGCTTAGAAGGA
Found at i:68464 original size:17 final size:16
Alignment explanation
Indices: 68432--68462 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
68422 GTTTTTCCTC
*
68432 TTTTTTTTCTTTTTTG
1 TTTTGTTTCTTTTTTG
68448 TTTTGTTTCTTTTTT
1 TTTTGTTTCTTTTTT
68463 TGGAAAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.87
Consensus pattern (16 bp):
TTTTGTTTCTTTTTTG
Found at i:72737 original size:97 final size:97
Alignment explanation
Indices: 72570--72777 Score: 226
Period size: 97 Copynumber: 2.2 Consensus size: 97
72560 CCACTCGAAG
* * ** * * *
72570 GAATAGGGTTGGAATGTCCCAGATGATGACCATTTAAGTAAAAATTAGATTTAAATTTTAACAAG
1 GAATAGGGTTGGAGTGTCCCAGATGATAAAAATTTAAGCAAAAATAAGATTTAAACTTTAACAAG
* * **
72635 TTTAAAAGCAGGG-TTAGAGTA-CCTCCTCGGAA
66 CTTAAAAAC-GGGTTTAGAGTATCC-CCTCAAAA
* * *
72667 GAATAGGGTTGGAGTGTCCCTA-ATGATAAAAATTTAGGCAAAAATAAGATTTAAACTTTGACGA
1 GAATAGGGTTGGAGTGTCCC-AGATGATAAAAATTTAAGCAAAAATAAGATTTAAACTTTAACAA
72731 GCTTAAAAACGGGTTTAGAGTATCCCCTCAAAA
65 GCTTAAAAACGGGTTTAGAGTATCCCCTCAAAA
*
72764 G-ATGGGGTTGGAGT
1 GAATAGGGTTGGAGT
72778 ATTTCCAATG
Statistics
Matches: 93, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
96 15 0.16
97 75 0.81
98 3 0.03
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.28
Consensus pattern (97 bp):
GAATAGGGTTGGAGTGTCCCAGATGATAAAAATTTAAGCAAAAATAAGATTTAAACTTTAACAAG
CTTAAAAACGGGTTTAGAGTATCCCCTCAAAA
Found at i:75016 original size:21 final size:21
Alignment explanation
Indices: 74956--75018 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
74946 AATCTATAAA
*
74956 ATTGCCTGCATGTATCGATAC
1 ATTGCCAGCATGTATCGATAC
** * *
74977 ATT-AAAGAATGTACCGATAC
1 ATTGCCAGCATGTATCGATAC
*
74997 ATTGCCAGCATGTATTGATAC
1 ATTGCCAGCATGTATCGATAC
75018 A
1 A
75019 AGTTTTCCAA
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (21 bp):
ATTGCCAGCATGTATCGATAC
Found at i:76578 original size:23 final size:23
Alignment explanation
Indices: 76526--76603 Score: 68
Period size: 22 Copynumber: 3.3 Consensus size: 23
76516 AATAAATTAT
* *
76526 TTATGTTTTACTTATAAATTATATGA
1 TTAT-TTTTACTTA-AAAATA-ATAA
* * *
76552 TTATTTTTATTTTAGAATAATAA
1 TTATTTTTACTTAAAAATAATAA
76575 TTA-TTTTACTTAAAAATAATAA
1 TTATTTTTACTTAAAAATAATAA
76597 TATATTT
1 T-TATTT
76604 GCTCATCTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
22 17 0.40
23 8 0.19
24 6 0.14
25 7 0.17
26 4 0.10
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.54
Consensus pattern (23 bp):
TTATTTTTACTTAAAAATAATAA
Found at i:78820 original size:16 final size:16
Alignment explanation
Indices: 78782--78825 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
78772 TTACTATCAA
*
78782 TATTCATGAACTTTAAT
1 TATTCATGAA-TTTAAG
*
78799 TATTCATGAATTTGAG
1 TATTCATGAATTTAAG
78815 TATTCATGAAT
1 TATTCATGAAT
78826 CATGTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (16 bp):
TATTCATGAATTTAAG
Found at i:78868 original size:17 final size:16
Alignment explanation
Indices: 78846--78903 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 16
78836 CCTAAATGGT
*
78846 ATTATGAACATTAATGA
1 ATTATGAA-ATTCATGA
78863 ATTATGTAAATTCATGA
1 ATTATG-AAATTCATGA
78880 ATT-TGAATATTCATGA
1 ATTATGAA-ATTCATGA
*
78896 ACTATGAA
1 ATTATGAA
78904 TATACATGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
15 2 0.06
16 12 0.33
17 20 0.56
18 2 0.06
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (16 bp):
ATTATGAAATTCATGA
Found at i:78905 original size:17 final size:16
Alignment explanation
Indices: 78848--78917 Score: 61
Period size: 17 Copynumber: 4.2 Consensus size: 16
78838 TAAATGGTAT
* *
78848 TATGAACATTAATGAA
1 TATGAATATTCATGAA
78864 TTATGTAA-ATTCATGAA
1 -TATG-AATATTCATGAA
*
78881 TTTGAATATTCATGAA
1 TATGAATATTCATGAA
*
78897 CTATGAATATACATGATA
1 -TATGAATATTCATGA-A
78915 TAT
1 TAT
78918 TCATGAATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
15 2 0.04
16 12 0.27
17 28 0.62
18 3 0.07
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (16 bp):
TATGAATATTCATGAA
Found at i:78912 original size:33 final size:34
Alignment explanation
Indices: 78780--78912 Score: 96
Period size: 33 Copynumber: 3.9 Consensus size: 34
78770 TGTTACTATC
*
78780 AATATTCATGAACT-T-TAATTATTCATGAATTTG
1 AATATTCATGAACTATGTAA-TATACATGAATTTG
* * *
78813 AGTATTCATGAA-TCATGTATATACCTAAATGGTATTATG
1 AATATTCATGAACT-ATGTA-ATA--TACAT-GAATT-TG
* * * *
78852 AACATTAATGAATTATGTAA-ATTCATGAATTTG
1 AATATTCATGAACTATGTAATATACATGAATTTG
78885 AATATTCATGAACTATG-AATATACATGA
1 AATATTCATGAACTATGTAATATACATGA
78913 TATATTCATG
Statistics
Matches: 76, Mismatches: 14, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
32 3 0.04
33 34 0.45
34 5 0.07
35 7 0.09
36 1 0.01
37 4 0.05
38 5 0.07
39 16 0.21
40 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (34 bp):
AATATTCATGAACTATGTAATATACATGAATTTG
Found at i:80050 original size:15 final size:15
Alignment explanation
Indices: 80030--80064 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
80020 AATCAATATT
*
80030 TTTTTTATTTATTGG
1 TTTTTTATATATTGG
80045 TTTTTTATATATTGG
1 TTTTTTATATATTGG
80060 TTTTT
1 TTTTT
80065 GACATCTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.74
Consensus pattern (15 bp):
TTTTTTATATATTGG
Done.