Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold89
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: 5168001
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 33045 characters in sequence are not A, C, G, or T
File 3 of 27
Found at i:281981 original size:19 final size:20
Alignment explanation
Indices: 281957--282005 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
281947 CATTATTAAA
*
281957 TTATATTAAAATAT-TATTT
1 TTATATTAAAATATATATAT
*
281976 TTATA-TAATATATATATAT
1 TTATATTAAAATATATATAT
281995 TTATAATTAAA
1 TTAT-ATTAAA
282006 CTTATATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 7 0.29
19 13 0.54
20 1 0.04
21 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATATTAAAATATATATAT
Found at i:282014 original size:60 final size:60
Alignment explanation
Indices: 281961--282077 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 60
281951 ATTAAATTAT
281961 ATTAAAATATTATTTTTATA-TAATATATATATATT-TATAATTAAACTTATATTAAAAA
1 ATTAAAATATTATTTTTATATTAATATATATATATTCTATAATTAAACTTATATTAAAAA
**** * * *
282019 ATTTTGTTATTATTTTTATATTAATATTTATATATTCTATAATTAAATTTAAATTAAAA
1 ATTAAAATATTATTTTTATATTAATATATATATATTCTATAATTAAACTTATATTAAAA
282078 TTTTTTTATT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 16 0.32
59 14 0.28
60 20 0.40
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (60 bp):
ATTAAAATATTATTTTTATATTAATATATATATATTCTATAATTAAACTTATATTAAAAA
Found at i:282078 original size:58 final size:57
Alignment explanation
Indices: 281968--282087 Score: 170
Period size: 58 Copynumber: 2.1 Consensus size: 57
281958 TATATTAAAA
*
281968 TATTATTTTTATATAATATATATATATTTATAATTAAACTTATATTAAAAAATTTTGT
1 TATTATTTTTATATAATATATATATATTTATAATTAAACTTAAATT-AAAAATTTTGT
* * *
282026 TATTATTTTTATATTAATATTTATATATTCTATAATTAAATTTAAATT-AAAATTTTTT
1 TATTATTTTTATA-TAATATATATATATT-TATAATTAAACTTAAATTAAAAATTTTGT
282084 TATT
1 TATT
282088 GAATGAAAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
58 26 0.46
59 14 0.25
60 16 0.29
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.57
Consensus pattern (57 bp):
TATTATTTTTATATAATATATATATATTTATAATTAAACTTAAATTAAAAATTTTGT
Found at i:286940 original size:12 final size:13
Alignment explanation
Indices: 286925--286977 Score: 54
Period size: 14 Copynumber: 4.0 Consensus size: 13
286915 CATTTATAAA
286925 AATAATTTTA-AT
1 AATAATTTTATAT
286937 AATAATTTATATAT
1 AATAATTT-TATAT
* *
286951 TATAATTTTATTT
1 AATAATTTTATAT
*
286964 AAAATATTTTATAT
1 AATA-ATTTTATAT
286978 TTATATAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
12 8 0.24
13 8 0.24
14 17 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AATAATTTTATAT
Found at i:287002 original size:62 final size:65
Alignment explanation
Indices: 286926--287069 Score: 158
Period size: 62 Copynumber: 2.3 Consensus size: 65
286916 ATTTATAAAA
* * * *
286926 ATAATTTTAATAATAATTTATA-TATTATAATTTTATTTAAA-ATATT-TTATATTTA-TATAAA
1 ATAATTATATTAATAATTTATATTA-TATAAATTTA--AAAATATATTATTATATTTATTATAAA
286987 TTT
63 TTT
* *
286990 -T-ATTATATTAATAATTTATATTATATAAATTTAAAAATATATTATTTTATTTATTATAATTTT
1 ATAATTATATTAATAATTTATATTATATAAATTTAAAAATATATTATTATATTTATTATAAATTT
287053 ATAATTATATTAA-AATT
1 ATAATTATATTAATAATT
287070 ATTAAATCTA
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
60 3 0.04
61 5 0.07
62 34 0.50
63 11 0.16
64 5 0.07
65 10 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (65 bp):
ATAATTATATTAATAATTTATATTATATAAATTTAAAAATATATTATTATATTTATTATAAATTT
Found at i:287022 original size:15 final size:15
Alignment explanation
Indices: 286971--287062 Score: 62
Period size: 15 Copynumber: 5.8 Consensus size: 15
286961 TTTAAAATAT
286971 TTTATATTTATATAAA
1 TTTATA-TTATATAAA
286987 TTT-TATTATATTAATAA
1 TTTATATTATA-T-A-AA
287004 TTTATATTATATAAA
1 TTTATATTATATAAA
* * * *
287019 TTTAAAAATATATTAT
1 TTT-ATATTATATAAA
*
287035 TTTAT-TTATTATAAT
1 TTTATATTA-TATAAA
287050 TTTATAATTATAT
1 TTTAT-ATTATAT
287063 TAAAATTATT
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 7 0.11
15 19 0.31
16 19 0.31
17 9 0.15
18 7 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTATATTATATAAA
Found at i:287048 original size:31 final size:31
Alignment explanation
Indices: 286968--287064 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 31
286958 TTATTTAAAA
* ** *
286968 TATTTTATATTTATATAAATTTTATTATATTAA
1 TATTTTATA-TTATATAAATTTAAAAATA-TAT
*
287001 TAATTTATATTATATAAATTTAAAAATATAT
1 TATTTTATATTATATAAATTTAAAAATATAT
* * *
287032 TATTTTAT-TTATTATAATTTTATAATTATAT
1 TATTTTATATTA-TATAAATTTAAAAATATAT
287063 TA
1 TA
287065 AAATTATTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
30 3 0.06
31 27 0.50
32 16 0.30
33 8 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
TATTTTATATTATATAAATTTAAAAATATAT
Found at i:289067 original size:17 final size:18
Alignment explanation
Indices: 289041--289089 Score: 75
Period size: 17 Copynumber: 2.8 Consensus size: 18
289031 TTTTCAATTA
289041 TATAATTTATATTATCTT
1 TATAATTTATATTATCTT
*
289059 TAT-ATTTATA-TATTTT
1 TATAATTTATATTATCTT
289075 TATAATTTATATTAT
1 TATAATTTATATTAT
289090 ATATTGAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 8 0.29
17 14 0.50
18 6 0.21
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TATAATTTATATTATCTT
Found at i:290109 original size:22 final size:22
Alignment explanation
Indices: 290084--290126 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
290074 TCGCCAAGAG
290084 GAAAAAAAAAAAAAAAGAAAAA
1 GAAAAAAAAAAAAAAAGAAAAA
* *
290106 GAAAAAGAAAAAAAGAGAAAA
1 GAAAAAAAAAAAAAAAGAAAA
290127 GGGTAAACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (22 bp):
GAAAAAAAAAAAAAAAGAAAAA
Found at i:290116 original size:20 final size:21
Alignment explanation
Indices: 290087--290127 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
290077 CCAAGAGGAA
290087 AAAAAAAAAAAAAGA-AAAAG
1 AAAAAAAAAAAAAGAGAAAAG
*
290107 AAAAAGAAAAAAAGAGAAAAG
1 AAAAAAAAAAAAAGAGAAAAG
290128 GGTAAACGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAAAAGAGAAAAG
Found at i:290124 original size:16 final size:15
Alignment explanation
Indices: 290084--290126 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 15
290074 TCGCCAAGAG
290084 GAAAAAAAA-AAAAA
1 GAAAAAAAAGAAAAA
*
290098 -AAGAAAAAGAAAAA
1 GAAAAAAAAGAAAAA
290112 GAAAAAAAGAGAAAA
1 GAAAAAAA-AGAAAA
290127 GGGTAAACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 7 0.29
14 5 0.21
15 6 0.25
16 6 0.25
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
GAAAAAAAAGAAAAA
Found at i:290127 original size:7 final size:6
Alignment explanation
Indices: 290084--290117 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
290074 TCGCCAAGAG
290084 GAAAAA -AAAAA -AAAAA GAAAAA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
290118 AAGAGAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.37
6 17 0.63
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:296247 original size:18 final size:18
Alignment explanation
Indices: 296204--296255 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
296194 GTTTGGGAAA
* **
296204 GGGGAGGGCCGCGGAGGG
1 GGGGAGGGCAGCAAAGGG
296222 GGGAGAGGGCAGCAAAGGG
1 GGG-GAGGGCAGCAAAGGG
*
296241 GGGGAGGGCGGCAAA
1 GGGGAGGGCAGCAAA
296256 ATAAGGAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.23, C:0.13, G:0.63, T:0.00
Consensus pattern (18 bp):
GGGGAGGGCAGCAAAGGG
Found at i:299575 original size:20 final size:20
Alignment explanation
Indices: 299518--299575 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
299508 CAAAATAATA
*
299518 ATTTAATA-ATTTATTATAT
1 ATTTAATATAATTATTATAT
* * *
299537 A-TTAAAATAAATATAATAT
1 ATTTAATATAATTATTATAT
*
299556 ATTTAATATACTTATTATAT
1 ATTTAATATAATTATTATAT
299576 TTCTGCAGAC
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
18 5 0.17
19 10 0.34
20 14 0.48
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTAATATAATTATTATAT
Found at i:300084 original size:22 final size:22
Alignment explanation
Indices: 300043--300108 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
300033 ATCTAAAATT
* *
300043 ATATTATTTATTTTATTATTAAA
1 ATATT-TTTATATTAATATTAAA
* *
300066 ATATTTTTATATTAATATTTAT
1 ATATTTTTATATTAATATTAAA
* *
300088 ATATTTATAAATTAA-ATTAAA
1 ATATTTTTATATTAATATTAAA
300109 TTAAATTAAG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 4 0.11
22 26 0.74
23 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATATTTTTATATTAATATTAAA
Found at i:300304 original size:22 final size:22
Alignment explanation
Indices: 300276--300323 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
300266 TGAAGATATG
300276 TTAGTTTATTAGTAGTAATTAA
1 TTAGTTTATTAGTAGTAATTAA
300298 TTAGTTTATTAGTAGTAATTAA
1 TTAGTTTATTAGTAGTAATTAA
300320 TTAG
1 TTAG
300324 AACCAACCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (22 bp):
TTAGTTTATTAGTAGTAATTAA
Found at i:300597 original size:8 final size:8
Alignment explanation
Indices: 300584--300650 Score: 54
Period size: 8 Copynumber: 8.8 Consensus size: 8
300574 TTAAAATATA
300584 ATATAAAT
1 ATATAAAT
300592 ATATAAAT
1 ATATAAAT
300600 ATA-AAA-
1 ATATAAAT
*
300606 A-ATTAA-
1 ATATAAAT
*
300612 ACATAAAT
1 ATATAAAT
*
300620 -TATTAAT
1 ATATAAAT
300627 ATATTAAAAT
1 ATA-T-AAAT
300637 ATATAAAT
1 ATATAAAT
300645 ATATAA
1 ATATAA
300651 TATTTTATGT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
5 1 0.02
6 4 0.08
7 12 0.25
8 23 0.48
9 2 0.04
10 6 0.12
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATAAAT
Found at i:300838 original size:8 final size:8
Alignment explanation
Indices: 300811--300876 Score: 53
Period size: 8 Copynumber: 7.8 Consensus size: 8
300801 ATTTAAAAAT
300811 TATATAAA
1 TATATAAA
300819 TATGAGATAAA
1 TAT---ATAAA
300830 TATATAAA
1 TATATAAA
*
300838 TATAAAATA
1 TATATAA-A
300847 TAATATAAA
1 T-ATATAAA
300856 T-TATAAA
1 TATATAAA
*
300863 AATATAAA
1 TATATAAA
*
300871 AATATA
1 TATATA
300877 TTATATTTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
7 6 0.12
8 26 0.53
9 4 0.08
10 5 0.10
11 8 0.16
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (8 bp):
TATATAAA
Found at i:300845 original size:35 final size:35
Alignment explanation
Indices: 300770--300876 Score: 94
Period size: 35 Copynumber: 3.1 Consensus size: 35
300760 ATGATATGAT
* * * * * *
300770 TAAAATATAAAATAAATAATTAAAATA-GAATATT
1 TAAAATATAATATAAATTATAAAAATATAAAAATA
* *
300804 TAAAA-ATTATATAAA-TATGAGATAAATATATAAATA
1 TAAAATATAATATAAATTAT-A-A-AAATATAAAAATA
300840 TAAAATATAATATAAATTATAAAAATATAAAAATA
1 TAAAATATAATATAAATTATAAAAATATAAAAATA
300875 TA
1 TA
300877 TTATATTTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
32 2 0.04
33 8 0.14
34 6 0.11
35 19 0.33
36 9 0.16
37 10 0.18
38 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (35 bp):
TAAAATATAATATAAATTATAAAAATATAAAAATA
Found at i:301018 original size:20 final size:21
Alignment explanation
Indices: 300989--301038 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
300979 TAAAACTAAT
* *
300989 AAATTTAAATATGATATA-AA
1 AAATTAAAATATAATATATAA
301009 AAATTAAAATATAATATATAA
1 AAATTAAAATATAATATATAA
301030 AAATATAAA
1 AAAT-TAAA
301039 TAAATTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 16 0.62
21 6 0.23
22 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AAATTAAAATATAATATATAA
Found at i:301022 original size:15 final size:15
Alignment explanation
Indices: 301002--301049 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
300992 TTTAAATATG
301002 ATATAAAAAATTAAA
1 ATATAAAAAATTAAA
* * *
301017 ATATAATATATAAAA
1 ATATAAAAAATTAAA
301032 ATATAAATAAATTAAA
1 ATATAAA-AAATTAAA
301048 AT
1 AT
301050 TTATATATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATATAAAAAATTAAA
Found at i:301037 original size:30 final size:33
Alignment explanation
Indices: 301002--301063 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 33
300992 TTTAAATATG
301002 ATATAAA-AAATTAAAATATA-ATA-TATAAAA
1 ATATAAATAAATTAAAATATATATATTATAAAA
*
301032 ATATAAATAAATTAAAATTTATATATTATAAA
1 ATATAAATAAATTAAAATATATATATTATAAA
301064 TTATTAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.25
31 12 0.43
32 3 0.11
33 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (33 bp):
ATATAAATAAATTAAAATATATATATTATAAAA
Found at i:301047 original size:31 final size:32
Alignment explanation
Indices: 301002--301095 Score: 95
Period size: 32 Copynumber: 2.9 Consensus size: 32
300992 TTTAAATATG
301002 ATATAAAAAATTAAAATATA-ATA-TATAAAA
1 ATATAAAAAATTAAAATATATATATTATAAAA
*
301032 ATATAAATAAATTAAAATTTATATATTAT-AAA
1 ATATAAA-AAATTAAAATATATATATTATAAAA
* * * *
301064 TTATTAAACAATCAAAATATATAAATATATAA
1 ATA-TAAAAAATTAAAATATATATAT-TATAA
301096 TATTAATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
30 7 0.13
31 12 0.23
32 22 0.42
33 10 0.19
34 1 0.02
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (32 bp):
ATATAAAAAATTAAAATATATATATTATAAAA
Found at i:302079 original size:18 final size:17
Alignment explanation
Indices: 302056--302090 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
302046 TTTATCTTAA
302056 TTTATAATAATTAATTTT
1 TTTATAATAATT-ATTTT
*
302074 TTTATATTAATTATTTT
1 TTTATAATAATTATTTT
302091 AAAAGATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTATAATAATTATTTT
Found at i:307473 original size:32 final size:32
Alignment explanation
Indices: 307427--307497 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
307417 ATAGGTTGGA
* *
307427 AAGCGCTAAGGCGCTAAGCGCATCCCACGTGG
1 AAGCGCTAAAGCGCTAAGCGCATCCAACGTGG
* *
307459 ATGCGCTAAAGCGCTCAGCGCATCCAACGTGG
1 AAGCGCTAAAGCGCTAAGCGCATCCAACGTGG
307491 AAGCGCT
1 AAGCGCT
307498 GAGCGCCTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.25, C:0.31, G:0.30, T:0.14
Consensus pattern (32 bp):
AAGCGCTAAAGCGCTAAGCGCATCCAACGTGG
Found at i:313404 original size:21 final size:21
Alignment explanation
Indices: 313347--313407 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 21
313337 ATCAACCAAA
313347 AAAAATTTAAAGTTC-TATAAAT
1 AAAAATTTAAA-TTCATAT-AAT
*
313369 AAAAA--TAAA-TCATATATT
1 AAAAATTTAAATTCATATAAT
313387 AAAAATTTAAATTCATATAAT
1 AAAAATTTAAATTCATATAAT
313408 TATACCAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 9 0.27
19 3 0.09
20 8 0.24
21 8 0.24
22 5 0.15
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAAATTTAAATTCATATAAT
Found at i:313487 original size:138 final size:142
Alignment explanation
Indices: 313206--313884 Score: 386
Period size: 143 Copynumber: 4.7 Consensus size: 142
313196 ATTACAATAT
* * *
313206 AAATTTAAACTTCTACAAATAGAAATAAATTATAGCTTAAAAAATTTAAACTCATATAATCATAC
1 AAATTTAAACTTCTACAAATAAAAATAAATCATAGATTAAAAAATTTAAACTCATATAATCATAC
* * * * * *
313271 CCTAAAGATAAATTTAAACTTTTACAAATAAAAATGAATATACCTAAAAAAATTTAAATTCATAT
66 CCTAAAGATAAATTTAAACTTATACAAAGAAAAATAAATATAACTAAAAAAATTTAAACTCATAA
313336 AATCAACCAAAAA
131 AATCAA-CAAAAA
* * * * *
313349 AAATTTAAAGTTCTATAAATAAAAATAAATCATATATT-AAAAATTTAAATTCATATAATTATA-
1 AAATTTAAACTTCTACAAATAAAAATAAATCATAGATTAAAAAATTTAAACTCATATAATCATAC
* * * *
313412 CC-AAA-A-AAGTTTAAACTTATACAAAGAAAGATAAATAATAACT-TAAAAATTTAAACTCGTA
66 CCTAAAGATAAATTTAAACTTATACAAAGAAAAATAAAT-ATAACTAAAAAAATTTAAACTCATA
313473 AAATCATA-ATAAAA
130 AAATCA-ACA-AAAA
* * * ** * *
313487 AAATCAAATCTAAACTACTACAAATAAAGATAAATAATACTTTAAAAAAATTTAAACTCGTATAG
1 AAAT----T-TAAACTTCTACAAATAAAAATAAATCATAGATT-AAAAAATTTAAACTCATATAA
* * * * * * **
313552 TCATACTCAAAAAATAAATTTAAACTTTTATAAATAAAAATAAAT-TATACTTCAAAAATTTAAA
60 TCATACCCTAAAGATAAATTTAAACTTATACAAAGAAAAATAAATATA-ACTAAAAAAATTTAAA
** *
313616 CTTGTAAATCATAAACCCCAAAAAA
124 CTCATAAA--ATCAA---C-AAAAA
* * * *** *
313641 TAAATTT-TACTTTTAC-AA-AAAAA-AAGT-ATATCCT-AAAAATTTAAACTTATATAATCATA
1 -AAATTTAAACTTCTACAAATAAAAATAAATCATAGATTAAAAAATTTAAACTCATATAATCATA
* * * * * * *
313700 -TCTAAAAAATAAATATAAACTTTTACAAATAAAAATATATAATATACT--AAAAATTTGAACTC
65 CCCT-AAAGATAAATTTAAACTTATACAAAGAAAAATAAAT-ATA-ACTAAAAAAATTTAAACTC
*
313762 ATATAAT-AACCCAAAGAA
127 ATAAAATCAA--CAAA-AA
* *** * ** * *
313780 CAAATTTAAACTTTTACAAATGGGAATAAATTATACCTTCAAAAATTTAAGCTCATATAATCTTA
1 -AAATTTAAACTTCTACAAATAAAAATAAATCATAGATTAAAAAATTTAAACTCATATAATC--A
* * * * * *
313845 AACCTCAAAAAATAAATTTTAACTTCTACAAATAAAAATA
63 TACC-CTAAAGATAAATTTAAACTTATACAAAGAAAAATA
313885 TATTATGCTC
Statistics
Matches: 425, Mismatches: 73, Indels: 71
0.75 0.13 0.12
Matches are distributed among these distances:
137 1 0.00
138 56 0.13
139 18 0.04
140 13 0.03
141 6 0.01
142 28 0.07
143 131 0.31
144 5 0.01
145 51 0.12
146 4 0.01
147 11 0.03
148 36 0.08
149 50 0.12
150 2 0.00
151 4 0.01
154 4 0.01
155 5 0.01
ACGTcount: A:0.54, C:0.12, G:0.03, T:0.31
Consensus pattern (142 bp):
AAATTTAAACTTCTACAAATAAAAATAAATCATAGATTAAAAAATTTAAACTCATATAATCATAC
CCTAAAGATAAATTTAAACTTATACAAAGAAAAATAAATATAACTAAAAAAATTTAAACTCATAA
AATCAACAAAAA
Found at i:313535 original size:75 final size:71
Alignment explanation
Indices: 313423--313629 Score: 227
Period size: 76 Copynumber: 2.8 Consensus size: 71
313413 CAAAAAAGTT
*
313423 TAAACTTATACAAAGAAAGATAAATAATAACTTAAAAATTTAAACTCGTAAAATCATAATAAAAA
1 TAAAC-TATACAAATAAAGATAAATAAT-ACTTAAAAATTTAAACTCGTAAAATCATAATAAAAA
313488 AATCAAATC
64 AAT-AAATC
* * * *
313497 TAAACTACTACAAATAAAGATAAATAATACTTTAAAAAAATTTAAACTCGTATAGTCATACTCAA
1 TAAACTA-TACAAATAAAGATAAATAATAC-TT--AAAAATTTAAACTCGTAAAATCATAATAAA
*
313562 AAAATAAATT
62 AAAATAAATC
* * * * *
313572 TAAACTTTTATAAATAAAAATAAATTATACTTCAAAAATTTAAACTTGT-AAATCATAA
1 TAAAC-TATACAAATAAAGATAAATAATACTT-AAAAATTTAAACTCGTAAAATCATAA
313630 ACCCCAAAAA
Statistics
Matches: 113, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
72 6 0.05
73 19 0.17
74 28 0.25
75 28 0.25
76 32 0.28
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.30
Consensus pattern (71 bp):
TAAACTATACAAATAAAGATAAATAATACTTAAAAATTTAAACTCGTAAAATCATAATAAAAAAA
TAAATC
Found at i:313638 original size:75 final size:75
Alignment explanation
Indices: 313204--313920 Score: 490
Period size: 69 Copynumber: 9.9 Consensus size: 75
313194 TAATTACAAT
* * * *
313204 ATAAATTTAAACTTCTACAAATAGAAATAAATTATAGCTTAAAAAATTTAAACTCATATAATCAT
1 ATAAATTTAAACTTTTACAAATAAAAATAAATTATA-CTTCAAAAATTTAAACTTATATAATCAT
* *
313269 --ACCCTAAAG
65 AAACCCAAAAA
* **
313278 ATAAATTTAAACTTTTACAAATAAAAATGAA-TATACCTAAAAAAATTTAAA-TTCATATAATC-
1 ATAAATTTAAACTTTTACAAATAAAAATAAATTATA-CTTCAAAAATTTAAACTT-ATATAATCA
313340 --AA-CC-AAAA
64 TAAACCCAAAAA
* * *
313348 A-AAATTTAAAGTTCTATAAATAAAAATAAATCATATA-TT-AAAAATTTAAA-TTCATATAAT-
1 ATAAATTTAAACTTTTACAAATAAAAATAAAT--TATACTTCAAAAATTTAAACTT-ATATAATC
*
313408 -TATA-CC--AAA
63 ATAAACCCAAAAA
* * * * * ** *
313417 A-AAGTTTAAACTTATACAAAGAAAGATAAATAATAACTT-AAAAATTTAAACTCGTAAAATCAT
1 ATAAATTTAAACTTTTACAAATAAAAATAAATTAT-ACTTCAAAAATTTAAACTTATATAATCAT
313480 AATA---AAAAA
65 AA-ACCCAAAAA
* ** * * * ** *
313489 ATCAAATCTAAACTACTACAAATAAAGATAAATAATACTTTAAAAAAATTTAAACTCGTATAGTC
1 AT-AAATTTAAACTTTTACAAATAAAAATAAATTATAC-TT-CAAAAATTTAAACTTATATAATC
*
313554 AT--ACTCAAAAA
63 ATAAACCCAAAAA
* *
313565 ATAAATTTAAACTTTTATAAATAAAAATAAATTATACTTCAAAAATTTAAACTTGTA-AATCATA
1 ATAAATTTAAACTTTTACAAATAAAAATAAATTATACTTCAAAAATTTAAACTTATATAATCATA
313629 AACCCCAAAAA
66 AA-CCCAAAAA
* * *
313640 ATAAATTT-TACTTTTAC--A-AAAAA-AAAGTATA-TCCTAAAAATTTAAACTTATATAATCAT
1 ATAAATTTAAACTTTTACAAATAAAAATAAATTATACTTC-AAAAATTTAAACTTATATAATCAT
* *
313699 --ATCTAAAAA
65 AAACCCAAAAA
* * * *
313708 ATAAATATAAACTTTTACAAATAAAAATATATAATATAC-T-AAAAATTTGAACTCATAT-A--A
1 ATAAATTTAAACTTTTACAAATAAAAATA-A-ATTATACTTCAAAAATTTAAACTTATATAATCA
*
313768 T-AACCCAAAGA
64 TAAACCCAAAAA
* *** * * *
313779 ACAAATTTAAACTTTTACAAATGGGAATAAATTATACCTTCAAAAATTTAAGCTCATATAATCTT
1 ATAAATTTAAACTTTTACAAATAAAAATAAATTATA-CTTCAAAAATTTAAACTTATATAATCAT
313844 AAACCTCAAAAA
65 AAACC-CAAAAA
* * * * *
313856 ATAAATTTTAACTTCTACAAATAAAAATATATTATGC-TCTAAAAATTTAAATTTATATAATCAT
1 ATAAATTTAAACTTTTACAAATAAAAATAAATTATACTTC-AAAAATTTAAACTTATATAATCAT
313920 A
65 A
313921 CAAACTTCTA
Statistics
Matches: 518, Mismatches: 79, Indels: 90
0.75 0.11 0.13
Matches are distributed among these distances:
67 2 0.00
68 14 0.03
69 108 0.21
70 36 0.07
71 47 0.09
72 39 0.08
73 63 0.12
74 69 0.13
75 52 0.10
76 55 0.11
77 33 0.06
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.32
Consensus pattern (75 bp):
ATAAATTTAAACTTTTACAAATAAAAATAAATTATACTTCAAAAATTTAAACTTATATAATCATA
AACCCAAAAA
Found at i:313973 original size:58 final size:58
Alignment explanation
Indices: 313865--313976 Score: 134
Period size: 58 Copynumber: 1.9 Consensus size: 58
313855 AATAAATTTT
* * * * * *
313865 AACTTCTACAAATAAAAATATATTATGCTCTAAAAATTTAAATTTATATAATCATACA
1 AACTTCTACAAACAAAAATAAATAATACTCTAAAAATTTAAACTCATATAATCATACA
* * * *
313923 AACTTCTATAAACAAAGATAAATAATACTCTAAAATTTTAAACTCGTATAATCA
1 AACTTCTACAAACAAAAATAAATAATACTCTAAAAATTTAAACTCATATAATCA
313977 ACTTAAAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
58 44 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.34
Consensus pattern (58 bp):
AACTTCTACAAACAAAAATAAATAATACTCTAAAAATTTAAACTCATATAATCATACA
Found at i:313998 original size:71 final size:72
Alignment explanation
Indices: 313922--314242 Score: 362
Period size: 73 Copynumber: 4.4 Consensus size: 72
313912 ATAATCATAC
* * * * * * *
313922 AAACTTCTATAAACAAAGATAAATAATACTCTAAAATTTTAAACTCGTATAATCA-ACTTAAAAA
1 AAACTTCTACAAATAAAAATAAATTATACTTTAAAATTTTAAACTCATATAATCATACCTAAAAA
*
313986 TAAATGT
66 TAAATTT
* *
313993 AAACTTCTACAAATAAAAATAAATTATACCTTTAAAAATTTAAACTCATATAATTATACCTAAAA
1 AAACTTCTACAAATAAAAATAAATTATA-CTTTAAAATTTTAAACTCATATAATCATACCTAAAA
314058 A-ACATATTT
65 ATA-A-ATTT
* * * ** * *
314067 AAATTTCTACAAATCAAAATAAATTATAGTTTAAAATTTTAAACTCGCATAATCA-AACAAAAAA
1 AAACTTCTACAAATAAAAATAAATTATACTTTAAAATTTTAAACTCATATAATCATACCTAAAAA
314131 TAAATTT
66 TAAATTT
* * * *
314138 AAACTTTTACAAATAAAAATAAATTATACTTTTAAAA-TTTAAACTTATATAATCATGCCCTACA
1 AAACTTCTACAAATAAAAATAAATTATAC-TTTAAAATTTTAAACTCATATAATCAT-ACCTAAA
314202 AATAAATTT
64 AATAAATTT
* *
314211 AAATTTCTACAAATAAAAATAAATAATACTTT
1 AAACTTCTACAAATAAAAATAAATTATACTTT
314243 TAATCAAATT
Statistics
Matches: 209, Mismatches: 33, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
71 68 0.33
72 42 0.20
73 70 0.33
74 29 0.14
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.34
Consensus pattern (72 bp):
AAACTTCTACAAATAAAAATAAATTATACTTTAAAATTTTAAACTCATATAATCATACCTAAAAA
TAAATTT
Found at i:314180 original size:26 final size:26
Alignment explanation
Indices: 314126--314175 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
314116 TAATCAAACA
314126 AAAAATAAATTTAAACTTTTACAAAT
1 AAAAATAAATTTAAACTTTTACAAAT
*
314152 AAAAATAAA-TTATACTTTTA-AAAT
1 AAAAATAAATTTAAACTTTTACAAAT
314176 TTAAACTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.17
25 10 0.43
26 9 0.39
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (26 bp):
AAAAATAAATTTAAACTTTTACAAAT
Found at i:314233 original size:20 final size:20
Alignment explanation
Indices: 314197--314234 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
314187 TAATCATGCC
**
314197 CTACAAATAAATTTAAATTT
1 CTACAAATAAAAATAAATTT
314217 CTACAAATAAAAATAAAT
1 CTACAAATAAAAATAAAT
314235 AATACTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.32
Consensus pattern (20 bp):
CTACAAATAAAAATAAATTT
Found at i:314245 original size:145 final size:145
Alignment explanation
Indices: 313926--314242 Score: 435
Period size: 145 Copynumber: 2.2 Consensus size: 145
313916 TCATACAAAC
* * * * * *
313926 TTCTATAAACAAAGATAAATAATACTCTAAAATTTTAAACTCGTATAATCAACTTAAAAATAAAT
1 TTCTACAAATAAAAATAAATAATACTTTAAAATTTTAAACTCGCATAATCAACTAAAAAATAAAT
*
313991 GTAAACTTCTACAAATAAAAATAAATTATACCTTTAAAAATTTAAACTCATATAATTATACCTAA
66 GTAAACTTCTACAAATAAAAATAAATTATACCTTTAAAAATTTAAACTCATATAATCATACCTAA
314056 AAAACATATTTAAAT
131 AAAACATATTTAAAT
* * *
314071 TTCTACAAATCAAAATAAATTATAGTTTAAAATTTTAAACTCGCATAATCAAAC-AAAAAATAAA
1 TTCTACAAATAAAAATAAATAATACTTTAAAATTTTAAACTCGCATAATC-AACTAAAAAATAAA
* * * * *
314135 TTTAAACTTTTACAAATAAAAATAAATTATA-CTTTTAAAATTTAAACTTATATAATCATGCCCT
65 TGTAAACTTCTACAAATAAAAATAAATTATACCTTTAAAAATTTAAACTCATATAATCAT-ACCT
*
314199 ACAAATA-A-ATTTAAAT
129 A-AAAAACATATTTAAAT
314215 TTCTACAAATAAAAATAAATAATACTTT
1 TTCTACAAATAAAAATAAATAATACTTT
314243 TAATCAAATT
Statistics
Matches: 150, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
144 58 0.39
145 85 0.57
146 7 0.05
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.34
Consensus pattern (145 bp):
TTCTACAAATAAAAATAAATAATACTTTAAAATTTTAAACTCGCATAATCAACTAAAAAATAAAT
GTAAACTTCTACAAATAAAAATAAATTATACCTTTAAAAATTTAAACTCATATAATCATACCTAA
AAAACATATTTAAAT
Found at i:314660 original size:20 final size:19
Alignment explanation
Indices: 314621--314673 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
314611 TTTCCTGTGA
314621 TTTTTA-TTT-TTTAAAA-
1 TTTTTATTTTATTTAAAAT
314637 -TTTTATTTTAATTTAAAAT
1 TTTTTATTTT-ATTTAAAAT
314656 TTTTTATTTTATTTAAAA
1 TTTTTATTTTATTTAAAA
314674 ATTAATAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 5 0.16
16 3 0.09
18 7 0.22
19 8 0.25
20 9 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTTATTTTATTTAAAAT
Found at i:315897 original size:6 final size:6
Alignment explanation
Indices: 315881--315909 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
315871 TAAGATAAGA
315881 TAAAAT T-AAAT TAAAAT TAAAAT TAAAAT
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT
315910 GATAAGTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
TAAAAT
Found at i:325019 original size:2 final size:2
Alignment explanation
Indices: 325012--325040 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
325002 GAAATAGAAA
325012 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
325041 AACCCAGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:326003 original size:12 final size:13
Alignment explanation
Indices: 325980--326004 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
325970 AGTAATAATT
325980 ACTTTAAAAAAAA
1 ACTTTAAAAAAAA
325993 ACTTTAAAAAAA
1 ACTTTAAAAAAA
326005 TCAACAAAAC
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (13 bp):
ACTTTAAAAAAAA
Found at i:330846 original size:19 final size:19
Alignment explanation
Indices: 330818--330858 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
330808 ATTTAATATT
330818 TTATTATTTA-ATTATAAAA
1 TTATTATTTATATT-TAAAA
*
330837 TTATTTTTTATATTTAAAA
1 TTATTATTTATATTTAAAA
330856 TTA
1 TTA
330859 AAATTTTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTATTTATATTTAAAA
Found at i:331226 original size:2 final size:2
Alignment explanation
Indices: 331221--331256 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
331211 CGTCTTTCAT
331221 TA TA TA TA 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 TA TA TA TA
331257 GTGGAGCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:332273 original size:7 final size:7
Alignment explanation
Indices: 332248--332306 Score: 52
Period size: 7 Copynumber: 8.6 Consensus size: 7
332238 ACTGTCAATG
*
332248 TAATAAA
1 TAATATA
*
332255 TAATTATT
1 TAA-TATA
332263 TAATATA
1 TAATATA
332270 TAATATA
1 TAATATA
*
332277 TAA-CTA
1 TAATATA
332283 TAA-ATA
1 TAATATA
332289 TAATATA
1 TAATATA
332296 -AATTATA
1 TAA-TATA
332303 TAAT
1 TAAT
332307 TAAAAAATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
6 12 0.28
7 24 0.56
8 7 0.16
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (7 bp):
TAATATA
Found at i:336617 original size:26 final size:26
Alignment explanation
Indices: 336588--336660 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 26
336578 AGGCAATCCC
* *
336588 TAATATTAAATATAATTATAT-AAATA
1 TAATA-TAAATAAAAATATATAAAATA
*
336614 TAATATAAATAAAAATATTTAAAATA
1 TAATATAAATAAAAATATATAAAATA
* * *
336640 TAACATGATATAAATATATAT
1 TAATAT-AAATAAAAATATAT
336661 TTTAAAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
25 12 0.32
26 15 0.39
27 11 0.29
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (26 bp):
TAATATAAATAAAAATATATAAAATA
Found at i:339761 original size:60 final size:60
Alignment explanation
Indices: 339693--339809 Score: 225
Period size: 60 Copynumber: 1.9 Consensus size: 60
339683 TCCAGCAAGG
*
339693 ACCCAGCTCAATGTATGAAAAGATCAGAAAACTAACTACAACTTAATATGCATAAAACAT
1 ACCCAGCTCAATGTATAAAAAGATCAGAAAACTAACTACAACTTAATATGCATAAAACAT
339753 ACCCAGCTCAATGTATAAAAAGATCAGAAAACTAACTACAACTTAATATGCATAAAA
1 ACCCAGCTCAATGTATAAAAAGATCAGAAAACTAACTACAACTTAATATGCATAAAA
339810 TATAACCGTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.50, C:0.20, G:0.09, T:0.21
Consensus pattern (60 bp):
ACCCAGCTCAATGTATAAAAAGATCAGAAAACTAACTACAACTTAATATGCATAAAACAT
Found at i:344538 original size:34 final size:35
Alignment explanation
Indices: 344492--344561 Score: 81
Period size: 34 Copynumber: 2.0 Consensus size: 35
344482 ATTATTTACT
*
344492 ATTTTTTAAAATGTTAAATTCTTTA-TTAAACTAA
1 ATTTTTTAAAATGGTAAATTCTTTATTTAAACTAA
* * *
344526 ATTTTTCT-AAATGGTAATTTTTTTATTTAAATTAA
1 ATTTTT-TAAAATGGTAAATTCTTTATTTAAACTAA
344561 A
1 A
344562 AAATGACTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
34 20 0.67
35 10 0.33
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (35 bp):
ATTTTTTAAAATGGTAAATTCTTTATTTAAACTAA
Found at i:344990 original size:21 final size:21
Alignment explanation
Indices: 344966--345011 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
344956 TATAGGTATA
*
344966 ATTTTGATAATATTTAATATG
1 ATTTTCATAATATTTAATATG
* *
344987 ATTTTCATAGTTTTTAATATG
1 ATTTTCATAATATTTAATATG
345008 ATTT
1 ATTT
345012 AATTTTTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.57
Consensus pattern (21 bp):
ATTTTCATAATATTTAATATG
Found at i:348937 original size:26 final size:26
Alignment explanation
Indices: 348900--348990 Score: 89
Period size: 26 Copynumber: 3.5 Consensus size: 26
348890 GCACTTTCAG
348900 TTATATAATAAATGAAATAATAATATT
1 TTAT-TAATAAATGAAATAATAATATT
*
348927 TTATTAATAAAT-AAAT-ATAAAATT
1 TTATTAATAAATGAAATAATAATATT
** * * *
348951 TTAAAAATAAATATAAATAATCATAAT
1 TTATTAATAAAT-GAAATAATAATATT
348978 TTA-TAATAAATGA
1 TTATTAATAAATGA
348991 CATCATTAGT
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
24 17 0.32
25 5 0.09
26 19 0.36
27 12 0.23
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.38
Consensus pattern (26 bp):
TTATTAATAAATGAAATAATAATATT
Found at i:350014 original size:26 final size:25
Alignment explanation
Indices: 349984--350057 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 25
349974 AGTAAAGTTT
*
349984 ATAAAAAAATTATTAAA-CAAAAATTA
1 ATAAAAAAATTA--AAATAAAAAATTA
* *
350010 ATAAATAAATTAAAATAAAAAATTT
1 ATAAAAAAATTAAAATAAAAAATTA
*
350035 ATAAAAAATAATAAAATAAAAAA
1 ATAAAAAA-ATTAAAATAAAAAA
350058 AAGAAATGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 3 0.07
25 14 0.34
26 24 0.59
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.26
Consensus pattern (25 bp):
ATAAAAAAATTAAAATAAAAAATTA
Found at i:350038 original size:25 final size:25
Alignment explanation
Indices: 350002--350057 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
349992 ATTATTAAAC
350002 AAAAATTAATAAATAAAT-TAAAATA
1 AAAAATTAATAAA-AAATATAAAATA
*
350027 AAAAATTTATAAAAAATAATAAAATA
1 AAAAATTAATAAAAAAT-ATAAAATA
350053 AAAAA
1 AAAAA
350058 AAGAAATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 4 0.14
25 12 0.43
26 12 0.43
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (25 bp):
AAAAATTAATAAAAAATATAAAATA
Found at i:350048 original size:10 final size:11
Alignment explanation
Indices: 350002--350050 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
349992 ATTATTAAAC
350002 AAAAATTAATA
1 AAAAATTAATA
350013 AATAAATTAAAATA
1 AA-AAATT--AATA
*
350027 AAAAATTTATA
1 AAAAATTAATA
350038 AAAAA-TAATA
1 AAAAATTAATA
350048 AAA
1 AAA
350051 TAAAAAAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
10 7 0.21
11 10 0.30
12 5 0.15
13 5 0.15
14 6 0.18
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAAATTAATA
Found at i:350149 original size:14 final size:14
Alignment explanation
Indices: 350130--350222 Score: 58
Period size: 14 Copynumber: 7.1 Consensus size: 14
350120 CATAATTTTT
350130 ATTTCATGCATTTC
1 ATTTCATGCATTTC
350144 ATTTCATGCA-TT-
1 ATTTCATGCATTTC
* **
350156 -TTACATAAAATTTC
1 ATTTCAT-GCATTTC
*
350170 A-TGCATGCATTTC
1 ATTTCATGCATTTC
*
350183 A---CAT-AATTTC
1 ATTTCATGCATTTC
350193 ATTTCATGCATTTTC
1 ATTTCATGCA-TTTC
*
350208 ATTTCATACATTTC
1 ATTTCATGCATTTC
350222 A
1 A
350223 CGTAACATTC
Statistics
Matches: 61, Mismatches: 9, Indels: 18
0.69 0.10 0.20
Matches are distributed among these distances:
10 6 0.10
11 8 0.13
12 1 0.02
13 13 0.21
14 20 0.33
15 13 0.21
ACGTcount: A:0.29, C:0.19, G:0.05, T:0.46
Consensus pattern (14 bp):
ATTTCATGCATTTC
Found at i:350177 original size:39 final size:39
Alignment explanation
Indices: 350104--350183 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 39
350094 TCATTGCATA
* * *
350104 CATTTCATGCATTTCACATAATTTTTATTTCATGCATTT
1 CATTTCATGCATTTCACATAAATTTCATTGCATGCATTT
*
350143 CATTTCATGCATTTTACATAAAATTTCA-TGCATGCATTT
1 CATTTCATGCATTTCACAT-AAATTTCATTGCATGCATTT
350182 CA
1 CA
350184 CATAATTTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
39 30 0.83
40 6 0.17
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.46
Consensus pattern (39 bp):
CATTTCATGCATTTCACATAAATTTCATTGCATGCATTT
Found at i:350187 original size:64 final size:64
Alignment explanation
Indices: 350109--350275 Score: 246
Period size: 64 Copynumber: 2.6 Consensus size: 64
350099 GCATACATTT
* * * *
350109 CATGCATTTCACATAATTTTTATTTCATGCATTTCATTTCATGCATTTTACATAAAATTTCATG
1 CATGCATTTCACATAATTTTCATTTCATGCATTTCATTTCATACATTTCACATAAAATTCCATG
* *
350173 CATGCATTTCACATAA-TTTCATTTCATGCATTTTCATTTCATACATTTCACGTAACATTCCATG
1 CATGCATTTCACATAATTTTCATTTCATGCA-TTTCATTTCATACATTTCACATAAAATTCCATG
* *
350237 CATGCATTTTACATAATTTTCATGTCATGCATTTCATTT
1 CATGCATTTCACATAATTTTCATTTCATGCATTTCATTT
350276 TAAGCACGTA
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
63 13 0.14
64 67 0.72
65 13 0.14
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.46
Consensus pattern (64 bp):
CATGCATTTCACATAATTTTCATTTCATGCATTTCATTTCATACATTTCACATAAAATTCCATG
Found at i:350207 original size:15 final size:15
Alignment explanation
Indices: 350189--350220 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
350179 TTTCACATAA
*
350189 TTTCATTTCATGCAT
1 TTTCATTTCATACAT
350204 TTTCATTTCATACAT
1 TTTCATTTCATACAT
350219 TT
1 TT
350221 CACGTAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.19, G:0.03, T:0.56
Consensus pattern (15 bp):
TTTCATTTCATACAT
Found at i:350207 original size:25 final size:26
Alignment explanation
Indices: 350139--350208 Score: 94
Period size: 25 Copynumber: 2.8 Consensus size: 26
350129 TATTTCATGC
350139 ATTTCATTTCATGCATTTT-ACATAAA
1 ATTTCATTTCATGCATTTTCACAT-AA
*
350165 ATTTCA-TGCATGCA-TTTCACAT-A
1 ATTTCATTTCATGCATTTTCACATAA
350188 ATTTCATTTCATGCATTTTCA
1 ATTTCATTTCATGCATTTTCA
350209 TTTCATACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
23 7 0.18
24 10 0.26
25 16 0.41
26 6 0.15
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.46
Consensus pattern (26 bp):
ATTTCATTTCATGCATTTTCACATAA
Found at i:350307 original size:64 final size:64
Alignment explanation
Indices: 350103--350308 Score: 173
Period size: 64 Copynumber: 3.2 Consensus size: 64
350093 GTCATTGCAT
* * *
350103 ACATTTC--ATGCATTTCACATAATTTTTATTTCATGCATTTCATTTCATGCA-T-TTTACATA-
1 ACATTTCATATGCATTTCACATAATTTTCATTTCATGCATTTCATTTTAAGCACTATTT-CA-AG
350163 A
64 A
* * *
350164 A-ATTTCATGCATGCATTTCACATAA-TTTCATTTCATGCATTTTCA-TTTCA-TAC-ATTTCAC
1 ACATTTCAT--ATGCATTTCACATAATTTTCATTTCATGCA-TTTCATTTTAAGCACTATTTCAA
350224 GTA
63 G-A
* * *
350227 ACATTCCATGCATGCATTTTACATAATTTTCATGTCATGCATTTCATTTTAAGCACGTATTTCAA
1 ACATTTCAT--ATGCATTTCACATAATTTTCATTTCATGCATTTCATTTTAAGCAC-TATTTCAA
350292 GA
63 GA
350294 ACATTTCAT-TGCATT
1 ACATTTCATATGCATT
350309 GCTTTCATGC
Statistics
Matches: 117, Mismatches: 13, Indels: 27
0.75 0.08 0.17
Matches are distributed among these distances:
60 5 0.04
61 1 0.01
62 3 0.03
63 20 0.17
64 53 0.45
65 17 0.15
66 2 0.02
67 9 0.08
68 7 0.06
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.44
Consensus pattern (64 bp):
ACATTTCATATGCATTTCACATAATTTTCATTTCATGCATTTCATTTTAAGCACTATTTCAAGA
Found at i:354868 original size:16 final size:15
Alignment explanation
Indices: 354786--354869 Score: 59
Period size: 16 Copynumber: 5.5 Consensus size: 15
354776 ATGACATAAA
*
354786 TAAA-ATATAATATA
1 TAAATATATAATATT
*
354800 TAAATATGTTAATATT
1 TAAATAT-ATAATATT
*
354816 TACATAATATAA-ATT
1 TAAAT-ATATAATATT
*
354831 ATAAATATATCAAAATT
1 -TAAATATAT-AATATT
354848 T--ATATATAATATTT
1 TAAATATATAATA-TT
354862 TAAATATA
1 TAAATATA
354870 ATTTTTATAG
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
13 3 0.05
14 13 0.24
15 9 0.16
16 25 0.45
17 5 0.09
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (15 bp):
TAAATATATAATATT
Found at i:362627 original size:2 final size:2
Alignment explanation
Indices: 362620--362649 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
362610 CAATTTTCTA
362620 AT AT 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 AT AT
362650 TTGTAGATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:364039 original size:18 final size:16
Alignment explanation
Indices: 364007--364046 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
363997 TACTTATAAA
364007 ATTATA-TAAAATTAT
1 ATTATATTAAAATTAT
364022 ATTATATTAATAATTTAT
1 ATTATATTAA-AA-TTAT
364040 ATTATAT
1 ATTATAT
364047 AAATTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.27
16 3 0.14
17 2 0.09
18 11 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTATATTAAAATTAT
Found at i:365063 original size:20 final size:19
Alignment explanation
Indices: 365037--365090 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
365027 CATAATCATA
365037 AATAAATTATTTTATATTT
1 AATAAATTATTTTATATTT
**
365056 ATATAAATT-TAATATA-TT
1 A-ATAAATTATTTTATATTT
*
365074 AATAATTTATTTTATAT
1 AATAAATTATTTTATAT
365091 AAATTTTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 6 0.22
20 7 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AATAAATTATTTTATATTT
Found at i:365078 original size:37 final size:38
Alignment explanation
Indices: 365037--365133 Score: 101
Period size: 37 Copynumber: 2.6 Consensus size: 38
365027 CATAATCATA
*
365037 AATAAATTATTTTATATTTATATAAATTTA-ATATATT
1 AATAAATTATTTTATATTTATATAAATATATATATATT
* ** * * *
365074 AATAATTTATTTTATATAAATTTTAATATATTTATATT
1 AATAAATTATTTTATATTTATATAAATATATATATATT
365112 -ATAAATTATTTT-TATATTATAT
1 AATAAATTATTTTATAT-TTATAT
365134 GATATTTTAT
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
36 3 0.06
37 38 0.81
38 6 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (38 bp):
AATAAATTATTTTATATTTATATAAATATATATATATT
Found at i:365091 original size:20 final size:19
Alignment explanation
Indices: 365041--365091 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 19
365031 ATCATAAATA
365041 AATTATTTTATAT-TTATAT
1 AATTATTTTATATATTA-AT
*
365060 AA--ATTTAATATATTAAT
1 AATTATTTTATATATTAAT
365077 AATTTATTTTATATA
1 AA-TTATTTTATATA
365092 AATTTTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
17 12 0.46
18 3 0.12
19 2 0.08
20 9 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AATTATTTTATATATTAAT
Found at i:365131 original size:23 final size:23
Alignment explanation
Indices: 365100--365152 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
365090 TAAATTTTAA
*
365100 TATATTTATATTATAAATTATTTT
1 TATA-TTATATGATAAATTATTTT
**
365124 TATATTATATGATATTTTATTTT
1 TATATTATATGATAAATTATTTT
*
365147 TTTATT
1 TATATT
365153 TGTATTGTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
TATATTATATGATAAATTATTTT
Found at i:365141 original size:18 final size:17
Alignment explanation
Indices: 365098--365132 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
365088 TATAAATTTT
*
365098 AATATATTTATATTATA
1 AATATTTTTATATTATA
365115 AATTATTTTTATATTATA
1 AA-TATTTTTATATTATA
365133 TGATATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AATATTTTTATATTATA
Found at i:365547 original size:29 final size:26
Alignment explanation
Indices: 365515--365584 Score: 61
Period size: 30 Copynumber: 2.6 Consensus size: 26
365505 ATTTAATTAG
365515 ATTTAAATTAATATTTAATAATTAAAAGT
1 ATTTAAATTAAT-TTTAATAA-TAAAA-T
* * *
365544 ATTTTTATTTAATTTTAATTATAAAAT
1 A-TTTAAATTAATTTTAATAATAAAAT
*
365571 ATATAAA-TAATTTT
1 ATTTAAATTAATTTT
365585 TAATTTTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
25 7 0.21
26 3 0.09
27 2 0.06
28 5 0.15
29 8 0.24
30 9 0.26
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (26 bp):
ATTTAAATTAATTTTAATAATAAAAT
Found at i:365614 original size:15 final size:16
Alignment explanation
Indices: 365594--365635 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
365584 TTAATTTTTA
365594 TTAAATATAAAT-AAT
1 TTAAATATAAATGAAT
365609 TTAAAT-T-AATGGAAT
1 TTAAATATAAAT-GAAT
365624 TTAAATATAAAT
1 TTAAATATAAAT
365636 TAAAAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.13
14 1 0.04
15 15 0.65
16 1 0.04
17 3 0.13
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (16 bp):
TTAAATATAAATGAAT
Found at i:367659 original size:14 final size:14
Alignment explanation
Indices: 367619--367663 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
367609 AATTTTTTTA
367619 TATATTTAAATAATT
1 TATATTTAAAT-ATT
367634 ATATATTT--ATATT
1 -TATATTTAAATATT
367647 TATATTTAAATATT
1 TATATTTAAATATT
367661 TAT
1 TAT
367664 CGTATAGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 7 0.26
13 3 0.11
14 10 0.37
16 7 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATATTTAAATATT
Found at i:369157 original size:17 final size:16
Alignment explanation
Indices: 369126--369159 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
369116 AATACATAAA
*
369126 TATTTTATATTAATAT
1 TATTTAATATTAATAT
369142 TATTTAATATTTAATAT
1 TATTTAATA-TTAATAT
369159 T
1 T
369160 TAATAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTTAATATTAATAT
Found at i:374413 original size:37 final size:35
Alignment explanation
Indices: 374358--374432 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 35
374348 ATTTGTGCTG
* *
374358 ATATATTTTTATATATTTTAATTATATTAAAAATATT
1 ATATATTTATATAAATTTTAA-TATATTAAAAAT-TT
*
374395 ATATATTTATATAAATTTTAATATATTAATAATTT
1 ATATATTTATATAAATTTTAATATATTAAAAATTT
374430 ATA
1 ATA
374433 ATATAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 5 0.14
36 11 0.31
37 19 0.54
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (35 bp):
ATATATTTATATAAATTTTAATATATTAAAAATTT
Found at i:374426 original size:18 final size:18
Alignment explanation
Indices: 374372--374437 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 18
374362 ATTTTTATAT
374372 ATTTTAATTATATTAA-AA
1 ATTTTAA-TATATTAATAA
*
374390 ATATT-ATATATTTATATAA
1 ATTTTAATATA-TTA-ATAA
374409 ATTTTAATATATTAAT-A
1 ATTTTAATATATTAATAA
374426 ATTTATAATATA
1 ATTT-TAATATA
374438 AATTTGTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
16 4 0.10
17 9 0.22
18 14 0.34
19 9 0.22
20 5 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTTAATATATTAATAA
Found at i:374765 original size:20 final size:18
Alignment explanation
Indices: 374717--374765 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
374707 TTAAATTATT
374717 ATTATAAATATATTTTAA
1 ATTATAAATATATTTTAA
* * * *
374735 ATGATATTATATTTTTTTA
1 ATTATA-AATATATTTTAA
374754 ATTATAAATATA
1 ATTATAAATATA
374766 ATAAATATTT
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTATAAATATATTTTAA
Found at i:375218 original size:16 final size:16
Alignment explanation
Indices: 375192--375231 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
375182 GTTATTTTTT
*
375192 TTTAGTATTGATAT-A
1 TTTAATATTGATATAA
375207 TATTAATATTGATATAA
1 T-TTAATATTGATATAA
375224 TTTAATAT
1 TTTAATAT
375232 ATTATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 19 0.86
17 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTAATATTGATATAA
Found at i:378077 original size:28 final size:28
Alignment explanation
Indices: 378046--378099 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
378036 CATTCACATT
378046 GCAAAATTGCAGTCCAAGTTACAATCAG
1 GCAAAATTGCAGTCCAAGTTACAATCAG
378074 GCAAAATTGCAGTCCAAGTTACAATC
1 GCAAAATTGCAGTCCAAGTTACAATC
378100 GTCCCGTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (28 bp):
GCAAAATTGCAGTCCAAGTTACAATCAG
Found at i:381449 original size:12 final size:12
Alignment explanation
Indices: 381415--381456 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
381405 TAATAATTAA
381415 ATTTATTATA-T
1 ATTTATTATATT
381426 ATTT-TTATATT
1 ATTTATTATATT
*
381437 ATTTATAATATT
1 ATTTATTATATT
*
381449 ATTAATTA
1 ATTTATTA
381457 AATTTTACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 5 0.19
11 9 0.35
12 12 0.46
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTTATTATATT
Found at i:383549 original size:2 final size:2
Alignment explanation
Indices: 383542--383568 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
383532 CAGCTAAAGA
383542 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
383569 ATCTTTCATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:385901 original size:17 final size:17
Alignment explanation
Indices: 385863--385925 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 17
385853 TATTCATCGA
*
385863 AAATTAATTTAATTAATA-
1 AAATT-ATTTAA-AAATAT
385881 AAATTATTTAAAAATAT
1 AAATTATTTAAAAATAT
*
385898 AAATAATTTTAAATAATAT
1 AAATTA-TTTAAA-AATAT
*
385917 TAATTATTT
1 AAATTATTT
385926 TCTCTGTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
16 4 0.11
17 11 0.29
18 14 0.37
19 9 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AAATTATTTAAAAATAT
Found at i:389840 original size:24 final size:25
Alignment explanation
Indices: 389810--389859 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
389800 TGATTTAGCT
389810 TTGCA-TTTTCCCTTTGCACGATGC
1 TTGCATTTTTCCCTTTGCACGATGC
389834 TTGCATTTTTCCCTTTGCACGATGC
1 TTGCATTTTTCCCTTTGCACGATGC
389859 T
1 T
389860 GTTTAACCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.12, C:0.28, G:0.16, T:0.44
Consensus pattern (25 bp):
TTGCATTTTTCCCTTTGCACGATGC
Found at i:390252 original size:14 final size:14
Alignment explanation
Indices: 390218--390249 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
390208 TATTTAAAAA
390218 TTTTTAAATTATAT
1 TTTTTAAATTATAT
390232 TTTTTAAA-TATAT
1 TTTTTAAATTATAT
390245 TTTTT
1 TTTTT
390250 TAATCTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTTAAATTATAT
Found at i:396200 original size:7 final size:8
Alignment explanation
Indices: 396183--396207 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
396173 AAGCCCCCAA
396183 TTTCTTTT
1 TTTCTTTT
396191 TTTCTTTT
1 TTTCTTTT
396199 TTTCTTTT
1 TTTCTTTT
396207 T
1 T
396208 AAATAGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTCTTTT
Found at i:400103 original size:6 final size:6
Alignment explanation
Indices: 400098--400137 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
400088 TGATATTGAA
* *
400098 GATGAA GATGAA GATGAG GATGAG GATGAG GATGAG GATG
1 GATGAG GATGAG GATGAG GATGAG GATGAG GATGAG GATG
400138 CTGAAGAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.38, C:0.00, G:0.45, T:0.17
Consensus pattern (6 bp):
GATGAG
Found at i:407534 original size:4 final size:4
Alignment explanation
Indices: 407525--407552 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
407515 TCTTACTTTG
407525 AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA
407553 GATGAATCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:408290 original size:17 final size:19
Alignment explanation
Indices: 408270--408304 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
408260 TTTTAATCTT
408270 AATAT-ATT-TATAATATA
1 AATATAATTATATAATATA
408287 AATATAATTATATAATAT
1 AATATAATTATATAATAT
408305 GATACAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATATAATTATATAATATA
Found at i:408561 original size:18 final size:19
Alignment explanation
Indices: 408539--408584 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 19
408529 AAAAAATAAT
408539 TAAAAAAAGATACAACAC-A
1 TAAAAAAAGATA-AACACTA
*
408558 -AAAAATAATATAAACACTA
1 TAAAAA-AAGATAAACACTA
408577 TAAAAAAA
1 TAAAAAAA
408585 CTATTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 10 0.43
19 8 0.35
20 5 0.22
ACGTcount: A:0.72, C:0.11, G:0.02, T:0.15
Consensus pattern (19 bp):
TAAAAAAAGATAAACACTA
Found at i:410190 original size:2 final size:2
Alignment explanation
Indices: 410177--410222 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
410167 TGCTATCTTT
*
410177 TA TA TG TA TA TA TA 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 TA TA TA TA TA TA TA
410219 TA TA
1 TA TA
410223 GACATTTTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:414570 original size:3 final size:3
Alignment explanation
Indices: 414562--414588 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
414552 AAAAAACAAT
414562 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
414589 GCTTGAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:417459 original size:168 final size:168
Alignment explanation
Indices: 417181--417516 Score: 663
Period size: 168 Copynumber: 2.0 Consensus size: 168
417171 TTCACTCTTT
417181 GAGAGCTTAAAAGAACATGTATCCACCATTTTGACAATCACCCAAATAGTAGAAAAGATGTTTTA
1 GAGAGCTTAAAAGAACATGTATCCACCATTTTGACAATCACCCAAATAGTAGAAAAGATGTTTTA
*
417246 ACCCCGGGTCTGGATGCGAGCCATAAGAGCCTGTCATCCAGAACACTACTGTTGTACTCATTGCC
66 ACCCCGGGTCTGGATGCGAGCCATAAGAACCTGTCATCCAGAACACTACTGTTGTACTCATTGCC
417311 ATCCTTCTAATATACATGTCTTTAACATAAGCTCCTCC
131 ATCCTTCTAATATACATGTCTTTAACATAAGCTCCTCC
417349 GAGAGCTTAAAAGAACATGTATCCACCATTTTGACAATCACCCAAATAGTAGAAAAGATGTTTTA
1 GAGAGCTTAAAAGAACATGTATCCACCATTTTGACAATCACCCAAATAGTAGAAAAGATGTTTTA
417414 ACCCCGGGTCTGGATGCGAGCCATAAGAACCTGTCATCCAGAACACTACTGTTGTACTCATTGCC
66 ACCCCGGGTCTGGATGCGAGCCATAAGAACCTGTCATCCAGAACACTACTGTTGTACTCATTGCC
417479 ATCCTTCTAATATACATGTCTTTAACATAAGCTCCTCC
131 ATCCTTCTAATATACATGTCTTTAACATAAGCTCCTCC
417517 TTCCCACGGC
Statistics
Matches: 167, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
168 167 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (168 bp):
GAGAGCTTAAAAGAACATGTATCCACCATTTTGACAATCACCCAAATAGTAGAAAAGATGTTTTA
ACCCCGGGTCTGGATGCGAGCCATAAGAACCTGTCATCCAGAACACTACTGTTGTACTCATTGCC
ATCCTTCTAATATACATGTCTTTAACATAAGCTCCTCC
Found at i:419423 original size:25 final size:25
Alignment explanation
Indices: 419394--419441 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
419384 TTTTATATAT
* *
419394 TTTTTAATTTATTTTTA-AAATTTAA
1 TTTTT-ATTAATTTTAATAAATTTAA
419419 TTTTTATTAATTTTAATAAATTT
1 TTTTTATTAATTTTAATAAATTT
419442 TTATTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTTTATTAATTTTAATAAATTTAA
Found at i:419430 original size:10 final size:10
Alignment explanation
Indices: 419415--419454 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
419405 TTTTTAAAAT
419415 TTAATTTTTA
1 TTAATTTTTA
*
419425 TTAATTTTAA
1 TTAATTTTTA
*
419435 TAAATTTTTA
1 TTAATTTTTA
*
419445 TTAAATTTTA
1 TTAATTTTTA
419455 AAAATATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTAATTTTTA
Found at i:419440 original size:20 final size:20
Alignment explanation
Indices: 419417--419459 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
419407 TTTAAAATTT
419417 AATTTTTATT-AATTTTAATA
1 AATTTTTATTAAATTTTAA-A
419437 AATTTTTATTAAATTTTAAA
1 AATTTTTATTAAATTTTAAA
419457 AAT
1 AAT
419460 ATATAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AATTTTTATTAAATTTTAAA
Found at i:419449 original size:11 final size:11
Alignment explanation
Indices: 419417--419453 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
419407 TTTAAAATTT
419417 AATTTTTATT-
1 AATTTTTATTA
*
419427 AA-TTTTAATA
1 AATTTTTATTA
419437 AATTTTTATTA
1 AATTTTTATTA
419448 AATTTT
1 AATTTT
419454 AAAAATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
9 6 0.26
10 4 0.17
11 13 0.57
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
AATTTTTATTA
Found at i:419503 original size:21 final size:22
Alignment explanation
Indices: 419479--419526 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
419469 AATATATATT
*
419479 TATATAATAAAAATAATA-TAA
1 TATATAATAAAAATAAAATTAA
*
419500 TATAT-ATAAATATAAAATTAA
1 TATATAATAAAAATAAAATTAA
419521 TATATA
1 TATATA
419527 TTTTAGATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TATATAATAAAAATAAAATTAA
Found at i:419522 original size:29 final size:28
Alignment explanation
Indices: 419455--419527 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
419445 TTAAATTTTA
* **
419455 AAAATATATAATTTAATATATATTTATAT
1 AAAATA-ATAATATAATATATATAAATAT
*
419484 AATAAAAATAATATAATATATATAAATAT
1 AA-AATAATAATATAATATATATAAATAT
419513 AAAATTAATATATAT
1 AAAA-TAATA-ATAT
419528 TTTAGATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.06
29 27 0.75
30 7 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
AAAATAATAATATAATATATATAAATAT
Found at i:420370 original size:13 final size:14
Alignment explanation
Indices: 420342--420374 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
420332 AAAATTATTA
*
420342 TTTTAAGTAATGAT
1 TTTTAACTAATGAT
420356 TTTTAACTAAT-AT
1 TTTTAACTAATGAT
420369 TTTTAA
1 TTTTAA
420375 TAAAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TTTTAACTAATGAT
Found at i:423502 original size:28 final size:28
Alignment explanation
Indices: 423439--423502 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
423429 GTTTTTTAAA
* *
423439 TTTAAAATTTAATTATGATTTGATCTTT
1 TTTAAAATTAAATTATGATTTAATCTTT
* *
423467 TTT-TAATTAAGATTTTGATTTAAT-TTT
1 TTTAAAATTAA-ATTATGATTTAATCTTT
423494 TTTAAAATT
1 TTTAAAATT
423503 TTGAATTACG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (28 bp):
TTTAAAATTAAATTATGATTTAATCTTT
Found at i:423516 original size:22 final size:22
Alignment explanation
Indices: 423473--423516 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
423463 CTTTTTTTAA
* * *
423473 TTAAGATTTTGATTTAATTTTT
1 TTAAAATTTTGAATTAAGTTTT
*
423495 TTAAAATTTTGAATTACGTTTT
1 TTAAAATTTTGAATTAAGTTTT
423517 AAAACTTATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (22 bp):
TTAAAATTTTGAATTAAGTTTT
Found at i:424025 original size:30 final size:30
Alignment explanation
Indices: 423991--424051 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
423981 TCTAGCTTTG
*
423991 CACCTTAGCTTGGACTTTTCCAAGCACAAA
1 CACCTTAGCTTGGACTTTCCCAAGCACAAA
424021 CACCTTAGCTTGGACTTTCCCAAGCACAAA
1 CACCTTAGCTTGGACTTTCCCAAGCACAAA
424051 C
1 C
424052 CCAAGTGCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.33, G:0.13, T:0.25
Consensus pattern (30 bp):
CACCTTAGCTTGGACTTTCCCAAGCACAAA
Found at i:426434 original size:32 final size:32
Alignment explanation
Indices: 426397--426463 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
426387 TAAGAATCTA
*
426397 TAAAGATAA-AATTTATAGAGTTTAGACTGATC
1 TAAAGA-AAGAATTGATAGAGTTTAGACTGATC
* * *
426429 TAAAGAAAGAGTTGATAGAGTTTATACTTATC
1 TAAAGAAAGAATTGATAGAGTTTAGACTGATC
426461 TAA
1 TAA
426464 GATTTTAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 2 0.07
32 28 0.93
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.34
Consensus pattern (32 bp):
TAAAGAAAGAATTGATAGAGTTTAGACTGATC
Found at i:428738 original size:11 final size:11
Alignment explanation
Indices: 428722--428747 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
428712 ATCCCGAAAG
428722 TTATCTTGTTT
1 TTATCTTGTTT
428733 TTATCTTGTTT
1 TTATCTTGTTT
428744 TTAT
1 TTAT
428748 TTTTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.12, C:0.08, G:0.08, T:0.73
Consensus pattern (11 bp):
TTATCTTGTTT
Found at i:429005 original size:9 final size:9
Alignment explanation
Indices: 428993--429035 Score: 54
Period size: 8 Copynumber: 5.0 Consensus size: 9
428983 ATTTTTTCTT
428993 TTTTTTTAA
1 TTTTTTTAA
*
429002 TTTTTATAA
1 TTTTTTTAA
*
429011 TGTTTTT-A
1 TTTTTTTAA
429019 TTTTTTT-A
1 TTTTTTTAA
429027 TTTTTTTAA
1 TTTTTTTAA
429036 ATAAATATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 15 0.52
9 14 0.48
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:429714 original size:25 final size:25
Alignment explanation
Indices: 429679--429737 Score: 109
Period size: 25 Copynumber: 2.3 Consensus size: 25
429669 CTAATTTTTC
429679 TTCTAAATTCAAATCAAATTTATCAA
1 TTCT-AATTCAAATCAAATTTATCAA
429705 TTCTAATTCAAATCAAATTTATCAA
1 TTCTAATTCAAATCAAATTTATCAA
429730 TTCTAATT
1 TTCTAATT
429738 AAGTCCAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 29 0.88
26 4 0.12
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (25 bp):
TTCTAATTCAAATCAAATTTATCAA
Found at i:429755 original size:24 final size:25
Alignment explanation
Indices: 429679--429755 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 25
429669 CTAATTTTTC
*
429679 TTCTAAATTCAAATCAAATTTATCAA
1 TTCT-AATTCAAATCAAATTCATCAA
*
429705 TTCTAATTCAAATCAAATTTATCAA
1 TTCTAATTCAAATCAAATTCATCAA
* * *
429730 TTCTAATT-AAGTCCAATTCATGAA
1 TTCTAATTCAAATCAAATTCATCAA
429754 TT
1 TT
429756 TTACGGTTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
24 14 0.30
25 29 0.62
26 4 0.09
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.40
Consensus pattern (25 bp):
TTCTAATTCAAATCAAATTCATCAA
Found at i:429858 original size:26 final size:27
Alignment explanation
Indices: 429815--429865 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
429805 TTTATAAATT
* *
429815 AAATAATTATTTTCATAAAATTTTTAA
1 AAATAATTATTATAATAAAATTTTTAA
*
429842 AAATAA-TATTATAATAATATTTTT
1 AAATAATTATTATAATAAAATTTTT
429866 TATTTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
AAATAATTATTATAATAAAATTTTTAA
Found at i:431667 original size:25 final size:27
Alignment explanation
Indices: 431642--431693 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
431632 TTATAATTAT
431642 AATTTAA-AATATT-ATATATTTATATA
1 AATTTAATAATATTAATA-ATTTATATA
*
431668 AATTTAATTATATTAATAATTTATAT
1 AATTTAATAATATTAATAATTTATAT
431694 TATATAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
27 13 0.57
28 3 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
AATTTAATAATATTAATAATTTATATA
Found at i:431679 original size:20 final size:19
Alignment explanation
Indices: 431656--431698 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
431646 TAAAATATTA
431656 TATATTTATATAAATTTA-AT
1 TATATTTA-AT-AATTTATAT
431676 TATA-TTAATAATTTATAT
1 TATATTTAATAATTTATAT
431694 TATAT
1 TATAT
431699 AAATTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 6 0.29
18 8 0.38
19 3 0.14
20 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATTTAATAATTTATAT
Found at i:431680 original size:14 final size:14
Alignment explanation
Indices: 431661--431709 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 14
431651 TATTATATAT
431661 TTATATAAATTTAA
1 TTATATAAATTTAA
431675 TTATATTAATAATTTATA
1 TTATA-T-A-AATTTA-A
431693 TTATATAAATTTTAA
1 TTATATAAA-TTTAA
431708 TT
1 TT
431710 TTTTTAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
14 5 0.17
15 6 0.20
16 6 0.20
17 7 0.23
18 6 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTATATAAATTTAA
Found at i:431695 original size:18 final size:18
Alignment explanation
Indices: 431668--431740 Score: 67
Period size: 18 Copynumber: 3.8 Consensus size: 18
431658 TATTTATATA
431668 AATTTA-ATTATATTAAT
1 AATTTATATTATATTAAT
*
431685 AATTTATATTATATAAATTTT
1 AATTTATATTATATTAA---T
*
431706 AATTTTTTTAATTATATTAAT
1 AA--TTTAT-ATTATATTAAT
431727 AATTTATATTATAT
1 AATTTATATTATAT
431741 AATTTTTAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
17 6 0.13
18 16 0.36
19 4 0.09
21 6 0.13
23 4 0.09
24 9 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
AATTTATATTATATTAAT
Found at i:431710 original size:21 final size:21
Alignment explanation
Indices: 431684--431752 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
431674 ATTATATTAA
431684 TAATTTATATTATATAAATTT
1 TAATTTATATTATATAAATTT
* * *
431705 TAATTT-TTTTA-ATTATATTAA
1 TAATTTATATTATA-TAAATT-T
*
431726 TAATTTATATTATATAATTTT
1 TAATTTATATTATATAAATTT
431747 TAATTT
1 TAATTT
431753 TTAATAAGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
19 1 0.03
20 9 0.24
21 18 0.49
22 8 0.22
23 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TAATTTATATTATATAAATTT
Found at i:431722 original size:42 final size:42
Alignment explanation
Indices: 431670--431754 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
431660 TTTATATAAA
431670 TTTAATTATATTAATAATTTATATTATATAAATTTTAATTTT
1 TTTAATTATATTAATAATTTATATTATATAAATTTTAATTTT
*
431712 TTTAATTATATTAATAATTTATATTATATAATTTTTAATTTT
1 TTTAATTATATTAATAATTTATATTATATAAATTTTAATTTT
431754 T
1 T
431755 AATAAGATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (42 bp):
TTTAATTATATTAATAATTTATATTATATAAATTTTAATTTT
Found at i:431765 original size:42 final size:42
Alignment explanation
Indices: 431672--431782 Score: 136
Period size: 42 Copynumber: 2.6 Consensus size: 42
431662 TATATAAATT
* *
431672 TAATTATATTAATAATTTATATTATATAAATTTTAATTTTTT
1 TAATGATATTAATAATTTATATTATATAAATTTTAATTTTTA
* *
431714 TAATTATATTAATAATTTATATTATATAATTTTTAATTTTTAA
1 TAATGATATTAATAATTTATATTATATAAATTTTAATTTTT-A
* *
431757 TAA-GATATTGAT-ATATATATATATAT
1 TAATGATATTAATAATTTATAT-TATAT
431783 TGTTTTGGCA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
41 7 0.11
42 52 0.84
43 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (42 bp):
TAATGATATTAATAATTTATATTATATAAATTTTAATTTTTA
Found at i:434593 original size:31 final size:31
Alignment explanation
Indices: 434525--434594 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
434515 AGGATATGGT
* *
434525 TATATAAATATATTAAATATATATAATATAA
1 TATATTAATATATTAAATATAAATAATATAA
*
434556 -ATTATTAATATATTAAATTTTAAATAA-ATAA
1 TA-TATTAATATATTAAA-TATAAATAATATAA
434587 TATATTAA
1 TATATTAA
434595 ATACAATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
30 1 0.03
31 24 0.73
32 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
TATATTAATATATTAAATATAAATAATATAA
Found at i:436437 original size:70 final size:70
Alignment explanation
Indices: 436324--436458 Score: 182
Period size: 70 Copynumber: 1.9 Consensus size: 70
436314 TAGGTTTTAC
* *
436324 AAATAATTGAGTTTAAAATTGAATACAGGAATTGAATTAATTTTTATTAAATAAATAAACTTAAT
1 AAATAATTGAGTTTAAAATTGAATACAAGAATCGAATTAATTTTTATTAAATAAATAAACTTAAT
436389 GGAGT
66 GGAGT
* * * * **
436394 AAATAATTTATTTTAAAATTGAGTATAAGAATCGAACTT-ATTTTTATTAGGTAAATAAACTTAA
1 AAATAATTGAGTTTAAAATTGAATACAAGAATCGAA-TTAATTTTTATTAAATAAATAAACTTAA
436458 T
65 T
436459 AGAATGAACT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
70 54 0.96
71 2 0.04
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.39
Consensus pattern (70 bp):
AAATAATTGAGTTTAAAATTGAATACAAGAATCGAATTAATTTTTATTAAATAAATAAACTTAAT
GGAGT
Found at i:437346 original size:9 final size:9
Alignment explanation
Indices: 437332--437356 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
437322 AAGCCCCGTG
437332 GTGGTGGCC
1 GTGGTGGCC
437341 GTGGTGGCC
1 GTGGTGGCC
437350 GTGGTGG
1 GTGGTGG
437357 AGGAAGAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.60, T:0.24
Consensus pattern (9 bp):
GTGGTGGCC
Found at i:440355 original size:45 final size:42
Alignment explanation
Indices: 440269--440356 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 42
440259 ATAATTAAAA
* *
440269 TTTATTTTTATTTTAATATTATATTAATAAAAATATTAATTT
1 TTTAATTTTATTTTAATATTATATTAATAAAAATATGAATTT
*
440311 TTTAATTTTATTATTTATATTATATATAA-AAAAATAACTGAATTT
1 TTTAATTTTATT-TTAATATTATAT-TAATAAAAAT-A-TGAATTT
440356 T
1 T
440357 GTGTTATTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
42 11 0.28
43 17 0.44
44 4 0.10
45 7 0.18
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (42 bp):
TTTAATTTTATTTTAATATTATATTAATAAAAATATGAATTT
Found at i:440903 original size:24 final size:25
Alignment explanation
Indices: 440875--440952 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 25
440865 TAAAAAAGTT
440875 ATTAAATT-ATTAATAAT-TAAATAA
1 ATTAAATTAATTAA-AATATAAATAA
440899 ATT-AATTAATTAAAATATAAATAA
1 ATTAAATTAATTAAAATATAAATAA
* * *
440923 ATT-AATCAA-TAAAAAATAATTAA
1 ATTAAATTAATTAAAATATAAATAA
440946 A-TAAATT
1 ATTAAATT
440953 TAACATAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
22 1 0.02
23 23 0.49
24 23 0.49
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (25 bp):
ATTAAATTAATTAAAATATAAATAA
Found at i:440908 original size:20 final size:21
Alignment explanation
Indices: 440877--440945 Score: 67
Period size: 24 Copynumber: 3.4 Consensus size: 21
440867 AAAAAGTTAT
440877 TAAATT-ATTAATAAT-TAAA
1 TAAATTAATTAATAATATAAA
440896 TAAATTAATTAATTAAAATATAAA
1 TAAATTAATTAA-T--AATATAAA
*
440920 TAAATTAATCAATAA-A-AAA
1 TAAATTAATTAATAATATAAA
440939 T-AATTAA
1 TAAATTAA
440946 ATAAATTTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
18 6 0.14
19 10 0.23
20 6 0.14
21 3 0.07
23 4 0.09
24 15 0.34
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATTAATTAATAATATAAA
Found at i:441667 original size:19 final size:18
Alignment explanation
Indices: 441645--441690 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
441635 AAATTTTTTA
441645 TTAATTTATAAATAATAAT
1 TTAATTTATAAAT-ATAAT
441664 TTAAATATT-TAAATATAAT
1 TT-AAT-TTATAAATATAAT
441683 TTAATTTA
1 TTAATTTA
441691 AATTAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 2 0.08
18 3 0.12
19 9 0.38
20 8 0.33
21 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATTTATAAATATAAT
Found at i:442556 original size:27 final size:26
Alignment explanation
Indices: 442526--442612 Score: 95
Period size: 27 Copynumber: 3.3 Consensus size: 26
442516 TAATAATTTT
442526 AAATATAATATGAATATGATATATAAA
1 AAATATAATAT-AATATGATATATAAA
*
442553 AAATATAATAATAATATGATATAAAAA
1 AAATATAAT-ATAATATGATATATAAA
* * *
442580 ATAATATTATACAATAT-AAATATAAA
1 A-AATATAATATAATATGATATATAAA
*
442606 ATATATA
1 AAATATA
442613 TCAAAATTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
25 4 0.08
26 8 0.16
27 30 0.59
28 9 0.18
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (26 bp):
AAATATAATATAATATGATATATAAA
Found at i:442612 original size:22 final size:23
Alignment explanation
Indices: 442494--442612 Score: 66
Period size: 22 Copynumber: 5.6 Consensus size: 23
442484 CACTTCCTAA
442494 ATAAGTAAT-TATAC-AT-TAAAT
1 ATAA-TAATATATACAATATAAAT
* *
442515 TTAATAAT-TTTA-AATAT-AAT
1 ATAATAATATATACAATATAAAT
*
442535 ATGAAT-ATGATATATAA-A-AAAT
1 AT-AATAAT-ATATACAATATAAAT
**
442557 ATAATAATA-ATATGATATAAA-
1 ATAATAATATATACAATATAAAT
442578 A-AATAATATTATACAATATAAAT
1 ATAATAATA-TATACAATATAAAT
442601 ATAA-AATATATA
1 ATAATAATATATA
442613 TCAAAATTTA
Statistics
Matches: 77, Mismatches: 7, Indels: 27
0.69 0.06 0.24
Matches are distributed among these distances:
20 27 0.35
21 13 0.17
22 28 0.36
23 7 0.09
24 2 0.03
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (23 bp):
ATAATAATATATACAATATAAAT
Found at i:442624 original size:12 final size:12
Alignment explanation
Indices: 442599--442632 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
442589 TACAATATAA
*
442599 ATAT-AAAATAT
1 ATATCAAAATTT
442610 ATATCAAAATTT
1 ATATCAAAATTT
442622 ATATCAAAATT
1 ATATCAAAATT
442633 ATGTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATCAAAATTT
Found at i:442880 original size:13 final size:14
Alignment explanation
Indices: 442852--442886 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
442842 TTAAATATGA
442852 TTAATATAATATAT
1 TTAATATAATATAT
442866 TTAATATAA-ATAT
1 TTAATATAATATAT
*
442879 TTTATATA
1 TTAATATA
442887 CATTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAATATAATATAT
Found at i:443565 original size:17 final size:18
Alignment explanation
Indices: 443539--443579 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
443529 TGAGATAATA
*
443539 TTAATATTATA-TTATTT
1 TTAATTTTATATTTATTT
443556 TTAATTTTATATTTATTT
1 TTAATTTTATATTTATTT
443574 TTAATT
1 TTAATT
443580 AAATTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTAATTTTATATTTATTT
Done.