Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008353.1 Hibiscus syriacus cultivar Beakdansim tig00111088_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2583621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 1 of 13
Found at i:4756 original size:38 final size:39
Alignment explanation
Indices: 4705--4783 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 39
4695 TTAACAGTAG
* *
4705 ATGCAGCTTTCCC-TTGGTAGAGGATGAGTCAC-CGGGTA
1 ATGCAACTTTCCCTTTAGTAGAGGATGAGTC-CTCGGGTA
*
4743 ATGCAACTTTCCCTTTAGTAGCGGATGAGTCCTCGGGTA
1 ATGCAACTTTCCCTTTAGTAGAGGATGAGTCCTCGGGTA
4782 AT
1 AT
4784 ACTCGGGTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 13 0.36
39 23 0.64
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (39 bp):
ATGCAACTTTCCCTTTAGTAGAGGATGAGTCCTCGGGTA
Found at i:7409 original size:17 final size:17
Alignment explanation
Indices: 7387--7427 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
7377 AAAAGTTAGT
*
7387 AAAAAAATAAAC-AAATA
1 AAAAAAAT-AACGAAAGA
7404 AAAAAAATAACGAAAGA
1 AAAAAAATAACGAAAGA
7421 AAAAAAA
1 AAAAAAA
7428 AATACAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.83, C:0.05, G:0.05, T:0.07
Consensus pattern (17 bp):
AAAAAAATAACGAAAGA
Found at i:8535 original size:30 final size:29
Alignment explanation
Indices: 8477--8536 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
8467 TAAGGGATTA
* *
8477 AATAAAAAAAAAATTTAAAGTACCAAAAT
1 AATAAAAAAAAAATTTAAAGAACAAAAAT
* *
8506 AATACAAACAAAAATTTAAAGAATAAAAAT
1 AATA-AAAAAAAAATTTAAAGAACAAAAAT
8536 A
1 A
8537 GTATTAACAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (29 bp):
AATAAAAAAAAAATTTAAAGAACAAAAAT
Found at i:14004 original size:17 final size:16
Alignment explanation
Indices: 13982--14032 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
13972 CCGTGTCCCG
*
13982 ACCCGGATGTTACGGGT
1 ACCCGGATATT-CGGGT
*
13999 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
*
14014 ACCCGGATTTTGCGGGT
1 ACCCGGATATT-CGGGT
14031 AC
1 AC
14033 TCGGTAATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 11 0.39
16 4 0.14
17 13 0.46
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.24
Consensus pattern (16 bp):
ACCCGGATATTCGGGT
Found at i:14245 original size:10 final size:9
Alignment explanation
Indices: 14230--14254 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
14220 ATAATTATAT
14230 ATAAAAAAA
1 ATAAAAAAA
14239 ATAAAAAAA
1 ATAAAAAAA
14248 ATAAAAA
1 ATAAAAA
14255 CTAACCGGGT
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:17230 original size:53 final size:53
Alignment explanation
Indices: 17168--17268 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
17158 TACAAATAAA
*
17168 ATTTCAGGGTAGGCA-TCATCCGTAAAATAAGTAACTAATCGAAGAAAACTCAT
1 ATTTCAGGGTAGGCACT-ATCAGTAAAATAAGTAACTAATCGAAGAAAACTCAT
* * * *
17221 ATTTCAGGGTGGGCACTATTAGTAAAATAAGTACCTAATCGAATAAAA
1 ATTTCAGGGTAGGCACTATCAGTAAAATAAGTAACTAATCGAAGAAAA
17269 TTTGGATTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 41 0.98
54 1 0.02
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.26
Consensus pattern (53 bp):
ATTTCAGGGTAGGCACTATCAGTAAAATAAGTAACTAATCGAAGAAAACTCAT
Found at i:20062 original size:19 final size:19
Alignment explanation
Indices: 20024--20064 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
20014 CATAATTATT
* **
20024 GCAACGAATTTGGACTATC
1 GCAACGAATTTGAAAAATC
20043 GCAACGAATTTGAAAAATC
1 GCAACGAATTTGAAAAATC
20062 GCA
1 GCA
20065 TTGCGATAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (19 bp):
GCAACGAATTTGAAAAATC
Found at i:24974 original size:30 final size:29
Alignment explanation
Indices: 24903--24979 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 29
24893 ATTATGGCAT
* *
24903 TAATCTCCTAAAATCTTAAATTTCATACTC
1 TAATCT-CTAAATTCTTAAATTTCAGACTC
*
24933 AAATCTCTAAATTCTTAAATTTCAAGACTC
1 TAATCTCTAAATTCTTAAATTTC-AGACTC
24963 TAATCTCTAAATT-TTAA
1 TAATCTCTAAATTCTTAA
24980 TTAAATTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 20 0.48
30 22 0.52
ACGTcount: A:0.39, C:0.19, G:0.01, T:0.40
Consensus pattern (29 bp):
TAATCTCTAAATTCTTAAATTTCAGACTC
Found at i:26371 original size:35 final size:35
Alignment explanation
Indices: 26322--26399 Score: 113
Period size: 35 Copynumber: 2.2 Consensus size: 35
26312 CACAAACATT
26322 AATTACATTCTAAACC-CTAAATTCCAAAATACTTA
1 AATTACATTCTAAACCTC-AAATTCCAAAATACTTA
* * *
26357 AATTACATTTTAAACCTCAAATTTCAAAATACTTC
1 AATTACATTCTAAACCTCAAATTCCAAAATACTTA
26392 AATTACAT
1 AATTACAT
26400 GCCCAACCCC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 38 0.97
36 1 0.03
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.35
Consensus pattern (35 bp):
AATTACATTCTAAACCTCAAATTCCAAAATACTTA
Found at i:26413 original size:35 final size:35
Alignment explanation
Indices: 26322--26415 Score: 98
Period size: 35 Copynumber: 2.7 Consensus size: 35
26312 CACAAACATT
* * *
26322 AATTACATTCTAAACCCTAAATTCCAAAATACTTA
1 AATTACATGCCAAACCCCAAATTCCAAAATACTTA
*** * * *
26357 AATTACATTTTAAACCTCAAATTTCAAAATACTTC
1 AATTACATGCCAAACCCCAAATTCCAAAATACTTA
*
26392 AATTACATGCCCAACCCCAAATTC
1 AATTACATGCCAAACCCCAAATTC
26416 ATAATCCATT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.43, C:0.26, G:0.01, T:0.31
Consensus pattern (35 bp):
AATTACATGCCAAACCCCAAATTCCAAAATACTTA
Found at i:27165 original size:143 final size:142
Alignment explanation
Indices: 26898--27179 Score: 456
Period size: 143 Copynumber: 2.0 Consensus size: 142
26888 AAACTATTTA
* * ** *
26898 AATTAGAACCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACTCGAATATTCA
1 AATTAGAACCAAATAATATTATAATATGATAAATATTTATAATTAAAAATAAACTCGAAAATTCA
*
26963 ATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTAAACTATTTTA
66 ATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTAAACTATTTTA
*
27028 TAAACTGAACTT
131 TAAAATGAACTT
*
27040 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAAAAATAAACTCGAAAATTC
1 AATTAGAACCAAATAATATTATAATATGATAAATATTTATAATT-AAAAATAAACTCGAAAATTC
* * *
27105 AATTCAATTCAACTTGATTTGAATTTTATAAACTCAAATCGAAAAAATTTTGAGTCAACTATTTT
65 AATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTAAACTATTTT
27170 ATAAAATGAA
130 ATAAAATGAA
27180 ATGAGTATTT
Statistics
Matches: 128, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
142 41 0.32
143 87 0.68
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (142 bp):
AATTAGAACCAAATAATATTATAATATGATAAATATTTATAATTAAAAATAAACTCGAAAATTCA
ATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTAAACTATTTTA
TAAAATGAACTT
Found at i:27375 original size:35 final size:35
Alignment explanation
Indices: 27336--27429 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 35
27326 AATGTATTAT
* * *
27336 GAATTTGGGGTTGGGTATGTAATTGAAGTATTTTG
1 GAATTTGGGGTTGAGAATGTAATTAAAGTATTTTG
* *
27371 GAATTTGAGGTTTAGAATGTAATTAAAGTATTTTG
1 GAATTTGGGGTTGAGAATGTAATTAAAGTATTTTG
* * *
27406 GACTTTGGGGTTTATAATGTAATT
1 GAATTTGGGGTTGAGAATGTAATT
27430 GATGACTGTG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.28, C:0.01, G:0.28, T:0.44
Consensus pattern (35 bp):
GAATTTGGGGTTGAGAATGTAATTAAAGTATTTTG
Found at i:46081 original size:28 final size:30
Alignment explanation
Indices: 46044--46102 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
46034 AGATTTGATT
*
46044 AAAATTTAGAT-TC-AGGTCTTGAAATTTA
1 AAAATTTAGATATCTAGGTATTGAAATTTA
*
46072 AAAATTTAGATATCTGGGTATTGAAATTTA
1 AAAATTTAGATATCTAGGTATTGAAATTTA
46102 A
1 A
46103 GGTTTTAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 11 0.41
29 2 0.07
30 14 0.52
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (30 bp):
AAAATTTAGATATCTAGGTATTGAAATTTA
Found at i:46423 original size:20 final size:20
Alignment explanation
Indices: 46398--46449 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
46388 TAGTTGAAAA
46398 TCGCGTTGCGATTTTCCACT
1 TCGCGTTGCGATTTTCCACT
*
46418 TCGCGTTGCGGTTTTCCACT
1 TCGCGTTGCGATTTTCCACT
46438 TCGCGTTGCGAT
1 TCGCGTTGCGAT
46450 AGTCTACAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.08, C:0.29, G:0.25, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCACT
Found at i:47123 original size:6 final size:6
Alignment explanation
Indices: 47114--47138 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
47104 GCCGTCCGTC
47114 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
47139 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:47318 original size:21 final size:21
Alignment explanation
Indices: 47255--47318 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
47245 ACAACTGTAG
47255 ACTATCGCAACGCGAAATG-A
1 ACTATCGCAACGCGAAATGCA
** ** *
47275 AAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
47296 ACTATCGCAACACGAAATGCA
1 ACTATCGCAACGCGAAATGCA
47317 AC
1 AC
47319 GCGAATTTGC
Statistics
Matches: 32, Mismatches: 11, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.17
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:49176 original size:23 final size:23
Alignment explanation
Indices: 49150--49202 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
49140 GAATAAGAAA
49150 TCATTAAAAATAAATATTCAACC
1 TCATTAAAAATAAATATTCAACC
*
49173 TCATTAAGAATAAATATTCAACC
1 TCATTAAAAATAAATATTCAACC
49196 TCATTAA
1 TCATTAA
49203 TCGGTGAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (23 bp):
TCATTAAAAATAAATATTCAACC
Found at i:60067 original size:2 final size:2
Alignment explanation
Indices: 60062--60096 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
60052 TATATATGGT
60062 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60097 TAGAAGATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:63978 original size:24 final size:24
Alignment explanation
Indices: 63951--63999 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
63941 CACTTCTTGT
63951 TATGTTTTGTTGCCACTCGCATGC
1 TATGTTTTGTTGCCACTCGCATGC
63975 TATGTTTTGTTGCCACTCGCATGC
1 TATGTTTTGTTGCCACTCGCATGC
63999 T
1 T
64000 CACTACTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.43
Consensus pattern (24 bp):
TATGTTTTGTTGCCACTCGCATGC
Found at i:66430 original size:12 final size:12
Alignment explanation
Indices: 66413--66446 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
66403 AGCTGGTAAA
*
66413 TTATATATATGT
1 TTATATATATAT
66425 TTATATATATAT
1 TTATATATATAT
*
66437 ATATATATAT
1 TTATATATAT
66447 CACACATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (12 bp):
TTATATATATAT
Found at i:80540 original size:16 final size:16
Alignment explanation
Indices: 80515--80552 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
80505 ATGATTAATA
*
80515 TTTA-ATAAATATTTT
1 TTTATATAAATATTAT
*
80530 TTTATATAAATGTTAT
1 TTTATATAAATATTAT
80546 TTTATAT
1 TTTATAT
80553 TTATTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTATATAAATATTAT
Found at i:87235 original size:2 final size:2
Alignment explanation
Indices: 87228--87257 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
87218 TAATCATTGA
87228 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
87258 GTACCAGAAC
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:92359 original size:38 final size:42
Alignment explanation
Indices: 92273--92359 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 42
92263 TTTAATAAGT
* *
92273 TAAAAAAATATTTATATATTTTATTTAAAAAAATTTAAATTA
1 TAAAAAAATATTTATATATTTTATTTAAAAAAATTAAAAATA
*
92315 -ATAAAAAATATTTA-AT-TTTT-TTT-ACAAAATTAAAAATA
1 TA-AAAAAATATTTATATATTTTATTTAAAAAAATTAAAAATA
92353 TAAAAAA
1 TAAAAAA
92360 GTTGAATGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
38 17 0.43
39 4 0.10
40 4 0.10
41 3 0.08
42 12 0.30
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (42 bp):
TAAAAAAATATTTATATATTTTATTTAAAAAAATTAAAAATA
Found at i:97399 original size:18 final size:19
Alignment explanation
Indices: 97378--97415 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
97368 ATTAAGAAAA
*
97378 AATA-TTATTTAAAATATT
1 AATATTTATTTAAAAAATT
*
97396 AATATTTTTTTAAAAAATT
1 AATATTTATTTAAAAAATT
97415 A
1 A
97416 TGATATAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATTTATTTAAAAAATT
Found at i:97409 original size:19 final size:19
Alignment explanation
Indices: 97385--97461 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 19
97375 AAAAATATTA
97385 TTTAAAATATTAATATTTT
1 TTTAAAATATTAATATTTT
*
97404 TTTAAAAAATTATGATATAATGTT
1 TTTAAAATATTA--ATAT--T-TT
97428 ATTTAAAATATT-AT-TTTT
1 -TTTAAAATATTAATATTTT
97446 TATTAAAAATATTAAT
1 T-TT-AAAATATTAAT
97462 TTCGCTACTT
Statistics
Matches: 47, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
17 1 0.02
18 4 0.09
19 20 0.43
20 2 0.04
21 5 0.11
22 2 0.04
23 1 0.02
24 2 0.04
25 10 0.21
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (19 bp):
TTTAAAATATTAATATTTT
Found at i:100384 original size:29 final size:27
Alignment explanation
Indices: 100352--100407 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
100342 TGTATGTTAT
100352 TTTATTTCA-CCTTTATTATGTTTTATTTA
1 TTTATTT-ATCCTTT-TTAT-TTTTATTTA
100381 TTTATTTATTCCTTTTTATTTTTATTT
1 TTTATTTA-TCCTTTTTATTTTTATTT
100408 GTACATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 9 0.36
29 11 0.44
30 5 0.20
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTATTTATCCTTTTTATTTTTATTTA
Found at i:100499 original size:27 final size:27
Alignment explanation
Indices: 100469--100535 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
100459 AGTTTTTTTA
100469 TTTTATTTATTACTATTATATATATCT
1 TTTTATTTATTACTATTATATATATCT
* *
100496 TTTTATTTACTT-TTATTGTATATATCT
1 TTTTATTTA-TTACTATTATATATATCT
100523 TTATTA-TTATTAC
1 TT-TTATTTATTAC
100536 CATCATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 2 0.06
27 27 0.79
28 5 0.15
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.64
Consensus pattern (27 bp):
TTTTATTTATTACTATTATATATATCT
Found at i:112154 original size:106 final size:105
Alignment explanation
Indices: 111783--112487 Score: 1151
Period size: 105 Copynumber: 6.7 Consensus size: 105
111773 AGGTTTTACC
*
111783 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
111848 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAATTT
111888 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
111953 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAATTT
** *
111993 CAGAGCCAATTTCTGCTTCACAACGAGGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
112058 ACGAAGGGACCACTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ACTTCTCAATTT
*
112099 CAGAGCCAATTTCAACCTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
112164 ACGAAGGGACCGCTGGTTGTCAATAAACATTTC-CTAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTC-AATTT
* *
112204 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
112269 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ACTTCTCAATTT
* * *
112310 CGGTGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
112375 ACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCCAACTT
66 ACGAAGGGACCGCTGGTTGTCAACAAA-CACTTCTCAATTT
* ***
112416 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAATATAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
112481 ACGAAGG
66 ACGAAGG
112488 AGCTATATAC
Statistics
Matches: 561, Mismatches: 34, Indels: 9
0.93 0.06 0.01
Matches are distributed among these distances:
104 1 0.00
105 289 0.52
106 270 0.48
107 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAATTT
Found at i:112178 original size:211 final size:210
Alignment explanation
Indices: 111783--112487 Score: 1178
Period size: 211 Copynumber: 3.3 Consensus size: 210
111773 AGGTTTTACC
*
111783 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
111848 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAATTTCAACTTCACAAC
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAAC
*
111912 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
131 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT
*
111977 GAACATTTCTCAATTT
196 AAACATTTC-CAATTT
** *
111993 CAGAGCCAATTTCTGCTTCACAACGAGGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
112058 ACGAAGGGACCACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACCTCACAAC
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAAC
112123 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT
131 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT
112188 AAACATTTCCTAATTT
196 AAACATTTCC-AATTT
* *
112204 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
112269 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCGGTGCCAATTTCAACTTCACAGC
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAAC
112334 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT
131 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT
* * *
112399 AAATAACTTCCCAACTT
196 AAA-CA-TTTCCAATTT
* ***
112416 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAATATAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
112481 ACGAAGG
66 ACGAAGG
112488 AGCTATATAC
Statistics
Matches: 463, Mismatches: 28, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
210 89 0.19
211 299 0.65
212 71 0.15
213 4 0.01
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (210 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAAC
GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT
AAACATTTCCAATTT
Found at i:114331 original size:29 final size:27
Alignment explanation
Indices: 114299--114354 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
114289 TGTATGTTAT
114299 TTTATTTCA-CCTTTATTATGTTTTATTTA
1 TTTATTT-ATCCTTT-TTAT-TTTTATTTA
114328 TTTATTTATTCCTTTTTATTTTTATTT
1 TTTATTTA-TCCTTTTTATTTTTATTT
114355 GTACATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 9 0.36
29 11 0.44
30 5 0.20
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTATTTATCCTTTTTATTTTTATTTA
Found at i:114437 original size:27 final size:27
Alignment explanation
Indices: 114407--114473 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
114397 AGTTTTTTTA
114407 TTTTATTTATTACTATTATATATATCT
1 TTTTATTTATTACTATTATATATATCT
* *
114434 TTTTATTTACTT-TTATTGTATATATCT
1 TTTTATTTA-TTACTATTATATATATCT
114461 TTATTA-TTATTAC
1 TT-TTATTTATTAC
114474 CATCATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 2 0.06
27 27 0.79
28 5 0.15
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.64
Consensus pattern (27 bp):
TTTTATTTATTACTATTATATATATCT
Found at i:116805 original size:22 final size:22
Alignment explanation
Indices: 116778--116823 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
116768 ACTTCATCCT
116778 TTTTCG-GACTGGGAATCGGAGC
1 TTTTCGAG-CTGGGAATCGGAGC
116800 TTTTCGAGCTGGGAATCGGAGC
1 TTTTCGAGCTGGGAATCGGAGC
116822 TT
1 TT
116824 CAACATGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.17, C:0.17, G:0.35, T:0.30
Consensus pattern (22 bp):
TTTTCGAGCTGGGAATCGGAGC
Found at i:128641 original size:20 final size:19
Alignment explanation
Indices: 128616--128682 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
128606 TATTATTTAA
128616 TTATTTGAATTGTAATGTTT
1 TTATTT-AATTGTAATGTTT
*
128636 TTATTTAA-T-T-ATTTTT
1 TTATTTAATTGTAATGTTT
*
128652 ATTATTTAGTTTGTAATGTTT
1 -TTATTTA-ATTGTAATGTTT
128673 TTATTTAATT
1 TTATTTAATT
128683 TTCACTTGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
16 5 0.13
17 8 0.21
18 1 0.03
19 5 0.13
20 14 0.37
21 5 0.13
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (19 bp):
TTATTTAATTGTAATGTTT
Found at i:128652 original size:14 final size:14
Alignment explanation
Indices: 128608--128654 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
128598 AATATTTTTA
128608 TTATTTAATTATTT
1 TTATTTAATTATTT
** *
128622 GAATTGTAA-TGTTT
1 TTATT-TAATTATTT
128636 TTATTTAATTATTT
1 TTATTTAATTATTT
128650 TTATT
1 TTATT
128655 ATTTAGTTTG
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
13 3 0.12
14 19 0.76
15 3 0.12
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (14 bp):
TTATTTAATTATTT
Found at i:128656 original size:37 final size:39
Alignment explanation
Indices: 128605--128682 Score: 117
Period size: 37 Copynumber: 2.1 Consensus size: 39
128595 CTTAATATTT
128605 TTATTATTTAATTATTT-GAATTGTAATGTTTTTATTTAA
1 TTATTATTTAATTATTTAG-ATTGTAATGTTTTTATTTAA
*
128644 TTATT-TTT-ATTATTTAGTTTGTAATGTTTTTATTTAA
1 TTATTATTTAATTATTTAGATTGTAATGTTTTTATTTAA
128681 TT
1 TT
128683 TTCACTTGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
37 28 0.76
38 4 0.11
39 5 0.14
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (39 bp):
TTATTATTTAATTATTTAGATTGTAATGTTTTTATTTAA
Found at i:128770 original size:23 final size:23
Alignment explanation
Indices: 128744--128787 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
128734 ACTGAGACTT
128744 CATAAACAACAATTACATCGTCA
1 CATAAACAACAATTACATCGTCA
*
128767 CATAATCAACAATTACATCGT
1 CATAAACAACAATTACATCGT
128788 TGGAGAGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (23 bp):
CATAAACAACAATTACATCGTCA
Found at i:129492 original size:51 final size:51
Alignment explanation
Indices: 129416--129518 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
129406 TTATAGGGGA
129416 GGGGATGAGCGAATAACCGAGAGAGATAAGGCTCAGGTAATAATGGAAGGC
1 GGGGATGAGCGAATAACCGAGAGAGATAAGGCTCAGGTAATAATGGAAGGC
129467 GGGGATGAGCGAATAACCGAGAGAGATAAGGCTCAGGTAATAATGGAAGGC
1 GGGGATGAGCGAATAACCGAGAGAGATAAGGCTCAGGTAATAATGGAAGGC
129518 G
1 G
129519 CGCCTCATGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.37, C:0.12, G:0.38, T:0.14
Consensus pattern (51 bp):
GGGGATGAGCGAATAACCGAGAGAGATAAGGCTCAGGTAATAATGGAAGGC
Found at i:131109 original size:20 final size:20
Alignment explanation
Indices: 131084--131121 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
131074 ATCCTATTCC
131084 CTGGTAATCTTACATTCCTA
1 CTGGTAATCTTACATTCCTA
131104 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
131122 GTGAACCAAA
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:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCTA
Found at i:133635 original size:2 final size:2
Alignment explanation
Indices: 133560--133626 Score: 116
Period size: 2 Copynumber: 33.5 Consensus size: 2
133550 CGTTGGCTCC
133560 TA TA TA 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
* *
133602 TA TA TA TA TA TA TA TG TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
133627 GCATATATAC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:134449 original size:23 final size:23
Alignment explanation
Indices: 134423--134466 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
134413 CACCACAGCT
*
134423 CGTATAAATGCACCGAAGTGCTG
1 CGTAGAAATGCACCGAAGTGCTG
* *
134446 CGTAGAATTGCACCGTAGTGC
1 CGTAGAAATGCACCGAAGTGC
134467 CATATAAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCTG
Found at i:134743 original size:31 final size:31
Alignment explanation
Indices: 134707--134779 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
134697 ATTTACATAC
134707 CTTTATCACATGAACATATCATGTTCCATCA
1 CTTTATCACATGAACATATCATGTTCCATCA
134738 CTTTATCACATGAACATATCATGTTCCATCA
1 CTTTATCACATGAACATATCATGTTCCATCA
134769 CTTTATCACAT
1 CTTTATCACAT
134780 AGCTTATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (31 bp):
CTTTATCACATGAACATATCATGTTCCATCA
Found at i:136553 original size:33 final size:33
Alignment explanation
Indices: 136511--136579 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
136501 TTAAGGCAAT
136511 GCAGCACCATCAAGTACCATACCAGAATATCAG
1 GCAGCACCATCAAGTACCATACCAGAATATCAG
136544 GCAGCACCATCAAGTACCATACCAGAATATCAG
1 GCAGCACCATCAAGTACCATACCAGAATATCAG
136577 GCA
1 GCA
136580 CAATCCCATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.39, C:0.30, G:0.16, T:0.14
Consensus pattern (33 bp):
GCAGCACCATCAAGTACCATACCAGAATATCAG
Found at i:142484 original size:16 final size:16
Alignment explanation
Indices: 142463--142498 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
142453 ATTTTACTCT
142463 ATTCCCAAACGTCAGG
1 ATTCCCAAACGTCAGG
142479 ATTCCCAAACGTCAGG
1 ATTCCCAAACGTCAGG
142495 ATTC
1 ATTC
142499 GAACCCTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.22
Consensus pattern (16 bp):
ATTCCCAAACGTCAGG
Found at i:144202 original size:16 final size:16
Alignment explanation
Indices: 144181--144211 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
144171 CATTAAAATG
144181 ATTTTTTTAATTATAA
1 ATTTTTTTAATTATAA
*
144197 ATTTTTTTTATTATA
1 ATTTTTTTAATTATA
144212 TTTTAAGATA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTTTTAATTATAA
Found at i:151517 original size:16 final size:16
Alignment explanation
Indices: 151496--151528 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
151486 TATATGACAC
151496 TGCTTCATAAATATAA
1 TGCTTCATAAATATAA
151512 TGCTTCATAAATATAA
1 TGCTTCATAAATATAA
151528 T
1 T
151529 CGGACTCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (16 bp):
TGCTTCATAAATATAA
Found at i:153593 original size:23 final size:22
Alignment explanation
Indices: 153550--153593 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
153540 TTTAATCAAG
* * *
153550 AATAAAACATCATTGATTAAAA
1 AATAAAACATCAATAACTAAAA
153572 AATATAAACATCAATAACTAAA
1 AATA-AAACATCAATAACTAAA
153594 TTTATCACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.61, C:0.11, G:0.02, T:0.25
Consensus pattern (22 bp):
AATAAAACATCAATAACTAAAA
Found at i:155172 original size:37 final size:37
Alignment explanation
Indices: 155096--155172 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
155086 TTTTTATATT
*
155096 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
155133 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
155170 TTT
1 TTT
155173 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:156002 original size:37 final size:37
Alignment explanation
Indices: 155939--156045 Score: 115
Period size: 37 Copynumber: 2.9 Consensus size: 37
155929 ATTTAAATAA
* * * * * *
155939 TAAACGAATACAAATGAACGAACATAAACGAGCGGATG
1 TAAACGAACAC-AATAAATGAACATAAACGAACGAACG
* * * *
155977 TAAACGAGCACGATAAATGAACATAAACAAATGAACG
1 TAAACGAACACAATAAATGAACATAAACGAACGAACG
156014 TAAACGAACACAATAAATGAACATAAACGAAC
1 TAAACGAACACAATAAATGAACATAAACGAAC
156046 CTCCACAAAC
Statistics
Matches: 55, Mismatches: 14, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
37 46 0.84
38 9 0.16
ACGTcount: A:0.54, C:0.17, G:0.16, T:0.13
Consensus pattern (37 bp):
TAAACGAACACAATAAATGAACATAAACGAACGAACG
Found at i:171162 original size:2 final size:2
Alignment explanation
Indices: 171150--171181 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
171140 CTATCCTATC
171150 AT AT A- 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 AT AT AT A
171182 ATAATAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:171187 original size:3 final size:3
Alignment explanation
Indices: 171179--171203 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
171169 ATATATATAT
171179 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
171204 AATCGATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:172469 original size:2 final size:2
Alignment explanation
Indices: 172462--172489 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
172452 TATTTTATTA
172462 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
172490 TTCTTAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:172583 original size:44 final size:44
Alignment explanation
Indices: 172533--172621 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
172523 TTTTGATCAC
*
172533 GTTTTTCAATAAAGACTAAATGTGTTTGACCTCGGAGGAAAGAT
1 GTTTTTCAATAAAGACTAAATGTGTTTGACATCGGAGGAAAGAT
172577 GTTTTTCAATAAAGACTAAATGTGTTTGACATCGGAGGAAAGAT
1 GTTTTTCAATAAAGACTAAATGTGTTTGACATCGGAGGAAAGAT
172621 G
1 G
172622 ATCAGACAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (44 bp):
GTTTTTCAATAAAGACTAAATGTGTTTGACATCGGAGGAAAGAT
Found at i:183750 original size:27 final size:29
Alignment explanation
Indices: 183697--183750 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
183687 ATTATTTTAA
*
183697 ATATTTTAAAAATCAATTTTATAAAATAT
1 ATATTTTAAAAATCAATTTGATAAAATAT
*
183726 ATATTTTAAAAA-C-ATTTGATTAAAT
1 ATATTTTAAAAATCAATTTGATAAAAT
183751 GTTTTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 10 0.43
28 1 0.04
29 12 0.52
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (29 bp):
ATATTTTAAAAATCAATTTGATAAAATAT
Found at i:183760 original size:38 final size:38
Alignment explanation
Indices: 183713--183809 Score: 158
Period size: 38 Copynumber: 2.5 Consensus size: 38
183703 TAAAAATCAA
183713 TTTTATAAAATATATATTTTAAAAACATTTGATTAAATG
1 TTTT-TAAAATATATATTTTAAAAACATTTGATTAAATG
* *
183752 TTTTTAAAATATATATTTAAAAAATATTTGATTAAATG
1 TTTTTAAAATATATATTTTAAAAACATTTGATTAAATG
*
183790 TTTTAAAAATATATATTTTA
1 TTTTTAAAATATATATTTTA
183810 TGTTTTTAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
38 50 0.93
39 4 0.07
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (38 bp):
TTTTTAAAATATATATTTTAAAAACATTTGATTAAATG
Found at i:184452 original size:20 final size:20
Alignment explanation
Indices: 184423--184460 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
184413 AACACGCTGG
*
184423 GCATCTGAGGCCATCCGAGA
1 GCATCCGAGGCCATCCGAGA
184443 GCATCCGAGGCCATCCGA
1 GCATCCGAGGCCATCCGA
184461 CCGAGGCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.34, G:0.29, T:0.13
Consensus pattern (20 bp):
GCATCCGAGGCCATCCGAGA
Found at i:184502 original size:23 final size:23
Alignment explanation
Indices: 184476--184521 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
184466 GCTATTTGAA
*
184476 CGAGCTATGCGAGGGCAA-CCGAG
1 CGAGCTATCCGAGGG-AAGCCGAG
184499 CGAGCTATCCGAGGGAAGCCGAG
1 CGAGCTATCCGAGGGAAGCCGAG
184522 TGAGGGTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.26, C:0.26, G:0.39, T:0.09
Consensus pattern (23 bp):
CGAGCTATCCGAGGGAAGCCGAG
Found at i:184678 original size:29 final size:29
Alignment explanation
Indices: 184595--184680 Score: 136
Period size: 29 Copynumber: 3.0 Consensus size: 29
184585 GAGCAAGGGT
*
184595 AGGTCGCCCGGAGTGCATGGTGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
*
184624 AGGTCGCCCGGAGTGCATGGCTACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
* *
184653 AGGTCGCCCGGAGTGTATGACGACCTAC
1 AGGTCGCCCGGAGTGCATGGCGACCTAC
184681 GGCCAACACT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.21, C:0.29, G:0.33, T:0.17
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:188397 original size:29 final size:29
Alignment explanation
Indices: 188324--188406 Score: 125
Period size: 29 Copynumber: 2.9 Consensus size: 29
188314 GTGTTGGCCG
*
188324 GGTCACCATGCACT-CTGGGCGACCTTGTA
1 GGTCGCCATGCACTCCT-GGCGACCTTGTA
188353 GGTCGCCATGCACTCCTGGCGACCTTGTA
1 GGTCGCCATGCACTCCTGGCGACCTTGTA
188382 GGTCGCCATGCACTCCAT-GCGACCT
1 GGTCGCCATGCACTCC-TGGCGACCT
188407 ACCCTTGCTC
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
29 48 0.94
30 3 0.06
ACGTcount: A:0.16, C:0.35, G:0.27, T:0.23
Consensus pattern (29 bp):
GGTCGCCATGCACTCCTGGCGACCTTGTA
Found at i:188498 original size:29 final size:29
Alignment explanation
Indices: 188465--188520 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
188455 TCCCAACACA
*
188465 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
* *
188494 TAGGTCGTCATGCACTCCGGGTGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
188521 ACCCTGGCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.12, C:0.34, G:0.30, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:188573 original size:33 final size:33
Alignment explanation
Indices: 188536--188608 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
188526 GGCTCGGCTT
* *
188536 CCCTCGGATTCCCTCGCATAGCTCGTTCGGTTG
1 CCCTCGGATGCCCTCGCATAGCTCGTTCGGATG
*
188569 CCCTCGGATGCCCTCGCATAGCTTGTTCGGATG
1 CCCTCGGATGCCCTCGCATAGCTCGTTCGGATG
*
188602 GCCTCGG
1 CCCTCGG
188609 TCGGATGGCC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.10, C:0.36, G:0.27, T:0.27
Consensus pattern (33 bp):
CCCTCGGATGCCCTCGCATAGCTCGTTCGGATG
Found at i:188614 original size:14 final size:14
Alignment explanation
Indices: 188595--188654 Score: 66
Period size: 14 Copynumber: 3.9 Consensus size: 14
188585 CATAGCTTGT
188595 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
188609 TCGGATGGCCTCGGATG
1 TCGGATGGCCTC-G--G
188626 CTCTCGGATGGCCTCGG
1 ---TCGGATGGCCTCGG
188643 TCGGATGGCCTC
1 TCGGATGGCCTC
188655 AGATGCCCAG
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
14 24 0.60
15 1 0.03
17 2 0.05
19 1 0.03
20 12 0.30
ACGTcount: A:0.08, C:0.30, G:0.38, T:0.23
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:188622 original size:10 final size:10
Alignment explanation
Indices: 188609--188642 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
188599 ATGGCCTCGG
188609 TCGGATGGCC
1 TCGGATGGCC
188619 TCGGAT-GCTC
1 TCGGATGGC-C
188629 TCGGATGGCC
1 TCGGATGGCC
188639 TCGG
1 TCGG
188643 TCGGATGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 18 0.82
11 2 0.09
ACGTcount: A:0.09, C:0.29, G:0.38, T:0.24
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:188638 original size:34 final size:34
Alignment explanation
Indices: 188595--188660 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
188585 CATAGCTTGT
*
188595 TCGGATGGCCTCGGTCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGTCGGATGGCCTCAGATGCTC
188629 TCGGATGGCCTCGGTCGGATGGCCTCAGATGC
1 TCGGATGGCCTCGGTCGGATGGCCTCAGATGC
188661 CCAGCGTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.11, C:0.29, G:0.38, T:0.23
Consensus pattern (34 bp):
TCGGATGGCCTCGGTCGGATGGCCTCAGATGCTC
Found at i:188736 original size:29 final size:29
Alignment explanation
Indices: 188699--188756 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
188689 GCAATCTCTT
* *
188699 GTAGCTCGCCGGGAAGACATGGTGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* *
188728 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
188757 CGGCCAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.22, C:0.26, G:0.36, T:0.16
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:194186 original size:105 final size:105
Alignment explanation
Indices: 193665--194418 Score: 1289
Period size: 105 Copynumber: 7.3 Consensus size: 105
193655 TCGGATGAGT
* ** * *
193665 TTCTTCTCATTATGAACTCTTCTGGAAATGTCGATTCACCTCCTTC-GGGGTGAATTTGAAAGGA
1 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAAGGA
*
193729 ACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAG
66 ACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAG
* *
193769 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGA
1 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAAGGA
*
193834 AC-GGCTCTTCTCATTACGAACCCCTCTCCTTTAGGACG-G
66 ACAGGCTCTTCTCATTACGAA-CCTTCTCCTTTAGGACGAG
193873 TTCTTCTCATTATGAA--CTTCTGGAAATGTTTGGGTCACCTCCTTCTGTGGTGGATTTGAAAGG
1 TTCTTCTCATTATGAACTCTTCTGGAAATG-TTGGGTCACCTCCTTCTGTGGTGGATTTGAAAGG
*
193936 AACATGCTC-TCTCATTACGAACCTTCTCCTTTA-GACGAG
65 AACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAG
193975 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTC--T-GTGGATTTGAAAGGA
1 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAAGGA
194037 ACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAG
66 ACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAG
194077 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAAGGA
1 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAAGGA
* *
194142 AAAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAG
66 ACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAG
194182 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAAGGA
1 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAAGGA
194247 ACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAG
66 ACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAG
194287 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTC-CCTCCTTCTGTGGTGGATTTG-AAGGA
1 TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAAGGA
194350 ACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAG
66 ACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAG
*
194390 TTCTTCCCATTATGAACTCTTCTGGAAAT
1 TTCTTCTCATTATGAACTCTTCTGGAAAT
194419 ATTGATTGGT
Statistics
Matches: 622, Mismatches: 16, Indels: 25
0.94 0.02 0.04
Matches are distributed among these distances:
100 22 0.04
101 29 0.05
102 92 0.15
103 136 0.22
104 116 0.19
105 227 0.36
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (105 bp):
TTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAAGGA
ACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGACGAG
Found at i:195286 original size:54 final size:51
Alignment explanation
Indices: 195147--195314 Score: 162
Period size: 51 Copynumber: 3.2 Consensus size: 51
195137 ATTTACAGTT
** * **
195147 ATCAAGAAACCCCTAAATTAGGCTTAGCTTCTTTCAAAAGTT--TTAAAAAAA
1 ATCAAGAAACCCCTAAATTAGGCTTAATTTCTTT-GAAA-TTCATTTGAAAAA
** *
195198 ATCAAGAAACCCCTGAAACCA-GCTTAATTTCTTTGACAATTCATTTGAAAAC
1 ATCAAGAAACCCCT-AAATTAGGCTTAATTTCTTTGA-AATTCATTTGAAAAA
*
195250 ATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTGAACGTTCATTTGAGAAAA
1 ATCAAGAAACCCCT--AAATTAGGCTTAATTTCTTTGAA-ATTCATTTGA-AAAA
195305 ATCAAGAAAC
1 ATCAAGAAAC
195315 TTTCGAAAAT
Statistics
Matches: 96, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
50 3 0.03
51 27 0.28
52 24 0.25
53 5 0.05
54 24 0.25
55 13 0.14
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.29
Consensus pattern (51 bp):
ATCAAGAAACCCCTAAATTAGGCTTAATTTCTTTGAAATTCATTTGAAAAA
Found at i:195369 original size:54 final size:53
Alignment explanation
Indices: 195198--195868 Score: 719
Period size: 54 Copynumber: 12.6 Consensus size: 53
195188 TTTAAAAAAA
** * * * * *
195198 ATCAAGAAACCCCTG-AAACCAG-CTTAATTTCTTTGACAATTCATTTGAAAAC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAACTCATTTGAAATC
** * * * * * **
195250 ATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTT-GAACGTTCATTTGAGAAAA
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAC--TCATTTGA-AATC
* *
195305 ATCAAGAAACTT-TCGAAAATCAGACTTAGTTTCTTTAAAACACATTTGAAAAGC
1 ATCAAGAAACTTCT-GAAAATCAGACTTAGTTTCTTTAAAACTCATTTG-AAATC
* *
195359 GTCAAGAAACTTCTAAAAATCAGACTTAGTTTCTTTAAAAAACTCATTTGAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT--AAAACTCATTTGAAATC
* *
195414 AT---GAAACTTCTGAAAATCAGACTTAGTTTCGTTGAAAACTTATTTGAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTC-TTTAAAACTCATTTGAAATC
*
195465 ATCAAGAAACTTCTGAAAATCAGACTT--TTTCTTTAAAAACTCA-CTGAAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAACTCATTTG-AAATC
* * *
195517 ATCATGAAACTTCTGAAAATCAGACTTAGTTTCATTGAAAACTTATTTGAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTC-TTTAAAACTCATTTGAAATC
* *
195571 ATCAAGAAACTTCTGAAAATAAGACTT--TTTCTTTAAAACCTCACTTGAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAA-CTCATTTGAAATC
* * *
195623 GTCAAG-AACTTCTGAAAATAAGACTTAGTTTCTTTAAAAGCTCATTTAAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAA-CTCATTTGAAATC
* * *
195676 ATCAAGAAACTTCTGAAAATCAGACTTAATTT-TTTGAAAGCTCATTTGAAATT
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAACTCATTTGAAATC
* *
195729 GTCAAGAAACTTCTGAAAATCAGACTTA-TTTCTTTGAAAGCTCATTT-AAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAACTCATTTGAAATC
*
195781 ATCAAGAAACTTCTG-AAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAA-CTCATTT-GAAATC
*
195835 ATCAAGAAACTTCTGAAGATCAGACTTAGTTTCT
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCT
195869 AAAAAAACAC
Statistics
Matches: 536, Mismatches: 51, Indels: 61
0.83 0.08 0.09
Matches are distributed among these distances:
51 63 0.12
52 140 0.26
53 90 0.17
54 170 0.32
55 59 0.11
56 14 0.03
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.33
Consensus pattern (53 bp):
ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAACTCATTTGAAATC
Found at i:195442 original size:106 final size:103
Alignment explanation
Indices: 195303--195868 Score: 653
Period size: 106 Copynumber: 5.3 Consensus size: 103
195293 CATTTGAGAA
* * * *
195303 AAATCAAGAAACTT-TCGAAAATCAGACTTAGTTTCTTTAAAACACATTTGAAAAGCGTCAAGAA
1 AAATCATGAAACTTCT-GAAAATCAGACTTAGTTTCTTTAAAACTCATTTG-AAATCATCAAGAA
*
195367 ACTTCTAAAAATCAGACTTAGTTTCTTTAAAAAACTCATTTG
64 ACTTCTGAAAATCAGACTTA-TTTCTTT-AAAAACTCATTTG
* *
195409 AAATCATGAAACTTCTGAAAATCAGACTTAGTTTCGTTGAAAACTTATTTGAAATCATCAAGAAA
1 AAATCATGAAACTTCTGAAAATCAGACTTAGTTTC-TTTAAAACTCATTTGAAATCATCAAGAAA
*
195474 CTTCTGAAAATCAGACTT-TTTCTTTAAAAACTCA-CTG
65 CTTCTGAAAATCAGACTTATTTCTTTAAAAACTCATTTG
* *
195511 AAAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCATTGAAAACTTATTTGAAATCATCAA
1 --AA--ATCATGAAACTTCTGAAAATCAGACTTAGTTTC-TTTAAAACTCATTTGAAATCATCAA
* * *
195576 GAAACTTCTGAAAATAAGACTT-TTTCTTTAAAACCTCACTTG
61 GAAACTTCTGAAAATCAGACTTATTTCTTTAAAAACTCATTTG
* * * *
195618 AAATCGTCAAGAACTTCTGAAAATAAGACTTAGTTTCTTTAAAAGCTCATTTAAAATCATCAAGA
1 AAATCAT-GA-AACTTCTGAAAATCAGACTTAGTTTCTTTAAAA-CTCATTTGAAATCATCAAGA
* *
195683 AACTTCTGAAAATCAGACTTAATTT-TTTGAAAGCTCATTTG
63 AACTTCTGAAAATCAGACTT-ATTTCTTTAAAAACTCATTTG
* *
195724 AAATTGTCAAGAAACTTCTGAAAATCAGACTTA-TTTCTTTGAAAGCTCATTT-AAATCATCAAG
1 AAA---TCATGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAACTCATTTGAAATCATCAAG
* *
195787 AAACTTCTG-AAATCAGACTTAGTTTCTTTAAAAGCTCATTTAA
62 AAACTTCTGAAAATCAGACTTA-TTTCTTTAAAAACTCATTT-G
*
195830 AAATCATCAAGAAACTTCTGAAGATCAGACTTAGTTTCT
1 AAATCAT---GAAACTTCTGAAAATCAGACTTAGTTTCT
195869 AAAAAAACAC
Statistics
Matches: 406, Mismatches: 31, Indels: 45
0.84 0.06 0.09
Matches are distributed among these distances:
102 2 0.00
103 17 0.04
104 30 0.07
105 98 0.24
106 210 0.52
107 46 0.11
108 1 0.00
109 2 0.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (103 bp):
AAATCATGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAACTCATTTGAAATCATCAAGAAAC
TTCTGAAAATCAGACTTATTTCTTTAAAAACTCATTTG
Found at i:195536 original size:158 final size:157
Alignment explanation
Indices: 195305--195868 Score: 707
Period size: 158 Copynumber: 3.6 Consensus size: 157
195295 TTTGAGAAAA
* * *
195305 ATCAAGAAACTT-TCGAAAATCAGACTTAGTTTCTTT-AAAACACATTTGAAAAGCGTCAAGAAA
1 ATCAAGAAACTTCT-GAAAATCAGACTTA-TTTCTTTAAAAACTCATTTGAAAATCATCAAGAAA
*
195368 CTTCTAAAAATCAGACTTAGTTTCTTTAAAAAACTCATTTGAAATCATGAAACTTCTGAAAATCA
64 CTTCTGAAAATCAGACTTAGTTTCTTT-AAAAACTCATTTGAAATCATGAAACTTCTGAAAATCA
*
195433 GACTTAGTTTCGTTGAAAACTTATTTGAAATC
128 GACTTA-TTTC-TTGAAAACTCATTTGAAATC
* *
195465 ATCAAGAAACTTCTGAAAATCAGACTT-TTTCTTTAAAAACTCA-CTGAAAATCATCATGAAACT
1 ATCAAGAAACTTCTGAAAATCAGACTTATTTCTTTAAAAACTCATTTGAAAATCATCAAGAAACT
* * * *
195528 TCTGAAAATCAGACTTAGTTTCATTGAAAACTTATTTGAAATCATCAAGAAACTTCTGAAAATAA
66 TCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAATCAT---GAAACTTCTGAAAATCA
* *
195593 GACTT-TTTCTTTAAAACCTCACTTGAAATC
128 GACTTATTTCTTGAAAA-CTCATTTGAAATC
* * *
195623 GTCAAG-AACTTCTGAAAATAAGACTTAGTTTCTTTAAAAGCTCATTT-AAAATCATCAAGAAAC
1 ATCAAGAAACTTCTGAAAATCAGACTTA-TTTCTTTAAAAACTCATTTGAAAATCATCAAGAAAC
* * * *
195686 TTCTGAAAATCAGACTTAATTT-TTTGAAAGCTCATTTGAAATTGTCAAGAAACTTCTGAAAATC
65 TTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAA---TCATGAAACTTCTGAAAATC
*
195750 AGACTTATTTCTTTGAAAGCTCATTT-AAATC
127 AGACTTATTTC-TTGAAAACTCATTTGAAATC
* *
195781 ATCAAGAAACTTCTG-AAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCATCAAGAAAC
1 ATCAAGAAACTTCTGAAAATCAGACTTA-TTTCTTTAAAAACTCATTTGAAAATCATCAAGAAAC
*
195845 TTCTGAAGATCAGACTTAGTTTCT
65 TTCTGAAAATCAGACTTAGTTTCT
195869 AAAAAAACAC
Statistics
Matches: 356, Mismatches: 31, Indels: 34
0.85 0.07 0.08
Matches are distributed among these distances:
157 43 0.12
158 144 0.40
159 112 0.31
160 53 0.15
161 4 0.01
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (157 bp):
ATCAAGAAACTTCTGAAAATCAGACTTATTTCTTTAAAAACTCATTTGAAAATCATCAAGAAACT
TCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAATCATGAAACTTCTGAAAATCAGAC
TTATTTCTTGAAAACTCATTTGAAATC
Found at i:197853 original size:18 final size:18
Alignment explanation
Indices: 197810--197864 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
197800 GTTGGATCTG
* **
197810 TCTATTTCTTTTTTTTTAA
1 TCTATTT-TTTCTTTTTCT
197829 TCT-TTTTTTCTTTTTCT
1 TCTATTTTTTCTTTTTCT
*
197846 TCTATTTTTTCTCTTTCT
1 TCTATTTTTTCTTTTTCT
197864 T
1 T
197865 TTTTCTGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 11 0.35
18 17 0.55
19 3 0.10
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.76
Consensus pattern (18 bp):
TCTATTTTTTCTTTTTCT
Found at i:197854 original size:12 final size:11
Alignment explanation
Indices: 197839--197923 Score: 68
Period size: 12 Copynumber: 7.5 Consensus size: 11
197829 TCTTTTTTTC
197839 TTTTTCTTCTAT
1 TTTTTCTTCT-T
197851 TTTTTC-TCTT
1 TTTTTCTTCTT
197861 TCTTTT-TTCTGT
1 T-TTTTCTTCT-T
* *
197873 TTTTTTTTCTG
1 TTTTTCTTCTT
*
197884 TGTTTC-TCTTT
1 TTTTTCTTC-TT
197895 TTTTTCTTTCTT
1 TTTTTC-TTCTT
197907 TTTTTCTTTCTT
1 TTTTTC-TTCTT
197919 TTTTT
1 TTTTT
197924 GTGTTTTTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
10 4 0.07
11 24 0.39
12 31 0.51
13 2 0.03
ACGTcount: A:0.01, C:0.15, G:0.04, T:0.80
Consensus pattern (11 bp):
TTTTTCTTCTT
Found at i:197868 original size:33 final size:30
Alignment explanation
Indices: 197831--197913 Score: 85
Period size: 33 Copynumber: 2.6 Consensus size: 30
197821 TTTTTTAATC
* *
197831 TTTTTTTCTTTTTCTTCTATTTTTTCTCTTTCT
1 TTTTTTTCTTTTT-TTCT-GTGTTTCTCTTT-T
*
197864 TTTTTCTGTTTTTTTTTCTGTGTTTCTCTTTT
1 TTTTT-T-TCTTTTTTTCTGTGTTTCTCTTTT
197896 TTTTCTTTCTTTTTTTCT
1 TTTT-TTTCTTTTTTTCT
197914 TTCTTTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
31 10 0.23
32 6 0.14
33 16 0.37
34 5 0.12
35 6 0.14
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.80
Consensus pattern (30 bp):
TTTTTTTCTTTTTTTCTGTGTTTCTCTTTT
Found at i:197876 original size:53 final size:54
Alignment explanation
Indices: 197814--197957 Score: 147
Period size: 53 Copynumber: 2.7 Consensus size: 54
197804 GATCTGTCTA
197814 TTTCT-TTTTTTTTAATCTTTTTTTCTTTTTCTTCTAT-TTTTTCTCTTTCTTT
1 TTTCTGTTTTTTTTAATCTTTTTTTCTTTTTCTTCTATCTTTTTCTCTTTCTTT
* * * *
197866 TTTCTGTTTTTTTT--TCTGTGTTTCTCTTTTTTTTCTTTCTTTTTTTCTTTCTTT
1 TTTCTGTTTTTTTTAATCT-T-TTTTTCTTTTTCTTCTATCTTTTTCTCTTTCTTT
* * *
197920 TTT-TGTGTTTTTTATAT-ATCTTTTCTTTTTCTCTCTAT
1 TTTCTGTTTTTTTTA-ATCTTTTTTTCTTTTTCT-TCTAT
197958 GTTGTCAATT
Statistics
Matches: 74, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
51 3 0.04
52 6 0.08
53 42 0.57
54 22 0.30
56 1 0.01
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (54 bp):
TTTCTGTTTTTTTTAATCTTTTTTTCTTTTTCTTCTATCTTTTTCTCTTTCTTT
Found at i:197896 original size:42 final size:42
Alignment explanation
Indices: 197814--197929 Score: 121
Period size: 42 Copynumber: 2.7 Consensus size: 42
197804 GATCTGTCTA
* *
197814 TTTCTTTTTTT-TTAATCTTTTTTTCTTTTTCTTCTATTTTTTCTC
1 TTTCTTTTTTTCTT--T-TTTTTTTCTGTGT-TTCTATTTTTTCTC
* *
197859 TTTC-TTTTTTCTGTTTTTTTTTCTGTGTTTCTCTTTTTTTTC
1 TTTCTTTTTTTCT-TTTTTTTTTCTGTGTTTCTATTTTTTCTC
*
197901 TTTCTTTTTTTCTTTCTTTTTT-TGTGTTT
1 TTTCTTTTTTTCTTTTTTTTTTCTGTGTTT
197930 TTTATATATC
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
41 7 0.11
42 24 0.38
43 19 0.30
44 7 0.11
45 5 0.08
46 1 0.02
ACGTcount: A:0.03, C:0.14, G:0.04, T:0.79
Consensus pattern (42 bp):
TTTCTTTTTTTCTTTTTTTTTTCTGTGTTTCTATTTTTTCTC
Found at i:197898 original size:31 final size:33
Alignment explanation
Indices: 197831--197913 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 33
197821 TTTTTTAATC
* *
197831 TTTT-TTTCTTTTTCTTCTATTTTTTCTCTTTCTT
1 TTTTCTTTCTTTTT-TTCT-GTGTTTCTCTTTCTT
197865 TTTTCTGTT-TTTTTTTCTGTGTTTCTC-TT-TT
1 TTTTCT-TTCTTTTTTTCTGTGTTTCTCTTTCTT
197896 TTTTCTTTCTTTTTTTCT
1 TTTTCTTTCTTTTTTTCT
197914 TTCTTTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
30 2 0.05
31 17 0.39
32 2 0.05
33 7 0.16
34 8 0.18
35 6 0.14
36 2 0.05
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.80
Consensus pattern (33 bp):
TTTTCTTTCTTTTTTTCTGTGTTTCTCTTTCTT
Found at i:199343 original size:21 final size:23
Alignment explanation
Indices: 199302--199352 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
199292 ATGCACATGC
199302 AAATG-AAAAGATACAAAAATGG
1 AAATGCAAAAGATACAAAAATGG
* *
199324 GAATGCAAAA-ATAC-AAAATGT
1 AAATGCAAAAGATACAAAAATGG
199345 AAATGCAA
1 AAATGCAA
199353 CAAAGGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 13 0.52
22 8 0.32
23 4 0.16
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (23 bp):
AAATGCAAAAGATACAAAAATGG
Found at i:202049 original size:15 final size:13
Alignment explanation
Indices: 202021--202076 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
202011 GTAGTATTAT
202021 ATAAATATATATA
1 ATAAATATATATA
202034 ATAAATATATA-A
1 ATAAATATATATA
*
202046 AT-AATATACGTAAA
1 ATAAATATA--TATA
*
202060 ATAAATACATAATA
1 ATAAATATAT-ATA
202074 ATA
1 ATA
202077 TACATAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
11 6 0.17
12 3 0.08
13 14 0.39
14 8 0.22
15 5 0.14
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (13 bp):
ATAAATATATATA
Found at i:202049 original size:25 final size:24
Alignment explanation
Indices: 202021--202090 Score: 70
Period size: 26 Copynumber: 2.8 Consensus size: 24
202011 GTAGTATTAT
* *
202021 ATAAATATATATAATAAATATATA
1 ATAAATATATAAAATAAATACATA
202045 A-ATAATATACGTAAAATAAATACATA
1 ATA-AATATA--TAAAATAAATACATA
*
202071 ATAATATACATAAAATAAAT
1 ATAA-ATATATAAAATAAAT
202091 GTGTAATACA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
23 1 0.03
24 7 0.18
25 10 0.26
26 15 0.39
27 5 0.13
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (24 bp):
ATAAATATATAAAATAAATACATA
Found at i:202063 original size:14 final size:13
Alignment explanation
Indices: 202024--202088 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 13
202014 GTATTATATA
*
202024 AATATA-TATAAT
1 AATATACTAAAAT
202036 AA-ATA-TATAAAT
1 AATATACTA-AAAT
202048 AATATACGTAAAAT
1 AATATAC-TAAAAT
*
202062 AA-ATAC-ATAAT
1 AATATACTAAAAT
202073 AATATACATAAAAT
1 AATATAC-TAAAAT
202087 AA
1 AA
202089 ATGTGTAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
11 11 0.26
12 11 0.26
13 7 0.16
14 12 0.28
15 2 0.05
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31
Consensus pattern (13 bp):
AATATACTAAAAT
Found at i:202098 original size:25 final size:25
Alignment explanation
Indices: 202033--202090 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
202023 AAATATATAT
* *
202033 AATAAATATATAAATAATATACGTAA
1 AATAAATACAT-AATAATATACATAA
202059 AATAAATACATAATAATATACATAA
1 AATAAATACATAATAATATACATAA
202084 AATAAAT
1 AATAAAT
202091 GTGTAATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 20 0.67
26 10 0.33
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (25 bp):
AATAAATACATAATAATATACATAA
Found at i:204316 original size:31 final size:31
Alignment explanation
Indices: 204269--204331 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
204259 GATATCCCTT
204269 AGTGATCACATATTAATTAAATAAAAACGAA
1 AGTGATCACATATTAATTAAATAAAAACGAA
* * *
204300 AGTGATTACATTTTAATTAAATAAAAGCGAA
1 AGTGATCACATATTAATTAAATAAAAACGAA
204331 A
1 A
204332 ATAACTACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.29
Consensus pattern (31 bp):
AGTGATCACATATTAATTAAATAAAAACGAA
Found at i:204545 original size:32 final size:32
Alignment explanation
Indices: 204504--204602 Score: 189
Period size: 32 Copynumber: 3.1 Consensus size: 32
204494 TATAGGTGAC
204504 TAAGGACTCATAACTTAAAATTTCCCAAGGTA
1 TAAGGACTCATAACTTAAAATTTCCCAAGGTA
204536 TAAGGACTCATAACTTAAAATTTCCCAAGGTA
1 TAAGGACTCATAACTTAAAATTTCCCAAGGTA
*
204568 TAAGGACTCATAACTTAAAATTTCCTAAGGTA
1 TAAGGACTCATAACTTAAAATTTCCCAAGGTA
204600 TAA
1 TAA
204603 TAACCCTGTT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.29
Consensus pattern (32 bp):
TAAGGACTCATAACTTAAAATTTCCCAAGGTA
Found at i:205196 original size:9 final size:9
Alignment explanation
Indices: 205182--205215 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
205172 TAAAAGGGAA
205182 AAATAAAAT
1 AAATAAAAT
205191 AAATAAAAT
1 AAATAAAAT
205200 AAAT-AAAT
1 AAATAAAAT
205208 AAGATAAA
1 AA-ATAAA
205216 GGAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:205670 original size:2 final size:2
Alignment explanation
Indices: 205663--205693 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
205653 TATTAAAGAA
205663 AT AT 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 AT AT A
205694 ACATAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:206190 original size:34 final size:35
Alignment explanation
Indices: 206113--206192 Score: 126
Period size: 37 Copynumber: 2.3 Consensus size: 35
206103 ATAGTATAAC
206113 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA--AAAAT
*
206150 TTTATCCTATTTTTAGGAGTTTGAATCCT-AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
206184 TCTATCCTA
1 TCTATCCTA
206193 ATCCTAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
34 13 0.32
37 28 0.68
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
Found at i:207536 original size:10 final size:10
Alignment explanation
Indices: 207518--207557 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
207508 TTATATAAAA
*
207518 GAATTAAATC
1 GAATCAAATC
207528 GAATCAAATC
1 GAATCAAATC
*
207538 GAATCGAATC
1 GAATCAAATC
207548 GAATCAAATC
1 GAATCAAATC
207558 TAATTGTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.23
Consensus pattern (10 bp):
GAATCAAATC
Found at i:207537 original size:5 final size:5
Alignment explanation
Indices: 207524--207557 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
207514 AAAAGAATTA
* *
207524 AATCG AATCA AATCG AATCG AATCG AATCA AATC
1 AATCG AATCG AATCG AATCG AATCG AATCG AATC
207558 TAATTGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.21
Consensus pattern (5 bp):
AATCG
Found at i:208352 original size:2 final size:2
Alignment explanation
Indices: 208345--208372 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
208335 AGGTAGGCAC
208345 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
208373 TAATAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:208429 original size:22 final size:22
Alignment explanation
Indices: 208399--208441 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
208389 TTATATTTAT
208399 ATAGATATAATAAAACTTCAGA
1 ATAGATATAATAAAACTTCAGA
* *
208421 ATAGGTATAATAAAATTTCAG
1 ATAGATATAATAAAACTTCAG
208442 GATAAACACG
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:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (22 bp):
ATAGATATAATAAAACTTCAGA
Found at i:212693 original size:28 final size:28
Alignment explanation
Indices: 212653--212709 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
212643 CGTCACGACG
212653 GATCAATATGATACTTATTTGTTATCAT
1 GATCAATATGATACTTATTTGTTATCAT
212681 GATCAATATGATACTTATTTGTTATCAT
1 GATCAATATGATACTTATTTGTTATCAT
212709 G
1 G
212710 TTGATCTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.46
Consensus pattern (28 bp):
GATCAATATGATACTTATTTGTTATCAT
Found at i:215428 original size:22 final size:21
Alignment explanation
Indices: 215402--215460 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 21
215392 AAATATAATT
215402 TATATTAAATTATTTTAAAAA
1 TATATTAAATTATTTTAAAAA
*
215423 GTATATTTATAA-TATTATAAAAA
1 -TATA-TTA-AATTATTTTAAAAA
*
215446 TATTTTAAATTATTT
1 TATATTAAATTATTT
215461 ATTTAATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 2 0.06
21 7 0.23
22 7 0.23
23 13 0.42
24 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TATATTAAATTATTTTAAAAA
Found at i:223552 original size:59 final size:55
Alignment explanation
Indices: 223391--223555 Score: 161
Period size: 59 Copynumber: 2.9 Consensus size: 55
223381 TTAAAAAATA
*
223391 AGTACCTAAAGTATACCATCTTTTTCATCCAA-GTACCTAAAGATTTTTTTTGGTCGG
1 AGTACCTAAAGTATACCA-CTTTTTCAT-CAAGGTACCTAAA-ATATTTTTTGGTCGG
* * * * ** *
223448 AGTACTTAAAGTATACCACTTTTTCATCTAGATATCTAAGGTATTTTTTGGTCAAAGT
1 AGTACCTAAAGTATACCACTTTTTCATCAAGGTACCTAAAATATTTTTTGGTC---GG
* * *
223506 AGGTACCTAAAGTATAGCACTTTTTCATAAAGGTGCCTAAAATATTTTTT
1 A-GTACCTAAAGTATACCACTTTTTCATCAAGGTACCTAAAATATTTTTT
223556 AATAAATGCC
Statistics
Matches: 86, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
55 13 0.15
56 15 0.17
57 17 0.20
58 2 0.02
59 39 0.45
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (55 bp):
AGTACCTAAAGTATACCACTTTTTCATCAAGGTACCTAAAATATTTTTTGGTCGG
Found at i:227937 original size:56 final size:56
Alignment explanation
Indices: 227819--227995 Score: 221
Period size: 56 Copynumber: 3.2 Consensus size: 56
227809 ATTATTTTTC
* * * * * ** *
227819 TAGATATATTTGATTTCGGGATCCCTA-TTTTATGATTTTTAATGGTAACAACTAA
1 TAGATATACTCGATTTCGGGAACCCTATTTTTATGCTTATTAATGACAACAACTGA
* * *
227874 TAAATATACTCGATTTCGGGACCCCTATTTTTATGCTTCTTAATGACAACAACTGA
1 TAGATATACTCGATTTCGGGAACCCTATTTTTATGCTTATTAATGACAACAACTGA
* * *
227930 TAGATATATTCGATTTCGGGAACTCTATTTTTATGCTTATTAATGACAACAATTGA
1 TAGATATACTCGATTTCGGGAACCCTATTTTTATGCTTATTAATGACAACAACTGA
227986 TAGATATACT
1 TAGATATACT
227996 TTTTTTCAAT
Statistics
Matches: 105, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
55 23 0.22
56 82 0.78
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.40
Consensus pattern (56 bp):
TAGATATACTCGATTTCGGGAACCCTATTTTTATGCTTATTAATGACAACAACTGA
Found at i:228781 original size:79 final size:79
Alignment explanation
Indices: 228650--228808 Score: 293
Period size: 79 Copynumber: 2.0 Consensus size: 79
228640 ATTAATAAAG
228650 AATCAAGATACAACAAAAAGCTTACAAGGGTCACCCTCCCGTTTTGTTCAAACCCTCAACTCAAG
1 AATCAAGATACAACAAAAAGCTTACAAGGGTCACCCTCCCGTTTTGTTCAAACCCTCAACTCAAG
228715 CTAACTTAAAACTT
66 CTAACTTAAAACTT
*
228729 AATCAAGATGCAACAAAAAGCTTACAAGGGTCACCCTCCCGTTTT-TCTCAAACCCTCAACTCAA
1 AATCAAGATACAACAAAAAGCTTACAAGGGTCACCCTCCCGTTTTGT-TCAAACCCTCAACTCAA
228793 GCTAACTTAAAACTT
65 GCTAACTTAAAACTT
228808 A
1 A
228809 CCTATCAAGA
Statistics
Matches: 78, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
78 1 0.01
79 77 0.99
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.24
Consensus pattern (79 bp):
AATCAAGATACAACAAAAAGCTTACAAGGGTCACCCTCCCGTTTTGTTCAAACCCTCAACTCAAG
CTAACTTAAAACTT
Found at i:242178 original size:60 final size:60
Alignment explanation
Indices: 242105--242227 Score: 221
Period size: 60 Copynumber: 2.0 Consensus size: 60
242095 TACGCTGGAT
242105 ATGCATTCTGCTGGTTGAAATAAAACGGTGGCAGTGTCGTGG-TCGATGTTCCGAAACCAG
1 ATGCATTCTGCTGGTTGAAATAAAACGGTGGCAGTGTCGTGGCT-GATGTTCCGAAACCAG
*
242165 ATGCATTCTGCTGGTTGAAATAAAACGGTGGCATTGTCGTGGCTGATGTTCCGAAACCAG
1 ATGCATTCTGCTGGTTGAAATAAAACGGTGGCAGTGTCGTGGCTGATGTTCCGAAACCAG
242225 ATG
1 ATG
242228 GACCAGCCTG
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
60 60 0.98
61 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (60 bp):
ATGCATTCTGCTGGTTGAAATAAAACGGTGGCAGTGTCGTGGCTGATGTTCCGAAACCAG
Found at i:246607 original size:28 final size:27
Alignment explanation
Indices: 246568--246630 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
246558 AAAATTTGTT
* *
246568 TTCGCCCTG-AAATCTTATAAGTTCAAG
1 TTCGCCCTGAAAAT-TTAAAAATTCAAG
246595 TTCGCCCCTGAAAATTTAAAAATTCAAG
1 TTCG-CCCTGAAAATTTAAAAATTCAAG
*
246623 TTCACCCT
1 TTCGCCCT
246631 TAACATAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 8 0.26
28 19 0.61
29 4 0.13
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (27 bp):
TTCGCCCTGAAAATTTAAAAATTCAAG
Found at i:249802 original size:21 final size:21
Alignment explanation
Indices: 249778--249817 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
249768 TTTATTTTAT
249778 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
249799 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
249818 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:249865 original size:33 final size:33
Alignment explanation
Indices: 249812--249910 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
249802 TTTGTTTCAA
249812 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
249844 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
249877 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
249910 T
1 T
249911 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:249939 original size:13 final size:13
Alignment explanation
Indices: 249896--249950 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
249886 TTGGAAGTAT
249896 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
249909 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
249923 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
249936 TTAAGTATTTGAA
1 TTAAGTATTTCAA
249949 TT
1 TT
249951 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:250172 original size:21 final size:21
Alignment explanation
Indices: 250146--250202 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
250136 TGGAGCGTGG
*
250146 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
250167 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
250188 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
250203 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:250524 original size:15 final size:17
Alignment explanation
Indices: 250498--250529 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
250488 TTCTATGGGA
250498 AAAAACCGGATC-GGAT
1 AAAAACCGGATCTGGAT
250514 AAAAACC-GATCTGGAT
1 AAAAACCGGATCTGGAT
250530 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.16
Consensus pattern (17 bp):
AAAAACCGGATCTGGAT
Found at i:251532 original size:24 final size:24
Alignment explanation
Indices: 251500--251546 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
251490 GGCTAGAAGG
* * *
251500 TAAATTTTTAACTTTATTTTTTAA
1 TAAAATTTTAAATTTATTATTTAA
251524 TAAAATTTTAAATTTATTATTTA
1 TAAAATTTTAAATTTATTATTTA
251547 TTATTTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TAAAATTTTAAATTTATTATTTAA
Found at i:252183 original size:35 final size:36
Alignment explanation
Indices: 252138--252245 Score: 146
Period size: 35 Copynumber: 3.0 Consensus size: 36
252128 GGCAACCAAC
252138 TTTGAAAAAATGGTTTTTAAAGTTTGGTAAATGTTTA
1 TTTG-AAAAATGGTTTTTAAAGTTTGGTAAATGTTTA
* * *
252175 TTTG-AAAATGGTTTTCAAAGTTTGATAAATGTTTC
1 TTTGAAAAATGGTTTTTAAAGTTTGGTAAATGTTTA
* *
252210 TTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 TTTGAAAAATGGTTTTT-AAAGTTTGGTAAATGTTT
252246 GTAGAAAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
35 32 0.52
36 10 0.16
37 20 0.32
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (36 bp):
TTTGAAAAATGGTTTTTAAAGTTTGGTAAATGTTTA
Found at i:252204 original size:21 final size:20
Alignment explanation
Indices: 252145--252205 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
252135 AACTTTGAAA
*
252145 AAATGGTTTTTAAAGTTTGGT
1 AAATGG-TTTTAAAGTTTGAT
252166 AAAT-G-TTT--A-TTTGA-
1 AAATGGTTTTAAAGTTTGAT
252180 AAATGGTTTTCAAAGTTTGAT
1 AAATGGTTTT-AAAGTTTGAT
252201 AAATG
1 AAATG
252206 TTTCTTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 14
0.68 0.02 0.30
Matches are distributed among these distances:
14 4 0.12
15 5 0.16
16 4 0.12
18 3 0.09
19 1 0.03
20 6 0.19
21 9 0.28
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (20 bp):
AAATGGTTTTAAAGTTTGAT
Found at i:256777 original size:21 final size:21
Alignment explanation
Indices: 256753--256812 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
256743 AACTTTGAAA
256753 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
256774 AAAT-G-TTTC-----TTGGA
1 AAATGGTTTTCAAAGTTTGGT
256788 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
256809 AAAT
1 AAAT
256813 ATTTCTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 8 0.27
15 1 0.03
16 4 0.13
19 4 0.13
20 1 0.03
21 12 0.40
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.42
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:256791 original size:35 final size:36
Alignment explanation
Indices: 256745--256853 Score: 157
Period size: 35 Copynumber: 3.0 Consensus size: 36
256735 TGGCAACCAA
256745 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
256782 C-TTGGAAAATGGTTTTCAAAGTTTGGTAAATATTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
256817 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
256854 GTAGAAAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
35 30 0.47
36 11 0.17
37 23 0.36
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:258892 original size:3 final size:3
Alignment explanation
Indices: 258886--259025 Score: 208
Period size: 3 Copynumber: 46.7 Consensus size: 3
258876 TTTTTATCCA
* *
258886 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
258934 TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TGT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
258982 TAT TAT TAT TAT TTT TAT TAT TAT TAT TAT TAT TTT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
259026 AATATATTAA
Statistics
Matches: 121, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 121 1.00
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:261175 original size:17 final size:17
Alignment explanation
Indices: 261155--261201 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
261145 CAAATTTTTT
261155 TTATTTTTATTTATTTA
1 TTATTTTTATTTATTTA
*
261172 TTATTTTTATAATATTTA
1 TTATTTTTAT-TTATTTA
261190 -TATGTTTTATTT
1 TTAT-TTTTATTT
261202 GCAAGTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (17 bp):
TTATTTTTATTTATTTA
Found at i:271818 original size:1 final size:1
Alignment explanation
Indices: 271812--271896 Score: 62
Period size: 1 Copynumber: 85.0 Consensus size: 1
271802 ATGCTTGAAG
* * * * * * * * * *
271812 AAAAAAAAAGAAAAAAAAAAGAAAAGAAAAAAGAAAAGAAAGAAAAGAAAAAAGAAAAGAAAATA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
271877 ATAGAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAA
271897 GGGGGTCAAG
Statistics
Matches: 60, Mismatches: 24, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 60 1.00
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (1 bp):
A
Found at i:271825 original size:5 final size:5
Alignment explanation
Indices: 271809--271897 Score: 69
Period size: 5 Copynumber: 17.6 Consensus size: 5
271799 ATTATGCTTG
* *
271809 AAGAA AAAAA AAGAAA AAAAA AAGAA AAGAAAA AAGAA AAG-A AAGAA
1 AAGAA AAGAA AAG-AA AAGAA AAGAA AAG--AA AAGAA AAGAA AAGAA
* *
271856 AAGAAAA AAGAA AAGAA AATAA TAGAA AA-AA AA-AA AA-AA AAG
1 AAG--AA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAG
271898 GGGGTCAAGG
Statistics
Matches: 69, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
4 16 0.23
5 39 0.57
6 4 0.06
7 10 0.14
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.02
Consensus pattern (5 bp):
AAGAA
Found at i:271829 original size:12 final size:12
Alignment explanation
Indices: 271812--271897 Score: 93
Period size: 12 Copynumber: 6.8 Consensus size: 12
271802 ATGCTTGAAG
271812 AAAAAAAAAG-A
1 AAAAAAAAAGAA
271823 AAAAAAAAAGAA
1 AAAAAAAAAGAA
*
271835 AAGAAAAAAGAA
1 AAAAAAAAAGAA
271847 AAGAAAGAAAAGAA
1 AA-AAA-AAAAGAA
*
271861 AAAAGAAAAGAA
1 AAAAAAAAAGAA
*
271873 AATAATAGAAAAAAA
1 AA-AA-A-AAAAGAA
271888 AAAAAAAAAG
1 AAAAAAAAAG
271898 GGGGTCAAGG
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
11 10 0.16
12 27 0.43
13 7 0.11
14 11 0.17
15 8 0.13
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:271835 original size:21 final size:22
Alignment explanation
Indices: 271815--271896 Score: 98
Period size: 21 Copynumber: 3.8 Consensus size: 22
271805 CTTGAAGAAA
*
271815 AAAAAAGAAAAAAAAAAGAAAAG
1 AAAAAAGAAAAGAAAAA-AAAAG
*
271838 AAAAAAGAAAAGAAAG-AAAAG
1 AAAAAAGAAAAGAAAAAAAAAG
* *
271859 AAAAAAGAAAAGAAAATAATAG
1 AAAAAAGAAAAGAAAAAAAAAG
271881 AAAAAA-AAAA-AAAAAA
1 AAAAAAGAAAAGAAAAAA
271897 GGGGGTCAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.09
21 24 0.45
22 10 0.19
23 14 0.26
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.02
Consensus pattern (22 bp):
AAAAAAGAAAAGAAAAAAAAAG
Found at i:271840 original size:26 final size:26
Alignment explanation
Indices: 271809--271895 Score: 84
Period size: 26 Copynumber: 3.1 Consensus size: 26
271799 ATTATGCTTG
271809 AAGAAAAAAAAAGAAAAAAAAAAGAA
1 AAGAAAAAAAAAGAAAAAAAAAAGAA
271835 AAGAAAAAAGAAAAGAAAGAAAAGAAAAAAGAA
1 AAG----AA-AAAA-AAAGAAAA-AAAAAAGAA
* * *
271868 AAGAAAATAATAGAAAAAAAAAAAAA
1 AAGAAAAAAAAAGAAAAAAAAAAGAA
271894 AA
1 AA
271896 AGGGGGTCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
26 13 0.25
27 7 0.14
28 3 0.06
29 2 0.04
30 2 0.04
31 4 0.08
32 8 0.16
33 12 0.24
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (26 bp):
AAGAAAAAAAAAGAAAAAAAAAAGAA
Found at i:273571 original size:52 final size:52
Alignment explanation
Indices: 273043--273550 Score: 939
Period size: 52 Copynumber: 9.8 Consensus size: 52
273033 TGAATATGCT
273043 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
*
273095 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCATAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAA
273147 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
*
273199 CATAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
273251 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
273303 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
273355 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
*
273407 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCATAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAA
273459 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
* *
273511 CATAGCATTTTCTGGAAGTGTTCTTTGAGATATCTGATCT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
273551 AATTGGATAG
Statistics
Matches: 444, Mismatches: 8, Indels: 8
0.97 0.02 0.02
Matches are distributed among these distances:
51 4 0.01
52 436 0.98
53 4 0.01
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.38
Consensus pattern (52 bp):
CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
Found at i:274519 original size:113 final size:114
Alignment explanation
Indices: 274183--275317 Score: 1708
Period size: 113 Copynumber: 9.8 Consensus size: 114
274173 CAAAGATTTG
*
274183 AATTCATCAAATTGATGGATCATTCATTTT-CAGAGGAAGAGTTCATAATGAGAAGAACTCGTCA
1 AATTCATC-ACTTGATGGATCATTC-TTTTCCAGA-GAA-AGTTCATAATGAGAAGAA--C-TCA
274247 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
59 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
274303 AATTCATCACTTGATGGATCATTCTTTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AATTCATCACTTGATGGATCATTCTTTTCCAGAGAA-AGTTCATAATGAGAAGAA--C-TCATCT
* *** *
274368 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
62 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
* * *
274421 AATCCATCATTTGGTGGATCA-TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
274485 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
274534 AATTCATCACTTGATGGATCATTCTTTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AATTCATCACTTGATGGATCATTCTTTTCCAGAGAA-AGTTCATAATGAGAAGAA--C-TCATCT
* *** *
274599 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
62 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
* * *
274652 AATCCATCATTTGGTGGATCA-TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
274716 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
274765 AATTCATCACTTGATGGATCATTCTTTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AATTCATCACTTGATGGATCATTCTTTTCCAGAGAA-AGTTCATAATGAGAAGAA--C-TCATCT
* *** *
274830 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
62 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
* * *
274883 AATCCATCATTTGGTGGATCA-TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
274947 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
274996 AATTCATCACTTGATGGATCA-TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
275060 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
* * *
275109 AATTCATCACTTGATGGATTATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATTTGAAG
1 AATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
275174 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
* * * *
275223 AATTCATCAGTTGATGGATCA-ACATTACCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AATTCATCACTTGATGGATCATTCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAA
* *
275286 GAAGGAAGAAAAAGTTCATAACGAGAAGAACT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACT
275318 CATCAAGAGC
Statistics
Matches: 937, Mismatches: 65, Indels: 33
0.91 0.06 0.03
Matches are distributed among these distances:
112 1 0.00
113 392 0.42
114 137 0.15
115 36 0.04
116 54 0.06
117 44 0.05
118 246 0.26
119 19 0.02
120 8 0.01
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.30
Consensus pattern (114 bp):
AATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTA
Found at i:274628 original size:231 final size:231
Alignment explanation
Indices: 274198--275315 Score: 1891
Period size: 231 Copynumber: 4.9 Consensus size: 231
274188 ATCAAATTGA
274198 TGGATCATTCATTTT-CAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGA
1 TGGATCA-TC-TTTTCCAGA-GAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGA
274262 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGGATCATTC
59 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGGATCATTC
274327 TTTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAA
124 TTTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAA
274392 TGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGG
189 TGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGG
274435 TGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
1 TGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
274500 CATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGGATCATTCTTTTCCA
66 CATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGGATCATTCTTTTCCA
274565 GAGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
131 GAGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
274630 AATTTGTTCAACCTTTTACCTGAATCCATCATTTGG
196 AATTTGTTCAACCTTTTACCTGAATCCATCATTTGG
274666 TGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
1 TGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
274731 CATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGGATCATTCTTTTCCA
66 CATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGGATCATTCTTTTCCA
274796 GAGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
131 GAGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
274861 AATTTGTTCAACCTTTTACCTGAATCCATCATTTGG
196 AATTTGTTCAACCTTTTACCTGAATCCATCATTTGG
274897 TGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
1 TGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
274962 CATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGGATCA-TCTTTTCCA
66 CATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGGATCATTCTTTTCCA
275026 GAGAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
131 GAGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
* *** * * * *
275087 AACTTGTTCAACCTTTTGTTTAAATTCATCACTTGA
196 AATTTGTTCAACCTTTTACCTGAATCCATCATTTGG
* * *
275123 TGGATTATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATTTGAAGAAGGAAGAAGAAGT
1 TGGATCA-TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* * * * * * *
275188 TCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAGTTGATGGATCA-ACATTACC
65 TCATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGGATCATTCTTTTCC
* *
275252 AG-GTAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAAAAGTTCATAACGAGA
130 AGAG-AAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
275312 AGAA
194 AGAA
275316 CTCATCAAGA
Statistics
Matches: 858, Mismatches: 20, Indels: 16
0.96 0.02 0.02
Matches are distributed among these distances:
226 72 0.08
227 173 0.20
229 18 0.02
230 14 0.02
231 542 0.63
232 1 0.00
234 18 0.02
235 7 0.01
236 6 0.01
237 7 0.01
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (231 bp):
TGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
CATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGGATCATTCTTTTCCA
GAGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
AATTTGTTCAACCTTTTACCTGAATCCATCATTTGG
Found at i:275572 original size:3 final size:3
Alignment explanation
Indices: 275566--275705 Score: 199
Period size: 3 Copynumber: 46.7 Consensus size: 3
275556 TTTTTATCCA
* * *
275566 TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
275614 TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TGT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
275662 TAT TAT TAT TAT TTT TAT TAT TAT TAT TAT TAT TTT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
275706 AATATATTAA
Statistics
Matches: 119, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 119 1.00
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:282648 original size:21 final size:21
Alignment explanation
Indices: 282617--282767 Score: 107
Period size: 21 Copynumber: 7.3 Consensus size: 21
282607 CAATTTACAT
*
282617 ATTCGCATTGCGATAGTCCAA
1 ATTCGCGTTGCGATAGTCCAA
* ** *
282638 GTTCGCGTTGCGATTTTTCAA
1 ATTCGCGTTGCGATAGTCCAA
*
282659 ATT--CGTTGCGATAGTCGAA
1 ATTCGCGTTGCGATAGTCCAA
* *
282678 GTTCGCGTTGCGATTTATTCCAA
1 ATTCGCGTTGCGA--TAGTCCAA
* *
282701 ATT--CATTACGATAGTCCAA
1 ATTCGCGTTGCGATAGTCCAA
* *
282720 GTTCGCGTTGCGATTTATTCCAA
1 ATTCGCGTTGCGA--TAGTCCAA
282743 ATT--CGTTGCGATAGTCCAA
1 ATTCGCGTTGCGATAGTCCAA
*
282762 AATCGC
1 ATTCGC
282768 AACGACTGGT
Statistics
Matches: 96, Mismatches: 24, Indels: 20
0.69 0.17 0.14
Matches are distributed among these distances:
19 32 0.33
21 47 0.49
23 17 0.18
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (21 bp):
ATTCGCGTTGCGATAGTCCAA
Found at i:282703 original size:42 final size:42
Alignment explanation
Indices: 282624--282761 Score: 235
Period size: 42 Copynumber: 3.3 Consensus size: 42
282614 CATATTCGCA
282624 TTGCGATAGTCCAAGTTCGCGTTGCGATTT-TT-CAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
282664 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCA
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
282706 TTACGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
282748 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
282762 AATCGCAACG
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
40 29 0.32
41 2 0.02
42 59 0.66
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:282859 original size:6 final size:6
Alignment explanation
Indices: 282848--282878 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
282838 GAAGACACGT
282848 ATTACC ATTACC ATTACC ATTACC ATTACC A
1 ATTACC ATTACC ATTACC ATTACC ATTACC A
282879 CGACCACGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
ATTACC
Done.