Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1611
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: 379729
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 3 of 3
Found at i:342094 original size:22 final size:22
Alignment explanation
Indices: 342026--342094 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
342016 GGCACCTTCA
*
342026 CCTTTAAGTCCAATGTAGCTGG
1 CCTTTAAGTCCAATATAGCTGG
* * * *
342048 CCTTGAA-T-CAACACA-TTGG
1 CCTTTAAGTCCAATATAGCTGG
342067 CACCTTTAAGTCCAATATAGCTGG
1 --CCTTTAAGTCCAATATAGCTGG
342091 CCTT
1 CCTT
342095 GAATCAGCAT
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 3 0.09
20 4 0.12
21 7 0.21
22 11 0.33
23 5 0.15
24 3 0.09
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (22 bp):
CCTTTAAGTCCAATATAGCTGG
Found at i:342140 original size:52 final size:54
Alignment explanation
Indices: 342070--342218 Score: 176
Period size: 52 Copynumber: 2.8 Consensus size: 54
342060 ACATTGGCAC
342070 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CATTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
* * ** * *
342122 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCATTTTCTCAT
* * * * *
342177 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
342219 TCTTTATCAC
Statistics
Matches: 78, Mismatches: 16, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
52 37 0.47
54 6 0.08
55 35 0.45
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.34
Consensus pattern (54 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
Found at i:342337 original size:49 final size:49
Alignment explanation
Indices: 342235--342338 Score: 136
Period size: 49 Copynumber: 2.1 Consensus size: 49
342225 TCACTCTTCT
* * * * *
342235 CATCATCATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
1 CATCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGA
* * *
342284 CATCTTCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGA
1 CATCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGA
342333 CATCTT
1 CATCTT
342339 TTTTCTCATC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (49 bp):
CATCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGA
Found at i:342359 original size:171 final size:171
Alignment explanation
Indices: 342070--342464 Score: 673
Period size: 171 Copynumber: 2.3 Consensus size: 171
342060 ACATTGGCAC
*
342070 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTTCAAT
* *
342135 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
63 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTCAAGCCCAATATCGTTGACC
342200 ATGAATCAACATATTGGCATCTTTATCACTCTTCTCATCATCAT
128 ATGAATCAACATATTGGCATCTTTATCACTCTTCTCATCATCAT
* *
342244 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
*
342309 GCTGGCCTTGAATCAGCACGTTGACATCTTTTTTCTCATCTTCAAGCCCAATATCGTTGACCATG
66 GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTCAAGCCCAATATCGTTGACCATG
* *
342374 AATCAACATATTGGCATCTTTATCACTTTTCTCATCTTCAT
131 AATCAACATATTGGCATCTTTATCACTCTTCTCATCATCAT
* *
342415 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
342465 ATCTCTAAAA
Statistics
Matches: 210, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
171 167 0.80
172 5 0.02
174 38 0.18
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (171 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTCAAGCCCAATATCGTTGACCATG
AATCAACATATTGGCATCTTTATCACTCTTCTCATCATCAT
Found at i:343290 original size:33 final size:33
Alignment explanation
Indices: 343253--343319 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
343243 TTCAACGATT
343253 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
343286 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
343319 T
1 T
343320 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:343291 original size:13 final size:13
Alignment explanation
Indices: 343273--343297 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
343263 CATAAAATGT
343273 TGTATCGATACAA
1 TGTATCGATACAA
343286 TGTATCGATACA
1 TGTATCGATACA
343298 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:343381 original size:13 final size:13
Alignment explanation
Indices: 343363--343387 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
343353 ATTACTCACA
343363 TGTATCGATACAT
1 TGTATCGATACAT
343376 TGTATCGATACA
1 TGTATCGATACA
343388 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:343524 original size:52 final size:52
Alignment explanation
Indices: 343396--343516 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
343386 CACTGATCTT
*
343396 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
343448 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
343500 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
343517 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:350756 original size:1 final size:1
Alignment explanation
Indices: 350752--350781 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
350742 AAAAAGATGC
*
350752 AAAAAAAAAAAAAAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
350782 CCCCTTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:351798 original size:61 final size:63
Alignment explanation
Indices: 351723--352382 Score: 440
Period size: 61 Copynumber: 10.3 Consensus size: 63
351713 TTTTTAACGT
* * * * *
351723 CCACGACTCAGTGGCA-TTTTTTC-TTTAAAGCCCACAATTCCGTGGCACCTCATCTTTAAGT
1 CCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCTCTTCTTTAAGC
* * * *
351784 CCACAACTCCGTGGCAC-----CCTTTTACAGCCCACAATTCCGTGGCACCTCATCTTTAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCTCTTCTTTAAGC
* *
351842 CCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCA-CTCTTC--AAA
1 CCACAACTCCGTGGCA--CTTTTT-TCTTTT-AAAGCCCACAACTCCGTGGCACCTCTTCTTTAA
351904 GC
62 GC
* * *
351906 CCACGACTCCGTGGCAC-----TC-TTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAA
1 CCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACC-TCTTC--TTT-AA
351965 GC
62 GC
* *
351967 CCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCA-CTC-T-TTAAA
1 CCACAACTCCGTGGCA--CTTTTT-TCTTTT-AAAGCCCACAACTCCGTGGCACCTCTTCTTTAA
352029 GC
62 GC
* * * *
352031 CCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAA
1 CCACAACTCCGTGGCACTTTTTTCTTTT-AAAGCCCACAACTCCGTGGCACC-TCTTC-TTT--A
352096 AGC
61 AGC
* * * *
352099 CCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACGACTCCGTGGCA-CTCTT-TTTAAAGC
1 CCACAACTCCGTGGCACTTTTTTCTTTT-AAAGCCCACAACTCCGTGGCACCTCTTCTTT-AAGC
* ** * *
352162 CCACAACTCTGTGGCACTCTTTTTCCTCCT-AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT
1 CCACAACTCCGTGGCACT-TTTTT-CTTTTAAAGCCCACAACTCCGTGGCAC-C-TCTT-CTT-T
352226 AAGC
60 AAGC
* * * * *
352230 CCACAACTCCGTGGCA-----TCCTTTT-AAGCCCATAACTCCGTGGCACTTTTTTCATCTTTGA
1 CCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCAC----CTCTTCTTTAA
*
352289 GT
62 GC
* *
352291 CCATAACTCCGTGGCACCTTTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTT
1 CCACAACTCCGTGGCA-C--TTTTTTCTTTTAAAGCCCACAACTCCGTGGCAC-C-TCTT--C-T
*
352356 TTAAGT
58 TTAAGC
352362 CCACAACTCCGTGGCATCTTT
1 CCACAACTCCGTGGCA-CTTT
352383 CTCCCTTCCT
Statistics
Matches: 484, Mismatches: 56, Indels: 110
0.74 0.09 0.17
Matches are distributed among these distances:
54 20 0.04
55 3 0.01
56 6 0.01
57 1 0.00
58 52 0.11
60 1 0.00
61 99 0.20
62 10 0.02
63 45 0.09
64 47 0.10
65 6 0.01
66 19 0.04
67 20 0.04
68 76 0.16
69 13 0.03
70 24 0.05
71 42 0.09
ACGTcount: A:0.20, C:0.35, G:0.14, T:0.31
Consensus pattern (63 bp):
CCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCTCTTCTTTAAGC
Found at i:351890 original size:125 final size:125
Alignment explanation
Indices: 351749--352245 Score: 551
Period size: 125 Copynumber: 3.9 Consensus size: 125
351739 TTTTTTCTTT
* * * * *
351749 AAAGCCCACAATTCCGTGGCACCTCATCTTTAAGTCCACAACTCCGTGGCACCCTTTTACAGCCC
1 AAAGCCCACGACTCCGTGGCA-CTC-T-TTAAAGCCCACAACTCCGTGGCACCCTTTTAAAGCCC
* *
351814 ACAATTCCGTGGCACC-TCATC-TTT-AAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTC
63 ACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTC
* * * *
351874 AAAGCCCACGACTCCGTGGCACTCTTCAAAGCCCACGACTCCGTGGCACTC-TTCAAAGCCCACA
1 AAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAAGCCCACA
*
351938 ACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTC
66 ACTCCGTGGCACCTTCTTCT-TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTC
*
351999 AAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAG
1 AAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCA-C--C--CTTTT-AAAG
* * *
352064 CCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCAC-C-TTCT-TCTTT
60 CCCACAACTCCGTGGCACCTTCTTCTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCTCTTT
352126 TC
124 TC
* * *
352128 AAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCTCCTA
1 AAAGCCCACGACTCCGTGGCACTC--TTTAAAGCCCACAACTCCGTGGCAC-C-CTTT--T--AA
* * *
352193 AGCCCACAACTCTGTGGCACTCTTTTTCCTTCT-AAGCCCACAACTCCGTGGCA
58 AGCCCACAACTCCGTGGCAC-CTTCTT-CTTTTAAAGCCCACAACTCCGTGGCA
352246 TCCTTTTAAG
Statistics
Matches: 327, Mismatches: 26, Indels: 32
0.85 0.07 0.08
Matches are distributed among these distances:
121 23 0.07
122 24 0.07
123 1 0.00
124 6 0.02
125 100 0.31
126 1 0.00
128 4 0.01
129 33 0.10
130 6 0.02
131 71 0.22
132 54 0.17
133 4 0.01
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (125 bp):
AAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAAGCCCACA
ACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTC
Found at i:351901 original size:27 final size:27
Alignment explanation
Indices: 351871--351949 Score: 149
Period size: 27 Copynumber: 2.9 Consensus size: 27
351861 TTTTTCTCTT
351871 TTCAAAGCCCACGACTCCGTGGCACTC
1 TTCAAAGCCCACGACTCCGTGGCACTC
351898 TTCAAAGCCCACGACTCCGTGGCACTC
1 TTCAAAGCCCACGACTCCGTGGCACTC
*
351925 TTCAAAGCCCACAACTCCGTGGCAC
1 TTCAAAGCCCACGACTCCGTGGCAC
351950 CTTTTTCTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.24, C:0.41, G:0.18, T:0.18
Consensus pattern (27 bp):
TTCAAAGCCCACGACTCCGTGGCACTC
Found at i:351971 original size:34 final size:33
Alignment explanation
Indices: 351714--352382 Score: 456
Period size: 34 Copynumber: 20.9 Consensus size: 33
351704 TCAAATACCT
* * * * *
351714 TTTTAACGTCCACGACTCAGTGGCA-TTTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
* **
351746 -TTTAAAGCCCACAATTCCGTGGCACC-TCATC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
*
351777 -TTT-AAGTCCACAACTCCGTGGCACC-----C
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
* * **
351803 TTTTACAGCCCACAATTCCGTGGCACC-TCATC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
351835 -TTT-AAGCCCACAACTCCGTGGCACTCTTTTTCTC
1 TTTTAAAGCCCACAACTCCGTGGCAC-C-TTTT-TC
*
351869 TTTTCAAAGCCCACGACTCCGTGGCA-C----TC
1 TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
* *
351898 -TTCAAAGCCCACGACTCCGTGGCA-C----TC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
*
351925 -TTCAAAGCCCACAACTCCGTGGCACCTTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
351957 TGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTC
1 T-TTTAAAGCCCACAACTCCGTGGCAC-C-TTTT-TC
*
351994 TTTTCAAAGCCCACGACTCCGTGGCA-C----TC
1 TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
* *
352023 -TTTAAAGCCCACAACTCTGTGGCACCTTCTTC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
* *
352055 TTTTCAAAGCCCACAACTCTGTGGCACCTTCTTC
1 TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
* *
352089 TTTTCAAAGCCCACAACTCTGTGGCACCTTCTTC
1 TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
* *
352123 TTTTCAAAGCCCACGACTCCGTGGCA-C--TCT-
1 TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
*
352153 TTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCC
1 TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-C
** *
352188 TCCT-AAGCCCACAACTCTGTGGCACTCTTTTTCC
1 TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-C
* *
352222 TTCT-AAGCCCACAACTCCGTGGCA-----TCC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
* *
352249 TTTT-AAGCCCATAACTCCGTGGCACTTTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
* * *
352281 ATCTTT-GAGTCCATAACTCCGTGGCACCTTTTTTTTC
1 -T-TTTAAAGCCCACAACTCCGTGGCACC---TTTTTC
352318 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT--C
* *
352354 TTTT-AAGTCCACAACTCCGTGGCATCTTT
1 TTTTAAAGCCCACAACTCCGTGGCACCTTT
352383 CTCCCTTCCT
Statistics
Matches: 538, Mismatches: 47, Indels: 102
0.78 0.07 0.15
Matches are distributed among these distances:
26 1 0.00
27 92 0.17
28 27 0.05
29 23 0.04
30 43 0.08
31 31 0.06
32 7 0.01
33 8 0.01
34 196 0.36
35 30 0.06
36 31 0.06
37 49 0.09
ACGTcount: A:0.20, C:0.35, G:0.14, T:0.32
Consensus pattern (33 bp):
TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
Found at i:352016 original size:98 final size:96
Alignment explanation
Indices: 351898--352216 Score: 368
Period size: 98 Copynumber: 3.3 Consensus size: 96
351888 CGTGGCACTC
*
351898 TTCAAAGCCCACGACTCCGTGGCACTCTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTA
1 TTCAAAGCCCACAACTCCGTGGCACTCTTCAAAGCCCACAACTCCGTGGCACC-TTTTCT-TTTA
*
351963 AAGCCCACAACTCCGTGGCACTCTTTTTCTCTT
64 AAGCCCACAACTCTGTGGCACTCTTTTTCTCTT
* * *
351996 TTCAAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCA
1 TTCAAAGCCCACAACTCCGTGGCACTCTTCAAAGCCCACAACTCCGTGGCACCTT-TTCTTTT-A
*
352061 AAGCCCACAACTCTGTGGCAC-C-TTCT-TCTT
64 AAGCCCACAACTCTGTGGCACTCTTTTTCTCTT
* * *
352091 TTCAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACGACTCCGTGGCA-C-TCT-
1 TTCAAAGCCCACAACTCCGTGGCA----C-TC--TTCAAAGCCCACAACTCCGTGGCACCTTTTC
352153 TTTTAAAGCCCACAACTCTGTGGCACTCTTTTTC-C--
59 TTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCTCTT
* * *
352188 TCCTAAGCCCACAACTCTGTGGCACTCTT
1 TTCAAAGCCCACAACTCCGTGGCACTCTT
352217 TTTCCTTCTA
Statistics
Matches: 196, Mismatches: 13, Indels: 32
0.81 0.05 0.13
Matches are distributed among these distances:
90 2 0.01
92 2 0.01
93 1 0.01
95 26 0.13
96 3 0.02
97 50 0.26
98 81 0.41
99 6 0.03
100 3 0.02
101 1 0.01
102 21 0.11
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.30
Consensus pattern (96 bp):
TTCAAAGCCCACAACTCCGTGGCACTCTTCAAAGCCCACAACTCCGTGGCACCTTTTCTTTTAAA
GCCCACAACTCTGTGGCACTCTTTTTCTCTT
Found at i:352173 original size:97 final size:97
Alignment explanation
Indices: 351898--352350 Score: 395
Period size: 97 Copynumber: 4.7 Consensus size: 97
351888 CGTGGCACTC
*
351898 TTCAAAGCCCACGACTCCGTGGCA----C-TC-TTCAAAGCCCACAACTCCGTGGCACCTTTTTC
1 TTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTCAAAGCCCACAACTCCGTGGCA-C----TC
*
351957 TGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCTT
61 TTTTTAAAGCCCACAACTCCGTGGCACTC-TTTT-TCTT
* *
351996 TTCAAAGCCCACGACTCCGTGGCA----C-TCTTT-AAAGCCCACAACTCTGTGGCACCTTCTTC
1 TTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTCAAAGCCCACAACTCCGTGGCA-C-TC-T-
* *
352055 TTTTCAAAGCCCACAACTCTGTGGCAC-CTTCTTCTT
62 TTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCTT
* *
352091 TTCAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACGACTCCGTGGCACTCTTTT
1 TTCAAAGCCCACAACTCCGTGGCACCTTCTTC-TTTCAAAGCCCACAACTCCGTGGCACTCTTTT
* *
352156 TAAAGCCCACAACTCTGTGGCACTCTTTTTC-C
65 TAAAGCCCACAACTCCGTGGCACTCTTTTTCTT
* * * * * * *
352188 TCCTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCA-TCCTTT
1 TTCAAAGCCCACAACTCCGTGGCAC-CTTCTTCTTTCAAAGCCCACAACTCCGTGGCACTCTTTT
*
352252 T-AAGCCCATAACTCCGTGGCACT-TTTTTCATCT
65 TAAAGCCCACAACTCCGTGGCACTCTTTTTC-T-T
* * * * *
352285 TT--GAGTCCATAACTCCGTGGCACCTTTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
1 TTCAAAGCCCACAACTCCGTGGCACC---TTCTTCTTTCAAAGCCCACAACTCCGTGGCACTCTT
352348 TTT
63 TTT
352351 CCCTTTTAAG
Statistics
Matches: 306, Mismatches: 29, Indels: 40
0.82 0.08 0.11
Matches are distributed among these distances:
94 7 0.02
95 66 0.22
96 10 0.03
97 100 0.33
98 92 0.30
99 4 0.01
100 4 0.01
101 4 0.01
102 19 0.06
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.32
Consensus pattern (97 bp):
TTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTCAAAGCCCACAACTCCGTGGCACTCTTTTT
AAAGCCCACAACTCCGTGGCACTCTTTTTCTT
Found at i:352196 original size:63 final size:63
Alignment explanation
Indices: 351922--352219 Score: 341
Period size: 63 Copynumber: 4.6 Consensus size: 63
351912 CTCCGTGGCA
* *
351922 CTCTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCT
1 CTCTTCAAAGCCCACAACTCCGTGGCA-C----TCTTTTTAAAGCCCACAACTCTGTGGCAC-CT
*
351987 TTTT
60 TCTT
*
351991 CTCTTTTCAAAGCCCACGACTCCGTGGCACTC--TTTAAAGCCCACAACTCTGTGGCACCTTCTT
1 CTC--TTCAAAGCCCACAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCTGTGGCACCTTCTT
* *
352054 CTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTT
1 CTCTTCAAAGCCCACAACTCCGTGGCA-C-TC-T-TTTT-AAAGCCCACAACTCTGTGGCACCTT
352119 CTT
61 CTT
* * *
352122 CTTTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
1 CTCTTCAAAGCCCACAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCTGTGGCAC-CTTCTT
* * *
352186 C-CTCCTAAGCCCACAACTCTGTGGCACTCTTTTT
1 CTCTTCAAAGCCCACAACTCCGTGGCACTCTTTTT
352220 CCTTCTAAGC
Statistics
Matches: 205, Mismatches: 14, Indels: 26
0.84 0.06 0.11
Matches are distributed among these distances:
61 22 0.11
62 1 0.00
63 59 0.29
64 34 0.17
65 1 0.00
66 4 0.02
67 4 0.02
68 53 0.26
69 3 0.01
70 1 0.00
71 23 0.11
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.32
Consensus pattern (63 bp):
CTCTTCAAAGCCCACAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCTGTGGCACCTTCTT
Found at i:352279 original size:27 final size:27
Alignment explanation
Indices: 352219--352272 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
352209 GCACTCTTTT
*
352219 TCCTTCTAAGCCCACAACTCCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
*
352246 TCCTTTTAAGCCCATAACTCCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
352273 CTTTTTTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.37, G:0.15, T:0.26
Consensus pattern (27 bp):
TCCTTTTAAGCCCACAACTCCGTGGCA
Found at i:352335 original size:36 final size:34
Alignment explanation
Indices: 352248--352382 Score: 146
Period size: 35 Copynumber: 3.9 Consensus size: 34
352238 CCGTGGCATC
*
352248 CTTTTAAGCCCATAACTCCGTGGCACTTTTTTCAT
1 CTTTTAAGCCCACAACTCCGTGGCACTTTTTT-AT
* * * *
352283 C-TTTGAGTCCATAACTCCGTGGCACCTTTTTTTT
1 CTTTTAAGCCCACAACTCCGTGGCA-CTTTTTTAT
**
352317 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 CTTTT-AAGCCCACAACTCCGTGGCACT-TTTTTAT
*
352353 CTTTTAAGTCCACAACTCCGTGGCATCTTT
1 CTTTTAAGCCCACAACTCCGTGGCA-CTTT
352383 CTCCCTTCCT
Statistics
Matches: 86, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
34 23 0.27
35 34 0.40
36 29 0.34
ACGTcount: A:0.19, C:0.30, G:0.13, T:0.39
Consensus pattern (34 bp):
CTTTTAAGCCCACAACTCCGTGGCACTTTTTTAT
Found at i:352388 original size:34 final size:34
Alignment explanation
Indices: 352247--352389 Score: 144
Period size: 36 Copynumber: 4.1 Consensus size: 34
352237 TCCGTGGCAT
* *
352247 CCTTTTAAGCCCATAACTCCGTGGCA-CTTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCATCTTTTTC
* * * * * *
352280 CATCTTTGAGTCCATAACTCCGTGGCACCTTTTTTT
1 CCT-TTTAAGCCCACAACTCCGTGGCATC-TTTTTC
*
352316 TCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
1 CCTTTT-AAGCCCACAACTCCGTGGCA-TCTTTTTC
* *
352352 CCTTTTAAGTCCACAACTCCGTGGCATCTTTCTC
1 CCTTTTAAGCCCACAACTCCGTGGCATCTTTTTC
352386 CCTT
1 CCTT
352390 CCTAAAGCCC
Statistics
Matches: 92, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
33 2 0.02
34 32 0.35
35 23 0.25
36 34 0.37
37 1 0.01
ACGTcount: A:0.17, C:0.32, G:0.12, T:0.38
Consensus pattern (34 bp):
CCTTTTAAGCCCACAACTCCGTGGCATCTTTTTC
Found at i:352396 original size:71 final size:70
Alignment explanation
Indices: 352253--352402 Score: 178
Period size: 71 Copynumber: 2.1 Consensus size: 70
352243 GCATCCTTTT
* * * * **
352253 AAGCCCATAACTCCGTGGCACTTTTTTCATCTTTGAGTCCATAACTCCGTGGCACCTTTTTTTTC
1 AAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTCTCCC
*
352318 TTTTA
66 TTCTA
* *
352323 AAGCCCACAACTCCGTGGCACTCTTTTTC-CCTTTTAAGTCCACAACTCCGTGGCATC-TTTCTC
1 AAGCCCACAACTCCGTGGCACT-TTTTTCATC-TTTAAGTCCACAACTCCGTGGCACCTTTTCTC
352386 CCTTCCTA
64 CCTT-CTA
352394 AAGCCCACA
1 AAGCCCACA
352403 CAAGTCGGTG
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
70 29 0.43
71 39 0.57
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (70 bp):
AAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTCTCCC
TTCTA
Found at i:352430 original size:33 final size:35
Alignment explanation
Indices: 352387--352456 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 35
352377 ATCTTTCTCC
352387 CTTCCTAAAGCCCACACAAGTCGGTGGCAA-CCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
352421 CTTCC-AAAGCCCACACAAGTCGGTGGCAACCCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
352455 CT
1 CT
352457 AAGCCCAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 24 0.69
34 11 0.31
ACGTcount: A:0.26, C:0.37, G:0.17, T:0.20
Consensus pattern (35 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
Found at i:352520 original size:49 final size:49
Alignment explanation
Indices: 352456--354106 Score: 2017
Period size: 49 Copynumber: 33.9 Consensus size: 49
352446 GCAACCCTTC
*
352456 TAAGCCCAATATAGCTGGCCTTGAATCAGCATC-TTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCA-CATTGGCATCTTCATCTT
*
352505 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * *
352548 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
*
352597 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
352640 TAAGTCCAATATCGCTGGCATTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
352689 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
352738 TAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCATCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
352787 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * *
352836 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
352885 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * *
352934 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
352983 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
353032 TAAGTCCAATATTGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * *
353081 TAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
353130 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * * *
353179 TAGGTCCAATATCGCTGGCCTTGAATCAACATATTGGCATCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
353228 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * *
353277 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
353326 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
353375 TAAGTCCAATATTGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
353424 TAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCATCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
353473 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * *
353522 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
353571 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * *
353620 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
353669 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * *
353718 TAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
353767 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
353816 TAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCATCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* * * *
353865 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* *
353914 TAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
* *
353957 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG--CATCTT-CATCTT
* * * *
354009 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAT-C----T-TCATCTT
* * * * * *
354064 TAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTT
354107 TATCACTCTT
Statistics
Matches: 1366, Mismatches: 208, Indels: 56
0.84 0.13 0.03
Matches are distributed among these distances:
43 113 0.08
45 5 0.00
47 2 0.00
48 1 0.00
49 1166 0.85
50 5 0.00
52 35 0.03
54 1 0.00
55 37 0.03
56 1 0.00
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
Found at i:352764 original size:98 final size:98
Alignment explanation
Indices: 352451--354039 Score: 2305
Period size: 98 Copynumber: 16.4 Consensus size: 98
352441 CGGTGGCAAC
* * * *
352451 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATG
*
352516 TAGCTGGCCTTGAATCAGCACATTGG------CA
65 TAGCTGGCCTTGACTCAGCACATTGGCACCTTCA
* * * *
352544 CCTTTAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
*
352609 AGCTGGCCTTGAATCAGCACATTGG------CA
66 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
*
352636 CCTTTAAGTCCAATATCGCTGGCATTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
352701 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
66 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
*
352734 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCATCATCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
352799 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
66 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
352832 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
352897 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
66 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
352930 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
352995 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
66 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
* * * * * * *
353028 CCTTTAAGTCCAATATTGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTTTAAGTCCAATAT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
* * * * *
353093 TGCTGGCCTTGAATCAGCATATTGGCATCATCA
66 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
* * * * * * * * * *
353126 TCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTTTAGGTCCAATAT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
* * * * * *
353191 CGCTGGCCTTGAATCAACATATTGGCATCATCA
66 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
* * * * * * * * *
353224 TCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTTTAAGTCCAATAT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
* * * * *
353289 CGCTGGCCTTGAATCAGCATATTGGCATCATCA
66 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
* * * * * * * * *
353322 TCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCTTTAAGTCCAATAT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
*
353387 TGCTGGCCTTGACTCAGCACATTGGCACCTTCA
66 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
*
353420 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCATCATCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
353485 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
66 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
353518 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
353583 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
66 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
353616 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
353681 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
66 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
*
353714 CCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
353779 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
66 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
*
353812 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCATCATCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
353877 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
66 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
* * * * *
353910 CCTTTAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGG---CA-C--CTTTAAGTCCAATAT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
* * *
353969 AGCTGGCCTTGAATCAGCATATTGGCACATTTTCCA
66 AGCTGGCCTTGACTCAGCACATTGGCAC--CTT-CA
* * * *
354005 TCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCA
354040 CGTTGACATC
Statistics
Matches: 1426, Mismatches: 61, Indels: 16
0.95 0.04 0.01
Matches are distributed among these distances:
92 210 0.15
93 4 0.00
94 3 0.00
95 36 0.03
98 1173 0.82
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (98 bp):
CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
Found at i:353978 original size:22 final size:22
Alignment explanation
Indices: 353910--353978 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
353900 GGCACCTTCA
*
353910 CCTTTAAGTCCAATGTAGCTGG
1 CCTTTAAGTCCAATATAGCTGG
* * * *
353932 CCTTGAA-T-CAACACA-TTGG
1 CCTTTAAGTCCAATATAGCTGG
353951 CACCTTTAAGTCCAATATAGCTGG
1 --CCTTTAAGTCCAATATAGCTGG
353975 CCTT
1 CCTT
353979 GAATCAGCAT
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 3 0.09
20 4 0.12
21 7 0.21
22 11 0.33
23 5 0.15
24 3 0.09
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (22 bp):
CCTTTAAGTCCAATATAGCTGG
Found at i:354024 original size:52 final size:54
Alignment explanation
Indices: 353954--354102 Score: 176
Period size: 52 Copynumber: 2.8 Consensus size: 54
353944 ACATTGGCAC
353954 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CATTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
* * ** * *
354006 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCATTTTCTCAT
* * * * *
354061 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
354103 TCTTTATCAC
Statistics
Matches: 78, Mismatches: 16, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
52 37 0.47
54 6 0.08
55 35 0.45
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.34
Consensus pattern (54 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCATTTTCTCAT
Found at i:354221 original size:49 final size:49
Alignment explanation
Indices: 354119--354222 Score: 136
Period size: 49 Copynumber: 2.1 Consensus size: 49
354109 TCACTCTTCT
* * * * *
354119 CATCATCATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
1 CATCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGA
* * *
354168 CATCTTCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGA
1 CATCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGA
354217 CATCTT
1 CATCTT
354223 TTTTCTCATC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (49 bp):
CATCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGA
Found at i:354243 original size:171 final size:171
Alignment explanation
Indices: 353954--354348 Score: 673
Period size: 171 Copynumber: 2.3 Consensus size: 171
353944 ACATTGGCAC
*
353954 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTTCAAT
* *
354019 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCC
63 GTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTCAAGCCCAATATCGTTGACC
354084 ATGAATCAACATATTGGCATCTTTATCACTCTTCTCATCATCAT
128 ATGAATCAACATATTGGCATCTTTATCACTCTTCTCATCATCAT
* *
354128 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
*
354193 GCTGGCCTTGAATCAGCACGTTGACATCTTTTTTCTCATCTTCAAGCCCAATATCGTTGACCATG
66 GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTCAAGCCCAATATCGTTGACCATG
* *
354258 AATCAACATATTGGCATCTTTATCACTTTTCTCATCTTCAT
131 AATCAACATATTGGCATCTTTATCACTCTTCTCATCATCAT
* *
354299 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
354349 ATCTCTAAAA
Statistics
Matches: 210, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
171 167 0.80
172 5 0.02
174 38 0.18
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (171 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTA
GCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTCAAGCCCAATATCGTTGACCATG
AATCAACATATTGGCATCTTTATCACTCTTCTCATCATCAT
Found at i:355174 original size:33 final size:33
Alignment explanation
Indices: 355137--355203 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
355127 TTCAACGATT
355137 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
355170 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
355203 T
1 T
355204 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:355175 original size:13 final size:13
Alignment explanation
Indices: 355157--355181 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
355147 CATAAAATGT
355157 TGTATCGATACAA
1 TGTATCGATACAA
355170 TGTATCGATACA
1 TGTATCGATACA
355182 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:355265 original size:13 final size:13
Alignment explanation
Indices: 355247--355271 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
355237 ATTACTCACA
355247 TGTATCGATACAT
1 TGTATCGATACAT
355260 TGTATCGATACA
1 TGTATCGATACA
355272 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:355408 original size:52 final size:52
Alignment explanation
Indices: 355280--355400 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
355270 CACTGATCTT
*
355280 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
355332 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
355384 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
355401 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:358549 original size:15 final size:16
Alignment explanation
Indices: 358513--358553 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
358503 TTAATTAAAA
*
358513 TTATAAAATTATAATT
1 TTATATAATTATAATT
358529 TT-TATAATT-TAATT
1 TTATATAATTATAATT
358543 TTATATAATTA
1 TTATATAATTA
358554 ATATAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 7 0.32
15 13 0.59
16 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATAATTATAATT
Found at i:360873 original size:17 final size:17
Alignment explanation
Indices: 360840--360874 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
360830 AATAATATTG
*
360840 TTTTGATTTTCTAAAAA
1 TTTTGATTTTATAAAAA
360857 TTTTGATTTTATTAAAAA
1 TTTTGATTTTA-TAAAAA
360875 ATAACATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTTGATTTTATAAAAA
Found at i:361718 original size:155 final size:152
Alignment explanation
Indices: 361254--361800 Score: 376
Period size: 155 Copynumber: 3.5 Consensus size: 152
361244 TCAGGAAGAT
* * * * * * *
361254 GAACCTACCCTAAACACACACCCTTGGCATAAAAGCAACTCAGTGATTACTTAGTAATTAGTTCT
1 GAACCTATCCTAAACACACA-CCTTGGCATAAAAGCACCT-AGTGA-TACCTAGGACTAATTTCT
* * * * * * * **
361319 AAAAAAATTACCAAAATGCCCCT--AGATAAACGTTTGACGTGAAAGTATCTCAGTAACTTTAAA
63 AAAGAAATTACCAAAATACCCCTAGAGATATACATTTGAC-TTAAAATATCTCGGTAACCCTAAA
* * *
361382 AGAAACAAAGAA-GATAAGAAAATGAT
127 AGACACAAA-AATGATAAGAAAAGGAC
* * ** * * *
361408 GAAACTATCATAAATGCACACCTTTAGTATAAAAGCAACCTAGTGACTACCTAAGACTTAATTT-
1 GAACCTATCCTAAACACACACC-TTGGCATAAAAGC-ACCTAGTGA-TACCTAGGAC-TAATTTC
* *
361472 TAAAAGAAATTACCAAAATACCTCTATG-G-TTTACATTTGA-TATAAAAGTAT-TCGAGTAACC
62 T-AAAGAAATTACCAAAATACCCCTA-GAGATATACATTTGACT-TAAAA-TATCTCG-GTAACC
** * ** *
361533 CTAAGTGACACGAAAATGA-ACCTAAGAGGAC
122 CTAAAAGACACAAAAATGATA-AGAAAAGGAC
* *
361564 GAACCTATCCTAAACACACACCATTGGCATAAAAGCGACCTAGTGATGGCCTAGGACTCATTTCT
1 GAACCTATCCTAAACACACACC-TTGGCATAAAAGC-ACCTAGTGAT-ACCTAGGACTAATTTCT
* * * *
361629 TATGAAATTACCAAAATACCCCTAGAGATATACCTTTGACTTAAAATATCTTGGTAACCCTAAAA
63 AAAGAAATTACCAAAATACCCCTAGAGATATACATTTGACTTAAAATATCTCGGTAACCCTAAAA
361694 GACACAAAAATGATAAGAAAAGGAC
128 GACACAAAAATGATAAGAAAAGGAC
* * * * * * * ***
361719 GCATCTATCTTAAATACACACCTTAGGCATAAAAGTAACCCAGTGACTACTTAGGACTCGGTTCT
1 GAACCTATCCTAAACACACACCTT-GGCATAAAAG-CACCTAGTGA-TACCTAGGACTAATTTCT
361784 AACA-AAATTACCAAAAT
63 AA-AGAAATTACCAAAAT
361801 GCCTTTAGGG
Statistics
Matches: 300, Mismatches: 70, Indels: 45
0.72 0.17 0.11
Matches are distributed among these distances:
153 2 0.01
154 42 0.14
155 158 0.53
156 96 0.32
157 2 0.01
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (152 bp):
GAACCTATCCTAAACACACACCTTGGCATAAAAGCACCTAGTGATACCTAGGACTAATTTCTAAA
GAAATTACCAAAATACCCCTAGAGATATACATTTGACTTAAAATATCTCGGTAACCCTAAAAGAC
ACAAAAATGATAAGAAAAGGAC
Found at i:363280 original size:16 final size:17
Alignment explanation
Indices: 363249--363284 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
363239 TACGTAATGT
*
363249 ATCGATTTTCACTGTTC
1 ATCGATGTTCACTGTTC
363266 ATCGATGTT-ACTGTTC
1 ATCGATGTTCACTGTTC
363282 ATC
1 ATC
363285 ACTATTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.44
Consensus pattern (17 bp):
ATCGATGTTCACTGTTC
Found at i:363311 original size:13 final size:13
Alignment explanation
Indices: 363293--363330 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
363283 TCACTATTCA
*
363293 TGTATCGATACAT
1 TGTATCGATACAG
363306 TGTATCGATACAG
1 TGTATCGATACAG
363319 TGTATCGATACA
1 TGTATCGATACA
363331 CTATAAATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:363445 original size:20 final size:20
Alignment explanation
Indices: 363402--363445 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
363392 TTTAAATGCA
* *
363402 TGTATCGATACATTATAAAT
1 TGTATCGATACATTAGAAAG
* *
363422 TGTATCGATACATTGGAACG
1 TGTATCGATACATTAGAAAG
363442 TGTA
1 TGTA
363446 AGTGCGGAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTAGAAAG
Found at i:363864 original size:34 final size:35
Alignment explanation
Indices: 363801--363867 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
363791 CTAAGTGATT
363801 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
363837 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
363868 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:365754 original size:13 final size:13
Alignment explanation
Indices: 365736--365795 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
365726 TTACCACTGT
365736 TTGTATCGATACA
1 TTGTATCGATACA
*
365749 TTGTATCGATATA
1 TTGTATCGATACA
365762 -TG-A-CG--A-A
1 TTGTATCGATACA
365769 TTGTATCGATACA
1 TTGTATCGATACA
365782 TTGTATCGATACA
1 TTGTATCGATACA
365795 T
1 T
365796 GATGCTTGTA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
7 1 0.03
8 3 0.08
9 1 0.03
10 4 0.10
11 1 0.03
12 3 0.08
13 27 0.68
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:369646 original size:52 final size:51
Alignment explanation
Indices: 369584--369768 Score: 228
Period size: 52 Copynumber: 3.6 Consensus size: 51
369574 AAATAACGAG
* * * *
369584 GTTGGAGTATCCTCGATTGTGGAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGAGGAAAATTGGT-GTTTTGAAAATAAAATCGGA
* * *
369636 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGG-
1 GTTGGAGTATCCCCGATT-GAGGAAAATTGGTGTTTTGAAAATAAAATCGGA
*
369687 GATTGGAGTATCCCCGATTGAGGAAAAATTAGTGTTTTGAAAATAAAATCGGA
1 G-TTGGAGTATCCCCGATTGAGG-AAAATTGGTGTTTTGAAAATAAAATCGGA
* * *
369740 GTTGGAATATCCCCGATTGTGGAGAATTG
1 GTTGGAGTATCCCCGATTGAGGAAAATTG
369769 AGAAACTCAA
Statistics
Matches: 114, Mismatches: 15, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
51 9 0.08
52 94 0.82
53 11 0.10
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGAGGAAAATTGGTGTTTTGAAAATAAAATCGGA
Found at i:372142 original size:13 final size:13
Alignment explanation
Indices: 372124--372149 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
372114 ACAAAGATCC
372124 ATGTATCGATACA
1 ATGTATCGATACA
372137 ATGTATCGATACA
1 ATGTATCGATACA
372150 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:372145 original size:33 final size:33
Alignment explanation
Indices: 372103--372169 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
372093 AAAATTTCCA
***
372103 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
372136 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
372169 A
1 A
372170 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:372213 original size:19 final size:19
Alignment explanation
Indices: 372189--372256 Score: 94
Period size: 19 Copynumber: 3.9 Consensus size: 19
372179 CAGTAGCTAA
372189 TTATGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
372208 TTATGTATCGATAC---A-
1 TTATGTATCGATACAAAAC
372223 -T-TGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
372240 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
372257 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 1 0.02
19 28 0.65
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.34
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:372229 original size:13 final size:13
Alignment explanation
Indices: 372211--372235 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
372201 ACAAAACTTA
372211 TGTATCGATACAT
1 TGTATCGATACAT
372224 TGTATCGATACA
1 TGTATCGATACA
372236 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:372233 original size:32 final size:32
Alignment explanation
Indices: 372192--372254 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
372182 TAGCTAATTA
372192 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
372224 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
372255 AATTGTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:373306 original size:59 final size:59
Alignment explanation
Indices: 373001--374234 Score: 1593
Period size: 59 Copynumber: 21.3 Consensus size: 59
372991 ATAAAGTGTA
* * * * * *
373001 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTT----G-AAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
373056 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* * **
373111 TCCTACTCTTTAAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-----AAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* * **
373166 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGTG
* *
373227 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* **
373286 TCCCGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
*
373341 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* *
373401 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* * *
373460 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGAAAATGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* * *
373519 TCCCGCTCGTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* *
373578 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
*
373637 TCCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
1 T-CCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
*
373692 TCCTGCTCTTTGAGGATTGAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* *
373746 TCCTGCTCTTTGAGGATTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* *
373805 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
*
373864 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* *
373918 TCCTGCTCTTTGAGGATTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* * *
373977 TCCTGTTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
* * * * * **
374036 TCCCGCTCTTTGAGGACTGAAGGTGCTACCAACTTGTGTGGGTTTTAAGAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
** *
374095 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
** * **
374155 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGGGGGCTTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGC-TTTAAAA-GAAAAGGTG
*
374217 TCCTGCTCTCTGAGGACT
1 TCCTGCTCTTTGAGGACT
374235 AAAAAGCGGA
Statistics
Matches: 1076, Mismatches: 69, Indels: 61
0.89 0.06 0.05
Matches are distributed among these distances:
54 148 0.14
55 189 0.18
56 3 0.00
57 1 0.00
58 2 0.00
59 482 0.45
60 196 0.18
61 30 0.03
62 25 0.02
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.27
Consensus pattern (59 bp):
TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
Found at i:373919 original size:172 final size:169
Alignment explanation
Indices: 373024--374208 Score: 1537
Period size: 172 Copynumber: 6.9 Consensus size: 169
373014 GGAGTAAAAA
* *
373024 GTGCCACCAACTCGTGTGGGCTTTG-AAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCA
1 GTGCCACCAACTTGTGTGGGCTTTGAAAAGGTGTCCTGCTCTTTGAGGACTG-AAGGTGCCACCA
* * **
373088 ACTTGTGTGGGCTTT--AAG---AGGTGTCCTACTCTTTAAGGACTGGAAAATGCCACCAACTTG
65 ACTTGTGTGGGCTTTAAAAGAAAAGGTGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTG
* *
373148 TGTGGGCTTT-AAAAGGTGTCCTGCTCTTTGGGGACTGAAAG
129 TGTGGGCTTTGAAAAGGTGTCCCGCTCTTTGAGGACTG-AAG
**
373189 GTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCC
1 GTGCCACCAACTTGTGTGGGCTTTGAAAAG-----GTGTCCTGCTCTTTGAGGACTGAAGGTGCC
* * * **
373254 ACCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAAAATGCCACCAA
61 ACCAACTTGTGTGGGCTTTAAAAGAAAAGGTGTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAA
*
373319 CTTGTGTGGGCTTTG-AAAGGTGTCCTGCTCTTTGAGGACTGAAAG
125 CTTGTGTGGGCTTTGAAAAGGTGTCCCGCTCTTTGAGGACTG-AAG
*
373364 GTGCCACCAACTTGTGTGGGCTTTGAAAGAAAAGGTGTCCCGCTCTTTGAGGACTGAAGGTGCCA
1 GTGCCACCAACTTGTGTGGGCTTT----GAAAAGGTGTCCTGCTCTTTGAGGACTGAAGGTGCCA
* *
373429 CCAACTTGTGTGGGCTTTAAAAGAAAATGTGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACT
62 CCAACTTGTGTGGGCTTTAAAAGAAAAGGTGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACT
* * *
373494 TGTATGGGCTTTAAAAGAAAATGTGTCCCGCTCGTTGAGGACTGAAG
127 TGTGTGGGCTTT----GAAAAGGTGTCCCGCTCTTTGAGGACTGAAG
* *
373541 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGTGTCCCGCTCTTTGAGGACTGAAGGTGCCA
1 GTGCCACCAACTTGTGTGGGCTTT----GAAAAGGTGTCCTGCTCTTTGAGGACTGAAGGTGCCA
* *
373606 CCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCCGCTCTTTGAGGACTGAAGGTGCCACCAAC
62 CCAACTTGTGTGGGCTTTAAAAGAAAAGGTGT-CCTGCTCTTTGAGGACTGAAGGTGCCACCAAC
* *
373671 TTGTGTGGGCTTTG-AAAGGTGTCCTGCTCTTTGAGGATTGAAG
126 TTGTGTGGGCTTTGAAAAGGTGTCCCGCTCTTTGAGGACTGAAG
*
373714 GTGCCACCAACTTGTGTGGGCTTTG-AAAGGTGTCCTGCTCTTTGAGGATTGAAGGTGCCACCAA
1 GTGCCACCAACTTGTGTGGGCTTTGAAAAGGTGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAA
*
373778 CTTGTGTGGGCTTTAAGAGAAAAGGTGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTG
66 CTTGTGTGGGCTTTAAAAGAAAAGGTGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTG
*
373843 TGGGCTTTAAGAGAAAAAGTGTCCCGCTCTTTGAGGACTGAAG
131 TGGGCTTT----GAAAAGGTGTCCCGCTCTTTGAGGACTGAAG
*
373886 GTGCCACCAACTTGTGTGGGCTTTG-AAAGGTGTCCTGCTCTTTGAGGATTGAAGGTGCCACCAA
1 GTGCCACCAACTTGTGTGGGCTTTGAAAAGGTGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAA
* *
373950 CTTGTGTGGGCTTTAAGAGAAAAGGTGTCCTGTTCTTTGAGGACTGAAGGTGCCACCAACTTGTG
66 CTTGTGTGGGCTTTAAAAGAAAAGGTGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTG
*
374015 TGGGCTTTAAGAGAAAAAGTGTCCCGCTCTTTGAGGACTGAAG
131 TGGGCTTT----GAAAAGGTGTCCCGCTCTTTGAGGACTGAAG
* * * ** **
374058 GTGCTACCAACTTGTGTGGGTTTTAAGAGAAAAAGCATCCTGCTCTTTGAGGACTAGAAAATGCC
1 GTGCCACCAACTTGTGTGGGCTTT----GAAAAGGTGTCCTGCTCTTTGAGGACT-GAAGGTGCC
* **
374123 ACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAA
61 ACCAACTTGTGTGGGCTTTAAAAGAAAAGGTGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAA
* *
374188 CTTGTGGGGGCTTTTAAAAGG
125 CTTGTGTGGGCTTTGAAAAGG
374209 AAAAGGCATC
Statistics
Matches: 930, Mismatches: 55, Indels: 60
0.89 0.05 0.06
Matches are distributed among these distances:
165 24 0.03
166 4 0.00
167 44 0.05
168 62 0.07
169 1 0.00
170 26 0.03
171 22 0.02
172 222 0.24
173 73 0.08
174 77 0.08
175 104 0.11
176 1 0.00
177 118 0.13
178 121 0.13
179 31 0.03
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (169 bp):
GTGCCACCAACTTGTGTGGGCTTTGAAAAGGTGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAA
CTTGTGTGGGCTTTAAAAGAAAAGGTGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTG
TGGGCTTTGAAAAGGTGTCCCGCTCTTTGAGGACTGAAG
Found at i:375244 original size:18 final size:19
Alignment explanation
Indices: 375223--375266 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
375213 TCTCTTTTTC
375223 TTTGTTTTATTTTTTTG-T
1 TTTGTTTTATTTTTTTGCT
*
375241 TTTGTTTTTTTTTTTTGCT
1 TTTGTTTTATTTTTTTGCT
375260 TTT-TTTT
1 TTTGTTTT
375267 TTGAAGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.86
Consensus pattern (19 bp):
TTTGTTTTATTTTTTTGCT
Found at i:375267 original size:14 final size:13
Alignment explanation
Indices: 375217--375268 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
375207 CTTTTCTCTC
*
375217 TTTTTCTTTGTTTTA
1 TTTTT-TTT-TTTTG
*
375232 TTTTTTTGTTTTG
1 TTTTTTTTTTTTG
375245 TTTTTTTTTTTTG
1 TTTTTTTTTTTTG
375258 CTTTTTTTTTT
1 -TTTTTTTTTT
375269 GAAGAGAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 16 0.48
14 12 0.36
15 5 0.15
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.87
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:375267 original size:18 final size:18
Alignment explanation
Indices: 375217--375268 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
375207 CTTTTCTCTC
* *
375217 TTTTT-CTTTGTTTTATT
1 TTTTTGCTTTTTTTTTTT
375234 TTTTTG-TTTTGTTTTTTT
1 TTTTTGCTTTT-TTTTTTT
375252 TTTTTGCTTTTTTTTTT
1 TTTTTGCTTTTTTTTTT
375269 GAAGAGAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 8 0.27
18 18 0.60
19 4 0.13
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.87
Consensus pattern (18 bp):
TTTTTGCTTTTTTTTTTT
Done.