Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold360
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: 397502
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
File 3 of 3
Found at i:290564 original size:26 final size:27
Alignment explanation
Indices: 290535--290595 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
290525 TTTAAAAATT
290535 TATTTTATTATTTA-TTATATTATTA-A
1 TATTTTATT-TTTATTTATATTATTATA
* *
290561 TATTTTATTTTTATTTTTATTTTTATA
1 TATTTTATTTTTATTTATATTATTATA
290588 TATTTTAT
1 TATTTTAT
290596 AATTAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 4 0.13
26 18 0.58
27 9 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (27 bp):
TATTTTATTTTTATTTATATTATTATA
Found at i:290636 original size:26 final size:27
Alignment explanation
Indices: 290590--290642 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
290580 TTTTTATATA
*
290590 TTTTATAATTAAATTTAAA-TTAAATT
1 TTTTATAATTAAATATAAATTTAAATT
*
290616 TTTTATTATTAAATA-ATAATTTAAATT
1 TTTTATAATTAAATATA-AATTTAAATT
290643 AAATTAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 1 0.04
26 15 0.65
27 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTTTATAATTAAATATAAATTTAAATT
Found at i:290855 original size:4 final size:4
Alignment explanation
Indices: 290848--290884 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
290838 TTTTTTTCTT
290848 TTTA TTTA TTTA TTTA TTTA -TTA -TTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
290885 GCTGAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 6 0.19
4 26 0.81
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:291181 original size:25 final size:25
Alignment explanation
Indices: 291147--291222 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 25
291137 AAAAAGTACA
*
291147 TATTTTATTAT-TGTTAGATAAATTT
1 TATTTTATTATAT-TTAAATAAATTT
291172 TATTTTATTATATTTAAATAAATTT
1 TATTTTATTATATTTAAATAAATTT
** *
291197 T-TAAT-TTATATCTAAATAAAATTT
1 TATTTTATTATATTTAAAT-AAATTT
291221 TA
1 TA
291223 ACATAAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
23 11 0.25
24 9 0.20
25 23 0.52
26 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (25 bp):
TATTTTATTATATTTAAATAAATTT
Found at i:291212 original size:23 final size:23
Alignment explanation
Indices: 291179--291223 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
291169 TTTTATTTTA
* *
291179 TTATATTTAAATAAATTTTTAAT
1 TTATATCTAAATAAAATTTTAAT
291202 TTATATCTAAATAAAATTTTAA
1 TTATATCTAAATAAAATTTTAA
291224 CATAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TTATATCTAAATAAAATTTTAAT
Found at i:292679 original size:15 final size:15
Alignment explanation
Indices: 292649--292698 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
292639 TATTTTATTT
292649 TAAT-AATTAA-TAA
1 TAATAAATTAATTAA
292662 TAATAAATTAATTAA
1 TAATAAATTAATTAA
* * *
292677 TAAAAAATTATTTTA
1 TAATAAATTAATTAA
292692 TAATAAA
1 TAATAAA
292699 CTAAACTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
13 4 0.13
14 6 0.19
15 21 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATAAATTAATTAA
Found at i:293275 original size:15 final size:15
Alignment explanation
Indices: 293255--293285 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
293245 AACAACTAAT
293255 AAATATGTTAACGTA
1 AAATATGTTAACGTA
*
293270 AAATATGTTAATGTA
1 AAATATGTTAACGTA
293285 A
1 A
293286 TAGACATACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.13, T:0.35
Consensus pattern (15 bp):
AAATATGTTAACGTA
Found at i:294253 original size:71 final size:70
Alignment explanation
Indices: 294133--294275 Score: 216
Period size: 71 Copynumber: 2.0 Consensus size: 70
294123 TTTAATTCTT
* * *
294133 AAATAAATATATCACCGCTACCTAATTCTTCTAACATGCGCTGACGCCATGCTCAATAATTTCAT
1 AAATAAATATATCACCGCTACCTAACTCTTCTAACATGCGCTGACGCCATGCTCAAAAAATTCAT
294198 AAACC
66 AAACC
* *
294203 AAATAAATAATATCACCGCTACCTAACTCTTCTAATAT-CTGCTGATGCCATGCTCAAAAAATTC
1 AAATAAAT-ATATCACCGCTACCTAACTCTTCTAACATGC-GCTGACGCCATGCTCAAAAAATTC
294267 ATAAACC
64 ATAAACC
294274 AA
1 AA
294276 TCTTATACAC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
70 9 0.14
71 57 0.86
ACGTcount: A:0.38, C:0.26, G:0.08, T:0.28
Consensus pattern (70 bp):
AAATAAATATATCACCGCTACCTAACTCTTCTAACATGCGCTGACGCCATGCTCAAAAAATTCAT
AAACC
Found at i:300523 original size:2 final size:2
Alignment explanation
Indices: 300516--300546 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
300506 GAGAGTACTT
*
300516 GA GA GA GA GA GA GA GA GA GA GA CA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
300547 GGTGGCGAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:300566 original size:35 final size:35
Alignment explanation
Indices: 300527--300596 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
300517 AGAGAGAGAG
*
300527 AGAGAGAGAGACAGAGAGAGGGTGGCGAGGGGTTC
1 AGAGAGAGACACAGAGAGAGGGTGGCGAGGGGTTC
*
300562 AGAGAGAGACAGAGAGAGAGGGTGGCGAGGGGTTC
1 AGAGAGAGACACAGAGAGAGGGTGGCGAGGGGTTC
300597 GGTGTGGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.31, C:0.09, G:0.51, T:0.09
Consensus pattern (35 bp):
AGAGAGAGACACAGAGAGAGGGTGGCGAGGGGTTC
Found at i:301079 original size:42 final size:41
Alignment explanation
Indices: 300957--301093 Score: 161
Period size: 41 Copynumber: 3.3 Consensus size: 41
300947 TTTCTTATTA
* * * *
300957 AAAAATATTTCATATTAAACATGAATTACCATCTAAAAAAT
1 AAAAATATTTTATATTAAACATAAATTATCATTTAAAAAAT
300998 AAAAATATTTTATATTAAACATAAATTATCATTTAAAAAAT
1 AAAAATATTTTATATTAAACATAAATTATCATTTAAAAAAT
* *
301039 AAAAATTATTTTATGTTAAATC-TCAAATTATTATTT-AAAAAT
1 AAAAA-TATTTTATATTAAA-CAT-AAATTATCATTTAAAAAAT
*
301081 AATAAAAATTTTA
1 AA-AAATATTTTA
301094 AAAAATATTC
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
41 42 0.49
42 28 0.33
43 15 0.18
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.39
Consensus pattern (41 bp):
AAAAATATTTTATATTAAACATAAATTATCATTTAAAAAAT
Found at i:301099 original size:55 final size:54
Alignment explanation
Indices: 301038--301513 Score: 470
Period size: 53 Copynumber: 8.8 Consensus size: 54
301028 ATTTAAAAAA
* * *
301038 TAAAAATTATTTTATGTTAAATCTCAAATTATTATTTAAAAATAATAAAAATTT
1 TAAAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAAATTT
* * *
301092 TAAAAAATATTCTATATTAAATCCCAAATTACCATTTAAACAATAATAAAAATTT
1 TAAAAAATATTTTATATTAAATCTCAAATTACTATTTAAA-AATAATAAAAATTT
* *
301147 TAAAAAAAATATTTTATACTAAA-CTCCATATTACTATTTAAAAATAATAAAAATTTT
1 T--AAAAAATATTTTATATTAAATCT-CAAATTACTATTTAAAAATAATAAAAA-TTT
* * * ** * **
301204 TTAAAAATATTTTATATCAAATTTTGAATTATTATCCAAAAATAATAAATAATTT
1 TAAAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAA-AATTT
* ** *
301259 T-AAAAATA-TTTATATTAAATTTTGAATTAGTATTT-AAAATAAT-AAAATTT
1 TAAAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAAATTT
* * * *
301309 AAAAAAATATTTAAT-TTAAATATCGAATTACTATTTAAAAATAATAAAAATTT
1 TAAAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAAATTT
* * * *
301362 T-AAAAATATTTTATATTAAATTTAAAATTATTATTTAAAAATAA-AAAAA-AT
1 TAAAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAAATTT
* *
301413 AAAAAATATATTTTATATTAAATCTCGAATTACTATTTAAAAGATAATAAAAA--T
1 TAAAAA-ATATTTTATATTAAATCTCAAATTACTATTTAAAA-ATAATAAAAATTT
** * *
301467 TAATATGTATGTATTTATATTAAATCTTAAATTACTATTTAAAAATA
1 TAA-A-AAATAT-TTTATATTAAATCTCAAATTACTATTTAAAAATA
301514 TTTTATATTA
Statistics
Matches: 355, Mismatches: 48, Indels: 37
0.81 0.11 0.08
Matches are distributed among these distances:
50 5 0.01
51 28 0.08
52 41 0.12
53 86 0.24
54 48 0.14
55 67 0.19
56 44 0.12
57 36 0.10
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (54 bp):
TAAAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAATAAAAATTT
Found at i:301394 original size:157 final size:159
Alignment explanation
Indices: 301038--301469 Score: 514
Period size: 157 Copynumber: 2.7 Consensus size: 159
301028 ATTTAAAAAA
* * *
301038 TAAAAATTATTTTATGTTAAATCTCAAATTATTATTTAAAAATAATAAAAATTTTAAAAAATATT
1 TAAAAA-TATTTTATATTAAATTTAAAATTATTATTTAAAAATAATAAAAATTTT-AAAAATATT
* * * *
301103 CTATATTAAATCCCAAATTACCATTTAAACAATAATAAAAATTTTAAAAAAAATATTTTATACTA
64 -TATATTAAATCTCGAATTACTATTTAAA-AATAAT-AAAA-TTT-AAAAAAATATTTAATACTA
*
301168 AACTCCATATTACTATTTAAAAATAATAAAAATTTTT
124 AAATCCATATTACTATTTAAAAATAATAAAAA-TTTT
* ** **
301205 TAAAAATATTTTATATCAAATTTTGAATTATTATCCAAAAATAATAAATAATTTTAAAAATATTT
1 TAAAAATATTTTATATTAAATTTAAAATTATTATTTAAAAATAATAAA-AATTTTAAAAATATTT
* * * *
301270 ATATTAAATTTTGAATTAGTATTT-AAAATAATAAAATTTAAAAAAATATTTAAT-TTAAATATC
65 ATATTAAATCTCGAATTACTATTTAAAAATAATAAAATTTAAAAAAATATTTAATACTAAA-ATC
*
301333 GA-ATTACTATTTAAAAATAATAAAAA-TTT
129 CATATTACTATTTAAAAATAATAAAAATTTT
* **
301362 TAAAAATATTTTATATTAAATTTAAAATTATTATTTAAAAATAA-AAAAAATAAAAAATATATTT
1 TAAAAATATTTTATATTAAATTTAAAATTATTATTTAAAAATAATAAAAATTTTAAAA-ATA-TT
*
301426 TATATTAAATCTCGAATTACTATTTAAAAGATAATAAAAATTAA
64 TATATTAAATCTCGAATTACTATTTAAAA-ATAATAAAATTTAA
301470 TATGTATGTA
Statistics
Matches: 230, Mismatches: 29, Indels: 20
0.82 0.10 0.07
Matches are distributed among these distances:
155 7 0.03
156 6 0.03
157 66 0.29
158 3 0.01
159 41 0.18
160 17 0.07
161 3 0.01
162 4 0.02
163 6 0.03
164 2 0.01
165 19 0.08
166 44 0.19
167 12 0.05
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (159 bp):
TAAAAATATTTTATATTAAATTTAAAATTATTATTTAAAAATAATAAAAATTTTAAAAATATTTA
TATTAAATCTCGAATTACTATTTAAAAATAATAAAATTTAAAAAAATATTTAATACTAAAATCCA
TATTACTATTTAAAAATAATAAAAATTTT
Found at i:301521 original size:91 final size:86
Alignment explanation
Indices: 301415--301600 Score: 228
Period size: 86 Copynumber: 2.1 Consensus size: 86
301405 AAAAAAATAA
* ** *
301415 AAAATATATTTTATATTAAATCTCGAATTACTATTTAAAAGATAATAAAAATTAATATGTATGTA
1 AAAA-ATATTTTATATTAAATCTCGAATTA-TATTTAAAAAATAA-AAAAA-TAA-AAATATAT-
301480 TTTATATTAAATCTTAAATTACTATTT
60 TTTATATTAAATCTTAAATTACTATTT
* * * *
301507 AAAAATATTTTATATTAAATCTTGATTTATTTTTAAAAAATAACAAAATAAAAATATATTTTATA
1 AAAAATATTTTATATTAAATCTCGAATTATATTTAAAAAATAAAAAAATAAAAATATATTTTATA
*
301572 TTAAATTTTAAATTACTATTT
66 TTAAATCTTAAATTACTATTT
301593 AAATAATA
1 AAA-AATA
301601 ATAATAAATT
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
86 29 0.35
87 9 0.11
88 3 0.04
89 4 0.05
90 12 0.14
91 23 0.27
92 4 0.05
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (86 bp):
AAAAATATTTTATATTAAATCTCGAATTATATTTAAAAAATAAAAAAATAAAAATATATTTTATA
TTAAATCTTAAATTACTATTT
Found at i:301710 original size:51 final size:50
Alignment explanation
Indices: 301507--301768 Score: 158
Period size: 51 Copynumber: 5.1 Consensus size: 50
301497 ATTACTATTT
* ** * * *
301507 AAAAATATTTTATATTAAATCTTGATTTAT-TTTTAAAA-AATAACAAAATA
1 AAAAATATTTTATAAT-AATCTAAATTAATATTTAAAAATAATAA-AAATTA
* * * *
301557 AAAATATATTTTATATTAAATTTTAAATTACTATTTAAATAATAATAATAAATTTT
1 AAAA-ATATTTTATAAT-AA-TCTAAATTAATATTTAAA-AATAATAA-AAA-TTA
* * * * *
301613 AAAAATATTTCGTATTA-AATCTCAAATTATTTTTTAAATAT-TTAAAAATTA
1 AAAAATATTT--TATAATAATCT-AAATTAATATTTAAAAATAATAAAAATTA
301664 AAAAATATTTTATAATAATCTAGAATTAATATTTAAAAATAATAAAAAATTA
1 AAAAATATTTTATAATAATCTA-AATTAATATTTAAAAATAAT-AAAAATTA
* * * * * * *
301716 AAATATGTTATATCAA-ATTATAAATTACTTTTTAAAAA-AATAAAAATTA
1 AAAAATATTTTAT-AATAATCTAAATTAATATTTAAAAATAATAAAAATTA
301765 AAAA
1 AAAA
301769 TGGTTTACAT
Statistics
Matches: 168, Mismatches: 30, Indels: 29
0.74 0.13 0.13
Matches are distributed among these distances:
49 16 0.10
50 26 0.15
51 42 0.25
52 31 0.18
53 10 0.06
54 6 0.04
55 29 0.17
56 5 0.03
57 3 0.02
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (50 bp):
AAAAATATTTTATAATAATCTAAATTAATATTTAAAAATAATAAAAATTA
Found at i:305063 original size:13 final size:13
Alignment explanation
Indices: 305045--305069 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
305035 GTAAGATTAG
305045 TGTATCGATACAA
1 TGTATCGATACAA
305058 TGTATCGATACA
1 TGTATCGATACA
305070 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:305146 original size:19 final size:18
Alignment explanation
Indices: 305122--305186 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
305112 AACTGTACAT
305122 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAA-TTA
305141 TGTATCGATAC---A-T-
1 TGTATCGATACAAAATTA
305154 TGTATCGATACAACAATTA
1 TGTATCGATACAA-AATTA
305173 TGTATCGATACAAA
1 TGTATCGATACAAA
305187 TCGTTGAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 1 0.03
17 1 0.03
18 2 0.05
19 24 0.60
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (18 bp):
TGTATCGATACAAAATTA
Found at i:305158 original size:32 final size:32
Alignment explanation
Indices: 305117--305184 Score: 120
Period size: 32 Copynumber: 2.1 Consensus size: 32
305107 TTCGTAACTG
305117 TACATTGTATCGATACAA-AACTTATGTATCGA
1 TACATTGTATCGATACAACAA-TTATGTATCGA
305149 TACATTGTATCGATACAACAATTATGTATCGA
1 TACATTGTATCGATACAACAATTATGTATCGA
305181 TACA
1 TACA
305185 AATCGTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 33 0.94
33 2 0.06
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (32 bp):
TACATTGTATCGATACAACAATTATGTATCGA
Found at i:305159 original size:13 final size:13
Alignment explanation
Indices: 305141--305165 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
305131 ACAAAACTTA
305141 TGTATCGATACAT
1 TGTATCGATACAT
305154 TGTATCGATACA
1 TGTATCGATACA
305166 ACAATTATGT
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:306369 original size:22 final size:22
Alignment explanation
Indices: 306341--306383 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
306331 GGGGTTGTTT
*
306341 CAGTTAAAGTTATATATACATC
1 CAGTTAAAATTATATATACATC
*
306363 CAGTTAAAATTATATGTACAT
1 CAGTTAAAATTATATATACAT
306384 TAGTTATAGT
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:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (22 bp):
CAGTTAAAATTATATATACATC
Found at i:306649 original size:22 final size:22
Alignment explanation
Indices: 306593--306649 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
306583 ATGAAAAGTT
*
306593 ATATGTATATTCAGTTAAAATC
1 ATATGTATATTTAGTTAAAATC
** *
306615 ATATGTACGTTTAGTTATAATC
1 ATATGTATATTTAGTTAAAATC
306637 ATATGTATATTTA
1 ATATGTATATTTA
306650 ATTTTATTCG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.46
Consensus pattern (22 bp):
ATATGTATATTTAGTTAAAATC
Found at i:306971 original size:22 final size:22
Alignment explanation
Indices: 306917--306963 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
306907 TAAAGTCATA
* * *
306917 TATATTCAGTTATAATTATATG
1 TATATACAATTATAATCATATG
306939 TATATACAATTATAATCATATG
1 TATATACAATTATAATCATATG
306961 TAT
1 TAT
306964 GTTTAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.47
Consensus pattern (22 bp):
TATATACAATTATAATCATATG
Found at i:307126 original size:51 final size:50
Alignment explanation
Indices: 307060--307309 Score: 297
Period size: 52 Copynumber: 4.9 Consensus size: 50
307050 GTTTTAAATT
* * * *
307060 TTTTTAAATAGTAATTCAGGACTTAATATAAATTTTTTTATTTTTTTATTA
1 TTTTTAAAGAGTAATTCAAGATTTAATATAAATATTTTTA-TTTTTTATTA
* * * *
307111 TTTTTAAACAATAATTTAAGATTTAATATAAAATATTTTTAAATTTTTATTA
1 TTTTTAAAGAGTAATTCAAGATTTAATAT-AAATATTTTT-ATTTTTTATTA
* * *
307163 TCTTTAAATAGTAATTCAAGATTTAATATAAATATATTTTTAATTTTTATTA
1 TTTTTAAAGAGTAATTCAAGATTTAATAT-AA-ATATTTTTATTTTTTATTA
* *
307215 TTTTTAAAGAGTAATTCAAGATTTAATAAAAAATATTTTCATTTTTTATTA
1 TTTTTAAAGAGTAATTCAAGATTTAAT-ATAAATATTTTTATTTTTTATTA
* *
307266 -TTTT-AAGAGTAATTCAAGATTTAATAAAAATATTTTAATTTTTT
1 TTTTTAAAGAGTAATTCAAGATTTAATATAAATATTTTTATTTTTT
307310 TTTACTATTT
Statistics
Matches: 178, Mismatches: 17, Indels: 11
0.86 0.08 0.05
Matches are distributed among these distances:
48 18 0.10
49 21 0.12
50 4 0.02
51 41 0.23
52 84 0.47
53 10 0.06
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (50 bp):
TTTTTAAAGAGTAATTCAAGATTTAATATAAATATTTTTATTTTTTATTA
Found at i:307217 original size:104 final size:102
Alignment explanation
Indices: 307061--307308 Score: 337
Period size: 103 Copynumber: 2.5 Consensus size: 102
307051 TTTTAAATTT
* * *
307061 TTTTAAATAGTAATTCAGGACTTAATATAAAT-T-TTTTTATTTTTTTATTATTTTTAAACAATA
1 TTTTAAATAGTAATTCAAGATTTAATATAAATATATTTTTA-ATTTTTATTATTTTTAAACAATA
* *
307124 ATTTAAGATTTAATATAAAATATTTTTAAATTTTTATTA
65 ATTCAAGATTTAATAAAAAATA-TTTTAAATTTTTATTA
* *
307163 TCTTTAAATAGTAATTCAAGATTTAATATAAATATATTTTTAATTTTTATTATTTTTAAAGAGTA
1 T-TTTAAATAGTAATTCAAGATTTAATATAAATATATTTTTAATTTTTATTATTTTTAAACAATA
* *
307228 ATTCAAGATTTAATAAAAAATATTTTCATTTTTTATTA
65 ATTCAAGATTTAATAAAAAATATTTTAAATTTTTATTA
*
307266 TTTT-AAGAGTAATTCAAGATTTAATA-AAA-ATA-TTTTAATTTTT
1 TTTTAAATAGTAATTCAAGATTTAATATAAATATATTTTTAATTTTT
307309 TTTTACTATT
Statistics
Matches: 133, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
98 11 0.08
99 3 0.02
100 3 0.02
101 21 0.16
102 4 0.03
103 44 0.33
104 41 0.31
105 6 0.05
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (102 bp):
TTTTAAATAGTAATTCAAGATTTAATATAAATATATTTTTAATTTTTATTATTTTTAAACAATAA
TTCAAGATTTAATAAAAAATATTTTAAATTTTTATTA
Found at i:307619 original size:51 final size:54
Alignment explanation
Indices: 307481--307702 Score: 213
Period size: 50 Copynumber: 4.3 Consensus size: 54
307471 ATAATAAACT
* *
307481 ATTTTATTA-TATTTTAAATAGTCAGTTGAG-ATTTAATATAAAA-AT-ATTTTTA
1 ATTTT-TTATTATTTTAAATAGTAATTTGAGTATTTAATATAAAATATGA-TTTTA
* * *
307533 AATTTTTATTATTTTTAAATCA-TAA-TT-AATATTTAAGATAAAATATGGATTTTA
1 ATTTTTTATTA-TTTTAAAT-AGTAATTTGAGTATTTAATATAAAATAT-GATTTTA
307587 A-TTTTT-TT-TTTTAAATAGTAATTTG-GTATTTAATAT-AAA-AT-ATTTTA
1 ATTTTTTATTATTTTAAATAGTAATTTGAGTATTTAATATAAAATATGATTTTA
* *
307634 ATTTTTTATTATTTTAAATAGTAATTTGAG-ATTTAATATAAAATATGCTTTTCT
1 ATTTTTTATTATTTTAAATAGTAATTTGAGTATTTAATATAAAATATGATTTT-A
*
307688 TTTTTTTATTATTTT
1 ATTTTTTATTATTTT
307703 TAATTAACAA
Statistics
Matches: 143, Mismatches: 9, Indels: 34
0.77 0.05 0.18
Matches are distributed among these distances:
47 7 0.05
48 5 0.03
49 5 0.03
50 40 0.28
51 19 0.13
52 24 0.17
53 21 0.15
54 21 0.15
55 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (54 bp):
ATTTTTTATTATTTTAAATAGTAATTTGAGTATTTAATATAAAATATGATTTTA
Found at i:307694 original size:101 final size:103
Alignment explanation
Indices: 307492--307680 Score: 262
Period size: 101 Copynumber: 1.9 Consensus size: 103
307482 TTTTATTATA
*
307492 TTTTAAATAGTCAGTTGAGATTTAATATAAAAATATTTTTAAATTTTTATTATTTTTAAATCATA
1 TTTTAAATAGTAAGTTGAGATTTAATATAAAAATATTTTTAAATTTTTATTATTTTTAAATCATA
*
307557 ATTAATATTTAAGATAAAATATGGATTTTAATTTTTTT
66 ATTAAGATTTAAGATAAAATATGGATTTTAATTTTTTT
* *
307595 TTTTAAATAGTAATTTG-GTATTTAATAT-AAAATA-TTTTAATTTTTTATTA-TTTTAAAT-AG
1 TTTTAAATAGTAAGTTGAG-ATTTAATATAAAAATATTTTTAAATTTTTATTATTTTTAAATCA-
* *
307655 TAATTTGAGATTTAATATAAAATATG
64 TAA-TTAAGATTTAAGATAAAATATG
307681 CTTTTCTTTT
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
99 1 0.01
100 11 0.14
101 34 0.44
102 7 0.09
103 24 0.31
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.51
Consensus pattern (103 bp):
TTTTAAATAGTAAGTTGAGATTTAATATAAAAATATTTTTAAATTTTTATTATTTTTAAATCATA
ATTAAGATTTAAGATAAAATATGGATTTTAATTTTTTT
Found at i:310145 original size:2 final size:2
Alignment explanation
Indices: 310138--310170 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
310128 TGCAAGTAAA
*
310138 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
310171 AAAAATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:310482 original size:4 final size:4
Alignment explanation
Indices: 310473--310515 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
310463 GATTTGAATT
* * * *
310473 ATAA ATAA ATAT ATAA ATAT ATAA ATAT ATAA ATAT ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
310516 TATATATATA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (4 bp):
ATAA
Found at i:310494 original size:2 final size:2
Alignment explanation
Indices: 310481--310531 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
310471 TTATAAATAA
* * * *
310481 AT AT AT AA AT AT AT AA AT AT AT AA AT AT AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
310523 AT AT AT AT A
1 AT AT AT AT A
310532 AGCACTAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:310531 original size:8 final size:8
Alignment explanation
Indices: 310477--310527 Score: 93
Period size: 8 Copynumber: 6.4 Consensus size: 8
310467 TGAATTATAA
310477 ATAAATAT
1 ATAAATAT
310485 ATAAATAT
1 ATAAATAT
310493 ATAAATAT
1 ATAAATAT
310501 ATAAATAT
1 ATAAATAT
310509 ATAAATAT
1 ATAAATAT
*
310517 ATATATAT
1 ATAAATAT
310525 ATA
1 ATA
310528 TATAAGCACT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
8 42 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATAAATAT
Found at i:316102 original size:44 final size:43
Alignment explanation
Indices: 316053--316137 Score: 152
Period size: 44 Copynumber: 2.0 Consensus size: 43
316043 GTATCGATGC
*
316053 ATTGAAGAATGTATCGATACATTTGGTTCAAAAACCCAGAATAT
1 ATTGAAGAATGTATCGATACATTTGGGTC-AAAACCCAGAATAT
316097 ATTGAAGAATGTATCGATACATTTGGGTCAAAACCCAGAAT
1 ATTGAAGAATGTATCGATACATTTGGGTCAAAACCCAGAAT
316138 GTATCGATAC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 12 0.30
44 28 0.70
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (43 bp):
ATTGAAGAATGTATCGATACATTTGGGTCAAAACCCAGAATAT
Found at i:321948 original size:31 final size:31
Alignment explanation
Indices: 321913--322001 Score: 115
Period size: 31 Copynumber: 2.9 Consensus size: 31
321903 CAGCTTCCAA
* *
321913 CAGCTCGATCTTCTTCAAGCTTCCACGCCAG
1 CAGCTCGAGCCTCTTCAAGCTTCCACGCCAG
* **
321944 CAGCTCGAGCCTCTTCTAGCTTCCACGGTAG
1 CAGCTCGAGCCTCTTCAAGCTTCCACGCCAG
* *
321975 TAGCTCGAGCCTCTTCCAGCTTCCACG
1 CAGCTCGAGCCTCTTCAAGCTTCCACG
322002 AACACAGCAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.17, C:0.38, G:0.19, T:0.26
Consensus pattern (31 bp):
CAGCTCGAGCCTCTTCAAGCTTCCACGCCAG
Found at i:322020 original size:21 final size:21
Alignment explanation
Indices: 321991--322060 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
321981 GAGCCTCTTC
*
321991 CAGCTTCCACGAACACAGCAG
1 CAGCATCCACGAACACAGCAG
*
322012 CAGCATCCACGAGCATGACAGCAG
1 CAGCATCCACGA--A-CACAGCAG
* *
322036 TAGTATCCACGAACACAGCAG
1 CAGCATCCACGAACACAGCAG
322057 CAGC
1 CAGC
322061 TCGAGCCTCT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
21 20 0.51
22 1 0.03
23 1 0.03
24 17 0.44
ACGTcount: A:0.34, C:0.34, G:0.21, T:0.10
Consensus pattern (21 bp):
CAGCATCCACGAACACAGCAG
Found at i:322057 original size:24 final size:23
Alignment explanation
Indices: 321996--322059 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
321986 TCTTCCAGCT
321996 TCCACGAACACAGCAGC--AGCA
1 TCCACGAACACAGCAGCAGAGCA
* * *
322017 TCCACGAGCA-TGACAGCAGTAGTA
1 TCCACGAACACAG-CAGCAG-AGCA
322041 TCCACGAACACAGCAGCAG
1 TCCACGAACACAGCAGCAG
322060 CTCGAGCCTC
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
20 1 0.03
21 13 0.39
24 18 0.55
25 1 0.03
ACGTcount: A:0.36, C:0.33, G:0.22, T:0.09
Consensus pattern (23 bp):
TCCACGAACACAGCAGCAGAGCA
Found at i:322170 original size:32 final size:32
Alignment explanation
Indices: 322108--322171 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
322098 CCACGAGCAC
**
322108 TCCAACAGCGACAACATCCACTAACAGTAGCT
1 TCCAACAGCGACAACATAAACTAACAGTAGCT
* *
322140 TCCAGCAGCGACAACATTAAAC-AACGGTAGCT
1 TCCAACAGCGACAACA-TAAACTAACAGTAGCT
322172 CTAGCAATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 24 0.89
33 3 0.11
ACGTcount: A:0.38, C:0.31, G:0.16, T:0.16
Consensus pattern (32 bp):
TCCAACAGCGACAACATAAACTAACAGTAGCT
Found at i:322959 original size:13 final size:13
Alignment explanation
Indices: 322941--322988 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
322931 AGTAAAATTT
322941 TAAAAAAATATAA
1 TAAAAAAATATAA
322954 T-AAAAAATAATAA
1 TAAAAAAAT-ATAA
*
322967 CAAAATAAA-ATAA
1 TAAAA-AAATATAA
322980 TAAAAAAAT
1 TAAAAAAAT
322989 CTTTTCATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 10 0.34
13 13 0.45
14 3 0.10
15 3 0.10
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (13 bp):
TAAAAAAATATAA
Found at i:322978 original size:16 final size:16
Alignment explanation
Indices: 322957--322988 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
322947 AATATAATAA
*
322957 AAAATAATAACAAAAT
1 AAAATAATAAAAAAAT
322973 AAAATAATAAAAAAAT
1 AAAATAATAAAAAAAT
322989 CTTTTCATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAATAATAAAAAAAT
Found at i:327467 original size:22 final size:23
Alignment explanation
Indices: 327423--327467 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
327413 ATATTCATGG
*
327423 CATTCATTCAACATTTTCATAAT
1 CATTCATTCAACATTTGCATAAT
* *
327446 CATTCA-TCAATATTTGCCTAAT
1 CATTCATTCAACATTTGCATAAT
327468 TCAAATTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.33, C:0.22, G:0.02, T:0.42
Consensus pattern (23 bp):
CATTCATTCAACATTTGCATAAT
Found at i:335629 original size:42 final size:42
Alignment explanation
Indices: 335582--336510 Score: 961
Period size: 42 Copynumber: 22.2 Consensus size: 42
335572 CATTAAACTT
* * *
335582 CTGAAGACTTTCCTTTCCTTAGTCTACCTGTCGACTTTGACC
1 CTGAAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * * * *
335624 CTGAAGACTTTCCTTTCCTTAGTCTACCTATTGGCTGTGACC
1 CTGAAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* *
335666 CTGAAGACTTTCCTACCCTTAGTCTGTCTGTCGGCTTTGACC
1 CTGAAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* *
335708 CTAGAA-ACTTTTCTTCCCTTAGTTTGCCTGTCGGCTTTGACC
1 CT-GAAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * *
335750 TTGAAGACTTTCCTTCCCTTAGTCTGCTTGTCGGTTTTGACC
1 CTGAAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
*
335792 CT-AGAGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACC
1 CTGA-AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * *
335834 CTGGAGACTTTTCTTCCCTTATTCTGCCTGTCGGCTTTGACC
1 CTGAAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* *
335876 CT-AGAGACTTTCCTTCCCTTAGTCTGCTTGTCGGCTTTGATC
1 CTGA-AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* *
335918 CT-AGAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTAACT
1 CTGA-AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * ** *
335960 TTGGAGACTTTTTTTCCTTTAGTCTGCCTGTCGGCTTTGACC
1 CTGAAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * *
336002 CT-AGAGACTTTCCTACCCTTAGTCTGCCTTTCAGCTTTGACC
1 CTGA-AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * * * * *
336044 TTGGAGACTTTTCTTCCCTTAATCTGCATGTCGTCTTTGA-C
1 CTGAAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * * *
336085 CTCAAAGACTTTTCTTCCCTTAGTTTGCTTGTCGGCTTTGACC
1 CT-GAAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * *
336128 CT-AGAGACTTTTCTACCCTTAGTCTGCCTATCGGCTTTGA-C
1 CTGA-AGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * * *
336169 CTGGAGACTTTCTTTCCCTTAGTCTGCTTGTTGGCTTTGACC
1 CTGAAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* *
336211 TTGAAGACTTT-CTTACCCTTAGTCTGCTTGTCGGCTTTGACC
1 CTGAAGACTTTCCTT-CCCTTAGTCTGCCTGTCGGCTTTGACC
* *
336253 CT--AGACTTTCCTACCCTCAGTCTGCCTGTCGGCTTTGACC
1 CTGAAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * * * **
336293 TTGGAGACTTT-CTTACCCTGAGTCTACCTGTCAACTTTGACC
1 CTGAAGACTTTCCTT-CCCTTAGTCTGCCTGTCGGCTTTGACC
* *
336335 CTGAAGACTTTCCTTCCCTCAGTCTGCCCGTCGGC-TTGACC
1 CTGAAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * * * * * *
336376 TTGGAGATTTTTCTACCCTTAGTCTCCCTATCGGCTTTGACC
1 CTGAAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
* * * * *
336418 TTGGAGACTTT-TTTACCCTTAGCCTACCTGTCGG-TCTTGACC
1 CTGAAGACTTTCCTT-CCCTTAGTCTGCCTGTCGGCT-TTGACC
* * * * *
336460 CTGGAGACTTTTCTACCCTCAGTCTGCCTGTTGGCTTTGACC
1 CTGAAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
336502 CTGAAGACT
1 CTGAAGACT
336511 GCCTTATCTA
Statistics
Matches: 740, Mismatches: 123, Indels: 48
0.81 0.14 0.05
Matches are distributed among these distances:
40 33 0.04
41 80 0.11
42 616 0.83
43 11 0.01
ACGTcount: A:0.14, C:0.30, G:0.18, T:0.38
Consensus pattern (42 bp):
CTGAAGACTTTCCTTCCCTTAGTCTGCCTGTCGGCTTTGACC
Found at i:337030 original size:31 final size:30
Alignment explanation
Indices: 336986--337057 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
336976 TTTATTTGAT
*
336986 ATAAAATATAATAATAGTAGAAATTAA-A-AA
1 ATAAAA-A-AATAATAATAGAAATTAATAGAA
*
337016 TTAAAAAAATAATAATAGAAATTAATAGAA
1 ATAAAAAAATAATAATAGAAATTAATAGAA
337046 ATAAAAAAATAA
1 ATAAAAAAATAA
337058 AAAAAATCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 17 0.46
29 2 0.05
30 18 0.49
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (30 bp):
ATAAAAAAATAATAATAGAAATTAATAGAA
Found at i:337727 original size:31 final size:31
Alignment explanation
Indices: 337679--337765 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 31
337669 ACCAACTTCC
* *
337679 AGCAGCTTGAGCTTCTTCCAGCTTTCAC-GCT
1 AGCAGCTCGAGCCTCTTCCAGCTTTCACAG-T
*
337710 AGCAGCTCGAGCCTCTTCCAGCTTCCACAGT
1 AGCAGCTCGAGCCTCTTCCAGCTTTCACAGT
* *
337741 AGTAGCTCCAGCCTCTTCCAG-TTTC
1 AGCAGCTCGAGCCTCTTCCAGCTTTC
337766 CACGAACACA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
30 3 0.06
31 45 0.92
32 1 0.02
ACGTcount: A:0.17, C:0.36, G:0.18, T:0.29
Consensus pattern (31 bp):
AGCAGCTCGAGCCTCTTCCAGCTTTCACAGT
Found at i:338137 original size:29 final size:29
Alignment explanation
Indices: 338095--338153 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
338085 CAAAGAAGAA
338095 AAACGATAATGGTAGACATCAAGGTTAAC
1 AAACGATAATGGTAGACATCAAGGTTAAC
*
338124 AAACGGTAATGGTAGACATCAAGGTTAAC
1 AAACGATAATGGTAGACATCAAGGTTAAC
338153 A
1 A
338154 TATTTAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (29 bp):
AAACGATAATGGTAGACATCAAGGTTAAC
Found at i:341121 original size:98 final size:96
Alignment explanation
Indices: 340920--341097 Score: 227
Period size: 98 Copynumber: 1.9 Consensus size: 96
340910 TATTATATTA
340920 AAAAAATACAAACATGATAGCCAGATCTGATTTTAAACAACTCATCCAAGAAAAAAGAATGCCAC
1 AAAAAATACAAACATGATAGCCAGATCTGATTTTAAACAA--CATCCAAGAAAAAAGAATGCCAC
* * ** * * **
340985 CTTAATATAATATCATAAACATGATATTATATT
64 CTTAATATAAGAGCATAAACAACAAATCATAAC
*
341018 AAAAAATACAAACATGATAGCCAGATCTGATTTTAAACAA-ATCCAAGGAAAAAGAATGCCACCT
1 AAAAAATACAAACATGATAGCCAGATCTGATTTTAAACAACATCCAAGAAAAAAGAATGCCACCT
341082 TAA-A-ACAGAGCATAAA
66 TAATATA-AGAGCATAAA
341098 ACGCAACAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
93 1 0.01
94 9 0.12
95 26 0.34
98 40 0.53
ACGTcount: A:0.51, C:0.17, G:0.10, T:0.22
Consensus pattern (96 bp):
AAAAAATACAAACATGATAGCCAGATCTGATTTTAAACAACATCCAAGAAAAAAGAATGCCACCT
TAATATAAGAGCATAAACAACAAATCATAAC
Found at i:342256 original size:20 final size:20
Alignment explanation
Indices: 342233--342273 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
342223 AAATATTTTA
342233 TTTATAAAT-TAATAAAAAAT
1 TTTA-AAATATAATAAAAAAT
*
342253 TTTAAAATATTATAAAAAAT
1 TTTAAAATATAATAAAAAAT
342273 T
1 T
342274 ATTTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTAAAATATAATAAAAAAT
Found at i:344195 original size:6 final size:6
Alignment explanation
Indices: 344184--344211 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
344174 GTAAAATATA
344184 ATAATT ATAATT ATAATT ATAATT ATAA
1 ATAATT ATAATT ATAATT ATAATT ATAA
344212 AAAAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
ATAATT
Found at i:344249 original size:20 final size:20
Alignment explanation
Indices: 344204--344250 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
344194 TTATAATTAT
*
344204 AATTATAAAAAAATTTAATG
1 AATTTTAAAAAAATTTAATG
* *
344224 ATTTTTAAAATAATTT-ATG
1 AATTTTAAAAAAATTTAATG
344243 AAATTTTA
1 -AATTTTA
344251 TAATTATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
AATTTTAAAAAAATTTAATG
Found at i:344530 original size:6 final size:6
Alignment explanation
Indices: 344519--344546 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
344509 TTGTATTGCT
344519 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
344547 AAAAATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:344861 original size:13 final size:13
Alignment explanation
Indices: 344843--344871 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
344833 ATAATTAACG
344843 ATAAATTTTTAAT
1 ATAAATTTTTAAT
344856 ATAAATTTTTAAT
1 ATAAATTTTTAAT
344869 ATA
1 ATA
344872 TTTATAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATAAATTTTTAAT
Found at i:345938 original size:11 final size:11
Alignment explanation
Indices: 345915--345947 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
345905 TTTTTTATTT
345915 ATTTAAA-TAA
1 ATTTAAATTAA
345925 ATTTAAATTAA
1 ATTTAAATTAA
345936 ATTTAAATTAA
1 ATTTAAATTAA
345947 A
1 A
345948 AATATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 7 0.32
11 15 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATTTAAATTAA
Found at i:346786 original size:21 final size:21
Alignment explanation
Indices: 346762--346802 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
346752 AAATATATAT
*
346762 TAATATAATTATTATAAAAAA
1 TAATATAAATATTATAAAAAA
*
346783 TAATATAAATATTGTAAAAA
1 TAATATAAATATTATAAAAA
346803 TTATTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
TAATATAAATATTATAAAAAA
Found at i:346801 original size:57 final size:57
Alignment explanation
Indices: 346695--346802 Score: 132
Period size: 57 Copynumber: 1.9 Consensus size: 57
346685 AATATAATTA
* * *
346695 AAATATATATTTTAAAATTTATATAACAAATAATTATTAATATGTTAAAAACTTTAT
1 AAATATATATTATAAAATTTATATAAAAAATAATTATAAATATGTTAAAAACTTTAT
*
346752 AAATATATATTAATATAA-TTATTATAAAAAATAA-TATAAATAT-TGTAAAAA
1 AAATATATATT-ATAAAATTTA-TATAAAAAATAATTATAAATATGT-TAAAAA
346803 TTATTAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
56 1 0.02
57 28 0.64
58 15 0.34
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (57 bp):
AAATATATATTATAAAATTTATATAAAAAATAATTATAAATATGTTAAAAACTTTAT
Found at i:347147 original size:14 final size:14
Alignment explanation
Indices: 347128--347159 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
347118 TAGATATTTA
347128 AAAATATTAAAATT
1 AAAATATTAAAATT
347142 AAAATATTAAAATT
1 AAAATATTAAAATT
347156 AAAA
1 AAAA
347160 AATAAGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATATTAAAATT
Found at i:347540 original size:32 final size:32
Alignment explanation
Indices: 347445--347542 Score: 103
Period size: 32 Copynumber: 3.1 Consensus size: 32
347435 TAAATATAAA
* *
347445 TAAATTTAAATATAATTTAAATTAT--TTATTT
1 TAAATTTAAATA-AATATAAATTATAATTATAT
* * *
347476 ATAAATATAAATCAATA-AAATTTTAATTATAT
1 -TAAATTTAAATAAATATAAATTATAATTATAT
*
347508 TAAATTTAAATAAATATACATTATAATTATAT
1 TAAATTTAAATAAATATAAATTATAATTATAT
347540 TAA
1 TAA
347543 TGGGAGGACT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
30 6 0.11
31 17 0.31
32 31 0.57
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (32 bp):
TAAATTTAAATAAATATAAATTATAATTATAT
Found at i:347808 original size:33 final size:30
Alignment explanation
Indices: 347771--347860 Score: 92
Period size: 33 Copynumber: 2.8 Consensus size: 30
347761 TTGAATTAGG
*
347771 TTAAATTTTTAAATTTTTAGATTATTTTGTAA
1 TTAAATTTTTAAATTTTAAG-TTATTTTG-AA
*
347803 TTTAAATTATTTTAATTTTAAGTTATTTTGAA
1 -TTAAATT-TTTAAATTTTAAGTTATTTTGAA
347835 TTAAGATTATTTTAAA-TTTAAGTTAT
1 TTAA-A-T-TTTTAAATTTTAAGTTAT
347861 GACAATGGTC
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
31 4 0.08
32 13 0.26
33 21 0.42
34 12 0.24
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (30 bp):
TTAAATTTTTAAATTTTAAGTTATTTTGAA
Found at i:347811 original size:17 final size:16
Alignment explanation
Indices: 347786--347860 Score: 64
Period size: 16 Copynumber: 4.6 Consensus size: 16
347776 TTTTTAAATT
*
347786 TTTAGATTATTTTGTAA
1 TTTAAATTATTTT-TAA
347803 TTTAAATTA-TTTTAA
1 TTTAAATTATTTTTAA
* *
347818 TTTTAAGTTATTTTGAA
1 -TTTAAATTATTTTTAA
*
347835 -TTAAGATTATTTTAAA
1 TTTAA-ATTATTTTTAA
*
347851 TTTAAGTTAT
1 TTTAAATTAT
347861 GACAATGGTC
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
15 7 0.15
16 24 0.50
17 17 0.35
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (16 bp):
TTTAAATTATTTTTAA
Found at i:347828 original size:16 final size:15
Alignment explanation
Indices: 347800--347860 Score: 70
Period size: 16 Copynumber: 3.9 Consensus size: 15
347790 GATTATTTTG
*
347800 TAATTTAAATTATTT
1 TAATTTAAGTTATTT
347815 TAATTTTAAGTTATTT
1 TAA-TTTAAGTTATTT
347831 TGAA-TTAAGATTATTT
1 T-AATTTAAG-TTATTT
347847 TAAATTTAAGTTAT
1 T-AATTTAAGTTAT
347861 GACAATGGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
15 8 0.20
16 25 0.62
17 7 0.17
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (15 bp):
TAATTTAAGTTATTT
Found at i:347849 original size:32 final size:33
Alignment explanation
Indices: 347771--347860 Score: 114
Period size: 32 Copynumber: 2.8 Consensus size: 33
347761 TTGAATTAGG
* *
347771 TTAAATT-TTTAAATTTTTAGATTATTTTGTAAT
1 TTAAATTATTTTAATTTTAAG-TTATTTTGTAAT
347804 TTAAATTATTTTAATTTTAAGTTATTTTG-AA-
1 TTAAATTATTTTAATTTTAAGTTATTTTGTAAT
*
347835 TTAAGATTATTTTAAATTTAAGTTAT
1 TTAA-ATTATTTTAATTTTAAGTTAT
347861 GACAATGGTC
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
31 4 0.08
32 22 0.42
33 15 0.29
34 11 0.21
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (33 bp):
TTAAATTATTTTAATTTTAAGTTATTTTGTAAT
Found at i:348604 original size:14 final size:14
Alignment explanation
Indices: 348567--348628 Score: 63
Period size: 15 Copynumber: 4.3 Consensus size: 14
348557 CGTAGGAAAA
*
348567 AATA-TTTAATTTT
1 AATATTTTAAATTT
*
348580 TATATTATTAAATTT
1 AATATT-TTAAATTT
348595 AATATTTTAAATTT
1 AATATTTTAAATTT
*
348609 ATATTTTTTAAATTAT
1 A-ATATTTTAAATT-T
348625 AATA
1 AATA
348629 AATAAAGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 3 0.08
14 10 0.25
15 25 0.62
16 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AATATTTTAAATTT
Found at i:348614 original size:13 final size:13
Alignment explanation
Indices: 348578--348615 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
348568 ATATTTAATT
348578 TTTATATTATTAAA
1 TTTATATT-TTAAA
348592 TTTAATATTTTAAA
1 TTT-ATATTTTAAA
348606 TTTATATTTT
1 TTTATATTTT
348616 TTAAATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.30
14 11 0.48
15 5 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTATATTTTAAA
Found at i:349765 original size:14 final size:14
Alignment explanation
Indices: 349729--349770 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
349719 AATTAATAGC
*
349729 ATAAA-TTT-TTAT
1 ATAAATTTTATTAA
349741 ATAATATTTTATTAA
1 ATAA-ATTTTATTAA
349756 ATAAATTTTATTAA
1 ATAAATTTTATTAA
349770 A
1 A
349771 ATTAAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 4 0.15
13 1 0.04
14 14 0.54
15 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATTTTATTAA
Found at i:351447 original size:18 final size:17
Alignment explanation
Indices: 351424--351471 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
351414 GGTAACATAA
351424 ATTTAAATTTGAAAAGTT
1 ATTTAAATTTGAAAA-TT
351442 ATTTAAAAATTT-AAAATT
1 ATTT--AAATTTGAAAATT
*
351460 TTTTAAATTTGA
1 ATTTAAATTTGA
351472 TTTAATTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 6 0.23
17 1 0.04
18 9 0.35
19 4 0.15
20 6 0.23
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
ATTTAAATTTGAAAATT
Found at i:351545 original size:16 final size:16
Alignment explanation
Indices: 351526--351594 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
351516 TTTGAAATTG
351526 TTTAAATTTAAAATAA
1 TTTAAATTTAAAATAA
*
351542 TTTAAATTTAAAATTA
1 TTTAAATTTAAAATAA
**
351558 TTTAAACGTAAAATAA
1 TTTAAATTTAAAATAA
*
351574 TTTAAATTTAAAATTA
1 TTTAAATTTAAAATAA
351590 TTTAA
1 TTTAA
351595 TCTCAAAATA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (16 bp):
TTTAAATTTAAAATAA
Found at i:351602 original size:16 final size:15
Alignment explanation
Indices: 351520--351603 Score: 60
Period size: 16 Copynumber: 5.3 Consensus size: 15
351510 GTGGATTTTG
* *
351520 AAATTGTTTAAATTTA
1 AAATTATTT-AATCTA
* *
351536 AAATAATTTAAATTTA
1 AAATTATTT-AATCTA
*
351552 AAATTATTTAAACGTA
1 AAATTATTTAATC-TA
* *
351568 AAATAATTTAAATTTA
1 AAATTATTT-AATCTA
351584 AAATTATTTAATCTCA
1 AAATTATTTAATCT-A
351600 AAAT
1 AAAT
351604 AAGAGATTAA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
15 6 0.11
16 47 0.85
17 2 0.04
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (15 bp):
AAATTATTTAATCTA
Found at i:351605 original size:32 final size:32
Alignment explanation
Indices: 351520--351594 Score: 123
Period size: 32 Copynumber: 2.3 Consensus size: 32
351510 GTGGATTTTG
* **
351520 AAATTGTTTAAATTTAAAATAATTTAAATTTA
1 AAATTATTTAAACGTAAAATAATTTAAATTTA
351552 AAATTATTTAAACGTAAAATAATTTAAATTTA
1 AAATTATTTAAACGTAAAATAATTTAAATTTA
351584 AAATTATTTAA
1 AAATTATTTAA
351595 TCTCAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (32 bp):
AAATTATTTAAACGTAAAATAATTTAAATTTA
Found at i:352142 original size:2 final size:2
Alignment explanation
Indices: 352135--352180 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
352125 CCTTTTAGTG
352135 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
352177 TA TA
1 TA TA
352181 AATGATCTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:352512 original size:35 final size:35
Alignment explanation
Indices: 352473--352544 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
352463 TATTTTAAAG
* *
352473 AATTTGTATATGAATAATTAATTTAAAAAATTTAA
1 AATTTATATATAAATAATTAATTTAAAAAATTTAA
*
352508 AATTTATATATAAATAATTATTTTAAAAAATTTAA
1 AATTTATATATAAATAATTAATTTAAAAAATTTAA
352543 AA
1 AA
352545 ATCGCTATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (35 bp):
AATTTATATATAAATAATTAATTTAAAAAATTTAA
Found at i:352822 original size:6 final size:6
Alignment explanation
Indices: 352808--352838 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
352798 TTATTTGGGC
*
352808 CTGTGT CTGTCT CTGTCT CTGTCT CTGTCT C
1 CTGTCT CTGTCT CTGTCT CTGTCT CTGTCT C
352839 CGTGTCTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.32, G:0.19, T:0.48
Consensus pattern (6 bp):
CTGTCT
Found at i:356177 original size:103 final size:103
Alignment explanation
Indices: 356052--356257 Score: 304
Period size: 103 Copynumber: 2.0 Consensus size: 103
356042 CAGTTTCTTA
* * * *
356052 AATTCTTTACACCTGATTTGGTTGTGGTAGCTCATATTGGTACCTTATTTCTTCTCCATGAAGCA
1 AATTCTTTAAACCTGATTTGGTTGTGGTAGCTCATATTGATACCTCATTTCTTCACCATGAAGCA
* * *
356117 ATTTCTTTTATATTGTTTTCTCTATCAAGGAGTAATGG
66 ATTTCTTTTATAGTCTTTTCTCCATCAAGGAGTAATGG
* * *
356155 AATTCTTTAAACCTGTTTTGGTTTTGGTAGCTCATCTTGATACCTCATTTCTTCACCATGAAGCA
1 AATTCTTTAAACCTGATTTGGTTGTGGTAGCTCATATTGATACCTCATTTCTTCACCATGAAGCA
* *
356220 ATTTCTTTTATAGTCTTTTCTCCATTAAGGAGTGATGG
66 ATTTCTTTTATAGTCTTTTCTCCATCAAGGAGTAATGG
356258 GGTTGATTGG
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
103 91 1.00
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.44
Consensus pattern (103 bp):
AATTCTTTAAACCTGATTTGGTTGTGGTAGCTCATATTGATACCTCATTTCTTCACCATGAAGCA
ATTTCTTTTATAGTCTTTTCTCCATCAAGGAGTAATGG
Found at i:359796 original size:22 final size:22
Alignment explanation
Indices: 359769--359818 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
359759 ATTTAATAAA
359769 ATATATTTGTAT-ATTAATATTT
1 ATATATTTGTATAATTAA-ATTT
*
359791 ATATATTTTTATAATTAAATTT
1 ATATATTTGTATAATTAAATTT
*
359813 AAATAT
1 ATATAT
359819 AAATATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATATTTGTATAATTAAATTT
Found at i:360967 original size:44 final size:44
Alignment explanation
Indices: 360911--361055 Score: 133
Period size: 44 Copynumber: 3.3 Consensus size: 44
360901 TAATGCTTTT
*
360911 AACAATTAATTATGAATAAAACTCTTAAGTAATTAAATCTTATCA
1 AACAATTAATTAT-AATAAAACTATTAAGTAATTAAATCTTATCA
* * * *
360956 AACAA-TAATTATAAAATAAAAATATT--TTAAAT-AATACTT-T-T
1 AACAATTAATTAT--AATAAAACTATTAAGTAATTAAAT-CTTATCA
*
360997 AACAATTAATTATATATAAAACTTTTAAGTAATTAAATCTTATCA
1 AACAATTAATTATA-ATAAAACTATTAAGTAATTAAATCTTATCA
*
361042 AATAA-TAATTATAA
1 AACAATTAATTATAA
361056 AATCAGAATC
Statistics
Matches: 79, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
40 1 0.01
41 14 0.18
42 11 0.14
43 15 0.19
44 19 0.24
45 19 0.24
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (44 bp):
AACAATTAATTATAATAAAACTATTAAGTAATTAAATCTTATCA
Found at i:361023 original size:39 final size:39
Alignment explanation
Indices: 360894--361029 Score: 112
Period size: 39 Copynumber: 3.3 Consensus size: 39
360884 AACTACAATA
* *
360894 TTTTAAATAATGCTTTTAACAATTAATTATGAATAAAAC
1 TTTTAAATAATACTTTTAACAATTAATTATAAATAAAAC
* * * *
360933 TCTTAAGTAATTAAATCTTATCAAACAA-TAATTATAAAATAAAAATA
1 TTTTAAATAA-T--A-CTT-T-TAACAATTAATTAT-AAAT-AAAA-C
*
360980 TTTTAAATAATACTTTTAACAATTAATTATATATAAAAC
1 TTTTAAATAATACTTTTAACAATTAATTATAAATAAAAC
*
361019 TTTTAAGTAAT
1 TTTTAAATAAT
361030 TAAATCTTAT
Statistics
Matches: 75, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
39 18 0.24
40 5 0.07
41 8 0.11
42 8 0.11
43 6 0.08
44 9 0.12
45 8 0.11
46 5 0.07
47 8 0.11
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.40
Consensus pattern (39 bp):
TTTTAAATAATACTTTTAACAATTAATTATAAATAAAAC
Found at i:361026 original size:86 final size:86
Alignment explanation
Indices: 360890--361058 Score: 295
Period size: 86 Copynumber: 2.0 Consensus size: 86
360880 GTAAAACTAC
*
360890 AATATTTTAAATAATGCTTTTAACAATTAATTATGAATAAAACTCTTAAGTAATTAAATCTTATC
1 AATATTTTAAATAATACTTTTAACAATTAATTATGAATAAAACTCTTAAGTAATTAAATCTTATC
360955 AAACAATAATTATAAAATAAA
66 AAACAATAATTATAAAATAAA
*
360976 AATATTTTAAATAATACTTTTAACAATTAATTAT-ATATAAAACTTTTAAGTAATTAAATCTTAT
1 AATATTTTAAATAATACTTTTAACAATTAATTATGA-ATAAAACTCTTAAGTAATTAAATCTTAT
*
361040 CAAATAATAATTATAAAAT
65 CAAACAATAATTATAAAAT
361059 CAGAATCTAC
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
85 1 0.01
86 78 0.99
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (86 bp):
AATATTTTAAATAATACTTTTAACAATTAATTATGAATAAAACTCTTAAGTAATTAAATCTTATC
AAACAATAATTATAAAATAAA
Found at i:361693 original size:32 final size:31
Alignment explanation
Indices: 361657--361724 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 31
361647 AAAATACTTT
*
361657 TATTAAATAATAA-TATTTATTATTGTTTATTA
1 TATTAAATAATAACCATTTATT-TTG-TTATTA
**
361689 TATTATTTAATAACCATTTATTTTGTTATTA
1 TATTAAATAATAACCATTTATTTTGTTATTA
361720 TATTA
1 TATTA
361725 TAGATTGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 11 0.34
32 14 0.44
33 7 0.22
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (31 bp):
TATTAAATAATAACCATTTATTTTGTTATTA
Found at i:365837 original size:17 final size:17
Alignment explanation
Indices: 365817--365864 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
365807 TTAAACAGAT
365817 CTCATTTTTTATCTAAA
1 CTCATTTTTTATCTAAA
*
365834 CTCATTTTTAATCT-AA
1 CTCATTTTTTATCTAAA
365850 -T-A-TTTTTATCTAAA
1 CTCATTTTTTATCTAAA
365864 C
1 C
365865 CTCCAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 8 0.30
14 3 0.11
15 1 0.04
16 2 0.07
17 13 0.48
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.52
Consensus pattern (17 bp):
CTCATTTTTTATCTAAA
Found at i:367427 original size:18 final size:18
Alignment explanation
Indices: 367388--367427 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
367378 GCTCTCAATT
367388 CTTT-AATTTATTTAAAA
1 CTTTAAATTTATTTAAAA
* *
367405 ATTTAAATTTATTTTAAA
1 CTTTAAATTTATTTAAAA
367423 CTTTA
1 CTTTA
367428 CTATTTTAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
CTTTAAATTTATTTAAAA
Found at i:369090 original size:24 final size:24
Alignment explanation
Indices: 369044--369091 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
369034 TAAATTTTTT
* *
369044 TATATTATCATTCATGAATAAAAA
1 TATATTATCATTCATAAAGAAAAA
369068 TATACTTATCATTCA-AAAGAAAAA
1 TATA-TTATCATTCATAAAGAAAAA
369092 CAATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
TATATTATCATTCATAAAGAAAAA
Found at i:369280 original size:2 final size:2
Alignment explanation
Indices: 369273--369310 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
369263 TATTACATAC
*
369273 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
369311 GATAAAGGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:369579 original size:2 final size:2
Alignment explanation
Indices: 369572--369613 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
369562 ATGAGTTGTC
369572 AT AT AT AT AT AT 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 AT AT AT AT AT AT
369614 TTCACCATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:370849 original size:19 final size:19
Alignment explanation
Indices: 370827--370880 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
370817 TAAATTTTAA
370827 TATATTTTTATATTTATGT
1 TATATTTTTATATTTATGT
* *
370846 TATAATTTTATATTATATTT
1 TATATTTTTATATT-TATGT
370866 TA-ATTATTT-TATTTA
1 TATATT-TTTATATTTA
370881 ATTATATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.07
19 19 0.63
20 9 0.30
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TATATTTTTATATTTATGT
Found at i:370861 original size:13 final size:12
Alignment explanation
Indices: 370761--370896 Score: 58
Period size: 12 Copynumber: 11.6 Consensus size: 12
370751 ACTCGTGAAT
*
370761 TTATATTATAT-
1 TTATATTTTATA
*
370772 TTATATTTTTTA
1 TTATATTTTATA
370784 TTATATTTTTATATA
1 TTATA--TTT-TATA
*
370799 TTAATAATTTATA
1 TT-ATATTTTATA
** *
370812 TTATA-TAAATT
1 TTATATTTTATA
*
370823 TTAATATATT-T-
1 TT-ATATTTTATA
*
370834 TTATA-TTTATG
1 TTATATTTTATA
370845 TTATAATTTTATA
1 TTAT-ATTTTATA
370858 TTATATTTTA-A
1 TTATATTTTATA
370869 -T-TATTTTAT-
1 TTATATTTTATA
*
370878 TTA-ATTATATAA
1 TTATATTTTAT-A
370890 TTATATT
1 TTATATT
370897 GTGTTTAAAA
Statistics
Matches: 95, Mismatches: 13, Indels: 32
0.68 0.09 0.23
Matches are distributed among these distances:
9 9 0.09
10 12 0.13
11 21 0.22
12 22 0.23
13 18 0.19
14 5 0.05
15 5 0.05
16 3 0.03
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:370869 original size:42 final size:42
Alignment explanation
Indices: 370766--370863 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
370756 TGAATTTATA
** *
370766 TTATATT-TATATTTTTTATTATATTTTTATATATTAATAAT
1 TTATATTATATAAATTTTAATATATTTTTATATATTAATAAT
*
370807 TTATATTATATAAATTTTAATATATTTTTATATTTATGTTATAATT
1 TTATATTATATAAATTTTAATATATTTTTATA--TAT-TAATAA-T
370853 TTATATTATAT
1 TTATATTATAT
370864 TTTAATTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
41 7 0.15
42 21 0.44
44 3 0.06
45 5 0.10
46 12 0.25
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (42 bp):
TTATATTATATAAATTTTAATATATTTTTATATATTAATAAT
Found at i:370876 original size:40 final size:39
Alignment explanation
Indices: 370766--370891 Score: 101
Period size: 44 Copynumber: 3.0 Consensus size: 39
370756 TGAATTTATA
* *
370766 TTATATTTATATTTTTTATTATATTTTTATATATTAATAATT
1 TTATA-TTATA-TTTTAATTAT-TTTATATATATTAATAATT
* * *
370808 TATATTATATAAATTTTAATATATTTTTATATTTATGTTATAATT
1 T-TA-TAT-TATATTTTAAT-TA-TTTTATATATAT-TAATAATT
*
370853 TTATATTATATTTTAATTATTTTATTTA-ATTATATAATT
1 TTATATTATATTTTAATTATTTTATATATATTA-ATAATT
370892 ATATTGTGTT
Statistics
Matches: 68, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
38 1 0.01
39 8 0.12
40 7 0.10
41 2 0.03
42 11 0.16
43 12 0.18
44 18 0.26
45 9 0.13
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (39 bp):
TTATATTATATTTTAATTATTTTATATATATTAATAATT
Found at i:370879 original size:46 final size:42
Alignment explanation
Indices: 370766--370888 Score: 94
Period size: 46 Copynumber: 2.8 Consensus size: 42
370756 TGAATTTATA
*
370766 TTATATTTATATTTT--TTATTATATTTTTATATATTAATAAT
1 TTATA-TTATATTTTAATTATTTTATTTTTATATATTAATAAT
* *
370807 TTATATTATA--TAAATT-TTAATATATTTTTATATTTATGTTATAATT
1 TTATATTATATTTTAATTATT--T-TATTTTTATA--TAT-TAATAA-T
370853 TTATATTATATTTTAATTATTTTATTTAATTATATA
1 TTATATTATATTTTAATTATTTTATTT--TTATATA
370889 ATTATATTGT
Statistics
Matches: 64, Mismatches: 4, Indels: 23
0.70 0.04 0.25
Matches are distributed among these distances:
38 1 0.02
39 2 0.03
40 7 0.11
41 5 0.08
42 10 0.16
44 3 0.05
45 5 0.08
46 18 0.28
47 1 0.02
48 10 0.16
49 2 0.03
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (42 bp):
TTATATTATATTTTAATTATTTTATTTTTATATATTAATAAT
Found at i:371235 original size:20 final size:20
Alignment explanation
Indices: 371212--371267 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
371202 TACATATCTA
371212 AAAATTTATTTTAATATTTT
1 AAAATTTATTTTAATATTTT
* ** *
371232 AAAATATATTAAAATA-ATT
1 AAAATTTATTTTAATATTTT
*
371251 AAAA-TTATTTTTATATT
1 AAAATTTATTTTAATATT
371268 AATATTTAAA
Statistics
Matches: 26, Mismatches: 9, Indels: 3
0.68 0.24 0.08
Matches are distributed among these distances:
18 7 0.27
19 6 0.23
20 13 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AAAATTTATTTTAATATTTT
Found at i:371264 original size:44 final size:43
Alignment explanation
Indices: 371216--371312 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 43
371206 TATCTAAAAA
* *
371216 TTTATTTTAATATTTTAAAATATATTA-AAATAATTAAAATTATT
1 TTTATATTAATA-TTT-AAATATATTATAAATAATTAAAATAATT
* * *
371260 TTTATATTAATATTTAAATATTTTATAATTAATTTAAATAATT
1 TTTATATTAATATTTAAATATATTATAAATAATTAAAATAATT
371303 TTT-TATTAAT
1 TTTATATTAAT
371313 TAAATAATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 16 0.34
43 20 0.43
44 11 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (43 bp):
TTTATATTAATATTTAAATATATTATAAATAATTAAAATAATT
Found at i:371283 original size:21 final size:22
Alignment explanation
Indices: 371259--371312 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
371249 TTAAAATTAT
371259 TTTTATATTAATATTTAAAT-A
1 TTTTATATTAATATTTAAATAA
371280 TTTTATAATT-A-ATTTAAATAA
1 TTTTAT-ATTAATATTTAAATAA
*
371301 TTTTTTATTAAT
1 TTTTATATTAAT
371313 TAAATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 11 0.39
21 14 0.50
22 3 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTATATTAATATTTAAATAA
Found at i:371314 original size:24 final size:23
Alignment explanation
Indices: 371246--371315 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 23
371236 TATATTAAAA
*
371246 TAATTAAAATTATTTTTATATTAA-
1 TAATTTAAA-TATTTTT-TATTAAT
371270 T-ATTTAAATA--TTTTA-TAAT
1 TAATTTAAATATTTTTTATTAAT
371289 TAATTTAAATAATTTTTTATTAAT
1 TAATTTAAAT-ATTTTTTATTAAT
371313 TAA
1 TAA
371316 ATAATAACTT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 11 0.28
21 1 0.03
22 2 0.05
23 11 0.28
24 8 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TAATTTAAATATTTTTTATTAAT
Found at i:371796 original size:20 final size:18
Alignment explanation
Indices: 371770--371825 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
371760 AAATTTTTTT
371770 TTAAATATTTAATAAATAA
1 TTAAATATTTAATAAAT-A
* * *
371789 TATTAATATTAAATAAGTA
1 T-TAAATATTTAATAAATA
371808 TTAAATATTTAAATAAAT
1 TTAAATATTT-AATAAAT
371826 GTTTTATAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
18 7 0.24
19 9 0.31
20 13 0.45
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TTAAATATTTAATAAATA
Found at i:371819 original size:19 final size:16
Alignment explanation
Indices: 371782--371823 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 16
371772 AAATATTTAA
371782 TAAATAATATTAATAT
1 TAAATAATATTAATAT
371798 TAAATAAGTATTAAATATT
1 TAAATAA-TATT-AATA-T
371817 TAAATAA
1 TAAATAA
371824 ATGTTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.30
17 4 0.17
18 4 0.17
19 8 0.35
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
TAAATAATATTAATAT
Found at i:373625 original size:22 final size:22
Alignment explanation
Indices: 373597--373639 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
373587 AATAAATATT
373597 AAATATAT-TTTATAATTAATAA
1 AAATATATATTTA-AATTAATAA
*
373619 AAATATATATTTAATTTAATA
1 AAATATATATTTAAATTAATA
373640 TAATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATATATATTTAAATTAATAA
Found at i:374248 original size:17 final size:16
Alignment explanation
Indices: 374205--374252 Score: 78
Period size: 16 Copynumber: 2.9 Consensus size: 16
374195 TACTTTTATA
*
374205 AAAATTATTTAAATTT
1 AAAATAATTTAAATTT
374221 AAAATAATTTAAATTT
1 AAAATAATTTAAATTT
374237 AAAATCAATTTAAATT
1 AAAAT-AATTTAAATT
374253 GATTTGGCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 20 0.67
17 10 0.33
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAATAATTTAAATTT
Found at i:374818 original size:22 final size:22
Alignment explanation
Indices: 374761--374819 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
374751 TTTTTATATT
* *
374761 TATATATTAATAAATATTATAA
1 TATATAATAATAAATATTAAAA
*
374783 TATTATAAT-GTAAATATTAAAA
1 TA-TATAATAATAAATATTAAAA
374805 TATATAATAATAAAT
1 TATATAATAATAAAT
374820 TTTTATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 6 0.19
22 20 0.65
23 5 0.16
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TATATAATAATAAATATTAAAA
Found at i:375119 original size:22 final size:23
Alignment explanation
Indices: 375094--375163 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 23
375084 TTATGATGAG
375094 ATTTTATTTAAATAAATTAAAA-
1 ATTTTATTTAAATAAATTAAAAT
*
375116 A-TTTATATAATATAAATTAAAAT
1 ATTTTATTTAA-ATAAATTAAAAT
* *
375139 TTTTTATTAAAATATAA-TAAAAT
1 ATTTTATTTAAATA-AATTAAAAT
375162 AT
1 AT
375164 AAAATCTTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 8 0.21
22 12 0.31
23 10 0.26
24 9 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTTATTTAAATAAATTAAAAT
Found at i:375120 original size:21 final size:21
Alignment explanation
Indices: 375096--375144 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
375086 ATGATGAGAT
375096 TTTATTTAA-ATAAATTAAAAA
1 TTTATTTAATATAAATT-AAAA
*
375117 TTTATATAATATAAATTAAAA
1 TTTATTTAATATAAATTAAAA
375138 TTT-TTTA
1 TTTATTTA
375145 TTAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 15 0.60
22 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTATTTAATATAAATTAAAA
Found at i:375178 original size:29 final size:28
Alignment explanation
Indices: 375120--375198 Score: 70
Period size: 30 Copynumber: 2.7 Consensus size: 28
375110 TTAAAAATTT
*
375120 ATATAATATAAAT-TAAAATTTTTTATTAAA
1 ATATAATA-AAATATAAAA--TCTTATTAAA
375150 ATATAATAAAATATAAAATCTTACTTAAA
1 ATATAATAAAATATAAAATCTTA-TTAAA
* * *
375179 AAATGATAAATTTATAAAAT
1 ATATAATAAA-ATATAAAAT
375199 ATTTTATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
28 4 0.10
29 17 0.40
30 21 0.50
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (28 bp):
ATATAATAAAATATAAAATCTTATTAAA
Found at i:375937 original size:55 final size:54
Alignment explanation
Indices: 375871--375980 Score: 193
Period size: 55 Copynumber: 2.0 Consensus size: 54
375861 AACTTCTGCT
*
375871 AAAATCAACTAATTGGACTTTGTTTTGAGTAAAATATTTTATCCCAATGAAATTG
1 AAAATCAACTAATTAGACTTTGTTTTGAGTAAAATATTTTAT-CCAATGAAATTG
*
375926 AAAATCAACTAATTAGACTTTGTTTTGAGTAAAATATTTTATCCGATGAAATTG
1 AAAATCAACTAATTAGACTTTGTTTTGAGTAAAATATTTTATCCAATGAAATTG
375980 A
1 A
375981 GATTAGATGT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
54 12 0.23
55 41 0.77
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (54 bp):
AAAATCAACTAATTAGACTTTGTTTTGAGTAAAATATTTTATCCAATGAAATTG
Found at i:376791 original size:12 final size:13
Alignment explanation
Indices: 376771--376808 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
376761 TTTTCACACA
376771 TAAAATTTTA-AT
1 TAAAATTTTATAT
*
376783 TAAATTTTTATAT
1 TAAAATTTTATAT
*
376796 GAAAATTTTATAT
1 TAAAATTTTATAT
376809 CAAATTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
TAAAATTTTATAT
Found at i:376815 original size:12 final size:12
Alignment explanation
Indices: 376770--376816 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
376760 ATTTTCACAC
376770 ATAAAATTTTA-
1 ATAAAATTTTAT
*
376781 ATTAAATTTTTAT
1 A-TAAAATTTTAT
376794 ATGAAAATTTTAT
1 AT-AAAATTTTAT
*
376807 ATCAAATTTT
1 ATAAAATTTT
376817 TGACATAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 1 0.03
12 17 0.57
13 12 0.40
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (12 bp):
ATAAAATTTTAT
Found at i:376817 original size:13 final size:13
Alignment explanation
Indices: 376784--376817 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
376774 AATTTTAATT
*
376784 AAATTTTTATATG
1 AAATTTTTATATC
*
376797 AAAATTTTATATC
1 AAATTTTTATATC
376810 AAATTTTT
1 AAATTTTT
376818 GACATAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (13 bp):
AAATTTTTATATC
Found at i:384884 original size:20 final size:21
Alignment explanation
Indices: 384857--384913 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
384847 TCAAAAACCT
384857 AGAATGTATCAATACAATG-A
1 AGAATGTATCAATACAATGCA
* * *
384877 ATAATGTATCGATACATTGCA
1 AGAATGTATCAATACAATGCA
*
384898 AGCATGTATCAATACA
1 AGAATGTATCAATACA
384914 TTAACTTATA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (21 bp):
AGAATGTATCAATACAATGCA
Found at i:386059 original size:3 final size:3
Alignment explanation
Indices: 386051--386092 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
386041 CATGAAAAAT
386051 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
386093 ATATCAATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:386787 original size:20 final size:20
Alignment explanation
Indices: 386739--386798 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
386729 TCAAATTTCT
*
386739 ATGAATTGTATCGATACAATTA
1 ATGAA-TGTATCGATAC-ATAA
* *
386761 GTGAATGTATTGATACATAA
1 ATGAATGTATCGATACATAA
386781 ATGAATGTATCGATACAT
1 ATGAATGTATCGATACAT
386799 GCCTAAAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 19 0.58
21 10 0.30
22 4 0.12
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (20 bp):
ATGAATGTATCGATACATAA
Found at i:396041 original size:22 final size:22
Alignment explanation
Indices: 396011--396055 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
396001 AAATATGAAA
396011 ATTTACCTGCATGTATCGATAC
1 ATTTACCTGCATGTATCGATAC
*
396033 ATTTTCCTGCATGTATCGATAC
1 ATTTACCTGCATGTATCGATAC
396055 A
1 A
396056 AAGATCATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (22 bp):
ATTTACCTGCATGTATCGATAC
Found at i:397129 original size:90 final size:92
Alignment explanation
Indices: 396809--397352 Score: 575
Period size: 92 Copynumber: 5.9 Consensus size: 92
396799 ATAGGATGTT
* * *
396809 AATGTGCTGATTCAAGGCCAGCTA-TTTGAACTTAAAGATGGAAAATGTGGCCAATATGCTGATT
1 AATGGGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT-G--AAGGT-GCCAATATGCTGATT
396873 CAAGGCCAGCTATATTGGACTTAAAAG-GTGCC
62 CAAGGCCAGCTATATTGGACTT-AAAGTG-GCC
** *
396905 AATATGCTGATTCAAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTG-TT
1 AATGGGCTGATTC-AAGGCCAGCTACATTGAACTTAAAGAT-G--AAGGTGCCAATATGCTGATT
* *
396969 C-AGGCTAGCAATATTGGACTTAAAG-GTGCC
62 CAAGGCCAGCTATATTGGACTTAAAGTG-GCC
* * * *
396999 AATGTGGCTGATTCAAGGCCAGCTACATTGGACTTGAAGATGAAGGTG-CAATAGGCCTGATTTA
1 AATG-GGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGGTGCCAATATG-CTGATTCA
*
397063 AGGCCAAC-ATATTGGACTT-AAGTGGCC
64 AGGCCAGCTATATTGGACTTAAAGTGGCC
* * *
397090 AATTGGGTTGATTC-AGGCCAGCTATATTGAACTTAAAGATGAAGGTGTCAATATGCT-ATTCAA
1 AA-TGGGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
397153 GGCCAGCTATATTGGAACTTAAAGGTGGCC
65 GGCCAGCTATATTGG-ACTTAAA-GTGGCC
* * *
397183 AATGTGCTGATTTCAA-G-CAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCGGATTCAA
1 AATGGGCTGA-TTCAAGGCCAGCTACATTGAACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
397246 GGCCAGCTA-ATTGGACTTAAAGGTGGCC
65 GGCCAGCTATATTGGACTTAAA-GTGGCC
* * * *
397274 -ATGTGCTGATGCAA-GCCAGCTA-ATTG-GCTTAAAGATGAAGGGGCCAATATGCTGA-TCAAG
1 AATGGGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGGTGCCAATATGCTGATTCAAG
* *
397334 GCCAGCGATATTGGGCTTA
66 GCCAGCTATATTGGACTTA
397353 GAAGGTTTGC
Statistics
Matches: 398, Mismatches: 32, Indels: 44
0.84 0.07 0.09
Matches are distributed among these distances:
87 12 0.03
88 35 0.09
89 20 0.05
90 60 0.15
91 48 0.12
92 64 0.16
93 34 0.09
94 38 0.10
95 26 0.07
96 15 0.04
97 23 0.06
98 23 0.06
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (92 bp):
AATGGGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGGTGCCAATATGCTGATTCAAG
GCCAGCTATATTGGACTTAAAGTGGCC
Found at i:397160 original size:48 final size:48
Alignment explanation
Indices: 397100--397346 Score: 190
Period size: 48 Copynumber: 5.4 Consensus size: 48
397090 AATTGGGTTG
*
397100 ATTC-AGGCCAGCTATATTGAACTTAAAGATGAAGGTGTCAATATGCT
1 ATTCAAGGCCAGCTATATTGAACTTAAAGATGAAGGTGCCAATATGCT
* *
397147 ATTCAAGGCCAGCTATATTGGAACTTAAAG--G--TG-GCCAATGTGCT
1 ATTCAAGGCCAGCTATATT-GAACTTAAAGATGAAGGTGCCAATATGCT
* * *
397191 GATTTCAA-G-CAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCGG
1 -A-TTCAAGGCCAGCTATATTGAACTTAAAGATGAAGGTGCCAATATGC-T
* * *
397240 ATTCAAGGCCAGCTA-ATTGGACTTAAAG--G--TG-GCC-ATGTGCT
1 ATTCAAGGCCAGCTATATTGAACTTAAAGATGAAGGTGCCAATATGCT
* * *
397281 GATGCAA-GCCAGCTA-ATTG-GCTTAAAGATGAAGGGGCCAATATGCT
1 -ATTCAAGGCCAGCTATATTGAACTTAAAGATGAAGGTGCCAATATGCT
*
397327 GA-TCAAGGCCAGCGATATTG
1 -ATTCAAGGCCAGCTATATTG
397347 GGCTTAGAAG
Statistics
Matches: 162, Mismatches: 17, Indels: 42
0.73 0.08 0.19
Matches are distributed among these distances:
40 7 0.04
41 12 0.07
42 11 0.07
43 12 0.07
44 20 0.12
45 10 0.06
46 21 0.13
47 15 0.09
48 38 0.23
49 16 0.10
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (48 bp):
ATTCAAGGCCAGCTATATTGAACTTAAAGATGAAGGTGCCAATATGCT
Found at i:397227 original size:182 final size:181
Alignment explanation
Indices: 396809--397358 Score: 559
Period size: 182 Copynumber: 3.0 Consensus size: 181
396799 ATAGGATGTT
* * * * *
396809 AATGT-GCTGATTCAAGGCCAGCTA-TTTGAACTTAAAGATGGAAAATGTGGCCAATATGCTGAT
1 AATGTGGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGT-GCCAATAGGCGGAT
* ** *
396872 TCAAGGCCAGCTATATTGGACTTAAAAGGT-GCCAATATGCTGATTCAAAGGCCAGCTACATTGA
62 TCAAGGCCAACTA-ATTGGACTT-AAAGGTGGCC-ATGGGCTGATGC--AGGCCAGCTA-ATTGA
* * *
396936 ACTTAAAGATGGAAAATGTGCCAATATGCTGTTC-AGGCTAGCAATATTGGACTTAAAGGTGCC
121 ACTTAAAGAT-G--AAGGTGCCAATATGCTATTCAAGGCCAGCAATATTGGACTTAAAGGTGCC
* * *
396999 AATGTGGCTGATTCAAGGCCAGCTACATTGGACTTGAAGATGAAGGTG-CAATAGGCCTGATTTA
1 AATGTGGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATAGG-CGGATTCA
* *
397063 AGGCCAAC-ATATTGGACTT-AA-GTGGCCAATTGGGTTGATTCAGGCCAGCTATATTGAACTTA
65 AGGCCAACTA-ATTGGACTTAAAGGTGGCC-A-TGGGCTGATGCAGGCCAGCTA-ATTGAACTTA
* *
397125 AAGATGAAGGTGTCAATATGCTATTCAAGGCCAGCTATATTGGAACTTAAAGGTGGCC
126 AAGATGAAGGTGCCAATATGCTATTCAAGGCCAGCAATATTGG-ACTTAAAGGT-GCC
*
397183 AATGT-GCTGATTTCAA-G-CAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCGGATTCA
1 AATGTGGCTGA-TTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATAGGCGGATTCA
* * * *
397245 AGGCCAGCTAATTGGACTTAAAGGTGGCCATGTGCTGATGCAAGCCAGCTAATTG-GCTTAAAGA
65 AGGCCAACTAATTGGACTTAAAGGTGGCCATGGGCTGATGCAGGCCAGCTAATTGAACTTAAAGA
* * *
397309 TGAAGGGGCCAATATGCTGA-TCAAGGCCAGCGATATTGGGCTTAGAAGGT
130 TGAAGGTGCCAATATGCT-ATTCAAGGCCAGCAATATTGGACTTA-AAGGT
397359 TTGCCACCGA
Statistics
Matches: 315, Mismatches: 30, Indels: 40
0.82 0.08 0.10
Matches are distributed among these distances:
179 4 0.01
180 47 0.15
181 22 0.07
182 81 0.26
183 27 0.09
184 46 0.15
185 7 0.02
186 8 0.03
187 17 0.05
188 15 0.05
189 4 0.01
190 5 0.02
191 20 0.06
192 12 0.04
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (181 bp):
AATGTGGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATAGGCGGATTCAA
GGCCAACTAATTGGACTTAAAGGTGGCCATGGGCTGATGCAGGCCAGCTAATTGAACTTAAAGAT
GAAGGTGCCAATATGCTATTCAAGGCCAGCAATATTGGACTTAAAGGTGCC
Found at i:397269 original size:134 final size:136
Alignment explanation
Indices: 396858--397306 Score: 379
Period size: 134 Copynumber: 3.3 Consensus size: 136
396848 GGAAAATGTG
*
396858 GCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAGGT-GCCAATATGCTGA-TTCAAA
1 GCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAGGTGGCCAATGTGCTGATTTC-AA
* * * *
396921 GGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTG-TTCAGGCTAGCAATATTG
65 GGCCAGCTACATTGGACTTAAAGAT-G--AA-GTGCCAATATGCGGATTCAGGCCAGCTATATTG
396985 GACTTAAAGGT
126 GACTTAAAGGT
* *
396996 GCCAATGTGGCTGATTCAAGGCCAGCTACATTGGACTTGAAGATGAAGGT-G-CAATAG-GCCTG
1 GCCAATAT-GCTGATTCAAGGCCAGCTATATTGGACTT--A-A--AAGGTGGCCAAT-GTG-CTG
* * *
397058 ATTT-AAGGCCAAC-ATATTGGACTT-AAG-T---G-GCCAAT-TGGGTTGATTCAGGCCAGCTA
58 ATTTCAAGGCCAGCTACATTGGACTTAAAGATGAAGTGCCAATATGCG--GATTCAGGCCAGCTA
*
397114 TATTGAACTTAAAGATGAAGGT
121 TATTGGACTT----A--AAGGT
*
397136 GTCAATATGCT-ATTCAAGGCCAGCTATATTGGAACTT-AAAGGTGGCCAATGTGCTGATTTCAA
1 GCCAATATGCTGATTCAAGGCCAGCTATATTGG-ACTTAAAAGGTGGCCAATGTGCTGATTTCAA
397199 -G-CAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCGGATTCAAGGCCAGCTA-ATTGGA
65 GGCCAGCTACATTGGACTTAAAGATGAA-GTGCCAATATGCGGATTC-AGGCCAGCTATATTGGA
397261 CTTAAAGGT
128 CTTAAAGGT
* *
397270 GGCC-ATGTGCTGATGCAA-GCCAGCTA-ATTGG-CTTAAA
1 -GCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
397307 GATGAAGGGG
Statistics
Matches: 254, Mismatches: 21, Indels: 78
0.72 0.06 0.22
Matches are distributed among these distances:
131 5 0.02
132 8 0.03
133 15 0.06
134 59 0.23
135 18 0.07
136 2 0.01
138 28 0.11
139 35 0.14
140 26 0.10
141 20 0.08
142 13 0.05
143 13 0.05
144 10 0.04
145 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (136 bp):
GCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAGGTGGCCAATGTGCTGATTTCAAG
GCCAGCTACATTGGACTTAAAGATGAAGTGCCAATATGCGGATTCAGGCCAGCTATATTGGACTT
AAAGGT
Found at i:397398 original size:33 final size:32
Alignment explanation
Indices: 397345--397502 Score: 164
Period size: 31 Copynumber: 5.0 Consensus size: 32
397335 CCAGCGATAT
*
397345 TGGGC-TTAG-AAGGTTTGCCACCGACTTTGTG
1 TGGGCTTTAGAAAGGGTTGCCACCGAC-TTGTG
** * *
397376 TGGGCTTTAGAACTGGTTGCCA-CAAATTGTG
1 TGGGCTTTAGAAAGGGTTGCCACCGACTTGTG
*
397407 TGGGCTTTAGAGAGGGTT-CCACCGACTTGTG
1 TGGGCTTTAGAAAGGGTTGCCACCGACTTGTG
* *
397438 TGGGCGTTGGAAAGGGTTGCCA-CGACTTGTG
1 TGGGCTTTAGAAAGGGTTGCCACCGACTTGTG
*
397469 TGGGCTTTTAAGAAGAAGGTTGCCACCGACTTGT
1 TGGGC-TTT-AGAA-AGGGTTGCCACCGACTTGT
Statistics
Matches: 103, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
30 3 0.03
31 61 0.59
32 11 0.11
33 11 0.11
34 9 0.09
35 8 0.08
ACGTcount: A:0.19, C:0.18, G:0.34, T:0.30
Consensus pattern (32 bp):
TGGGCTTTAGAAAGGGTTGCCACCGACTTGTG
Found at i:397442 original size:62 final size:63
Alignment explanation
Indices: 397345--397502 Score: 187
Period size: 62 Copynumber: 2.5 Consensus size: 63
397335 CCAGCGATAT
* * **
397345 TGGGC-TTAGA-AGGTTTGCCACCGACTTTGTGTGGGCTTTAGAACTGGTTGCCACAAATTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGAC-TTGTGTGGGCGTTAGAAAGGGTTGCCACAAATTGTG
* * *
397407 TGGGCTTTAGAGAGGGTT-CCACCGACTTGTGTGGGCGTTGGAAAGGGTTGCCACGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCGTTAGAAAGGGTTGCCACAAATTGTG
*
397469 TGGGCTTTTAAGAAGAAGGTTGCCACCGACTTGT
1 TGGGC-TTT-AG-AGAGGGTTGCCACCGACTTGT
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
62 40 0.49
63 16 0.20
64 7 0.09
65 7 0.09
66 12 0.15
ACGTcount: A:0.19, C:0.18, G:0.34, T:0.30
Consensus pattern (63 bp):
TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCGTTAGAAAGGGTTGCCACAAATTGTG
Done.