Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008150.1 Hibiscus syriacus cultivar Beakdansim tig00110716_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3012591
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 14
Found at i:1271215 original size:20 final size:20
Alignment explanation
Indices: 1271186--1271224 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1271176 CGGTAATTAG
1271186 CGTTGCGAATTTGAAAATCA
1 CGTTGCGAATTTGAAAATCA
*
1271206 CGTTGTGAATTTGAAAATC
1 CGTTGCGAATTTGAAAATC
1271225 GCATTGCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (20 bp):
CGTTGCGAATTTGAAAATCA
Found at i:1271294 original size:20 final size:20
Alignment explanation
Indices: 1271262--1271310 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1271252 TCGGTAATTA
* *
1271262 GCATTGTGAATTTGAATATC
1 GCATTGCGAATTTGAAAATC
*
1271282 GCGTTGCGAATTTGAAAATC
1 GCATTGCGAATTTGAAAATC
1271302 GCATTGCGA
1 GCATTGCGA
1271311 TATTACGGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (20 bp):
GCATTGCGAATTTGAAAATC
Found at i:1271368 original size:134 final size:134
Alignment explanation
Indices: 1271206--1271450 Score: 393
Period size: 134 Copynumber: 1.8 Consensus size: 134
1271196 TTGAAAATCA
* * *
1271206 CGTTGTGAATTTGAAAATCGCATTGCGATAGTACTATTTACCTATATCGGTAATTAGCATTGTGA
1 CGTTGCGAATATGAAAATCGCATTGCGATAGTACTATTTACCTATATCGGTAATTAGCATTGCGA
* *
1271271 ATTTGAATATCGCGTTGCGAATT-TGAAAATCGCATTGCGATATTACGGTTTACCTATTTCGGTA
66 ATTTGAAAATCGCATTGCGAATTGTGAAAATCGCATTGCGAT-TTACGGTTTACCTATTTCGGTA
1271335 ATTAG
130 ATTAG
* * *
1271340 CGTTGCGAATATGAAAATCGCATTGCGATAGTACTGTTTACCTATATCGGTAATTCGCGTTGCGA
1 CGTTGCGAATATGAAAATCGCATTGCGATAGTACTATTTACCTATATCGGTAATTAGCATTGCGA
*
1271405 ATTTGAAAATCGCATTGCGAATTGTGAAAATTGCATTGCGATTTAC
66 ATTTGAAAATCGCATTGCGAATTGTGAAAATCGCATTGCGATTTAC
1271451 CTATTATCGT
Statistics
Matches: 101, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
134 84 0.83
135 17 0.17
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.36
Consensus pattern (134 bp):
CGTTGCGAATATGAAAATCGCATTGCGATAGTACTATTTACCTATATCGGTAATTAGCATTGCGA
ATTTGAAAATCGCATTGCGAATTGTGAAAATCGCATTGCGATTTACGGTTTACCTATTTCGGTAA
TTAG
Found at i:1271379 original size:57 final size:57
Alignment explanation
Indices: 1271282--1271424 Score: 241
Period size: 57 Copynumber: 2.5 Consensus size: 57
1271272 TTTGAATATC
* *
1271282 GCGTTGCGAATTTGAAAATCGCATTGCGATATTACGGTTTACCTATTTCGGTAATTA
1 GCGTTGCGAATTTGAAAATCGCATTGCGATAGTACGGTTTACCTATATCGGTAATTA
* * *
1271339 GCGTTGCGAATATGAAAATCGCATTGCGATAGTACTGTTTACCTATATCGGTAATTC
1 GCGTTGCGAATTTGAAAATCGCATTGCGATAGTACGGTTTACCTATATCGGTAATTA
1271396 GCGTTGCGAATTTGAAAATCGCATTGCGA
1 GCGTTGCGAATTTGAAAATCGCATTGCGA
1271425 ATTGTGAAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 80 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (57 bp):
GCGTTGCGAATTTGAAAATCGCATTGCGATAGTACGGTTTACCTATATCGGTAATTA
Found at i:1271422 original size:20 final size:21
Alignment explanation
Indices: 1271394--1271445 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1271384 TATCGGTAAT
*
1271394 TCGCGTTGCGAATT-TGAAAA
1 TCGCATTGCGAATTGTGAAAA
1271414 TCGCATTGCGAATTGTGAAAA
1 TCGCATTGCGAATTGTGAAAA
*
1271435 TTGCATTGCGA
1 TCGCATTGCGA
1271446 TTTACCTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (21 bp):
TCGCATTGCGAATTGTGAAAA
Found at i:1271465 original size:20 final size:20
Alignment explanation
Indices: 1271440--1271485 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1271430 GAAAATTGCA
* *
1271440 TTGCGATTTACCTATTATCG
1 TTGCGATTTACATATTAGCG
*
1271460 TTGCGATTTACATATTCGCG
1 TTGCGATTTACATATTAGCG
1271480 TTGCGA
1 TTGCGA
1271486 ATTTGGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (20 bp):
TTGCGATTTACATATTAGCG
Found at i:1271499 original size:134 final size:131
Alignment explanation
Indices: 1271226--1271548 Score: 339
Period size: 134 Copynumber: 2.4 Consensus size: 131
1271216 TTGAAAATCG
* * * * *
1271226 CATTGCGATAGTACTATTTACCTATATCGGTAATTAGCATTGTGAATTTGAATATCGCGTTGCGA
1 CATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCATTGCGA
* * *
1271291 ATTTGAAAATCGCATTGCGATATTACGGTTTACCTATTTCGGTAATTAGCGTTGCGAATATGAAA
66 ATTTGAAAATCGCATTGCGATATTACGCTTTACCGATTTCGATAATTAGCGTTGCGAATATGAAA
1271356 A
131 A
*
1271357 TCGCATTGCGATAGTACTGTTTACCTATATCGGTAATTCGCGTTGCGAATTTGAAAATCGCATTG
1 ---CATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCATTG
* *
1271422 CGAATTGTGAAAATTGCATTGCGAT-TTAC-CTATTATCGTTGCGATTTAC-AT-ATTCGCGTTG
63 CGAATT-TGAAAATCGCATTGCGATATTACGCT-TTA-C----CGATTT-CGATAATTAGCGTTG
*
1271483 CGAATTTGGAAAA
120 CGAATAT-GAAAA
* * **
1271496 TTGCGTTGGGATAGTGGTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
1 ---CATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
1271549 TAGGATACCC
Statistics
Matches: 162, Mismatches: 18, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
133 1 0.01
134 69 0.43
135 18 0.11
138 15 0.09
139 58 0.36
140 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.37
Consensus pattern (131 bp):
CATTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCATTGCGA
ATTTGAAAATCGCATTGCGATATTACGCTTTACCGATTTCGATAATTAGCGTTGCGAATATGAAA
A
Found at i:1272237 original size:20 final size:20
Alignment explanation
Indices: 1272212--1272258 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1272202 TCGGTAATTA
*
1272212 GCGTTGCAAATTTGAAAATC
1 GCGTTGCAAATATGAAAATC
*
1272232 GCGTTGCGAATATGAAAATC
1 GCGTTGCAAATATGAAAATC
*
1272252 GCATTGC
1 GCGTTGC
1272259 GATAGTACTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (20 bp):
GCGTTGCAAATATGAAAATC
Found at i:1272242 original size:77 final size:77
Alignment explanation
Indices: 1272101--1272552 Score: 522
Period size: 77 Copynumber: 5.8 Consensus size: 77
1272091 AATGCCCCAC
* * *
1272101 TTGCGATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAATATCACGTTACGAAT
1 TTGCGATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAAT
1272166 TTGAAAATCGCA
66 TTGAAAATCGCA
* * *
1272178 TTGCGATAGTATTGTTTACCTTTGTCGGTAATTAGCGTTGCAAATTTGAAAATCGCGTTGCGAAT
1 TTGCGATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAAT
*
1272243 ATGAAAATCGCA
66 TTGAAAATCGCA
* * *
1272255 TTGCGATAGTACTGTTTACCTATATCGGTAATTCGCGTTGCGAATTTGAAAATCGCATTGCGAAT
1 TTGCGATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAAT
1272320 TTGGAAAATCGCA
66 TT-GAAAATCGCA
*** * * *
1272333 TTGCGA-A-T-TTGGAAAATCGC-A-ATGCGATTTACCTATTATCGTTGCG-ATTT-ACATATTC
1 TTGCGATAGTATT-GTTTA-C-CTATAT-CG--GTA---ATTAGCGTTGCGAATTTGA-A-AATC
*
1272391 GCGTTGCGAATTTGGAAAATCGCG
55 GCGTTGCGAATTT-GAAAATCGCA
* *
1272415 TTGCGATAGTATTGTTTACCTATATCGGTAATTAGCGTTCCGAATTTGAAAATCGCGTTGTGAAT
1 TTGCGATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAAT
1272480 TTGAAAATCGCA
66 TTGAAAATCGCA
* * * * *
1272492 TTGCGATAGTACTATTTACCTATATCTGTAATTAGTGTTGCGAATTTGAAAATCGCATTGC
1 TTGCGATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGC
1272553 TATAGTACTG
Statistics
Matches: 316, Mismatches: 40, Indels: 38
0.80 0.10 0.10
Matches are distributed among these distances:
75 1 0.00
76 5 0.02
77 198 0.63
78 42 0.13
79 7 0.02
80 2 0.01
81 7 0.02
82 42 0.13
83 5 0.02
84 5 0.02
85 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (77 bp):
TTGCGATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCGTTGCGAAT
TTGAAAATCGCA
Found at i:1272328 original size:21 final size:21
Alignment explanation
Indices: 1272287--1272359 Score: 121
Period size: 21 Copynumber: 3.5 Consensus size: 21
1272277 TATCGGTAAT
*
1272287 TCGCGTTGCGAATTT-GAAAA
1 TCGCATTGCGAATTTGGAAAA
1272307 TCGCATTGCGAATTTGGAAAA
1 TCGCATTGCGAATTTGGAAAA
1272328 TCGCATTGCGAATTTGGAAAA
1 TCGCATTGCGAATTTGGAAAA
*
1272349 TCGCAATGCGA
1 TCGCATTGCGA
1272360 TTTACCTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 14 0.28
21 36 0.72
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (21 bp):
TCGCATTGCGAATTTGGAAAA
Found at i:1272378 original size:20 final size:20
Alignment explanation
Indices: 1272355--1272399 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1272345 AAAATCGCAA
* *
1272355 TGCGATTTACCTATTATCGT
1 TGCGATTTACATATTAGCGT
*
1272375 TGCGATTTACATATTCGCGT
1 TGCGATTTACATATTAGCGT
1272395 TGCGA
1 TGCGA
1272400 ATTTGGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (20 bp):
TGCGATTTACATATTAGCGT
Found at i:1272567 original size:57 final size:57
Alignment explanation
Indices: 1272469--1272612 Score: 225
Period size: 57 Copynumber: 2.5 Consensus size: 57
1272459 TTTGAAAATC
* *
1272469 GCGTTGTGAATTTGAAAATCGCATTGCGATAGTACTATTTACCTATATCTGTAATTA
1 GCGTTGCGAATTTGAAAATCGCATTGCGATAGTACTATTTACCTATATCGGTAATTA
* * *
1272526 GTGTTGCGAATTTGAAAATCGCATTGCTATAGTACTGTTTACCTATATCGGTAATTA
1 GCGTTGCGAATTTGAAAATCGCATTGCGATAGTACTATTTACCTATATCGGTAATTA
* *
1272583 GCGTTGCAAATTTGAAAATCACATTGCGAT
1 GCGTTGCGAATTTGAAAATCGCATTGCGAT
1272613 TTACCTATTA
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 78 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (57 bp):
GCGTTGCGAATTTGAAAATCGCATTGCGATAGTACTATTTACCTATATCGGTAATTA
Found at i:1272647 original size:20 final size:20
Alignment explanation
Indices: 1272606--1272654 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1272596 GAAAATCACA
*
1272606 TTGCGATTTACCTATTATCG
1 TTGCGATTTACCTATTAGCG
* *
1272626 TTGTGATTTACCTATTCGCG
1 TTGCGATTTACCTATTAGCG
1272646 TTGCGATTT
1 TTGCGATTT
1272655 TGGAACATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.47
Consensus pattern (20 bp):
TTGCGATTTACCTATTAGCG
Found at i:1276944 original size:11 final size:9
Alignment explanation
Indices: 1276925--1276986 Score: 56
Period size: 9 Copynumber: 6.7 Consensus size: 9
1276915 TTGACTTTGG
1276925 TTTTTTCTT
1 TTTTTTCTT
* *
1276934 CTTTTTCTC
1 TTTTTTCTT
1276943 TTTTTT-TT
1 TTTTTTCTT
1276951 TTTTTTCTT
1 TTTTTTCTT
1276960 TTTTAATT-TT
1 TTTT--TTCTT
1276970 CTTTTTCTCTT
1 -TTTTT-TCTT
1276981 TTTTTT
1 TTTTTT
1276987 GCAACGGTGG
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
8 7 0.16
9 20 0.47
10 8 0.19
11 8 0.19
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:1276945 original size:23 final size:23
Alignment explanation
Indices: 1276919--1276962 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1276909 CGGTTTTTGA
1276919 CTTTGGTTTTTTCTTCTTTTTCT
1 CTTTGGTTTTTTCTTCTTTTTCT
** *
1276942 CTTTTTTTTTTTTTTCTTTTT
1 CTTTGGTTTTTTCTTCTTTTT
1276963 TAATTTTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.82
Consensus pattern (23 bp):
CTTTGGTTTTTTCTTCTTTTTCT
Found at i:1276969 original size:21 final size:21
Alignment explanation
Indices: 1276932--1276984 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1276922 TGGTTTTTTC
1276932 TTCTTTTTCTC--TTTT--TT
1 TTCTTTTTCTCTTTTTTAATT
1276949 TT-TTTTT-TCTTTTTTAATT
1 TTCTTTTTCTCTTTTTTAATT
1276968 TTCTTTTTCTCTTTTTT
1 TTCTTTTTCTCTTTTTT
1276985 TTGCAACGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.07
16 5 0.17
17 6 0.20
19 4 0.13
20 5 0.17
21 8 0.27
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (21 bp):
TTCTTTTTCTCTTTTTTAATT
Found at i:1276969 original size:23 final size:23
Alignment explanation
Indices: 1276925--1276986 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
1276915 TTGACTTTGG
* *
1276925 TTTTTTCTTCTTTTTCTCTTTTT
1 TTTTTTCTTCTTTTTCTATTTTC
*
1276948 TTTTTTTTTCTTTTT-TAATTTTC
1 TTTTTTCTTCTTTTTCT-ATTTTC
*
1276971 TTTTTCTCTTTTTTTT
1 TTTTT-TCTTCTTTTT
1276987 GCAACGGTGG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 1 0.03
23 23 0.72
24 8 0.25
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTTTCTTCTTTTTCTATTTTC
Found at i:1276982 original size:13 final size:12
Alignment explanation
Indices: 1276932--1276986 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 12
1276922 TGGTTTTTTC
1276932 TTCTTTTTCTCTT
1 TTCTTTTT-TCTT
1276945 TT-TTTTTT-TT
1 TTCTTTTTTCTT
*
1276955 TTCTTTTTTAATT
1 TTCTTTTTT-CTT
1276968 TTCTTTTTCTCTT
1 TTCTTTTT-TCTT
1276981 TT-TTTT
1 TTCTTTT
1276987 GCAACGGTGG
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
10 4 0.11
11 7 0.19
12 9 0.24
13 16 0.43
14 1 0.03
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.84
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:1291849 original size:18 final size:18
Alignment explanation
Indices: 1291806--1291850 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1291796 CCAATGATTT
*
1291806 GATGTTGCACTCCAAGTC
1 GATGTTGTACTCCAAGTC
*
1291824 TATGTTGTACTCCAAGTC
1 GATGTTGTACTCCAAGTC
1291842 GATGTTGTA
1 GATGTTGTA
1291851 TTGATCCAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (18 bp):
GATGTTGTACTCCAAGTC
Found at i:1292949 original size:27 final size:27
Alignment explanation
Indices: 1292919--1292993 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
1292909 AAAGGGGATT
*
1292919 AAAAGGAATAAAGATTAAAAAGAACTC
1 AAAAGGAATAAAGATTAAAAAGAAATC
* * * * *
1292946 AAAACGAAAAAAATATTAAAAGGAAATT
1 AAAA-GGAATAAAGATTAAAAAGAAATC
*
1292974 AAAAAGAATAAAGATTAAAA
1 AAAAGGAATAAAGATTAAAA
1292994 GTGTCGAAAC
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
27 16 0.43
28 21 0.57
ACGTcount: A:0.68, C:0.04, G:0.12, T:0.16
Consensus pattern (27 bp):
AAAAGGAATAAAGATTAAAAAGAAATC
Found at i:1292977 original size:28 final size:27
Alignment explanation
Indices: 1292888--1292994 Score: 99
Period size: 27 Copynumber: 3.9 Consensus size: 27
1292878 TATTTATAAG
* * *
1292888 AATTAAAAGAAATAAATATTTAAAGGG
1 AATTAAAAGAAATAAAGATTAAAAGGA
* * *
1292915 GATTAAAAGGAATAAAGATTAAAAAGA
1 AATTAAAAGAAATAAAGATTAAAAGGA
* * * *
1292942 ACTCAAAACGAAAAAAATATTAAAAGGA
1 AATTAAAA-GAAATAAAGATTAAAAGGA
1292970 AATTAAAA-AGAATAAAGATTAAAAG
1 AATTAAAAGA-AATAAAGATTAAAAG
1292995 TGTCGAAACG
Statistics
Matches: 61, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
26 1 0.02
27 39 0.64
28 21 0.34
ACGTcount: A:0.64, C:0.03, G:0.14, T:0.20
Consensus pattern (27 bp):
AATTAAAAGAAATAAAGATTAAAAGGA
Found at i:1295771 original size:52 final size:52
Alignment explanation
Indices: 1295651--1295829 Score: 200
Period size: 51 Copynumber: 3.5 Consensus size: 52
1295641 ATGATAAGTC
* ** * *
1295651 TGCTCCCTATTTCTTCAGAGAGTATAGGACTTAATCTTCAA-CAAATGTATC
1 TGCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAATAAAATGTATA
* * * *
1295702 CGCTCCCTATTCCTTCAGAGAGTATAGGAGTCGGTCTTCAATAAAATGTGTA
1 TGCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAATAAAATGTATA
* * * *
1295754 TGCTCCTTATTCCTTCAGAGAGTATAAGACTCGATCTTCAAT-AAACGTATC
1 TGCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAATAAAATGTATA
** *
1295805 CACTCCCTATTGCTTCAGAGAGTAT
1 TGCTCCCTATTCCTTCAGAGAGTAT
1295830 GGAACTCAAA
Statistics
Matches: 106, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
51 62 0.58
52 44 0.42
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (52 bp):
TGCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAATAAAATGTATA
Found at i:1295942 original size:54 final size:54
Alignment explanation
Indices: 1295824--1296493 Score: 1137
Period size: 54 Copynumber: 12.4 Consensus size: 54
1295814 TTGCTTCAGA
* * *
1295824 GAGTATGGAACTCAAACGTCTTCTTCTTACGGG-TCGCTCCCTCTTTATCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
** *
1295877 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTTACTCCTTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1295931 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1295985 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1296039 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCT-TTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* *
1296092 GAGTATGGAACTCGAACATCTTCTTCTTACGAGTTCGCTCTCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* * *
1296146 GAGTATGGATCTCGAATATCTTCTGCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1296200 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* * * * *
1296254 GAGTATGGAACTCGAACATATTCTTCATACGGGTTCACTTCCTCTTTTTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1296308 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
*
1296362 GAGTATGAAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* * *
1296416 GAGTATGAAACTCGAACATATTCTTCTTACGGGTTCGCTCTCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
*
1296470 GAGTATGAAACTCGAACATCTTCT
1 GAGTATGGAACTCGAACATCTTCT
1296494 GCTTTACCAC
Statistics
Matches: 582, Mismatches: 33, Indels: 3
0.94 0.05 0.00
Matches are distributed among these distances:
53 82 0.14
54 500 0.86
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.36
Consensus pattern (54 bp):
GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:1301201 original size:72 final size:72
Alignment explanation
Indices: 1301084--1301233 Score: 255
Period size: 72 Copynumber: 2.1 Consensus size: 72
1301074 CCCTAACATG
*
1301084 TTCTTGATCAGTTGCTAACATCACATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAGTCT
1 TTCTTGATCAGTTGCTAACATCACATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAATCT
1301149 TCATATT
66 TCATATT
* * * *
1301156 TTCTTGATCATTTGCTATCATCACATTGGTTGTACCACTAACATTCAGATTTTCACCCGAAATCT
1 TTCTTGATCAGTTGCTAACATCACATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAATCT
1301221 TCATATT
66 TCATATT
1301228 TTCTTG
1 TTCTTG
1301234 TGTAATAGGG
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (72 bp):
TTCTTGATCAGTTGCTAACATCACATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAATCT
TCATATT
Found at i:1303966 original size:20 final size:21
Alignment explanation
Indices: 1303941--1304033 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
1303931 TTTTCCCAAT
*
1303941 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1303961 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
* *
1303982 TTGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1304002 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1304023 TCGCAATGCGA
1 TCGCAATGCGA
1304034 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1304047 original size:20 final size:20
Alignment explanation
Indices: 1304022--1304114 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
1304012 AATTGGGAAA
*
1304022 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1304042 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1304063 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1304083 -TTGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1304102 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1304115 TTACATAGCG
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
19 16 0.28
20 27 0.47
21 14 0.25
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1304048 original size:41 final size:41
Alignment explanation
Indices: 1303941--1304033 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
1303931 TTTTCCCAAT
1303941 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
1303982 TTGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1304023 TCGCAATGCGA
1 TCGCAATGCGA
1304034 TACTGACTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1304064 original size:41 final size:40
Alignment explanation
Indices: 1304019--1304095 Score: 100
Period size: 41 Copynumber: 1.9 Consensus size: 40
1304009 GCGAATTGGG
* * *
1304019 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACT-TCGCAACGCGATAATAA
* *
1304060 AAAATCGCAACGAGATACTTACTTTGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTTCGCAACGCGATA
1304096 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 11 0.35
41 20 0.65
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (40 bp):
AAAATCGCAACGAGATACTGACTTCGCAACGCGATAATAA
Found at i:1304090 original size:19 final size:20
Alignment explanation
Indices: 1304064--1304110 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
1304054 TAATAAAAAA
*
1304064 TCGCAACGAGATACTTACTT
1 TCGCAACGAGATACTGACTT
*
1304084 T-GCAACGCGATACTGACTT
1 TCGCAACGAGATACTGACTT
1304103 TCGCAACG
1 TCGCAACG
1304111 CGATTTACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGCAACGAGATACTGACTT
Found at i:1304709 original size:19 final size:19
Alignment explanation
Indices: 1304687--1304871 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
1304677 GAAACCAAAA
*
1304687 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1304706 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1304725 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1304744 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1304764 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1304780 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1304797 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
1304811 TCTCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1304830 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1304850 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1304870 TC
1 TC
1304872 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.44
20 48 0.35
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1304764 original size:39 final size:38
Alignment explanation
Indices: 1304687--1304871 Score: 165
Period size: 33 Copynumber: 5.1 Consensus size: 38
1304677 GAAACCAAAA
*
1304687 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
1304725 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
1304764 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * **
1304797 TCGCGTTGCGA--TTC---TCTCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
1304830 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
1304870 TC
1 TC
1304872 AACCAAAAGA
Statistics
Matches: 122, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
31 3 0.02
33 37 0.30
34 10 0.08
35 1 0.01
36 3 0.02
38 21 0.17
39 30 0.25
40 17 0.14
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:1304848 original size:20 final size:20
Alignment explanation
Indices: 1304825--1304871 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1304815 ATTGCGATAG
1304825 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCGATTC
* *
1304845 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTC
1304865 TCATTTC
1 TCATTTC
1304872 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:1306926 original size:42 final size:42
Alignment explanation
Indices: 1306866--1306988 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
1306856 GCCCGACTCG
* * *
1306866 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
1306908 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
1306950 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
1306989 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1306946 original size:21 final size:21
Alignment explanation
Indices: 1306922--1306988 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1306912 TCATTCCTCG
1306922 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1306943 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1306964 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1306985 AGAG
1 AGAG
1306989 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1308348 original size:14 final size:14
Alignment explanation
Indices: 1308329--1308364 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1308319 ATTGTTTAAT
1308329 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1308343 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1308357 TGATTTGT
1 TGATTTGT
1308365 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1308564 original size:19 final size:19
Alignment explanation
Indices: 1308542--1308706 Score: 153
Period size: 19 Copynumber: 9.5 Consensus size: 19
1308532 CGAAATTAAA
*
1308542 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1308561 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1308580 TTCGCATTACGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1308599 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
1308615 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1308632 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
1308646 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1308665 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
1308681 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1308698 TTCGCATTG
1 TTCGCATTG
1308707 AGATAGTAAT
Statistics
Matches: 116, Mismatches: 15, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
14 23 0.20
16 13 0.11
17 13 0.11
19 67 0.58
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:1308631 original size:33 final size:33
Alignment explanation
Indices: 1308546--1308706 Score: 207
Period size: 33 Copynumber: 4.7 Consensus size: 33
1308536 ATTAAATTCG
*
1308546 CGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
1 CGTTGCGATTTTCATTTCGCATTGCGA--TTC-TCT
* *
1308582 CGCATTACGATTTTCATTTCGCATTGCGATTCCCT
1 CG--TTGCGATTTTCATTTCGCATTGCGATTCTCT
* **
1308617 CGTTGCGATTTTCATTTCGCATTGCGAAAT-TAG
1 CGTTGCGATTTTCATTTCGCATTGCG-ATTCTCT
1308650 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1308683 CGTTGCGATTTTCATTTCGCATTG
1 CGTTGCGATTTTCATTTCGCATTG
1308707 AGATAGTAAT
Statistics
Matches: 110, Mismatches: 11, Indels: 11
0.83 0.08 0.08
Matches are distributed among these distances:
32 2 0.02
33 74 0.67
34 2 0.02
35 3 0.03
36 5 0.05
38 24 0.22
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1308685 original size:66 final size:67
Alignment explanation
Indices: 1308546--1308711 Score: 235
Period size: 66 Copynumber: 2.4 Consensus size: 67
1308536 ATTAAATTCG
* *
1308546 CGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTACGATTTTCATTTCGCATTGCGA
1 CGTTGCGATTTTCATTTCGCATTGCGA---T-AATTAGCATTACGATTTTCATTTCGCATTGCGA
1308611 TTCCCT
62 TTCCCT
* * *
1308617 CGTTGCGATTTTCATTTCGCATTGCGA-AATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATAATTAGCATTACGATTTTCATTTCGCATTGCGATTCC
1308681 CT
66 CT
*
1308683 CGTTGCGATTTTCATTTCGCATTGAGATA
1 CGTTGCGATTTTCATTTCGCATTGCGATA
1308712 GTAATTTCCG
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
66 60 0.68
67 1 0.01
71 27 0.31
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.43
Consensus pattern (67 bp):
CGTTGCGATTTTCATTTCGCATTGCGATAATTAGCATTACGATTTTCATTTCGCATTGCGATTCC
CT
Found at i:1311017 original size:12 final size:12
Alignment explanation
Indices: 1311000--1311024 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1310990 TCTTCGGGGA
1311000 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1311012 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1311024 C
1 C
1311025 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1311238 original size:24 final size:24
Alignment explanation
Indices: 1311211--1311257 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1311201 CAAAATCCGT
* *
1311211 GTATTGACCAATATCAAAGTTCGG
1 GTATTGAACAAGATCAAAGTTCGG
*
1311235 GTATTGAACAAGATCAAATTTCG
1 GTATTGAACAAGATCAAAGTTCG
1311258 AATACTGACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (24 bp):
GTATTGAACAAGATCAAAGTTCGG
Found at i:1312366 original size:39 final size:38
Alignment explanation
Indices: 1312299--1312372 Score: 112
Period size: 39 Copynumber: 1.9 Consensus size: 38
1312289 ATTCATTTGA
*
1312299 CTATCGCAACGCGAAATGACTATCGCAACGCGAAATGG
1 CTATCGCAACGCGAAATGACTATCGCAACGAGAAATGG
**
1312337 CTATCGCAACGCGAAAATGGTTATCGCAACGAGAAA
1 CTATCGCAACGCG-AAATGACTATCGCAACGAGAAA
1312373 ATCGCAATGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 13 0.41
39 19 0.59
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.16
Consensus pattern (38 bp):
CTATCGCAACGCGAAATGACTATCGCAACGAGAAATGG
Found at i:1312374 original size:20 final size:19
Alignment explanation
Indices: 1312299--1312372 Score: 112
Period size: 19 Copynumber: 3.8 Consensus size: 19
1312289 ATTCATTTGA
*
1312299 CTATCGCAACGCGAAATGA
1 CTATCGCAACGCGAAATGG
1312318 CTATCGCAACGCGAAATGG
1 CTATCGCAACGCGAAATGG
1312337 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCG-AAATGG
* *
1312357 TTATCGCAACGAGAAA
1 CTATCGCAACGCGAAA
1312373 ATCGCAATGC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
19 34 0.67
20 17 0.33
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.16
Consensus pattern (19 bp):
CTATCGCAACGCGAAATGG
Found at i:1312434 original size:19 final size:19
Alignment explanation
Indices: 1312393--1312460 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
1312383 GAAATGAAAA
1312393 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1312409 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1312426 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1312445 TTGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1312461 TCGTTGCGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 29 0.63
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1314507 original size:20 final size:19
Alignment explanation
Indices: 1314472--1314537 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
1314462 GAAACTTAAA
1314472 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1314491 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1314511 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1314530 ATCGCAAC
1 ATCGCAAC
1314538 ACAAAATCGG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
19 23 0.57
20 17 0.43
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1314560 original size:32 final size:32
Alignment explanation
Indices: 1314511--1314588 Score: 113
Period size: 32 Copynumber: 2.4 Consensus size: 32
1314501 GGAAATGGCT
*
1314511 ATCGCAATGCGAAATGAAAATCGCAAC-ACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
*
1314543 ATCGGAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
*
1314575 ATCGCAACGTGAAA
1 ATCGCAACGCGAAA
1314589 CACAAATCGC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 10 0.24
32 31 0.76
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:1314578 original size:14 final size:14
Alignment explanation
Indices: 1314527--1314583 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
1314517 ATGCGAAATG
1314527 AAAATCGCAAC-AC
1 AAAATCGCAACGAC
* *
1314540 AAAATCGGAACGCGAA
1 AAAATCGCAA--CGAC
1314556 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1314572 AAAATCGCAACG
1 AAAATCGCAACG
1314584 TGAAACACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
13 9 0.26
14 11 0.31
15 1 0.03
16 6 0.17
18 8 0.23
ACGTcount: A:0.49, C:0.25, G:0.18, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1314617 original size:19 final size:19
Alignment explanation
Indices: 1314595--1314662 Score: 120
Period size: 19 Copynumber: 3.6 Consensus size: 19
1314585 GAAACACAAA
1314595 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1314614 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
1314632 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1314651 TCGCATTGCGAT
1 TCGCATTGCGAT
1314663 AGCCATTTCC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
18 17 0.37
19 29 0.63
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1314669 original size:19 final size:19
Alignment explanation
Indices: 1314595--1314690 Score: 113
Period size: 19 Copynumber: 5.1 Consensus size: 19
1314585 GAAACACAAA
*
1314595 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATATTCATT
*
1314614 TCGCGTTGCGAT-TTCATT
1 TCGCATTGCGATATTCATT
*
1314632 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATATTCATT
**
1314651 TCGCATTGCGATAGCCATT
1 TCGCATTGCGATATTCATT
* *
1314670 TCCGCGTTGCGATAGTCATT
1 T-CGCATTGCGATATTCATT
1314690 T
1 T
1314691 TCGTGTTGCG
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
18 17 0.25
19 34 0.50
20 17 0.25
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TCGCATTGCGATATTCATT
Found at i:1314681 original size:20 final size:19
Alignment explanation
Indices: 1314610--1314701 Score: 78
Period size: 19 Copynumber: 4.8 Consensus size: 19
1314600 TTGCGATTTT
**
1314610 CATTTCGCGTTGCGAT-TT
1 CATTTCGCGTTGCGATAGC
* ***
1314628 CATTTCGCATTGCGATTTT
1 CATTTCGCGTTGCGATAGC
*
1314647 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1314666 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1314686 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1314702 AAGTAAACTA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
18 15 0.23
19 23 0.36
20 23 0.36
21 3 0.05
ACGTcount: A:0.15, C:0.23, G:0.22, T:0.40
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1315150 original size:18 final size:18
Alignment explanation
Indices: 1315124--1315168 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1315114 GTCGATCAGA
*
1315124 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1315142 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1315160 TGATGGCTC
1 TGATGGCTC
1315169 CCGAAATGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1316508 original size:20 final size:20
Alignment explanation
Indices: 1316483--1316520 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1316473 AATAGTTTCT
1316483 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1316503 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1316521 GAGAGAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1316806 original size:22 final size:22
Alignment explanation
Indices: 1316781--1316824 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1316771 GATTTAGATA
1316781 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
1316803 GACGGATTTCGTCGGATATGGG
1 GACGGATTTCGCCGGAGATGGG
1316825 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.16, G:0.43, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1317037 original size:20 final size:20
Alignment explanation
Indices: 1317012--1317105 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1317002 GATTATGTAT
1317012 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1317032 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
1317052 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
1317073 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1317093 TATCGCATTGCGA
1 TATCGCGTTGCGA
1317106 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1317077 original size:41 final size:41
Alignment explanation
Indices: 1317032--1317109 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
1317022 CGAAAGTCAG
* * *
1317032 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
1317073 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
1317110 CCCAATTCGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:1317106 original size:20 final size:20
Alignment explanation
Indices: 1316992--1317106 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1316982 CGCTTTGAAA
*
1316992 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
1317013 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
1317033 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
1317053 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1317074 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1317094 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1317107 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1317125 original size:41 final size:41
Alignment explanation
Indices: 1317095--1317187 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 41
1317085 ATAGTCAGTA
* * *
1317095 TCGCATTGCGATTTTCCCAATTCGTGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* *
1317136 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
1317177 TCGCATTGCGA
1 TCGCATTGCGA
1317188 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:1317126 original size:21 final size:21
Alignment explanation
Indices: 1317095--1317170 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1317085 ATAGTCAGTA
*
1317095 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* * **
1317116 TCGTGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
*
1317136 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
1317157 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
1317171 ACTTATTCGC
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 15 0.35
21 28 0.65
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:1317144 original size:20 final size:20
Alignment explanation
Indices: 1317121--1317187 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
1317111 CCAATTCGTG
1317121 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
* ** *
1317141 TTGCGATTTTCCCAATTCGCG
1 TTGCGA-TTTACTTATTCGCA
1317162 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
1317182 TTGCGA
1 TTGCGA
1317188 ATTGGGAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (20 bp):
TTGCGATTTACTTATTCGCA
Found at i:1325562 original size:17 final size:18
Alignment explanation
Indices: 1325540--1325577 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1325530 GAAAAACAAA
* *
1325540 ATGGGCT-TGTATCTAAT
1 ATGGGCTATCTATATAAT
1325557 ATGGGCTATCTATATAAT
1 ATGGGCTATCTATATAAT
1325575 ATG
1 ATG
1325578 AAAACATAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (18 bp):
ATGGGCTATCTATATAAT
Found at i:1326978 original size:15 final size:14
Alignment explanation
Indices: 1326956--1326994 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 14
1326946 ATAGAAACAT
1326956 ATTTATTTCTATAA
1 ATTTATTTCTATAA
1326970 ATCTTATTTATCTATAA
1 AT-TTA-TT-TCTATAA
1326987 ATTTATTT
1 ATTTATTT
1326995 TATTTTATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 3 0.14
15 5 0.23
16 5 0.23
17 9 0.41
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTATTTCTATAA
Found at i:1326997 original size:17 final size:17
Alignment explanation
Indices: 1326963--1326994 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1326953 CATATTTATT
1326963 TCTATAAATCTTATTTA
1 TCTATAAATCTTATTTA
1326980 TCTATAAAT-TTATTT
1 TCTATAAATCTTATTT
1326995 TATTTTATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.56
Consensus pattern (17 bp):
TCTATAAATCTTATTTA
Found at i:1335285 original size:21 final size:21
Alignment explanation
Indices: 1335248--1335330 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
1335238 TTTTTGTGCA
1335248 GAGGGAATCGA-TCCCCCCCT
1 GAGGGAATCGATTCCCCCCCT
**
1335268 GAGGGAATCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCCCT
* *
1335289 GAAGGGGAACCGATTCCCCCCACA
1 G-A-GGGAATCGATTCCCCCC-CT
*
1335313 G-GGGAATCGATACCCCCC
1 GAGGGAATCGATTCCCCCC
1335331 TGGGGTTCTG
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
20 11 0.22
21 23 0.45
22 1 0.02
23 15 0.29
24 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCCCT
Found at i:1337683 original size:12 final size:12
Alignment explanation
Indices: 1337666--1337691 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1337656 AATTACTAAA
1337666 ATGTTTTGTTAT
1 ATGTTTTGTTAT
1337678 ATGTTTTGTTAT
1 ATGTTTTGTTAT
1337690 AT
1 AT
1337692 CAAAAAGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.15, T:0.65
Consensus pattern (12 bp):
ATGTTTTGTTAT
Found at i:1340460 original size:36 final size:36
Alignment explanation
Indices: 1340298--1340548 Score: 231
Period size: 36 Copynumber: 6.7 Consensus size: 36
1340288 ATTTCCAAAG
* *
1340298 AAACTATATATTATATGTTTTCAAGAA-CATTTTAAAA
1 AAACTATATATTATACGTTTTCAA-AACCATTTT-TAA
* * * * *
1340335 AAAGCCATATATTATATGTTTTCCAAAATGCGTTTTCAA
1 AAA-CTATATATTATACGTTTT-CAAAA-CCATTTTTAA
*
1340374 AAACTATATTATGTAT--GTTTTCCAAAACTATTTTTAAAGAA
1 AAACTATA-TAT-TATACGTTTT-CAAAACCATTTTT----AA
* *
1340415 AAACCATATATTATACGTTTTCAAAACCGTTTTTAA
1 AAACTATATATTATACGTTTTCAAAACCATTTTTAA
1340451 AAACTATATATTATACGTTTTCAAAACCATTTTTAAA
1 AAACTATATATTATACGTTTTCAAAACCATTTTT-AA
* *
1340488 AAACTATATATTATATGTTTTCAAAA-TATTTTTAA
1 AAACTATATATTATACGTTTTCAAAACCATTTTTAA
* *
1340523 AAACTATATATTATACGCTTTAAAAA
1 AAACTATATATTATACGTTTTCAAAA
1340549 ACTATATTAT
Statistics
Matches: 183, Mismatches: 18, Indels: 28
0.80 0.08 0.12
Matches are distributed among these distances:
35 25 0.14
36 40 0.22
37 34 0.19
38 34 0.19
39 14 0.08
40 22 0.12
41 14 0.08
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.41
Consensus pattern (36 bp):
AAACTATATATTATACGTTTTCAAAACCATTTTTAA
Found at i:1340570 original size:22 final size:22
Alignment explanation
Indices: 1340513--1340571 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
1340503 TGTTTTCAAA
1340513 ATAT-TTTTAAAAACTATATATT
1 ATATGTTTTAAAAAC-ATATATT
* *
1340535 ATACGCTTTAAAAA-ACTATATT
1 ATATGTTTTAAAAACA-TATATT
1340557 ATATGTTTTCAAAAA
1 ATATGTTTT-AAAAA
1340572 TACGTTTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
21 1 0.03
22 16 0.53
23 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (22 bp):
ATATGTTTTAAAAACATATATT
Found at i:1340611 original size:39 final size:36
Alignment explanation
Indices: 1340535--1340646 Score: 143
Period size: 36 Copynumber: 3.0 Consensus size: 36
1340525 ACTATATATT
* * *
1340535 ATACGCTTTAAAAAACTATATTATATGTTTTCAAAA
1 ATACGTTTTAAAAACCTATATTATATATTTTCAAAA
*
1340571 ATACGTTTTGAAAAACCATATATTATATTTTTTTCAAAA
1 ATACGTTTT-AAAAACC-TATATTATA-TATTTTCAAAA
* *
1340610 ATACGTTTTCAAAACCTATACTATATATTTTCAAAA
1 ATACGTTTTAAAAACCTATATTATATATTTTCAAAA
1340646 A
1 A
1340647 CTATATTTGA
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
36 19 0.28
37 14 0.21
38 15 0.22
39 19 0.28
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.40
Consensus pattern (36 bp):
ATACGTTTTAAAAACCTATATTATATATTTTCAAAA
Found at i:1340651 original size:97 final size:93
Alignment explanation
Indices: 1340457--1340653 Score: 218
Period size: 97 Copynumber: 2.1 Consensus size: 93
1340447 TTAAAAACTA
* * * *
1340457 TATATTATACGTTTTCAAAACCATTTTTAAAAAACTATATATTATATGTTTTCAAAATATTTTTA
1 TATATTATACGTTTTCAAAAACAGTTTTAAAAAACCATATATTATATGTTTTCAAAATATTTTCA
1340522 AAAACTATATATTATACGCTTTAAAAAAC
66 AAAACTATATATTATAC-CTTTAAAAAAC
* * * *
1340551 TATATTATATGTTTTCAAAAATACGTTTTGAAAAACCATATATTATATTTTTTTCAAAAATACGT
1 TATATTATACGTTTTCAAAAACA-GTTTTAAAAAACCATATATTATA-TGTTTTC-AAAATA--T
* * *
1340616 TTTCAAAACCTATACTA-TATA-TTTTCAAAAAC
61 TTTCAAAAACTATA-TATTATACCTTTAAAAAAC
1340648 TATATT
1 TATATT
1340654 TGAAATTATT
Statistics
Matches: 86, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
94 20 0.23
95 20 0.23
96 6 0.07
97 21 0.24
99 17 0.20
100 2 0.02
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.43
Consensus pattern (93 bp):
TATATTATACGTTTTCAAAAACAGTTTTAAAAAACCATATATTATATGTTTTCAAAATATTTTCA
AAAACTATATATTATACCTTTAAAAAAC
Found at i:1351787 original size:12 final size:12
Alignment explanation
Indices: 1351769--1351800 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1351759 TTAATAAGAA
1351769 AAAAATAATAAT
1 AAAAATAATAAT
*
1351781 CAAAATAATAAT
1 AAAAATAATAAT
1351793 AAAAATAA
1 AAAAATAA
1351801 AAATTCCTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:1353844 original size:38 final size:37
Alignment explanation
Indices: 1353796--1353937 Score: 128
Period size: 38 Copynumber: 3.7 Consensus size: 37
1353786 ATTTCCAAAG
1353796 AAACTATATATTATATGTTTTCAAAAGCATTTTTAAA
1 AAACTATATATTATATGTTTTCAAAAGCATTTTTAAA
* * * *
1353833 AACACCATATATTATATGTTTTTCAACATGC-GTTTTCAA
1 AA-ACTATATATTATATG-TTTTCAA-AAGCATTTTTAAA
* *
1353872 AAACTATAT-TATATATGTTTTCGAGAACCATTTTTAAAGAA
1 AAACTATATAT-TATATGTTTTC-AAAAGCATTTTT--A-AA
*
1353913 AAATTATATATTATAT-TTTTCAAAA
1 AAACTATATATTATATGTTTTCAAAA
1353938 CTATATATTA
Statistics
Matches: 83, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
37 10 0.12
38 31 0.37
39 18 0.22
40 8 0.10
41 15 0.18
42 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (37 bp):
AAACTATATATTATATGTTTTCAAAAGCATTTTTAAA
Found at i:1353874 original size:40 final size:38
Alignment explanation
Indices: 1353801--1353875 Score: 105
Period size: 40 Copynumber: 1.9 Consensus size: 38
1353791 CAAAGAAACT
*
1353801 ATATATTATATGTTTTCAAAAGCATTTTTAAAAACACC
1 ATATATTATATGTTTTCAAAAGCATTTTCAAAAACACC
* *
1353839 ATATATTATATGTTTTTCAACATGCGTTTTCAAAAAC
1 ATATATTATATG-TTTTCAA-AAGCATTTTCAAAAAC
1353876 TATATTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 12 0.38
39 7 0.22
40 13 0.41
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (38 bp):
ATATATTATATGTTTTCAAAAGCATTTTCAAAAACACC
Found at i:1353937 original size:22 final size:23
Alignment explanation
Indices: 1353912--1353961 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
1353902 TTTTTAAAGA
* *
1353912 AAAATTATATATTATA-TTTTTC
1 AAAACTATATATTATACGTTTTC
1353934 AAAACTATATATTATACGTTTTC
1 AAAACTATATATTATACGTTTTC
1353957 AAAAC
1 AAAAC
1353962 CGCTTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (23 bp):
AAAACTATATATTATACGTTTTC
Found at i:1353942 original size:63 final size:60
Alignment explanation
Indices: 1353864--1353998 Score: 157
Period size: 63 Copynumber: 2.2 Consensus size: 60
1353854 TTCAACATGC
* * * *
1353864 GTTTTCAAAAACTATAT-TATATATGTTTTCGAGAACCATTTTTAAAGAAAAATTATATATTATA
1 GTTTTC-AAAACTATATAT-TATACGTTTTC-AAAACCACTTTT--A-AAAAACTATATATTATA
1353928 T
60 T
*
1353929 -TTTTCAAAACTATATATTATACGTTTTCAAAACCGCTTTTAAAAAACTATATATTATAT
1 GTTTTCAAAACTATATATTATACGTTTTCAAAACCACTTTTAAAAAACTATATATTATAT
1353988 GTTTTCAAAAC
1 GTTTTCAAAAC
1353999 CGTTTTTAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
59 17 0.27
60 11 0.17
62 9 0.14
63 20 0.32
64 6 0.10
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (60 bp):
GTTTTCAAAACTATATATTATACGTTTTCAAAACCACTTTTAAAAAACTATATATTATAT
Found at i:1353984 original size:37 final size:36
Alignment explanation
Indices: 1353934--1354033 Score: 155
Period size: 36 Copynumber: 2.8 Consensus size: 36
1353924 TATATTTTTC
1353934 AAAACTATATATTATACGTTTTCAAAACCGCTTTTAA
1 AAAACTATATATTATACGTTTTCAAAACCG-TTTTAA
* *
1353971 AAAACTATATATTATATGTTTTCAAAACCGTTTTTA
1 AAAACTATATATTATACGTTTTCAAAACCGTTTTAA
* *
1354007 AAAACAATATATTATACATTTTCAAAA
1 AAAACTATATATTATACGTTTTCAAAA
1354034 ACTATATTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
36 29 0.50
37 29 0.50
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.39
Consensus pattern (36 bp):
AAAACTATATATTATACGTTTTCAAAACCGTTTTAA
Found at i:1354034 original size:60 final size:60
Alignment explanation
Indices: 1353978--1354094 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 60
1353968 TAAAAAACTA
* * *
1353978 TATATTATATG-TTTTCAAAA-CCGTTTTTAAAAACAATATATTATACATTTTCAAAAAC
1 TATATTATATGTTTTTAAAAATACGTTTTGAAAAACAATATATTATACATTTTCAAAAAC
* *
1354036 TATATTATATGTTTTTAAAAATACGTTTTGAAAAACTATATATTATACCTTTTCAAAAA
1 TATATTATATGTTTTTAAAAATACGTTTTGAAAAACAATATATTATACATTTTCAAAAA
1354095 TGCGTTTTCA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
58 11 0.21
59 8 0.15
60 33 0.63
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (60 bp):
TATATTATATGTTTTTAAAAATACGTTTTGAAAAACAATATATTATACATTTTCAAAAAC
Found at i:1354035 original size:37 final size:37
Alignment explanation
Indices: 1353928--1354033 Score: 160
Period size: 37 Copynumber: 2.9 Consensus size: 37
1353918 ATATATTATA
*
1353928 TTTTTCAAAACTATATATTATACGTTTTCAAAACCGC
1 TTTTTAAAAACTATATATTATACGTTTTCAAAACCGC
* *
1353965 TTTTAAAAAACTATATATTATATGTTTTCAAAACCG-
1 TTTTTAAAAACTATATATTATACGTTTTCAAAACCGC
* *
1354001 TTTTTAAAAACAATATATTATACATTTTCAAAA
1 TTTTTAAAAACTATATATTATACGTTTTCAAAA
1354034 ACTATATTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
36 29 0.47
37 33 0.53
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.42
Consensus pattern (37 bp):
TTTTTAAAAACTATATATTATACGTTTTCAAAACCGC
Found at i:1354050 original size:22 final size:23
Alignment explanation
Indices: 1353999--1354056 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
1353989 TTTTCAAAAC
1353999 CGTTTTTAAAAACAATATATTATA
1 CGTTTTTAAAAAC-ATATATTATA
* *
1354023 CATTTTCAAAAAC-TATATTATA
1 CGTTTTTAAAAACATATATTATA
*
1354045 TGTTTTTAAAAA
1 CGTTTTTAAAAA
1354057 TACGTTTTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 18 0.62
24 11 0.38
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (23 bp):
CGTTTTTAAAAACATATATTATA
Found at i:1354070 original size:36 final size:36
Alignment explanation
Indices: 1354020--1354130 Score: 125
Period size: 36 Copynumber: 3.0 Consensus size: 36
1354010 ACAATATATT
* * *
1354020 ATACATTTTCAAAAACTATATTATATGTTTTTAAAA
1 ATACGTTTTCAAAAACTATATTATATATTTTCAAAA
*
1354056 ATACGTTTTGAAAAACTATA-TATTATACCTTTTCAAAA
1 ATACGTTTTCAAAAACTATATTA-TATA--TTTTCAAAA
* * *
1354094 ATGCGTTTTCAAAACCTATACTATATATTTTCAAAA
1 ATACGTTTTCAAAAACTATATTATATATTTTCAAAA
1354130 A
1 A
1354131 CTATATATTC
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
35 2 0.03
36 31 0.48
38 29 0.45
39 2 0.03
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.41
Consensus pattern (36 bp):
ATACGTTTTCAAAAACTATATTATATATTTTCAAAA
Found at i:1356774 original size:14 final size:14
Alignment explanation
Indices: 1356755--1356781 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1356745 ACATTAAGGG
1356755 GTGTATCGATACCT
1 GTGTATCGATACCT
1356769 GTGTATCGATACC
1 GTGTATCGATACC
1356782 CACAGGCAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (14 bp):
GTGTATCGATACCT
Found at i:1358141 original size:18 final size:18
Alignment explanation
Indices: 1358118--1358154 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1358108 GTTCTTAAGG
1358118 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
*
1358136 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
1358154 A
1 A
1358155 TGTGTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:1358930 original size:2 final size:2
Alignment explanation
Indices: 1358923--1358949 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1358913 GTGTTATAAC
1358923 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1358950 TTGAAAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1359069 original size:7 final size:7
Alignment explanation
Indices: 1359057--1359081 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1359047 TAATTATAAA
1359057 AGGGGTT
1 AGGGGTT
1359064 AGGGGTT
1 AGGGGTT
1359071 AGGGGTT
1 AGGGGTT
1359078 AGGG
1 AGGG
1359082 TTGAAGTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.60, T:0.24
Consensus pattern (7 bp):
AGGGGTT
Found at i:1359101 original size:12 final size:13
Alignment explanation
Indices: 1359079--1359112 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
1359069 TTAGGGGTTA
1359079 GGGTTGA-AGTTG
1 GGGTTGAGAGTTG
1359091 GGGTT-AGAGTTG
1 GGGTTGAGAGTTG
1359103 GGGTTGAGAG
1 GGGTTGAGAG
1359113 AGAAGAGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.05
12 15 0.75
13 4 0.20
ACGTcount: A:0.18, C:0.00, G:0.53, T:0.29
Consensus pattern (13 bp):
GGGTTGAGAGTTG
Found at i:1359108 original size:18 final size:18
Alignment explanation
Indices: 1359065--1359108 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1359055 AAAGGGGTTA
*
1359065 GGGGTTAGGGGTTAGGGTT
1 GGGGTT-GGGGTTAGAGTT
**
1359084 GAAGTTGGGGTTAGAGTT
1 GGGGTTGGGGTTAGAGTT
1359102 GGGGTTG
1 GGGGTTG
1359109 AGAGAGAAGA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.14, C:0.00, G:0.55, T:0.32
Consensus pattern (18 bp):
GGGGTTGGGGTTAGAGTT
Found at i:1359500 original size:19 final size:18
Alignment explanation
Indices: 1359463--1359506 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
1359453 GGACATGGTG
*
1359463 AATAATATTTTTTATTAAA
1 AATAA-ATTTTTTAATAAA
1359482 AATAAATTTTTTAAATAAA
1 AATAAATTTTTT-AATAAA
*
1359501 TATAAA
1 AATAAA
1359507 CGTGACACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATAAATTTTTTAATAAA
Found at i:1360217 original size:2 final size:2
Alignment explanation
Indices: 1360210--1360234 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1360200 CTTGTAGCGG
1360210 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1360235 CACACACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1361894 original size:2 final size:2
Alignment explanation
Indices: 1361889--1361919 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1361879 CCATTTAGCG
1361889 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1361920 TTTTCTGGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1363247 original size:25 final size:26
Alignment explanation
Indices: 1363172--1363248 Score: 68
Period size: 25 Copynumber: 3.0 Consensus size: 26
1363162 TGAGCCAACC
1363172 TATTCCTGGTCATTATAGCATCACTA
1 TATTCCTGGTCATTATAGCATCACTA
* * * * * ** *
1363198 TAAT-CTTGTTATTTTGGTTTTACTA
1 TATTCCTGGTCATTATAGCATCACTA
1363223 -ATTCCTGGTCATTATAGCATCACTA
1 TATTCCTGGTCATTATAGCATCACTA
1363248 T
1 T
1363249 GATCTTGTTA
Statistics
Matches: 33, Mismatches: 16, Indels: 4
0.62 0.30 0.08
Matches are distributed among these distances:
24 2 0.06
25 28 0.85
26 3 0.09
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (26 bp):
TATTCCTGGTCATTATAGCATCACTA
Found at i:1363248 original size:50 final size:50
Alignment explanation
Indices: 1363173--1363272 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
1363163 GAGCCAACCT
*
1363173 ATTCCTGGTCATTATAGCATCACTATAATCTTGTTATTTTGGTTTTACTA
1 ATTCCTGGTCATTATAGCATCACTATAATCTTGTTATTTTAGTTTTACTA
*
1363223 ATTCCTGGTCATTATAGCATCACTATGATCTTGTTATTTTAGTTTTACTA
1 ATTCCTGGTCATTATAGCATCACTATAATCTTGTTATTTTAGTTTTACTA
1363273 TTTATATGGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (50 bp):
ATTCCTGGTCATTATAGCATCACTATAATCTTGTTATTTTAGTTTTACTA
Found at i:1375754 original size:26 final size:26
Alignment explanation
Indices: 1375723--1375774 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1375713 TTTAAGTAAG
1375723 TTTTCATTTTCTACTAAAGTATCGAA
1 TTTTCATTTTCTACTAAAGTATCGAA
1375749 TTTTCATTTTCTACTAAAGTATCGAA
1 TTTTCATTTTCTACTAAAGTATCGAA
1375775 AGTATAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (26 bp):
TTTTCATTTTCTACTAAAGTATCGAA
Found at i:1389094 original size:9 final size:9
Alignment explanation
Indices: 1389039--1389095 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
1389029 AAAACAAAGG
1389039 AAAAT-GAT
1 AAAATAGAT
*
1389047 AAAATAAAT
1 AAAATAGAT
*
1389056 ACAAATAGAC
1 A-AAATAGAT
*
1389066 AAAATAAAT
1 AAAATAGAT
*
1389075 AAAAT-GGT
1 AAAATAGAT
1389083 AAAATAGAT
1 AAAATAGAT
1389092 AAAA
1 AAAA
1389096 ATAAAACATA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
8 11 0.29
9 20 0.53
10 7 0.18
ACGTcount: A:0.68, C:0.04, G:0.09, T:0.19
Consensus pattern (9 bp):
AAAATAGAT
Found at i:1389535 original size:19 final size:17
Alignment explanation
Indices: 1389503--1389538 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
1389493 AATAAAAACC
1389503 AAAAAGAAAAAATAATA
1 AAAAAGAAAAAATAATA
1389520 AAAAAGAACTAAAATAATA
1 AAAAAGAA--AAAATAATA
1389539 GATAGTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
19 9 0.53
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAAAGAAAAAATAATA
Found at i:1389562 original size:13 final size:13
Alignment explanation
Indices: 1389544--1389569 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1389534 TAATAGATAG
1389544 TAAACAAATAAAA
1 TAAACAAATAAAA
1389557 TAAACAAATAAAA
1 TAAACAAATAAAA
1389570 ATACATATTA
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:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
TAAACAAATAAAA
Found at i:1391532 original size:85 final size:85
Alignment explanation
Indices: 1391366--1392906 Score: 1678
Period size: 85 Copynumber: 18.0 Consensus size: 85
1391356 TACTATGTGG
* * * * * * * * ** *
1391366 TTGATATGCCATCGAGCTCAATGGAATCGAACTCGACA-GTTTTTGTCGACAGATAGCTTTTATC
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAACCCTTCTC
* * *
1391430 GACTTAAGCTATGCTGTAAAT
65 GCCTTGAGTTATGCTGTAAAT
* ** * * * * * *
1391451 TTGACATGCCAATGAGCTGAATGGAATCGAACTCGAAGATATTTATTGATAGATAACCCTTCTCG
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCG
*
1391516 CCTTGAGTTATACTGTAAAT
66 CCTTGAGTTATGCTGTAAAT
* *
1391536 TGGATATGCCTTTGAGCTGATTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCG
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCG
*
1391601 CCTTGAGTTATGCTGCAAAT
66 CCTTGAGTTATGCTGTAAAT
* * * *
1391621 TTGATATGACTTTGAACTGAGTGTAATCGAACTCGAAGGTCTTTTGATGACAGATAGCCCTTCTC
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTC
*
1391686 GCCTTGAGCTATGCTGTAAAT
65 GCCTTGAGTTATGCTGTAAAT
* ** * * *
1391707 TTGATGTGCCTCGGAGCTGAGTGTAATCAAACTC-AAGGGGTCTTGGTTGACAGATAACCATTCT
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAA--GGTCTTTGTTGACAGATAACCCTTCT
*
1391771 CGCCTTGAGTTATGCTATAAAT
64 CGCCTTGAGTTATGCTGTAAAT
* * * * * ** *
1391793 TTGATATGCCTTTGAGCTGAGTATAATCAAACTCGAAGGTCTTTTGATAACATATAGGCCTTCTT
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTC
* * *
1391858 TCCTTGAGCTATACTGTAAAT
65 GCCTTGAGTTATGCTGTAAAT
* * * *
1391879 TTGATGTACCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCA
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCG
*
1391944 CCTTGAGTTATGTTGTAAA-
66 CCTTGAGTTATGCTGTAAAT
* * * * *
1391963 TTAATATG-CTTTGAGATGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAAATAGCCCTTCTC
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTC
**
1392027 GCCTTGAGCCATGCTGTAAAT
65 GCCTTGAGTTATGCTGTAAAT
* * * * * *
1392048 TTAATGTGCCTTTCAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTAACAGATAACCCTTCTTG
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCG
*
1392113 CCTTGAGTTATACTGTAAA-
66 CCTTGAGTTATGCTGTAAAT
* *
1392132 TTGATATGCCTTTGAGCTGAGTGTAATCGATCTCGAAGGTCTTGGTTGACAGATAACCCTTCTCG
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCG
*
1392197 CCTTGAGTTATGCTATAAA-
66 CCTTGAGTTATGCTGTAAAT
* * * * *
1392216 TTAATATGCCTTTGAGCTAAGTGTAATCGATCTCGAATGTCTTTGTGATGACAAATAACCCTTCT
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGT--TGACAGATAACCCTTCT
* *
1392281 CGCCTTGAGCTATGTTGTAAAT
64 CGCCTTGAGTTATGCTGTAAAT
* * * * * *
1392303 TTGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTATTGGTTGATAGATAACCCTTATCG
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCG
*
1392368 CCTTGAGTTATGTTGTAAA-
66 CCTTGAGTTATGCTGTAAAT
* * * * * *
1392387 TTGACATGCCTTTGAGCTGTGTGTAATCAAACTTGAAGGTCTTTTGTTGACAGATAGCCCTTCTA
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTC
* *
1392452 ACCTTGAGCTATGCTGTAAAT
65 GCCTTGAGTTATGCTGTAAAT
* * * **
1392473 TTGATGTGCCTTTGAGCTGAGTATAATCGAACTCGAAGGTCTTGGTTGATGGATAACCCTTCTCG
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCG
1392538 CCTTGAGTTATGCTGTAAA-
66 CCTTGAGTTATGCTGTAAAT
* * * *
1392557 TTGATATGCCTTTGAGTTGGGAGTAATCGAACTCGAAGGTATTTTGTTGACAGATAACCCTTCTC
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT-CTTTGTTGACAGATAACCCTTCTC
* *
1392622 GCCTTAAGCTATGCTGTAAAT
65 GCCTTGAGTTATGCTGTAAAT
** * * *
1392643 TTGACGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTGGTTTACAGATAACCCTTCTCG
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCG
*
1392708 CCTTGAGTTACTTGAGTTATGTTGTAAA-
66 -C--------CTTGAGTTATGCTGTAAAT
* ** * * * * *
1392736 TTGATACGTTTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTCGACAAATAGCCTTTCTTG
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCG
* ***
1392801 CCTTGAGCTATGCTACGAAT
66 CCTTGAGTTATGCTGTAAAT
* *
1392821 TGGATATGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTC
1 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTC
* * * *
1392886 ACATTGAGCTATGCTGCAAAT
65 GCCTTGAGTTATGCTGTAAAT
1392907 AGAAAAAAAT
Statistics
Matches: 1216, Mismatches: 213, Indels: 53
0.82 0.14 0.04
Matches are distributed among these distances:
83 30 0.02
84 244 0.20
85 457 0.38
86 373 0.31
87 44 0.04
92 1 0.00
93 52 0.04
94 15 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (85 bp):
TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCG
CCTTGAGTTATGCTGTAAAT
Found at i:1405940 original size:22 final size:21
Alignment explanation
Indices: 1405914--1405957 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
1405904 TTAGTGCAGA
*
1405914 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCC-TGAAG
1405936 GGGAACCGATACCCCCTGAAG
1 GGGAACCGATACCCCCTGAAG
1405957 G
1 G
1405958 TTCTGTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.27, C:0.30, G:0.30, T:0.14
Consensus pattern (21 bp):
GGGAACCGATACCCCCTGAAG
Found at i:1405950 original size:21 final size:22
Alignment explanation
Indices: 1405914--1405957 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1405904 TTAGTGCAGA
* *
1405914 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCCTGAAG
1405936 GGGAACCGATA-CCCCCTGAAG
1 GGGAACCGATACCCCCCTGAAG
1405957 G
1 G
1405958 TTCTGTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.27, C:0.30, G:0.30, T:0.14
Consensus pattern (22 bp):
GGGAACCGATACCCCCCTGAAG
Found at i:1410495 original size:13 final size:13
Alignment explanation
Indices: 1410477--1410504 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1410467 TGCTCCATGA
1410477 AAAAAAGAGAAAG
1 AAAAAAGAGAAAG
1410490 AAAAAAGAGAAAG
1 AAAAAAGAGAAAG
1410503 AA
1 AA
1410505 CAACATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAAAGAGAAAG
Found at i:1413289 original size:19 final size:18
Alignment explanation
Indices: 1413258--1413317 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
1413248 AAAGCAAAGG
*
1413258 AAAAATGATAAAATAAAT
1 AAAAATGACAAAATAAAT
1413276 AAAAATAGACAAAATAAAT
1 AAAAAT-GACAAAATAAAT
** *
1413295 -AAAATGGTAAAATAGAT
1 AAAAATGACAAAATAAAT
1413312 AAAAAT
1 AAAAAT
1413318 TAAAATACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
17 9 0.25
18 16 0.44
19 11 0.31
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.20
Consensus pattern (18 bp):
AAAAATGACAAAATAAAT
Found at i:1413314 original size:9 final size:9
Alignment explanation
Indices: 1413259--1413315 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
1413249 AAGCAAAGGA
1413259 AAAAT-GAT
1 AAAATAGAT
*
1413267 AAAATAAAT
1 AAAATAGAT
*
1413276 AAAAATAGAC
1 -AAAATAGAT
*
1413286 AAAATAAAT
1 AAAATAGAT
*
1413295 AAAAT-GGT
1 AAAATAGAT
1413303 AAAATAGAT
1 AAAATAGAT
1413312 AAAA
1 AAAA
1413316 ATTAAAATAC
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
8 11 0.29
9 20 0.53
10 7 0.18
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (9 bp):
AAAATAGAT
Found at i:1413380 original size:21 final size:21
Alignment explanation
Indices: 1413326--1413390 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
1413316 ATTAAAATAC
*
1413326 AAAATGAAAAA-AAA-ATAAAA
1 AAAAT-AAAAACAAAGACAAAA
*
1413346 TAAAAT-AAAGCAAAGACAAAA
1 -AAAATAAAAACAAAGACAAAA
*
1413367 AAAATAAAAACAAAGGAGAAAA
1 AAAATAAAAACAAA-GACAAAA
1413389 AA
1 AA
1413391 GTAATGGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
19 3 0.08
20 8 0.22
21 17 0.47
22 8 0.22
ACGTcount: A:0.78, C:0.05, G:0.09, T:0.08
Consensus pattern (21 bp):
AAAATAAAAACAAAGACAAAA
Found at i:1413427 original size:22 final size:21
Alignment explanation
Indices: 1413402--1413443 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1413392 TAATGGAATT
* *
1413402 AAAATAAAAACAAGAACAAAAA
1 AAAAGAAAAAAAAGAA-AAAAA
1413424 AAAAGAAAAAAAAGAAAAAA
1 AAAAGAAAAAAAAGAAAAAA
1413444 GGATAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.86, C:0.05, G:0.07, T:0.02
Consensus pattern (21 bp):
AAAAGAAAAAAAAGAAAAAAA
Found at i:1413689 original size:26 final size:23
Alignment explanation
Indices: 1413642--1413723 Score: 67
Period size: 23 Copynumber: 3.4 Consensus size: 23
1413632 AATGCAGGAA
* *
1413642 AAAAAATATTAAAAACCA-AAAAG
1 AAAAAATAATAAAAA-AATAAAAG
*
1413665 AAAAAATAATAAAAAAGAACTAAAAT
1 AAAAAATAAT-AAAAA-AA-TAAAAG
* *
1413691 AATAGATAATAAAAAAATAAAAG
1 AAAAAATAATAAAAAAATAAAAG
1413714 AAACAAATAA
1 AAA-AAATAA
1413724 AAATATATAT
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
23 16 0.35
24 13 0.28
25 5 0.11
26 12 0.26
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.15
Consensus pattern (23 bp):
AAAAAATAATAAAAAAATAAAAG
Found at i:1413691 original size:19 final size:17
Alignment explanation
Indices: 1413659--1413694 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
1413649 ATTAAAAACC
1413659 AAAAAGAAAAAATAATA
1 AAAAAGAAAAAATAATA
1413676 AAAAAGAACTAAAATAATA
1 AAAAAGAA--AAAATAATA
1413695 GATAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
19 9 0.53
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAAAGAAAAAATAATA
Found at i:1413725 original size:18 final size:19
Alignment explanation
Indices: 1413685--1413725 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
1413675 AAAAAAGAAC
* *
1413685 TAAAATAATAGATAATAAA
1 TAAAATAAAAGATAACAAA
1413704 -AAAATAAAAGA-AACAAA
1 TAAAATAAAAGATAACAAA
1413721 TAAAA
1 TAAAA
1413726 ATATATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (19 bp):
TAAAATAAAAGATAACAAA
Found at i:1414113 original size:21 final size:20
Alignment explanation
Indices: 1414086--1414135 Score: 82
Period size: 21 Copynumber: 2.5 Consensus size: 20
1414076 CATCGCCTCG
*
1414086 CCGACCGCCGTAGACCAGCA
1 CCGACCGCCGTAGACCAACA
1414106 CCGAACCGCCGTAGACCAACA
1 CCG-ACCGCCGTAGACCAACA
1414127 CCGACCGCC
1 CCGACCGCC
1414136 ACTCATCGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.26, C:0.48, G:0.22, T:0.04
Consensus pattern (20 bp):
CCGACCGCCGTAGACCAACA
Found at i:1415147 original size:13 final size:13
Alignment explanation
Indices: 1415129--1415153 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1415119 AGAAGGCTGA
1415129 CAAATTTATTAAC
1 CAAATTTATTAAC
1415142 CAAATTTATTAA
1 CAAATTTATTAA
1415154 GATTTTAAAT
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:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (13 bp):
CAAATTTATTAAC
Found at i:1426661 original size:45 final size:46
Alignment explanation
Indices: 1426598--1426765 Score: 207
Period size: 46 Copynumber: 3.7 Consensus size: 46
1426588 ATCATTTTCA
* *
1426598 CATTTATGGAATCCTTTCATGCATGTT-ATGTACCATTATGCA-TTT
1 CATTTATGGCATCCTTTCATGCCT-TTAATGTACCATTATGCATTTT
* * * *
1426643 CATTTATGGCATCTTTTCATTCCTTTAATGCACCGTTATGCATTTT
1 CATTTATGGCATCCTTTCATGCCTTTAATGTACCATTATGCATTTT
* *
1426689 CATTTATGACATCCTTTCATGCCTTTAATGCT-CCATTAAGCATTTT
1 CATTTATGGCATCCTTTCATGCCTTTAATG-TACCATTATGCATTTT
* *
1426735 CATTTATGGCAACCTTTCATGCCTTTTATGT
1 CATTTATGGCATCCTTTCATGCCTTTAATGT
1426766 CAATTAAATG
Statistics
Matches: 105, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
44 2 0.02
45 34 0.32
46 69 0.66
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.45
Consensus pattern (46 bp):
CATTTATGGCATCCTTTCATGCCTTTAATGTACCATTATGCATTTT
Found at i:1427208 original size:22 final size:22
Alignment explanation
Indices: 1427166--1427219 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1427156 TGGCTCCTCA
1427166 GTATCGATAC--CCATACCATG
1 GTATCGATACTACCATACCATG
*
1427186 GTATCGATACTACCATACTATG
1 GTATCGATACTACCATACCATG
*
1427208 GTACCGATACTA
1 GTATCGATACTA
1427220 TGTTATGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 10 0.33
22 20 0.67
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (22 bp):
GTATCGATACTACCATACCATG
Found at i:1427289 original size:20 final size:21
Alignment explanation
Indices: 1427261--1427310 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
1427251 GTTTTGAAGG
*
1427261 GTATTGATACCTTCCC-TTCA
1 GTATCGATACCTTCCCTTTCA
*
1427281 GTATCGATA-CTTCCCTTTCG
1 GTATCGATACCTTCCCTTTCA
1427301 GTATCGATAC
1 GTATCGATAC
1427311 TGATTGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.20, C:0.28, G:0.14, T:0.38
Consensus pattern (21 bp):
GTATCGATACCTTCCCTTTCA
Found at i:1431545 original size:46 final size:46
Alignment explanation
Indices: 1431436--1431598 Score: 204
Period size: 46 Copynumber: 3.6 Consensus size: 46
1431426 ATCAAATTCA
* *
1431436 CATTTATGGCATCCTTTCATGCCTTTTATGCACCATTATACA-TTT
1 CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATACATTTT
*** * *
1431481 CATTTACAACAGCCTTTCATGCCTTTAATGTACCGTTATACATTTT
1 CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATACATTTT
* * * *
1431527 CATTTATGGCATCATTTCATTCCTTTAATGCACTGTTATGCATTTT
1 CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATACATTTT
1431573 CATTT-TGGGCATCCTTTCATGCCTTT
1 CATTTAT-GGCATCCTTTCATGCCTTT
1431599 TATGTCAATT
Statistics
Matches: 98, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
45 36 0.37
46 62 0.63
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.45
Consensus pattern (46 bp):
CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATACATTTT
Found at i:1432060 original size:54 final size:54
Alignment explanation
Indices: 1431955--1432594 Score: 818
Period size: 54 Copynumber: 11.9 Consensus size: 54
1431945 GTGCCTGTAT
* *
1431955 GGTTATTCATCCACATAGGATGAATT-CGTGAAATACACACTTAGTGACGAAAC
1 GGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAAC
* * * *
1432008 AGTCATTCATCCACATAGGATGAATTTCATGAAATGCACACTTAGTGCCGAAAC
1 GGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAAC
* * * *
1432062 GGTTATTCAT-CACATAGGATGAATTCCATGAAATGCAGACTTAGTGTCGAAAT
1 GGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAAC
* * *
1432115 GGTTATTCATCAACATAGGATGAATTCCGTGAAATGTACACTTAGTGTCGAAAC
1 GGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAAC
* * *
1432169 GGTTATTCATCCACATAGAATGAATTCCGTGAAATGCACATTTAGTACCGAAAC
1 GGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAAC
* * **
1432223 AGTTATTCATCCAAATAGGATGAATTCCGTGAAATGCACACTTAGTGCTAAAAC
1 GGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAAC
* * * * *
1432277 GGTTATTCATCCATATAGGATGAGTTCCATAAAATGCACACTTAGTGCCGAAAT
1 GGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAAC
* *
1432331 GGTTATTCATCCACATAGGATGAATTCTGTGAAATGCACACTTAGTGTCGAAAC
1 GGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAAC
** ** ** * * * *
1432385 AATTATTTGTCCACATAAAATAAATTCCGTAAAATGCACACTTAATGTCGAAAC
1 GGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAAC
* * * ** *
1432439 GTTTATTCATCTACTTAGGATGAATTTTGTGAAATGCACACTTAGTGCCGAAAT
1 GGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAAC
* *
1432493 GGTTATTCATCCACATAGGATGAATTTCGTGAAATGCACACTTAGTGACGAAAC
1 GGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAAC
* * * *
1432547 -GATATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCC
1 GGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCC
1432595 TATTTGGTAA
Statistics
Matches: 504, Mismatches: 81, Indels: 4
0.86 0.14 0.01
Matches are distributed among these distances:
53 115 0.23
54 389 0.77
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (54 bp):
GGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAAC
Found at i:1433084 original size:20 final size:20
Alignment explanation
Indices: 1433013--1433076 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
1433003 TGTTTTGAAG
*
1433013 GGTATCGATACCTTCCCTTT-
1 GGTATCGATA-CTCCCCTTTC
*
1433033 AGTATCGATACTCCCCTTTC
1 GGTATCGATACTCCCCTTTC
1433053 GGTATCGATACTCCCCTTTC
1 GGTATCGATACTCCCCTTTC
1433073 GGTA
1 GGTA
1433077 CTGATACTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.20
20 32 0.80
ACGTcount: A:0.17, C:0.31, G:0.16, T:0.36
Consensus pattern (20 bp):
GGTATCGATACTCCCCTTTC
Found at i:1438447 original size:13 final size:13
Alignment explanation
Indices: 1438431--1438455 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1438421 CCCCACATGA
1438431 AATGAAAAAAATG
1 AATGAAAAAAATG
1438444 AATGAAAAAAAT
1 AATGAAAAAAAT
1438456 CAAATTGTGA
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:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (13 bp):
AATGAAAAAAATG
Found at i:1439074 original size:20 final size:20
Alignment explanation
Indices: 1439045--1439082 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1439035 AGAGCTCATA
*
1439045 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1439065 TAGGAGCATATAGTTGCA
1 TAGGAGCATATAGATGCA
1439083 CGTGGTGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.32
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1452539 original size:3 final size:3
Alignment explanation
Indices: 1452533--1452592 Score: 111
Period size: 3 Copynumber: 19.7 Consensus size: 3
1452523 TTTAATAATA
1452533 ATT ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1452579 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
1452593 ATCTCTGTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1455078 original size:9 final size:9
Alignment explanation
Indices: 1455042--1455078 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
1455032 AATTTGAGGA
1455042 TATTTTATT
1 TATTTTATT
* *
1455051 AATTTTAAT
1 TATTTTATT
1455060 TATTTTATT
1 TATTTTATT
1455069 TATTTTATT
1 TATTTTATT
1455078 T
1 T
1455079 TGTATCCATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TATTTTATT
Found at i:1459394 original size:11 final size:11
Alignment explanation
Indices: 1459378--1459405 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1459368 AGCTTCAACT
1459378 CAATTTTCAAG
1 CAATTTTCAAG
1459389 CAATTTTCAAG
1 CAATTTTCAAG
1459400 CAATTT
1 CAATTT
1459406 ACTTAGGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (11 bp):
CAATTTTCAAG
Found at i:1460891 original size:44 final size:45
Alignment explanation
Indices: 1460841--1460979 Score: 210
Period size: 46 Copynumber: 3.1 Consensus size: 45
1460831 GTAACCATGC
*
1460841 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
1460885 AAATAAGCTTATGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGG-AATAAATGGTAAGTATATTGGTA
* *
1460931 AAATAAACTTACGAGCTTATGGAATGAATGGTAAGTATA-TGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1460975 AAATA
1 AAATA
1460980 TTGGATATAC
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
44 31 0.36
45 17 0.20
46 38 0.44
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:1473368 original size:40 final size:40
Alignment explanation
Indices: 1473313--1473434 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
1473303 TGCAGGTTTA
1473313 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
1473353 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1473393 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1473433 TA
1 TA
1473435 GCACTACGGT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:1473589 original size:46 final size:46
Alignment explanation
Indices: 1473539--1473660 Score: 129
Period size: 46 Copynumber: 2.6 Consensus size: 46
1473529 GTAACCATGC
*
1473539 AAATAAGCTTATGAGCTTACGGAA-CAATGGCAAGTATATTGAAAAA
1 AAATAAGCTTATGAGCTTACGGAATAAATGGCAAGTATATTG-AAAA
* * * * **
1473585 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTACGGAA--TAAATGGCAAGTATATTGAAAA
* *
1473633 AAATAAGCTTATGAGCTTATGGGATAAA
1 AAATAAGCTTATGAGCTTACGGAATAAA
1473661 AGGTAAGAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
46 26 0.41
48 24 0.38
49 14 0.22
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (46 bp):
AAATAAGCTTATGAGCTTACGGAATAAATGGCAAGTATATTGAAAA
Found at i:1473649 original size:48 final size:46
Alignment explanation
Indices: 1473539--1473654 Score: 135
Period size: 48 Copynumber: 2.5 Consensus size: 46
1473529 GTAACCATGC
* *
1473539 AAATAAGCTTATGAGCTTACGGAACAATGGCAAGTATATTGAAAAA
1 AAATAAGCTTATGAGCTTATGGAAAAATGGCAAGTATATTGAAAAA
* * * **
1473585 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTG-GTAA
1 AAATAAGCTTATGAGCTTATGGAA---AAATGGCAAGTATATTGAAAAA
1473633 AAATAAGCTTATGAGCTTATGG
1 AAATAAGCTTATGAGCTTATGG
1473655 GATAAAAGGT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 22 0.37
48 23 0.39
49 14 0.24
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.30
Consensus pattern (46 bp):
AAATAAGCTTATGAGCTTATGGAAAAATGGCAAGTATATTGAAAAA
Done.