Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000867.1 Hibiscus syriacus cultivar Beakdansim tig00001674_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: 604573
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 1 of 3
Found at i:2510 original size:16 final size:17
Alignment explanation
Indices: 2489--2523 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2479 AGGTATGCAT
2489 ATAGAT-AAATAAATTG
1 ATAGATCAAATAAATTG
*
2505 ATAGATCAAGTAAATTG
1 ATAGATCAAATAAATTG
2522 AT
1 AT
2524 GGGCTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.31
Consensus pattern (17 bp):
ATAGATCAAATAAATTG
Found at i:6140 original size:2 final size:2
Alignment explanation
Indices: 6135--6160 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6125 AACACACGCT
6135 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
6161 GTGGTCAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9739 original size:24 final size:26
Alignment explanation
Indices: 9711--9760 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
9701 TGATTTTATG
*
9711 TTAGG-GAGT-TGAACTTTTAAAATT
1 TTAGGAGAGTGTGAACTTATAAAATT
9735 TTAGGAGAGTGTGAACTTATAAAATT
1 TTAGGAGAGTGTGAACTTATAAAATT
9761 CTAGAGGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.22
25 4 0.17
26 14 0.61
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (26 bp):
TTAGGAGAGTGTGAACTTATAAAATT
Found at i:12283 original size:22 final size:21
Alignment explanation
Indices: 12246--12310 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
12236 TTTTACCCCC
*
12246 AATCTCAAATCATAAACTCTA
1 AATCTCAAATCATAAACCCTA
*
12267 AATCTCAAAATCTTAAACCCTA
1 AATCTC-AAATCATAAACCCTA
* * * *
12289 AAGCTTACATCTTAAACCCTA
1 AATCTCAAATCATAAACCCTA
12310 A
1 A
12311 CCTTAAAGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 21 0.55
22 17 0.45
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.28
Consensus pattern (21 bp):
AATCTCAAATCATAAACCCTA
Found at i:12689 original size:2 final size:2
Alignment explanation
Indices: 12682--12706 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12672 AGAAGCATGA
12682 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
12707 GACAGGGGTC
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:16324 original size:31 final size:31
Alignment explanation
Indices: 16289--16347 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
16279 TATAAAATAC
*
16289 TGATAAGTTTAATGATCCTTTTATAATAATT
1 TGATAAGTTTAATGATCATTTTATAATAATT
16320 TGATAAGTTTAATGATCATTTTATAATA
1 TGATAAGTTTAATGATCATTTTATAATA
16348 GTAACTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.47
Consensus pattern (31 bp):
TGATAAGTTTAATGATCATTTTATAATAATT
Found at i:28760 original size:5 final size:5
Alignment explanation
Indices: 28745--28790 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
28735 TTGATGATTA
* * *
28745 AATTT ATTTT AATTT AATTT AATAT -ATTT -ATTT ATTTT AATTT AAT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AAT
28791 GTATTTATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
4 7 0.21
5 27 0.79
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
AATTT
Found at i:28778 original size:23 final size:23
Alignment explanation
Indices: 28746--28798 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
28736 TGATGATTAA
28746 ATTTATTTTAATTTAATTTAATAT
1 ATTTA-TTTAATTTAATTTAATAT
* *
28770 ATTTATTTATTTTAATTTAATGT
1 ATTTATTTAATTTAATTTAATAT
28793 ATTTAT
1 ATTTAT
28799 ATTCTACCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
ATTTATTTAATTTAATTTAATAT
Found at i:29570 original size:17 final size:17
Alignment explanation
Indices: 29548--29582 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29538 AATTGGGGCC
29548 AAATGA-TAGAATATATA
1 AAATGACTA-AATATATA
29565 AAATGACTAAATATATA
1 AAATGACTAAATATATA
29582 A
1 A
29583 TTATATCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.60, C:0.03, G:0.09, T:0.29
Consensus pattern (17 bp):
AAATGACTAAATATATA
Found at i:36265 original size:16 final size:15
Alignment explanation
Indices: 36245--36320 Score: 58
Period size: 13 Copynumber: 5.4 Consensus size: 15
36235 TTTTTATAAA
36245 ATATATATTTTAATT
1 ATATATATTTTAATT
*
36260 ACTATAT-TTATATATT
1 A-TATATATTTTA-ATT
36276 AT-TATATTTTAATT
1 ATATATATTTTAATT
*
36290 AT-TA-ATTATAATT
1 ATATATATTTTAATT
*
36303 A-ATAT-TATTAATT
1 ATATATATTTTAATT
36316 A-ATAT
1 ATATAT
36321 TATTATATTC
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
13 22 0.43
14 10 0.20
15 10 0.20
16 9 0.18
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATATATTTTAATT
Found at i:36309 original size:30 final size:30
Alignment explanation
Indices: 36222--36310 Score: 82
Period size: 30 Copynumber: 3.1 Consensus size: 30
36212 ATTTTCAAAA
* *
36222 TATATTATAATTATT-TTTATAA--AATA-
1 TATATTTTAATTATTAATTATAATTAATAT
* *
36248 TATATTTTAATTACTATATT-T-ATATATTAT
1 TATATTTTAATTATTA-ATTATAAT-TAATAT
36278 TATATTTTAATTATTAATTATAATTAATAT
1 TATATTTTAATTATTAATTATAATTAATAT
36308 TAT
1 TAT
36311 TAATTAATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
26 14 0.29
27 1 0.02
28 2 0.04
29 6 0.12
30 24 0.49
31 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (30 bp):
TATATTTTAATTATTAATTATAATTAATAT
Found at i:36314 original size:56 final size:59
Alignment explanation
Indices: 36222--36342 Score: 137
Period size: 56 Copynumber: 2.1 Consensus size: 59
36212 ATTTTCAAAA
* *
36222 TATATTATAATTATTTTTATAAAATATATATTTTAATTACTA-TATT-TA-T-ATATTAT
1 TATATTATAATTATTATTATAAAATATATATTTTAATTAATATTATTATATTCAT-TTAT
* *
36278 TATATTTTAATTATTAATTAT-AATTA-ATATTATTAATTAATATTATTATATTCATTTAT
1 TATATTATAATTATT-ATTATAAAATATATATT-TTAATTAATATTATTATATTCATTTAT
36337 TATATT
1 TATATT
36343 CATTTAATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
55 5 0.09
56 27 0.49
57 8 0.15
58 2 0.04
59 11 0.20
60 2 0.04
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (59 bp):
TATATTATAATTATTATTATAAAATATATATTTTAATTAATATTATTATATTCATTTAT
Found at i:36317 original size:13 final size:13
Alignment explanation
Indices: 36279--36338 Score: 63
Period size: 13 Copynumber: 4.7 Consensus size: 13
36269 ATATATTATT
36279 ATATT-TTAATTA
1 ATATTATTAATTA
*
36291 TTAATTA-TAATTA
1 AT-ATTATTAATTA
36304 ATATTATTAATTA
1 ATATTATTAATTA
*
36317 ATATTATTATATTC
1 ATATTATTA-ATTA
36331 AT-TTATTA
1 ATATTATTA
36339 TATTCATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
12 5 0.12
13 31 0.76
14 5 0.12
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
ATATTATTAATTA
Found at i:36339 original size:13 final size:13
Alignment explanation
Indices: 36307--36348 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
36297 ATAATTAATA
*
36307 TTATTA-ATTAAT
1 TTATTATATTCAT
36319 ATTATTATATTCAT
1 -TTATTATATTCAT
36333 TTATTATATTCAT
1 TTATTATATTCAT
36346 TTA
1 TTA
36349 ATTTTTACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 22 0.81
14 5 0.19
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATTATATTCAT
Found at i:41816 original size:19 final size:20
Alignment explanation
Indices: 41785--41823 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
41775 CAAACACTCC
41785 TCTCTTATTCTTCATCATTT
1 TCTCTTATTCTTCATCATTT
*
41805 TCTCTT-TTCTTCTTCATTT
1 TCTCTTATTCTTCATCATTT
41824 CTTAAGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.10, C:0.26, G:0.00, T:0.64
Consensus pattern (20 bp):
TCTCTTATTCTTCATCATTT
Found at i:44770 original size:90 final size:90
Alignment explanation
Indices: 44612--44795 Score: 350
Period size: 90 Copynumber: 2.0 Consensus size: 90
44602 ACAACGAAAT
44612 TCCCCAATGCTAGCCTGTTAGACTTTAATAGCACTTCTAAACAAGAACTAACAACACTTCTATAA
1 TCCCCAATGCTAGCCTGTTAGACTTTAATAGCACTTCTAAACAAGAACTAACAACACTTCTATAA
*
44677 GCAATGCTAGCTTGCTAGTGCTCTA
66 GCAATGCTAGCTTGCTAGGGCTCTA
*
44702 TCCCTAATGCTAGCCTGTTAGACTTTAATAGCACTTCTAAACAAGAACTAACAACACTTCTATAA
1 TCCCCAATGCTAGCCTGTTAGACTTTAATAGCACTTCTAAACAAGAACTAACAACACTTCTATAA
44767 GCAATGCTAGCTTGCTAGGGCTCTA
66 GCAATGCTAGCTTGCTAGGGCTCTA
44792 TCCC
1 TCCC
44796 AGCTATCATG
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 92 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.29
Consensus pattern (90 bp):
TCCCCAATGCTAGCCTGTTAGACTTTAATAGCACTTCTAAACAAGAACTAACAACACTTCTATAA
GCAATGCTAGCTTGCTAGGGCTCTA
Found at i:48582 original size:99 final size:99
Alignment explanation
Indices: 48468--48652 Score: 334
Period size: 99 Copynumber: 1.9 Consensus size: 99
48458 ACAAGCTTAC
* * *
48468 TGTTGTGGGTCTGGGAAATGGATCCTGCCAACTCTGCATTTAAGGGACAGAAACTACCCTTCATG
1 TGTTGCGGGTCTGGGAAATGGATCCTGCCAACTCTGCAATCAAGGGACAGAAACTACCCTTCATG
48533 CTCTTAAAGATTGCTCCTTTGCAAGAGGTGCTGT
66 CTCTTAAAGATTGCTCCTTTGCAAGAGGTGCTGT
*
48567 TGTTGCGGGTCTGGGAAATGGATCCTGCCAACTCTGCAATCAAGGGACTGAAACTACCCTTCATG
1 TGTTGCGGGTCTGGGAAATGGATCCTGCCAACTCTGCAATCAAGGGACAGAAACTACCCTTCATG
48632 CTCTTAAAGATTGCTCCTTTG
66 CTCTTAAAGATTGCTCCTTTG
48653 AAAAAGAAGT
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
99 82 1.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (99 bp):
TGTTGCGGGTCTGGGAAATGGATCCTGCCAACTCTGCAATCAAGGGACAGAAACTACCCTTCATG
CTCTTAAAGATTGCTCCTTTGCAAGAGGTGCTGT
Found at i:56424 original size:12 final size:13
Alignment explanation
Indices: 56407--56435 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
56397 ATTTTGTGTT
56407 TTTTTA-TTTTTA
1 TTTTTATTTTTTA
56419 TTTTTATTTTTTA
1 TTTTTATTTTTTA
56432 TTTT
1 TTTT
56436 AAATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:58949 original size:21 final size:21
Alignment explanation
Indices: 58925--58966 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
58915 GCATGTAGCT
58925 GCAATTTAATTCTTGGATCGG
1 GCAATTTAATTCTTGGATCGG
58946 GCAATTTAATTCTTGGATCGG
1 GCAATTTAATTCTTGGATCGG
58967 ATAGTCCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (21 bp):
GCAATTTAATTCTTGGATCGG
Found at i:62698 original size:42 final size:42
Alignment explanation
Indices: 62649--62732 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
62639 ATACCGTTGT
*
62649 AAGTATGTGTTAAGTGCTACACTTT-TTTATTTTATTCACTTA
1 AAGTATGTGTTAAGTGCTA-AATTTGTTTATTTTATTCACTTA
*
62691 AAGTATGTGTTAAGTGCTAAATTTGTTTATTTTATTGACTTA
1 AAGTATGTGTTAAGTGCTAAATTTGTTTATTTTATTCACTTA
62733 CGTTGGTGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
41 4 0.10
42 35 0.90
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.50
Consensus pattern (42 bp):
AAGTATGTGTTAAGTGCTAAATTTGTTTATTTTATTCACTTA
Found at i:62768 original size:93 final size:92
Alignment explanation
Indices: 62597--62769 Score: 213
Period size: 93 Copynumber: 1.9 Consensus size: 92
62587 TACATCGGTG
* * * * **
62597 TAAATATGCGTTAAGTGCTATATGTTTTTATTTTATTTACTTATACCGTTGTAAGTATGTGTTAA
1 TAAATATGCGTTAAGTGCTAAATGTTTTTATTTTATTGACTTACACCGGTGTAAGTATACGTTAA
62662 GTGCTACACTTTTTTATTTTATTCACT
66 GTGCTACACTTTTTTATTTTATTCACT
* ***
62689 TAAAGTATGTGTTAAGTGCTAAAT-TTGTTTATTTTATTGACTTACGTTGGTGTAAGTATACGTT
1 TAAA-TATGCGTTAAGTGCTAAATGTT-TTTATTTTATTGACTTACACCGGTGTAAGTATACGTT
* *
62753 AATTGCTACATTTTTTT
64 AAGTGCTACACTTTTTT
62770 GTAGTAAGAA
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
92 6 0.09
93 61 0.91
ACGTcount: A:0.25, C:0.09, G:0.15, T:0.50
Consensus pattern (92 bp):
TAAATATGCGTTAAGTGCTAAATGTTTTTATTTTATTGACTTACACCGGTGTAAGTATACGTTAA
GTGCTACACTTTTTTATTTTATTCACT
Found at i:73438 original size:39 final size:39
Alignment explanation
Indices: 73369--73505 Score: 152
Period size: 39 Copynumber: 3.5 Consensus size: 39
73359 AACCAAAGCA
* * * *
73369 GGACTTGCCA-CTCTTGACGCAGCAGAATGCTCATCATCC
1 GGACTTG-CAGCTCTCGATGCAACAGGATGCTCATCATCC
* * *
73408 AGACTTGCAACTCTCGATGTAACTA-GATGCTCATCATCC
1 GGACTTGCAGCTCTCGATGCAAC-AGGATGCTCATCATCC
* *
73447 GGACTTGCAGCTCTCGATGCAGCAGGATGCTCATCACCC
1 GGACTTGCAGCTCTCGATGCAACAGGATGCTCATCATCC
*
73486 GGGCTTGCAGCTCTCGATGC
1 GGACTTGCAGCTCTCGATGC
73506 TCCAACATGT
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
38 3 0.04
39 79 0.95
40 1 0.01
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (39 bp):
GGACTTGCAGCTCTCGATGCAACAGGATGCTCATCATCC
Found at i:73520 original size:39 final size:39
Alignment explanation
Indices: 73395--73521 Score: 128
Period size: 39 Copynumber: 3.3 Consensus size: 39
73385 ACGCAGCAGA
* * * * * * *
73395 ATGCTCATCATCCAGACTTGCAACTCTCGATGTAACTAG
1 ATGCTCATCACCCGGACTTGCAGCTCTCGATGCACCAAC
* * **
73434 ATGCTCATCATCCGGACTTGCAGCTCTCGATGCAGCAGG
1 ATGCTCATCACCCGGACTTGCAGCTCTCGATGCACCAAC
* *
73473 ATGCTCATCACCCGGGCTTGCAGCTCTCGATGCTCCAAC
1 ATGCTCATCACCCGGACTTGCAGCTCTCGATGCACCAAC
*
73512 ATGTTCATCA
1 ATGCTCATCA
73522 ACTGCGCCTG
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (39 bp):
ATGCTCATCACCCGGACTTGCAGCTCTCGATGCACCAAC
Found at i:73520 original size:78 final size:78
Alignment explanation
Indices: 73369--73521 Score: 175
Period size: 78 Copynumber: 2.0 Consensus size: 78
73359 AACCAAAGCA
* * * *
73369 GGACTTGCCACTCTTGACGCAGCAGAATGCTCATCATCCAGACTTGCAACTCTCGATGTAACTAG
1 GGACTTGCCACTCTCGACGCAGCAGAATGCTCATCACCCAGACTTGCAACTCTCGATGTAACAAC
73434 ATGCTCATCATCC
66 ATGCTCATCATCC
* * * * * *
73447 GGACTTG-CAGCTCTCGATGCAGCAGGATGCTCATCACCCGGGCTTGCAGCTCTCGATGCT-CCA
1 GGACTTGCCA-CTCTCGACGCAGCAGAATGCTCATCACCCAGACTTGCAACTCTCGATG-TAACA
*
73510 ACATGTTCATCA
64 ACATGCTCATCA
73522 ACTGCGCCTG
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
77 2 0.03
78 59 0.95
79 1 0.02
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (78 bp):
GGACTTGCCACTCTCGACGCAGCAGAATGCTCATCACCCAGACTTGCAACTCTCGATGTAACAAC
ATGCTCATCATCC
Found at i:91781 original size:105 final size:105
Alignment explanation
Indices: 91599--92582 Score: 1799
Period size: 105 Copynumber: 9.4 Consensus size: 105
91589 AGGTTTTACC
*
91599 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
91664 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
91704 CAGAGCCAATTTCAACTTCACAACGAAGGTTATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
91769 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
91809 CAGAGCCAATTTCAACTTCCCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
91874 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTTAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
91914 CAGAGCCAATTTCAACTTCACAACGAAGGAT-TTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
91978 ATGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
92018 TAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
** *
92083 ACGAAAAGACCGCTGGTTGTCAACAAATATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
92123 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
92188 ACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
92228 TAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
92293 ACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
92333 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTTAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
92398 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
92438 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACTCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
92503 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
92543 CAGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
92583 GGAACAATAC
Statistics
Matches: 852, Mismatches: 26, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
104 100 0.12
105 752 0.88
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:95262 original size:52 final size:47
Alignment explanation
Indices: 95198--95581 Score: 187
Period size: 54 Copynumber: 7.3 Consensus size: 47
95188 TTTTAAAATA
*
95198 ATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATTTT-AAAT-AA-T-TTAT-AAATATGGATTG
* *
95250 ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAAATAATTTATTTTAAATAATTTATAAATATGGATTG
* * * *
95297 ATTTATGTTAAAATGAATTGATTTATTTT-AATAATTTATTAGTATGAATTG
1 ATTTATTTTAAAAT--A---ATTTATTTTAAATAATTTATAAATATGGATTG
* * * *
95348 ATTTATTTT-AAACAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATT--T-T-AAATAATTTA---T-AAATATGGATTG
* * * *
95402 ATTTATTATTGTAGTTTATGGATTGATTTATTTTAAATAATTTATTATTATGGATTG
1 ATTTA-T-TT-TA----A---AATAATTTATTTTAAATAATTTATAAATATGGATTG
* * **
95459 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATATATTG
1 ATTTATTTT-AAA-AT--A---ATTTATTTTAAATAATTTATAAATATGGATTG
* *
95513 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTT-AAA-AT--A---ATTTATTTTAAATAATTTATAAATATGGATTG
95567 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
95582 TAGATTGATT
Statistics
Matches: 273, Mismatches: 27, Indels: 66
0.75 0.07 0.18
Matches are distributed among these distances:
45 7 0.03
47 24 0.09
48 7 0.03
49 3 0.01
50 13 0.05
51 34 0.12
52 34 0.12
53 4 0.01
54 105 0.38
55 4 0.01
56 3 0.01
57 16 0.06
58 1 0.00
61 7 0.03
62 2 0.01
63 1 0.00
65 8 0.03
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (47 bp):
ATTTATTTTAAAATAATTTATTTTAAATAATTTATAAATATGGATTG
Found at i:95279 original size:14 final size:15
Alignment explanation
Indices: 95138--95285 Score: 181
Period size: 15 Copynumber: 9.5 Consensus size: 15
95128 TAATAAGGTT
95138 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
95153 ATTTATTTTGAAATA
1 ATTTATTTTAAAATA
*
95168 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
95183 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
95198 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
95213 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
95228 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
95247 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
95265 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
95279 ATTTATT
1 ATTTATT
95286 AGTATGGATT
Statistics
Matches: 116, Mismatches: 10, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
14 12 0.10
15 84 0.72
16 4 0.03
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.03
22 6 0.05
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:95370 original size:32 final size:32
Alignment explanation
Indices: 95309--95391 Score: 141
Period size: 32 Copynumber: 2.6 Consensus size: 32
95299 TTATGTTAAA
*
95309 ATGAATTGATTTATTTT-AATAATTTATTAGT
1 ATGAATTGATTTATTTTAAACAATTTATTAGT
95340 ATGAATTGATTTATTTTAAACAATTTATTAGT
1 ATGAATTGATTTATTTTAAACAATTTATTAGT
*
95372 ATGGATTGATTTATTTTAAA
1 ATGAATTGATTTATTTTAAA
95392 ATATGGATTG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 17 0.35
32 32 0.65
ACGTcount: A:0.36, C:0.01, G:0.11, T:0.52
Consensus pattern (32 bp):
ATGAATTGATTTATTTTAAACAATTTATTAGT
Found at i:95382 original size:130 final size:131
Alignment explanation
Indices: 95241--95844 Score: 547
Period size: 130 Copynumber: 4.6 Consensus size: 131
95231 TATTATAAAA
*
95241 TATGGATTGATTTATTTTAAAATA-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATGT
1 TATGGATTGATTTATTTTAAAATATATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTT
*
95305 TAAAATGAATTGATTTATTTTAATAATTTA-TTAGTAT-GAATTGATTTATTTTAAACAATTTAT
66 TAAAAT-AATTGATTTATTTTAATAATTTATTTAGTATAG-ATTGATTTATTTTAAATAATTTAT
95368 TAG
129 TAG
* *
95371 TATGGATTGATTTATTTTAAAATATGGATTGA-TTT--ATTATTGTAGTT--TATGGATTGATTT
1 TATGGATTGATTTATTTTAAAATAT--ATTTATTTTAAATAATT-TA-TTAGTATGGATTGATTT
* * * * * *
95431 ATTTT-AAATAATTTA-TTATTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAT
62 ATTTTAAAATAATTGATTTATT-T-TAATAATTTA-TTT--AGTATAGATTGATTTATTTTAAAT
95494 AATTTATTAG
122 AATTTATTAG
**
95504 TATATATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TATGGATTGATTTATTTT-AAA-AT--A-T-ATTTATTTTAAATAATTTATTAGTATGGATTGAT
* * * * *
95569 TTATTTTAAAAT-ATAGATTGA--TT-AT--TGTAGTT-GTATAGTTTGATTTATTTTAAATAAT
60 TTATTTTAAAATAATTGATTTATTTTAATAATTTATTTAGTATAGATTGATTTATTTTAAATAAT
95627 TTATTAG
125 TTATTAG
*
95634 TATGGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATTGATTGAT
1 TATGGATTGATTTATTTT-AAA-AT--A-T-ATTTATTTTAAATAATTTATTAGTATGGATTGAT
*
95699 TTATTTTAAAATATAGATTGATTTATTTTAAATAATTTA-TTATTATAGATTGATTTATTTTAAA
60 TTATTTT-AAA-ATA-ATTGATTTATTTT-AATAATTTATTTAGTATAGATTGATTTATTTTAAA
95763 TAATTTATT--
121 TAATTTATTAG
* * * * *
95772 TATAGATTTATTTATTTTAAAATATAGATGA-TTT--ATTATTGTAATT-GTATGGATTGATTTA
1 TATGGATTGATTTATTTTAAAATATA-TTTATTTTAAATAATT-T-ATTAGTATGGATTGATTTA
95833 TTTT-AAATAATT
63 TTTTAAAATAATT
95845 TATTAGTATG
Statistics
Matches: 398, Mismatches: 38, Indels: 79
0.77 0.07 0.15
Matches are distributed among these distances:
127 8 0.02
128 9 0.02
129 13 0.03
130 149 0.37
131 26 0.07
132 14 0.04
133 55 0.14
134 15 0.04
135 2 0.01
136 5 0.01
137 9 0.02
138 25 0.06
139 4 0.01
140 58 0.15
141 6 0.02
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.53
Consensus pattern (131 bp):
TATGGATTGATTTATTTTAAAATATATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTT
TAAAATAATTGATTTATTTTAATAATTTATTTAGTATAGATTGATTTATTTTAAATAATTTATTA
G
Found at i:95383 original size:18 final size:18
Alignment explanation
Indices: 95362--95409 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
95352 ATTTTAAACA
*
95362 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
95380 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
95402 ATTTATTA
1 ATTTATTA
95410 TTGTAGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:95396 original size:22 final size:22
Alignment explanation
Indices: 95371--95438 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
95361 AATTTATTAG
95371 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
***
95393 TATGGATTGATTTATTATTGTAGTT
1 TATGGATTGATTTA-T-TT-TAAAA
95418 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
95439 TAATTTATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 16 0.42
23 3 0.08
24 3 0.08
25 16 0.42
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:95458 original size:32 final size:32
Alignment explanation
Indices: 95417--95871 Score: 173
Period size: 32 Copynumber: 14.7 Consensus size: 32
95407 TTATTGTAGT
95417 TTATGGATTGATTTATTTTAAATAATTTATTA
1 TTATGGATTGATTTATTTTAAATAATTTATTA
95449 TTATGGATTGATTTA-TTT---TAA---A--A
1 TTATGGATTGATTTATTTTAAATAATTTATTA
95472 -TATGGATTGATTTATTTTAAATAATTTATTA
1 TTATGGATTGATTTATTTTAAATAATTTATTA
* **
95503 GTATATATTGATTTA-TTT---TAA---A--A
1 TTATGGATTGATTTATTTTAAATAATTTATTA
95526 -TATGGATTGATTTATTTTAAATAATTTATTA
1 TTATGGATTGATTTATTTTAAATAATTTATTA
* **
95557 GTATGGATTGATTTATTTTAAA-ATATAGATTGA
1 TTATGGATTGATTTATTTTAAATA-ATTTATT-A
* ** * *
95590 TTATTGTAGTTGTATAGTT-TGATTTATTTTAAATAATTTA
1 TTA-TGGA-TTG-AT--TTAT--TTTA-AATAATTTA-TTA
* * * *
95630 TTA-GTATGGATTGA-TTT--AT--TTTA-AA
1 TTATGGATTGATTTATTTTAAATAATTTATTA
* *
95655 ATATAGATTGATTTATTTTAAATAATTTATTA
1 TTATGGATTGATTTATTTTAAATAATTTATTA
* *
95687 GTATTGATTGATTTATTTT--A-AA---A-TA
1 TTATGGATTGATTTATTTTAAATAATTTATTA
95712 -TA--GATTGATTTATTTTAAATAATTTATTA
1 TTATGGATTGATTTATTTTAAATAATTTATTA
*
95741 TTATAGATTGATTTATTTTAAATAATTTA-T-
1 TTATGGATTGATTTATTTTAAATAATTTATTA
* *
95771 TTATAGATTTATTTATTTTAAAATATAGATGATTTATTA
1 TTATGGATTGATTTATTTT--AA-AT--A--ATTTATTA
*
95810 TTGTAATTGTATGGATTGATTTATTTTAAATAATTTATTA
1 -T-T-ATGG-----ATTGATTTATTTTAAATAATTTATTA
*
95850 GTATGGATTGATTTATTTTAAA
1 TTATGGATTGATTTATTTTAAA
95872 ATATTAATTG
Statistics
Matches: 324, Mismatches: 32, Indels: 134
0.66 0.07 0.27
Matches are distributed among these distances:
22 40 0.12
23 8 0.02
24 3 0.01
25 9 0.03
26 14 0.04
27 5 0.02
28 7 0.02
29 9 0.03
30 21 0.06
31 14 0.04
32 116 0.36
33 5 0.02
34 4 0.01
35 4 0.01
36 4 0.01
37 11 0.03
38 7 0.02
39 4 0.01
40 15 0.05
41 4 0.01
42 4 0.01
44 2 0.01
45 2 0.01
47 12 0.04
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (32 bp):
TTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:95464 original size:18 final size:17
Alignment explanation
Indices: 95416--95468 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 17
95406 ATTATTGTAG
95416 TTTATGGATTGATTTAT
1 TTTATGGATTGATTTAT
* *
95433 TTTA---AATAATTTAT
1 TTTATGGATTGATTTAT
95447 TATTATGGATTGATTTAT
1 T-TTATGGATTGATTTAT
95465 TTTA
1 TTTA
95469 AAATATGGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
14 9 0.32
15 3 0.11
17 7 0.25
18 9 0.32
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.58
Consensus pattern (17 bp):
TTTATGGATTGATTTAT
Found at i:95466 original size:22 final size:22
Alignment explanation
Indices: 95450--95492 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
95440 AATTTATTAT
95450 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
95472 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
95493 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:95482 original size:54 final size:54
Alignment explanation
Indices: 95265--95591 Score: 378
Period size: 54 Copynumber: 6.1 Consensus size: 54
95255 TTTTAAAATA
* *
95265 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATGTT-AAA-ATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* **
95317 ATTTATTTT-AATAATTTATTAGTATGAATTGATTTATTTTAAACA-ATTTATTAG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA-ATATGGATT-G
** * ** * * * ***
95371 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTATTGTAGTTTATGGATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TAAAATATGGATTG
*
95427 ATTTATTTTAAATAATTTATTATTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
**
95481 ATTTATTTTAAATAATTTATTAGTATATATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
95535 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
95589 ATT
1 ATT
95592 ATTGTAGTTG
Statistics
Matches: 229, Mismatches: 35, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
51 29 0.13
52 11 0.05
53 6 0.03
54 133 0.58
55 15 0.07
56 13 0.06
57 22 0.10
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:95587 original size:22 final size:22
Alignment explanation
Indices: 95562--95730 Score: 88
Period size: 22 Copynumber: 6.8 Consensus size: 22
95552 TATTAGTATG
95562 GATTGATTTATTTTAAAATATA
1 GATTGATTTATTTTAAAATATA
* ***
95584 GATTGA-TTATTGTAGTTGTATA
1 GATTGATTTATTTTA-AAATATA
*
95606 GTTTGATTTATTTTAAATAATTTATTA
1 GATTGATTTATTTT-AA-AA--TA-TA
*
95633 GTATGGATTGATTTATTTTAAAATATA
1 G-ATTGA-T---TTATTTTAAAATATA
95660 GATTGATTTATTTTAAATAATTTATTA
1 GATTGATTTATTTT-AA-AA--TA-TA
95687 GTATTGATTGATTTATTTTAAAATATA
1 G-ATTGA-T---TTATTTTAAAATATA
95714 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
95731 TAATTTATTA
Statistics
Matches: 113, Mismatches: 12, Indels: 44
0.67 0.07 0.26
Matches are distributed among these distances:
21 7 0.06
22 32 0.28
23 8 0.07
24 3 0.03
25 2 0.02
26 13 0.12
27 12 0.11
28 12 0.11
29 2 0.02
30 4 0.04
31 4 0.04
32 14 0.12
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATA
Found at i:95589 original size:76 final size:76
Alignment explanation
Indices: 95504--95676 Score: 267
Period size: 76 Copynumber: 2.3 Consensus size: 76
95494 AATTTATTAG
* *
95504 TATATATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
95569 TTATTTTAAAA
66 TTATTTTAAAA
* *** *
95580 TATAGATTGA-TTATTGTAGTTGTATAGTTTGATTTATTTTAAATAATTTATTAGTATGGATTGA
1 TATAGATTGATTTATTTTA-AAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
95644 TTTATTTTAAAA
65 TTTATTTTAAAA
95656 TATAGATTGATTTATTTTAAA
1 TATAGATTGATTTATTTTAAA
95677 TAATTTATTA
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
75 7 0.08
76 71 0.84
77 7 0.08
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (76 bp):
TATAGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
TTATTTTAAAA
Found at i:95645 original size:184 final size:185
Alignment explanation
Indices: 95339--95762 Score: 701
Period size: 184 Copynumber: 2.3 Consensus size: 185
95329 AATTTATTAG
* *
95339 TATGAATTGATTTATTTTAAACAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT-GA-TGAT
* * *
95404 TTATTATTGTAGTTTATGGATTGATTTATTTTAAATAATTTATTATTATGGATTGATTTATTTTA
64 TGATTATTGTAGTTTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA
*
95469 AAATATGGATTGATTTATTTTAAATAATTTATTAGTATAT-ATTGATTTATTTTAAAA
129 AAATATAGATTGATTTATTTTAAATAATTTATTAGTAT-TGATTGATTTATTTTAAAA
95526 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT-A-GATTG
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGATGATTG
*
95589 ATTATTGTAGTTGTATAGTTTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAA
66 ATTATTGTAGTT-TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAA
95654 AATATAGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAA
130 AATATAGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAA
* * *
95710 TATAGATTGATTTATTTTAAATAATTTATTATTATAGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
95763 TAATTTATTT
Statistics
Matches: 225, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
183 17 0.08
184 152 0.68
185 1 0.00
187 55 0.24
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (185 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGATGATTG
ATTATTGTAGTTTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
ATATAGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAA
Found at i:95902 original size:54 final size:55
Alignment explanation
Indices: 95608--95898 Score: 332
Period size: 54 Copynumber: 5.4 Consensus size: 55
95598 GTTGTATAGT
*
95608 TTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA-TAGA
1 TTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATTAGA
*
95662 TTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAATA-TAGA
1 TTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATTAGA
* *
95716 TTGATTTATTTTAAATAATTTATTATTATAGATTGATTTATTTT-AAATAATT-TA
1 TTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAAT-ATTAGA
* ** ** * * * **
95770 TTTATAGA-TTTATTTATTTTA-AAATATAGA-TGATTTATTATTGTAAT-TGTATGGA
1 TTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATT-TTAAAATAT-TA--GA
*
95825 TTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTA-A
1 TTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATTAGA
95879 TTGATTTATTTT-AATAATTT
1 TTGATTTATTTTAAATAATTT
95899 TATTGTAGTT
Statistics
Matches: 200, Mismatches: 25, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
51 10 0.05
52 10 0.05
53 25 0.12
54 115 0.57
55 7 0.04
56 10 0.05
57 13 0.06
58 10 0.05
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (55 bp):
TTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATTAGA
Found at i:95950 original size:31 final size:31
Alignment explanation
Indices: 95915--95973 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
95905 AGTTGTATGT
* *
95915 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
95946 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
95974 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:96338 original size:5 final size:5
Alignment explanation
Indices: 96328--96353 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
96318 TGACTTAGAA
96328 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
96354 ATAATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:99070 original size:21 final size:23
Alignment explanation
Indices: 99028--99086 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
99018 CGACCCAAAA
*
99028 TAATAAAAAAATATTATTTTTATT
1 TAATAAAAAAATATTA-TTTTAAT
*
99052 TAATAAAAACA-ATTA-TTTAAT
1 TAATAAAAAAATATTATTTTAAT
99073 TAA-AAAAATAATAT
1 TAATAAAAA-AATAT
99087 ATAGATAGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 5 0.17
21 9 0.30
22 2 0.07
23 4 0.13
24 10 0.33
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
TAATAAAAAAATATTATTTTAAT
Found at i:102455 original size:24 final size:25
Alignment explanation
Indices: 102410--102464 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
102400 AAATTCATAT
102410 ATAT-ATTTAAAAACTAAGATAA-C
1 ATATGATTTAAAAACTAAGATAATC
*
102433 ATATGATTTAAAAA-TATATATAATTC
1 ATATGATTTAAAAACTA-AGATAA-TC
102459 ATATGA
1 ATATGA
102465 ATTATCAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 6 0.22
24 14 0.52
26 7 0.26
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.36
Consensus pattern (25 bp):
ATATGATTTAAAAACTAAGATAATC
Found at i:108211 original size:18 final size:18
Alignment explanation
Indices: 108188--108223 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
108178 TCTAATGTGG
108188 CAGTTTCTAGAAGGTCCA
1 CAGTTTCTAGAAGGTCCA
108206 CAGTTTCTAGAAGGTCCA
1 CAGTTTCTAGAAGGTCCA
108224 GTCAGTGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (18 bp):
CAGTTTCTAGAAGGTCCA
Found at i:109413 original size:60 final size:60
Alignment explanation
Indices: 109346--109478 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 60
109336 TTTAAATTGA
* **
109346 TCCTTAAACTTTTAAATATTATAATAGC-ATCCCCAAACTATGACTCT-TATTCTAAGTTAG
1 TCCTTAAACTTTTAAACATTATAAT-GCAATCCCCAAACTATGACTCTCT-TTCTAAACTAG
* * * * *
109406 TCCTTAAACTTTTGAACATTCTAATTCAATCCCTAAACTATGAGTCTCTTTCTAAACTAG
1 TCCTTAAACTTTTAAACATTATAATGCAATCCCCAAACTATGACTCTCTTTCTAAACTAG
*
109466 TCCCTAAACTTTT
1 TCCTTAAACTTTT
109479 GAATCTTCCA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 1 0.02
60 60 0.97
61 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (60 bp):
TCCTTAAACTTTTAAACATTATAATGCAATCCCCAAACTATGACTCTCTTTCTAAACTAG
Found at i:112025 original size:18 final size:18
Alignment explanation
Indices: 112002--112037 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
111992 AACCCCAAAA
*
112002 TTAATATAAGTGACACTC
1 TTAATACAAGTGACACTC
*
112020 TTAATACAAGTGTCACTC
1 TTAATACAAGTGACACTC
112038 CTGTGATTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.33
Consensus pattern (18 bp):
TTAATACAAGTGACACTC
Found at i:112547 original size:2 final size:2
Alignment explanation
Indices: 112540--112569 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
112530 GAATCAATCA
112540 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
112570 ATTTTAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:114253 original size:22 final size:21
Alignment explanation
Indices: 114201--114262 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
114191 ATATAATTTG
114201 TATTAATAAT--AATAATAAT
1 TATTAATAATAAAATAATAAT
*
114220 TAATAA-ACATAAACATAATAAT
1 TATTAATA-ATAAA-ATAATAAT
**
114242 TATTAATAATAATTTAATAAT
1 TATTAATAATAAAATAATAAT
114263 ATTTTTGTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 1 0.03
19 7 0.21
21 8 0.24
22 17 0.50
23 1 0.03
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (21 bp):
TATTAATAATAAAATAATAAT
Found at i:126272 original size:7 final size:7
Alignment explanation
Indices: 126260--126285 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
126250 CTCTATTATC
126260 TTTAAAA
1 TTTAAAA
126267 TTTAAAA
1 TTTAAAA
126274 TTTAAAA
1 TTTAAAA
126281 TTTAA
1 TTTAA
126286 TTTCAATAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TTTAAAA
Found at i:126637 original size:2 final size:2
Alignment explanation
Indices: 126630--126663 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
126620 AAGCTCTTGC
126630 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
126664 TAACTTTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:127255 original size:11 final size:11
Alignment explanation
Indices: 127234--127271 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
127224 TATAATTATT
127234 TAAATAATTAAA
1 TAAA-AATTAAA
127246 TAAAAATTAAA
1 TAAAAATTAAA
*
127257 TAAAAAATAAA
1 TAAAAATTAAA
127268 -AAAA
1 TAAAA
127272 TTTAGGTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
TAAAAATTAAA
Found at i:127270 original size:19 final size:19
Alignment explanation
Indices: 127233--127269 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
127223 ATATAATTAT
*
127233 TTAAATAATTAAATAAAAA
1 TTAAATAATAAAATAAAAA
127252 TTAAATAA-AAAATAAAAA
1 TTAAATAATAAAATAAAAA
127270 AATTTAGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
TTAAATAATAAAATAAAAA
Found at i:135910 original size:2 final size:2
Alignment explanation
Indices: 135903--135931 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
135893 ATCATCTGCG
135903 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 T
135932 TATTGTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:146322 original size:24 final size:24
Alignment explanation
Indices: 146259--146324 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
146249 TTTAAATTAT
* * *
146259 AAACGAACACAAA-TGAACGAATAT
1 AAACGAACA-AAAGTAAACAAATAC
** *
146283 AAACGAACGGATGTAAACAAATAC
1 AAACGAACAAAAGTAAACAAATAC
146307 AAACGAACAAAAGTAAAC
1 AAACGAACAAAAGTAAAC
146325 GAACATAAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
23 1 0.03
24 31 0.97
ACGTcount: A:0.59, C:0.17, G:0.14, T:0.11
Consensus pattern (24 bp):
AAACGAACAAAAGTAAACAAATAC
Found at i:146809 original size:18 final size:18
Alignment explanation
Indices: 146752--146810 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
146742 GTATTTTATT
146752 TATGATAAACATCAATTC
1 TATGATAAACATCAATTC
* * *
146770 TATTAATTAAACCTTCTA-TC
1 TA-TGA-TAAA-CATCAATTC
146790 TATGATAAACATCAATTC
1 TATGATAAACATCAATTC
146808 TAT
1 TAT
146811 TATCACTTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
17 4 0.13
18 11 0.35
19 4 0.13
20 8 0.26
21 4 0.13
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (18 bp):
TATGATAAACATCAATTC
Found at i:146875 original size:129 final size:131
Alignment explanation
Indices: 146642--146884 Score: 427
Period size: 129 Copynumber: 1.9 Consensus size: 131
146632 TATTTTTTGT
146642 ATTAAACCTTCTATCTATGATAAACATCAATTCTATTATCACTTATCCACTATATGTATATATTT
1 ATTAAACCTTCTATCTATGATAAACATCAATTCTATTATCACTTATCCAC-ATA-GTATATATTT
* *
146707 AGATTCTATGATTATCCTACGTAGTAACATCAAATGTATTTTATTTATGATAAACATCAATTCTA
64 AGATTATATGATTATCCTACGTAATAACATCAAATGTATTTTATTTATGATAAACATCAATTCTA
146772 TTA
129 TTA
146775 ATTAAACCTTCTATCTATGATAAACATCAATTCTATTATCACTTATCCAC-TA-TATATATTTAG
1 ATTAAACCTTCTATCTATGATAAACATCAATTCTATTATCACTTATCCACATAGTATATATTTAG
*
146838 ATTATATGGTTATCCTACGTAATAACATCAAATGTATTTTATTTATG
66 ATTATATGATTATCCTACGTAATAACATCAAATGTATTTTATTTATG
146885 CACAATATGA
Statistics
Matches: 107, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
129 55 0.51
131 2 0.02
133 50 0.47
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42
Consensus pattern (131 bp):
ATTAAACCTTCTATCTATGATAAACATCAATTCTATTATCACTTATCCACATAGTATATATTTAG
ATTATATGATTATCCTACGTAATAACATCAAATGTATTTTATTTATGATAAACATCAATTCTATT
A
Found at i:149642 original size:32 final size:32
Alignment explanation
Indices: 149606--149666 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
149596 GTTAATAACT
*
149606 ATTTTGTAACAGCTAAATAAAACTTAATGATC
1 ATTTTGAAACAGCTAAATAAAACTTAATGATC
* * * *
149638 ATTTTGAAATAGTTCAATAAAATTTAATG
1 ATTTTGAAACAGCTAAATAAAACTTAATG
149667 GTTATTTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (32 bp):
ATTTTGAAACAGCTAAATAAAACTTAATGATC
Found at i:154884 original size:2 final size:2
Alignment explanation
Indices: 154877--154904 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
154867 AGAACTAAAT
154877 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
154905 AGAAAGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:159133 original size:39 final size:39
Alignment explanation
Indices: 159079--159155 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
159069 CATTGGATGA
* * *
159079 CTGGCTCAAGGACATGCCGGCAGTTGTATAGGGCATTTT
1 CTGGCTCAAGGACATGCCAGCAGTGGCATAGGGCATTTT
159118 CTGGCTCAAGGACATGCCAGCAGTGGCATAGGGCATTT
1 CTGGCTCAAGGACATGCCAGCAGTGGCATAGGGCATTT
159156 GATTTGCTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.25
Consensus pattern (39 bp):
CTGGCTCAAGGACATGCCAGCAGTGGCATAGGGCATTTT
Found at i:160461 original size:11 final size:11
Alignment explanation
Indices: 160426--160465 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
160416 TCGAGACTCG
160426 AGCTCGATTGA
1 AGCTCGATTGA
* *
160437 AGCTCAATTCA
1 AGCTCGATTGA
*
160448 AGCTCGTTTGA
1 AGCTCGATTGA
160459 AGCTCGA
1 AGCTCGA
160466 AGACGGGTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.28
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:162586 original size:13 final size:13
Alignment explanation
Indices: 162549--162599 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
162539 TCATATAATC
162549 AGATTTAGGTTTA
1 AGATTTAGGTTTA
* *
162562 GGGATTGA-GTTTA
1 -AGATTTAGGTTTA
*
162575 TGATTTAGGTTTA
1 AGATTTAGGTTTA
*
162588 AGATTTATGTTT
1 AGATTTAGGTTT
162600 TAGAGTTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
12 5 0.17
13 20 0.67
14 5 0.17
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.49
Consensus pattern (13 bp):
AGATTTAGGTTTA
Found at i:166135 original size:3 final size:3
Alignment explanation
Indices: 166129--166177 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
166119 ATTTTAAAAT
*
166129 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
166175 TTA
1 TTA
166178 CAAAACCCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:167409 original size:15 final size:14
Alignment explanation
Indices: 167389--167447 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 14
167379 ATCCATTAGT
167389 TTTTAATATTATTA
1 TTTTAATATTATTA
*
167403 CTTTTAAT-TTTTTAA
1 -TTTTAATATTATT-A
*
167418 TTTTAATTATTGTTA
1 TTTTAA-TATTATTA
*
167433 TTTT-ATTTTATTA
1 TTTTAATATTATTA
167446 TT
1 TT
167448 ACGTTTGATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 8 0.22
14 11 0.30
15 14 0.38
16 4 0.11
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (14 bp):
TTTTAATATTATTA
Found at i:167522 original size:14 final size:15
Alignment explanation
Indices: 167505--167537 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
167495 TATTATTAAG
167505 TTATATAA-ATATAT
1 TTATATAATATATAT
*
167519 TTATATAATATTTAT
1 TTATATAATATATAT
167534 TTAT
1 TTAT
167538 TTATTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATAATATATAT
Found at i:167895 original size:137 final size:135
Alignment explanation
Indices: 167615--167893 Score: 305
Period size: 137 Copynumber: 2.0 Consensus size: 135
167605 AAATAAACAT
* * * * *
167615 ATTTTGATATGTATTTATTATTTAATATCTAAGAAAAGAGCTGTCTTAAAATACCTAGAAGTCTT
1 ATTTTAATATGTATTTATTATTTAATATCAAAGAAAAGAACTGTCTTAAAACACCTAGAAGTATT
** * * ** *
167680 TTCTGATATTCTTAAATAAATAAATGTCTTACTTTTATAAATTGTATATATTAATCTATTTTTTA
66 TTCTGATATTCTTAAATAAATAAACATCTTACTTTTATAAATTATAAATATTAATCTAAATTATA
167745 GATAA
131 GATAA
* * *
167750 ATGTTTTAATATTTATTTATTTTTTAATATCAAAGGAAAGAACTGTCTTAAAACACCTAGAAGCT
1 A--TTTTAATATGTATTTATTATTTAATATCAAAGAAAAGAACTGTCTTAAAACACCTAGAAG-T
*
167815 ATTTTCTGATATT-TCTAAATAAATAAACATCTTA-TTTATATAAATTAATAAAT-TTACT-TAA
63 ATTTTCTGATATTCT-TAAATAAATAAACATCTTACTTT-TATAAATT-ATAAATATTAATCT-A
167876 AATTATAGTAATAA
124 AATTATAG--ATAA
167890 ATTT
1 ATTT
167894 AAATTAAATA
Statistics
Matches: 119, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
135 1 0.01
137 58 0.49
138 51 0.43
139 4 0.03
140 5 0.04
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (135 bp):
ATTTTAATATGTATTTATTATTTAATATCAAAGAAAAGAACTGTCTTAAAACACCTAGAAGTATT
TTCTGATATTCTTAAATAAATAAACATCTTACTTTTATAAATTATAAATATTAATCTAAATTATA
GATAA
Found at i:172965 original size:18 final size:20
Alignment explanation
Indices: 172928--172965 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
172918 CACGGAATGT
*
172928 AAGATTATCAATACGAATAA
1 AAGATTATCAAGACGAATAA
172948 AAGATTATC-AGA-GAATAA
1 AAGATTATCAAGACGAATAA
172966 GATTACTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.55, C:0.08, G:0.13, T:0.24
Consensus pattern (20 bp):
AAGATTATCAAGACGAATAA
Found at i:173190 original size:37 final size:39
Alignment explanation
Indices: 173098--173195 Score: 112
Period size: 38 Copynumber: 2.5 Consensus size: 39
173088 ATTTATTTTT
173098 TTAACAAATTTAAAAATATTTATATATTTTCTTTAAAAAA
1 TTAA-AAATTTAAAAATATTTATATATTTTCTTTAAAAAA
* * * *
173138 TT-TAAATTCATAAA-ATTTATATAATTTT-TTTACAAAA
1 TTAAAAATTTAAAAATATTTATAT-ATTTTCTTTAAAAAA
*
173175 TTAAAAATTTAAAAATGTTTA
1 TTAAAAATTTAAAAATATTTA
173196 ATGAAAGGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
37 18 0.38
38 23 0.49
39 4 0.09
40 2 0.04
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (39 bp):
TTAAAAATTTAAAAATATTTATATATTTTCTTTAAAAAA
Found at i:178721 original size:21 final size:21
Alignment explanation
Indices: 178692--178732 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
178682 TCGTGATTGT
* *
178692 GACCGTCGCGGGCGCTATTAA
1 GACCATCGCGAGCGCTATTAA
*
178713 GACCATCGCGATCGCTATTA
1 GACCATCGCGAGCGCTATTA
178733 CGGTCTTCAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.29, G:0.27, T:0.22
Consensus pattern (21 bp):
GACCATCGCGAGCGCTATTAA
Found at i:179997 original size:18 final size:20
Alignment explanation
Indices: 179965--180005 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
179955 GCCTTTTAAC
179965 ATTTTTAATGATATT-ATCG
1 ATTTTTAATGATATTGATCG
*
179984 ATTTTTAAT-TTATTGATCG
1 ATTTTTAATGATATTGATCG
180003 ATT
1 ATT
180006 AATCAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (20 bp):
ATTTTTAATGATATTGATCG
Found at i:185995 original size:2 final size:2
Alignment explanation
Indices: 185984--186013 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
185974 TCTATGATGT
185984 TA TA -A 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
186014 GGTAAAGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:206583 original size:33 final size:33
Alignment explanation
Indices: 206522--206627 Score: 113
Period size: 39 Copynumber: 3.0 Consensus size: 33
206512 AAATTTAATG
*
206522 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAA-TTTGAATAATATAATTTATATTTTAAAT
*
206556 TTAAATTTGAATAATATTATTTTTATTTTTATTTTAAAT
1 TTAAATTTGAATAATA-TA-----ATTTATATTTTAAAT
*
206595 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTT-GAATAATATAATTTATATTTTAAA
206628 AACATTTATC
Statistics
Matches: 62, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
33 10 0.16
34 20 0.32
39 24 0.39
40 8 0.13
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (33 bp):
TTAAATTTGAATAATATAATTTATATTTTAAAT
Found at i:206592 original size:39 final size:40
Alignment explanation
Indices: 206541--206624 Score: 134
Period size: 39 Copynumber: 2.1 Consensus size: 40
206531 GAATACTATA
* * *
206541 ATTTATATTTTAAATTTAAATTT-GAATAATATTATTTTT
1 ATTTTTATTTTAAATTTAAATTTCGAATAATATAATTTGT
206580 ATTTTTATTTTAAATTTAAATTTCGAATAATATAATTTGT
1 ATTTTTATTTTAAATTTAAATTTCGAATAATATAATTTGT
206620 ATTTT
1 ATTTT
206625 AAAAACATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 22 0.54
40 19 0.46
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (40 bp):
ATTTTTATTTTAAATTTAAATTTCGAATAATATAATTTGT
Found at i:208050 original size:21 final size:21
Alignment explanation
Indices: 208024--208079 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
208014 TATGCCATCT
208024 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
208045 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
208066 CCGCCA-GGTTACAT
1 CCG-CAGGGTTACAT
208080 GCATTTATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.20, C:0.34, G:0.25, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:213751 original size:37 final size:36
Alignment explanation
Indices: 213676--213751 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
213666 TTTTTATATT
*
213676 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
*
213712 TTTAAGTTTT-TAAAGAAAA-TATATAAATATTTTACAA
1 TTTAA-TTTTGTAAA-AAAATTATATAAATATTAT-CAA
213749 TTT
1 TTT
213752 GTAATATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 22 0.63
37 13 0.37
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.46
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:222185 original size:40 final size:41
Alignment explanation
Indices: 222140--222219 Score: 117
Period size: 40 Copynumber: 1.9 Consensus size: 41
222130 AATGAGCCAT
*
222140 TTGTTCGTATTTGTTCATTTAAT-TAAACGAACATAAAAAC
1 TTGTTCATATTTGTTCATTTAATATAAACGAACATAAAAAC
*
222180 TTGTTCATATTTGTTCGTTTAATAAATAAACGAACATAAA
1 TTGTTCATATTTGTTCATTTAAT--ATAAACGAACATAAA
222220 CAAACTTCCC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
40 21 0.60
43 14 0.40
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (41 bp):
TTGTTCATATTTGTTCATTTAATATAAACGAACATAAAAAC
Found at i:222597 original size:16 final size:17
Alignment explanation
Indices: 222572--222603 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
222562 ATTTTTATAG
222572 ATTT-ATTTTTATTAAA
1 ATTTAATTTTTATTAAA
222588 ATTTAATTTTTATTAA
1 ATTTAATTTTTATTAA
222604 CATCAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTAATTTTTATTAAA
Found at i:223763 original size:19 final size:21
Alignment explanation
Indices: 223739--223781 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
223729 CTTGATCACA
223739 AATAGAATG-AAA-AAATATT
1 AATAGAATGAAAACAAATATT
223758 AATAGAATGAAAACAAATATT
1 AATAGAATGAAAACAAATATT
223779 AAT
1 AAT
223782 TTAATAGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 9 0.41
20 3 0.14
21 10 0.45
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (21 bp):
AATAGAATGAAAACAAATATT
Found at i:223919 original size:25 final size:25
Alignment explanation
Indices: 223885--223940 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
223875 TGTATGTTGT
*
223885 AATAAACAAATAGCTCACATTTTAA
1 AATAAACAAATAACTCACATTTTAA
223910 AATAAACAAATAACTCACATTTTAA
1 AATAAACAAATAACTCACATTTTAA
*
223935 ACTAAA
1 AATAAA
223941 ATGATCTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.55, C:0.16, G:0.02, T:0.27
Consensus pattern (25 bp):
AATAAACAAATAACTCACATTTTAA
Found at i:228482 original size:15 final size:16
Alignment explanation
Indices: 228459--228493 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
228449 AACTTTTATT
228459 ATTAATTTGTAAT-AA
1 ATTAATTTGTAATGAA
*
228474 ATTAGTTTGTAATGAA
1 ATTAATTTGTAATGAA
228490 ATTA
1 ATTA
228494 TTTTAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (16 bp):
ATTAATTTGTAATGAA
Found at i:228664 original size:127 final size:127
Alignment explanation
Indices: 228524--228760 Score: 370
Period size: 127 Copynumber: 1.9 Consensus size: 127
228514 AACTCATCAT
228524 GTCGACATGATGAGTCCCGCTA-TTTTTAATTATTTTAAA-TTAAAAATAATTGCTTAATTTTTA
1 GTCGACATGATGAGTCCCGCTATTTTTTAATTATTTTAAATTTAAAAA-AATTG-TTAATTTTTA
* * * *
228587 AAATATATATTTTATATAGAATCATCACATCAATGTGACAATTTCTTCCAATGAAAGTCTTCAC
64 AAAAAAATATTTTATATAGAATCATCACATCAACGTGACAAATTCTTCCAATGAAAGTCTTCAC
*
228651 GTCGACATGATGAGTCCCGCTATTTTTTAATTATTTTAAATTTAAAAAAATTGTTTATTTTTAAA
1 GTCGACATGATGAGTCCCGCTATTTTTTAATTATTTTAAATTTAAAAAAATTGTTAATTTTTAAA
* * *
228716 AAAAATATTTTATATGGAATTATCACATCGACGTGACAAATTCTT
66 AAAAATATTTTATATAGAATCATCACATCAACGTGACAAATTCTT
228761 AAAAATATAT
Statistics
Matches: 100, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
127 71 0.71
128 22 0.22
129 7 0.07
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (127 bp):
GTCGACATGATGAGTCCCGCTATTTTTTAATTATTTTAAATTTAAAAAAATTGTTAATTTTTAAA
AAAAATATTTTATATAGAATCATCACATCAACGTGACAAATTCTTCCAATGAAAGTCTTCAC
Found at i:242501 original size:30 final size:33
Alignment explanation
Indices: 242467--242528 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
242457 TAAATTCATA
242467 TCTTAA-CATTAAA-A-ATATTTTTTATTTTTG
1 TCTTAACCATTAAATACATATTTTTTATTTTTG
*
242497 TCTTAACTCATTAAATACATTTTTTTTATTTT
1 TCTTAAC-CATTAAATACATATTTTTTATTTT
242529 AACTTAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 6 0.22
32 7 0.26
33 1 0.04
34 13 0.48
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.58
Consensus pattern (33 bp):
TCTTAACCATTAAATACATATTTTTTATTTTTG
Found at i:242577 original size:29 final size:29
Alignment explanation
Indices: 242522--242682 Score: 144
Period size: 30 Copynumber: 5.5 Consensus size: 29
242512 TACATTTTTT
*
242522 TTATTTTAACTTAAAAAATATATTTTAGTC
1 TTATTTTAACTT-AAAAATATATTTTAATC
*
242552 TTATTCTAACTTAAAAATATATTTTAATC
1 TTATTTTAACTTAAAAATATATTTTAATC
* *
242581 TTATTTTATTCTTAAAAATATATTTTAATT
1 TTATTTTA-ACTTAAAAATATATTTTAATC
* * * ** *
242611 TTATTTTAGCTCAAAAA-GTATTTTGTTT
1 TTATTTTAACTTAAAAATATATTTTAATC
* * * * *
242639 TTATCTTAACTTATGAGATATATTTTACTT
1 TTATTTTAACTTA-AAAATATATTTTAATC
*
242669 TTATTTTAATTTAA
1 TTATTTTAACTTAA
242683 GATATCTTTT
Statistics
Matches: 107, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
28 18 0.17
29 32 0.30
30 57 0.53
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (29 bp):
TTATTTTAACTTAAAAATATATTTTAATC
Found at i:242718 original size:24 final size:25
Alignment explanation
Indices: 242691--242742 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
242681 AAGATATCTT
242691 TTTAAAAATCAATATAAAAAT-ATA
1 TTTAAAAATCAATATAAAAATAATA
* * * *
242715 TTTATAAGTTAATATAAGAATAATA
1 TTTAAAAATCAATATAAAAATAATA
242740 TTT
1 TTT
242743 TTTTAAAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (25 bp):
TTTAAAAATCAATATAAAAATAATA
Found at i:242756 original size:27 final size:28
Alignment explanation
Indices: 242715--242804 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 28
242705 TAAAAATATA
242715 TTTATAAGTTAATATAAGAATAATATTTT
1 TTTA-AAGTTAATATAAGAATAATATTTT
*
242744 TTTAAAGTT-ATATAAGAATAAGATATATT
1 TTTAAAGTTAATATAAGAAT-A-ATATTTT
* * *
242773 TTT-AAGTTAAAATAAGAGTAA-ACTTT
1 TTTAAAGTTAATATAAGAATAATATTTT
242799 TTTAAA
1 TTTAAA
242805 ATAAAATAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
26 6 0.12
27 13 0.25
28 12 0.23
29 21 0.40
ACGTcount: A:0.47, C:0.01, G:0.09, T:0.43
Consensus pattern (28 bp):
TTTAAAGTTAATATAAGAATAATATTTT
Found at i:242774 original size:29 final size:26
Alignment explanation
Indices: 242709--242781 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 26
242699 TCAATATAAA
*
242709 AATATATTTATAAGTTAATATAAGAAT
1 AATATATTTTTAAGTT-ATATAAGAAT
*
242736 AATATTTTTTTAAAGTTATATAAGAAT
1 AATATATTTTT-AAGTTATATAAGAAT
242763 AAGATATATTTTTAAGTTA
1 -A-ATATATTTTTAAGTTA
242782 AAATAAGAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 19 0.47
28 12 0.30
29 9 0.22
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (26 bp):
AATATATTTTTAAGTTATATAAGAAT
Found at i:242787 original size:29 final size:27
Alignment explanation
Indices: 242709--242864 Score: 110
Period size: 26 Copynumber: 5.8 Consensus size: 27
242699 TCAATATAAA
*
242709 AATATATTTATAAGTTAATATAAGAAT
1 AATATATTTTTAAGTTAATATAAGAAT
*
242736 AATATTTTTTTAAAGTT-ATATAAGAAT
1 AATATATTTTT-AAGTTAATATAAGAAT
* *
242763 AAGATATATTTTTAAGTTAAAATAAGAGT
1 -A-ATATATTTTTAAGTTAATATAAGAAT
** *
242792 AA-ACT-TTTTTAAAATAAAATAA-AA-
1 AATA-TATTTTTAAGTTAATATAAGAAT
* * * *
242816 AATATATTTAATAATTTAAGATAAAAAT
1 AATATATTT-TTAAGTTAATATAAGAAT
242844 AAT-T-TTTTTAATGTTAATATA
1 AATATATTTTTAA-GTTAATATA
242865 TAAATTTAAT
Statistics
Matches: 103, Mismatches: 15, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
24 3 0.03
25 8 0.08
26 36 0.35
27 24 0.23
28 15 0.15
29 17 0.17
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (27 bp):
AATATATTTTTAAGTTAATATAAGAAT
Found at i:246375 original size:18 final size:18
Alignment explanation
Indices: 246331--246378 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
246321 TTTTTAAAGA
* *
246331 AAATATATAAATATTTTCC
1 AAATATAT-AATATTATAC
*
246350 AACT-TATAATATTATAC
1 AAATATATAATATTATAC
246367 AAATATATAATA
1 AAATATATAATA
246379 CGGATAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 11 0.46
18 10 0.42
19 3 0.12
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATATATAATATTATAC
Found at i:247263 original size:11 final size:11
Alignment explanation
Indices: 247247--247290 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
247237 ATAATCATAT
247247 TAATTTTTTTA
1 TAATTTTTTTA
*
247258 TAA-TTTTTCA
1 TAATTTTTTTA
*
247268 -GATTTTTTTA
1 TAATTTTTTTA
247278 TAATTTTTTTA
1 TAATTTTTTTA
247289 TA
1 TA
247291 TTTATAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
9 1 0.04
10 12 0.44
11 14 0.52
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (11 bp):
TAATTTTTTTA
Found at i:247323 original size:16 final size:15
Alignment explanation
Indices: 247292--247331 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
247282 TTTTTTATAT
247292 TTATAA-AATTAATA
1 TTATAATAATTAATA
247306 TTATAATAATTAAATA
1 TTATAATAATT-AATA
247322 TTATGAATAA
1 TTAT-AATAA
247332 AGTAAAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.26
15 4 0.17
16 8 0.35
17 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
TTATAATAATTAATA
Found at i:248636 original size:133 final size:130
Alignment explanation
Indices: 248456--248799 Score: 367
Period size: 128 Copynumber: 2.6 Consensus size: 130
248446 ACGGGTTGTC
* * * *
248456 ATGCCTAATTGCGATGCCTGCCTTGGTTCGTGAAAGAAGATTCCGAGCACGAGTTTTTCCCTTCC
1 ATGCCTAATTGCGAGGCCTACCTTGGTTCATGAAAGAAGATTCCGAGCACGAGTCTTTCCCTTCC
* * * * ***
248521 ATTCAACCATTACATTATGTTTGACGGTTAATAAGAGCTGACGATTGTTGTC-T-GGTTGTCTT-
66 ATTCAACCATTACATTATGTATGACGGTTAAGAAGAGC-GACCATTGCTGTCTTCAAATG-CTTG
248583 CAA
129 C-A
* * * * *
248586 ATGCTTTGCAATTGTGAGGCCTACCTTAGTTCATGGAAGAAGATTCCGAGCACGGGTCTTTCCCT
1 ATGC-CT--AATTGCGAGGCCTACCTTGGTTCATGAAAGAAGATTCCGAGCACGAGTCTTTCCCT
* * *
248651 T--GTTCAACCATTACA-TATGTATGATGGTTAAGAAGAGCGGCCATTGCTGTCTTCAAATGCTT
63 TCCATTCAACCATTACATTATGTATGACGGTTAAGAAGAGCGACCATTGCTGTCTTCAAATGCTT
248713 GGCA
128 -GCA
* * * *
248717 ATGCCTAATTGCGAGGCCTACCTTGGTTCTTGAAAGAAGATTCCGAGCACAAATCTTTCCCTCCC
1 ATGCCTAATTGCGAGGCCTACCTTGGTTCATGAAAGAAGATTCCGAGCACGAGTCTTTCCCTTCC
*
248782 ATTCAACCATTCCATTAT
66 ATTCAACCATTACATTAT
248800 ATCTGACCAT
Statistics
Matches: 174, Mismatches: 30, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
128 49 0.28
129 10 0.06
130 41 0.24
131 24 0.14
132 1 0.01
133 49 0.28
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (130 bp):
ATGCCTAATTGCGAGGCCTACCTTGGTTCATGAAAGAAGATTCCGAGCACGAGTCTTTCCCTTCC
ATTCAACCATTACATTATGTATGACGGTTAAGAAGAGCGACCATTGCTGTCTTCAAATGCTTGCA
Found at i:257102 original size:22 final size:22
Alignment explanation
Indices: 257074--257117 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
257064 ATACTCGGTT
257074 CTGTCCTTGAGGGAAAGCTTTC
1 CTGTCCTTGAGGGAAAGCTTTC
257096 CTGTCCTTGAGGGAAAGCTTTC
1 CTGTCCTTGAGGGAAAGCTTTC
257118 TTCAACAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (22 bp):
CTGTCCTTGAGGGAAAGCTTTC
Found at i:265078 original size:31 final size:31
Alignment explanation
Indices: 265016--265083 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
265006 TAGTAGTATC
*
265016 TAATTTTTTAATTCAATTAAGTACTTGAATT
1 TAATTTTTTAATTCAATTAAGTACTTAAATT
* * *
265047 TAATTTTTTTATTCAAATT-GGTATTTAAATT
1 TAATTTTTTAATTC-AATTAAGTACTTAAATT
265078 TAATTT
1 TAATTT
265084 CATCGTTCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (31 bp):
TAATTTTTTAATTCAATTAAGTACTTAAATT
Found at i:281789 original size:30 final size:31
Alignment explanation
Indices: 281754--281817 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
281744 ATAAGTAAAA
*
281754 ATAAATTTATAAGTTATCTA-TTTTTATATG
1 ATAAATTTATAACTTATCTATTTTTTATATG
*
281784 ATAAATTTATAACTTATTTATTTTTTATATG
1 ATAAATTTATAACTTATCTATTTTTTATATG
281815 ATA
1 ATA
281818 CTTAAATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (31 bp):
ATAAATTTATAACTTATCTATTTTTTATATG
Found at i:283886 original size:21 final size:21
Alignment explanation
Indices: 283862--283903 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
283852 TTCATATAGC
283862 AAATAATTCGTCATGACTGCT
1 AAATAATTCGTCATGACTGCT
*
283883 AAATAATTTGTCATGACTGCT
1 AAATAATTCGTCATGACTGCT
283904 GAATGAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (21 bp):
AAATAATTCGTCATGACTGCT
Found at i:284662 original size:17 final size:18
Alignment explanation
Indices: 284630--284664 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
284620 GGTCCCCGGG
284630 TGGATCTGCGGTTGGATT
1 TGGATCTGCGGTTGGATT
284648 TGGATCTGC-GTTGGATT
1 TGGATCTGCGGTTGGATT
284665 GGACTGGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.11, C:0.11, G:0.37, T:0.40
Consensus pattern (18 bp):
TGGATCTGCGGTTGGATT
Found at i:291889 original size:19 final size:19
Alignment explanation
Indices: 291852--291891 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
291842 CCTATATATA
* **
291852 ATTCGATTTAATTGGATTC
1 ATTCAATTTAATTCAATTC
291871 ATTCAATTTAATTCAATTC
1 ATTCAATTTAATTCAATTC
291890 AT
1 AT
291892 GCTCTTGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.47
Consensus pattern (19 bp):
ATTCAATTTAATTCAATTC
Found at i:293691 original size:13 final size:13
Alignment explanation
Indices: 293673--293698 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
293663 ATTAAATACT
293673 AGTAACATAATTG
1 AGTAACATAATTG
293686 AGTAACATAATTG
1 AGTAACATAATTG
293699 CTAACTAAGG
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:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
AGTAACATAATTG
Found at i:297340 original size:29 final size:29
Alignment explanation
Indices: 297308--297367 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
297298 TGGTAATAAT
* * *
297308 AAATTAAAGGGCTAAAACAGAAAAATAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
* *
297337 AAATTAAAAGACTAAAATAGCAAAACAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
297366 AA
1 AA
297368 CGTAGGGACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.65, C:0.08, G:0.13, T:0.13
Consensus pattern (29 bp):
AAATTAAAAGACTAAAACAGAAAAACAGA
Found at i:298977 original size:3 final size:3
Alignment explanation
Indices: 298965--299007 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
298955 ATGTAAAATG
*
298965 TAA T-A TAA TAA T-A TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
299008 ATAACGATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:299354 original size:43 final size:43
Alignment explanation
Indices: 299298--299501 Score: 157
Period size: 43 Copynumber: 4.7 Consensus size: 43
299288 TTAGGTGATA
*
299298 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTATGGTTG
* ** *
299341 ACACGGCTCCTACGTGATGAGGAGATCTGG---TCTGGGGAATG
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTATGG-TTG
* * * ** ** * *
299382 GCACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCT-ATGGT--TG
* *
299428 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCCATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTATGGTTG
* *
299471 ACACGACTCCTACGTGATGAGGAGATCTGGT
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGT
299502 CTGGGGATGA
Statistics
Matches: 125, Mismatches: 26, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
40 5 0.04
41 28 0.22
42 2 0.02
43 53 0.42
44 3 0.02
45 6 0.05
46 27 0.22
47 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (43 bp):
ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTATGGTTG
Found at i:299415 original size:130 final size:129
Alignment explanation
Indices: 299218--299548 Score: 466
Period size: 130 Copynumber: 2.6 Consensus size: 129
299208 GTGACAAGGT
* * * * ** *
299218 TCCTACATAATGAGGAAATCTGATC-GAGGGATGACACTTCTCCTACGTGATGAAGAGTTCTTGG
1 TCCTACGTGATGAGGAGATCTGGTCTG-GGGATGACACGGCTCATACGTGATGAAGAGTTC-TGG
* * *
299282 CCATCTTTAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGG
64 CCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCCATGGTTGACACGA
299347 C
129 C
*
299348 TCCTACGTGATGAGGAGATCTGGTCTGGGGAATGGCACGGCTCATACGTGATGAAGAGTTCTGGC
1 TCCTACGTGATGAGGAGATCTGGTCTGGGG-ATGACACGGCTCATACGTGATGAAGAGTTCTGGC
*
299413 CATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCCATGGTTGACACGAC
65 CATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCCATGGTTGACACGAC
* * * * * *
299478 TCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGTTCCTATGTGATGAGGACTACTGGCC
1 TCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
299543 ATCTTA
66 ATCTTA
299549 GGAATAATGG
Statistics
Matches: 179, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
129 33 0.18
130 119 0.66
131 27 0.15
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.27
Consensus pattern (129 bp):
TCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
ATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCCATGGTTGACACGAC
Found at i:299762 original size:35 final size:36
Alignment explanation
Indices: 299711--299790 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 36
299701 CGAGACAAAA
* * **
299711 TTTGTTTTTAAGGGAAAC-GTTCTCAAAGAT-GTTTAT
1 TTTG-TTTCAAGGGAAACAGAT-TCAAAGATGGTAAAT
299747 TTTGTTTCAAGGGAAACAGATTCAAAGATGGTAAAT
1 TTTGTTTCAAGGGAAACAGATTCAAAGATGGTAAAT
299783 TTTGTTTC
1 TTTGTTTC
299791 CAAAGAAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 20 0.53
36 18 0.47
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACAGATTCAAAGATGGTAAAT
Found at i:300072 original size:15 final size:15
Alignment explanation
Indices: 300048--300091 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
300038 AAGATGATCT
*
300048 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
300063 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
300078 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
300092 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:300236 original size:40 final size:40
Alignment explanation
Indices: 300187--300266 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
300177 GTTTTAATAA
*
300187 AAACAATCTCCAAGGTGGGTAGTTTT-AAAAGAAATTGTCT
1 AAACAATCTCAAAGGTGGGTA-TTTTCAAAAGAAATTGTCT
* * *
300227 AAACGATCTCAAATGTGGGTATTTTCAAAAGAAGTTGTCT
1 AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
300267 CGAGAGACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (40 bp):
AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
Found at i:300366 original size:64 final size:62
Alignment explanation
Indices: 300248--300371 Score: 167
Period size: 64 Copynumber: 2.0 Consensus size: 62
300238 AATGTGGGTA
* * * *
300248 TTTTCAAAAGAAGTTGTCTCGAGAGACAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTT
1 TTTTCAAAAGAAATTGTCTCAAGAGAAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
* * *
300310 TTTTCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAATAGACTCAAAGAT
1 TTTTCAAAAGAAATTGTC-TCAAGAGA-AAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
300372 GGATTACATC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
62 17 0.32
63 6 0.11
64 30 0.57
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (62 bp):
TTTTCAAAAGAAATTGTCTCAAGAGAAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
Found at i:300644 original size:64 final size:64
Alignment explanation
Indices: 300551--300788 Score: 259
Period size: 67 Copynumber: 3.6 Consensus size: 64
300541 AAAGATTTAC
* * * * * * *
300551 TTCAAGAGAAACTGTCTCAAGAAATACAAAATTCATTTT-AAGAGAAACAGATTCAAAGA-TTTT
1 TTCAAAAGAAATTATCTCAAGAGAGACAAAATT--TTTTCAA-AGAAACAAACTCAAAGATTTTT
300614 -T
63 GT
*
300615 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGCTTCCAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAATTATCTCAAGAGAGACAAAATTTT--TT-CAAAGAAACAAACTCAAAGATTTTT
300680 GT
63 GT
*
300682 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAATTATCTCAAGAGAGACAAAA-TTT-TTTC-AAAGAAACAAACTCAAAGATTTTT
300747 GT
63 GT
*
300749 TTCAAAA-AAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 TTCAAAAGAAATTATCTCAAGAGAGACAAAA-TTT-TTTCA
300789 GACTCAGAGA
Statistics
Matches: 154, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
62 2 0.01
64 29 0.19
65 16 0.10
66 36 0.23
67 67 0.44
68 3 0.02
69 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (64 bp):
TTCAAAAGAAATTATCTCAAGAGAGACAAAATTTTTTCAAAGAAACAAACTCAAAGATTTTTGT
Found at i:300660 original size:37 final size:37
Alignment explanation
Indices: 300604--300729 Score: 124
Period size: 37 Copynumber: 3.6 Consensus size: 37
300594 GAAACAGATT
300604 CAAAGATTTT-TTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAA-ATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
* * ** * *
300641 CAAAATTTTGCTTCCAAAGAAACAAAC-TCA-A-AG-
1 CAAAATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
*
300674 ---ATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAAATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
300708 CAAAATTTTGTTTCAAAAGAAA
1 CAAAATTTTGTTTCAAAAGAAA
300730 CAAACTCAAA
Statistics
Matches: 67, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
30 18 0.27
31 2 0.03
32 1 0.01
33 2 0.03
34 2 0.03
35 1 0.01
36 7 0.10
37 34 0.51
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (37 bp):
CAAAATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
Found at i:300699 original size:67 final size:67
Alignment explanation
Indices: 300593--300788 Score: 299
Period size: 67 Copynumber: 3.0 Consensus size: 67
300583 TCATTTTAAG
* * *
300593 AGAAACAGATTCAAAGA-TTTT-TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGCTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGCTTCA
300656 AA
66 AA
*
300658 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGCTTCA
300723 AA
66 AA
* * * *
300725 AGAAACAAACTCAAAGATTTTTGTTTCAAAA-AAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGCTTCA
300789 GACTCAGAGA
Statistics
Matches: 122, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
65 15 0.12
66 34 0.28
67 73 0.60
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (67 bp):
AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGCTTCA
AA
Found at i:300866 original size:27 final size:27
Alignment explanation
Indices: 300836--300985 Score: 169
Period size: 27 Copynumber: 5.4 Consensus size: 27
300826 CAAAACTTTG
* * *
300836 TTTCAAAATAAATAGACTCAAAGATTT
1 TTTCAAAAGAAACAAACTCAAAGATTT
*
300863 TTTCAAACGAAAC-AACTCAAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGA-TTT
* *
300890 TATTCAAAAGGAACAAACTCCAAGATTTT
1 T-TTCAAAAGAAACAAACTCAAAGA-TTT
*
300919 TATTCAAAAGGAACAAACTCAAAGATTT
1 T-TTCAAAAGAAACAAACTCAAAGATTT
*
300947 TTTCAAGAGGAAA-AAACTCAAAGATTT
1 TTTCAA-AAGAAACAAACTCAAAGATTT
300974 TTTCAAAAGAAA
1 TTTCAAAAGAAA
300986 TTGTCTTTAA
Statistics
Matches: 108, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
26 14 0.13
27 39 0.36
28 18 0.17
29 37 0.34
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (27 bp):
TTTCAAAAGAAACAAACTCAAAGATTT
Found at i:300916 original size:29 final size:27
Alignment explanation
Indices: 300851--300982 Score: 176
Period size: 29 Copynumber: 4.8 Consensus size: 27
300841 AAATAAATAG
* *
300851 ACTCAAAGATTTTTTCAAACGAAAC-A
1 ACTCAAAGATTTTTTCAAAAGGAACAA
300877 ACTCAAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGA-TTTT-TTCAAAAGGAACAA
*
300906 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGA-TTTT-TTCAAAAGGAACAA
* *
300935 ACTCAAAGATTTTTTCAAGAGGAAAAA
1 ACTCAAAGATTTTTTCAAAAGGAACAA
300962 ACTCAAAGATTTTTTCAAAAG
1 ACTCAAAGATTTTTTCAAAAG
300983 AAATTGTCTT
Statistics
Matches: 96, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
26 9 0.09
27 36 0.38
28 14 0.15
29 37 0.39
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (27 bp):
ACTCAAAGATTTTTTCAAAAGGAACAA
Found at i:300964 original size:56 final size:55
Alignment explanation
Indices: 300851--300985 Score: 184
Period size: 56 Copynumber: 2.4 Consensus size: 55
300841 AAATAAATAG
* *
300851 ACTCAAAGATTTTTTCAAACGAAACAACTCAAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATTTTTATTCAAAAGGAAAAA
* * *
300906 ACTCCAAGATTTTTATTCAAAAGGAACAAACTCAAAGA-TTTT-TTCAAGAGGAAAAA
1 ACTCAAAGA-TTTT-TTCAAAAGAAAC-AACTCAAAGATTTTTATTCAAAAGGAAAAA
300962 ACTCAAAGATTTTTTCAAAAGAAA
1 ACTCAAAGATTTTTTCAAAAGAAA
300986 TTGTCTTTAA
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
54 10 0.14
55 12 0.17
56 24 0.34
57 14 0.20
58 10 0.14
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.27
Consensus pattern (55 bp):
ACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATTTTTATTCAAAAGGAAAAA
Found at i:301309 original size:37 final size:36
Alignment explanation
Indices: 301224--301322 Score: 103
Period size: 37 Copynumber: 2.8 Consensus size: 36
301214 GAGAAAATGA
* * *
301224 TGTCTCAAGCGAGACGAAATTTG--CTTTAAGATAC
1 TGTCTCAAGCGAGACAAAATTTGTTTTTTAAGAAAC
* ** *
301258 AGTCTCAAATGAGACAAAATTTGTTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTTA-AGAAAC
*
301295 TGTCTCAAGCGAGACAAAGTTTGTTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTTT
301323 GAGAAAACGA
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
34 19 0.37
36 4 0.08
37 28 0.55
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.34
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTTAAGAAAC
Found at i:301337 original size:36 final size:37
Alignment explanation
Indices: 301225--301344 Score: 99
Period size: 37 Copynumber: 3.4 Consensus size: 37
301215 AGAAAATGAT
* * *
301225 GTCTCAAGCGAGACGAAATTTG--CTTTA-AG-ATAC
1 GTCTCAAGCGAGACAAAATTTGTTTTTTAGAGAAAAC
** **
301258 AGTCTCAAATGAGACAAAATTTGTTTTTTAGAGAAATT
1 -GTCTCAAGCGAGACAAAATTTGTTTTTTAGAGAAAAC
*
301296 GTCTCAAGCGAGACAAAGTTTG-TTTTT-GAGAAAAC
1 GTCTCAAGCGAGACAAAATTTGTTTTTTAGAGAAAAC
*
301331 GATCTCAAGTGAGA
1 G-TCTCAAGCGAGA
301345 TCAACTTTGT
Statistics
Matches: 68, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
34 19 0.28
35 7 0.10
36 20 0.29
37 21 0.31
38 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (37 bp):
GTCTCAAGCGAGACAAAATTTGTTTTTTAGAGAAAAC
Found at i:301483 original size:105 final size:102
Alignment explanation
Indices: 301296--301533 Score: 270
Period size: 105 Copynumber: 2.3 Consensus size: 102
301286 TAGAGAAATT
*
301296 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGA-AAACGATCTCAAGTGAGATCAACTTTGTTTAA
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAAATAAACGATCTCAAGTGAGATCAACTTTGTTTAA
* *
301359 TGCGAAACAAATTCGAAATTT-TGATCTCAAAGGGAAAAG
64 TGCGAAACAAATTCAAAATTTGT-ATCTCAAAGGAAAAAG
* *
301398 GTCTCAAGCGAGACGAAATTTGTTTTGAAATAAACAAGAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTGAAATAAAC--G-ATCTCAA-GTGAGATCAACTTTGTTT
* * * *
301462 -TTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
62 AAT-GCGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAAG
* *
301503 GTCTCAAGCGAGACGCAATTTGTTTTAAAAT
1 GTCTCAAGCGAGACGAAATTTGTTTTGAAAT
301534 TTTCAAAATT
Statistics
Matches: 117, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
101 7 0.06
102 22 0.19
103 3 0.03
104 4 0.03
105 80 0.68
106 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (102 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAAATAAACGATCTCAAGTGAGATCAACTTTGTTTAATG
CGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAAG
Found at i:301632 original size:36 final size:37
Alignment explanation
Indices: 301548--301656 Score: 114
Period size: 38 Copynumber: 2.9 Consensus size: 37
301538 AAAATTTGTG
*
301548 GAAAAATGTCTCAAGCGAGACATAATTTG-TTTTAGA
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAGA
* *
301584 GAGAAAGTTGTCTCAAGCGAGATAAAATTTGTTTTTA-A
1 GA-AAA-ATGTCTCAAGCGAGACAAAATTTGTTTTTAGA
* * * *
301622 GAAAACTGTCTCTAGTGAGACGAAACTTTGTTTTT
1 GAAAAATGTCTCAAGCGAGAC-AAAATTTGTTTTT
301657 TTAATAAGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
36 14 0.23
37 18 0.30
38 24 0.39
39 5 0.08
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (37 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAGA
Found at i:301893 original size:4 final size:4
Alignment explanation
Indices: 301884--301915 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
301874 TCAATATGAA
301884 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
301916 TTTTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:302010 original size:4 final size:4
Alignment explanation
Indices: 301994--302170 Score: 306
Period size: 4 Copynumber: 45.0 Consensus size: 4
301984 ATGCAAATTT
**
301994 TATG TAT- TATG TATG TATG --TG TACA TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
302039 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
302087 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
302135 TATG TATG TATG TATG TATA TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG
302171 CTTTTCTCGA
Statistics
Matches: 164, Mismatches: 6, Indels: 6
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.01
3 3 0.02
4 159 0.97
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:303372 original size:12 final size:11
Alignment explanation
Indices: 303344--303381 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
303334 TCCTCTTTTG
*
303344 TTCTTTGCTTT
1 TTCTTTGATTT
303355 TTCTTTGATTT
1 TTCTTTGATTT
303366 TTGCTTTGATTT
1 TT-CTTTGATTT
303378 TTCT
1 TTCT
303382 CTTTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:303386 original size:18 final size:17
Alignment explanation
Indices: 303365--303411 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
303355 TTCTTTGATT
303365 TTTGCTTTGATTTTTCTC
1 TTTGCTTTGATTTTT-TC
303383 TTTGCTCTTTG-TTTTTTC
1 TTTG--CTTTGATTTTTTC
*
303401 TTTGGTTTGAT
1 TTTGCTTTGAT
303412 CTTTGCACTC
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 4 0.16
17 1 0.04
18 10 0.40
19 5 0.20
20 5 0.20
ACGTcount: A:0.04, C:0.13, G:0.15, T:0.68
Consensus pattern (17 bp):
TTTGCTTTGATTTTTTC
Found at i:303677 original size:13 final size:13
Alignment explanation
Indices: 303659--303683 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
303649 ATCCCCAGGG
303659 GATTAATTTTTAA
1 GATTAATTTTTAA
303672 GATTAATTTTTA
1 GATTAATTTTTA
303684 TTTAAATGAA
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:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
GATTAATTTTTAA
Done.