Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006573.1 Hibiscus syriacus cultivar Beakdansim tig00016106_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: 1218788
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:948186 original size:21 final size:21
Alignment explanation
Indices: 948160--948204 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
948150 AGATAGTTGT
948160 ATCAACGACTTGATCAATTGC
1 ATCAACGACTTGATCAATTGC
948181 ATCAACGACTTGATCAATTGC
1 ATCAACGACTTGATCAATTGC
948202 ATC
1 ATC
948205 GTTTGAGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.29
Consensus pattern (21 bp):
ATCAACGACTTGATCAATTGC
Found at i:949123 original size:23 final size:23
Alignment explanation
Indices: 949091--949142 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
949081 GAGAATAAAT
* *
949091 TCTCACGAAGACGTCGCTTTTAC
1 TCTCACGAAGACATCGCTTTCAC
*
949114 TCTCATGAAGACATCGCTTTCAC
1 TCTCACGAAGACATCGCTTTCAC
949137 TCTCAC
1 TCTCAC
949143 TTAAAGGGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.23, C:0.33, G:0.13, T:0.31
Consensus pattern (23 bp):
TCTCACGAAGACATCGCTTTCAC
Found at i:955785 original size:20 final size:20
Alignment explanation
Indices: 955760--955812 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
955750 CCCATCAAGA
955760 AGTATCGATACTCGGGGCCT
1 AGTATCGATACTCGGGGCCT
955780 AGTATCGATACTCGGGGCCT
1 AGTATCGATACTCGGGGCCT
*
955800 AGTATCGAAACTC
1 AGTATCGATACTC
955813 AGGGATTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (20 bp):
AGTATCGATACTCGGGGCCT
Found at i:956182 original size:21 final size:22
Alignment explanation
Indices: 956156--956196 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
956146 AGTTTCATTC
*
956156 AGAATTGAA-AAGGGAAACCAA
1 AGAATTCAATAAGGGAAACCAA
*
956177 AGAATTCAATGAGGGAAACC
1 AGAATTCAATAAGGGAAACC
956197 TTCTAATAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.51, C:0.12, G:0.24, T:0.12
Consensus pattern (22 bp):
AGAATTCAATAAGGGAAACCAA
Found at i:960524 original size:18 final size:19
Alignment explanation
Indices: 960483--960529 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
960473 CAACTTTTGG
960483 TCAAAGTCAACAAGTCATA
1 TCAAAGTCAACAAGTCATA
**
960502 TCAAAGTCAACATTTCA-A
1 TCAAAGTCAACAAGTCATA
960520 TCAAAGTCAA
1 TCAAAGTCAA
960530 TAGTTTAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.23
Consensus pattern (19 bp):
TCAAAGTCAACAAGTCATA
Found at i:960575 original size:20 final size:20
Alignment explanation
Indices: 960547--960590 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
960537 GATTAGTTCA
* *
960547 AGTTTACTCAGTTGGGTTTG
1 AGTTAACTCAGTTGGATTTG
* *
960567 AGTTAACTCGGTTTGATTTG
1 AGTTAACTCAGTTGGATTTG
960587 AGTT
1 AGTT
960591 GACTTAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.18, C:0.09, G:0.27, T:0.45
Consensus pattern (20 bp):
AGTTAACTCAGTTGGATTTG
Found at i:970721 original size:10 final size:11
Alignment explanation
Indices: 970699--970727 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
970689 ATAACCAAAA
970699 CATAAATATAT
1 CATAAATATAT
970710 CATAAA-ATAT
1 CATAAATATAT
970720 CATAAATA
1 CATAAATA
970728 AAATATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (11 bp):
CATAAATATAT
Found at i:975590 original size:21 final size:19
Alignment explanation
Indices: 975552--975597 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
975542 AATTAATCCT
975552 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
975572 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
975593 A-TAAT
1 ACTAAT
975598 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:993087 original size:21 final size:21
Alignment explanation
Indices: 993063--993142 Score: 97
Period size: 21 Copynumber: 3.7 Consensus size: 21
993053 AAAGTGCCAT
993063 AGTACACAAAGTACTACTACA
1 AGTACACAAAGTACTACTACA
* * * *
993084 AGTACACGAAGTGCTCCTGTCA
1 AGTACACAAAGTACTACT-ACA
*
993106 TAGTACACAAAGTACTACTCCA
1 -AGTACACAAAGTACTACTACA
993128 AGTACACAAAGTACT
1 AGTACACAAAGTACT
993143 CTTACGAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 30 0.61
22 4 0.08
23 15 0.31
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.21
Consensus pattern (21 bp):
AGTACACAAAGTACTACTACA
Found at i:997183 original size:25 final size:25
Alignment explanation
Indices: 997149--997196 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
997139 ATTTATAACT
997149 CAAATAAGA-TAAAATAATCATATTC
1 CAAATAAGATTAAAAT-ATCATATTC
* *
997174 CAAATCAGATTAAGATATCATAT
1 CAAATAAGATTAAAATATCATAT
997197 GCACATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.29
Consensus pattern (25 bp):
CAAATAAGATTAAAATATCATATTC
Found at i:1000864 original size:21 final size:21
Alignment explanation
Indices: 1000808--1000852 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1000798 TAAAAACTAA
* * *
1000808 AAAATTAAAAGTTTAGATACT
1 AAAATTGATAGTTTAAATACT
1000829 AAAATTGATAGTTTAAATACT
1 AAAATTGATAGTTTAAATACT
1000850 AAA
1 AAA
1000853 CATATAGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.33
Consensus pattern (21 bp):
AAAATTGATAGTTTAAATACT
Found at i:1008845 original size:21 final size:21
Alignment explanation
Indices: 1008797--1008845 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1008787 AAATTTTTTT
*
1008797 AGTTAATTAGTTTGTTAGTATA
1 AGTT-ATTACTTTGTTAGTATA
*
1008819 AATTATTACTTTGTTAGT-TGA
1 AGTTATTACTTTGTTAGTAT-A
1008840 AGTTAT
1 AGTTAT
1008846 ATTATATTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 19 0.83
22 3 0.13
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (21 bp):
AGTTATTACTTTGTTAGTATA
Found at i:1008853 original size:28 final size:30
Alignment explanation
Indices: 1008822--1008884 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 30
1008812 TAGTATAAAT
1008822 TATTACTTTGTTAGTTGAAG-T-TATATTA
1 TATTACTTTGTTAGTTGAAGTTATATATTA
* *
1008850 TATTAGTTTGTTAGTTTAAGTTATATATTA
1 TATTACTTTGTTAGTTGAAGTTATATATTA
1008880 TATTA
1 TATTA
1008885 TATAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 18 0.58
29 1 0.03
30 12 0.39
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.56
Consensus pattern (30 bp):
TATTACTTTGTTAGTTGAAGTTATATATTA
Found at i:1008943 original size:44 final size:49
Alignment explanation
Indices: 1008842--1008958 Score: 145
Period size: 44 Copynumber: 2.4 Consensus size: 49
1008832 TTAGTTGAAG
1008842 TTATATTATATTAGTTTGTTAGTTTAAGTTATATATTATATTATATAAAAAA
1 TTAT-TTA-ATTAGTTTGTTAGTTTAAGTTATATA-TATATTATATAAAAAA
* *
1008894 TTATTTAATTAGTTTCTTAGTTTAAGTTAT-TA-A-A-TGTA-AAAAAA
1 TTATTTAATTAGTTTGTTAGTTTAAGTTATATATATATTATATAAAAAA
*
1008938 TTATTTAATTAATTTGTTAGT
1 TTATTTAATTAGTTTGTTAGT
1008959 GTGTTTAAAC
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
44 25 0.41
45 3 0.05
46 1 0.02
47 1 0.02
49 2 0.03
50 22 0.36
51 3 0.05
52 4 0.07
ACGTcount: A:0.38, C:0.01, G:0.09, T:0.52
Consensus pattern (49 bp):
TTATTTAATTAGTTTGTTAGTTTAAGTTATATATATATTATATAAAAAA
Found at i:1009251 original size:10 final size:10
Alignment explanation
Indices: 1009236--1009263 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1009226 AAGAAACAAT
1009236 AAAGGAAAAG
1 AAAGGAAAAG
1009246 AAAGGAAAAG
1 AAAGGAAAAG
1009256 AAAGGAAA
1 AAAGGAAA
1009264 GGAAGAAGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (10 bp):
AAAGGAAAAG
Found at i:1009404 original size:15 final size:16
Alignment explanation
Indices: 1009380--1009409 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1009370 AATTTATTCC
1009380 TGTTTAAAAAATATTG
1 TGTTTAAAAAATATTG
1009396 TGTTT-AAAAATATT
1 TGTTTAAAAAATATT
1009410 TATTGTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (16 bp):
TGTTTAAAAAATATTG
Found at i:1009439 original size:19 final size:19
Alignment explanation
Indices: 1009385--1009439 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
1009375 ATTCCTGTTT
*
1009385 AAAAAATATTGTG-TTTAA
1 AAAAAATATTTTGTTTTAA
**
1009403 AAATATTTATTGTTGTTTTAA
1 AAA-AAATATT-TTGTTTTAA
1009424 AAAAAATATTTTGTTT
1 AAAAAATATTTTGTTT
1009440 AATTTATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 3 0.10
19 11 0.38
20 7 0.24
21 8 0.28
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (19 bp):
AAAAAATATTTTGTTTTAA
Found at i:1009526 original size:20 final size:20
Alignment explanation
Indices: 1009501--1009565 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
1009491 TATAATCTTA
1009501 AAATTTGTTTGATATTTAAC
1 AAATTTGTTTGATATTTAAC
* *
1009521 AAATTTGATTGATTAATTAAC
1 AAATTTGTTTGA-TATTTAAC
* *
1009542 AAATTTGTTTAATATTTAAA
1 AAATTTGTTTGATATTTAAC
1009562 AAAT
1 AAAT
1009566 AAAAAATATT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 21 0.55
21 17 0.45
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (20 bp):
AAATTTGTTTGATATTTAAC
Found at i:1009542 original size:21 final size:20
Alignment explanation
Indices: 1009501--1009548 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
1009491 TATAATCTTA
* *
1009501 AAATTTGTTTGATATTTAAC
1 AAATTTGATTGATAATTAAC
1009521 AAATTTGATTGATTAATTAAC
1 AAATTTGATTGA-TAATTAAC
1009542 AAATTTG
1 AAATTTG
1009549 TTTAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (20 bp):
AAATTTGATTGATAATTAAC
Found at i:1009693 original size:16 final size:17
Alignment explanation
Indices: 1009659--1009697 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
1009649 ATAAATAATT
1009659 ATCAGTATTCATTAGTAA
1 ATCA-TATTCATTAGTAA
*
1009677 ATCATATT-ATTATTAA
1 ATCATATTCATTAGTAA
1009693 ATCAT
1 ATCAT
1009698 TAAATATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 4 0.20
18 4 0.20
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (17 bp):
ATCATATTCATTAGTAA
Found at i:1010556 original size:30 final size:30
Alignment explanation
Indices: 1010520--1010585 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
1010510 AAATGGATTT
* *
1010520 AGTTTAGTGACCAAATTATAAA-TTTGGTAA
1 AGTTTAGTGACCAAAGTATAAACTTT-GAAA
*
1010550 AGTTTAGTGACTAAAGTATAAACTTTGAAA
1 AGTTTAGTGACCAAAGTATAAACTTTGAAA
1010580 AGTTTA
1 AGTTTA
1010586 AGGACTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 29 0.91
31 3 0.09
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.36
Consensus pattern (30 bp):
AGTTTAGTGACCAAAGTATAAACTTTGAAA
Found at i:1011824 original size:9 final size:9
Alignment explanation
Indices: 1011810--1011881 Score: 63
Period size: 9 Copynumber: 8.0 Consensus size: 9
1011800 ATTCCAATAC
*
1011810 TGGAATTTC
1 TGGAATTTA
* *
1011819 TTGAATTTT
1 TGGAATTTA
*
1011828 TTGAATTTA
1 TGGAATTTA
*
1011837 TGGAATTTT
1 TGGAATTTA
*
1011846 TTGAATTTA
1 TGGAATTTA
*
1011855 TGGAATTTC
1 TGGAATTTA
*
1011864 TGGAATTTT
1 TGGAATTTA
*
1011873 TGGTATTTA
1 TGGAATTTA
1011882 AAATTTAAGT
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.25, C:0.03, G:0.18, T:0.54
Consensus pattern (9 bp):
TGGAATTTA
Found at i:1011835 original size:18 final size:18
Alignment explanation
Indices: 1011821--1011862 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
1011811 GGAATTTCTT
1011821 GAATTTTTTGAATTTATG
1 GAATTTTTTGAATTTATG
1011839 GAATTTTTTGAATTTATG
1 GAATTTTTTGAATTTATG
1011857 GAATTT
1 GAATTT
1011863 CTGGAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.55
Consensus pattern (18 bp):
GAATTTTTTGAATTTATG
Found at i:1011869 original size:18 final size:18
Alignment explanation
Indices: 1011809--1011871 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 18
1011799 AATTCCAATA
* *
1011809 CTGGAATTTCTTGAATTT
1 CTGGAATTTATGGAATTT
* *
1011827 TTTGAATTTATGGAATTT
1 CTGGAATTTATGGAATTT
* *
1011845 TTTGAATTTATGGAATTT
1 CTGGAATTTATGGAATTT
1011863 CTGGAATTT
1 CTGGAATTT
1011872 TTGGTATTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.25, C:0.05, G:0.17, T:0.52
Consensus pattern (18 bp):
CTGGAATTTATGGAATTT
Found at i:1011872 original size:27 final size:27
Alignment explanation
Indices: 1011809--1011873 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
1011799 AATTCCAATA
* * *
1011809 CTGGAATTTCTTGAATTTTTTGAATTT
1 CTGGAATTTTTTGAATTTATGGAATTT
*
1011836 ATGGAATTTTTTGAATTTATGGAATTT
1 CTGGAATTTTTTGAATTTATGGAATTT
1011863 CTGGAATTTTT
1 CTGGAATTTTT
1011874 GGTATTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.25, C:0.05, G:0.17, T:0.54
Consensus pattern (27 bp):
CTGGAATTTTTTGAATTTATGGAATTT
Found at i:1011880 original size:27 final size:27
Alignment explanation
Indices: 1011810--1011881 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
1011800 ATTCCAATAC
* *
1011810 TGGAATTTCTT-GAATTTTTTGAATTTA
1 TGGAATTT-TTGGAATTTATGGAATTTA
* *
1011837 TGGAATTTTTTGAATTTATGGAATTTC
1 TGGAATTTTTGGAATTTATGGAATTTA
*
1011864 TGGAATTTTTGGTATTTA
1 TGGAATTTTTGGAATTTA
1011882 AAATTTAAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 2 0.05
27 37 0.95
ACGTcount: A:0.25, C:0.03, G:0.18, T:0.54
Consensus pattern (27 bp):
TGGAATTTTTGGAATTTATGGAATTTA
Found at i:1013076 original size:38 final size:38
Alignment explanation
Indices: 1013019--1013097 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
1013009 CTTAAGGAGT
* *
1013019 GGTCCTACGGGACATAGATGACATCCTTCGGGATGATA
1 GGTCCTACGGGACACAGATGACATCCTGCGGGATGATA
*
1013057 GGTCCTACGGGATACAGATGACATCCTGCGGGATGATA
1 GGTCCTACGGGACACAGATGACATCCTGCGGGATGATA
1013095 GGT
1 GGT
1013098 AATTCGAGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.23
Consensus pattern (38 bp):
GGTCCTACGGGACACAGATGACATCCTGCGGGATGATA
Found at i:1013142 original size:21 final size:21
Alignment explanation
Indices: 1013100--1013143 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1013090 TGATAGGTAA
**
1013100 TTCGAGATATACATATGGTCC
1 TTCGAGATATACATATAATCC
* *
1013121 TTCGGGATATATATATAATCC
1 TTCGAGATATACATATAATCC
1013142 TT
1 TT
1013144 TGGAATATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (21 bp):
TTCGAGATATACATATAATCC
Found at i:1013199 original size:21 final size:21
Alignment explanation
Indices: 1013106--1013200 Score: 61
Period size: 21 Copynumber: 4.5 Consensus size: 21
1013096 GTAATTCGAG
* * *
1013106 ATATACATATGGTCCTTCGGG
1 ATATATATATGGTCCTTTGGA
**
1013127 ATATATATATAATCCTTTGGA
1 ATATATATATGGTCCTTTGGA
* *
1013148 ATAT-T-TATGCGATTCTTCAGG-
1 ATATATATATG-G-TCCTT-TGGA
* *
1013169 ACACATATATGGTCCTTTGGA
1 ATATATATATGGTCCTTTGGA
1013190 ATATATATATG
1 ATATATATATG
1013201 TTATTCTTAA
Statistics
Matches: 53, Mismatches: 15, Indels: 12
0.66 0.19 0.15
Matches are distributed among these distances:
19 3 0.06
20 3 0.06
21 39 0.74
22 4 0.08
23 4 0.08
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.39
Consensus pattern (21 bp):
ATATATATATGGTCCTTTGGA
Found at i:1013426 original size:30 final size:31
Alignment explanation
Indices: 1013357--1013427 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
1013347 ATACATGGGT
*
1013357 TAATACATGGGCTTATAAAAGATCTCAATAA
1 TAATACATGGGCTTATAAAAGATATCAATAA
*
1013388 TAATACATGGGTTTATAAAAGATATCAA-AA
1 TAATACATGGGCTTATAAAAGATATCAATAA
1013418 GT-ATACATGG
1 -TAATACATGG
1013428 AATAATACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 10 0.27
31 27 0.73
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (31 bp):
TAATACATGGGCTTATAAAAGATATCAATAA
Found at i:1016624 original size:21 final size:22
Alignment explanation
Indices: 1016586--1016629 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
1016576 AAATTACTAA
*
1016586 TAATGATTTATTATTAAT-ATT
1 TAATGATTTATTAGTAATGATT
1016607 TAATGATTTGA-TAGTAATGATT
1 TAATGATTT-ATTAGTAATGATT
1016629 T
1 T
1016630 TAGGGTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.52
Consensus pattern (22 bp):
TAATGATTTATTAGTAATGATT
Found at i:1016901 original size:11 final size:11
Alignment explanation
Indices: 1016827--1016907 Score: 51
Period size: 11 Copynumber: 7.4 Consensus size: 11
1016817 AAAATTATAA
*
1016827 TAATGACTTAG
1 TAATGATTTAG
*
1016838 TAATGATTATTAA
1 TAATGA-T-TTAG
*
1016851 TAATGATTTAT
1 TAATGATTTAG
* *
1016862 TATTAATATT--
1 TAATGAT-TTAG
* *
1016872 TAATGATATAC
1 TAATGATTTAG
1016883 TAATGATTTAG
1 TAATGATTTAG
1016894 TAATGA-TTAG
1 TAATGATTTAG
1016904 TAAT
1 TAAT
1016908 AATGAAATTA
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
9 1 0.02
10 13 0.24
11 29 0.53
12 3 0.05
13 9 0.16
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (11 bp):
TAATGATTTAG
Found at i:1016953 original size:52 final size:52
Alignment explanation
Indices: 1016879--1016985 Score: 187
Period size: 52 Copynumber: 2.1 Consensus size: 52
1016869 ATTTAATGAT
* *
1016879 ATACTAATGATTTAGTAATGATTAGTAATAATGAAATTATAATAATGATTTG
1 ATACTAAAGATTTAGTAATGATTAGTAATAATGAAATTATAACAATGATTTG
*
1016931 ATACTAAAGATTTAGTAATGATTAGTAATAATGAAATTATTACAATGATTTG
1 ATACTAAAGATTTAGTAATGATTAGTAATAATGAAATTATAACAATGATTTG
1016983 ATA
1 ATA
1016986 AATAGTTGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.39
Consensus pattern (52 bp):
ATACTAAAGATTTAGTAATGATTAGTAATAATGAAATTATAACAATGATTTG
Found at i:1017007 original size:16 final size:16
Alignment explanation
Indices: 1016978--1017016 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1016968 TATTACAATG
*
1016978 ATTTGATAAATAGTTGA
1 ATTT-ATAAATAGTCGA
*
1016995 ATTTATAACTAGTCGA
1 ATTTATAAATAGTCGA
1017011 ATTTAT
1 ATTTAT
1017017 CTTTATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (16 bp):
ATTTATAAATAGTCGA
Found at i:1018122 original size:44 final size:44
Alignment explanation
Indices: 1018072--1018220 Score: 221
Period size: 44 Copynumber: 3.4 Consensus size: 44
1018062 TTCAAAATAT
*
1018072 TTACCATTTATCCCATAAGCTCGTAAGC-TATTTTACTAACATAC
1 TTACCATTTAT-CCATAAGCTCGTAAGCTTATTTTACCAACATAC
*
1018116 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAACATAC
* *
1018160 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATACAC
1 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAACATAC
*
1018204 TTTCCA-TTATTCCATAA
1 TTACCATTTA-TCCATAA
1018221 CCATATACCA
Statistics
Matches: 99, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
43 19 0.19
44 80 0.81
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (44 bp):
TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAACATAC
Found at i:1018192 original size:24 final size:24
Alignment explanation
Indices: 1018121--1018192 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
1018111 CATACTTACC
1018121 ATTTATCCATAAGCTCGTAAGCTT
1 ATTTATCCATAAGCTCGTAAGCTT
*
1018145 ATTT-TACCAATATA-CT--T-A-C-C
1 ATTTAT-CC-ATA-AGCTCGTAAGCTT
1018165 ATTTATCCATAAGCTCGTAAGCTT
1 ATTTATCCATAAGCTCGTAAGCTT
1018189 ATTT
1 ATTT
1018193 TACCAATACA
Statistics
Matches: 36, Mismatches: 2, Indels: 20
0.62 0.03 0.34
Matches are distributed among these distances:
18 1 0.03
19 5 0.14
20 6 0.17
21 3 0.08
22 2 0.06
23 3 0.08
24 10 0.28
25 5 0.14
26 1 0.03
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (24 bp):
ATTTATCCATAAGCTCGTAAGCTT
Found at i:1018633 original size:21 final size:22
Alignment explanation
Indices: 1018595--1018635 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1018585 CAAAATAACA
1018595 TTCATGATAAAAATCATATATG
1 TTCATGATAAAAATCATATATG
*
1018617 TTCATGAT-AACATCATATA
1 TTCATGATAAAAATCATATA
1018636 CAAAAATCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (22 bp):
TTCATGATAAAAATCATATATG
Found at i:1022155 original size:18 final size:19
Alignment explanation
Indices: 1022132--1022174 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1022122 CAACAGCACA
*
1022132 TAACTGCTC-TTAACAAGC
1 TAACTGCTCGTTAACAAAC
1022150 TAACTGCTCGTTTAACAAAC
1 TAACTGCTCG-TTAACAAAC
1022170 TAACT
1 TAACT
1022175 ACCATTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
20 13 0.59
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (19 bp):
TAACTGCTCGTTAACAAAC
Found at i:1026784 original size:18 final size:19
Alignment explanation
Indices: 1026761--1026803 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1026751 CAGCAGCACA
*
1026761 TAACTGCTC-TTAACAAGC
1 TAACTGCTCGTTAACAAAC
1026779 TAACTGCTCGTTTAACAAAC
1 TAACTGCTCG-TTAACAAAC
1026799 TAACT
1 TAACT
1026804 ACCATTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
20 13 0.59
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (19 bp):
TAACTGCTCGTTAACAAAC
Found at i:1029990 original size:24 final size:24
Alignment explanation
Indices: 1029962--1030050 Score: 92
Period size: 24 Copynumber: 3.7 Consensus size: 24
1029952 TTTCTATTAT
* *
1029962 AATACCTGACATGGATTCTGATC-
1 AATACTTGACCTGGATTCTGATCG
*
1029985 AGATACTTAACCTGGATTCTGATCG
1 A-ATACTTGACCTGGATTCTGATCG
* *
1030010 AATACTTGACCTGGATTTTGATATG
1 AATACTTGACCTGGATTCTGAT-CG
*
1030035 -ATAATTGACCTGGATT
1 AATACTTGACCTGGATT
1030051 ATGTTTTGAT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
23 1 0.02
24 53 0.95
25 2 0.04
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (24 bp):
AATACTTGACCTGGATTCTGATCG
Found at i:1035254 original size:24 final size:24
Alignment explanation
Indices: 1035226--1035314 Score: 83
Period size: 24 Copynumber: 3.7 Consensus size: 24
1035216 ATTTTATTAT
* *
1035226 AATACCTGACATGGATTCTGATC-
1 AATACTTGACCTGGATTCTGATCG
* *
1035249 AGATACTTAACCTGAATTCTGATCG
1 A-ATACTTGACCTGGATTCTGATCG
* *
1035274 AATACTTGACCTGGATTTTGATATG
1 AATACTTGACCTGGATTCTGAT-CG
*
1035299 -ATAATTGACCTGGATT
1 AATACTTGACCTGGATT
1035315 ATGTTTTGAT
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
23 1 0.02
24 51 0.94
25 2 0.04
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (24 bp):
AATACTTGACCTGGATTCTGATCG
Found at i:1037872 original size:4 final size:4
Alignment explanation
Indices: 1037863--1037890 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1037853 GAGATTTTGA
1037863 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1037891 GTAAATTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:1040588 original size:24 final size:24
Alignment explanation
Indices: 1040536--1040624 Score: 92
Period size: 24 Copynumber: 3.7 Consensus size: 24
1040526 ATTCTATTAT
* * *
1040536 AATACCTGACATGGATTCTGA-TC
1 AATACTTGACCTGGATTCTGATTG
*
1040559 AGATACTTAACCTGGATTCTGATTG
1 A-ATACTTGACCTGGATTCTGATTG
*
1040584 AATACTTGACCTGGATTTTGATATG
1 AATACTTGACCTGGATTCTGAT-TG
*
1040609 -ATAATTGACCTGGATT
1 AATACTTGACCTGGATT
1040625 ATGTTTTGAT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
23 1 0.02
24 51 0.91
25 4 0.07
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (24 bp):
AATACTTGACCTGGATTCTGATTG
Found at i:1044795 original size:44 final size:44
Alignment explanation
Indices: 1044745--1044893 Score: 212
Period size: 44 Copynumber: 3.4 Consensus size: 44
1044735 TTCAAAATAT
*
1044745 TTACCATTTATCCCATAAGCTCGTAAGC-TATTTTACTAACATAC
1 TTACCATTTAT-CCATAAGCTCGTAAGCTTATTTTACCAACATAC
*
1044789 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAACATAC
* * *
1044833 TTACCATTTATCCATAAGATCGTAAGCTTATTTTACCAATACAC
1 TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAACATAC
*
1044877 TTGCCA-TTATTCCATAA
1 TTACCATTTA-TCCATAA
1044894 CCATATACCA
Statistics
Matches: 98, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
43 19 0.19
44 79 0.81
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (44 bp):
TTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAACATAC
Found at i:1045086 original size:59 final size:59
Alignment explanation
Indices: 1044994--1045122 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 59
1044984 CATAGTGCAA
* * * **
1044994 TCCCGAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAG
* ** *
1045053 TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAG
1045112 TCCCGAATATG
1 TCCCGAATATG
1045123 CAGCCTGCTG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:1047824 original size:23 final size:23
Alignment explanation
Indices: 1047798--1047841 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1047788 AAATTATAAT
*
1047798 AATAATAAAATTGATTTAAATCA
1 AATAATAAAATTAATTTAAATCA
* *
1047821 AATAATATAGTTAATTTAAAT
1 AATAATAAAATTAATTTAAAT
1047842 AATAATTAAT
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:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (23 bp):
AATAATAAAATTAATTTAAATCA
Found at i:1049872 original size:29 final size:29
Alignment explanation
Indices: 1049835--1049911 Score: 145
Period size: 29 Copynumber: 2.7 Consensus size: 29
1049825 TCGCCGGGAC
*
1049835 TGCACGGCGACCTGCTTGGGCGCTCGGAG
1 TGCATGGCGACCTGCTTGGGCGCTCGGAG
1049864 TGCATGGCGACCTGCTTGGGCGCTCGGAG
1 TGCATGGCGACCTGCTTGGGCGCTCGGAG
1049893 TGCATGGCGACCTGCTTGG
1 TGCATGGCGACCTGCTTGG
1049912 TCACGGGGCT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.10, C:0.29, G:0.40, T:0.21
Consensus pattern (29 bp):
TGCATGGCGACCTGCTTGGGCGCTCGGAG
Found at i:1049925 original size:29 final size:29
Alignment explanation
Indices: 1049835--1049934 Score: 110
Period size: 29 Copynumber: 3.4 Consensus size: 29
1049825 TCGCCGGGAC
* * *
1049835 TGCACGGCGACCTGCTTGGGCGCTCGGAG
1 TGCATGGCGACCTGCTTGGGCACGCGGAG
* *
1049864 TGCATGGCGACCTGCTTGGGCGCTCGGAG
1 TGCATGGCGACCTGCTTGGGCACGCGGAG
* * **
1049893 TGCATGGCGACCTGCTTGGTCACGGGGCT
1 TGCATGGCGACCTGCTTGGGCACGCGGAG
*
1049922 TGCATGACGACCT
1 TGCATGGCGACCT
1049935 AGAGGCGTGC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.12, C:0.29, G:0.38, T:0.21
Consensus pattern (29 bp):
TGCATGGCGACCTGCTTGGGCACGCGGAG
Found at i:1054225 original size:23 final size:24
Alignment explanation
Indices: 1054188--1054250 Score: 92
Period size: 23 Copynumber: 2.6 Consensus size: 24
1054178 AATTTTTAAT
*
1054188 TTAAACTATACAAATATAAAAAAA
1 TTAAACTATAAAAATATAAAAAAA
1054212 TTAAA-TATAAAAATATAAAAAAA
1 TTAAACTATAAAAATATAAAAAAA
*
1054235 TTAAATTACTAAAAAT
1 TTAAACTA-TAAAAAT
1054251 TATTAACCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
23 22 0.61
24 7 0.19
25 7 0.19
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (24 bp):
TTAAACTATAAAAATATAAAAAAA
Found at i:1055815 original size:26 final size:24
Alignment explanation
Indices: 1055753--1055815 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 24
1055743 CATTTTAATC
1055753 AAAATATTA-ATTATTAAAATATTT
1 AAAATATTATATTATT-AAATATTT
1055777 AAAATA-TAT-TTATT-AATACTTCT
1 AAAATATTATATTATTAAATA-TT-T
1055800 AATAATATTATATTAT
1 AA-AATATTATATTAT
1055816 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
21 4 0.12
22 2 0.06
23 10 0.30
24 10 0.30
25 3 0.09
26 4 0.12
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATTATATTATTAAATATTT
Found at i:1056013 original size:23 final size:23
Alignment explanation
Indices: 1055966--1056038 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
1055956 TATGTATTTA
*
1055966 ATATTAATATAATA-ATCTAATAAT
1 ATATTAATA-AATATATTTAA-AAT
*
1055990 ATTTTAATAAATATATTTAAAAT
1 ATATTAATAAATATATTTAAAAT
** * *
1056013 ATACCAATTAATATTTTTAAAAT
1 ATATTAATAAATATATTTAAAAT
1056036 ATA
1 ATA
1056039 ATATAACACT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
23 28 0.68
24 13 0.32
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATTAATAAATATATTTAAAAT
Found at i:1056150 original size:20 final size:21
Alignment explanation
Indices: 1056126--1056180 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
1056116 TTAATAAAAT
1056126 TATAAAAATAATATTTTAATA
1 TATAAAAATAATATTTTAATA
*
1056147 -ATAAATAA-ATTATTTTAATA
1 TATAAA-AATAATATTTTAATA
*
1056167 TTTTAAAAATAATA
1 -TATAAAAATAATA
1056181 ATATTAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
20 16 0.59
21 4 0.15
22 7 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TATAAAAATAATATTTTAATA
Found at i:1056525 original size:9 final size:8
Alignment explanation
Indices: 1056486--1056516 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
1056476 CTGGTCTGCT
1056486 CCTTTCCC
1 CCTTTCCC
1056494 CCTTTCCC
1 CCTTTCCC
1056502 CCTTTCCC
1 CCTTTCCC
1056510 CCTTTCC
1 CCTTTCC
1056517 TCCATTTCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (8 bp):
CCTTTCCC
Found at i:1057167 original size:22 final size:22
Alignment explanation
Indices: 1057068--1057161 Score: 106
Period size: 22 Copynumber: 4.4 Consensus size: 22
1057058 TTGAAAATCG
1057068 CGTTGCGATAGTCTC-CAGTTGT
1 CGTTGCGATAGTC-CACAGTTGT
** *
1057090 CGTTGCGATTTTCCA-A-AT-T
1 CGTTGCGATAGTCCACAGTTGT
*
1057109 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCCACAGTTGT
*
1057131 TGTTGCGATAGTCCACAGTTGT
1 CGTTGCGATAGTCCACAGTTGT
1057153 CGTTGCGAT
1 CGTTGCGAT
1057162 TTTCCAAATT
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
19 13 0.22
20 2 0.03
21 3 0.05
22 40 0.69
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (22 bp):
CGTTGCGATAGTCCACAGTTGT
Found at i:1057823 original size:6 final size:6
Alignment explanation
Indices: 1057786--1057837 Score: 69
Period size: 5 Copynumber: 9.5 Consensus size: 6
1057776 CGCCGTCTCG
1057786 GGTCG- GGTCG- GGTCGT -GTCGT -GTCGT -GTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1057829 GGTCGT GGT
1 GGTCGT GGT
1057838 AATACGTGTC
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.56
6 20 0.44
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1057939 original size:22 final size:22
Alignment explanation
Indices: 1057914--1058010 Score: 101
Period size: 22 Copynumber: 4.5 Consensus size: 22
1057904 TTTTATTTTA
1057914 ACTATCACAACGACAACTGTAG
1 ACTATCACAACGACAACTGTAG
*
1057936 ACTATCGCAACGACAACTGTAG
1 ACTATCACAACGACAACTGTAG
* **
1057958 ACTATCGCAACGA-ATTTG-A-
1 ACTATCACAACGACAACTGTAG
** *
1057977 AAAATCACAACGATAACTGTAG
1 ACTATCACAACGACAACTGTAG
*
1057999 ACTATCTCAACG
1 ACTATCACAACG
1058011 CGAAATGTAA
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 10 0.16
20 4 0.07
21 4 0.07
22 43 0.70
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.21
Consensus pattern (22 bp):
ACTATCACAACGACAACTGTAG
Found at i:1058830 original size:23 final size:22
Alignment explanation
Indices: 1058796--1058846 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
1058786 TTTGTAATTG
1058796 ATTTTTCGAAAAATGTTTCCTC
1 ATTTTTCGAAAAATGTTTCCTC
1058818 ATTTTTCGAAAAATGTTTCCTC
1 ATTTTTCGAAAAATGTTTCCTC
1058840 ATTTTTC
1 ATTTTTC
1058847 AGTGTTTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.18, G:0.08, T:0.49
Consensus pattern (22 bp):
ATTTTTCGAAAAATGTTTCCTC
Found at i:1059045 original size:28 final size:27
Alignment explanation
Indices: 1058980--1059045 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 27
1058970 TATAAACACT
1058980 TAAAATATTATTATTTTATATATTTAA
1 TAAAATATTATTATTTTATATATTTAA
*
1059007 TATTAATA-TATTATTTTTAGTATCATTTTAA
1 TA-AAATATTATTA-TTTTA-TAT-A-TTTAA
1059038 TAAAATAT
1 TAAAATAT
1059046 CAATAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
27 7 0.23
28 9 0.29
29 3 0.10
30 5 0.16
31 7 0.23
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (27 bp):
TAAAATATTATTATTTTATATATTTAA
Found at i:1059133 original size:29 final size:29
Alignment explanation
Indices: 1059101--1059157 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1059091 ATATATTTAT
*
1059101 TATTATAATTATATTATCATAATATATAC
1 TATTATAATTATATTATAATAATATATAC
* * *
1059130 TATTATACTTTTATTTTAATAATATATA
1 TATTATAATTATATTATAATAATATATA
1059158 ATAAATTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (29 bp):
TATTATAATTATATTATAATAATATATAC
Found at i:1059524 original size:14 final size:14
Alignment explanation
Indices: 1059482--1059524 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1059472 AATTATAGAT
*
1059482 ATAATATTTCAATA
1 ATAATATTTAAATA
*
1059496 ATAATATTTACATA
1 ATAATATTTAAATA
1059510 ACTAATA-TTAAATA
1 A-TAATATTTAAATA
1059524 A
1 A
1059525 ATTAATCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAATATTTAAATA
Found at i:1059786 original size:9 final size:9
Alignment explanation
Indices: 1059758--1059802 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
1059748 TATATTTAAT
1059758 ATTTAA-TA
1 ATTTAATTA
1059766 ATTTCAATTA
1 ATTT-AATTA
*
1059776 ATTTGATTA
1 ATTTAATTA
1059785 ATTTAATTA
1 ATTTAATTA
1059794 A-TTAATTA
1 ATTTAATTA
1059802 A
1 A
1059803 ATATTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 12 0.36
9 15 0.45
10 6 0.18
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (9 bp):
ATTTAATTA
Found at i:1067655 original size:18 final size:18
Alignment explanation
Indices: 1067632--1067673 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1067622 GTCATAACCC
1067632 GACCCGACCCAACACGTT
1 GACCCGACCCAACACGTT
* *
1067650 GACCCGACCCGACCCGTT
1 GACCCGACCCAACACGTT
1067668 GACCCG
1 GACCCG
1067674 TTAACCGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.48, G:0.21, T:0.10
Consensus pattern (18 bp):
GACCCGACCCAACACGTT
Found at i:1070047 original size:12 final size:12
Alignment explanation
Indices: 1070032--1070101 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
1070022 GATACATGAC
1070032 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1070044 CTGATTTCTGAT
1 CTGAATTCTGTT
* *
1070056 ATGGATTCTGTT
1 CTGAATTCTGTT
*
1070068 ATG-ATATCTGTT
1 CTGAAT-TCTGTT
1070080 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1070092 TTGATTTCTG
1 CTGAATTCTG
1070102 ATATCTTCGT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.17, C:0.13, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:1070063 original size:24 final size:24
Alignment explanation
Indices: 1070033--1070105 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
1070023 ATACATGACC
*
1070033 TGAATTCTGTTCTGATTTCTGATA
1 TGAATTCTGTTATGATTTCTGATA
* * * *
1070057 TGGATTCTGTTATGATATCTGTTC
1 TGAATTCTGTTATGATTTCTGATA
*
1070081 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTATGATTTCTGATA
1070105 T
1 T
1070106 CTTCGTTTAA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.19, C:0.11, G:0.18, T:0.52
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATA
Found at i:1070073 original size:48 final size:48
Alignment explanation
Indices: 1070012--1070105 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
1070002 TCCGACTTGA
*
1070012 ATTCTATTCTGATA-CATGACCTGAATTCTGTTCTGATTTCTGATATGG
1 ATTCTATTATGATATC-TGACCTGAATTCTGTTCTGATTTCTGATATGG
* ** *
1070060 ATTCTGTTATGATATCTGTTCTGAATTCTGTTTTGATTTCTGATAT
1 ATTCTATTATGATATCTGACCTGAATTCTGTTCTGATTTCTGATAT
1070106 CTTCGTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 39 0.98
49 1 0.03
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (48 bp):
ATTCTATTATGATATCTGACCTGAATTCTGTTCTGATTTCTGATATGG
Found at i:1072790 original size:40 final size:40
Alignment explanation
Indices: 1072746--1072855 Score: 184
Period size: 40 Copynumber: 2.8 Consensus size: 40
1072736 ACCGTAGTGC
*
1072746 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
1072786 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
1072826 TAAACATAAGGTCGTTCCCACCATATACAC
1 TACACATAAGGTCGTGCCCACCATATACAC
1072856 TTAGTGTCCT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1075072 original size:20 final size:20
Alignment explanation
Indices: 1075042--1075089 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1075032 AATGATTTGG
1075042 TTTTG-AAAGCAAAATTG-AA
1 TTTTGAAAAGCAAAA-TGAAA
1075061 TTTTGAAAAGCAAAATGAAA
1 TTTTGAAAAGCAAAATGAAA
1075081 TTTTGAAAA
1 TTTTGAAAA
1075090 ATTATTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.31
Consensus pattern (20 bp):
TTTTGAAAAGCAAAATGAAA
Found at i:1077859 original size:39 final size:39
Alignment explanation
Indices: 1077816--1077926 Score: 152
Period size: 39 Copynumber: 2.8 Consensus size: 39
1077806 AGTGTGAAAT
* * *
1077816 TATTTGAATTAATAATTTTGATTAACTATAACTGTATCC
1 TATTTGAATTAGTAGTTTAGATTAACTATAACTGTATCC
* *
1077855 TATTT-AATTTAGTAGTTTAGATTAACTATAACTTTATCT
1 TATTTGAA-TTAGTAGTTTAGATTAACTATAACTGTATCC
*
1077894 TATTTGATTTAGTAGTTTAGATTAACTATAACT
1 TATTTGAATTAGTAGTTTAGATTAACTATAACT
1077927 CCATTTTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
38 2 0.03
39 61 0.95
40 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.09, T:0.49
Consensus pattern (39 bp):
TATTTGAATTAGTAGTTTAGATTAACTATAACTGTATCC
Found at i:1083421 original size:20 final size:20
Alignment explanation
Indices: 1083396--1083435 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1083386 AATGTGTTAT
*
1083396 GGTGAACAAAATAAGGAATG
1 GGTGAACAAAACAAGGAATG
1083416 GGTGAACAAAACAAGGAATG
1 GGTGAACAAAACAAGGAATG
1083436 ATTAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.30, T:0.12
Consensus pattern (20 bp):
GGTGAACAAAACAAGGAATG
Found at i:1094964 original size:89 final size:89
Alignment explanation
Indices: 1094811--1095068 Score: 417
Period size: 89 Copynumber: 2.9 Consensus size: 89
1094801 TACGTAGAGC
* * * * *
1094811 TTACCCTAAGCACATAGCAAAAGGGAGCCAACCTAAGGATATTTCTTGGGGCCTATGGGTCTACC
1 TTACCCTAAGCACACAAC-AAAGGGAACCAACCTAAGGATATTCCTTGGGGCCTATGGGCCTACC
1094876 CAAGGGTATCCTTAGATCCATAGGG
65 CAAGGGTATCCTTAGATCCATAGGG
1094901 TTACCCTAAGCACACAACAAAGGGAACCAACCTAAGGATATTCCTTGGGGCCTATGGGCCTACCC
1 TTACCCTAAGCACACAACAAAGGGAACCAACCTAAGGATATTCCTTGGGGCCTATGGGCCTACCC
*
1094966 AAGGGTATCCTTAGATCCGTAGGG
66 AAGGGTATCCTTAGATCCATAGGG
* ** *
1094990 TTACCCTAAGCACACAATAAAGGGAATAAACCTAAGGATATGCCTTGGGGCCTATGGGCCTACCC
1 TTACCCTAAGCACACAACAAAGGGAACCAACCTAAGGATATTCCTTGGGGCCTATGGGCCTACCC
1095055 AAGGGTATCCTTAG
66 AAGGGTATCCTTAG
1095069 GTCTGTAATG
Statistics
Matches: 158, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 142 0.90
90 16 0.10
ACGTcount: A:0.30, C:0.25, G:0.24, T:0.22
Consensus pattern (89 bp):
TTACCCTAAGCACACAACAAAGGGAACCAACCTAAGGATATTCCTTGGGGCCTATGGGCCTACCC
AAGGGTATCCTTAGATCCATAGGG
Found at i:1097771 original size:18 final size:17
Alignment explanation
Indices: 1097748--1097790 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1097738 ATATATACAT
1097748 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
1097766 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1097783 ATAA-AATA
1 ATAATAATA
1097791 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1097798 original size:60 final size:56
Alignment explanation
Indices: 1097680--1097790 Score: 134
Period size: 59 Copynumber: 1.9 Consensus size: 56
1097670 AATTAAAGAA
* * * **
1097680 ATATATATAGAATAATAATAAAATATAGTAAAAAAATAAATGAAATAATTTAATAT
1 ATATATATACAATAATAATAAAACATAATAAAAAAATAAATGAAATAAAATAATAT
1097736 ATATATATACATATAATAATAATAACATGAATAATAAAAATAAATG-AATAAAATA
1 ATATATATACA-ATAATAATAA-AACAT-AATAA-AAAAATAAATGAAATAAAATA
1097791 TCCATATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
56 10 0.22
57 10 0.22
58 4 0.09
59 11 0.24
60 11 0.24
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (56 bp):
ATATATATACAATAATAATAAAACATAATAAAAAAATAAATGAAATAAAATAATAT
Found at i:1098224 original size:37 final size:36
Alignment explanation
Indices: 1098181--1098282 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
1098171 ATAGTAGAAC
1098181 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
1098218 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
1098252 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1098283 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:1099226 original size:106 final size:105
Alignment explanation
Indices: 1098830--1099347 Score: 690
Period size: 106 Copynumber: 5.0 Consensus size: 105
1098820 CATTGTTCCA
* * * * ** *
1098830 AGTCCAATATCCTCCATCGTGAAGTTGAAATTGGTTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGTG-ATTGGGAAGTTG-TTGTTGACAA
* * * * *
1098894 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** * *
1098936 AGTCCAATATCCTTCTTTGTGAAGTTGAAATTGAATC--TGAAT--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGTGATTGGGAAGTTGTTGTTGACAAGC
*
1098996 AGCGCTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1099036 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-TAGATTGGGAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGT-GATTGGGAAGTTGTTGTTGACAAG
*
1099100 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1099141 AGTCCAATATTCTTCGTTGTGAAGTTTGAAATTGGCTCTGTGATTGGGAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAG-TTGAAATTGGCTCTGTGATTGGGAAGTTGTTGTTGACAAG
*
1099206 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** * *
1099247 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGTGATTGGGAAGTTG-TTGTTGACAAG
* * *
1099312 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1099348 CCTCGAGTGC
Statistics
Matches: 372, Mismatches: 31, Indels: 18
0.88 0.07 0.04
Matches are distributed among these distances:
100 80 0.22
101 1 0.00
102 9 0.02
104 6 0.02
105 100 0.27
106 175 0.47
107 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGTGATTGGGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1100125 original size:67 final size:66
Alignment explanation
Indices: 1099990--1100147 Score: 201
Period size: 68 Copynumber: 2.4 Consensus size: 66
1099980 AAGATATCTG
* * **
1099990 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA-
1100055 TT
65 TT
* * * * *
1100057 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGATAAAATT-TGTTTTAGGGGAAATAAATTCAAAGG
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA
1100121 TT
65 TT
*
1100123 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
1100148 ATAGACGAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 23 0.29
68 31 0.39
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:1100163 original size:65 final size:67
Alignment explanation
Indices: 1099991--1100173 Score: 183
Period size: 65 Copynumber: 2.7 Consensus size: 67
1099981 AGATATCTGT
* * * * * ** *
1099991 TGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATT-TGTTTTAAGGGAAATAAATTCAAAGAGT
1100056 TTG
65 TTG
* * * *
1100059 TGTTTCAAGAGTAACTGTCTCAAGGGAGATAAAATTTGTTTTAGGGGAAATAAATTCAAAG-GTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
1100123 T-
66 TG
* * * *
1100124 TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-GAAAATTTGTTTTAAGGGAAA
1100174 CTGTCTCAAG
Statistics
Matches: 97, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
65 37 0.38
66 7 0.07
67 22 0.23
68 31 0.32
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
TG
Found at i:1100174 original size:36 final size:35
Alignment explanation
Indices: 1100123--1100403 Score: 254
Period size: 36 Copynumber: 8.0 Consensus size: 35
1100113 TTCAAAGGTT
* *
1100123 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
1100159 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
1100194 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * * **
1100232 TTGTTTCAA-ATAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGA-GAAAC-TGTCTCAAGAGAGACAAAA
*
1100261 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
1100296 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
*
1100333 TTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
1100368 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1100404 CTCTTCTAGT
Statistics
Matches: 200, Mismatches: 29, Indels: 32
0.77 0.11 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.09
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 9 0.05
36 132 0.66
37 33 0.17
38 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:1100233 original size:138 final size:137
Alignment explanation
Indices: 1100071--1100384 Score: 405
Period size: 138 Copynumber: 2.3 Consensus size: 137
1100061 TTTCAAGAGT
* * * * *
1100071 AACTGTCTCAAGGGAGATAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* *
1100136 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
1100200 TCCAAAAGA
129 TCCAAAAGA
** *** * *
1100209 AACTGTCTCAAGGGAGACGGAATTTGTTTCAAATAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * * * *
1100274 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTT
66 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
1100339 CAAGAGA
131 CAAAAGA
* *
1100346 AACTGTCTAAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
1100385 TGTCTCAAGA
Statistics
Matches: 148, Mismatches: 27, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
137 47 0.32
138 101 0.68
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:1100910 original size:18 final size:18
Alignment explanation
Indices: 1100883--1100918 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1100873 TGTTGAATCC
* *
1100883 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
1100901 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1100919 TTGATGTTGA
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:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:1101410 original size:22 final size:22
Alignment explanation
Indices: 1101333--1101403 Score: 124
Period size: 22 Copynumber: 3.2 Consensus size: 22
1101323 TTGTGTTTGG
*
1101333 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
1101355 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
1101377 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTTGATGC
1101399 TCAAA
1 TCAAA
1101404 AGATTGATGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:1102125 original size:16 final size:16
Alignment explanation
Indices: 1102080--1102132 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
1102070 TTCTTGTTTC
* *
1102080 TCTTTTTCTTTGTTTTT
1 TCTTTTGCTTT-TTTGT
*
1102097 TTTTTTGCTTTTTTGCT
1 TCTTTTGCTTTTTTG-T
1102114 TCTTTT-CTTTTTTGT
1 TCTTTTGCTTTTTTGT
1102129 TCTT
1 TCTT
1102133 GATTGGATCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 5 0.16
16 11 0.35
17 15 0.48
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (16 bp):
TCTTTTGCTTTTTTGT
Found at i:1103301 original size:8 final size:8
Alignment explanation
Indices: 1103285--1103323 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1103275 AATGTAGATG
1103285 AAAATGCA
1 AAAATGCA
*
1103293 AAAAGGCA
1 AAAATGCA
1103301 AAAATGC-
1 AAAATGCA
1103308 AAAATGCA
1 AAAATGCA
*
1103316 AGAATGCA
1 AAAATGCA
1103324 CGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:1103311 original size:15 final size:15
Alignment explanation
Indices: 1103285--1103323 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1103275 AATGTAGATG
1103285 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
1103301 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
1103316 AGAATGCA
1 AAAATGCA
1103324 CGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:1106455 original size:18 final size:17
Alignment explanation
Indices: 1106432--1106474 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1106422 ATATATACAT
1106432 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
1106450 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1106467 ATAA-AATA
1 ATAATAATA
1106475 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1106475 original size:58 final size:57
Alignment explanation
Indices: 1106364--1106475 Score: 129
Period size: 61 Copynumber: 1.9 Consensus size: 57
1106354 TATTAAAGAA
* *
1106364 ATATATATATATAATAATAAAATAGTAAAAAAATAAATGAAAATAATTTAATATATATAT
1 ATATACATATATAATAATAAAATAATAAAAAAATAAATG-AAATAA--TAATATATATAT
*
1106424 ATATACATATAATAATAATAACATGAATAATAAAAATAAATG-AATAA-AATAT
1 ATATACATAT-ATAATAATAAAAT-AATAA-AAAAATAAATGAAATAATAATAT
1106476 CCATATAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
58 5 0.11
60 9 0.20
61 17 0.37
62 4 0.09
63 11 0.24
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (57 bp):
ATATACATATATAATAATAAAATAATAAAAAAATAAATGAAATAATAATATATATAT
Found at i:1106908 original size:37 final size:36
Alignment explanation
Indices: 1106865--1106966 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
1106855 ATAGTAGAAC
1106865 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
1106902 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
1106936 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1106967 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:1107452 original size:13 final size:13
Alignment explanation
Indices: 1107434--1107473 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1107424 TTTAACTTTT
1107434 TGGTCAAAGTCAA
1 TGGTCAAAGTCAA
*
1107447 TGGTCAAAGTTAA
1 TGGTCAAAGTCAA
*
1107460 CGGTCAATAGTCAA
1 TGGTCAA-AGTCAA
1107474 CAGTAGTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 18 0.78
14 5 0.22
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.25
Consensus pattern (13 bp):
TGGTCAAAGTCAA
Found at i:1111880 original size:18 final size:16
Alignment explanation
Indices: 1111848--1111911 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
1111838 ACGAAAAAGA
1111848 GAAAAATGAAA-AAAAT
1 GAAAAA-GAAATAAAAT
*
1111864 GAAAAAGAAGAATAAAAA
1 GAAAAAG-A-AATAAAAT
*
1111882 GAAAAAGAAATGAAAT
1 GAAAAAGAAATAAAAT
*
1111898 GAAAAATAAATAAA
1 GAAAAAGAAATAAA
1111912 TAAATAAAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 1 0.03
16 25 0.62
17 3 0.08
18 11 0.28
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (16 bp):
GAAAAAGAAATAAAAT
Found at i:1111908 original size:16 final size:15
Alignment explanation
Indices: 1111848--1111922 Score: 60
Period size: 16 Copynumber: 4.6 Consensus size: 15
1111838 ACGAAAAAGA
*
1111848 GAAAAATGAAAAAAAT
1 GAAAAA-GAAATAAAT
*
1111864 GAAAAAGAAGAATAAAAA
1 GAAAAAG-A-AAT-AAAT
1111882 GAAAAAGAAATGAAAT
1 GAAAAAGAAAT-AAAT
*
1111898 GAAAAATAAATAAAT
1 GAAAAAGAAATAAAT
*
1111913 AAATAAAGAA
1 GAA-AAAGAA
1111923 GGAAAAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
15 7 0.15
16 28 0.58
17 3 0.06
18 10 0.21
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.12
Consensus pattern (15 bp):
GAAAAAGAAATAAAT
Found at i:1114159 original size:143 final size:144
Alignment explanation
Indices: 1113935--1114200 Score: 435
Period size: 143 Copynumber: 1.8 Consensus size: 144
1113925 ATACACATAT
* *
1113935 ACACTTTCAAACACATTTTGAAACACTTATTGGAAATGGTGGTTGTCATGATCAACCTTACATGG
1 ACACTTTAAAACACATTTTGAAACACTTATTGGAAA--GTGGTTGTAATGATCAACCTTACATGG
* *
1114000 ACAAAAAAAATTTCACTCATCCATGGATAGTGAAGTTATTCCACTTATCCTTAACACATTCATAT
64 ACAAAAAAAATTTCACTCAACCATGGATAGTGAAGTTATTCCACTCATCCTTAACACATTCATAT
1114065 ATATATATATATACAC
129 ATATATATATATACAC
* *
1114081 ACACTTTAAAATACATTTTGAAACACTTATTGGAAA-TGGTTGTAATGATCAACCTTATATGGAC
1 ACACTTTAAAACACATTTTGAAACACTTATTGGAAAGTGGTTGTAATGATCAACCTTACATGGAC
* *
1114145 AAAAAAAATTTCACTCAACCATGGATAGTGAAGTTGTTCTACTCATCCTTAACACA
66 AAAAAAAATTTCACTCAACCATGGATAGTGAAGTTATTCCACTCATCCTTAACACA
1114201 CACACACACA
Statistics
Matches: 112, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
143 78 0.70
146 34 0.30
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (144 bp):
ACACTTTAAAACACATTTTGAAACACTTATTGGAAAGTGGTTGTAATGATCAACCTTACATGGAC
AAAAAAAATTTCACTCAACCATGGATAGTGAAGTTATTCCACTCATCCTTAACACATTCATATAT
ATATATATATACAC
Found at i:1116735 original size:118 final size:117
Alignment explanation
Indices: 1116498--1116891 Score: 429
Period size: 118 Copynumber: 3.4 Consensus size: 117
1116488 AAAAAGAGGA
** *
1116498 GGATCAATCA-TTTCAAA-GAGAATTCATAATGAGAAGAACTTTTAC-AAAGAGGGACAAAAAGT
1 GGATCAA-CATTTTCAAAGGAGAATTCATAATGAGAAGAACTCGT-CTAAAGAGGGAGAAAAAGT
* * * * *
1116560 TCAAAATGAGAAGAACATGTTAGACTTTTTTCTCAAGTCCATTACAAAAGGAGGT
64 TCATAATGAGAAGAACTTGTTTGACCTTTTTCTCAAGTCCATCACAAAAGGA-GT
* * *
1116615 GGATCAACATTTTCAAAGGTGAGTTCATAATGAGAAGAACTCGTCTAAAGAGGGAGAATAAGTTC
1 GGATCAACATTTTCAAAGGAGAATTCATAATGAGAAGAACTCGTCTAAAGAGGGAGAAAAAGTTC
* * ** * *
1116680 ATAATGAGAAGAACTTATTTGACCCTTAGCTCAAGTCCATCACAGAATGATGT
66 ATAATGAGAAGAACTTGTTTGACCTTTTTCTCAAGTCCATCACAAAAGGA-GT
* * * * * * *
1116733 GGATCAATATTTTCAATGGAGAGTTCAAAATGAGAAGAACTCGT-TCGACGAAGGAGAAAAAGTT
1 GGATCAACATTTTCAAAGGAGAATTCATAATGAGAAGAACTCGTCT-AAAGAGGGAGAAAAAGTT
* *
1116797 CATAATAAGAAGAACTTGTTTGACCTTTTTCTCAAGTCAATCACAAAAGGAGTT
65 CATAATGAGAAGAACTTGTTTGACCTTTTTCTCAAGTCCATCACAAAAGGAG-T
* * *
1116851 GGACCAAAATTTTCAATAGGA-AATTCACAATGAGAAGAACT
1 GGATCAACATTTTCAA-AGGAGAATTCATAATGAGAAGAACT
1116892 TGTCCAAAAA
Statistics
Matches: 232, Mismatches: 39, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
116 2 0.01
117 17 0.07
118 210 0.91
119 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (117 bp):
GGATCAACATTTTCAAAGGAGAATTCATAATGAGAAGAACTCGTCTAAAGAGGGAGAAAAAGTTC
ATAATGAGAAGAACTTGTTTGACCTTTTTCTCAAGTCCATCACAAAAGGAGT
Found at i:1119887 original size:43 final size:43
Alignment explanation
Indices: 1119844--1120027 Score: 244
Period size: 43 Copynumber: 4.3 Consensus size: 43
1119834 TGTTTGTCCA
* * * *
1119844 ACAAACGCCGCAATAGGTGTTGATAATTGGCGGCATTTTTCCA
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTCCC
* * *
1119887 ACAAACGCCGCAATAGGTGTTGAGATTTACCAGCGTTTTTCCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTCCC
* *
1119930 ACAAACGCCGCAATAGATGTTGAGATTTAGCGGCGTTTTTCCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTCCC
* * *
1119973 ACAAACGCTGCAATAGGTCTTGATATTTAGCGGCA-TTTTCCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTCCC
*
1120015 ACAAACACCGCAA
1 ACAAACGCCGCAA
1120028 AAGATCTGGT
Statistics
Matches: 124, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 18 0.15
43 106 0.85
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (43 bp):
ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCATTTTTCCC
Found at i:1120249 original size:21 final size:21
Alignment explanation
Indices: 1120223--1120281 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1120213 ATTTTCCAAT
*
1120223 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
1120244 AAACTTAAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
**
1120265 AAAAATGAAATCCATAA
1 AAACTTGAAATCCATAA
1120282 TAATAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:1127868 original size:42 final size:42
Alignment explanation
Indices: 1127796--1127944 Score: 133
Period size: 42 Copynumber: 3.6 Consensus size: 42
1127786 TCGGTTCAAA
* * * *
1127796 AAAGTACGAGTATTTAGTGGTGTTTGTGCTTAAAACGCCACT
1 AAAGTACGAGTATCTAGCGGCGTTTATGCTTAAAACGCCACT
* *
1127838 AAAGTACGAGTATCTGGCGGCGTTTATGCTTAAAATGCCACT
1 AAAGTACGAGTATCTAGCGGCGTTTATGCTTAAAACGCCACT
* * * * * * *
1127880 AAAGTAC-ATTATTTTGAGGCATTTAT-ATAAAAACGCCACT
1 AAAGTACGAGTATCTAGCGGCGTTTATGCTTAAAACGCCACT
* *
1127920 ATAA-TATGAGTATTTAGCGGCGTTT
1 A-AAGTACGAGTATCTAGCGGCGTTT
1127945 GTATAAAAAA
Statistics
Matches: 86, Mismatches: 19, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
40 14 0.16
41 29 0.34
42 43 0.50
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (42 bp):
AAAGTACGAGTATCTAGCGGCGTTTATGCTTAAAACGCCACT
Found at i:1127916 original size:82 final size:80
Alignment explanation
Indices: 1127827--1128087 Score: 231
Period size: 82 Copynumber: 3.2 Consensus size: 80
1127817 GTTTGTGCTT
* * * *
1127827 AAAACGCCACTAAAGTACGAGTATCTGGCGGCGTTTATGCTTAAAATGCCACTAAAGTACATTAT
1 AAAACGCCACTAAA-TACGAGTATATAGCGGCGTTTGT-CTAAAAATGCCACTAAAGTACATTAT
*
1127892 TTTGAGGCATTTATATA
64 TTTGAGGCATTTGTATA
* * * *
1127909 AAAACGCCACTATAATATGAGTATTTAGCGGCGTTTGTATAAAAAATGCCGCTAAAG-AC-TCGT
1 AAAACGCCACTA-AATACGAGTATATAGCGGCGTTTGTCT-AAAAATGCCACTAAAGTACAT--T
* *
1127972 ACTATAGAGGCATTTGTATA
62 A-TTTTGAGGCATTTGTATA
* * * * * *
1127992 AAAACGCCACTAAATCACGAGTCTATAGCCGCGTTTGTTCTAAAAACGCCACTAAATTACAGT-C
1 AAAACGCCACTAAAT-ACGAGTATATAGCGGCGTTTG-TCTAAAAATGCCACTAAAGTACATTAT
* *
1128056 TTTCACGGCGTTTGTATA
64 TTTGA-GGCATTTGTATA
*
1128074 AAAACACCACTAAA
1 AAAACGCCACTAAA
1128088 GTAAATTATT
Statistics
Matches: 144, Mismatches: 25, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
80 1 0.01
81 5 0.03
82 74 0.51
83 60 0.42
84 4 0.03
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (80 bp):
AAAACGCCACTAAATACGAGTATATAGCGGCGTTTGTCTAAAAATGCCACTAAAGTACATTATTT
TGAGGCATTTGTATA
Found at i:1128018 original size:41 final size:40
Alignment explanation
Indices: 1127905--1128227 Score: 189
Period size: 41 Copynumber: 8.0 Consensus size: 40
1127895 GAGGCATTTA
* * *
1127905 TATAAAAACGCCACTATAATATGAGTATTTAGCGGCGTTTG
1 TATAAAAACGCCACTA-AATACGAGTCTATAGCGGCGTTTG
* * * ** * *
1127946 TATAAAAAATGCCGCTAAAGACTCGTACTATAGAGGCATTTG
1 TAT-AAAAACGCCACTAAATACGAGT-CTATAGCGGCGTTTG
*
1127988 TATAAAAACGCCACTAAATCACGAGTCTATAGCCGCGTTTG
1 TATAAAAACGCCACTAAAT-ACGAGTCTATAGCGGCGTTTG
* *
1128029 TTCTAAAAACGCCACTAAATTAC-AGTCTTTCA-CGGCGTTTG
1 -TATAAAAACGCCACTAAA-TACGAGTCTAT-AGCGGCGTTTG
* * * * * *
1128070 TATAAAAACACCACTAAAGTA-AATTATTTAGCGACGTTTG
1 TATAAAAACGCCACTAAA-TACGAGTCTATAGCGGCGTTTG
** * *
1128110 TATAAAAAACGCCGGTAAAGACTCA-TACTATAGCGGCGTTTG
1 TAT-AAAAACGCCACTAAATAC-GAGT-CTATAGCGGCGTTTG
* * * *
1128152 TACAAAACCGCCACTAAAT--TAGTCTTTAGCGGCG--T-
1 TATAAAAACGCCACTAAATACGAGTCTATAGCGGCGTTTG
* * * *
1128187 T-TAAAAACGCCGCTATAGTACGAGTCTTTACCGGCGTTTG
1 TATAAAAACGCCACTA-AATACGAGTCTATAGCGGCGTTTG
1128227 T
1 T
1128228 TCTAGAAATG
Statistics
Matches: 215, Mismatches: 48, Indels: 39
0.71 0.16 0.13
Matches are distributed among these distances:
34 11 0.05
35 3 0.01
36 1 0.00
37 13 0.06
38 11 0.05
39 3 0.01
40 36 0.17
41 72 0.33
42 64 0.30
43 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (40 bp):
TATAAAAACGCCACTAAATACGAGTCTATAGCGGCGTTTG
Found at i:1128036 original size:42 final size:40
Alignment explanation
Indices: 1127984--1128087 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 40
1127974 TATAGAGGCA
1127984 TTTGTATAAAAACGCCACTAAATCACGAGTCTAT-AGCCGCG
1 TTTGTATAAAAACGCCACTAAATCAC-AGTCTATCA-CCGCG
* * * *
1128025 TTTGTTCTAAAAACGCCACTAAATTACAGTCTTTCACGGCG
1 TTTG-TATAAAAACGCCACTAAATCACAGTCTATCACCGCG
*
1128066 TTTGTATAAAAACACCACTAAA
1 TTTGTATAAAAACGCCACTAAA
1128088 GTAAATTATT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
40 16 0.29
41 18 0.33
42 21 0.38
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (40 bp):
TTTGTATAAAAACGCCACTAAATCACAGTCTATCACCGCG
Found at i:1143400 original size:20 final size:20
Alignment explanation
Indices: 1143361--1143400 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1143351 AATAAGTCAG
* *
1143361 TAGTATTGATAATCAGAGGT
1 TAGTATTGATAACCAAAGGT
*
1143381 TAGTATTGATACCCAAAGGT
1 TAGTATTGATAACCAAAGGT
1143401 CATTATTGGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGTATTGATAACCAAAGGT
Found at i:1147158 original size:16 final size:16
Alignment explanation
Indices: 1147139--1147183 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
1147129 AGGAGAGGGC
*
1147139 GGTCAAAGGATGATTT
1 GGTCAAAGAATGATTT
1147155 GGTCAAAGAATGATTT
1 GGTCAAAGAATGATTT
*
1147171 GGTTAAAGAATGA
1 GGTCAAAGAATGA
1147184 AAAAGGGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.38, C:0.04, G:0.29, T:0.29
Consensus pattern (16 bp):
GGTCAAAGAATGATTT
Found at i:1159757 original size:18 final size:18
Alignment explanation
Indices: 1159734--1159776 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1159724 TTGTATGTGC
1159734 ATTGAGATTCATAGGTGA
1 ATTGAGATTCATAGGTGA
*
1159752 ATTGAGATTCATAGGTGC
1 ATTGAGATTCATAGGTGA
1159770 ATTGAGA
1 ATTGAGA
1159777 CAAACTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.33
Consensus pattern (18 bp):
ATTGAGATTCATAGGTGA
Found at i:1160033 original size:54 final size:54
Alignment explanation
Indices: 1159969--1160086 Score: 137
Period size: 54 Copynumber: 2.2 Consensus size: 54
1159959 AACGGTGCAT
* * **
1159969 TTTCGGCACTAAATGTGCAACCCATGGTATTCATAATGTGTTTATGAATGACCA
1 TTTCGGCACTAAATATGCAACCCATGGAATTCATAATACGTTTATGAATGACCA
* ** * * **
1160023 TTTCAGCACTATGTATGCAATCCATGGAATTCATAATACGTTTGTGAATTTCCA
1 TTTCGGCACTAAATATGCAACCCATGGAATTCATAATACGTTTATGAATGACCA
1160077 TTTCGGCACT
1 TTTCGGCACT
1160087 TTGGTGCAAT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (54 bp):
TTTCGGCACTAAATATGCAACCCATGGAATTCATAATACGTTTATGAATGACCA
Found at i:1165809 original size:25 final size:22
Alignment explanation
Indices: 1165772--1165816 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
1165762 ATCATCAAAA
*
1165772 AGAAAATAAAATATTATAATGAAT
1 AGAAAA-AAAA-ATAATAATGAAT
1165796 AGAAAAAAATAATAATAATGA
1 AGAAAAAAA-AATAATAATGA
1165817 CATAAAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (22 bp):
AGAAAAAAAAATAATAATGAAT
Found at i:1171841 original size:9 final size:9
Alignment explanation
Indices: 1171823--1171878 Score: 60
Period size: 9 Copynumber: 6.1 Consensus size: 9
1171813 CATTCATCAG
*
1171823 AAAAGAAAA
1 AAAAGGAAA
1171832 AAAAGGAAA
1 AAAAGGAAA
*
1171841 AAAAAGAAA
1 AAAAGGAAA
1171850 AAAA-GAAA
1 AAAAGGAAA
*
1171858 AAGATATGAAA
1 AA-A-AGGAAA
1171869 AAAAGGAAA
1 AAAAGGAAA
1171878 A
1 A
1171879 GAAATTGAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
8 6 0.15
9 27 0.66
10 2 0.05
11 6 0.15
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (9 bp):
AAAAGGAAA
Found at i:1171856 original size:27 final size:28
Alignment explanation
Indices: 1171823--1171878 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1171813 CATTCATCAG
1171823 AAAAGAAAAA-AAAGGAAAAAAAAGAAA
1 AAAAGAAAAAGAAAGGAAAAAAAAGAAA
* * *
1171850 AAAAGAAAAAGATATGAAAAAAAGGAAA
1 AAAAGAAAAAGAAAGGAAAAAAAAGAAA
1171878 A
1 A
1171879 GAAATTGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (28 bp):
AAAAGAAAAAGAAAGGAAAAAAAAGAAA
Found at i:1171879 original size:19 final size:19
Alignment explanation
Indices: 1171821--1171882 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
1171811 CTCATTCATC
1171821 AGAAAAGAAAAAAAAGGAAA
1 AGAAAAG-AAAAAAAGGAAA
*
1171841 A-AAAAGAAAAAAAGAAAA
1 AGAAAAGAAAAAAAGGAAA
* *
1171859 AGATATGAAAAAAAGGAAA
1 AGAAAAGAAAAAAAGGAAA
1171878 AGAAA
1 AGAAA
1171883 TTGAATCAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
18 12 0.33
19 23 0.64
20 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (19 bp):
AGAAAAGAAAAAAAGGAAA
Found at i:1174933 original size:43 final size:44
Alignment explanation
Indices: 1174865--1174983 Score: 136
Period size: 43 Copynumber: 2.8 Consensus size: 44
1174855 ACGAATGAGC
* * * * *
1174865 CATCCACAATGTCAACTCCATGACGAAGGATATCGTGCCCAC-A
1 CATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCAACAA
*
1174908 CATCCACGATTTCAACTTCACGACGAAGGATATCGTGTCAACAA
1 CATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCAACAA
** *
1174952 CAT--TGGATTTCAACTTCACAACGAAGGATATC
1 CATCCACGATTTCAACTTCACGACGAAGGATATC
1174984 CAATTCAAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
42 26 0.39
43 36 0.55
44 4 0.06
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.23
Consensus pattern (44 bp):
CATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCAACAA
Found at i:1175422 original size:261 final size:261
Alignment explanation
Indices: 1174957--1175538 Score: 916
Period size: 261 Copynumber: 2.2 Consensus size: 261
1174947 AACAACATTG
* *
1174957 GATTTCAACTTCACAACGAAGGATATCCAATTCAAATCTCAACTTCACAGCAAATGGGCTTCCCA
1 GATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAGCAAAGGGGCTTCCCA
* * *
1175022 GTTTCATTAAGAGCTAATTTCAACTTCACGGCAAAGGATATTGGACTCGAAACAACAACAATGCG
66 GTTTCATTAAGAGCTAATTTCAACTTCACGGCAAAGGACATTGGACTCGAAACAACAACAATACA
* * * *
1175087 ACCCTTGGATTTCAACTTCATAACGAAGTATATCCAATTCTAGGCTCAACTTCACGACGAAGGGG
131 ACCCTTGGATTTCAACTTCACAACGAAGGATATCCAATTCGAGGCTCAACTTCACGAAGAAGGGG
* *
1175152 TCATCCACGATTTTAACTTCACGACGAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGAT-
196 CCATCCACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGATA
*
1175216 G
261 A
* *
1175217 GTATTTCAACTTCACAACAAAGGATATCCAATTCAAAGCTCAACTTCACAGCGAAGGGGCTTCCC
1 G-ATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAGCAAAGGGGCTTCCC
* * * * * *
1175282 AGTTTCATTCAGAGCTAATTTCAACTTCACTGCGAATGACATTGGACTCGAAACAACAGCAATAT
65 AGTTTCATTAAGAGCTAATTTCAACTTCACGGCAAAGGACATTGGACTCGAAACAACAACAATAC
* *
1175347 AACCCTTGGATTTCAACTTCACAATGAAGGATATCCAATTCGAGGCTCAACTTCACGAAGAATGG
130 AACCCTTGGATTTCAACTTCACAACGAAGGATATCCAATTCGAGGCTCAACTTCACGAAGAAGGG
1175412 GCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGAT
195 GCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGAT
1175477 AA
260 AA
* *
1175479 GATTTCAACTTCACAACGAAGGATATCCAATTCGAGGCTCAACTTCAC-GACAAAGGGGCT
1 GATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAG-CAAAGGGGCT
1175539 ATTCACGATA
Statistics
Matches: 293, Mismatches: 26, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
260 2 0.01
261 290 0.99
262 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (261 bp):
GATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAGCAAAGGGGCTTCCCA
GTTTCATTAAGAGCTAATTTCAACTTCACGGCAAAGGACATTGGACTCGAAACAACAACAATACA
ACCCTTGGATTTCAACTTCACAACGAAGGATATCCAATTCGAGGCTCAACTTCACGAAGAAGGGG
CCATCCACGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGATA
A
Found at i:1175555 original size:124 final size:124
Alignment explanation
Indices: 1175355--1175584 Score: 381
Period size: 124 Copynumber: 1.9 Consensus size: 124
1175345 ATAACCCTTG
* *
1175355 GATTTCAACTTCACAATGAAGGATATCCAATTCGAGGCTCAACTTCACGAAGAATGGGCCATCCA
1 GATTTCAACTTCACAACGAAGGATATCCAATTCGAGGCTCAACTTCACGAAGAAGGGGCCATCCA
* *
1175420 CGATTTCAACTTCACGACGAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGATAA
66 CGATATCAACTTCACGACGAAGGATATCGTGTCCAACAGCAACATTCATCTTTAGATAA
* *
1175479 GATTTCAACTTCACAACGAAGGATATCCAATTCGAGGCTCAACTTCACGACA-AAGGGGCTATTC
1 GATTTCAACTTCACAACGAAGGATATCCAATTCGAGGCTCAACTTCACGA-AGAAGGGGCCATCC
*
1175543 ACGATATCAACTTCACGGCGAAGGATATCGTGTCCAACAGCA
65 ACGATATCAACTTCACGACGAAGGATATCGTGTCCAACAGCA
1175585 GCAATGCATC
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
124 97 0.99
125 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (124 bp):
GATTTCAACTTCACAACGAAGGATATCCAATTCGAGGCTCAACTTCACGAAGAAGGGGCCATCCA
CGATATCAACTTCACGACGAAGGATATCGTGTCCAACAGCAACATTCATCTTTAGATAA
Found at i:1175805 original size:137 final size:137
Alignment explanation
Indices: 1175633--1176017 Score: 544
Period size: 137 Copynumber: 2.8 Consensus size: 137
1175623 TCGTGTCCAT
* *
1175633 CAACCTCATTCTTAGATAGCCAAATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTTT
1 CAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTTT
* * * *
1175698 AAAGATGGACAAACGTCCTGATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTTATCAC
66 AAAGATGGACAAACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAAAACTCCTCATCAC
1175763 GA-AGGAG
131 -ATAGGAG
1175770 CAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGG-ACCAGTGTTATCTCAAATATCTT
1 CAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCA-TGTTATCTCAAATATCTT
* *
1175834 TAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAAAACTCCTCATCA
65 TAAAGATGGACAAACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAAAACTCCTCATCA
1175899 CATAGGAG
130 CATAGGAG
* * * * *
1175907 C--CGAGTAATTCTTAAACATCGAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCT
1 CAAC-A-TCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCT
* * * * *
1175970 TTAACGAGGGTCAAATGTCCTCATCACGAAGGAACAATGTCATACACC
64 TTAAAGATGGACAAACGTCCTCATCACGAAGGAACAATGTCATCCACC
1176018 AATTGGATCT
Statistics
Matches: 224, Mismatches: 19, Indels: 10
0.89 0.08 0.04
Matches are distributed among these distances:
135 1 0.00
136 6 0.03
137 213 0.95
138 4 0.02
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.24
Consensus pattern (137 bp):
CAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTTT
AAAGATGGACAAACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAAAACTCCTCATCAC
ATAGGAG
Found at i:1176185 original size:3 final size:3
Alignment explanation
Indices: 1176179--1176206 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1176169 AGACTATCAA
1176179 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1176207 GTAGTAGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1182488 original size:20 final size:20
Alignment explanation
Indices: 1182446--1182496 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
1182436 AAAATAATTG
1182446 AATTTC-ACATCATAACATC
1 AATTTCAACATCATAACATC
*
1182465 AATTTCAACACTCA-AACATT
1 AATTTCAACA-TCATAACATC
1182485 AATTTCTAACAT
1 AATTTC-AACAT
1182497 AGTAAATCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 6 0.21
20 15 0.54
21 7 0.25
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTTCAACATCATAACATC
Found at i:1187239 original size:31 final size:32
Alignment explanation
Indices: 1187201--1187286 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 32
1187191 ATTTGATTTT
*
1187201 TTTTAAATAAAATATTAATTTAATC-CTTAAA
1 TTTTAAATAAAATATTAATTTAATCAATTAAA
* * * *
1187232 TTTTAAATAAAACATCAATTT-AGCAATTGAA
1 TTTTAAATAAAATATTAATTTAATCAATTAAA
*
1187263 TTTTAAATAAAATATTAGTTTAAT
1 TTTTAAATAAAATATTAATTTAAT
1187287 TCTTTAATCT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
30 2 0.05
31 41 0.93
32 1 0.02
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (32 bp):
TTTTAAATAAAATATTAATTTAATCAATTAAA
Found at i:1188345 original size:31 final size:30
Alignment explanation
Indices: 1188310--1188400 Score: 101
Period size: 31 Copynumber: 3.0 Consensus size: 30
1188300 AATTTTGAAA
*
1188310 ATTTTATATAAATTTTAACGATTAAATTAAT
1 ATTTTATATAAAATTTAA-GATTAAATTAAT
* * *
1188341 ATTTTATTTAAAAGTTAAGATTAATTTAAT
1 ATTTTATATAAAATTTAAGATTAAATTAAT
* * *
1188371 ATTTTATCTAAAATTCAAATATTAAATTAA
1 ATTTTATATAAAATT-TAAGATTAAATTAA
1188401 AAGTTAATCA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
30 24 0.48
31 26 0.52
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (30 bp):
ATTTTATATAAAATTTAAGATTAAATTAAT
Found at i:1188370 original size:30 final size:31
Alignment explanation
Indices: 1188310--1188400 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 31
1188300 AATTTTGAAA
**
1188310 ATTTTATATAAATTTTAACGATTAAATTAAT
1 ATTTTATATAAAAGTTAACGATTAAATTAAT
* *
1188341 ATTTTATTTAAAAGTTAA-GATTAATTTAAT
1 ATTTTATATAAAAGTTAACGATTAAATTAAT
* **
1188371 ATTTTATCTAAAA-TTCAAATATTAAATTAA
1 ATTTTATATAAAAGTT-AACGATTAAATTAA
1188401 AAGTTAATCA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
29 2 0.04
30 25 0.49
31 24 0.47
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTTTATATAAAAGTTAACGATTAAATTAAT
Found at i:1188791 original size:40 final size:40
Alignment explanation
Indices: 1188736--1188855 Score: 231
Period size: 40 Copynumber: 3.0 Consensus size: 40
1188726 AACATCTTTT
1188736 TATAAGATTTAAACCAGAGATCTATTAAACTTAATAAGAA
1 TATAAGATTTAAACCAGAGATCTATTAAACTTAATAAGAA
1188776 TATAAGATTTAAACCAGAGATCTATTAAACTTAATAAGAA
1 TATAAGATTTAAACCAGAGATCTATTAAACTTAATAAGAA
*
1188816 TATAAGATTTAAACCAGAGATCTATTGAACTTAATAAGAA
1 TATAAGATTTAAACCAGAGATCTATTAAACTTAATAAGAA
1188856 GCAACCAAAC
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (40 bp):
TATAAGATTTAAACCAGAGATCTATTAAACTTAATAAGAA
Found at i:1189105 original size:16 final size:16
Alignment explanation
Indices: 1189086--1189116 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1189076 TTTTTATTAT
*
1189086 TTTTATTTAATTTTAA
1 TTTTAGTTAATTTTAA
1189102 TTTTAGTTAATTTTA
1 TTTTAGTTAATTTTA
1189117 GGGACCAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTAGTTAATTTTAA
Found at i:1191990 original size:38 final size:38
Alignment explanation
Indices: 1191948--1192063 Score: 196
Period size: 38 Copynumber: 3.1 Consensus size: 38
1191938 TCGGTAATTC
*
1191948 GTTCATTTATATACGTGTATGTTCATTCGTTTATGTTT
1 GTTCATTTATGTACGTGTATGTTCATTCGTTTATGTTT
* *
1191986 GTTCATTTATGTACGTGTATGTACGTTCGTTTATGTTT
1 GTTCATTTATGTACGTGTATGTTCATTCGTTTATGTTT
*
1192024 GTTCATTTATGTACGTGTATGTTCATTCATTTATGTTT
1 GTTCATTTATGTACGTGTATGTTCATTCGTTTATGTTT
1192062 GT
1 GT
1192064 GTATGTTCGT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 72 1.00
ACGTcount: A:0.17, C:0.10, G:0.18, T:0.54
Consensus pattern (38 bp):
GTTCATTTATGTACGTGTATGTTCATTCGTTTATGTTT
Found at i:1192044 original size:24 final size:24
Alignment explanation
Indices: 1192025--1192071 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1192015 TTTATGTTTG
1192025 TTCATTTATGTACGTGTATGTTCA
1 TTCATTTATGTACGTGTATGTTCA
**
1192049 TTCATTTATGTTTGTGTATGTTC
1 TTCATTTATGTACGTGTATGTTC
1192072 GTTTATATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.55
Consensus pattern (24 bp):
TTCATTTATGTACGTGTATGTTCA
Found at i:1192395 original size:23 final size:23
Alignment explanation
Indices: 1192272--1192395 Score: 101
Period size: 23 Copynumber: 5.4 Consensus size: 23
1192262 TTGTTGTTTA
* *
1192272 GTTCGTTCA-GTTAATTTA-TGT
1 GTTCGTTTACGTTCATTTATTGT
* * * *
1192293 GTTCGATTAGGTTCATTTGTTAT
1 GTTCGTTTACGTTCATTTATTGT
* *
1192316 GTTCGTTTATGTTCATCTATTGT
1 GTTCGTTTACGTTCATTTATTGT
* *
1192339 GTTCGTTTATGTTCGTTCGT-TTGT
1 GTTCGTTTACGTTCATT--TATTGT
* *
1192363 GTTCATTTACGTTCGTTTATTGT
1 GTTCGTTTACGTTCATTTATTGT
1192386 GTTCGTTTAC
1 GTTCGTTTAC
1192396 ATCCTTTCGT
Statistics
Matches: 83, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
21 7 0.08
22 8 0.10
23 48 0.58
24 19 0.23
25 1 0.01
ACGTcount: A:0.13, C:0.12, G:0.20, T:0.55
Consensus pattern (23 bp):
GTTCGTTTACGTTCATTTATTGT
Found at i:1192405 original size:47 final size:47
Alignment explanation
Indices: 1192312--1192412 Score: 121
Period size: 47 Copynumber: 2.1 Consensus size: 47
1192302 GGTTCATTTG
* * ** *
1192312 TTATGTTCGTTTATGTTCATCTATTGTGTTCGTTTATGTTCGTTCGT
1 TTATGTTCATTTACGTTCATCTATTGTGTTCGTTTACATCCGTTCGT
* * * *
1192359 TTGTGTTCATTTACGTTCGTTTATTGTGTTCGTTTACATCCTTTCGT
1 TTATGTTCATTTACGTTCATCTATTGTGTTCGTTTACATCCGTTCGT
1192406 TTATGTT
1 TTATGTT
1192413 TGTTCATTTG
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.11, C:0.14, G:0.18, T:0.57
Consensus pattern (47 bp):
TTATGTTCATTTACGTTCATCTATTGTGTTCGTTTACATCCGTTCGT
Done.