Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 111 of 187
Found at i:33150749 original size:19 final size:19
Alignment explanation
Indices: 33150698--33150749 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
33150688 TTTTTTATAA
*
33150698 TTTTTATAATT-TTTAAAT
1 TTTTTAAAATTATTTAAAT
**
33150716 TTTTTAAAAAAATTT-AAT
1 TTTTTAAAATTATTTAAAT
33150734 TGTTTTAAAATTATTT
1 T-TTTTAAAATTATTT
33150750 TCATTATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTTAAAATTATTTAAAT
Found at i:33150879 original size:61 final size:61
Alignment explanation
Indices: 33150784--33150910 Score: 173
Period size: 61 Copynumber: 2.1 Consensus size: 61
33150774 TTAAAAAAAC
* * * *
33150784 TAATTAATTGCTAAAGTGGCAATCCACATGTATGACACAGTTCAACAAAGTTAATAAAAGT
1 TAATTAATTGCTAAAGTGACAATCCACATATATGACACACTTAAACAAAGTTAATAAAAGT
* * ** *
33150845 TAATTAATTGCTTACGTGACAATCCATGTATATGACACACTTAAACATAGTTAATAAAAGT
1 TAATTAATTGCTAAAGTGACAATCCACATATATGACACACTTAAACAAAGTTAATAAAAGT
33150906 TAATT
1 TAATT
33150911 TTTTCCATCT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (61 bp):
TAATTAATTGCTAAAGTGACAATCCACATATATGACACACTTAAACAAAGTTAATAAAAGT
Found at i:33152532 original size:63 final size:61
Alignment explanation
Indices: 33152465--33152626 Score: 143
Period size: 62 Copynumber: 2.6 Consensus size: 61
33152455 TAATTTTTTG
* *
33152465 AAAATTTTAATTAGGTTCCTCCAAAATTTTTAAAAATTATT-ATTAAACCTTTGAGAAAAT-TTA
1 AAAATTTTAATTAGG-TCCTCCAAAATTTTTAAAAATT-TTCATAAAACCTCT-A-AAAATATTA
* * * ** *
33152528 AAAATTTCAATTA-GACTCTTCAATTTTTGTTAAAAATTTTCATAAAACCTCTAAAATTATTA
1 AAAATTTTAATTAGGTC-CTCCAAAATTT-TTAAAAATTTTCATAAAACCTCTAAAAATATTA
* *
33152590 AAAGTTTTAATTA-GACCTACCAAAATTTTTAAAAATT
1 AAAATTTTAATTAGGTCCT-CCAAAATTTTTAAAAATT
33152627 CCGACTAAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
61 16 0.20
62 35 0.43
63 30 0.37
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (61 bp):
AAAATTTTAATTAGGTCCTCCAAAATTTTTAAAAATTTTCATAAAACCTCTAAAAATATTA
Found at i:33152992 original size:61 final size:60
Alignment explanation
Indices: 33152927--33153046 Score: 150
Period size: 61 Copynumber: 2.0 Consensus size: 60
33152917 TTTTTTTATC
* * * * * *
33152927 ACCTAATTATGAAAAGTTATAAAAAGATCACTTAATTATGTTTTTTTTTTCTTTTTTGGTT
1 ACCTAATTACGAAAAGTAACAAAAAGACCACTCAACTATG-TTTTTTTTTCTTTTTTGGTT
* * *
33152988 ACCTAATTACGAAAAGTAACCAAATGGCCACTCAACTATGTTTTTTTTTCTTTTTTGGT
1 ACCTAATTACGAAAAGTAACAAAAAGACCACTCAACTATGTTTTTTTTTCTTTTTTGGT
33153047 CACTAGCTAG
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
60 19 0.38
61 31 0.62
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (60 bp):
ACCTAATTACGAAAAGTAACAAAAAGACCACTCAACTATGTTTTTTTTTCTTTTTTGGTT
Found at i:33153528 original size:63 final size:62
Alignment explanation
Indices: 33153460--33153584 Score: 162
Period size: 62 Copynumber: 2.0 Consensus size: 62
33153450 GTTGGTGACC
* * * * *
33153460 AAAAAAGAA-AAACCATAAATAAGTGGCTATTTTATAACTTTTCATAGTTGGGTGACAAAAAA
1 AAAAAAAAACAAACCAT-AATAAGTGACCATTTTAGAACTTTTCATAGTTGAGTGACAAAAAA
* * *
33153522 AAAAAAAAACAGACCATAATGAGTGACCATTTTAGAACTTTTCATAGTTGAGTGACCAAAAA
1 AAAAAAAAACAAACCATAATAAGTGACCATTTTAGAACTTTTCATAGTTGAGTGACAAAAAA
33153584 A
1 A
33153585 TTTCATAGTT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
62 48 0.89
63 6 0.11
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (62 bp):
AAAAAAAAACAAACCATAATAAGTGACCATTTTAGAACTTTTCATAGTTGAGTGACAAAAAA
Found at i:33153593 original size:24 final size:24
Alignment explanation
Indices: 33153561--33153608 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
33153551 TTTTAGAACT
*
33153561 TTTCATAGTTGAGTGACCAAAAAA
1 TTTCATAGTTGAGTGACAAAAAAA
*
33153585 TTTCATAGTTGGGTGACAAAAAAA
1 TTTCATAGTTGAGTGACAAAAAAA
33153609 AAAAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (24 bp):
TTTCATAGTTGAGTGACAAAAAAA
Found at i:33153606 original size:86 final size:87
Alignment explanation
Indices: 33153499--33153672 Score: 332
Period size: 88 Copynumber: 2.0 Consensus size: 87
33153489 TTTTATAACT
33153499 TTTCATAGTTGGGTGAC-AAAAAAAAAAAAAAACAGACCATAATGAGTGACCATTTTAGAACTTT
1 TTTCATAGTTGGGTGACAAAAAAAAAAAAAAAACAGACCATAATGAGTGACCATTTTAGAACTTT
33153563 TCATAGTTGAGTGACCAAAAAA
66 TCATAGTTGAGTGACCAAAAAA
33153585 TTTCATAGTTGGGTGACAAAAAAAAAAAAAAAAACAGACCATAATGAGTGACCATTTTAGAACTT
1 TTTCATAGTTGGGTGAC-AAAAAAAAAAAAAAAACAGACCATAATGAGTGACCATTTTAGAACTT
33153650 TTCATAGTTGAGTGACCAAAAAA
65 TTCATAGTTGAGTGACCAAAAAA
33153673 GAAAATCATA
Statistics
Matches: 86, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
86 17 0.20
88 69 0.80
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.25
Consensus pattern (87 bp):
TTTCATAGTTGGGTGACAAAAAAAAAAAAAAAACAGACCATAATGAGTGACCATTTTAGAACTTT
TCATAGTTGAGTGACCAAAAAA
Found at i:33159071 original size:24 final size:24
Alignment explanation
Indices: 33159042--33159087 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
33159032 GAAAAATATT
33159042 AAATATATATA-TTTTTTATTTTTA
1 AAATATA-ATAGTTTTTTATTTTTA
33159066 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
33159088 CAGTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:33159198 original size:9 final size:9
Alignment explanation
Indices: 33159184--33159211 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
33159174 TTTTGTTACA
33159184 ACAATTAAT
1 ACAATTAAT
33159193 ACAATTAAT
1 ACAATTAAT
33159202 ACAATTAAT
1 ACAATTAAT
33159211 A
1 A
33159212 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:33159233 original size:68 final size:68
Alignment explanation
Indices: 33159154--33159363 Score: 388
Period size: 68 Copynumber: 3.1 Consensus size: 68
33159144 TCAAGTTTGT
*
33159154 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
33159219 AAA
66 AAA
33159222 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
33159287 AAA
66 AAA
33159290 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
33159353 AAT
66 AAA
33159356 TTTACTAA
1 TTTACTAA
33159364 CAATTAATTT
Statistics
Matches: 140, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
66 27 0.19
67 1 0.01
68 112 0.80
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:33159264 original size:9 final size:9
Alignment explanation
Indices: 33159252--33159279 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
33159242 TTTTATTACA
33159252 ACAATTAAT
1 ACAATTAAT
33159261 ACAATTAAT
1 ACAATTAAT
33159270 ACAATTAAT
1 ACAATTAAT
33159279 A
1 A
33159280 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:33159373 original size:16 final size:16
Alignment explanation
Indices: 33159352--33159393 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
33159342 AATAATTTGA
* *
33159352 TAATTTTACTAACAAT
1 TAATTTTAATAAAAAT
33159368 TAATTTTAATAAAAAT
1 TAATTTTAATAAAAAT
*
33159384 TAGTTTTAAT
1 TAATTTTAAT
33159394 TTTATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAAAAAT
Found at i:33159377 original size:22 final size:20
Alignment explanation
Indices: 33159352--33159419 Score: 54
Period size: 22 Copynumber: 3.4 Consensus size: 20
33159342 AATAATTTGA
33159352 TAATTTTACTAACAATTAATTT
1 TAATTTTA-TAA-AATTAATTT
*
33159374 TAA---TA-AAAATTAGTTT
1 TAATTTTATAAAATTAATTT
*
33159390 TAATTTTATTAAAAAATAATTT
1 TAATTTTA-T-AAAATTAATTT
33159412 TAATTTTA
1 TAATTTTA
33159420 ATTAAAAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
16 11 0.30
17 2 0.05
19 4 0.11
22 20 0.54
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (20 bp):
TAATTTTATAAAATTAATTT
Found at i:33159426 original size:22 final size:23
Alignment explanation
Indices: 33159367--33159427 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
33159357 TTACTAACAA
*
33159367 TTAATTTTAA-TAAAAATTAGTT
1 TTAATTTTAATTAAAAATTAATT
*
33159389 TTAATTTT-ATTAAAAAATAATT
1 TTAATTTTAATTAAAAATTAATT
33159411 TTAATTTTAATTAAAAA
1 TTAATTTTAATTAAAAA
33159428 CAGGTCGGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 1 0.03
22 26 0.74
23 8 0.23
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TTAATTTTAATTAAAAATTAATT
Found at i:33164413 original size:24 final size:24
Alignment explanation
Indices: 33164379--33164440 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
33164369 CCTTTTTGAG
* *
33164379 CCATTTCGTACCGAAAATCCCATT
1 CCATTTCGTACCAAAAATCCCATA
* *
33164403 CCATTTTGTACCAAAAATCCGATA
1 CCATTTCGTACCAAAAATCCCATA
33164427 CCATTTCGTACCAA
1 CCATTTCGTACCAA
33164441 TACCCAATTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.32, C:0.31, G:0.08, T:0.29
Consensus pattern (24 bp):
CCATTTCGTACCAAAAATCCCATA
Found at i:33166240 original size:26 final size:26
Alignment explanation
Indices: 33166204--33166265 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
33166194 ACATATTTTC
33166204 TCAAAATTTTACCAAGGGCAAAATCA
1 TCAAAATTTTACCAAGGGCAAAATCA
* * *
33166230 TCAAAATTTTACTATGGGTAAAATCA
1 TCAAAATTTTACCAAGGGCAAAATCA
33166256 TCAAAATTTT
1 TCAAAATTTT
33166266 GTTTGGGGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.32
Consensus pattern (26 bp):
TCAAAATTTTACCAAGGGCAAAATCA
Found at i:33171890 original size:20 final size:20
Alignment explanation
Indices: 33171847--33171888 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
33171837 TAAAGAAAGT
33171847 AAATGCAATGGAAAGTAATG
1 AAATGCAATGGAAAGTAATG
33171867 AAATGCAAAT-GAAAGTAA-G
1 AAATGC-AATGGAAAGTAATG
33171886 AAA
1 AAA
33171889 ATTTGGAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 14 0.67
21 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.17
Consensus pattern (20 bp):
AAATGCAATGGAAAGTAATG
Found at i:33172357 original size:15 final size:16
Alignment explanation
Indices: 33172337--33172366 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33172327 TGGTGCCTTG
33172337 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
33172352 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
33172367 AGCATGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:33175232 original size:15 final size:15
Alignment explanation
Indices: 33175208--33175238 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33175198 TACGGTGTAT
*
33175208 TGGTGCTTGATAACA
1 TGGTGATTGATAACA
33175223 TGGTGATTGATAACA
1 TGGTGATTGATAACA
33175238 T
1 T
33175239 AGTGTCTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.35
Consensus pattern (15 bp):
TGGTGATTGATAACA
Found at i:33201523 original size:21 final size:20
Alignment explanation
Indices: 33201485--33201547 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
33201475 ATTCAATTTC
33201485 TCAATCC-AAT-ATA-CATT
1 TCAATCCAAATAATATCATT
33201502 TCAATACCACAATAAT-TCATT
1 TCAAT-CCA-AATAATATCATT
*
33201523 T-AATTCAAATAATATCATT
1 TCAATCCAAATAATATCATT
33201542 TGCAAT
1 T-CAAT
33201548 TTCCATTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
17 5 0.14
18 8 0.22
19 8 0.22
20 6 0.16
21 10 0.27
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TCAATCCAAATAATATCATT
Found at i:33205971 original size:25 final size:25
Alignment explanation
Indices: 33205909--33206015 Score: 114
Period size: 25 Copynumber: 4.3 Consensus size: 25
33205899 GTACATATAT
*
33205909 GCTCATACGAGCT-ATGAATCGGTAT
1 GCTCATACGAGCTGA-GAATCGGTAA
33205934 GCTCTCATA--AGCT-ATGAATCGGTAA
1 G--CTCATACGAGCTGA-GAATCGGTAA
* *
33205959 GCTCATACGAGCTGAAAATCTGTAA
1 GCTCATACGAGCTGAGAATCGGTAA
*
33205984 GCTCATACAAGCTGAGAATCGGTAA
1 GCTCATACGAGCTGAGAATCGGTAA
33206009 GCTCATA
1 GCTCATA
33206016 AGAGTTGTGG
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
23 6 0.08
25 58 0.82
26 1 0.01
27 6 0.08
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (25 bp):
GCTCATACGAGCTGAGAATCGGTAA
Found at i:33222105 original size:25 final size:25
Alignment explanation
Indices: 33222077--33222152 Score: 125
Period size: 25 Copynumber: 3.0 Consensus size: 25
33222067 TTAGGGTTAT
33222077 TGATTTATAGCTCATGAGAGCATAC
1 TGATTTATAGCTCATGAGAGCATAC
*
33222102 TGATTTATAGCACATGAGAGCATAC
1 TGATTTATAGCTCATGAGAGCATAC
* *
33222127 CGATTTATAGCTCGTGAGAGCATAC
1 TGATTTATAGCTCATGAGAGCATAC
33222152 T
1 T
33222153 AATCTTTAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (25 bp):
TGATTTATAGCTCATGAGAGCATAC
Found at i:33222173 original size:50 final size:50
Alignment explanation
Indices: 33222078--33222201 Score: 139
Period size: 50 Copynumber: 2.5 Consensus size: 50
33222068 TAGGGTTATT
* *
33222078 GATTTATAGCTCATGAGAGCATACTGATTTATAGCACATGAGAGCATACC
1 GATTTATAGCTCGTGAGAGCATACTAATTTATAGCACATGAGAGCATACC
*
33222128 GATTTATAGCTCGTGAGAGCATACTAATCTT-TAGTTCA-AT-TGAGCATACC
1 GATTTATAGCTCGTGAGAGCATACTAAT-TTATAG--CACATGAGAGCATACC
* *
33222178 GATTCACAGCTCGT-ATGAGCATAC
1 GATTTATAGCTCGTGA-GAGCATAC
33222202 ACGTACATGA
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
49 1 0.02
50 58 0.89
51 4 0.06
52 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (50 bp):
GATTTATAGCTCGTGAGAGCATACTAATTTATAGCACATGAGAGCATACC
Found at i:33226218 original size:50 final size:49
Alignment explanation
Indices: 33226124--33226219 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 49
33226114 TATTGAGGTT
* *
33226124 ATGAGAGGTCCCATGTAGACCATGTCTGGGACATGGAGTTGGCACCAAG
1 ATGAGAGGTCCCACGTAGACCATGTCTGGGACATGGAGTGGGCACCAAG
*
33226173 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGTA-TGGGCACC
1 ATGAGAGGTCCCACGT-AGACCATGTCTGGGACATGG-AGTGGGCACC
33226220 GATATGAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
49 14 0.33
50 27 0.64
51 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.32, T:0.20
Consensus pattern (49 bp):
ATGAGAGGTCCCACGTAGACCATGTCTGGGACATGGAGTGGGCACCAAG
Found at i:33226241 original size:50 final size:50
Alignment explanation
Indices: 33226132--33226246 Score: 126
Period size: 50 Copynumber: 2.3 Consensus size: 50
33226122 TTATGAGAGG
* * **
33226132 TCCCATGT-AGACCATGTCTGGGACATGGAGTTGGCACCAAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGAGTGGGCACCAAGATGAAAAC
** * *
33226181 TCCCCCGTAAGACCATGTCTGGGACATGGTA-TGGGCACCGATATGAAAAC
1 TCCCATGTAAGACCATGTCTGGGACATGG-AGTGGGCACCAAGATGAAAAC
*
33226231 TCCCGTGTAAGACCAT
1 TCCCATGTAAGACCAT
33226247 ATCTAGGATA
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
49 6 0.11
50 47 0.87
51 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGAGTGGGCACCAAGATGAAAAC
Found at i:33226545 original size:20 final size:20
Alignment explanation
Indices: 33226520--33226568 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
33226510 TGAGTTATTT
33226520 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
33226540 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
33226560 AAG-AAGCAA
1 AAGTAAGCAA
33226569 AGACCACGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:33237639 original size:21 final size:23
Alignment explanation
Indices: 33237613--33237654 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
33237603 GGTAGGAATG
33237613 TTTTTGAAAAA-CT-TGCATTGA
1 TTTTTGAAAAAGCTCTGCATTGA
33237634 TTTTTGAAAAAGCTCTGCATT
1 TTTTTGAAAAAGCTCTGCATT
33237655 AACATCCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.58
22 2 0.11
23 6 0.32
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (23 bp):
TTTTTGAAAAAGCTCTGCATTGA
Found at i:33238153 original size:47 final size:47
Alignment explanation
Indices: 33238099--33238193 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
33238089 AATTAGTATT
33238099 TGATAAGATTATGCATGAAGCTTGGTTTTTATTAAAACCTGACAAAA
1 TGATAAGATTATGCATGAAGCTTGGTTTTTATTAAAACCTGACAAAA
33238146 TGATAAGATTATGCATGAAGCTTGGTTTTTATTAAAACCTGACAAAA
1 TGATAAGATTATGCATGAAGCTTGGTTTTTATTAAAACCTGACAAAA
33238193 T
1 T
33238194 CACTCTTTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.35
Consensus pattern (47 bp):
TGATAAGATTATGCATGAAGCTTGGTTTTTATTAAAACCTGACAAAA
Found at i:33247647 original size:20 final size:22
Alignment explanation
Indices: 33247595--33247662 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 22
33247585 TGTCACTCAG
*
33247595 TCACACTGGCGTGTGCCTCCTT
1 TCACACAGGCGTGTGCCTCCTT
* *
33247617 TTACACAGGCGTGTG-CTTC-T
1 TCACACAGGCGTGTGCCTCCTT
* *
33247637 TCACACGGGCGTGTTCCT-CTT
1 TCACACAGGCGTGTGCCTCCTT
33247658 TCACA
1 TCACA
33247663 TGGGTGTGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 14 0.37
21 11 0.29
22 13 0.34
ACGTcount: A:0.13, C:0.32, G:0.22, T:0.32
Consensus pattern (22 bp):
TCACACAGGCGTGTGCCTCCTT
Found at i:33257529 original size:21 final size:20
Alignment explanation
Indices: 33257503--33257549 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
33257493 CATGAGGGAA
33257503 ATGTATCGA-TACATCCCTTAG
1 ATGTATC-ACTACAT-CCTTAG
*
33257524 ATGTATCACTACATCTTTAG
1 ATGTATCACTACATCCTTAG
33257544 ATGTAT
1 ATGTAT
33257550 TGGTACAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (20 bp):
ATGTATCACTACATCCTTAG
Found at i:33258266 original size:13 final size:13
Alignment explanation
Indices: 33258248--33258272 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33258238 TATTTTATTT
33258248 TAGAAAATTTTTG
1 TAGAAAATTTTTG
33258261 TAGAAAATTTTT
1 TAGAAAATTTTT
33258273 AAAATACCAT
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:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TAGAAAATTTTTG
Found at i:33258431 original size:18 final size:17
Alignment explanation
Indices: 33258408--33258441 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
33258398 CCCAAATATA
*
33258408 GAAATATATATATATAAG
1 GAAATAAATATA-ATAAG
33258426 GAAATAAATATAATAA
1 GAAATAAATATAATAA
33258442 AAGTCTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (17 bp):
GAAATAAATATAATAAG
Found at i:33259681 original size:3 final size:3
Alignment explanation
Indices: 33259673--33259715 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
33259663 TTTTTAATCC
33259673 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
33259716 TCTTCTTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:33259870 original size:23 final size:22
Alignment explanation
Indices: 33259843--33259902 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
33259833 CGACATTACC
*
33259843 TTTAAACTTATTATTATTATAAT
1 TTTAAA-TTATTATTACTATAAT
* *
33259866 TTTAAAATGTAATA-TACTATTAT
1 TTT-AAAT-TATTATTACTATAAT
33259889 TTTAAATTATTATT
1 TTTAAATTATTATT
33259903 GACATGTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
21 4 0.13
22 5 0.17
23 14 0.47
24 7 0.23
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTAAATTATTATTACTATAAT
Found at i:33259933 original size:21 final size:21
Alignment explanation
Indices: 33259909--33259952 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
33259899 TATTGACATG
*
33259909 TTTTAAATTTATCATACATTT
1 TTTTAAATCTATCATACATTT
* * *
33259930 TTTTATATCTATTATATATTT
1 TTTTAAATCTATCATACATTT
33259951 TT
1 TT
33259953 ATCTTCAAAC
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:0.07, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTAAATCTATCATACATTT
Found at i:33264531 original size:18 final size:19
Alignment explanation
Indices: 33264489--33264532 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
33264479 AATTTTAAAC
33264489 TATTTTAGGAAAATTTTTA
1 TATTTTAGGAAAATTTTTA
*
33264508 TATTTTA-GAAAGTTTATTA
1 TATTTTAGGAAAATTT-TTA
33264527 T-TTTTA
1 TATTTTA
33264533 AAATTTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (19 bp):
TATTTTAGGAAAATTTTTA
Found at i:33265074 original size:20 final size:20
Alignment explanation
Indices: 33265029--33265081 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
33265019 CAAAGATTAC
33265029 AAAATAATTCAAAATAATTTT
1 AAAA-AATTCAAAATAATTTT
* *
33265050 CAAAAATTCAAAAT-GTTTAT
1 AAAAAATTCAAAATAATTT-T
*
33265070 AAAAATTTCAAA
1 AAAAAATTCAAA
33265082 TTTTTATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 3 0.11
20 21 0.78
21 3 0.11
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:33273332 original size:8 final size:8
Alignment explanation
Indices: 33273319--33273377 Score: 55
Period size: 8 Copynumber: 7.1 Consensus size: 8
33273309 CCATGACTTG
33273319 TTTTTATT
1 TTTTTATT
33273327 TTTTTATT
1 TTTTTATT
* *
33273335 TTTATCTT
1 TTTTTATT
**
33273343 TTTCCATT
1 TTTTTATT
33273351 TTGTTTATT
1 TT-TTTATT
33273360 TTTTTATT
1 TTTTTATT
*
33273368 ATTTCTATT
1 -TTTTTATT
33273377 T
1 T
33273378 CTATTTTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 28 0.68
9 13 0.32
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTTATT
Found at i:33273384 original size:32 final size:33
Alignment explanation
Indices: 33273321--33273389 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
33273311 ATGACTTGTT
* *
33273321 TTTATTTTTTTATTTTTATCTTTTTCCATTTTG
1 TTTATTTTTTTATTATTATCTATTTCCATTTTG
* *
33273354 TTTATTTTTTTATTATT-TCTATTTCTATTTTT
1 TTTATTTTTTTATTATTATCTATTTCCATTTTG
33273386 TTTA
1 TTTA
33273390 AAAAAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 16 0.50
33 16 0.50
ACGTcount: A:0.14, C:0.07, G:0.01, T:0.77
Consensus pattern (33 bp):
TTTATTTTTTTATTATTATCTATTTCCATTTTG
Found at i:33280128 original size:25 final size:25
Alignment explanation
Indices: 33280100--33280171 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 25
33280090 AATTTTCTTG
33280100 AAATTTTATTGGGGTAAAATCGTCA
1 AAATTTTATTGGGGTAAAATCGTCA
* *
33280125 AAATTTTAGTGGGGGTAAAATTGTCA
1 AAATTTTA-TTGGGGTAAAATCGTCA
*
33280151 AAGATTTTACTGGGGTAAAAT
1 AA-ATTTTATTGGGGTAAAAT
33280172 TTGGGTGAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
25 8 0.20
26 27 0.66
27 6 0.15
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.35
Consensus pattern (25 bp):
AAATTTTATTGGGGTAAAATCGTCA
Found at i:33280754 original size:37 final size:37
Alignment explanation
Indices: 33280704--33280775 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
33280694 AAGAGAATAA
*
33280704 TGGAAAATATCGTTTGGTTGAAAGCTAGAAAATATAG
1 TGGAAAATATCGTTTGGTTGAAAGCCAGAAAATATAG
33280741 TGGAAAATATCGTTTGGTTGAAAGCCAGAAAATAT
1 TGGAAAATATCGTTTGGTTGAAAGCCAGAAAATAT
33280776 CAAGGATTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (37 bp):
TGGAAAATATCGTTTGGTTGAAAGCCAGAAAATATAG
Found at i:33289159 original size:26 final size:26
Alignment explanation
Indices: 33289125--33289188 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
33289115 TGAATGAATT
*
33289125 TTGTCAAAATTTTAGCAGGGGCAAAA
1 TTGTAAAAATTTTAGCAGGGGCAAAA
* * *
33289151 TTGTAAAAATTTTATCGGGGGTAAAA
1 TTGTAAAAATTTTAGCAGGGGCAAAA
*
33289177 TTGTTAAAATTT
1 TTGTAAAAATTT
33289189 ACGGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (26 bp):
TTGTAAAAATTTTAGCAGGGGCAAAA
Found at i:33293424 original size:18 final size:18
Alignment explanation
Indices: 33293398--33293432 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33293388 TTATGCACGC
*
33293398 TCACATATCATTTTCATT
1 TCACATATCACTTTCATT
*
33293416 TCACTTATCACTTTCAT
1 TCACATATCACTTTCAT
33293433 ATAATTCACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACATATCACTTTCATT
Found at i:33296094 original size:18 final size:18
Alignment explanation
Indices: 33296071--33296106 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
33296061 TAATTAAAAT
33296071 AGTTACATATAGGAACAA
1 AGTTACATATAGGAACAA
*
33296089 AGTTACATATAGTAACAA
1 AGTTACATATAGGAACAA
33296107 CTTAATCGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25
Consensus pattern (18 bp):
AGTTACATATAGGAACAA
Found at i:33297647 original size:21 final size:21
Alignment explanation
Indices: 33297621--33297667 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
33297611 ATGTTCGTAC
33297621 ACCATATACCATATACCATAT
1 ACCATATACCATATACCATAT
* * *
33297642 ACCATATACCTTATACCTTGT
1 ACCATATACCATATACCATAT
33297663 ACCAT
1 ACCAT
33297668 GCCGCCATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (21 bp):
ACCATATACCATATACCATAT
Found at i:33297660 original size:7 final size:7
Alignment explanation
Indices: 33297621--33297658 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
33297611 ATGTTCGTAC
33297621 ACCATAT
1 ACCATAT
33297628 ACCATAT
1 ACCATAT
33297635 ACCATAT
1 ACCATAT
33297642 ACCATAT
1 ACCATAT
*
33297649 ACCTTAT
1 ACCATAT
33297656 ACC
1 ACC
33297659 TTGTACCATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (7 bp):
ACCATAT
Found at i:33298600 original size:16 final size:18
Alignment explanation
Indices: 33298567--33298601 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
33298557 ATTCTTGTCA
33298567 AAAATATATAATAATTAT
1 AAAATATATAATAATTAT
33298585 AAAATA-ATAA-AATTAT
1 AAAATATATAATAATTAT
33298601 A
1 A
33298602 CTTAAATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATATATAATAATTAT
Found at i:33307117 original size:17 final size:19
Alignment explanation
Indices: 33307083--33307120 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
33307073 TCAAAAGTAT
*
33307083 AAAAATTTAGAAATTATAA
1 AAAAATATAGAAATTATAA
33307102 AAAAATATA-AAATATATAA
1 AAAAATATAGAAAT-TATAA
33307121 TAAATTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (19 bp):
AAAAATATAGAAATTATAA
Found at i:33308705 original size:10 final size:10
Alignment explanation
Indices: 33308656--33308703 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
33308646 TAAACTCCCA
33308656 AAAGATAAAT
1 AAAGATAAAT
** *
33308666 AAATTTAATT
1 AAAGATAAAT
*
33308676 CAAGATAAAT
1 AAAGATAAAT
33308686 AAAGATAAAT
1 AAAGATAAAT
33308696 AAA-ATAAA
1 AAAGATAAA
33308704 ATCCTAAATT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
9 5 0.17
10 25 0.83
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:33308747 original size:15 final size:14
Alignment explanation
Indices: 33308726--33308761 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
33308716 ATAATCCTTA
*
33308726 ATAATTATCTTAAT
1 ATAATTATCCTAAT
33308740 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
33308755 ATAATTA
1 ATAATTA
33308762 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:33309362 original size:16 final size:18
Alignment explanation
Indices: 33309325--33309372 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 18
33309315 ATATTTTTTC
*
33309325 TTTTCTATTTATTT-TTA
1 TTTTATATTTATTTATTA
33309342 TTTTA-ATTTATTTATTA
1 TTTTATATTTATTTATTA
33309359 -TTTATATTT-TTTAT
1 TTTTATATTTATTTAT
33309373 GCTTTAGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 17 0.61
17 11 0.39
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTATATTTATTTATTA
Found at i:33310120 original size:3 final size:3
Alignment explanation
Indices: 33310112--33310142 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
33310102 ATAATCACAG
33310112 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA C
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA C
33310143 CAAAATCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:33310522 original size:22 final size:21
Alignment explanation
Indices: 33310497--33310556 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
33310487 GCTGAGGCGT
* *
33310497 GGTGCTTGGGTGCAGGGATAAG
1 GGTGCTTGGCTGCAGGAAT-AG
*
33310519 GGTGGTTGGCTGCAGGAATAG
1 GGTGCTTGGCTGCAGGAATAG
*
33310540 GGTAGTTTGGCTGCAGG
1 GGT-GCTTGGCTGCAGG
33310557 CATTCTGGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.15
22 28 0.85
ACGTcount: A:0.17, C:0.10, G:0.48, T:0.25
Consensus pattern (21 bp):
GGTGCTTGGCTGCAGGAATAG
Found at i:33314238 original size:15 final size:14
Alignment explanation
Indices: 33314217--33314252 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
33314207 ATAATCCTTA
*
33314217 ATAATTATCTTAAT
1 ATAATTATCCTAAT
33314231 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
33314246 ATAATTA
1 ATAATTA
33314253 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:33316524 original size:9 final size:9
Alignment explanation
Indices: 33316506--33316590 Score: 107
Period size: 9 Copynumber: 9.4 Consensus size: 9
33316496 GTAGTGATTC
33316506 AATTCGGTT
1 AATTCGGTT
*
33316515 AATTCAGTT
1 AATTCGGTT
33316524 AATTCGGTT
1 AATTCGGTT
*
33316533 AATTCGGGT
1 AATTCGGTT
*
33316542 AATCCGGTT
1 AATTCGGTT
*
33316551 AATTTGGTT
1 AATTCGGTT
*
33316560 AATTCGGGT
1 AATTCGGTT
**
33316569 AATTTAGTT
1 AATTCGGTT
33316578 AATTCGGTT
1 AATTCGGTT
33316587 AATT
1 AATT
33316591 TTTAACCAAA
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 62 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (9 bp):
AATTCGGTT
Found at i:33316538 original size:27 final size:27
Alignment explanation
Indices: 33316506--33316590 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
33316496 GTAGTGATTC
*
33316506 AATTCGGTTAATTCAGTTAATTCGGTT
1 AATTCGGGTAATTCAGTTAATTCGGTT
* * *
33316533 AATTCGGGTAATCCGGTTAATTTGGTT
1 AATTCGGGTAATTCAGTTAATTCGGTT
*
33316560 AATTCGGGTAATTTAGTTAATTCGGTT
1 AATTCGGGTAATTCAGTTAATTCGGTT
33316587 AATT
1 AATT
33316591 TTTAACCAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (27 bp):
AATTCGGGTAATTCAGTTAATTCGGTT
Found at i:33321298 original size:13 final size:13
Alignment explanation
Indices: 33321280--33321312 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
33321270 AATATTGTAT
*
33321280 ATAATTTTTATTA
1 ATAATTTTTAATA
33321293 ATAATTTTTAATA
1 ATAATTTTTAATA
33321306 ATAATTT
1 ATAATTT
33321313 ATATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATAATTTTTAATA
Found at i:33321335 original size:26 final size:25
Alignment explanation
Indices: 33321278--33321335 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
33321268 GTAATATTGT
* * * *
33321278 ATATAATTTTTATTAATAATTTTTA
1 ATATAATTTATATTAAAAAATTTGA
33321303 ATAATAATTTATATATAAAAAATTTGA
1 AT-ATAATTTATAT-TAAAAAATTTGA
33321330 ATATAA
1 ATATAA
33321336 AAATTATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 2 0.07
26 14 0.52
27 11 0.41
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
ATATAATTTATATTAAAAAATTTGA
Found at i:33324854 original size:15 final size:15
Alignment explanation
Indices: 33324834--33324865 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
33324824 ATTGCACAAC
33324834 TTAATAGTAAAGCAT
1 TTAATAGTAAAGCAT
33324849 TTAATAGTAAAGCAT
1 TTAATAGTAAAGCAT
33324864 TT
1 TT
33324866 CAGTCTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (15 bp):
TTAATAGTAAAGCAT
Found at i:33325402 original size:16 final size:16
Alignment explanation
Indices: 33325381--33325413 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
33325371 CAAAACAATG
33325381 AATATTTGAGATGATA
1 AATATTTGAGATGATA
*
33325397 AATATTTTAGATGATA
1 AATATTTGAGATGATA
33325413 A
1 A
33325414 GCTAGACCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.39
Consensus pattern (16 bp):
AATATTTGAGATGATA
Found at i:33326129 original size:20 final size:20
Alignment explanation
Indices: 33326104--33326164 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
33326094 GCAGCAGATG
33326104 GGGAAATAAGAAGGAAAAAA
1 GGGAAATAAGAAGGAAAAAA
* *
33326124 GGGAAATAA-TATG----AA
1 GGGAAATAAGAAGGAAAAAA
33326139 GGGAAATAAGAAGGAAAAAA
1 GGGAAATAAGAAGGAAAAAA
33326159 GGGAAA
1 GGGAAA
33326165 CGCAGAGATG
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 11 0.34
16 2 0.06
19 2 0.06
20 17 0.53
ACGTcount: A:0.61, C:0.00, G:0.31, T:0.08
Consensus pattern (20 bp):
GGGAAATAAGAAGGAAAAAA
Found at i:33339193 original size:63 final size:63
Alignment explanation
Indices: 33339037--33339195 Score: 164
Period size: 63 Copynumber: 2.5 Consensus size: 63
33339027 TTGTCTGTCT
* * *
33339037 GTGTGGTCT-TAAATCCCAAACAGTGAGTCACACGACCTGAACACACGCCCGTGTCTTTGGCCC
1 GTGTAGTCTATAAATCAC-AACAGTGAGTCACACGACCTGAACACACGCCCGTGTCCTTGGCCC
* * * * *
33339100 GTGTAGTCTCTAAATCACAATATTGGGTCACACGGCCTAGATA-A-ACGCCCGTGTCCTTGGCCC
1 GTGTAGTCTATAAATCACAACAGTGAGTCACACGACCT-GA-ACACACGCCCGTGTCCTTGGCCC
* *
33339163 TTGT-GATTTATAAATCACAACAGTGAGTCACAC
1 GTGTAG-TCTATAAATCACAACAGTGAGTCACAC
33339196 AGCTTAGACA
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
62 1 0.01
63 67 0.85
64 10 0.13
65 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (63 bp):
GTGTAGTCTATAAATCACAACAGTGAGTCACACGACCTGAACACACGCCCGTGTCCTTGGCCC
Found at i:33342542 original size:19 final size:20
Alignment explanation
Indices: 33342520--33342557 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
33342510 GATTTATTTT
33342520 TATTAA-TAA-ATAAAGTAAA
1 TATTAAGTAATAT-AAGTAAA
33342539 TATTAAGTAATATAAGTAA
1 TATTAAGTAATATAAGTAA
33342558 TAAACAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 9 0.53
21 2 0.12
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (20 bp):
TATTAAGTAATATAAGTAAA
Found at i:33342559 original size:19 final size:19
Alignment explanation
Indices: 33342520--33342557 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
33342510 GATTTATTTT
33342520 TATTAATAAATAAAGTAAA
1 TATTAATAAATAAAGTAAA
33342539 TATTAAGT-AATATAAGTAA
1 TATTAA-TAAATA-AAGTAA
33342558 TAAACAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (19 bp):
TATTAATAAATAAAGTAAA
Found at i:33343798 original size:20 final size:20
Alignment explanation
Indices: 33343771--33343893 Score: 103
Period size: 20 Copynumber: 6.2 Consensus size: 20
33343761 TGTACGGGAC
33343771 TACACTTCGGTGCCTCTGTT
1 TACACTTCGGTGCCTCTGTT
*
33343791 TGCACTTCGGTGCCTCTG-T
1 TACACTTCGGTGCCTCTGTT
* *
33343810 TACACTTCGGTG-TTCCTATT
1 TACACTTCGGTGCCT-CTGTT
* *
33343830 CACACTTCGATGCCTCTGATT
1 TACACTTCGGTGCCTCTG-TT
* * * *
33343851 GCACAATT--GTGTCTCTGTC
1 -TACACTTCGGTGCCTCTGTT
33343870 TACACTTCGGTGCCTCTG-T
1 TACACTTCGGTGCCTCTGTT
33343889 TACAC
1 TACAC
33343894 ATCTACGATG
Statistics
Matches: 80, Mismatches: 16, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
18 6 0.08
19 20 0.25
20 45 0.56
21 3 0.04
22 6 0.08
ACGTcount: A:0.14, C:0.30, G:0.19, T:0.37
Consensus pattern (20 bp):
TACACTTCGGTGCCTCTGTT
Found at i:33353270 original size:19 final size:18
Alignment explanation
Indices: 33353246--33353281 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
33353236 CTTCAAATGT
*
33353246 TCACATGGTCTGAGCCATG
1 TCACATGGACTG-GCCATG
33353265 TCACATGGACTGGCCAT
1 TCACATGGACTGGCCAT
33353282 ATGGTCGCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (18 bp):
TCACATGGACTGGCCATG
Found at i:33356015 original size:26 final size:27
Alignment explanation
Indices: 33355960--33356030 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 27
33355950 AATTTTCTTG
* **
33355960 AAATTTTATCGAGGGT-AAAATAGTTT
1 AAATTTTATCAAGGGTAAAAATAGTCA
33355986 AAATTTTATCAAGGGTAAAAAT-GTCA
1 AAATTTTATCAAGGGTAAAAATAGTCA
* *
33356012 AAATTTTATTAGGGGTAAA
1 AAATTTTATCAAGGGTAAA
33356031 TTTGGGGTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 34 0.87
27 5 0.13
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.35
Consensus pattern (27 bp):
AAATTTTATCAAGGGTAAAAATAGTCA
Found at i:33360367 original size:95 final size:93
Alignment explanation
Indices: 33360258--33360457 Score: 228
Period size: 95 Copynumber: 2.1 Consensus size: 93
33360248 AACATAACCT
* *
33360258 CATGTTT-ATCGTCTT-ATCGGACTACCCCGTGTTTATTGTCCCGGTGGACTCTC-TATGTTGCC
1 CATGTTTAAT-GTCTTGAT-GGACTACCCCGTGTTTATTATCCCAGTGGACTC-CATATGTTGCC
* *
33360320 ATAGTCAAGCTATGGTCTTACACAAT-ATAACTC
63 ATAGCCAAGCTATCGTCTTACAC-ATCAT-AC-C
* * * *
33360353 CATGTTTAATGTCTTGGTGGATTACCCCGTGTTTATTATCCTAGTGGACTCCATATGTTGTCATA
1 CATGTTTAATGTCTTGATGGACTACCCCGTGTTTATTATCCCAGTGGACTCCATATGTTGCCATA
* *
33360418 GCCGAGCTATCGTCTTACACGTCATACC
66 GCCAAGCTATCGTCTTACACATCATACC
33360446 CATGTTTAATGT
1 CATGTTTAATGT
33360458 ACTAGCGAAC
Statistics
Matches: 91, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
93 13 0.14
94 4 0.04
95 71 0.78
96 3 0.03
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.37
Consensus pattern (93 bp):
CATGTTTAATGTCTTGATGGACTACCCCGTGTTTATTATCCCAGTGGACTCCATATGTTGCCATA
GCCAAGCTATCGTCTTACACATCATACC
Found at i:33362830 original size:16 final size:16
Alignment explanation
Indices: 33362809--33362856 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
33362799 TGGATTGTTT
33362809 TTAAGTATATTATATG
1 TTAAGTATATTATATG
33362825 TTAAGTTATATT-TAT-
1 TTAAG-TATATTATATG
33362840 TTAA-TA-A-TATATG
1 TTAAGTATATTATATG
33362853 TTAA
1 TTAA
33362857 AATAATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
11 1 0.03
12 4 0.14
13 6 0.21
15 4 0.14
16 8 0.28
17 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (16 bp):
TTAAGTATATTATATG
Found at i:33367915 original size:17 final size:16
Alignment explanation
Indices: 33367895--33367932 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
33367885 ATTTAATCAA
33367895 TTAATTAAATTAATTTC
1 TTAATTAAA-TAATTTC
*
33367912 TTAATTAAATAATTTT
1 TTAATTAAATAATTTC
33367928 TTAAT
1 TTAAT
33367933 CTAATTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAATTAAATAATTTC
Found at i:33369971 original size:23 final size:22
Alignment explanation
Indices: 33369915--33369972 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
33369905 ATTCTCATTT
*
33369915 AGTTAAAAAATATATTTTTTGAA
1 AGTT-AAAAATATATTATTTGAA
* *
33369938 ATTGTACAAATATATTATTTGATA
1 AGT-TAAAAATATATTATTTGA-A
33369962 AGTTAAAAATA
1 AGTTAAAAATA
33369973 AACAAGTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
23 24 0.86
24 4 0.14
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (22 bp):
AGTTAAAAATATATTATTTGAA
Found at i:33373849 original size:17 final size:17
Alignment explanation
Indices: 33373827--33373865 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
33373817 ACTGCAGGGG
33373827 TCACACGGCCATGTGAC
1 TCACACGGCCATGTGAC
33373844 TCACACGGCCATGTGAC
1 TCACACGGCCATGTGAC
33373861 TCACA
1 TCACA
33373866 TGGCTGAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.26, C:0.36, G:0.21, T:0.18
Consensus pattern (17 bp):
TCACACGGCCATGTGAC
Found at i:33376841 original size:13 final size:14
Alignment explanation
Indices: 33376823--33376851 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
33376813 GTAGGATACT
33376823 AACTAAAAT-ATGA
1 AACTAAAATCATGA
33376836 AACTAAAATCATGA
1 AACTAAAATCATGA
33376850 AA
1 AA
33376852 GGTAGGGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.21
Consensus pattern (14 bp):
AACTAAAATCATGA
Found at i:33377369 original size:28 final size:28
Alignment explanation
Indices: 33377310--33377428 Score: 170
Period size: 28 Copynumber: 4.3 Consensus size: 28
33377300 GTAAACACGC
**
33377310 CATGAAAGAAAAA-CCTTCT-TGACGAAT
1 CATGAAAGAAAAAGCCTT-TGTGGTGAAT
* *
33377337 TATGAAAGAAAAAGCATTTGTGGTGAAT
1 CATGAAAGAAAAAGCCTTTGTGGTGAAT
33377365 CATGAAAGAAAAAGCCTTTGTGGTGAAT
1 CATGAAAGAAAAAGCCTTTGTGGTGAAT
33377393 CATGAAAGAAAAAGCCTTTGTGGTGAAT
1 CATGAAAGAAAAAGCCTTTGTGGTGAAT
*
33377421 CATCAAAG
1 CATGAAAG
33377429 GATCGCTTTA
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
27 13 0.16
28 70 0.84
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (28 bp):
CATGAAAGAAAAAGCCTTTGTGGTGAAT
Found at i:33387851 original size:26 final size:26
Alignment explanation
Indices: 33387815--33387986 Score: 166
Period size: 26 Copynumber: 6.5 Consensus size: 26
33387805 TTAAGTTTTC
33387815 GCCACAAAGCCTTTCTTTCATATTAT
1 GCCACAAAGCCTTTCTTTCATATTAT
33387841 GCCACAAAGCCTTTCTTTCATATTAT
1 GCCACAAAGCCTTTCTTTCATATTAT
**
33387867 GCCACAAAGATTTTCTTTCATATTAT
1 GCCACAAAGCCTTTCTTTCATATTAT
* * * *
33387893 GCTATAAAGGCC-TCCTTTCATATTAC
1 GCCACAAA-GCCTTTCTTTCATATTAT
* * * * *
33387919 ACCAGAAAGACTTTTTTTTTCATATTAC
1 GCCACAAAG-C-CTTTCTTTCATATTAT
* * *
33387947 GTCATAAAGGCTTTCTTTCATATTAT
1 GCCACAAAGCCTTTCTTTCATATTAT
* *
33387973 GCCATAAAGGCTTT
1 GCCACAAAGCCTTT
33387987 TTTTTCCTAA
Statistics
Matches: 120, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
25 1 0.01
26 100 0.83
27 1 0.01
28 18 0.15
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (26 bp):
GCCACAAAGCCTTTCTTTCATATTAT
Found at i:33387955 original size:54 final size:54
Alignment explanation
Indices: 33387855--33387991 Score: 163
Period size: 54 Copynumber: 2.6 Consensus size: 54
33387845 CAAAGCCTTT
* *
33387855 CTTTCATATTATGCCACAAAGA--TTTTCTTTCATATTATGCTATAAAGGCCTC
1 CTTTCATATTATGCCACAAAGACTTTTTTTTTCATATTACGCTATAAAGGCCTC
** * * *
33387907 CTTTCATATTACACCAGAAAGACTTTTTTTTTCATATTACG-TCATAAAGGCTTT
1 CTTTCATATTATGCCACAAAGACTTTTTTTTTCATATTACGCT-ATAAAGGCCTC
* *
33387961 CTTTCATATTATGCCATAAAGGCTTTTTTTT
1 CTTTCATATTATGCCACAAAGACTTTTTTTT
33387992 CCTAACGTGT
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
52 19 0.27
53 1 0.01
54 51 0.72
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (54 bp):
CTTTCATATTATGCCACAAAGACTTTTTTTTTCATATTACGCTATAAAGGCCTC
Found at i:33390751 original size:33 final size:35
Alignment explanation
Indices: 33390713--33390782 Score: 85
Period size: 33 Copynumber: 2.1 Consensus size: 35
33390703 ATATTTCTAT
33390713 AATTTTTGA-AAATTTA-ATACTTTGTATTATA-AA
1 AATTTTT-ATAAATTTATATACTTTGTATTATATAA
* *
33390746 AA-TTTTATATATTTATATATTTTGTATTATATAA
1 AATTTTTATAAATTTATATACTTTGTATTATATAA
33390780 AAT
1 AAT
33390783 ATATCATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
31 1 0.03
32 10 0.32
33 16 0.52
34 4 0.13
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (35 bp):
AATTTTTATAAATTTATATACTTTGTATTATATAA
Found at i:33393297 original size:17 final size:16
Alignment explanation
Indices: 33393264--33393306 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
33393254 GAAAATTGTC
33393264 ATTTTTGGGAAACTTTT
1 ATTTTT-GGAAACTTTT
* *
33393281 CTTCTTTGGAAAGTTTT
1 ATT-TTTGGAAACTTTT
33393298 ATTTTTGGA
1 ATTTTTGGA
33393307 CTTTTTAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 6 0.27
17 13 0.59
18 3 0.14
ACGTcount: A:0.21, C:0.07, G:0.19, T:0.53
Consensus pattern (16 bp):
ATTTTTGGAAACTTTT
Found at i:33395366 original size:15 final size:15
Alignment explanation
Indices: 33395346--33395375 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
33395336 CTTCAGCAAT
33395346 ATAATGTGAAGTCAC
1 ATAATGTGAAGTCAC
33395361 ATAATGTGAAGTCAC
1 ATAATGTGAAGTCAC
33395376 GCATTTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (15 bp):
ATAATGTGAAGTCAC
Found at i:33395677 original size:13 final size:14
Alignment explanation
Indices: 33395659--33395687 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
33395649 TATGCTTAAT
33395659 TACATAATTT-TTG
1 TACATAATTTATTG
33395672 TACATAATTTATTG
1 TACATAATTTATTG
33395686 TA
1 TA
33395688 ACACCCCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (14 bp):
TACATAATTTATTG
Found at i:33427657 original size:5 final size:5
Alignment explanation
Indices: 33427647--33427673 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
33427637 GATTGTGATG
33427647 ATTAA ATTAA ATTAA ATTAA ATTAA AT
1 ATTAA ATTAA ATTAA ATTAA ATTAA AT
33427674 GCAAATAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTAA
Found at i:33429276 original size:15 final size:14
Alignment explanation
Indices: 33429241--33429273 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
33429231 TAATTAAGTA
33429241 AAATTCACTCATAT
1 AAATTCACTCATAT
33429255 AAATTCACTCATAT
1 AAATTCACTCATAT
33429269 AAATT
1 AAATT
33429274 TCACATACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATTCACTCATAT
Found at i:33436942 original size:25 final size:25
Alignment explanation
Indices: 33436874--33437049 Score: 111
Period size: 25 Copynumber: 7.4 Consensus size: 25
33436864 CAAAGATACA
* * *
33436874 CCACAAAGGCATCATATGGGATACG
1 CCACAAAGGCATTATATGGAATATG
* **
33436899 CCATAAAGGC--TA-ACAGAATATG
1 CCACAAAGGCATTATATGGAATATG
* *
33436921 CCACAAAAGCATTATATGGAATACG
1 CCACAAAGGCATTATATGGAATATG
* * *
33436946 CCATAAAGGC--TA-ACGAAATATG
1 CCACAAAGGCATTATATGGAATATG
*
33436968 CCACAAAGGCATCT-TATAGAATATG
1 CCACAAAGGCAT-TATATGGAATATG
* *
33436993 CCATAAAGGC--TA-ATAGAATATG
1 CCACAAAGGCATTATATGGAATATG
* * **
33437015 CCAAAAAGGCATCATATGGAATACA
1 CCACAAAGGCATTATATGGAATATG
33437040 CCACAAAGGC
1 CCACAAAGGC
33437050 TAACAGAATA
Statistics
Matches: 113, Mismatches: 27, Indels: 22
0.70 0.17 0.14
Matches are distributed among these distances:
22 50 0.44
23 3 0.03
24 3 0.03
25 57 0.50
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (25 bp):
CCACAAAGGCATTATATGGAATATG
Found at i:33436945 original size:47 final size:47
Alignment explanation
Indices: 33436874--33437059 Score: 250
Period size: 47 Copynumber: 4.0 Consensus size: 47
33436864 CAAAGATACA
* *
33436874 CCACAAAGGCATCATATGGGATACGCCATAAAGGCTAACAGAATATG
1 CCACAAAAGCATCATATGGAATACGCCATAAAGGCTAACAGAATATG
*
33436921 CCACAAAAGCATTATATGGAATACGCCATAAAGGCTAAC-GAAATATG
1 CCACAAAAGCATCATATGGAATACGCCATAAAGGCTAACAG-AATATG
* * * * *
33436968 CCACAAAGGCATCTTATAGAATATGCCATAAAGGCTAATAGAATATG
1 CCACAAAAGCATCATATGGAATACGCCATAAAGGCTAACAGAATATG
* *
33437015 CCA-AAAAGGCATCATATGGAATACACCACAAAGGCTAACAGAATA
1 CCACAAAA-GCATCATATGGAATACGCCATAAAGGCTAACAGAATA
33437060 CACAACAAAG
Statistics
Matches: 120, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
46 4 0.03
47 115 0.96
48 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (47 bp):
CCACAAAAGCATCATATGGAATACGCCATAAAGGCTAACAGAATATG
Found at i:33436970 original size:22 final size:21
Alignment explanation
Indices: 33436898--33437024 Score: 67
Period size: 22 Copynumber: 5.5 Consensus size: 21
33436888 TATGGGATAC
*
33436898 GCCATAAAGGCTAACAGAATAT
1 GCCATAAAGGCTAAGA-AATAT
* * * *
33436920 GCCACAAAAGCATTATATGGAATAC
1 GCCATAAAGGC--TA-A-GAAATAT
33436945 GCCATAAAGGCTAACGAAATAT
1 GCCATAAAGGCTAA-GAAATAT
*
33436967 GCCACAAAGGCATCTTATAG-AATAT
1 GCCATAAAGG---C-TA-AGAAATAT
*
33436992 GCCATAAAGGCTAATAGAATAT
1 GCCATAAAGGCTAAGA-AATAT
*
33437014 GCCAAAAAGGC
1 GCCATAAAGGC
33437025 ATCATATGGA
Statistics
Matches: 80, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
20 1 0.01
21 2 0.03
22 40 0.50
23 2 0.03
24 2 0.03
25 29 0.36
26 3 0.04
27 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (21 bp):
GCCATAAAGGCTAAGAAATAT
Found at i:33437061 original size:22 final size:23
Alignment explanation
Indices: 33437033--33437080 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
33437023 GCATCATATG
*
33437033 GAATACACCACAAAGGCT-AACA
1 GAATACACAACAAAGGCTAAACA
*
33437055 GAATACACAACAAAGGTTAAACA
1 GAATACACAACAAAGGCTAAACA
33437078 GAA
1 GAA
33437081 AACCATCCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.54, C:0.21, G:0.15, T:0.10
Consensus pattern (23 bp):
GAATACACAACAAAGGCTAAACA
Found at i:33437068 original size:94 final size:94
Alignment explanation
Indices: 33436843--33437070 Score: 280
Period size: 94 Copynumber: 2.4 Consensus size: 94
33436833 AGATTTGTCA
* * * * *
33436843 GAATACACCACAAGGGTTAGACAAAGATACACCACAAAGGCATCATATGGGATACGCCATAAAGG
1 GAATACACCACAAAGGCTA-ACAGA-ATACACCACAAAGGCATCATATAGAATACGCCATAAAGG
*
33436908 CTAACAGAATATGCCACAAAAGCATTATATG
64 CTAACAGAATATGCCACAAAAGCATCATATG
* * ** * *
33436939 GAATACGCCATAAAGGCTAAC-GAAATATGCCACAAAGGCATCTTATAGAATATGCCATAAAGGC
1 GAATACACCACAAAGGCTAACAG-AATACACCACAAAGGCATCATATAGAATACGCCATAAAGGC
*
33437003 TAATAGAATATGCCA-AAAAGGCATCATATG
65 TAACAGAATATGCCACAAAA-GCATCATATG
*
33437033 GAATACACCACAAAGGCTAACAGAATACACAACAAAGG
1 GAATACACCACAAAGGCTAACAGAATACACCACAAAGG
33437071 TTAAACAGAA
Statistics
Matches: 111, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
93 4 0.04
94 88 0.79
95 4 0.04
96 15 0.14
ACGTcount: A:0.45, C:0.20, G:0.18, T:0.17
Consensus pattern (94 bp):
GAATACACCACAAAGGCTAACAGAATACACCACAAAGGCATCATATAGAATACGCCATAAAGGCT
AACAGAATATGCCACAAAAGCATCATATG
Found at i:33442057 original size:29 final size:29
Alignment explanation
Indices: 33442000--33442061 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
33441990 GGATGGGAGG
*
33442000 GAAGTAAAAGTTTTGGGAAAAAGTGAAAA
1 GAAGTAAAAGTTTAGGGAAAAAGTGAAAA
33442029 GAAGTAAAAGTATTAGGGAAAAAGT-AAAA
1 GAAGTAAAAGT-TTAGGGAAAAAGTGAAAA
33442058 -AAGT
1 GAAGT
33442062 TTAGGGATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 4 0.13
29 15 0.48
30 12 0.39
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.19
Consensus pattern (29 bp):
GAAGTAAAAGTTTAGGGAAAAAGTGAAAA
Found at i:33443849 original size:27 final size:26
Alignment explanation
Indices: 33443805--33443859 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
33443795 ATCAAAACTT
* *
33443805 TATTTATTATATATTTTTTAATAAATA
1 TATTTATTACATAATTTTT-ATAAATA
*
33443832 TATTTATTACATAATTTTTATATATA
1 TATTTATTACATAATTTTTATAAATA
33443858 TA
1 TA
33443860 ATAATATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (26 bp):
TATTTATTACATAATTTTTATAAATA
Found at i:33444193 original size:22 final size:22
Alignment explanation
Indices: 33444131--33444202 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
33444121 TTTATTCAAA
* **
33444131 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
33444153 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
33444175 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
33444197 CATGAG
1 CATGAG
33444203 GGATCAAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:33444843 original size:13 final size:14
Alignment explanation
Indices: 33444814--33444851 Score: 60
Period size: 13 Copynumber: 2.7 Consensus size: 14
33444804 TATTCGAAGC
33444814 AAACATAAAAACAAA
1 AAACA-AAAAACAAA
33444829 AAACAAAAAAC-AA
1 AAACAAAAAACAAA
33444842 AAACAAAAAA
1 AAACAAAAAA
33444852 AGAAAAGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 12 0.52
14 6 0.26
15 5 0.22
ACGTcount: A:0.84, C:0.13, G:0.00, T:0.03
Consensus pattern (14 bp):
AAACAAAAAACAAA
Found at i:33444852 original size:14 final size:14
Alignment explanation
Indices: 33444814--33444857 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
33444804 TATTCGAAGC
*
33444814 AAACATAAAAACAA
1 AAACAAAAAAACAA
33444828 AAA-ACAAAAAACAA
1 AAACA-AAAAAACAA
*
33444842 AAACAAAAAAAGAA
1 AAACAAAAAAACAA
33444856 AA
1 AA
33444858 GGTTTTTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 1 0.04
14 24 0.92
15 1 0.04
ACGTcount: A:0.84, C:0.11, G:0.02, T:0.02
Consensus pattern (14 bp):
AAACAAAAAAACAA
Found at i:33444857 original size:7 final size:7
Alignment explanation
Indices: 33444814--33444851 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
33444804 TATTCGAAGC
33444814 AAACATAA
1 AAACA-AA
33444822 AAACAAA
1 AAACAAA
33444829 AAACAAA
1 AAACAAA
33444836 AAAC-AA
1 AAACAAA
33444842 AAACAAA
1 AAACAAA
33444849 AAA
1 AAA
33444852 AGAAAAGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.21
7 18 0.62
8 5 0.17
ACGTcount: A:0.84, C:0.13, G:0.00, T:0.03
Consensus pattern (7 bp):
AAACAAA
Found at i:33446604 original size:17 final size:17
Alignment explanation
Indices: 33446582--33446620 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
33446572 TTGTAGACCG
* *
33446582 AAAATTATCGTTTTAGT
1 AAAATTAACCTTTTAGT
*
33446599 AAAATTAACCTTTTATT
1 AAAATTAACCTTTTAGT
33446616 AAAAT
1 AAAAT
33446621 GATTAAATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (17 bp):
AAAATTAACCTTTTAGT
Found at i:33457438 original size:94 final size:94
Alignment explanation
Indices: 33457277--33457647 Score: 381
Period size: 94 Copynumber: 3.9 Consensus size: 94
33457267 ATGAAACCAT
* * * * * *
33457277 AAATCCTATACCCCTAAAGTTGCAGTGGGTCGGATTAAAGCTACAATAGCGAATATTATCTCCCT
1 AAATCTTATACCCATGAAGTTGTAGTGGGTCGGATTGAAGCTACAATAGCGAATCTTATCTCCCT
* * *
33457342 GAAGCTGCAGTGGAGCAAGATAAAGCTAC
66 GAAGTTGTAGTGGAGCAAGATGAAGCTAC
* * *
33457371 AAATCTTATACCACAT-AAGTTGTAGTAGGTCAGATTGAAGTTACAATAGCGAATCTTATCTCCC
1 AAATCTTATACC-CATGAAGTTGTAGTGGGTCGGATTGAAGCTACAATAGCGAATCTTATCTCCC
*
33457435 TGAAGTTATAGTGGAGCAAGATGAAGCTAC
65 TGAAGTTGTAGTGGAGCAAGATGAAGCTAC
* * * *
33457465 AAATTTCTATACCCCTGAA-TTGTAGTGGGTCGGATTGAAACTACGATAGCGAATCTTATCTCCC
1 AAATCT-TATACCCATGAAGTTGTAGTGGGTCGGATTGAAGCTACAATAGCGAATCTTATCTCCC
* * *
33457529 TGAAGTTGTAGCGGAACAAGATGAGGCTAC
65 TGAAGTTGTAGTGGAGCAAGATGAAGCTAC
* * * * * * * * * *
33457559 AAATCCTATATCCC-TAAAATTGCAATGGAAT-GGATTGAAACTACAATGGCAAATCTTATCTTC
1 AAATCTTATA-CCCATGAAGTTGTAGTGG-GTCGGATTGAAGCTACAATAGCGAATCTTATCTCC
* * *
33457622 TTGAAGTTGCAATGGAGCAAGATGAA
64 CTGAAGTTGTAGTGGAGCAAGATGAA
33457648 ACTGTAACAC
Statistics
Matches: 232, Mismatches: 39, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
93 7 0.03
94 214 0.92
95 11 0.05
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (94 bp):
AAATCTTATACCCATGAAGTTGTAGTGGGTCGGATTGAAGCTACAATAGCGAATCTTATCTCCCT
GAAGTTGTAGTGGAGCAAGATGAAGCTAC
Found at i:33457617 original size:188 final size:189
Alignment explanation
Indices: 33457282--33457647 Score: 429
Period size: 188 Copynumber: 1.9 Consensus size: 189
33457272 ACCATAAATC
33457282 CTATACCCCTAAAGTTGCAGTGGGTCGGATTAAAGCTACAATAGCGAATATTATCTCCCTGAAGC
1 CTATACCCCTAAAGTTGCAGTGGGTCGGATTAAAGCTACAATAGCGAATATTATCTCCCTGAAGC
* * * * * * **
33457347 TGCAGTGGAGCAAGATAAAGCTACAAATCTTATACCACATAAGTTGTAGTAGGTCAGATTGAAGT
66 TGCAGCGGAACAAGATAAAGCTACAAATCCTATACCACATAAATTGCAATAGGTCAGATTGAAAC
* * *
33457412 TACAATAGCGAATCTTATCTCCCTGAAGTTATAGTGGAGCAAGATGAAGCTACAAATTT
131 TACAATAGCAAATCTTATCTCCCTGAAGTTACAATGGAGCAAGATGAAGCTACAAATTT
* * * *
33457471 CTATACCCCTGAA-TTGTAGTGGGTCGGATTGAAA-CTACGATAGCGAATCTTATCTCCCTGAAG
1 CTATACCCCTAAAGTTGCAGTGGGTCGGATT-AAAGCTACAATAGCGAATATTATCTCCCTGAAG
* * * * *
33457534 TTGTAGCGGAACAAGATGAGGCTACAAATCCTATATCC-C-TAAAATTGCAAT-GGAAT-GGATT
65 CTGCAGCGGAACAAGATAAAGCTACAAATCCTATA-CCACAT-AAATTGCAATAGG--TCAGATT
* * * *
33457595 GAAACTACAATGGCAAATCTTATCTTCTTGAAGTTGCAATGGAGCAAGATGAA
126 GAAACTACAATAGCAAATCTTATCTCCCTGAAGTTACAATGGAGCAAGATGAA
33457648 ACTGTAACAC
Statistics
Matches: 148, Mismatches: 24, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
187 3 0.02
188 127 0.86
189 18 0.12
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (189 bp):
CTATACCCCTAAAGTTGCAGTGGGTCGGATTAAAGCTACAATAGCGAATATTATCTCCCTGAAGC
TGCAGCGGAACAAGATAAAGCTACAAATCCTATACCACATAAATTGCAATAGGTCAGATTGAAAC
TACAATAGCAAATCTTATCTCCCTGAAGTTACAATGGAGCAAGATGAAGCTACAAATTT
Found at i:33464179 original size:274 final size:275
Alignment explanation
Indices: 33463676--33464182 Score: 724
Period size: 274 Copynumber: 1.8 Consensus size: 275
33463666 ATGTTGCATC
* * *
33463676 TAGAGCTTGTATTTTGGTAGTGCTGCAAACAAATTGGTGACATTTTAGTAGGGACAGTTCAGGGT
1 TAGAGCATGAATTTTGGTAGTGCTGCAAACAAATCGGTGACATTTTAGTAGGGACA-TTCAGGGT
**
33463741 ACAAAGTTGTATGACCTTTCGATTTAGCTGCTGGATCATCTTTTTAATCTGCCTTTAAGAATTTT
65 ACAAAGTTGTATGACCTTTCGATTTAGCTGCTGGATCATCTTTTTAATCCACCTTTAAGAATTTT
* * *
33463806 GAGCATGGGTTTGCAGGAATTAGTTTGTGCATTAAAGAGATGAGATGGCTAATATTTAGTATTTA
130 GAGCACGGGTTTGCAGGAAGTAGTTTGTACATTAAAGAGATGAGATGGCTAATATTTAGTATTTA
* * * * *
33463871 GCGTCAAATGGTACTATCAAAGGTTATTATTGATGAAAACATTCACTTCCAGACATCTGAGATAA
195 GCATCAAAGGGTACAAACAAAGGTTATCATTGATGAAAACATTCACTTCCAGACATCTGAGATAA
33463936 CATATCATGTAGTATT
260 CATATCATGTAGTATT
*
33463952 TAGAGCATGAATTTTGGTAGTGCTGCAAACAAATCGGTGAC-TTTTATTAGGGAC-TTCA-GGTA
1 TAGAGCATGAATTTTGGTAGTGCTGCAAACAAATCGGTGACATTTTAGTAGGGACATTCAGGGTA
33464014 CAAAAGTTGTATGACCTTT-GATTTAGCTGCT-GACTCATC-TTTTAATTCCACCTTTAAGAA-T
66 C-AAAGTTGTATGACCTTTCGATTTAGCTGCTGGA-TCATCTTTTTAA-TCCACCTTTAAGAATT
* * * *
33464075 TT-AGCACGGCTAGTTTTGCAGGCAGTATTTTGTACCTTAAAGAGATGAGATGGCTAATATTTTG
128 TTGAGCACGG---G-TTTGCAGGAAGTAGTTTGTACATTAAAGAGATGAGATGGCTAATATTTAG
33464139 TATTTAGCATCAAAGGGTACAAACAAAGGTTATCATTGATGAAA
189 TATTTAGCATCAAAGGGTACAAACAAAGGTTATCATTGATGAAA
33464183 CCTTACATCT
Statistics
Matches: 206, Mismatches: 18, Indels: 16
0.86 0.08 0.07
Matches are distributed among these distances:
270 6 0.03
271 11 0.05
272 34 0.17
273 22 0.11
274 83 0.40
275 12 0.06
276 38 0.18
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.35
Consensus pattern (275 bp):
TAGAGCATGAATTTTGGTAGTGCTGCAAACAAATCGGTGACATTTTAGTAGGGACATTCAGGGTA
CAAAGTTGTATGACCTTTCGATTTAGCTGCTGGATCATCTTTTTAATCCACCTTTAAGAATTTTG
AGCACGGGTTTGCAGGAAGTAGTTTGTACATTAAAGAGATGAGATGGCTAATATTTAGTATTTAG
CATCAAAGGGTACAAACAAAGGTTATCATTGATGAAAACATTCACTTCCAGACATCTGAGATAAC
ATATCATGTAGTATT
Found at i:33472166 original size:71 final size:71
Alignment explanation
Indices: 33472086--33472218 Score: 162
Period size: 71 Copynumber: 1.9 Consensus size: 71
33472076 TTATGAGTTG
* * * *
33472086 CAAGTAATTCTTTC-ATGTACTACGAGCTACTTAATTTTTTAGAAGCC-TTTCATATTTTAAGTT
1 CAAGTAATTCCTTCTAT-TACTACAAACTACTTAATTTCTTAGAA-CCTTTTCATATTTTAAGTT
33472149 TTGTATTT
64 TTGTATTT
* * * *
33472157 CAAGTAATTCCTTCTATTGCTACAAATTAGTTAATTTCTTAGAACCTTTTCATGTTTTAAGT
1 CAAGTAATTCCTTCTATTACTACAAACTACTTAATTTCTTAGAACCTTTTCATATTTTAAGT
33472219 AATTCTTTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
70 2 0.04
71 48 0.92
72 2 0.04
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.47
Consensus pattern (71 bp):
CAAGTAATTCCTTCTATTACTACAAACTACTTAATTTCTTAGAACCTTTTCATATTTTAAGTTTT
GTATTT
Found at i:33472509 original size:57 final size:55
Alignment explanation
Indices: 33472440--33472567 Score: 159
Period size: 56 Copynumber: 2.3 Consensus size: 55
33472430 TTCAAGTTTT
* *
33472440 AAGTAATTCTTTCATGTATTACT-AATTACTTACTTTCTTAACACTCTTTCATATTTG
1 AAGTAA-TCTTTCATGTATTA-TGAATTA-TTAATTTCTTAAAACTCTTTCATATTTG
* * *
33472497 AAGTAACTCTTTCATGTATTATGGATTATTAATTTCTTAAAACTCTTTCATGTTTT
1 AAGTAA-TCTTTCATGTATTATGAATTATTAATTTCTTAAAACTCTTTCATATTTG
33472553 AAGTAATACTTTCAT
1 AAGTAAT-CTTTCAT
33472568 ATTTTACGAA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
55 1 0.02
56 38 0.60
57 24 0.38
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (55 bp):
AAGTAATCTTTCATGTATTATGAATTATTAATTTCTTAAAACTCTTTCATATTTG
Found at i:33472557 original size:56 final size:56
Alignment explanation
Indices: 33472428--33472611 Score: 194
Period size: 57 Copynumber: 3.2 Consensus size: 56
33472418 TTAAGTAACA
* * *
33472428 CTTTCAAGTTTTAAGTAATTCTTTCATGTATTACT-AATTACTTACTTTCTTAACACT
1 CTTTCATGTTTTAAGTAA-TCTTTCATGTATTA-TGAATTACTTAATTTCTTAAAACT
* * *
33472485 CTTTCATATTTGAAGTAACTCTTTCATGTATTATGGATTA-TTAATTTCTTAAAACT
1 CTTTCATGTTTTAAGTAA-TCTTTCATGTATTATGAATTACTTAATTTCTTAAAACT
* * * * * *
33472541 CTTTCATGTTTTAAGTAATACTTTCATATTTTACGAATAACTTAATTTATTAGAA-T
1 CTTTCATGTTTTAAGTAAT-CTTTCATGTATTATGAATTACTTAATTTCTTAAAACT
33472597 CATTTCATGTTTTAA
1 C-TTTCATGTTTTAA
33472612 TTGTCTTTTT
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
55 1 0.01
56 48 0.45
57 58 0.54
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.49
Consensus pattern (56 bp):
CTTTCATGTTTTAAGTAATCTTTCATGTATTATGAATTACTTAATTTCTTAAAACT
Found at i:33478341 original size:19 final size:20
Alignment explanation
Indices: 33478319--33478361 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
33478309 TGAGGGAGGA
33478319 ACAC-GACCGTGTGTAGGTG
1 ACACAGACCGTGTGTAGGTG
*
33478338 ACACATGCCCGTGTGTAGGTG
1 ACACA-GACCGTGTGTAGGTG
33478359 ACA
1 ACA
33478362 TAAGTCCGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
21 17 0.81
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.21
Consensus pattern (20 bp):
ACACAGACCGTGTGTAGGTG
Found at i:33478370 original size:21 final size:21
Alignment explanation
Indices: 33478325--33478374 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
33478315 AGGAACACGA
*
33478325 CCGTGTGTAGGTGACACATGC
1 CCGTGTGTAGGTGACACAAGC
* *
33478346 CCGTGTGTAGGTGACATAAGT
1 CCGTGTGTAGGTGACACAAGC
33478367 CCGTGTGT
1 CCGTGTGT
33478375 CCAGGGAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.18, C:0.20, G:0.34, T:0.28
Consensus pattern (21 bp):
CCGTGTGTAGGTGACACAAGC
Found at i:33479217 original size:5 final size:5
Alignment explanation
Indices: 33479207--33479240 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
33479197 ATTACCAAGA
33479207 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
33479241 ATGAACTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:33481876 original size:16 final size:17
Alignment explanation
Indices: 33481836--33481876 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
33481826 CATGATTCGA
33481836 TTATTAAACTAATTTAT
1 TTATTAAACTAATTTAT
*
33481853 TTGTTAAA-TAA-TTAT
1 TTATTAAACTAATTTAT
33481868 TTATATAAA
1 TTAT-TAAA
33481877 ATTGAGTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 7 0.33
16 7 0.33
17 7 0.33
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TTATTAAACTAATTTAT
Found at i:33500134 original size:18 final size:19
Alignment explanation
Indices: 33500113--33500149 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
33500103 TTCAATTCTA
33500113 ATTTGACCC-AAAATATTT
1 ATTTGACCCAAAAATATTT
*
33500131 ATTTTACCCAAAAATATTT
1 ATTTGACCCAAAAATATTT
33500150 TAAAACTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.41
Consensus pattern (19 bp):
ATTTGACCCAAAAATATTT
Found at i:33504836 original size:21 final size:21
Alignment explanation
Indices: 33504810--33504856 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
33504800 GTTAATTATT
*
33504810 CCCTGAATTGCACATACGTGC
1 CCCTGAATTACACATACGTGC
33504831 CCCTGAATTACACATACGTGC
1 CCCTGAATTACACATACGTGC
33504852 CCCTG
1 CCCTG
33504857 TTTATACTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.23
Consensus pattern (21 bp):
CCCTGAATTACACATACGTGC
Found at i:33515849 original size:21 final size:20
Alignment explanation
Indices: 33515816--33515858 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
33515806 GTTCTAATTC
33515816 TAAAAATTATAAAATATATT
1 TAAAAATTATAAAATATATT
* *
33515836 TAAAAATATTTAAAATATTTT
1 TAAAAAT-TATAAAATATATT
33515857 TA
1 TA
33515859 TATTTACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAAAATTATAAAATATATT
Found at i:33515858 original size:11 final size:11
Alignment explanation
Indices: 33515825--33515858 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
33515815 CTAAAAATTA
33515825 TAAAATATATT
1 TAAAATATATT
33515836 TAAAA-ATATT
1 TAAAATATATT
*
33515846 TAAAATATTTT
1 TAAAATATATT
33515857 TA
1 TA
33515859 TATTTACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TAAAATATATT
Found at i:33516320 original size:8 final size:9
Alignment explanation
Indices: 33516269--33516327 Score: 57
Period size: 9 Copynumber: 6.4 Consensus size: 9
33516259 TTTAAAAATA
33516269 AATTTTTAT
1 AATTTTTAT
*
33516278 AATTTATATT
1 AATTTTTA-T
* * *
33516288 TACTTTTAA
1 AATTTTTAT
33516297 AATTTTTA-
1 AATTTTTAT
33516305 AGATTTTTAT
1 A-ATTTTTAT
33516315 AATTTTTAT
1 AATTTTTAT
33516324 AATT
1 AATT
33516328 AGGACTAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
8 1 0.03
9 32 0.80
10 7 0.17
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (9 bp):
AATTTTTAT
Found at i:33519302 original size:15 final size:16
Alignment explanation
Indices: 33519278--33519316 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
33519268 ATATTCTTCA
*
33519278 TTTCCCTTACTTTCCC
1 TTTCCTTTACTTTCCC
33519294 -TTCCTTTACTTTCCC
1 TTTCCTTTACTTTCCC
33519309 TTTCCTTT
1 TTTCCTTT
33519317 CCCTCTCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTCCTTTACTTTCCC
Found at i:33519659 original size:15 final size:16
Alignment explanation
Indices: 33519622--33519664 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
33519612 AGTAATATCC
33519622 TATCCAAATCTGAAAT
1 TATCCAAATCTGAAAT
* * *
33519638 TACCCAATTCT-AGAT
1 TATCCAAATCTGAAAT
33519653 TATCCAAATCTG
1 TATCCAAATCTG
33519665 GAAAAAAAAC
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (16 bp):
TATCCAAATCTGAAAT
Found at i:33533406 original size:15 final size:14
Alignment explanation
Indices: 33533366--33533405 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
33533356 TTGAGACCAC
*
33533366 AAATTTGATGTTGAA
1 AAATTT-ATTTTGAA
33533381 AAATTTATTTTGAA
1 AAATTTATTTTGAA
33533395 AAATTTATTTT
1 AAATTTATTTT
33533406 TATTATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (14 bp):
AAATTTATTTTGAA
Found at i:33550507 original size:27 final size:27
Alignment explanation
Indices: 33550477--33550564 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 27
33550467 TATAACCATG
*
33550477 AAGGCTTCCT-TTATGGAGATTGCCACA
1 AAGGCTTCCTATT-TAGAGATTGCCACA
*
33550504 AAGGCTTTCCTATTTAGAGTTTGCCACA
1 AAGGC-TTCCTATTTAGAGATTGCCACA
*
33550532 AAGGCTGT-C-ATTTCAAAGATTTGCCACA
1 AAGGCT-TCCTATTT-AGAGA-TTGCCACA
33550560 AAGGC
1 AAGGC
33550565 CTTTTTTAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
26 4 0.08
27 10 0.19
28 36 0.69
29 2 0.04
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (27 bp):
AAGGCTTCCTATTTAGAGATTGCCACA
Found at i:33550527 original size:28 final size:28
Alignment explanation
Indices: 33550496--33550564 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
33550486 TTTATGGAGA
* *
33550496 TTGCCACAAAGGCTTTCCTATTT-AGAG-T
1 TTGCCACAAAGGCTGT-C-ATTTCAAAGAT
33550524 TTGCCACAAAGGCTGTCATTTCAAAGAT
1 TTGCCACAAAGGCTGTCATTTCAAAGAT
33550552 TTGCCACAAAGGC
1 TTGCCACAAAGGC
33550565 CTTTTTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 4 0.11
27 4 0.11
28 29 0.78
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (28 bp):
TTGCCACAAAGGCTGTCATTTCAAAGAT
Found at i:33550687 original size:57 final size:57
Alignment explanation
Indices: 33550526--33550698 Score: 192
Period size: 57 Copynumber: 3.1 Consensus size: 57
33550516 TTTAGAGTTT
* * * *
33550526 GCCACAAAGGCTGTCA-TTT-CAAAGATTTGCCACAAAGGCCT-T-TTTTAATAGGTTC
1 GCCACAAAGGCT-TAACTTTCCAAAGTTTTTCCACAAAGG-CTATCATTTAATAGGTTC
* * * * * *
33550581 GCCTCAAAGGCTTAACTTTCCAGAGTTTTTCCACAAAGGTTGTCGTTTAATAGATTC
1 GCCACAAAGGCTTAACTTTCCAAAGTTTTTCCACAAAGGCTATCATTTAATAGGTTC
* *
33550638 GCCACAAAGGCTTAACTTTCCAAAGTTTTTCCATAAAGGCTATCATTTAACAGGTTC
1 GCCACAAAGGCTTAACTTTCCAAAGTTTTTCCACAAAGGCTATCATTTAATAGGTTC
33550695 GCCA
1 GCCA
33550699 TAGTGACTTT
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
54 2 0.02
55 15 0.15
56 17 0.17
57 64 0.65
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (57 bp):
GCCACAAAGGCTTAACTTTCCAAAGTTTTTCCACAAAGGCTATCATTTAATAGGTTC
Found at i:33550986 original size:53 final size:53
Alignment explanation
Indices: 33550829--33550987 Score: 185
Period size: 53 Copynumber: 3.0 Consensus size: 53
33550819 TTAATTTTCC
* * * *
33550829 CCATATGATGCCATAACCCACCAGTTATAATCTTACACGATATGGTCTTATTT
1 CCATATGATGACATAAACCACCAGTTATGATCTTACACGATATGGTCTTCTTT
* * * *
33550882 CCATATGATGACATAAACCACTAGTTATGGTCTTACACGATTTGGTTTTCTTT
1 CCATATGATGACATAAACCACCAGTTATGATCTTACACGATATGGTCTTCTTT
* * * * *
33550935 CCATATGGT-ATCATAATCCACCAGTTACGATCTTACATGATATGATCTTCTTT
1 CCATATGATGA-CATAAACCACCAGTTATGATCTTACACGATATGGTCTTCTTT
33550988 AGTGCTATGG
Statistics
Matches: 88, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
52 1 0.01
53 87 0.99
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (53 bp):
CCATATGATGACATAAACCACCAGTTATGATCTTACACGATATGGTCTTCTTT
Found at i:33551925 original size:22 final size:22
Alignment explanation
Indices: 33551900--33551942 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
33551890 TTTTGATGTA
33551900 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
33551922 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
33551943 GAACAATAAA
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:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:33552902 original size:2 final size:2
Alignment explanation
Indices: 33552895--33552929 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
33552885 TTCAAATTCG
33552895 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33552930 TGTTTGGGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33554075 original size:4 final size:4
Alignment explanation
Indices: 33554066--33554092 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
33554056 TAGCTTGATG
33554066 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
33554093 TAATTTGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:33555995 original size:11 final size:11
Alignment explanation
Indices: 33555979--33556020 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
33555969 TGGGTGAAAT
33555979 TATTTTAATAA
1 TATTTTAATAA
*
33555990 TATTTTATTAAGA
1 TATTTTAAT-A-A
33556003 TATTTTAATAA
1 TATTTTAATAA
33556014 TATTTTA
1 TATTTTA
33556021 TTTATTTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 16 0.59
12 2 0.07
13 9 0.33
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
TATTTTAATAA
Done.