Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 132 of 206
Found at i:40041539 original size:87 final size:87
Alignment explanation
Indices: 40041424--40041604 Score: 227
Period size: 87 Copynumber: 2.1 Consensus size: 87
40041414 AACCATCACT
* * * * * * *
40041424 TTTCATTAATCGATAGTCGTCACCATCCCTTTTCATAGTTGATGGTCGTTACCATCCCTTTTCGC
1 TTTCA-TAATCGATAGTCATCACCATCCCTTTTCACAATTGATGGTCATCACCATCCATTTTCAC
40041489 AATAGATAGCCGAAGCTATCCCG
65 AATAGATAGCCGAAGCTATCCCG
* * * *
40041512 TTTCATATTCGATGGTCATCACCATCCCTTTTCACAATTGATGGTCATCACCCTCCATTTTCATA
1 TTTCATAATCGATAGTCATCACCATCCCTTTTCACAATTGATGGTCATCACCATCCATTTTCACA
* * *
40041577 ATCGATAGCCGAAGCTATCTCT
66 ATAGATAGCCGAAGCTATCCCG
40041599 TTTCAT
1 TTTCAT
40041605 TGGTCGATGA
Statistics
Matches: 79, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
87 74 0.94
88 5 0.06
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (87 bp):
TTTCATAATCGATAGTCATCACCATCCCTTTTCACAATTGATGGTCATCACCATCCATTTTCACA
ATAGATAGCCGAAGCTATCCCG
Found at i:40041574 original size:58 final size:58
Alignment explanation
Indices: 40041393--40041582 Score: 163
Period size: 58 Copynumber: 3.3 Consensus size: 58
40041383 TGTTATGTCT
* * * *
40041393 CTTTTCATATTCGATGGTCGA-AACCATCACTTTTCATTAATCGATAGTCGTCACCATCC
1 CTTTTCATATTCGATGGTC-ATAACCATCCCTTTTCA-CAATAGATAGTCATCACCATCC
* * * * *
40041452 CTTTTCATAGTT-GATGGTCGTTACCATCCCTTTTCGCAATAGATAGCCGA--AGCTATCC
1 CTTTTCATA-TTCGATGGTCATAACCATCCCTTTTCACAATAGATAGTC-ATCA-CCATCC
* * * * *
40041510 CGTTTCATATTCGATGGTCATCACCATCCCTTTTCACAATTGATGGTCATCACCCTCC
1 CTTTTCATATTCGATGGTCATAACCATCCCTTTTCACAATAGATAGTCATCACCATCC
* *
40041568 ATTTTCATAATCGAT
1 CTTTTCATATTCGAT
40041583 AGCCGAAGCT
Statistics
Matches: 103, Mismatches: 21, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
57 4 0.04
58 68 0.66
59 29 0.28
60 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (58 bp):
CTTTTCATATTCGATGGTCATAACCATCCCTTTTCACAATAGATAGTCATCACCATCC
Found at i:40045729 original size:23 final size:23
Alignment explanation
Indices: 40045698--40045819 Score: 163
Period size: 23 Copynumber: 5.3 Consensus size: 23
40045688 ATAAGTGCCA
* *
40045698 CACTAATATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
40045721 CACTGATATGTAGCTGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
40045744 CACTAAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
40045767 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
40045790 CACTGAAATGTAACCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
40045813 CACTGAT
1 CACTGAT
40045820 CAATAACATT
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 84 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:40045765 original size:46 final size:46
Alignment explanation
Indices: 40045698--40045819 Score: 199
Period size: 46 Copynumber: 2.7 Consensus size: 46
40045688 ATAAGTGCCA
* * *
40045698 CACTAATATGTAGTCGAAGCTACCACTGATATGTAGCTGTAGCTAC
1 CACTAAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
40045744 CACTAAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
1 CACTAAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
* *
40045790 CACTGAAATGTAACCGAAGCTACCACTGAT
1 CACTAAAATGTAGCCGAAGCTACCACTGAT
40045820 CAATAACATT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (46 bp):
CACTAAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
Found at i:40050209 original size:12 final size:12
Alignment explanation
Indices: 40050192--40050216 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40050182 AACCTCACAC
40050192 GCCCGTGTGCTA
1 GCCCGTGTGCTA
40050204 GCCCGTGTGCTA
1 GCCCGTGTGCTA
40050216 G
1 G
40050217 GACATGTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.32, G:0.36, T:0.24
Consensus pattern (12 bp):
GCCCGTGTGCTA
Found at i:40056205 original size:36 final size:36
Alignment explanation
Indices: 40056151--40056221 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
40056141 ATTAAACTCT
* * *
40056151 ATTCAGTTAAGCAGCCTTTTGGCTCTATTTTGACTG
1 ATTCAGTTAAGCAACCTTTTGGATCTATTCTGACTG
*
40056187 ATTCAGTTCAA-CAACCTTTTGTATCTATTCTGACT
1 ATTCAGTT-AAGCAACCTTTTGGATCTATTCTGACT
40056222 AATGCGCTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 28 0.93
37 2 0.07
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (36 bp):
ATTCAGTTAAGCAACCTTTTGGATCTATTCTGACTG
Found at i:40063819 original size:26 final size:24
Alignment explanation
Indices: 40063786--40063834 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
40063776 TGCATGTGAG
* *
40063786 CAAAATGAGTTTGTTTTGAATATGA
1 CAAAATGAATATGTTTTG-ATATGA
40063811 CAAATATGAATATGTTTTGATATG
1 CAAA-ATGAATATGTTTTGATATG
40063835 TTCGATTGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.41
Consensus pattern (24 bp):
CAAAATGAATATGTTTTGATATGA
Found at i:40066568 original size:12 final size:13
Alignment explanation
Indices: 40066544--40066572 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
40066534 GGGCTATAAC
40066544 TATTGCATTTATT
1 TATTGCATTTATT
40066557 TATTGC-TTTATT
1 TATTGCATTTATT
40066569 TATT
1 TATT
40066573 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:40071613 original size:34 final size:34
Alignment explanation
Indices: 40071570--40071639 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
40071560 ATTTTCATAC
*
40071570 AGTCAAACGTACACCGTAACTGGTTATTCTATAA
1 AGTCAAACGTACACCATAACTGGTTATTCTATAA
* *
40071604 AGTCAAACGTACACCATAATTGGTTGTTCTATAA
1 AGTCAAACGTACACCATAACTGGTTATTCTATAA
40071638 AG
1 AG
40071640 GCTAATGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (34 bp):
AGTCAAACGTACACCATAACTGGTTATTCTATAA
Found at i:40072757 original size:42 final size:42
Alignment explanation
Indices: 40072661--40072757 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 42
40072651 CGTTCCAACA
* **
40072661 ACACGGGCATGTGAGGCCATTTCGAAAGTTTCACGGCCTGGT
1 ACACGGGCATGTGAGGCCATTTCGAAAGTTACACGGCCTGAC
* ** * * * *
40072703 AGATTGGTATGTGAGGGCATTTTGAAAGTTACACGGCTTGAC
1 ACACGGGCATGTGAGGCCATTTCGAAAGTTACACGGCCTGAC
40072745 ACACGGGCATGTG
1 ACACGGGCATGTG
40072758 GCTTGGCCAT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.26
Consensus pattern (42 bp):
ACACGGGCATGTGAGGCCATTTCGAAAGTTACACGGCCTGAC
Found at i:40074900 original size:13 final size:14
Alignment explanation
Indices: 40074882--40074910 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40074872 TTTCTACTTG
40074882 TTTAA-TTTTCTTT
1 TTTAATTTTTCTTT
40074895 TTTAATTTTTCTTT
1 TTTAATTTTTCTTT
40074909 TT
1 TT
40074911 GCACTTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTAATTTTTCTTT
Found at i:40082350 original size:41 final size:41
Alignment explanation
Indices: 40082318--40082479 Score: 236
Period size: 41 Copynumber: 4.0 Consensus size: 41
40082308 CCCGTTAGAC
*
40082318 TTATAGCCTGATTCAGATCACCGACACGTAGCCTGCTAGGT
1 TTATAACCTGATTCAGATCACCGACACGTAGCCTGCTAGGT
*
40082359 TTATAACCTGATTTAGATCACC-AGCACGTAGCCTGCTAGGT
1 TTATAACCTGATTCAGATCACCGA-CACGTAGCCTGCTAGGT
* *
40082400 TTATAACCTGATTCAGATCACTGGCACGTAGCCTGCTAGGT
1 TTATAACCTGATTCAGATCACCGACACGTAGCCTGCTAGGT
* * **
40082441 TTATAACCTGATTTAGATCACCGGCAATTAGCCTGCTAG
1 TTATAACCTGATTCAGATCACCGACACGTAGCCTGCTAG
40082480 ACTTAAAGTC
Statistics
Matches: 110, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
40 1 0.01
41 109 0.99
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (41 bp):
TTATAACCTGATTCAGATCACCGACACGTAGCCTGCTAGGT
Found at i:40082442 original size:82 final size:82
Alignment explanation
Indices: 40082318--40082479 Score: 270
Period size: 82 Copynumber: 2.0 Consensus size: 82
40082308 CCCGTTAGAC
*
40082318 TTATAGCCTGATTCAGATCACCGACACGTAGCCTGCTAGGTTTATAACCTGATTTAGATCACCAG
1 TTATAACCTGATTCAGATCACCGACACGTAGCCTGCTAGGTTTATAACCTGATTTAGATCACCAG
*
40082383 CACGTAGCCTGCTAGGT
66 CAAGTAGCCTGCTAGGT
* * *
40082400 TTATAACCTGATTCAGATCACTGGCACGTAGCCTGCTAGGTTTATAACCTGATTTAGATCACCGG
1 TTATAACCTGATTCAGATCACCGACACGTAGCCTGCTAGGTTTATAACCTGATTTAGATCACCAG
*
40082465 CAATTAGCCTGCTAG
66 CAAGTAGCCTGCTAG
40082480 ACTTAAAGTC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (82 bp):
TTATAACCTGATTCAGATCACCGACACGTAGCCTGCTAGGTTTATAACCTGATTTAGATCACCAG
CAAGTAGCCTGCTAGGT
Found at i:40083267 original size:12 final size:12
Alignment explanation
Indices: 40083222--40083274 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
40083212 AATAACTTTT
**
40083222 ATATATATATGT
1 ATATATATATAC
*
40083234 ATATATATTCTAGC
1 ATATATA-TATA-C
40083248 ATTATATATATAC
1 A-TATATATATAC
40083261 ATATATATATAC
1 ATATATATATAC
40083273 AT
1 AT
40083275 GCTTATTCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 20 0.59
13 4 0.12
14 4 0.12
15 6 0.18
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (12 bp):
ATATATATATAC
Found at i:40086119 original size:22 final size:22
Alignment explanation
Indices: 40086087--40086163 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
40086077 TACAGAGGCA
*
40086087 ATGTTGCGACACACCAAGTCCT
1 ATGTTGTGACACACCAAGTCCT
*
40086109 ATGTTGTGACACACCAAGTCAT
1 ATGTTGTGACACACCAAGTCCT
40086131 ATGTTGTGACACACCAAGTCCT
1 ATGTTGTGACACACCAAGTCCT
40086153 ATGTTGTGACA
1 ATGTTGTGACA
40086164 TCCTCAGGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (22 bp):
ATGTTGTGACACACCAAGTCCT
Found at i:40094828 original size:22 final size:22
Alignment explanation
Indices: 40094803--40094844 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
40094793 ATTTATTTTT
40094803 ATTATATTATT-TATTTTAAACC
1 ATTATA-TATTATATTTTAAACC
*
40094825 ATTATATATTATCTTTTAAA
1 ATTATATATTATATTTTAAA
40094845 ATTCTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTATATATTATATTTTAAACC
Found at i:40094924 original size:26 final size:26
Alignment explanation
Indices: 40094894--40094960 Score: 84
Period size: 25 Copynumber: 2.6 Consensus size: 26
40094884 ATATGTTATA
40094894 TATTATTTATTTATTTTAAACTATTT
1 TATTATTTATTTATTTTAAACTATTT
* * *
40094920 TATTA-TTATTCATTTTAAGCTTTTT
1 TATTATTTATTTATTTTAAACTATTT
40094945 TATGTATTT-TTTATTT
1 TAT-TATTTATTTATTT
40094961 GAAGTCTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 20 0.57
26 13 0.37
27 2 0.06
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.67
Consensus pattern (26 bp):
TATTATTTATTTATTTTAAACTATTT
Found at i:40100567 original size:21 final size:21
Alignment explanation
Indices: 40100541--40100580 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
40100531 TGGATTCTAT
*
40100541 AGGTCATGTTCCCCAGAGACC
1 AGGTCATATTCCCCAGAGACC
40100562 AGGTCATATTCCCCAGAGA
1 AGGTCATATTCCCCAGAGA
40100581 ACAAATCAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.20
Consensus pattern (21 bp):
AGGTCATATTCCCCAGAGACC
Found at i:40101350 original size:143 final size:143
Alignment explanation
Indices: 40101122--40101680 Score: 764
Period size: 143 Copynumber: 3.9 Consensus size: 143
40101112 GTTATATCAG
* * * * *
40101122 GCGAATCTTATTTCCTTGACGTTGTAGTGGAACA-ATTAAAGCTACCAATTATGGCAGATCTTAT
1 GCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTAT
* * * * *
40101186 CCTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACTAGCCTTATCTCCTTAAAGTTGCAGCGAAG
66 CTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACAAGCCTTATCTCCCTGAAGTTGCAGCGGAG
40101251 CAGACTGAAGACA
131 CAGACTGAAGACA
* *
40101264 GCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACCAATTATGGTGGATCTTAT
1 GCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTAT
* * * *
40101329 CTTTCTAAAGTTGCAGTGGAGCAGATTGGAGCCACAAGCCTTATATCCCTGAAGTTGTAGCGGAG
66 CTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACAAGCCTTATCTCCCTGAAGTTGCAGCGGAG
40101394 CAGACTGAAGACA
131 CAGACTGAAGACA
* * * *
40101407 GCGAATATTATTTCCCTGGCGTTGCAATAGAACAGATTAAAGCTACAAATTGTGGCGGATCTTAT
1 GCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTAT
* * *
40101472 CTTCCTGAAA-TTGCAGTGGAGTAGATTAAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGCGGA
66 CTTCCT-AAAGTTGCAGTGGAGCAGATTGAAGCCACAAGCCTTATCTCCCTGAAGTTGCAGCGGA
*
40101536 GCAGACTGAACACA
130 GCAGACTGAAGACA
* * *
40101550 GCGAATCTTACTTCCCTAGCGTTGGAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTAT
1 GCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTAT
* * * * * * * *
40101615 CTTCCTGAAGTTGCAATAGAGCAAATTGAAGCCACCGATCC-TATCTCCCTGAAGTTGTAGTGGA
66 CTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCA-CAAGCCTTATCTCCCTGAAGTTGCAGCGGA
40101679 GC
130 GC
40101681 GGATTAAAAC
Statistics
Matches: 368, Mismatches: 45, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
142 33 0.09
143 328 0.89
144 7 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (143 bp):
GCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTAT
CTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACAAGCCTTATCTCCCTGAAGTTGCAGCGGAG
CAGACTGAAGACA
Found at i:40103281 original size:22 final size:22
Alignment explanation
Indices: 40103256--40103319 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
40103246 CGTTTATTTT
40103256 TATTATATTATT-TATTTTAAAC
1 TATTATA-TATTATATTTTAAAC
* *
40103278 TATTATATATTATCTTTTAAAA
1 TATTATATATTATATTTTAAAC
40103300 T-TCTCATATATTAT-TTTTAA
1 TAT-T-ATATATTATATTTTAA
40103320 TAAAGAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
21 5 0.14
22 23 0.62
23 9 0.24
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTATATATTATATTTTAAAC
Found at i:40103415 original size:26 final size:25
Alignment explanation
Indices: 40103349--40103425 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 25
40103339 ATATGTTATA
** *
40103349 TATTATTTATTTATTTTAAACTATTT
1 TATTA-TTATTTATTTTAAGTTTTTT
*
40103375 TATTATTATTCATTTTAAGTTTTTT
1 TATTATTATTTATTTTAAGTTTTTT
* * *
40103400 TATGTATTGTTTATTTGAAGTCTTTT
1 TAT-TATTATTTATTTTAAGTTTTTT
40103426 ATCATTTATT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 19 0.45
26 23 0.55
ACGTcount: A:0.25, C:0.04, G:0.06, T:0.65
Consensus pattern (25 bp):
TATTATTATTTATTTTAAGTTTTTT
Found at i:40104635 original size:19 final size:19
Alignment explanation
Indices: 40104593--40104637 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
40104583 TTTTACGGAA
* *
40104593 AATGTTTTATACATTTTCC
1 AATGTTTTATACATCTTAC
*
40104612 AATGTTTTATATATCTTAC
1 AATGTTTTATACATCTTAC
*
40104631 TATGTTT
1 AATGTTT
40104638 ACTTCAAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.11, G:0.07, T:0.56
Consensus pattern (19 bp):
AATGTTTTATACATCTTAC
Found at i:40104907 original size:16 final size:18
Alignment explanation
Indices: 40104886--40104918 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
40104876 ATATTTAGTC
40104886 ATATAA-TAA-ATAATTA
1 ATATAATTAATATAATTA
40104902 ATATAATTAATATAATT
1 ATATAATTAATATAATT
40104919 TCTTAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATAATTAATATAATTA
Found at i:40104909 original size:9 final size:9
Alignment explanation
Indices: 40104886--40104918 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
40104876 ATATTTAGTC
40104886 ATATAA-TA
1 ATATAATTA
40104894 A-ATAATTA
1 ATATAATTA
40104902 ATATAATTA
1 ATATAATTA
40104911 ATATAATT
1 ATATAATT
40104919 TCTTAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 4 0.17
8 4 0.17
9 15 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
ATATAATTA
Found at i:40104964 original size:13 final size:13
Alignment explanation
Indices: 40104948--40104974 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40104938 TTAATATTAA
40104948 AATTTAAAATAAT
1 AATTTAAAATAAT
40104961 AATTTAAAATAAT
1 AATTTAAAATAAT
40104974 A
1 A
40104975 TTCTTCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATTTAAAATAAT
Found at i:40114806 original size:101 final size:102
Alignment explanation
Indices: 40114690--40114874 Score: 275
Period size: 101 Copynumber: 1.8 Consensus size: 102
40114680 AAAGTGATGG
* ** *
40114690 TCACGTGTGTAGTACTATGTACAGGCTACGACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACATGTGTAGTACTATGTACAGGCTACGACACGTACCAGATAGTGAT-GGTCACATGTGTAGT
40114753 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
* * * *
40114791 TCACATGTGTAGTACTATGTGCAGGCTACTACACGTATCGGATAGTGATGGTCACATGTGTAGTA
1 TCACATGTGTAGTACTATGTACAGGCTACGACACGTACCAGATAGTGATGGTCACATGTGTAGTA
40114856 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
40114875 TGAACCGGTA
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
101 35 0.47
102 35 0.47
103 4 0.05
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (102 bp):
TCACATGTGTAGTACTATGTACAGGCTACGACACGTACCAGATAGTGATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:40114809 original size:51 final size:50
Alignment explanation
Indices: 40114690--40114874 Score: 196
Period size: 51 Copynumber: 3.7 Consensus size: 50
40114680 AAAGTGATGG
* * * * * * *
40114690 TCACGTGTGTAGTACTATGTACAGGCTACGACGTGTACCAGA-A-TGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-AT-GA
*
40114740 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCT-TCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAG-TAT-GA
** * *
40114791 TCACATGTGTAGTACTATGTGCAGGCTACTACACGTATCGGATAGTGATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-ATGA
40114842 TCACATGTGTAGTACTATGTGCAGGCTACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
40114875 TGAACCGGTA
Statistics
Matches: 114, Mismatches: 16, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
50 36 0.32
51 76 0.67
52 1 0.01
53 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTATGA
Found at i:40114882 original size:102 final size:101
Alignment explanation
Indices: 40114690--40114882 Score: 271
Period size: 102 Copynumber: 1.9 Consensus size: 101
40114680 AAAGTGATGG
* ** *
40114690 TCACGTGTGTAGTACTATGTACAGGCTACGACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
1 TCACATGTGTAGTACTATGTACAGGCTACGACACGTACCAGAATGATAGGTCACATGTGTAGTAC
*
40114755 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
66 TATGTGCAGGCTACTATGCGAACCGGATAGCTTCGA
* * * *
40114791 TCACATGTGTAGTACTATGTGCAGGCTACTACACGTATCGGATAGTGAT-GGTCACATGTGTAGT
1 TCACATGTGTAGTACTATGTACAGGCTACGACACGTACCAGA-A-TGATAGGTCACATGTGTAGT
*
40114855 ACTATGTGCAGGCTACTATGTGAACCGG
64 ACTATGTGCAGGCTACTATGCGAACCGG
40114883 TATCATTAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
101 35 0.44
102 41 0.51
103 4 0.05
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.28
Consensus pattern (101 bp):
TCACATGTGTAGTACTATGTACAGGCTACGACACGTACCAGAATGATAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGAACCGGATAGCTTCGA
Found at i:40121666 original size:20 final size:23
Alignment explanation
Indices: 40121627--40121667 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
40121617 AATGCAATAT
40121627 TAAAAGTGCTAACTAAAATGTCC
1 TAAAAGTGCTAACTAAAATGTCC
40121650 TAAAA-TGC-AAC-AAAATGT
1 TAAAAGTGCTAACTAAAATGT
40121668 ACTTAAGTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 3 0.17
23 5 0.28
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (23 bp):
TAAAAGTGCTAACTAAAATGTCC
Found at i:40123837 original size:82 final size:82
Alignment explanation
Indices: 40123744--40123904 Score: 304
Period size: 82 Copynumber: 2.0 Consensus size: 82
40123734 TTGTATTAAT
*
40123744 TTTTTGGATAAACTTTAATTTTTTAGGGGTATGAGCAACAATAGATTTTTATTTGTTTCTGTGCT
1 TTTTTGAATAAACTTTAATTTTTTAGGGGTATGAGCAACAATAGATTTTTATTTGTTTCTGTGCT
40123809 ATTTTAGAATTTTAGAA
66 ATTTTAGAATTTTAGAA
40123826 TTTTTGAATAAACTTTAATTTTTTAGGGGTATGAGCAACAATAGATTTTTATTTGTTTCTGTGCT
1 TTTTTGAATAAACTTTAATTTTTTAGGGGTATGAGCAACAATAGATTTTTATTTGTTTCTGTGCT
*
40123891 GTTTTAGAATTTTA
66 ATTTTAGAATTTTA
40123905 TATGTAGGAA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.50
Consensus pattern (82 bp):
TTTTTGAATAAACTTTAATTTTTTAGGGGTATGAGCAACAATAGATTTTTATTTGTTTCTGTGCT
ATTTTAGAATTTTAGAA
Found at i:40135220 original size:19 final size:19
Alignment explanation
Indices: 40135196--40135233 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
40135186 TCTTATAAAA
*
40135196 CTAATTAGAAATTTTTATT
1 CTAATTAGAAAATTTTATT
40135215 CTAATTAGAAAATTTTATT
1 CTAATTAGAAAATTTTATT
40135234 AATTACAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (19 bp):
CTAATTAGAAAATTTTATT
Found at i:40138502 original size:110 final size:110
Alignment explanation
Indices: 40138309--40138581 Score: 289
Period size: 110 Copynumber: 2.5 Consensus size: 110
40138299 TTATAATGCT
* ** * * *
40138309 AATCAGACTAGTAGTTCATGACATGAAGACATGTGTAAGACCATGTGGTAGAGACCTATGACATT
1 AATCAGACTAGTAGATCACAACATGAAGACATGTGTAAGACCACGTGGTAGAAACCCATGACATT
*
40138374 ATATGACAATGAGGATATTCATGGTGTAGCCTATGGTGAGATGTA
66 ATACGACAATGAGGATATTCATGGTGTAGCCTATGGTGAGATGTA
* * * *
40138419 AATCAGACTAGTAGATCACAACATTAAGATATGTGTAAGACCACGTGGTATAAACCCATGGCATT
1 AATCAGACTAGTAGATCACAACATGAAGACATGTGTAAGACCACGTGGTAGAAACCCATGACATT
* * * * ***
40138484 ATACGACAATGGGGATATTCATGTTGTATCGTCCAGTGAGATGTA
66 ATACGACAATGAGGATATTCATGGTGTAGCCTATGGTGAGATGTA
* * * * * * *
40138529 AA-CCGAACT-GCTGGATCACAATATGAAGATATGTATAAGACCATGTGGGAGAA
1 AATCAG-ACTAG-TAGATCACAACATGAAGACATGTGTAAGACCACGTGGTAGAA
40138582 GCCCCACGGT
Statistics
Matches: 135, Mismatches: 26, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
109 3 0.02
110 132 0.98
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (110 bp):
AATCAGACTAGTAGATCACAACATGAAGACATGTGTAAGACCACGTGGTAGAAACCCATGACATT
ATACGACAATGAGGATATTCATGGTGTAGCCTATGGTGAGATGTA
Found at i:40142713 original size:114 final size:114
Alignment explanation
Indices: 40142513--40142735 Score: 410
Period size: 114 Copynumber: 2.0 Consensus size: 114
40142503 ATGCTAAACC
* *
40142513 CTTATGCAAATTATTGGAGAAGGATACAACATTCAACTTTGATGAAGAATGTTTGAGAGATTTTA
1 CTTATGCAAATTATTGGAGAAGGATACAACATTCAAATTTGATGAAAAATGTTTGAGAGATTTTA
* *
40142578 ATGATTTGAAGAATCGATTAGTTTTAGCACCAATTATCGTCACATAGGA
66 AAGATTTGAAGAATCGATTAGTTTCAGCACCAATTATCGTCACATAGGA
40142627 CTTATGCAAATTATTGGAGAAGGATACAACATTCAAATTTGATGAAAAATGTTTGAGAGATTTTA
1 CTTATGCAAATTATTGGAGAAGGATACAACATTCAAATTTGATGAAAAATGTTTGAGAGATTTTA
40142692 AAGATTTGAAGAATCGATTAGTTTCAGCACCAATTATCGTCACA
66 AAGATTTGAAGAATCGATTAGTTTCAGCACCAATTATCGTCACA
40142736 CGGGATTGGT
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 105 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (114 bp):
CTTATGCAAATTATTGGAGAAGGATACAACATTCAAATTTGATGAAAAATGTTTGAGAGATTTTA
AAGATTTGAAGAATCGATTAGTTTCAGCACCAATTATCGTCACATAGGA
Found at i:40144928 original size:17 final size:17
Alignment explanation
Indices: 40144890--40144929 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
40144880 AAATAATGTA
40144890 TTATTATATATTATATT
1 TTATTATATATTATATT
*
40144907 ATATTATATATTA-ATTT
1 TTATTATATATTATA-TT
40144924 TTATTA
1 TTATTA
40144930 ACCTTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATTATATATTATATT
Found at i:40150712 original size:37 final size:37
Alignment explanation
Indices: 40150662--40150736 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
40150652 CATTAGCCTT
40150662 GCATAACTTCCAAGATTATTATGATTAAATTGTTTTA
1 GCATAACTTCCAAGATTATTATGATTAAATTGTTTTA
40150699 GCATAACTTCCAAGATTATTATGATTAAATTGTTTTA
1 GCATAACTTCCAAGATTATTATGATTAAATTGTTTTA
40150736 G
1 G
40150737 TATAGAGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.43
Consensus pattern (37 bp):
GCATAACTTCCAAGATTATTATGATTAAATTGTTTTA
Found at i:40166231 original size:17 final size:17
Alignment explanation
Indices: 40166206--40166241 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
40166196 TATCGGTTAG
*
40166206 AATAAAAAATATT-AAA
1 AATAAAAAAAATTCAAA
40166222 AATAAAAAAAATTCAAA
1 AATAAAAAAAATTCAAA
40166239 AAT
1 AAT
40166242 TTCGGTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (17 bp):
AATAAAAAAAATTCAAA
Found at i:40167590 original size:20 final size:20
Alignment explanation
Indices: 40167545--40167594 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
40167535 ATGCAATACT
40167545 AAAATTTTTAACAAATATCG
1 AAAATTTTTAACAAATATCG
* *
40167565 -ATATTTTTAACATGATAT-G
1 AAAATTTTTAACA-AATATCG
40167584 AAAATTTTTAA
1 AAAATTTTTAA
40167595 TTGATGCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (20 bp):
AAAATTTTTAACAAATATCG
Found at i:40167715 original size:20 final size:19
Alignment explanation
Indices: 40167656--40167720 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
40167646 AGATACACAG
*
40167656 AGAAATTTTGATA-CTCGATT
1 AGAAA-TTTGATATCACG-TT
***
40167676 AGAAATTTGATATTGTGTT
1 AGAAATTTGATATCACGTT
40167695 AGAAATATTGATATCACGTT
1 AGAAAT-TTGATATCACGTT
40167715 A-AAATT
1 AGAAATT
40167721 ATTAGCATCA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.51
20 17 0.46
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (19 bp):
AGAAATTTGATATCACGTT
Found at i:40168497 original size:17 final size:18
Alignment explanation
Indices: 40168475--40168508 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40168465 GGTGATAAGT
40168475 AAAAG-AATAAGAAAATA
1 AAAAGAAATAAGAAAATA
*
40168492 AAAAGAAATGAGAAAAT
1 AAAAGAAATAAGAAAAT
40168509 CTAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (18 bp):
AAAAGAAATAAGAAAATA
Found at i:40170789 original size:50 final size:50
Alignment explanation
Indices: 40170686--40170802 Score: 153
Period size: 50 Copynumber: 2.3 Consensus size: 50
40170676 AGGTATCATA
* * ** *
40170686 TAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCG
1 TAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAACTCCCACG
* * *
40170736 TAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCTATG
1 TAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAACTCCCACG
*
40170786 TAAGACCATATCTGGGA
1 TAAGACCATGTCTGGGA
40170803 TATGACATTG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAACTCCCACG
Found at i:40171116 original size:20 final size:20
Alignment explanation
Indices: 40171078--40171116 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40171068 TAAGCAAGCA
*
40171078 AGTAAGTAAACAAGTAAGTG
1 AGTAAGTAAACAAGAAAGTG
*
40171098 AGTAAGTAAAGAAGAAAGT
1 AGTAAGTAAACAAGAAAGT
40171117 AAAGATCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.26, T:0.18
Consensus pattern (20 bp):
AGTAAGTAAACAAGAAAGTG
Found at i:40174599 original size:5 final size:5
Alignment explanation
Indices: 40174589--40174627 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
40174579 GCCTAAGATG
* *
40174589 TGAAT TGAAT TGAAT TGAAT ATGAAT TGTAT TAAAT TGA
1 TGAAT TGAAT TGAAT TGAAT -TGAAT TGAAT TGAAT TGA
40174628 GTTAAGTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (5 bp):
TGAAT
Found at i:40175100 original size:25 final size:25
Alignment explanation
Indices: 40175065--40175175 Score: 99
Period size: 25 Copynumber: 4.5 Consensus size: 25
40175055 ACACATCACA
* *
40175065 GCTCTTAGGAGCGTCTCGATATATG
1 GCTCTTCGGAGCTTCTCGATATATG
40175090 GCTCTTCGGAGCTTAC-CG--ATATG
1 GCTCTTCGGAGCTT-CTCGATATATG
* *
40175113 GCTGGCTT--GAACTTCCCGATATATG
1 GCT--CTTCGGAGCTTCTCGATATATG
*
40175138 GCTATTCGGAGCTTCTCGAT-TAATG
1 GCTCTTCGGAGCTTCTCGATAT-ATG
40175163 GCTCTTCGGAGCT
1 GCTCTTCGGAGCT
40175176 ACCTGTCATT
Statistics
Matches: 70, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
22 1 0.01
23 17 0.24
24 1 0.01
25 50 0.71
26 1 0.01
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.32
Consensus pattern (25 bp):
GCTCTTCGGAGCTTCTCGATATATG
Found at i:40175210 original size:73 final size:73
Alignment explanation
Indices: 40175072--40175210 Score: 160
Period size: 73 Copynumber: 1.9 Consensus size: 73
40175062 ACAGCTCTTA
** *
40175072 GGAGCGTCTCGATATATGGCTCTTCGGAGCTTACCGATATGGCTGGCTTGAACTTCCCGATATAT
1 GGAGCGTCTCGATATATGGCTCTTCGGAGCTTACCGATATGGCTCACATGAACTTCCCGATATAT
40175137 GGCTATTC
66 GGCTATTC
* * *
40175145 GGAGCTTCTCGAT-TAATGGCTCTTCGGAGC-TACCTG-TCATTGGCTCACATGAGCTTCCTGA-
1 GGAGCGTCTCGATAT-ATGGCTCTTCGGAGCTTACC-GAT-A-TGGCTCACATGAACTTCCCGAT
40175206 ATATG
62 ATATG
40175211 ACTTATGAGC
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
72 6 0.11
73 34 0.61
74 16 0.29
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (73 bp):
GGAGCGTCTCGATATATGGCTCTTCGGAGCTTACCGATATGGCTCACATGAACTTCCCGATATAT
GGCTATTC
Found at i:40180992 original size:79 final size:79
Alignment explanation
Indices: 40180901--40181050 Score: 255
Period size: 79 Copynumber: 1.9 Consensus size: 79
40180891 CCGGAAAAAA
* ** *
40180901 TGGTTTTGGGGCCACAAATCCGATGAGTAAGTTCGTAAATATTATTATTTAATATTTATGAGTCA
1 TGGTTTCGGGGCCACAAATCCGACAAGTAAGTTCATAAATATTATTATTTAATATTTATGAGTCA
40180966 AATATGGGAAACAG
66 AATATGGGAAACAG
*
40180980 TGGTTTCGGGGCCACAAATTCGACAAGTAAGTTCATAAATATTATTATTTAATATTTATGAGTCA
1 TGGTTTCGGGGCCACAAATCCGACAAGTAAGTTCATAAATATTATTATTTAATATTTATGAGTCA
40181045 AATATG
66 AATATG
40181051 ATTTTAAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 66 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (79 bp):
TGGTTTCGGGGCCACAAATCCGACAAGTAAGTTCATAAATATTATTATTTAATATTTATGAGTCA
AATATGGGAAACAG
Found at i:40185876 original size:27 final size:27
Alignment explanation
Indices: 40185838--40185899 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
40185828 TAACCATATC
*
40185838 ACAAACATATCATCATGCATCCTCAAG
1 ACAACCATATCATCATGCATCCTCAAG
40185865 ACAACCATATCATCATGCATCCTCAAG
1 ACAACCATATCATCATGCATCCTCAAG
40185892 ACAACCAT
1 ACAACCAT
40185900 TTATAATTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.40, C:0.32, G:0.06, T:0.21
Consensus pattern (27 bp):
ACAACCATATCATCATGCATCCTCAAG
Found at i:40188193 original size:12 final size:12
Alignment explanation
Indices: 40188178--40188202 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40188168 CCCAATCAAA
40188178 TAATCAATTAAT
1 TAATCAATTAAT
40188190 TAATCAATTAAT
1 TAATCAATTAAT
40188202 T
1 T
40188203 CATACAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATCAATTAAT
Found at i:40189858 original size:78 final size:79
Alignment explanation
Indices: 40189729--40189903 Score: 235
Period size: 78 Copynumber: 2.2 Consensus size: 79
40189719 AGCACAAAAT
*
40189729 CCTGCTAGGCACTAAGCTTGAATAACACACTGACACGAAGCCTACTAGGCACTAAGCAT-TTAAC
1 CCTGCTAGGCACTAAGCTTGAATAACACACTGACACGAAGCCTACTAGGCACTAAGCATAATAAC
40189793 ACACAAGCATGAAG
66 ACACAAGCATGAAG
* * * * * *
40189807 CCTGCTAGGCACTATGCTTGAATAATACACTGGCAGGAAGCCTGCTAGGCACTAAGCCTGAATAA
1 CCTGCTAGGCACTAAGCTTGAATAACACACTGACACGAAGCCTACTAGGCACTAAGCAT-AATAA
**
40189872 CACACTGGCATGAAG
65 CACACAAGCATGAAG
* *
40189887 CCTGCTAAGTACTAAGC
1 CCTGCTAGGCACTAAGC
40189904 CTAAACAATC
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
78 53 0.64
80 30 0.36
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (79 bp):
CCTGCTAGGCACTAAGCTTGAATAACACACTGACACGAAGCCTACTAGGCACTAAGCATAATAAC
ACACAAGCATGAAG
Found at i:40189904 original size:40 final size:40
Alignment explanation
Indices: 40189729--40189905 Score: 214
Period size: 40 Copynumber: 4.5 Consensus size: 40
40189719 AGCACAAAAT
* * *
40189729 CCTGCTAGGCACTAAGCTTGAATAACACACTGACACGAAG
1 CCTGCTAGGCACTAAGCCTGAATAACACACTGGCATGAAG
* * * **
40189769 CCTACTAGGCACTAAGCAT--TTAACACACAAGCATGAAG
1 CCTGCTAGGCACTAAGCCTGAATAACACACTGGCATGAAG
* * * *
40189807 CCTGCTAGGCACTATGCTTGAATAATACACTGGCAGGAAG
1 CCTGCTAGGCACTAAGCCTGAATAACACACTGGCATGAAG
40189847 CCTGCTAGGCACTAAGCCTGAATAACACACTGGCATGAAG
1 CCTGCTAGGCACTAAGCCTGAATAACACACTGGCATGAAG
* *
40189887 CCTGCTAAGTACTAAGCCT
1 CCTGCTAGGCACTAAGCCT
40189906 AAACAATCAT
Statistics
Matches: 114, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
38 30 0.26
40 84 0.74
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (40 bp):
CCTGCTAGGCACTAAGCCTGAATAACACACTGGCATGAAG
Found at i:40198032 original size:25 final size:25
Alignment explanation
Indices: 40198002--40198050 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
40197992 AAAATTGCCT
* * *
40198002 TTGTGGTAAGTTATCTATAAAGCCA
1 TTGTGGAAAATTATCTAAAAAGCCA
40198027 TTGTGGAAAATTATCTAAAAAGCC
1 TTGTGGAAAATTATCTAAAAAGCC
40198051 TATACGGCGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (25 bp):
TTGTGGAAAATTATCTAAAAAGCCA
Found at i:40200765 original size:27 final size:27
Alignment explanation
Indices: 40200727--40200783 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
40200717 TAGAAATGAG
*
40200727 AATGATCCTGGTCTTAACAATAATCCA
1 AATGATCCTGGTCTCAACAATAATCCA
* *
40200754 AATGGTCCTGGTCTCAATAATAATCCA
1 AATGATCCTGGTCTCAACAATAATCCA
40200781 AAT
1 AAT
40200784 TTTTAGGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (27 bp):
AATGATCCTGGTCTCAACAATAATCCA
Found at i:40205087 original size:43 final size:43
Alignment explanation
Indices: 40205027--40205117 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
40205017 CTTTGAGTTC
* *
40205027 ATTA-CAAGATTTCCTTGATTAA-ATAAATGTATTATATATTTT
1 ATTACCAAGATTTACTTGATTAAGA-AAATGCATTATATATTTT
* *
40205069 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATGTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
40205112 ATTACC
1 ATTACC
40205118 TTGCATATGT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 4 0.09
43 38 0.88
44 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
Found at i:40205469 original size:43 final size:43
Alignment explanation
Indices: 40205370--40205634 Score: 273
Period size: 43 Copynumber: 6.2 Consensus size: 43
40205360 GATATGGTTT
* ** * * *
40205370 TAGCGGCGTTTGCGTGAAAAGCGCTGCTACAGGTC-TGTTCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * **
40205412 TAGTGGCGTCTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * *
40205455 TAGCGGCGTTTGTGGAAAAAGTGCTGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGATCTA
** * *
40205498 TAGCGGCGTTTGCAAAAAAAGCGCCGCTAAAGATCTTGAGCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * * * *
40205541 TAGTGGCATTTGTG-AATAAGCGCCGCTAAAGGTCCTGATTTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * * * *
40205583 TAGCGGCGTTTATTAAAAAATCGCTGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGATCTA
40205626 TAGCGGCGT
1 TAGCGGCGT
40205635 ATATTTCTAT
Statistics
Matches: 185, Mismatches: 36, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
42 62 0.34
43 123 0.66
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (43 bp):
TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGATCTA
Found at i:40205627 original size:85 final size:86
Alignment explanation
Indices: 40205428--40205632 Score: 268
Period size: 85 Copynumber: 2.4 Consensus size: 86
40205418 CGTCTGTGGG
* * * *
40205428 AAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAAAAGTGCTGCTAAAGGTCTTG
1 AAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCATTTGTGGAAAAAGCGCCGCTAAAGGTCCTG
*
40205493 ATCTATAGCGGCGTTTGCAAA
66 ATCTATAGCGGCGTTTACAAA
* * * *
40205514 AAAAGCGCCGCTAAAGATCTTGAGCTATAGTGGCATTTGT-GAATAAGCGCCGCTAAAGGTCCTG
1 AAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCATTTGTGGAAAAAGCGCCGCTAAAGGTCCTG
* **
40205578 ATTTATAGCGGCGTTTATTAA
66 ATCTATAGCGGCGTTTACAAA
* * *
40205599 AAAATCGCTGCTAAAGGTCCTGATCTATAGCGGC
1 AAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGC
40205633 GTATATTTCT
Statistics
Matches: 101, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
85 65 0.64
86 36 0.36
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.27
Consensus pattern (86 bp):
AAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCATTTGTGGAAAAAGCGCCGCTAAAGGTCCTG
ATCTATAGCGGCGTTTACAAA
Found at i:40206005 original size:20 final size:22
Alignment explanation
Indices: 40205972--40206012 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
40205962 AGACCAATTT
40205972 TTCTCCTAAATTTT-AATTTAA
1 TTCTCCTAAATTTTCAATTTAA
*
40205993 TTCT-CTAATTTTTCAATTTA
1 TTCTCCTAAATTTTCAATTTA
40206013 TTGAATTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (22 bp):
TTCTCCTAAATTTTCAATTTAA
Found at i:40224159 original size:16 final size:16
Alignment explanation
Indices: 40224138--40224206 Score: 129
Period size: 16 Copynumber: 4.3 Consensus size: 16
40224128 TTGGTTGGCT
40224138 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
40224154 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
*
40224170 GTAATGGAATAGAAGC
1 GTAATGGAATAGAGGC
40224186 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
40224202 GTAAT
1 GTAAT
40224207 AGCAATTCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.39, C:0.06, G:0.35, T:0.20
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:40224250 original size:45 final size:44
Alignment explanation
Indices: 40224186--40224282 Score: 142
Period size: 44 Copynumber: 2.2 Consensus size: 44
40224176 GAATAGAAGC
40224186 GTAATGGAATAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG-AATTC-ATGTGTTTGGTTGAAT
* *
40224231 GTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAAT
*
40224275 GGAATGGA
1 GTAATGGA
40224283 GGTGTAATAG
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 24 0.50
45 23 0.48
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAAT
Found at i:40226117 original size:33 final size:33
Alignment explanation
Indices: 40226075--40226141 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
40226065 TAAAACAACG
40226075 CAACTTTAATATAACACCACAAGAAACCTAATA
1 CAACTTTAATATAACACCACAAGAAACCTAATA
40226108 CAACTTTAATATAACACCACAAGAAACCTAATA
1 CAACTTTAATATAACACCACAAGAAACCTAATA
40226141 C
1 C
40226142 TTACCAAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.51, C:0.25, G:0.03, T:0.21
Consensus pattern (33 bp):
CAACTTTAATATAACACCACAAGAAACCTAATA
Found at i:40227276 original size:14 final size:15
Alignment explanation
Indices: 40227250--40227283 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
40227240 AAGAAGAAGC
40227250 AGAAATCTGGAGAAA
1 AGAAATCTGGAGAAA
40227265 AGAAAT-TGGAGAAA
1 AGAAATCTGGAGAAA
40227279 AGAAA
1 AGAAA
40227284 AGAAATGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.59, C:0.03, G:0.26, T:0.12
Consensus pattern (15 bp):
AGAAATCTGGAGAAA
Found at i:40227282 original size:19 final size:22
Alignment explanation
Indices: 40227260--40227304 Score: 69
Period size: 19 Copynumber: 2.2 Consensus size: 22
40227250 AGAAATCTGG
40227260 AGAAAAGAAAT-TG-G-AGAAA
1 AGAAAAGAAATGTGAGAAGAAA
40227279 AGAAAAGAAATGTGAGAAGAAA
1 AGAAAAGAAATGTGAGAAGAAA
40227301 AGAA
1 AGAA
40227305 GCTTACAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.48
20 2 0.09
21 1 0.04
22 9 0.39
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (22 bp):
AGAAAAGAAATGTGAGAAGAAA
Found at i:40232383 original size:50 final size:50
Alignment explanation
Indices: 40232301--40232423 Score: 201
Period size: 50 Copynumber: 2.5 Consensus size: 50
40232291 TTACATTTCT
* *
40232301 AGTAAGGCATGTTAGTTGCTAACCAGCTTGGCGTTATGGGTGATGCCATC
1 AGTAGGGCATGTTAGTTGCTAACCAGCCTGGCGTTATGGGTGATGCCATC
* *
40232351 GGTAGGGCATGTTAGTTACTAACCAGCCTGGCGTTATGGGTGATGCCATC
1 AGTAGGGCATGTTAGTTGCTAACCAGCCTGGCGTTATGGGTGATGCCATC
*
40232401 AGTAGGGTATGTTAGTTGCTAAC
1 AGTAGGGCATGTTAGTTGCTAAC
40232424 AATGGCAAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (50 bp):
AGTAGGGCATGTTAGTTGCTAACCAGCCTGGCGTTATGGGTGATGCCATC
Found at i:40232624 original size:66 final size:66
Alignment explanation
Indices: 40232518--40232649 Score: 219
Period size: 66 Copynumber: 2.0 Consensus size: 66
40232508 ATGGGATCCG
* * * *
40232518 AGGTTAGTACAAGGAAGGGCTTGGGAAATAGTGAGAAAATGTGAAAAATGGATTTCTTGTATATA
1 AGGTTAGCACAAGGAAGGGCATGGGAAAGAGTGAAAAAATGTGAAAAATGGATTTCTTGTATATA
40232583 A
66 A
*
40232584 AGGTTAGCATAAGGAAGGGCATGGGAAAGAGTGAAAAAATGTGAAAAATGGATTTCTTGTATATA
1 AGGTTAGCACAAGGAAGGGCATGGGAAAGAGTGAAAAAATGTGAAAAATGGATTTCTTGTATATA
40232649 A
66 A
40232650 TGCATGTTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.41, C:0.05, G:0.29, T:0.26
Consensus pattern (66 bp):
AGGTTAGCACAAGGAAGGGCATGGGAAAGAGTGAAAAAATGTGAAAAATGGATTTCTTGTATATA
A
Found at i:40234617 original size:35 final size:35
Alignment explanation
Indices: 40234577--40234645 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
40234567 GTGGTAGAAG
* *
40234577 TTAAAATAAGGAGGTAAAATGGTAAAGTGGTTAAA
1 TTAAAATAAGAAGGTAAAATGGTAAAGTGATTAAA
* *
40234612 TTAAAATAAGAAGGTGAAGTGGTAAAGTGATTAA
1 TTAAAATAAGAAGGTAAAATGGTAAAGTGATTAA
40234646 CTGTTTCTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (35 bp):
TTAAAATAAGAAGGTAAAATGGTAAAGTGATTAAA
Found at i:40234984 original size:17 final size:16
Alignment explanation
Indices: 40234962--40235003 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
40234952 TCATTTGCTA
40234962 TCATTTTCTCATTTTTT
1 TCATTTTCTCA-TTTTT
40234979 TCA-TTTCTTCATTTTT
1 TCATTTTC-TCATTTTT
40234995 T-ATTTTCTC
1 TCATTTTCTC
40235004 TCTTTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.13
16 14 0.61
17 6 0.26
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (16 bp):
TCATTTTCTCATTTTT
Found at i:40235010 original size:17 final size:17
Alignment explanation
Indices: 40234964--40235012 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 17
40234954 ATTTGCTATC
*
40234964 ATTTTCTCAT-TTTTTTC
1 ATTTTCTC-TCTTTTTTT
*
40234981 A-TTTCT-TCATTTTTT
1 ATTTTCTCTCTTTTTTT
40234996 ATTTTCTCTCTTTTTTT
1 ATTTTCTCTCTTTTTTT
40235013 GAAAAACAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
14 1 0.04
15 6 0.23
16 10 0.38
17 9 0.35
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTCTCTCTTTTTTT
Found at i:40236177 original size:14 final size:14
Alignment explanation
Indices: 40236155--40236189 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
40236145 AAATGTGAGC
*
40236155 ATGTTTACATGCAA
1 ATGTGTACATGCAA
40236169 ATGTGTACATGCAA
1 ATGTGTACATGCAA
40236183 ATGTGTA
1 ATGTGTA
40236190 TAATTGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (14 bp):
ATGTGTACATGCAA
Found at i:40236755 original size:19 final size:19
Alignment explanation
Indices: 40236728--40236776 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
40236718 TGCTCTTGGA
*
40236728 TATGAACTTTTTAATAAAT
1 TATGGACTTTTTAATAAAT
* * **
40236747 TATGGACTTTATATTATTT
1 TATGGACTTTTTAATAAAT
40236766 TATGGACTTTT
1 TATGGACTTTT
40236777 ATAGACTTTG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.53
Consensus pattern (19 bp):
TATGGACTTTTTAATAAAT
Found at i:40237847 original size:18 final size:18
Alignment explanation
Indices: 40237824--40237860 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40237814 ACTCATGTAT
40237824 TATGTTGCTATGCGAACC
1 TATGTTGCTATGCGAACC
* *
40237842 TATGTTGTTTTGCGAACC
1 TATGTTGCTATGCGAACC
40237860 T
1 T
40237861 TAATAATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (18 bp):
TATGTTGCTATGCGAACC
Found at i:40240589 original size:2 final size:2
Alignment explanation
Indices: 40240582--40240606 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40240572 TGATTTTCTT
40240582 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 T
40240607 TCTGTTTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40242317 original size:6 final size:6
Alignment explanation
Indices: 40242307--40242336 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
40242297 ACACATATAC
*
40242307 ATATGC ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA
40242337 TCTCAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (6 bp):
ATATGA
Found at i:40243705 original size:17 final size:19
Alignment explanation
Indices: 40243670--40243707 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
40243660 AATAATTTTT
40243670 AAATTATAAAAAATCTAAA
1 AAATTATAAAAAATCTAAA
*
40243689 AAATTA-AACAAAT-TAAA
1 AAATTATAAAAAATCTAAA
40243706 AA
1 AA
40243708 TTTTAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 6 0.33
19 6 0.33
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATTATAAAAAATCTAAA
Found at i:40244690 original size:37 final size:31
Alignment explanation
Indices: 40244613--40244672 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
40244603 ATTATACTGT
**
40244613 TGGTTTTAATTATGGGGATTGGATGTGAAAA
1 TGGTTTTAATTATGGCCATTGGATGTGAAAA
40244644 TGGTTTTAATTATGGCCATTGGATGTGAA
1 TGGTTTTAATTATGGCCATTGGATGTGAA
40244673 TAAAATAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.03, G:0.30, T:0.40
Consensus pattern (31 bp):
TGGTTTTAATTATGGCCATTGGATGTGAAAA
Found at i:40248155 original size:30 final size:30
Alignment explanation
Indices: 40248120--40248182 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
40248110 ACACTGTTTC
40248120 CATTTACTGAAAGTATGTGATTAGTGAGGA
1 CATTTACTGAAAGTATGTGATTAGTGAGGA
* *
40248150 CATTTATTGAAAGTATGTGATTTGTGAGGA
1 CATTTACTGAAAGTATGTGATTAGTGAGGA
40248180 CAT
1 CAT
40248183 GCTGAGCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (30 bp):
CATTTACTGAAAGTATGTGATTAGTGAGGA
Found at i:40265201 original size:12 final size:13
Alignment explanation
Indices: 40265184--40265213 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
40265174 CTCATACATG
40265184 AATAAATAAA-GC
1 AATAAATAAATGC
40265196 AATAAATAAATGC
1 AATAAATAAATGC
40265209 AATAA
1 AATAA
40265214 TTATAGCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:40288540 original size:20 final size:20
Alignment explanation
Indices: 40288517--40288567 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
40288507 TATGTACGTA
*
40288517 TATATATATATTATACTTTC
1 TATATATATATTATAATTTC
* *
40288537 TATACATATTTTATAATTTC
1 TATATATATATTATAATTTC
40288557 TATATATATAT
1 TATATATATAT
40288568 ATATGTAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATATATATTATAATTTC
Found at i:40288582 original size:52 final size:52
Alignment explanation
Indices: 40288515--40288675 Score: 118
Period size: 54 Copynumber: 3.1 Consensus size: 52
40288505 TATATGTACG
40288515 TATA-TATATAT--ATTATACTTTCTATACATATTTTATAATTTCTATATATA
1 TATACTATATATGCATTATACTTTCTAT-CATATTTTATAATTTCTATATATA
* * * *
40288565 TATA-TATGTAAT-CATTAT-CTTTATGATCTATATATTTATTAACTTATATATATA
1 TATACTATAT-ATGCATTATACTTTCT-ATC-ATAT-TTTA-TAATTTCTATATATA
* ** * * *
40288619 TGTACGTATATATGTTTTATATTTTCTATCCACATTTTATAATTTCTATATGTA
1 TATAC-TATATATGCATTATACTTTCTAT-CATATTTTATAATTTCTATATATA
40288673 TAT
1 TAT
40288676 TTTCTTTATT
Statistics
Matches: 85, Mismatches: 15, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
50 8 0.09
51 8 0.09
52 11 0.13
53 4 0.05
54 30 0.35
55 6 0.07
56 13 0.15
57 5 0.06
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (52 bp):
TATACTATATATGCATTATACTTTCTATCATATTTTATAATTTCTATATATA
Found at i:40288629 original size:108 final size:106
Alignment explanation
Indices: 40288458--40288675 Score: 303
Period size: 108 Copynumber: 2.0 Consensus size: 106
40288448 TTTTTAAGTT
* *
40288458 TATATATGTAATTATTATTTTATGATTTATAAATTTATTACCTTATATATATGTACGTATATATA
1 TATATATGTAATCATTATTTTATGATCTATAAATTTATTACCTTATATATATGTACG-ATATATA
*
40288523 TATATTATACTTTCTATACATATTTTATAATTTCTATATATA
65 TATATTATACTTTCTATACACATTTTATAATTTCTATATATA
* *
40288565 TATATATGTAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACG-TATA
1 TATATATGTAATCATTAT-TTTATGATCTATAAATTTATT-ACCT-TATATATATGTACGATATA
* * * * *
40288629 TATGTTTTATATTTTCTATCCACATTTTATAATTTCTATATGTA
63 TATATATTATACTTTCTATACACATTTTATAATTTCTATATATA
40288673 TAT
1 TAT
40288676 TTTCTTTATT
Statistics
Matches: 98, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
107 17 0.17
108 64 0.65
109 3 0.03
110 14 0.14
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (106 bp):
TATATATGTAATCATTATTTTATGATCTATAAATTTATTACCTTATATATATGTACGATATATAT
ATATTATACTTTCTATACACATTTTATAATTTCTATATATA
Found at i:40289013 original size:16 final size:16
Alignment explanation
Indices: 40288988--40289019 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40288978 CTTTTACTCG
40288988 ATTTTAAAAATAGAAA
1 ATTTTAAAAATAGAAA
*
40289004 ATTTTTAAAATAGAAA
1 ATTTTAAAAATAGAAA
40289020 TAATACTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (16 bp):
ATTTTAAAAATAGAAA
Found at i:40290038 original size:96 final size:96
Alignment explanation
Indices: 40289918--40290101 Score: 305
Period size: 96 Copynumber: 1.9 Consensus size: 96
40289908 TACTTTCTTA
*
40289918 TCTAGTTGGATATTTAATTAGACATTGGAAACCCTTATGATCTTTTGAACTAGACCAATAACATT
1 TCTAGTTGGATATTTAATTAGACATTGGAAACCCTTATGATCTTTTGAACTACACCAATAACATT
**
40289983 GCACAAAAGGTGATTTCTCAATCATCTTCTC
66 GCACAAAAGGTGATAGCTCAATCATCTTCTC
* * * *
40290014 TCTATTTGGATATTTAATTGGACATTGGAAACCCTTATGATCTTTTGAACTACACTAATAATATT
1 TCTAGTTGGATATTTAATTAGACATTGGAAACCCTTATGATCTTTTGAACTACACCAATAACATT
40290079 GCACAAAAGGTGATAGCTCAATC
66 GCACAAAAGGTGATAGCTCAATC
40290102 GTATTCCTCC
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 81 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.35
Consensus pattern (96 bp):
TCTAGTTGGATATTTAATTAGACATTGGAAACCCTTATGATCTTTTGAACTACACCAATAACATT
GCACAAAAGGTGATAGCTCAATCATCTTCTC
Found at i:40298791 original size:11 final size:12
Alignment explanation
Indices: 40298766--40298792 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40298756 CATTTTAGTA
40298766 TTTTTGTTCATT
1 TTTTTGTTCATT
40298778 TTTTTGTTCATT
1 TTTTTGTTCATT
40298790 TTT
1 TTT
40298793 CCATAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTTGTTCATT
Found at i:40304329 original size:10 final size:9
Alignment explanation
Indices: 40304316--40304361 Score: 51
Period size: 8 Copynumber: 5.1 Consensus size: 9
40304306 CTCTTTTTCC
40304316 TTATTTTATT
1 TTATTTTA-T
40304326 TTATTTTAT
1 TTATTTTAT
*
40304335 TTA-TTTAC
1 TTATTTTAT
40304343 TTA-TTTAT
1 TTATTTTAT
40304351 TTATTATTAT
1 TTATT-TTAT
40304361 T
1 T
40304362 CGTATGTCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 14 0.44
9 5 0.16
10 13 0.41
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (9 bp):
TTATTTTAT
Found at i:40306120 original size:6 final size:6
Alignment explanation
Indices: 40306109--40306165 Score: 78
Period size: 6 Copynumber: 9.5 Consensus size: 6
40306099 AGTTTATTTG
* * *
40306109 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TATTGT TTGTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
*
40306157 TGTTAT TTT
1 TTTTAT TTT
40306166 CTTCAATTTG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:40314749 original size:25 final size:24
Alignment explanation
Indices: 40314698--40314751 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
40314688 GTCAGTAGGG
*
40314698 TTACCGATTTCAGCTCGTGAGAGC
1 TTACCGATTTCAGCTCGTGAGACC
*
40314722 TTACTGATTCTCAGCTCGT-ATGACC
1 TTACCGATT-TCAGCTCGTGA-GACC
40314747 TTACC
1 TTACC
40314752 AATATTCAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (24 bp):
TTACCGATTTCAGCTCGTGAGACC
Found at i:40315047 original size:24 final size:23
Alignment explanation
Indices: 40315015--40315059 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
40315005 AGGTTATTAC
40315015 ATGATACATAGTTATAT-GAAATGG
1 ATGATACAT-G-TATATGGAAATGG
40315039 ATGATACATGTATATGGAAAT
1 ATGATACATGTATATGGAAAT
40315060 ATGATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 6 0.30
24 9 0.45
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.33
Consensus pattern (23 bp):
ATGATACATGTATATGGAAATGG
Found at i:40317125 original size:50 final size:50
Alignment explanation
Indices: 40317001--40317228 Score: 244
Period size: 50 Copynumber: 4.6 Consensus size: 50
40316991 GATAATAACA
* ** * * *
40317001 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCAT-GCAT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* * * ** * *
40317050 TGCCAATGCCATATCCCAGATATGGTCTTATATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* ** *
40317100 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCTTCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* *
40317150 TGCCAACT-CCATGTCCCAGACATGGTCTTACATGGGACCTCTCCTCTCGG
1 TGCCAA-TGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* *
40317200 TGCCAACGCCATGTCCCAGACATGCTCTT
1 TGCCAATGCCATGTCCCAGACATGGTCTT
40317229 CTCGGTGCCA
Statistics
Matches: 148, Mismatches: 28, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
49 38 0.26
50 109 0.74
51 1 0.01
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
Found at i:40317237 original size:34 final size:34
Alignment explanation
Indices: 40317194--40317262 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
40317184 GGACCTCTCC
40317194 TCTCGGTGCCAACGCCATGTCCCAGACATGCTCT
1 TCTCGGTGCCAACGCCATGTCCCAGACATGCTCT
*
40317228 TCTCGGTGCCAACGCCATGTCCCAGACATGGTCT
1 TCTCGGTGCCAACGCCATGTCCCAGACATGCTCT
40317262 T
1 T
40317263 ACATGGGACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.17, C:0.36, G:0.22, T:0.25
Consensus pattern (34 bp):
TCTCGGTGCCAACGCCATGTCCCAGACATGCTCT
Found at i:40317282 original size:84 final size:84
Alignment explanation
Indices: 40317140--40317307 Score: 300
Period size: 84 Copynumber: 2.0 Consensus size: 84
40317130 CGGGGGACCT
* * *
40317140 CTCTTCTCAGTGCCAACTCCATGTCCCAGACATGGTCTTACATGGGACCTCTCCTCTCGGTGCCA
1 CTCTTCTCAGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCCA
40317205 ACGCCATGTCCCAGACATG
66 ACGCCATGTCCCAGACATG
*
40317224 CTCTTCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCCA
1 CTCTTCTCAGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCCA
40317289 ACGCCATGTCCCAGACATG
66 ACGCCATGTCCCAGACATG
40317308 GTTTTACATG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.20, C:0.36, G:0.20, T:0.24
Consensus pattern (84 bp):
CTCTTCTCAGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCCA
ACGCCATGTCCCAGACATG
Found at i:40317303 original size:50 final size:50
Alignment explanation
Indices: 40317228--40317325 Score: 169
Period size: 50 Copynumber: 2.0 Consensus size: 50
40317218 GACATGCTCT
*
40317228 TCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCA
1 TCTCGATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCA
* *
40317278 TCTCGATGCCAACGCCATGTCCCAGACATGGTTTTACATGGGATCTCT
1 TCTCGATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
40317326 TTACCCAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.20, C:0.32, G:0.21, T:0.27
Consensus pattern (50 bp):
TCTCGATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCA
Found at i:40322225 original size:17 final size:18
Alignment explanation
Indices: 40322197--40322230 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40322187 TCTCCCAAAA
*
40322197 TTCAATTTTATTTAATTT
1 TTCAATTTTATTAAATTT
40322215 TTCAA-TTTATTAAATT
1 TTCAATTTTATTAAATT
40322231 ATTAGTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCAATTTTATTAAATTT
Found at i:40337149 original size:31 final size:32
Alignment explanation
Indices: 40337114--40337174 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
40337104 TATTTTATTC
*
40337114 TTAA-TTTTGTTATTATTTTAAAGGCATTTTT
1 TTAATTTTTGTTATTATTTTAAAAGCATTTTT
40337145 TTAATTTTTGTTATTATTTTAAAAGCATTT
1 TTAATTTTTGTTATTATTTTAAAAGCATTT
40337175 ACGTTACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.61
Consensus pattern (32 bp):
TTAATTTTTGTTATTATTTTAAAAGCATTTTT
Found at i:40337306 original size:11 final size:11
Alignment explanation
Indices: 40337290--40337320 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
40337280 TATATATATT
40337290 TAAAAATTATA
1 TAAAAATTATA
*
40337301 TAAAAATAATA
1 TAAAAATTATA
40337312 TAAAAATTA
1 TAAAAATTA
40337321 ATACGGCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:40342182 original size:24 final size:23
Alignment explanation
Indices: 40342150--40342298 Score: 87
Period size: 24 Copynumber: 6.5 Consensus size: 23
40342140 AAATACTTTT
*
40342150 TAAAGAAATAATATAAATATATA
1 TAAATAAATAATATAAATATATA
* *
40342173 TACAAAAAATAA-ATAATATAAATTA
1 TA-AATAAATAATATAA-ATATA-TA
**
40342198 TTTATAAATATATATACAA-A-A-A
1 TAAATAAATA-ATATA-AATATATA
* *
40342220 TAAATAAAT-ATTTAAATA-ATT
1 TAAATAAATAATATAAATATATA
* * *
40342241 TATA-AAATAATATAAATACTTTT
1 TAAATAAATAATATAAATA-TATA
40342264 TAAATAAATAATATAAATATATA
1 TAAATAAATAATATAAATATATA
*
40342287 TACAAAAAATAA
1 TA-AATAAATAA
40342299 ATGATATAAA
Statistics
Matches: 97, Mismatches: 16, Indels: 25
0.70 0.12 0.18
Matches are distributed among these distances:
19 2 0.02
20 10 0.10
21 11 0.11
22 8 0.08
23 15 0.15
24 41 0.42
25 5 0.05
26 4 0.04
27 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (23 bp):
TAAATAAATAATATAAATATATA
Found at i:40342186 original size:28 final size:28
Alignment explanation
Indices: 40342155--40342309 Score: 102
Period size: 28 Copynumber: 5.5 Consensus size: 28
40342145 CTTTTTAAAG
40342155 AAATAATATAAATATATATACAAAAAAT
1 AAATAATATAAATATATATACAAAAAAT
* *
40342183 AAATAATATAAATTATTTATA-AATATATAT
1 AAATAATATAAA-TATATATACAA-A-AAAT
* ** *
40342213 ACAA-AA-ATAAATAAATATTTAAATAAT
1 A-AATAATATAAATATATATACAAAAAAT
** * * ***
40342240 TTATAAAAT-AATATAAATACTTTTTAAAT
1 AAATAATATAAATATATATAC--AAAAAAT
40342269 AAATAATATAAATATATATACAAAAAAT
1 AAATAATATAAATATATATACAAAAAAT
*
40342297 AAATGATATAAAT
1 AAATAATATAAAT
40342310 TATTTATAAA
Statistics
Matches: 92, Mismatches: 25, Indels: 20
0.67 0.18 0.15
Matches are distributed among these distances:
26 1 0.01
27 11 0.12
28 38 0.41
29 24 0.26
30 16 0.17
31 2 0.02
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.35
Consensus pattern (28 bp):
AAATAATATAAATATATATACAAAAAAT
Found at i:40342211 original size:41 final size:40
Alignment explanation
Indices: 40342164--40342256 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 40
40342154 GAAATAATAT
* *
40342164 AAATATATATACAAA-AAATAAATAATATAAATTATTTATA
1 AAATATATATAAAAATAAATAAAT-ATATAAATAATTTATA
* *
40342204 AATATATATACAAAAATAAATAAATATTTAAATAATTTATA
1 AA-ATATATATAAAAATAAATAAATATATAAATAATTTATA
40342245 AAATA-ATATAAA
1 AAATATATATAAA
40342257 TACTTTTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
39 6 0.13
40 5 0.11
41 27 0.59
42 8 0.17
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (40 bp):
AAATATATATAAAAATAAATAAATATATAAATAATTTATA
Found at i:40344830 original size:16 final size:16
Alignment explanation
Indices: 40344806--40344873 Score: 52
Period size: 16 Copynumber: 4.3 Consensus size: 16
40344796 TCAAGATAAG
*
40344806 TATTGGATAAATTTAA
1 TATTAGATAAATTTAA
*
40344822 TATTAGATATA-TTAA
1 TATTAGATAAATTTAA
*
40344837 -ATTA-ATAGAATATAA
1 TATTAGATA-AATTTAA
* *
40344852 TATTAAATTTAATTTAA
1 TATTAGA-TAAATTTAA
40344869 TATTA
1 TATTA
40344874 AATTTATTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
13 3 0.07
14 5 0.12
15 7 0.17
16 13 0.32
17 12 0.29
18 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (16 bp):
TATTAGATAAATTTAA
Found at i:40344887 original size:17 final size:17
Alignment explanation
Indices: 40344850--40344884 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40344840 AATAGAATAT
*
40344850 AATATTAAATTTAATTT
1 AATATTAAATTTAATTA
40344867 AATATTAAATTT-ATTA
1 AATATTAAATTTAATTA
40344883 AA
1 AA
40344885 ATAATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATATTAAATTTAATTA
Found at i:40348375 original size:11 final size:11
Alignment explanation
Indices: 40348345--40348378 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
40348335 ATCGCAAGTG
40348345 AATTAATTCTAA
1 AATTAATTC-AA
*
40348357 AATAAATTCAA
1 AATTAATTCAA
40348368 AATTAATTCAA
1 AATTAATTCAA
40348379 CTTGGGTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (11 bp):
AATTAATTCAA
Found at i:40348712 original size:20 final size:19
Alignment explanation
Indices: 40348670--40348716 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
40348660 ACATAAGTTC
40348670 TAATTAAAGTAAGTTAAGT
1 TAATTAAAGTAAGTTAAGT
*
40348689 TAATTAAA-TAAAGATTATGT
1 TAATTAAAGT-AAG-TTAAGT
40348709 TAATTAAA
1 TAATTAAA
40348717 CCAAATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 1 0.04
19 11 0.44
20 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
TAATTAAAGTAAGTTAAGT
Found at i:40357931 original size:103 final size:103
Alignment explanation
Indices: 40357752--40358120 Score: 605
Period size: 103 Copynumber: 3.6 Consensus size: 103
40357742 TAGCCGTTAT
** * *
40357752 TGGTGGATCCCGCACTTTGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
40357817 AATCAGCACATAGCAACCCCCTTTTTATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTTATTTCAAAGATA
40357855 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
*
40357920 AATCAGCACATAGCAACCCCCTGTTTATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTTATTTCAAAGATA
40357958 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
**
40358023 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTT-TTATTTCAAAGATA
* * * **
40358062 TGGTGGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
40358121 TTTATATACA
Statistics
Matches: 251, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
103 186 0.74
104 64 0.25
105 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (103 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTTATTTCAAAGATA
Found at i:40358482 original size:29 final size:29
Alignment explanation
Indices: 40358449--40358512 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
40358439 TAATCCACCA
40358449 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
40358478 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
40358508 CCCAA
1 CCCAA
40358513 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:40358486 original size:30 final size:30
Alignment explanation
Indices: 40358456--40358512 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
40358446 CCACCCAACT
40358456 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
40358485 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
40358513 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:40367065 original size:73 final size:73
Alignment explanation
Indices: 40366946--40367100 Score: 242
Period size: 73 Copynumber: 2.1 Consensus size: 73
40366936 AAAAAATATC
*
40366946 AAATAAAATCTTGTTAAACAGCGGGAATAAATTCTGAAACAGATTTTATTTAATTCAATTC-AAT
1 AAATAAAATCTTGTTAAACAGCGGGAATAAATTCTGAAACAGATTTT-TTTAAATCAATTCTAAT
40367010 TTGGAAACA
65 TTGGAAACA
* * *
40367019 AAATAAAATCTTGTTAAATAGTGGGAATAAA-TCTCGAAACAGATTTTTTTAAATCTATTCTAAT
1 AAATAAAATCTTGTTAAACAGCGGGAATAAATTCT-GAAACAGATTTTTTTAAATCAATTCTAAT
40367083 TTGGAAACA
65 TTGGAAACA
40367092 AAATAAAAT
1 AAATAAAAT
40367101 GAAATAAAAT
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
72 14 0.18
73 62 0.82
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.34
Consensus pattern (73 bp):
AAATAAAATCTTGTTAAACAGCGGGAATAAATTCTGAAACAGATTTTTTTAAATCAATTCTAATT
TGGAAACA
Found at i:40367250 original size:87 final size:88
Alignment explanation
Indices: 40367088--40367275 Score: 236
Period size: 87 Copynumber: 2.1 Consensus size: 88
40367078 CTAATTTGGA
* * * *
40367088 AACAAAATAAAATGAAATAAAATATTGTTAAATGACGAGAAAAAAAATCCCAAAATAGATTTTAT
1 AACAAAATCAAATCAAATAAAATATTATTAAATGACGAG-AAAAAAATCACAAAATAGATTTTAT
40367153 TTAATTTAATTTCTC-GTTTTTGAC
65 TTAATTTAATTTCTCAGTTTTTG-C
* * * * * *
40367177 AACAAAATCAAATCAAATAAATTTTTATTAAATGATGAG-AATAAATCACGAAATATATTTTATT
1 AACAAAATCAAATCAAATAAAATATTATTAAATGACGAGAAAAAAATCACAAAATAGATTTTATT
* *
40367241 TAATTTAATTTTTCATTTTTTGC
66 TAATTTAATTTCTCAGTTTTTGC
40367264 AACAAAATCAAA
1 AACAAAATCAAA
40367276 ATGTAATAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
87 47 0.55
88 6 0.07
89 33 0.38
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (88 bp):
AACAAAATCAAATCAAATAAAATATTATTAAATGACGAGAAAAAAATCACAAAATAGATTTTATT
TAATTTAATTTCTCAGTTTTTGC
Found at i:40369600 original size:38 final size:38
Alignment explanation
Indices: 40369558--40369643 Score: 93
Period size: 38 Copynumber: 2.2 Consensus size: 38
40369548 GGCCCATTTT
*
40369558 TAAAATAAACATTAAAAAATTATTTTAAAAATAAAAAA
1 TAAAATAAACATTAAAAAAGTATTTTAAAAATAAAAAA
** ** *
40369596 TAAAA-AATTTATTTTAAAAGTATTTTAAAATTAAAAAA
1 TAAAATAA-ACATTAAAAAAGTATTTTAAAAATAAAAAA
40369634 TAAAAATAAA
1 T-AAAATAAA
40369644 AAATATATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
37 2 0.05
38 30 0.79
39 4 0.11
40 2 0.05
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (38 bp):
TAAAATAAACATTAAAAAAGTATTTTAAAAATAAAAAA
Found at i:40369609 original size:27 final size:26
Alignment explanation
Indices: 40369553--40369614 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
40369543 AGCCCGGCCC
* * *
40369553 ATTTTTAAAATAAACATTAAAAAATT
1 ATTTTAAAAATAAAAAATAAAAAATT
40369579 ATTTTAAAAATAAAAAATAAAAAATTT
1 ATTTTAAAAATAAAAAATAAAAAA-TT
40369606 ATTTTAAAA
1 ATTTTAAAA
40369615 GTATTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 21 0.66
27 11 0.34
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
ATTTTAAAAATAAAAAATAAAAAATT
Found at i:40376262 original size:20 final size:20
Alignment explanation
Indices: 40376239--40376278 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
40376229 TATATAAAAA
40376239 TAAAATTACATATAGAGGAG
1 TAAAATTACATATAGAGGAG
40376259 TAAAATTACATATAGAGGAG
1 TAAAATTACATATAGAGGAG
40376279 CTCTTTTCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (20 bp):
TAAAATTACATATAGAGGAG
Found at i:40377309 original size:152 final size:152
Alignment explanation
Indices: 40377028--40377344 Score: 528
Period size: 152 Copynumber: 2.1 Consensus size: 152
40377018 AAGTCTAAAT
* *
40377028 ACCATAAGAAATTAGTTTAAATATAACAAAAATATTATTAAGCACATAATAATCAAACATGCAAT
1 ACCAAAAGAAATTAGTTTAAATATAACAAAAAGATTATTAAGCACATAATAATCAAACATGCAAT
*
40377093 CTTTATGTGCATGATTATGATAATCCAAATATTTTTATAAAACATATATGCAAGTTTTCTAAAAT
66 CTTTATGTGCATGATTACGATAATCCAAATATTTTTATAAAACATATATGCAAGTTTTCTAAAAT
*
40377158 TTCCTACCCATTTCCGCTGCAC
131 TTCCTACCCATTTCCGCTACAC
* *
40377180 ACTAAAAGAAATTAGTTTAAATATAACAAAAAGATTGTTAAGCACATAATAATCAAACATGCAAT
1 ACCAAAAGAAATTAGTTTAAATATAACAAAAAGATTATTAAGCACATAATAATCAAACATGCAAT
*
40377245 CTTTATGTGCATGATTACGATAATGCAAATATTTTTATAAAACATATATG-ACAGTTTTCTAAAA
66 CTTTATGTGCATGATTACGATAATCCAAATATTTTTATAAAACATATATGCA-AGTTTTCTAAAA
* *
40377309 TTTCTTACCCATTTCTGCTACAC
130 TTTCCTACCCATTTCCGCTACAC
*
40377332 ACCAAAAGGAATT
1 ACCAAAAGAAATT
40377345 CCTCAAAAAT
Statistics
Matches: 153, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
151 1 0.01
152 152 0.99
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.33
Consensus pattern (152 bp):
ACCAAAAGAAATTAGTTTAAATATAACAAAAAGATTATTAAGCACATAATAATCAAACATGCAAT
CTTTATGTGCATGATTACGATAATCCAAATATTTTTATAAAACATATATGCAAGTTTTCTAAAAT
TTCCTACCCATTTCCGCTACAC
Found at i:40385223 original size:21 final size:23
Alignment explanation
Indices: 40385199--40385251 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 23
40385189 CTAATTATTC
40385199 TAAAAAAA-T-ACAAAAATAAAA
1 TAAAAAAATTAACAAAAATAAAA
40385220 TAAAATGAAATTGAACAAAAATAAAA
1 TAAAA--AAATT-AACAAAAATAAAA
40385246 TAAAAA
1 TAAAAA
40385252 GAAAATTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 5 0.19
23 3 0.11
24 2 0.07
26 17 0.63
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.17
Consensus pattern (23 bp):
TAAAAAAATTAACAAAAATAAAA
Found at i:40391147 original size:23 final size:23
Alignment explanation
Indices: 40391110--40391154 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
40391100 ACGCCAGTTC
40391110 TGTAATATCCCGAAAATTACTAT
1 TGTAATATCCCGAAAATTACTAT
40391133 TGTAATA-CCCTGAAAATTACTA
1 TGTAATATCCC-GAAAATTACTA
40391155 CAGTGAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (23 bp):
TGTAATATCCCGAAAATTACTAT
Found at i:40394323 original size:50 final size:50
Alignment explanation
Indices: 40394226--40394513 Score: 326
Period size: 50 Copynumber: 5.6 Consensus size: 50
40394216 TGTGAGCCAG
* *
40394226 TGTAAGACCATGTCTGGAACATGGCATTGGCATTCTTGAGATTATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCA--C-CGAG---ATGAGAGGTCCCA
40394282 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* * * *
40394332 TGCAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGTGGGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* * * * * *
40394382 TGTAAAACCATGTTTGGGACATGGCGTTGGCACCGGGATGATAGGTCCCC
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* * * * **
40394432 CGTATGACCATGTCTAGGACATGGCATGGGCACCG-GTATGAGAACTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG-ATGAGAGGTCCCA
* *
40394482 TGTAAGACCATATCTGGGATATGGCATTGGCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCA
40394514 GTATAGAAAA
Statistics
Matches: 200, Mismatches: 31, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
49 1 0.00
50 164 0.82
53 3 0.01
54 1 0.00
56 31 0.16
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.23
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
Found at i:40396611 original size:25 final size:25
Alignment explanation
Indices: 40396528--40396662 Score: 115
Period size: 25 Copynumber: 5.6 Consensus size: 25
40396518 TTGATATGCA
* *
40396528 CTAATGAA-CAGAGAGCACTAAAGTG
1 CTAAT-AATCAGAGAGCACCAACGTG
*
40396553 CT-AT-A-CAGAGAGCA-CAGATGTG
1 CTAATAATCAGAGAGCACCA-ACGTG
** *
40396575 CT-A-AA-CAGAGAGCACTGACATG
1 CTAATAATCAGAGAGCACCAACGTG
40396597 CTAATAATCAGAGAGCACCAACGTG
1 CTAATAATCAGAGAGCACCAACGTG
* * *
40396622 CTAGTAGTCAGAGAGCACCAATGTG
1 CTAATAATCAGAGAGCACCAACGTG
40396647 CTAATAATCAGAGAGC
1 CTAATAATCAGAGAGC
40396663 GCGCTAAAGT
Statistics
Matches: 90, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
21 1 0.01
22 32 0.36
23 1 0.01
24 4 0.04
25 52 0.58
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (25 bp):
CTAATAATCAGAGAGCACCAACGTG
Found at i:40397740 original size:5 final size:5
Alignment explanation
Indices: 40397732--40397772 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
40397722 TTGTTTTATG
*
40397732 AATAT AATAAT AATAT AATAT TATAAT AATAT AATAT AATA
1 AATAT AAT-AT AATAT AATAT AAT-AT AATAT AATAT AATA
40397773 ACTTACTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 23 0.72
6 9 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:40397757 original size:16 final size:16
Alignment explanation
Indices: 40397732--40397773 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
40397722 TTGTTTTATG
40397732 AATATAATAATAATAT
1 AATATAATAATAATAT
*
40397748 AATATTATAATAATAT
1 AATATAATAATAATAT
40397764 AATATAATAA
1 AATATAATAA
40397774 CTTACTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATAATAATAATAT
Found at i:40397773 original size:8 final size:8
Alignment explanation
Indices: 40397738--40397767 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
40397728 TATGAATATA
40397738 ATAATAAT
1 ATAATAAT
*
40397746 ATAATATT
1 ATAATAAT
40397754 ATAATAAT
1 ATAATAAT
40397762 ATAATA
1 ATAATA
40397768 TAATAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAATAAT
Found at i:40398460 original size:23 final size:23
Alignment explanation
Indices: 40398426--40398476 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
40398416 GGGAGAGAAA
*
40398426 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
40398449 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
40398472 AGTAA
1 TGTAA
40398477 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:40400428 original size:21 final size:22
Alignment explanation
Indices: 40400398--40400438 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
40400388 TTCGTGTAAC
*
40400398 TTGAATTATAT-TATTAGATGA
1 TTGAAATATATATATTAGATGA
40400419 TTGAAATATATATATTAGAT
1 TTGAAATATATATATTAGAT
40400439 TGAGAAACTG
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:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (22 bp):
TTGAAATATATATATTAGATGA
Found at i:40409452 original size:41 final size:41
Alignment explanation
Indices: 40409406--40409489 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
40409396 TATTATATAA
40409406 CCATATTTTTCATGTAAAATCATATGTGATCTTGTAATAGC
1 CCATATTTTTCATGTAAAATCATATGTGATCTTGTAATAGC
40409447 CCATATTTTTCATGTAAAATCATATGTGATCTTGTAATAGC
1 CCATATTTTTCATGTAAAATCATATGTGATCTTGTAATAGC
40409488 CC
1 CC
40409490 GTATCGAACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (41 bp):
CCATATTTTTCATGTAAAATCATATGTGATCTTGTAATAGC
Found at i:40418566 original size:25 final size:25
Alignment explanation
Indices: 40418549--40418660 Score: 161
Period size: 25 Copynumber: 4.5 Consensus size: 25
40418539 CAGCTCATAT
*
40418549 GAGCTTACCGTTATTCAGCTTGGAG
1 GAGCTTACCGTTATTCAGCTCGGAG
* * * *
40418574 AAGCTTCCCGTTATTCAACTCAGAG
1 GAGCTTACCGTTATTCAGCTCGGAG
* *
40418599 GAGTTTACCATTATTCAGCTCGGAG
1 GAGCTTACCGTTATTCAGCTCGGAG
40418624 GAGCTTACCGTTATTCAGCTCGGAG
1 GAGCTTACCGTTATTCAGCTCGGAG
40418649 GAGCTTACCGTT
1 GAGCTTACCGTT
40418661 TACAGCTTGT
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 74 1.00
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.30
Consensus pattern (25 bp):
GAGCTTACCGTTATTCAGCTCGGAG
Found at i:40426127 original size:54 final size:54
Alignment explanation
Indices: 40426000--40426128 Score: 150
Period size: 54 Copynumber: 2.4 Consensus size: 54
40425990 CAGAATAGGT
* * * *** *
40426000 CTTACACAATGTGGTCTTCATTACCCCATATGATGCCACAGCAAATGGCTAGGC
1 CTTACACTATATGGTCTTCTTTACCCCATATGATGCCACAGCAAACAACTAAGC
* * ** *
40426054 CTTACACTATATGCTCTTCTTTTCCCTGTATGATGCCATAGCAAACAACTAAGC
1 CTTACACTATATGGTCTTCTTTACCCCATATGATGCCACAGCAAACAACTAAGC
40426108 CTTACACTATATGGTCTTCTT
1 CTTACACTATATGGTCTTCTT
40426129 GCCATGGTCA
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (54 bp):
CTTACACTATATGGTCTTCTTTACCCCATATGATGCCACAGCAAACAACTAAGC
Found at i:40427421 original size:20 final size:20
Alignment explanation
Indices: 40427396--40427434 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
40427386 TACTTTCTTT
40427396 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
40427416 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
40427435 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Done.