Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 136 of 199
Found at i:41212284 original size:79 final size:79
Alignment explanation
Indices: 41212189--41212336 Score: 190
Period size: 79 Copynumber: 1.9 Consensus size: 79
41212179 ACGCACATAC
* * * *
41212189 GTGCCCTGTTTGTACTTTGATACCCCTGAATGCACACACGTG-CCCTATCTTTACTTCGACACCC
1 GTGCCCTGTTTGTACTTCGATACACCTGAATGCACACACGTGCCCCTATATGTACTTCGACACCC
41212253 CTGATTGCACACGT
66 CTGATTGCACACGT
* * * * **
41212267 GTGCCCATGTTTGTACTTCGGTACACTTGATTGCACATACGTGCCCCTATATGTACTTCGGTACC
1 GTGCCC-TGTTTGTACTTCGATACACCTGAATGCACACACGTGCCCCTATATGTACTTCGACACC
41212332 CCTGA
65 CCTGA
41212337 ACACATTTAC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
78 6 0.10
79 30 0.52
80 22 0.38
ACGTcount: A:0.19, C:0.31, G:0.18, T:0.32
Consensus pattern (79 bp):
GTGCCCTGTTTGTACTTCGATACACCTGAATGCACACACGTGCCCCTATATGTACTTCGACACCC
CTGATTGCACACGT
Found at i:41212298 original size:40 final size:40
Alignment explanation
Indices: 41212136--41212330 Score: 115
Period size: 39 Copynumber: 4.9 Consensus size: 40
41212126 AATATTTGTA
* * * * * *
41212136 TGATTGCACATATGTGCCCCTATTTGTACTTCAGTACCCT
1 TGATTGCACACACGTGCCCATATATGTACTTCGGTACACT
* ** * * * * * * *
41212176 TAAACGCACATACGTGCCC-TGTTTGTACTTTGATACCCC
1 TGATTGCACACACGTGCCCATATATGTACTTCGGTACACT
* * * ** * *
41212215 TGAATGCACACACGTGCCC-TATCTTTACTTCGACACCCC
1 TGATTGCACACACGTGCCCATATATGTACTTCGGTACACT
** * *
41212254 TGATTGCACACGTGTGCCCATGTTTGTACTTCGGTACACT
1 TGATTGCACACACGTGCCCATATATGTACTTCGGTACACT
* *
41212294 TGATTGCACATACGTGCCCCTATATGTACTTCGGTAC
1 TGATTGCACACACGTGCCCATATATGTACTTCGGTAC
41212331 CCCTGAACAC
Statistics
Matches: 121, Mismatches: 33, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
39 62 0.51
40 59 0.49
ACGTcount: A:0.21, C:0.30, G:0.17, T:0.32
Consensus pattern (40 bp):
TGATTGCACACACGTGCCCATATATGTACTTCGGTACACT
Found at i:41214043 original size:15 final size:16
Alignment explanation
Indices: 41214017--41214054 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
41214007 TTTTTATAGA
41214017 ATTTTCTATAAT-TTCT
1 ATTTT-TATAATATTCT
*
41214033 ATTTTTATAATATTTT
1 ATTTTTATAATATTCT
41214049 ATTTTT
1 ATTTTT
41214055 TCATAACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTTATAATATTCT
Found at i:41214181 original size:19 final size:19
Alignment explanation
Indices: 41214159--41214202 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
41214149 ATTTTAAAAT
41214159 TTTTATAATATTGTAATAA
1 TTTTATAATATTGTAATAA
41214178 TTTTATAATATTGTAATAA
1 TTTTATAATATTGTAATAA
41214197 TGTTTA
1 T-TTTA
41214203 GGCTTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (19 bp):
TTTTATAATATTGTAATAA
Found at i:41215367 original size:81 final size:82
Alignment explanation
Indices: 41215216--41215375 Score: 214
Period size: 81 Copynumber: 2.0 Consensus size: 82
41215206 TTTTTCTTGG
** *
41215216 TTTTTGTTAAAATAAAAAGACTAAAATACCCTCAAATAATATGACTCATTTTAATTACGAATGGG
1 TTTTTGTTAAAATAAAAAGACTAAAATACCCTCAAATAATATGACTCATTTTAATTACGAAAAGA
*
41215281 TATTTTCGTAATTTCCT
66 CATTTTCGTAATTTCCT
* * * * * *
41215298 TTTTTGTTAAAATGAAAATATTAAAATA-CTTCAAATAATATGACTCATTTTAATTATGAAAATA
1 TTTTTGTTAAAATAAAAAGACTAAAATACCCTCAAATAATATGACTCATTTTAATTACGAAAAGA
*
41215362 CATTTTCTTAATTT
66 CATTTTCGTAATTT
41215376 TTTAATCAAG
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
81 42 0.63
82 25 0.37
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (82 bp):
TTTTTGTTAAAATAAAAAGACTAAAATACCCTCAAATAATATGACTCATTTTAATTACGAAAAGA
CATTTTCGTAATTTCCT
Found at i:41216023 original size:22 final size:22
Alignment explanation
Indices: 41215995--41216039 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
41215985 TTATGTTGAT
*
41215995 TCATAGAGCTGATTTCTAGGGA
1 TCATAGAACTGATTTCTAGGGA
* *
41216017 TCATAGAATTGATTTGTAGGGA
1 TCATAGAACTGATTTCTAGGGA
41216039 T
1 T
41216040 TTGGTTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.09, G:0.27, T:0.36
Consensus pattern (22 bp):
TCATAGAACTGATTTCTAGGGA
Found at i:41216053 original size:23 final size:23
Alignment explanation
Indices: 41216024--41216077 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
41216014 GGATCATAGA
* * *
41216024 ATTGATTTGTAGGGATTTGGTTT
1 ATTGATTTGCAAGGATTTGGTTC
41216047 ATTGATTTGCAAGGATTTGGTTC
1 ATTGATTTGCAAGGATTTGGTTC
41216070 ATTGATTT
1 ATTGATTT
41216078 CTTTCCTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.20, C:0.04, G:0.26, T:0.50
Consensus pattern (23 bp):
ATTGATTTGCAAGGATTTGGTTC
Found at i:41220273 original size:22 final size:22
Alignment explanation
Indices: 41220245--41220289 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
41220235 ACAGTTAGAT
*
41220245 TCATAGAGCTGATTTGTAGGGA
1 TCATAGAACTGATTTGTAGGGA
*
41220267 TCATAGAATTGATTTGTAGGGA
1 TCATAGAACTGATTTGTAGGGA
41220289 T
1 T
41220290 TTTTTTCTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (22 bp):
TCATAGAACTGATTTGTAGGGA
Found at i:41220428 original size:6 final size:6
Alignment explanation
Indices: 41220417--41220490 Score: 148
Period size: 6 Copynumber: 12.3 Consensus size: 6
41220407 TTTGATGCTA
41220417 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
41220465 ATACAT ATACAT ATACAT ATACAT AT
1 ATACAT ATACAT ATACAT ATACAT AT
41220491 GTTGGAATCC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
ATACAT
Found at i:41220531 original size:32 final size:32
Alignment explanation
Indices: 41220490--41220552 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
41220480 CATATACATA
41220490 TGTTGGAATCCCTATAATTAAGGATAGAAATT
1 TGTTGGAATCCCTATAATTAAGGATAGAAATT
*
41220522 TGTTGGAATCCCTATAATTAATGATAGAAAT
1 TGTTGGAATCCCTATAATTAAGGATAGAAAT
41220553 CTTACCTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTTGGAATCCCTATAATTAAGGATAGAAATT
Found at i:41229308 original size:17 final size:17
Alignment explanation
Indices: 41229286--41229318 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41229276 TTTCATAAAT
*
41229286 AATGGTGCATTTGAAAG
1 AATGGTGCAATTGAAAG
41229303 AATGGTGCAATTGAAA
1 AATGGTGCAATTGAAA
41229319 TTTATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.27, T:0.27
Consensus pattern (17 bp):
AATGGTGCAATTGAAAG
Found at i:41230288 original size:8 final size:8
Alignment explanation
Indices: 41230275--41230304 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
41230265 ACTTATTTCA
41230275 TTTTTTAT
1 TTTTTTAT
41230283 TTTTTTAT
1 TTTTTTAT
41230291 TTTTTTAT
1 TTTTTTAT
41230299 TTTTTT
1 TTTTTT
41230305 GTCCTTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTAT
Found at i:41231549 original size:6 final size:6
Alignment explanation
Indices: 41231540--41231571 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
41231530 TTATGTTCTA
41231540 TTTATT TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TT
41231572 CCTTTATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:41243611 original size:19 final size:18
Alignment explanation
Indices: 41243569--41243613 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
41243559 TTATTAGGAA
*
41243569 AGAATGGAGAAGAGAAAG
1 AGAATGGGGAAGAGAAAG
*
41243587 AAAATGGGGAAGAAGAAAG
1 AGAATGGGGAAG-AGAAAG
*
41243606 GGAATGGG
1 AGAATGGG
41243614 AGTTTGCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.42, T:0.07
Consensus pattern (18 bp):
AGAATGGGGAAGAGAAAG
Found at i:41245983 original size:2 final size:2
Alignment explanation
Indices: 41245976--41246037 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
41245966 NNNNNNNNAG
** *
41245976 TA TA TA TA TA TA CG TA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41246018 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
41246038 ATAAACATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:41254152 original size:13 final size:13
Alignment explanation
Indices: 41254134--41254197 Score: 110
Period size: 13 Copynumber: 4.9 Consensus size: 13
41254124 AGTTCTTCAT
41254134 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
41254147 TGCTTTTCAGAAG
1 TGCTTTTGAGAAG
41254160 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
41254173 TGCTTTTCAGAAG
1 TGCTTTTGAGAAG
41254186 TGCTTTTGAGAA
1 TGCTTTTGAGAA
41254198 ATTTGAGTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.23, C:0.11, G:0.27, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:41254163 original size:26 final size:26
Alignment explanation
Indices: 41254134--41254197 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
41254124 AGTTCTTCAT
41254134 TGCTTTTGAGAAGTGCTTTTCAGAAG
1 TGCTTTTGAGAAGTGCTTTTCAGAAG
41254160 TGCTTTTGAGAAGTGCTTTTCAGAAG
1 TGCTTTTGAGAAGTGCTTTTCAGAAG
41254186 TGCTTTTGAGAA
1 TGCTTTTGAGAA
41254198 ATTTGAGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.23, C:0.11, G:0.27, T:0.39
Consensus pattern (26 bp):
TGCTTTTGAGAAGTGCTTTTCAGAAG
Found at i:41258078 original size:19 final size:19
Alignment explanation
Indices: 41258014--41258141 Score: 68
Period size: 19 Copynumber: 6.7 Consensus size: 19
41258004 AAAATTATTA
*
41258014 TTTTTAAAATTTTTA-ATT
1 TTTTTAAAATTTTTATAAT
* * *
41258032 TTATTTATATACTCTTTAGAATT
1 TT-TTTA-A-AATTTTTATAA-T
41258055 TTTTTAAAATTTTTATAAT
1 TTTTTAAAATTTTTATAAT
**
41258074 TTTTTAAAA--AATATAA-
1 TTTTTAAAATTTTTATAAT
* **
41258090 ATTTTGGAATTTTTATAAT
1 TTTTTAAAATTTTTATAAT
**
41258109 TATTTT-AAATTTAAATAAT
1 T-TTTTAAAATTTTTATAAT
41258128 TATTTTAAAATTTT
1 T-TTTTAAAATTTT
41258142 GAACATTATT
Statistics
Matches: 82, Mismatches: 18, Indels: 18
0.69 0.15 0.15
Matches are distributed among these distances:
16 6 0.07
17 5 0.06
18 7 0.09
19 30 0.37
20 19 0.23
21 7 0.09
22 5 0.06
23 3 0.04
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTTAAAATTTTTATAAT
Found at i:41262475 original size:74 final size:73
Alignment explanation
Indices: 41262354--41262529 Score: 259
Period size: 74 Copynumber: 2.4 Consensus size: 73
41262344 TTACGTAAAT
* *
41262354 AATACAAAGTTTATTATTTAAATTACAAAAAACCCTAAAATTAATAACTGAAATGG-CAAAAAAG
1 AATACAAAG-TTA-TATTTAAATTACAAAAAACCCTAAAATTAATAACTAAAATGGAAAAAAAAG
41262418 TCATTACATA
64 TCATTACATA
*
41262428 AATACAAAGTTGACTATTTAAATTACAAAAATCCCTAAAATTAATAACTAAAATGGAAAAAAAAA
1 AATACAAAGTT-A-TATTTAAATTACAAAAAACCCTAAAATTAATAACTAAAATGG-AAAAAAAA
41262493 GTCATTACATA
63 GTCATTACATA
41262504 AATACAAAG-T-TATTTAAATTACAAAA
1 AATACAAAGTTATATTTAAATTACAAAA
41262530 CCGCCTAAAA
Statistics
Matches: 95, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
72 16 0.17
73 2 0.02
74 50 0.53
75 1 0.01
76 26 0.27
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (73 bp):
AATACAAAGTTATATTTAAATTACAAAAAACCCTAAAATTAATAACTAAAATGGAAAAAAAAGTC
ATTACATA
Found at i:41264941 original size:103 final size:101
Alignment explanation
Indices: 41264815--41265290 Score: 483
Period size: 97 Copynumber: 4.9 Consensus size: 101
41264805 AGTTACATTA
*
41264815 TAAAAAATTTACATTAATGAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAACCT
1 TAAAAAA-TTACATTAATAAAAAATCACAAAACACTAAACTAAACACTAACAA-TT-TATAACCT
41264880 AATCATAAATTACTAACAAAATAACTATAAAATTATTTT
63 AATCATAAATTACTAACAAAATAACTATAAAATTATTTT
* * **
41264919 TAAAAAATTACATTATTAAAAAATTACAAAATC-CTAAACTAAACACTAACAATTTATAAAATAA
1 TAAAAAATTACATTAATAAAAAATCACAAAA-CACTAAACTAAACACTAACAATTTATAACCTAA
* * * * *
41264983 TCATAAATTATTAAAAAAATAACTACAACATT-TTTAAA
65 TCATAAATTACTAACAAAATAACTATAAAATTATTT--T
* * * *
41265021 AAAAAAATTACATTACTGATAAATCACAAAACAC---A--AAACACTAACAATTTATAACCTAAT
1 TAAAAAATTACATTAATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATAACCTAAT
41265081 CATAAATTACTAACAAAATAACTATAAAATTATTTTT
66 CATAAATTACTAACAAAATAACTATAAAATTA-TTTT
* * * *
41265118 TTAAAATTTACATTACTAAAAAATCACAAAACAC---A--AAACATTAACAATTTATAACCTAAT
1 TAAAAAATTACATTAATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATAACCTAAT
*
41265178 CATAAATTAATAACAAAATAA-T-TAACAA--A----
66 CATAAATTACTAACAAAATAACTATAA-AATTATTTT
* * * * * *
41265207 -ATAAATTTACATTAATAAAAAATCAAAAAATACTAAACTAAACAC-AACAATTTAGAACATAAT
1 TAAAAAATTACATTAATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATAACCTAAT
* *
41265270 CCTAAATTACTACCAAAATAA
66 CATAAATTACTAACAAAATAA
41265291 TTTTAAACTA
Statistics
Matches: 320, Mismatches: 40, Indels: 36
0.81 0.10 0.09
Matches are distributed among these distances:
88 28 0.09
91 1 0.00
92 34 0.11
93 5 0.02
94 1 0.00
95 3 0.01
96 3 0.01
97 124 0.39
99 4 0.01
100 3 0.01
101 37 0.12
102 29 0.09
103 40 0.12
104 8 0.03
ACGTcount: A:0.57, C:0.14, G:0.01, T:0.28
Consensus pattern (101 bp):
TAAAAAATTACATTAATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATAACCTAAT
CATAAATTACTAACAAAATAACTATAAAATTATTTT
Found at i:41265840 original size:17 final size:17
Alignment explanation
Indices: 41265800--41265850 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
41265790 CGATATATAT
*
41265800 ATATATTTTTAAAAATA
1 ATATATTTTTAAAAAAA
41265817 ATATATTTTTATAAAAAA
1 ATATATTTTTA-AAAAAA
*
41265835 AT-TA-TTATAAAAAAA
1 ATATATTTTTAAAAAAA
41265850 A
1 A
41265851 GTGTTGGTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 7 0.23
16 4 0.13
17 13 0.42
18 7 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATATTTTTAAAAAAA
Found at i:41275391 original size:17 final size:15
Alignment explanation
Indices: 41275357--41275385 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41275347 GCTTTAGTGG
41275357 TTGATAATGCCACAT
1 TTGATAATGCCACAT
41275372 TTGATAATGCCACA
1 TTGATAATGCCACA
41275386 CATTTGTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (15 bp):
TTGATAATGCCACAT
Found at i:41276909 original size:51 final size:51
Alignment explanation
Indices: 41276833--41276938 Score: 212
Period size: 51 Copynumber: 2.1 Consensus size: 51
41276823 TCAGAAACTA
41276833 GCACAATAAAGGGAGTATGCAGGAAAAGGGTGCATGTGTGAAAATAGTAGT
1 GCACAATAAAGGGAGTATGCAGGAAAAGGGTGCATGTGTGAAAATAGTAGT
41276884 GCACAATAAAGGGAGTATGCAGGAAAAGGGTGCATGTGTGAAAATAGTAGT
1 GCACAATAAAGGGAGTATGCAGGAAAAGGGTGCATGTGTGAAAATAGTAGT
41276935 GCAC
1 GCAC
41276939 GTTGTATGAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.39, C:0.09, G:0.33, T:0.19
Consensus pattern (51 bp):
GCACAATAAAGGGAGTATGCAGGAAAAGGGTGCATGTGTGAAAATAGTAGT
Found at i:41285610 original size:14 final size:15
Alignment explanation
Indices: 41285576--41285613 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
41285566 GGTTTTTGTA
41285576 ATAATAAAATAAAAG
1 ATAATAAAATAAAAG
* *
41285591 ATAATAACATAAAGG
1 ATAATAAAATAAAAG
41285606 A-AATAAAA
1 ATAATAAAA
41285614 GTTCAAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (15 bp):
ATAATAAAATAAAAG
Found at i:41289616 original size:8 final size:8
Alignment explanation
Indices: 41289605--41289629 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
41289595 ACTTTCATAA
41289605 TTTCACTT
1 TTTCACTT
41289613 TTTCACTT
1 TTTCACTT
41289621 TTTCACTT
1 TTTCACTT
41289629 T
1 T
41289630 CAATCACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTCACTT
Found at i:41289717 original size:23 final size:22
Alignment explanation
Indices: 41289674--41289717 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
41289664 TTCTAAGTCG
41289674 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
41289697 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
41289718 TTAGTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:41289821 original size:45 final size:45
Alignment explanation
Indices: 41289763--41289855 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 45
41289753 ACAGATACTT
* * *
41289763 GGTGGATTAAGCACATAGCAACCACTTTATTAATCAATGATGTCC
1 GGTGGAATAAGCACATAGCAACCACCTTACTAATCAATGATGTCC
* *
41289808 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTTC
1 GGTGGAATAAGCACATAGCAACCACCTTACTAATCAATGATGTCC
41289853 GGT
1 GGT
41289856 TCACATAGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (45 bp):
GGTGGAATAAGCACATAGCAACCACCTTACTAATCAATGATGTCC
Found at i:41289919 original size:51 final size:50
Alignment explanation
Indices: 41289861--41290043 Score: 188
Period size: 51 Copynumber: 3.6 Consensus size: 50
41289851 TCGGTTCACA
* * * *
41289861 TAGTAGCCTGCACATAGTAGTACACATGTGACCATTACCATCCGATATACG
1 TAGTAGCCTACACATAGTACTACACACGTGACCA-TACCATCCGGTATACG
* * * * * *
41289912 TAGTAGCCTACACATAGTACTACATACGTGATCGAAACTATCCGGTATGCA
1 TAGTAGCCTACACATAGTACTACACACGTGA-CCATACCATCCGGTATACG
* * * *
41289963 TAGTAGCCTACACATAGTACTACACATGCGACC-TATCATTCCGGTACACG
1 TAGTAGCCTACACATAGTACTACACACGTGACCATACCA-TCCGGTATACG
**
41290013 TAGTAGCCTGGACATAGTACTACACACGTGA
1 TAGTAGCCTACACATAGTACTACACACGTGA
41290044 TCATCACTTT
Statistics
Matches: 106, Mismatches: 24, Indels: 5
0.79 0.18 0.04
Matches are distributed among these distances:
49 2 0.02
50 36 0.34
51 66 0.62
52 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTACACATAGTACTACACACGTGACCATACCATCCGGTATACG
Found at i:41290042 original size:101 final size:101
Alignment explanation
Indices: 41289859--41290045 Score: 268
Period size: 101 Copynumber: 1.8 Consensus size: 101
41289849 GTTCGGTTCA
* * * *
41289859 CATAGTAGCCTGCACATAGTAGTACACATGTGACCATTACCATCCGATATACGTAGTAGCCTACA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTACA
*
41289924 CATAGTACTACATACGTGATCGAAACTATCCGGTATG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTATG
* * **
41289961 CATAGTAGCCTACACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTGGA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTACA
41290025 CATAGTACTACACACGTGATC
65 CATAGTACTACACACGTGATC
41290046 ATCACTTTCA
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
100 4 0.05
101 39 0.52
102 32 0.43
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTACACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTACAC
ATAGTACTACACACGTGATCGAAACTATCCGGTATG
Found at i:41302893 original size:20 final size:22
Alignment explanation
Indices: 41302865--41302906 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
41302855 AATTTAGCCA
*
41302865 TTTATTTTAATT-TTA-ATTTT
1 TTTAATTTAATTGTTACATTTT
41302885 TTTAATTTAATTGTTACATTTT
1 TTTAATTTAATTGTTACATTTT
41302907 AATTTTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 3 0.16
22 5 0.26
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTAATTTAATTGTTACATTTT
Found at i:41302927 original size:29 final size:28
Alignment explanation
Indices: 41302865--41302931 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 28
41302855 AATTTAGCCA
41302865 TTTATT-TTA-ATTTTAATTTTTTTAAT
1 TTTATTGTTACATTTTAATTTTTTTAAT
* *
41302891 TTAATTGTTACATTTTAATTTTTCTTATT
1 TTTATTGTTACATTTTAATTTTT-TTAAT
41302920 TTTATTGTTACA
1 TTTATTGTTACA
41302932 GGTTCTTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.14
27 3 0.09
28 12 0.34
29 15 0.43
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.67
Consensus pattern (28 bp):
TTTATTGTTACATTTTAATTTTTTTAAT
Found at i:41306309 original size:22 final size:22
Alignment explanation
Indices: 41306244--41306327 Score: 73
Period size: 27 Copynumber: 3.6 Consensus size: 22
41306234 CTGAACTATC
41306244 TTTATTTTATTGTTATT-TGT-T
1 TTTATTTTATT-TTATTATGTAT
41306265 TTTATTTTATTTTCCAAACTTATGTAT
1 TTTATTTTATTTT----A-TTATGTAT
* *
41306292 TTTATTTTATTTTATTATGCAC
1 TTTATTTTATTTTATTATGTAT
41306314 TTTATTATTATTTT
1 TTTATT-TTATTTT
41306328 TTCGAATTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
20 2 0.04
21 11 0.21
22 12 0.23
23 8 0.15
24 1 0.02
25 2 0.04
26 3 0.06
27 14 0.26
ACGTcount: A:0.21, C:0.06, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTATTTTATTTTATTATGTAT
Found at i:41308575 original size:49 final size:49
Alignment explanation
Indices: 41308503--41308617 Score: 169
Period size: 49 Copynumber: 2.3 Consensus size: 49
41308493 CTACACGAGC
* * * *
41308503 TGAACGATTTCACATGGCCATACCACACGGTCGTGTGATCC-ACATAGGT
1 TGAACCATTCCACATGGCCATACCACACAGTCGTGTGA-CCAACACAGGT
*
41308552 TGAACTATTCCACATGGCCATACCACACAGTCGTGTGACCAACACAGGT
1 TGAACCATTCCACATGGCCATACCACACAGTCGTGTGACCAACACAGGT
41308601 TGAACCATTCCACATGG
1 TGAACCATTCCACATGG
41308618 TCGTTGACCT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
48 2 0.03
49 58 0.97
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (49 bp):
TGAACCATTCCACATGGCCATACCACACAGTCGTGTGACCAACACAGGT
Found at i:41313057 original size:151 final size:150
Alignment explanation
Indices: 41312714--41313277 Score: 689
Period size: 151 Copynumber: 3.7 Consensus size: 150
41312704 CAAAATAGTT
* * * *
41312714 AAAAAAATAAAAACTTTATTCTAAAATTTTAAAATTTCATTTAAAATGACTT-AAAAAACATGTT
1 AAAAAAATCAAAACTTTATTTTAAAATTTTAAAATTTCCTTTAAAATGACTTAAAAAAACATATT
* *** *
41312778 TTTATTTTTCAAAATCTAAAATTTCTCTCTCTCTTTTT-TTTAAAACACTGTTTTTCTTAAAGAT
66 TTTATTTTTCAAAATCTAAACTTTCTC-CT-T-TTTTTAAAAAAAACACTATTTTTCTTAAAGAT
41312842 TAAAGCTTTTATTTTGAAGTAGTTTG
128 TAAAGCTTTTATTTT--A-TAGTTTG
* * * *
41312868 ACAAAAATCAAAACTTTGTTTTAAACA-TTTAAACTTTCCTTTAAAATGACTTAAAAAAACAAAT
1 AAAAAAATCAAAACTTTATTTTAAA-ATTTTAAAATTTCCTTTAAAATGACTTAAAAAAACATAT
41312932 TTTTATTTTTCAAAATCTAAACTTTCTCCTTTTTTTAAAAAAAACACTATTTTTCTTAAAAGATT
65 TTTTATTTTTCAAAATCTAAACTTTCTCCTTTTTTTAAAAAAAACACTATTTTTCTT-AAAGATT
*
41312997 AAAGTTTTTATTTTATAGTTTG
129 AAAGCTTTTATTTTATAGTTTG
*
41313019 AAAAAAATCAAAACTTTGTTTTAAAATTTTAAAATTTCCTTTAAAATGAC-TAACAAAAACATAT
1 AAAAAAATCAAAACTTTATTTTAAAATTTTAAAATTTCCTTTAAAATGACTTAA-AAAAACATAT
* *
41313083 TTTTATTTTTCAAAATCTAAACTTTCTCC---TTTTAAAAAAAACCACTATTCTTCTTGAAGATT
65 TTTTATTTTTCAAAATCTAAACTTTCTCCTTTTTTTAAAAAAAA-CACTATTTTTCTTAAAGATT
*
41313145 AAAGCTTTTACTTTGAAATAG-TTG
129 AAAGCTTTTA-TTT--TATAGTTTG
* * * *
41313169 AAAAAAAAATCAAAAATTTATTTTAAAATTTTAAATTTTCCTTTAAAATAACTAAAAAAAACATA
1 --AAAAAAATCAAAACTTTATTTTAAAATTTTAAAATTTCCTTTAAAATGACTTAAAAAAACATA
* * *
41313234 TTTTTACTTGTT-AAAATCTAAACTTTCT-CGTTTTTAAAAAAAAA
64 TTTTTA-TTTTTCAAAATCTAAACTTTCTCCTTTTTTTAAAAAAAA
41313278 TAAAAAATTT
Statistics
Matches: 365, Mismatches: 28, Indels: 34
0.85 0.07 0.08
Matches are distributed among these distances:
148 27 0.07
149 15 0.04
150 7 0.02
151 96 0.26
152 83 0.23
153 23 0.06
154 77 0.21
155 37 0.10
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.42
Consensus pattern (150 bp):
AAAAAAATCAAAACTTTATTTTAAAATTTTAAAATTTCCTTTAAAATGACTTAAAAAAACATATT
TTTATTTTTCAAAATCTAAACTTTCTCCTTTTTTTAAAAAAAACACTATTTTTCTTAAAGATTAA
AGCTTTTATTTTATAGTTTG
Found at i:41313624 original size:3 final size:3
Alignment explanation
Indices: 41313616--41313651 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
41313606 GTAAAAAATG
41313616 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41313652 GTAGTAGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:41317339 original size:20 final size:20
Alignment explanation
Indices: 41317316--41317356 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
41317306 TGAAAAACAC
41317316 ATATAAAAATGAAAAATAAA
1 ATATAAAAATGAAAAATAAA
** *
41317336 ATATGCAAATGAAAAGTAAA
1 ATATAAAAATGAAAAATAAA
41317356 A
1 A
41317357 ACAAAAGCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.68, C:0.02, G:0.10, T:0.20
Consensus pattern (20 bp):
ATATAAAAATGAAAAATAAA
Found at i:41334812 original size:15 final size:15
Alignment explanation
Indices: 41334792--41334826 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
41334782 TTATTGTAAA
41334792 AAAATTTTTGATTTT
1 AAAATTTTTGATTTT
41334807 AAAA-TTTTGATTTT
1 AAAATTTTTGATTTT
41334821 AAAATT
1 AAAATT
41334827 CAATGAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (15 bp):
AAAATTTTTGATTTT
Found at i:41338758 original size:45 final size:45
Alignment explanation
Indices: 41338654--41338784 Score: 147
Period size: 45 Copynumber: 2.9 Consensus size: 45
41338644 GCTATACGCC
* * *
41338654 TAAAAATAAGTAAGACCATAGTTGAAAGATGCTATGGTATCACGA
1 TAAAAATGAGTAAGACTATAGTTGAAAGATGCTATGGCATCACGA
* * * * * *
41338699 TATAATTGAGTAAGACTATGGTTGAACGATGCTATGACATCATGA
1 TAAAAATGAGTAAGACTATAGTTGAAAGATGCTATGGCATCACGA
* *
41338744 TAAAAATGACTAAGA-TCATAGTTGAAAGACGCTATGGCATC
1 TAAAAATGAGTAAGACT-ATAGTTGAAAGATGCTATGGCATC
41338785 CTAGTAGCCC
Statistics
Matches: 69, Mismatches: 16, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
44 1 0.01
45 68 0.99
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (45 bp):
TAAAAATGAGTAAGACTATAGTTGAAAGATGCTATGGCATCACGA
Found at i:41353502 original size:24 final size:23
Alignment explanation
Indices: 41353449--41353502 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
41353439 TCAAAATATA
41353449 AAAAT-ATTATATTAAATGAAAT
1 AAAATAATTATATTAAATGAAAT
41353471 AAACATAATTATATTAATAAT-AAAT
1 AAA-ATAATTATATT-A-AATGAAAT
41353496 AAAATAA
1 AAAATAA
41353503 AAACCTCCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 3 0.11
23 2 0.07
24 12 0.43
25 8 0.29
26 3 0.11
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAATAATTATATTAAATGAAAT
Found at i:41354326 original size:3 final size:3
Alignment explanation
Indices: 41354318--41354347 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
41354308 TAACTTTCCT
41354318 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41354348 ATTCTAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:41366999 original size:19 final size:20
Alignment explanation
Indices: 41366962--41367000 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
41366952 CCAAAAACGT
**
41366962 AAATTTATTTATTTTAATTA
1 AAATTTATTTATTGCAATTA
41366982 AAATTTATTT-TTGCAATTA
1 AAATTTATTTATTGCAATTA
41367001 TTGCCTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (20 bp):
AAATTTATTTATTGCAATTA
Found at i:41368749 original size:2 final size:2
Alignment explanation
Indices: 41368742--41368775 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
41368732 TTTAAAAATA
*
41368742 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41368776 TCGAACTCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41369879 original size:20 final size:21
Alignment explanation
Indices: 41369856--41369901 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
41369846 AAAAAAAGAA
41369856 ATTTTGA-AATTTTAAAAATT
1 ATTTTGATAATTTTAAAAATT
* *
41369876 ATTTTGATTATTTTTAAAATT
1 ATTTTGATAATTTTAAAAATT
41369897 -TTTTG
1 ATTTTG
41369902 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.59
Consensus pattern (21 bp):
ATTTTGATAATTTTAAAAATT
Found at i:41370128 original size:2 final size:2
Alignment explanation
Indices: 41370121--41370159 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
41370111 TACTCATGTA
41370121 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41370160 GATGTATGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41370851 original size:51 final size:51
Alignment explanation
Indices: 41370796--41370898 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
41370786 AATTCCTTCC
* *
41370796 CATAAATCAGCAGAGCATGATTAGTTCCATGCTCAACTAATTTCCTTTTAG
1 CATAAATCAACAGAGAATGATTAGTTCCATGCTCAACTAATTTCCTTTTAG
*
41370847 CATAAATCAACAGAGAATGATTAGTTCCATGCTCAATTAATTTCCTTTTAG
1 CATAAATCAACAGAGAATGATTAGTTCCATGCTCAACTAATTTCCTTTTAG
41370898 C
1 C
41370899 TTTAGCTTGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (51 bp):
CATAAATCAACAGAGAATGATTAGTTCCATGCTCAACTAATTTCCTTTTAG
Found at i:41371529 original size:15 final size:14
Alignment explanation
Indices: 41371506--41371554 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
41371496 TGCAATTGTT
41371506 TTTATTTTATTTTAA
1 TTTATTTTATTTT-A
* *
41371521 TTTACTTTATATTTG
1 TTTATTTTAT-TTTA
*
41371536 TTTATTTTATTTTC
1 TTTATTTTATTTTA
41371550 TTTAT
1 TTTAT
41371555 CAACTAAACC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 8 0.28
15 18 0.62
16 3 0.10
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:41371533 original size:22 final size:21
Alignment explanation
Indices: 41371468--41371554 Score: 65
Period size: 22 Copynumber: 4.0 Consensus size: 21
41371458 TGATTCACCG
*
41371468 ATTTGATTTT-ATTTCTTTA-
1 ATTTTATTTTAATTTCTTTAT
41371487 ATTTTATTTTGCAATTGT-TTT-T
1 ATTTTATTTT--AATT-TCTTTAT
41371509 ATTTTATTTTAATTTACTTTAT
1 ATTTTATTTTAATTT-CTTTAT
*
41371531 ATTTGTTTATTTTATTTTCTTTAT
1 A--T-TTTATTTTAATTTCTTTAT
41371555 CAACTAAACC
Statistics
Matches: 55, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
19 10 0.18
20 4 0.07
21 3 0.05
22 18 0.33
23 1 0.02
24 7 0.13
25 12 0.22
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.70
Consensus pattern (21 bp):
ATTTTATTTTAATTTCTTTAT
Found at i:41375583 original size:12 final size:12
Alignment explanation
Indices: 41375538--41375586 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
41375528 NNNNNNCTTT
41375538 TAAAAGTATATTA
1 TAAAA-TATATTA
*
41375551 TAAAATAAAAGTTA
1 TAAAAT-ATA-TTA
41375565 TTAAAATATATTA
1 -TAAAATATATTA
41375578 TAAAATATA
1 TAAAATATA
41375587 ATTCATCACA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 10 0.32
13 10 0.32
14 5 0.16
15 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (12 bp):
TAAAATATATTA
Found at i:41376963 original size:13 final size:12
Alignment explanation
Indices: 41376933--41376966 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
41376923 AAACTGGACA
41376933 TTTA-TTTATTT
1 TTTATTTTATTT
41376944 TTTATTTTATTT
1 TTTATTTTATTT
41376956 TATTATTTTAT
1 T-TTATTTTAT
41376967 GCATGTGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.19
12 8 0.38
13 9 0.43
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:41377362 original size:41 final size:41
Alignment explanation
Indices: 41377236--41377365 Score: 113
Period size: 41 Copynumber: 3.1 Consensus size: 41
41377226 TCCGGTTGGC
* *
41377236 AAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGAT
1 AAGACTTGATGCGATCTACTCTACTGTAACTTCAGAGAGAT
** * * *
41377277 AAGATCGGTTTCTTCTG-TCTATTCCACTGTAA-TCTCAG-GAAGAT
1 AAGA-C--TTGATGC-GATCTACTCTACTGTAACT-TCAGAG-AGAT
*
41377321 AAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGAT
1 AAGACTTGATGCGATCTACTCTACTGTAACTTCAGAGAGAT
41377362 AAGA
1 AAGA
41377366 TCCTTTATTT
Statistics
Matches: 67, Mismatches: 13, Indels: 18
0.68 0.13 0.18
Matches are distributed among these distances:
40 1 0.01
41 32 0.48
42 3 0.04
43 3 0.04
44 27 0.40
45 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (41 bp):
AAGACTTGATGCGATCTACTCTACTGTAACTTCAGAGAGAT
Found at i:41377388 original size:85 final size:85
Alignment explanation
Indices: 41377236--41377406 Score: 227
Period size: 85 Copynumber: 2.0 Consensus size: 85
41377226 TCCGGTTGGC
* * * * * * *
41377236 AAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCGGTTTCTTCTGTCTATTC
1 AAGACCTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCGCTTTATTCTATCCACTC
41377301 CACTGTAATCTCAGGAAGAT
66 CACTGTAATCTCAGGAAGAT
* * *
41377321 AAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATC-CTTTATTTTAATCCGCT
1 AAGACCTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCGCTTTATTCT-ATCCACT
*
41377385 CCACTGTAATCTCAGGGAGAT
65 CCACTGTAATCTCAGGAAGAT
41377406 A
1 A
41377407 GGATTACTAA
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
84 6 0.08
85 68 0.92
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (85 bp):
AAGACCTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCGCTTTATTCTATCCACTC
CACTGTAATCTCAGGAAGAT
Found at i:41377405 original size:44 final size:44
Alignment explanation
Indices: 41377343--41377677 Score: 184
Period size: 44 Copynumber: 7.5 Consensus size: 44
41377333 GATCTACTCT
41377343 ACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCC
1 ACTGTAATC-TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCC
* * * * * * * *
41377387 ACTGTAATCTCAGGGAGATAGGATTAC-TAACTTCAATCTGCCCC
1 ACTGTAATCTCAGAGAGATAAGA-TCCTTTATTTTAATCCGCTCC
* * * * * * *
41377431 GCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATGCGATCTACTC
1 ACTGTAATCTCAGAGAGATAAGA--TC---CTTTATTTTAATCCG--CT-C-C
41377484 TACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCC
1 -ACTGTAATC-TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCC
* * * * * *
41377529 ACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGCTCC
1 ACTGTAATCTCAGAGAGATAAGATCCT-TTA-TTTTAATCCGCTCC
* * * * * ** *
41377573 GCCGTAATCTCAGAGAGATAAGAT--TTGA-TGTGATCTACTCT
1 ACTGTAATCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCC
*
41377614 ACTGTAA-CTTCAGAGAGATAAGATCCCTTATTTTAATCCGCTCC
1 ACTGTAATC-TCAGAGAGATAAGATCCTTTATTTTAATCCGCTCC
*
41377658 ACTGTAATCTCAGGGAGATA
1 ACTGTAATCTCAGAGAGATA
41377678 GGATTACTAG
Statistics
Matches: 217, Mismatches: 53, Indels: 42
0.70 0.17 0.13
Matches are distributed among these distances:
40 1 0.00
41 28 0.13
42 1 0.00
43 5 0.02
44 129 0.59
45 8 0.04
46 1 0.00
47 2 0.01
48 1 0.00
49 16 0.07
51 1 0.00
52 3 0.01
53 2 0.01
54 19 0.09
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (44 bp):
ACTGTAATCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCC
Found at i:41377630 original size:129 final size:129
Alignment explanation
Indices: 41377469--41377701 Score: 448
Period size: 129 Copynumber: 1.8 Consensus size: 129
41377459 GGCTTCAATC
*
41377469 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGT
1 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCCTTATTTTAATCCGCTCCACTGT
41377534 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCCGTAATCTCAGAGAGATAAGATT
66 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCCGTAATCTCAGAGAGATAAGATT
*
41377598 TGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCCTTATTTTAATCCGCTCCACTGT
1 TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCCTTATTTTAATCCGCTCCACTGT
41377663 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCC
66 AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCC
41377702 ACCACTGCCA
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 102 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (129 bp):
TGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCCTTATTTTAATCCGCTCCACTGT
AATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCCGTAATCTCAGAGAGATAAGATT
Found at i:41377701 original size:44 final size:44
Alignment explanation
Indices: 41377519--41377703 Score: 157
Period size: 44 Copynumber: 4.3 Consensus size: 44
41377509 CCTTTATTTT
* * *
41377519 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGAGAGATAAGATTACTAGCTTC
* * *
41377563 AATCTGCTCCGCCGTAATCTCAGAGAGATAAGATT--T-GATGT-
1 AATCTGCTCCACTGTAATCTCAGAGAGATAAGATTACTAGCT-TC
* * * ** * *
41377604 GATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCCTTA-TTTT
1 AATCTGCTCCACTGTAATC-TCAGAGAGATAAGATTAC-TAGCTTC
* * *
41377648 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGAGAGATAAGATTACTAGCTTC
41377692 AATCTGCTCCAC
1 AATCTGCTCCAC
41377704 CACTGCCAGG
Statistics
Matches: 108, Mismatches: 24, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
40 1 0.01
41 29 0.27
42 2 0.02
43 3 0.03
44 72 0.67
45 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGAGAGATAAGATTACTAGCTTC
Found at i:41391511 original size:13 final size:12
Alignment explanation
Indices: 41391481--41391514 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
41391471 AAACTGGACA
41391481 TTTA-TTTATTT
1 TTTATTTTATTT
41391492 TTTATTTTATTT
1 TTTATTTTATTT
41391504 TATTATTTTAT
1 T-TTATTTTAT
41391515 GTATGTAGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.19
12 8 0.38
13 9 0.43
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:41403549 original size:2 final size:2
Alignment explanation
Indices: 41403542--41403569 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41403532 CTCGTAATGT
41403542 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
41403570 ATGATAGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:41412751 original size:23 final size:22
Alignment explanation
Indices: 41412709--41412753 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
41412699 GTTTTAAAAG
41412709 TCGAATTTAATATCTAATTGTA
1 TCGAATTTAATATCTAATTGTA
*
41412731 TCGATTTTATATAT-TATATTGTA
1 TCGAATTTA-ATATCTA-ATTGTA
41412754 CAAAATGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (22 bp):
TCGAATTTAATATCTAATTGTA
Found at i:41422900 original size:26 final size:26
Alignment explanation
Indices: 41422863--41422924 Score: 106
Period size: 26 Copynumber: 2.3 Consensus size: 26
41422853 CAGCCCATTG
*
41422863 GGACAATAAACACGGGGAAGTTTGCCA
1 GGAC-ATAAACACGGGGAAGTCTGCCA
41422890 GGACATAAACACGGGGAAGTCTGCCA
1 GGACATAAACACGGGGAAGTCTGCCA
41422916 GGACATAAA
1 GGACATAAA
41422925 ACATGGAGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 30 0.88
27 4 0.12
ACGTcount: A:0.39, C:0.19, G:0.29, T:0.13
Consensus pattern (26 bp):
GGACATAAACACGGGGAAGTCTGCCA
Found at i:41428390 original size:15 final size:17
Alignment explanation
Indices: 41428367--41428399 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
41428357 CTAATCACAA
41428367 TTAACTTAATT-ATCCT
1 TTAACTTAATTAATCCT
41428383 TTAA-TTAATTAATCCT
1 TTAACTTAATTAATCCT
41428399 T
1 T
41428400 AAGCATGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAACTTAATTAATCCT
Found at i:41435018 original size:41 final size:41
Alignment explanation
Indices: 41434984--41435118 Score: 225
Period size: 41 Copynumber: 3.3 Consensus size: 41
41434974 ACCGGCTTTT
*
41434984 AGCCTGCTAGACTTATAGTTCGAAATGTTTCACCGGCATCA
1 AGCCTGCTAGACTTATAGTCCGAAATGTTTCACCGGCATCA
*
41435025 AGCCTGCTAGATTTATAGTCCGAAATGTTTCACCGGCATCA
1 AGCCTGCTAGACTTATAGTCCGAAATGTTTCACCGGCATCA
* **
41435066 AGCCTGCTAGACTTATAGTCCAAAATGTTTCACTAGCATCA
1 AGCCTGCTAGACTTATAGTCCGAAATGTTTCACCGGCATCA
41435107 AGCCTGCTAGAC
1 AGCCTGCTAGAC
41435119 ATAAAGTCTG
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 88 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCCGAAATGTTTCACCGGCATCA
Found at i:41435283 original size:36 final size:36
Alignment explanation
Indices: 41435243--41435315 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
41435233 TAAAAATTCA
41435243 GCTCAAAATTTATAACCTTTATCTTTGAATCACAGG
1 GCTCAAAATTTATAACCTTTATCTTTGAATCACAGG
41435279 GCTCAAAATTTATAACCTTTATCTTTGAATCACAGG
1 GCTCAAAATTTATAACCTTTATCTTTGAATCACAGG
41435315 G
1 G
41435316 ATATATAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (36 bp):
GCTCAAAATTTATAACCTTTATCTTTGAATCACAGG
Found at i:41435323 original size:30 final size:31
Alignment explanation
Indices: 41435253--41435323 Score: 81
Period size: 36 Copynumber: 2.2 Consensus size: 31
41435243 GCTCAAAATT
*
41435253 TATAACCTTTATCTTTGAATCACAGGGCTCAAAATT
1 TATAACCTTTATCTTTGAATCACAGGG-----AATA
41435289 TATAACCTTTATCTTTGAATCACAGGG-ATA
1 TATAACCTTTATCTTTGAATCACAGGGAATA
41435319 TATAA
1 TATAA
41435324 AGTTCAATCA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
30 7 0.21
36 27 0.79
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (31 bp):
TATAACCTTTATCTTTGAATCACAGGGAATA
Found at i:41435840 original size:2 final size:2
Alignment explanation
Indices: 41435825--41435862 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
41435815 TTCGATCCAA
* *
41435825 AT AT AT AC AA AT AT AT -T AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41435863 CCTTTAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:41436170 original size:2 final size:2
Alignment explanation
Indices: 41436163--41436192 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
41436153 ATAGATTTAC
41436163 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41436193 GTTGATTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41438666 original size:47 final size:47
Alignment explanation
Indices: 41438589--41438724 Score: 191
Period size: 47 Copynumber: 2.9 Consensus size: 47
41438579 AACGGAGGAA
* *
41438589 CTAGTCGGCAGTTCATCTGCTCGACCAGTGGTTTATACACAACATATT
1 CTAGTCGACAG-TCATCTGCTCGACCAGTGGTTTATCCACAACATATT
* * * *
41438637 CTAGTCGACAGTCATCTGCTTGACTAGTGGTTTATCCATAACGTATT
1 CTAGTCGACAGTCATCTGCTCGACCAGTGGTTTATCCACAACATATT
* *
41438684 CTAGTTGACAGTCATTTGCTCGACCAGTGGTTTATCCACAA
1 CTAGTCGACAGTCATCTGCTCGACCAGTGGTTTATCCACAA
41438725 TGCATTAGTA
Statistics
Matches: 77, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
47 67 0.87
48 10 0.13
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (47 bp):
CTAGTCGACAGTCATCTGCTCGACCAGTGGTTTATCCACAACATATT
Found at i:41438853 original size:91 final size:91
Alignment explanation
Indices: 41438693--41438861 Score: 216
Period size: 91 Copynumber: 1.9 Consensus size: 91
41438683 TCTAGTTGAC
* * ** * *
41438693 AGTCATTTGCTCGACCAGTGGTTTATCCACAATGCATTAGTAGCTTTTATTTATACAAGTGGATA
1 AGTCATCTGCTCAACCAGTGGTTTATCCACAACACATTAGCAGCTTTTATTCATACAAGTGGATA
41438758 GTTCATCCACCAATATTCTAATCGGT
66 GTTCATCCACCAATATTCTAATCGGT
* * *
41438784 AGTCATCTGCTCAACTAGTGGTTTATCCACAACATATTAGCAGCTTTTATCTGCATA-GAG-GGA
1 AGTCATCTGCTCAACCAGTGGTTTATCCACAACACATTAGCAGCTTTTAT-T-CATACAAGTGGA
*
41438847 TGGTTCATCCACCAA
64 TAGTTCATCCACCAA
41438862 AATATTTATC
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
91 60 0.91
92 3 0.05
93 3 0.05
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (91 bp):
AGTCATCTGCTCAACCAGTGGTTTATCCACAACACATTAGCAGCTTTTATTCATACAAGTGGATA
GTTCATCCACCAATATTCTAATCGGT
Found at i:41444180 original size:2 final size:2
Alignment explanation
Indices: 41444173--41444197 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41444163 TATAAAAGGA
41444173 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
41444198 AGGAAATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41444626 original size:17 final size:17
Alignment explanation
Indices: 41444604--41444654 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 17
41444594 GTTAATTTTC
41444604 ATAATTTTATATTTT-AA
1 ATAATTTTAT-TTTTAAA
41444621 ATAATTTTAGTTTTTAAA
1 ATAATTTTA-TTTTTAAA
41444639 AGTAATTTTATGTTTT
1 A-TAATTTTAT-TTTT
41444655 TTGAATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 13 0.43
18 5 0.17
19 12 0.40
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
ATAATTTTATTTTTAAA
Found at i:41446321 original size:29 final size:28
Alignment explanation
Indices: 41446257--41446331 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 28
41446247 GTTTTAATTT
*
41446257 TTTTATTTTT-AATTAATAAATATATTA
1 TTTTATTTTTAAATTAATAAATATACTA
*
41446284 TTTTCATTTTTAAATTTTAATTAATA-ACTA
1 TTTT-ATTTTTAAA--TTAATAAATATACTA
*
41446314 TTTTATTTATAAAATTAA
1 TTTTATTT-TTAAATTAA
41446332 ATAATAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
27 4 0.10
28 10 0.25
29 6 0.15
30 11 0.28
31 9 0.22
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTTATTTTTAAATTAATAAATATACTA
Found at i:41448769 original size:2 final size:2
Alignment explanation
Indices: 41448762--41448795 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
41448752 CTGAACCTGA
41448762 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41448796 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41448907 original size:2 final size:2
Alignment explanation
Indices: 41448900--41448933 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
41448890 NNNNNNTAGA
41448900 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41448934 GTTCAAGCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41449844 original size:13 final size:13
Alignment explanation
Indices: 41449826--41449851 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41449816 TTTTATTTAA
41449826 CCTTATAGAATTT
1 CCTTATAGAATTT
41449839 CCTTATAGAATTT
1 CCTTATAGAATTT
41449852 AGAACTGCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
CCTTATAGAATTT
Found at i:41459811 original size:28 final size:28
Alignment explanation
Indices: 41459765--41459828 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
41459755 TTATTCGGTA
* * *
41459765 ACAGT-ACAGTGTGGGCCTTAGTCCGAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
41459792 ACAGTAACAATGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
41459820 ACAGTAACA
1 ACAGTAACA
41459829 GTGCAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 5 0.15
28 28 0.85
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.22
Consensus pattern (28 bp):
ACAGTAACAATGTGGGCCTTAGCCCAAT
Found at i:41459959 original size:23 final size:24
Alignment explanation
Indices: 41459933--41459982 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
41459923 CCAATATTGC
* *
41459933 AGCA-AAGCTGCTAGTAATAGTAT
1 AGCAGAAGCTGCCAGTAACAGTAT
41459956 AGCAGGGAAGCTGCCAGTAACAGTAT
1 AGCA--GAAGCTGCCAGTAACAGTAT
41459982 A
1 A
41459983 TGTGGCAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 4 0.18
26 18 0.82
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.20
Consensus pattern (24 bp):
AGCAGAAGCTGCCAGTAACAGTAT
Found at i:41460274 original size:28 final size:27
Alignment explanation
Indices: 41460174--41460280 Score: 133
Period size: 27 Copynumber: 3.9 Consensus size: 27
41460164 GGTATAACAG
41460174 TCATTTTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
* * *
41460201 TCATTTTACTCTACGAGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
*
41460228 TCATTTTACCCTATGGGGGGTATTTCAA
1 TCATTTTACCCTAT-GGGGGTATTTCGA
* * *
41460256 TCATTTAACCTTATAGGGGTCATTT
1 TCATTTTACCCTATGGGGGT-ATTT
41460281 TACCCTGTAG
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
27 41 0.60
28 27 0.40
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGA
Found at i:41460303 original size:27 final size:27
Alignment explanation
Indices: 41460273--41460334 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
41460263 ACCTTATAGG
41460273 GGTCATTTTACCCTGTAGAGGTATTTT
1 GGTCATTTTACCCTGTAGAGGTATTTT
*
41460300 GGTCATTTTACCCTGTAGGGGTATTTT
1 GGTCATTTTACCCTGTAGAGGTATTTT
41460327 GGTCATTT
1 GGTCATTT
41460335 ATTAACCTCT
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:0.16, C:0.15, G:0.24, T:0.45
Consensus pattern (27 bp):
GGTCATTTTACCCTGTAGAGGTATTTT
Found at i:41464720 original size:41 final size:41
Alignment explanation
Indices: 41464628--41464819 Score: 185
Period size: 41 Copynumber: 4.7 Consensus size: 41
41464618 GATACCACAT
* * **
41464628 CGGCATAAAGCCTGCTAGGTATAAAG-CTTAT-TAGA-ATAC
1 CGGCATAAAGCCTGCTAGGCACAAAGCCAGATAT-GATATAC
*
41464667 ACTGGCATAAAGCCTACTAGGCACAAAGCCAGATATGATATAC
1 -C-GGCATAAAGCCTGCTAGGCACAAAGCCAGATATGATATAC
* * * * *
41464710 CGGCACAAAGCCTGCTAGGCATAAAGCCTGATATGGTACAC
1 CGGCATAAAGCCTGCTAGGCACAAAGCCAGATATGATATAC
* * *
41464751 CGGCATGAAGCCTGCTAGGCATAAAGCCAGATATAAT-TCAC
1 CGGCATAAAGCCTGCTAGGCACAAAGCCAGATATGATAT-AC
* *
41464792 CGGCATAAAGCCTGTTAGGCACAGAGCC
1 CGGCATAAAGCCTGCTAGGCACAAAGCC
41464820 CAAATATCAC
Statistics
Matches: 126, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
40 1 0.01
41 114 0.90
42 6 0.05
43 5 0.04
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.19
Consensus pattern (41 bp):
CGGCATAAAGCCTGCTAGGCACAAAGCCAGATATGATATAC
Found at i:41464769 original size:82 final size:82
Alignment explanation
Indices: 41464628--41464812 Score: 232
Period size: 82 Copynumber: 2.3 Consensus size: 82
41464618 GATACCACAT
* * *
41464628 CGGCATAAAGCCTGCTAGGTATAAAGCTTATTAGAATACACTGGCATAAAGCCTACTAGGCACAA
1 CGGCATAAAGCCTGCTAGGCATAAAGCTGATTAGAATACACCGGCATAAAGCCTACTAGGCACAA
*
41464693 AGCCAGATATGATAT-AC
66 AGCCAGATATAAT-TCAC
* * * * *
41464710 CGGCACAAAGCCTGCTAGGCATAAAGCCTGA-TATG-GTACACCGGCATGAAGCCTGCTAGGCAT
1 CGGCATAAAGCCTGCTAGGCATAAAG-CTGATTA-GAATACACCGGCATAAAGCCTACTAGGCAC
41464773 AAAGCCAGATATAATTCAC
64 AAAGCCAGATATAATTCAC
*
41464792 CGGCATAAAGCCTGTTAGGCA
1 CGGCATAAAGCCTGCTAGGCA
41464813 CAGAGCCCAA
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
81 1 0.01
82 84 0.94
83 4 0.04
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (82 bp):
CGGCATAAAGCCTGCTAGGCATAAAGCTGATTAGAATACACCGGCATAAAGCCTACTAGGCACAA
AGCCAGATATAATTCAC
Found at i:41475224 original size:3 final size:3
Alignment explanation
Indices: 41475216--41475280 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
41475206 ATAAAACGGA
41475216 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
41475264 AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AA
41475281 TGGTACTAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:41493201 original size:50 final size:44
Alignment explanation
Indices: 41493116--41493239 Score: 185
Period size: 50 Copynumber: 2.7 Consensus size: 44
41493106 AGATATTTTG
41493116 GAGGTGAATTAAATTTTGGATAAGTAATTTACGGAGTTATATTA
1 GAGGTGAATTAAATTTTGGATAAGTAATTTACGGAGTTATATTA
*
41493160 GAGGTGAATTAAATTTTGGCAATATTATTAATATTTACGGAGTTATATTA
1 GAGGTGAATTAAATTTTGG--ATA--AGT-A-ATTTACGGAGTTATATTA
41493210 GAGGTGAATTAAATTTTGGATAAGTAATTT
1 GAGGTGAATTAAATTTTGGATAAGTAATTT
41493240 TCATGAGTTA
Statistics
Matches: 72, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
44 23 0.32
45 1 0.01
46 5 0.07
48 5 0.07
49 1 0.01
50 37 0.51
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.40
Consensus pattern (44 bp):
GAGGTGAATTAAATTTTGGATAAGTAATTTACGGAGTTATATTA
Found at i:41493810 original size:3 final size:3
Alignment explanation
Indices: 41493802--41493862 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
41493792 AATGACTAAA
41493802 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41493850 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
41493863 GTACCATCTC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:41497533 original size:21 final size:21
Alignment explanation
Indices: 41497509--41497605 Score: 61
Period size: 21 Copynumber: 4.6 Consensus size: 21
41497499 CCATGAGGGT
*
41497509 TGAACAGAAGCTCACAAGAGC
1 TGAACAGAAGCTCAAAAGAGC
* * * *
41497530 TGAACGGAAAC-CTAAAAGGGT
1 TGAACAGAAGCTC-AAAAGAGC
* *
41497551 TAAACAAAAGCTCAAAAGAGC
1 TGAACAGAAGCTCAAAAGAGC
* * * * * *
41497572 TGAACGGAAACTGATATGAGT
1 TGAACAGAAGCTCAAAAGAGC
41497593 TGAACAGAAGCTC
1 TGAACAGAAGCTC
41497606 GTGAGAGCTA
Statistics
Matches: 52, Mismatches: 22, Indels: 4
0.67 0.28 0.05
Matches are distributed among these distances:
20 1 0.02
21 50 0.96
22 1 0.02
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (21 bp):
TGAACAGAAGCTCAAAAGAGC
Found at i:41497540 original size:42 final size:41
Alignment explanation
Indices: 41497494--41497605 Score: 125
Period size: 42 Copynumber: 2.7 Consensus size: 41
41497484 GTGCTAAATA
*
41497494 GAAACCCATGAGGGTTGAACAGAAGCTCACAAGAGCTGAACG
1 GAAACCCAT-AGGGTTGAACAGAAGCTCAAAAGAGCTGAACG
* * * *
41497536 GAAACCTAAAAGGGTTAAACAAAAGCTCAAAAGAGCTGAACG
1 GAAACC-CATAGGGTTGAACAGAAGCTCAAAAGAGCTGAACG
** *
41497578 GAAACTGATATGAGTTGAACAGAAGCTC
1 GAAACCCATA-GGGTTGAACAGAAGCTC
41497606 GTGAGAGCTA
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 54 0.95
43 1 0.02
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (41 bp):
GAAACCCATAGGGTTGAACAGAAGCTCAAAAGAGCTGAACG
Found at i:41497614 original size:42 final size:42
Alignment explanation
Indices: 41497507--41497605 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 42
41497497 ACCCATGAGG
* *
41497507 GTTGAACAGAAGCTCACAAGAGCTGAACGGAAACCTAAAAGG
1 GTTGAACAGAAGCTCAAAAGAGCTGAACGGAAACCTAAAAGA
* * * *
41497549 GTTAAACAAAAGCTCAAAAGAGCTGAACGGAAA-CTGATATGA
1 GTTGAACAGAAGCTCAAAAGAGCTGAACGGAAACCT-AAAAGA
41497591 GTTGAACAGAAGCTC
1 GTTGAACAGAAGCTC
41497606 GTGAGAGCTA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 2 0.04
42 46 0.96
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.15
Consensus pattern (42 bp):
GTTGAACAGAAGCTCAAAAGAGCTGAACGGAAACCTAAAAGA
Found at i:41499157 original size:26 final size:26
Alignment explanation
Indices: 41499124--41499178 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
41499114 AATTAGGCTA
41499124 AAAATTAATTCAACGTTAGAACTATT
1 AAAATTAATTCAACGTTAGAACTATT
41499150 AAAATTAATTCAACGTTAGAACTATT
1 AAAATTAATTCAACGTTAGAACTATT
41499176 AAA
1 AAA
41499179 TTTGAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (26 bp):
AAAATTAATTCAACGTTAGAACTATT
Found at i:41503035 original size:3 final size:3
Alignment explanation
Indices: 41503029--41503076 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
41503019 ACAACAGTAG
41503029 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
41503077 TGGTACTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:41510878 original size:16 final size:17
Alignment explanation
Indices: 41510857--41510888 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
41510847 AAATATGCAA
41510857 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
41510873 TCACATAACTTCATAT
1 TCACATAACTTCATAT
41510889 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:41511115 original size:43 final size:42
Alignment explanation
Indices: 41511057--41511205 Score: 180
Period size: 43 Copynumber: 3.5 Consensus size: 42
41511047 CAATGCCAAC
*
41511057 GTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCATT
1 GTCCCAGACGTGGTCTTACACGTAATCACATATCGATGCCA-T
*
41511100 GTCCCAGACAG-GGTCTTACACG-AATCAAATA-CGATGCCAAT
1 GTCCCAGAC-GTGGTCTTACACGTAATCACATATCGATGCC-AT
* * *
41511141 GTCCCAGACATGGTCTTACACGTAAACACA-AGTCGATGCCGAC
1 GTCCCAGACGTGGTCTTACACGTAATCACATA-TCGATGCC-AT
41511184 GTCCCAGACGTGGTCTTACACG
1 GTCCCAGACGTGGTCTTACACG
41511206 ATAACATATA
Statistics
Matches: 92, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
41 29 0.32
42 14 0.15
43 48 0.52
44 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (42 bp):
GTCCCAGACGTGGTCTTACACGTAATCACATATCGATGCCAT
Found at i:41511190 original size:84 final size:84
Alignment explanation
Indices: 41511049--41511206 Score: 223
Period size: 84 Copynumber: 1.9 Consensus size: 84
41511039 GACTCGTACA
* * * *
41511049 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCATTGTCCCAGACAG-GG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCATCGTCCCAGAC-GTGG
41511113 TCTTACACGAATCAAATACG
65 TCTTACACGAATCAAATACG
*
41511133 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCGATGCCGA-CGTCCCAGACGTG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATA-TCGATGCC-ATCGTCCCAGACGTG
41511196 GTCTTACACGA
64 GTCTTACACGA
41511207 TAACATATAC
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
83 2 0.03
84 63 0.95
85 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCATCGTCCCAGACGTGGT
CTTACACGAATCAAATACG
Found at i:41532704 original size:44 final size:45
Alignment explanation
Indices: 41532648--41532766 Score: 177
Period size: 50 Copynumber: 2.6 Consensus size: 45
41532638 GATATTTTGA
41532648 AGGTGAATTAAATTTTGGATAAGTA-ATTTACGGAGTTATATTAG
1 AGGTGAATTAAATTTTGGATAAGTATATTTACGGAGTTATATTAG
*
41532692 AGGTGAATTAAATTTTGGCAATATTATTAATATTTACGGAGTTATATTAG
1 AGGTGAATTAAATTTTGG--ATA--AGT-ATATTTACGGAGTTATATTAG
41532742 AGGTGAATTAAATTTTGGATAAGTA
1 AGGTGAATTAAATTTTGGATAAGTA
41532767 GTTTTCATGA
Statistics
Matches: 67, Mismatches: 2, Indels: 11
0.84 0.03 0.14
Matches are distributed among these distances:
44 18 0.27
45 1 0.01
46 5 0.07
48 5 0.07
49 1 0.01
50 37 0.55
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.39
Consensus pattern (45 bp):
AGGTGAATTAAATTTTGGATAAGTATATTTACGGAGTTATATTAG
Found at i:41532954 original size:10 final size:10
Alignment explanation
Indices: 41532935--41532982 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
41532925 AGTTGTATGT
*
41532935 ATTATGTCAA
1 ATTATATCAA
41532945 ATTATATCAA
1 ATTATATCAA
*
41532955 ATTATAATAAA
1 ATTAT-ATCAA
41532966 TATTATATCAA
1 -ATTATATCAA
41532977 ATTATA
1 ATTATA
41532983 ATGAAATANN
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 20 0.61
11 8 0.24
12 5 0.15
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (10 bp):
ATTATATCAA
Found at i:41532973 original size:22 final size:23
Alignment explanation
Indices: 41532945--41532990 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
41532935 ATTATGTCAA
41532945 ATTATATCAAATTATAAT-AAAT
1 ATTATATCAAATTATAATGAAAT
41532967 ATTATATCAAATTATAATGAAAT
1 ATTATATCAAATTATAATGAAAT
41532990 A
1 A
41532991 NNNNNNNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (23 bp):
ATTATATCAAATTATAATGAAAT
Found at i:41533939 original size:43 final size:43
Alignment explanation
Indices: 41533878--41533965 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
41533868 CATTACTAAG
41533878 TGTGAGTCTAGACAAATCCCTATCGCTTAAAAGGGTTGAGATT
1 TGTGAGTCTAGACAAATCCCTATCGCTTAAAAGGGTTGAGATT
41533921 TGTGAGTCTAGACAAATCCCTATCGCTTAAAAGGGTTGAGATT
1 TGTGAGTCTAGACAAATCCCTATCGCTTAAAAGGGTTGAGATT
41533964 TG
1 TG
41533966 GATCCTTGCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Consensus pattern (43 bp):
TGTGAGTCTAGACAAATCCCTATCGCTTAAAAGGGTTGAGATT
Found at i:41545579 original size:41 final size:43
Alignment explanation
Indices: 41545478--41545594 Score: 134
Period size: 41 Copynumber: 2.8 Consensus size: 43
41545468 GACTCGTACA
* * * *
41545478 ATGCCAACGTTCCAGAC-GTGGTCTTACATGTAATCACATATCG
1 ATGCCAATGTGCCAGACAG-GGTCTTACACGTAATCAAATATCG
*
41545521 ATGCCACTGTGCCAGACAGGGTCTTACACG-AATCAAATA-CG
1 ATGCCAATGTGCCAGACAGGGTCTTACACGTAATCAAATATCG
*
41545562 ATGCCAATGT-CCAAGACATGGTCTTACACGTAA
1 ATGCCAATGTGCC-AGACAGGGTCTTACACGTAA
41545595 ACACAAGTCA
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
40 2 0.03
41 27 0.42
42 10 0.16
43 24 0.38
44 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.24
Consensus pattern (43 bp):
ATGCCAATGTGCCAGACAGGGTCTTACACGTAATCAAATATCG
Found at i:41552485 original size:16 final size:17
Alignment explanation
Indices: 41552464--41552495 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
41552454 AAATATGCAA
41552464 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
41552480 TCACATAACTTCATAT
1 TCACATAACTTCATAT
41552496 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:41552722 original size:43 final size:43
Alignment explanation
Indices: 41552656--41552855 Score: 207
Period size: 43 Copynumber: 4.7 Consensus size: 43
41552646 GACTCGTACA
* * * *
41552656 ATGCCAACGTCCCAGACATGGTCTTACATGTAATCACATA-TCG
1 ATGCCGACGTCCCAGACAGGGTCTTACACGTAAACACA-AGTCG
* *
41552699 ATGCC-ATTGTCCCAGACAGGGTCTTACACG-AATCA-AA-TACG
1 ATGCCGA-CGTCCCAGACAGGGTCTTACACGTAAACACAAGT-CG
* * * *
41552740 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACAAGTTG
1 ATGCCGACGTCCCAGACAGGGTCTTACACGTAAACACAAGTCG
*
41552783 ATGCCGACGTCCCAGAC-GTGGTCTTACACGTAAACACAAGTTG
1 ATGCCGACGTCCCAGACAG-GGTCTTACACGTAAACACAAGTCG
41552826 ATGCCGACGTCCCAGAC-GTGGTCTTACACG
1 ATGCCGACGTCCCAGACAG-GGTCTTACACG
41552856 ATAACATATA
Statistics
Matches: 141, Mismatches: 9, Indels: 14
0.86 0.05 0.09
Matches are distributed among these distances:
40 2 0.01
41 30 0.21
42 11 0.08
43 97 0.69
44 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (43 bp):
ATGCCGACGTCCCAGACAGGGTCTTACACGTAAACACAAGTCG
Found at i:41552797 original size:84 final size:86
Alignment explanation
Indices: 41552656--41552855 Score: 241
Period size: 84 Copynumber: 2.3 Consensus size: 86
41552646 GACTCGTACA
* * *
41552656 ATGCCAACGTCCCAGACATGGTCTTACATGTAATCACATATCGATGCCATTGTCCCAGACAG-GG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCATCGTCCCAGAC-GTGG
*
41552720 TCTTACACG-AATCA-AA-TACG
65 TCTTACACGTAAACACAAGT-CG
* *
41552740 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTTGATGCCGA-CGTCCCAGACGTG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATA-TCGATGCC-ATCGTCCCAGACGTG
*
41552803 GTCTTACACGTAAACACAAGTTG
64 GTCTTACACGTAAACACAAGTCG
* *
41552826 ATGCCGACGTCCCAGACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACATGGTCTTACACG
41552856 ATAACATATA
Statistics
Matches: 100, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
83 2 0.02
84 62 0.62
85 5 0.05
86 30 0.30
87 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (86 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCATCGTCCCAGACGTGGT
CTTACACGTAAACACAAGTCG
Found at i:41567515 original size:44 final size:45
Alignment explanation
Indices: 41567459--41567577 Score: 177
Period size: 50 Copynumber: 2.6 Consensus size: 45
41567449 GATATTTTGA
41567459 AGGTGAATTAAATTTTGGATAAGTA-ATTTACGGAGTTATATTAG
1 AGGTGAATTAAATTTTGGATAAGTATATTTACGGAGTTATATTAG
*
41567503 AGGTGAATTAAATTTTGGCAATATTATTAATATTTACGGAGTTATATTAG
1 AGGTGAATTAAATTTTGG--ATA--AGT-ATATTTACGGAGTTATATTAG
41567553 AGGTGAATTAAATTTTGGATAAGTA
1 AGGTGAATTAAATTTTGGATAAGTA
41567578 GTTTTCATGA
Statistics
Matches: 67, Mismatches: 2, Indels: 11
0.84 0.03 0.14
Matches are distributed among these distances:
44 18 0.27
45 1 0.01
46 5 0.07
48 5 0.07
49 1 0.01
50 37 0.55
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.39
Consensus pattern (45 bp):
AGGTGAATTAAATTTTGGATAAGTATATTTACGGAGTTATATTAG
Found at i:41567765 original size:10 final size:10
Alignment explanation
Indices: 41567746--41567793 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
41567736 AGTTGTATGT
*
41567746 ATTATGTCAA
1 ATTATATCAA
41567756 ATTATATCAA
1 ATTATATCAA
*
41567766 ATTATAATAAA
1 ATTAT-ATCAA
41567777 TATTATATCAA
1 -ATTATATCAA
41567788 ATTATA
1 ATTATA
41567794 ATGAAATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 20 0.61
11 8 0.24
12 5 0.15
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (10 bp):
ATTATATCAA
Found at i:41567784 original size:22 final size:23
Alignment explanation
Indices: 41567756--41567802 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
41567746 ATTATGTCAA
41567756 ATTATATCAAATTATAAT-AAAT
1 ATTATATCAAATTATAATGAAAT
41567778 ATTATATCAAATTATAATGAAAT
1 ATTATATCAAATTATAATGAAAT
41567801 AT
1 AT
41567803 AATAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (23 bp):
ATTATATCAAATTATAATGAAAT
Found at i:41567788 original size:32 final size:32
Alignment explanation
Indices: 41567745--41567810 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
41567735 AAGTTGTATG
*
41567745 TATTATGTCAAATTAT-ATCAAATTATAATAAA
1 TATTATATCAAATTATAATCAAA-TATAATAAA
*
41567777 TATTATATCAAATTATAATGAAATATAATAAA
1 TATTATATCAAATTATAATCAAATATAATAAA
41567809 TA
1 TA
41567811 AATAAATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 26 0.84
33 5 0.16
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (32 bp):
TATTATATCAAATTATAATCAAATATAATAAA
Found at i:41568179 original size:3 final size:3
Alignment explanation
Indices: 41568171--41568195 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
41568161 AATGACTAAA
41568171 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
41568196 GTACCATCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:41568755 original size:43 final size:43
Alignment explanation
Indices: 41568694--41568781 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
41568684 CCTTACTAAG
41568694 TGTGAGTCTAGACAAATCCCTATCGCTTAAAAGGGTTGAGATT
1 TGTGAGTCTAGACAAATCCCTATCGCTTAAAAGGGTTGAGATT
41568737 TGTGAGTCTAGACAAATCCCTATCGCTTAAAAGGGTTGAGATT
1 TGTGAGTCTAGACAAATCCCTATCGCTTAAAAGGGTTGAGATT
41568780 TG
1 TG
41568782 GATCCTTGCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Consensus pattern (43 bp):
TGTGAGTCTAGACAAATCCCTATCGCTTAAAAGGGTTGAGATT
Found at i:41573854 original size:21 final size:21
Alignment explanation
Indices: 41573830--41573935 Score: 77
Period size: 21 Copynumber: 5.0 Consensus size: 21
41573820 CCATGAGGGT
41573830 TGAACAGAAGCTCATAAGAGC
1 TGAACAGAAGCTCATAAGAGC
* * * * * *
41573851 TGAACGGAAACCCAAAAGGGT
1 TGAACAGAAGCTCATAAGAGC
* * *
41573872 TAAACAAAAGCTCAAAAGAGC
1 TGAACAGAAGCTCATAAGAGC
* * * * *
41573893 TGAACGGAAACTGATATGAGT
1 TGAACAGAAGCTCATAAGAGC
*
41573914 TGAACAGAAGCTCATGAGAGC
1 TGAACAGAAGCTCATAAGAGC
41573935 T
1 T
41573936 AAATGGAAAG
Statistics
Matches: 58, Mismatches: 27, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.43, C:0.17, G:0.25, T:0.15
Consensus pattern (21 bp):
TGAACAGAAGCTCATAAGAGC
Found at i:41573861 original size:42 final size:41
Alignment explanation
Indices: 41573788--41573944 Score: 143
Period size: 42 Copynumber: 3.8 Consensus size: 41
41573778 GCCCGAAGGC
* * * **
41573788 TGAACAGAAACACATAAGTGCTAAATAGAAACCCATGAGGGT
1 TGAACAGAAGCTCATAAGAGCTAAACGGAAACCCAT-AGGGT
* *
41573830 TGAACAGAAGCTCATAAGAGCTGAACGGAAACCCAAAAGGGT
1 TGAACAGAAGCTCATAAGAGCTAAACGGAAACCC-ATAGGGT
* * * * ** *
41573872 TAAACAAAAGCTCAAAAGAGCTGAACGGAAACTGATATGAGT
1 TGAACAGAAGCTCATAAGAGCTAAACGGAAACCCATA-GGGT
* *
41573914 TGAACAGAAGCTCATGAGAGCTAAATGGAAA
1 TGAACAGAAGCTCATAAGAGCTAAACGGAAA
41573945 GTAAACACGA
Statistics
Matches: 93, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
41 2 0.02
42 90 0.97
43 1 0.01
ACGTcount: A:0.45, C:0.16, G:0.24, T:0.15
Consensus pattern (41 bp):
TGAACAGAAGCTCATAAGAGCTAAACGGAAACCCATAGGGT
Found at i:41578682 original size:3 final size:3
Alignment explanation
Indices: 41578662--41578717 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
41578652 ATAAAACAGA
* * *
41578662 AAC AAC AGC AGC AGC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
41578710 AAC AAC AA
1 AAC AAC AA
41578718 TGGTACTAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.62, C:0.32, G:0.05, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:41586596 original size:3 final size:3
Alignment explanation
Indices: 41586544--41586583 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
41586534 AAAACGGGAC
41586544 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
41586584 GGTACTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:41596101 original size:16 final size:17
Alignment explanation
Indices: 41596080--41596111 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
41596070 AAATATGCAA
41596080 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
41596096 TCACATAACTTCATAT
1 TCACATAACTTCATAT
41596112 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:41596338 original size:43 final size:43
Alignment explanation
Indices: 41596272--41596442 Score: 174
Period size: 43 Copynumber: 4.0 Consensus size: 43
41596262 GACTCGTACA
*
41596272 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCATATATCG
1 ATGCCAACGTCCCAGACAG-GGTCTTACACGTAATCATATATCG
*
41596315 ATGCC-ACTGTCCCAGACAGGGTCTTACACG-AATCAAATA-CG
1 ATGCCAAC-GTCCCAGACAGGGTCTTACACGTAATCATATATCG
* * * * * *
41596356 ATGCCAATGTCCTAGACATGGTCTTACACATAAACACA-AGTCG
1 ATGCCAACGTCCCAGACAGGGTCTTACACGTAATCATATA-TCG
* *
41596399 ATGCCGACGTCCCAGACATGGTCTTACACGATAA-CATATATCG
1 ATGCCAACGTCCCAGACAGGGTCTTACACG-TAATCATATATCG
41596442 A
1 A
41596443 AAATCCTATG
Statistics
Matches: 107, Mismatches: 13, Indels: 16
0.79 0.10 0.12
Matches are distributed among these distances:
41 27 0.25
42 16 0.15
43 59 0.55
44 5 0.05
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACAGGGTCTTACACGTAATCATATATCG
Found at i:41596413 original size:84 final size:84
Alignment explanation
Indices: 41596272--41596429 Score: 212
Period size: 84 Copynumber: 1.9 Consensus size: 84
41596262 GACTCGTACA
* ** * *
41596272 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCATATATCGATGCCACTGTCCCAGACAGGGT
1 ATGCCAACGTCCCAGACATGGTCTTACACATAAACACATATCGATGCCACTGTCCCAGACAGGGT
41596337 CTTACACGAATCAAATACG
66 CTTACACGAATCAAATACG
* * *
41596356 ATGCCAATGTCCTAGACATGGTCTTACACATAAACACA-AGTCGATGCCGAC-GTCCCAGACATG
1 ATGCCAACGTCCCAGACATGGTCTTACACATAAACACATA-TCGATGCC-ACTGTCCCAGACAGG
41596419 GTCTTACACGA
64 GTCTTACACGA
41596430 TAACATATAT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
83 1 0.02
84 61 0.95
85 2 0.03
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATGGTCTTACACATAAACACATATCGATGCCACTGTCCCAGACAGGGT
CTTACACGAATCAAATACG
Found at i:41614047 original size:21 final size:21
Alignment explanation
Indices: 41614023--41614128 Score: 68
Period size: 21 Copynumber: 5.0 Consensus size: 21
41614013 CCATGAGGGT
41614023 TGAACAGAAGCTCATAAGAGC
1 TGAACAGAAGCTCATAAGAGC
* * * * * *
41614044 TGAACGGAAACCCAAAAGGGT
1 TGAACAGAAGCTCATAAGAGC
* * *
41614065 TAAACAAAAGCTCAAAAGAGC
1 TGAACAGAAGCTCATAAGAGC
* * * * * *
41614086 TAAACGGAAACTGATATGAGT
1 TGAACAGAAGCTCATAAGAGC
*
41614107 TGAACAGAAGCTCATGAGAGC
1 TGAACAGAAGCTCATAAGAGC
41614128 T
1 T
41614129 AAATGGAAAG
Statistics
Matches: 58, Mismatches: 27, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (21 bp):
TGAACAGAAGCTCATAAGAGC
Found at i:41614054 original size:42 final size:41
Alignment explanation
Indices: 41613981--41614137 Score: 152
Period size: 42 Copynumber: 3.8 Consensus size: 41
41613971 GCCCGAAGGC
* * * **
41613981 TGAACAGAAACACATAAGTGCTAAATAGAAACCCATGAGGGT
1 TGAACAGAAGCTCATAAGAGCTAAACGGAAACCCAT-AGGGT
* *
41614023 TGAACAGAAGCTCATAAGAGCTGAACGGAAACCCAAAAGGGT
1 TGAACAGAAGCTCATAAGAGCTAAACGGAAACCC-ATAGGGT
* * * ** *
41614065 TAAACAAAAGCTCAAAAGAGCTAAACGGAAACTGATATGAGT
1 TGAACAGAAGCTCATAAGAGCTAAACGGAAACCCATA-GGGT
* *
41614107 TGAACAGAAGCTCATGAGAGCTAAATGGAAA
1 TGAACAGAAGCTCATAAGAGCTAAACGGAAA
41614138 GTAAACACGA
Statistics
Matches: 93, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
41 2 0.02
42 90 0.97
43 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.15
Consensus pattern (41 bp):
TGAACAGAAGCTCATAAGAGCTAAACGGAAACCCATAGGGT
Found at i:41615411 original size:28 final size:28
Alignment explanation
Indices: 41615371--41615429 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
41615361 TTTGAAATTG
41615371 TAATTACACTCTCTACATTGGTATTCAC
1 TAATTACACTCTCTACATTGGTATTCAC
41615399 TAATTACACTCTCTACATTGGTATTCAC
1 TAATTACACTCTCTACATTGGTATTCAC
41615427 TAA
1 TAA
41615430 CTCTCCACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.39
Consensus pattern (28 bp):
TAATTACACTCTCTACATTGGTATTCAC
Found at i:41616069 original size:3 final size:3
Alignment explanation
Indices: 41616061--41616092 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
41616051 ATAAAACGGG
41616061 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
41616093 TAATAATGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:41620178 original size:35 final size:36
Alignment explanation
Indices: 41620118--41620188 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 36
41620108 CAAGTAAGGA
* *
41620118 AGATGATGAAAATGTATGCGCTGATTAGGAAGGTAT
1 AGATGATGAAAATGTATACGCTGATTAGAAAGGTAT
*
41620154 AGATGATG-AAATGTATACGTTGATTAGAAAGGTAT
1 AGATGATGAAAATGTATACGCTGATTAGAAAGGTAT
41620189 CTGCCAATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 24 0.75
36 8 0.25
ACGTcount: A:0.38, C:0.04, G:0.28, T:0.30
Consensus pattern (36 bp):
AGATGATGAAAATGTATACGCTGATTAGAAAGGTAT
Found at i:41620188 original size:19 final size:18
Alignment explanation
Indices: 41620139--41620188 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 18
41620129 ATGTATGCGC
*
41620139 TGATTAGGAAGGTATAGA
1 TGATTAGAAAGGTATAGA
* *
41620157 TGA-T-GAAATGTATACGT
1 TGATTAGAAAGGTATA-GA
41620174 TGATTAGAAAGGTAT
1 TGATTAGAAAGGTAT
41620189 CTGCCAATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
16 8 0.32
17 5 0.20
18 4 0.16
19 8 0.32
ACGTcount: A:0.38, C:0.02, G:0.28, T:0.32
Consensus pattern (18 bp):
TGATTAGAAAGGTATAGA
Found at i:41623714 original size:48 final size:46
Alignment explanation
Indices: 41623658--41623794 Score: 179
Period size: 47 Copynumber: 2.9 Consensus size: 46
41623648 CCCATTTTTA
* *
41623658 TTTAAAATTTTAAAAATTAAAAAGTATTTT-AATATATTTTTAAAATAT
1 TTTAAAATTTAAAAAATTAAAAAGTATTTTAAAAATA-TTTT--AATAT
* *
41623706 TTTTAAATTAAAAAAATTAAAAAAGTATTTTAAAAATATTTTAATAT
1 TTTAAAATTTAAAAAATT-AAAAAGTATTTTAAAAATATTTTAATAT
*
41623753 TTTAAAATTTAAAAAATTAAAAAGTA-TGTAAAAATATTTTAA
1 TTTAAAATTTAAAAAATTAAAAAGTATTTTAAAAATATTTTAA
41623795 ATTAAAAATA
Statistics
Matches: 80, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
45 15 0.19
46 8 0.10
47 21 0.26
48 15 0.19
49 16 0.20
50 5 0.06
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (46 bp):
TTTAAAATTTAAAAAATTAAAAAGTATTTTAAAAATATTTTAATAT
Found at i:41625174 original size:2 final size:2
Alignment explanation
Indices: 41625163--41625202 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
41625153 AACTCATACT
*
41625163 TA TA TA -A TA TA TA TA TA TA TG TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41625203 GATAAATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41625436 original size:28 final size:29
Alignment explanation
Indices: 41625404--41625505 Score: 102
Period size: 28 Copynumber: 3.5 Consensus size: 29
41625394 AATTACCTGT
*
41625404 AAAATTTATTATATATAAAAT-AT-TTTAA
1 AAAATTTAATATA-ATAAAATAATATTTAA
*
41625432 AAAATTAAATATAAT-AAATAATATTTAA
1 AAAATTTAATATAATAAAATAATATTTAA
* * *
41625460 ATAATTTAATATAATGATAAATGATGTTTAA
1 AAAATTTAATATAAT-A-AAATAATATTTAA
*
41625491 ATAATTTAATATAAT
1 AAAATTTAATATAAT
41625506 GATACATGAA
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
26 4 0.06
27 4 0.06
28 29 0.46
31 26 0.41
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (29 bp):
AAAATTTAATATAATAAAATAATATTTAA
Found at i:41625438 original size:50 final size:50
Alignment explanation
Indices: 41625374--41625602 Score: 127
Period size: 50 Copynumber: 4.4 Consensus size: 50
41625364 ATCTTAAATG
** *
41625374 TATTTTAAGTAATTAATATAAATTACCTGTAAAATTTATTATATATAAAA
1 TATTTTAAAAAATTAATATAAATTACATGTAAAATTTATTATATATAAAA
* * * *
41625424 TATTTTAAAAAATTAAATATAATAAATAATATTTAAATAATTTAATATA-ATGATAAA
1 TATTTTAAAAAATT--A-AT-ATAAATTACATGT-AA-AATTTATTATATAT-A-AAA
* * *
41625481 TGATGTTTAAATAATTTAATAT-AATGATACATG-AAACA--TA--A-ATCTTAAA
1 T-AT-TTTAAA-AAATTAATATAAAT--TACATGTAAA-ATTTATTATATATAAAA
*
41625530 TGCATTTTAAATAATTAATATAAATTACCA-GTAAAATTTATTATATATAAAA
1 T--ATTTTAAAAAATTAATATAAATTA-CATGTAAAATTTATTATATATAAAA
41625582 TATTTT-AAAAATTAAATATAA
1 TATTTTAAAAAATT-AATATAA
41625603 TAAAAAGATT
Statistics
Matches: 135, Mismatches: 19, Indels: 50
0.66 0.09 0.25
Matches are distributed among these distances:
47 4 0.03
48 13 0.10
49 21 0.16
50 27 0.20
51 3 0.02
52 8 0.06
53 4 0.03
54 10 0.07
55 10 0.07
56 13 0.10
57 9 0.07
58 3 0.02
59 6 0.04
60 4 0.03
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (50 bp):
TATTTTAAAAAATTAATATAAATTACATGTAAAATTTATTATATATAAAA
Done.