Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 134 of 185
Found at i:41503363 original size:106 final size:102
Alignment explanation
Indices: 41503218--41503515 Score: 347
Period size: 100 Copynumber: 2.9 Consensus size: 102
41503208 CATTTGGATA
41503218 AAGAGATCCCATGTAAGACCATGTTTGGGACATGACATTGGCATCATTGAGATTATGAGAGGTCC
1 AAGAGATCCCATGTAAGACCATGTTTGGGACATGACATTGGCA-CA-TGAGA--ATGAGAGGTCC
*
41503283 CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
62 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* * * * * **
41503324 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC-CGAG-ATGAGAGGTCCCCCG
1 AAGAGATCCCATGTAAGACCATGTTTGGGACATGACATTGGCACATGAGAATGAGAGGTCCCATG
* * *
41503387 TAAGACCATATCTGGGACATGGCATGGGCACCGATAT
66 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* * * * **
41503424 AAGA-ACTCCCATGTAAGACCATATTTGGGATATGACATTGGCA-AT-ACAA-GAAACATCCCAT
1 AAGAGA-TCCCATGTAAGACCATGTTTGGGACATGACATTGGCACATGAGAATGAGAGGTCCCAT
*
41503485 GTAAGACCATGTCTGGGACATGGCTTTGGCA
65 GTAAGACCATGTCTGGGACATGGCATTGGCA
41503516 TGTTATTATC
Statistics
Matches: 162, Mismatches: 27, Indels: 13
0.80 0.13 0.06
Matches are distributed among these distances:
99 36 0.22
100 83 0.51
103 3 0.02
105 1 0.01
106 39 0.24
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.22
Consensus pattern (102 bp):
AAGAGATCCCATGTAAGACCATGTTTGGGACATGACATTGGCACATGAGAATGAGAGGTCCCATG
TAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
Found at i:41505845 original size:21 final size:21
Alignment explanation
Indices: 41505805--41505845 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
41505795 TCAAAGGTAA
*
41505805 ATAAACAATATCATACACTTT
1 ATAAACAATATCATAAACTTT
41505826 ATAAA-AATATCATCAAACTT
1 ATAAACAATATCAT-AAACTT
41505846 ACAACTTCAA
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:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAAACAATATCATAAACTTT
Found at i:41506581 original size:57 final size:58
Alignment explanation
Indices: 41506482--41506607 Score: 166
Period size: 57 Copynumber: 2.2 Consensus size: 58
41506472 AAGGCATCGC
* *
41506482 AACACATCCCTTCTAAACACACCAAAGCGCACCTAAGTGCTAAACCCAAAGGCAAGAG
1 AACACATCCCTTCTAAACACACCAAAGAGCACCTAAGTGCTAAACCCAAAGGCAACAG
* *** *
41506540 ATCACATCCCTTC-AAACACACTTGAGAGCACAC-AAGTGCTAAACCCGAAGGCAACAG
1 AACACATCCCTTCTAAACACACCAAAGAGCAC-CTAAGTGCTAAACCCAAAGGCAACAG
41506597 AACACATCCCT
1 AACACATCCCT
41506608 ATTGGCATGC
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
57 46 0.78
58 13 0.22
ACGTcount: A:0.40, C:0.33, G:0.13, T:0.13
Consensus pattern (58 bp):
AACACATCCCTTCTAAACACACCAAAGAGCACCTAAGTGCTAAACCCAAAGGCAACAG
Found at i:41507443 original size:20 final size:20
Alignment explanation
Indices: 41507420--41507464 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
41507410 AAGATGTTCA
41507420 ATAATCCAATAAGAAATTCT
1 ATAATCCAATAAGAAATTCT
***
41507440 ATAATTTTATAAGAAATTCT
1 ATAATCCAATAAGAAATTCT
41507460 ATAAT
1 ATAAT
41507465 TTTTAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (20 bp):
ATAATCCAATAAGAAATTCT
Found at i:41507464 original size:40 final size:40
Alignment explanation
Indices: 41507388--41507464 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 40
41507378 TTATAATATG
* * **
41507388 ATAAGAGATTCAATAATGTTGTAAGATGTTCAATAATCCA
1 ATAAGAAATTCAATAATGTTATAAGAAATTCAATAATCCA
* * *
41507428 ATAAGAAATTCTATAATTTTATAAGAAATTCTATAAT
1 ATAAGAAATTCAATAATGTTATAAGAAATTCAATAAT
41507465 TTTTAATAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.36
Consensus pattern (40 bp):
ATAAGAAATTCAATAATGTTATAAGAAATTCAATAATCCA
Found at i:41507465 original size:20 final size:20
Alignment explanation
Indices: 41507428--41507467 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
41507418 CAATAATCCA
41507428 ATAAGAAATTCTATAATTTT
1 ATAAGAAATTCTATAATTTT
41507448 ATAAGAAATTCTATAATTTT
1 ATAAGAAATTCTATAATTTT
41507468 TAATAATTTT
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:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
ATAAGAAATTCTATAATTTT
Found at i:41507476 original size:30 final size:30
Alignment explanation
Indices: 41507440--41507496 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
41507430 AAGAAATTCT
*
41507440 ATAATTTTATAA-GAAATTCTATAATTTTTA
1 ATAATTTTA-AAGGAAATTCAATAATTTTTA
*
41507470 ATAATTTTAAAGGAGATTCAATAATTT
1 ATAATTTTAAAGGAAATTCAATAATTT
41507497 ACAAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (30 bp):
ATAATTTTAAAGGAAATTCAATAATTTTTA
Found at i:41508969 original size:11 final size:11
Alignment explanation
Indices: 41508940--41508972 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
41508930 AAAGAAAAAA
*
41508940 TTATAAAATTA
1 TTATAAAATTT
41508951 TT-TAAAATTT
1 TTATAAAATTT
41508961 TTATAAAATTT
1 TTATAAAATTT
41508972 T
1 T
41508973 AACATTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTATAAAATTT
Found at i:41509139 original size:19 final size:19
Alignment explanation
Indices: 41509115--41509170 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
41509105 GTAGATTATG
41509115 AATTTTTTAATTTTTTAAT
1 AATTTTTTAATTTTTTAAT
** *
41509134 AATTTTCGAA-GTTTTAAT
1 AATTTTTTAATTTTTTAAT
*
41509152 -ATTTTTTGAGTTTTTTAAT
1 AATTTTTT-AATTTTTTAAT
41509171 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
17 5 0.18
18 8 0.29
19 15 0.54
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (19 bp):
AATTTTTTAATTTTTTAAT
Found at i:41509166 original size:18 final size:18
Alignment explanation
Indices: 41509116--41509175 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
41509106 TAGATTATGA
* *
41509116 ATTTTTTAATTTTTTAAT
1 ATTTTTTGAGTTTTTAAT
* *
41509134 AATTTTCGAAG-TTTTAAT
1 ATTTTTTG-AGTTTTTAAT
41509152 ATTTTTTGAGTTTTTTAAT
1 ATTTTTTGAG-TTTTTAAT
41509171 -TTTTT
1 ATTTTT
41509176 AAAAACTTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
17 2 0.06
18 23 0.70
19 8 0.24
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.67
Consensus pattern (18 bp):
ATTTTTTGAGTTTTTAAT
Found at i:41516297 original size:40 final size:40
Alignment explanation
Indices: 41516260--41516485 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
41516250 GCTACTCGTT
* *
41516260 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
41516300 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41516340 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** *
41516380 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
** * * * *
41516420 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
41516461 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
41516486 CATCATTCAA
Statistics
Matches: 171, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
39 3 0.02
40 156 0.91
41 12 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:41520332 original size:21 final size:21
Alignment explanation
Indices: 41520307--41520354 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
41520297 CTAAACATGG
*
41520307 CCGTGTGGCTA-TCTCACACAC
1 CCGTGTGACTACTC-CACACAC
41520328 CCGTGTGACTACTCCACACAC
1 CCGTGTGACTACTCCACACAC
41520349 CCGTGT
1 CCGTGT
41520355 ATCCAACCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.19, C:0.40, G:0.19, T:0.23
Consensus pattern (21 bp):
CCGTGTGACTACTCCACACAC
Found at i:41520372 original size:147 final size:147
Alignment explanation
Indices: 41520113--41520401 Score: 479
Period size: 147 Copynumber: 2.0 Consensus size: 147
41520103 ACACGCCGTC
* *
41520113 TGTCCAGAACGTTTGATAGAGCCCAGACCGTATGGCTCCAAACATGGCTGTGTGGTTATCCCACA
1 TGTCCAGAACGTTTGATAGAGCCCAGACCGTATGGCTCCAAACATGGCCGTGTGGCTATCCCACA
* * * **
41520178 CGCCCGTGTGACTACTCCACACACCCATGTGTCCAACCGTGTGCTTACCTGTGTAACTCACTGAC
66 CACCCGTGTGACTACTCCACACACCCATGTATCCAACCGTGTACTTACCCATGTAACTCACTGAC
41520243 TTGGCTCACACGTCATG
131 TTGGCTCACACGTCATG
* * *
41520260 TGTCCAGAACGTTTGATAGAGCCCAGACTGTATGGCTCTAAACATGGCCGTGTGGCTATCTCACA
1 TGTCCAGAACGTTTGATAGAGCCCAGACCGTATGGCTCCAAACATGGCCGTGTGGCTATCCCACA
*
41520325 CACCCGTGTGACTACTCCACACACCCGTGTATCCAACCGTGTACTTACCCATGTAACTCACTGAC
66 CACCCGTGTGACTACTCCACACACCCATGTATCCAACCGTGTACTTACCCATGTAACTCACTGAC
41520390 TTGGCTCACACG
131 TTGGCTCACACG
41520402 CCCGTGTCTC
Statistics
Matches: 131, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
147 131 1.00
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (147 bp):
TGTCCAGAACGTTTGATAGAGCCCAGACCGTATGGCTCCAAACATGGCCGTGTGGCTATCCCACA
CACCCGTGTGACTACTCCACACACCCATGTATCCAACCGTGTACTTACCCATGTAACTCACTGAC
TTGGCTCACACGTCATG
Found at i:41525196 original size:90 final size:89
Alignment explanation
Indices: 41525037--41525288 Score: 233
Period size: 90 Copynumber: 2.8 Consensus size: 89
41525027 ATAAGCTCAT
* * * * * * *
41525037 TGCTCTTAATAAGTTCATAGCCCAGATTTTGGGTGGTCTTGCT-AGGACGGACTTGATGAATTCA
1 TGCTCTTAATGAGTTCATAACCCAG-GTTTGGGTGGTCCTACTGA-GACGAACTTGATGAACTCA
* *
41525101 CCGAATTTATAAGATGAAG-TACTAGA
64 CCGAATTTATAAGAT-AAGCCACTAAA
*
41525127 TGCTCTTAATGAGTTCATAACCCATGGTTTGGGTGGTCCTATTGAGACGAACTTGATGAAC-CTA
1 TGCTCTTAATGAGTTCATAACCCA-GGTTTGGGTGGTCCTACTGAGACGAACTTGATGAACTC-A
* * *
41525191 TCGAATTTATAGGGTAAGCCACTAAA
64 CCGAATTTATAAGATAAGCCACTAAA
* * * * * *
41525217 TGTTCTTAATGAATTCATATCCCAGGCTTTAGGTGGTCCTAGTGAGAC-AGACTTGATGAATTCA
1 TGCTCTTAATGAGTTCATAACCCAGG-TTTGGGTGGTCCTACTGAGACGA-ACTTGATGAACTCA
*
41525281 CTGAATTT
64 CCGAATTT
41525289 TTAAACTGAG
Statistics
Matches: 134, Mismatches: 21, Indels: 14
0.79 0.12 0.08
Matches are distributed among these distances:
89 7 0.05
90 124 0.93
91 3 0.02
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (89 bp):
TGCTCTTAATGAGTTCATAACCCAGGTTTGGGTGGTCCTACTGAGACGAACTTGATGAACTCACC
GAATTTATAAGATAAGCCACTAAA
Found at i:41526167 original size:45 final size:46
Alignment explanation
Indices: 41526116--41526221 Score: 112
Period size: 44 Copynumber: 2.4 Consensus size: 46
41526106 TTTTTAAGTA
*
41526116 TGTATTAATTAGGGTTATAAG-GTTTGTTAAATTATGGTTAATGATT
1 TGTATTAATTAGGGTTATAAGTGTTTGTT-AATTAGGGTTAATGATT
* * * * *
41526162 T-TATT-ATTATGGTCATTAGTGTTTGTTAATTAGGGTTTATGGTT
1 TGTATTAATTAGGGTTATAAGTGTTTGTTAATTAGGGTTAATGATT
*
41526206 TGT-TAAATTAGGGTTA
1 TGTATTAATTAGGGTTA
41526222 ATGATTTTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
44 27 0.56
45 20 0.42
46 1 0.02
ACGTcount: A:0.26, C:0.01, G:0.23, T:0.50
Consensus pattern (46 bp):
TGTATTAATTAGGGTTATAAGTGTTTGTTAATTAGGGTTAATGATT
Found at i:41526206 original size:21 final size:21
Alignment explanation
Indices: 41526120--41526220 Score: 71
Period size: 23 Copynumber: 4.6 Consensus size: 21
41526110 TAAGTATGTA
*
41526120 TTAATTAGGGTTATAAGGTTTG
1 TTAATTAGGGTT-TATGGTTTG
* * *
41526142 TTAAATTATGGTTAATGATTT-
1 TT-AATTAGGGTTTATGGTTTG
* *
41526163 TATTATTATGGTCATTA-GTGTTTG
1 T-TAATTAGGGT--TTATG-GTTTG
41526187 TTAATTAGGGTTTATGGTTTG
1 TTAATTAGGGTTTATGGTTTG
41526208 TTAAATTAGGGTT
1 TT-AATTAGGGTT
41526221 AATGATTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
21 19 0.31
22 20 0.32
23 22 0.35
24 1 0.02
ACGTcount: A:0.26, C:0.01, G:0.23, T:0.50
Consensus pattern (21 bp):
TTAATTAGGGTTTATGGTTTG
Found at i:41526213 original size:66 final size:66
Alignment explanation
Indices: 41526118--41526303 Score: 237
Period size: 66 Copynumber: 2.8 Consensus size: 66
41526108 TTTAAGTATG
* *
41526118 TATTAATTAGGGTTATAAGGTTTGTTAAATTATGGTTAATGATTTTATTATTATGGTCATTAGTG
1 TATTAATTAGGGTT-TAAGGTTTGTTAAATTAAGGTTAATGATTTTATTATTAGGGTCATTAGTG
41526183 TT
65 TT
* * * * **
41526185 TGTTAATTAGGGTTTATGGTTTGTTAAATTAGGGTTAATGATTTTATTATGAGGGTTTTTAGTGT
1 TATTAATTAGGGTTTAAGGTTTGTTAAATTAAGGTTAATGATTTTATTATTAGGGTCATTAGTGT
41526250 T
66 T
* * * * * *
41526251 TATAAATTAAGGTTTAAAGTTTATTAATTTAAGATTAATGATTTTATTATTAG
1 TATTAATTAGGGTTTAAGGTTTGTTAAATTAAGGTTAATGATTTTATTATTAG
41526304 AGTTTTAGGG
Statistics
Matches: 102, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
66 89 0.87
67 13 0.13
ACGTcount: A:0.30, C:0.01, G:0.19, T:0.51
Consensus pattern (66 bp):
TATTAATTAGGGTTTAAGGTTTGTTAAATTAAGGTTAATGATTTTATTATTAGGGTCATTAGTGT
T
Found at i:41526855 original size:36 final size:36
Alignment explanation
Indices: 41526804--41526875 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
41526794 TTTTAGAAGA
*
41526804 ATAGAAGTTCGTAGGGAAGACATAAGTTGGAGCAAT
1 ATAGAAGTTCATAGGGAAGACATAAGTTGGAGCAAT
*
41526840 ATAGAAGTTCATAGGGAAGGCATAAGTTGGAGCAAT
1 ATAGAAGTTCATAGGGAAGACATAAGTTGGAGCAAT
41526876 GGTACTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.39, C:0.08, G:0.31, T:0.22
Consensus pattern (36 bp):
ATAGAAGTTCATAGGGAAGACATAAGTTGGAGCAAT
Found at i:41533248 original size:50 final size:50
Alignment explanation
Indices: 41533145--41533377 Score: 218
Period size: 50 Copynumber: 4.6 Consensus size: 50
41533135 GGGAATGAGA
*
41533145 TCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--TGAG---ATGAGAGG
*
41533201 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGG
* * * * **
41533251 TCCC-TCGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGG
* * * ** * * * **
41533301 TCCCATGTAAGACCATATCTGGGATATGACATTGGCGGT-ACAAGAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGG
*
41533350 TCACATGTAAGACCATGTCTGGGACATG
1 TCCCATGTAAGACCATGTCTGGGACATG
41533378 AATTTGGCAT
Statistics
Matches: 150, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
49 31 0.21
50 78 0.52
51 1 0.01
53 4 0.03
55 1 0.01
56 35 0.23
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGG
Found at i:41533544 original size:22 final size:22
Alignment explanation
Indices: 41533518--41533562 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
41533508 TTATAAGAGT
41533518 TAAGAACATATTCTGTTATCAA
1 TAAGAACATATTCTGTTATCAA
41533540 TAAGAACATATTCTGTTATCAA
1 TAAGAACATATTCTGTTATCAA
41533562 T
1 T
41533563 TGAAAACCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (22 bp):
TAAGAACATATTCTGTTATCAA
Found at i:41539596 original size:16 final size:17
Alignment explanation
Indices: 41539572--41539604 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
41539562 CAAAATCTAA
*
41539572 CCATTTTAACC-TAAAT
1 CCATGTTAACCATAAAT
41539588 CCATGTTAACCATAAAT
1 CCATGTTAACCATAAAT
41539605 GCAAGGGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.33
Consensus pattern (17 bp):
CCATGTTAACCATAAAT
Found at i:41549039 original size:12 final size:12
Alignment explanation
Indices: 41549022--41549053 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
41549012 TACCCAATTA
41549022 AATTAATTCTAT
1 AATTAATTCTAT
41549034 AATTAATTCTAT
1 AATTAATTCTAT
41549046 AATTAATT
1 AATTAATT
41549054 TAATTTAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTAATTCTAT
Found at i:41551739 original size:42 final size:41
Alignment explanation
Indices: 41551685--41551821 Score: 132
Period size: 42 Copynumber: 3.3 Consensus size: 41
41551675 CAGTACACAT
*
41551685 AGTGCATTATCAGACAAGTCGAAGCAAATATACTAGCACGTA
1 AGTGCATCATCAGACAA-TCGAAGCAAATATACTAGCACGTA
* * * *
41551727 AGTGCATCATCAGATGAATTGAAGCAAATATACTAGTACATA
1 AGTGCATCATCAGA-CAATCGAAGCAAATATACTAGCACGTA
* * * * *
41551769 AGTGAATCATC-GAATAAACCAAAACAAATATACTAGCACGTA
1 AGTGCATCATCAG-A-CAATCGAAGCAAATATACTAGCACGTA
*
41551811 AGTACATCATC
1 AGTGCATCATC
41551822 GGATAAACTG
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
41 1 0.01
42 75 0.96
43 2 0.03
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (41 bp):
AGTGCATCATCAGACAATCGAAGCAAATATACTAGCACGTA
Found at i:41553700 original size:17 final size:17
Alignment explanation
Indices: 41553678--41553710 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
41553668 TAATTTCTCA
41553678 TTATTTATTTCTTTTTG
1 TTATTTATTTCTTTTTG
41553695 TTATTTATTTCTTTTT
1 TTATTTATTTCTTTTT
41553711 ATTCCTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.79
Consensus pattern (17 bp):
TTATTTATTTCTTTTTG
Found at i:41556307 original size:20 final size:20
Alignment explanation
Indices: 41556279--41556318 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
41556269 GGGATGATAA
*
41556279 TGATGATTTTAAAATCATTT
1 TGATAATTTTAAAATCATTT
41556299 TGATAATTTTAAAATCATTT
1 TGATAATTTTAAAATCATTT
41556319 GCTGACGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (20 bp):
TGATAATTTTAAAATCATTT
Found at i:41562522 original size:16 final size:16
Alignment explanation
Indices: 41562501--41562533 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
41562491 ACTATAGTGG
*
41562501 AATGAGTTTATGATTA
1 AATGAGTTTATAATTA
41562517 AATGAGTTTATAATTA
1 AATGAGTTTATAATTA
41562533 A
1 A
41562534 TAGTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (16 bp):
AATGAGTTTATAATTA
Found at i:41564946 original size:18 final size:18
Alignment explanation
Indices: 41564925--41564959 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41564915 TTAAAAATTC
*
41564925 ATATTTTTTATTTTTAAT
1 ATATTTTTTAATTTTAAT
41564943 ATATTTTTTAATTTTAA
1 ATATTTTTTAATTTTAA
41564960 AATACATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
ATATTTTTTAATTTTAAT
Found at i:41571584 original size:23 final size:22
Alignment explanation
Indices: 41571533--41571584 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
41571523 CCTCGTCTTT
41571533 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTGTTTCTTTTTCTAAC
*
41571555 -TCATTTTCTTTTCTTTCTTC-AAC
1 TTC-TTTT-GTTTCTTT-TTCTAAC
41571578 TTCTTTT
1 TTCTTTT
41571585 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 4 0.16
23 14 0.56
24 5 0.20
ACGTcount: A:0.10, C:0.21, G:0.02, T:0.67
Consensus pattern (22 bp):
TTCTTTTGTTTCTTTTTCTAAC
Found at i:41571599 original size:18 final size:18
Alignment explanation
Indices: 41571578--41571616 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
41571568 TTTCTTCAAC
* *
41571578 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
41571596 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
41571614 TTC
1 TTC
41571617 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:41581002 original size:7 final size:7
Alignment explanation
Indices: 41580990--41581035 Score: 92
Period size: 7 Copynumber: 6.6 Consensus size: 7
41580980 AGTCGATTGA
41580990 TATTTAG
1 TATTTAG
41580997 TATTTAG
1 TATTTAG
41581004 TATTTAG
1 TATTTAG
41581011 TATTTAG
1 TATTTAG
41581018 TATTTAG
1 TATTTAG
41581025 TATTTAG
1 TATTTAG
41581032 TATT
1 TATT
41581036 ATGTATATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (7 bp):
TATTTAG
Found at i:41581713 original size:18 final size:18
Alignment explanation
Indices: 41581687--41581721 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41581677 AGGTGCGTTT
*
41581687 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
41581705 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
41581722 TCATTTTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:41582184 original size:43 final size:45
Alignment explanation
Indices: 41582128--41582213 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 45
41582118 ATATTTTGAA
*
41582128 TATTTTGAAATTATTTTATGTAA-AAAAAAGAAATTT-TTTGAGT
1 TATTTTGAAATTATTTGATGTAATAAAAAAGAAATTTATTTGAGT
* * *
41582171 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGA
1 TATTTTGAAATTATTTGATGTAATAAAAAAGAAATTTATTTGA
41582214 TGTAATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 21 0.57
44 11 0.30
45 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.48
Consensus pattern (45 bp):
TATTTTGAAATTATTTGATGTAATAAAAAAGAAATTTATTTGAGT
Found at i:41582215 original size:25 final size:25
Alignment explanation
Indices: 41582181--41582293 Score: 123
Period size: 25 Copynumber: 4.7 Consensus size: 25
41582171 TATTTTGATA
41582181 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
41582206 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
** *
41582231 TT-TTTCGA-GT--T-ATTTTG-A-T
1 TTATTT-GATGTAATAAAATAGAAGT
41582250 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
41582276 TTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAA
41582294 ACCCTAACCT
Statistics
Matches: 72, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
19 1 0.01
20 5 0.07
21 8 0.11
22 1 0.01
23 1 0.01
24 8 0.11
25 47 0.65
26 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.44
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:41582248 original size:70 final size:69
Alignment explanation
Indices: 41582138--41582294 Score: 280
Period size: 70 Copynumber: 2.3 Consensus size: 69
41582128 TATTTTGAAA
*
41582138 TTATTTTATGTAA-AAAAAAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAG
1 TTATTTGATGTAATAAAAAAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAG
41582202 AAGT
66 AAGT
*
41582206 TTATTTGATGTAATAAAATAGAAATTTTTTCGAGTTATTTTGATATTATTTGATGTAATAAAATA
1 TTATTTGATGTAATAAAAAAGAAATTTTTT-GAGTTATTTTGATATTATTTGATGTAATAAAATA
41582271 GAAGT
65 GAAGT
41582276 TTATTTGATGTAATAAAAA
1 TTATTTGATGTAATAAAAA
41582295 CCCTAACCTA
Statistics
Matches: 84, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
68 12 0.14
69 15 0.18
70 57 0.68
ACGTcount: A:0.41, C:0.01, G:0.13, T:0.45
Consensus pattern (69 bp):
TTATTTGATGTAATAAAAAAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAG
AAGT
Found at i:41582347 original size:23 final size:23
Alignment explanation
Indices: 41582317--41582682 Score: 200
Period size: 29 Copynumber: 14.5 Consensus size: 23
41582307 TAAAAACCCT
41582317 AAACCCTAACCTAATTTAATTAA
1 AAACCCTAACCTAATTTAATTAA
41582340 AAACCCTAACCTTAACCTAATTTAATTAA
1 AAA--C---CC-TAACCTAATTTAATTAA
41582369 AAACCCTAAACC----TTAACTTAA
1 AAACCCT-AACCTAATTTAA-TTAA
*
41582390 AAACCCTAAACCTTAA-CT--TTAA
1 AAACCCT-AACC-TAATTTAATTAA
41582412 AAACCCTAACCTAATTTAA-TACA
1 AAACCCTAACCTAATTTAATTA-A
*
41582435 AAACTCTAACCTAATTTAATTAA
1 AAACCCTAACCTAATTTAATTAA
41582458 AAACCCTAAACC----TTAACTTAA
1 AAACCCT-AACCTAATTTAA-TTAA
41582479 AAACCCTAACCTAATTTAA-TACA
1 AAACCCTAACCTAATTTAATTA-A
*
41582502 AAACCCTAACCTAAACCTTAATTAA
1 AAACCCTAACCT-AA-TTTAATTAA
41582527 AAACCCTAACCCTAACCTAAATTAATTAA
1 AAACCCTAA-CCTAA--T---TTAATTAA
41582556 AAACCCTAACCCTAACATAAATTAATTAAAA
1 AAACCCTAA-CCT-A-AT---TTAATT--AA
41582587 ACCCTAACCCTAACCTAATTTAATTAAA
1 A----AACCCTAACCTAATTTAATT-AA
41582615 AATCCTACCCCTAACCTAATTTAATTAA
1 AA----A-CCCTAACCTAATTTAATTAA
41582643 AAACCCTAACCCTAACCTAAATTAATTAA
1 AAACCCTAA-CCTAA--T---TTAATTAA
41582672 AAACCCTAACC
1 AAACCCTAACC
41582683 CTAACCCTAA
Statistics
Matches: 286, Mismatches: 6, Indels: 97
0.74 0.02 0.25
Matches are distributed among these distances:
20 15 0.05
21 32 0.11
22 15 0.05
23 49 0.17
24 25 0.09
25 18 0.06
26 7 0.02
27 1 0.00
28 13 0.05
29 92 0.32
30 1 0.00
31 4 0.01
32 2 0.01
33 1 0.00
34 3 0.01
35 8 0.03
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (23 bp):
AAACCCTAACCTAATTTAATTAA
Found at i:41582355 original size:29 final size:30
Alignment explanation
Indices: 41582303--41582385 Score: 150
Period size: 29 Copynumber: 2.8 Consensus size: 30
41582293 AACCCTAACC
*
41582303 TAATTAAAAACCCTAAACCCTAACCTAATT
1 TAATTAAAAACCCTAAACCTTAACCTAATT
41582333 TAATTAAAAACCCT-AACCTTAACCTAATT
1 TAATTAAAAACCCTAAACCTTAACCTAATT
41582362 TAATTAAAAACCCTAAACCTTAAC
1 TAATTAAAAACCCTAAACCTTAAC
41582386 TTAAAAACCC
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 28 0.55
30 23 0.45
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (30 bp):
TAATTAAAAACCCTAAACCTTAACCTAATT
Found at i:41582390 original size:21 final size:21
Alignment explanation
Indices: 41582361--41582487 Score: 120
Period size: 21 Copynumber: 5.9 Consensus size: 21
41582351 TTAACCTAAT
41582361 TTAA-TTAAAAACCCTAAACC
1 TTAACTTAAAAACCCTAAACC
41582381 TTAACTTAAAAACCCTAAACC
1 TTAACTTAAAAACCCTAAACC
41582402 TTAACTTTAAAAACCCT-AACC
1 TTAAC-TTAAAAACCCTAAACC
* *
41582423 -TAATTTAATACAAAACTCT-AACC
1 TTAA-CT--TA-AAAACCCTAAACC
41582446 TAATTTAA-TTAAAAACCCTAAACC
1 ----TTAACTTAAAAACCCTAAACC
41582470 TTAACTTAAAAACCCTAA
1 TTAACTTAAAAACCCTAA
41582488 CCTAATTTAA
Statistics
Matches: 91, Mismatches: 3, Indels: 25
0.76 0.03 0.21
Matches are distributed among these distances:
20 12 0.13
21 38 0.42
22 13 0.14
23 18 0.20
24 6 0.07
26 1 0.01
28 3 0.03
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (21 bp):
TTAACTTAAAAACCCTAAACC
Found at i:41582474 original size:89 final size:92
Alignment explanation
Indices: 41582317--41582564 Score: 310
Period size: 89 Copynumber: 2.6 Consensus size: 92
41582307 TAAAAACCCT
41582317 AAACCCTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAACCT
1 AAACCCTAACCTAATTTAATTAAAAA-CCT-A-CTTAACCTAATTTAATTAAAAACCCTAAACCT
41582382 TAACTTAAAAACCCTAAACCTTAACTT-TA-A
63 TAACTTAAAAACCCT-AACC-TAACTTATACA
41582412 AAACCCTAACCTAATTTAA-TACAAAA-CT-C-TAACCTAATTTAATTAAAAACCCTAAACCTTA
1 AAACCCTAACCTAATTTAATTA-AAAACCTACTTAACCTAATTTAATTAAAAACCCTAAACCTTA
*
41582473 ACTTAAAAACCCTAACCTAATTTAATACA
65 ACTTAAAAACCCTAACCTAACTT-ATACA
* * *
41582502 AAACCCTAACCTAAACCTTAATTAAAAACCCTAACCCTAACCTAAATTAATTAAAAACCCTAA
1 AAACCCTAACCT-AA-TTTAATTAAAAA-CCT-A-CTTAACCTAATTTAATTAAAAACCCTAA
41582565 CCCTAACATA
Statistics
Matches: 137, Mismatches: 3, Indels: 23
0.84 0.02 0.14
Matches are distributed among these distances:
87 5 0.04
88 4 0.03
89 47 0.34
90 14 0.10
91 2 0.01
92 8 0.06
93 4 0.03
94 4 0.03
95 23 0.17
97 1 0.01
98 25 0.18
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.27
Consensus pattern (92 bp):
AAACCCTAACCTAATTTAATTAAAAACCTACTTAACCTAATTTAATTAAAAACCCTAAACCTTAA
CTTAAAAACCCTAACCTAACTTATACA
Found at i:41582497 original size:67 final size:70
Alignment explanation
Indices: 41582373--41582535 Score: 278
Period size: 67 Copynumber: 2.4 Consensus size: 70
41582363 AATTAAAAAC
41582373 CCTAAACCTTAACTTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATACAAAA
1 CCTAAACCTTAA-TTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATACAAAA
*
41582438 CTCTAA
65 CCCTAA
*
41582444 CCT-AA-TTTAATTAAAAACCCTAAACCTTAAC-TTAAAAACCCTAACCTAATTTAATACAAAAC
1 CCTAAACCTTAATTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATACAAAAC
41582506 CCTAA
66 CCTAA
41582511 CCTAAACCTTAATTAAAAACCCTAA
1 CCTAAACCTTAATTAAAAACCCTAA
41582536 CCCTAACCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
67 38 0.44
68 23 0.26
69 21 0.24
70 2 0.02
71 3 0.03
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (70 bp):
CCTAAACCTTAATTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATACAAAAC
CCTAA
Found at i:41582526 original size:29 final size:29
Alignment explanation
Indices: 41582480--41583034 Score: 749
Period size: 29 Copynumber: 19.1 Consensus size: 29
41582470 TTAACTTAAA
41582480 AACCCTAACCTAATTTAA-TACAAAACCCT
1 AACCCTAACCTAATTTAATTA-AAAACCCT
41582509 AA-CCTAAACC----TTAATTAAAAACCCT
1 AACCCT-AACCTAATTTAATTAAAAACCCT
*
41582534 AACCCTAACCTAAATTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
41582563 AACCCTAACATAAATTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
41582592 AACCCTAACCTAATTTAATTAAAAATCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
41582621 ACCCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
41582650 AACCCTAACCTAAATTAATTAAAAACCCTAACCCT
1 AACCCTAACCTAATTTAATT--AAA----AACCCT
41582685 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
41582714 AACCCTAACCTAATTTAATTAAAAAACCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
41582743 AACACTAACCTAATTTAATTAAAGACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
41582772 AACCCTAACCTAAATTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
41582801 AATCCTAACCTAAATTAATT-AAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
41582829 AAACCCTAACCTAATTTAATTAAAGACCCT
1 -AACCCTAACCTAATTTAATTAAAAACCCT
*
41582859 AACCCTAACCTAATTTAATTAAAAAACCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
41582888 AACCCTAACCTAATTTAATTAAAGACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
41582917 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
41582946 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
41582975 AACCCTAACCCCAACCTAATTTAATTAAAAACCCT
1 AACCCT------AACCTAATTTAATTAAAAACCCT
41583010 AA-CCT-A---AA-TTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
41583033 AA
1 AA
41583035 ACTAAGTTAA
Statistics
Matches: 480, Mismatches: 25, Indels: 48
0.87 0.05 0.09
Matches are distributed among these distances:
23 17 0.04
24 2 0.00
25 18 0.04
26 5 0.01
27 1 0.00
28 11 0.02
29 360 0.75
30 7 0.01
31 3 0.01
33 3 0.01
34 3 0.01
35 50 0.10
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.26
Consensus pattern (29 bp):
AACCCTAACCTAATTTAATTAAAAACCCT
Found at i:41583013 original size:23 final size:23
Alignment explanation
Indices: 41582981--41583044 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
41582971 CCCTAACCCT
* *
41582981 AACCCCAACCTAATTTAATTAAA
1 AACCCTAACCTAAATTAATTAAA
41583004 AACCCTAACCTAAATTAATTAAA
1 AACCCTAACCTAAATTAATTAAA
* *
41583027 AACCCTAAACTAAGTTAA
1 AACCCTAACCTAAATTAA
41583045 CAATGTTACA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.50, C:0.23, G:0.02, T:0.25
Consensus pattern (23 bp):
AACCCTAACCTAAATTAATTAAA
Found at i:41583194 original size:116 final size:116
Alignment explanation
Indices: 41583041--41583394 Score: 609
Period size: 116 Copynumber: 3.1 Consensus size: 116
41583031 CTAAACTAAG
* * * *
41583041 TTAACAATGTTACATTCACGTAATGTTAGATTGGGAAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
*
41583106 TAATTTTACATAATTTGATAATTTTACTAACCACTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
*
41583157 TTAATAATTTTACATTCACATAATGGTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
41583222 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
* * * *
41583273 TAAATAATTTTACATTCACATAATGTTAGATTTCGAAAAATGTTTTGATTGGTACTAGCAATTAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
*
41583338 TAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
41583389 TTAATA
1 TTAATA
41583395 CAATTTATCA
Statistics
Matches: 225, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 225 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (116 bp):
TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
Found at i:41583411 original size:17 final size:18
Alignment explanation
Indices: 41583370--41583411 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
41583360 TTTACTAACC
* *
41583370 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
41583388 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
41583405 ATTAATA
1 ATTAATA
41583412 ATTTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:41586582 original size:124 final size:125
Alignment explanation
Indices: 41586422--41586775 Score: 557
Period size: 124 Copynumber: 2.8 Consensus size: 125
41586412 CCCAAACAAG
*
41586422 CTACTGTAGCAAAAGCGCGTCTACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
41586487 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAT-TTTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCTTACATGAC
* * * *
41586546 CTACTGTAGCAAAAGTGCGTCCACAAGGCCACGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
41586611 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATAATTATTTCTTCCGTGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTC--AAAAAATAATTATTTCTTACATGAC
* *
41586673 CTACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAAGCATCCTT
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAAT-AGCATCCTG
** *
41586738 CTAGAAGCGATTTTATACTATTTTATCAGAAATGTCAA
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
41586776 CTCGAAATTA
Statistics
Matches: 209, Mismatches: 17, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
124 95 0.45
126 9 0.04
127 64 0.31
128 41 0.20
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCTTACATGAC
Found at i:41588070 original size:17 final size:17
Alignment explanation
Indices: 41588048--41588081 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41588038 ATATTTATCA
41588048 ATAAAATAAAAATAATT
1 ATAAAATAAAAATAATT
41588065 ATAAAATAAAAATAATT
1 ATAAAATAAAAATAATT
41588082 TTTTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATAAAAATAATT
Found at i:41594561 original size:19 final size:19
Alignment explanation
Indices: 41594539--41594585 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
41594529 ATTGGAACGT
* *
41594539 AAAGTGCATATTGGCGCAC
1 AAAGTGCATACTGGCACAC
*
41594558 AAAGCGCATACTGGCACAC
1 AAAGTGCATACTGGCACAC
*
41594577 GAAGTGCAT
1 AAAGTGCAT
41594586 CTTGACGTGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (19 bp):
AAAGTGCATACTGGCACAC
Found at i:41601589 original size:41 final size:41
Alignment explanation
Indices: 41601527--41601697 Score: 213
Period size: 41 Copynumber: 4.2 Consensus size: 41
41601517 ATTATTGCTT
*
41601527 AATTGCACATATGTGCTCC-TGTTTGTACTTCGGTACCCCTA
1 AATTGCACATACGTGC-CCTTGTTTGTACTTCGGTACCCCTA
* *
41601568 AATTGAACATACGTGTCCC-TGTTTGTACTTCGGTAACCCTA
1 AATTGCACATACGTG-CCCTTGTTTGTACTTCGGTACCCCTA
* * *
41601609 AATTGCACATATGTGCCCTTATTTGTACTTCGGTACCCCTG
1 AATTGCACATACGTGCCCTTGTTTGTACTTCGGTACCCCTA
* * * *
41601650 AATTGCACATACATGCCCTTTTTTATACTTCGGTACCTCTA
1 AATTGCACATACGTGCCCTTGTTTGTACTTCGGTACCCCTA
41601691 AA-TGCAC
1 AATTGCAC
41601698 TTTTTTCCTG
Statistics
Matches: 114, Mismatches: 14, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
40 8 0.07
41 105 0.92
42 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (41 bp):
AATTGCACATACGTGCCCTTGTTTGTACTTCGGTACCCCTA
Found at i:41609091 original size:27 final size:27
Alignment explanation
Indices: 41609055--41609132 Score: 138
Period size: 27 Copynumber: 2.9 Consensus size: 27
41609045 AAATGTGAAG
*
41609055 GGGGTTGCTAAGTGCTGATTCCCGCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
41609082 GGGGTTGCTAAGTGCTGATTCCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
*
41609109 GAGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
41609133 GACTCATTGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (27 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:41609188 original size:129 final size:130
Alignment explanation
Indices: 41608953--41609208 Score: 415
Period size: 129 Copynumber: 2.0 Consensus size: 130
41608943 GAATATAAAG
* * *
41608953 GGGGTTGCTAAGTGCTTATTCCCCCAAGGGGTTTCTAAGTGCTGATTCCCCGAATCATTGGTGGT
1 GGGGTTGCTAAGTGCTGATTCCCCCAAGAGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGT
* * * *
41609018 TGTTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGGGGTTGCTAAGTGCTGA-TTCCCGCAA
66 TGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTTCCCGCAA
*
41609082 GGGGTTGCTAAGTGCTGATTCCCCCAAGAGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGT
1 GGGGTTGCTAAGTGCTGATTCCCCCAAGAGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGT
* *
41609147 TGCTAAGTGCTGATCCCATCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGTTGATTTCCCG
66 TGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTTCCCG
41609209 AATCACTGGT
Statistics
Matches: 116, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
129 110 0.95
130 6 0.05
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (130 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAAGAGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGT
TGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTTCCCGCAA
Found at i:41614205 original size:22 final size:22
Alignment explanation
Indices: 41614177--41614226 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
41614167 GGGTCATGTC
*
41614177 TTGTCTCAAGACATAAGAC-CAT
1 TTGTCTCAAGACAT-ACACTCAT
*
41614199 TTGTCTCAAGATATACACTCAT
1 TTGTCTCAAGACATACACTCAT
41614221 TTGTCT
1 TTGTCT
41614227 TGAGATAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (22 bp):
TTGTCTCAAGACATACACTCAT
Found at i:41617902 original size:40 final size:40
Alignment explanation
Indices: 41617804--41618106 Score: 387
Period size: 40 Copynumber: 7.6 Consensus size: 40
41617794 TCCTCGTTCA
* * * * *
41617804 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
41617843 AATGCCTTCGGGACATAACCCGGATTTAACAACTTGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
41617883 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41617923 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41617963 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
41618003 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
41618043 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
41618083 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41618107 CAGCATTCAA
Statistics
Matches: 238, Mismatches: 22, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 36 0.15
40 194 0.82
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:41625890 original size:40 final size:40
Alignment explanation
Indices: 41625792--41626094 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
41625782 TCCTCGTTCA
* * * * *
41625792 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
41625831 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
41625871 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41625911 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41625951 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
41625991 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
41626031 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
41626071 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41626095 CAGCATTCAA
Statistics
Matches: 240, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 37 0.15
40 195 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:41627665 original size:12 final size:13
Alignment explanation
Indices: 41627639--41627667 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
41627629 TGCGAAATTC
41627639 AAATAGTGAAATG
1 AAATAGTGAAATG
41627652 AAATAGTG-AATG
1 AAATAGTGAAATG
41627664 AAAT
1 AAAT
41627668 TATATTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (13 bp):
AAATAGTGAAATG
Found at i:41633173 original size:24 final size:23
Alignment explanation
Indices: 41633128--41633173 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
41633118 TACCTTTTCA
**
41633128 TTATACTTTATTTTGATTAATTT
1 TTATACTTTATTTTGAAAAATTT
*
41633151 TTATAACTTTATTTTTAAAAATT
1 TTAT-ACTTTATTTTGAAAAATT
41633174 CGATTTTTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (23 bp):
TTATACTTTATTTTGAAAAATTT
Found at i:41646040 original size:15 final size:15
Alignment explanation
Indices: 41646022--41646061 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
41646012 AAAATACATG
41646022 ATAATAAATATAAGA
1 ATAATAAATATAAGA
41646037 ATAATAGAA-ATAAGA
1 ATAATA-AATATAAGA
*
41646052 ATAACAAATA
1 ATAATAAATA
41646062 AATAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.09
15 18 0.82
16 2 0.09
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.23
Consensus pattern (15 bp):
ATAATAAATATAAGA
Found at i:41646049 original size:24 final size:24
Alignment explanation
Indices: 41645973--41646042 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
41645963 GAGGAATAAA
*
41645973 AATAATAAACATAATGAAACA-A-AT
1 AATAATAAAAATAA-GAAA-ATACAT
*
41645997 AAAAATAAAAATAAGAAAATACAT
1 AATAATAAAAATAAGAAAATACAT
* *
41646021 GATAATAAATATAAGAATAATA
1 AATAATAAAAATAAGAA-AATA
41646043 GAAATAAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
22 1 0.03
23 5 0.13
24 28 0.74
25 4 0.11
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (24 bp):
AATAATAAAAATAAGAAAATACAT
Found at i:41646055 original size:21 final size:19
Alignment explanation
Indices: 41646024--41646086 Score: 54
Period size: 21 Copynumber: 3.1 Consensus size: 19
41646014 AATACATGAT
*
41646024 AATAAATATAAGAATAATAGA
1 AATAAAAATAA-AATAA-AGA
* *
41646045 AATAAGAATAACAAATAAATA
1 AATAAAAAT-A-AAATAAAGA
*
41646066 AATAAAAATAAAATAAGGA
1 AATAAAAATAAAATAAAGA
41646085 AA
1 AA
41646087 AAGAAGGGGA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 9 0.26
20 1 0.03
21 17 0.50
22 6 0.18
23 1 0.03
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.19
Consensus pattern (19 bp):
AATAAAAATAAAATAAAGA
Found at i:41653183 original size:17 final size:18
Alignment explanation
Indices: 41653150--41653185 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
41653140 CCCATTATCT
*
41653150 TTTTTTTCCATTATTTAA
1 TTTTTTTCCACTATTTAA
41653168 TTTTTTTCCACT-TTTAA
1 TTTTTTTCCACTATTTAA
41653185 T
1 T
41653186 CGTAGCTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTTTCCACTATTTAA
Found at i:41665435 original size:25 final size:26
Alignment explanation
Indices: 41665401--41665451 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
41665391 CATTAAAGTT
41665401 AAAAAAGAATTTCAATTA-TCCCAAA
1 AAAAAAGAATTTCAATTATTCCCAAA
41665426 AAAAAAGAATTTCAATTATTCCCAAA
1 AAAAAAGAATTTCAATTATTCCCAAA
41665452 TTTTAATTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.55, C:0.16, G:0.04, T:0.25
Consensus pattern (26 bp):
AAAAAAGAATTTCAATTATTCCCAAA
Found at i:41667612 original size:10 final size:10
Alignment explanation
Indices: 41667593--41667622 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
41667583 AGGTGGTTGG
41667593 TTAGTGGGAT
1 TTAGTGGGAT
*
41667603 TTAGTAGGAT
1 TTAGTGGGAT
41667613 TTAGTGGGAT
1 TTAGTGGGAT
41667623 ATGGGTAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (10 bp):
TTAGTGGGAT
Found at i:41668431 original size:36 final size:36
Alignment explanation
Indices: 41668352--41668450 Score: 117
Period size: 36 Copynumber: 2.8 Consensus size: 36
41668342 GTAAGCTGTG
* * * *
41668352 TGAGGCACACGACCATGTGAAATCATGTAGTCCGTG
1 TGAGGCACACGACCGTGTGAAATCATATAGGCCGTA
*
41668388 TGAGGCACACGACCGTGTGAAATCATATAGGCCTTA
1 TGAGGCACACGACCGTGTGAAATCATATAGGCCGTA
* * **
41668424 TGGGGCACATGGTCGTGTGAAATCATA
1 TGAGGCACACGACCGTGTGAAATCATA
41668451 CAGATCGTGT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (36 bp):
TGAGGCACACGACCGTGTGAAATCATATAGGCCGTA
Found at i:41678488 original size:41 final size:43
Alignment explanation
Indices: 41678381--41678539 Score: 135
Period size: 41 Copynumber: 3.7 Consensus size: 43
41678371 CTATCGAACA
* * * * **
41678381 ATGCCAACGTCCCAGACGTGGTCTTACATGCTATCTCATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGCAATCAAATATCG
* * *
41678424 ATGCCACTGTCCCGGACAGGGTCTTACACG-AATCAAATA-CG
1 ATGCCAATGTCCCAGACATGGTCTTACACGCAATCAAATATCG
* ** *
41678465 ATGCCAATGTCCTAGACATGGTCTTACACATAATCGCATATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGCAAT--CAAATATCG
* *
41678510 ATGCC-ATCATCCCAGACTTGGTCTTACACG
1 ATGCCAAT-GTCCCAGACATGGTCTTACACG
41678540 AGAACACATA
Statistics
Matches: 92, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
41 27 0.29
42 9 0.10
43 24 0.26
44 7 0.08
45 25 0.27
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGCAATCAAATATCG
Found at i:41683053 original size:28 final size:28
Alignment explanation
Indices: 41683013--41683094 Score: 137
Period size: 28 Copynumber: 2.9 Consensus size: 28
41683003 AAAACGTATA
* *
41683013 AAAATGGAAGCCTTTATCGCAATCTATG
1 AAAATGGAAGCCTTTGTGGCAATCTATG
*
41683041 AAAATAGAAGCCTTTGTGGCAATCTATG
1 AAAATGGAAGCCTTTGTGGCAATCTATG
41683069 AAAATGGAAGCCTTTGTGGCAATCTA
1 AAAATGGAAGCCTTTGTGGCAATCTA
41683095 AGGAAAGGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (28 bp):
AAAATGGAAGCCTTTGTGGCAATCTATG
Found at i:41683109 original size:28 final size:28
Alignment explanation
Indices: 41683013--41683110 Score: 126
Period size: 28 Copynumber: 3.5 Consensus size: 28
41683003 AAAACGTATA
* * *
41683013 AAAATGGAAGCCTTTATCGCAATCTATG
1 AAAATGGAAGCCTTTGTGGCAATCTAAG
* *
41683041 AAAATAGAAGCCTTTGTGGCAATCTATG
1 AAAATGGAAGCCTTTGTGGCAATCTAAG
41683069 AAAATGGAAGCCTTTGTGGCAATCTAAG
1 AAAATGGAAGCCTTTGTGGCAATCTAAG
*
41683097 GAAA-GGAACGCCTT
1 AAAATGGAA-GCCTT
41683111 CATGGTGCAT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 4 0.06
28 59 0.94
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (28 bp):
AAAATGGAAGCCTTTGTGGCAATCTAAG
Found at i:41684442 original size:66 final size:66
Alignment explanation
Indices: 41684349--41684480 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
41684339 GATAACTAAA
41684349 AAAATTGGAACAACCTTATGTGTAAATAGGAAACCTATCCTGGCATTATAAAAGTTGAAAATAGA
1 AAAATTGGAACAACCTTATGTGTAAATAGGAAACCTATCCTGGCATTATAAAAGTTGAAAATAGA
41684414 T
66 T
41684415 AAAATTGGAACAACCTTATGTGTAAATAGGAAACCTATCCTGGCATTATAAAAGTTGAAAATAGA
1 AAAATTGGAACAACCTTATGTGTAAATAGGAAACCTATCCTGGCATTATAAAAGTTGAAAATAGA
41684480 T
66 T
41684481 CAATATAGAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (66 bp):
AAAATTGGAACAACCTTATGTGTAAATAGGAAACCTATCCTGGCATTATAAAAGTTGAAAATAGA
T
Found at i:41684733 original size:18 final size:17
Alignment explanation
Indices: 41684693--41684735 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
41684683 AATACTTTAA
*
41684693 ATAT-AAAATTATAAAT
1 ATATAAAAATAATAAAT
*
41684709 GTATAAAAATAATATAAT
1 ATATAAAAATAATA-AAT
41684727 ATATAAAAA
1 ATATAAAAA
41684736 AACTGCCACG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 8 0.36
18 11 0.50
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
ATATAAAAATAATAAAT
Found at i:41685454 original size:22 final size:22
Alignment explanation
Indices: 41685421--41685469 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
41685411 AAAGTAATTG
*
41685421 ACTAAAATATAAATGTAAAAAA
1 ACTAAAATATAAATGAAAAAAA
*
41685443 ACTAGAAA-ATAAGTGAAAAAAA
1 ACTA-AAATATAAATGAAAAAAA
41685465 A-TAAA
1 ACTAAA
41685470 CTGAATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.08
21 2 0.08
22 17 0.71
23 3 0.12
ACGTcount: A:0.69, C:0.04, G:0.08, T:0.18
Consensus pattern (22 bp):
ACTAAAATATAAATGAAAAAAA
Found at i:41703105 original size:16 final size:18
Alignment explanation
Indices: 41703070--41703107 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41703060 ATTCTTATTT
*
41703070 AAATAAAATACATTAGTA
1 AAATAAAATACATAAGTA
41703088 AAATAAAATA-A-AAGTA
1 AAATAAAATACATAAGTA
41703104 AAAT
1 AAAT
41703108 CCATATAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 1 0.05
18 10 0.53
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATAAAATACATAAGTA
Found at i:41709462 original size:33 final size:33
Alignment explanation
Indices: 41709420--41709503 Score: 123
Period size: 33 Copynumber: 2.5 Consensus size: 33
41709410 AATCAGCAGG
*
41709420 TTGGGCCTGGTCATGGTGGTACCAGATAACAGA
1 TTGGGCCTGGTCATGGTGGTACCAGACAACAGA
* *
41709453 TTGGGCCTGGTCATGGTGGTACCTGGCAACAGA
1 TTGGGCCTGGTCATGGTGGTACCAGACAACAGA
* *
41709486 TTGGGCCTGCTAATGGTG
1 TTGGGCCTGGTCATGGTG
41709504 CAGTTGGGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.26
Consensus pattern (33 bp):
TTGGGCCTGGTCATGGTGGTACCAGACAACAGA
Found at i:41721449 original size:120 final size:120
Alignment explanation
Indices: 41721236--41721473 Score: 440
Period size: 120 Copynumber: 2.0 Consensus size: 120
41721226 AGACTATTAT
* *
41721236 AGAAATATATTAAATTTTGGTCTAATAATTTTATTTAATTGATAGTTAATTAAGATACAAGTGTA
1 AGAAATATATTAAAGTTTGGTCTAATAATTTTATTTAATTGATAGTTAATAAAGATACAAGTGTA
*
41721301 ATGATCATAAAGTTAGTGATATCGAAAAATACAGTTTTAGAACCCCATTTTCAAA
66 ATGATCATAAAGTTAGTGATATCGAAAAATACAGTTTTAGAACACCATTTTCAAA
*
41721356 AGAAATATATTAAAGTTTGGTCTAATAATTTTATTTAATTGATAGTTAATAAAGGTACAAGTGTA
1 AGAAATATATTAAAGTTTGGTCTAATAATTTTATTTAATTGATAGTTAATAAAGATACAAGTGTA
41721421 ATGATCATAAAGTTAGTGATATCGAAAAATACAGTTTTAGAACACCATTTTCA
66 ATGATCATAAAGTTAGTGATATCGAAAAATACAGTTTTAGAACACCATTTTCA
41721474 TAAACTGAGA
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 114 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (120 bp):
AGAAATATATTAAAGTTTGGTCTAATAATTTTATTTAATTGATAGTTAATAAAGATACAAGTGTA
ATGATCATAAAGTTAGTGATATCGAAAAATACAGTTTTAGAACACCATTTTCAAA
Found at i:41723658 original size:22 final size:22
Alignment explanation
Indices: 41723578--41723660 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 22
41723568 AATTGGTTGA
* *
41723578 GTTTGGTTAGTTAATGAACTAT
1 GTTTGTTTAGTTGATGAACTAT
* * *
41723600 GTTTGCTTAGTTGATG-AGTTT
1 GTTTGTTTAGTTGATGAACTAT
**
41723621 GTGTT-TATTAAATGATGAACTAT
1 GT-TTGT-TTAGTTGATGAACTAT
41723644 GTTTGTTTAGTTGATGA
1 GTTTGTTTAGTTGATGA
41723661 GTACATAGGT
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
21 5 0.11
22 35 0.76
23 6 0.13
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (22 bp):
GTTTGTTTAGTTGATGAACTAT
Found at i:41733302 original size:7 final size:7
Alignment explanation
Indices: 41733292--41733349 Score: 52
Period size: 7 Copynumber: 8.4 Consensus size: 7
41733282 TTTAAATTAA
41733292 AAATATT
1 AAATATT
41733299 AAAT-TT
1 AAATATT
*
41733305 AAAGTA-A
1 AAA-TATT
41733312 AAATA-T
1 AAATATT
41733318 AAAT-TT
1 AAATATT
41733324 ATAATATT
1 A-AATATT
41733332 AAATATT
1 AAATATT
41733339 AAAATATT
1 -AAATATT
41733347 AAA
1 AAA
41733350 AAAGACTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
6 13 0.30
7 20 0.47
8 10 0.23
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (7 bp):
AAATATT
Found at i:41733320 original size:19 final size:20
Alignment explanation
Indices: 41733281--41733324 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
41733271 AATTAGGTTT
*
41733281 ATTTAAATTAAAAATATTAA
1 ATTTAAAGTAAAAATATTAA
41733301 ATTTAAAGTAAAAATA-TAA
1 ATTTAAAGTAAAAATATTAA
41733320 ATTTA
1 ATTTA
41733325 TAATATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
ATTTAAAGTAAAAATATTAA
Found at i:41733544 original size:22 final size:22
Alignment explanation
Indices: 41733493--41733556 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
41733483 ATTAATTTTT
*
41733493 AATAAAATTTT-AAAA-TATATA
1 AATAAAATTTTAAAAATTA-AAA
*
41733514 ATTATAAATTTTAAAAATTAAAA
1 AATA-AAATTTTAAAAATTAAAA
* *
41733537 AATAAAATATAAAAAATTAA
1 AATAAAATTTTAAAAATTAA
41733557 TTTAAATTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
21 3 0.09
22 21 0.60
23 9 0.26
24 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AATAAAATTTTAAAAATTAAAA
Found at i:41733583 original size:23 final size:23
Alignment explanation
Indices: 41733544--41733597 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 23
41733534 AAAAATAAAA
41733544 TATAAAAAATTAATTTA-AA-TT
1 TATAAAAAATTAATTTAGAATTT
41733565 TATAAAAAATTATATTTTAGAATTT
1 TATAAAAAATTA-A-TTTAGAATTT
41733590 TATAAAAA
1 TATAAAAA
41733598 TATTTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 12 0.41
22 1 0.03
23 4 0.14
24 2 0.07
25 10 0.34
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TATAAAAAATTAATTTAGAATTT
Found at i:41733608 original size:11 final size:11
Alignment explanation
Indices: 41733592--41733620 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
41733582 TAGAATTTTA
41733592 TAAAAATATTT
1 TAAAAATATTT
41733603 TAAAAATATTT
1 TAAAAATATTT
41733614 TAAAAAT
1 TAAAAAT
41733621 TTTATATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:41733620 original size:22 final size:21
Alignment explanation
Indices: 41733576--41733620 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
41733566 ATAAAAAATT
*
41733576 ATATTTTAGAATTTTATAAAA
1 ATATTTTAAAATTTTATAAAA
41733597 ATATTTTAAAAATATTT-TAAAA
1 ATATTTT-AAAAT-TTTATAAAA
41733619 AT
1 AT
41733621 TTTATATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 11 0.52
23 3 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
ATATTTTAAAATTTTATAAAA
Found at i:41738870 original size:8 final size:8
Alignment explanation
Indices: 41738857--41738902 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
41738847 TAGTAAAATA
41738857 ATATTTAT
1 ATATTTAT
*
41738865 ATATTTAA
1 ATATTTAT
* *
41738873 AAATAATAT
1 ATAT-TTAT
41738882 ATATTTAT
1 ATATTTAT
41738890 ATATTTAT
1 ATATTTAT
41738898 ATATT
1 ATATT
41738903 CAAACCCCCC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
8 26 0.84
9 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
ATATTTAT
Found at i:41744684 original size:11 final size:11
Alignment explanation
Indices: 41744668--41744706 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
41744658 ACTACTATAT
41744668 ATTACTATTAA
1 ATTACTATTAA
*
41744679 ATTACTACTCTAT
1 ATTACTA-T-TAA
41744692 ATTACTATTAA
1 ATTACTATTAA
41744703 ATTA
1 ATTA
41744707 AGTTAGAGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 13 0.54
12 2 0.08
13 9 0.38
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTACTATTAA
Found at i:41744692 original size:24 final size:24
Alignment explanation
Indices: 41744657--41744706 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
41744647 GGATCAACCC
41744657 TACTACTATATATTACTATTAAAT
1 TACTACTATATATTACTATTAAAT
*
41744681 TACTACTCTATATTACTATTAAAT
1 TACTACTATATATTACTATTAAAT
41744705 TA
1 TA
41744707 AGTTAGAGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (24 bp):
TACTACTATATATTACTATTAAAT
Found at i:41744697 original size:13 final size:12
Alignment explanation
Indices: 41744657--41744698 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
41744647 GGATCAACCC
41744657 TACTACTATATAT
1 TACTACT-TATAT
*
41744670 TACTA-TTAAAT
1 TACTACTTATAT
41744681 TACTACTCTATAT
1 TACTACT-TATAT
41744694 TACTA
1 TACTA
41744699 TTAAATTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.36
12 2 0.08
13 14 0.56
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (12 bp):
TACTACTTATAT
Found at i:41749148 original size:24 final size:24
Alignment explanation
Indices: 41749104--41749153 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
41749094 CGCAATAAAG
*
41749104 AATTTAAAAATTATCAAAAATCAA
1 AATTTAAAAAGTATCAAAAATCAA
* *
41749128 AATTATAAAAAGT-TCATAAATTAA
1 AATT-TAAAAAGTATCAAAAATCAA
41749152 AA
1 AA
41749154 AAAAACATGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (24 bp):
AATTTAAAAAGTATCAAAAATCAA
Found at i:41749535 original size:17 final size:17
Alignment explanation
Indices: 41749513--41749555 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
41749503 TGATAAACTT
* *
41749513 AAAAAATTAAGTGCGGA
1 AAAAAATTAAGTACGAA
*
41749530 AAAAAA-TAAGTACTAA
1 AAAAAATTAAGTACGAA
41749546 AAAAAATTAA
1 AAAAAATTAA
41749556 AAGTTGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.65, C:0.05, G:0.12, T:0.19
Consensus pattern (17 bp):
AAAAAATTAAGTACGAA
Found at i:41753018 original size:20 final size:21
Alignment explanation
Indices: 41752978--41753018 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
41752968 AACTTGGTCA
* *
41752978 TTTTCCTATAAAATAAGTTTT
1 TTTTCCTATAAAACAACTTTT
41752999 TTTTCCTAT-AAACAACTTTT
1 TTTTCCTATAAAACAACTTTT
41753019 AAAGCGTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.32, C:0.15, G:0.02, T:0.51
Consensus pattern (21 bp):
TTTTCCTATAAAACAACTTTT
Found at i:41753218 original size:26 final size:26
Alignment explanation
Indices: 41753188--41753257 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 26
41753178 ATACATATCT
41753188 AATTATTTATATTTAGTCA-TATAATA
1 AATTATTTATATTTA-TCATTATAATA
* *
41753214 AATTATTAATATAATTTATTATTTTAATA
1 AATTATT--TAT-ATTTATCATTATAATA
41753243 AATTATTTAATATTT
1 AATTATTT-ATATTT
41753258 CAATTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
26 7 0.19
27 5 0.14
28 7 0.19
29 18 0.49
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (26 bp):
AATTATTTATATTTATCATTATAATA
Found at i:41753227 original size:16 final size:16
Alignment explanation
Indices: 41753206--41753255 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 16
41753196 ATATTTAGTC
41753206 ATATAATAAATTATTA
1 ATATAATAAATTATTA
41753222 ATATAAT---TTATTA
1 ATATAATAAATTATTA
* *
41753235 TTTTAATAAATTATTTA
1 ATATAATAAATTA-TTA
41753252 ATAT
1 ATAT
41753256 TTCAATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 11 0.42
16 10 0.38
17 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:41753231 original size:29 final size:30
Alignment explanation
Indices: 41753198--41753255 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
41753188 AATTATTTAT
41753198 ATTTAGTCA-TATAATAAATTA-TTAATATA
1 ATTTA-TCATTATAATAAATTATTTAATATA
* *
41753227 ATTTATTATTTTAATAAATTATTTAATAT
1 ATTTATCATTATAATAAATTATTTAATAT
41753256 TTCAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 16 0.64
30 7 0.28
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
ATTTATCATTATAATAAATTATTTAATATA
Found at i:41753607 original size:7 final size:7
Alignment explanation
Indices: 41753595--41753635 Score: 66
Period size: 7 Copynumber: 5.9 Consensus size: 7
41753585 TACGCAAAAA
41753595 AAAATAT
1 AAAATAT
41753602 AAAATAT
1 AAAATAT
41753609 AAAATAT
1 AAAATAT
41753616 AAAAT-T
1 AAAATAT
41753622 ATAAATAT
1 A-AAATAT
41753630 AAAATA
1 AAAATA
41753636 AACTCAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 2 0.06
7 28 0.88
8 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAAATAT
Found at i:41765379 original size:25 final size:25
Alignment explanation
Indices: 41765351--41765400 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
41765341 CTCGTTTCCA
*
41765351 TTTCTCTTATTTGCCATTTCAATAT
1 TTTCTCATATTTGCCATTTCAATAT
*
41765376 TTTCTCATCTTTGCCATTTCAATAT
1 TTTCTCATATTTGCCATTTCAATAT
41765401 CAATCACATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.20, C:0.22, G:0.04, T:0.54
Consensus pattern (25 bp):
TTTCTCATATTTGCCATTTCAATAT
Found at i:41766506 original size:15 final size:14
Alignment explanation
Indices: 41766486--41766516 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
41766476 TTCCCCTTTC
41766486 TTCTTTCTTTCTCTT
1 TTCTTTCTTT-TCTT
41766501 TTCTTTCTTTTCTT
1 TTCTTTCTTTTCTT
41766515 TT
1 TT
41766517 AAATTTGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
TTCTTTCTTTTCTT
Found at i:41769105 original size:50 final size:50
Alignment explanation
Indices: 41769030--41769222 Score: 251
Period size: 50 Copynumber: 3.8 Consensus size: 50
41769020 ATTTGGGTAA
*
41769030 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* *
41769080 AGAGGTCCCATGTAAGACCATGTCTGGGACATGACGTTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
*** * * * *
41769130 AGAGGTCCCCCATAAGACCGTGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * *
41769180 AGAACATCCCATGTAAGACCATGTCTGGGACATAGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
41769223 TGTTATTATC
Statistics
Matches: 121, Mismatches: 21, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
50 90 0.74
51 31 0.26
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:41769899 original size:12 final size:12
Alignment explanation
Indices: 41769882--41769914 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
41769872 TGGCCCGCCC
41769882 ATATTAATTTTT
1 ATATTAATTTTT
41769894 ATATT-ATTTTT
1 ATATTAATTTTT
41769905 ATA-TAATTTT
1 ATATTAATTTT
41769915 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:41770084 original size:30 final size:30
Alignment explanation
Indices: 41770040--41770102 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
41770030 ACTTAACAAG
*
41770040 CAAATGCCTCTAAAATAATGACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
41770070 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
41770100 CAA
1 CAA
41770103 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.56, C:0.14, G:0.05, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:41771550 original size:24 final size:26
Alignment explanation
Indices: 41771503--41771552 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
41771493 TTTAAAATAC
* *
41771503 TTTAAAAATATTTTTATTTTTTTATT
1 TTTAAAAATATTTTTATGTGTTTATT
41771529 TTTAAAAAT-TTTTT-TGTGTTTATT
1 TTTAAAAATATTTTTATGTGTTTATT
41771553 AAAAATCGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 5 0.23
26 9 0.41
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (26 bp):
TTTAAAAATATTTTTATGTGTTTATT
Found at i:41779296 original size:44 final size:43
Alignment explanation
Indices: 41779209--41779548 Score: 154
Period size: 44 Copynumber: 7.8 Consensus size: 43
41779199 GACTTGATGC
* * * *
41779209 AATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTT
1 AATCCGCTCCACTACAACTTCAGAGAGATAAGAT-TATGACTTT
* * *
41779253 AATCCGGTCCACTACAACTTCAGGGAGATAGGATTATCGACTTT
1 AATCCGCTCCACTACAACTTCAGAGAGATAAGATTAT-GACTTT
* * *
41779297 AATCTGCTCCACTGCAACCTCAGAGAGATAAGATT-TG-CTTCTT
1 AATCCGCTCCACTACAACTTCAGAGAGATAAGATTATGAC-T-TT
** * * *** * * * **
41779340 CGTTCTGCCCCACTGTGACTTCAGGGGGATAAGACT-TGTTTTCT
1 -AATCCGCTCCACTACAACTTCAGAGAGATAAGATTATGACTT-T
* * * * * * *
41779384 CAGTCTGCTCTACTGCAACCTCAGGGAGATAAGACCTAATG-C---
1 -AATCCGCTCCACTACAACTTCAGAGAGATAAGA--TTATGACTTT
* * * *
41779426 AATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTT
1 AATCCGCTCCACTACAACTTCAGAGAGATAAGAT-TATGACTTT
* * * * * *
41779470 AATCCGCTACACTACAACTTTAGGGAGATAGGATTATCGGCTTC
1 AATCCGCTCCACTACAACTTCAGAGAGATAAGATTAT-GACTTT
* * *
41779514 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
1 AATCCGCTCCACTACAACTTCAGAGAGATAAGATT
41779549 TGCCATCTTC
Statistics
Matches: 225, Mismatches: 56, Indels: 30
0.72 0.18 0.10
Matches are distributed among these distances:
39 1 0.00
40 2 0.01
41 30 0.13
42 2 0.01
43 10 0.04
44 178 0.79
47 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (43 bp):
AATCCGCTCCACTACAACTTCAGAGAGATAAGATTATGACTTT
Found at i:41779696 original size:128 final size:127
Alignment explanation
Indices: 41779539--41780075 Score: 767
Period size: 128 Copynumber: 4.2 Consensus size: 127
41779529 AACTTCAGGG
* *
41779539 AGATAAGATTTGCCATCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCA
1 AGATAAGATTTGCC-GCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
* ** * * **
41779604 ACCTATTCCACAACTGACCAGGGATATACGACTTGTGGCTTAAATCTGCTTTTTTACACTTGA
65 ACCTACTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * *
41779667 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTTCTA
1 AGATAAGATTTGCCG-CTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
* *
41779732 ACCTACTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATTTACTTCCTTACACTTGA
65 ACCTACTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
*
41779795 AGATAAGATTTGCCGCTTTCGATCTACTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
1 AGATAAGATTTGCCGC-TTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
* * * *
41779860 A-CT--T-CATTGCTGACCAGGGACATAGGACTTGAGGCTTAAATTTGCTTTCTTACACTTGA
65 ACCTACTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
* * *
41779919 AGATAAGATTTGCCGCTTTCGATCTACTCCGTTACCGCTTAGGGAGACAAGATCTGTAATTTCCA
1 AGATAAGATTTGCCGC-TTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
* * *
41779984 ACCTACTCCACTGCTAACCAGGGACATAGGACTTGTAGCTTGAATCTGCTTCCTTACACTTGA
65 ACCTACTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
*
41780047 AGATAAGATTTGTCGCTTCCGATCTGCTC
1 AGATAAGATTTGCCGCTT-CGATCTGCTC
41780076 TGTAATTTCC
Statistics
Matches: 369, Mismatches: 33, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
124 115 0.31
125 3 0.01
127 6 0.02
128 245 0.66
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (127 bp):
AGATAAGATTTGCCGCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAA
CCTACTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGA
Found at i:41779989 original size:252 final size:255
Alignment explanation
Indices: 41779539--41780071 Score: 788
Period size: 252 Copynumber: 2.1 Consensus size: 255
41779529 AACTTCAGGG
* * *
41779539 AGATAAGATTTGCC-ATCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCC
1 AGATAAGATTTGCCGCT-TTCGATCTACTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCC
* * *
41779603 AACCTATTCCACAACTGACCAGGGATATACGACTTGTGGCTTAAATCTGCTTTTTTACACTTGAA
65 AACC-ATTCCACAACTGACCAGGGACATACGACTTGAGGCTTAAATCTGCTTTCTTACACTTGAA
* * * *
41779668 GATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTTCTAA
129 GATAAGATTCGCCGTCTTCGATCTACTCCGCTACCGCTTAGGGAGACAAGATCTGTAATTTCCAA
* * *
41779733 CCTACTCCACTGCTGACCAGGGACATAGGACTTGTGGCTTAAATTTACTTCCTTACACTTGA
194 CCTACTCCACTGCTAACCAGGGACATAGGACTTGTAGCTTAAATCTACTTCCTTACACTTGA
41779795 AGATAAGATTTGCCGCTTTCGATCTACTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
1 AGATAAGATTTGCCGCTTTCGATCTACTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
*** * *
41779860 A-C-TT-CATTGCTGACCAGGGACATAGGACTTGAGGCTTAAATTTGCTTTCTTACACTTGAAGA
66 ACCATTCCACAACTGACCAGGGACATACGACTTGAGGCTTAAATCTGCTTTCTTACACTTGAAGA
* *
41779922 TAAGATTTGCCG-CTTTCGATCTACTCCGTTACCGCTTAGGGAGACAAGATCTGTAATTTCCAAC
131 TAAGATTCGCCGTC-TTCGATCTACTCCGCTACCGCTTAGGGAGACAAGATCTGTAATTTCCAAC
* *
41779986 CTACTCCACTGCTAACCAGGGACATAGGACTTGTAGCTTGAATCTGCTTCCTTACACTTGA
195 CTACTCCACTGCTAACCAGGGACATAGGACTTGTAGCTTAAATCTACTTCCTTACACTTGA
* *
41780047 AGATAAGATTTGTCGCTTCCGATCT
1 AGATAAGATTTGCCGCTTTCGATCT
41780072 GCTCTGTAAT
Statistics
Matches: 251, Mismatches: 24, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
251 1 0.00
252 185 0.74
253 2 0.01
255 1 0.00
256 61 0.24
257 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (255 bp):
AGATAAGATTTGCCGCTTTCGATCTACTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCA
ACCATTCCACAACTGACCAGGGACATACGACTTGAGGCTTAAATCTGCTTTCTTACACTTGAAGA
TAAGATTCGCCGTCTTCGATCTACTCCGCTACCGCTTAGGGAGACAAGATCTGTAATTTCCAACC
TACTCCACTGCTAACCAGGGACATAGGACTTGTAGCTTAAATCTACTTCCTTACACTTGA
Found at i:41780150 original size:103 final size:103
Alignment explanation
Indices: 41779971--41780159 Score: 351
Period size: 103 Copynumber: 1.8 Consensus size: 103
41779961 GGAGACAAGA
*
41779971 TCTGTAATTTCCAACCTACTCCACTGCTAACCAGGGACATAGGACTTGTAGCTTGAATCTGCTTC
1 TCTGTAATTTCCAACCTACTCCACTACTAACCAGGGACATAGGACTTGTAGCTTGAATCTGCTTC
41780036 CTTACACTTGAAGATAAGATTTGTCGCTTCCGATCTGC
66 CTTACACTTGAAGATAAGATTTGTCGCTTCCGATCTGC
*
41780074 TCTGTAATTTCCAACCTACTCCACTACTAACCAGGGACATAGGACTTGTGGCTTGAATCTGCTTC
1 TCTGTAATTTCCAACCTACTCCACTACTAACCAGGGACATAGGACTTGTAGCTTGAATCTGCTTC
*
41780139 CTTACACTTGAAGGTAAGATT
66 CTTACACTTGAAGATAAGATT
41780160 CACCGTCTTT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 83 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (103 bp):
TCTGTAATTTCCAACCTACTCCACTACTAACCAGGGACATAGGACTTGTAGCTTGAATCTGCTTC
CTTACACTTGAAGATAAGATTTGTCGCTTCCGATCTGC
Found at i:41781542 original size:7 final size:7
Alignment explanation
Indices: 41781523--41781586 Score: 87
Period size: 7 Copynumber: 9.0 Consensus size: 7
41781513 TTAGCCTCTC
41781523 CATTTTT
1 CATTTTT
41781530 -ACTTTTT
1 CA-TTTTT
41781537 CATTTTTT
1 CA-TTTTT
41781545 CATTTTT
1 CATTTTT
41781552 CATTTTT
1 CATTTTT
41781559 CA-TTTT
1 CATTTTT
41781565 CATTTTT
1 CATTTTT
41781572 CATTTTT
1 CATTTTT
41781579 CATATTTT
1 CAT-TTTT
41781587 TTTGACTTAG
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
6 7 0.13
7 33 0.63
8 12 0.23
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (7 bp):
CATTTTT
Found at i:41781557 original size:13 final size:13
Alignment explanation
Indices: 41781523--41781577 Score: 74
Period size: 13 Copynumber: 4.0 Consensus size: 13
41781513 TTAGCCTCTC
*
41781523 CATTTTTACTTTTT
1 CATTTTT-CATTTT
41781537 CATTTTTTCATTTTT
1 CA-TTTTTCA-TTTT
41781552 CATTTTTCATTTT
1 CATTTTTCATTTT
41781565 CATTTTTCATTTT
1 CATTTTTCATTTT
41781578 TCATATTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
13 17 0.45
14 10 0.26
15 11 0.29
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (13 bp):
CATTTTTCATTTT
Found at i:41781566 original size:20 final size:20
Alignment explanation
Indices: 41781523--41781581 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 20
41781513 TTAGCCTCTC
41781523 CATTTTT-ACTTTTTCATTTTTT
1 CATTTTTCA-TTTTTCA--TTTT
41781545 CATTTTTCATTTTTCATTTT
1 CATTTTTCATTTTTCATTTT
41781565 CATTTTTCATTTTTCAT
1 CATTTTTCATTTTTCAT
41781582 ATTTTTTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
20 21 0.58
22 14 0.39
23 1 0.03
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (20 bp):
CATTTTTCATTTTTCATTTT
Found at i:41782487 original size:6 final size:6
Alignment explanation
Indices: 41782459--41782504 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
41782449 CTTCTCTCTT
* * * *
41782459 TTTTCA TTTTCA TTTTGG CTTTGA TTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
41782505 TCTTTTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (6 bp):
TTTTGA
Found at i:41782520 original size:16 final size:17
Alignment explanation
Indices: 41782495--41782532 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
41782485 TTGATTTTGA
41782495 TTTTGATTTT-TCTTTT
1 TTTTGATTTTATCTTTT
*
41782511 TTTTGTTTTTGATCTTTT
1 TTTTGATTTT-ATCTTTT
41782529 TTTT
1 TTTT
41782533 TGGATTGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
18 10 0.53
ACGTcount: A:0.05, C:0.05, G:0.08, T:0.82
Consensus pattern (17 bp):
TTTTGATTTTATCTTTT
Found at i:41782520 original size:22 final size:21
Alignment explanation
Indices: 41782489--41782533 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
41782479 TTGATTTTGA
*
41782489 TTTTGATTTTGATTTTTCTTTT
1 TTTTGATTTTGATCTTT-TTTT
*
41782511 TTTTGTTTTTGATCTTTTTTT
1 TTTTGATTTTGATCTTTTTTT
41782532 TT
1 TT
41782534 GGATTGGATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.07, C:0.04, G:0.09, T:0.80
Consensus pattern (21 bp):
TTTTGATTTTGATCTTTTTTT
Found at i:41796692 original size:3 final size:3
Alignment explanation
Indices: 41796684--41796708 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
41796674 TCGTTGCATC
41796684 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
41796709 TGTAGTGTAC
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:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:41799443 original size:3 final size:3
Alignment explanation
Indices: 41799435--41799485 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
41799425 AGTCCCCATT
*
41799435 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41799483 TTA
1 TTA
41799486 CTACTACTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:41799694 original size:12 final size:12
Alignment explanation
Indices: 41799677--41799705 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
41799667 TATGCATACC
41799677 TACATATTTTAA
1 TACATATTTTAA
41799689 TACATATTTTAA
1 TACATATTTTAA
41799701 TACAT
1 TACAT
41799706 TCATTTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (12 bp):
TACATATTTTAA
Found at i:41801100 original size:39 final size:41
Alignment explanation
Indices: 41800999--41801102 Score: 99
Period size: 44 Copynumber: 2.5 Consensus size: 41
41800989 GGTTCGCTGT
*
41800999 AATGGAATAGA-GGTGTAATAGTAATTCAATTGTTTGGTTG
1 AATGGAATAGATGCTGTAATAGTAATTCAATTGTTTGGTTG
* *
41801039 AATGGAATGGAATAGAACTGTAATAGT-ATTC-TTGTGTTTGGTTG
1 AATGGAATAG-AT-G--CTGTAATAGTAATTCAAT-TGTTTGGTTG
*
41801083 AATGGAAT-GATGTTGTAATA
1 AATGGAATAGATGCTGTAATA
41801103 ACATAAGGAA
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
39 7 0.13
40 9 0.17
41 2 0.04
42 2 0.04
43 3 0.06
44 22 0.41
45 9 0.17
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.38
Consensus pattern (41 bp):
AATGGAATAGATGCTGTAATAGTAATTCAATTGTTTGGTTG
Found at i:41801408 original size:59 final size:59
Alignment explanation
Indices: 41801213--41801410 Score: 185
Period size: 59 Copynumber: 3.4 Consensus size: 59
41801203 TATTAATATA
* * *
41801213 AATAATAAATAATTTAAT--CATAT--TTTAACATAATTATTATTAAATATAATTTAAT
1 AATAATATATAATTTAATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAAT
* * * * * * **
41801268 AAAAATATATAATTTAATAAAATTCTTAATATT-AAAT-ATTCTTATATGAATTTACTAAAAT
1 AATAATATATAATTTAATAAAA-T-ATAAT-TTAAAATAATTATTAT-TAAATATAATTTAAT
* *
41801329 CATAATATATAATACT-ATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAAT
1 AATAATATATAAT-TTAATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAAT
41801388 AATAATATATAATTTAATAAAAT
1 AATAATATATAATTTAATAAAAT
41801411 TCAATATAAT
Statistics
Matches: 108, Mismatches: 23, Indels: 20
0.72 0.15 0.13
Matches are distributed among these distances:
55 16 0.15
57 1 0.01
58 4 0.04
59 38 0.35
60 15 0.14
61 31 0.29
62 3 0.03
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.43
Consensus pattern (59 bp):
AATAATATATAATTTAATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAAT
Found at i:41801491 original size:117 final size:119
Alignment explanation
Indices: 41801242--41801476 Score: 384
Period size: 117 Copynumber: 2.0 Consensus size: 119
41801232 ATATTTTAAC
*
41801242 ATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATAT
1 ATAACTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC-TAATATTAAATAT
* *
41801307 TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAA
65 TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAAATAATGTAAA
* * *
41801362 ATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAATTC-AATA-TAATTATT
1 ATAACTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTAATATTAAATATT
*
41801425 CTTATATGAATTTACTAAAGTCATAATATATAATACTATAAAAAATAATGTA
66 CTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAAATAATGTA
41801477 TAATCTACTT
Statistics
Matches: 110, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
117 56 0.51
118 4 0.04
120 50 0.45
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (119 bp):
ATAACTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTAATATTAAATATT
CTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAAATAATGTAAA
Found at i:41801493 original size:120 final size:119
Alignment explanation
Indices: 41801236--41801473 Score: 408
Period size: 120 Copynumber: 2.0 Consensus size: 119
41801226 TTAATCATAT
*
41801236 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC-TAATATT
*
41801301 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
65 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAAATAA
*
41801356 TTTAAAATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAATTC-AATA-TA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTAATATTA
* *
41801419 ATTATTCTTATATGAATTTACTAAAGTCATAATATATAATACTATAAAAAATAA
66 AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAAATAA
41801473 T
1 T
41801474 GTATAATCTA
Statistics
Matches: 113, Mismatches: 5, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
117 54 0.48
118 4 0.04
120 55 0.49
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (119 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTAATATTA
AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAAATAA
Found at i:41802935 original size:49 final size:49
Alignment explanation
Indices: 41802863--41802966 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
41802853 AGAAAAAAAC
* * *
41802863 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
41802912 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
*
41802961 ATATTA
1 AAATTA
41802967 TAACACATGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.33
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
Found at i:41812874 original size:87 final size:88
Alignment explanation
Indices: 41812699--41812874 Score: 309
Period size: 87 Copynumber: 2.0 Consensus size: 88
41812689 AGCGCTATCG
*
41812699 TGCGTTGAGAAAAATTCCTAACCATCAATGCAAATGCTCTTTTTTTTTTAGTCTACCATCTTCAG
1 TGCGTTGAGAAAAATTCCTAACCATCAATGCAAATGCTCTATTTTTTTTAGTCTACCATCTTCAG
41812764 TTCGATTAGAATGGGTGAGAAGA
66 TTCGATTAGAATGGGTGAGAAGA
* *
41812787 TGCGTTGAGCAAAATTCCTAACCATCAATGCAAATGCTC-ATTTTTTTTAGTCTACCTTCTTCAG
1 TGCGTTGAGAAAAATTCCTAACCATCAATGCAAATGCTCTATTTTTTTTAGTCTACCATCTTCAG
*
41812851 TTCGATTGGAATGGGTGAGAAGA
66 TTCGATTAGAATGGGTGAGAAGA
41812874 T
1 T
41812875 TTCTTTTTGA
Statistics
Matches: 84, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
87 46 0.55
88 38 0.45
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (88 bp):
TGCGTTGAGAAAAATTCCTAACCATCAATGCAAATGCTCTATTTTTTTTAGTCTACCATCTTCAG
TTCGATTAGAATGGGTGAGAAGA
Found at i:41814601 original size:16 final size:16
Alignment explanation
Indices: 41814577--41814627 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
41814567 TGAATTACTA
41814577 ATTATAGCTCTATTCC
1 ATTATAGCTCTATTCC
* * *
41814593 ATTACAGCTTTATTAC
1 ATTATAGCTCTATTCC
*
41814609 ATTATAACTCTATTCC
1 ATTATAGCTCTATTCC
41814625 ATT
1 ATT
41814628 CTCCCTAACC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45
Consensus pattern (16 bp):
ATTATAGCTCTATTCC
Found at i:41814695 original size:16 final size:16
Alignment explanation
Indices: 41814671--41814706 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41814661 TGGTTCACTA
* *
41814671 TAATGGAATAGAGTTG
1 TAATAGAATAGAGCTG
41814687 TAATAGAATAGAGCTG
1 TAATAGAATAGAGCTG
41814703 TAAT
1 TAAT
41814707 CAGTAATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.31
Consensus pattern (16 bp):
TAATAGAATAGAGCTG
Found at i:41814906 original size:14 final size:14
Alignment explanation
Indices: 41814887--41814915 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41814877 GGATTATTAT
41814887 TAAAAATAATTTAA
1 TAAAAATAATTTAA
41814901 TAAAAATAATTTAA
1 TAAAAATAATTTAA
41814915 T
1 T
41814916 CATATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAAATAATTTAA
Found at i:41815318 original size:26 final size:27
Alignment explanation
Indices: 41815282--41815345 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
41815272 GGCCGGGCCC
* * *
41815282 ATTTTTAAAAT-AAATATTAAAAAATT
1 ATTTTAAAAATAAAAAATAAAAAAATT
41815308 ATTTTAAAAATAAAAAAAATAAAAAAATT
1 ATTTTAAAAAT--AAAAAATAAAAAAATT
41815337 ATTTTAAAA
1 ATTTTAAAA
41815346 GTATTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 10 0.31
29 22 0.69
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
ATTTTAAAAATAAAAAATAAAAAAATT
Found at i:41831232 original size:36 final size:36
Alignment explanation
Indices: 41831175--41831263 Score: 160
Period size: 36 Copynumber: 2.5 Consensus size: 36
41831165 CCCAACTACT
*
41831175 GTATACGTGAACAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
*
41831211 GTATACGTGAATAGTATTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
41831247 GTATACGTGAATAGTAC
1 GTATACGTGAATAGTAC
41831264 CGTAAACGGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.30
Consensus pattern (36 bp):
GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
Found at i:41831266 original size:18 final size:18
Alignment explanation
Indices: 41831175--41831267 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
41831165 CCCAACTACT
* *
41831175 GTATACGTGAACAGTACT
1 GTATACGTGAATAGTACC
*
41831193 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
**
41831211 GTATACGTGAATAGTATT
1 GTATACGTGAATAGTACC
*
41831229 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
41831247 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
41831265 GTA
1 GTA
41831268 AACGGTCGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:41831829 original size:11 final size:11
Alignment explanation
Indices: 41831802--41831844 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
41831792 TGACCTTTTC
41831802 AAGGTATGGG-
1 AAGGTATGGGA
*
41831812 TAGGTATGGGA
1 AAGGTATGGGA
*
41831823 AAGGTATGGGC
1 AAGGTATGGGA
41831834 AAGGTATGGGA
1 AAGGTATGGGA
41831845 TATATTCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (11 bp):
AAGGTATGGGA
Done.