Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 188 of 208
Found at i:58805819 original size:57 final size:59
Alignment explanation
Indices: 58805740--58805854 Score: 155
Period size: 57 Copynumber: 1.9 Consensus size: 59
58805730 GCTAAATCCA
* * *
58805740 TTTTCCACATATTCTTCGGGAGGGTTATATC-A-A-GATCACCCGTCCGGGCTAGAGCT
1 TTTTCCACATATTATTCAGGAGGGCTATATCGATAGGATCACCCGTCCGGGCTAGAGCT
58805796 TTTTCACACATATTATTCAGGAGGGCTATATCAGGATAGGATCACCCGTCCGGGCTAGA
1 TTTTC-CACATATTATTCAGGAGGGCTATATC--GATAGGATCACCCGTCCGGGCTAGA
58805855 TTCTTTTTAC
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
56 5 0.10
57 23 0.46
60 1 0.02
61 1 0.02
62 20 0.40
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.29
Consensus pattern (59 bp):
TTTTCCACATATTATTCAGGAGGGCTATATCGATAGGATCACCCGTCCGGGCTAGAGCT
Found at i:58807462 original size:8 final size:8
Alignment explanation
Indices: 58807449--58807473 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
58807439 ATATATACTA
58807449 AATAAAAT
1 AATAAAAT
58807457 AATAAAAT
1 AATAAAAT
58807465 AATAAAAT
1 AATAAAAT
58807473 A
1 A
58807474 TCTTTTAAAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:58810436 original size:19 final size:18
Alignment explanation
Indices: 58810408--58810451 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
58810398 ATTGATTAGT
**
58810408 TTAATTAATTTTTTAAAA
1 TTAATTAATTAATTAAAA
58810426 TTAATTTAATTAATTAAAA
1 TTAA-TTAATTAATTAAAA
*
58810445 TTTATTA
1 TTAATTA
58810452 TGAAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATTAATTAATTAAAA
Found at i:58817465 original size:18 final size:18
Alignment explanation
Indices: 58817442--58817479 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
58817432 CTCTTTATAT
58817442 ATGAGTTCTGTTAATTTC
1 ATGAGTTCTGTTAATTTC
58817460 ATGAGTTCTGTTAATTTC
1 ATGAGTTCTGTTAATTTC
58817478 AT
1 AT
58817480 CAATGGTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.50
Consensus pattern (18 bp):
ATGAGTTCTGTTAATTTC
Found at i:58819456 original size:42 final size:42
Alignment explanation
Indices: 58819390--58819532 Score: 164
Period size: 42 Copynumber: 3.4 Consensus size: 42
58819380 GTATATGGCC
* * *
58819390 TTGGATATGGCATTGAAGATGGGAACCAGTTAGGTACAGCCA
1 TTGGATATGGCATTGGAGAAGGGAACCAGTTAGGTACAGGCA
* *
58819432 TTGGATATGGCATTGGAGAAGGGAACCGGGTAGGTACAGGCA
1 TTGGATATGGCATTGGAGAAGGGAACCAGTTAGGTACAGGCA
* * **
58819474 TTGGAAATGGCA-TGG-GAAGTGGGAACCAGTTAGGAATGGGCA
1 TTGGATATGGCATTGGAGAA--GGGAACCAGTTAGGTACAGGCA
*
58819516 TTGGGTATGGCATTGGA
1 TTGGATATGGCATTGGA
58819533 AATGGGGGTC
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
40 3 0.04
41 3 0.04
42 75 0.89
43 3 0.04
ACGTcount: A:0.29, C:0.11, G:0.38, T:0.22
Consensus pattern (42 bp):
TTGGATATGGCATTGGAGAAGGGAACCAGTTAGGTACAGGCA
Found at i:58819551 original size:42 final size:42
Alignment explanation
Indices: 58819504--58819628 Score: 103
Period size: 42 Copynumber: 3.0 Consensus size: 42
58819494 GGGAACCAGT
58819504 TAGGAATGGGCATTGGGTATGGCATTGGAAATGGGGGTCA-A
1 TAGGAATGGGCATTGGGTATGGCATTGGAAATGGGGGTCAGA
* * * * * ***
58819545 TCAGGAAAT-AGCA-TGGGATTTGGTATCGGAAATGCGAACCAGA
1 T-AGG-AATGGGCATTGGG-TATGGCATTGGAAATGGGGGTCAGA
* * *
58819588 TGGGAATGGGTATCGGGTATGGCATTGGAAATGGGGGTCAG
1 TAGGAATGGGCATTGGGTATGGCATTGGAAATGGGGGTCAG
58819629 GCCGGAAATA
Statistics
Matches: 59, Mismatches: 19, Indels: 11
0.66 0.21 0.12
Matches are distributed among these distances:
41 8 0.14
42 43 0.73
43 8 0.14
ACGTcount: A:0.28, C:0.10, G:0.39, T:0.23
Consensus pattern (42 bp):
TAGGAATGGGCATTGGGTATGGCATTGGAAATGGGGGTCAGA
Found at i:58819715 original size:42 final size:42
Alignment explanation
Indices: 58819656--58819759 Score: 154
Period size: 42 Copynumber: 2.5 Consensus size: 42
58819646 ATATGGCATA
* *
58819656 GGATATGGCACTGGAAATGGGAACCAGTTAGGAACTGGTATC
1 GGATATGGTACTGGAAATGGGAACCAGTTAGGAACCGGTATC
* *
58819698 GGATATGGTATTGGAAATGGGAACCAGTTAGGAACCGGTATT
1 GGATATGGTACTGGAAATGGGAACCAGTTAGGAACCGGTATC
* *
58819740 GGATTTGGTACCGGAAATGG
1 GGATATGGTACTGGAAATGG
58819760 AGGTCAGTCA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.30, C:0.12, G:0.35, T:0.24
Consensus pattern (42 bp):
GGATATGGTACTGGAAATGGGAACCAGTTAGGAACCGGTATC
Found at i:58821871 original size:13 final size:13
Alignment explanation
Indices: 58821855--58821881 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58821845 AAAGAAAAAG
58821855 AAAAAAGGATTCA
1 AAAAAAGGATTCA
58821868 AAAAAAGGATTCA
1 AAAAAAGGATTCA
58821881 A
1 A
58821882 GAAGAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAAAAGGATTCA
Found at i:58827171 original size:9 final size:9
Alignment explanation
Indices: 58827081--58827174 Score: 111
Period size: 9 Copynumber: 10.4 Consensus size: 9
58827071 TTAGTGATTC
58827081 AATTCGGTT
1 AATTCGGTT
58827090 AATTCTGG-T
1 AATTC-GGTT
*
58827099 AATTCGGGT
1 AATTCGGTT
58827108 AATTCAGG-T
1 AATTC-GGTT
58827117 AATTCGGTT
1 AATTCGGTT
*
58827126 AATTCGGGT
1 AATTCGGTT
*
58827135 AATTCTGTT
1 AATTCGGTT
58827144 AATTCGGTT
1 AATTCGGTT
*
58827153 AATTAGGTT
1 AATTCGGTT
*
58827162 AATTCAGTT
1 AATTCGGTT
58827171 AATT
1 AATT
58827175 TTTAACCAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
8 4 0.05
9 66 0.89
10 4 0.05
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:58833540 original size:27 final size:27
Alignment explanation
Indices: 58833465--58833529 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
58833455 AAAAACTTTT
* *
58833465 CTTTCATATTACACCACAAAGGTGTTC
1 CTTTCATATTGCGCCACAAAGGTGTTC
58833492 CTTTCATATTGCGCCACAAAGGTGTTC
1 CTTTCATATTGCGCCACAAAGGTGTTC
58833519 CTTTCATATTG
1 CTTTCATATTG
58833530 TGTCATAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (27 bp):
CTTTCATATTGCGCCACAAAGGTGTTC
Found at i:58835977 original size:13 final size:13
Alignment explanation
Indices: 58835956--58836021 Score: 80
Period size: 13 Copynumber: 5.1 Consensus size: 13
58835946 AGTATAGCAA
58835956 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
58835969 TGTTTTTGAAAAG
1 TGCTTTTGAAAAG
*
58835982 TG-TTGTGGAAAAG
1 TGCTT-TTGAAAAG
* *
58835995 TACTTTTGAGAAG
1 TGCTTTTGAAAAG
58836008 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
58836021 T
1 T
58836022 TTGGTTTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
12 2 0.05
13 40 0.91
14 2 0.05
ACGTcount: A:0.30, C:0.05, G:0.26, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:58839338 original size:12 final size:12
Alignment explanation
Indices: 58839321--58839345 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58839311 CGTTCGACCC
58839321 TTGTTTTTGACA
1 TTGTTTTTGACA
58839333 TTGTTTTTGACA
1 TTGTTTTTGACA
58839345 T
1 T
58839346 AATCAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TTGTTTTTGACA
Found at i:58844952 original size:19 final size:20
Alignment explanation
Indices: 58844918--58844960 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
58844908 GTTTGTGGGG
58844918 TTTT-TTTAAAATATTT-TA
1 TTTTATTTAAAATATTTATA
58844936 TTTTATTTATAAA-ATTTATA
1 TTTTATTTA-AAATATTTATA
58844956 TTTTA
1 TTTTA
58844961 ATAAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.18
19 8 0.36
20 10 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTATTTAAAATATTTATA
Found at i:58857809 original size:33 final size:33
Alignment explanation
Indices: 58857764--58857835 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
58857754 AAATACCTTC
58857764 AAGAAAGAGTCGAGGCACCAATGCTGATGGACA
1 AAGAAAGAGTCGAGGCACCAATGCTGATGGACA
* *
58857797 AAGAAAGGGTCGAGGCACCAATGCTGATGGATA
1 AAGAAAGAGTCGAGGCACCAATGCTGATGGACA
58857830 AAGAAA
1 AAGAAA
58857836 ACCACTTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.42, C:0.15, G:0.31, T:0.12
Consensus pattern (33 bp):
AAGAAAGAGTCGAGGCACCAATGCTGATGGACA
Found at i:58861273 original size:294 final size:294
Alignment explanation
Indices: 58860743--58861328 Score: 1091
Period size: 294 Copynumber: 2.0 Consensus size: 294
58860733 AACGACCAAG
*
58860743 CAAATCATGAGATTCGAATACTATTGGTCCACAATGGAAGGGGATTGTATTAGTTATGCCAAGAG
1 CAAATCATGAGATTCGAATACTATTGGTCCACAATAGAAGGGGATTGTATTAGTTATGCCAAGAG
58860808 ATTTCATAAATGCCAAATTTATGGAGACAAAATTCATGTACCTCATTCACTTCTTCACATTACAA
66 ATTTCATAAATGCCAAATTTATGGAGACAAAATTCATGTACCTCATTCACTTCTTCACATTACAA
*
58860873 CTTCTCCATGTCCTTTCTTTATGTAGGGCATGAATGTTATTGGGTCGATCTCGCCAAAAGCTTTC
131 CTTCTCCATGTCCTTTCTCTATGTAGGGCATGAATGTTATTGGGTCGATCTCGCCAAAAGCTTTC
* *
58860938 AATGGGCATCGAATAATCTTTGTGGTCATCAACTGCTTCACCAAGTGGGTAGAAAACACTTCTTA
196 AATGGGCATCGAATAATCTTTATGGTCATCAACTACTTCACCAAGTGGGTAGAAAACACTTCTTA
58861003 CACTAATGTCACGAAGACGATAATCAATAAATGC
261 CACTAATGTCACGAAGACGATAATCAATAAATGC
*
58861037 CAAATCATGAGATTCGAATATTATTGGTCCACAATAGAAGGGGATTGTATTAGTTATGCCAAGAG
1 CAAATCATGAGATTCGAATACTATTGGTCCACAATAGAAGGGGATTGTATTAGTTATGCCAAGAG
58861102 ATTTCATAAATGCCAAATTTATGGAGACAAAATTCATGTACCTCATTCACTTCTTCACATTACAA
66 ATTTCATAAATGCCAAATTTATGGAGACAAAATTCATGTACCTCATTCACTTCTTCACATTACAA
* *
58861167 CTTCTCCATGTCCTTTCTCTATGTAGGGCATGGATGTTATTGGGTTGATCTCGCCAAAAGCTTTC
131 CTTCTCCATGTCCTTTCTCTATGTAGGGCATGAATGTTATTGGGTCGATCTCGCCAAAAGCTTTC
* *
58861232 AATGGGCATCGATTCATCTTTATGGTCATCAACTACTTCACCAAGTGGGTAGAAAACACTTCTTA
196 AATGGGCATCGAATAATCTTTATGGTCATCAACTACTTCACCAAGTGGGTAGAAAACACTTCTTA
58861297 CACTAATGTCACGAAGACGATAATCAATAAAT
261 CACTAATGTCACGAAGACGATAATCAATAAAT
58861329 TCTTGAAGAA
Statistics
Matches: 283, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
294 283 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (294 bp):
CAAATCATGAGATTCGAATACTATTGGTCCACAATAGAAGGGGATTGTATTAGTTATGCCAAGAG
ATTTCATAAATGCCAAATTTATGGAGACAAAATTCATGTACCTCATTCACTTCTTCACATTACAA
CTTCTCCATGTCCTTTCTCTATGTAGGGCATGAATGTTATTGGGTCGATCTCGCCAAAAGCTTTC
AATGGGCATCGAATAATCTTTATGGTCATCAACTACTTCACCAAGTGGGTAGAAAACACTTCTTA
CACTAATGTCACGAAGACGATAATCAATAAATGC
Found at i:58862366 original size:44 final size:44
Alignment explanation
Indices: 58862318--58862473 Score: 170
Period size: 44 Copynumber: 3.5 Consensus size: 44
58862308 GAAGTTGCAG
*
58862318 TGGAGCAGATTAAAGCTACAAATCTAATCTCCCTGAAATTACAA
1 TGGAGTAGATTAAAGCTACAAATCTAATCTCCCTGAAATTACAA
* * * ** *
58862362 TGGAGTAGATTGAAGCTACAAATCTTAT-TCTCCTGAAGTTGTAG
1 TGGAGTAGATTAAAGCTACAAATCTAATCTC-CCTGAAATTACAA
* * ** *
58862406 TGGAATAGATTAAAGCTACAAATCTAATCTCCCTGAAGTTGTAG
1 TGGAGTAGATTAAAGCTACAAATCTAATCTCCCTGAAATTACAA
* *
58862450 TGGAGTAGATTGAAGCAACAAATC
1 TGGAGTAGATTAAAGCTACAAATC
58862474 CTATACCTAT
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
43 2 0.02
44 93 0.96
45 2 0.02
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (44 bp):
TGGAGTAGATTAAAGCTACAAATCTAATCTCCCTGAAATTACAA
Found at i:58862417 original size:88 final size:88
Alignment explanation
Indices: 58862294--58862473 Score: 270
Period size: 88 Copynumber: 2.0 Consensus size: 88
58862284 TACTATAGCG
* * *
58862294 AATCTTATTTTTCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTAATCTCCCTGAAATTA
1 AATCTTATTCTCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAATCTAATCTCCCTGAAATTA
*
58862359 CAATGGAGTAGATTGAAGCTACA
66 CAATGGAGTAGATTGAAGCAACA
* * * *
58862382 AATCTTATTCTCCTGAAGTTGTAGTGGAATAGATTAAAGCTACAAATCTAATCTCCCTGAAGTTG
1 AATCTTATTCTCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAATCTAATCTCCCTGAAATTA
* *
58862447 TAGTGGAGTAGATTGAAGCAACA
66 CAATGGAGTAGATTGAAGCAACA
58862470 AATC
1 AATC
58862474 CTATACCTAT
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 82 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.31
Consensus pattern (88 bp):
AATCTTATTCTCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAATCTAATCTCCCTGAAATTA
CAATGGAGTAGATTGAAGCAACA
Found at i:58862487 original size:44 final size:44
Alignment explanation
Indices: 58862305--58862490 Score: 157
Period size: 44 Copynumber: 4.2 Consensus size: 44
58862295 ATCTTATTTT
* * *
58862305 TCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAAT-CTA-ATCTC
1 TCTGAAGTTGTAGTGGAGTAGATTGAAGCTACAAATCCTATA-C-C
* * ** * * *
58862349 CCTGAAATTACAATGGAGTAGATTGAAGCTACAAATCTTAT-TC
1 TCTGAAGTTGTAGTGGAGTAGATTGAAGCTACAAATCCTATACC
* *
58862392 TCCTGAAGTTGTAGTGGAATAGATTAAAGCTACAAAT-CTA-ATCTC
1 T-CTGAAGTTGTAGTGGAGTAGATTGAAGCTACAAATCCTATA-C-C
* *
58862437 CCTGAAGTTGTAGTGGAGTAGATTGAAGCAACAAATCCTATACC
1 TCTGAAGTTGTAGTGGAGTAGATTGAAGCTACAAATCCTATACC
*
58862481 TATGAAGTTG
1 TCTGAAGTTG
58862491 CAATGGGTCA
Statistics
Matches: 111, Mismatches: 23, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
43 3 0.03
44 100 0.90
45 7 0.06
46 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (44 bp):
TCTGAAGTTGTAGTGGAGTAGATTGAAGCTACAAATCCTATACC
Found at i:58862487 original size:88 final size:88
Alignment explanation
Indices: 58862307--58862512 Score: 261
Period size: 88 Copynumber: 2.3 Consensus size: 88
58862297 CTTATTTTTC
*
58862307 TGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTAATCTCCCTGAAATTACAATGGAGTAGAT
1 TGAAGTTGCAGTGGAACAGATTAAAGCTACAAATCTAATCTCCCTGAAATTACAATGGAGTAGAT
* * * *
58862372 TGAAGCTACAAATCTTATTCTCC
66 TGAAGCAACAAATCCTATCCTCA
* * * ** *
58862395 TGAAGTTGTAGTGGAATAGATTAAAGCTACAAATCTAATCTCCCTGAAGTTGTAGTGGAGTAGAT
1 TGAAGTTGCAGTGGAACAGATTAAAGCTACAAATCTAATCTCCCTGAAATTACAATGGAGTAGAT
58862460 TGAAGCAACAAATCCTATACCT-A
66 TGAAGCAACAAATCCTAT-CCTCA
* ** *
58862483 TGAAGTTGCAATGGGTCAGATTAAATCTAC
1 TGAAGTTGCAGTGGAACAGATTAAAGCTAC
58862513 CATAGCAAAT
Statistics
Matches: 100, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
88 98 0.98
89 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (88 bp):
TGAAGTTGCAGTGGAACAGATTAAAGCTACAAATCTAATCTCCCTGAAATTACAATGGAGTAGAT
TGAAGCAACAAATCCTATCCTCA
Found at i:58862578 original size:138 final size:138
Alignment explanation
Indices: 58862418--58862710 Score: 401
Period size: 138 Copynumber: 2.1 Consensus size: 138
58862408 GAATAGATTA
* ** * *
58862418 AAGCTACAAATCTAATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCAACAAATCCTATACCTA
1 AAGCTACAAATCTTATCTCCCTGAAGTTGTAGTCAAGCAGATTGAAGCAACAAATCCCATACCTA
* *
58862483 TGAAGTTGCAATGGGTC-AGATTAAATCTACCATAGCAAATCTTATCTCCCTT-AAGTTGTAGTA
66 TGAAGTTGCAATGGGTCGA-ATTAAATCTACCATAGCAAATATTATCT-CCTTGAAGTTGCAGTA
58862546 AAACAAGATG
129 AAACAAGATG
* * *
58862556 AAGCTACAAATCTTATGTCCCTGAAGTTGTAGTCAAGCAGATTGAAGCGACAAATCCCATACCTC
1 AAGCTACAAATCTTATCTCCCTGAAGTTGTAGTCAAGCAGATTGAAGCAACAAATCCCATACCTA
* * **
58862621 TGAAGTTGCAGTGGGTCGAATTAAATTTACCATAGCAAATATTATCTCCTTGAAGTTGCAGTGGA
66 TGAAGTTGCAATGGGTCGAATTAAATCTACCATAGCAAATATTATCTCCTTGAAGTTGCAGTAAA
**
58862686 ATGAGATG
131 ACAAGATG
*
58862694 AAGATACAAATCTTATC
1 AAGCTACAAATCTTATC
58862711 CATCTCTGAG
Statistics
Matches: 135, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
137 4 0.03
138 130 0.96
139 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (138 bp):
AAGCTACAAATCTTATCTCCCTGAAGTTGTAGTCAAGCAGATTGAAGCAACAAATCCCATACCTA
TGAAGTTGCAATGGGTCGAATTAAATCTACCATAGCAAATATTATCTCCTTGAAGTTGCAGTAAA
ACAAGATG
Found at i:58862583 original size:44 final size:44
Alignment explanation
Indices: 58862518--58862611 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
58862508 TCTACCATAG
* *
58862518 CAAATCTTATCTCCCTTAAGTTGTAGTAAAACAAGA-TGAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGTAGTAAAAC-AGATTGAAGCGA
* * *
58862562 CAAATCTTATGTCCCTGAAGTTGTAGTCAAGCAGATTGAAGCGA
1 CAAATCTTATCTCCCTGAAGTTGTAGTAAAACAGATTGAAGCGA
58862606 CAAATC
1 CAAATC
58862612 CCATACCTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 3 0.07
44 41 0.93
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGTAGTAAAACAGATTGAAGCGA
Found at i:58865311 original size:22 final size:23
Alignment explanation
Indices: 58865286--58865336 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
58865276 AAAAGTGATA
*
58865286 TAATTATCATGT-AAACATTAAC
1 TAATTATCATATAAAACATTAAC
*
58865308 TAATTTTCATATAGAAACATTAAC
1 TAATTATCATATA-AAACATTAAC
58865332 TAATT
1 TAATT
58865337 GCCACAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 10 0.40
24 15 0.60
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (23 bp):
TAATTATCATATAAAACATTAAC
Found at i:58883420 original size:162 final size:162
Alignment explanation
Indices: 58883179--58883531 Score: 573
Period size: 162 Copynumber: 2.2 Consensus size: 162
58883169 CAATTGGGAA
* * *
58883179 CAGCTCTTTATCCTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAA
1 CAGCTCTCTATCTTCAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAA
* * *
58883244 TTTCAACTTATTGC-ATTCAGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTGTGGTTGATACT
66 TTTCAACTTATTGCAATT-AGTGACTTGTAATTCCCTTAGGCATTGGAAGATTATGGTTGATACT
*
58883308 TGTGAGTCTTGGATTATTTCTTCCATTCCAAAG
130 TGTGAGTCTTGAATTATTTCTTCCATTCCAAAG
* *
58883341 CGGCTCTCTATCTTCAGAGTTTGCAATTTCTCAAGACTATTAGCAACACACATTGGGAAGAGAAA
1 CAGCTCTCTATCTTCAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAA
* *
58883406 TTTCAATTTATTGCAATTTGTGACTTGTAATTCCCTTAGGCATTGGAAGATTATGGTTGATACTT
66 TTTCAACTTATTGCAATTAGTGACTTGTAATTCCCTTAGGCATTGGAAGATTATGGTTGATACTT
58883471 GTGAGTCTTGAATTATTTCTTCCATTCCAAAG
131 GTGAGTCTTGAATTATTTCTTCCATTCCAAAG
**
58883503 CAATTCTCTATCTTCAGAGTTTGCAATTT
1 CAGCTCTCTATCTTCAGAGTTTGCAATTT
58883532 GGGCGCATTT
Statistics
Matches: 176, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
162 173 0.98
163 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.37
Consensus pattern (162 bp):
CAGCTCTCTATCTTCAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAA
TTTCAACTTATTGCAATTAGTGACTTGTAATTCCCTTAGGCATTGGAAGATTATGGTTGATACTT
GTGAGTCTTGAATTATTTCTTCCATTCCAAAG
Found at i:58890121 original size:32 final size:32
Alignment explanation
Indices: 58890085--58890149 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
58890075 CAGTTTTTAC
*
58890085 TAACTCATATAGCTTTTTGAAAATAAACTAAG
1 TAACTCATATAGCTTTCTGAAAATAAACTAAG
*
58890117 TAACTTATATAGCTTTCTGAAAATAAACTAAG
1 TAACTCATATAGCTTTCTGAAAATAAACTAAG
58890149 T
1 T
58890150 TTTCTTCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.35
Consensus pattern (32 bp):
TAACTCATATAGCTTTCTGAAAATAAACTAAG
Found at i:58890162 original size:22 final size:24
Alignment explanation
Indices: 58890131--58890175 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
58890121 TTATATAGCT
*
58890131 TTCTGAAAATAAACTAA-GTTTTC
1 TTCTGAAAATAAACAAATGTTTTC
58890154 TTCT-AAAATAAACAAATGTTTT
1 TTCTGAAAATAAACAAATGTTTT
58890176 AAAATCAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (24 bp):
TTCTGAAAATAAACAAATGTTTTC
Found at i:58890782 original size:29 final size:29
Alignment explanation
Indices: 58890712--58890787 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
58890702 ATAAATATTT
* *
58890712 TTTTATTTTTTTATTTTTTAAAAGTAATAA
1 TTTTATTTTATTA-TTTTTAAAAATAATAA
* * *
58890742 TATTAATATATTATTTTTAAAAATAATAA
1 TTTTATTTTATTATTTTTAAAAATAATAA
*
58890771 TTTTATTTTATTGTTTT
1 TTTTATTTTATTATTTT
58890788 AATATTTCAT
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 28 0.76
30 9 0.24
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (29 bp):
TTTTATTTTATTATTTTTAAAAATAATAA
Found at i:58891720 original size:40 final size:39
Alignment explanation
Indices: 58891674--58891810 Score: 159
Period size: 40 Copynumber: 3.4 Consensus size: 39
58891664 GCGTTTGGAC
*
58891674 AAAAAACGCTGCTAAAAATCAAGCATTAGCGGCGCTTTA
1 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTA
* *
58891713 AATAAAACGCCGCTAAAGACCAAGCATTAGCGGCGCTTTCA
1 AA-AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTT-A
** * * *
58891754 GGAAAACGCCGCCAAAAAT-GAGCATTAGCGGCGTTTTTCA
1 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCG-CTTT-A
58891794 AAAAAACGCCGCTAAAA
1 AAAAAACGCCGCTAAAA
58891811 CCCTAAGCCC
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
39 15 0.18
40 66 0.80
41 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (39 bp):
AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTA
Found at i:58891895 original size:41 final size:42
Alignment explanation
Indices: 58891837--58891951 Score: 180
Period size: 41 Copynumber: 2.8 Consensus size: 42
58891827 CGACCTTTCG
58891837 GGGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
1 GGGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
** * *
58891879 -GGCTTTTAGCGGCGTTTTCCAAGAAGCGCCGCTAATGCTTA
1 GGGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
58891920 GGGC-TTTAGCGGCGTTTTTGAAAAAGCGCCGC
1 GGGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGC
58891952 AAAAACATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
41 62 0.95
42 3 0.05
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.28
Consensus pattern (42 bp):
GGGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
Found at i:58892407 original size:7 final size:7
Alignment explanation
Indices: 58892395--58892434 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
58892385 ATGTTGTGAT
58892395 TTAGGGG
1 TTAGGGG
58892402 TTAGGGG
1 TTAGGGG
58892409 TTAGGGG
1 TTAGGGG
*
58892416 TTAGGGA
1 TTAGGGG
*
58892423 TT-TGGG
1 TTAGGGG
58892429 TTAGGG
1 TTAGGG
58892435 TTTAAGGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 4 0.14
7 24 0.86
ACGTcount: A:0.15, C:0.00, G:0.53, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:58892513 original size:7 final size:7
Alignment explanation
Indices: 58892503--58892591 Score: 88
Period size: 7 Copynumber: 12.7 Consensus size: 7
58892493 TAGTAGTTAT
58892503 GGGTTTG
1 GGGTTTG
58892510 GGGTTTG
1 GGGTTTG
* *
58892517 GGATTTA
1 GGGTTTG
58892524 GGGTTTG
1 GGGTTTG
*
58892531 GGGTTTA
1 GGGTTTG
*
58892538 GGGTTAG
1 GGGTTTG
* *
58892545 AGGTTTA
1 GGGTTTG
*
58892552 GGGTTAG
1 GGGTTTG
58892559 GGGTTTG
1 GGGTTTG
*
58892566 GGATTTG
1 GGGTTTG
*
58892573 GGGTTAG
1 GGGTTTG
*
58892580 GGGTTAG
1 GGGTTTG
58892587 GGGTT
1 GGGTT
58892592 AAGGGTTAGA
Statistics
Matches: 65, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 65 1.00
ACGTcount: A:0.11, C:0.00, G:0.51, T:0.38
Consensus pattern (7 bp):
GGGTTTG
Found at i:58892529 original size:14 final size:14
Alignment explanation
Indices: 58892503--58892598 Score: 97
Period size: 14 Copynumber: 6.9 Consensus size: 14
58892493 TAGTAGTTAT
*
58892503 GGGTTTGGGGTTTG
1 GGGTTTAGGGTTTG
*
58892517 GGATTTAGGGTTTG
1 GGGTTTAGGGTTTG
*
58892531 GGGTTTAGGGTTAG
1 GGGTTTAGGGTTTG
* *
58892545 AGGTTTAGGGTTAG
1 GGGTTTAGGGTTTG
58892559 GGGTTT-GGGATTTG
1 GGGTTTAGGG-TTTG
*
58892573 GGG-TTAGGGGTTAG
1 GGGTTTA-GGGTTTG
*
58892587 GGGTTAAGGGTT
1 GGGTTTAGGGTT
58892599 AGAGGTTAAG
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
13 5 0.07
14 59 0.86
15 5 0.07
ACGTcount: A:0.12, C:0.00, G:0.50, T:0.38
Consensus pattern (14 bp):
GGGTTTAGGGTTTG
Found at i:58892592 original size:7 final size:7
Alignment explanation
Indices: 58892485--58892606 Score: 79
Period size: 7 Copynumber: 17.4 Consensus size: 7
58892475 TAAATAAGGT
58892485 TTAGGGG
1 TTAGGGG
**
58892492 TTAGTAG
1 TTAGGGG
*
58892499 TTATGGG
1 TTAGGGG
*
58892506 TTTGGGG
1 TTAGGGG
* *
58892513 TTTGGGAT
1 TTAGGG-G
58892521 TTA-GGG
1 TTAGGGG
*
58892527 TTTGGGG
1 TTAGGGG
58892534 TTTA-GGG
1 -TTAGGGG
*
58892541 TTAGAGGT
1 TTAG-GGG
58892549 TTA-GGG
1 TTAGGGG
58892555 TTAGGGG
1 TTAGGGG
* *
58892562 TTTGGGA
1 TTAGGGG
*
58892569 TTTGGGG
1 TTAGGGG
58892576 TTAGGGG
1 TTAGGGG
58892583 TTAGGGG
1 TTAGGGG
*
58892590 TTAAGGG
1 TTAGGGG
*
58892597 TTAGAGG
1 TTAGGGG
58892604 TTA
1 TTA
58892607 AGAGTTAGTG
Statistics
Matches: 88, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
6 10 0.11
7 69 0.78
8 9 0.10
ACGTcount: A:0.16, C:0.00, G:0.47, T:0.38
Consensus pattern (7 bp):
TTAGGGG
Found at i:58892597 original size:21 final size:21
Alignment explanation
Indices: 58892482--58892606 Score: 90
Period size: 21 Copynumber: 5.9 Consensus size: 21
58892472 TATTAAATAA
** *
58892482 GGTTTAGGGGTTAGTAGTTATG
1 GGTTTA-GGGTTAGGGGTTAGG
* * *
58892504 GGTTTGGGGTTTGGGATTTA-G
1 GGTTTAGGGTTAGGG-GTTAGG
* ** *
58892525 GGTTTGGGGTTTAGGGTTAGA
1 GGTTTAGGGTTAGGGGTTAGG
*
58892546 GGTTTAGGGTTAGGGGTTTGG
1 GGTTTAGGGTTAGGGGTTAGG
* *
58892567 GATTTGGGGTTAGGGGTTAGG
1 GGTTTAGGGTTAGGGGTTAGG
* *
58892588 GGTTAAGGGTTAGAGGTTA
1 GGTTTAGGGTTAGGGGTTA
58892607 AGAGTTAGTG
Statistics
Matches: 81, Mismatches: 20, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
20 3 0.04
21 70 0.86
22 8 0.10
ACGTcount: A:0.15, C:0.00, G:0.47, T:0.38
Consensus pattern (21 bp):
GGTTTAGGGTTAGGGGTTAGG
Found at i:58892599 original size:14 final size:14
Alignment explanation
Indices: 58892523--58892614 Score: 87
Period size: 14 Copynumber: 6.6 Consensus size: 14
58892513 TTTGGGATTT
* *
58892523 AGGGTTTGGGGTTT
1 AGGGTTAGGGGTTA
* *
58892537 AGGGTTAGAGGTTT
1 AGGGTTAGGGGTTA
58892551 AGGGTTAGGGGTT-
1 AGGGTTAGGGGTTA
* *
58892564 TGGGATTTGGGGTTA
1 AGGG-TTAGGGGTTA
*
58892579 GGGGTTAGGGGTTA
1 AGGGTTAGGGGTTA
*
58892593 AGGGTTAGAGGTTA
1 AGGGTTAGGGGTTA
*
58892607 AGAGTTAG
1 AGGGTTAG
58892615 TGATTTAAGG
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
13 3 0.05
14 60 0.91
15 3 0.05
ACGTcount: A:0.18, C:0.00, G:0.48, T:0.34
Consensus pattern (14 bp):
AGGGTTAGGGGTTA
Found at i:58892613 original size:21 final size:21
Alignment explanation
Indices: 58892573--58892613 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
58892563 TTGGGATTTG
* * *
58892573 GGGTTAGGGGTTAGGGGTTAA
1 GGGTTAGAGGTTAAGAGTTAA
58892594 GGGTTAGAGGTTAAGAGTTA
1 GGGTTAGAGGTTAAGAGTTA
58892614 GTGATTTAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.46, T:0.29
Consensus pattern (21 bp):
GGGTTAGAGGTTAAGAGTTAA
Found at i:58892922 original size:7 final size:7
Alignment explanation
Indices: 58892912--58892943 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
58892902 GTAGTTATGG
58892912 GTTTGGT
1 GTTTGGT
*
58892919 GTTTGGG
1 GTTTGGT
58892926 GTTTGGT
1 GTTTGGT
58892933 GTTTGGT
1 GTTTGGT
58892940 GTTT
1 GTTT
58892944 AGGGTTAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.44, T:0.56
Consensus pattern (7 bp):
GTTTGGT
Found at i:58892927 original size:14 final size:13
Alignment explanation
Indices: 58892905--58892974 Score: 59
Period size: 14 Copynumber: 5.1 Consensus size: 13
58892895 GGGGTTAGTA
*
58892905 GTTATGGGTTTGG
1 GTTAGGGGTTTGG
*
58892918 TGTTTGGGGTTTGG
1 -GTTAGGGGTTTGG
* *
58892932 TGTTTGGTGTTTAGG
1 -GTTAGGGGTTT-GG
*
58892947 GTTAGAGGTTTAGG
1 GTTAGGGGTTT-GG
58892961 GTTAGGGGTTTGG
1 GTTAGGGGTTTGG
58892974 G
1 G
58892975 ATTTAGGGTC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
13 3 0.06
14 43 0.90
15 2 0.04
ACGTcount: A:0.09, C:0.00, G:0.47, T:0.44
Consensus pattern (13 bp):
GTTAGGGGTTTGG
Found at i:58892957 original size:21 final size:20
Alignment explanation
Indices: 58892905--58892957 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
58892895 GGGGTTAGTA
*
58892905 GTTATGGGTTTGGTGTTTGGG
1 GTTA-GGGTTTGGTGTTTAGG
*
58892926 GTTTGGTGTTTGGTGTTTAGG
1 GTTAGG-GTTTGGTGTTTAGG
58892947 GTTAGAGGTTT
1 GTTAG-GGTTT
58892958 AGGGTTAGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 2 0.07
21 24 0.89
22 1 0.04
ACGTcount: A:0.08, C:0.00, G:0.43, T:0.49
Consensus pattern (20 bp):
GTTAGGGTTTGGTGTTTAGG
Found at i:58892969 original size:21 final size:21
Alignment explanation
Indices: 58892945--58893007 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
58892935 TTGGTGTTTA
58892945 GGGTTAGAGGTTTAGGGTTAG
1 GGGTTAGAGGTTTAGGGTTAG
* *
58892966 GGGTTTG-GGATTTAGGGTCAG
1 GGGTTAGAGG-TTTAGGGTTAG
* *
58892987 GGGTTAGAGGTTAAGAGTTAG
1 GGGTTAGAGGTTTAGGGTTAG
58893008 TGATTTAAGG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 2 0.06
21 30 0.88
22 2 0.06
ACGTcount: A:0.21, C:0.02, G:0.46, T:0.32
Consensus pattern (21 bp):
GGGTTAGAGGTTTAGGGTTAG
Found at i:58893429 original size:5 final size:5
Alignment explanation
Indices: 58893419--58893450 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
58893409 AAAACCAATC
58893419 AATAT AATAT AATAT AATAT AATAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT AA
58893451 AAATAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:58893641 original size:22 final size:21
Alignment explanation
Indices: 58893616--58893679 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
58893606 GTACTCTTAA
*
58893616 TTATTTTATTTTTTCTAATTTG
1 TTATTTAATTTTTT-TAATTTG
*
58893638 TTATTAAAATTTTTTTAATTTG
1 TTATT-TAATTTTTTTAATTTG
* * *
58893660 GTGTTTGATTTTTTTAATTT
1 TTATTTAATTTTTTTAATTT
58893680 AGTACTTAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
21 13 0.37
22 15 0.43
23 7 0.20
ACGTcount: A:0.22, C:0.02, G:0.08, T:0.69
Consensus pattern (21 bp):
TTATTTAATTTTTTTAATTTG
Found at i:58897282 original size:43 final size:43
Alignment explanation
Indices: 58897217--58897441 Score: 335
Period size: 43 Copynumber: 5.3 Consensus size: 43
58897207 ATGGCACTTT
** * **
58897217 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAAGTTATGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* * * * *
58897260 TAGCGGCGTTCGTGAGAGAAGCGTCGCTAAAAGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
58897303 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
*
58897346 TAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
*
58897389 TAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
58897431 TAGCGGCGTTT
1 TAGCGGCGTTT
58897442 ATTTCTAAAA
Statistics
Matches: 168, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
42 36 0.21
43 132 0.79
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.25
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
Found at i:58902726 original size:41 final size:41
Alignment explanation
Indices: 58902676--58902764 Score: 151
Period size: 41 Copynumber: 2.2 Consensus size: 41
58902666 CAAAAATCAC
* *
58902676 CTAATTACATCAAGTACATTAAAAACTTAGTTCAAATCTAA
1 CTAAGTACATCAAGTACATTAAAAACTTACTTCAAATCTAA
*
58902717 CTAAGTACATCAAGTACATTAACAACTTACTTCAAATCTAA
1 CTAAGTACATCAAGTACATTAAAAACTTACTTCAAATCTAA
58902758 CTAAGTA
1 CTAAGTA
58902765 GCAAAACATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (41 bp):
CTAAGTACATCAAGTACATTAAAAACTTACTTCAAATCTAA
Found at i:58902751 original size:22 final size:22
Alignment explanation
Indices: 58902680--58902751 Score: 53
Period size: 22 Copynumber: 3.4 Consensus size: 22
58902670 AATCACCTAA
*
58902680 TTACATCAAGTACATTAAAAAC
1 TTACATCAAGTACATTAACAAC
** *
58902702 TTAGTTCAAAT-C--TAACTAA-
1 TTACATCAAGTACATTAAC-AAC
*
58902721 GTACATCAAGTACATTAACAAC
1 TTACATCAAGTACATTAACAAC
*
58902743 TTACTTCAA
1 TTACATCAA
58902752 ATCTAACTAA
Statistics
Matches: 35, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
19 10 0.29
20 3 0.09
21 3 0.09
22 19 0.54
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (22 bp):
TTACATCAAGTACATTAACAAC
Found at i:58903066 original size:14 final size:13
Alignment explanation
Indices: 58903038--58903063 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58903028 GTGAGCAATT
58903038 TAAAAAAATTCAA
1 TAAAAAAATTCAA
58903051 TAAAAAAATTCAA
1 TAAAAAAATTCAA
58903064 ATAGTTATGA
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:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAAAAAATTCAA
Found at i:58909530 original size:25 final size:24
Alignment explanation
Indices: 58909491--58909545 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
58909481 AACTCCTCCC
58909491 CTTTC-TCTCACTTTTTTTCCTTTCT
1 CTTTCTTCTCACTTTTTTT--TTTCT
*
58909516 -TTTCTTCTCTCTTTTTTTTTTCT
1 CTTTCTTCTCACTTTTTTTTTTCT
58909539 CTTTCTT
1 CTTTCTT
58909546 TGAAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 5 0.19
24 10 0.37
25 12 0.44
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (24 bp):
CTTTCTTCTCACTTTTTTTTTTCT
Found at i:58909538 original size:15 final size:14
Alignment explanation
Indices: 58909501--58909546 Score: 60
Period size: 13 Copynumber: 3.3 Consensus size: 14
58909491 CTTTCTCTCA
58909501 CTTTTTTTC-CTTT
1 CTTTTTTTCTCTTT
58909514 CTTTTCTTCTCTCTTT
1 CTTTT-TT-TCTCTTT
58909530 -TTTTTTTCTCTTT
1 CTTTTTTTCTCTTT
58909543 CTTT
1 CTTT
58909547 GAAAAAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 12 0.41
14 7 0.24
15 6 0.21
16 4 0.14
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
CTTTTTTTCTCTTT
Found at i:58912501 original size:26 final size:25
Alignment explanation
Indices: 58912455--58912508 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
58912445 ATAATCAAGA
58912455 ATATAATAATAAAGCATTTAAATCAT
1 ATATAATAATAAAGCATTTAAA-CAT
* *
58912481 ATATAAT-ATAATGCTTATTAAACAT
1 ATATAATAATAAAGCAT-TTAAACAT
58912506 ATA
1 ATA
58912509 AACTTACCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (25 bp):
ATATAATAATAAAGCATTTAAACAT
Found at i:58912857 original size:16 final size:16
Alignment explanation
Indices: 58912836--58912868 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
58912826 ATTGTTTAAC
58912836 TCACAATAAATATTCA
1 TCACAATAAATATTCA
58912852 TCACAATAAATATTCA
1 TCACAATAAATATTCA
58912868 T
1 T
58912869 TTTCTTCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (16 bp):
TCACAATAAATATTCA
Found at i:58913735 original size:10 final size:9
Alignment explanation
Indices: 58913706--58913740 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
58913696 AAATTAATTT
58913706 ATTTTTATA
1 ATTTTTATA
58913715 ATTTTTATA
1 ATTTTTATA
*
58913724 ATTTTATTTA
1 ATTTT-TATA
58913734 ATTTTTA
1 ATTTTTA
58913741 AGGCTTAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
ATTTTTATA
Found at i:58913737 original size:28 final size:30
Alignment explanation
Indices: 58913674--58913740 Score: 86
Period size: 28 Copynumber: 2.3 Consensus size: 30
58913664 AATGAGAAGA
58913674 TTAATTTTTATGAAATTTTATAAAATTAAT
1 TTAATTTTTATGAAATTTTATAAAATTAAT
* * *
58913704 TT-ATTTTTAT-AATTTTTAT-AATTTTAT
1 TTAATTTTTATGAAATTTTATAAAATTAAT
58913731 TTAATTTTTA
1 TTAATTTTTA
58913741 AGGCTTAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 8 0.24
28 15 0.45
29 8 0.24
30 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (30 bp):
TTAATTTTTATGAAATTTTATAAAATTAAT
Found at i:58925097 original size:79 final size:79
Alignment explanation
Indices: 58925010--58925165 Score: 267
Period size: 79 Copynumber: 2.0 Consensus size: 79
58925000 TTTTAAATTA
* * * *
58925010 AAATTAAATTATAATTTTTACGATAGTAAAATTGTAATTTTATCGTTTTAATAACCTAAATTTTT
1 AAATTAAATTATAAATTTTACGATAGTAAAATTATAATTTTATCATTTTAATAACCTAAATCTTT
58925075 ATAATTTTTAAAAG
66 ATAATTTTTAAAAG
*
58925089 AAATTAAATTATAAATTTTATGATAGTAAAATTATAATTTTATCATTTTAATAACCTAAATCTTT
1 AAATTAAATTATAAATTTTACGATAGTAAAATTATAATTTTATCATTTTAATAACCTAAATCTTT
58925154 ATAATTTTTAAA
66 ATAATTTTTAAA
58925166 GGATTAAATC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 72 1.00
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (79 bp):
AAATTAAATTATAAATTTTACGATAGTAAAATTATAATTTTATCATTTTAATAACCTAAATCTTT
ATAATTTTTAAAAG
Found at i:58933994 original size:82 final size:82
Alignment explanation
Indices: 58933892--58934992 Score: 1471
Period size: 82 Copynumber: 13.4 Consensus size: 82
58933882 TGTGTTTTTA
* * * * *
58933892 GTCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGTGATCTACTCCACTACTGCTTAGGG-G
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
58933956 AATAAGATCTGTGGTTCT
66 -ATAAGATCTGTGGTTCT
* * * * *
58933974 GTCTACTCCACTATTACTTAGGGACATAAGACTTGGTGCGATCTGCTCCACTACTGCTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
*
58934039 ATAAGATCTATGGTTCT
66 ATAAGATCTGTGGTTCT
* * *
58934056 GTCTGCCCCAATATTTCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
58934121 ATAAGATCTGTGGTTCT
66 ATAAGATCTGTGGTTCT
* *
58934138 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGTTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
58934203 ATAAGATCTGTGGTTCT
66 ATAAGATCTGTGGTTCT
* *
58934220 GTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
*
58934285 ATAAGATCTATGGTTCT
66 ATAAGATCTGTGGTTCT
* *
58934302 GTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCACTATTGCTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
58934367 ATAAGATCTGTGGTTCT
66 ATAAGATCTGTGGTTCT
* *
58934384 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCAATCTGCTCCACTACTGCTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
58934449 ATAAGATCTGTGGTTCT
66 ATAAGATCTGTGGTTCT
58934466 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
58934531 ATAAGATCTGTGGTTCT
66 ATAAGATCTGTGGTTCT
*
58934548 GTCTGCTCCACTATTGCTTAGGGTGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
*
58934613 ATAAGATCTG-GTTTCTTTT
66 ATAAGATCTGTGGTTC---T
* *
58934632 GTCTACTCCACTAATGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
* *
58934697 ATAAGA-CT-TGATGC-
66 ATAAGATCTGTGGTTCT
* * *
58934711 GATCTTCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTCTG-TCTGCTCCACTATTGCTTAG
1 G-TCTGCTCCACTATTGCTTAGGGAGATAAGA-CT-TGATGC-GATCTGCTCCACTATTGCTTAG
* *
58934775 GGAGATAAGA-CT-TGATGC-
62 GGAGATAAGATCTGTGGTTCT
* * * * *
58934793 GATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGGTTTCTTTTG-TCTGCTCCACTACTACTT
1 G-TCTGCTCCACTATTGCTTAGGGAGATAAGA-CTTGATGC----GATCTGCTCCACTATTGCTT
* *
58934857 AGGGAGATAAGA-CT-TGATGC-
60 AGGGAGATAAGATCTGTGGTTCT
* * *
58934877 GATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGGTTTCTTTTG-TCTGCTCCACTATTGCTT
1 G-TCTGCTCCACTATTGCTTAGGGAGATAAGA-CTTGATGC----GATCTGCTCCACTATTGCTT
* *
58934941 AGGGAGATAAGA-CT-T-GATGT
60 AGGGAGATAAGATCTGTGGTTCT
*
58934961 GATCTGCTCCACTACTGCTTAGGGAGATAAGA
1 G-TCTGCTCCACTATTGCTTAGGGAGATAAGA
58934993 TCTGGTTTCT
Statistics
Matches: 949, Mismatches: 57, Indels: 24
0.92 0.06 0.02
Matches are distributed among these distances:
79 1 0.00
80 28 0.03
81 10 0.01
82 688 0.72
83 7 0.01
84 215 0.23
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (82 bp):
GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
ATAAGATCTGTGGTTCT
Found at i:58935329 original size:50 final size:50
Alignment explanation
Indices: 58935067--58935594 Score: 187
Period size: 50 Copynumber: 10.6 Consensus size: 50
58935057 GTCGGGGAAC
** * * *
58935067 AAGATTCATCGTTGTAGCTTCAATCTGATCCACTGCATCGACAAGAAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTACACTGCATCGCCAAGAAAGT
* * ** * * * * ** * * *
58935117 AAGATTCACTGTTGCGGCTTCAATCTTTTAAATTGTAAT-ATCAGGGAAGC
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTACACTG-CATCGCCAAGAAAGT
* * ** * *
58935167 AAGATTCGCCGTCGTAGCTTTAATCTACTGCACTGTA-CTGCC-AGAGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTACACTGCATC-GCCAAGA-AAGT
* * * * * ** *
58935217 GAGATTCGCCGTTGTGGCTTCAATCTCTTTA-ATTGCAAT-GTCGGGGAA-T
1 AAGATTCGCCGTTGTAGCTTCAATCT-GTTACACTGC-ATCGCCAAGAAAGT
* *
58935266 AAGATTCGCCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAAGAAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTACACTGCATCGCCAAGAAAGT
** * * * ** *
58935316 AAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAAT-ATCAAGAAAGC
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTACACTGC-ATCGCCAAGAAAGT
* * * * *
58935366 AAGATTCGCCATCGTAGCTTTAATCTGCTACACTGTA-CTGCC-AGAGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTACACTGCATC-GCCAAGA-AAGT
* * ** * * * * * * * *
58935416 GAGATTCGTCGTTGCGGCTTCAATCTTTTAAATTGTAAT-GTCGAGGAAGC
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTACACTG-CATCGCCAAGAAAGT
* * *** * *
58935466 AAGATTCGCTGTTGTAGCTTTAATCTGCCCCACTGCATCGCCATGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTACACTGCATCGCCAAGAAAGT
** * * * * * * ** * *
58935516 AAGATTCGTTGTTGCAGCTTCAATCTTTTAAATTGTAAT-GTCGGGGAAGC
1 AAGATTCGCCGTTGTAGCTTCAATCTGTTACACTG-CATCGCCAAGAAAGT
58935566 AAGATTCGCCGTTGTAGCTTCAATCTGTT
1 AAGATTCGCCGTTGTAGCTTCAATCTGTT
58935595 CCACAATATA
Statistics
Matches: 331, Mismatches: 127, Indels: 40
0.66 0.26 0.08
Matches are distributed among these distances:
48 3 0.01
49 42 0.13
50 274 0.83
51 12 0.04
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (50 bp):
AAGATTCGCCGTTGTAGCTTCAATCTGTTACACTGCATCGCCAAGAAAGT
Found at i:58935350 original size:199 final size:199
Alignment explanation
Indices: 58935010--58935591 Score: 878
Period size: 199 Copynumber: 2.9 Consensus size: 199
58935000 TCTGTTTGCT
* *
58935010 AGAGAAGTGAGATTCGCTGTTGTGGCTTCAATCTCTTTAATTGCAATGTCGGGGAACAAGATTCA
1 AGAGAAGTGAGATTCGCCGTTGTGGCTTCAATCTCTTTAATTGCAATGTCGGGGAACAAGATTCG
* * *
58935075 TCGTTGTAGCTTCAATCTGATCCACTGCATCGACAAGAAAGTAAGATTCACTGTTGCGGCTTCAA
66 CCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAAGAAAGTAAGATTCGCTGTTGCGGCTTCAA
*
58935140 TCTTTTAAATTGTAATATCAGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTACTGCACTGTAC
131 TCTTTTAAATTGTAATATCAGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTACTACACTGTAC
58935205 TGCC
196 TGCC
*
58935209 AGAGAAGTGAGATTCGCCGTTGTGGCTTCAATCTCTTTAATTGCAATGTCGGGGAATAAGATTCG
1 AGAGAAGTGAGATTCGCCGTTGTGGCTTCAATCTCTTTAATTGCAATGTCGGGGAACAAGATTCG
*
58935274 CCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAAGAAAGTAAGATTCGCCGTTGCGGCTTCAA
66 CCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAAGAAAGTAAGATTCGCTGTTGCGGCTTCAA
* * * * *
58935339 TCTTTTAAATTGCAATATCAAGAAAGCAAGATTCGCCATCGTAGCTTTAATCTGCTACACTGTAC
131 TCTTTTAAATTGTAATATCAGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTACTACACTGTAC
58935404 TGCC
196 TGCC
* * * *
58935408 AGAGAAGTGAGATTCGTCGTTGCGGCTTCAATCT-TTTAAATTGTAATGTCGAGGAAGCAAGATT
1 AGAGAAGTGAGATTCGCCGTTGTGGCTTCAATCTCTTT-AATTGCAATGTCGGGGAA-CAAGATT
* * ** * * * *
58935472 CGCTGTTGTAGCTTTAATCTGCCCCACTGCATCGCCATGGAAGTAAGATTCGTTGTTGCAGCTTC
64 CGCCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAAGAAAGTAAGATTCGCTGTTGCGGCTTC
* * * *
58935537 AATCTTTTAAATTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCT
129 AATCTTTTAAATTGTAATATCAGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCT
58935592 GTTCCACAAT
Statistics
Matches: 346, Mismatches: 35, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
198 3 0.01
199 234 0.68
200 109 0.32
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.31
Consensus pattern (199 bp):
AGAGAAGTGAGATTCGCCGTTGTGGCTTCAATCTCTTTAATTGCAATGTCGGGGAACAAGATTCG
CCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAAGAAAGTAAGATTCGCTGTTGCGGCTTCAA
TCTTTTAAATTGTAATATCAGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTACTACACTGTAC
TGCC
Found at i:58935592 original size:100 final size:99
Alignment explanation
Indices: 58935013--58935598 Score: 653
Period size: 100 Copynumber: 5.9 Consensus size: 99
58935003 GTTTGCTAGA
* * * **
58935013 GAAGTGAGATTCGCTGTTGTGGCTTCAATCTCTTT-AATTGCAATGTCGGGGAA-CAAGATTCAT
1 GAAGTAAGATTCGCCGTTGCGGCTTCAATCT-TTTAAATTGCAATGTCGGGGAAGCAAGATTCGC
* *
58935076 CGTTGTAGCTTCAATCTGATCCACTGCATCGACAAG
65 CGTTGTAGCTTCAATCTGCTCCACTGCATCG-CCAG
* * * * * *
58935112 AAAGTAAGATTCACTGTTGCGGCTTCAATCTTTTAAATTGTAATATCAGGGAAGCAAGATTCGCC
1 GAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTCGCC
* * * * *
58935177 GTCGTAGCTTTAATCTACTGCACTGTA-CTGCCAG
66 GTTGTAGCTTCAATCTGCTCCACTGCATC-GCCAG
* * *
58935211 AGAAGTGAGATTCGCCGTTGTGGCTTCAATCTCTTT-AATTGCAATGTCGGGGAA-TAAGATTCG
1 -GAAGTAAGATTCGCCGTTGCGGCTTCAATCT-TTTAAATTGCAATGTCGGGGAAGCAAGATTCG
*
58935274 CCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAAG
64 CCGTTGTAGCTTCAATCTGCTCCACTGCATCGCC-AG
* * ** *
58935311 AAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATATCAAGAAAGCAAGATTCGCC
1 GAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTCGCC
* * * * *
58935376 ATCGTAGCTTTAATCTGCTACACTGTA-CTGCCAG
66 GTTGTAGCTTCAATCTGCTCCACTGCATC-GCCAG
* * * *
58935410 AGAAGTGAGATTCGTCGTTGCGGCTTCAATCTTTTAAATTGTAATGTCGAGGAAGCAAGATTCGC
1 -GAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTCGC
* * *
58935475 TGTTGTAGCTTTAATCTGCCCCACTGCATCGCCATG
65 CGTTGTAGCTTCAATCTGCTCCACTGCATCGCCA-G
** * *
58935511 GAAGTAAGATTCGTTGTTGCAGCTTCAATCTTTTAAATTGTAATGTCGGGGAAGCAAGATTCGCC
1 GAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTCGCC
*
58935576 GTTGTAGCTTCAATCTGTTCCAC
66 GTTGTAGCTTCAATCTGCTCCAC
58935599 AATATAGGAA
Statistics
Matches: 408, Mismatches: 66, Indels: 25
0.82 0.13 0.05
Matches are distributed among these distances:
98 6 0.01
99 125 0.31
100 272 0.67
101 5 0.01
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (99 bp):
GAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTCGCC
GTTGTAGCTTCAATCTGCTCCACTGCATCGCCAG
Found at i:58935744 original size:43 final size:45
Alignment explanation
Indices: 58935598--58936140 Score: 473
Period size: 44 Copynumber: 12.5 Consensus size: 45
58935588 ATCTGTTCCA
* * *
58935598 CAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCAC-GC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTAC
* * * * * * * *
58935642 CAATACATGAAGAAAAGATTTGCTTTCTTGGATCTACTTCGCCAC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTAC
* * *
58935687 CAGTATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTAC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTAC
* * * *
58935730 CAATATAAGAAGACAGGACCTGCTATCTTCGATCTGC--CA--A-
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTAC
* * * *
58935770 C---ATAGGAAGACAAGATCTACTTTCTTCGATCTACTCCACCAC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTAC
* *
58935812 CAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTAC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTAC
* * *
58935855 CAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACTGC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTAC
* * * * * * * *
58935900 CAACACAGGAAGACAAGATCTACT-TTTTTGATCTACTCCGCCAC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTAC
* *
58935944 CAATATGGGAAGACAAGATCTGC-ATCCTT-GATCCACTTC-CTAC
1 CAATATAGGAAGACAAGATCTGCTAT-CTTCGATCTACTTCACTAC
* *
58935987 CAATATAGGAAGACAAGGTCTGC-ATCTTCGATCCACTTC-CTAC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTAC
* * *
58936030 CAATATAGGAAGACAGGATTTGC-ATCTTCGATCCACTTC-CTAC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTAC
* * * * *
58936073 CAATATAGGAAGATAGGACCTGCTATCTTTGATCTACTTCAC-GC
1 CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTAC
* * *
58936117 CAAAACATGAAGACAAGATCTGCT
1 CAATATAGGAAGACAAGATCTGCT
58936141 TTAATGACTT
Statistics
Matches: 401, Mismatches: 80, Indels: 36
0.78 0.15 0.07
Matches are distributed among these distances:
37 27 0.07
39 2 0.00
40 1 0.00
41 2 0.00
42 5 0.01
43 144 0.36
44 160 0.40
45 60 0.15
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (45 bp):
CAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTAC
Found at i:58935762 original size:132 final size:132
Alignment explanation
Indices: 58935598--58936025 Score: 626
Period size: 125 Copynumber: 3.3 Consensus size: 132
58935588 ATCTGTTCCA
* * * *
58935598 CAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAAAAGATTT
1 CAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCCAACACAGGAAGACAAGATCT
* * * *
58935663 GCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCT
66 ACTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCT
58935728 AC
131 AC
* *
58935730 CAATATAAGAAGACAGGACCTGCTATCTTCGA--T-C-T---GCCAACATAGGAAGACAAGATCT
1 CAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCCAACACAGGAAGACAAGATCT
*
58935788 ACTTTCTTCGATCTACTCCACCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCT
66 ACTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCT
58935853 AC
131 AC
58935855 CAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACTGCCAACACAGGAAGACAAGATC
1 CAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCAC-GCCAACACAGGAAGACAAGATC
*
58935920 TACTTT-TTTGATCTACTCCGCCACCAATATGGGAAGACAAGATCTGCATCCTT-GATCCACTTC
65 TACTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATCTGCAT-CTTCGATCCACTTC
58935983 CTAC
129 CTAC
* *
58935987 CAATATAGGAAGACAAGG-TCTGC-ATCTTCGATCCACTTC
1 CAATATAGGAAGAC-AGGACCTGCTATCTTCGATCTACTTC
58936026 CTACCAATAT
Statistics
Matches: 269, Mismatches: 17, Indels: 21
0.88 0.06 0.07
Matches are distributed among these distances:
125 111 0.41
127 1 0.00
128 2 0.01
129 2 0.01
130 1 0.00
131 15 0.06
132 104 0.39
133 33 0.12
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (132 bp):
CAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCCAACACAGGAAGACAAGATCT
ACTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCT
AC
Found at i:58936344 original size:15 final size:15
Alignment explanation
Indices: 58936304--58936344 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
58936294 TAACTAGATG
58936304 TGTATGAATGATATT
1 TGTATGAATGATATT
*
58936319 TGCATTGAATGATATT
1 TGTA-TGAATGATATT
58936335 TGTATGAATG
1 TGTATGAATG
58936345 CAGAATGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.44
Consensus pattern (15 bp):
TGTATGAATGATATT
Found at i:58936833 original size:109 final size:103
Alignment explanation
Indices: 58936647--58936838 Score: 269
Period size: 109 Copynumber: 1.8 Consensus size: 103
58936637 GAAAAATGCT
58936647 TGAAAAAGATTATCAAAATAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAATCAATC
1 TGAAAAAGATTATCAAAATAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAATCAATC
58936712 AAGACAGAAAATTTTGCTGAGATACGAGATGTATAAGA
66 AAGACAGAAAATTTTGCTGAGATACGAGATGTATAAGA
**
58936750 TGAAAAAGATTATCACAATGGATAAGATGGAAA-TTTGTTGAGAGCAAAAGCTCTAAATGAACAA
1 TGAAAAAGATTATCA-AA---ATAA-AT-GAAATTTTGTTGAGAGC-AAAGCTCTAAACAAACAA
* * *
58936814 ATTAATCAAGATAGCAAATTTTGCT
59 ATCAATCAAGACAGAAAATTTTGCT
58936839 AGAATAAAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 8
0.86 0.06 0.09
Matches are distributed among these distances:
103 15 0.19
104 2 0.03
107 4 0.05
108 14 0.18
109 42 0.55
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.26
Consensus pattern (103 bp):
TGAAAAAGATTATCAAAATAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAATCAATC
AAGACAGAAAATTTTGCTGAGATACGAGATGTATAAGA
Found at i:58936880 original size:45 final size:47
Alignment explanation
Indices: 58936812--58936899 Score: 117
Period size: 45 Copynumber: 1.9 Consensus size: 47
58936802 CTAAATGAAC
* *
58936812 AAATTAATCAAGATAGCAAATTTTG-CTAGAATA-AAAAATGAGAAT
1 AAATTAATCAAGATAGCAAATTTTGTCGAAAATACAAAAATGAGAAT
* **
58936857 AAATTAATCAAGATGGCGTATTTTGTCGAAAATACAAAAATGA
1 AAATTAATCAAGATAGCAAATTTTGTCGAAAATACAAAAATGA
58936900 ATAAAATGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 22 0.61
46 6 0.17
47 8 0.22
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (47 bp):
AAATTAATCAAGATAGCAAATTTTGTCGAAAATACAAAAATGAGAAT
Found at i:58936902 original size:45 final size:43
Alignment explanation
Indices: 58936804--58936904 Score: 112
Period size: 45 Copynumber: 2.3 Consensus size: 43
58936794 CAAAAGCTCT
* * *
58936804 AAATGAACAAATTAATCAAGATAGCAAATTTTGCTAGAATAAA
1 AAATGAATAAATTAATCAAGATAGCAAATTTTGCGAAAATAAA
* **
58936847 AAATGAGAATAAATTAATCAAGATGGCGTATTTTGTCGAAAATACAA
1 AAAT--GAATAAATTAATCAAGATAGCAAATTTTG-CGAAAATA-AA
58936894 AAATGAATAAA
1 AAATGAATAAA
58936905 ATGGAAATAG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
43 4 0.08
45 32 0.67
46 6 0.12
47 6 0.12
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.26
Consensus pattern (43 bp):
AAATGAATAAATTAATCAAGATAGCAAATTTTGCGAAAATAAA
Found at i:58937194 original size:12 final size:11
Alignment explanation
Indices: 58937177--58937219 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
58937167 CCTCTCCTTT
58937177 TTCTTTTTGTTA
1 TTCTTTTT-TTA
*
58937189 TTCTTTTCTT-
1 TTCTTTTTTTA
58937199 TTCTTTTTTTA
1 TTCTTTTTTTA
58937210 TTTCTTTTTT
1 -TTCTTTTTT
58937220 CAAGTGAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.33
11 2 0.07
12 16 0.59
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (11 bp):
TTCTTTTTTTA
Found at i:58937200 original size:22 final size:22
Alignment explanation
Indices: 58937175--58937217 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
58937165 GGCCTCTCCT
58937175 TTTTCTTTTTGTTA-TTCTTTTC
1 TTTTCTTTTT-TTATTTCTTTTC
58937197 TTTTCTTTTTTTATTTCTTTT
1 TTTTCTTTTTTTATTTCTTTT
58937218 TTCAAGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (22 bp):
TTTTCTTTTTTTATTTCTTTTC
Found at i:58937695 original size:14 final size:13
Alignment explanation
Indices: 58937678--58937716 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
58937668 GTTCTCTTTT
58937678 TTTTTGTTTTTGTG
1 TTTTTGTTTTTG-G
58937692 TTTTTGGTTTTTGG
1 TTTTT-GTTTTTGG
58937706 TTTTT-TTTTTG
1 TTTTTGTTTTTG
58937717 CCTTTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
14 11 0.46
15 7 0.29
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (13 bp):
TTTTTGTTTTTGG
Found at i:58937711 original size:8 final size:7
Alignment explanation
Indices: 58937677--58937710 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
58937667 TGTTCTCTTT
*
58937677 TTTTTTG
1 TTTTTGG
58937684 TTTTTGTG
1 TTTTTG-G
58937692 TTTTTGG
1 TTTTTGG
58937699 TTTTTGG
1 TTTTTGG
58937706 TTTTT
1 TTTTT
58937711 TTTTTGCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (7 bp):
TTTTTGG
Found at i:58939183 original size:62 final size:62
Alignment explanation
Indices: 58938998--58939184 Score: 302
Period size: 62 Copynumber: 3.0 Consensus size: 62
58938988 CTAAACTCGA
* * * * *
58938998 CGTACTTTTGGATTTTAGGAAATTTACTGTATGCAATGAAACGTAATGTTGATGCATGAATA
1 CGTATTTTTGGATTTTAGGAAATTTATTGCATGCAATGAAATGTAATGTTGATGCATGAATG
* *
58939060 CGTATTTTTGGATTTTAAGAAATTTATTGCATGCAATGAAATTTAATGTTGATGCATGAATG
1 CGTATTTTTGGATTTTAGGAAATTTATTGCATGCAATGAAATGTAATGTTGATGCATGAATG
*
58939122 CGTATTTTTGGATTTTAGGAAATTTATTGCATGCGATGAAATGTAATGTTGATGCATGAATG
1 CGTATTTTTGGATTTTAGGAAATTTATTGCATGCAATGAAATGTAATGTTGATGCATGAATG
58939184 C
1 C
58939185 AAAAAAGAGA
Statistics
Matches: 115, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 115 1.00
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (62 bp):
CGTATTTTTGGATTTTAGGAAATTTATTGCATGCAATGAAATGTAATGTTGATGCATGAATG
Found at i:58943754 original size:20 final size:20
Alignment explanation
Indices: 58943731--58943771 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
58943721 TTAAATTAAA
*
58943731 ATTAATTATAAATAATTTTT
1 ATTAATTATAAATAATATTT
* *
58943751 ATTAATTTTTAATAATATTT
1 ATTAATTATAAATAATATTT
58943771 A
1 A
58943772 ATATTTTCTA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTAATTATAAATAATATTT
Found at i:58943756 original size:10 final size:10
Alignment explanation
Indices: 58943741--58943809 Score: 56
Period size: 10 Copynumber: 7.0 Consensus size: 10
58943731 ATTAATTATA
58943741 AATAATTTTT
1 AATAATTTTT
*
58943751 ATTAATTTTT
1 AATAATTTTT
*
58943761 AATAATATTT
1 AATAATTTTT
58943771 AAT-ATTTTCT
1 AATAATTTT-T
*
58943781 -AT-ATTTTA
1 AATAATTTTT
58943789 AATAATTATTT
1 AATAATT-TTT
58943800 -ATAAATTTTT
1 AAT-AATTTTT
58943810 TGAACAACCA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
9 13 0.27
10 29 0.60
11 6 0.12
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (10 bp):
AATAATTTTT
Found at i:58944504 original size:17 final size:17
Alignment explanation
Indices: 58944490--58944524 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
58944480 TATTTTTTTA
58944490 TTTTTCTTCTTTTTTCT
1 TTTTTCTTCTTTTTTCT
58944507 TTTTTCTTC-TTTTTCT
1 TTTTTCTTCTTTTTTCT
58944523 TT
1 TT
58944525 CCTTATTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTCTTTTTTCT
Found at i:58944644 original size:12 final size:12
Alignment explanation
Indices: 58944627--58944712 Score: 70
Period size: 12 Copynumber: 7.1 Consensus size: 12
58944617 TCTTCCCTTC
58944627 TCCTTCTTTTCT
1 TCCTTCTTTTCT
*
58944639 TCCTTCTCTTCT
1 TCCTTCTTTTCT
*
58944651 TCCTT-TTTTCC
1 TCCTTCTTTTCT
58944662 TCCTT-TTTTCTTT
1 TCCTTCTTTTC--T
58944675 TCCTTTCTCTTTCT
1 TCC-TTCT-TTTCT
*
58944689 TTCTT-TTTTCT
1 TCCTTCTTTTCT
* *
58944700 TCTTTCTTCTCT
1 TCCTTCTTTTCT
58944712 T
1 T
58944713 TTCTCCCCTT
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
11 22 0.37
12 23 0.38
13 5 0.08
14 5 0.08
15 1 0.02
16 4 0.07
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (12 bp):
TCCTTCTTTTCT
Found at i:58944644 original size:23 final size:23
Alignment explanation
Indices: 58944618--58944666 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
58944608 GCGTCCCCTT
*
58944618 CTTCCCTTC-TCCTTCTTTTCTTC
1 CTTCCCTTCTTCCTT-TTTTCCTC
*
58944641 CTTCTCTTCTTCCTTTTTTCCTC
1 CTTCCCTTCTTCCTTTTTTCCTC
58944664 CTT
1 CTT
58944667 TTTTCTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (23 bp):
CTTCCCTTCTTCCTTTTTTCCTC
Found at i:58944676 original size:39 final size:39
Alignment explanation
Indices: 58944630--58944718 Score: 87
Period size: 39 Copynumber: 2.3 Consensus size: 39
58944620 TCCCTTCTCC
58944630 TTCTTTTCTTCC-T-TCTCTTCTTCCTTTTTTCCTCCTTT-T
1 TTCTTTTC-TCCTTCTCT-TTCTTCCTTTTTT-CTCCTTTCT
* * *
58944669 TTCTTTTC-CTTTCTCTTTCTTTCTTTTTTCTTCTTTCT
1 TTCTTTTCTCCTTCTCTTTCTTCCTTTTTTCTCCTTTCT
58944707 TCTCTTTTCTCC
1 T-TCTTTTCTCC
58944719 CCTTTTTCGT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
37 7 0.17
38 15 0.37
39 18 0.44
40 1 0.02
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (39 bp):
TTCTTTTCTCCTTCTCTTTCTTCCTTTTTTCTCCTTTCT
Found at i:58944687 original size:27 final size:27
Alignment explanation
Indices: 58944645--58944718 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
58944635 TTCTTCCTTC
58944645 TCTTCTTCCTT-T-TTTCCTCCTTTTT
1 TCTTCTTCCTTCTCTTTCCTCCTTTTT
* *
58944670 TCTT-TTCCTTTCTCTTTCTTTCTTTTT
1 TCTTCTTCC-TTCTCTTTCCTCCTTTTT
* *
58944697 TCTTCTTTCTTCTCTTTTCTCC
1 TCTTCTTCCTTCTCTTTCCTCC
58944719 CCTTTTTCGT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
24 4 0.10
25 6 0.15
26 1 0.03
27 25 0.64
28 3 0.08
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (27 bp):
TCTTCTTCCTTCTCTTTCCTCCTTTTT
Found at i:58944709 original size:17 final size:17
Alignment explanation
Indices: 58944629--58944716 Score: 61
Period size: 20 Copynumber: 4.7 Consensus size: 17
58944619 TTCCCTTCTC
58944629 CTTCTTTTCTTCCTTCTCTT
1 CTTCTTTT-TT-CTTCT-TT
*
58944649 CTTCCTTTTTTCCTCCTTT
1 CTT-CTTTTTT-CTTCTTT
*
58944668 TTTCTTTTCCTT-TCTCTTT
1 CTTCTTTT--TTCT-TCTTT
58944687 CTTTCTTTTTTCTTCTTT
1 C-TTCTTTTTTCTTCTTT
*
58944705 CTTCTCTTTTCT
1 CTTCTTTTTTCT
58944717 CCCCTTTTTC
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
17 10 0.18
18 14 0.25
19 9 0.16
20 19 0.33
21 5 0.09
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CTTCTTTTTTCTTCTTT
Found at i:58944769 original size:9 final size:9
Alignment explanation
Indices: 58944755--58944788 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
58944745 GCTTAGGTAC
58944755 GACGGTGAT
1 GACGGTGAT
58944764 GACGGTGATT
1 GACGGTGA-T
58944774 G-CGGTGAT
1 GACGGTGAT
58944782 GACGGTG
1 GACGGTG
58944789 GCGGCACGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.09
9 19 0.83
10 2 0.09
ACGTcount: A:0.18, C:0.12, G:0.47, T:0.24
Consensus pattern (9 bp):
GACGGTGAT
Found at i:58945538 original size:76 final size:75
Alignment explanation
Indices: 58945351--58946530 Score: 1432
Period size: 76 Copynumber: 15.3 Consensus size: 75
58945341 TTTCTTTCTG
* * * * * * * * * * *
58945351 TTTGAAAAATAGAAATCGAAAATAGCTCAGTGTGCGACCCGAAGCTCAACTCATCTATTGGATTA
1 TTTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTA
58945416 TGAG-T--TT
66 TGAGTTGATT
* * *
58945423 TTTGAAAATAAACAGAAATTGAAAATACCTCAGCCTGTGACCCGAGGCTCAACTCACCTCTCGGA
1 TTTG--AA-AAACAGAAATTGAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCA
*
58945488 TTATGATTTGATT
63 TTATGAGTTGATT
* * * *
58945501 TTTGAAAAAACAGAAATTGAAAATACCTCTGCATGTGACCCGAGGCTCAACTCACCTCTTGAATT
1 TTTG-AAAAACAGAAATTGAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATT
58945566 ATGAGTTGATT
65 ATGAGTTGATT
* * ** * *
58945577 TTTGAAAAAATAGAAATTGAAAGTACCTTAGTGTGCGACCCGAGGCTCAACTCACCTCTCGCATT
1 TTTG-AAAAACAGAAATTGAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATT
58945642 ATGAGTTGATT
65 ATGAGTTGATT
* ** * *
58945653 TTTGAAAAAATAGAAATTGAAAATACCTCAACGTGCGACCCGAGGATCAACTCACCTCTCGCATT
1 TTTG-AAAAACAGAAATTGAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATT
* *
58945718 TTGAGTTCATTT
65 ATGAGTTGA-TT
* * * *
58945730 TTTCGAAAAACATAAAATGAAAAATACCTCGGCGTGTGACCCAAGGCTCAACTCATCTCTCGCAT
1 TTT-GAAAAACAGAAATTG-AAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAT
58945795 TATGAGTTGATTTT
64 TATGAGTTGA--TT
* * *
58945809 CTTTTAAAAACA-AAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCATCTCTCGCATT
1 -TTTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATT
58945873 ATGAGTTGATT
65 ATGAGTTGATT
* * * *
58945884 TTTGAAAAAATAGAAATTGAAAAATACCTCAGCATGTGACTCGAGGCTCAACTCACCTCTCGCAT
1 TTTG-AAAAACAGAAATTG-AAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAT
58945949 TATGAGTTGATT
64 TATGAGTTGATT
*
58945961 TTTGAAAAACATAAATTGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATT
1 TTTGAAAAACAGAAATTG-AAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATT
58946026 ATGAGTTGATTTTTT
65 ATGAGTTGA----TT
* * * * *
58946041 TTTGTAAAACAAAAATTAAAAATACCTCGGTGTGCGACCCGAGGCTCAACTCACCTCTCGCATTA
1 TTTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTA
58946106 TGAGTTGATT
66 TGAGTTGATT
*
58946116 TTTGAAAAACATAAATTGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATT
1 TTTGAAAAACAGAAATTG-AAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATT
58946181 ATGAGTTGATTTTTTT
65 ATGAGTTGA-----TT
* * * *
58946197 TTTGTAAAACAGAAATTAAAAATACCTCGGTGTGCGACCCGAGGCTCAACTCACCTCTCGCATTA
1 TTTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTA
58946262 TGAGTTGATT
66 TGAGTTGATT
* * **
58946272 TTTGAAAAAACTGAAATTGAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTAACAT
1 TTTG-AAAAACAGAAATTG-AAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAT
*
58946337 TAAGAGTTGATT
64 TATGAGTTGATT
*
58946349 TTTGAAAAACAGAAATTGAAAAATACCCCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATT
1 TTTGAAAAACAGAAATTG-AAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATT
58946414 ATGAGTTGATTTT
65 ATGAGTTGA--TT
* * * *
58946427 TTTGAAAAACATAAATTGAAAATACCTCAGCGTGCGACCAGAGGCTCAACTCACCTCTCGCATTA
1 TTTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTA
* *
58946492 GGAGTTGTTTTTT
66 TGAGTTG---ATT
*
58946505 TTTGAAAAACAGATATTGAAAATACC
1 TTTGAAAAACAGAAATTGAAAATACC
58946531 ATAGCATTGT
Statistics
Matches: 981, Mismatches: 96, Indels: 56
0.87 0.08 0.05
Matches are distributed among these distances:
72 4 0.00
74 5 0.01
75 83 0.08
76 398 0.41
77 234 0.24
78 104 0.11
79 63 0.06
80 73 0.07
81 17 0.02
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (75 bp):
TTTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTA
TGAGTTGATT
Found at i:58945885 original size:155 final size:153
Alignment explanation
Indices: 58945355--58947244 Score: 1631
Period size: 154 Copynumber: 12.0 Consensus size: 153
58945345 TTTCTGTTTG
* * * * * * * * * *
58945355 AAAAATAGAAATCGAAAATAGCTCAGTGTGCGACCCGAAGCTCAACTCATCTATTGGATTATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAG
*** * * * *
58945420 TT--TTTTGAAAATAAACAGAAATTG-AAAATACCTCAGCCTGTGACCCGAGGCTCAACTCACCT
66 TTGATTTTTTGAA-AAACATAAAATGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCT
* * *
58945482 CTCGGATTATGATTTGATTTTTGA
130 CTCGCATTATGAGTTGATTTTTTA
* * * *
58945506 AAAAACAGAAATTGAAAATACCTCTGCATGTGACCCGAGGCTCAACTCACCTCTTGAATTATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAG
* ** * *
58945571 TTGA-TTTTTGAAAAA-ATAGAAATTG-AAAGTACCTTAGTGTGCGACCCGAGGCTCAACTCACC
66 TTGATTTTTTGAAAAACATA-AAA-TGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACC
*
58945633 TCTCGCATTATGAGTTGATTTTTGA
129 TCTCGCATTATGAGTTGATTTTTTA
* * * * *
58945658 AAAAATAGAAATTGAAAATACCTCAACGTGCGACCCGAGGATCAACTCACCTCTCGCATTTTGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAG
* * *
58945723 TTCATTTTTTCGAAAAACATAAAATGAAAAATACCTCGGCGTGTGACCCAAGGCTCAACTCATCT
66 TTGATTTTTT-GAAAAACATAAAATGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCT
*
58945788 CTCGCATTATGAGTTGATTTTCTTTT
130 CTCGCATTATGAGTTGA-TTT-TTTA
*
58945814 AAAAACA-AAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCATCTCTCGCATTATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAG
* * *
58945878 TTGA-TTTTTGAAAAA-ATAGAAATTGAAAAATACCTCAGCATGTGACTCGAGGCTCAACTCACC
66 TTGATTTTTTGAAAAACATA-AAA-TGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACC
*
58945941 TCTCGCATTATGAGTTGA-TTTTTG
129 TCTCGCATTATGAGTTGATTTTTTA
* *
58945965 AAAAACATAAATTGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGA
1 AAAAACAGAAATTG-AAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGA
* * * *
58946030 GTTGATTTTTTTTTGTAAAACA-AAAATTAAAAATACCTCGGTGTGCGACCCGAGGCTCAACTCA
65 GTTGA---TTTTTTGAAAAACATAAAATGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCA
*
58946094 CCTCTCGCATTATGAGTTGA-TTTTTG
127 CCTCTCGCATTATGAGTTGATTTTTTA
* *
58946120 AAAAACATAAATTGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGA
1 AAAAACAGAAATTG-AAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGA
* * * * *
58946185 GTTGATTTTTTTTTTGTAAAACA-GAAATTAAAAATACCTCGGTGTGCGACCCGAGGCTCAACTC
65 GTTGA----TTTTTTGAAAAACATAAAATGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTC
*
58946249 ACCTCTCGCATTATGAGTTGATTTTTGA
126 ACCTCTCGCATTATGAGTTGATTTTTTA
* * * ** *
58946277 AAAAACTGAAATTGAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTAACATTAAGA
1 AAAAACAGAAATTG-AAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGA
* * *
58946342 GTTGA-TTTTTGAAAAACAGAAATTGAAAAATACCCCGGCGTGTGACCCGAGGCTCAACTCACCT
65 GTTGATTTTTTGAAAAACATAAAATGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCT
*
58946406 CTCGCATTATGAGTTGATTTTTTTG
130 CTCGCATTATGAGTTGA-TTTTTTA
* * * *
58946431 AAAAACATAAATTGAAAATACCTCAGCGTGCGACCAGAGGCTCAACTCACCTCTCGCATTAGGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAG
* * * * * * * *
58946496 TTGTTTTTTTTTGAAAAACAGATATTG-AAAATACCAT-AGCATTGTTTTTTTTTGAAAAACAGA
66 TTG--ATTTTTTGAAAAACATAAAATGAAAAATACC-TCGGC---G------TGTG---ACCCGA
*** * * * * * * * **
58946559 AATTGAAAAT-ACC-ATAGCATGCGACCCGAGGCTCAACTCACCTCTCGCATT-
116 GGCT-CAACTCACCTCTCGCAT--TA--TGA-G-T----TGA--T-T--TTTTA
** *** ** **
58946610 ATGAGTTGATTTTTTGAAAAATAGAAATTGAAAATACCTCAGCGTACGACCCGAGGCTCAACTCA
1 AAAAACAGA--AATTGAAA--------------ATACCTCAGCGTGTGACCCGAGGCTCAACTCA
* * * **
58946675 ACTCTCGCATTATGAGTTGATTTTTTTTGAAAAACATAAATTG-AAAATACCTCAGCGTACGACC
50 CCTCTCGCATTATGAGTTGA--TTTTTTGAAAAACATAAAATGAAAAATACCTCGGCGTGTGACC
*
58946739 CGAGGCTCAACTCACCTCTCGCATT-TGAGTTGATTTTTTTG
113 CGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTTTA
* * * * *
58946780 AAAAACATAAATTG-AAATACCTCAGCGTGCGGCCCGAGACTCAACCCACCTCTCGCATTATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAG
** * * * *
58946844 TTGATTTTTTTGAAAAACAT-AAATTTACAATACCTCAGCGTGCGACCAGAGGCTCAACTCACCT
66 TTGA-TTTTTTGAAAAACATAAAATGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCT
* *
58946908 CTCGCATTATAAGTTGA-TTTTTG
130 CTCGCATTATGAGTTGATTTTTTA
* *
58946931 AAAAACAGAAATTAAAAAAATACCCCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
1 AAAAACAGAAATT--GAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATG
* * *
58946996 AGTTGATTTTTGGAAAAAAACA-AAAATTAAAAAATACCTCGGCATGTG-CCCGAGGCTCAACTC
64 AGTTGATTTTTTG--AAAAACATAAAA-TGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTC
* *
58947059 ACCTCTCGTATTATGAGTTGA-TTTTTG
126 ACCTCTCGCATTATGAGTTGATTTTTTA
* * *
58947086 AAAAACAAAAATTGAAAAATACCTCAGCGTGCGACCTGAGGCTCAACTCACCTCTCGCATTATGA
1 AAAAACAGAAATTG-AAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGA
* * * * *
58947151 GTTGATTCTTGGAAAAGAACATAAATTAAAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCAC
65 GTTGATTTTTTG-AAA-AACATAAAATGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCAC
* * *
58947215 CTCTCACATTATGAGTTGACTTTTGA
128 CTCTCGCATTATGAGTTGATTTTTTA
58947241 AAAA
1 AAAA
58947245 CATAAAAAGA
Statistics
Matches: 1460, Mismatches: 190, Indels: 174
0.80 0.10 0.10
Matches are distributed among these distances:
150 2 0.00
151 92 0.06
152 203 0.14
153 236 0.16
154 298 0.20
155 271 0.19
156 123 0.08
157 79 0.05
158 2 0.00
164 3 0.00
166 5 0.00
167 10 0.01
168 7 0.00
169 2 0.00
170 5 0.00
171 2 0.00
172 2 0.00
173 2 0.00
176 2 0.00
177 2 0.00
178 2 0.00
179 5 0.00
180 2 0.00
181 6 0.00
182 3 0.00
183 8 0.01
184 5 0.00
186 2 0.00
192 1 0.00
194 1 0.00
195 77 0.05
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.28
Consensus pattern (153 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAG
TTGATTTTTTGAAAAACATAAAATGAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTC
TCGCATTATGAGTTGATTTTTTA
Found at i:58946553 original size:41 final size:41
Alignment explanation
Indices: 58946496--58946578 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
58946486 GCATTAGGAG
*
58946496 TTGTTTTTTTTTGAAAAACAGATATTGAAAATACCATAGCA
1 TTGTTTTTTTTTGAAAAACAGAAATTGAAAATACCATAGCA
58946537 TTGTTTTTTTTTGAAAAACAGAAATTGAAAATACCATAGCA
1 TTGTTTTTTTTTGAAAAACAGAAATTGAAAATACCATAGCA
58946578 T
1 T
58946579 GCGACCCGAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.39
Consensus pattern (41 bp):
TTGTTTTTTTTTGAAAAACAGAAATTGAAAATACCATAGCA
Found at i:58946682 original size:195 final size:197
Alignment explanation
Indices: 58946347--58946725 Score: 618
Period size: 195 Copynumber: 1.9 Consensus size: 197
58946337 TAAGAGTTGA
* * * *
58946347 TTTTTGAAAAACAGAAATTGAAAAATACCCCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCA
1 TTTTTGAAAAACAGAAATTGAAAAATACCACAGCATGCGACCCGAGGCTCAACTCACCTCTCGCA
* *
58946412 TTATGAGTTGATTTTTTTGAAAAACATAAATTGAAAATACCTCAGCGTGCGACCAGAGGCTCAAC
66 TTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTACGACCAGAGGCTCAAC
* * *
58946477 TCACCTCTCGCATTAGGAGTTGTTTTTTTTTGAAAAACAGATATTGAAAATACCATAGCATTGTT
131 TCAACTCTCGCATTAGGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAATACCATAGCATTGTT
58946542 TT
196 TT
*
58946544 TTTTTGAAAAACAGAAATTG-AAAATACCATAGCATGCGACCCGAGGCTCAACTCACCTCTCGCA
1 TTTTTGAAAAACAGAAATTGAAAAATACCACAGCATGCGACCCGAGGCTCAACTCACCTCTCGCA
* *
58946608 TTATGAGTTGA-TTTTTTGAAAAATAGAAATTGAAAATACCTCAGCGTACGACCCGAGGCTCAAC
66 TTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTACGACCAGAGGCTCAAC
* *
58946672 TCAACTCTCGCATTATGAGTTGATTTTTTTTGAAAAACATAAATTGAAAATACC
131 TCAACTCTCGCATTAGGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAATACC
58946726 TCAGCGTACG
Statistics
Matches: 168, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
195 98 0.58
196 50 0.30
197 20 0.12
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (197 bp):
TTTTTGAAAAACAGAAATTGAAAAATACCACAGCATGCGACCCGAGGCTCAACTCACCTCTCGCA
TTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTACGACCAGAGGCTCAAC
TCAACTCTCGCATTAGGAGTTGATTTTTTTTGAAAAACAGAAATTGAAAATACCATAGCATTGTT
TT
Found at i:58946743 original size:78 final size:76
Alignment explanation
Indices: 58946543--58947250 Score: 919
Period size: 76 Copynumber: 9.2 Consensus size: 76
58946533 AGCATTGTTT
* *
58946543 TTTTTTGAAAAACAGAAATTGAAAATACCAT-AGCATGCGACCCGAGGCTCAACTCACCTCTCGC
1 TTTTTTGAAAAACATAAATTGAAAATACC-TCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGC
58946607 ATTATGAGTTGA
65 ATTATGAGTTGA
* * * *
58946619 TTTTTTGAAAAATAGAAATTGAAAATACCTCAGCGTACGACCCGAGGCTCAACTCAACTCTCGCA
1 TTTTTTGAAAAACATAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCA
58946684 TTATGAGTTGA
66 TTATGAGTTGA
*
58946695 TTTTTTTTGAAAAACATAAATTGAAAATACCTCAGCGTACGACCCGAGGCTCAACTCACCTCTCG
1 --TTTTTTGAAAAACATAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCG
58946760 CATT-TGAGTTGA
64 CATTATGAGTTGA
* * *
58946772 TTTTTTTGAAAAACATAAATTG-AAATACCTCAGCGTGCGGCCCGAGACTCAACCCACCTCTCGC
1 -TTTTTTGAAAAACATAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGC
58946836 ATTATGAGTTGA
65 ATTATGAGTTGA
* * *
58946848 TTTTTTTGAAAAACATAAATTTACAATACCTCAGCGTGCGACCAGAGGCTCAACTCACCTCTCGC
1 -TTTTTTGAAAAACATAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGC
*
58946913 ATTATAAGTTGA
65 ATTATGAGTTGA
* * * *
58946925 -TTTTTGAAAAACAGAAATTAAAAAAATACCCCAGCGTGTGACCCGAGGCTCAACTCACCTCTCG
1 TTTTTTGAAAAACATAAATT--GAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCG
58946989 CATTATGAGTTGA
64 CATTATGAGTTGA
* * * * * *
58947002 TTTTTGGAAAAAAACAAAAATTAAAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTC
1 TTTTTTG--AAAAACATAAATT-GAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTC
*
58947066 GTATTATGAGTTGA
63 GCATTATGAGTTGA
* *
58947080 -TTTTTGAAAAACAAAAATTGAAAAATACCTCAGCGTGCGACCTGAGGCTCAACTCACCTCTCGC
1 TTTTTTGAAAAACATAAATTG-AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGC
58947144 ATTATGAGTTGA
65 ATTATGAGTTGA
* * * * * *
58947156 TTCTTGGAAAAGAACATAAATTAAAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTC
1 TTTTTTG-AAA-AACATAAATT-GAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTC
*
58947220 ACATTATGAGTTGA
63 GCATTATGAGTTGA
*
58947234 -CTTTTGAAAAACATAAA
1 TTTTTTGAAAAACATAAA
58947251 AAGAAATAAT
Statistics
Matches: 566, Mismatches: 50, Indels: 33
0.87 0.08 0.05
Matches are distributed among these distances:
75 96 0.17
76 158 0.28
77 118 0.21
78 141 0.25
79 41 0.07
80 12 0.02
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.27
Consensus pattern (76 bp):
TTTTTTGAAAAACATAAATTGAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCA
TTATGAGTTGA
Found at i:58950954 original size:25 final size:25
Alignment explanation
Indices: 58950901--58950954 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
58950891 TAGAGTCTTG
***
58950901 TGTTTATAAAATCTCTTCAGTGTTG
1 TGTTTATAAAATCTCTTCAGTGAAC
**
58950926 TGTTTATAAAATCTCTTCTTTGAAC
1 TGTTTATAAAATCTCTTCAGTGAAC
58950951 TGTT
1 TGTT
58950955 GCCCCCAAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.50
Consensus pattern (25 bp):
TGTTTATAAAATCTCTTCAGTGAAC
Found at i:58956249 original size:20 final size:20
Alignment explanation
Indices: 58956224--58956274 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
58956214 TTGTTTTAAA
*
58956224 TAAATTTTTAGTTTAGGATT
1 TAAATTTTTAGTTTAGGATC
* * *
58956244 TAAATTTATAATTTAGGGTC
1 TAAATTTTTAGTTTAGGATC
*
58956264 TAAAATTTTAG
1 TAAATTTTTAG
58956275 GATATAAAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49
Consensus pattern (20 bp):
TAAATTTTTAGTTTAGGATC
Found at i:58956275 original size:15 final size:15
Alignment explanation
Indices: 58956255--58956303 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
58956245 AAATTTATAA
*
58956255 TTTAGGGTCTAAAAT
1 TTTAGGGTATAAAAT
*
58956270 TTTAGGATATAAAA-
1 TTTAGGGTATAAAAT
58956284 TTTAGGGTTATAAAAT
1 TTTAGGG-TATAAAAT
58956300 TTTA
1 TTTA
58956304 TAAAAACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 6 0.21
15 19 0.66
16 4 0.14
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.43
Consensus pattern (15 bp):
TTTAGGGTATAAAAT
Found at i:58956702 original size:14 final size:14
Alignment explanation
Indices: 58956683--58956722 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
58956673 TTGATTGTCA
58956683 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
58956697 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
58956711 GGAAAATGTTTT
1 GTAAAATGTTTT
58956723 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:58956731 original size:20 final size:20
Alignment explanation
Indices: 58956706--58956745 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
58956696 CGTAAAATGA
*
58956706 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
58956726 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
58956746 AGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:58956735 original size:34 final size:35
Alignment explanation
Indices: 58956691--58956757 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
58956681 CAGTAAAATG
* *
58956691 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
*
58956725 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
58956758 CTGTTATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:58961776 original size:20 final size:20
Alignment explanation
Indices: 58961751--58961788 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
58961741 CTTTTCGTTC
58961751 ACAATCACAATACGTAATAG
1 ACAATCACAATACGTAATAG
58961771 ACAATCACAATACGTAAT
1 ACAATCACAATACGTAAT
58961789 TTAGGAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.21, G:0.08, T:0.21
Consensus pattern (20 bp):
ACAATCACAATACGTAATAG
Found at i:58965338 original size:27 final size:27
Alignment explanation
Indices: 58965299--58965393 Score: 127
Period size: 27 Copynumber: 3.5 Consensus size: 27
58965289 AAAGGTTGTT
* * * *
58965299 AAATAATCGTAATGCCCCTGTAGGATA
1 AAATGATCGTAATACCCCTATAGGGTA
* *
58965326 AAATGATCATAATTCCCCTATAGGGTA
1 AAATGATCGTAATACCCCTATAGGGTA
*
58965353 AAATGACCGTAATACCCCTATAGGGTA
1 AAATGATCGTAATACCCCTATAGGGTA
58965380 AAATGATCGTAATA
1 AAATGATCGTAATA
58965394 TTCTCGAGAT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (27 bp):
AAATGATCGTAATACCCCTATAGGGTA
Found at i:58965471 original size:24 final size:25
Alignment explanation
Indices: 58965430--58965476 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
58965420 CTATGGTTAA
*
58965430 ATGACTGATTTATCTGTG-TTTGGT
1 ATGACCGATTTATCTGTGATTTGGT
* *
58965454 ATGACCGATTTGTTTGTGATTTG
1 ATGACCGATTTATCTGTGATTTG
58965477 AATGACTGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.17, C:0.09, G:0.26, T:0.49
Consensus pattern (25 bp):
ATGACCGATTTATCTGTGATTTGGT
Found at i:58965719 original size:32 final size:32
Alignment explanation
Indices: 58965673--58965875 Score: 230
Period size: 32 Copynumber: 6.4 Consensus size: 32
58965663 GCTGTGATGC
* *
58965673 TACTAATGGCTTTGTGCCGGTCATATTACTGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* *
58965705 TACTGATGGCTTTGTACTGATCATATTACTGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* *
58965737 TACTGATGGCTTTATGCTGATCATATTA-TCGT
1 TACTGATGGCTTTGTGCCGATCATATTACT-GT
* * *
58965769 TACTGATGGCTTTATGTCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* * * *
58965801 TACTGATGGCTGTGTACCGATCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* * *
58965833 TACTGATGGCTTTGTGCCAAACATATTACT-A
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
*
58965864 TACTTATGGCTT
1 TACTGATGGCTT
58965876 GTAGCCTGTT
Statistics
Matches: 146, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
31 12 0.08
32 134 0.92
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACTGT
Found at i:58965858 original size:96 final size:96
Alignment explanation
Indices: 58965673--58965860 Score: 259
Period size: 96 Copynumber: 2.0 Consensus size: 96
58965663 GCTGTGATGC
* * * * * * *
58965673 TACTAATGGCTTTGTGCCGGTCATATTACTGTTACTGATGGCTTTGTACTGATCATATTACTGTT
1 TACTAATGGCTTTATGCCGATCATATTACCGTTACTGATGGCTGTGTACCGATCATATCACTGCT
** *
58965738 ACTGATGGCTTTATGCTGATCATATTATCGT
66 ACTGATGGCTTTATGCCAAACATATTATCGT
* *
58965769 TACTGATGGCTTTATGTCGATCATATTACCGTTACTGATGGCTGTGTACCGATCATATCACTGCT
1 TACTAATGGCTTTATGCCGATCATATTACCGTTACTGATGGCTGTGTACCGATCATATCACTGCT
*
58965834 ACTGATGGCTTTGTGCCAAACATATTA
66 ACTGATGGCTTTATGCCAAACATATTA
58965861 CTATACTTAT
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
96 79 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (96 bp):
TACTAATGGCTTTATGCCGATCATATTACCGTTACTGATGGCTGTGTACCGATCATATCACTGCT
ACTGATGGCTTTATGCCAAACATATTATCGT
Found at i:58969676 original size:23 final size:25
Alignment explanation
Indices: 58969628--58969683 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
58969618 TATAGTTATG
58969628 AAAAATAATTACATATATAAAATAA
1 AAAAATAATTACATATATAAAATAA
**
58969653 AAAAATAATTACATA-AT-ATTTAA
1 AAAAATAATTACATATATAAAATAA
58969676 AAAAATAA
1 AAAAATAA
58969684 ATATGCGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 12 0.41
24 2 0.07
25 15 0.52
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.29
Consensus pattern (25 bp):
AAAAATAATTACATATATAAAATAA
Found at i:58971448 original size:128 final size:130
Alignment explanation
Indices: 58971164--58971451 Score: 286
Period size: 128 Copynumber: 2.2 Consensus size: 130
58971154 CTTCAATCTA
* * *
58971164 CTCCTCTGCAACTTCAGGGAGATAAGACTAGATGTGATATGCTCTATGCAACTTCAGAGAATAAG
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATATGCTCTATGCAACTTCAAAGAATAAG
* *
58971229 ATCCAAGATTTGTGGTTCTAATCCGCTCCATTGCAACTTCAGGAGGATAAGACTTGCTTACTTAG
66 ATCCAAGA--TGT-GTTCTAATCCGCTCCACTGCAACTTCAGGAGGATAAGACTTGCTTA-TTAA
*
58971294 TCTG
127 CCTG
* ** * * * *
58971298 CTCCACTACCTCTTTAGAGAGATAAGACTAGATGCGATCTGCTC-ACTGCAACTTCAAAGAGTTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATATGCTCTA-TGCAACTTCAAAGA-ATA
* * *
58971362 TGATCCAA-A-GT-TT-TAATCCGCTCCACTGCAACTTCAGG-GAGATAGGATTATCGGC-T-TT
64 AGATCCAAGATGTGTTCTAATCCGCTCCACTGCAACTTCAGGAG-GATAAGACT-T--GCTTATT
58971420 AACCTG
125 AACCTG
58971426 CTCCACTGCAACTTCAGGGAGATAAG
1 CTCCACTGCAACTTCAGGGAGATAAG
58971452 GTTTCCAATC
Statistics
Matches: 127, Mismatches: 21, Indels: 18
0.77 0.13 0.11
Matches are distributed among these distances:
127 1 0.01
128 58 0.46
129 3 0.02
130 1 0.01
131 4 0.03
133 1 0.01
134 50 0.39
135 9 0.07
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (130 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATATGCTCTATGCAACTTCAAAGAATAAG
ATCCAAGATGTGTTCTAATCCGCTCCACTGCAACTTCAGGAGGATAAGACTTGCTTATTAACCTG
Found at i:58971635 original size:217 final size:217
Alignment explanation
Indices: 58971260--58971842 Score: 880
Period size: 217 Copynumber: 2.7 Consensus size: 217
58971250 TCCGCTCCAT
* ** * *
58971260 TGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTACCTCTTTAGAGAGATAAGA
1 TGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
* * * * *
58971325 CTAGATGCGATCTGCTCACTGCAACTTCAAAG-AGTTATGATCCAAAGTTTTAATCCGCTCCACT
66 CTAGATGGGATCTGCTCTCTGCAACTTCAGAGAAATAAT-ATCCAAAGTTTTAATCCGCTCCACT
* *
58971389 GCAACTTCAGGGAGATAGGATTATCGGCTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGGT
130 GCAACTTCAGGGAGATAGGACTATCGGCTTTAACCTGCTCCACTGCAACTTCAGGAAGATAAGGT
58971454 TTCCAATCTGCAGTCTGCCTCAC
195 TTCCAATCTGCAGTCTGCCTCAC
58971477 TGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 TGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
* * * * *
58971542 CTAGATGGGATATGCTCTCTACAACTTCAGAGAAATAATATCCAAGGTTCTAATCCGCTCCACTA
66 CTAGATGGGATCTGCTCTCTGCAACTTCAGAGAAATAATATCCAAAGTTTTAATCCGCTCCACTG
*
58971607 CAACTTCAGGGAGATAGGACTATCGGCTTTAACCTGCTCTACTGCAACTTCAGGAAGATAAGGTT
131 CAACTTCAGGGAGATAGGACTATCGGCTTTAACCTGCTCCACTGCAACTTCAGGAAGATAAGGTT
* *
58971672 TGCAATCTTCAGTCTGCCTCAC
196 TCCAATCTGCAGTCTGCCTCAC
* * * *
58971694 TGTAACTTCAGGAGGATAAAACTTGCTTACTTAGTCTGCTCCCCTGCAACTTCAAGGAGATAAGA
1 TGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
* * * * *
58971759 CTAGATGGGATCTACTCTCTGCAACTTCAGAGAGATAAGATCCAATGTTTTAATCCTCTCCACTG
66 CTAGATGGGATCTGCTCTCTGCAACTTCAGAGAAATAATATCCAAAGTTTTAATCCGCTCCACTG
*
58971824 CAACTTCAGGGAAATAGGA
131 CAACTTCAGGGAGATAGGA
58971843 TTATTGGCCA
Statistics
Matches: 331, Mismatches: 34, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
217 327 0.99
218 4 0.01
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (217 bp):
TGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
CTAGATGGGATCTGCTCTCTGCAACTTCAGAGAAATAATATCCAAAGTTTTAATCCGCTCCACTG
CAACTTCAGGGAGATAGGACTATCGGCTTTAACCTGCTCCACTGCAACTTCAGGAAGATAAGGTT
TCCAATCTGCAGTCTGCCTCAC
Found at i:58976353 original size:23 final size:23
Alignment explanation
Indices: 58976327--58976373 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
58976317 GTAATTATAA
58976327 ATACATGTGTAATAAATATATGT
1 ATACATGTGTAATAAATATATGT
* *
58976350 ATACATTTGTAATTAATATATGT
1 ATACATGTGTAATAAATATATGT
58976373 A
1 A
58976374 CATACTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (23 bp):
ATACATGTGTAATAAATATATGT
Found at i:58976515 original size:13 final size:13
Alignment explanation
Indices: 58976484--58976523 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
58976474 AACGAAACAG
*
58976484 AGAAGGAAAG-AA
1 AGAAAGAAAGAAA
*
58976496 GGAAAGAAAGAAA
1 AGAAAGAAAGAAA
58976509 AGAAAGAAAGAAA
1 AGAAAGAAAGAAA
58976522 AG
1 AG
58976524 GGAAAATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAGAAA
Found at i:58977704 original size:45 final size:45
Alignment explanation
Indices: 58977634--58977734 Score: 139
Period size: 45 Copynumber: 2.2 Consensus size: 45
58977624 GCCGACTACT
* * * *
58977634 GTTACTGTTTCCGATTCGGCGCTTTGTGTGTCGAATACTGTTACC
1 GTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATACTGTTACC
* * *
58977679 GTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATATTGTTACT
1 GTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATACTGTTACC
58977724 GTTACTGTTAC
1 GTTACTGTTAC
58977735 TACTTCCGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.43
Consensus pattern (45 bp):
GTTACTGTTACAGATTCAGCACTTTGTGTGTCGAATACTGTTACC
Found at i:58978865 original size:17 final size:17
Alignment explanation
Indices: 58978824--58978866 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
58978814 ACGTGGCATG
* *
58978824 TACCTAAATAATGTATA
1 TACCTAAGTAATATATA
58978841 TACCTAAGTAATATATA
1 TACCTAAGTAATATATA
58978858 TACCTAAGT
1 TACCTAAGT
58978867 GATGTAAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (17 bp):
TACCTAAGTAATATATA
Found at i:58980729 original size:27 final size:26
Alignment explanation
Indices: 58980681--58980732 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
58980671 ACGCGCCCTT
* * *
58980681 CTTCTTTTCTGTCTTTTTTCTGGCTC
1 CTTCTTTTCTGTCCTCTGTCTGGCTC
58980707 CTTCTTTCTCTGTCCTCTGTCTGGCT
1 CTTCTTT-TCTGTCCTCTGTCTGGCT
58980733 TGTATCCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.00, C:0.31, G:0.13, T:0.56
Consensus pattern (26 bp):
CTTCTTTTCTGTCCTCTGTCTGGCTC
Found at i:58987215 original size:20 final size:20
Alignment explanation
Indices: 58987186--58987228 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
58987176 AACGTGTTGA
*
58987186 ATTCCTAATAATGAGTTCTT
1 ATTCCCAATAATGAGTTCTT
58987206 ATTCCCAATAATGAGTTCTT
1 ATTCCCAATAATGAGTTCTT
58987226 ATT
1 ATT
58987229 TTTTGATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.44
Consensus pattern (20 bp):
ATTCCCAATAATGAGTTCTT
Found at i:58993770 original size:21 final size:19
Alignment explanation
Indices: 58993743--58993792 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
58993733 ATTCATGAAA
*
58993743 ATAAAAATATGTATATATAT
1 ATAAAAATATGTATACA-AT
* *
58993763 ATTAAAAAAATTTATACAAT
1 A-TAAAAATATGTATACAAT
58993783 ATAAAAATAT
1 ATAAAAATAT
58993793 ACGTAAGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 8 0.32
20 4 0.16
21 13 0.52
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (19 bp):
ATAAAAATATGTATACAAT
Found at i:58994014 original size:18 final size:18
Alignment explanation
Indices: 58993993--58994027 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
58993983 TAAATATATG
* *
58993993 TATATATAAATTATAAAA
1 TATATAAAAAATATAAAA
58994011 TATATAAAAAATATAAA
1 TATATAAAAAATATAAA
58994028 TAAGTATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TATATAAAAAATATAAAA
Found at i:58994016 original size:20 final size:19
Alignment explanation
Indices: 58993965--58994045 Score: 60
Period size: 22 Copynumber: 4.2 Consensus size: 19
58993955 AAAAATTTAG
* *
58993965 AAAATATGTATATAGATAT
1 AAAATATATATATAAATAT
58993984 AAATATATGTATATATAAATTAT
1 AAA-ATA--TATATATAAA-TAT
*
58994007 AAAATATATA-AAAAATAT
1 AAAATATATATATAAATAT
*
58994025 -AAATA-AGTATATATATAT
1 AAAATATA-TATATAAATAT
58994043 AAA
1 AAA
58994046 TCAAAGATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
16 1 0.02
17 7 0.14
18 9 0.18
19 9 0.18
20 7 0.14
22 11 0.22
23 6 0.12
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
AAAATATATATATAAATAT
Found at i:58994041 original size:51 final size:51
Alignment explanation
Indices: 58993886--58994042 Score: 131
Period size: 51 Copynumber: 3.1 Consensus size: 51
58993876 ATGGATGTAA
** * * * * *
58993886 ATATGTATATGCAAATTAGAAAGTATA-AAAAATATATAAGTACGTACATAT
1 ATATGTATATATAAATTATAAAATATATAAAAA-ATATAAATAAGTATATAT
* * * * * ** *
58993937 AAATATATATAT-ACTTATAAAA-ATTTAGAAAATATGTATATAGATATAAAT
1 ATATGTATATATAAATTATAAAATATATAAAAAATATAAATA-AG-TATATAT
58993988 ATATGTATATATAAATTATAAAATATATAAAAAATATAAATAAGTATATAT
1 ATATGTATATATAAATTATAAAATATATAAAAAATATAAATAAGTATATAT
58994039 ATAT
1 ATAT
58994043 AAATCAAAGA
Statistics
Matches: 78, Mismatches: 23, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
49 8 0.10
50 12 0.15
51 33 0.42
52 11 0.14
53 14 0.18
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.36
Consensus pattern (51 bp):
ATATGTATATATAAATTATAAAATATATAAAAAATATAAATAAGTATATAT
Found at i:58994336 original size:3 final size:3
Alignment explanation
Indices: 58994266--58994320 Score: 76
Period size: 3 Copynumber: 18.3 Consensus size: 3
58994256 GAAATATAGC
* *
58994266 AAT AAT AAC AAT AAT -AT AGAT AAT AAT ACT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
58994311 AAT AAT AAT A
1 AAT AAT AAT A
58994321 TATTAGTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:59005594 original size:27 final size:27
Alignment explanation
Indices: 59005553--59005620 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
59005543 ATACATGAAT
*
59005553 TCATTTCA-ATATTCATATCCCATTTCA
1 TCATTTCATAT-TTCATATCCCATCTCA
* *
59005580 TCATTTCATATTTCATTTCTCATCTCA
1 TCATTTCATATTTCATATCCCATCTCA
*
59005607 T-A-TTCATTTTTCAT
1 TCATTTCATATTTCAT
59005621 CCTTGTCATC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 11 0.31
26 1 0.03
27 22 0.61
28 2 0.06
ACGTcount: A:0.25, C:0.24, G:0.00, T:0.51
Consensus pattern (27 bp):
TCATTTCATATTTCATATCCCATCTCA
Found at i:59005607 original size:19 final size:18
Alignment explanation
Indices: 59005573--59005621 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
59005563 ATTCATATCC
*
59005573 CATTTCATCATTTCATATTT
1 CATTTC-TCATCTCATA-TT
59005593 CATTTCTCATCTCATATT
1 CATTTCTCATCTCATATT
*
59005611 CATTTTTCATC
1 CATTTCTCATC
59005622 CTTGTCATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 12 0.44
19 9 0.33
20 6 0.22
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.53
Consensus pattern (18 bp):
CATTTCTCATCTCATATT
Found at i:59010737 original size:27 final size:27
Alignment explanation
Indices: 59010715--59010851 Score: 85
Period size: 27 Copynumber: 5.1 Consensus size: 27
59010705 TGACAAACAT
***
59010715 TACTCTTACATATTTCGCCACAATGGC
1 TACTCTTACATATTTCGCCACAAAAAC
* *
59010742 TACTATTACATATTTTGCCACAAAAAC
1 TACTCTTACATATTTCGCCACAAAAAC
* * ** ** ***
59010769 AACTCTTTCATATTTTACGGCAATGGC
1 TACTCTTACATATTTCGCCACAAAAAC
* * *
59010796 TATTCTTTCATATTTCACCACAAAAAC
1 TACTCTTACATATTTCGCCACAAAAAC
* * * *
59010823 TAATCTTTCATATTTTGCCACAAATAC
1 TACTCTTACATATTTCGCCACAAAAAC
59010850 TA
1 TA
59010852 GCCTTTCCTG
Statistics
Matches: 84, Mismatches: 26, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 84 1.00
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (27 bp):
TACTCTTACATATTTCGCCACAAAAAC
Found at i:59010793 original size:54 final size:54
Alignment explanation
Indices: 59010735--59010838 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 54
59010725 TATTTCGCCA
**
59010735 CAATGGCTACTATTACATATTTTGCCACAAAAAC-AACTCTTTCATATTTTACGG
1 CAATGGCTACTATTACATATTTCACCACAAAAACTAA-TCTTTCATATTTTACGG
* * *
59010789 CAATGGCTATTCTTTCATATTTCACCACAAAAACTAATCTTTCATATTTT
1 CAATGGCTACTATTACATATTTCACCACAAAAACTAATCTTTCATATTTT
59010839 GCCACAAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
54 42 0.95
55 2 0.05
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (54 bp):
CAATGGCTACTATTACATATTTCACCACAAAAACTAATCTTTCATATTTTACGG
Found at i:59010857 original size:27 final size:27
Alignment explanation
Indices: 59010800--59010858 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
59010790 AATGGCTATT
*
59010800 CTTTCATATTTCACCACAAAAACTAAT
1 CTTTCATATTTCACCACAAAAACTAAC
** * *
59010827 CTTTCATATTTTGCCACAAATACTAGC
1 CTTTCATATTTCACCACAAAAACTAAC
59010854 CTTTC
1 CTTTC
59010859 CTGACATGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.37
Consensus pattern (27 bp):
CTTTCATATTTCACCACAAAAACTAAC
Found at i:59013633 original size:11 final size:11
Alignment explanation
Indices: 59013617--59013647 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
59013607 GAGGGAGTAG
59013617 TTTATTTTTGA
1 TTTATTTTTGA
*
59013628 TTTATTTTAGA
1 TTTATTTTTGA
59013639 TTTATTTTT
1 TTTATTTTT
59013648 TTAAGTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (11 bp):
TTTATTTTTGA
Found at i:59020638 original size:22 final size:22
Alignment explanation
Indices: 59020613--59020655 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
59020603 CGATTTGAGT
*
59020613 GCATGAATGATTAAAGCAAATA
1 GCATGAATGATTAAAACAAATA
59020635 GCATGAATGATTAAAACAAAT
1 GCATGAATGATTAAAACAAAT
59020656 TTGATTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.23
Consensus pattern (22 bp):
GCATGAATGATTAAAACAAATA
Found at i:59023253 original size:13 final size:13
Alignment explanation
Indices: 59023235--59023261 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59023225 TTCAACCAAT
59023235 TTTCAATTGCAGC
1 TTTCAATTGCAGC
59023248 TTTCAATTGCAGC
1 TTTCAATTGCAGC
59023261 T
1 T
59023262 CTATATCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (13 bp):
TTTCAATTGCAGC
Found at i:59024232 original size:21 final size:21
Alignment explanation
Indices: 59024203--59024244 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
59024193 TAACAAAACC
*
59024203 TTTGATATAATAATAATTTTA
1 TTTGATATAATAACAATTTTA
*
59024224 TTTGGTATAATAACAATTTTA
1 TTTGATATAATAACAATTTTA
59024245 GTCCTCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.50
Consensus pattern (21 bp):
TTTGATATAATAACAATTTTA
Found at i:59024384 original size:28 final size:29
Alignment explanation
Indices: 59024336--59024394 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
59024326 AGAACATTAT
*
59024336 AAATTTAAAATTAAATAAAAGT-AGATAA
1 AAATTTAAAATTAAATAAAAGTGAGAGAA
59024364 AAATTTCAAAATTAAAT-AAAGTGAGAGAA
1 AAATTT-AAAATTAAATAAAAGTGAGAGAA
59024393 AA
1 AA
59024395 TGAAGGATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.63, C:0.02, G:0.10, T:0.25
Consensus pattern (29 bp):
AAATTTAAAATTAAATAAAAGTGAGAGAA
Found at i:59027211 original size:24 final size:24
Alignment explanation
Indices: 59027179--59027305 Score: 84
Period size: 25 Copynumber: 5.2 Consensus size: 24
59027169 GAGCCTATAT
* *
59027179 CAGGTAGCTCCGAATAGCACTTAA
1 CAGGAAGCTCCGAAGAGCACTTAA
59027203 CAGGAAGCTCCGAAGAGCACTTTAA
1 CAGGAAGCTCCGAAGAGCAC-TTAA
* * *
59027228 CA-GAGAGCACTGAATAGTCA-TATAA
1 CAGGA-AGCTCCGAAGAG-CACT-TAA
* *
59027253 CGGGAAGCT-C-AAGCGAACAC-TAA
1 CAGGAAGCTCCGAA--GAGCACTTAA
*
59027276 CGGGAAGCTCCGAAGAGCACTTTAA
1 CAGGAAGCTCCGAAGAGCAC-TTAA
59027301 CAGGA
1 CAGGA
59027306 GGTTCACAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 23
0.69 0.11 0.20
Matches are distributed among these distances:
23 19 0.24
24 24 0.30
25 32 0.41
26 4 0.05
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (24 bp):
CAGGAAGCTCCGAAGAGCACTTAA
Found at i:59038342 original size:25 final size:26
Alignment explanation
Indices: 59038306--59038356 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
59038296 GTTGTGTTTA
59038306 AAAATTTAACATTTTAGTCAATATTT
1 AAAATTTAACATTTTAGTCAATATTT
59038332 AAAA-TTAACATTTTAGTCAATATTT
1 AAAATTTAACATTTTAGTCAATATTT
59038357 TTATTAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (26 bp):
AAAATTTAACATTTTAGTCAATATTT
Found at i:59042004 original size:22 final size:22
Alignment explanation
Indices: 59041968--59042013 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
59041958 AAAAAAAATG
*
59041968 AAAATAGAAACAAAATAATAAA
1 AAAATAGAAACAAAACAATAAA
* * *
59041990 AAAATAGCAAGAAAACAGTAAA
1 AAAATAGAAACAAAACAATAAA
59042012 AA
1 AA
59042014 GAACAACAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.74, C:0.07, G:0.09, T:0.11
Consensus pattern (22 bp):
AAAATAGAAACAAAACAATAAA
Found at i:59047026 original size:73 final size:74
Alignment explanation
Indices: 59046870--59047051 Score: 185
Period size: 72 Copynumber: 2.5 Consensus size: 74
59046860 CGCAGCTATT
* * * *
59046870 ATGAACGTCCCGTTAAATGGCTCTTCGTGAGCTTCCTAATTATTGGATCTCCGAAGCTTCCCGAT
1 ATGAACTTCCCGATAAATGGCTATTCGTGAGCTTCCTAATTAATGGATCTCCGAAGCTTCCCGAT
59046935 ATGGCTCGC
66 ATGGCTCGC
* * * * *
59046944 TTGAACTTCCCGATAAATGGCTATTCG-GAGCTTCCT-ATTAATGGCTCTTCGGAG-TTACCCGT
1 ATGAACTTCCCGATAAATGGCTATTCGTGAGCTTCCTAATTAATGGATCTCCGAAGCTT-CCCGA
59047006 TATTGGCTCGC
65 TA-TGGCTCGC
* * * * *
59047017 ATGAGCTTCCTGAT-TATGGCTCTT-ATGAGCTTCCT
1 ATGAACTTCCCGATAAATGGCTATTCGTGAGCTTCCT
59047052 GTTATACAGC
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
71 2 0.02
72 37 0.41
73 28 0.31
74 23 0.26
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.34
Consensus pattern (74 bp):
ATGAACTTCCCGATAAATGGCTATTCGTGAGCTTCCTAATTAATGGATCTCCGAAGCTTCCCGAT
ATGGCTCGC
Done.