Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008031.1 Hibiscus syriacus cultivar Beakdansim tig00110511_pilon, whole genome shotgun sequence
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: 1788856
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1325309 original size:37 final size:39
Alignment explanation
Indices: 1325231--1325309 Score: 90
Period size: 42 Copynumber: 2.0 Consensus size: 39
1325221 ATTTCCCTTT
*
1325231 TTTTATCTTATTTTGTTTTATCTTTATTTTCCCACTTTTTTA
1 TTTTATCTTATTTTGTTTTATCTTTATTTT--C-CTCTTTTA
* *
1325273 TTTTATTTTGTTTTGTTTTAT-TTTATTTT-CTCTTTTA
1 TTTTATCTTATTTTGTTTTATCTTTATTTTCCTCTTTTA
1325310 ACATTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
37 7 0.21
41 8 0.24
42 19 0.56
ACGTcount: A:0.13, C:0.10, G:0.04, T:0.73
Consensus pattern (39 bp):
TTTTATCTTATTTTGTTTTATCTTTATTTTCCTCTTTTA
Found at i:1325370 original size:63 final size:63
Alignment explanation
Indices: 1325289--1325430 Score: 162
Period size: 64 Copynumber: 2.2 Consensus size: 63
1325279 TTTGTTTTGT
* * * * * *
1325289 TTTATTTTATTTTCTCTTTTAACATTTTTTTAT-TTTTTATTTT-TTGAATTTAATATTTTCTTC
1 TTTA-TTTATTTTTTCTTTTAACATTTATATATATATATATTTTATT-AATTTAATATTTACTTC
**
1325352 ATTTATTTATTTTTTCTTTTAACATTTATATATATATATATTTTATTTTTTTAATATTTACTTC
1 -TTTATTTATTTTTTCTTTTAACATTTATATATATATATATTTTATTAATTTAATATTTACTTC
1325416 TTTGATTTATTTTTT
1 TTT-ATTTATTTTTT
1325431 AAATTTAATT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 28 0.42
64 37 0.55
65 2 0.03
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.70
Consensus pattern (63 bp):
TTTATTTATTTTTTCTTTTAACATTTATATATATATATATTTTATTAATTTAATATTTACTTC
Found at i:1325372 original size:16 final size:16
Alignment explanation
Indices: 1325266--1325372 Score: 53
Period size: 15 Copynumber: 6.8 Consensus size: 16
1325256 ATTTTCCCAC
*
1325266 TTTTTTATTTTATTT-
1 TTTTTTCTTTTATTTA
* *
1325281 TGTTTTGTTTTATTTTA
1 TTTTTTCTTTTA-TTTA
* **
1325298 TTTTCTCTTTTA-ACA
1 TTTTTTCTTTTATTTA
1325313 TTTTTT-TATTT-TTTA
1 TTTTTTCT-TTTATTTA
** *
1325328 TTTTTTGAATTTA-ATA
1 TTTTTT-CTTTTATTTA
*
1325344 TTTTCTTCATTTATTTA
1 TTTT-TTCTTTTATTTA
1325361 TTTTTTCTTTTA
1 TTTTTTCTTTTA
1325373 ACATTTATAT
Statistics
Matches: 68, Mismatches: 15, Indels: 17
0.68 0.15 0.17
Matches are distributed among these distances:
14 1 0.01
15 26 0.38
16 24 0.35
17 17 0.25
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTTTTCTTTTATTTA
Found at i:1325438 original size:33 final size:31
Alignment explanation
Indices: 1325324--1325444 Score: 91
Period size: 33 Copynumber: 3.7 Consensus size: 31
1325314 TTTTTTATTT
*
1325324 TTTATTTTTTGAATTTAATATTTTCTTCATTTA
1 TTTATTTTTT-AATTTAATATTTACTTC-TTTA
** * * *
1325357 TTTATTTTTTCTTTTAACATTTA-TATATATA
1 TTTATTTTTTAATTTAATATTTACT-TCTTTA
* **
1325388 TATATTTTATTTTTTTAATATTTACTTCTTTGA
1 TTTATTTT-TTAATTTAATATTTACTTCTTT-A
*
1325421 TTTATTTTTTAAATTTAATTTTTA
1 TTTATTTTTT-AATTTAATATTTA
1325445 TTTGATATTT
Statistics
Matches: 68, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
31 11 0.16
32 28 0.41
33 29 0.43
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (31 bp):
TTTATTTTTTAATTTAATATTTACTTCTTTA
Found at i:1330685 original size:69 final size:69
Alignment explanation
Indices: 1330554--1330685 Score: 176
Period size: 69 Copynumber: 1.9 Consensus size: 69
1330544 GTCTCGCACG
* * * * *
1330554 GGAGCCCCTAAAGGTTAGAGTGTCTCGCATGAGAGCATCTAATCATAATTATTTCGGGTGACTCG
1 GGAGCCCCGAAAGGTTAGAGTGTCTCGCACGAGAACATCTAATCATAATTATTTCAGATGACTCG
1330619 TATT
66 TATT
* * *
1330623 GGAGCCCCGAAGGGTTAGAGTGTCTCGTACGGGAACA-CTTAATCATAATTATTTCAGATGACT
1 GGAGCCCCGAAAGGTTAGAGTGTCTCGCACGAGAACATC-TAATCATAATTATTTCAGATGACT
1330686 TGCACGGGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
68 1 0.02
69 53 0.98
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (69 bp):
GGAGCCCCGAAAGGTTAGAGTGTCTCGCACGAGAACATCTAATCATAATTATTTCAGATGACTCG
TATT
Found at i:1334003 original size:18 final size:19
Alignment explanation
Indices: 1333956--1333995 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1333946 AACTTTTTTC
*
1333956 AAAGTCAACGGGTCAAGTT
1 AAAGTCAATGGGTCAAGTT
*
1333975 AAAGTCAATGGGTCAGGTT
1 AAAGTCAATGGGTCAAGTT
1333994 AA
1 AA
1333996 TTCAATGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.23
Consensus pattern (19 bp):
AAAGTCAATGGGTCAAGTT
Found at i:1336089 original size:19 final size:20
Alignment explanation
Indices: 1336065--1336115 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
1336055 TATGTAAGCA
1336065 GTATCGATACCAAGAGG-GG
1 GTATCGATACCAAGAGGAGG
* * * *
1336084 GTATCGTTACTATGAGGATG
1 GTATCGATACCAAGAGGAGG
1336104 GTATCGATACCA
1 GTATCGATACCA
1336116 TTGTTAACAG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
GTATCGATACCAAGAGGAGG
Found at i:1336161 original size:19 final size:19
Alignment explanation
Indices: 1336137--1336178 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1336127 ATGTAAAAAT
1336137 AGTATCGGTACCGTGATGG
1 AGTATCGGTACCGTGATGG
1336156 AGTATCGGTACCGTGATGG
1 AGTATCGGTACCGTGATGG
1336175 AGTA
1 AGTA
1336179 GTATTGATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.24, C:0.14, G:0.36, T:0.26
Consensus pattern (19 bp):
AGTATCGGTACCGTGATGG
Found at i:1345547 original size:21 final size:21
Alignment explanation
Indices: 1345521--1345561 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1345511 AAACCATTCA
1345521 GGGGGGAATCGGTACCCTCTT
1 GGGGGGAATCGGTACCCTCTT
*
1345542 GGGGGGAATCGGTTCCCTCT
1 GGGGGGAATCGGTACCCTCT
1345562 GAGAAATCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.24, G:0.39, T:0.24
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCTCTT
Found at i:1346365 original size:47 final size:47
Alignment explanation
Indices: 1346293--1346648 Score: 525
Period size: 47 Copynumber: 7.6 Consensus size: 47
1346283 AAACCGAATA
*
1346293 CATAACTAAAAATGCATG-ACAGGATGCATTAAGGTATGAAAGGATGC
1 CATAACTAAAAATGCATGAAC-GGATGCATTAAGGCATGAAAGGATGC
* * * *
1346340 TATAACTAAAAATGAATGAATGGATGCATTAAGGAATGAAAGGATGC
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* *
1346387 CATAACTAAAAATGCATGAACAGATGCATTAAGGTATGAAAGGATGC
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* *
1346434 CATAACTAAAAATGCATGAACGGATTCATTAAGGCATAAAAGGATGC
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
*
1346481 CATAACTAAAATTGCATGAACGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* * * *
1346528 CATAACTAAAAATACATTAACGGACGCATTAAGGCATAAAAGGATGC
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
** *
1346575 CATAACTAAAAATGCATGAAAAGATACATTAAGGCATGAAAGGATGC
1 CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
* *
1346622 CATAACTAAAAATGAATGAAAGGATGC
1 CATAACTAAAAATGCATGAACGGATGC
1346649 TATAACTAAA
Statistics
Matches: 277, Mismatches: 31, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
47 276 1.00
48 1 0.00
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.21
Consensus pattern (47 bp):
CATAACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGC
Found at i:1346417 original size:94 final size:94
Alignment explanation
Indices: 1346293--1346888 Score: 711
Period size: 94 Copynumber: 6.6 Consensus size: 94
1346283 AAACCGAATA
* *
1346293 CATAACTAAAAATGCATG-ACAGGATGCATTAAGGTATGAAAGGATGCTATAACTAAAAATGAAT
1 CATAACTAAAAATGCATGAACA-GATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGAAT
* * *
1346357 GAATGGATGCATTAAGGAATGAAAGGATGC
65 GAACGGATGCATTAAGGCATAAAAGGATGC
* *
1346387 CATAACTAAAAATGCATGAACAGATGCATTAAGGTATGAAAGGATGCCATAACTAAAAATGCATG
1 CATAACTAAAAATGCATGAACAGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGAATG
*
1346452 AACGGATTCATTAAGGCATAAAAGGATGC
66 AACGGATGCATTAAGGCATAAAAGGATGC
* *
1346481 CATAACTAAAATTGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAAT-ACAT
1 CATAACTAAAAATGCATGAACAGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGA-AT
* *
1346545 TAACGGACGCATTAAGGCATAAAAGGATGC
65 GAACGGATGCATTAAGGCATAAAAGGATGC
* *
1346575 CATAACTAAAAATGCATGAAAAGATACATTAAGGCATGAAAGGATGCCATAACTAAAAATGAATG
1 CATAACTAAAAATGCATGAACAGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGAATG
*
1346640 AAAGGATGC-TATAA--C-TAAAA--ATG-
66 AACGGATGCAT-TAAGGCATAAAAGGATGC
* * *
1346663 CATGAAC---AAATGCAT------T------AAGGCATGAAAGGATTCCATAACTAAAAATGCAT
1 CAT-AACTAAAAATGCATGAACAGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGAAT
* * *
1346713 GAACAGATGCATTAAGACATGAAAGGATGC
65 GAACGGATGCATTAAGGCATAAAAGGATGC
* * * *
1346743 CATAACTAAAAATGCATGAACAAATACATTAAGTCATGAAAGGATGCCATAACTAAAAATGCATG
1 CATAACTAAAAATGCATGAACAGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGAATG
* * *
1346808 AAAGGATGCATTAAGGCATGAAAGGACGC
66 AACGGATGCATTAAGGCATAAAAGGATGC
*
1346837 CATAACTAAAAATGCATGAA-TGTATGCATTAAGGCATGAAAGGATGCCATAA
1 CATAACTAAAAATGCATGAACAG-ATGCATTAAGGCATGAAAGGATGCCATAA
1346889 ATGAAATTAA
Statistics
Matches: 437, Mismatches: 37, Indels: 56
0.82 0.07 0.11
Matches are distributed among these distances:
74 43 0.10
75 1 0.00
76 1 0.00
77 4 0.01
79 6 0.01
80 3 0.01
82 8 0.02
86 8 0.02
88 3 0.01
89 6 0.01
91 5 0.01
92 1 0.00
93 1 0.00
94 343 0.78
95 4 0.01
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.21
Consensus pattern (94 bp):
CATAACTAAAAATGCATGAACAGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGAATG
AACGGATGCATTAAGGCATAAAAGGATGC
Found at i:1346648 original size:27 final size:27
Alignment explanation
Indices: 1346610--1346668 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
1346600 ACATTAAGGC
1346610 ATGAAAGGATGCCATAACTAAAAATGA
1 ATGAAAGGATGCCATAACTAAAAATGA
* *
1346637 ATGAAAGGATGCTATAACTAAAAATGC
1 ATGAAAGGATGCCATAACTAAAAATGA
1346664 ATGAA
1 ATGAA
1346669 CAAATGCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.51, C:0.10, G:0.19, T:0.20
Consensus pattern (27 bp):
ATGAAAGGATGCCATAACTAAAAATGA
Found at i:1346706 original size:47 final size:47
Alignment explanation
Indices: 1346637--1346888 Score: 389
Period size: 47 Copynumber: 5.4 Consensus size: 47
1346627 CTAAAAATGA
*
1346637 ATGAAAGGATGCTATAACTAAAAATGCATGAACAAATGCATTAAGGC
1 ATGAAAGGATGCCATAACTAAAAATGCATGAACAAATGCATTAAGGC
* * *
1346684 ATGAAAGGATTCCATAACTAAAAATGCATGAACAGATGCATTAAGAC
1 ATGAAAGGATGCCATAACTAAAAATGCATGAACAAATGCATTAAGGC
* *
1346731 ATGAAAGGATGCCATAACTAAAAATGCATGAACAAATACATTAAGTC
1 ATGAAAGGATGCCATAACTAAAAATGCATGAACAAATGCATTAAGGC
*
1346778 ATGAAAGGATGCCATAACTAAAAATGCATGAA-AGGATGCATTAAGGC
1 ATGAAAGGATGCCATAACTAAAAATGCATGAACA-AATGCATTAAGGC
* ***
1346825 ATGAAAGGACGCCATAACTAAAAATGCATGAATGTATGCATTAAGGC
1 ATGAAAGGATGCCATAACTAAAAATGCATGAACAAATGCATTAAGGC
1346872 ATGAAAGGATGCCATAA
1 ATGAAAGGATGCCATAA
1346889 ATGAAATTAA
Statistics
Matches: 188, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
46 1 0.01
47 187 0.99
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.21
Consensus pattern (47 bp):
ATGAAAGGATGCCATAACTAAAAATGCATGAACAAATGCATTAAGGC
Found at i:1346722 original size:74 final size:74
Alignment explanation
Indices: 1346566--1346715 Score: 248
Period size: 74 Copynumber: 2.0 Consensus size: 74
1346556 TTAAGGCATA
1346566 AAAGGATGCCATAACTAAAAATGCATGAAAAGATACATTAAGGCATGAAAGGATGCCATAACTAA
1 AAAGGATGCCATAACTAAAAATGCATGAAAAGATACATTAAGGCATGAAAGGATGCCATAACTAA
1346631 AAATGAATG
66 AAATGAATG
* * *
1346640 AAAGGATGCTATAACTAAAAATGCATGAACAA-ATGCATTAAGGCATGAAAGGATTCCATAACTA
1 AAAGGATGCCATAACTAAAAATGCATGAA-AAGATACATTAAGGCATGAAAGGATGCCATAACTA
*
1346704 AAAATGCATG
65 AAAATGAATG
1346714 AA
1 AA
1346716 CAGATGCATT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
74 69 0.97
75 2 0.03
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.20
Consensus pattern (74 bp):
AAAGGATGCCATAACTAAAAATGCATGAAAAGATACATTAAGGCATGAAAGGATGCCATAACTAA
AAATGAATG
Found at i:1346734 original size:121 final size:121
Alignment explanation
Indices: 1346516--1346762 Score: 386
Period size: 121 Copynumber: 2.0 Consensus size: 121
1346506 GCATTAAGGC
* **
1346516 ATGAAAGGATGCCATAACTAAAAATACATTAACGGACGCATTAAGGCATAAAAGGATGCCATAAC
1 ATGAAAGGATGCCATAACTAAAAATACATGAACAAACGCATTAAGGCATAAAAGGATGCCATAAC
*
1346581 TAAAAATGCATGAAAAGATACATTAAGGCATGAAAGGATGCCATAACTAAAAATGA
66 TAAAAATGCATGAAAAGATACATTAAGACATGAAAGGATGCCATAACTAAAAATGA
* * * * *
1346637 ATGAAAGGATGCTATAACTAAAAATGCATGAACAAATGCATTAAGGCATGAAAGGATTCCATAAC
1 ATGAAAGGATGCCATAACTAAAAATACATGAACAAACGCATTAAGGCATAAAAGGATGCCATAAC
* * *
1346702 TAAAAATGCATGAACAGATGCATTAAGACATGAAAGGATGCCATAACTAAAAATGC
66 TAAAAATGCATGAAAAGATACATTAAGACATGAAAGGATGCCATAACTAAAAATGA
1346758 ATGAA
1 ATGAA
1346763 CAAATACATT
Statistics
Matches: 114, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
121 114 1.00
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (121 bp):
ATGAAAGGATGCCATAACTAAAAATACATGAACAAACGCATTAAGGCATAAAAGGATGCCATAAC
TAAAAATGCATGAAAAGATACATTAAGACATGAAAGGATGCCATAACTAAAAATGA
Found at i:1346750 original size:168 final size:168
Alignment explanation
Indices: 1346472--1346816 Score: 557
Period size: 168 Copynumber: 2.1 Consensus size: 168
1346462 TTAAGGCATA
* **
1346472 AAAGGATGCCATAACTAAAATTGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAA
1 AAAGGATGCCATAACTAAAAATGCATGAACAAATGCATTAAGGCATGAAAGGATGCCATAACTAA
* * *
1346537 AAATACATTAACGGACGCATTAAGGCATAAAAGGATGCCATAACTAAAAATGCATGAA-AAGATA
66 AAATACATGAACAGACGCATTAAGACATAAAAGGATGCCATAACTAAAAATGCATGAACAA-ATA
1346601 CATTAAGGCATGAAAGGATGCCATAACTAAAAATGAATG
130 CATTAAGGCATGAAAGGATGCCATAACTAAAAATGAATG
* *
1346640 AAAGGATGCTATAACTAAAAATGCATGAACAAATGCATTAAGGCATGAAAGGATTCCATAACTAA
1 AAAGGATGCCATAACTAAAAATGCATGAACAAATGCATTAAGGCATGAAAGGATGCCATAACTAA
* * *
1346705 AAATGCATGAACAGATGCATTAAGACATGAAAGGATGCCATAACTAAAAATGCATGAACAAATAC
66 AAATACATGAACAGACGCATTAAGACATAAAAGGATGCCATAACTAAAAATGCATGAACAAATAC
* *
1346770 ATTAAGTCATGAAAGGATGCCATAACTAAAAATGCATG
131 ATTAAGGCATGAAAGGATGCCATAACTAAAAATGAATG
1346808 AAAGGATGC
1 AAAGGATGC
1346817 ATTAAGGCAT
Statistics
Matches: 163, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
168 161 0.99
169 2 0.01
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (168 bp):
AAAGGATGCCATAACTAAAAATGCATGAACAAATGCATTAAGGCATGAAAGGATGCCATAACTAA
AAATACATGAACAGACGCATTAAGACATAAAAGGATGCCATAACTAAAAATGCATGAACAAATAC
ATTAAGGCATGAAAGGATGCCATAACTAAAAATGAATG
Found at i:1346793 original size:215 final size:215
Alignment explanation
Indices: 1346422--1346856 Score: 681
Period size: 215 Copynumber: 2.0 Consensus size: 215
1346412 GCATTAAGGT
** *
1346422 ATGAAAGGATGCCATAACTAAAAATGCATGAACGGATTCATTAAGGCATAAAAGGATGCCATAAC
1 ATGAAAGGATGCCATAACTAAAAATGCATGAACAAATGCATTAAGGCATAAAAGGATGCCATAAC
* * * * **
1346487 TAAAATTGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATACATTAACGGA
66 TAAAAATGCATGAACAGATGCATTAAGACATGAAAGGATGCCATAACTAAAAATACATGAACAAA
*
1346552 CGCATTAAGGCATAAAAGGATGCCATAACTAAAAATGCATGAAAAGATACATTAAGGCATGAAAG
131 CACATTAAGGCATAAAAGGATGCCATAACTAAAAATGCATGAAAAGATACATTAAGGCATGAAAG
*
1346617 GATGCCATAACTAAAAATGA
196 GACGCCATAACTAAAAATGA
* * *
1346637 ATGAAAGGATGCTATAACTAAAAATGCATGAACAAATGCATTAAGGCATGAAAGGATTCCATAAC
1 ATGAAAGGATGCCATAACTAAAAATGCATGAACAAATGCATTAAGGCATAAAAGGATGCCATAAC
*
1346702 TAAAAATGCATGAACAGATGCATTAAGACATGAAAGGATGCCATAACTAAAAATGCATGAACAAA
66 TAAAAATGCATGAACAGATGCATTAAGACATGAAAGGATGCCATAACTAAAAATACATGAACAAA
* * * * *
1346767 TACATTAAGTCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAG
131 CACATTAAGGCATAAAAGGATGCCATAACTAAAAATGCATGAAAAGATACATTAAGGCATGAAAG
*
1346832 GACGCCATAACTAAAAATGC
196 GACGCCATAACTAAAAATGA
1346852 ATGAA
1 ATGAA
1346857 TGTATGCATT
Statistics
Matches: 199, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
215 199 1.00
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (215 bp):
ATGAAAGGATGCCATAACTAAAAATGCATGAACAAATGCATTAAGGCATAAAAGGATGCCATAAC
TAAAAATGCATGAACAGATGCATTAAGACATGAAAGGATGCCATAACTAAAAATACATGAACAAA
CACATTAAGGCATAAAAGGATGCCATAACTAAAAATGCATGAAAAGATACATTAAGGCATGAAAG
GACGCCATAACTAAAAATGA
Found at i:1346815 original size:27 final size:27
Alignment explanation
Indices: 1346777--1346856 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
1346767 TACATTAAGT
1346777 CATGAAAGGATGCCATAACTAAAAATG
1 CATGAAAGGATGCCATAACTAAAAATG
*
1346804 CATGAAAGGATG-CAT---T---AAGG
1 CATGAAAGGATGCCATAACTAAAAATG
*
1346824 CATGAAAGGACGCCATAACTAAAAATG
1 CATGAAAGGATGCCATAACTAAAAATG
1346851 CATGAA
1 CATGAA
1346857 TGTATGCATT
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
20 14 0.33
21 3 0.07
23 1 0.02
24 1 0.02
26 3 0.07
27 21 0.49
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.17
Consensus pattern (27 bp):
CATGAAAGGATGCCATAACTAAAAATG
Found at i:1346828 original size:20 final size:20
Alignment explanation
Indices: 1346803--1346883 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 20
1346793 AACTAAAAAT
1346803 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1346823 GCATGAAAGGACGCCATAACTAAAAAT
1 GCATGAAAGGATG-CAT---T---AAG
* *
1346850 GCATGAATGTATGCATTAAG
1 GCATGAAAGGATGCATTAAG
1346870 GCATGAAAGGATGC
1 GCATGAAAGGATGC
1346884 CATAAATGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
20 26 0.57
21 3 0.07
23 1 0.02
24 1 0.02
26 3 0.07
27 12 0.26
ACGTcount: A:0.41, C:0.14, G:0.26, T:0.20
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:1352786 original size:20 final size:21
Alignment explanation
Indices: 1352761--1352816 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
1352751 GATACAAGTA
*
1352761 GTATCGATACTGATG-TGGAG
1 GTATCGATACTGATGATGAAG
* *
1352781 GTATCGATAC-CATGATGAAT
1 GTATCGATACTGATGATGAAG
1352801 GTATCGATACTG-TGAT
1 GTATCGATACTGATGAT
1352817 TGGAAAATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (21 bp):
GTATCGATACTGATGATGAAG
Found at i:1353266 original size:54 final size:54
Alignment explanation
Indices: 1353175--1353636 Score: 602
Period size: 54 Copynumber: 8.6 Consensus size: 54
1353165 TTATGTACAG
* * *
1353175 AATTCATAATAAGGTTATGAACGACCATATCGACACTATGTGTGCAACCCAAAA
1 AATTCATAATAAGTTTATGAACGACCGTATCGACACTATGTGTGCAACCCACAA
* *
1353229 AATTCATAATAAGTTTATGAATGGCCGTATC-AGCACTATGTGTGCAACCCACAA
1 AATTCATAATAAGTTTATGAACGACCGTATCGA-CACTATGTGTGCAACCCACAA
*
1353283 AATTCATAATAAGTTTATGAGCGACCGTATCGACACTATGTGTGCAACCCACAA
1 AATTCATAATAAGTTTATGAACGACCGTATCGACACTATGTGTGCAACCCACAA
* * * *
1353337 AATTCATAACAAGTTTATGAATGACCGTATCGACACTATGTGTGCAACCCATAG
1 AATTCATAATAAGTTTATGAACGACCGTATCGACACTATGTGTGCAACCCACAA
* ** * * * ** **
1353391 AATTCATAATAAGTTTATGAAAGATTGTATCGGCACTATGTGCGTAATGCATGA
1 AATTCATAATAAGTTTATGAACGACCGTATCGACACTATGTGTGCAACCCACAA
* *
1353445 AATTCATAATAAGTTTATGAACGACCGTATTGACACTATGTGTGCAACCCACGA
1 AATTCATAATAAGTTTATGAACGACCGTATCGACACTATGTGTGCAACCCACAA
* * * *
1353499 AATTCATAATAAGTTTATGAACGACTGTATCGACACTATGCGTCCAACCCACAG
1 AATTCATAATAAGTTTATGAACGACCGTATCGACACTATGTGTGCAACCCACAA
* * * * *
1353553 AATTCATAATAAGTTTATGAACGACCGTATAGGCACTAAGTTTGCAACCCACAG
1 AATTCATAATAAGTTTATGAACGACCGTATCGACACTATGTGTGCAACCCACAA
* * *
1353607 AATTCATAATGAGCTTATGAATGACCGTAT
1 AATTCATAATAAGTTTATGAACGACCGTAT
1353637 TTCCACTACG
Statistics
Matches: 356, Mismatches: 50, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
53 1 0.00
54 354 0.99
55 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (54 bp):
AATTCATAATAAGTTTATGAACGACCGTATCGACACTATGTGTGCAACCCACAA
Found at i:1363025 original size:2 final size:2
Alignment explanation
Indices: 1363020--1363104 Score: 161
Period size: 2 Copynumber: 42.5 Consensus size: 2
1363010 TATATATATA
1363020 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
1363062 TG TG TG TG TG TG TG TG TG TG TG TG TG TT TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1363104 T
1 T
1363105 ATGTATGTTT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1363220 original size:73 final size:73
Alignment explanation
Indices: 1363133--1363277 Score: 220
Period size: 73 Copynumber: 2.0 Consensus size: 73
1363123 ATATGATATA
* *
1363133 TGTTAATTTGAGTGGTGTAAATACATATTTACATTAACTGGTGTAAGTATGTGATAAGTTCATT-
1 TGTTAATTTCAGTGGTGTAAATACATATTAACATTAACTGGTGTAAGTATGTGATAAGTTCATTA
1363197 GATATAATG
66 G-TATAATG
* * * *
1363206 TGTTAATTTCAGTGGTGTAAATACATGTTAACTTTAATTGGTGTAAGTATGTTATAAGTTCATTA
1 TGTTAATTTCAGTGGTGTAAATACATATTAACATTAACTGGTGTAAGTATGTGATAAGTTCATTA
1363271 GTATAAT
66 GTATAAT
1363278 ATTTGTTACT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
73 64 0.98
74 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (73 bp):
TGTTAATTTCAGTGGTGTAAATACATATTAACATTAACTGGTGTAAGTATGTGATAAGTTCATTA
GTATAATG
Found at i:1363326 original size:75 final size:73
Alignment explanation
Indices: 1363148--1363339 Score: 192
Period size: 73 Copynumber: 2.6 Consensus size: 73
1363138 ATTTGAGTGG
* * * *
1363148 TGTAAATACATATTTACATTAACTGGTGTAAGTATGTGATAAGTTCATTGATATAATGTGTTAAT
1 TGTAAATACATGTTAACTTTAACTAGTGTAAGTATGTGATAAGTTCATTGATATAATGTGTTAAT
* **
1363213 TTCAGTGG
66 TTCACTAA
* * * *
1363221 TGTAAATACATGTTAACTTTAATTGGTGTAAGTATGTTATAAGTTCATT-AGTATAATATTTGTT
1 TGTAAATACATGTTAACTTTAACTAGTGTAAGTATGTGATAAGTTCATTGA-TAT-A-ATGTGTT
*
1363285 ACTTTCACTAA
63 AATTTCACTAA
* * *
1363296 TGTAAATATATGTTAAAGTTT-ACTAGTGTAAGT-TGTGGTAAGTT
1 TGTAAATACATGTT-AACTTTAACTAGTGTAAGTATGTGATAAGTT
1363340 TTTTGGATAA
Statistics
Matches: 99, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
72 1 0.01
73 47 0.47
74 10 0.10
75 36 0.36
76 5 0.05
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (73 bp):
TGTAAATACATGTTAACTTTAACTAGTGTAAGTATGTGATAAGTTCATTGATATAATGTGTTAAT
TTCACTAA
Found at i:1363365 original size:28 final size:28
Alignment explanation
Indices: 1363324--1363378 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1363314 TTTACTAGTG
* *
1363324 TAAGTTGTGGTAAGTTTTTTGG-ATAAA
1 TAAGTTGTGATAAGTTTATTGGTATAAA
1363351 TAAGTATGTGATAAGTTTATTGGTATAA
1 TAAGT-TGTGATAAGTTTATTGGTATAA
1363379 TATATTTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.21
28 15 0.62
29 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.44
Consensus pattern (28 bp):
TAAGTTGTGATAAGTTTATTGGTATAAA
Found at i:1364088 original size:33 final size:34
Alignment explanation
Indices: 1364013--1364088 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 34
1364003 CATGAAAGTC
*
1364013 CATGTTATGATATAAGATATTTCCATGGAAGTTT
1 CATGTTATGATATAAGATATTTCAATGGAAGTTT
*
1364047 -ATGTTATGATATAAGTTATTTCAAT-GATA-TTT
1 CATGTTATGATATAAGATATTTCAATGGA-AGTTT
*
1364079 CATGCTATGA
1 CATGTTATGA
1364089 ATTCATGTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
32 5 0.14
33 32 0.86
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (34 bp):
CATGTTATGATATAAGATATTTCAATGGAAGTTT
Found at i:1366382 original size:22 final size:23
Alignment explanation
Indices: 1366357--1366416 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
1366347 TCAGATGTTA
** *
1366357 TAACTCTTGCTATTATATC-ATG
1 TAACTCTTGAAATTAAATCAATG
*
1366379 TAACTCCTGAAATTAAATCAATG
1 TAACTCTTGAAATTAAATCAATG
*
1366402 TAACTC-TGATATTAA
1 TAACTCTTGAAATTAA
1366417 CAGTTTGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 23 0.72
23 9 0.28
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
TAACTCTTGAAATTAAATCAATG
Found at i:1366406 original size:23 final size:21
Alignment explanation
Indices: 1366368--1366416 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
1366358 AACTCTTGCT
*
1366368 ATTATATCATGTAACTCCTGAA
1 ATTAAATCATGTAACT-CTGAA
*
1366390 ATTAAATCAATGTAACTCTGAT
1 ATTAAATC-ATGTAACTCTGAA
1366412 ATTAA
1 ATTAA
1366417 CAGTTTGCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (21 bp):
ATTAAATCATGTAACTCTGAA
Found at i:1366692 original size:12 final size:12
Alignment explanation
Indices: 1366672--1366702 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1366662 GACATGTATT
*
1366672 ACCACGACCACG
1 ACCATGACCACG
1366684 ACCATGACCACG
1 ACCATGACCACG
1366696 ACCATGA
1 ACCATGA
1366703 GCGAGCCGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.42, G:0.16, T:0.06
Consensus pattern (12 bp):
ACCATGACCACG
Found at i:1369158 original size:32 final size:32
Alignment explanation
Indices: 1369112--1369177 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
1369102 AAGTTAAGCC
*
1369112 GCCAAGTCAGAAATGGGAGGCACGAATTCGGT
1 GCCAAGTCAAAAATGGGAGGCACGAATTCGGT
1369144 GCCAAGTCAAAAATGGGAGGCACGAATTCGGT
1 GCCAAGTCAAAAATGGGAGGCACGAATTCGGT
1369176 GC
1 GC
1369178 AATTAATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.32, C:0.20, G:0.33, T:0.15
Consensus pattern (32 bp):
GCCAAGTCAAAAATGGGAGGCACGAATTCGGT
Found at i:1371312 original size:35 final size:35
Alignment explanation
Indices: 1371249--1371348 Score: 119
Period size: 35 Copynumber: 2.7 Consensus size: 35
1371239 TTTCGTCCTA
*
1371249 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
1371286 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
1371321 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
1371349 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 22 0.39
36 18 0.32
37 16 0.29
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:1371874 original size:37 final size:37
Alignment explanation
Indices: 1371810--1371905 Score: 108
Period size: 37 Copynumber: 2.6 Consensus size: 37
1371800 TCAATTGATT
*
1371810 TTTTTTACACTATATATTA-TTAT-TATATATACATATA
1 TTTTTTA-AATAT-TATTATTTATATATATATACATATA
* *
1371847 TTTTTTAGATATTATTATTTATATATATATATATATA
1 TTTTTTAAATATTATTATTTATATATATATACATATA
* *
1371884 TATTTAAAATATT-TTATTTATA
1 TTTTTTAAATATTATTATTTATA
1371906 AGCGTATTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
35 5 0.10
36 16 0.31
37 30 0.59
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (37 bp):
TTTTTTAAATATTATTATTTATATATATATACATATA
Found at i:1372059 original size:29 final size:29
Alignment explanation
Indices: 1372027--1372095 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
1372017 ATTATATGTA
1372027 TATTTTTATATTTGATTTATATATTTATT
1 TATTTTTATATTTGATTTATATATTTATT
* * * * *
1372056 TATTTTTATTTTTGGTTTTTTTATTTGTT
1 TATTTTTATATTTGATTTATATATTTATT
*
1372085 TA-TATTATATT
1 TATTTTTATATT
1372096 ATATTTTCAT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
28 7 0.21
29 26 0.79
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (29 bp):
TATTTTTATATTTGATTTATATATTTATT
Found at i:1372184 original size:4 final size:4
Alignment explanation
Indices: 1372171--1372257 Score: 51
Period size: 4 Copynumber: 22.2 Consensus size: 4
1372161 TATATATTAA
1372171 TATT TCATT TATT TATT TATT TATT T-TT CT-TT TA-T T-TT TATT TA-T
1 TATT T-ATT TATT TATT TATT TATT TATT -TATT TATT TATT TATT TATT
* * * * *
1372216 T-TT TACT TATT TTTAT TCTT TATT TTTT TCATT TATT CATT T
1 TATT TATT TATT TAT-T TATT TATT TATT T-ATT TATT TATT T
1372258 TTTCCCTCTA
Statistics
Matches: 65, Mismatches: 9, Indels: 18
0.71 0.10 0.20
Matches are distributed among these distances:
3 11 0.17
4 44 0.68
5 10 0.15
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:1372195 original size:21 final size:19
Alignment explanation
Indices: 1372178--1372252 Score: 59
Period size: 20 Copynumber: 4.0 Consensus size: 19
1372168 TAATATTTCA
1372178 TTTATTTATTT-ATTTATT
1 TTTATTTATTTCATTTATT
* *
1372196 TTTCTTTTATTTTTATTTATT
1 TTT-ATTTA-TTTCATTTATT
*
1372217 TTTACTTA-TT--TTTATT
1 TTTATTTATTTCATTTATT
*
1372233 CTTTATTTTTTTCATTTATT
1 -TTTATTTATTTCATTTATT
1372253 CATTTTTTCC
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
16 6 0.13
17 6 0.13
18 7 0.16
19 4 0.09
20 12 0.27
21 10 0.22
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTATTTATTTCATTTATT
Found at i:1372214 original size:10 final size:10
Alignment explanation
Indices: 1372178--1372232 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
1372168 TAATATTTCA
1372178 TTTATTTA--
1 TTTATTTATT
1372186 TTTATTTATT
1 TTTATTTATT
*
1372196 TTTCTTTTATT
1 TTT-ATTTATT
1372207 TTTATTTATT
1 TTTATTTATT
*
1372217 TTTACTTATT
1 TTTATTTATT
1372227 TTTATT
1 TTTATT
1372233 CTTTATTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
8 8 0.20
10 23 0.57
11 9 0.22
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTATTTATT
Found at i:1372225 original size:20 final size:20
Alignment explanation
Indices: 1372186--1372232 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
1372176 CATTTATTTA
1372186 TTTATTTATTTTTCTTTTATT
1 TTTATTTATTTTTC-TTTATT
1372207 TTTATTTATTTTTAC-TTATT
1 TTTATTTATTTTT-CTTTATT
1372227 TTTATT
1 TTTATT
1372233 CTTTATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.44
21 13 0.52
22 1 0.04
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTATTTATTTTTCTTTATT
Found at i:1372228 original size:25 final size:26
Alignment explanation
Indices: 1372182--1372244 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
1372172 ATTTCATTTA
1372182 TTTATTTATTTATT-TT-TCTTTTATT-
1 TTTATTTATTT-TTCTTAT-TTTTATTC
1372207 TTTATTTATTTTTACTTATTTTTATTC
1 TTTATTTATTTTT-CTTATTTTTATTC
1372234 TTTATTT-TTTT
1 TTTATTTATTTT
1372245 CATTTATTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
24 2 0.06
25 11 0.32
26 13 0.38
27 8 0.24
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (26 bp):
TTTATTTATTTTTCTTATTTTTATTC
Found at i:1372251 original size:26 final size:26
Alignment explanation
Indices: 1372200--1372252 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
1372190 TTTATTTTTC
* *
1372200 TTTTATTTTTATTTATTTTTACTTAT
1 TTTTATTCTTATTTATTTTCACTTAT
*
1372226 TTTTATTCTTTATTT-TTTTCATTTAT
1 TTTTATTC-TTATTTATTTTCACTTAT
1372252 T
1 T
1372253 CATTTTTTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTTATTCTTATTTATTTTCACTTAT
Found at i:1374089 original size:7 final size:7
Alignment explanation
Indices: 1374072--1374105 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
1374062 GAACATCTCA
1374072 TGCATTTT
1 TGCA-TTT
1374080 TGCATTT
1 TGCATTT
1374087 TGCATTT
1 TGCATTT
1374094 TGCATTT
1 TGCATTT
1374101 TGCAT
1 TGCAT
1374106 CTACATTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 22 0.85
8 4 0.15
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (7 bp):
TGCATTT
Found at i:1375275 original size:22 final size:22
Alignment explanation
Indices: 1375252--1375313 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
1375242 CAAAAAGGGC
1375252 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAGAAAAAA-AAAAGAAGCA
* *
1375275 AAAAAGGAAAAAACAAGAA-CA
1 AAAAAGAAAAAAAAAAGAAGCA
1375296 AAAAAGAAAGAACAAAAA
1 AAAAAGAAA-AA-AAAAA
1375314 TAAAAAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.30
22 8 0.24
23 15 0.45
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAGAAGCA
Found at i:1375304 original size:20 final size:20
Alignment explanation
Indices: 1375252--1375320 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
1375242 CAAAAAGGGC
*
1375252 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAG-AAAAA-ACAAGAA-CA
1375275 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAGAACA
* * *
1375296 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAGAACA
1375316 AAAAA
1 AAAAA
1375321 AGGGGACAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 17 0.41
21 7 0.17
22 6 0.15
23 10 0.24
24 1 0.02
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAGAACA
Found at i:1375960 original size:22 final size:22
Alignment explanation
Indices: 1375932--1375982 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1375922 CCCCATCAAT
1375932 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
* *
1375954 CCTTTGAGCATTAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
1375976 CCTTTGA
1 CCTTTGA
1375983 CCAAACACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.27
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:1376894 original size:36 final size:36
Alignment explanation
Indices: 1376841--1376953 Score: 138
Period size: 36 Copynumber: 3.1 Consensus size: 36
1376831 CGTGCTCACC
* *
1376841 ATTGTCTCTCTTAAGACAGTTTCCCTTGAAACAAAC
1 ATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA
* * *
1376877 TTTGTCTTTCTTGAGACAGTTTCCCTTGAAAAAAAA
1 ATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA
* *
1376913 ATT-TCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
1 ATTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAA
1376949 CATTG
1 -ATTG
1376954 AAAACATTTC
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
35 25 0.39
36 36 0.56
37 3 0.05
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (36 bp):
ATTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA
Found at i:1377061 original size:102 final size:101
Alignment explanation
Indices: 1376860--1377315 Score: 734
Period size: 102 Copynumber: 4.5 Consensus size: 101
1376850 CTTAAGACAG
** * * * * *
1376860 TTTCCCTTGAAACAAACTTTGTCTTTCTTGAGACAGTTTCCCTTGAAAAAAAAATT-TCTCCCTT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTGTCTCCCTT
1376924 GAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 GAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
1376960 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGTCTCCAT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATT-TGTCTCCCT
* *
1377025 TGAGACAGTTTCTCTTGAAATATAAACATTGGAAACA
65 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
1377062 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA-TTTGTCTCCCT
1377127 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
65 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
1377164 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAACTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA-TTTGTCTCCCT
1377229 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
65 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
1377266 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAAATAGTTTCTCTTGAAACA
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1377316 TAAACATTGA
Statistics
Matches: 330, Mismatches: 23, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
100 47 0.14
102 281 0.85
103 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.36
Consensus pattern (101 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTGTCTCCCTT
GAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:1377129 original size:37 final size:37
Alignment explanation
Indices: 1377062--1377148 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
1377052 ATTGGAAACA
** * *
1377062 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1377098 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
1377135 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
1377149 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:1377224 original size:37 final size:38
Alignment explanation
Indices: 1377181--1377255 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 38
1377171 TGAAATGAAT
* *
1377181 TTTGTCTCTCTTGAGATAGTTTCCCTCGAAACA-AAAC
1 TTTGTCTCCCTTGAGACAGTTTCCCTCGAAACATAAAC
* *
1377218 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTTGTCTCCCTTGAGACAGTTTCCCTCGAAACATAAAC
1377256 ATTGAAAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
37 29 0.88
38 4 0.12
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (38 bp):
TTTGTCTCCCTTGAGACAGTTTCCCTCGAAACATAAAC
Found at i:1377305 original size:65 final size:65
Alignment explanation
Indices: 1377221--1377380 Score: 293
Period size: 65 Copynumber: 2.5 Consensus size: 65
1377211 ACAAAACTTT
*
1377221 GTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTC
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTC
* *
1377286 GTCTCTCTTGAAATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTC
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTC
1377351 GTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACA
1377381 AAATTTTGTC
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 90 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (65 bp):
GTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTC
Found at i:1377323 original size:167 final size:169
Alignment explanation
Indices: 1377098--1377415 Score: 523
Period size: 167 Copynumber: 1.9 Consensus size: 169
1377088 CTTGAGATAG
* *
1377098 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAAACAGTTTCTCTTGAAACATAAACATTGAAAAC
* *
1377163 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAACTTTGTCTCCC
66 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAACTTTGTCTCCC
1377228 TTGAGACAG-TTTCTCTTGAAACATAAACATTGAAAACA
131 TTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACA
** * *
1377266 TTTCCCTTGAAA-TGAATTTCGTCTCTCTTGAAATAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAAACAGTTTCTCTTGAAACATAAACATTGAAAAC
* * *
1377330 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCCC
66 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAACTTTGTCTCCC
1377395 TTGAGACAGTTTTCTCTTGAA
131 TTGAGACAGTTTTCTCTTGAA
1377416 GCATCATCTT
Statistics
Matches: 138, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
167 115 0.83
168 23 0.17
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (169 bp):
TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAAACAGTTTCTCTTGAAACATAAACATTGAAAAC
ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAACTTTGTCTCCC
TTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:1377558 original size:37 final size:37
Alignment explanation
Indices: 1377488--1377559 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
1377478 TGGAACTAAG
* * **
1377488 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
* *
1377525 TTTTGTCTCCCTTAAGACCGTTTCCCTTGAAACAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAA
1377560 CAAATATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.40
Consensus pattern (37 bp):
TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
Found at i:1378119 original size:159 final size:159
Alignment explanation
Indices: 1377882--1378219 Score: 604
Period size: 159 Copynumber: 2.1 Consensus size: 159
1377872 CAACACAAGT
1377882 TCAACTTCACAACGAAGGGACGGCTAGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTA
1 TCAACTTCACAACGAA-GGACGGCTAGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTA
1377947 ACTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTAAACTTCACAGCGAAGGGGCGGCT
65 ACTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTAAACTTCACAGCGAAGGGGCGGCT
*
1378012 GACTGTCGACAAACAATTTCGGAGCCAATC
130 GACTGTCGACAAACAATTTCGGAGCCAAAC
* *
1378042 TCAACTTCACAACGAAGGACGGCTGGTTGTCAATAATAATTTCCCAGTTTCAGGGCCAATTTTAA
1 TCAACTTCACAACGAAGGACGGCTAGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTAA
* *
1378107 CTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTG
66 CTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTAAACTTCACAGCGAAGGGGCGGCTG
*
1378172 ACTGTCGACAAGCAATTTCGGAGCCAAAC
131 ACTGTCGACAAACAATTTCGGAGCCAAAC
*
1378201 TCAACTTCACAGCGAAGGA
1 TCAACTTCACAACGAAGGA
1378220 TATTGGACTC
Statistics
Matches: 171, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
159 155 0.91
160 16 0.09
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (159 bp):
TCAACTTCACAACGAAGGACGGCTAGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTTAA
CTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTAAACTTCACAGCGAAGGGGCGGCTG
ACTGTCGACAAACAATTTCGGAGCCAAAC
Found at i:1378593 original size:106 final size:105
Alignment explanation
Indices: 1378042--1378760 Score: 642
Period size: 109 Copynumber: 6.9 Consensus size: 105
1378032 GGAGCCAATC
* * * * * *
1378042 TCAACTTCACAACGAA-GGACGGCTGGTTGTCAA-TAATAATTTCCCAGTTTCAGGGCCAATTTT
1 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-TCAATTTCAGAGCCAATTTC
* * * *
1378105 AACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGC
65 AACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
* * ** * * * **
1378146 TCAACTTCACAGCGAAGGGGCGGCTGACTGT---C-GACAA---GCAATTTCGGAGCCAAACTCA
1 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCAATTTCAGAGCCAATTTCA
*
1378204 ACTTCACAGCGAAGGATATTGGACTCGAGACAACAGAAGT
66 ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
* * * * *
1378244 TCAACTTCACAGCGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCTATTCCAGAGCCGATTTC
1 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-TCAATTTCAGAGCCAATTTC
* * * * *
1378309 AACTCCACAACGGAGGATATCGTGCTACCCGAGACAACACAAGT
65 AACTTCACAGCGAAGGATAT--TG-GACTCGAGACAACACAAGT
* * * ** *
1378353 TTAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTTCA-TCCGCGATTT
1 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTTCAATTTCAGAGC-CAATTT
* * *
1378417 CAACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACACAAGT
64 CAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAGT
* * *
1378462 TCAACTTCACAACGAAGGAACGGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGTCAATTTC
1 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTC-AATTTCAGAGCCAATTTC
* *
1378527 AACTTCGCAGCGAAGGATATTGGACTCAAGACAACACAAGT
65 AACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
* * * * *
1378568 TCAACTTCACAATGAAGGGACGGCTGATTGTCAAC-AA-GA-TTTC--GTTCAGAGTCAATTTCA
1 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCAATTTCAGAGCCAATTTCA
* * * *
1378628 TCTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGC
66 ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
* * ** * * * *
1378668 TCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGTTCCAGAACCAATTTC
1 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-TCAATTTCAGAGCCAATTTC
* *
1378733 AACTTCACAGCGGAGGATATTGAACTCG
65 AACTTCACAGCGAAGGATATTGGACTCG
1378761 GAACAATATT
Statistics
Matches: 503, Mismatches: 87, Indels: 48
0.79 0.14 0.08
Matches are distributed among these distances:
98 77 0.15
100 81 0.16
101 3 0.01
102 8 0.02
103 6 0.01
104 16 0.03
105 13 0.03
106 115 0.23
107 2 0.00
108 8 0.02
109 170 0.34
110 4 0.01
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (105 bp):
TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCAATTTCAGAGCCAATTTCA
ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGT
Found at i:1379288 original size:35 final size:35
Alignment explanation
Indices: 1379221--1379320 Score: 112
Period size: 36 Copynumber: 2.7 Consensus size: 35
1379211 TTTCGTCCTA
1379221 CTAGGATTCAAACT-CTCAAAAGTAGGATAGAATTATG
1 CTAGGATTC-AACTCCT-AAAA-TAGGATAGAATTATG
*
1379258 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTATG
** *
1379293 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
1379321 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
35 17 0.30
36 21 0.38
37 18 0.32
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTATG
Found at i:1379794 original size:2 final size:2
Alignment explanation
Indices: 1379789--1379861 Score: 50
Period size: 2 Copynumber: 39.5 Consensus size: 2
1379779 TTTTTTACAC
* * * *
1379789 TA TA TA T- TA T- TA T- TA TA TA TA CA TA TA T- TT TT TA GA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1379827 T- TA T- TA TT TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1379862 TTTTAAAATA
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
1 6 0.11
2 50 0.89
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1379843 original size:37 final size:37
Alignment explanation
Indices: 1379779--1379853 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 37
1379769 TTCAATTGAT
1379779 TTTTTTACACTATATATTATTATTATATATACATATA
1 TTTTTTACACTATATATTATTATTATATATACATATA
* *
1379816 TTTTTTAGA-TAT-TATTATTTATATATATATATATATA
1 TTTTTTACACTATATATTA-TTAT-TATATATACATATA
1379853 T
1 T
1379854 ATACATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 5 0.15
36 7 0.21
37 22 0.65
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.57
Consensus pattern (37 bp):
TTTTTTACACTATATATTATTATTATATATACATATA
Found at i:1380201 original size:22 final size:20
Alignment explanation
Indices: 1380173--1380220 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 20
1380163 TATTTATTTA
*
1380173 TTTATTTATTTTTCCTTTTATT
1 TTTATTTATTTTTAC--TTATT
1380195 TTTATTTATTTTTACTTATT
1 TTTATTTATTTTTACTTATT
1380215 TTTATT
1 TTTATT
1380221 CTTCATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 11 0.44
22 14 0.56
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTATTTATTTTTACTTATT
Found at i:1380202 original size:4 final size:4
Alignment explanation
Indices: 1380150--1380183 Score: 59
Period size: 4 Copynumber: 8.2 Consensus size: 4
1380140 TATATATTAA
1380150 TATT TCATT TATT TATT TATT TATT TATT TATT T
1 TATT T-ATT TATT TATT TATT TATT TATT TATT T
1380184 TTCCTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:1381727 original size:109 final size:108
Alignment explanation
Indices: 1381481--1381727 Score: 284
Period size: 109 Copynumber: 2.3 Consensus size: 108
1381471 GTTTAGTGCC
* * * *
1381481 TTTTTGCATTTTGGACACCTGTAGGACT-AAATCTGGTATTTCCCCTTTTTCGTGCATATTATGT
1 TTTTTGCATTTTGGTCATCTGTAGGACTGAAATCT-GTATTTCCCCTTTTCCGTGCATATTATAT
* * * *
1381545 AATTATTGGTTTATTCTTTGTTTAGTCCCTCTAAGTTTCGCACG
65 AATTATTGGCTTATTCTTTGATTAGTCCCTCTAAGTTTAGAACG
* * * * *
1381589 TTTTTGTATTCTGGTCATCTGTGAGGACTGAAATCAT-TATTTTCCCTTTTCCTTGCATGTTATA
1 TTTTTGCATTTTGGTCATCTGT-AGGACTGAAATC-TGTATTTCCCCTTTTCCGTGCATATTATA
* *
1381653 TATTTATTGGCTTATT-TGTTGATTAGTCCCTCTAAGTTTAGAATG
64 TAATTATTGGCTTATTCT-TTGATTAGTCCCTCTAAGTTTAGAACG
*
1381698 TTTTTGCATTTTGGTCATATGTAGTGACTG
1 TTTTTGCATTTTGGTCATCTGTAG-GACTG
1381728 TTTAATTTTT
Statistics
Matches: 116, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
108 21 0.18
109 89 0.77
110 5 0.04
111 1 0.01
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.48
Consensus pattern (108 bp):
TTTTTGCATTTTGGTCATCTGTAGGACTGAAATCTGTATTTCCCCTTTTCCGTGCATATTATATA
ATTATTGGCTTATTCTTTGATTAGTCCCTCTAAGTTTAGAACG
Found at i:1382019 original size:25 final size:25
Alignment explanation
Indices: 1381985--1382043 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
1381975 TAATCCTTTT
*
1381985 TTTTTGTTATT-CATTTTATTTTTAA
1 TTTTT-TTATTGCATTTTATTTCTAA
**
1382010 TGTTTTTTATTGTTTTTTATTTCTAA
1 T-TTTTTTATTGCATTTTATTTCTAA
1382036 TTTTTTTA
1 TTTTTTTA
1382044 ATTGGGTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 13 0.45
26 16 0.55
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (25 bp):
TTTTTTTATTGCATTTTATTTCTAA
Found at i:1382053 original size:25 final size:26
Alignment explanation
Indices: 1381999--1382055 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
1381989 TGTTATTCAT
* **
1381999 TTTATTTTTAATGTTTTTTATTGTTT
1 TTTATTTCTAATGTTTTTTATTGTGG
1382025 TTTATTTCTAAT-TTTTTTAATTG-GG
1 TTTATTTCTAATGTTTTTT-ATTGTGG
1382050 TTTATT
1 TTTATT
1382056 ATTCGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 12 0.44
26 15 0.56
ACGTcount: A:0.18, C:0.02, G:0.09, T:0.72
Consensus pattern (26 bp):
TTTATTTCTAATGTTTTTTATTGTGG
Found at i:1393145 original size:18 final size:18
Alignment explanation
Indices: 1393124--1393165 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1393114 CAGAAACAAA
*
1393124 AAAAATAAGAAAGAAAAT
1 AAAAAGAAGAAAGAAAAT
*
1393142 AAAAAGAAGAATGAAAAT
1 AAAAAGAAGAAAGAAAAT
1393160 AAAAAG
1 AAAAAG
1393166 GAGGGTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (18 bp):
AAAAAGAAGAAAGAAAAT
Found at i:1394488 original size:139 final size:139
Alignment explanation
Indices: 1394238--1394753 Score: 737
Period size: 139 Copynumber: 3.7 Consensus size: 139
1394228 GAAGGGTTTG
*
1394238 TAATGAGAAGAACTCATCCGATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTAAACCTTA
1 TAATGAGAAGAACTCATCCGATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
* ** * * *
1394303 GCTCGATTCATTGCATATGGAGGTGAATCAGCAACGCCTCACTCGAGGAATCAACATTTCCAGTG
66 GCTTGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATTTCCAGTG
1394368 GAGAGTTCA
131 GAGAGTTCA
* * *
1394377 TAATGAGAAAAACTCATCCGACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
1 TAATGAGAAGAACTCATCCGATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
* * * *
1394442 GCTTGATTCGTCACAAATGGAGTTGAATCAACAACACCTTACTCGAGGGATCAACATTTCCAGTG
66 GCTTGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATTTCCAGTG
1394507 GAGAGTTCA
131 GAGAGTTCA
* *
1394516 TAATGAGAAGAACTAATCCGATGAGGGAGAAAAAGTTAATAATGAGAAGAACTTGTTCAACCTTA
1 TAATGAGAAGAACTCATCCGATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
* * * * * * * *
1394581 CCTTAATTAATCACATATGGAGTTGAATCAGTAGCATCTCACTCGAGGGATCAATATTTCTAGTG
66 GCTTGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATTTCCAGTG
1394646 GAGAGTTCA
131 GAGAGTTCA
* * * *
1394655 AAATGAGAATAACTCATCCAATGAGGGAGAAAAAGTTTATAATGAGAAGAACTTGTTCAACCTTA
1 TAATGAGAAGAACTCATCCGATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
* *
1394720 GCTTGTTTCCATCACATAAGGAGTTGGAA-CAGCA
66 GCTTGATT-CATCACATATGGAGTT-GAATCAGCA
1394754 CCGACCTTTG
Statistics
Matches: 333, Mismatches: 42, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
139 312 0.94
140 18 0.05
141 3 0.01
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (139 bp):
TAATGAGAAGAACTCATCCGATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
GCTTGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATTTCCAGTG
GAGAGTTCA
Found at i:1395490 original size:36 final size:37
Alignment explanation
Indices: 1395417--1395503 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 37
1395407 TCTGCTTTCA
*
1395417 CAGTTTCGAATAACAACAAAAAAGGGAAAAAACTTTTT
1 CAGTTTCGAAAAACAACAAAAAA-GGAAAAAACTTTTT
* * *
1395455 -AGTTTCGAAAAATATCAAAAAA-GAAAAACCATTTTT
1 CAGTTTCGAAAAACAACAAAAAAGGAAAAAAC-TTTTT
*
1395491 CAGTATCGAAAAA
1 CAGTTTCGAAAAA
1395504 GAAGAGACAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
35 7 0.17
36 5 0.12
37 30 0.71
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (37 bp):
CAGTTTCGAAAAACAACAAAAAAGGAAAAAACTTTTT
Found at i:1396080 original size:108 final size:109
Alignment explanation
Indices: 1395911--1396111 Score: 255
Period size: 108 Copynumber: 1.9 Consensus size: 109
1395901 TCACACATAG
* *
1395911 GTCCCATTAGGTTTAGTACGTTTTTGCATTATGGTCACCTATAGGGACCAAATCTTGTA-TTTCC
1 GTCCCATTAGGTTTAGCACGTTTTTGCATTATGGTCACCTATAGGGACCAAATCGTGTATTTTCC
* *
1395975 CTTTTTCGTGCATGTTATGTAATTATTGGTTTATTCGTTGTTTA
66 CTTTTCCGTGCATGTTATATAATTATTGGTTTATTCGTTGTTTA
* * * * * *
1396019 GTCCCTTTAGGTTTAGCACGTTTTTGCGTTCTGGTCATCTGT-GAGGACTGAAATCGT-TATTTT
1 GTCCCATTAGGTTTAGCACGTTTTTGCATTATGGTCACCTATAG-GGAC-CAAATCGTGTATTTT
* *
1396082 CCCTTTTCCTTGCATGTTATATATTTATTG
64 CCCTTTTCCGTGCATGTTATATAATTATTG
1396112 CCCTATTTGT
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
107 1 0.01
108 42 0.54
109 35 0.45
ACGTcount: A:0.18, C:0.17, G:0.19, T:0.46
Consensus pattern (109 bp):
GTCCCATTAGGTTTAGCACGTTTTTGCATTATGGTCACCTATAGGGACCAAATCGTGTATTTTCC
CTTTTCCGTGCATGTTATATAATTATTGGTTTATTCGTTGTTTA
Found at i:1402684 original size:81 final size:81
Alignment explanation
Indices: 1402595--1402969 Score: 570
Period size: 81 Copynumber: 4.6 Consensus size: 81
1402585 CATATAACCT
* * * *
1402595 TTCATCTAACTTGCATGATTGACACTTTTCTTTCAAATGCACAGCTAGGCCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTTATCTTTTACT
1402660 CAACGGTATTGAATCG
66 CAACGGTATTGAATCG
** *
1402676 TTCATCTAACTGGCATAATTGACACATTTCTACCAAATGCACAACTAGGCCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTTATCTTTTACT
* *
1402741 CGACGGGATTGAATCG
66 CAACGGTATTGAATCG
* *
1402757 TTCATCTAACTGGCATAATTGACACATTTCTGTAAAATGCACAGCTAGGTCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTTATCTTTTACT
1402822 CAACGGTATTGAATCG
66 CAACGGTATTGAATCG
* * * *
1402838 TTCATCTATCTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGACCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTTATCTTTTACT
* * *
1402903 CGACGATATTGAATTG
66 CAACGGTATTGAATCG
* *
1402919 TTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGTTAGGCC
1 TTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCC
1402970 TCAAAGGCAC
Statistics
Matches: 265, Mismatches: 29, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 265 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (81 bp):
TTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCCATTTATCTTTTACT
CAACGGTATTGAATCG
Found at i:1403028 original size:68 final size:68
Alignment explanation
Indices: 1402919--1403106 Score: 331
Period size: 68 Copynumber: 2.8 Consensus size: 68
1402909 TATTGAATTG
* *
1402919 TTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1402984 CCT
66 CCT
*
1402987 TTCATCTAACTGGCACAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1403052 CCT
66 CCT
* *
1403055 TTCATCTAACTGGCATAAATGACAACTTTATGTCAAATGCACAGTTAGGCCT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCT
1403107 ATTAATCTTT
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 114 1.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:1403449 original size:55 final size:55
Alignment explanation
Indices: 1403318--1403475 Score: 223
Period size: 55 Copynumber: 2.9 Consensus size: 55
1403308 ACATATATTT
* * *
1403318 CCCATACAGAAATTCATACACTTAGTATGGATTTCTTAG--TT-CGCACATATTG
1 CCCATACAGAAATTCATACACTTAGTATGGATTTCTTAGTTTTGCACACAAAGTG
* * *
1403370 CCCATACAAAAATTTATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTG
1 CCCATACAGAAATTCATACACTTAGTATGGATTTCTTAGTTTTGCACACAAAGTG
1403425 CCCATACAGAAATTCATACACTTAGTATGGATTTCTTAAGTTTTTGCACAC
1 CCCATACAGAAATTCATACACTTAGTATGGATTTCTT-AG-TTTTGCACAC
1403476 TTAGTTCCAT
Statistics
Matches: 92, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
52 36 0.39
54 2 0.02
55 42 0.46
56 2 0.02
57 10 0.11
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (55 bp):
CCCATACAGAAATTCATACACTTAGTATGGATTTCTTAGTTTTGCACACAAAGTG
Found at i:1406838 original size:20 final size:20
Alignment explanation
Indices: 1406801--1406839 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1406791 AGATTGAGTG
* * *
1406801 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
1406821 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
1406840 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:1407067 original size:20 final size:21
Alignment explanation
Indices: 1407021--1407081 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
1407011 TTCCCCTGTG
1407021 GGGGGAATCGGTTCTCCTTCAAA
1 GGGGGAATCGGTTC-CC-TCAAA
1407044 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
1407064 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1407082 TGCATCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 2 0.06
23 14 0.39
ACGTcount: A:0.18, C:0.25, G:0.34, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1407068 original size:21 final size:21
Alignment explanation
Indices: 1407020--1407081 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
1407010 ATTCCCCTGT
1407020 GGGGGGAATCGGTTCTCCTTCAA
1 GGGGGGAATCGGTTC-CC-TCAA
*
1407043 AGGGGGAATCGGTTCCCTCAA
1 GGGGGGAATCGGTTCCCTCAA
*
1407064 GGGGGG-ATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
1407082 TGCATCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 11 0.31
21 9 0.25
22 2 0.06
23 14 0.39
ACGTcount: A:0.18, C:0.24, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:1409095 original size:12 final size:12
Alignment explanation
Indices: 1409078--1409109 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
1409068 ATGGTTCTCC
1409078 AACGTCATGTCT
1 AACGTCATGTCT
1409090 AACGTCATGTCT
1 AACGTCATGTCT
1409102 AACGTCAT
1 AACGTCAT
1409110 TTGTATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (12 bp):
AACGTCATGTCT
Found at i:1413725 original size:19 final size:20
Alignment explanation
Indices: 1413687--1413725 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1413677 TTTTCTAAAT
*
1413687 TTAAGATAAGGAATAATAGG
1 TTAAGATAAGGAAAAATAGG
*
1413707 TTAAGATAA-TAAAAATAGG
1 TTAAGATAAGGAAAAATAGG
1413726 GTAATAGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.21, T:0.26
Consensus pattern (20 bp):
TTAAGATAAGGAAAAATAGG
Found at i:1420554 original size:51 final size:51
Alignment explanation
Indices: 1420484--1420585 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
1420474 AATACTAACA
1420484 TAGTTAACCATTAAATTAGAAACTTTGAACTAACAAACGGTTGGTATAGTG
1 TAGTTAACCATTAAATTAGAAACTTTGAACTAACAAACGGTTGGTATAGTG
* *
1420535 TAGTTAACCATTAAATTAGAAACTTTGAACTAACGAACGGTTGGTTTAGTG
1 TAGTTAACCATTAAATTAGAAACTTTGAACTAACAAACGGTTGGTATAGTG
1420586 GGATAAGATA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (51 bp):
TAGTTAACCATTAAATTAGAAACTTTGAACTAACAAACGGTTGGTATAGTG
Found at i:1426156 original size:13 final size:14
Alignment explanation
Indices: 1426138--1426172 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1426128 AACAATTAAA
*
1426138 TTTTAAAATG-CAC
1 TTTTAAAAAGACAC
1426151 TTTTAAAAAGACAC
1 TTTTAAAAAGACAC
1426165 TTTTAAAA
1 TTTTAAAA
1426173 GTCATTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (14 bp):
TTTTAAAAAGACAC
Found at i:1428426 original size:2 final size:2
Alignment explanation
Indices: 1428419--1428475 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1428409 ACGTTTCTAT
1428419 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1428461 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1428476 CTAAAATCTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1430725 original size:23 final size:26
Alignment explanation
Indices: 1430699--1430754 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
1430689 ATATAAACTC
*
1430699 TATTA-ATTATT-TATTAAAAATTA-
1 TATTATATTATTATAATAAAAATTAT
*
1430722 TATTATATTATTATAATAATAATTAT
1 TATTATATTATTATAATAAAAATTAT
1430748 TATTATA
1 TATTATA
1430755 AAAATAAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 5 0.18
24 6 0.21
25 10 0.36
26 7 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TATTATATTATTATAATAAAAATTAT
Found at i:1430750 original size:18 final size:18
Alignment explanation
Indices: 1430727--1430761 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1430717 AATTATATTA
*
1430727 TATTATTATAATAATAAT
1 TATTATTATAAAAATAAT
1430745 TATTATTATAAAAATAA
1 TATTATTATAAAAATAA
1430762 AGTAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTATTATAAAAATAAT
Found at i:1431167 original size:32 final size:32
Alignment explanation
Indices: 1431126--1431190 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1431116 GACTAAGATA
1431126 ATTATAAAATAATATATGTTCAAAAAATTTCT
1 ATTATAAAATAATATATGTTCAAAAAATTTCT
*
1431158 ATTATAAAATAATATCTGTTCAAAAAATTTCT
1 ATTATAAAATAATATATGTTCAAAAAATTTCT
1431190 A
1 A
1431191 AAGAATTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.40
Consensus pattern (32 bp):
ATTATAAAATAATATATGTTCAAAAAATTTCT
Found at i:1434730 original size:55 final size:56
Alignment explanation
Indices: 1434646--1434758 Score: 210
Period size: 55 Copynumber: 2.0 Consensus size: 56
1434636 ATGCTTTAAA
1434646 TTAGGGTTTAAATTTATGAACGAGGTGAACGTTTTC-AAAAAATGGTAAGCCACTT
1 TTAGGGTTTAAATTTATGAACGAGGTGAACGTTTTCAAAAAAATGGTAAGCCACTT
1434701 TTAGGGTTTAAATTTATGAACGAGGTGAACGTTTTCAGAAAAAATGGTAAGCCACTT
1 TTAGGGTTTAAATTTATGAACGAGGTGAACGTTTTCA-AAAAAATGGTAAGCCACTT
1434758 T
1 T
1434759 GGTGGTTTCA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
55 36 0.64
57 20 0.36
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.33
Consensus pattern (56 bp):
TTAGGGTTTAAATTTATGAACGAGGTGAACGTTTTCAAAAAAATGGTAAGCCACTT
Found at i:1438180 original size:64 final size:65
Alignment explanation
Indices: 1438107--1438261 Score: 206
Period size: 65 Copynumber: 2.4 Consensus size: 65
1438097 CACCCTAATC
*
1438107 CGAATGCATTTTGTGTACCGATGCACA-ACCATACATCGATGTACTCCT-GATTTTCTTGAAACA
1 CGAATGCATTTTGTGTAACGATGCACAGACCATACATCGATGTACTCCTGGATTTT-TTGAAACA
1438170 T
65 T
* * * * *
1438171 CGAATGCATTTTATGTAACGATGCAAAGACCATGCATCGCTGTACTCTTGGATTTTTTGAAACAT
1 CGAATGCATTTTGTGTAACGATGCACAGACCATACATCGATGTACTCCTGGATTTTTTGAAACAT
* * *
1438236 CGAATGTAATTAGTGTAACGATGCAC
1 CGAATGCATTTTGTGTAACGATGCAC
1438262 CCCAAGTGTA
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 24 0.31
65 48 0.62
66 6 0.08
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (65 bp):
CGAATGCATTTTGTGTAACGATGCACAGACCATACATCGATGTACTCCTGGATTTTTTGAAACAT
Found at i:1443362 original size:23 final size:23
Alignment explanation
Indices: 1443336--1443406 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
1443326 TGAAGTGTAC
1443336 CGATGCATCCTTTGAATATGCAT
1 CGATGCATCCTTTGAATATGCAT
* * *
1443359 CGATACA--CTATGAAGATGCA-
1 CGATGCATCCTTTGAATATGCAT
*
1443379 CTGATGCAATCC-TTGAATGTGCAT
1 C-GATGC-ATCCTTTGAATATGCAT
1443403 CGAT
1 CGAT
1443407 ACCTATGCAG
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
20 1 0.03
21 15 0.42
22 1 0.03
23 17 0.47
24 2 0.06
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (23 bp):
CGATGCATCCTTTGAATATGCAT
Found at i:1443402 original size:44 final size:43
Alignment explanation
Indices: 1443309--1443425 Score: 157
Period size: 43 Copynumber: 2.7 Consensus size: 43
1443299 TTTTGTGCAT
*
1443309 TGTGCATCGATACACTATGAAGTGTACCGATGCATCCTTTGAA
1 TGTGCATCGATACACTATGAAGTGCACCGATGCATCCTTTGAA
* *
1443352 TATGCATCGATACACTATGAAGATGCACTGATGCAATCC-TTGAA
1 TGTGCATCGATACACTATGAAG-TGCACCGATGC-ATCCTTTGAA
* *
1443396 TGTGCATCGATAC-CTATGCAGTGCATCGAT
1 TGTGCATCGATACACTATGAAGTGCACCGAT
1443426 ACACTCGTCG
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
42 7 0.11
43 28 0.43
44 26 0.40
45 4 0.06
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (43 bp):
TGTGCATCGATACACTATGAAGTGCACCGATGCATCCTTTGAA
Found at i:1445655 original size:64 final size:65
Alignment explanation
Indices: 1445552--1445675 Score: 162
Period size: 64 Copynumber: 1.9 Consensus size: 65
1445542 ATGCAAAACC
* * * *
1445552 ATGCATCGATGCACTCCTGATTTTATTTAAAAATTGAATGTATTTA-TGTACCAATGCACATACT
1 ATGCATCGATGCACTCCTGATCTTATTGAAAAATCGAATGTAATTAGTGTACCAATGCACATACT
* * *
1445616 ATGCATCGATGCACTCCTGGCTCTT-TTGAAACATCGAATGTAATTAGTGTACCGATGCAC
1 ATGCATCGATGCACTCCT-GATCTTATTGAAAAATCGAATGTAATTAGTGTACCAATGCAC
1445676 CCCAAGTGTA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
64 35 0.69
65 16 0.31
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (65 bp):
ATGCATCGATGCACTCCTGATCTTATTGAAAAATCGAATGTAATTAGTGTACCAATGCACATACT
Found at i:1452942 original size:25 final size:25
Alignment explanation
Indices: 1452907--1452958 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1452897 CAATGGTATG
*
1452907 TAGTAGTGAGTGATTTTGAGGAACA
1 TAGTAGAGAGTGATTTTGAGGAACA
*
1452932 TAGTAGAGAGTGGTTTTGAGGAACA
1 TAGTAGAGAGTGATTTTGAGGAACA
1452957 TA
1 TA
1452959 CTATCCAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.33, T:0.31
Consensus pattern (25 bp):
TAGTAGAGAGTGATTTTGAGGAACA
Found at i:1459313 original size:24 final size:24
Alignment explanation
Indices: 1459284--1459333 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
1459274 CAATAATCTG
*
1459284 TTTGTTTATGTTCATTCATTTATA
1 TTTGTTTATGTTCATTCACTTATA
*
1459308 TTTGTTTATGTTCGTTCACTTATA
1 TTTGTTTATGTTCATTCACTTATA
1459332 TT
1 TT
1459334 CAACCTAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.62
Consensus pattern (24 bp):
TTTGTTTATGTTCATTCACTTATA
Found at i:1463262 original size:2 final size:2
Alignment explanation
Indices: 1463255--1463297 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1463245 ACAATGCAGG
1463255 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1463297 T
1 T
1463298 CCTTTATGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1465840 original size:2 final size:2
Alignment explanation
Indices: 1465833--1465862 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1465823 TCAATCTACA
1465833 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1465863 TTATTGACGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1466801 original size:30 final size:30
Alignment explanation
Indices: 1466767--1466838 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
1466757 TTCTCCCATG
* * *
1466767 TCCCATTATCTTATTCACTATCCTCTCCTA
1 TCCCAGTATCTTACTAACTATCCTCTCCTA
1466797 TCCCAGTATCTTACTAACTATCCTCTCCTA
1 TCCCAGTATCTTACTAACTATCCTCTCCTA
*
1466827 TCTCAGTATCTT
1 TCCCAGTATCTT
1466839 CAACTCCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.21, C:0.35, G:0.03, T:0.42
Consensus pattern (30 bp):
TCCCAGTATCTTACTAACTATCCTCTCCTA
Found at i:1470171 original size:2 final size:2
Alignment explanation
Indices: 1470164--1470190 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1470154 TCAATTTACA
1470164 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1470191 AAATTTACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1478025 original size:3 final size:3
Alignment explanation
Indices: 1478007--1478084 Score: 138
Period size: 3 Copynumber: 25.7 Consensus size: 3
1477997 CTATCAAAAA
*
1478007 TAT TAT AAT ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1478053 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1478085 CTACTACTAC
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
3 70 0.97
4 2 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1482533 original size:31 final size:29
Alignment explanation
Indices: 1482498--1482571 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 29
1482488 CAAATCAAAG
1482498 CAAAGAGAAAAAGAACAAAGAGAAAAAGAAC
1 CAAAGAGAAAAAGAACAAAGA-AAAAA-AAC
* * *
1482529 CAAAGAAAAATAAAGAGCAAAGAAAAAAAAG
1 CAAAG-AGAA-AAAGAACAAAGAAAAAAAAC
*
1482560 TAAAGAGAAAAA
1 CAAAGAGAAAAA
1482572 AAATAAAAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
29 3 0.08
30 3 0.08
31 11 0.31
32 8 0.22
33 11 0.31
ACGTcount: A:0.73, C:0.07, G:0.18, T:0.03
Consensus pattern (29 bp):
CAAAGAGAAAAAGAACAAAGAAAAAAAAC
Found at i:1482563 original size:21 final size:21
Alignment explanation
Indices: 1482534--1482600 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
1482524 AGAACCAAAG
*
1482534 AAAAATAAAGAGCAAAGAAAA-
1 AAAAGTAAAGAG-AAAGAAAAT
*
1482555 AAAAGTAAAGAGAAAAAAAAT
1 AAAAGTAAAGAGAAAGAAAAT
**
1482576 AAAAACAAAGAGAAA-AAAAT
1 AAAAGTAAAGAGAAAGAAAAT
1482596 AAAAG
1 AAAAG
1482601 AAAAAGCAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.78, C:0.03, G:0.13, T:0.06
Consensus pattern (21 bp):
AAAAGTAAAGAGAAAGAAAAT
Found at i:1482568 original size:16 final size:16
Alignment explanation
Indices: 1482494--1482574 Score: 80
Period size: 16 Copynumber: 5.2 Consensus size: 16
1482484 AGATCAAATC
1482494 AAAGCAAAGAGAAAAA
1 AAAGCAAAGAGAAAAA
*
1482510 GAA-CAAAGAGAAAAA
1 AAAGCAAAGAGAAAAA
* *
1482525 GAACCAAAGA-AAAATA
1 AAAGCAAAGAGAAAA-A
1482541 AAGAGC-AA-AGAAAAA
1 AA-AGCAAAGAGAAAAA
*
1482556 AAAGTAAAGAGAAAAA
1 AAAGCAAAGAGAAAAA
1482572 AAA
1 AAA
1482575 TAAAAACAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
14 2 0.04
15 25 0.45
16 26 0.47
17 2 0.04
ACGTcount: A:0.74, C:0.06, G:0.17, T:0.02
Consensus pattern (16 bp):
AAAGCAAAGAGAAAAA
Found at i:1482572 original size:15 final size:15
Alignment explanation
Indices: 1482494--1482573 Score: 83
Period size: 15 Copynumber: 5.2 Consensus size: 15
1482484 AGATCAAATC
1482494 AAAGCAAAGAGAAAA
1 AAAGCAAAGAGAAAA
1482509 AGAA-CAAAGAGAAAA
1 A-AAGCAAAGAGAAAA
* *
1482524 AGAACCAAAGAAAAATA
1 A-AAGCAAAGAGAAA-A
1482541 AAGAGCAAAGA-AAAA
1 AA-AGCAAAGAGAAAA
*
1482556 AAAGTAAAGAGAAAA
1 AAAGCAAAGAGAAAA
1482571 AAA
1 AAA
1482574 ATAAAAACAA
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
14 7 0.12
15 26 0.46
16 15 0.26
17 9 0.16
ACGTcount: A:0.74, C:0.06, G:0.17, T:0.03
Consensus pattern (15 bp):
AAAGCAAAGAGAAAA
Found at i:1482585 original size:35 final size:35
Alignment explanation
Indices: 1482507--1482605 Score: 109
Period size: 36 Copynumber: 2.9 Consensus size: 35
1482497 GCAAAGAGAA
**
1482507 AAAGAACAAAGAGAAAAAGAACCAAAG---AAAAAT
1 AAAGAACAAAGAGAAAAA-AATAAAAGAAAAAAAAT
*
1482540 AAAGAGCAAAGA-AAAAAAAGTAAAGAGAAAAAAAAT
1 AAAGAACAAAGAGAAAAAAA-TAAA-AGAAAAAAAAT
1482576 AAA-AACAAAGAGAAAAAAATAAAAGAAAAA
1 AAAGAACAAAGAGAAAAAAATAAAAGAAAAA
1482606 GCAAAGAGCG
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
31 2 0.04
32 7 0.12
33 13 0.23
34 7 0.12
35 11 0.20
36 16 0.29
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.04
Consensus pattern (35 bp):
AAAGAACAAAGAGAAAAAAATAAAAGAAAAAAAAT
Found at i:1483689 original size:33 final size:33
Alignment explanation
Indices: 1483647--1483715 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
1483637 AGAATCAGTG
1483647 TTGAAGCAATCAACATCGAATATTACGGCATCT
1 TTGAAGCAATCAACATCGAATATTACGGCATCT
* * *
1483680 TTGAAGCAATCAACATCGAATGTTAGGGTATCT
1 TTGAAGCAATCAACATCGAATATTACGGCATCT
1483713 TTG
1 TTG
1483716 GGGATTCAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Consensus pattern (33 bp):
TTGAAGCAATCAACATCGAATATTACGGCATCT
Found at i:1483952 original size:38 final size:37
Alignment explanation
Indices: 1483861--1483969 Score: 141
Period size: 38 Copynumber: 2.9 Consensus size: 37
1483851 TGAAACACTT
*
1483861 ATCTTTGAGTCTGTTTCACTTTAAACAAAGA-AAAGAA
1 ATCTTTGAGTTTGTTTCACTTTAAACAAA-ACAAAGAA
* *
1483898 ATATTTGAGTTTGTTTCACTTGAAACAAAACAAA-AA
1 ATCTTTGAGTTTGTTTCACTTTAAACAAAACAAAGAA
*
1483934 TCATCTTTGAGTTTGTTTCCCTTTAAACAAAACAAA
1 --ATCTTTGAGTTTGTTTCACTTTAAACAAAACAAA
1483970 TATCTATGAG
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
36 3 0.05
37 29 0.46
38 31 0.49
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (37 bp):
ATCTTTGAGTTTGTTTCACTTTAAACAAAACAAAGAA
Found at i:1484875 original size:55 final size:55
Alignment explanation
Indices: 1484801--1484963 Score: 222
Period size: 55 Copynumber: 3.0 Consensus size: 55
1484791 CTATACGGAA
* * *
1484801 ATTCATCAACTCATTATGAATTTCGTGGGTTTGCACACAAAGTGTC-TGTACGGTG
1 ATTCATCAACCCATGATGAATTTCGTGGATTTGCACACAAAGTG-CATGTACGGTG
* *
1484856 ATTCATCAACCCATGATGAATTCCGTGGATTTGCACACAAAGTGCATGTATGGTG
1 ATTCATCAACCCATGATGAATTTCGTGGATTTGCACACAAAGTGCATGTACGGTG
* * *
1484911 ATTCATCAACCTATGATTAA-TTCTGTGGATTTGCACACAAAGTGCTTGTACGG
1 ATTCATCAACCCATGATGAATTTC-GTGGATTTGCACACAAAGTGCATGTACGG
1484964 CCCATGATGA
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
54 3 0.03
55 93 0.97
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (55 bp):
ATTCATCAACCCATGATGAATTTCGTGGATTTGCACACAAAGTGCATGTACGGTG
Found at i:1485040 original size:2 final size:2
Alignment explanation
Indices: 1485033--1485061 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1485023 TATCAATGCA
1485033 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1485062 ACAACATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1485448 original size:34 final size:34
Alignment explanation
Indices: 1485405--1485484 Score: 124
Period size: 34 Copynumber: 2.4 Consensus size: 34
1485395 ACCCCCTTCT
*
1485405 GGTATCGATACCAAAAATAGGTTCGATGTTGCCG
1 GGTATCGATACCAAAAATAGATTCGATGTTGCCG
* **
1485439 GGTATCGATACCAAAATTAGATTCGATGTTGCTT
1 GGTATCGATACCAAAAATAGATTCGATGTTGCCG
1485473 GGTATCGATACC
1 GGTATCGATACC
1485485 CTTATCATGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (34 bp):
GGTATCGATACCAAAAATAGATTCGATGTTGCCG
Found at i:1492839 original size:32 final size:31
Alignment explanation
Indices: 1492798--1492985 Score: 155
Period size: 32 Copynumber: 5.9 Consensus size: 31
1492788 AGTCGAGGGT
*
1492798 TTACCTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATG-TCTTCGGAACATATGGACAGAA
* * *
1492830 TTACCTATGTCTTTTGGGACATATGGATAGAA
1 TTACCTATGTC-TTCGGAACATATGGACAGAA
* *
1492862 TTACCTATGTCTTTCAGAACATATGGACATAA
1 TTACCTATGTC-TTCGGAACATATGGACAGAA
* ** *
1492894 TTACCTATGCCTTTTGAGACATATGGACAGTA
1 TTACCTATGTCTTCGGA-ACATATGGACAGAA
** * *
1492926 -TACCTATGTTCTAAGGAACATGTGGACAG-T
1 TTACCTATG-TCTTCGGAACATATGGACAGAA
* * *
1492956 TTACCTAGGTTCTTCGGGACCTATGGACAG
1 TTACCTATG-TCTTCGGAACATATGGACAG
1492986 TTGTCGAGGT
Statistics
Matches: 126, Mismatches: 26, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
31 48 0.38
32 78 0.62
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (31 bp):
TTACCTATGTCTTCGGAACATATGGACAGAA
Found at i:1492899 original size:64 final size:63
Alignment explanation
Indices: 1492814--1492934 Score: 188
Period size: 64 Copynumber: 1.9 Consensus size: 63
1492804 ATGTTCTACG
* * *
1492814 GAACATATGGACAGAATTACCTATGTCTTTTGGGACATATGGATAGAATTACCTATGTCTTTCA
1 GAACATATGGACAGAATTACCTATGCCTTTTGAGACATATGGACAGAA-TACCTATGTCTTTCA
* *
1492878 GAACATATGGACATAATTACCTATGCCTTTTGAGACATATGGACAGTATACCTATGT
1 GAACATATGGACAGAATTACCTATGCCTTTTGAGACATATGGACAGAATACCTATGT
1492935 TCTAAGGAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
63 9 0.17
64 43 0.83
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (63 bp):
GAACATATGGACAGAATTACCTATGCCTTTTGAGACATATGGACAGAATACCTATGTCTTTCA
Found at i:1492983 original size:31 final size:31
Alignment explanation
Indices: 1492912--1492987 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
1492902 GCCTTTTGAG
* *
1492912 ACATATGGACAGTATACCTATGTTCTAAGGA
1 ACATATGGACAGTTTACCTAGGTTCTAAGGA
* ** *
1492943 ACATGTGGACAGTTTACCTAGGTTCTTCGGG
1 ACATATGGACAGTTTACCTAGGTTCTAAGGA
*
1492974 ACCTATGGACAGTT
1 ACATATGGACAGTT
1492988 GTCGAGGTTC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (31 bp):
ACATATGGACAGTTTACCTAGGTTCTAAGGA
Found at i:1497387 original size:55 final size:55
Alignment explanation
Indices: 1497269--1497388 Score: 141
Period size: 55 Copynumber: 2.2 Consensus size: 55
1497259 TGTGAGTTTA
* ** * *** * *
1497269 CACACAAAGTGCCTGTACGGTGATTCATCAACCCATGATGAATTTTATGGATTTG
1 CACACAAAGTCCCTGTACAATGATTCATCAACCCATAATGAATCCCAAGGATATG
**
1497324 CATGCAAAGTCCCTGTACAATGATTCATCAACCCATAATGAATCCCAAGGATATG
1 CACACAAAGTCCCTGTACAATGATTCATCAACCCATAATGAATCCCAAGGATATG
1497379 CACACAAAGT
1 CACACAAAGT
1497389 GCCCGTAGTA
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (55 bp):
CACACAAAGTCCCTGTACAATGATTCATCAACCCATAATGAATCCCAAGGATATG
Found at i:1497431 original size:2 final size:2
Alignment explanation
Indices: 1497424--1497465 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1497414 TATCAATGCA
1497424 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1497466 TTAACAACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1497872 original size:20 final size:22
Alignment explanation
Indices: 1497847--1497899 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1497837 GATGTTGTCG
1497847 GGTATCGATACT-CT-TACCAT
1 GGTATCGATACTACTATACCAT
* *
1497867 GGTATCGATACTACTATTCTAT
1 GGTATCGATACTACTATACCAT
1497889 GGTATCGATAC
1 GGTATCGATAC
1497900 CCCCTTCCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 12 0.41
21 2 0.07
22 15 0.52
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (22 bp):
GGTATCGATACTACTATACCAT
Found at i:1497916 original size:95 final size:95
Alignment explanation
Indices: 1497779--1497975 Score: 279
Period size: 95 Copynumber: 2.1 Consensus size: 95
1497769 CAGAGTACTA
* * * *
1497779 ATACTTCTATACTATGGTACCAATACCCCCTTCCGGTATCGATCCCAAAATTAGGTTTGATGTTG
1 ATACTACTATACTATGGTACCAATACCCCCTTCCGGTATCGATACCAAAATTAGATTTGATATTG
*
1497844 -TCGGGTATCGATACTCTTACCATGGTATCG
66 CT-GGGTATCGATACCCTTACCATGGTATCG
* * * *
1497874 ATACTACTATTCTATGGTATCGATACCCCCTTCCGGTATCGATACTAAAATTAGATTTGATATTG
1 ATACTACTATACTATGGTACCAATACCCCCTTCCGGTATCGATACCAAAATTAGATTTGATATTG
* *
1497939 CTTGGTATCGATACCCTTATCATGGTATCG
66 CTGGGTATCGATACCCTTACCATGGTATCG
1497969 ATACTAC
1 ATACTAC
1497976 CTCGTCGGTA
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
95 89 0.99
96 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (95 bp):
ATACTACTATACTATGGTACCAATACCCCCTTCCGGTATCGATACCAAAATTAGATTTGATATTG
CTGGGTATCGATACCCTTACCATGGTATCG
Found at i:1499906 original size:55 final size:55
Alignment explanation
Indices: 1499788--1500055 Score: 308
Period size: 55 Copynumber: 4.9 Consensus size: 55
1499778 CTATACGGAA
* * * * * *
1499788 ATTCATCAACTCATTATGAATTCCTTGGGTTTGCACAC--AGTGTTTGTACGGTG
1 ATTCATCAACCCATGATGAATTCCATGGATTTGCACACAAAGTGCTTGTACGATG
* *
1499841 ATTCATCAACCCATGATGAATTCCGTGGATTTGCACACAAAGTGCATGTACGATG
1 ATTCATCAACCCATGATGAATTCCATGGATTTGCACACAAAGTGCTTGTACGATG
* * * * * *
1499896 ATTCATCAACCTATAATTAATTCTATGGATTCGCACACAAAGTGCCTGTAC-AGTG
1 ATTCATCAACCCATGATGAATTCCATGGATTTGCACACAAAGTGCTTGTACGA-TG
* * * *
1499951 ATTCATCAACCCATGATGAATTTCATGTATTTGCGCACAAAGTGCTTGTACGGTG
1 ATTCATCAACCCATGATGAATTCCATGGATTTGCACACAAAGTGCTTGTACGATG
* * * *
1500006 ATTCATCAACCCATTATGAATCCCTTGGATATGCACACAAAGTGCTTGTA
1 ATTCATCAACCCATGATGAATTCCATGGATTTGCACACAAAGTGCTTGTA
1500056 GTACACATAG
Statistics
Matches: 180, Mismatches: 31, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
53 34 0.19
54 1 0.01
55 145 0.81
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (55 bp):
ATTCATCAACCCATGATGAATTCCATGGATTTGCACACAAAGTGCTTGTACGATG
Found at i:1500551 original size:95 final size:95
Alignment explanation
Indices: 1500415--1500602 Score: 277
Period size: 95 Copynumber: 2.0 Consensus size: 95
1500405 ACCGATACTT
** * * * *
1500415 CTATACTATGGTATTGATACCTCCTTCCGGTATCGATACCAAAATTAGGTTTGATGTTGCCTAGT
1 CTATACTATGGTACCGATACCCCCTTCCAGTATCGATACCAAAATTAGATTCGATGTTGCCTAGT
*
1500480 ACTGATACCCTTACCATGGTATTGATACAA
66 ACTGATACCCTTACCAAGGTATTGATACAA
* *
1500510 CTATACTATGGTACCGATACCCCCTTCCAGTATCGATACCAAAATTAGATTCGATGTTGCTTGGT
1 CTATACTATGGTACCGATACCCCCTTCCAGTATCGATACCAAAATTAGATTCGATGTTGCCTAGT
* *
1500575 ATTGATACCCTTATCAAGGTATTGATAC
66 ACTGATACCCTTACCAAGGTATTGATAC
1500603 TACCTCTTCG
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
95 82 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (95 bp):
CTATACTATGGTACCGATACCCCCTTCCAGTATCGATACCAAAATTAGATTCGATGTTGCCTAGT
ACTGATACCCTTACCAAGGTATTGATACAA
Found at i:1502650 original size:2 final size:2
Alignment explanation
Indices: 1502643--1502701 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
1502633 AACCATTGAA
1502643 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
1502685 CC TC TC CC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
1502702 GGCAAAACGG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:1503254 original size:30 final size:29
Alignment explanation
Indices: 1503211--1503329 Score: 109
Period size: 30 Copynumber: 4.0 Consensus size: 29
1503201 GGATTATTTT
* *
1503211 TATTTTCT-ATTTTAGCCCCTTAAGTTTC
1 TATTTTTTGATTTTAGTCCCTTAAGTTTC
*
1503239 TATTTTTGTGATTTTAGTCCCTTAAATGTTTG
1 TATTTTT-TGATTTTAGTCCCTT-AA-GTTTC
*
1503271 T-TTTTATTG-TATTAGTCCCTTAAGTTTC
1 TATTTT-TTGATTTTAGTCCCTTAAGTTTC
* **
1503299 TATTTTTATTATTTTAGTCATTTAAGTTTC
1 TATTTTT-TGATTTTAGTCCCTTAAGTTTC
1503329 T
1 T
1503330 GTTGTTACTG
Statistics
Matches: 74, Mismatches: 9, Indels: 14
0.76 0.09 0.14
Matches are distributed among these distances:
28 12 0.16
29 8 0.11
30 40 0.54
31 8 0.11
32 6 0.08
ACGTcount: A:0.19, C:0.13, G:0.10, T:0.58
Consensus pattern (29 bp):
TATTTTTTGATTTTAGTCCCTTAAGTTTC
Found at i:1503344 original size:30 final size:28
Alignment explanation
Indices: 1503290--1503403 Score: 102
Period size: 30 Copynumber: 3.8 Consensus size: 28
1503280 TATTAGTCCC
* *
1503290 TTAAGTTTCTATTTTTATTATTTTAGTCAT
1 TTAAGTTTCT-GTTTTACTATTTTAGTC-T
*
1503320 TTAAGTTTCTGTTGTTACTGTTTTAGCTCT
1 TTAAGTTTCTGTT-TTACTATTTTAG-TCT
* * *
1503350 TTAAATTTCTGTTTGTGCCATTTTAGTCCT
1 TTAAGTTTCTGTTT-TACTATTTTAGT-CT
*
1503380 TTAAGTTTCTGTTTTTCTTATTTT
1 TTAAGTTTCTGTTTTAC-TATTTT
1503404 GGTCCATGAA
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
29 6 0.09
30 61 0.88
31 2 0.03
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.61
Consensus pattern (28 bp):
TTAAGTTTCTGTTTTACTATTTTAGTCT
Found at i:1503359 original size:60 final size:60
Alignment explanation
Indices: 1503220--1503392 Score: 179
Period size: 60 Copynumber: 2.9 Consensus size: 60
1503210 TTATTTTCTA
* * * * * *
1503220 TTTTAGCCCCTTAAGTTTCTATTTTTGTGATTTTAGTCCCTTAAATGTT-TGTTTTTATTG
1 TTTTAGCTCCTTAAGTTTCTATTTTTGTCATTTTAGTCCTTTAAGT-TTCTGTTGTTACTG
* * * *
1503280 TATTAG-TCCCTTAAGTTTCTATTTTTATTATTTTAGTCATTTAAGTTTCTGTTGTTACTG
1 TTTTAGCT-CCTTAAGTTTCTATTTTTGTCATTTTAGTCCTTTAAGTTTCTGTTGTTACTG
* * * * *
1503340 TTTTAGCTCTTTAAATTTCTGTTTGTGCCATTTTAGTCCTTTAAGTTTCTGTT
1 TTTTAGCTCCTTAAGTTTCTATTTTTGTCATTTTAGTCCTTTAAGTTTCTGTT
1503393 TTTCTTATTT
Statistics
Matches: 92, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
59 2 0.02
60 89 0.97
61 1 0.01
ACGTcount: A:0.17, C:0.13, G:0.13, T:0.57
Consensus pattern (60 bp):
TTTTAGCTCCTTAAGTTTCTATTTTTGTCATTTTAGTCCTTTAAGTTTCTGTTGTTACTG
Found at i:1503483 original size:20 final size:20
Alignment explanation
Indices: 1503458--1503495 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1503448 GGGTTGGAAT
* *
1503458 ATTCGTTTGTATTTATTTCA
1 ATTCGTATGTATATATTTCA
1503478 ATTCGTATGTATATATTT
1 ATTCGTATGTATATATTT
1503496 GTATGTATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.08, G:0.11, T:0.58
Consensus pattern (20 bp):
ATTCGTATGTATATATTTCA
Found at i:1508044 original size:14 final size:14
Alignment explanation
Indices: 1508003--1508049 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 14
1507993 TTCTTCCTCT
1508003 TCTTTAGTCTTTAA
1 TCTTTAGTCTTTAA
*
1508017 TC--TAGTCTCT--
1 TCTTTAGTCTTTAA
1508027 TCTTTAGTCTTTAA
1 TCTTTAGTCTTTAA
1508041 TCTTTAGTC
1 TCTTTAGTC
1508050 GAACCCCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
10 2 0.07
12 14 0.52
14 11 0.41
ACGTcount: A:0.17, C:0.19, G:0.09, T:0.55
Consensus pattern (14 bp):
TCTTTAGTCTTTAA
Found at i:1510414 original size:35 final size:35
Alignment explanation
Indices: 1510368--1510439 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
1510358 CCAAAAAAGA
* * *
1510368 AGAGTTAGATTAGGAGTTAAATACTAGTCTAAAAT
1 AGAGTTAGATTAAGACTCAAATACTAGTCTAAAAT
*
1510403 AGAGTTGGATTAAGACTCAAATACTAGTCTAAAAT
1 AGAGTTAGATTAAGACTCAAATACTAGTCTAAAAT
1510438 AG
1 AG
1510440 GGTTTTTTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.43, C:0.08, G:0.19, T:0.29
Consensus pattern (35 bp):
AGAGTTAGATTAAGACTCAAATACTAGTCTAAAAT
Found at i:1510837 original size:16 final size:18
Alignment explanation
Indices: 1510814--1510852 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
1510804 ATTATATGGA
1510814 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
1510830 T-TTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
1510847 TATTAT
1 TATTAT
1510853 ACGTATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.10
16 9 0.45
17 5 0.25
18 4 0.20
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:1510908 original size:2 final size:2
Alignment explanation
Indices: 1510903--1510927 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1510893 TTACTTTATT
1510903 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1510928 TTCTTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1511101 original size:2 final size:2
Alignment explanation
Indices: 1511096--1511120 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1511086 CTTATAACTT
1511096 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1511121 TTTTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1511276 original size:41 final size:39
Alignment explanation
Indices: 1511231--1511307 Score: 100
Period size: 41 Copynumber: 1.9 Consensus size: 39
1511221 AGGGCCCATT
* *
1511231 TTTTTATTTTATTTCTAACTAAAGTCTCTCTCACTTTCCTC
1 TTTTTATCTTATTTCTAACTAAAG-CCCTC-CACTTTCCTC
* *
1511272 TTTTTGTCTTATTTCTGACTAAAGCCCTCCACTTTC
1 TTTTTATCTTATTTCTAACTAAAGCCCTCCACTTTC
1511308 GGTGAAGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 7 0.22
40 4 0.12
41 21 0.66
ACGTcount: A:0.18, C:0.26, G:0.05, T:0.51
Consensus pattern (39 bp):
TTTTTATCTTATTTCTAACTAAAGCCCTCCACTTTCCTC
Done.