Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold7
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: 6555642
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 349864 characters in sequence are not A, C, G, or T
File 27 of 37
Found at i:4631615 original size:22 final size:23
Alignment explanation
Indices: 4631589--4631635 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
4631579 TCATATGGTC
4631589 AATTTAA-TTTAAT-TTAATAAAA
1 AATTTAATTTTAATGTTAA-AAAA
4631611 AATTTAATTTTAATGTTAAAAAA
1 AATTTAATTTTAATGTTAAAAAA
4631634 AA
1 AA
4631636 GCCTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.30
23 12 0.52
24 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
AATTTAATTTTAATGTTAAAAAA
Found at i:4638416 original size:20 final size:21
Alignment explanation
Indices: 4638367--4638424 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
4638357 TCTGGAAGGA
* *
4638367 AATTGTATCGATATATTTTTT
1 AATTGTATCGATACATTTCTT
*
4638388 AAATGTATCGATACATTTCTT
1 AATTGTATCGATACATTTCTT
4638409 -ATTGTATCGATACATT
1 AATTGTATCGATACATT
4638425 CTGGGTGTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (21 bp):
AATTGTATCGATACATTTCTT
Found at i:4641378 original size:33 final size:32
Alignment explanation
Indices: 4641298--4641451 Score: 141
Period size: 33 Copynumber: 4.8 Consensus size: 32
4641288 AAAGTAACCT
** *
4641298 TTCAAAGTCCATGACTCAGTGGCATC-TCTTC
1 TTCAAAGTCCACAACTCAGTGGCATCTTTTTC
* *
4641329 -TCCAAGTCTACAACTCAGTGGCATCATTTTTC
1 TTCAAAGTCCACAACTCAGTGGCATC-TTTTTC
* *
4641361 TTCAAAGTCCACGACTCAGTGGCATCTTTTTTT
1 TTCAAAGTCCACAACTCAGTGGCATC-TTTTTC
* * *
4641394 TTCAAAGTCCACTACTCTGTGGCACCCTTTTTC
1 TTCAAAGTCCACAACTCAGTGGCA-TCTTTTTC
** *
4641427 ATTTTAAGTCCACAACTCCGTGGCA
1 -TTCAAAGTCCACAACTCAGTGGCA
4641452 CCCTTTAAAG
Statistics
Matches: 100, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
30 21 0.21
32 4 0.04
33 54 0.54
34 21 0.21
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (32 bp):
TTCAAAGTCCACAACTCAGTGGCATCTTTTTC
Found at i:4641561 original size:31 final size:31
Alignment explanation
Indices: 4641457--4641709 Score: 222
Period size: 33 Copynumber: 7.9 Consensus size: 31
4641447 TGGCACCCTT
* * *
4641457 TAAAGCCCACAGAAGTCGGTGACAACCTTTCTC
1 TAAAGCCCACACAAGTCAGTGGCAACC-TT-TC
* * *
4641490 TAAAACCCACACAAGTCAGTGACAACCCTTCTA
1 TAAAGCCCACACAAGTCAGTGGCAA-CCTT-TC
**
4641523 TAAAGCCCACACAAGTTGGTGGCAACCTTTC
1 TAAAGCCCACACAAGTCAGTGGCAACCTTTC
*
4641554 TAAAGCCCACACATGTCAGTGGCAACAC-TTC
1 TAAAGCCCACACAAGTCAGTGGCAAC-CTTTC
* * * *
4641585 TAAAGCCCACATAAGTCAATGGCACCCTTCTT
1 TAAAGCCCACACAAGTCAGTGGCAACCTT-TC
**
4641617 TAAAGCCCACACAAGTTGGTGGCAATCCTTTTC
1 TAAAGCCCACACAAGTCAGTGGCAA-CC-TTTC
* * *
4641650 CAAAGCCCACACAAGTC-GATAGCAACCCCCTTC
1 TAAAGCCCACACAAGTCAG-TGGCAA--CCTTTC
*
4641683 AAAAGCCCACACAAGTCAGTGGCAACC
1 TAAAGCCCACACAAGTCAGTGGCAACC
4641710 ATCTTAAAAA
Statistics
Matches: 181, Mismatches: 30, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
30 1 0.01
31 52 0.29
32 27 0.15
33 94 0.52
34 7 0.04
ACGTcount: A:0.33, C:0.32, G:0.15, T:0.19
Consensus pattern (31 bp):
TAAAGCCCACACAAGTCAGTGGCAACCTTTC
Found at i:4641959 original size:113 final size:113
Alignment explanation
Indices: 4641806--4642031 Score: 267
Period size: 113 Copynumber: 2.0 Consensus size: 113
4641796 CATTTCTTTC
* * * * ** * **
4641806 TAAGTCCAATGTTGTTGTCCTTTAATCAGCACATTGGCACCTTT-TTTTTTCTTAAGTTCAATAT
1 TAAGTCCAATGTTCTAGTCCTTAAATCAGCACATTAGCACCTTTGTCATCT-TTAAGCCCAATAT
*
4641870 CACCGGCCTTGAATCAACATATTGGCACCTTTATCATTCTTCTCATCTT
65 CACCGGCCTTAAATCAACATATTGGCACCTTTATCATTCTTCTCATCTT
*
4641919 TAAGTCCAATGTCTCTAGT-CTTAAATTAGCACATTAGCACCTTTGTCATCTTTAAGCCCAATAT
1 TAAGTCCAATGT-TCTAGTCCTTAAATCAGCACATTAGCACCTTTGTCATCTTTAAGCCCAATAT
* * * * * *
4641983 CTCTGTCCTTAAATCATCATATTGGCAGCTTTATCATTCTTCTTATCTT
65 CACCGGCCTTAAATCAACATATTGGCACCTTTATCATTCTTCTCATCTT
4642032 CAAGCCTGAT
Statistics
Matches: 94, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
113 87 0.93
114 7 0.07
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (113 bp):
TAAGTCCAATGTTCTAGTCCTTAAATCAGCACATTAGCACCTTTGTCATCTTTAAGCCCAATATC
ACCGGCCTTAAATCAACATATTGGCACCTTTATCATTCTTCTCATCTT
Found at i:4648121 original size:20 final size:20
Alignment explanation
Indices: 4648096--4648220 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
4648086 AATAAACTAG
4648096 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
4648116 ATGTATCGATACATTTGGGTAAAAAAACAGA
1 ATGTATCGATACA-TT--G------AA-A-A
4648147 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
* * *
4648167 ATGTATCGATACATTTATAC
1 ATGTATCGATACATTGAAAA
* *
4648187 ATATATCGATACATTAAAAA
1 ATGTATCGATACATTGAAAA
*
4648207 ATGTATTGATACAT
1 ATGTATCGATACAT
4648221 CTGGATAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
20 59 0.69
21 3 0.04
22 2 0.02
23 1 0.01
28 1 0.01
29 2 0.02
30 3 0.04
31 14 0.16
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:4650683 original size:32 final size:30
Alignment explanation
Indices: 4650647--4650705 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
4650637 GAAATCAAAT
4650647 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
4650679 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
4650706 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:4651005 original size:13 final size:13
Alignment explanation
Indices: 4650987--4651012 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4650977 ATATTTTTTG
4650987 TGTATCGATACAT
1 TGTATCGATACAT
4651000 TGTATCGATACAT
1 TGTATCGATACAT
4651013 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4651027 original size:32 final size:33
Alignment explanation
Indices: 4650966--4651030 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
4650956 TACAAGCCAA
* *
4650966 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TCTTGGTGTATCGATACAT
4651000 TGTATCGATACATA-CTTGGTGTATCGATACA
1 TGTATCGATACATATCTTGGTGTATCGATACA
4651031 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 15 0.52
34 14 0.48
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATATCTTGGTGTATCGATACAT
Found at i:4656524 original size:13 final size:13
Alignment explanation
Indices: 4656506--4656531 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4656496 ATATTTTTTG
4656506 TGTATCGATACAT
1 TGTATCGATACAT
4656519 TGTATCGATACAT
1 TGTATCGATACAT
4656532 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4656546 original size:32 final size:33
Alignment explanation
Indices: 4656485--4656549 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
4656475 TACAAGCCAA
* *
4656485 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TCTTGGTGTATCGATACAT
4656519 TGTATCGATACATA-CTTGGTGTATCGATACA
1 TGTATCGATACATATCTTGGTGTATCGATACA
4656550 AGTTTGCCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 15 0.52
34 14 0.48
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATATCTTGGTGTATCGATACAT
Found at i:4658722 original size:78 final size:78
Alignment explanation
Indices: 4658622--4658775 Score: 175
Period size: 78 Copynumber: 2.0 Consensus size: 78
4658612 AACTAATCCT
* * * *
4658622 TTAGGGCCATTTGGGTACTTTTAAGTTAAAACCA-AGCCTTTAGGTTTAGTTTAGCACTTTAATG
1 TTAGGGCCATTTGAGTAATTTTAAG-TAAAACCAGAGCCTTAAGATTTAGTTTAGCACTTTAATG
*
4658686 TCTAAATCAAACAC
65 TCTAAAGCAAACAC
* * * * * * * *
4658700 TTAGGGCCATTTTAGTAATTTTATGTCAATCTAGAGCCTTAAGATTTAGTTTGGCATTTTCATGT
1 TTAGGGCCATTTGAGTAATTTTAAGTAAAACCAGAGCCTTAAGATTTAGTTTAGCACTTTAATGT
4658765 CTAAAGCAAAC
66 CTAAAGCAAAC
4658776 TTTTAAGTTC
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
77 5 0.08
78 57 0.92
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Consensus pattern (78 bp):
TTAGGGCCATTTGAGTAATTTTAAGTAAAACCAGAGCCTTAAGATTTAGTTTAGCACTTTAATGT
CTAAAGCAAACAC
Found at i:4658797 original size:78 final size:78
Alignment explanation
Indices: 4658656--4658803 Score: 170
Period size: 78 Copynumber: 1.9 Consensus size: 78
4658646 GTTAAAACCA
* * * * * *
4658656 AGCCTTTAGGTTTAGTTTAGCACTTTAATGTCTAAATCAAACACTTAGGGCCATTTTAGTAATTT
1 AGCCTTAAGATTTAGTTTAGCACTTTAATGTCTAAAGCAAACACTTAAGGCCATGTTAATAATTT
*
4658721 TATGTCAATCTAG
66 CATGTCAATCTAG
* * * ** **
4658734 AGCCTTAAGATTTAGTTTGGCATTTTCATGTCTAAAGCAAACTTTTAAGTTCATGTTAATAATTT
1 AGCCTTAAGATTTAGTTTAGCACTTTAATGTCTAAAGCAAACACTTAAGGCCATGTTAATAATTT
4658799 CATGT
66 CATGT
4658804 TCATTCCGAG
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
78 56 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (78 bp):
AGCCTTAAGATTTAGTTTAGCACTTTAATGTCTAAAGCAAACACTTAAGGCCATGTTAATAATTT
CATGTCAATCTAG
Found at i:4661238 original size:24 final size:24
Alignment explanation
Indices: 4661206--4661252 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
4661196 AATGTAATCG
4661206 ATACATGAAAAGTGATGAACAGTT
1 ATACATGAAAAGTGATGAACAGTT
* *
4661230 ATACGTGAACAGTGATGAACAGT
1 ATACATGAAAAGTGATGAACAGT
4661253 AATGTATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (24 bp):
ATACATGAAAAGTGATGAACAGTT
Found at i:4661337 original size:19 final size:20
Alignment explanation
Indices: 4661313--4661363 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
4661303 ACAATTCATG
4661313 ATGTATCGATACCAAG-AAC
1 ATGTATCGATACCAAGCAAC
* *
4661332 ATGTATCGATACTAAGCAAT
1 ATGTATCGATACCAAGCAAC
4661352 ATGTATCGATAC
1 ATGTATCGATAC
4661364 ATCTGGGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (20 bp):
ATGTATCGATACCAAGCAAC
Found at i:4661357 original size:20 final size:19
Alignment explanation
Indices: 4661292--4661364 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 19
4661282 ATTGCCAGTT
*
4661292 TATGTATCGATACAATTC-A
1 TATGTATCGATACAA-GCAA
4661311 TGATGTATCGATACCAAG-AA
1 T-ATGTATCGATA-CAAGCAA
*
4661331 CATGTATCGATACTAAGCAA
1 TATGTATCGATAC-AAGCAA
4661351 TATGTATCGATACA
1 TATGTATCGATACA
4661365 TCTGGGTGTG
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 1 0.02
19 16 0.35
20 26 0.57
21 3 0.07
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.30
Consensus pattern (19 bp):
TATGTATCGATACAAGCAA
Found at i:4665456 original size:51 final size:52
Alignment explanation
Indices: 4665372--4665575 Score: 259
Period size: 51 Copynumber: 3.9 Consensus size: 52
4665362 TGAAGTATCC
*
4665372 TTTAAAAATAATTAAAAATT-AAAAATACTTTATATTAAATCTCAAATTATTA
1 TTTAAAAATAA-TAAAAATTAAAAAATATTTTATATTAAATCTCAAATTATTA
** *
4665424 TTTAAAAATAAT-AAAATTAAAAAATATTTTATATTAAATCTTGAGTTATTA
1 TTTAAAAATAATAAAAATTAAAAAATATTTTATATTAAATCTCAAATTATTA
* * ** * *
4665475 ATTAAAAATATTAAAAATTAAAAAAATATTTTCCATTAAATCTAAAATAATTA
1 TTTAAAAATAATAAAAATT-AAAAAATATTTTATATTAAATCTCAAATTATTA
*
4665528 TTTAAAAAATAATAAAAACTTAAAAAATATTTTTTATTAAATCTCAAA
1 TTT-AAAAATAATAAAAA-TTAAAAAATATTTTATATTAAATCTCAAA
4665576 ATATAGTAAA
Statistics
Matches: 130, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
50 6 0.05
51 39 0.30
52 17 0.13
53 29 0.22
54 37 0.28
55 2 0.02
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (52 bp):
TTTAAAAATAATAAAAATTAAAAAATATTTTATATTAAATCTCAAATTATTA
Found at i:4665533 original size:104 final size:106
Alignment explanation
Indices: 4665373--4665571 Score: 298
Period size: 104 Copynumber: 1.9 Consensus size: 106
4665363 GAAGTATCCT
* * *
4665373 TTAAAAATAATTAAAAATTAAAAATACTTTATATTAAATCTCAAATTATTATTT-AAAAATAAT-
1 TTAAAAATAATTAAAAATTAAAAATACTTTACATTAAATCTAAAATAATTATTTAAAAAATAATA
4665436 AAAA-TTAAAAAATATTTTATATTAAATCTTGAGTTATTAA
66 AAAACTTAAAAAATATTTTATATTAAATCTTGAGTTATTAA
* *
4665476 TTAAAAAT-ATTAAAAATTAAAAAAATATTTTCCATTAAATCTAAAATAATTATTTAAAAAATAA
1 TTAAAAATAATTAAAAATT--AAAAATACTTTACATTAAATCTAAAATAATTATTTAAAAAATAA
*
4665540 TAAAAACTTAAAAAATATTTTTTATTAAATCT
64 TAAAAACTTAAAAAATATTTTATATTAAATCT
4665572 CAAAATATAG
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
102 10 0.12
103 8 0.09
104 30 0.35
105 9 0.11
106 4 0.05
107 24 0.28
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.40
Consensus pattern (106 bp):
TTAAAAATAATTAAAAATTAAAAATACTTTACATTAAATCTAAAATAATTATTTAAAAAATAATA
AAAACTTAAAAAATATTTTATATTAAATCTTGAGTTATTAA
Found at i:4665605 original size:2 final size:2
Alignment explanation
Indices: 4665598--4665622 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4665588 AAAGATTAAT
4665598 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
4665623 TGGAACATAC
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:4666489 original size:24 final size:21
Alignment explanation
Indices: 4666462--4666516 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
4666452 ATTTATTTTT
4666462 AAATAAATAATTATTAATATAATA
1 AAATAAATAA-TATTAA-A-AATA
* *
4666486 AAATTATTAATATTAAAAATA
1 AAATAAATAATATTAAAAATA
*
4666507 ATATAAATAA
1 AAATAAATAA
4666517 AATATAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 11 0.42
22 1 0.04
23 6 0.23
24 8 0.31
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATAAATAATATTAAAAATA
Found at i:4667075 original size:54 final size:54
Alignment explanation
Indices: 4666992--4667100 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
4666982 TGATTAAAGA
*
4666992 AGTGTTTTTATTTTTTATTTTTTTGGGTTTAACTCTATATATATATATATATAT
1 AGTGTTTTTATTTTTTATTTTTTTCGGTTTAACTCTATATATATATATATATAT
4667046 AGTGTTTTTATTTTTTATTTTTTTCGGTTTAACTCTATATATATATATATATAT
1 AGTGTTTTTATTTTTTATTTTTTTCGGTTTAACTCTATATATATATATATATAT
4667100 A
1 A
4667101 TATATAGCCT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.27, C:0.05, G:0.08, T:0.61
Consensus pattern (54 bp):
AGTGTTTTTATTTTTTATTTTTTTCGGTTTAACTCTATATATATATATATATAT
Found at i:4667086 original size:2 final size:2
Alignment explanation
Indices: 4667081--4667106 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4667071 GGTTTAACTC
4667081 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
4667107 GCCTTGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4668136 original size:14 final size:13
Alignment explanation
Indices: 4668111--4668135 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4668101 ATGAAATATC
4668111 AAACTTAAAAAAT
1 AAACTTAAAAAAT
4668124 AAACTTAAAAAA
1 AAACTTAAAAAA
4668136 AAATAAAATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (13 bp):
AAACTTAAAAAAT
Found at i:4668938 original size:24 final size:22
Alignment explanation
Indices: 4668877--4668938 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 22
4668867 TTTTAAAAGA
4668877 TTTTAAAAATTT-ATTAAATAT
1 TTTTAAAAATTTAATTAAATAT
* *
4668898 TTTTTAAAATTTAAATTAAGTTAAT
1 TTTTAAAAATTT-AATTAA-AT-AT
4668923 TTTTAAAAATTTAATT
1 TTTTAAAAATTTAATT
4668939 TATTTTATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 11 0.32
23 5 0.15
24 5 0.15
25 13 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTAAAAATTTAATTAAATAT
Found at i:4671272 original size:20 final size:21
Alignment explanation
Indices: 4671238--4671302 Score: 80
Period size: 20 Copynumber: 3.0 Consensus size: 21
4671228 AATTCAAAAA
4671238 TTTGACAATTTGTATCGATACAT
1 TTTG-CAA-TTGTATCGATACAT
4671261 TATT-C-ATTGTATCGATACAT
1 T-TTGCAATTGTATCGATACAT
*
4671281 TTTGCAAATGTATCGATACAT
1 TTTGCAATTGTATCGATACAT
4671302 T
1 T
4671303 CAGGCATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
19 2 0.05
20 16 0.42
21 16 0.42
22 1 0.03
23 1 0.03
24 2 0.05
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (21 bp):
TTTGCAATTGTATCGATACAT
Found at i:4673846 original size:28 final size:28
Alignment explanation
Indices: 4673784--4673856 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
4673774 TTAAACAATT
* **
4673784 GGAGATACTCCAACCCCGTTATTTCATC
1 GGAGATACTCCAACCCCATTATTTCAGA
*
4673812 GGAGATACTCCAACCCCATTATTTCCGA
1 GGAGATACTCCAACCCCATTATTTCAGA
* *
4673840 GGGGATACTCTAACCCC
1 GGAGATACTCCAACCCC
4673857 GCCTTTATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.25
Consensus pattern (28 bp):
GGAGATACTCCAACCCCATTATTTCAGA
Found at i:4674117 original size:51 final size:51
Alignment explanation
Indices: 4673949--4674118 Score: 225
Period size: 51 Copynumber: 3.3 Consensus size: 51
4673939 TATTTTCGAG
* * * * *
4673949 GGGATACTCCAACCCCGATTTTATTTTTAAAATACCAAATTTTCACAATCG
1 GGGATACTCCAACCCTGATTTTATTTTCAAAACACCAATTTTTCACAATCA
* *
4674000 GGGATACTCCAACTCC-GATTTTATTTCCAAAACACCAATTTCTCACAATCA
1 GGGATACTCCAAC-CCTGATTTTATTTTCAAAACACCAATTTTTCACAATCA
* * * *
4674051 TGGATACTCCAACCCTAATTTTATTTTCAAAACACCAATTTTTTATAATCA
1 GGGATACTCCAACCCTGATTTTATTTTCAAAACACCAATTTTTCACAATCA
4674102 GGGATACTCCAACCCTG
1 GGGATACTCCAACCCTG
4674119 TTATTTTCGA
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
50 2 0.02
51 99 0.96
52 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.32
Consensus pattern (51 bp):
GGGATACTCCAACCCTGATTTTATTTTCAAAACACCAATTTTTCACAATCA
Found at i:4674122 original size:26 final size:28
Alignment explanation
Indices: 4674093--4674146 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
4674083 CACCAATTTT
4674093 TTATAATC-A-GGGATACTCCAACCCTG
1 TTATAATCGAGGGGATACTCCAACCCTG
**
4674119 TTATTTTCGAGGGGATACTCCAACCCTG
1 TTATAATCGAGGGGATACTCCAACCCTG
4674147 ATTTTATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.25
27 1 0.04
28 17 0.71
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (28 bp):
TTATAATCGAGGGGATACTCCAACCCTG
Found at i:4681458 original size:21 final size:21
Alignment explanation
Indices: 4681415--4681455 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
4681405 TAATATTTAG
*
4681415 TTAATATTTTAATATATATAA
1 TTAATATTTTAATATATAAAA
*
4681436 TTAAT-TTTTAATTTATAAAA
1 TTAATATTTTAATATATAAAA
4681456 ATTTATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTAATATTTTAATATATAAAA
Found at i:4684819 original size:79 final size:80
Alignment explanation
Indices: 4684629--4685098 Score: 455
Period size: 79 Copynumber: 6.0 Consensus size: 80
4684619 TTCTACCATT
* * * * *
4684629 GGGGATACTTCAACCCCGGTTTTATTTTC-AAAACACCGATTTTTCATAA-CGGGGGTACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAA
4684692 TCCCT-TTATTTC-GA
66 -CCCTGTTATTTCTGA
* ** * *
4684706 GGGGATACTCTAACCTTGGTTTTATTTTC-AAAACACCAATTTTTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAA
*
4684770 CCTTGTTATTTCTGA
66 CCCTGTTATTTCTGA
* * *
4684785 GGGGATACTCCAACCCCGATTTTATTTTC-AAAACAACAA-TTTTCTACCATCGGGGATACTCTA
1 GGGGATACTCCAACCCCGATTTTATTTTCTAAAACACCAATTTTTC-ACAATCGGGGATACTCCA
*
4684848 A-CTTCGTTATTT-TCGA
65 ACCCT-GTTATTTCT-GA
* * * *
4684864 GGAGATACTTCAACCTC-AGTTTTA-TTTCTAAAACACCAAATTTTCACAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGA-TTTTATTTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCA
* *
4684927 ACCCCGTTATTTTTGA
65 ACCCTGTTATTTCTGA
* * * * * * *
4684943 AGGGATACTCAAACTCCAGTTTTTA-TTTCAAAAACACCGATTTTTCACAATCGGGGATATTCCA
1 GGGGATACTCCAAC-CCCGATTTTATTTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCA
**
4685007 ACCCCATTATTTCTGA
65 ACCCTGTTATTTCTGA
* ** * *
4685023 GGGAATACTCCAACCCTTATTTT-TATTTCTAAAACACCGATTTTTCACAATCGGGGATAGTCCA
1 GGGGATACTCCAACCCCGATTTTAT-TTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCA
4685087 ACACC-GTTATTT
65 AC-CCTGTTATTT
4685099 TCGAGGGAGT
Statistics
Matches: 332, Mismatches: 45, Indels: 29
0.82 0.11 0.07
Matches are distributed among these distances:
77 47 0.14
78 34 0.10
79 131 0.39
80 118 0.36
81 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (80 bp):
GGGGATACTCCAACCCCGATTTTATTTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAA
CCCTGTTATTTCTGA
Found at i:4684915 original size:158 final size:156
Alignment explanation
Indices: 4684629--4685098 Score: 506
Period size: 158 Copynumber: 3.0 Consensus size: 156
4684619 TTCTACCATT
* * *
4684629 GGGGATACTTCAACCCCGGTTTTATTTTCAAAACACCGATTTTT--CATAACGGGGGTACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTTACCAT--CGGGGATACTCCAA
* * *
4684692 -TCCCTT-TATTTCGAGGGGATAC-TCTAACCTTGGTTTTATTT-TCAAAACACCAATTTTTCAT
64 CTCCATTAT-TTTCGA-GGGATACTTC-AACCTTAGTTTTATTTCT-AAAACACCAATTTTTCAC
**
4684753 AATCGGGGATACTCCAACCTTGTTATTTCTGA
125 AATCGGGGATACTCCAACCCCGTTATTTCTGA
* * *
4684785 GGGGATACTCCAACCCCGATTTTATTTTCAAAACAACAATTTTCTACCATCGGGGATACTCTAAC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTT-TACCATCGGGGATACTCCAAC
* * * *
4684850 TTCGTTATTTTCGAGGAGATACTTCAACCTCAGTTTTATTTCTAAAACACCAAATTTTCACAATC
65 TCCATTATTTTCGAGG-GATACTTCAACCTTAGTTTTATTTCTAAAACACCAATTTTTCACAATC
*
4684915 GGGGATACTCCAACCCCGTTATTTTTGA
129 GGGGATACTCCAACCCCGTTATTTCTGA
* * * * * *
4684943 AGGGATACTCAAACTCCAGTTTTTA-TTTCAAAAACACCGATTTTTCACAATCGGGGATATTCCA
1 GGGGATACTCCAAC-CCCGATTTTATTTTC-AAAACACCGATTTTT-ACCATCGGGGATACTCCA
* * * *
4685007 ACCCCATTA-TTTCTGAGGGAATACTCCAACCCTTATTTTTATTTCTAAAACACCGATTTTTCAC
63 ACTCCATTATTTTC-GAGGG-ATACTTCAA-CCTTAGTTTTATTTCTAAAACACCAATTTTTCAC
* *
4685071 AATCGGGGATAGTCCAACACCGTTATTT
125 AATCGGGGATACTCCAACCCCGTTATTT
4685099 TCGAGGGAGT
Statistics
Matches: 266, Mismatches: 34, Indels: 24
0.82 0.10 0.07
Matches are distributed among these distances:
156 39 0.15
157 15 0.06
158 96 0.36
159 60 0.23
160 56 0.21
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (156 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTTACCATCGGGGATACTCCAACT
CCATTATTTTCGAGGGATACTTCAACCTTAGTTTTATTTCTAAAACACCAATTTTTCACAATCGG
GGATACTCCAACCCCGTTATTTCTGA
Found at i:4685007 original size:80 final size:78
Alignment explanation
Indices: 4684630--4685118 Score: 444
Period size: 80 Copynumber: 6.2 Consensus size: 78
4684620 TCTACCATTG
* * * * *
4684630 GGGATACTTC-AACCCCGGTTTTATTTTCAAAACACCGATTTTTCATAA-CGGGGGTACTCCAAT
1 GGGATAC-TCAAACCCAGTTTTTATTTTCAAAACACCGATTTTTCACAATCGGGGATACTCCAAC
*
4684693 CCCTTTA-TTTCGA
65 CCCGTTATTTTCGA
* ** * * *
4684706 GGGGATACTCTAACCTTGGTTTTATTTTCAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
1 -GGGATACTCAAACCCAGTTTTTATTTTCAAAACACCGATTTTTCACAATCGGGGATACTCCAAC
**
4684771 CTTGTTA-TTTCTGA
65 CCCGTTATTTTC-GA
* * * * * * *
4684785 GGGGATACTCCAACCCCGATTTTATTTTCAAAACAAC-AATTTTCTACCATCGGGGATACTCTAA
1 -GGGATACTCAAACCCAGTTTTTATTTTCAAAACACCGATTTTTC-ACAATCGGGGATACTCCAA
**
4684849 CTTCGTTATTTTCGA
64 CCCCGTTATTTTCGA
* *
4684864 GGAGATACTTC-AACCTCAG-TTTTA-TTTCTAAAACACCAAATTTTCACAATCGGGGATACTCC
1 GG-GATAC-TCAAACC-CAGTTTTTATTTTC-AAAACACCGATTTTTCACAATCGGGGATACTCC
*
4684926 AACCCCGTTATTTTTGAA
62 AACCCCGTTATTTTCG-A
*
4684944 GGGATACTCAAACTCCAGTTTTTA-TTTCAAAAACACCGATTTTTCACAATCGGGGATATTCCAA
1 GGGATACTCAAAC-CCAGTTTTTATTTTC-AAAACACCGATTTTTCACAATCGGGGATACTCCAA
*
4685008 CCCCATTA-TTTCTGA
64 CCCCGTTATTTTC-GA
* *
4685023 GGGAATACTCCAACCCTTA-TTTTTA-TTTCTAAAACACCGATTTTTCACAATCGGGGATAGTCC
1 GGG-ATACTCAAACCC--AGTTTTTATTTTC-AAAACACCGATTTTTCACAATCGGGGATACTCC
*
4685086 AACACCGTTATTTTCGA
62 AACCCCGTTATTTTCGA
*
4685103 GGGAGTACTCTAACCC
1 GGGA-TACTCAAACCC
4685119 TAGTATATTC
Statistics
Matches: 354, Mismatches: 38, Indels: 37
0.83 0.09 0.09
Matches are distributed among these distances:
76 2 0.01
77 42 0.12
78 35 0.10
79 128 0.36
80 142 0.40
81 5 0.01
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (78 bp):
GGGATACTCAAACCCAGTTTTTATTTTCAAAACACCGATTTTTCACAATCGGGGATACTCCAACC
CCGTTATTTTCGA
Found at i:4685454 original size:13 final size:13
Alignment explanation
Indices: 4685436--4685462 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4685426 ACATTATGTT
4685436 TTGTATCGATACA
1 TTGTATCGATACA
4685449 TTGTATCGATACA
1 TTGTATCGATACA
4685462 T
1 T
4685463 GTTAATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:4685472 original size:19 final size:19
Alignment explanation
Indices: 4685448--4685503 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
4685438 GTATCGATAC
**
4685448 ATTGTATCGATACATGTTA
1 ATTGTATCGATACATGACA
*
4685467 ATTGTATCAATACATGGACA
1 ATTGTATCGATACAT-GACA
4685487 ATTGTATCGATACATGA
1 ATTGTATCGATACATGA
4685504 GATTGGTAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (19 bp):
ATTGTATCGATACATGACA
Found at i:4685491 original size:20 final size:20
Alignment explanation
Indices: 4685448--4685502 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
4685438 GTATCGATAC
**
4685448 ATTGTATCGATACAT-GTTA
1 ATTGTATCGATACATGGACA
*
4685467 ATTGTATCAATACATGGACA
1 ATTGTATCGATACATGGACA
4685487 ATTGTATCGATACATG
1 ATTGTATCGATACATG
4685503 AGATTGGTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:4685557 original size:20 final size:20
Alignment explanation
Indices: 4685532--4685597 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
4685522 TTTCACTGTT
4685532 TGTATCGATACATGGTACAA
1 TGTATCGATACATGGTACAA
4685552 TGTATCGATACA---T----
1 TGTATCGATACATGGTACAA
4685565 TGTATCGATACATGGTACAA
1 TGTATCGATACATGGTACAA
4685585 TGTATCGATACAT
1 TGTATCGATACAT
4685598 TGTATCGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 12 0.31
16 1 0.03
17 1 0.03
20 25 0.64
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATGGTACAA
Found at i:4685568 original size:13 final size:13
Alignment explanation
Indices: 4685547--4685610 Score: 68
Period size: 13 Copynumber: 5.4 Consensus size: 13
4685537 CGATACATGG
*
4685547 TACAATGTATCGA
1 TACATTGTATCGA
4685560 TACATTGTATCGA
1 TACATTGTATCGA
4685573 TACA-TG----G-
1 TACATTGTATCGA
*
4685580 TACAATGTATCGA
1 TACATTGTATCGA
4685593 TACATTGTATCGA
1 TACATTGTATCGA
4685606 TACAT
1 TACAT
4685611 GATGAATTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
7 4 0.09
8 3 0.07
12 3 0.07
13 33 0.77
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:4685630 original size:33 final size:33
Alignment explanation
Indices: 4685531--4685611 Score: 162
Period size: 33 Copynumber: 2.5 Consensus size: 33
4685521 CTTTCACTGT
4685531 TTGTATCGATACATGGTACAATGTATCGATACA
1 TTGTATCGATACATGGTACAATGTATCGATACA
4685564 TTGTATCGATACATGGTACAATGTATCGATACA
1 TTGTATCGATACATGGTACAATGTATCGATACA
4685597 TTGTATCGATACATG
1 TTGTATCGATACATG
4685612 ATGAATTGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACATGGTACAATGTATCGATACA
Found at i:4691965 original size:20 final size:22
Alignment explanation
Indices: 4691921--4691967 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
4691911 AATTTTCCAC
4691921 AAAT-TTTCACTTTTTCACTTCA
1 AAATCTTTCACTTTTTCAC-TCA
4691943 AAATCTTTCA-TTTTTCA-TCA
1 AAATCTTTCACTTTTTCACTCA
4691963 AAATC
1 AAATC
4691968 ATCAACAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.33
22 11 0.46
23 5 0.21
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATCTTTCACTTTTTCACTCA
Found at i:4694329 original size:20 final size:20
Alignment explanation
Indices: 4694286--4694340 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
4694276 GTATCGATAC
* **
4694286 ATTGTATCAATACAT-GTTA
1 ATTGTATCGATACATGGACA
4694305 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
4694325 ATTGTATCGATACATG
1 ATTGTATCGATACATG
4694341 AGATTGGCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:4701344 original size:62 final size:62
Alignment explanation
Indices: 4701273--4702337 Score: 928
Period size: 62 Copynumber: 17.3 Consensus size: 62
4701263 TTTTCAACCT
* ** *
4701273 TTTAGTCCTCAAAGAGCATGACACCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCATCC
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * * *
4701335 TTTTGTCCTCAAAGAGCATGACGCCTTTTT-TTTTCGAAGCCTACACGAGTTGGTGGCACCC
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * *
4701396 TTTAGTCCTCAAAGATCATGATGCCGTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* ** *
4701458 TTTAGTCCTCAAATATTAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCC
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * *** ** * *
4701520 TTTAGTCCTCAAAGAGTAGGACGCCTTCTCCTT-TTTTCCTTTGTCCTCA-AAAAGCATGAT-GC
1 TTTAGTCCTCAAAGAGCAGGATGCCTT-T--TTCTTTT-CAAAG-CC-CACACGAG-TTGGTGGC
4701582 A--C
59 ACCC
***** * * ** ** * ** * *
4701584 TTTA-T--T-------TTTTTTTCC-TTTGC-CCTCAAAGAGCAAGACAC-ATTTCAT-TCTCCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTC-AA-AGC-CCACACGAGTTGGTGGC-AC-
4701635 TTTTCC
61 ----CC
* * * *
4701641 TTTA-TCCTCAAAGAGTAAGATGTCTTTTTCTTTT-AAAGCCCACACGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* *** * * *
4701701 TTTAGTCCTCAAAGAGTAGGGCACCTTTTCCTTTT-AAAGCCCATACGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * *
4701762 TTTAGTCTTCAAAGAGC--GA-GACACTTTTCCTTTTGAAAGCCCACACGAGTTGGTGGCACCC
1 TTTAGTCCTCAAAGAGCAGGATG-C-CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * *
4701823 TTTAGTCCTCAAAGAGCAGGACGCTTTTTTCTTTTTAAAGCCCACACTAGTTGGTGGCA-CC
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * * * * *
4701884 TTTAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAACCTATACAAGTTGATGGCATCC
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * * *
4701946 TTTTGTCCTCAAAGAGTAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGTACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * *
4702008 TTTAGTCCTCAAAGAGTAGGATACCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGTACCC
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * * * * *
4702070 TTTTGCCCTCAAAGAGCAAGACGCCTTTTTCTTTTTAAAGCCCACACTAGTTGGTGGCAACC
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * *
4702132 TTTAGTCCTCTAAA-AGCAGGATGCCTTTTTCTTTTCAAAGCCTATATGAGTTGGTGGCACTC
1 TTTAGTCCTC-AAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* *
4702194 TTTAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAAG-CCACACGAGTTAGTGGCACCC
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTC-AAAGCCCACACGAGTTGGTGGCACCC
** *
4702256 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCTTACATGAGTTGGTGGCACCC
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
*
4702318 TTTAGTCCTTAAAGAGCAGG
1 TTTAGTCCTCAAAGAGCAGG
4702338 CGAGTTGGTG
Statistics
Matches: 817, Mismatches: 140, Indels: 92
0.78 0.13 0.09
Matches are distributed among these distances:
49 5 0.01
50 5 0.01
51 2 0.00
52 1 0.00
53 1 0.00
54 3 0.00
57 6 0.01
59 3 0.00
60 16 0.02
61 218 0.27
62 496 0.61
63 12 0.01
64 14 0.02
65 11 0.01
66 14 0.02
67 9 0.01
68 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (62 bp):
TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
Found at i:4701642 original size:42 final size:41
Alignment explanation
Indices: 4701545--4701660 Score: 121
Period size: 40 Copynumber: 2.8 Consensus size: 41
4701535 GTAGGACGCC
* *
4701545 TTCTCCTTTTTTCCTTTGTCCTCAAAAAGCATGATGCACTTTA
1 TTCTCC-TTTTTCCTTTGTCCTCAAAGAGCAAGA-GCACTTTA
* *
4701588 TT-T-TTTTTTCCTTTGCCCTCAAAGAGCAAGA-CACATTTCA
1 TTCTCCTTTTTCCTTTGTCCTCAAAGAGCAAGAGCAC-TTT-A
* *
4701628 TTCTCCTTTTTCCTTTATCCTCAAAGAGTAAGA
1 TTCTCCTTTTTCCTTTGTCCTCAAAGAGCAAGA
4701661 TGTCTTTTTC
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
38 3 0.05
39 3 0.05
40 27 0.44
41 1 0.02
42 25 0.41
43 2 0.03
ACGTcount: A:0.23, C:0.25, G:0.09, T:0.42
Consensus pattern (41 bp):
TTCTCCTTTTTCCTTTGTCCTCAAAGAGCAAGAGCACTTTA
Found at i:4702100 original size:124 final size:123
Alignment explanation
Indices: 4701273--4701546 Score: 361
Period size: 123 Copynumber: 2.2 Consensus size: 123
4701263 TTTTCAACCT
* ** *
4701273 TTTAGTCCTCAAAGAGCATGACACCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCATCCTTT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTT
* * * *
4701338 TGTCCTCAAAGAGCATGACGCCTTTTT-TTTTCGAAGCCTACACGAGTTGGTGGCACCC
66 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-CC
* * *
4701396 TTTAGTCCTCAAAGATCATGATGCCGTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTT
* ** * *
4701461 AGTCCTCAAATATTAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCC
66 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-CC
* *
4701520 TTTAGTCCTCAAAGAGTAGGACGCCTT
1 TTTAGTCCTCAAAGAGCAGGATGCCTT
4701547 CTCCTTTTTT
Statistics
Matches: 131, Mismatches: 19, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
123 81 0.62
124 50 0.38
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (123 bp):
TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTT
AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
Found at i:4702343 original size:36 final size:36
Alignment explanation
Indices: 4702303--4702373 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
4702293 AAGCTTACAT
*
4702303 GAGTTGGTGGCACCCTTTAGTCCTTAAAGAGCAGGC
1 GAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGC
* *
4702339 GAGTTGGTGGCATCTTTTAGTCCTCAAAGAGCAGG
1 GAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGG
4702374 ACACACTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.27
Consensus pattern (36 bp):
GAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGC
Found at i:4702454 original size:43 final size:42
Alignment explanation
Indices: 4702358--4702711 Score: 392
Period size: 43 Copynumber: 8.4 Consensus size: 42
4702348 GCATCTTTTA
* * *
4702358 GTCCTCAAAGAGCAGGACACACTTCATTTTCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTCCTTTTTTCCTTT
* *
4702400 GTCCTCGAAGAGCAGGACGCACTTTATTTCCTTCTTTTCTTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTCCTT-TTTTCCTTT
* * *
4702443 GTCCTCAAAGAGCAAGACACA-TTTCATTTCCTCCTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTT-ATTTCCT-TTTTTCCTTT
* * * * * *
4702486 ATACTCAAAGAGTAGGACACATTTTATTTCTTTTTTTCCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTCCTTTTTT-CCTTT
*
4702529 GTCCTCAAAGAGCAGGATGCACTTTATTT-CTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTCCTTTTTTCCTTT
* * *
4702570 GTCCTCAAAGAGCATGATGCA-TTTCATTTCATTCTTTTCCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTT-ATTTCCTT-TTTT-CCTTT
* * *
4702614 GTCCTCAAAGAGTAGGACGCACTTTATTTCCTTTTCTCTTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTCCTTTTTTCCTTT
* * *
4702656 ATCCTCAAAGAACAGGACGCACTTCATTTCCTTTTTT-CTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTCCTTTTTTCCTTT
*
4702697 GTCCTCGAAGAGCAG
1 GTCCTCAAAGAGCAG
4702712 AACATACTCT
Statistics
Matches: 262, Mismatches: 40, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
40 3 0.01
41 44 0.17
42 80 0.31
43 99 0.38
44 33 0.13
45 3 0.01
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.41
Consensus pattern (42 bp):
GTCCTCAAAGAGCAGGACGCACTTTATTTCCTTTTTTCCTTT
Found at i:4702594 original size:127 final size:128
Alignment explanation
Indices: 4702361--4702710 Score: 456
Period size: 127 Copynumber: 2.7 Consensus size: 128
4702351 TCTTTTAGTC
* * *
4702361 CTCAAAGAGCAGGACACACTTCATTT-TCTTTTTTCCTTTGTCCTCGAAGAGCAGGACGCACTTT
1 CTCAAAGAGTAGGACACACTTTATTTCT-TTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTT
* *
4702425 ATTTCCTTCTTTTCTTTTGTCCTCAAAGAGCAAGACACATTTCATTTCCTCCTTTT-CCTTTATA
65 ATTTCCTT-TTTTCCTTTGTCCTCAAAGAGCAAGACACATTTCATTTCATCCTTTTCCCTTTATA
* *
4702489 CTCAAAGAGTAGGACACATTTTATTTCTTTTTTTCCCTTTGTCCTCAAAGAGCAGGATGCACTTT
1 CTCAAAGAGTAGGACACACTTTATTTCTTTTTTT-CCTTTGTCCTCAAAGAGCAGGACGCACTTT
* ** * * *
4702554 ATTT-CTTTTTTCCTTTGTCCTCAAAGAGCATGATGCATTTCATTTCATTCTTTTCCCTTTGTC
65 ATTTCCTTTTTTCCTTTGTCCTCAAAGAGCAAGACACATTTCATTTCATCCTTTTCCCTTTATA
* * * * * * *
4702617 CTCAAAGAGTAGGACGCACTTTATTTCCTTTTCTCTTTTATCCTCAAAGAACAGGACGCACTTCA
1 CTCAAAGAGTAGGACACACTTTATTTCTTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTTA
*
4702682 TTTCCTTTTTT-CTTTGTCCTCGAAGAGCA
66 TTTCCTTTTTTCCTTTGTCCTCAAAGAGCA
4702711 GAACATACTC
Statistics
Matches: 195, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
127 87 0.45
128 75 0.38
129 33 0.17
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.41
Consensus pattern (128 bp):
CTCAAAGAGTAGGACACACTTTATTTCTTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTTA
TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAAGACACATTTCATTTCATCCTTTTCCCTTTATA
Found at i:4702814 original size:40 final size:38
Alignment explanation
Indices: 4702728--4702823 Score: 111
Period size: 40 Copynumber: 2.5 Consensus size: 38
4702718 CTCTTTTCCT
* * * *
4702728 CTTTATCCTTAAGGAGCAGGACACTTTCCTTTTTTTTT
1 CTTTGTCCTTAAGGAGTAGGACACTTTCATTTTTTTTC
* *
4702766 CTTTGTCCTCAAGGAGTAGGACCCATTTCATTCTTTTTTC
1 CTTTGTCCTTAAGGAGTAGGACAC-TTTCATT-TTTTTTC
*
4702806 CTTTGTCCTTAATGAGTA
1 CTTTGTCCTTAAGGAGTA
4702824 AGACGTACTC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 20 0.42
39 6 0.12
40 22 0.46
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.45
Consensus pattern (38 bp):
CTTTGTCCTTAAGGAGTAGGACACTTTCATTTTTTTTC
Found at i:4703472 original size:20 final size:20
Alignment explanation
Indices: 4703447--4703503 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
4703437 TTTTCATAAT
4703447 TTGTATCGATACATTCTTCA
1 TTGTATCGATACATTCTTCA
* ** *
4703467 TTGTATTGATATTTTTTTCA
1 TTGTATCGATACATTCTTCA
4703487 TTGTATCGATACATTCT
1 TTGTATCGATACATTCT
4703504 GGGTTTAACG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.53
Consensus pattern (20 bp):
TTGTATCGATACATTCTTCA
Found at i:4704479 original size:2 final size:2
Alignment explanation
Indices: 4704472--4704507 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
4704462 CATTCCTCCT
*
4704472 AC AC AC AC AC AC AC AC AC AC GC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
4704508 CTCTATCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.50, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4707074 original size:13 final size:13
Alignment explanation
Indices: 4707043--4707085 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
4707033 TTCAACAAAA
4707043 AAAGAAAAAA-AG
1 AAAGAAAAAAGAG
4707055 AAA-AAAAAAGAG
1 AAAGAAAAAAGAG
*
4707067 AAAGAAAATAGAG
1 AAAGAAAAAAGAG
4707080 -AAGAAA
1 AAAGAAA
4707086 TAGAAACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 6 0.21
12 14 0.50
13 8 0.29
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (13 bp):
AAAGAAAAAAGAG
Found at i:4711753 original size:13 final size:13
Alignment explanation
Indices: 4711735--4711759 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4711725 CAATTTTTTG
4711735 TGTATCGATACAT
1 TGTATCGATACAT
4711748 TGTATCGATACA
1 TGTATCGATACA
4711760 AACTTGGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4711775 original size:32 final size:33
Alignment explanation
Indices: 4711715--4711778 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
4711705 TACAAGCCAA
** *
4711715 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
4711748 TGTATCGATACAA-ACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
4711779 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:4712451 original size:40 final size:41
Alignment explanation
Indices: 4712405--4712495 Score: 107
Period size: 39 Copynumber: 2.3 Consensus size: 41
4712395 TTTTCTTTCT
**
4712405 CCCTTAATTAAAG-TAATTTTAACAAATTCGTACATTCTCC
1 CCCTTAATTAAAGATAATTTTAACAAATTCACACATTCTCC
* *
4712445 CCCTTAA-T-AAGATAATTTTAGCAAATTCACGCATTCTCC
1 CCCTTAATTAAAGATAATTTTAACAAATTCACACATTCTCC
* *
4712484 CCTTTTATTAAA
1 CCCTTAATTAAA
4712496 AAATCTCCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
38 3 0.07
39 29 0.69
40 8 0.19
41 2 0.05
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.37
Consensus pattern (41 bp):
CCCTTAATTAAAGATAATTTTAACAAATTCACACATTCTCC
Found at i:4713873 original size:21 final size:20
Alignment explanation
Indices: 4713844--4713886 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
4713834 GGCTAGTGTG
*
4713844 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
4713865 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
4713885 GG
1 GG
4713887 TGGTGCTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.30, G:0.44, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:4714345 original size:13 final size:13
Alignment explanation
Indices: 4714329--4714365 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
4714319 AATCCCCCTA
*
4714329 TATCGATACAGTG
1 TATCGATACAATG
4714342 TATCGATACAATG
1 TATCGATACAATG
4714355 TATCGATACAA
1 TATCGATACAA
4714366 AGAAAAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:4716460 original size:15 final size:15
Alignment explanation
Indices: 4716440--4716470 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4716430 ATTTCGTTTG
*
4716440 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
4716455 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
4716470 G
1 G
4716471 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:4717013 original size:25 final size:25
Alignment explanation
Indices: 4716985--4717052 Score: 109
Period size: 27 Copynumber: 2.6 Consensus size: 25
4716975 AAATTATGGC
4716985 AACCGAATTGATTACCCAATTCACT
1 AACCGAATTGATTACCCAATTCACT
*
4717010 AACCGAATTGGTTCTACCCAATTCACT
1 AACCGAATT-GAT-TACCCAATTCACT
4717037 AACCGAATTGATTACC
1 AACCGAATTGATTACC
4717053 TTTAAGGCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
25 13 0.33
26 4 0.10
27 22 0.56
ACGTcount: A:0.34, C:0.28, G:0.10, T:0.28
Consensus pattern (25 bp):
AACCGAATTGATTACCCAATTCACT
Found at i:4717592 original size:20 final size:20
Alignment explanation
Indices: 4717567--4717631 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
4717557 TACAAGCCAA
4717567 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATTTTTTG
4717587 TGTATCGATAC-A-----T-
1 TGTATCGATACAATTTTTTG
4717600 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATTTTTTG
4717620 TGTATCGATACA
1 TGTATCGATACA
4717632 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 2 0.05
19 2 0.05
20 23 0.61
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (20 bp):
TGTATCGATACAATTTTTTG
Found at i:4717605 original size:13 final size:13
Alignment explanation
Indices: 4717587--4717644 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
4717577 CAATTTTTTG
4717587 TGTATCGATACAT
1 TGTATCGATACAT
4717600 TGTATCGATACAATTTTTT
1 TGTATCGATAC-A-----T
4717619 GTGTATCGATACAT
1 -TGTATCGATACAT
4717633 TGTATCGATACA
1 TGTATCGATACA
4717645 AACTTGGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 23 0.61
14 2 0.05
19 2 0.05
20 11 0.29
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4717609 original size:33 final size:33
Alignment explanation
Indices: 4717567--4717663 Score: 160
Period size: 33 Copynumber: 3.0 Consensus size: 33
4717557 TACAAGCCAA
4717567 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATTTTTTGTGTATCGATACAT
4717600 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATTTTTTGTGTATCGATACAT
** *
4717633 TGTATCGATACAA-ACTTGGTGTATCGATACA
1 TGTATCGATACAATTTTTTGTGTATCGATACA
4717664 AGTTTGGCTA
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 15 0.25
33 46 0.75
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATTTTTTGTGTATCGATACAT
Found at i:4726829 original size:20 final size:20
Alignment explanation
Indices: 4726804--4726857 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
4726794 GTATCGATAC
**
4726804 AATGTATCGATACATGACTA
1 AATGTATCGATACATGAAAA
*
4726824 AATGTATCGATACTTGAAAA
1 AATGTATCGATACATGAAAA
4726844 AATGTATCGATACA
1 AATGTATCGATACA
4726858 AGTCATTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATGAAAA
Found at i:4726927 original size:13 final size:13
Alignment explanation
Indices: 4726909--4726933 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4726899 ACACACAGTA
4726909 TGTATCGATACAT
1 TGTATCGATACAT
4726922 TGTATCGATACA
1 TGTATCGATACA
4726934 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4728449 original size:28 final size:28
Alignment explanation
Indices: 4728368--4728449 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
4728358 TTTTGGAGAT
*
4728368 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
4728396 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
4728424 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
4728450 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:4728592 original size:51 final size:51
Alignment explanation
Indices: 4728432--4728602 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
4728422 GAAATAACGA
* * *
4728432 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
4728484 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
4728537 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
4728588 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
4728603 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:4728648 original size:27 final size:28
Alignment explanation
Indices: 4728585--4728660 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
4728575 AAAATAAAGT
*
4728585 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
4728613 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
4728640 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
4728661 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:4728703 original size:55 final size:51
Alignment explanation
Indices: 4728644--4728779 Score: 143
Period size: 51 Copynumber: 2.6 Consensus size: 51
4728634 GATTAACGGG
* *
4728644 GTTGGAGTGTCCCCGATTGTGAAGAAATTGATGTTTTTTTGGAAA-TAAAATCGGA
1 GTTGGAGTATCCCCGATTGTG-AGAAATTAATG---TTTT-GAAAGTAAAATCGGA
*
4728699 GTTGGAGTATCCCCGATTAT-AGAAAATTAATGTTTTGAAAGTAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAG-AAATTAATGTTTTGAAAGTAAAATCGGA
* *
4728750 GTTGGAATATCCTCGATTGTG-GAGAATTAA
1 GTTGGAGTATCCCCGATTGTGAGA-AATTAA
4728780 GCAACTCAAC
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
50 5 0.07
51 38 0.54
53 2 0.03
54 8 0.11
55 18 0.25
ACGTcount: A:0.32, C:0.10, G:0.25, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAGAAATTAATGTTTTGAAAGTAAAATCGGA
Found at i:4731143 original size:13 final size:13
Alignment explanation
Indices: 4731125--4731150 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4731115 ACAAAGATCC
4731125 ATGTATCGATACA
1 ATGTATCGATACA
4731138 ATGTATCGATACA
1 ATGTATCGATACA
4731151 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4731146 original size:33 final size:33
Alignment explanation
Indices: 4731104--4731170 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4731094 AAAATTTCCA
***
4731104 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
4731137 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
4731170 A
1 A
4731171 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:4731214 original size:19 final size:18
Alignment explanation
Indices: 4731190--4731257 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
4731180 CAGTAGCTAA
4731190 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
4731209 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
4731224 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
4731241 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
4731258 TCGTTGGATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:4731230 original size:13 final size:13
Alignment explanation
Indices: 4731212--4731236 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4731202 ACAATACTTA
4731212 TGTATCGATACAT
1 TGTATCGATACAT
4731225 TGTATCGATACA
1 TGTATCGATACA
4731237 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4731234 original size:32 final size:32
Alignment explanation
Indices: 4731193--4731255 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
4731183 TAGCTAATTA
*
4731193 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
4731225 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
4731256 AATCGTTGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:4731319 original size:21 final size:22
Alignment explanation
Indices: 4731293--4731350 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
4731283 GTTGGGACCC
*
4731293 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACATTTGTACAAA
*
4731314 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTACAAA
*
4731335 TGTATCGATATATTTG
1 TGTATCGATACATTTG
4731351 GAATTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 4 0.13
21 25 0.81
22 2 0.06
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (22 bp):
TGTATCGATACATTTGTACAAA
Found at i:4732007 original size:55 final size:55
Alignment explanation
Indices: 4731912--4732708 Score: 965
Period size: 55 Copynumber: 14.3 Consensus size: 55
4731902 ATAAAGTGTA
* * * * * * *
4731912 TCCTTCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
4731967 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
4732022 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAA-ATAAAAAG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGT-----G
** * *
4732081 CATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 --TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
4732138 TCCTGCTCTTTGAGGACTGGAAA--TACCACCAACTTGTGTGGGATTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
**
4732192 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
* ** * *
4732253 TCCTGCTCTTTGAGGACTAAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
4732308 TCCTGCTCTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
4732361 TCCTGCTCTTCGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
4732416 TCCTGCTTTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
4732471 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
4732526 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAGCTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
4732581 TCCTGCTCTTTGAGGTCTGGAAA-ATGCCACCAACTTAG-GTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTT-GTGTGGGCTTTGAAAGGTG
* *
4732636 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
4732691 TCCTGCTCTTTAAGGACT
1 TCCTGCTCTTTGAGGACT
4732709 AAAAAGCGGA
Statistics
Matches: 659, Mismatches: 53, Indels: 60
0.85 0.07 0.08
Matches are distributed among these distances:
53 54 0.08
54 57 0.09
55 432 0.66
56 19 0.03
57 1 0.00
59 1 0.00
60 4 0.01
61 90 0.14
62 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:4732046 original size:26 final size:26
Alignment explanation
Indices: 4731958--4732047 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
4731948 GTGTGGGCTT
* *
4731958 TGAAAGGCGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
4731984 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
*
4732011 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
4732039 TGAAAGGTG
1 TGAAAGGTG
4732048 CCACCAACTT
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
25 3 0.06
26 16 0.34
27 9 0.19
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:4732071 original size:29 final size:29
Alignment explanation
Indices: 4731984--4732072 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
4731974 CTTTGAGGAC
4731984 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
** *
4732013 T-AAGAGGTGTCCTGC-TCTT-TG-GGGAC--
1 TGAA-AGGTG-CCACCAACTTGTGTGGG-CTT
4732039 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
4732068 TGAAA
1 TGAAA
4732073 ATAAAAAGCA
Statistics
Matches: 45, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
25 3 0.07
26 9 0.20
27 8 0.18
28 8 0.18
29 14 0.31
30 3 0.07
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.28
Consensus pattern (29 bp):
TGAAAGGTGCCACCAACTTGTGTGGGCTT
Found at i:4732548 original size:27 final size:27
Alignment explanation
Indices: 4732466--4732548 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 27
4732456 GGGCTTTAAG
4732466 AGGTGTCCTGCTCTTTGAGGACTGGAA
1 AGGTGTCCTGCTCTTTGAGGACTGGAA
* ** * * * *
4732493 A-ATG-CCACCAACTTGTGTGGGCTTTGAA
1 AGGTGTCCTGC-TCTT-TGAGGAC-TGGAA
4732521 AGGTGTCCTGCTCTTTGAGGACTGGAA
1 AGGTGTCCTGCTCTTTGAGGACTGGAA
4732548 A
1 A
4732549 ATGCCACCAG
Statistics
Matches: 37, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.14
27 11 0.30
28 10 0.27
29 5 0.14
30 3 0.08
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (27 bp):
AGGTGTCCTGCTCTTTGAGGACTGGAA
Found at i:4733715 original size:13 final size:12
Alignment explanation
Indices: 4733691--4733749 Score: 66
Period size: 13 Copynumber: 4.8 Consensus size: 12
4733681 CTTTTCTCTC
*
4733691 TTTTTCTTTGTT
1 TTTTTTTTTGTT
4733703 TTGTTTTTTTG-T
1 TT-TTTTTTTGTT
*
4733715 TTTTTTTTTCTT
1 TTTTTTTTTGTT
*
4733727 TTTTTTTTTGCCT
1 TTTTTTTTTG-TT
4733740 TTTTTTTTTG
1 TTTTTTTTTG
4733750 AAGAGAAGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
11 7 0.17
12 15 0.38
13 18 0.45
ACGTcount: A:0.00, C:0.07, G:0.08, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:4733741 original size:14 final size:12
Alignment explanation
Indices: 4733674--4733748 Score: 62
Period size: 14 Copynumber: 5.8 Consensus size: 12
4733664 CTTAAGTAGG
4733674 TTTTTTTCTTTTC
1 TTTTTTT-TTTTC
* *
4733687 TCTCTTTTTCTTTG
1 T-T-TTTTTTTTTC
4733701 TTTTGTTTTTTT-
1 TTTT-TTTTTTTC
*
4733713 GTTTTTTTTTTC
1 TTTTTTTTTTTC
4733725 TTTTTTTTTTTGCC
1 TTTTTTTTTTT--C
4733739 TTTTTTTTTT
1 TTTTTTTTTT
4733749 GAAGAGAAGG
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
11 7 0.14
12 15 0.29
13 8 0.16
14 16 0.31
15 5 0.10
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:4733742 original size:24 final size:24
Alignment explanation
Indices: 4733690--4733747 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
4733680 TCTTTTCTCT
* *
4733690 CTTTTTCTTTGTTTTGTTTTTTTG
1 CTTTTTTTTTCTTTTGTTTTTTTG
*
4733714 TTTTTTTTTTCTTTT-TTTTTTTG
1 CTTTTTTTTTCTTTTGTTTTTTTG
4733737 CCTTTTTTTTT
1 -CTTTTTTTTT
4733748 TGAAGAGAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 8 0.28
24 21 0.72
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (24 bp):
CTTTTTTTTTCTTTTGTTTTTTTG
Found at i:4733746 original size:36 final size:39
Alignment explanation
Indices: 4733675--4733749 Score: 95
Period size: 36 Copynumber: 2.0 Consensus size: 39
4733665 TTAAGTAGGT
*
4733675 TTTTTTCTTTTCTCTCTTTTTCTTTGTTTTGTTTTTTTG
1 TTTTTTCTTTTCTCTCTTTTTCTTTGCTTTGTTTTTTTG
*
4733714 TTTTTT-TTTTCT-T-TTTTTTTTTGCCTTT-TTTTTTTG
1 TTTTTTCTTTTCTCTCTTTTTCTTTG-CTTTGTTTTTTTG
4733750 AAGAGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
36 17 0.52
37 4 0.12
38 6 0.18
39 6 0.18
ACGTcount: A:0.00, C:0.11, G:0.07, T:0.83
Consensus pattern (39 bp):
TTTTTTCTTTTCTCTCTTTTTCTTTGCTTTGTTTTTTTG
Found at i:4746221 original size:28 final size:29
Alignment explanation
Indices: 4746149--4746232 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 29
4746139 TTTTGGAGAT
*
4746149 AATAACGAGGTTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTTGGAGT-ATCCC-CGATGA
* *
4746178 AGTAACGGGGTTTGGAGTATCCCCGATGA
1 AATAACGAGGTTTGGAGTATCCCCGATGA
*
4746207 AATAACGAGG-TTGGAGTATCCTCGAT
1 AATAACGAGGTTTGGAGTATCCCCGAT
4746233 TGTGAAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
27 2 0.04
28 19 0.40
29 26 0.55
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
AATAACGAGGTTTGGAGTATCCCCGATGA
Found at i:4746375 original size:51 final size:51
Alignment explanation
Indices: 4746215--4746385 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
4746205 GAAATAACGA
* * *
4746215 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
4746267 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
4746320 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
4746371 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
4746386 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:4813701 original size:33 final size:33
Alignment explanation
Indices: 4813658--4813722 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
4813648 TTTGGGACAA
* **
4813658 TGTATCGATACAATTTTTCATGTATCGATACAT
1 TGTATCGATACAATATGCCATGTATCGATACAT
* *
4813691 TGTATTGATACAATATGCCATGTATTGATACA
1 TGTATCGATACAATATGCCATGTATCGATACA
4813723 AACAGTGGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACAATATGCCATGTATCGATACAT
Found at i:4813797 original size:19 final size:20
Alignment explanation
Indices: 4813752--4813805 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
4813742 TTGTTAGTTT
**
4813752 CATGTATCGATACAATCGTG
1 CATGTATCGATACAATCGAA
*
4813772 TATGTATCGATACAAT-GAA
1 CATGTATCGATACAATCGAA
4813791 CATGTATCGATACAA
1 CATGTATCGATACAA
4813806 CATATCGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATCGAA
Found at i:4813834 original size:33 final size:32
Alignment explanation
Indices: 4813776--4813837 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
4813766 ATCGTGTATG
*
4813776 TATCGATACAATGAACATGTATCGATACAACA
1 TATCGATACAAAGAACATGTATCGATACAACA
4813808 TATCGATACAAAGCATA-ATGTATCGATACA
1 TATCGATACAAAG-A-ACATGTATCGATACA
4813838 TCTGGATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 12 0.44
33 14 0.52
34 1 0.04
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.26
Consensus pattern (32 bp):
TATCGATACAAAGAACATGTATCGATACAACA
Found at i:4816372 original size:20 final size:20
Alignment explanation
Indices: 4816347--4816444 Score: 98
Period size: 20 Copynumber: 5.6 Consensus size: 20
4816337 TAGTAACCTC
4816347 TGTATCGATACAAAGAACAT
1 TGTATCGATACAAAGAACAT
4816367 TGTATCGAT----A-AA-A-
1 TGTATCGATACAAAGAACAT
4816380 TGTATCGATACAAAGAACAT
1 TGTATCGATACAAAGAACAT
4816400 TGTATCGAT----A-AA-A-
1 TGTATCGATACAAAGAACAT
4816413 TGTATCGATACAAAGAACAT
1 TGTATCGATACAAAGAACAT
4816433 TGTATCGATACA
1 TGTATCGATACA
4816445 TCTGGGTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 28
0.70 0.00 0.30
Matches are distributed among these distances:
13 18 0.28
14 2 0.03
15 4 0.06
16 2 0.03
17 2 0.03
18 4 0.06
19 2 0.03
20 30 0.47
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (20 bp):
TGTATCGATACAAAGAACAT
Found at i:4816389 original size:33 final size:33
Alignment explanation
Indices: 4816347--4816442 Score: 192
Period size: 33 Copynumber: 2.9 Consensus size: 33
4816337 TAGTAACCTC
4816347 TGTATCGATACAAAGAACATTGTATCGATAAAA
1 TGTATCGATACAAAGAACATTGTATCGATAAAA
4816380 TGTATCGATACAAAGAACATTGTATCGATAAAA
1 TGTATCGATACAAAGAACATTGTATCGATAAAA
4816413 TGTATCGATACAAAGAACATTGTATCGATA
1 TGTATCGATACAAAGAACATTGTATCGATA
4816443 CATCTGGGTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (33 bp):
TGTATCGATACAAAGAACATTGTATCGATAAAA
Found at i:4823045 original size:11 final size:11
Alignment explanation
Indices: 4823031--4823080 Score: 75
Period size: 11 Copynumber: 4.5 Consensus size: 11
4823021 CAATCCATAG
4823031 TTTTTTTTTCA
1 TTTTTTTTTCA
4823042 TTTTCTTTTTCA
1 TTTT-TTTTTCA
4823054 -TTTTTTTTCA
1 TTTTTTTTTCA
*
4823064 TTTTTTTCTCA
1 TTTTTTTTTCA
4823075 TTTTTT
1 TTTTTT
4823081 GAACATCACC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
10 7 0.19
11 22 0.61
12 7 0.19
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTTTTCA
Found at i:4823708 original size:19 final size:20
Alignment explanation
Indices: 4823675--4823718 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
4823665 GTTCATAGCA
*
4823675 AAAAAATAAATAAATAACCT
1 AAAAAATAAATAAATAACAT
*
4823695 AAAAAATAAA-AAATTACAT
1 AAAAAATAAATAAATAACAT
4823714 AAAAA
1 AAAAA
4823719 CAAACTAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (20 bp):
AAAAAATAAATAAATAACAT
Found at i:4823826 original size:118 final size:119
Alignment explanation
Indices: 4823703--4823927 Score: 344
Period size: 120 Copynumber: 1.9 Consensus size: 119
4823693 CTAAAAAATA
* * * * *
4823703 AAAAATTACATAAAAACAAACTAACATAAACTAATTTGACATAAAAAA-ATAAAGACTTTCCCTC
1 AAAAATTACACAAAAACAAACTAACATAAACTAATTCGACATAAAAAATAGAAAAACCTTCCCTC
4823767 AAAGTTAAAACAAACATTATCCTCAATGTTTATAAATAAAAGAGAAGGAATAAG
66 AAAGTTAAAACAAACATTATCCTCAATGTTTATAAATAAAAGAGAAGGAATAAG
* *
4823821 AAAAATTACACAAAAATAAACTAACGTAAACTAATTCGACATAAAAAATTAGAAAAACCTTCCCT
1 AAAAATTACACAAAAACAAACTAACATAAACTAATTCGACATAAAAAA-TAGAAAAACCTTCCCT
* * *
4823886 CAAAGTTAAAACAAATATTGTCCTTAATGTTTATAAATAAAA
65 CAAAGTTAAAACAAACATTATCCTCAATGTTTATAAATAAAA
4823928 AAATAACAAA
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
118 44 0.46
120 51 0.54
ACGTcount: A:0.54, C:0.14, G:0.07, T:0.25
Consensus pattern (119 bp):
AAAAATTACACAAAAACAAACTAACATAAACTAATTCGACATAAAAAATAGAAAAACCTTCCCTC
AAAGTTAAAACAAACATTATCCTCAATGTTTATAAATAAAAGAGAAGGAATAAG
Found at i:4825381 original size:19 final size:18
Alignment explanation
Indices: 4825354--4825396 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
4825344 TACCTGAAAA
*
4825354 AAATAAAAATAAATTAAAT
1 AAATAAAAATAAAAT-AAT
*
4825373 AAATTAAAATAAAATAAT
1 AAATAAAAATAAAATAAT
4825391 AAATAA
1 AAATAA
4825397 GAAAAGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATAAAAATAAAATAAT
Found at i:4826857 original size:17 final size:17
Alignment explanation
Indices: 4826835--4826867 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4826825 CTATTTAGTC
4826835 ATGTCAAAATAATCATA
1 ATGTCAAAATAATCATA
4826852 ATGTCAAAATAATCAT
1 ATGTCAAAATAATCAT
4826868 TCGCTTGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (17 bp):
ATGTCAAAATAATCATA
Found at i:4827437 original size:20 final size:20
Alignment explanation
Indices: 4827394--4827447 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
4827384 ACCCTTCAAC
*
4827394 TGTATCGATACATGATTAAAT
1 TGTATCGATACATCA-TAAAT
4827415 TGTATCGATACATCA-AGAAT
1 TGTATCGATACATCATA-AAT
*
4827435 TGTATCTATACAT
1 TGTATCGATACAT
4827448 TTGGTCTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 1 0.03
20 15 0.50
21 14 0.47
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATCATAAAT
Found at i:4827979 original size:34 final size:33
Alignment explanation
Indices: 4827887--4828021 Score: 180
Period size: 34 Copynumber: 4.0 Consensus size: 33
4827877 GAAGTGATTG
** *
4827887 AAAGGTTCCCTCTTAGCTTTTGAAAAGGATAGGGA
1 AAAGGTTCTATCTTAGC-CTTGAAAA-GATAGGGA
*
4827922 AGAGGTTCTATCTTAGCCTTGAAAAGATAGGGA
1 AAAGGTTCTATCTTAGCCTTGAAAAGATAGGGA
4827955 AAAGGTTCTATCTTAGCCTGTGAAAAGATAGGGA
1 AAAGGTTCTATCTTAGCCT-TGAAAAGATAGGGA
* *
4827989 ATAGGCTCTATCTTAGCCTTCGAAAAGATAGGG
1 AAAGGTTCTATCTTAGCCTT-GAAAAGATAGGG
4828022 TTGTAAGCTT
Statistics
Matches: 91, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
33 27 0.30
34 50 0.55
35 14 0.15
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (33 bp):
AAAGGTTCTATCTTAGCCTTGAAAAGATAGGGA
Found at i:4828014 original size:68 final size:68
Alignment explanation
Indices: 4827887--4828021 Score: 200
Period size: 68 Copynumber: 2.0 Consensus size: 68
4827877 GAAGTGATTG
* * * *
4827887 AAAGGTTCCCTCTTAGCTTTTGAAAAGGATAGGGAAGAGGTTCTATCTTAGCCTTGAAAAGATAG
1 AAAGGTTCCATCTTAGCCTGTGAAAAGGATAGGGAAGAGGCTCTATCTTAGCCTTGAAAAGATAG
4827952 GGA
66 GGA
* *
4827955 AAAGGTTCTATCTTAGCCTGTGAAAA-GATAGGGAATAGGCTCTATCTTAGCCTTCGAAAAGATA
1 AAAGGTTCCATCTTAGCCTGTGAAAAGGATAGGGAAGAGGCTCTATCTTAGCCTT-GAAAAGATA
4828019 GGG
65 GGG
4828022 TTGTAAGCTT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
67 26 0.43
68 34 0.57
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (68 bp):
AAAGGTTCCATCTTAGCCTGTGAAAAGGATAGGGAAGAGGCTCTATCTTAGCCTTGAAAAGATAG
GGA
Found at i:4830574 original size:12 final size:12
Alignment explanation
Indices: 4830557--4830585 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
4830547 ATTTTGAAAA
4830557 TTGATTTTGATG
1 TTGATTTTGATG
4830569 TTGATTTTGATG
1 TTGATTTTGATG
4830581 TTGAT
1 TTGAT
4830586 CATGTGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.24, T:0.59
Consensus pattern (12 bp):
TTGATTTTGATG
Found at i:4830766 original size:20 final size:20
Alignment explanation
Indices: 4830741--4830778 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4830731 TGGATTTTTC
*
4830741 CAAAATGTATCGATACATTG
1 CAAAATGTATCAATACATTG
4830761 CAAAATGTATCAATACAT
1 CAAAATGTATCAATACAT
4830779 CTAGGTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.29
Consensus pattern (20 bp):
CAAAATGTATCAATACATTG
Found at i:4830963 original size:21 final size:21
Alignment explanation
Indices: 4830914--4830963 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
4830904 ATCTTCCAAT
4830914 CATCAAA-TTCTTCAAATACA
1 CATCAAATTTCTTCAAATACA
* *
4830934 CCTCGAATTTCTTCAAA-AGCA
1 CATCAAATTTCTTCAAATA-CA
4830955 CATCAAATT
1 CATCAAATT
4830964 CCTTTATTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.40, C:0.26, G:0.04, T:0.30
Consensus pattern (21 bp):
CATCAAATTTCTTCAAATACA
Found at i:4833982 original size:34 final size:34
Alignment explanation
Indices: 4833912--4834048 Score: 195
Period size: 34 Copynumber: 4.0 Consensus size: 34
4833902 CGAAGTGATT
* *
4833912 AAGAGGTTCTATCTTAGCCTTTGAAAAAGATCGGG
1 AAGAGGTTCTATCTTAGCCTGTG-AAAAGATAGGG
4833947 AAGAGGTTCTATCTTAGCCTGTGAAAAGATAGGG
1 AAGAGGTTCTATCTTAGCCTGTGAAAAGATAGGG
* *
4833981 AAAAAGTTCTATCTTAGCCTGTGAAAAGATAGGG
1 AAGAGGTTCTATCTTAGCCTGTGAAAAGATAGGG
* *
4834015 AAGAGGTTATATCTTAGCCT-TCAGAAAGATAGGG
1 AAGAGGTTCTATCTTAGCCTGTGA-AAAGATAGGG
4834049 TTGTAAGGTT
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
33 2 0.02
34 69 0.74
35 22 0.24
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.27
Consensus pattern (34 bp):
AAGAGGTTCTATCTTAGCCTGTGAAAAGATAGGG
Found at i:4836622 original size:31 final size:31
Alignment explanation
Indices: 4836573--4836689 Score: 135
Period size: 31 Copynumber: 3.8 Consensus size: 31
4836563 AAGGCTACTG
4836573 TGGGTCGTGGTAGCACCTTTAGGGGTTGTTT
1 TGGGTCGTGGTAGCACCTTTAGGGGTTGTTT
* * *
4836604 TGGGTTGTCGTAGTACCTTTAGGGGTTGTTT
1 TGGGTCGTGGTAGCACCTTTAGGGGTTGTTT
* * *
4836635 TGGGTCGTGGCAGCACCTCTAGGGGCTGTTT
1 TGGGTCGTGGTAGCACCTTTAGGGGTTGTTT
* * * * *
4836666 TAGGTCATGGCAACACCTCTAGGG
1 TGGGTCGTGGTAGCACCTTTAGGG
4836690 CCGTTTCATA
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 74 1.00
ACGTcount: A:0.13, C:0.17, G:0.36, T:0.34
Consensus pattern (31 bp):
TGGGTCGTGGTAGCACCTTTAGGGGTTGTTT
Found at i:4837093 original size:30 final size:31
Alignment explanation
Indices: 4837045--4837102 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
4837035 ATGTTTTTCA
* *
4837045 TGCATTTTGATTTTATTTAAGGGCCATTGTG
1 TGCATTTTGATATTATTTAAGGACCATTGTG
4837076 TGCATTTT-ATATTATTTAAGGACCATT
1 TGCATTTTGATATTATTTAAGGACCATT
4837103 TTGAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.48
Consensus pattern (31 bp):
TGCATTTTGATATTATTTAAGGACCATTGTG
Found at i:4843611 original size:55 final size:56
Alignment explanation
Indices: 4843442--4843633 Score: 164
Period size: 55 Copynumber: 3.5 Consensus size: 56
4843432 GTCGTGGTTG
* * * *
4843442 AAATTGGCACTAAAAT-ATGAAAGCTTAAGAGTAGTCA-ATAGGTTTCATCCCAG-TT
1 AAATTGGCACTAAAATGA-GAAAGCCTAAGACTACT-AGATAAGTTTCATCCCAGTTT
* * * * * *
4843497 AAAATGGCA-TTAAATGAGAAAGCCTAAGAGCAACT-GACT-AGGTTCATCCCACTTG
1 AAATTGGCACTAAAATGAGAAAGCCTAAGA-CTACTAGA-TAAGTTTCATCCCAGTTT
* *
4843552 AAATTGGCACTAAAATGAGAAAGCTTGAGACTACTAGATAAGTTTC-TCCCAGTTT
1 AAATTGGCACTAAAATGAGAAAGCCTAAGACTACTAGATAAGTTTCATCCCAGTTT
* *
4843607 AAATTAGCACAAAAAATGAGAAAGCCT
1 AAATTGGCAC-TAAAATGAGAAAGCCT
4843634 GAGAGTAGCT
Statistics
Matches: 107, Mismatches: 21, Indels: 17
0.74 0.14 0.12
Matches are distributed among these distances:
54 27 0.25
55 42 0.39
56 38 0.36
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (56 bp):
AAATTGGCACTAAAATGAGAAAGCCTAAGACTACTAGATAAGTTTCATCCCAGTTT
Found at i:4846283 original size:13 final size:13
Alignment explanation
Indices: 4846265--4846292 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4846255 AATTCTTCAC
4846265 GTATCGATACAAT
1 GTATCGATACAAT
4846278 GTATCGATACAAT
1 GTATCGATACAAT
4846291 GT
1 GT
4846293 GCCATGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:4846365 original size:20 final size:19
Alignment explanation
Indices: 4846338--4846393 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
4846328 TTGCCAGTTT
**
4846338 CATGTATCGATACAATCGTG
1 CATGTATCGATACAAT-GAA
* *
4846358 CTTGTATCGATATAATGAA
1 CATGTATCGATACAATGAA
4846377 CATGTATCGATACAATG
1 CATGTATCGATACAATG
4846394 TATCGATACA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:4846396 original size:13 final size:13
Alignment explanation
Indices: 4846378--4846403 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4846368 TATAATGAAC
4846378 ATGTATCGATACA
1 ATGTATCGATACA
4846391 ATGTATCGATACA
1 ATGTATCGATACA
4846404 TCTGGATATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4853332 original size:33 final size:33
Alignment explanation
Indices: 4853289--4853353 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
4853279 TTTGGGACAA
* **
4853289 TGTATCGATACAATTTTTCATGTATCGATACAT
1 TGTATCGATACAATATGCCATGTATCGATACAT
* *
4853322 TGTATTGATACAATATGCCATGTATTGATACA
1 TGTATCGATACAATATGCCATGTATCGATACA
4853354 AACAGTGGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACAATATGCCATGTATCGATACAT
Found at i:4853428 original size:19 final size:20
Alignment explanation
Indices: 4853383--4853436 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
4853373 TTGTTAGTTT
**
4853383 CATGTATCGATACAATCGTG
1 CATGTATCGATACAATCGAA
*
4853403 TATGTATCGATACAAT-GAA
1 CATGTATCGATACAATCGAA
4853422 CATGTATCGATACAA
1 CATGTATCGATACAA
4853437 CATATCGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATCGAA
Found at i:4853465 original size:33 final size:32
Alignment explanation
Indices: 4853407--4853468 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
4853397 ATCGTGTATG
*
4853407 TATCGATACAATGAACATGTATCGATACAACA
1 TATCGATACAAAGAACATGTATCGATACAACA
4853439 TATCGATACAAAGCATA-ATGTATCGATACA
1 TATCGATACAAAG-A-ACATGTATCGATACA
4853469 TCTGGATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 12 0.44
33 14 0.52
34 1 0.04
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.26
Consensus pattern (32 bp):
TATCGATACAAAGAACATGTATCGATACAACA
Found at i:4856004 original size:20 final size:20
Alignment explanation
Indices: 4855979--4856076 Score: 98
Period size: 20 Copynumber: 5.6 Consensus size: 20
4855969 TAGTAACCTC
4855979 TGTATCGATACAAAGAACAT
1 TGTATCGATACAAAGAACAT
4855999 TGTATCGAT----A-AA-A-
1 TGTATCGATACAAAGAACAT
4856012 TGTATCGATACAAAGAACAT
1 TGTATCGATACAAAGAACAT
4856032 TGTATCGAT----A-AA-A-
1 TGTATCGATACAAAGAACAT
4856045 TGTATCGATACAAAGAACAT
1 TGTATCGATACAAAGAACAT
4856065 TGTATCGATACA
1 TGTATCGATACA
4856077 TCTGGGTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 28
0.70 0.00 0.30
Matches are distributed among these distances:
13 18 0.28
14 2 0.03
15 4 0.06
16 2 0.03
17 2 0.03
18 4 0.06
19 2 0.03
20 30 0.47
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (20 bp):
TGTATCGATACAAAGAACAT
Found at i:4856021 original size:33 final size:33
Alignment explanation
Indices: 4855979--4856074 Score: 192
Period size: 33 Copynumber: 2.9 Consensus size: 33
4855969 TAGTAACCTC
4855979 TGTATCGATACAAAGAACATTGTATCGATAAAA
1 TGTATCGATACAAAGAACATTGTATCGATAAAA
4856012 TGTATCGATACAAAGAACATTGTATCGATAAAA
1 TGTATCGATACAAAGAACATTGTATCGATAAAA
4856045 TGTATCGATACAAAGAACATTGTATCGATA
1 TGTATCGATACAAAGAACATTGTATCGATA
4856075 CATCTGGGTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (33 bp):
TGTATCGATACAAAGAACATTGTATCGATAAAA
Found at i:4862677 original size:11 final size:11
Alignment explanation
Indices: 4862663--4862712 Score: 75
Period size: 11 Copynumber: 4.5 Consensus size: 11
4862653 CAATCCATAG
4862663 TTTTTTTTTCA
1 TTTTTTTTTCA
4862674 TTTTCTTTTTCA
1 TTTT-TTTTTCA
4862686 -TTTTTTTTCA
1 TTTTTTTTTCA
*
4862696 TTTTTTTCTCA
1 TTTTTTTTTCA
4862707 TTTTTT
1 TTTTTT
4862713 GAACATCACC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
10 7 0.19
11 22 0.61
12 7 0.19
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTTTTCA
Found at i:4863340 original size:19 final size:20
Alignment explanation
Indices: 4863307--4863350 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
4863297 GTTCATAGCA
*
4863307 AAAAAATAAATAAATAACCT
1 AAAAAATAAATAAATAACAT
*
4863327 AAAAAATAAA-AAATTACAT
1 AAAAAATAAATAAATAACAT
4863346 AAAAA
1 AAAAA
4863351 CAAACTAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (20 bp):
AAAAAATAAATAAATAACAT
Found at i:4863458 original size:118 final size:119
Alignment explanation
Indices: 4863335--4863559 Score: 344
Period size: 120 Copynumber: 1.9 Consensus size: 119
4863325 CTAAAAAATA
* * * * *
4863335 AAAAATTACATAAAAACAAACTAACATAAACTAATTTGACATAAAAAA-ATAAAGACTTTCCCTC
1 AAAAATTACACAAAAACAAACTAACATAAACTAATTCGACATAAAAAATAGAAAAACCTTCCCTC
4863399 AAAGTTAAAACAAACATTATCCTCAATGTTTATAAATAAAAGAGAAGGAATAAG
66 AAAGTTAAAACAAACATTATCCTCAATGTTTATAAATAAAAGAGAAGGAATAAG
* *
4863453 AAAAATTACACAAAAATAAACTAACGTAAACTAATTCGACATAAAAAATTAGAAAAACCTTCCCT
1 AAAAATTACACAAAAACAAACTAACATAAACTAATTCGACATAAAAAA-TAGAAAAACCTTCCCT
* * *
4863518 CAAAGTTAAAACAAATATTGTCCTTAATGTTTATAAATAAAA
65 CAAAGTTAAAACAAACATTATCCTCAATGTTTATAAATAAAA
4863560 AAATAACAAA
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
118 44 0.46
120 51 0.54
ACGTcount: A:0.54, C:0.14, G:0.07, T:0.25
Consensus pattern (119 bp):
AAAAATTACACAAAAACAAACTAACATAAACTAATTCGACATAAAAAATAGAAAAACCTTCCCTC
AAAGTTAAAACAAACATTATCCTCAATGTTTATAAATAAAAGAGAAGGAATAAG
Found at i:4865013 original size:19 final size:18
Alignment explanation
Indices: 4864986--4865028 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
4864976 TACCTGAAAA
*
4864986 AAATAAAAATAAATTAAAT
1 AAATAAAAATAAAAT-AAT
*
4865005 AAATTAAAATAAAATAAT
1 AAATAAAAATAAAATAAT
4865023 AAATAA
1 AAATAA
4865029 GAAAAGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATAAAAATAAAATAAT
Found at i:4866545 original size:69 final size:69
Alignment explanation
Indices: 4866408--4866547 Score: 160
Period size: 69 Copynumber: 2.0 Consensus size: 69
4866398 AAAATTACAG
* ** * *
4866408 AATAGTCCTTAAATACATGAAATTATGTAATAGTCCTAAAATCATGAAAAATGATTAAAATGGTC
1 AATAGTCCTAAAATACATGAAATTACATAATAGTCCTAAAATCATGAAAAATGATTAAAATAGCC
4866473 CTAA
66 CTAA
* * *
4866477 AATAGTCCTAAAATATATGAAATTACATAATAGTCCCTATAAT-AT-AGAAAATG-TTCTAAATA
1 AATAGTCCTAAAATACATGAAATTACATAATAGT-CCTAAAATCATGA-AAAATGATT-AAAATA
4866539 GCCCTAA
63 GCCCTAA
4866546 AA
1 AA
4866548 ATCATGGAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
68 3 0.05
69 50 0.83
70 7 0.12
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (69 bp):
AATAGTCCTAAAATACATGAAATTACATAATAGTCCTAAAATCATGAAAAATGATTAAAATAGCC
CTAA
Found at i:4866558 original size:59 final size:58
Alignment explanation
Indices: 4866476--4866628 Score: 159
Period size: 59 Copynumber: 2.6 Consensus size: 58
4866466 AATGGTCCTA
* * *
4866476 AAATAGTCCTAAAATAT-ATGAAATTACATAATAGTCCCTATAATATAGAAAATGTTCT
1 AAATAGACCTAAAA-ATCATGAAATTACATAATAGTCCCTATAACATAGAAAAGGTTCT
* * * * * *
4866534 AAATAGCCCTAAAAATCATGGAAATTACATGATAGGCCCTATAGCATGGAAAAGGTTTT
1 AAATAGACCTAAAAATCAT-GAAATTACATAATAGTCCCTATAACATAGAAAAGGTTCT
*
4866593 ATA-AGAACCT-AAAATACATGAAATTACATAATAGTC
1 AAATAG-ACCTAAAAAT-CATGAAATTACATAATAGTC
4866629 AATACATCAT
Statistics
Matches: 79, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
57 2 0.03
58 37 0.47
59 40 0.51
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (58 bp):
AAATAGACCTAAAAATCATGAAATTACATAATAGTCCCTATAACATAGAAAAGGTTCT
Found at i:4866664 original size:58 final size:58
Alignment explanation
Indices: 4866601--4866801 Score: 181
Period size: 58 Copynumber: 3.5 Consensus size: 58
4866591 TTATAAGAAC
* * * *
4866601 CTAAAATACATGAAATTACATAATAGTCAATACATCATAAAAAATGACTAAAATAGCT
1 CTAAAATGCATGAAATTACATAATAGTCCATAAATCATGAAAAATGACTAAAATAGCT
* * * * * * *
4866659 TTAAAATGCAT-AAAATAGCATCATGGTCCTTAAATCATGAAAAATGACCAAAATGGCT
1 CTAAAATGCATGAAATTA-CATAATAGTCCATAAATCATGAAAAATGACTAAAATAGCT
* * * * ** *
4866717 CTAAAGTGCATGAAATAACATAATAATCCCTAAATCATGAAAAATGACTAGCATAACT
1 CTAAAATGCATGAAATTACATAATAGTCCATAAATCATGAAAAATGACTAAAATAGCT
* * *
4866775 -TCAAAATGTATGAAATTATATAGTAGT
1 CT-AAAATGCATGAAATTACATAATAGT
4866802 ACTTAATTTG
Statistics
Matches: 110, Mismatches: 30, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
57 6 0.05
58 100 0.91
59 4 0.04
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (58 bp):
CTAAAATGCATGAAATTACATAATAGTCCATAAATCATGAAAAATGACTAAAATAGCT
Found at i:4869234 original size:27 final size:27
Alignment explanation
Indices: 4869196--4869248 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
4869186 TATTATAAGT
4869196 AATTCGCCACTTCAAGGAATCTAACTA
1 AATTCGCCACTTCAAGGAATCTAACTA
4869223 AATTCGCCACTTCAAGGAATCTAACT
1 AATTCGCCACTTCAAGGAATCTAACT
4869249 TGAACTGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.26
Consensus pattern (27 bp):
AATTCGCCACTTCAAGGAATCTAACTA
Found at i:4871277 original size:15 final size:15
Alignment explanation
Indices: 4871267--4871296 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4871257 TTTTAAAGAC
4871267 TTAA-TAATTAAAAA
1 TTAACTAATTAAAAA
4871281 TTAACTAATTAAAAA
1 TTAACTAATTAAAAA
4871296 T
1 T
4871297 AAAAAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAACTAATTAAAAA
Found at i:4872882 original size:16 final size:16
Alignment explanation
Indices: 4872861--4872917 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
4872851 TAAAATTTTC
*
4872861 GGATCATTTTAGGTTT
1 GGATCATTTCAGGTTT
*
4872877 GGATCATTTCGGGTTT
1 GGATCATTTCAGGTTT
*
4872893 GGATCATTTCAGGTTC
1 GGATCATTTCAGGTTT
*
4872909 AGATCATTT
1 GGATCATTT
4872918 TGGATTTTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.44
Consensus pattern (16 bp):
GGATCATTTCAGGTTT
Done.