Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 95 of 207
Found at i:28082253 original size:90 final size:88
Alignment explanation
Indices: 28082096--28082261 Score: 235
Period size: 90 Copynumber: 1.8 Consensus size: 88
28082086 TCTATTTGTC
* * *
28082096 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTCTTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--CACACGCTGAGGTCTTTTAAATT
28082161 CTGTTCTTCAATTTCTGTTCGTAAA
64 CTGTTCTTCAATTTCTGTTCGTAAA
*
28082186 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCTGAGGTATTTTTAAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCACACGCTGAGGT-CTTTTAAA-T
*
28082250 TCTGTTTTTCAA
63 TCTGTTCTTCAA
28082262 AAAAATCAAC
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
88 11 0.16
89 6 0.09
90 49 0.72
91 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (88 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACACGCTGAGGTCTTTTAAATTCT
GTTCTTCAATTTCTGTTCGTAAA
Found at i:28082296 original size:76 final size:75
Alignment explanation
Indices: 28082170--28082368 Score: 303
Period size: 76 Copynumber: 2.7 Consensus size: 75
28082160 TCTGTTCTTC
* *
28082170 AATTTCTGTTCGTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
1 AATTTCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
*
28082235 AGGTATTTTTA
66 AGGTA-ATTTA
* * *
28082246 AATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGGACACGCTG
1 AATTTCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
*
28082311 AGGTAATTTC
66 AGGTAATTTA
*
28082321 AATTTCTGTTTGTC--AAAAATTAACTCATATTGCGAGAGGTGAGTTGAG
1 AATTTCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
28082369 TCCGGCTCAC
Statistics
Matches: 113, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
73 32 0.28
75 16 0.14
76 65 0.58
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (75 bp):
AATTTCTGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
AGGTAATTTA
Found at i:28082368 original size:239 final size:237
Alignment explanation
Indices: 28081922--28082418 Score: 718
Period size: 239 Copynumber: 2.1 Consensus size: 237
28081912 ATGCTGAGGT
* * * *
28081922 TTTTCAATTTCTGTTTGTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGTCTCGCTCAC
1 TTTTCAATTTCTGTTCGTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGC-CAC
* * *
28081987 ATGCTGAGGTCTTTTTAATTTCTTTCAATGATATTTTTCAAAAATCAACTCATATTGCAAAGGTG
65 ACGCTGAGGTATTTTTAA--TATTTC-ATG--ATTTTTCAAAAATCAACTCATATTGCAAAGGTG
28082052 AGTTGAGCCTCGGACACGCTGAGTAATTTCAATTTCTATTTGTCAAAAATTAACTCATATTGCGA
125 AGTTGAGCCTCGGACACGCTGAGTAATTTCAATTTCTATTTGTCAAAAATTAACTCATATTGCGA
28082117 GAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTCTTTTCAA-TTCTG-
190 GAGGTGAGTTGAGCC-CGGCTCACATGCTGAGGTCTTTTCAATTTCTGC
*
28082164 TTCTTCAATTTCTGTTCGTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG-GA
1 TT-TTCAATTTCTGTTCGTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GCCA
28082228 CACGCTGAGGTATTTTTAA-ATTTC-TG-TTTTTCAAAAAAATCAACTCATATTGCGAAAGGTGA
64 CACGCTGAGGTATTTTTAATATTTCATGATTTTTC--AAAAATCAACTCATATTGC-AAAGGTGA
*
28082290 GTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCG
126 GTTGAGCCTC-GGACACGCTGA-GTAATTTCAATTTCTATTTGTCAAAAATTAACTCATATTGCG
* *
28082355 AGAGGTGAGTTGAGTCCGGCTCACATGCTGAGGTCTTTTTAATTTCTGC
189 AGAGGTGAGTTGAGCCCGGCTCACATGCTGAGGTCTTTTCAATTTCTGC
*
28082404 TTTTGAATTTCTGTT
1 TTTTCAATTTCTGTT
28082419 TTTTCAATTT
Statistics
Matches: 234, Mismatches: 12, Indels: 21
0.88 0.04 0.08
Matches are distributed among these distances:
234 6 0.03
236 19 0.08
237 20 0.09
238 36 0.15
239 77 0.33
240 2 0.01
242 20 0.09
243 53 0.23
244 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (237 bp):
TTTTCAATTTCTGTTCGTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGCCACA
CGCTGAGGTATTTTTAATATTTCATGATTTTTCAAAAATCAACTCATATTGCAAAGGTGAGTTGA
GCCTCGGACACGCTGAGTAATTTCAATTTCTATTTGTCAAAAATTAACTCATATTGCGAGAGGTG
AGTTGAGCCCGGCTCACATGCTGAGGTCTTTTCAATTTCTGC
Found at i:28082623 original size:75 final size:75
Alignment explanation
Indices: 28082510--28082757 Score: 337
Period size: 76 Copynumber: 3.3 Consensus size: 75
28082500 AAATCTACTT
*
28082510 TTGCGAGAAGTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAA
1 TTGCGAGAGGTGAGTTGAGCC-TTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAA
28082575 ATCAACTCATA
65 ATCAACTCATA
* *
28082586 TTGTGAGAGGTGAGTTGAGCCTTGCTCACGTGATGAGCTATTTTCAATTTCTGCTTTTCAAAAAA
1 TTGCGAGAGGTGAGTTGAGCCTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTC-AAAAA
28082651 ATCAACTCATA
65 ATCAACTCATA
* ** *
28082662 TTGCGAGAGGTGAGTTGAG--TTCGGGTCACACGCTGAGGC-GTTTTCAATTTCTGC-TTTC--A
1 TTGCGAGAGGTGAGTTGAGCCTT--GCTCACGTGCTGA-GCTATTTTCAATTTCTGCTTTTCAAA
28082721 AAATCAACTCATA
63 AAATCAACTCATA
*
28082734 TTGCGAGATGTGAGTTGAGCCTTG
1 TTGCGAGAGGTGAGTTGAGCCTTG
28082758 GGTTTACATG
Statistics
Matches: 156, Mismatches: 10, Indels: 16
0.86 0.05 0.09
Matches are distributed among these distances:
72 33 0.21
74 4 0.03
75 41 0.26
76 76 0.49
77 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (75 bp):
TTGCGAGAGGTGAGTTGAGCCTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAAA
TCAACTCATA
Found at i:28083502 original size:30 final size:30
Alignment explanation
Indices: 28083466--28083596 Score: 226
Period size: 30 Copynumber: 4.4 Consensus size: 30
28083456 ACTTTTCTCA
28083466 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
28083496 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
28083526 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
28083556 ACTAGCCACACCTTCTCCACCACCAAATCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
28083586 ACTAGCCACAC
1 ACTAGCCACAC
28083597 TGCTCCATTA
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 95 1.00
ACGTcount: A:0.27, C:0.49, G:0.04, T:0.20
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:28083531 original size:60 final size:60
Alignment explanation
Indices: 28083466--28083638 Score: 226
Period size: 60 Copynumber: 2.9 Consensus size: 60
28083456 ACTTTTCTCA
* *
28083466 ACTAGCCACACCTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCCACTAGCCACACCTTCTCCACCACCAAATCC
* *
28083526 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTCTCCACCACCAAATCC
1 ACTAGCCACACCTTTTCCACCACCAACTCCACTAGCCACACCTTCTCCACCACCAAATCC
** ** * *
28083586 ACTAGCCACA-CTGCTCCATTACCTACTCCACTAACCACA-CTTGCTCCA-CACCA
1 ACTAGCCACACCTTTTCCACCACCAACTCCACTAGCCACACCTT-CTCCACCACCA
28083639 CTTGTACCTA
Statistics
Matches: 100, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
58 8 0.08
59 27 0.27
60 65 0.65
ACGTcount: A:0.27, C:0.48, G:0.04, T:0.21
Consensus pattern (60 bp):
ACTAGCCACACCTTTTCCACCACCAACTCCACTAGCCACACCTTCTCCACCACCAAATCC
Found at i:28083633 original size:30 final size:30
Alignment explanation
Indices: 28083466--28083638 Score: 194
Period size: 30 Copynumber: 5.8 Consensus size: 30
28083456 ACTTTTCTCA
*
28083466 ACTAGCCACACCTT-TTCCACCACCAACTCC
1 ACTAGCCACA-CTTGCTCCACCACCAACTCC
*
28083496 ACTAGCCACACCTT-TTCCACCACCAACTCC
1 ACTAGCCACA-CTTGCTCCACCACCAACTCC
* **
28083526 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACTTGCTCCACCACCAACTCC
*
28083556 ACTAGCCACACCTT-CTCCACCACCAAATCC
1 ACTAGCCACA-CTTGCTCCACCACCAACTCC
** *
28083586 ACTAGCCACAC-TGCTCCATTACCTACTCC
1 ACTAGCCACACTTGCTCCACCACCAACTCC
*
28083615 ACTAACCACACTTGCTCCA-CACCA
1 ACTAGCCACACTTGCTCCACCACCA
28083639 CTTGTACCTA
Statistics
Matches: 128, Mismatches: 11, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
28 1 0.01
29 29 0.23
30 95 0.74
31 3 0.02
ACGTcount: A:0.27, C:0.48, G:0.04, T:0.21
Consensus pattern (30 bp):
ACTAGCCACACTTGCTCCACCACCAACTCC
Found at i:28084244 original size:25 final size:25
Alignment explanation
Indices: 28084216--28084359 Score: 87
Period size: 25 Copynumber: 5.6 Consensus size: 25
28084206 ATATTACGTA
* *
28084216 TATATATATTTTATACTATTTTATT
1 TATATATATTTAATACTATATTATT
* *
28084241 TATATATCTTTAATATTATATTATT
1 TATATATATTTAATACTATATTATT
* * *
28084266 TATATATATATT-TTTCTACATGTTATCT
1 TATATATAT-TTAATACT--ATATTAT-T
*
28084294 TATGTATATATCTT-A-ACTATATTATG
1 TA--TATATAT-TTAATACTATATTATT
* * *
28084320 TATATATTTTTAACACTATATTATG
1 TATATATATTTAATACTATATTATT
* *
28084345 TACATATTTTTAATA
1 TATATATATTTAATA
28084360 TTATCACGTA
Statistics
Matches: 94, Mismatches: 17, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
23 2 0.02
24 7 0.07
25 55 0.59
26 4 0.04
27 12 0.13
28 3 0.03
29 2 0.02
30 9 0.10
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (25 bp):
TATATATATTTAATACTATATTATT
Found at i:28084496 original size:16 final size:15
Alignment explanation
Indices: 28084477--28084556 Score: 52
Period size: 16 Copynumber: 4.7 Consensus size: 15
28084467 ATTTCTATTT
28084477 TATTTTTTATTTTCAA
1 TATTTTTTATTTT-AA
28084493 TATTAATTATTATTATTCTAA
1 TATT--TT-TTA-T-TT-TAA
*
28084514 TATTTTGATATTTTAA
1 TATTTT-TTATTTTAA
*
28084530 TATTTTATATTTTATA
1 TATTTTTTATTTTA-A
*
28084546 TATTTATTATT
1 TATTTTTTATT
28084557 CACATCATTG
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
15 8 0.15
16 23 0.43
17 2 0.04
18 3 0.06
19 7 0.13
20 1 0.02
21 8 0.15
22 1 0.02
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (15 bp):
TATTTTTTATTTTAA
Found at i:28084541 original size:7 final size:7
Alignment explanation
Indices: 28084513--28084552 Score: 53
Period size: 8 Copynumber: 5.3 Consensus size: 7
28084503 TATTATTCTA
28084513 ATATTTT
1 ATATTTT
28084520 GATATTTT
1 -ATATTTT
28084528 AATATTTT
1 -ATATTTT
28084536 ATATTTT
1 ATATTTT
28084543 ATATATTT
1 ATAT-TTT
28084551 AT
1 AT
28084553 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
7 11 0.37
8 19 0.63
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (7 bp):
ATATTTT
Found at i:28084552 original size:15 final size:15
Alignment explanation
Indices: 28084506--28084550 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
28084496 TAATTATTAT
*
28084506 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
28084522 TATTTTAATATTTTA
1 TATTTTAATATTTTA
28084537 TATTTTATATATTT
1 TATTTTA-ATATTT
28084551 ATTATTCACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 8 0.30
16 19 0.70
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:28086424 original size:17 final size:18
Alignment explanation
Indices: 28086404--28086438 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28086394 ATTTATTGGT
*
28086404 ATTAT-TAATTTTTTTAA
1 ATTATATAATTATTTTAA
28086421 ATTATATAATTATTTTAA
1 ATTATATAATTATTTTAA
28086439 GTTTTGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTATATAATTATTTTAA
Found at i:28087310 original size:15 final size:16
Alignment explanation
Indices: 28087284--28087313 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28087274 CTCTCAAACA
28087284 AAATTACAAAATAAAT
1 AAATTACAAAATAAAT
28087300 AAATT-CAAAATAAA
1 AAATTACAAAATAAA
28087314 CTTCAAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATTACAAAATAAAT
Found at i:28090393 original size:3 final size:3
Alignment explanation
Indices: 28090387--28090417 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
28090377 AGTATAAAAA
28090387 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
28090418 GAGTTTTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:28096163 original size:22 final size:22
Alignment explanation
Indices: 28096122--28096163 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28096112 AAAATACATT
* **
28096122 AATATTTTTTTTGTTTTTTAGG
1 AATATGTTTTTTGTAATTTAGG
28096144 AATATGTTTTTTGTAATTTA
1 AATATGTTTTTTGTAATTTA
28096164 TCAAGAGTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (22 bp):
AATATGTTTTTTGTAATTTAGG
Found at i:28104117 original size:9 final size:9
Alignment explanation
Indices: 28104103--28104142 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
28104093 TATAAGAGAG
28104103 CTCTCTAAA
1 CTCTCTAAA
28104112 CTCTCTAAA
1 CTCTCTAAA
28104121 CTCTCTAAA
1 CTCTCTAAA
28104130 --CTCTAAA
1 CTCTCTAAA
28104137 CTCTCT
1 CTCTCT
28104143 CTAAACTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.24
9 22 0.76
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (9 bp):
CTCTCTAAA
Found at i:28104133 original size:16 final size:17
Alignment explanation
Indices: 28104103--28104142 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
28104093 TATAAGAGAG
28104103 CTCTCTAAACTCTCTAAA
1 CTCTCTAAAC-CTCTAAA
28104121 CTCTCTAAA-CTCTAAA
1 CTCTCTAAACCTCTAAA
28104137 CTCTCT
1 CTCTCT
28104143 CTAAACTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 13 0.59
18 9 0.41
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (17 bp):
CTCTCTAAACCTCTAAA
Found at i:28118022 original size:29 final size:29
Alignment explanation
Indices: 28117980--28118042 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
28117970 GGCCTAGATT
* * *
28117980 GTGTGTCATACATGACCTGTCACACTGCC
1 GTGTGTCACACATGACCTGGCACACGGCC
* *
28118009 GTGTGTCGCACATGGCCTGGCACACGGCC
1 GTGTGTCACACATGACCTGGCACACGGCC
28118038 GTGTG
1 GTGTG
28118043 GCATCGATAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (29 bp):
GTGTGTCACACATGACCTGGCACACGGCC
Found at i:28121197 original size:15 final size:15
Alignment explanation
Indices: 28121172--28121213 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
28121162 AAGCTAATAT
28121172 AAAAG-ATTTTGAGA
1 AAAAGAATTTTGAGA
*
28121186 AAAAGAATTTTGCGA
1 AAAAGAATTTTGAGA
28121201 AAAAGAATTTTGA
1 AAAAGAATTTTGA
28121214 CTTGCATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.50, C:0.02, G:0.19, T:0.29
Consensus pattern (15 bp):
AAAAGAATTTTGAGA
Found at i:28130674 original size:25 final size:24
Alignment explanation
Indices: 28130646--28130743 Score: 92
Period size: 25 Copynumber: 4.0 Consensus size: 24
28130636 ATAAGCTATG
* *
28130646 AATCGATATGCTCTCACGAGCTGTA
1 AATCGGTAAGCTCTCACGAGCTG-A
28130671 AATCGGTAAGCTCAT-ACGAGCTGA
1 AATCGGTAAGCTC-TCACGAGCTGA
* *
28130695 GAATTGGTAAGCTCTCATGAGCTGCA
1 -AATCGGTAAGCTCTCACGAGCTG-A
*
28130721 AATCGGTAATCTCAT-ACGAGCTG
1 AATCGGTAAGCTC-TCACGAGCTG
28130744 TGGTGTGTCT
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
24 2 0.03
25 56 0.92
26 3 0.05
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (24 bp):
AATCGGTAAGCTCTCACGAGCTGA
Found at i:28137523 original size:37 final size:37
Alignment explanation
Indices: 28137476--28137551 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
28137466 AGTAATAGCT
*
28137476 TTTCCATGTATTTCATGTATATATATACCTATAATAG
1 TTTCCATGTATTTCATGTATATATATACCTACAATAG
*
28137513 TTTCCATGTATTTCATGTATATATATACCTGCAATAG
1 TTTCCATGTATTTCATGTATATATATACCTACAATAG
28137550 TT
1 TT
28137552 CCTATCAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.46
Consensus pattern (37 bp):
TTTCCATGTATTTCATGTATATATATACCTACAATAG
Found at i:28137747 original size:25 final size:25
Alignment explanation
Indices: 28137678--28137791 Score: 83
Period size: 25 Copynumber: 4.6 Consensus size: 25
28137668 ATGCACGTAT
* * *
28137678 GCTCATACGAGCTATGAAA-AGGTAT
1 GCTCATACGAGCTA-CAAATCGGTAA
* * *
28137703 GCTC-TAACAAGCTATAAATCAGTAA
1 GCTCAT-ACGAGCTACAAATCGGTAA
*
28137728 GCTCATACGAGCTGA-GAATCGGTAA
1 GCTCATACGAGCT-ACAAATCGGTAA
* *
28137753 GCTC-TCATGAACTACAAATCGGTAA
1 GCTCAT-ACGAGCTACAAATCGGTAA
28137778 GCTCATACGAGCTA
1 GCTCATACGAGCTA
28137792 TGGTGTGTCC
Statistics
Matches: 69, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
24 6 0.09
25 60 0.87
26 3 0.04
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (25 bp):
GCTCATACGAGCTACAAATCGGTAA
Found at i:28137757 original size:50 final size:50
Alignment explanation
Indices: 28137678--28137793 Score: 137
Period size: 50 Copynumber: 2.3 Consensus size: 50
28137668 ATGCACGTAT
* *
28137678 GCTCATACGAGCTATGAAAAGGTATGCTCT-AACAAGCTATAAATCAGTAA
1 GCTCATACGAGCTATGAAAAGGTAAGCTCTCAACAA-CTACAAATCAGTAA
** ** *
28137728 GCTCATACGAGCTGA-GAATCGGTAAGCTCTCATGAACTACAAATCGGTAA
1 GCTCATACGAGCT-ATGAAAAGGTAAGCTCTCAACAACTACAAATCAGTAA
28137778 GCTCATACGAGCTATG
1 GCTCATACGAGCTATG
28137794 GTGTGTCCGC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
49 1 0.02
50 51 0.91
51 4 0.07
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (50 bp):
GCTCATACGAGCTATGAAAAGGTAAGCTCTCAACAACTACAAATCAGTAA
Found at i:28141970 original size:121 final size:121
Alignment explanation
Indices: 28141814--28142055 Score: 387
Period size: 121 Copynumber: 2.0 Consensus size: 121
28141804 TAGGGCGAGA
* * * *
28141814 CTATTATTGTTTTCTCGATGGATACTTGTGGTATAATCAGATTATAGTAGCGCTAGAAGATCAAC
1 CTATTACTATTTTCTCAATGGATACTTGTGGTATAATCAGATTATAATAGCGCTAGAAGATCAAC
* *
28141879 AAAAAACAACATTCACATGCCCATACGATACATTTGCACTTAGACGCATGTCATTT
66 AAAAAACAACATTCACATGCCCATACGATACACTTGCACTTAGACGCATGCCATTT
*
28141935 CTATTACTATTTTCTCAATGGATACTTG-GGATATAATCAGATTATAATTGCGCTAGAAGATCAA
1 CTATTACTATTTTCTCAATGGATACTTGTGG-TATAATCAGATTATAATAGCGCTAGAAGATCAA
* *
28141999 CACAAAACAACATTCACATGCCCATACGATACACTTGCATTTAGACGCATGCCATTT
65 CAAAAAACAACATTCACATGCCCATACGATACACTTGCACTTAGACGCATGCCATTT
28142056 GGTTTATATA
Statistics
Matches: 111, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
120 2 0.02
121 109 0.98
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (121 bp):
CTATTACTATTTTCTCAATGGATACTTGTGGTATAATCAGATTATAATAGCGCTAGAAGATCAAC
AAAAAACAACATTCACATGCCCATACGATACACTTGCACTTAGACGCATGCCATTT
Found at i:28146550 original size:17 final size:17
Alignment explanation
Indices: 28146528--28146561 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28146518 ATGACTCAAT
28146528 GAGAAGCACTCTTACGA
1 GAGAAGCACTCTTACGA
28146545 GAGAAGCACTCTTACGA
1 GAGAAGCACTCTTACGA
28146562 AAATATTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (17 bp):
GAGAAGCACTCTTACGA
Found at i:28148293 original size:28 final size:28
Alignment explanation
Indices: 28148233--28148287 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
28148223 AATATAATAT
*
28148233 AATTA-TAAAATATTTAAATTTTACTTA
1 AATTATTAAAATATTTAAATTTTAATTA
28148260 AATTATTAAAATA-TTAAATTTTAATTA
1 AATTATTAAAATATTTAAATTTTAATTA
28148287 A
1 A
28148288 TTTTATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
AATTATTAAAATATTTAAATTTTAATTA
Found at i:28151523 original size:17 final size:16
Alignment explanation
Indices: 28151491--28151540 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
28151481 TTTCAAAAAG
*
28151491 AAAAAAACAAATAAATA
1 AAAAAAATAAA-AAATA
28151508 AATAAAAATAAAAAATA
1 AA-AAAAATAAAAAATA
*
28151525 AAACCAAATAAAAAAT
1 AAA-AAAATAAAAAAT
28151541 TAAAGGTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 1 0.03
17 20 0.69
18 8 0.28
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAAAAATAAAAAATA
Found at i:28153210 original size:17 final size:17
Alignment explanation
Indices: 28153176--28153213 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
28153166 AGTTATTCAC
*
28153176 TTTTATTTTATTTCATT
1 TTTTATTTTATTTAATT
28153193 TTTTAATTTT-TTTAATT
1 TTTT-ATTTTATTTAATT
28153210 TTTT
1 TTTT
28153214 TTAAATCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTATTTTATTTAATT
Found at i:28164238 original size:37 final size:37
Alignment explanation
Indices: 28164188--28164266 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
28164178 TTATTACGAA
* * *
28164188 GTCTTACCTGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
* *
28164225 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCTG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
28164262 GTCTT
1 GTCTT
28164267 TAGAGCTCGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
37 34 0.94
38 2 0.06
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:28164463 original size:47 final size:47
Alignment explanation
Indices: 28164385--28164989 Score: 924
Period size: 47 Copynumber: 13.1 Consensus size: 47
28164375 CCCTTCGGGA
* * * * * * *
28164385 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28164432 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28164479 CTTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28164526 CTTATTACATATATACACTTTCACATTCATCACAT----C----GG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28164564 C-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
28164610 CTTATTACATATATACACTTTCACATTCATCACATCAGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28164657 CTTATCACATATATACACGTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28164704 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28164751 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28164798 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28164845 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28164892 CTTATCAAATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28164939 CTTATCACATATTTACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28164986 CTTA
1 CTTA
28164990 CTATCATTTC
Statistics
Matches: 519, Mismatches: 29, Indels: 20
0.91 0.05 0.04
Matches are distributed among these distances:
37 32 0.06
38 1 0.00
39 2 0.00
41 1 0.00
43 1 0.00
45 2 0.00
46 1 0.00
47 479 0.92
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28170392 original size:88 final size:88
Alignment explanation
Indices: 28170294--28170651 Score: 434
Period size: 88 Copynumber: 4.1 Consensus size: 88
28170284 GTGGAGTAGG
* * *
28170294 TCGAAGACACTCGCCTTGCCTCCTTGGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCT
1 TCGAAGACACTAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGATAGCAGATCTTGCCT
* * *
28170359 TCCTATACTGACTGTGAAACAGA
66 TCCTATACTGACAGCGAAGCAGA
* * * *
28170382 TCGAAGACACTAGACTTGCCTCCCTGGGTTGCAGCGGAGTAGGTTAAAAATAGCAGATCTTGCCT
1 TCGAAGACACTAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGATAGCAGATCTTGCCT
28170447 TCCTGCAT-C-GACAGCGAAGCAGA
66 TCCT--ATACTGACAGCGAAGCAGA
* *
28170470 TCGAAGACACTAGCCTTTCCTCCCTGGGTTGCAGCAGAGCAGGTTGAAGATAGCAGATCTTGCCT
1 TCGAAGACACTAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGATAGCAGATCTTGCCT
** * *
28170535 TCCTGCAATGGCAGCGAAGCAGA
66 TCCTATACTGACAGCGAAGCAGA
* * * * *
28170558 TCAAAGACACCAGCCTTGCCTCCCTGGGTTGCAGTGGAGCAGGTTGAA-AGCACCAGATCTTGCC
1 TCGAAGACACTAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGA-TAGCAGATCTTGCC
* * * **
28170622 TTCTTGTACTGTCAATGAAGCAGA
65 TTCCTATACTGACAGCGAAGCAGA
28170646 TCGAAG
1 TCGAAG
28170652 CCAATAATCC
Statistics
Matches: 231, Mismatches: 34, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
87 1 0.00
88 227 0.98
89 1 0.00
90 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.23
Consensus pattern (88 bp):
TCGAAGACACTAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGATAGCAGATCTTGCCT
TCCTATACTGACAGCGAAGCAGA
Found at i:28170620 original size:44 final size:44
Alignment explanation
Indices: 28170308--28170622 Score: 170
Period size: 44 Copynumber: 7.2 Consensus size: 44
28170298 AGACACTCGC
* * * *
28170308 CTTGCCTCCTTGGGTTGCAGTGGAGCAGGTTGAAGATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGACACCAGAT
* **** * * * * * * *
28170352 CTTGCCTTCCTATACTGACTGTGAAACAGATCGAAGACACTAGA-
1 CTTGCCTCCCTGGGTTG-CAGCGGAGCAGGTTGAAGACACCAGAT
* * * * *
28170396 CTTGCCTCCCTGGGTTGCAGCGGAGTAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGACACCAGAT
* ** * * * * * *
28170440 CTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACTAG-C
1 CTTGCCTCCCTGGGTTG-CAGCGGAGCAGGTTGAAGACACCAGAT
* * * *
28170484 CTTTCCTCCCTGGGTTGCAGCAGAGCAGGTTGAAGATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGACACCAGAT
* ** * * * ** *
28170528 CTTGCCTTCCTGCAATGGCAGCGAAGCAGATCAAAGACACCAG-C
1 CTTGCCTCCCTG-GGTTGCAGCGGAGCAGGTTGAAGACACCAGAT
*
28170572 CTTGCCTCCCTGGGTTGCAGTGGAGCAGGTTGAA-AGCACCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGA-CACCAGAT
28170616 CTTGCCT
1 CTTGCCT
28170623 TCTTGTACTG
Statistics
Matches: 183, Mismatches: 81, Indels: 14
0.66 0.29 0.05
Matches are distributed among these distances:
42 1 0.01
43 52 0.28
44 76 0.42
45 54 0.30
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (44 bp):
CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTGAAGACACCAGAT
Found at i:28170789 original size:44 final size:45
Alignment explanation
Indices: 28170740--28170844 Score: 122
Period size: 44 Copynumber: 2.4 Consensus size: 45
28170730 TGGATCACAT
*
28170740 CAAGTCTTATTTCCCTGAGGTTACAGCGGAGCAAACTGAGAA-AG
1 CAAGTCTTATTTCCCTGAAGTTACAGCGGAGCAAACTGAGAATAG
** * * * *
28170784 CAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAGAATAG
1 CAAGTCTTATTTCCCTGAAGTTACAGCGGAGCAAACTGAGAATAG
* *
28170829 CAAATCTTACTTCCCT
1 CAAGTCTTATTTCCCT
28170845 AACGGTGTAG
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
44 35 0.71
45 14 0.29
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.25
Consensus pattern (45 bp):
CAAGTCTTATTTCCCTGAAGTTACAGCGGAGCAAACTGAGAATAG
Found at i:28170999 original size:44 final size:44
Alignment explanation
Indices: 28170936--28171084 Score: 162
Period size: 44 Copynumber: 3.5 Consensus size: 44
28170926 TTACAAATCC
*
28170936 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCT
* ** *** * *
28170980 TATCTCTCT-AGAGTTGCAGTAGAGTAGA-TCGCAT-CATG-TCT
1 TATCTCTCTGA-AGTTGCAGTGGAGCGGATTAAAATAAAAGATCT
*
28171021 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCT
*
28171065 TATCTTTCTGAAGTTGCAGT
1 TATCTCTCTGAAGTTGCAGT
28171085 AGAGTAGATC
Statistics
Matches: 80, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
41 25 0.31
42 6 0.08
43 6 0.08
44 43 0.54
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Consensus pattern (44 bp):
TATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCT
Found at i:28171036 original size:41 final size:41
Alignment explanation
Indices: 28170977--28171124 Score: 154
Period size: 41 Copynumber: 3.5 Consensus size: 41
28170967 AAATAAAAGA
*
28170977 TCTTATCTCTCT-AGAGTTGCAGTAGAGTAGATCGCATCATG
1 TCTTATCTCTCTGA-AGTTGCAGTAGAGTAGATCGCATCAAG
* * ** *** *
28171018 TCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAG
1 TCTTATCTCTCTGAAGTTGCAGTAGAGTAGA-TCGCAT-CAAG
* *
28171061 ATCTTATCTTTCTGAAGTTGCAGTAGAGTAGATCGCATCAGG
1 -TCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAAG
28171103 TCTTATCTCTCTGAAGTTGCAG
1 TCTTATCTCTCTGAAGTTGCAG
28171125 CGGAGCAGAC
Statistics
Matches: 83, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
41 46 0.55
42 6 0.07
43 5 0.06
44 26 0.31
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (41 bp):
TCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAAG
Found at i:28171080 original size:85 final size:85
Alignment explanation
Indices: 28170936--28171130 Score: 338
Period size: 85 Copynumber: 2.3 Consensus size: 85
28170926 TTACAAATCC
28170936 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTAGAGTTGCAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTAGAGTTGCAGTA
*
28171001 GAGTAGATCGCATCATGTCT
66 GAGTAGATCGCATCAGGTCT
*
28171021 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTTTCT-GAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTAG-AGTTGCAGT
28171085 AGAGTAGATCGCATCAGGTCT
65 AGAGTAGATCGCATCAGGTCT
* *
28171106 TATCTCTCTGAAGTTGCAGCGGAGC
1 TATCTCCCTGAAGTTGCAGTGGAGC
28171131 AGACCGAAGA
Statistics
Matches: 105, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
84 1 0.01
85 104 0.99
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (85 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTAGAGTTGCAGTA
GAGTAGATCGCATCAGGTCT
Found at i:28171370 original size:173 final size:172
Alignment explanation
Indices: 28171149--28171570 Score: 655
Period size: 173 Copynumber: 2.4 Consensus size: 172
28171139 GAATTACAGA
** * * *
28171149 TCTTATCTCCCTAAGCAGTAGCAGAGCAAATCAAAGATGACAGATCTTATCTCCCTAAGCAGTAG
1 TCTTATCTCCCTAAGTTGCAGCAGAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAGTAG
28171214 TGGAGCAGATTGTAGCCAGTAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAATAAAAG
66 TGGAGCAGATTGTAGCCAGTAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAATAAAAG
* *
28171279 ATATTATCTCTCTAGAGTTGCAGTAGAGTAGATCGCATCATG
131 ATATTATCTCTCTAGAGTTGCAGTAGAGTAGATCACATCAGG
*
28171321 TCTTATCTCCCTAAAGTTGCAGCAGAGCAGATCGAAGATGGCAGATCTTATCTCCCTAAGCAGTA
1 TCTTATCTCCCT-AAGTTGCAGCAGAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAGTA
* *
28171386 GTGGAACAGATTGTAGCCAGTAATCCTATCTCCCTGAAGTTGTAGTGGAGCGTATTAAAATAAAA
65 GTGGAGCAGATTGTAGCCAGTAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAATAAAA
* *
28171451 GATCTTATCTCTCTGGAGTTGCAGTAGAGTAGATCACATCAGG
130 GATATTATCTCTCTAGAGTTGCAGTAGAGTAGATCACATCAGG
* * * * *
28171494 TCTTATCTCTCTGAAGTTGCAGCGGAGCAGACCGAAGAATTACAGATATTATCTCCCTAAGCAGT
1 TCTTATCTCCCT-AAGTTGCAGCAGAGCAGATCGAAG-ATGACAGATCTTATCTCCCTAAGCAGT
*
28171559 AGCGGAGCAGAT
64 AGTGGAGCAGAT
28171571 CGAAGATGGC
Statistics
Matches: 227, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
172 12 0.05
173 181 0.80
174 34 0.15
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (172 bp):
TCTTATCTCCCTAAGTTGCAGCAGAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAGTAG
TGGAGCAGATTGTAGCCAGTAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAATAAAAG
ATATTATCTCTCTAGAGTTGCAGTAGAGTAGATCACATCAGG
Found at i:28171598 original size:218 final size:218
Alignment explanation
Indices: 28171345--28171960 Score: 980
Period size: 218 Copynumber: 2.8 Consensus size: 218
28171335 AGTTGCAGCA
*
28171345 GAGCAGATCGAAGATGGCAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATTGTAGCCAGTAAT
1 GAGCAGATCGAAGATGGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGTAGCCAGTAAT
* * *
28171410 CCTATCTCCCTGAAGTTGTAGTGGAGCGTATTAAAATAAAAGATCTTATCTCTCTGGAGTTGCAG
66 CCTATCTCCCTGAAGTTGAAGTGGAGCGAATTAAAATAAAAGATCTTATCTCTCTGAAGTTGCAG
* *
28171475 TAGAGTAGATCACATCAGGTCTTATCTCTCTGAAGTTGCAGCGGAGCAGACCGAAGAATTACAGA
131 TAGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACCGAAGAATTACAGA
28171540 TATTATCTCCCTAAGCAGTAGCG
196 TATTATCTCCCTAAGCAGTAGCG
*
28171563 GAGCAGATCGAAGATGGCAGATCTAATCTCCCTAAGCAGTAGTGGAGCAGATTGTAGCCAGTAAT
1 GAGCAGATCGAAGATGGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGTAGCCAGTAAT
* * *
28171628 CCTATCTCCCTGAAGTTAAAGTGGAGCGAATTAAAATAAAAGATATTATCTCTCTAAAGTTGCAG
66 CCTATCTCCCTGAAGTTGAAGTGGAGCGAATTAAAATAAAAGATCTTATCTCTCTGAAGTTGCAG
*
28171693 TAGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGAATTACAGA
131 TAGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACCGAAGAATTACAGA
* * * *
28171758 TCTTATCTCCTTAAGCATTAGTG
196 TATTATCTCCCTAAGCAGTAGCG
* * * * * * *
28171781 GAGCAGATTGAAGATGACAAATCTTATCTCCCTAAGCAGTAGTAGAGCAGATTGAAACTAGTAAT
1 GAGCAGATCGAAGATGGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGTAGCCAGTAAT
* * * * *
28171846 CCTATCTCTCTGAAGTTGCAGTGGAGTGGATTAAAATAAAAGATCTTATCTCTCTGAAGTGGCAG
66 CCTATCTCCCTGAAGTTGAAGTGGAGCGAATTAAAATAAAAGATCTTATCTCTCTGAAGTTGCAG
*
28171911 TAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGA
131 TAGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGA
28171961 TCAAGGAAGC
Statistics
Matches: 366, Mismatches: 32, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
218 366 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (218 bp):
GAGCAGATCGAAGATGGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGTAGCCAGTAAT
CCTATCTCCCTGAAGTTGAAGTGGAGCGAATTAAAATAAAAGATCTTATCTCTCTGAAGTTGCAG
TAGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACCGAAGAATTACAGA
TATTATCTCCCTAAGCAGTAGCG
Found at i:28171599 original size:44 final size:45
Alignment explanation
Indices: 28171514--28171614 Score: 141
Period size: 44 Copynumber: 2.3 Consensus size: 45
28171504 CTGAAGTTGC
* * *
28171514 AGCGGAGCAGACCGAAGAATTACAGATATTATCTCCCTAAGCAGT
1 AGCGGAGCAGATCGAAGAATGACAGATATAATCTCCCTAAGCAGT
* *
28171559 AGCGGAGCAGATCGAAG-ATGGCAGATCTAATCTCCCTAAGCAGT
1 AGCGGAGCAGATCGAAGAATGACAGATATAATCTCCCTAAGCAGT
*
28171603 AGTGGAGCAGAT
1 AGCGGAGCAGAT
28171615 TGTAGCCAGT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
44 34 0.68
45 16 0.32
ACGTcount: A:0.34, C:0.21, G:0.27, T:0.19
Consensus pattern (45 bp):
AGCGGAGCAGATCGAAGAATGACAGATATAATCTCCCTAAGCAGT
Found at i:28171742 original size:391 final size:392
Alignment explanation
Indices: 28171021--28171790 Score: 1310
Period size: 391 Copynumber: 2.0 Consensus size: 392
28171011 CATCATGTCT
*
28171021 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTTTCTGAAGTTGCAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTGCAGTA
* *
28171086 GAGTAGATCGCATCAGGTCTTATCTCTCTGAAGTTGCAGCGGAGCAGACCGAAGAATTACAGATC
66 GAGTAGATCACATCAGGTCTTATCTCTCTGAAGTTGCAGCGGAGCAGACCGAAGAATTACAGATA
*
28171151 TTATCTCCCTAAGCAGTAGCAGAGCAAATCAAAGATGACAGATCTTATCTCCCTAAGCAGTAGTG
131 TTATCTCCCTAAGCAGTAGCAGAGCAAATCAAAGATGACAGATCTAATCTCCCTAAGCAGTAGTG
** *
28171216 GAGCAGATTGTAGCCAGTAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAATAAAAGAT
196 GAGCAGATTGTAGCCAGTAATCCTATCTCCCTGAAGTTAAAGTGGAGCGAATTAAAATAAAAGAT
* *
28171281 ATTATCTCTCTAGAGTTGCAGTAGAGTAGATCGCATCATGTCTTATCTCCCTAAAGTTGCAGCAG
261 ATTATCTCTCTAAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTAAAGTTGCAGCAG
*
28171346 AGCAGA-TCGAAG-ATGGCAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATTGTAGCCAGTAA
326 AGCAGACT-GAAGAATGACAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATTGTAGCCAGTAA
28171409 TCC
390 TCC
* * *
28171412 TATCTCCCTGAAGTTGTAGTGGAGCGTATTAAAATAAAAGATCTTATCTCTCTGGAGTTGCAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTGCAGTA
28171477 GAGTAGATCACATCAGGTCTTATCTCTCTGAAGTTGCAGCGGAGCAGACCGAAGAATTACAGATA
66 GAGTAGATCACATCAGGTCTTATCTCTCTGAAGTTGCAGCGGAGCAGACCGAAGAATTACAGATA
* * * *
28171542 TTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCAGATCTAATCTCCCTAAGCAGTAGTG
131 TTATCTCCCTAAGCAGTAGCAGAGCAAATCAAAGATGACAGATCTAATCTCCCTAAGCAGTAGTG
28171607 GAGCAGATTGTAGCCAGTAATCCTATCTCCCTGAAGTTAAAGTGGAGCGAATTAAAATAAAAGAT
196 GAGCAGATTGTAGCCAGTAATCCTATCTCCCTGAAGTTAAAGTGGAGCGAATTAAAATAAAAGAT
* *
28171672 ATTATCTCTCTAAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGG
261 ATTATCTCTCTAAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTAAAGTTGCAGCAG
* * * *
28171737 AGCAGACTGAAGAATTACAGATCTTATCTCCTTAAGCATTAGTGGAGCAGATTG
326 AGCAGACTGAAGAATGACAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATTG
28171791 AAGATGACAA
Statistics
Matches: 354, Mismatches: 23, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
391 317 0.90
392 37 0.10
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (392 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTGCAGTA
GAGTAGATCACATCAGGTCTTATCTCTCTGAAGTTGCAGCGGAGCAGACCGAAGAATTACAGATA
TTATCTCCCTAAGCAGTAGCAGAGCAAATCAAAGATGACAGATCTAATCTCCCTAAGCAGTAGTG
GAGCAGATTGTAGCCAGTAATCCTATCTCCCTGAAGTTAAAGTGGAGCGAATTAAAATAAAAGAT
ATTATCTCTCTAAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTAAAGTTGCAGCAG
AGCAGACTGAAGAATGACAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATTGTAGCCAGTAAT
CC
Found at i:28171817 original size:44 final size:45
Alignment explanation
Indices: 28171712--28171836 Score: 144
Period size: 44 Copynumber: 2.8 Consensus size: 45
28171702 TCGCATCAGG
** * * * * *
28171712 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGAATTACAGA
1 TCTTATCTCCCT-AAGCAGTAGTGGAGCAGATTGAAGAATGACAAA
* *
28171758 TCTTATCTCCTTAAGCATTAGTGGAGCAGATTGAAG-ATGACAAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAATGACAAA
*
28171802 TCTTATCTCCCTAAGCAGTAGTAGAGCAGATTGAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAA
28171837 ACTAGTAATC
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
44 38 0.57
45 18 0.27
46 11 0.16
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (45 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAATGACAAA
Found at i:28172280 original size:17 final size:18
Alignment explanation
Indices: 28172250--28172283 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28172240 TCAAAAAGAA
28172250 AAAAACAAATAAATAAAT
1 AAAAACAAATAAATAAAT
*
28172268 AAAAATAAA-AAATAAA
1 AAAAACAAATAAATAAA
28172284 GCCAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAAACAAATAAATAAAT
Found at i:28177570 original size:49 final size:49
Alignment explanation
Indices: 28177498--28177595 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
28177488 ATTTGGGAAC
*
28177498 GTCAGAAATAGATAAGTTTTTGTAATGCTCCCCTACTTTCCTATTACTT
1 GTCAGAAATAGATAAGTTTTTGTAATGCTCCCCTACTTTCATATTACTT
28177547 GTCAGAAATAGATAAGTTTTTGTAATGCTCCCCTACTTTCATATTACTT
1 GTCAGAAATAGATAAGTTTTTGTAATGCTCCCCTACTTTCATATTACTT
28177596 TCCTTGTTCG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (49 bp):
GTCAGAAATAGATAAGTTTTTGTAATGCTCCCCTACTTTCATATTACTT
Found at i:28189481 original size:17 final size:18
Alignment explanation
Indices: 28189459--28189496 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
28189449 ATATTTAGTC
28189459 ATATAATAAATTA-TTTA
1 ATATAATAAATTATTTTA
**
28189476 ATATAATTTATTATTTTA
1 ATATAATAAATTATTTTA
28189494 ATA
1 ATA
28189497 AATTATTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATAATAAATTATTTTA
Found at i:28189485 original size:30 final size:30
Alignment explanation
Indices: 28189451--28189509 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
28189441 AATTATTTAT
28189451 ATTTAGTCA-TATAATAAATTATTTAATATA
1 ATTTA-TCATTATAATAAATTATTTAATATA
* * *
28189481 ATTTATTATTTTAATAAATTATTTGATAT
1 ATTTATCATTATAATAAATTATTTAATAT
28189510 TTCAATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (30 bp):
ATTTATCATTATAATAAATTATTTAATATA
Found at i:28189500 original size:17 final size:17
Alignment explanation
Indices: 28189468--28189500 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28189458 CATATAATAA
28189468 ATTATTTAATATAATTT
1 ATTATTTAATATAATTT
28189485 ATTATTTTAATA-AATT
1 ATTA-TTTAATATAATT
28189501 ATTTGATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTATTTAATATAATTT
Found at i:28189606 original size:15 final size:15
Alignment explanation
Indices: 28189588--28189644 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
28189578 TATCAATATT
28189588 AATATTTTAATAATA
1 AATATTTTAATAATA
*
28189603 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
28189622 AATATATTAATAATA
1 AATATTTTAATAATA
*
28189637 AATGTTTT
1 AATATTTT
28189645 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:28191137 original size:26 final size:26
Alignment explanation
Indices: 28191108--28191158 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
28191098 GGGTTTTATT
*
28191108 CTTGTAGACTAAGAAACTAAAATTAA
1 CTTGTAGAATAAGAAACTAAAATTAA
* *
28191134 CTTGTAGAATAAGAACCTATAATTA
1 CTTGTAGAATAAGAAACTAAAATTA
28191159 GGGTAACTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (26 bp):
CTTGTAGAATAAGAAACTAAAATTAA
Found at i:28194354 original size:13 final size:13
Alignment explanation
Indices: 28194338--28194362 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28194328 CAAAATGTAC
28194338 AATATAAATAAAT
1 AATATAAATAAAT
28194351 AATATAAATAAA
1 AATATAAATAAA
28194363 ATAAAATAAT
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:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATATAAATAAAT
Found at i:28195066 original size:26 final size:26
Alignment explanation
Indices: 28195037--28195086 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
28195027 TTTTTTTGGC
28195037 TTCATAAGCAAGCCCTGACTTTTGCT
1 TTCATAAGCAAGCCCTGACTTTTGCT
28195063 TTCATAAGCAAGCCCTGACTTTTG
1 TTCATAAGCAAGCCCTGACTTTTG
28195087 TTGTCCCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (26 bp):
TTCATAAGCAAGCCCTGACTTTTGCT
Found at i:28204954 original size:67 final size:67
Alignment explanation
Indices: 28204883--28205067 Score: 271
Period size: 67 Copynumber: 2.7 Consensus size: 67
28204873 TACCTGACAT
* * *
28204883 CATAGCCCAGCTATGGTCTTACACAGTATACCCTATGTTTAATGTCTTGGCGGACTTCTTTTGTT
1 CATAGCCTAGCTATGGTCTTACACAGTATACCCTATGTTTAATGTCCTGGCGGACTTCCTTTGTT
28204948 GC
66 GC
* * *
28204950 CATAGTCTAGCTATGGTCTTACACAATATACCCTATGTTTAATGTCCTGGTGGACTTCCTTTGTT
1 CATAGCCTAGCTATGGTCTTACACAGTATACCCTATGTTTAATGTCCTGGCGGACTTCCTTTGTT
28205015 GC
66 GC
* * *
28205017 CATAGCCTAGCTATGTTCTTACATAGTATATACCCCATGTTTAATGTCCTG
1 CATAGCCTAGCTATGGTCTTACACAG--TATACCCTATGTTTAATGTCCTG
28205068 ACGGGCTCTT
Statistics
Matches: 105, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
67 83 0.79
69 22 0.21
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (67 bp):
CATAGCCTAGCTATGGTCTTACACAGTATACCCTATGTTTAATGTCCTGGCGGACTTCCTTTGTT
GC
Found at i:28211921 original size:17 final size:16
Alignment explanation
Indices: 28211896--28211941 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
28211886 GACAACCCAA
28211896 TTTTAT-TTTTATTTT
1 TTTTATATTTTATTTT
*
28211911 TTTTATATTTTA-CTT
1 TTTTATATTTTATTTT
*
28211926 TTTTCTATTTTATTTT
1 TTTTATATTTTATTTT
28211942 CTTGCATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 19 0.73
16 7 0.27
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTATATTTTATTTT
Found at i:28220061 original size:79 final size:82
Alignment explanation
Indices: 28219950--28220134 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
28219940 GCTACTCGTT
* * *
28219950 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
28220013 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
28220030 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
28220093 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
28220110 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28220135 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:28220134 original size:40 final size:40
Alignment explanation
Indices: 28219931--28220134 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
28219921 CGGAATTTAA
** *
28219931 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
28219971 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
28220011 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
28220050 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
28220090 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
28220130 CCGGA
1 CCGGA
28220135 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:28227954 original size:39 final size:39
Alignment explanation
Indices: 28227907--28228088 Score: 192
Period size: 39 Copynumber: 4.6 Consensus size: 39
28227897 GCTACTCGTT
*
28227907 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTT-TAGTAACTCGCA
* *
28227947 C-ATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTTAGTAACTCGCA
** *
28227986 CAAATGCCTTC-GGACTTAGCCCGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTTAGTAACTCGCA
* * * * *
28228024 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGG-TTTAGTAAC-TCGCA
28228065 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
28228089 ACATCATTCA
Statistics
Matches: 119, Mismatches: 17, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
38 26 0.22
39 52 0.44
40 30 0.25
41 11 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTTAGTAACTCGCA
Found at i:28232324 original size:50 final size:50
Alignment explanation
Indices: 28232265--28232365 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
28232255 AATTACGAAC
28232265 CAAACACAAAACCAAAAATGATTTATTAGTTTCAGTAAGAAAGTAATTCT
1 CAAACACAAAACCAAAAATGATTTATTAGTTTCAGTAAGAAAGTAATTCT
*
28232315 CAAACACAAAACCAAAAATGATTTATTAGTTTTAGTAAGAAAGTAATTCT
1 CAAACACAAAACCAAAAATGATTTATTAGTTTCAGTAAGAAAGTAATTCT
28232365 C
1 C
28232366 TCTCAATAGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.29
Consensus pattern (50 bp):
CAAACACAAAACCAAAAATGATTTATTAGTTTCAGTAAGAAAGTAATTCT
Found at i:28235414 original size:27 final size:28
Alignment explanation
Indices: 28235329--28235426 Score: 162
Period size: 28 Copynumber: 3.5 Consensus size: 28
28235319 TAAATTGTAC
28235329 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
*
28235357 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
*
28235385 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
*
28235412 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28235427 GACTTAATAT
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
27 23 0.34
28 44 0.66
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGCTTGATTATGT
Found at i:28235437 original size:27 final size:27
Alignment explanation
Indices: 28235329--28235439 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 27
28235319 TAAATTGTAC
* *
28235329 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* * *
28235357 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
28235385 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
28235412 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
28235439 A
1 A
28235440 CTTTTGAATC
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
27 29 0.38
28 47 0.62
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:28237592 original size:24 final size:24
Alignment explanation
Indices: 28237564--28237751 Score: 87
Period size: 24 Copynumber: 7.6 Consensus size: 24
28237554 ATATAATAAA
28237564 AAGCTCATAAGAGCCATAATCGAG
1 AAGCTCATAAGAGCCATAATCGAG
** *
28237588 AAGCTCATGCGAGCCAATAA-CGGG
1 AAGCTCATAAGAGCC-ATAATCGAG
* ** *
28237612 TAGCTCCGAAGAGCCATTAA-CGTG
1 AAGCTCATAAGAGCCA-TAATCGAG
* *
28237636 AAGCTC-TAGATAGCCATATATCGGG
1 AAGCTCATA-AGAGCCATA-ATCGAG
*** * *
28237661 AAGCTCCGGAGAGCGATTAAT-TAGG
1 AAGCTCATAAGAGCCA-TAATCGA-G
* *
28237686 AAGCTCACAAAGAGCCTTTAATCGAG
1 AAGCTCA-TAAGAGCC-ATAATCGAG
* *
28237712 AAGCTCATGAAGAGCCATATAACGGG
1 AAGCTCAT-AAGAGCCATA-ATCGAG
*
28237738 ACGCTCATAAGAGC
1 AAGCTCATAAGAGC
28237752 TGTGGTGTGC
Statistics
Matches: 121, Mismatches: 30, Indels: 25
0.69 0.17 0.14
Matches are distributed among these distances:
23 4 0.03
24 44 0.36
25 35 0.29
26 37 0.31
27 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (24 bp):
AAGCTCATAAGAGCCATAATCGAG
Found at i:28240751 original size:43 final size:43
Alignment explanation
Indices: 28240654--28240752 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
28240644 TTACTTCGAT
* *
28240654 TTATCCAATGATGCACTGTGTGTGCCAGTATAACTGCTTTCGC
1 TTATCCAATGATGCACTATATGTGCCAGTATAACTGCTTTCGC
* ** * *
28240697 TTTTCTGATGATGCACTATATGTGCCAGTATAATTGC-TTCGG
1 TTATCCAATGATGCACTATATGTGCCAGTATAACTGCTTTCGC
28240739 TATATCCAATGATG
1 T-TATCCAATGATG
28240753 TACTTACGGT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
42 5 0.11
43 40 0.89
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.37
Consensus pattern (43 bp):
TTATCCAATGATGCACTATATGTGCCAGTATAACTGCTTTCGC
Found at i:28246584 original size:22 final size:21
Alignment explanation
Indices: 28246559--28246621 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
28246549 GCCAGTTAAT
28246559 AGAACGGCTAAAAGCCATAAGC
1 AGAACGGCTAAAAGCCATAA-C
* *
28246581 AGAAAGGC-AGAAAGCCTTGAAC
1 AGAACGGCTA-AAAGCCAT-AAC
*
28246603 AGAACGGCTACAAGCCATA
1 AGAACGGCTAAAAGCCATA
28246622 CACTTCCTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
21 2 0.06
22 28 0.85
23 3 0.09
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (21 bp):
AGAACGGCTAAAAGCCATAAC
Found at i:28250232 original size:25 final size:27
Alignment explanation
Indices: 28250204--28250264 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
28250194 AGGGGTAAAA
* *
28250204 TGGTAATTTTA-CCTTC-GGGGTATTT
1 TGGTCATTTTACCCTTCAAGGGTATTT
28250229 TGGTCATTTTACCCTTCAAGGGTATTT
1 TGGTCATTTTACCCTTCAAGGGTATTT
*
28250256 CGGTCATTT
1 TGGTCATTT
28250265 GATAACCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 10 0.32
26 5 0.16
27 16 0.52
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.46
Consensus pattern (27 bp):
TGGTCATTTTACCCTTCAAGGGTATTT
Found at i:28254816 original size:43 final size:43
Alignment explanation
Indices: 28254750--28255033 Score: 296
Period size: 43 Copynumber: 6.7 Consensus size: 43
28254740 TTTTGGAAAT
* *
28254750 AAACGCCGCTATAGACCATGACCTTTAGCGGCACTTTCCTC-AC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCACTTT-CTCAAC
* * * *
28254793 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTT-TCCAT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCACTTTCTCAAC
* * * *
28254835 AAACGCCGCTATAGATCAGGATCTTTAACGGCGCTTT-TACAAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCACTTTCT-CAAC
* * *
28254878 AAACGCCGCTATAGCTCAAGACCTTTAGCGGCGATTTTC-CTAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGC-ACTTTCTCAAC
* * * *
28254921 AAACGCCGCTATAGATCAAGATCTTTAGCGGCGCTTTTTCTAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCACTTTCTCAAC
*
28254964 AAACGCCGC-ATAGATCAAGACCTTTAGCGGCACTTTTATCGAA-
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCAC-TTTCTC-AAC
28255007 AAACGCCGCTATAGAAT-AA-ACCTTTAG
1 AAACGCCGCTATAG-ATCAAGACCTTTAG
28255034 TGATGCTTCT
Statistics
Matches: 208, Mismatches: 24, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
41 2 0.01
42 62 0.30
43 132 0.63
44 10 0.05
45 2 0.01
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCACTTTCTCAAC
Found at i:28254891 original size:85 final size:83
Alignment explanation
Indices: 28254748--28255021 Score: 343
Period size: 85 Copynumber: 3.2 Consensus size: 83
28254738 ATTTTTGGAA
* * * * *
28254748 ATAAACGCCGCTATAGACCATGACCTTTAGCGGCACTTTCCTCACAAACGCCGCTATAGATCAGG
1 ATAAACGCCGCTATAGATCAAGATCTTTAGCGGCGCTTT--TCACAAACGCCGCTATAGATCAAG
28254813 ACCTTTAGCGGCGCTTTTCC
64 ACCTTTAGCGGCGCTTTTCC
* * *
28254833 ATAAACGCCGCTATAGATCAGGATCTTTAACGGCGCTTTTACAACAAACGCCGCTATAGCTCAAG
1 ATAAACGCCGCTATAGATCAAGATCTTTAGCGGCGCTTTT-C-ACAAACGCCGCTATAGATCAAG
*
28254898 ACCTTTAGCGGCGATTTTCC
64 ACCTTTAGCGGCGCTTTTCC
*
28254918 TACAAACGCCGCTATAGATCAAGATCTTTAGCGGCGCTTTTTCTACAAACGCCGC-ATAGATCAA
1 -ATAAACGCCGCTATAGATCAAGATCTTTAGCGGCGC-TTTTC-ACAAACGCCGCTATAGATCAA
* *
28254982 GACCTTTAGCGGCACTTTTATCG
63 GACCTTTAGCGGCGC-TTT-TCC
*
28255005 AAAAACGCCGCTATAGA
1 ATAAACGCCGCTATAGA
28255022 ATAAACCTTT
Statistics
Matches: 166, Mismatches: 17, Indels: 11
0.86 0.09 0.06
Matches are distributed among these distances:
83 1 0.01
84 1 0.01
85 94 0.57
86 64 0.39
87 6 0.04
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (83 bp):
ATAAACGCCGCTATAGATCAAGATCTTTAGCGGCGCTTTTCACAAACGCCGCTATAGATCAAGAC
CTTTAGCGGCGCTTTTCC
Found at i:28254978 original size:128 final size:129
Alignment explanation
Indices: 28254750--28255021 Score: 383
Period size: 128 Copynumber: 2.1 Consensus size: 129
28254740 TTTTGGAAAT
* *
28254750 AAACGCCGCTATAGACCATGACCTTTAGCGGCACTTTCCTCACAAACGCCGCTATAGATCAGGAC
1 AAACGCCGCTATAGACCAAGACCTTTAGCGGCACTTTCCTCACAAACGCCGCTATAGATCAAGAC
* * * *
28254815 CTTTAGCGGCGCTTTTCCATAAACGCCGCTATAGATCAGGATCTTTAACGGCGCTTTTA-C-AA
66 CTTTAGCGGCGCTTTTCCACAAACGCCGCTATAGATCAAGACCTTTAACGGCACTTTTATCGAA
*
28254877 CAAACGCCGCTATAG-CTCAAGACCTTTAGCGGCGATTTTCCT-ACAAACGCCGCTATAGATCAA
1 -AAACGCCGCTATAGAC-CAAGACCTTTAGCGGC-ACTTTCCTCACAAACGCCGCTATAGATCAA
* * *
28254940 GATCTTTAGCGGCGCTTTTTCTACAAACGCCGC-ATAGATCAAGACCTTTAGCGGCACTTTTATC
63 GACCTTTAGCGGCGC-TTTTCCACAAACGCCGCTATAGATCAAGACCTTTAACGGCACTTTTATC
28255004 GAA
127 GAA
28255007 AAACGCCGCTATAGA
1 AAACGCCGCTATAGA
28255022 ATAAACCTTT
Statistics
Matches: 128, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
127 1 0.01
128 88 0.69
129 37 0.29
130 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (129 bp):
AAACGCCGCTATAGACCAAGACCTTTAGCGGCACTTTCCTCACAAACGCCGCTATAGATCAAGAC
CTTTAGCGGCGCTTTTCCACAAACGCCGCTATAGATCAAGACCTTTAACGGCACTTTTATCGAA
Found at i:28258534 original size:103 final size:105
Alignment explanation
Indices: 28258413--28258611 Score: 321
Period size: 103 Copynumber: 1.9 Consensus size: 105
28258403 ACAAAGAATT
*
28258413 TTTCATTTTGAACAAAATGACGCAGTTTTACTATTCTAAAAATTTTTTA-T-TTTTTTATAAATT
1 TTTCATTTTGAACAAAATGACGCAGTTTTACTATGCTAAAAATTTTTTATTGTTTTTTATAAATT
*
28258476 GATTTATTTTTTGCGTCGTTTTAATAAAAAAACGCCGCTA
66 GATTTATTTTTTGCGGCGTTTTAATAAAAAAACGCCGCTA
* *
28258516 TTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTGTTTTTTATAAA
1 TTTCATTTTGAACAAAATGACGCAGTTTTACTATGCTAAAAATTTTTTA--TTGTTTTTTATAAA
*
28258581 TTGATTTATTTTTTGCGGCGTTTTTATAAAA
64 TTGATTTATTTTTTGCGGCGTTTTAATAAAA
28258612 TTTGATCGGG
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
103 46 0.53
106 1 0.01
107 40 0.46
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (105 bp):
TTTCATTTTGAACAAAATGACGCAGTTTTACTATGCTAAAAATTTTTTATTGTTTTTTATAAATT
GATTTATTTTTTGCGGCGTTTTAATAAAAAAACGCCGCTA
Found at i:28259418 original size:19 final size:17
Alignment explanation
Indices: 28259394--28259451 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 17
28259384 CTTTTTTTCA
28259394 AACAAAAAAATAACAGAAT
1 AACAAAAAAATAA-A-AAT
28259413 AACAAAAAAATAAAAAT
1 AACAAAAAAATAAAAAT
*
28259430 AA-AATAAAATAATAAA-
1 AACAAAAAAATAA-AAAT
28259446 AACAAA
1 AACAAA
28259452 TCCTAACCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 11 0.31
17 10 0.29
18 1 0.03
19 13 0.37
ACGTcount: A:0.79, C:0.07, G:0.02, T:0.12
Consensus pattern (17 bp):
AACAAAAAAATAAAAAT
Found at i:28262560 original size:49 final size:47
Alignment explanation
Indices: 28262245--28262697 Score: 674
Period size: 47 Copynumber: 9.6 Consensus size: 47
28262235 CCCTTCGGGA
* * * * * *
28262245 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28262291 CTCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CT-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28262339 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28262386 CTTATCACATATATACACTTTCACATTCATCACATCGGCAATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28262433 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28262480 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28262527 CTTATCACATATATATACGCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28262576 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28262625 CTTATCACATATATACACTTTCACATTCATTACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
28262672 CTTACCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
28262698 CACAATTATC
Statistics
Matches: 375, Mismatches: 28, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
46 2 0.01
47 280 0.75
48 2 0.01
49 91 0.24
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28265764 original size:45 final size:45
Alignment explanation
Indices: 28265715--28265824 Score: 159
Period size: 45 Copynumber: 2.4 Consensus size: 45
28265705 AAAAATGAGC
*
28265715 AAGACCATGACTGAAAGACATTATGGCATCATGATTCTATCAAGT
1 AAGACCATGACTGAAAGACATTATGGCATCACGATTCTATCAAGT
* * * *
28265760 AAGACCATGACTGAAAAACATTATGGTATTACGATTCTATCGAGT
1 AAGACCATGACTGAAAGACATTATGGCATCACGATTCTATCAAGT
28265805 AAGACCAT-AGCTGAAAGACA
1 AAGACCATGA-CTGAAAGACA
28265825 CTATAGTATC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 1 0.02
45 57 0.98
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (45 bp):
AAGACCATGACTGAAAGACATTATGGCATCACGATTCTATCAAGT
Found at i:28281447 original size:36 final size:35
Alignment explanation
Indices: 28281400--28281467 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
28281390 CACCTGTTAA
*
28281400 AATGTTCAATGTGGTACTTCAAATTTAATTTTTCAT
1 AATGTCCAATGTGG-ACTTCAAATTTAATTTTTCAT
* *
28281436 AATGTCCAATGTGGACTTGAACTTTAATTTTT
1 AATGTCCAATGTGGACTTCAAATTTAATTTTT
28281468 GTATATCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 16 0.55
36 13 0.45
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (35 bp):
AATGTCCAATGTGGACTTCAAATTTAATTTTTCAT
Found at i:28282579 original size:20 final size:20
Alignment explanation
Indices: 28282551--28282599 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
28282541 ATATATCCTG
*
28282551 ATTTTATTTGATTTCAATCA
1 ATTTGATTTGATTTCAATCA
*
28282571 ATTTGATTTGATTTTAATCA
1 ATTTGATTTGATTTCAATCA
*
28282591 AATTGATTT
1 ATTTGATTT
28282600 AATTGCTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.55
Consensus pattern (20 bp):
ATTTGATTTGATTTCAATCA
Found at i:28283077 original size:22 final size:23
Alignment explanation
Indices: 28283044--28283087 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
28283034 CAATTTATAT
28283044 TTTATTTTATATATAAATATTTG
1 TTTATTTTATATATAAATATTTG
* *
28283067 TTTA-TTTATATTTATATATTT
1 TTTATTTTATATATAAATATTT
28283088 ATTCGCTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTATTTTATATATAAATATTTG
Found at i:28283079 original size:14 final size:14
Alignment explanation
Indices: 28283036--28283089 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
28283026 AAATTATTCA
28283036 ATTTATAT-TTTAT
1 ATTTATATATTTAT
**
28283049 -TTTATATATAAAT
1 ATTTATATATTTAT
* *
28283062 ATTTGTTTATTTAT
1 ATTTATATATTTAT
28283076 ATTTATATATTTAT
1 ATTTATATATTTAT
28283090 TCGCTAACGT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
12 7 0.23
13 3 0.10
14 21 0.68
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (14 bp):
ATTTATATATTTAT
Found at i:28296978 original size:33 final size:33
Alignment explanation
Indices: 28296936--28297002 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
28296926 CATACAAGAC
28296936 TTGGGTATTTCTTATGAAAGAAAAATTTGTGGT
1 TTGGGTATTTCTTATGAAAGAAAAATTTGTGGT
28296969 TTGGGTATTTCTTATGAAAGAAAAATTTGTGGT
1 TTGGGTATTTCTTATGAAAGAAAAATTTGTGGT
28297002 T
1 T
28297003 GAAAGAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.03, G:0.24, T:0.43
Consensus pattern (33 bp):
TTGGGTATTTCTTATGAAAGAAAAATTTGTGGT
Found at i:28297007 original size:19 final size:19
Alignment explanation
Indices: 28296983--28297051 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
28296973 GTATTTCTTA
28296983 TGAAAGAAAAATTTGTGGT
1 TGAAAGAAAAATTTGTGGT
* ***
28297002 TGAAAG-AATATTTCAAGT
1 TGAAAGAAAAATTTGTGGT
** *
28297020 CTTCAAGAAAATTTTGTGGT
1 -TGAAAGAAAAATTTGTGGT
28297040 TGAAAGAAAAAT
1 TGAAAGAAAAAT
28297052 GGGGTTACAG
Statistics
Matches: 34, Mismatches: 14, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 8 0.24
19 19 0.56
20 7 0.21
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.32
Consensus pattern (19 bp):
TGAAAGAAAAATTTGTGGT
Found at i:28300430 original size:44 final size:44
Alignment explanation
Indices: 28300376--28300464 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
28300366 AATAATGATA
28300376 GTTAACTGATTGGATGACTTAAAATCTATACGAACAATAAAATG
1 GTTAACTGATTGGATGACTTAAAATCTATACGAACAATAAAATG
28300420 GTTAACTGATTGGATGACTTAAAATCTATACGAACAATAAAATG
1 GTTAACTGATTGGATGACTTAAAATCTATACGAACAATAAAATG
28300464 G
1 G
28300465 ACGTTTTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (44 bp):
GTTAACTGATTGGATGACTTAAAATCTATACGAACAATAAAATG
Found at i:28306841 original size:34 final size:34
Alignment explanation
Indices: 28306802--28306870 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
28306792 TAGATAATTT
28306802 TAAAGAGTTTTATTAGGGTTCAATTACTCTTGTA
1 TAAAGAGTTTTATTAGGGTTCAATTACTCTTGTA
28306836 TAAAGAGTTTTATTAGGGTTCAATTACTCTTGTA
1 TAAAGAGTTTTATTAGGGTTCAATTACTCTTGTA
28306870 T
1 T
28306871 TTTACCTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.45
Consensus pattern (34 bp):
TAAAGAGTTTTATTAGGGTTCAATTACTCTTGTA
Found at i:28317988 original size:21 final size:21
Alignment explanation
Indices: 28317960--28318015 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
28317950 AACAACGGTG
*
28317960 GCAGTGAGATTAGTTACTGTA
1 GCAGTGAGATTAGATACTGTA
* *
28317981 GCGGTGAGATTGGATACTGTA
1 GCAGTGAGATTAGATACTGTA
28318002 GCAGTGAGATTAGA
1 GCAGTGAGATTAGA
28318016 AACAATGGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (21 bp):
GCAGTGAGATTAGATACTGTA
Found at i:28335654 original size:27 final size:27
Alignment explanation
Indices: 28335592--28335654 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
28335582 CCATTTAAGA
* *
28335592 TCAAGCCATGGTCATCAACAACCTTTG
1 TCAAACCATGGTCATCAACAACCTATG
* *
28335619 -CAGATCCATGGTGATCAACAACCTATG
1 TCA-AACCATGGTCATCAACAACCTATG
28335646 TCAAACCAT
1 TCAAACCAT
28335655 ATTACCAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 2 0.07
27 26 0.87
28 2 0.07
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (27 bp):
TCAAACCATGGTCATCAACAACCTATG
Found at i:28335769 original size:144 final size:144
Alignment explanation
Indices: 28335509--28335783 Score: 514
Period size: 144 Copynumber: 1.9 Consensus size: 144
28335499 CCTGTGGCTT
*
28335509 ATATTACCAACTATGATTTCCATCCAGTACAAATCAATGAGCGAGTGGCAAAACAACCTAGGAGG
1 ATATTACCAACTATGATTCCCATCCAGTACAAATCAATGAGCGAGTGGCAAAACAACCTAGGAGG
28335574 AAGAGACCCCATTTAAGATCAAGCCATGGTCATCAACAACCTTTGCAGATCCATGGTGATCAACA
66 AAGAGACCCCATTTAAGATCAAGCCATGGTCATCAACAACCTTTGCAGATCCATGGTGATCAACA
28335639 ACCTATGTCAAACC
131 ACCTATGTCAAACC
28335653 ATATTACCAACTATGATTCCCATCCAGTACAAATCAATGAGCGAGTGGCAAAACAACCTAGGAGG
1 ATATTACCAACTATGATTCCCATCCAGTACAAATCAATGAGCGAGTGGCAAAACAACCTAGGAGG
* * *
28335718 AAGAGACCTCGTTTAAGATCAAGCCATGGTCATCAACAACCTTTGCCGATCCATGGTGATCAACA
66 AAGAGACCCCATTTAAGATCAAGCCATGGTCATCAACAACCTTTGCAGATCCATGGTGATCAACA
28335783 A
131 A
28335784 TCTGTACTAA
Statistics
Matches: 127, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 127 1.00
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.21
Consensus pattern (144 bp):
ATATTACCAACTATGATTCCCATCCAGTACAAATCAATGAGCGAGTGGCAAAACAACCTAGGAGG
AAGAGACCCCATTTAAGATCAAGCCATGGTCATCAACAACCTTTGCAGATCCATGGTGATCAACA
ACCTATGTCAAACC
Found at i:28335779 original size:27 final size:27
Alignment explanation
Indices: 28335737--28335873 Score: 125
Period size: 27 Copynumber: 5.1 Consensus size: 27
28335727 CGTTTAAGAT
* * *
28335737 CAAGCCATGGTCATCAACAACCTTTGC
1 CAAGCCATGGTGATCAACAACCTGTAC
* * *
28335764 CGATCCATGGTGATCAACAATCTGTAC
1 CAAGCCATGGTGATCAACAACCTGTAC
*
28335791 TAAGCCATGGTGATCAACAACCAATGT--
1 CAAGCCATGGTGATCAACAACC--TGTAC
* ** *
28335818 CAAACCACAGTGATCAACAATCTGTAC
1 CAAGCCATGGTGATCAACAACCTGTAC
* *
28335845 CAAGCTATGGTGATCAACAACCTGGAC
1 CAAGCCATGGTGATCAACAACCTGTAC
28335872 CA
1 CA
28335874 CGGCATTATG
Statistics
Matches: 85, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
25 3 0.04
27 79 0.93
29 3 0.04
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (27 bp):
CAAGCCATGGTGATCAACAACCTGTAC
Found at i:28340781 original size:43 final size:43
Alignment explanation
Indices: 28340578--28340781 Score: 300
Period size: 43 Copynumber: 4.7 Consensus size: 43
28340568 TTTTAAAAAT
*
28340578 AAACGCCGCTAAAGACCAAGACCTTTAGCGGAGCTTTCCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCCCAC
* * ***
28340621 AAATGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTGTCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCCCAC
* *
28340664 AAACGCCGCTAAATACCAAGACCTTTAGCGACGCTTTCCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCCCAC
*
28340707 AAACGCCACTAAAGACCAAGACCTTTAGCGGCGCTTTCCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCCCAC
* * *
28340750 AAACGCCGCTAAAGACTATGACCATTAGCGGC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGC
28340782 ATTTTTTCCT
Statistics
Matches: 141, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 141 1.00
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.19
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCCCAC
Found at i:28340830 original size:42 final size:42
Alignment explanation
Indices: 28340578--28340830 Score: 165
Period size: 43 Copynumber: 5.9 Consensus size: 42
28340568 TTTTAAAAAT
* * **
28340578 AAACGCCGCTAAAGACCA-AGACCTTTAGCGGAGCTTTCCCCAC
1 AAACGACGCTAAAGA--ATAGACCTTTAGCGGCGCTTTTTCCAC
* *
28340621 AAATGCCGCTAAAGACCAT-GACCTTTAGCGGCGCTTTTGT-CAC
1 AAACGACGCTAAAGA--ATAGACCTTTAGCGGCGCTTTT-TCCAC
* * * **
28340664 AAACGCCGCTAAATACCA-AGACCTTTAGCGACGCTTTCCCCAC
1 AAACGACGCTAAAGA--ATAGACCTTTAGCGGCGCTTTTTCCAC
* * **
28340707 AAACGCCACTAAAGACCA-AGACCTTTAGCGGCGCTTTCCCCAC
1 AAACGACGCTAAAGA--ATAGACCTTTAGCGGCGCTTTTTCCAC
* * * ** *
28340750 AAACGCCGCTAAAGACTATGACCATTAGCGGCATTTTTTCCTC
1 AAACGACGCTAAAGAATA-GACCTTTAGCGGCGCTTTTTCCAC
* * *
28340793 AAACGACGTTATAGAATAGACCTTTAGCGACGCTTTTT
1 AAACGACGCTAAAGAATAGACCTTTAGCGGCGCTTTTT
28340831 AGAAAAACAC
Statistics
Matches: 176, Mismatches: 28, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
42 17 0.10
43 159 0.90
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (42 bp):
AAACGACGCTAAAGAATAGACCTTTAGCGGCGCTTTTTCCAC
Found at i:28343290 original size:9 final size:9
Alignment explanation
Indices: 28343276--28343319 Score: 88
Period size: 9 Copynumber: 4.9 Consensus size: 9
28343266 CAGCAATGGT
28343276 TGTAACCTC
1 TGTAACCTC
28343285 TGTAACCTC
1 TGTAACCTC
28343294 TGTAACCTC
1 TGTAACCTC
28343303 TGTAACCTC
1 TGTAACCTC
28343312 TGTAACCT
1 TGTAACCT
28343320 GTTTGTGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.23, C:0.32, G:0.11, T:0.34
Consensus pattern (9 bp):
TGTAACCTC
Found at i:28344332 original size:14 final size:14
Alignment explanation
Indices: 28344292--28344325 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
28344282 AATCCTAGAT
*
28344292 CCCTAACTCCTAAC
1 CCCTAACTCTTAAC
28344306 CCCTAACTCTTAAC
1 CCCTAACTCTTAAC
28344320 CCCTAA
1 CCCTAA
28344326 ACCTTAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.47, G:0.00, T:0.24
Consensus pattern (14 bp):
CCCTAACTCTTAAC
Found at i:28344341 original size:21 final size:20
Alignment explanation
Indices: 28344317--28344357 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
28344307 CCTAACTCTT
*
28344317 AACCCCTAAACCTTAAATCCC
1 AACCCCTAAACCAT-AATCCC
*
28344338 AACCCTTAAACCATAATCCC
1 AACCCCTAAACCATAATCCC
28344358 TAAATCTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (20 bp):
AACCCCTAAACCATAATCCC
Found at i:28345481 original size:41 final size:41
Alignment explanation
Indices: 28345423--28345736 Score: 380
Period size: 41 Copynumber: 7.7 Consensus size: 41
28345413 AATATTTTTT
* * * *
28345423 GCGGCGCTTTTTCAAAAACGCCACTAAAGACCCAAGCATTA
1 GCGGCGCTTCTTAAAAAACGCCGCTAAAGACCCGAGCATTA
*
28345464 GCGGCGCTTCTTAAAAAACGCCGCTAAATACCCGAGCATTA
1 GCGGCGCTTCTTAAAAAACGCCGCTAAAGACCCGAGCATTA
* * * *
28345505 GCGGCGCTTCTTCAAAAGCGCCGCTAAAGTCCTGAGCATTA
1 GCGGCGCTTCTTAAAAAACGCCGCTAAAGACCCGAGCATTA
* *
28345546 GCGGCGCTTCTTGAAAAATGCCGCTAAAGACCCGAGCATTA
1 GCGGCGCTTCTTAAAAAACGCCGCTAAAGACCCGAGCATTA
*
28345587 GCGGCGCTTCTTGAAAAACGCCGCTAAAGACCCGAGCATTA
1 GCGGCGCTTCTTAAAAAACGCCGCTAAAGACCCGAGCATTA
* * * * * *
28345628 GCGGCGCTTATTTAAAAATGCCGTTAAAGCCCCGAGAATTA
1 GCGGCGCTTCTTAAAAAACGCCGCTAAAGACCCGAGCATTA
* * * *
28345669 GCGGTGCTT-TTCAAAAAACACCGCTAAAGCCCCGAGAATTA
1 GCGGCGCTTCTT-AAAAAACGCCGCTAAAGACCCGAGCATTA
* *
28345710 GTGGCGCTT-TTCAAAAAACGCCACTAA
1 GCGGCGCTTCTT-AAAAAACGCCGCTAA
28345737 CGCCTCGAAA
Statistics
Matches: 241, Mismatches: 31, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 2 0.01
41 239 0.99
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (41 bp):
GCGGCGCTTCTTAAAAAACGCCGCTAAAGACCCGAGCATTA
Found at i:28345825 original size:39 final size:38
Alignment explanation
Indices: 28345776--28345909 Score: 133
Period size: 40 Copynumber: 3.4 Consensus size: 38
28345766 TGTGCTTGGG
* * *
28345776 TTTTTTGCGGCGCTTTCTGAAAAATGCCGCTAATGCTCA
1 TTTTTAGCGGCG-TTTATGAAAAACGCCGCTAATGCTCA
* * * * *
28345815 TTTTTAGCGGCATTTTTCAAAAAACGCCGCTAATACTGGA
1 TTTTTAGCGGCGTTTAT-GAAAAACGCCGCTAATGCT-CA
* *
28345855 TCTTTAGCGGCGTTTATGAAGAAGCGCCGCTAATGCTCAA
1 TTTTTAGCGGCGTTTATGAA-AAACGCCGCTAATGCTC-A
28345895 TTTTTAGCGGCGTTT
1 TTTTTAGCGGCGTTT
28345910 TTTATCCAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
38 4 0.05
39 28 0.37
40 44 0.58
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (38 bp):
TTTTTAGCGGCGTTTATGAAAAACGCCGCTAATGCTCA
Found at i:28351727 original size:16 final size:16
Alignment explanation
Indices: 28351706--28351736 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28351696 CTCACTACTA
28351706 TGTCTTTTATATTTTC
1 TGTCTTTTATATTTTC
28351722 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
28351737 GCATGCATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.10, G:0.06, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:28356043 original size:42 final size:43
Alignment explanation
Indices: 28355943--28356045 Score: 100
Period size: 43 Copynumber: 2.4 Consensus size: 43
28355933 ACAATGCAAC
* * * * *
28355943 GTCCCAAACGTGGTCTTACATGTAATCAAATATTGATGCTGTT
1 GTCCCAAACATGGTCTTACACGAAATCAAATATCGATGCTGAT
** * * **
28355986 GTCTTAGACAGGGTCTTACACGAAATCGTATA-CGATGCTGAT
1 GTCCCAAACATGGTCTTACACGAAATCAAATATCGATGCTGAT
28356028 GTCCCAAACATGGTCTTA
1 GTCCCAAACATGGTCTTA
28356046 AATGTAAATC
Statistics
Matches: 45, Mismatches: 15, Indels: 1
0.74 0.25 0.02
Matches are distributed among these distances:
42 22 0.49
43 23 0.51
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (43 bp):
GTCCCAAACATGGTCTTACACGAAATCAAATATCGATGCTGAT
Found at i:28357231 original size:13 final size:13
Alignment explanation
Indices: 28357213--28357237 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28357203 CCAAATGATA
28357213 AAATTTTCACACG
1 AAATTTTCACACG
28357226 AAATTTTCACAC
1 AAATTTTCACAC
28357238 ATATAAACCA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:28359956 original size:16 final size:16
Alignment explanation
Indices: 28359924--28359954 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28359914 CAAAATCAGT
28359924 GAAAAGAAAATACAAA
1 GAAAAGAAAATACAAA
28359940 GAAAAGAAAAT-CAAA
1 GAAAAGAAAATACAAA
28359955 AGCACAAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.74, C:0.06, G:0.13, T:0.06
Consensus pattern (16 bp):
GAAAAGAAAATACAAA
Found at i:28368137 original size:199 final size:198
Alignment explanation
Indices: 28367797--28368194 Score: 652
Period size: 199 Copynumber: 2.0 Consensus size: 198
28367787 ATCATTGGTG
* * * *
28367797 GTAAGTTGGGTTTCTGTTCGTTCTTGGTTTTCAATTTGCTTGTAAATCCGTTAAATTGATGTTGA
1 GTAAGTTGGGTTTCTGTTCATTCTTGGTTGTCAATTTGCTTGTAAATCCATTAAAATGATGTTGA
*
28367862 GTATCTTGATTATAGGCTTTGGAGTGCTCAGGGACTGATTTAGCATCAAAGAGAACTAGGTGAGT
66 GTATCTTGATTATAGGCTTTGGAGTGCTCAGGGACTGATTTAGCATCAAAGAGAACCAGGTGAGT
* * * *
28367927 ACCAGAAACGCAAAGAAAAATGGATTCGGTGAAAAGCTAAAATTGCTTGTTGTTTGGACAGCAGT
131 ACCAGAAACGCAAA-AAAAAAGGATTCAGTGAAAAGCTAAAATTGCTTGCTGTTTGGACAGCAGC
28367992 AGTA
195 AGTA
*
28367996 GTAAGTTGGGTTTCTGTTCATTCTTGGTTGTCAATTTTCTTGTAAATCCATTAAAATGATGTTGA
1 GTAAGTTGGGTTTCTGTTCATTCTTGGTTGTCAATTTGCTTGTAAATCCATTAAAATGATGTTGA
* * *
28368061 GTATCTTGATTATAGGCTTTGGAGTGCTCGGGGACTGTTTTAGCATCAAAGAGAACCAGGTGTGT
66 GTATCTTGATTATAGGCTTTGGAGTGCTCAGGGACTGATTTAGCATCAAAGAGAACCAGGTGAGT
* *
28368126 ACCAGAAACGCAAAAAAAAAGGATTTAGTGAAAAGCTGAAATTGCTTGCTGTTTGGACAGCAGCA
131 ACCAGAAACGCAAAAAAAAAGGATTCAGTGAAAAGCTAAAATTGCTTGCTGTTTGGACAGCAGCA
28368191 GTA
196 GTA
28368194 G
1 G
28368195 GCTAATTTTG
Statistics
Matches: 184, Mismatches: 15, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
198 49 0.27
199 135 0.73
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (198 bp):
GTAAGTTGGGTTTCTGTTCATTCTTGGTTGTCAATTTGCTTGTAAATCCATTAAAATGATGTTGA
GTATCTTGATTATAGGCTTTGGAGTGCTCAGGGACTGATTTAGCATCAAAGAGAACCAGGTGAGT
ACCAGAAACGCAAAAAAAAAGGATTCAGTGAAAAGCTAAAATTGCTTGCTGTTTGGACAGCAGCA
GTA
Found at i:28368483 original size:45 final size:41
Alignment explanation
Indices: 28368445--28368522 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
28368435 ATTTAAATTA
*
28368445 TTAATGAGTCTAATTACTACTTAATGCCTTATTATATTTTT
1 TTAATGAATCTAATTACTACTTAATGCCTTATTATATTTTT
* *
28368486 TTAATTAATCTAATTACTACTTGATGCCTTATTATAT
1 TTAATGAATCTAATTACTACTTAATGCCTTATTATAT
28368523 ATCTAATGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.31, C:0.13, G:0.06, T:0.50
Consensus pattern (41 bp):
TTAATGAATCTAATTACTACTTAATGCCTTATTATATTTTT
Found at i:28368568 original size:36 final size:35
Alignment explanation
Indices: 28368537--28368605 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
28368527 AATGTAATTT
28368537 TTAATTAAATTGAATGGAAGTTTATGGATGTATAAG
1 TTAATTAAATTGAATGGAAG-TTATGGATGTATAAG
* * *
28368573 TTAATTCAATTGAATGTAAGTTATGGAAGTATA
1 TTAATTAAATTGAATGGAAGTTATGGATGTATA
28368606 TGTATTTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 12 0.40
36 18 0.60
ACGTcount: A:0.39, C:0.01, G:0.20, T:0.39
Consensus pattern (35 bp):
TTAATTAAATTGAATGGAAGTTATGGATGTATAAG
Found at i:28368854 original size:75 final size:76
Alignment explanation
Indices: 28368757--28368920 Score: 231
Period size: 75 Copynumber: 2.2 Consensus size: 76
28368747 CAGTTATCCA
** * *
28368757 ACTAGCGCCGGGTGCAATAATTTGTCGACTCGTTCGACTAGTGCTGGGCACACTATTGATCTTGT
1 ACTAGCGCTAGGTGCAATAATTTGTCGACTCGTTCGACTAGTGCTGGGCACACCATTGATCATGT
**
28368822 CG-GTTATTCG
66 CGAGTTAAACG
* * * *
28368832 GCTAGCGCTAGGTGTAATAATTTGTCGACTCGTTTGACTAGTGTTGGGCACACCATTGATCATGT
1 ACTAGCGCTAGGTGCAATAATTTGTCGACTCGTTCGACTAGTGCTGGGCACACCATTGATCATGT
28368897 CGAGTTAAACG
66 CGAGTTAAACG
28368908 ACTAGCGCTAGGT
1 ACTAGCGCTAGGT
28368921 ACAAAAACCT
Statistics
Matches: 77, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
75 59 0.77
76 18 0.23
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (76 bp):
ACTAGCGCTAGGTGCAATAATTTGTCGACTCGTTCGACTAGTGCTGGGCACACCATTGATCATGT
CGAGTTAAACG
Found at i:28372506 original size:20 final size:20
Alignment explanation
Indices: 28372457--28372500 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
28372447 TATCAATCCA
28372457 GTATCAATACT-TTTCTTAAG
1 GTATCAATA-TATTTCTTAAG
28372477 GTATCAATATATTTCTTAAG
1 GTATCAATATATTTCTTAAG
28372497 GTAT
1 GTAT
28372501 AGATATTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (20 bp):
GTATCAATATATTTCTTAAG
Found at i:28372852 original size:216 final size:216
Alignment explanation
Indices: 28372472--28372899 Score: 725
Period size: 216 Copynumber: 2.0 Consensus size: 216
28372462 AATACTTTTC
* *
28372472 TTAAGGTATCAATATATTTCTTAAGGTATAGATATTCCTGCTTCAACGGTTACTGAAATCAACAT
1 TTAAGGTATCAATATATTTCCTAAGGTATAGATATTCCTGCTTCAACGGTCACTGAAATCAACAT
* * *
28372537 TATTTACAAAAAATATCGATACCCTTTTAGTTGGTATCGATACTCGTTGCTGCAGGTGAATTTAA
66 TATTTACAAAAAATATCGATACCCTTTTAGTTGGTATCGATACTCGTTGCTACAGGTAAAGTTAA
* *
28372602 TGACCTAGTATTTCATCCCAACAGCTACATTCACTTCTACAACAACCACAATGGTTGAAAATCAA
131 TGACCTAGTATTTCATCCCAACAGCTACATTCACTTCTACAACAACCACAACGGTTGAAAATAAA
28372667 TTAGAGGGTATAAATACCATT
196 TTAGAGGGTATAAATACCATT
*
28372688 TTAAGGTATCAATATATTTCCTAAGGTATAGATATTCCTGCTTCAACGGTCACTGAAATCATCAT
1 TTAAGGTATCAATATATTTCCTAAGGTATAGATATTCCTGCTTCAACGGTCACTGAAATCAACAT
* *
28372753 TATTTACAAAAAATATCGTTACCTTTTTAGTTGGTATCGATACTCGTTGCTACAGGTAAAGTTAA
66 TATTTACAAAAAATATCGATACCCTTTTAGTTGGTATCGATACTCGTTGCTACAGGTAAAGTTAA
*
28372818 TGATCTAGTATTTCATCCCAA-AGGCT-CAATTCACTTCTACAACAACCACAACGGTTGAAAATA
131 TGACCTAGTATTTCATCCCAACA-GCTAC-ATTCACTTCTACAACAACCACAACGGTTGAAAATA
28372881 AATTAGAGGGTATAAATAC
194 AATTAGAGGGTATAAATAC
28372900 TATCTTCCAA
Statistics
Matches: 199, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
215 2 0.01
216 197 0.99
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (216 bp):
TTAAGGTATCAATATATTTCCTAAGGTATAGATATTCCTGCTTCAACGGTCACTGAAATCAACAT
TATTTACAAAAAATATCGATACCCTTTTAGTTGGTATCGATACTCGTTGCTACAGGTAAAGTTAA
TGACCTAGTATTTCATCCCAACAGCTACATTCACTTCTACAACAACCACAACGGTTGAAAATAAA
TTAGAGGGTATAAATACCATT
Found at i:28388059 original size:21 final size:21
Alignment explanation
Indices: 28388025--28388066 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28388015 TGAACATAAA
*
28388025 AATAAAAATAAAAATGGAAAT
1 AATAAAAATAAAAATGAAAAT
* *
28388046 AATAATAATGAAAATGAAAAT
1 AATAAAAATAAAAATGAAAAT
28388067 TTTCTTTTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (21 bp):
AATAAAAATAAAAATGAAAAT
Found at i:28393459 original size:17 final size:17
Alignment explanation
Indices: 28393433--28393480 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
28393423 TCAGATTTTG
28393433 ATACCCATATCTTTCTA
1 ATACCCATATCTTTCTA
* *
28393450 ATACCTATATCTTTCTG
1 ATACCCATATCTTTCTA
*
28393467 ATTCCCATATCTTT
1 ATACCCATATCTTT
28393481 GACTTTCTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.25, C:0.27, G:0.02, T:0.46
Consensus pattern (17 bp):
ATACCCATATCTTTCTA
Found at i:28398567 original size:41 final size:41
Alignment explanation
Indices: 28398512--28398702 Score: 310
Period size: 41 Copynumber: 4.6 Consensus size: 41
28398502 CTTAATTTAA
* * * *
28398512 CAGATTCACCGGCACTTAGCCTACTAGGCTTATAGCCTAATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
*
28398554 CAGATCACTGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
*
28398595 CAAATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
28398636 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
*
28398677 CAGATCACCAGCACTTAGCCTGCTAG
1 CAGATCACCGGCACTTAGCCTGCTAG
28398703 ACGTATAGTC
Statistics
Matches: 140, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
41 136 0.97
42 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
Found at i:28406343 original size:41 final size:41
Alignment explanation
Indices: 28406290--28406480 Score: 328
Period size: 41 Copynumber: 4.6 Consensus size: 41
28406280 CTTAATTTAA
* * *
28406290 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTAATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
28406332 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
*
28406373 CAAATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
28406414 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
*
28406455 CAGAACACCGGCACTTAGCCTGCTAG
1 CAGATCACCGGCACTTAGCCTGCTAG
28406481 ACGTATAGTC
Statistics
Matches: 143, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
41 139 0.97
42 4 0.03
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
Found at i:28408803 original size:17 final size:17
Alignment explanation
Indices: 28408781--28408830 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
28408771 TCTCAGATTT
28408781 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
*
28408798 TGATACCTATATCTTTC
1 TGATACCCATATCTTTC
28408815 TGATACCCATATCTTT
1 TGATACCCATATCTTT
28408831 GACTTTCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.24, C:0.26, G:0.06, T:0.44
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:28409496 original size:27 final size:27
Alignment explanation
Indices: 28409466--28409540 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
28409456 CCATTCCTAA
* *
28409466 TTTGCCACAAAGAC-ATTCTTTTCAGAT
1 TTTGCCACAAAGGCTATTCTTTT-AGAG
28409493 TTTGCCACAAAGGCTATTCTTTTAGAG
1 TTTGCCACAAAGGCTATTCTTTTAGAG
*
28409520 TTCGCCACAAAGGCTATTCTT
1 TTTGCCACAAAGGCTATTCTT
28409541 AGTTTTTGTG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 36 0.82
28 8 0.18
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.36
Consensus pattern (27 bp):
TTTGCCACAAAGGCTATTCTTTTAGAG
Found at i:28418170 original size:24 final size:24
Alignment explanation
Indices: 28418142--28418215 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
28418132 TTATAAATTA
28418142 AATTATAATTATTTTTAAATGTTT
1 AATTATAATTATTTTTAAATGTTT
* ** *
28418166 AATTATCACAACTTTT--A---TT
1 AATTATAATTATTTTTAAATGTTT
28418185 AAGTTATAATTATTTTTAAATGTTT
1 AA-TTATAATTATTTTTAAATGTTT
28418210 AATTAT
1 AATTAT
28418216 TACAACTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
19 4 0.11
20 10 0.28
22 2 0.06
24 16 0.44
25 4 0.11
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (24 bp):
AATTATAATTATTTTTAAATGTTT
Found at i:28418192 original size:44 final size:44
Alignment explanation
Indices: 28418138--28418228 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
28418128 ATAATTATAA
28418138 ATTAAATTATAATTATTTTTAAATGTTTAATTATCACAACTTTT
1 ATTAAATTATAATTATTTTTAAATGTTTAATTATCACAACTTTT
* *
28418182 ATTAAGTTATAATTATTTTTAAATGTTTAATTATTACAACTTTT
1 ATTAAATTATAATTATTTTTAAATGTTTAATTATCACAACTTTT
28418226 ATT
1 ATT
28418229 TTAATTTAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.54
Consensus pattern (44 bp):
ATTAAATTATAATTATTTTTAAATGTTTAATTATCACAACTTTT
Found at i:28418225 original size:24 final size:24
Alignment explanation
Indices: 28418154--28418226 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
28418144 TTATAATTAT
*
28418154 TTTTAAATGTTTAATTATCACAAC
1 TTTTAAATGTTTAATTATTACAAC
28418178 TTTTATTAA-GTTATAATTA-T-----
1 TTTTA--AATGTT-TAATTATTACAAC
28418198 TTTTAAATGTTTAATTATTACAAC
1 TTTTAAATGTTTAATTATTACAAC
28418222 TTTTA
1 TTTTA
28418227 TTTTAATTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 20
0.64 0.02 0.34
Matches are distributed among these distances:
18 8 0.21
19 4 0.11
20 5 0.13
24 10 0.26
25 3 0.08
26 8 0.21
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (24 bp):
TTTTAAATGTTTAATTATTACAAC
Found at i:28420732 original size:17 final size:17
Alignment explanation
Indices: 28420710--28420743 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28420700 TGGTTACTTA
28420710 GCTTGAGAATACCTCTT
1 GCTTGAGAATACCTCTT
28420727 GCTTGAGAATACCTCTT
1 GCTTGAGAATACCTCTT
28420744 TCTTCACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (17 bp):
GCTTGAGAATACCTCTT
Found at i:28427183 original size:24 final size:24
Alignment explanation
Indices: 28427111--28427184 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 24
28427101 TCATGAATTG
* *
28427111 GAAATCGATAAGCTTATACGAGTT
1 GAAATCGATAAGCTCATACGAGCT
* * *
28427135 GACAATC-AGTAAACTC-TCCCAAGCT
1 GA-AATCGA-TAAGCTCAT-ACGAGCT
28427160 GAAATCGATAAGCTCATACGAGCT
1 GAAATCGATAAGCTCATACGAGCT
28427184 G
1 G
28427185 TGGTGTGTCC
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
24 20 0.54
25 17 0.46
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (24 bp):
GAAATCGATAAGCTCATACGAGCT
Found at i:28437153 original size:27 final size:28
Alignment explanation
Indices: 28437123--28437175 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
28437113 TATTCAGTGA
28437123 CAGTA-CAATGAGGGCCTTAGCCCAATT
1 CAGTAGCAATGAGGGCCTTAGCCCAATT
* *
28437150 CAGTAGCAGTGTGGGCCTTAGCCCAA
1 CAGTAGCAATGAGGGCCTTAGCCCAA
28437176 CACAGTATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (28 bp):
CAGTAGCAATGAGGGCCTTAGCCCAATT
Found at i:28437166 original size:28 final size:28
Alignment explanation
Indices: 28437134--28437210 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 28
28437124 AGTACAATGA
*
28437134 GGGCCTTAGCCCAATTCAGTAGCAGTGT
1 GGGCCTTAGCCCAATACAGTAGCAGTGT
* *
28437162 GGGCCTTAGCCCAACACAGTATCAGTGT
1 GGGCCTTAGCCCAATACAGTAGCAGTGT
* *
28437190 GGACCTTAGCGCAATACAGTA
1 GGGCCTTAGCCCAATACAGTA
28437211 ACATTACAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (28 bp):
GGGCCTTAGCCCAATACAGTAGCAGTGT
Found at i:28437610 original size:27 final size:27
Alignment explanation
Indices: 28437580--28438209 Score: 533
Period size: 27 Copynumber: 23.5 Consensus size: 27
28437570 GGGGTATAAA
*
28437580 ATCATTTTACCCTAT-GAGGGTATTTTG
1 ATCATTTTACCCT-TCGAGGGTATTTCG
* * *
28437607 ATCATTTTACCTTTCGAGGTTATTT-T
1 ATCATTTTACCCTTCGAGGGTATTTCG
*
28437633 AGTCATTTTACCCTTC-AGGGTATTTCA
1 A-TCATTTTACCCTTCGAGGGTATTTCG
* *
28437660 ATTATTTTAACCTTCGAGGGTATTTC-
1 ATCATTTTACCCTTCGAGGGTATTTCG
*
28437686 ATCATTTTACCCTTCGAGGGTATTTTG
1 ATCATTTTACCCTTCGAGGGTATTTCG
*
28437713 ATCATTTTACCCTTCAAGGGTATTTCG
1 ATCATTTTACCCTTCGAGGGTATTTCG
* *
28437740 GTCATATTACCCTTCGA-GGTATTTC-
1 ATCATTTTACCCTTCGAGGGTATTTCG
* *
28437765 AGTCATTTTACCCTAT-GGGGGTAATTCG
1 A-TCATTTTACCCT-TCGAGGGTATTTCG
* * *
28437793 GTCATTTCT-CCCTAT-GGGGGCATTTC-
1 ATCATTT-TACCCT-TCGAGGGTATTTCG
28437819 ATTCATTTCT-CCCTTCGAGGGTATTTCG
1 A-TCATTT-TACCCTTCGAGGGTATTTCG
* * * * *
28437847 GTTATTTCACCCTTTGGGGGTATTTCG
1 ATCATTTTACCCTTCGAGGGTATTTCG
*
28437874 ATCATTTTACTCTTCGAGGG-ATTTC-
1 ATCATTTTACCCTTCGAGGGTATTTCG
*
28437899 AGTCATTTTACCCTTCGAGGGTATTTAG
1 A-TCATTTTACCCTTCGAGGGTATTTCG
* * * * *
28437927 GTGATCTTACCCTTTGGGGGTATTTCG
1 ATCATTTTACCCTTCGAGGGTATTTCG
* *
28437954 ATCATTTTATCCTTCG-GGAGTATTTCA
1 ATCATTTTACCCTTCGAGG-GTATTTCG
*
28437981 ATCATTTTACCCTTCG-GAGGTAATTCG
1 ATCATTTTACCCTTCGAG-GGTATTTCG
* * *
28438008 GTCATTTTACCCTTTGTA-AGTGA-TTCG
1 ATCATTTTACCCTTCG-AGGGT-ATTTCG
* * ** * *
28438035 GTCATTTTAACCTTTTTA-GGTAATCCG
1 ATCATTTT-ACCCTTCGAGGGTATTTCG
* *
28438062 ATCATTTTACCCTTCGGGGGTAATTCG
1 ATCATTTTACCCTTCGAGGGTATTTCG
* *
28438089 ATCATTTTACCCTTCAAGGGTATTTCA
1 ATCATTTTACCCTTCGAGGGTATTTCG
* *
28438116 ATCATTTTACCCTTCGGGGGTAATTCG
1 ATCATTTTACCCTTCGAGGGTATTTCG
*
28438143 ATCATTTTACCCATCGAGGGTATTTCG
1 ATCATTTTACCCTTCGAGGGTATTTCG
* * *
28438170 GTTATTTTACCCTTC-AGGAGTAATTCG
1 ATCATTTTACCCTTCGAGG-GTATTTCG
*
28438197 GTCATTTTACCCT
1 ATCATTTTACCCT
28438210 ACTGGGGTAA
Statistics
Matches: 494, Mismatches: 83, Indels: 52
0.79 0.13 0.08
Matches are distributed among these distances:
25 1 0.00
26 100 0.20
27 384 0.78
28 9 0.02
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (27 bp):
ATCATTTTACCCTTCGAGGGTATTTCG
Found at i:28438845 original size:12 final size:12
Alignment explanation
Indices: 28438827--28438856 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28438817 TGGATAAGAG
28438827 AAGGGAAGAGAA
1 AAGGGAAGAGAA
*
28438839 GAGGGAAGAGAA
1 AAGGGAAGAGAA
28438851 AAGGGA
1 AAGGGA
28438857 TTCGACAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (12 bp):
AAGGGAAGAGAA
Found at i:28441249 original size:359 final size:359
Alignment explanation
Indices: 28440590--28441281 Score: 1249
Period size: 359 Copynumber: 1.9 Consensus size: 359
28440580 GGCCCTAACA
*
28440590 TTCGACGATTGCCTCTTATTACTTACCAATCTTGGTATACCTCTTAACTGTCACAAGGCCATTTG
1 TTCGACGATTGCCTCTTATTACTTACCAATCTTGGTATACCTCTTAACTGTCACAAGGCCATTCG
*
28440655 GCAAGGTCCAAAATCAGTATGAAAAATTAATCACATGCATAAAATATACCATTTCTTAAACACTA
66 GCAAGGTCCAAAATCAATATGAAAAATTAATCACATGCATAAAATATACCATTTCTTAAACACTA
*
28440720 ATACACACAAAAGGTTAGACCCACACCTTATTTACATGAATCTAATACACTAACATCATCGCAAC
131 ATACACACAAAAGGTTAAACCCACACCTTATTTACATGAATCTAATACACTAACATCATCGCAAC
*
28440785 TTCTACAACTTAAATCTAGACAGCTCTAGACCAGATCTGTACACAACATGAATGAAACTCGATTA
196 TTCTACAACTTAAATCTAGACAACTCTAGACCAGATCTGTACACAACATGAATGAAACTCGATTA
28440850 AAACTAGCCTTTAAAAACACCTATAAGGTTCAAACAGAACAAGGATTAACAATGTCAAATCAAAT
261 AAACTAGCCTTTAAAAACACCTATAAGGTTCAAACAGAACAAGGATTAACAATGTCAAATCAAAT
28440915 TCAATTTTACCAATCTTGGTATACCTCTTAACTG
326 TCAATTTTACCAATCTTGGTATACCTCTTAACTG
*
28440949 TTCGACGATTGCCTCTTATTACTTACCAATCTTGGTATACCTCTTAACTGTCACAAGGCTATTCG
1 TTCGACGATTGCCTCTTATTACTTACCAATCTTGGTATACCTCTTAACTGTCACAAGGCCATTCG
*
28441014 GCAAGGTCCAAAATCAATATGCAAAATTAATCACATGCATAAAATATACCATTTCTTAAACACTA
66 GCAAGGTCCAAAATCAATATGAAAAATTAATCACATGCATAAAATATACCATTTCTTAAACACTA
* * * * * *
28441079 ATACTCACAAAAGGTTAAATCCACACCTTATTTACATGAATCTGATGCACTAACGTCATTGCAAC
131 ATACACACAAAAGGTTAAACCCACACCTTATTTACATGAATCTAATACACTAACATCATCGCAAC
28441144 TTCTACAACTTAAATCTAGACAACTCTAGACCAGATCTGTACACAACATGAATGAAACTCGATTA
196 TTCTACAACTTAAATCTAGACAACTCTAGACCAGATCTGTACACAACATGAATGAAACTCGATTA
* * *
28441209 AAACTAGCCTTTAGAAACCCCTATAAGGTTCGAACAGAACAAGGATTAACAATGTCAAATCAAAT
261 AAACTAGCCTTTAAAAACACCTATAAGGTTCAAACAGAACAAGGATTAACAATGTCAAATCAAAT
28441274 TCAATTTT
326 TCAATTTT
28441282 TGATCACTTA
Statistics
Matches: 318, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
359 318 1.00
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.28
Consensus pattern (359 bp):
TTCGACGATTGCCTCTTATTACTTACCAATCTTGGTATACCTCTTAACTGTCACAAGGCCATTCG
GCAAGGTCCAAAATCAATATGAAAAATTAATCACATGCATAAAATATACCATTTCTTAAACACTA
ATACACACAAAAGGTTAAACCCACACCTTATTTACATGAATCTAATACACTAACATCATCGCAAC
TTCTACAACTTAAATCTAGACAACTCTAGACCAGATCTGTACACAACATGAATGAAACTCGATTA
AAACTAGCCTTTAAAAACACCTATAAGGTTCAAACAGAACAAGGATTAACAATGTCAAATCAAAT
TCAATTTTACCAATCTTGGTATACCTCTTAACTG
Found at i:28442082 original size:526 final size:523
Alignment explanation
Indices: 28441038--28442608 Score: 1971
Period size: 526 Copynumber: 3.0 Consensus size: 523
28441028 CAATATGCAA
* * *
28441038 AATTAATCACATGCATAAAATATACCATTTCTTAAACACTAATACTCACAAAAGGTTAAATCCAC
1 AATTAATCACATGCATAAAATATACCATTT-TTTAACACTAATACACA-AAAAGGTTAAACCCAC
* *** * *
28441103 ACCTTATTTACATGAATCTGATGCACTAACGTC-ATTGCAACTTCTACAACTTAAATCTAGACAA
64 ACCTAATTTATGCGAATCTGATGCACTAACG-CAATTGCAACTTCTACAACTTAGATCTAGACAG
* *
28441167 CTCTAGACCAGATCTGTACACAACATGAATGAAACTCGATTAAAACTAGCCTTTAGAAACCCCTA
128 CTCTAGACCGGATCTGTACACAACATGAATGAAACTCGATTAAAACCAGCCTTTAGAAACCCCTA
* * **
28441232 TAAGGTTCGAACAGAACAAGGATTAACAATGTCAAATCAAATTCAATTTTTGATCACTTACTTAC
193 TAAGGTTCGACCAGAACAAGGATTAACAGTGTCAAATCGGATTCAA-TTTTG-TCACTTACTTAC
* * * * ** *
28441297 TCTATTGTGATATATAACGAAGACATGAATGAGTTTTGATGTCATTACTGATCCATGACATTTGG
256 TCTATT-CGATATATAACAAAGACA-GAATGAGTTTAGATGTCACTGTTGATCCATGACATTCGG
28441362 ATTAGGTCCTTCAATCAAAATAACACTCAAAAGTTAGTATAGAATATTCGACTATGCCACCAGTA
319 ATTAGGTCCTTCAATCAAAATAACACTCAAAAGTTAGTATAGAATATTCGACTATGCCACCAGTA
* * * *
28441427 ACATTCAACCAAAGTAGAAAACAAAGGAAGAAGGAAACGAGATAAGATCTGATTGAAAGAAAAAC
384 ACATTTAACCAAAGCAAAAAACAAAGGAAGAAGGAAACGAGATAAGATCTGATCGAAAGAAAAAC
* *
28441492 TACTTACTCCACATGAACGACAGATACGAAGAACCAATCAAAAATCCAAGCAGTACATATGAATT
449 TACTTACTCCACATGAACGACAGATACGAAGAACCAATCAAAAATCCAAGCAATACAGATGAATT
28441557 C-AGCTAGAAT
514 CGAG-TAGAAT
* *
28441567 AATTAATCACATGTATAAAATATACCATTTTTTAACACTAATACACAAAAAGGTCAAACCCACAC
1 AATTAATCACATGCATAAAATATACCATTTTTTAACACTAATACACAAAAAGGTTAAACCCACAC
* *
28441632 CTAATTTATGCGAATCCGATACACTAACGCAATTGCAACTTCTACAACTTAGATCTAGACAGCTC
66 CTAATTTATGCGAATCTGATGCACTAACGCAATTGCAACTTCTACAACTTAGATCTAGACAGCTC
* *
28441697 TAGACCGGATTTGTACACAACATGAATGAAACTCGATTAAAACCAGCCATTAGAAA-CCCTATAA
131 TAGACCGGATCTGTACACAACATGAATGAAACTCGATTAAAACCAGCCTTTAGAAACCCCTATAA
*
28441761 GGTTTGACCAGAACAAGGATTAACAGTGTCAAATCGGATTCAATATTTGGTCACTTACTTACTCT
196 GGTTCGACCAGAACAAGGATTAACAGTGTCAAATCGGATTCAAT-TTT-GTCACTTACTTACTCT
* * *
28441826 ATCTCGATTTATAACAAAGACACAAATGAGTTTAGATGTCACTGTTGATCCATGACGTTCGGATT
259 AT-TCGATATATAACAAAGACA-GAATGAGTTTAGATGTCACTGTTGATCCATGACATTCGGATT
* * * * * *
28441891 AAGTCCTCCAATCAAAATAACAATCAAAAGCTAGTAAAGAATATTTGACTATGCCACCAGTAACA
322 AGGTCCTTCAATCAAAATAACACTCAAAAGTTAGTATAGAATATTCGACTATGCCACCAGTAACA
** * * * *
28441956 TTTGTCCAAAGCAAAAAATC-AAGGGAGAAGGAACCGAGATCAGATCTGATCGAAAGAAAAATTA
387 TTTAACCAAAGCAAAAAA-CAAAGGAAGAAGGAAACGAGATAAGATCTGATCGAAAGAAAAACTA
* * * *
28442020 CTTACTCTAC-TAGAACGACAGATTCGAAGAACCAATGAAAAATCTAAGCAATATC-GATGAATT
451 CTTACTCCACAT-GAACGACAGATACGAAGAACCAATCAAAAATCCAAGCAATA-CAGATGAATT
28442083 CGAGTAGAAT
514 CGAGTAGAAT
* * * *
28442093 AATTAATCACATGCATAAAATATACCTTTTTTTAAACACTAATACACACAAATGTTAGACCCACA
1 AATTAATCACATGCATAAAATATACCATTTTTT-AACACTAATACACAAAAAGGTTAAACCCACA
** *
28442158 CCTAATTTATGTC-AATCTGATGCACTAACATAATCGCAACTTCTACAACTTAGATCTAGACAGC
65 CCTAATTTATG-CGAATCTGATGCACTAACGCAATTGCAACTTCTACAACTTAGATCTAGACAGC
* * * *
28442222 TCTAGATCGGATCTGTACACAAAATGAATGAAACTCAATTAAAATCAGCCTTTAGAAACCCCTAT
129 TCTAGACCGGATCTGTACACAACATGAATGAAACTCGATTAAAACCAGCCTTTAGAAACCCCTAT
* * * * *
28442287 AAGGTTCGGCCAGAACAAGGACTAACAGTGTCAAATCGGATTCAATTTT-T-AATCACTTACTAT
194 AAGGTTCGACCAGAACAAGGATTAACAGTGTCAAATCGGATTCAATTTTGTCACTTACTTACTCT
* * * *
28442350 ATTTCGATATAGAACAAAGACTAGAATGAGTCTCA-ATGTCACTGTTGATCCATGGCATTCGTAT
259 A-TTCGATATATAACAAAGAC-AGAATGAGT-TTAGATGTCACTGTTGATCCATGACATTCGGAT
* * *
28442414 TAGGTCCTTCAATCAAAATAACACTCAAAAGTTAGTATAGAAAATTCGGCTATGCCACCAATAAC
321 TAGGTCCTTCAATCAAAATAACACTCAAAAGTTAGTATAGAATATTCGACTATGCCACCAGTAAC
* * * * * * * **
28442479 ATTTAGA-CAAATCAGAAAATACAGGAAGAAGGAAACAAGATAAAATTTTGATTAAAAGAAAAAC
386 ATTTA-ACCAAAGCAAAAAACAAAGGAAGAAGGAAACGAGATAAGA-TCTGATCGAAAGAAAAAC
* * * * * * ** * *
28442543 TATTTATTCAACCA-AAACAACAAATTTGAAGTACCAAGT-AAAAATCCAAGCAGTACAGATGAA
449 TACTTACTCCA-CATGAACGACAGATACGAAGAACCAA-TCAAAAATCCAAGCAATACAGATGAA
28442606 TTC
512 TTC
28442609 AACCAGAATA
Statistics
Matches: 902, Mismatches: 119, Indels: 46
0.85 0.11 0.04
Matches are distributed among these distances:
524 149 0.17
525 70 0.08
526 321 0.36
527 268 0.30
528 65 0.07
529 29 0.03
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.26
Consensus pattern (523 bp):
AATTAATCACATGCATAAAATATACCATTTTTTAACACTAATACACAAAAAGGTTAAACCCACAC
CTAATTTATGCGAATCTGATGCACTAACGCAATTGCAACTTCTACAACTTAGATCTAGACAGCTC
TAGACCGGATCTGTACACAACATGAATGAAACTCGATTAAAACCAGCCTTTAGAAACCCCTATAA
GGTTCGACCAGAACAAGGATTAACAGTGTCAAATCGGATTCAATTTTGTCACTTACTTACTCTAT
TCGATATATAACAAAGACAGAATGAGTTTAGATGTCACTGTTGATCCATGACATTCGGATTAGGT
CCTTCAATCAAAATAACACTCAAAAGTTAGTATAGAATATTCGACTATGCCACCAGTAACATTTA
ACCAAAGCAAAAAACAAAGGAAGAAGGAAACGAGATAAGATCTGATCGAAAGAAAAACTACTTAC
TCCACATGAACGACAGATACGAAGAACCAATCAAAAATCCAAGCAATACAGATGAATTCGAGTAG
AAT
Found at i:28449008 original size:18 final size:19
Alignment explanation
Indices: 28448981--28449019 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
28448971 TGCTTGTTTG
*
28448981 TTATTTTTTTCTTTT-CTT
1 TTATTATTTTCTTTTGCTT
28448999 TTATTATTTTCTTTTGCTT
1 TTATTATTTTCTTTTGCTT
28449018 TT
1 TT
28449020 CTTGTGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.08, C:0.10, G:0.03, T:0.79
Consensus pattern (19 bp):
TTATTATTTTCTTTTGCTT
Found at i:28452801 original size:41 final size:41
Alignment explanation
Indices: 28452744--28452868 Score: 198
Period size: 41 Copynumber: 3.0 Consensus size: 41
28452734 AGTGACAATT
* *
28452744 TACTTGCGATACAATTTAAACCATCACAACTATTCTTAAAA
1 TACTTGTGATACAATTTAAACCATCACAACTATTGTTAAAA
28452785 TACTTGTGATACAATTTAAACCATCACAACTATTGTTAAAA
1 TACTTGTGATACAATTTAAACCATCACAACTATTGTTAAAA
* *
28452826 -AGCCTGTGATACAATTTAAACCATCATAACTATTGTTAAAA
1 TA-CTTGTGATACAATTTAAACCATCACAACTATTGTTAAAA
28452867 TA
1 TA
28452869 GTAACCAAGT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
40 1 0.01
41 76 0.97
42 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (41 bp):
TACTTGTGATACAATTTAAACCATCACAACTATTGTTAAAA
Found at i:28466677 original size:22 final size:22
Alignment explanation
Indices: 28466612--28466691 Score: 76
Period size: 22 Copynumber: 3.7 Consensus size: 22
28466602 TACTATTTTC
*
28466612 TCTTTTAAACAGTAATTTATCTGA
1 TCTTTTAAACA-T-ATTTATTTGA
**
28466636 TCTTTTCTACATA---ATTTGA
1 TCTTTTAAACATATTTATTTGA
28466655 TCTTTTAAACATATTTATTTGA
1 TCTTTTAAACATATTTATTTGA
**
28466677 TCTTTTCTACATATT
1 TCTTTTAAACATATT
28466692 AAGTCACTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
19 16 0.35
22 20 0.43
23 1 0.02
24 9 0.20
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.53
Consensus pattern (22 bp):
TCTTTTAAACATATTTATTTGA
Found at i:28470947 original size:23 final size:23
Alignment explanation
Indices: 28470921--28470966 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
28470911 ACTACTCGTA
28470921 TCCATTCTTCAACTCTTAAATAG
1 TCCATTCTTCAACTCTTAAATAG
*
28470944 TCCATTCTTGAACTCTTAAATAG
1 TCCATTCTTCAACTCTTAAATAG
28470967 AATGATAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (23 bp):
TCCATTCTTCAACTCTTAAATAG
Found at i:28473629 original size:223 final size:226
Alignment explanation
Indices: 28473242--28473695 Score: 781
Period size: 223 Copynumber: 2.0 Consensus size: 226
28473232 TAGGTTAGTG
* **
28473242 AGAATTTTCTAACGGTAGTGACTAAATTACATTTTTTTTTATTTGAGGGATCAAAATGAAAGGGC
1 AGAATTTTCTAACGGTAGTGACTAAATTACAGTTTTTTTTATTTGAGGGATCAAAATGAAAGCAC
*
28473307 TTAAAAAGTTGGGTAATCAACTAGGTAGTTTATCTTAATTTATTTTATTTAATTTTATAGCAATA
66 TTAAAAAGTTGGGTAACCAACTAGGTAGTTTATCTTAATTTATTTTATTTAATTTTATAGCAATA
28473372 TAGGAGGACATGGGTTCGAGTGTACTGAATCTCATTATCCTCTTATTTAT-GG-AGA-AG-GACT
131 TAGGAGGACATGGGTTCGAGTGTACTGAATCTCATTATCCTCTTATTTATAGGTAGAGAGAGACT
*
28473433 ATGTATAGTTTTAAACATTGTCTTCTCAAAA
196 ATATATAGTTTTAAACATTGTCTTCTCAAAA
*
28473464 AGAATTTTCTAACGGTAGTGACTAAATTACAAGTTTTTTTTATTTGAGGGATTAAAATGAAAGCA
1 AGAATTTTCTAACGGTAGTGACTAAATTAC-AGTTTTTTTTATTTGAGGGATCAAAATGAAAGCA
28473529 CTTAAAAAGTTGGGTAACCAACTAGGTAGTTTATCTTAATTTATTTTATTTAATTTTATAGCAAT
65 CTTAAAAAGTTGGGTAACCAACTAGGTAGTTTATCTTAATTTATTTTATTTAATTTTATAGCAAT
* *
28473594 ATAGGAGGACATGGGTTCGAGTGTATTGAATCTCATTATCCTCTTATTTATAGGTTGGAGAGAGA
130 ATAGGAGGACATGGGTTCGAGTGTACTGAATCTCATTATCCTCTTATTTATAGG-TAGAGAGAGA
*
28473659 CTATATATAGTTTTAAACATTGTTTTCTCAAAA
194 CTATATATAGTTTTAAACATTGTCTTCTCAAAA
28473692 AGAA
1 AGAA
28473696 CATATATGAA
Statistics
Matches: 217, Mismatches: 9, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
222 30 0.14
223 144 0.66
224 2 0.01
226 2 0.01
227 2 0.01
228 37 0.17
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (226 bp):
AGAATTTTCTAACGGTAGTGACTAAATTACAGTTTTTTTTATTTGAGGGATCAAAATGAAAGCAC
TTAAAAAGTTGGGTAACCAACTAGGTAGTTTATCTTAATTTATTTTATTTAATTTTATAGCAATA
TAGGAGGACATGGGTTCGAGTGTACTGAATCTCATTATCCTCTTATTTATAGGTAGAGAGAGACT
ATATATAGTTTTAAACATTGTCTTCTCAAAA
Done.