Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009460.1 Hibiscus syriacus cultivar Beakdansim tig00113722_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2853300
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 11 of 14
Found at i:2012945 original size:60 final size:60
Alignment explanation
Indices: 2012872--2012998 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 60
2012862 ATAGCCAGGT
* * *
2012872 GACCATTTTGTAACTTTTAATAATC-AGGGGA-TTCAACAAAACAATACTCTATAGTCGA-AG
1 GACCATTATGTAACCTTTAATAATCGA-GGGACTT-AACAAAACAATACCCTATAGTC-ATAG
* * *
2012932 GACCATTATGTAACCTTTAATAATCGATGGACTTAATAAAGCAATACCCTATAGTCATAG
1 GACCATTATGTAACCTTTAATAATCGAGGGACTTAACAAAACAATACCCTATAGTCATAG
2012992 GACCATT
1 GACCATT
2012999 TGCATTCTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
59 1 0.02
60 54 0.93
61 3 0.05
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (60 bp):
GACCATTATGTAACCTTTAATAATCGAGGGACTTAACAAAACAATACCCTATAGTCATAG
Found at i:2015043 original size:20 final size:19
Alignment explanation
Indices: 2015007--2015045 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2014997 GTATTTTCGT
* *
2015007 AAATAGCATATATAAATAA
1 AAATAGCAAATAGAAATAA
2015026 AAATAAGCAAATAGAAATAA
1 AAAT-AGCAAATAGAAATAA
2015046 TTAAAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.21
Consensus pattern (19 bp):
AAATAGCAAATAGAAATAA
Found at i:2025256 original size:2 final size:2
Alignment explanation
Indices: 2025249--2025277 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2025239 TTGCTACTTA
2025249 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2025278 TATTGTAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2026489 original size:43 final size:42
Alignment explanation
Indices: 2026440--2026760 Score: 315
Period size: 43 Copynumber: 7.5 Consensus size: 42
2026430 TCTATTACGC
* * *
2026440 CGTTTTTTGAAAAAACGCCGCAAAAAGTCGATATCTATAGCGG
1 CGTTTTTGGAAAAAACGCCGCAAAAAGTC-AGACCTATAGCGG
* * * ** *
2026483 CATTTTTGGAATAAACGCCGCAAAAAGTTATGATATATAACGG
1 CGTTTTTGGAAAAAACGCCGCAAAAAGTCA-GACCTATAGCGG
* * * *
2026526 CGTTTCTAGAAAAAACGCCGCAAAAGGTCAGATCTATAGCGG
1 CGTTTTTGGAAAAAACGCCGCAAAAAGTCAGACCTATAGCGG
* **
2026568 CGTTTTTGGATACAAACGCCGC-AAAAGAAAAGACCTATA-CTGG
1 CGTTTTTGGA-AAAAACGCCGCAAAAAG-TCAGACCTATAGC-GG
* * * *
2026611 CGTTTTTAGAACAAACGCCGCAAAAGGTCAGACCTATAGAGG
1 CGTTTTTGGAAAAAACGCCGCAAAAAGTCAGACCTATAGCGG
* * *
2026653 CGTTTTTGGACATAAACGCCACAAAAAGTCAGACCTATAACGG
1 CGTTTTTGGA-AAAAACGCCGCAAAAAGTCAGACCTATAGCGG
2026696 CGTTTTT-GAATACAAACGCCGCAAAAAGTCAGACCTATAGCGG
1 CGTTTTTGGAA-A-AAACGCCGCAAAAAGTCAGACCTATAGCGG
* *
2026739 CGTTTTTTGATACAAACGCCGC
1 CGTTTTTGGA-AAAAACGCCGC
2026761 TAATTACCTT
Statistics
Matches: 230, Mismatches: 37, Indels: 22
0.80 0.13 0.08
Matches are distributed among these distances:
41 1 0.00
42 57 0.25
43 169 0.73
44 2 0.01
45 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (42 bp):
CGTTTTTGGAAAAAACGCCGCAAAAAGTCAGACCTATAGCGG
Found at i:2026572 original size:128 final size:125
Alignment explanation
Indices: 2026406--2026760 Score: 349
Period size: 128 Copynumber: 2.8 Consensus size: 125
2026396 GTTTGAGAAC
* * *
2026406 AAAAAACGCCACAATAGGTCAATATCTATTACGCCGTTTTTTGAAAAAACGCCGCAAAAAGTCGA
1 AAAAAACGCCACAAAAGGTC-AGATCTA-TACGGCGTTTTTTGAAAAAACGCCGCAAAAAGTC-A
* * * * * * *
2026471 TATCTATAGCGGCATTTTTGGAATAAACGCCGCAAAAAGTTATGATATATA-ACGGCGTTTCTAG
63 GACCTATAGCGGCGTTTTTAGAACAAACGCCGCAAAAAGTCA-GACATATAGA-GGCGTTTCTAG
* * * **
2026535 AAAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGC-AAAAGAAAA
1 AAAAAACGCCACAAAAGGTCAGATCTATA-CGGCGTTTTTTGA-AAAAACGCCGCAAAAAG-TCA
* * * *
2026599 GACCTATA-CTGGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGACCTATAGAGGCGTTTTTGG
63 GACCTATAGC-GGCGTTTTTAGAACAAACGCCGCAAAAAGTCAGACATATAGAGGCGTTTCTAG
* * *
2026662 ACATAAACGCCACAAAAAGTCAGACCTATAACGGCG-TTTTTGAATACAAACGCCGCAAAAAGTC
1 A-AAAAACGCCACAAAAGGTCAGATCTAT-ACGGCGTTTTTTGAA-A-AAACGCCGCAAAAAGTC
*
2026726 AGACCTATAGCGGCGTTTTTTGATACAAACGCCGC
62 AGACCTATAGCGGCGTTTTTAGA-ACAAACGCCGC
2026761 TAATTACCTT
Statistics
Matches: 186, Mismatches: 28, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
126 1 0.01
127 25 0.13
128 114 0.61
129 46 0.25
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (125 bp):
AAAAAACGCCACAAAAGGTCAGATCTATACGGCGTTTTTTGAAAAAACGCCGCAAAAAGTCAGAC
CTATAGCGGCGTTTTTAGAACAAACGCCGCAAAAAGTCAGACATATAGAGGCGTTTCTAG
Found at i:2026576 original size:85 final size:84
Alignment explanation
Indices: 2026443--2026760 Score: 363
Period size: 85 Copynumber: 3.7 Consensus size: 84
2026433 ATTACGCCGT
* * * * *
2026443 TTTTTGAAAAAACGCCGCAAAAAGTCGATATCTATAGCGGCATTTTTGGA-ATAAACGCCGCAAA
1 TTTTAGAAAAAACGCCGCAAAAAGTC-AGACCTATAGCGGCGTTTTTGGATACAAACGCCGCAAA
* **
2026507 AAGTTATGATATATAACGGCG
65 AAG-TAAGACCTATAACGGCG
* *
2026528 TTTCTAGAAAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAACGCCGC-AA
1 TTT-TAGAAAAAACGCCGCAAAAAGTCAGACCTATAGCGGCGTTTTTGGATACAAACGCCGCAAA
*
2026592 AAGAAAAGACCTAT-ACTGGCG
65 AAG-TAAGACCTATAAC-GGCG
* * * * * *
2026613 TTTTTAGAACAAACGCCGCAAAAGGTCAGACCTATAGAGGCGTTTTTGGACATAAACGCCACAAA
1 -TTTTAGAAAAAACGCCGCAAAAAGTCAGACCTATAGCGGCGTTTTTGGATACAAACGCCGCAAA
*
2026678 AAGTCAGACCTATAACGGCG
65 AAGTAAGACCTATAACGGCG
* *
2026698 TTTTTGAATACAAACGCCGCAAAAAGTCAGACCTATAGCGGCGTTTTTTGATACAAACGCCGC
1 TTTTAGAA-A-AAACGCCGCAAAAAGTCAGACCTATAGCGGCGTTTTTGGATACAAACGCCGC
2026761 TAATTACCTT
Statistics
Matches: 199, Mismatches: 26, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
84 9 0.05
85 103 0.52
86 87 0.44
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (84 bp):
TTTTAGAAAAAACGCCGCAAAAAGTCAGACCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAA
AGTAAGACCTATAACGGCG
Found at i:2030306 original size:41 final size:41
Alignment explanation
Indices: 2030261--2030768 Score: 552
Period size: 41 Copynumber: 12.3 Consensus size: 41
2030251 TCGTAAACAC
** * * * *
2030261 AAACGCCACTATGGTACAAGTGTATAGCGGCGTTTGAATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
2030302 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
2030343 AAATGTCAATAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * *
2030384 AAATGCCACTAAATTACGAGTCTTTAGCGACGTTTGTAAACA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA-A
* * * * * * *
2030426 CAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAA
1 -AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
2030468 AAATGCCACTAAAGTACGCGTCTTTAGCGGAGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
*
2030509 AAACGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * *
2030550 AAATGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTAAACA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA-A
* * * * *
2030592 CAAACACCACTATAGTAC-ATGTGTATAACGGCGTTTGTATAA
1 -AAACGCCACTAAAGTACGA-GTCTTTAGCGGCGTTTGTATAA
* * *
2030634 AAACGCCACTAAAGTACAATTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * *
2030675 AAATGCCACTAAATTACGAGTCTTTAGCGGTGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
* * * *
2030716 AAACGCCACTAAAGTACTACTCTTTTGCAGCGTTTGT-TGAAA
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTAT--AA
2030758 AAACGCCACTA
1 AAACGCCACTA
2030769 TCGATGAACC
Statistics
Matches: 392, Mismatches: 67, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
40 1 0.00
41 312 0.80
42 19 0.05
43 60 0.15
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
Found at i:2030469 original size:125 final size:125
Alignment explanation
Indices: 2030302--2030768 Score: 372
Period size: 125 Copynumber: 3.7 Consensus size: 125
2030292 GTTTGAATAA
* * * * * *
2030302 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGTCAATAAAGTACGAGTCTT
1 AAACGCCACTAAAGTACAAGTCTATAACGACGTTTGAATAAAAATGCCAATAAAGTACGAGTCTT
* * *
2030367 TAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGACGTTTGTAAACAC
66 TAGCGGAGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGACGTTTGTAAACAC
* * * *
2030427 AAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAATGCCACTAAAGTACGCGTCTT
1 AAACGCCACTAAAGTACAAGTCTATAACGACGTTTGAATAAAAATGCCAATAAAGTACGAGTCTT
* * *
2030492 TAGCGGAGTTTGTATAAAAACGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATA-A-
66 TAGCGGAGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGACGTTTGTAAACAC
* * ** * * * ** * *
2030550 AAATGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTAA-ACACAAACACCACTATAGTAC-ATG
1 AAACGCCACTAAAGTACAAGTCTATAACGACGTTTG-AATA-A-AAATGCCAATAAAGTACGA-G
* * * * * * * * *
2030613 TGTATAACGGCGTTTGTATAAAAACGCCACTAAAGTACAATTCTATAGCGGCGTTTGTATA-A-
62 TCTTTAGCGGAGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGACGTTTGTAAACAC
* * * * * ** * * * * *
2030675 AAATGCCACTAAATTACGAGTCTTTAGCGGTGTTTGTATAAAAACGCCACTAAAGTACTACTCTT
1 AAACGCCACTAAAGTACAAGTCTATAACGACGTTTGAATAAAAATGCCAATAAAGTACGAGTCTT
* * *
2030740 TTGCAGCGTTTGT-TGAAAAAACGCCACTA
66 TAGCGGAGTTTGTAT--AAAAACGCCACTA
2030769 TCGATGAACC
Statistics
Matches: 286, Mismatches: 48, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
122 1 0.00
123 55 0.19
124 20 0.07
125 210 0.73
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (125 bp):
AAACGCCACTAAAGTACAAGTCTATAACGACGTTTGAATAAAAATGCCAATAAAGTACGAGTCTT
TAGCGGAGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGACGTTTGTAAACAC
Found at i:2030532 original size:166 final size:166
Alignment explanation
Indices: 2030253--2030728 Score: 763
Period size: 166 Copynumber: 2.9 Consensus size: 166
2030243 TGCGGCATTC
* *
2030253 GTAAACACAAACGCCACTATGGTACAAGTGTATAGCGGCGTTTGAATAAAAACGCCACTAAAGTA
1 GTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAACGCCACTAAAGTA
* *
2030318 CGAGTCTTTAGCGGCGTTTGTATAAAAATGTCAATAAAGTACGAGTCTTTAGCGGCGTTTGTATA
66 CGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA
2030383 AAAATGCCACTAAATTACGAGTCTTTAGCGACGTTT
131 AAAATGCCACTAAATTACGAGTCTTTAGCGACGTTT
* *
2030419 GTAAACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAATGCCACTAAAGTA
1 GTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAACGCCACTAAAGTA
* * * *
2030484 CGCGTCTTTAGCGGAGTTTGTATAAAAACGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATA
66 CGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA
* *
2030549 AAAATGCCACTAAATTATGAGTCTTTAGCGGCGTTT
131 AAAATGCCACTAAATTACGAGTCTTTAGCGACGTTT
* * *
2030585 GTAAACACAAACACCACTATAGTACATGTGTATAACGGCGTTTGTATAAAAACGCCACTAAAGTA
1 GTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAACGCCACTAAAGTA
* * * * *
2030650 CAATTCTATAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGTGTTTGTATA
66 CGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA
*
2030715 AAAACGCCACTAAA
131 AAAATGCCACTAAA
2030729 GTACTACTCT
Statistics
Matches: 283, Mismatches: 27, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
166 283 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (166 bp):
GTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAACGCCACTAAAGTA
CGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA
AAAATGCCACTAAATTACGAGTCTTTAGCGACGTTT
Found at i:2031151 original size:23 final size:22
Alignment explanation
Indices: 2031102--2031154 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
2031092 TCACATCTTT
** *
2031102 TTCATATGAATAATTATACCTA
1 TTCATATGAATAAACACACCTA
*
2031124 ATCATATGAATCAAACACACCTA
1 TTCATATGAAT-AAACACACCTA
2031147 TTCATATG
1 TTCATATG
2031155 TGTTGGGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.34
Consensus pattern (22 bp):
TTCATATGAATAAACACACCTA
Found at i:2033609 original size:21 final size:21
Alignment explanation
Indices: 2033583--2033622 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2033573 TCTGCTGAAA
* *
2033583 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGCTGTGGAGTATG
2033604 CTCCACCTGCTGTGGAGTA
1 CTCCACCTGCTGTGGAGTA
2033623 CTACTTGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.33
Consensus pattern (21 bp):
CTCCACCTGCTGTGGAGTATG
Found at i:2037408 original size:9 final size:9
Alignment explanation
Indices: 2037394--2037450 Score: 54
Period size: 7 Copynumber: 7.0 Consensus size: 9
2037384 CCAAAGATGT
2037394 CAACTTTGC
1 CAACTTTGC
2037403 CAACTTT--
1 CAACTTTGC
* *
2037410 TAATTTTGC
1 CAACTTTGC
2037419 CAACTTT--
1 CAACTTTGC
2037426 CAACTTTGC
1 CAACTTTGC
2037435 CAACTTT--
1 CAACTTTGC
2037442 CAACTTTGC
1 CAACTTTGC
2037451 TAATATTTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
7 19 0.50
9 19 0.50
ACGTcount: A:0.25, C:0.28, G:0.07, T:0.40
Consensus pattern (9 bp):
CAACTTTGC
Found at i:2037419 original size:16 final size:16
Alignment explanation
Indices: 2037393--2037450 Score: 98
Period size: 16 Copynumber: 3.6 Consensus size: 16
2037383 ACCAAAGATG
2037393 TCAACTTTGCCAACTT
1 TCAACTTTGCCAACTT
* *
2037409 TTAATTTTGCCAACTT
1 TCAACTTTGCCAACTT
2037425 TCAACTTTGCCAACTT
1 TCAACTTTGCCAACTT
2037441 TCAACTTTGC
1 TCAACTTTGC
2037451 TAATATTTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.24, C:0.28, G:0.07, T:0.41
Consensus pattern (16 bp):
TCAACTTTGCCAACTT
Found at i:2040514 original size:22 final size:21
Alignment explanation
Indices: 2040489--2040545 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
2040479 ATCAATTCTA
*
2040489 ATGAATAGTCACATCTTTTCAT
1 ATGAATA-TCACATCTATTCAT
*
2040511 ATGAATCAACACATCTATTCAT
1 ATGAAT-ATCACATCTATTCAT
2040533 ATGAATAATCACA
1 ATGAAT-ATCACA
2040546 CCTCTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.33
Consensus pattern (21 bp):
ATGAATATCACATCTATTCAT
Found at i:2044344 original size:86 final size:86
Alignment explanation
Indices: 2044237--2044413 Score: 198
Period size: 86 Copynumber: 2.1 Consensus size: 86
2044227 AGTGTCGCAA
* * ** * *
2044237 TAGGTGTTGTTATTTAGCGGCG-TTTGTCACAAAAATGCCACAATAGGTTTTTATGTTTAGCGGC
1 TAGGTGTTGATATTTAGCGGCGTTTTGTCA-AAAAACGCCACAATAGGTGATGATGTTTAGCGAC
2044301 GTTT-TCCCCACAAACGCCACAG
65 GTTTCT-CCCACAAACGCCACAG
* * *
2044323 TAGGTGTTGATATTTTA-CGGCGTTTTTTCAACAAACGCCGCAATAGGTGATGATGTTTAGCGAC
1 TAGGTGTTGATA-TTTAGCGGCGTTTTGTCAAAAAACGCCACAATAGGTGATGATGTTTAGCGAC
* * *
2044387 GTTTCTCCCATAAACGTCGCAG
65 GTTTCTCCCACAAACGCCACAG
2044409 TAGGT
1 TAGGT
2044414 TTTCAGATTA
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
86 65 0.86
87 11 0.14
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (86 bp):
TAGGTGTTGATATTTAGCGGCGTTTTGTCAAAAAACGCCACAATAGGTGATGATGTTTAGCGACG
TTTCTCCCACAAACGCCACAG
Found at i:2044402 original size:43 final size:42
Alignment explanation
Indices: 2044232--2044413 Score: 150
Period size: 43 Copynumber: 4.2 Consensus size: 42
2044222 AAAATAGTGT
* * * * *
2044232 CGCAATAGGTGTTGTTATTTAGCGGCGTTTGTCACAAAAATGC
1 CGCAATAGGTGTTGATGTTTAGCGGCGTTT-TCCCACAAACGC
* * *
2044275 CACAATAGGTTTTTATGTTTAGCGGCGTTTTCCCCACAAACGC
1 CGCAATAGGTGTTGATGTTTAGCGGCGTTTT-CCCACAAACGC
* * * * *
2044318 CACAGTAGGTGTTGATATTTTA-CGGCGTTTTTTCAACAAACGC
1 CGCAATAGGTGTTGAT-GTTTAGCGGCG-TTTTCCCACAAACGC
* * * *
2044361 CGCAATAGGTGATGATGTTTAGCGACGTTTCTCCCATAAACGT
1 CGCAATAGGTGTTGATGTTTAGCGGCGTTT-TCCCACAAACGC
*
2044404 CGCAGTAGGT
1 CGCAATAGGT
2044414 TTTCAGATTA
Statistics
Matches: 110, Mismatches: 24, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
42 8 0.07
43 94 0.85
44 8 0.07
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (42 bp):
CGCAATAGGTGTTGATGTTTAGCGGCGTTTTCCCACAAACGC
Found at i:2044616 original size:43 final size:43
Alignment explanation
Indices: 2044517--2044627 Score: 111
Period size: 43 Copynumber: 2.6 Consensus size: 43
2044507 TTTAGTGGCG
* *
2044517 TTTTTTTATAA-AAACGCCGCTAAA-GTTCGGTATATCGCGGCG
1 TTTTTTT-TAACAAACACCGCTAAATGTTCGGTATATCGCGGCA
* ** *
2044559 TTTGTAGTATACAAACACCGCTAAATGTAT-GGTATATTGCGGCA
1 TTTTTTTTA-ACAAACACCGCTAAATGT-TCGGTATATCGCGGCA
*
2044603 TTTTTTTTAACAAACCCCGCTAAAT
1 TTTTTTTTAACAAACACCGCTAAAT
2044628 AACACAAAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
41 2 0.04
42 5 0.09
43 27 0.49
44 20 0.36
45 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (43 bp):
TTTTTTTTAACAAACACCGCTAAATGTTCGGTATATCGCGGCA
Found at i:2044973 original size:23 final size:21
Alignment explanation
Indices: 2044943--2045021 Score: 122
Period size: 21 Copynumber: 3.8 Consensus size: 21
2044933 GCTGATATGT
2044943 TGCTTCTCTCTGTGCTGTCGC
1 TGCTTCTCTCTGTGCTGTCGC
2044964 TGCTTCTCTCTGTGCTGTCGC
1 TGCTTCTCTCTGTGCTGTCGC
* *
2044985 TGCTTCTCTCTGTGTTGCCGC
1 TGCTTCTCTCTGTGCTGTCGC
* *
2045006 TGCTTCTTTCTCTGCT
1 TGCTTCTCTCTGTGCT
2045022 TTCGTTACTG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.00, C:0.33, G:0.22, T:0.46
Consensus pattern (21 bp):
TGCTTCTCTCTGTGCTGTCGC
Found at i:2045072 original size:21 final size:21
Alignment explanation
Indices: 2045014--2045072 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
2045004 GCTGCTTCTT
* * *
2045014 TCTCTGCTTTCGTTACTGCTC
1 TCTCTGCTTCCCTTGCTGCTC
**
2045035 TGGCTGCTTCCGC-TGCTGCTC
1 TCTCTGCTTCC-CTTGCTGCTC
2045056 TCTCTGCTTCCCTTGCT
1 TCTCTGCTTCCCTTGCT
2045073 TCATTTTCCG
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.02, C:0.37, G:0.19, T:0.42
Consensus pattern (21 bp):
TCTCTGCTTCCCTTGCTGCTC
Found at i:2047977 original size:41 final size:42
Alignment explanation
Indices: 2047927--2048024 Score: 105
Period size: 41 Copynumber: 2.4 Consensus size: 42
2047917 GCGTTTGTGG
*
2047927 TATAAACGCCACTACAT-TAAC-ACTATATTGCGACA-TTTTAGC
1 TATAAACGCCACTAAATGT--CTACTATATTGCGACATTTTTA-C
* *
2047969 TA-AAACGCCGCTAAATGTCTACTATATTGCGGCATTTTTAC
1 TATAAACGCCACTAAATGTCTACTATATTGCGACATTTTTAC
*
2048010 TATAAACGCCGCTAA
1 TATAAACGCCACTAA
2048025 TATTTAACCT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
40 1 0.02
41 28 0.57
42 20 0.41
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.31
Consensus pattern (42 bp):
TATAAACGCCACTAAATGTCTACTATATTGCGACATTTTTAC
Found at i:2051568 original size:23 final size:23
Alignment explanation
Indices: 2051524--2051569 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2051514 ATGACATGGA
** *
2051524 GATGATGTGGAAGGTGATGTGGC
1 GATGATGTGGAAGCCGACGTGGC
*
2051547 GATGATGTGGCAGCCGACGTGGC
1 GATGATGTGGAAGCCGACGTGGC
2051570 TTATGATCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.13, G:0.46, T:0.22
Consensus pattern (23 bp):
GATGATGTGGAAGCCGACGTGGC
Found at i:2055298 original size:15 final size:15
Alignment explanation
Indices: 2055275--2055305 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2055265 GAAGAGGAGG
*
2055275 AGAAGAAGAATAAGA
1 AGAAAAAGAATAAGA
2055290 AGAAAAAGAATAAGA
1 AGAAAAAGAATAAGA
2055305 A
1 A
2055306 TAAGACAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (15 bp):
AGAAAAAGAATAAGA
Found at i:2058649 original size:14 final size:15
Alignment explanation
Indices: 2058603--2058650 Score: 73
Period size: 14 Copynumber: 3.3 Consensus size: 15
2058593 ACCCGTTTCG
2058603 TTTTCTTTTAATTT-
1 TTTTCTTTTAATTTA
*
2058617 GTTTCTTTTAATTTA
1 TTTTCTTTTAATTTA
2058632 TTTTC-TTTAATTTA
1 TTTTCTTTTAATTTA
2058646 TTTTC
1 TTTTC
2058651 AATCATTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 27 0.87
15 4 0.13
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTTCTTTTAATTTA
Found at i:2066084 original size:35 final size:34
Alignment explanation
Indices: 2065999--2066085 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
2065989 AAAATAATTT
* *
2065999 TAAATACAACAAACTTACAATAAGTATTAGATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
2066033 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
2066071 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
2066086 ACTGAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 4 0.09
38 10 0.23
ACGTcount: A:0.53, C:0.10, G:0.09, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:2074009 original size:11 final size:11
Alignment explanation
Indices: 2073978--2074025 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
2073968 GAAAATATTA
2073978 ATATTA-AAAT
1 ATATTATAAAT
2073988 ATAATTATAAAT
1 AT-ATTATAAAT
* *
2074000 ATATTTTAAAA
1 ATATTATAAAT
2074011 ATATTATAAAT
1 ATATTATAAAT
2074022 ATAT
1 ATAT
2074026 ATGATAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 2 0.06
11 24 0.75
12 6 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATATTATAAAT
Found at i:2074027 original size:13 final size:13
Alignment explanation
Indices: 2073978--2074032 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 13
2073968 GAAAATATTA
2073978 ATATTA-AAATAT
1 ATATTATAAATAT
2073990 A-ATTATAAATAT
1 ATATTATAAATAT
2074002 AT-TT-TAAA-A-
1 ATATTATAAATAT
2074011 ATATTATAAATAT
1 ATATTATAAATAT
*
2074024 ATATGATAA
1 ATATTATAA
2074033 TTTAAATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
9 2 0.06
10 3 0.08
11 12 0.33
12 11 0.31
13 8 0.22
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
ATATTATAAATAT
Found at i:2078738 original size:45 final size:46
Alignment explanation
Indices: 2078689--2078776 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
2078679 GAACATCGAA
* *
2078689 TGCATTTTATGCATCGATGCAC-ATACCATGCATCAATGCACTTAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCAATGCACTTAG
*
2078734 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACT
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCAATGCACT
2078777 CAGGCTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.54
46 18 0.46
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCAATGCACTTAG
Found at i:2094433 original size:17 final size:18
Alignment explanation
Indices: 2094395--2094435 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
2094385 GTTTAATTTC
*
2094395 TTTTATTTTAAATCATTA
1 TTTTATTTGAAATCATTA
*
2094413 -TTTATTTGCAAT-ATTA
1 TTTTATTTGAAATCATTA
2094429 TTTTATT
1 TTTTATT
2094436 ATTACTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTATTTGAAATCATTA
Found at i:2094444 original size:12 final size:11
Alignment explanation
Indices: 2094424--2094486 Score: 53
Period size: 11 Copynumber: 5.8 Consensus size: 11
2094414 TTATTTGCAA
2094424 TATTATTTTAT
1 TATTATTTTAT
2094435 TATTACTTTTA-
1 TATTA-TTTTAT
*
2094446 TA-T-TTTAAT
1 TATTATTTTAT
*
2094455 TA-TAGCTTTAAT
1 TATTA--TTTTAT
2094467 TATTATTTTAT
1 TATTATTTTAT
2094478 TATTATTTT
1 TATTATTTT
2094487 TATCTTAATC
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
8 4 0.09
9 3 0.07
10 1 0.02
11 21 0.48
12 13 0.30
13 2 0.05
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:2094463 original size:20 final size:19
Alignment explanation
Indices: 2094427--2094489 Score: 56
Period size: 19 Copynumber: 3.1 Consensus size: 19
2094417 TTTGCAATAT
2094427 TATTTTATTATTACTTTTA
1 TATTTTATTATTACTTTTA
2094446 TATTTTAATTA-TAGCTTTAATTA
1 TATTTT-ATTATTA-C-TT--TTA
*
2094469 TTATTTTATTATTATTTTTA
1 -TATTTTATTATTACTTTTA
2094489 T
1 T
2094490 CTTAATCATA
Statistics
Matches: 36, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
19 9 0.25
20 8 0.22
21 2 0.06
22 2 0.06
23 7 0.19
24 8 0.22
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTTTATTATTACTTTTA
Found at i:2094666 original size:17 final size:18
Alignment explanation
Indices: 2094646--2094683 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2094636 CATATTGTTT
2094646 TATTTTA-ATTATTTTAA
1 TATTTTATATTATTTTAA
*
2094663 TA-TTTATATTTTTTTAA
1 TATTTTATATTATTTTAA
2094680 TATT
1 TATT
2094684 AAGAAATGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
16 4 0.22
17 13 0.72
18 1 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTTTATATTATTTTAA
Found at i:2102349 original size:24 final size:25
Alignment explanation
Indices: 2102309--2102359 Score: 95
Period size: 24 Copynumber: 2.1 Consensus size: 25
2102299 CATATCTGTC
2102309 CAGTGTTATGATAAAATATTTACAG
1 CAGTGTTATGATAAAATATTTACAG
2102334 CAGTGTTATGAT-AAATATTTACAG
1 CAGTGTTATGATAAAATATTTACAG
2102358 CA
1 CA
2102360 ACATCTACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (25 bp):
CAGTGTTATGATAAAATATTTACAG
Found at i:2105491 original size:18 final size:18
Alignment explanation
Indices: 2105455--2105493 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2105445 GTGCATATGC
**
2105455 TCCACCCCCTGGAGGATA
1 TCCACCCCCTGGAACATA
*
2105473 TCCACCTCCTGGAACATA
1 TCCACCCCCTGGAACATA
2105491 TCC
1 TCC
2105494 TCATCCCGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.41, G:0.15, T:0.21
Consensus pattern (18 bp):
TCCACCCCCTGGAACATA
Found at i:2105567 original size:15 final size:15
Alignment explanation
Indices: 2105543--2105609 Score: 98
Period size: 15 Copynumber: 4.5 Consensus size: 15
2105533 ATATGGAGGA
* *
2105543 TATCCCCCTCAAGGG
1 TATCCACCTCAAGGT
* *
2105558 TATCCGCCTCAAAGT
1 TATCCACCTCAAGGT
2105573 TATCCACCTCAAGGT
1 TATCCACCTCAAGGT
2105588 TATCCACCTCAAGGT
1 TATCCACCTCAAGGT
2105603 TATCCAC
1 TATCCAC
2105610 TAGGTGGCTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.25, C:0.36, G:0.13, T:0.25
Consensus pattern (15 bp):
TATCCACCTCAAGGT
Found at i:2109883 original size:23 final size:23
Alignment explanation
Indices: 2109815--2109875 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
2109805 ACATTTTATA
*
2109815 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGTAATTCTACG
*
2109838 TGGCACTTCGGTTTAATTCTACG
1 TGGCACTTCGGTGTAATTCTACG
*
2109861 TGGCACTTAGGTGTA
1 TGGCACTTCGGTGTA
2109876 TTTATACGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.34
Consensus pattern (23 bp):
TGGCACTTCGGTGTAATTCTACG
Found at i:2113545 original size:21 final size:21
Alignment explanation
Indices: 2113503--2113545 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2113493 TTTCTAGGAT
* *
2113503 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
2113524 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
2113545 A
1 A
2113546 ACGAACCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:2115214 original size:23 final size:23
Alignment explanation
Indices: 2115146--2115206 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
2115136 ACATTTTATA
2115146 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
2115169 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
2115192 TGTCACTTAGGTGCA
1 TGGCACTTCGGTGCA
2115207 TTTATACGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:2120365 original size:117 final size:120
Alignment explanation
Indices: 2120201--2120438 Score: 439
Period size: 117 Copynumber: 2.0 Consensus size: 120
2120191 ACATATATAT
2120201 CTCTGCATTCTGTATGGCAACAACAACAATAACAAATCTCTGAAGCTCCTATGACCTGGTTGAGT
1 CTCTGCATTCTGTATGGCAACAACAACAATAACAAATCTCTGAAGCTCCTATGACCTGGTTGAG-
2120266 TCAAGATC-ACACAGAGTTCTTTCATTTCCCTTTCATCTATTTGGTCAAGCACCTA
65 TCAAGATCAACACAGAGTTCTTTCATTTCCCTTTCATCTATTTGGTCAAGCACCTA
2120321 CTCTGC-TTCTGTATGGC-ACAACAACAAT-ACAAATCTCTGAAGCTCCTATGACCTGGTTGAGT
1 CTCTGCATTCTGTATGGCAACAACAACAATAACAAATCTCTGAAGCTCCTATGACCTGGTTGAGT
2120383 CAAGATCAACACAGAGTTCTTTCATTTCCCTTTCATCTATTTGGTCAAGCACCTA
66 CAAGATCAACACAGAGTTCTTTCATTTCCCTTTCATCTATTTGGTCAAGCACCTA
2120438 C
1 C
2120439 CCCACATTGC
Statistics
Matches: 117, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
116 8 0.07
117 81 0.69
118 11 0.09
119 11 0.09
120 6 0.05
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (120 bp):
CTCTGCATTCTGTATGGCAACAACAACAATAACAAATCTCTGAAGCTCCTATGACCTGGTTGAGT
CAAGATCAACACAGAGTTCTTTCATTTCCCTTTCATCTATTTGGTCAAGCACCTA
Found at i:2133635 original size:31 final size:31
Alignment explanation
Indices: 2133580--2133689 Score: 157
Period size: 31 Copynumber: 3.5 Consensus size: 31
2133570 AGTTTCAAAA
* * * *
2133580 ATAACAAATTAGTCATTAATATTATTAATTT
1 ATAACAAATCAATCACTAACATTATTAATTT
* *
2133611 ATAATAAATCAATCACTAACATTATCAATTT
1 ATAACAAATCAATCACTAACATTATTAATTT
*
2133642 GTAACAAATCAATCACTAACATTATTAATTT
1 ATAACAAATCAATCACTAACATTATTAATTT
2133673 ATAACAAATCAATCACT
1 ATAACAAATCAATCACT
2133690 CGACCTTGAC
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 69 1.00
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.36
Consensus pattern (31 bp):
ATAACAAATCAATCACTAACATTATTAATTT
Found at i:2133639 original size:16 final size:16
Alignment explanation
Indices: 2133618--2133666 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
2133608 TTTATAATAA
2133618 ATCAATCACTAACATT
1 ATCAATCACTAACATT
*** *
2133634 ATCAATTTGTAACA-A
1 ATCAATCACTAACATT
2133649 ATCAATCACTAACATT
1 ATCAATCACTAACATT
2133665 AT
1 AT
2133667 TAATTTATAA
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.33
Consensus pattern (16 bp):
ATCAATCACTAACATT
Found at i:2134265 original size:71 final size:71
Alignment explanation
Indices: 2134177--2134322 Score: 249
Period size: 71 Copynumber: 2.1 Consensus size: 71
2134167 GATGAATAGA
** *
2134177 AAAT-AGGTGATTCAAAATGGTGAATGCCAGATAGTGCTACCATGTTCAGGAGAGTATCAGGTCA
1 AAATGAGGTGATTCAAAATGGTGAATGCCAGATAGTGCTACCACATTCAGGAGAGTATCAAGTCA
2134241 ATGATT
66 ATGATT
*
2134247 AAATGAGGTGATTCAAAATGGTGAATGTCAGATAGTGCTACCACATTCAGGAGAGTATCAAGTCA
1 AAATGAGGTGATTCAAAATGGTGAATGCCAGATAGTGCTACCACATTCAGGAGAGTATCAAGTCA
2134312 ATGATT
66 ATGATT
2134318 AAATG
1 AAATG
2134323 GATATTGATG
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
70 4 0.06
71 67 0.94
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (71 bp):
AAATGAGGTGATTCAAAATGGTGAATGCCAGATAGTGCTACCACATTCAGGAGAGTATCAAGTCA
ATGATT
Found at i:2135364 original size:14 final size:14
Alignment explanation
Indices: 2135345--2135374 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2135335 TAAAGGGATC
2135345 GTTCGTTCATTTAT
1 GTTCGTTCATTTAT
*
2135359 GTTCGTTCGTTTAT
1 GTTCGTTCATTTAT
2135373 GT
1 GT
2135375 CTATTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.13, G:0.20, T:0.57
Consensus pattern (14 bp):
GTTCGTTCATTTAT
Found at i:2137292 original size:31 final size:31
Alignment explanation
Indices: 2137251--2137344 Score: 107
Period size: 31 Copynumber: 3.0 Consensus size: 31
2137241 ATTTTAAAAC
* * *
2137251 GACATAATAATACCACATGTATATAGACATT
1 GACATGATAATATCATATGTATATAGACATT
* * *
2137282 GACATGATAATATCATGTGTACATAAACATT
1 GACATGATAATATCATATGTATATAGACATT
* * *
2137313 GAGATGATAGTATCATATGTATATAGGCATT
1 GACATGATAATATCATATGTATATAGACATT
2137344 G
1 G
2137345 GCAATATCAC
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (31 bp):
GACATGATAATATCATATGTATATAGACATT
Found at i:2137686 original size:13 final size:13
Alignment explanation
Indices: 2137668--2137701 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2137658 CCAAAATTTT
*
2137668 TAATTTTTTAAAA
1 TAATTTTATAAAA
*
2137681 TAATTTTATATAA
1 TAATTTTATAAAA
2137694 TAATTTTA
1 TAATTTTA
2137702 ATAATTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATTTTATAAAA
Found at i:2137710 original size:13 final size:12
Alignment explanation
Indices: 2137673--2137711 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
2137663 ATTTTTAATT
2137673 TTTTAA-AATAA
1 TTTTAATAATAA
2137684 TTTTATATAATAA
1 TTTTA-ATAATAA
2137697 TTTTAATAATTAA
1 TTTTAATAA-TAA
2137710 TT
1 TT
2137712 AAAATCAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.20
12 5 0.20
13 15 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTTAATAATAA
Found at i:2138906 original size:12 final size:12
Alignment explanation
Indices: 2138891--2138973 Score: 53
Period size: 12 Copynumber: 6.9 Consensus size: 12
2138881 CATAAATCAA
*
2138891 AACATAATTCAG
1 AACAGAATTCAG
* *
2138903 AACA-TATATCAT
1 AACAGAAT-TCAG
*
2138915 AACAGAATCCAG
1 AACAGAATTCAG
* *
2138927 ATCAGAAATCAG
1 AACAGAATTCAG
2138939 AACAGAATTCAG
1 AACAGAATTCAG
** *
2138951 GTCATGTA-TCAG
1 AACA-GAATTCAG
2138963 AACAGAATTCA
1 AACAGAATTCA
2138974 AGTCGGAAAT
Statistics
Matches: 51, Mismatches: 16, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
11 4 0.08
12 43 0.84
13 4 0.08
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:2138908 original size:24 final size:24
Alignment explanation
Indices: 2138881--2138973 Score: 78
Period size: 24 Copynumber: 3.9 Consensus size: 24
2138871 ACGGAGATAT
*
2138881 CATAAATCAAAACATAATTCAGAA
1 CATAAATCAAAACAGAATTCAGAA
* * * *
2138905 CATATATCATAACAGAATCCAGAT
1 CATAAATCAAAACAGAATTCAGAA
* * **
2138929 CAGAAATCAGAACAGAATTCAGGT
1 CATAAATCAAAACAGAATTCAGAA
** *
2138953 CATGTATCAGAACAGAATTCA
1 CATAAATCAAAACAGAATTCA
2138974 AGTCGGAAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (24 bp):
CATAAATCAAAACAGAATTCAGAA
Found at i:2138948 original size:48 final size:47
Alignment explanation
Indices: 2138879--2138987 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 47
2138869 AAACGGAGAT
* * * *
2138879 ATCATAAATCAAAACATAATTCAGAACATATATCATAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACATATATCAGAACAGAATCCA
** * *
2138926 GATCAGAAATCAGAACAGAATTCAGGTCATGTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACATATATCAGAACAGAATCCA
*
2138974 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
2138988 TAAAATATTT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
47 1 0.02
48 50 0.98
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACATATATCAGAACAGAATCCA
Found at i:2138985 original size:24 final size:25
Alignment explanation
Indices: 2138910--2138987 Score: 74
Period size: 24 Copynumber: 3.2 Consensus size: 25
2138900 CAGAACATAT
* *
2138910 ATCATAACAGAA-TCCAGATCA-GAA
1 ATCAGAACAGAATTCAAG-TCAGGAA
* * *
2138934 ATCAGAACAGAATTCAGGTCATG-T
1 ATCAGAACAGAATTCAAGTCAGGAA
2138958 ATCAGAACAGAATTCAAGTC-GGAA
1 ATCAGAACAGAATTCAAGTCAGGAA
2138982 ATCAGA
1 ATCAGA
2138988 TAAAATATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
23 1 0.02
24 39 0.89
25 4 0.09
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.19
Consensus pattern (25 bp):
ATCAGAACAGAATTCAAGTCAGGAA
Found at i:2140728 original size:36 final size:36
Alignment explanation
Indices: 2140681--2140753 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
2140671 GATAAATTAT
2140681 AATCTACATATCCATGACTGATTCTTTTATCACTTA
1 AATCTACATATCCATGACTGATTCTTTTATCACTTA
* *
2140717 AATCTACATATCGATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGACTGATTCTTTTATCACTTA
2140753 A
1 A
2140754 TTTCAGAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (36 bp):
AATCTACATATCCATGACTGATTCTTTTATCACTTA
Found at i:2141450 original size:13 final size:13
Alignment explanation
Indices: 2141415--2141444 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2141405 GTCAACGGGT
2141415 CGGGGCGGGTGAA
1 CGGGGCGGGTGAA
2141428 CGGGGCGGGTGAA
1 CGGGGCGGGTGAA
2141441 CGGG
1 CGGG
2141445 TTGGGTCGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.17, G:0.63, T:0.07
Consensus pattern (13 bp):
CGGGGCGGGTGAA
Found at i:2144755 original size:2 final size:2
Alignment explanation
Indices: 2144748--2144781 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2144738 ACTGAGCTTG
2144748 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2144782 ATGGTTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2146282 original size:2 final size:2
Alignment explanation
Indices: 2146233--2146265 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2146223 GTACATATTC
2146233 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2146266 TCGAATCCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2148635 original size:2 final size:2
Alignment explanation
Indices: 2148628--2148664 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2148618 TAAGAAAATA
2148628 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2148665 GGTTCCCAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2153466 original size:15 final size:17
Alignment explanation
Indices: 2153443--2153484 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
2153433 AGAAAAAAGA
*
2153443 GAGAGAAAGATGAG-AG
1 GAGAAAAAGATGAGAAG
2153459 GA-AAAAAGA-GAGAAG
1 GAGAAAAAGATGAGAAG
2153474 GAGAAAAAGAT
1 GAGAAAAAGAT
2153485 AGACAAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 3 0.14
15 10 0.45
16 9 0.41
ACGTcount: A:0.60, C:0.00, G:0.36, T:0.05
Consensus pattern (17 bp):
GAGAAAAAGATGAGAAG
Found at i:2153883 original size:16 final size:18
Alignment explanation
Indices: 2153853--2153886 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2153843 TTATATATAC
2153853 TATTATTTATATTTGGTA
1 TATTATTTATATTTGGTA
2153871 TATTATTT-T-TTTGGTA
1 TATTATTTATATTTGGTA
2153887 ACATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (18 bp):
TATTATTTATATTTGGTA
Found at i:2154943 original size:23 final size:22
Alignment explanation
Indices: 2154912--2154980 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
2154902 CACCACAGCT
*
2154912 CGTATAATTGCACCTAAGTGCCA
1 CGTAGAATTGCACCT-AGTGCCA
* *
2154935 CTTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACC-TAGTGCCA
*
2154958 CGTAGAATTGTACCGTAGTGCCA
1 CGTAGAATTGCACC-TAGTGCCA
2154981 TATAATAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (22 bp):
CGTAGAATTGCACCTAGTGCCA
Found at i:2155121 original size:103 final size:103
Alignment explanation
Indices: 2154996--2155213 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
2154986 TAATGTCCAT
* * *
2154996 AAGGACCACATATCATTCCTTAAGAATTATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
2155061 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
2155099 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
2155164 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
2155202 AAGGACCACATA
1 AAGGACCACATA
2155214 GACCCTCTAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:2155725 original size:21 final size:21
Alignment explanation
Indices: 2155701--2155743 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2155691 TCATATTCGT
*
2155701 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
2155722 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
2155743 T
1 T
2155744 AGCCCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:2161540 original size:103 final size:103
Alignment explanation
Indices: 2161409--2161626 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
2161399 TAATATCCAT
* *
2161409 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
* *
2161474 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATATTCCAAAGAATACATATATCTCCCG
2161512 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
2161577 GACCTCACACATATTCCAAAGAATACATATATCTCCCG
66 GACCTCACACATATTCCAAAGAATACATATATCTCCCG
* *
2161615 AAAGACTACATA
1 AAGGACCACATA
2161627 GACCCTCTAC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.24
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGGTGTCTCACCA
GACCTCACACATATTCCAAAGAATACATATATCTCCCG
Found at i:2162145 original size:18 final size:19
Alignment explanation
Indices: 2162108--2162144 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2162098 TTTTTTATTA
*
2162108 TGGGGGAATCGGTTCCCCC
1 TGGGGGAATCGATTCCCCC
*
2162127 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
2162145 TCTAGCGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (19 bp):
TGGGGGAATCGATTCCCCC
Found at i:2162196 original size:21 final size:21
Alignment explanation
Indices: 2162172--2162214 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2162162 TCATATTCGT
*
2162172 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
2162193 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
2162214 T
1 T
2162215 AGCCCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:2163007 original size:88 final size:88
Alignment explanation
Indices: 2162858--2163034 Score: 354
Period size: 88 Copynumber: 2.0 Consensus size: 88
2162848 CTCTTCCATC
2162858 ATTCTACTTAAATCACCAAATGCTGAAACTTTACAAATTAATCACTAACCCGGCATGGAGGATGT
1 ATTCTACTTAAATCACCAAATGCTGAAACTTTACAAATTAATCACTAACCCGGCATGGAGGATGT
2162923 TACACATTACTCCATTTTTTCAT
66 TACACATTACTCCATTTTTTCAT
2162946 ATTCTACTTAAATCACCAAATGCTGAAACTTTACAAATTAATCACTAACCCGGCATGGAGGATGT
1 ATTCTACTTAAATCACCAAATGCTGAAACTTTACAAATTAATCACTAACCCGGCATGGAGGATGT
2163011 TACACATTACTCCATTTTTTCAT
66 TACACATTACTCCATTTTTTCAT
2163034 A
1 A
2163035 AATAACTAAA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.33
Consensus pattern (88 bp):
ATTCTACTTAAATCACCAAATGCTGAAACTTTACAAATTAATCACTAACCCGGCATGGAGGATGT
TACACATTACTCCATTTTTTCAT
Found at i:2167806 original size:34 final size:34
Alignment explanation
Indices: 2167757--2167864 Score: 99
Period size: 34 Copynumber: 3.1 Consensus size: 34
2167747 TTGTTTTGCA
*
2167757 TGAAAAATTTCATCTCACTCGAGACATTTTCTCT
1 TGAAAATTTTCATCTCACTCGAGACATTTTCTCT
** * * * *
2167791 TGAATTTTTTTATCTCGCTTGAGATAGTTTTCTCT
1 TGAAAATTTTCATCTCACTCGAGACA-TTTTCTCT
* * * * *
2167826 TTAAAATTTTCGTCGCACTCGAGACAGTTTCTTT
1 TGAAAATTTTCATCTCACTCGAGACATTTTCTCT
2167860 TGAAA
1 TGAAA
2167865 CAATTTATTT
Statistics
Matches: 54, Mismatches: 19, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
34 29 0.54
35 25 0.46
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.44
Consensus pattern (34 bp):
TGAAAATTTTCATCTCACTCGAGACATTTTCTCT
Found at i:2171551 original size:16 final size:16
Alignment explanation
Indices: 2171530--2171567 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2171520 AAAAATAATT
2171530 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
2171546 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
2171562 T-ATAAA
1 TAATAAA
2171568 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:2171811 original size:11 final size:11
Alignment explanation
Indices: 2171732--2171812 Score: 51
Period size: 11 Copynumber: 7.3 Consensus size: 11
2171722 TTATATACGT
*
2171732 TAATAGTAAAA
1 TAATATTAAAA
* *
2171743 TAATAATAATA
1 TAATATTAAAA
2171754 TAATAGTTATAAA
1 TAATA-TTA-AAA
*
2171767 T-ATATATATAA
1 TAATAT-TAAAA
2171778 TAACT-TTAAAA
1 TAA-TATTAAAA
*
2171789 -AACATTAAAA
1 TAATATTAAAA
*
2171799 TAATATTAGAA
1 TAATATTAAAA
2171810 TAA
1 TAA
2171813 AAATAATATA
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
10 8 0.15
11 33 0.61
12 9 0.17
13 4 0.07
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (11 bp):
TAATATTAAAA
Found at i:2172323 original size:35 final size:37
Alignment explanation
Indices: 2172282--2172353 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
2172272 AACATAGCAA
2172282 AATTCTATCCTA-TTTTAAGAG-TTGAATCCTAGTAG
1 AATTCTATCCTATTTTTAAGAGTTTGAATCCTAGTAG
* *
2172317 AATTCTATCTTATTTTTGAGAGTTTGAATCCTAGTAG
1 AATTCTATCCTATTTTTAAGAGTTTGAATCCTAGTAG
2172354 GACGAAAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 11 0.33
36 8 0.24
37 14 0.42
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.43
Consensus pattern (37 bp):
AATTCTATCCTATTTTTAAGAGTTTGAATCCTAGTAG
Found at i:2173119 original size:106 final size:108
Alignment explanation
Indices: 2172817--2173440 Score: 607
Period size: 109 Copynumber: 5.9 Consensus size: 108
2172807 GTTCCGAGTC
* * * * **
2172817 CAATATCCTCCG-CTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAGTCAG
1 CAATATCCTCCGTC-GTGGAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
* * * *
2172881 CCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGT-C-
65 CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
* * * * * * * *
2172923 TAATATCCTTCG-CTGTGAAGATGAAATTGACTCTG-AA---CGAAA-T-CTTGTTGACAATCAG
1 CAATATCCTCCGTC-GTGGAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
2172981 CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-C-
65 CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
* * * *
2173023 CAATATCCTTCG-C-TGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGACAACCA
1 CAATATCCTCCGTCGTG-G-AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCA
* *
2173086 GCTGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCA
64 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCA
* * ** * * **
2173132 CGATATCCTCCGTCGTGGAGTTGAAA-TCGCGGATGAAACT-GAAAAGTTGTTCATTGACAACCA
1 CAATATCCTCCGTCGTGGAGTTGAAATTGGC-TCTGAAATTGGGAAA-TTGTTTGTTGACAACCA
* * *
2173195 GCCGTCCCTTCGTTGTGAAGTTGGACTTGTGTTTTCTCGGGTAGCA
64 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCA
* * * * * *
2173241 CGATATCCTCCGTCGTGGAGTTGAAATCGGTTCTGGAATTGGGAAGTTGTTCGTTGACAACCAGC
1 CAATATCCTCCGTCGTGGAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGC
* *
2173306 CATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCA
66 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCA
* * * * * *
2173350 CGATATCCTCCGTCGTGGAGTTGAAATCGGTTCCGAAATTGGGAAATTG-TTGTTGGCAACCAGA
1 CAATATCCTCCGTCGTGGAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGC
2173414 CGTCCCTTCGTTGTGAAGTTGAACTTG
66 CGTCCCTTCGTTGTGAAGTTGAACTTG
2173441 ACTCTAGCTA
Statistics
Matches: 444, Mismatches: 57, Indels: 32
0.83 0.11 0.06
Matches are distributed among these distances:
98 2 0.00
100 78 0.18
101 3 0.01
102 4 0.01
104 3 0.01
105 3 0.01
106 82 0.18
108 47 0.11
109 214 0.48
110 6 0.01
111 2 0.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (108 bp):
CAATATCCTCCGTCGTGGAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGC
CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
Found at i:2174100 original size:67 final size:67
Alignment explanation
Indices: 2174020--2174178 Score: 216
Period size: 67 Copynumber: 2.4 Consensus size: 67
2174010 GAAATGAAAT
*
2174020 TTTGTTTTAAGGGAGATA-AAT-TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTC-ATGGGAGA
1 TTTGTTTCAAGGGA-A-ACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAT-GGAGA
2174082 CAAAA
63 CAAAA
* *
2174087 TTTGTTTCGAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAAACTGTCTCAATGGAGACAA
1 TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAATGGAGACAA
2174152 AA
66 AA
* **
2174154 TTTATTTCAAGGGAAATTATCTCAA
1 TTTGTTTCAAGGGAAACAATCTCAA
2174179 GAGAGACGAA
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 75 0.91
68 2 0.02
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (67 bp):
TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAATGGAGACAA
AA
Found at i:2174177 original size:36 final size:35
Alignment explanation
Indices: 2174122--2174529 Score: 157
Period size: 36 Copynumber: 11.8 Consensus size: 35
2174112 AGGTTTTGTG
* *
2174122 TTTCAAGAGAAACTGTCTCAATGGAGACAAAATTTA
1 TTTCAAGGGAAACTATCTCAA-GGAGACAAAATTTA
* * *
2174158 TTTCAAGGGAAATTATCTCAAGAGAGACGAAATTCA
1 TTTCAAGGGAAACTATCTCAAG-GAGACAAAATTTA
* * *
2174194 TTTCAAGGGAAA-TGTTTTCAA--TG------TTTA
1 TTTCAAGGGAAACT-ATCTCAAGGAGACAAAATTTA
* * *
2174221 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG
1 --TTTCAAGGGAAACTATCTCAA-GGAGACAAAA-TTTA
*
2174260 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
1 TTTCAAGGGAAACTATCTCAAG-GAGACAAAATTTA
* * **
2174296 TTTCAAGGGAAA-TGTTTC-------CAATGTTTA
1 TTTCAAGGGAAACTATCTCAAGGAGACAAAATTTA
* * * *
2174323 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTG
1 --TTTCAAGGGAAACTATCTCAA-GGAGACAAAA-TTTA
* *
2174362 TTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCA
1 TTTCAAGGGAAACTATCTCAAG-GAGACAAAATTTA
* * *
2174398 TTTCAAGGGAAA-TGTTTTCAA--TG------TTTA
1 TTTCAAGGGAAACT-ATCTCAAGGAGACAAAATTTA
* * * *
2174425 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAAATTTG
1 --TTTCAAGGGAAACTATCTCAA-GGAG-ACAAAATTTA
* * *
2174464 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTTTG
1 TTTCAAGGGAAACTATCTCAAG-GAGACAAAATTTA
*
2174500 TTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TTTCAAGGGAAACTATCTCAAG-GAGACAA
2174530 TGGTGAGCAC
Statistics
Matches: 280, Mismatches: 48, Indels: 88
0.67 0.12 0.21
Matches are distributed among these distances:
27 11 0.04
29 43 0.15
30 7 0.03
32 2 0.01
33 2 0.01
35 7 0.03
36 119 0.43
37 78 0.28
38 2 0.01
39 9 0.03
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (35 bp):
TTTCAAGGGAAACTATCTCAAGGAGACAAAATTTA
Found at i:2174272 original size:37 final size:37
Alignment explanation
Indices: 2174221--2174529 Score: 239
Period size: 37 Copynumber: 8.9 Consensus size: 37
2174211 TCAATGTTTA
* *
2174221 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
2174258 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * **
2174294 CATTTCAAGGGAAA-TGTTTC--------CAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * *
2174322 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
2174360 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
2174396 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * * *
2174424 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAAATT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
2174462 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
2174498 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
2174530 TGGTGAGCAC
Statistics
Matches: 209, Mismatches: 38, Indels: 50
0.70 0.13 0.17
Matches are distributed among these distances:
27 3 0.01
28 3 0.01
29 25 0.12
30 8 0.04
32 1 0.00
33 1 0.00
34 1 0.00
35 6 0.03
36 65 0.31
37 89 0.43
38 7 0.03
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:2174297 original size:102 final size:102
Alignment explanation
Indices: 2174120--2174511 Score: 660
Period size: 102 Copynumber: 3.9 Consensus size: 102
2174110 AAAGGTTTTG
* * * *
2174120 TGTTTCAAGAGAAACTGTCTCAATGGAGACAAAA-TTTATTTCAAGGGAAATTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
2174184 ACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
2174221 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
2174286 ACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
2174323 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
2174388 ACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
2174425 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* **
2174490 ACAAAGTTTGTTTCAAGGGAAA
66 ACAAAATTCATTTCAAGGGAAA
2174512 CTGTCTCAAG
Statistics
Matches: 276, Mismatches: 14, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
101 33 0.12
102 243 0.88
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.29
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:2176091 original size:22 final size:21
Alignment explanation
Indices: 2176029--2176084 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
2176019 CTTTTTGTTC
* * *
2176029 CCTTTTTTATTTTTGTTCTTT
1 CCTTTTTTGTTCTTGTTTTTT
2176050 -CTTTTTTGTTCTTGTTTTTT
1 CCTTTTTTGTTCTTGTTTTTT
2176070 CCTTTTTTGCTTCTT
1 CCTTTTTTG-TTCTT
2176085 TTCTTTTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.57
21 8 0.27
22 5 0.17
ACGTcount: A:0.02, C:0.16, G:0.07, T:0.75
Consensus pattern (21 bp):
CCTTTTTTGTTCTTGTTTTTT
Found at i:2179456 original size:21 final size:20
Alignment explanation
Indices: 2179424--2179463 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2179414 ATAATAAATA
*
2179424 TAATAACGAAAAAAATAATT
1 TAATAAAGAAAAAAATAATT
*
2179444 TAATAAAGTAAAATAATAAT
1 TAATAAAG-AAAAAAATAAT
2179464 AATGTAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAATAAAGAAAAAAATAATT
Found at i:2179465 original size:16 final size:16
Alignment explanation
Indices: 2179444--2179481 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2179434 AAAAATAATT
2179444 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
2179460 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
2179476 T-ATAAA
1 TAATAAA
2179482 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:2179728 original size:11 final size:11
Alignment explanation
Indices: 2179646--2179729 Score: 55
Period size: 11 Copynumber: 7.3 Consensus size: 11
2179636 TTATATACGT
*
2179646 TAATAGTAAAA
1 TAATATTAAAA
*
2179657 TAATAATAAATA
1 TAATATTAAA-A
2179669 TAATAGTTATAAA
1 TAATA-TTA-AAA
*
2179682 TATATATATATAA
1 TA-ATAT-TAAAA
2179695 TAACT-TTAAAA
1 TAA-TATTAAAA
*
2179706 -AACATTAAAA
1 TAATATTAAAA
*
2179716 TAATATTAGAA
1 TAATATTAAAA
2179727 TAA
1 TAA
2179730 AAATAATTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
10 8 0.14
11 24 0.41
12 8 0.14
13 11 0.19
14 7 0.12
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (11 bp):
TAATATTAAAA
Found at i:2180242 original size:35 final size:37
Alignment explanation
Indices: 2180172--2180271 Score: 105
Period size: 35 Copynumber: 2.8 Consensus size: 37
2180162 GTGCTTGTGG
* * * * *
2180172 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTATTTTTAAGAGTTTGAATCCTAGCAAAATTCT
*
2180209 ATCCTA-TTTTAAGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTTAAGAGTTTGAATCCTAGCAAAATTCT
* **
2180244 ATCTTATTTTTGTGAGTTTGAATCCTAG
1 ATCCTATTTTTAAGAGTTTGAATCCTAG
2180272 TAGGACGAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
35 21 0.40
36 14 0.27
37 17 0.33
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAAGAGTTTGAATCCTAGCAAAATTCT
Found at i:2189607 original size:47 final size:45
Alignment explanation
Indices: 2189537--2189662 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
2189527 TATAAAATCT
* *
2189537 CTTACCATTTATCCCATAAGCTCGTAAACTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
2189582 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
2189629 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
2189663 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 36 0.51
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:2189811 original size:40 final size:40
Alignment explanation
Indices: 2189767--2189888 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
2189757 ACCGTAGTGC
2189767 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2189807 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2189847 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2189887 TA
1 TA
2189889 TAAACCTGCA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:2193676 original size:16 final size:15
Alignment explanation
Indices: 2193655--2193702 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
2193645 TGAAATATTT
2193655 TTTTTTTCATTTCTCA
1 TTTTTTTC-TTTCTCA
2193671 TTTTTTTC--TCT-A
1 TTTTTTTCTTTCTCA
2193683 TTTCTTTTCTTTCTCA
1 TTT-TTTTCTTTCTCA
2193699 TTTT
1 TTTT
2193703 CATTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 4 0.14
13 8 0.29
15 4 0.14
16 12 0.43
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTTTCTTTCTCA
Found at i:2193707 original size:34 final size:33
Alignment explanation
Indices: 2193653--2193742 Score: 103
Period size: 34 Copynumber: 2.6 Consensus size: 33
2193643 AGTGAAATAT
*
2193653 TTTTTTTTTCATTTCTCATTTTTTTCTCTAT-TTC-
1 TTTTCTTTTCATTT-TCATTTTTTT-TCT-TCTTCG
2193687 TTTTCTTTCTCATTTTCATTTTTTTTCTTCTTCG
1 TTTTCTTT-TCATTTTCATTTTTTTTCTTCTTCG
*
2193721 TTTTCGTTTTCGTTTTCATTTT
1 TTTTC-TTTTCATTTTCATTTT
2193743 CTATTTTCAT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
32 1 0.02
33 6 0.12
34 34 0.68
35 9 0.18
ACGTcount: A:0.07, C:0.18, G:0.03, T:0.72
Consensus pattern (33 bp):
TTTTCTTTTCATTTTCATTTTTTTTCTTCTTCG
Found at i:2193750 original size:7 final size:6
Alignment explanation
Indices: 2193658--2193762 Score: 64
Period size: 6 Copynumber: 17.7 Consensus size: 6
2193648 AATATTTTTT
2193658 TTTTCA TTTCTCA TTTT-- TTTCTC- TATTTC- TTTTC- TTTCTCA TTTTCA
1 TTTTCA TTT-TCA TTTTCA TTT-TCA T-TTTCA TTTTCA TTT-TCA TTTTCA
* * *
2193705 TTTT-- TTTTC- TTCTTCG TTTTCG TTTTCG TTTTCA TTTTCTA TTTTCA
1 TTTTCA TTTTCA TT-TTCA TTTTCA TTTTCA TTTTCA TTTTC-A TTTTCA
2193752 TTTTCTA TTTT
1 TTTTC-A TTTT
2193763 TTTTCTTCTT
Statistics
Matches: 87, Mismatches: 1, Indels: 21
0.80 0.01 0.19
Matches are distributed among these distances:
4 7 0.08
5 10 0.11
6 46 0.53
7 24 0.28
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.70
Consensus pattern (6 bp):
TTTTCA
Found at i:2193751 original size:13 final size:13
Alignment explanation
Indices: 2193733--2193762 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2193723 TTCGTTTTCG
2193733 TTTTCATTTTCTA
1 TTTTCATTTTCTA
2193746 TTTTCATTTTCTA
1 TTTTCATTTTCTA
2193759 TTTT
1 TTTT
2193763 TTTTCTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTCATTTTCTA
Found at i:2193774 original size:17 final size:17
Alignment explanation
Indices: 2193657--2193784 Score: 63
Period size: 17 Copynumber: 7.3 Consensus size: 17
2193647 AAATATTTTT
*
2193657 TTTTTCATTTCTCATTT-
1 TTTTTCTTTTCT-ATTTC
2193674 TTTTCTCTATTTCT-TTTC
1 TTTT-TCT-TTTCTATTTC
*
2193692 TTTCTCATTTTC-ATTT-
1 TTTTTC-TTTTCTATTTC
2193708 TTTTTCTTCTTCGT-TTTC
1 TTTTTCTT-TTC-TATTTC
*
2193726 GTTTTCGTTTTC-ATTTTC
1 TTTTTC-TTTTCTA-TTTC
2193744 TATTTTCATTTTCTATTT-
1 T-TTTTC-TTTTCTATTTC
* *
2193762 TTTTTCTTCTTCTGTTTG
1 TTTTTCTT-TTCTATTTC
2193780 TTTTT
1 TTTTT
2193785 TTCTTCTTCT
Statistics
Matches: 88, Mismatches: 7, Indels: 31
0.70 0.06 0.25
Matches are distributed among these distances:
15 2 0.02
16 10 0.11
17 31 0.35
18 24 0.27
19 20 0.23
20 1 0.01
ACGTcount: A:0.07, C:0.17, G:0.04, T:0.72
Consensus pattern (17 bp):
TTTTTCTTTTCTATTTC
Found at i:2195345 original size:47 final size:45
Alignment explanation
Indices: 2195275--2195400 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
2195265 TATAAAATCT
*
2195275 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
2195320 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
2195367 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
2195401 GCATGGTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 37 0.51
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:2195548 original size:40 final size:40
Alignment explanation
Indices: 2195504--2195625 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
2195494 ACCGTAGTGC
2195504 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
2195544 TACACATAAGGTCGTGCCCACCATATACTCCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
2195584 TACACATAAGGTCGTGTCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2195624 TA
1 TA
2195626 TAAACCTGCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:2198697 original size:15 final size:16
Alignment explanation
Indices: 2198664--2198702 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2198654 CTGTTTCAAT
*
2198664 TTTATTTTTACTTTAG
1 TTTATTTTGACTTTAG
*
2198680 TTTATTTTGGCTTT-G
1 TTTATTTTGACTTTAG
2198695 TTTATTTT
1 TTTATTTT
2198703 CTTGGTGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.13, C:0.05, G:0.10, T:0.72
Consensus pattern (16 bp):
TTTATTTTGACTTTAG
Found at i:2199561 original size:2 final size:2
Alignment explanation
Indices: 2199554--2199578 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2199544 CCCGATTCTT
2199554 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2199579 TTTTAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2199730 original size:101 final size:102
Alignment explanation
Indices: 2199554--2199756 Score: 390
Period size: 101 Copynumber: 2.0 Consensus size: 102
2199544 CCCGATTCTT
*
2199554 TCTCTCTCTCTCTCTCTCTCTCTCTTTTTAAATATAAGTGAAAGTACATACTAAATTGAACATAA
1 TCTCTATCTCTCTCTCTCTCTCTCTTTTTAAATATAAGTGAAAGTACATACTAAATTGAACATAA
2199619 GATGAACTTTGAAGTTCAAGCTGTGAAGACAATAAAA
66 GATGAACTTTGAAGTTCAAGCTGTGAAGACAATAAAA
2199656 TCTCTATCTCTCTCTCTCTCTCTC-TTTTAAATATAAGTGAAAGTACATACTAAATTGAACATAA
1 TCTCTATCTCTCTCTCTCTCTCTCTTTTTAAATATAAGTGAAAGTACATACTAAATTGAACATAA
2199720 GATGAACTTTGAAGTTCAAGCTGTGAAGACAATAAAA
66 GATGAACTTTGAAGTTCAAGCTGTGAAGACAATAAAA
2199757 ATTAAGGACT
Statistics
Matches: 100, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
101 77 0.77
102 23 0.23
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (102 bp):
TCTCTATCTCTCTCTCTCTCTCTCTTTTTAAATATAAGTGAAAGTACATACTAAATTGAACATAA
GATGAACTTTGAAGTTCAAGCTGTGAAGACAATAAAA
Found at i:2199882 original size:11 final size:11
Alignment explanation
Indices: 2199866--2199904 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2199856 CAATATATTC
2199866 ACGAATATTAA
1 ACGAATATTAA
**
2199877 ACGAATATGTTC
1 ACGAATAT-TAA
2199889 ACGAATATTAA
1 ACGAATATTAA
2199900 ACGAA
1 ACGAA
2199905 CCAAACACGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.26
Consensus pattern (11 bp):
ACGAATATTAA
Found at i:2199883 original size:23 final size:23
Alignment explanation
Indices: 2199857--2199904 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
2199847 AACATATAAC
2199857 AATATATTCACGAATATTAAACG
1 AATATATTCACGAATATTAAACG
*
2199880 AATATGTTCACGAATATTAAACG
1 AATATATTCACGAATATTAAACG
2199903 AA
1 AA
2199905 CCAAACACGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.29
Consensus pattern (23 bp):
AATATATTCACGAATATTAAACG
Found at i:2202104 original size:14 final size:14
Alignment explanation
Indices: 2202082--2202111 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2202072 AGGCTTCCTT
*
2202082 TTCAGATGCATTCA
1 TTCAAATGCATTCA
2202096 TTCAAATGCATTCA
1 TTCAAATGCATTCA
2202110 TT
1 TT
2202112 AATTGATTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (14 bp):
TTCAAATGCATTCA
Found at i:2202610 original size:28 final size:24
Alignment explanation
Indices: 2202544--2202606 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
2202534 ACAAGCATCG
2202544 AATTTTTCAAATAAAAATAATTCTT
1 AATTTTT-AAATAAAAATAATTCTT
2202569 AATTTTTAAATAAAAATAATTCTT
1 AATTTTTAAATAAAAATAATTCTT
*
2202593 AATTTTCAAATAAA
1 AATTTTTAAATAAA
2202607 TAAATAAAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
24 30 0.81
25 7 0.19
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (24 bp):
AATTTTTAAATAAAAATAATTCTT
Found at i:2203380 original size:13 final size:13
Alignment explanation
Indices: 2203362--2203394 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2203352 AGCATTGTGA
*
2203362 AAAGAAAATAATG
1 AAAGAAAATAAAG
2203375 AAAGAAAATAAAG
1 AAAGAAAATAAAG
2203388 AAAGAAA
1 AAAGAAA
2203395 GGTCGATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (13 bp):
AAAGAAAATAAAG
Found at i:2205919 original size:18 final size:18
Alignment explanation
Indices: 2205875--2205921 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
2205865 ATAAATGAAT
*
2205875 AAAATAAATAATTATTGA
1 AAAATAAATAATTAATGA
2205893 ATAAA-AAATAA-TAATGA
1 A-AAATAAATAATTAATGA
2205910 GAAAATAAATAA
1 -AAAATAAATAA
2205922 AATAGAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 8 0.32
18 14 0.56
19 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (18 bp):
AAAATAAATAATTAATGA
Found at i:2210903 original size:25 final size:25
Alignment explanation
Indices: 2210866--2210914 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2210856 AATCTATGTA
2210866 AAAATTAACTAAAACAAGTCAATGC
1 AAAATTAACTAAAACAAGTCAATGC
* *
2210891 AAAATTCATTAAAACAAGTCAATG
1 AAAATTAACTAAAACAAGTCAATG
2210915 AATTTGTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.55, C:0.14, G:0.08, T:0.22
Consensus pattern (25 bp):
AAAATTAACTAAAACAAGTCAATGC
Found at i:2212448 original size:22 final size:21
Alignment explanation
Indices: 2212419--2212477 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 21
2212409 ATATATCGGT
2212419 AATTGAGTTGCGAAATTGGCG
1 AATTGAGTTGCGAAATTGGCG
*
2212440 AATTAGAGTTGCGAAATTTGCG
1 AATT-GAGTTGCGAAATTGGCG
2212462 AATTCGAGTTGCGAAA
1 AATT-GAGTTGCGAAA
2212478 AATGAAATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 4 0.11
22 31 0.89
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (21 bp):
AATTGAGTTGCGAAATTGGCG
Found at i:2212459 original size:120 final size:120
Alignment explanation
Indices: 2212207--2212437 Score: 309
Period size: 120 Copynumber: 1.9 Consensus size: 120
2212197 TTATATTTTG
* * * * * **
2212207 CAACACGAATTTGTCAAATTTGAAACTTAGTTTTTAAATTGGCGAATTTGAATTTTTTATTAAAT
1 CAACATGAATTTGTCAAATTCGAAACTCAGTTTTCAAATTGGCGAATTCGAATTTTTTACCAAAT
* * * *
2212272 TTTTCTATCGTGTTTACCTATATCGGTAATTGAGTTGCGAAATTGGTCAAATTCA
66 TTTTCTACCATATTTACATATATCGGTAATTGAGTTGCGAAATTGGTCAAATTCA
* ** **
2212327 CAACATGAATTTGTCAAATTCGCAACTCAGTTTTCAAATTGGCGAATTCGGTTTTTTTACCGGAT
1 CAACATGAATTTGTCAAATTCGAAACTCAGTTTTCAAATTGGCGAATTCGAATTTTTTACCAAAT
*
2212392 TTTTTTACCATATTTACATATATCGGTAATTGAGTTGCGAAATTGG
66 TTTTCTACCATATTTACATATATCGGTAATTGAGTTGCGAAATTGG
2212438 CGAATTAGAG
Statistics
Matches: 94, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
120 94 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.41
Consensus pattern (120 bp):
CAACATGAATTTGTCAAATTCGAAACTCAGTTTTCAAATTGGCGAATTCGAATTTTTTACCAAAT
TTTTCTACCATATTTACATATATCGGTAATTGAGTTGCGAAATTGGTCAAATTCA
Found at i:2212500 original size:20 final size:21
Alignment explanation
Indices: 2212462--2212500 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2212452 GAAATTTGCG
2212462 AATTCGAGTTGCGAAAAATGA
1 AATTCGAGTTGCGAAAAATGA
*
2212483 AATTCGCGTTGC-AAAAAT
1 AATTCGAGTTGCGAAAAAT
2212501 TTTCATGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.26
Consensus pattern (21 bp):
AATTCGAGTTGCGAAAAATGA
Found at i:2212556 original size:20 final size:20
Alignment explanation
Indices: 2212508--2212563 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
2212498 AATTTTCATG
* *
2212508 TTCGAGTTGCGAATT-CTAC
1 TTCGAGTTGCGAATTCCAAA
*
2212527 TTCTGTGTTGCGAATTCCAAA
1 TTC-GAGTTGCGAATTCCAAA
2212548 TTCGAGTTGCGAATTC
1 TTCGAGTTGCGAATTC
2212564 ATTTGTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 3 0.10
20 23 0.74
21 5 0.16
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (20 bp):
TTCGAGTTGCGAATTCCAAA
Found at i:2215545 original size:30 final size:30
Alignment explanation
Indices: 2215507--2215583 Score: 147
Period size: 30 Copynumber: 2.6 Consensus size: 30
2215497 GAACAATTTG
2215507 GTTA-GTGATTTGATTGACATAATTAAATA
1 GTTAGGTGATTTGATTGACATAATTAAATA
2215536 GTTAGGTGATTTGATTGACATAATTAAATA
1 GTTAGGTGATTTGATTGACATAATTAAATA
2215566 GTTAGGTGATTTGATTGA
1 GTTAGGTGATTTGATTGA
2215584 TAAAAGTTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 4 0.09
30 43 0.91
ACGTcount: A:0.34, C:0.03, G:0.22, T:0.42
Consensus pattern (30 bp):
GTTAGGTGATTTGATTGACATAATTAAATA
Found at i:2219301 original size:2 final size:2
Alignment explanation
Indices: 2219292--2219331 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2219282 ATATATTTTG
2219292 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2219332 TACAAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2221959 original size:58 final size:58
Alignment explanation
Indices: 2221869--2221985 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
2221859 CCTTTCGATC
2221869 GCATTTTTGTCGAGTGCACTCCTGAAGATATTAGAAATGTCGATGGTAACAAAAAGAT
1 GCATTTTTGTCGAGTGCACTCCTGAAGATATTAGAAATGTCGATGGTAACAAAAAGAT
2221927 GCATTTTTGTCGAGTGCACTCCTGAAGATATTAGAAATGTCGATGGTAACAAAAAGAT
1 GCATTTTTGTCGAGTGCACTCCTGAAGATATTAGAAATGTCGATGGTAACAAAAAGAT
2221985 G
1 G
2221986 AAGATCGAAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (58 bp):
GCATTTTTGTCGAGTGCACTCCTGAAGATATTAGAAATGTCGATGGTAACAAAAAGAT
Found at i:2222436 original size:26 final size:26
Alignment explanation
Indices: 2222406--2222457 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
2222396 AAACAGGGTC
2222406 ACATGAGCCAGAAGTCAAGTGCTAGG
1 ACATGAGCCAGAAGTCAAGTGCTAGG
*
2222432 ACATGAGCCAGAGGTCAAGTGCTAGG
1 ACATGAGCCAGAAGTCAAGTGCTAGG
2222458 GGCGCTGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.19, G:0.33, T:0.15
Consensus pattern (26 bp):
ACATGAGCCAGAAGTCAAGTGCTAGG
Found at i:2232288 original size:18 final size:17
Alignment explanation
Indices: 2232256--2232290 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2232246 CCCAGAGTTA
*
2232256 TTTTGTTTTTTATATAT
1 TTTTATTTTTTATATAT
2232273 TTTTATTTTATTATATAT
1 TTTTATTTT-TTATATAT
2232291 ATATATATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTATTTTTTATATAT
Found at i:2233380 original size:20 final size:20
Alignment explanation
Indices: 2233357--2233409 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2233347 AAATGACGTG
2233357 TTTCCCTTTAAATATTATGC
1 TTTCCCTTTAAATATTATGC
* *
2233377 TTTCCCTTTAAATATTGTGT
1 TTTCCCTTTAAATATTATGC
2233397 TTTCCCTTTAAAT
1 TTTCCCTTTAAAT
2233410 CTGTTTGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.53
Consensus pattern (20 bp):
TTTCCCTTTAAATATTATGC
Found at i:2233525 original size:10 final size:11
Alignment explanation
Indices: 2233500--2233548 Score: 50
Period size: 10 Copynumber: 4.7 Consensus size: 11
2233490 GTCCTTTCTA
2233500 TTTATTTAATT
1 TTTATTTAATT
2233511 TTTATTTAA-T
1 TTTATTTAATT
*
2233521 TTTA-TTATTT
1 TTTATTTAATT
* *
2233531 TTTA-CTAACT
1 TTTATTTAATT
2233541 TTTATTTA
1 TTTATTTA
2233549 TCTTTGTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
9 3 0.10
10 17 0.55
11 11 0.35
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTATTTAATT
Found at i:2233577 original size:3 final size:3
Alignment explanation
Indices: 2233555--2233602 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
2233545 TTTATCTTTG
2233555 TTA TCTA TT- TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2233598 ATA TT
1 TTA TT
2233603 TTTTCTCTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 6 0.15
3 30 0.77
4 3 0.08
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2235474 original size:21 final size:21
Alignment explanation
Indices: 2235448--2235502 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
2235438 AAGGAACAAA
*
2235448 CATTGGATACACCACCTCAAG
1 CATTGGACACACCACCTCAAG
2235469 CATTGGACACACCACCTCAAG
1 CATTGGACACACCACCTCAAG
2235490 CATTGGACACACC
1 CATTGGACACACC
2235503 TTATCCACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.36, G:0.15, T:0.16
Consensus pattern (21 bp):
CATTGGACACACCACCTCAAG
Found at i:2236462 original size:95 final size:93
Alignment explanation
Indices: 2236278--2236520 Score: 294
Period size: 94 Copynumber: 2.7 Consensus size: 93
2236268 TATAATATTA
* *
2236278 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAAAGCCCGACTTTATGGAT
1 TATATATACAATAAAGCTTGAGCTATCCCTCTAGAGCAATTGGTTAAAAGCCCGACTTTATGGAT
* * *
2236343 AATATTCAGTTAGCCTGATAAAGGTGAT
66 AAGATTCAGCTAACCTGATAAAGGTGAT
*
2236371 TATACTATACAATAAAGCTTGAGCTATCCCTCTA-AGGCAATTGGTTAAAAGCCCTGGCTTTATG
1 TATA-TATACAATAAAGCTTGAGCTATCCCTCTAGA-GCAATTGGTTAAAAGCCC-GACTTTATG
2236435 GATAAGATTCAGCTAACCTGATAAAGGTG--
63 GATAAGATTCAGCTAACCTGATAAAGGTGAT
* *
2236464 --T-T-TAC-AT--A--TTGAGCTATCCCTCTAGAGCAATTGGTTAAACGCCCTAGCTTTATGGA
1 TATATATACAATAAAGCTTGAGCTATCCCTCTAGAGCAATTGGTTAAAAGCCCGA-CTTTATGGA
2236520 T
65 T
2236521 TCAACTAGCC
Statistics
Matches: 136, Mismatches: 9, Indels: 20
0.82 0.05 0.12
Matches are distributed among these distances:
83 43 0.32
84 1 0.01
85 1 0.01
87 2 0.01
88 3 0.02
89 1 0.01
91 1 0.01
93 5 0.04
94 45 0.33
95 34 0.25
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (93 bp):
TATATATACAATAAAGCTTGAGCTATCCCTCTAGAGCAATTGGTTAAAAGCCCGACTTTATGGAT
AAGATTCAGCTAACCTGATAAAGGTGAT
Found at i:2237666 original size:43 final size:43
Alignment explanation
Indices: 2237549--2237666 Score: 139
Period size: 43 Copynumber: 2.7 Consensus size: 43
2237539 GGCCATCCAT
* * ** *
2237549 GATTTCAGCTCCACGACGGAGGATATCGTACCCACGGATCCAC
1 GATTTCAACTCCACGACGGAGGATATCGTGCCCACACAACCAC
* * *
2237592 GATTTCAACTCCTCGACGGAGGATATTGTGCCCACACAACCGC
1 GATTTCAACTCCACGACGGAGGATATCGTGCCCACACAACCAC
*
2237635 GATTTCAACTCCACAAC-GACGGATATCGTGCC
1 GATTTCAACTCCACGACGGA-GGATATCGTGCC
2237667 AACTCTAGAT
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 2 0.03
43 61 0.97
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.20
Consensus pattern (43 bp):
GATTTCAACTCCACGACGGAGGATATCGTGCCCACACAACCAC
Found at i:2238099 original size:37 final size:36
Alignment explanation
Indices: 2238008--2238268 Score: 218
Period size: 37 Copynumber: 7.2 Consensus size: 36
2237998 AATTTACTCA
2238008 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
2238045 AAATAAATTTTATCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
2238081 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 -AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
2238118 AAACAAA------ATCT-TTGA-ATATGTTT-TACATT-
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCT-C-TTG
* * * *
2238147 AAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* **
2238183 GAACTATGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
2238220 GAACAAATTTTGTCTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAA-----T-TTTGTCTCTCTTGAGACAGTTTCTCTTG
2238262 AAACAAA
1 AAACAAA
2238269 ATCTTTGAAT
Statistics
Matches: 179, Mismatches: 24, Indels: 37
0.75 0.10 0.15
Matches are distributed among these distances:
28 3 0.02
29 16 0.09
30 5 0.03
35 4 0.02
36 45 0.25
37 72 0.40
41 1 0.01
42 33 0.18
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:2238267 original size:144 final size:139
Alignment explanation
Indices: 2238008--2238350 Score: 458
Period size: 144 Copynumber: 2.4 Consensus size: 139
2237998 AATTTACTCA
* * * * * *
2238008 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT-GAAATAAATTTTATCTCTCTTGAGACAG
1 AAACAAA-TTTTGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
*
2238072 TTTCCCTTGAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAATAT
65 TTTCCCTTGAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATAT
2238137 GTTTTACATT-
130 GTTTT-CATTG
* *
2238147 AAACAAATTTCGTCTCCCTTGAGACAATTTCTTTTGGAACTATGTTTTGTCTCTCTTGAGACAGT
1 AAACAAATTTTGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGT
* *
2238212 TTCTCTTG-GAACAAATTTTGTCTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTG
66 TTCCCTTGAAAACAAA-----T-TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTG
*
2238276 AATATGTTTTCCTTG
125 AATATGTTTTCATTG
* *
2238291 AAACAAATTTTGTCTCCCTTGAGACAGTTTTCTTTCGGAACTAAGTTTTGTCTCTCTTGA
1 AAACAAATTTTGTCTCCCTTGAGACA-ATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGA
2238351 AACAAAATTT
Statistics
Matches: 179, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
138 30 0.17
139 39 0.22
143 4 0.02
144 76 0.42
145 30 0.17
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (139 bp):
AAACAAATTTTGTCTCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGT
TTCCCTTGAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATG
TTTTCATTG
Found at i:2238361 original size:22 final size:22
Alignment explanation
Indices: 2238336--2238377 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2238326 CGGAACTAAG
* *
2238336 TTTTGTCTCTCTTGAAACAAAA
1 TTTTGCCTCCCTTGAAACAAAA
*
2238358 TTTTGCCTCCCTTGAGACAA
1 TTTTGCCTCCCTTGAAACAA
2238378 TTTCTCTTGA
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:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (22 bp):
TTTTGCCTCCCTTGAAACAAAA
Found at i:2239194 original size:18 final size:17
Alignment explanation
Indices: 2239140--2239188 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2239130 TTGGACCCTT
* *
2239140 AGTGCATCGATACACTAA
1 AGTGCATCGATGCA-TCA
2239158 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
2239176 AGTGCATTCGATG
1 AGTGCA-TCGATG
2239189 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:2239228 original size:64 final size:64
Alignment explanation
Indices: 2239160--2239369 Score: 239
Period size: 65 Copynumber: 3.2 Consensus size: 64
2239150 TACACTAAGA
* *
2239160 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGTTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTTG
**
2239224 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATATCCAGAGTGCATCGATGCATGGT-
2239288 T-
63 TG
* * * ** *
2239289 GTGCATTGATGCATGAAATGCATTCAATG-TTCAATTTAATTCATGA-TGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ATCCA-GAGTGCATCGATGCATGG-T
2239352 TG
63 TG
*
2239354 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
2239370 CTTGATAAAT
Statistics
Matches: 123, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 47 0.38
65 67 0.54
66 4 0.03
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTTG
Found at i:2239750 original size:40 final size:40
Alignment explanation
Indices: 2239692--2239775 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 40
2239682 TTTTGAAAAA
*
2239692 TTACTCCCCCTTACTACAACACTTCTCCCCTTTAACACTT
1 TTACTCACCCTTACTACAACACTTCTCCCCTTTAACACTT
* * * *
2239732 TTACTCACCCTTATTACAATATTTCTCCCCTTTGACACTT
1 TTACTCACCCTTACTACAACACTTCTCCCCTTTAACACTT
2239772 TTAC
1 TTAC
2239776 ACTTCTTTCC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.23, C:0.37, G:0.01, T:0.39
Consensus pattern (40 bp):
TTACTCACCCTTACTACAACACTTCTCCCCTTTAACACTT
Found at i:2242083 original size:20 final size:21
Alignment explanation
Indices: 2242026--2242087 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
2242016 TCGGTGCACC
*
2242026 TTCATGGTGTATCGATGCATA
1 TTCAAGGTGTATCGATGCATA
*
2242047 TTCAAGGATGCATCGATGCAT-
1 TTCAAGG-TGTATCGATGCATA
*
2242068 TGT-TAGGTGTATCGATGCAT
1 T-TCAAGGTGTATCGATGCAT
2242088 GAAGCACAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 12 0.34
21 10 0.29
22 13 0.37
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (21 bp):
TTCAAGGTGTATCGATGCATA
Found at i:2247408 original size:20 final size:20
Alignment explanation
Indices: 2247385--2247422 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2247375 CAAGAATATA
2247385 CTCCAATTCTTGAGAACACT
1 CTCCAATTCTTGAGAACACT
2247405 CTCCAATTCTTGAGAACA
1 CTCCAATTCTTGAGAACA
2247423 TTCTTTCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.29, G:0.11, T:0.29
Consensus pattern (20 bp):
CTCCAATTCTTGAGAACACT
Found at i:2248070 original size:65 final size:64
Alignment explanation
Indices: 2247872--2248081 Score: 241
Period size: 65 Copynumber: 3.2 Consensus size: 64
2247862 TGCACTAAGA
* * ** *
2247872 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGTTG
*
2247936 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGATGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGGT
2247999 AT-
63 -TG
* *
2248001 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCATGG-TT
2248065 G
64 G
*
2248066 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
2248082 CTTTGATAAA
Statistics
Matches: 125, Mismatches: 11, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 52 0.42
65 64 0.51
66 1 0.01
67 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGTTG
Done.