Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008703.1 Hibiscus syriacus cultivar Beakdansim tig00111742_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: 1275178
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:305758 original size:21 final size:22
Alignment explanation
Indices: 305725--305766 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
305715 GTTATAAATT
*
305725 ATAATTTGAATAACTC-GAATA
1 ATAACTTGAATAACTCAGAATA
*
305746 ATAACTTGGATAACTCAGAAT
1 ATAACTTGAATAACTCAGAAT
305767 TTTTTATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (22 bp):
ATAACTTGAATAACTCAGAATA
Found at i:306069 original size:18 final size:17
Alignment explanation
Indices: 306037--306070 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
306027 TCGATTTAAG
306037 TTCATCAACCATTAACT
1 TTCATCAACCATTAACT
*
306054 TTCATTAACTCATTAAC
1 TTCATCAAC-CATTAAC
306071 GAAAGAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.38
Consensus pattern (17 bp):
TTCATCAACCATTAACT
Found at i:312673 original size:39 final size:39
Alignment explanation
Indices: 312619--312693 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
312609 CTTGTAGACC
* *
312619 CAGTAAGGGCATACCCTGTGCAAAAAGAAGAGGAGCTTG
1 CAGTAAGGACATACCCTGAGCAAAAAGAAGAGGAGCTTG
* * **
312658 CAGTAAGGACTTACCCTGAGCACAAAGCTGAGGAGC
1 CAGTAAGGACATACCCTGAGCAAAAAGAAGAGGAGC
312694 CTGTGGAAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.35, C:0.21, G:0.29, T:0.15
Consensus pattern (39 bp):
CAGTAAGGACATACCCTGAGCAAAAAGAAGAGGAGCTTG
Found at i:312761 original size:44 final size:43
Alignment explanation
Indices: 312660--312959 Score: 220
Period size: 44 Copynumber: 6.8 Consensus size: 43
312650 GGAGCTTGCA
* * * ** * *
312660 GTAAGGACTTACCCTGAGCACAAAGCTGAGGAGCCTGTGGAAAGCG
1 GTAAGGTCTTACCCT-TGCACATAGCAAAGGAGCCTAT-GAAA-TG
*
312706 GTAAGGTCTTACCCTTGCACATAGCAAAGGATCCTATGGAAATG
1 GTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTAT-GAAATG
* * * * * *
312750 TTAAGGTCTTACCCTGGCACATAGTAGAGGAGTCTTTAGAAATG
1 GTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTAT-GAAATG
* * * *
312794 GTAAGGTTTTACCCTTACACACAGCAGAGGAGCCT-TCAGAAATG
1 GTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTAT--GAAATG
*
312838 GTAAGGTCTCACCCTTG--CATA-CAATAGAAGAGCCCTCA-GAAATG
1 GTAAGGTCTTACCCTTGCACATAGCAA-AG--GAG-CCT-ATGAAATG
* *
312882 GTAA-GTCTTACCCTTGCACAAAGTAGAA-GAGCCTTCAT-AAATG
1 GTAAGGTCTTACCCTTGCACATAGCA-AAGGAGCC-T-ATGAAATG
312925 GTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCT
1 GTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCT
312960 TCATAAACTT
Statistics
Matches: 206, Mismatches: 33, Indels: 33
0.76 0.12 0.12
Matches are distributed among these distances:
41 2 0.01
42 7 0.03
43 30 0.15
44 123 0.60
45 27 0.13
46 16 0.08
47 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.23
Consensus pattern (43 bp):
GTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTATGAAATG
Found at i:312807 original size:88 final size:87
Alignment explanation
Indices: 312660--312960 Score: 261
Period size: 88 Copynumber: 3.4 Consensus size: 87
312650 GGAGCTTGCA
* * * * *
312660 GTAAGGACTTACCCTGAGCACAAAGCT-GAGGAGCCTGTGGAAAGCGGTAAGGTCTTACCCTTGC
1 GTAAGGTCTTACCCTG-GCACATAG-TAGAGGAGCCTTTAGAAA-TGGTAAGGTCTTACCCTTGC
* *
312724 ACATAGCAAAGGATCCTATGGAAATG
63 ACAAAGCAAAGGAGCCTAT-GAAATG
* * * *
312750 TTAAGGTCTTACCCTGGCACATAGTAGAGGAGTCTTTAGAAATGGTAAGGTTTTACCCTTACACA
1 GTAAGGTCTTACCCTGGCACATAGTAGAGGAGCCTTTAGAAATGGTAAGGTCTTACCCTTGCACA
* *
312815 CAGCAGAGGAGCCT-TCAGAAATG
66 AAGCAAAGGAGCCTAT--GAAATG
* * * * * * * *
312838 GTAAGGTCTCACCCTTGCATACAATAGAAGAGCCCTCAGAAATGGTAA-GTCTTACCCTTGCACA
1 GTAAGGTCTTACCCTGGCACATAGTAGAGGAGCCTTTAGAAATGGTAAGGTCTTACCCTTGCACA
*
312902 AAGTAGAA-GAGCCTTCAT-AAATG
66 AAGCA-AAGGAGCC-T-ATGAAATG
* * *
312925 GTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTT
1 GTAAGGTCTTACCCTGGCACATAGTAGAGGAGCCTT
312961 CATAAACTTC
Statistics
Matches: 169, Mismatches: 36, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
87 56 0.33
88 78 0.46
89 20 0.12
90 15 0.09
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.23
Consensus pattern (87 bp):
GTAAGGTCTTACCCTGGCACATAGTAGAGGAGCCTTTAGAAATGGTAAGGTCTTACCCTTGCACA
AAGCAAAGGAGCCTATGAAATG
Found at i:312966 original size:44 final size:44
Alignment explanation
Indices: 312705--312962 Score: 276
Period size: 44 Copynumber: 5.9 Consensus size: 44
312695 TGTGGAAAGC
* *
312705 GGTAAGGTCTTACCCTTGCACATAGCAAAGGATCCTAT-GGAAAT
1 GGTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCT-TCAGAAAT
* * * * * *
312749 GTTAAGGTCTTACCCTGGCACATAGTAGAGGAGTCTTTAGAAAT
1 GGTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTTCAGAAAT
* * * *
312793 GGTAAGGTTTTACCCTTACACACAGCAGAGGAGCCTTCAGAAAT
1 GGTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTTCAGAAAT
* *
312837 GGTAAGGTCTCACCCTTG--CATA-CAATAGAAGAGCCCTCAGAAAT
1 GGTAAGGTCTTACCCTTGCACATAGCAA-AG--GAGCCTTCAGAAAT
* * *
312881 GGTAA-GTCTTACCCTTGCACAAAGTAGAA-GAGCCTTCATAAAT
1 GGTAAGGTCTTACCCTTGCACATAGCA-AAGGAGCCTTCAGAAAT
312924 GGTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTTCA
1 GGTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTTCA
312963 TAAACTTCAT
Statistics
Matches: 176, Mismatches: 28, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
41 2 0.01
42 5 0.03
43 31 0.18
44 132 0.75
45 3 0.02
46 2 0.01
47 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (44 bp):
GGTAAGGTCTTACCCTTGCACATAGCAAAGGAGCCTTCAGAAAT
Found at i:319443 original size:16 final size:17
Alignment explanation
Indices: 319422--319454 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
319412 GATTATTTGG
319422 TTTGGATATTT-GTTTT
1 TTTGGATATTTAGTTTT
*
319438 TTTGGATGTTTAGTTTT
1 TTTGGATATTTAGTTTT
319455 GGTTTGTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.12, C:0.00, G:0.21, T:0.67
Consensus pattern (17 bp):
TTTGGATATTTAGTTTT
Found at i:319754 original size:13 final size:13
Alignment explanation
Indices: 319736--319762 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
319726 TAGTAAGGGG
319736 AAGTAATTTTTCA
1 AAGTAATTTTTCA
319749 AAGTAATTTTTCA
1 AAGTAATTTTTCA
319762 A
1 A
319763 TAGATTAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (13 bp):
AAGTAATTTTTCA
Found at i:319774 original size:20 final size:20
Alignment explanation
Indices: 319749--319790 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
319739 TAATTTTTCA
*
319749 AAGTAATTTTTCAATAGATT
1 AAGTAATTTTTCAAAAGATT
*
319769 AAGTAATTTTTTAAAAGATT
1 AAGTAATTTTTCAAAAGATT
319789 AA
1 AA
319791 AATCTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (20 bp):
AAGTAATTTTTCAAAAGATT
Found at i:323174 original size:2 final size:2
Alignment explanation
Indices: 323167--323200 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
323157 TTTAACCATA
323167 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
323201 CTTTCTGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:325438 original size:20 final size:20
Alignment explanation
Indices: 325413--325469 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
325403 TTTATTTATG
* *
325413 GCATCCTTTTAAGCCTTAAT
1 GCATCCTTTCAAGCATTAAT
*
325433 GCATCCTTTCATGCATTAAT
1 GCATCCTTTCAAGCATTAAT
*
325453 GCATCCTTTCATGCATT
1 GCATCCTTTCAAGCATT
325470 TTATTTATGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.40
Consensus pattern (20 bp):
GCATCCTTTCAAGCATTAAT
Found at i:325527 original size:34 final size:34
Alignment explanation
Indices: 325484--325706 Score: 185
Period size: 34 Copynumber: 5.9 Consensus size: 34
325474 TTATGGCATC
*
325484 CTTTCATGCCAATAATGCACCCATATGCATTATT
1 CTTTTATGCCAATAATGCACCCATATGCATTATT
* *
325518 CTTTTATGCCGATAATGCACCCATATACATTTCAGCTAT
1 CTTTTATGCCAATAATGCACCCATATGCA-TT-A--T-T
325557 GGCATCCTTTAATGCCAATAATGCACCCATATGCATTATT
1 --C-T--TTT-ATGCCAATAATGCACCCATATGCATTATT
*
325597 CTTTTATGCCGATAATGCACCCATATGGATTTCATCTATT
1 CTTTTATGCCAATAATGCACCCATAT-G----CAT-TATT
*
325637 GCATTCTTTCATGCAAATAATGCACCCATATGCATTATT
1 -C--T-TTT-ATGCCAATAATGCACCCATATGCATTATT
**
325676 CTTTTATGCCGCTAATGCACCCATATGCATT
1 CTTTTATGCCAATAATGCACCCATATGCATT
325707 TCAGCGATGA
Statistics
Matches: 156, Mismatches: 11, Indels: 44
0.74 0.05 0.21
Matches are distributed among these distances:
34 69 0.44
35 9 0.06
36 2 0.01
37 1 0.01
38 3 0.02
39 8 0.05
40 8 0.05
41 3 0.02
42 1 0.01
43 2 0.01
44 9 0.06
45 41 0.26
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (34 bp):
CTTTTATGCCAATAATGCACCCATATGCATTATT
Found at i:325563 original size:79 final size:79
Alignment explanation
Indices: 325475--325761 Score: 484
Period size: 79 Copynumber: 3.6 Consensus size: 79
325465 GCATTTTATT
325475 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
*
325540 ATATACATTTCAGC
66 ATATGCATTTCAGC
*
325554 TATGGCATCCTTTAATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
* *
325619 ATATGGATTTCATC
66 ATATGCATTTCAGC
* * * *
325633 TATTGCATTCTTTCATGCAAATAATGCACCCATATGCATTATTCTTTTATGCCGCTAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
325698 ATATGCATTTCAGC
66 ATATGCATTTCAGC
* *
325712 GATGACATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTAT
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTAT
325762 TCATTCGTTT
Statistics
Matches: 192, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 192 1.00
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (79 bp):
TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGCACCC
ATATGCATTTCAGC
Found at i:325644 original size:45 final size:43
Alignment explanation
Indices: 325594--325747 Score: 121
Period size: 45 Copynumber: 3.7 Consensus size: 43
325584 CATATGCATT
* *
325594 ATTCTTTTATGCCGATAATGCACCCATATGGATTTCATCTATTGC
1 ATTCTTTCATGCCAATAATGCACCCATATGGATTTCA-C-ATTGC
*
325639 ATTCTTTCATGCAAATAATGCACCCATAT-G------CATT--
1 ATTCTTTCATGCCAATAATGCACCCATATGGATTTCACATTGC
* ** *
325673 ATTCTTTTATGCCGCTAATGCACCCATATGCATTTCAGCGA-TGAC
1 ATTCTTTCATGCCAATAATGCACCCATATGGATTTCA-C-ATTG-C
*
325718 ATCCTTTCATGCCAATAATGCACCCATATG
1 ATTCTTTCATGCCAATAATGCACCCATATG
325748 CATTATTCTT
Statistics
Matches: 85, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
34 25 0.29
36 3 0.04
37 1 0.01
42 2 0.02
43 1 0.01
44 1 0.01
45 52 0.61
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.35
Consensus pattern (43 bp):
ATTCTTTCATGCCAATAATGCACCCATATGGATTTCACATTGC
Found at i:326212 original size:22 final size:19
Alignment explanation
Indices: 326162--326237 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 19
326152 ATTTTTGACT
* *
326162 CTATAGTATCGATACCCCTA
1 CTATGGTATCGATA-CTCTA
*
326182 CCATGGTATCGATACTACTATA
1 CTATGGTATCGATACT-C--TA
*
326204 CTATGGTATTGATACTCTA
1 CTATGGTATCGATACTCTA
*
326223 CTATGGTATCTATAC
1 CTATGGTATCGATAC
326238 CATTTTTGCA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
19 16 0.35
20 13 0.28
21 1 0.02
22 16 0.35
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (19 bp):
CTATGGTATCGATACTCTA
Found at i:326287 original size:20 final size:21
Alignment explanation
Indices: 326262--326312 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
326252 TCTTTGAAAT
*
326262 GGTATCGATACTT-TCCCTTC
1 GGTATCGATACTTACCCCTTC
326282 GGTATCGATA-TTACCCCTTC
1 GGTATCGATACTTACCCCTTC
326302 GGTATCGATAC
1 GGTATCGATAC
326313 CGATTGAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (21 bp):
GGTATCGATACTTACCCCTTC
Found at i:327466 original size:34 final size:34
Alignment explanation
Indices: 327411--327554 Score: 108
Period size: 34 Copynumber: 3.9 Consensus size: 34
327401 TTATGACATC
* * *
327411 CTTTCATGCCAATAATACACCCATATGCATTATT
1 CTTTTATGCCGATAATGCACCCATATGCATTATT
* *
327445 CTTTTATGCTGATAATGCACCCATATGTATTTCAGCGATGGCAT
1 CTTTTATGCCGATAATGCACCCATATGCA-TT-----AT----T
* *
327489 CCTTTCATGCCAATAATGCACCCATATGCATTATT
1 -CTTTTATGCCGATAATGCACCCATATGCATTATT
**
327524 CTTTTATGCCGATAATGTGCCCATATGCATT
1 CTTTTATGCCGATAATGCACCCATATGCATT
327555 TCAACGATGG
Statistics
Matches: 86, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
34 51 0.59
35 3 0.03
39 2 0.02
40 2 0.02
44 3 0.03
45 25 0.29
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.36
Consensus pattern (34 bp):
CTTTTATGCCGATAATGCACCCATATGCATTATT
Found at i:327538 original size:79 final size:79
Alignment explanation
Indices: 327407--327676 Score: 423
Period size: 79 Copynumber: 3.4 Consensus size: 79
327397 TTATTTATGA
*
327407 CATCCTTTCATGCCAATAATACACCCATATGCATTATTCTTTTATGCTGATAATGCACCCATATG
1 CATCCTTTCATGCCAATAATACACCCATATGCATTATTCTTTTATGCCGATAATGCACCCATATG
*
327472 TATTTCAGCGATGG
66 CATTTCAGCGATGG
* **
327486 CATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGTGCCCATATG
1 CATCCTTTCATGCCAATAATACACCCATATGCATTATTCTTTTATGCCGATAATGCACCCATATG
*
327551 CATTTCAACGATGG
66 CATTTCAGCGATGG
* * * * *
327565 CATCCTTTCATTCCAATAACACACCCATATTCATTATTCTTTAATGTCGATAATGCACCCATATG
1 CATCCTTTCATGCCAATAATACACCCATATGCATTATTCTTTTATGCCGATAATGCACCCATATG
*
327630 CATTTCAGCTATGG
66 CATTTCAGCGATGG
*
327644 CATACTTTCATGCCAATAATACACCCATATGCA
1 CATCCTTTCATGCCAATAATACACCCATATGCA
327677 ACCAAAACCC
Statistics
Matches: 171, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 171 1.00
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (79 bp):
CATCCTTTCATGCCAATAATACACCCATATGCATTATTCTTTTATGCCGATAATGCACCCATATG
CATTTCAGCGATGG
Found at i:329786 original size:18 final size:17
Alignment explanation
Indices: 329762--329810 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
329752 CCGTTGACCA
*
329762 GTCCGACCCGACCTGTT
1 GTCCGACCCGACCAGTT
329779 GATCCGACCCGACCAGTT
1 G-TCCGACCCGACCAGTT
*
329797 GTCCCGACACGACC
1 GT-CCGACCCGACC
329811 GTCGACCGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.18, C:0.43, G:0.22, T:0.16
Consensus pattern (17 bp):
GTCCGACCCGACCAGTT
Found at i:329872 original size:30 final size:29
Alignment explanation
Indices: 329830--329982 Score: 112
Period size: 28 Copynumber: 5.6 Consensus size: 29
329820 TGACCGGGTT
* *
329830 ATATTTTAGTAATTATTTTGAAAATGGTG
1 ATATTTTTGTAATTATTTTAAAAATGGTG
329859 ATATCTTTTGTAATTATTTTAAAAATGGTG
1 ATAT-TTTTGTAATTATTTTAAAAATGGTG
* *
329889 TTATTTTCGTAATT-TTTT--AAA---TG
1 ATATTTTTGTAATTATTTTAAAAATGGTG
* ***
329912 ATATTTTCGT-A--A-TTTAAAAAAAATG
1 ATATTTTTGTAATTATTTTAAAAATGGTG
* * *
329937 ATATTTTGGTAATT-TTTTGAAAATAGTG
1 ATATTTTTGTAATTATTTTAAAAATGGTG
*
329965 ATATTTTTGTAAATATTT
1 ATATTTTTGTAATTATTT
329983 CTTAAAAGGG
Statistics
Matches: 101, Mismatches: 11, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
20 3 0.03
22 4 0.04
23 11 0.11
25 11 0.11
26 4 0.04
28 26 0.26
29 16 0.16
30 26 0.26
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (29 bp):
ATATTTTTGTAATTATTTTAAAAATGGTG
Found at i:329901 original size:29 final size:29
Alignment explanation
Indices: 329830--329909 Score: 108
Period size: 30 Copynumber: 2.8 Consensus size: 29
329820 TGACCGGGTT
*
329830 ATATTTTAGTAATTATTTTGAAAATGGTG
1 ATATTTTAGTAATTATTTTAAAAATGGTG
*
329859 ATATCTTTTGTAATTATTTTAAAAATGGTG
1 ATAT-TTTAGTAATTATTTTAAAAATGGTG
* *
329889 TTATTTTCGTAATT-TTTTAAA
1 ATATTTTAGTAATTATTTTAAA
329910 TGATATTTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 7 0.15
29 13 0.28
30 26 0.57
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.53
Consensus pattern (29 bp):
ATATTTTAGTAATTATTTTAAAAATGGTG
Found at i:337113 original size:21 final size:21
Alignment explanation
Indices: 337083--337124 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
337073 TTTAAACCGG
*
337083 GTTGACCGGTTCGACCCGACC
1 GTTGACCGGTCCGACCCGACC
*
337104 GTTGATCGGTCCGACCCGACC
1 GTTGACCGGTCCGACCCGACC
337125 CGACCCGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.38, G:0.29, T:0.19
Consensus pattern (21 bp):
GTTGACCGGTCCGACCCGACC
Found at i:341181 original size:18 final size:17
Alignment explanation
Indices: 341160--341194 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
341150 TCTATATAAA
*
341160 GGGGTATCGATATCCTAT
1 GGGGTATCCATA-CCTAT
341178 GGGGTATCCATACCTAT
1 GGGGTATCCATACCTAT
341195 TTTGCATTCG
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:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (17 bp):
GGGGTATCCATACCTAT
Found at i:341578 original size:19 final size:19
Alignment explanation
Indices: 341554--341590 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
341544 ATGCAAAAAT
341554 AGTATCGATACCATAGTAG
1 AGTATCGATACCATAGTAG
*
341573 AGTATCGGTACCATAGTA
1 AGTATCGATACCATAGTA
341591 TAATAGTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (19 bp):
AGTATCGATACCATAGTAG
Found at i:341774 original size:45 final size:43
Alignment explanation
Indices: 341719--342000 Score: 190
Period size: 34 Copynumber: 7.0 Consensus size: 43
341709 ATAAAAGAAT
*
341719 AATGCATATGGGTCCATTATTGGCATGAAAGGATGCCATAACTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAA-T-A
* *
341764 AATGCATATGGGTGGATTATCGGCAT-AAA--A-G----AAT-
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATA
*
341798 AATGCATATGGGTGCATTATAT--CATGAAAGGATGCCATCGATAA
1 AATGCATATGGGTGCATTAT-TGGCATGAAAGGATGCCAT-AAT-A
* *
341842 AATGCATATGGGTGAATTATCGGCAT-AAA--A-G----AAT-
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATA
* *
341876 AATTCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATA-AT-A
341921 AATGCATATGGGTGCATTATTGGCAT--AA--A----ATAAT-
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATA
* * *
341955 AATGCATATTGGTGCATTATTGGTATGAAAGGATACCATAAATA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAT-AATA
341999 AA
1 AA
342001 ATGAAATTTA
Statistics
Matches: 185, Mismatches: 17, Indels: 71
0.68 0.06 0.26
Matches are distributed among these distances:
33 3 0.02
34 69 0.37
35 3 0.02
36 7 0.04
37 7 0.04
38 2 0.01
41 3 0.02
42 7 0.04
43 6 0.03
44 27 0.15
45 51 0.28
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.28
Consensus pattern (43 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATA
Found at i:341900 original size:157 final size:157
Alignment explanation
Indices: 341613--342003 Score: 595
Period size: 157 Copynumber: 2.5 Consensus size: 157
341603 TACCCCTACC
* *
341613 ATGGGTGCATTATTGGCATAAAAGAATAATGCATATGTGTGCATTATTGGAATGGAAGGATGCCA
1 ATGGGTGCATTATTGGCATAAAAGAATAATGCATATGGGTGCATTATT-GAATGAAAGGATGCCA
* *
341678 TAGCTGAAATGCATATGGGTGAATTATCGACATAAAAGAATAATGCATATGGGTCCATTATTGGC
65 TAGATAAAATGCATATGGGTGAATTATCGACATAAAAGAATAATGCATATGGGTCCATTATTGGC
341743 ATGAAAGGATGCCATAACTGAAATGCAT
130 ATGAAAGGATGCCATAACTGAAATGCAT
* * *
341771 ATGGGTGGATTATCGGCATAAAAGAATAATGCATATGGGTGCATTATAT-CATGAAAGGATGCCA
1 ATGGGTGCATTATTGGCATAAAAGAATAATGCATATGGGTGCATTAT-TGAATGAAAGGATGCCA
* * * *
341835 TCGATAAAATGCATATGGGTGAATTATCGGCATAAAAGAATAATTCATATGGGTGCATTATTGGC
65 TAGATAAAATGCATATGGGTGAATTATCGACATAAAAGAATAATGCATATGGGTCCATTATTGGC
*
341900 ATGAAAGGATGCCATAGCTGAAATGCAT
130 ATGAAAGGATGCCATAACTGAAATGCAT
* * * *
341928 ATGGGTGCATTATTGGCATAAAATAATAATGCATATTGGTGCATTATTGGTATGAAAGGATACCA
1 ATGGGTGCATTATTGGCATAAAAGAATAATGCATATGGGTGCATTATT-GAATGAAAGGATGCCA
*
341993 TAAATAAAATG
65 TAGATAAAATG
342004 AAATTTAACA
Statistics
Matches: 210, Mismatches: 20, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
156 1 0.00
157 142 0.68
158 66 0.31
159 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (157 bp):
ATGGGTGCATTATTGGCATAAAAGAATAATGCATATGGGTGCATTATTGAATGAAAGGATGCCAT
AGATAAAATGCATATGGGTGAATTATCGACATAAAAGAATAATGCATATGGGTCCATTATTGGCA
TGAAAGGATGCCATAACTGAAATGCAT
Found at i:342003 original size:79 final size:79
Alignment explanation
Indices: 341613--341994 Score: 570
Period size: 79 Copynumber: 4.8 Consensus size: 79
341603 TACCCCTACC
* * * * *
341613 ATGGGTGCATTATTGGCATAAAAGAATAATGCATATGTGTGCATTATTGGAATGGAAGGATGCCA
1 ATGGGTGAATTATCGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA
341678 TAGCTGAAATGCAT
66 TAGCTGAAATGCAT
* *
341692 ATGGGTGAATTATCGACATAAAAGAATAATGCATATGGGTCCATTATTGGCATGAAAGGATGCCA
1 ATGGGTGAATTATCGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA
*
341757 TAACTGAAATGCAT
66 TAGCTGAAATGCAT
*
341771 ATGGGTGGATTATCGGCATAAAAGAATAATGCATATGGGTGCATTATAT--CATGAAAGGATGCC
1 ATGGGTGAATTATCGGCATAAAAGAATAATGCATATGGGTGCATTAT-TGGCATGAAAGGATGCC
* * *
341834 ATCGATAAAATGCAT
65 ATAGCTGAAATGCAT
*
341849 ATGGGTGAATTATCGGCATAAAAGAATAATTCATATGGGTGCATTATTGGCATGAAAGGATGCCA
1 ATGGGTGAATTATCGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA
341914 TAGCTGAAATGCAT
66 TAGCTGAAATGCAT
* * * * * *
341928 ATGGGTGCATTATTGGCATAAAATAATAATGCATATTGGTGCATTATTGGTATGAAAGGATACCA
1 ATGGGTGAATTATCGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA
341993 TA
66 TA
341995 AATAAAATGA
Statistics
Matches: 273, Mismatches: 27, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
77 1 0.00
78 70 0.26
79 201 0.74
80 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (79 bp):
ATGGGTGAATTATCGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA
TAGCTGAAATGCAT
Found at i:345173 original size:42 final size:42
Alignment explanation
Indices: 345114--345199 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
345104 ATTATACTAT
345114 TAAATTAAATGTTAATTTTGTTAAAAAAATAATATGAAAGTA
1 TAAATTAAATGTTAATTTTGTTAAAAAAATAATATGAAAGTA
345156 TAAATTAAATGTTAATTTTGTTAAAAAAATAATATGAAAGTA
1 TAAATTAAATGTTAATTTTGTTAAAAAAATAATATGAAAGTA
345198 TA
1 TA
345200 TATCATATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.38
Consensus pattern (42 bp):
TAAATTAAATGTTAATTTTGTTAAAAAAATAATATGAAAGTA
Found at i:347293 original size:32 final size:32
Alignment explanation
Indices: 347252--347314 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
347242 TGATAAGTTC
347252 CATTATTTATTCCTCATTTGCTTATTGTTGTA
1 CATTATTTATTCCTCATTTGCTTATTGTTGTA
347284 CATTATTTATTCCTCATTTGCTTATTGTTGT
1 CATTATTTATTCCTCATTTGCTTATTGTTGT
347315 TACTAACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.17, C:0.16, G:0.10, T:0.57
Consensus pattern (32 bp):
CATTATTTATTCCTCATTTGCTTATTGTTGTA
Found at i:347342 original size:48 final size:50
Alignment explanation
Indices: 347286--347426 Score: 146
Period size: 49 Copynumber: 2.9 Consensus size: 50
347276 TTGTTGTACA
* ** *
347286 TTAT-TTATTCCTCATTTGCTTATTGTTGTTACTAACT-TTTTTTGT-CT
1 TTATGTTATTCCTCATGTGCTTATTGTTGCAACAAACTCTTTTTTGTCCT
** *
347333 TTATGTTATTTGTCATGTGCTTATTGTTGCAACAAACTCTTTTTTTTCCT
1 TTATGTTATTCCTCATGTGCTTATTGTTGCAACAAACTCTTTTTTGTCCT
** * **
347383 TTATGTT-TTTGTAATGTGCTTATTGTTATAACAAACTCTTTTTT
1 TTATGTTATTCCTCATGTGCTTATTGTTGCAACAAACTCTTTTTT
347427 AGGCTTTATG
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
47 4 0.05
48 27 0.33
49 41 0.51
50 9 0.11
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.57
Consensus pattern (50 bp):
TTATGTTATTCCTCATGTGCTTATTGTTGCAACAAACTCTTTTTTGTCCT
Found at i:347400 original size:49 final size:49
Alignment explanation
Indices: 347302--347442 Score: 178
Period size: 49 Copynumber: 2.9 Consensus size: 49
347292 ATTCCTCATT
* * *
347302 TGCTTATTGTTGTTACTAACT-TTTTTTGTCTTTATGTTATTTGTCATG
1 TGCTTATTGTTGTAACAAACTCTTTTTTGTCTTTATGTTATTTGTAATG
* *
347350 TGCTTATTGTTGCAACAAACTCTTTTTTTTCCTTTATGTT-TTTGTAATG
1 TGCTTATTGTTGTAACAAACTCTTTTTTGT-CTTTATGTTATTTGTAATG
* * *
347399 TGCTTATTGTTATAACAAACTCTTTTTTAGGCTTTATGTAATTT
1 TGCTTATTGTTGTAACAAACTCTTTTTT-GTCTTTATGTTATTT
347443 TATTTTAGGT
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
48 18 0.23
49 49 0.62
50 12 0.15
ACGTcount: A:0.19, C:0.12, G:0.13, T:0.56
Consensus pattern (49 bp):
TGCTTATTGTTGTAACAAACTCTTTTTTGTCTTTATGTTATTTGTAATG
Found at i:352518 original size:29 final size:29
Alignment explanation
Indices: 352475--352541 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
352465 CTTGAACAAA
* *
352475 TTGACTCAGACGGGTTGACTCAGGCCGAG
1 TTGACTCGGACGGGTTGACTCAGACCGAG
* *
352504 TTTACTCGGACGGGTTGACTCAGACTGAG
1 TTGACTCGGACGGGTTGACTCAGACCGAG
352533 TTGACTCGG
1 TTGACTCGG
352542 TGACTGGACT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.19, C:0.22, G:0.33, T:0.25
Consensus pattern (29 bp):
TTGACTCGGACGGGTTGACTCAGACCGAG
Found at i:352537 original size:15 final size:14
Alignment explanation
Indices: 352475--352539 Score: 67
Period size: 14 Copynumber: 4.5 Consensus size: 14
352465 CTTGAACAAA
*
352475 TTGACTCAGACGGG
1 TTGACTCAGACGAG
*
352489 TTGACTCAGGCCGAG
1 TTGACTCA-GACGAG
* * *
352504 TTTACTCGGACGGG
1 TTGACTCAGACGAG
352518 TTGACTCAGACTGAG
1 TTGACTCAGAC-GAG
352533 TTGACTC
1 TTGACTC
352540 GGTGACTGGA
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
14 21 0.52
15 19 0.47
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (14 bp):
TTGACTCAGACGAG
Found at i:353779 original size:3 final size:3
Alignment explanation
Indices: 353773--353891 Score: 238
Period size: 3 Copynumber: 39.7 Consensus size: 3
353763 TATTGTATAT
353773 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
353821 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
353869 ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA AT
353892 GGTAAAGTAT
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 116 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:363340 original size:18 final size:19
Alignment explanation
Indices: 363306--363341 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
363296 GAACCAAATA
363306 TTACAAACTAAAAACCCAT
1 TTACAAACTAAAAACCCAT
*
363325 TTACAAA-TATAAACCCA
1 TTACAAACTAAAAACCCA
363342 AACATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (19 bp):
TTACAAACTAAAAACCCAT
Found at i:364837 original size:240 final size:238
Alignment explanation
Indices: 364382--365072 Score: 870
Period size: 240 Copynumber: 2.9 Consensus size: 238
364372 GGAGCTCTTC
*
364382 AGAAAAATCAGTTTTCACG-AAAGATTTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTCGA
1 AGAAAAATCAGTTTTCA-GAAAAGATTTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTGA
* * * *
364446 AAATCATGTGAAAACATCCCACCCGAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGTTT
65 AAATCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGG-CCGAAGGACTTATCATCTTGTTC
* * * *
364511 GAAAGACTTATAGATGACCCGAATGATTTAAGTATCATATTCGAAAGACTTACTGATGGCCAGAA
129 GAAAGACTTATAGATGACCCGAATGATTTAAGCATCATGTTCGAAAGACTGACTGATGACCAGAA
* * * *
364576 GGACTTACTTAGTAAGAAACTTTGGAAATCAATTTCTTACTTTTCA
194 AGACTCACTCAATAAGAAACTTTGGAAATCAATTTCTT-CTTTTCA
* * **
364622 AGAAAAGTCAGTTTTCAGAAAAGATTTAAATGAGAAACTTTGGAAACCGTTTTCTCATTTTTGAA
1 AGAAAAATCAGTTTTCAGAAAAGATTTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTGAA
* * * * * *
364687 AATCATGTGAAAACAACTTGCCTGAAGGTCTTATGGATGGCTCGAAGGACTTATCATCTTGCTCA
66 AATCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGC-CGAAGGACTTATCATCTTGTTCG
* * * * * *
364752 AAAGACTTATAGATGACCCAAAAGATCTAAGCATCATGTTCAAAAGACTGATTGATGACCTGAAA
130 AAAGACTTATAGATGACCCGAATGATTTAAGCATCATGTTCGAAAGACTGACTGATGACCAGAAA
* ** * *
364817 GACTCACTCAATATGAAACTTTGGAAATCGTTTTCTTTTTTTCT
195 GACTCACTCAATAAGAAACTTTGGAAATCAATTTCTTCTTTTCA
* *
364861 AGAAAAATCAATTTTCAGAAAAGATTTAAATGAGAAACTTTGGAAATCACATTCTCATTTTTCGA
1 AGAAAAATCAGTTTTCAGAAAAGATTTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTT-GA
* **
364926 AAATCATGTGAAAACATCCTACCCCAAGGTCTTATGGATGGCCTGAATTACTTATCATCTTGTTC
65 AAATCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCC-GAAGGACTTATCATCTTGTTC
* * * * *
364991 GAAAGAC-T-TA-ATGACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACTAATGGCCCGAA
129 GAAAGACTTATAGATGACCCGAATGATTTAAGCATCATGTTCGAAAGACTGACTGATGACCAGAA
* *
365053 TGACTTACT-AATCAAGAAAC
194 AGACTCACTCAAT-AAGAAAC
365073 CCTTGAAAAC
Statistics
Matches: 384, Mismatches: 62, Indels: 13
0.84 0.14 0.03
Matches are distributed among these distances:
236 3 0.01
237 55 0.14
238 2 0.01
239 65 0.17
240 259 0.67
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (238 bp):
AGAAAAATCAGTTTTCAGAAAAGATTTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTGAA
AATCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCGAAGGACTTATCATCTTGTTCGA
AAGACTTATAGATGACCCGAATGATTTAAGCATCATGTTCGAAAGACTGACTGATGACCAGAAAG
ACTCACTCAATAAGAAACTTTGGAAATCAATTTCTTCTTTTCA
Found at i:370163 original size:17 final size:17
Alignment explanation
Indices: 370141--370177 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
370131 TATAACAACT
370141 TATTGTATAAATCTCCA
1 TATTGTATAAATCTCCA
370158 TATTGTATAAATCTCCA
1 TATTGTATAAATCTCCA
370175 TAT
1 TAT
370178 ACGTTGAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.43
Consensus pattern (17 bp):
TATTGTATAAATCTCCA
Found at i:371344 original size:29 final size:30
Alignment explanation
Indices: 371288--371344 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
371278 GCGTGAGACC
* *
371288 AGACAAAAGGAAGTCAAGTTAGTAGAAACA
1 AGACAAAAAGAAGTCAAGTTAATAGAAACA
*
371318 AGACAAAAAGAA-TCAAGTTAATTGAAA
1 AGACAAAAAGAAGTCAAGTTAATAGAAA
371345 TGATTAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.56, C:0.09, G:0.19, T:0.16
Consensus pattern (30 bp):
AGACAAAAAGAAGTCAAGTTAATAGAAACA
Found at i:374794 original size:3 final size:3
Alignment explanation
Indices: 374786--374827 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
374776 TTGGTTTGTA
374786 AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
374828 TCGAGGTAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:374811 original size:20 final size:20
Alignment explanation
Indices: 374786--374824 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
374776 TTGGTTTGTA
374786 AATAATAATAATAATAATAT
1 AATAATAATAATAATAATAT
374806 AATAATAATAATAATAATA
1 AATAATAATAATAATAATA
374825 ATATCGAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAATAATAATAATAATAT
Found at i:385634 original size:21 final size:21
Alignment explanation
Indices: 385592--385643 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
385582 TCGAAAAAAA
* *
385592 GAGAAAAAATAGCAGCATTTC
1 GAGAAAAAAAAGAAGCATTTC
385613 GAGAAAAAAAAGAAG-ATGTTC
1 GAGAAAAAAAAGAAGCAT-TTC
*
385634 GA-AAGAAAAA
1 GAGAAAAAAAA
385644 TAAAAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.58, C:0.08, G:0.21, T:0.13
Consensus pattern (21 bp):
GAGAAAAAAAAGAAGCATTTC
Found at i:386743 original size:25 final size:25
Alignment explanation
Indices: 386699--386762 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 25
386689 AGTTTTATTA
* *
386699 AAGCTTTCTCTTTTCATTTTATTTTTC
1 AAGCTTTAT-TTTTCATTTTA-CTTTC
*
386726 AAGTTTTATTTTTC-TTTTACTTTC
1 AAGCTTTATTTTTCATTTTACTTTC
*
386750 ATGCTTTATTTTT
1 AAGCTTTATTTTT
386763 AAATATGCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 15 0.47
25 5 0.16
26 5 0.16
27 7 0.22
ACGTcount: A:0.16, C:0.14, G:0.05, T:0.66
Consensus pattern (25 bp):
AAGCTTTATTTTTCATTTTACTTTC
Found at i:389766 original size:21 final size:21
Alignment explanation
Indices: 389732--389783 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
389722 TTACTTTTTG
* *
389732 GTCAACGGTCAAAGGTCAATA
1 GTCAACGGTTAAAGGTCAACA
*
389753 GTCAATGGTTAAAGGTCAACA
1 GTCAACGGTTAAAGGTCAACA
389774 GTCAACGGTT
1 GTCAACGGTT
389784 TGGTCCAGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (21 bp):
GTCAACGGTTAAAGGTCAACA
Found at i:392025 original size:165 final size:165
Alignment explanation
Indices: 391666--392117 Score: 622
Period size: 165 Copynumber: 2.7 Consensus size: 165
391656 AAAACATATT
* * * *
391666 TTTATTCAAAAACCATATTAATCCCTCTAACTGAACACTCCATAATGTGTAGGTTCCCTAGAAAC
1 TTTA-TCAAAAACCATAGTAATCCCTCCAACCGAACACTCCATAATGTGTAGGTTCCCTAGAACC
* * *
391731 ATACACCCACCTA-CACACCAAGTAAGGACTTACCTTGAGTACAAAGCAGAAGAGCCTACAGTAA
65 ATACACCCACC-AGCACACCTAGTAAGG-C---CC-TGAGCATAAAGCAGAAGAGCCTACAGTAA
* *
391795 TGGTAACAGTAACTTCCTCTAACAACACCCTCCCATAAAACA
124 TGGTAACAATAACTTCCTCCAACAACACCCTCCCATAAAACA
* * *
391837 TTTATCAAAAACTATAGTAATCCCTCCAACCGAACACTCCATGATGTGTAGGTTCCCTAGAGCCA
1 TTTATCAAAAACCATAGTAATCCCTCCAACCGAACACTCCATAATGTGTAGGTTCCCTAGAACCA
* *
391902 TACACCCACCAGCACACCTAGTAAGGCCCTGAGCATAAAGCA-AAGAAGTCTACAGTAGCT-GTA
66 TACACCCACCAGCACACCTAGTAAGGCCCTGAGCATAAAGCAGAAG-AGCCTACAGTA-ATGGTA
*
391965 ACAATAACTTCCTCCAACAATACCCTCCCATAAAACA
129 ACAATAACTTCCTCCAACAACACCCTCCCATAAAACA
* *
392002 TTTATCAAAAACCATAGTAATCCCTCCAATCGAACACTCCATAATGTGTAGGTTCCCCAGAACCA
1 TTTATCAAAAACCATAGTAATCCCTCCAACCGAACACTCCATAATGTGTAGGTTCCCTAGAACCA
* * *
392067 TACACCCACCAGTACACCTAGTAAGGCCCTGAGCATAAAGCCGAGGAGCCT
66 TACACCCACCAGCACACCTAGTAAGGCCCTGAGCATAAAGCAGAAGAGCCT
392118 GTAGATATAC
Statistics
Matches: 253, Mismatches: 24, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
164 3 0.01
165 162 0.64
166 5 0.02
169 2 0.01
170 77 0.30
171 4 0.02
ACGTcount: A:0.36, C:0.30, G:0.13, T:0.21
Consensus pattern (165 bp):
TTTATCAAAAACCATAGTAATCCCTCCAACCGAACACTCCATAATGTGTAGGTTCCCTAGAACCA
TACACCCACCAGCACACCTAGTAAGGCCCTGAGCATAAAGCAGAAGAGCCTACAGTAATGGTAAC
AATAACTTCCTCCAACAACACCCTCCCATAAAACA
Found at i:392218 original size:24 final size:24
Alignment explanation
Indices: 392179--392247 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
392169 GAATGGAGAT
* * * *
392179 ATCATAAATCAAAACATAATTCTG
1 ATCAGAAATCAGAACAAAATTCAG
* *
392203 GTCAGATATCAGAACAAAATTCAG
1 ATCAGAAATCAGAACAAAATTCAG
*
392227 ATCGGAAATCAGAACAGAAAT
1 ATCAGAAATCAGAACA-AAAT
392248 CATATAAAAT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
24 31 0.89
25 4 0.11
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCAGAACAAAATTCAG
Found at i:399043 original size:21 final size:21
Alignment explanation
Indices: 399017--399060 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
399007 ACTTAAAATA
399017 TGCATCGATGCACTACTACAG
1 TGCATCGATGCACTACTACAG
*
399038 TGCATCGATGCACTGCTACAG
1 TGCATCGATGCACTACTACAG
399059 TG
1 TG
399061 ATTTCCGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (21 bp):
TGCATCGATGCACTACTACAG
Found at i:399652 original size:87 final size:86
Alignment explanation
Indices: 399454--400488 Score: 1304
Period size: 87 Copynumber: 12.1 Consensus size: 86
399444 TATCAATCTT
* * *
399454 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACTAATATACTTATCA-TTATTCCATAAG
1 CTTACCATTT-TTCCATAAGCTCGTAAGCTTATTTTAC-AATCTACTTA-CATTTTTTCCATAAG
399518 CTCGTAAGCTTATTTTATCAATATA
63 CTCGTAAGCTTATTTTA-CAATATA
* * * * ** **
399543 CTTACCATTATACTATAAGCTCGTAAGCTTATTTTACATTCTACTTATTTTTTTTTATATAAGCT
1 CTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTA-CATTTTTTCCATAAGCT
*
399608 CTTAAGCTTATTTTACAATATA
65 CGTAAGCTTATTTTACAATATA
* * *
399630 CTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTACAATATACCTACCAGTTTTTCCATAAGCT
1 CTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTA-CATTTTTTCCATAAGCT
*
399695 CATAAGCTTATTTTACCAATATA
65 CGTAAGCTTATTTTA-CAATATA
* * *
399718 ATTACCATTATTT-CATAAGCTCATAAGCTTATTTTACCAATATACTTACCA-TTTTTCCATAAG
1 CTTACCATT-TTTCCATAAGCTCGTAAGCTTATTTTA-CAATCTACTTA-CATTTTTTCCATAAG
*
399781 CTCGTAAGCTTATTTTACAATCTA
63 CTCGTAAGCTTATTTTACAATATA
*
399805 CTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTACCATTATTT-CATAAGCT
1 CTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTA-CATTTTTTCCATAAGCT
399869 CGTAAGCTTATTTTACCAATATA
65 CGTAAGCTTATTTTA-CAATATA
399892 CTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTACCA-TTTTT-CATAAGCT
1 CTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTA-CATTTTTTCCATAAGCT
*
399955 CGTAAGCTTATTTTACAATCTA
65 CGTAAGCTTATTTTACAATATA
* *
399977 CTTACCATTATTT-CATAAGCTCGTAAACTTATTTTACCAATGTACTTACCA-TTTTTCCATAAG
1 CTTACCATT-TTTCCATAAGCTCGTAAGCTTATTTTA-CAATCTACTTA-CATTTTTTCCATAAG
*
400040 CTCGTAAGCTTATTTTACAATCTA
63 CTCGTAAGCTTATTTTACAATATA
* * *
400064 CTTACCATTTTT-CATAAGCTCGTAATCTTATTTTACAATCTATTTACCATTATTT-CATAAGCT
1 CTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTA-CATTTTTTCCATAAGCT
400127 CGTAAGCTTATTTTACCAATATA
65 CGTAAGCTTATTTTA-CAATATA
* *
400150 CTTATCATTTTTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTACCA-TTTTTCCATAAACT
1 CTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTA-CATTTTTTCCATAAGCT
*
400214 CGTAAGCTTATTTTACAATCTA
65 CGTAAGCTTATTTTACAATATA
*
400236 CTTACCATTATTT-CATAAGCTCGTAAGCTTATTTTACCAATATACTTACATTTTTTCCATAAGC
1 CTTACCATT-TTTCCATAAGCTCGTAAGCTTATTTTA-CAATCTACTTACATTTTTTCCATAAGC
*
400300 TCGTAAGCTTATTTTACAATCTA
64 TCGTAAGCTTATTTTACAATATA
*
400323 CTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTACCATTATTT-CATAAGCT
1 CTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTA-CATTTTTTCCATAAGCT
400387 --T--G----TTTTACCAATATA
65 CGTAAGCTTATTTTA-CAATATA
*
400402 CTTACCATTTTTCC---A-----TAAGCTTATTTTACAATCTAATTACCA-TTTTT-CATAAGCT
1 CTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTA-CATTTTTTCCATAAGCT
400457 CGTAAGCTTATTTTACCAATATA
65 CGTAAGCTTATTTTA-CAATATA
*
400480 CTCACCATT
1 CTTACCATT
400489 ATATATATAT
Statistics
Matches: 860, Mismatches: 58, Indels: 67
0.87 0.06 0.07
Matches are distributed among these distances:
70 12 0.01
71 26 0.03
72 1 0.00
74 1 0.00
76 1 0.00
78 26 0.03
79 20 0.02
82 1 0.00
84 1 0.00
85 72 0.08
86 197 0.23
87 362 0.42
88 115 0.13
89 25 0.03
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (86 bp):
CTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTACATTTTTTCCATAAGCTC
GTAAGCTTATTTTACAATATA
Found at i:399657 original size:43 final size:43
Alignment explanation
Indices: 399447--400488 Score: 1389
Period size: 43 Copynumber: 24.4 Consensus size: 43
399437 CATTTCTTAT
* *
399447 CAATCTTCTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA
1 CAATCTACTTACCATTT-TTCCATAAGCTCGTAAGCTTATTTTA
* * *
399491 CTAATATACTTATCATTATTCCATAAGCTCGTAAGCTTATTTTA
1 C-AATCTACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
* * * *
399535 TCAATATACTTACCATTATACTATAAGCTCGTAAGCTTATTTTA
1 -CAATCTACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
* *** ** *
399579 CATTCTACTTATTTTTTTTTATATAAGCTCTTAAGCTTATTTTA
1 CAATCTACTTA-CCATTTTTCCATAAGCTCGTAAGCTTATTTTA
*
399623 CAATATACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
1 CAATCTACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
* * *
399666 CAATATACCTACCAGTTTTTCCATAAGCTCATAAGCTTATTTTA
1 CAATCTACTTACCA-TTTTTCCATAAGCTCGTAAGCTTATTTTA
* * *
399710 CCAATATAATTACCATTATTT-CATAAGCTCATAAGCTTATTTTA
1 -CAATCTACTTACCATT-TTTCCATAAGCTCGTAAGCTTATTTTA
*
399754 CCAATATACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
1 -CAATCTACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
399798 CAATCTACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
1 CAATCTACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
399841 CAATCTACTTACCATTATTT-CATAAGCTCGTAAGCTTATTTTA
1 CAATCTACTTACCATT-TTTCCATAAGCTCGTAAGCTTATTTTA
*
399884 CCAATATACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
1 -CAATCTACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
399928 CAATCTACTTACCATTTTT-CATAAGCTCGTAAGCTTATTTTA
1 CAATCTACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
*
399970 CAATCTACTTACCATTATTT-CATAAGCTCGTAAACTTATTTTA
1 CAATCTACTTACCATT-TTTCCATAAGCTCGTAAGCTTATTTTA
*
400013 CCAATGTACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
1 -CAATCTACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
*
400057 CAATCTACTTACCATTTTT-CATAAGCTCGTAATCTTATTTTA
1 CAATCTACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
*
400099 CAATCTATTTACCATTATTT-CATAAGCTCGTAAGCTTATTTTA
1 CAATCTACTTACCATT-TTTCCATAAGCTCGTAAGCTTATTTTA
* *
400142 CCAATATACTTATCATTTTTCCATAAGCTCGTAAGCTTATTTTA
1 -CAATCTACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
*
400186 CAATCTACTTACCATTTTTCCATAAACTCGTAAGCTTATTTTA
1 CAATCTACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
400229 CAATCTACTTACCATTATTT-CATAAGCTCGTAAGCTTATTTTA
1 CAATCTACTTACCATT-TTTCCATAAGCTCGTAAGCTTATTTTA
*
400272 CCAATATACTTA-CATTTTTTCCATAAGCTCGTAAGCTTATTTTA
1 -CAATCTACTTACCA-TTTTTCCATAAGCTCGTAAGCTTATTTTA
400316 CAATCTACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
1 CAATCTACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
400359 CAATCTACTTACCATTATTT-CATAAGCT--T--G----TTTTA
1 CAATCTACTTACCATT-TTTCCATAAGCTCGTAAGCTTATTTTA
*
400394 CCAATATACTTACCATTTTTCC---A-----TAAGCTTATTTTA
1 -CAATCTACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
*
400430 CAATCTAATTACCATTTTT-CATAAGCTCGTAAGCTTATTTTA
1 CAATCTACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
* *
400472 CCAATATACTCACCATT
1 -CAATCTACTTACCATT
400489 ATATATATAT
Statistics
Matches: 903, Mismatches: 56, Indels: 79
0.87 0.05 0.08
Matches are distributed among these distances:
30 1 0.00
32 1 0.00
33 1 0.00
34 1 0.00
35 25 0.03
36 21 0.02
37 1 0.00
39 1 0.00
41 1 0.00
42 89 0.10
43 386 0.43
44 347 0.38
45 28 0.03
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (43 bp):
CAATCTACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA
Found at i:400010 original size:21 final size:21
Alignment explanation
Indices: 399944--400010 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
399934 ACTTACCATT
*
399944 TTTCATAAGCTCGTAAGCTTA
1 TTTCATAAGCTCGTAAACTTA
* * * * *
399965 TTTTACAATCTAC-TTACCATTA
1 TTTCATAAGCT-CGTAAAC-TTA
399987 TTTCATAAGCTCGTAAACTTA
1 TTTCATAAGCTCGTAAACTTA
400008 TTT
1 TTT
400011 TACCAATGTA
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.43
Consensus pattern (21 bp):
TTTCATAAGCTCGTAAACTTA
Found at i:400247 original size:22 final size:22
Alignment explanation
Indices: 400178--400248 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
400168 GCTCGTAAGC
400178 TTATTTTACAATCTACTTACCA
1 TTATTTTACAATCTACTTACCA
* * * * *
400200 TT-TTTCCATAAACT-CGTAAGC-
1 TTATTT-TACAATCTAC-TTACCA
400221 TTATTTTACAATCTACTTACCA
1 TTATTTTACAATCTACTTACCA
400243 TTATTT
1 TTATTT
400249 CATAAGCTCG
Statistics
Matches: 34, Mismatches: 10, Indels: 10
0.63 0.19 0.19
Matches are distributed among these distances:
21 14 0.41
22 20 0.59
ACGTcount: A:0.30, C:0.21, G:0.03, T:0.46
Consensus pattern (22 bp):
TTATTTTACAATCTACTTACCA
Found at i:400342 original size:35 final size:34
Alignment explanation
Indices: 400303--400456 Score: 173
Period size: 35 Copynumber: 4.2 Consensus size: 34
400293 CATAAGCTCG
400303 TAAGCTTATTTTACAATCTACTTACCATTTTTCCATAA
1 TAAGCTTATTTTACAATCTACTTACCATTTTT-C---A
400341 GCTCGTAAGCTTATTTTACAATCTACTTACCATTATTTCA
1 -----TAAGCTTATTTTACAATCTACTTACCATT-TTTCA
* *
400381 TAAGCTTGTTTTACCAATATACTTACCATTTTTCCA
1 TAAGCTTATTTTA-CAATCTACTTACCATTTTT-CA
*
400417 TAAGCTTATTTTACAATCTAATTACCATTTTTCA
1 TAAGCTTATTTTACAATCTACTTACCATTTTTCA
400451 TAAGCT
1 TAAGCT
400457 CGTAAGCTTA
Statistics
Matches: 103, Mismatches: 5, Indels: 15
0.84 0.04 0.12
Matches are distributed among these distances:
34 8 0.08
35 32 0.31
36 29 0.28
40 1 0.01
43 30 0.29
44 3 0.03
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (34 bp):
TAAGCTTATTTTACAATCTACTTACCATTTTTCA
Found at i:400377 original size:22 final size:22
Alignment explanation
Indices: 400308--400378 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
400298 GCTCGTAAGC
400308 TTATTTTACAATCTACTTACCA
1 TTATTTTACAATCTACTTACCA
* * * * *
400330 TT-TTTCCATAAGCT-CGTAAGC-
1 TTATTT-TACAATCTAC-TTACCA
400351 TTATTTTACAATCTACTTACCA
1 TTATTTTACAATCTACTTACCA
400373 TTATTT
1 TTATTT
400379 CATAAGCTTG
Statistics
Matches: 34, Mismatches: 10, Indels: 10
0.63 0.19 0.19
Matches are distributed among these distances:
21 14 0.41
22 20 0.59
ACGTcount: A:0.28, C:0.21, G:0.04, T:0.46
Consensus pattern (22 bp):
TTATTTTACAATCTACTTACCA
Found at i:400770 original size:58 final size:57
Alignment explanation
Indices: 400576--401166 Score: 488
Period size: 59 Copynumber: 10.1 Consensus size: 57
400566 TAGAACTCTC
* * * ** **
400576 AGTGCTCCAT-TTGAAATATCATATAATTAATATGATTTCCTTCTCATTTTAGCACACAA
1 AGTGCTCCATATTGAAAT-CCATA-CATTAGTATGATTTCCTTAACATTTTAGCACA-TT
* * * * *
400635 AGTGC-CC-TATTCAATAATTCATACCATTTGTATGA-TTCTTTTACCATTTTTAGCACATAT
1 AGTGCTCCATATT-GA-AATCCATA-CATTAGTATGATTTC-CTTAACA-TTTTAGCACAT-T
* * * *
400695 AATGC-CCTATATGGAAATCCATATATTCA-TATGATTTCCTTAAAATTTTAGCACACTT
1 AGTGCTCC-ATATTGAAATCCATACATT-AGTATGATTTCCTTAACATTTTAGCACA-TT
*
400753 AGTGCTCCATATTGAAATCCATACACTTAGTATGATTT-CTTATCATTTTAGCACATT
1 AGTGCTCCATATTGAAATCCATACA-TTAGTATGATTTCCTTAACATTTTAGCACATT
* * * *
400810 CAGTGCTCCATATGGAAATACATACACTTAGTATGATTCCCTTACCATTTTAGCACATAT
1 -AGTGCTCCATATTGAAATCCATACA-TTAGTATGATTTCCTTAACATTTTAGCACAT-T
* * *
400870 AATGC-CC-TATTTGGAAATCCATATATTCAATATGATTTCCTTAACATTTTAGCACACTT
1 AGTGCTCCATA-TT-GAAATCCATACATT-AGTATGATTTCCTTAACATTTTAGCACA-TT
*
400929 AGTGCTCCATATTGAAATCCATACACTTAGTATGATTT-CTTATCATTTTAGCACATT
1 AGTGCTCCATATTGAAATCCATACA-TTAGTATGATTTCCTTAACATTTTAGCACATT
* * * *
400986 CAGTGCTCCATATGGAAATACATACATTTAGTATGATTCCCTTATCATTTTAGCACATAT
1 -AGTGCTCCATATTGAAATCCATACA-TTAGTATGATTTCCTTAACATTTTAGCACAT-T
* * * *
401046 AATGC-CC-TATTTGGAAATCCATATATTCAATATGATTTCCTTAACCTTTTAGCACACTT
1 AGTGCTCCATA-TT-GAAATCCATACATT-AGTATGATTTCCTTAACATTTTAGCACA-TT
* * * *
401105 AGTGCTTCATATTGAAATCCATACACTTAGTATGATTT-CTTATCGTTTTTGCACATAT
1 AGTGCTCCATATTGAAATCCATACA-TTAGTATGATTTCCTTAACATTTTAGCACAT-T
401163 AGTG
1 AGTG
401167 TCATTCCGTA
Statistics
Matches: 439, Mismatches: 58, Indels: 71
0.77 0.10 0.12
Matches are distributed among these distances:
57 10 0.02
58 167 0.38
59 210 0.48
60 44 0.10
61 5 0.01
62 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (57 bp):
AGTGCTCCATATTGAAATCCATACATTAGTATGATTTCCTTAACATTTTAGCACATT
Found at i:400907 original size:176 final size:176
Alignment explanation
Indices: 400664--401160 Score: 888
Period size: 176 Copynumber: 2.8 Consensus size: 176
400654 CATACCATTT
** *
400664 GTATGATTCTTTTACCATTTTTAGCACATATAATGCCCTATATGGAAATCCATATATTC-ATATG
1 GTATGATTCCCTTACCA-TTTTAGCACATATAATGCCCTATTTGGAAATCCATATATTCAATATG
*
400728 ATTTCCTTAAAATTTTAGCACACTTAGTGCTCCATATTGAAATCCATACACTTAGTATGATTTCT
65 ATTTCCTTAACATTTTAGCACACTTAGTGCTCCATATTGAAATCCATACACTTAGTATGATTTCT
400793 TATCATTTTAGCACATTCAGTGCTCCATATGGAAATACATACACTTA
130 TATCATTTTAGCACATTCAGTGCTCCATATGGAAATACATACACTTA
400840 GTATGATTCCCTTACCATTTTAGCACATATAATGCCCTATTTGGAAATCCATATATTCAATATGA
1 GTATGATTCCCTTACCATTTTAGCACATATAATGCCCTATTTGGAAATCCATATATTCAATATGA
400905 TTTCCTTAACATTTTAGCACACTTAGTGCTCCATATTGAAATCCATACACTTAGTATGATTTCTT
66 TTTCCTTAACATTTTAGCACACTTAGTGCTCCATATTGAAATCCATACACTTAGTATGATTTCTT
*
400970 ATCATTTTAGCACATTCAGTGCTCCATATGGAAATACATACATTTA
131 ATCATTTTAGCACATTCAGTGCTCCATATGGAAATACATACACTTA
*
401016 GTATGATTCCCTTATCATTTTAGCACATATAATGCCCTATTTGGAAATCCATATATTCAATATGA
1 GTATGATTCCCTTACCATTTTAGCACATATAATGCCCTATTTGGAAATCCATATATTCAATATGA
* *
401081 TTTCCTTAACCTTTTAGCACACTTAGTGCTTCATATTGAAATCCATACACTTAGTATGATTTCTT
66 TTTCCTTAACATTTTAGCACACTTAGTGCTCCATATTGAAATCCATACACTTAGTATGATTTCTT
* *
401146 ATCGTTTTTGCACAT
131 ATCATTTTAGCACAT
401161 ATAGTGTCAT
Statistics
Matches: 310, Mismatches: 10, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
175 40 0.13
176 270 0.87
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (176 bp):
GTATGATTCCCTTACCATTTTAGCACATATAATGCCCTATTTGGAAATCCATATATTCAATATGA
TTTCCTTAACATTTTAGCACACTTAGTGCTCCATATTGAAATCCATACACTTAGTATGATTTCTT
ATCATTTTAGCACATTCAGTGCTCCATATGGAAATACATACACTTA
Found at i:401512 original size:19 final size:19
Alignment explanation
Indices: 401466--401558 Score: 125
Period size: 19 Copynumber: 4.8 Consensus size: 19
401456 TTTTGGCCTT
*
401466 TATGCATCGATGCA-TTCTA
1 TATGCATCGATGCACTGC-A
401485 TAGTGCATCGATGCACTGCA
1 TA-TGCATCGATGCACTGCA
*
401505 TATGCATCGATGCACTGCC
1 TATGCATCGATGCACTGCA
* *
401524 TATGCATCGATGCACTACC
1 TATGCATCGATGCACTGCA
401543 TATGCATCGATGCACT
1 TATGCATCGATGCACT
401559 TATTGTATTC
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
19 52 0.75
20 15 0.22
21 2 0.03
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (19 bp):
TATGCATCGATGCACTGCA
Found at i:403726 original size:43 final size:43
Alignment explanation
Indices: 403657--403755 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 43
403647 TCAAAGTCAA
* * *
403657 CGGGTCATGTTAAAGTCAACGAGTTGGGTTAAACAGTTCGGGT
1 CGGGTCATGTCAAAGTCAACGAGTTGGGTCAAACAGTTCGAGT
* * * *
403700 TGGGTCATGTCAAAGTCAATGGGTTGGGTCAAACAGTTTGAGT
1 CGGGTCATGTCAAAGTCAACGAGTTGGGTCAAACAGTTCGAGT
*
403743 CGGGTCAGGTCAA
1 CGGGTCATGTCAA
403756 GGGTTTGGGT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.25, C:0.14, G:0.33, T:0.27
Consensus pattern (43 bp):
CGGGTCATGTCAAAGTCAACGAGTTGGGTCAAACAGTTCGAGT
Found at i:403747 original size:24 final size:23
Alignment explanation
Indices: 403720--403773 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
403710 CAAAGTCAAT
403720 GGGTTGGGTCAAACAGTTTGAGTC
1 GGGTTGGGTC-AACAGTTTGAGTC
** ** *
403744 GGGTCAGGTCAAGGGTTTGGGTC
1 GGGTTGGGTCAACAGTTTGAGTC
403767 GGGTTGG
1 GGGTTGG
403774 ATTGGTTCAA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.15, C:0.11, G:0.46, T:0.28
Consensus pattern (23 bp):
GGGTTGGGTCAACAGTTTGAGTC
Found at i:407945 original size:19 final size:20
Alignment explanation
Indices: 407898--407948 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 20
407888 AATTTAACTC
407898 TGGTCAAAGTCAACGGGTCAGGT
1 TGGTCAAAGTCAACGGGT---GT
407921 TGGGTCAAAGTCAACGGGT-T
1 T-GGTCAAAGTCAACGGGTGT
407941 TGGTCAAA
1 TGGTCAAA
407949 CAGTTCAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 7 0.26
20 2 0.07
23 1 0.04
24 17 0.63
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (20 bp):
TGGTCAAAGTCAACGGGTGT
Found at i:414019 original size:21 final size:20
Alignment explanation
Indices: 413979--414020 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
413969 CCAACTTACA
*
413979 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
413999 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
414020 A
1 A
414021 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:417141 original size:16 final size:17
Alignment explanation
Indices: 417122--417167 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
417112 TCAAATTAAG
417122 ATTTAATATAAT-TATT
1 ATTTAATATAATATATT
*
417138 ATTTATTAT-ATATATT
1 ATTTAATATAATATATT
*
417154 ATTGATATATAATA
1 ATTTA-ATATAATA
417168 AAAAATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 2 0.08
16 16 0.67
17 3 0.12
18 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
ATTTAATATAATATATT
Found at i:419029 original size:113 final size:113
Alignment explanation
Indices: 418813--419453 Score: 1029
Period size: 113 Copynumber: 5.7 Consensus size: 113
418803 GATAAAATCT
* **
418813 AGCAAAAGGTT-AAGCAAGTTCTTCTCATTATGAAC-TCTTTCTTCC-TCTTCAGATGGGTTCTT
1 AGCAAAAAGTTGAA-CAAGTTCTTCTCATTATGAACTTC-TTCTTCCTTCTTCAGATGAATTCTT
* * * * * * *
418875 CTCATTATGAACACCT-TCTGGAAATGTTGATCCATCGAGTGATGTATTTA
64 CTCATTATGAAC-TCTAACTGGCACTGCTGATCCACCGAGTGATGAATTTA
* *
418925 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCT
* *
418990 TATTATGAACTCAAACTGGCACTGCTGATCCACCGAGTGATGAATTTA
66 CATTATGAACTCTAACTGGCACTGCTGATCCACCGAGTGATGAATTTA
* * *
419038 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCATGAGATGAATTCTTCT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCT
419103 CATTATGAACTCTAACTGGCACTGCTGATCCACCGAGTGATGAATTTA
66 CATTATGAACTCTAACTGGCACTGCTGATCCACCGAGTGATGAATTTA
*
419151 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTACTTCTTCAGATGAATTCTTCT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCT
419216 CATTATGAACTCTAACTGGCACTGCTGATCCACCGAGTGATGAATTTA
66 CATTATGAACTCTAACTGGCACTGCTGATCCACCGAGTGATGAATTTA
*
419264 AGTAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCT
*
419329 CATTATGAACTCTAAGTGGCACTGCTGATCCACCGAGTGATGAATTTA
66 CATTATGAACTCTAACTGGCACTGCTGATCCACCGAGTGATGAATTTA
* *
419377 AGCAAAAAGTTGAACAAGTTTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCT
419442 CATTATGAACTC
66 CATTATGAACTC
419454 GACCTGGAAT
Statistics
Matches: 496, Mismatches: 29, Indels: 7
0.93 0.05 0.01
Matches are distributed among these distances:
112 39 0.08
113 457 0.92
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (113 bp):
AGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCT
CATTATGAACTCTAACTGGCACTGCTGATCCACCGAGTGATGAATTTA
Found at i:420337 original size:114 final size:114
Alignment explanation
Indices: 420174--420507 Score: 553
Period size: 114 Copynumber: 2.9 Consensus size: 114
420164 GATCATGCAG
* * * * * * * *
420174 TTCATCTTTTAATTCCAATGATT-AGTTCTGTGGTTCTTACCGAACCAGATCAGATGACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGA-TTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAG
* *
420238 AAAACTTCCAGAAGATTCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
65 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
420288 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
420353 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
420402 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
*
420467 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTTTACTA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTA
420508 CGAGAACGTA
Statistics
Matches: 208, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
114 207 1.00
115 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:420832 original size:19 final size:17
Alignment explanation
Indices: 420804--420852 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
420794 AAAATAAAAG
*
420804 AATAAGTTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
420823 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
420839 AATAAATTGAATTT
1 AATAAATTGAATTT
420853 AGAGAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 3 0.12
19 10 0.38
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:421211 original size:1 final size:1
Alignment explanation
Indices: 421207--421269 Score: 72
Period size: 1 Copynumber: 63.0 Consensus size: 1
421197 TGACCCCCTC
* * * * * *
421207 TTTTTTCTTTTTTTTTCTTTTTTCTTTTTTTTTTTTTTTCTTTTTTTTTTCTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
421270 CTTCAAGCAT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (1 bp):
T
Found at i:421227 original size:17 final size:16
Alignment explanation
Indices: 421207--421269 Score: 108
Period size: 16 Copynumber: 3.9 Consensus size: 16
421197 TGACCCCCTC
421207 TTTTTTCTTTTTTTTT
1 TTTTTTCTTTTTTTTT
421223 CTTTTTTCTTTTTTTTT
1 -TTTTTTCTTTTTTTTT
421240 TTTTTTCTTTTTTTTT
1 TTTTTTCTTTTTTTTT
*
421256 TCTTTTCTTTTTTT
1 TTTTTTCTTTTTTT
421270 CTTCAAGCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
16 29 0.64
17 16 0.36
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (16 bp):
TTTTTTCTTTTTTTTT
Found at i:421236 original size:24 final size:23
Alignment explanation
Indices: 421205--421272 Score: 102
Period size: 23 Copynumber: 2.9 Consensus size: 23
421195 CTTGACCCCC
421205 TCTTTTTTCTTTTTTTTTCTTTTT
1 TCTTTTTT-TTTTTTTTTCTTTTT
421229 TCTTTTTTTTTTTTTTTCTTTTT
1 TCTTTTTTTTTTTTTTTCTTTTT
421252 T-TTTTCTTTTCTTTTTTTCTT
1 TCTTTT-TTTT-TTTTTTTCTT
421273 CAAGCATAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.10
23 20 0.48
24 18 0.43
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (23 bp):
TCTTTTTTTTTTTTTTTCTTTTT
Found at i:434646 original size:17 final size:15
Alignment explanation
Indices: 434611--434639 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
434601 TTTAAAATAA
434611 TTAA-AATAATATAT
1 TTAATAATAATATAT
434625 TTAATAATAATATAT
1 TTAATAATAATATAT
434640 CTATAATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAATAATAATATAT
Found at i:435236 original size:30 final size:30
Alignment explanation
Indices: 435197--435298 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 30
435187 AAGAATGGTT
* * *
435197 AAATTTTAATTTGACCTCT-GAATTTAGATA
1 AAATATTAATTTGACCT-TAAAATTTACATA
435227 AAATATTAATTTGACCTTAAAATTTACATA
1 AAATATTAATTTGACCTTAAAATTTACATA
* * * * *
435257 AAATACTAATCTAACTCTTAAAATCTATATA
1 AAATATTAATTTGAC-CTTAAAATTTACATA
*
435288 AAATATGAATT
1 AAATATTAATT
435299 AACCCCTAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
29 1 0.02
30 37 0.63
31 21 0.36
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (30 bp):
AAATATTAATTTGACCTTAAAATTTACATA
Found at i:437021 original size:15 final size:16
Alignment explanation
Indices: 437001--437033 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
436991 TAAATCAATA
437001 TATTA-TTTTATAATT
1 TATTATTTTTATAATT
437016 TATTATTTTTATAATT
1 TATTATTTTTATAATT
437032 TA
1 TA
437034 AACACTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTATTTTTATAATT
Found at i:442787 original size:40 final size:40
Alignment explanation
Indices: 442750--442831 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 40
442740 CATTTGTTTG
* *
442750 TGTTCATTCTTTTAATTAAACGAATAGAAAACTTTGTTCA
1 TGTTCATTCATTTAATTAAACAAATAGAAAACTTTGTTCA
*
442790 TGTTCATTCATTTAATTAAACAAATATAAAA-TCTTGTTCA
1 TGTTCATTCATTTAATTAAACAAATAGAAAACT-TTGTTCA
442830 TG
1 TG
442832 AACTTACCGC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 1 0.03
40 37 0.97
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.43
Consensus pattern (40 bp):
TGTTCATTCATTTAATTAAACAAATAGAAAACTTTGTTCA
Found at i:445786 original size:36 final size:36
Alignment explanation
Indices: 445745--445820 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
445735 ATTTTCGGGA
*
445745 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
445781 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
445817 TTTT
1 TTTT
445821 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:448994 original size:3 final size:3
Alignment explanation
Indices: 448986--449021 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
448976 GGTTTTAAAA
448986 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
449022 TTACTAATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:452770 original size:25 final size:25
Alignment explanation
Indices: 452742--452793 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
452732 AAAAGAAAGA
452742 CAAATTAGTGAATTTGTGGAAAATC
1 CAAATTAGTGAATTTGTGGAAAATC
452767 CAAATTAGTGAATTTGTGGAAAATC
1 CAAATTAGTGAATTTGTGGAAAATC
452792 CA
1 CA
452794 TAGTCTGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (25 bp):
CAAATTAGTGAATTTGTGGAAAATC
Found at i:458645 original size:18 final size:18
Alignment explanation
Indices: 458622--458656 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
458612 AAATAAAAAA
458622 TTGTTTTTGATTTAATTG
1 TTGTTTTTGATTTAATTG
458640 TTGTTTTTGATTTAATT
1 TTGTTTTTGATTTAATT
458657 ATATTGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (18 bp):
TTGTTTTTGATTTAATTG
Found at i:460978 original size:44 final size:44
Alignment explanation
Indices: 460915--461011 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 44
460905 TTATTACTGG
* ** * *
460915 TATCGATATTACTTTACATAGTGGCATCGATACTCCTTG-GACGA
1 TATCGATACTACTACACATAGTAGCATCAATACTCCTTGAGA-GA
* *
460959 TATCGATACTACTACACATAGTAGTATCAATACTCCTTGAGAGG
1 TATCGATACTACTACACATAGTAGCATCAATACTCCTTGAGAGA
461003 TATCGATAC
1 TATCGATAC
461012 CGTTGAGTTG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 43 0.96
45 2 0.04
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (44 bp):
TATCGATACTACTACACATAGTAGCATCAATACTCCTTGAGAGA
Found at i:464084 original size:15 final size:15
Alignment explanation
Indices: 464053--464118 Score: 73
Period size: 15 Copynumber: 4.3 Consensus size: 15
464043 AGATCAAGTT
464053 AAAACAAAGAAAAAAGA
1 AAAACAAAG--AAAAGA
464070 AAAACAAAGAAAAGA
1 AAAACAAAGAAAAGA
464085 AAAACAAAGAAAA-A
1 AAAACAAAGAAAAGA
*
464099 AAGAA-AAAAACAAAGA
1 AA-AACAAAGA-AAAGA
464115 AAAA
1 AAAA
464119 AGAGGACAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
14 7 0.16
15 26 0.58
16 3 0.07
17 9 0.20
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAACAAAGAAAAGA
Found at i:464090 original size:32 final size:34
Alignment explanation
Indices: 464053--464117 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
464043 AGATCAAGTT
464053 AAAACAAAG-AAAAAAG-AAAAACAAAGAAAAGA
1 AAAACAAAGAAAAAAAGAAAAAACAAAGAAAAGA
464085 AAAACAAAGAAAAAAAGAAAAAAACAAAGAAAA
1 AAAACAAAGAAAAAAAG-AAAAAACAAAGAAAA
464118 AAGAGGACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 9 0.30
33 7 0.23
35 14 0.47
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (34 bp):
AAAACAAAGAAAAAAAGAAAAAACAAAGAAAAGA
Found at i:465430 original size:35 final size:36
Alignment explanation
Indices: 465357--465436 Score: 101
Period size: 35 Copynumber: 2.2 Consensus size: 36
465347 CATCTCACTA
*
465357 GAGACAGTCTTTCTTAAAAACGAATTTTGTCTCGCTT
1 GAGACAGTCTTTCTTAAAAAC-AATTTTGTCCCGCTT
* *
465394 GAGACA-TTTTTCTTAAAAA-AACTTTTGTCCCTCTT
1 GAGACAGTCTTTCTTAAAAACAA-TTTTGTCCCGCTT
465429 GAGACAGT
1 GAGACAGT
465437 TTCCCTTGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
34 2 0.05
35 17 0.45
36 13 0.34
37 6 0.16
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (36 bp):
GAGACAGTCTTTCTTAAAAACAATTTTGTCCCGCTT
Found at i:465493 original size:64 final size:64
Alignment explanation
Indices: 465402--465625 Score: 263
Period size: 64 Copynumber: 3.5 Consensus size: 64
465392 TTGAGACATT
*
465402 TTTCTTAAAAA-AACTTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACACAAACATTGAGATTG
1 TTTCTTAAAAACAACTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACAAACATTGAGATTG
*
465465 TTTCTTAAAAACAACTTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACACAAACATTGAGATTG
1 TTTCTTAAAAACAACTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACAAACATTGAGATTG
** * * * * * * * *
465529 TTTCTCTTGAAACAAAATTTAGTCTCTCTTGAGAAAGTTTCTCTTGAAACATAATCTTTGAGATC
1 TTTCT-TAAAAAC-AACTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACAAACATTGAGATT
465594 G
64 G
* **
465595 TTTCCCTTGAAATGAA-TTTTGTCTCTCTTGA
1 TTT--CTTAAAAACAACTTTTGTCTCTCTTGA
465626 AACACCATCT
Statistics
Matches: 138, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
63 11 0.08
64 55 0.40
65 19 0.14
66 48 0.35
67 3 0.02
68 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (64 bp):
TTTCTTAAAAACAACTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACAAACATTGAGATTG
Found at i:465590 original size:66 final size:65
Alignment explanation
Indices: 465416--465625 Score: 269
Period size: 66 Copynumber: 3.2 Consensus size: 65
465406 TTAAAAAAAC
* ** *
465416 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAACACAAACATTGAGATTGTTTCT-TAAAAACAAC
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACAAACATTGAGATTGTTTCTCTTGAAACAAA
*
465480 TTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACACAAACATTGAGATTGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACAAACATTGAGATTGTTTCTCTTGAAAC-AA
465545 A
65 A
* * * * * * * * **
465546 TTTAGTCTCTCTTGAGAAAGTTTCTCTTGAAACATAATCTTTGAGATCGTTTCCCTTGAAATGAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACAAACATTGAGATTGTTTCTCTTGAAACAAA
465611 TTTTGTCTCTCTTGA
1 TTTTGTCTCTCTTGA
465626 AACACCATCT
Statistics
Matches: 127, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
64 52 0.41
65 21 0.17
66 54 0.43
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.39
Consensus pattern (65 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACAAACATTGAGATTGTTTCTCTTGAAACAAA
Found at i:465641 original size:50 final size:50
Alignment explanation
Indices: 465568--465673 Score: 167
Period size: 50 Copynumber: 2.1 Consensus size: 50
465558 TGAGAAAGTT
* *
465568 TCTCTTGAAACATAATCTTTGAGATCGTTTCCCTTGAAATGAATTTTGTC
1 TCTCTTGAAACACAATCTTTGAGATCGTTTCCCTTGAAATGAATTTTATC
* *
465618 TCTCTTGAAACACCATCTTTGAGATCGTTTCCTTTGAAATGAATTTTATC
1 TCTCTTGAAACACAATCTTTGAGATCGTTTCCCTTGAAATGAATTTTATC
*
465668 TTTCTT
1 TCTCTT
465674 TAGATAGTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (50 bp):
TCTCTTGAAACACAATCTTTGAGATCGTTTCCCTTGAAATGAATTTTATC
Found at i:465687 original size:65 final size:65
Alignment explanation
Indices: 465618--465845 Score: 185
Period size: 65 Copynumber: 3.6 Consensus size: 65
465608 GAATTTTGTC
* * ** * *
465618 TCTCTTGAAACACCATCTTTGAGATCGTTTCCTTTGAAATGAA-TTTTATCTTTCTTTAGATAGT
1 TCTCTTGAAACACCATCTTTGAGATCGTTTCCCTTGAAA-CAAGTTTTATCTCCCTTGAGACAGT
465682 T
65 T
* * *
465683 TCTCTTGAAACATCATCTTTGAGATTGTTTCCCTTGAAACAAGTTTTGTCTCCCTTGAGACAGTT
1 TCTCTTGAAACACCATCTTTGAGATCGTTTCCCTTGAAACAAGTTTTATCTCCCTTGAGACAGTT
* * *
465748 TCTCTTG--A-A--A----T-AAATTGTTTCCCTTGAAACAAAG-TTTGTCTCCCTTGAGACAGT
1 TCTCTTGAAACACCATCTTTGAGATCGTTTCCCTTGAAAC-AAGTTTTATCTCCCTTGAGACAGT
465802 T
65 T
** * *
465803 TCTCTTGAAACAAAAATCTTTGA-CTCTATTTCCCTTGAAACAA
1 TCTCTTGAAAC-ACCATCTTTGAGATC-GTTTCCCTTGAAACAA
465846 AATTTTGTCT
Statistics
Matches: 136, Mismatches: 13, Indels: 28
0.77 0.07 0.16
Matches are distributed among these distances:
55 46 0.34
56 4 0.03
57 1 0.01
59 1 0.01
60 1 0.01
61 1 0.01
62 1 0.01
63 1 0.01
64 2 0.01
65 64 0.47
66 14 0.10
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (65 bp):
TCTCTTGAAACACCATCTTTGAGATCGTTTCCCTTGAAACAAGTTTTATCTCCCTTGAGACAGTT
Found at i:465736 original size:21 final size:20
Alignment explanation
Indices: 465707--465795 Score: 73
Period size: 21 Copynumber: 4.7 Consensus size: 20
465697 ATCTTTGAGA
*
465707 TTGTTTCCCTTGAAACAAGTT
1 TTGTCTCCCTTGAAACAAG-T
*
465728 TTGTCTCCCTTGAGAC-AG-
1 TTGTCTCCCTTGAAACAAGT
* *
465746 TT-TCT--CTTGAAATAA-A
1 TTGTCTCCCTTGAAACAAGT
*
465762 TTGTTTCCCTTGAAACAAAGT
1 TTGTCTCCCTTGAAAC-AAGT
465783 TTGTCTCCCTTGA
1 TTGTCTCCCTTGA
465796 GACAGTTTCT
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
15 6 0.11
16 3 0.06
17 5 0.09
18 2 0.04
19 7 0.13
20 4 0.08
21 26 0.49
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (20 bp):
TTGTCTCCCTTGAAACAAGT
Found at i:465772 original size:55 final size:55
Alignment explanation
Indices: 465706--465812 Score: 198
Period size: 55 Copynumber: 1.9 Consensus size: 55
465696 CATCTTTGAG
465706 ATTGTTTCCCTTGAAAC-AAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAATAA
1 ATTGTTTCCCTTGAAACAAAG-TTTGTCTCCCTTGAGACAGTTTCTCTTGAAATAA
465761 ATTGTTTCCCTTGAAACAAAGTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA
1 ATTGTTTCCCTTGAAACAAAGTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA
465813 CAAAAATCTT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
55 48 0.94
56 3 0.06
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (55 bp):
ATTGTTTCCCTTGAAACAAAGTTTGTCTCCCTTGAGACAGTTTCTCTTGAAATAA
Found at i:465773 original size:19 final size:20
Alignment explanation
Indices: 465745--465795 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
465735 CCTTGAGACA
* *
465745 GTTTCTCTTGAAATAAA-TT
1 GTTTCCCTTGAAACAAAGTT
465764 GTTTCCCTTGAAACAAAGTTT
1 GTTTCCCTTGAAACAAAG-TT
*
465785 GTCTCCCTTGA
1 GTTTCCCTTGA
465796 GACAGTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 15 0.56
21 12 0.44
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (20 bp):
GTTTCCCTTGAAACAAAGTT
Found at i:465953 original size:40 final size:40
Alignment explanation
Indices: 465893--466031 Score: 120
Period size: 40 Copynumber: 3.4 Consensus size: 40
465883 GCCAGCTATT
* *
465893 CTCATCACGTAGGAACCGTGTCATCCACTGACAATATCTC
1 CTCATCATGTAGGAGCCGTGTCATCCACTGACAATATCTC
* * *
465933 CTCATCATGCAGGAGTCGTGTCA-CC-CTTAGATAACTAGTCGTC
1 CTCATCATGTAGGAGCCGTGTCATCCAC-T-GACAA-TA-TC-TC
* * * * * *
465976 CTCATCACGTAAGAACCGTGTCATCCACCGACCAGATCTC
1 CTCATCATGTAGGAGCCGTGTCATCCACTGACAATATCTC
466016 CTCATCATGTAGGAGC
1 CTCATCATGTAGGAGC
466032 TGCGCCAACC
Statistics
Matches: 75, Mismatches: 17, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
38 1 0.01
39 3 0.04
40 38 0.51
41 4 0.05
42 3 0.04
43 23 0.31
44 2 0.03
45 1 0.01
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (40 bp):
CTCATCATGTAGGAGCCGTGTCATCCACTGACAATATCTC
Found at i:466044 original size:83 final size:83
Alignment explanation
Indices: 465893--466069 Score: 257
Period size: 83 Copynumber: 2.1 Consensus size: 83
465883 GCCAGCTATT
* * * * * *
465893 CTCATCACGTAGGAACCGTGTCATCCACTGACAATATCTCCTCATCATGCAGGAGTCGTGTCACC
1 CTCATCACGTAAGAACCGTGTCATCCACCGACAAGATCTCCTCATCATGCAGGAGTCGCGCCAAC
*
465958 CTTAGATAACTAGTCGTC
66 CTTAGATAACCAGTCGTC
* *
465976 CTCATCACGTAAGAACCGTGTCATCCACCGACCAGATCTCCTCATCATGTAGGAG-CTGCGCCAA
1 CTCATCACGTAAGAACCGTGTCATCCACCGACAAGATCTCCTCATCATGCAGGAGTC-GCGCCAA
466040 CCTTAGATAACCAGTCGTC
65 CCTTAGATAACCAGTCGTC
466059 CTCATCACGTA
1 CTCATCACGTA
466070 GGATTCATGT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
82 1 0.01
83 83 0.99
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (83 bp):
CTCATCACGTAAGAACCGTGTCATCCACCGACAAGATCTCCTCATCATGCAGGAGTCGCGCCAAC
CTTAGATAACCAGTCGTC
Found at i:466374 original size:3 final size:3
Alignment explanation
Indices: 466366--466395 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
466356 GTCTTAAACA
466366 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
466396 TTACTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:472613 original size:2 final size:2
Alignment explanation
Indices: 472608--472683 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
472598 ACACACACAC
472608 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
472650 AT AT AT AT AT AT AT AT AT -T 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 A
472684 ATTTCGTTTA
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 72 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:486944 original size:3 final size:3
Alignment explanation
Indices: 486936--486998 Score: 54
Period size: 3 Copynumber: 20.7 Consensus size: 3
486926 TTTAATAAAT
* * * * * * *
486936 TAA TAA TAA CAA CAA TAA CAA TAA CAA TAA CAA CAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
486984 TAAA TAA TAA TAA TA
1 T-AA TAA TAA TAA TA
486999 TTTTTGTAGA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (3 bp):
TAA
Found at i:486991 original size:13 final size:13
Alignment explanation
Indices: 486973--486998 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
486963 TAACAACAAC
486973 AATAATAATAATA
1 AATAATAATAATA
486986 AATAATAATAATA
1 AATAATAATAATA
486999 TTTTTGTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:487486 original size:131 final size:130
Alignment explanation
Indices: 487186--487635 Score: 458
Period size: 131 Copynumber: 3.4 Consensus size: 130
487176 GTACTGGTCG
* * * ** * *
487186 TCTAAGGGTGACACGGA-TCCTACATGATGAGGATATCTGGTCGGTGGATGACACAGTT-TCTAC
1 TCTAAGGTTGACA-TGACTCCTACGTGATGAGGAGGTCTTGTCGGTGGATGACACGGTTCT-TAC
* ** *
487249 GTGATAAGGATGACATGCCATCTTTAGGGAGGGTGATAACACAGTTCCTACGCGATGAGGATGAT
64 GTGATGAGGATGACATGCCATCTTTAGGGA---TGATAACATGGTTCCTACGTGATGAGGATGAT
*
487314 TGATTA
126 AG-TTA
* * * *
487320 TCTAGGGGTGGCATGACTCCTACGTGATGAGGAGGTCTTGTCGGTGGATGACATGGTTCTTACGT
1 TCTAAGGTTGACATGACTCCTACGTGATGAGGAGGTCTTGTCGGTGGATGACACGGTTCTTACGT
* * *
487385 GATGAGGATGATAGGCCATCTTTAGGGATGATAACATGGTTCCTACATGATGAGGATGAGTAGTT
66 GATGAGGATGACATGCCATCTTTAGGGATGATAACATGGTTCCTACGTGATGAGGATGA-TAGTT
487450 A
130 A
* * * * * * * * *
487451 TCTAAGTTTGACATGGCTACTACGTGATGAGGAGGTC-CGACCAGTAGATGAGACGGTTCCTACG
1 TCTAAGGTTGACATGACTCCTACGTGATGAGGAGGTCTTG-TCGGTGGATGACACGGTTCTTACG
* * * * * *
487515 TGTTGAGGACGACATGCTATCTTTAGGGATTATAACATGATTCCTACGTGATGAGGATGACTGGT
65 TGATGAGGATGACATGCCATCTTTAGGGATGATAACATGGTTCCTACGTGATGAGGATGA-TAGT
487580 TA
129 TA
* *
487582 TCTAAGGTTGACACGACTCCTATGTGATGAGGAGGT-TTGGTCGGTGGATGACAC
1 TCTAAGGTTGACATGACTCCTACGTGATGAGGAGGTCTT-GTCGGTGGATGACAC
487636 TACTCCTGCG
Statistics
Matches: 260, Mismatches: 50, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
130 1 0.00
131 177 0.68
132 3 0.01
133 2 0.01
134 76 0.29
135 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.28
Consensus pattern (130 bp):
TCTAAGGTTGACATGACTCCTACGTGATGAGGAGGTCTTGTCGGTGGATGACACGGTTCTTACGT
GATGAGGATGACATGCCATCTTTAGGGATGATAACATGGTTCCTACGTGATGAGGATGATAGTTA
Found at i:487795 original size:66 final size:66
Alignment explanation
Indices: 487678--487968 Score: 291
Period size: 66 Copynumber: 4.4 Consensus size: 66
487668 GTAAGGATAA
* * * * * * *
487678 TGTTTCAAGGGAAACAAACACAAAGA-TGATGCTTCAAAAAGAAGCTGTCTCAAGAGAGACAAAA
1 TGTTTCAAGGGAAACAATCTCAAAGATTGGTGTTTC-AAGAGAAACTGTCTCAAGGGAGACAAAA
487742 TT
65 TT
* * * *
487744 GGTTTCAAGGGAAACGATCTCAAAGATGGGTGTTTCAAGAGAAACTATCTCAA-GGAGGACAAAA
1 TGTTTCAAGGGAAACAATCTCAAAGATTGGTGTTTCAAGAGAAACTGTCTCAAGGGA-GACAAAA
*
487808 CT
65 TT
* * * * **
487810 TGTTTCAATGGAAACAAT-TCAAAGTTTGGTGTTTCATGAAAAACTGTCTTGAGGGAGACAAAAT
1 TGTTTCAAGGGAAACAATCTCAAAGATTGGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT
487874 T
66 T
* * * * * * * *
487875 TATTTCAAGGGAAATAATCTCTAAGTTTGGTGTTTCATGAGAAACTGTATCGAGGGAGGCAAAAT
1 TGTTTCAAGGGAAACAATCTCAAAGATTGGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT
487940 T
66 T
* *
487941 TGTTTCAAGAGAAACAAACTCAAAGATT
1 TGTTTCAAGGGAAACAATCTCAAAGATT
487969 ATAAATTTTG
Statistics
Matches: 184, Mismatches: 37, Indels: 8
0.80 0.16 0.03
Matches are distributed among these distances:
65 52 0.28
66 126 0.68
67 6 0.03
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (66 bp):
TGTTTCAAGGGAAACAATCTCAAAGATTGGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT
T
Found at i:489326 original size:16 final size:16
Alignment explanation
Indices: 489305--489339 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
489295 GCTTCTTGTC
*
489305 TCTTTTTCTTTTCTTT
1 TCTTTTACTTTTCTTT
*
489321 TCTTTTACTTTTTTTT
1 TCTTTTACTTTTCTTT
489337 TCT
1 TCT
489340 CAATTTACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (16 bp):
TCTTTTACTTTTCTTT
Found at i:489371 original size:14 final size:13
Alignment explanation
Indices: 489350--489397 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
489340 CAATTTACTA
489350 TTTTTTTCTTTGC
1 TTTTTTTCTTTGC
489363 TTATTTTTCTTTG-
1 TT-TTTTTCTTTGC
489376 TTTTCTTT-TTTGC
1 TTTT-TTTCTTTGC
*
489389 TTCTTTTCT
1 TTTTTTTCT
489398 CTTTTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
12 9 0.30
13 11 0.37
14 10 0.33
ACGTcount: A:0.02, C:0.15, G:0.06, T:0.77
Consensus pattern (13 bp):
TTTTTTTCTTTGC
Found at i:489387 original size:26 final size:26
Alignment explanation
Indices: 489350--489413 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
489340 CAATTTACTA
*
489350 TTTTTTTCTTTGCTTATTTT-TCTTT
1 TTTTTTTATTTGCTTATTTTCTCTTT
*
489375 GTTTTCTTT-TTTGCTTCTTTTCTCTTT
1 -TTTT-TTTATTTGCTTATTTTCTCTTT
489402 TTTTTTTATTTG
1 TTTTTTTATTTG
489414 ATCTTCGCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
25 3 0.09
26 23 0.68
27 8 0.24
ACGTcount: A:0.03, C:0.12, G:0.06, T:0.78
Consensus pattern (26 bp):
TTTTTTTATTTGCTTATTTTCTCTTT
Found at i:490738 original size:28 final size:27
Alignment explanation
Indices: 490679--490737 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 27
490669 GAAATGTTTG
490679 AAAATGCTTAAAAATGAAATGCAGATGC
1 AAAATGC-TAAAAATGAAATGCAGATGC
*
490707 AAAATGC-AAAAATGCAAATGTAGATGC
1 AAAATGCTAAAAATG-AAATGCAGATGC
490734 AAAA
1 AAAA
490738 AGATTGATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 7 0.24
27 15 0.52
28 7 0.24
ACGTcount: A:0.54, C:0.10, G:0.17, T:0.19
Consensus pattern (27 bp):
AAAATGCTAAAAATGAAATGCAGATGC
Found at i:493595 original size:20 final size:20
Alignment explanation
Indices: 493556--493595 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
493546 ATTTATTTGG
*
493556 ATTTTTTCTAATTTTTATCT
1 ATTTTTTCTAATTTTGATCT
493576 ATTTTTT-TAATGTTTGATCT
1 ATTTTTTCTAAT-TTTGATCT
493596 GCTTTCGGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (20 bp):
ATTTTTTCTAATTTTGATCT
Found at i:494080 original size:3 final size:3
Alignment explanation
Indices: 494072--494105 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
494062 AAAAATGATG
494072 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
494106 TTTGTAGGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:501395 original size:90 final size:89
Alignment explanation
Indices: 501241--501418 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 89
501231 TAACACACCC
*
501241 TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTGAAATTAATTAAATCTATATT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATT
* * *
501306 TAATTAATTGGAATTTAATATTCA
66 GAATTAATTGAAATTAAATATTCA
* *
501330 TTTTATATCCAAGTTACCCTAATTATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATAT
501395 TGAATTAATTGAAATTAAATATTC
65 TGAATTAATTGAAATTAAATATTC
501419 GGGGTTATTA
Statistics
Matches: 82, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 31 0.38
90 51 0.62
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.46
Consensus pattern (89 bp):
TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATT
GAATTAATTGAAATTAAATATTCA
Found at i:505018 original size:2 final size:2
Alignment explanation
Indices: 505011--505042 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
505001 TGTTTGTCTC
505011 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
505043 GTGTCCAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:509896 original size:98 final size:99
Alignment explanation
Indices: 509727--509927 Score: 289
Period size: 98 Copynumber: 2.0 Consensus size: 99
509717 ATATACCATG
* *
509727 TTACTCGAAGGGTAACTTCCAAAATTGGGACGAATACTGAAAATATTCCTTTTTTTGCACGGACT
1 TTACTCGAAGGGTAACTTCCAAAATTGGGACGAATACTGAAAATATTCCTCTTTTTGCACAGACT
* * *
509792 GAGTCATAATAGATAAGATACTTTGGTATACTT-
66 GAGTCATAAAAAATAAGATAATTTGGTATACTTA
** * * *
509825 TTACTCGCGGGGTAACTTCCAAAATTGGGACGAATACTGACAATATTTCC-CTTTTTGCACATAT
1 TTACTCGAAGGGTAACTTCCAAAATTGGGACGAATACTGAAAATA-TTCCTCTTTTTGCACAGAC
509889 TGAGTCATAAAAAATAAGATAATTTGGTATACTTA
65 TGAGTCATAAAAAATAAGATAATTTGGTATACTTA
509924 TTAC
1 TTAC
509928 ATAACGATTA
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
98 83 0.91
99 8 0.09
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (99 bp):
TTACTCGAAGGGTAACTTCCAAAATTGGGACGAATACTGAAAATATTCCTCTTTTTGCACAGACT
GAGTCATAAAAAATAAGATAATTTGGTATACTTA
Found at i:510883 original size:32 final size:32
Alignment explanation
Indices: 510845--510917 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 32
510835 GGCCTGAGAG
*
510845 CTACCCAAGGAAAAACCTCGGGGCCTTACAAC
1 CTACCCAAGGAAAAACCTCGGGGCCTCACAAC
* * * *
510877 CTACCCAAGGAAATACCTTGGGGCCTCAGAGC
1 CTACCCAAGGAAAAACCTCGGGGCCTCACAAC
510909 CTACCCAAG
1 CTACCCAAG
510918 TGTCACCTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.32, C:0.34, G:0.21, T:0.14
Consensus pattern (32 bp):
CTACCCAAGGAAAAACCTCGGGGCCTCACAAC
Found at i:513556 original size:110 final size:109
Alignment explanation
Indices: 513235--513773 Score: 496
Period size: 110 Copynumber: 4.9 Consensus size: 109
513225 AATAGGTATG
* * * * * * * * *
513235 CTCCATCTTCTTTTAGGGAGTATAGGACTCAAAACATATTCAAAAAATGGATCTGATCCATCTTC
1 CTCCCTCTTCTTTCAAGGAGTATAGGACTCAAAA-ATCTTCAGAAAATGGGTCCGCTCCCTCTTC
* * ** * * * *
513300 TTT-ATGGGAATATAGGACTCGAAATTTTTTTAAAAAATTGGTCCA
65 TTTCA-GGGAGTATAGGACTTGAAAAATCTTCAGAAAATGGGTCCA
* * * * * * ** *
513345 CTCCCTCTTTTTTCATGGAGTATAGGACTCGAACAATCTT-TGAAAAATAGGTCTGCTCTATATT
1 CTCCCTCTTCTTTCAAGGAGTATAGGACTC-AAAAATCTTCAG-AAAATGGGTCCGCTCCCTCTT
* * * *
513409 CTTTCAGGGAGCATAGGAC-TCAAAACAACTTCAGAAAATGGGTTCA
64 CTTTCAGGGAGTATAGGACTTGAAAA-ATCTTCAGAAAATGGGTCCA
513455 CTCCCT-TTACTTTCAAGGAGTATAGGACTCAAAATATCTTCAGAAAATGGGTCCGCTCCCTCTT
1 CTCCCTCTT-CTTTCAAGGAGTATAGGACTCAAAA-ATCTTCAGAAAATGGGTCCGCTCCCTCTT
* * * *
513519 CTTTCAGGGAGTATAGGACTTGAAAACTCTTCGGAAAACGGGTCCG
64 CTTTCAGGGAGTATAGGACTTGAAAAATCTTCAGAAAATGGGTCCA
* * ** * *
513565 CTCCCTCTTCTCTCAAGGAGTA-AGGACTTGAAAAATCTTTGGAGAATGGGTCCACTCCCTCTTC
1 CTCCCTCTTCTTTCAAGGAGTATAGGAC-TCAAAAATCTTCAGAAAATGGGTCCGCTCCCTCTTC
* * * * * *
513629 TCTCAGGGAGTATAGGACGTAAAAAATCTTCAGAAATTAGGTCCG
65 TTTCAGGGAGTATAGGACTTGAAAAATCTTCAGAAAATGGGTCCA
* *
513674 CTCCCTCTTCTTTCAAGGAGTATAGGACTCAAAAAATCTTTA-AAAGACGGGTCCGCTCCCTCTT
1 CTCCCTCTTCTTTCAAGGAGTATAGGACTC-AAAAATCTTCAGAAA-ATGGGTCCGCTCCCTCTT
* *
513738 CTTTTAGGGAGTATAGGACTTGAAAAATCTTTAGAA
64 CTTTCAGGGAGTATAGGACTTGAAAAATCTTCAGAA
513774 CTCTTCTTTC
Statistics
Matches: 349, Mismatches: 67, Indels: 26
0.79 0.15 0.06
Matches are distributed among these distances:
109 100 0.29
110 237 0.68
111 12 0.03
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (109 bp):
CTCCCTCTTCTTTCAAGGAGTATAGGACTCAAAAATCTTCAGAAAATGGGTCCGCTCCCTCTTCT
TTCAGGGAGTATAGGACTTGAAAAATCTTCAGAAAATGGGTCCA
Found at i:513660 original size:164 final size:165
Alignment explanation
Indices: 513333--513769 Score: 472
Period size: 164 Copynumber: 2.7 Consensus size: 165
513323 ATTTTTTTAA
* * * * * * **
513333 AAAATTGGTCCACTCCCTCTTTTTTCATGGAGTATAGGACTCGAACAATCTTTGAAAA-ATAGGT
1 AAAATAGGTCCGCTCCCTCTTCTTTCAAGGAGTATAGGACTCAAAAAATC-TTGAAAAGACGGGT
* ** * * * * * * ** * *
513397 CTGCTCTATATTCTTTCAGGGAGCATAGGAC-TCAAAACAACTTCAGAAAATGGGTTCACTCCCT
65 CCGCTCCCTCTTCTCTCAAGGAGTATAGGACTTGAAAA-ATCTTTGGAGAATGGGTCCACTCCCT
* *
513461 TTACTTTCAAGGAGTATAGGACTCAAAATATCTTCAG
129 TTACTCTCAAGGAGTATAGGACTCAAAAAATCTTCAG
* * ** * *
513498 AAAATGGGTCCGCTCCCTCTTCTTTCAGGGAGTATAGGACTTGAAAACTCTTCGGAAA-ACGGGT
1 AAAATAGGTCCGCTCCCTCTTCTTTCAAGGAGTATAGGACTCAAAAAATCTT-GAAAAGACGGGT
513562 CCGCTCCCTCTTCTCTCAAGGAGTA-AGGACTTGAAAAATCTTTGGAGAATGGGTCCACTCCCTC
65 CCGCTCCCTCTTCTCTCAAGGAGTATAGGACTTGAAAAATCTTTGGAGAATGGGTCCACTCCCT-
*
513626 TT-CTCTCAGGGAGTATAGGACGT-AAAAAATCTTCAG
129 TTACTCTCAAGGAGTATAGGAC-TCAAAAAATCTTCAG
* *
513662 AAATTAGGTCCGCTCCCTCTTCTTTCAAGGAGTATAGGACTCAAAAAATCTTTAAAAGACGGGTC
1 AAAATAGGTCCGCTCCCTCTTCTTTCAAGGAGTATAGGACTCAAAAAATCTTGAAAAGACGGGTC
* * *
513727 CGCTCCCTCTTCTTTTAGGGAGTATAGGACTTGAAAAATCTTT
66 CGCTCCCTCTTCTCTCAAGGAGTATAGGACTTGAAAAATCTTT
513770 AGAACTCTTC
Statistics
Matches: 229, Mismatches: 37, Indels: 12
0.82 0.13 0.04
Matches are distributed among these distances:
163 3 0.01
164 131 0.57
165 95 0.41
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (165 bp):
AAAATAGGTCCGCTCCCTCTTCTTTCAAGGAGTATAGGACTCAAAAAATCTTGAAAAGACGGGTC
CGCTCCCTCTTCTCTCAAGGAGTATAGGACTTGAAAAATCTTTGGAGAATGGGTCCACTCCCTTT
ACTCTCAAGGAGTATAGGACTCAAAAAATCTTCAG
Found at i:513764 original size:55 final size:54
Alignment explanation
Indices: 513234--513770 Score: 420
Period size: 55 Copynumber: 9.8 Consensus size: 54
513224 AAATAGGTAT
* * * * * * *
513234 GCTCCATCTTCTTTTAGGGAGTATAGGAC-TCAAAACATATTCAAAAAATGGATCT
1 GCTCCCTCTTCTTTCAGGGAGTATAGGACTTGAAAA-ATCTT-TAAAAATGGGTCC
* * * * ** * *
513289 GATCCATCTTCTTT-ATGGGAATATAGGACTCGAAATTTTTTTAAAAAATTGGTCC
1 GCTCCCTCTTCTTTCA-GGGAGTATAGGACTTGAAAAATCTTT-AAAAATGGGTCC
* * * * * * *
513344 ACTCCCTCTTTTTTCATGGAGTATAGGACTCGAACAATCTTTGAAAAATAGGTCT
1 GCTCCCTCTTCTTTCAGGGAGTATAGGACTTGAAAAATCTTT-AAAAATGGGTCC
** * * * * * *
513399 GCTCTATATTCTTTCAGGGAGCATAGGAC-TCAAAACAACTTCAGAAAATGGGTTC
1 GCTCCCTCTTCTTTCAGGGAGTATAGGACTTGAAAA-ATCTTTA-AAAATGGGTCC
* * * *
513454 ACTCCCT-TTACTTTCAAGGAGTATAGGAC-TCAAAATATCTTCAGAAAATGGGTCC
1 GCTCCCTCTT-CTTTCAGGGAGTATAGGACTTGAAAA-ATCTTTA-AAAATGGGTCC
* ** *
513509 GCTCCCTCTTCTTTCAGGGAGTATAGGACTTGAAAACTCTTCGGAAAACGGGTCC
1 GCTCCCTCTTCTTTCAGGGAGTATAGGACTTGAAAAATCTT-TAAAAATGGGTCC
* * * *
513564 GCTCCCTCTTCTCTCAAGGAGTA-AGGACTTGAAAAATCTTTGGAGAATGGGTCC
1 GCTCCCTCTTCTTTCAGGGAGTATAGGACTTGAAAAATCTTT-AAAAATGGGTCC
* * * * * * *
513618 ACTCCCTCTTCTCTCAGGGAGTATAGGACGTAAAAAATCTTCAGAAATTAGGTCC
1 GCTCCCTCTTCTTTCAGGGAGTATAGGACTTGAAAAATCTTTA-AAAATGGGTCC
* ** *
513673 GCTCCCTCTTCTTTCAAGGAGTATAGGACTCAAAAAATCTTTAAAAGACGGGTCC
1 GCTCCCTCTTCTTTCAGGGAGTATAGGACTTGAAAAATCTTTAAAA-ATGGGTCC
*
513728 GCTCCCTCTTCTTTTAGGGAGTATAGGACTTGAAAAATCTTTA
1 GCTCCCTCTTCTTTCAGGGAGTATAGGACTTGAAAAATCTTTA
513771 GAACTCTTCT
Statistics
Matches: 386, Mismatches: 82, Indels: 28
0.78 0.17 0.06
Matches are distributed among these distances:
54 57 0.15
55 318 0.82
56 11 0.03
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (54 bp):
GCTCCCTCTTCTTTCAGGGAGTATAGGACTTGAAAAATCTTTAAAAATGGGTCC
Found at i:516666 original size:105 final size:104
Alignment explanation
Indices: 516515--516722 Score: 256
Period size: 105 Copynumber: 2.0 Consensus size: 104
516505 TTGTAATTTT
* * * * *
516515 CCTTTATCAGGCTTGCTGATTCTTATCTATAAAGCTAGGGCATTTAACCAATTTCTCTAGAGGGA
1 CCTTTATCAGGATTGCTGAATCTTATCCATAAAGCTAGGGCATTTAACCAATTCCTCTAAAGGGA
* * *
516580 TAGCTCAAGTTTTA-TTGTATATATATATATATGATAATCA
66 CAACTCAAGCTTTAGTT-TATATATATA-ATATGATAATCA
* * ** *
516620 CCTTTATCAGGATTGTTGAATCTTATCCATAAAGCTGGGGTGTTTAACTAATTCCTCTAAAGGGA
1 CCTTTATCAGGATTGCTGAATCTTATCCATAAAGCTAGGGCATTTAACCAATTCCTCTAAAGGGA
* *
516685 CAACTCAAGCTTTAGTTTCTATATATAATATTATAATC
66 CAACTCAAGCTTTAGTTTATATATATAATATGATAATC
516723 TGGGTATACA
Statistics
Matches: 87, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
104 10 0.11
105 75 0.86
106 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (104 bp):
CCTTTATCAGGATTGCTGAATCTTATCCATAAAGCTAGGGCATTTAACCAATTCCTCTAAAGGGA
CAACTCAAGCTTTAGTTTATATATATAATATGATAATCA
Found at i:533459 original size:12 final size:13
Alignment explanation
Indices: 533442--533472 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
533432 ACCTATATTT
533442 AAAAAACAAA-TA
1 AAAAAACAAACTA
533454 AAAAAACAAACTA
1 AAAAAACAAACTA
533467 AAAAAA
1 AAAAAA
533473 TCGATGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.84, C:0.10, G:0.00, T:0.06
Consensus pattern (13 bp):
AAAAAACAAACTA
Found at i:534224 original size:15 final size:15
Alignment explanation
Indices: 534206--534236 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
534196 GAATTCTAAA
534206 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
534221 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
534236 T
1 T
534237 CTATTTGTTG
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:537589 original size:20 final size:20
Alignment explanation
Indices: 537546--537591 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
537536 CCTGGCAATG
* *
537546 AACCGACTGAAAACCGATAG
1 AACCGGCTGAAAACCGATAA
* *
537566 AACCGGCTGAAAACTGGTAA
1 AACCGGCTGAAAACCGATAA
537586 AACCGG
1 AACCGG
537592 GGTGAACCGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (20 bp):
AACCGGCTGAAAACCGATAA
Found at i:540681 original size:24 final size:24
Alignment explanation
Indices: 540642--540697 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
540632 AAACATAATT
*
540642 CAGGTCAAGTAGCATATCAGAATC
1 CAGGTCAAGTAGCATATCAAAATC
* *
540666 CATGTCAAGTATCATATCAAAATC
1 CAGGTCAAGTAGCATATCAAAATC
540690 CAGGTCAA
1 CAGGTCAA
540698 AAATCAGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.23
Consensus pattern (24 bp):
CAGGTCAAGTAGCATATCAAAATC
Found at i:540703 original size:24 final size:24
Alignment explanation
Indices: 540654--540703 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
540644 GGTCAAGTAG
* * **
540654 CATATCAGAATCCATGTCAAGTAT
1 CATATCAAAATCCAGGTCAAAAAT
540678 CATATCAAAATCCAGGTCAAAAAT
1 CATATCAAAATCCAGGTCAAAAAT
540702 CA
1 CA
540704 GATAAACTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.44, C:0.22, G:0.10, T:0.24
Consensus pattern (24 bp):
CATATCAAAATCCAGGTCAAAAAT
Found at i:541446 original size:29 final size:28
Alignment explanation
Indices: 541408--541574 Score: 201
Period size: 29 Copynumber: 5.8 Consensus size: 28
541398 TTATCACCCT
541408 TTTTAAAAATAATTACAAAAATAGCACAC
1 TTTTAAAAATAATTACAAAAATAGCAC-C
541437 TTTTAAAAATAATTACAAAAATAGCACC
1 TTTTAAAAATAATTACAAAAATAGCACC
* *
541465 ATTTTTAAATTAATTACAAAAATAGCACC
1 -TTTTAAAAATAATTACAAAAATAGCACC
* *
541494 ATTTTTAAAATAATTACGAAAATAGCACCC
1 -TTTTAAAAATAATTACAAAAATAGCA-CC
* * *
541524 TTTAAAAAATGATTAC-AAAATAGCACAT
1 TTTTAAAAATAATTACAAAAATAGCAC-C
* *
541552 TTTTTAAAATAATTACGAAAATA
1 TTTTAAAAATAATTACAAAAATA
541575 ACACTCGGGC
Statistics
Matches: 123, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
27 1 0.01
28 23 0.19
29 97 0.79
30 2 0.02
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (28 bp):
TTTTAAAAATAATTACAAAAATAGCACC
Found at i:541487 original size:58 final size:58
Alignment explanation
Indices: 541402--541574 Score: 242
Period size: 58 Copynumber: 3.0 Consensus size: 58
541392 ACACAATTAT
* *
541402 CACCCTTTTTAAAAATAATTACAAAAATAGCACACTTTTAAAAATAATTACAAAAATAG
1 CACCCTTTTT-AAAATAATTACAAAAATAGCACACTTTTTAAAATAATTACGAAAATAG
* *
541461 CACCATTTTTAAATTAATTACAAAAATAGCAC-CATTTTTAAAATAATTACGAAAATAG
1 CACCCTTTTTAAAATAATTACAAAAATAGCACAC-TTTTTAAAATAATTACGAAAATAG
** * *
541519 CACCCTTTAAAAAATGATTAC-AAAATAGCACATTTTTTAAAATAATTACGAAAATA
1 CACCCTTTTTAAAATAATTACAAAAATAGCACACTTTTTAAAATAATTACGAAAATA
541575 ACACTCGGGC
Statistics
Matches: 102, Mismatches: 10, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
57 34 0.33
58 59 0.58
59 9 0.09
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.31
Consensus pattern (58 bp):
CACCCTTTTTAAAATAATTACAAAAATAGCACACTTTTTAAAATAATTACGAAAATAG
Found at i:541539 original size:87 final size:87
Alignment explanation
Indices: 541402--541574 Score: 251
Period size: 87 Copynumber: 2.0 Consensus size: 87
541392 ACACAATTAT
* *
541402 CACCCTTTTTAAAAATAATTACAAAAATAGCACACTTTTAAAAATAATTACAAAAATAGCACCA-
1 CACCATTTTTAAAAATAATTACAAAAATAGCACACTTTAAAAAATAATTAC-AAAATAGCA-CAT
*
541466 TTTTTAAATTAATTACAAAAATAG
64 TTTTTAAAATAATTACAAAAATAG
* * *
541490 CACCATTTTT-AAAATAATTACGAAAATAGCACCCTTTAAAAAATGATTACAAAATAGCACATTT
1 CACCATTTTTAAAAATAATTACAAAAATAGCACACTTTAAAAAATAATTACAAAATAGCACATTT
*
541554 TTTAAAATAATTACGAAAATA
66 TTTAAAATAATTACAAAAATA
541575 ACACTCGGGC
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
85 2 0.03
86 30 0.39
87 36 0.47
88 9 0.12
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.31
Consensus pattern (87 bp):
CACCATTTTTAAAAATAATTACAAAAATAGCACACTTTAAAAAATAATTACAAAATAGCACATTT
TTTAAAATAATTACAAAAATAG
Found at i:541625 original size:22 final size:22
Alignment explanation
Indices: 541595--541647 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
541585 AACGGTCCAT
*
541595 GGTCGGGTCAACAGTCGGGACG
1 GGTCAGGTCAACAGTCGGGACG
* * *
541617 GTTCAGGTCAACGGTCGGGTCG
1 GGTCAGGTCAACAGTCGGGACG
541639 GGTCAGGTC
1 GGTCAGGTC
541648 GAACCGGTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.15, C:0.23, G:0.43, T:0.19
Consensus pattern (22 bp):
GGTCAGGTCAACAGTCGGGACG
Found at i:543638 original size:17 final size:16
Alignment explanation
Indices: 543596--543643 Score: 64
Period size: 17 Copynumber: 3.1 Consensus size: 16
543586 TAGAAACACA
543596 TAAAATATAAAAGAA-
1 TAAAATATAAAAGAAT
*
543611 T-AAACATAAAAGAAT
1 TAAAATATAAAAGAAT
543626 CTAAAATATAAAAGAAT
1 -TAAAATATAAAAGAAT
543643 T
1 T
543644 TCAGGGCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 12 0.43
15 1 0.04
16 2 0.07
17 13 0.46
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.23
Consensus pattern (16 bp):
TAAAATATAAAAGAAT
Found at i:545411 original size:21 final size:21
Alignment explanation
Indices: 545387--545428 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
545377 AAGGAAGTGT
545387 TTCAACGACTAAAAGAAGTAG
1 TTCAACGACTAAAAGAAGTAG
545408 TTCAACGACTAAAAGAAGTAG
1 TTCAACGACTAAAAGAAGTAG
545429 AACTTAACCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.19, T:0.19
Consensus pattern (21 bp):
TTCAACGACTAAAAGAAGTAG
Found at i:553379 original size:95 final size:95
Alignment explanation
Indices: 553209--553382 Score: 233
Period size: 95 Copynumber: 1.8 Consensus size: 95
553199 AATGATGTGG
* * * * *
553209 GTATCGATACTATGAGGAAGGTATCGATACCATTGATTCCAGAATGCAAAAATGGTATTGATACT
1 GTATCGATACTAAGAGAAAGATATCGATACCATGGATTCCAGAATGCAAAAATGGTATCGATACT
** *
553274 TTAGTGGAGTATCGATACTATAGTATATGA
66 AAAGTAGAGTATCGATACTATAGTATATGA
* * *
553304 GTATCGATACTAAGAGAAAGATATCGATACCATGGATTCCAGAATGTAGAAATTGTATCGATACT
1 GTATCGATACTAAGAGAAAGATATCGATACCATGGATTCCAGAATGCAAAAATGGTATCGATACT
553369 AAAAG-AGAGTATCG
66 -AAAGTAGAGTATCG
553383 GTACGCTCTC
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
95 65 0.97
96 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (95 bp):
GTATCGATACTAAGAGAAAGATATCGATACCATGGATTCCAGAATGCAAAAATGGTATCGATACT
AAAGTAGAGTATCGATACTATAGTATATGA
Found at i:558612 original size:11 final size:11
Alignment explanation
Indices: 558596--558624 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
558586 TAGTTTGATA
558596 TCGATTTAATC
1 TCGATTTAATC
558607 TCGATTTAATC
1 TCGATTTAATC
558618 TCGATTT
1 TCGATTT
558625 TTATTTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.48
Consensus pattern (11 bp):
TCGATTTAATC
Done.