Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold126
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: 2080828
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 191490 characters in sequence are not A, C, G, or T
File 3 of 13
Found at i:303325 original size:20 final size:20
Alignment explanation
Indices: 303300--303357 Score: 84
Period size: 19 Copynumber: 3.0 Consensus size: 20
303290 CTGCCAGTTT
*
303300 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTA
*
303320 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGTA
303339 CATGTATCGATAC-ATTGTA
1 CATGTATCGATACAATTGTA
303358 TCGATACAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 18 0.53
20 15 0.44
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGTA
Found at i:303359 original size:13 final size:13
Alignment explanation
Indices: 303341--303365 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
303331 ACAATGAACA
303341 TGTATCGATACAT
1 TGTATCGATACAT
303354 TGTATCGATACA
1 TGTATCGATACA
303366 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:303382 original size:33 final size:32
Alignment explanation
Indices: 303322--303387 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 32
303312 CAATTGTCCA
*
303322 TGTATCGATACAATGAACATGTATCGATACAT
1 TGTATCGATACAAAGAACATGTATCGATACAT
303354 TGTATCGATACAAAGCATA-ATGTATCGATACAT
1 TGTATCGATACAAAG-A-ACATGTATCGATACAT
303387 T
1 T
303388 TGGGTCTGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 14 0.45
33 16 0.52
34 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (32 bp):
TGTATCGATACAAAGAACATGTATCGATACAT
Found at i:304034 original size:53 final size:52
Alignment explanation
Indices: 303959--304073 Score: 171
Period size: 53 Copynumber: 2.2 Consensus size: 52
303949 TTTGATAAAA
* *
303959 AAAAATTT-CTCCCCCTTGATAATCGGTTAAAAAGATTTT-TCTCCCCTTTGAT
1 AAAAATTTATTCCCCCTTGATAATCAGTTAAAAAGATTTTCT-TCCCC-TTGAT
*
304011 AAAAATTTATTCCCTCTTGATAATCAGTTAAAAAGATTTTCTTCCCCTTGAT
1 AAAAATTTATTCCCCCTTGATAATCAGTTAAAAAGATTTTCTTCCCCTTGAT
304063 AAAAATTTATT
1 AAAAATTTATT
304074 TTCAAAACAA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
52 24 0.41
53 33 0.57
54 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (52 bp):
AAAAATTTATTCCCCCTTGATAATCAGTTAAAAAGATTTTCTTCCCCTTGAT
Found at i:304062 original size:52 final size:53
Alignment explanation
Indices: 303959--304073 Score: 173
Period size: 52 Copynumber: 2.2 Consensus size: 53
303949 TTTGATAAAA
* *
303959 AAAAATTT-CTCCCCCTTGATAATCGGTTAAAAAGATTTTTCTCCCCTTTGAT
1 AAAAATTTATTCCCCCTTGATAATCAGTTAAAAAGATTTTTCTCCCCTTTGAT
*
304011 AAAAATTTATTCCCTCTTGATAATCAGTTAAAAAGA-TTTTCTTCCCC-TTGAT
1 AAAAATTTATTCCCCCTTGATAATCAGTTAAAAAGATTTTTC-TCCCCTTTGAT
304063 AAAAATTTATT
1 AAAAATTTATT
304074 TTCAAAACAA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
52 29 0.50
53 29 0.50
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (53 bp):
AAAAATTTATTCCCCCTTGATAATCAGTTAAAAAGATTTTTCTCCCCTTTGAT
Found at i:305470 original size:21 final size:21
Alignment explanation
Indices: 305441--305483 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
305431 AGTGGGTGTA
* *
305441 GGAGCTGCCCGGTTGCGACCTG
1 GGAGCTG-CCGATTACGACCTG
305463 GGAG-TGCCGATTACGACCTG
1 GGAGCTGCCGATTACGACCTG
305483 G
1 G
305484 AGGTGGCTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 13 0.68
21 2 0.11
22 4 0.21
ACGTcount: A:0.14, C:0.28, G:0.40, T:0.19
Consensus pattern (21 bp):
GGAGCTGCCGATTACGACCTG
Found at i:305801 original size:21 final size:21
Alignment explanation
Indices: 305763--305804 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
305753 ATGATTTTGA
* * *
305763 TGAAAAATGAGTATTTTGAAG
1 TGAAAAATAAGAAATTTGAAG
305784 TGAAAAATAAGAAATTTGAAG
1 TGAAAAATAAGAAATTTGAAG
305805 AAGATTTGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (21 bp):
TGAAAAATAAGAAATTTGAAG
Found at i:312109 original size:20 final size:20
Alignment explanation
Indices: 312084--312137 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
312074 GTTTGAAGCA
312084 ATGTATCGATACAAT-T-CATC
1 ATGTATCGATACAATGTGC--C
312104 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTGCC
312124 ATGTATCGATACAA
1 ATGTATCGATACAA
312138 ATAGTGGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTGCC
Found at i:315759 original size:20 final size:20
Alignment explanation
Indices: 315733--315787 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
315723 CTGTTAGTTT
*
315733 CATGTATTGATACAATTGAG
1 CATGTATCGATACAATTGAG
* *
315753 TATGTATCGATA-TATTGAG
1 CATGTATCGATACAATTGAG
315772 CATGTATCGATACAAT
1 CATGTATCGATACAAT
315788 GTATCGATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:315791 original size:13 final size:13
Alignment explanation
Indices: 315773--315799 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
315763 TATATTGAGC
315773 ATGTATCGATACA
1 ATGTATCGATACA
315786 ATGTATCGATACA
1 ATGTATCGATACA
315799 A
1 A
315800 AGCATAATGT
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:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:316685 original size:20 final size:20
Alignment explanation
Indices: 316644--316696 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
316634 CACACCTAGA
**
316644 TGTATCGATACAT-GTTAAT
1 TGTATCGATACATGGACAAT
316663 TGTATCGATACATGGACAAT
1 TGTATCGATACATGGACAAT
316683 TGTATCGATACATG
1 TGTATCGATACATG
316697 AGATTGGCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGGACAAT
Found at i:322897 original size:13 final size:13
Alignment explanation
Indices: 322879--322919 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
322869 ACAATATTCC
*
322879 TTGTATTGATACA
1 TTGTATCGATACA
*
322892 TTGTATCGATAGA
1 TTGTATCGATACA
*
322905 CTGTATCGATACA
1 TTGTATCGATACA
322918 TT
1 TT
322920 AGGTACTGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:325473 original size:91 final size:91
Alignment explanation
Indices: 325330--325523 Score: 370
Period size: 91 Copynumber: 2.1 Consensus size: 91
325320 TACATAGGTA
*
325330 TTTGTATCGATACATTATGGTAGACTTAGGCTACAAAGGTCAAAACCCTTGAATGTATCGATTCA
1 TTTGTATCGATACATTATGGTAGACTTAGGCTACAAAGGTCAAAACCCTTGAATGTATCGATACA
325395 CACCCAGATGTATTGATACATTACGC
66 CACCCAGATGTATTGATACATTACGC
325421 TTTGTATCGATACATTATGGTAGACTTAGGCTACAAAGGTCAAAACCCTTGAATGTATCGATACA
1 TTTGTATCGATACATTATGGTAGACTTAGGCTACAAAGGTCAAAACCCTTGAATGTATCGATACA
*
325486 CACCCAGATGTATTGATACATTATGC
66 CACCCAGATGTATTGATACATTACGC
325512 TTTGTATCGATA
1 TTTGTATCGATA
325524 TATGGACAAT
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 101 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (91 bp):
TTTGTATCGATACATTATGGTAGACTTAGGCTACAAAGGTCAAAACCCTTGAATGTATCGATACA
CACCCAGATGTATTGATACATTACGC
Found at i:325613 original size:13 final size:13
Alignment explanation
Indices: 325592--325622 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
325582 CGATACATGG
*
325592 TACAATGTATCGA
1 TACATTGTATCGA
325605 TACATTGTATCGA
1 TACATTGTATCGA
325618 TACAT
1 TACAT
325623 GATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:325618 original size:33 final size:33
Alignment explanation
Indices: 325576--325642 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
325566 CTATCACTGT
*
325576 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
*
325609 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
325642 T
1 T
325643 AGCTTGTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:326475 original size:13 final size:13
Alignment explanation
Indices: 326457--326481 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
326447 ATAATGCACA
326457 GTATCGATACATT
1 GTATCGATACATT
326470 GTATCGATACAT
1 GTATCGATACAT
326482 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:326606 original size:20 final size:20
Alignment explanation
Indices: 326567--326614 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
326557 ACTATTTGTG
*
326567 TCGATACA-CACAAGATGTA
1 TCGATACATCACAAAATGTA
*
326586 TCGATACATCCCAAAATGTA
1 TCGATACATCACAAAATGTA
326606 TCGATACAT
1 TCGATACAT
326615 TGGCTTGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (20 bp):
TCGATACATCACAAAATGTA
Found at i:330175 original size:13 final size:13
Alignment explanation
Indices: 330157--330204 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 13
330147 ATAAGTTTTA
330157 TATCGATACAATG
1 TATCGATACAATG
330170 TATCGATACATAAGTTG
1 TATCGATAC--AA--TG
330187 TATCGATACAATG
1 TATCGATACAATG
330200 TATCG
1 TATCG
330205 CTACGTAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 16 0.52
15 4 0.13
17 11 0.35
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:330190 original size:17 final size:17
Alignment explanation
Indices: 330136--330196 Score: 67
Period size: 17 Copynumber: 3.7 Consensus size: 17
330126 ATTCAGTAAA
330136 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG--T
*
330155 TATATCGATAC--AA--
1 TGTATCGATACATAAGT
330168 TGTATCGATACATAAGT
1 TGTATCGATACATAAGT
330185 TGTATCGATACA
1 TGTATCGATACA
330197 ATGTATCGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
13 10 0.28
15 2 0.06
17 14 0.39
19 10 0.28
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (17 bp):
TGTATCGATACATAAGT
Found at i:330193 original size:30 final size:31
Alignment explanation
Indices: 330134--330204 Score: 117
Period size: 30 Copynumber: 2.3 Consensus size: 31
330124 ACATTCAGTA
330134 AATGTATCGATACATAAGTTTTATATCGATAC
1 AATGTATCGATACATAAG-TTTATATCGATAC
*
330166 AATGTATCGATACATAAG-TTGTATCGATAC
1 AATGTATCGATACATAAGTTTATATCGATAC
330196 AATGTATCG
1 AATGTATCG
330205 CTACGTAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
30 20 0.53
32 18 0.47
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (31 bp):
AATGTATCGATACATAAGTTTATATCGATAC
Found at i:330267 original size:13 final size:13
Alignment explanation
Indices: 330249--330274 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
330239 ATTAAGAAAA
330249 TGTATCGATACAT
1 TGTATCGATACAT
330262 TGTATCGATACAT
1 TGTATCGATACAT
330275 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:332636 original size:52 final size:52
Alignment explanation
Indices: 332564--332697 Score: 171
Period size: 52 Copynumber: 2.6 Consensus size: 52
332554 TTAGGTTTCT
** * *
332564 CAATTTTTGACAACCGGGGATACTCCAACCCCGGTTTTATTTTCA-AAACAC
1 CAATTTTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCACAAACAC
** *
332615 CAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTTCACAAACAC
1 CAATTTTCC-ACAATCGGGGATACTCCAACCCCGATTTTATTTTCACAAACAC
* *
332668 CAATTTTTCACAATCGAGGATACTCCAACC
1 CAATTTTCCACAATCGGGGATACTCCAACC
332698 TCGTTATTTC
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
51 7 0.10
52 48 0.70
53 14 0.20
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.31
Consensus pattern (52 bp):
CAATTTTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCACAAACAC
Found at i:332817 original size:79 final size:77
Alignment explanation
Indices: 332710--332943 Score: 245
Period size: 79 Copynumber: 2.9 Consensus size: 77
332700 GTTATTTCAT
** * * *
332710 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACCCCAACCTCGGCTTTATTTCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACC-CAGTTTTATTTCCAAAATAT
*
332775 TGATTTCTCAAAAT
65 T-ATTTCTCAAAAC
* * *
332789 TGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAATCCCAATTTTATTTCC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAA-CCCAGTTTTATTTCCAAAAT-A
* *
332853 TCTATTTTTCACAAC
64 T-TATTTCTCAAAAC
* * * * *
332868 CGGGGATACTCTAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGTTATTATCTCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCAGTT-TTATTTCCAAAATAT
332933 TAAATTTCTCA
65 T--ATTTCTCA
332944 TCGGGACATA
Statistics
Matches: 128, Mismatches: 20, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
78 9 0.07
79 106 0.83
80 13 0.10
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (77 bp):
CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCAGTTTTATTTCCAAAATATT
ATTTCTCAAAAC
Found at i:343429 original size:13 final size:13
Alignment explanation
Indices: 343411--343440 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
343401 ACAATTCTTC
343411 ATGTATCGATACA
1 ATGTATCGATACA
343424 ATGTATCGATACA
1 ATGTATCGATACA
343437 ATGT
1 ATGT
343441 GCTATGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:343430 original size:33 final size:33
Alignment explanation
Indices: 343388--343457 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 33
343378 GCCGTTTGGG
343388 ACAATGTATCAATACAAT-T-CTTCATGTATCGAT
1 ACAATGTATCAATACAATGTGC-T-ATGTATCGAT
*
343421 ACAATGTATCGATACAATGTGCTATGTATCGAT
1 ACAATGTATCAATACAATGTGCTATGTATCGAT
343454 ACAA
1 ACAA
343458 ATAGTGGTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
33 31 0.91
34 2 0.06
35 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (33 bp):
ACAATGTATCAATACAATGTGCTATGTATCGAT
Found at i:343544 original size:13 final size:13
Alignment explanation
Indices: 343526--343551 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
343516 TACAATTAAC
343526 TTGTATCGATACA
1 TTGTATCGATACA
343539 TTGTATCGATACA
1 TTGTATCGATACA
343552 AAGCATAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:343941 original size:21 final size:23
Alignment explanation
Indices: 343916--343963 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
343906 GATACTTTGG
343916 ATTATTT-TTACTTG-AAAACAT
1 ATTATTTATTACTTGAAAAACAT
*
343937 ATTATTTATTGCTTGAAAAACAT
1 ATTATTTATTACTTGAAAAACAT
343960 -TTAT
1 ATTAT
343964 ACTTAACTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 10 0.42
23 7 0.29
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (23 bp):
ATTATTTATTACTTGAAAAACAT
Found at i:344061 original size:249 final size:249
Alignment explanation
Indices: 343611--344106 Score: 675
Period size: 249 Copynumber: 2.0 Consensus size: 249
343601 TTTGACCTTT
343611 GTAGCATAAGTCAACCTTAATGTATCGATACAAATACCTATGTATCGATACTTTGGTTCATTCAT
1 GTAGCATAAGTCAACCTTAATGTATCGATACAAATACCTATGTATCGATACTTTGGTTCATTCAT
*
343676 AATGGAAAACGTTTGATTTAAGGCTTGAAAACATTTATACGAACCTCTAAAACATTATTAATATT
66 AATGGAAAACATTTGATTTAAGGCTTGAAAACATTTATACGAACCTCTAAAACATTATTAATATT
*
343741 GAAAATCAATTAGAAGAAGGTTTTTAGAGTATCTTTGAATGAATAAAACTTATTACGGTTTTTCA
131 GAAAATCAATTAGAAGAAGGTTTTTAGAGTATCTTTGAATGAATAAAACTTATTACGATTTTTCA
* *
343806 AAGTATTTTTCATTTTTATTCA-ATCTTTGTTATATCAAAATCAAGATCCTAACA
196 AAGTATTTTTCAGTTTTATTCATA-CTTTGTTATATCAAAACCAAGATCCTAACA
* ** **
343860 GTAGCTTAAGTCAACCTTTGTGTATCGATACAAATACCTATGTATCGATACTTTGGATT-ATTTT
1 GTAGCATAAGTCAACCTTAATGTATCGATACAAATACCTATGTATCGATACTTTGG-TTCATTCA
* * ** * *
343924 TACTTGAAAACATATT-ATTTATTGCTTGAAAAACATTTATACTTAA-CTCTAAAACATCT-TTG
65 TAATGGAAAACAT-TTGATTTAAGGCTTG-AAAACATTTATAC-GAACCTCTAAAACAT-TATTA
* * * *
343986 ATATTGAAAATCATTTTG-AGCAAGG-TTTTAGAGTAT-TTTTAAGTGAATAAAACTTGTTACGA
126 ATATTGAAAATCAATTAGAAG-AAGGTTTTTAGAGTATCTTTGAA-TGAATAAAACTTATTACGA
* *
344048 TTTTTCCAAGTATTTTTCGGTTTTATTCATACTTTGTTATATCAAAACCAAGATCCTAA
189 TTTTTCAAAGTATTTTTCAGTTTTATTCATACTTTGTTATATCAAAACCAAGATCCTAA
344107 TACCTTCGAC
Statistics
Matches: 218, Mismatches: 21, Indels: 16
0.85 0.08 0.06
Matches are distributed among these distances:
248 5 0.02
249 159 0.73
250 51 0.23
251 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.39
Consensus pattern (249 bp):
GTAGCATAAGTCAACCTTAATGTATCGATACAAATACCTATGTATCGATACTTTGGTTCATTCAT
AATGGAAAACATTTGATTTAAGGCTTGAAAACATTTATACGAACCTCTAAAACATTATTAATATT
GAAAATCAATTAGAAGAAGGTTTTTAGAGTATCTTTGAATGAATAAAACTTATTACGATTTTTCA
AAGTATTTTTCAGTTTTATTCATACTTTGTTATATCAAAACCAAGATCCTAACA
Found at i:344388 original size:156 final size:154
Alignment explanation
Indices: 344106--344620 Score: 547
Period size: 155 Copynumber: 3.3 Consensus size: 154
344096 CAAGATCCTA
* * * *
344106 ATACCTTCGACGTAAAAGTACCCGATACCCTTAAAGGACTTAAAAAGAATTTTAAAGGGGGTGAA
1 ATACCTTCGACGTAAAAGTACCCGATACCCTTAAAGGACTTAAAAAGGATTTAAAATGGGATGAA
* ** *
344171 -CTATACTAAATACCCACTTTTGGCATAAAAGTGGACCCGGTGATAACCTAGGACTTGATTCTAA
66 CCTATCCTAAATACCCAC-TTTGATATAAAAGTGGACCTGGTGATAACCTAGGACTTGATTCTAA
*
344235 AAAATTACCAAAATGCCCTTAGGGG
130 AAAATTACCAAAATACCCTTAGGGG
* *
344260 ATACCTTCGACGTAAAAGTATCCC-AGTACCCTTAAAGGACTTAGAAAGGATATAAAATGGGATG
1 ATACCTTCGACGTAAAAGTA-CCCGA-TACCCTTAAAGGACTTAAAAAGGATTTAAAATGGGATG
* * * *
344324 AACCTATCCTAAATACCCTTCTTCT-ATATAAAAGTGGACCTGGTGATAACTTAAGACTCGATTC
64 AACCTATCCTAAATACCC-ACTT-TGATATAAAAGTGGACCTGGTGATAACCTAGGACTTGATTC
* * * * *
344388 TAAAATATCACCAAAATCCCCCTAGAGG
127 TAAAAAATTACCAAAATACCCTTAGGGG
* * * * *** * * *
344416 ATACCTTTGGCATGAAAGTACTTAATACCCCTAAAGGACTTAAAAAGG-TTTAAGATGGAATGAA
1 ATACCTTCGACGTAAAAGTACCCGATACCCTTAAAGGACTTAAAAAGGATTTAAAATGGGATGAA
* * * * * *
344480 CCTATCCTAAATGCCCACCTTTGGCATA-AAAAGCGGACCTAGTGACAACCTAGGAGTTGGTTCT
66 CCTATCCTAAATACCCA-CTTT-G-ATATAAAAGTGGACCTGGTGATAACCTAGGACTTGATTCT
**
344544 AAAAAATTATGAAAATACCCTT-GAGGG
128 AAAAAATTACCAAAATACCCTTAG-GGG
* *
344571 ATACCTTCGATGTAGAAGTACCCGATACCCTTAAAGGACTTAAAAAGGAT
1 ATACCTTCGACGTAAAAGTACCCGATACCCTTAAAGGACTTAAAAAGGAT
344621 GACAAAAGGT
Statistics
Matches: 292, Mismatches: 57, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
153 1 0.00
154 53 0.18
155 143 0.49
156 93 0.32
157 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (154 bp):
ATACCTTCGACGTAAAAGTACCCGATACCCTTAAAGGACTTAAAAAGGATTTAAAATGGGATGAA
CCTATCCTAAATACCCACTTTGATATAAAAGTGGACCTGGTGATAACCTAGGACTTGATTCTAAA
AAATTACCAAAATACCCTTAGGGG
Found at i:345416 original size:169 final size:161
Alignment explanation
Indices: 345032--345463 Score: 480
Period size: 169 Copynumber: 2.7 Consensus size: 161
345022 TGAAAGTTTC
* * * * * *
345032 ATTTTGTACCTTGATGGATGCCCGAAAAGATAAGAAAA-ATTTTGAAATC-TTTATACCCTTACG
1 ATTTCGTACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTGAAATCTTTTATACCCCTACG
* * * * *
345095 GATCTCCATAGGAATATAAAAGA-T-AAAAA--ATTAAAGTTCCTCTCAGTTATGAAAGTATTAG
66 GA-CCCCA-AAGAATATAAAAGATTAAAAAATGATTAAAGTTCATCTCAATTATGAAAGTATTAA
*
345156 CTTAATTTTATTTATTTGTTTTCGAAAAATACA
129 CTTAATTTTATTTATTTATTTTCGAAAAATACA
* * * * *
345189 TTTTCGTATCTTAATGGAAACTCGAAAAGATACGAAATGTTTTTGAAATCTTTTATACCCCTACG
1 ATTTCGTACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTGAAATCTTTTATACCCCTACG
* * * * * *
345254 GACCCCCAAATGAATATAGATGATTAGAAAAATGATTAATATTTTATTTCAATTATGAAAGTGTT
66 GA-CCCCAAA-GAATATAAAAGATTA-AAAAATGATTAA-AGTTCATCTCAATTATGAAAGTATT
* *
345319 AATTTAATTTTATTTATTTATACATTTTCGAAAAATATA
127 AACTTAATTTTATTTA-TT-T--ATTTTCGAAAAATACA
* *
345358 ATTTCGTACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTGACATCTTTTATACCCCTATG
1 ATTTCGTACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTGAAATCTTTTATACCCCTACG
345423 GACCCCATAAGAATATAAAAGATTAAAAAATGATTAAAGTT
66 GACCCCA-AAGAATATAAAAGATTAAAAAATGATTAAAGTT
345464 TAAATATCTT
Statistics
Matches: 225, Mismatches: 36, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
157 29 0.13
158 11 0.05
159 29 0.13
160 1 0.00
162 5 0.02
164 5 0.02
165 33 0.15
166 5 0.02
167 13 0.06
168 18 0.08
169 76 0.34
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.36
Consensus pattern (161 bp):
ATTTCGTACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTGAAATCTTTTATACCCCTACG
GACCCCAAAGAATATAAAAGATTAAAAAATGATTAAAGTTCATCTCAATTATGAAAGTATTAACT
TAATTTTATTTATTTATTTTCGAAAAATACA
Found at i:348010 original size:18 final size:19
Alignment explanation
Indices: 347987--348022 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
347977 TTAATTTATC
*
347987 AAAGAAAATAA-TAAAAAA
1 AAAGAAAAAAAGTAAAAAA
348005 AAAGAAAAAAAGTAAAAA
1 AAAGAAAAAAAGTAAAAA
348023 TGTAGGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.83, C:0.00, G:0.08, T:0.08
Consensus pattern (19 bp):
AAAGAAAAAAAGTAAAAAA
Found at i:352566 original size:21 final size:21
Alignment explanation
Indices: 352519--352572 Score: 85
Period size: 20 Copynumber: 2.6 Consensus size: 21
352509 TGACATGGTC
352519 TTGTATCGATACATTTACTTA
1 TTGTATCGATACATTTACTTA
352540 -TGTATCGATACA-TTACATTA
1 TTGTATCGATACATTTAC-TTA
352560 TTGTATCGATACA
1 TTGTATCGATACA
352573 ATTTGTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.13
20 15 0.48
21 12 0.39
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TTGTATCGATACATTTACTTA
Found at i:353519 original size:149 final size:148
Alignment explanation
Indices: 353247--353789 Score: 590
Period size: 149 Copynumber: 3.6 Consensus size: 148
353237 TTTGTAACCA
* * * **
353247 TTTTCAAGTCC-CTTCA-GATCACC-GAGCACTTCTAAGTTGATGGTAAATCTTAGGGATATTTT
1 TTTTCAAGTCCTC-T-AGGATCACCAG-GCACTTCTAAGTCGATGGTAGACCTTAGGGACCTTTT
* *** * * * * * *
353309 AGCATTTTTCTTGAAACTTAGCCCTATGAACCTACC-AGGTCCGCTTCTACATCGAATGTATGAA
63 A-TATTTTTCCCAAAACCTAGTCCTATGAAACTACCGA-GTCCACTTCTACAGCGAAAGTATGAA
353373 TTAGGAGTAGGTTCGCTTTTACT
126 TTAGGAGTAGGTTCGCTTTTACT
*
353396 TTTTCAAGTCCTCTAGGATCACTAGGCACTTCTAAGTCGATGGTAGACCTTAGGGACCTTTTATC
1 TTTTCAAGTCCTCTAGGATCACCAGGCACTTCTAAGTCGATGGTAGACCTTAGGGACCTTTTAT-
* * * * * *
353461 ATTTTTCCCAAAATCTAGTCCTATGAAACTACTGAGTTCACTTTTACGGCGAAGGTATGAATTAG
65 ATTTTTCCCAAAACCTAGTCCTATGAAACTACCGAGTCCACTTCTACAGCGAAAGTATGAATTAG
* *
353526 GATTAGGTTCGCTTTTACC
130 GAGTAGGTTCGCTTTTACT
* * * * * *
353545 TTTTCAAGTCCTCTAAGATCACCAAGCACTTCTAAGTCAATGGTAGGCCTTAAGGACCTTTTCGT
1 TTTTCAAGTCCTCTAGGATCACCAGGCACTTCTAAGTCGATGGTAGACCTTAGGGACCTTTT-AT
** * * *
353610 ATTTTTCCTGAAACCTAGTCCTATAAAACTACCGGGTCCACTTCTACATCGAAAGTATGAATTAG
65 ATTTTTCCCAAAACCTAGTCCTATGAAACTACCGAGTCCACTTCTACAGCGAAAGTATGAATTAG
*
353675 AAGTAGGTTCGCTTTTACT
130 GAGTAGGTTCGCTTTTACT
* * * * *
353694 TTTTCAAGTCTTCTAGGTTCACCGGGCACTTCTAAGTCGATGGAAGACCTTAGGGACCATTTAGT
1 TTTTCAAGTCCTCTAGGATCACCAGGCACTTCTAAGTCGATGGTAGACCTTAGGGACCTTTTA-T
* * *
353759 TTTTTTCCCAAAACCTAGTCTTGTGAAACTA
65 ATTTTTCCCAAAACCTAGTCCTATGAAACTA
353790 TCAAGCCGCT
Statistics
Matches: 326, Mismatches: 61, Indels: 14
0.81 0.15 0.03
Matches are distributed among these distances:
148 1 0.00
149 321 0.98
150 4 0.01
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (148 bp):
TTTTCAAGTCCTCTAGGATCACCAGGCACTTCTAAGTCGATGGTAGACCTTAGGGACCTTTTATA
TTTTTCCCAAAACCTAGTCCTATGAAACTACCGAGTCCACTTCTACAGCGAAAGTATGAATTAGG
AGTAGGTTCGCTTTTACT
Found at i:353788 original size:298 final size:298
Alignment explanation
Indices: 353247--353789 Score: 775
Period size: 298 Copynumber: 1.8 Consensus size: 298
353237 TTTGTAACCA
* * ** * * *
353247 TTTTCAAGTCCCTTCAGATCACCGAGCACTTCTAAGTTGATGGTAAATCTTAGGGATATTTTAGC
1 TTTTCAAGTCCCTTAAGATCACCAAGCACTTCTAAGTCAATGGTAAACCTTAAGGACATTTTAGC
* * * * * *
353312 ATTTTTCTTGAAACTTAGCCCTATGAACCTACCAGGTCCGCTTCTACATCGAATGTATGAATTAG
66 ATTTTTCCTGAAACCTAGCCCTATAAAACTACCAGGTCCACTTCTACATCGAAAGTATGAATTAG
* * *
353377 GAGTAGGTTCGCTTTTACTTTTTCAAGTCCTCTAGGATCACTAGGCACTTCTAAGTCGATGGTAG
131 AAGTAGGTTCGCTTTTACTTTTTCAAGTCCTCTAGGATCACCAGGCACTTCTAAGTCGATGGAAG
* *
353442 ACCTTAGGGACCTTTTATCATTTTTCCCAAAATCTAGTCCTATGAAACTACTGAGTTCACTTTTA
196 ACCTTAGGGACCATTTATCATTTTTCCCAAAACCTAGTCCTATGAAACTACTGAGTTCACTTTTA
353507 CGGCGAAGGTATGAATTAGGATTAGGTTCGCTTTTACC
261 CGGCGAAGGTATGAATTAGGATTAGGTTCGCTTTTACC
** * *
353545 TTTTCAAGT-CCTCTAAGATCACCAAGCACTTCTAAGTCAATGGTAGGCCTTAAGGACCTTTTCG
1 TTTTCAAGTCCCT-TAAGATCACCAAGCACTTCTAAGTCAATGGTAAACCTTAAGGACATTTTAG
* * *
353609 TATTTTTCCTGAAACCTAGTCCTATAAAACTACCGGGTCCACTTCTACATCGAAAGTATGAATTA
65 CATTTTTCCTGAAACCTAGCCCTATAAAACTACCAGGTCCACTTCTACATCGAAAGTATGAATTA
* * *
353674 GAAGTAGGTTCGCTTTTACTTTTTCAAGTCTTCTAGGTTCACCGGGCACTTCTAAGTCGATGGAA
130 GAAGTAGGTTCGCTTTTACTTTTTCAAGTCCTCTAGGATCACCAGGCACTTCTAAGTCGATGGAA
* * *
353739 GACCTTAGGGACCATTTAGT-TTTTTTCCCAAAACCTAGTCTTGTGAAACTA
195 GACCTTAGGGACCATTTA-TCATTTTTCCCAAAACCTAGTCCTATGAAACTA
353790 TCAAGCCGCT
Statistics
Matches: 212, Mismatches: 31, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
297 3 0.01
298 208 0.98
299 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (298 bp):
TTTTCAAGTCCCTTAAGATCACCAAGCACTTCTAAGTCAATGGTAAACCTTAAGGACATTTTAGC
ATTTTTCCTGAAACCTAGCCCTATAAAACTACCAGGTCCACTTCTACATCGAAAGTATGAATTAG
AAGTAGGTTCGCTTTTACTTTTTCAAGTCCTCTAGGATCACCAGGCACTTCTAAGTCGATGGAAG
ACCTTAGGGACCATTTATCATTTTTCCCAAAACCTAGTCCTATGAAACTACTGAGTTCACTTTTA
CGGCGAAGGTATGAATTAGGATTAGGTTCGCTTTTACC
Found at i:358093 original size:52 final size:52
Alignment explanation
Indices: 358008--358188 Score: 308
Period size: 52 Copynumber: 3.5 Consensus size: 52
357998 CAAAATATGA
*
358008 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
* *
358060 AAACTTGCCTGCATGTATCGATACATTTAATAGTGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
*
358112 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
* *
358164 AAATTTACCTGCATGTTTCGATACA
1 AAATTTGCCTGCATGTATCGATACA
358189 ATGTATCGAT
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 121 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
Found at i:358281 original size:13 final size:13
Alignment explanation
Indices: 358263--358287 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
358253 ACAAAAAATA
358263 TGTATCGATACAT
1 TGTATCGATACAT
358276 TGTATCGATACA
1 TGTATCGATACA
358288 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:359218 original size:55 final size:52
Alignment explanation
Indices: 359118--359538 Score: 286
Period size: 43 Copynumber: 8.7 Consensus size: 52
359108 GAAAAGTGAT
* * * * * * *
359118 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTCG-GCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATT-GAACTTAAAGATG-G-A
* *
359172 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
359225 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
359268 AAAGGTGCCAATGTGATGATTCAAGGCCAACTACATTGGACTTAAAGA---A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
359317 GAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
359360 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
359409 GAAGGTGCCAATATGGTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
359452 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
359501 GAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTG
359539 GGCTTAGAAG
Statistics
Matches: 304, Mismatches: 38, Indels: 55
0.77 0.10 0.14
Matches are distributed among these distances:
43 111 0.37
44 3 0.01
46 1 0.00
48 2 0.01
49 107 0.35
51 1 0.00
52 32 0.11
53 6 0.02
54 6 0.02
55 35 0.12
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
Found at i:359288 original size:43 final size:44
Alignment explanation
Indices: 359226--359549 Score: 393
Period size: 43 Copynumber: 7.1 Consensus size: 44
359216 AAAGATGGAA
359226 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA-
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAG
* * * *
359269 AAGGTGCCAATGTGATGATTCAAGGCCAACTACATTGGACTTAAAGAAG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-----AG
*
359318 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAG
* *
359361 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-----AG
*
359410 AAGGTGCCAATATGGTGATTCAAGGCCAGCTATATTGGACTTA-
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAG
* *
359453 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-----AG
*
359502 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAG
359546 AAGG
1 AAGG
359550 GTTGCCACCG
Statistics
Matches: 242, Mismatches: 21, Indels: 35
0.81 0.07 0.12
Matches are distributed among these distances:
43 116 0.48
44 8 0.03
48 3 0.01
49 115 0.48
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (44 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAG
Found at i:359355 original size:92 final size:92
Alignment explanation
Indices: 359172--359549 Score: 639
Period size: 92 Copynumber: 4.1 Consensus size: 92
359162 AAGATGAGAA
* * *
359172 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTGCCAAT
359237 ATGCTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
359268 AAAGGTGCCAATGTGATGATTCAAGGCCAACTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
*
359333 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
359360 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
359425 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
359452 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
*
359517 TGATTCAAGGCCAGCTATATTGGGCTT
66 TGATTCAAGGCCAGCTATATTGGACTT
359544 AGAAGG
1 A-AAGG
359550 GTTGCCACCG
Statistics
Matches: 269, Mismatches: 12, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
92 221 0.82
93 4 0.01
95 39 0.14
96 5 0.02
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:359630 original size:32 final size:32
Alignment explanation
Indices: 359537--359968 Score: 660
Period size: 32 Copynumber: 13.5 Consensus size: 32
359527 CCAGCTATAT
359537 TGGGC-TTAGA-AGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
*
359567 TGGGCTTTAGAGAGGG-TGCTACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
*
359598 TGGGCTTTAGAGAGGGTTGCCATCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
359630 TGGGCTTT-GAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAG-AGGGTTGCCACCGACTTGTG
359662 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
*
359694 TGGGCTTTAGAGAGGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
359726 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
*
359758 TGGGCTTT-GAGAAGGGTTGCCACTGACTTGTG
1 TGGGCTTTAGAG-AGGGTTGCCACCGACTTGTG
* *
359790 TGGGCTTTAGAGAAGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
* *
359822 TAGGCTTTAGAGGGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
* * *
359854 TGGGCTTTGGAAAAGGGTTGCCACCGACTTGTA
1 TGGGCTTTAG-AGAGGGTTGCCACCGACTTGTG
* *
359887 TGGGCTTTGGAAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
359919 TGGGCTTT-GAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAG-AGGGTTGCCACCGACTTGTG
359951 TGGGCTTTAGAGAAGGGT
1 TGGGCTTTAGAG-AGGGT
359969 GAAAGATGCC
Statistics
Matches: 371, Mismatches: 21, Indels: 17
0.91 0.05 0.04
Matches are distributed among these distances:
30 5 0.01
31 43 0.12
32 279 0.75
33 44 0.12
ACGTcount: A:0.17, C:0.18, G:0.37, T:0.28
Consensus pattern (32 bp):
TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
Found at i:360109 original size:34 final size:34
Alignment explanation
Indices: 359970--361266 Score: 1408
Period size: 34 Copynumber: 39.8 Consensus size: 34
359960 GAGAAGGGTG
* * *
359970 AAAGA-TGCCACGAAGTTGTGGACTTAAAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* * * *
360003 CAAG-GTGCCACGAAGTTGTGGACTTTAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAA-GGAA
*
360038 AAAGAGTGCCACGGAGTTGTGGGCTT------TA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* * *
360066 AAAGGGTGCCACAGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* *
360100 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
* * *
360135 AAAG-GTGCCATGGAGTTATGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
*
360168 AAAGAGTGCCACGGAGTTGTGGGCTTTGAA--AA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* * *
360200 GAAG-GTGCCACGGAGTCGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
360233 AAAGAGTGCCACGGAGTTGTGGGCTT-------A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* *
360260 AAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
360294 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* * *
360328 AAATAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
* *
360363 AAAG-GTGCCACAGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* * *
360396 AAAGAGTGCCATGGACTTGTGGGCTTTGAA--AA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* * *
360428 GAAG-GTGCCACGGAGTCGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
*
360461 AAAGAGTGCCATGGAGTTGTGGGCTT-------A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* *
360488 AAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG-AA
*
360523 AAAGAGTGCCATGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* *
360557 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
*
360592 AAAG-GTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* *
360625 AAAGAGTGCCACGGAGTTGTGGGCTTTGCA-G-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* ** *
360657 GAAG-GTGCCACGGAGTCCTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
*
360690 AAAGAGTGCCACAGAGTTGTGGGCTT-------A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* * *
360717 AAAGGGTGCCACGGAGTTATGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
360751 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* * *
360785 AAAGAGTGTCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
** *
360820 AAAG-GTGCCACAAAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
*
360853 AAAGAGTGCCACGGAGTTGTGGGCTTTGAA--AA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* * *
360885 GAAG-GTGCCACGGAGTCGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
360918 AAAGAGTGCCACGGAGTTGTGGGCTT-------A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* *
360945 AAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
360979 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* *
361013 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
* *
361048 AAAG-GTGCCACGAAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
*
361081 AAAGAGTGCCACGGAGTTGTGGGCTTTGAA--AA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* * *
361113 GAAG-GTGCCACGGAGTCGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
361146 AAAGAGTGCCACGGAGTTGT-GGCTT-------A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* ** *
361172 AAAGGGTGCCATTGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
361206 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
361240 AAAGAGTGCCACGGAGTTGTGGGCTTA
1 AAAGAGTGCCACGGAGTTGTGGGCTTA
361267 AAATGGTGCC
Statistics
Matches: 1054, Mismatches: 138, Indels: 143
0.79 0.10 0.11
Matches are distributed among these distances:
26 18 0.02
27 101 0.10
28 24 0.02
31 106 0.10
32 25 0.02
33 110 0.10
34 555 0.53
35 98 0.09
36 17 0.02
ACGTcount: A:0.33, C:0.13, G:0.35, T:0.20
Consensus pattern (34 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
Found at i:360325 original size:228 final size:228
Alignment explanation
Indices: 360065--361357 Score: 2212
Period size: 228 Copynumber: 5.7 Consensus size: 228
360055 TGTGGGCTTT
* * *
360065 AAAAGGGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
** *
360130 AAGAAAAAGGTGCCATGGAGTTATGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
66 AAGAAAAAGGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
360195 GAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTA
131 GAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTA
360260 AAAGGGTGCCACGGAGTTGTGGACTTAGAAGGA
196 AAAGGGTGCCACGGAGTTGTGGACTTAGAAGGA
*
360293 AAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAATAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
* *
360358 AAGAAAAAGGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCATGGACTTGTGGGCTTT
66 AAGAAAAAGGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
*
360423 GAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTA
131 GAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTA
360488 AAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAA
196 AAAGGGTGCCACGGAGTTGTGGACTTAGAAGG-A
*
360522 AAAAGAGTGCCATGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
*
360587 AAGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
66 AAGAAAAAGGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
* * * *
360652 GCAGAGAAGGTGCCACGGAGTCCTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTA
131 GAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTA
*
360717 AAAGGGTGCCACGGAGTTATGGACTTAGAAGGA
196 AAAGGGTGCCACGGAGTTGTGGACTTAGAAGGA
*
360750 AAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGTCACGGAGTTGTGGGCTTTAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
*
360815 AAGAAAAAGGTGCCACAAAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
66 AAGAAAAAGGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
360880 GAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTA
131 GAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTA
360945 AAAGGGTGCCACGGAGTTGTGGACTTAGAAGGA
196 AAAGGGTGCCACGGAGTTGTGGACTTAGAAGGA
360978 AAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
361043 AAGAAAAAGGTGCCAC-GAAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
66 AAGAAAAAGGTGCCACAG-AGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
361107 TGAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGT-GGCTT
130 TGAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
**
361171 AAAAGGGTGCCATTGAGTTGTGGACTTAGAAGGA
195 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGA
361205 AAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT---
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
* * * **
361266 ---AAAATGGTGCCACAGAGTTGTGGACTTAAAAGG-AAAATAGTGCCACATAGTTGTGGGCTTT
66 AAGAAAAAGGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
* **
361327 GTAGAA-AAGGATGCCACTAAGTCGTGGACTT
131 G-AAAAGAAGG-TGCCACGGAGTCGTGGACTT
361358 TAAGAAGGTA
Statistics
Matches: 1018, Mismatches: 42, Indels: 18
0.94 0.04 0.02
Matches are distributed among these distances:
219 30 0.03
220 50 0.05
221 1 0.00
226 2 0.00
227 96 0.09
228 622 0.61
229 217 0.21
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.20
Consensus pattern (228 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
AAGAAAAAGGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
GAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTA
AAAGGGTGCCACGGAGTTGTGGACTTAGAAGGA
Found at i:360936 original size:457 final size:456
Alignment explanation
Indices: 360065--361357 Score: 2237
Period size: 457 Copynumber: 2.9 Consensus size: 456
360055 TGTGGGCTTT
* * *
360065 AAAAGGGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
* *
360130 AAGAAAAAGGTGCCATGGAGTTATGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
66 AAGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
360195 GAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTA
131 GAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTA
360260 AAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAG
196 AAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAG
*
360325 GAAAAATAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAG
261 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAG
* *
360390 AAGGAAAAAGAGTGCCATGGACTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAG
326 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAG
*
360455 AAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAGAAGG
391 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAGAAGG
360520 AA
456 -A
*
360522 AAAAGAGTGCCATGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
360587 AAGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
66 AAGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
* * * *
360652 GCAGAGAAGGTGCCACGGAGTCCTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTA
131 GAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTA
*
360717 AAAGGGTGCCACGGAGTTATGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAG
196 AAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAG
* *
360782 GAAAAAGAGTGTCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAAAGTTGTGGACTTAG
261 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAG
360847 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAG
326 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAG
360912 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAGAAGG
391 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAGAAGG
360977 A
456 A
360978 AAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
*
361043 AAGAAAAAGGTGCCACGAAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
66 AAGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
361108 GAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGT-GGCTTA
131 GAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTA
**
361172 AAAGGGTGCCATTGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAG
196 AAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAG
* *
361237 GAAAAAGAGTGCCACGGAGTTGTGGGC-TT------AAAATGGTGCCACAGAGTTGTGGACTTAA
261 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAG
* ** * **
361295 AAGG-AAAATAGTGCCACATAGTTGTGGGCTTTGTAGAA-AAGGATGCCACTAAGTCGTGGACTT
326 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTG-AAAAGAAGG-TGCCACGGAGTCGTGGACTT
361358 TAAGAAGGTA
Statistics
Matches: 798, Mismatches: 36, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
447 30 0.04
448 51 0.06
454 2 0.00
455 94 0.12
456 183 0.23
457 438 0.55
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.20
Consensus pattern (456 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
AAGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
GAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTA
AAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAG
GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAG
AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAG
AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAGAAGG
A
Found at i:361209 original size:60 final size:61
Alignment explanation
Indices: 361046--361237 Score: 287
Period size: 65 Copynumber: 3.1 Consensus size: 61
361036 CTTTAAAAAG
* *
361046 AAAAAGGTGCCACGAAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT
*
361108 GAAAAGAAGGTGCCACGGAGTCGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGT-GGCTT
1 -AAAAG--GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
**
361171 AAAAGGGTGCCATTGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
*
361232 AGAAGG
1 AAAAGG
361238 AAAAAGAGTG
Statistics
Matches: 119, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
60 47 0.39
61 10 0.08
62 5 0.04
63 6 0.05
64 3 0.03
65 48 0.40
ACGTcount: A:0.32, C:0.12, G:0.36, T:0.20
Consensus pattern (61 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
Found at i:361286 original size:61 final size:60
Alignment explanation
Indices: 361211--361325 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
361201 AGGAAAAAGA
* * * *
361211 GTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAATG
1 GTGCCACAGAGTTGTGGACTTAAAAGG-AAAAGAGTGCCACAGAGTTGTGGGCTTAAAATG
* *
361272 GTGCCACAGAGTTGTGGACTTAAAAGGAAAATAGTGCCACATAGTTGTGGGCTT
1 GTGCCACAGAGTTGTGGACTTAAAAGGAAAAGAGTGCCACAGAGTTGTGGGCTT
361326 TGTAGAAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
60 24 0.50
61 24 0.50
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (60 bp):
GTGCCACAGAGTTGTGGACTTAAAAGGAAAAGAGTGCCACAGAGTTGTGGGCTTAAAATG
Found at i:361494 original size:16 final size:17
Alignment explanation
Indices: 361463--361500 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
361453 GATGCAAATA
* *
361463 ATGATGTTATTGATGTT
1 ATGATGTCATTGATGTC
361480 ATGATGTCA-TGATGTC
1 ATGATGTCATTGATGTC
361496 ATGAT
1 ATGAT
361501 TACAGCACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (17 bp):
ATGATGTCATTGATGTC
Found at i:369485 original size:52 final size:52
Alignment explanation
Indices: 369407--369587 Score: 326
Period size: 52 Copynumber: 3.5 Consensus size: 52
369397 CAAAATATAA
*
369407 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
369459 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
* *
369511 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATTTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
*
369563 AAATTTACCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
369588 AAGATCAGTG
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
Found at i:369614 original size:13 final size:13
Alignment explanation
Indices: 369596--369620 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
369586 CAAAGATCAG
369596 TGTATCGATACAA
1 TGTATCGATACAA
369609 TGTATCGATACA
1 TGTATCGATACA
369621 TTTGAGTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:369700 original size:13 final size:13
Alignment explanation
Indices: 369682--369706 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
369672 ACAAAAAATA
369682 TGTATCGATACAT
1 TGTATCGATACAT
369695 TGTATCGATACA
1 TGTATCGATACA
369707 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:369702 original size:32 final size:33
Alignment explanation
Indices: 369661--369726 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
369651 AGTAGCTTAA
369661 ATTGTATCGATACAA-AAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
369693 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
369726 A
1 A
369727 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Found at i:370087 original size:32 final size:33
Alignment explanation
Indices: 370030--370091 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
370020 GGTGTCTACA
* *
370030 GTATTGATACATTTTGGGATGTATCGATACGCT
1 GTATCGATACATCTTGGGATGTATCGATACGCT
*
370063 GTATCGATACATCTTGTG-TGTATCGATAC
1 GTATCGATACATCTTGGGATGTATCGATAC
370092 AAACAGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 11 0.42
33 15 0.58
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.39
Consensus pattern (33 bp):
GTATCGATACATCTTGGGATGTATCGATACGCT
Found at i:370224 original size:34 final size:33
Alignment explanation
Indices: 370177--370253 Score: 118
Period size: 34 Copynumber: 2.3 Consensus size: 33
370167 TTTGGTCATA
*
370177 TATCGATACAATGTATCGATATTGTGCAATCTGG
1 TATCGATACAATGTATCGATACTGTGCAATCT-G
* *
370211 TATCGATATAATGTTTCGATACTGTGCAATCTG
1 TATCGATACAATGTATCGATACTGTGCAATCTG
370244 TATCGATACA
1 TATCGATACA
370254 TTTGAAGGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 10 0.26
34 29 0.74
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (33 bp):
TATCGATACAATGTATCGATACTGTGCAATCTG
Found at i:370265 original size:20 final size:20
Alignment explanation
Indices: 370242--370282 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
370232 CTGTGCAATC
*
370242 TGTATCGATACATTTGAAGG
1 TGTATCGATACATTTCAAGG
*
370262 TGTATCGATACTTTTCAAGG
1 TGTATCGATACATTTCAAGG
370282 T
1 T
370283 TTTGACCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTTCAAGG
Found at i:374458 original size:89 final size:90
Alignment explanation
Indices: 374261--374468 Score: 255
Period size: 89 Copynumber: 2.4 Consensus size: 90
374251 GGTGTTGATA
* * *
374261 CATCATAAAGCCTGATTTT-TTTAGGGCAAGGTACAGCCCATACATTCCTAATCATATCCTCTTC
1 CATCATAAAGCCTGATTTTCCTTAGGGCAAGGTACAACCCATACATTCCCAATCATATCCTCTTC
* *
374325 ATCCAACCACTATATGGCATTGATG
66 ATCCAACCACTACATGGCATTAATG
** * *
374350 CATCACCAAGCTTGA-TTTCCTTAGGGCAAGGTGCAACCCATACATTCCCAATCATAT-CTCCTT
1 CATCATAAAGCCTGATTTTCCTTAGGGCAAGGTACAACCCATACATTCCCAATCATATCCT-CTT
* * *
374413 CATTCAACCATTACATGGTATTAATG
65 CATCCAACCACTACATGGCATTAATG
*
374439 -ATCATAAAGCCTGATTTTCC-TAAGGCAAGG
1 CATCATAAAGCCTGATTTTCCTTAGGGCAAGG
374469 ATATCTCGAC
Statistics
Matches: 100, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
88 25 0.25
89 75 0.75
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (90 bp):
CATCATAAAGCCTGATTTTCCTTAGGGCAAGGTACAACCCATACATTCCCAATCATATCCTCTTC
ATCCAACCACTACATGGCATTAATG
Found at i:374781 original size:35 final size:35
Alignment explanation
Indices: 374730--374802 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
374720 GCTAATTTTT
* *
374730 TTTCCATCATTGTTTGGATGTATCTGGTCAAACTC
1 TTTCCATCATTGTTTGGATATATCTAGTCAAACTC
* * *
374765 TTTCTATCATTTTTTGGCTATATCTAGTCAAACTC
1 TTTCCATCATTGTTTGGATATATCTAGTCAAACTC
374800 TTT
1 TTT
374803 TCACCATCGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (35 bp):
TTTCCATCATTGTTTGGATATATCTAGTCAAACTC
Found at i:374959 original size:44 final size:43
Alignment explanation
Indices: 374853--375180 Score: 302
Period size: 44 Copynumber: 7.5 Consensus size: 43
374843 TCAGTATGAT
* **
374853 GTATGGTTACCACCCTGGTC-AGATTCTTTTCATCCTACTTGAC
1 GTATGGTTACCACCCTGGTCAAG-TTCTTTTCATTCTGTTTGAC
374896 GTATGGTTACCACCCTGGTCAAGTTCTTTTCATTCATGTTTGAC
1 GTATGGTTACCACCCTGGTCAAGTTCTTTTCATTC-TGTTTGAC
* ** * *
374940 GTATGGTTACCACCTTGGTCAAACTCTTTTCATTTCGGTATGAC
1 GTATGGTTACCACCCTGGTCAAGTTCTTTTCA-TTCTGTTTGAC
* * ** *
374984 GTATGGTTACCTCCCTGGTC-AGATTCTTTTCATCCTACTTGAT
1 GTATGGTTACCACCCTGGTCAAG-TTCTTTTCATTCTGTTTGAC
*
375027 GTATGGTTACCACCCTGGTCAAGTTTTTTTCATTCATGTTTGAC
1 GTATGGTTACCACCCTGGTCAAGTTCTTTTCATTC-TGTTTGAC
* *** * * *
375071 GTATGGTTACCACACTGGTCAAACCCTTCTCATTTTGGTCTGAC
1 GTATGGTTACCACCCTGGTCAAGTTCTTTTCATTCT-GTTTGAC
* * * * *
375115 TTATGGTTACCACCTTGGTC-AGATTCTTTTTATTCTAATTTGAT
1 GTATGGTTACCACCCTGGTCAAG-TTCTTTTCATTCT-GTTTGAC
* **
375159 GCATGGTTACCACTTTGGTCAA
1 GTATGGTTACCACCCTGGTCAA
375181 ATCTGCTTCC
Statistics
Matches: 228, Mismatches: 48, Indels: 16
0.78 0.16 0.05
Matches are distributed among these distances:
43 68 0.30
44 156 0.68
45 4 0.02
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.40
Consensus pattern (43 bp):
GTATGGTTACCACCCTGGTCAAGTTCTTTTCATTCTGTTTGAC
Found at i:375031 original size:87 final size:86
Alignment explanation
Indices: 374849--375092 Score: 287
Period size: 87 Copynumber: 2.8 Consensus size: 86
374839 CATTTCAGTA
* *
374849 TGATGTATGGTTACCACCCTGGTCAGATTCTTTTCA-TCCTACTTGACGTATGGTTACCACCCTG
1 TGATGTATGGTTACCACCCTGGTCAAATTCTTTTCATTCGTA--TGACGTATGGTTACCACCCTG
**
374913 GTCAAGTTCTTTTCATTCATGTT
64 GTCAAGTTCTTTTCATTCATACT
* * * *
374936 TGACGTATGGTTACCACCTTGGTCAAACTCTTTTCATTTCGGTATGACGTATGGTTACCTCCCTG
1 TGATGTATGGTTACCACCCTGGTCAAATTCTTTTCA-TTC-GTATGACGTATGGTTACCACCCTG
*
375001 GTC-AGATTCTTTTCA-TCCTACT
64 GTCAAG-TTCTTTTCATTCATACT
* * * *
375023 TGATGTATGGTTACCACCCTGGTCAAGTTTTTTTCATTCATGTTTGACGTATGGTTACCACACTG
1 TGATGTATGGTTACCACCCTGGTCAAATTCTTTTCATTC--GTATGACGTATGGTTACCACCCTG
375088 GTCAA
64 GTCAA
375093 ACCCTTCTCA
Statistics
Matches: 133, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
86 3 0.02
87 93 0.70
88 33 0.25
89 2 0.02
90 2 0.02
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.39
Consensus pattern (86 bp):
TGATGTATGGTTACCACCCTGGTCAAATTCTTTTCATTCGTATGACGTATGGTTACCACCCTGGT
CAAGTTCTTTTCATTCATACT
Found at i:375066 original size:131 final size:131
Alignment explanation
Indices: 374827--375180 Score: 521
Period size: 131 Copynumber: 2.7 Consensus size: 131
374817 CTAGACCTGC
* * *
374827 TCAATCTCTTCTCATTTCAGTATGATGTATGGTTACCACCCTGGTCAGATTCTTTTCATCCTACT
1 TCAAACTCTTCTCATTTCGGTATGACGTATGGTTACCACCCTGGTCAGATTCTTTTCATCCTACT
*
374892 TGACGTATGGTTACCACCCTGGTCAAGTTCTTTTCATTCATGTTTGACGTATGGTTACCAC-CTT
66 TGATGTATGGTTACCACCCTGGTCAAGTTCTTTTCATTCATGTTTGACGTATGGTTACCACAC-T
374956 GG
130 GG
* *
374958 TCAAACTCTTTTCATTTCGGTATGACGTATGGTTACCTCCCTGGTCAGATTCTTTTCATCCTACT
1 TCAAACTCTTCTCATTTCGGTATGACGTATGGTTACCACCCTGGTCAGATTCTTTTCATCCTACT
*
375023 TGATGTATGGTTACCACCCTGGTCAAGTTTTTTTCATTCATGTTTGACGTATGGTTACCACACTG
66 TGATGTATGGTTACCACCCTGGTCAAGTTCTTTTCATTCATGTTTGACGTATGGTTACCACACTG
375088 G
131 G
* * * * * * * *
375089 TCAAACCCTTCTCATTTTGGTCTGACTTATGGTTACCACCTTGGTCAGATTCTTTTTATTCTAAT
1 TCAAACTCTTCTCATTTCGGTATGACGTATGGTTACCACCCTGGTCAGATTCTTTTCATCCT-AC
* **
375154 TTGATGCATGGTTACCACTTTGGTCAA
65 TTGATGTATGGTTACCACCCTGGTCAA
375181 ATCTGCTTCC
Statistics
Matches: 201, Mismatches: 20, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
131 175 0.87
132 26 0.13
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (131 bp):
TCAAACTCTTCTCATTTCGGTATGACGTATGGTTACCACCCTGGTCAGATTCTTTTCATCCTACT
TGATGTATGGTTACCACCCTGGTCAAGTTCTTTTCATTCATGTTTGACGTATGGTTACCACACTG
G
Found at i:376588 original size:10 final size:11
Alignment explanation
Indices: 376562--376587 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
376552 GGGTTAATCT
376562 AAAAATATTGA
1 AAAAATATTGA
376573 AAAAATATTGA
1 AAAAATATTGA
376584 AAAA
1 AAAA
376588 TCACTTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (11 bp):
AAAAATATTGA
Found at i:380754 original size:165 final size:167
Alignment explanation
Indices: 380342--380772 Score: 609
Period size: 165 Copynumber: 2.6 Consensus size: 167
380332 TGGGTTTAAA
* *
380342 ATTTTGAAAATTCATAAAATATTATTATTTATTTCATATTAATTCATTTTTCAAAAAATTCATTC
1 ATTTTTAAAATTCATAAAATATTATTATTTATTTTATATTAATTCATTTTTC-AAAAATTCATTC
* * * *
380407 ATTTCCATAAATTTTGAATTTTTTCATTGAAATTCTTCTTTTTTCGAAATACGGAGTTTTCGACT
65 ATTTCCATAAATTTTGAATTTTTTCCTTGAAATTCTCCTTTTTTCAAAATACAGAGTTTTCGACT
* * ** *
380472 CCGTAATTTTTTTCGGGGGGATTTTTCTTATTTTTTTT
130 CCGCAATTTTTTTCGAGGGGATTTTTCTTAGGTTTTTG
*
380510 ATTTTTAAAATTCATCAAATATTATTATTTATTTCT-TATTAATTCAGTTTTT-AAAAATTCATT
1 ATTTTTAAAATTCATAAAATATTATTATTTATTT-TATATTAATTCA-TTTTTCAAAAATTCATT
* * * *
380573 CATTTCTATAAATTTTGAATTATTTCCTTGAAATTCTCCTTTTTTCAAAATACAGATTTTTCTAC
64 CATTTCCATAAATTTTGAATTTTTTCCTTGAAATTCTCCTTTTTTCAAAATACAGAGTTTTCGAC
*
380638 TCTGCAA-TTTTTTCGAGGGGATTTTTCTT-GGTTTTTG
129 TCCGCAATTTTTTTCGAGGGGATTTTTCTTAGGTTTTTG
* * *
380675 ATTTTTAAAATTCATAAAATATTATTATTTATTTTATATTAATTTATTTTTCAAAAATTAATTTA
1 ATTTTTAAAATTCATAAAATATTATTATTTATTTTATATTAATTCATTTTTCAAAAATTCATTCA
* *
380740 TTTCCATGAATTTTGAATTTTTTTCTTGAAATT
66 TTTCCATAAATTTTGAATTTTTTCCTTGAAATT
380773 TTTAGAGGGA
Statistics
Matches: 234, Mismatches: 25, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
164 6 0.03
165 87 0.37
166 21 0.09
167 73 0.31
168 42 0.18
169 5 0.02
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (167 bp):
ATTTTTAAAATTCATAAAATATTATTATTTATTTTATATTAATTCATTTTTCAAAAATTCATTCA
TTTCCATAAATTTTGAATTTTTTCCTTGAAATTCTCCTTTTTTCAAAATACAGAGTTTTCGACTC
CGCAATTTTTTTCGAGGGGATTTTTCTTAGGTTTTTG
Found at i:381369 original size:12 final size:12
Alignment explanation
Indices: 381341--381393 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
381331 AATTTAGCTG
381341 AAAAAAAATCA-A
1 AAAAAAAAT-AGA
*
381353 CAAAAAAATAGA
1 AAAAAAAATAGA
*
381365 AAAAAAAAGAGA
1 AAAAAAAATAGA
381377 AAGAAAAAA-AGA
1 AA-AAAAAATAGA
381389 AAAAA
1 AAAAA
381394 CAAGAAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 4 0.11
12 26 0.72
13 6 0.17
ACGTcount: A:0.83, C:0.04, G:0.09, T:0.04
Consensus pattern (12 bp):
AAAAAAAATAGA
Found at i:381383 original size:24 final size:25
Alignment explanation
Indices: 381355--381409 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
381345 AAAATCAACA
*
381355 AAAAAATAGAAAAAAAAAGAGAA-AG
1 AAAAAA-AGAAAAAAAAAGAAAATAG
*
381380 AAAAAAAGAAAAAACAAGAAAATAG
1 AAAAAAAGAAAAAAAAAGAAAATAG
381405 AAAAA
1 AAAAA
381410 CTAGTTAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.82, C:0.02, G:0.13, T:0.04
Consensus pattern (25 bp):
AAAAAAAGAAAAAAAAAGAAAATAG
Found at i:382536 original size:148 final size:148
Alignment explanation
Indices: 382286--382552 Score: 326
Period size: 148 Copynumber: 1.8 Consensus size: 148
382276 TTTTTCATCC
* * * * *
382286 AATAAAAATTATCACCTAAATTTTTTAAAATTTCTAATATTCCCATGGGTATCCATGGAGGTATG
1 AATAAAAATTATCACCTAAATTTTTTAAAATTTCCAATATTCCCATAGGCATCCATGAAGGTAAG
* * * * * * *
382351 AAAATTTTTAAAACTTTTCGTATTTTTTTGGTTCTCCATTAAGGTATGAAATAATTTCTTTGGGA
66 AAAATTTTAAAAACTTTTCGTATCTTTTCGATCCTCCATTAAGGCACGAAATAATTTCTTTGGGA
382416 AATAAAAAAGTTAAATTA
131 AATAAAAAAGTTAAATTA
* * *
382434 AATAAAAATTATGATCCT-AATTTTTTAGAATTTCCAATATTCCTATAGGCAT-C-TGTAAGGGT
1 AATAAAAATTATCA-CCTAAATTTTTTAAAATTTCCAATATTCCCATAGGCATCCATG-AA-GGT
*
382496 AAGAAAATTTTAAAAACATTTT-GTGTCTTTTCGATCCTCCATTAAGGCACGAAATAA
63 AAGAAAATTTTAAAAAC-TTTTCGTATCTTTTCGATCCTCCATTAAGGCACGAAATAA
382553 AAATTTTCAA
Statistics
Matches: 99, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
146 2 0.02
147 2 0.02
148 88 0.89
149 7 0.07
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (148 bp):
AATAAAAATTATCACCTAAATTTTTTAAAATTTCCAATATTCCCATAGGCATCCATGAAGGTAAG
AAAATTTTAAAAACTTTTCGTATCTTTTCGATCCTCCATTAAGGCACGAAATAATTTCTTTGGGA
AATAAAAAAGTTAAATTA
Found at i:383176 original size:155 final size:154
Alignment explanation
Indices: 382921--383350 Score: 434
Period size: 155 Copynumber: 2.8 Consensus size: 154
382911 GCCCGCTTTA
* * * * * *
382921 ATGTCGAAGGTGGGTATTTAGGATAGGTTCATCCCAT-TTTGTAACCCTTTTTAAGTCCTTTAGA
1 ATGTCAAAGGTAGATATTAAGGATAGGTTCATCCCATCTAT-T-ATCCTTTTTAAGTCCTTTAG-
* * * * * *
382985 GATATCGGGCACTTCTACGTCGAAGATATCCCTTAGGGGCATTTTCGTAGTTTTTTAGAACCGAG
63 GGTATCGGGTACTTTTACGTCGAAGATATCCCTTAGGGGCATTTTCGTAATTTTTCAAAACCGAG
* * * *
383050 TCTTAGGATGTCCCTAG-GTCTATTCTT
128 TCCTAAGATAT-CATAGAGTCTATTCTT
* * *
383077 ATGTCAAAGGTTGATATGTAA-GATAGGTTCATCTCATCTATTATCTTTTTTAAGTCCTTTACGG
1 ATGTCAAAGGTAGATAT-TAAGGATAGGTTCATCCCATCTATTATCCTTTTTAAGTCCTTTA-GG
** * * * * *
383141 GTATTAGGTACTTTTATGTCGAAGATATCCTTTAGGGCCATTTTCATAATTTTTCAAAATCGAGT
64 GTATCGGGTACTTTTACGTCGAAGATATCCCTTAGGGGCATTTTCGTAATTTTTCAAAACCGAGT
* * * * *
383206 CCTAAGTTATCATCGAGTTTGTTTTT
129 CCTAAGATATCATAGAGTCTATTCTT
* * *
383232 CTGTCGAAGGTAGATATTAAGGATAGGTTCATCCCATCTATTATCCTTTTTAAGTTCTTTAGGGG
1 ATGTCAAAGGTAGATATTAAGGATAGGTTCATCCCATCTATTATCCTTTTTAAGTCCTTTA-GGG
* * * *
383297 TATCGGGTACTTTTACGACGAAGGTATCCCTAAGGAGCATTTTCGTAATTTTTC
65 TATCGGGTACTTTTACGTCGAAGATATCCCTTAGGGGCATTTTCGTAATTTTTC
383351 TTGAACTTAG
Statistics
Matches: 222, Mismatches: 47, Indels: 11
0.79 0.17 0.04
Matches are distributed among these distances:
154 6 0.03
155 181 0.82
156 31 0.14
157 4 0.02
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.40
Consensus pattern (154 bp):
ATGTCAAAGGTAGATATTAAGGATAGGTTCATCCCATCTATTATCCTTTTTAAGTCCTTTAGGGT
ATCGGGTACTTTTACGTCGAAGATATCCCTTAGGGGCATTTTCGTAATTTTTCAAAACCGAGTCC
TAAGATATCATAGAGTCTATTCTT
Found at i:387035 original size:112 final size:113
Alignment explanation
Indices: 386848--387084 Score: 352
Period size: 112 Copynumber: 2.1 Consensus size: 113
386838 CAGTTACTTG
* * * * * ** *
386848 AGTATCGATACTTGCTGTCCAAAAATTCGAATTTTAGTTACTGCGAAGGCTTGTATCGATACAAT
1 AGTATCAATACTTGCTGTCCAAAAATTCAAATTTTAGCTACTACCAAGAATGGTATCGATACAAT
*
386913 CACACTAGGTATCGATACCACACCCT-GGTTATTGATACCAAGCCTTCA
66 CACACTAGGTATCGATACCACACCCTAGG-TATTGATACCAAGCCCTCA
386961 AGTATCAATACTTGCTGTCCAAAAA-TCAAATTTTAGCTACTACCAAGAATGGTATCGATACAAT
1 AGTATCAATACTTGCTGTCCAAAAATTCAAATTTTAGCTACTACCAAGAATGGTATCGATACAAT
387025 CACACTAGGTATCGATACCACACCCTAGGTATTGATACCAAGCCCTCA
66 CACACTAGGTATCGATACCACACCCTAGGTATTGATACCAAGCCCTCA
* *
387073 TGTATTAATACT
1 AGTATCAATACT
387085 ACACATGGAA
Statistics
Matches: 112, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
112 86 0.77
113 26 0.23
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (113 bp):
AGTATCAATACTTGCTGTCCAAAAATTCAAATTTTAGCTACTACCAAGAATGGTATCGATACAAT
CACACTAGGTATCGATACCACACCCTAGGTATTGATACCAAGCCCTCA
Found at i:387054 original size:20 final size:21
Alignment explanation
Indices: 387011--387064 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
387001 TACCAAGAAT
*
387011 GGTATCGATACAATCACACTA
1 GGTATCGATACCATCACACTA
*
387032 GGTATCGATACCA-CACCCTA
1 GGTATCGATACCATCACACTA
*
387052 GGTATTGATACCA
1 GGTATCGATACCA
387065 AGCCCTCATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (21 bp):
GGTATCGATACCATCACACTA
Found at i:389097 original size:80 final size:80
Alignment explanation
Indices: 388989--389166 Score: 213
Period size: 80 Copynumber: 2.3 Consensus size: 80
388979 TTTGACACAA
* ** * *
388989 CTTAGGA--TCATTTT-ACTAATTTCCATAAAAAATTGAGTT-TTTTAGGATCATGTAGCACTTT
1 CTTAGGAGGTCATTTTAAGTAATTTCCATAAAAAA-CCAATTCTTTTAGGATCATGCAGCACTTT
**
389050 CATGTCATGCATGTCC
65 CATGTCAAACATGTCC
* *
389066 CTTAGGAGGTCATTTTAAGTAATTTCCATAAAAAACCAATTCTTTTAGGGTGATGCAGCACTTTC
1 CTTAGGAGGTCATTTTAAGTAATTTCCATAAAAAACCAATTCTTTTAGGATCATGCAGCACTTTC
389131 ATGTCAAACATGTCC
66 ATGTCAAACATGTCC
* *
389146 TTTAAGAGGTCA-TTTAAGTAA
1 CTTAGGAGGTCATTTTAAGTAA
389167 CAACATGAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
77 7 0.08
79 19 0.22
80 60 0.70
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (80 bp):
CTTAGGAGGTCATTTTAAGTAATTTCCATAAAAAACCAATTCTTTTAGGATCATGCAGCACTTTC
ATGTCAAACATGTCC
Found at i:393092 original size:166 final size:164
Alignment explanation
Indices: 392891--393604 Score: 630
Period size: 166 Copynumber: 4.3 Consensus size: 164
392881 TAATAAATAT
* * * *
392891 AAAAAAATTG-AAAACTCA-CAAAATAAATTGAATTTTTTGAAACTGATTTAATGAGAATTT-AA
1 AAAAAAA-TGAAAAACTCATAAAAATAAA-TGAATTTTTTAAAAATGATTTAAT-ATAATTTAAA
** * * * * *
392953 TGACAATATTAGATGAATTTTAAAAATTTTAAATCGCGAAAAATGCCCCCAAAAATATTTATGGA
63 TGATGATATTTGATGAATATTAAAAATTTTGAA-C-CGAAAAATCCCCCCAAAAACATTTATGGA
*
393018 ATAAAAAACTCGATTTTTCAAAAATAAGAGAATTTCAAG
126 ATAGAAAACTCGATTTTTCAAAAATAAGAGAATTTCAAG
* * * * *
393057 AAAAAAATGAAAAGCTCATGAAAATAAATGAATTTTTCAAAAATGATTCATTATAATTTAAATGA
1 AAAAAAATGAAAAACTCATAAAAATAAATGAATTTTTTAAAAATGATTTAATATAATTTAAATGA
*
393122 TGATATTTGATGAATATTAAAAAGTTTGAACCGAGAAAATCCCCCTCAAAAACATTTATGGAATA
66 TGATATTTGATGAATATTAAAAATTTTGAACCGA-AAAATCCCCC-CAAAAACATTTATGGAATA
* * * * *
393187 GAAAACTCGGTTTTTTAGAAATAAGGGATTTTCAAG
129 GAAAACTCGATTTTTCAAAAATAAGAGAATTTCAAG
* * * * * *
393223 GAAAAAATGAAAAACTTATAAAAATAAATGGA-TTTTTCAAATTGATTTACTATAATTTAAATGA
1 AAAAAAATGAAAAACTCATAAAAATAAATGAATTTTTTAAAAATGATTTAATATAATTTAAATGA
*
393287 TGATATTTGATGAATATTAAAAATTTTGAACAAGAAAAA-CCCCCCAGAAAACATTTATGGAATA
66 TGATATTTGATGAATATTAAAAATTTTGAAC-CGAAAAATCCCCCCA-AAAACATTTATGGAATA
*
393351 GAAAACTCGATTTTTCAAAAAT-AGCGAATTTTCAAGG
129 GAAAACTCGATTTTTCAAAAATAAGAGAA-TTTCAA-G
* * ** * *
393388 AAAAAAA-GAAAAAATCATAAAAATAAGTG-GCTTTTTCAAAATGGA-TTAA-ATAATGATTAGA
1 AAAAAAATGAAAAACTCATAAAAATAAATGAATTTTTTAAAAAT-GATTTAATATAAT--TTAAA
* * * * * * *
393449 TAATAATATTTGATAAAGT-TTAAAAATTTT-AATTCGATGAAAATCCTCTCAAAAAAATTTATG
63 TGATGATATTTGATGAA-TATTAAAAATTTTGAA-CCGA--AAAATCCCCCCAAAAACATTTATG
* * * * * *
393512 GAAAAGAAAACTCTATATTTTGAGAACACAAG-GAATTCCAA-
124 GAATAGAAAACTCGAT-TTTTCA-AAAATAAGAGAATTTCAAG
* * * * * *
393553 AAGAAAATAAAAAACTCCTAGAACA-AAATGAATTTTTCAAAACTGATTTAAT
1 AAAAAAATGAAAAACTCATA-AAAATAAATGAATTTTTTAAAAATGATTTAAT
393605 TGTAACTAAA
Statistics
Matches: 450, Mismatches: 72, Indels: 50
0.79 0.13 0.09
Matches are distributed among these distances:
163 11 0.02
164 86 0.19
165 123 0.27
166 184 0.41
167 38 0.08
168 6 0.01
169 2 0.00
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (164 bp):
AAAAAAATGAAAAACTCATAAAAATAAATGAATTTTTTAAAAATGATTTAATATAATTTAAATGA
TGATATTTGATGAATATTAAAAATTTTGAACCGAAAAATCCCCCCAAAAACATTTATGGAATAGA
AAACTCGATTTTTCAAAAATAAGAGAATTTCAAG
Found at i:393590 original size:330 final size:331
Alignment explanation
Indices: 392892--393602 Score: 752
Period size: 330 Copynumber: 2.1 Consensus size: 331
392882 AATAAATATA
** * ** * *
392892 AAAAAATTGAAAACTCA-CAAAATAAATTGAATTTTTTGAAACTGATTTAATGAGAATTT-AATG
1 AAAAAATAAAAAACTCATAAAAATAAA-TGAATTTTTCAAAACTGATTTACT-ATAATTTAAATG
** * ** * *
392955 ACAATATTAGATGAATTTTAAAAATTTTAAATCGCGAAAAATGCCCCCAAAAATATTTATGGAAT
64 ATGATATTAGATGAATATTAAAAATTTTAAATCAAGAAAAATCCCCCCAAAAACATTTATGGAAT
** *
393020 AAAAAACTCGATTTTTCAAAAATAAGAGAATTTCAAGAAAAAAATGAAAAGCTCATGAAAATAAA
129 AAAAAACTCGATTTTTCAAAAATAAGAGAATTTCAAGAAAAAAATGAAAAAATCATAAAAATAAA
* * * *
393085 TGAATTTTTCAAAAATGATTCATTATAATTTAAATGATGATATTTGATGAATATTAAAAAGTTTG
194 TGAATTTTTCAAAAATGATTCATAATAATTTAAATAATAATATTTGATAAATATTAAAAAGTTTG
* * * * *
393150 AACCGAGAAAATCCCCCTCAAAAACATTTATGGAATAGAAAACTCGGTTTTTTAGAAATAAGGGA
259 AACCGAGAAAATCCCCCTCAAAAAAATTTATGGAAAAGAAAACTCGATTTTTGAGAAACAAGGGA
* *
393215 TTTTCAAGG
324 ATTCCAA-G
* * * *
393224 AAAAAATGAAAAACTTATAAAAATAAATGGATTTTTC-AAATTGATTTACTATAATTTAAATGAT
1 AAAAAATAAAAAACTCATAAAAATAAATGAATTTTTCAAAACTGATTTACTATAATTTAAATGAT
* *
393288 GATATTTGATGAATATTAAAAATTTTGAA-CAAGAAAAA-CCCCCCAGAAAACATTTATGGAATA
66 GATATTAGATGAATATTAAAAATTTTAAATCAAGAAAAATCCCCCCA-AAAACATTTATGGAATA
* *
393351 GAAAACTCGATTTTTCAAAAAT-AGCGAATTTTCAAGGAAAAAAA-GAAAAAATCATAAAAATAA
130 AAAAACTCGATTTTTCAAAAATAAGAGAA-TTTCAA-GAAAAAAATGAAAAAATCATAAAAATAA
* ** *
393414 GTGGCTTTTTC-AAAATGGATT-A-AATAATGATTAGATAATAATATTTGATAAAGT-TTAAAAA
193 ATGAATTTTTCAAAAAT-GATTCATAATAAT--TTAAATAATAATATTTGATAAA-TATTAAAAA
* * * *
393475 -TTTTAATTCGATGAAAAT-CCTCTCAAAAAAATTTATGGAAAAGAAAACTCTATATTTTGAGAA
254 GTTTGAA-CCGA-GAAAATCCCCCTCAAAAAAATTTATGGAAAAGAAAACTCGAT-TTTTGAGAA
393538 CACAA-GGAATTCCAA-
316 -ACAAGGGAATTCCAAG
* *
393553 AAGAAAATAAAAAACTCCTAGAACA-AAATGAATTTTTCAAAACTGATTTA
1 AA-AAAATAAAAAACTCATA-AAAATAAATGAATTTTTCAAAACTGATTTA
393603 ATTGTAACTA
Statistics
Matches: 315, Mismatches: 48, Indels: 33
0.80 0.12 0.08
Matches are distributed among these distances:
328 5 0.02
329 24 0.08
330 168 0.53
331 85 0.27
332 25 0.08
333 8 0.03
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (331 bp):
AAAAAATAAAAAACTCATAAAAATAAATGAATTTTTCAAAACTGATTTACTATAATTTAAATGAT
GATATTAGATGAATATTAAAAATTTTAAATCAAGAAAAATCCCCCCAAAAACATTTATGGAATAA
AAAACTCGATTTTTCAAAAATAAGAGAATTTCAAGAAAAAAATGAAAAAATCATAAAAATAAATG
AATTTTTCAAAAATGATTCATAATAATTTAAATAATAATATTTGATAAATATTAAAAAGTTTGAA
CCGAGAAAATCCCCCTCAAAAAAATTTATGGAAAAGAAAACTCGATTTTTGAGAAACAAGGGAAT
TCCAAG
Found at i:394668 original size:60 final size:59
Alignment explanation
Indices: 394604--394775 Score: 247
Period size: 60 Copynumber: 2.9 Consensus size: 59
394594 TAGGCAGATA
* * * *
394604 AAGAAAGGCTGGACCAAACACAATCAAGCGAGGTAAGATTTGATCAAGTACAATCAAATG
1 AAGAAAGACT-GACCGAACACAGTCAAGCGAGGTAAGATTTGATCGAGTACAATCAAATG
*
394664 AAGAAAGACATGACCGAATACAGTCAAGC-AGGGTAAGATTTGATCGAGTACAATCAAATG
1 AAGAAAGAC-TGACCGAACACAGTCAAGCGA-GGTAAGATTTGATCGAGTACAATCAAATG
*
394724 AAGAAAGACTTGATCGAACACAGTCAAGCGAGGTAAGATTTGATCGAGTACA
1 AAGAAAGAC-TGACCGAACACAGTCAAGCGAGGTAAGATTTGATCGAGTACA
394776 GTTGTAGACA
Statistics
Matches: 101, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
59 1 0.01
60 98 0.97
61 2 0.02
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.18
Consensus pattern (59 bp):
AAGAAAGACTGACCGAACACAGTCAAGCGAGGTAAGATTTGATCGAGTACAATCAAATG
Found at i:394777 original size:30 final size:30
Alignment explanation
Indices: 394627--394777 Score: 124
Period size: 30 Copynumber: 5.0 Consensus size: 30
394617 CCAAACACAA
* *
394627 TCAAGCGAGGTAAGATTTGATCAAGTACAA
1 TCAAGCGAGGTAAGATTTGATCGAGTACAG
** * * ** * *
394657 TCAAATGAAGAAAGACATGACCGAATACAG
1 TCAAGCGAGGTAAGATTTGATCGAGTACAG
*
394687 TCAAGC-AGGGTAAGATTTGATCGAGTACAA
1 TCAAGCGA-GGTAAGATTTGATCGAGTACAG
** * * * **
394717 TCAAATGAAGAAAGACTTGATCGAACACAG
1 TCAAGCGAGGTAAGATTTGATCGAGTACAG
394747 TCAAGCGAGGTAAGATTTGATCGAGTACAG
1 TCAAGCGAGGTAAGATTTGATCGAGTACAG
394777 T
1 T
394778 TGTAGACACC
Statistics
Matches: 85, Mismatches: 34, Indels: 4
0.69 0.28 0.03
Matches are distributed among these distances:
29 1 0.01
30 83 0.98
31 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.21
Consensus pattern (30 bp):
TCAAGCGAGGTAAGATTTGATCGAGTACAG
Found at i:395205 original size:13 final size:13
Alignment explanation
Indices: 395187--395211 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
395177 TTATTCAATG
395187 TATCGATACATTT
1 TATCGATACATTT
395200 TATCGATACATT
1 TATCGATACATT
395212 GATCTTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (13 bp):
TATCGATACATTT
Found at i:395209 original size:33 final size:33
Alignment explanation
Indices: 395167--395230 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
395157 CAAGGCAATG
395167 TATCGATACATT-ATTCAATGTATCGATACATTT
1 TATCGATACATTGA-TCAATGTATCGATACATTT
**
395200 TATCGATACATTGATCTTTGTATCGATACAT
1 TATCGATACATTGATCAATGTATCGATACAT
395231 CTGGGAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (33 bp):
TATCGATACATTGATCAATGTATCGATACATTT
Found at i:398465 original size:30 final size:30
Alignment explanation
Indices: 398412--398561 Score: 85
Period size: 30 Copynumber: 5.1 Consensus size: 30
398402 CATTGCGACA
* *
398412 ACAGTTAAATGAGGATAA-TCTTGATCGAGT
1 ACAGTTAAATGAAGA-AAGACTTGATCGAGT
* *
398442 ACAGTTAAATGAAGAAAGACTTGACCGAAT
1 ACAGTTAAATGAAGAAAGACTTGATCGAGT
* * * * *
398472 ATAG-TCAA-GCAAG-TA-ATTTGATCAAGT
1 ACAGTTAAATG-AAGAAAGACTTGATCGAGT
* * * *
398499 CCAGTTAAATGAAAAAAGACTTGATCAAAT
1 ACAGTTAAATGAAGAAAGACTTGATCGAGT
* * * * *
398529 ACAGTCAAATGAGGTAAGATTTGACCGAGT
1 ACAGTTAAATGAAGAAAGACTTGATCGAGT
398559 ACA
1 ACA
398562 ATCAAATAAG
Statistics
Matches: 87, Mismatches: 27, Indels: 12
0.69 0.21 0.10
Matches are distributed among these distances:
27 10 0.11
28 7 0.08
29 10 0.11
30 60 0.69
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.25
Consensus pattern (30 bp):
ACAGTTAAATGAAGAAAGACTTGATCGAGT
Found at i:398520 original size:57 final size:58
Alignment explanation
Indices: 398427--398536 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 58
398417 TAAATGAGGA
* * * *
398427 TAATCTTGATCGAGTACAGTTAAATGAAGAAAGACTTGACCGAATATAGTCAAGCAAG
1 TAATCTTGATCAAGTACAGTTAAATGAAAAAAGACTTGACCAAATACAGTCAAGCAAG
* *
398485 TAAT-TTGATCAAGTCCAGTTAAATGAAAAAAGACTTGATCAAATACAGTCAA
1 TAATCTTGATCAAGTACAGTTAAATGAAAAAAGACTTGACCAAATACAGTCAA
398537 ATGAGGTAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 42 0.91
58 4 0.09
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (58 bp):
TAATCTTGATCAAGTACAGTTAAATGAAAAAAGACTTGACCAAATACAGTCAAGCAAG
Found at i:398731 original size:30 final size:30
Alignment explanation
Indices: 398673--398798 Score: 96
Period size: 30 Copynumber: 4.1 Consensus size: 30
398663 GGCATGACGA
* *
398673 AATACAGTCAA-CCAAGGGTGAAATTTGATCG
1 AATACAGTCAAGCGAA-GGT-AGATTTGATCG
* *
398704 AATACAGTTAAGCGAAGGTAGATTTGATCA
1 AATACAGTCAAGCGAAGGTAGATTTGATCG
** * *
398734 AATACAGTCAAATG-AGGAAAGATTTGACCG
1 AATACAGTCAAGCGAAGG-TAGATTTGATCG
* *
398764 AATATAGTCAAGC-AAGAGTGAAATTTGATCG
1 AATACAGTCAAGCGAAG-GT-AGATTTGATCG
398795 AATA
1 AATA
398799 TAGACAAATA
Statistics
Matches: 74, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
29 3 0.04
30 41 0.55
31 27 0.36
32 3 0.04
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (30 bp):
AATACAGTCAAGCGAAGGTAGATTTGATCG
Found at i:398790 original size:61 final size:60
Alignment explanation
Indices: 398695--398849 Score: 168
Period size: 61 Copynumber: 2.6 Consensus size: 60
398685 CAAGGGTGAA
* * * * *
398695 ATTTGATCGAATACAGTTAAGCGAAGGTAGATTTGATCAAATACAGTCAAATGAGGAAAG
1 ATTTGATCGAATATAGTCAAGCGAAGGTAAATTTGATCAAATACAGACAAATAAGGAAAG
* * *
398755 ATTTGACCGAATATAGTCAAGC-AAGAGTGAAATTTGATCGAATATAGACAAATAAGGAAAG
1 ATTTGATCGAATATAGTCAAGCGAAG-GT-AAATTTGATCAAATACAGACAAATAAGGAAAG
** * * *
398816 GGTTGATCGAATATAGTCAAACAAAGGTGAATTT
1 ATTTGATCGAATATAGTCAAGCGAAGGTAAATTT
398850 TGGGGAAGAG
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
59 3 0.04
60 26 0.33
61 47 0.59
62 3 0.04
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.25
Consensus pattern (60 bp):
ATTTGATCGAATATAGTCAAGCGAAGGTAAATTTGATCAAATACAGACAAATAAGGAAAG
Found at i:399682 original size:1 final size:1
Alignment explanation
Indices: 399676--399737 Score: 52
Period size: 1 Copynumber: 62.0 Consensus size: 1
399666 TTATTTATTC
* * ** * * * *
399676 TTTTTTTTTGTTTTTTTGTTTTTTTTTTTTGCTTTCTTCTTTTTTTTATTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
399738 ATTACCCCAT
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.03, C:0.05, G:0.05, T:0.87
Consensus pattern (1 bp):
T
Found at i:402648 original size:11 final size:11
Alignment explanation
Indices: 402634--402670 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
402624 AAATAAAAAC
402634 AAAAAAATCCA
1 AAAAAAATCCA
*
402645 AAAAAAATCAA
1 AAAAAAATCCA
402656 AAAAAAAT-CA
1 AAAAAAATCCA
402666 AAAAA
1 AAAAA
402671 TCAAAGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 6 0.25
11 18 0.75
ACGTcount: A:0.81, C:0.11, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAAATCCA
Found at i:403595 original size:74 final size:74
Alignment explanation
Indices: 403491--403635 Score: 191
Period size: 74 Copynumber: 2.0 Consensus size: 74
403481 GCAGCTTCCA
* * * * * * * *
403491 CGAACATCGACAGTAGCTCTAGCAGCTTCCAACAGTGACAACATCCACCAACAGCAGCAGTAGCT
1 CGAACACCGACAGCAGCTCCAGCAACTTCCAACAGCGACAACATCCACAAACAGCAACAGGAGCT
*
403556 TCCAGCTCG
66 CCCAGCTCG
* *
403565 CGAACACCGGCAGCAGCTCCAGCAACTTCCAACAGCGACAGCATCCACAAACAGCAACAGGAGCT
1 CGAACACCGACAGCAGCTCCAGCAACTTCCAACAGCGACAACATCCACAAACAGCAACAGGAGCT
403630 CCCAGC
66 CCCAGC
403636 CCACGAGCAC
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.32, C:0.37, G:0.19, T:0.12
Consensus pattern (74 bp):
CGAACACCGACAGCAGCTCCAGCAACTTCCAACAGCGACAACATCCACAAACAGCAACAGGAGCT
CCCAGCTCG
Found at i:403660 original size:74 final size:73
Alignment explanation
Indices: 403488--403660 Score: 186
Period size: 74 Copynumber: 2.3 Consensus size: 73
403478 CTAGCAGCTT
* * * * * * * *
403488 CCACGAACATCGACAGTAGCTCTAGCAGCTTCCAACAGTGACAACATCCACCAACAGCAGCAGTA
1 CCACGAACACCG-CAGCAGCTCCAGCAACTTCCAACAGCGACAACATCCACAAACAGCAACAGGA
*
403553 GCTTCCAGC
65 GCTCCCAGC
* * *
403562 TCGCGAACACCGGCAGCAGCTCCAGCAACTTCCAACAGCGACAGCATCCACAAACAGCAACAGGA
1 CCACGAACACC-GCAGCAGCTCCAGCAACTTCCAACAGCGACAACATCCACAAACAGCAACAGGA
403627 GCTCCCAGC
65 GCTCCCAGC
*
403636 CCACGAGCACTC-CAGCAGCTTCCAG
1 CCACGAACAC-CGCAGCAGC-TCCAG
403661 TAGCGACAAC
Statistics
Matches: 81, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
73 7 0.09
74 72 0.89
75 2 0.02
ACGTcount: A:0.31, C:0.38, G:0.19, T:0.12
Consensus pattern (73 bp):
CCACGAACACCGCAGCAGCTCCAGCAACTTCCAACAGCGACAACATCCACAAACAGCAACAGGAG
CTCCCAGC
Found at i:405471 original size:56 final size:57
Alignment explanation
Indices: 405258--405447 Score: 321
Period size: 57 Copynumber: 3.3 Consensus size: 57
405248 TATAATAATA
* *
405258 AAAATCCTTCGTATCCTCCC-AGTGCTCCAAAAGGGTATGAAAGACATTTTGGCCTTG
1 AAAACCCTTTGTATCCTCCCGA-TGCTCCAAAAGGGTATGAAAGACATTTTGGCCTTG
405315 AAAACCCTTTGTATCCTCCCGATGCTCCAAAAGGGTATGAAAGACATTTTGGCCTTG
1 AAAACCCTTTGTATCCTCCCGATGCTCCAAAAGGGTATGAAAGACATTTTGGCCTTG
405372 AAAACCCTTTGTATCCTCCCGATGCTCCAAAAGGGTATGAAAGACATTTTGGCCTTG
1 AAAACCCTTTGTATCCTCCCGATGCTCCAAAAGGGTATGAAAGACATTTTGGCCTTG
*
405429 AAAA-CCTTTATATTCCTCC
1 AAAACCCTTTGTA-TCCTCC
405448 GAGCTTCTAG
Statistics
Matches: 128, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
56 7 0.05
57 120 0.94
58 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (57 bp):
AAAACCCTTTGTATCCTCCCGATGCTCCAAAAGGGTATGAAAGACATTTTGGCCTTG
Found at i:415538 original size:189 final size:189
Alignment explanation
Indices: 415212--415593 Score: 665
Period size: 189 Copynumber: 2.0 Consensus size: 189
415202 CCATGCCAAC
* *
415212 GGACATAAAATGGCAAGGCAGATTATGAGATTGGGCTACTTCTGGATGACTATGGAAGGAGATTG
1 GGACACAAAATGGCAAGGCAGATTATGAGATTGGGCTACTTCTAGATGACTATGGAAGGAGATTG
* ** * *
415277 CATTACATATGCTTGAAAATGCCACAAATGCCAGATCTATGCTGACAAAATTCATGTTTCCCTAT
66 CATTAAATATGCCCGAAAATGCCACAAATGCCAGATCTATGCCGACAAAATTCATGTTTCCCCAT
*
415342 CAAAATTACATGTCATCACTATGCCATGGCCTTTCTCTATATGGGGCATGGACGTCATT
131 CAAAATTACATGTCATCACTATGCCATGGCCTTTCTCTATATGGGGCATGGACATCATT
* * *
415401 GGACACAAAATGGCAAGGTAGATTGTGAGATTGGGCTTCTTCTAGATGACTATGGAAGGAGATTG
1 GGACACAAAATGGCAAGGCAGATTATGAGATTGGGCTACTTCTAGATGACTATGGAAGGAGATTG
415466 CATTAAATATGCCCGAAAATGCCACAAATGCCAGATCTATGCCGACAAAATTCATGTTTCCCCAT
66 CATTAAATATGCCCGAAAATGCCACAAATGCCAGATCTATGCCGACAAAATTCATGTTTCCCCAT
415531 CAAAATTACATGTCATCACTATGCCATGGCCTTTCTCTATATGGGGCATGGACATCATT
131 CAAAATTACATGTCATCACTATGCCATGGCCTTTCTCTATATGGGGCATGGACATCATT
415590 GGAC
1 GGAC
415594 CTATTACTCC
Statistics
Matches: 182, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
189 182 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (189 bp):
GGACACAAAATGGCAAGGCAGATTATGAGATTGGGCTACTTCTAGATGACTATGGAAGGAGATTG
CATTAAATATGCCCGAAAATGCCACAAATGCCAGATCTATGCCGACAAAATTCATGTTTCCCCAT
CAAAATTACATGTCATCACTATGCCATGGCCTTTCTCTATATGGGGCATGGACATCATT
Found at i:417566 original size:43 final size:43
Alignment explanation
Indices: 417491--418113 Score: 398
Period size: 43 Copynumber: 14.6 Consensus size: 43
417481 TTTTTTCGTA
* * *
417491 CCCTTAGTCTGCTTGTC-GTCTTTGACCCTAGAGACTTTCCTAT
1 CCCTCAGTCTGCCTGTCAG-CTTTGACCCTGGAGACTTTCCTAT
* * * * *
417534 CCCTCAGTCTGCCTGTCAGTTTTAACCATAGAGAC-TGCCT-T
1 CCCTCAGTCTGCCTGTCAGCTTTGACCCTGGAGACTTTCCTAT
** * * * * * *
417575 AGCTAAAGTCTGTCT-ACCGACTTTGACCCTAGAGACTTTTCTAT
1 CCCT-CAGTCTGCCTGTCAG-CTTTGACCCTGGAGACTTTCCTAT
* * * *
417619 CCCTCTGTCTGCTTATCAGCTTTGACCCTGGAGAC-TGCCTTAT
1 CCCTCAGTCTGCCTGTCAGCTTTGACCCTGGAGACTTTCC-TAT
* * *
417662 --CTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTAT
1 CCCT-CAGTCTGCCTGTCAGCTTTGACCCTGGAGACTTTCCTAT
* * * * * *
417704 CCTTCAGTCTGCCTATCAGTTTTGACCATGGAAAC-TGCCTTAT
1 CCCTCAGTCTGCCTGTCAGCTTTGACCCTGGAGACTTTCC-TAT
* *
417747 --CTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTAT
1 CCCT-CAGTCTGCCTGTCAGCTTTGACCCTGGAGACTTTCCTAT
* *
417789 CCCTCAGTCTGCTTGTCAGCTTTGACCCTGGAGAC-TGCCTTAT
1 CCCTCAGTCTGCCTGTCAGCTTTGACCCTGGAGACTTTCC-TAT
* * * * * *
417832 --CTAAATTCTGCCTATCGGCTTTGACCTTGGAGACTTTCTTAT
1 CCCT-CAGTCTGCCTGTCAGCTTTGACCCTGGAGACTTTCCTAT
* *
417874 CCCTCAGTCTGCCTGTCAACTTTGACCCTGGAGACTTTCTTAT
1 CCCTCAGTCTGCCTGTCAGCTTTGACCCTGGAGACTTTCCTAT
* * ** * ** *
417917 CCCTCAGTCTACCTATTGGCTTTGACCTTGGAGACAGTCTTAT
1 CCCTCAGTCTGCCTGTCAGCTTTGACCCTGGAGACTTTCCTAT
* * * * *
417960 --CTAGAGTCTGCATGTCGGCTTTGACCTTGGAAACTTTCCTAT
1 CCCT-CAGTCTGCCTGTCAGCTTTGACCCTGGAGACTTTCCTAT
* * * * * *
418002 ACCTAAGTCTGCCTATCGGCTTTGACCCTAGAGACCTTT-TTA-
1 CCCTCAGTCTGCCTGTCAGCTTTGACCCTGGAGA-CTTTCCTAT
* * * * * *
418044 CTCTAAGTCTGCTTGTCGGCTTTGACCTTAGAGACTTTCCTAT
1 CCCTCAGTCTGCCTGTCAGCTTTGACCCTGGAGACTTTCCTAT
* * **
418087 CCTTTAGTCTGCCTGTTGGCTTTGACC
1 CCCTCAGTCTGCCTGTCAGCTTTGACC
418114 TGGGAGAATC
Statistics
Matches: 449, Mismatches: 104, Indels: 54
0.74 0.17 0.09
Matches are distributed among these distances:
41 16 0.04
42 178 0.40
43 238 0.53
44 17 0.04
ACGTcount: A:0.17, C:0.28, G:0.18, T:0.36
Consensus pattern (43 bp):
CCCTCAGTCTGCCTGTCAGCTTTGACCCTGGAGACTTTCCTAT
Found at i:417653 original size:85 final size:85
Alignment explanation
Indices: 417496--418079 Score: 586
Period size: 85 Copynumber: 6.9 Consensus size: 85
417486 TCGTACCCTT
* * * * * *
417496 AGTCTGCTTGTCGTCTTTGACCCTAGAGACTTTCCTATCCCTCAGTCTGCCTGTCAGTTTTAACC
1 AGTCTGCCTATCGGCTTTGACCCTGGAGACTTTCCTATCCCTCAGTCTGCCTGTCAGCTTTGACC
* * *
417561 ATAGAGACTGCCTTAGCTAA
66 CTGGAGACTGCCTTATCTAA
* * * * * * * *
417581 AGTCTGTCTACCGACTTTGACCCTAGAGACTTTTCTATCCCTCTGTCTGCTTATCAGCTTTGACC
1 AGTCTGCCTATCGGCTTTGACCCTGGAGACTTTCCTATCCCTCAGTCTGCCTGTCAGCTTTGACC
417646 CTGGAGACTGCCTTATCTAA
66 CTGGAGACTGCCTTATCTAA
* * * * *
417666 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTATCCTTCAGTCTGCCTATCAGTTTTGACC
1 AGTCTGCCTATCGGCTTTGACCCTGGAGACTTTCCTATCCCTCAGTCTGCCTGTCAGCTTTGACC
* *
417731 ATGGAAACTGCCTTATCTAA
66 CTGGAGACTGCCTTATCTAA
* *
417751 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTATCCCTCAGTCTGCTTGTCAGCTTTGACC
1 AGTCTGCCTATCGGCTTTGACCCTGGAGACTTTCCTATCCCTCAGTCTGCCTGTCAGCTTTGACC
417816 CTGGAGACTGCCTTATCTAA
66 CTGGAGACTGCCTTATCTAA
* * * *
417836 ATTCTGCCTATCGGCTTTGACCTTGGAGACTTTCTTATCCCTCAGTCTGCCTGTCAACTTTGACC
1 AGTCTGCCTATCGGCTTTGACCCTGGAGACTTTCCTATCCCTCAGTCTGCCTGTCAGCTTTGACC
** *
417901 CTGGAGACTTTCTTATCCCT-C
66 CTGGAGACTGCCTTAT--CTAA
* * * ** * * * *
417922 AGTCTACCTATTGGCTTTGACCTTGGAGACAGTCTTAT--CTAGAGTCTGCATGTCGGCTTTGAC
1 AGTCTGCCTATCGGCTTTGACCCTGGAGACTTTCCTATCCCT-CAGTCTGCCTGTCAGCTTTGAC
* * * *
417985 CTTGGAAACTTTCCTATACCT-A
65 CCTGGAGAC-TGCCT-TATCTAA
* * * * * *
418007 AGTCTGCCTATCGGCTTTGACCCTAGAGACCTTT-TTA-CTCTAAGTCTGCTTGTCGGCTTTGAC
1 AGTCTGCCTATCGGCTTTGACCCTGGAGA-CTTTCCTATCCCTCAGTCTGCCTGTCAGCTTTGAC
* *
418070 CTTAGAGACT
65 CCTGGAGACT
418080 TTCCTATCCT
Statistics
Matches: 424, Mismatches: 67, Indels: 17
0.83 0.13 0.03
Matches are distributed among these distances:
84 3 0.01
85 376 0.89
86 41 0.10
87 4 0.01
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.35
Consensus pattern (85 bp):
AGTCTGCCTATCGGCTTTGACCCTGGAGACTTTCCTATCCCTCAGTCTGCCTGTCAGCTTTGACC
CTGGAGACTGCCTTATCTAA
Found at i:417888 original size:213 final size:213
Alignment explanation
Indices: 417625--418120 Score: 586
Period size: 213 Copynumber: 2.3 Consensus size: 213
417615 CTATCCCTCT
* * **
417625 GTCTGCTTATCAGCTTTGACCCTGGAGACTGCCTTAT--CTAAAGTCTGCCTGTCGGCTTTGACC
1 GTCTGCTTATCGGCTTTGACCTTGGAGACTTTCTTATCCCT-AAGTCTGCCTGTCGGCTTTGACC
* * * *
417688 TTGGAGACTTTCCTATCCTTCAGTCTGCCTATCAGTTTTGACCATGGAAACTGCCTTATCTAAAG
65 TTGGAGACTTTCCTATCCCTCAGTCTACCTATCAGCTTTGACCATGGAAACAGCCTTATCTAAAG
* * * * * *
417753 TCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTATCCCTCAGTCTGCTTGTCAGCTTTGACCCT
130 TCTGCATGTCGGCTTTGACCCTGGAAACTTTCCTATACCTAAGTCTGCCTATCAGCTTTGACCCT
*
417818 GGAGA-CTGCCTTA-TCTAAA
195 AGAGACCT-CCTTACTCT-AA
* * * ** *
417837 TTCTGCCTATCGGCTTTGACCTTGGAGACTTTCTTATCCCTCAGTCTGCCTGTCAACTTTGACCC
1 GTCTGCTTATCGGCTTTGACCTTGGAGACTTTCTTATCCCTAAGTCTGCCTGTCGGCTTTGACCT
* ** * * * *
417902 TGGAGACTTTCTTATCCCTCAGTCTACCTATTGGCTTTGACCTTGGAGACAGTCTTATCTAGAGT
66 TGGAGACTTTCCTATCCCTCAGTCTACCTATCAGCTTTGACCATGGAAACAGCCTTATCTAAAGT
* *
417967 CTGCATGTCGGCTTTGACCTTGGAAACTTTCCTATACCTAAGTCTGCCTATCGGCTTTGACCCTA
131 CTGCATGTCGGCTTTGACCCTGGAAACTTTCCTATACCTAAGTCTGCCTATCAGCTTTGACCCTA
**
418032 GAGACCTTTTTACTCTAA
196 GAGACCTCCTTACTCTAA
* * * * * *
418050 GTCTGCTTGTCGGCTTTGACCTTAGAGACTTTCCTATCCTTTAGTCTGCCTGTTGGCTTTGACCT
1 GTCTGCTTATCGGCTTTGACCTTGGAGACTTTCTTATCCCTAAGTCTGCCTGTCGGCTTTGACCT
*
418115 GGGAGA
66 TGGAGA
418121 ATCTTTTCTT
Statistics
Matches: 236, Mismatches: 44, Indels: 7
0.82 0.15 0.02
Matches are distributed among these distances:
212 31 0.13
213 198 0.84
214 7 0.03
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.35
Consensus pattern (213 bp):
GTCTGCTTATCGGCTTTGACCTTGGAGACTTTCTTATCCCTAAGTCTGCCTGTCGGCTTTGACCT
TGGAGACTTTCCTATCCCTCAGTCTACCTATCAGCTTTGACCATGGAAACAGCCTTATCTAAAGT
CTGCATGTCGGCTTTGACCCTGGAAACTTTCCTATACCTAAGTCTGCCTATCAGCTTTGACCCTA
GAGACCTCCTTACTCTAA
Found at i:418098 original size:128 final size:128
Alignment explanation
Indices: 417510--418114 Score: 515
Period size: 128 Copynumber: 4.7 Consensus size: 128
417500 TGCTTGTCGT
* * * * * * * * *
417510 CTTTGACCCTAGAGACTTTCCTATCCCTCAGTCTGCCTGTCAGTTTTAACCATAGAGAC-TGCCT
1 CTTTGACCCTGGAGACTTTCTTATCCCTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCC-
* * * * * * * * * ** *
417574 TAGCTAAAGTCTGTCTACCGACTTTGACCCTAGAGACTTTTCTATCCCTCTGTCTGCTTATCAG
65 TATCTAAAGTCTGCCTATCGGCTTTGACCTTGGAAACTTTCCTATACCTAAGTCTGCCTATCAG
**
417638 CTTTGACCCTGGAGACTGCCTTAT--CTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCC
1 CTTTGACCCTGGAGACTTTCTTATCCCT-AAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCC
** * * * * * * *
417701 TATCCTTCAGTCTGCCTATCAGTTTTGACCATGGAAAC-TGCCT-TATCTAAAGTCTGCCTGTCG
65 TAT-CTAAAGTCTGCCTATCGGCTTTGACCTTGGAAACTTTCCTATACCT-AAGTCTGCCTATCA
417764 G
128 G
* * * * * *
417765 CTTTGACCCTGGAGACTTTCCTATCCCTCAGTCTGCTTGTCAGCTTTGACCCTGGAGAC-TGCCT
1 CTTTGACCCTGGAGACTTTCTTATCCCTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCC-
* * * * * * *
417829 TATCTAAATTCTGCCTATCGGCTTTGACCTTGGAGACTTTCTTATCCCTCAGTCTGCCTGTCAA
65 TATCTAAAGTCTGCCTATCGGCTTTGACCTTGGAAACTTTCCTATACCTAAGTCTGCCTATCAG
* * * * ** *
417893 CTTTGACCCTGGAGACTTTCTTATCCCTCAGTCTACCTATTGGCTTTGACCTTGGAGACAGTCTT
1 CTTTGACCCTGGAGACTTTCTTATCCCTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCT
* * * *
417958 ATCTAGAGTCTGCATGTCGGCTTTGACCTTGGAAACTTTCCTATACCTAAGTCTGCCTATCGG
66 ATCTAAAGTCTGCCTATCGGCTTTGACCTTGGAAACTTTCCTATACCTAAGTCTGCCTATCAG
* * * *
418021 CTTTGACCCTAGAGACCTTT-TTA-CTCTAAGTCTGCTTGTCGGCTTTGACCTTAGAGACTTTCC
1 CTTTGACCCTGGAGA-CTTTCTTATCCCTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCC
** * *
418084 TATCCTTTAGTCTGCCTGTTGGCTTTGACCT
65 TAT-CTAAAGTCTGCCTATCGGCTTTGACCT
418115 GGGAGAATCT
Statistics
Matches: 376, Mismatches: 89, Indels: 24
0.77 0.18 0.05
Matches are distributed among these distances:
126 5 0.01
127 124 0.33
128 237 0.63
129 10 0.03
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (128 bp):
CTTTGACCCTGGAGACTTTCTTATCCCTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCT
ATCTAAAGTCTGCCTATCGGCTTTGACCTTGGAAACTTTCCTATACCTAAGTCTGCCTATCAG
Found at i:418628 original size:10 final size:10
Alignment explanation
Indices: 418610--418682 Score: 75
Period size: 11 Copynumber: 7.6 Consensus size: 10
418600 AATTAAAAAT
418610 AAAAA-CAAA
1 AAAAATCAAA
418619 AAAAATCAAAA
1 AAAAATC-AAA
418630 AAAAATCAAA
1 AAAAATCAAA
418640 AAAAATC--A
1 AAAAATCAAA
418648 AAAAATC-AA
1 AAAAATCAAA
*
418657 AGAAAT-AAA
1 AAAAATCAAA
*
418666 AAAATTTCAAA
1 AAAA-ATCAAA
418677 AAAAAT
1 AAAAAT
418683 GTGAAAGAAC
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
8 8 0.15
9 16 0.30
10 13 0.24
11 17 0.31
ACGTcount: A:0.78, C:0.08, G:0.01, T:0.12
Consensus pattern (10 bp):
AAAAATCAAA
Found at i:418629 original size:21 final size:21
Alignment explanation
Indices: 418597--418652 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
418587 AGTAGAAATC
* *
418597 AAAAATTAAAAATAAAAACAAA
1 AAAAATCAAAAA-AAAATCAAA
418619 AAAAATCAAAAAAAAATCAAA
1 AAAAATCAAAAAAAAATCAAA
418640 AAAAATCAAAAAA
1 AAAAATCAAAAAA
418653 TCAAAGAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (21 bp):
AAAAATCAAAAAAAAATCAAA
Found at i:418630 original size:11 final size:11
Alignment explanation
Indices: 418597--418652 Score: 71
Period size: 11 Copynumber: 5.2 Consensus size: 11
418587 AGTAGAAATC
*
418597 AAAAATTAAAA
1 AAAAATCAAAA
*
418608 ATAAAAAC-AAA
1 A-AAAATCAAAA
418619 AAAAATCAAAA
1 AAAAATCAAAA
418630 AAAAATC-AAA
1 AAAAATCAAAA
418640 AAAAATCAAAA
1 AAAAATCAAAA
418651 AA
1 AA
418653 TCAAAGAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
10 15 0.38
11 20 0.51
12 4 0.10
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (11 bp):
AAAAATCAAAA
Found at i:418662 original size:17 final size:18
Alignment explanation
Indices: 418592--418682 Score: 71
Period size: 17 Copynumber: 4.8 Consensus size: 18
418582 TAATAAGTAG
418592 AAATCAAAAATTAAA-AATAA
1 AAATCAAAAA--AAATAA-AA
418612 AAA-CAAAAAAAATCAAAAAA
1 AAATCAAAAAAAAT---AAAA
*
418632 AAATCAAAAAAAATCAAA
1 AAATCAAAAAAAATAAAA
*
418650 AAATC-AAAGAAATAAAA
1 AAATCAAAAAAAATAAAA
418667 AAATTTCAAAAAAAAT
1 AAA--TCAAAAAAAAT
418683 GTGAAAGAAC
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
17 16 0.27
18 8 0.14
19 8 0.14
20 15 0.25
21 12 0.20
ACGTcount: A:0.77, C:0.08, G:0.01, T:0.14
Consensus pattern (18 bp):
AAATCAAAAAAAATAAAA
Found at i:418669 original size:29 final size:28
Alignment explanation
Indices: 418592--418669 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 28
418582 TAATAAGTAG
*
418592 AAATCAAAAATTAAAAATAAAAACAAAAA
1 AAATCAAAAAATAAAAA-AAAAACAAAAA
*
418621 AAATCAAAAAA-AAATCAAAAAAA-ATCAAA
1 AAATCAAAAAATAAA--AAAAAAACA-AAAA
418650 AAATCAAAGAAATAAAAAAA
1 AAATCAAA-AAATAAAAAAA
418670 TTTCAAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
28 4 0.10
29 30 0.71
30 5 0.12
31 3 0.07
ACGTcount: A:0.79, C:0.08, G:0.01, T:0.12
Consensus pattern (28 bp):
AAATCAAAAAATAAAAAAAAAACAAAAA
Found at i:425191 original size:20 final size:20
Alignment explanation
Indices: 425149--425203 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
425139 AAATTCCCAG
**
425149 ATGTATCGATACAAAGATCA
1 ATGTATCGATACATTGATCA
425169 ATGTATCGATACATTGAAT-A
1 ATGTATCGATACATTG-ATCA
*
425189 ATGTATTGATACATT
1 ATGTATCGATACATT
425204 TCCTTGGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTGATCA
Found at i:427127 original size:12 final size:12
Alignment explanation
Indices: 427106--427139 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
427096 TTATGAATGT
*
427106 ATGTGCATGTAC
1 ATGTGTATGTAC
427118 ATGTGTATGTAC
1 ATGTGTATGTAC
*
427130 AAGTGTATGT
1 ATGTGTATGT
427140 TTGTATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.38
Consensus pattern (12 bp):
ATGTGTATGTAC
Found at i:429882 original size:174 final size:170
Alignment explanation
Indices: 429580--429901 Score: 407
Period size: 174 Copynumber: 1.9 Consensus size: 170
429570 GGATAAATTC
* * * * * *
429580 ATTTAATTCATTTTGATTGTTATTTATTTAATTATTTTGCAAAAAATTATTTCGTACTTGACGAA
1 ATTTAATTCATTATGATTATTATTTATTTAATTATTTTGAAAAAAATCATTTCATACCTGACGAA
* *
429645 AAACCGAAAGAATACGAAAAGTTTTAAAGATTTTTATACCCCTACGGAAATCCATAGGAATAATA
66 AAACCGAAAGAATACGAAAAGTTTTAAAGATTTCTATACCCCTACGGAAATCCATAAGAATAATA
429710 GAAATATATAAAAAATGATCAAGTTTATTCTGAAAGGTTGG
131 GAAATAT-TAAAAAATGATCAAGTTTATTCTGAAAGGTTGG
*
429751 ATTTATATT-ATTATGATTATTATTTATTTAATTAATTTTTTTAAAAAAATCATTTCATACCTGA
1 ATTTA-ATTCATTATGATTATTATTTATTTAATT-A--TTTTGAAAAAAATCATTTCATACCTGA
* * * * * * *
429815 -TAGAAATCGAAAGAATACGAAAGGTTTTCGAATATTTCTATACCCTTACGGATAA-CCATAAGA
62 CGAAAAACCGAAAGAATACGAAAAGTTTT-AAAGATTTCTATACCCCTACGGA-AATCCATAAGA
*
429878 ATAATAGAAATATTTAAAAATGAT
125 ATAATAGAAATATTAAAAAATGAT
429902 TGAAATGAAA
Statistics
Matches: 128, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
171 27 0.21
172 4 0.03
173 34 0.27
174 61 0.48
175 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (170 bp):
ATTTAATTCATTATGATTATTATTTATTTAATTATTTTGAAAAAAATCATTTCATACCTGACGAA
AAACCGAAAGAATACGAAAAGTTTTAAAGATTTCTATACCCCTACGGAAATCCATAAGAATAATA
GAAATATTAAAAAATGATCAAGTTTATTCTGAAAGGTTGG
Found at i:430655 original size:10 final size:10
Alignment explanation
Indices: 430640--430697 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
430630 GTAAGACTTT
430640 TTTTTTCTTC
1 TTTTTTCTTC
*
430650 TTTTTTTTTC
1 TTTTTTCTTC
*
430660 TCTCTTTT-TTA
1 T-T-TTTTCTTC
430671 TTTTTT-TTC
1 TTTTTTCTTC
430680 -TTTTTCTCTC
1 TTTTTTCT-TC
430690 TTTTTTCT
1 TTTTTTCT
430698 CACTTGCCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
8 5 0.12
9 7 0.17
10 13 0.32
11 11 0.28
12 4 0.10
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTTCTTC
Found at i:430683 original size:26 final size:27
Alignment explanation
Indices: 430636--430695 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
430626 AGATGTAAGA
*
430636 CTTTTTTTTTCTTCTTTTTTTTTCTCT
1 CTTTTTTTTTCTTCTTTCTTTTTCTCT
430663 CTTTTTTATTT-TT-TTTCTTTTTCTCT
1 CTTTTTT-TTTCTTCTTTCTTTTTCTCT
430689 CTTTTTT
1 CTTTTTT
430696 CTCACTTGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
26 19 0.61
27 9 0.29
28 3 0.10
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.82
Consensus pattern (27 bp):
CTTTTTTTTTCTTCTTTCTTTTTCTCT
Found at i:431515 original size:164 final size:162
Alignment explanation
Indices: 431178--431709 Score: 588
Period size: 164 Copynumber: 3.2 Consensus size: 162
431168 AAAAAAATTC
* * * * ** * * **
431178 AAAACTCA-CAAAATAAATTGAATTTTCTGAAACTGATTTAATGGGAATTCAATGACAATA-TTA
1 AAAACTCATAAAAATAAA-TGAATTTTTTAAAACTGATTTACTATGATTTAAATGATGATATTTA
* * *
431241 GATAAATTTTAAAAATTTTAAACTGAGAAAAATCTCTCCAAAAACATTTATGGAATAGAAAACTC
65 -ATGAATATTAAAAATTTTGAACTGAGAAAAA-C-CTCCAAAAACATTTATGGAATAGAAAACTC
* ** * * *
431306 AGTTTTTTGGAAACAGTGA-AATTTCAAAGAAAAATAA
127 -GATTTTTCAAAACAG-GAGATTTTCAAGGAAAAATGA
431343 AAAACTCATAAAAATAAATGAATTTTTTAAAACTGATTTACTATGATTTAAATGATGATATTTAA
1 AAAACTCATAAAAATAAATGAATTTTTTAAAACTGATTTACTATGATTTAAATGATGATATTTAA
* **
431408 TGAATATTAAAAATTTTGAACTAAGAAAAACCTCCTGAAACTATTTATGGAATAGAAAACTCGAT
66 TGAATATTAAAAATTTTGAACTGAGAAAAACCTCCAAAAAC-ATTTATGGAATAGAAAACTCGAT
431473 TTTTCAAAAGCAGGAGATTTTCAAGGAAAAATGA
130 TTTTCAAAA-CAGGAGATTTTCAAGGAAAAATGA
* * * * *
431507 AAAACTCATAAAAATAAATAAATTTTTTTAAACTGATTTACTATGATATAAACGATGATATTTGA
1 AAAACTCATAAAAATAAATGAATTTTTTAAAACTGATTTACTATGATTTAAATGATGATATTTAA
* *
431572 TGAATATTAAAAATTTTGAACTGAGAAAAACCTTCCAAAAACATTTATTGAATAGAAAAGTC-AC
66 TGAATATTAAAAATTTTGAACTGAGAAAAACC-TCCAAAAACATTTATGGAATAGAAAACTCGA-
* * * *
431636 TTTTTCGAAAATAATG-GATTTTCAAAGAAAAAAAGA
129 TTTTTC-AAAA-CAGGAGATTTTC-AAGGAAAAATGA
** *
431672 AAAACTCATAAAAATAAATGGCTTTTTCAAAACTGATT
1 AAAACTCATAAAAATAAATGAATTTTTTAAAACTGATT
431710 AAATGGTGAT
Statistics
Matches: 316, Mismatches: 42, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
163 20 0.06
164 161 0.51
165 124 0.39
166 11 0.03
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.32
Consensus pattern (162 bp):
AAAACTCATAAAAATAAATGAATTTTTTAAAACTGATTTACTATGATTTAAATGATGATATTTAA
TGAATATTAAAAATTTTGAACTGAGAAAAACCTCCAAAAACATTTATGGAATAGAAAACTCGATT
TTTCAAAACAGGAGATTTTCAAGGAAAAATGA
Found at i:433179 original size:17 final size:17
Alignment explanation
Indices: 433159--433191 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
433149 TTTAATTTAT
433159 AATTATT-CATTCAATTG
1 AATTATTGC-TTCAATTG
433176 AATTATTGCTTCAATT
1 AATTATTGCTTCAATT
433192 AAATAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (17 bp):
AATTATTGCTTCAATTG
Found at i:433977 original size:32 final size:32
Alignment explanation
Indices: 433941--434003 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
433931 AAATATTTTT
433941 AATTTAAAT-TTAATTATAAAT-ATTAATAAAAA
1 AATTTAAATATT-ATTATAAATAATTAA-AAAAA
* *
433973 AATTTTAATATTATTTTAAATAATTAAAAAA
1 AATTTAAATATTATTATAAATAATTAAAAAA
434004 CTTTGACAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 20 0.74
33 7 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
AATTTAAATATTATTATAAATAATTAAAAAAA
Found at i:437100 original size:18 final size:18
Alignment explanation
Indices: 437077--437113 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
437067 TTCATACAGA
437077 GTGAATAATCGTAATTAT
1 GTGAATAATCGTAATTAT
*
437095 GTGAATCATCGTAATTAT
1 GTGAATAATCGTAATTAT
437113 G
1 G
437114 AAATAAGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (18 bp):
GTGAATAATCGTAATTAT
Found at i:441130 original size:17 final size:17
Alignment explanation
Indices: 441086--441145 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
441076 TGACACATTA
* * *
441086 ATATATATATCTTACTT
1 ATATCTATATTTTAATT
441103 ATAT-TATATTTTATATT
1 ATATCTATATTTTA-ATT
*
441120 GTATC-ATATTTTAATT
1 ATATCTATATTTTAATT
441136 ATATCTATAT
1 ATATCTATAT
441146 CTTTTCAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 15 0.42
17 21 0.58
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.57
Consensus pattern (17 bp):
ATATCTATATTTTAATT
Found at i:445081 original size:22 final size:22
Alignment explanation
Indices: 445038--445082 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
445028 ATTCATTCCT
*
445038 AAATTTTAGGAATTGAATTCCC
1 AAATTTTAGGAATTGAACTCCC
* *
445060 AAATTTTAGGTATTTAACTCCC
1 AAATTTTAGGAATTGAACTCCC
445082 A
1 A
445083 CTAGAAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
AAATTTTAGGAATTGAACTCCC
Found at i:448470 original size:33 final size:33
Alignment explanation
Indices: 448428--448492 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
448418 GGGCCAAATG
**
448428 TATCGATACAATT-ATTGTTGTATCGATACAATA
1 TATCGATACAATTCA-TCATGTATCGATACAATA
*
448461 TATCGATACATTTCATCATGTATCGATACAAT
1 TATCGATACAATTCATCATGTATCGATACAAT
448493 TCGATTATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (33 bp):
TATCGATACAATTCATCATGTATCGATACAATA
Found at i:448616 original size:33 final size:32
Alignment explanation
Indices: 448553--448616 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
448543 TATTTTATGG
* *
448553 TGTATCGATACAATGAAAATGTATCGATACAA
1 TGTATCGATACAAAGAAAATGTATCAATACAA
* *
448585 TGTATTGATACAAAGCAATATGTATCAATACA
1 TGTATCGATACAAAG-AAAATGTATCAATACA
448617 TCTGGGTGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (32 bp):
TGTATCGATACAAAGAAAATGTATCAATACAA
Found at i:449227 original size:28 final size:30
Alignment explanation
Indices: 449196--449254 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
449186 AATCGAAACA
449196 TTTC-TTTTATG-AA-CTCTCCTCTATTTGT
1 TTTCATTTTATGCAATCTCTCC-CTATTTGT
*
449224 TTTCATTTTATGCAATCTCTCCCTTTTTGT
1 TTTCATTTTATGCAATCTCTCCCTATTTGT
449254 T
1 T
449255 ATAAAGCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 4 0.15
29 7 0.26
30 10 0.37
31 6 0.22
ACGTcount: A:0.14, C:0.22, G:0.07, T:0.58
Consensus pattern (30 bp):
TTTCATTTTATGCAATCTCTCCCTATTTGT
Found at i:451372 original size:30 final size:30
Alignment explanation
Indices: 451338--451397 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
451328 ATAACCTAAG
451338 CCATCTTTGTCAAAGAATGCTCTTTGAGTT
1 CCATCTTTGTCAAAGAATGCTCTTTGAGTT
451368 CCATCTTTGTCAAAGAATGCTCTTTGAGTT
1 CCATCTTTGTCAAAGAATGCTCTTTGAGTT
451398 TCTAACATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (30 bp):
CCATCTTTGTCAAAGAATGCTCTTTGAGTT
Found at i:451511 original size:22 final size:21
Alignment explanation
Indices: 451482--451533 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
451472 AGTTAATTCA
*
451482 TCATTTTCTTTTTGTAACTCATT
1 TCATTTTCTTTTT-CAACTCA-T
451505 TC-TTTTCTTTTTCAACTCAT
1 TCATTTTCTTTTTCAACTCAT
451525 TCATTTTCT
1 TCATTTTCT
451534 CCTCTAGTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 3 0.11
21 12 0.44
22 10 0.37
23 2 0.07
ACGTcount: A:0.15, C:0.21, G:0.02, T:0.62
Consensus pattern (21 bp):
TCATTTTCTTTTTCAACTCAT
Found at i:452498 original size:426 final size:426
Alignment explanation
Indices: 451705--452536 Score: 1594
Period size: 426 Copynumber: 2.0 Consensus size: 426
451695 GTATTAGAAT
451705 TGTTAGGATCTTGGTTTTGATATAACAAAGGATTGAATAAAACCGAGAATTATTATGAAAATACC
1 TGTTAGGATCTTGGTTTTGATATAACAAAGGATTGAATAAAACCGAGAATTATTATGAAAATACC
*
451770 AAAAATGTGTTTTATTCAATTAAGTACTTTATAAATTTTGTACCAAATGATTTTTGATTCACCAA
66 AAAAATGTGTTTTATTCAATTAAGTACTTTATAAATTTTGTACCAAATGATATTTGATTCACCAA
451835 ATGTTTTCTAGTTAAGTATAAATGTTTTCAAGGCTTAAAATGATTGATTTTTAAGATAAAATATA
131 ATGTTTTCTAGTTAAGTATAAATGTTTTCAAGGCTTAAAATGATTGATTTTTAAGATAAAATATA
*
451900 TCAAAGTATCGATACATAGGTATTTGTATCGAAACATTAAGGTTGACTTAGGCTAAAATGGTCAA
196 TCAAAGTATCAATACATAGGTATTTGTATCGAAACATTAAGGTTGACTTAGGCTAAAATGGTCAA
*
451965 AACCCTTAAAAGTATCGATACACAATTCAAAGTATCGATACATGTTGCAATGTATCGATACATGA
261 AACCCTTAAAAGTATCGATACACAATTCAAAGTATCAATACATGTTGCAATGTATCGATACATGA
452030 AAAATATGTATCGATACATGTCATTGGGATTTCTTGGCAGTAGCCAAACTTGTATCGATACACCA
326 AAAATATGTATCGATACATGTCATTGGGATTTCTTGGCAGTAGCCAAACTTGTATCGATACACCA
452095 AGTATGTATCGATACATCAGAAAAATGTATCGATAC
391 AGTATGTATCGATACATCAGAAAAATGTATCGATAC
* *
452131 TGTTAGGATCTTGGTTTTGATATGACAAAGGATTGAATAAAACCG-GAAATTATTTTGAAAATAC
1 TGTTAGGATCTTGGTTTTGATATAACAAAGGATTGAATAAAACCGAG-AATTATTATGAAAATAC
452195 CAAAAATGTGTTTTATTCAATTAAGTACTTTATAAATTTTGTACCAAATGATATTTGATTCACCA
65 CAAAAATGTGTTTTATTCAATTAAGTACTTTATAAATTTTGTACCAAATGATATTTGATTCACCA
452260 AATGTTTTCTAGTTAAGTATAAATGTTTTCAAGGCTTAAAATGATTGATTTTTAAGATAAAATAT
130 AATGTTTTCTAGTTAAGTATAAATGTTTTCAAGGCTTAAAATGATTGATTTTTAAGATAAAATAT
*
452325 ATCAAAGTATCAATACATAGGTATTTGTATCGATACATTAAGGTTGACTTAGGCTAAAATGGTCA
195 ATCAAAGTATCAATACATAGGTATTTGTATCGAAACATTAAGGTTGACTTAGGCTAAAATGGTCA
452390 AAACCCTTAAAAGTATCGATACACAATTCAAAGTATCAATACATGTTGCAATGTATCGATACATG
260 AAACCCTTAAAAGTATCGATACACAATTCAAAGTATCAATACATGTTGCAATGTATCGATACATG
452455 AAAAATATGTATCGATACATGTCATTGGGATTTCTTGGCAGTAGCCAAACTTGTATCGATACACC
325 AAAAATATGTATCGATACATGTCATTGGGATTTCTTGGCAGTAGCCAAACTTGTATCGATACACC
452520 AAGTATGTATCGATACA
390 AAGTATGTATCGATACA
452537 ATGTATCGAT
Statistics
Matches: 399, Mismatches: 6, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
425 1 0.00
426 398 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (426 bp):
TGTTAGGATCTTGGTTTTGATATAACAAAGGATTGAATAAAACCGAGAATTATTATGAAAATACC
AAAAATGTGTTTTATTCAATTAAGTACTTTATAAATTTTGTACCAAATGATATTTGATTCACCAA
ATGTTTTCTAGTTAAGTATAAATGTTTTCAAGGCTTAAAATGATTGATTTTTAAGATAAAATATA
TCAAAGTATCAATACATAGGTATTTGTATCGAAACATTAAGGTTGACTTAGGCTAAAATGGTCAA
AACCCTTAAAAGTATCGATACACAATTCAAAGTATCAATACATGTTGCAATGTATCGATACATGA
AAAATATGTATCGATACATGTCATTGGGATTTCTTGGCAGTAGCCAAACTTGTATCGATACACCA
AGTATGTATCGATACATCAGAAAAATGTATCGATAC
Found at i:452542 original size:13 final size:13
Alignment explanation
Indices: 452524--452549 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
452514 TACACCAAGT
452524 ATGTATCGATACA
1 ATGTATCGATACA
452537 ATGTATCGATACA
1 ATGTATCGATACA
452550 TCAGAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:452566 original size:33 final size:32
Alignment explanation
Indices: 452506--452569 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
452496 TAGCCAAACT
**
452506 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
*
452538 TGTATCGATACATCAGAAAATGTATCGATACA
1 TGTATCGATACACCA-AAAATGTATCGATACA
452570 TTAGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:453070 original size:34 final size:35
Alignment explanation
Indices: 453007--453073 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
452997 TTAAGTGATT
453007 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
453043 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
453074 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:454194 original size:21 final size:21
Alignment explanation
Indices: 454168--454209 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
454158 AATCAACCGT
* *
454168 TCAAGATGATGATGAAGATGA
1 TCAAGAGGATGATGAAAATGA
*
454189 TCAAGAGGTTGATGAAAATGA
1 TCAAGAGGATGATGAAAATGA
454210 AGAAATGGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.24
Consensus pattern (21 bp):
TCAAGAGGATGATGAAAATGA
Found at i:454771 original size:84 final size:84
Alignment explanation
Indices: 454598--454758 Score: 200
Period size: 84 Copynumber: 1.9 Consensus size: 84
454588 ACTCAAAGAA
* * * * * *
454598 GAAAATAAATCAATAAGTGTAGAGAATGATTTTCTTGAAAAGAAATTAAGTGAATTAGAGAAGAA
1 GAAAATAAATCAATAAGTGTAGAAAATAATTTTCTTAAAAAGAAAATAAATGAAATAGAGAAGAA
*
454663 TATGAAAGAGTTACAAAAT
66 TAAGAAAGAGTTACAAAAT
* * *
454682 GAAAATAAATCAATGAGTTTAGAAAATAATTCTT-TTAAAAAGAAAATAAATGAAATAGAGGAGA
1 GAAAATAAATCAATAAGTGTAGAAAATAATT-TTCTTAAAAAGAAAATAAATGAAATAGAGAAGA
454746 A-AAGAAATGAGTT
65 ATAAGAAA-GAGTT
454759 GCAAGTGGAA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
83 5 0.08
84 58 0.89
85 2 0.03
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.25
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAAAATAATTTTCTTAAAAAGAAAATAAATGAAATAGAGAAGAA
TAAGAAAGAGTTACAAAAT
Found at i:458022 original size:20 final size:19
Alignment explanation
Indices: 457967--458022 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
457957 AAAACCCTTA
*
457967 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
457987 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
458007 AATGTATCGATACATG
1 AAAGTATCGATACATG
458023 AAAAATATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:465061 original size:13 final size:13
Alignment explanation
Indices: 465043--465068 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
465033 ACATCATTCT
465043 TTGTATCGATACA
1 TTGTATCGATACA
465056 TTGTATCGATACA
1 TTGTATCGATACA
465069 GGGGGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:467648 original size:19 final size:21
Alignment explanation
Indices: 467626--467678 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
467616 TAGCCAAACT
*
467626 TGTATCGATACA-C-CAAGTA
1 TGTATCGATACATCACAAATA
*
467645 TGTATCGATACATCAGAAATA
1 TGTATCGATACATCACAAATA
467666 TGTATCGATACAT
1 TGTATCGATACAT
467679 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.40
20 1 0.03
21 17 0.57
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATCACAAATA
Found at i:470214 original size:317 final size:317
Alignment explanation
Indices: 469639--470274 Score: 1060
Period size: 317 Copynumber: 2.0 Consensus size: 317
469629 GTGGGTGAAT
*
469639 TGGTTCTAATGGAAAATTAAAACTTTTGAGACAAGTGTGATAAAAACAAATCGAATAATAAAGAG
1 TGGTTCTAATGAAAAATTAAAACTTTTGAGACAAGTGTGATAAAAACAAATCGAATAATAAAGAG
* * *
469704 AATAAAGGTAAGAGATATCACACACGAGATTTATAGAGGTTCAGTTCAAACACGACACCTAGTCC
66 AATAAAGGTAAGAGATATCACACACAAGATTTATAGAGATTCAGTCCAAACACGACACCTAGTCC
* * *
469769 TTTCTCCTTGGCACTTCCTTGCCAAGTGGTTACCATAATTCACTAATAAAATTATTACCTTTGAG
131 TATCTCCTTGACACTTCCTTGCCAAGTGGTTACCACAATTCACTAATAAAATTATTACCTTTGAG
* * * * *
469834 GCTAAGGTATAACCTTATAACACTATCTTTTTTAAGGCTAAGATAGATTCTCTTCCCTATCTTTT
196 GCTAAGGTATAACCTTACAACACTATCTTTTTGAAGGCTAAGATAAAATCTCTTCCATATCTTTT
* * *
469899 CAAAGGCTAAGATAGAACTTCTCAATCACTTTGAGAATTATACCCAAAATTCTTAAG
261 CAAAGGCTAAGATAAAACCTCTCAATCACTTTGAGAATTATACCCAAAATTCTCAAG
*
469956 TGGTTCTAATGAAAAATTAAAACTTTTGAGATAAGTGTGATAAAAACAAATCGAATAATAAAGAG
1 TGGTTCTAATGAAAAATTAAAACTTTTGAGACAAGTGTGATAAAAACAAATCGAATAATAAAGAG
470021 AATAAAGGTAAGAGATATCACACACAAGATTTATAGAGATTC-GATCCAAACAC-AGCACCTAGT
66 AATAAAGGTAAGAGATATCACACACAAGATTTATAGAGATTCAG-TCCAAACACGA-CACCTAGT
* * *
470084 CCTATCTTCTTGATACTTCCTTGCCAAGTGGTTACCACAATTCACTAATAAAATTGTTACCTTTG
129 CCTATCTCCTTGACACTTCCTTGCCAAGTGGTTACCACAATTCACTAATAAAATTATTACCTTTG
*
470149 AGGCTAAGGTATAATCTTACAACACTATCTTTTTGAAGGCTAAGATAAAATCTCTTCCATATCTT
194 AGGCTAAGGTATAACCTTACAACACTATCTTTTTGAAGGCTAAGATAAAATCTCTTCCATATCTT
470214 TTCAAAGGCTAAGATAAAACCTCTCAATCACTTTGAGAATTATACCCAAAATTCTCAAG
259 TTCAAAGGCTAAGATAAAACCTCTCAATCACTTTGAGAATTATACCCAAAATTCTCAAG
470273 TG
1 TG
470275 ATTGCTAACA
Statistics
Matches: 297, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
316 2 0.01
317 295 0.99
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (317 bp):
TGGTTCTAATGAAAAATTAAAACTTTTGAGACAAGTGTGATAAAAACAAATCGAATAATAAAGAG
AATAAAGGTAAGAGATATCACACACAAGATTTATAGAGATTCAGTCCAAACACGACACCTAGTCC
TATCTCCTTGACACTTCCTTGCCAAGTGGTTACCACAATTCACTAATAAAATTATTACCTTTGAG
GCTAAGGTATAACCTTACAACACTATCTTTTTGAAGGCTAAGATAAAATCTCTTCCATATCTTTT
CAAAGGCTAAGATAAAACCTCTCAATCACTTTGAGAATTATACCCAAAATTCTCAAG
Found at i:471745 original size:1 final size:1
Alignment explanation
Indices: 471741--471825 Score: 53
Period size: 1 Copynumber: 85.0 Consensus size: 1
471731 CTTCTTTTTT
* * * * * * * * * *
471741 AAAAAAAACAAAAAACAAAAAACAAAAAACAAAAAACAAAAAACAAAGAAAACAAAACAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
471806 GAAAACAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAA
471826 TAGAGAAAAG
Statistics
Matches: 58, Mismatches: 26, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.85, C:0.12, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:471755 original size:7 final size:7
Alignment explanation
Indices: 471743--471824 Score: 98
Period size: 7 Copynumber: 11.9 Consensus size: 7
471733 TCTTTTTTAA
471743 AAAAAAC
1 AAAAAAC
471750 AAAAAAC
1 AAAAAAC
471757 AAAAAAC
1 AAAAAAC
471764 AAAAAAC
1 AAAAAAC
471771 AAAAAAC
1 AAAAAAC
471778 AAAAAAC
1 AAAAAAC
471785 AAAGAAA-
1 AAA-AAAC
*
471792 ACAAAAC
1 AAAAAAC
*
471799 -AAAAAG
1 AAAAAAC
*
471805 AGAAAAC
1 AAAAAAC
471812 AAAACAA-
1 AAAA-AAC
471819 AAAAAA
1 AAAAAA
471825 ATAGAGAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
6 9 0.14
7 51 0.78
8 5 0.08
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Done.