Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005024.1 Hibiscus syriacus cultivar Beakdansim tig00011277_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 902903
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
File 2 of 3
Found at i:221551 original size:16 final size:16
Alignment explanation
Indices: 221530--221606 Score: 118
Period size: 16 Copynumber: 4.8 Consensus size: 16
221520 TAATAAATAA
*
221530 ACGAAGATAAACGAAC
1 ACGAACATAAACGAAC
*
221546 ACGAAGATAAACGAAC
1 ACGAACATAAACGAAC
*
221562 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
221578 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
221594 ACGAACATAAACG
1 ACGAACATAAACG
221607 TTGGAGACCC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 58 1.00
ACGTcount: A:0.56, C:0.19, G:0.16, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:226255 original size:2 final size:2
Alignment explanation
Indices: 226248--226273 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
226238 TCATTAACAA
226248 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
226274 GATGTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:229311 original size:79 final size:76
Alignment explanation
Indices: 229174--229316 Score: 173
Period size: 79 Copynumber: 1.8 Consensus size: 76
229164 CAATAAAATA
* *
229174 TTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTGAATTATAATC-TTTAATGT
1 TTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTAAATTACAATCTTTTAATGT
229238 TTATTTAAAAC
66 TTATTTAAAAC
* * * *
229249 TTATTTAATT-ATTCCAAATTATATATACCAATTAAAAGAGTTGTAATCTAAATTACATTCTTTT
1 TTATTTAATTAATT-C-AATTAAATATA-C-ATT-AAAGACTTATAATCTAAATTACAATCTTTT
229313 AATG
61 AATG
229317 CTTACTTACT
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
74 3 0.05
75 11 0.20
76 10 0.18
77 1 0.02
78 3 0.05
79 21 0.38
80 7 0.12
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (76 bp):
TTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTAAATTACAATCTTTTAATGT
TTATTTAAAAC
Found at i:232141 original size:17 final size:17
Alignment explanation
Indices: 232111--232152 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
232101 CTTTTCCCTT
*
232111 TCTTT-GAGAGAAATTC
1 TCTTTCGAGAAAAATTC
232127 TCTTTCGAGAAAAATTC
1 TCTTTCGAGAAAAATTC
232144 -CTGTTCGAG
1 TCT-TTCGAG
232153 CAACAAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (17 bp):
TCTTTCGAGAAAAATTC
Found at i:251518 original size:54 final size:54
Alignment explanation
Indices: 251454--251841 Score: 496
Period size: 54 Copynumber: 7.2 Consensus size: 54
251444 CTTTGGGGCA
* * * *
251454 CACACGTAGTGCAGATGCGGTCATTCATAAACTTATTATGAATTTCGTGGGTTA
1 CACACTTAGTGCAGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTG
* *
251508 CACACTTAGTGCTA-ATACGGTTGTTCATAAACTTATTATGAATTTTGTGGGTTG
1 CACACTTAGTGC-AGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTG
* *
251562 CACACTTAGTACCGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTG
1 CACACTTAGTGCAGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTG
* * * *
251616 CACACTTTGTGCCGATACGGTCTTTCATAAACTTATTATGAATTTAGTGGGTTG
1 CACACTTAGTGCAGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTG
* * *
251670 CACACTTAGTGCCGATACGATCCTTCAT-AACTTATTATGAA-TTCTGTGGGTTG
1 CACACTTAGTGCAGATACGGTCGTTCATAAACTTATTATGAATTTC-GTGGGTTG
* * * * * *
251723 CACACTTAGTGCTGATATGGTCATTAATAAACTTATTATGAATTCCATGGGTTG
1 CACACTTAGTGCAGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTG
* * * *
251777 CACACTTAATGCCA-ATACGGTTGTTCATAAACTTATTATGAATTACGTGGATTG
1 CACACTTAGTG-CAGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTG
251831 CACACTTAGTG
1 CACACTTAGTG
251842 TCGATAGTAC
Statistics
Matches: 293, Mismatches: 35, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
52 2 0.01
53 44 0.15
54 243 0.83
55 4 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (54 bp):
CACACTTAGTGCAGATACGGTCGTTCATAAACTTATTATGAATTTCGTGGGTTG
Found at i:251762 original size:161 final size:162
Alignment explanation
Indices: 251454--251847 Score: 533
Period size: 161 Copynumber: 2.4 Consensus size: 162
251444 CTTTGGGGCA
* * * * * *
251454 CACACGTAGTGCAGATGCGGTCATTCATAAACTTATTATGAATTTCGTGGGTTACACACTTAGTG
1 CACACTTAGTGCCGATACGGTCTTTCATAAACTTATTATGAATTTAGTGGGTTGCACACTTAGTG
** * ** *
251519 CTAATACGGTTGTTCATAAACTTATTATGAATTTTGTGGGTTGCACACTTAGTACCGATACGGTC
66 CCGATACGATCCTTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTACCGATACGGTC
* * * *
251584 GTTCATAAACTTATTATGAATTTCGTGGGTTG
131 ATTAATAAACTTATTATGAATTCCATGGGTTG
*
251616 CACACTTTGTGCCGATACGGTCTTTCATAAACTTATTATGAATTTAGTGGGTTGCACACTTAGTG
1 CACACTTAGTGCCGATACGGTCTTTCATAAACTTATTATGAATTTAGTGGGTTGCACACTTAGTG
* * *
251681 CCGATACGATCCTTCAT-AACTTATTATGAATTCTGTGGGTTGCACACTTAGTGCTGATATGGTC
66 CCGATACGATCCTTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTACCGATACGGTC
251745 ATTAATAAACTTATTATGAATTCCATGGGTTG
131 ATTAATAAACTTATTATGAATTCCATGGGTTG
* * *
251777 CACACTTAATGCCAATACGGT-TGTTCATAAACTTATTATGAA-TTACGTGGATTGCACACTTAG
1 CACACTTAGTGCCGATACGGTCT-TTCATAAACTTATTATGAATTTA-GTGGGTTGCACACTTAG
*
251840 TGTCGATA
64 TGCCGATA
251848 GTACACATAG
Statistics
Matches: 205, Mismatches: 25, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
160 4 0.02
161 131 0.64
162 70 0.34
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (162 bp):
CACACTTAGTGCCGATACGGTCTTTCATAAACTTATTATGAATTTAGTGGGTTGCACACTTAGTG
CCGATACGATCCTTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTACCGATACGGTC
ATTAATAAACTTATTATGAATTCCATGGGTTG
Found at i:258172 original size:54 final size:54
Alignment explanation
Indices: 258062--258468 Score: 528
Period size: 54 Copynumber: 7.5 Consensus size: 54
258052 TCATTAAAAG
* * * * * * *
258062 TTCTTTGGGGTGCACACGTAGTGCCGATATGCTCATTCATAAACTTATTAGGAA
1 TTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAA
* * * * *
258116 TTCTGTGGGTTGAACACTTACTACCGATACGGTTGTTCATAAACTTATTATAAA
1 TTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAA
* *
258170 TTCTATGGGTTGCACACTTAGTGCGGATACGGTCGTTCATAAACTTATTATGAA
1 TTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAA
* * *
258224 TTCTGTGGGTTGCACACTTAGTGTCAATACGGTCGTTCATAAATTTATTATGAA
1 TTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAA
* * * *
258278 TTCCGTGGGTTGCACACTTAGTGCTGATACGGTCATTCATAAACTTATTCTGAA
1 TTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAA
* * *
258332 TTATATGGGTTGCACACTTAGTTCCGATACGGTCGTTCATAAAACTTATTATGAA
1 TTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCAT-AAACTTATTATGAA
* * * * *
258387 TTATGTGGGTTGCAC-CTTAGTGTCGGTATGGTCATTCATAAACTTATTATGAA
1 TTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAA
*
258440 TTCTGTGGGTTGCACACTTAGTGTCGATA
1 TTCTGTGGGTTGCACACTTAGTGCCGATA
258469 GTACACATAA
Statistics
Matches: 305, Mismatches: 46, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
53 28 0.09
54 250 0.82
55 27 0.09
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37
Consensus pattern (54 bp):
TTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAA
Found at i:259619 original size:8 final size:8
Alignment explanation
Indices: 259608--259634 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
259598 CCCTTTCATC
259608 CTTCCATT
1 CTTCCATT
259616 CTTCCATT
1 CTTCCATT
259624 CTTCCATT
1 CTTCCATT
259632 CTT
1 CTT
259635 ACTAATTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.37, G:0.00, T:0.52
Consensus pattern (8 bp):
CTTCCATT
Found at i:266502 original size:182 final size:184
Alignment explanation
Indices: 266195--266561 Score: 720
Period size: 182 Copynumber: 2.0 Consensus size: 184
266185 ACACAAACGA
266195 TATAATAGTTCAAGGACATCACTTCTACTGTTTACACAAACAGTAAAGTAAATATAATGTCACGA
1 TATAATAGTTCAAGGACATCACTTCTACTGTTTACACAAACAGTAAAGTAAATATAATGTCACGA
266260 GAGAAGGTTTAAAGGAGAACACTTACTTATCCTATGAAACTATCGATCATAGAGTCTATCGCCAC
66 GAGAAGGTTTAAAGGAGAACACTTACTTATCCTATGAAACTATCGATCATAGAGTCTATCGCCAC
266325 ATCATGTTTAAATG-TTTTGATAAAATCATCAATTTCA-TCATGTGGGGGATTG
131 ATCATGTTTAAATGTTTTTGATAAAATCATCAATTTCATTCATGTGGGGGATTG
266377 TATAATAGTTCAAGGACATCACTTCTACTGTTTACACAAACAGTAAAGTAAATATAATGTCACGA
1 TATAATAGTTCAAGGACATCACTTCTACTGTTTACACAAACAGTAAAGTAAATATAATGTCACGA
266442 GAGAAGGTTTAAAGGAGAACACTTACTTATCCTATGAAACTATCGATCATAGAGTCTATCGCCAC
66 GAGAAGGTTTAAAGGAGAACACTTACTTATCCTATGAAACTATCGATCATAGAGTCTATCGCCAC
266507 ATCATGTTTAAATGTTTTTGATAAAATCATCAATTTCATTCATGTGGGGGATTG
131 ATCATGTTTAAATGTTTTTGATAAAATCATCAATTTCATTCATGTGGGGGATTG
266561 T
1 T
266562 TGGAAAAAGA
Statistics
Matches: 183, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
182 144 0.79
183 23 0.13
184 16 0.09
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (184 bp):
TATAATAGTTCAAGGACATCACTTCTACTGTTTACACAAACAGTAAAGTAAATATAATGTCACGA
GAGAAGGTTTAAAGGAGAACACTTACTTATCCTATGAAACTATCGATCATAGAGTCTATCGCCAC
ATCATGTTTAAATGTTTTTGATAAAATCATCAATTTCATTCATGTGGGGGATTG
Found at i:268932 original size:32 final size:32
Alignment explanation
Indices: 268873--268933 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
268863 ATCAACATTG
* * *
268873 TATTCAGATAATGCATAGTAGAGTTAGTATTA
1 TATTCAGATAATGCATAGCAAAATTAGTATTA
268905 TATTCAGATAATGCATAGCAAAATTAGTA
1 TATTCAGATAATGCATAGCAAAATTAGTA
268934 GTGCATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.34
Consensus pattern (32 bp):
TATTCAGATAATGCATAGCAAAATTAGTATTA
Found at i:269473 original size:20 final size:20
Alignment explanation
Indices: 269448--269604 Score: 210
Period size: 20 Copynumber: 7.8 Consensus size: 20
269438 TTTTTCGACT
269448 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
269468 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
269488 ATCGCAATGCGAATATATAA
1 ATCGCAATGCGAATATGTAA
* *
269508 ATCGCAATGCGATTATG-ACT
1 ATCGCAATGCGAATATGTA-A
269528 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
** *
269548 ATCGCAATGCGGTTATG-ACT
1 ATCGCAATGCGAATATGTA-A
269568 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
269588 ATCACAATGCGATTATG
1 ATCGCAATGCGAATATG
269605 ACTATCGCAA
Statistics
Matches: 119, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 115 0.97
21 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:269496 original size:40 final size:40
Alignment explanation
Indices: 269444--269614 Score: 281
Period size: 40 Copynumber: 4.3 Consensus size: 40
269434 GCTATTTTTC
*
269444 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAATAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
* *
269484 GTA-AATCGCAATGCGAATATATAAATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
*
269524 GACTATCGCAATGCGAATATGTAAATCGCAATGCGGTTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
*
269564 GACTATCGCAATGCGAATATGTAAATCACAATGCGATTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
269604 GACTATCGCAA
1 GACTATCGCAA
269615 CTCGATTCTG
Statistics
Matches: 121, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
39 1 0.01
40 119 0.98
41 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (40 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
Found at i:269620 original size:20 final size:20
Alignment explanation
Indices: 269444--269634 Score: 153
Period size: 20 Copynumber: 9.6 Consensus size: 20
269434 GCTATTTTTC
*
269444 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
* *
269464 GTA-AATCGCAATGCGAATAT
1 G-ACTATCGCAATGCGATTAT
*
269484 GTA-AATCGCAATGCGAATATAT
1 G-ACTATCGCAATGCG-AT-TAT
*
269506 -A-AATCGCAATGCGATTAT
1 GACTATCGCAATGCGATTAT
*
269524 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
* *
269544 GTA-AATCGCAATGCGGTTAT
1 G-ACTATCGCAATGCGATTAT
*
269564 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
* *
269584 GTA-AATCACAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
*
269604 GACTATCGCAACT-CGATTCT
1 GACTATCGCAA-TGCGATTAT
*
269624 GACTGTCGCAA
1 GACTATCGCAA
269635 CACTGAATTT
Statistics
Matches: 144, Mismatches: 17, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
18 3 0.02
19 5 0.03
20 128 0.89
21 5 0.03
22 3 0.02
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:269627 original size:60 final size:60
Alignment explanation
Indices: 269444--269634 Score: 221
Period size: 60 Copynumber: 3.2 Consensus size: 60
269434 GCTATTTTTC
269444 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAATATGTAAATCGCAATGCGAATATAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAATATGTAAATCGCAATGCG-AT-TAT
* * * *
269506 -A-AATCGCAATGCGATTATG-ACTATCGCAATGCGAATATGTAAATCGCAATGCGGTTAT
1 GACTATCGCAATGCGAATATGTA-AATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
* * * *
269564 GACTATCGCAATGCGAATATGTAAATCACAATGCGATTATG-ACTATCGCAACT-CGATTCT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAATATGTA-AATCGCAA-TGCGATTAT
*
269624 GACTGTCGCAA
1 GACTATCGCAA
269635 CACTGAATTT
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
58 3 0.03
59 4 0.04
60 100 0.91
61 3 0.03
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (60 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
Found at i:270490 original size:24 final size:24
Alignment explanation
Indices: 270439--270492 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
270429 GTATTCAAAA
* *
270439 TTTGATCTTGGTTAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
270463 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
270487 TTTGAT
1 TTTGAT
270493 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:273024 original size:20 final size:20
Alignment explanation
Indices: 272996--273143 Score: 121
Period size: 20 Copynumber: 7.7 Consensus size: 20
272986 GTTTAACATT
*
272996 TTTGTCTATCGCAACGCGAA
1 TTTGACTATCGCAACGCGAA
*
273016 TTTGACTATCGCAACG-GCTA
1 TTTGACTATCGCAACGCG-AA
273036 TTTGACTATCGCAA--C-AA
1 TTTGACTATCGCAACGCGAA
**
273053 ---GAAAATCGCAACGCGAA
1 TTTGACTATCGCAACGCGAA
* * *
273070 TTTGACTATCACAATGCAAA
1 TTTGACTATCGCAACGCGAA
* * *
273090 TTTGAGTATCGCAATGAGAA
1 TTTGACTATCGCAACGCGAA
* * *
273110 TTTGATTATCGCAACGGGTA
1 TTTGACTATCGCAACGCGAA
273130 TTTGACTATCGCAA
1 TTTGACTATCGCAA
273144 TGAGAAAATC
Statistics
Matches: 101, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
14 9 0.09
16 1 0.01
17 3 0.03
19 1 0.01
20 87 0.86
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (20 bp):
TTTGACTATCGCAACGCGAA
Found at i:273120 original size:94 final size:94
Alignment explanation
Indices: 273002--273184 Score: 267
Period size: 94 Copynumber: 1.9 Consensus size: 94
272992 CATTTTTGTC
* *
273002 TATCGCAACGCGAATTTGACTATCGCAACGGCTATTTGACTATCGCAACAAGAAAATCGCAACGC
1 TATCGCAACGAGAATTTGACTATCGCAACGGCTATTTGACTATCGCAACAAGAAAATCGCAAAGC
* *
273067 GAATTTGACTATCACAATGCAAATTTGAG
66 GAATTAGACTATCACAACGCAAATTTGAG
* * * **
273096 TATCGCAATGAGAATTTGATTATCGCAACGGGTATTTGACTATCGCAATGAGAAAATCGCAAAGC
1 TATCGCAACGAGAATTTGACTATCGCAACGGCTATTTGACTATCGCAACAAGAAAATCGCAAAGC
* *
273161 GTATTAGACTATCGCAACGCAAAT
66 GAATTAGACTATCACAACGCAAAT
273185 GACTTTCGCG
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
94 78 1.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (94 bp):
TATCGCAACGAGAATTTGACTATCGCAACGGCTATTTGACTATCGCAACAAGAAAATCGCAAAGC
GAATTAGACTATCACAACGCAAATTTGAG
Found at i:273212 original size:20 final size:20
Alignment explanation
Indices: 273187--273225 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
273177 ACGCAAATGA
*
273187 CTTTCGCGTTGCGATTTTGT
1 CTTTCGCATTGCGATTTTGT
273207 CTTTCGCATTGCGATTTTG
1 CTTTCGCATTGCGATTTTG
273226 AGTTTAGCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.08, C:0.21, G:0.23, T:0.49
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGT
Found at i:273399 original size:14 final size:14
Alignment explanation
Indices: 273339--273400 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
273329 CACAAATAAG
*
273339 AATTATTTACACATC
1 AATT-TTTACAAATC
**
273354 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
273369 AACTTTTACAAATC
1 AATTTTTACAAATC
*
273383 AATTTTTATAAATC
1 AATTTTTACAAATC
273397 AATT
1 AATT
273401 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:275411 original size:18 final size:19
Alignment explanation
Indices: 275388--275433 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
275378 GAAACTTAAA
275388 ATCGCAACACG-AATGACT
1 ATCGCAACACGAAATGACT
*
275406 ATCGCAACGCGAAAATGACT
1 ATCGCAACACG-AAATGACT
275426 ATCGCAAC
1 ATCGCAAC
275434 GAGAGAATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 10 0.40
20 15 0.60
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.15
Consensus pattern (19 bp):
ATCGCAACACGAAATGACT
Found at i:277475 original size:20 final size:20
Alignment explanation
Indices: 277435--277523 Score: 81
Period size: 20 Copynumber: 4.5 Consensus size: 20
277425 TCTGAAACTT
277435 AAAATCGCAACACGAAAAATG
1 AAAATCGCAACACG-AAAATG
277456 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
277476 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** * *
277496 ACTATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
277515 AAAATCGCA
1 AAAATCGCA
277524 TTGCGATTCT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
19 7 0.12
20 38 0.64
21 14 0.24
ACGTcount: A:0.46, C:0.24, G:0.16, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:277936 original size:22 final size:21
Alignment explanation
Indices: 277905--277960 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
277895 GATGGAGATA
277905 GACGGATTTCGCGGGAGATGGG
1 GACGGATTTCGC-GGAGATGGG
*
277927 GACTGATTTCGTCGGAGATGGG
1 GACGGATTTCG-CGGAGATGGG
*
277949 GACGGATGTCGC
1 GACGGATTTCGC
277961 CTTAGAGAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 28 0.93
23 1 0.03
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.21
Consensus pattern (21 bp):
GACGGATTTCGCGGAGATGGG
Found at i:278154 original size:20 final size:20
Alignment explanation
Indices: 278124--278237 Score: 129
Period size: 20 Copynumber: 5.7 Consensus size: 20
278114 GCGCTTTGAA
*
278124 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* * *
278144 CATCGCGTTGCGACAGTCGG
1 AATCGCGTTGCGATAGTCAG
* *
278164 AATCGTGTTGCGATAGTCAA
1 AATCGCGTTGCGATAGTCAG
* *
278184 AATCTCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
278204 AATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
* *
278224 ACTCGCATTGCGAT
1 AATCGCGTTGCGAT
278238 TTACATATTC
Statistics
Matches: 76, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.27
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:278235 original size:60 final size:60
Alignment explanation
Indices: 278122--278261 Score: 165
Period size: 60 Copynumber: 2.3 Consensus size: 60
278112 TGGCGCTTTG
* * **
278122 AAAATCGCATTGCGATAGTCAGCATCGCGTTGCGACAGTCGGAATCGTGTTGCGATAGTC
1 AAAATCGCATTGCGATAGTCAGAATCGCGTTGCGACAGTCAGAATCGCATTGCGATAGTC
* * * * *
278182 AAAATCTCATTGCGATAGTCAGAATCGCGTTGCGATAGTCATACTCGCATTGCGAT-TTAC
1 AAAATCGCATTGCGATAGTCAGAATCGCGTTGCGACAGTCAGAATCGCATTGCGATAGT-C
* *
278242 ATATTCGCATTGCGATAGTC
1 AAAATCGCATTGCGATAGTC
278262 GGAAAATCGC
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
59 1 0.01
60 66 0.99
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (60 bp):
AAAATCGCATTGCGATAGTCAGAATCGCGTTGCGACAGTCAGAATCGCATTGCGATAGTC
Found at i:278255 original size:40 final size:40
Alignment explanation
Indices: 278124--278272 Score: 138
Period size: 40 Copynumber: 3.7 Consensus size: 40
278114 GCGCTTTGAA
** * * *
278124 AATCGCATTGCGATAGTCAGCATCGCGTTGCGACAGTCGG
1 AATCGCATTGCGATAGTCAAAATCGCATTGCGATAGTCAG
** *
278164 AATCGTGTTGCGATAGTCAAAATCTCATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAAAATCGCATTGCGATAGTCAG
* * * * *
278204 AATCGCGTTGCGATAGTCATACTCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGTCAAAATCGCATTGCGATAGT-CAG
*
278244 ATTCGCATTGCGATAGTCGGAAAATCGCA
1 AATCGCATTGCGATAGTC--AAAATCGCA
278273 ACGCGAATTT
Statistics
Matches: 88, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
39 1 0.01
40 80 0.91
42 7 0.08
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (40 bp):
AATCGCATTGCGATAGTCAAAATCGCATTGCGATAGTCAG
Found at i:278371 original size:19 final size:19
Alignment explanation
Indices: 278347--278383 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
278337 CGATACCGGA
*
278347 GATCGCGTTGCGAATTATC
1 GATCGCATTGCGAATTATC
*
278366 GATCGCATTGCGATTTAT
1 GATCGCATTGCGAATTAT
278384 TTGGTCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (19 bp):
GATCGCATTGCGAATTATC
Found at i:283215 original size:22 final size:22
Alignment explanation
Indices: 283189--283242 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
283179 ACTGTATTCG
283189 GGGACGTGTCACTAAATAGTTT
1 GGGACGTGTCACTAAATAGTTT
283211 GGGACGTGTCACTAAATAGTTT
1 GGGACGTGTCACTAAATAGTTT
*
283233 GGGATGTGTC
1 GGGACGTGTC
283243 TCGATGCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.24, C:0.13, G:0.31, T:0.31
Consensus pattern (22 bp):
GGGACGTGTCACTAAATAGTTT
Found at i:291031 original size:34 final size:36
Alignment explanation
Indices: 290958--291033 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 36
290948 AATTTAATCA
*
290958 AAATTA-TAAATATAATAATAATATATAAATAGTTT
1 AAATTATTAAATATAATAATAATATATAAATAATTT
* * *
290993 -AATTATTAAA-ATATTAATAA-ATTTGAATAATTT
1 AAATTATTAAATATAATAATAATATATAAATAATTT
291026 AAATTATT
1 AAATTATT
291034 TTTTAGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 10 0.29
34 21 0.60
35 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (36 bp):
AAATTATTAAATATAATAATAATATATAAATAATTT
Found at i:293851 original size:2 final size:2
Alignment explanation
Indices: 293844--293874 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
293834 ACTTTATTTT
293844 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
293875 TACTTTGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:293943 original size:24 final size:24
Alignment explanation
Indices: 293916--293962 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
293906 TTTATTTCTG
*
293916 TTTTTTAATTTATTAC-TATTATT
1 TTTTTTAATTTAATACTTATTATT
*
293939 TTTTTTATTTTAATACTTATTATT
1 TTTTTTAATTTAATACTTATTATT
293963 ACTATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTTTAATTTAATACTTATTATT
Found at i:305061 original size:43 final size:43
Alignment explanation
Indices: 304978--305061 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
304968 ACGAATAGGC
* * *
304978 CATCCACGATTTCAACTCCACGACGGATGATATCGTACCCACA
1 CATCCACAATTTCAACTCCACGACGGAGGATATCGGACCCACA
* ** *
305021 CATCCACAATTTTAACTTTACGACGGAGGATATTGGACCCA
1 CATCCACAATTTCAACTCCACGACGGAGGATATCGGACCCA
305062 GAGCAATACA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.24
Consensus pattern (43 bp):
CATCCACAATTTCAACTCCACGACGGAGGATATCGGACCCACA
Found at i:306555 original size:24 final size:24
Alignment explanation
Indices: 306523--306574 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
306513 TTTCTTTTAT
*
306523 TTATGTTTTTTTA-TTTATTAC-TA
1 TTAT-TTTTTTTATTTTAATACTTA
306546 TTATTTTTTTTATTTTAATACTTA
1 TTATTTTTTTTATTTTAATACTTA
306570 TTATT
1 TTATT
306575 ACTATTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 8 0.31
23 11 0.42
24 7 0.27
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (24 bp):
TTATTTTTTTTATTTTAATACTTA
Found at i:306810 original size:24 final size:23
Alignment explanation
Indices: 306783--306833 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
306773 ATTTATTTTG
*
306783 TATTTTCT-TTGTATTTTTTCTCAT
1 TATTTT-TATTGT-TTTTTTATCAT
*
306807 TATTTTTATTGTTTTTTTATTAT
1 TATTTTTATTGTTTTTTTATCAT
306830 TATT
1 TATT
306834 AGATTCGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.75
Consensus pattern (23 bp):
TATTTTTATTGTTTTTTTATCAT
Found at i:308196 original size:9 final size:9
Alignment explanation
Indices: 308182--308214 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
308172 TGTTAAATTT
308182 TAAAATAAA
1 TAAAATAAA
308191 TAAAATAAA
1 TAAAATAAA
308200 T-AAATAAA
1 TAAAATAAA
308208 TAAAATA
1 TAAAATA
308215 TTTAAAGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
TAAAATAAA
Found at i:308321 original size:34 final size:34
Alignment explanation
Indices: 308278--308348 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
308268 AAGTGAACTG
308278 CAAGAGAAAAACAAAAGGTTAGGAGACCAAATTA
1 CAAGAGAAAAACAAAAGGTTAGGAGACCAAATTA
*
308312 CAAGAGAAAAACAAAAGGTTAGGAGACGAAATTA
1 CAAGAGAAAAACAAAAGGTTAGGAGACCAAATTA
308346 CAA
1 CAA
308349 AATATAAGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.56, C:0.11, G:0.21, T:0.11
Consensus pattern (34 bp):
CAAGAGAAAAACAAAAGGTTAGGAGACCAAATTA
Found at i:309537 original size:2 final size:2
Alignment explanation
Indices: 309504--309560 Score: 63
Period size: 2 Copynumber: 31.5 Consensus size: 2
309494 TTAAATAAAA
*
309504 AT AT A- AT AA AT A- AT AT AT A- AT AT -T AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
309541 AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT A
309561 CTTGTAATAC
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
1 6 0.13
2 41 0.87
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:310882 original size:54 final size:54
Alignment explanation
Indices: 310818--311089 Score: 411
Period size: 54 Copynumber: 5.0 Consensus size: 54
310808 AATTTATATG
*
310818 TTGTGAATTACCGTATCGGCACTATGTGTGCAACCCATGTAATTCATAATGAGT
1 TTGTGAATTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGT
* *
310872 TTGTGAATTACCGTATCGACACTATGTGTGCAACCCATGTAATTCATAATGAGT
1 TTGTGAATTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGT
* *
310926 TTATGAATTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATTAGT
1 TTGTGAATTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGT
* * *
310980 TTGTGAATTACCATATCGACACTATGTGTGCAACTCACGTAATTCATAATGAGT
1 TTGTGAATTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGT
* * * *
311034 TTGTAAATTACCGTATCGAG-ACTATGTGTGCAAAACCACATAATTTATAATGAGT
1 TTGTGAATTACCGTATCG-GCACTATGTGTGC-AACCCACGTAATTCATAATGAGT
311089 T
1 T
311090 AAATATTAAA
Statistics
Matches: 199, Mismatches: 17, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
54 179 0.90
55 20 0.10
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (54 bp):
TTGTGAATTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGT
Found at i:317668 original size:54 final size:54
Alignment explanation
Indices: 317583--317885 Score: 410
Period size: 54 Copynumber: 5.6 Consensus size: 54
317573 AATGTATATG
* *
317583 TTGTGAATTACCATATCGACTCTATATGTGCAACCCACGTAATTCATAATTAGT
1 TTGTGAATTACCATATCGACACTATGTGTGCAACCCACGTAATTCATAATTAGT
* * * *
317637 TTATGAATTACCGTGTCGGCACTATGTGTGCAACCCACGTAATTCATAATTAGT
1 TTGTGAATTACCATATCGACACTATGTGTGCAACCCACGTAATTCATAATTAGT
* * * * *
317691 TTGTGAATTATCATATCGACACTATGTGTGCAACCAATGTAATTCATTATGAGT
1 TTGTGAATTACCATATCGACACTATGTGTGCAACCCACGTAATTCATAATTAGT
* * * *
317745 TTGTGATTTACCGTATC-AGCACTATGTATGCTACCCACGTAATTCATAATTAGT
1 TTGTGAATTACCATATCGA-CACTATGTGTGCAACCCACGTAATTCATAATTAGT
* * *
317799 TTGTGAATTACCCTATCGACACTATGCGTGCAACCCACGTAATTCATAATGAGT
1 TTGTGAATTACCATATCGACACTATGTGTGCAACCCACGTAATTCATAATTAGT
* *
317853 TTATAAATTACCATATCGACACTATGTGTGCAA
1 TTGTGAATTACCATATCGACACTATGTGTGCAA
317886 AACCATGAAA
Statistics
Matches: 213, Mismatches: 34, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
53 1 0.00
54 211 0.99
55 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (54 bp):
TTGTGAATTACCATATCGACACTATGTGTGCAACCCACGTAATTCATAATTAGT
Found at i:318397 original size:2 final size:2
Alignment explanation
Indices: 318390--319331 Score: 664
Period size: 2 Copynumber: 541.0 Consensus size: 2
318380 AATATAAAAT
318390 TA TA TA TA -A TA TA TA TA -A TA TA -A TA T- TA TA TA CTA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
318428 TA TA -A TT TA TA TA -A TA TA -A TA TA TA -A TA TA CA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
318465 TA TG TA CTA TA TA -A TA TA TA -A TA TA TA CTA CTA TA AA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA -TA TA TA TA TA
318506 TA TA -A TA T- TA -A TA TA TA -A TA TA TA -A TA TA -A TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
318541 TA TA -A TA TA TA TA -A TA TA TA TA -A TA TA -A TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
318578 GA TA TA -A TA TA -A TA TA -A TA TA -A TA TA -A TA TA -A TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
318614 TA TA -A TA TA -A TA -A TA TA -A TA TA -A TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
318650 TA AA TA -A TA -A TA TA TA -A TA TA -A TA TA TA -A TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
318686 TA -A TA TA -A TA TA -A TA TA -A TA TA -A TA TA TA TA -A TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
318721 TA TA TA TA -A TA TA -A TA TA -A TA TA -A TA TA -A TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
318757 TA TA TA -A TA TA TA TA AA TA CTA TA TA -A TA -A TA AA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
318796 TA -A TA TA TA TA TA TA -A TA TA -A TA TA TA -A TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
318833 -A TA -A TA TA -A TA TA -A TA TA -A TA TA -A TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
318868 TA TA -A TA TA -A TA TA -A TA TA -A TA TA -A TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
318904 TA TA -A TA TA -A TA -A TA TA TA TA -A TA TA -A TA TA -A TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
318940 TA TA -A TA TA -A TA TA TA -A TA TA -A TA TA -A TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
318977 -A TA TA -A TA TA -A TA T- TA CTA -A TA TA -A TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
319013 TA -A TA TA -A TA TA -A TA TA -A TA TA -A TA TA -A TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
319048 TA -A TA TA AA TA TA -A TA TA -A TA TA -A TA TA -A TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
319084 TA TA TA -A TA TA -A TA -A TA -A TA TA -A TA TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
319121 TA TA -A TA TA TA -A TA TA -A TA TA TA TA AA TA GA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
319159 TA TA -A TA TA -A TA TA -A TA TA -A TA TA -A TA TA -A TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
319194 TA TA -A TA TA -A TA TA -A TA -A TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
319231 TA TA -A TA TA -A TA TA TA -A TA TA -A TA TA TA TA -A TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
319267 TA TA TA -A TA TA -A TA TA -A T- TA -A TA TA -A TA -A TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
319301 TA TA -A TA TA -A TA TA -A TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
319332 ATAACATCTT
Statistics
Matches: 757, Mismatches: 32, Indels: 302
0.69 0.03 0.28
Matches are distributed among these distances:
1 146 0.19
2 598 0.79
3 13 0.02
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (2 bp):
TA
Found at i:318401 original size:5 final size:5
Alignment explanation
Indices: 318378--319334 Score: 1135
Period size: 5 Copynumber: 189.2 Consensus size: 5
318368 TTACAATACC
* * *
318378 ATAAT ATAAA ATTATAT ATAAT AT-AT ATAAT ATAAT ATTAT ATACT ATAAT
1 ATAAT ATAAT A-TA-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* *
318429 ATAAT -TTAT ATAAT ATAATAT ATAAT ATACAT ATAAT AT-GT ACT-AT
1 ATAAT ATAAT ATAAT AT-A-AT ATAAT ATA-AT ATAAT ATAAT A-TAAT
*
318475 ATAAT AT-AT AATATAT ACTACT ATAA- ATATAT ATAAT ATTAAT AT-AT
1 ATAAT ATAAT -ATA-AT A-TAAT ATAAT ATA-AT ATAAT A-TAAT ATAAT
318522 A-ATAT ATAAT ATAAT ATAAT ATAAT AT-AT ATAAT AT-AT ATAAT ATAAT
1 ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
318570 ATAAT ATAGAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-AAT ATAAT
1 ATAAT ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
318620 AT-A- ATAAT ATAAT ATAAT ATAAT ATATAT ATAA- ATAAT A-ATAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT ATA-AT ATAAT
318668 ATAATAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT ATAAT
1 AT-A-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
318719 AATATAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT ATAAT AT-AT
1 -ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
318769 ATAA- ATACTAT ATAAT AATAA- ATAAT ATAAT AT-AT AT-AT ATAAT
1 ATAAT ATA--AT ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
318813 ATAATAT ATAAT ATAAT AT-A- ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT
1 AT-A-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
318862 ATAATAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATATAT ATAAT
1 AT-A-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT
318910 ATAAT AATATAT ATAAT ATAAT ATAAT A-AAT ATAAT ATAATAT ATAAT
1 ATAAT -ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT AT-A-AT ATAAT
*
318958 ATAAT ATAAT ATATAA ATAAT ATAAT ATAAT AT--T ACTAAT ATAAT ATAAT
1 ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT ATAAT
319008 AT-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AAT
319058 ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT ATAAT ATAAT AATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT
*
319108 ATAA- AT-AT ATATAT ATAATAT ATAAT ATAAT AT-AT ATAAAT AGATAT
1 ATAAT ATAAT ATA-AT AT-A-AT ATAAT ATAAT ATAAT AT-AAT ATA-AT
319155 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
319205 ATAAT A-ATAT ATATAT ATATAT ATAAT ATAAT ATAATAT ATAAT ATAAT
1 ATAAT ATA-AT ATA-AT ATA-AT ATAAT ATAAT AT-A-AT ATAAT ATAAT
319254 AT-AT ATAAT ATAATAT ATAAT ATAAT ATAAT -TAAT AT-A- ATAAT ATAAT
1 ATAAT ATAAT AT-A-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
319302 ATAAT ATAAT ATAAT ATATAT ATAAAT ATAAT A
1 ATAAT ATAAT ATAAT ATA-AT AT-AAT ATAAT A
319335 ACATCTTGAG
Statistics
Matches: 854, Mismatches: 16, Indels: 164
0.83 0.02 0.16
Matches are distributed among these distances:
3 9 0.01
4 102 0.12
5 579 0.68
6 116 0.14
7 48 0.06
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:322309 original size:25 final size:25
Alignment explanation
Indices: 322253--322309 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
322243 TTAACTTGAC
*
322253 AAACACGAACGAAACTCACTTCATA
1 AAACTCGAACGAAACTCACTTCATA
322278 AAACTCGAACGAAACTCACTTCATA
1 AAACTCGAACGAAACTCACTTCATA
*
322303 AAGCTCG
1 AAACTCG
322310 GACATTACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.44, C:0.28, G:0.11, T:0.18
Consensus pattern (25 bp):
AAACTCGAACGAAACTCACTTCATA
Found at i:324364 original size:24 final size:24
Alignment explanation
Indices: 324332--324384 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
324322 GATAGTTACA
*
324332 GAAGCTTGTACTTTTACAGCCGAT
1 GAAGCTTGTACTTTTACAGCAGAT
* *
324356 GAAGCTTGTGCTTTTGCAGCAGAT
1 GAAGCTTGTACTTTTACAGCAGAT
324380 GAAGC
1 GAAGC
324385 CTATGCTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (24 bp):
GAAGCTTGTACTTTTACAGCAGAT
Found at i:324391 original size:24 final size:24
Alignment explanation
Indices: 324342--324400 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
324332 GAAGCTTGTA
* * * *
324342 CTTTTACAGCCGATGAAGCTTGTG
1 CTTTTGCAGCAGATGAAGCCTATG
324366 CTTTTGCAGCAGATGAAGCCTATG
1 CTTTTGCAGCAGATGAAGCCTATG
*
324390 CTTTTGAAGCA
1 CTTTTGCAGCA
324401 TGTGAGTCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (24 bp):
CTTTTGCAGCAGATGAAGCCTATG
Found at i:326889 original size:18 final size:18
Alignment explanation
Indices: 326866--326900 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
326856 GTGAGTTAAG
326866 AATAATAATCAAAATAAT
1 AATAATAATCAAAATAAT
*
326884 AATAATAATGAAAATAA
1 AATAATAATCAAAATAA
326901 AAATTCCTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (18 bp):
AATAATAATCAAAATAAT
Found at i:329234 original size:22 final size:20
Alignment explanation
Indices: 329221--329345 Score: 83
Period size: 19 Copynumber: 6.6 Consensus size: 20
329211 TAAATGTTAT
329221 ATAAA-AATATAATAAA-TA
1 ATAAATAATATAATAAATTA
329239 ATAAATAATATAATAAA-TA
1 ATAAATAATATAATAAATTA
*
329258 AT-AAT-ATAT-ATATATATA
1 ATAAATAATATAATAAAT-TA
*
329276 ATATATAATATAATATAA-TA
1 ATAAATAATATAATA-AATTA
* * *
329296 ATATATACTAT-ATATA-T-
1 ATAAATAATATAATAAATTA
*
329313 ATATATAATAT-ATATAATATA
1 ATAAATAATATAATA-AAT-TA
329334 ATAAATAATATA
1 ATAAATAATATA
329346 TATATATTAT
Statistics
Matches: 87, Mismatches: 8, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
16 4 0.05
17 17 0.20
18 15 0.17
19 20 0.23
20 17 0.20
21 13 0.15
22 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAAATAATATAATAAATTA
Found at i:329241 original size:7 final size:7
Alignment explanation
Indices: 329229--329343 Score: 69
Period size: 7 Copynumber: 15.9 Consensus size: 7
329219 ATATAAAAAT
329229 ATAATAA
1 ATAATAA
329236 ATAATAA
1 ATAATAA
329243 ATAAT--
1 ATAATAA
329248 ATAATAA
1 ATAATAA
329255 ATAAT-A
1 ATAATAA
*
329261 AT-ATAT
1 ATAATAA
329267 ATATATATA
1 ATA-ATA-A
329276 ATATATAA
1 ATA-ATAA
329284 TATAATATA
1 -ATAATA-A
*
329293 ATAATAT
1 ATAATAA
* *
329300 ATACTAT
1 ATAATAA
*
329307 AT-ATAT
1 ATAATAA
329313 ATATATAA
1 ATA-ATAA
329321 TATATATAA
1 -ATA-ATAA
329330 TATAATAA
1 -ATAATAA
329338 ATAATA
1 ATAATA
329344 TATATATATT
Statistics
Matches: 91, Mismatches: 6, Indels: 22
0.76 0.05 0.18
Matches are distributed among these distances:
5 7 0.08
6 10 0.11
7 31 0.34
8 20 0.22
9 23 0.25
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (7 bp):
ATAATAA
Found at i:329253 original size:15 final size:15
Alignment explanation
Indices: 329229--329343 Score: 92
Period size: 17 Copynumber: 7.2 Consensus size: 15
329219 ATATAAAAAT
329229 ATAATAAATAATA-A
1 ATAATAAATAATATA
329243 ATAATATAATAA-ATA
1 ATAATA-AATAATATA
329258 ATAATATATATATATATA
1 ATAATA-A-ATA-ATATA
329276 ATATATAATATAATATA
1 ATA-ATAA-ATAATATA
* *
329293 ATAATATATACTATA
1 ATAATAAATAATATA
*
329308 TATATATATATAATATA
1 -ATA-ATAAATAATATA
329325 TATAATATAATAA-ATA
1 -ATAATA-AATAATATA
329341 ATA
1 ATA
329344 TATATATATT
Statistics
Matches: 88, Mismatches: 4, Indels: 17
0.81 0.04 0.16
Matches are distributed among these distances:
14 7 0.08
15 24 0.27
16 15 0.17
17 28 0.32
18 11 0.12
19 3 0.03
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (15 bp):
ATAATAAATAATATA
Found at i:329268 original size:2 final size:2
Alignment explanation
Indices: 329261--329356 Score: 104
Period size: 2 Copynumber: 52.5 Consensus size: 2
329251 ATAAATAATA
329261 AT AT AT AT AT AT AT A- AT AT AT A- AT AT A- AT AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
329298 AT AT ACT AT AT AT AT AT AT AT A- AT AT AT AT A- AT AT A- AT AA
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
329338 AT A- AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT A
329357 CCATCGTTGA
Statistics
Matches: 81, Mismatches: 2, Indels: 22
0.77 0.02 0.21
Matches are distributed among these distances:
1 10 0.12
2 69 0.85
3 2 0.02
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:329289 original size:42 final size:41
Alignment explanation
Indices: 329227--329356 Score: 175
Period size: 42 Copynumber: 3.3 Consensus size: 41
329217 TTATATAAAA
329227 ATATA-ATA-AATAATAA-ATAATATAATAAATAATAATAT
1 ATATATATATAATAATAATATAATATAATAAATAATAATAT
*
329265 ATATATATATAATATATAATATAATATAAT-AATATATACTAT
1 ATATATATATAATA-ATAATATAATATAATAAATA-ATAATAT
329307 ATATATATAT-ATAATATATATAATATAATAAATAAT-ATAT
1 ATATATATATAATAATA-ATATAATATAATAAATAATAATAT
329347 ATATAT-TATA
1 ATATATATATA
329357 CCATCGTTGA
Statistics
Matches: 82, Mismatches: 2, Indels: 14
0.84 0.02 0.14
Matches are distributed among these distances:
38 5 0.06
39 6 0.07
40 16 0.20
41 25 0.30
42 30 0.37
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (41 bp):
ATATATATATAATAATAATATAATATAATAAATAATAATAT
Found at i:339328 original size:20 final size:20
Alignment explanation
Indices: 339303--339344 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
339293 TTTAGGTATC
*
339303 GATATTAAGCCTTCGATATG
1 GATATTAAGCCTCCGATATG
*
339323 GATATTAATCCTCCGATATG
1 GATATTAAGCCTCCGATATG
339343 GA
1 GA
339345 GACCAGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (20 bp):
GATATTAAGCCTCCGATATG
Found at i:341109 original size:25 final size:26
Alignment explanation
Indices: 341081--341131 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
341071 AAGAGGAGAA
341081 GAAGAAGAAGAA-AATATG-AAGAAAT
1 GAAGAAGAA-AAGAATATGAAAGAAAT
*
341106 GAAGAGGAAAAGAATATGAAAGAAAT
1 GAAGAAGAAAAGAATATGAAAGAAAT
341132 AAATAGGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 2 0.09
25 14 0.61
26 7 0.30
ACGTcount: A:0.63, C:0.00, G:0.25, T:0.12
Consensus pattern (26 bp):
GAAGAAGAAAAGAATATGAAAGAAAT
Found at i:342467 original size:23 final size:23
Alignment explanation
Indices: 342441--342492 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
342431 GATCAGTATA
* *
342441 TATATAT-ATATATATATGACATG
1 TATATATGAT-TATAAATAACATG
*
342464 TATATATGATTTTAAATAACATG
1 TATATATGATTATAAATAACATG
342487 TATATA
1 TATATA
342493 CTAAATAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (23 bp):
TATATATGATTATAAATAACATG
Found at i:345043 original size:15 final size:15
Alignment explanation
Indices: 345023--345063 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
345013 AAAAAGGAAA
345023 AAATAATAAAATAAT
1 AAATAATAAAATAAT
*
345038 AAATAATAATAGTAAT
1 AAATAATAA-AATAAT
345054 AAA-AATAAAA
1 AAATAATAAAA
345064 ATAAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 1 0.04
15 14 0.61
16 8 0.35
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (15 bp):
AAATAATAAAATAAT
Found at i:348055 original size:5 final size:5
Alignment explanation
Indices: 348045--348146 Score: 53
Period size: 5 Copynumber: 20.0 Consensus size: 5
348035 ATGTTCAGAA
* ** * *
348045 AAAAT AAAAT AAAAT TAGTT AAAAT AAAAT -AAAT AGAAT GAAAAT AAAGT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT
**** * * * *
348095 TTGCT AAAAAT AAAAT AAAAT GAAAAT AAAAC GAAAT AAAGT AAAAC AAAAT
1 AAAAT -AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
348147 GGGTTGTCTC
Statistics
Matches: 68, Mismatches: 25, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
4 4 0.06
5 54 0.79
6 10 0.15
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:351110 original size:15 final size:15
Alignment explanation
Indices: 351090--351130 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
351080 AAGAAGGGAC
351090 AAATAATAAAATAAT
1 AAATAATAAAATAAT
*
351105 AAATAATAATAGTAAT
1 AAATAATAA-AATAAT
351121 AAA-AATAAAA
1 AAATAATAAAA
351131 GGGATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 1 0.04
15 14 0.61
16 8 0.35
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (15 bp):
AAATAATAAAATAAT
Found at i:351112 original size:18 final size:18
Alignment explanation
Indices: 351091--351128 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
351081 AGAAGGGACA
351091 AATAATA-AAATAATAAAT
1 AATAATAGAAATAA-AAAT
*
351109 AATAATAGTAATAAAAAT
1 AATAATAGAAATAAAAAT
351127 AA
1 AA
351129 AAGGGATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
AATAATAGAAATAAAAAT
Found at i:352941 original size:21 final size:18
Alignment explanation
Indices: 352910--353000 Score: 111
Period size: 17 Copynumber: 5.2 Consensus size: 18
352900 GATTAATACC
*
352910 CTAGTTT-AATGAATGAA
1 CTAGTTTGATTGAATGAA
352927 CTAGTTTGATT-AATGAA
1 CTAGTTTGATTGAATGAA
352944 CTAGCTTT-ATTGAATGAA
1 CTAG-TTTGATTGAATGAA
352962 CTAGTTTGATT-AATGAA
1 CTAGTTTGATTGAATGAA
*
352979 CTAGCTTT-ATTCAATGAA
1 CTAG-TTTGATTGAATGAA
352997 CTAG
1 CTAG
353001 ATGCATGAAT
Statistics
Matches: 67, Mismatches: 1, Indels: 11
0.85 0.01 0.14
Matches are distributed among these distances:
17 36 0.54
18 31 0.46
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.38
Consensus pattern (18 bp):
CTAGTTTGATTGAATGAA
Found at i:352961 original size:35 final size:35
Alignment explanation
Indices: 352910--353000 Score: 157
Period size: 35 Copynumber: 2.6 Consensus size: 35
352900 GATTAATACC
*
352910 CTAG-TTTAATGAATGAACTAGTTTGATTAATGAA
1 CTAGCTTTATTGAATGAACTAGTTTGATTAATGAA
352944 CTAGCTTTATTGAATGAACTAGTTTGATTAATGAA
1 CTAGCTTTATTGAATGAACTAGTTTGATTAATGAA
*
352979 CTAGCTTTATTCAATGAACTAG
1 CTAGCTTTATTGAATGAACTAG
353001 ATGCATGAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
34 4 0.07
35 50 0.93
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.38
Consensus pattern (35 bp):
CTAGCTTTATTGAATGAACTAGTTTGATTAATGAA
Found at i:353010 original size:52 final size:52
Alignment explanation
Indices: 352910--353013 Score: 131
Period size: 52 Copynumber: 2.0 Consensus size: 52
352900 GATTAATACC
* **
352910 CTAGTTTAATGAATGAACTAGTTTGATTAATGAACTAGCTTTATTGAATGAA
1 CTAGTTTAATGAATGAACTAGTTTGATTAATGAACTAGATGCATTGAATGAA
* *
352962 CTAGTTTGATTAATGAACTAGCTTT-ATTCAATGAACTAGATGCA-TGAATGAA
1 CTAGTTTAATGAATGAACTAG-TTTGATT-AATGAACTAGATGCATTGAATGAA
353014 TTAGCTTACT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
52 30 0.67
53 15 0.33
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (52 bp):
CTAGTTTAATGAATGAACTAGTTTGATTAATGAACTAGATGCATTGAATGAA
Found at i:353029 original size:52 final size:52
Alignment explanation
Indices: 352921--353029 Score: 116
Period size: 52 Copynumber: 2.1 Consensus size: 52
352911 TAGTTTAATG
* ** * *
352921 AATGAACTAGTTTGATTAATGAACTAGCTTTATTGAATGAACTAGTTTGATT
1 AATGAACTAGTTTGATTAATGAACTAGATGCATTGAATGAACTAGCTTGATA
*
352973 AATGAACTAGCTTT-ATTCAATGAACTAGATGCA-TGAATGAATTAGCTT-ACTA
1 AATGAACTAG-TTTGATT-AATGAACTAGATGCATTGAATGAACTAGCTTGA-TA
353025 AATGA
1 AATGA
353030 TCTAAATATG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
51 1 0.02
52 32 0.67
53 15 0.31
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (52 bp):
AATGAACTAGTTTGATTAATGAACTAGATGCATTGAATGAACTAGCTTGATA
Found at i:361597 original size:94 final size:95
Alignment explanation
Indices: 361426--361619 Score: 259
Period size: 94 Copynumber: 2.1 Consensus size: 95
361416 TACTTATGGG
* * *
361426 GTATCAATACTAAAAGAAAAGTATCGATACCATGGATTCTAGAATGCCAAAATGGTATCGATATT
1 GTATCAAAACTAAAAGAAAAGTATCGATACCATGGATTCAAGAATGCCAAAATGGTATCAATATT
* *
361491 GAAAGGGAGTATCGGTACCATAGTATATAA
66 GAAAGGGAGTATCAGTACCATAGTATAGAA
* * ** *
361521 GTATCAAAACTAGAAGAAGAGTATCGATACTGTGGA-TCAAGAATG-TAGAAATGGTATCAATAC
1 GTATCAAAACTAAAAGAAAAGTATCGATACCATGGATTCAAGAATGCCA-AAATGGTATCAATA-
361584 TT-AAAGGGAGTATCAGTACCATAGTATAGAA
64 TTGAAAGGGAGTATCAGTACCATAGTATAGAA
361615 GTATC
1 GTATC
361620 GATACCATGG
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
93 1 0.01
94 53 0.61
95 33 0.38
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (95 bp):
GTATCAAAACTAAAAGAAAAGTATCGATACCATGGATTCAAGAATGCCAAAATGGTATCAATATT
GAAAGGGAGTATCAGTACCATAGTATAGAA
Found at i:362709 original size:32 final size:34
Alignment explanation
Indices: 362648--362715 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
362638 ATTCTTCTGA
362648 ATACCTAACCTTCATCTAAGAAATGGACATTTCC
1 ATACCTAACCTTCATCTAAGAAATGGACATTTCC
362682 ATACCTAACCTTCATCT-A-AAATGGACATTTCC
1 ATACCTAACCTTCATCTAAGAAATGGACATTTCC
362714 AT
1 AT
362716 GCCTCTTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 16 0.47
33 1 0.03
34 17 0.50
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.31
Consensus pattern (34 bp):
ATACCTAACCTTCATCTAAGAAATGGACATTTCC
Found at i:362815 original size:24 final size:24
Alignment explanation
Indices: 362771--362820 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
362761 ATAAAGAACC
*
362771 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
362795 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
362819 AA
1 AA
362821 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:372497 original size:55 final size:55
Alignment explanation
Indices: 372292--372475 Score: 305
Period size: 55 Copynumber: 3.3 Consensus size: 55
372282 TACCAAATGA
* * *
372292 CACTATGTGTGCAAAACTAACAAGTTCATAATAAGTTTATGAATTTCCATATGGC
1 CACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATGGC
* *
372347 CACTTTGTGAGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATGGC
1 CACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATGGC
* *
372402 CACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGG
1 CACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATGGC
372457 CACTGTGTGTGCAAAACTA
1 CACTGTGTGTGCAAAACTA
372476 TAAGTTTATG
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 121 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (55 bp):
CACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATGGC
Found at i:372497 original size:110 final size:98
Alignment explanation
Indices: 372396--372593 Score: 235
Period size: 97 Copynumber: 2.0 Consensus size: 98
372386 TGAATTTCCA
*
372396 TATGGCCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACT
1 TATGGGCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACT
* * * **
372461 GTGTGTGCAAAACT-ATAAGTTTATGAAT-TTTCT
66 GTGTGTGCAAAACTAAGAAATTCAT-AATAAGT-T
* *
372494 TATGGGTACTGT-T-TGCCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCAC
1 TATGGGCACTGTGTGTG-CAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAC
* * *
372557 TGTGTGTGC-AAATTAAAAAATTCCTAATAAGTT
65 TGTGTGTGCAAAACTAAGAAATTCATAATAAGTT
372590 TATG
1 TATG
372594 AATTTACGTA
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
96 14 0.16
97 63 0.72
98 10 0.11
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (98 bp):
TATGGGCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACT
GTGTGTGCAAAACTAAGAAATTCATAATAAGTT
Found at i:372498 original size:43 final size:42
Alignment explanation
Indices: 372432--372517 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 42
372422 GAAATTCATA
372432 ATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTG-CAAAACT
1 ATAAGTTTATGAATTTCCGTATGGGCACTGT-T-TGCCAAAACT
* * *
372475 ATAAGTTTATGAATTTTCTTATGGGTACTGTTTGCCAAAACT
1 ATAAGTTTATGAATTTCCGTATGGGCACTGTTTGCCAAAACT
372517 A
1 A
372518 AGAAATTCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
41 2 0.05
42 9 0.23
43 28 0.72
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (42 bp):
ATAAGTTTATGAATTTCCGTATGGGCACTGTTTGCCAAAACT
Found at i:372539 original size:54 final size:54
Alignment explanation
Indices: 372475--372604 Score: 174
Period size: 54 Copynumber: 2.4 Consensus size: 54
372465 GTGCAAAACT
* * *
372475 ATAAGTTTATGAATTTTCTTATGGGTACTGT-T-TGCCAAAACTAAGAAATTCATA
1 ATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTG-C-AAACTAAAAAATTCATA
* *
372529 ATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTGCAAATTAAAAAATTCCTA
1 ATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTGCAAACTAAAAAATTCATA
*
372583 ATAAGTTTATGAATTTACGTAT
1 ATAAGTTTATGAATTTTCGTAT
372605 TTGGTAGTGG
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
54 64 0.94
55 2 0.03
56 2 0.03
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (54 bp):
ATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTGCAAACTAAAAAATTCATA
Found at i:372544 original size:97 final size:98
Alignment explanation
Indices: 372377--372568 Score: 316
Period size: 97 Copynumber: 2.0 Consensus size: 98
372367 GAAATTCATA
372377 ATAAGTTTATGAATTTCCATATGGCCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTAT
1 ATAAGTTTATGAATTTCCATATGGCCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTAT
372442 GAATTTCCGTATGGGCACTGTGTGTGCAAAACT
66 GAATTTCCGTATGGGCACTGTGTGTGCAAAACT
* * **
372475 ATAAGTTTATGAATTTTCTTATGGGTACTGT-T-TGCCAAAACTAAGAAATTCATAATAAGTTTA
1 ATAAGTTTATGAATTTCCATATGGCCACTGTGTGTG-CAAAACTAAGAAATTCATAATAAGTTTA
*
372538 TGAATTTTCGTATGGGCACTGTGTGTGCAAA
65 TGAATTTCCGTATGGGCACTGTGTGTGCAAA
372569 TTAAAAAATT
Statistics
Matches: 88, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
96 2 0.02
97 59 0.67
98 27 0.31
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (98 bp):
ATAAGTTTATGAATTTCCATATGGCCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTAT
GAATTTCCGTATGGGCACTGTGTGTGCAAAACT
Found at i:372622 original size:152 final size:153
Alignment explanation
Indices: 372322--372604 Score: 428
Period size: 152 Copynumber: 1.9 Consensus size: 153
372312 CAAGTTCATA
*
372322 ATAAGTTTATGAATTTCCATATGGCCACTTTGTGAGCAAAACTAAGAAATTCATAATAAGTTTAT
1 ATAAGTTTATGAATTTCCATATGGCCACTTTGTGACCAAAACTAAGAAATTCATAATAAGTTTAT
* *
372387 GAATTTCCATATGGCCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGT
66 GAATTTCCATATGGCCACTGTGTGTGCAAAACTAAAAAATTCATAATAAGTTTATGAATTTACGT
372452 ATGGGCACTGTGTGTGCAAAACT
131 ATGGGCACTGTGTGTGCAAAACT
* * **
372475 ATAAGTTTATGAATTTTCTTATGGGTACTGTT-TG-CCAAAACTAAGAAATTCATAATAAGTTTA
1 ATAAGTTTATGAATTTCCATATGGCCACT-TTGTGACCAAAACTAAGAAATTCATAATAAGTTTA
* * * * *
372538 TGAATTTTCGTATGGGCACTGTGTGTGC-AAATTAAAAAATTCCTAATAAGTTTATGAATTTACG
65 TGAATTTCCATATGGCCACTGTGTGTGCAAAACTAAAAAATTCATAATAAGTTTATGAATTTACG
372602 TAT
130 TAT
372605 TTGGTAGTGG
Statistics
Matches: 117, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
151 35 0.30
152 53 0.45
153 27 0.23
154 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (153 bp):
ATAAGTTTATGAATTTCCATATGGCCACTTTGTGACCAAAACTAAGAAATTCATAATAAGTTTAT
GAATTTCCATATGGCCACTGTGTGTGCAAAACTAAAAAATTCATAATAAGTTTATGAATTTACGT
ATGGGCACTGTGTGTGCAAAACT
Found at i:379285 original size:55 final size:55
Alignment explanation
Indices: 379206--379561 Score: 554
Period size: 55 Copynumber: 6.5 Consensus size: 55
379196 ATTACCAAAT
* * *
379206 GGCACTATGTGTGAAAAACGAAGAAATTCATAATAAGTTTATGAATTTCTGTATG
1 GGCACTATGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * *
379261 GGAACTACGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATG
1 GGCACTATGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * *
379316 GGAACTACGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTACGTATG
1 GGCACTATGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
*
379371 GGCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
1 GGCACTATGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
*
379426 GGCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
1 GGCACTATGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
*
379481 GGCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
1 GGCACTATGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * *
379536 AGCA-T-TGTGTGTAAGAATTAAGAAAT
1 GGCACTATGTGTGCAA-AACTAAGAAAT
379562 AAGAAATAAG
Statistics
Matches: 287, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
53 8 0.03
54 11 0.04
55 268 0.93
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (55 bp):
GGCACTATGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
Found at i:379559 original size:7 final size:7
Alignment explanation
Indices: 379547--379577 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
379537 GCATTGTGTG
*
379547 TAAGAAT
1 TAAGAAA
379554 TAAGAAA
1 TAAGAAA
379561 TAAGAAA
1 TAAGAAA
379568 TAAGAAA
1 TAAGAAA
379575 TAA
1 TAA
379578 AATTCATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (7 bp):
TAAGAAA
Found at i:379566 original size:14 final size:14
Alignment explanation
Indices: 379547--379581 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
379537 GCATTGTGTG
379547 TAAGAATTAAGAAA
1 TAAGAATTAAGAAA
*
379561 TAAGAAATAAGAAA
1 TAAGAATTAAGAAA
379575 TAA-AATT
1 TAAGAATT
379582 CATAATAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 3 0.16
14 16 0.84
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (14 bp):
TAAGAATTAAGAAA
Found at i:385779 original size:18 final size:18
Alignment explanation
Indices: 385756--385790 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
385746 TCTGAGTATT
385756 TGTCCCGAA-GGACCACTA
1 TGTCCC-AATGGACCACTA
385774 TGTCCCAATGGACCACT
1 TGTCCCAATGGACCACT
385791 GATTATCCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCAATGGACCACTA
Found at i:395423 original size:3 final size:3
Alignment explanation
Indices: 395417--395470 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
395407 AATTATTATT
* * * *
395417 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA AAA TAA TAA TGA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
395465 TAA TAA
1 TAA TAA
395471 AAAAAATGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:395451 original size:24 final size:24
Alignment explanation
Indices: 395417--395473 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
395407 AATTATTATT
*
395417 TAATAATAATAATAATAATGATAA
1 TAATAAAAATAATAATAATGATAA
*
395441 TAATAAAAATAATAATGATGATAA
1 TAATAAAAATAATAATAATGATAA
395465 TAATAAAAA
1 TAATAAAAA
395474 AAATGGTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (24 bp):
TAATAAAAATAATAATAATGATAA
Found at i:395927 original size:20 final size:20
Alignment explanation
Indices: 395898--396144 Score: 231
Period size: 20 Copynumber: 12.3 Consensus size: 20
395888 AATCTGTAAA
395898 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
**
395918 TCATAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
395938 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
395958 TCGCAACACTGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
395978 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
395998 TCGCAACGC-GAA-TCTGTAAA-
1 TCGCAACACAGAAGTC---AAAT
*
396018 TCGTAACAC-GAATTTGT-AAAT
1 TCGCAACACAGAA---GTCAAAT
396039 T-GCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
396058 TTGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
** *
396078 TCGCAACACTTAATTTCAAAT
1 TCGCAACACAGAA-GTCAAAT
*
396099 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* *
396119 TCGTAACGC-GAAAGTCAAAT
1 TCGCAACACAG-AAGTCAAAT
396139 TCGCAA
1 TCGCAA
396145 AACGCGTTTA
Statistics
Matches: 188, Mismatches: 24, Indels: 30
0.78 0.10 0.12
Matches are distributed among these distances:
18 4 0.02
19 9 0.05
20 148 0.79
21 26 0.14
24 1 0.01
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.21
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:395966 original size:60 final size:61
Alignment explanation
Indices: 395873--396144 Score: 285
Period size: 60 Copynumber: 4.5 Consensus size: 61
395863 ACCCAGTTTC
* * ** *
395873 CAAATTCGCAACGCGAATCTGT-AAA-TCGCAACACAGAA-GTCAAATTCATAACACAGAAGT
1 CAAATTCGCAACGCG-AT-AGTCAAATTCGCAACACTGAATGTCAAATTCGCAACACAAAAGT
395933 CAAATTCGCAACGCGATAGTCAAATTCGCAACACTGAA-GTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACTGAATGTCAAATTCGCAACACAAAAGT
* * *
395993 CAAATTCGCAACGCGAATCTGT-AAA-TCGTAACAC-GAATTTGT-AAATT-GCAACACAGAAGT
1 CAAATTCGCAACGCG-AT-AGTCAAATTCGCAACACTGAA--TGTCAAATTCGCAACACAAAAGT
* * * *
396053 CAAATTTGCAACACAGA-AGTCAAATTCGCAACACTTAATTTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGC-GATAGTCAAATTCGCAACACTGAATGTCAAATTCGCAACACAAAAGT
* *
396114 CAAATTCGTAACGCGAAAGTCAAATTCGCAA
1 CAAATTCGCAACGCGATAGTCAAATTCGCAA
396145 AACGCGTTTA
Statistics
Matches: 180, Mismatches: 18, Indels: 27
0.80 0.08 0.12
Matches are distributed among these distances:
58 4 0.02
59 13 0.07
60 109 0.61
61 50 0.28
62 4 0.02
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.21
Consensus pattern (61 bp):
CAAATTCGCAACGCGATAGTCAAATTCGCAACACTGAATGTCAAATTCGCAACACAAAAGT
Found at i:398480 original size:21 final size:21
Alignment explanation
Indices: 398456--398505 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
398446 GTTAGGGGAG
*
398456 TTACGTGATGAGCTCGGTGCT
1 TTACGTGATGAGCTCGGTACT
* *
398477 TTACGTCATGAGGTCGGTACT
1 TTACGTGATGAGCTCGGTACT
398498 TTACGTGA
1 TTACGTGA
398506 AGACAATGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGCTCGGTACT
Found at i:398628 original size:21 final size:21
Alignment explanation
Indices: 398586--398631 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
398576 TGTGCGCTAT
* * *
398586 GTGATGAGGTATCTACTTTAC
1 GTGATGAGGTAGCCACTCTAC
*
398607 GTGATGAGGTAGCCGCTCTAC
1 GTGATGAGGTAGCCACTCTAC
398628 GTGA
1 GTGA
398632 GATTGTTTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
GTGATGAGGTAGCCACTCTAC
Found at i:398964 original size:21 final size:21
Alignment explanation
Indices: 398913--399031 Score: 116
Period size: 21 Copynumber: 5.7 Consensus size: 21
398903 GATTCACCTG
** *
398913 TCATCGTTCAAGAGGTGCGTC
1 TCATCGTTCAAGAGGCCCCTC
*
398934 AT-ATCGTTCAAGAGGCTCCTC
1 -TCATCGTTCAAGAGGCCCCTC
*
398955 TCATCATTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
398976 CCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
*
398997 TCATCGTTCAATG-GGTCCCTC
1 TCATCGTTCAA-GAGGCCCCTC
*
399018 CCATCGTTCAAGAG
1 TCATCGTTCAAGAG
399032 CCCGATTCAC
Statistics
Matches: 80, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.03
21 76 0.95
22 2 0.03
ACGTcount: A:0.21, C:0.33, G:0.21, T:0.25
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:400491 original size:65 final size:65
Alignment explanation
Indices: 400388--400531 Score: 245
Period size: 66 Copynumber: 2.2 Consensus size: 65
400378 TTTTACATTG
400388 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA-TTTTTTGCTTGTTTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGTA
* * *
400452 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTTCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
400517 A
65 A
400518 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
400532 GTTTTAAATT
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
64 17 0.23
65 19 0.25
66 39 0.52
ACGTcount: A:0.30, C:0.01, G:0.17, T:0.51
Consensus pattern (65 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGTA
Found at i:400516 original size:66 final size:64
Alignment explanation
Indices: 400357--400531 Score: 244
Period size: 66 Copynumber: 2.6 Consensus size: 64
400347 TGGGTACACC
400357 TTTTTTTCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTGTTTAATTGATGAGGAAATAAG
1 TTTTTTTCTTGTTTAATTG-ATTTGT--A---AAAGTTGATTTGTTTAATTGATGAGGAAATAAG
400421 AATTA
60 AATTA
* * *
400426 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTA
1 TTTTTTTCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA
400491 TTTTTTTTCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 -TTTTTTTCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
400532 GTTTTAAATT
Statistics
Matches: 99, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
64 17 0.17
65 19 0.19
66 39 0.39
67 1 0.01
68 4 0.04
69 19 0.19
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.54
Consensus pattern (64 bp):
TTTTTTTCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
Found at i:400821 original size:6 final size:6
Alignment explanation
Indices: 400812--400846 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
400802 TTGTGATTGG
**
400812 GATTTT GATTTT GATTGC GATTTT GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
400847 CCTTTTCCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:400828 original size:18 final size:18
Alignment explanation
Indices: 400805--400845 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
400795 AAGCCGGTTG
*
400805 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
400823 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
400841 TGATT
1 TGATT
400846 TCCTTTTCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.02, G:0.24, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:404115 original size:19 final size:18
Alignment explanation
Indices: 404072--404120 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
404062 CAAAACATTT
*
404072 GTGTTGCGAAACTAAAAC
1 GTGTTGCGAAATTAAAAC
* *
404090 CTGTTGCGAAATTAAATTC
1 GTGTTGCGAAATTAAA-AC
404109 GTGTTGC-AAATT
1 GTGTTGCGAAATT
404121 CGAAAATTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (18 bp):
GTGTTGCGAAATTAAAAC
Found at i:404152 original size:19 final size:19
Alignment explanation
Indices: 404112--404187 Score: 80
Period size: 19 Copynumber: 3.9 Consensus size: 19
404102 TAAATTCGTG
* *
404112 TTGCAAATTCGAAAATTGAA
1 TTGCAAATTTG-AAATTCAA
404132 TTGCAAATTTGAAATTCAA
1 TTGCAAATTTGAAATTCAA
* **
404151 TTGCGAATTTGAAATTCCG
1 TTGCAAATTTGAAATTCAA
**
404170 TTGTGAATTTGAAATTCA
1 TTGCAAATTTGAAATTCA
404188 GTGTTGCGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 39 0.80
20 10 0.20
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (19 bp):
TTGCAAATTTGAAATTCAA
Found at i:404166 original size:38 final size:39
Alignment explanation
Indices: 404124--404202 Score: 88
Period size: 38 Copynumber: 2.0 Consensus size: 39
404114 GCAAATTCGA
*
404124 AAATTGAATTGCAAATTTGAAATTCA-ATTGCGAATTTG
1 AAATTCAATTGCAAATTTGAAATTCAGATTGCGAATTTG
** ** *
404162 AAATTCCGTTGTGAATTTGAAATTCAGTGTTGCGAATTTG
1 AAATTCAATTGCAAATTTGAAATTCAG-ATTGCGAATTTG
404202 A
1 A
404203 CTATCACGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
38 21 0.64
40 12 0.36
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (39 bp):
AAATTCAATTGCAAATTTGAAATTCAGATTGCGAATTTG
Found at i:404235 original size:20 final size:20
Alignment explanation
Indices: 404188--404392 Score: 183
Period size: 20 Copynumber: 10.3 Consensus size: 20
404178 TTGAAATTCA
404188 GTGTTGCGAATTTGAC-TAT
1 GTGTTGCGAATTTGACTTAT
** *
404207 CACGATGCGAATTTGACTTAT
1 -GTGTTGCGAATTTGACTTAT
*
404228 GTGTTGCGAATTTGATTTAT
1 GTGTTGCGAATTTGACTTAT
**
404248 GTGTTGCG-ATTT-ACAAATT
1 GTGTTGCGAATTTGACTTA-T
* *
404267 CGTGTTGCGATTTATAGA-TT-C
1 -GTGTTGCGAATT-T-GACTTAT
* *
404288 GCGTTGCGAATTTGACTTTT
1 GTGTTGCGAATTTGACTTAT
404308 GTGTTGCGAA-TTGACTTCA-
1 GTGTTGCGAATTTGACTT-AT
404327 GTGTTGCGAATTTGAC-TAT
1 GTGTTGCGAATTTGACTTAT
*
404346 CGCGTTGCGAATTTGACTTAT
1 -GTGTTGCGAATTTGACTTAT
*
404367 GTGTTGCGAATTTGACTTCT
1 GTGTTGCGAATTTGACTTAT
404387 GTGTTG
1 GTGTTG
404393 TGATTTACAA
Statistics
Matches: 149, Mismatches: 22, Indels: 28
0.75 0.11 0.14
Matches are distributed among these distances:
18 5 0.03
19 26 0.17
20 108 0.72
21 8 0.05
22 1 0.01
24 1 0.01
ACGTcount: A:0.20, C:0.13, G:0.25, T:0.42
Consensus pattern (20 bp):
GTGTTGCGAATTTGACTTAT
Found at i:404331 original size:139 final size:139
Alignment explanation
Indices: 404184--404440 Score: 433
Period size: 139 Copynumber: 1.8 Consensus size: 139
404174 GAATTTGAAA
*
404184 TTCAGTGTTGCGAATTTGACTATCACGATGCGAATTTGACTTATGTGTTGCGAATTTGATTTATG
1 TTCAGTGTTGCGAATTTGACTATCACGATGCGAATTTGACTTATGTGTTGCGAATTTGACTTATG
* * * *
404249 TGTTGCGATTTACAAATTCGTGTTGCGATTTATAGATTCGCGTTGCGAATTTGACTTTTGTGTTG
66 TGTTGCGATTTACAAATTCGCGTTGCAATTTACAGATTCGAGTTGCGAATTTGACTTTTGTGTTG
404314 CGAATTGAC
131 CGAATTGAC
* * *
404323 TTCAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTGCGAATTTGACTTCTG
1 TTCAGTGTTGCGAATTTGACTATCACGATGCGAATTTGACTTATGTGTTGCGAATTTGACTTATG
*
404388 TGTTGTGATTTACAAATTCGCGTTGCAATTTACAGATTCGAGTTGCGAATTTG
66 TGTTGCGATTTACAAATTCGCGTTGCAATTTACAGATTCGAGTTGCGAATTTG
404441 GAAACTGGGT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
139 109 1.00
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (139 bp):
TTCAGTGTTGCGAATTTGACTATCACGATGCGAATTTGACTTATGTGTTGCGAATTTGACTTATG
TGTTGCGATTTACAAATTCGCGTTGCAATTTACAGATTCGAGTTGCGAATTTGACTTTTGTGTTG
CGAATTGAC
Found at i:404413 original size:40 final size:40
Alignment explanation
Indices: 404151--404418 Score: 143
Period size: 40 Copynumber: 6.8 Consensus size: 40
404141 TGAAATTCAA
* * *
404151 TTGCGAATTTGA-AATTC-CGTTGTGAATTTGAAATTCAGTG
1 TTGCGAATTT-ACAATTCGCGTTGCGAATTTG-ACTTCTGTG
* * * *
404191 TTGCGAATTTGACTA-TCACGATGCGAATTTGACTTATGTG
1 TTGCGAATTT-ACAATTCGCGTTGCGAATTTGACTTCTGTG
* * * *
404231 TTGCGAATTT-GATTTATGTGTTGCG-ATTT-ACAAATTC-GTG
1 TTGCGAATTTACAATT-CGCGTTGCGAATTTGAC---TTCTGTG
* *
404271 TTGCG-ATTTATAGATTCGCGTTGCGAATTTGACTTTTGTG
1 TTGCGAATTTACA-ATTCGCGTTGCGAATTTGACTTCTGTG
* * *
404311 TTGCGAATTGAC--TTCAGTGTTGCGAATTTGACTATC-GCG
1 TTGCGAATTTACAATTC-GCGTTGCGAATTTGACT-TCTGTG
* *
404350 TTGCGAATTTGAC--TTATGTGTTGCGAATTTGACTTCTGTG
1 TTGCGAATTT-ACAATT-CGCGTTGCGAATTTGACTTCTGTG
*
404390 TTGTG-ATTTACAAATTCGCGTTGC-AATTT
1 TTGCGAATTTAC-AATTCGCGTTGCGAATTT
404419 ACAGATTCGA
Statistics
Matches: 177, Mismatches: 30, Indels: 43
0.71 0.12 0.17
Matches are distributed among these distances:
38 7 0.04
39 49 0.28
40 93 0.53
41 26 0.15
42 2 0.01
ACGTcount: A:0.22, C:0.13, G:0.23, T:0.42
Consensus pattern (40 bp):
TTGCGAATTTACAATTCGCGTTGCGAATTTGACTTCTGTG
Found at i:404418 original size:20 final size:21
Alignment explanation
Indices: 404395--404439 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
404385 CTGTGTTGTG
*
404395 ATTTACAAATTCGCGTTGC-A
1 ATTTACAAATTCGAGTTGCGA
*
404415 ATTTACAGATTCGAGTTGCGA
1 ATTTACAAATTCGAGTTGCGA
404436 ATTT
1 ATTT
404440 GGAAACTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (21 bp):
ATTTACAAATTCGAGTTGCGA
Found at i:404828 original size:64 final size:64
Alignment explanation
Indices: 404748--404875 Score: 220
Period size: 64 Copynumber: 2.0 Consensus size: 64
404738 CTTAAAACTA
*
404748 TCTTTCTTAAAGAGAACATCATTTGCAACAACCAAAGTCTCGAGAATGGCCTCTACGGTTTGAG
1 TCTTTCTTAAAGAGAACATCATTTGCAACAACCAAAGTCTCGAGAATGGACTCTACGGTTTGAG
* * *
404812 TCTTTGTTAAAGAGAACATCATTTGCATCAACCAAAGTCTCGAGACTGGACTCTACGGTTTGAG
1 TCTTTCTTAAAGAGAACATCATTTGCAACAACCAAAGTCTCGAGAATGGACTCTACGGTTTGAG
404876 AAAGGACCTC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (64 bp):
TCTTTCTTAAAGAGAACATCATTTGCAACAACCAAAGTCTCGAGAATGGACTCTACGGTTTGAG
Found at i:405838 original size:28 final size:27
Alignment explanation
Indices: 405805--405887 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 27
405795 GGTATTATAA
* *
405805 TTTAGAATTTATAATTTTTTTTGAGATT
1 TTTAGAATTTAGAA-GTTTTTTGAGATT
*
405833 TTTAGAAATTTAGGAGTTTTTTGAGATT
1 TTTAG-AATTTAGAAGTTTTTTGAGATT
* **
405861 TTCTGGAATTTAAGGTGTTTTTTGAGA
1 TT-TAGAATTT-AGAAGTTTTTTGAGA
405888 ATTTAATAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 24 0.51
29 23 0.49
ACGTcount: A:0.27, C:0.01, G:0.19, T:0.53
Consensus pattern (27 bp):
TTTAGAATTTAGAAGTTTTTTGAGATT
Found at i:405880 original size:29 final size:28
Alignment explanation
Indices: 405821--405887 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
405811 ATTTATAATT
405821 TTTTTTGAGATTTTTAGAAATTTAGGAG
1 TTTTTTGAGATTTTTAGAAATTTAGGAG
* *
405849 TTTTTTGAGATTTTCT-GGAATTTAAGGTG
1 TTTTTTGAGATTTT-TAGAAATTT-AGGAG
405878 TTTTTTGAGA
1 TTTTTTGAGA
405888 ATTTAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 20 0.57
29 15 0.43
ACGTcount: A:0.24, C:0.01, G:0.22, T:0.52
Consensus pattern (28 bp):
TTTTTTGAGATTTTTAGAAATTTAGGAG
Found at i:408620 original size:45 final size:45
Alignment explanation
Indices: 408529--409010 Score: 601
Period size: 45 Copynumber: 10.7 Consensus size: 45
408519 TATTTATTAT
* * * * *
408529 TTTCATTTATGGAATCCTTTTTATTACTTTTAATGCACCATTATGCA
1 TTTCATTTATGGCATCC-TTTCA-TGCCTTTAATGCACCGTTATGCA
* * *
408576 TTTTATTTATGACATCCTTTCATGCCTTTAATGTACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* * *
408621 TTTCATTTATGACATCCTTTCATGCATTTAATGCACCATTATAG-A
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTAT-GCA
* * * *
408666 TGTCAATTATGGCATCCTTTCAAGCCTTTAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* * *
408711 TTT-AGTTTATGGTATCCATTAATGCCTTTAATGCACCGTTATGCA
1 TTTCA-TTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* ** *
408756 TTTCATTTATGTCATCCTTTTGTGCCTTTAATGCATCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* * *
408801 ATTCATTTATGGCATGCTTTCATTCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* * *
408846 TTTCATTTATGACATCCTTTCATGCCTTTAATGAACCTTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* * *
408891 TTTCATTTATGACATCCTTTCATTCCTTTAATGCACCGTTATGTA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* *
408936 TTT-ATTTATGGCATCCTTTCATGCCTTTAATGCTCCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
*
408980 TTTCATTTATGGCATCCTTTCATTCCTTTAA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAA
409011 ACTGAGTTAG
Statistics
Matches: 377, Mismatches: 53, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
44 41 0.11
45 316 0.84
46 6 0.02
47 14 0.04
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
Found at i:408964 original size:21 final size:21
Alignment explanation
Indices: 408801--409009 Score: 74
Period size: 21 Copynumber: 9.4 Consensus size: 21
408791 TCGTTATGCA
* *
408801 ATTCATTTATGGCATGCTTTC
1 ATTCCTTTATGGCATCCTTTC
408822 ATTCCTTTAAT-GCA-CCGTTATGC
1 ATTCCTTT-ATGGCATCC-TT-T-C
* *
408845 ATTTCATTTATGACATCCTTTC
1 A-TTCCTTTATGGCATCCTTTC
* *
408867 ATGCCTTTAAT-G-AACCTTTATGC
1 ATTCCTTT-ATGGCATCC-TT-T-C
* *
408890 ATTTCATTTATGACATCCTTTC
1 A-TTCCTTTATGGCATCCTTTC
*
408912 ATTCCTTTAAT-GCA-CCGTTATGT
1 ATTCCTTT-ATGGCATCC-TT-T-C
**
408935 ATTTATTTATGGCATCCTTTC
1 ATTCCTTTATGGCATCCTTTC
*
408956 ATGCCTTTAAT-GC-TCCATTATGC
1 ATTCCTTT-ATGGCATCC-TT-T-C
*
408979 ATTTCATTTATGGCATCCTTTC
1 A-TTCCTTTATGGCATCCTTTC
409001 ATTCCTTTA
1 ATTCCTTTA
409010 AACTGAGTTA
Statistics
Matches: 137, Mismatches: 24, Indels: 54
0.64 0.11 0.25
Matches are distributed among these distances:
20 9 0.07
21 45 0.33
22 21 0.15
23 26 0.19
24 28 0.20
25 8 0.06
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (21 bp):
ATTCCTTTATGGCATCCTTTC
Found at i:409306 original size:54 final size:54
Alignment explanation
Indices: 409246--409419 Score: 170
Period size: 55 Copynumber: 3.2 Consensus size: 54
409236 TTTACGTGGG
* *
409246 TTGCACACCCACTACTAGTACGAAAATTCATAAACTTATTATGAA-TTCTTAGTT
1 TTGCACACACAGTACTA-TACGAAAATTCATAAACTTATTATGAATTTCTTAGTT
** * * * **
409300 TTGCACACACAGTGGTCATACTAAAATTCATAAATTTATTATGAATTTCATAACT
1 TTGCACACACAGTACT-ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTT
* * * * * *
409355 TTGCACACATAGTGCCCATACGGAAATTCATACACTTATTATAAATTTCTTAGTTT
1 TTGCACACACAGT-ACTATACGAAAATTCATAAACTTATTATGAATTTCTTAG-TT
409411 TTGCACACA
1 TTGCACACA
409420 TAGTGCCATT
Statistics
Matches: 95, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
54 37 0.39
55 48 0.51
56 10 0.11
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.36
Consensus pattern (54 bp):
TTGCACACACAGTACTATACGAAAATTCATAAACTTATTATGAATTTCTTAGTT
Found at i:409383 original size:55 final size:55
Alignment explanation
Indices: 409264--409426 Score: 202
Period size: 55 Copynumber: 3.0 Consensus size: 55
409254 CCACTACTAG
* * **
409264 TACGAAAATTCATAAACTTATTATGAA-TTCTTAGTTTTGCACACACAGTGGTCA
1 TACGAAAATTCATAAACTTATTATGAATTTCTTAATTTTGCACACATAGTGCCCA
* * * *
409318 TACTAAAATTCATAAATTTATTATGAATTTCATAACTTTGCACACATAGTGCCCA
1 TACGAAAATTCATAAACTTATTATGAATTTCTTAATTTTGCACACATAGTGCCCA
* * * *
409373 TACGGAAATTCATACACTTATTATAAATTTCTTAGTTTTTGCACACATAGTGCC
1 TACGAAAATTCATAAACTTATTATGAATTTCTTA-ATTTTGCACACATAGTGCC
409427 ATTTGGTAAT
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
54 25 0.27
55 49 0.54
56 17 0.19
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (55 bp):
TACGAAAATTCATAAACTTATTATGAATTTCTTAATTTTGCACACATAGTGCCCA
Found at i:412404 original size:13 final size:13
Alignment explanation
Indices: 412386--412419 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
412376 AATGGACAAT
412386 TTTGAAAACTAA-G
1 TTTGAAAAC-AAGG
412399 TTTGAAAACAAGG
1 TTTGAAAACAAGG
412412 TTTGAAAA
1 TTTGAAAA
412420 TCAATATACG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 2 0.10
13 18 0.90
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (13 bp):
TTTGAAAACAAGG
Found at i:417933 original size:32 final size:32
Alignment explanation
Indices: 417887--417957 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
417877 TCCATTGAAA
*
417887 AAAGAAGGCTTGTTGACGGGCATTGAATCGAG
1 AAAGAAGGCTTGTTGAAGGGCATTGAATCGAG
*
417919 AAAGGAGGCTTGTTGAAGGGCATTGAATCGAG
1 AAAGAAGGCTTGTTGAAGGGCATTGAATCGAG
*
417951 AACGAAG
1 AAAGAAG
417958 TCGGAGTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.11, G:0.35, T:0.20
Consensus pattern (32 bp):
AAAGAAGGCTTGTTGAAGGGCATTGAATCGAG
Found at i:424137 original size:90 final size:90
Alignment explanation
Indices: 424043--424221 Score: 277
Period size: 90 Copynumber: 2.0 Consensus size: 90
424033 AGGGCATACG
* * ** *
424043 TTCATGCCTTTAGTTCACTTTTATGCATTTTATTTATGGAATCCTTTCATGCCTTTAATGCACCA
1 TTCATGCCTTTAATGCACCGTTATGCATTTTAATTATGGAATCCTTTCATGCCTTTAATGCACCA
424108 TTATGCATTTCATTTATGAAATCCT
66 TTATGCATTTCATTTATGAAATCCT
* *
424133 TTCATGCCTTTAATGCACCGTTATGCATTTTAATTATGGCATCCTTTCATGCCTTTAATGCACCG
1 TTCATGCCTTTAATGCACCGTTATGCATTTTAATTATGGAATCCTTTCATGCCTTTAATGCACCA
* *
424198 TTATGCGTTTCATTTATGACATCC
66 TTATGCATTTCATTTATGAAATCC
424222 CATTATGCAT
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (90 bp):
TTCATGCCTTTAATGCACCGTTATGCATTTTAATTATGGAATCCTTTCATGCCTTTAATGCACCA
TTATGCATTTCATTTATGAAATCCT
Found at i:424221 original size:45 final size:45
Alignment explanation
Indices: 424025--424221 Score: 243
Period size: 45 Copynumber: 4.4 Consensus size: 45
424015 TATTCATTAT
* * * * * * **
424025 TTTCATTTAGGGCATACGTTCATGCCTTTAGTTCACTTTTATGCA
1 TTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGCA
* *
424070 TTTTATTTATGGA-ATCCTTTCATGCCTTTAATGCACCATTATGCA
1 TTTCATTTAT-GACATCCTTTCATGCCTTTAATGCACCGTTATGCA
*
424115 TTTCATTTATGAAATCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGCA
* * * *
424160 TTTTAATTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCG
1 TTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGCA
424205 TTTCATTTATGACATCC
1 TTTCATTTATGACATCC
424222 CATTATGCAT
Statistics
Matches: 131, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
44 2 0.02
45 128 0.98
46 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.44
Consensus pattern (45 bp):
TTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGCA
Found at i:424233 original size:71 final size:71
Alignment explanation
Indices: 424153--424292 Score: 199
Period size: 71 Copynumber: 2.0 Consensus size: 71
424143 TAATGCACCG
* * * * *
424153 TTATGCATTTTAATTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCGTTTCATTTATGAC
1 TTATGCATTTCAATTATGGAATCCTTTCATGACTTTAATGCACCATTATGCATTTCATTTATGAC
424218 ATCCCA
66 ATCCCA
* * * *
424224 TTATGCATTTCATTTATGGAATCCTTTCATGACTTTAATGCCCCATTATGCATTTTATTTATGGC
1 TTATGCATTTCAATTATGGAATCCTTTCATGACTTTAATGCACCATTATGCATTTCATTTATGAC
424289 ATCC
66 ATCC
424293 TTTCATGCCT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.44
Consensus pattern (71 bp):
TTATGCATTTCAATTATGGAATCCTTTCATGACTTTAATGCACCATTATGCATTTCATTTATGAC
ATCCCA
Found at i:424247 original size:116 final size:116
Alignment explanation
Indices: 424105--424337 Score: 385
Period size: 116 Copynumber: 2.0 Consensus size: 116
424095 CTTTAATGCA
* *
424105 CCATTATGCATTTCATTTATGAAATCCTTTCATGCCTTTAATGCACCGTTATGCATTTTAATTAT
1 CCATTATGCATTTCATTTATGAAATCCTTTCATGACTTTAATGCACCATTATGCATTTTAATTAT
* * *
424170 GGCATCCTTTCATGCCTTTAATGCACCGTTATGCGTTTCATTTATGACATC
66 GGCATCCTTTCATGCCTTTAATGAACAGTTATGCATTTCATTTATGACATC
* * *
424221 CCATTATGCATTTCATTTATGGAATCCTTTCATGACTTTAATGCCCCATTATGCATTTTATTTAT
1 CCATTATGCATTTCATTTATGAAATCCTTTCATGACTTTAATGCACCATTATGCATTTTAATTAT
*
424286 GGCATCCTTTCATGCCTTTAATGAACAGTTATGCATTTCATTTATGGCATC
66 GGCATCCTTTCATGCCTTTAATGAACAGTTATGCATTTCATTTATGACATC
424337 C
1 C
424338 TTTCATGTCT
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
116 108 1.00
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (116 bp):
CCATTATGCATTTCATTTATGAAATCCTTTCATGACTTTAATGCACCATTATGCATTTTAATTAT
GGCATCCTTTCATGCCTTTAATGAACAGTTATGCATTTCATTTATGACATC
Found at i:424270 original size:45 final size:45
Alignment explanation
Indices: 424221--424441 Score: 345
Period size: 45 Copynumber: 4.9 Consensus size: 45
424211 TTATGACATC
* * *
424221 CCATTATGCATTTCATTTATGGAATCCTTTCATGACTTTAATGCC
1 CCATTATGCATTTCATTTATGGCATCCTTTCATGCCTTTAATGCA
*
424266 CCATTATGCATTTTATTTATGGCATCCTTTCATGCCTTTAATG-A
1 CCATTATGCATTTCATTTATGGCATCCTTTCATGCCTTTAATGCA
* *
424310 ACAGTTATGCATTTCATTTATGGCATCCTTTCATGTCTTTAATGCA
1 CCA-TTATGCATTTCATTTATGGCATCCTTTCATGCCTTTAATGCA
* *
424356 CCGTTATGCATTTCATTTATGGCATCCTTTCATGCATTTAATGCA
1 CCATTATGCATTTCATTTATGGCATCCTTTCATGCCTTTAATGCA
*
424401 CCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTTTAA
1 CCATTATGCATTTCATTTATGGCATCCTTTCATGCCTTTAA
424442 ACTCAGTTCG
Statistics
Matches: 162, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
44 2 0.01
45 158 0.98
46 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (45 bp):
CCATTATGCATTTCATTTATGGCATCCTTTCATGCCTTTAATGCA
Found at i:424393 original size:161 final size:161
Alignment explanation
Indices: 424062--424394 Score: 524
Period size: 161 Copynumber: 2.1 Consensus size: 161
424052 TTAGTTCACT
* *
424062 TTTATGCATTTTATTTATGGAATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGA
1 TTTATGCATTTCATTTATGGAATCCTTTCATGACTTTAATGCACCATTATGCATTTCATTTATGA
* * *
424127 AATCCTTTCATGCCTTTAATGCACCGTTATGCATTTTAATTATGGCATCCTTTCATGCCTTTAAT
66 AATCCTTTCATGCCTTTAATGAACAGTTATGCATTTCAATTATGGCATCCTTTCATGCCTTTAAT
*
424192 GCACCGTTATGCGTTTCATTTATGACATCCC
131 GCACCGTTATGCATTTCATTTATGACATCCC
* * * *
424223 ATTATGCATTTCATTTATGGAATCCTTTCATGACTTTAATGCCCCATTATGCATTTTATTTATGG
1 TTTATGCATTTCATTTATGGAATCCTTTCATGACTTTAATGCACCATTATGCATTTCATTTATGA
* * *
424288 CATCCTTTCATGCCTTTAATGAACAGTTATGCATTTCATTTATGGCATCCTTTCATGTCTTTAAT
66 AATCCTTTCATGCCTTTAATGAACAGTTATGCATTTCAATTATGGCATCCTTTCATGCCTTTAAT
*
424353 GCACCGTTATGCATTTCATTTATGGCAT-CC
131 GCACCGTTATGCATTTCATTTATGACATCCC
424383 TTTCATGCATTT
1 TTT-ATGCATTT
424395 AATGCACCGT
Statistics
Matches: 156, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
160 4 0.03
161 152 0.97
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.44
Consensus pattern (161 bp):
TTTATGCATTTCATTTATGGAATCCTTTCATGACTTTAATGCACCATTATGCATTTCATTTATGA
AATCCTTTCATGCCTTTAATGAACAGTTATGCATTTCAATTATGGCATCCTTTCATGCCTTTAAT
GCACCGTTATGCATTTCATTTATGACATCCC
Found at i:424411 original size:19 final size:19
Alignment explanation
Indices: 424347--424413 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 19
424337 CTTTCATGTC
424347 TTTAATGCACCGTTATGCA
1 TTTAATGCACCGTTATGCA
*
424366 TTTCATTTATGGCATCCTTTCATGCA
1 TTT-A---AT-GCA-CCGTT-ATGCA
424392 TTTAATGCACCGTTATGCA
1 TTTAATGCACCGTTATGCA
424411 TTT
1 TTT
424414 CATTTATGGC
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
19 11 0.28
20 5 0.13
21 3 0.08
22 2 0.05
23 2 0.05
24 3 0.08
25 5 0.13
26 8 0.21
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.43
Consensus pattern (19 bp):
TTTAATGCACCGTTATGCA
Found at i:424829 original size:57 final size:55
Alignment explanation
Indices: 424648--424854 Score: 197
Period size: 55 Copynumber: 3.7 Consensus size: 55
424638 CCAATACGGT
* ** * * * * **
424648 AATTCATAAACTTATTAT-AATTTACGT-GGGTTGCACACCCACTACCAATACGGA
1 AATTCATAAACTTATTATGAATTT-CTTAGTTTTGCACACACAATGCCCATACTAA
* *
424702 AATTTATAAACTTATTAT-ATATTTCTTAGTTTTGCACACACAATTCCCATACTAA
1 AATTCATAAACTTATTATGA-ATTTCTTAGTTTTGCACACACAATGCCCATACTAA
* * * *
424757 AATTCATAAATTTATTATGAATTTCATAGTTTTGCACACACACAGTGCCCGT-TTGAA
1 AATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACA-A-TGCCCATACT-AA
424814 AATTCATAAACTTATTATGAATTTCTTAGTTCTTGCACACA
1 AATTCATAAACTTATTATGAATTTCTTAGTT-TTGCACACA
424855 TAGTACCATT
Statistics
Matches: 128, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
54 20 0.16
55 60 0.47
56 3 0.02
57 36 0.28
58 9 0.07
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (55 bp):
AATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAATGCCCATACTAA
Found at i:425267 original size:34 final size:34
Alignment explanation
Indices: 425222--425336 Score: 194
Period size: 34 Copynumber: 3.4 Consensus size: 34
425212 TACTATAATG
* *
425222 TGGTACCGATACCATTTCTGTATTCTGTAACCAA
1 TGGTATCGATACCATTTCTGCATTCTGTAACCAA
*
425256 TGATATCGATACCATTTCTGCATTCTGTAACCAA
1 TGGTATCGATACCATTTCTGCATTCTGTAACCAA
*
425290 TGGTATCGATACCATTTCTGCATTCTGTGACCAA
1 TGGTATCGATACCATTTCTGCATTCTGTAACCAA
425324 TGGTATCGATACC
1 TGGTATCGATACC
425337 TTCTCCACAA
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 76 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (34 bp):
TGGTATCGATACCATTTCTGCATTCTGTAACCAA
Found at i:425365 original size:88 final size:88
Alignment explanation
Indices: 425258--425444 Score: 302
Period size: 88 Copynumber: 2.1 Consensus size: 88
425248 GTAACCAATG
*** *
425258 ATATCGATACCATTTCTGCATTCTGTAACCAATGGTATCGATACCATTTCTGCATTCTGTGACCA
1 ATATCGATACCATTTCTGCATTCTGTAACCAACAATATCGATACCATTTCTGCATTCTGTAACCA
425323 ATGGTATCGATACCTTCTCCACA
66 ATGGTATCGATACCTTCTCCACA
* *
425346 ATATCGATACCATTTCTGCATTTTGTAACCAACAATATCGATACCATTTCTGCATTTTGTAACCA
1 ATATCGATACCATTTCTGCATTCTGTAACCAACAATATCGATACCATTTCTGCATTCTGTAACCA
*
425411 ATGGTATCGATATCTTCTCCACA
66 ATGGTATCGATACCTTCTCCACA
*
425434 GTATCGATACC
1 ATATCGATACC
425445 CCCTCTCAGT
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 91 1.00
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (88 bp):
ATATCGATACCATTTCTGCATTCTGTAACCAACAATATCGATACCATTTCTGCATTCTGTAACCA
ATGGTATCGATACCTTCTCCACA
Found at i:425422 original size:34 final size:34
Alignment explanation
Indices: 425343--425411 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
425333 TACCTTCTCC
425343 ACAATATCGATACCATTTCTGCATTTTGTAACCA
1 ACAATATCGATACCATTTCTGCATTTTGTAACCA
425377 ACAATATCGATACCATTTCTGCATTTTGTAACCA
1 ACAATATCGATACCATTTCTGCATTTTGTAACCA
425411 A
1 A
425412 TGGTATCGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (34 bp):
ACAATATCGATACCATTTCTGCATTTTGTAACCA
Found at i:429249 original size:18 final size:19
Alignment explanation
Indices: 429209--429249 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
429199 AATAAGTAAA
* *
429209 TATGAGATTAGAAGCATTG
1 TATGAGATTAAAAACATTG
429228 TATGAGATTAAAAACA-TG
1 TATGAGATTAAAAACATTG
429246 TATG
1 TATG
429250 GAAAAGTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (19 bp):
TATGAGATTAAAAACATTG
Found at i:430060 original size:54 final size:54
Alignment explanation
Indices: 429966--430218 Score: 330
Period size: 54 Copynumber: 4.7 Consensus size: 54
429956 CTATGTGTAC
* * ** * *
429966 TATCGGCACTAAGTGTGCAACACATGGAATTCATATTAAGTTTATGAACGATCG
1 TATCGACACTAAGTGTGCAACCCAAAGAATTCATAATAAGTTTATGAACGACCG
* *
430020 TATCGATACTAAGTGTGCAACCCAAAGAATCCATAATAAGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCAAAGAATTCATAATAAGTTTATGAACGACCG
* *
430074 TATCGACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACTG
1 TATCGACACTAAGTGTGCAACCCAAAGAATTCATAATAAGTTTATGAACGACCG
* * *
430128 TATCGATACTAAGTGTGCAACCC-ACGTAATTTATAATAAGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCAAAG-AATTCATAATAAGTTTATGAACGACCG
* * *
430182 TATCGGCACTATGTGTGCACCCCAAAGAACTT-ATAAT
1 TATCGACACTAAGTGTGCAACCCAAAGAA-TTCATAAT
430219 GATTTGAAAA
Statistics
Matches: 174, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 169 0.97
55 4 0.02
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (54 bp):
TATCGACACTAAGTGTGCAACCCAAAGAATTCATAATAAGTTTATGAACGACCG
Found at i:432715 original size:15 final size:15
Alignment explanation
Indices: 432690--432733 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
432680 ATTCATATTC
432690 AAAAA-AAAAAAGAA
1 AAAAAGAAAAAAGAA
*
432704 AGAAAGAAAAAAGAA
1 AAAAAGAAAAAAGAA
432719 AAAAAGAAAAAAGAA
1 AAAAAGAAAAAAGAA
432734 GTAGAAGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 4 0.15
15 23 0.85
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAGAA
Found at i:432716 original size:7 final size:7
Alignment explanation
Indices: 432690--432733 Score: 63
Period size: 7 Copynumber: 6.1 Consensus size: 7
432680 ATTCATATTC
432690 AAAAA-A
1 AAAAAGA
432696 AAAAAGA
1 AAAAAGA
432703 AAGAAAGA
1 AA-AAAGA
432711 AAAAAGAA
1 AAAAAG-A
432719 AAAAAGA
1 AAAAAGA
432726 AAAAAGA
1 AAAAAGA
432733 A
1 A
432734 GTAGAAGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
6 5 0.14
7 16 0.46
8 14 0.40
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:435321 original size:260 final size:259
Alignment explanation
Indices: 434829--435425 Score: 799
Period size: 260 Copynumber: 2.3 Consensus size: 259
434819 GCTTTTCAAT
**
434829 GTTTCTCATTT-AATATTTTCAGAAAATGAAATTTATGAAAAGTAAGAAAGCT-ATTTCTGAAGT
1 GTTTCTCATTTAAATATTTTCAGAAAATGAAATTTATGAAAAGTAAGAAAG-TGATTTCCAAAGT
* * *
434892 TTCTTACCTAGT-AACTATTTCCAAAATTGGTAAGTCATTCGGGCCATTAGTAAGTCTTTCGAGT
65 TTCTTACCTAATAAACTATTTCCAAAATTGGAAAGTCATTCAGGCCATTAGTAAGTCTTTCGAGT
* * * * *
434956 ATGATGGTTAAATCCTTCGGGTCATTTATAAGCCTTTCGAGCAAGATGATAAGTCCTTTGGGCCA
130 ATAATGCTTAAATCCTTCGGGCCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCATTGGGCCA
* * * **
435021 TCCACAAGACCTTCGGGCAGGATGTTTTCACATTATTTTCGAAAAATGATAAAGCGGTTTACAAA
195 TCCACAAGACATTCGGGCAGGATGTTTTCACATGATTTTCGAAAAATGAGAAAGCAATTTACAAA
* * *
435086 GTTTCTCATTTAAATCTTTTCAGAAAAGTGAAATTTGTGAAAAGTAAGAATGTGATTTCCAAAGT
1 GTTTCTCATTTAAATATTTTCAGAAAA-TGAAATTTATGAAAAGTAAGAAAGTGATTTCCAAAGT
* *
435151 TTCTTACCTAATAAACTATTTTCAAAATTGGAAAGTCTTTCAGGCCATTAGTAAGTCTTTCGA-T
65 TTCTTACCTAATAAACTATTTCCAAAATTGGAAAGTCATTCAGGCCATTAGTAAGTCTTTCGAGT
* * * *
435215 CCA-AATGCTTAAATCCTTTGGGCCATCTATAAGTCTTTTGAGTAAGATGATAAGTCCATTGGGC
130 --ATAATGCTTAAATCCTTCGGGCCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCATTGGGC
** *
435279 CATTTACAAGACATTCGGGCAGGATGTTTTCACATGATTTTCGAAAAATGAGAAAGCAATTTCCA
193 CATCCACAAGACATTCGGGCAGGATGTTTTCACATGATTTTCGAAAAATGAGAAAGCAATTTACA
435344 AA
258 AA
* * * * **
435346 GTTTCTCATTTAAATATTTTCTGAAATTTGATATTTTTTGAAAAGTAAGAAAACGATTTCCAAAG
1 GTTTCTCATTTAAATATTTTCAGAAA-ATGA-AATTTATGAAAAGTAAGAAAGTGATTTCCAAAG
*
435411 TTTCTTACTTAATAA
64 TTTCTTACCTAATAA
435426 GTCCTTTAGG
Statistics
Matches: 296, Mismatches: 36, Indels: 12
0.86 0.10 0.03
Matches are distributed among these distances:
257 11 0.04
258 15 0.05
259 43 0.15
260 184 0.62
261 43 0.15
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (259 bp):
GTTTCTCATTTAAATATTTTCAGAAAATGAAATTTATGAAAAGTAAGAAAGTGATTTCCAAAGTT
TCTTACCTAATAAACTATTTCCAAAATTGGAAAGTCATTCAGGCCATTAGTAAGTCTTTCGAGTA
TAATGCTTAAATCCTTCGGGCCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCATTGGGCCAT
CCACAAGACATTCGGGCAGGATGTTTTCACATGATTTTCGAAAAATGAGAAAGCAATTTACAAA
Found at i:435883 original size:6 final size:6
Alignment explanation
Indices: 435873--435916 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
435863 TGTCTGGTAT
* *
435873 ATTATT ATTATT ATT-TA ATTATA ATTATA ATTATA ATTATA ATT
1 ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA ATT
435917 TTTTATTTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
5 4 0.11
6 32 0.89
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (6 bp):
ATTATA
Found at i:435989 original size:24 final size:23
Alignment explanation
Indices: 435960--436009 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
435950 ATCGGACCCA
* *
435960 AAATTACATCAGCCAACCAGGCCC
1 AAATTAAATCACCCAACCA-GCCC
*
435984 AAATTAAATCACCCAACTAGCCC
1 AAATTAAATCACCCAACCAGCCC
436007 AAA
1 AAA
436010 CCCTAGCCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.44, C:0.34, G:0.08, T:0.14
Consensus pattern (23 bp):
AAATTAAATCACCCAACCAGCCC
Found at i:441804 original size:16 final size:18
Alignment explanation
Indices: 441767--441806 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
441757 ATGAAGACTG
*
441767 TAAAATTAATGTTTTCAT
1 TAAAATTAATATTTTCAT
441785 TAAAATTAA-ATTTT-AT
1 TAAAATTAATATTTTCAT
441801 TAAAAT
1 TAAAAT
441807 GGAAAACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 4 0.19
18 9 0.43
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
TAAAATTAATATTTTCAT
Found at i:450184 original size:13 final size:13
Alignment explanation
Indices: 450166--450190 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
450156 AGATATTATT
450166 TCCATCACCATTA
1 TCCATCACCATTA
450179 TCCATCACCATT
1 TCCATCACCATT
450191 CATGCCCTTA
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:0.28, C:0.40, G:0.00, T:0.32
Consensus pattern (13 bp):
TCCATCACCATTA
Done.