Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, 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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 3 of 100
Found at i:224707 original size:15 final size:15
Alignment explanation
Indices: 224687--224719 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
224677 CACTTTCCCC
224687 CGGATGGGCGGACAT
1 CGGATGGGCGGACAT
*
224702 CGGATGGGTGGACAT
1 CGGATGGGCGGACAT
224717 CGG
1 CGG
224720 GCCTTGCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.48, T:0.15
Consensus pattern (15 bp):
CGGATGGGCGGACAT
Found at i:229228 original size:387 final size:387
Alignment explanation
Indices: 228514--229286 Score: 1314
Period size: 387 Copynumber: 2.0 Consensus size: 387
228504 CATTATGCAG
* * *
228514 ATGCTCTTCTAACTAAATGTTGTTCTGGTGTGAATTCTTTTTCATCCTTTCCCACCCATTTGTCC
1 ATGCTCTGCTAACTAAATATTGTTCTGGTGTGAATTCTTTTTCATCCTTTCCAACCCATTTGTCC
* *
228579 TTCTACCCTGAGAAGCCTTTGATGATTTGTTTCAGGCTTTTTGCCAGCATGGGAGCAACCACCAG
66 TTCTACCCTGAGAAGCCTTTGATGATTTGTTACAGGCGTTTTGCCAGCATGGGAGCAACCACCAG
* *
228644 CACAGGAGCATGAAAAGCCCTTTTGATTCTACAATTGCGCTGGATATGTGAGGAAATACTGCTTA
131 CACAGGAGCATGAAAAGCCCTTTTGATTCTACAATTGCGCGGGATATGTGAGGAAATACGGCTTA
228709 GAACATTAACATTAATCCCCGAGGTTCCTTTCTCACTATTGTTAGTTCCATCCAATTGCAACTTG
196 GAACATTAACATTAATCCCCGAGGTTCCTTTCTCACTATTGTTAGTTCCATCCAATTGCAACTTG
*
228774 CTTTTGATTGGGTTTAGCTTTGTTGATAAATTATGCTTGTATATCTCTGCTGCTGATAGGGATTT
261 CTTTTGATTGGGTTTAGCTTTGTTGATAAATTATGCTTGTATATCTCTGCTGCTGATAGGAATTT
*
228839 AAGAGATGGTGAATGCTTTTCTTTCATTCGGCTGTTGCACCTCATCATTACATGAAAGAAAT
326 AAGAAATGGTGAATGCTTTTCTTTCATTCGGCTGTTGCACCTCATCATTACATGAAAGAAAT
* *
228901 ATGCTCTGCTAACTAAATATTGTTCTGGTGTGTATTCTTTTTCATCCTTTCCAACCCATTTGTTC
1 ATGCTCTGCTAACTAAATATTGTTCTGGTGTGAATTCTTTTTCATCCTTTCCAACCCATTTGTCC
* *
228966 TTCTACCCTGAGAAGCCTTTGATGATTTGTTACAGGCGTTTTGCCAGCATGGGAGCGACCACCTG
66 TTCTACCCTGAGAAGCCTTTGATGATTTGTTACAGGCGTTTTGCCAGCATGGGAGCAACCACCAG
* *
229031 CAC-GGCAGTATGAAAAGCCCTTTTGATTCTACAATTGTGCGGGATATGTGAGGAAATACGGCTT
131 CACAGG-AGCATGAAAAGCCCTTTTGATTCTACAATTGCGCGGGATATGTGAGGAAATACGGCTT
** * **
229095 AGAATGTTAACATTAGTCCTTGAGGTTCCTTTCTCACTATTGTTAGTTCCATCCAATTGCAACTT
195 AGAACATTAACATTAATCCCCGAGGTTCCTTTCTCACTATTGTTAGTTCCATCCAATTGCAACTT
* *
229160 GCTTTTGATTTGGTTTAGGTTTGTTGATAAATTATGCTTGTATATCTCTGCTGCTGATAGGAATT
260 GCTTTTGATTGGGTTTAGCTTTGTTGATAAATTATGCTTGTATATCTCTGCTGCTGATAGGAATT
* *
229225 TAAGAAATGGTGAATGCTTTTCTTTCATTTGGCTGTTGCACCTCTTCATTACATGAAAGAAA
325 TAAGAAATGGTGAATGCTTTTCTTTCATTCGGCTGTTGCACCTCATCATTACATGAAAGAAA
229287 GATCTTCATG
Statistics
Matches: 361, Mismatches: 24, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
386 2 0.01
387 359 0.99
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (387 bp):
ATGCTCTGCTAACTAAATATTGTTCTGGTGTGAATTCTTTTTCATCCTTTCCAACCCATTTGTCC
TTCTACCCTGAGAAGCCTTTGATGATTTGTTACAGGCGTTTTGCCAGCATGGGAGCAACCACCAG
CACAGGAGCATGAAAAGCCCTTTTGATTCTACAATTGCGCGGGATATGTGAGGAAATACGGCTTA
GAACATTAACATTAATCCCCGAGGTTCCTTTCTCACTATTGTTAGTTCCATCCAATTGCAACTTG
CTTTTGATTGGGTTTAGCTTTGTTGATAAATTATGCTTGTATATCTCTGCTGCTGATAGGAATTT
AAGAAATGGTGAATGCTTTTCTTTCATTCGGCTGTTGCACCTCATCATTACATGAAAGAAAT
Found at i:237677 original size:16 final size:15
Alignment explanation
Indices: 237565--237678 Score: 54
Period size: 16 Copynumber: 7.2 Consensus size: 15
237555 AAAGATAAAA
*
237565 AAATATATATATACAT
1 AAATA-ATAAATACAT
237581 AAATAATAAAATACACAT
1 AAATAAT-AAAT--ACAT
* * *
237599 AAATATTAACAAAAAAT
1 AAATAAT-A-AATACAT
* *
237616 AGATAAATAAATATAT
1 AAAT-AATAAATACAT
* *
237632 ACATATATTAATACAT
1 AAATA-ATAAATACAT
237648 -AATAAT-AATA-AT
1 AAATAATAAATACAT
237660 AAATAATACAATACAT
1 AAATAATA-AATACAT
237676 AAA
1 AAA
237679 ATACAAAAGA
Statistics
Matches: 76, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
12 2 0.03
13 10 0.13
14 2 0.03
15 10 0.13
16 29 0.38
17 7 0.09
18 14 0.18
19 2 0.03
ACGTcount: A:0.63, C:0.07, G:0.01, T:0.29
Consensus pattern (15 bp):
AAATAATAAATACAT
Found at i:237954 original size:43 final size:43
Alignment explanation
Indices: 237904--238170 Score: 254
Period size: 43 Copynumber: 6.2 Consensus size: 43
237894 AGAAGAGCTA
* *
237904 TATTTATTTTTCAAAAGTCATTTAGCCTCTGTTTAGAGAAGCCT
1 TATTTATTTTTC-AAAGTCGTTGAGCCTCTGTTTAGAGAAGCCT
* * * *
237948 TA-TTATTTCTCAAAAGTCGTTGAGTCTCTGTTTAGAGGAGCCC
1 TATTTATTTTTC-AAAGTCGTTGAGCCTCTGTTTAGAGAAGCCT
* ** * * * *
237991 TATTTATTTTTCTTAA-TTATTGAGCCTCTGCTTATAGGAGTCT
1 TATTTATTTTTC-AAAGTCGTTGAGCCTCTGTTTAGAGAAGCCT
* * * * *
238034 TATTTATTTTTCAAAGTTGTTAAGCTTCTGCTTAGAAAAG-CT
1 TATTTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGAAGCCT
* *
238076 TATTTATTTTTTAAAGTCGTTGAGCCTTTGTTTAGACG-AGCCT
1 TATTTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGA-GAAGCCT
* * * *
238119 TATTTATTTATCAAAGTCGTTGAGTCTCTATTTAGGGAAGCCT
1 TATTTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGAAGCCT
238162 TATTTATTT
1 TATTTATTT
238171 GTTAAGCTTT
Statistics
Matches: 182, Mismatches: 36, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
42 37 0.20
43 133 0.73
44 12 0.07
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.45
Consensus pattern (43 bp):
TATTTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGAAGCCT
Found at i:238142 original size:128 final size:130
Alignment explanation
Indices: 237904--238147 Score: 289
Period size: 128 Copynumber: 1.9 Consensus size: 130
237894 AGAAGAGCTA
* * *
237904 TATTTATTTTTCAAAAGTCATTTAGCCTCTGTTTAGAGAAGCCTTATTATTTCTCAAAAGTCGTT
1 TATTTATTTTTCAAAAGTCATTAAGCCTCTGCTTAGAAAAGCCTTATTATTTCTCAAAAGTCGTT
* * * * *
237969 GAGTCTCTGTTTAGAGGAGCCCTATTTATTTTTCTTAATTATTGAGCCTCTGCTTATAGGAGTCT
66 GAGCCTCTGTTTAGACGAGCCCTATTTATTTATCTAAATCATTGAGCCTCTGCTTATAGGAGTCT
** * **
238034 TATTTATTTTTC-AAAGTTGTTAAGCTTCTGCTTAGAAAAG-CTTATTTATTT-TTTAAAGTCGT
1 TATTTATTTTTCAAAAGTCATTAAGCCTCTGCTTAGAAAAGCCTTA-TTATTTCTCAAAAGTCGT
* * * *
238096 TGAGCCTTTGTTTAGACGAGCCTTATTTATTTATC-AAAGTCGTTGAGTCTCT
65 TGAGCCTCTGTTTAGACGAGCCCTATTTATTTATCTAAA-TCATTGAGCCTCT
238148 ATTTAGGGAA
Statistics
Matches: 95, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
127 2 0.02
128 53 0.56
129 28 0.29
130 12 0.13
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (130 bp):
TATTTATTTTTCAAAAGTCATTAAGCCTCTGCTTAGAAAAGCCTTATTATTTCTCAAAAGTCGTT
GAGCCTCTGTTTAGACGAGCCCTATTTATTTATCTAAATCATTGAGCCTCTGCTTATAGGAGTCT
Found at i:239179 original size:9 final size:9
Alignment explanation
Indices: 239159--239200 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
239149 TCTTGTTTGG
239159 ATTTTAATTT
1 ATTTT-ATTT
239169 ATTTTATTT
1 ATTTTATTT
*
239178 A-TTTAGTT
1 ATTTTATTT
239186 ATTTTATTT
1 ATTTTATTT
239195 ATTTTA
1 ATTTTA
239201 AAAGTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 7 0.24
9 17 0.59
10 5 0.17
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (9 bp):
ATTTTATTT
Found at i:239483 original size:13 final size:13
Alignment explanation
Indices: 239450--239483 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
239440 AAAAGAGAAA
*
239450 AATAAAAAATTTT
1 AATAAAAAATTTG
239463 AATAAAAAATTTGG
1 AATAAAAAATTT-G
239477 AATAAAA
1 AATAAAA
239484 TACTAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (13 bp):
AATAAAAAATTTG
Found at i:242743 original size:8 final size:8
Alignment explanation
Indices: 242730--242773 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
242720 ATTAATTTTG
242730 TATTTATA
1 TATTTATA
242738 TATTTATA
1 TATTTATA
*
242746 TAATTATA
1 TATTTATA
242754 TATTTA-A
1 TATTTATA
*
242761 -ATTTTTA
1 TATTTATA
242768 TATTTA
1 TATTTA
242774 AAAAATAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
6 4 0.13
7 2 0.07
8 24 0.80
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATTTATA
Found at i:254419 original size:15 final size:15
Alignment explanation
Indices: 254399--254430 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
254389 ATGTCGGTGT
254399 AGGTGAGAACTTCAA
1 AGGTGAGAACTTCAA
254414 AGGTGAGAACTTCAA
1 AGGTGAGAACTTCAA
254429 AG
1 AG
254431 TTGCAGCTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.28, T:0.19
Consensus pattern (15 bp):
AGGTGAGAACTTCAA
Found at i:254983 original size:18 final size:19
Alignment explanation
Indices: 254969--255007 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
254959 TAATTTCTTA
254969 ATAA-TATTTTTTTTCATT
1 ATAAGTATTTTTTTTCATT
254987 ATAATGTATTTTTTTT-ATT
1 ATAA-GTATTTTTTTTCATT
255006 AT
1 AT
255008 CATTATGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 5 0.26
20 10 0.53
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
ATAAGTATTTTTTTTCATT
Found at i:262680 original size:2 final size:2
Alignment explanation
Indices: 262673--262713 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
262663 GTTTCATTTC
262673 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
262714 CCATTCCAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:264589 original size:2 final size:2
Alignment explanation
Indices: 264582--264607 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
264572 ATCTCTTTAA
264582 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
264608 GGAAATGGAA
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:270844 original size:2 final size:2
Alignment explanation
Indices: 270837--270867 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
270827 TTATTTATTA
270837 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
270868 ACCACAAGTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:278504 original size:15 final size:15
Alignment explanation
Indices: 278473--278501 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
278463 ATGAGATGGG
278473 GGAAAAGAAGAGAAA
1 GGAAAAGAAGAGAAA
278488 GGAAAAGAA-AGAAA
1 GGAAAAGAAGAGAAA
278502 AGGGGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (15 bp):
GGAAAAGAAGAGAAA
Found at i:282044 original size:25 final size:25
Alignment explanation
Indices: 282016--282065 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
282006 AGTTGTAGTG
282016 AGAAATAGTTGAACTTTACCATGGT
1 AGAAATAGTTGAACTTTACCATGGT
282041 AGAAATAGTTGAACTTTACCATGGT
1 AGAAATAGTTGAACTTTACCATGGT
282066 TAAGTCAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (25 bp):
AGAAATAGTTGAACTTTACCATGGT
Found at i:287369 original size:12 final size:14
Alignment explanation
Indices: 287354--287385 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
287344 TTTAATTTTT
287354 TATTTATAT-A-TA
1 TATTTATATAATTA
287366 TATTTATATAATTA
1 TATTTATATAATTA
287380 TATTTA
1 TATTTA
287386 AAAAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.50
13 1 0.06
14 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTTATATAATTA
Found at i:294630 original size:14 final size:15
Alignment explanation
Indices: 294611--294639 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
294601 TATCAATTTA
294611 AAAAATTT-ATAAAT
1 AAAAATTTAATAAAT
294625 AAAAATTTAATAAAT
1 AAAAATTTAATAAAT
294640 TCAAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAATTTAATAAAT
Found at i:296377 original size:16 final size:16
Alignment explanation
Indices: 296356--296391 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
296346 ATTAAAAATC
*
296356 ATCATAAGTCATCATA
1 ATCATAAATCATCATA
*
296372 ATCATAAATCATCATT
1 ATCATAAATCATCATA
296388 ATCA
1 ATCA
296392 ATCGTTTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.33
Consensus pattern (16 bp):
ATCATAAATCATCATA
Found at i:302224 original size:7 final size:7
Alignment explanation
Indices: 302213--302246 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
302203 ATACCAATTG
*
302213 CTGAGGG
1 CTGAGGA
302220 CTGAGGA
1 CTGAGGA
*
302227 CTGAGCA
1 CTGAGGA
302234 CTGAGGA
1 CTGAGGA
302241 CTGAGG
1 CTGAGG
302247 GTCGCCCGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.24, C:0.18, G:0.44, T:0.15
Consensus pattern (7 bp):
CTGAGGA
Found at i:302506 original size:17 final size:15
Alignment explanation
Indices: 302475--302511 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 15
302465 TAAATTTATT
302475 CAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAA
302490 CAAAAACAAAAACAAAA
1 CAAAAA-AAAAA-AAAA
302507 CAAAA
1 CAAAA
302512 GAAAGATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
16 5 0.25
17 9 0.45
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (15 bp):
CAAAAAAAAAAAAAA
Found at i:303733 original size:2 final size:2
Alignment explanation
Indices: 303726--303753 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
303716 ATATAATAGA
303726 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
303754 CTCACAAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:306019 original size:21 final size:23
Alignment explanation
Indices: 305995--306046 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
305985 ATAATTTAAC
* *
305995 ATATATATTTTA-ATATTTATA-
1 ATATATATTTCATATATATATAT
306016 ATATAATATTTCATATATATATAT
1 ATAT-ATATTTCATATATATATAT
306040 ATATATA
1 ATATATA
306047 AAATAGCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 7 0.27
23 11 0.42
24 4 0.15
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATATATTTCATATATATATAT
Found at i:310108 original size:2 final size:2
Alignment explanation
Indices: 310103--310165 Score: 72
Period size: 2 Copynumber: 31.5 Consensus size: 2
310093 CATGTGTGTG
* * * *
310103 TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA CA TA TA TG TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
310145 GA TA TA TA TA CA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
310166 TTTGTTTCAT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:314502 original size:2 final size:2
Alignment explanation
Indices: 314489--314522 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
314479 TAGACATGAC
* *
314489 AT AT AT AC AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
314523 GGCTTGGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:315692 original size:2 final size:2
Alignment explanation
Indices: 315681--315727 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
315671 ACACACACAC
*
315681 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
315723 AT AT A
1 AT AT A
315728 CACACACACA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:325568 original size:2 final size:2
Alignment explanation
Indices: 325561--325590 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
325551 TGGCAGGGTG
325561 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
325591 GCAGAATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:336087 original size:2 final size:2
Alignment explanation
Indices: 336080--336107 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
336070 TGGTGTTAGC
336080 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
336108 AACCATGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:351369 original size:3 final size:3
Alignment explanation
Indices: 351363--351391 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
351353 TAAGCATGTG
351363 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
351392 CCTCCCATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:351548 original size:2 final size:2
Alignment explanation
Indices: 351543--351569 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
351533 GAGGCAACGC
351543 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 T
351570 GGAAGATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:353540 original size:16 final size:17
Alignment explanation
Indices: 353510--353546 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
353500 AATTGTTACA
353510 AAATAAAAAATATAA-T
1 AAATAAAAAATATAATT
353526 AAAT-AAAAATAATAATT
1 AAATAAAAAAT-ATAATT
353543 AAAT
1 AAAT
353547 CAATTTCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 8 0.42
17 5 0.26
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATAAAAAATATAATT
Found at i:353653 original size:27 final size:28
Alignment explanation
Indices: 353590--353657 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 28
353580 TTTTCTAAAT
353590 AAATATCAAATCAATCTAGAATATTACTAG
1 AAATATC--ATCAATCTAGAATATTACTAG
353620 AATAATATCATCAATCTAGAATATTACTAG
1 -A-AATATCATCAATCTAGAATATTACTAG
353650 -AATATCAT
1 AAATATCAT
353658 TGGCACCCCG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
27 8 0.22
30 21 0.58
31 1 0.03
32 6 0.17
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (28 bp):
AAATATCATCAATCTAGAATATTACTAG
Found at i:358001 original size:41 final size:41
Alignment explanation
Indices: 357909--358007 Score: 103
Period size: 41 Copynumber: 2.4 Consensus size: 41
357899 ATCAATATCT
* * *
357909 AATATTCTCTAAATTAATATCAAATCAATCTAAAAATTACTAT
1 AATATTAT-TAAAATAATATC-AATCAATCTAAAAATTACTAA
*
357952 AATATTATTAAAATAATATC-ATCAATCTAGAATATTA-TCAA
1 AATATTATTAAAATAATATCAATCAATCTA-AAAATTACT-AA
*
357993 AATATTATTAGAATA
1 AATATTATTAAAATA
358008 TCATTAACAG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
40 10 0.20
41 21 0.43
42 11 0.22
43 7 0.14
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (41 bp):
AATATTATTAAAATAATATCAATCAATCTAAAAATTACTAA
Found at i:360248 original size:7 final size:7
Alignment explanation
Indices: 360223--360257 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
360213 ATGTATAAAA
360223 GAAATAT
1 GAAATAT
* *
360230 GGAATTT
1 GAAATAT
360237 GAAATAT
1 GAAATAT
360244 GAAATAT
1 GAAATAT
360251 GAAATAT
1 GAAATAT
360258 AATAGAAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.31
Consensus pattern (7 bp):
GAAATAT
Found at i:362139 original size:22 final size:22
Alignment explanation
Indices: 362113--362154 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
362103 TGTATATTTA
*
362113 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCTCTAAAATTAAG
362135 TATTTGTATCTCTAAAATTA
1 TATTTGTATCTCTAAAATTA
362155 GGATAGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (22 bp):
TATTTGTATCTCTAAAATTAAG
Found at i:366961 original size:5 final size:6
Alignment explanation
Indices: 366944--366968 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
366934 CACATTAGCC
366944 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
366969 ACAAATGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:372633 original size:13 final size:13
Alignment explanation
Indices: 372614--372643 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
372604 GTTTTAGATG
372614 AAATTTTTTG-AT
1 AAATTTTTTGCAT
372626 AAATTTTTTGCAT
1 AAATTTTTTGCAT
372639 AAATT
1 AAATT
372644 AAATGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (13 bp):
AAATTTTTTGCAT
Found at i:378919 original size:95 final size:95
Alignment explanation
Indices: 378753--378933 Score: 308
Period size: 95 Copynumber: 1.9 Consensus size: 95
378743 CTCGGTGCCG
*
378753 ACAGAGGCCACAGTGGACATATTCCTGAAAGACGTCACATTATGTCCCCAAAACGAATAAAAGAA
1 ACAGAGGCCACAGTGGACATATTCCTGAAAGACGGCACATTATGTCCCCAAAACGAATAAAAGAA
* * *
378818 CTTCCTTTTAGTCACATTCACACGGTCCCT
66 CCTCCTTTTAATAACATTCACACGGTCCCT
* *
378848 ACAGAGGCCACAGTGGACATATTCCTGAAAGACGGCACATTATGTCCCTAAAAGGAATAAAAGAA
1 ACAGAGGCCACAGTGGACATATTCCTGAAAGACGGCACATTATGTCCCCAAAACGAATAAAAGAA
378913 CCTCCTTTTAATAACATTCAC
66 CCTCCTTTTAATAACATTCAC
378934 GTAACACTTA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
95 80 1.00
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (95 bp):
ACAGAGGCCACAGTGGACATATTCCTGAAAGACGGCACATTATGTCCCCAAAACGAATAAAAGAA
CCTCCTTTTAATAACATTCACACGGTCCCT
Found at i:384331 original size:2 final size:2
Alignment explanation
Indices: 384324--384359 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
384314 AGTAGTGTAC
384324 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
384360 CTCCAACAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:387523 original size:24 final size:25
Alignment explanation
Indices: 387496--387551 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
387486 TTAAGTATAA
* *
387496 AAATTTTTA-TTTTTTATTGATTAC
1 AAATCTTTATTTTTTTATTAATTAC
*
387520 AAATCTTTATTTTTTTATTAATTAT
1 AAATCTTTATTTTTTTATTAATTAC
387545 AAATCTT
1 AAATCTT
387552 GATGTTGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (25 bp):
AAATCTTTATTTTTTTATTAATTAC
Found at i:391322 original size:2 final size:2
Alignment explanation
Indices: 391317--391350 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
391307 TTTCCTTTCC
*
391317 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
391351 TAATGTGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:396218 original size:40 final size:40
Alignment explanation
Indices: 396174--396254 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
396164 TCTTGTGACT
*
396174 ACCAAAATCCTCTTGTTCATCATTTACAAGTCATTAGAAC
1 ACCAAAATCCTCGTGTTCATCATTTACAAGTCATTAGAAC
396214 ACCAAAATCCTCGTGTTCATCATTTACAAGTCATTAGAAC
1 ACCAAAATCCTCGTGTTCATCATTTACAAGTCATTAGAAC
396254 A
1 A
396255 TAGTTGATGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.36, C:0.25, G:0.09, T:0.31
Consensus pattern (40 bp):
ACCAAAATCCTCGTGTTCATCATTTACAAGTCATTAGAAC
Found at i:398552 original size:15 final size:15
Alignment explanation
Indices: 398532--398560 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
398522 ATCAGGGTCA
398532 ATTTTTATATAAACG
1 ATTTTTATATAAACG
398547 ATTTTTATATAAAC
1 ATTTTTATATAAAC
398561 AAATAAAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.48
Consensus pattern (15 bp):
ATTTTTATATAAACG
Found at i:401641 original size:26 final size:26
Alignment explanation
Indices: 401591--401645 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
401581 ACCAATTAAA
401591 GAAAGAAAAGTAACTAGCCAAAAGGT
1 GAAAGAAAAGTAACTAGCCAAAAGGT
*
401617 GAAAGAAAAGTACCTAGCCAAAAGGT
1 GAAAGAAAAGTAACTAGCCAAAAGGT
401643 GAA
1 GAA
401646 CATCCTCAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.53, C:0.13, G:0.24, T:0.11
Consensus pattern (26 bp):
GAAAGAAAAGTAACTAGCCAAAAGGT
Found at i:402381 original size:21 final size:20
Alignment explanation
Indices: 402357--402398 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
402347 AGGGGGAGAG
402357 GGTGGAGGATAAGAAGAAGGA
1 GGTGGAGGATAAGAAG-AGGA
* *
402378 GGTGTAGGATAAGCAGAGGA
1 GGTGGAGGATAAGAAGAGGA
402398 G
1 G
402399 AGATTTTGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.38, C:0.02, G:0.48, T:0.12
Consensus pattern (20 bp):
GGTGGAGGATAAGAAGAGGA
Found at i:420591 original size:3 final size:3
Alignment explanation
Indices: 420578--420630 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
420568 GTTTCAGTTG
*
420578 ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
420626 ATA AT
1 ATA AT
420631 TCCAGTAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:428138 original size:17 final size:20
Alignment explanation
Indices: 428100--428138 Score: 57
Period size: 17 Copynumber: 2.1 Consensus size: 20
428090 TTATATCTTA
428100 ATTTTATATATAAATATAAT
1 ATTTTATATATAAATATAAT
428120 ATTTT-TAT-TAAAT-TAAT
1 ATTTTATATATAAATATAAT
428137 AT
1 AT
428139 ATTAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 5 0.26
19 3 0.16
20 5 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTTATATATAAATATAAT
Found at i:428793 original size:10 final size:10
Alignment explanation
Indices: 428778--428807 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
428768 ATTAAATTTT
428778 TATATTTTAA
1 TATATTTTAA
428788 TATATTTTAA
1 TATATTTTAA
428798 T-TATTTTAA
1 TATATTTTAA
428807 T
1 T
428808 TGATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:430096 original size:18 final size:18
Alignment explanation
Indices: 430055--430096 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
430045 ATGAGGTGAT
430055 AAAATAAAATAATAATTA
1 AAAATAAAATAATAATTA
* *
430073 TAAATAAAATTAT-ATTA
1 AAAATAAAATAATAATTA
430090 AATAATA
1 AA-AATA
430097 TTGTTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATAAAATAATAATTA
Found at i:430715 original size:155 final size:149
Alignment explanation
Indices: 430359--430715 Score: 328
Period size: 150 Copynumber: 2.3 Consensus size: 149
430349 AAGTGTGAAC
* * * ** * * * *
430359 TCTAAAAATATTAATAGTGAACGACATAAAT-ACATTTATAAATTTTAAGAAATAACAAATTTAC
1 TCTAAAAATGTTAAAAATGAATAACATAAATCA-AATTATAAATATTAA-AAACAACAAATTTAA
* * **
430423 TTTAAATTTTTAGCATTATTTATTTATTTAATAATGATTATTTATCATTAAATCTATATTTTATT
64 TTTAAATTTCTAGCATTATTTATTTATTTAATAAAGATTATTTATCATTAAAAATATATTTTATT
430488 AGTTAGTTATTTAAATTTAAA
129 AGTTAGTTATTTAAATTTAAA
* **** *
430509 TCTAAAAGTGTTAAAAATGAATAACATAAATGTCTTTATAAATTTTAAAAAACAACAAATTTATA
1 TCTAAAAATGTTAAAAATGAATAACATAAATCAAATTATAAATATT-AAAAACAACAAATTTA-A
* * *
430574 TTTCAATTTCTAGCATTTTTTTATTTATTTAATAAAGATTATTTGTCATTAAAAATATAGCTTTT
64 TTTAAATTTCTAGCA-TTATTTATTTATTTAATAAAGATTATTTATCATTAAAAATATA---TTT
*
430639 TATTTGTTAGTTATTTAAATTTAAA
125 TATTAGTTAGTTATTTAAATTTAAA
* * *
430664 TCAATTAAAAAT-TTACAAAT-AA-AATATATATCAAATTA-AACTATATTAAAAA
1 TC---TAAAAATGTTAAAAATGAATAACATAAATCAAATTATAA--ATATTAAAAA
430716 TTTATTTGTG
Statistics
Matches: 168, Mismatches: 27, Indels: 19
0.79 0.13 0.09
Matches are distributed among these distances:
150 50 0.30
151 15 0.09
152 38 0.23
154 2 0.01
155 44 0.26
156 6 0.04
157 7 0.04
158 6 0.04
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (149 bp):
TCTAAAAATGTTAAAAATGAATAACATAAATCAAATTATAAATATTAAAAACAACAAATTTAATT
TAAATTTCTAGCATTATTTATTTATTTAATAAAGATTATTTATCATTAAAAATATATTTTATTAG
TTAGTTATTTAAATTTAAA
Found at i:431107 original size:17 final size:17
Alignment explanation
Indices: 431085--431124 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
431075 AGATTAATCG
*
431085 AAATTAAAGTTCATACT
1 AAATTAAAGTTCATACA
431102 AAATTAAAGTTCATACA
1 AAATTAAAGTTCATACA
431119 AAATTA
1 AAATTA
431125 TAAATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.33
Consensus pattern (17 bp):
AAATTAAAGTTCATACA
Found at i:431148 original size:23 final size:24
Alignment explanation
Indices: 431101--431148 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
431091 AAGTTCATAC
*
431101 TAAATTAAAGTTCATACAAAATTA
1 TAAATTAAAGTTCATAAAAAATTA
431125 TAAATTAAA-TT-ATAAAAAAATTA
1 TAAATTAAAGTTCAT-AAAAAATTA
431148 T
1 T
431149 TCAAAAAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 2 0.09
23 11 0.50
24 9 0.41
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (24 bp):
TAAATTAAAGTTCATAAAAAATTA
Found at i:432198 original size:44 final size:44
Alignment explanation
Indices: 432146--432253 Score: 144
Period size: 44 Copynumber: 2.5 Consensus size: 44
432136 TAATAGTATA
* * *
432146 TAGTAAATCATTGATAATTTTATAGTAAATTATTGACAATTTAG
1 TAGTAAATCAATGATAATTTTATAGCAAATTATTGACAACTTAG
* * * *
432190 TAGTAAATCACTAATAATGTTATAGCAAATTATTGATAACTTAG
1 TAGTAAATCAATGATAATTTTATAGCAAATTATTGACAACTTAG
*
432234 TTGTAAATCAATGATAATTT
1 TAGTAAATCAATGATAATTT
432254 AGTATAAATT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (44 bp):
TAGTAAATCAATGATAATTTTATAGCAAATTATTGACAACTTAG
Found at i:432253 original size:66 final size:65
Alignment explanation
Indices: 432102--432262 Score: 159
Period size: 66 Copynumber: 2.5 Consensus size: 65
432092 CTAAAACTCA
** * * * *
432102 ATAGTAAATCAATGATAACATGGTAGCAAATGCATAATAGTATATAGTAAATCATTGATAATTTT
1 ATAGTAAATCAATGATAATTTAGTAGTAAATGCATAATAGTATATAGCAAATCATTGATAATCTT
* * * *
432167 ATAGTAAATTATTGACAATTTAGTAGTAAAT-CACTAATAATGT-TATAGCAAATTATTGATAA-
1 ATAGTAAATCAATGATAATTTAGTAGTAAATGCA-TAAT-A-GTATATAGCAAATCATTGATAAT
432229 CTT
63 CTT
*
432232 AGTTGTAAATCAATGATAATTTAGTA-TAAAT
1 A-TAGTAAATCAATGATAATTTAGTAGTAAAT
432263 TAATAATGAT
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
64 2 0.03
65 36 0.46
66 38 0.49
67 2 0.03
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (65 bp):
ATAGTAAATCAATGATAATTTAGTAGTAAATGCATAATAGTATATAGCAAATCATTGATAATCTT
Found at i:432255 original size:22 final size:22
Alignment explanation
Indices: 432146--432262 Score: 114
Period size: 22 Copynumber: 5.4 Consensus size: 22
432136 TAATAGTATA
432146 TAGTAAATCATTGATAATTTTA-
1 TAGTAAATCATTGATAA-TTTAG
* *
432168 TAGTAAATTATTGACAATTTAG
1 TAGTAAATCATTGATAATTTAG
* *
432190 TAGTAAATCACTAATAATGTTA-
1 TAGTAAATCATTGATAAT-TTAG
* * *
432212 TAGCAAATTATTGATAACTTAG
1 TAGTAAATCATTGATAATTTAG
* *
432234 TTGTAAATCAATGATAATTTAG
1 TAGTAAATCATTGATAATTTAG
432256 TA-TAAAT
1 TAGTAAAT
432263 TAATAATGAT
Statistics
Matches: 75, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
21 12 0.16
22 60 0.80
23 3 0.04
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (22 bp):
TAGTAAATCATTGATAATTTAG
Found at i:432286 original size:22 final size:22
Alignment explanation
Indices: 432183--432286 Score: 77
Period size: 22 Copynumber: 4.8 Consensus size: 22
432173 AATTATTGAC
* * *
432183 AATTTAGTAGTAAATCACTAAT
1 AATTTAGTTGTAAATTAATAAT
* * * *
432205 AATGTTA-TAGCAAATTATTGAT
1 AAT-TTAGTTGTAAATTAATAAT
* * *
432227 AACTTAGTTGTAAATCAATGAT
1 AATTTAGTTGTAAATTAATAAT
*
432249 AATTTAG-TATAAATTAATAAT
1 AATTTAGTTGTAAATTAATAAT
*
432270 GATTTAGTTGTAAATTA
1 AATTTAGTTGTAAATTA
432287 GTTAATTATT
Statistics
Matches: 64, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
21 20 0.31
22 41 0.64
23 3 0.05
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (22 bp):
AATTTAGTTGTAAATTAATAAT
Found at i:432344 original size:22 final size:21
Alignment explanation
Indices: 432285--432362 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 21
432275 AGTTGTAAAT
* *
432285 TAGTTAATTATTAACAACTTCT-
1 TAGTAAATTA-TAATAACTT-TA
*
432307 TAGTAAATCATCAATAACTTTA
1 TAGTAAATTAT-AATAACTTTA
*
432329 TAGTAAATTAGTAATAATTTTA
1 TAGTAAATTA-TAATAACTTTA
*
432351 TAATAAATTATA
1 TAGTAAATTATA
432363 GTAAATTAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
21 4 0.09
22 42 0.89
23 1 0.02
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (21 bp):
TAGTAAATTATAATAACTTTA
Found at i:432364 original size:32 final size:32
Alignment explanation
Indices: 432326--432393 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
432316 ATCAATAACT
*
432326 TTATAGTAAATTAGTAATAATTTTATAATAAA
1 TTATAGTAAATTAGTAATAACTTTATAATAAA
432358 TTATAGTAAATTAGTAATAACTTTATAATAAA
1 TTATAGTAAATTAGTAATAACTTTATAATAAA
432390 TTAT
1 TTAT
432394 CTATAACTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (32 bp):
TTATAGTAAATTAGTAATAACTTTATAATAAA
Found at i:432370 original size:76 final size:76
Alignment explanation
Indices: 432258--432434 Score: 200
Period size: 76 Copynumber: 2.4 Consensus size: 76
432248 TAATTTAGTA
* * ** * * *
432258 TAAATTAATAATGATTTAGTTGTAAA-T-TAGTTAATTATTAACAACTTCT-TAGTAAATCATCA
1 TAAATTAGTAATAATTTAGTAATAAATTATAGTAAATTAGTAACAACTT-TATAATAAATCATCA
*
432320 ATAACTTTATAG
65 ATAACTTAATAG
* * *
432332 TAAATTAGTAATAATTTTA-TAATAAATTATAGTAAATTAGTAATAACTTTATAATAAATTATCT
1 TAAATTAGTAATAA-TTTAGTAATAAATTATAGTAAATTAGTAACAACTTTATAATAAATCATCA
432396 ATAACTTAATAG
65 ATAACTTAATAG
*
432408 TAAATTATTAATAATTTAGTAATAAAT
1 TAAATTAGTAATAATTTAGTAATAAAT
432435 CATTTATAAC
Statistics
Matches: 86, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
74 17 0.20
75 10 0.12
76 59 0.69
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.42
Consensus pattern (76 bp):
TAAATTAGTAATAATTTAGTAATAAATTATAGTAAATTAGTAACAACTTTATAATAAATCATCAA
TAACTTAATAG
Found at i:432414 original size:44 final size:44
Alignment explanation
Indices: 432360--432456 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 44
432350 ATAATAAATT
*
432360 ATAGTAAATTAGTAATAACTTTA-TAATAAATTATCTATAACTTA
1 ATAGTAAATTAGTAATAA-TTTAGTAATAAATCATCTATAACTTA
* *
432404 ATAGTAAATTATTAATAATTTAGTAATAAATCATTTATAACTTA
1 ATAGTAAATTAGTAATAATTTAGTAATAAATCATCTATAACTTA
* *
432448 GTAATAAAT
1 ATAGTAAAT
432457 CATCTATAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 4 0.09
44 43 0.91
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (44 bp):
ATAGTAAATTAGTAATAATTTAGTAATAAATCATCTATAACTTA
Found at i:432445 original size:66 final size:66
Alignment explanation
Indices: 432374--432498 Score: 173
Period size: 66 Copynumber: 1.9 Consensus size: 66
432364 TAAATTAGTA
* * *
432374 ATAACTTTA-TAATAAATTATCTATAACTTAAT-AGTAAATTATTAATAATTTAGTAATAAATCA
1 ATAAC-TTAGTAATAAATCATCTATAACTTAATGA-TAAATTAATAATAATTTAGAAATAAATCA
432437 TTT
64 TTT
* *
432440 ATAACTTAGTAATAAATCATCTATAACTTAGTGATAAATTAATGATAATTTAGAAATAA
1 ATAACTTAGTAATAAATCATCTATAACTTAATGATAAATTAATAATAATTTAGAAATAA
432499 TCAATGATAA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
65 3 0.06
66 48 0.92
67 1 0.02
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (66 bp):
ATAACTTAGTAATAAATCATCTATAACTTAATGATAAATTAATAATAATTTAGAAATAAATCATT
T
Found at i:432454 original size:11 final size:10
Alignment explanation
Indices: 432326--432434 Score: 74
Period size: 11 Copynumber: 10.1 Consensus size: 10
432316 ATCAATAACT
*
432326 TTATAGTAAA
1 TTATAATAAA
*
432336 TTAGTAATAATT
1 TTA-TAATAA-A
432348 TTATAATAAA
1 TTATAATAAA
*
432358 TTATAGTAAA
1 TTATAATAAA
*
432368 TTAGTAATAACT
1 TTA-TAATAA-A
432380 TTATAATAAA
1 TTATAATAAA
* *
432390 TTATCTATAAC
1 TTAT-AATAAA
*
432401 TTAATAGTAAA
1 TT-ATAATAAA
*
432412 TTATTAATAAT
1 TTA-TAATAAA
432423 TTAGTAATAAA
1 TTA-TAATAAA
432434 T
1 T
432435 CATTTATAAC
Statistics
Matches: 76, Mismatches: 16, Indels: 13
0.72 0.15 0.12
Matches are distributed among these distances:
10 20 0.26
11 48 0.63
12 8 0.11
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (10 bp):
TTATAATAAA
Found at i:432457 original size:22 final size:22
Alignment explanation
Indices: 432374--432478 Score: 115
Period size: 22 Copynumber: 4.8 Consensus size: 22
432364 TAAATTAGTA
*
432374 ATAACTTTA-TAATAAATTATCT
1 ATAAC-TTAGTAATAAATCATCT
* * *
432396 ATAACTTAATAGTAAATTAT-T
1 ATAACTTAGTAATAAATCATCT
* *
432417 AATAATTTAGTAATAAATCATTT
1 -ATAACTTAGTAATAAATCATCT
432440 ATAACTTAGTAATAAATCATCT
1 ATAACTTAGTAATAAATCATCT
*
432462 ATAACTTAGTGATAAAT
1 ATAACTTAGTAATAAAT
432479 TAATGATAAT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
21 4 0.06
22 67 0.93
23 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.41
Consensus pattern (22 bp):
ATAACTTAGTAATAAATCATCT
Found at i:432487 original size:22 final size:22
Alignment explanation
Indices: 432336--432498 Score: 102
Period size: 22 Copynumber: 7.5 Consensus size: 22
432326 TTATAGTAAA
* * * *
432336 TTAGTAATAATTTTATAATAAA
1 TTAGTAATAAATTAATTATAAC
* * *
432358 TTA-TAGTAAATTAGTAATAAC
1 TTAGTAATAAATTAATTATAAC
432379 TTTA-TAATAAATT-ATCTATAAC
1 -TTAGTAATAAATTAAT-TATAAC
* * *
432401 TTAATAGTAAATT-ATTAATAAT
1 TTAGTAATAAATTAATT-ATAAC
* *
432423 TTAGTAATAAATCATTTATAAC
1 TTAGTAATAAATTAATTATAAC
*
432445 TTAGTAATAAA-TCATCTATAAC
1 TTAGTAATAAATTAAT-TATAAC
* * *
432467 TTAGTGATAAATTAATGATAAT
1 TTAGTAATAAATTAATTATAAC
*
432489 TTAGAAATAA
1 TTAGTAATAA
432499 TCAATGATAA
Statistics
Matches: 110, Mismatches: 24, Indels: 14
0.74 0.16 0.09
Matches are distributed among these distances:
21 19 0.17
22 86 0.78
23 5 0.05
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (22 bp):
TTAGTAATAAATTAATTATAAC
Found at i:432830 original size:22 final size:22
Alignment explanation
Indices: 432756--432830 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
432746 TAATTTATTG
* * * *
432756 ATAAATTAATAGTAAATCATAA
1 ATAACTTAGTAGTAAATAATTA
* *
432778 ATAACTTAGTAGTAATTCAATTG
1 ATAACTTAGTAGTAAAT-AATTA
*
432801 ATAGCTTAGTAGTAAATAATTA
1 ATAACTTAGTAGTAAATAATTA
432823 ATAACTTA
1 ATAACTTA
432831 ACAGCTAATT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
22 25 0.60
23 17 0.40
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (22 bp):
ATAACTTAGTAGTAAATAATTA
Found at i:433034 original size:22 final size:22
Alignment explanation
Indices: 432993--433137 Score: 73
Period size: 22 Copynumber: 6.6 Consensus size: 22
432983 TAAATTAGTT
* * * *
432993 AATCATTGATAATTTTATAGCA
1 AATCATTTATAACTTCATAGAA
433015 AATCATTTATAACTTCATAGAA
1 AATCATTTATAACTTCATAGAA
* * *
433037 AATTAGTTATAACTTTAT-GATA
1 AATCATTTATAACTTCATAGA-A
* **
433059 AATTATCAATAACTT-AGTA-ATA
1 AATCATTTATAACTTCA-TAGA-A
* * *
433081 AATCATTCATAACTTAATAGTA
1 AATCATTTATAACTTCATAGAA
* * *
433103 AATCATTGATAATTTAATA-ATA
1 AATCATTTATAACTTCATAGA-A
*
433125 AATCATTAATAAC
1 AATCATTTATAAC
433138 ATAATAATAA
Statistics
Matches: 98, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
21 3 0.03
22 94 0.96
23 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.39
Consensus pattern (22 bp):
AATCATTTATAACTTCATAGAA
Found at i:433136 original size:66 final size:66
Alignment explanation
Indices: 433014--433149 Score: 159
Period size: 66 Copynumber: 2.1 Consensus size: 66
433004 ATTTTATAGC
* * * * * * *
433014 AAATCATTTATAACTTCATAGAAAATTAGTTATAACTTTATGATAAATTATCAATAACTTAGTAA
1 AAATCATTCATAACTTAATAGAAAATCAGTTATAACTTTATAATAAATCATCAATAACATAATAA
433079 T
66 T
* *
433080 AAATCATTCATAACTTAATAGTAAATCA-TTGATAA-TTTAATAATAAATCATTAATAACATAAT
1 AAATCATTCATAACTTAATAGAAAATCAGTT-ATAACTTT-ATAATAAATCATCAATAACATAAT
433143 AAT
64 AAT
433146 AAAT
1 AAAT
433150 TAGTTATAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
65 5 0.08
66 54 0.92
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (66 bp):
AAATCATTCATAACTTAATAGAAAATCAGTTATAACTTTATAATAAATCATCAATAACATAATAA
T
Found at i:433158 original size:22 final size:22
Alignment explanation
Indices: 433014--433149 Score: 123
Period size: 22 Copynumber: 6.2 Consensus size: 22
433004 ATTTTATAGC
* *
433014 AAATCATTTATAACTTCATAGA-
1 AAATCATTAATAACTTAATA-AT
* * *
433036 AAATTAGTT-ATAACTTTATGAT
1 AAATCA-TTAATAACTTAATAAT
* * *
433058 AAATTATCAATAACTTAGTAAT
1 AAATCATTAATAACTTAATAAT
* *
433080 AAATCATTCATAACTTAATAGT
1 AAATCATTAATAACTTAATAAT
* *
433102 AAATCATTGATAATTTAATAAT
1 AAATCATTAATAACTTAATAAT
*
433124 AAATCATTAATAACATAATAAT
1 AAATCATTAATAACTTAATAAT
433146 AAAT
1 AAAT
433150 TAGTTATAAT
Statistics
Matches: 93, Mismatches: 18, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
21 2 0.02
22 89 0.96
23 2 0.02
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (22 bp):
AAATCATTAATAACTTAATAAT
Found at i:433231 original size:22 final size:23
Alignment explanation
Indices: 433173--433232 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 23
433163 TTATCAATGT
* *
433173 TAATTTAGTTGT-AATTTATTGA
1 TAATTAAGTTGTAAATTAATTGA
433195 TAACTTAA--TGATAAATTAATT-A
1 TAA-TTAAGTTG-TAAATTAATTGA
433217 TAATTAAGTTGTAAAT
1 TAATTAAGTTGTAAAT
433233 CAGTGATAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
21 6 0.19
22 13 0.42
23 12 0.39
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.47
Consensus pattern (23 bp):
TAATTAAGTTGTAAATTAATTGA
Found at i:440410 original size:2 final size:2
Alignment explanation
Indices: 440403--440436 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
440393 AATGAAGATG
440403 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
440437 GACGGTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:440651 original size:21 final size:22
Alignment explanation
Indices: 440621--440672 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
440611 GATATTTTTA
440621 AATA-TTTATA-TTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
440641 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
440663 AATATTTTAT
1 AATATTTTAT
440673 TAATTTCAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 20 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:440786 original size:2 final size:2
Alignment explanation
Indices: 440779--440813 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
440769 ATGTCATCCC
440779 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
440814 GTACTCACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:441302 original size:21 final size:21
Alignment explanation
Indices: 441276--441319 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
441266 TTTGCAGATG
441276 TCGGGATTTTTCTCCTTATCC
1 TCGGGATTTTTCTCCTTATCC
441297 TCGGGATTTTTCTCCTTATCC
1 TCGGGATTTTTCTCCTTATCC
441318 TC
1 TC
441320 ATCTTTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.30, G:0.14, T:0.48
Consensus pattern (21 bp):
TCGGGATTTTTCTCCTTATCC
Found at i:443713 original size:15 final size:16
Alignment explanation
Indices: 443687--443716 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
443677 TCATAGAGAA
443687 AAGGACAATAATTAAC
1 AAGGACAATAATTAAC
443703 AAGGA-AATAATTAA
1 AAGGACAATAATTAA
443717 AGTAATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (16 bp):
AAGGACAATAATTAAC
Found at i:447282 original size:23 final size:23
Alignment explanation
Indices: 447252--447298 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
447242 CCTTTTCGAG
447252 CCCATAAATTCTACAAGTCTGAC
1 CCCATAAATTCTACAAGTCTGAC
*
447275 CCCATAAATTCTAGAAGTCTGAC
1 CCCATAAATTCTACAAGTCTGAC
447298 C
1 C
447299 GGTGTACATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.26
Consensus pattern (23 bp):
CCCATAAATTCTACAAGTCTGAC
Found at i:450741 original size:28 final size:28
Alignment explanation
Indices: 450682--450745 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
450672 AGTAAATCCC
* * *
450682 AACA-CTAACTTTCATAAACTATTAACA
1 AACATCTAACCTTCATAAACCACTAACA
*
450709 AACATCTAACCTTCATAAACCACTAATA
1 AACATCTAACCTTCATAAACCACTAACA
*
450737 CACATCTAA
1 AACATCTAA
450746 TTTTTTATCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
27 4 0.13
28 27 0.87
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (28 bp):
AACATCTAACCTTCATAAACCACTAACA
Found at i:458054 original size:30 final size:30
Alignment explanation
Indices: 458018--458079 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
458008 AATTTTTGCA
458018 ACTTCATAAACACATGAAAAGCTCACTCCC
1 ACTTCATAAACACATGAAAAGCTCACTCCC
458048 ACTTCATAAACACATGAAAAGCTCACTCCC
1 ACTTCATAAACACATGAAAAGCTCACTCCC
458078 AC
1 AC
458080 ATTATAATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.34, G:0.06, T:0.19
Consensus pattern (30 bp):
ACTTCATAAACACATGAAAAGCTCACTCCC
Found at i:460814 original size:21 final size:21
Alignment explanation
Indices: 460781--460837 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 21
460771 ATAAATATAT
* *
460781 AATATATTCAAAAAT-TAAAGA
1 AATAAATTTAAAAATATAAA-A
*
460802 AATAAATTTAAAAGTATAAAA
1 AATAAATTTAAAAATATAAAA
460823 AATAATATTATAAAA
1 AATAA-ATT-TAAAA
460838 TTTTTATGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 18 0.60
22 7 0.23
23 5 0.17
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (21 bp):
AATAAATTTAAAAATATAAAA
Found at i:461060 original size:28 final size:29
Alignment explanation
Indices: 460982--461060 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 29
460972 ACTTTCTTGA
460982 AAAAAATTAAAATACTTATAAACTTATGTTTG
1 AAAAAA-TAAAATAC-TATAAA-TTATGTTTG
*
461014 AAAAAATAAAAT--TATAAATTTTGGTTTG
1 AAAAAATAAAATACTATAAATTAT-GTTTG
461042 -AAAAATAAAATACTA-AAAT
1 AAAAAATAAAATACTATAAAT
461061 AAAAAATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
27 14 0.33
28 15 0.35
29 2 0.05
31 6 0.14
32 6 0.14
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (29 bp):
AAAAAATAAAATACTATAAATTATGTTTG
Found at i:461530 original size:18 final size:16
Alignment explanation
Indices: 461502--461545 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
461492 CTTCTTTAGC
*
461502 TTTTTTT-TTTATTATT
1 TTTTTTTCTTTA-TACT
461518 TTTTTTTGCTTTATACT
1 TTTTTTT-CTTTATACT
461535 TTTTTTTCTTT
1 TTTTTTTCTTT
461546 TAAATAGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 11 0.44
17 10 0.40
18 4 0.16
ACGTcount: A:0.09, C:0.07, G:0.02, T:0.82
Consensus pattern (16 bp):
TTTTTTTCTTTATACT
Found at i:471394 original size:2 final size:2
Alignment explanation
Indices: 471387--471416 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
471377 GAGTGCACCA
471387 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
471417 TGGTAGTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:477345 original size:18 final size:18
Alignment explanation
Indices: 477284--477355 Score: 58
Period size: 18 Copynumber: 4.0 Consensus size: 18
477274 TTTAAATATG
*
477284 ATATGAATAAAAAATATAA
1 ATAT-AATAAAAATTATAA
* * *
477303 AAATAATATAATTTA-AA
1 ATATAATAAAAATTATAA
*
477320 ATTTTAATAAAAATTATAA
1 A-TATAATAAAAATTATAA
*
477339 ATATAATTAAAA-TATAA
1 ATATAATAAAAATTATAA
477356 TTTTTTATAT
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
17 8 0.20
18 27 0.66
19 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (18 bp):
ATATAATAAAAATTATAA
Found at i:482781 original size:15 final size:15
Alignment explanation
Indices: 482751--482867 Score: 115
Period size: 15 Copynumber: 8.1 Consensus size: 15
482741 TAATTTTACT
*
482751 TATTAAT-AATATTA
1 TATTAATAAATAATA
482765 TATTAATAAAT-A-A
1 TATTAATAAATAATA
482778 TA-TAAT-AATAATA
1 TATTAATAAATAATA
482791 TATTAATAAATATTATCA
1 TATTAATAAATA--AT-A
* *
482809 TATTTATTAATAAT-
1 TATTAATAAATAATA
482823 TATT-AT-AATAATA
1 TATTAATAAATAATA
*
482836 TACTAATAAATAATA
1 TATTAATAAATAATA
482851 TATTAATAAATAATA
1 TATTAATAAATAATA
482866 TA
1 TA
482868 AAGAATAATA
Statistics
Matches: 87, Mismatches: 5, Indels: 21
0.77 0.04 0.19
Matches are distributed among these distances:
11 3 0.03
12 11 0.13
13 11 0.13
14 17 0.20
15 30 0.34
16 2 0.02
17 2 0.02
18 11 0.13
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
TATTAATAAATAATA
Found at i:482785 original size:26 final size:25
Alignment explanation
Indices: 482754--482859 Score: 105
Period size: 26 Copynumber: 4.4 Consensus size: 25
482744 TTTTACTTAT
*
482754 TAATAATATTATATTAATAAATAATA
1 TAATAATAATATATTAATAAAT-ATA
482780 TAATAATAATATATTAATAAATAT-
1 TAATAATAATATATTAATAAATATA
* *
482804 T-ATCAT-ATTTATTAAT-AAT-TA
1 TAATAATAATATATTAATAAATATA
* *
482825 TTATAATAATATACTAATAAATAATA
1 TAATAATAATATATTAATAAAT-ATA
*
482851 TATTAATAA
1 TAATAATAA
482860 ATAATATAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
20 1 0.02
21 4 0.06
22 13 0.20
23 12 0.18
24 4 0.06
25 2 0.03
26 30 0.45
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TAATAATAATATATTAATAAATATA
Found at i:482851 original size:48 final size:49
Alignment explanation
Indices: 482759--482855 Score: 126
Period size: 48 Copynumber: 2.0 Consensus size: 49
482749 CTTATTAATA
*
482759 ATATTATATTAATAAATAATATAATAATAATATATTAATAAATATTATC
1 ATATTATATTAATAAATAATATAATAATAATATATAAATAAATATTATC
* *
482808 ATATT-TATTAATAATTATTATAATAAT-ATACTAATAAATAATATATTA
1 ATATTATATTAATAAATAATATAATAATAATA-T-ATAAATAA-ATATTA
482856 ATAAATAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
47 3 0.07
48 21 0.50
49 12 0.29
50 6 0.14
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (49 bp):
ATATTATATTAATAAATAATATAATAATAATATATAAATAAATATTATC
Found at i:482878 original size:45 final size:42
Alignment explanation
Indices: 482754--482877 Score: 137
Period size: 42 Copynumber: 2.9 Consensus size: 42
482744 TTTTACTTAT
* *
482754 TAAT-AATATTATATTAATAAATAATAT-AATAATAATATAT
1 TAATAAATAATATATTAATAAATAATATAAATAATAATATAC
* * *
482794 TAATAAATATTATCATATTTATTAATAAT-TATTATAATAATATAC
1 TAATAAATA--AT-ATATTAATAAATAATATA-AATAATAATATAC
*
482839 TAATAAATAATATATTAATAAATAATATAAAGAATAATA
1 TAATAAATAATATATTAATAAATAATATAAATAATAATA
482878 AATAGTTTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
40 4 0.06
41 4 0.06
42 21 0.31
43 6 0.09
44 13 0.19
45 20 0.29
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (42 bp):
TAATAAATAATATATTAATAAATAATATAAATAATAATATAC
Found at i:482970 original size:9 final size:9
Alignment explanation
Indices: 482956--483003 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
482946 TAATTATTTT
482956 TAATTTTAA
1 TAATTTTAA
482965 TAATTTTAA
1 TAATTTTAA
*
482974 TAA--TAAA
1 TAATTTTAA
482981 TAATTTTTAA
1 TAA-TTTTAA
482991 T-ATTTTAA
1 TAATTTTAA
482999 TAATT
1 TAATT
483004 ATATTAATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
7 6 0.18
8 7 0.21
9 16 0.48
10 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TAATTTTAA
Found at i:485264 original size:90 final size:84
Alignment explanation
Indices: 485130--485304 Score: 242
Period size: 90 Copynumber: 2.0 Consensus size: 84
485120 TGAACTTTCT
* * *
485130 TTACCAAATAATGGGGACTTGACTAACATTGTTCCGATGCAATTCTGTGCTTGTTTCTTTTCATT
1 TTACCAAATAATGGAGACTTGACAAACATTGTTCCGATGCAATTCTGTGCTTGTTTC-CTT--TT
485195 TCTTTTCTTTTTTTCCAGTGATCAA
63 T-TTTT-TTTTTTT-CAGTGATCAA
* * *
485220 TTACCAAGTAATGGAGACTTGACAAACATTGTTCTGATGCAATTCTGTTCTTGTTTCCTTTTTTT
1 TTACCAAATAATGGAGACTTGACAAACATTGTTCCGATGCAATTCTGTGCTTGTTTCCTTTTTTT
485285 TTTTTTTTTCAGTGATCAA
66 TTTTTTTTTCAGTGATCAA
485304 T
1 T
485305 ATCTTTGTCT
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
84 11 0.14
85 7 0.09
86 4 0.05
87 3 0.04
89 2 0.03
90 52 0.66
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (84 bp):
TTACCAAATAATGGAGACTTGACAAACATTGTTCCGATGCAATTCTGTGCTTGTTTCCTTTTTTT
TTTTTTTTTCAGTGATCAA
Found at i:491522 original size:2 final size:2
Alignment explanation
Indices: 491515--491555 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
491505 CTTGCCTTTG
*
491515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
491556 AATCTTTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:491834 original size:15 final size:14
Alignment explanation
Indices: 491814--491844 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
491804 AGGACTGATT
491814 AAGGGAAAGGAAAGG
1 AAGGGAAA-GAAAGG
491829 AAGGGAAAGAAAGG
1 AAGGGAAAGAAAGG
491843 AA
1 AA
491845 AAAGAATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (14 bp):
AAGGGAAAGAAAGG
Found at i:493293 original size:25 final size:26
Alignment explanation
Indices: 493254--493303 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
493244 AGCAAGTGAT
*
493254 GGGTAAATGTTATATTGGGACTAAAC
1 GGGTAAATGTCATATTGGGACTAAAC
493280 GGGT-AATGTCATATTGGGACTAAA
1 GGGTAAATGTCATATTGGGACTAAA
493304 ATATTGCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (26 bp):
GGGTAAATGTCATATTGGGACTAAAC
Found at i:493518 original size:22 final size:20
Alignment explanation
Indices: 493470--493508 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
493460 ATATCAGCTA
*
493470 ATAGTACAATATGTATATAT
1 ATAGTACAATATATATATAT
493490 ATAGTACAATATATATATA
1 ATAGTACAATATATATATA
493509 CATATTGTAC
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:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (20 bp):
ATAGTACAATATATATATAT
Found at i:497485 original size:2 final size:2
Alignment explanation
Indices: 497478--497512 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
497468 TTGTTAAGTC
497478 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
497513 TTATCTATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:500269 original size:15 final size:15
Alignment explanation
Indices: 500249--500281 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
500239 TAAATCATCA
500249 TTATCAATCAAATCG
1 TTATCAATCAAATCG
*
500264 TTATCATTCAAATCG
1 TTATCAATCAAATCG
500279 TTA
1 TTA
500282 GCTACGGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (15 bp):
TTATCAATCAAATCG
Found at i:501905 original size:1 final size:1
Alignment explanation
Indices: 501899--501923 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
501889 AAATAGTCCC
501899 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
501924 CGGGTATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:513761 original size:6 final size:6
Alignment explanation
Indices: 513750--513791 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
513740 GAAGTTAGCT
513750 CAATCC CAATCC CAATCC CAATCC CAATCC CAATCC C-ATCC C
1 CAATCC CAATCC CAATCC CAATCC CAATCC CAATCC CAATCC C
513792 CCATCTGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.14
6 31 0.86
ACGTcount: A:0.31, C:0.52, G:0.00, T:0.17
Consensus pattern (6 bp):
CAATCC
Found at i:524574 original size:18 final size:19
Alignment explanation
Indices: 524535--524574 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
524525 TAAAAAAATA
* *
524535 AAATTTAAATTTATTTATT
1 AAATTTAAATTTATATAAT
524554 AAATTT-AATTTATATAAT
1 AAATTTAAATTTATATAAT
524572 AAA
1 AAA
524575 AATTAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATTTAAATTTATATAAT
Found at i:524580 original size:19 final size:18
Alignment explanation
Indices: 524531--524580 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
524521 AAATTAAAAA
524531 AATAAAATTTAAATTTATT
1 AATAAAATTT-AATTTATT
* *
524550 TATTAAATTTAATTTATAT
1 AATAAAATTTAATTTAT-T
*
524569 AATAAAAATTAA
1 AATAAAATTTAA
524581 AAAATAGAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATAAAATTTAATTTATT
Found at i:528508 original size:25 final size:25
Alignment explanation
Indices: 528480--528543 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
528470 TGAGTTGAAG
* *
528480 TTTAAATTTCATTTAAA-ATTCATT
1 TTTAAATTTCAATTAAACATTAATT
*
528504 ATTTAGAA-TTCAATTAAACTTTAATT
1 -TTTA-AATTTCAATTAAACATTAATT
*
528530 TTTAAATTTAAATT
1 TTTAAATTTCAATT
528544 TAATTTGAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
24 2 0.06
25 23 0.72
26 7 0.22
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTAAATTTCAATTAAACATTAATT
Found at i:528833 original size:30 final size:32
Alignment explanation
Indices: 528793--528865 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 32
528783 ACTTATTTGA
* *
528793 TAAATTAAATT-ATTCAAATTTGATTTAACAA-
1 TAAATCAAATTGATT-AAATTTGACTTAACAAT
* *
528824 T-AATCAAATTGCTTAAATTTGACTTAATAAT
1 TAAATCAAATTGATTAAATTTGACTTAACAAT
528855 TAAATCAAATT
1 TAAATCAAATT
528866 TGAATCTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 22 0.63
31 4 0.11
32 9 0.26
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (32 bp):
TAAATCAAATTGATTAAATTTGACTTAACAAT
Found at i:532635 original size:17 final size:18
Alignment explanation
Indices: 532615--532648 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
532605 TATGGACATA
532615 ATTTTATTATT-ATGGTG
1 ATTTTATTATTCATGGTG
*
532632 ATTTTGTTATTCATGGT
1 ATTTTATTATTCATGGT
532649 TTTGAATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.21, C:0.03, G:0.18, T:0.59
Consensus pattern (18 bp):
ATTTTATTATTCATGGTG
Found at i:532978 original size:16 final size:15
Alignment explanation
Indices: 532954--532994 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
532944 ATATTATTTG
532954 TTTTAATTTATAAAT
1 TTTTAATTTATAAAT
532969 TTTATAATTT-T-AAT
1 TTT-TAATTTATAAAT
*
532983 TTTTTATTTATA
1 TTTTAATTTATA
532995 TATCATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
13 5 0.23
14 7 0.32
15 4 0.18
16 6 0.27
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTAATTTATAAAT
Found at i:534255 original size:25 final size:25
Alignment explanation
Indices: 534227--534290 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
534217 ATTATTAACA
534227 AATATTTTATTTGTAAATAAATA-AT
1 AATATTTTATTTGTAAATAAA-AGAT
* * *
534252 AATAATTTAGTT-TAGATAAAAGAT
1 AATATTTTATTTGTAAATAAAAGAT
*
534276 ATATATTTAATTTGT
1 A-ATATTTTATTTGT
534291 TCAATAATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
23 1 0.03
24 10 0.33
25 18 0.60
26 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (25 bp):
AATATTTTATTTGTAAATAAAAGAT
Found at i:538599 original size:36 final size:35
Alignment explanation
Indices: 538551--538668 Score: 182
Period size: 36 Copynumber: 3.3 Consensus size: 35
538541 CTAATAACTT
*
538551 CATTTGTGTACTTGAAAAACTTAATGAGAGTCGTGA
1 CATTTGTTTACTTGAAAAACTTAATGA-AGTCGTGA
538587 CATTTGTTTACTTGAAAAACTTAATGCAAGTCGTGA
1 CATTTGTTTACTTGAAAAACTTAATG-AAGTCGTGA
* *
538623 CATTTGTTTACATGAAAAACTTAATGAAAGTTGTGA
1 CATTTGTTTACTTGAAAAACTTAATG-AAGTCGTGA
538659 CATTTGTTTA
1 CATTTGTTTA
538669 TTGGAATTGA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
36 76 0.99
37 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (35 bp):
CATTTGTTTACTTGAAAAACTTAATGAAGTCGTGA
Found at i:540905 original size:14 final size:15
Alignment explanation
Indices: 540878--540906 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
540868 TGGATGCGTC
540878 TTGATTTCCTCCAAG
1 TTGATTTCCTCCAAG
540893 TTGATTT-CTCCAAG
1 TTGATTTCCTCCAAG
540907 AGATAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (15 bp):
TTGATTTCCTCCAAG
Found at i:541354 original size:21 final size:21
Alignment explanation
Indices: 541328--541369 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
541318 TGATACAATT
541328 TTTAATTTCAATCTTTAAAAG
1 TTTAATTTCAATCTTTAAAAG
541349 TTTAATTTCAATCTTTAAAAG
1 TTTAATTTCAATCTTTAAAAG
541370 ACGAAAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.48
Consensus pattern (21 bp):
TTTAATTTCAATCTTTAAAAG
Found at i:546071 original size:24 final size:24
Alignment explanation
Indices: 546043--546101 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
546033 TAATAATTTA
* **
546043 AAATATGACATAATAATATGATAT
1 AAATATGACATAAAAATAAAATAT
*
546067 AAATATGATATAAAAATAAAATAT
1 AAATATGACATAAAAATAAAATAT
*
546091 AAAAATGACAT
1 AAATATGACAT
546102 GATTTAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (24 bp):
AAATATGACATAAAAATAAAATAT
Found at i:546083 original size:13 final size:13
Alignment explanation
Indices: 546042--546096 Score: 60
Period size: 13 Copynumber: 4.4 Consensus size: 13
546032 TTAATAATTT
*
546042 AAAATATGACATA
1 AAAATATGATATA
*
546055 ATAATATGATAT-
1 AAAATATGATATA
546067 -AAATATGATATA
1 AAAATATGATATA
**
546079 AAAATAAAATATA
1 AAAATATGATATA
546092 AAAAT
1 AAAAT
546097 GACATGATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 10 0.29
13 25 0.71
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (13 bp):
AAAATATGATATA
Found at i:550542 original size:16 final size:16
Alignment explanation
Indices: 550521--550557 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
550511 CAAGAATTAA
550521 CAAGGAGTTGAAGTTT
1 CAAGGAGTTGAAGTTT
550537 CAAGGAGTTGAAGTTT
1 CAAGGAGTTGAAGTTT
550553 CAAGG
1 CAAGG
550558 CTTTGGAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.27
Consensus pattern (16 bp):
CAAGGAGTTGAAGTTT
Found at i:553529 original size:12 final size:12
Alignment explanation
Indices: 553512--553547 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
553502 TTTGTCTTAG
*
553512 TGATGATGAGGA
1 TGATGATGAAGA
553524 TGATGATGAAGA
1 TGATGATGAAGA
*
553536 GGATGATGAAGA
1 TGATGATGAAGA
553548 AGCTCTCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.22
Consensus pattern (12 bp):
TGATGATGAAGA
Found at i:553532 original size:15 final size:15
Alignment explanation
Indices: 553512--553549 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
553502 TTTGTCTTAG
*
553512 TGATGATGAGGATGA
1 TGATGAAGAGGATGA
553527 TGATGAAGAGGATGA
1 TGATGAAGAGGATGA
*
553542 TGAAGAAG
1 TGATGAAG
553550 CTCTCTTGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.21
Consensus pattern (15 bp):
TGATGAAGAGGATGA
Found at i:575085 original size:116 final size:115
Alignment explanation
Indices: 574806--575322 Score: 745
Period size: 116 Copynumber: 4.6 Consensus size: 115
574796 GAGCAAGCTT
* * ** * *
574806 CACTTTCCATTAGC-AAAACACAC-AAAAACAAGCCAATCCCACCTCTCAGAATCTTAACTTTCT
1 CACTTTCCATTAGCAAAAACATACGAAAAGCAAGAAAATCCAACCTCTCAAAATCTTAACTTTCT
574869 TCACTATTGCAACACAAAACATGAAACCAACAAACCAAAC---G--AATC
66 TCACTATTGCAACACAAAACATGAAACCAACAAACCAAACATGGACAATC
* * *
574914 CACATTCCATTAGCAAAAACATACGAAAAACAGGAAAATCCAACCTCTCAAAATCTTAACTTTCT
1 CACTTTCCATTAGCAAAAACATACGAAAAGCAAGAAAATCCAACCTCTCAAAATCTTAACTTTCT
*
574979 TCCCTATTGCAACACAAAACATGAAACCAACAAACCAAACGATGGACAATC
66 TCACTATTGCAACACAAAACATGAAACCAACAAACCAAAC-ATGGACAATC
575030 CACTTTCCATTAGCAAAAACATACGAAAAGCAAGAAAATCCAACCTCTCAAAATCTTAACTTTCT
1 CACTTTCCATTAGCAAAAACATACGAAAAGCAAGAAAATCCAACCTCTCAAAATCTTAACTTTCT
*
575095 TCACTGTTGCAACACAAAACATGAAA-C--C-AA-CAAA-ATGGACAATC
66 TCACTATTGCAACACAAAACATGAAACCAACAAACCAAACATGGACAATC
* * * *
575139 CACTTTCCATTAGCAAATACATACGAAAAGTAAGAAAATCCAACCTCTCAAAAGCTTAGCTTTCT
1 CACTTTCCATTAGCAAAAACATACGAAAAGCAAGAAAATCCAACCTCTCAAAATCTTAACTTTCT
575204 TCACTATTGCAACACAAAACATGAAACCAACAAACCAAACGATGGACAATC
66 TCACTATTGCAACACAAAACATGAAACCAACAAACCAAAC-ATGGACAATC
* **
575255 CACTTTCCATTAGCAAAAACATACGAAAAAGCGAGAAAATCCAACCTCTCAAAAATCCCAACTTT
1 CACTTTCCATTAGCAAAAACATACG-AAAAGCAAGAAAATCCAACCTCTC-AAAATCTTAACTTT
575320 CTT
64 CTT
575323 GAACTTTTAA
Statistics
Matches: 367, Mismatches: 25, Indels: 24
0.88 0.06 0.06
Matches are distributed among these distances:
108 13 0.04
109 104 0.28
110 75 0.20
111 4 0.01
112 3 0.01
113 3 0.01
114 5 0.01
115 1 0.00
116 124 0.34
117 22 0.06
118 13 0.04
ACGTcount: A:0.44, C:0.28, G:0.08, T:0.20
Consensus pattern (115 bp):
CACTTTCCATTAGCAAAAACATACGAAAAGCAAGAAAATCCAACCTCTCAAAATCTTAACTTTCT
TCACTATTGCAACACAAAACATGAAACCAACAAACCAAACATGGACAATC
Found at i:575204 original size:225 final size:226
Alignment explanation
Indices: 574806--575322 Score: 797
Period size: 225 Copynumber: 2.3 Consensus size: 226
574796 GAGCAAGCTT
* * ** * *
574806 CACTTTCCATTAGC-AAAACACAC-AAAAACAAGCCAATCCCACCTCTCAGAATCTTAACTTTCT
1 CACTTTCCATTAGCAAAAACATACGAAAAGCAAGAAAATCCAACCTCTCAAAATCTTAACTTTCT
*
574869 TCACTATTGCAACACAAAACATGAAACCAACAAACCAAACGAATCCACATTCCATTAGCAAAAAC
66 TCACTATTGCAACACAAAACATGAAACCAACAAAACAAACGAATCCACATTCCATTAGCAAAAAC
* * *
574934 ATACGAAAAACAGGAAAATCCAACCTCTCAAAATCTTAACTTTCTTCCCTATTGCAACACAAAAC
131 ATACGAAAAACAAGAAAATCCAACCTCTCAAAAGCTTAACTTTCTTCACTATTGCAACACAAAAC
574999 ATGAAACCAACAAACCAAACGATGGACAATC
196 ATGAAACCAACAAACCAAACGATGGACAATC
575030 CACTTTCCATTAGCAAAAACATACGAAAAGCAAGAAAATCCAACCTCTCAAAATCTTAACTTTCT
1 CACTTTCCATTAGCAAAAACATACGAAAAGCAAGAAAATCCAACCTCTCAAAATCTTAACTTTCT
* *** * *
575095 TCACTGTTGCAACACAAAACATGAAACCAACAAAATGGAC-AATCCACTTTCCATTAGCAAATAC
66 TCACTATTGCAACACAAAACATGAAACCAACAAAACAAACGAATCCACATTCCATTAGCAAAAAC
** *
575159 ATACGAAAAGTAAGAAAATCCAACCTCTCAAAAGCTTAGCTTTCTTCACTATTGCAACACAAAAC
131 ATACGAAAAACAAGAAAATCCAACCTCTCAAAAGCTTAACTTTCTTCACTATTGCAACACAAAAC
575224 ATGAAACCAACAAACCAAACGATGGACAATC
196 ATGAAACCAACAAACCAAACGATGGACAATC
* **
575255 CACTTTCCATTAGCAAAAACATACGAAAAAGCGAGAAAATCCAACCTCTCAAAAATCCCAACTTT
1 CACTTTCCATTAGCAAAAACATACG-AAAAGCAAGAAAATCCAACCTCTC-AAAATCTTAACTTT
575320 CTT
64 CTT
575323 GAACTTTTAA
Statistics
Matches: 267, Mismatches: 22, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
224 14 0.05
225 145 0.54
226 93 0.35
227 15 0.06
ACGTcount: A:0.44, C:0.28, G:0.08, T:0.20
Consensus pattern (226 bp):
CACTTTCCATTAGCAAAAACATACGAAAAGCAAGAAAATCCAACCTCTCAAAATCTTAACTTTCT
TCACTATTGCAACACAAAACATGAAACCAACAAAACAAACGAATCCACATTCCATTAGCAAAAAC
ATACGAAAAACAAGAAAATCCAACCTCTCAAAAGCTTAACTTTCTTCACTATTGCAACACAAAAC
ATGAAACCAACAAACCAAACGATGGACAATC
Found at i:576307 original size:11 final size:11
Alignment explanation
Indices: 576291--576329 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
576281 TTAATAATGA
576291 TTAAATTAAAT
1 TTAAATTAAAT
**
576302 TTAAATTTTAT
1 TTAAATTAAAT
*
576313 TTAAATTAATT
1 TTAAATTAAAT
576324 TTAAAT
1 TTAAAT
576330 AATTTATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:577036 original size:17 final size:16
Alignment explanation
Indices: 577010--577043 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
577000 TTGTTGAGTC
*
577010 ATATTCAAGCAATTTA
1 ATATTCAAGCAAATTA
577026 ATATATCAAGCAAATTA
1 ATAT-TCAAGCAAATTA
577043 A
1 A
577044 GTTTAAGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.32
Consensus pattern (16 bp):
ATATTCAAGCAAATTA
Found at i:578112 original size:23 final size:23
Alignment explanation
Indices: 578085--578129 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
578075 AAAAATTTAA
578085 TTTTAATG-TATTTAATATTAAAG
1 TTTT-ATGATATTTAATATTAAAG
* *
578108 TTTTATGATTTTTAATGTTAAA
1 TTTTATGATATTTAATATTAAA
578130 AAAATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (23 bp):
TTTTATGATATTTAATATTAAAG
Found at i:582110 original size:12 final size:13
Alignment explanation
Indices: 582076--582116 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
582066 ATTTTTTGTG
582076 TTAATATAAA-TT
1 TTAATATAAATTT
*
582088 ATAATATAAATTT
1 TTAATATAAATTT
582101 TTAATA-AAATATT
1 TTAATATAAAT-TT
582114 TTA
1 TTA
582117 TAAATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 13 0.52
13 12 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTAATATAAATTT
Found at i:589088 original size:2 final size:2
Alignment explanation
Indices: 589075--589114 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
589065 CAAGTTAGGA
*
589075 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
589115 TTCACGCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:595105 original size:48 final size:48
Alignment explanation
Indices: 595048--595145 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
595038 GCACCCTTTC
595048 AGTCTTCTCTAGTCCACTCACAAACAAACATACACACCCATAAGACGT
1 AGTCTTCTCTAGTCCACTCACAAACAAACATACACACCCATAAGACGT
595096 AGTCTTCTCTAGTCCACTCACAAACAAACATACACACCCATAAGACGT
1 AGTCTTCTCTAGTCCACTCACAAACAAACATACACACCCATAAGACGT
595144 AG
1 AG
595146 AGCCCTAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.38, C:0.33, G:0.09, T:0.20
Consensus pattern (48 bp):
AGTCTTCTCTAGTCCACTCACAAACAAACATACACACCCATAAGACGT
Found at i:595313 original size:43 final size:43
Alignment explanation
Indices: 595252--595334 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 43
595242 ATAACCATAA
595252 AAACTTGCCCATTAAGAAT-CCTTCTCCTCTT-AGAATTCTTGTC
1 AAACTTGCCCATTAAGAATCCCTT-TCCTCTTGA-AATTCTTGTC
* *
595295 AAACTTGTCTATTAAGAATCCCTTTCCTCTTGAAATTCTT
1 AAACTTGCCCATTAAGAATCCCTTTCCTCTTGAAATTCTT
595335 CTTTTGTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
43 31 0.86
44 5 0.14
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (43 bp):
AAACTTGCCCATTAAGAATCCCTTTCCTCTTGAAATTCTTGTC
Found at i:595386 original size:11 final size:11
Alignment explanation
Indices: 595370--595412 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
595360 AGCAATATCT
595370 AACAAATCTCA
1 AACAAATCTCA
*
595381 AACAAATCCCA
1 AACAAATCTCA
*
595392 AACAAATCTAA
1 AACAAATCTCA
595403 AACAAATCTC
1 AACAAATCTC
595413 TTATGAGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (11 bp):
AACAAATCTCA
Done.