Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008017.1 Hibiscus syriacus cultivar Beakdansim tig00110483_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: 3132588
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 15
Found at i:692552 original size:36 final size:37
Alignment explanation
Indices: 692422--692560 Score: 154
Period size: 41 Copynumber: 3.6 Consensus size: 37
692412 GCGTTGCATT
* *
692422 TCGCGTTGCGATAGTGTACAGTGTCGTTGCAATTTTCC
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTT-C
* *
692460 ATTTCGCGTTGCGATAGTGTACATTGTCGTTGCGATTTTCCATC
1 ---TCGCGTTGCGATAGTCTACAGTGTCGTTGCGA-TTT---TC
*
692504 TCGCGTTGCGATAGTCTACAGTGTCGTTACGATTTTC
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
692541 -CGCGTTGCGATAGTCTACAG
1 TCGCGTTGCGATAGTCTACAG
692561 GATTTTCCAA
Statistics
Matches: 89, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
36 20 0.22
37 2 0.02
40 3 0.03
41 59 0.66
42 3 0.03
44 1 0.01
45 1 0.01
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.37
Consensus pattern (37 bp):
TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
Found at i:693352 original size:21 final size:21
Alignment explanation
Indices: 693297--693476 Score: 101
Period size: 21 Copynumber: 8.9 Consensus size: 21
693287 TTTTTAATTT
693297 ACTGTAGACTATCGCAACGA-
1 ACTGTAGACTATCGCAACGAC
* * **
693317 A-TTTGGAAAATCGCAACGAC
1 ACTGTAGACTATCGCAACGAC
693337 ACTGTAGACTATCGCAACG-C
1 ACTGTAGACTATCGCAACGAC
** ** *
693357 GA-AATAGAAAATCGCAGCGA-
1 -ACTGTAGACTATCGCAACGAC
* **
693377 A--ATAGAAAATCGCAACGAC
1 ACTGTAGACTATCGCAACGAC
*
693396 ACTGTACACTATCGCAACGAC
1 ACTGTAGACTATCGCAACGAC
*
693417 ATTGTAGACTATCGCAACG-C
1 ACTGTAGACTATCGCAACGAC
* **
693437 GAAATG-A-AAAATCGCAACGAC
1 --ACTGTAGACTATCGCAACGAC
*
693458 ACTATAGACTATCGCAACG
1 ACTGTAGACTATCGCAACG
693477 CAAAAAAAAA
Statistics
Matches: 121, Mismatches: 27, Indels: 23
0.71 0.16 0.13
Matches are distributed among these distances:
18 16 0.13
19 18 0.15
20 27 0.22
21 57 0.47
22 3 0.02
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (21 bp):
ACTGTAGACTATCGCAACGAC
Found at i:693378 original size:18 final size:18
Alignment explanation
Indices: 693355--693390 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
693345 CTATCGCAAC
693355 GCGAAATAGAAAATCGCA
1 GCGAAATAGAAAATCGCA
693373 GCGAAATAGAAAATCGCA
1 GCGAAATAGAAAATCGCA
693391 ACGACACTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.17, G:0.22, T:0.11
Consensus pattern (18 bp):
GCGAAATAGAAAATCGCA
Found at i:693455 original size:41 final size:41
Alignment explanation
Indices: 693299--693565 Score: 180
Period size: 41 Copynumber: 6.6 Consensus size: 41
693289 TTTAATTTAC
* * *
693299 TGTAGACTATCGCAA--CGAATTTGGAAAATCGCAACGACAC
1 TGTAGACTATCGCAACGCGAA-ATGAAAAATCGCAACGACAT
*
693339 TGTAGACTATCGCAACGCGAAAT-AGAAAATCGCAGCGA-A-
1 TGTAGACTATCGCAACGCGAAATGA-AAAATCGCAACGACAT
* ** * **
693378 -ATAGAAAATCGCAA--CGACACTGTACACTATCGCAACGACAT
1 TGTAGACTATCGCAACGCGA-AATG-A-AAAATCGCAACGACAT
*
693419 TGTAGACTATCGCAACGCGAAATGAAAAATCGCAACGACAC
1 TGTAGACTATCGCAACGCGAAATGAAAAATCGCAACGACAT
* * ** *
693460 TATAGACTATCGCAACGCAAAAAAAAAAATCGCAACG-CGGT
1 TGTAGACTATCGCAACGCGAAATGAAAAATCGCAACGAC-AT
* * *
693501 TTTCA-ACTATCGCAACGCAAAATGAAAAATCGCATCG-CGAT
1 TGT-AGACTATCGCAACGCGAAATGAAAAATCGCAACGAC-AT
* *
693542 TTTCA-ACTATCGCAACACGAAATG
1 TGT-AGACTATCGCAACGCGAAATG
693566 CAGCGCGAAT
Statistics
Matches: 183, Mismatches: 31, Indels: 25
0.77 0.13 0.10
Matches are distributed among these distances:
36 3 0.02
37 2 0.01
38 11 0.06
39 11 0.06
40 18 0.10
41 115 0.63
42 17 0.09
43 3 0.02
44 3 0.02
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (41 bp):
TGTAGACTATCGCAACGCGAAATGAAAAATCGCAACGACAT
Found at i:693460 original size:62 final size:60
Alignment explanation
Indices: 693299--693477 Score: 213
Period size: 62 Copynumber: 3.0 Consensus size: 60
693289 TTTAATTTAC
* *
693299 TGTAGACTATCGCAA-CGAATTTGGAAAATCGCAACGACACTGTAGACTATCGCAACGCGA
1 TGTAGACTATCGCAAGCGAA-ATGAAAAATCGCAACGACACTGTAGACTATCGCAACGCGA
** ** *
693359 AATAGAAAATCGC-AGCGAAAT-AGAAAATCGCAACGACACTGTACACTATCGCAACGAC-A
1 TGTAGACTATCGCAAGCGAAATGA-AAAATCGCAACGACACTGTAGACTATCGCAACG-CGA
*
693418 TTGTAGACTATCGCAACGCGAAATGAAAAATCGCAACGACACTATAGACTATCGCAACGC
1 -TGTAGACTATCGCAA-GCGAAATGAAAAATCGCAACGACACTGTAGACTATCGCAACGC
693478 AAAAAAAAAA
Statistics
Matches: 99, Mismatches: 13, Indels: 13
0.79 0.10 0.10
Matches are distributed among these distances:
59 35 0.35
60 23 0.23
61 2 0.02
62 38 0.38
63 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (60 bp):
TGTAGACTATCGCAAGCGAAATGAAAAATCGCAACGACACTGTAGACTATCGCAACGCGA
Found at i:693534 original size:20 final size:20
Alignment explanation
Indices: 693427--693534 Score: 56
Period size: 20 Copynumber: 5.3 Consensus size: 20
693417 ATTGTAGACT
*
693427 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCAAAATGAAAA
** **
693447 ATCGCAACGACACTAT-AGACT
1 ATCGCAACG-CAAAATGA-AAA
**
693468 ATCGCAACGCAAAAAAAAAA
1 ATCGCAACGCAAAATGAAAA
**** * **
693488 ATCGCAACGCGGTTTTCAACT
1 ATCGCAACGC-AAAATGAAAA
693509 ATCGCAACGCAAAATGAAAA
1 ATCGCAACGCAAAATGAAAA
693529 ATCGCA
1 ATCGCA
693535 TCGCGATTTT
Statistics
Matches: 59, Mismatches: 25, Indels: 8
0.64 0.27 0.09
Matches are distributed among these distances:
20 33 0.56
21 26 0.44
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCAAAATGAAAA
Found at i:695399 original size:30 final size:30
Alignment explanation
Indices: 695365--695464 Score: 93
Period size: 30 Copynumber: 3.4 Consensus size: 30
695355 AATTGAAAAA
*
695365 ATATAATATATGTATATAATATAAGTTTAT
1 ATATAATATATATATATAATATAAGTTTAT
* *
695395 ATATAAAATATATATATAA-ACTATGTTTAT
1 ATATAATATATATATATAATA-TAAGTTTAT
*
695425 ATTATAA-ACTATATA-ATTATTATAAG-TTAT
1 A-TATAATA-TATATATA-TAATATAAGTTTAT
695455 ATAT-ATATAT
1 ATATAATATAT
695465 GCTTATATGA
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
28 4 0.07
29 5 0.08
30 33 0.56
31 16 0.27
32 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (30 bp):
ATATAATATATATATATAATATAAGTTTAT
Found at i:695404 original size:19 final size:18
Alignment explanation
Indices: 695362--695412 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
695352 AAAAATTGAA
*
695362 AAAATATAATATATGTAT
1 AAAATATAATATATATAT
* *
695380 ATAATATAAGTTTATATAT
1 AAAATATAA-TATATATAT
695399 AAAATAT-ATATATA
1 AAAATATAATATATA
695413 AACTATGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 5 0.19
18 9 0.33
19 13 0.48
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (18 bp):
AAAATATAATATATATAT
Found at i:695444 original size:20 final size:19
Alignment explanation
Indices: 695403--695438 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
695393 ATATATAAAA
*
695403 TATATATATAAACTATGTT
1 TATATATATAAACTATATT
695422 TATAT-TATAAACTATAT
1 TATATATATAAACTATAT
695439 AATTATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (19 bp):
TATATATATAAACTATATT
Found at i:695567 original size:2 final size:2
Alignment explanation
Indices: 695560--695600 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
695550 ATTTATATTC
*
695560 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA 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
695601 AAATTCAAAG
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:695736 original size:19 final size:19
Alignment explanation
Indices: 695737--695797 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
695727 ATTTAGAGGG
695737 ATTTAGAGGGGAAA-TGAGAA
1 ATTTAGA-GGGAAATTGAG-A
* *
695757 ATTTAGAGGG-AATAGAAA
1 ATTTAGAGGGAAATTGAGA
*
695775 ATTTTGGAGGGAAATTGAGA
1 A-TTTAGAGGGAAATTGAGA
695795 ATT
1 ATT
695798 GAGATTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
18 4 0.12
19 15 0.45
20 14 0.42
ACGTcount: A:0.43, C:0.00, G:0.31, T:0.26
Consensus pattern (19 bp):
ATTTAGAGGGAAATTGAGA
Found at i:696046 original size:2 final size:2
Alignment explanation
Indices: 696036--696285 Score: 93
Period size: 2 Copynumber: 126.5 Consensus size: 2
696026 ATTGAAAAAA
* *
696036 AT AT A- AT AT AT AT AT AT AT A- AT AT A- AGT TT AT AT AT A- AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
696075 AT AT AT AT AT AA ACT AT AT TT AT AT -T AT AA ACT AT AT A- AT -T
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* *
696116 AT -T AT A- AGT -T AT AT AT AT AA AT -T AT GCT -T AT AT GA- ACT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT -AT AT AT AT -AT A-T
* * * * *
696154 AT AT AT AT AT AA ACT AT AT AT GT AA ACT AT AT AT GT AT AA ACT
1 AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT A-T
* * * * *
696197 AT A- AA AA AGT AT AT AGT TT AT AA ACT AT A- AT TT AT AT -T A-
1 AT AT AT AT A-T AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT
*
696236 AT AT AGT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
696279 AT AT AT A
1 AT AT AT A
696286 ATTCAAAGTG
Statistics
Matches: 186, Mismatches: 31, Indels: 62
0.67 0.11 0.22
Matches are distributed among these distances:
1 17 0.09
2 156 0.84
3 13 0.07
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:696070 original size:17 final size:15
Alignment explanation
Indices: 696036--696287 Score: 109
Period size: 15 Copynumber: 16.5 Consensus size: 15
696026 ATTGAAAAAA
696036 ATATAATATATATAT
1 ATATAATATATATAT
*
696051 ATATAATATAAGTTTAT
1 ATATAATAT-A-TATAT
*
696068 ATATAAAATATATAT
1 ATATAATATATATAT
*
696083 ATA-AACTATATTTAT
1 ATATAA-TATATATAT
696098 ATTATAA-ACTATATAATT
1 A-TATAATA-TATAT-A-T
696116 ATTATAAGT-TATATAT
1 A-TATAA-TATATATAT
*
696132 ATA-AAT-TATGCT-T
1 ATATAATATAT-ATAT
696145 ATATGAACTATATATAT
1 ATAT-AA-TATATATAT
*
696162 ATA-AACTATATATGT
1 ATATAA-TATATATAT
* *
696177 A-A-ACTATATATGT
1 ATATAATATATATAT
* *
696190 ATA-AACTATA-AAAA
1 ATATAA-TATATATAT
* *
696204 AGTAT-ATAGTTTATAA
1 A-TATAATA-TATATAT
*
696220 ACTATAATTTATAT-T
1 A-TATAATATATATAT
* *
696235 AATATAGTATTTATAT
1 -ATATAATATATATAT
696251 ATAT-ATATATATAT
1 ATATAATATATATAT
696265 ATATATATATATATAT
1 ATATA-ATATATATAT
696281 ATATAAT
1 ATATAAT
696288 TCAAAGTGAG
Statistics
Matches: 185, Mismatches: 25, Indels: 54
0.70 0.09 0.20
Matches are distributed among these distances:
13 18 0.10
14 25 0.14
15 64 0.35
16 40 0.22
17 25 0.14
18 13 0.07
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (15 bp):
ATATAATATATATAT
Found at i:696079 original size:30 final size:30
Alignment explanation
Indices: 696036--696136 Score: 100
Period size: 31 Copynumber: 3.2 Consensus size: 30
696026 ATTGAAAAAA
696036 ATATAATATATATATATATAATATAAGTTTAT
1 ATATAA-A-ATATATATATAATATAAGTTTAT
696068 ATATAAAATATATATATAA-ACTATA-TTTAT
1 ATATAAAATATATATATAATA-TA-AGTTTAT
* *
696098 ATTATAAACTATATA-ATTATTATAAGTTATAT
1 A-TATAAAATATATATA-TAATATAAGTT-TAT
696130 ATATAAA
1 ATATAAA
696137 TTATGCTTAT
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
29 1 0.02
30 22 0.37
31 26 0.43
32 11 0.18
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (30 bp):
ATATAAAATATATATATAATATAAGTTTAT
Found at i:696453 original size:29 final size:30
Alignment explanation
Indices: 696396--696453 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
696386 TGATAATATA
*
696396 GGGAAATTGAGAATTTAGAGGGATTTAGAG
1 GGGAAATTGAGAATTTAGAGGGATATAGAG
696426 GGGAAA-TGAGAAATTTAGAGGGA-ATAGA
1 GGGAAATTGAG-AATTTAGAGGGATATAGA
696454 AAATTTTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.41, C:0.00, G:0.36, T:0.22
Consensus pattern (30 bp):
GGGAAATTGAGAATTTAGAGGGATATAGAG
Found at i:696675 original size:681 final size:668
Alignment explanation
Indices: 695336--696680 Score: 2372
Period size: 681 Copynumber: 2.0 Consensus size: 668
695326 AAAAATACAA
*
695336 TAAATTGCATTCATTTAAAAATTGAAAAAATATAATATATGTATATAATATAAGTTTATATATAA
1 TAAATTGCATTCATTTAAAAATTGAAAAAATATAATATATATATATAATATAAGTTTATATATAA
*
695401 AATATATATATAAACTATGTTTATATTATAAACTATATAATTATTATAAGTTATATATATATATG
66 AATATATATATAAACTATATTTATATTATAAACTATATAATTATTATAAGTTATATATATATATG
695466 CTTATATGAACTATATATATATAAACTATATATGTAAACTATATATGTATAAACTATAAAAAAGT
131 CTTATATGAACTATATATATATAAACTATATATGTAAACTATATATGTATAAACTATAAAAAAGT
*
695531 ATATAATTTATAAACTATAATTTATATTCATATATATATATATATATATATATATATATATATAA
196 ATATAATTTATAAACTATAATTTATATTAATATATATATATATATATATATATATATATATATAA
695596 ATATAAAATTCAAAGTGAGTGGTGGGAGAAAACTTTTTAAAATAAAGATTTTTTTGTGTGAATTT
261 ATATAAAATTCAAAGTGAGTGGTGGGAGAAAACTTTTTAAAATAAAGATTTTTTTGTGTGAA-TT
*
695661 TTTTTTTATTTTATTTGGGAATTTAGAGGAAAATTGAGAAATTTTGAGAATATAGGGAAATTGAG
325 GTTTTTTATTTTATTTGGGAATTTAGAGGAAAATTGAGAAATTTTGAGAATATAGGGAAATTGAG
*
695726 AATTTAGAGGGATTTAGAGGGGAAATGAGAAATTTAGAGGGAATAGAAAATTTTGGAGGGAAATT
390 AATTTAGAGGGATTTAGAGGGGAAATGAGAAATTTAGAGGGAATAGAAAATTTTGGAGAGAAATT
* *
695791 GAGAATTGAGATTTTATTTGGAAAGATATTTTGGGTTAATTAGGCTCATGCTCCTCCAACAATCA
455 GAGAATTGAGATTTTATTTGGAAAGATATTTTAGGTTAATTAGGCTCATGCTCATCCAACAATCA
* *
695856 TCATGTTTTCACTTGTATTTGATTTTTGATTTCTTTCATTTTAGTCATTGTTTAATTGTAAATAT
520 TCATGTTTCCACTTGTATTTGATTTTTGATTTCTTTCATTTTAGTCATTATTTAATTGTAAATAT
*
695921 CTTCTTGAATTCTCAATTCGATACAATTTAATCATGTATACATTCTAATTACTTTTAATTGTATG
585 CTTCTTGAATTCTCAATTCGATACAATTTAATCATGTATACATTCTAATTACTTTTAATTATATG
695986 TATGTGTGTGTGTGTATAG
650 TATGTGTGTGTGTGTATAG
696005 TAAATTGCATTCATTTAAAAAATTGAAAAAAATATAATATATATATATATAATATAAGTTTATAT
1 TAAATTGCATTCATTT-AAAAATTG-AAAAAATAT-A-ATATATATATATAATATAAGTTTATAT
696070 ATAAAATATATATATAAACTATATTTATATTATAAACTATATAATTATTATAAGTTATATATATA
62 ATAAAATATATATATAAACTATATTTATATTATAAACTATATAATTATTATAAGTTATATATAT-
696135 AATTATGCTTATATGAACTATATATATATAAACTATATATGTAAACTATATATGTATAAACTATA
126 -A-TATGCTTATATGAACTATATATATATAAACTATATATGTAAACTATATATGTATAAACTATA
*
696200 AAAAAGTATATAGTTTATAAACTATAATTTATATTAATATAGTATTTATATATATATATATATAT
189 AAAAAGTATATAATTTATAAACTATAATTTATATTAATATA-TA--TATATATATATATATATAT
696265 ATATATATATATATATATATAATTCAAAGTGAGTGGTGGGAGAAAACTTTTTAAAATAAAGATTT
251 ATATATATA-A-ATATA-A-AATTCAAAGTGAGTGGTGGGAGAAAACTTTTTAAAATAAAGATTT
* *
696330 TTTTGTGTGAA-TGTTTTTTATTTTATTTGGGAATTTAGAGGGAAATTGAGAAATTTTGATAATA
312 TTTTGTGTGAATTGTTTTTTATTTTATTTGGGAATTTAGAGGAAAATTGAGAAATTTTGAGAATA
696394 TAGGGAAATTGAGAATTTAGAGGGATTTAGAGGGGAAATGAGAAATTTAGAGGGAATAGAAAATT
377 TAGGGAAATTGAGAATTTAGAGGGATTTAGAGGGGAAATGAGAAATTTAGAGGGAATAGAAAATT
696459 TTGGAGAGAAATTGAGAATTGAGATTTTATTTGGAAAGATATTTTAGGTTAATTAGGCTCATGCT
442 TTGGAGAGAAATTGAGAATTGAGATTTTATTTGGAAAGATATTTTAGGTTAATTAGGCTCATGCT
*
696524 CATCCAACAATCATCAT-TCTTCCACTTGTATTTGATTTTTGTTTTCTTTCATTTTAGTCATTAT
507 CATCCAACAATCATCATGT-TTCCACTTGTATTTGATTTTTGATTTCTTTCATTTTAGTCATTAT
*
696588 TTAATTGTAAATATCTTCTTGAATTCTCAATTCGATATAATTTAATCATGTATACATTCTAATTA
571 TTAATTGTAAATATCTTCTTGAATTCTCAATTCGATACAATTTAATCATGTATACATTCTAATTA
*
696653 CTTTTAATTA-ATTGTGTGTGTGTGTGTG
636 CTTTTAATTATA-TGTATGTGTGTGTGTG
696681 CGCGCGCGGG
Statistics
Matches: 644, Mismatches: 16, Indels: 20
0.95 0.02 0.03
Matches are distributed among these distances:
669 16 0.02
670 8 0.01
671 9 0.01
672 1 0.00
673 89 0.14
675 1 0.00
676 101 0.16
677 2 0.00
679 28 0.04
680 3 0.00
681 329 0.51
682 1 0.00
683 56 0.09
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (668 bp):
TAAATTGCATTCATTTAAAAATTGAAAAAATATAATATATATATATAATATAAGTTTATATATAA
AATATATATATAAACTATATTTATATTATAAACTATATAATTATTATAAGTTATATATATATATG
CTTATATGAACTATATATATATAAACTATATATGTAAACTATATATGTATAAACTATAAAAAAGT
ATATAATTTATAAACTATAATTTATATTAATATATATATATATATATATATATATATATATATAA
ATATAAAATTCAAAGTGAGTGGTGGGAGAAAACTTTTTAAAATAAAGATTTTTTTGTGTGAATTG
TTTTTTATTTTATTTGGGAATTTAGAGGAAAATTGAGAAATTTTGAGAATATAGGGAAATTGAGA
ATTTAGAGGGATTTAGAGGGGAAATGAGAAATTTAGAGGGAATAGAAAATTTTGGAGAGAAATTG
AGAATTGAGATTTTATTTGGAAAGATATTTTAGGTTAATTAGGCTCATGCTCATCCAACAATCAT
CATGTTTCCACTTGTATTTGATTTTTGATTTCTTTCATTTTAGTCATTATTTAATTGTAAATATC
TTCTTGAATTCTCAATTCGATACAATTTAATCATGTATACATTCTAATTACTTTTAATTATATGT
ATGTGTGTGTGTGTATAG
Found at i:696721 original size:10 final size:10
Alignment explanation
Indices: 696704--696754 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 10
696694 GCGCACGCGC
696704 GCGCGTGCAT
1 GCGCGTGCAT
*
696714 GCGTGTGCAT
1 GCGCGTGCAT
*
696724 GCGCGTGCGT
1 GCGCGTGCAT
*
696734 GTGCGTGC--
1 GCGCGTGCAT
*
696742 GTGCGTGCAT
1 GCGCGTGCAT
696752 GCG
1 GCG
696755 TGCGTGTATC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
8 8 0.24
10 26 0.76
ACGTcount: A:0.06, C:0.25, G:0.45, T:0.24
Consensus pattern (10 bp):
GCGCGTGCAT
Found at i:696741 original size:4 final size:4
Alignment explanation
Indices: 696726--696880 Score: 224
Period size: 4 Copynumber: 39.2 Consensus size: 4
696716 GTGTGCATGC
* ** *
696726 GCGT GCGT --GT GCGT GCGT GCGT GCAT GCGT GCGT GTAT CCGT GCGT
1 GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT
* *
696772 CCGT CCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT
1 GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT
* *
696820 CCGT GCGT GCGT GCGT GCGT GCGT GCGT CCGT GCGT GCGT GCGT GCGT
1 GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCGT
696868 GCGT GCGT GCGT G
1 GCGT GCGT GCGT G
696881 ATAAAGTATA
Statistics
Matches: 135, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
2 2 0.01
4 133 0.99
ACGTcount: A:0.01, C:0.27, G:0.46, T:0.26
Consensus pattern (4 bp):
GCGT
Found at i:697052 original size:2 final size:2
Alignment explanation
Indices: 696992--697043 Score: 77
Period size: 2 Copynumber: 25.0 Consensus size: 2
696982 ATAAATCATG
*
696992 TA TA GTA TA TA TA AA CTA 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 TA TA TA TA
697036 TA TA TA TA
1 TA TA TA TA
697044 AACTATATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 43 0.93
3 3 0.07
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:697166 original size:14 final size:14
Alignment explanation
Indices: 697155--697185 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
697145 ACCTAAACTT
697155 TAAACCAAAAACAC
1 TAAACCAAAAACAC
*
697169 TAAACCAAAAACCC
1 TAAACCAAAAACAC
697183 TAA
1 TAA
697186 TGTAAATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.29, G:0.00, T:0.10
Consensus pattern (14 bp):
TAAACCAAAAACAC
Found at i:697574 original size:20 final size:21
Alignment explanation
Indices: 697525--697575 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
697515 TAAATAATTT
*
697525 TATATAATATGTATGTATAAAC
1 TATAT-ATATGTATATATAAAC
* *
697547 CATGTATA-GTATATATAAAC
1 TATATATATGTATATATAAAC
697567 TATATATAT
1 TATATATAT
697576 AACCTCTCTC
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 17 0.74
21 3 0.13
22 3 0.13
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (21 bp):
TATATATATGTATATATAAAC
Found at i:698468 original size:2 final size:2
Alignment explanation
Indices: 698461--698503 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
698451 AAAACAAAAG
698461 TA TA TA TA 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 TA TA TA TA
698503 T
1 T
698504 GTAACACCGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:701840 original size:24 final size:24
Alignment explanation
Indices: 701737--701824 Score: 140
Period size: 24 Copynumber: 3.7 Consensus size: 24
701727 TTCTATTATA
* * *
701737 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTTTGATCTG
*
701761 ATATTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTTTGATCTG
701785 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTTTGATCTG
701809 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
701825 ATGTTATGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.39
Consensus pattern (24 bp):
ATACTTGACCTGGATTTTGATCTG
Found at i:703975 original size:15 final size:15
Alignment explanation
Indices: 703955--703998 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
703945 AACCCGACCC
703955 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
703970 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
*
703985 AACCGCTGTTGACC
1 GACC-C-GTTGACC
703999 AAAACTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 18 0.69
16 1 0.04
17 7 0.27
ACGTcount: A:0.16, C:0.34, G:0.25, T:0.25
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:706539 original size:24 final size:24
Alignment explanation
Indices: 706442--706529 Score: 133
Period size: 24 Copynumber: 3.7 Consensus size: 24
706432 TTCTAATATA
* *
706442 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCTG
706466 ATACTTGACCTGGATTCTGAT-TG
1 ATACTTGACCTGGATTCTGATCTG
*
706489 AATACTTGACCTGGATTTTGATCTG
1 -ATACTTGACCTGGATTCTGATCTG
706514 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
706530 ATGTTATGAT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
23 1 0.02
24 56 0.95
25 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCTG
Found at i:706545 original size:24 final size:24
Alignment explanation
Indices: 706437--706539 Score: 109
Period size: 24 Copynumber: 4.3 Consensus size: 24
706427 TTGATTTCTA
* * *
706437 ATATAATACCTGACCTGGATTCTG
1 ATATGATACTTGACCTGGATTATG
** *
706461 ATCGGATACTTGACCTGGATTCTG
1 ATATGATACTTGACCTGGATTATG
*
706485 AT-TGAATACTTGACCTGGATTTTG
1 ATATG-ATACTTGACCTGGATTATG
*
706509 ATCTGATACTTGACCTGGATTATG
1 ATATGATACTTGACCTGGATTATG
*
706533 TTATGAT
1 ATATGAT
706540 TTTTGATATA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
23 1 0.01
24 65 0.96
25 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (24 bp):
ATATGATACTTGACCTGGATTATG
Found at i:707362 original size:15 final size:17
Alignment explanation
Indices: 707344--707380 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
707334 TAAATAATTT
707344 TATATAA-TATGTAT-G
1 TATATAACTATGTATAG
707359 TATA-AACTATGTATAG
1 TATATAACTATGTATAG
707375 TATATA
1 TATATA
707381 TAAACTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.11
15 11 0.58
16 5 0.26
17 1 0.05
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (17 bp):
TATATAACTATGTATAG
Found at i:707401 original size:20 final size:20
Alignment explanation
Indices: 707344--707485 Score: 86
Period size: 20 Copynumber: 7.2 Consensus size: 20
707334 TAAATAATTT
*
707344 TATATAATATGTATGTATAAAC
1 TATAT-ATA-GTATATATAAAC
*
707366 TATGTATAGTATATATAAAC
1 TATATATAGTATATATAAAC
*
707386 TATATA-AGTA-ATAT--AT
1 TATATATAGTATATATAAAC
* *
707402 TTTATATAGTTTATATATATA-
1 TATATATAG--TATATATAAAC
* *
707423 TATATATAGTTTATATATA-
1 TATATATAGTATATATAAAC
*
707442 TATATATA-TATATATATA-
1 TATATATAGTATATATAAAC
*
707460 TATATATA-TAACTATATAAAA
1 TATATATAGT-A-TATATAAAC
707481 TATAT
1 TATAT
707486 TACTTATATA
Statistics
Matches: 102, Mismatches: 9, Indels: 19
0.78 0.07 0.15
Matches are distributed among these distances:
16 6 0.06
17 2 0.02
18 22 0.22
19 24 0.24
20 27 0.26
21 16 0.16
22 5 0.05
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (20 bp):
TATATATAGTATATATAAAC
Found at i:707485 original size:2 final size:2
Alignment explanation
Indices: 707370--707469 Score: 98
Period size: 2 Copynumber: 49.0 Consensus size: 2
707360 ATAAACTATG
* *
707370 TA TA GTA TA TA TA AA CTA TA TA -A GTA -A TA TA T- TT TA TA TA
1 TA TA -TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA
* *
707410 GTT TA TA TA TA TA TA TA TA TA GTT 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 TA TA TA TA
707454 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
707470 ACTATATAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
1 3 0.04
2 74 0.89
3 6 0.07
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:707558 original size:7 final size:7
Alignment explanation
Indices: 707548--707615 Score: 55
Period size: 7 Copynumber: 9.7 Consensus size: 7
707538 TTATAGAAAT
707548 CCTAAAC
1 CCTAAAC
707555 CCTAAAC
1 CCTAAAC
707562 CCTAAAC
1 CCTAAAC
*
707569 CATAAAC
1 CCTAAAC
**
707576 TTTAAAC
1 CCTAAAC
*
707583 CATAAAC
1 CCTAAAC
*
707590 ACTAAAC
1 CCTAAAC
** *
707597 AATAAAT
1 CCTAAAC
*
707604 CATAAAC
1 CCTAAAC
707611 CCTAA
1 CCTAA
707616 TATAAATGGA
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.19
Consensus pattern (7 bp):
CCTAAAC
Found at i:707567 original size:14 final size:14
Alignment explanation
Indices: 707548--707602 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
707538 TTATAGAAAT
*
707548 CCTAAACCCTAAAC
1 CCTAAACCATAAAC
707562 CCTAAACCATAAAC
1 CCTAAACCATAAAC
**
707576 TTTAAACCATAAAC
1 CCTAAACCATAAAC
* *
707590 ACTAAACAATAAA
1 CCTAAACCATAAA
707603 TCATAAACCC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18
Consensus pattern (14 bp):
CCTAAACCATAAAC
Found at i:707615 original size:21 final size:21
Alignment explanation
Indices: 707548--707615 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
707538 TTATAGAAAT
** *
707548 CCTAAACCCTAAACCCTAAAC
1 CCTAAACAATAAACCATAAAC
* **
707569 CATAAACTTTAAACCATAAAC
1 CCTAAACAATAAACCATAAAC
* *
707590 ACTAAACAATAAATCATAAAC
1 CCTAAACAATAAACCATAAAC
707611 CCTAA
1 CCTAA
707616 TATAAATGGA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.19
Consensus pattern (21 bp):
CCTAAACAATAAACCATAAAC
Found at i:707861 original size:20 final size:21
Alignment explanation
Indices: 707824--707899 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 21
707814 AAATAATTTT
*
707824 ATATAATATGTATGTATAAACC
1 ATAT-ATATGTATATATAAACC
* *
707846 ATGTATA-GTATATATAAACT
1 ATATATATGTATATATAAACC
* *
707866 ATATATATGTATA-ATATA-T
1 ATATATATGTATATATAAACC
*
707885 ATATATATATATATA
1 ATATATATGTATATA
707900 AATTATATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
19 13 0.28
20 22 0.48
21 8 0.17
22 3 0.07
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (21 bp):
ATATATATGTATATATAAACC
Found at i:707889 original size:21 final size:21
Alignment explanation
Indices: 707849--707908 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
707839 ATAAACCATG
*
707849 TATA-GTAT-ATATAAACTATA
1 TATATGTATAATATATA-TATA
707869 TATATGTATAATATATATATA
1 TATATGTATAATATATATATA
*
707890 TATATATATAA-AT-TATATA
1 TATATGTATAATATATATATA
707909 AAATAAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
19 6 0.17
20 6 0.17
21 18 0.50
22 6 0.17
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (21 bp):
TATATGTATAATATATATATA
Found at i:707926 original size:2 final size:2
Alignment explanation
Indices: 707849--707908 Score: 61
Period size: 2 Copynumber: 30.0 Consensus size: 2
707839 ATAAACCATG
* *
707849 TA TA GTA TA TA TA AA CTA TA TA TA TG TA TA -A TA TA 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
*
707892 TA TA TA TA AA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA
707909 AAATAAATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
1 2 0.04
2 43 0.90
3 3 0.06
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:707992 original size:7 final size:7
Alignment explanation
Indices: 707982--708041 Score: 59
Period size: 7 Copynumber: 8.6 Consensus size: 7
707972 TAGTTTATAG
*
707982 AAACTCT
1 AAACACT
*
707989 AAACCCT
1 AAACACT
*
707996 AAACTCT
1 AAACACT
*
708003 AAACCCT
1 AAACACT
708010 AAACACT
1 AAACACT
708017 AAAC-CAT
1 AAACAC-T
708024 AAACACT
1 AAACACT
*
708031 AAACATT
1 AAACACT
708038 AAAC
1 AAAC
708042 CATAAACAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
6 1 0.02
7 44 0.96
8 1 0.02
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.18
Consensus pattern (7 bp):
AAACACT
Found at i:708011 original size:21 final size:21
Alignment explanation
Indices: 707982--708049 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
707972 TAGTTTATAG
* *
707982 AAACTCTAAACCCTAAACTC-T
1 AAACACTAAACACTAAAC-CAT
*
708003 AAACCCTAAACACTAAACCAT
1 AAACACTAAACACTAAACCAT
*
708024 AAACACTAAACATTAAACCAT
1 AAACACTAAACACTAAACCAT
708045 AAACA
1 AAACA
708050 ATAATGTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 1 0.02
21 41 0.98
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18
Consensus pattern (21 bp):
AAACACTAAACACTAAACCAT
Found at i:708049 original size:14 final size:14
Alignment explanation
Indices: 707982--708034 Score: 79
Period size: 14 Copynumber: 3.8 Consensus size: 14
707972 TAGTTTATAG
*
707982 AAACTCTAAACCCT
1 AAACACTAAACCCT
*
707996 AAACTCTAAACCCT
1 AAACACTAAACCCT
*
708010 AAACACTAAACCAT
1 AAACACTAAACCCT
708024 AAACACTAAAC
1 AAACACTAAAC
708035 ATTAAACCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.17
Consensus pattern (14 bp):
AAACACTAAACCCT
Found at i:708249 original size:23 final size:24
Alignment explanation
Indices: 708219--708268 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
708209 TTATTTTTTC
*
708219 TTTATATAAATTGAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
708242 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
708266 TTT
1 TTT
708269 TTCTTTGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:708340 original size:13 final size:13
Alignment explanation
Indices: 708307--708333 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
708297 TAATTTACAT
708307 TTAAATAATTTTA
1 TTAAATAATTTTA
708320 TTAAATAATTTTA
1 TTAAATAATTTTA
708333 T
1 T
708334 ATAATAAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:708376 original size:27 final size:26
Alignment explanation
Indices: 708289--708379 Score: 73
Period size: 30 Copynumber: 3.3 Consensus size: 26
708279 TATTAATCAT
708289 GTTTTATCTAATTTACATT-TA-AATAA
1 GTTTTAT-TAATTTA-ATTATATAATAA
*
708315 -TTTTATTAA-ATAATTTTATATAATAA
1 GTTTTATTAATTTAA--TTATATAATAA
708341 GTCTATTTATTAATTTAATTATCATAATAA
1 G--T-TTTATTAATTTAATTAT-ATAATAA
708371 GTTTTATTA
1 GTTTTATTA
708380 TAACATTTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 19
0.72 0.03 0.26
Matches are distributed among these distances:
22 1 0.02
23 2 0.04
24 5 0.09
25 8 0.15
26 5 0.09
27 7 0.13
28 1 0.02
29 5 0.09
30 16 0.30
31 3 0.06
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (26 bp):
GTTTTATTAATTTAATTATATAATAA
Found at i:708573 original size:17 final size:16
Alignment explanation
Indices: 708534--708579 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
708524 TACAGATCAT
*
708534 GTTAAAAACAGGTCAG
1 GTTAAAAACAGGTCAA
*
708550 GTTAAAAACATGTCAA
1 GTTAAAAACAGGTCAA
*
708566 GTTGAAAACAGGTC
1 GTTAAAAACAGGTC
708580 GGGTAATACC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (16 bp):
GTTAAAAACAGGTCAA
Found at i:708679 original size:31 final size:32
Alignment explanation
Indices: 708604--708680 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
708594 ATTTACCAGG
708604 TCAATCTCGGGTTCGAGTTCATATCAGTCGGAT
1 TCAAT-TCGGGTTCGAGTTCATATCAGTCGGAT
* * **
708637 GCAGTTCGGGTTCGAGTATCATAT-TTTCGG-T
1 TCAATTCGGGTTCGAGT-TCATATCAGTCGGAT
708668 TCAATTCGGGTTC
1 TCAATTCGGGTTC
708681 AGGTCGTTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
31 12 0.32
32 16 0.43
33 9 0.24
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.36
Consensus pattern (32 bp):
TCAATTCGGGTTCGAGTTCATATCAGTCGGAT
Found at i:718679 original size:90 final size:90
Alignment explanation
Indices: 718526--718692 Score: 307
Period size: 90 Copynumber: 1.9 Consensus size: 90
718516 CCTAACACAC
*
718526 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
718591 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGGAATTTAATAAT
* *
718616 CCTTTTATATCCAAGTTACCGTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
718681 ATTTAATTAATT
66 ATTTAATTAATT
718693 CAAATTAAAT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 74 1.00
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.46
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGGAATTTAATAAT
Found at i:733954 original size:28 final size:26
Alignment explanation
Indices: 733923--733982 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
733913 GCTTCATAGG
733923 AAAAAATAGTAGTTCGAAAAGAAAAGAA
1 AAAAAAT-GTAGTTCGAAAA-AAAAGAA
* * * *
733951 AAAAGATGTTGTTCGAAAAAAGAGAG
1 AAAAAATGTAGTTCGAAAAAAAAGAA
733977 AAAAAA
1 AAAAAA
733983 GACATGAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 10 0.37
27 11 0.41
28 6 0.22
ACGTcount: A:0.62, C:0.03, G:0.20, T:0.15
Consensus pattern (26 bp):
AAAAAATGTAGTTCGAAAAAAAAGAA
Found at i:736507 original size:18 final size:19
Alignment explanation
Indices: 736478--736513 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
736468 ATACTTCCCT
736478 AGCTGTGGTATCGATACCA
1 AGCTGTGGTATCGATACCA
736497 AGCTG-GGTATCGATACC
1 AGCTGTGGTATCGATACC
736514 CATTTTGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (19 bp):
AGCTGTGGTATCGATACCA
Found at i:742037 original size:17 final size:18
Alignment explanation
Indices: 741998--742039 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
741988 AAAAAGTGTT
*
741998 CTTGAAAGAAAAATGAAT
1 CTTGAAAGAAAAATGAAG
* *
742016 ATTGAATGAAAAAT-AAG
1 CTTGAAAGAAAAATGAAG
742033 CTTGAAA
1 CTTGAAA
742040 TGCTCAAACT
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.55, C:0.05, G:0.17, T:0.24
Consensus pattern (18 bp):
CTTGAAAGAAAAATGAAG
Found at i:742362 original size:18 final size:17
Alignment explanation
Indices: 742308--742356 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
742298 TTGGACCCTT
* *
742308 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
742326 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
742344 AGTGCATTCGATG
1 AGTGCA-TCGATG
742357 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:742461 original size:65 final size:65
Alignment explanation
Indices: 742328--742487 Score: 193
Period size: 65 Copynumber: 2.5 Consensus size: 65
742318 TGCACTAAGA
* *
742328 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGACTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCAGAGTGCATCGATGCATGACTG
* * * *
742392 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAACATCCTCG-GTGCATCGGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCC-AGAGTGCATCGATGCAT-G-A
742456 -T-
63 CTG
* *
742457 GTGCATCAATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
742488 CAATTTAATT
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
64 28 0.33
65 52 0.62
66 3 0.04
67 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCAGAGTGCATCGATGCATGACTG
Found at i:742526 original size:65 final size:64
Alignment explanation
Indices: 742328--742537 Score: 182
Period size: 65 Copynumber: 3.2 Consensus size: 64
742318 TGCACTAAGA
* * * * *
742328 GTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AA-AT-AGCCAGAGTGCATCGATGCATGAC
1 GTGCATCAATGCATCAAATGCATTCGATGTTTTATAACATCA-TC-G-GTGCATCGATGCATGAT
742390 TG
63 TG
* * * *
742392 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAACATCCTCGGTGCATCGGTGCATGGTAT
1 GTGCATCAATGCATCAAATGCATTCGATGTTTT-ATAACATCATCGGTGCATCGATGCATGAT-T
742457 -
64 G
* *
742457 GTGCATCAATGCATGAAATGCATTCGATGTTCAATT-TAA-TTCAT-GGTGCATCGATGCATGAA
1 GTGCATCAATGCATCAAATGCATTCGATGTT---TTATAACATCATCGGTGCATCGATGCATG-A
742519 TTG
62 TTG
*
742522 GTGCATCAGTGCATCA
1 GTGCATCAATGCATCA
742538 CTCTGAAAAA
Statistics
Matches: 121, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
64 47 0.39
65 62 0.51
66 7 0.06
67 3 0.02
68 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (64 bp):
GTGCATCAATGCATCAAATGCATTCGATGTTTTATAACATCATCGGTGCATCGATGCATGATTG
Found at i:743016 original size:2 final size:2
Alignment explanation
Indices: 743009--743052 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
742999 AATTGATTAA
743009 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
743051 AT
1 AT
743053 CTTAAGCTGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:744506 original size:23 final size:23
Alignment explanation
Indices: 744480--744533 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
744470 GGTGGAGGAG
744480 GAACGAGATTAGGAGGTTGGTTT
1 GAACGAGATTAGGAGGTTGGTTT
744503 GAACGAGATTAGGAGGTTGGTTT
1 GAACGAGATTAGGAGGTTGGTTT
744526 GAACGAGA
1 GAACGAGA
744534 ACGACAAGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.30, C:0.06, G:0.39, T:0.26
Consensus pattern (23 bp):
GAACGAGATTAGGAGGTTGGTTT
Found at i:750718 original size:65 final size:64
Alignment explanation
Indices: 750520--750729 Score: 155
Period size: 65 Copynumber: 3.2 Consensus size: 64
750510 TGCACAAAGA
* * * * * * * *
750520 GTGCATCGATGCATCAAGTGCATTCGA-TGTTTCAAAATAGCCAT-AGTACATCGATGCATGACT
1 GTGCATCAATGCATCAAATGCATTCGAGT-TTTCATAACA-TCATCGGTGCATCGATGCATGATT
750583 G
64 G
* * *
750584 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAACATCCTCGGTGCATC-AGTGCATGGTA
1 GTGCATCAATGCATCAAATGCATTCGA-GTTTTCATAACATCATCGGTGCATCGA-TGCATGAT-
750648 T-
63 TG
* *
750649 GTGCATCAATGCATGAAATGCATTCGA-TTTTCAATTTAA-TTCAT-GGTGCATCGATGCATGAA
1 GTGCATCAATGCATCAAATGCATTCGAGTTTTC-A--TAACATCATCGGTGCATCGATGCATG-A
750711 TTG
62 TTG
**
750714 GTGCATCGGTGCATCA
1 GTGCATCAATGCATCA
750730 CTCTGAAAAA
Statistics
Matches: 118, Mismatches: 17, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
63 5 0.04
64 45 0.38
65 63 0.53
66 5 0.04
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (64 bp):
GTGCATCAATGCATCAAATGCATTCGAGTTTTCATAACATCATCGGTGCATCGATGCATGATTG
Found at i:756362 original size:27 final size:27
Alignment explanation
Indices: 756324--756378 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
756314 ATGAAGATCT
*
756324 TGATGTTGTGGACTTTCAAGTTCAAAG
1 TGATGTTATGGACTTTCAAGTTCAAAG
*
756351 TGATGTTATGGAGTTTCAAGTTCAAAG
1 TGATGTTATGGACTTTCAAGTTCAAAG
756378 T
1 T
756379 AGTGATGGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.38
Consensus pattern (27 bp):
TGATGTTATGGACTTTCAAGTTCAAAG
Found at i:757526 original size:47 final size:44
Alignment explanation
Indices: 757310--757523 Score: 298
Period size: 43 Copynumber: 4.9 Consensus size: 44
757300 GATAGACTTG
757310 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAAC
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAAC
*
757354 -TTTT-TTTATTTTGTTTCTTAATGTTTTTATTTAACTATTG--C
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTA-TGAAC
*
757395 TTTTTTATTTA-TTTGTTTCTTAATGTTTTTATTTAATTAT-AGGC
1 -TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGA-AC
757439 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATTATGAAC
1 TTTTTATTTATTTTGTTTCTTAATG--TTT-TTATTTAATTATGAAC
*
757486 ATTTTATTTATTTTGTTTCTTAATGTTTTTA-TTAATTA
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTA
757524 ATTGTTTGAA
Statistics
Matches: 154, Mismatches: 4, Indels: 25
0.84 0.02 0.14
Matches are distributed among these distances:
41 1 0.01
42 33 0.21
43 54 0.35
44 22 0.14
45 3 0.02
46 3 0.02
47 37 0.24
48 1 0.01
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (44 bp):
TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAAC
Found at i:757555 original size:91 final size:91
Alignment explanation
Indices: 757311--757567 Score: 209
Period size: 85 Copynumber: 2.9 Consensus size: 91
757301 ATAGACTTGT
* * * * *
757311 TTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTAT-GAACTTT--TTTTATTTTGTTTCTT
1 TTTTATTTA-TTTGTTTCTTAATGTTTTTATTTAATTATAG-GCTTTGAATTTAGTTTGTATCTA
* *
757373 AATG--T-T-TTTATTTAACTATTG--CTT
64 AATGTTTCTATTTATTTAATTA-TGAAC-A
** * * *
757397 TTTTATTTATTTGTTTCTTAATGTTTTTATTTAATTATAGGCTTTTTATTTATTTTGTTTCTTAA
1 TTTTATTTATTTGTTTCTTAATGTTTTTATTTAATTATAGGCTTTGAATTTAGTTTGTATCTAAA
*
757462 TGTTTTTA-TTATTTAATTATGAACA
66 TGTTTCTATTTATTTAATTATGAACA
*
757487 TTTTATTTATTTTGTTTCTTAATGTTTTTA-TTAATTA-ATTG-TTTGAATTGTAACGTTTGTAT
1 TTTTATTTA-TTTGTTTCTTAATGTTTTTATTTAATTATA-GGCTTTGAATT-T-A-GTTTGTAT
757549 -TAAATGTTTCTATTTATTT
61 CTAAATGTTTCTATTTATTT
757568 TTATTATTTA
Statistics
Matches: 145, Mismatches: 11, Indels: 24
0.81 0.06 0.13
Matches are distributed among these distances:
85 33 0.23
86 10 0.07
87 19 0.13
89 10 0.07
90 29 0.20
91 32 0.22
92 12 0.08
ACGTcount: A:0.22, C:0.05, G:0.08, T:0.65
Consensus pattern (91 bp):
TTTTATTTATTTGTTTCTTAATGTTTTTATTTAATTATAGGCTTTGAATTTAGTTTGTATCTAAA
TGTTTCTATTTATTTAATTATGAACA
Found at i:757575 original size:129 final size:125
Alignment explanation
Indices: 757308--757583 Score: 303
Period size: 129 Copynumber: 2.1 Consensus size: 125
757298 TCGATAGACT
*
757308 TGTTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAACTTTTTTTATTTTGTTTCTT
1 TGTTATTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAACTTTTTTTATTTTGTTTCTT
** * * *
757373 AATGTTTTTATTTAACTATTGCTTTTTTATTTATTTGTTTCTTAATGTTTTTATTTAATTA
66 AATGTTTTTATTTAACTATTGC-TTTGAATTTATTTGTATCTAAATGTTTCTATTTAATTA
*
757434 TAGGCTTTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATTATGAACATTTTATTTATTT
1 T--G-TTATTATTTATTTTGTTTCTTAATG--TTT-TTATTTAATTATGAAC-TTTT-TTTATTT
*
757499 TGTTTCTTAATGTTTTTA-TTAATTAATTG-TTTGAATTGTAACGTTTGTAT-TAAATGTTTCTA
58 TGTTTCTTAATGTTTTTATTTAACT-ATTGCTTTGAATT-T-A--TTTGTATCTAAATGTTTCTA
757561 TTT-ATT-
118 TTTAATTA
*
757567 T-TTATTATTTAGTTTGT
1 TGTTATTATTTATTTTGT
757584 AATGTTTTTA
Statistics
Matches: 129, Mismatches: 8, Indels: 23
0.81 0.05 0.14
Matches are distributed among these distances:
126 1 0.01
128 1 0.01
129 39 0.30
131 3 0.02
132 22 0.17
133 11 0.09
134 33 0.26
135 13 0.10
136 6 0.05
ACGTcount: A:0.22, C:0.04, G:0.09, T:0.65
Consensus pattern (125 bp):
TGTTATTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAACTTTTTTTATTTTGTTTCTT
AATGTTTTTATTTAACTATTGCTTTGAATTTATTTGTATCTAAATGTTTCTATTTAATTA
Found at i:766353 original size:356 final size:356
Alignment explanation
Indices: 765700--766404 Score: 1356
Period size: 356 Copynumber: 2.0 Consensus size: 356
765690 TTTATTTTCA
*
765700 TTTATTGAACTCTGTTTATTTTAGCATCTGTACTGATCTTGTGCAGGTTCTGATGCACCCTTATG
1 TTTATTGAACTCTGTCTATTTTAGCATCTGTACTGATCTTGTGCAGGTTCTGATGCACCCTTATG
*
765765 ATCATTTCTCTTGGAATGGTGTTTTATTAATTATAAGGATTTAAACTTGGTACTTCTTTATCTGT
66 ATCATGTCTCTTGGAATGGTGTTTTATTAATTATAAGGATTTAAACTTGGTACTTCTTTATCTGT
*
765830 GATTGCTATGCGCTGGTGCTAACCATGATGCATAAAGAGAGGAGAAGTAATGGAATGACATCTAT
131 GATGGCTATGCGCTGGTGCTAACCATGATGCATAAAGAGAGGAGAAGTAATGGAATGACATCTAT
*
765895 TCAGTCTTATCTAGGGAAATTGGCTTGAATCATTATTTTCTGGTTGTGTTCTTTATCAGAAATGA
196 TCAGCCTTATCTAGGGAAATTGGCTTGAATCATTATTTTCTGGTTGTGTTCTTTATCAGAAATGA
765960 TTCTGCTAGCTAGATTCCTCTGGAAAGACTTGAAAATGATATATTGCAAGACCACATTGTTTATA
261 TTCTGCTAGCTAGATTCCTCTGGAAAGACTTGAAAATGATATATTGCAAGACCACATTGTTTATA
766025 TTGCCCCGTCTCTCTATATCGAGACCACATT
326 TTGCCCCGTCTCTCTATATCGAGACCACATT
766056 TTTATTGAACTCTGTCTATTTTAGCATCTGTACTGATCTTGTGCAGGTTCTGATGCACCCTTATG
1 TTTATTGAACTCTGTCTATTTTAGCATCTGTACTGATCTTGTGCAGGTTCTGATGCACCCTTATG
766121 ATCATGTCTCTTGGAATGGTGTTTTATTAATTATAAGGATTTAAACTTGGTACTTCTTTATCTGT
66 ATCATGTCTCTTGGAATGGTGTTTTATTAATTATAAGGATTTAAACTTGGTACTTCTTTATCTGT
*
766186 GATGGCTATGCTCTGGTGCTAACCATGATGCATAAAGAGAGGAGAAGTAATGGAATGACATCTAT
131 GATGGCTATGCGCTGGTGCTAACCATGATGCATAAAGAGAGGAGAAGTAATGGAATGACATCTAT
*
766251 TCAGCCTTATCTAGGGAAATTGGCTTGAATCATTATTTTCTGGTTGTGTTCTTTATCGGAAATGA
196 TCAGCCTTATCTAGGGAAATTGGCTTGAATCATTATTTTCTGGTTGTGTTCTTTATCAGAAATGA
766316 TTCTGCTAGCTAGATTCCTCTGGAAAGACTTGAAAATGATATATTGCAAGACCACATTGTTTATA
261 TTCTGCTAGCTAGATTCCTCTGGAAAGACTTGAAAATGATATATTGCAAGACCACATTGTTTATA
766381 TTGCCCCGTCTCTCTATATCGAGA
326 TTGCCCCGTCTCTCTATATCGAGA
766405 TCCCTCATAA
Statistics
Matches: 343, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
356 343 1.00
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (356 bp):
TTTATTGAACTCTGTCTATTTTAGCATCTGTACTGATCTTGTGCAGGTTCTGATGCACCCTTATG
ATCATGTCTCTTGGAATGGTGTTTTATTAATTATAAGGATTTAAACTTGGTACTTCTTTATCTGT
GATGGCTATGCGCTGGTGCTAACCATGATGCATAAAGAGAGGAGAAGTAATGGAATGACATCTAT
TCAGCCTTATCTAGGGAAATTGGCTTGAATCATTATTTTCTGGTTGTGTTCTTTATCAGAAATGA
TTCTGCTAGCTAGATTCCTCTGGAAAGACTTGAAAATGATATATTGCAAGACCACATTGTTTATA
TTGCCCCGTCTCTCTATATCGAGACCACATT
Found at i:776675 original size:35 final size:35
Alignment explanation
Indices: 776629--776701 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
776619 ATATAAACTC
* *
776629 TAAACTCTAAACTTTAAACCTTAAATCC-TATCACA
1 TAAACTCTAAACCTTAAACCCTAAA-CCTTATCACA
776664 TAAACTCTAAACCTTAAACCCTAAACCTTATCACA
1 TAAACTCTAAACCTTAAACCCTAAACCTTATCACA
776699 TAA
1 TAA
776702 TTAGTTATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 2 0.06
35 33 0.94
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (35 bp):
TAAACTCTAAACCTTAAACCCTAAACCTTATCACA
Found at i:776681 original size:14 final size:14
Alignment explanation
Indices: 776622--776693 Score: 60
Period size: 14 Copynumber: 5.1 Consensus size: 14
776612 CCCTAATATA
776622 TAAACTCTAAA-CT
1 TAAACTCTAAACCT
*
776635 CTAAACTTTAAACCT
1 -TAAACTCTAAACCT
* *
776650 TAAA-TCCT-ATCACA
1 TAAACT-CTAAAC-CT
776664 TAAACTCTAAACCT
1 TAAACTCTAAACCT
*
776678 TAAACCCTAAACCT
1 TAAACTCTAAACCT
776692 TA
1 TA
776694 TCACATAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
13 3 0.07
14 38 0.83
15 5 0.11
ACGTcount: A:0.43, C:0.28, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAACTCTAAACCT
Found at i:777110 original size:12 final size:11
Alignment explanation
Indices: 777083--777116 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
777073 TCGTTAAGAA
777083 CTCGAGTCGAG
1 CTCGAGTCGAG
*
777094 TTCGAGTTCGAG
1 CTCGAG-TCGAG
777106 CTCGAGTCGAG
1 CTCGAGTCGAG
777117 TCCATTCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.18, C:0.24, G:0.35, T:0.24
Consensus pattern (11 bp):
CTCGAGTCGAG
Found at i:778699 original size:25 final size:25
Alignment explanation
Indices: 778671--778720 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
778661 AAAAATGTGA
778671 TGAACAAATAT-TTTTTAAATTAAAT
1 TGAACAAA-ATCTTTTTAAATTAAAT
*
778696 TGAATAAAATGCTTTTTAAATTAAA
1 TGAACAAAAT-CTTTTTAAATTAAA
778721 CTAAATTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 2 0.09
25 7 0.32
26 13 0.59
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (25 bp):
TGAACAAAATCTTTTTAAATTAAAT
Found at i:779529 original size:25 final size:25
Alignment explanation
Indices: 779495--779542 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
779485 AGATTTCAAG
779495 GAAGATTGTCCTCGCTTCAGTACTA
1 GAAGATTGTCCTCGCTTCAGTACTA
779520 GAAGATTGTCCTCGCTTCAGTAC
1 GAAGATTGTCCTCGCTTCAGTAC
779543 ATATTTCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (25 bp):
GAAGATTGTCCTCGCTTCAGTACTA
Found at i:785807 original size:16 final size:16
Alignment explanation
Indices: 785782--785813 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
785772 ATTTTAAAAT
785782 TAAATCATTAATTAAA
1 TAAATCATTAATTAAA
*
785798 TAAATTATTAATTAAA
1 TAAATCATTAATTAAA
785814 AAAAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAATCATTAATTAAA
Found at i:799539 original size:8 final size:8
Alignment explanation
Indices: 799526--799603 Score: 56
Period size: 8 Copynumber: 9.9 Consensus size: 8
799516 TATTAATATT
799526 TATAATAA
1 TATAATAA
799534 TATAATTTAA
1 TATAA--TAA
*
799544 TATAATAT
1 TATAATAA
*
799552 TAT-AT-T
1 TATAATAA
*
799558 TATAATAT
1 TATAATAA
799566 TATAATAA
1 TATAATAA
*
799574 AATAATCAA
1 TATAAT-AA
*
799583 T-T-ATAT
1 TATAATAA
799589 TATAATAA
1 TATAATAA
799597 TATAATA
1 TATAATA
799604 TAAGATATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
6 6 0.11
7 7 0.12
8 34 0.60
9 2 0.04
10 8 0.14
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (8 bp):
TATAATAA
Found at i:799562 original size:32 final size:31
Alignment explanation
Indices: 799516--799602 Score: 106
Period size: 32 Copynumber: 2.7 Consensus size: 31
799506 AAAATATATT
*
799516 TATTAATATTTATAATAATATAATTTAATATAA
1 TATT-ATATTTATAATAATATAA-TTAAAATAA
*
799549 TATTATATTTATAATATTATAA-TAAAATAA
1 TATTATATTTATAATAATATAATTAAAATAA
799579 TCAATTATA-TTATAATAATATAAT
1 T--ATTATATTTATAATAATATAAT
799603 ATAAGATATT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
30 8 0.17
31 13 0.27
32 23 0.48
33 4 0.08
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (31 bp):
TATTATATTTATAATAATATAATTAAAATAA
Found at i:799589 original size:37 final size:42
Alignment explanation
Indices: 799510--799592 Score: 113
Period size: 40 Copynumber: 2.1 Consensus size: 42
799500 ATATTTAAAA
* *
799510 TATATTTATTAATATTTATAATAATATAATTTAATATAATAT
1 TATATTTATTAATATTTATAATAAAATAATTCAATATAATAT
799552 TATATTTA-TAATA-TTATAATAAAATAA-TCAAT-T-ATAT
1 TATATTTATTAATATTTATAATAAAATAATTCAATATAATAT
799589 TATA
1 TATA
799593 ATAATATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
37 8 0.21
38 1 0.03
39 4 0.10
40 13 0.33
41 5 0.13
42 8 0.21
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (42 bp):
TATATTTATTAATATTTATAATAAAATAATTCAATATAATAT
Found at i:799611 original size:23 final size:23
Alignment explanation
Indices: 799562--799612 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
799552 TATATTTATA
**
799562 ATATTATAATAAAATAATCAATT
1 ATATTATAATAAAATAATCAAAG
*
799585 ATATTATAATAATATAAT-ATAAG
1 ATATTATAATAAAATAATCA-AAG
799608 ATATT
1 ATATT
799613 TTTTTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATTATAATAAAATAATCAAAG
Found at i:800365 original size:46 final size:46
Alignment explanation
Indices: 800298--800389 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
800288 ACGAACAACT
800298 AAATGAAAAAAAAATCTTGTTCGTGAAGAAATTTAGCTTATTTGTG
1 AAATGAAAAAAAAATCTTGTTCGTGAAGAAATTTAGCTTATTTGTG
800344 AAATGAAAAAAAAATCTTGTTCGTGAAGAAATTTAGCTTATTTGTG
1 AAATGAAAAAAAAATCTTGTTCGTGAAGAAATTTAGCTTATTTGTG
800390 TTCGTTCGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (46 bp):
AAATGAAAAAAAAATCTTGTTCGTGAAGAAATTTAGCTTATTTGTG
Found at i:803513 original size:29 final size:30
Alignment explanation
Indices: 803470--803530 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 30
803460 GGATCTGTTA
803470 GTTTGATTTAACTTAGGATCCAAATAAGTC
1 GTTTGATTTAACTTAGGATCCAAATAAGTC
803500 GTTTGA-TTAACTTAGGATCCAAATAAGTC
1 GTTTGATTTAACTTAGGATCCAAATAAGTC
803529 GT
1 GT
803531 AAGAATTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (30 bp):
GTTTGATTTAACTTAGGATCCAAATAAGTC
Found at i:805949 original size:41 final size:41
Alignment explanation
Indices: 805904--805982 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
805894 CGTTTTTTCA
*
805904 ACAAACACCGCAAAAGACTAG-TAATTTAGCGGCGTTTTGAT
1 ACAAACACCACAAAAGACTAGAT-ATTTAGCGGCGTTTTGAT
** * *
805945 ACAAATGCCACAAAAGAGTAGATATTTAGTGGCGTTTT
1 ACAAACACCACAAAAGACTAGATATTTAGCGGCGTTTT
805983 TTTTTATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 31 0.97
42 1 0.03
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (41 bp):
ACAAACACCACAAAAGACTAGATATTTAGCGGCGTTTTGAT
Found at i:806577 original size:22 final size:22
Alignment explanation
Indices: 806549--806595 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
806539 GTTTTTTAGG
806549 TTTCGAATAGAAAAATAATAGC
1 TTTCGAATAGAAAAATAATAGC
*
806571 TTTCGAATAGGAAAATAATAGC
1 TTTCGAATAGAAAAATAATAGC
806593 TTT
1 TTT
806596 TGAAAACGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.32
Consensus pattern (22 bp):
TTTCGAATAGAAAAATAATAGC
Found at i:807766 original size:83 final size:83
Alignment explanation
Indices: 807667--807934 Score: 265
Period size: 83 Copynumber: 3.2 Consensus size: 83
807657 CGATATATAA
* * *
807667 TTGTACATTAGCGGCGTTTTTATACAAATGCCGCAATAGGT-TAAATCTATAGTGTC-TTTTTAT
1 TTGTACTTTAGCGGCGTTTTTATAAAAATGCCGCAATAGGTGT-AATCTATAGTGGCATTTTT-T
** *
807730 CAAAAAATGCCGCAAAATAT
64 CAAAAAACACCACAAAATAT
* * * * * * * *
807750 TTGTACTTTAGGGGCGTTGTTATAGAAACGTCGTAATAGGTGTAATTTATATTGGCATTTTTTCA
1 TTGTACTTTAGCGGCGTTTTTATAAAAATGCCGCAATAGGTGTAATCTATAGTGGCATTTTTTCA
*
807815 AAAAACACCATAAAATAT
66 AAAAACACCACAAAATAT
** *
807833 TCATACTTTAGCGGCGTTTATATAAAAATGCCGCAATAGGTGTAATCTATAGTGGCATTTTTT-A
1 TTGTACTTTAGCGGCGTTTTTATAAAAATGCCGCAATAGGTGTAATCTATAGTGGCATTTTTTCA
* ** *
807897 GACAAATGCCATAAAATAGT
66 -AAAAACACCACAAAATA-T
*
807917 TT-TACTTTAGCAGCGTTT
1 TTGTACTTTAGCGGCGTTT
807935 GAATATAAAC
Statistics
Matches: 151, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
82 1 0.01
83 142 0.94
84 8 0.05
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (83 bp):
TTGTACTTTAGCGGCGTTTTTATAAAAATGCCGCAATAGGTGTAATCTATAGTGGCATTTTTTCA
AAAAACACCACAAAATAT
Found at i:810096 original size:28 final size:28
Alignment explanation
Indices: 810056--810118 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
810046 CGTTTGCTTG
*
810056 TGTGTGTACGAGCCAGTGCATTCGTGTA
1 TGTGTGTACGAGCCAATGCATTCGTGTA
810084 TGTGTGTACGAGCCAATGCATTCGTGTA
1 TGTGTGTACGAGCCAATGCATTCGTGTA
810112 TGTGTGT
1 TGTGTGT
810119 GTTTATATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.17, C:0.16, G:0.32, T:0.35
Consensus pattern (28 bp):
TGTGTGTACGAGCCAATGCATTCGTGTA
Found at i:815071 original size:21 final size:21
Alignment explanation
Indices: 815047--815105 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
815037 GAAGCAAGGG
*
815047 AAGCACAAAGAGCAGCAGCGA
1 AAGCACAAAGAGAAGCAGCGA
* * *
815068 AAGCAGAGAGAGAAGCAGCGG
1 AAGCACAAAGAGAAGCAGCGA
* * *
815089 CAGCATAGAGAGAAGCA
1 AAGCACAAAGAGAAGCA
815106 TTATATCAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.46, C:0.19, G:0.34, T:0.02
Consensus pattern (21 bp):
AAGCACAAAGAGAAGCAGCGA
Found at i:815454 original size:44 final size:44
Alignment explanation
Indices: 815403--815489 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
815393 AAAATATTTA
* * * *
815403 ATATACCATATATTTTGCGACATTTGTACCCTAAAAACACCGCT
1 ATATACCAGACATTTAGCGACATTTGTACCCAAAAAACACCGCT
* * *
815447 ATATACCAGACCTTTAGCGGCATTTGTATCCAAAAAACACCGC
1 ATATACCAGACATTTAGCGACATTTGTACCCAAAAAACACCGC
815490 GAAATATCTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.28
Consensus pattern (44 bp):
ATATACCAGACATTTAGCGACATTTGTACCCAAAAAACACCGCT
Found at i:815598 original size:43 final size:43
Alignment explanation
Indices: 815551--815803 Score: 319
Period size: 43 Copynumber: 5.9 Consensus size: 43
815541 GCATTTTACG
* *
815551 GCGTTTGTGGGAAAAATGCCGCTAAATCTCAACACCTATTGCA
1 GCGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTATTGCA
* * *
815594 GCGTTTGTGATAAAAACGCCGCTAAATCTCAAAACCTATTAC-
1 GCGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTATTGCA
* * *
815636 GACATTTGTGTGAAAAACGCCGTTAAATCTCAACACCTATTGCA
1 G-CGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTATTGCA
* * * **
815680 GCGTTTGTGAGAAAAAAGCCGCTAAATATCAAAACCTATTGGG
1 GCGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTATTGCA
* **
815723 GCGTTTATGAGAAAAACGCCGCTAAATCTCAACACCTATTGTG
1 GCGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTATTGCA
* * *
815766 GCATTTGTGGGAAAAACGCCGCTAAACCTCAACACCTA
1 GCGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTA
815804 ACAAACGCCG
Statistics
Matches: 180, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
42 1 0.01
43 178 0.99
44 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (43 bp):
GCGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTATTGCA
Found at i:815656 original size:129 final size:129
Alignment explanation
Indices: 815522--815800 Score: 335
Period size: 129 Copynumber: 2.2 Consensus size: 129
815512 CATTTAGGAC
* * * * * * * *
815522 AACGCCGCTATAT-ACATACGCATTTTACGGCGTTTGTGGGAAAAATGCCGCTAAATCTCAACAC
1 AACGCCGCTAAATCACA-ACACATATTACAGCGTTTGTGAGAAAAAAGCCGCTAAATATCAAAAC
* * *
815586 CTATTGCAGCGTTTGTGATAAAAACGCCGCTAAATCTCAAAACCTATTACGACATTTGTGTGAAA
65 CTATTGCAGCGTTTATGAGAAAAACGCCGCTAAATCTCAAAACCTATTACGACATTTGTGGGAAA
* * * *
815651 AACGCCGTTAAATCTCAACACCTATTGCAGCGTTTGTGAGAAAAAAGCCGCTAAATATCAAAACC
1 AACGCCGCTAAATCACAACACATATTACAGCGTTTGTGAGAAAAAAGCCGCTAAATATCAAAACC
** * ** *
815716 TATTGGGGCGTTTATGAGAAAAACGCCGCTAAATCTCAACACCTATTGTGGCATTTGTGGGAAA
66 TATTGCAGCGTTTATGAGAAAAACGCCGCTAAATCTCAAAACCTATTACGACATTTGTGGGAAA
* *
815780 AACGCCGCTAAACCTCAACAC
1 AACGCCGCTAAATCACAACAC
815801 CTAACAAACG
Statistics
Matches: 126, Mismatches: 23, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
129 124 0.98
130 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (129 bp):
AACGCCGCTAAATCACAACACATATTACAGCGTTTGTGAGAAAAAAGCCGCTAAATATCAAAACC
TATTGCAGCGTTTATGAGAAAAACGCCGCTAAATCTCAAAACCTATTACGACATTTGTGGGAAA
Found at i:815801 original size:129 final size:129
Alignment explanation
Indices: 815551--815803 Score: 371
Period size: 129 Copynumber: 2.0 Consensus size: 129
815541 GCATTTTACG
* * * * * *
815551 GCGTTTGTGGGAAAAATGCCGCTAAATCTCAACACCTATTGCAGCGTTTGTGATAAAAACGCCGC
1 GCGTTTGTGAGAAAAAAGCCGCTAAATATCAAAACCTATTGCAGCGTTTATGAGAAAAACGCCGC
* * *
815616 TAAATCTCAAAACCTATTACGACATTTGTGTGAAAAACGCCGTTAAATCTCAACACCTATTGCA
66 TAAATCTCAAAACCTATTACGACATTTGTGGGAAAAACGCCGCTAAACCTCAACACCTATTGCA
**
815680 GCGTTTGTGAGAAAAAAGCCGCTAAATATCAAAACCTATTGGGGCGTTTATGAGAAAAACGCCGC
1 GCGTTTGTGAGAAAAAAGCCGCTAAATATCAAAACCTATTGCAGCGTTTATGAGAAAAACGCCGC
* ** *
815745 TAAATCTCAACACCTATTGTGGCATTTGTGGGAAAAACGCCGCTAAACCTCAACACCTA
66 TAAATCTCAAAACCTATTACGACATTTGTGGGAAAAACGCCGCTAAACCTCAACACCTA
815804 ACAAACGCCG
Statistics
Matches: 109, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
129 109 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (129 bp):
GCGTTTGTGAGAAAAAAGCCGCTAAATATCAAAACCTATTGCAGCGTTTATGAGAAAAACGCCGC
TAAATCTCAAAACCTATTACGACATTTGTGGGAAAAACGCCGCTAAACCTCAACACCTATTGCA
Found at i:815824 original size:27 final size:27
Alignment explanation
Indices: 815779--815830 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
815769 TTTGTGGGAA
*
815779 AAACGCCGCTAAACCTCAACACCTAAC
1 AAACGCCGCTAAACATCAACACCTAAC
**
815806 AAACGCCGCTAATTATCAACACCTA
1 AAACGCCGCTAAACATCAACACCTA
815831 TTGTGGCGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.37, G:0.08, T:0.15
Consensus pattern (27 bp):
AAACGCCGCTAAACATCAACACCTAAC
Found at i:820286 original size:11 final size:11
Alignment explanation
Indices: 820262--820306 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
820252 TTGGTGCTAG
820262 AAACAAGATAA
1 AAACAAGATAA
* *
820273 AAATAAGATTA
1 AAACAAGATAA
820284 AAACAAGATAA
1 AAACAAGATAA
820295 AGAA-AAGATAA
1 A-AACAAGATAA
820306 A
1 A
820307 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:820290 original size:22 final size:22
Alignment explanation
Indices: 820262--820303 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
820252 TTGGTGCTAG
820262 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
820284 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
820304 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:820715 original size:15 final size:17
Alignment explanation
Indices: 820690--820726 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
820680 TAAAGGTCCT
*
820690 AAATAACTAATGAA-TA
1 AAATAACTAATAAACTA
820706 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
820722 AAATA
1 AAATA
820727 TCTTAACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:824157 original size:14 final size:14
Alignment explanation
Indices: 824140--824167 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
824130 ATTTTGGCTT
824140 TTTTGTTTTTTTTG
1 TTTTGTTTTTTTTG
824154 TTTTGTTTTTTTTG
1 TTTTGTTTTTTTTG
824168 AAAAAAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (14 bp):
TTTTGTTTTTTTTG
Found at i:824510 original size:11 final size:10
Alignment explanation
Indices: 824486--824530 Score: 54
Period size: 11 Copynumber: 4.2 Consensus size: 10
824476 TTTGTGCTGG
824486 AAAAAAGATA
1 AAAAAAGATA
824496 AAAATAAGATTA
1 AAAA-AAGA-TA
*
824508 AAACAAGATA
1 AAAAAAGATA
824518 AAGAAAAGATA
1 AA-AAAAGATA
824529 AA
1 AA
824531 TGAATTGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 8 0.27
11 17 0.57
12 5 0.17
ACGTcount: A:0.73, C:0.02, G:0.11, T:0.13
Consensus pattern (10 bp):
AAAAAAGATA
Found at i:831560 original size:49 final size:49
Alignment explanation
Indices: 831466--831560 Score: 113
Period size: 49 Copynumber: 1.9 Consensus size: 49
831456 AAGTCCAACA
* * * *
831466 AATTTAACAAAATAAAGTAAGTATTAAATGAGAAATAATAAAAAATTAC
1 AATTTAACAAAATAAAGTAAATATCAAATGAGAAAAAAAAAAAAATTAC
*
831515 AATTTAACAAAATAAAGTAAATA-CAAAT-ATAATAAAAAAACAAAAT
1 AATTTAACAAAATAAAGTAAATATCAAATGAGAA-AAAAAAA-AAAAT
831561 CTATCGATGC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
47 3 0.08
48 9 0.23
49 27 0.69
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.24
Consensus pattern (49 bp):
AATTTAACAAAATAAAGTAAATATCAAATGAGAAAAAAAAAAAAATTAC
Found at i:833726 original size:17 final size:17
Alignment explanation
Indices: 833704--833737 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
833694 CCTTCCATTA
*
833704 TATATTTGCAAAATATT
1 TATATTAGCAAAATATT
*
833721 TATATTAGTAAAATATT
1 TATATTAGCAAAATATT
833738 AAATAAAGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (17 bp):
TATATTAGCAAAATATT
Found at i:833747 original size:17 final size:18
Alignment explanation
Indices: 833727--833767 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
833717 TATTTATATT
833727 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
833744 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
833762 ATTAAA
1 AGTAAA
833768 TATAGAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:840252 original size:43 final size:44
Alignment explanation
Indices: 840097--840255 Score: 150
Period size: 44 Copynumber: 3.8 Consensus size: 44
840087 TTTATGAATT
* * *
840097 TAGCGGCATTTTTTGGATAC--ACGCCGCAGAAGGTGTGATATA
1 TAGCGGCATTTTTTGGATACAAACGCCGCAAAAGGTATGGTATA
* * * * * *
840139 TAGCGG---TGTTCGTATAAAAACGCCGTAAAATGTATGGTATA
1 TAGCGGCATTTTTTGGATACAAACGCCGCAAAAGGTATGGTATA
* * *
840180 TAGCGGCGTTTTTTGGATACAAACACCGCAAAAGGTCTGGTATA
1 TAGCGGCATTTTTTGGATACAAACGCCGCAAAAGGTATGGTATA
* *
840224 TAGTGGCATTTTTT-GTTACAAACGCCGCAAAA
1 TAGCGGCATTTTTTGGATACAAACGCCGCAAAA
840256 TATTTAAATT
Statistics
Matches: 91, Mismatches: 21, Indels: 9
0.75 0.17 0.07
Matches are distributed among these distances:
39 7 0.08
41 23 0.25
42 6 0.07
43 16 0.18
44 39 0.43
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (44 bp):
TAGCGGCATTTTTTGGATACAAACGCCGCAAAAGGTATGGTATA
Found at i:840687 original size:23 final size:21
Alignment explanation
Indices: 840659--840736 Score: 129
Period size: 21 Copynumber: 3.7 Consensus size: 21
840649 TGATATGTTA
*
840659 CTTCTCTCTGTGCTGCCGCTG
1 CTTCTCTCTGTGCTTCCGCTG
840680 CTTCTCTCTGTGCTTCCGCTG
1 CTTCTCTCTGTGCTTCCGCTG
840701 CTTCTCTCTGTGCTTCCGCTG
1 CTTCTCTCTGTGCTTCCGCTG
* *
840722 CTGCTCTCTCTGCTT
1 CTTCTCTCTGTGCTT
840737 TCCTCGCTTC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.00, C:0.38, G:0.19, T:0.42
Consensus pattern (21 bp):
CTTCTCTCTGTGCTTCCGCTG
Found at i:840695 original size:12 final size:12
Alignment explanation
Indices: 840678--840733 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
840668 GTGCTGCCGC
840678 TGCTTCTCTCTG
1 TGCTTCTCTCTG
*
840690 TGCTTC-CGC--
1 TGCTTCTCTCTG
840699 TGCTTCTCTCTG
1 TGCTTCTCTCTG
*
840711 TGCTTC-CGCTG
1 TGCTTCTCTCTG
840722 CTGC-TCTCTCTG
1 -TGCTTCTCTCTG
840734 CTTTCCTCGC
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
9 6 0.17
10 2 0.06
11 8 0.23
12 19 0.54
ACGTcount: A:0.00, C:0.38, G:0.20, T:0.43
Consensus pattern (12 bp):
TGCTTCTCTCTG
Found at i:846544 original size:42 final size:40
Alignment explanation
Indices: 846453--846572 Score: 136
Period size: 41 Copynumber: 3.0 Consensus size: 40
846443 ATGGACAATG
**
846453 ACGGTGTTTATTAAAAACA-CCACTAAGGGA-AAAACTTTT
1 ACGGTGTTTATTAAAAA-AGCCACTAAGGGACAAAACTACT
* **
846492 GCGGCATTTATTACAAAAATGCCACTAAGGGACAAAACTACT
1 ACGGTGTTTATTA-AAAAA-GCCACTAAGGGACAAAACTACT
*
846534 ACGGTGTTTATTGAAAAAAGCCACTAAAGGACAAAACTA
1 ACGGTGTTTATT-AAAAAAGCCACTAAGGGACAAAACTA
846573 TTGCGGCGTT
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
39 11 0.16
40 4 0.06
41 30 0.45
42 21 0.31
43 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (40 bp):
ACGGTGTTTATTAAAAAAGCCACTAAGGGACAAAACTACT
Found at i:846640 original size:41 final size:41
Alignment explanation
Indices: 846571--846722 Score: 175
Period size: 41 Copynumber: 3.8 Consensus size: 41
846561 AGGACAAAAC
*
846571 TATTGCGGCG-TTTGT-A-AAACGCCGCTAAAGTACATGGA
1 TATTGCGGCGTTTTGTCACAAACGCCACTAAAGTACATGGA
* * * * *
846609 TATTGCGGCATTTGGTCACAGACGCCACTAAAGTACAGGGC
1 TATTGCGGCGTTTTGTCACAAACGCCACTAAAGTACATGGA
** * * *
846650 TATTATGGCGTTTTCTCACAAATGCCACTAAAGTACATGGT
1 TATTGCGGCGTTTTGTCACAAACGCCACTAAAGTACATGGA
*
846691 TATTGCGGCGTTTTGTCACAAACACCACTAAA
1 TATTGCGGCGTTTTGTCACAAACGCCACTAAA
846723 TTAAGAGTAT
Statistics
Matches: 91, Mismatches: 20, Indels: 3
0.80 0.18 0.03
Matches are distributed among these distances:
38 9 0.10
39 4 0.04
40 1 0.01
41 77 0.85
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (41 bp):
TATTGCGGCGTTTTGTCACAAACGCCACTAAAGTACATGGA
Found at i:848068 original size:22 final size:22
Alignment explanation
Indices: 848042--848094 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
848032 TTTTCACGTT
*
848042 TTCAAAATCTATTATTTTCCTA
1 TTCAAAAGCTATTATTTTCCTA
*
848064 TTCAAAAGCTATTATTTTTCTA
1 TTCAAAAGCTATTATTTTCCTA
*
848086 TTCGAAAGC
1 TTCAAAAGC
848095 AGAAAAACAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (22 bp):
TTCAAAAGCTATTATTTTCCTA
Found at i:851108 original size:16 final size:16
Alignment explanation
Indices: 851087--851207 Score: 69
Period size: 16 Copynumber: 7.8 Consensus size: 16
851077 TTCAGAAAAG
851087 AAAAAATAATAAATAT
1 AAAAAATAATAAATAT
* *
851103 AAAAAATATTAAA-AG
1 AAAAAATAATAAATAT
* *
851118 AGAAAGTAA-AAATA-
1 AAAAAATAATAAATAT
*
851132 AAACAA-AATAAA-AT
1 AAAAAATAATAAATAT
*
851146 AAAAAAGTGGGAA-AAATAA
1 AAAAAA-T---AATAAATAT
*
851165 AAAAATATAAT-AATAA
1 AAAAA-ATAATAAATAT
851181 AAAAAAT-ATAAATAT
1 AAAAAATAATAAATAT
*
851196 AATAAATAATAA
1 AAAAAATAATAA
851208 TAATAAAGAT
Statistics
Matches: 80, Mismatches: 12, Indels: 26
0.68 0.10 0.22
Matches are distributed among these distances:
13 3 0.04
14 16 0.20
15 20 0.25
16 28 0.35
18 3 0.04
19 9 0.11
20 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.20
Consensus pattern (16 bp):
AAAAAATAATAAATAT
Found at i:851182 original size:15 final size:15
Alignment explanation
Indices: 851164--851214 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 15
851154 GGGAAAAATA
851164 AAAAAATATAATAAT
1 AAAAAATATAATAAT
851179 AAAAAAAATATAA-ATAT
1 --AAAAAATATAATA-AT
*
851196 AATAAATAATAATAAT
1 AAAAAAT-ATAATAAT
851212 AAA
1 AAA
851215 GATAAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 6 0.21
16 9 0.31
17 14 0.48
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAAAATATAATAAT
Found at i:851255 original size:93 final size:93
Alignment explanation
Indices: 851158--851383 Score: 309
Period size: 93 Copynumber: 2.4 Consensus size: 93
851148 AAAAGTGGGA
851158 AAAATAAAAAAA-TATAATAATAAAAAA-AA-T--ATAAATATAATAAATAATAATAATAAAGAT
1 AAAATAAAAAAATTA-AATAA-AAAAAATAATTAAATAAATATAATAAATAAT-A-AATAAAGAT
851218 AAAAAGAGGGTTTTTAAAAGTTATTTTTAAAAT
62 -AAAAGAGGGTTTTTAAAAGTTATTTTTAAAAT
* * *
851251 AAAATATAAGAATTAAATAAAAATAATAATTAAATAAATATAATAAATAATAAATAAAGATAAAA
1 AAAATAAAAAAATTAAATAAAAAAAATAATTAAATAAATATAATAAATAATAAATAAAGATAAAA
*
851316 GAGGGTTTTTAAAAGTTGTTTTTAAAAT
66 GAGGGTTTTTAAAAGTTATTTTTAAAAT
* * *
851344 AAAATATAAGAATTAAATAAAAATAATAATTAAATAAATA
1 AAAATAAAAAAATTAAATAAAAAAAATAATTAAATAAATA
851384 ATCTATAGAG
Statistics
Matches: 124, Mismatches: 4, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
92 5 0.04
93 88 0.71
94 12 0.10
95 1 0.01
96 18 0.15
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.31
Consensus pattern (93 bp):
AAAATAAAAAAATTAAATAAAAAAAATAATTAAATAAATATAATAAATAATAAATAAAGATAAAA
GAGGGTTTTTAAAAGTTATTTTTAAAAT
Found at i:851281 original size:17 final size:17
Alignment explanation
Indices: 851247--851296 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
851237 GTTATTTTTA
*
851247 AAATAAAATATAAGAATT
1 AAATAAAA-ATAATAATT
851265 AAATAAAAATAATAATT
1 AAATAAAAATAATAATT
*
851282 AAATAAATATAATAA
1 AAATAAAAATAATAA
851297 ATAATAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 22 0.73
18 8 0.27
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (17 bp):
AAATAAAAATAATAATT
Found at i:851290 original size:21 final size:20
Alignment explanation
Indices: 851247--851308 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
851237 GTTATTTTTA
* *
851247 AAATAAAAT--ATAAGAATT
1 AAATAAAATAAATAATAAAT
851265 AAATAAAA-ATAATAATTAAAT
1 AAATAAAATA-AATAA-TAAAT
*
851286 AAATATAATAAATAATAAAT
1 AAATAAAATAAATAATAAAT
851306 AAA
1 AAA
851309 GATAAAAGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 8 0.22
20 12 0.33
21 15 0.42
22 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (20 bp):
AAATAAAATAAATAATAAAT
Found at i:851295 original size:20 final size:19
Alignment explanation
Indices: 851247--851313 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 19
851237 GTTATTTTTA
*
851247 AAATAAAAT-ATAAGAATT
1 AAATAAAATAATAATAATT
851265 AAAT-AAA-AATAATAATT
1 AAATAAAATAATAATAATT
851282 AAATAAATATAATAAATAA-T
1 AAATAAA-ATAAT-AATAATT
851302 AAATAAAGATAA
1 AAATAAA-ATAA
851314 AAGAGGGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
17 15 0.36
18 6 0.14
19 1 0.02
20 15 0.36
21 5 0.12
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (19 bp):
AAATAAAATAATAATAATT
Found at i:851374 original size:17 final size:18
Alignment explanation
Indices: 851340--851381 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
851330 GTTGTTTTTA
851340 AAATAAAATATAAGAATT
1 AAATAAAATATAAGAATT
*
851358 AAATAAAA-ATAATAATT
1 AAATAAAATATAAGAATT
851375 AAATAAA
1 AAATAAA
851382 TAATCTATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
AAATAAAATATAAGAATT
Found at i:851780 original size:11 final size:12
Alignment explanation
Indices: 851748--851780 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
851738 GAAGTGTGCG
851748 AAAATAGAGAGA
1 AAAATAGAGAGA
*
851760 AAACTAGAGAGA
1 AAAATAGAGAGA
851772 AAAAT-GAGA
1 AAAATAGAGA
851781 TTTATTCCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.64, C:0.03, G:0.24, T:0.09
Consensus pattern (12 bp):
AAAATAGAGAGA
Found at i:855827 original size:3 final size:3
Alignment explanation
Indices: 855819--855882 Score: 62
Period size: 3 Copynumber: 21.3 Consensus size: 3
855809 ACTGTGCAAC
* *
855819 AAG AAG AAG AAG AAG AAG AAG AAG AATG AAG GAG -GG AAG AA- ATA-
1 AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG A-AG
855863 AAG AAGG AAG AAG AAG AAG A
1 AAG AA-G AAG AAG AAG AAG A
855883 CCTGGGGGTG
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
2 3 0.06
3 44 0.83
4 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:859667 original size:18 final size:19
Alignment explanation
Indices: 859644--859696 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
859634 AATACATGTC
*
859644 AGTAAAATTAAAGT-AATA
1 AGTAAAATTAAAATAAATA
*
859662 ATTAAAA-TAAAATAAATA
1 AGTAAAATTAAAATAAATA
*
859680 AGAAAAATT-AAATAAAT
1 AGTAAAATTAAAATAAAT
859697 TAACTTTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 5 0.17
18 23 0.79
19 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (19 bp):
AGTAAAATTAAAATAAATA
Found at i:862902 original size:15 final size:14
Alignment explanation
Indices: 862879--862908 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
862869 TCAACAATAG
862879 TTTTTTTTTTTATT
1 TTTTTTTTTTTATT
862893 TTTTTGTTTTTTATT
1 TTTTT-TTTTTTATT
862908 T
1 T
862909 GATAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.07, C:0.00, G:0.03, T:0.90
Consensus pattern (14 bp):
TTTTTTTTTTTATT
Found at i:862934 original size:126 final size:130
Alignment explanation
Indices: 862764--863024 Score: 460
Period size: 129 Copynumber: 2.0 Consensus size: 130
862754 TGTTTTGGAT
862764 TTTTTATTGTTTTTTATTTGATAAATAATACTGTCTTTTAGTCTAAATATAAT-AAT-ATTATTA
1 TTTTTATTGTTTTTTATTTGATAAATAATACTGTCTTTTAGTCTAAATATAATAAATAATTATTA
*
862827 TGTCACGTTTTATTATTATATTAATAACGTTTATTA-TTATTATCAACAATAGTTTTTTTTTTTA
66 TGTCACGTTTTATTATTATATTAATAACGTTTATTATTTATTATCAACAATAGTTTTTTATTTTA
862891 TTTTT-TTGTTTTTTATTTGATAAATATATACTGTC-TTTAGTCTAAATATAATAGAATAATTAT
1 TTTTTATTGTTTTTTATTTGATAAATA-ATACTGTCTTTTAGTCTAAATATAATA-AATAATTAT
862954 TATGTCACGTTTTATTATTATATTAATAACGTTTATTATTTATTATCAACAATAGTTTTTTATTT
64 TATGTCACGTTTTATTATTATATTAATAACGTTTATTATTTATTATCAACAATAGTTTTTTATTT
863019 TA
129 TA
863021 TTTT
1 TTTT
863025 AATTTTTAAT
Statistics
Matches: 128, Mismatches: 1, Indels: 7
0.94 0.01 0.05
Matches are distributed among these distances:
126 38 0.30
127 13 0.10
128 3 0.02
129 43 0.34
130 31 0.24
ACGTcount: A:0.31, C:0.06, G:0.07, T:0.56
Consensus pattern (130 bp):
TTTTTATTGTTTTTTATTTGATAAATAATACTGTCTTTTAGTCTAAATATAATAAATAATTATTA
TGTCACGTTTTATTATTATATTAATAACGTTTATTATTTATTATCAACAATAGTTTTTTATTTTA
Found at i:863629 original size:17 final size:17
Alignment explanation
Indices: 863607--863656 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
863597 AAATTCTTCT
863607 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
*
863624 AACA-T--T-GATACTCA
1 AACATTCATAGAAAC-CA
863638 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
863655 AA
1 AA
863657 ACATGAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 4 0.15
14 7 0.27
15 1 0.04
16 1 0.04
17 9 0.35
18 4 0.15
ACGTcount: A:0.52, C:0.22, G:0.06, T:0.20
Consensus pattern (17 bp):
AACATTCATAGAAACCA
Found at i:865339 original size:7 final size:7
Alignment explanation
Indices: 865327--865369 Score: 86
Period size: 7 Copynumber: 6.1 Consensus size: 7
865317 TCAATTCTGG
865327 GATTCCA
1 GATTCCA
865334 GATTCCA
1 GATTCCA
865341 GATTCCA
1 GATTCCA
865348 GATTCCA
1 GATTCCA
865355 GATTCCA
1 GATTCCA
865362 GATTCCA
1 GATTCCA
865369 G
1 G
865370 GCTTCTGCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (7 bp):
GATTCCA
Found at i:866089 original size:42 final size:42
Alignment explanation
Indices: 866042--866136 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
866032 GATGAAAACA
* * * * *
866042 TTTTGTTACTAGTTTTAGTTGGTAA-TTGACGATGACAATTGT
1 TTTTGTCACTAGTCTTAATTGGTAATTTG-CGACGACAATTAT
866084 TTTTGTCACTAGTCTTAATTGGTAATTTGCGACGACAATTAT
1 TTTTGTCACTAGTCTTAATTGGTAATTTGCGACGACAATTAT
866126 TTTTGTCACTA
1 TTTTGTCACTA
866137 TTGAAATGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 44 0.94
43 3 0.06
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.46
Consensus pattern (42 bp):
TTTTGTCACTAGTCTTAATTGGTAATTTGCGACGACAATTAT
Found at i:870030 original size:13 final size:12
Alignment explanation
Indices: 869997--870032 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
869987 TAATGGGCAA
869997 AATTTTGAAAAC
1 AATTTTGAAAAC
*
870009 TATTTTGAAAAC
1 AATTTTGAAAAC
870021 AATGTTTGAAAA
1 AAT-TTTGAAAA
870033 TTCATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (12 bp):
AATTTTGAAAAC
Found at i:870532 original size:23 final size:22
Alignment explanation
Indices: 870501--870569 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 22
870491 TGGTACACCT
870501 AGGAGTGTATCGATACATATTCA
1 AGGA-TGTATCGATACATATTCA
*
870524 AGGAATGTATCGGTACATATTCA
1 AGG-ATGTATCGATACATATTCA
870547 TA-G-TGTATCGATACATA-TCA
1 -AGGATGTATCGATACATATTCA
870567 AGG
1 AGG
870570 GGGTATTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
19 1 0.02
20 4 0.10
21 13 0.32
23 21 0.51
24 2 0.05
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (22 bp):
AGGATGTATCGATACATATTCA
Found at i:870575 original size:21 final size:22
Alignment explanation
Indices: 870505--870575 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 22
870495 ACACCTAGGA
870505 GTGTATCGATACATATTCAAGG
1 GTGTATCGATACATATTCAAGG
* *
870527 AATGTATCGGTACATATTCATA--
1 -GTGTATCGATACATATTCA-AGG
870549 GTGTATCGATACATA-TCAAGG
1 GTGTATCGATACATATTCAAGG
*
870570 GGGTAT
1 GTGTAT
870576 TGAAACCCAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
19 1 0.03
20 3 0.08
21 18 0.45
23 17 0.43
24 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (22 bp):
GTGTATCGATACATATTCAAGG
Found at i:872696 original size:37 final size:37
Alignment explanation
Indices: 872638--872734 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
872628 CTTTTTCGTC
*
872638 CTACTAGAATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
872675 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
872712 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
872735 GATAAGATCC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:873302 original size:21 final size:21
Alignment explanation
Indices: 873212--873303 Score: 82
Period size: 21 Copynumber: 4.3 Consensus size: 21
873202 TTTTTTACAC
873212 TATATA-TTATTATTATATATA
1 TATATATTTATTATT-TATATA
* * *
873233 CATATATTTTTTATTTATTTA
1 TATATATTTATTATTTATATA
* *
873254 TAT-TCATTTGGTTATTTTTA-A
1 TATAT-ATTT-ATTATTTATATA
873275 TACTATATTTATTATTTATATA
1 TA-TATATTTATTATTTATATA
873297 TATATAT
1 TATATAT
873304 ATATATATAC
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
20 1 0.02
21 32 0.57
22 22 0.39
23 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (21 bp):
TATATATTTATTATTTATATA
Found at i:873478 original size:13 final size:13
Alignment explanation
Indices: 873460--873492 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
873450 TGTTTACTTT
873460 TATATTTGGTTTA
1 TATATTTGGTTTA
873473 TATATTTGGTTTA
1 TATATTTGGTTTA
873486 TATATTT
1 TATATTT
873493 AGTACCTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (13 bp):
TATATTTGGTTTA
Found at i:875332 original size:16 final size:16
Alignment explanation
Indices: 875311--875343 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
875301 TAATAAATAA
875311 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
875327 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
875343 A
1 A
875344 AATTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:875419 original size:53 final size:55
Alignment explanation
Indices: 875327--875449 Score: 232
Period size: 53 Copynumber: 2.3 Consensus size: 55
875317 ATAAACGAAC
875327 ACGAACATAAACGAACAAATTATTTTTTGTTCATGTTCGTTTATTTAATAAATAA
1 ACGAACATAAACGAACAAATTATTTTTTGTTCATGTTCGTTTATTTAATAAATAA
875382 ACGAACATAAACGAAC-AATT-TTTTTTGTTCATGTTCGTTTATTTAATAAATAA
1 ACGAACATAAACGAACAAATTATTTTTTGTTCATGTTCGTTTATTTAATAAATAA
875435 ACGAACATAAACGAA
1 ACGAACATAAACGAA
875450 TACGAACATA
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
53 48 0.71
54 4 0.06
55 16 0.24
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (55 bp):
ACGAACATAAACGAACAAATTATTTTTTGTTCATGTTCGTTTATTTAATAAATAA
Found at i:875446 original size:10 final size:10
Alignment explanation
Indices: 875431--875499 Score: 64
Period size: 10 Copynumber: 7.7 Consensus size: 10
875421 TATTTAATAA
875431 ATAAACGAAC
1 ATAAACGAAC
875441 ATAAACG-A-
1 ATAAACGAAC
875449 AT--ACGAAC
1 ATAAACGAAC
*
875457 ATAAGCGAAC
1 ATAAACGAAC
875467 ATAAACG-A-
1 ATAAACGAAC
875475 AT--ACGAAC
1 ATAAACGAAC
*
875483 ATAAGCGAAC
1 ATAAACGAAC
875493 ATAAACG
1 ATAAACG
875500 TTGGAGACCC
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
6 6 0.13
7 2 0.04
8 8 0.17
9 2 0.04
10 29 0.62
ACGTcount: A:0.55, C:0.19, G:0.14, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:875456 original size:16 final size:16
Alignment explanation
Indices: 875435--875491 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
875425 TAATAAATAA
875435 ACGAACATAAACGAAT
1 ACGAACATAAACGAAT
875451 ACGAACAT-AA-G---
1 ACGAACATAAACGAAT
875462 -CGAACATAAACGAAT
1 ACGAACATAAACGAAT
*
875477 ACGAACATAAGCGAA
1 ACGAACATAAACGAA
875492 CATAAACGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
10 7 0.21
11 2 0.06
12 1 0.03
14 1 0.03
15 2 0.06
16 21 0.62
ACGTcount: A:0.54, C:0.19, G:0.16, T:0.11
Consensus pattern (16 bp):
ACGAACATAAACGAAT
Found at i:875467 original size:26 final size:26
Alignment explanation
Indices: 875431--875499 Score: 129
Period size: 26 Copynumber: 2.7 Consensus size: 26
875421 TATTTAATAA
*
875431 ATAAACGAACATAAACGAATACGAAC
1 ATAAGCGAACATAAACGAATACGAAC
875457 ATAAGCGAACATAAACGAATACGAAC
1 ATAAGCGAACATAAACGAATACGAAC
875483 ATAAGCGAACATAAACG
1 ATAAGCGAACATAAACG
875500 TTGGAGACCC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.55, C:0.19, G:0.14, T:0.12
Consensus pattern (26 bp):
ATAAGCGAACATAAACGAATACGAAC
Done.