Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007243.1 Hibiscus syriacus cultivar Beakdansim tig00019193_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: 78452
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:4532 original size:62 final size:61
Alignment explanation
Indices: 4440--4564 Score: 191
Period size: 63 Copynumber: 2.0 Consensus size: 61
4430 ACTAAACTCA
*
4440 GACTCAAATTAGAAATAAATC-AAAATTTTAAAATCAAATCAAATTAAAACCTATTAAATTC
1 GACTCAAATTAGAAATAAATCAAAAATTTAAAAATCAAATCAAATT-AAACCTATTAAATTC
*
4501 GACTCAAATTA-AAAGTAAAATCAAAAATTTAAAAATCAAATCAAATTAAATCTATTAAATTC
1 GACTCAAATTAGAAA-T-AAATCAAAAATTTAAAAATCAAATCAAATTAAACCTATTAAATTC
4563 GA
1 GA
4565 ATCGAGTATT
Statistics
Matches: 59, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
60 3 0.05
61 12 0.20
62 21 0.36
63 23 0.39
ACGTcount: A:0.55, C:0.12, G:0.04, T:0.29
Consensus pattern (61 bp):
GACTCAAATTAGAAATAAATCAAAAATTTAAAAATCAAATCAAATTAAACCTATTAAATTC
Found at i:4616 original size:3 final size:3
Alignment explanation
Indices: 4608--4666 Score: 93
Period size: 3 Copynumber: 19.3 Consensus size: 3
4598 CAAACTGTAC
4608 AAT AAT AAT AAT -AT AAT AAT ATAT AAT ATAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT
4654 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
4667 GTCTTCGTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:9692 original size:3 final size:3
Alignment explanation
Indices: 9684--9735 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
9674 CTTTACCAAA
9684 TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9730 TAT TAT
1 TAT TAT
9736 ATATGAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 43 0.91
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:9712 original size:17 final size:17
Alignment explanation
Indices: 9684--9735 Score: 95
Period size: 17 Copynumber: 3.0 Consensus size: 17
9674 CTTTACCAAA
9684 TATTATTATTATTATTAT
1 TATTA-TATTATTATTAT
9702 TATTATATTATTATTAT
1 TATTATATTATTATTAT
9719 TATTATATTATTATTAT
1 TATTATATTATTATTAT
9736 ATATGAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 29 0.85
18 5 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTATATTATTATTAT
Found at i:11946 original size:6 final size:6
Alignment explanation
Indices: 11935--11971 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
11925 ATAATATTGC
* *
11935 GGATTT GGATTT GGATTT GGATTT GAATTT AGATTT G
1 GGATTT GGATTT GGATTT GGATTT GGATTT GGATTT G
11972 AAGATATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.49
Consensus pattern (6 bp):
GGATTT
Found at i:15958 original size:2 final size:2
Alignment explanation
Indices: 15951--15980 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15941 AATAATCCAT
15951 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
15981 AAATAATAAA
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):
TA
Found at i:17122 original size:23 final size:23
Alignment explanation
Indices: 17096--17174 Score: 122
Period size: 23 Copynumber: 3.4 Consensus size: 23
17086 ATTTAAATGA
17096 TAAACAAACACAATAAACGAACG
1 TAAACAAACACAATAAACGAACG
17119 TAAACAAACACAATAAACGAACG
1 TAAACAAACACAATAAACGAACG
* * *
17142 TAAACGAACACAAAAAATGAACG
1 TAAACAAACACAATAAACGAACG
*
17165 TAAACGAACA
1 TAAACAAACA
17175 TAAATGAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.61, C:0.20, G:0.10, T:0.09
Consensus pattern (23 bp):
TAAACAAACACAATAAACGAACG
Found at i:22305 original size:2 final size:2
Alignment explanation
Indices: 22298--22339 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
22288 GAATTCACAT
22298 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
22340 AATCAATCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23252 original size:2 final size:2
Alignment explanation
Indices: 23247--23284 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
23237 GTGTGACCAA
23247 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
23285 TAAAATCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23591 original size:2 final size:2
Alignment explanation
Indices: 23586--23686 Score: 202
Period size: 2 Copynumber: 50.5 Consensus size: 2
23576 TCACACACAC
23586 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
23628 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
23670 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
23687 GTCAATCATA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 99 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25030 original size:23 final size:23
Alignment explanation
Indices: 24987--25031 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
24977 TTACCCTTTA
**
24987 TTTTAAATAATTTATCTTTATAT
1 TTTTAAATAATTTATAATTATAT
*
25010 TTTTAACTAATTTATAATTATA
1 TTTTAAATAATTTATAATTATA
25032 CGCTGAGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTAAATAATTTATAATTATAT
Found at i:26674 original size:151 final size:152
Alignment explanation
Indices: 26473--26746 Score: 388
Period size: 151 Copynumber: 1.8 Consensus size: 152
26463 TACAAAATAA
* ** * * *
26473 TATATATAATATACGTTGAAAGGTTAATAATTTGATGATAAACGATCATACCTCAACTTATATAG
1 TATATATAATATACGTTCAAAGAATAATAATTTGATAATAAACGACCATACCCCAACTTATATAG
* * *
26538 TATTTAAACTCAAAACTTTAAGGAATAATAACAAATCTTATAAGCACGAAAATTAATACATAATT
66 TATTTAAACCCAAAACTTTAAGGAATAACAACAAATCTTATAACCACGAAAATTAATACATAATT
26603 AGTACATTATATATATATTATG
131 AGTACATTATATATATATTATG
* * **
26625 TATATAT-ATATACGTTCAAAGAATAATAATTTGGTAATGAACGACCATACCCCTGCTTATATAG
1 TATATATAATATACGTTCAAAGAATAATAATTTGATAATAAACGACCATACCCCAACTTATATAG
* * * *
26689 TATTTGAACCCAAAACTTTAAGGATTAACAATAAATCTTATAACCACGATAATTAATA
66 TATTTAAACCCAAAACTTTAAGGAATAACAACAAATCTTATAACCACGAAAATTAATA
26747 AATTATATAT
Statistics
Matches: 105, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
151 98 0.93
152 7 0.07
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (152 bp):
TATATATAATATACGTTCAAAGAATAATAATTTGATAATAAACGACCATACCCCAACTTATATAG
TATTTAAACCCAAAACTTTAAGGAATAACAACAAATCTTATAACCACGAAAATTAATACATAATT
AGTACATTATATATATATTATG
Found at i:27141 original size:10 final size:10
Alignment explanation
Indices: 27126--27154 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
27116 TTATGTGTTA
27126 TAAATTTTAT
1 TAAATTTTAT
27136 TAAATTTTAT
1 TAAATTTTAT
27146 T-AATTTTAT
1 TAAATTTTAT
27155 GCAATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TAAATTTTAT
Found at i:27181 original size:2 final size:2
Alignment explanation
Indices: 27174--27204 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
27164 ATGAATCCTG
27174 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
27205 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:27209 original size:2 final size:2
Alignment explanation
Indices: 27204--27237 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
27194 ACACACACAC
27204 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
27238 TATGTATAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27756 original size:10 final size:10
Alignment explanation
Indices: 27741--27769 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
27731 TTATGTGTTA
27741 TAAATTTTAT
1 TAAATTTTAT
27751 TAAATTTTAT
1 TAAATTTTAT
27761 T-AATTTTAT
1 TAAATTTTAT
27770 GCAATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TAAATTTTAT
Found at i:27780 original size:615 final size:613
Alignment explanation
Indices: 26610--28435 Score: 2826
Period size: 615 Copynumber: 3.0 Consensus size: 613
26600 ATTAGTACAT
**
26610 TATATATATATTATGTATA-TATATATACGTTCAAAGAATAATAATTTGGTAATGAACGACCATA
1 TATATATATATTATGTATAGGGT-TATACGTTCAAAGAATAATAATTTGGTAATGAACGACCATA
26674 CCCCTGCTTATATAGTATTTGAACCCAAAACTTTAAGGATTAACAATAAATCTTATAACCACGAT
65 CCCCTGCTTATATAGTATTTGAACCCAAAACTTTAAGGATTAACAATAAATCTTATAACCACGAT
26739 AATTAATAAATTATATATATATATAAGGATAAGATCCACTTGCACTATGTAAAACTAATAAATTT
130 AATTAATAAATTATATATATATAT--GGATAAGATCCACTTGCACTATGTAAAACTAATAAATTT
26804 TACACCAATTTATAAAACATTAGATTTAAATAAATAAATGGCTTATATTTAATTAAAATTTATAA
193 TACACCAATTTAT-AAACATTAGATTTAAATAAATAAATGGCTTATATTTAATTAAAATTTATAA
* *
26869 TTCATACATGAATATTTCTTTATCTCACAATAAAACAATATTTTTTTCTTTTTAGGGTTAGGATT
257 TTCATACATAAATATTTCTTTATCTCACAATAAAACAATATTTTTTTCCTTTTAGGGTTAGGATT
* * *
26934 TAGGATTTAAAGGGTTAAGATTTAAGGTTTAGACTATAGGGTTTAGGTTTTGATGTTCATGATTT
322 TAGGATTTAAAGGGTTAAGATTTAAGGTTTAGAATATAAGGTTTAGGTTTTGATGTTCACGATTT
26999 AGTGTTTAGGATATGATGTGGGTTCGGGATTAGGGTTTGAAATTTTGTGTTTAAGGTTTAAAATT
387 AGTGTTTAGGATATGATGTGGGTTCGGGATTAGGGTTTGAAATTTTGTGTTTAAGGTTTAAAATT
27064 TGAGATTGCGATAAAAGAGATATTATTCTACTGTGAGTTAAAAGATATTTATTTATGTGTTATAA
452 TGAGATTGCGATAAAAGAGATATTATTCTACTGTGAGTTAAAAGATATTTATTTATGTGTTATAA
27129 ATTTTATTAAATTTTATTAATTTTATGCAATATAAATGAATCCTGACACACACACACACACACAC
517 ATTTTATTAAATTTTATTAATTTTATGCAATATAAATGAATCCTG-CACACACACACACACACAC
27194 ACACACACACATATATATATATATATATATATA
581 ACACACACACATATATATATATATATATATATA
*
27227 TATATATATATTATGTATAGGGTTATACGTTCAAAGAATAATAATTTGGTAATGAACGATCATAC
1 TATATATATATTATGTATAGGGTTATACGTTCAAAGAATAATAATTTGGTAATGAACGACCATAC
27292 CCCTGCTTATATAGTATTTGAACCCAAAACTTTAAGGATTAACAATAAATCTTATAACCACGATA
66 CCCTGCTTATATAGTATTTGAACCCAAAACTTTAAGGATTAACAATAAATCTTATAACCACGATA
27357 ATTAATAAATTATATATATATATGGATAAGATCCACTTGCACTATGTAAAACTAATAAATTTTAC
131 ATTAATAAATTATATATATATATGGATAAGATCCACTTGCACTATGTAAAACTAATAAATTTTAC
27422 ACCAATTTATAAACATTAGATTTAAATAAATAAATGGCTTATATTTAATTAAAATTTATAATTCA
196 ACCAATTTATAAACATTAGATTTAAATAAATAAATGGCTTATATTTAATTAAAATTTATAATTCA
* *
27487 TACATAAATATTTATTTATCTCACAATAAAACAATATTTTTTTCCTTTTAGAGTTAGGATTTAGG
261 TACATAAATATTTCTTTATCTCACAATAAAACAATATTTTTTTCCTTTTAGGGTTAGGATTTAGG
*
27552 ATTTAAAGGGTTAAGATTTAAGGTTTAGAATATAAGGTTTAGGTTTTGATGTTCACAATTTAGTG
326 ATTTAAAGGGTTAAGATTTAAGGTTTAGAATATAAGGTTTAGGTTTTGATGTTCACGATTTAGTG
27617 TTTAGGATATGATGTGGGTTCAGGGATTAGGGTTTGAAATTTTGTGTTTAAGGTTTAAAATTTGA
391 TTTAGGATATGATGTGGGTTC-GGGATTAGGGTTTGAAATTTTGTGTTTAAGGTTTAAAATTTGA
*
27682 GATTGCGATAAAAGAGAGATTATTCTACTGTGAGTTAAAAGATATTTATTTATGTGTTATAAATT
455 GATTGCGATAAAAGAGATATTATTCTACTGTGAGTTAAAAGATATTTATTTATGTGTTATAAATT
*
27747 TTATTAAATTTTATTAATTTTATGCAATATAAATGAATCATG-------------ACACACACAC
520 TTATTAAATTTTATTAATTTTATGCAATATAAATGAATCCTGCACACACACACACACACACACAC
27799 ACACAC------------------ATATA
585 ACACACATATATATATATATATATATATA
27810 TATATATATATTATGTATAGGGTTATACGTTCAAAGAATAATAATTTGGTAATGAACGACCATAC
1 TATATATATATTATGTATAGGGTTATACGTTCAAAGAATAATAATTTGGTAATGAACGACCATAC
*
27875 CCATGCTTATATAGTATTTGAACCCAAAACTTTAAGGATTAACAATAAATCTTATAACCACGATA
66 CCCTGCTTATATAGTATTTGAACCCAAAACTTTAAGGATTAACAATAAATCTTATAACCACGATA
*
27940 ATTAATAAATTATATATAGATATATATGGATAAGATCCACTTACACTATGTAAAACTAATAAATT
131 ATTAATAAA-T-TATAT--ATATATATGGATAAGATCCACTTGCACTATGTAAAACTAATAAATT
*
28005 TTACACCAATTTATAAACATTATATTTAAATAAATAAATGGCTTATATTTAATTAAAATTTATAA
192 TTACACCAATTTATAAACATTAGATTTAAATAAATAAATGGCTTATATTTAATTAAAATTTATAA
* * * *
28070 TTCGTAAATAAATATTTCTTTACCTCGCAATAAAACAATA-TTTTTTCCTTTTAGGGTTAGGATT
257 TTCATACATAAATATTTCTTTATCTCACAATAAAACAATATTTTTTTCCTTTTAGGGTTAGGATT
* * * * * *
28134 TAGGATTTAAATGGTTAATATTTAAGGTTTATG-ATAT-AGGATTTAAGTTTTAATGTTTACGGT
322 TAGGATTTAAAGGGTTAAGATTTAAGGTTTA-GAATATAAGG-TTTAGGTTTTGATGTTCACGAT
* * * * ** *
28197 TTAGTGTTTAGGATATGATGTGGGTTTGGGGATTGGGGTTTAAAATATTAAGTTTAGGGTTTAAA
385 TTAGTGTTTAGGATATGATGTGGG-TTCGGGATTAGGGTTTGAAATTTTGTGTTTAAGGTTTAAA
* *
28262 ATTTGAGATTGCAATAAAAGAGATATTATTCTATTGTGAGTTAAAAGATATTTATTTATGTG---
449 ATTTGAGATTGCGATAAAAGAGATATTATTCTACTGTGAGTTAAAAGATATTTATTTATGTGTTA
*
28324 ------TTA-TAAATTTTATTAATTTTATGCAGTATAAATGAATCCT-CACACACACACACACAC
514 TAAATTTTATTAAATTTTATTAATTTTATGCAATATAAATGAATCCTGCACACACACACACACAC
* * * * *
28381 ACATATATATATATATATATATATATATATATATA
579 ACACACACACACATATATATATATATATATATATA
*
28416 TATATATATATATATATATA
1 TATATATATAT-TATGTATA
28436 CTACCTTGAC
Statistics
Matches: 1120, Mismatches: 48, Indels: 92
0.89 0.04 0.07
Matches are distributed among these distances:
576 35 0.03
577 3 0.00
583 142 0.13
584 1 0.00
585 8 0.01
586 187 0.17
587 147 0.13
588 11 0.01
601 16 0.01
606 16 0.01
607 7 0.01
614 198 0.18
615 200 0.18
617 148 0.13
618 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (613 bp):
TATATATATATTATGTATAGGGTTATACGTTCAAAGAATAATAATTTGGTAATGAACGACCATAC
CCCTGCTTATATAGTATTTGAACCCAAAACTTTAAGGATTAACAATAAATCTTATAACCACGATA
ATTAATAAATTATATATATATATGGATAAGATCCACTTGCACTATGTAAAACTAATAAATTTTAC
ACCAATTTATAAACATTAGATTTAAATAAATAAATGGCTTATATTTAATTAAAATTTATAATTCA
TACATAAATATTTCTTTATCTCACAATAAAACAATATTTTTTTCCTTTTAGGGTTAGGATTTAGG
ATTTAAAGGGTTAAGATTTAAGGTTTAGAATATAAGGTTTAGGTTTTGATGTTCACGATTTAGTG
TTTAGGATATGATGTGGGTTCGGGATTAGGGTTTGAAATTTTGTGTTTAAGGTTTAAAATTTGAG
ATTGCGATAAAAGAGATATTATTCTACTGTGAGTTAAAAGATATTTATTTATGTGTTATAAATTT
TATTAAATTTTATTAATTTTATGCAATATAAATGAATCCTGCACACACACACACACACACACACA
CACACATATATATATATATATATATATA
Found at i:28209 original size:35 final size:36
Alignment explanation
Indices: 28130--28210 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 36
28120 TTAGGGTTAG
28130 GATTTAGGATTTAAATGGTTAATATTTAAGGTTTAT
1 GATTTAGGATTTAAATGGTTAATATTTAAGGTTTAT
* * * * *
28166 GATATAGGATTTAAGT-TTTAATGTTTACGGTTTAGT
1 GATTTAGGATTTAAATGGTTAATATTTAAGGTTTA-T
28202 G-TTTAGGAT
1 GATTTAGGAT
28211 ATGATGTGGG
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
35 22 0.58
36 16 0.42
ACGTcount: A:0.30, C:0.01, G:0.22, T:0.47
Consensus pattern (36 bp):
GATTTAGGATTTAAATGGTTAATATTTAAGGTTTAT
Found at i:28381 original size:586 final size:583
Alignment explanation
Indices: 27222--28415 Score: 1855
Period size: 586 Copynumber: 2.0 Consensus size: 583
27212 ATATATATAT
*
27222 ATATATATATATATATTATGTATAGGGTTATACGTTCAAAGAATAATAATTTGGTAATGAACGAT
1 ATATATATATATATATTATGTATAGGGTTATACGTTCAAAGAATAATAATTTGGTAATGAACGAC
27287 CATACCCCTGCTTATATAGTATTTGAACCCAAAACTTTAAGGATTAACAATAAATCTTATAACCA
66 CATACCCCTGCTTATATAGTATTTGAACCCAAAACTTTAAGGATTAACAATAAATCTTATAACCA
27352 CGATAATTAATAAA-T-TATATATATATATGGATAAGATCCACTTGCACTATGTAAAACTAATAA
131 CGATAATTAATAAATTATATATATATATATGGATAAGATCCACTTGCACTATGTAAAACTAATAA
27415 ATTTTACACCAATTTATAAACATTAGATTTAAATAAATAAATGGCTTATATTTAATTAAAATTTA
196 ATTTTACACCAATTTATAAACATTAGATTTAAATAAATAAATGGCTTATATTTAATTAAAATTTA
* *
27480 TAATTCATACATAAATATTTATTTATCTCACAATAAAACAATATTTTTTTCCTTTTAGAGTTAGG
261 TAATTCATACATAAATATTTCTTTATCTCACAATAAAACAATATTTTTTTCCTTTTAGGGTTAGG
*
27545 ATTTAGGATTTAAAGGGTTAAGATTTAAGGTTTAGAATATAAGGTTTAGGTTTTGATGTTCACAA
326 ATTTAGGATTTAAAGGGTTAAGATTTAAGGTTTAG-ATAT-AGGTTTAGGTTTTGATGTTCACGA
*
27610 TTTAGTGTTTAGGATATGATGTGGGTTCAGGGATTAGGGTTTGAAATTTTGTGTTTAAGGTTTAA
389 TTTAGTGTTTAGGATATGATGTGGGTTTAGGGATTAGGGTTTGAAATTTTGTGTTTAAGGTTTAA
*
27675 AATTTGAGATTGCGATAAAAGAGAGATTATTCTACTGTGAGTTAAAAGATATTTATTTATGTGTT
454 AATTTGAGATTGCGATAAAAGAGATATTATTCTACTGTGAGTTAAAAGATATTTATTTATGTGTT
* ** * * * *
27740 ATAAATTTTATTAAATTTTAT-TAAT-TTTATGCAAT-AT-AAATGA-ATCATGACACACACACA
519 ATAAATTTTATT-AATTTTATGCAATATAAATG-AATCCTCACA-CACA-CA-CACACACACACA
27800 CACAC
579 CACAC
27805 ATATATATATATATATTATGTATAGGGTTATACGTTCAAAGAATAATAATTTGGTAATGAACGAC
1 ATATATATATATATATTATGTATAGGGTTATACGTTCAAAGAATAATAATTTGGTAATGAACGAC
*
27870 CATACCCATGCTTATATAGTATTTGAACCCAAAACTTTAAGGATTAACAATAAATCTTATAACCA
66 CATACCCCTGCTTATATAGTATTTGAACCCAAAACTTTAAGGATTAACAATAAATCTTATAACCA
*
27935 CGATAATTAATAAATTATATATAGATATATATGGATAAGATCCACTTACACTATGTAAAACTAAT
131 CGATAATTAATAAATTATATAT--ATATATATGGATAAGATCCACTTGCACTATGTAAAACTAAT
*
28000 AAATTTTACACCAATTTATAAACATTATATTTAAATAAATAAATGGCTTATATTTAATTAAAATT
194 AAATTTTACACCAATTTATAAACATTAGATTTAAATAAATAAATGGCTTATATTTAATTAAAATT
* * * *
28065 TATAATTCGTAAATAAATATTTCTTTACCTCGCAATAAAACAATA-TTTTTTCCTTTTAGGGTTA
259 TATAATTCATACATAAATATTTCTTTATCTCACAATAAAACAATATTTTTTTCCTTTTAGGGTTA
* * * * *
28129 GGATTTAGGATTTAAATGGTTAATATTTAAGGTTTATGATATAGGATTTAAGTTTTAATGTTTAC
324 GGATTTAGGATTTAAAGGGTTAAGATTTAAGGTTTA-GATATAGG-TTTAGGTTTTGATGTTCAC
* * * * * ** *
28194 GGTTTAGTGTTTAGGATATGATGTGGGTTTGGGGATTGGGGTTTAAAATATTAAGTTTAGGGTTT
387 GATTTAGTGTTTAGGATATGATGTGGGTTTAGGGATTAGGGTTTGAAATTTTGTGTTTAAGGTTT
* *
28259 AAAATTTGAGATTGCAATAAAAGAGATATTATTCTATTGTGAGTTAAAAGATATTTATTTATGTG
452 AAAATTTGAGATTGCGATAAAAGAGATATTATTCTACTGTGAGTTAAAAGATATTTATTTATGTG
* * * *
28324 TTATAAATTTTATTAATTTTATGCAGTATAAATGAATCCTCACACACACACACACACACATATAT
517 TTATAAATTTTATTAATTTTATGCAATATAAATGAATCCTCACACACACACACACACACACACAC
*
28389 AT
582 AC
*
28391 ATATATATATATATATATATATATA
1 ATATATATATATATAT-TATGTATA
28416 TATATATATA
Statistics
Matches: 558, Mismatches: 41, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
583 142 0.25
584 1 0.00
585 16 0.03
586 236 0.42
587 160 0.29
588 3 0.01
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (583 bp):
ATATATATATATATATTATGTATAGGGTTATACGTTCAAAGAATAATAATTTGGTAATGAACGAC
CATACCCCTGCTTATATAGTATTTGAACCCAAAACTTTAAGGATTAACAATAAATCTTATAACCA
CGATAATTAATAAATTATATATATATATATGGATAAGATCCACTTGCACTATGTAAAACTAATAA
ATTTTACACCAATTTATAAACATTAGATTTAAATAAATAAATGGCTTATATTTAATTAAAATTTA
TAATTCATACATAAATATTTCTTTATCTCACAATAAAACAATATTTTTTTCCTTTTAGGGTTAGG
ATTTAGGATTTAAAGGGTTAAGATTTAAGGTTTAGATATAGGTTTAGGTTTTGATGTTCACGATT
TAGTGTTTAGGATATGATGTGGGTTTAGGGATTAGGGTTTGAAATTTTGTGTTTAAGGTTTAAAA
TTTGAGATTGCGATAAAAGAGATATTATTCTACTGTGAGTTAAAAGATATTTATTTATGTGTTAT
AAATTTTATTAATTTTATGCAATATAAATGAATCCTCACACACACACACACACACACACACAC
Found at i:28388 original size:2 final size:2
Alignment explanation
Indices: 28383--28435 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
28373 ACACACACAC
28383 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
28425 AT AT AT AT AT A
1 AT AT AT AT AT A
28436 CTACCTTGAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29740 original size:38 final size:39
Alignment explanation
Indices: 29697--29782 Score: 113
Period size: 41 Copynumber: 2.2 Consensus size: 39
29687 AACTTAACGT
*
29697 TAAATTTTGAACGGA-G-TACTAAAATGAAACAAAAAAC
1 TAAATTTTGAACGGAGGATACTAAAATCAAACAAAAAAC
* *
29734 TAAAATTTTTAACGGATGGATTCTAAAATCAAACAAAAAAC
1 T-AAATTTTGAACGGA-GGATACTAAAATCAAACAAAAAAC
29775 TAAATTTT
1 TAAATTTT
29783 ACGTATGATT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
37 1 0.02
38 13 0.31
40 8 0.19
41 20 0.48
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.28
Consensus pattern (39 bp):
TAAATTTTGAACGGAGGATACTAAAATCAAACAAAAAAC
Found at i:31828 original size:15 final size:15
Alignment explanation
Indices: 31808--31859 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
31798 TTTACTTCAT
31808 AATGATTAAGCGCTG
1 AATGATTAAGCGCTG
*
31823 AATGATTCAGAGGCTCTG
1 AATGATT-A-A-GCGCTG
* *
31841 TATGATTAAGCGTTG
1 AATGATTAAGCGCTG
31856 AATG
1 AATG
31860 TGACATGCTG
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 14 0.48
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.31
Consensus pattern (15 bp):
AATGATTAAGCGCTG
Found at i:34501 original size:83 final size:83
Alignment explanation
Indices: 34397--34574 Score: 338
Period size: 83 Copynumber: 2.1 Consensus size: 83
34387 ACTTTGTATA
* *
34397 GTAGTATCGATACCATTGACATAGTATTTATACCACCAGGCCCCAACAGCTAGTAACGACTAGTT
1 GTAGTATCGATACCATAGACATAGTATTGATACCACCAGGCCCCAACAGCTAGTAACGACTAGTT
34462 GATTTAAAAATAACAAAG
66 GATTTAAAAATAACAAAG
34480 GTAGTATCGATACCATAGACATAGTATTGATACCACCAGGCCCCAACAGCTAGTAACGACTAGTT
1 GTAGTATCGATACCATAGACATAGTATTGATACCACCAGGCCCCAACAGCTAGTAACGACTAGTT
34545 GATTTAAAAATAACAAAG
66 GATTTAAAAATAACAAAG
34563 GTAGTATCGATA
1 GTAGTATCGATA
34575 TTCCCTTTAG
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 93 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.25
Consensus pattern (83 bp):
GTAGTATCGATACCATAGACATAGTATTGATACCACCAGGCCCCAACAGCTAGTAACGACTAGTT
GATTTAAAAATAACAAAG
Found at i:36476 original size:22 final size:20
Alignment explanation
Indices: 36442--36482 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
36432 AATATTTTGA
*
36442 TATATTATCAATATATTTAT
1 TATATTATCAATAAATTTAT
36462 TATATTATTCAAATAAATTTA
1 TATATTA-TC-AATAAATTTA
36483 AATTTTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 9 0.50
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TATATTATCAATAAATTTAT
Found at i:36501 original size:18 final size:17
Alignment explanation
Indices: 36475--36518 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
36465 ATTATTCAAA
*
36475 TAAATTTAAATTTTGTTT
1 TAAATTTAAATATT-TTT
*
36493 TACATTTAAATATTTTT
1 TAAATTTAAATATTTTT
36510 TAAATTTAA
1 TAAATTTAA
36519 CTAATATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
TAAATTTAAATATTTTT
Found at i:47565 original size:3 final size:3
Alignment explanation
Indices: 47550--47589 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
47540 CTAATTCAAT
*
47550 TTA TTA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
47590 GAATAATCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:47996 original size:2 final size:2
Alignment explanation
Indices: 47989--48020 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
47979 ATAATTTTAA
47989 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
48021 TCAAATAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54359 original size:18 final size:20
Alignment explanation
Indices: 54336--54378 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
54326 ACGAAATAAA
54336 CATCGAATGCA-A-GGAGTG
1 CATCGAATGCATAGGGAGTG
54354 CATCG-ATGCATAGGGAGTG
1 CATCGAATGCATAGGGAGTG
54373 CATCGA
1 CATCGA
54379 TACACCCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.23
18 6 0.27
19 11 0.50
ACGTcount: A:0.30, C:0.19, G:0.33, T:0.19
Consensus pattern (20 bp):
CATCGAATGCATAGGGAGTG
Found at i:58522 original size:45 final size:45
Alignment explanation
Indices: 58473--58930 Score: 462
Period size: 45 Copynumber: 10.4 Consensus size: 45
58463 GTCACAGTTG
* * * * **
58473 TCTCTTTTTTCATCTTCTCAGCTGAGTCATTCACTTCCACAGCTC
1 TCTCTTTCTTCACCTTCTCAGCTGAGCCATTCACTTTCACAGCAA
58518 TCTCTTTCTTCACCTTCTCAGCTGAGCCATTCACTTTCACAGCAA
1 TCTCTTTCTTCACCTTCTCAGCTGAGCCATTCACTTTCACAGCAA
* * *
58563 TCTCCTTCTTCACCTTCTCTGCTGAG-C--T-A-TTT-ACAGTCGA
1 TCTCTTTCTTCACCTTCTCAGCTGAGCCATTCACTTTCACAG-CAA
* * * * **
58603 TGTCGTCTCTTTCATCTTCTCAGCTGAGCCATTCACTTTCACAACTG
1 TCTC-TTTC-TTCACCTTCTCAGCTGAGCCATTCACTTTCACAGCAA
*
58650 TCTCTTTCTTCACCTTCTCAGCTGTGCCATTCACTTTCACAGCAA
1 TCTCTTTCTTCACCTTCTCAGCTGAGCCATTCACTTTCACAGCAA
58695 TCTCTTTCTTCACCTTCTCAGCTGAGCCATTCACTTTCACAGCAA
1 TCTCTTTCTTCACCTTCTCAGCTGAGCCATTCACTTTCACAGCAA
* * * * **
58740 TCTC-TT-TTCACCTTCTCTGCTGAGCTATTTACTGTCA-ATGCCG
1 TCTCTTTCTTCACCTTCTCAGCTGAGCCATTCACTTTCACA-GCAA
* *
58783 TCTC--T-TTCATCTTCTCAGCTGAGCCATTCACTTTCACGGCAA
1 TCTCTTTCTTCACCTTCTCAGCTGAGCCATTCACTTTCACAGCAA
* ** * * **
58825 TCTCTTTCTTCACCTTCTCTGCTGAGTTATTTACTGTCA-ATGCCG
1 TCTCTTTCTTCACCTTCTCAGCTGAGCCATTCACTTTCACA-GCAA
* *
58870 TCTC---CTTCATCTTCTCAGCTGAGCCATTCACTTTCACGGCAA
1 TCTCTTTCTTCACCTTCTCAGCTGAGCCATTCACTTTCACAGCAA
58912 TCTCTTTCTTCACCTTCTC
1 TCTCTTTCTTCACCTTCTC
58931 TGCTAAGCTA
Statistics
Matches: 336, Mismatches: 58, Indels: 38
0.78 0.13 0.09
Matches are distributed among these distances:
39 4 0.01
40 8 0.02
41 3 0.01
42 83 0.25
43 34 0.10
44 4 0.01
45 186 0.55
46 4 0.01
47 7 0.02
48 3 0.01
ACGTcount: A:0.17, C:0.34, G:0.11, T:0.39
Consensus pattern (45 bp):
TCTCTTTCTTCACCTTCTCAGCTGAGCCATTCACTTTCACAGCAA
Found at i:58643 original size:87 final size:87
Alignment explanation
Indices: 58526--58977 Score: 635
Period size: 87 Copynumber: 5.2 Consensus size: 87
58516 TCTCTCTTTC
* *
58526 TTCACCTTCTCAGCTGAGCCATTCACTTTCACAGCAATCTCCTTCTTCACCTTCTCTGCTGAGCT
1 TTCATCTTCTCAGCTGAGCCATTCACTTTCACAGCAATCTCTTTCTTCACCTTCTCTGCTGAGCT
* * *
58591 ATTTACAGTCGATGTCGTCTCT
66 ATTTACTGTCAATGCCGTCTCT
* ** * * *
58613 TTCATCTTCTCAGCTGAGCCATTCACTTTCACAACTGTCTCTTTCTTCACCTTCTCAGCTGTGCC
1 TTCATCTTCTCAGCTGAGCCATTCACTTTCACAGCAATCTCTTTCTTCACCTTCTCTGCTGAGCT
* * **
58678 ATTCACTTTCACA-GCAATCTCTTT
66 ATTTACTGTCA-ATGCCGTCTC--T
*
58702 CTTCACCTTCTCAGCTGAGCCATTCACTTTCACAGCAATCTC-TT-TTCACCTTCTCTGCTGAGC
1 -TTCATCTTCTCAGCTGAGCCATTCACTTTCACAGCAATCTCTTTCTTCACCTTCTCTGCTGAGC
58765 TATTTACTGTCAATGCCGTCTCT
65 TATTTACTGTCAATGCCGTCTCT
* *
58788 TTCATCTTCTCAGCTGAGCCATTCACTTTCACGGCAATCTCTTTCTTCACCTTCTCTGCTGAGTT
1 TTCATCTTCTCAGCTGAGCCATTCACTTTCACAGCAATCTCTTTCTTCACCTTCTCTGCTGAGCT
*
58853 ATTTACTGTCAATGCCGTCTCC
66 ATTTACTGTCAATGCCGTCTCT
* *
58875 TTCATCTTCTCAGCTGAGCCATTCACTTTCACGGCAATCTCTTTCTTCACCTTCTCTGCTAAGCT
1 TTCATCTTCTCAGCTGAGCCATTCACTTTCACAGCAATCTCTTTCTTCACCTTCTCTGCTGAGCT
*
58940 ATTTACTGTCAATGAC--CTCT
66 ATTTACTGTCAATGCCGTCTCT
58960 TTCATCTTCTCAGCTGAG
1 TTCATCTTCTCAGCTGAG
58978 TTATTTATTG
Statistics
Matches: 324, Mismatches: 34, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
85 60 0.19
86 3 0.01
87 188 0.58
88 33 0.10
89 3 0.01
90 37 0.11
ACGTcount: A:0.17, C:0.33, G:0.12, T:0.38
Consensus pattern (87 bp):
TTCATCTTCTCAGCTGAGCCATTCACTTTCACAGCAATCTCTTTCTTCACCTTCTCTGCTGAGCT
ATTTACTGTCAATGCCGTCTCT
Found at i:58674 original size:24 final size:24
Alignment explanation
Indices: 58647--58718 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 24
58637 ACTTTCACAA
58647 CTGTCTCTTTCTTCACCTTCTCAG
1 CTGTCTCTTTCTTCACCTTCTCAG
* * *
58671 CTGTGC-C---ATTCACTTTCACAG
1 CTGT-CTCTTTCTTCACCTTCTCAG
**
58692 CAATCTCTTTCTTCACCTTCTCAG
1 CTGTCTCTTTCTTCACCTTCTCAG
58716 CTG
1 CTG
58719 AGCCATTCAC
Statistics
Matches: 33, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
20 1 0.03
21 14 0.42
24 17 0.52
25 1 0.03
ACGTcount: A:0.14, C:0.36, G:0.10, T:0.40
Consensus pattern (24 bp):
CTGTCTCTTTCTTCACCTTCTCAG
Found at i:58692 original size:21 final size:21
Alignment explanation
Indices: 58623--58692 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
58613 TTCATCTTCT
*
58623 CAGCTGAGCCATTCACTTTCA
1 CAGCTGTGCCATTCACTTTCA
* * * *
58644 CAACTGT-CTCTTTCTTCACCTTCT
1 CAGCTGTGC-C---ATTCACTTTCA
58668 CAGCTGTGCCATTCACTTTCA
1 CAGCTGTGCCATTCACTTTCA
58689 CAGC
1 CAGC
58693 AATCTCTTTC
Statistics
Matches: 35, Mismatches: 9, Indels: 10
0.65 0.17 0.19
Matches are distributed among these distances:
20 1 0.03
21 18 0.51
24 15 0.43
25 1 0.03
ACGTcount: A:0.19, C:0.36, G:0.11, T:0.34
Consensus pattern (21 bp):
CAGCTGTGCCATTCACTTTCA
Found at i:59090 original size:45 final size:45
Alignment explanation
Indices: 59015--59294 Score: 272
Period size: 45 Copynumber: 6.2 Consensus size: 45
59005 ATCTCTCTGT
* * * * **
59015 TGAGCTGTTTACTGTCATGGCCATCTCTTTCTTCATCTTCTCAGG
1 TGAGCTATTTACTGTCAAGGCCGTCTCTTTCTTCACCTTCTCAAC
*** * * * *
59060 TGCTTTATTTATTGTCAAGGCTGCCACTTTCTTCACCTTCTCAAC
1 TGAGCTATTTACTGTCAAGGCCGTCTCTTTCTTCACCTTCTCAAC
59105 TGAGCTATTTACTGTCAAGGCCGTCTCTTTCTTCACCTTCTCAAC
1 TGAGCTATTTACTGTCAAGGCCGTCTCTTTCTTCACCTTCTCAAC
* *
59150 TGAGCTATTTACTGTCAAGGCCGTCTCTTTCTTCATCTTCTCAGC
1 TGAGCTATTTACTGTCAAGGCCGTCTCTTTCTTCACCTTCTCAAC
* ** * ** * *
59195 TGAGCTATTTACTGGCGTGGCCGTCTCTTTTTTCATATTTTCAGC
1 TGAGCTATTTACTGTCAAGGCCGTCTCTTTCTTCACCTTCTCAAC
* ** * * * * * *
59240 CGAATTATTTATTTTCAAGGCCATCTCTTTGTTCATCTTCTCAGC
1 TGAGCTATTTACTGTCAAGGCCGTCTCTTTCTTCACCTTCTCAAC
59285 TGAGCTATTT
1 TGAGCTATTT
59295 CTTGAAGTTG
Statistics
Matches: 192, Mismatches: 43, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 192 1.00
ACGTcount: A:0.16, C:0.26, G:0.15, T:0.42
Consensus pattern (45 bp):
TGAGCTATTTACTGTCAAGGCCGTCTCTTTCTTCACCTTCTCAAC
Found at i:59132 original size:90 final size:90
Alignment explanation
Indices: 58472--59294 Score: 431
Period size: 90 Copynumber: 9.4 Consensus size: 90
58462 TGTCACAGTT
* * ** *
58472 GTCTCTTTTTTCATCTTCTCAGCTGAG-TCATTCACT-TCCACAGCTC-TCTCTTTCTTCACCTT
1 GTCTCTTTCTTCATCTTCTCAGCTGAGCT-ATTTACTGT-CATGGC-CGTCTCTTTCTTCATCTT
*** * *
58534 CTCAGCTGAGCCATTCACTT-TCACA-GCA
63 CTCAGCTGAATTATTTA-TTGTCA-AGGCC
* * * * * *
58562 ATCTCCTTCTTCACCTTCTCTGCTGAGCTATTTACAGTCGAT-GTCGTCTC--T-TTCATCTTCT
1 GTCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTC-ATGGCCGTCTCTTTCTTCATCTTCT
*** * * *
58623 CAGCTGAGCCATTCACTT-TCACA-ACT
65 CAGCTGAATTATTTA-TTGTCA-AGGCC
* * * * * ** ** *
58649 GTCTCTTTCTTCACCTTCTCAGCTGTGCCATTCACTTTCACAGCAATCTCTTTCTTCACCTTCTC
1 GTCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTCATGGCCGTCTCTTTCTTCATCTTCTC
*** * *
58714 AGCTGAGCCATTCACTT-TCACA-GCA
66 AGCTGAATTATTTA-TTGTCA-AGGCC
* * *
58739 ATCTC-TT-TTCACCTTCTCTGCTGAGCTATTTACTGTCAAT-GCCGTCTC--T-TTCATCTTCT
1 GTCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTC-ATGGCCGTCTCTTTCTTCATCTTCT
*** * * *
58798 CAGCTGAGCCATTCACTT-TCACGGCA
65 CAGCTGAATTATTTA-TTGTCAAGGCC
* * * *
58824 ATCTCTTTCTTCACCTTCTCTGCTGAGTTATTTACTGTCAAT-GCCGTCTC---CTTCATCTTCT
1 GTCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTC-ATGGCCGTCTCTTTCTTCATCTTCT
*** * * *
58885 CAGCTGAGCCATTCACTT-TCACGGCA
65 CAGCTGAATTATTTA-TTGTCAAGGCC
* * * * *
58911 ATCTCTTTCTTCACCTTCTCTGCTAAGCTATTTACTGTCAAT-GAC--CTC--T-TTCATCTTCT
1 GTCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTC-ATGGCCGTCTCTTTCTTCATCTTCT
* * *
58970 CAGCTGAGTTATTTATTGT--A-TCT
65 CAGCTGAATTATTTATTGTCAAGGCC
* * * *
58993 GTCTCTTGTC-TCATC-TCTCTGTTGAGCTGTTTACTGTCATGGCCATCTCTTTCTTCATCTTCT
1 GTCTCTT-TCTTCATCTTCTCAGCTGAGCTATTTACTGTCATGGCCGTCTCTTTCTTCATCTTCT
* ** *
59056 CAGGTGCTTTATTTATTGTCAAGGCT
65 CAGCTGAATTATTTATTGTCAAGGCC
* * * * * *
59082 GCCACTTTCTTCACCTTCTCAACTGAGCTATTTACTGTCAAGGCCGTCTCTTTCTTCACCTTCTC
1 GTCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTCATGGCCGTCTCTTTCTTCATCTTCTC
* ** *
59147 AACTGAGCTATTTACTGTCAAGGCC
66 AGCTGAATTATTTATTGTCAAGGCC
* * * * *
59172 GTCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGGCGTGGCCGTCTCTTTTTTCATATTTTC
1 GTCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTCATGGCCGTCTCTTTCTTCATCTTCTC
* *
59237 AGCCGAATTATTTATTTTCAAGGCC
66 AGCTGAATTATTTATTGTCAAGGCC
* *
59262 ATCTCTTTGTTCATCTTCTCAGCTGAGCTATTT
1 GTCTCTTTCTTCATCTTCTCAGCTGAGCTATTT
59295 CTTGAAGTTG
Statistics
Matches: 612, Mismatches: 94, Indels: 54
0.81 0.12 0.07
Matches are distributed among these distances:
80 2 0.00
81 22 0.04
82 11 0.02
83 5 0.01
84 2 0.00
85 65 0.11
86 30 0.05
87 187 0.31
88 35 0.06
89 16 0.03
90 234 0.38
91 3 0.00
ACGTcount: A:0.17, C:0.30, G:0.13, T:0.41
Consensus pattern (90 bp):
GTCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGTCATGGCCGTCTCTTTCTTCATCTTCTC
AGCTGAATTATTTATTGTCAAGGCC
Found at i:59409 original size:44 final size:44
Alignment explanation
Indices: 59372--59461 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
59362 TCTCAGATGG
*
59372 ACTATTCACCGTCAAGGCCATCTCTTGTCTGTCTTCTCAGCCAA
1 ACTATTCACCGTCAAGGCCATCTCTTGTCTGTCTTCTCAGACAA
* *
59416 ACTATTCACCGTCAAGGCCATCTCTTGTTTGTCTTCTCAGCCAA
1 ACTATTCACCGTCAAGGCCATCTCTTGTCTGTCTTCTCAGACAA
59460 AC
1 AC
59462 CATTGAGGCT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.32
Consensus pattern (44 bp):
ACTATTCACCGTCAAGGCCATCTCTTGTCTGTCTTCTCAGACAA
Found at i:59610 original size:108 final size:107
Alignment explanation
Indices: 59422--59637 Score: 389
Period size: 108 Copynumber: 2.0 Consensus size: 107
59412 CCAAACTATT
59422 CACCGTCAAGGCCATCTCTTGTTTGTCTTCTCAGCCAAACCATTGAGGCTCTGTTCCACAATATG
1 CACCGTCAAGGCCATCTCTTGTTTGTCTTCTCAGCCAAACCATTGAGGCTCTGTTCCACAATATG
59487 CATGTTAGTAGTGCTTGAGACCTTCTCTGAACTTGGCTTTGG
66 CATGTTAGTAGTGCTTGAGACCTTCTCTGAACTTGGCTTTGG
* *
59529 CACCGTCAAGGCCATCTCTTTGTTTGTCTTCTCAGCCAAACTATTGAGGCTGTGTTCCACAATAT
1 CACCGTCAAGGCCATCTC-TTGTTTGTCTTCTCAGCCAAACCATTGAGGCTCTGTTCCACAATAT
59594 -CTATGTTAGTAGTGCTTGAGACCTTCTCTGAACTTGGCTTTGG
65 GC-ATGTTAGTAGTGCTTGAGACCTTCTCTGAACTTGGCTTTGG
59637 C
1 C
59638 TTTTCAAATT
Statistics
Matches: 105, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
107 19 0.18
108 86 0.82
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.35
Consensus pattern (107 bp):
CACCGTCAAGGCCATCTCTTGTTTGTCTTCTCAGCCAAACCATTGAGGCTCTGTTCCACAATATG
CATGTTAGTAGTGCTTGAGACCTTCTCTGAACTTGGCTTTGG
Found at i:65364 original size:30 final size:30
Alignment explanation
Indices: 65319--65375 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
65309 AAACGTAACA
65319 CGTTTAATACCTAAACTATCAATTTTTATC
1 CGTTTAATACCTAAACTATCAATTTTTATC
* * * *
65349 CGTTTAGTACTTAAACTTTTAATTTTT
1 CGTTTAATACCTAAACTATCAATTTTT
65376 TCCCAAAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.49
Consensus pattern (30 bp):
CGTTTAATACCTAAACTATCAATTTTTATC
Found at i:68057 original size:54 final size:54
Alignment explanation
Indices: 67990--68134 Score: 155
Period size: 56 Copynumber: 2.6 Consensus size: 54
67980 CTCTATTTTT
* * * *
67990 TAGATATATTCGATTTCGAGCCCCATTTTTTTGTTTCTTAATGACAACAACTGA
1 TAGATATACTCGATTTCGAGCCCTATTTTTTTGCTTATTAATGACAACAACTGA
* * * * * *
68044 TATATATACTCGATTTCGGGGGCCCTATTTTTATACTTATTAATGACAACAATTTA
1 TAGATATACTCGATTTC--GAGCCCTATTTTTTTGCTTATTAATGACAACAACTGA
*
68100 TAGATATACTCGATTTCAAGACTCCTATTTTTTTG
1 TAGATATACTCGATTTCGAG-C-CCTATTTTTTTG
68135 GGCCCTACAC
Statistics
Matches: 72, Mismatches: 15, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
54 16 0.22
55 1 0.01
56 55 0.76
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (54 bp):
TAGATATACTCGATTTCGAGCCCTATTTTTTTGCTTATTAATGACAACAACTGA
Found at i:71768 original size:19 final size:20
Alignment explanation
Indices: 71727--71785 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
71717 CTTTGTATAG
71727 TAGTATCGATACCATAGGCA
1 TAGTATCGATACCATAGGCA
71747 TAGTATCGATACCATA-GCA
1 TAGTATCGATACCATAGGCA
71766 TAGTATCGATACCATTAGGC
1 TAGTATCGATACCA-TAGGC
71786 CCCAACGGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
19 17 0.46
20 18 0.49
21 2 0.05
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (20 bp):
TAGTATCGATACCATAGGCA
Done.