Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008311.1 Hibiscus syriacus cultivar Beakdansim tig00111002_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: 1790494
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1712596 original size:8 final size:8
Alignment explanation
Indices: 1712585--1712649 Score: 55
Period size: 8 Copynumber: 7.9 Consensus size: 8
1712575 TATTTAAATA
1712585 TATATTAT
1 TATATTAT
1712593 TATATGTA-
1 TATAT-TAT
*
1712601 TATGTATAT
1 TATAT-TAT
1712610 GTATATGTA-
1 -TATAT-TAT
1712619 TAT-TTAT
1 TATATTAT
1712626 TATATTAT
1 TATATTAT
1712634 TATATTAT
1 TATATTAT
1712642 TAATATTA
1 T-ATATTA
1712650 ATATCAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
6 2 0.04
7 4 0.09
8 27 0.57
9 8 0.17
10 6 0.13
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (8 bp):
TATATTAT
Found at i:1712604 original size:6 final size:6
Alignment explanation
Indices: 1712593--1712621 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1712583 TATATATTAT
1712593 TATATG TATATG TATATG TATATG TATAT
1 TATATG TATATG TATATG TATATG TATAT
1712622 TTATTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (6 bp):
TATATG
Found at i:1717506 original size:54 final size:54
Alignment explanation
Indices: 1717425--1717692 Score: 349
Period size: 54 Copynumber: 5.0 Consensus size: 54
1717415 ATAACCTACA
* * * *
1717425 GTCGTTCATAAACATACTATAAATTTTGTGGTTTGCACACTTAGTGTCGATA-G
1 GTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATACG
* * * * * *
1717478 AGTCGTTTATAAACATATTATGAATTTTGTGGGTTGCAAACATAGTGTTGCTACG
1 -GTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATACG
* *
1717533 CTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACGCTTAGTGTCGATACG
1 GTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATACG
* **
1717587 GTCGTTCATAAAAATATTATGAATTCCATGGGTTGCACACTTAGTGTCGATACG
1 GTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATACG
* * * *
1717641 GTCATTCATAGATATATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATA
1 GTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATA
1717693 GTACACATTG
Statistics
Matches: 186, Mismatches: 27, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
54 185 0.99
55 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (54 bp):
GTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATACG
Found at i:1721087 original size:54 final size:53
Alignment explanation
Indices: 1721004--1721273 Score: 333
Period size: 54 Copynumber: 5.0 Consensus size: 53
1720994 CATAACCTAC
* * * * *
1721004 GGTCGTTCATAAACATACTATAAATTTTGTGGCTTGCACACTTAGTGTCAATA
1 GGTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATA
* * * *
1721057 GAGTCGTTCATAAACATATTATGAATTTTGTGGGTTGCAAACTTAGTGTTGCTA
1 G-GTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATA
* *
1721111 CGCTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACGCTTAGTGTCGATA
1 -GGTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATA
* * ** *
1721165 CAGTCGTTCATAAAAATATTATGAATTCCATGGGTTGCACACTTAGTGTTGATA
1 -GGTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATA
* * *
1721219 CGGTCATTCATAGATATATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATA
1 -GGTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATA
1721273 G
1 G
1721274 TACACATAGT
Statistics
Matches: 188, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
53 2 0.01
54 185 0.98
55 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (53 bp):
GGTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATA
Found at i:1721189 original size:108 final size:108
Alignment explanation
Indices: 1721000--1721272 Score: 393
Period size: 108 Copynumber: 2.5 Consensus size: 108
1720990 CTCACATAAC
* * * * * *
1721000 CTACGGTCGTTCATAAACATACTATAAATTTTGTGGCTTGCACACTTAGTGTCAATAGAGTCGTT
1 CTACGGTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATACAGTCGTT
* ***
1721065 CATAAACATATTATGAATTTTGTGGGTTGCAAACTTAGTGTTG
66 CATAAAAATATTATGAATTCCATGGGTTGCAAACTTAGTGTTG
* *
1721108 CTACGCTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACGCTTAGTGTCGATACAGTCGTT
1 CTACGGTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATACAGTCGTT
*
1721173 CATAAAAATATTATGAATTCCATGGGTTGCACACTTAGTGTTG
66 CATAAAAATATTATGAATTCCATGGGTTGCAAACTTAGTGTTG
* * * *
1721216 ATACGGTCATTCATAGATATATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATA
1 CTACGGTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATA
1721273 GTACACATAG
Statistics
Matches: 146, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
108 146 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (108 bp):
CTACGGTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTCGATACAGTCGTT
CATAAAAATATTATGAATTCCATGGGTTGCAAACTTAGTGTTG
Found at i:1724606 original size:54 final size:55
Alignment explanation
Indices: 1724543--1724814 Score: 320
Period size: 54 Copynumber: 5.0 Consensus size: 55
1724533 TCACATAACC
* * * * * *
1724543 TACG-GTCGTTTATAAACATACTATAAATTTTATGGTTTGCACACTTAGTGTCAA
1 TACGAGTCGTTCATAAACATATTATGAATTCTATGGGTTGCACACTTAGTGTCGA
* * * *
1724597 TA-GAGTCGTTCATAAACATATTATGAATTTTGTGGGTTGCACACTTAGTGTTGC
1 TACGAGTCGTTCATAAACATATTATGAATTCTATGGGTTGCACACTTAGTGTCGA
* * *
1724651 TACG-CTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACGCTTAGTGTCGA
1 TACGAGTCGTTCATAAACATATTATGAATTCTATGGGTTGCACACTTAGTGTCGA
* *
1724705 TACGA-TCGTTCATAAAAATATTATGAATTCCATGGGTTGCACACTTAGTGTCGA
1 TACGAGTCGTTCATAAACATATTATGAATTCTATGGGTTGCACACTTAGTGTCGA
* * * ** *
1724759 TACGA-TCATTCATATATATATTATGAATTCCGTGGGTTGCACACTTAGTGCCGA
1 TACGAGTCGTTCATAAACATATTATGAATTCTATGGGTTGCACACTTAGTGTCGA
1724813 TA
1 TA
1724815 GTACACATAG
Statistics
Matches: 193, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
53 1 0.01
54 191 0.99
55 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (55 bp):
TACGAGTCGTTCATAAACATATTATGAATTCTATGGGTTGCACACTTAGTGTCGA
Found at i:1728154 original size:54 final size:54
Alignment explanation
Indices: 1728086--1728356 Score: 314
Period size: 54 Copynumber: 5.0 Consensus size: 54
1728076 TCACATAACC
* * * *
1728086 TACGGTCGTTCATAAACATACTATAAATTATGTGGTTTTCACACTTAGTGTCGA
1 TACGGTCGTTCATAAACATATTATGAATTATGTGGGTTGCACACTTAGTGTCGA
* * *
1728140 TA-GAGTCGTTCATAAACATATTATGAATTTTGTGGGTTGCACACTTAGTGTTGC
1 TACG-GTCGTTCATAAACATATTATGAATTATGTGGGTTGCACACTTAGTGTCGA
* * *
1728194 TACGCTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACGCTTAGTGT-GA
1 TACGGTCGTTCATAAACATATTATGAATTATGTGGGTTGCACACTTAGTGTCGA
* * ***
1728247 TATGGTCGTTCATAAAAATATTATGAATTCCATGGGTTGCACACTTAGTGTCGA
1 TACGGTCGTTCATAAACATATTATGAATTATGTGGGTTGCACACTTAGTGTCGA
* * * * * *
1728301 TACGATCATTCATATATATATTATGAATT-TCGTGGGTTGCACACTTTGTGCCGA
1 TACGGTCGTTCATAAACATATTATGAATTAT-GTGGGTTGCACACTTAGTGTCGA
1728355 TA
1 TA
1728357 GTACTAATAT
Statistics
Matches: 187, Mismatches: 26, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
53 47 0.25
54 139 0.74
55 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.37
Consensus pattern (54 bp):
TACGGTCGTTCATAAACATATTATGAATTATGTGGGTTGCACACTTAGTGTCGA
Found at i:1728287 original size:107 final size:107
Alignment explanation
Indices: 1728085--1728357 Score: 334
Period size: 107 Copynumber: 2.5 Consensus size: 107
1728075 CTCACATAAC
* * * * *
1728085 CTACGGTCGTTCATAAACATACTATAAATTATGTGGTTTTCACACTTAGTGTCGATAGAGTCGTT
1 CTACGATCGTTCATAAACATATTATGAATT-TGTGGGTTGCACACTTAGTGTCGATAGAGTCGTT
* *** *
1728150 CATAAACATATTATGAATTTTGTGGGTTGCACACTTAGTGTTG
65 CATAAAAATATTATGAATTCCATGGGTTGCACACTTAGTGTCG
* *
1728193 CTACGCTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACGCTTAGTGT-GATATG-GTCGT
1 CTACGATCGTTCATAAACATATTATGAATT-TGTGGGTTGCACACTTAGTGTCGATA-GAGTCGT
1728256 TCATAAAAATATTATGAATTCCATGGGTTGCACACTTAGTGTCG
64 TCATAAAAATATTATGAATTCCATGGGTTGCACACTTAGTGTCG
* * * * * *
1728300 ATACGATCATTCATATATATATTATGAATTTCGTGGGTTGCACACTTTGTGCCGATAG
1 CTACGATCGTTCATAAACATATTATGAATTT-GTGGGTTGCACACTTAGTGTCGATAG
1728358 TACTAATATA
Statistics
Matches: 142, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
106 1 0.01
107 91 0.64
108 50 0.35
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (107 bp):
CTACGATCGTTCATAAACATATTATGAATTTGTGGGTTGCACACTTAGTGTCGATAGAGTCGTTC
ATAAAAATATTATGAATTCCATGGGTTGCACACTTAGTGTCG
Found at i:1732889 original size:54 final size:54
Alignment explanation
Indices: 1732831--1733573 Score: 808
Period size: 54 Copynumber: 13.8 Consensus size: 54
1732821 AGTCATTAAC
* ** * * * ***
1732831 AAACTCATTGTGAATTTTTTCGGTTGCACACATAGTGCCAATAAGGAAATTCAT
1 AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATAAGGTCGTTCAT
* * * * *
1732885 AAACTCATTATGAGTTCCGTGGGTTACACACTTAGTGCCGATACGATCGTTCAT
1 AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATAAGGTCGTTCAT
* *
1732939 AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTTCCGATACGGTCGTTCAT
1 AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATAAGGTCGTTCAT
* * * *
1732993 AAACTCATCATGAA-TTCGTGGGTTGCACACATAGTGCTGATACGAG-CGTTCAT
1 AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATAAG-GTCGTTCAT
* * * *
1733046 AAACTCATTATGAA-TTCTGTGGGTTACACACTTAGTGCCAATACGGTCATTCAT
1 AAACTCATTATGAATTTC-GTGGGTTGCACACTTAGTGCCGATAAGGTCGTTCAT
1733100 AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATAAGGTCGTTCAT
1 AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATAAGGTCGTTCAT
*** *
1733154 AAACTCATTATGAA-TTCTGTGGGTTGCACACTTAGTGTTAATACGGTCGTTCAT
1 AAACTCATTATGAATTTC-GTGGGTTGCACACTTAGTGCCGATAAGGTCGTTCAT
* * * *
1733208 AAACTCATTATGAATTCCATGGGTTGCACACTTAGTGCTGATACGGTCGTTCAT
1 AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATAAGGTCGTTCAT
** *
1733262 AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGTTGATACGG-CAGTTCAT
1 AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATAAGGTC-GTTCAT
* * ** * *
1733316 AAA-TGTATTATGAATTTTGTGGGTTGCACACTT-GTGTTGATACGGTCATTCAT
1 AAACT-CATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATAAGGTCGTTCAT
* * * * *
1733369 AAACAT-ATTATGAATTGCGTGAGTTGCACACTTAGTGTCGATACGGTCTTTCAT
1 AAAC-TCATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATAAGGTCGTTCAT
* * ** *
1733423 AAACAT-ATTTTGAATTCCGTGGGTTGCACACTTAGTGCTAATACGGTCGTTCAT
1 AAAC-TCATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATAAGGTCGTTCAT
* * * *
1733477 AAA-TATATTATGAATTTCGTGGGTTGCACACTTAGTGTCAATACGGTCGTTCAT
1 AAACT-CATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATAAGGTCGTTCAT
*
1733531 AAACAT-ATTATGAATCAT-GTGGGTTGCACACTTAGTGCCGATA
1 AAAC-TCATTATGAAT-TTCGTGGGTTGCACACTTAGTGCCGATA
1733574 GTACACAAAG
Statistics
Matches: 606, Mismatches: 66, Indels: 34
0.86 0.09 0.05
Matches are distributed among these distances:
52 1 0.00
53 100 0.17
54 497 0.82
55 7 0.01
56 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (54 bp):
AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATAAGGTCGTTCAT
Found at i:1732945 original size:108 final size:108
Alignment explanation
Indices: 1732831--1733573 Score: 927
Period size: 108 Copynumber: 6.9 Consensus size: 108
1732821 AGTCATTAAC
* ** * * * * ***
1732831 AAACTCATTGTGAATTTTTTCGGTTGCACACATAGTGCCAATAAGGAAATTCATAAACTCATTAT
1 AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGTCAATACGGTCGTTCATAAACTCATTAT
* * * *
1732896 GAGTTCCGTGGGTTACACACTTAGTGCCGATACGATCGTTCAT
66 GAATTCCGTGGGTTGCACACTTAGTGCTGATACGGTCGTTCAT
* *
1732939 AAACTCATTATGAATTTCGTGGGTTGCACACTTAGT-TCCGATACGGTCGTTCATAAACTCATCA
1 AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGT-CAATACGGTCGTTCATAAACTCATTA
*
1733003 TGAATT-CGTGGGTTGCACACATAGTGCTGATACGAG-CGTTCAT
65 TGAATTCCGTGGGTTGCACACTTAGTGCTGATACG-GTCGTTCAT
* * *
1733046 AAACTCATTATGAA-TTCTGTGGGTTACACACTTAGTGCCAATACGGTCATTCATAAACTCATTA
1 AAACTCATTATGAATTTC-GTGGGTTGCACACTTAGTGTCAATACGGTCGTTCATAAACTCATTA
* * *
1733110 TGAATTTCGTGGGTTGCACACTTAGTGCCGATAAGGTCGTTCAT
65 TGAATTCCGTGGGTTGCACACTTAGTGCTGATACGGTCGTTCAT
*
1733154 AAACTCATTATGAA-TTCTGTGGGTTGCACACTTAGTGTTAATACGGTCGTTCATAAACTCATTA
1 AAACTCATTATGAATTTC-GTGGGTTGCACACTTAGTGTCAATACGGTCGTTCATAAACTCATTA
*
1733218 TGAATTCCATGGGTTGCACACTTAGTGCTGATACGGTCGTTCAT
65 TGAATTCCGTGGGTTGCACACTTAGTGCTGATACGGTCGTTCAT
** *
1733262 AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGTTGATACGG-CAGTTCATAAA-TGTATT
1 AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGTCAATACGGTC-GTTCATAAACT-CATT
** * *
1733325 ATGAATTTTGTGGGTTGCACACTT-GTGTTGATACGGTCATTCAT
64 ATGAATTCCGTGGGTTGCACACTTAGTGCTGATACGGTCGTTCAT
* * * *
1733369 AAACAT-ATTATGAATTGCGTGAGTTGCACACTTAGTGTCGATACGGTCTTTCATAAACAT-ATT
1 AAAC-TCATTATGAATTTCGTGGGTTGCACACTTAGTGTCAATACGGTCGTTCATAAAC-TCATT
* *
1733432 TTGAATTCCGTGGGTTGCACACTTAGTGCTAATACGGTCGTTCAT
64 ATGAATTCCGTGGGTTGCACACTTAGTGCTGATACGGTCGTTCAT
*
1733477 AAA-TATATTATGAATTTCGTGGGTTGCACACTTAGTGTCAATACGGTCGTTCATAAACAT-ATT
1 AAACT-CATTATGAATTTCGTGGGTTGCACACTTAGTGTCAATACGGTCGTTCATAAAC-TCATT
* *
1733540 ATGAA-TCATGTGGGTTGCACACTTAGTGCCGATA
64 ATGAATTC-CGTGGGTTGCACACTTAGTGCTGATA
1733574 GTACACAAAG
Statistics
Matches: 560, Mismatches: 58, Indels: 34
0.86 0.09 0.05
Matches are distributed among these distances:
106 4 0.01
107 188 0.34
108 364 0.65
109 4 0.01
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (108 bp):
AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGTCAATACGGTCGTTCATAAACTCATTAT
GAATTCCGTGGGTTGCACACTTAGTGCTGATACGGTCGTTCAT
Found at i:1733361 original size:269 final size:270
Alignment explanation
Indices: 1732809--1733573 Score: 1001
Period size: 269 Copynumber: 2.8 Consensus size: 270
1732799 AGTGCACATA
* * * * * ** * * *
1732809 TAGTGCCATTACAGTCATTAACAAACTCATTGTGAATTTTTTCGGTTGCACACATAGTGCCAATA
1 TAGTGCCAATACGGTCATTCATAAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATA
** * * ** *
1732874 AGGAAATTCATAAACTCATTATGAGTTCCGTGGGTTACACACTTAGTGCCGATACGATCGTTCAT
66 AGGTCATTCATAAACTCATTATGAATTCCGTGGGTTGCACACTTAGTGCTAATACGGTCGTTCAT
* * *
1732939 AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTTCCGATACGGTCGTTCATAAACTCATCAT
131 AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGCTGATACGGTCGTTCATAAACTCATTAT
*
1733004 GAA-TTCGTGGGTTGCACACATAGTGCTGATACGAGCGTTCATAAACTCATTATGAATTCTGTGG
196 GAATTTCGTGGGTTGCACACTTAGTGCTGATACGAGCGTTCATAAACTCATTATGAATTCTGTGG
1733068 GTTACACACT
261 GTTACACACT
1733078 TAGTGCCAATACGGTCATTCATAAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATA
1 TAGTGCCAATACGGTCATTCATAAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATA
* * *
1733143 AGGTCGTTCATAAACTCATTATGAATTCTGTGGGTTGCACACTTAGTGTTAATACGGTCGTTCAT
66 AGGTCATTCATAAACTCATTATGAATTCCGTGGGTTGCACACTTAGTGCTAATACGGTCGTTCAT
* *
1733208 AAACTCATTATGAATTCCATGGGTTGCACACTTAGTGCTGATACGGTCGTTCATAAACTCATTAT
131 AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGCTGATACGGTCGTTCATAAACTCATTAT
* * *
1733273 GAATTTCGTGGGTTGCACACTTAGTGTTGATACG-GCAGTTCATAAA-TGTATTATGAATTTTGT
196 GAATTTCGTGGGTTGCACACTTAGTGCTGATACGAGC-GTTCATAAACT-CATTATGAATTCTGT
*
1733336 GGGTTGCACACT
259 GGGTTACACACT
*** * * *
1733348 T-GTGTTGATACGGTCATTCATAAACAT-ATTATGAATTGCGTGAGTTGCACACTTAGTGTCGAT
1 TAGTGCCAATACGGTCATTCATAAAC-TCATTATGAATTTCGTGGGTTGCACACTTAGTGCCGAT
* * *
1733411 ACGGTCTTTCATAAACAT-ATTTTGAATTCCGTGGGTTGCACACTTAGTGCTAATACGGTCGTTC
65 AAGGTCATTCATAAAC-TCATTATGAATTCCGTGGGTTGCACACTTAGTGCTAATACGGTCGTTC
* *
1733475 ATAAA-TATATTATGAATTTCGTGGGTTGCACACTTAGTG-TCAATACGGTCGTTCATAAACAT-
129 ATAAACT-CATTATGAATTTCGTGGGTTGCACACTTAGTGCT-GATACGGTCGTTCATAAAC-TC
* *
1733537 ATTATGAATCAT-GTGGGTTGCACACTTAGTGCCGATA
191 ATTATGAAT-TTCGTGGGTTGCACACTTAGTGCTGATA
1733574 GTACACAAAG
Statistics
Matches: 439, Mismatches: 48, Indels: 18
0.87 0.10 0.04
Matches are distributed among these distances:
268 2 0.00
269 371 0.85
270 66 0.15
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (270 bp):
TAGTGCCAATACGGTCATTCATAAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGCCGATA
AGGTCATTCATAAACTCATTATGAATTCCGTGGGTTGCACACTTAGTGCTAATACGGTCGTTCAT
AAACTCATTATGAATTTCGTGGGTTGCACACTTAGTGCTGATACGGTCGTTCATAAACTCATTAT
GAATTTCGTGGGTTGCACACTTAGTGCTGATACGAGCGTTCATAAACTCATTATGAATTCTGTGG
GTTACACACT
Found at i:1734473 original size:41 final size:41
Alignment explanation
Indices: 1734437--1734627 Score: 136
Period size: 41 Copynumber: 4.7 Consensus size: 41
1734427 TAAACGCAGT
* *
1734437 TAAAGATTCGTACTATAGCGGTGTTTGTATACAAACGCCAC
1 TAAAGACTCGTACTATAGCGGCGTTTGTATACAAACGCCAC
* * * * *
1734478 TAAAGACTCGTACTTTAGTGGCGTTTTTATACAAATGTCAC
1 TAAAGACTCGTACTATAGCGGCGTTTGTATACAAACGCCAC
* * * * * * * *
1734519 TATAGACTAGTACTTTAGTGGCATTTTTATACAAATGCCGC
1 TAAAGACTCGTACTATAGCGGCGTTTGTATACAAACGCCAC
* * * * * *
1734560 TATAA-ACTAGTACT-TTG-GGCCTTTTCTATACAAATGCCGC
1 TA-AAGACTCGTACTATAGCGG-CGTTTGTATACAAACGCCAC
* *
1734600 TAAAGACTCGTACTTTAGTGGCGTTTGT
1 TAAAGACTCGTACTATAGCGGCGTTTGT
1734628 TTTTACAAAC
Statistics
Matches: 125, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
39 4 0.03
40 30 0.24
41 88 0.70
42 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (41 bp):
TAAAGACTCGTACTATAGCGGCGTTTGTATACAAACGCCAC
Found at i:1734601 original size:40 final size:41
Alignment explanation
Indices: 1734464--1734621 Score: 196
Period size: 41 Copynumber: 3.9 Consensus size: 41
1734454 GCGGTGTTTG
* * *
1734464 TATACAAACGCCACTAAAGACTCGTACTTTAGTGGCGTTTT
1 TATACAAATGCCACTAAAGACTAGTACTTTAGTGGCATTTT
* *
1734505 TATACAAATGTCACTATAGACTAGTACTTTAGTGGCATTTT
1 TATACAAATGCCACTAAAGACTAGTACTTTAGTGGCATTTT
* *
1734546 TATACAAATGCCGCTATAA-ACTAGTACTTT-G-GGCCTTTT
1 TATACAAATGCCACTA-AAGACTAGTACTTTAGTGGCATTTT
* *
1734585 CTATACAAATGCCGCTAAAGACTCGTACTTTAGTGGC
1 -TATACAAATGCCACTAAAGACTAGTACTTTAGTGGC
1734622 GTTTGTTTTT
Statistics
Matches: 102, Mismatches: 10, Indels: 9
0.84 0.08 0.07
Matches are distributed among these distances:
39 9 0.09
40 27 0.26
41 62 0.61
42 4 0.04
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (41 bp):
TATACAAATGCCACTAAAGACTAGTACTTTAGTGGCATTTT
Found at i:1737799 original size:43 final size:42
Alignment explanation
Indices: 1737742--1737823 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
1737732 TGGCGTTTGG
* * * * *
1737742 AAAAATGTCGCTAAATATCATAATCTTTAGCGGTGTTTGTAAT
1 AAAAATGCCACTAAA-AACATAACCTTTAGCGGCGTTTGTAAT
*
1737785 AAAAATGCCACTAAAAACATTACCTTTAGCGGCGTTTGT
1 AAAAATGCCACTAAAAACATAACCTTTAGCGGCGTTTGT
1737824 GAACGACAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
42 20 0.61
43 13 0.39
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (42 bp):
AAAAATGCCACTAAAAACATAACCTTTAGCGGCGTTTGTAAT
Found at i:1739758 original size:3 final size:3
Alignment explanation
Indices: 1739697--1739744 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
1739687 TTCATTTGAT
* * *
1739697 TTA TTA TTA TTA TTA TTA TCA TCA TTA TTA TCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1739745 AAAAAATTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1740122 original size:22 final size:22
Alignment explanation
Indices: 1740097--1740156 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
1740087 CACGCCGAGC
1740097 TCTATGGTGAGTCACCACCATA
1 TCTATGGTGAGTCACCACCATA
1740119 TCTATGGTGAGTCACCACCATA
1 TCTATGGTGAGTCACCACCATA
* *
1740141 GCTATGGTGACTCACC
1 TCTATGGTGAGTCACC
1740157 TAGGCCAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (22 bp):
TCTATGGTGAGTCACCACCATA
Found at i:1741300 original size:17 final size:19
Alignment explanation
Indices: 1741264--1741300 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1741254 CATGGAATAC
1741264 AATATTATAATTTTATAAT
1 AATATTATAATTTTATAAT
*
1741283 AATATT-TATTTTTA-AAT
1 AATATTATAATTTTATAAT
1741300 A
1 A
1741301 TCAAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTATAATTTTATAAT
Found at i:1742031 original size:2 final size:2
Alignment explanation
Indices: 1742024--1742076 Score: 76
Period size: 2 Copynumber: 27.5 Consensus size: 2
1742014 CCAAAATTTT
1742024 TA TA TA TA CT- TA T- TA T- 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
1742064 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1742077 TATTTTTTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.06
2 43 0.91
3 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1743788 original size:14 final size:14
Alignment explanation
Indices: 1743761--1743797 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1743751 AAATAATTTA
* *
1743761 CATTTACATTTTTG
1 CATTTGCATCTTTG
1743775 CATTTGCATCTTTG
1 CATTTGCATCTTTG
1743789 CATTTGCAT
1 CATTTGCAT
1743798 TTGTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51
Consensus pattern (14 bp):
CATTTGCATCTTTG
Found at i:1746354 original size:1 final size:1
Alignment explanation
Indices: 1746348--1746435 Score: 86
Period size: 1 Copynumber: 88.0 Consensus size: 1
1746338 ACTCATTCAT
* ** * * * *
1746348 AAAAAAAAGAAAAAAAAAAGGAAAAAAGAAAAAGAAAAAAAGAAAAAAAGAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
1746413 AAGAAAAAAGAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAA
1746436 GAATAAAGGA
Statistics
Matches: 69, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (1 bp):
A
Found at i:1746362 original size:7 final size:7
Alignment explanation
Indices: 1746350--1746448 Score: 95
Period size: 6 Copynumber: 14.6 Consensus size: 7
1746340 TCATTCATAA
1746350 AAAAAAG
1 AAAAAAG
1746357 -AAAAA-
1 AAAAAAG
*
1746362 AAAAAGG
1 AAAAAAG
1746369 AAAAAAG
1 AAAAAAG
1746376 -AAAAAG
1 AAAAAAG
1746382 AAAAAAAG
1 -AAAAAAG
1746390 AAAAAA-
1 AAAAAAG
1746396 AGAAAAA-
1 A-AAAAAG
1746403 AAAAAA-
1 AAAAAAG
1746409 AAAAAAG
1 AAAAAAG
1746416 AAAAAAG
1 AAAAAAG
1746423 -AAAAAG
1 AAAAAAG
1746429 AAAAAAAG
1 -AAAAAAG
*
1746437 AATAAAGG
1 AA-AAAAG
1746445 AAAA
1 AAAA
1746449 TTGAATCAAG
Statistics
Matches: 80, Mismatches: 3, Indels: 18
0.79 0.03 0.18
Matches are distributed among these distances:
6 33 0.41
7 29 0.36
8 18 0.22
ACGTcount: A:0.86, C:0.00, G:0.13, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:1746362 original size:8 final size:8
Alignment explanation
Indices: 1746349--1746448 Score: 102
Period size: 8 Copynumber: 12.5 Consensus size: 8
1746339 CTCATTCATA
1746349 AAAAAAAG
1 AAAAAAAG
1746357 AAAAAAA-
1 AAAAAAAG
1746364 AAAGGAAAA-
1 AAA--AAAAG
1746373 AAGAAAAAG
1 AA-AAAAAG
1746382 AAAAAAAG
1 AAAAAAAG
1746390 AAAAAAAG
1 AAAAAAAG
1746398 AAAAAAA-
1 AAAAAAAG
1746405 AAAAAAA-
1 AAAAAAAG
1746412 AAAGAAAA-
1 AAA-AAAAG
1746420 AAGAAAAAG
1 AA-AAAAAG
1746429 AAAAAAAG
1 AAAAAAAG
* *
1746437 AATAAAGG
1 AAAAAAAG
1746445 AAAA
1 AAAA
1746449 TTGAATCAAG
Statistics
Matches: 82, Mismatches: 3, Indels: 14
0.83 0.03 0.14
Matches are distributed among these distances:
7 13 0.16
8 57 0.70
9 11 0.13
10 1 0.01
ACGTcount: A:0.86, C:0.00, G:0.13, T:0.01
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1746380 original size:25 final size:25
Alignment explanation
Indices: 1746351--1746435 Score: 122
Period size: 25 Copynumber: 3.5 Consensus size: 25
1746341 CATTCATAAA
1746351 AAAAAGAAAAAAAAAAGGAAAAAAG
1 AAAAAGAAAAAAAAAAGGAAAAAAG
*
1746376 AAAAAG---AAAAAAAGAAAAAAAG
1 AAAAAGAAAAAAAAAAGGAAAAAAG
* *
1746398 AAAAAAAAAAAAAAAAAGAAAAAAG
1 AAAAAGAAAAAAAAAAGGAAAAAAG
1746423 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
1746436 GAATAAAGGA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
22 20 0.38
25 32 0.62
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (25 bp):
AAAAAGAAAAAAAAAAGGAAAAAAG
Found at i:1746419 original size:47 final size:49
Alignment explanation
Indices: 1746349--1746448 Score: 168
Period size: 47 Copynumber: 2.1 Consensus size: 49
1746339 CTCATTCATA
1746349 AAAAAAAGAAAAAAAAAAGGAAAAAAGAAAAAGAAAAAAAGAAAAAAAG
1 AAAAAAAGAAAAAAAAAAGGAAAAAAGAAAAAGAAAAAAAGAAAAAAAG
* *
1746398 AAAAAAA-AAAAAAAAAA-GAAAAAAGAAAAAGAAAAAAAGAATAAAGG
1 AAAAAAAGAAAAAAAAAAGGAAAAAAGAAAAAGAAAAAAAGAAAAAAAG
1746445 AAAA
1 AAAA
1746449 TTGAATCAAG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 32 0.65
48 10 0.20
49 7 0.14
ACGTcount: A:0.86, C:0.00, G:0.13, T:0.01
Consensus pattern (49 bp):
AAAAAAAGAAAAAAAAAAGGAAAAAAGAAAAAGAAAAAAAGAAAAAAAG
Found at i:1747065 original size:32 final size:32
Alignment explanation
Indices: 1747029--1747090 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
1747019 GTCAGACACA
*
1747029 AGAAGTATCTCTACGAGATGAGCATAACAACG
1 AGAAGTATCTCTACAAGATGAGCATAACAACG
*
1747061 AGAAGTATCTCTACAAGATGAGTATAACAA
1 AGAAGTATCTCTACAAGATGAGCATAACAA
1747091 TCATTTCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (32 bp):
AGAAGTATCTCTACAAGATGAGCATAACAACG
Found at i:1749600 original size:75 final size:75
Alignment explanation
Indices: 1749500--1749672 Score: 233
Period size: 75 Copynumber: 2.3 Consensus size: 75
1749490 ATCAACAAGA
** * * *
1749500 AGCAAATGTTGGGGTATGCTGAAAGCCTATTTCAATCAGAATGAATAATGTTCACACATTTTGAA
1 AGCAAATGTTGGGCCATGCTGAAAGCCCATTTCAATCAGAATAAAGAATGTTCACACATTTTGAA
*
1749565 CGCTTGTATT
66 CGCTTATATT
* * *
1749575 AGCCAATAT-TTGGG-CATGCTGAAAGCCCCTTTCAATCAGAATAAAGAATGTTGACGCATTTTG
1 AG-CAA-ATGTTGGGCCATGCTGAAAGCCCATTTCAATCAGAATAAAGAATGTTCACACATTTTG
1749638 AACGCTTATATT
64 AACGCTTATATT
1749650 AGCAAATGTTGGGCCATGCTGAA
1 AGCAAATGTTGGGCCATGCTGAA
1749673 GGTCTGTATC
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
73 2 0.02
74 8 0.09
75 66 0.77
76 8 0.09
77 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (75 bp):
AGCAAATGTTGGGCCATGCTGAAAGCCCATTTCAATCAGAATAAAGAATGTTCACACATTTTGAA
CGCTTATATT
Found at i:1751328 original size:37 final size:36
Alignment explanation
Indices: 1751220--1751353 Score: 135
Period size: 36 Copynumber: 3.7 Consensus size: 36
1751210 ACTATTTCCC
1751220 AAATTTATCTCACTTGAGATTATTTTTCTTAAAACA
1 AAATTTATCTCACTTGAGATTATTTTTCTTAAAACA
* * * ** **
1751256 AAATTTGTCTCGCTTGAGA-CAGTTTCACTCGAAACA
1 AAATTTATCTCACTTGAGATTA-TTTTTCTTAAAACA
1751292 ACAATTTATCTCACTTGAGATTATTTTTCTTAAAACA
1 A-AATTTATCTCACTTGAGATTATTTTTCTTAAAACA
* ** * *
1751329 AGATTCGTCTCGCTTGAGATAATTT
1 AAATTTATCTCACTTGAGATTATTT
1751354 CACTAGAAAC
Statistics
Matches: 76, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
35 1 0.01
36 47 0.62
37 27 0.36
38 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (36 bp):
AAATTTATCTCACTTGAGATTATTTTTCTTAAAACA
Found at i:1751340 original size:73 final size:73
Alignment explanation
Indices: 1751221--1751365 Score: 245
Period size: 73 Copynumber: 2.0 Consensus size: 73
1751211 CTATTTCCCA
* * *
1751221 AATTTATCTCACTTGAGATTATTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
1 AATTTATCTCACTTGAGATTATTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAATTTCACTA
1751286 GAAACAAC
66 GAAACAAC
* *
1751294 AATTTATCTCACTTGAGATTATTTTTCTTAAAACAAGATTCGTCTCGCTTGAGATAATTTCACTA
1 AATTTATCTCACTTGAGATTATTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAATTTCACTA
1751359 GAAACAA
66 GAAACAA
1751366 ACATTTCCAT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 67 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (73 bp):
AATTTATCTCACTTGAGATTATTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAATTTCACTA
GAAACAAC
Found at i:1751364 original size:36 final size:36
Alignment explanation
Indices: 1751220--1751371 Score: 119
Period size: 36 Copynumber: 4.2 Consensus size: 36
1751210 ACTATTTCCC
* * * **
1751220 AAATTTATCTCACTTGAGATTATTTTTCTTA-AAACA
1 AAATTTGTCTCGCTTGAGATAATTTCAC-TAGAAACA
* * *
1751256 AAATTTGTCTCGCTTGAGACAGTTTCACTCGAAACA
1 AAATTTGTCTCGCTTGAGATAATTTCACTAGAAACA
* * * **
1751292 ACAATTTATCTCACTTGAGATTATTTTTCTTA-AAACA
1 A-AATTTGTCTCGCTTGAGATAATTTCAC-TAGAAACA
* *
1751329 AGATTCGTCTCGCTTGAGATAATTTCACTAGAAACA
1 AAATTTGTCTCGCTTGAGATAATTTCACTAGAAACA
1751365 AACATTT
1 AA-ATTT
1751372 CCATCACTTA
Statistics
Matches: 86, Mismatches: 25, Indels: 9
0.72 0.21 0.08
Matches are distributed among these distances:
35 3 0.03
36 53 0.62
37 29 0.34
38 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (36 bp):
AAATTTGTCTCGCTTGAGATAATTTCACTAGAAACA
Found at i:1751532 original size:17 final size:17
Alignment explanation
Indices: 1751510--1751572 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
1751500 CAACTTTTCC
1751510 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
* *
1751527 AGAAGAACTCATCTGAAGAATG
1 AGAAGAAGT--TC---ATAATG
*
1751549 AGAAGAAGTTCATAATA
1 AGAAGAAGTTCATAATG
1751566 AGAAGAA
1 AGAAGAA
1751573 CTTGTTCAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
17 19 0.53
19 2 0.06
20 2 0.06
22 13 0.36
ACGTcount: A:0.51, C:0.08, G:0.22, T:0.19
Consensus pattern (17 bp):
AGAAGAAGTTCATAATG
Found at i:1751999 original size:3 final size:3
Alignment explanation
Indices: 1751919--1751981 Score: 99
Period size: 3 Copynumber: 21.0 Consensus size: 3
1751909 TTTATTTGAT
* * *
1751919 TTA TTA TTA TTA ATA TTA TTA TTA TTA TTA TTA TTA TCA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1751967 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
1751982 ATAAAAAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1756137 original size:27 final size:27
Alignment explanation
Indices: 1756099--1756161 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
1756089 AACTGCATTT
1756099 GTTGCTGTTGGCTCTGTACAAGGTTAG
1 GTTGCTGTTGGCTCTGTACAAGGTTAG
1756126 GTTGCTGTTGGCTCTGTACAAGGTTAG
1 GTTGCTGTTGGCTCTGTACAAGGTTAG
1756153 GTTGCTGTT
1 GTTGCTGTT
1756162 CCATCTGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.13, C:0.14, G:0.33, T:0.40
Consensus pattern (27 bp):
GTTGCTGTTGGCTCTGTACAAGGTTAG
Found at i:1756168 original size:27 final size:27
Alignment explanation
Indices: 1756099--1756169 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 27
1756089 AACTGCATTT
*
1756099 GTTGCTGTTGGCTCTGTACAAGGTTAG
1 GTTGCTGTTGCCTCTGTACAAGGTTAG
*
1756126 GTTGCTGTTGGCTCTGTACAAGGTTAG
1 GTTGCTGTTGCCTCTGTACAAGGTTAG
1756153 GTTGCTGTT-CCATCTGT
1 GTTGCTGTTGCC-TCTGT
1756170 TGTTGATTCT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
26 1 0.02
27 41 0.98
ACGTcount: A:0.13, C:0.17, G:0.31, T:0.39
Consensus pattern (27 bp):
GTTGCTGTTGCCTCTGTACAAGGTTAG
Found at i:1761209 original size:15 final size:16
Alignment explanation
Indices: 1761175--1761208 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
1761165 CAAATAGTAT
1761175 ATATAATAAGTTAGAAAA
1 ATATAATAAGTT--AAAA
1761193 ATATAATAAGTTAAAA
1 ATATAATAAGTTAAAA
1761209 TTTCATTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
18 12 0.75
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (16 bp):
ATATAATAAGTTAAAA
Found at i:1764306 original size:15 final size:15
Alignment explanation
Indices: 1764273--1764307 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1764263 GGCTTTTTAG
* *
1764273 CCCGCACCGTTTAAG
1 CCCGCACCGTTAAAA
1764288 CCCGCACCGTTAAAA
1 CCCGCACCGTTAAAA
1764303 CCCGC
1 CCCGC
1764308 GGGCTAAACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.46, G:0.17, T:0.14
Consensus pattern (15 bp):
CCCGCACCGTTAAAA
Found at i:1765749 original size:15 final size:15
Alignment explanation
Indices: 1765713--1765753 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1765703 GTCCTTAAAT
* *
1765713 TTTAGGAATTCTTGA
1 TTTAGGTATTTTTGA
1765728 TTTAGGTATTTTTGA
1 TTTAGGTATTTTTGA
1765743 TTTAGGTATTT
1 TTTAGGTATTT
1765754 AAACTTCTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.22, C:0.02, G:0.20, T:0.56
Consensus pattern (15 bp):
TTTAGGTATTTTTGA
Found at i:1768206 original size:42 final size:42
Alignment explanation
Indices: 1768159--1768290 Score: 221
Period size: 42 Copynumber: 3.2 Consensus size: 42
1768149 ATAAAAAAGT
*
1768159 AAATAAATAACACCATAACACCATTAAGTTTCAATAAGTCTA
1 AAATAAATAACACCATAACACCATTAAGTCTCAATAAGTCTA
1768201 AAATAAATAACACCATAACACCATTAAGTCTCAATAAGTCTA
1 AAATAAATAACACCATAACACCATTAAGTCTCAATAAGTCTA
* * *
1768243 AAATAAATAACACCATAATACTAATAAGTCTCAATAAGTCT-
1 AAATAAATAACACCATAACACCATTAAGTCTCAATAAGTCTA
1768284 AAATAAA
1 AAATAAA
1768291 ATCAACATCA
Statistics
Matches: 86, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
41 7 0.08
42 79 0.92
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.25
Consensus pattern (42 bp):
AAATAAATAACACCATAACACCATTAAGTCTCAATAAGTCTA
Found at i:1769090 original size:20 final size:21
Alignment explanation
Indices: 1769051--1769092 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
1769041 GAAAGAGATA
1769051 ATTCAATTTGTGCTTCACAAT
1 ATTCAATTTGTGCTTCACAAT
*
1769072 ATTCAATTT-TGCTTGACAAT
1 ATTCAATTTGTGCTTCACAAT
1769092 A
1 A
1769093 AATTGGATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.43
Consensus pattern (21 bp):
ATTCAATTTGTGCTTCACAAT
Found at i:1770753 original size:30 final size:31
Alignment explanation
Indices: 1770693--1770761 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 31
1770683 CAACCATTCA
* * * *
1770693 CAACTTTTCCAAAATTATTAAATTGGTCCCC
1 CAACTTTTCAAAAATTATCAAAATGATCCCC
1770724 CAACTTTTCAAAAATTA-CAAAATGATCCCC
1 CAACTTTTCAAAAATTATCAAAATGATCCCC
*
1770754 CAAATTTT
1 CAACTTTT
1770762 TCGAAGGATT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.33
Consensus pattern (31 bp):
CAACTTTTCAAAAATTATCAAAATGATCCCC
Found at i:1771486 original size:31 final size:31
Alignment explanation
Indices: 1771458--1771534 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
1771448 CCAAGACATG
* *
1771458 TCAAACTTATCATCTTCCAAAATAAGACACC
1 TCAACCTTATCATCTTCCAAAAAAAGACACC
*
1771489 TCAACCTTATCGTCTTCCAAAAAAAGACACC
1 TCAACCTTATCATCTTCCAAAAAAAGACACC
1771520 TCAACCTTATCATCT
1 TCAACCTTATCATCT
1771535 CCCATAAGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.38, C:0.31, G:0.04, T:0.27
Consensus pattern (31 bp):
TCAACCTTATCATCTTCCAAAAAAAGACACC
Found at i:1785084 original size:7 final size:7
Alignment explanation
Indices: 1785072--1785102 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1785062 CTTTGCATCA
1785072 TATTCTT
1 TATTCTT
*
1785079 TATTCTG
1 TATTCTT
1785086 TATTCTT
1 TATTCTT
1785093 TATTCTT
1 TATTCTT
1785100 TAT
1 TAT
1785103 ATTCCAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.16, C:0.13, G:0.03, T:0.68
Consensus pattern (7 bp):
TATTCTT
Found at i:1788467 original size:24 final size:24
Alignment explanation
Indices: 1788435--1788503 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
1788425 TACAGAAGAC
*
1788435 GAAGTTTGTGCTTTTGCAGCAGAT
1 GAAGCTTGTGCTTTTGCAGCAGAT
1788459 GAAGCTTGTGCTTTTGCAGCAGAT
1 GAAGCTTGTGCTTTTGCAGCAGAT
*
1788483 GAAGCTTGTGCTTTTACAGCA
1 GAAGCTTGTGCTTTTGCAGCA
1788504 TATAAGTCCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.35
Consensus pattern (24 bp):
GAAGCTTGTGCTTTTGCAGCAGAT
Done.