Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008911.1 Hibiscus syriacus cultivar Beakdansim tig00112211_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: 76582
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:359 original size:124 final size:124
Alignment explanation
Indices: 138--526 Score: 500
Period size: 124 Copynumber: 3.1 Consensus size: 124
128 CACGATATCC
* * * * * * *
138 TTCGTCGTGAAGTTGAAATCGTGGAGGGCCCATTCGTTGTGAAGTTGAGCCTTTATTTAGATATA
1 TTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATC
* * *
203 CTTCGTCGTGAAGTTGAAATCCAATCTGAAGATGAATGTTGTTGGT-AGGCGCAATTCCA
66 CTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGA-GCACAATTCCA
*
262 TTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCATTGAATTGGATATC
1 TTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATC
* * * * *
327 CTTCGTCGTGAAGTTGAAATCCAATATAAAGATAAATGTTACTGGTGAGCACGATTCCC
66 CTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACAATTCCA
* * *
386 TTCGTAGTGAAGTTAAAACCGTGGATGACCCATTCGGTGTGAAGTTGAGCCTTGAATTGGATATC
1 TTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATC
* * *
451 ATTCGTCGTGAAGTTGAAATTCAATCTCAAGATGAATGTTGCT--TCGAGTCA-AATATCC-
66 CTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGT-GAG-CACAAT-TCCA
*
509 TTCGTCGGGAAGTTGAAA
1 TTCGTCGTGAAGTTGAAA
527 TTGATTCTGA
Statistics
Matches: 231, Mismatches: 30, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
122 1 0.00
123 20 0.09
124 209 0.90
125 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (124 bp):
TTCGTCGTGAAGTTGAAACCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATC
CTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACAATTCCA
Found at i:608 original size:64 final size:64
Alignment explanation
Indices: 517--726 Score: 285
Period size: 64 Copynumber: 3.3 Consensus size: 64
507 CCTTCGTCGG
* * * * *
517 GAAGTTGAAATTGATTCTGAATGAAACTGGGAAGCCGTTTGTTTAGTTCAATATCATTCGCTGT
1 GAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTGTTGAGTCCAATATCATTCGCTGT
* * *
581 GAAGTTGAAATTGACTCTGAATTAAACTAGAAAGTCGTTTGTTGAGTCCAATATCATTCACTGT
1 GAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTGTTGAGTCCAATATCATTCGCTGT
* * * * * * *
645 GAAGTTAAAATTGACTTTGAATGAAACTGAAAAGTTGTTTATTGAGTCCAATATCCTTCGTTGT
1 GAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTGTTGAGTCCAATATCATTCGCTGT
709 GAAGTTGAAATTGACTCT
1 GAAGTTGAAATTGACTCT
727 AAAAACTGCA
Statistics
Matches: 126, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 126 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.36
Consensus pattern (64 bp):
GAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTGTTGAGTCCAATATCATTCGCTGT
Found at i:1935 original size:12 final size:12
Alignment explanation
Indices: 1918--1942 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1908 ACTGCCACAA
1918 TTTCAAACATAT
1 TTTCAAACATAT
1930 TTTCAAACATAT
1 TTTCAAACATAT
1942 T
1 T
1943 GAAAAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTCAAACATAT
Found at i:2670 original size:22 final size:22
Alignment explanation
Indices: 2645--2702 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
2635 ATGTTGATGT
2645 TGTTTTATTTTAATTTAGTCAC
1 TGTTTTATTTTAATTTAGTCAC
* * *
2667 TG-TTAATTTCTGATTTAGTTAC
1 TGTTTTATTT-TAATTTAGTCAC
2689 --TTTTATTTTAATTT
1 TGTTTTATTTTAATTT
2703 TTGCATGTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
20 5 0.17
21 12 0.41
22 12 0.41
ACGTcount: A:0.22, C:0.07, G:0.09, T:0.62
Consensus pattern (22 bp):
TGTTTTATTTTAATTTAGTCAC
Found at i:2995 original size:27 final size:28
Alignment explanation
Indices: 2965--3019 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
2955 CTTTTAGATA
* *
2965 TTAACATTTTC-TTATTTTTTTTTATTT
1 TTAACATTTTCATCATTTTTATTTATTT
2992 TTAACATTTTCATCATTTTTATTTATTT
1 TTAACATTTTCATCATTTTTATTTATTT
3020 ATATTGTGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (28 bp):
TTAACATTTTCATCATTTTTATTTATTT
Found at i:5286 original size:22 final size:20
Alignment explanation
Indices: 5229--5282 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
5219 AAAATGAAAA
5229 AAATTAAAATAACAGTAGCT
1 AAATTAAAATAACAGTAGCT
*
5249 AAATCAGAAATTAACAGT-GACT
1 AAATTA-AAA-TAACAGTAG-CT
5271 AAATTAAAATAA
1 AAATTAAAATAA
5283 AACAACATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 8 0.28
21 7 0.24
22 14 0.48
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.24
Consensus pattern (20 bp):
AAATTAAAATAACAGTAGCT
Found at i:6494 original size:83 final size:84
Alignment explanation
Indices: 6340--6495 Score: 215
Period size: 83 Copynumber: 1.9 Consensus size: 84
6330 GAAAGTAGTT
* * * *
6340 GCTGAGTGTAATCGAACTCGAAGGTGTTTTATTGGCAGATGACCCTTCTTGCCTTGAGCTATGCT
1 GCTGAGTGTAATAGAACTCGAAGGTGTTTTATTGGCAGATAACCCTTCTAGCCTTAAGCTATGCT
*
6405 GCAAATGATGTGTCTTTGA
66 ACAAATGATGTGTCTTTGA
* * **
6424 GCTGAGTGTAATAGAACTCGAAGGT-TTTTGTTGGCAGATAACCTTTCTAGCCTTAATTTATGCT
1 GCTGAGTGTAATAGAACTCGAAGGTGTTTTATTGGCAGATAACCCTTCTAGCCTTAAGCTATGCT
*
6488 ATAAATGA
66 ACAAATGA
6496 ACACAATATT
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
83 38 0.61
84 24 0.39
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (84 bp):
GCTGAGTGTAATAGAACTCGAAGGTGTTTTATTGGCAGATAACCCTTCTAGCCTTAAGCTATGCT
ACAAATGATGTGTCTTTGA
Found at i:6816 original size:64 final size:64
Alignment explanation
Indices: 6742--6972 Score: 313
Period size: 64 Copynumber: 3.6 Consensus size: 64
6732 ATGTTGCTTC
* * * * * *
6742 GAGTCCAATATCCTTCG-TCATGAAGTTGAAATT-AGTTTTGAATGAAACTGGGAAGCCGTTTGT
1 GAGTCCAATATCATTCGCT-GTGAAGTTGAAATTGA-CTCTGAATGAAACTGGAAAGTCGTTTGT
6805 T
64 T
* * *
6806 GAGTCCAATATCCTTCGCTGTGAATTTGAAATTGACTCTGAATGAAATTGGAAAGTCGTTTGTT
1 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTGTT
* *
6870 GAGTTCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTGTT
* *
6934 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTAACTCT
1 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCT
6973 AAAAACTGCA
Statistics
Matches: 150, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
64 148 0.99
65 2 0.01
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.35
Consensus pattern (64 bp):
GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTGTT
Found at i:9260 original size:92 final size:92
Alignment explanation
Indices: 9098--9282 Score: 334
Period size: 92 Copynumber: 2.0 Consensus size: 92
9088 ACTCGTTCAA
*
9098 TTATTCCACCTTAGAAGGTAACATAAATTCATTCGTTTAAAGGATTAAGCAAATATGAAAAATCA
1 TTATTCCACCTTAGAAGGTAACATAAATTCATTCGTTTAAAAGATTAAGCAAATATGAAAAATCA
*
9163 TAAACGTGTTCAAACAAAACAATACTC
66 AAAACGTGTTCAAACAAAACAATACTC
* *
9190 TTATTCCACCTTAGAATGTAATATAAATTCATTCGTTTAAAAGATTAAGCAAATATGAAAAATCA
1 TTATTCCACCTTAGAAGGTAACATAAATTCATTCGTTTAAAAGATTAAGCAAATATGAAAAATCA
9255 AAAACGTGTTCAAACAAAACAATACTC
66 AAAACGTGTTCAAACAAAACAATACTC
9282 T
1 T
9283 CAGTGCAAAT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 89 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (92 bp):
TTATTCCACCTTAGAAGGTAACATAAATTCATTCGTTTAAAAGATTAAGCAAATATGAAAAATCA
AAAACGTGTTCAAACAAAACAATACTC
Found at i:11088 original size:7 final size:7
Alignment explanation
Indices: 11078--11103 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
11068 TCAAATAATA
11078 AATTTAT
1 AATTTAT
11085 AATTTAT
1 AATTTAT
11092 AATTTAT
1 AATTTAT
11099 AATTT
1 AATTT
11104 TCGCTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
AATTTAT
Found at i:14984 original size:37 final size:37
Alignment explanation
Indices: 14894--14998 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
14884 TCTTTTCGTC
14894 ATACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 ATACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* **
14931 TTGTTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 ATACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * * *
14968 ATACTATTATTTAAACTCATAAAGATAGGAT
1 ATACTAGGATTCAAACTCCTAAAAATAGGAT
14999 TCACAAACAT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (37 bp):
ATACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:15450 original size:2 final size:2
Alignment explanation
Indices: 15443--15467 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15433 CCTTATTATT
15443 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
15468 TTAATTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15692 original size:29 final size:27
Alignment explanation
Indices: 15660--15751 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 27
15650 CTATGATTAC
15660 TATTTTTTAGTTAATATTATATGTATATT
1 TATTTTTTA-TTAATATTATAT-TATATT
*
15689 TATTTTTCATTTATTATATTATTATTACTATT
1 TATTTTTTA-TTA--ATATTA-TATTA-TATT
* *
15721 TAGTATTTTATT-ATATTATA-TATATA
1 TA-TTTTTTATTAATATTATATTATATT
15747 TATTT
1 TATTT
15752 ATATATATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
25 2 0.04
26 5 0.10
27 2 0.04
28 2 0.04
29 17 0.33
31 8 0.15
32 11 0.21
33 5 0.10
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (27 bp):
TATTTTTTATTAATATTATATTATATT
Found at i:15712 original size:8 final size:9
Alignment explanation
Indices: 15700--15826 Score: 121
Period size: 8 Copynumber: 14.7 Consensus size: 9
15690 ATTTTTCATT
15700 TATTATAT-
1 TATTATATA
15708 TATTAT-TA
1 TATTATATA
15716 CTATT-TAGTA
1 -TATTATA-TA
*
15726 TTTTAT-TA
1 TATTATATA
15734 TATTATATA
1 TATTATATA
*
15743 TA-TATATT
1 TATTATATA
15751 TA-TATATA
1 TATTATATA
15759 TA-TATATA
1 TATTATATA
15767 TA-TATATA
1 TATTATATA
15775 TA-TATATA
1 TATTATATA
15783 TA-TATATA
1 TATTATATA
15791 TATATATATA
1 TAT-TATATA
15801 TATATATATA
1 TAT-TATATA
15811 TATATATATA
1 TAT-TATATA
15821 TATTAT
1 TATTAT
15827 TTATTTTCAT
Statistics
Matches: 107, Mismatches: 4, Indels: 15
0.85 0.03 0.12
Matches are distributed among these distances:
7 1 0.01
8 60 0.56
9 14 0.13
10 32 0.30
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (9 bp):
TATTATATA
Found at i:15720 original size:6 final size:5
Alignment explanation
Indices: 15673--15842 Score: 88
Period size: 6 Copynumber: 32.0 Consensus size: 5
15663 TTTTTAGTTA
*
15673 ATATT ATATGT ATATT -TATTT TTCATT -TATT ATATT ATTATT ACTATTT
1 ATATT ATAT-T ATATT ATA-TT AT-ATT ATATT ATATT A-TATT A-TA-TT
*
15722 AGTATT TTATT ATATT ATA-T ATA-T ATATT -TA-T ATATAT ATATAT
1 A-TATT ATATT ATATT ATATT ATATT ATATT ATATT ATAT-T ATAT-T
15766 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
1 ATAT-T ATAT-T ATAT-T ATAT-T ATAT-T ATAT-T ATAT-T ATAT-T ATAT-T
15820 ATATT AT-TT AT-TT -TCATT ATATT
1 ATATT ATATT ATATT AT-ATT ATATT
15843 TTTAGTTTCT
Statistics
Matches: 147, Mismatches: 4, Indels: 28
0.82 0.02 0.16
Matches are distributed among these distances:
3 2 0.01
4 23 0.16
5 33 0.22
6 83 0.56
7 6 0.04
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:15744 original size:2 final size:2
Alignment explanation
Indices: 15732--15823 Score: 168
Period size: 2 Copynumber: 46.5 Consensus size: 2
15722 AGTATTTTAT
*
15732 TA TA T- TA TA TA TA TA TA TT 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
15773 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
15815 TA TA TA TA T
1 TA TA TA TA T
15824 TATTTATTTT
Statistics
Matches: 87, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 86 0.99
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17135 original size:19 final size:19
Alignment explanation
Indices: 17111--17147 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
17101 ACCTTACTAA
17111 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
17130 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
17148 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:20588 original size:7 final size:7
Alignment explanation
Indices: 20576--20656 Score: 76
Period size: 7 Copynumber: 11.6 Consensus size: 7
20566 CAATAAGAAC
20576 AAAAAGA
1 AAAAAGA
20583 AAAAAGA
1 AAAAAGA
20590 AAAAAGA
1 AAAAAGA
20597 AAAGAAGCA
1 AAA-AAG-A
20606 AAAAAGA
1 AAAAAGA
*
20613 AGAAA-A
1 AAAAAGA
*
20619 CAAAAGA
1 AAAAAGA
20626 AAAAAGA
1 AAAAAGA
* *
20633 AAGAA-C
1 AAAAAGA
**
20639 AAAAATC
1 AAAAAGA
20646 AAAAAGA
1 AAAAAGA
20653 AAAA
1 AAAA
20657 GGGATAAAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
6 8 0.13
7 43 0.70
8 6 0.10
9 4 0.07
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.01
Consensus pattern (7 bp):
AAAAAGA
Found at i:20608 original size:23 final size:24
Alignment explanation
Indices: 20582--20626 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
20572 GAACAAAAAG
*
20582 AAAAAAGAA-AAAAGAAAAGAAGC
1 AAAAAAGAAGAAAACAAAAGAAGC
20605 AAAAAAGAAGAAAACAAAAGAA
1 AAAAAAGAAGAAAACAAAAGAA
20627 AAAAGAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (24 bp):
AAAAAAGAAGAAAACAAAAGAAGC
Found at i:20643 original size:20 final size:20
Alignment explanation
Indices: 20570--20654 Score: 82
Period size: 20 Copynumber: 4.1 Consensus size: 20
20560 AAGATTCAAT
*
20570 AAGAACAAAAAGAAAAAAGA
1 AAGAAAAAAAAGAAAAAAGA
*
20590 AAAAAGAAAAGAAGCAAAAAAG-
1 AAGAA-AAAA-AAG-AAAAAAGA
20612 AAGAAAACAAAAGAAAAAAGA
1 AAGAAAA-AAAAGAAAAAAGA
* **
20633 AAGAACAAAAATCAAAAAGA
1 AAGAAAAAAAAGAAAAAAGA
20653 AA
1 AA
20655 AAGGGATAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
20 24 0.44
21 14 0.26
22 9 0.17
23 7 0.13
ACGTcount: A:0.79, C:0.06, G:0.14, T:0.01
Consensus pattern (20 bp):
AAGAAAAAAAAGAAAAAAGA
Found at i:22835 original size:317 final size:317
Alignment explanation
Indices: 22255--23211 Score: 1515
Period size: 317 Copynumber: 3.0 Consensus size: 317
22245 ATATCGTGCC
* * *
22255 ACTCGAGACAACACAAGTTCAACCTCACGACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
* *
22320 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACT
* * *
22385 TCACGACGAAGAGACCGTTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
* *
22450 ACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
196 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTG
22515 TCAATAAACAACTTCCCAATTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
261 TCAATAAACAACTTCCCAATTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* **
22572 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTTTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
22637 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACT
* *
22702 TCACGACGAAGGGACCGCTGGTTGTTAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
*
22767 ATAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTG
196 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTG
* * **
22832 TCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA-AAAAGGATATTGG
261 TCAATAAACAACTTCCCAATTT-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
22889 ACTCCAGACAACGCAAGTTCAACTTCACAAACGAAGGGACGGCTTGTTGTCAACAAACAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCAC-GACGAAGGGACGGCTGGTTGTCAACAAACAACTTCC
* *
22954 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTTAAC
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAAC
* * * *
23019 TTCACAACGAAGGGACAGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTT
130 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTT
* ** * *
23084 CACAGCGAAGGATATTGGACTCGAGACAATACAAGTTCAACTTCACAACT-AAGGGACGGCTGGT
195 CACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA-TGAAGGGACCGCTGGT
* * * *
23148 TGTCAATAAACAATTTCCCAGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
259 TGTCAATAAACAACTTCCCAATT-TAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
23208 ACTC
1 ACTC
23212 GGAACAAGGC
Statistics
Matches: 587, Mismatches: 47, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
317 303 0.52
318 269 0.46
319 15 0.03
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (317 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACT
TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTG
TCAATAAACAACTTCCCAATTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:23212 original size:106 final size:106
Alignment explanation
Indices: 22255--23211 Score: 1504
Period size: 106 Copynumber: 9.0 Consensus size: 106
22245 ATATCGTGCC
* * * *
22255 ACTCGAGACAACACAAGTTCAACCTCACGACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
22320 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
22361 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGAGACCGTTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
22426 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
22467 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
22532 AATTT-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
**
22572 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTTTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
22637 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
22678 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
22743 AATTTCAGAGCCAATTTCAACTTCATAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
22784 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
22849 AATTTCAGAGCCAATTTCAACTTCACAA-AAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
22889 ACTCCAGACAACGCAAGTTCAACTTCACAAACGAAGGGACGGCTTGTTGTCAACAAACAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCAC-GACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC
22954 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
22996 ACTCGAGACAACACAAGTTTAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
23061 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* ** * * * * *
23102 ACTCGAGACAATACAAGTTCAACTTCACAACTAAGGGACGGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
23167 AGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
23208 ACTC
1 ACTC
23212 GGAACAAGGC
Statistics
Matches: 791, Mismatches: 57, Indels: 6
0.93 0.07 0.01
Matches are distributed among these distances:
105 140 0.18
106 615 0.78
107 36 0.05
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:24012 original size:37 final size:37
Alignment explanation
Indices: 23961--24057 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
23951 CATTTTCGTC
23961 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
23998 TTACTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** *
24035 CTACTATTATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
24058 TATATGATCC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:24821 original size:26 final size:27
Alignment explanation
Indices: 24791--24909 Score: 82
Period size: 25 Copynumber: 4.7 Consensus size: 27
24781 TTTATTTTTC
24791 ATTTATTTATTATTATTATTAT-TACT
1 ATTTATTTATTATTATTATTATATACT
*
24817 ATTTA-ATATT-TTA-TA-TATATACAT
1 ATTTATTTATTATTATTATTATATAC-T
* *
24841 ACATT-TTTA-TATTTTTA-TATATA-T
1 A-TTTATTTATTATTATTATTATATACT
*
24865 ATATATTTTATTATT-TTATT-TATACT
1 ATTTA-TTTATTATTATTATTATATACT
24891 ATTTATTTATT-TTCATTAT
1 ATTTATTTATTATT-ATTAT
24910 ATTTTTAGTT
Statistics
Matches: 73, Mismatches: 7, Indels: 26
0.69 0.07 0.25
Matches are distributed among these distances:
22 3 0.04
23 6 0.08
24 10 0.14
25 27 0.37
26 27 0.37
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (27 bp):
ATTTATTTATTATTATTATTATATACT
Found at i:24975 original size:31 final size:30
Alignment explanation
Indices: 24935--25003 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
24925 GCTCTTATTA
*
24935 TTATTTTTTTTTAAAAATACTTTATCTTTT
1 TTATTTTTTTGTAAAAATACTTTATCTTTT
* * * *
24965 TTATTCTTTTTGTATATATATTTTATCTTCAT
1 TTATT-TTTTTGTAAAAATACTTTATCTT-TT
24997 TTATTTT
1 TTATTTT
25004 ATTTTATTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
30 5 0.16
31 21 0.66
32 6 0.19
ACGTcount: A:0.23, C:0.07, G:0.01, T:0.68
Consensus pattern (30 bp):
TTATTTTTTTGTAAAAATACTTTATCTTTT
Found at i:25019 original size:24 final size:24
Alignment explanation
Indices: 24992--25074 Score: 64
Period size: 24 Copynumber: 3.5 Consensus size: 24
24982 ATATTTTATC
24992 TTCATTTATTTTATTTTATTCAAT
1 TTCATTTATTTTATTTTATTCAAT
* * * *
25016 TTCATTTTTTTTGTTTCATCCAA-
1 TTCATTTATTTTATTTTATTCAAT
**
25039 TT-ATTTTATGTTTATTATTATT-GGT
1 TTCA-TTTAT-TTTATT-TTATTCAAT
25064 TTCATTTATTT
1 TTCATTTATTT
25075 CCTTGATTTA
Statistics
Matches: 44, Mismatches: 10, Indels: 10
0.69 0.16 0.16
Matches are distributed among these distances:
22 1 0.02
23 6 0.14
24 26 0.59
25 10 0.23
26 1 0.02
ACGTcount: A:0.20, C:0.08, G:0.05, T:0.66
Consensus pattern (24 bp):
TTCATTTATTTTATTTTATTCAAT
Found at i:25661 original size:39 final size:40
Alignment explanation
Indices: 25605--25730 Score: 150
Period size: 39 Copynumber: 3.2 Consensus size: 40
25595 GAAGCAGCAG
*
25605 TTATAACACTATGTTGGACACAACATTTCACCCTCCAATT
1 TTATAACACTAAGTTGGACACAACATTTCACCCTCCAATT
* *
25645 TTATAATAC-AAGTTGGAGACAACATTTCACCCTCCAATT
1 TTATAACACTAAGTTGGACACAACATTTCACCCTCCAATT
* * * *
25684 TTATCACACTAAGTT-G-CATAACATTTCACACGCCAATT
1 TTATAACACTAAGTTGGACACAACATTTCACCCTCCAATT
*
25722 CTAATAACA
1 -TTATAACA
25731 AACCCAAGGC
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
38 18 0.25
39 42 0.58
40 13 0.18
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.31
Consensus pattern (40 bp):
TTATAACACTAAGTTGGACACAACATTTCACCCTCCAATT
Found at i:28829 original size:2 final size:2
Alignment explanation
Indices: 28822--28855 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28812 TAATTACTTA
28822 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
28856 GAATTGTAAT
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:31164 original size:2 final size:2
Alignment explanation
Indices: 31157--31234 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
31147 ATGGGTGTTA
31157 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
31199 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
31235 TAAAGTAAAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32063 original size:26 final size:25
Alignment explanation
Indices: 32000--32058 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
31990 AATATATTTT
*
32000 TATTTTTTGATTAACTTAAAAGAATA
1 TATTTTTTTATTAAC-TAAAAGAATA
*
32026 TATTTTGTTATTAA-TAAAAGAATA
1 TATTTTTTTATTAACTAAAAGAATA
32050 -ATTCTTTTT
1 TATT-TTTTT
32059 TTATTGACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 3 0.10
24 14 0.48
26 12 0.41
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (25 bp):
TATTTTTTTATTAACTAAAAGAATA
Found at i:32719 original size:3 final size:3
Alignment explanation
Indices: 32711--32755 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
32701 AATTTTTTCT
*
32711 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
32756 CCCATTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:34021 original size:17 final size:17
Alignment explanation
Indices: 34009--34044 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
33999 AATGGAATTT
34009 TGGTCGAAATGGAACGA
1 TGGTCGAAATGGAACGA
34026 TGGTCGAAATGGAACGA
1 TGGTCGAAATGGAACGA
34043 TG
1 TG
34045 CTCCAACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.11, G:0.36, T:0.19
Consensus pattern (17 bp):
TGGTCGAAATGGAACGA
Found at i:40005 original size:28 final size:28
Alignment explanation
Indices: 39962--40045 Score: 150
Period size: 28 Copynumber: 3.0 Consensus size: 28
39952 ATATATTTAT
* *
39962 ATGGTTATATGGTTGATGATTCAAGTGA
1 ATGGTTATATGATTGATGATACAAGTGA
39990 ATGGTTATATGATTGATGATACAAGTGA
1 ATGGTTATATGATTGATGATACAAGTGA
40018 ATGGTTATATGATTGATGATACAAGTGA
1 ATGGTTATATGATTGATGATACAAGTGA
40046 GTCACTTTCC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (28 bp):
ATGGTTATATGATTGATGATACAAGTGA
Found at i:48749 original size:2 final size:2
Alignment explanation
Indices: 48742--48787 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
48732 ATTCACCGAG
48742 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
48784 AT AT
1 AT AT
48788 GAGATAAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50411 original size:30 final size:30
Alignment explanation
Indices: 50375--50446 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
50365 GGGAAGATAA
*
50375 GAAGATGAGAGGGAAGAGAAGAAACGGAGT
1 GAAGATGAGAGGGAAGAGAAGAAACAGAGT
50405 GAAGATGAGAGGGAAGAGAAGAAACAGAGT
1 GAAGATGAGAGGGAAGAGAAGAAACAGAGT
50435 GAAGATGAGAGG
1 GAAGATGAGAGG
50447 AAAAATCATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.47, C:0.03, G:0.43, T:0.07
Consensus pattern (30 bp):
GAAGATGAGAGGGAAGAGAAGAAACAGAGT
Found at i:51662 original size:138 final size:137
Alignment explanation
Indices: 51539--51786 Score: 367
Period size: 138 Copynumber: 1.8 Consensus size: 137
51529 AATATATTAT
*
51539 TAAA-TAAAACAAATGAATAGAAATAAATATACAGATAATAATAAAA-G-AAAAAATATATGTTT
1 TAAAGTAAAACAAA-AAATAGAAA-AAATATACAGATAATAATAAAAGGAAAAAAATATATGTTT
* *
51601 ATATACGCTATCAATAATACTTAAAATAATAAAATTAACGATGGTTATGTATAGAGATAAATAAA
64 ATATACGCTATCAATAATACTTAAAATAATAAAAATAACGATGATTATGTATAGAGATAAATAAA
51666 ATAAATACA
129 ATAAATACA
** * * *
51675 TAAAGTAAATGAAAAAATATAAAGAATATACATATAATAATAAAAGGGAAAAAAATATATGTTTA
1 TAAAGTAAAACAAAAAATAGAAAAAATATACAGATAATAATAAAA-GGAAAAAAATATATGTTTA
*
51740 TATACGCTATCAATGATACTTAAAATAATAAAAATAACGATGATTAT
65 TATACGCTATCAATAATACTTAAAATAATAAAAATAACGATGATTAT
51787 ATGTATATAT
Statistics
Matches: 99, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
135 20 0.20
136 11 0.11
137 8 0.08
138 60 0.61
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.28
Consensus pattern (137 bp):
TAAAGTAAAACAAAAAATAGAAAAAATATACAGATAATAATAAAAGGAAAAAAATATATGTTTAT
ATACGCTATCAATAATACTTAAAATAATAAAAATAACGATGATTATGTATAGAGATAAATAAAAT
AAATACA
Found at i:51864 original size:48 final size:46
Alignment explanation
Indices: 51790--51894 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 46
51780 TGATTATATG
*
51790 TATATATATATATGTATAATAAAATAAAATAAAA-ATATACAT-AAAA
1 TATATATATATATATATAATAAAATAAAATAAAATA-ATA-ATGAAAA
*
51836 TATATATATATATATA-AATAAAGGAATAAAATATAATAATAATGAAAA
1 TATATATATATATATATAAT-AA--AATAAAATAAAATAATAATGAAAA
51884 TATAGTATATA
1 TATA-TATATA
51895 ATAATAGTAG
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
45 3 0.06
46 17 0.33
47 2 0.04
48 22 0.43
49 7 0.14
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (46 bp):
TATATATATATATATATAATAAAATAAAATAAAATAATAATGAAAA
Found at i:53763 original size:105 final size:105
Alignment explanation
Indices: 53640--54414 Score: 1505
Period size: 105 Copynumber: 7.4 Consensus size: 105
53630 GTATTGTTCA
53640 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
53705 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
53745 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
53810 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
53850 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
*
53915 CAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
53955 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
54020 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
54060 TAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
54125 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
54165 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
54230 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
54270 TAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
54335 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
54375 TAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
54415 GGTGAAACCT
Statistics
Matches: 663, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 663 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:54620 original size:12 final size:12
Alignment explanation
Indices: 54603--54663 Score: 108
Period size: 12 Copynumber: 5.2 Consensus size: 12
54593 AAATGTTTGA
54603 TGATTTTTTTTT
1 TGATTTTTTTTT
54615 TGA-TTTTTTTT
1 TGATTTTTTTTT
54626 TGATTTTTTTTT
1 TGATTTTTTTTT
54638 TGA-TTTTTTTT
1 TGATTTTTTTTT
54649 TGATTTTTTTTT
1 TGATTTTTTTTT
54661 TGA
1 TGA
54664 AGATGCTCCT
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
11 22 0.47
12 25 0.53
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (12 bp):
TGATTTTTTTTT
Found at i:54623 original size:11 final size:11
Alignment explanation
Indices: 54607--54660 Score: 99
Period size: 11 Copynumber: 4.8 Consensus size: 11
54597 GTTTGATGAT
54607 TTTTTTTTTGA
1 TTTTTTTTTGA
54618 TTTTTTTTTGA
1 TTTTTTTTTGA
54629 TTTTTTTTTTGA
1 -TTTTTTTTTGA
54641 TTTTTTTTTGA
1 TTTTTTTTTGA
54652 TTTTTTTTT
1 TTTTTTTTT
54661 TGAAGATGCT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
11 31 0.74
12 11 0.26
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTGA
Found at i:54632 original size:23 final size:23
Alignment explanation
Indices: 54603--54663 Score: 122
Period size: 23 Copynumber: 2.7 Consensus size: 23
54593 AAATGTTTGA
54603 TGATTTTTTTTTTGATTTTTTTT
1 TGATTTTTTTTTTGATTTTTTTT
54626 TGATTTTTTTTTTGATTTTTTTT
1 TGATTTTTTTTTTGATTTTTTTT
54649 TGATTTTTTTTTTGA
1 TGATTTTTTTTTTGA
54664 AGATGCTCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (23 bp):
TGATTTTTTTTTTGATTTTTTTT
Found at i:55317 original size:64 final size:64
Alignment explanation
Indices: 55194--55318 Score: 142
Period size: 64 Copynumber: 2.0 Consensus size: 64
55184 CTTTTTCCTC
* * * *** *
55194 TTTTTTCTTTTTTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCCAAACGTTTTTTTTCTTTTT
1 TTTTTTCTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCCAAACGAAGTATTTCTTTTT
* * * * *
55258 TTTTTTTTTTTTTTAACTTAGGACGCCCTCTCGGGTTTTCATCCTAAGCGAAGTATTTCTT
1 TTTTTTCTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCCAAACGAAGTATTTCTT
55319 GACTGCGTCC
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
64 49 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.52
Consensus pattern (64 bp):
TTTTTTCTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCCAAACGAAGTATTTCTTTTT
Found at i:64724 original size:20 final size:20
Alignment explanation
Indices: 64686--64729 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
64676 ATGGTTAGTA
*
64686 AAATAAAAATAAATGGAAAT
1 AAATAAAAATAAATAGAAAT
64706 AAATAAAAATAACA-AGAAAT
1 AAATAAAAATAA-ATAGAAAT
64726 AAAT
1 AAAT
64730 GGCAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (20 bp):
AAATAAAAATAAATAGAAAT
Found at i:66473 original size:2 final size:2
Alignment explanation
Indices: 66456--66494 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
66446 ATAAAATAAA
* *
66456 AT AT AC AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
66495 AAGGATAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:72394 original size:10 final size:11
Alignment explanation
Indices: 72381--72416 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
72371 TTGCAAAAGG
72381 TTATAA-AAAA
1 TTATAATAAAA
72391 TTATAATAAAA
1 TTATAATAAAA
72402 TT-TAATAAAA
1 TTATAATAAAA
72412 -TATAA
1 TTATAA
72417 ATTATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 1 0.04
10 17 0.71
11 6 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TTATAATAAAA
Found at i:73393 original size:179 final size:182
Alignment explanation
Indices: 73073--73728 Score: 858
Period size: 182 Copynumber: 3.6 Consensus size: 182
73063 ATACAAATGA
* * * * * * * * *
73073 AAAATGGATCGCTCCATAGCAATATTACAGGTACAAATATGACAAAACCGGTC-CCAAAATGACA
1 AAAATGTATCGATCCAAAACAATATAACAGGTAAAAATATGATAAAACCAGTCTCAAAAATGACA
* * * *
73137 AAACTGGTAAAACGCTACCAGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGAAACTTT
66 AAACCGGTAAAAAGTTACCAGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
* * * *
73202 CTGAATTTAAAAGAGAAGAAGTTATAGAGCCTATAAAGCGTCGATACTTTA-
131 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAG
** * *
73253 AAAAAATATCGATCCACAACAATATTACAGGT-AAAATATGATAAAACCAGTCTCAAAAATGACA
1 AAAATGTATCGATCCAAAACAATATAACAGGTAAAAATATGATAAAACCAGTCTCAAAAATGACA
** *
73317 AAACCGG-AAAAAGTTACTGGATATATTGAAAGTGTCGATAATTTAATATTAGTATCGACACTTT
66 AAACCGGTAAAAAGTTACCAGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
*
73381 CTGAATTTAAAAGAGAAGAAGTTATAGCGTCTAAAAAGTGTCGACACTTTATG
131 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTA-G
** * * *
73434 AAAATGTATCGATCCTTACCAATATAACAGGTAAAAATATGATAAAA-TATGTCTAAAAAATGAC
1 AAAATGTATCGATCCAAAACAATATAACAGGTAAAAATATGATAAAACCA-GTCTCAAAAATGAC
* * * *
73498 AAAACCGG-AAAAAGATACCGGATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACACTT
65 AAAACCGGTAAAAAGTTACCAGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
* *
73562 TCTTAATTTAAAAGAGAAGAAGTTATAGCGCTTAAAAAGTGTCGACACTTTATG
130 TCTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTA-G
* *
73616 AAAATGTATCGATCCAAAACAATATAACAGGTAAAAATATGATAAAATCGGTCTC-AAAATGACA
1 AAAATGTATCGATCCAAAACAATATAACAGGTAAAAATATGATAAAACCAGTCTCAAAAATGACA
* * * *
73680 AAGCCGGTAAATAGTTACCAGATATGTTGAAAGTGTCGATACTTTAATA
66 AAACCGGTAAAAAGTTACCAGATATATTGAAAGTGTCGATAATTTAATA
73729 AGTACGCGTA
Statistics
Matches: 419, Mismatches: 50, Indels: 12
0.87 0.10 0.02
Matches are distributed among these distances:
179 114 0.27
180 42 0.10
181 42 0.10
182 221 0.53
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAATGTATCGATCCAAAACAATATAACAGGTAAAAATATGATAAAACCAGTCTCAAAAATGACA
AAACCGGTAAAAAGTTACCAGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGACACTTTAG
Found at i:74134 original size:18 final size:19
Alignment explanation
Indices: 74111--74155 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
74101 TAGTTAATAT
74111 TTATAGGTA-AAAATGATA
1 TTATAGGTAGAAAATGATA
74129 TTATAGGTAGAAAATGATA
1 TTATAGGTAGAAAATGATA
*
74148 TTTTAGGT
1 TTATAGGT
74156 TGTATAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (19 bp):
TTATAGGTAGAAAATGATA
Found at i:75451 original size:22 final size:22
Alignment explanation
Indices: 75401--75455 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
75391 AATGTTTTTG
75401 TTTT-TTATATAAAATGATAGTA
1 TTTTATTATATAAAATGATAG-A
*
75423 TAGTTATTATATAAAATGATA-A
1 T-TTTATTATATAAAATGATAGA
75445 CTTTTATTATA
1 -TTTTATTATA
75456 AATGCAGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 10 0.36
23 3 0.11
24 15 0.54
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (22 bp):
TTTTATTATATAAAATGATAGA
Done.