Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000940.1 Hibiscus syriacus cultivar Beakdansim tig00001878_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: 108592
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:16371 original size:31 final size:31
Alignment explanation
Indices: 16298--16363 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
16288 CAAACAGTCA
* *
16298 GGGACCATATTGCAAATAGACTAAATGTTTG
1 GGGACCATATTGCAAACAGACTAAATGTTAG
16329 GGGACCATATTGCAAACAGACTAAATGTTAG
1 GGGACCATATTGCAAACAGACTAAATGTTAG
16360 GGGA
1 GGGA
16364 TTGTATTGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (31 bp):
GGGACCATATTGCAAACAGACTAAATGTTAG
Found at i:19789 original size:2 final size:2
Alignment explanation
Indices: 19782--19811 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19772 TGCAAGCTTA
19782 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
19812 TGATGATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20083 original size:14 final size:14
Alignment explanation
Indices: 20064--20105 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
20054 TCGGATGCTC
20064 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
20078 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
20092 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
20106 ATGCCCAGCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.07, C:0.29, G:0.43, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:20108 original size:10 final size:10
Alignment explanation
Indices: 20044--20077 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
20034 CATAGCTCGG
20044 TCGGATGGCC
1 TCGGATGGCC
20054 TCGGAT-GCTC
1 TCGGATGGC-C
20064 TCGGATGGCC
1 TCGGATGGCC
20074 TCGG
1 TCGG
20078 TCGGATGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 18 0.82
11 2 0.09
ACGTcount: A:0.09, C:0.29, G:0.38, T:0.24
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:23727 original size:12 final size:12
Alignment explanation
Indices: 23696--23721 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
23686 GAACTTCTAC
23696 GATGAAGAAGGA
1 GATGAAGAAGGA
23708 GATGAAGAAGGA
1 GATGAAGAAGGA
23720 GA
1 GA
23722 GAAAGAGGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.42, T:0.08
Consensus pattern (12 bp):
GATGAAGAAGGA
Found at i:27090 original size:2 final size:2
Alignment explanation
Indices: 27083--27109 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27073 AAATATTTGG
27083 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 A
27110 AAAGTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33127 original size:27 final size:27
Alignment explanation
Indices: 33074--33128 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
33064 TATGTTGGAA
* * *
33074 AATAAATTTATAAAAAATTATAGGAAT
1 AATAAAGTTATAAAAAATTAAAAGAAT
**
33101 AATAAAGTTATAAAATCTTAAAAGAAT
1 AATAAAGTTATAAAAAATTAAAAGAAT
33128 A
1 A
33129 CAAATATATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (27 bp):
AATAAAGTTATAAAAAATTAAAAGAAT
Found at i:43099 original size:60 final size:59
Alignment explanation
Indices: 43025--43136 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 59
43015 AATGATATCC
** *
43025 TAATTATAGGGTGTTGTTTTGTTGAGTCTC-CCGACTATTAAAAAATACTAAATAATCCTT
1 TAATTATAGGGTGTTACTTTGTTGAGT-TCACCAACTATTAAAAAATAC-AAATAATCCTT
* *
43085 TAATTATAGTGTGTTACTTTGTTGAGTTCACCAACTATTAAAAATTACAAAT
1 TAATTATAGGGTGTTACTTTGTTGAGTTCACCAACTATTAAAAAATACAAAT
43137 GATCACTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
59 6 0.13
60 40 0.87
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (59 bp):
TAATTATAGGGTGTTACTTTGTTGAGTTCACCAACTATTAAAAAATACAAATAATCCTT
Found at i:44656 original size:21 final size:21
Alignment explanation
Indices: 44632--44671 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
44622 CCCTAAATTA
*
44632 TAAACATTAAACACTAAACCC
1 TAAACACTAAACACTAAACCC
* *
44653 TAAACCCTAAACCCTAAAC
1 TAAACACTAAACACTAAAC
44672 TCCAACTTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (21 bp):
TAAACACTAAACACTAAACCC
Found at i:48129 original size:42 final size:42
Alignment explanation
Indices: 48070--48189 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
48060 TTTCCCCGAA
*
48070 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
*
48112 TTCCCATGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
48154 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
48190 TGTAATTCAT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:48419 original size:21 final size:21
Alignment explanation
Indices: 48378--48419 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
48368 TAATTATTAA
*
48378 AATATTTAAAATATATTTATT
1 AATATTTAAAATATATATATT
*
48399 AATATTTATAATA-ATAATATT
1 AATATTTAAAATATAT-ATATT
48420 GTATTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATATTTAAAATATATATATT
Found at i:48453 original size:29 final size:30
Alignment explanation
Indices: 48389--48463 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 30
48379 ATATTTAAAA
48389 TATATTTATTAATATTTATAATAATAATAT
1 TATATTTATTAATATTTATAATAATAATAT
*
48419 TGTATTT-TTAATA-TTATAA-AATAATCAAT
1 TATATTTATTAATATTTATAATAATAAT--AT
*
48448 TATATTATAATAATAT
1 TATATT-TATTAATAT
48464 AAGATATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
27 6 0.16
28 6 0.16
29 13 0.35
30 7 0.19
31 5 0.14
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (30 bp):
TATATTTATTAATATTTATAATAATAATAT
Found at i:48544 original size:29 final size:29
Alignment explanation
Indices: 48448--48547 Score: 100
Period size: 28 Copynumber: 3.5 Consensus size: 29
48438 AATAATCAAT
* * *
48448 TATATTATAATAATATAA-GATATTATTTT
1 TATATT-TAATAATAGAATAATATTATTTA
* *
48477 TAT-TTTAATAATATAATAA-ATTTTTTTA
1 TATATTTAATAATAGAATAATA-TTATTTA
48505 TATATTTAATAAT-GAATAATATTATTTA
1 TATATTTAATAATAGAATAATATTATTTA
48533 TATATTTCAATAATA
1 TATATTT-AATAATA
48548 TTTTAGTAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
27 12 0.20
28 29 0.48
29 19 0.32
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (29 bp):
TATATTTAATAATAGAATAATATTATTTA
Found at i:48792 original size:20 final size:20
Alignment explanation
Indices: 48714--48783 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
48704 TTTCCAGATG
48714 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
48734 TTTTTCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
48754 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
48774 TTTTCCAGAA
1 TTTTCCAGAA
48784 TTCAAATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:48792 original size:40 final size:40
Alignment explanation
Indices: 48714--48792 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
48704 TTTCCAGATG
* * **
48714 TTTTCCAGAAATGTAATTCATTTTTCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
48754 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
48793 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:48802 original size:15 final size:15
Alignment explanation
Indices: 48766--48847 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
48756 TTACAGAAAT
**
48766 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
48781 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
48795 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
48810 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
48825 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
48840 GTAATTCA
1 GTAATTCA
48848 TTTTCTGGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:48818 original size:30 final size:30
Alignment explanation
Indices: 48766--48847 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
48756 TTACAGAAAT
48766 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
48795 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
48825 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
48848 TTTTCTGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:48840 original size:45 final size:44
Alignment explanation
Indices: 48766--48852 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
48756 TTACAGAAAT
**
48766 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
48810 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTTC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTC
48853 TGGAAAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:49625 original size:31 final size:31
Alignment explanation
Indices: 49579--49648 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
49569 ATTTTAAATG
* * *
49579 TAACAAACTGGTTACTAACATTATCAATTTA
1 TAACAAATTGATTACTAACATCATCAATTTA
** **
49610 TAACAAATTGATTACTGTCATCATTGATTTA
1 TAACAAATTGATTACTAACATCATCAATTTA
49641 TAACAAAT
1 TAACAAAT
49649 CAGTCATTCA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.37
Consensus pattern (31 bp):
TAACAAATTGATTACTAACATCATCAATTTA
Found at i:59415 original size:77 final size:78
Alignment explanation
Indices: 59277--59440 Score: 251
Period size: 77 Copynumber: 2.1 Consensus size: 78
59267 GTTCCTACTT
* ** *
59277 TAGTTTTTCATGAATAGATCGAGATAGAGATTAACAAGGTGATTATTCTTGAAAATTTTAAATTT
1 TAGTTTTTCATGAATAGATAGAGATAGAGACCAAC-AGGTGATTATTCTTGAAAATTTTAAAATT
59342 TTATATAATTTAAA
65 TTATATAATTTAAA
*
59356 TAGTTTTTCATGAATGGATAGAGATAGAGACCAAC-GGTGATTATTCTTGAAAATTTTAAAATTT
1 TAGTTTTTCATGAATAGATAGAGATAGAGACCAACAGGTGATTATTCTTGAAAATTTTAAAATTT
59420 TATATAATTTAAA
66 TATATAATTTAAA
59433 -ATGTTTTT
1 TA-GTTTTT
59441 ATTAATATTT
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
76 1 0.01
77 47 0.59
79 31 0.39
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (78 bp):
TAGTTTTTCATGAATAGATAGAGATAGAGACCAACAGGTGATTATTCTTGAAAATTTTAAAATTT
TATATAATTTAAA
Found at i:60745 original size:83 final size:83
Alignment explanation
Indices: 60651--60805 Score: 247
Period size: 83 Copynumber: 1.9 Consensus size: 83
60641 AACTTGAAAT
* * **
60651 TTTTTTGAGTCGAGTTGAATTTATGAAATTACAACTTGAAGTTAATTTGAGTCAAATTTCCACGA
1 TTTTTCGAGTCGAGTCGAATTTATGAAATTACAACTTGAAGTTAATTCAAGTCAAATTTCCACGA
60716 GTCGAGTCTAAAAACCAA
66 GTCGAGTCTAAAAACCAA
* * *
60734 TTTTTCGAGTCGAGTCGAGTTTATGAAATTACAACTTGAAGTTAATTCAAGTCAAGTTTTCACGA
1 TTTTTCGAGTCGAGTCGAATTTATGAAATTACAACTTGAAGTTAATTCAAGTCAAATTTCCACGA
60799 GTCGAGT
66 GTCGAGT
60806 AAAGTCGAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 65 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (83 bp):
TTTTTCGAGTCGAGTCGAATTTATGAAATTACAACTTGAAGTTAATTCAAGTCAAATTTCCACGA
GTCGAGTCTAAAAACCAA
Found at i:64926 original size:17 final size:17
Alignment explanation
Indices: 64904--64940 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
64894 GGATTCAAAA
*
64904 GATTATATTTAGAACTT
1 GATTATATATAGAACTT
64921 GATTATATATAGAACTT
1 GATTATATATAGAACTT
64938 GAT
1 GAT
64941 ATCACTTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (17 bp):
GATTATATATAGAACTT
Found at i:69569 original size:13 final size:13
Alignment explanation
Indices: 69551--69582 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
69541 TCTCATTTGG
69551 TCTCTCTGCGCTC
1 TCTCTCTGCGCTC
69564 TCTCTCTGCGCTC
1 TCTCTCTGCGCTC
69577 TCTCTC
1 TCTCTC
69583 GTCTCTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.47, G:0.12, T:0.41
Consensus pattern (13 bp):
TCTCTCTGCGCTC
Found at i:70552 original size:3 final size:3
Alignment explanation
Indices: 70544--70575 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
70534 AAAAATGAAA
70544 AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT A
70576 TATATATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:70568 original size:22 final size:22
Alignment explanation
Indices: 70547--70591 Score: 69
Period size: 19 Copynumber: 2.2 Consensus size: 22
70537 AATGAAAAAT
70547 AATAATAATA-ATA-ATA-ATA
1 AATAATAATATATATATACATA
70566 AATAATAATATATATATACATA
1 AATAATAATATATATATACATA
70588 AATA
1 AATA
70592 TTTTCAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.43
20 3 0.13
21 3 0.13
22 7 0.30
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAATAATATATATATACATA
Found at i:70714 original size:71 final size:73
Alignment explanation
Indices: 70638--70827 Score: 218
Period size: 71 Copynumber: 2.7 Consensus size: 73
70628 TTTTTTTCTT
* * *
70638 AAACTATATAATATACGAATGTTTTCAACATGTTTTCAAAA-ATATTATATAAGTTTTCAAAAAC
1 AAACTATATAATATACAAATGTTTTCAAAATGTTTTCAAAACATAATATATAAGTTTTCAAAAAC
70702 GTTTT-AA
66 GTTTTCAA
* **
70709 AAACTATATAATATATAAATGTTTTCAAAATGTTTTCAAAACTATAATATATGTGTTTTCAAAAA
1 AAACTATATAATATACAAATGTTTTCAAAATGTTTTCAAAAC-ATAATATATAAGTTTTCAAAAA
*
70774 TGTTTTCAA
65 CGTTTTCAA
* *
70783 AAA-T-TAT-ATATA-TAAT-TTTTCAAAATGATTTT-AAAA-ATTATATAT
1 AAACTATATAATATACAAATGTTTTCAAAATG-TTTTCAAAACATAATATAT
70828 TATATATATT
Statistics
Matches: 106, Mismatches: 9, Indels: 12
0.83 0.07 0.09
Matches are distributed among these distances:
67 8 0.08
69 15 0.14
70 7 0.07
71 43 0.41
72 3 0.03
73 25 0.24
74 5 0.05
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (73 bp):
AAACTATATAATATACAAATGTTTTCAAAATGTTTTCAAAACATAATATATAAGTTTTCAAAAAC
GTTTTCAA
Found at i:70741 original size:11 final size:11
Alignment explanation
Indices: 70725--70749 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
70715 TATAATATAT
70725 AAATGTTTTCA
1 AAATGTTTTCA
70736 AAATGTTTTCA
1 AAATGTTTTCA
70747 AAA
1 AAA
70750 CTATAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:70779 original size:12 final size:12
Alignment explanation
Indices: 70762--70786 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
70752 ATAATATATG
70762 TGTTTTCAAAAA
1 TGTTTTCAAAAA
70774 TGTTTTCAAAAA
1 TGTTTTCAAAAA
70786 T
1 T
70787 TATATATATA
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:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TGTTTTCAAAAA
Found at i:70825 original size:34 final size:34
Alignment explanation
Indices: 70655--70827 Score: 176
Period size: 34 Copynumber: 4.9 Consensus size: 34
70645 ATAATATACG
*
70655 AATGTTTTCAACATGTTTTCAAAAA-TAT-TATAT
1 AATGTTTTCAAAATGTTTT-AAAAATTATATATAT
*
70688 AA-GTTTTCAAAAACGTTTTAAAAACTATATAATATAT
1 AATGTTTTC-AAAATGTTTTAAAAA-T-TAT-ATATAT
* *
70725 AAATGTTTTCAAAATGTTTTCAAAACTATA-ATAT
1 -AATGTTTTCAAAATGTTTTAAAAATTATATATAT
*
70759 ATGTGTTTTCAAAAATGTTTTCAAAAATTATATATAT
1 A-ATGTTTTC-AAAATGTTTT-AAAAATTATATATAT
70796 AAT-TTTTCAAAATGATTTTAAAAATTATATAT
1 AATGTTTTCAAAATG-TTTTAAAAATTATATAT
70828 TATATATATT
Statistics
Matches: 118, Mismatches: 9, Indels: 25
0.78 0.06 0.16
Matches are distributed among these distances:
32 11 0.09
33 11 0.09
34 30 0.25
35 23 0.19
36 12 0.10
37 10 0.08
38 15 0.13
39 6 0.05
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (34 bp):
AATGTTTTCAAAATGTTTTAAAAATTATATATAT
Found at i:71919 original size:166 final size:166
Alignment explanation
Indices: 71526--72509 Score: 1746
Period size: 166 Copynumber: 6.0 Consensus size: 166
71516 CTTGCCATGA
* * * * * *
71526 TAAATGATATGACTTCGAAGTTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAGCCCTTCTT
1 TAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTC
* * *
71591 GACTTAAGCTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
66 GACTTAAGCTATTCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTGG
* * *
71656 TTGG---CAGATAACCCTTCTTGACTTAAGTTATGCTG
130 -TGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTG
* *
71691 CAAATGGTGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTC
1 TAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTC
* *
71756 GACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGGT
66 GACTTAAGCTATTCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGT
71821 GGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTG
131 GGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTG
71857 TAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTC
1 TAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTC
71922 GACTTAAGCTATTCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGT
66 GACTTAAGCTATTCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGT
71987 GGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTG
131 GGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTG
72023 TAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTC
1 TAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTC
72088 GACTTAAGCTATTCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGT
66 GACTTAAGCTATTCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGT
72153 GGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTG
131 GGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTG
72189 TAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTC
1 TAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTC
72254 GACTTAAGCTATTCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGT
66 GACTTAAGCTATTCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGT
72319 GGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTG
131 GGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTG
72355 TAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTC
1 TAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTC
72420 GACTTAAGCTATTCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGT
66 GACTTAAGCTATTCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGT
* *
72485 GG---CAGATAGCCCTTCTGGCCTTGAG
131 GGTCACAGATAACCCTTCTAGCCTTGAG
72510 CTAAGCTGCA
Statistics
Matches: 796, Mismatches: 20, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
163 24 0.03
164 4 0.01
165 114 0.14
166 654 0.82
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (166 bp):
TAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTC
GACTTAAGCTATTCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGT
GGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTG
Found at i:78034 original size:13 final size:13
Alignment explanation
Indices: 78016--78047 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
78006 TCTCATTTGG
78016 TCTCTCTGCGCTC
1 TCTCTCTGCGCTC
78029 TCTCTCTGCGCTC
1 TCTCTCTGCGCTC
78042 TCTCTC
1 TCTCTC
78048 GTCTCTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.47, G:0.12, T:0.41
Consensus pattern (13 bp):
TCTCTCTGCGCTC
Found at i:79013 original size:3 final size:3
Alignment explanation
Indices: 79005--79042 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
78995 TTAAAAAATG
79005 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT A
79043 TATATATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:79183 original size:71 final size:73
Alignment explanation
Indices: 79107--79296 Score: 218
Period size: 71 Copynumber: 2.7 Consensus size: 73
79097 TTTTTTTCTT
* * *
79107 AAACTATATAATATACGAATGTTTTCAACATGTTTTCAAAA-ATATTATATAAGTTTTCAAAAAC
1 AAACTATATAATATACAAATGTTTTCAAAATGTTTTCAAAACATAATATATAAGTTTTCAAAAAC
79171 GTTTT-AA
66 GTTTTCAA
* **
79178 AAACTATATAATATATAAATGTTTTCAAAATGTTTTCAAAACTATAATATATGTGTTTTCAAAAA
1 AAACTATATAATATACAAATGTTTTCAAAATGTTTTCAAAAC-ATAATATATAAGTTTTCAAAAA
*
79243 TGTTTTCAA
65 CGTTTTCAA
* *
79252 AAA-T-TAT-ATATA-TAAT-TTTTCAAAATGATTTT-AAAA-ATTATATAT
1 AAACTATATAATATACAAATGTTTTCAAAATG-TTTTCAAAACATAATATAT
79297 TATATATATT
Statistics
Matches: 106, Mismatches: 9, Indels: 12
0.83 0.07 0.09
Matches are distributed among these distances:
67 8 0.08
69 15 0.14
70 7 0.07
71 43 0.41
72 3 0.03
73 25 0.24
74 5 0.05
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (73 bp):
AAACTATATAATATACAAATGTTTTCAAAATGTTTTCAAAACATAATATATAAGTTTTCAAAAAC
GTTTTCAA
Found at i:79210 original size:11 final size:11
Alignment explanation
Indices: 79194--79218 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
79184 TATAATATAT
79194 AAATGTTTTCA
1 AAATGTTTTCA
79205 AAATGTTTTCA
1 AAATGTTTTCA
79216 AAA
1 AAA
79219 CTATAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:79248 original size:12 final size:12
Alignment explanation
Indices: 79231--79255 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
79221 ATAATATATG
79231 TGTTTTCAAAAA
1 TGTTTTCAAAAA
79243 TGTTTTCAAAAA
1 TGTTTTCAAAAA
79255 T
1 T
79256 TATATATATA
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:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TGTTTTCAAAAA
Found at i:79294 original size:34 final size:34
Alignment explanation
Indices: 79124--79296 Score: 176
Period size: 34 Copynumber: 4.9 Consensus size: 34
79114 ATAATATACG
*
79124 AATGTTTTCAACATGTTTTCAAAAA-TAT-TATAT
1 AATGTTTTCAAAATGTTTT-AAAAATTATATATAT
*
79157 AA-GTTTTCAAAAACGTTTTAAAAACTATATAATATAT
1 AATGTTTTC-AAAATGTTTTAAAAA-T-TAT-ATATAT
* *
79194 AAATGTTTTCAAAATGTTTTCAAAACTATA-ATAT
1 -AATGTTTTCAAAATGTTTTAAAAATTATATATAT
*
79228 ATGTGTTTTCAAAAATGTTTTCAAAAATTATATATAT
1 A-ATGTTTTC-AAAATGTTTT-AAAAATTATATATAT
79265 AAT-TTTTCAAAATGATTTTAAAAATTATATAT
1 AATGTTTTCAAAATG-TTTTAAAAATTATATAT
79297 TATATATATT
Statistics
Matches: 118, Mismatches: 9, Indels: 25
0.78 0.06 0.16
Matches are distributed among these distances:
32 11 0.09
33 11 0.09
34 30 0.25
35 23 0.19
36 12 0.10
37 10 0.08
38 15 0.13
39 6 0.05
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (34 bp):
AATGTTTTCAAAATGTTTTAAAAATTATATATAT
Found at i:79637 original size:37 final size:37
Alignment explanation
Indices: 79595--79670 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
79585 ATTAAGTATG
79595 AATTTTTAAAATATATATATATAAAATTTGGACACCA
1 AATTTTTAAAATATATATATATAAAATTTGGACACCA
79632 AATTTTTAAAATATATATATATAAAATTTGGACACCA
1 AATTTTTAAAATATATATATATAAAATTTGGACACCA
79669 AA
1 AA
79671 ATTGAATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (37 bp):
AATTTTTAAAATATATATATATAAAATTTGGACACCA
Found at i:79681 original size:39 final size:37
Alignment explanation
Indices: 79601--79681 Score: 126
Period size: 37 Copynumber: 2.1 Consensus size: 37
79591 TATGAATTTT
**
79601 TAAAATATATATATATAAAATTTGGACACCAAATTTT
1 TAAAATATATATATATAAAATTTGGACACCAAATTAA
79638 TAAAATATATATATATAAAATTTGGACACCAAAATTGAA
1 TAAAATATATATATATAAAATTTGGACACC-AAATT-AA
79677 TAAAA
1 TAAAA
79682 GGGGCTAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
37 30 0.75
38 5 0.12
39 5 0.12
ACGTcount: A:0.53, C:0.07, G:0.06, T:0.33
Consensus pattern (37 bp):
TAAAATATATATATATAAAATTTGGACACCAAATTAA
Found at i:83548 original size:17 final size:18
Alignment explanation
Indices: 83505--83545 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
83495 GAATTATATT
83505 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
83522 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
83540 ATTAAA
1 AGTAAA
83546 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:83624 original size:10 final size:10
Alignment explanation
Indices: 83587--83626 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
83577 CTTAAACAGA
*
83587 GAGAGTATTT
1 GAGAGAATTT
* *
83597 GAGAGAAATC
1 GAGAGAATTT
83607 GAGAGAATTT
1 GAGAGAATTT
83617 GAGAGAATTT
1 GAGAGAATTT
83627 AGTGTGATGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.40, C:0.03, G:0.30, T:0.28
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:85271 original size:2 final size:2
Alignment explanation
Indices: 85264--85289 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
85254 AGTTAATACA
85264 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
85290 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86124 original size:3 final size:3
Alignment explanation
Indices: 86118--86188 Score: 99
Period size: 3 Copynumber: 23.7 Consensus size: 3
86108 TTTTTTTTTA
* *
86118 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TGT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
86164 TAT TAT TAT TA- TAT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
86189 CATTTTACAC
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
2 2 0.03
3 55 0.92
4 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:86301 original size:25 final size:25
Alignment explanation
Indices: 86273--86346 Score: 114
Period size: 25 Copynumber: 3.0 Consensus size: 25
86263 CTGAACCACC
86273 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
86298 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
* * *
86323 AACAAATTAGGGTTT-TAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
86347 TCCCCCTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
24 8 0.17
25 38 0.83
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:88322 original size:63 final size:63
Alignment explanation
Indices: 88254--88383 Score: 154
Period size: 63 Copynumber: 2.1 Consensus size: 63
88244 CAATGTGTGT
* * * * *
88254 TTTTTAAATAGT-AATTTATTTTATTTTATGTAAATGTCAATTTGCATTTGTATTCAATTCACA
1 TTTTTAAATAATCAATTTATTTTATTGTATGCAAACGTCAATTT-CATTTATATTCAATTCACA
** * * *
88317 TTTTTAGTTAATCAATTTATTTTGTTGTATGCAAACGTCAATTTTATTTATATTCGATTCACA
1 TTTTTAAATAATCAATTTATTTTATTGTATGCAAACGTCAATTTCATTTATATTCAATTCACA
88380 TTTT
1 TTTT
88384 ATCAAAAGGG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
63 29 0.52
64 27 0.48
ACGTcount: A:0.29, C:0.09, G:0.08, T:0.53
Consensus pattern (63 bp):
TTTTTAAATAATCAATTTATTTTATTGTATGCAAACGTCAATTTCATTTATATTCAATTCACA
Found at i:94123 original size:14 final size:14
Alignment explanation
Indices: 94104--94131 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
94094 CAGATTAAGA
94104 ACACATACATACAT
1 ACACATACATACAT
94118 ACACATACATACAT
1 ACACATACATACAT
94132 GATACATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (14 bp):
ACACATACATACAT
Found at i:94609 original size:30 final size:29
Alignment explanation
Indices: 94575--94756 Score: 112
Period size: 30 Copynumber: 5.6 Consensus size: 29
94565 TCTTAAGATA
94575 GTTTCTGTTGAAACAAAAATCTTTGAGTTT
1 GTTTCT-TTGAAACAAAAATCTTTGAGTTT
* * * *
94605 GTTTCTTTGAAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTG-AAACAAAA------ATCT-TTGAGTTT
94642 GTTTCTTTTGAAACAAAAATCTTTGAGTTT
1 GTTTC-TTTGAAACAAAAATCTTTGAGTTT
* * * *
94672 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTT-GAAACAAAA------ATCT-TTGAGTTT
94709 GTTTCTGTTGAAACAAAAATCTTTGAGTTT
1 GTTTCT-TTGAAACAAAAATCTTTGAGTTT
94739 GTTTCTTTGGAAACAAAA
1 GTTTCTTT-GAAACAAAA
94757 TTTTGTCTCT
Statistics
Matches: 117, Mismatches: 16, Indels: 38
0.68 0.09 0.22
Matches are distributed among these distances:
29 8 0.07
30 53 0.45
31 6 0.05
36 6 0.05
37 38 0.32
38 6 0.05
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (29 bp):
GTTTCTTTGAAACAAAAATCTTTGAGTTT
Found at i:94619 original size:67 final size:67
Alignment explanation
Indices: 94484--94851 Score: 518
Period size: 67 Copynumber: 5.6 Consensus size: 67
94474 ATTTTTCTAA
* *
94484 AAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG--A-AAAAATCTTTGAGTTTGTTTCTT
1 AAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTCTTGAAACAAAAATCTTTGAGTTTGTTTCTT
94545 TG
66 TG
* *
94547 GAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTGTTGAAACAAAAATCTTTGAGTTTGTTTCTT
1 AAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTCTTGAAACAAAAATCTTTGAGTTTGTTTCTT
94612 TG
66 TG
*
94614 AAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTT
1 AAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTCTTGAAACAAAAATCTTTGAGTTTGTTTCTT
94679 TG
66 TG
* *
94681 GAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTGTTGAAACAAAAATCTTTGAGTTTGTTTCTT
1 AAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTCTTGAAACAAAAATCTTTGAGTTTGTTTCTT
94746 TG
66 TG
* * * * *
94748 GAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTG-AA-AAAAATCTTTGAATCTGTTTCTC
1 AAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTCTTGAAACAAAAATCTTTGAGTTTGTTTCT-
94811 TT-
65 TTG
** * * *
94813 AAAA-TGAATTTTGTATCTCTTGAGACAGTTTCTCTTGAA
1 AAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTCTTGAA
94852 GTAAATCTTT
Statistics
Matches: 279, Mismatches: 20, Indels: 10
0.90 0.06 0.03
Matches are distributed among these distances:
63 4 0.01
64 55 0.20
65 24 0.09
66 5 0.02
67 191 0.68
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (67 bp):
AAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTCTTGAAACAAAAATCTTTGAGTTTGTTTCTT
TG
Found at i:95342 original size:17 final size:15
Alignment explanation
Indices: 95311--95349 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
95301 AGTCTTTTCA
95311 CTTGAAACATTCTCT
1 CTTGAAACATTCTCT
*
95326 CTTGAAACATTTTCT
1 CTTGAAACATTCTCT
*
95341 CTTAAAACA
1 CTTGAAACA
95350 AGATCATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.38
Consensus pattern (15 bp):
CTTGAAACATTCTCT
Found at i:95499 original size:64 final size:64
Alignment explanation
Indices: 95355--95514 Score: 173
Period size: 64 Copynumber: 2.5 Consensus size: 64
95345 AAACAAGATC
* * *
95355 ATCTTTGAGTTTGTTTCTCTGGAAAC--AGTGTTTTATCCCTTGAAACAATTTCTTTTGAAAAAA
1 ATCTTTGAGTTTGTTTCTTTGGAAACAAAAT-TTTTATCCCTCGAAACAATTTCTTTTGAAAAAA
* * * * * * * * *
95418 ATCATTGAATCTCTTTCTTTGGAAACAAAATTTTGTGTCTCTCGAGACAGTTTC-TTTGAGAAAA
1 ATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTT-TATCCCTCGAAACAATTTCTTTTGAAAAAA
95482 ATCTTTGAGTTTGTTTCTTTGGAAACAAAATTT
1 ATCTTTGAGTTTGTTTCTTTGGAAACAAAATTT
95515 ACCATCTTTG
Statistics
Matches: 78, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
63 21 0.27
64 41 0.53
65 16 0.21
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (64 bp):
ATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTTATCCCTCGAAACAATTTCTTTTGAAAAAA
Found at i:95894 original size:28 final size:28
Alignment explanation
Indices: 95844--95897 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
95834 TCAAAATCCA
* *
95844 ATCTTTGAGTTTGTTTCTATTGAAACAC
1 ATCTTTGAGTTGGTTCCTATTGAAACAC
95872 ATCTTTGAGTTGGTCTCCT-TTGAAAC
1 ATCTTTGAGTTGGT-TCCTATTGAAAC
95898 CATTATCCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (28 bp):
ATCTTTGAGTTGGTTCCTATTGAAACAC
Found at i:95976 original size:46 final size:45
Alignment explanation
Indices: 95926--96252 Score: 258
Period size: 46 Copynumber: 7.5 Consensus size: 45
95916 CCAGCCGTCC
* *
95926 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAGCCGTGTCATCACC-TTAGATGGCCAGAACTCT
* * *
95972 TCATCACGTATGAGCCGTGTCATTC-CC--CGA---CCAGATCTCT
1 TCATCACGTAGGAGCCGTGTCA-TCACCTTAGATGGCCAGAACTCT
* ** * *
96012 TCATCACGTAGGAGCCGTGTCA--ACCATAGATAACCAG-CCGTCC
1 TCATCACGTAGGAGCCGTGTCATCACCTTAGATGGCCAGAAC-TCT
* *
96055 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAGCCGTGTCATCACC-TTAGATGGCCAGAACTCT
* * *
96101 TCATCACGTATGAGCCGTGTCATTC-CC--CGA---CCAGATCTCT
1 TCATCACGTAGGAGCCGTGTCA-TCACCTTAGATGGCCAGAACTCT
* ** * *
96141 TCATCACGTAGGAGCCGTGTCA--ACCATAGATAACCAG-CCGTCC
1 TCATCACGTAGGAGCCGTGTCATCACCTTAGATGGCCAGAAC-TCT
* *
96184 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAGCCGTGTCATCACC-TTAGATGGCCAGAACTCT
*
96230 TCATCACGTATGAGCCGTGTCAT
1 TCATCACGTAGGAGCCGTGTCAT
96253 TCCCCGACCA
Statistics
Matches: 222, Mismatches: 35, Indels: 48
0.73 0.11 0.16
Matches are distributed among these distances:
38 4 0.02
40 64 0.29
42 2 0.01
43 56 0.25
45 6 0.03
46 84 0.38
47 6 0.03
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.26
Consensus pattern (45 bp):
TCATCACGTAGGAGCCGTGTCATCACCTTAGATGGCCAGAACTCT
Found at i:96017 original size:40 final size:39
Alignment explanation
Indices: 95962--96291 Score: 178
Period size: 40 Copynumber: 7.8 Consensus size: 39
95952 CTTTAGATGG
* *
95962 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCA-TCCCAGA
* * *
96002 CCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCATCC-CAG---A
* * * *
96045 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGA
1 CCAGAAC-TCTTCATCACGTAGGAGCCGTGTCATC-CC---AGA
* *
96088 TGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGA
1 ---CCAGAACTCTTCATCACGTAGGAGCCGTGTCA-TCCCAGA
* * *
96131 CCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCATCC-CAG---A
* * * *
96174 CCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGA
1 CCAGAAC-TCTTCATCACGTAGGAGCCGTGTCATC-CC---AGA
* *
96217 TGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGA
1 ---CCAGAACTCTTCATCACGTAGGAGCCGTGTCA-TCCCAGA
** * * *
96260 CCAGATGTCCTCATCACGTAGGAACCATGTCA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCA
96292 CCCTTAGACG
Statistics
Matches: 222, Mismatches: 40, Indels: 56
0.70 0.13 0.18
Matches are distributed among these distances:
39 4 0.02
40 88 0.40
42 2 0.01
43 62 0.28
44 2 0.01
46 58 0.26
47 6 0.03
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.25
Consensus pattern (39 bp):
CCAGAACTCTTCATCACGTAGGAGCCGTGTCATCCCAGA
Found at i:96320 original size:129 final size:129
Alignment explanation
Indices: 95908--96291 Score: 732
Period size: 129 Copynumber: 3.0 Consensus size: 129
95898 CATTATCCCT
95908 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTT
1 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTT
95973 CATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACC
66 CATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACC
96037 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTT
1 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTT
96102 CATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACC
66 CATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACC
96166 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTT
1 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTT
* * * *
96231 CATCACGTATGAGCCGTGTCATTCCCCGACCAGATGTCCTCATCACGTAGGAACCATGTCA
66 CATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCA
96292 CCCTTAGACG
Statistics
Matches: 251, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 251 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (129 bp):
ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTT
CATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACC
Found at i:96494 original size:3 final size:3
Alignment explanation
Indices: 96488--96555 Score: 93
Period size: 3 Copynumber: 22.7 Consensus size: 3
96478 TTTTTTTTTA
* *
96488 TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TGT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
*
96534 TAT TAT TA- TAT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
96556 CATTTTACAC
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 2 0.04
3 52 0.91
4 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:96668 original size:25 final size:25
Alignment explanation
Indices: 96640--96738 Score: 164
Period size: 25 Copynumber: 4.0 Consensus size: 25
96630 CTGAACCACC
96640 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
96665 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
96690 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
* * *
96715 AACAAATTAGGGTTT-TAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
96739 TCCCCTAATG
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
24 8 0.11
25 63 0.89
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:103482 original size:33 final size:34
Alignment explanation
Indices: 103438--103504 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
103428 AATAGGAATT
*
103438 ACAACTTCTCTC-AATCTAAAAGGAGAAAACAATA
1 ACAACTTCTCTCTAAT-AAAAAGGAGAAAACAATA
*
103472 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAAT
1 ACAACTTCTCTC-TAATAAAAAGGAGAAAACAAT
103505 TCTCAAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 7 0.24
34 20 0.69
35 2 0.07
ACGTcount: A:0.49, C:0.18, G:0.10, T:0.22
Consensus pattern (34 bp):
ACAACTTCTCTCTAATAAAAAGGAGAAAACAATA
Found at i:108154 original size:18 final size:18
Alignment explanation
Indices: 108131--108166 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
108121 TCGGTTCATT
108131 TGTTTAATGTTTGTGAAC
1 TGTTTAATGTTTGTGAAC
108149 TGTTTAATGTTTGTGAAC
1 TGTTTAATGTTTGTGAAC
108167 ATAAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.22, T:0.50
Consensus pattern (18 bp):
TGTTTAATGTTTGTGAAC
Found at i:108467 original size:19 final size:19
Alignment explanation
Indices: 108443--108481 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
108433 GTTTGTTTAT
108443 TAAATGAACATTATACGAA
1 TAAATGAACATTATACGAA
108462 TAAATGAACATTATACGAA
1 TAAATGAACATTATACGAA
108481 T
1 T
108482 GATTTATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.28
Consensus pattern (19 bp):
TAAATGAACATTATACGAA
Done.