Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007882.1 Hibiscus syriacus cultivar Beakdansim tig00110260_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: 1274288
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:5835 original size:82 final size:82
Alignment explanation
Indices: 5743--5898 Score: 312
Period size: 82 Copynumber: 1.9 Consensus size: 82
5733 AAAAATATGA
5743 TTTAATGTCATCTAATATTTCACTTCTAACAAGTCTTTTATCTCTATACTAACGTTCATTTTAAT
1 TTTAATGTCATCTAATATTTCACTTCTAACAAGTCTTTTATCTCTATACTAACGTTCATTTTAAT
5808 GTCATTTTATGACAACT
66 GTCATTTTATGACAACT
5825 TTTAATGTCATCTAATATTTCACTTCTAACAAGTCTTTTATCTCTATACTAACGTTCATTTTAAT
1 TTTAATGTCATCTAATATTTCACTTCTAACAAGTCTTTTATCTCTATACTAACGTTCATTTTAAT
5890 GTCATTTTA
66 GTCATTTTA
5899 AGATGACAAC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (82 bp):
TTTAATGTCATCTAATATTTCACTTCTAACAAGTCTTTTATCTCTATACTAACGTTCATTTTAAT
GTCATTTTATGACAACT
Found at i:7064 original size:20 final size:20
Alignment explanation
Indices: 7035--7074 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
7025 TAATCTTATT
*
7035 CACTGGTAATCTTACATTCC
1 CACTGATAATCTTACATTCC
*
7055 CACTGATAATCTTATATTCC
1 CACTGATAATCTTACATTCC
7075 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.38
Consensus pattern (20 bp):
CACTGATAATCTTACATTCC
Found at i:12687 original size:12 final size:13
Alignment explanation
Indices: 12664--12692 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
12654 TTTTAATAAA
12664 ATTAATAAAAATT
1 ATTAATAAAAATT
12677 ATTAA-AAAAATT
1 ATTAATAAAAATT
12689 ATTA
1 ATTA
12693 TTTTTATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTAATAAAAATT
Found at i:21770 original size:21 final size:20
Alignment explanation
Indices: 21746--21803 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 20
21736 ATCCTCGCTA
21746 TGTATCGATACACTATGAATG
1 TGTATCGATACACT-TGAATG
*
21767 TGTACCGATACATTCCTTGAATG
1 TGTATCGATACA---CTTGAATG
*
21790 TATATCGATACACT
1 TGTATCGATACACT
21804 CAGAAGAGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 2 0.06
21 11 0.35
23 16 0.52
24 2 0.06
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (20 bp):
TGTATCGATACACTTGAATG
Found at i:25261 original size:24 final size:24
Alignment explanation
Indices: 25234--25291 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
25224 GTTCTTGTAG
25234 TATCGATATTAATATCAATACCAA
1 TATCGATATTAATATCAATACCAA
* * * **
25258 TATCGACATCAGTATTGATACCAA
1 TATCGATATTAATATCAATACCAA
*
25282 TATCAATATT
1 TATCGATATT
25292 GTCCAATACC
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.34
Consensus pattern (24 bp):
TATCGATATTAATATCAATACCAA
Found at i:26700 original size:55 final size:55
Alignment explanation
Indices: 26505--26851 Score: 414
Period size: 55 Copynumber: 6.3 Consensus size: 55
26495 TTTATTAAGA
* * **
26505 TGCACACTTAGTGCCTATACGG-TAGTTCATCAACTCATGATGAATT--ATGTGGGT
1 TGCACACATAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTCCATG-GATT
** * * * *
26559 TGCATGCATAGTGCTTGTACGGTTGTTCATCAACTCATGATGAATTTCGTGGA-T
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCATGGATT
* * *
26613 TGGACACATAGTTCCTGTACGATTATTCATCAACTCATGATGAATTCCATGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCATGGATT
* * *
26668 TGCACACATAGTGCATGTATGGTTATTCATCAACTCATGATGAATTCCATGGACT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCATGGATT
* * *** *
26723 TGTACACATGGTGCCTGTAAAATTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCATGGATT
* * *
26778 TGCATACATAGTGTCTGTATGGTTATTCATCAACTCATGATGAATTCCATGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCATGGATT
*
26833 TGCACACATAGTACCTGTA
1 TGCACACATAGTGCCTGTA
26852 ATACACATAG
Statistics
Matches: 247, Mismatches: 42, Indels: 7
0.83 0.14 0.02
Matches are distributed among these distances:
54 83 0.34
55 162 0.66
56 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (55 bp):
TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCATGGATT
Found at i:31210 original size:90 final size:89
Alignment explanation
Indices: 31054--31216 Score: 281
Period size: 90 Copynumber: 1.8 Consensus size: 89
31044 ACACACCCTT
*
31054 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATAATTA
31119 ATTAATTAGAATTTAATAATCCTC
66 ATTAATTAGAATTTAATAATCCTC
* * *
31143 TTATATCCAAGTTACCCTAATCATATTGGGGATTTTATTATTTCAAATTAATTAAATCTATAATT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATATATAATT
31208 AATTAATTA
65 AATTAATTA
31217 ATTGAAATTA
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
89 29 0.42
90 40 0.58
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATAATTA
ATTAATTAGAATTTAATAATCCTC
Found at i:34752 original size:20 final size:21
Alignment explanation
Indices: 34727--34776 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
34717 GATGAACAAC
34727 ATCGATACTAAATAGGT-A-GT
1 ATCGATACTAAATA-GTAAGGT
*
34747 ATCGATAC-CAATAGTAAGGT
1 ATCGATACTAAATAGTAAGGT
34767 ATCGATACTA
1 ATCGATACTA
34777 TAATGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 2 0.08
19 5 0.20
20 18 0.72
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (21 bp):
ATCGATACTAAATAGTAAGGT
Found at i:35392 original size:57 final size:57
Alignment explanation
Indices: 35275--35392 Score: 150
Period size: 57 Copynumber: 2.1 Consensus size: 57
35265 TGTTCAATGG
* *
35275 GAATAAATGATAATTTCAATAATGTTATATGAAACACTATGAGTATATGTTTTATGT
1 GAATAAATGATAATTTCAATAATGTTATATGAAACACTATGAGTATATGTTCTATAT
* * **
35332 GAATAAATGATAGGTTT-AGTAATGTTATATGAAATGCTATGAGTA-ATTGTTCTATAT
1 GAATAAATGATA-ATTTCAATAATGTTATATGAAACACTATGAGTATA-TGTTCTATAT
35389 GAAT
1 GAAT
35393 TAATATTAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
56 1 0.02
57 49 0.92
58 3 0.06
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.40
Consensus pattern (57 bp):
GAATAAATGATAATTTCAATAATGTTATATGAAACACTATGAGTATATGTTCTATAT
Found at i:35619 original size:24 final size:24
Alignment explanation
Indices: 35576--35640 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
35566 TACGCGGTCA
* *
35576 TTCGGGACAAA-TCTATGTGGCAC
1 TTCGGTACAAATTCTACGTGGCAC
*
35599 TTCGGTACATATTCTACGTGGCAC
1 TTCGGTACAAATTCTACGTGGCAC
*
35623 TTTGGTACAAATTCTACG
1 TTCGGTACAAATTCTACG
35641 CGACAGTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 9 0.25
24 27 0.75
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.32
Consensus pattern (24 bp):
TTCGGTACAAATTCTACGTGGCAC
Found at i:41183 original size:57 final size:57
Alignment explanation
Indices: 41108--41295 Score: 227
Period size: 57 Copynumber: 3.3 Consensus size: 57
41098 TTTACGTGAT
* * *
41108 TATGTTCTATGGGAATAAATGATAATTTGAATAATGTTATATGAAACACTATGAGTA
1 TATGTTCTATGTGAATAAATGATAATTTGAGTAATGTTATATGAAATACTATGAGTA
* * * * *
41165 TGTGTTTTATGTGAATAAATGATAAGTTGAGTAATGCTATATGAAATGCTATGAGTA
1 TATGTTCTATGTGAATAAATGATAATTTGAGTAATGTTATATGAAATACTATGAGTA
* *
41222 -ACTGTTCTATGTAAATAAAT-ATTAAATTTGGGTAATGTTATATGAAATACTATGAGTA
1 TA-TGTTCTATGTGAATAAATGA-T-AATTTGAGTAATGTTATATGAAATACTATGAGTA
* *
41280 TAAGTTTTATGTGAAT
1 TATGTTCTATGTGAAT
41296 TTGAATAATG
Statistics
Matches: 109, Mismatches: 18, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
56 1 0.01
57 66 0.61
58 41 0.38
59 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.39
Consensus pattern (57 bp):
TATGTTCTATGTGAATAAATGATAATTTGAGTAATGTTATATGAAATACTATGAGTA
Found at i:41424 original size:23 final size:23
Alignment explanation
Indices: 41398--41477 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
41388 GGTTCTACAC
41398 GGTCCTTCGGGACAATTCTATGT
1 GGTCCTTCGGGACAATTCTATGT
** * *
41421 GGTCAATCGGGACAAATTCTACGC
1 GGTCCTTCGGGAC-AATTCTATGT
** *
41445 GGTCCTTCAAGACAAATCTATGT
1 GGTCCTTCGGGACAATTCTATGT
41468 GG-CACTTCGG
1 GGTC-CTTCGG
41478 TGAAAACTCT
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
22 1 0.02
23 24 0.57
24 17 0.40
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.28
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCTATGT
Found at i:41448 original size:24 final size:23
Alignment explanation
Indices: 41390--41448 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
41380 GAGTCGAGGG
* **
41390 TTCTACACGGTCCTTCGGGACAA
1 TTCTACGCGGTCAATCGGGACAA
* *
41413 TTCTATGTGGTCAATCGGGACAAA
1 TTCTACGCGGTCAATCGGGAC-AA
41437 TTCTACGCGGTC
1 TTCTACGCGGTC
41449 CTTCAAGACA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (23 bp):
TTCTACGCGGTCAATCGGGACAA
Found at i:41489 original size:47 final size:47
Alignment explanation
Indices: 41391--41490 Score: 114
Period size: 47 Copynumber: 2.1 Consensus size: 47
41381 AGTCGAGGGT
* ** * *
41391 TCTACACGGTCCTTCGGGACAATTCTATGTGGTCAATCGGGACAAAT
1 TCTACGCGGTCCTTCAAGACAAATCTATGTGGTCAATCGGGACAAAC
*
41438 TCTACGCGGTCCTTCAAGACAAATCTATGTGG-CACTTCGGTGA-AAAC
1 TCTACGCGGTCCTTCAAGACAAATCTATGTGGTCA-ATCGG-GACAAAC
41485 TCTACG
1 TCTACG
41491 TGATAGTTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
46 2 0.04
47 41 0.91
48 2 0.04
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (47 bp):
TCTACGCGGTCCTTCAAGACAAATCTATGTGGTCAATCGGGACAAAC
Found at i:43109 original size:35 final size:35
Alignment explanation
Indices: 43008--43111 Score: 136
Period size: 35 Copynumber: 2.9 Consensus size: 35
42998 GTTCAATAGA
*
43008 GTGTCATGTGTCGTAATTAGATAATGCACCAACAAT
1 GTGTCATGTGTCGTATTTAGATAATGCA-CAACAAT
* * * *
43044 GTGTCATGTGTCGCATTCAGATAATACACAATAAT
1 GTGTCATGTGTCGTATTTAGATAATGCACAACAAT
**
43079 GTGTCATGTGTCGTATTTAGAGCATGCACAACA
1 GTGTCATGTGTCGTATTTAGATAATGCACAACA
43112 GTCAATCATT
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
35 33 0.58
36 24 0.42
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (35 bp):
GTGTCATGTGTCGTATTTAGATAATGCACAACAAT
Found at i:44394 original size:23 final size:23
Alignment explanation
Indices: 44359--44407 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
44349 GGCCGAACCA
** * *
44359 AACCGTTGGCCTGACTCGACTCG
1 AACCGTTAACCTGACCCGACGCG
44382 AACCGTTAACCTGACCCGACGCG
1 AACCGTTAACCTGACCCGACGCG
44405 AAC
1 AAC
44408 TGTTTGACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.24, C:0.37, G:0.22, T:0.16
Consensus pattern (23 bp):
AACCGTTAACCTGACCCGACGCG
Found at i:53763 original size:22 final size:21
Alignment explanation
Indices: 53740--53819 Score: 60
Period size: 21 Copynumber: 3.8 Consensus size: 21
53730 AGAACCCCAG
*
53740 GGGGGTATCGATTCCCCTGTA
1 GGGGGAATCGATTCCCCTGTA
*
53761 GGGGGAATCGGTTCCCCT-TCAAA
1 GGGGGAATCGATTCCCCTGT---A
*
53784 GGGGGAATCGGTTCCCTCATG--
1 GGGGGAATCGATTCCC-C-TGTA
53805 GGGGG-ATCGATTCCC
1 GGGGGAATCGATTCCC
53820 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
20 10 0.20
21 21 0.42
23 17 0.34
24 1 0.02
25 1 0.02
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
GGGGGAATCGATTCCCCTGTA
Found at i:53813 original size:20 final size:21
Alignment explanation
Indices: 53760--53821 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
53750 ATTCCCCTGT
53760 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTT-CCC-TCAA
53783 AGGGGGAATCGGTTCCCTC-A
1 AGGGGGAATCGGTTCCCTCAA
* * *
53803 TGGGGGGATCGATTCCCTC
1 AGGGGGAATCGGTTCCCTC
53822 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 17 0.47
21 2 0.06
22 3 0.08
23 14 0.39
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.23
Consensus pattern (21 bp):
AGGGGGAATCGGTTCCCTCAA
Found at i:70353 original size:12 final size:12
Alignment explanation
Indices: 70336--70369 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
70326 TCATGTAGGA
70336 AATTGAAGTTTG
1 AATTGAAGTTTG
70348 AATTGAA-TTTG
1 AATTGAAGTTTG
70359 ATATTGAAGTT
1 A-ATTGAAGTT
70370 ATTGTAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.25
12 13 0.65
13 2 0.10
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (12 bp):
AATTGAAGTTTG
Found at i:75931 original size:21 final size:21
Alignment explanation
Indices: 75907--75977 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
75897 AGCAACTTCA
* **
75907 CAAGAAAAGTTGGTTATGTCC
1 CAAGAAAAGCTGGTTACATCC
75928 CAAGAAAAGCTGGTTACATCC
1 CAAGAAAAGCTGGTTACATCC
* ** *
75949 CAGGAAAAGCTAATTGCATCC
1 CAAGAAAAGCTGGTTACATCC
*
75970 CAGGAAAA
1 CAAGAAAA
75978 ATTCCAAAGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (21 bp):
CAAGAAAAGCTGGTTACATCC
Found at i:80158 original size:5 final size:5
Alignment explanation
Indices: 80134--80190 Score: 73
Period size: 5 Copynumber: 11.6 Consensus size: 5
80124 TTTATAAAAC
* *
80134 TTTAT TTCAT TATA- TTTAT TTTAT TTTGA- TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT-AT TTTAT TTTAT TTTAT TTTAT
80183 TTTAT TTT
1 TTTAT TTT
80191 TCTCTAAACA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
4 4 0.09
5 40 0.89
6 1 0.02
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:107147 original size:17 final size:17
Alignment explanation
Indices: 107117--107150 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
107107 TTCTTTATCC
**
107117 TTATTTCTTTTATTTAT
1 TTATTTCTAATATTTAT
107134 TTATTTCTAATATTTAT
1 TTATTTCTAATATTTAT
107151 CTTTTTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTTCTAATATTTAT
Found at i:109852 original size:21 final size:23
Alignment explanation
Indices: 109827--109868 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
109817 AAAATATCAA
109827 ATTTAA-CAAGTATAA-CAAACT
1 ATTTAATCAAGTATAATCAAACT
*
109848 ATTTAATCACGTATAATCAAA
1 ATTTAATCAAGTATAATCAAA
109869 ATATAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.31
Consensus pattern (23 bp):
ATTTAATCAAGTATAATCAAACT
Found at i:116212 original size:20 final size:21
Alignment explanation
Indices: 116183--116222 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
116173 TAATGACCTT
116183 ATGTTATCACAT-AAATATTA
1 ATGTTATCACATGAAATATTA
* *
116203 ATGTTCTCACTTGAAATATT
1 ATGTTATCACATGAAATATT
116223 TTATTAAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (21 bp):
ATGTTATCACATGAAATATTA
Found at i:117301 original size:22 final size:22
Alignment explanation
Indices: 117273--117314 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
117263 CAAACCATTC
117273 AGGGGGAATCGGTACCCTCTTT
1 AGGGGGAATCGGTACCCTCTTT
* *
117295 AGGGGGAATTGGTTCCCTCT
1 AGGGGGAATCGGTACCCTCT
117315 GGCCAATCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.21, G:0.33, T:0.29
Consensus pattern (22 bp):
AGGGGGAATCGGTACCCTCTTT
Found at i:119052 original size:2 final size:2
Alignment explanation
Indices: 119045--119085 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
119035 TGAATCCAAT
119045 TA TA TA TA TA TA TA TA TA TA TA T- 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
119086 ACTATTCCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:127146 original size:24 final size:24
Alignment explanation
Indices: 127110--127163 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
127100 AAAACTGTCG
*
127110 CGTAGAATTTGTACCAAAGTGCCA
1 CGTAGAATATGTACCAAAGTGCCA
*
127134 CGTAGAATATGTACCGAAGTGCCA
1 CGTAGAATATGTACCAAAGTGCCA
*
127158 CATAGA
1 CGTAGA
127164 TTTGTCCCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (24 bp):
CGTAGAATATGTACCAAAGTGCCA
Found at i:127397 original size:58 final size:57
Alignment explanation
Indices: 127321--127456 Score: 150
Period size: 57 Copynumber: 2.4 Consensus size: 57
127311 CATAAAACTT
* ** * *
127321 ATAGTATTTCACATAACATTACCCAAATTTAAT-ATTAATTCATATAGAACA-ATTACTC
1 ATAGTATTTCATATAACATTA-CCAAACCT-ATCATTAATTCACATAAAACATA-TACTC
* * *
127379 ATAGCATTTCATATAACATTACTAAACCTATCATTTATTCACATAAAACATATACTC
1 ATAGTATTTCATATAACATTACCAAACCTATCATTAATTCACATAAAACATATACTC
*
127436 ATAGTGTTTCATATAACATTA
1 ATAGTATTTCATATAACATTA
127457 TTGAAATTAT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
56 2 0.03
57 44 0.67
58 20 0.30
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.37
Consensus pattern (57 bp):
ATAGTATTTCATATAACATTACCAAACCTATCATTAATTCACATAAAACATATACTC
Found at i:133593 original size:24 final size:24
Alignment explanation
Indices: 133566--133617 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
133556 AACGGATATA
*
133566 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
133590 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
133614 TCAA
1 TCAA
133618 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:133618 original size:24 final size:24
Alignment explanation
Indices: 133586--133703 Score: 159
Period size: 24 Copynumber: 4.9 Consensus size: 24
133576 AAACATAAAT
*
133586 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
*
133610 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
133634 CAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
133658 CATGTC-AGATATCAGATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
*
133682 CATGTCAAGTATCAGATCAGAA
1 CAGGTCAAGTATCAGATCAGAA
133704 ATCAAATCGA
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
23 5 0.06
24 79 0.92
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:133720 original size:48 final size:47
Alignment explanation
Indices: 133589--133720 Score: 151
Period size: 48 Copynumber: 2.7 Consensus size: 47
133579 CATAAATCAG
* *
133589 GTCAAGTATCATATCAGAAATCAGGTCAAGTAA-CAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAAATCAAGTCAA--AATCAGATCAGAATCCAA
* * *
133637 GTCAAGTATCAGATCAG-AATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAAT-CAAGTCA-AAATCAGATCAGAATCCAA
*
133685 GTCAAGTATCAGATCAGAAATCAAATCGAAAATCAG
1 GTCAAGTATCAGATCAGAAATCAAGTC-AAAATCAG
133721 GTAAAATATT
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
47 4 0.06
48 63 0.88
49 5 0.07
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (47 bp):
GTCAAGTATCAGATCAGAAATCAAGTCAAAATCAGATCAGAATCCAA
Found at i:136165 original size:7 final size:7
Alignment explanation
Indices: 136153--136184 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
136143 TGGTCAACTC
136153 CGGTCAA
1 CGGTCAA
136160 CGGTCAA
1 CGGTCAA
136167 CGGGTCAA
1 C-GGTCAA
136175 CGGTCAA
1 CGGTCAA
136182 CGG
1 CGG
136185 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:136174 original size:15 final size:15
Alignment explanation
Indices: 136154--136200 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
136144 GGTCAACTCC
136154 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
136169 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
136184 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
136197 GGTC
1 GGTC
136201 GGTTCGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:136209 original size:18 final size:17
Alignment explanation
Indices: 136184--136258 Score: 86
Period size: 18 Copynumber: 4.5 Consensus size: 17
136174 ACGGTCAACG
136184 GGTCGGGTCAACGGGTC
1 GGTCGGGTCAACGGGTC
136201 GGTTCGGGTCAAC--G--
1 GG-TCGGGTCAACGGGTC
*
136215 GGTCGGGTAAACGGGTC
1 GGTCGGGTCAACGGGTC
136232 GGATCGGGTCAACGGGTC
1 GG-TCGGGTCAACGGGTC
136250 GGGTCGGGT
1 -GGTCGGGT
136259 TGTGACCGGT
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
13 9 0.18
14 2 0.04
15 1 0.02
16 1 0.02
17 4 0.08
18 30 0.61
19 2 0.04
ACGTcount: A:0.13, C:0.20, G:0.48, T:0.19
Consensus pattern (17 bp):
GGTCGGGTCAACGGGTC
Found at i:136228 original size:31 final size:31
Alignment explanation
Indices: 136176--136253 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
136166 ACGGGTCAAC
* *
136176 GGTCAACGGGTCGGGTCAACGGGTCGGTTCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGATCG
136207 GGTCAACGGGTCGGGTAAACGGGTCGGATCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGATCG
136238 GGTCAACGGGTCGGGT
1 GGTCAACGGGTCGGGT
136254 CGGGTTGTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.15, C:0.21, G:0.46, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACGGGTCGGATCG
Found at i:136254 original size:13 final size:13
Alignment explanation
Indices: 136161--136233 Score: 65
Period size: 13 Copynumber: 5.1 Consensus size: 13
136151 TCCGGTCAAC
*
136161 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
136176 GGTCAACGGGTCG
1 GGTCAACGGGTCG
136189 GGTCAACGGGTCGGTTCG
1 GGTCAAC--G--GG-TCG
136207 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
136220 GGTAAACGGGTCG
1 GGTCAACGGGTCG
136233 G
1 G
136234 ATCGGGTCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
13 23 0.45
14 2 0.04
15 13 0.25
16 1 0.02
17 2 0.04
18 10 0.20
ACGTcount: A:0.18, C:0.22, G:0.44, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:138441 original size:24 final size:24
Alignment explanation
Indices: 138414--138465 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
138404 AACGGATATA
*
138414 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
138438 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
138462 TCAA
1 TCAA
138466 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:138466 original size:24 final size:24
Alignment explanation
Indices: 138434--138551 Score: 159
Period size: 24 Copynumber: 4.9 Consensus size: 24
138424 AAACATAAAT
*
138434 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
*
138458 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
138482 CAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
138506 CATGTC-AGATATCAGATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
*
138530 CATGTCAAGTATCAGATCAGAA
1 CAGGTCAAGTATCAGATCAGAA
138552 ATCAAATCGA
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
23 5 0.06
24 79 0.92
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:138568 original size:48 final size:47
Alignment explanation
Indices: 138437--138568 Score: 151
Period size: 48 Copynumber: 2.7 Consensus size: 47
138427 CATAAATCAG
* *
138437 GTCAAGTATCATATCAGAAATCAGGTCAAGTAA-CAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAAATCAAGTCAA--AATCAGATCAGAATCCAA
* * *
138485 GTCAAGTATCAGATCAG-AATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAAT-CAAGTCA-AAATCAGATCAGAATCCAA
*
138533 GTCAAGTATCAGATCAGAAATCAAATCGAAAATCAG
1 GTCAAGTATCAGATCAGAAATCAAGTC-AAAATCAG
138569 GTAAAATATT
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
47 4 0.06
48 63 0.88
49 5 0.07
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (47 bp):
GTCAAGTATCAGATCAGAAATCAAGTCAAAATCAGATCAGAATCCAA
Found at i:141010 original size:7 final size:7
Alignment explanation
Indices: 140998--141029 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
140988 TGGTCAACTC
140998 CGGTCAA
1 CGGTCAA
141005 CGGTCAA
1 CGGTCAA
141012 CGGGTCAA
1 C-GGTCAA
141020 CGGTCAA
1 CGGTCAA
141027 CGG
1 CGG
141030 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:141019 original size:15 final size:15
Alignment explanation
Indices: 140999--141045 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
140989 GGTCAACTCC
140999 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
141014 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
141029 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
141042 GGTC
1 GGTC
141046 GGTTCGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:141054 original size:18 final size:17
Alignment explanation
Indices: 141029--141103 Score: 86
Period size: 18 Copynumber: 4.5 Consensus size: 17
141019 ACGGTCAACG
141029 GGTCGGGTCAACGGGTC
1 GGTCGGGTCAACGGGTC
141046 GGTTCGGGTCAAC--G--
1 GG-TCGGGTCAACGGGTC
*
141060 GGTCGGGTAAACGGGTC
1 GGTCGGGTCAACGGGTC
141077 GGATCGGGTCAACGGGTC
1 GG-TCGGGTCAACGGGTC
141095 GGGTCGGGT
1 -GGTCGGGT
141104 TGTGACCGGT
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
13 9 0.18
14 2 0.04
15 1 0.02
16 1 0.02
17 4 0.08
18 30 0.61
19 2 0.04
ACGTcount: A:0.13, C:0.20, G:0.48, T:0.19
Consensus pattern (17 bp):
GGTCGGGTCAACGGGTC
Found at i:141073 original size:31 final size:31
Alignment explanation
Indices: 141021--141098 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
141011 ACGGGTCAAC
* *
141021 GGTCAACGGGTCGGGTCAACGGGTCGGTTCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGATCG
141052 GGTCAACGGGTCGGGTAAACGGGTCGGATCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGATCG
141083 GGTCAACGGGTCGGGT
1 GGTCAACGGGTCGGGT
141099 CGGGTTGTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.15, C:0.21, G:0.46, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACGGGTCGGATCG
Found at i:141099 original size:13 final size:13
Alignment explanation
Indices: 141006--141078 Score: 65
Period size: 13 Copynumber: 5.1 Consensus size: 13
140996 TCCGGTCAAC
*
141006 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
141021 GGTCAACGGGTCG
1 GGTCAACGGGTCG
141034 GGTCAACGGGTCGGTTCG
1 GGTCAAC--G--GG-TCG
141052 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
141065 GGTAAACGGGTCG
1 GGTCAACGGGTCG
141078 G
1 G
141079 ATCGGGTCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
13 23 0.45
14 2 0.04
15 13 0.25
16 1 0.02
17 2 0.04
18 10 0.20
ACGTcount: A:0.18, C:0.22, G:0.44, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:145062 original size:55 final size:55
Alignment explanation
Indices: 144995--145341 Score: 423
Period size: 55 Copynumber: 6.3 Consensus size: 55
144985 CTATGTGTAT
* *
144995 TACAGGTACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACCA
1 TACAGGCACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACCG
* * ***
145050 TACAGGCACTATGTATGCAAATCCACGGAATTCATCATGAGTTGATGAATAATTT
1 TACAGGCACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACCG
* * *
145105 TACAGGCACCATGTGTGCAAGTCCATGGAATTCATCATGAGTTGATGAATAACCA
1 TACAGGCACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACCG
* *
145160 TACATGCACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAATCG
1 TACAGGCACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACCG
* * * * * *
145215 TACATGAACTATGTGT-CCAATCCACGAAATTCATCATGAGTTGATGAACAACCG
1 TACAGGCACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACCG
* ** **
145269 TACAAGCACTATGCATGCAACCCACAT--AATTCATCATGAGTTGATGAACT-ACCG
1 TACAGGCACTATGTGTGCAAATC-CATGGAATTCATCATGAGTTGATGAA-TAACCG
* *
145323 TATAGGCACTAAGTGTGCA
1 TACAGGCACTATGTGTGCA
145342 TCTTAATAAA
Statistics
Matches: 251, Mismatches: 38, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
54 84 0.33
55 165 0.66
56 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (55 bp):
TACAGGCACTATGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACCG
Found at i:146610 original size:24 final size:24
Alignment explanation
Indices: 146555--146612 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
146545 GGTATTGGAC
*
146555 AATATTGATATTGGTATCAATACT
1 AATATCGATATTGGTATCAATACT
* * ** *
146579 GATGTCGATATTGGTATTGATATT
1 AATATCGATATTGGTATCAATACT
146603 AATATCGATA
1 AATATCGATA
146613 CTACAAGAAC
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (24 bp):
AATATCGATATTGGTATCAATACT
Found at i:148154 original size:2 final size:2
Alignment explanation
Indices: 148147--148219 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
148137 TCAAATAACC
148147 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
148189 AT 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 A
148220 CATTCAAGTT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:150146 original size:21 final size:21
Alignment explanation
Indices: 150097--150154 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 21
150087 TACTCTTCTG
*
150097 AGTGTATCGATATACATTCA-
1 AGTGTATCGATACACATTCAT
*
150117 AGGAATGTATCGGTACACATTCAT
1 A-G--TGTATCGATACACATTCAT
150141 AGTGTATCGATACA
1 AGTGTATCGATACA
150155 TAGCGAGGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 1 0.03
21 12 0.39
23 17 0.55
24 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (21 bp):
AGTGTATCGATACACATTCAT
Found at i:150167 original size:42 final size:42
Alignment explanation
Indices: 150079--150175 Score: 101
Period size: 42 Copynumber: 2.3 Consensus size: 42
150069 ACCTGATGAG
* *
150079 TGTATCGGTACTCTTCTGAGTGTATCGATATACATTCAAGGAA
1 TGTATCGGTACACTTCTGAGTGTATCGA-ATACATGCAAGGAA
*
150122 TGTATCGGTACACATTCAT-AGTGTATCG-ATACATAGCGAGG-A
1 TGTATCGGTACAC-TTC-TGAGTGTATCGAATACAT-GCAAGGAA
*
150164 TGTATCGATACA
1 TGTATCGGTACA
150176 TAGGTATCGA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
42 18 0.38
43 16 0.34
44 12 0.26
45 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (42 bp):
TGTATCGGTACACTTCTGAGTGTATCGAATACATGCAAGGAA
Found at i:155886 original size:21 final size:21
Alignment explanation
Indices: 155860--155899 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
155850 GTTAGGAGCG
155860 TAGGTGTATCGGTACACTCTC
1 TAGGTGTATCGGTACACTCTC
155881 TAGGTGTATCGGTACACTC
1 TAGGTGTATCGGTACACTC
155900 AATGTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.33
Consensus pattern (21 bp):
TAGGTGTATCGGTACACTCTC
Found at i:159064 original size:42 final size:43
Alignment explanation
Indices: 158969--159065 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 43
158959 GTACGACGAC
* ***
158969 TTTAATATAAAATTAATGAAAAATATTATTTATTTTATTATTTT
1 TTTAAT-TAAAATTAATGAAAAATATTATCTAAAATATTATTTT
*
159013 ATTAA-TAAAATTAAT-AAAAA-ATTATCTAAAATATTATTATT
1 TTTAATTAAAATTAATGAAAAATATTATCTAAAATATTATT-TT
159054 TTTAATTAAAAT
1 TTTAATTAAAAT
159066 ATTATTGAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
40 14 0.31
41 11 0.24
42 16 0.36
44 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (43 bp):
TTTAATTAAAATTAATGAAAAATATTATCTAAAATATTATTTT
Found at i:166100 original size:82 final size:82
Alignment explanation
Indices: 166004--166159 Score: 312
Period size: 82 Copynumber: 1.9 Consensus size: 82
165994 GTTGTCATCT
166004 TAAAATGACATTAAAATGAACGTTAGTATAGAGATAAAAGACTTGTTAGAAGTGAAATATTAGAT
1 TAAAATGACATTAAAATGAACGTTAGTATAGAGATAAAAGACTTGTTAGAAGTGAAATATTAGAT
166069 GACATTAAAAGTTGTCA
66 GACATTAAAAGTTGTCA
166086 TAAAATGACATTAAAATGAACGTTAGTATAGAGATAAAAGACTTGTTAGAAGTGAAATATTAGAT
1 TAAAATGACATTAAAATGAACGTTAGTATAGAGATAAAAGACTTGTTAGAAGTGAAATATTAGAT
166151 GACATTAAA
66 GACATTAAA
166160 TCATATTTTT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (82 bp):
TAAAATGACATTAAAATGAACGTTAGTATAGAGATAAAAGACTTGTTAGAAGTGAAATATTAGAT
GACATTAAAAGTTGTCA
Found at i:175956 original size:5 final size:5
Alignment explanation
Indices: 175946--175971 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
175936 TGACTTAGAA
175946 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
175972 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:177743 original size:3 final size:3
Alignment explanation
Indices: 177737--177761 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
177727 CTGAAACTTC
177737 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
177762 GTATCTCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:178810 original size:42 final size:42
Alignment explanation
Indices: 178716--178873 Score: 166
Period size: 42 Copynumber: 3.8 Consensus size: 42
178706 GTTTGTTATA
* * *
178716 AAACGCCGC-AAATACT-AAACTTTAGTGGCGTTTCT-TGTC-C
1 AAACGCCGCTATATACTCATACTTTAGTGGCGTTT-TAAG-CAC
* *
178756 AAAGGCCGCTATATACTCATAGTTTAGTGGCGTTTTAAGCAC
1 AAACGCCGCTATATACTCATACTTTAGTGGCGTTTTAAGCAC
* *
178798 AAACGCCACTATATACTCGTACTTTAGTGGC-TTTTAAGCAC
1 AAACGCCGCTATATACTCATACTTTAGTGGCGTTTTAAGCAC
* *
178839 AAACGCCGCTAAATTCT-AGTACTTTAGTGGCGTTT
1 AAACGCCGCTATATACTCA-TACTTTAGTGGCGTTT
178874 GTATATTAAA
Statistics
Matches: 99, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
40 8 0.08
41 44 0.44
42 47 0.47
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (42 bp):
AAACGCCGCTATATACTCATACTTTAGTGGCGTTTTAAGCAC
Found at i:178845 original size:41 final size:42
Alignment explanation
Indices: 178734--178873 Score: 169
Period size: 42 Copynumber: 3.4 Consensus size: 42
178724 CAAATACTAA
* * *
178734 ACTTTAGTGGCGTTTCT-TGTC-CAAAGGCCGCTATATACTCAT
1 ACTTTAGTGGCGTTT-TAAG-CACAAACGCCGCTATATACTCGT
* *
178776 AGTTTAGTGGCGTTTTAAGCACAAACGCCACTATATACTCGT
1 ACTTTAGTGGCGTTTTAAGCACAAACGCCGCTATATACTCGT
* * *
178818 ACTTTAGTGGC-TTTTAAGCACAAACGCCGCTAAATTCTAGT
1 ACTTTAGTGGCGTTTTAAGCACAAACGCCGCTATATACTCGT
178859 ACTTTAGTGGCGTTT
1 ACTTTAGTGGCGTTT
178874 GTATATTAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
41 39 0.46
42 46 0.54
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Consensus pattern (42 bp):
ACTTTAGTGGCGTTTTAAGCACAAACGCCGCTATATACTCGT
Found at i:182575 original size:43 final size:43
Alignment explanation
Indices: 182509--182763 Score: 232
Period size: 43 Copynumber: 6.0 Consensus size: 43
182499 AAATTAGCCG
* *
182509 CGTTTGTTCCAAAAAATGTCGCTATATATCTGATCTTTTGCGA
1 CGTTTGTTCCAAAAAATGTCGCTATAGATCTGACCTTTTGCGA
* * *
182552 CGTTTGATCCAAAAAATGCCGCTATAGATCAGACCTTTTGCGA
1 CGTTTGTTCCAAAAAATGTCGCTATAGATCTGACCTTTTGCGA
* * * *
182595 TGTTTGTTCCAAAAAATGTCGCTATAGATCTGACCTATTGTGG
1 CGTTTGTTCCAAAAAATGTCGCTATAGATCTGACCTTTTGCGA
* ** * * * *
182638 CGTTTGTTCTAAAAACGGT-GCTATAGATATCATCCTTTTGTGG
1 CGTTTGTTCCAAAAAATGTCGCTATAGATCTGA-CCTTTTGCGA
* * * * *
182681 CGTTTATTCC--AAAACGCCGCTATAAATATCGACCTTTTGCGA
1 CGTTTGTTCCAAAAAATGTCGCTATAGATCT-GACCTTTTGCGA
* *
182723 CGTTTGTTCCAAAAACA--CCGCTATAGATCTTGACCTATTGC
1 CGTTTGTTCCAAAAA-ATGTCGCTATAGATC-TGACCTTTTGC
182764 AGCGTTTTTG
Statistics
Matches: 173, Mismatches: 32, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
41 4 0.02
42 38 0.22
43 126 0.73
44 4 0.02
45 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (43 bp):
CGTTTGTTCCAAAAAATGTCGCTATAGATCTGACCTTTTGCGA
Found at i:184462 original size:20 final size:20
Alignment explanation
Indices: 184434--184482 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
184424 CAGTACAATG
* *
184434 GTATCGATATA-AGCCCTTTA
1 GTATTGATATAGA-CCCTTCA
*
184454 GTATTGATATCGACCCTTCA
1 GTATTGATATAGACCCTTCA
184474 GTATTGATA
1 GTATTGATA
184483 CCTACACTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (20 bp):
GTATTGATATAGACCCTTCA
Found at i:186861 original size:2 final size:2
Alignment explanation
Indices: 186856--186900 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
186846 TGTGTGTGTG
* * * *
186856 TA TA TA TA TA TA TA TA TA GA TA TA GA TA TA GA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
186898 TA T
1 TA T
186901 TTCATGTAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (2 bp):
TA
Found at i:186865 original size:6 final size:6
Alignment explanation
Indices: 186857--186897 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
186847 GTGTGTGTGT
* *
186857 ATATAT ATATAT ATATAG ATATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
186898 TATTTCATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (6 bp):
ATATAG
Found at i:187185 original size:15 final size:14
Alignment explanation
Indices: 187161--187190 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
187151 ATCACAAGGG
187161 AACAAACATAAGTC
1 AACAAACATAAGTC
187175 AACATAACATAAGTC
1 AACA-AACATAAGTC
187190 A
1 A
187191 TATCGTATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.57, C:0.20, G:0.07, T:0.17
Consensus pattern (14 bp):
AACAAACATAAGTC
Found at i:188374 original size:26 final size:26
Alignment explanation
Indices: 188333--188407 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
188323 GGCATAATTC
* *
188333 ATTTAAAAAAAATAAG-ACTTATTTA
1 ATTTTAAAAAAATAAGAAATTATTTA
*
188358 ATTTTTAAAAAATTAAGAAATTATTTA
1 A-TTTTAAAAAAATAAGAAATTATTTA
* *
188385 ATTTTAAAATAA-AAGCAATTATT
1 ATTTTAAAAAAATAAGAAATTATT
188408 AAAGTATTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
25 11 0.26
26 22 0.52
27 9 0.21
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (26 bp):
ATTTTAAAAAAATAAGAAATTATTTA
Found at i:188404 original size:25 final size:26
Alignment explanation
Indices: 188339--188407 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 26
188329 ATTCATTTAA
*
188339 AAAAAATAAG-ACTTATTTAATTTTT
1 AAAAAATAAGAAATTATTTAATTTTT
188364 AAAAAATTAAGAAATTATTTAA-TTTT
1 AAAAAA-TAAGAAATTATTTAATTTTT
*
188390 AAAATAA-AAGCAATTATT
1 AAAA-AATAAGAAATTATT
188408 AAAGTATTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
25 16 0.41
26 12 0.31
27 11 0.28
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (26 bp):
AAAAAATAAGAAATTATTTAATTTTT
Found at i:188847 original size:19 final size:19
Alignment explanation
Indices: 188823--188862 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
188813 TCTAGAAAAA
188823 TATTTTCTATTTTTATTTT
1 TATTTTCTATTTTTATTTT
* *
188842 TATTTTCTGTTTTTGTTTT
1 TATTTTCTATTTTTATTTT
188861 TA
1 TA
188863 GAAAATAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.78
Consensus pattern (19 bp):
TATTTTCTATTTTTATTTT
Found at i:195593 original size:16 final size:18
Alignment explanation
Indices: 195572--195607 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
195562 ATTTAACTCA
195572 AAATTATTT-A-AAATTT
1 AAATTATTTGATAAATTT
195588 AAATTATTTGATAAATTT
1 AAATTATTTGATAAATTT
195606 AA
1 AA
195608 CAACAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 1 0.06
18 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AAATTATTTGATAAATTT
Found at i:205190 original size:20 final size:20
Alignment explanation
Indices: 205165--205212 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
205155 TTTTAGTTAC
* *
205165 ATATATTTACATATACATTT
1 ATATATTTACACACACATTT
*
205185 ATATATTTTCACACACATTT
1 ATATATTTACACACACATTT
205205 ATATATTT
1 ATATATTT
205213 GGATATAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTTACACACACATTT
Found at i:208165 original size:24 final size:24
Alignment explanation
Indices: 208150--208195 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
208140 TATAATTTGC
208150 ACCGAAGTGCCACATAGAATATGA
1 ACCGAAGTGCCACATAGAATATGA
208174 ACCGAAGTGCCACATAG-ATATG
1 ACCGAAGTGCCACATAGAATATG
208196 TCCAGATGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (24 bp):
ACCGAAGTGCCACATAGAATATGA
Found at i:208412 original size:40 final size:40
Alignment explanation
Indices: 208368--208449 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
208358 TATTCTTTAC
* *
208368 TCAAATATAACATATTCACATAGCATATATTCGCGTAGAA
1 TCAAATATAACATATTCACATAGCATATATTCACATAGAA
208408 TCAAATATAACATATTCACATAGCATATATTCACATAGAA
1 TCAAATATAACATATTCACATAGCATATATTCACATAGAA
208448 TC
1 TC
208450 TTTTCATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.30
Consensus pattern (40 bp):
TCAAATATAACATATTCACATAGCATATATTCACATAGAA
Found at i:208455 original size:15 final size:15
Alignment explanation
Indices: 208419--208448 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
208409 CAAATATAAC
*
208419 ATATTCACATAGCAT
1 ATATTCACATAGAAT
208434 ATATTCACATAGAAT
1 ATATTCACATAGAAT
208449 CTTTTCATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (15 bp):
ATATTCACATAGAAT
Found at i:208470 original size:15 final size:15
Alignment explanation
Indices: 208452--208505 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
208442 ATAGAATCTT
208452 TTCATATAAAACACA
1 TTCATATAAAACACA
*
208467 TTCACATATATAACACA
1 TT--CATATAAAACACA
** *
208484 TTCGCATAGAACACA
1 TTCATATAAAACACA
208499 TTCATAT
1 TTCATAT
208506 TTTAATAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 17 0.55
17 14 0.45
ACGTcount: A:0.44, C:0.22, G:0.04, T:0.30
Consensus pattern (15 bp):
TTCATATAAAACACA
Found at i:208479 original size:19 final size:17
Alignment explanation
Indices: 208454--208491 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
208444 AGAATCTTTT
*
208454 CATATAAAACACATTCA
1 CATATATAACACATTCA
*
208471 CATATATAACACATTCG
1 CATATATAACACATTCA
208488 CATA
1 CATA
208492 GAACACATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.24, G:0.03, T:0.26
Consensus pattern (17 bp):
CATATATAACACATTCA
Found at i:215205 original size:24 final size:24
Alignment explanation
Indices: 215170--215248 Score: 97
Period size: 25 Copynumber: 3.3 Consensus size: 24
215160 TGAAGTGCCA
* *
215170 CATAG-ATATGTCCCAAAGGACCG
1 CATAGAATTTGTCCCGAAGGACCG
* *
215193 CGTAGAATTTGTCCCGAAGGACCA
1 CATAGAATTTGTCCCGAAGGACCG
*
215217 CATAGAAATTTGTCCCGAATGACCG
1 CATAG-AATTTGTCCCGAAGGACCG
215242 CATAGAA
1 CATAGAA
215249 CTCTCTACTC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
23 4 0.09
24 21 0.45
25 22 0.47
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (24 bp):
CATAGAATTTGTCCCGAAGGACCG
Found at i:215232 original size:25 final size:25
Alignment explanation
Indices: 215178--215248 Score: 99
Period size: 25 Copynumber: 2.9 Consensus size: 25
215168 CACATAGATA
* *
215178 TGTCCCAAAGGACCGCGTAG-AATT
1 TGTCCCGAAGGACCGCATAGAAATT
*
215202 TGTCCCGAAGGACCACATAGAAATT
1 TGTCCCGAAGGACCGCATAGAAATT
*
215227 TGTCCCGAATGACCGCATAGAA
1 TGTCCCGAAGGACCGCATAGAA
215249 CTCTCTACTC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
24 17 0.41
25 24 0.59
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20
Consensus pattern (25 bp):
TGTCCCGAAGGACCGCATAGAAATT
Found at i:219209 original size:20 final size:20
Alignment explanation
Indices: 219180--219229 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
219170 CATCCATGTA
*
219180 TTACTTAATTTCTATTTTGG
1 TTACTCAATTTCTATTTTGG
219200 TTACTCAATTTCTATTTTGG
1 TTACTCAATTTCTATTTTGG
219220 TTACTCAATT
1 TTACTCAATT
219230 ATTATATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.14, G:0.08, T:0.56
Consensus pattern (20 bp):
TTACTCAATTTCTATTTTGG
Found at i:223823 original size:19 final size:19
Alignment explanation
Indices: 223801--223843 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
223791 ATGCATCGAA
223801 GCACTCTAAGTGCACCGAT
1 GCACTCTAAGTGCACCGAT
*
223820 GCACTCTTAGTGCACCGAT
1 GCACTCTAAGTGCACCGAT
223839 GCACT
1 GCACT
223844 GAGAGTCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.23
Consensus pattern (19 bp):
GCACTCTAAGTGCACCGAT
Found at i:228683 original size:21 final size:22
Alignment explanation
Indices: 228634--228695 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
228624 ATACCCCCAT
228634 AAGGGAACCGATTCCCCCTTTG
1 AAGGGAACCGATTCCCCCTTTG
228656 AATGGGAACCGATTCCCTCC-TTG
1 AA-GGGAACCGATTCCC-CCTTTG
* *
228679 -AGGGAATCGATACCCCC
1 AAGGGAACCGATTCCCCC
228696 CATGGGTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 2 0.06
21 12 0.33
22 3 0.08
23 17 0.47
24 2 0.06
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.21
Consensus pattern (22 bp):
AAGGGAACCGATTCCCCCTTTG
Found at i:232249 original size:20 final size:20
Alignment explanation
Indices: 232224--232262 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
232214 TTTTCAAGGG
232224 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
232244 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
232263 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:234289 original size:29 final size:29
Alignment explanation
Indices: 234257--234312 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
234247 TGAGGCGTAT
* *
234257 TGTTTG-AATTTGTTTTTTTAACTTTCTAA
1 TGTTTGAAACTTG-TTTTTGAACTTTCTAA
234286 TGTTTGAAACTTGTTTTTGAACTTTCT
1 TGTTTGAAACTTGTTTTTGAACTTTCT
234313 TTGGATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.20, C:0.09, G:0.12, T:0.59
Consensus pattern (29 bp):
TGTTTGAAACTTGTTTTTGAACTTTCTAA
Found at i:236393 original size:84 final size:84
Alignment explanation
Indices: 236131--236903 Score: 620
Period size: 84 Copynumber: 9.3 Consensus size: 84
236121 TAAAGAAACT
* * * * * * * *
236131 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTTTCTG-CTAACAAAAGTCCTTCGAGTTCAACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTC-ACCAAAAGACCTTTGAGTTCGACTAC
236195 GCTCAGCTCCAAGGCACATC
65 GCTCAGCTCCAAGGCACATC
* * * * * * *
236215 ATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CC-AAAGACCCTTGAGTTTGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACG
* * * * *
236276 CACAGCTTCGAGGGCACGTT
66 CTCAGC-TCCAAGGCACATC
* * * * * *
236296 ACTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACG
* *
236361 CTCAACTCAAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* * * * * *
236380 AATTGGAGTATAACTTAAGTCGAGAAGGGCTATCTGGCAACCAAAAGACCTTCGAGTTCGACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTC-ACCAAAAGACCTTTGAGTTCGACTAC
* *
236445 GTTCAGCTCCAAGACACATC
65 GCTCAGCTCCAAGGCACATC
* * * * * * *** * * *
236465 TTTTGTAGTATAGCTTAAGTCAAGAAGGGCTATCT-T--CC-AAAGACCCCCGAGTTTGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACG
* *
236526 CTCAGCTTCGAGGGCACATC
66 CTCAGC-TCCAAGGCACATC
* ** * * * * *
236546 ATTTACAATATAACTCAAGGCTAAAAGGGTTATCTGTCACCAAAAGTCCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACG
* * *
236611 CTCAGCTTCAAGGTATATC
66 CTCAGCTCCAAGGCACATC
** * * * * *
236630 ATTTGCATAATAGCTTAAGTCGATAAGGGTTATCTGCCATCAAAAGACCTTTGAGTTTGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACG
* *
236695 TTCAGCTCCAAGGCATATC
66 CTCAGCTCCAAGGCACATC
* ** * * *
236714 ATTCGCAGCATGGCTTAAGTCGAGAAGGGTTATCTG---CC-AAAGACCCTTGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACG
* * *
236775 CTCAACTTCGAGGGCACATC
66 CTCAGC-TCCAAGGCACATC
* * * * * *
236795 ATTTACAACATAACTGAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACG
236859 CTCAGCTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* *
236878 ATTTGCAACATAGCTTAAGTCGAGAA
1 ATTTGCAGCATAACTTAAGTCGAGAA
236904 AAGCTATCTG
Statistics
Matches: 533, Mismatches: 141, Indels: 31
0.76 0.20 0.04
Matches are distributed among these distances:
80 67 0.13
81 113 0.21
82 1 0.00
83 32 0.06
84 204 0.38
85 116 0.22
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (84 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACG
CTCAGCTCCAAGGCACATC
Found at i:236411 original size:165 final size:165
Alignment explanation
Indices: 236139--236917 Score: 687
Period size: 165 Copynumber: 4.7 Consensus size: 165
236129 CTATTTGCAG
* * * *
236139 CATAACTCAAGGCTAGAAGGGTTTTCTG-CTAACAAAAGTCCTTCGAGTTCAACTACGCTCAGCT
1 CATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCT
*
236203 CCAAGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTT
65 CCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTT
* * * * * * *
236268 TGATTACACACAGCTTCGAGGGCACGTTACTTACAA
130 CGACTACACTCAGCTTCGAAGGCACATCATTTACAA
* *
236304 CATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACGCTCAACTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * * * *
236369 AAAGGCACATCAATTGGAGTATAACTTAAGTCGAGAAGGGCTATCTGGCAACCAAAAGA-CCTTC
66 CAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT-G---CC-AAAGACCCTT-
** * * * ** *
236433 GAGTTCGACTACGTTCAGC-TCCAAGACACATCTTTTGTAG
125 GAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAA
* * * * * * ** * * *
236473 TATAGCTTAAGTCAAGAAGGGCTATCT-T--CC-AAAGACCCCCGAGTTTGATTACACTCAGCTT
1 CATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGC-T
* * * ** * * * * * * * *
236534 CGAGGGCACATCATTTACAATATAACTCAAGGCTAAAAGGGTTATCTGTCACCAAAAGTCCTTTG
65 CCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CC-AAAGACCCTTG
* * * *
236599 AGTTCGACTACGCTCAGCTTC-AAGGTATATCATTTGCATA
126 AGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACA-A
* * * * * * * * * *
236639 -ATAGCTTAAGTCGATAAGGGTTATCTGCCATCAAAAGACCTTTGAGTTTGACTACGTTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * * *
236703 CAAGGCATATCATTCGCAGCATGGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTTGAGTTC
66 CAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTC
* * *
236768 GATTACACTCAACTTCGAGGGCACATCATTTACAA
131 GACTACACTCAGCTTCGAAGGCACATCATTTACAA
*
236803 CATAACTGAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTC
1 CATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* **
236867 CAAGGCACATCATTTGCAACATAGCTTAAGTCGAGAAAAGCTATCTGCCAA
66 CAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
236918 CCGAAGACCT
Statistics
Matches: 486, Mismatches: 111, Indels: 35
0.77 0.18 0.06
Matches are distributed among these distances:
164 100 0.21
165 222 0.46
166 46 0.09
168 38 0.08
169 61 0.13
170 19 0.04
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.26
Consensus pattern (165 bp):
CATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
CAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTC
GACTACACTCAGCTTCGAAGGCACATCATTTACAA
Found at i:236649 original size:250 final size:250
Alignment explanation
Indices: 236171--236962 Score: 1074
Period size: 250 Copynumber: 3.2 Consensus size: 250
236161 TTTCTGCTAA
* * *
236171 CAAAAGTCCTTCGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTC
1 CAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTC
* * * *
236236 GAGAAGGGCTATCTGCCAAAGACCCTTGAGTTTGATTACACACAGCTTCGAGGGCACGTTACTTA
66 GAGAAGGGCTATCTGCCAAAGACCCTTGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTA
*
236301 CAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACGCTCAA
131 CAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACGCTCAG
* * *
236366 C-TCAAAGGCACATCAATTGGAGT-ATAACTTAAGTCGAGAAGGGCTATCTGGCAAC
196 CTTC-AAGGCACATCATTTGCA-TAATAGCTTAAGTCGAGAAGGGCTATCTGGCAAC
* * *
236421 CAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGACACATCTTTTGTAGTATAGCTTAAGTC
1 CAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTC
* * **
236486 AAGAAGGGCTATCTTCCAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTA
66 GAGAAGGGCTATCTGCCAAAGACCCTTGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTA
* * *
236551 CAATATAACTCAAGGCTAAAAGGGTTATCTGTCACCAAAAGTCCTTTGAGTTCGACTACGCTCAG
131 CAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACGCTCAG
* * * * * *
236616 CTTCAAGGTATATCATTTGCATAATAGCTTAAGTCGATAAGGGTTATCT-GCCAT
196 CTTCAAGGCACATCATTTGCATAATAGCTTAAGTCGAGAAGGGCTATCTGGCAAC
* * * * * *
236670 CAAAAGACCTTTGAGTTTGACTACGTTCAGCTCCAAGGCATATCATTCGCAGCATGGCTTAAGTC
1 CAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTC
* * *
236735 GAGAAGGGTTATCTGCCAAAGACCCTTGAGTTCGATTACACTCAACTTCGAGGGCACATCATTTA
66 GAGAAGGGCTATCTGCCAAAGACCCTTGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTA
* *
236800 CAACATAACTGAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAG
131 CAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACGCTCAG
* ** *
236864 CTCCAAGGCACATCATTTGCA-ACATAGCTTAAGTCGAGAAAAGCTATCTGCCAAC
196 CTTCAAGGCACATCATTTGCATA-ATAGCTTAAGTCGAGAAGGGCTATCTGGCAAC
* * * ** * *
236919 C-GAAGACCTTCGAGTTTGATTATATTCAGCTCAAAGGCATATCA
1 CAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCA
236963 AATTTTACAG
Statistics
Matches: 474, Mismatches: 64, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
247 1 0.00
248 103 0.22
249 154 0.32
250 214 0.45
251 2 0.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.26
Consensus pattern (250 bp):
CAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTC
GAGAAGGGCTATCTGCCAAAGACCCTTGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTA
CAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCGACTACGCTCAG
CTTCAAGGCACATCATTTGCATAATAGCTTAAGTCGAGAAGGGCTATCTGGCAAC
Found at i:241623 original size:29 final size:29
Alignment explanation
Indices: 241591--241646 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
241581 TGAGGCGTAT
* *
241591 TGTTTG-AATTTGTTTTTTTAACTTTCTAA
1 TGTTTGAAACTTG-TTTTTGAACTTTCTAA
241620 TGTTTGAAACTTGTTTTTGAACTTTCT
1 TGTTTGAAACTTGTTTTTGAACTTTCT
241647 TTGGATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.20, C:0.09, G:0.12, T:0.59
Consensus pattern (29 bp):
TGTTTGAAACTTGTTTTTGAACTTTCTAA
Found at i:243637 original size:80 final size:80
Alignment explanation
Indices: 243506--243750 Score: 269
Period size: 80 Copynumber: 3.0 Consensus size: 80
243496 TCTGCTAACA
* ***
243506 AAAGACCTTCGAGTTCAACTATGTTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTTGA
1 AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTTGA
243571 GAAGGGTTATCTGCC
66 GAAGGGTTATCTGCC
* * * * * * *
243586 AAAGACCTT-GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCT
1 AAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAA-GTT
243650 -AGAAGGGTTATCTGTCACC
64 GAGAAGGGTTATCTG---CC
* ** *
243669 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAATATAGCTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTTGA
** *
243734 GAAAAGCTATCTGCC
66 GAAGGGTTATCTGCC
243749 AA
1 AA
243751 CCGAAGACCT
Statistics
Matches: 133, Mismatches: 25, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
79 14 0.11
80 53 0.40
81 2 0.02
82 1 0.01
83 46 0.35
84 17 0.13
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (80 bp):
AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTTGA
GAAGGGTTATCTGCC
Found at i:243760 original size:84 final size:82
Alignment explanation
Indices: 243507--243795 Score: 287
Period size: 84 Copynumber: 3.5 Consensus size: 82
243497 CTGCTAACAA
* * * *
243507 AAGACCTTCGAGTTCAACTATGTTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTTGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
243572 AAGGGTTATCTGCCA--
66 AAGGGTTATCTGCCACC
* * * * * * * * *
243587 AAGACCTT-GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTA
1 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
*
243651 GAAGGGTTATCTGTCACC
65 GAAGGGTTATCTGCCACC
**
243669 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAATATAGCTTAAGTCGA
1 -AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
** *
243734 GAAAAGCTATCTGCCAACC
65 GAAGGGTTATCTGCC-ACC
* * * ** * *
243753 GAAGACCTTCCAGTTTGATTACTTTCAGCTCAAAGGCATATCA
1 -AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCA
243796 AATTTTACAG
Statistics
Matches: 166, Mismatches: 37, Indels: 8
0.79 0.18 0.04
Matches are distributed among these distances:
79 14 0.08
80 51 0.31
83 46 0.28
84 55 0.33
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (82 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
AAGGGTTATCTGCCACC
Found at i:253412 original size:6 final size:6
Alignment explanation
Indices: 253401--253448 Score: 52
Period size: 5 Copynumber: 8.7 Consensus size: 6
253391 TCGAAATATC
253401 AAAAAT AAAAAT -AAAAT -AAAAT AAAAA- AAAAA- AAAAA- AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
253444 GAAAA
1 -AAAA
253449 GGAAAATTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
5 25 0.64
6 10 0.26
7 4 0.10
ACGTcount: A:0.88, C:0.00, G:0.02, T:0.10
Consensus pattern (6 bp):
AAAAAT
Found at i:258550 original size:25 final size:24
Alignment explanation
Indices: 258522--258574 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
258512 TATAGAAATT
258522 AATATAAACTAAT-ATTAATAAATAA
1 AATATAAAC-AATAATTAA-AAATAA
* *
258547 AATATTAACAATAATTAAAATTAA
1 AATATAAACAATAATTAAAAATAA
258571 AATA
1 AATA
258575 GAATTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (24 bp):
AATATAAACAATAATTAAAAATAA
Found at i:259733 original size:30 final size:31
Alignment explanation
Indices: 259693--259759 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 31
259683 TTCGGGTTGC
*
259693 TTTTCGGTTCGAGTTG-TTTGGTTC-GAGTTA
1 TTTTCAGTTCGAGTTGCTTTGGTTCAGA-TTA
259723 TTTTCAGTTCGAGTTGCTTTTGGTTCAGATTA
1 TTTTCAGTTCGAGTTGC-TTTGGTTCAGATTA
259755 TTTTC
1 TTTTC
259760 GATTCGGGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 15 0.45
32 16 0.48
33 2 0.06
ACGTcount: A:0.12, C:0.12, G:0.24, T:0.52
Consensus pattern (31 bp):
TTTTCAGTTCGAGTTGCTTTGGTTCAGATTA
Found at i:259748 original size:16 final size:16
Alignment explanation
Indices: 259662--259748 Score: 90
Period size: 16 Copynumber: 5.5 Consensus size: 16
259652 TCTGGTTAAA
*
259662 TTTGGTTTGAGTTGCT
1 TTTGGTTCGAGTTGCT
* *
259678 TTTTGTTCGGGTTGCT
1 TTTGGTTCGAGTTGCT
259694 TTTCGGTTCGAGTTG--
1 TTT-GGTTCGAGTTGCT
*
259709 TTTGGTTCGAGTT-AT
1 TTTGGTTCGAGTTGCT
*
259724 TTTCAGTTCGAGTTGCT
1 TTT-GGTTCGAGTTGCT
259741 TTTGGTTC
1 TTTGGTTC
259749 AGATTATTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
14 10 0.17
15 6 0.10
16 29 0.50
17 13 0.22
ACGTcount: A:0.07, C:0.11, G:0.29, T:0.53
Consensus pattern (16 bp):
TTTGGTTCGAGTTGCT
Found at i:275546 original size:20 final size:20
Alignment explanation
Indices: 275521--275568 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
275511 AAGCAAACAC
275521 AATAATTTTATTTAAAATCA
1 AATAATTTTATTTAAAATCA
275541 AATAATTTTATTTAAAATCA
1 AATAATTTTATTTAAAATCA
275561 AATAATTT
1 AATAATTT
275569 ATGTATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (20 bp):
AATAATTTTATTTAAAATCA
Found at i:292218 original size:20 final size:20
Alignment explanation
Indices: 292185--292223 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
292175 TGGATTTCAC
* *
292185 CGTCGATGACCAACAGCCGA
1 CGTCGATCAACAACAGCCGA
*
292205 CGTCGATCAACAACGGCCG
1 CGTCGATCAACAACAGCCG
292224 GTGAGACGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.36, G:0.26, T:0.10
Consensus pattern (20 bp):
CGTCGATCAACAACAGCCGA
Found at i:292643 original size:6 final size:6
Alignment explanation
Indices: 292570--292673 Score: 54
Period size: 6 Copynumber: 17.2 Consensus size: 6
292560 AATTTAATCA
* * *
292570 TTTTAT TATTCT TTTTA- TTCT-T TTTTA- TTTTA- TTTTAT TTCTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT-TTAT
* * * * *
292615 TATATAT ATTTTATT TATTTAT TTTTAT TTTTAT TATTAC TATTAT TATTAT
1 T-TTTAT -TTTTA-T T-TTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
*
292667 TATTAT T
1 TTTTAT T
292674 ATTCATATTA
Statistics
Matches: 79, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
5 16 0.20
6 42 0.53
7 14 0.18
8 7 0.09
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTTAT
Found at i:292674 original size:9 final size:9
Alignment explanation
Indices: 292572--292688 Score: 77
Period size: 9 Copynumber: 13.2 Consensus size: 9
292562 TTTAATCATT
*
292572 TTATTATTC
1 TTATTATTA
* *
292581 TTTTTATTC
1 TTATTATTA
292590 TT-TT-TTA
1 TTATTATTA
292597 TT-TTATT-
1 TTATTATTA
*
292604 TTATTTCTTA
1 TTA-TTATTA
292614 TTA-TATATA
1 TTATTAT-TA
292623 TT-TTATTTA
1 TTATTA-TTA
*
292632 TTTATTTTTA
1 -TTATTATTA
*
292642 TTTTTATTA
1 TTATTATTA
*
292651 TTACTATTA
1 TTATTATTA
292660 TTATTATTA
1 TTATTATTA
292669 TTATTATTCA
1 TTATTATT-A
292679 -TATTATTA
1 TTATTATTA
292687 TT
1 TT
292689 TCCTTTTTAT
Statistics
Matches: 87, Mismatches: 10, Indels: 22
0.73 0.08 0.18
Matches are distributed among these distances:
7 8 0.09
8 7 0.08
9 60 0.69
10 10 0.11
11 2 0.02
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (9 bp):
TTATTATTA
Found at i:292674 original size:15 final size:15
Alignment explanation
Indices: 292572--292688 Score: 77
Period size: 15 Copynumber: 7.9 Consensus size: 15
292562 TTTAATCATT
* *
292572 TTATTATTCTTTTTA
1 TTATTATTATTATTA
*
292587 TTCTT-TT-TTATT-
1 TTATTATTATTATTA
*
292599 TTATT-TTATTTCTTA
1 TTATTATTA-TTATTA
292614 TTA-TATATATT-TTA
1 TTATTAT-TATTATTA
* *
292628 TTTATTTATTTTTATTT
1 -TTA-TTATTATTATTA
*
292645 TTATTATTACTATTA
1 TTATTATTATTATTA
292660 TTATTATTATTATTA
1 TTATTATTATTATTA
292675 TTCA-TATTATTATT
1 TT-ATTATTATTATT
292689 TCCTTTTTAT
Statistics
Matches: 82, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
12 6 0.07
13 4 0.05
14 10 0.12
15 48 0.59
16 9 0.11
17 5 0.06
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (15 bp):
TTATTATTATTATTA
Found at i:292904 original size:5 final size:5
Alignment explanation
Indices: 292896--292959 Score: 51
Period size: 5 Copynumber: 12.6 Consensus size: 5
292886 TATTTTTATT
* * * *
292896 TTTTA TTTTA TTTTA TTTT- TCTTTGT TTTTG TTTTA TTTT- TTTCA TTTTG
1 TTTTA TTTTA TTTTA TTTTA T-TTT-A TTTTA TTTTA TTTTA TTTTA TTTTA
292946 TTTTA TTTTTA TTT
1 TTTTA -TTTTA TTT
292960 ATGATACCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
4 4 0.08
5 35 0.73
6 8 0.17
7 1 0.02
ACGTcount: A:0.11, C:0.03, G:0.05, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:292911 original size:10 final size:9
Alignment explanation
Indices: 292894--292961 Score: 64
Period size: 10 Copynumber: 6.9 Consensus size: 9
292884 TATATTTTTA
292894 TTTTTTATT
1 TTTTTTATT
292903 TTATTTTATT
1 TT-TTTTATT
*
292913 TTTCTTTGTTT
1 TTT-TTT-ATT
292924 TTGTTTTATT
1 TT-TTTTATT
*
292934 TTTTTCATT
1 TTTTTTATT
292943 TTGTTTTATT
1 TT-TTTTATT
292953 TTTATTTAT
1 TTT-TTTAT
292962 GATACCAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
9 12 0.24
10 29 0.59
11 7 0.14
12 1 0.02
ACGTcount: A:0.12, C:0.03, G:0.04, T:0.81
Consensus pattern (9 bp):
TTTTTTATT
Found at i:298229 original size:64 final size:64
Alignment explanation
Indices: 298090--298452 Score: 487
Period size: 64 Copynumber: 5.8 Consensus size: 64
298080 CAACTTTTAA
* * *
298090 AGTCAATTTCAA-TTCACAGTGAAGGATATTGGACTCAACAAATAAGTTT-CAGTTTCATTCAG
1 AGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTCAG
*
298152 AGTCAATTTCAACTTCACAGCGAAGGATATTAGAGA-T-AACAAACAACTTTCCAATTTCATTCA
1 AGTCAATTTCAACTTCACAGCGAAGGATATT-G-GACTCAACAAACAACTTTCCAGTTTCATTCA
*
298215 A
64 G
* * *
298216 AGTCAATTTCAACTTCACAGCGAAAGATATTGGACTCAACAAACAATTTTCTAGTTTCATTCAG
1 AGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTCAG
* *
298280 AGTCAATTTCAACTTCATAGCCAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTCAG
1 AGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTCAG
*
298344 AGTCAATTTCAACTTCACAGCGAAGGATATTGGACT-------CAAGTTTCCAGTTTCATTCAG
1 AGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTCAG
* *
298401 AGTCAATTTCAACTTCACAACGAAAGATATTGGACTCGAAACAATACAACTT
1 AGTCAATTTCAACTTCACAGCGAAGGATATTGGACTC--AACAA-ACAACTT
298453 ACACAAGATT
Statistics
Matches: 264, Mismatches: 21, Indels: 27
0.85 0.07 0.09
Matches are distributed among these distances:
57 54 0.20
62 14 0.05
63 30 0.11
64 159 0.60
65 2 0.01
67 5 0.02
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.30
Consensus pattern (64 bp):
AGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTCAG
Found at i:298415 original size:57 final size:57
Alignment explanation
Indices: 298327--298437 Score: 204
Period size: 57 Copynumber: 1.9 Consensus size: 57
298317 AACAAACAAC
* *
298327 TTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAG
1 TTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAAGATATTGGACTCAAG
298384 TTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAAGATATTGGACTC
1 TTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAAGATATTGGACTC
298438 GAAACAATAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (57 bp):
TTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAAGATATTGGACTCAAG
Found at i:299049 original size:86 final size:86
Alignment explanation
Indices: 298803--299087 Score: 414
Period size: 85 Copynumber: 3.3 Consensus size: 86
298793 CCCAATGTAG
* * *
298803 CATAACTCAAGGCAAGAA-GGTTATTTGTC-ATCAAAGACCTTCGAGTTCGATTACACTCAGCTC
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAATCAAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
298866 AAAGGCACATCCAATTTACAC
66 AAAGGCACATCAAATTTACAA
* * *
298887 CATAACTCAAGGCGAGAAGGGTTATCTGTCAA-CCAAGACCTTCGAGTTCGATTATACTCAGCTC
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAATCAAAGACCTTCGAGTTCGATTACACTCAGCTC
*
298951 AAAGGCACATCAAATTTATAA
66 AAAGGCACATCAAATTTACAA
* * * * *
298972 TATAGCTCAAGGCGAGAAGGGTTATTTGTCAATAAAAGGCCTTCGAGTTCGATTACATTCAGCTC
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAATCAAAGACCTTCGAGTTCGATTACACTCAGCTC
*
299037 AAAGGCATATCAAATTTACAA
66 AAAGGCACATCAAATTTACAA
299058 CATAGCTCAAGGCGAGAAGGGTTATCTGTC
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTC
299088 GACAAAAACT
Statistics
Matches: 179, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
84 17 0.09
85 87 0.49
86 75 0.42
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (86 bp):
CATAGCTCAAGGCGAGAAGGGTTATCTGTCAATCAAAGACCTTCGAGTTCGATTACACTCAGCTC
AAAGGCACATCAAATTTACAA
Found at i:300802 original size:3 final size:3
Alignment explanation
Indices: 300759--300858 Score: 64
Period size: 3 Copynumber: 32.7 Consensus size: 3
300749 TTTAATCATT
* *
300759 TTA TTA TTC TT- TT- TTA TT- TTA TTTC TTA TTA TATA TATA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA T-TA T-TA TTA -TTA
* * * *
300805 TTTC TTT TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTC TGA
1 -TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
300851 TTA TTA TT
1 TTA TTA TT
300859 TTCTTTTTAT
Statistics
Matches: 80, Mismatches: 10, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
2 8 0.10
3 54 0.68
4 18 0.22
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:300814 original size:53 final size:52
Alignment explanation
Indices: 300757--300869 Score: 124
Period size: 53 Copynumber: 2.1 Consensus size: 52
300747 AATTTAATCA
* * *
300757 TTTTATTATTCTTTTTTATT-TTATTTCTTATTATATATAT-ATTATT-TATTTCT
1 TTTTATTATT-ATTATTATTATTA-TTATTATTATAT-TATGATTATTAT-TTTCT
*
300810 TTTTATTTATTATTATTATTATTATTATTATTATATTCTGATTATTATTTTCT
1 TTTTA-TTATTATTATTATTATTATTATTATTATATTATGATTATTATTTTCT
300863 TTTTATT
1 TTTTATT
300870 CTATTTATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
52 4 0.08
53 39 0.75
54 9 0.17
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (52 bp):
TTTTATTATTATTATTATTATTATTATTATTATATTATGATTATTATTTTCT
Found at i:300868 original size:14 final size:14
Alignment explanation
Indices: 300819--300869 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
300809 TTTTTATTTA
*
300819 TTATTATTATTATTA
1 TTATTATTATT-TTC
*
300834 TTATTATTATATTC
1 TTATTATTATTTTC
*
300848 TGATTATTATTTTC
1 TTATTATTATTTTC
*
300862 TTTTTATT
1 TTATTATT
300870 CTATTTATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 20 0.67
15 10 0.33
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (14 bp):
TTATTATTATTTTC
Found at i:301035 original size:18 final size:17
Alignment explanation
Indices: 301008--301205 Score: 63
Period size: 16 Copynumber: 12.0 Consensus size: 17
300998 CTGTTTTTTA
301008 CTTA-TTTTATTATATTT
1 CTTATTTTTATT-TATTT
*
301025 CTTATTTTTATTTTTTT
1 CTTATTTTTATTTATTT
*
301042 CTTTTCTTTTATTT-TGTT
1 CTTAT-TTTTATTTAT-TT
* * *
301060 -TTGTTTTTCTTTGTTT
1 CTTATTTTTATTTATTT
301076 -TTATTTTTATTCT-TGTT
1 CTTATTTTTATT-TAT-TT
*
301093 TTTA-TTTTATTT-TGTT
1 CTTATTTTTATTTAT-TT
301109 -TTATTTTT-TATT-TTT
1 CTTATTTTTAT-TTATTT
301124 -TTA-TTTT-TTTATTTT
1 CTTATTTTTATTTA-TTT
* *
301139 CATT-TTTTCATTTTTTGT
1 C-TTATTTTTATTTATT-T
*
301157 TTTATTTTTATTTATGTT
1 CTTATTTTTATTTAT-TT
*
301175 AC-CA-TTTTA-TTATTT
1 -CTTATTTTTATTTATTT
*
301190 -TTATTTTTACTTATTT
1 CTTATTTTTATTTATTT
301206 TATTTTTTCT
Statistics
Matches: 145, Mismatches: 14, Indels: 45
0.71 0.07 0.22
Matches are distributed among these distances:
13 2 0.01
14 6 0.04
15 19 0.13
16 41 0.28
17 41 0.28
18 35 0.24
19 1 0.01
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.77
Consensus pattern (17 bp):
CTTATTTTTATTTATTT
Found at i:301037 original size:6 final size:6
Alignment explanation
Indices: 301020--301169 Score: 84
Period size: 6 Copynumber: 24.8 Consensus size: 6
301010 TATTTTATTA
*
301020 TATTTCT TATTTT TATTTT T-TTCTT T-TCTTT TATTTT GT-TTTGT TTTTCTT
1 TATTT-T TATTTT TATTTT TATT-TT TAT-TTT TATTTT -TATTT-T TATT-TT
* * * *
301071 TGTTTT TATTTT TATTCT TGTTTT TA-TTT TA-TTT T-GTTT TATTTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TA-TTTT
* *
301117 TATTTT T-TTAT T-TTTT TATTTT CATTTTT TCATTTT T-TGTTT TATTTT
1 TATTTT TATTTT TATTTT TATTTT TA-TTTT T-ATTTT TAT-TTT TATTTT
301165 TATTT
1 TATTT
301170 ATGTTACCAT
Statistics
Matches: 117, Mismatches: 11, Indels: 31
0.74 0.07 0.19
Matches are distributed among these distances:
5 24 0.21
6 61 0.52
7 30 0.26
8 2 0.02
ACGTcount: A:0.11, C:0.05, G:0.04, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:301061 original size:15 final size:16
Alignment explanation
Indices: 301029--301174 Score: 127
Period size: 16 Copynumber: 8.8 Consensus size: 16
301019 ATATTTCTTA
*
301029 TTTTTATTTTTTTCTTT
1 TTTTTATTTTGTT-TTT
*
301046 TCTTTTATTTTGTTTTG
1 T-TTTTATTTTGTTTTT
*
301063 TTTTT-CTTTGTTTTT
1 TTTTTATTTTGTTTTT
301078 ATTTTTATTCTTGTTTTT
1 -TTTTTATT-TTGTTTTT
*
301096 ATTTTATTTTGTTTTAT
1 TTTTTATTTTGTTTT-T
301113 TTTTTATTTT-TTTATT
1 TTTTTATTTTGTTT-TT
*
301129 TTTTTATTTTCATTTTT
1 TTTTTATTTT-GTTTTT
** *
301146 TCATT-TTTTGTTTTA
1 TTTTTATTTTGTTTTT
301161 TTTTTATTTATGTT
1 TTTTTATTT-TGTT
301175 ACCATTTTAT
Statistics
Matches: 106, Mismatches: 13, Indels: 20
0.76 0.09 0.14
Matches are distributed among these distances:
15 15 0.14
16 37 0.35
17 32 0.30
18 22 0.21
ACGTcount: A:0.10, C:0.04, G:0.05, T:0.81
Consensus pattern (16 bp):
TTTTTATTTTGTTTTT
Found at i:301132 original size:49 final size:46
Alignment explanation
Indices: 301009--301169 Score: 139
Period size: 49 Copynumber: 3.3 Consensus size: 46
300999 TGTTTTTTAC
* *
301009 TTATTTTATTATATTTCTTATTTTTATTTTTTTCTTTTCTTTTATTTTGTT
1 TTATTTT-TTAT-TTTTTTATTTTTA-TTTTAT-TTTT-TTTTATTTTGTT
* *
301060 TTGTTTTTCT-TTGTTTTTATTTTTATTCTTGTTTTTATTTTATTTTGTT
1 TTATTTTT-TATT-TTTTTATTTTTATT-TTATTTTT-TTTTATTTTGTT
*
301109 TTATTTTTTATTTTTTTATTTTTTTATTTTCATTTTTTCATT-TTTTGTT
1 TTATTTTTTATTTTTTTA--TTTTTATTTT-ATTTTTT-TTTATTTTGTT
301158 TTA-TTTTTATTT
1 TTATTTTTTATTT
301170 ATGTTACCAT
Statistics
Matches: 95, Mismatches: 7, Indels: 19
0.79 0.06 0.16
Matches are distributed among these distances:
48 16 0.17
49 41 0.43
50 31 0.33
51 7 0.07
ACGTcount: A:0.12, C:0.04, G:0.04, T:0.80
Consensus pattern (46 bp):
TTATTTTTTATTTTTTTATTTTTATTTTATTTTTTTTTATTTTGTT
Found at i:301146 original size:8 final size:7
Alignment explanation
Indices: 301009--301213 Score: 72
Period size: 7 Copynumber: 28.3 Consensus size: 7
300999 TGTTTTTTAC
301009 TTATTTT
1 TTATTTT
301016 ATTATATTT
1 -TTAT-TTT
301025 CTTA-TTT
1 -TTATTTT
301032 TTATTTT
1 TTATTTT
*
301039 TT-TCTT
1 TTATTTT
*
301045 TTCTTTT
1 TTATTTT
301052 ATT-TTGTT
1 -TTATT-TT
*
301060 TTGTTTT
1 TTATTTT
*
301067 TCTTTGTTT
1 T-TAT-TTT
301076 TTA-TTT
1 TTATTTT
*
301082 TTA-TTC
1 TTATTTT
*
301088 TT-GTTT
1 TTATTTT
301094 TTATTTT
1 TTATTTT
301101 ATT-TTGTT
1 -TTATT-TT
301109 TTATTTT
1 TTATTTT
301116 TTATTTTT
1 TTA-TTTT
301124 TTATTTT
1 TTATTTT
301131 TT-TATTT
1 TTAT-TTT
*
301138 TCATTTT
1 TTATTTT
301145 TTCATTTT
1 TT-ATTTT
*
301153 TTGTTTT
1 TTATTTT
301160 ATT-TTTAT
1 -TTATTT-T
*
301168 TTATGTTA
1 TTAT-TTT
**
301176 CCATTTT
1 TTATTTT
301183 ATTA-TTT
1 -TTATTTT
301190 TTA-TTT
1 TTATTTT
301196 TTACTTATT
1 TTA-TT-TT
301205 TTATTTT
1 TTATTTT
301212 TT
1 TT
301214 CTCTCTTCTT
Statistics
Matches: 155, Mismatches: 17, Indels: 51
0.70 0.08 0.23
Matches are distributed among these distances:
6 32 0.21
7 62 0.40
8 44 0.28
9 17 0.11
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (7 bp):
TTATTTT
Found at i:301163 original size:82 final size:80
Alignment explanation
Indices: 301011--301213 Score: 207
Period size: 82 Copynumber: 2.4 Consensus size: 80
301001 TTTTTTACTT
* *
301011 ATTTTATTATATTTCTTATTTTTATTTTTTTCTTTTCTTTTATTTTGTTTTGTTTTTCTTTGTTT
1 ATTTTA-T-TATTT-TTATTTTTATTTTTTT-ATTT-TTTTATTTTATTTTGTTTTTCTTTGTTT
***
301076 TTATTTTTATTCT-TGTTTTT
61 TTATTTTTATT-TATGTTACC
*
301096 ATTTTATTTTGTTTTATTTTTTATTTTTTTATTTTTTTATTTTCATTTT-TTCATTT-TTTG-TT
1 ATTTTATTAT-TTTTA-TTTTTATTTTTTTATTTTTTTATTTT-ATTTTGTT--TTTCTTTGTTT
301158 TTATTTTTATTTATGTTACC
61 TTATTTTTATTTATGTTACC
*
301178 ATTTTATTATTTTTATTTTTACTTATTTTATTTTTT
1 ATTTTATTATTTTTATTTTTA-TTTTTTTATTTTTT
301214 CTCTCTTCTT
Statistics
Matches: 103, Mismatches: 8, Indels: 18
0.80 0.06 0.14
Matches are distributed among these distances:
80 6 0.06
81 19 0.18
82 37 0.36
83 16 0.16
84 19 0.18
85 6 0.06
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (80 bp):
ATTTTATTATTTTTATTTTTATTTTTTTATTTTTTTATTTTATTTTGTTTTTCTTTGTTTTTATT
TTTATTTATGTTACC
Found at i:301164 original size:5 final size:5
Alignment explanation
Indices: 301009--301144 Score: 59
Period size: 5 Copynumber: 26.4 Consensus size: 5
300999 TGTTTTTTAC
* * *
301009 TTATT TTATT ATATTT CTTATT TT-TAT TT-TT TTCTT TTCTT TTATT
1 TTATT TTATT TTA-TT -TTATT TTAT-T TTATT TTATT TTATT TTATT
* * * *
301055 TTGTT TTGTT TT-TCT TTGTTT TTATTT TTATT CTTGTTT TTATT TTATT
1 TTATT TTATT TTAT-T TT-ATT TTA-TT TTATT -TT-ATT TTATT TTATT
* *
301104 TTGTT TTATT TT-TT ATTTTT TTA-T TT-TT TTATT TTCATT TT
1 TTATT TTATT TTATT -TTATT TTATT TTATT TTATT TT-ATT TT
301145 TTCATTTTTT
Statistics
Matches: 106, Mismatches: 10, Indels: 29
0.73 0.07 0.20
Matches are distributed among these distances:
4 13 0.12
5 65 0.61
6 23 0.22
7 5 0.05
ACGTcount: A:0.12, C:0.04, G:0.04, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:301213 original size:16 final size:15
Alignment explanation
Indices: 301002--301212 Score: 76
Period size: 15 Copynumber: 13.3 Consensus size: 15
300992 TTATTACTGT
301002 TTTTTACTTATTTTATTA
1 TTTTTA-TTA-TTT-TTA
* *
301020 TATTTCTTATTTTTA
1 TTTTTATTATTTTTA
*
301035 TTTTT-TT-CTTTT-
1 TTTTTATTATTTTTA
* * *
301047 CTTTTATTTTGTTTTG
1 TTTTTATTAT-TTTTA
* *
301063 TTTTTCTTTGTTTTTA
1 TTTTT-ATTATTTTTA
* *
301079 TTTTTATTCTTGTTTT
1 TTTTTATTATT-TTTA
*
301095 TATTTTATTTTGTTTTA
1 T-TTTTATTAT-TTTTA
301112 TTTTTTATT-TTTTTA
1 -TTTTTATTATTTTTA
*
301127 TTTTT-TTATTTTCA
1 TTTTTATTATTTTTA
*
301141 TTTTTTCATTTTTTGTTTTA
1 -TTTTT-A--TTAT-TTTTA
*
301161 TTTTTATT-TATGTTA
1 TTTTTATTAT-TTTTA
*
301176 CCATTTTATTATTTTTA
1 --TTTTTATTATTTTTA
301193 TTTTTACTTA-TTTTA
1 TTTTTA-TTATTTTTA
301208 TTTTT
1 TTTTT
301213 TCTCTCTTCT
Statistics
Matches: 150, Mismatches: 23, Indels: 43
0.69 0.11 0.20
Matches are distributed among these distances:
12 4 0.03
13 8 0.05
14 12 0.08
15 45 0.30
16 26 0.17
17 35 0.23
18 8 0.05
19 8 0.05
20 4 0.03
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (15 bp):
TTTTTATTATTTTTA
Found at i:302503 original size:23 final size:23
Alignment explanation
Indices: 302477--302545 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
302467 CACCACAGCT
*
302477 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
302500 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
302523 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
302546 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:308791 original size:2 final size:2
Alignment explanation
Indices: 308784--308814 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
308774 ACAACAATCT
308784 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
308815 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:313704 original size:20 final size:20
Alignment explanation
Indices: 313679--313716 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
313669 ATTCATCCTA
313679 GTTCATCCAATATCGATAAT
1 GTTCATCCAATATCGATAAT
* *
313699 GTTCATCTAGTATCGATA
1 GTTCATCCAATATCGATA
313717 CTTGAACCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (20 bp):
GTTCATCCAATATCGATAAT
Found at i:327208 original size:23 final size:22
Alignment explanation
Indices: 327164--327208 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
327154 AATGTCATGG
* *
327164 GGGAACCGATACCCCCACAGGA
1 GGGAACCAATACCCCCAAAGGA
*
327186 GGGAACCAATTCCCCCTAAAGGA
1 GGGAACCAATACCCCC-AAAGGA
327209 AGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.33, C:0.33, G:0.24, T:0.09
Consensus pattern (22 bp):
GGGAACCAATACCCCCAAAGGA
Found at i:328879 original size:23 final size:24
Alignment explanation
Indices: 328834--328879 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
328824 AATCTTATAT
* *
328834 GGCACTACGGTGCAAATTCTACGC
1 GGCACTACGATGCAAATTATACGC
*
328858 GGCACTTCGATGC-AATTATACG
1 GGCACTACGATGCAAATTATACG
328880 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (24 bp):
GGCACTACGATGCAAATTATACGC
Found at i:334488 original size:9 final size:9
Alignment explanation
Indices: 334439--334488 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
334429 TCAGTATTGA
334439 AATTTTTGG
1 AATTTTTGG
334448 AATTTCTT-G
1 AATTT-TTGG
*
334457 AATTTATGG
1 AATTTTTGG
*
334466 AATTTATGG
1 AATTTTTGG
334475 AATTTTTGG
1 AATTTTTGG
*
334484 TATTT
1 AATTT
334489 GAAATTTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
8 1 0.03
9 33 0.92
10 2 0.06
ACGTcount: A:0.26, C:0.02, G:0.18, T:0.54
Consensus pattern (9 bp):
AATTTTTGG
Found at i:334488 original size:18 final size:18
Alignment explanation
Indices: 334439--334488 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
334429 TCAGTATTGA
* *
334439 AATTTTTGGAATTTCTTG
1 AATTTTTGGAATTTATGG
*
334457 AATTTATGGAATTTATGG
1 AATTTTTGGAATTTATGG
*
334475 AATTTTTGGTATTT
1 AATTTTTGGAATTT
334489 GAAATTTAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.26, C:0.02, G:0.18, T:0.54
Consensus pattern (18 bp):
AATTTTTGGAATTTATGG
Found at i:335605 original size:38 final size:38
Alignment explanation
Indices: 335563--335658 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 38
335553 GCATCTTTTG
* *
335563 GGATGACAGGTCATTCGGGACACAGATTACATCCTTCA
1 GGATGATAGGTCATTCGGGACACAGATGACATCCTTCA
* * *
335601 GGATGATAGGTCCTTCAGGACACAGATGACATCCTTCG
1 GGATGATAGGTCATTCGGGACACAGATGACATCCTTCA
*
335639 GGATGATAGGTCTTTCGGGA
1 GGATGATAGGTCATTCGGGA
335659 TATTTATACG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (38 bp):
GGATGATAGGTCATTCGGGACACAGATGACATCCTTCA
Found at i:335766 original size:30 final size:30
Alignment explanation
Indices: 335730--335819 Score: 126
Period size: 30 Copynumber: 3.0 Consensus size: 30
335720 GAGTTCTCAG
335730 TAATGTACATGGGCTTATAAAAGATATCAA
1 TAATGTACATGGGCTTATAAAAGATATCAA
* *
335760 TAATGTACATTGGCTTATAAAAGATATCAT
1 TAATGTACATGGGCTTATAAAAGATATCAA
* * * *
335790 TACTGTATATGGGCCTAAAAAAGATATCAA
1 TAATGTACATGGGCTTATAAAAGATATCAA
335820 AAGTATACAT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (30 bp):
TAATGTACATGGGCTTATAAAAGATATCAA
Found at i:338279 original size:14 final size:14
Alignment explanation
Indices: 338268--338374 Score: 76
Period size: 16 Copynumber: 7.4 Consensus size: 14
338258 TAAAAAAACT
338268 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
338282 AAAAAGAAGAAGAAAG
1 AAAAAGAA-AA-AAAG
* * *
338298 AAGAAG-AAAGAAC
1 AAAAAGAAAAAAAG
338311 AAAAAGAACAAAAAG
1 AAAAAGAA-AAAAAG
338326 --AAAGAACAAAAAG
1 AAAAAGAA-AAAAAG
* *
338339 AAGGAACAAAAAAAGG
1 AA-AAAGAAAAAAA-G
*
338355 AAAACAGAAAAAATG
1 AAAA-AGAAAAAAAG
338370 AAAAA
1 AAAAA
338375 ACAATGAGAG
Statistics
Matches: 73, Mismatches: 11, Indels: 18
0.72 0.11 0.18
Matches are distributed among these distances:
13 20 0.27
14 12 0.16
15 18 0.25
16 23 0.32
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.01
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:338285 original size:13 final size:13
Alignment explanation
Indices: 338269--338373 Score: 61
Period size: 13 Copynumber: 7.3 Consensus size: 13
338259 AAAAAAACTA
338269 AAAAGAAAAAAAG
1 AAAAGAAAAAAAG
338282 AAAAAGAAGAAGAAAG
1 -AAAAGAA-AA-AAAG
*
338298 AAGAAGAAAGAACA-
1 AA-AAGAAA-AAAAG
338312 AAAAGAACAAAAAG
1 AAAAGAA-AAAAAG
338326 -AAAGAACAAAAAG
1 AAAAGAA-AAAAAG
*
338339 AAGGAACAAAAAAAGG
1 AA--AAGAAAAAAA-G
*
338355 AAAACAGAAAAAATG
1 -AAA-AGAAAAAAAG
338370 AAAA
1 AAAA
338374 AACAATGAGA
Statistics
Matches: 74, Mismatches: 5, Indels: 25
0.71 0.05 0.24
Matches are distributed among these distances:
13 22 0.30
14 14 0.19
15 14 0.19
16 22 0.30
17 2 0.03
ACGTcount: A:0.76, C:0.05, G:0.18, T:0.01
Consensus pattern (13 bp):
AAAAGAAAAAAAG
Done.