Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2195_ERROPOS1964815+
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: 398699
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 1 of 2
Found at i:221 original size:16 final size:17
Alignment explanation
Indices: 195--229 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
185 CTTGAGTTTC
*
195 TTGAGTTATTTTAGGTT
1 TTGAGTTATTTTAGATT
212 TTGA-TTATTTTAGATT
1 TTGAGTTATTTTAGATT
228 TT
1 TT
230 AATCAAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.20, C:0.00, G:0.17, T:0.63
Consensus pattern (17 bp):
TTGAGTTATTTTAGATT
Found at i:786 original size:3 final size:3
Alignment explanation
Indices: 778--802 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
768 AATAGATATA
778 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
803 GAGCAACAAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3944 original size:15 final size:14
Alignment explanation
Indices: 3918--3947 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3908 TGAAATCTCC
3918 AATAAAAATAAATA
1 AATAAAAATAAATA
3932 AATAAATAATAAATA
1 AATAAA-AATAAATA
3947 A
1 A
3948 GCAAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAAAAATAAATA
Found at i:9531 original size:24 final size:24
Alignment explanation
Indices: 9504--9555 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
9494 TTAGTAAGTC
*
9504 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
9528 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
9552 AAAT
1 AAAT
9556 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:11502 original size:24 final size:24
Alignment explanation
Indices: 11475--11526 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
11465 TTAGTAAGTC
*
11475 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
11499 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
11523 AAAT
1 AAAT
11527 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:13697 original size:24 final size:24
Alignment explanation
Indices: 13670--13721 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
13660 TTAGTAAGTC
*
13670 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
13694 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
13718 AAAT
1 AAAT
13722 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:31581 original size:23 final size:23
Alignment explanation
Indices: 31521--31583 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
31511 ATGGGGTAGG
* *
31521 ATCTAAATCTGTATCTGTTATGC
1 ATCTGAATCTGTATTTGTTATGC
*
31544 ATCTGAATCTATATTTGTTATGC
1 ATCTGAATCTGTATTTGTTATGC
* **
31567 ATTTGTGTCTGTATTTG
1 ATCTGAATCTGTATTTG
31584 CTTCCTAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.22, C:0.13, G:0.16, T:0.49
Consensus pattern (23 bp):
ATCTGAATCTGTATTTGTTATGC
Found at i:32755 original size:26 final size:26
Alignment explanation
Indices: 32706--32772 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
32696 TCTTCAACTC
**
32706 TTTAAATTT-ATAAAGAAAAAATTAT
1 TTTAAATTTCATTTAGAAAAAATTAT
32731 TTTAAATTTCATTTAGAAAAAATTAT
1 TTTAAATTTCATTTAGAAAAAATTAT
32757 TTTAAATTTCATTTAG
1 TTTAAATTTCATTTAG
32773 TTTTTCGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
25 9 0.23
26 30 0.77
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (26 bp):
TTTAAATTTCATTTAGAAAAAATTAT
Found at i:38261 original size:27 final size:27
Alignment explanation
Indices: 38205--38264 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
38195 CTTTAAATAT
**
38205 TTTTTTATAAATATATTTGTTATTTAA
1 TTTTTTATAAATATATTTGTTACATAA
*
38232 TTTTTTATAAATATATTTGTTACATGA
1 TTTTTTATAAATATATTTGTTACATAA
38259 TTTTTT
1 TTTTTT
38265 CCACCCATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (27 bp):
TTTTTTATAAATATATTTGTTACATAA
Found at i:40824 original size:18 final size:18
Alignment explanation
Indices: 40779--40830 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
40769 GGCTCACAAT
*
40779 ACACATA-GGATCGCAATA
1 ACACATAGGGTTCGC-ATA
*
40797 ACAAAT-GGGTTCGCATA
1 ACACATAGGGTTCGCATA
40814 ACACATAGGGTTCGCAT
1 ACACATAGGGTTCGCAT
40831 TACATAGGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 8 0.28
18 21 0.72
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (18 bp):
ACACATAGGGTTCGCATA
Found at i:40837 original size:16 final size:16
Alignment explanation
Indices: 40816--40846 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40806 TTCGCATAAC
*
40816 ACATAGGGTTCGCATT
1 ACATAGGATTCGCATT
40832 ACATAGGATTCGCAT
1 ACATAGGATTCGCAT
40847 GCCTTACTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (16 bp):
ACATAGGATTCGCATT
Found at i:40884 original size:18 final size:18
Alignment explanation
Indices: 40861--40895 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
40851 TACTATTCAT
40861 TACTATTCATTACTGACC
1 TACTATTCATTACTGACC
40879 TACTATTCATTACTGAC
1 TACTATTCATTACTGAC
40896 TGCCGAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.40
Consensus pattern (18 bp):
TACTATTCATTACTGACC
Found at i:40892 original size:10 final size:10
Alignment explanation
Indices: 40850--40874 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
40840 TTCGCATGCC
40850 TTACTATTCA
1 TTACTATTCA
40860 TTACTATTCA
1 TTACTATTCA
40870 TTACT
1 TTACT
40875 GACCTACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.20, G:0.00, T:0.52
Consensus pattern (10 bp):
TTACTATTCA
Found at i:47880 original size:6 final size:7
Alignment explanation
Indices: 47864--47888 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
47854 ATATTTTCTA
47864 TTTTAAT
1 TTTTAAT
47871 TTTTAAT
1 TTTTAAT
47878 TTTTAAT
1 TTTTAAT
47885 TTTT
1 TTTT
47889 TTATAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTAAT
Found at i:64943 original size:8 final size:8
Alignment explanation
Indices: 64927--64957 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
64917 CTTTGTTATA
*
64927 TCTTCTTT
1 TCTTTTTT
64935 TCTTTTTT
1 TCTTTTTT
64943 TCTTTTTT
1 TCTTTTTT
64951 TCTTTTT
1 TCTTTTT
64958 CTCATATCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TCTTTTTT
Found at i:65826 original size:20 final size:19
Alignment explanation
Indices: 65791--65831 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
65781 AAAAATAACA
65791 TTAATAATAATTTTAATAT
1 TTAATAATAATTTTAATAT
65810 TTAAGTAAT-ATTCTTAATAT
1 TTAA-TAATAATT-TTAATAT
65830 TT
1 TT
65832 TATTTAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
TTAATAATAATTTTAATAT
Found at i:66420 original size:30 final size:30
Alignment explanation
Indices: 66386--66443 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
66376 GTAATGACAT
66386 TAATGGTAAATGAC-AAATAATAAAAGTATG
1 TAATGG-AAATGACAAAATAATAAAAGTATG
* *
66416 TAATGGCAATGACTAAAATGATAAAAGT
1 TAATGGAAATGAC-AAAATAATAAAAGT
66444 TTACAGACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.25
30 6 0.25
31 12 0.50
ACGTcount: A:0.52, C:0.05, G:0.17, T:0.26
Consensus pattern (30 bp):
TAATGGAAATGACAAAATAATAAAAGTATG
Found at i:66754 original size:31 final size:32
Alignment explanation
Indices: 66709--66770 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
66699 CCCTATACAT
66709 TAATTCGATCAATTTTAAACCATGTACTTTTC
1 TAATTCGATCAATTTTAAACCATGTACTTTTC
* **
66741 TAATT-GATTAATTTTAATTCATGTACTTTT
1 TAATTCGATCAATTTTAAACCATGTACTTTT
66771 GACCCAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.31, C:0.13, G:0.06, T:0.50
Consensus pattern (32 bp):
TAATTCGATCAATTTTAAACCATGTACTTTTC
Found at i:71479 original size:16 final size:16
Alignment explanation
Indices: 71458--71494 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
71448 CTTTTGCAAA
*
71458 ATTTTATATATTTTTT
1 ATTTTAGATATTTTTT
71474 ATTTTAGATATTTTTT
1 ATTTTAGATATTTTTT
*
71490 GTTTT
1 ATTTT
71495 TGAACTACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (16 bp):
ATTTTAGATATTTTTT
Found at i:71838 original size:26 final size:28
Alignment explanation
Indices: 71793--71871 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 28
71783 ATCTCAAAAT
*
71793 TATACATGAATTTTAATTTAATGTGCAATTG
1 TATACATGAACTTTAA-TT-A-GTGCAATTG
71824 TATACATGAACTTTAATTTAGTGCAATTG
1 TATACATGAACTTTAA-TTAGTGCAATTG
*
71853 TATACATGAAACTCTAATT
1 TATACATG-AACTTTAATT
71872 GTGGCTTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 19 0.42
30 8 0.18
31 18 0.40
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (28 bp):
TATACATGAACTTTAATTAGTGCAATTG
Found at i:71848 original size:29 final size:31
Alignment explanation
Indices: 71793--71871 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
71783 ATCTCAAAAT
*
71793 TATACATGAATTTTAATTTAATGTGCAATTG
1 TATACATGAACTTTAATTTAATGTGCAATTG
71824 TATACATGAACTTTAATTT-A-GTGCAATTG
1 TATACATGAACTTTAATTTAATGTGCAATTG
*
71853 TATACATGAAACTCTAATT
1 TATACATG-AACTTTAATT
71872 GTGGCTTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
29 17 0.38
30 10 0.22
31 18 0.40
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (31 bp):
TATACATGAACTTTAATTTAATGTGCAATTG
Found at i:73868 original size:34 final size:34
Alignment explanation
Indices: 73830--73898 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
73820 CCAAAAGAAC
*
73830 ATAAACATATCAATGTCGGACACATACATAGCTA
1 ATAAACATATCAATGTCAGACACATACATAGCTA
*
73864 ATAAACATATCAATGTCAGACACATACATATCTA
1 ATAAACATATCAATGTCAGACACATACATAGCTA
73898 A
1 A
73899 CAAGTCAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.25
Consensus pattern (34 bp):
ATAAACATATCAATGTCAGACACATACATAGCTA
Found at i:74722 original size:31 final size:31
Alignment explanation
Indices: 74680--74741 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
74670 GTTGAGCCTG
*
74680 ATGGCAGTAAAATAATTAGTACCAATTGAAC
1 ATGGCAATAAAATAATTAGTACCAATTGAAC
74711 ATGGCAATAAAATAATTAGTACCAATTGAAC
1 ATGGCAATAAAATAATTAGTACCAATTGAAC
74742 TTAAAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.26
Consensus pattern (31 bp):
ATGGCAATAAAATAATTAGTACCAATTGAAC
Found at i:83328 original size:29 final size:25
Alignment explanation
Indices: 83303--83361 Score: 102
Period size: 24 Copynumber: 2.4 Consensus size: 25
83293 TATATATAAA
83303 ATATATATTTGATTAAAAAT-AAAT
1 ATATATATTTGATTAAAAATAAAAT
*
83327 ATATATATTTGATTAAAAATAAAAA
1 ATATATATTTGATTAAAAATAAAAT
83352 ATATATATTT
1 ATATATATTT
83362 AATATATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 20 0.61
25 13 0.39
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (25 bp):
ATATATATTTGATTAAAAATAAAAT
Found at i:88247 original size:19 final size:19
Alignment explanation
Indices: 88225--88262 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
88215 AAATTAATAC
88225 TTATATATTAAATCAAAGA
1 TTATATATTAAATCAAAGA
*
88244 TTATATATTACATCAAAGA
1 TTATATATTAAATCAAAGA
88263 GCACGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
TTATATATTAAATCAAAGA
Found at i:88466 original size:22 final size:22
Alignment explanation
Indices: 88441--88485 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
88431 GTTCTTACAA
88441 GAATCTCCATTATACTTCTCAT
1 GAATCTCCATTATACTTCTCAT
88463 GAATCTCCATTATACTTCTCAT
1 GAATCTCCATTATACTTCTCAT
88485 G
1 G
88486 GAGGGTACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (22 bp):
GAATCTCCATTATACTTCTCAT
Found at i:92331 original size:10 final size:10
Alignment explanation
Indices: 92308--92340 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
92298 AAACGAGAGC
92308 AAAAAGAAAG
1 AAAAAGAAAG
92318 -AAAAGAAAG
1 AAAAAGAAAG
*
92327 AAAAAGAGAG
1 AAAAAGAAAG
92337 AAAA
1 AAAA
92341 TCTTCCATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:95804 original size:9 final size:9
Alignment explanation
Indices: 95790--95822 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
95780 GAGGATTTGG
95790 TTAATTAAA
1 TTAATTAAA
95799 TTAATTAAA
1 TTAATTAAA
*
95808 TTAACTAAA
1 TTAATTAAA
95817 TTAATT
1 TTAATT
95823 TTCTAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (9 bp):
TTAATTAAA
Found at i:104275 original size:46 final size:46
Alignment explanation
Indices: 104189--104278 Score: 117
Period size: 46 Copynumber: 2.0 Consensus size: 46
104179 ATATATAAAA
* *
104189 AAATCTATTCATGCTTTAGATAGCACATTCTCGAAGTCAAGCCAGC
1 AAATCTAATCATGCTTTAGATAGCACAATCTCGAAGTCAAGCCAGC
* * * * *
104235 AAATCTAATCATGCTTTAGATTGGAGAATCTTGAATTCAAGCCA
1 AAATCTAATCATGCTTTAGATAGCACAATCTCGAAGTCAAGCCA
104279 AAATTTCTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (46 bp):
AAATCTAATCATGCTTTAGATAGCACAATCTCGAAGTCAAGCCAGC
Found at i:128406 original size:286 final size:286
Alignment explanation
Indices: 127894--128467 Score: 1058
Period size: 286 Copynumber: 2.0 Consensus size: 286
127884 ACAGAGAGGA
127894 CAAGGCAGCAAAAATTGTTGAACTTGAGGAGAGACTTTGAGAATTTGAAGATGAAGGAAGAAAAA
1 CAAGGCAGCAAAAATTGTTGAACTTGAGGAGAGACTTTGAGAATTTGAAGATGAAGGAAGAAAAA
*
127959 ACTGTCAAGCAGTATTTTGACAGGATTATGGCTGTGGTAAACAGCATAAAGCTCCTTGGTGAGCA
66 ACTGTCAAGCAGTATTTTGACAGGATTATGGCTGTGGTAAACAACATAAAGCTCCTTGGTGAGCA
*
128024 GTTCAGTGAAGCAAAGATAATGGAGAATGTGATTTCAACCTTACCAGAGAGGTATGAGGCAAAAA
131 GTTCAGTGAAGCAAAGATAATGGAGAAGGTGATTTCAACCTTACCAGAGAGGTATGAGGCAAAAA
*
128089 TCTCATCTCTCGAAGACTCAAGGGATCTGACCAGTATTCCCTTAACAAAGCTCATTAATGCTCTA
196 TCTCATCTCTCGAAGACTCAAGGGATCTGACCAGCATTCCCTTAACAAAGCTCATTAATGCTCTA
*
128154 TATGCACCAGAGCAGAGAAGAGCTAG
261 TATGCACAAGAGCAGAGAAGAGCTAG
* *
128180 CAAGGCAGCAACAATTGTTGAACTTGAGGAGAGACTTTGAGAATTTGAAGATGAAGGAAGAAGAA
1 CAAGGCAGCAAAAATTGTTGAACTTGAGGAGAGACTTTGAGAATTTGAAGATGAAGGAAGAAAAA
128245 ACTGTCAAGCAGTATTTTGACAGGATTATGGCTGTGGTAAACAACATAAAGCTCCTTGGTGAGCA
66 ACTGTCAAGCAGTATTTTGACAGGATTATGGCTGTGGTAAACAACATAAAGCTCCTTGGTGAGCA
*
128310 GTTCAGTGAAGCAAAGATAGTGGAGAAGGTGATTTCAACCTTACCAGAGAGGTATGAGGCAAAAA
131 GTTCAGTGAAGCAAAGATAATGGAGAAGGTGATTTCAACCTTACCAGAGAGGTATGAGGCAAAAA
* *
128375 TCTCATCTCTCGAAGACTCAAGGGATCTGACCAGCATTCCCTTAACAGAGTTCATTAATGCTCTA
196 TCTCATCTCTCGAAGACTCAAGGGATCTGACCAGCATTCCCTTAACAAAGCTCATTAATGCTCTA
*
128440 TATGCATAAGAGCAGAGAAGAGCTAG
261 TATGCACAAGAGCAGAGAAGAGCTAG
128466 CA
1 CA
128468 GACTGGAGAA
Statistics
Matches: 278, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
286 278 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (286 bp):
CAAGGCAGCAAAAATTGTTGAACTTGAGGAGAGACTTTGAGAATTTGAAGATGAAGGAAGAAAAA
ACTGTCAAGCAGTATTTTGACAGGATTATGGCTGTGGTAAACAACATAAAGCTCCTTGGTGAGCA
GTTCAGTGAAGCAAAGATAATGGAGAAGGTGATTTCAACCTTACCAGAGAGGTATGAGGCAAAAA
TCTCATCTCTCGAAGACTCAAGGGATCTGACCAGCATTCCCTTAACAAAGCTCATTAATGCTCTA
TATGCACAAGAGCAGAGAAGAGCTAG
Found at i:133516 original size:42 final size:42
Alignment explanation
Indices: 133469--133555 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
133459 TGCAAGGAAC
133469 CTGCAACATCTTCAGT-TGAGACTAGAGAATT-CTTGAGCTTAT
1 CTGCAACATCTTCA-TCTGAGACTAGAG-ATTCCTTGAGCTTAT
** * * *
133511 CTGCAAGGTCTTCATCTGAGAGTTGAGATTCCTTGATCTTAT
1 CTGCAACATCTTCATCTGAGACTAGAGATTCCTTGAGCTTAT
133553 CTG
1 CTG
133556 GTATGGATAC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
41 4 0.11
42 34 0.89
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.36
Consensus pattern (42 bp):
CTGCAACATCTTCATCTGAGACTAGAGATTCCTTGAGCTTAT
Found at i:134007 original size:15 final size:16
Alignment explanation
Indices: 133982--134012 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
133972 TTTATGCATA
133982 CTTTATTATCTTCATC
1 CTTTATTATCTTCATC
133998 CTTT-TTATCTTCATC
1 CTTTATTATCTTCATC
134013 TGTAGTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (16 bp):
CTTTATTATCTTCATC
Found at i:142366 original size:4 final size:4
Alignment explanation
Indices: 142359--142401 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
142349 TTATATATGT
*
142359 ATGG ATGG ATAG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATG
142402 TGTGTGTATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.28, C:0.00, G:0.47, T:0.26
Consensus pattern (4 bp):
ATGG
Found at i:142899 original size:6 final size:6
Alignment explanation
Indices: 142888--142921 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
142878 ATAATATTAT
*
142888 ATATAG ATATAG ATATAG TTATAG ATATAG ATAT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATAT
142922 CTGACAACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (6 bp):
ATATAG
Found at i:145936 original size:30 final size:29
Alignment explanation
Indices: 145902--145966 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
145892 AAAAAATATA
*
145902 TTGAAA-TTAACCGAAATATATGTTTTTGTC
1 TTGAAAGTTAACCGAAATA-ATG-TTATGTC
* *
145932 TTGAAAGTTAACTGAATTAATGTTATGTC
1 TTGAAAGTTAACCGAAATAATGTTATGTC
145961 TTGAAA
1 TTGAAA
145967 CACTACATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 12 0.39
30 9 0.29
31 10 0.32
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (29 bp):
TTGAAAGTTAACCGAAATAATGTTATGTC
Found at i:148397 original size:25 final size:25
Alignment explanation
Indices: 148363--148412 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
148353 TCCTTGCCTA
148363 ACCCTCTAGCTTCACCCTGCATGCG
1 ACCCTCTAGCTTCACCCTGCATGCG
148388 ACCCTCTAGCTTCACCCTGCATGCG
1 ACCCTCTAGCTTCACCCTGCATGCG
148413 TTATCTCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.44, G:0.16, T:0.24
Consensus pattern (25 bp):
ACCCTCTAGCTTCACCCTGCATGCG
Found at i:148471 original size:15 final size:16
Alignment explanation
Indices: 148441--148471 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
148431 AATTTGTTGG
148441 TTTATAATATATATTT
1 TTTATAATATATATTT
148457 TTTATAATA-ATATTT
1 TTTATAATATATATTT
148472 AAAGAGTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATAATATATATTT
Found at i:158864 original size:18 final size:18
Alignment explanation
Indices: 158824--158866 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
158814 GTTCAAGGTG
158824 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
158842 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
158860 TAATTAA
1 TAATTAA
158867 AAACCTAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:159806 original size:16 final size:17
Alignment explanation
Indices: 159782--159814 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
159772 TAATATTTTA
159782 TCTCATATATT-TGTTT
1 TCTCATATATTATGTTT
*
159798 TCTCTTATATTATGTTT
1 TCTCATATATTATGTTT
159815 AGGTTTAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (17 bp):
TCTCATATATTATGTTT
Found at i:165322 original size:32 final size:32
Alignment explanation
Indices: 165284--165347 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
165274 TTTAAATCCG
*
165284 AAATATCTAAATC-TAAAA-TAATTTAAAATAAA
1 AAATATC-AAAACATAAAATTAA-TTAAAATAAA
*
165316 AAATATCAAAACATAAAATTAATTAGAATAAA
1 AAATATCAAAACATAAAATTAATTAAAATAAA
165348 CTAATTTGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 4 0.14
32 21 0.75
33 3 0.11
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (32 bp):
AAATATCAAAACATAAAATTAATTAAAATAAA
Found at i:167322 original size:12 final size:11
Alignment explanation
Indices: 167274--167323 Score: 50
Period size: 13 Copynumber: 4.4 Consensus size: 11
167264 TTTTTCAATA
167274 TTTTTTATAA-
1 TTTTTTATAAT
167284 -TTTTTATAACT
1 TTTTTTATAA-T
167295 TCTTTTTATAAAT
1 T-TTTTTAT-AAT
167308 TTTGTTTATAAT
1 TTT-TTTATAAT
167320 TTTT
1 TTTT
167324 ATGATTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
9 9 0.26
11 1 0.03
12 8 0.24
13 14 0.41
14 2 0.06
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (11 bp):
TTTTTTATAAT
Found at i:168090 original size:195 final size:190
Alignment explanation
Indices: 167761--168143 Score: 538
Period size: 192 Copynumber: 2.0 Consensus size: 190
167751 TTCAAACTTT
*
167761 TTTTTTTGCATTCAATTGAGTATTAAAACTTTTAAAATGTATCAGAAAGGCCATCAAAATTAAAA
1 TTTTTTTGCATTCAATTGAGTATTAAAACTTTTAAAATGTATCAAAAAGGCCATCAAAATTAAAA
* * *
167826 AAAGAAATGAAGCTCTTGCTTTTTTTTTTGCACTCAATTGGTTACTTGAACTGCTAAAATGCATC
66 AAAGAAATGAAGCTCTTGCTTTTTTTTTTGCACTCAACTGGGTACTTGAACTACTAAAATGCATC
* *
167891 AAAAAG-CCCTAAGATTTTTTCAAAAAATAAAAAATAAAAATTAAGCCCCTGCTTTTTTTTTA
131 AAAAAGACCCTAAGACTTTTTCAAAAAAT--AAAATAAAAATTAAGCCCCT-ATTTTTTTTTA
* ** *
167953 TTTTTTTGCATTCAATTG-GATATTTAAACTTTTAAAATGTATCAAAAATTCCCTCAAAATTAAA
1 TTTTTTTGCATTCAATTGAG-TATTAAAACTTTTAAAATGTATCAAAAAGGCCATCAAAATT---
* *
168017 AAAAAAAAGCAATTAAGCTCTTGCTTTTTTTTTT-CACTCAACTGGGTACTTGAACTACTAAAAT
62 -AAAAAAAGAAATGAAGCTCTTGCTTTTTTTTTTGCACTCAACTGGGTACTTGAACTACTAAAAT
* * *
168081 GCATCAAAAAGACTCTCAGACTTTTTCAAAAAATAAAATAAAAATTAATCCCCTATTTTTTTT
126 GCATCAAAAAGACCCTAAGACTTTTTCAAAAAATAAAATAAAAATTAAGCCCCTATTTTTTTT
168144 CACTCAATTG
Statistics
Matches: 170, Mismatches: 15, Indels: 11
0.87 0.08 0.06
Matches are distributed among these distances:
191 1 0.01
192 54 0.32
193 8 0.05
194 19 0.11
195 38 0.22
196 50 0.29
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (190 bp):
TTTTTTTGCATTCAATTGAGTATTAAAACTTTTAAAATGTATCAAAAAGGCCATCAAAATTAAAA
AAAGAAATGAAGCTCTTGCTTTTTTTTTTGCACTCAACTGGGTACTTGAACTACTAAAATGCATC
AAAAAGACCCTAAGACTTTTTCAAAAAATAAAATAAAAATTAAGCCCCTATTTTTTTTTA
Found at i:168376 original size:28 final size:27
Alignment explanation
Indices: 168281--168378 Score: 101
Period size: 27 Copynumber: 3.5 Consensus size: 27
168271 TAAAAGTTAT
*
168281 AAAAATGATTAAATTTTAATAAAAATATA
1 AAAAAT-ATAAAATTTT-ATAAAAATATA
*
168310 AAAAA-ATTAAATTTTATTAAAAAT-TA
1 AAAAATATAAAATTTTA-TAAAAATATA
*
168336 GAAAAATTGTAAAATTTTATAAAAATCATA
1 -AAAAA-TATAAAATTTTATAAAAAT-ATA
168366 AAAAATATAAAAT
1 AAAAATATAAAAT
168379 GTATGAAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
26 3 0.05
27 22 0.37
28 14 0.23
29 19 0.32
30 2 0.03
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (27 bp):
AAAAATATAAAATTTTATAAAAATATA
Found at i:174377 original size:14 final size:14
Alignment explanation
Indices: 174355--174392 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
174345 ACCTAAACCC
*
174355 AAACCCTAAACTTT
1 AAACCCTAAACATT
*
174369 AAACTCTAAACATT
1 AAACCCTAAACATT
174383 AAACCCTAAA
1 AAACCCTAAA
174393 TTTGGTCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACCCTAAACATT
Found at i:174422 original size:13 final size:13
Alignment explanation
Indices: 174404--174429 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
174394 TTGGTCTTTT
174404 GGTTTAAGGTTTG
1 GGTTTAAGGTTTG
174417 GGTTTAAGGTTTG
1 GGTTTAAGGTTTG
174430 AGTTCAGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.46
Consensus pattern (13 bp):
GGTTTAAGGTTTG
Found at i:174439 original size:20 final size:20
Alignment explanation
Indices: 174416--174465 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
174406 TTTAAGGTTT
* *
174416 GGGTTTAAGGTTTGAGTTCA
1 GGGTTCAAGGTTCGAGTTCA
*
174436 GGGTTCAAGGTTCGAGTTTA
1 GGGTTCAAGGTTCGAGTTCA
*
174456 GGATTCAAGG
1 GGGTTCAAGG
174466 CTGAGGTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.08, G:0.36, T:0.34
Consensus pattern (20 bp):
GGGTTCAAGGTTCGAGTTCA
Found at i:177902 original size:38 final size:38
Alignment explanation
Indices: 177851--177927 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
177841 CAGTCCGATC
177851 GTTGAAACAAACTCAAATTTAGAAATGTCACTTTTGAA
1 GTTGAAACAAACTCAAATTTAGAAATGTCACTTTTGAA
*
177889 GTTGAAATAAACTCAAATTTAGAAATGTCACTTTTGAA
1 GTTGAAACAAACTCAAATTTAGAAATGTCACTTTTGAA
177927 G
1 G
177928 GGGAAACTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (38 bp):
GTTGAAACAAACTCAAATTTAGAAATGTCACTTTTGAA
Found at i:179955 original size:23 final size:23
Alignment explanation
Indices: 179928--179971 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
179918 TAACTATCAT
*
179928 TAAAATAATAAAGTAAA-TAAACA
1 TAAAAGAATAAAG-AAACTAAACA
179951 TAAAAGAATAAAGAAACTAAA
1 TAAAAGAATAAAGAAACTAAA
179972 AGAATAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.18
Consensus pattern (23 bp):
TAAAAGAATAAAGAAACTAAACA
Found at i:179973 original size:17 final size:18
Alignment explanation
Indices: 179941--179984 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
179931 AATAATAAAG
*
179941 TAAATAAACATAAAAGAA
1 TAAAGAAACATAAAAGAA
179959 TAAAGAAAC-TAAAAGAA
1 TAAAGAAACATAAAAGAA
179976 TAAAAGAAA
1 T-AAAGAAA
179985 GAAATGAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.73, C:0.05, G:0.09, T:0.14
Consensus pattern (18 bp):
TAAAGAAACATAAAAGAA
Found at i:180453 original size:17 final size:18
Alignment explanation
Indices: 180431--180464 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
180421 TAAATGAGTT
180431 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
180448 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
180465 AAAAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:180930 original size:21 final size:22
Alignment explanation
Indices: 180902--180965 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
180892 GCTTTGCCAA
180902 TCAGGCACTATATGTGTCGTAT
1 TCAGGCACTATATGTGTCGTAT
* **
180924 T-AGGCACCACGTGTGTCGT-T
1 TCAGGCACTATATGTGTCGTAT
* *
180944 TCAGGCACTTTATGTGTTGTAT
1 TCAGGCACTATATGTGTCGTAT
180966 ACTGTTACTG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (22 bp):
TCAGGCACTATATGTGTCGTAT
Found at i:187436 original size:50 final size:50
Alignment explanation
Indices: 187333--188031 Score: 771
Period size: 50 Copynumber: 13.9 Consensus size: 50
187323 CATTGAGATT
*
187333 ATGAGAGGTCCCATGTAAGATCATGTCT-GGACATGG-AGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCA-TTGGCACCGAG
* *
187382 ATGAGAGGTCCCATGTAAGATCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
** * *
187432 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
** *
187482 ATGAGAACATCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCCTTGAG
1 ATGAG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG
* * *
187536 ATCATAAGAGGTCCCATATAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ---ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
* *
187589 ACGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
* * *
187639 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGCCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
* ** * * * *
187689 ATGGGAGGTCCCCCGTAAGACTATGTCTGGGACATGGCATGGGCACCAAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
** * * * *
187739 ATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGTA--GTAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AG
* * ** *
187788 AAGAAACATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
* * *
187838 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGCCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
* ** * * *
187888 ATGGGAGGTCCCCCGTAAGACTATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
** * * * *
187938 ATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGTA--GTAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AG
* * **
187987 AAGAAACATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
188032 TGTTATCAGA
Statistics
Matches: 547, Mismatches: 90, Indels: 26
0.83 0.14 0.04
Matches are distributed among these distances:
48 1 0.00
49 105 0.19
50 358 0.65
51 35 0.06
52 2 0.00
53 3 0.01
54 2 0.00
55 2 0.00
56 35 0.06
57 4 0.01
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
Found at i:187857 original size:199 final size:199
Alignment explanation
Indices: 187390--188031 Score: 917
Period size: 199 Copynumber: 3.2 Consensus size: 199
187380 AGATGAGAGG
* **
187390 TCCCATGTAAGATCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCA
* * * * * * ** ** *
187455 TGTCTGGGACATGGCATGGGCACCGATATGAGAACATCCCATGTAAGACCATGTCTGGGACATGG
66 TGTCTAGGACATGCCGTTGGCACCGAGATG-GGAGGTCCCCCGTAAGACTATGTCTGGGACATGG
** * ** * * * * *
187520 CATTAGCATCCTTGAGATCATAAGAGGTCCCATATAAGACCATGTCTGGGACATGGCGTTGGCAC
130 CATGGGCA-CC---A-AT-ATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGTA-
* * * **
187585 CG-AGACGAGAGG
188 -GTACAAGAAACA
187597 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCA
187662 TGTCTAGGACATGCCGTTGGCACCGAGATGGGAGGTCCCCCGTAAGACTATGTCTGGGACATGGC
66 TGTCTAGGACATGCCGTTGGCACCGAGATGGGAGGTCCCCCGTAAGACTATGTCTGGGACATGGC
187727 ATGGGCACCAATATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGTAGTACAAGA
131 ATGGGCACCAATATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGTAGTACAAGA
187792 AACA
196 AACA
187796 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCA
187861 TGTCTAGGACATGCCGTTGGCACCGAGATGGGAGGTCCCCCGTAAGACTATGTCTGGGACATGGC
66 TGTCTAGGACATGCCGTTGGCACCGAGATGGGAGGTCCCCCGTAAGACTATGTCTGGGACATGGC
*
187926 ATGGGCACCGATATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGTAGTACAAGA
131 ATGGGCACCAATATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGTAGTACAAGA
187991 AACA
196 AACA
*
187995 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
188032 TGTTATCAGA
Statistics
Matches: 403, Mismatches: 31, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
198 1 0.00
199 239 0.59
200 37 0.09
201 2 0.00
202 1 0.00
205 2 0.00
206 34 0.08
207 87 0.22
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (199 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCA
TGTCTAGGACATGCCGTTGGCACCGAGATGGGAGGTCCCCCGTAAGACTATGTCTGGGACATGGC
ATGGGCACCAATATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGTAGTACAAGA
AACA
Found at i:192539 original size:26 final size:26
Alignment explanation
Indices: 192513--192562 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
192503 AATCTTTTGA
192513 AATATAATAT-ATTTA-TAATATTATG
1 AATATAATATAATTTACT-ATATTATG
*
192538 AATATAATTTAATTTACTATATTAT
1 AATATAATATAATTTACTATATTAT
192563 TGTTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 12 0.55
27 1 0.05
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (26 bp):
AATATAATATAATTTACTATATTATG
Found at i:193424 original size:9 final size:8
Alignment explanation
Indices: 193376--193455 Score: 52
Period size: 8 Copynumber: 9.2 Consensus size: 8
193366 TTTTATTAAC
*
193376 TTTTTTCT
1 TTTTTTAT
193384 TTTTCTTAAT
1 TTTT-TT-AT
*
193394 TTTTTTCT
1 TTTTTTAT
*
193402 TTTTCTTAAG
1 TTTT-TT-AT
*
193412 TTTTATAT
1 TTTTTTAT
*
193420 TTTTTTCT
1 TTTTTTAT
*
193428 TATTTTAT
1 TTTTTTAT
193436 TTTGTTTAT
1 TTT-TTTAT
193445 TTTATTTAT
1 TTT-TTTAT
193454 TT
1 TT
193456 ATTGTTATTA
Statistics
Matches: 55, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
8 24 0.44
9 22 0.40
10 9 0.16
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.78
Consensus pattern (8 bp):
TTTTTTAT
Found at i:193433 original size:18 final size:19
Alignment explanation
Indices: 193364--193437 Score: 84
Period size: 18 Copynumber: 4.0 Consensus size: 19
193354 TTTAATTTTA
* *
193364 CTTTTTATTAACTTT-TTT
1 CTTTTTCTTAATTTTATTT
193382 CTTTTTCTTAATTTT-TTT
1 CTTTTTCTTAATTTTATTT
193400 CTTTTTCTTAAGTTTTATATT
1 CTTTTTCTTAA-TTTTAT-TT
193421 -TTTTTCTT-ATTTTATTT
1 CTTTTTCTTAATTTTATTT
193438 TGTTTATTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
17 2 0.04
18 33 0.65
19 5 0.10
20 9 0.18
21 2 0.04
ACGTcount: A:0.15, C:0.09, G:0.01, T:0.74
Consensus pattern (19 bp):
CTTTTTCTTAATTTTATTT
Found at i:193444 original size:14 final size:14
Alignment explanation
Indices: 193427--193464 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
193417 TATTTTTTTC
*
193427 TTATTTTATTTTGT
1 TTATTTTATTTTAT
193441 TTATTTTA-TTTAT
1 TTATTTTATTTTAT
193454 TTATTGTTATT
1 TTATT-TTATT
193465 AATTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 9 0.43
14 11 0.52
15 1 0.05
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (14 bp):
TTATTTTATTTTAT
Found at i:193549 original size:23 final size:24
Alignment explanation
Indices: 193499--193542 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
193489 ATTTGAAATG
*
193499 TTTTATAATATATATTTTTTAAGA
1 TTTTATAATATATATTTTTAAAGA
193523 TTTTA-AATAT-TATTTTTAAA
1 TTTTATAATATATATTTTTAAA
193543 TTATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 5 0.26
24 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TTTTATAATATATATTTTTAAAGA
Found at i:193558 original size:32 final size:34
Alignment explanation
Indices: 193510--193580 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
193500 TTTATAATAT
193510 ATATTTTTTAAGATTTTAAATATTA-TTTTTAAA
1 ATATTTTTTAAGATTTTAAATATTATTTTTTAAA
* *
193543 TTATTTTTTAA-ATTTTGAATATTATTTTTTAAA
1 ATATTTTTTAAGATTTTAAATATTATTTTTTAAA
193576 ATATT
1 ATATT
193581 AAATATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 12 0.35
33 22 0.65
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (34 bp):
ATATTTTTTAAGATTTTAAATATTATTTTTTAAA
Found at i:193567 original size:21 final size:22
Alignment explanation
Indices: 193534--193594 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
193524 TTTAAATATT
*
193534 ATTTTTAA-ATTATTTTTT-AA
1 ATTTTAAATATTATTTTTTAAA
*
193554 ATTTTGAATATTATTTTTTAAA
1 ATTTTAAATATTATTTTTTAAA
*
193576 ATATTAAATATATATTTTT
1 ATTTTAAATAT-TATTTTT
193595 AATTATATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.20
21 10 0.29
22 11 0.31
23 7 0.20
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
ATTTTAAATATTATTTTTTAAA
Found at i:193595 original size:22 final size:21
Alignment explanation
Indices: 193542--193610 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 21
193532 TTATTTTTAA
* * *
193542 ATTATTTTTTAAATTTTGAAT
1 ATTATTTTTAAAATATTAAAT
193563 ATTATTTTTTAAAATATTAAAT
1 ATTA-TTTTTAAAATATTAAAT
* *
193585 ATATATTTTTAATTATATAAAAT
1 AT-TATTTTTAA-AATATTAAAT
193608 ATT
1 ATT
193611 TAAATATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 4 0.10
22 24 0.60
23 12 0.30
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (21 bp):
ATTATTTTTAAAATATTAAAT
Found at i:193690 original size:22 final size:23
Alignment explanation
Indices: 193657--193715 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
193647 TTTTTTTAAT
193657 ATTTTTAATATTATTTAATT-TG
1 ATTTTTAATATTATTTAATTATG
*
193679 -TTTTATAATATT-TTAAATTATG
1 ATTTT-TAATATTATTTAATTATG
193701 ATTTTTAA-ATTATTT
1 ATTTTTAATATTATTT
193716 TTAAAGATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
21 13 0.42
22 14 0.45
23 4 0.13
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (23 bp):
ATTTTTAATATTATTTAATTATG
Found at i:194018 original size:16 final size:16
Alignment explanation
Indices: 193999--194058 Score: 50
Period size: 19 Copynumber: 3.6 Consensus size: 16
193989 AATAAAAAAA
193999 ATTTAAAAAAATATTT
1 ATTTAAAAAAATATTT
*
194015 ATTTGTTAAAAAATAAATTT
1 A--T-TTAAAAAA-ATATTT
* *
194035 ATTTAAAAATATATAT
1 ATTTAAAAAAATATTT
194051 A-TTAAAAA
1 ATTTAAAAA
194059 GTAAAAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
15 7 0.19
16 6 0.17
17 7 0.19
18 2 0.06
19 8 0.22
20 6 0.17
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
ATTTAAAAAAATATTT
Found at i:194093 original size:19 final size:19
Alignment explanation
Indices: 194038--194093 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 19
194028 TAAATTTATT
194038 TAAAAATATATATATTAAAAAG
1 TAAAAAT-TA-ATATT-AAAAG
194060 TAAAAATTTAA-ATTAAAAG
1 TAAAAA-TTAATATTAAAAG
194079 TTAAAAA-TAATATTA
1 -TAAAAATTAATATTA
194094 TAAGATCACA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
18 3 0.10
19 9 0.29
20 9 0.29
21 1 0.03
22 8 0.26
23 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (19 bp):
TAAAAATTAATATTAAAAG
Found at i:202667 original size:16 final size:15
Alignment explanation
Indices: 202642--202671 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
202632 TATGATTCTC
202642 TAATTAAAATTTTAA
1 TAATTAAAATTTTAA
202657 TAATATAAAATTTTA
1 TAAT-TAAAATTTTA
202672 GAAAGAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTAAAATTTTAA
Found at i:203099 original size:14 final size:16
Alignment explanation
Indices: 203067--203117 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 16
203057 TTACCAAATG
203067 ATTTTTTAATATTTAT
1 ATTTTTTAATATTTAT
*
203083 ATTTTTT-AT-TTTTT
1 ATTTTTTAATATTTAT
203097 ATTTTTTGAAATATTTTAT
1 ATTTTTT--AATA-TTTAT
203116 AT
1 AT
203118 AGTCGTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 11 0.39
15 2 0.07
16 7 0.25
17 2 0.07
19 6 0.21
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (16 bp):
ATTTTTTAATATTTAT
Found at i:203904 original size:17 final size:19
Alignment explanation
Indices: 203882--203920 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
203872 AGTATCATAA
203882 TTTTTA-TTTTTAAAT-TT
1 TTTTTATTTTTTAAATGTT
203899 TTTTTATTTTTTAAATGTT
1 TTTTTATTTTTTAAATGTT
203918 TTT
1 TTT
203921 GTTTTTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
18 9 0.45
19 5 0.25
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (19 bp):
TTTTTATTTTTTAAATGTT
Found at i:203925 original size:17 final size:18
Alignment explanation
Indices: 203882--203926 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
203872 AGTATCATAA
*
203882 TTTTTA-TTTTTAAATTT
1 TTTTTATTTTTTAAATTG
203899 TTTTTATTTTTTAAA-TG
1 TTTTTATTTTTTAAATTG
*
203916 TTTTTGTTTTT
1 TTTTTATTTTT
203927 GTTTCTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (18 bp):
TTTTTATTTTTTAAATTG
Found at i:203926 original size:18 final size:18
Alignment explanation
Indices: 203888--203926 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
203878 ATAATTTTTA
*
203888 TTTTTAAATTTTTTTTAT
1 TTTTTAAATTTTTTGTAT
203906 TTTTTAAATGTTTTTGT-T
1 TTTTTAAAT-TTTTTGTAT
203924 TTT
1 TTT
203927 GTTTCTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (18 bp):
TTTTTAAATTTTTTGTAT
Found at i:208023 original size:59 final size:60
Alignment explanation
Indices: 207912--208025 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 60
207902 GTAATATAAC
* **
207912 ATTTGGTATCGAAACTTGATATTTTTTTTTCAAATTTGATACCTAATTTTTTTTTGTCCA
1 ATTTGGTATCGAAACTTGATATTTTTTTTTCAAATTTGACACCTAAGCTTTTTTTGTCCA
* * *
207972 ATTTGGTATCTAAACTTGAT-TTTTTTTTTCTAATTTGGCACCTAAGCTTTTTTT
1 ATTTGGTATCGAAACTTGATATTTTTTTTTCAAATTTGACACCTAAGCTTTTTTT
208026 AGGTTTATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
59 29 0.60
60 19 0.40
ACGTcount: A:0.23, C:0.12, G:0.11, T:0.54
Consensus pattern (60 bp):
ATTTGGTATCGAAACTTGATATTTTTTTTTCAAATTTGACACCTAAGCTTTTTTTGTCCA
Found at i:208023 original size:60 final size:60
Alignment explanation
Indices: 207912--208025 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
207902 GTAATATAAC
* *
207912 ATTTGGTATCGAAACTTGATATTTTTTTTTCAAATTTGATACCTAATTTTTTTTTGTCCA
1 ATTTGGTATCGAAACTTGATATTTTTTTTTCAAATTTGACACCTAACTTTTTTTTGTCCA
* * *
207972 ATTTGGTATCTAAACTTGAT-TTTTTTTTTCTAATTTGGCACCTAAGCTTTTTTT
1 ATTTGGTATCGAAACTTGATATTTTTTTTTCAAATTTGACACCTAA-CTTTTTTT
208026 AGGTTTATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 22 0.46
60 26 0.54
ACGTcount: A:0.23, C:0.12, G:0.11, T:0.54
Consensus pattern (60 bp):
ATTTGGTATCGAAACTTGATATTTTTTTTTCAAATTTGACACCTAACTTTTTTTTGTCCA
Found at i:209489 original size:39 final size:40
Alignment explanation
Indices: 209402--209489 Score: 97
Period size: 39 Copynumber: 2.2 Consensus size: 40
209392 TTCTCCCATA
* * * *
209402 ATATCTATATATATACATATAATATTGTTACAACTTATAT
1 ATATATATACATATACATATAAGATTGTTACAACTGATAT
* * **
209442 AGACATATACATATA-ATATAAGATTGTTGGAACTGATAT
1 ATATATATACATATACATATAAGATTGTTACAACTGATAT
209481 ATATATATA
1 ATATATATA
209490 TACATGTATG
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
39 27 0.71
40 11 0.29
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (40 bp):
ATATATATACATATACATATAAGATTGTTACAACTGATAT
Found at i:210831 original size:12 final size:12
Alignment explanation
Indices: 210810--210862 Score: 97
Period size: 12 Copynumber: 4.4 Consensus size: 12
210800 AGAAGAAATA
*
210810 AAAGAGGAGAAG
1 AAAGAAGAGAAG
210822 AAAGAAGAGAAG
1 AAAGAAGAGAAG
210834 AAAGAAGAGAAG
1 AAAGAAGAGAAG
210846 AAAGAAGAGAAG
1 AAAGAAGAGAAG
210858 AAAGA
1 AAAGA
210863 TGATGAGCCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (12 bp):
AAAGAAGAGAAG
Found at i:212330 original size:16 final size:15
Alignment explanation
Indices: 212305--212334 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
212295 TAAGATTCTC
212305 TAATTAAAATTTTAA
1 TAATTAAAATTTTAA
212320 TAATATAAAATTTTA
1 TAAT-TAAAATTTTA
212335 GAAAGAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTAAAATTTTAA
Found at i:213655 original size:26 final size:25
Alignment explanation
Indices: 213592--213655 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
213582 TAATTTACTC
*
213592 TTTAATTTAATGT-ATATAATATAA
1 TTTAATTTAATATAATATAATATAA
213616 TTTATAAATTT-ATA-AATATAATATAA
1 -TT-T-AATTTAATATAATATAATATAA
213642 TTTAATTTAATATA
1 TTTAATTTAATATA
213656 GAAGTATCGG
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
23 5 0.15
24 4 0.12
25 5 0.15
26 14 0.42
27 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TTTAATTTAATATAATATAATATAA
Found at i:218015 original size:17 final size:17
Alignment explanation
Indices: 217993--218026 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
217983 GATTGCTAAG
217993 AAATAAAATTGAAATTC
1 AAATAAAATTGAAATTC
218010 AAATAAAATTGAAATTC
1 AAATAAAATTGAAATTC
218027 GATTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (17 bp):
AAATAAAATTGAAATTC
Found at i:218042 original size:11 final size:11
Alignment explanation
Indices: 218028--218069 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
218018 TTGAAATTCG
218028 ATTTTTTTATA
1 ATTTTTTTATA
218039 ATTTTTTTATAA
1 ATTTTTTTAT-A
*
218051 ATTTTGATTAT-
1 ATTTT-TTTATA
218062 ATTTTTTT
1 ATTTTTTT
218070 TGTTACACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 2 0.07
11 15 0.56
12 6 0.22
13 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (11 bp):
ATTTTTTTATA
Found at i:226835 original size:9 final size:9
Alignment explanation
Indices: 226821--226869 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
226811 GTAGTGATTC
226821 AATTCGGTT
1 AATTCGGTT
*
226830 AATTCGGGT
1 AATTCGGTT
* *
226839 AATCCGGGT
1 AATTCGGTT
226848 AATTCGGTT
1 AATTCGGTT
226857 AATTCGGTT
1 AATTCGGTT
226866 AATT
1 AATT
226870 TTTAACCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (9 bp):
AATTCGGTT
Found at i:235378 original size:19 final size:18
Alignment explanation
Indices: 235350--235389 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
235340 AATATAATAG
*
235350 TAAAATAATAGCAAAACAA
1 TAAAAAAATAGCAAAA-AA
*
235369 TAAAAAAATAGTAAAAAA
1 TAAAAAAATAGCAAAAAA
235387 TAA
1 TAA
235390 TATTTTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.17
Consensus pattern (18 bp):
TAAAAAAATAGCAAAAAA
Found at i:242820 original size:25 final size:25
Alignment explanation
Indices: 242792--242876 Score: 64
Period size: 25 Copynumber: 3.2 Consensus size: 25
242782 CATTTCATAA
242792 TTTTTCTTAATTTGGTATCTAAATT
1 TTTTTCTTAATTTGGTATCTAAATT
* * *
242817 TTTTACTCAATTTGATATTCT-AATT
1 TTTTTCTTAATTTGGTA-TCTAAATT
*
242842 TGACCCATTTTCTTAATTTGGTACCTAAATT
1 T------TTTTCTTAATTTGGTATCTAAATT
242873 TTTT
1 TTTT
242877 AGGCTCGATT
Statistics
Matches: 45, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
25 22 0.49
26 3 0.07
30 2 0.04
31 18 0.40
ACGTcount: A:0.25, C:0.13, G:0.07, T:0.55
Consensus pattern (25 bp):
TTTTTCTTAATTTGGTATCTAAATT
Found at i:242907 original size:56 final size:56
Alignment explanation
Indices: 242791--242933 Score: 157
Period size: 56 Copynumber: 2.5 Consensus size: 56
242781 CCATTTCATA
* *
242791 ATTTTTCTTAATTTGGTATCTAAATTTTTTACTCAATTTGATATTCTAATTTGACCC
1 ATTTTTCTTAATTTGGTATCTAAATTTTTTACTCAATTTGATATTCAAACTTGA-CC
* * * *
242848 A-TTTTCTTAATTTGGTACCTAAATTTTTTAGGCTCGATTTGGTACTT-AAACTTG-TC
1 ATTTTTCTTAATTTGGTATCTAAATTTTTTA--CTCAATTTGATA-TTCAAACTTGACC
* *
242904 ATTTTTCTTAATTTTGTATTTAAATTTTTT
1 ATTTTTCTTAATTTGGTATCTAAATTTTTT
242934 TTAGATTCAA
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
56 30 0.41
57 26 0.36
58 15 0.21
59 2 0.03
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.55
Consensus pattern (56 bp):
ATTTTTCTTAATTTGGTATCTAAATTTTTTACTCAATTTGATATTCAAACTTGACC
Found at i:245727 original size:151 final size:151
Alignment explanation
Indices: 245453--245760 Score: 580
Period size: 151 Copynumber: 2.0 Consensus size: 151
245443 TAACTATTGA
245453 ATTAAAATGTTAAAATATGAAAAGTACATAGATTAAATTCTAACTCCATGAAAGTACAGGGACTA
1 ATTAAAATGTTAAAATATGAAAAGTACATAGATTAAATTCTAACTCCATGAAAGTACAGGGACTA
*
245518 GTAGCACATTTTGACCATTGTTAAATTATGCATAATATTATTTATTAACAAATATAAACCCAATA
66 GTAGCACATTTTGACCATTATTAAATTATGCATAATATTATTTATTAACAAATATAAACCCAATA
245583 ACTTAAATAAACTATACATAT
131 ACTTAAATAAACTATACATAT
* *
245604 ATTAAAATGTTGAAATATGAAAAGTACATAGATTAAATTCTAAGTCCATGAAAGTACAGGGACTA
1 ATTAAAATGTTAAAATATGAAAAGTACATAGATTAAATTCTAACTCCATGAAAGTACAGGGACTA
*
245669 GTAGCACATTTTGACCATTATTAAATTATGCATAATATTATTTATTAATAAATATAAACCCAATA
66 GTAGCACATTTTGACCATTATTAAATTATGCATAATATTATTTATTAACAAATATAAACCCAATA
245734 ACTTAAATAAACTATACATAT
131 ACTTAAATAAACTATACATAT
245755 ATTAAA
1 ATTAAA
245761 CTTATTTTTT
Statistics
Matches: 153, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
151 153 1.00
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (151 bp):
ATTAAAATGTTAAAATATGAAAAGTACATAGATTAAATTCTAACTCCATGAAAGTACAGGGACTA
GTAGCACATTTTGACCATTATTAAATTATGCATAATATTATTTATTAACAAATATAAACCCAATA
ACTTAAATAAACTATACATAT
Found at i:248133 original size:14 final size:15
Alignment explanation
Indices: 248100--248132 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
248090 AAGAAAAGAG
248100 AAAATTTAAAAATAA
1 AAAATTTAAAAATAA
*
248115 AAAATTTAAAAGTAA
1 AAAATTTAAAAATAA
248130 AAA
1 AAA
248133 TATGTTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
AAAATTTAAAAATAA
Found at i:254372 original size:18 final size:19
Alignment explanation
Indices: 254350--254396 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
254340 TATGAATGTT
254350 TTATTTTTTA-ATTTCCAAA
1 TTATTTTTTATATTT-CAAA
* *
254369 -TATTTTATATATTTTAAA
1 TTATTTTTTATATTTCAAA
254387 TTATTTTTTA
1 TTATTTTTTA
254397 CGTGGCATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTTTTATATTTCAAA
Found at i:255599 original size:179 final size:176
Alignment explanation
Indices: 255289--255632 Score: 476
Period size: 179 Copynumber: 1.9 Consensus size: 176
255279 ATGTTACACA
* *
255289 TTTTAAAAGGCTAATGGTCAAAATTAGCTAAAAAAGAATAGGAGCAAAATTGACAAAAGATGTAA
1 TTTTAAAAGGCTAATGGTCAAAATTAGCTAAAAAAGAATAAGAGCAAAATTGACAAAAGATGCAA
* * * **
255354 ACGTTGAGAATTAAATTAATAAAAAATTCAGATTTGTCATTTAAACCAATTAACTTGACTTTAAA
66 ACATTGAGAACTAAATTAATAAAAAAATCAGATTTGTCATTTAAACCAATTAACTTGAAATTAAA
*
255419 TCTAATTCAATTGAATTTGATTATTAAATATAAAAAAATTGACTCC
131 TCTAATTCAATCGAATTTGATTATTAAATATAAAAAAATTGACTCC
* * * *
255465 TTTTGAAATGCTAATGGTCAAATTTAGCTTAAAAAAAAAGAATAAGAGTAAAATTGACAAAAGAT
1 TTTTAAAAGGCTAATGGTCAAAATTAGC-T---AAAAAAGAATAAGAGCAAAATTGACAAAAGAT
* *
255530 GCAAACATTGAGAGCTAAATTGAA-AAAAAAAT-GGATTTGTCATTTAAACCAATTAACTTGAAA
62 GCAAACATTGAGAACTAAATT-AATAAAAAAATCAGATTTGTCATTTAAACCAATTAACTTGAAA
** *
255593 TTAAATCTAATTCGGTCGAATTTGATTATTAAGTATAAAA
126 TTAAATCTAATTCAATCGAATTTGATTATTAAATATAAAA
255633 TATTTGAATC
Statistics
Matches: 146, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
176 25 0.17
177 1 0.01
179 64 0.44
180 54 0.37
181 2 0.01
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (176 bp):
TTTTAAAAGGCTAATGGTCAAAATTAGCTAAAAAAGAATAAGAGCAAAATTGACAAAAGATGCAA
ACATTGAGAACTAAATTAATAAAAAAATCAGATTTGTCATTTAAACCAATTAACTTGAAATTAAA
TCTAATTCAATCGAATTTGATTATTAAATATAAAAAAATTGACTCC
Found at i:267820 original size:26 final size:26
Alignment explanation
Indices: 267772--267821 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
267762 TAGAAAATTC
*
267772 AATTAATTAAATTTATTTAATTAAAA
1 AATTAATTAAATTTATTGAATTAAAA
*
267798 AATTAATT-AATTTACTTGGATTAA
1 AATTAATTAAATTTA-TTGAATTAA
267822 CATCCACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (26 bp):
AATTAATTAAATTTATTGAATTAAAA
Found at i:267948 original size:20 final size:22
Alignment explanation
Indices: 267917--267962 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
267907 ATTTCGTAAC
*
267917 AAAACGATAACA-TAAGTGATT
1 AAAACGATAACATTAAATGATT
267938 AAAAC-ATAACATTAAATGATT
1 AAAACGATAACATTAAATGATT
267959 AAAA
1 AAAA
267963 TACAACTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.24
Consensus pattern (22 bp):
AAAACGATAACATTAAATGATT
Found at i:271759 original size:13 final size:14
Alignment explanation
Indices: 271741--271778 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
271731 AATCTAAATC
*
271741 TAATTATAA-AAAA
1 TAATTAAAATAAAA
271754 TAATTAAAATAAAA
1 TAATTAAAATAAAA
271768 TATATTAAAAT
1 TA-ATTAAAAT
271779 TACGATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.36
14 6 0.27
15 8 0.36
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAATTAAAATAAAA
Found at i:271767 original size:15 final size:15
Alignment explanation
Indices: 271750--271778 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
271740 CTAATTATAA
271750 AAAATA-ATTAAAAT
1 AAAATATATTAAAAT
271764 AAAATATATTAAAAT
1 AAAATATATTAAAAT
271779 TACGATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATATATTAAAAT
Found at i:272689 original size:31 final size:32
Alignment explanation
Indices: 272622--272691 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
272612 AAATTAAATG
* * **
272622 TTCTTATGAAAAATTAATTCTTTCACATTTTT
1 TTCTTATGAAAAATTAAATCGTTCACAAATTT
*
272654 TTCTTATGAAAAATTAAAT-GTTCATAAATTT
1 TTCTTATGAAAAATTAAATCGTTCACAAATTT
272685 TTCTTAT
1 TTCTTAT
272692 ATAATTATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
31 15 0.45
32 18 0.55
ACGTcount: A:0.34, C:0.10, G:0.04, T:0.51
Consensus pattern (32 bp):
TTCTTATGAAAAATTAAATCGTTCACAAATTT
Found at i:278788 original size:17 final size:15
Alignment explanation
Indices: 278752--278790 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
278742 TTATTTATCA
*
278752 TTTTTATTTCTTTCT
1 TTTTTATTTCTTTAT
278767 TTTTTATTTCTGTTTAT
1 TTTTTATTTC--TTTAT
278784 TTTTTAT
1 TTTTTAT
278791 ACATATATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
17 11 0.52
ACGTcount: A:0.10, C:0.08, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTTATTTCTTTAT
Found at i:279729 original size:3 final size:3
Alignment explanation
Indices: 279721--279780 Score: 93
Period size: 3 Copynumber: 20.0 Consensus size: 3
279711 AATCTTTTTC
* *
279721 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT AAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
279769 TAT TGT TAT TAT
1 TAT TAT TAT TAT
279781 GTTAGTTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:280079 original size:21 final size:21
Alignment explanation
Indices: 280054--280096 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
280044 TTCTACATAC
280054 ATATCTTTGATTTATATATAT
1 ATATCTTTGATTTATATATAT
280075 ATATCTTTGATTTATATATAT
1 ATATCTTTGATTTATATATAT
280096 A
1 A
280097 ATTATAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56
Consensus pattern (21 bp):
ATATCTTTGATTTATATATAT
Found at i:282947 original size:24 final size:24
Alignment explanation
Indices: 282894--282948 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
282884 TTCTATATTT
*
282894 TATTTAATATATAATTAATTTTAA
1 TATTTAATATATAATAAATTTTAA
* * *
282918 TTTTTATTATATAA-AAATATTTTA
1 TATTTAATATATAATAAAT-TTTAA
282942 TATTTAA
1 TATTTAA
282949 AATAATGAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TATTTAATATATAATAAATTTTAA
Found at i:283117 original size:33 final size:33
Alignment explanation
Indices: 283043--283117 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
283033 ATAGGAATAC
* * * * *
283043 ATATCTTTGATTTATATACATACTTATATATAT
1 ATATCTATAATTTATATACACACCTATAGATAT
283076 AT-TCCTATAATTTATATACACACCTATAGATAT
1 ATAT-CTATAATTTATATACACACCTATAGATAT
283109 ATATCTATA
1 ATATCTATA
283118 CAAATTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
32 1 0.03
33 33 0.94
34 1 0.03
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.45
Consensus pattern (33 bp):
ATATCTATAATTTATATACACACCTATAGATAT
Found at i:283147 original size:24 final size:24
Alignment explanation
Indices: 283119--283167 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
283109 ATATCTATAC
283119 AAATTTTTATTTTCACAAATACAT
1 AAATTTTTATTTTCACAAATACAT
**
283143 AAATTTTTATTTTCATGAATACAT
1 AAATTTTTATTTTCACAAATACAT
283167 A
1 A
283168 TATACTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (24 bp):
AAATTTTTATTTTCACAAATACAT
Found at i:283176 original size:24 final size:24
Alignment explanation
Indices: 283125--283176 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
283115 ATACAAATTT
**
283125 TTATTTTCACAAATACATAAATTT
1 TTATTTTCACAAATACATAAATAC
** *
283149 TTATTTTCATGAATACATATATAC
1 TTATTTTCACAAATACATAAATAC
283173 TTAT
1 TTAT
283177 ATGTTTTCAT
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:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (24 bp):
TTATTTTCACAAATACATAAATAC
Found at i:283209 original size:2 final size:2
Alignment explanation
Indices: 283197--283233 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
283187 CCTACAATTT
*
283197 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
283234 TTTTTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:283713 original size:71 final size:71
Alignment explanation
Indices: 283597--283731 Score: 216
Period size: 71 Copynumber: 1.9 Consensus size: 71
283587 TCTTTTCAAA
* * * * *
283597 CTCAAGTTTTAACCGATCTTGGGAATTAAGAAGAGATCGTGTCCTAACTCACTGGGCATGATCCT
1 CTCAAGTTTTAAACGATCTCGGAAATTAAGAAAAGATCGTGTCCTAACTCACTAGGCATGATCCT
283662 TTTTTC
66 TTTTTC
*
283668 CTCAAGTTTTAAACGATCTCGGAAATTAAGAAAAGATCGTGTCCTAACTTACTAGGCATGATCC
1 CTCAAGTTTTAAACGATCTCGGAAATTAAGAAAAGATCGTGTCCTAACTCACTAGGCATGATCC
283732 CCTTTTTTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 58 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (71 bp):
CTCAAGTTTTAAACGATCTCGGAAATTAAGAAAAGATCGTGTCCTAACTCACTAGGCATGATCCT
TTTTTC
Found at i:284633 original size:17 final size:17
Alignment explanation
Indices: 284611--284643 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
284601 TATAATTATC
284611 ATAATT-TTTATTAAATT
1 ATAATTATTT-TTAAATT
284628 ATAATTATTTTTAAAT
1 ATAATTATTTTTAAAT
284644 GTCCATGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATAATTATTTTTAAATT
Found at i:289405 original size:2 final size:2
Alignment explanation
Indices: 289398--289430 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
289388 AATATGTATA
289398 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
289431 CAAGAAGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:291827 original size:48 final size:48
Alignment explanation
Indices: 291752--291846 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
291742 TCATGAATGT
291752 ATTTTATTAATTAAAGCTATAAATACTTGCTAATAAGGTAAAATTAAG
1 ATTTTATTAATTAAAGCTATAAATACTTGCTAATAAGGTAAAATTAAG
* * *
291800 ATTTTATTAATTAAAGCTATAAGTACTTGCTAATAAGTTCAAATTAA
1 ATTTTATTAATTAAAGCTATAAATACTTGCTAATAAGGTAAAATTAA
291847 TTTCTTTCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.39
Consensus pattern (48 bp):
ATTTTATTAATTAAAGCTATAAATACTTGCTAATAAGGTAAAATTAAG
Found at i:329980 original size:16 final size:16
Alignment explanation
Indices: 329959--329991 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
329949 ACTATAGCTG
329959 CTTAGATTGTAATGCT
1 CTTAGATTGTAATGCT
329975 CTTAGATTGTAATGCT
1 CTTAGATTGTAATGCT
329991 C
1 C
329992 AGATGCAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.42
Consensus pattern (16 bp):
CTTAGATTGTAATGCT
Found at i:334741 original size:30 final size:30
Alignment explanation
Indices: 334705--334765 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
334695 ATAATAAAAG
334705 TTTAAATTGAGAACCCTAAAGGCATGCCCA
1 TTTAAATTGAGAACCCTAAAGGCATGCCCA
334735 TTTAAATTGAGAACCCTAAAGGCATGCCCA
1 TTTAAATTGAGAACCCTAAAGGCATGCCCA
334765 T
1 T
334766 CACCGATAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (30 bp):
TTTAAATTGAGAACCCTAAAGGCATGCCCA
Found at i:336943 original size:2 final size:2
Alignment explanation
Indices: 336938--336962 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
336928 AAAAACAAGT
336938 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
336963 AATTAGAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:343949 original size:24 final size:24
Alignment explanation
Indices: 343899--343950 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
343889 TTAGTAAGTC
* **
343899 AAATAAATTATGCTAATAAATGTT
1 AAATAAATTATACTAATAAATACT
*
343923 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
343947 AAAT
1 AAAT
343951 CTTCTGGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:344081 original size:34 final size:35
Alignment explanation
Indices: 344034--344102 Score: 131
Period size: 34 Copynumber: 2.0 Consensus size: 35
344024 AACAATAAGA
344034 AAAATAAATAAAACATTGGAAGTTATTTAACTATT
1 AAAATAAATAAAACATTGGAAGTTATTTAACTATT
344069 AAAA-AAATAAAACATTGGAAGTTATTTAACTATT
1 AAAATAAATAAAACATTGGAAGTTATTTAACTATT
344103 TTTTTAACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 30 0.88
35 4 0.12
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAATAAATAAAACATTGGAAGTTATTTAACTATT
Found at i:345366 original size:34 final size:35
Alignment explanation
Indices: 345322--345388 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
345312 CAGTAAAATA
*
345322 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
345356 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
345389 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:347443 original size:6 final size:6
Alignment explanation
Indices: 347434--347459 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
347424 AAAAAGAAAA
347434 AGTTTT AGTTTT AGTTTT AGTTTT AG
1 AGTTTT AGTTTT AGTTTT AGTTTT AG
347460 AACAACTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (6 bp):
AGTTTT
Found at i:347704 original size:30 final size:30
Alignment explanation
Indices: 347670--347734 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
347660 AAATAGTATC
* *
347670 TTTATAATTTTTA-AAGAATTAAATTAAAAT
1 TTTATAATTTTTAGAA-AACTAAAGTAAAAT
*
347700 TTTATTATTTTTAGGAAAACTAAAGTAAAAT
1 TTTATAATTTTTA-GAAAACTAAAGTAAAAT
347731 TTTA
1 TTTA
347735 ACTTTACTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 12 0.40
31 16 0.53
32 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (30 bp):
TTTATAATTTTTAGAAAACTAAAGTAAAAT
Found at i:355452 original size:38 final size:38
Alignment explanation
Indices: 355394--355474 Score: 144
Period size: 38 Copynumber: 2.1 Consensus size: 38
355384 AAATTTATTG
* *
355394 TGAAATTATGTTATAGATAGGAAGTATAGGGTCCTTAA
1 TGAAATTATGTTACAAATAGGAAGTATAGGGTCCTTAA
355432 TGAAATTATGTTACAAATAGGAAGTATAGGGTCCTTAA
1 TGAAATTATGTTACAAATAGGAAGTATAGGGTCCTTAA
355470 TGAAA
1 TGAAA
355475 GAATGTGAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (38 bp):
TGAAATTATGTTACAAATAGGAAGTATAGGGTCCTTAA
Found at i:359151 original size:4 final size:4
Alignment explanation
Indices: 359142--359172 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
359132 ATACAGAAAA
359142 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAA
359173 GAAATTTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:364947 original size:30 final size:30
Alignment explanation
Indices: 364913--364983 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 30
364903 ACAGAAAAAC
364913 TAGTTTACTCTTTGATCTAACACACATGAT
1 TAGTTTACTCTTTGATCTAACACACATGAT
**
364943 TAGTTTA-TCTTTGATCTAACATTCATGAT
1 TAGTTTACTCTTTGATCTAACACACATGAT
*
364972 TAATTTAC-CTTT
1 TAGTTTACTCTTT
364984 TCCTAAAGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 30 0.81
30 7 0.19
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.46
Consensus pattern (30 bp):
TAGTTTACTCTTTGATCTAACACACATGAT
Found at i:366302 original size:25 final size:25
Alignment explanation
Indices: 366268--366332 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 25
366258 GAATTATTCT
366268 GTTAAAAATTTCATTTATGTTTACA
1 GTTAAAAATTTCATTTATGTTTACA
366293 GTTAAAAATTGGTTTTCATTTATGTTTACA
1 GTTAAAAA-----TTTCATTTATGTTTACA
366323 GTTAAAAATT
1 GTTAAAAATT
366333 GGTTTTTGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
25 10 0.29
30 25 0.71
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (25 bp):
GTTAAAAATTTCATTTATGTTTACA
Found at i:366312 original size:30 final size:30
Alignment explanation
Indices: 366276--366338 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
366266 CTGTTAAAAA
366276 TTTCATTTATGTTTACAGTTAAAAATTGGT
1 TTTCATTTATGTTTACAGTTAAAAATTGGT
366306 TTTCATTTATGTTTACAGTTAAAAATTGGT
1 TTTCATTTATGTTTACAGTTAAAAATTGGT
366336 TTT
1 TTT
366339 TGTACGTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (30 bp):
TTTCATTTATGTTTACAGTTAAAAATTGGT
Found at i:367023 original size:31 final size:31
Alignment explanation
Indices: 366985--367046 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
366975 TTTCACAAAA
366985 AAGATTTAACTGTTTTGAGTAGAATTAGATC
1 AAGATTTAACTGTTTTGAGTAGAATTAGATC
367016 AAGATTTAACTGTTTTGAGTAGAATTAGATC
1 AAGATTTAACTGTTTTGAGTAGAATTAGATC
367047 CTTGTACATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.39
Consensus pattern (31 bp):
AAGATTTAACTGTTTTGAGTAGAATTAGATC
Found at i:373799 original size:13 final size:13
Alignment explanation
Indices: 373781--373806 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
373771 CAATCAAATG
373781 CACACAAAATAAT
1 CACACAAAATAAT
373794 CACACAAAATAAT
1 CACACAAAATAAT
373807 ATTAATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (13 bp):
CACACAAAATAAT
Found at i:375301 original size:26 final size:27
Alignment explanation
Indices: 375272--375330 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 27
375262 CATTTAGAAA
375272 ACGCCACACAA-GCAATC-ATAT-AGAGT
1 ACGCCACA-AAGGCAATCAAT-TCAGAGT
375298 ACGCCACAAAGGCAATCAATTCAGAGT
1 ACGCCACAAAGGCAATCAATTCAGAGT
375325 ACGCCA
1 ACGCCA
375331 TGGACTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
25 2 0.07
26 15 0.50
27 13 0.43
ACGTcount: A:0.41, C:0.29, G:0.17, T:0.14
Consensus pattern (27 bp):
ACGCCACAAAGGCAATCAATTCAGAGT
Found at i:379909 original size:8 final size:9
Alignment explanation
Indices: 379887--379912 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
379877 AATGATAAAG
379887 TAAAAATAT
1 TAAAAATAT
379896 TAAAAATAT
1 TAAAAATAT
379905 TAAAAATA
1 TAAAAATA
379913 ATGTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
TAAAAATAT
Found at i:384475 original size:44 final size:46
Alignment explanation
Indices: 384347--384477 Score: 130
Period size: 44 Copynumber: 2.9 Consensus size: 46
384337 ATAAAAGATT
* *
384347 TAGTCAATGCCAAAAACCACACGCAAGGTTAAAGGCACTTGACAGA
1 TAGTCAATGCCAAAAAACACACACAAGGTTAAAGGCACTTGACAGA
* * ** *
384393 -AGAT-AACG-CAAGGATAACACTTA-AAGGATAAAGGCACTT-A-AGA
1 TAG-TCAATGCCAA--AAAACACACACAAGGTTAAAGGCACTTGACAGA
384436 TAGTCAATGCCAAAAAACACACACAAGGTTAAAGGCACTTGA
1 TAGTCAATGCCAAAAAACACACACAAGGTTAAAGGCACTTGA
384478 GAGAGAGAGA
Statistics
Matches: 65, Mismatches: 12, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
43 11 0.17
44 24 0.37
45 24 0.37
46 6 0.09
ACGTcount: A:0.45, C:0.20, G:0.19, T:0.16
Consensus pattern (46 bp):
TAGTCAATGCCAAAAAACACACACAAGGTTAAAGGCACTTGACAGA
Done.