Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 75 of 97
Found at i:29897262 original size:18 final size:19
Alignment explanation
Indices: 29897221--29897263 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
29897211 TAATTATAAA
29897221 ATATAAAATAAATATTAGT
1 ATATAAAATAAATATTAGT
* *
29897240 A-ATAAAATATATATT-TT
1 ATATAAAATAAATATTAGT
29897257 ATATAAA
1 ATATAAA
29897264 TTTAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.86
19 1 0.05
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
ATATAAAATAAATATTAGT
Found at i:29897313 original size:14 final size:14
Alignment explanation
Indices: 29897274--29897314 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
29897264 TTTAAAAATA
29897274 ATATATA-ATAT-T
1 ATATATATATATGT
29897286 ATATATAT-TGATGT
1 ATATATATAT-ATGT
29897300 ATATATATATATGT
1 ATATATATATATGT
29897314 A
1 A
29897315 GAGAATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 8 0.32
13 2 0.08
14 14 0.56
15 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (14 bp):
ATATATATATATGT
Found at i:29898881 original size:22 final size:22
Alignment explanation
Indices: 29898775--29898946 Score: 95
Period size: 22 Copynumber: 7.7 Consensus size: 22
29898765 TTGAATATAA
*
29898775 TAAA-TATAATAAAGAGTATTATT
1 TAAATTATAATAAA-AATATTA-T
29898798 TAAATT-TAATGAATAATATATT-T
1 TAAATTATAAT-AA-AA-ATATTAT
** * *
29898821 TATCTTTTAATATTAAATATTAT
1 TAAATTATAATA-AAAATATTAT
*
29898844 TTAATTATAATAAAAAGT-TTAAT
1 TAAATTATAATAAAAA-TATT-AT
* *
29898867 TAACTTCTAATAAAAATATTAT
1 TAAATTATAATAAAAATATTAT
29898889 TAAATTATAATAAAAATATGT-T
1 TAAATTATAATAAAAATAT-TAT
** * * *
29898911 TGTATTTTAGTGAAAATATTAT
1 TAAATTATAATAAAAATATTAT
*
29898933 T-AATTATAGTAAAA
1 TAAATTATAATAAAA
29898947 GTTATTTTGA
Statistics
Matches: 115, Mismatches: 22, Indels: 26
0.71 0.13 0.16
Matches are distributed among these distances:
21 11 0.10
22 47 0.41
23 44 0.38
24 8 0.07
25 5 0.04
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
TAAATTATAATAAAAATATTAT
Found at i:29911573 original size:20 final size:21
Alignment explanation
Indices: 29911538--29911595 Score: 70
Period size: 19 Copynumber: 2.9 Consensus size: 21
29911528 ATAAAAATTA
*
29911538 TATATTTTTTATTATATTATTT
1 TATATTTTATA-TATATTATTT
29911560 T-TATTTTATATATA-TATTT
1 TATATTTTATATATATTATTT
29911579 TATATTTT-TAT-TATTAT
1 TATATTTTATATATATTAT
29911596 ATATTTTTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
18 2 0.06
19 12 0.36
20 10 0.30
21 8 0.24
22 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TATATTTTATATATATTATTT
Found at i:29911577 original size:13 final size:13
Alignment explanation
Indices: 29911561--29911599 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
29911551 ATATTATTTT
29911561 TATTTTATATATA
1 TATTTTATATATA
* *
29911574 TATTTTATATTTT
1 TATTTTATATATA
29911587 TATTATTATATAT
1 TATT-TTATATAT
29911600 TTTTCATAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTTATATATA
Found at i:29911679 original size:9 final size:9
Alignment explanation
Indices: 29911667--29911702 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
29911657 ATTATTTTTA
29911667 TTTTTTATT
1 TTTTTTATT
29911676 TTTTTTATT
1 TTTTTTATT
29911685 TTTTTATATT
1 TTTTT-TATT
29911695 TTTTTTAT
1 TTTTTTAT
29911703 AGTTTGTGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTATT
Found at i:29911680 original size:16 final size:17
Alignment explanation
Indices: 29911656--29911699 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
29911646 TTCATATATA
*
29911656 TATTATTTTTA-TTTTT
1 TATTTTTTTTATTTTTT
29911672 TATTTTTTTTATTTTTT
1 TATTTTTTTTATTTTTT
29911689 TATATTTTTTT
1 TAT-TTTTTTT
29911700 TATAGTTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 10 0.40
17 8 0.32
18 7 0.28
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (17 bp):
TATTTTTTTTATTTTTT
Found at i:29911687 original size:10 final size:10
Alignment explanation
Indices: 29911667--29911700 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
29911657 ATTATTTTTA
29911667 TTTTTTA-TT
1 TTTTTTATTT
29911676 TTTTTTATTT
1 TTTTTTATTT
*
29911686 TTTTATATTT
1 TTTTTTATTT
29911696 TTTTT
1 TTTTT
29911701 ATAGTTTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:29911848 original size:17 final size:18
Alignment explanation
Indices: 29911803--29911853 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
29911793 TTTTCACAAA
*
29911803 TTAATTATTTATTATATGT
1 TTAATTA-TTATTATATAT
29911822 TTGAATTATTATTATATAT
1 TT-AATTATTATTATATAT
*
29911841 TT-ATTATTTTTAT
1 TTAATTATTATTAT
29911854 CAAGTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 10 0.34
19 14 0.48
20 5 0.17
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (18 bp):
TTAATTATTATTATATAT
Found at i:29912271 original size:15 final size:15
Alignment explanation
Indices: 29912234--29912270 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
29912224 AATGATTTTG
29912234 ATTTTTTTACTTATT
1 ATTTTTTTACTTATT
29912249 ATTATTTTT-CTTA-T
1 ATT-TTTTTACTTATT
29912263 ATTTTTTT
1 ATTTTTTT
29912271 TAATTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 5 0.24
14 4 0.19
15 7 0.33
16 5 0.24
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTTTTTACTTATT
Found at i:29912894 original size:129 final size:131
Alignment explanation
Indices: 29912675--29912924 Score: 396
Period size: 129 Copynumber: 1.9 Consensus size: 131
29912665 CCGGCAAACT
* *
29912675 CCCCTTGGTCGCCGATCAGGTGCTGCTGCTCTCCTTCCTGTGCCGTGTACGGTGGAGCGACGGTC
1 CCCCTTGGTCGACGATCAGGTACTGCTGCTCTCCTTCCTGTGCCGTGTACGGTGGAGCGACGGTC
*
29912740 AAGCTTCCTCGACTGCCGATCTGTTGGAGGA-CCCACGCCGACGAACTCTTCCTGCCGGCGCGAA
66 AAGCTTCCTCGACCGCCGATCTGTTGGAGGACCCCACGCCGACGAACTCTTCCTGCCGGCGCGAA
29912804 C
131 C
* * *
29912805 CCCCTTGG-CGACGATCGGGTACTGCTGTTCTCCTTCCTGTGCCGTGTACGGTGGAGCGACGGTG
1 CCCCTTGGTCGACGATCAGGTACTGCTGCTCTCCTTCCTGTGCCGTGTACGGTGGAGCGACGGTC
* *
29912869 AAGCTTCCTCTACCGCCGATCTGTTGGAGGACCCCCCCCGCCGACGAACTCTTCCT
66 AAGCTTCCTCGACCGCCGATCTGTTGGAGGA--CCCCACGCCGACGAACTCTTCCT
29912925 TAGCTCCGCT
Statistics
Matches: 109, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
129 80 0.73
130 8 0.07
132 21 0.19
ACGTcount: A:0.13, C:0.36, G:0.28, T:0.23
Consensus pattern (131 bp):
CCCCTTGGTCGACGATCAGGTACTGCTGCTCTCCTTCCTGTGCCGTGTACGGTGGAGCGACGGTC
AAGCTTCCTCGACCGCCGATCTGTTGGAGGACCCCACGCCGACGAACTCTTCCTGCCGGCGCGAA
C
Found at i:29916306 original size:13 final size:13
Alignment explanation
Indices: 29916288--29916312 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29916278 GGATAAATTG
29916288 TGATTTTATAAAA
1 TGATTTTATAAAA
29916301 TGATTTTATAAA
1 TGATTTTATAAA
29916313 TTTTCTAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:29920642 original size:14 final size:15
Alignment explanation
Indices: 29920601--29920645 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
29920591 AGATTAGAGA
29920601 TTTT-GATTATAAAG-
1 TTTTGGATT-TAAAGT
29920615 TTTTGGATTTTAAAGT
1 TTTTGGA-TTTAAAGT
29920631 TTTTGG-TTTAAAGT
1 TTTTGGATTTAAAGT
29920645 T
1 T
29920646 GTTTTAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 13 0.46
15 7 0.25
16 8 0.29
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.56
Consensus pattern (15 bp):
TTTTGGATTTAAAGT
Found at i:29934472 original size:15 final size:16
Alignment explanation
Indices: 29934452--29934487 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
29934442 TCTTTCCTGT
29934452 TTTTTGTTC-ATTATA
1 TTTTTGTTCTATTATA
*
29934467 TTTTTGTTCTTTTATA
1 TTTTTGTTCTATTATA
29934483 TTTTT
1 TTTTT
29934488 TTATGAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.75
Consensus pattern (16 bp):
TTTTTGTTCTATTATA
Found at i:29934586 original size:22 final size:22
Alignment explanation
Indices: 29934561--29934606 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
29934551 AATTTTTAAG
* *
29934561 TTTTTTTTT-CAA-TTTTGTTT
1 TTTTTTTTTGTAATTTTTGATT
29934581 TTTTTTTTTGTAATTTTTGATT
1 TTTTTTTTTGTAATTTTTGATT
29934603 TTTT
1 TTTT
29934607 ACTATTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 2 0.09
22 11 0.50
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (22 bp):
TTTTTTTTTGTAATTTTTGATT
Found at i:29936734 original size:9 final size:10
Alignment explanation
Indices: 29936713--29936749 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
29936703 ATTTTTTACC
29936713 TTTATATATT
1 TTTATATATT
*
29936723 TTTTTA-ATT
1 TTTATATATT
29936732 TTTATATATT
1 TTTATATATT
29936742 TTTA-ATAT
1 TTTATATAT
29936750 AATTAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 12 0.50
10 12 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTATATATT
Found at i:29936909 original size:2 final size:2
Alignment explanation
Indices: 29936902--29936958 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
29936892 TTAAATATTA
*
29936902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA 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
29936944 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
29936959 CTATCAATTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29940075 original size:17 final size:15
Alignment explanation
Indices: 29940036--29940082 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
29940026 AAAAGATAAT
* *
29940036 AAATAATAAGATATA
1 AAATAAAAAGAGATA
29940051 AAATAAAAAGAGATA
1 AAATAAAAAGAGATA
*
29940066 AATATGAAAAG-GATA
1 AA-ATAAAAAGAGATA
29940081 AA
1 AA
29940083 GATTTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 21 0.75
16 7 0.25
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (15 bp):
AAATAAAAAGAGATA
Found at i:29940747 original size:45 final size:44
Alignment explanation
Indices: 29940679--29940787 Score: 130
Period size: 45 Copynumber: 2.4 Consensus size: 44
29940669 GAAATGAAAA
* *
29940679 TATTTAA-ATATTATTTAACTATAATAAACATTATAAAGAATAT
1 TATTTAATATATTATTTAACTATAATAAACATAACAAAGAATAT
* * **
29940722 TATTTAATATTATTATTTGAGTATAATAAATGTAACAAAGAATAT
1 TATTTAATA-TATTATTTAACTATAATAAACATAACAAAGAATAT
29940767 TATTTAATTAGTATTATTTAA
1 TATTTAA-TA-TATTATTTAA
29940788 ATTTAATGAA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
43 7 0.13
44 1 0.02
45 36 0.65
46 11 0.20
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.45
Consensus pattern (44 bp):
TATTTAATATATTATTTAACTATAATAAACATAACAAAGAATAT
Found at i:29940878 original size:23 final size:22
Alignment explanation
Indices: 29940822--29940895 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 22
29940812 TTTTAATATT
* *
29940822 AAATATTATTTAATTATAATAA
1 AAATATTATTAAATCATAATAA
* * *
29940844 AAGGT-TTAATTATATCCTAATACA
1 AA-ATATT-ATTAAATCATAATA-A
*
29940868 AAATATTATTAAATTATAATAA
1 AAATATTATTAAATCATAATAA
29940890 AAATAT
1 AAATAT
29940896 GTTTGTATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
22 11 0.28
23 23 0.59
24 5 0.13
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.41
Consensus pattern (22 bp):
AAATATTATTAAATCATAATAA
Found at i:29941995 original size:181 final size:184
Alignment explanation
Indices: 29941630--29941999 Score: 559
Period size: 183 Copynumber: 2.0 Consensus size: 184
29941620 AATTTTTTAA
* *
29941630 AAAAGATAAAATTATAGAATTAAATAAATACATTCTCCAATGATGAAATCTAAAAAAATCCAAAA
1 AAAAGATAAAATTAAAGAATTAAATAAATACATACTCCAATGATGAAATCTAAAAAAATCCAAAA
** * * * *
29941695 GTGGTTTCTTGGGAATTTCTAGGTGAGAGAATTTTCCAAAATTTTACCATAAGTGTTTGGGAGAT
66 GTGACTTCTTGAGAATTTCTAAGTGAGAGAATTTTCCAAAATTTTACCAT-AGGGCTTGGGAGAT
** *
29941760 TTTGGGAAATTTTCGATATCAAGAATTTTTATTTATTTTGAAAAACTAATAAAAT
130 TTTGAAAAATTTTCAATATCAAGAATTTTTATTTATTTTGAAAAACTAATAAAAT
*
29941815 AAAAGATAAAATTAAAGAATTAAATAAATA-A-ACTCCAATGATGAAATCTCAAGAAAA-CCAAA
1 AAAAGATAAAATTAAAGAATTAAATAAATACATACTCCAATGATGAAATCT-AAAAAAATCCAAA
* *
29941877 AGTGACTTCTTGAGAATTTGTAAGTGAGAGAATTTTCCAAAATTTTACCAT-GGGCTTGGGTGAT
65 AGTGACTTCTTGAGAATTTCTAAGTGAGAGAATTTTCCAAAATTTTACCATAGGGCTTGGGAGAT
*
29941941 TTTGAAAAATTTTCAATATCAAGAATTTTTATTTATTTTGAAAAATTAATAAAAT
130 TTTGAAAAATTTTCAATATCAAGAATTTTTATTTATTTTGAAAAACTAATAAAAT
29941996 AAAA
1 AAAA
29942000 ATAGAAAAGA
Statistics
Matches: 169, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
181 65 0.38
183 68 0.40
184 7 0.04
185 29 0.17
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.34
Consensus pattern (184 bp):
AAAAGATAAAATTAAAGAATTAAATAAATACATACTCCAATGATGAAATCTAAAAAAATCCAAAA
GTGACTTCTTGAGAATTTCTAAGTGAGAGAATTTTCCAAAATTTTACCATAGGGCTTGGGAGATT
TTGAAAAATTTTCAATATCAAGAATTTTTATTTATTTTGAAAAACTAATAAAAT
Found at i:29943078 original size:121 final size:120
Alignment explanation
Indices: 29942941--29943177 Score: 271
Period size: 121 Copynumber: 2.0 Consensus size: 120
29942931 AAAAATTATC
* * * * * * *
29942941 TATTCAAATAGAATGTTTCTTAAAAAAAGATATATCGT-AAAAATCAATTAGGTATTTAGTTACA
1 TATTCAAATAAAATGTTTCTT--AAAAAGACATATAGTAAAAAATAAATGAAGTATTTAATTACA
****
29943005 TTAAAATATTAAATATATTGTTATAT-AAATCAACAAAATTATATTTATAAACACATA
64 TTAAAATATTAAATATATAAAAAT-TGAAATCAACAAAATTATATTTATAAACACATA
* * * *
29943062 TATTTAAATAAAATGTTTCTTTAAAAGACATATAGTAAAAAAATAAATGAATTATTTAATTATAT
1 TATTCAAATAAAATGTTTCTTAAAAAGACATATAGT-AAAAAATAAATGAAGTATTTAATTACAT
* *
29943127 TAAACTATTAAATATATAAAAATTGTAATCAACAAAATTATATTTATAAAC
65 TAAAATATTAAATATATAAAAATTGAAATCAACAAAATTATATTTATAAAC
29943178 GCGCTTATAT
Statistics
Matches: 96, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
119 12 0.12
120 1 0.01
121 83 0.86
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (120 bp):
TATTCAAATAAAATGTTTCTTAAAAAGACATATAGTAAAAAATAAATGAAGTATTTAATTACATT
AAAATATTAAATATATAAAAATTGAAATCAACAAAATTATATTTATAAACACATA
Found at i:29949584 original size:28 final size:31
Alignment explanation
Indices: 29949531--29949589 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
29949521 TGAGATAAAA
29949531 TAAAAAATTATTAATAATTTAAAATTAAATAT
1 TAAAAAATTATTAATAATTT-AAATTAAATAT
29949563 TAAAAAATTA-TAATAA-TT-AATTAAATA
1 TAAAAAATTATTAATAATTTAAATTAAATA
29949590 AAAAATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 9 0.33
30 2 0.07
31 6 0.22
32 10 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (31 bp):
TAAAAAATTATTAATAATTTAAATTAAATAT
Found at i:29950007 original size:155 final size:156
Alignment explanation
Indices: 29949724--29950039 Score: 535
Period size: 155 Copynumber: 2.0 Consensus size: 156
29949714 ACTGTATATT
* * *
29949724 AAATGTGTAGAATTTATAATCTTTATGTGTTCACTTAATTATCATTTTAATTTTCTAATATTTTT
1 AAATGTCTAGAATTTATAATCTTTATGTGTTCACCTAATTATCATTTTAATTTTCTAAAATTTTT
29949789 TAATTATACTTTAATACACATGTGAGAACTTGTAAACCACTTGTAAAATTTAAATATTTTCATAG
66 TAATTATACTTTAATACACATGTGAGAACTTGTAAACCACTTGTAAAATTTAAATATTTTCATAG
29949854 TAGGTATATCCCATAATGCACTACCC
131 TAGGTATATCCCATAATGCACTACCC
* * *
29949880 AAATGTCTAGAGTTTATAATTTTTAT-TGTTCACCTAATTATCATTTTTATTTTCTAAAATTTTT
1 AAATGTCTAGAATTTATAATCTTTATGTGTTCACCTAATTATCATTTTAATTTTCTAAAATTTTT
*
29949944 TAATTATACTTTTATACACATGTGAGAACTTGTAAACCACTTGTAAAATTTAAATATTTTCATAG
66 TAATTATACTTTAATACACATGTGAGAACTTGTAAACCACTTGTAAAATTTAAATATTTTCATAG
* * *
29950009 TAGGTGTATTCCATAGTGCACTACCC
131 TAGGTATATCCCATAATGCACTACCC
29950035 AAATG
1 AAATG
29950040 CATTGATATG
Statistics
Matches: 150, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
155 127 0.85
156 23 0.15
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (156 bp):
AAATGTCTAGAATTTATAATCTTTATGTGTTCACCTAATTATCATTTTAATTTTCTAAAATTTTT
TAATTATACTTTAATACACATGTGAGAACTTGTAAACCACTTGTAAAATTTAAATATTTTCATAG
TAGGTATATCCCATAATGCACTACCC
Found at i:29963946 original size:13 final size:13
Alignment explanation
Indices: 29963928--29963952 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29963918 TTTCATAAAA
29963928 TTTATAAAATCAT
1 TTTATAAAATCAT
29963941 TTTATAAAATCA
1 TTTATAAAATCA
29963953 CAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:29970266 original size:15 final size:15
Alignment explanation
Indices: 29970246--29970291 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
29970236 ATTTTAAAAT
29970246 AACTTTAAAACCAAA
1 AACTTTAAAACCAAA
*
29970261 AACTTTAAAATTC-AA
1 AACTTTAAAA-CCAAA
*
29970276 AGCTTTAAAACCAAA
1 AACTTTAAAACCAAA
29970291 A
1 A
29970292 TCTCTGATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 1 0.04
15 24 0.92
16 1 0.04
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (15 bp):
AACTTTAAAACCAAA
Found at i:29977241 original size:2 final size:2
Alignment explanation
Indices: 29977234--29977290 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
29977224 NNNNNNNNNN
29977234 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29977276 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
29977291 GGGCCTGGCA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29982001 original size:32 final size:32
Alignment explanation
Indices: 29981965--29982027 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
29981955 CGATGTAAAG
* * *
29981965 CTGTTTGGTTATCTGTTAATGTTTAAAGTTTA
1 CTGTTTGATTATCTATTAATGTGTAAAGTTTA
29981997 CTGTTTGATTATCTATTAATGTGTAAAGTTT
1 CTGTTTGATTATCTATTAATGTGTAAAGTTT
29982028 GAGTGTATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.24, C:0.06, G:0.17, T:0.52
Consensus pattern (32 bp):
CTGTTTGATTATCTATTAATGTGTAAAGTTTA
Found at i:29984602 original size:19 final size:21
Alignment explanation
Indices: 29984564--29984602 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
29984554 AAGAATAAAA
*
29984564 ATAATTTATTTTATAAAATAG
1 ATAATTTATTTCATAAAATAG
29984585 ATAA-TTATTTCA-AAAATA
1 ATAATTTATTTCATAAAATA
29984603 ATGACAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (21 bp):
ATAATTTATTTCATAAAATAG
Found at i:29984825 original size:25 final size:24
Alignment explanation
Indices: 29984796--29984843 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
29984786 TTAATGTTGG
29984796 ATAAAAAA-TGAAATAAAATGATAAT
1 ATAAAAAAGT-AAATAAAAT-ATAAT
*
29984821 ATAAATAAGTAAATAAAATATAA
1 ATAAAAAAGTAAATAAAATATAA
29984844 GTAAATATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 16 0.76
26 1 0.05
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (24 bp):
ATAAAAAAGTAAATAAAATATAAT
Found at i:29985887 original size:14 final size:14
Alignment explanation
Indices: 29985868--29985897 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
29985858 ATATATTACT
29985868 ATCAGAGATACAGC
1 ATCAGAGATACAGC
29985882 ATCAGAGATACAGC
1 ATCAGAGATACAGC
29985896 AT
1 AT
29985898 AGATGTAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (14 bp):
ATCAGAGATACAGC
Found at i:29985978 original size:2 final size:2
Alignment explanation
Indices: 29985973--29986004 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29985963 TTACTATCAG
29985973 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
29986005 GCAAGAACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29986078 original size:15 final size:15
Alignment explanation
Indices: 29986058--29986093 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
29986048 CCTCTGCTTC
29986058 TTCTTCTTCATGGCT
1 TTCTTCTTCATGGCT
29986073 TTCTTCTTCATGGCT
1 TTCTTCTTCATGGCT
29986088 TTCTTC
1 TTCTTC
29986094 AGTGCAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.06, C:0.28, G:0.11, T:0.56
Consensus pattern (15 bp):
TTCTTCTTCATGGCT
Found at i:29986078 original size:18 final size:17
Alignment explanation
Indices: 29986053--29986093 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
29986043 TTAGTCCTCT
29986053 GCTTCTTCTTCTTCATG
1 GCTTCTTCTTCTTCATG
29986070 GC-T-TTCTTCTTCATG
1 GCTTCTTCTTCTTCATG
29986085 GCTTTCTTC
1 GC-TTCTTC
29986094 AGTGCAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 14 0.67
16 1 0.05
17 3 0.14
18 3 0.14
ACGTcount: A:0.05, C:0.29, G:0.12, T:0.54
Consensus pattern (17 bp):
GCTTCTTCTTCTTCATG
Found at i:29990635 original size:17 final size:17
Alignment explanation
Indices: 29990613--29990648 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
29990603 GGTCTTTGGA
29990613 AAAAATAAAGATAGATT
1 AAAAATAAAGATAGATT
*
29990630 AAAAATAAGGATAGATT
1 AAAAATAAAGATAGATT
29990647 AA
1 AA
29990649 GGTTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.22
Consensus pattern (17 bp):
AAAAATAAAGATAGATT
Found at i:29991944 original size:212 final size:211
Alignment explanation
Indices: 29991577--29991960 Score: 597
Period size: 212 Copynumber: 1.8 Consensus size: 211
29991567 TAAAACTATA
* * * * * *
29991577 ATGTTATAATGTTTTATATCAAAGTTTATATAAATAATAATTAATTATAAATAATATGTTATAAA
1 ATGTTATAATATTTTATATCAAAATTTATATAAATAATAACTAATCATAAACAATAGGTTATAAA
* **
29991642 ATCTAAGGTGATAACTAATAAAGTTATTAAATATAATTATATAAATAAAATCTATTATAAGTAAT
66 AACTAAACTGATAACTAATAAAGTTATTAAATATAATTATATAAATAAAATCTATTATAAGTAAT
** *
29991707 AGTAATGGTTATATATAAATTAAATATATGTATATATAATATTACTTTATTATATATAGAGAAAA
131 AGTAATACTTATATATAAATTAAATATAAGTATATAT-ATATTACTTTATTATATATAGAGAAAA
29991772 TTAATGATACAATTTAT
195 TTAATGATACAATTTAT
*
29991789 ATGTTATAATATTTTGTATCAAAATTTATATAAATAATAACTAATCATAAACAATAGGTTATAAA
1 ATGTTATAATATTTTATATCAAAATTTATATAAATAATAACTAATCATAAACAATAGGTTATAAA
* * * *
29991854 AACTAAACTGATAACTAATAAAGTTATTAAGTGTAATTATATAAATAAAATTTATTATAAGTTAT
66 AACTAAACTGATAACTAATAAAGTTATTAAATATAATTATATAAATAAAATCTATTATAAGTAAT
*
29991919 AGTATTACTTATATATAAATTAAATATAAGTATATATATATT
131 AGTAATACTTATATATAAATTAAATATAAGTATATATATATT
29991961 TATACAATTA
Statistics
Matches: 154, Mismatches: 18, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
211 5 0.03
212 149 0.97
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (211 bp):
ATGTTATAATATTTTATATCAAAATTTATATAAATAATAACTAATCATAAACAATAGGTTATAAA
AACTAAACTGATAACTAATAAAGTTATTAAATATAATTATATAAATAAAATCTATTATAAGTAAT
AGTAATACTTATATATAAATTAAATATAAGTATATATATATTACTTTATTATATATAGAGAAAAT
TAATGATACAATTTAT
Found at i:29991993 original size:22 final size:20
Alignment explanation
Indices: 29991949--29991995 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
29991939 TAAATATAAG
* *
29991949 TATATATATATTTATACAAT
1 TATATATATATTCATAAAAT
29991969 TATATATATATTCATAAAAT
1 TATATATATATTCATAAAAT
*
29991989 TTTATAT
1 TATATAT
29991996 TACGAAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
TATATATATATTCATAAAAT
Found at i:29998970 original size:44 final size:45
Alignment explanation
Indices: 29998907--29998996 Score: 137
Period size: 44 Copynumber: 2.0 Consensus size: 45
29998897 ATCCTTGATG
* *
29998907 ACTGCATCAACAGTTTTCCCATGGTTCCAC-TTTAAACTCTCCAT
1 ACTGCATCAACAGGTTTCCCACGGTTCCACTTTTAAACTCTCCAT
* *
29998951 ACTGCATCCATAGGTTTCCCACGGTTCCACTTTTAAACTCTCCAT
1 ACTGCATCAACAGGTTTCCCACGGTTCCACTTTTAAACTCTCCAT
29998996 A
1 A
29998997 TACTTTTCTG
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 26 0.63
45 15 0.37
ACGTcount: A:0.24, C:0.32, G:0.10, T:0.33
Consensus pattern (45 bp):
ACTGCATCAACAGGTTTCCCACGGTTCCACTTTTAAACTCTCCAT
Found at i:30010492 original size:5 final size:5
Alignment explanation
Indices: 30010479--30010518 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
30010469 TAACTCGATA
* *
30010479 TAACC TAACT TAACT TGACT T-ACT TAACT TAACT TAACT T
1 TAACT TAACT TAACT TAACT TAACT TAACT TAACT TAACT T
30010519 GGGCCACGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.40
Consensus pattern (5 bp):
TAACT
Found at i:30010573 original size:15 final size:15
Alignment explanation
Indices: 30010553--30010603 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
30010543 TTCTTAAAAC
30010553 AACTTTAAAATCAAA
1 AACTTTAAAATCAAA
* *
30010568 AACTTTGAAATCCAA
1 AACTTTAAAATCAAA
*
30010583 AGCTTTAAAATCAAA
1 AACTTTAAAATCAAA
*
30010598 ATCTTT
1 AACTTT
30010604 GATCTTTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (15 bp):
AACTTTAAAATCAAA
Found at i:30015620 original size:5 final size:5
Alignment explanation
Indices: 30015607--30015646 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
30015597 TAACTCGATA
* *
30015607 TAACC TAACT TAACT TGACT T-ACT TAACT TAACT TAACT T
1 TAACT TAACT TAACT TAACT TAACT TAACT TAACT TAACT T
30015647 GGGCCACGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.40
Consensus pattern (5 bp):
TAACT
Found at i:30015701 original size:15 final size:15
Alignment explanation
Indices: 30015681--30015731 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
30015671 TTCTTAAAAC
30015681 AACTTTAAAATCAAA
1 AACTTTAAAATCAAA
* *
30015696 AACTTTGAAATCCAA
1 AACTTTAAAATCAAA
*
30015711 AGCTTTAAAATCAAA
1 AACTTTAAAATCAAA
*
30015726 ATCTTT
1 AACTTT
30015732 GATCTTTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (15 bp):
AACTTTAAAATCAAA
Found at i:30020748 original size:5 final size:5
Alignment explanation
Indices: 30020735--30020774 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
30020725 TAACTCGATA
* *
30020735 TAACC TAACT TAACT TGACT T-ACT TAACT TAACT TAACT T
1 TAACT TAACT TAACT TAACT TAACT TAACT TAACT TAACT T
30020775 GGGCCACGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.40
Consensus pattern (5 bp):
TAACT
Found at i:30020829 original size:15 final size:15
Alignment explanation
Indices: 30020809--30020859 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
30020799 TTCTTAAAAC
30020809 AACTTTAAAATCAAA
1 AACTTTAAAATCAAA
* *
30020824 AACTTTGAAATCCAA
1 AACTTTAAAATCAAA
*
30020839 AGCTTTAAAATCAAA
1 AACTTTAAAATCAAA
*
30020854 ATCTTT
1 AACTTT
30020860 GATCTTTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (15 bp):
AACTTTAAAATCAAA
Found at i:30024480 original size:21 final size:21
Alignment explanation
Indices: 30024439--30024480 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
30024429 TTGACTATCA
* *
30024439 ATCAATAGTTGTTGTGTATCT
1 ATCAATAGTTGTTATGAATCT
30024460 ATCAATAGTTGTTCAT-AATCT
1 ATCAATAGTTGTT-ATGAATCT
30024481 TTGATGTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (21 bp):
ATCAATAGTTGTTATGAATCT
Found at i:30027208 original size:17 final size:17
Alignment explanation
Indices: 30027176--30027208 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
30027166 TATAACAAAA
30027176 CAAAATAACAATAACAT
1 CAAAATAACAATAACAT
30027193 CAAATATAACAA-AACA
1 CAAA-ATAACAATAACA
30027209 AAATTCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.67, C:0.18, G:0.00, T:0.15
Consensus pattern (17 bp):
CAAAATAACAATAACAT
Found at i:30031474 original size:75 final size:75
Alignment explanation
Indices: 30031380--30031525 Score: 215
Period size: 75 Copynumber: 1.9 Consensus size: 75
30031370 CTAACATATT
* *
30031380 ATAATAAATGATGATGGACAAGATAACATGA-CTACATGATATTTTTCACCCTT-CATGTTAGCA
1 ATAATAAACGATGATGGACAAGATAACATGATC-ACACGATATTTTTCA-CCTTCCATGTTAGCA
*
30031443 TCACATGATGTC
64 TCAAATGATGTC
* *
30031455 ATAATAAACGATGATGGACAAGATAACATGATCACGCGATATTTTTCATCTTCCATGTTAGCATC
1 ATAATAAACGATGATGGACAAGATAACATGATCACACGATATTTTTCACCTTCCATGTTAGCATC
30031520 AAATGA
66 AAATGA
30031526 GTATAAAATG
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
74 3 0.05
75 60 0.94
76 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (75 bp):
ATAATAAACGATGATGGACAAGATAACATGATCACACGATATTTTTCACCTTCCATGTTAGCATC
AAATGATGTC
Found at i:30031942 original size:41 final size:42
Alignment explanation
Indices: 30031843--30031943 Score: 150
Period size: 41 Copynumber: 2.4 Consensus size: 42
30031833 AATATGTAAC
* * *
30031843 ACGACACGACACGATTAACACGTTTATTAAACGTGTTAATAT
1 ACGACACGACACGATTAACACGTTTACTAAACATGTCAATAT
*
30031885 ACGACACGACACGATTAGCACGTTTACT-AACATGTCAATAT
1 ACGACACGACACGATTAACACGTTTACTAAACATGTCAATAT
*
30031926 ACGACACGACATGATTAA
1 ACGACACGACACGATTAA
30031944 TAACACATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 27 0.51
42 26 0.49
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.25
Consensus pattern (42 bp):
ACGACACGACACGATTAACACGTTTACTAAACATGTCAATAT
Found at i:30031967 original size:18 final size:18
Alignment explanation
Indices: 30031944--30031982 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
30031934 ACATGATTAA
30031944 TAACACATTTAACAAGAT
1 TAACACATTTAACAAGAT
* *
30031962 TAACACGTTTAACATGAT
1 TAACACATTTAACAAGAT
30031980 TAA
1 TAA
30031983 ATAAAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (18 bp):
TAACACATTTAACAAGAT
Found at i:30033038 original size:2 final size:2
Alignment explanation
Indices: 30033031--30033064 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30033021 NNNNNNNNNA
30033031 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
30033065 TTTCTTATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30041737 original size:17 final size:17
Alignment explanation
Indices: 30041711--30041745 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
30041701 CATATATATA
*
30041711 TATATATATAATTATTT
1 TATATATATAAATATTT
*
30041728 TATATGTATAAATATTT
1 TATATATATAAATATTT
30041745 T
1 T
30041746 TTTTTCATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TATATATATAAATATTT
Found at i:30048597 original size:6 final size:6
Alignment explanation
Indices: 30048588--30048616 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
30048578 GAGAAATTAG
30048588 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
30048617 TTGGTCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:30064471 original size:2 final size:2
Alignment explanation
Indices: 30064459--30064491 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
30064449 AACATTTCCC
*
30064459 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30064492 ATTNTAATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30064735 original size:299 final size:299
Alignment explanation
Indices: 30064197--30064794 Score: 1180
Period size: 299 Copynumber: 2.0 Consensus size: 299
30064187 CATGAAGCCG
30064197 TAATGCATTTATTACATAATTCTTTTTATAAATAAAGAAATGTTACAAACTATTTACAGATATAT
1 TAATGCATTTATTACATAATTCTTTTTATAAATAAAGAAATGTTACAAACTATTTACAGATATAT
30064262 ATTAAAATGATGTTTATAATTTTTGAATTCGGTGTAAATAATAATTAAACGGGTGTTTATAATCA
66 ATTAAAATGATGTTTATAATTTTTGAATTCGGTGTAAATAATAATTAAACGGGTGTTTATAATCA
30064327 CCCCTTAAAAACAAAAAAAATATTTACAATTAATGGACTAGTTTTATTAAATTAAAAAAACTAAT
131 CCCCTTAAAAACAAAAAAAATATTTACAATTAATGGACTAGTTTTATTAAATTAAAAAAACTAAT
30064392 ACATTAATTATAAATTTTTTTCTCAAAAAATATCATCCTTATCACCATTAATCAGCTAACATTTC
196 ACATTAATTATAAATTTTTTTCTCAAAAAATATCATCCTTATCACCATTAATCAGCTAACATTTC
30064457 CCATATC-TATATATATATATATATATATATATATAATT
261 CCATATCTTATATATATATATATATATATATATATAATT
30064495 NTAATGCATTTATTACATAATTCTTTTTATAAATAAAGAAATGTTACAAACTATTTACAGATATA
1 -TAATGCATTTATTACATAATTCTTTTTATAAATAAAGAAATGTTACAAACTATTTACAGATATA
30064560 TATTAAAATGATGTTTATAATTTTTGAATTCGGTGTAAATAATAATTAAACGGGTGTTTATAATC
65 TATTAAAATGATGTTTATAATTTTTGAATTCGGTGTAAATAATAATTAAACGGGTGTTTATAATC
30064625 ACCCCTTAAAAACAAAAAAAATATTTACAATTAATGGACTAGTTTTATTAAATTAAAAAAACTAA
130 ACCCCTTAAAAACAAAAAAAATATTTACAATTAATGGACTAGTTTTATTAAATTAAAAAAACTAA
30064690 TACATTAATTATAAATTTTTTTCTCAAAAAATATCATCCTTATCACCATTAATCAGCTAACATTT
195 TACATTAATTATAAATTTTTTTCTCAAAAAATATCATCCTTATCACCATTAATCAGCTAACATTT
30064755 CCCATATCTTATATATATATATATATATATATATATAATT
260 CCCATATCTTATATATATATATATATATATATATATAATT
30064795 GACAACTGAC
Statistics
Matches: 298, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
299 267 0.90
300 31 0.10
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (299 bp):
TAATGCATTTATTACATAATTCTTTTTATAAATAAAGAAATGTTACAAACTATTTACAGATATAT
ATTAAAATGATGTTTATAATTTTTGAATTCGGTGTAAATAATAATTAAACGGGTGTTTATAATCA
CCCCTTAAAAACAAAAAAAATATTTACAATTAATGGACTAGTTTTATTAAATTAAAAAAACTAAT
ACATTAATTATAAATTTTTTTCTCAAAAAATATCATCCTTATCACCATTAATCAGCTAACATTTC
CCATATCTTATATATATATATATATATATATATATAATT
Found at i:30064771 original size:2 final size:2
Alignment explanation
Indices: 30064764--30064791 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30064754 TCCCATATCT
30064764 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30064792 ATTGACAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30067531 original size:20 final size:20
Alignment explanation
Indices: 30067501--30067551 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
30067491 AATAATCATA
30067501 TTAATATAAATTATT-AATATT
1 TTAA-ATAAATT-TTAAATATT
30067522 TTAAATAAATTTTAAAATATT
1 TTAAATAAATTTT-AAATATT
30067543 TTAAA-AAAT
1 TTAAATAAAT
30067552 AAAAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.07
20 11 0.39
21 15 0.54
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAAATAAATTTTAAATATT
Found at i:30068000 original size:17 final size:17
Alignment explanation
Indices: 30067978--30068016 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
30067968 AAACTAAATG
30067978 GTAAAAATTATT-TTTTT
1 GTAAAAATT-TTCTTTTT
*
30067995 GTAAAACTTTTCTTTTT
1 GTAAAAATTTTCTTTTT
30068012 GTAAA
1 GTAAA
30068017 TTTTCAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (17 bp):
GTAAAAATTTTCTTTTT
Found at i:30069000 original size:20 final size:21
Alignment explanation
Indices: 30068977--30069022 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
30068967 ACTGTTCAAT
30068977 TTTTTA-TAAATAATTTGTTA
1 TTTTTATTAAATAATTTGTTA
* *
30068997 -TTTTATTTAATAATTTTTTA
1 TTTTTATTAAATAATTTGTTA
30069017 TATTTT
1 T-TTTT
30069023 TATTTTGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
19 5 0.24
20 12 0.57
22 4 0.19
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTTATTAAATAATTTGTTA
Found at i:30076184 original size:3 final size:3
Alignment explanation
Indices: 30076176--30076204 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
30076166 TTAAAATTTT
30076176 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
30076205 GTTCTACTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:30086628 original size:16 final size:17
Alignment explanation
Indices: 30086597--30086632 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
30086587 CATATTGTGC
*
30086597 AAAAAGAAATAGAAAGG
1 AAAAAGAAATAAAAAGG
30086614 AAAAAGAAA-AAAAAGG
1 AAAAAGAAATAAAAAGG
30086630 AAA
1 AAA
30086633 GAAATGGACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (17 bp):
AAAAAGAAATAAAAAGG
Found at i:30090280 original size:8 final size:8
Alignment explanation
Indices: 30090267--30090299 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
30090257 TTGCGCAGTC
30090267 TCTTTTTT
1 TCTTTTTT
30090275 TCTTTTTT
1 TCTTTTTT
30090283 TCTTTTTT
1 TCTTTTTT
30090291 CTCTTTTTT
1 -TCTTTTTT
30090300 GAAATGCTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TCTTTTTT
Found at i:30093957 original size:11 final size:10
Alignment explanation
Indices: 30093935--30093966 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
30093925 TACACTTGAC
30093935 ATATTTTTAT
1 ATATTTTTAT
30093945 ATATTTTTCAT
1 ATATTTTT-AT
30093956 ATATTTTTAT
1 ATATTTTTAT
30093966 A
1 A
30093967 ACGTTACTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (10 bp):
ATATTTTTAT
Found at i:30094013 original size:31 final size:32
Alignment explanation
Indices: 30093975--30094035 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
30093965 TAACGTTACT
*
30093975 GAATATTTTTCTA-ATTACAAAATATTTTTCA
1 GAATATTTTTATACATTACAAAATATTTTTCA
*
30094006 GAATATTTTTATACCATTGCAAAATATTTT
1 GAATATTTTTATA-CATTACAAAATATTTT
30094036 GTGATAACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 12 0.46
33 14 0.54
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.48
Consensus pattern (32 bp):
GAATATTTTTATACATTACAAAATATTTTTCA
Found at i:30094181 original size:79 final size:79
Alignment explanation
Indices: 30094067--30094557 Score: 903
Period size: 79 Copynumber: 6.2 Consensus size: 79
30094057 TTTCCTTATC
* * * *
30094067 ACAAAATATTTTAT-ATAATAAACTATTAAAAGACTTAATTTGGTCTTTGATTATTTTTCAGAAT
1 ACAAAATATTTTGTAATCATAAACTATTACAGGACTTAATTTGGTCTTTGATTATTTTTCAGAAT
30094131 ATTTTTATAACATT
66 ATTTTTATAACATT
30094145 ACAAAATATTTTGTAATCATAAACTATTACAGGACTTAATTTGGTCTTTGATTATTTTTCAGAAT
1 ACAAAATATTTTGTAATCATAAACTATTACAGGACTTAATTTGGTCTTTGATTATTTTTCAGAAT
30094210 ATTTTTATAACATT
66 ATTTTTATAACATT
30094224 ACAAAATATTTTGTAATCATAAACTATTACAGGACTTAATTTGGTCTTTGATTATTTTTCAGAAT
1 ACAAAATATTTTGTAATCATAAACTATTACAGGACTTAATTTGGTCTTTGATTATTTTTCAGAAT
30094289 ATTTTTATAACATT
66 ATTTTTATAACATT
30094303 ACAAAATATTTTGTAATCATAAACTATTACAGGACTTAATTTGGTCTTTGATTATTTTTCAGAAT
1 ACAAAATATTTTGTAATCATAAACTATTACAGGACTTAATTTGGTCTTTGATTATTTTTCAGAAT
30094368 ATTTTTATAACATT
66 ATTTTTATAACATT
30094382 ACAAAATATTTTGTAATCATAAACTATTACAGGACTTAATTTGGTCTTTGATTATTTTTCAGAAT
1 ACAAAATATTTTGTAATCATAAACTATTACAGGACTTAATTTGGTCTTTGATTATTTTTCAGAAT
30094447 ATTTTTATAACATT
66 ATTTTTATAACATT
* *
30094461 ACAAAATATTTTGTAATCATAAACTATTACAGGACTTAATTTGATCTTTTGATTATTTTTCACAA
1 ACAAAATATTTTGTAATCATAAACTATTACAGGACTTAATTTGGTC-TTTGATTATTTTTCAGAA
*
30094526 TATTTTTATAACACT
65 TATTTTTATAACATT
30094541 ACAAAATATTTTGTAAT
1 ACAAAATATTTTGTAAT
30094558 ATGTTACATG
Statistics
Matches: 404, Mismatches: 7, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
78 13 0.03
79 343 0.85
80 48 0.12
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (79 bp):
ACAAAATATTTTGTAATCATAAACTATTACAGGACTTAATTTGGTCTTTGATTATTTTTCAGAAT
ATTTTTATAACATT
Found at i:30100250 original size:23 final size:22
Alignment explanation
Indices: 30100218--30100289 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 22
30100208 ATACAAACAC
30100218 ATTTTTATTATAATTTAATAAT
1 ATTTTTATTATAATTTAATAAT
* **
30100240 ATTTTGTATTAGAAGCTAATTAA-
1 ATTTT-TATTATAATTTAA-TAAT
* *
30100263 ACCTTTTATTATAATTAAATAAT
1 A-TTTTTATTATAATTTAATAAT
30100286 ATTT
1 ATTT
30100290 AATATTAAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
22 10 0.27
23 21 0.57
24 6 0.16
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (22 bp):
ATTTTTATTATAATTTAATAAT
Found at i:30100387 original size:10 final size:10
Alignment explanation
Indices: 30100372--30100446 Score: 57
Period size: 10 Copynumber: 7.4 Consensus size: 10
30100362 ATATTCAAAT
30100372 AATAATATTA
1 AATAATATTA
*
30100382 AATAATATGCTT
1 AATAATAT--TA
*
30100394 TATAATATT-
1 AATAATATTA
* *
30100403 TATTATAATTA
1 AATAAT-ATTA
30100414 AATAATATT-
1 AATAATATTA
30100423 AAT-ATATTA
1 AATAATATTA
30100432 AATAATATTTA
1 AATAATA-TTA
30100443 AATA
1 AATA
30100447 TTTTCATTGC
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
8 5 0.09
9 11 0.21
10 18 0.34
11 11 0.21
12 8 0.15
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (10 bp):
AATAATATTA
Found at i:30100387 original size:45 final size:45
Alignment explanation
Indices: 30100327--30100420 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
30100317 ATTAAATTTA
* *
30100327 AATAATACTAAATAATATTCTTTATTACATTTATTAT-ATTCAAAT
1 AATAATACTAAATAATATGCTTTATAACATTTATTATAATT-AAAT
* *
30100372 AATAATATTAAATAATATGCTTTATAATATTTATTATAATTAAAT
1 AATAATACTAAATAATATGCTTTATAACATTTATTATAATTAAAT
30100417 AATA
1 AATA
30100421 TTAATATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 41 0.93
46 3 0.07
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (45 bp):
AATAATACTAAATAATATGCTTTATAACATTTATTATAATTAAAT
Found at i:30100433 original size:18 final size:19
Alignment explanation
Indices: 30100395--30100440 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
30100385 AATATGCTTT
*
30100395 ATAATATTTATTATAATTAA
1 ATAATA-TTAATATAATTAA
30100415 ATAATATTAATAT-ATTAA
1 ATAATATTAATATAATTAA
30100433 ATAATATT
1 ATAATATT
30100441 TAAATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 13 0.52
19 6 0.24
20 6 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAATATTAATATAATTAA
Found at i:30100447 original size:18 final size:18
Alignment explanation
Indices: 30100395--30100448 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
30100385 AATATGCTTT
*
30100395 ATAATATTTATTATAATTAA
1 ATAATATTTA-AAT-ATTAA
30100415 ATAATA-TTAATATATTAA
1 ATAATATTTAA-ATATTAA
30100433 ATAATATTTAAATATT
1 ATAATATTTAAATATT
30100449 TTCATTGCCC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 16 0.52
19 9 0.29
20 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATAATATTTAAATATTAA
Found at i:30101651 original size:125 final size:125
Alignment explanation
Indices: 30101450--30101699 Score: 428
Period size: 125 Copynumber: 2.0 Consensus size: 125
30101440 CCGAAAAGAT
30101450 GAAAATTATCTTTAAAAACAATGTATAATGTATAACACCTTAGAAAATTATCTTTAAACACAATA
1 GAAAATTATCTTTAAAAACAATGTATAATGTATAACACCTTAGAAAATTATCTTTAAACACAATA
* *
30101515 TATAATGTATCACGTTTCAGATTAATTTCATTGTTATCTATTTCCATTTTCACCAACACA
66 TATAATATATCACGCTTCAGATTAATTTCATTGTTATCTATTTCCATTTTCACCAACACA
* * * *
30101575 GAAATTTATCTTTAAAGACAATGTATAATGTATAACACCTTCGAAAATTATCTTTAAAGACAATA
1 GAAAATTATCTTTAAAAACAATGTATAATGTATAACACCTTAGAAAATTATCTTTAAACACAATA
* *
30101640 TATAATATATCACGCTTCAGATTAATTTCATTGTTATCTGTTTTCATTTTCACCAACACA
66 TATAATATATCACGCTTCAGATTAATTTCATTGTTATCTATTTCCATTTTCACCAACACA
30101700 CCACTTGTAG
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
125 117 1.00
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (125 bp):
GAAAATTATCTTTAAAAACAATGTATAATGTATAACACCTTAGAAAATTATCTTTAAACACAATA
TATAATATATCACGCTTCAGATTAATTTCATTGTTATCTATTTCCATTTTCACCAACACA
Found at i:30103868 original size:54 final size:54
Alignment explanation
Indices: 30103808--30103916 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
30103798 ATTGGAAAAG
30103808 ATAACCACATTTTCAACATCTAATTGCCCTGTCAAGCAATCCATTGGAAGATTC
1 ATAACCACATTTTCAACATCTAATTGCCCTGTCAAGCAATCCATTGGAAGATTC
30103862 ATAACCACATTTTCAACATCTAATTGCCCTGTCAAGCAATCCATTGGAAGATTC
1 ATAACCACATTTTCAACATCTAATTGCCCTGTCAAGCAATCCATTGGAAGATTC
30103916 A
1 A
30103917 ACGAAAAGGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (54 bp):
ATAACCACATTTTCAACATCTAATTGCCCTGTCAAGCAATCCATTGGAAGATTC
Found at i:30104830 original size:13 final size:14
Alignment explanation
Indices: 30104812--30104844 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
30104802 TTAATGCAGA
*
30104812 ACTTAA-GAATTTT
1 ACTTAAGGAATCTT
30104825 ACTTAAGGAATCTT
1 ACTTAAGGAATCTT
30104839 ACTTAA
1 ACTTAA
30104845 TTATGGCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (14 bp):
ACTTAAGGAATCTT
Found at i:30106198 original size:28 final size:29
Alignment explanation
Indices: 30106155--30106224 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
30106145 GGAGTGTAAA
*
30106155 AGAGAAACCAAAGAACAAAGAAGAAA-C-AG
1 AGAGAAA-GAAAGAACAAAG-AGAAACCGAG
30106184 AGAGAAAGAAAGAACAAAGAGAAAGCCGAG
1 AGAGAAAGAAAGAACAAAGAGAAA-CCGAG
30106214 AGAGAAAGAAA
1 AGAGAAAGAAA
30106225 CATAAAAGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 5 0.14
28 11 0.30
29 8 0.22
30 13 0.35
ACGTcount: A:0.64, C:0.10, G:0.26, T:0.00
Consensus pattern (29 bp):
AGAGAAAGAAAGAACAAAGAGAAACCGAG
Found at i:30108823 original size:14 final size:15
Alignment explanation
Indices: 30108798--30108836 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
30108788 TTAAAAAATT
30108798 TAAAAT-TTTAAC-A
1 TAAAATATTTAACAA
30108811 TAAAATATTTAACAA
1 TAAAATATTTAACAA
*
30108826 TAAAAAATTTA
1 TAAAATATTTA
30108837 TTTTAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.26
14 6 0.26
15 11 0.48
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAATATTTAACAA
Found at i:30109088 original size:17 final size:18
Alignment explanation
Indices: 30109066--30109102 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
30109056 ATGACAATTC
30109066 AATA-TTAAAAATTAAAA
1 AATATTTAAAAATTAAAA
30109083 AATATTTAAAAATTAAAA
1 AATATTTAAAAATTAAAA
30109101 AA
1 AA
30109103 AAAACCCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AATATTTAAAAATTAAAA
Found at i:30114154 original size:151 final size:153
Alignment explanation
Indices: 30113875--30114189 Score: 392
Period size: 151 Copynumber: 2.1 Consensus size: 153
30113865 TGCTATTTGC
* *
30113875 TATATCATGGACCCAGACATGTCTGAATTAAAACTTTCTTGCAAAAACATCCTTTTTTTTTCTAT
1 TATATTATGGACCCAGACATGTCTGAATTAAAACTTTCTTGCAAAAACATCCTCTTTTTTTC-AT
* * ** *
30113940 GTCTGCATGGGTCTTTGCATGTGTGTGAGTATCTGGTGGTGGTGGGAGTTTACATTTTGGAAATT
65 G-CTGCATGAGTCTGTGCATGTGCATGAGTATCTGGTGGTGGTGGGAGTATACATTTTGGAAATT
*
30114005 TGATATCATTAGC-AGGTGGAAGGTG
129 TGATAGCATTAGCAAGG-GGAAGGTG
*
30114030 TATATTATGGACCCAGACACT-TCTGAATTAAAAACGTTT-TTGCAAAATCATCC-CTTTTTTTC
1 TATATTATGGACCCAGACA-TGTCTGAATT-AAAAC-TTTCTTGCAAAAACATCCTCTTTTTTTC
* * *
30114092 -TG-TGTATTAGTCTGTGCATGTGCATGCA-TATCTGGTGGTGGTGGGGGTATACATTTTGGAAA
63 ATGCTGCATGAGTCTGTGCATGTGCATG-AGTATCTGGTGGTGGTGGGAGTATACATTTTGGAAA
*
30114154 TTTGATAGCATTATCAAGGGGAAGGTG
127 TTTGATAGCATTAGCAAGGGGAAGGTG
30114181 TATAATTAT
1 TAT-ATTAT
30114190 CTTGATATCC
Statistics
Matches: 141, Mismatches: 13, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
151 74 0.52
152 9 0.06
153 2 0.01
155 34 0.24
156 19 0.13
157 3 0.02
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (153 bp):
TATATTATGGACCCAGACATGTCTGAATTAAAACTTTCTTGCAAAAACATCCTCTTTTTTTCATG
CTGCATGAGTCTGTGCATGTGCATGAGTATCTGGTGGTGGTGGGAGTATACATTTTGGAAATTTG
ATAGCATTAGCAAGGGGAAGGTG
Found at i:30124156 original size:19 final size:19
Alignment explanation
Indices: 30124129--30124169 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
30124119 GCTCTGTAGT
*
30124129 TTTCGTTGTAATTCAATCC
1 TTTCATTGTAATTCAATCC
30124148 TTTCATTGTAATTCAATCC
1 TTTCATTGTAATTCAATCC
30124167 TTT
1 TTT
30124170 TTAAAGCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.07, T:0.51
Consensus pattern (19 bp):
TTTCATTGTAATTCAATCC
Found at i:30128138 original size:3 final size:3
Alignment explanation
Indices: 30128130--30128159 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
30128120 GACATTTAAC
30128130 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
30128160 CAAATGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:30132161 original size:2 final size:2
Alignment explanation
Indices: 30132149--30132184 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
30132139 TCGATACACG
*
30132149 AT AT CT 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
30132185 TGATTTAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30134890 original size:3 final size:3
Alignment explanation
Indices: 30134878--30134918 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
30134868 CTACTACTAC
*
30134878 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
30134919 ATCTCATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:30135368 original size:15 final size:15
Alignment explanation
Indices: 30135350--30135378 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
30135340 TTTACTTTAA
30135350 AAAATTCAATATTAT
1 AAAATTCAATATTAT
30135365 AAAATTCAATATTA
1 AAAATTCAATATTA
30135379 ACTGACATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATTCAATATTAT
Found at i:30149162 original size:21 final size:21
Alignment explanation
Indices: 30149133--30149177 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
30149123 TAGTGATGAT
* *
30149133 GAGGATGATGTTGATGAAGAG
1 GAGGATGATGATGAAGAAGAG
* *
30149154 GAGGGTGATGATGAAGGAGAG
1 GAGGATGATGATGAAGAAGAG
30149175 GAG
1 GAG
30149178 AAAGAGCAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.49, T:0.18
Consensus pattern (21 bp):
GAGGATGATGATGAAGAAGAG
Found at i:30154755 original size:2 final size:2
Alignment explanation
Indices: 30154748--30154780 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
30154738 GGTTTTCAGC
30154748 GA GA GA GA GA GA GA GA GA GA GA TGA GA G- GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA -GA GA GA GA GA G
30154781 GTTTAGAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.52, T:0.03
Consensus pattern (2 bp):
GA
Found at i:30157556 original size:2 final size:2
Alignment explanation
Indices: 30157549--30157588 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
30157539 TCATGCGCAG
30157549 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
30157589 TGGAGAAGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:30165543 original size:8 final size:8
Alignment explanation
Indices: 30165530--30165572 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
30165520 NNNTTTATTA
30165530 TATTTTTT
1 TATTTTTT
30165538 TATTTTTT
1 TATTTTTT
30165546 TATTTTATT
1 TATTTT-TT
*
30165555 T-TTTTTA
1 TATTTTTT
*
30165562 CATTTTTT
1 TATTTTTT
30165570 TAT
1 TAT
30165573 AGTTTGTGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 1 0.03
8 25 0.86
9 3 0.10
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.81
Consensus pattern (8 bp):
TATTTTTT
Found at i:30165561 original size:14 final size:13
Alignment explanation
Indices: 30165535--30165559 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30165525 TATTATATTT
30165535 TTTTATTTTTTTA
1 TTTTATTTTTTTA
30165548 TTTTATTTTTTT
1 TTTTATTTTTTT
30165560 TACATTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:30165631 original size:9 final size:9
Alignment explanation
Indices: 30165617--30165681 Score: 60
Period size: 9 Copynumber: 6.8 Consensus size: 9
30165607 AAATTGGTTG
30165617 TTTTTATTA
1 TTTTTATTA
30165626 TTTTTATTA
1 TTTTTATTA
30165635 -TTTTATTTA
1 TTTTTA-TTA
30165644 TTATTTATTA
1 TT-TTTATTA
30165654 TTTATATATATA
1 TTT-T-TAT-TA
* *
30165666 CTTTAATTA
1 TTTTTATTA
30165675 TTTTTAT
1 TTTTTAT
30165682 CAAGTAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
8 5 0.11
9 20 0.43
10 9 0.20
11 8 0.17
12 4 0.09
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTATTA
Found at i:30165649 original size:7 final size:7
Alignment explanation
Indices: 30165619--30165658 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
30165609 ATTGGTTGTT
30165619 TTTATTA
1 TTTATTA
30165626 TTT-TTA
1 TTTATTA
*
30165632 TTATTTTA
1 TT-TATTA
30165640 TTTATTA
1 TTTATTA
30165647 TTTATTA
1 TTTATTA
30165654 TTTAT
1 TTTAT
30165659 ATATATACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 5 0.17
7 20 0.67
8 5 0.17
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTATTA
Found at i:30166112 original size:12 final size:11
Alignment explanation
Indices: 30166078--30166114 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 11
30166068 GATTTTGATT
30166078 TTTTATTTATTA
1 TTTTATTTA-TA
30166090 TTTTATTTATA
1 TTTTATTTATA
30166101 TTTTAATTTATA
1 TTTT-ATTTATA
30166113 TT
1 TT
30166115 ACCATGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 6 0.25
12 18 0.75
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTATTTATA
Found at i:30168594 original size:31 final size:31
Alignment explanation
Indices: 30168557--30168616 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
30168547 ATATTATATT
30168557 TATTATTAAAGTATTTTCAAATATATTTTTA
1 TATTATTAAAGTATTTTCAAATATATTTTTA
*** *
30168588 TATTATTATTTTATTTTTAAATATATTTT
1 TATTATTAAAGTATTTTCAAATATATTTT
30168617 AAAATTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (31 bp):
TATTATTAAAGTATTTTCAAATATATTTTTA
Found at i:30168661 original size:3 final size:3
Alignment explanation
Indices: 30168649--30168678 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
30168639 AATTATTAAT
30168649 TAA TATA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TA
30168679 TCTCGAATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:30182752 original size:23 final size:23
Alignment explanation
Indices: 30182708--30182753 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
30182698 CTGTGCTCCC
*
30182708 GATTTCTCTTTCTCTCATTTTCA
1 GATTTCTCTTTCTCTCACTTTCA
*
30182731 GATTTTTCTTTC-CTGCACTTTCA
1 GATTTCTCTTTCTCT-CACTTTCA
30182754 AGACACCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.13, C:0.26, G:0.07, T:0.54
Consensus pattern (23 bp):
GATTTCTCTTTCTCTCACTTTCA
Found at i:30183211 original size:32 final size:32
Alignment explanation
Indices: 30183164--30183232 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
30183154 ATATGGCGTG
* *
30183164 CAATAATAATATTTTTTCAATCTAACGTGTAA
1 CAATAATAATATTTTTTCAATATAACATGTAA
* * *
30183196 CAATAATATTTTTTTTTCAATATGACATGTAA
1 CAATAATAATATTTTTTCAATATAACATGTAA
30183228 CAATA
1 CAATA
30183233 TAACTATGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.42
Consensus pattern (32 bp):
CAATAATAATATTTTTTCAATATAACATGTAA
Found at i:30183317 original size:45 final size:44
Alignment explanation
Indices: 30183215--30183328 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
30183205 TTTTTTTTCA
* * *
30183215 ATATGACATGTAACAATATAACTATGACGTGTCACGTGTTTTGT
1 ATATGACGTGTAACAATATAACCATGACGTGTCACATGTTTTGT
* **
30183259 ACATGGTGTGTAACAATATAACCATGACGTGTCACATGTTTTTGT
1 ATATGACGTGTAACAATATAACCATGACGTGTCACATG-TTTTGT
30183304 ATATGACGTGTAACAACT-TAACCAT
1 ATATGACGTGTAACAA-TATAACCAT
30183329 AAGGTGTAGC
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
44 32 0.54
45 26 0.44
46 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (44 bp):
ATATGACGTGTAACAATATAACCATGACGTGTCACATGTTTTGT
Found at i:30183402 original size:66 final size:66
Alignment explanation
Indices: 30183260--30183405 Score: 177
Period size: 66 Copynumber: 2.2 Consensus size: 66
30183250 GTGTTTTGTA
* * *
30183260 CATGGTGTGTAACAATATAACCATGACGTGTCACATGTTTTTGTATATGACGTGTAACAACTTAA
1 CATGGTGTGTAACAACATAACCATGACGTGTCACATGTTTTTGCATATGACGTGTAACAACCTAA
30183325 C
66 C
* * * * * * * *
30183326 CATAAG-GTGTAGCAACCTAACTATGTCGTGTCATATGTTTTTGCATATTACGTGTAACAGCCTA
1 CAT-GGTGTGTAACAACATAACCATGACGTGTCACATGTTTTTGCATATGACGTGTAACAACCTA
30183390 AC
65 AC
30183392 CATGGTGTGTAACA
1 CATGGTGTGTAACA
30183406 TGTTTTTATA
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
65 1 0.02
66 63 0.97
67 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (66 bp):
CATGGTGTGTAACAACATAACCATGACGTGTCACATGTTTTTGCATATGACGTGTAACAACCTAA
C
Found at i:30200161 original size:32 final size:32
Alignment explanation
Indices: 30200125--30200187 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
30200115 AAATTAATGT
*
30200125 AATATGGCTAAAAGACTGGAATCATAGTCAGC
1 AATATGGCTAAAAGACTGGAACCATAGTCAGC
*
30200157 AATATGGCTAAAAGACTGGAGCCATAGTCAG
1 AATATGGCTAAAAGACTGGAACCATAGTCAG
30200188 TGTAAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.21
Consensus pattern (32 bp):
AATATGGCTAAAAGACTGGAACCATAGTCAGC
Found at i:30206538 original size:6 final size:6
Alignment explanation
Indices: 30206529--30206560 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
30206519 TCCCATTATT
30206529 ATTCAA ATTCAA ATTCAA ATTCAA ATTCAA AT
1 ATTCAA ATTCAA ATTCAA ATTCAA ATTCAA AT
30206561 CCCTTCGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
ATTCAA
Found at i:30209404 original size:212 final size:212
Alignment explanation
Indices: 30209037--30209462 Score: 762
Period size: 212 Copynumber: 2.0 Consensus size: 212
30209027 TGTATTAAAT
* *
30209037 GTGTATGTGTACGTGTTTTAAATTTAAGACACAAATATTAAACGTGTCGTGTTCTTATTTTGCCT
1 GTGTATGTGTACGTGTTTCAAATTTAAGACACAAATATTAAACGTGTCGTGTTCTTATTTTACCT
* * * *
30209102 TAACGTGTTTCGTGTCTAATCGTATTTGACACGTTTACGATACGTTAATACGAATTGCTAGGTCT
66 TAACGTGTTTCGTGTCTAATCGTATCTGACACATTTACGACACGTTAACACGAATTGCTAGGTCT
*
30209167 ACTTTTAAGTAGGGATGCCATAATTTAAGCTATTTGTGACTTACTCTATTTTAACTTATTTAATT
131 ACTTTTAAGTAGGGATGCCATAATTTAAGCTATTTGCGACTTACTCTATTTTAACTTATTTAATT
30209232 GAGGTTGACTAATTCTA
196 GAGGTTGACTAATTCTA
*
30209249 GTGTATGTGTACGTGTTTCAAATTTAAGACACAAATATTAAACGTGTCGTGTTTTTATTTTACCT
1 GTGTATGTGTACGTGTTTCAAATTTAAGACACAAATATTAAACGTGTCGTGTTCTTATTTTACCT
* *
30209314 TAACGTGTTTCGTGTCTAATCGTGTCTGACACATTTACGACACGTTAACACGAATTGTTAGGTCT
66 TAACGTGTTTCGTGTCTAATCGTATCTGACACATTTACGACACGTTAACACGAATTGCTAGGTCT
30209379 ACTTTTAAGTAGGGATGCCATAATTTAAGCTATTTGCGACTTACTCTATTTTAACTTATTTAATT
131 ACTTTTAAGTAGGGATGCCATAATTTAAGCTATTTGCGACTTACTCTATTTTAACTTATTTAATT
30209444 GAGGTTGACTAATTCTA
196 GAGGTTGACTAATTCTA
30209461 GT
1 GT
30209463 TGCTAATTAC
Statistics
Matches: 204, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
212 204 1.00
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.41
Consensus pattern (212 bp):
GTGTATGTGTACGTGTTTCAAATTTAAGACACAAATATTAAACGTGTCGTGTTCTTATTTTACCT
TAACGTGTTTCGTGTCTAATCGTATCTGACACATTTACGACACGTTAACACGAATTGCTAGGTCT
ACTTTTAAGTAGGGATGCCATAATTTAAGCTATTTGCGACTTACTCTATTTTAACTTATTTAATT
GAGGTTGACTAATTCTA
Found at i:30209676 original size:18 final size:18
Alignment explanation
Indices: 30209655--30209689 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
30209645 TTATCCAAAC
*
30209655 AGTTATGTTTGTATAAAA
1 AGTTATATTTGTATAAAA
30209673 AGTTATATTTGTATAAA
1 AGTTATATTTGTATAAA
30209690 GAGACAGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (18 bp):
AGTTATATTTGTATAAAA
Found at i:30216521 original size:2 final size:2
Alignment explanation
Indices: 30216516--30216541 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30216506 TTTAAATTTA
30216516 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
30216542 TTATGTATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30216654 original size:102 final size:102
Alignment explanation
Indices: 30216535--30216737 Score: 352
Period size: 102 Copynumber: 2.0 Consensus size: 102
30216525 TATATATATA
* * *
30216535 TATATATTTATGTATTGTAGGCTTCTAACCACAATTTAAGCCTTAAAAGGTCACAATAATAATCA
1 TATATATATATATATTGTAGGCTTCAAACCACAATTTAAGCCTTAAAAGGTCACAATAATAATCA
*
30216600 CAACTTTAAAGTAACTTTCTTTGATAGTAACATTGCT
66 CAACTTTAAAGTAACTTTCCTTGATAGTAACATTGCT
*
30216637 TATATATATATATATTGTAGGCTTCAAACTACAATTTAAGCCTTAAAAGGTCACAATAATAATCA
1 TATATATATATATATTGTAGGCTTCAAACCACAATTTAAGCCTTAAAAGGTCACAATAATAATCA
*
30216702 CACCTTTAAAGTAACTTTCCTTGATAGTAACATTGC
66 CAACTTTAAAGTAACTTTCCTTGATAGTAACATTGC
30216738 AAAGCAGTAG
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 95 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.36
Consensus pattern (102 bp):
TATATATATATATATTGTAGGCTTCAAACCACAATTTAAGCCTTAAAAGGTCACAATAATAATCA
CAACTTTAAAGTAACTTTCCTTGATAGTAACATTGCT
Found at i:30217894 original size:20 final size:21
Alignment explanation
Indices: 30217869--30217914 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
30217859 CAAAACATGT
30217869 AGAAAGAGCCTTTC-CAAAAA
1 AGAAAGAGCCTTTCACAAAAA
*
30217889 AGAAAGAGCCTTTCACAGAAA
1 AGAAAGAGCCTTTCACAAAAA
30217910 AGAAA
1 AGAAA
30217915 AACCATGTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.52, C:0.17, G:0.17, T:0.13
Consensus pattern (21 bp):
AGAAAGAGCCTTTCACAAAAA
Found at i:30233036 original size:21 final size:20
Alignment explanation
Indices: 30233010--30233049 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
30233000 AAAAACTAAT
30233010 AAATAATAAAAAAATTAAAAG
1 AAATAA-AAAAAAATTAAAAG
* *
30233031 AAATAACATAAAATTAAAA
1 AAATAAAAAAAAATTAAAA
30233050 CAACTAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (20 bp):
AAATAAAAAAAAATTAAAAG
Found at i:30233041 original size:26 final size:26
Alignment explanation
Indices: 30232989--30233041 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
30232979 TTTTAATTCT
*
30232989 ATAAAAAATATAAAAACTAATAAATA
1 ATAAAAAATATAAAAACAAATAAATA
* *
30233015 ATAAAAAA-ATTAAAAGAAATAACATA
1 ATAAAAAATATAAAAACAAATAA-ATA
30233041 A
1 A
30233042 AATTAAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21
Consensus pattern (26 bp):
ATAAAAAATATAAAAACAAATAAATA
Found at i:30233045 original size:20 final size:20
Alignment explanation
Indices: 30233020--30233063 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
30233010 AAATAATAAA
*
30233020 AAAATTAAAAGAAATAACAT
1 AAAATTAAAACAAATAACAT
* *
30233040 AAAATTAAAACAACTAACTT
1 AAAATTAAAACAAATAACAT
30233060 AAAA
1 AAAA
30233064 GTAACCTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.68, C:0.09, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAATTAAAACAAATAACAT
Found at i:30233439 original size:23 final size:23
Alignment explanation
Indices: 30233391--30233498 Score: 83
Period size: 23 Copynumber: 4.4 Consensus size: 23
30233381 GGTTTGAACC
* *
30233391 TGGACTTGA-TTAGAACACGATC
1 TGGACTTGATTTGGAACACGATA
* *
30233413 TGGAGTTGATTTGGAGCACGATA
1 TGGACTTGATTTGGAACACGATA
*
30233436 TGGACTTGAGAACTTTGATTAGAACACGATC
1 TGGACTT--G-A-TTTG----GAACACGATA
*
30233467 TGGAGTTGATTTGGAACACGATA
1 TGGACTTGATTTGGAACACGATA
30233490 TGGACTTGA
1 TGGACTTGA
30233499 GAACTTTGTC
Statistics
Matches: 67, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
22 8 0.12
23 33 0.49
25 1 0.01
26 1 0.01
27 8 0.12
28 1 0.01
29 1 0.01
31 14 0.21
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.30
Consensus pattern (23 bp):
TGGACTTGATTTGGAACACGATA
Found at i:30233478 original size:54 final size:54
Alignment explanation
Indices: 30233396--30233506 Score: 213
Period size: 54 Copynumber: 2.1 Consensus size: 54
30233386 GAACCTGGAC
*
30233396 TTGATTAGAACACGATCTGGAGTTGATTTGGAGCACGATATGGACTTGAGAACT
1 TTGATTAGAACACGATCTGGAGTTGATTTGGAACACGATATGGACTTGAGAACT
30233450 TTGATTAGAACACGATCTGGAGTTGATTTGGAACACGATATGGACTTGAGAACT
1 TTGATTAGAACACGATCTGGAGTTGATTTGGAACACGATATGGACTTGAGAACT
30233504 TTG
1 TTG
30233507 TCTTCAAGGG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.31
Consensus pattern (54 bp):
TTGATTAGAACACGATCTGGAGTTGATTTGGAACACGATATGGACTTGAGAACT
Found at i:30234323 original size:21 final size:22
Alignment explanation
Indices: 30234297--30234345 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
30234287 TCATCCTTCG
30234297 ACAAAAAAATAAACTCTAGTT-
1 ACAAAAAAATAAACTCTAGTTA
* * *
30234318 ACAAAAAGATCAACTTTAGTTA
1 ACAAAAAAATAAACTCTAGTTA
30234340 ACAAAA
1 ACAAAA
30234346 GATTTGTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.57, C:0.14, G:0.06, T:0.22
Consensus pattern (22 bp):
ACAAAAAAATAAACTCTAGTTA
Found at i:30248113 original size:13 final size:12
Alignment explanation
Indices: 30248089--30248119 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
30248079 AGGAAATAAA
30248089 AGAGAATTAGAG
1 AGAGAATTAGAG
30248101 AGAGAATTTAGAG
1 AGAGAA-TTAGAG
30248114 AGAGAA
1 AGAGAA
30248120 GCTCTCTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (12 bp):
AGAGAATTAGAG
Found at i:30248393 original size:29 final size:29
Alignment explanation
Indices: 30248344--30248470 Score: 139
Period size: 29 Copynumber: 4.4 Consensus size: 29
30248334 AAAGATACAT
* * *
30248344 GTGAAAAGGTATAAGAAAAGAAGCTGTAC
1 GTGAACAGGTACAAGAGAAGAAGCTGTAC
* * *
30248373 GTGAACAAGTACAAAAGAAGAAGCTGCAC
1 GTGAACAGGTACAAGAGAAGAAGCTGTAC
*
30248402 GAGAACAGGTACAAGAGAAGAAGCTGTAC
1 GTGAACAGGTACAAGAGAAGAAGCTGTAC
* * *
30248431 ATGAATAGGTACAAGAGAAGAA-CGTGTAT
1 GTGAACAGGTACAAGAGAAGAAGC-TGTAC
*
30248460 GAGAACAGGTA
1 GTGAACAGGTA
30248471 TACGAGAACA
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
28 1 0.01
29 79 0.99
ACGTcount: A:0.46, C:0.11, G:0.28, T:0.14
Consensus pattern (29 bp):
GTGAACAGGTACAAGAGAAGAAGCTGTAC
Found at i:30248478 original size:58 final size:58
Alignment explanation
Indices: 30248350--30248478 Score: 161
Period size: 58 Copynumber: 2.2 Consensus size: 58
30248340 ACATGTGAAA
* *
30248350 AGGTATAAGAAAAGAAGCTGTACGTGAACAAGTACAAAAGAAGAAGCTGCACGAGAAC
1 AGGTATAAGAGAAGAAGCTGTACATGAACAAGTACAAAAGAAGAAGCTGCACGAGAAC
* * * * * *
30248408 AGGTACAAGAGAAGAAGCTGTACATGAATAGGTACAAGAGAAGAA-CGTGTATGAGAAC
1 AGGTATAAGAGAAGAAGCTGTACATGAACAAGTACAAAAGAAGAAGC-TGCACGAGAAC
*
30248466 AGGTATACGAGAA
1 AGGTATAAGAGAA
30248479 CAAGGTAGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
57 1 0.02
58 59 0.98
ACGTcount: A:0.47, C:0.12, G:0.28, T:0.14
Consensus pattern (58 bp):
AGGTATAAGAGAAGAAGCTGTACATGAACAAGTACAAAAGAAGAAGCTGCACGAGAAC
Found at i:30248799 original size:35 final size:35
Alignment explanation
Indices: 30248721--30248800 Score: 115
Period size: 35 Copynumber: 2.3 Consensus size: 35
30248711 CTACTTATTC
* ***
30248721 TAGTTGTTATACGTGAAGTAGTGCTTCACTTGTTT
1 TAGTTGTTCTACGTGAAGTAACACTTCACTTGTTT
*
30248756 TAGTTGTTCTACGTGAAGTAACACTTCATTTGTTT
1 TAGTTGTTCTACGTGAAGTAACACTTCACTTGTTT
30248791 TAGTTGTTCT
1 TAGTTGTTCT
30248801 CTGTATAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.47
Consensus pattern (35 bp):
TAGTTGTTCTACGTGAAGTAACACTTCACTTGTTT
Found at i:30256554 original size:13 final size:13
Alignment explanation
Indices: 30256538--30256565 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
30256528 AAAGAAAATC
30256538 AAGATTTACAAAG
1 AAGATTTACAAAG
30256551 AAGATTTACAAAG
1 AAGATTTACAAAG
30256564 AA
1 AA
30256566 ACCCTAACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.21
Consensus pattern (13 bp):
AAGATTTACAAAG
Found at i:30258151 original size:2 final size:2
Alignment explanation
Indices: 30258144--30258242 Score: 85
Period size: 2 Copynumber: 46.5 Consensus size: 2
30258134 TTTAGACGCC
*
30258144 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA NTCG T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -T-A TA TA
* *
30258187 GTA GTGA T- TGA TT TA GA CTA CTA TA TA TA TA TA TA TA TA TA TA
1 -TA -T-A TA T-A TA TA TA -TA -TA TA TA TA TA TA TA TA TA TA TA
30258230 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
30258243 CCGGACAATC
Statistics
Matches: 84, Mismatches: 5, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
1 2 0.02
2 69 0.82
3 12 0.14
4 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:30258218 original size:64 final size:63
Alignment explanation
Indices: 30258117--30258242 Score: 225
Period size: 64 Copynumber: 2.0 Consensus size: 63
30258107 TAAGATGAAG
*
30258117 TCGTTAGTAGTGATTGATTTAGACGCCTATATATATATATATATATATATATATATATATATA
1 TCGTTAGTAGTGATTGATTTAGACGACTATATATATATATATATATATATATATATATATATA
*
30258180 NTCGTTAGTAGTGATTGATTTAGACTACTATATATATATATATATATATATATATATATATAT
1 -TCGTTAGTAGTGATTGATTTAGACGACTATATATATATATATATATATATATATATATATAT
30258243 CCGGACAATC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.45
Consensus pattern (63 bp):
TCGTTAGTAGTGATTGATTTAGACGACTATATATATATATATATATATATATATATATATATA
Found at i:30269794 original size:38 final size:38
Alignment explanation
Indices: 30269743--30270140 Score: 298
Period size: 38 Copynumber: 10.2 Consensus size: 38
30269733 TAGTTTCAAG
* * *
30269743 ATTTTTAAAGTCATGTTGTCTCAGCTTTGAGGAGCCAC
1 ATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGTCTC
* *
30269781 ATTTTTAAAGTCATGTTGCCTTAGCTTTGAGCTTTGAGGAGCCAC
1 ATTTTTAAAGTCATGTTGCC-T--C----AGCTTTGAGGAGTCTC
30269826 ATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGTCTC
1 ATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGTCTC
* *
30269864 ATTTTTAAAGT-TTCGTTGCCTCAGTTTTGAGGAGTCTC
1 ATTTTTAAAGTCAT-GTTGCCTCAGCTTTGAGGAGTCTC
** * *
30269902 ATTTTTTAAAGTTTTGTTGCCTCAGTTTTGAGGAGTTTC
1 A-TTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGTCTC
* * *
30269941 ATTTTTAAAGT-TTCGTAGCCTCA-CTTTTGAAGAGT-TC
1 ATTTTTAAAGTCAT-GTTGCCTCAGC-TTTGAGGAGTCTC
* ** *
30269978 ATTTTTATAGTTTTGTTGCCTCAGCTTTGAGGAATCTC
1 ATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGTCTC
* * **
30270016 ATTTTAAAAAAAAAAGTC-TCATTG-CTCAATTTTGAGGAAGT-TC
1 ATTTT------TAAAGTCAT-GTTGCCTCAGCTTTGAGG-AGTCTC
*
30270059 ATTTTTAAAGT-TTCGTTGCCTCAGCTTTGAGGAGTCT-
1 ATTTTTAAAGTCAT-GTTGCCTCAGCTTTGAGGAGTCTC
* *
30270096 -TTTTTAAAGT-TTCGTTGCCTCAGTTTTGAGGAGT-TC
1 ATTTTTAAAGTCAT-GTTGCCTCAGCTTTGAGGAGTCTC
30270132 ATTTTTAAA
1 ATTTTTAAA
30270141 AAGTTTCGTT
Statistics
Matches: 307, Mismatches: 25, Indels: 57
0.79 0.06 0.15
Matches are distributed among these distances:
35 1 0.00
36 33 0.11
37 52 0.17
38 117 0.38
39 35 0.11
40 2 0.01
41 1 0.00
42 1 0.00
43 19 0.06
44 10 0.03
45 36 0.12
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (38 bp):
ATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGTCTC
Found at i:30269829 original size:45 final size:45
Alignment explanation
Indices: 30269765--30269856 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
30269755 ATGTTGTCTC
*
30269765 AGCTTTGAGGAGCCACATTTTTAAAGTCATGTTGCCTTAGCTTTG
1 AGCTTTGAGGAGCCACATTTTTAAAGTCATGTTGCCTCAGCTTTG
30269810 AGCTTTGAGGAGCCACATTTTTAAAGTCATGTTGCCTCAGCTTTG
1 AGCTTTGAGGAGCCACATTTTTAAAGTCATGTTGCCTCAGCTTTG
30269855 AG
1 AG
30269857 GAGTCTCATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (45 bp):
AGCTTTGAGGAGCCACATTTTTAAAGTCATGTTGCCTCAGCTTTG
Found at i:30269882 original size:83 final size:77
Alignment explanation
Indices: 30269743--30270128 Score: 283
Period size: 77 Copynumber: 4.9 Consensus size: 77
30269733 TAGTTTCAAG
* * * *
30269743 ATTTTTAAAGTCATGTTGTCTCAGCTTTGAGGAGCCACATTTTTAAAGTCAT-GTTGCCTTAGCT
1 ATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGTCTCATTTTTAAAGT-TTCGTTGCCTT--C-
30269807 TTGAGCTTTGAGGAGCCAC
62 ---AGCTTTGAGGAGCCAC
*
30269826 ATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGTCTCATTTTTAAAGTTTCGTTGCC-TCAGTT
1 ATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGTCTCATTTTTAAAGTTTCGTTGCCTTCAGCT
* *
30269890 TTGAGGAGTCTC
66 TTGAGGAGCCAC
** * * *
30269902 ATTTTTTAAAGTTTTGTTGCCTCAGTTTTGAGGAGTTTCATTTTTAAAGTTTCGTAGCC-TCA-C
1 A-TTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGTCTCATTTTTAAAGTTTCGTTGCCTTCAGC
* **
30269965 TTTTGAAGAG-TTC
65 -TTTGAGGAGCCAC
* ** * * * *
30269978 ATTTTTATAGTTTTGTTGCCTCAGCTTTGAGGAATCTCATTTTAAAAAAAAAAGTCTCATTG-C-
1 ATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGTCTCATTTT------TAAAGTTTCGTTGCCT
** **
30270041 TCAATTTTGAGGAAG-TTC
60 TCAGCTTTGAGG-AGCCAC
* *
30270059 ATTTTTAAAGT-TTCGTTGCCTCAGCTTTGAGGAGTCT--TTTTTAAAGTTTCGTTGCC-TCAGT
1 ATTTTTAAAGTCAT-GTTGCCTCAGCTTTGAGGAGTCTCATTTTTAAAGTTTCGTTGCCTTCAGC
30270120 TTTGAGGAG
65 TTTGAGGAG
30270129 TTCATTTTTA
Statistics
Matches: 259, Mismatches: 31, Indels: 36
0.79 0.10 0.11
Matches are distributed among these distances:
73 12 0.05
74 12 0.05
75 38 0.15
76 17 0.07
77 63 0.24
79 4 0.02
80 13 0.05
81 46 0.18
82 2 0.01
83 52 0.20
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (77 bp):
ATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGTCTCATTTTTAAAGTTTCGTTGCCTTCAGCT
TTGAGGAGCCAC
Found at i:30269921 original size:39 final size:37
Alignment explanation
Indices: 30269825--30270151 Score: 354
Period size: 38 Copynumber: 8.5 Consensus size: 37
30269815 TGAGGAGCCA
* *
30269825 CATTTTTAAAGTCAT-GTTGCCTCAGCTTTGAGGAGTCT
1 CATTTTTAAAGT-TTCGTTGCCTCAGTTTTGAGGAGT-T
30269863 CATTTTTAAAGTTTCGTTGCCTCAGTTTTGAGGAGTCT
1 CATTTTTAAAGTTTCGTTGCCTCAGTTTTGAGGAGT-T
*
30269901 CATTTTTTAAAGTTTTGTTGCCTCAGTTTTGAGGAGTTT
1 CA-TTTTTAAAGTTTCGTTGCCTCAGTTTTGAGGAG-TT
* * *
30269940 CATTTTTAAAGTTTCGTAGCCTCACTTTTGAAGAGTT
1 CATTTTTAAAGTTTCGTTGCCTCAGTTTTGAGGAGTT
* * * *
30269977 CATTTTTATAGTTTTGTTGCCTCAGCTTTGAGGAATCT
1 CATTTTTAAAGTTTCGTTGCCTCAGTTTTGAGGAGT-T
* * * *
30270015 CATTTTAAAAAAAAAAGTCTCATTG-CTCAATTTTGAGGAAGTT
1 CATTTT------TAAAGTTTCGTTGCCTCAGTTTTGAGG-AGTT
*
30270058 CATTTTTAAAGTTTCGTTGCCTCAGCTTTGAGGAG-T
1 CATTTTTAAAGTTTCGTTGCCTCAGTTTTGAGGAGTT
*
30270094 CTTTTTTAAAGTTTCGTTGCCTCAGTTTTGAGGAGTT
1 CATTTTTAAAGTTTCGTTGCCTCAGTTTTGAGGAGTT
30270131 CATTTTTAAAAAGTTTCGTTG
1 CATTTTT--AAAGTTTCGTTG
30270152 NTCTTTTTTA
Statistics
Matches: 244, Mismatches: 30, Indels: 29
0.81 0.10 0.10
Matches are distributed among these distances:
36 34 0.14
37 51 0.21
38 83 0.34
39 47 0.19
40 1 0.00
43 18 0.07
44 10 0.04
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (37 bp):
CATTTTTAAAGTTTCGTTGCCTCAGTTTTGAGGAGTT
Found at i:30269943 original size:77 final size:75
Alignment explanation
Indices: 30269825--30270140 Score: 404
Period size: 77 Copynumber: 4.1 Consensus size: 75
30269815 TGAGGAGCCA
**
30269825 CATTTTTAAAGTCATGTTGCCTCAGCTTTGAGGAGTCTCATTTTTAAAGTTTCGTTGCCTCAGTT
1 CATTTTTAAAGTTTTGTTGCCTCAGCTTTGAGGAGTCTCATTTTTAAAGTTTCGTTGCCTCAGTT
30269890 TTGAGGAGTCT
66 TTGAGGAGT-T
* * * *
30269901 CATTTTTTAAAGTTTTGTTGCCTCAGTTTTGAGGAGTTTCATTTTTAAAGTTTCGTAGCCTCACT
1 CA-TTTTTAAAGTTTTGTTGCCTCAGCTTTGAGGAGTCTCATTTTTAAAGTTTCGTTGCCTCAGT
*
30269966 TTTGAAGAGTT
65 TTTGAGGAGTT
* * * * *
30269977 CATTTTTATAGTTTTGTTGCCTCAGCTTTGAGGAATCTCATTTTAAAAAAAAAAGTCTCATTG-C
1 CATTTTTAAAGTTTTGTTGCCTCAGCTTTGAGGAGTCTCATTTT------TAAAGTTTCGTTGCC
*
30270041 TCAATTTTGAGGAAGTT
60 TCAGTTTTGAGG-AGTT
*
30270058 CATTTTTAAAGTTTCGTTGCCTCAGCTTTGAGGAGTCT--TTTTTAAAGTTTCGTTGCCTCAGTT
1 CATTTTTAAAGTTTTGTTGCCTCAGCTTTGAGGAGTCTCATTTTTAAAGTTTCGTTGCCTCAGTT
30270121 TTGAGGAGTT
66 TTGAGGAGTT
30270131 CATTTTTAAA
1 CATTTTTAAA
30270141 AAGTTTCGTT
Statistics
Matches: 207, Mismatches: 24, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
73 24 0.12
74 12 0.06
75 38 0.18
76 5 0.02
77 65 0.31
79 4 0.02
80 11 0.05
81 48 0.23
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.44
Consensus pattern (75 bp):
CATTTTTAAAGTTTTGTTGCCTCAGCTTTGAGGAGTCTCATTTTTAAAGTTTCGTTGCCTCAGTT
TTGAGGAGTT
Done.