Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 106 of 120
Found at i:31017067 original size:9 final size:9
Alignment explanation
Indices: 31017050--31017093 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
31017040 TTAAAACATA
31017050 ATAATTTTT
1 ATAATTTTT
*
31017059 ATAACTTTT
1 ATAATTTTT
31017068 ATTAATTTTT
1 A-TAATTTTT
31017078 AT--TTTTT
1 ATAATTTTT
31017085 ATAATTTTT
1 ATAATTTTT
31017094 TGTCACATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
7 7 0.23
9 15 0.50
10 8 0.27
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (9 bp):
ATAATTTTT
Found at i:31029259 original size:16 final size:15
Alignment explanation
Indices: 31029228--31029269 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
31029218 ACAAAATCAA
31029228 ATAAAAATTAATTAT
1 ATAAAAATTAATTAT
*
31029243 ATAAAAGTTACATTAT
1 ATAAAAATTA-ATTAT
31029259 ATAAAAATTAA
1 ATAAAAATTAA
31029270 ATGAGTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
ATAAAAATTAATTAT
Found at i:31029349 original size:38 final size:39
Alignment explanation
Indices: 31029305--31029388 Score: 134
Period size: 38 Copynumber: 2.2 Consensus size: 39
31029295 AAAAAAATCA
31029305 GTTATAATTAAACTTTTAATAAAATGATTTTGAACTTTT
1 GTTATAATTAAACTTTTAATAAAATGATTTTGAACTTTT
* * *
31029344 -TTATAATTAAACTTTTAATGAAATGATTTTTAATTTTT
1 GTTATAATTAAACTTTTAATAAAATGATTTTGAACTTTT
31029382 GTTATAA
1 GTTATAA
31029389 ACTTTATATG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 35 0.85
39 6 0.15
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (39 bp):
GTTATAATTAAACTTTTAATAAAATGATTTTGAACTTTT
Found at i:31029537 original size:22 final size:22
Alignment explanation
Indices: 31029512--31029774 Score: 185
Period size: 22 Copynumber: 11.3 Consensus size: 22
31029502 AATTAATTAT
31029512 AAAATAATTACAATATTCATAC
1 AAAATAATTACAATATTCATAC
31029534 AAAA-AATTACAATATTACAATATATC
1 AAAATAATTACAATATT-C---ATA-C
*** *
31029560 CCCA-AATTACAATATTAATAC
1 AAAATAATTACAATATTCATAC
* *
31029581 AAAAAAATTGCAATATTCATAC
1 AAAATAATTACAATATTCATAC
31029603 AAAATTATAATATTACAATATTCATAC
1 -AAA--AT-A-ATTACAATATTCATAC
* * *
31029630 AAAACAAATATAATATTCATAC
1 AAAATAATTACAATATTCATAC
31029652 AAAATTACTAAATTACAATATTCATAC
1 -AAA--A-T-AATTACAATATTCATAC
* *
31029679 AAAAAAATTGCAATATTCATAC
1 AAAATAATTACAATATTCATAC
31029701 AAAACTATAATATTACAATATTCATAC
1 -AAA--AT-A-ATTACAATATTCATAC
* * *
31029728 AAAAAAATTATAATATTTATAC
1 AAAATAATTACAATATTCATAC
31029750 --AA-AATTACAATATTCATAC
1 AAAATAATTACAATATTCATAC
31029769 AAAATA
1 AAAATA
31029775 CTAATCCAAA
Statistics
Matches: 191, Mismatches: 26, Indels: 48
0.72 0.10 0.18
Matches are distributed among these distances:
19 15 0.08
20 2 0.01
21 16 0.08
22 68 0.36
23 11 0.06
24 3 0.02
25 6 0.03
26 25 0.13
27 45 0.24
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (22 bp):
AAAATAATTACAATATTCATAC
Found at i:31029622 original size:49 final size:49
Alignment explanation
Indices: 31029565--31029763 Score: 296
Period size: 49 Copynumber: 4.1 Consensus size: 49
31029555 ATATCCCCAA
*
31029565 ATTACAATATTAATACAAAAAAATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAATTATAAT
31029614 ATTACAATATTCATACAAAACAAATAT--AATATTCATACAAAATTACTAA-
1 ATTACAATATTCATACAAAA-AAAT-TGCAATATTCATACAAAATTA-TAAT
*
31029663 ATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAACTATAAT
1 ATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAATTATAAT
** * *
31029712 ATTACAATATTCATACAAAAAAATTATAATATTTATACAAAATTACAAT
1 ATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAATTATAAT
31029761 ATT
1 ATT
31029764 CATACAAAAT
Statistics
Matches: 137, Mismatches: 7, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
47 1 0.01
48 7 0.05
49 121 0.88
50 7 0.05
51 1 0.01
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (49 bp):
ATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAATTATAAT
Found at i:31029681 original size:98 final size:98
Alignment explanation
Indices: 31029518--31029757 Score: 355
Period size: 98 Copynumber: 2.5 Consensus size: 98
31029508 TTATAAAATA
* ** *
31029518 ATTACAATATTCATAC-AAAAAATTACAATA-T--TACAATATATCCCCAAATTACAATATTAAT
1 ATTACAATATTCATACAAAAAAATTATAATATTCATACAA-A-ATTACTAAATTACAATATTAAT
*
31029579 ACAAAAAAATTGCAATATTCATACAAAATTATAAT
64 ACAAAAAAATTGCAATATTCATACAAAACTATAAT
*
31029614 ATTACAATATTCATACAAAACAAA-TATAATATTCATACAAAATTACTAAATTACAATATTCATA
1 ATTACAATATTCATACAAAA-AAATTATAATATTCATACAAAATTACTAAATTACAATATTAATA
31029678 CAAAAAAATTGCAATATTCATACAAAACTATAAT
65 CAAAAAAATTGCAATATTCATACAAAACTATAAT
*
31029712 ATTACAATATTCATACAAAAAAATTATAATATTTATACAAAATTAC
1 ATTACAATATTCATACAAAAAAATTATAATATTCATACAAAATTAC
31029758 AATATTCATA
Statistics
Matches: 131, Mismatches: 7, Indels: 10
0.89 0.05 0.07
Matches are distributed among these distances:
96 16 0.12
97 12 0.09
98 97 0.74
99 1 0.01
100 5 0.04
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.32
Consensus pattern (98 bp):
ATTACAATATTCATACAAAAAAATTATAATATTCATACAAAATTACTAAATTACAATATTAATAC
AAAAAAATTGCAATATTCATACAAAACTATAAT
Found at i:31029744 original size:30 final size:27
Alignment explanation
Indices: 31029591--31029731 Score: 169
Period size: 27 Copynumber: 5.6 Consensus size: 27
31029581 AAAAAAATTG
*
31029591 CAATATTCATACAAAATTATAATATTA
1 CAATATTCATACAAAACTATAATATTA
31029618 CAATATTCATACAAAAC-A-AATA-T-
1 CAATATTCATACAAAACTATAATATTA
*
31029641 -AATATTCATACAAAATTACTAA-ATTA
1 CAATATTCATACAAAACTA-TAATATTA
*
31029667 CAATATTCATAC-AAA--A-AA-ATTG
1 CAATATTCATACAAAACTATAATATTA
31029689 CAATATTCATACAAAACTATAATATTA
1 CAATATTCATACAAAACTATAATATTA
31029716 CAATATTCATACAAAA
1 CAATATTCATACAAAA
31029732 AAATTATAAT
Statistics
Matches: 99, Mismatches: 4, Indels: 22
0.79 0.03 0.18
Matches are distributed among these distances:
22 32 0.32
23 4 0.04
24 3 0.03
25 8 0.08
26 6 0.06
27 46 0.46
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (27 bp):
CAATATTCATACAAAACTATAATATTA
Found at i:31029755 original size:19 final size:19
Alignment explanation
Indices: 31029712--31029895 Score: 124
Period size: 19 Copynumber: 9.2 Consensus size: 19
31029702 AAACTATAAT
31029712 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCATAC---AAA
* *
31029734 ATTATAATATTTATACAAA
1 ATTACAATATTCATACAAA
31029753 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
* * *
31029772 A-TACTA-ATCCAAAACTATAA
1 ATTACAATATTC-ATAC-A-AA
*
31029792 A-TACAAATTTAATT-ATAAAATA
1 ATTAC-AA--T-ATTCATACAA-A
*
31029814 ATTACAATATTCATACAAC
1 ATTACAATATTCATACAAA
*
31029833 ATTACAATATTCATAAAAA
1 ATTACAATATTCATACAAA
*
31029852 ATTATAATATTCATACAAAAA
1 ATTACAATATTCATAC--AAA
*
31029873 AGTTAAAATATTCATACAAA
1 A-TTACAATATTCATACAAA
31029893 ATT
1 ATT
31029896 CTAATCTAAA
Statistics
Matches: 130, Mismatches: 18, Indels: 31
0.73 0.10 0.17
Matches are distributed among these distances:
17 3 0.02
18 7 0.05
19 58 0.45
20 16 0.12
21 6 0.05
22 33 0.25
23 5 0.04
25 2 0.02
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.33
Consensus pattern (19 bp):
ATTACAATATTCATACAAA
Found at i:31029869 original size:49 final size:47
Alignment explanation
Indices: 31029518--31029900 Score: 240
Period size: 49 Copynumber: 8.0 Consensus size: 47
31029508 TTATAAAATA
*
31029518 ATTACAATATTCATACAAAAAATTACAATA-T--TACAATA-TATCCCCAA-
1 ATTACAATATTCATAC-AAAAATTACAATATTCATACAAAATTAT----AAT
* *
31029565 ATTACAATATTAATACAAAAAAATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATAC--AAAAATTACAATATTCATACAAAATTATAAT
* *
31029614 ATTACAATATTCATACAAAACAAATATAATATTCATACAAAATTACTAA-
1 ATTACAATATTCATAC-AAA-AATTACAATATTCATACAAAATTA-TAAT
* *
31029663 ATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAACTATAAT
1 ATTACAATATTCATAC--AAAAATTACAATATTCATACAAAATTATAAT
* * *
31029712 ATTACAATATTCATACAAAAAAATTATAATATTTATACAAAATTACAAT
1 ATTACAATATTCATAC--AAAAATTACAATATTCATACAAAATTATAAT
* * * * * ***
31029761 ATTCATACAAAATACTAATCCAAAACTATA-AATA--CAAATTTAATTATAAAAT
1 A-T--TAC--AATATTCATACAAAAAT-TACAATATTCATACAAAATTAT--AAT
* *
31029813 AATTACAATATTCATAC-AACATTACAATATTCATAAAAAATTATAAT
1 -ATTACAATATTCATACAAAAATTACAATATTCATACAAAATTATAAT
* * *
31029860 ATT-C-ATA--CA-A-AAAAGTTAAAATATTCATACAAAATTCTAAT
1 ATTACAATATTCATACAAAAATTACAATATTCATACAAAATTATAAT
31029901 CTAAACTTTA
Statistics
Matches: 273, Mismatches: 40, Indels: 52
0.75 0.11 0.14
Matches are distributed among these distances:
41 26 0.10
42 2 0.01
44 3 0.01
45 1 0.00
46 5 0.02
47 25 0.09
48 30 0.11
49 127 0.47
50 18 0.07
51 6 0.02
52 19 0.07
53 3 0.01
54 8 0.03
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (47 bp):
ATTACAATATTCATACAAAAATTACAATATTCATACAAAATTATAAT
Found at i:31029883 original size:41 final size:38
Alignment explanation
Indices: 31029729--31029900 Score: 111
Period size: 41 Copynumber: 4.3 Consensus size: 38
31029719 TATTCATACA
* *
31029729 AAAAAATTATAATATTTATACAAAATTACAATATTCAT
1 AAAAAATTATAATATTCATACAAAATTAAAATATTCAT
* * *
31029767 ACAAAA-TACT-A-ATCCAAAACTATAAA-TACAAATTTAATT-AT
1 AAAAAATTA-TAATATTC-ATAC-A-AAATTA-AAA--T-ATTCAT
* * *
31029808 AAAATAATTACAATATTCATACAACATTACAATATTCAT
1 AAAA-AATTATAATATTCATACAAAATTAAAATATTCAT
31029847 AAAAAATTATAATATTCATACAAAAAAGTTAAAATATTCAT
1 AAAAAATTATAATATTCATAC--AAAA-TTAAAATATTCAT
* *
31029888 ACAAAATTCTAAT
1 AAAAAATTATAAT
31029901 CTAAACTTTA
Statistics
Matches: 101, Mismatches: 16, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
36 2 0.02
37 6 0.06
38 28 0.28
39 12 0.12
40 3 0.03
41 33 0.33
42 8 0.08
43 6 0.06
44 3 0.03
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.33
Consensus pattern (38 bp):
AAAAAATTATAATATTCATACAAAATTAAAATATTCAT
Found at i:31030697 original size:16 final size:16
Alignment explanation
Indices: 31030673--31030703 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31030663 ATTAATATTT
31030673 TTATAATATTTTTATC
1 TTATAATATTTTTATC
*
31030689 TTATCATATTTTTAT
1 TTATAATATTTTTAT
31030704 ATAATCTTTC
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:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATAATATTTTTATC
Found at i:31031510 original size:43 final size:44
Alignment explanation
Indices: 31031462--31031547 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
31031452 ATAGAAATGC
*
31031462 CATCTTAATTTT-CATTCAATCAAATTTTGGCAGTACAGTTTGG
1 CATCTTAATTTTGCATTCAATCAAATTTTGGCAGGACAGTTTGG
*
31031505 CATCTTAATTTTGCATTCAATCAAATTTTGGCAGGGCAGTTTG
1 CATCTTAATTTTGCATTCAATCAAATTTTGGCAGGACAGTTTG
31031548 ACATGGCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 12 0.30
44 28 0.70
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (44 bp):
CATCTTAATTTTGCATTCAATCAAATTTTGGCAGGACAGTTTGG
Found at i:31033843 original size:20 final size:20
Alignment explanation
Indices: 31033818--31033858 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
31033808 TCAATCAAAT
31033818 TTTGGCAAGGTAGTTTGGCA
1 TTTGGCAAGGTAGTTTGGCA
*
31033838 TTTGGCAGGGTAGTTTGGCA
1 TTTGGCAAGGTAGTTTGGCA
31033858 T
1 T
31033859 GACAATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.10, G:0.37, T:0.37
Consensus pattern (20 bp):
TTTGGCAAGGTAGTTTGGCA
Found at i:31043646 original size:186 final size:186
Alignment explanation
Indices: 31043327--31043707 Score: 717
Period size: 186 Copynumber: 2.0 Consensus size: 186
31043317 ATTTCTGTTC
*
31043327 TCATTTTGGATTTCTCTTCCTCTTACAGTATCAACCCCTCAAATGAATAAGTACATACTACATTT
1 TCATCTTGGATTTCTCTTCCTCTTACAGTATCAACCCCTCAAATGAATAAGTACATACTACATTT
31043392 TCACTTAGGTGAACCCACATTGATTGTTTCTCTGTATCTGATGGTTGTGTGTTTTTACCTATTAT
66 TCACTTAGGTGAACCCACATTGATTGTTTCTCTGTATCTGATGGTTGTGTGTTTTTACCTATTAT
*
31043457 TTCCTGCTTTCGGATCCAAAGCTGCCAGCCTGAACTTCCCTTTGTTTGCATCTAGA
131 TTCCTGCTTTCGGATCCAAAGCTACCAGCCTGAACTTCCCTTTGTTTGCATCTAGA
* *
31043513 TCATCTTGGATTTCTCTTCCTCTTACCGTATCAACCCCTCAAATGAATAAGTACATGCTACATTT
1 TCATCTTGGATTTCTCTTCCTCTTACAGTATCAACCCCTCAAATGAATAAGTACATACTACATTT
*
31043578 TCACTTAGGTGAACCCACATTGATTGTTTCTCTGTATCTGATGGTTGTGTGTTTTTAGCTATTAT
66 TCACTTAGGTGAACCCACATTGATTGTTTCTCTGTATCTGATGGTTGTGTGTTTTTACCTATTAT
31043643 TTCCTGCTTTCGGATCCAAAGCTACCAGCCTGAACTTCCCTTTGTTTGCATCTAGA
131 TTCCTGCTTTCGGATCCAAAGCTACCAGCCTGAACTTCCCTTTGTTTGCATCTAGA
31043699 TCATCTTGG
1 TCATCTTGG
31043708 CCTTGCTTCA
Statistics
Matches: 190, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
186 190 1.00
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.40
Consensus pattern (186 bp):
TCATCTTGGATTTCTCTTCCTCTTACAGTATCAACCCCTCAAATGAATAAGTACATACTACATTT
TCACTTAGGTGAACCCACATTGATTGTTTCTCTGTATCTGATGGTTGTGTGTTTTTACCTATTAT
TTCCTGCTTTCGGATCCAAAGCTACCAGCCTGAACTTCCCTTTGTTTGCATCTAGA
Found at i:31047183 original size:26 final size:28
Alignment explanation
Indices: 31047145--31047200 Score: 80
Period size: 26 Copynumber: 2.0 Consensus size: 28
31047135 ACATAAGGAC
31047145 TGGATCAAATTAGT-CC-TACTATTAAA
1 TGGATCAAATTAGTCCCGTACTATTAAA
*
31047171 TGGATCAATTTAGTCCCTGTACTATTAAA
1 TGGATCAAATTAGTCCC-GTACTATTAAA
31047200 T
1 T
31047201 TCAATGGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 13 0.50
27 2 0.08
29 11 0.42
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (28 bp):
TGGATCAAATTAGTCCCGTACTATTAAA
Found at i:31052622 original size:26 final size:26
Alignment explanation
Indices: 31052586--31052637 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
31052576 TAAATTGTGA
31052586 ATTAATCCTTTTAATTTTATTTTCTT
1 ATTAATCCTTTTAATTTTATTTTCTT
31052612 ATTAATCCTTTTAATTTTATTTTCTT
1 ATTAATCCTTTTAATTTTATTTTCTT
31052638 TACTTAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (26 bp):
ATTAATCCTTTTAATTTTATTTTCTT
Found at i:31061102 original size:31 final size:31
Alignment explanation
Indices: 31061067--31061139 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
31061057 AAAACTTAAC
31061067 AGTTTAGTGACTTAAATAAAAACTTTT-AAAT
1 AGTTTAGTGACTTAAATAAAAA-TTTTCAAAT
* *
31061098 AGTTTAGTGA-TTTAATGAAAATTTTCAAAT
1 AGTTTAGTGACTTAAATAAAAATTTTCAAAT
* *
31061128 AATTTAATGACT
1 AGTTTAGTGACT
31061140 ATTTTGTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 4 0.11
30 21 0.58
31 11 0.31
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.41
Consensus pattern (31 bp):
AGTTTAGTGACTTAAATAAAAATTTTCAAAT
Found at i:31065410 original size:13 final size:13
Alignment explanation
Indices: 31065392--31065418 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31065382 AAGTTAGACT
31065392 AGGAAAAGATAAC
1 AGGAAAAGATAAC
31065405 AGGAAAAGATAAC
1 AGGAAAAGATAAC
31065418 A
1 A
31065419 AAGTTTAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.22, T:0.07
Consensus pattern (13 bp):
AGGAAAAGATAAC
Found at i:31067283 original size:23 final size:23
Alignment explanation
Indices: 31067255--31067301 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
31067245 AGTGCGTTGA
31067255 AACGCATTATCCTCCTATTTATG
1 AACGCATTATCCTCCTATTTATG
31067278 AACGCATTATCCTCCTATTTATG
1 AACGCATTATCCTCCTATTTATG
31067301 A
1 A
31067302 GTTGGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.38
Consensus pattern (23 bp):
AACGCATTATCCTCCTATTTATG
Found at i:31072303 original size:22 final size:25
Alignment explanation
Indices: 31072272--31072338 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
31072262 CGGCCTGGAT
31072272 TATATA-TTAAATATATATATTTT-
1 TATATATTTAAATATATATATTTTA
*
31072295 TAT-T-TTTAATCAAATATATATTTTA
1 TATATATTTAA--ATATATATATTTTA
31072320 TATATATTT-AATATATATA
1 TATATATTTAAATATATATA
31072339 AAATATATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
22 5 0.14
23 3 0.08
24 20 0.56
25 3 0.08
26 2 0.06
27 3 0.08
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (25 bp):
TATATATTTAAATATATATATTTTA
Found at i:31072324 original size:11 final size:11
Alignment explanation
Indices: 31072307--31072337 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
31072297 TTTTTAATCA
31072307 AATATATATTT
1 AATATATATTT
*
31072318 TATATATATTT
1 AATATATATTT
31072329 AATATATAT
1 AATATATAT
31072338 AAAATATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
AATATATATTT
Found at i:31073157 original size:22 final size:22
Alignment explanation
Indices: 31073079--31073144 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
31073069 TAAATAAAAA
* **
31073079 AGCTTAGTACGTGAAACATGAG
1 AGCTTAGTACGTTAGCCATGAG
31073101 AGCTTAGTACGTTAGCCATGAG
1 AGCTTAGTACGTTAGCCATGAG
31073123 AGCTTAGTACGTTAGCCATGAG
1 AGCTTAGTACGTTAGCCATGAG
31073145 GGTTTAGTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (22 bp):
AGCTTAGTACGTTAGCCATGAG
Found at i:31073597 original size:5 final size:5
Alignment explanation
Indices: 31073554--31073580 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
31073544 GCTGATTGGT
31073554 AGAAA AGAAA AGAAA AGAAA AGAAA AG
1 AGAAA AGAAA AGAAA AGAAA AGAAA AG
31073581 CGGGAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:31077957 original size:13 final size:12
Alignment explanation
Indices: 31077923--31077962 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 12
31077913 ATTTTATTTT
31077923 TATT-TTTAAAA
1 TATTATTTAAAA
31077934 -A-TATTTAAAA
1 TATTATTTAAAA
31077944 TATTATTATAAAA
1 TATTATT-TAAAA
31077957 TATTAT
1 TATTAT
31077963 ATTTTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 1 0.04
10 8 0.32
11 1 0.04
12 4 0.16
13 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATTATTTAAAA
Found at i:31080452 original size:2 final size:2
Alignment explanation
Indices: 31080445--31080485 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
31080435 TAGTTGTTGG
31080445 TA TA TA TA TA TA 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 TA TA T
31080486 TGCAAAGTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31081967 original size:2 final size:2
Alignment explanation
Indices: 31081960--31081995 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
31081950 CTTAGAGAAT
31081960 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
31081996 AAAGTTGTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31085046 original size:21 final size:22
Alignment explanation
Indices: 31085015--31085055 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
31085005 GCTTGGTTGT
31085015 TTAAGTGTTTAATGATAGATTA
1 TTAAGTGTTTAATGATAGATTA
*
31085037 TTAAG-GTTTAATGTTAGAT
1 TTAAGTGTTTAATGATAGAT
31085056 ATACAAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (22 bp):
TTAAGTGTTTAATGATAGATTA
Found at i:31090888 original size:25 final size:25
Alignment explanation
Indices: 31090860--31090937 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 25
31090850 ACCTTAGCAC
* *
31090860 GCTCTCTGATTATTAACACGTTAGT
1 GCTCTCCGATTATTAACACATTAGT
*
31090885 GCTCTCCGATTATTAGCACATTAGT
1 GCTCTCCGATTATTAACACATTAGT
* * *
31090910 GCCCTCCG--T-TTAGCACATTTGT
1 GCTCTCCGATTATTAACACATTAGT
31090932 GCTCTC
1 GCTCTC
31090938 TGTATATTAC
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
22 17 0.36
23 1 0.02
25 29 0.62
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (25 bp):
GCTCTCCGATTATTAACACATTAGT
Found at i:31093512 original size:18 final size:18
Alignment explanation
Indices: 31093489--31093523 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31093479 TCGAAACTTC
31093489 ATTTTAAT-TTTTATACAA
1 ATTTTAATATTTT-TACAA
31093507 ATTTTAATATTTTTACA
1 ATTTTAATATTTTTACA
31093524 CAAAAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTAATATTTTTACAA
Found at i:31093915 original size:31 final size:29
Alignment explanation
Indices: 31093871--31093929 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
31093861 CAAAATTAAA
* *
31093871 AAAAAAACCTAAAATAATTAATAATAAATAG
1 AAAAAAACATAAAAGAA-TAA-AATAAATAG
*
31093902 AAAAAATCATAAAAGAATAAAATAAATA
1 AAAAAAACATAAAAGAATAAAATAAATA
31093930 AATTATAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.32
30 3 0.12
31 14 0.56
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.20
Consensus pattern (29 bp):
AAAAAAACATAAAAGAATAAAATAAATAG
Found at i:31098673 original size:19 final size:21
Alignment explanation
Indices: 31098627--31098673 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
31098617 ACATTCATTC
* *
31098627 AATTTAATCTCTATTTTTTTT
1 AATTTGATCTCTATTTTATTT
31098648 AATTTGATCTCTA-TTTATTT
1 AATTTGATCTCTATTTTATTT
31098668 -ATTTGA
1 AATTTGA
31098674 AGTAAATTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.25
20 6 0.25
21 12 0.50
ACGTcount: A:0.26, C:0.09, G:0.04, T:0.62
Consensus pattern (21 bp):
AATTTGATCTCTATTTTATTT
Found at i:31102879 original size:23 final size:24
Alignment explanation
Indices: 31102844--31102888 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
31102834 AATATGGCAA
31102844 GAAATTAAGTAGAAAAG-AAGTAT
1 GAAATTAAGTAGAAAAGTAAGTAT
31102867 GAAA-TAAGCTAGAAAAGTAAGT
1 GAAATTAAG-TAGAAAAGTAAGT
31102889 GAGCTTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.20
Consensus pattern (24 bp):
GAAATTAAGTAGAAAAGTAAGTAT
Found at i:31106812 original size:29 final size:30
Alignment explanation
Indices: 31106765--31106823 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
31106755 GAATTAGATC
31106765 AAATTAAAATTTTATGTATAAAATTATACA
1 AAATTAAAATTTTATGTATAAAATTATACA
*
31106795 AAATTAAAA-TTTGTGTATAAAATTATACA
1 AAATTAAAATTTTATGTATAAAATTATACA
31106824 TTAAACTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (30 bp):
AAATTAAAATTTTATGTATAAAATTATACA
Found at i:31106845 original size:31 final size:29
Alignment explanation
Indices: 31106779--31106845 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
31106769 TAAAATTTTA
* *
31106779 TGTATAAAATTATACAAAATTAAAATTTG
1 TGTATAAAATTATACAAAACTAAAATTCG
* *
31106808 TGTATAAAATTATACATTAAACTATAGTTCG
1 TGTATAAAATTATACA--AAACTAAAATTCG
31106839 TGTATAA
1 TGTATAA
31106846 TTTAAGATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 16 0.50
31 16 0.50
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (29 bp):
TGTATAAAATTATACAAAACTAAAATTCG
Found at i:31112522 original size:16 final size:17
Alignment explanation
Indices: 31112503--31112535 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
31112493 TTGTTTTCAT
*
31112503 ATTATTTTGG-GTTTGG
1 ATTAGTTTGGAGTTTGG
31112519 ATTAGTTTGGAGTTTGG
1 ATTAGTTTGGAGTTTGG
31112536 CTCATTCGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (17 bp):
ATTAGTTTGGAGTTTGG
Found at i:31113691 original size:18 final size:20
Alignment explanation
Indices: 31113655--31113692 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
31113645 GAAAAAAATA
31113655 TATTTTTATGAATAAGTATAT
1 TATTTTTATGAAT-AGTATAT
31113676 TATTTTTAT-AAT-GTATA
1 TATTTTTATGAATAGTATA
31113693 GCATGGACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
20 3 0.18
21 9 0.53
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (20 bp):
TATTTTTATGAATAGTATAT
Found at i:31125974 original size:25 final size:25
Alignment explanation
Indices: 31125923--31125980 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
31125913 GGTGCTTAGG
*
31125923 TGCTGTCCATTTTTTAGCATATCAA
1 TGCTGTCCATTTTTTAGCAAATCAA
*
31125948 TGCTGTCCATTTTTGTA-CAAATTAA
1 TGCTGTCCATTTTT-TAGCAAATCAA
*
31125973 TGTTGTCC
1 TGCTGTCC
31125981 GAGTGTTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 27 0.93
26 2 0.07
ACGTcount: A:0.22, C:0.19, G:0.14, T:0.45
Consensus pattern (25 bp):
TGCTGTCCATTTTTTAGCAAATCAA
Found at i:31126400 original size:31 final size:32
Alignment explanation
Indices: 31126365--31126451 Score: 131
Period size: 31 Copynumber: 2.8 Consensus size: 32
31126355 GGAGGAAAAC
**
31126365 TTATTGACTTAAATGCTAAATGTTGCTGTTG-
1 TTATTGACTTAAATGCTAAATGTTGCTACTGT
31126396 TTATTGACTTAAATGCTAAATGTTGCTACTGT
1 TTATTGACTTAAATGCTAAATGTTGCTACTGT
* *
31126428 TTATTGACTTAACTGCGAAATGTT
1 TTATTGACTTAAATGCTAAATGTT
31126452 AAGTGTTGCT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 29 0.57
32 22 0.43
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (32 bp):
TTATTGACTTAAATGCTAAATGTTGCTACTGT
Found at i:31128682 original size:18 final size:18
Alignment explanation
Indices: 31128661--31128706 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
31128651 TGAGTTTTTG
31128661 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
31128679 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
*
31128697 AGTTCGAATA
1 AATTCGAATA
31128707 TCAAACTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (18 bp):
AATTCGAATAACTCGAAT
Found at i:31128703 original size:9 final size:9
Alignment explanation
Indices: 31128661--31128706 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
31128651 TGAGTTTTTG
31128661 AATTCGAAT
1 AATTCGAAT
*
31128670 AACTCGAAT
1 AATTCGAAT
31128679 AATTCGAAT
1 AATTCGAAT
*
31128688 AACTCGAAT
1 AATTCGAAT
*
31128697 AGTTCGAAT
1 AATTCGAAT
31128706 A
1 A
31128707 TCAAACTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (9 bp):
AATTCGAAT
Found at i:31135977 original size:27 final size:28
Alignment explanation
Indices: 31135939--31135997 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 28
31135929 TAAAACTAAA
31135939 TTAATCGATCG-AACCGATCTAATTCGG
1 TTAATCGATCGTAACCGATCTAATTCGG
*
31135966 TTAATCGATCGATTAATCGATCTAATTCGG
1 TTAATCGATCG--TAACCGATCTAATTCGG
31135996 TT
1 TT
31135998 GGAGATCGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 11 0.39
30 17 0.61
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (28 bp):
TTAATCGATCGTAACCGATCTAATTCGG
Found at i:31141235 original size:2 final size:2
Alignment explanation
Indices: 31141228--31141258 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
31141218 TTGGCTCCAA
*
31141228 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31141259 GTCTCAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:31143471 original size:19 final size:19
Alignment explanation
Indices: 31143447--31143485 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
31143437 ATAGAAGTGA
*
31143447 ATAATTAATTCATATAAAT
1 ATAATTAATTCATAAAAAT
* *
31143466 ATAATTTATTTATAAAAAT
1 ATAATTAATTCATAAAAAT
31143485 A
1 A
31143486 ATATTTTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATTAATTCATAAAAAT
Found at i:31143998 original size:21 final size:21
Alignment explanation
Indices: 31143929--31143999 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
31143919 TAGTAATTCC
* *
31143929 AAATATCATATAAAA-AATAAA
1 AAATATAAT-TAAAATATTAAA
* *
31143950 AAATTATAATTAAATTATTAAT
1 AAA-TATAATTAAAATATTAAA
*
31143972 ATATATAATTAAAATATTAAA
1 AAATATAATTAAAATATTAAA
31143993 AAATATA
1 AAATATA
31144000 GAAATTATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 29 0.73
22 11 0.28
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATATAATTAAAATATTAAA
Found at i:31144149 original size:3 final size:3
Alignment explanation
Indices: 31144141--31144195 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
31144131 TTCCATTTTT
31144141 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
31144189 ATA ATA A
1 ATA ATA A
31144196 AATCATTCAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:31144871 original size:3 final size:3
Alignment explanation
Indices: 31144863--31144893 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
31144853 ATACTAAACT
31144863 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
31144894 TATTATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:31144898 original size:3 final size:3
Alignment explanation
Indices: 31144892--31144946 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
31144882 AATAATAATA
31144892 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
31144940 ATT ATT A
1 ATT ATT A
31144947 AATTTCGTAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:31151265 original size:16 final size:16
Alignment explanation
Indices: 31151240--31151270 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31151230 AAGAATAATA
31151240 ATTATATAATAATATC
1 ATTATATAATAATATC
*
31151256 ATTATTTAATAATAT
1 ATTATATAATAATAT
31151271 TAAATATATT
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTATATAATAATATC
Found at i:31154346 original size:29 final size:29
Alignment explanation
Indices: 31154314--31154371 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
31154304 TCAAGTTGTT
31154314 TCAAGATTATTAACAAATAACTAGTTTTA
1 TCAAGATTATTAACAAATAACTAGTTTTA
31154343 TCAAGATTATTAACAAATAACTAGTTTTA
1 TCAAGATTATTAACAAATAACTAGTTTTA
31154372 CTTCGATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (29 bp):
TCAAGATTATTAACAAATAACTAGTTTTA
Found at i:31160353 original size:17 final size:17
Alignment explanation
Indices: 31160333--31160365 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
31160323 ATTTTTTAAA
31160333 TGTCTATGTTTTGTCCT
1 TGTCTATGTTTTGTCCT
31160350 TGTCTATGTTTTGTCC
1 TGTCTATGTTTTGTCC
31160366 CCCAACCTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.18, G:0.18, T:0.58
Consensus pattern (17 bp):
TGTCTATGTTTTGTCCT
Found at i:31162645 original size:4 final size:4
Alignment explanation
Indices: 31162636--31162660 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
31162626 TTACTTTATG
31162636 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
31162661 ATGTCCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:31163485 original size:19 final size:17
Alignment explanation
Indices: 31163456--31163494 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
31163446 TATCAAATTT
*
31163456 AAAATTTAAAATTAATAA
1 AAAATTTAAAAATAA-AA
31163474 AAAATCTTAAAAATAAAA
1 AAAAT-TTAAAAATAAAA
31163492 AAA
1 AAA
31163495 TTCTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATTTAAAAATAAAA
Found at i:31164615 original size:2 final size:2
Alignment explanation
Indices: 31164608--31164661 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
31164598 AGCATCAACT
31164608 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
31164650 TA TA TA TA TA TA
1 TA TA TA TA TA TA
31164662 AACATGAGCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31166403 original size:5 final size:5
Alignment explanation
Indices: 31166393--31166420 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
31166383 CGGGCTACTA
31166393 CAACT CAACT CAACT CAACT CAACT CAA
1 CAACT CAACT CAACT CAACT CAACT CAA
31166421 GTCTCATTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.39, G:0.00, T:0.18
Consensus pattern (5 bp):
CAACT
Found at i:31171588 original size:32 final size:32
Alignment explanation
Indices: 31171545--31171656 Score: 172
Period size: 32 Copynumber: 3.5 Consensus size: 32
31171535 TGGGCTAAAC
* *
31171545 CGTGTGGGCCACAC-GAGCAAGGCCAATCTGAG
1 CGTGTGAGCCACACGGA-AAAGGCCAATCTGAG
*
31171577 CGTGTGAGCCACATGGAAAAGGCCAATCTGAG
1 CGTGTGAGCCACACGGAAAAGGCCAATCTGAG
*
31171609 CGTGTGAGCCACATGGAAAAGGCCAATCTGAG
1 CGTGTGAGCCACACGGAAAAGGCCAATCTGAG
31171641 CGTGTGAGCCACACGG
1 CGTGTGAGCCACACGG
31171657 GCATGTTAGC
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 73 0.97
33 2 0.03
ACGTcount: A:0.28, C:0.25, G:0.33, T:0.14
Consensus pattern (32 bp):
CGTGTGAGCCACACGGAAAAGGCCAATCTGAG
Found at i:31171686 original size:18 final size:18
Alignment explanation
Indices: 31171643--31171687 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
31171633 AATCTGAGCG
31171643 TGTGAG-CCACACGGGCA
1 TGTGAGCCCACACGGGCA
*
31171660 TGTTAGCCCACACGGGCA
1 TGTGAGCCCACACGGGCA
*
31171678 TGTGGGCCCA
1 TGTGAGCCCA
31171688 TAATTCTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.20, C:0.31, G:0.33, T:0.16
Consensus pattern (18 bp):
TGTGAGCCCACACGGGCA
Found at i:31175276 original size:42 final size:42
Alignment explanation
Indices: 31175230--31175334 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 42
31175220 GTGCTAAATA
* * * *
31175230 GAAACTCGTAAGGGTTAAA-TAGAAGCTCATAAGAGCTGAACG
1 GAAACCCGTAAGGGTTAAACT-GAAGCTCAAAAGAACTAAACG
* *
31175272 GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAACTAAACT
1 GAAACCCGTAAGGGTTAAACTGAAGCTCAAAAGAACTAAACG
31175314 GAAACCCAG-AAGGGTTAAACT
1 GAAACCC-GTAAGGGTTAAACT
31175335 AAAACTCATA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 53 0.98
43 1 0.02
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (42 bp):
GAAACCCGTAAGGGTTAAACTGAAGCTCAAAAGAACTAAACG
Found at i:31175377 original size:21 final size:21
Alignment explanation
Indices: 31175215--31175379 Score: 102
Period size: 21 Copynumber: 7.9 Consensus size: 21
31175205 CACAGAAGTA
*
31175215 CATAAGTGCTAAA-TAGAAACT
1 CATAAGAGCTAAACT-GAAACT
* * * *
31175236 CGTAAGGGTTAAA-TAGAAGCT
1 CATAAGAGCTAAACT-GAAACT
* * *
31175257 CATAAGAGCTGAACGGAAACC
1 CATAAGAGCTAAACTGAAACT
* * *
31175278 CATAAGGGTTAAACTGAAGCT
1 CATAAGAGCTAAACTGAAACT
* * *
31175299 CAAAAGAACTAAACTGAAACC
1 CATAAGAGCTAAACTGAAACT
* * * *
31175320 CAGAAGGGTTAAACTAAAACT
1 CATAAGAGCTAAACTGAAACT
* * *
31175341 CATATGAG-TTAACTGAAGCT
1 CATAAGAGCTAAACTGAAACT
31175361 CATAAGAGCTAAACTGAAA
1 CATAAGAGCTAAACTGAAA
31175380 GAAAATACGA
Statistics
Matches: 104, Mismatches: 38, Indels: 4
0.71 0.26 0.03
Matches are distributed among these distances:
20 16 0.15
21 88 0.85
ACGTcount: A:0.45, C:0.16, G:0.19, T:0.19
Consensus pattern (21 bp):
CATAAGAGCTAAACTGAAACT
Found at i:31182837 original size:18 final size:18
Alignment explanation
Indices: 31182814--31182848 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
31182804 GCTCTATGTT
31182814 TTTTTTATTTTTCTTTTA
1 TTTTTTATTTTTCTTTTA
*
31182832 TTTTTTCTTTTTCTTTT
1 TTTTTTATTTTTCTTTT
31182849 CGTTTTGAAA
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:0.06, C:0.09, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTTTATTTTTCTTTTA
Found at i:31182854 original size:18 final size:18
Alignment explanation
Indices: 31182815--31182854 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31182805 CTCTATGTTT
*
31182815 TTTTTATTTTTCTTTTAT
1 TTTTTATTTTTCTTTTAG
* *
31182833 TTTTTCTTTTTCTTTTCG
1 TTTTTATTTTTCTTTTAG
31182851 TTTT
1 TTTT
31182855 GAAAGAATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.10, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTTTATTTTTCTTTTAG
Found at i:31183813 original size:2 final size:2
Alignment explanation
Indices: 31183758--31183799 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
31183748 AATTCTTTAC
31183758 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31183800 TATTGGGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31186955 original size:60 final size:60
Alignment explanation
Indices: 31186862--31186982 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 60
31186852 ATAGGTTGGG
31186862 TTGAGTTCGAGTTAGGTTAATGCAAAAATTTTAAGGTCATTTTCTAGGTCCAAGTTTGAC
1 TTGAGTTCGAGTTAGGTTAATGCAAAAATTTTAAGGTCATTTTCTAGGTCCAAGTTTGAC
* *
31186922 TTGAGTTCGAGTTAGGTTAATGCAGAAATTTTAAGGTCATTTTTTAGGTCCAAGTTTGAC
1 TTGAGTTCGAGTTAGGTTAATGCAAAAATTTTAAGGTCATTTTCTAGGTCCAAGTTTGAC
31186982 T
1 T
31186983 CGAAATATGG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (60 bp):
TTGAGTTCGAGTTAGGTTAATGCAAAAATTTTAAGGTCATTTTCTAGGTCCAAGTTTGAC
Found at i:31187327 original size:22 final size:22
Alignment explanation
Indices: 31187272--31187346 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 22
31187262 TCCAAACAAT
* * *
31187272 AACAACAAAATAGTAGCAATAT
1 AACAACAAAATGGTAGCAAAAC
* *
31187294 AATAGCAAAATGGTAGCAAAAC
1 AACAACAAAATGGTAGCAAAAC
* * *
31187316 AACATCAAAATGGCAAC-AAAC
1 AACAACAAAATGGTAGCAAAAC
31187337 AACAACAAAA
1 AACAACAAAA
31187347 CAGCAGTGAA
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
21 13 0.30
22 30 0.70
ACGTcount: A:0.60, C:0.17, G:0.11, T:0.12
Consensus pattern (22 bp):
AACAACAAAATGGTAGCAAAAC
Found at i:31191300 original size:22 final size:22
Alignment explanation
Indices: 31191272--31191333 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
31191262 TACACCACAC
*
31191272 CAGTAGGCACCAAAGTGCTGAG
1 CAGTAGGCACCAAAGTGCTGAA
*
31191294 CAGTAGGCACTAAAGTGCTGAA
1 CAGTAGGCACCAAAGTGCTGAA
* *
31191316 CAATAGGCACCATAGTGC
1 CAGTAGGCACCAAAGTGC
31191334 AAATCAGTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.34, C:0.23, G:0.27, T:0.16
Consensus pattern (22 bp):
CAGTAGGCACCAAAGTGCTGAA
Found at i:31191374 original size:20 final size:22
Alignment explanation
Indices: 31191329--31191374 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
31191319 TAGGCACCAT
*
31191329 AGTGCAAATCAGTAGCCATTGA
1 AGTGCAAATCAGTAGCCATCGA
*
31191351 AGTGCAAA-CAGT-GGCATCGA
1 AGTGCAAATCAGTAGCCATCGA
31191371 AGTG
1 AGTG
31191375 TAATCCTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 4 0.18
22 8 0.36
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (22 bp):
AGTGCAAATCAGTAGCCATCGA
Found at i:31196190 original size:31 final size:29
Alignment explanation
Indices: 31196120--31196193 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 29
31196110 CTCTCGGGTT
* *
31196120 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTACGTTTGAAATGTA
* * *
31196149 ACGTTTTAGTCACTTACGTTAATGTAGTGTA
1 ACATTTTAGTCACTTACGTT--TGAAATGTA
31196180 ACATTTTAGTCACT
1 ACATTTTAGTCACT
31196194 GAGCTGTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 18 0.49
31 19 0.51
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.45
Consensus pattern (29 bp):
ACATTTTAGTCACTTACGTTTGAAATGTA
Found at i:31215614 original size:18 final size:19
Alignment explanation
Indices: 31215591--31215640 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
31215581 TAGAATTTTT
31215591 AAAAATTGTAAAAAAA-TA
1 AAAAATTGTAAAAAAATTA
*
31215609 AAAAATATATAAAAAAATTA
1 AAAAAT-TGTAAAAAAATTA
*
31215629 GAAAA-TGTAAAA
1 AAAAATTGTAAAA
31215641 TATTGTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 12 0.44
19 9 0.33
20 6 0.22
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (19 bp):
AAAAATTGTAAAAAAATTA
Found at i:31216032 original size:22 final size:22
Alignment explanation
Indices: 31215998--31216055 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
31215988 ATAAATCCTT
*
31215998 TCTCTAATATTCTCTCAATTTCC
1 TCTC-AATTTTCTCTCAATTTCC
* *
31216021 TCTCAATTTTCTCTCATTTTGC
1 TCTCAATTTTCTCTCAATTTCC
* *
31216043 TCTGAAATTTCTC
1 TCTCAATTTTCTC
31216056 CCAAATCCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.19, C:0.28, G:0.03, T:0.50
Consensus pattern (22 bp):
TCTCAATTTTCTCTCAATTTCC
Found at i:31217792 original size:30 final size:30
Alignment explanation
Indices: 31217758--31217829 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
31217748 GACAATGCAA
* * *
31217758 GCCCATCAACGAGGCCCAGACATTCACCCG
1 GCCCATCAACAAGGCCCAGACAATCACCAG
* * *
31217788 GCCCATCATCAATGCCCATACAATCACCAG
1 GCCCATCAACAAGGCCCAGACAATCACCAG
*
31217818 GCCCAGCAACAA
1 GCCCATCAACAA
31217830 CACCGACACA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.32, C:0.42, G:0.15, T:0.11
Consensus pattern (30 bp):
GCCCATCAACAAGGCCCAGACAATCACCAG
Found at i:31217929 original size:18 final size:18
Alignment explanation
Indices: 31217906--31217948 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
31217896 TGCCTGGTGC
* *
31217906 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
31217924 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
31217942 GTTTCCT
1 GTATCCT
31217949 TTTTCGAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:31221818 original size:126 final size:126
Alignment explanation
Indices: 31221593--31221872 Score: 481
Period size: 126 Copynumber: 2.2 Consensus size: 126
31221583 ACATGGGAGC
*
31221593 TTTTTTCAGGAGCTACTGTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGTACTTCTACTGA
1 TTTTTTCAGGAGCTACTGTAGCAAAAGCACATCCACGTGGGAGCTTCTTTCAGTACTTCTACTGA
*
31221658 CAAAGCATCCTGCTTAAAGCATTTTTGACACTGTTTGA-TCAGAAACGTCTACTCGAAATTA
66 CAAAGCATCCTGCTTAAAGCATTTTTGACACTGTTT-ACTAAGAAACGTCTACTCGAAATTA
* * * *
31221719 TTTTTTCAGGAGCTACTATAGCAAAAGCACGTCCACGTGGGAGCTTTTTTCAGTACTTCTGCTGA
1 TTTTTTCAGGAGCTACTGTAGCAAAAGCACATCCACGTGGGAGCTTCTTTCAGTACTTCTACTGA
*
31221784 CAAAGCATCCTGCTTAAAGCGTTTTTGACACTGTTTACTAAGAAACGTCTACTCGAAATTA
66 CAAAGCATCCTGCTTAAAGCATTTTTGACACTGTTTACTAAGAAACGTCTACTCGAAATTA
31221845 TTTTTTCAGGAGCTACTGTAGCAAAAGC
1 TTTTTTCAGGAGCTACTGTAGCAAAAGC
31221873 GCGTTCAACC
Statistics
Matches: 145, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
125 1 0.01
126 144 0.99
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (126 bp):
TTTTTTCAGGAGCTACTGTAGCAAAAGCACATCCACGTGGGAGCTTCTTTCAGTACTTCTACTGA
CAAAGCATCCTGCTTAAAGCATTTTTGACACTGTTTACTAAGAAACGTCTACTCGAAATTA
Found at i:31223076 original size:56 final size:56
Alignment explanation
Indices: 31222961--31223089 Score: 136
Period size: 56 Copynumber: 2.3 Consensus size: 56
31222951 AAAAAGATTA
* * *
31222961 TTAATATAAATAATAAATATTTTAATCATATTTTAACATAATTATTATTAAATATAAT
1 TTAATA-AAATAATAAATAATTTAATAAAATTTTAACATAATTATTATT-AATATAAT
* * *
31223019 TTAATAAAA-AATATATAATTTAATAAAATTCTTAATATAATTATTCTT-ATATGAAT
1 TTAATAAAATAATAAATAATTTAATAAAATT-TTAACATAATTATTATTAATAT-AAT
* *
31223075 TTACTAAAATCATAA
1 TTAATAAAATAATAA
31223090 TATATAATAG
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
55 4 0.07
56 28 0.47
57 21 0.36
58 6 0.10
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (56 bp):
TTAATAAAATAATAAATAATTTAATAAAATTTTAACATAATTATTATTAATATAAT
Found at i:31226235 original size:14 final size:14
Alignment explanation
Indices: 31226216--31226243 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31226206 GAGAGAAATC
31226216 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
31226230 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
31226244 GAAATGTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
TGGAGAAAAGAAAA
Found at i:31226243 original size:19 final size:18
Alignment explanation
Indices: 31226219--31226263 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
31226209 AGAAATCTGG
31226219 AGAAAAGAAAATG-GAGAAA
1 AGAAAAGAAAATGTGAG--A
31226238 AGAAAAG-AAATGTGAGA
1 AGAAAAGAAAATGTGAGA
31226255 AGAAAAGAA
1 AGAAAAGAA
31226264 GCGTACTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 6 0.25
19 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (18 bp):
AGAAAAGAAAATGTGAGA
Found at i:31226892 original size:29 final size:30
Alignment explanation
Indices: 31226830--31226894 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
31226820 TTTTCCCATC
*
31226830 TTGGTACCTAAAATTTTATTTGGTCACAAG
1 TTGGTACCTAAAATCTTATTTGGTCACAAG
* *
31226860 -TGGTACCTAAACTACTTATTT-TTC-CAAG
1 TTGGTACCTAAAAT-CTTATTTGGTCACAAG
31226888 TTGGTAC
1 TTGGTAC
31226895 TTCTGTTGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 4 0.13
29 20 0.67
30 6 0.20
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (30 bp):
TTGGTACCTAAAATCTTATTTGGTCACAAG
Found at i:31228137 original size:17 final size:16
Alignment explanation
Indices: 31228112--31228146 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
31228102 TTCCTGATTC
31228112 TTTTATTTGTTTGTTTT
1 TTTTATTTGTTT-TTTT
*
31228129 TTTTTTTTGTTTTTTT
1 TTTTATTTGTTTTTTT
31228145 TT
1 TT
31228147 CACTATTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.03, C:0.00, G:0.09, T:0.89
Consensus pattern (16 bp):
TTTTATTTGTTTTTTT
Found at i:31228143 original size:12 final size:13
Alignment explanation
Indices: 31228121--31228146 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31228111 CTTTTATTTG
31228121 TTTGTTTTTTTTT
1 TTTGTTTTTTTTT
31228134 TTTGTTTTTTTTT
1 TTTGTTTTTTTTT
31228147 CACTATTTAC
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TTTGTTTTTTTTT
Found at i:31228160 original size:15 final size:16
Alignment explanation
Indices: 31228142--31228174 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31228132 TTTTTGTTTT
31228142 TTTTTCA-CTATTTAC
1 TTTTTCAGCTATTTAC
*
31228157 TTTTTCAGTTATTTAC
1 TTTTTCAGCTATTTAC
31228173 TT
1 TT
31228175 ATTTGTCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.18, C:0.15, G:0.03, T:0.64
Consensus pattern (16 bp):
TTTTTCAGCTATTTAC
Found at i:31228237 original size:22 final size:23
Alignment explanation
Indices: 31228202--31228266 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 23
31228192 TTTTTATTGG
*
31228202 TTTTATAATATTTT-TAATGTATA
1 TTTTATAATATTTTATAATAT-TA
*
31228225 TTTTA-AATGTTTTATAATATTA
1 TTTTATAATATTTTATAATATTA
* *
31228247 TTTTTTAAAATTTTA-AATAT
1 TTTTATAATATTTTATAATAT
31228267 AAATTTTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
22 18 0.51
23 17 0.49
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (23 bp):
TTTTATAATATTTTATAATATTA
Found at i:31228273 original size:22 final size:22
Alignment explanation
Indices: 31228202--31228279 Score: 61
Period size: 23 Copynumber: 3.5 Consensus size: 22
31228192 TTTTTATTGG
* *
31228202 TTTTATAATATTTT-TAATGTATA
1 TTTTA-AA-ATTTTATAATATAAA
* **
31228225 TTTTAAATGTTTTATAATATTATT
1 TTTTAAA-ATTTTATAATA-TAAA
31228249 TTTTAAAATTTTA-AATATAAA
1 TTTTAAAATTTTATAATATAAA
31228270 TTTTAAAATT
1 TTTTAAAATT
31228280 ATTTAAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
21 12 0.26
22 11 0.23
23 14 0.30
24 10 0.21
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.58
Consensus pattern (22 bp):
TTTTAAAATTTTATAATATAAA
Found at i:31228326 original size:32 final size:33
Alignment explanation
Indices: 31228253--31228344 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 33
31228243 ATTATTTTTT
* * *
31228253 AAAATTTTAAATATAAATTTTAAAATTATTTAA
1 AAAAATTTAAATATAATTTTTTAAATTATTTAA
31228286 AAAAATTTAAATATAATTTTTTAAA-TA-TTATA
1 AAAAATTTAAATATAATTTTTTAAATTATTTA-A
* *
31228318 AAACATTTAAAATATATTATTTTTAAA
1 AAAAATTT-AAATATAAT-TTTTTAAA
31228345 GATATGACCT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
31 3 0.06
32 10 0.20
33 30 0.59
34 8 0.16
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (33 bp):
AAAAATTTAAATATAATTTTTTAAATTATTTAA
Found at i:31228419 original size:25 final size:25
Alignment explanation
Indices: 31228366--31228413 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
31228356 TCAAATTTAT
31228366 TATTTGTTTTATAATATTTTAAATG
1 TATTTGTTTTATAATATTTTAAATG
31228391 TATTT-TTTTA-AATTACTTTTAAA
1 TATTTGTTTTATAA-TA-TTTTAAA
31228414 GATATTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 2 0.10
24 7 0.33
25 12 0.57
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (25 bp):
TATTTGTTTTATAATATTTTAAATG
Found at i:31228441 original size:23 final size:23
Alignment explanation
Indices: 31228415--31228458 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
31228405 ACTTTTAAAG
* *
31228415 ATATTCAAACTTTTTAAAAAATT
1 ATATTCAAAATTTTAAAAAAATT
*
31228438 ATATTTAAAATTTTAAAAAAA
1 ATATTCAAAATTTTAAAAAAA
31228459 CAATATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATTCAAAATTTTAAAAAAATT
Found at i:31228464 original size:23 final size:23
Alignment explanation
Indices: 31228415--31228466 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
31228405 ACTTTTAAAG
* * * **
31228415 ATATTCAAACTTTTTAAAAAATT
1 ATATTTAAAATTTTAAAAAAACA
31228438 ATATTTAAAATTTTAAAAAAACA
1 ATATTTAAAATTTTAAAAAAACA
31228461 ATATTT
1 ATATTT
31228467 TATTTGGTGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (23 bp):
ATATTTAAAATTTTAAAAAAACA
Found at i:31228575 original size:8 final size:7
Alignment explanation
Indices: 31228546--31228573 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
31228536 TTTTAATATA
31228546 AAAATTT
1 AAAATTT
31228553 AAAATTT
1 AAAATTT
31228560 AAAATTT
1 AAAATTT
31228567 AAAATTT
1 AAAATTT
31228574 TATTTTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AAAATTT
Found at i:31238902 original size:14 final size:14
Alignment explanation
Indices: 31238897--31238938 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
31238887 ATATTATAAG
31238897 ACAAATAATAAAAA
1 ACAAATAATAAAAA
*
31238911 ACAAATAAAAAACAA
1 ACAAATAATAAA-AA
31238926 ACAAATAAATAAA
1 ACAAAT-AATAAA
31238939 CAGAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 8 0.33
16 5 0.21
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.12
Consensus pattern (14 bp):
ACAAATAATAAAAA
Found at i:31238947 original size:13 final size:12
Alignment explanation
Indices: 31238924--31238962 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
31238914 AATAAAAAAC
31238924 AAACAAATAAAT
1 AAACAAATAAAT
31238936 AAACAGAATAAAT
1 AAACA-AATAAAT
*
31238949 AAA-TAATAAAT
1 AAACAAATAAAT
31238960 AAA
1 AAA
31238963 GGACAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 10 0.40
12 5 0.20
13 10 0.40
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (12 bp):
AAACAAATAAAT
Found at i:31238949 original size:4 final size:4
Alignment explanation
Indices: 31238899--31238962 Score: 55
Period size: 4 Copynumber: 16.8 Consensus size: 4
31238889 ATTATAAGAC
* * * *
31238899 AAAT -AAT AAA- AAAC AAAT AAA- AAAC AAAC AAAT AAAT AAAC AGAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT
31238945 AAAT AAAT -AAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAA
31238963 GGACAAATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
3 12 0.24
4 36 0.71
5 3 0.06
ACGTcount: A:0.77, C:0.06, G:0.02, T:0.16
Consensus pattern (4 bp):
AAAT
Found at i:31238950 original size:17 final size:16
Alignment explanation
Indices: 31238897--31238954 Score: 77
Period size: 15 Copynumber: 3.8 Consensus size: 16
31238887 ATATTATAAG
31238897 ACAAAT-AATAAA-AA
1 ACAAATAAATAAACAA
31238911 ACAAATAAA-AAACAA
1 ACAAATAAATAAACAA
31238926 ACAAATAAATAAACAGA
1 ACAAATAAATAAACA-A
*
31238943 ATAAATAAATAA
1 ACAAATAAATAA
31238955 TAAATAAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
14 9 0.23
15 13 0.33
16 5 0.13
17 12 0.31
ACGTcount: A:0.76, C:0.09, G:0.02, T:0.14
Consensus pattern (16 bp):
ACAAATAAATAAACAA
Found at i:31238957 original size:39 final size:39
Alignment explanation
Indices: 31238914--31238993 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 39
31238904 ATAAAAAACA
*
31238914 AATAAA-AAACAAACAAATAAATAAACAGAATAAA-TAAAT
1 AATAAATAAA-AAACAAATAAAAAAACAGAA-AAAGTAAAT
** *
31238953 AATAAATAAAGGACAAATAAAAAAACTGAAAAAGTAAAT
1 AATAAATAAAAAACAAATAAAAAAACAGAAAAAGTAAAT
31238992 AA
1 AA
31238994 GGTAAAACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
38 3 0.09
39 29 0.83
40 3 0.09
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.15
Consensus pattern (39 bp):
AATAAATAAAAAACAAATAAAAAAACAGAAAAAGTAAAT
Found at i:31239008 original size:24 final size:24
Alignment explanation
Indices: 31238981--31239034 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
31238971 AAAAAAACTG
31238981 AAAAAGT-AAATAAGGTA-AAACAAA
1 AAAAAGTGAAA-AAGG-ACAAACAAA
*
31239005 AAAAAATGAAAAAGGACAAACAAA
1 AAAAAGTGAAAAAGGACAAACAAA
31239029 AAAAAG
1 AAAAAG
31239035 AACAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 1 0.04
24 22 0.85
25 3 0.12
ACGTcount: A:0.74, C:0.06, G:0.13, T:0.07
Consensus pattern (24 bp):
AAAAAGTGAAAAAGGACAAACAAA
Found at i:31239045 original size:15 final size:16
Alignment explanation
Indices: 31239013--31239050 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
31239003 AAAAAAAATG
*
31239013 AAAAAGGACAAACAAA
1 AAAAAGAACAAACAAA
*
31239029 AAAAAGAACAAATAAA
1 AAAAAGAACAAACAAA
31239045 AAAAAG
1 AAAAAG
31239051 CAGGGTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.79, C:0.08, G:0.11, T:0.03
Consensus pattern (16 bp):
AAAAAGAACAAACAAA
Found at i:31239757 original size:8 final size:8
Alignment explanation
Indices: 31239746--31239780 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
31239736 TTTAAAGTTT
31239746 TTTTAAAA
1 TTTTAAAA
31239754 TTTTAAATA
1 TTTTAAA-A
*
31239763 TATTAAAA
1 TTTTAAAA
31239771 TTTTAAAA
1 TTTTAAAA
31239779 TT
1 TT
31239781 GATTATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
TTTTAAAA
Found at i:31239770 original size:17 final size:18
Alignment explanation
Indices: 31239747--31239866 Score: 70
Period size: 17 Copynumber: 6.4 Consensus size: 18
31239737 TTAAAGTTTT
31239747 TTTAAAATTTTAAATATA
1 TTTAAAATTTTAAATATA
31239765 -TTAAAATTTTAAAATTGATTATA
1 TTTAAAATTTT--AA---A-TATA
* * *
31239788 TTTAACATTTTTTCAACATA
1 TTTAA-A-ATTTTAAATATA
*
31239808 CTTAAAATTTT-AATATA
1 TTTAAAATTTTAAATATA
*
31239825 TTTAAAATTCTTTAAGT-T-
1 TTTAAAA-T-TTTAAATATA
31239843 TTTAAAATTTTAAATATA
1 TTTAAAATTTTAAATATA
31239861 -TTAAAA
1 TTTAAAA
31239867 AATATTTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 29
0.68 0.08 0.25
Matches are distributed among these distances:
16 6 0.08
17 29 0.37
18 12 0.15
19 7 0.09
20 9 0.11
21 1 0.01
22 1 0.01
23 4 0.05
24 5 0.06
25 1 0.01
26 4 0.05
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (18 bp):
TTTAAAATTTTAAATATA
Found at i:31240019 original size:9 final size:9
Alignment explanation
Indices: 31240005--31240079 Score: 50
Period size: 9 Copynumber: 8.6 Consensus size: 9
31239995 TTAACATTTT
31240005 TTTAATATA
1 TTTAATATA
*
31240014 TTTAAT-TT
1 TTTAATATA
31240022 TTTAAATATA
1 TTT-AATATA
*
31240032 TTAAATATA
1 TTTAATATA
31240041 -TTAA-A-A
1 TTTAATATA
*
31240047 TTTATTATA
1 TTTAATATA
* * *
31240056 CTTAACATTT
1 TTTAATA-TA
31240066 TTTAATATA
1 TTTAATATA
31240075 TTTAA
1 TTTAA
31240080 ATTTTTTTAA
Statistics
Matches: 48, Mismatches: 12, Indels: 12
0.67 0.17 0.17
Matches are distributed among these distances:
6 1 0.02
7 4 0.08
8 8 0.17
9 26 0.54
10 9 0.19
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.55
Consensus pattern (9 bp):
TTTAATATA
Found at i:31240087 original size:19 final size:19
Alignment explanation
Indices: 31239995--31240104 Score: 73
Period size: 19 Copynumber: 5.5 Consensus size: 19
31239985 TTGTTTATGC
31239995 TTAACATTTTTTTAATATAT
1 TTAA-ATTTTTTTAATATAT
*
31240015 TT-AATTTTTTAAATATA-
1 TTAAATTTTTTTAATATAT
* *
31240032 TTAAATATATTAAAATTTATTATAC
1 TTAAAT-T-TT----TTTAATATAT
31240057 TTAACA-TTTTTTAATATAT
1 TTAA-ATTTTTTTAATATAT
* *
31240076 TTAAATTTTTTTAAGTTTTT
1 TTAAATTTTTTTAA-TATAT
31240096 TTAAATTTT
1 TTAAATTTT
31240105 AAATATATTA
Statistics
Matches: 72, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
17 2 0.03
18 17 0.24
19 22 0.31
20 16 0.22
23 2 0.03
24 8 0.11
25 4 0.06
26 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (19 bp):
TTAAATTTTTTTAATATAT
Found at i:31247177 original size:29 final size:30
Alignment explanation
Indices: 31247116--31247181 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
31247106 AAGTACAGCA
*
31247116 ACTAAAAGTGATCAATTCAAAAAGCATAAAG
1 ACTAAAAGTGATCAAAT-AAAAAGCATAAAG
* * *
31247147 ACTAAAATTGATCAAAT-AAAAGTATAGAG
1 ACTAAAAGTGATCAAATAAAAAGCATAAAG
31247176 ACTAAA
1 ACTAAA
31247182 TTTACAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 16 0.52
31 15 0.48
ACGTcount: A:0.56, C:0.11, G:0.12, T:0.21
Consensus pattern (30 bp):
ACTAAAAGTGATCAAATAAAAAGCATAAAG
Found at i:31247871 original size:13 final size:13
Alignment explanation
Indices: 31247853--31247880 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31247843 ATAATATATT
31247853 TATTAATTAAAAA
1 TATTAATTAAAAA
31247866 TATTAATTAAAAA
1 TATTAATTAAAAA
31247879 TA
1 TA
31247881 ATAAAAAAGC
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TATTAATTAAAAA
Found at i:31253041 original size:21 final size:20
Alignment explanation
Indices: 31253003--31253041 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
31252993 CAATATAATA
*
31253003 GCAAAAACAACAGCAAAACG
1 GCAAAAACAACAACAAAACG
*
31253023 GCAACAAACAACAATAAAA
1 GCAA-AAACAACAACAAAA
31253042 AAAAATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.64, C:0.23, G:0.10, T:0.03
Consensus pattern (20 bp):
GCAAAAACAACAACAAAACG
Found at i:31258639 original size:14 final size:14
Alignment explanation
Indices: 31258620--31258648 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
31258610 AATGATGAGA
31258620 TTCAGCCCATTATT
1 TTCAGCCCATTATT
31258634 TTCAGCCCATTATT
1 TTCAGCCCATTATT
31258648 T
1 T
31258649 AAGGGTGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.28, G:0.07, T:0.45
Consensus pattern (14 bp):
TTCAGCCCATTATT
Found at i:31268070 original size:12 final size:13
Alignment explanation
Indices: 31268053--31268081 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
31268043 CCGCTACATC
31268053 AAAAAAT-AATTT
1 AAAAAATAAATTT
31268065 AAAAAATAAATTT
1 AAAAAATAAATTT
31268078 AAAA
1 AAAA
31268082 TTACAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAAATAAATTT
Found at i:31268092 original size:9 final size:9
Alignment explanation
Indices: 31268078--31268108 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
31268068 AAATAAATTT
*
31268078 AAAATTACA
1 AAAATTATA
31268087 AAAATTATA
1 AAAATTATA
31268096 AAAATTATA
1 AAAATTATA
31268105 AAAA
1 AAAA
31268109 AAGAAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (9 bp):
AAAATTATA
Found at i:31269760 original size:5 final size:5
Alignment explanation
Indices: 31269744--31269775 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
31269734 CCACTTTTTT
31269744 GGCCC GGGCCC GGCCC GGCCC GGCCC GGCCC G
1 GGCCC -GGCCC GGCCC GGCCC GGCCC GGCCC G
31269776 AATAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.56, G:0.44, T:0.00
Consensus pattern (5 bp):
GGCCC
Found at i:31269835 original size:37 final size:37
Alignment explanation
Indices: 31269787--31269927 Score: 197
Period size: 37 Copynumber: 3.9 Consensus size: 37
31269777 ATAATAAATA
31269787 TTTTT-ATTTTTTAATTTTAAAATACTTTTAAAATATT
1 TTTTTAATTTTTTAATTTTAAAATA-TTTTAAAATATT
* *
31269824 TTTTTAATTTTTTAATTTTAAAATTTTTTAAAATACT
1 TTTTTAATTTTTTAATTTTAAAATATTTTAAAATATT
31269861 TTTTTAATTTTTTAATTTTAAAATATTTTAAAATACTT
1 TTTTTAATTTTTTAATTTTAAAATATTTTAAAATA-TT
31269899 TTTTT-A-TTTTT-ATTTT--AAT-TTTTAAAATA
1 TTTTTAATTTTTTAATTTTAAAATATTTTAAAATA
31269928 AAGTTTTGGT
Statistics
Matches: 98, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
32 10 0.10
33 3 0.03
35 5 0.05
36 5 0.05
37 51 0.52
38 24 0.24
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (37 bp):
TTTTTAATTTTTTAATTTTAAAATATTTTAAAATATT
Found at i:31269842 original size:7 final size:8
Alignment explanation
Indices: 31269823--31269879 Score: 51
Period size: 8 Copynumber: 6.5 Consensus size: 8
31269813 TTTAAAATAT
31269823 TTTTTTAA
1 TTTTTTAA
31269831 TTTTTTAA
1 TTTTTTAA
**
31269839 TTTTAAAA
1 TTTTTTAA
31269847 TTTTTTAAAATA
1 TTTTTT---A-A
31269859 CTTTTTTAA
1 -TTTTTTAA
31269868 TTTTTTAA
1 TTTTTTAA
31269876 TTTT
1 TTTT
31269880 AAAATATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
8 30 0.75
9 1 0.03
10 1 0.03
11 1 0.03
12 1 0.03
13 6 0.15
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (8 bp):
TTTTTTAA
Found at i:31271164 original size:23 final size:24
Alignment explanation
Indices: 31271138--31271182 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
31271128 TTGGTTTATG
31271138 AAAATATTTTT-TTTTAATTTTAA
1 AAAATATTTTTATTTTAATTTTAA
*
31271161 AAAATATTTTTATTTTTATTTT
1 AAAATATTTTTATTTTAATTTT
31271183 TTAAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
AAAATATTTTTATTTTAATTTTAA
Found at i:31272221 original size:4 final size:4
Alignment explanation
Indices: 31272212--31272236 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
31272202 AAAACTAATA
31272212 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
31272237 ATGTGAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:31278133 original size:108 final size:108
Alignment explanation
Indices: 31277942--31278594 Score: 1072
Period size: 108 Copynumber: 6.0 Consensus size: 108
31277932 ATATAACTAT
* * *
31277942 ATAAATCTCAACTTTTTGTTATTAACTAGCATAACAAAAATGGCGTAAGCCCTAAATCGATCTAA
1 ATAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
*
31278007 ACTCAACACAACCCTATTCCCTATCCCATCGAACCTCTTTGTA
66 ACTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTA
*
31278050 ATAAATCTCAACCTTTTGTTATTAACTATCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
1 ATAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
* *
31278115 ACTCAACACAACCTTATTCCCTATCCCATCGAACCTCTTTGTA
66 ACTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTA
* * *
31278158 ATAAATCTCAACCTTTTGTTATTAACTATCATAACAAAAACGGCGTAAACCCTAAATCGATCTAA
1 ATAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
*
31278223 ACTCAACACAACCCTATTTCCTATCCCATCCAACCTCTTTGTA
66 ACTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTA
* * * *
31278266 ATAAATCCCAACCTTTTGTTATTAACTAGCATAACAAAAATAACATAAACCCTAAATTGATCTAA
1 ATAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
31278331 ACTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTA
66 ACTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTA
* **
31278374 ATAAATCCCAATATTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
1 ATAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
* *
31278439 ACTCAACACAACCTTATTCCCTATCCCATCCAACCTTTTTGTA
66 ACTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTA
* * *
31278482 ATAAATCTCAACCTTTTGTTATTAATTAGCATAACGAAAATGACGTAAACCCTAAATCGATTTAA
1 ATAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
* *
31278547 ACTAAACACAACCCTATTCCCTAACCCATCCAACCTCTTTGTA
66 ACTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTA
31278590 TATAA
1 -ATAA
31278595 CTAAATATTG
Statistics
Matches: 509, Mismatches: 35, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
108 505 0.99
109 4 0.01
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (108 bp):
ATAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
ACTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTA
Found at i:31280093 original size:213 final size:214
Alignment explanation
Indices: 31279566--31280112 Score: 534
Period size: 206 Copynumber: 2.6 Consensus size: 214
31279556 AAAATCAGTT
* **
31279566 TTTTGGACTAAAAATGATAGCTTTCATGGGTCAAAGATCTATGGTGAATTTGAGGTGACTGATGA
1 TTTTGGAC-CAAAATGATAGCTTTCATATGTCAAAGATCTATGGTGAATTTGA-G-G--TGATGA
* * * * * * *
31279631 TCTAATTGGATTTATGGGG-TTGCTCTTTCCTTAATTATTAATTTATACAGTTATTCTCTACTTC
61 TCTAATTGGATTGATGGGGTTTTC-CTTCCCTTAATGATTAATATATACAGTTCTTCTCTACTTA
* * * *
31279695 AGTGTAAAGGGTGTTTTGCTATCTTTCTAGATTGATATCATGTTTGGTTTCATCAACTGCTATAT
125 AATGTAAAGGGTGTTTTGCCATCTTTCTACATTGATATCATGTTTGGTTTCATCAACTGCTAAAT
31279760 GTAATTCAACATTGAAAATTCACTC
190 GTAATTCAACATTGAAAATTCACTC
*
31279785 TTTTGGACTAAAATGATAGCTTTCATATGTCAAAGATCTAT-G-G----T--GGTGATGATCTAA
1 TTTTGGACCAAAATGATAGCTTTCATATGTCAAAGATCTATGGTGAATTTGAGGTGATGATCTAA
* * ** *
31279842 TTGGATTGATGGTGTTTTTCTTGACTGT-ATGATTAATATGTACAGTTCTTCTCTACTTAAATGT
66 TTGGATTGATGGGGTTTTCCTTCCCT-TAATGATTAATATATACAGTTCTTCTCTACTTAAATGT
* * * * **
31279906 AGAGGGTGTTTTGCCATCTCTTC-ACATTGA-ATAATTAGTTT-TTTTTATTTA-T-C-AAAT-T
130 AAAGGGTGTTTTGCCATCT-TTCTACATTGATATCA-T-GTTTGGTTTCATCAACTGCTAAATGT
* * *** *
31279964 ACATTGAATATTAGTTGATTCAGTC
192 A-ATTCAACATT-GAAAATTCACTC
* *
31279989 TTGTTGGACCAAAATGATAGATTTCATATGTCAAAGATCTATGGTGAATTTGAGGTGATGATCCA
1 TT-TTGGACCAAAATGATAGCTTTCATATGTCAAAGATCTATGGTGAATTTGAGGTGATGATCTA
* *
31280054 ATTGGATTGATGGGGTTTTCCGTCCCTTAATGATTAATATATATAGTTCTTCTCTACTT
65 ATTGGATTGATGGGGTTTTCCTTCCCTTAATGATTAATATATACAGTTCTTCTCTACTT
31280113 CAGAGTTACG
Statistics
Matches: 271, Mismatches: 40, Indels: 40
0.77 0.11 0.11
Matches are distributed among these distances:
202 2 0.01
203 11 0.04
204 11 0.04
205 41 0.15
206 89 0.33
207 11 0.04
208 1 0.00
209 1 0.00
211 1 0.00
212 2 0.01
213 61 0.23
216 1 0.00
217 1 0.00
218 30 0.11
219 8 0.03
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (214 bp):
TTTTGGACCAAAATGATAGCTTTCATATGTCAAAGATCTATGGTGAATTTGAGGTGATGATCTAA
TTGGATTGATGGGGTTTTCCTTCCCTTAATGATTAATATATACAGTTCTTCTCTACTTAAATGTA
AAGGGTGTTTTGCCATCTTTCTACATTGATATCATGTTTGGTTTCATCAACTGCTAAATGTAATT
CAACATTGAAAATTCACTC
Found at i:31282325 original size:2 final size:2
Alignment explanation
Indices: 31282318--31282378 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
31282308 TCGATGTAGT
31282318 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
31282360 AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC A
31282379 TGTATATATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:31288722 original size:28 final size:29
Alignment explanation
Indices: 31288686--31288754 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 29
31288676 TTTTTTATCA
31288686 TAAG-TGGTACTTAAACTA-TTTTCCCCC
1 TAAGTTGGTACTTAAACTATTTTTCCCCC
*
31288713 TAAGTTGGTACCTAAACTATTTTTTCCCCC
1 TAAGTTGGTACTTAAACTA-TTTTTCCCCC
*
31288743 -AAGTTGGAACTT
1 TAAGTTGGTACTT
31288755 TTGTCATTAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 4 0.11
28 13 0.36
29 10 0.28
30 9 0.25
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (29 bp):
TAAGTTGGTACTTAAACTATTTTTCCCCC
Found at i:31293664 original size:46 final size:46
Alignment explanation
Indices: 31293584--31293674 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
31293574 ACATTACTAT
* * *
31293584 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCAAAACAACATACCTAATTTTCAC
* * *
31293630 AACTCAGTATGGTTTTCTTTATCAAAATAACATACCTAATTTTCA
1 AACTCAGTATGGTTTTCTTCACCAAAACAACATACCTAATTTTCA
31293675 GACTTTGCCA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCAAAACAACATACCTAATTTTCAC
Found at i:31304651 original size:31 final size:31
Alignment explanation
Indices: 31304616--31304675 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
31304606 CCAGTGACTA
*
31304616 AAAT-AAAAGTTTTTGAATAGTTCAATGATTT
1 AAATAAAAACTTTTT-AATAGTTCAATGATTT
*
31304647 AAATAAAAACTTTTTAATAGTTCAGTGAT
1 AAATAAAAACTTTTTAATAGTTCAATGAT
31304676 CAAATTGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (31 bp):
AAATAAAAACTTTTTAATAGTTCAATGATTT
Found at i:31315076 original size:15 final size:15
Alignment explanation
Indices: 31315056--31315087 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31315046 TTACTTATTT
31315056 TCAAATCATCAATCA
1 TCAAATCATCAATCA
*
31315071 TCAAATCATTAATCA
1 TCAAATCATCAATCA
31315086 TC
1 TC
31315088 CTAACACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
TCAAATCATCAATCA
Found at i:31315677 original size:71 final size:71
Alignment explanation
Indices: 31315559--31315702 Score: 270
Period size: 71 Copynumber: 2.0 Consensus size: 71
31315549 ACTATCCTCT
*
31315559 TTTGAAATTGTCTCAATAGTTTCTACAACACTAGAAGTAATATAATGAGTTTTTACTACAAAAGT
1 TTTGAAATTGTCTCAATAGTTTCTACAACACTAGAAGTAATAAAATGAGTTTTTACTACAAAAGT
31315624 AAGTAG
66 AAGTAG
31315630 TTTGAAATTGTCTCAATAGTTTCTACAACACTAGAAGTAATAAAATGAGTTTTTACTACAAAAGT
1 TTTGAAATTGTCTCAATAGTTTCTACAACACTAGAAGTAATAAAATGAGTTTTTACTACAAAAGT
*
31315695 ATGTAG
66 AAGTAG
31315701 TT
1 TT
31315703 GTTTCCTTGA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (71 bp):
TTTGAAATTGTCTCAATAGTTTCTACAACACTAGAAGTAATAAAATGAGTTTTTACTACAAAAGT
AAGTAG
Found at i:31317755 original size:16 final size:18
Alignment explanation
Indices: 31317734--31317771 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
31317724 TTTTTTTTAG
31317734 ATTTTAAGA-TTA-TTTT
1 ATTTTAAGATTTATTTTT
*
31317750 ATTTTAATATTTATTTTT
1 ATTTTAAGATTTATTTTT
31317768 ATTT
1 ATTT
31317772 GGAAAGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 3 0.16
18 8 0.42
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
ATTTTAAGATTTATTTTT
Found at i:31319662 original size:2 final size:2
Alignment explanation
Indices: 31319655--31319688 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31319645 GTTGTGGAAT
31319655 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
31319689 GATGTAGTTA
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):
TA
Found at i:31320007 original size:36 final size:36
Alignment explanation
Indices: 31319960--31320193 Score: 159
Period size: 36 Copynumber: 6.4 Consensus size: 36
31319950 ATATCGTCAG
* *
31319960 TTTATCTGACTAGTGCTGGGCGTAAATCTTTGTCGA
1 TTTATCCGACTAGTGCTGGGCGCAAATCTTTGTCGA
* * * ** * *
31319996 TTTATTCGACTAGTGCAGGGCACATTTACTGT-TAG-
1 TTTATCCGACTAGTGCTGGGCGCAAAT-CTTTGTCGA
* * * * *
31320031 TTTATCCAACTAGCGCTGGGAGCAAATCTACTATCGA
1 TTTATCCGACTAGTGCTGGGCGCAAATCT-TTGTCGA
* *
31320068 TTTATCCGATTAGCGCTGGGCGCAAATCTTTGTCTG-
1 TTTATCCGACTAGTGCTGGGCGCAAATCTTTGTC-GA
* * * * * *
31320104 TTAATCCGACTAGTGCTGGGCACACATTTAATATCATCGG
1 TTTATCCGACTAGTGCTGGGCGCAAATCT--T-T-GTCGA
* *
31320144 TTTATCCGACTAGCGTTGGGCGCAAATCTTTGTCGA
1 TTTATCCGACTAGTGCTGGGCGCAAATCTTTGTCGA
*
31320180 TTTATTCGACTAGT
1 TTTATCCGACTAGT
31320194 TGTAACACCC
Statistics
Matches: 147, Mismatches: 41, Indels: 20
0.71 0.20 0.10
Matches are distributed among these distances:
34 2 0.01
35 20 0.14
36 65 0.44
37 31 0.21
38 2 0.01
39 2 0.01
40 25 0.17
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35
Consensus pattern (36 bp):
TTTATCCGACTAGTGCTGGGCGCAAATCTTTGTCGA
Found at i:31323657 original size:36 final size:36
Alignment explanation
Indices: 31323617--31323729 Score: 111
Period size: 36 Copynumber: 3.2 Consensus size: 36
31323607 ACTAGCGCTA
*
31323617 GGCACAAATATTTATCGATTTATTTGACTAGTGCAG
1 GGCACAAATATTTATCGATTTATTTAACTAGTGCAG
** * * * ** *
31323653 GGCACATCTA-CTGTCGGTTTACCTAACTAGTGCTG
1 GGCACAAATATTTATCGATTTATTTAACTAGTGCAG
* * *
31323688 GGCGCAAATTTTTATCGATTTATTTAACTAGTGCAA
1 GGCACAAATATTTATCGATTTATTTAACTAGTGCAG
31323724 GGCACA
1 GGCACA
31323730 TCTACTGCCG
Statistics
Matches: 55, Mismatches: 21, Indels: 2
0.71 0.27 0.03
Matches are distributed among these distances:
35 24 0.44
36 31 0.56
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (36 bp):
GGCACAAATATTTATCGATTTATTTAACTAGTGCAG
Found at i:31323683 original size:35 final size:35
Alignment explanation
Indices: 31323572--31323746 Score: 95
Period size: 36 Copynumber: 4.9 Consensus size: 35
31323562 AGGCTATTAC
**
31323572 ACTAGTGCAGGAG-ACATCTACTGTCGGTTTACCCG
1 ACTAGTGCAGG-GCACATCTACTGTCGGTTTACCTA
* ** * * * ** *
31323607 ACTAGCGCTA-GGCACAAATATTTATCGATTTATTTG
1 ACTAGTGC-AGGGCACATCTA-CTGTCGGTTTACCTA
31323643 ACTAGTGCAGGGCACATCTACTGTCGGTTTACCTA
1 ACTAGTGCAGGGCACATCTACTGTCGGTTTACCTA
* * ** * * **
31323678 ACTAGTGCTGGGCGCAAAT-TTTTATCGATTTATTTA
1 ACTAGTGC-AGG-GCACATCTACTGTCGGTTTACCTA
* *
31323714 ACTAGTGCAAGGCACATCTACTGCCGGTTTACC
1 ACTAGTGCAGGGCACATCTACTGTCGGTTTACC
31323747 CGACTAGCAC
Statistics
Matches: 97, Mismatches: 36, Indels: 14
0.66 0.24 0.10
Matches are distributed among these distances:
34 6 0.06
35 40 0.41
36 46 0.47
37 5 0.05
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.31
Consensus pattern (35 bp):
ACTAGTGCAGGGCACATCTACTGTCGGTTTACCTA
Done.