Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold65
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: 3097370
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.31
Warning! 315397 characters in sequence are not A, C, G, or T
File 8 of 17
Found at i:1702706 original size:16 final size:16
Alignment explanation
Indices: 1702661--1702697 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1702651 TTAAATTTAT
* *
1702661 TTTTAATATATAATTA
1 TTTTAAAATATTATTA
1702677 TTTTAAAATATTATTA
1 TTTTAAAATATTATTA
1702693 TTTTA
1 TTTTA
1702698 TATTTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTAAAATATTATTA
Found at i:1702845 original size:14 final size:13
Alignment explanation
Indices: 1702826--1702879 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 13
1702816 AAATAATAAA
1702826 ATAATACTATTTTG
1 ATAATA-TATTTTG
*
1702840 ATAATATATTTTAAA
1 ATAATATATTTT--G
1702855 ATAATAATATTTTG
1 ATAAT-ATATTTTG
*
1702869 ATAATAAATTT
1 ATAATATATTT
1702880 AAATATTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 11 0.32
14 11 0.32
15 5 0.15
16 7 0.21
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (13 bp):
ATAATATATTTTG
Found at i:1702879 original size:29 final size:29
Alignment explanation
Indices: 1702803--1702893 Score: 103
Period size: 29 Copynumber: 3.1 Consensus size: 29
1702793 CAAAATACAT
* ** *
1702803 TATTTTGTATAAAAAATAATAAAATAATAC
1 TATTTTG-ATAATAAATTTTAAAATAATAA
*
1702833 TATTTTGATAATATATTTTAAAATAATAA
1 TATTTTGATAATAAATTTTAAAATAATAA
1702862 TATTTTGATAATAAA-TTTAAATATTAATAA
1 TATTTTGATAATAAATTTTAAA-A-TAATAA
1702892 TA
1 TA
1702894 AAATGATAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
28 6 0.11
29 32 0.60
30 15 0.28
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (29 bp):
TATTTTGATAATAAATTTTAAAATAATAA
Found at i:1703429 original size:17 final size:17
Alignment explanation
Indices: 1703403--1703437 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1703393 TATTATAATT
* *
1703403 TTTATTAAAAATTTTAA
1 TTTATAAAAAACTTTAA
1703420 TTTATAAAAAACTTTAA
1 TTTATAAAAAACTTTAA
1703437 T
1 T
1703438 ATTAAATCAA
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:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTATAAAAAACTTTAA
Found at i:1703682 original size:11 final size:11
Alignment explanation
Indices: 1703663--1703693 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1703653 CCATCTGTAA
*
1703663 AATAAAAAAAT
1 AATATAAAAAT
1703674 AATATAAAAAT
1 AATATAAAAAT
1703685 AATATAAAA
1 AATATAAAA
1703694 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:1703699 original size:16 final size:16
Alignment explanation
Indices: 1703660--1703708 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1703650 GTCCCATCTG
1703660 TAAAA-TAAAA-AA-A
1 TAAAATTAAAATAATA
* *
1703673 TAATATAAAAATAATA
1 TAAAATTAAAATAATA
1703689 TAAAATTAAAATAATA
1 TAAAATTAAAATAATA
1703705 TAAA
1 TAAA
1703709 TATATAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 4 0.14
14 4 0.14
15 2 0.07
16 19 0.66
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAATTAAAATAATA
Found at i:1703732 original size:2 final size:2
Alignment explanation
Indices: 1703702--1703815 Score: 56
Period size: 2 Copynumber: 63.5 Consensus size: 2
1703692 AATTAAAATA
* * *
1703702 AT AT AA AT AT AT A- AT -T AT AT -T AA AT -T AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1703740 -T A- AT AT AT -T A- AA AT TT AT AT AA AT AA AT AT -T 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
* *
1703777 AT AT A- AT -T AT AT A- AT AT AT AT AA AT A- AT AT AA 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
1703815 A
1 A
1703816 AATTATGTCT
Statistics
Matches: 82, Mismatches: 17, Indels: 26
0.66 0.14 0.21
Matches are distributed among these distances:
1 13 0.16
2 69 0.84
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1703734 original size:14 final size:14
Alignment explanation
Indices: 1703717--1703789 Score: 62
Period size: 14 Copynumber: 5.1 Consensus size: 14
1703707 AATATATAAT
1703717 TATATTAAATTATA
1 TATATTAAATTATA
*
1703731 TATATT-TATTA-A
1 TATATTAAATTATA
1703743 TATATTAAAATTTATA
1 TATATT-AAA-TTATA
* *
1703759 TAAATAAATATTATA
1 TATATTAA-ATTATA
1703774 TATA-TATAATTATA
1 TATATTA-AATTATA
1703788 TA
1 TA
1703790 ATATATATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
12 7 0.15
13 4 0.09
14 16 0.34
15 14 0.30
16 6 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATATTAAATTATA
Found at i:1703777 original size:17 final size:18
Alignment explanation
Indices: 1703755--1703818 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 18
1703745 TATTAAAATT
1703755 TATATAAATAAATATTATA
1 TATATAAATAAATA-TATA
*
1703774 TATATATAAT-TATATAATA
1 TATATA-AATAAATAT-ATA
*
1703793 TATATAAAT-AATATAAA
1 TATATAAATAAATATATA
1703810 TATATAAAT
1 TATATAAAT
1703819 TATGTCTAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 11 0.28
18 8 0.20
19 18 0.45
20 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TATATAAATAAATATATA
Found at i:1703781 original size:21 final size:21
Alignment explanation
Indices: 1703755--1703812 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
1703745 TATTAAAATT
1703755 TATATAAATAAATATTATATA
1 TATATAAATAAATATTATATA
* * *
1703776 TATATAATTATATAATATATA
1 TATATAAATAAATATTATATA
*
1703797 TAAATAATATAAATAT
1 TATATAA-ATAAATAT
1703813 ATAAATTATG
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 24 0.83
22 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATATAAATAAATATTATATA
Found at i:1703808 original size:26 final size:26
Alignment explanation
Indices: 1703670--1703816 Score: 105
Period size: 26 Copynumber: 5.7 Consensus size: 26
1703660 TAAAATAAAA
*
1703670 AAATAATATAAA-A-ATAATATAAAATT
1 AAATAATATAAATATATAATAT-ATA-T
1703696 AAAATAATATAAATATATAAT-TATATT
1 -AAATAATATAAATATATAATATATA-T
* * *
1703723 AAATTATATATATTTATTAATATAT-T
1 AAATAATATAAATATA-TAATATATAT
*
1703749 AAA-ATTTATATAA-ATA-AATAT-TAT
1 AAATA-ATATA-AATATATAATATATAT
* *
1703773 ATAT-ATATAATTATATAATATATAT
1 AAATAATATAAATATATAATATATAT
1703798 AAATAATATAAATATATAA
1 AAATAATATAAATATATAA
1703817 ATTATGTCTA
Statistics
Matches: 95, Mismatches: 13, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
22 1 0.01
23 8 0.08
24 13 0.14
25 6 0.06
26 36 0.38
27 21 0.22
28 5 0.05
29 5 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AAATAATATAAATATATAATATATAT
Found at i:1705203 original size:17 final size:17
Alignment explanation
Indices: 1705161--1705195 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1705151 AAAAATTAAA
1705161 ATATATTTATATTGAAT
1 ATATATTTATATTGAAT
*
1705178 ATATATTTATATTTAAT
1 ATATATTTATATTGAAT
1705195 A
1 A
1705196 ATTATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATATATTTATATTGAAT
Found at i:1705569 original size:11 final size:10
Alignment explanation
Indices: 1705552--1705602 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 10
1705542 CCATTTTATT
1705552 TTTAAAATAA
1 TTTAAAATAA
1705562 TATTAAAAT-A
1 T-TTAAAATAA
*
1705572 TTTAAAATACC
1 TTTAAAATA-A
1705583 TTTATAAATAAA
1 TTTA-AAAT-AA
1705595 TTTAAAAT
1 TTTAAAAT
1705603 TTTATTATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
9 7 0.21
10 3 0.09
11 15 0.44
12 8 0.24
13 1 0.03
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (10 bp):
TTTAAAATAA
Found at i:1707796 original size:14 final size:15
Alignment explanation
Indices: 1707763--1707801 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
1707753 GTTGATTCAA
1707763 AATAAATTAAAATTG
1 AATAAATTAAAATTG
*
1707778 AATAAATTAAATTTG
1 AATAAATTAAAATTG
1707793 -ATAAATTAA
1 AATAAATTAA
1707802 TTTTATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (15 bp):
AATAAATTAAAATTG
Found at i:1708943 original size:2 final size:2
Alignment explanation
Indices: 1708936--1708964 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1708926 CAATGACATC
1708936 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1708965 AGTCCAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1709462 original size:5 final size:5
Alignment explanation
Indices: 1709448--1709516 Score: 56
Period size: 5 Copynumber: 14.0 Consensus size: 5
1709438 AAAAATTTTG
* *
1709448 TATAA TATAA CATAA AATAA TATAAA TATAA TATGAA TAT-A TA-AA TAT-A
1 TATAA TATAA TATAA TATAA TAT-AA TATAA TAT-AA TATAA TATAA TATAA
*
1709497 T-TAA TATTTA TATAA TATAA
1 TATAA TA-TAA TATAA TATAA
1709517 ATTATTAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
3 1 0.02
4 10 0.19
5 27 0.52
6 14 0.27
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (5 bp):
TATAA
Found at i:1709476 original size:21 final size:19
Alignment explanation
Indices: 1709451--1709496 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
1709441 AATTTTGTAT
1709451 AATATAACATAAAATAATATA
1 AATATAACAT-AAAT-ATATA
* *
1709472 AATATAATATGAATATATA
1 AATATAACATAAATATATA
1709491 AATATA
1 AATATA
1709497 TTAATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 11 0.48
20 3 0.13
21 9 0.39
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AATATAACATAAATATATA
Found at i:1711414 original size:18 final size:17
Alignment explanation
Indices: 1711393--1711426 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1711383 TAATTAATTT
1711393 ATATAATTATTATAAAAA
1 ATATAATTA-TATAAAAA
*
1711411 ATATTATTATATAAAA
1 ATATAATTATATAAAA
1711427 TTTAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTATATAAAAA
Found at i:1711418 original size:15 final size:15
Alignment explanation
Indices: 1711398--1711427 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1711388 AATTTATATA
1711398 ATTATTATAAAAAAT
1 ATTATTATAAAAAAT
*
1711413 ATTATTATATAAAAT
1 ATTATTATAAAAAAT
1711428 TTAATTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTATTATAAAAAAT
Found at i:1715583 original size:35 final size:35
Alignment explanation
Indices: 1715544--1715617 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
1715534 TTATATCTTT
* * *
1715544 CATAATGAGTGATGAATATCTTAGT-TTATTTTTTC
1 CATAACGAGTAATCAATATCTTA-TCTTATTTTTTC
*
1715579 CATAACGAGTAATCAATATCTTATCTTATTTTTTT
1 CATAACGAGTAATCAATATCTTATCTTATTTTTTC
1715614 CATA
1 CATA
1715618 TCTTCCAGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 1 0.03
35 33 0.97
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.47
Consensus pattern (35 bp):
CATAACGAGTAATCAATATCTTATCTTATTTTTTC
Found at i:1716029 original size:13 final size:14
Alignment explanation
Indices: 1716011--1716039 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1716001 AAAACTAGCT
1716011 AGATGATAAA-AAA
1 AGATGATAAATAAA
1716024 AGATGATAAATAAA
1 AGATGATAAATAAA
1716038 AG
1 AG
1716040 CTTATTGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (14 bp):
AGATGATAAATAAA
Found at i:1722789 original size:25 final size:24
Alignment explanation
Indices: 1722758--1722828 Score: 88
Period size: 26 Copynumber: 2.8 Consensus size: 24
1722748 GATAAATATT
1722758 ATTTTAAAATTTAATAAAAAATAA
1 ATTTTAAAATTTAATAAAAAATAA
* *
1722782 ATTATTAAAATTTAAATTAAAATATAT
1 ATT-TTAAAATTT-AA-TAAAAAATAA
*
1722809 ATTTTAAAATTTTATAAAAA
1 ATTTTAAAATTTAATAAAAA
1722829 TATATAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
24 8 0.20
25 10 0.25
26 11 0.28
27 11 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
ATTTTAAAATTTAATAAAAAATAA
Found at i:1722829 original size:25 final size:25
Alignment explanation
Indices: 1722751--1722834 Score: 109
Period size: 25 Copynumber: 3.4 Consensus size: 25
1722741 ATATGATGAT
1722751 AAATAT-TATTTTAAAATTTAATAA
1 AAATATATATTTTAAAATTTAATAA
* *
1722775 AAA-ATAAATTATTAAAATTTAAATTA
1 AAATATATATT-TTAAAATTT-AATAA
*
1722801 AAATATATATTTTAAAATTTTATAA
1 AAATATATATTTTAAAATTTAATAA
1722826 AAATATATA
1 AAATATATA
1722835 ATATGATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
23 2 0.04
24 6 0.12
25 21 0.41
26 16 0.31
27 6 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AAATATATATTTTAAAATTTAATAA
Found at i:1722917 original size:41 final size:40
Alignment explanation
Indices: 1722840--1722926 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 40
1722830 ATATAATATG
* *
1722840 ATAAATTTAAATATAATTAAATAATTTATTTATAAATATAA
1 ATAACTTTAAATAAAATTAAATAATTTATTTATAAAT-TAA
* *
1722881 ATAACTTTAAATAAAATTTAA-AATTTATATTCTAAATTAA
1 ATAACTTTAAATAAAATTAAATAATTTAT-TTATAAATTAA
1722921 ACTAAC
1 A-TAAC
1722927 ATTCACAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
40 11 0.28
41 29 0.73
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (40 bp):
ATAACTTTAAATAAAATTAAATAATTTATTTATAAATTAA
Found at i:1726120 original size:19 final size:20
Alignment explanation
Indices: 1726096--1726147 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1726086 ATTTGAGTGG
1726096 TAGTTTTTTAAA-AAATGAC
1 TAGTTTTTTAAATAAATGAC
* *
1726115 TAGTTTTTTAAATAAGTGAG
1 TAGTTTTTTAAATAAATGAC
*
1726135 TAATTTTTTAAAT
1 TAGTTTTTTAAAT
1726148 TTAAGTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (20 bp):
TAGTTTTTTAAATAAATGAC
Found at i:1726576 original size:2 final size:2
Alignment explanation
Indices: 1726569--1726614 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1726559 AAAATTTTTC
* *
1726569 AT AT AT AT AT AT AT AG AT AT AT AT GT 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
1726611 AT AT
1 AT AT
1726615 TATCTAATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1726736 original size:29 final size:29
Alignment explanation
Indices: 1726681--1726736 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
1726671 TAAAGTGTCA
* *
1726681 TATATTTATATAAATTAAAATTTTATATT
1 TATATTTATATAAATCAAAATTATATATT
* * *
1726710 TATATTTATATATATCCATATTATATA
1 TATATTTATATAAATCAAAATTATATA
1726737 GAAGCTTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (29 bp):
TATATTTATATAAATCAAAATTATATATT
Found at i:1728049 original size:57 final size:57
Alignment explanation
Indices: 1727985--1728159 Score: 264
Period size: 57 Copynumber: 3.1 Consensus size: 57
1727975 AAAATTTATC
*
1727985 TATTTTATATAAAAAACTACTTAAAAATTTAAAATTTTGCAATAAAAATAATTATTT
1 TATTTTATATAAAAAACTACTTAAAAATTTAAAATTTTGTAATAAAAATAATTATTT
* * *
1728042 TATTTTATACAAAAAATTACTTAAAAATTTAAAA-TTTGTAATAAAATAAAATT-TATT
1 TATTTTATATAAAAAACTACTTAAAAATTTAAAATTTTGTAATAAAA-ATAATTAT-TT
* *
1728099 TATTTTATATAAAAAACTATTTAAAAATTTAAAATTTGGTAATAAAAATAATTATTT
1 TATTTTATATAAAAAACTACTTAAAAATTTAAAATTTTGTAATAAAAATAATTATTT
1728156 TATT
1 TATT
1728160 CTAAAAAAAT
Statistics
Matches: 105, Mismatches: 9, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
56 12 0.11
57 81 0.77
58 12 0.11
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.43
Consensus pattern (57 bp):
TATTTTATATAAAAAACTACTTAAAAATTTAAAATTTTGTAATAAAAATAATTATTT
Found at i:1728742 original size:14 final size:13
Alignment explanation
Indices: 1728725--1728758 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1728715 TTATTTTTGA
1728725 TTTTTTATTAAGAT
1 TTTTTTATTAA-AT
*
1728739 TTTTTAATTAAAT
1 TTTTTTATTAAAT
1728752 TTTTTTA
1 TTTTTTA
1728759 AAATATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (13 bp):
TTTTTTATTAAAT
Found at i:1728759 original size:14 final size:14
Alignment explanation
Indices: 1728723--1728756 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1728713 TTTTATTTTT
1728723 GATTTTTT-ATTAA
1 GATTTTTTAATTAA
1728736 GATTTTTTAATTAA
1 GATTTTTTAATTAA
1728750 -ATTTTTT
1 GATTTTTT
1728757 TAAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (14 bp):
GATTTTTTAATTAA
Found at i:1738052 original size:50 final size:50
Alignment explanation
Indices: 1737949--1738042 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
1737939 TTTAAATTTT
* * * *
1737949 TTAA-AAATTTATAAATACTTTTTATATTTTATTAATCTTATATTTAAAA
1 TTAATAAATTTAAAAATACTTTTTATAATTTATTAATATAATATTTAAAA
*
1737998 TTAATAAATTTAAAAATATTTTTTA-AATTTATT-ATATAATATTTA
1 TTAATAAATTTAAAAATACTTTTTATAATTTATTAATATAATATTTA
1738043 TTATATTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
48 10 0.26
49 11 0.28
50 18 0.46
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (50 bp):
TTAATAAATTTAAAAATACTTTTTATAATTTATTAATATAATATTTAAAA
Found at i:1741034 original size:6 final size:6
Alignment explanation
Indices: 1741025--1741059 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1741015 AAAAAGAAAA
*
1741025 ACTAAC ACTAAC ACTAAC ACTAAC ACTAAC GCTAA
1 ACTAAC ACTAAC ACTAAC ACTAAC ACTAAC ACTAA
1741060 AAGTAATTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.49, C:0.31, G:0.03, T:0.17
Consensus pattern (6 bp):
ACTAAC
Found at i:1744705 original size:47 final size:47
Alignment explanation
Indices: 1744624--1744721 Score: 144
Period size: 47 Copynumber: 2.1 Consensus size: 47
1744614 ACATGAAGAG
* *
1744624 ATAAGTGATCAAGGTTTGAATTCATCTAAAGAACCATAGTCCAACCA
1 ATAAGTGATCAAGGTTGGAATTCATCCAAAGAACCATAGTCCAACCA
* *
1744671 ATAAGTGATCAAGGTTGGAA-TCTATCCAATGAACCATAGTCCAACTA
1 ATAAGTGATCAAGGTTGGAATTC-ATCCAAAGAACCATAGTCCAACCA
1744718 ATAA
1 ATAA
1744722 CAAAAGAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
46 2 0.04
47 44 0.96
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (47 bp):
ATAAGTGATCAAGGTTGGAATTCATCCAAAGAACCATAGTCCAACCA
Found at i:1746257 original size:23 final size:21
Alignment explanation
Indices: 1746204--1746258 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 21
1746194 TATAAAAAAT
*
1746204 AAAATATTATAAAATTAATTA
1 AAAATAATATAAAATTAATTA
1746225 AAAATTTAATATAAAATTAAATTTA
1 AAAA--TAATATAAAATT-AA-TTA
*
1746250 ATAATAATA
1 AAAATAATA
1746259 ATTCATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 4 0.14
23 16 0.57
24 2 0.07
25 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATAATATAAAATTAATTA
Found at i:1763254 original size:170 final size:165
Alignment explanation
Indices: 1762918--1763254 Score: 532
Period size: 170 Copynumber: 2.0 Consensus size: 165
1762908 GATTTTTACC
* *
1762918 TTTCAGACTTTAAATATCAGCGTGCAACAGTTGTCTAGGAGATTCAAGTATGTGTGCTATTAGTA
1 TTTCAGACTTTAAATATCAGCGTGCAACAGTTGTCTAGCAGATTCAAGTATGTGTGCCATTAGTA
* *
1762983 TAATCATCGCTGAATTTCAGCAAGTAGTTTCCCTAGTCTTTTCTGAATTTGCAAAGATTCTGGTT
66 TAATCATCGCTGAATTTCAACAAGTAGTTTCCATAGTCTTTTCTGAATTTGCAAAGATTCTGGTT
1763048 CTTATATACTATCATGGAGACTCTCAGAGAAGGGG
131 CTTATATACTATCATGGAGACTCTCAGAGAAGGGG
1763083 TTTCAGACTTTAAATATCAGCGTGCAACAGTTGTCTAGCAGATTCAAGTATGACTGTGTGCCATT
1 TTTCAGACTTTAAATATCAGCGTGCAACAGTTGTCTAGCAGATTCAAG--T-A-TGTGTGCCATT
** *
1763148 AGTATAATCATCGCTGAATTTCAACAAGTAGTTGTTGATAGTCTTTTCT-ACATTTGCGAAGATT
62 AGTATAATCATCGCTGAATTTCAACAAGTAGTT-TCCATAGTCTTTTCTGA-ATTTGCAAAGATT
* *
1763212 CTGGTTCTTATATACTATCATGGAGACTCTGAGAGGAGGGG
125 CTGGTTCTTATATACTATCATGGAGACTCTCAGAGAAGGGG
1763253 TT
1 TT
1763255 GTAGGGTTAA
Statistics
Matches: 157, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
165 47 0.30
167 1 0.01
168 1 0.01
169 43 0.27
170 65 0.41
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (165 bp):
TTTCAGACTTTAAATATCAGCGTGCAACAGTTGTCTAGCAGATTCAAGTATGTGTGCCATTAGTA
TAATCATCGCTGAATTTCAACAAGTAGTTTCCATAGTCTTTTCTGAATTTGCAAAGATTCTGGTT
CTTATATACTATCATGGAGACTCTCAGAGAAGGGG
Found at i:1764770 original size:22 final size:21
Alignment explanation
Indices: 1764744--1764787 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
1764734 GAATATTTTA
1764744 TTTT-ATTTAATAAGATTTGAAT
1 TTTTAATTT-ATAAGATTT-AAT
*
1764766 TTTTAATTTATTAGATTTAAT
1 TTTTAATTTATAAGATTTAAT
1764787 T
1 T
1764788 AACATTTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (21 bp):
TTTTAATTTATAAGATTTAAT
Found at i:1767378 original size:2 final size:2
Alignment explanation
Indices: 1767371--1767406 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1767361 TAAAAAGAAC
1767371 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
1767407 CATCTTGATG
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):
AT
Found at i:1771098 original size:7 final size:7
Alignment explanation
Indices: 1771086--1771125 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
1771076 AAATTGAGTT
1771086 AATTTTA
1 AATTTTA
1771093 AATTTTA
1 AATTTTA
1771100 AATTTT-
1 AATTTTA
1771106 AATTTT-
1 AATTTTA
1771112 AATTTTA
1 AATTTTA
*
1771119 ATTTTTA
1 AATTTTA
1771126 TTTTTAGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 12 0.39
7 19 0.61
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
AATTTTA
Found at i:1771100 original size:13 final size:13
Alignment explanation
Indices: 1771084--1771131 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
1771074 TCAAATTGAG
1771084 TTAATTTTAAATT
1 TTAATTTTAAATT
1771097 TTAAATTTT-AATT
1 TT-AATTTTAAATT
*
1771110 TTAATTTTAATTT
1 TTAATTTTAAATT
*
1771123 TTATTTTTA
1 TTAATTTTA
1771132 GACCACAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 6 0.19
13 19 0.61
14 6 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTAATTTTAAATT
Found at i:1771131 original size:6 final size:6
Alignment explanation
Indices: 1771084--1771129 Score: 65
Period size: 6 Copynumber: 7.3 Consensus size: 6
1771074 TCAAATTGAG
*
1771084 TTAATT TTAAATT TTAAATT TTAATT TTAATT TTAATT TTTATT TT
1 TTAATT TT-AATT TT-AATT TTAATT TTAATT TTAATT TTAATT TT
1771130 TAGACCACAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
6 25 0.66
7 13 0.34
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTAATT
Found at i:1771434 original size:2 final size:2
Alignment explanation
Indices: 1771427--1771459 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1771417 AGAAGAGTTA
*
1771427 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1771460 AGAGGAAGTT
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:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1772133 original size:19 final size:20
Alignment explanation
Indices: 1772104--1772141 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1772094 TATATAATTT
*
1772104 AAATTATAATTACAAATATA
1 AAATTATAATTAAAAATATA
1772124 AAATTA-AATTAAAAATAT
1 AAATTATAATTAAAAATAT
1772142 TTTACTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATTATAATTAAAAATATA
Found at i:1772619 original size:2 final size:2
Alignment explanation
Indices: 1772612--1772649 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1772602 GGCAGATCAC
1772612 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
1772650 TTAAGAGGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1774513 original size:29 final size:29
Alignment explanation
Indices: 1774476--1774564 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
1774466 TCTTGAACTC
*
1774476 TTTTAATTTT-TTAAAAATAAATTTTTATT
1 TTTTAATTTTATT-AAAATAAACTTTTATT
* * *
1774505 TTTTTATTTTATTTAAATAAACTTTTATC
1 TTTTAATTTTATTAAAATAAACTTTTATT
* * * *
1774534 ATTTGATTTATATTCAAATAAAATTTTATT
1 TTTTAATTT-TATTAAAATAAACTTTTATT
1774564 T
1 T
1774565 CAAATAAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 29 0.60
30 19 0.40
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (29 bp):
TTTTAATTTTATTAAAATAAACTTTTATT
Found at i:1774555 original size:30 final size:29
Alignment explanation
Indices: 1774490--1774562 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
1774480 AATTTTTTAA
* ** * *
1774490 AAATAAATTTTTATTTTTTTATTTTATTT
1 AAATAAAATTTTATCATTTGATTTTATTC
*
1774519 AAATAAACTTTTATCATTTGATTTATATTC
1 AAATAAAATTTTATCATTTGATTT-TATTC
1774549 AAATAAAATTTTAT
1 AAATAAAATTTTAT
1774563 TTCAAATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.56
Consensus pattern (29 bp):
AAATAAAATTTTATCATTTGATTTTATTC
Found at i:1774574 original size:18 final size:18
Alignment explanation
Indices: 1774540--1774573 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1774530 TATCATTTGA
1774540 TTTATATTCAAATAAAAT
1 TTTATATTCAAATAAAAT
1774558 TTTAT-TTCAAATAAAA
1 TTTATATTCAAATAAAA
1774574 AATTGATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTATATTCAAATAAAAT
Found at i:1774630 original size:29 final size:28
Alignment explanation
Indices: 1774594--1774666 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
1774584 TTAGTTAGGT
*
1774594 ATATATTAAAAATTAAAAATATATTTGA
1 ATATATTAAAAATTAAAAATATATTTAA
* * * *
1774622 ATGTAATTATAAATTAATAATTTATTTAA
1 ATAT-ATTAAAAATTAAAAATATATTTAA
1774651 ATATATCTAAAAATTA
1 ATATAT-TAAAAATTA
1774667 TCATTTGAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 5 0.14
29 31 0.86
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.42
Consensus pattern (28 bp):
ATATATTAAAAATTAAAAATATATTTAA
Found at i:1775331 original size:16 final size:16
Alignment explanation
Indices: 1775290--1775334 Score: 67
Period size: 14 Copynumber: 2.9 Consensus size: 16
1775280 ATATTTAAAC
1775290 TATTTAAAATATAAATA
1 TATTTAAAATA-AAATA
1775307 TATTT--AATAAAATA
1 TATTTAAAATAAAATA
1775321 TATTTAAAATAAAA
1 TATTTAAAATAAAA
1775335 AAATTAACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 10 0.38
15 4 0.15
16 7 0.27
17 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TATTTAAAATAAAATA
Found at i:1776568 original size:20 final size:22
Alignment explanation
Indices: 1776536--1776593 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
1776526 TATATTTATA
*
1776536 TAAATATTAATTTAAATTAAA-
1 TAAATAATAATTTAAATTAAAT
* *
1776557 TAAA-AATAATTTGATTTAAAT
1 TAAATAATAATTTAAATTAAAT
*
1776578 TAAATAATTATTTAAA
1 TAAATAATAATTTAAA
1776594 ATAATTATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 13 0.45
21 8 0.28
22 8 0.28
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAATAATAATTTAAATTAAAT
Found at i:1776637 original size:23 final size:21
Alignment explanation
Indices: 1776589--1776637 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
1776579 AAATAATTAT
1776589 TTAAAATAATTATTAAATTTA
1 TTAAAATAATTATTAAATTTA
* *
1776610 TTAAAATAATATTTTAATTCTTA
1 TTAAAATAAT-TATTAAAT-TTA
1776633 TTAAA
1 TTAAA
1776638 TCTATTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.42
22 6 0.25
23 8 0.33
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAAAATAATTATTAAATTTA
Found at i:1776926 original size:19 final size:19
Alignment explanation
Indices: 1776902--1776945 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1776892 TATTAAATAT
*
1776902 TAATTTAAATTAAATTAAA
1 TAATTTAAATTAAAATAAA
*
1776921 TAATTTAATTTAAAATAAA
1 TAATTTAAATTAAAATAAA
1776940 TAATTT
1 TAATTT
1776946 TTTAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAATTTAAATTAAAATAAA
Found at i:1776932 original size:24 final size:22
Alignment explanation
Indices: 1776893--1776940 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 22
1776883 AATTATCGTT
*
1776893 ATTAAATATTAATTTAAATTAA
1 ATTAAATATTAATTTAAAATAA
1776915 ATTAAATAATTTAATTTAAAATAA
1 ATTAAAT-A-TTAATTTAAAATAA
1776939 AT
1 AT
1776941 AATTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.30
23 1 0.04
24 15 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTAAATATTAATTTAAAATAA
Found at i:1779229 original size:25 final size:23
Alignment explanation
Indices: 1779191--1779237 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
1779181 ATTAAATTAA
1779191 ATTTAAAAAATTAAAATTAAAATTT
1 ATTTAAAAAATT-AAA-TAAAATTT
**
1779216 ATTTAAAATTTTAAATAAAATT
1 ATTTAAAAAATTAAATAAAATT
1779238 AACTTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 3 0.15
25 10 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTTAAAAAATTAAATAAAATTT
Found at i:1779270 original size:14 final size:14
Alignment explanation
Indices: 1779233--1779276 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1779223 ATTTTAAATA
*
1779233 AAATTAACTTATTT
1 AAATTAATTTATTT
*
1779247 AAAGTT-ATTTAATT
1 AAA-TTAATTTATTT
1779261 AAATTAATTTATTT
1 AAATTAATTTATTT
1779275 AA
1 AA
1779277 TAAAAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 2 0.08
14 21 0.84
15 2 0.08
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (14 bp):
AAATTAATTTATTT
Found at i:1779274 original size:18 final size:19
Alignment explanation
Indices: 1779251--1779293 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1779241 TTATTTAAAG
* *
1779251 TTATTTAATTAAATTAA-T
1 TTATTTAATAAAAATAATT
1779269 TTATTTAATAAAAATAATT
1 TTATTTAATAAAAATAATT
1779288 TTATTT
1 TTATTT
1779294 TTATATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATTTAATAAAAATAATT
Found at i:1779304 original size:18 final size:19
Alignment explanation
Indices: 1779283--1779327 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
1779273 TTAATAAAAA
* *
1779283 TAATTTTATTTTTA-TATT
1 TAATTTTAGTTTAATTATT
1779301 TAATTTTAGTTTAATTATT
1 TAATTTTAGTTTAATTATT
*
1779320 TAAATTTA
1 TAATTTTA
1779328 AATTAAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TAATTTTAGTTTAATTATT
Found at i:1783008 original size:27 final size:27
Alignment explanation
Indices: 1782976--1783035 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
1782966 ATTTAAAAAA
1782976 TATTAAAAATTAAA-AAAA-TATTTTT
1 TATTAAAAATTAAATAAAATTATTTTT
*
1783001 ATCATT-AAATTTAAATAAAATTATTTTT
1 -T-ATTAAAAATTAAATAAAATTATTTTT
1783029 TATTAAA
1 TATTAAA
1783036 TAAATAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
26 12 0.41
27 10 0.34
28 7 0.24
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
TATTAAAAATTAAATAAAATTATTTTT
Found at i:1783044 original size:27 final size:28
Alignment explanation
Indices: 1782975--1783045 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 28
1782965 TATTTAAAAA
*
1782975 ATATTAAA-AATTAA-AAAAATATTTTT
1 ATATTAAATAAATAATAAAAATATTTTT
** *
1783001 ATCATTAAATTTA-AATAAAATTATTTTT
1 AT-ATTAAATAAATAATAAAAATATTTTT
1783029 -TATTAAATAAATAATAA
1 ATATTAAATAAATAATAA
1783046 TTTAAAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
26 10 0.29
27 14 0.40
28 11 0.31
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (28 bp):
ATATTAAATAAATAATAAAAATATTTTT
Found at i:1783440 original size:19 final size:20
Alignment explanation
Indices: 1783416--1783453 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1783406 CATTTATTAT
1783416 TATTTAATT-TTAAATTAAA
1 TATTTAATTATTAAATTAAA
1783435 TATTTAATTATTAAATTAA
1 TATTTAATTATTAAATTAA
1783454 CTTTCTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTTAATTATTAAATTAAA
Found at i:1786527 original size:17 final size:16
Alignment explanation
Indices: 1786505--1786544 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
1786495 TATAAATAAA
*
1786505 ATAAATTTTTATATACT
1 ATAAATTTTTACATA-T
1786522 ATAAATTTTTACATAT
1 ATAAATTTTTACATAT
1786538 A-AAATTT
1 ATAAATTT
1786545 ATTTTCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.27
16 2 0.09
17 14 0.64
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (16 bp):
ATAAATTTTTACATAT
Found at i:1787214 original size:50 final size:50
Alignment explanation
Indices: 1787155--1787442 Score: 441
Period size: 50 Copynumber: 5.8 Consensus size: 50
1787145 TATACTTAGA
* * *
1787155 GTCAACAATTATGGTCATCTTTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1787205 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
1787255 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
1787305 GTCAACAATTACGGTCACCTCTCTCTATTGTCAAAGGTTGATGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* ** * *
1787355 GTCAATAATTATGATCATCTCTCTCTATTGTCAAAGGTTGATGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
** *
1787405 GTCAACAATTGCGGCCACATCTCTCTATTGTCAAAGGT
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGT
1787443 ACTTTTCACC
Statistics
Matches: 219, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 219 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:1789349 original size:20 final size:19
Alignment explanation
Indices: 1789295--1789350 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1789285 AAAACCCTTA
**
1789295 AAAGTATCGATACACAATTC
1 AAAGTATCGATACA-TGTTC
1789315 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
1789335 AAAGTATCGATACATG
1 AAAGTATCGATACATG
1789351 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:1789438 original size:13 final size:13
Alignment explanation
Indices: 1789420--1789445 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1789410 TACACAAAGT
1789420 ATGTATCGATACA
1 ATGTATCGATACA
1789433 ATGTATCGATACA
1 ATGTATCGATACA
1789446 CCAAAAAAAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1789466 original size:34 final size:32
Alignment explanation
Indices: 1789402--1789466 Score: 85
Period size: 34 Copynumber: 2.0 Consensus size: 32
1789392 TAGCCAAACT
** *
1789402 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCAATACAA
1789434 TGTATCGATACACCAAAAAAATGTATCAATACA
1 TGTATCGATACA-C-AAAAAATGTATCAATACA
1789467 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 12 0.43
33 1 0.04
34 15 0.54
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCAATACAA
Found at i:1795587 original size:20 final size:20
Alignment explanation
Indices: 1795515--1795593 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 20
1795505 TTTTTCAAAA
*
1795515 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATCTTTCT
* *
1795535 GTGTATCGATACATCTGGAAAATTCA
1 ATGTATCGATACATCT------TTCT
1795561 ATGTATCGATACATCTTTCT
1 ATGTATCGATACATCTTTCT
*
1795581 TTGTATCGATACA
1 ATGTATCGATACA
1795594 GGGGGATTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
20 29 0.62
26 18 0.38
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATCTTTCT
Found at i:1795738 original size:21 final size:20
Alignment explanation
Indices: 1795714--1795760 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
1795704 AAATCTTTTA
*
1795714 CAAAATAC-TTGTTTTTCACTT
1 CAAAATACATCGTTTTTCA--T
*
1795735 CAAATTACATCGTTTTTCAT
1 CAAAATACATCGTTTTTCAT
1795755 CAAAAT
1 CAAAAT
1795761 CAGCTTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.27
21 7 0.32
22 9 0.41
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACATCGTTTTTCAT
Found at i:1797317 original size:13 final size:13
Alignment explanation
Indices: 1797299--1797325 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1797289 ATCGCATATT
1797299 TATTTTATGGAAA
1 TATTTTATGGAAA
1797312 TATTTTATGGAAA
1 TATTTTATGGAAA
1797325 T
1 T
1797326 GTCTTCTATC
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:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TATTTTATGGAAA
Found at i:1797436 original size:24 final size:25
Alignment explanation
Indices: 1797390--1797441 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1797380 ATATGTATGC
1797390 AAATAAATTTTTGATTAAGGGGGAG
1 AAATAAATTTTTGATTAAGGGGGAG
1797415 AAATAAATTTTTGATTAAGGGGGAG
1 AAATAAATTTTTGATTAAGGGGGAG
1797440 AA
1 AA
1797442 TGCGCGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (25 bp):
AAATAAATTTTTGATTAAGGGGGAG
Found at i:1798068 original size:20 final size:19
Alignment explanation
Indices: 1798014--1798069 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1798004 AAAACCCTTA
**
1798014 AAAGTATCGATACACAATTC
1 AAAGTATCGATACA-TGTTC
1798034 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
1798054 AAAGTATCGATACATG
1 AAAGTATCGATACATG
1798070 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:1798145 original size:19 final size:21
Alignment explanation
Indices: 1798121--1798172 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1798111 TAGCCAAACT
**
1798121 TGTATCGATACA-C-AAAGTA
1 TGTATCGATACACCAAAAAAA
1798140 TGTATCGATACACCAAAAAAA
1 TGTATCGATACACCAAAAAAA
1798161 TGTATCGATACA
1 TGTATCGATACA
1798173 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.41
20 1 0.03
21 16 0.55
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.25
Consensus pattern (21 bp):
TGTATCGATACACCAAAAAAA
Found at i:1801788 original size:50 final size:50
Alignment explanation
Indices: 1801729--1801945 Score: 217
Period size: 50 Copynumber: 4.3 Consensus size: 50
1801719 ATACTTAGAG
* *
1801729 TCAACAATTATAGCCACCTCTCTCTATTGTCAAAAGTTGGTGAAGAATCA
1 TCAACAATTATAGCCACCTCTCTCTATTGTCAAAAGTTGATGAAAAATCA
* * *
1801779 TCAACAATTAT-GATCACCTCTCTCTATTGTCAAAAGTTGGTAAAAAATCA
1 TCAACAATTATAG-CCACCTCTCTCTATTGTCAAAAGTTGATGAAAAATCA
* * * * * *
1801829 TCAACAATTATGGCCACCTC-CTTCTATTATCAAAGGTTGATTAAGAATCG
1 TCAACAATTATAGCCACCTCTC-TCTATTGTCAAAAGTTGATGAAAAATCA
* * * *
1801879 TCAATAATTA-CGACCACCTCTCTATATTGTC-AAAGATCGATGAAAAATCA
1 TCAACAATTATAG-CCACCTCTCTCTATTGTCAAAAG-TTGATGAAAAATCA
* *
1801929 TCAATAATTACAGCCAC
1 TCAACAATTATAGCCAC
1801946 TTCTTTTTAT
Statistics
Matches: 140, Mismatches: 20, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
49 6 0.04
50 131 0.94
51 3 0.02
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (50 bp):
TCAACAATTATAGCCACCTCTCTCTATTGTCAAAAGTTGATGAAAAATCA
Found at i:1801964 original size:100 final size:100
Alignment explanation
Indices: 1801729--1801965 Score: 278
Period size: 100 Copynumber: 2.4 Consensus size: 100
1801719 ATACTTAGAG
* * * * *
1801729 TCAACAATTATAGCCACCTCTCTCTATTGTCAAAAGTTGGTGAAGAATCATCAACAATTATGATC
1 TCAACAATTATAGCCACCTCTTTCTATTGTCAAAGGTTGATGAAGAATCATCAACAATTACGACC
* * *
1801794 ACCTCTCTCTATTGTCAAAAGTTGGTAAAAAATCA
66 ACCTCTCTATATTGTCAAAAGTCGATAAAAAATCA
* * * * * *
1801829 TCAACAATTATGGCCACCTCCTTCTATTATCAAAGGTTGATTAAGAATCGTCAATAATTACGACC
1 TCAACAATTATAGCCACCTCTTTCTATTGTCAAAGGTTGATGAAGAATCATCAACAATTACGACC
*
1801894 ACCTCTCTATATTGTC-AAAGATCGATGAAAAATCA
66 ACCTCTCTATATTGTCAAAAG-TCGATAAAAAATCA
* * * * *
1801929 TCAATAATTACAGCCACTTCTTTTTATTGTGAAAGGT
1 TCAACAATTATAGCCACCTCTTTCTATTGTCAAAGGT
1801966 ACTTTTCACC
Statistics
Matches: 113, Mismatches: 23, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
99 4 0.04
100 109 0.96
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (100 bp):
TCAACAATTATAGCCACCTCTTTCTATTGTCAAAGGTTGATGAAGAATCATCAACAATTACGACC
ACCTCTCTATATTGTCAAAAGTCGATAAAAAATCA
Found at i:1802050 original size:2 final size:2
Alignment explanation
Indices: 1802043--1802076 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1802033 TGACAATTGA
*
1802043 AT AT AT AT AT AT AT AT AT GT 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
1802077 CCATATACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1802886 original size:21 final size:22
Alignment explanation
Indices: 1802840--1802886 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
1802830 ACTTTTGTAT
*
1802840 ATTTTTATATTTTTTATTAATG
1 ATTTTTATATTTTATATTAATG
1802862 -TTTTTATATATTTATA-TAA-G
1 ATTTTTATAT-TTTATATTAATG
1802882 ATTTT
1 ATTTT
1802887 AAAAGAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 1 0.05
21 16 0.73
22 5 0.23
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (22 bp):
ATTTTTATATTTTATATTAATG
Found at i:1803664 original size:42 final size:44
Alignment explanation
Indices: 1803597--1803687 Score: 116
Period size: 42 Copynumber: 2.1 Consensus size: 44
1803587 ATTTAAGAAG
*
1803597 TTAAATTTTAAAATATATTAATATTT-TT-AAT-ATATTTTACAA
1 TTAAATTTTAAAAAATATTAATATTTATTAAATAATATTTTA-AA
* **
1803639 TTAATTTTTAAAAAATATTTTTATTTATTAAATAATATTTTAAA
1 TTAAATTTTAAAAAATATTAATATTTATTAAATAATATTTTAAA
1803683 TTAAA
1 TTAAA
1803688 ATATTTTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 22 0.54
43 2 0.05
44 9 0.22
45 8 0.20
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (44 bp):
TTAAATTTTAAAAAATATTAATATTTATTAAATAATATTTTAAA
Found at i:1803680 original size:19 final size:19
Alignment explanation
Indices: 1803642--1803679 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1803632 TTTACAATTA
1803642 ATTTTTAAAAAATATTTTT
1 ATTTTTAAAAAATATTTTT
*
1803661 ATTTATTAAATAATATTTT
1 ATTT-TTAAAAAATATTTT
1803680 AAATTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTTAAAAAATATTTTT
Found at i:1804077 original size:13 final size:13
Alignment explanation
Indices: 1804059--1804088 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1804049 TATATTAATT
1804059 ATATTTTTAATAA
1 ATATTTTTAATAA
*
1804072 ATATTTTTAATCA
1 ATATTTTTAATAA
1804085 ATAT
1 ATAT
1804089 CACTATACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
ATATTTTTAATAA
Found at i:1804905 original size:2 final size:2
Alignment explanation
Indices: 1804900--1804929 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1804890 ATATATATAT
*
1804900 AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1804930 CGAGCTAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1807574 original size:38 final size:37
Alignment explanation
Indices: 1807516--1807587 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 37
1807506 AATATTAAAT
1807516 AAATTATATTGTTTGATAATTATAAATTTTGAATTTCAA
1 AAATTATATTGTTTGATAATT-TAAATTTT-AATTTCAA
** *
1807555 AAATTATA-TGTTTTTTAATTTTAATTTTAATTT
1 AAATTATATTGTTTGATAATTTAAATTTTAATTT
1807588 TATTAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 5 0.17
37 7 0.23
38 10 0.33
39 8 0.27
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.56
Consensus pattern (37 bp):
AAATTATATTGTTTGATAATTTAAATTTTAATTTCAA
Found at i:1807990 original size:3 final size:3
Alignment explanation
Indices: 1807982--1808055 Score: 69
Period size: 3 Copynumber: 24.7 Consensus size: 3
1807972 GACTTTAAAA
* * *
1807982 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TGT TGT TGA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
* * * *
1808027 TGT TAA AAT TTT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1808056 AACATATAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1808930 original size:17 final size:18
Alignment explanation
Indices: 1808910--1808951 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1808900 TTTATATAAA
1808910 ATTTTAA-ATATTTATAT
1 ATTTTAACATATTTATAT
*
1808927 ATTTGAATCATATTTATAT
1 ATTTTAA-CATATTTATAT
*
1808946 TTTTTA
1 ATTTTA
1808952 TATTATGTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 6 0.30
19 14 0.70
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
ATTTTAACATATTTATAT
Found at i:1809168 original size:21 final size:21
Alignment explanation
Indices: 1809121--1809169 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1809111 GATCCGATAA
1809121 ATATATATTAATTAAATTTATT
1 ATAT-TATTAATTAAATTTATT
* *
1809143 TTATTATTAATTTAATTT-TT
1 ATATTATTAATTAAATTTATT
1809163 GATATTA
1 -ATATTA
1809170 AATATATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 18 0.78
22 3 0.13
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATATTATTAATTAAATTTATT
Found at i:1809393 original size:13 final size:13
Alignment explanation
Indices: 1809375--1809399 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1809365 TTTAAAAATA
1809375 TAAATAACAAAAG
1 TAAATAACAAAAG
1809388 TAAATAACAAAA
1 TAAATAACAAAA
1809400 AATAAAATCG
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:0.72, C:0.08, G:0.04, T:0.16
Consensus pattern (13 bp):
TAAATAACAAAAG
Found at i:1810469 original size:105 final size:105
Alignment explanation
Indices: 1810354--1810563 Score: 269
Period size: 105 Copynumber: 2.0 Consensus size: 105
1810344 ATTTATTCAA
* * * *
1810354 AAAAATTAAATTTTAACTCTCTTGAACTTATATCTTTTAAAAATTTATTAACAACATTAAATGCT
1 AAAAATTAAATTTAAACTCTCTTAAACTTATATCTTTTAAAAATCTAATAACAACATTAAATGCT
* *
1810419 ATTTGAATTAAAACTCAATT-AATATAAATTTTGATCAATT
66 ATTTGAATTAAAACTC-ATTCAATAAAAAATTTGATCAATT
* * * * *** *
1810459 AAAAATTAAATTTAAATTTTCTTAAATTTATATTTTTTAAAAATCTAATAACCGTATTAAATGTT
1 AAAAATTAAATTTAAACTCTCTTAAACTTATATCTTTTAAAAATCTAATAACAACATTAAATGCT
*
1810524 ATTTGAATTAAAATTCATTCAATAAAAAATTTGATCAATT
66 ATTTGAATTAAAACTCATTCAATAAAAAATTTGATCAATT
1810564 TAAACGTGAT
Statistics
Matches: 89, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
104 3 0.03
105 86 0.97
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (105 bp):
AAAAATTAAATTTAAACTCTCTTAAACTTATATCTTTTAAAAATCTAATAACAACATTAAATGCT
ATTTGAATTAAAACTCATTCAATAAAAAATTTGATCAATT
Found at i:1810485 original size:16 final size:15
Alignment explanation
Indices: 1810464--1810499 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1810454 CAATTAAAAA
1810464 TTAAATTTAAATTTT
1 TTAAATTTAAATTTT
*
1810479 CTTAAATTTATATTTT
1 -TTAAATTTAAATTTT
1810495 TTAAA
1 TTAAA
1810500 AATCTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAAATTTAAATTTT
Found at i:1811466 original size:2 final size:2
Alignment explanation
Indices: 1811455--1811495 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
1811445 AATTTATAAC
*
1811455 TA TA -A TA TA TA TA TA TA TA TA TA TT TA TA TA -A CTA 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
1811496 ACTATAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 31 0.91
3 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1811496 original size:10 final size:9
Alignment explanation
Indices: 1811455--1811501 Score: 51
Period size: 10 Copynumber: 5.0 Consensus size: 9
1811445 AATTTATAAC
1811455 TATAATATA
1 TATAATATA
1811464 TAT-ATATA
1 TATAATATA
*
1811472 TATATATTTA
1 TATA-ATATA
1811482 TATAACTATA
1 TATAA-TATA
1811492 TATAACTATA
1 TATAA-TATA
1811502 ATTAAAAGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 8 0.24
9 4 0.12
10 21 0.64
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (9 bp):
TATAATATA
Found at i:1814021 original size:23 final size:25
Alignment explanation
Indices: 1813987--1814046 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 25
1813977 ATAAACTGAA
1813987 AAAATAAA-TATTGAATTTATATT-
1 AAAATAAATTATTGAATTTATATTG
* * *
1814010 ATAA-AAATTATTTAATTTTTATTG
1 AAAATAAATTATTGAATTTATATTG
1814034 AAAATAAATTATT
1 AAAATAAATTATT
1814047 AAATAAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 3 0.10
23 16 0.53
24 3 0.10
25 8 0.27
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (25 bp):
AAAATAAATTATTGAATTTATATTG
Found at i:1815542 original size:17 final size:17
Alignment explanation
Indices: 1815520--1815581 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
1815510 TTCATATTTT
1815520 TTTATATCATATTATAA
1 TTTATATCATATTATAA
* *
1815537 TTTATATTATATTTTAA
1 TTTATATCATATTATAA
* *
1815554 -TTATTTTTATATTAT-A
1 TTTA-TATCATATTATAA
1815570 TTTATATCATAT
1 TTTATATCATAT
1815582 AATCTTACTA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
16 10 0.27
17 27 0.73
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTATATCATATTATAA
Found at i:1815556 original size:11 final size:12
Alignment explanation
Indices: 1815528--1815581 Score: 69
Period size: 11 Copynumber: 4.8 Consensus size: 12
1815518 TTTTTATATC
*
1815528 ATATTATAATTT
1 ATATTATATTTT
1815540 ATATTATATTTT
1 ATATTATATTTT
1815552 A-ATTAT-TTTT
1 ATATTATATTTT
1815562 ATATTATA-TTT
1 ATATTATATTTT
*
1815573 ATATCATAT
1 ATATTATAT
1815582 AATCTTACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
10 5 0.14
11 20 0.54
12 12 0.32
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:1815748 original size:17 final size:15
Alignment explanation
Indices: 1815688--1815743 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
1815678 ATGAATCCGA
* *
1815688 TAAATATATATTAAT
1 TAAATATATTTTTAT
*
1815703 TAAATTTA-TTTTAT
1 TAAATATATTTTTAT
*
1815717 TATTAATTTATTTTTAT
1 TA--AATATATTTTTAT
1815734 TAAATATATT
1 TAAATATATT
1815744 ATTTTTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 6 0.18
15 14 0.41
16 6 0.18
17 8 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TAAATATATTTTTAT
Found at i:1818837 original size:2 final size:2
Alignment explanation
Indices: 1818830--1818859 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1818820 GAAAATTGAT
1818830 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1818860 TATTTGTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1819692 original size:31 final size:31
Alignment explanation
Indices: 1819657--1819719 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
1819647 TTGTGATTTT
1819657 TTTTTTACATATTAAATTATAAATTTAATTA
1 TTTTTTACATATTAAATTATAAATTTAATTA
* *
1819688 TTTTTTAGATATTAAATTATATATTTAATTA
1 TTTTTTACATATTAAATTATAAATTTAATTA
1819719 T
1 T
1819720 AAGTCAGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (31 bp):
TTTTTTACATATTAAATTATAAATTTAATTA
Found at i:1822757 original size:18 final size:20
Alignment explanation
Indices: 1822736--1822772 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
1822726 ATCGTACTTA
1822736 AAATTATAA-AT-TTAATAT
1 AAATTATAATATATTAATAT
*
1822754 AAATTTTAATATATTAATA
1 AAATTATAATATATTAATA
1822773 ATTTATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 2 0.12
20 6 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATTATAATATATTAATAT
Found at i:1822773 original size:18 final size:18
Alignment explanation
Indices: 1822752--1822848 Score: 60
Period size: 18 Copynumber: 5.6 Consensus size: 18
1822742 TAAATTTAAT
1822752 ATAAATTTTAATATATTA
1 ATAAATTTTAATATATTA
1822770 AT-AA--TT--TATATTA
1 ATAAATTTTAATATATTA
* *
1822783 TATAAATTTTAAAATATTT
1 -ATAAATTTTAATATATTA
* * *
1822802 ATATATTTTATTATATTT
1 ATAAATTTTAATATATTA
* * *
1822820 ATATTATTTTTATATAATA
1 ATA-AATTTTAATATATTA
*
1822839 ATATATTTTA
1 ATAAATTTTA
1822849 TTTTTTATCA
Statistics
Matches: 62, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
13 7 0.11
14 2 0.03
15 4 0.06
17 4 0.06
18 26 0.42
19 19 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATAAATTTTAATATATTA
Found at i:1822812 original size:34 final size:32
Alignment explanation
Indices: 1822750--1822817 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 32
1822740 TATAAATTTA
*
1822750 ATATAAATTTTAATATATTAATAATTTATATT
1 ATATAAATTTTAAAATATTAATAATTTATATT
*
1822782 ATATAAATTTTAAAATATTTATATATTT-TATT
1 ATATAAATTTTAAAATATTAATA-ATTTATATT
1822814 ATAT
1 ATAT
1822818 TTATATTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 29 0.88
33 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
ATATAAATTTTAAAATATTAATAATTTATATT
Found at i:1822820 original size:43 final size:42
Alignment explanation
Indices: 1822740--1822826 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 42
1822730 TACTTAAAAT
1822740 TATAAATTTAATATAAATTTTAATATATTAATAATTTATATTA
1 TATAAATTT-ATATAAATTTTAATATATTAATAATTTATATTA
* *
1822783 TATAAATTT-TA-AAATATTTATATATTTTATTATATTTATATTA
1 TATAAATTTATATAAAT-TTTA-ATATATTAATA-ATTTATATTA
1822826 T
1 T
1822827 TTTTATATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
40 4 0.10
41 6 0.15
42 9 0.23
43 20 0.51
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (42 bp):
TATAAATTTATATAAATTTTAATATATTAATAATTTATATTA
Found at i:1822829 original size:37 final size:37
Alignment explanation
Indices: 1822775--1822850 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 37
1822765 TATTAATAAT
* *
1822775 TTATATTATATAAATTTTAAAATATTTATATATTTTA
1 TTATATTATATAAATTTTAAAATAATAATATATTTTA
* * *
1822812 TTATATT-TATATTATTTTTATATAATAATATATTTTA
1 TTATATTATATA-AATTTTAAAATAATAATATATTTTA
1822849 TT
1 TT
1822851 TTTTATCATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
36 4 0.12
37 29 0.88
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (37 bp):
TTATATTATATAAATTTTAAAATAATAATATATTTTA
Found at i:1823025 original size:22 final size:22
Alignment explanation
Indices: 1822997--1823039 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1822987 ATTTAATTAT
*
1822997 TATTTTAATTTT-TTATATTTAG
1 TATTTT-ATTTTATTAAATTTAG
1823019 TATTTTATTTTATTAAATTTA
1 TATTTTATTTTATTAAATTTA
1823040 AACAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTTTATTTTATTAAATTTAG
Found at i:1825190 original size:19 final size:21
Alignment explanation
Indices: 1825151--1825192 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
1825141 ATACAATAAA
1825151 TTTATATTAAAGATCATATTT
1 TTTATATTAAAGATCATATTT
*
1825172 TTTA-ATTAAATAT-ATATTT
1 TTTATATTAAAGATCATATTT
1825191 TT
1 TT
1825193 ATCAAGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 8 0.40
21 4 0.20
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTATATTAAAGATCATATTT
Found at i:1825243 original size:20 final size:20
Alignment explanation
Indices: 1825218--1825261 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1825208 TATTTAATAC
*
1825218 TTAATATTAAAATTATTTAT
1 TTAATATTAAAATTATTTAA
* *
1825238 TTAATATTTAAATTTTTTAA
1 TTAATATTAAAATTATTTAA
1825258 TTAA
1 TTAA
1825262 ATGATTCAAT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTAATATTAAAATTATTTAA
Found at i:1826555 original size:16 final size:16
Alignment explanation
Indices: 1826536--1826598 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
1826526 TTGATTGATC
*
1826536 TAAATTTAAAATTATT
1 TAAATTTAAAATAATT
* * *
1826552 TAAAATCAAAATAACT
1 TAAATTTAAAATAATT
1826568 TAAATTTAAAAATAATT
1 TAAATTT-AAAATAATT
*
1826585 TAATATTTTAAATA
1 TAA-ATTTAAAATA
1826599 TCTAAATTAA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
16 17 0.46
17 16 0.43
18 4 0.11
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAATTTAAAATAATT
Found at i:1826581 original size:17 final size:18
Alignment explanation
Indices: 1826559--1826592 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1826549 ATTTAAAATC
1826559 AAAATAACTTAA-ATTTA
1 AAAATAACTTAATATTTA
*
1826576 AAAATAATTTAATATTT
1 AAAATAACTTAATATTT
1826593 TAAATATCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATAACTTAATATTTA
Found at i:1826605 original size:33 final size:31
Alignment explanation
Indices: 1826533--1826606 Score: 76
Period size: 33 Copynumber: 2.3 Consensus size: 31
1826523 ATTTTGATTG
*
1826533 ATCTAAATTTAAAATTATTTAAAATCAAAAT
1 ATCTAAATTTAAAATAATTTAAAATCAAAAT
* * **
1826564 AACTTAAATTTAAAAATAATTTAATATTTTAAAT
1 ATC-TAAATTT-AAAATAATTTAA-AATCAAAAT
1826598 ATCTAAATT
1 ATCTAAATT
1826607 AACTCAACCT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
31 2 0.06
32 7 0.21
33 17 0.50
34 8 0.24
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (31 bp):
ATCTAAATTTAAAATAATTTAAAATCAAAAT
Found at i:1827281 original size:28 final size:28
Alignment explanation
Indices: 1827237--1827291 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1827227 TGTTTAATTT
*
1827237 TTTTTAATTAATTTTTATTTAATTTTAA
1 TTTTTAATTAATTTTTATATAATTTTAA
*
1827265 TTTTTAA-TATTTATTTATATAATTTTA
1 TTTTTAATTAATT-TTTATATAATTTTA
1827292 TCTGATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTTTAATTAATTTTTATATAATTTTAA
Found at i:1830330 original size:17 final size:18
Alignment explanation
Indices: 1830301--1830335 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1830291 TATTTTTTAT
*
1830301 AAAAATTATAAATTATAA
1 AAAAATTATAAATAATAA
1830319 AAAAATTA-AAATAATAA
1 AAAAATTATAAATAATAA
1830336 TAACAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAATTATAAATAATAA
Found at i:1831495 original size:2 final size:2
Alignment explanation
Indices: 1831488--1831522 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1831478 TTTTCTTCCT
* *
1831488 TA TA TA TA TA TA TA TA TA TA TA AA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1831523 TTCGTTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1835248 original size:16 final size:16
Alignment explanation
Indices: 1835227--1835267 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1835217 AAACTTTTTT
1835227 ATTTAAATTCAAATTGA
1 ATTTAAATTCAAATT-A
*
1835244 A-TTAAGTTCAAATTA
1 ATTTAAATTCAAATTA
1835259 ATTTAAATT
1 ATTTAAATT
1835268 TAAAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 2 0.10
16 18 0.86
17 1 0.05
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (16 bp):
ATTTAAATTCAAATTA
Found at i:1839772 original size:21 final size:21
Alignment explanation
Indices: 1839731--1839772 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1839721 AAAGACTTTC
* *
1839731 ATATTTTTATTTTATTATTTT
1 ATATTTTAATTTAATTATTTT
1839752 ATATTTTAAATTTAATT-TTTT
1 ATATTTT-AATTTAATTATTTT
1839773 CATAAATTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
ATATTTTAATTTAATTATTTT
Found at i:1840823 original size:21 final size:20
Alignment explanation
Indices: 1840787--1840826 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1840777 ATTAATGAAA
*
1840787 TTATTAAAATATTAAATAAG
1 TTATTAAAATAATAAATAAG
1840807 TTATTAATAATAATAAATAA
1 TTATTAA-AATAATAAATAA
1840827 AGATAAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
TTATTAAAATAATAAATAAG
Found at i:1841537 original size:2 final size:2
Alignment explanation
Indices: 1841530--1841573 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1841520 GAGTGTGCGT
1841530 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1841571 TA T
1 TA T
1841574 TCCAATTTGC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1842900 original size:18 final size:16
Alignment explanation
Indices: 1842877--1842910 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
1842867 CATTGGTGTA
1842877 CCTTATAGATTGAGTATT
1 CCTTATA-ATTG-GTATT
1842895 CCTTATAATTGGTATT
1 CCTTATAATTGGTATT
1842911 GTTTACTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 4 0.25
18 7 0.44
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (16 bp):
CCTTATAATTGGTATT
Found at i:1848582 original size:20 final size:21
Alignment explanation
Indices: 1848553--1848591 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1848543 AAATTTTTAT
*
1848553 TAAATTTTAAT-TAAAATATA
1 TAAATATTAATATAAAATATA
1848573 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
1848592 ATATTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:1849128 original size:31 final size:31
Alignment explanation
Indices: 1849093--1849154 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
1849083 TTAAATATTA
*
1849093 AAATTTATATATT-TTATAATTA-AATTTAAAT
1 AAATTT-TATATTATTA-AATAATAATTTAAAT
*
1849124 AAATTTTTTATTATTAAATAATAATTTAAAT
1 AAATTTTATATTATTAAATAATAATTTAAAT
1849155 TTAATCACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
AAATTTTATATTATTAAATAATAATTTAAAT
Found at i:1851155 original size:38 final size:37
Alignment explanation
Indices: 1851089--1851164 Score: 93
Period size: 37 Copynumber: 2.0 Consensus size: 37
1851079 AAAATAAATT
**
1851089 TTATAATTTAAATATTTATATATTTTATATCTTATAA
1 TTATAATTTAAATATTTATATATTTTATAAATTATAA
1851126 TTAT-ATTTAAAATATTT-TATATTTATTATAAATTATAA
1 TTATAATTT-AAATATTTATATA-TT-TTATAAATTATAA
1851164 T
1 T
1851165 ACGTTAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 8 0.24
37 14 0.41
38 12 0.35
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (37 bp):
TTATAATTTAAATATTTATATATTTTATAAATTATAA
Found at i:1853124 original size:38 final size:39
Alignment explanation
Indices: 1853082--1853158 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
1853072 GTAATAATAA
* *
1853082 TAATAATAAT-ACTAAAAGG-AAAAGAAAGGAAAGGAAAT
1 TAATAA-AATAACTAAAAGGAAAAAGAAAAGAAAGCAAAT
* *
1853120 TAATAAAATAACTCAATGGAAAAAGAAAAGAAAGCAAAT
1 TAATAAAATAACTAAAAGGAAAAAGAAAAGAAAGCAAAT
1853159 GTGTATTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 3 0.09
38 13 0.39
39 17 0.52
ACGTcount: A:0.64, C:0.05, G:0.16, T:0.16
Consensus pattern (39 bp):
TAATAAAATAACTAAAAGGAAAAAGAAAAGAAAGCAAAT
Found at i:1854111 original size:15 final size:15
Alignment explanation
Indices: 1854091--1854120 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1854081 GAAACAACAA
1854091 ATAAAAATATATAAT
1 ATAAAAATATATAAT
*
1854106 ATAAAAATATTTAAT
1 ATAAAAATATATAAT
1854121 TATATGTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAAAAATATATAAT
Found at i:1854408 original size:21 final size:22
Alignment explanation
Indices: 1854384--1854436 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
1854374 AAAGAAAAAA
* *
1854384 AATAAAATATGATA-TAAAATT
1 AATAAAATATAAAATTAAAATT
*
1854405 AAT-AAATATAAAATTAATATT
1 AATAAAATATAAAATTAAAATT
1854426 AATATAAATAT
1 AATA-AAATAT
1854437 TTTTAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 8 0.31
21 12 0.46
23 6 0.23
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AATAAAATATAAAATTAAAATT
Found at i:1854415 original size:15 final size:16
Alignment explanation
Indices: 1854389--1854433 Score: 65
Period size: 15 Copynumber: 2.8 Consensus size: 16
1854379 AAAAAAATAA
*
1854389 AATATGATATAAAATT
1 AATATAATATAAAATT
1854405 AATA-AATATAAAATT
1 AATATAATATAAAATT
1854420 AATATTAATATAAA
1 AATA-TAATATAAA
1854434 TATTTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 14 0.54
16 4 0.15
17 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
AATATAATATAAAATT
Found at i:1854453 original size:10 final size:11
Alignment explanation
Indices: 1854388--1854453 Score: 50
Period size: 10 Copynumber: 6.3 Consensus size: 11
1854378 AAAAAAAATA
*
1854388 AAATATGATAT
1 AAATATTATAT
1854399 AAA-ATTA-AT
1 AAATATTATAT
* *
1854408 AAATATAAAAT
1 AAATATTATAT
*
1854419 TAATATTAATAT
1 AAATATT-ATAT
*
1854431 AAATATT-TTT
1 AAATATTATAT
1854441 AAAT-TTATAT
1 AAATATTATAT
1854451 AAA
1 AAA
1854454 ATAAATTATT
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
9 7 0.16
10 17 0.40
11 10 0.23
12 9 0.21
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
AAATATTATAT
Done.