Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 25 of 31
Found at i:5105472 original size:21 final size:21
Alignment explanation
Indices: 5105448--5105539 Score: 87
Period size: 21 Copynumber: 4.4 Consensus size: 21
5105438 AGGTTATCAT
5105448 AATTATATCAAAAATTATAAA
1 AATTATATCAAAAATTATAAA
* *
5105469 AATTATATTAAATATTACTAAA
1 AATTATATCAAAAATTA-TAAA
* * * *
5105491 ATTTACATCAAAAGTT-TTAA
1 AATTATATCAAAAATTATAAA
* * *
5105511 AATAATATAAAAAATTATCAA
1 AATTATATCAAAAATTATAAA
5105532 AATTATAT
1 AATTATAT
5105540 TAATATTATC
Statistics
Matches: 54, Mismatches: 15, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
20 14 0.26
21 25 0.46
22 15 0.28
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (21 bp):
AATTATATCAAAAATTATAAA
Found at i:5105574 original size:20 final size:20
Alignment explanation
Indices: 5105524--5105579 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
5105514 AATATAAAAA
*
5105524 ATTATCAAAATTATATTAAT
1 ATTATCACAATTATATTAAT
5105544 ATTATCACAATTATATTAAT
1 ATTATCACAATTATATTAAT
**
5105564 ATTATTGCAATTATAT
1 ATTATCACAATTATAT
5105580 CATAGGATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (20 bp):
ATTATCACAATTATATTAAT
Found at i:5105683 original size:20 final size:20
Alignment explanation
Indices: 5105655--5105697 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
5105645 ACGTTTGCCT
* *
5105655 AAATTATATGAAAAGTTATC
1 AAATCATATAAAAAGTTATC
5105675 AAATCATATAAAAAGTTATC
1 AAATCATATAAAAAGTTATC
5105695 AAA
1 AAA
5105698 ATGATAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (20 bp):
AAATCATATAAAAAGTTATC
Found at i:5105704 original size:19 final size:19
Alignment explanation
Indices: 5105660--5105706 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
5105650 TGCCTAAATT
*
5105660 ATATGAAAAGTTATCAAATC
1 ATATAAAAAGTTATCAAA-C
5105680 ATATAAAAAGTTATCAAA-
1 ATATAAAAAGTTATCAAAC
5105698 ATGATAAAA
1 AT-ATAAAA
5105707 TTATATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 2 0.08
19 6 0.24
20 17 0.68
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.28
Consensus pattern (19 bp):
ATATAAAAAGTTATCAAAC
Found at i:5105727 original size:21 final size:21
Alignment explanation
Indices: 5105691--5105921 Score: 125
Period size: 21 Copynumber: 11.1 Consensus size: 21
5105681 TATAAAAAGT
*
5105691 TATCAAAA-TGAT-AAAATTA
1 TATCAAAAGTTATCAAAATTA
* *
5105710 TATTAAAAGTTATCAAAATCA
1 TATCAAAAGTTATCAAAATTA
* *
5105731 TATCGAAAGTTATCAAAATCA
1 TATCAAAAGTTATCAAAATTA
*
5105752 TATCAATAA-TTA-CTAACATTA
1 TATCAA-AAGTTATC-AAAATTA
* * * *
5105773 TTTCAAACGTTACCAAATTTA
1 TATCAAAAGTTATCAAAATTA
*
5105794 TATCAAAAGTTATTAAAATTA
1 TATCAAAAGTTATCAAAATTA
* * ** * *
5105815 CATAAAAAAACTATTAAAATCA
1 TAT-CAAAAGTTATCAAAATTA
* * *
5105837 TA-CTAAAGGTTATGAAAATCA
1 TATC-AAAAGTTATCAAAATTA
** * *
5105858 TATCAACTGGTACCAAAATTA
1 TATCAAAAGTTATCAAAATTA
*
5105879 TATCAAATA-TTATTAAAATTA
1 TATCAAA-AGTTATCAAAATTA
* *
5105900 T-TCAAATGTTAACAAAATTA
1 TATCAAAAGTTATCAAAATTA
5105920 TA
1 TA
5105922 AGGTTATTAA
Statistics
Matches: 158, Mismatches: 42, Indels: 22
0.71 0.19 0.10
Matches are distributed among these distances:
19 7 0.04
20 21 0.13
21 111 0.70
22 19 0.12
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.33
Consensus pattern (21 bp):
TATCAAAAGTTATCAAAATTA
Found at i:5105906 original size:20 final size:21
Alignment explanation
Indices: 5105871--5105921 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
5105861 CAACTGGTAC
*
5105871 CAAAATTATATCAAATATTAT
1 CAAAATTATATCAAATATTAA
* *
5105892 TAAAATTAT-TCAAATGTTAA
1 CAAAATTATATCAAATATTAA
5105912 CAAAATTATA
1 CAAAATTATA
5105922 AGGTTATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (21 bp):
CAAAATTATATCAAATATTAA
Found at i:5105942 original size:19 final size:18
Alignment explanation
Indices: 5105913--5105951 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
5105903 AAATGTTAAC
5105913 AAAATTATAAGGTTATTA
1 AAAATTATAAGGTTATTA
5105931 AAAATGTATAAGGTTATTA
1 AAAAT-TATAAGGTTATTA
5105950 AA
1 AA
5105952 TTATTCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (18 bp):
AAAATTATAAGGTTATTA
Found at i:5109849 original size:20 final size:20
Alignment explanation
Indices: 5109826--5109867 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
5109816 CATTTCAAGC
* *
5109826 ATATATCGATTCATTCACTT
1 ATATATCGATACATTAACTT
5109846 ATATATCGATACATTAACTT
1 ATATATCGATACATTAACTT
5109866 AT
1 AT
5109868 TGTATCAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.43
Consensus pattern (20 bp):
ATATATCGATACATTAACTT
Found at i:5110686 original size:28 final size:28
Alignment explanation
Indices: 5110655--5110714 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 28
5110645 AATATGAGGT
5110655 ATTAAAATTAGTTAAG-ACTTTGTACTTC
1 ATTAAAATTAGTT-AGTACTTTGTACTTC
*
5110683 ATTAAAATTAGTTAGTATTTTGTACTTC
1 ATTAAAATTAGTTAGTACTTTGTACTTC
5110711 ATTA
1 ATTA
5110715 GTTGCTAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 2 0.07
28 28 0.93
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (28 bp):
ATTAAAATTAGTTAGTACTTTGTACTTC
Found at i:5110858 original size:29 final size:30
Alignment explanation
Indices: 5110824--5110892 Score: 51
Period size: 29 Copynumber: 2.4 Consensus size: 30
5110814 ATCGTTCTTA
5110824 AATTATAAATTTGATA-ATTTATATAT-TTAT
1 AATTAT-AATTT-ATATATTTATATATGTTAT
* *
5110854 -ATTATATTTATATATTTTTATAT--GTTAT
1 AATTATAATT-TATATATTTATATATGTTAT
5110882 AATTAT-ATTTA
1 AATTATAATTTA
5110893 AAGTTATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 11
0.70 0.07 0.24
Matches are distributed among these distances:
27 2 0.06
28 12 0.38
29 18 0.56
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (30 bp):
AATTATAATTTATATATTTATATATGTTAT
Found at i:5110906 original size:21 final size:21
Alignment explanation
Indices: 5110882--5110948 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
5110872 TATATGTTAT
5110882 AATTATATTTAAAGTTATTAA
1 AATTATATTTAAAGTTATTAA
* * *
5110903 AATTAT-TTAAAAAATTATAAA
1 AATTATATT-TAAAGTTATTAA
*
5110924 AATTATA-TTATAAGTTATTTA
1 AATTATATTTA-AAGTTATTAA
5110945 AATT
1 AATT
5110949 GCATCAAAGT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
20 3 0.08
21 33 0.92
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (21 bp):
AATTATATTTAAAGTTATTAA
Found at i:5112097 original size:14 final size:14
Alignment explanation
Indices: 5112078--5112126 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
5112068 ATTATTTTTG
5112078 TTATATATAAATAT
1 TTATATATAAATAT
*
5112092 TTATATATTAATAAT
1 TTATATATAAAT-AT
5112107 TTATTTTATATAAATAT
1 TTA---TATATAAATAT
5112124 TTA
1 TTA
5112127 CATGTTAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 11 0.38
15 5 0.17
17 5 0.17
18 8 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTATATATAAATAT
Found at i:5112116 original size:18 final size:18
Alignment explanation
Indices: 5112078--5112126 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 18
5112068 ATTATTTTTG
5112078 TTATATATAAATATTTA-
1 TTATATATAAATATTTAT
5112095 -TATAT-T-AATAATTTAT
1 TTATATATAAAT-ATTTAT
5112111 TT-TATATAAATATTTA
1 TTATATATAAATATTTA
5112127 CATGTTAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
14 3 0.11
15 6 0.22
16 8 0.30
17 7 0.26
18 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATATATAAATATTTAT
Found at i:5112466 original size:16 final size:17
Alignment explanation
Indices: 5112445--5112486 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
5112435 ATACGAATAC
5112445 ATAAATATATTAA-AAT
1 ATAAATATATTAAGAAT
*
5112461 ATAAATAAATTAAGAAT
1 ATAAATATATTAAGAAT
5112478 -TAACATATA
1 ATAA-ATATA
5112487 AAAATTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
ATAAATATATTAAGAAT
Found at i:5112730 original size:4 final size:4
Alignment explanation
Indices: 5112721--5112771 Score: 59
Period size: 4 Copynumber: 12.8 Consensus size: 4
5112711 TTTTTCTCTT
* * *
5112721 TTTC TTTC TTT- TTTT TTTCC TTCC TTTC TTCC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC TTTC
5112769 TTT
1 TTT
5112772 TTTTTTCAGC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
3 3 0.08
4 35 0.88
5 2 0.05
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:5112734 original size:12 final size:12
Alignment explanation
Indices: 5112713--5112775 Score: 56
Period size: 12 Copynumber: 4.9 Consensus size: 12
5112703 TATAAAATTT
*
5112713 TTTCTCTTTTTC
1 TTTCTTTTTTTC
5112725 TTTCTTTTTTT-
1 TTTCTTTTTTTC
5112736 TTTCCTTCCTTTCTTCC
1 TTT-CTT--TTT-TT-C
*
5112753 TTTCTTTCTTTC
1 TTTCTTTTTTTC
5112765 TTTCTTTTTTT
1 TTTCTTTTTTT
5112776 TTCAGCTGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
11 3 0.07
12 24 0.57
13 2 0.05
14 5 0.12
15 2 0.05
16 3 0.07
17 3 0.07
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTCTTTTTTTC
Found at i:5113625 original size:16 final size:17
Alignment explanation
Indices: 5113604--5113636 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
5113594 ATAGTTAATG
5113604 ATATTTTTAATT-TTTT
1 ATATTTTTAATTATTTT
5113620 ATATTTTTAATTATTTT
1 ATATTTTTAATTATTTT
5113637 TAATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
ATATTTTTAATTATTTT
Found at i:5113634 original size:10 final size:9
Alignment explanation
Indices: 5113604--5113641 Score: 53
Period size: 8 Copynumber: 4.3 Consensus size: 9
5113594 ATAGTTAATG
5113604 ATATTTTTA
1 ATATTTTTA
5113613 AT-TTTTT-
1 ATATTTTTA
5113620 ATATTTTTA
1 ATATTTTTA
5113629 ATTATTTTTA
1 A-TATTTTTA
5113639 ATA
1 ATA
5113642 AAAATTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
7 2 0.08
8 10 0.38
9 5 0.19
10 9 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATATTTTTA
Found at i:5113867 original size:19 final size:18
Alignment explanation
Indices: 5113835--5113873 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 18
5113825 ATATTACTTT
5113835 AAATATACAAAAAA-TAA
1 AAATATACAAAAAATTAA
5113852 AAATATGACAAAAAAATTAA
1 AAATAT-AC-AAAAAATTAA
5113872 AA
1 AA
5113874 CATAATGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 2 0.11
19 6 0.32
20 5 0.26
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (18 bp):
AAATATACAAAAAATTAA
Found at i:5114169 original size:12 final size:12
Alignment explanation
Indices: 5114152--5114212 Score: 58
Period size: 12 Copynumber: 5.4 Consensus size: 12
5114142 CAAAATATAC
5114152 ATATATATAAAA
1 ATATATATAAAA
5114164 ATATATATAAAA
1 ATATATATAAAA
*
5114176 A-AT-TAT--TA
1 ATATATATAAAA
*
5114184 ATATATAAAAAA
1 ATATATATAAAA
* *
5114196 ATTTATACAAAA
1 ATATATATAAAA
5114208 ATATA
1 ATATA
5114213 ATATTTTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
8 2 0.05
9 2 0.05
10 5 0.13
11 2 0.05
12 28 0.72
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (12 bp):
ATATATATAAAA
Found at i:5114190 original size:30 final size:29
Alignment explanation
Indices: 5114143--5114216 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 29
5114133 TACATATGAC
5114143 AAAATATACATATATATAAAAATATATATA-A
1 AAAATATA-ATATATA-AAAAA-ATATATACA
*
5114174 AAAATTATTAATATATAAAAAAATTTATACA
1 AAAA-TA-TAATATATAAAAAAATATATACA
5114205 AAAATATAATAT
1 AAAATATAATAT
5114217 TTTAAATACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
29 6 0.15
30 8 0.21
31 14 0.36
32 9 0.23
33 2 0.05
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.34
Consensus pattern (29 bp):
AAAATATAATATATAAAAAAATATATACA
Found at i:5114285 original size:6 final size:6
Alignment explanation
Indices: 5114270--5114321 Score: 70
Period size: 6 Copynumber: 8.5 Consensus size: 6
5114260 TTTCTTATCC
*
5114270 TTTC-T TTTCTT TTTCTT TTTCTT TCTCTT TTTCTTT CTTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTC-TT -TTTCTT TTTCTT
5114319 TTT
1 TTT
5114322 ACTTATGTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
5 4 0.10
6 30 0.71
7 4 0.10
8 4 0.10
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTCTT
Found at i:5114440 original size:32 final size:32
Alignment explanation
Indices: 5114394--5114454 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
5114384 GTTTGTGTAG
*
5114394 TTAAAATTAGATAT-ATAGATGAATATAAAAAA
1 TTAAAATTAGATATAAAAGAT-AATATAAAAAA
5114426 TTAAAATATA-ATATAAAAGATAATATAAA
1 TTAAAAT-TAGATATAAAAGATAATATAAA
5114455 TATAATATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
32 19 0.73
33 7 0.27
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (32 bp):
TTAAAATTAGATATAAAAGATAATATAAAAAA
Found at i:5114456 original size:18 final size:20
Alignment explanation
Indices: 5114415--5114462 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 20
5114405 TATATAGATG
5114415 AATATAAAAAATTAAAATAT
1 AATATAAAAAATTAAAATAT
*
5114435 AATATAAAAGATAATATAAATAT
1 AATATAAAA-A-ATTA-AAATAT
5114458 AATAT
1 AATAT
5114463 GAATACATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 9 0.38
21 1 0.04
22 3 0.12
23 11 0.46
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
AATATAAAAAATTAAAATAT
Found at i:5114461 original size:11 final size:11
Alignment explanation
Indices: 5114429--5114467 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5114419 TAAAAAATTA
5114429 AAATATAATAT
1 AAATATAATAT
*
5114440 AAAAGATAATAT
1 -AAATATAATAT
5114452 AAATATAATAT
1 AAATATAATAT
*
5114463 GAATA
1 AAATA
5114468 CATAAATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (11 bp):
AAATATAATAT
Found at i:5114597 original size:11 final size:11
Alignment explanation
Indices: 5114568--5114677 Score: 52
Period size: 11 Copynumber: 10.2 Consensus size: 11
5114558 GATATTTATA
*
5114568 AAAAAT-ATTT
1 AAAAATAATAT
*
5114578 AAAATATAACAT
1 AAAA-ATAATAT
5114590 AAAAATAATAT
1 AAAAATAATAT
* *
5114601 ATATATAATAT
1 AAAAATAATAT
*
5114612 AAATAT-ATAT
1 AAAAATAATAT
* *
5114622 AAATAT-ACAT
1 AAAAATAATAT
*
5114632 -AAAATAAAAT
1 AAAAATAATAT
*
5114642 AAATTATTAATAT
1 AAA--AATAATAT
5114655 ATAAAA-AATAT
1 A-AAAATAATAT
*
5114666 ATAAA-AATAT
1 AAAAATAATAT
5114676 AA
1 AA
5114678 TATTTTAAAT
Statistics
Matches: 79, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
9 4 0.05
10 29 0.37
11 30 0.38
12 7 0.09
13 7 0.09
14 2 0.03
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAAATAATAT
Found at i:5114610 original size:27 final size:25
Alignment explanation
Indices: 5114580--5114680 Score: 67
Period size: 26 Copynumber: 3.8 Consensus size: 25
5114570 AAATATTTAA
*
5114580 AATATAACATAAAAATAATATATATAT
1 AATATAA-ATAAAAATAA-ATATACAT
* *
5114607 AATATAAATATATATAAATATACAT
1 AATATAAATAAAAATAAATATACAT
* * * * *
5114632 AAAATAAAATAAATTATTAATATATAA
1 AATAT-AAATAAA-AATAAATATACAT
* *
5114659 AAAATATATAAAAATATAATAT
1 AATATAAATAAAAATA-AATAT
5114681 TTTAAATATA
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
25 13 0.22
26 25 0.42
27 22 0.37
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (25 bp):
AATATAAATAAAAATAAATATACAT
Found at i:5114643 original size:20 final size:20
Alignment explanation
Indices: 5114579--5114645 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 20
5114569 AAAATATTTA
5114579 AAATATAACATAAAAATAATAT
1 AAATAT-ACAT-AAAATAATAT
*
5114601 ATATATA-ATATAAATATATAT
1 AAATATACATA-AAATA-ATAT
*
5114622 AAATATACATAAAATAAAAT
1 AAATATACATAAAATAATAT
5114642 AAAT
1 AAAT
5114646 TATTAATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.03
20 14 0.36
21 16 0.41
22 8 0.21
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATATACATAAAATAATAT
Found at i:5114689 original size:35 final size:38
Alignment explanation
Indices: 5114578--5114709 Score: 100
Period size: 37 Copynumber: 3.5 Consensus size: 38
5114568 AAAAATATTT
*
5114578 AAAATATAACATAAAAATAATATATATATAATATAAATATAT-A
1 AAAATAT-ACAT-AAAATAA-A-ATA-ATTAT-TAAATATATAA
*
5114621 TAAATATACATAAAATAAAATAAATTATT-AATATATAA
1 AAAATATACATAAAATAAAAT-AATTATTAAATATATAA
* *
5114659 AAAATATATA-AAAATATAAT-ATT-TTAAATATA-AA
1 AAAATATACATAAAATAAAATAATTATTAAATATATAA
5114693 AAAA-A-ACATAAATATAA
1 AAAATATACATAAA-ATAA
5114710 GTACATAAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
32 2 0.03
33 4 0.05
34 11 0.14
35 9 0.12
37 16 0.21
38 10 0.13
39 6 0.08
40 2 0.03
41 7 0.09
42 4 0.05
43 6 0.08
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (38 bp):
AAAATATACATAAAATAAAATAATTATTAAATATATAA
Found at i:5114706 original size:32 final size:34
Alignment explanation
Indices: 5114616--5114709 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 34
5114606 TAATATAAAT
5114616 ATATATAAATATACATAAA-ATAAA-ATAAATTATTA
1 ATATATAAA-A-A-ATAAACATAAATATAAATTATTA
* * *
5114651 ATATATAAAAAATATATAAAAATATAATATT-TTA
1 ATATATAAAAAATAAACATAAATATAA-ATTATTA
5114685 A-ATATAAAAAA-AAACATAAATATAA
1 ATATATAAAAAATAAACATAAATATAA
5114710 GTACATAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
32 15 0.29
33 15 0.29
34 9 0.18
35 12 0.24
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (34 bp):
ATATATAAAAAATAAACATAAATATAAATTATTA
Found at i:5114732 original size:4 final size:4
Alignment explanation
Indices: 5114725--5114761 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
5114715 TAAATTTTTT
*
5114725 TTTC TTTC TTTC TTT- TTTC TTTC -TTC CTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
5114762 TATCAGCTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
3 6 0.20
4 24 0.80
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:5114742 original size:15 final size:15
Alignment explanation
Indices: 5114722--5114761 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
5114712 ACATAAATTT
*
5114722 TTTTTTCTTTCTTTC
1 TTTTTTCTTTCTTCC
5114737 TTTTTTCTTTCTTCC
1 TTTTTTCTTTCTTCC
*
5114752 TTCTTTCTTT
1 TTTTTTCTTT
5114762 TATCAGCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTCTTTCTTCC
Found at i:5114745 original size:11 final size:11
Alignment explanation
Indices: 5114729--5114762 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5114719 TTTTTTTTTC
5114729 TTTCTTTCTTT
1 TTTCTTTCTTT
*
5114740 TTTCTTTCTTC
1 TTTCTTTCTTT
*
5114751 CTTCTTTCTTT
1 TTTCTTTCTTT
5114762 T
1 T
5114763 ATCAGCTGAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTCTTTCTTT
Found at i:5114923 original size:16 final size:15
Alignment explanation
Indices: 5114900--5114984 Score: 74
Period size: 13 Copynumber: 6.0 Consensus size: 15
5114890 TTATAAATTT
5114900 TTTAATTAAATAAAA
1 TTTAATTAAATAAAA
5114915 TTATAATT-AATAAAA
1 TT-TAATTAAATAAAA
* *
5114930 TTTATTTAAA-AATA
1 TTTAATTAAATAAAA
5114944 TTTAA-TAAAT-AAA
1 TTTAATTAAATAAAA
**
5114957 TTTAA--AGTTAAAA
1 TTTAATTAAATAAAA
*
5114970 TTTAATTATATAAAA
1 TTTAATTAAATAAAA
5114985 AATTTATATA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
12 2 0.04
13 19 0.34
14 11 0.20
15 19 0.34
16 5 0.09
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (15 bp):
TTTAATTAAATAAAA
Found at i:5114996 original size:28 final size:27
Alignment explanation
Indices: 5114909--5114998 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 27
5114899 TTTTAATTAA
5114909 ATAAAATTATAATTAAT--AAAATTTAT
1 ATAAAATT-TAATTAATAAAAAATTTAT
* * * *
5114935 TTAAAA-ATATTTAATAAATAAATTTAA
1 ATAAAATTTAATTAATAAA-AAATTTAT
5114962 AGTTAAAATTTAATTATATAAAAAATTTAT
1 A--TAAAATTTAATTA-ATAAAAAATTTAT
5114992 ATAAAAT
1 ATAAAAT
5114999 ATAAGATAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
24 7 0.14
26 6 0.12
27 7 0.14
28 6 0.12
29 5 0.10
30 13 0.27
31 5 0.10
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (27 bp):
ATAAAATTTAATTAATAAAAAATTTAT
Found at i:5115026 original size:17 final size:17
Alignment explanation
Indices: 5114993--5115026 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5114983 AAAATTTATA
*
5114993 TAAAATATAAGATAAAT
1 TAAAATATAAGACAAAT
*
5115010 TAAAATATAATACAAAT
1 TAAAATATAAGACAAAT
5115027 ACAATATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (17 bp):
TAAAATATAAGACAAAT
Found at i:5115035 original size:24 final size:24
Alignment explanation
Indices: 5115008--5115057 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
5114998 TATAAGATAA
*
5115008 ATTAAAATATAA-TACAAATACAAT
1 ATTAAAAAATAATTA-AAATACAAT
5115032 ATTAAAAAATAATTAAAATACAAT
1 ATTAAAAAATAATTAAAATACAAT
5115056 AT
1 AT
5115058 GGCACAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTAAAAAATAATTAAAATACAAT
Found at i:5116016 original size:4 final size:4
Alignment explanation
Indices: 5115972--5116035 Score: 60
Period size: 4 Copynumber: 16.5 Consensus size: 4
5115962 ACATAATTTT
* * * * *
5115972 TTTC TTTT TTTC TTTC CTT- TTTC TTTT TTTC -TCC TTCC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
5116018 TTTT TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TT
5116036 GACAGAAATA
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
3 4 0.08
4 44 0.92
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:5116951 original size:37 final size:36
Alignment explanation
Indices: 5116907--5117015 Score: 120
Period size: 37 Copynumber: 3.0 Consensus size: 36
5116897 ATGAATACCG
5116907 TACATATAAAAATATACATAAAATAAAATAAATTATT
1 TACATATAAAAATATACATAAAATAAAATAAATT-TT
* *
5116944 TATATATAAAAAATATACA-AAAATATAAT--A-TTT
1 TACATAT-AAAAATATACATAAAATAAAATAAATTTT
5116977 TACATATAAAAA-ATAACATAAATATAAATATAAATTTT
1 TACATATAAAAATAT-ACATAAA-ATAAA-ATAAATTTT
5117015 T
1 T
5117016 TCTTTTTTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
31 2 0.03
32 8 0.13
33 11 0.18
34 5 0.08
35 3 0.05
37 16 0.27
38 15 0.25
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.35
Consensus pattern (36 bp):
TACATATAAAAATATACATAAAATAAAATAAATTTT
Found at i:5117007 original size:33 final size:34
Alignment explanation
Indices: 5116924--5117008 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 34
5116914 AAAAATATAC
* *
5116924 ATAAAATAAA-ATAAAT-TATTTATATATAAAAA
1 ATAACATAAATATAAATATATTTACATATAAAAA
*
5116956 ATATACAAAAATAT-AATAT-TTTACATATAAAAA
1 ATA-ACATAAATATAAATATATTTACATATAAAAA
5116989 ATAACATAAATATAAATATA
1 ATAACATAAATATAAATATA
5117009 AATTTTTTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
32 12 0.27
33 29 0.66
34 3 0.07
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (34 bp):
ATAACATAAATATAAATATATTTACATATAAAAA
Found at i:5119047 original size:54 final size:55
Alignment explanation
Indices: 5118966--5119074 Score: 148
Period size: 54 Copynumber: 2.0 Consensus size: 55
5118956 TGTTATAAAT
* * * * *
5118966 GTGTAACTGTATCAATACTTATTCATTAACA-TGTTTAAAATATGATAATTTAAC
1 GTGTAAATATATCAATACATATCCATTAACACTGTTTAAAATACGATAATTTAAC
* *
5119020 GTGTAAATATATCGATACATATCCATTAACACTTTTTAAAATACGATAATTTAAC
1 GTGTAAATATATCAATACATATCCATTAACACTGTTTAAAATACGATAATTTAAC
5119075 ATATCATAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
54 26 0.55
55 21 0.45
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (55 bp):
GTGTAAATATATCAATACATATCCATTAACACTGTTTAAAATACGATAATTTAAC
Found at i:5119451 original size:16 final size:17
Alignment explanation
Indices: 5119432--5119476 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
5119422 TAAATTAATT
*
5119432 AAATTATAATTT-TAAA
1 AAATTATAATTTGAAAA
* *
5119448 AAATAATTATTTGAAAA
1 AAATTATAATTTGAAAA
5119465 AAATTATAATTT
1 AAATTATAATTT
5119477 AAACTCTTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AAATTATAATTTGAAAA
Found at i:5119476 original size:17 final size:16
Alignment explanation
Indices: 5119432--5119479 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
5119422 TAAATTAATT
*
5119432 AAATTATAATTTTAAA
1 AAATTATAATTTAAAA
* *
5119448 AAATAATTATTTGAAAA
1 AAATTATAATTT-AAAA
5119465 AAATTATAATTTAAA
1 AAATTATAATTTAAA
5119480 CTCTTAAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AAATTATAATTTAAAA
Found at i:5119939 original size:10 final size:10
Alignment explanation
Indices: 5119906--5119943 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
5119896 CACCTGACAA
5119906 TTATATATTT
1 TTATATATTT
* *
5119916 ATAT-TATAT
1 TTATATATTT
5119925 TTATATATTT
1 TTATATATTT
5119935 TTATATATT
1 TTATATATT
5119944 AATCATGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATATATTT
Found at i:5120428 original size:21 final size:25
Alignment explanation
Indices: 5120380--5120427 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5120370 TTTATTAAAA
*
5120380 ATTTTTAAATAAATTACATAATTAT
1 ATTTTTAAATAAAATACATAATTAT
5120405 ATTTTTAAATAAAATA-A-AATTAT
1 ATTTTTAAATAAAATACATAATTAT
5120428 TGAATTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.27
24 1 0.05
25 15 0.68
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
ATTTTTAAATAAAATACATAATTAT
Found at i:5120744 original size:13 final size:14
Alignment explanation
Indices: 5120720--5120755 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5120710 ATATAAATAG
5120720 AAATTATTTTATTA-
1 AAATT-TTTTATTAC
5120734 AAATTTTTTATTAC
1 AAATTTTTTATTAC
5120748 AAATTTTT
1 AAATTTTT
5120756 GATTTTGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (14 bp):
AAATTTTTTATTAC
Found at i:5121028 original size:26 final size:26
Alignment explanation
Indices: 5120997--5121047 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
5120987 TTTTTTAAAC
* *
5120997 TTTATAAGTATAATTTAAATTATATA
1 TTTATAAATATAATTTAAAATATATA
*
5121023 TTTATAAATATATTTTAAAATATAT
1 TTTATAAATATAATTTAAAATATAT
5121048 GTCAATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
TTTATAAATATAATTTAAAATATATA
Found at i:5121034 original size:14 final size:13
Alignment explanation
Indices: 5121005--5121047 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
5120995 ACTTTATAAG
*
5121005 TATA-ATTTAAAT
1 TATATATTTAAAA
5121017 TATATATTTATAAA
1 TATATATTTA-AAA
5121031 TATAT-TTTAAAA
1 TATATATTTAAAA
5121043 TATAT
1 TATAT
5121048 GTCAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 12 0.43
13 9 0.32
14 7 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TATATATTTAAAA
Found at i:5121825 original size:34 final size:34
Alignment explanation
Indices: 5121759--5121943 Score: 255
Period size: 34 Copynumber: 5.5 Consensus size: 34
5121749 TAATAAAACT
* *
5121759 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
5121792 ATTGTTGACTAAATGGAAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
5121826 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
5121860 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
5121894 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
5121928 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
5121944 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 19, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 13 0.10
34 119 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:5122304 original size:19 final size:19
Alignment explanation
Indices: 5122248--5122310 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
5122238 TGGTTGTCGA
**
5122248 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
5122267 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
5122286 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
5122305 GTTACT
1 GGTACT
5122311 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:5126442 original size:34 final size:34
Alignment explanation
Indices: 5126376--5126560 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
5126366 AAGTGGGAGA
* *
5126376 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
5126409 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
5126443 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
5126477 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
5126511 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
5126545 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
5126561 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:5128006 original size:18 final size:18
Alignment explanation
Indices: 5127985--5128019 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5127975 TAAGTATTAT
5127985 TTTTAATATTTTATGACA
1 TTTTAATATTTTATGACA
*
5128003 TTTTGATATTTTATGAC
1 TTTTAATATTTTATGAC
5128020 CTAATAAAAA
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:0.29, C:0.06, G:0.09, T:0.57
Consensus pattern (18 bp):
TTTTAATATTTTATGACA
Found at i:5129951 original size:20 final size:19
Alignment explanation
Indices: 5129926--5129970 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
5129916 ATTTAAATTA
* *
5129926 ATTTAATTAATTTATTATTT
1 ATTTAATAAAATTATT-TTT
5129946 ATTTAATAAAATTATTTTT
1 ATTTAATAAAATTATTTTT
5129965 ATTTAA
1 ATTTAA
5129971 ATTTAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTAATAAAATTATTTTT
Found at i:5129978 original size:20 final size:20
Alignment explanation
Indices: 5129926--5129978 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
5129916 ATTTAAATTA
5129926 ATTTAA-TTAATTTATTATTT
1 ATTTAATTTAA-TTATTATTT
**
5129946 ATTTAATAAAATTATT-TTT
1 ATTTAATTTAATTATTATTT
5129965 ATTTAAATTTAATT
1 ATTT-AATTTAATT
5129979 TTAAAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 7 0.26
20 18 0.67
21 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTAATTTAATTATTATTT
Found at i:5129988 original size:11 final size:11
Alignment explanation
Indices: 5129974--5129999 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5129964 TATTTAAATT
5129974 TAATTTTAAAA
1 TAATTTTAAAA
5129985 TAATTTTAAAA
1 TAATTTTAAAA
5129996 TAAT
1 TAAT
5130000 AAATCAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:5130501 original size:20 final size:20
Alignment explanation
Indices: 5130461--5130501 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5130451 AAAAGCAAAA
*
5130461 AAATAAAATTTATTAATTAT
1 AAATAAAATTTATAAATTAT
5130481 AAATAAAATTT-TAAATATAT
1 AAATAAAATTTATAAAT-TAT
5130501 A
1 A
5130502 TATATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATAAAATTTATAAATTAT
Found at i:5137379 original size:12 final size:13
Alignment explanation
Indices: 5137353--5137377 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5137343 TATTTCATAA
5137353 AAAAATTATTTTT
1 AAAAATTATTTTT
5137366 AAAAATTATTTT
1 AAAAATTATTTT
5137378 AATATTTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAAAATTATTTTT
Found at i:5137530 original size:31 final size:32
Alignment explanation
Indices: 5137495--5137560 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 32
5137485 GTAAAACATT
5137495 TTTCAAAAATAGAAATAAACA-AAAAAATTAA
1 TTTCAAAAATAGAAATAAACATAAAAAATTAA
* *
5137526 TTTCAAAAATAGAAATAAACATCAAAAATTTA
1 TTTCAAAAATAGAAATAAACATAAAAAATTAA
5137558 TTT
1 TTT
5137561 GATTCTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 21 0.66
32 11 0.34
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.29
Consensus pattern (32 bp):
TTTCAAAAATAGAAATAAACATAAAAAATTAA
Found at i:5138738 original size:16 final size:16
Alignment explanation
Indices: 5138717--5138812 Score: 99
Period size: 16 Copynumber: 6.0 Consensus size: 16
5138707 CAAGTTAATT
*
5138717 GTTCGAATCATTTCGG
1 GTTCGAATCATTTCGA
* *
5138733 GTTCGAATTATTTTGA
1 GTTCGAATCATTTCGA
5138749 GTTC-AAGTCATTTCGA
1 GTTCGAA-TCATTTCGA
*
5138765 GTTCGAATCAGTTTTGA
1 GTTCGAATCA-TTTCGA
5138782 -TTC-AGATCATTTCGA
1 GTTCGA-ATCATTTCGA
*
5138797 GTTCGAATTATTTCGA
1 GTTCGAATCATTTCGA
5138813 ATTTTGGGTT
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
15 8 0.12
16 50 0.76
17 8 0.12
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.42
Consensus pattern (16 bp):
GTTCGAATCATTTCGA
Found at i:5138769 original size:32 final size:31
Alignment explanation
Indices: 5138723--5138809 Score: 122
Period size: 32 Copynumber: 2.7 Consensus size: 31
5138713 AATTGTTCGA
*
5138723 ATCATTTCGGGTTCGAATTATTTTGAGTTCA-
1 ATCATTTCGAGTTCGAATTATTTTGA-TTCAG
*
5138754 AGTCATTTCGAGTTCGAATCAGTTTTGATTCAG
1 A-TCATTTCGAGTTCGAATTA-TTTTGATTCAG
5138787 ATCATTTCGAGTTCGAATTATTT
1 ATCATTTCGAGTTCGAATTATTT
5138810 CGAATTTTGG
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
31 4 0.08
32 39 0.78
33 7 0.14
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44
Consensus pattern (31 bp):
ATCATTTCGAGTTCGAATTATTTTGATTCAG
Found at i:5139204 original size:2 final size:2
Alignment explanation
Indices: 5139197--5139235 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
5139187 TGCTTGTGAA
*
5139197 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5139236 CTAAGATCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5145455 original size:20 final size:20
Alignment explanation
Indices: 5145430--5145467 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5145420 TTTTAAATAT
5145430 TTAATA-TTAATATATTTTCA
1 TTAATATTTAA-ATATTTTCA
5145450 TTAATATTTAAATATTTT
1 TTAATATTTAAATATTTT
5145468 TTATAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
TTAATATTTAAATATTTTCA
Found at i:5145845 original size:20 final size:20
Alignment explanation
Indices: 5145820--5145878 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
5145810 AATAAATATT
5145820 AAATATAATTATAAAAATAA
1 AAATATAATTATAAAAATAA
* *
5145840 AAATATCATAATAAAAAATTTAA
1 AAATATAATTAT-AAAAA--TAA
5145863 AAAT-TAATT-TAAAAAT
1 AAATATAATTATAAAAAT
5145879 CAAATAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 1 0.03
20 15 0.47
21 6 0.19
22 3 0.09
23 7 0.22
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATATAATTATAAAAATAA
Found at i:5147988 original size:171 final size:171
Alignment explanation
Indices: 5147703--5148045 Score: 686
Period size: 171 Copynumber: 2.0 Consensus size: 171
5147693 TCCCATGGCC
5147703 TGCCATTCTGCTTACTATGCCTCCTTTTCATCTTCACCATTGAAAGGCTTTGCTACCAAGAACTC
1 TGCCATTCTGCTTACTATGCCTCCTTTTCATCTTCACCATTGAAAGGCTTTGCTACCAAGAACTC
5147768 AAAATTTAGGCCTTTTCGGCTTTAGGTTTCTTCCATTCCCCACAGTGATAGAGCCTCCTATAACA
66 AAAATTTAGGCCTTTTCGGCTTTAGGTTTCTTCCATTCCCCACAGTGATAGAGCCTCCTATAACA
5147833 CCCTTGTCTCTGAGGTATATATTTATTTATTTGTCTTCCCT
131 CCCTTGTCTCTGAGGTATATATTTATTTATTTGTCTTCCCT
5147874 TGCCATTCTGCTTACTATGCCTCCTTTTCATCTTCACCATTGAAAGGCTTTGCTACCAAGAACTC
1 TGCCATTCTGCTTACTATGCCTCCTTTTCATCTTCACCATTGAAAGGCTTTGCTACCAAGAACTC
5147939 AAAATTTAGGCCTTTTCGGCTTTAGGTTTCTTCCATTCCCCACAGTGATAGAGCCTCCTATAACA
66 AAAATTTAGGCCTTTTCGGCTTTAGGTTTCTTCCATTCCCCACAGTGATAGAGCCTCCTATAACA
5148004 CCCTTGTCTCTGAGGTATATATTTATTTATTTGTCTTCCCT
131 CCCTTGTCTCTGAGGTATATATTTATTTATTTGTCTTCCCT
5148045 T
1 T
5148046 CATTTAGAAA
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
171 172 1.00
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.39
Consensus pattern (171 bp):
TGCCATTCTGCTTACTATGCCTCCTTTTCATCTTCACCATTGAAAGGCTTTGCTACCAAGAACTC
AAAATTTAGGCCTTTTCGGCTTTAGGTTTCTTCCATTCCCCACAGTGATAGAGCCTCCTATAACA
CCCTTGTCTCTGAGGTATATATTTATTTATTTGTCTTCCCT
Found at i:5148292 original size:57 final size:57
Alignment explanation
Indices: 5148204--5148319 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 57
5148194 AATTTGTTCA
*
5148204 TGCACCTTTGGCTCTCATTTGTTCATTCATTTTGACTTGCTGGGGCTTTGCTTAGAC
1 TGCACATTTGGCTCTCATTTGTTCATTCATTTTGACTTGCTGGGGCTTTGCTTAGAC
5148261 TGCACATTTGGCTCTCATTTGTTCATTCATTTTGACTTGCTGGGGCTTTGCTTAGAC
1 TGCACATTTGGCTCTCATTTGTTCATTCATTTTGACTTGCTGGGGCTTTGCTTAGAC
5148318 TG
1 TG
5148320 TTTTAAGATT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (57 bp):
TGCACATTTGGCTCTCATTTGTTCATTCATTTTGACTTGCTGGGGCTTTGCTTAGAC
Found at i:5151557 original size:24 final size:23
Alignment explanation
Indices: 5151486--5151561 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 23
5151476 ACATATTGAA
*
5151486 TATTGAATT-TATTGTTA-ATTTT
1 TATTAAATTATATT-TTATATTTT
*
5151508 TATATAAATTATAAATTTT-TAATTT
1 TAT-TAAATTAT--ATTTTATATTTT
5151533 TATTAAATTATATTATTATATTTT
1 TATTAAATTATATT-TTATATTTT
5151557 TATTA
1 TATTA
5151562 TTAATAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
22 6 0.14
23 7 0.16
24 19 0.43
25 9 0.20
26 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (23 bp):
TATTAAATTATATTTTATATTTT
Found at i:5151558 original size:30 final size:31
Alignment explanation
Indices: 5151522--5151585 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
5151512 TAAATTATAA
*
5151522 ATTTTTAATT-TTATTAAATTATA-TTA-TTAT
1 ATTTTT-ATTATTAATAAATTA-AGTTATTTAT
5151552 ATTTTTATTATTAATAAATTAAGTTATTTAT
1 ATTTTTATTATTAATAAATTAAGTTATTTAT
5151583 ATT
1 ATT
5151586 AATTATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 4 0.13
30 19 0.63
31 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (31 bp):
ATTTTTATTATTAATAAATTAAGTTATTTAT
Found at i:5151595 original size:23 final size:23
Alignment explanation
Indices: 5151555--5151604 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5151545 TTATTATATT
*
5151555 TTTATTATTAATAAATTAAGTTA
1 TTTATTATTAATAAATTAAGTAA
*
5151578 TTTA-TATTAATTATATTAAGTAA
1 TTTATTATTAA-TAAATTAAGTAA
5151601 TTTA
1 TTTA
5151605 ATATAAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
TTTATTATTAATAAATTAAGTAA
Found at i:5159607 original size:20 final size:20
Alignment explanation
Indices: 5159569--5159609 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5159559 GAAAAACAAG
*
5159569 AAAACCCAGAAGAGTAATCA
1 AAAACCCAGAAGAGAAATCA
5159589 AAAACCCAGAA-AGGAAATCA
1 AAAACCCAGAAGA-GAAATCA
5159609 A
1 A
5159610 CAAATTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.59, C:0.20, G:0.15, T:0.07
Consensus pattern (20 bp):
AAAACCCAGAAGAGAAATCA
Found at i:5162466 original size:2 final size:2
Alignment explanation
Indices: 5162459--5162483 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5162449 CAATAGAGTT
5162459 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 T
5162484 GAATGACAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5164321 original size:2 final size:2
Alignment explanation
Indices: 5164314--5164361 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
5164304 ATGTCTAACA
5164314 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
5164356 AT AT AT
1 AT AT AT
5164362 TAAAATCGGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5164612 original size:26 final size:26
Alignment explanation
Indices: 5164583--5164655 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
5164573 TATCGATCTA
*
5164583 AAATTTTTATTAATTTATAA-AATTTT
1 AAATTTTTATTAAATTA-AATAATTTT
* *
5164609 AAATATATATTAAATTAAATAATTTT
1 AAATTTTTATTAAATTAAATAATTTT
*
5164635 TAATTTTTAATTAAA-TAAATA
1 AAATTTTT-ATTAAATTAAATA
5164656 CAATTGATCG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 2 0.05
26 31 0.79
27 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
AAATTTTTATTAAATTAAATAATTTT
Found at i:5165139 original size:27 final size:26
Alignment explanation
Indices: 5165089--5165159 Score: 79
Period size: 27 Copynumber: 2.7 Consensus size: 26
5165079 AAAATTAGAT
* *
5165089 AATTTTTAAAAAAATGAATAATATAAT
1 AATTTTTAAAAATAT-AATAATATAAA
* *
5165116 TATTTTTAAAAATATATATTATATAAA
1 AATTTTTAAAAATATA-ATAATATAAA
*
5165143 AAATTTTAAAAATATAA
1 AATTTTTAAAAATATAA
5165160 GACACATGCA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
26 2 0.05
27 35 0.95
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (26 bp):
AATTTTTAAAAATATAATAATATAAA
Found at i:5165275 original size:168 final size:167
Alignment explanation
Indices: 5164992--5165327 Score: 636
Period size: 168 Copynumber: 2.0 Consensus size: 167
5164982 AATTATTACT
*
5164992 AGACACATGCACAACAAGAACTTAGGCCAAGAAATATATATTTTTAAAAGAAAAAAATTTATATA
1 AGACACATGCACAACAAGAACTTAGGCCAAGAAATATATATTCTTAAAAGAAAAAAATTTATATA
5165057 CATGTGATTTATTTTTTAATAAAAAATTAGATAATTTTTAAAAAAATGAATAATATAATTATTTT
66 CATGTGATTTATTTTTTAATAAAAAATTAGATAATTTTTAAAAAAATGAATAATATAATTATTTT
5165122 TAAAAATATATATTATATAAAAAATTTTAAAAATATA
131 TAAAAATATATATTATATAAAAAATTTTAAAAATATA
5165159 AGACACATGCACAACAAGAACTTAGGCCAAGAAATATATATTCTTAAAAGAAAAAAATTTATATA
1 AGACACATGCACAACAAGAACTTAGGCCAAGAAATATATATTCTTAAAAGAAAAAAATTTATATA
* *
5165224 CTTGTGATTTATTTTTTTAATAAAAAATTAGATAATTTTTTAAAAAATGAATAATATAATTATTT
66 CATGTGATTTA-TTTTTTAATAAAAAATTAGATAATTTTTAAAAAAATGAATAATATAATTATTT
5165289 TTAAAAATATATATTATATAAAAAATTTTAAAAATATA
130 TTAAAAATATATATTATATAAAAAATTTTAAAAATATA
5165327 A
1 A
5165328 ATATTATTAA
Statistics
Matches: 165, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
167 74 0.45
168 91 0.55
ACGTcount: A:0.51, C:0.06, G:0.07, T:0.36
Consensus pattern (167 bp):
AGACACATGCACAACAAGAACTTAGGCCAAGAAATATATATTCTTAAAAGAAAAAAATTTATATA
CATGTGATTTATTTTTTAATAAAAAATTAGATAATTTTTAAAAAAATGAATAATATAATTATTTT
TAAAAATATATATTATATAAAAAATTTTAAAAATATA
Found at i:5165307 original size:27 final size:26
Alignment explanation
Indices: 5165260--5165327 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 26
5165250 ATTAGATAAT
**
5165260 TTTTTAAAAA-ATGAATAATATAATTA
1 TTTTTAAAAATAT-AATAATATAAAAA
*
5165286 TTTTTAAAAATATATATTATATAAAAA
1 TTTTTAAAAATATA-ATAATATAAAAA
*
5165313 ATTTTAAAAATATAA
1 TTTTTAAAAATATAA
5165328 ATATTATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 12 0.33
27 24 0.67
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (26 bp):
TTTTTAAAAATATAATAATATAAAAA
Found at i:5165342 original size:27 final size:26
Alignment explanation
Indices: 5165261--5165342 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 26
5165251 TTAGATAATT
* *
5165261 TTTTAAAAA-ATGAATAATA-TAATTAT
1 TTTTAAAAATAT-AATATTATTAA-TAA
*
5165287 TTTTAAAAATAT-ATATTATATAAAAAA
1 TTTTAAAAATATAATATTAT-T-AATAA
5165314 TTTTAAAAATATAAATATTATTAATAA
1 TTTTAAAAATAT-AATATTATTAATAA
5165341 TT
1 TT
5165343 AATAATTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
25 5 0.11
26 9 0.20
27 22 0.48
28 3 0.07
29 7 0.15
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (26 bp):
TTTTAAAAATATAATATTATTAATAA
Found at i:5166136 original size:20 final size:20
Alignment explanation
Indices: 5166113--5166168 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
5166103 ATTTTATTTT
*
5166113 TTAAAAT-TTTATTTAAAATA
1 TTAAAATATTTATAT-AAATA
*
5166133 TTAATATATTTATATAAATA
1 TTAAAATATTTATATAAATA
*
5166153 TCAAAATATATTATAT
1 TTAAAATAT-TTATAT
5166169 TATATAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAAATATTTATATAAATA
Found at i:5166223 original size:19 final size:21
Alignment explanation
Indices: 5166172--5166223 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 21
5166162 ATTATATTAT
*
5166172 ATAATTTTTAACATGTTAATAA
1 ATAATTTTT-ATATGTTAATAA
5166194 ATTAA-TTTTATAT-TTAAT-A
1 A-TAATTTTTATATGTTAATAA
5166213 ATAATTTTTAT
1 ATAATTTTTAT
5166224 TGTATCATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 3 0.11
19 8 0.30
20 5 0.19
21 3 0.11
22 5 0.19
23 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
ATAATTTTTATATGTTAATAA
Found at i:5166241 original size:17 final size:18
Alignment explanation
Indices: 5166196--5166241 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
5166186 GTTAATAAAT
5166196 TAATTTTATATTTAATAA
1 TAATTTTATATTTAATAA
*
5166214 TAATTTT-TATTGT-ATCA
1 TAATTTTATATT-TAATAA
5166231 T-ATTTTATATT
1 TAATTTTATATT
5166242 ATATTTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 5 0.20
17 12 0.48
18 8 0.32
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
TAATTTTATATTTAATAA
Found at i:5167033 original size:2 final size:2
Alignment explanation
Indices: 5167026--5167070 Score: 51
Period size: 2 Copynumber: 23.5 Consensus size: 2
5167016 ATGATTATTT
*
5167026 TA TA TA TA TA TA TA TA TA TA TCA TA T- TA TA T- TA TA TT TA -A
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
5167066 TA TA T
1 TA TA T
5167071 TTTTTATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 3 0.08
2 32 0.86
3 2 0.05
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5167080 original size:16 final size:16
Alignment explanation
Indices: 5167048--5167091 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
5167038 TATATATATC
* *
5167048 ATATTATATTATATTT
1 ATATTATTTTTTATTT
5167064 A-ATATATTTTTTATTT
1 ATAT-TATTTTTTATTT
5167080 ATATTATTTTTT
1 ATATTATTTTTT
5167092 TTCGGATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 2 0.08
16 20 0.83
17 2 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATATTATTTTTTATTT
Found at i:5167641 original size:13 final size:15
Alignment explanation
Indices: 5167618--5167649 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
5167608 TGGCCAAAAA
5167618 AAAGAAAAAAAGGT-
1 AAAGAAAAAAAGGTG
5167632 AAAG-AAAAAAGGTG
1 AAAGAAAAAAAGGTG
5167646 AAAG
1 AAAG
5167650 GGTATCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (15 bp):
AAAGAAAAAAAGGTG
Found at i:5167945 original size:17 final size:17
Alignment explanation
Indices: 5167925--5167974 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
5167915 TTATTATATC
5167925 TTTAAATATATTTAATA
1 TTTAAATATATTTAATA
* *
5167942 TTTATATAGAATTT-ATA
1 TTTAAATA-TATTTAATA
5167959 TTTAAA-AT-TTTAATA
1 TTTAAATATATTTAATA
5167974 T
1 T
5167975 ATTTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 3 0.11
15 4 0.15
16 1 0.04
17 15 0.56
18 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTAAATATATTTAATA
Found at i:5169264 original size:24 final size:26
Alignment explanation
Indices: 5169236--5169288 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
5169226 TTATATAAAT
5169236 TATAATT-TTTAGTAAAT-TAAAAAA
1 TATAATTATTTAGTAAATGTAAAAAA
* *
5169260 TATAATTATTTATTTAATGTAAAAAA
1 TATAATTATTTAGTAAATGTAAAAAA
5169286 TAT
1 TAT
5169289 GTTAATCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.28
25 8 0.32
26 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (26 bp):
TATAATTATTTAGTAAATGTAAAAAA
Found at i:5170763 original size:22 final size:21
Alignment explanation
Indices: 5170713--5170763 Score: 50
Period size: 24 Copynumber: 2.3 Consensus size: 21
5170703 CTTATTATGG
5170713 AATTTATATTATAACATTAATT
1 AATTTATATTATAACATTAA-T
* *
5170735 ATATTATATATTACAA-TTTAAT
1 A-ATT-TATATTATAACATTAAT
5170757 AATTTAT
1 AATTTAT
5170764 TCATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 3 0.12
21 3 0.12
22 3 0.12
23 7 0.28
24 9 0.36
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTTATATTATAACATTAAT
Found at i:5171213 original size:4 final size:4
Alignment explanation
Indices: 5171196--5171228 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
5171186 CTAAAAACAC
*
5171196 AATT AATC AATT AATT AATT AATT AATT -ATT AA
1 AATT AATT AATT AATT AATT AATT AATT AATT AA
5171229 ATATACAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (4 bp):
AATT
Found at i:5171438 original size:21 final size:24
Alignment explanation
Indices: 5171413--5171457 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
5171403 TATTAGAATG
5171413 AAAA-TTATCTTTT-TTT-AAATA
1 AAAATTTATCTTTTATTTCAAATA
*
5171434 AAAATTTATTTTTTATTTCAAATA
1 AAAATTTATCTTTTATTTCAAATA
5171458 TTTATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 8 0.40
23 3 0.15
24 5 0.25
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
AAAATTTATCTTTTATTTCAAATA
Found at i:5171566 original size:24 final size:25
Alignment explanation
Indices: 5171507--5171566 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
5171497 TATCTTATTC
* *
5171507 ATTTAATATAATAAATAATTTTATAT
1 ATTTAA-ATAATAAATAATTTAAAAT
* * *
5171533 AATTATATAAT-AATTATTTAAAAT
1 ATTTAAATAATAAATAATTTAAAAT
5171557 ATTTAAATAA
1 ATTTAAATAA
5171567 ATATATAAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
24 18 0.67
25 5 0.19
26 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTTAAATAATAAATAATTTAAAAT
Found at i:5171674 original size:21 final size:21
Alignment explanation
Indices: 5171658--5171699 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5171648 TGTTATTGAT
5171658 TTTAATTTTATAATTATAATA
1 TTTAATTTTATAATTATAATA
* *
5171679 TTTAATTTTATTATTTTAATA
1 TTTAATTTTATAATTATAATA
5171700 AGTAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTAATTTTATAATTATAATA
Found at i:5175360 original size:16 final size:17
Alignment explanation
Indices: 5175322--5175363 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
5175312 ATATTATATG
5175322 AATAT-TTTATTTTTTA
1 AATATATTTATTTTTTA
*
5175338 AAAATATTTA-TTTTTA
1 AATATATTTATTTTTTA
*
5175354 TATATATTTA
1 AATATATTTA
5175364 AATATAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AATATATTTATTTTTTA
Found at i:5177074 original size:12 final size:12
Alignment explanation
Indices: 5177057--5177102 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
5177047 TCATATAATA
5177057 TTTATATTATTT
1 TTTATATTATTT
*
5177069 TTTATATTATAT
1 TTTATATTATTT
5177081 TTTA-ATTATTT
1 TTTATATTATTT
*
5177092 TGTATAATTAT
1 TTTAT-ATTAT
5177103 ACATATCCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
11 9 0.31
12 15 0.52
13 5 0.17
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:5177101 original size:24 final size:24
Alignment explanation
Indices: 5177049--5177103 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
5177039 TCATATATTC
* *
5177049 ATATAATA-TTTATATTATTTTTT
1 ATATTATATTTTATATTATTTTGT
5177072 ATATTATATTTTA-ATTATTTTGT
1 ATATTATATTTTATATTATTTTGT
5177095 ATAATTATA
1 AT-ATTATA
5177104 CATATCCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
ATATTATATTTTATATTATTTTGT
Found at i:5177611 original size:21 final size:20
Alignment explanation
Indices: 5177585--5177625 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
5177575 TTAAATCGAG
5177585 TAAATATTTTTAAATAAAATT
1 TAAATATTTTTAAA-AAAATT
*
5177606 TAAATATTTTTTAAAAAATT
1 TAAATATTTTTAAAAAAATT
5177626 AATATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAATATTTTTAAAAAAATT
Found at i:5178866 original size:32 final size:36
Alignment explanation
Indices: 5178805--5178879 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 36
5178795 TATACATAAA
*
5178805 ATAAATAAAATTTATATATTATATGTATATGAATA-T
1 ATAAATAAAATTTATATATTATATATATAT-AATACT
5178841 ATAAATAAAATTT-TATA-TA-A-ATATATAATACT
1 ATAAATAAAATTTATATATTATATATATATAATACT
*
5178873 TTAAATA
1 ATAAATA
5178880 GACAAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
31 4 0.11
32 12 0.33
33 1 0.03
34 2 0.06
35 4 0.11
36 13 0.36
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (36 bp):
ATAAATAAAATTTATATATTATATATATATAATACT
Found at i:5182913 original size:22 final size:24
Alignment explanation
Indices: 5182866--5182914 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
5182856 ATATTTTTTA
*
5182866 TTTTTTAAAACAAATAACGATCAT
1 TTTTTTAAAACAAATAACGATAAT
*
5182890 TTTTTTAAAA-AAA-AACG-TAAA
1 TTTTTTAAAACAAATAACGATAAT
5182911 TTTT
1 TTTT
5182915 AAACTTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 6 0.26
22 4 0.17
23 3 0.13
24 10 0.43
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (24 bp):
TTTTTTAAAACAAATAACGATAAT
Found at i:5183217 original size:34 final size:34
Alignment explanation
Indices: 5183145--5183217 Score: 78
Period size: 34 Copynumber: 2.1 Consensus size: 34
5183135 AATTCGTAAA
** * *
5183145 GAAAAAAAAAAAAAAAAAAAAAGGCATCAAGCAT
1 GAAAAAAAAAAAAAAAAAAAAAGAAATCAACCAC
5183179 GAAAAAAAAAAAAAAAACAAAAA-AAATC-ACCTAC
1 GAAAAAAAAAAAAAAAA-AAAAAGAAATCAACC-AC
5183213 GAAAA
1 GAAAA
5183218 CATTAGCTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
33 2 0.06
34 26 0.79
35 5 0.15
ACGTcount: A:0.75, C:0.11, G:0.08, T:0.05
Consensus pattern (34 bp):
GAAAAAAAAAAAAAAAAAAAAAGAAATCAACCAC
Found at i:5183497 original size:23 final size:24
Alignment explanation
Indices: 5183471--5183516 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5183461 GCCACTCCAT
*
5183471 TTCATATT-TTTTTTTCTTTTTTC
1 TTCATATTCTTTCTTTCTTTTTTC
*
5183494 TTCATCTTCTTTCTTTCTTTTTT
1 TTCATATTCTTTCTTTCTTTTTT
5183517 ACCTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (24 bp):
TTCATATTCTTTCTTTCTTTTTTC
Found at i:5184827 original size:32 final size:32
Alignment explanation
Indices: 5184778--5185251 Score: 745
Period size: 32 Copynumber: 14.8 Consensus size: 32
5184768 AAAATGGTGA
* * *
5184778 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
5184810 TTTTAAATGGGTTGCCACCGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * * *
5184842 TTTTAAATGGGTTGCCACCAACTTCTGGGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
**
5184874 TTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5184906 TTTGAAATGGGTTGCCACCTACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5184938 TTT-AGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGA-AATGGGTTGCCACCGACTTGTGTGGGC
*
5184970 TTTGAAATGGGTTGCCACCGACTTGTGTAGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5185002 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5185034 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5185066 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5185098 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
5185130 TTTGGAATGGGTTGTCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5185162 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5185194 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
5185226 TTTGAAATGGG-TGCCACAGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
5185252 GATTTAAAAG
Statistics
Matches: 415, Mismatches: 25, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
31 14 0.03
32 400 0.96
33 1 0.00
ACGTcount: A:0.16, C:0.19, G:0.34, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:5185268 original size:27 final size:27
Alignment explanation
Indices: 5185234--5186465 Score: 1951
Period size: 27 Copynumber: 45.0 Consensus size: 27
5185224 GCTTTGAAAT
* *
5185234 GGGTGCCACAGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5185261 GGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5185288 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5185315 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
5185343 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
5185371 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5185398 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5185425 AGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
** * *
5185452 GAATGCCACGAAGTTATGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5185479 GGGTGCCACGGAGTTGTGGTCTTAAACA
1 GGGTGCCACGGAGTTGTGGACTTAAA-A
*
5185507 GGGATGCCACAGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
5185535 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5185562 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5185589 AGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
5185616 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5185643 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
5185670 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
5185698 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5185725 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5185752 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5185779 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5185806 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5185833 GGGTGCCACGGAGTTATGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5185860 GGGTGCCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
5185888 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* *
5185916 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5185943 GGGTGCCACGGAATTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
5185971 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5185998 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5186025 GGGTGCCACGGAGTTGTGGTCTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
5186053 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5186080 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5186107 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5186134 GGGTGCCACGGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
5186161 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
5186189 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
5186216 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
* *
5186244 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
5186271 GGGTACCACGGAGTTGTGGATTTTAAAA
1 GGGTGCCACGGAGTTGTGGA-CTTAAAA
*
5186299 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5186326 GGGGTGCCACGGAGTTGTGGATTTTAAAA
1 -GGGTGCCACGGAGTTGTGGA-CTTAAAA
*
5186355 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
5186382 GGGTACCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
5186410 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
5186437 GGATGCCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
5186465 G
1 G
5186466 AAAATGCCAC
Statistics
Matches: 1119, Mismatches: 72, Indels: 27
0.92 0.06 0.02
Matches are distributed among these distances:
27 761 0.68
28 331 0.30
29 27 0.02
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:5187536 original size:15 final size:15
Alignment explanation
Indices: 5187516--5187545 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5187506 AGGGTGAAAA
5187516 GGTTTTTTTTTTTTT
1 GGTTTTTTTTTTTTT
5187531 GGTTTTTTTTTTTTT
1 GGTTTTTTTTTTTTT
5187546 TTTTAGGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (15 bp):
GGTTTTTTTTTTTTT
Found at i:5193765 original size:22 final size:24
Alignment explanation
Indices: 5193718--5193766 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
5193708 ATATTTTTTA
*
5193718 TTTTTTAAAACAAATAACGATCAT
1 TTTTTTAAAACAAATAACGATAAT
*
5193742 TTTTTTAAAA-AAA-AACG-TAAA
1 TTTTTTAAAACAAATAACGATAAT
5193763 TTTT
1 TTTT
5193767 AAACTTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 6 0.26
22 4 0.17
23 3 0.13
24 10 0.43
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (24 bp):
TTTTTTAAAACAAATAACGATAAT
Found at i:5194068 original size:34 final size:34
Alignment explanation
Indices: 5193995--5194068 Score: 80
Period size: 36 Copynumber: 2.1 Consensus size: 34
5193985 AATAATTCGT
* *
5193995 AAAAAAAAAAAAAAAAAAAAAAAGGCATCAAGCATG
1 AAAAAAAAAAAAAAAAAAAAAAA-G-ATCAACCACG
5194031 AAAAAAAAAAAAAAAACAAAAAAA-ATC-ACCTACG
1 AAAAAAAAAAAAAAAA-AAAAAAAGATCAACC-ACG
5194065 AAAA
1 AAAA
5194069 CATTAGCTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
33 2 0.06
34 9 0.26
36 16 0.47
37 7 0.21
ACGTcount: A:0.77, C:0.11, G:0.07, T:0.05
Consensus pattern (34 bp):
AAAAAAAAAAAAAAAAAAAAAAAGATCAACCACG
Found at i:5194348 original size:23 final size:24
Alignment explanation
Indices: 5194322--5194367 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5194312 GCCACTCCAT
*
5194322 TTCATATT-TTTTTTTCTTTTTTC
1 TTCATATTCTTTCTTTCTTTTTTC
*
5194345 TTCATCTTCTTTCTTTCTTTTTT
1 TTCATATTCTTTCTTTCTTTTTT
5194368 ACCTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (24 bp):
TTCATATTCTTTCTTTCTTTTTTC
Found at i:5195189 original size:1 final size:1
Alignment explanation
Indices: 5195183--5195240 Score: 53
Period size: 1 Copynumber: 58.0 Consensus size: 1
5195173 CCACTCAAAA
* ** * * * *
5195183 TTTTTTTTCTTTTTTTTTTTTTTTTTTTTCCTTTTTTATTATTATTATTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5195241 AAAAAAACGA
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.07, C:0.05, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:5198189 original size:28 final size:28
Alignment explanation
Indices: 5198157--5198212 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
5198147 AATTCATGAT
5198157 ATATAA-ATTTTAAAATATTTATATATTA
1 ATATAATA-TTTAAAATATTTATATATTA
* * *
5198185 ATATAATATTTATATTATTTTTATATTA
1 ATATAATATTTAAAATATTTATATATTA
5198213 TGTTTAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
ATATAATATTTAAAATATTTATATATTA
Found at i:5198211 original size:11 final size:11
Alignment explanation
Indices: 5198193--5198232 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
5198183 TAATATAATA
5198193 TTTATATTATT
1 TTTATATTATT
*
5198204 TTTATATTATG
1 TTTATATTATT
*
5198215 TTTAAATTATT
1 TTTATATTATT
5198226 TTT-TATT
1 TTTATATT
5198233 TTGTATAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
10 3 0.12
11 22 0.88
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (11 bp):
TTTATATTATT
Found at i:5199566 original size:17 final size:16
Alignment explanation
Indices: 5199546--5199577 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
5199536 TTTAACGCAT
5199546 AAAAAATTTATATAAAG
1 AAAAAA-TTATATAAAG
5199563 AAAAAATTATATAAA
1 AAAAAATTATATAAA
5199578 TTTAAAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (16 bp):
AAAAAATTATATAAAG
Found at i:5199937 original size:16 final size:16
Alignment explanation
Indices: 5199913--5199943 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5199903 TTATTAATAA
5199913 AAAAGTTTATATAAAT
1 AAAAGTTTATATAAAT
*
5199929 AAAATTTTATATAAA
1 AAAAGTTTATATAAA
5199944 AATATAATAC
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:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
AAAAGTTTATATAAAT
Found at i:5201195 original size:50 final size:49
Alignment explanation
Indices: 5201131--5201289 Score: 228
Period size: 50 Copynumber: 3.2 Consensus size: 49
5201121 TATACTTAGA
* * *
5201131 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTAAATAATT
1 GTCAACAATTATGGCCACCTC-CTCTATTGTCAAAGGTTGGTAAAGAATC
*
5201181 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCC-TCTATTGTCAAAGGTTGGTAAAGAATC
* * *
5201231 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGGATA
1 GTCAACAATTATGGCCACCT-CCTCTATTGTCAAAGGTTGGTAAAGAATC
5201281 GTCAACAAT
1 GTCAACAAT
5201290 GGCAACAACT
Statistics
Matches: 101, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
49 1 0.01
50 98 0.97
51 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (49 bp):
GTCAACAATTATGGCCACCTCCTCTATTGTCAAAGGTTGGTAAAGAATC
Found at i:5205742 original size:50 final size:50
Alignment explanation
Indices: 5205683--5205891 Score: 294
Period size: 50 Copynumber: 4.2 Consensus size: 50
5205673 TATACTTAGA
*
5205683 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTAAAAAATC
1 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATC
* * *
5205733 GTCAACAATAATGGTCACCTCTCTCTATTGTCAAAGGTTGGTGAATAATT
1 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATC
* * *
5205783 GTCAACAATTATGGTCACCTC-CTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATAATGGCCACCTCTC-TCTATTGTCAAAGGTTGGTGAAAAATC
* * ** *
5205833 GTCAATAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGGATA
1 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATC
5205883 GTCAACAAT
1 GTCAACAAT
5205892 GGCAACAACT
Statistics
Matches: 145, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
49 1 0.01
50 143 0.99
51 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (50 bp):
GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATC
Found at i:5211380 original size:32 final size:32
Alignment explanation
Indices: 5211344--5211408 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
5211334 AAATAATATA
*
5211344 TTTAA-AGATAAAAATTTACATTTAAAAAATTT
1 TTTAACAGA-AAAAATTAACATTTAAAAAATTT
* * *
5211376 TTTAACAGAAAGAGTTAATATTTAAAAAATTT
1 TTTAACAGAAAAAATTAACATTTAAAAAATTT
5211408 T
1 T
5211409 ATTTTAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 25 0.89
33 3 0.11
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (32 bp):
TTTAACAGAAAAAATTAACATTTAAAAAATTT
Found at i:5213974 original size:23 final size:23
Alignment explanation
Indices: 5213943--5214009 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
5213933 TATAATTTTG
* *
5213943 ATGATTTTTGATATAATTTTTTT
1 ATGACTTTTGATATAATTTTCTT
* *
5213966 ATTACTTTTGATATTATTTTCTT
1 ATGACTTTTGATATAATTTTCTT
**
5213989 ATGACTTATAAATATAATTTT
1 ATGACTT-TTGATATAATTTT
5214010 GTTTTGAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 25 0.71
24 10 0.29
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (23 bp):
ATGACTTTTGATATAATTTTCTT
Found at i:5214213 original size:21 final size:21
Alignment explanation
Indices: 5214189--5214350 Score: 71
Period size: 21 Copynumber: 7.7 Consensus size: 21
5214179 TAATAAATAT
5214189 ATAATTTTTTATATAATTTTG
1 ATAATTTTTTATATAATTTTG
* * **
5214210 ATAATTTTATGTATAGCTTTG
1 ATAATTTTTTATATAATTTTG
** * *
5214231 ATAATCATTGATATAATTTTA
1 ATAATTTTTTATATAATTTTG
* *
5214252 ATAA-CTTTTATA-ATTGATTTG
1 ATAATTTTTTATATAAT--TTTG
* **
5214273 GTAATTTTGAATATAATTTT-
1 ATAATTTTTTATATAATTTTG
* * *
5214293 AGTAACTTTTAAAATAAATTTT-
1 A-TAATTTTTTATAT-AATTTTG
* * *
5214315 ATTAACTTTTTATATGATTTCG
1 A-TAATTTTTTATATAATTTTG
*
5214337 ATAATTTTTAATAT
1 ATAATTTTTTATAT
5214351 GACTTTATTA
Statistics
Matches: 102, Mismatches: 32, Indels: 14
0.69 0.22 0.09
Matches are distributed among these distances:
19 2 0.02
20 6 0.06
21 68 0.67
22 24 0.24
23 2 0.02
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (21 bp):
ATAATTTTTTATATAATTTTG
Found at i:5214326 original size:23 final size:23
Alignment explanation
Indices: 5214241--5214324 Score: 79
Period size: 22 Copynumber: 3.9 Consensus size: 23
5214231 ATAATCATTG
* *
5214241 ATATAATTTTAATAACTTTTATA
1 ATATAATTTTAGTAACTTTTAAA
* * *
5214264 AT-TGA-TTTGGTAA-TTTT-GA
1 ATATAATTTTAGTAACTTTTAAA
5214283 ATATAATTTTAGTAACTTTTAAA
1 ATATAATTTTAGTAACTTTTAAA
*
5214306 ATA-AATTTTATTAACTTTT
1 ATATAATTTTAGTAACTTTT
5214325 TATATGATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
19 3 0.06
20 6 0.12
21 13 0.27
22 21 0.43
23 6 0.12
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (23 bp):
ATATAATTTTAGTAACTTTTAAA
Found at i:5214479 original size:20 final size:20
Alignment explanation
Indices: 5214443--5214521 Score: 68
Period size: 20 Copynumber: 3.8 Consensus size: 20
5214433 CTTTTGCATA
*
5214443 ATTTGAATAATTTTTTATGTG
1 ATTTTAATAA-TTTTTATGTG
*
5214464 ATTTTAATAATTTTTATATG
1 ATTTTAATAATTTTTATGTG
* * * *
5214484 ATTTTGATAGCTTTTGATGTA
1 ATTTTAATA-ATTTTTATGTG
5214505 ATTTGTTAATAATTTTT
1 A-TT-TTAATAATTTTT
5214522 GTGGTGTTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
20 17 0.38
21 17 0.38
22 6 0.13
23 5 0.11
ACGTcount: A:0.29, C:0.01, G:0.11, T:0.58
Consensus pattern (20 bp):
ATTTTAATAATTTTTATGTG
Found at i:5214549 original size:17 final size:18
Alignment explanation
Indices: 5214529--5214590 Score: 65
Period size: 17 Copynumber: 3.4 Consensus size: 18
5214519 TTTGTGGTGT
5214529 TATAATTGTT-TATTTAA
1 TATAATTGTTATATTTAA
5214546 TATAATTGTTTATATTATAA
1 TATAATTG-TTATATT-TAA
* *
5214566 TATAAGTT-TTGTAATTAA
1 TATAA-TTGTTATATTTAA
5214584 TATAATT
1 TATAATT
5214591 ATATTTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 10 0.26
18 10 0.26
19 9 0.23
20 8 0.21
21 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (18 bp):
TATAATTGTTATATTTAA
Found at i:5214600 original size:20 final size:19
Alignment explanation
Indices: 5214577--5214624 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
5214567 ATAAGTTTTG
5214577 TAATTAATATAATTATATTT
1 TAATT-ATATAATTATATTT
* *
5214597 TAATTATTTAA-TATAATT
1 TAATTATATAATTATATTT
*
5214615 TAATTGTATA
1 TAATTATATA
5214625 TAATAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 14 0.58
19 5 0.21
20 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
TAATTATATAATTATATTT
Found at i:5214631 original size:42 final size:39
Alignment explanation
Indices: 5214585--5214681 Score: 92
Period size: 39 Copynumber: 2.5 Consensus size: 39
5214575 TGTAATTAAT
*
5214585 ATAATTATATTTTAATTATTTAATATAATTTAATTGTATATA
1 ATAATTATATTTTAATTATTTAATATAA-TT-ATT-TATAAA
* * *
5214627 ATAA-TATA--ATAATAATTTAATATTATTATTTATAAA
1 ATAATTATATTTTAATTATTTAATATAATTATTTATAAA
* *
5214663 ATTATAATATTTTAATTAT
1 ATAATTATATTTTAATTAT
5214682 GACATCTTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
36 8 0.18
37 6 0.14
38 2 0.05
39 20 0.45
41 4 0.09
42 4 0.09
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (39 bp):
ATAATTATATTTTAATTATTTAATATAATTATTTATAAA
Found at i:5214670 original size:23 final size:22
Alignment explanation
Indices: 5214635--5214681 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
5214625 TAATAATATA
*
5214635 ATAATAATTTAATATTATTATTT
1 ATAATAATTTAATATT-TTAATT
5214658 ATAA-AATTATAATATTTTAATT
1 ATAATAATT-TAATATTTTAATT
5214680 AT
1 AT
5214682 GACATCTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATAATAATTTAATATTTTAATT
Found at i:5215563 original size:15 final size:15
Alignment explanation
Indices: 5215540--5215596 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
5215530 GTGTTTATAC
*
5215540 AAAAATATAAATTTT
1 AAAATTATAAATTTT
5215555 AAAATTATAAATATTT
1 AAAATTATAAAT-TTT
*
5215571 AATATT-TAAAATTTTT
1 AAAATTAT-AAA-TTTT
*
5215587 AAATTTATAA
1 AAAATTATAA
5215597 TAAATAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
15 12 0.35
16 20 0.59
17 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AAAATTATAAATTTT
Done.