Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold374
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: 461091
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 3 of 4
Found at i:309252 original size:23 final size:23
Alignment explanation
Indices: 309226--309274 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
309216 AAGTTTCATA
309226 ATAAA-ATATTAT-TATATAAATAT
1 ATAAATATATT-TCTAT-TAAATAT
309249 ATAAATATATTTCTATTAAATAT
1 ATAAATATATTTCTATTAAATAT
309272 ATA
1 ATA
309275 TTATCTGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
ATAAATATATTTCTATTAAATAT
Found at i:309449 original size:20 final size:22
Alignment explanation
Indices: 309424--309463 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
309414 ATTTTTAACG
*
309424 TAATCATGA-AAAAA-ATAAGA
1 TAATCAAGACAAAAACATAAGA
309444 TAATCAAGACAAAAACATAA
1 TAATCAAGACAAAAACATAA
309464 AGGTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 5 0.29
22 4 0.24
ACGTcount: A:0.65, C:0.10, G:0.07, T:0.17
Consensus pattern (22 bp):
TAATCAAGACAAAAACATAAGA
Found at i:309727 original size:16 final size:15
Alignment explanation
Indices: 309701--309739 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
309691 TGTGAAGTAT
309701 ATAATAAAATAATAAA
1 ATAA-AAAATAATAAA
*
309717 ATATAAAAATAATTAA
1 ATA-AAAAATAATAAA
309733 ATAAAAA
1 ATAAAAA
309740 TATATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 16 0.76
17 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
ATAAAAAATAATAAA
Found at i:313768 original size:3 final size:3
Alignment explanation
Indices: 313760--313792 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
313750 CATTATTGTT
*
313760 ATC ATC ATC ATC ATC ATC ATC CTC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
313793 TTGAAAGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:314106 original size:14 final size:14
Alignment explanation
Indices: 314089--314136 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
314079 ATTTATTTGA
314089 TTTATATAATT-ATT
1 TTTA-ATAATTAATT
*
314103 TTTAAAAATTAATT
1 TTTAATAATTAATT
*
314117 TTTAATAATTTAAAT
1 TTTAATAA-TTAATT
314132 TTTAA
1 TTTAA
314137 ATTTTAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 5 0.17
14 14 0.48
15 10 0.34
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTAATAATTAATT
Found at i:314129 original size:15 final size:14
Alignment explanation
Indices: 314096--314137 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
314086 TGATTTATAT
314096 AATT-ATTTTTAAA
1 AATTAATTTTTAAA
314109 AATTAATTTTTAATA
1 AATTAATTTTTAA-A
* *
314124 ATTTAAATTTTAAA
1 AATTAATTTTTAAA
314138 TTTTAATATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 9 0.36
15 12 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AATTAATTTTTAAA
Found at i:314154 original size:22 final size:22
Alignment explanation
Indices: 314111--314156 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
314101 TTTTTAAAAA
* *
314111 TTAATTTTTAATAATTTAAATT
1 TTAAATTTTAATAATCTAAATT
314133 TTAAATTTTAAT-ATCTATAATT
1 TTAAATTTTAATAATCTA-AATT
314155 TT
1 TT
314157 TTTATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTAAATTTTAATAATCTAAATT
Found at i:314157 original size:23 final size:21
Alignment explanation
Indices: 314123--314173 Score: 50
Period size: 23 Copynumber: 2.4 Consensus size: 21
314113 AATTTTTAAT
*
314123 AATT-TAAATTTTAAATTTTA
1 AATTATAATTTTTAAATTTTA
**
314143 ATATCTATAATTTTTTTATTTTA
1 A-AT-TATAATTTTTAAATTTTA
314166 AATTATAA
1 AATTATAA
314174 ACTATTCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.04
21 7 0.28
22 3 0.12
23 14 0.56
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTATAATTTTTAAATTTTA
Found at i:314454 original size:18 final size:17
Alignment explanation
Indices: 314428--314462 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
314418 ATAAGTGCAG
314428 AATAAAAATATATATTAA
1 AATAAAAATATAT-TTAA
*
314446 AATATAAATATATTTAA
1 AATAAAAATATATTTAA
314463 TAATTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AATAAAAATATATTTAA
Found at i:314508 original size:31 final size:34
Alignment explanation
Indices: 314460--314521 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 34
314450 TAAATATATT
314460 TAATAATTTTATAATTTTTA-TAAAT-TATAAAA
1 TAATAATTTTATAATTTTTATTAAATATATAAAA
*
314492 TAATATTTTTAT-ATTTTTATTAAATATATA
1 TAATAATTTTATAATTTTTATTAAATATATA
314522 TTAAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 7 0.26
32 16 0.59
33 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (34 bp):
TAATAATTTTATAATTTTTATTAAATATATAAAA
Found at i:315288 original size:22 final size:23
Alignment explanation
Indices: 315258--315303 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
315248 ACATATGATT
315258 ATATAAAAATA-ATAT-ATATAAA
1 ATATAAAAA-ACATATGATATAAA
*
315280 ATATTAAAAACATATGATATAAA
1 ATATAAAAAACATATGATATAAA
315303 A
1 A
315304 AAATTTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 12 0.57
23 8 0.38
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
ATATAAAAAACATATGATATAAA
Found at i:316618 original size:42 final size:40
Alignment explanation
Indices: 316541--316622 Score: 94
Period size: 44 Copynumber: 2.0 Consensus size: 40
316531 AAATAGTATT
* * *
316541 AAAATATATTTTTATTTTAATATTTATAATTAAATTTAAATA
1 AAAATATATTTTTATTTAAATAATTAT-ATCAAA-TTAAATA
316583 AAAATATATTTTATTATTTAAATAATTAT-TCAAATTAAAT
1 AAAATATA-TTT-TTATTTAAATAATTATATCAAATTAAAT
316623 TAAATTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
41 6 0.17
42 12 0.34
43 3 0.09
44 14 0.40
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (40 bp):
AAAATATATTTTTATTTAAATAATTATATCAAATTAAATA
Found at i:317585 original size:20 final size:22
Alignment explanation
Indices: 317560--317619 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 22
317550 AAGGCAATAC
317560 AAAATTTTTATATT-TTA-AAT
1 AAAATTTTTATATTATTATAAT
**
317580 AAAATTTAAATAATTATTATAAT
1 AAAATTTTTAT-ATTATTATAAT
317603 ATAATATTTTTATATTA
1 A-AA-ATTTTTATATTA
317620 AAAAAAGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 9 0.29
21 3 0.10
22 3 0.10
23 4 0.13
24 6 0.19
25 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AAAATTTTTATATTATTATAAT
Found at i:317695 original size:23 final size:23
Alignment explanation
Indices: 317669--317712 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
317659 ATATAATTAT
*
317669 TTTAAAAAATAATATTTAATAAA
1 TTTAAAAAATAAAATTTAATAAA
* *
317692 TTTAATAATTAAAATTTAATA
1 TTTAAAAAATAAAATTTAATA
317713 TTTATAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTAAAAAATAAAATTTAATAAA
Found at i:317706 original size:14 final size:14
Alignment explanation
Indices: 317689--317722 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
317679 AATATTTAAT
317689 AAATTTAATAATTA
1 AAATTTAATAATTA
*
317703 AAATTTAATATTTA
1 AAATTTAATAATTA
*
317717 TAATTT
1 AAATTT
317723 TTTAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATTTAATAATTA
Found at i:317721 original size:28 final size:27
Alignment explanation
Indices: 317678--317771 Score: 71
Period size: 28 Copynumber: 3.2 Consensus size: 27
317668 TTTTAAAAAA
317678 TAATATTTAATAAATTTAATAATTAAAATT
1 TAATATTT-AT-AATTT-ATAATTAAAATT
* * *
317708 TAATATTTATAATTTTTTAATTTAAATA
1 TAATATTTATAA-TTTATAATTAAAATT
* * *
317736 TGATATATATAATACTTATATTTAAAATTT
1 TAATATTTATAAT--TTATAATTAAAA-TT
317766 TAATAT
1 TAATAT
317772 ATTAACATAA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
27 1 0.02
28 21 0.42
29 14 0.28
30 14 0.28
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
TAATATTTATAATTTATAATTAAAATT
Found at i:319839 original size:19 final size:16
Alignment explanation
Indices: 319815--319857 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 16
319805 GAGTCAAATT
319815 TTAAATAAAATTTTAATAA
1 TTAAATAAAA-TTT-A-AA
*
319834 TTAAATTAAATTTAAA
1 TTAAATAAAATTTAAA
319850 TTAAATAA
1 TTAAATAA
319858 TAAAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 9 0.41
17 1 0.05
18 3 0.14
19 9 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAAATAAAATTTAAA
Found at i:319871 original size:30 final size:27
Alignment explanation
Indices: 319837--319916 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 27
319827 TTAATAATTA
319837 AATTAAATTTAAATTAAATAATAAAAAATT
1 AATT-AATTT-AATTAAATAATAAAAAA-T
*
319867 AATTAATTTTAATT--ATAA-AAATAAT
1 AATTAA-TTTAATTAAATAATAAAAAAT
*
319892 ATATTAATATAATTAAATAATAAAA
1 A-ATTAATTTAATTAAATAATAAAA
319917 TAAATATTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
25 8 0.19
26 10 0.24
27 8 0.19
28 3 0.07
29 6 0.14
30 7 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
AATTAATTTAATTAAATAATAAAAAAT
Found at i:319872 original size:24 final size:26
Alignment explanation
Indices: 319836--319916 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 26
319826 TTTAATAATT
319836 AAATTAAATTTAAATTAAATAATAAA
1 AAATTAAATTTAAATTAAATAATAAA
* * *
319862 AAATT-AA-TTAATTTTAATTATAAA
1 AAATTAAATTTAAATTAAATAATAAA
* *
319886 AATAATATATTAATATAATTAAATAATAAA
1 AA-ATTAAATT--TA-AATTAAATAATAAA
319916 A
1 A
319917 TAAATATTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
24 16 0.39
25 4 0.10
26 6 0.15
27 1 0.02
29 2 0.05
30 12 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
AAATTAAATTTAAATTAAATAATAAA
Found at i:319923 original size:30 final size:29
Alignment explanation
Indices: 319848--319939 Score: 88
Period size: 30 Copynumber: 3.3 Consensus size: 29
319838 ATTAAATTTA
*
319848 AATTAAATAATAAAAAATTA-ATTAAT-T
1 AATTAAATAATAAAAAAATATATTAATAT
*
319875 --TT-AATTATAAAAATAATATATTAATAT
1 AATTAAATAATAAAAA-AATATATTAATAT
*
319902 AATTAAATAATAAAATAAATAT-TTAAATAA
1 AATTAAATAATAAAA-AAATATATT-AATAT
319932 AATTAAAT
1 AATTAAAT
319940 TTAAATAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
24 10 0.19
25 5 0.09
26 6 0.11
27 1 0.02
29 4 0.08
30 26 0.49
31 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
AATTAAATAATAAAAAAATATATTAATAT
Found at i:319943 original size:16 final size:17
Alignment explanation
Indices: 319910--319952 Score: 70
Period size: 16 Copynumber: 2.6 Consensus size: 17
319900 ATAATTAAAT
*
319910 AATAAAATAAATATTTA
1 AATAAAATTAATATTTA
319927 AATAAAATTAA-ATTTA
1 AATAAAATTAATATTTA
319943 AATAAAATTA
1 AATAAAATTA
319953 TTTTAAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATAAAATTAATATTTA
Found at i:320523 original size:15 final size:15
Alignment explanation
Indices: 320505--320548 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
320495 AACCGATCAA
320505 AATTAATTTTAATTT
1 AATTAATTTTAATTT
* *
320520 AATTTATTTAAATTT
1 AATTAATTTTAATTT
* *
320535 GATAAATTTTAATT
1 AATTAATTTTAATT
320549 AAATAAATTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
AATTAATTTTAATTT
Found at i:322752 original size:2 final size:2
Alignment explanation
Indices: 322745--322771 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
322735 AAATATCGAT
322745 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
322772 TGACAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:323718 original size:8 final size:8
Alignment explanation
Indices: 323707--323819 Score: 52
Period size: 8 Copynumber: 13.2 Consensus size: 8
323697 ATTAAATATA
323707 ATATAAAT
1 ATATAAAT
323715 ATATAAAT
1 ATATAAAT
*
323723 ATTTTAAA-
1 A-TATAAAT
* *
323731 ATTTATAT
1 ATATAAAT
323739 AATATAAAT
1 -ATATAAAT
*
323748 -TATTAAT
1 ATATAAAT
323755 ATATTAAAATTT
1 ATA-T-AAA--T
323767 ATATAAAT
1 ATATAAAT
323775 ATA-AAAT
1 ATATAAAT
*
323782 ATTTTAAAT
1 A-TATAAAT
323791 ATAATTATAAT
1 AT-A-TA-AAT
*
323802 ATAAAAAT
1 ATATAAAT
*
323810 ATACAAAT
1 ATATAAAT
323818 AT
1 AT
323820 CTTATGAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 26
0.69 0.08 0.22
Matches are distributed among these distances:
7 16 0.20
8 30 0.37
9 18 0.22
10 8 0.10
11 6 0.07
12 4 0.05
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (8 bp):
ATATAAAT
Found at i:323742 original size:27 final size:27
Alignment explanation
Indices: 323707--323811 Score: 88
Period size: 32 Copynumber: 3.6 Consensus size: 27
323697 ATTAAATATA
323707 ATATAAATATATAAATATTTTAAAATTT
1 ATAT-AATATATAAATATTTTAAAATTT
*
323735 ATATAATATAAATTATTAATATATTAAAATTT
1 ATATAATAT--A-TA--AATATTTTAAAATTT
*
323767 ATATAA-ATATAAAATATTTT-AAATATA
1 ATATAATATAT-AAATATTTTAAAAT-TT
*
323794 ATTATAATATAAAAATAT
1 A-TATAATATATAAATAT
323812 ACAAATATCT
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
26 4 0.06
27 14 0.22
28 16 0.25
29 6 0.09
30 2 0.03
31 2 0.03
32 20 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
ATATAATATATAAATATTTTAAAATTT
Found at i:323744 original size:33 final size:33
Alignment explanation
Indices: 323702--323793 Score: 123
Period size: 32 Copynumber: 2.7 Consensus size: 33
323692 AAATAATTAA
*
323702 ATATAATATAAATATATAAATATTTTAAAATTT
1 ATATAATATAAATATATAAATATATTAAAATTT
*
323735 ATATAATATAAAT-TATTAATATATTAAAATTT
1 ATATAATATAAATATATAAATATATTAAAATTT
*
323767 ATATAAATATAAAATATTTTAAATATA
1 ATAT-AATAT-AAATA-TATAAATATA
323794 ATTATAATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
32 21 0.41
33 18 0.35
34 4 0.08
36 8 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
ATATAATATAAATATATAAATATATTAAAATTT
Found at i:323762 original size:32 final size:32
Alignment explanation
Indices: 323702--323784 Score: 121
Period size: 33 Copynumber: 2.5 Consensus size: 32
323692 AAATAATTAA
* *
323702 ATATAATATAAATATATAAATATTTTAAAATTT
1 ATATAATATAAAT-TATTAATATATTAAAATTT
323735 ATATAATATAAATTATTAATATATTAAAATTT
1 ATATAATATAAATTATTAATATATTAAAATTT
*
323767 ATATAAATATAAAATATT
1 ATAT-AATATAAATTATT
323785 TTAAATATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 21 0.46
33 25 0.54
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
ATATAATATAAATTATTAATATATTAAAATTT
Found at i:323777 original size:20 final size:19
Alignment explanation
Indices: 323701--323781 Score: 63
Period size: 18 Copynumber: 4.7 Consensus size: 19
323691 AAAATAATTA
* *
323701 AATATAATATAAATATATA-
1 AATATATTA-AAATTTATAT
*
323720 AATATTTTAAAATTTATAT
1 AATATATTAAAATTTATAT
323739 -A-ATA-T-AAA-TTAT-T
1 AATATATTAAAATTTATAT
323752 AATATATTAAAATTTATAT
1 AATATATTAAAATTTATAT
323771 AA-ATA-TAAAAT
1 AATATATTAAAAT
323782 ATTTTAAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
13 1 0.02
14 5 0.10
15 6 0.12
16 2 0.04
17 11 0.22
18 16 0.31
19 10 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATATATTAAAATTTATAT
Found at i:323804 original size:33 final size:33
Alignment explanation
Indices: 323703--323812 Score: 110
Period size: 33 Copynumber: 3.5 Consensus size: 33
323693 AATAATTAAA
*
323703 TATAATATAAATATATAAATATTTTAAAAT-TT
1 TATAATATAAATATATAAATATTTTAAAATAAT
* *
323735 ATATAATATAAAT-TATTAATATATT--AA-AAT
1 -TATAATATAAATATATAAATATTTTAAAATAAT
323765 T-T-ATATAAATATA-AAATATTTTAAATATAAT
1 TATAATATAAATATATAAATATTTTAAA-ATAAT
*
323796 TATAATATAAAAATATA
1 TATAATATAAATATATA
323813 CAAATATCTT
Statistics
Matches: 62, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
27 15 0.24
28 3 0.05
29 2 0.03
30 4 0.06
31 4 0.06
32 11 0.18
33 22 0.35
34 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
TATAATATAAATATATAAATATTTTAAAATAAT
Found at i:324203 original size:3 final size:3
Alignment explanation
Indices: 324195--324226 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
324185 AATTTTAATT
324195 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
324227 TTGATATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:324456 original size:20 final size:20
Alignment explanation
Indices: 324423--324475 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
324413 ATTTTATGGT
*
324423 TTATATTAATTTAATTAAAA
1 TTATATTAATTTAATAAAAA
324443 TTATAATTAA-TTAATAAAAA
1 TTAT-ATTAATTTAATAAAAA
324463 -TAT-TTAAATTTAA
1 TTATATT-AATTTAA
324476 ATTTAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 2 0.07
18 2 0.07
19 7 0.24
20 13 0.45
21 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATATTAATTTAATAAAAA
Found at i:324478 original size:28 final size:29
Alignment explanation
Indices: 324437--324493 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
324427 ATTAATTTAA
324437 TTAAAATTATAA-TTAATTAATAAAAATAT
1 TTAAAATTATAATTTAATT-ATAAAAATAT
*
324466 TTAAATTTA-AATTTAATTATAAAAATAT
1 TTAAAATTATAATTTAATTATAAAAATAT
324494 AATTATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 12 0.46
29 14 0.54
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
TTAAAATTATAATTTAATTATAAAAATAT
Found at i:324489 original size:47 final size:47
Alignment explanation
Indices: 324430--324526 Score: 119
Period size: 47 Copynumber: 2.1 Consensus size: 47
324420 GGTTTATATT
*
324430 AATTTAATTAAAATTATAATTAATT-AATAAA-AATATTTAA-ATTTA
1 AATTTAATTAAAAATATAATT-ATTAAATAAATAATATTTAATATTTA
* *
324475 AATTTAATTATAAAAATATAATTATTAAATAAATACTTTTTAATATTTA
1 AATTTAA-T-TAAAAATATAATTATTAAATAAATAATATTTAATATTTA
324524 AAT
1 AAT
324527 ATTTTTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
45 7 0.16
46 4 0.09
47 18 0.41
48 7 0.16
49 8 0.18
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (47 bp):
AATTTAATTAAAAATATAATTATTAAATAAATAATATTTAATATTTA
Found at i:324800 original size:24 final size:24
Alignment explanation
Indices: 324754--324800 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
324744 ATGAATTTTA
*
324754 AAATATTAATAATTTATTTTATTT
1 AAATATTAATAATTTATTGTATTT
*
324778 AAATTTTAATAACTTTA-TGTATT
1 AAATATTAATAA-TTTATTGTATT
324801 CAAGTTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
AAATATTAATAATTTATTGTATTT
Found at i:326244 original size:11 final size:11
Alignment explanation
Indices: 326228--326271 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
326218 ATTAAATTTA
*
326228 TATATTTGTAT
1 TATATTTATAT
326239 TATATTTATAT
1 TATATTTATAT
326250 TAT-TTTATATT
1 TATATTTATA-T
326261 TATATTT-TAT
1 TATATTTATAT
326271 T
1 T
326272 TTAAAAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 8 0.27
11 19 0.63
12 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (11 bp):
TATATTTATAT
Found at i:326245 original size:19 final size:17
Alignment explanation
Indices: 326236--326271 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
326226 TATATATTTG
326236 TATTATATTTATATTAT
1 TATTATATTTATATTAT
326253 T-TTATATTTATATT-T
1 TATTATATTTATATTAT
326268 TATT
1 TATT
326272 TTAAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 2 0.11
16 15 0.83
17 1 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTATATTTATATTAT
Found at i:326247 original size:6 final size:6
Alignment explanation
Indices: 326228--326272 Score: 53
Period size: 5 Copynumber: 8.2 Consensus size: 6
326218 ATTAAATTTA
*
326228 TATATT TGTA-T TATATT TATA-T TAT-TT TATATT TATATT T-TATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
326272 T
1 T
326273 TAAAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
5 17 0.50
6 17 0.50
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (6 bp):
TATATT
Found at i:327299 original size:25 final size:24
Alignment explanation
Indices: 327232--327305 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 24
327222 TTAAAGTACA
*
327232 TTTAAAATAAATAATAAAAAATTAATT
1 TTTAAAAT-AA-AATATAAAA-TAATT
*
327259 TTTAAAATAAAATATATAATAATAT
1 TTTAAAATAAAATATAAAATAAT-T
* **
327284 TTTAATATAATTTATAAAATAA
1 TTTAAAATAAAATATAAAATAA
327306 AAAAATTATT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
24 4 0.10
25 26 0.65
26 2 0.05
27 8 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TTTAAAATAAAATATAAAATAATT
Found at i:328377 original size:11 final size:12
Alignment explanation
Indices: 328348--328415 Score: 60
Period size: 11 Copynumber: 6.2 Consensus size: 12
328338 TAATTACTAT
328348 TTATAAAATTAA
1 TTATAAAATTAA
*
328360 --ATAAAATTTA
1 TTATAAAATTAA
328370 TT-TAAAATTAA
1 TTATAAAATTAA
328381 TTATAAAA-T-A
1 TTATAAAATTAA
328391 -TATAAATATTAA
1 TTATAAA-ATTAA
*
328403 -TATAAAAATAA
1 TTATAAAATTAA
328414 TT
1 TT
328416 TTTTAATATT
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
9 6 0.13
10 11 0.24
11 16 0.35
12 13 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TTATAAAATTAA
Found at i:328385 original size:33 final size:33
Alignment explanation
Indices: 328348--328415 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
328338 TAATTACTAT
* * *
328348 TTATAAAATTAAATAAA-ATTTATTTAAAATTAA
1 TTATAAAA-TAAATAAATATTAATATAAAAATAA
*
328381 TTATAAAATATATAAATATTAATATAAAAATAA
1 TTATAAAATAAATAAATATTAATATAAAAATAA
328414 TT
1 TT
328416 TTTTAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 7 0.23
33 23 0.77
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
TTATAAAATAAATAAATATTAATATAAAAATAA
Found at i:328396 original size:21 final size:21
Alignment explanation
Indices: 328349--328409 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
328339 AATTACTATT
328349 TATAAAATTAA-ATAAAATTTA
1 TATAAAATTAATATAAAA-TTA
*
328370 TTTAAAATTAATTATAAAA-TA
1 TATAAAATTAA-TATAAAATTA
328391 TATAAATATTAATATAAAA
1 TATAAA-ATTAATATAAAA
328410 ATAATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 24 0.69
22 5 0.14
23 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TATAAAATTAATATAAAATTA
Found at i:330069 original size:16 final size:16
Alignment explanation
Indices: 330030--330073 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
330020 ATCACCACTA
*
330030 TTTATT-ATTTAAATT
1 TTTATTAATATAAATT
330045 TAATTATTAATATAAATT
1 T--TTATTAATATAAATT
330063 TTTATTAATAT
1 TTTATTAATAT
330074 TTTAATACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 1 0.04
16 10 0.40
17 5 0.20
18 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTATTAATATAAATT
Found at i:330495 original size:21 final size:22
Alignment explanation
Indices: 330440--330502 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 22
330430 TAAATATTTG
330440 AATCTATTAAATTATTTTTCAAA
1 AATCTATTAAATTATTTTTC-AA
*
330463 AATACAAAATTAAATTATTTTTC-A
1 AAT-C--TATTAAATTATTTTTCAA
330487 AATCTATTAAATTATT
1 AATCTATTAAATTATT
330503 GTACATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
21 11 0.31
23 4 0.11
24 5 0.14
26 15 0.43
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (22 bp):
AATCTATTAAATTATTTTTCAA
Found at i:330866 original size:19 final size:20
Alignment explanation
Indices: 330822--330881 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 20
330812 AAATATTGAT
*
330822 ATAAAAT-TAATTTTTAATA
1 ATAAAATATAATTTTAAATA
* *
330841 CTTAAATAT-ATTTTAAATA
1 ATAAAATATAATTTTAAATA
*
330860 ATAAAATAAAATATTTAGAATA
1 ATAAAATATAAT-TTTA-AATA
330882 TGATCTTACC
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 20 0.65
20 3 0.10
21 4 0.13
22 4 0.13
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
ATAAAATATAATTTTAAATA
Found at i:332282 original size:179 final size:180
Alignment explanation
Indices: 331899--332450 Score: 697
Period size: 179 Copynumber: 3.0 Consensus size: 180
331889 AAGTCATAAT
*
331899 TTAGATATTTTTCCATCTTTAAGAGCTTTA-CTTTCCTTAATGAATGGTTTAAGTTTAGTAAGAG
1 TTAGATATTTTTCCATATTTAAGAGCTTTATC-TTCCTTAATGAATGGTTTAAGTTTAGTAAGAG
*
331963 TAATTTTAAATATTTATTTATTTATTTATTTT-GAAAAAATAAATTTTGAATTGAGCTCTTAGAA
65 TAATTTTAAATA--TA-TT-TTTATTTATTTTGGAAAAAATAAATTTTGAATTGAACTCTTAGAA
* * * **
332027 AAGAAAGATGACATTTATTTTTG-TTTTCATAAGTAATAACATGGTGACAATTT-TGG
126 AAGTAAGATAACATGTATTTTTGCTTTT-ATAAGT-ATAACATGGTGAC-ATTTCTTA
*
332083 TTAGATATTTTTCCATATTTAAGATCTTTATCTTCCTTAATGAATGGTTTAAGTTTAGTAAGAGT
1 TTAGATATTTTTCCATATTTAAGAGCTTTATCTTCCTTAATGAATGGTTTAAGTTTAGTAAGAGT
332148 AATTTTAAATA-A-TTTTATTTATTTTGGAAAAAATAAATTTTGAATTGAACTCTTAGAAAAGTA
66 AATTTTAAATATATTTTTATTTATTTTGGAAAAAATAAATTTTGAATTGAACTCTTAGAAAAGTA
*
332211 AGA-AAAATGTATTTTTGCTTTTATAAGTACTAACATGGTGACATTTCTTA
131 AGATAACATGTATTTTTGCTTTTATAAGTA-TAACATGGTGACATTTCTTA
* * * *
332261 TTCAGATATTTTTCCATATTTAAGAGCTTTATTTTCCTTAATTAATGATTTAATTTTAGTAAGAG
1 TT-AGATATTTTTCCATATTTAAGAGCTTTATCTTCCTTAATGAATGGTTTAAGTTTAGTAAGAG
* * * *
332326 TAATTTTACTAAATATTTATTTATTTTTTATTTTGAAAAAAAATAAA-TTTGAATTTAATTCTTA
65 TAA-TTT--TAAATA--TATTT-TTATTTATTTTG-GAAAAAATAAATTTTGAATTGAACTCTTA
* * * *
332390 GAATAGTAAGATACCATGTATTTTTGCTTTTATAAGCGATAACATGATGACATTTCTTA
123 GAAAAGTAAGATAACATGTATTTTTGCTTTTATAAG-TATAACATGGTGACATTTCTTA
332449 TT
1 TT
332451 TAGGACTCCT
Statistics
Matches: 328, Mismatches: 23, Indels: 30
0.86 0.06 0.08
Matches are distributed among these distances:
177 5 0.02
178 44 0.13
179 103 0.31
180 3 0.01
181 1 0.00
182 6 0.02
184 72 0.22
185 2 0.01
186 2 0.01
187 36 0.11
188 53 0.16
189 1 0.00
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (180 bp):
TTAGATATTTTTCCATATTTAAGAGCTTTATCTTCCTTAATGAATGGTTTAAGTTTAGTAAGAGT
AATTTTAAATATATTTTTATTTATTTTGGAAAAAATAAATTTTGAATTGAACTCTTAGAAAAGTA
AGATAACATGTATTTTTGCTTTTATAAGTATAACATGGTGACATTTCTTA
Found at i:335484 original size:2 final size:2
Alignment explanation
Indices: 335477--335537 Score: 86
Period size: 2 Copynumber: 30.5 Consensus size: 2
335467 TTTATAACTT
* * * *
335477 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA CA CA CA 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
335519 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
335538 GATTGAGAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:336044 original size:25 final size:27
Alignment explanation
Indices: 336016--336084 Score: 88
Period size: 25 Copynumber: 2.6 Consensus size: 27
336006 AAAATTATTT
* *
336016 TATTTAAATTTAATTTTAAAA-AAT-A
1 TATTTAAAATTAATATTAAAATAATAA
336041 TATTTAAAATTAATATTAAAATAATAA
1 TATTTAAAATTAATATTAAAATAATAA
* *
336068 TATTTTATATTAATATT
1 TATTTAAAATTAATATT
336085 TATATATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 19 0.50
26 3 0.08
27 16 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TATTTAAAATTAATATTAAAATAATAA
Found at i:336056 original size:13 final size:13
Alignment explanation
Indices: 336016--336086 Score: 58
Period size: 13 Copynumber: 5.5 Consensus size: 13
336006 AAAATTATTT
*
336016 TATTTAAATTTAA
1 TATTTAAAATTAA
*
336029 T-TTTAAAA-AATA
1 TATTTAAAATTA-A
336041 TATTTAAAATTAA
1 TATTTAAAATTAA
336054 TA-TTAAAATAATAA
1 TATTTAAAAT--TAA
* *
336068 TATTTTATATTAA
1 TATTTAAAATTAA
336081 TATTTA
1 TATTTA
336087 TATATTTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
11 1 0.02
12 15 0.33
13 19 0.41
14 6 0.13
15 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TATTTAAAATTAA
Found at i:336079 original size:21 final size:21
Alignment explanation
Indices: 336053--336139 Score: 59
Period size: 21 Copynumber: 3.8 Consensus size: 21
336043 TTTAAAATTA
336053 ATATTAAAATAATAATATTTT
1 ATATTAAAATAATAATATTTT
* *
336074 ATATTAATAT-TTATATATTTT
1 ATATTAAAATAATA-ATATTTT
*
336095 ATAATTCATTTTAAATAAAAATATTTT
1 AT-ATT-A----AAATAATAATATTTT
336122 AATTATTAAAATAATAAT
1 -A-TATTAAAATAATAAT
336140 TTCAGTTGAT
Statistics
Matches: 50, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
20 2 0.04
21 18 0.36
22 3 0.06
23 10 0.20
27 11 0.22
28 5 0.10
29 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (21 bp):
ATATTAAAATAATAATATTTT
Found at i:337356 original size:19 final size:18
Alignment explanation
Indices: 337332--337376 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
337322 TTATAAACAA
337332 AAATATAATAAAAATTATT
1 AAATATAATAAAAATT-TT
*
337351 AAATAT-ATTAAAATTTT
1 AAATATAATAAAAATTTT
337368 AAATATAAT
1 AAATATAAT
337377 TGATACACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 8 0.33
18 10 0.42
19 6 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATATAATAAAAATTTT
Found at i:337371 original size:17 final size:18
Alignment explanation
Indices: 337332--337374 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
337322 TTATAAACAA
337332 AAATATAATAAAAATTATT
1 AAATAT-ATAAAAATTATT
*
337351 AAATATATTAAAATT-TT
1 AAATATATAAAAATTATT
337368 AAATATA
1 AAATATA
337375 ATTGATACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.39
18 8 0.35
19 6 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATATATAAAAATTATT
Found at i:337597 original size:2 final size:2
Alignment explanation
Indices: 337590--337635 Score: 67
Period size: 2 Copynumber: 23.0 Consensus size: 2
337580 AGAATGTGTC
*
337590 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT -T AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
337632 AT AT
1 AT AT
337636 TTGTAAGACT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:338620 original size:23 final size:26
Alignment explanation
Indices: 338594--338644 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 26
338584 ATAATATAAT
338594 TAAT-ATTAAAAAAAAGA-T-AAGAA
1 TAATAATTAAAAAAAAGATTAAAGAA
* *
338617 TAATAATTCAAAGAAAGATTAAAGAA
1 TAATAATTAAAAAAAAGATTAAAGAA
338643 TA
1 TA
338645 GGACAATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 11 0.48
25 1 0.04
26 7 0.30
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.24
Consensus pattern (26 bp):
TAATAATTAAAAAAAAGATTAAAGAA
Found at i:339624 original size:15 final size:16
Alignment explanation
Indices: 339606--339635 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
339596 TATTTAAATA
339606 TTATAT-AATTTATAT
1 TTATATAAATTTATAT
339621 TTATATAAATTTATA
1 TTATATAAATTTATA
339636 CAATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATATAAATTTATAT
Found at i:340038 original size:217 final size:220
Alignment explanation
Indices: 339621--340062 Score: 640
Period size: 217 Copynumber: 2.0 Consensus size: 220
339611 TAATTTATAT
* *
339621 TTATATAAATTTATACAATATTATAATATGAACATTAAAAATATAAATAAAATATGTTATTTATA
1 TTATATAAATTTATACAATATTATAATATGAAAATTAAAAATAT--AGAAAATATGTTATTTATA
* *
339686 TTTTACACTTATTAAAATGACAATAAAAAAATATTAAAGATAAAAAAAATCATATTTTATTTTTT
64 TTTTACACTTATTAAAAAGACAAGAAAAAAATATTAAAGATAAAAAAAATCATATTTTATTTTTT
* * ** * * *
339751 TAAGAAAAAAATCAACTAATAAGTGAAGATAAAATTTGAAATTTGAATTATCGGATCGGGTCAAA
129 TAAGAAAAAAATCAACTAATAAGTCAAGATAAAAATTGAAATCCGAATTACCAGATCGGATCAAA
* * *
339816 ATTGATACTGATATTATAATTAAATTA
194 ATTGATACTAATATTACAATTAAACTA
* *
339843 TTATATAAATTTATATAATATTGTAATATGAAAATTAAAAATAT-GAAAATATGTTATTTATATT
1 TTATATAAATTTATACAATATTATAATATGAAAATTAAAAATATAGAAAATATGTTATTTATATT
* *
339907 TTACAACTTATTAAAAAGACAAGAAAAAAATATTAAGGAT-AAAAAAATTATATTTTA-TTTTTT
66 TTAC-ACTTATTAAAAAGACAAGAAAAAAATATTAAAGATAAAAAAAATCATATTTTATTTTTTT
*
339970 AAG-AAAAAATCAACTAATAAGTCAAGATAAAAATTGAAATCCGAATTGCCAGATCGGATCAAAA
130 AAGAAAAAAATCAACTAATAAGTCAAGATAAAAATTGAAATCCGAATTACCAGATCGGATCAAAA
* *
340034 TTGATGCTAATATTACACTTAAACTA
195 TTGATACTAATATTACAATTAAACTA
340060 TTA
1 TTA
340063 AGCATGAAAG
Statistics
Matches: 198, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
217 77 0.39
218 9 0.05
219 39 0.20
220 32 0.16
222 41 0.21
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (220 bp):
TTATATAAATTTATACAATATTATAATATGAAAATTAAAAATATAGAAAATATGTTATTTATATT
TTACACTTATTAAAAAGACAAGAAAAAAATATTAAAGATAAAAAAAATCATATTTTATTTTTTTA
AGAAAAAAATCAACTAATAAGTCAAGATAAAAATTGAAATCCGAATTACCAGATCGGATCAAAAT
TGATACTAATATTACAATTAAACTA
Found at i:344189 original size:12 final size:12
Alignment explanation
Indices: 344172--344197 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
344162 ATTTAATTTT
344172 ATTAATATAAAA
1 ATTAATATAAAA
344184 ATTAATATAAAA
1 ATTAATATAAAA
344196 AT
1 AT
344198 ATTTTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATTAATATAAAA
Found at i:344388 original size:24 final size:26
Alignment explanation
Indices: 344343--344394 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
344333 TTTTAATAAA
*
344343 TTTAATATATTAAATATAAAAATATTT
1 TTTAAAATATTAAATATAAAAAT-TTT
344370 TTTAAAATATT-AAT-T-AAAATTTT
1 TTTAAAATATTAAATATAAAAATTTT
344393 TT
1 TT
344395 AAATTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 5 0.21
24 5 0.21
25 1 0.04
26 3 0.12
27 10 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTAAAATATTAAATATAAAAATTTT
Found at i:345107 original size:23 final size:24
Alignment explanation
Indices: 345080--345135 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 24
345070 AATATATTAA
*
345080 AATATTAAAATTATTTTTA-AATT
1 AATATTTAAATTATTTTTATAATT
*
345103 AATATTTATA-TATTTTTATAATT
1 AATATTTAAATTATTTTTATAATT
345126 AA-ATTTAAAT
1 AATATTTAAAT
345136 AAAAATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AATATTTAAATTATTTTTATAATT
Found at i:346627 original size:15 final size:15
Alignment explanation
Indices: 346603--346646 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 15
346593 AATTATGTCA
346603 TTTA-ATTAAATATT
1 TTTATATTAAATATT
346617 TTTATATTAAAAATATT
1 TTTATATT--AAATATT
*
346634 TTTATATTTAATA
1 TTTATATTAAATA
346647 CTTATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 4 0.15
15 7 0.27
17 15 0.58
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTATATTAAATATT
Found at i:346632 original size:17 final size:17
Alignment explanation
Indices: 346581--346641 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 17
346571 ATTTTTTAAA
346581 TTTTATATTAAAAATTAT
1 TTTTATATTAAAAA-TAT
346599 GTCATTTA-ATT--AAATAT
1 -T--TTTATATTAAAAATAT
346616 TTTTATATTAAAAATAT
1 TTTTATATTAAAAATAT
346633 TTTTATATT
1 TTTTATATT
346642 TAATACTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 4 0.11
15 3 0.08
16 1 0.03
17 18 0.49
18 3 0.08
19 1 0.03
20 3 0.08
21 4 0.11
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTTATATTAAAAATAT
Found at i:348190 original size:15 final size:15
Alignment explanation
Indices: 348158--348186 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
348148 AATAATACCT
348158 TAATAAAATAATAAA
1 TAATAAAATAATAAA
348173 TAATAAAA-AATAAA
1 TAATAAAATAATAAA
348187 ATAAAATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
TAATAAAATAATAAA
Found at i:348640 original size:15 final size:15
Alignment explanation
Indices: 348620--348649 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
348610 CTTGGGTGTG
348620 TATATATAAATATAT
1 TATATATAAATATAT
*
348635 TATATATATATATAT
1 TATATATAAATATAT
348650 ATGAGTGATA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATATATAAATATAT
Found at i:349275 original size:19 final size:18
Alignment explanation
Indices: 349230--349280 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
349220 GATTGTTGAA
*
349230 AAATAATT-ACATTAAAT
1 AAATAATTAAAATTAAAT
349247 AAATAATTAAATATTAAA-
1 AAATAATTAAA-ATTAAAT
*
349265 AAATATTTTAAAATTA
1 AAATA-ATTAAAATTA
349281 CACACTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 8 0.28
18 10 0.34
19 11 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATAATTAAAATTAAAT
Found at i:350020 original size:20 final size:21
Alignment explanation
Indices: 349992--350030 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
349982 TTAAAAAATT
349992 AATTATTATAT-ATTTTTATC
1 AATTATTATATAATTTTTATC
*
350012 AATTTTTATATAATTTTTA
1 AATTATTATATAATTTTTA
350031 GGTCGGTATG
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:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
AATTATTATATAATTTTTATC
Found at i:350195 original size:2 final size:2
Alignment explanation
Indices: 350188--350212 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
350178 AAATTATCAA
350188 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 A
350213 AAATTTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:350562 original size:18 final size:18
Alignment explanation
Indices: 350522--350585 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
350512 CATAATTATT
350522 TAATTAAAAATAAATTAA
1 TAATTAAAAATAAATTAA
* * *
350540 GAATTAAAAATTATTTAA
1 TAATTAAAAATAAATTAA
* *
350558 TAATTTAATTAA-AAATTTA
1 TAA-TTAA-AAATAAATTAA
350577 TAATTAAAA
1 TAATTAAAA
350586 TTTTTAAATA
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
17 1 0.03
18 21 0.60
19 11 0.31
20 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
TAATTAAAAATAAATTAA
Found at i:350582 original size:14 final size:14
Alignment explanation
Indices: 350563--350611 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 14
350553 TTTAATAATT
350563 TAATTAAAAATTTA
1 TAATTAAAAATTTA
*
350577 TAATT-AAAATTTT
1 TAATTAAAAATTTA
* *
350590 TAA--ATAATTTTA
1 TAATTAAAAATTTA
350602 TAATTAAAAA
1 TAATTAAAAA
350612 AATAAAAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
12 8 0.31
13 10 0.38
14 8 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATTAAAAATTTA
Found at i:350586 original size:36 final size:38
Alignment explanation
Indices: 350514--350599 Score: 97
Period size: 41 Copynumber: 2.2 Consensus size: 38
350504 TTTTTTTTCA
*
350514 TAATTATTTAATTAAAAATAAATTAAGAATTAAAAATTATT
1 TAATAATTTAATTAAAAAT--ATTAAGAATTAAAAATT-TT
*
350555 TAATAATTTAATTAAAAAT-TT-ATAATT-AAAATTTT
1 TAATAATTTAATTAAAAATATTAAGAATTAAAAATTTT
350590 TAAATAATTT
1 T-AATAATTT
350600 TATAATTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
35 3 0.07
36 14 0.33
37 5 0.12
38 2 0.05
41 18 0.43
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (38 bp):
TAATAATTTAATTAAAAATATTAAGAATTAAAAATTTT
Found at i:350807 original size:22 final size:23
Alignment explanation
Indices: 350742--350810 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 23
350732 TAATAAAATT
350742 TTTAAA-AAATATTTTATATTAATA
1 TTTAAATAAA-ATTTTATATTAA-A
*
350766 TTT--ATATAATTTTATAATTAAA
1 TTTAAATAAAATTTTAT-ATTAAA
350788 TTTAAATAAAATTTT-TATTAAA
1 TTTAAATAAAATTTTATATTAAA
350810 T
1 T
350811 AATAATAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
22 19 0.49
23 8 0.21
24 12 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAAATAAAATTTTATATTAAA
Found at i:351244 original size:20 final size:20
Alignment explanation
Indices: 351219--351260 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
351209 ATAATTTTTT
351219 ATTTAAAT-TTAATTATAAAA
1 ATTTAAATATTAA-TATAAAA
351239 ATTTAAATATTAATATAAAA
1 ATTTAAATATTAATATAAAA
351259 AT
1 AT
351261 AATTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTTAAATATTAATATAAAA
Found at i:352507 original size:22 final size:22
Alignment explanation
Indices: 352473--352527 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
352463 ATTTTATATT
352473 ATTATCAATTATTTTAATTACG
1 ATTATCAATTATTTTAATTACG
* *
352495 ATTA-CAATATATTTTTATTAGG
1 ATTATCAAT-TATTTTAATTACG
*
352517 CTTATCAATTA
1 ATTATCAATTA
352528 GTCGAGCTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 4 0.14
22 20 0.71
23 4 0.14
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.49
Consensus pattern (22 bp):
ATTATCAATTATTTTAATTACG
Found at i:354199 original size:14 final size:15
Alignment explanation
Indices: 354165--354198 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
354155 TTTGTACTAC
354165 TTTTTATTTTAATTT
1 TTTTTATTTTAATTT
354180 TTTTTATTTTAATTT
1 TTTTTATTTTAATTT
354195 TTTT
1 TTTT
354199 AAAAACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTATTTTAATTT
Found at i:354400 original size:17 final size:17
Alignment explanation
Indices: 354380--354430 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
354370 TAAATAATAT
*
354380 TTAAATATCTATTTTTA
1 TTAAAAATCTATTTTTA
* *
354397 TTAAAAATTTAGTTTTA
1 TTAAAAATCTATTTTTA
354414 TTAAAAAATCTATTTTT
1 TT-AAAAATCTATTTTT
354431 TATGTGAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (17 bp):
TTAAAAATCTATTTTTA
Found at i:355607 original size:20 final size:20
Alignment explanation
Indices: 355579--355625 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
355569 AGAATGTTTT
*
355579 AAAATATAAAAATGTAAA-AA
1 AAAAAATAAAAAT-TAAATAA
*
355599 AAAAAATAATAATTAAATTAA
1 AAAAAATAAAAATTAAA-TAA
355620 AAAAAA
1 AAAAAA
355626 ATTTCATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.17
20 11 0.48
21 8 0.35
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (20 bp):
AAAAAATAAAAATTAAATAA
Found at i:356038 original size:17 final size:17
Alignment explanation
Indices: 356016--356050 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
356006 TTGAATCGAT
356016 TTAAAATAA-ATAAAAAA
1 TTAAAA-AATATAAAAAA
356033 TTAAAAAATATAAAAAA
1 TTAAAAAATATAAAAAA
356050 T
1 T
356051 GATTAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TTAAAAAATATAAAAAA
Found at i:362815 original size:24 final size:24
Alignment explanation
Indices: 362780--362834 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
362770 TATTTTTCCC
*
362780 ATTTATATATTTTAATA-ATTTATT
1 ATTTATAAATTTTAATATA-TTATT
362804 ATTTATAAATTTTAATATATTATT
1 ATTTATAAATTTTAATATATTATT
*
362828 ATATATA
1 ATTTATA
362835 TATATTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTTATAAATTTTAATATATTATT
Found at i:362896 original size:18 final size:18
Alignment explanation
Indices: 362861--362895 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
362851 TTTAAGCTTC
362861 AATTTTTAATAATATTTT
1 AATTTTTAATAATATTTT
362879 AATTTTTAA-AATATTTT
1 AATTTTTAATAATATTTT
362896 TTATATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AATTTTTAATAATATTTT
Found at i:362933 original size:16 final size:17
Alignment explanation
Indices: 362914--362953 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
362904 TTTAATATTT
362914 ATATTTAATAAATAT-A
1 ATATTTAATAAATATAA
*
362930 ATATAT-ATAAATATAA
1 ATATTTAATAAATATAA
362946 ATATTTAA
1 ATATTTAA
362954 ATTATCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 8 0.40
16 11 0.55
17 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATTTAATAAATATAA
Found at i:362941 original size:15 final size:14
Alignment explanation
Indices: 362921--362955 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
362911 TTTATATTTA
362921 ATAAATATAATATAT
1 ATAAATATAA-ATAT
362936 ATAAATATAAATAT
1 ATAAATATAAATAT
*
362950 TTAAAT
1 ATAAAT
362956 TATCATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAAATATAAATAT
Found at i:363011 original size:6 final size:6
Alignment explanation
Indices: 362994--363046 Score: 61
Period size: 6 Copynumber: 8.5 Consensus size: 6
362984 AAAAAATTAA
* * *
362994 ATATTT AAATTT TTATTT TTATTT AATATTT ATATTT ATATTT AATATTT
1 ATATTT ATATTT ATATTT ATATTT -ATATTT ATATTT ATATTT -ATATTT
363044 ATA
1 ATA
363047 ATAAATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 30 0.73
7 11 0.27
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATATTT
Found at i:363023 original size:13 final size:12
Alignment explanation
Indices: 362994--363046 Score: 61
Period size: 13 Copynumber: 4.2 Consensus size: 12
362984 AAAAAATTAA
*
362994 ATATTTAAATTT
1 ATATTTATATTT
* *
363006 TTATTTTTATTT
1 ATATTTATATTT
363018 AATATTTATATTT
1 -ATATTTATATTT
363031 ATATTTAATATTT
1 ATATTT-ATATTT
363044 ATA
1 ATA
363047 ATAAATATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
12 15 0.44
13 19 0.56
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATATTTATATTT
Found at i:363029 original size:19 final size:19
Alignment explanation
Indices: 362994--363046 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
362984 AAAAAATTAA
*
362994 ATATTTAA-ATTTTTATTT
1 ATATTTAATATTTATATTT
*
363012 TTATTTAATATTTATATTT
1 ATATTTAATATTTATATTT
363031 ATATTTAATATTTATA
1 ATATTTAATATTTATA
363047 ATAAATATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
18 7 0.23
19 24 0.77
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATATTTAATATTTATATTT
Found at i:363910 original size:3 final size:3
Alignment explanation
Indices: 363902--363948 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
363892 AGGGTTGCTT
363902 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
363949 GTCATTGTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:366118 original size:99 final size:99
Alignment explanation
Indices: 365947--366145 Score: 364
Period size: 99 Copynumber: 2.0 Consensus size: 99
365937 GTATTTTTAG
365947 TAGCAAACTTCTAAATTTAAAAGAAGATGTTTGCTTGGCTGGGTTCAAGATTTGCAATGATAGCT
1 TAGCAAACTTCTAAATTTAAAAGAAGATGTTTGCTTGGCTGGGTTCAAGATTTGCAATGATAGCT
*
366012 ATTAAATTACTTGATATGCCATGAGTTAGATTAC
66 ATTAAATTACTTGATATGCCAGGAGTTAGATTAC
366046 TAGCAAACTTCTAAATTTAAAA-AGAGATGTTTGCTTGGCTGGGTTCAAGATTTGCAATGATAGC
1 TAGCAAACTTCTAAATTTAAAAGA-AGATGTTTGCTTGGCTGGGTTCAAGATTTGCAATGATAGC
*
366110 TATTAAATTACTTGGTATGCCAGGAGTTAGATTAC
65 TATTAAATTACTTGATATGCCAGGAGTTAGATTAC
366145 T
1 T
366146 GTGTTTCATG
Statistics
Matches: 97, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
98 1 0.01
99 96 0.99
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (99 bp):
TAGCAAACTTCTAAATTTAAAAGAAGATGTTTGCTTGGCTGGGTTCAAGATTTGCAATGATAGCT
ATTAAATTACTTGATATGCCAGGAGTTAGATTAC
Found at i:372857 original size:23 final size:24
Alignment explanation
Indices: 372817--372862 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
372807 TGTTTTTTAA
*
372817 TTATATAATATATTATTT-TATTT
1 TTATATAATATATAATTTATATTT
* *
372840 TTATATATTATGTAATTTATATT
1 TTATATAATATATAATTTATATT
372863 ATATAAACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TTATATAATATATAATTTATATTT
Found at i:372867 original size:23 final size:22
Alignment explanation
Indices: 372812--372868 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 22
372802 GTATTTGTTT
*
372812 TTTA-ATTATATAATATATTAT
1 TTTATATTATATAATATATTAA
*
372833 TTTAT-TTTTAT-ATATTATGTAA
1 TTTATATTATATAATA-TAT-TAA
372855 TTTATATTATATAA
1 TTTATATTATATAA
372869 ACATTAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 3 0.11
21 12 0.43
22 7 0.25
23 5 0.18
24 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTATATTATATAATATATTAA
Found at i:375149 original size:3 final size:3
Alignment explanation
Indices: 375141--375175 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
375131 TTTTCAGGGC
375141 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
375176 CATTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:388000 original size:22 final size:20
Alignment explanation
Indices: 387962--388002 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 20
387952 TAAATATTAA
387962 TTAAATAAATAATTTTAATT
1 TTAAATAAATAATTTTAATT
387982 TTAAATATAATAATATTTAAT
1 TTAAATA-AATAAT-TTTAAT
388003 AAAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 6 0.32
22 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAAATAAATAATTTTAATT
Found at i:388117 original size:32 final size:31
Alignment explanation
Indices: 388047--388117 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
388037 TATAAAATTA
*
388047 AAATTAA--AAAATTAAATTTTATCACTTTT
1 AAATTAATTAAAATTAAATTTTATCAATTTT
* *
388076 AATAATAATTAAAATTAATATTTTATTAATTTT
1 AA-ATTAATTAAAATTAA-ATTTTATCAATTTT
388109 AAATTAATT
1 AAATTAATT
388118 TTTATCAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 2 0.06
30 4 0.12
32 14 0.41
33 14 0.41
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (31 bp):
AAATTAATTAAAATTAAATTTTATCAATTTT
Found at i:388721 original size:16 final size:15
Alignment explanation
Indices: 388696--388727 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
388686 TTAATGTATT
388696 AAAAAATAATAAATA
1 AAAAAATAATAAATA
388711 AAAATAATAATAAATA
1 AAAA-AATAATAAATA
388727 A
1 A
388728 GATCTCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (15 bp):
AAAAAATAATAAATA
Found at i:389119 original size:14 final size:15
Alignment explanation
Indices: 389100--389138 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
389090 CATTTTATAT
389100 TAAATATAAT-TACA
1 TAAATATAATATACA
*
389114 TAAATATAATATATA
1 TAAATATAATATACA
389129 TAAA-ATAATA
1 TAAATATAATA
389139 AAAATATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAATATAATATACA
Found at i:389220 original size:17 final size:17
Alignment explanation
Indices: 389168--389221 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
389158 ATATATATTT
389168 TAAAATTTATAT-AA-A
1 TAAAATTTATATAAATA
389183 -AAAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
389198 TCAAAATTTATATAAATA
1 T-AAAATTTATATAAATA
389216 TAAAAT
1 TAAAAT
389222 ATTTTAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
12 1 0.03
13 5 0.16
14 5 0.16
15 1 0.03
17 9 0.28
18 8 0.25
19 3 0.09
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:392023 original size:23 final size:22
Alignment explanation
Indices: 391973--392015 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
391963 ATCGAAAAAA
391973 ATTTCGATGCATATTAACTCGT
1 ATTTCGATGCATATTAACTCGT
*
391995 ATTTTCTATGCATATTAACTC
1 A-TTTCGATGCATATTAACTC
392016 ATTATTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (22 bp):
ATTTCGATGCATATTAACTCGT
Found at i:392356 original size:19 final size:20
Alignment explanation
Indices: 392332--392373 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
392322 AATCCGGCTC
392332 AAAATAAT-T-TTTTTATATT
1 AAAATAATATATTTTTAT-TT
392351 AAAATAATATATTTTTATTT
1 AAAATAATATATTTTTATTT
392371 AAA
1 AAA
392374 TTTAATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.38
20 6 0.29
21 7 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AAAATAATATATTTTTATTT
Found at i:392714 original size:12 final size:13
Alignment explanation
Indices: 392694--392762 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 13
392684 ATATAAAAAT
*
392694 TTATATTTTTGTA
1 TTATATTTTTATA
392707 TTAT-TTTTTATA
1 TTATATTTTTATA
*
392719 TTTTATTATGTTATAA
1 TTATATT-T-TTAT-A
*
392735 TTATATTTAATATA
1 TTATATTT-TTATA
* *
392749 TTTTATTTTGATA
1 TTATATTTTTATA
392762 T
1 T
392763 CAATTTTAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
12 10 0.23
13 10 0.23
14 9 0.20
15 8 0.18
16 7 0.16
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (13 bp):
TTATATTTTTATA
Found at i:395035 original size:14 final size:15
Alignment explanation
Indices: 395016--395048 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
395006 AGTATGTGCT
395016 TTCTC-TGGACTTAG
1 TTCTCTTGGACTTAG
395030 TTCTCTTTGGACTTAG
1 TTCTC-TTGGACTTAG
395046 TTC
1 TTC
395049 AAGTAGGCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
16 12 0.71
ACGTcount: A:0.12, C:0.21, G:0.18, T:0.48
Consensus pattern (15 bp):
TTCTCTTGGACTTAG
Found at i:395471 original size:36 final size:36
Alignment explanation
Indices: 395422--395498 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 36
395412 GATCATTATT
** *
395422 AATATAATAAAATATTTTTATTTAAAATTAATTATAAA
1 AATATAATAAAATATTAATA-TAAAAATT-ATTATAAA
*
395460 AATAT-AT-AAATATTAATATAAAAATTATTTTAAA
1 AATATAATAAAATATTAATATAAAAATTATTATAAA
395494 AATAT
1 AATAT
395499 TTCATTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
34 12 0.34
35 7 0.20
36 9 0.26
37 2 0.06
38 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (36 bp):
AATATAATAAAATATTAATATAAAAATTATTATAAA
Found at i:395478 original size:12 final size:12
Alignment explanation
Indices: 395445--395496 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
395435 ATTTTTATTT
395445 AAAATTAATTATA
1 AAAATTAA-TATA
395458 AAAA-T-ATATA
1 AAAATTAATATA
*
395468 AATATTAATATA
1 AAAATTAATATA
* *
395480 AAAATTATTTTA
1 AAAATTAATATA
395492 AAAAT
1 AAAAT
395497 ATTTCATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
10 7 0.21
11 2 0.06
12 20 0.61
13 4 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:395566 original size:29 final size:29
Alignment explanation
Indices: 395510--395588 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 29
395500 TCATTATTTT
*
395510 TTAACACT-AATTTAAATTTACAA-ATTAAA
1 TTAA-ACTAAATTTAAATTTA-AACTTTAAA
395539 TTAAACTAAATTTAAATTTAAACTTTAAA
1 TTAAACTAAATTTAAATTTAAACTTTAAA
*
395568 --AAA--AAATTTAAATCTAAACTT
1 TTAAACTAAATTTAAATTTAAACTT
395589 CAAAAAAACT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
25 17 0.37
27 3 0.07
28 5 0.11
29 21 0.46
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (29 bp):
TTAAACTAAATTTAAATTTAAACTTTAAA
Found at i:395567 original size:7 final size:6
Alignment explanation
Indices: 395518--395567 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
395508 TTTTAACACT
* *
395518 AATTTA AATTTA CAAATTA AA-TTA AA-CTA AATTTA AATTTA AACTTTA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA AATTTA AA-TTTA
395566 AA
1 AA
395568 AAAAAATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
5 9 0.24
6 18 0.47
7 11 0.29
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (6 bp):
AATTTA
Found at i:395575 original size:25 final size:25
Alignment explanation
Indices: 395546--395596 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
395536 AAATTAAACT
* *
395546 AAATTTAAATTTAAACTTTAAAAAA
1 AAATTTAAATCTAAACTTCAAAAAA
395571 AAATTTAAATCTAAACTTCAAAAAA
1 AAATTTAAATCTAAACTTCAAAAAA
395596 A
1 A
395597 CTAACTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (25 bp):
AAATTTAAATCTAAACTTCAAAAAA
Found at i:402622 original size:3 final size:3
Alignment explanation
Indices: 402614--402646 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
402604 TTTCCCGTGT
402614 TTA TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
402647 GTCTTTTGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:402774 original size:21 final size:19
Alignment explanation
Indices: 402729--402768 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
402719 TTTTTAGATC
*
402729 AATTATTTTTGATAAATAA
1 AATTATTTTTGAAAAATAA
*
402748 AATTATTTTTTAAAAATAA
1 AATTATTTTTGAAAAATAA
402767 AA
1 AA
402769 AATTATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
AATTATTTTTGAAAAATAA
Found at i:402783 original size:23 final size:24
Alignment explanation
Indices: 402757--402802 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
402747 AAATTATTTT
402757 TTAAAA-AT-AAAAAATTATAAATA
1 TTAAAATATCAAAAAATTA-AAATA
*
402780 TTAAAATATCAAAATATTAAAAT
1 TTAAAATATCAAAAAATTAAAAT
402803 TTATATTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
TTAAAATATCAAAAAATTAAAATA
Found at i:402785 original size:16 final size:16
Alignment explanation
Indices: 402766--402807 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
402756 TTTAAAAATA
402766 AAAAATTATAAATATT
1 AAAAATTATAAATATT
*
402782 AAAATATCA-AAATATT
1 AAAA-ATTATAAATATT
*
402798 AAAATTTATA
1 AAAAATTATA
402808 TTGTATGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
15 2 0.10
16 16 0.76
17 3 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAAATTATAAATATT
Found at i:402786 original size:8 final size:8
Alignment explanation
Indices: 402764--402802 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
402754 TTTTTAAAAA
*
402764 TAAAAAAT
1 TAAAATAT
402772 TATAAATAT
1 TA-AAATAT
402781 TAAAATAT
1 TAAAATAT
*
402789 CAAAATAT
1 TAAAATAT
402797 TAAAAT
1 TAAAAT
402803 TTATATTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (8 bp):
TAAAATAT
Found at i:404145 original size:16 final size:15
Alignment explanation
Indices: 404124--404153 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
404114 TTTAAAAAAG
404124 AAGAAGAAGAAGAAAC
1 AAGAAGAA-AAGAAAC
404140 AAGAAGAAAAGAAA
1 AAGAAGAAAAGAAA
404154 GAATGGATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.73, C:0.03, G:0.23, T:0.00
Consensus pattern (15 bp):
AAGAAGAAAAGAAAC
Found at i:407489 original size:21 final size:21
Alignment explanation
Indices: 407465--407506 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
407455 AAAAATTTAT
407465 TTTTAT-ATTAATATTTATATA
1 TTTTATAATTAA-ATTTATATA
407486 TTTTATAATTAAATTTATATA
1 TTTTATAATTAAATTTATATA
407507 AAAATAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTATAATTAAATTTATATA
Found at i:407515 original size:20 final size:20
Alignment explanation
Indices: 407490--407533 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
407480 TATATATTTT
407490 ATAATTAAATTTATATAAA-A
1 ATAATTAAATTTA-ATAAATA
**
407510 ATAATTTTATTTAATAAATA
1 ATAATTAAATTTAATAAATA
407530 ATAA
1 ATAA
407534 ATCAAGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAATTAAATTTAATAAATA
Found at i:407530 original size:17 final size:17
Alignment explanation
Indices: 407484--407531 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
407474 AATATTTATA
* * *
407484 TATTTTATAATTAAATT
1 TATTTAATAAATAATTT
*
407501 TATATAA-AAATAATTT
1 TATTTAATAAATAATTT
407517 TATTTAATAAATAAT
1 TATTTAATAAATAAT
407532 AAATCAAGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTTAATAAATAATTT
Found at i:407980 original size:24 final size:27
Alignment explanation
Indices: 407928--407978 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
407918 TATATATATT
*
407928 TAATTGTTAAATTTTTTTGATATTAAA
1 TAATTGTTAAATTTTTTTAATATTAAA
*
407955 TAATT-TT-AATTTTTTTAATTTTAA
1 TAATTGTTAAATTTTTTTAATATTAA
407979 TATGTACAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 15 0.68
26 2 0.09
27 5 0.23
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (27 bp):
TAATTGTTAAATTTTTTTAATATTAAA
Found at i:408525 original size:27 final size:27
Alignment explanation
Indices: 408493--408544 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
408483 ATGATAAAAT
*
408493 ATAATAAAAA-ATTAATATATTATAAAG
1 ATAATAAAAATA-TAATATAATATAAAG
*
408520 ATAATATAAATATAATATAATATAA
1 ATAATAAAAATATAATATAATATAA
408545 TATAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (27 bp):
ATAATAAAAATATAATATAATATAAAG
Found at i:408527 original size:11 final size:11
Alignment explanation
Indices: 408506--408556 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
408496 ATAAAAAATT
*
408506 AATATATTATA
1 AATATAATATA
*
408517 AAGATAATATA
1 AATATAATATA
408528 AATATAATAT-
1 AATATAATATA
408538 AATATAATATA
1 AATATAATATA
408549 ATATATAA
1 A-ATATAA
408557 ATATTTAGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
10 10 0.29
11 19 0.54
12 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
AATATAATATA
Found at i:408528 original size:5 final size:5
Alignment explanation
Indices: 408490--408553 Score: 65
Period size: 5 Copynumber: 12.2 Consensus size: 5
408480 TTTATGATAA
* * * *
408490 AATAT AATAA AAAATT AATAT ATTAT AAAGAT AATAT AAATAT AATAT
1 AATAT AATAT AATA-T AATAT AATAT -AATAT AATAT -AATAT AATAT
408538 AATAT AATAT AATAT A
1 AATAT AATAT AATAT A
408554 TAAATATTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
5 37 0.77
6 11 0.23
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:409869 original size:21 final size:22
Alignment explanation
Indices: 409833--409873 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
409823 TTGAAAACTC
409833 GAAGAAAATGTGAATGATCTTA
1 GAAGAAAATGTGAATGATCTTA
409855 GAAGAAAAT-TGAATGATCT
1 GAAGAAAATGTGAATGATCT
409874 AAATATCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.46, C:0.05, G:0.22, T:0.27
Consensus pattern (22 bp):
GAAGAAAATGTGAATGATCTTA
Found at i:413396 original size:2 final size:2
Alignment explanation
Indices: 413389--413416 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
413379 AAAATTAGGA
413389 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
413417 TCATTCAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:422329 original size:6 final size:6
Alignment explanation
Indices: 422320--422347 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
422310 TTCATTTTCA
422320 ATTTGC ATTTGC ATTTGC ATTTGC ATTT
1 ATTTGC ATTTGC ATTTGC ATTTGC ATTT
422348 CAGTTTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.54
Consensus pattern (6 bp):
ATTTGC
Found at i:422875 original size:17 final size:18
Alignment explanation
Indices: 422837--422899 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 18
422827 ACTTTATGTT
*
422837 TAATATATAATTTTTTTAA
1 TAATATA-AATATTTTTAA
* *
422856 TAA-ATAAGTATTTTTCA
1 TAATATAAATATTTTTAA
422873 TAATATAAATA-TTTT-A
1 TAATATAAATATTTTTAA
*
422889 TATTATAAATA
1 TAATATAAATA
422900 ATTAACAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
16 11 0.29
17 15 0.39
18 9 0.24
19 3 0.08
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
TAATATAAATATTTTTAA
Found at i:422989 original size:21 final size:21
Alignment explanation
Indices: 422948--422988 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
422938 TTTTAAATAG
* *
422948 TTTAATAATGTTGTGATAAAA
1 TTTAAAAATGTTGTGAAAAAA
422969 TTTAAAAATGTT-TGAAAAAA
1 TTTAAAAATGTTGTGAAAAAA
422989 AGACTTACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (21 bp):
TTTAAAAATGTTGTGAAAAAA
Found at i:423200 original size:21 final size:22
Alignment explanation
Indices: 423167--423211 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
423157 CTGGTCTAAT
423167 TTAATTATAAAATTTATAAATA
1 TTAATTATAAAATTTATAAATA
* *
423189 TTAATT-TAAAATTTTTTAATA
1 TTAATTATAAAATTTATAAATA
423210 TT
1 TT
423212 TTATTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATTATAAAATTTATAAATA
Done.