Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold40
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: 3440810
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 28138 characters in sequence are not A, C, G, or T
File 17 of 24
Found at i:2215146 original size:2 final size:2
Alignment explanation
Indices: 2215139--2215167 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2215129 GGGGAAAGAC
2215139 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2215168 ATATAACACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2218191 original size:2 final size:2
Alignment explanation
Indices: 2218184--2218209 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2218174 TCTAATGTGC
2218184 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
2218210 TCACACCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2219720 original size:30 final size:30
Alignment explanation
Indices: 2219680--2219739 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
2219670 TTTTAATTTT
* *
2219680 TATAATATTAAAT-AAATATTTTATTTTTAA
1 TATAAAATT-AATGAAATATTTTATATTTAA
2219710 TATAAAATTAATGAAATATTTTATATTTAA
1 TATAAAATTAATGAAATATTTTATATTTAA
2219740 AAAATTTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 3 0.11
30 24 0.89
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (30 bp):
TATAAAATTAATGAAATATTTTATATTTAA
Found at i:2224660 original size:32 final size:31
Alignment explanation
Indices: 2224613--2224691 Score: 79
Period size: 32 Copynumber: 2.5 Consensus size: 31
2224603 AATTAAAATA
* * *
2224613 TTAATATATTAATATTTTTTATTATATAATTT
1 TTAACATATTAATATTATAT-TTATATAATTT
* *
2224645 TTAACATATTTATATTATATTTATATTATTT
1 TTAACATATTAATATTATATTTATATAATTT
* *
2224676 TT-TCATATTACTATTA
1 TTAACATATTAATATTA
2224692 CTCAAATAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 11 0.28
31 12 0.31
32 16 0.41
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (31 bp):
TTAACATATTAATATTATATTTATATAATTT
Found at i:2224664 original size:43 final size:44
Alignment explanation
Indices: 2224568--2224676 Score: 109
Period size: 43 Copynumber: 2.5 Consensus size: 44
2224558 AATTCGTATC
* *
2224568 ATATTATTATTATTATTTTTTTATTTTATAATTTTAATTAAAATATT
1 ATATTA-TATTAATA-TTTTTTATTATATAATTTT-ATTAAAATATT
*
2224615 A-A-TATATTAATATTTTTTATTATATAA-TTT-TTAACATATTT
1 ATATTATATTAATATTTTTTATTATATAATTTTATTAAAATA-TT
*
2224656 ATATTATATTTATATTATTTT
1 ATATTATATTAATATT-TTTT
2224677 TTCATATTAC
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
40 7 0.13
41 3 0.06
42 4 0.07
43 25 0.46
44 11 0.20
45 2 0.04
46 1 0.02
47 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (44 bp):
ATATTATATTAATATTTTTTATTATATAATTTTATTAAAATATT
Found at i:2225043 original size:12 final size:12
Alignment explanation
Indices: 2225026--2225051 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2225016 TTGTTGTTTG
2225026 AATTTTTTTTTT
1 AATTTTTTTTTT
2225038 AATTTTTTTTTT
1 AATTTTTTTTTT
2225050 AA
1 AA
2225052 GTTTGTTTTG
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
AATTTTTTTTTT
Found at i:2225120 original size:15 final size:15
Alignment explanation
Indices: 2225093--2225135 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2225083 AATTACTCAA
2225093 ATATTTTTAAAATTT
1 ATATTTTTAAAATTT
*
2225108 ATATATTTT-AAATTA
1 ATAT-TTTTAAAATTT
*
2225123 AAATTTTTAAAAT
1 ATATTTTTAAAAT
2225136 AAAAATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTTTAAAATTT
Found at i:2225346 original size:15 final size:16
Alignment explanation
Indices: 2225318--2225350 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2225308 TTTTGATTTT
*
2225318 AATTCTAATTTTTATA
1 AATTCTAATCTTTATA
2225334 AATT-TAATCTTTATA
1 AATTCTAATCTTTATA
2225349 AA
1 AA
2225351 CAAAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTCTAATCTTTATA
Found at i:2227440 original size:3 final size:3
Alignment explanation
Indices: 2227432--2227471 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2227422 AAACGTTTAG
2227432 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2227472 GGAAAATCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2229716 original size:14 final size:14
Alignment explanation
Indices: 2229699--2229740 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
2229689 TTCTTAAAAT
2229699 ATTTTAAAAATATAA
1 ATTTTAAAAATA-AA
*
2229714 TTTTTAAAAA-AAA
1 ATTTTAAAAATAAA
2229727 ATTATTAAAAATAA
1 ATT-TTAAAAATAA
2229741 TTTTTTAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.17
14 8 0.35
15 11 0.48
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATTTTAAAAATAAA
Found at i:2229724 original size:27 final size:28
Alignment explanation
Indices: 2229671--2229748 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 28
2229661 AATTTAATAG
*** *
2229671 TATTAAAAATAAATTTTATTCTTAAAATAT
1 TATTAAAAATAAA-TTT-TTAAAAAAAAAT
2229701 T-TTAAAAATATAATTTTTAAAAAAAAAT
1 TATTAAAAATA-AATTTTTAAAAAAAAAT
*
2229729 TATTAAAAATAATTTTTTAA
1 TATTAAAAATAAATTTTTAA
2229749 TCATTAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
28 17 0.41
29 21 0.51
30 3 0.07
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (28 bp):
TATTAAAAATAAATTTTTAAAAAAAAAT
Found at i:2229742 original size:13 final size:14
Alignment explanation
Indices: 2229694--2229742 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
2229684 TTTTATTCTT
2229694 AAAAT-ATT-TTAA
1 AAAATAATTATTAA
*
2229706 AAATATAATTTTTAA
1 AAA-ATAATTATTAA
*
2229721 AAAAAAATTATT-A
1 AAAATAATTATTAA
2229734 AAAATAATT
1 AAAATAATT
2229743 TTTTAATCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 3 0.10
13 11 0.35
14 10 0.32
15 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAATAATTATTAA
Found at i:2229748 original size:14 final size:14
Alignment explanation
Indices: 2229695--2229748 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
2229685 TTTATTCTTA
2229695 AAATATTTTAAAAAT
1 AAAT-TTTTAAAAAT
*
2229710 ATAATTTTTAAAAAA
1 A-AATTTTTAAAAAT
*
2229725 AAATTATTAAAAAT
1 AAATTTTTAAAAAT
*
2229739 AATTTTTTAA
1 AAATTTTTAA
2229749 TCATTAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
14 19 0.58
15 11 0.33
16 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATTTTTAAAAAT
Found at i:2230606 original size:16 final size:17
Alignment explanation
Indices: 2230580--2230613 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2230570 TAATAATTTT
2230580 TTAAAATAAATTAAAAA
1 TTAAAATAAATTAAAAA
*
2230597 TTAAAA-AAATTATAAA
1 TTAAAATAAATTAAAAA
2230613 T
1 T
2230614 AGATTTAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAAAATAAATTAAAAA
Found at i:2231159 original size:21 final size:21
Alignment explanation
Indices: 2231133--2231182 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
2231123 TAAATAAATA
*
2231133 AAATTTTATA-TTTAATTATTT
1 AAATTTTAAATTTTAA-TATTT
2231154 AAATTTTAAATTTTAATATTT
1 AAATTTTAAATTTTAATATTT
2231175 ATAATTTT
1 A-AATTTT
2231183 TTAATCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AAATTTTAAATTTTAATATTT
Found at i:2233885 original size:5 final size:5
Alignment explanation
Indices: 2233875--2233899 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2233865 ATGCCAATGA
2233875 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
2233900 TGTGACAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:2235464 original size:3 final size:3
Alignment explanation
Indices: 2235456--2235497 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
2235446 TTATGACTTC
2235456 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2235498 TATTCAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2236727 original size:2 final size:2
Alignment explanation
Indices: 2236720--2236748 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2236710 AAAATAAAAT
2236720 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2236749 ATTTCTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2236736 original size:13 final size:13
Alignment explanation
Indices: 2236718--2236745 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2236708 CAAAAATAAA
2236718 ATTATATATATAT
1 ATTATATATATAT
2236731 ATTATATATATAT
1 ATTATATATATAT
2236744 AT
1 AT
2236746 ATAATTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATATATATAT
Found at i:2237014 original size:4 final size:4
Alignment explanation
Indices: 2237007--2237032 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2236997 CAAGTAAAAA
2237007 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
2237033 TGCAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2237393 original size:54 final size:53
Alignment explanation
Indices: 2237330--2237434 Score: 124
Period size: 53 Copynumber: 2.0 Consensus size: 53
2237320 TTAATTTAAG
*
2237330 TTAAAATTAAAATTATTATTATAAATT-AA-TAAAAAATAAAAAATTATTTTTATA
1 TTAAAATTAAAA-TATT-TTAT-AATTAAATTAAAAAATAAAAAATTATATTTATA
* * * *
2237384 TTAATATTAATATATTTTATAATTAAATTTAAATATAAAAAATTATATTTA
1 TTAAAATTAAAATATTTTATAATTAAATTAAAAAATAAAAAATTATATTTA
2237435 ATTGGGATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
51 4 0.09
52 6 0.14
53 24 0.55
54 10 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (53 bp):
TTAAAATTAAAATATTTTATAATTAAATTAAAAAATAAAAAATTATATTTATA
Found at i:2237473 original size:20 final size:20
Alignment explanation
Indices: 2237448--2237493 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2237438 GGGATAAACT
2237448 TAATATATAACACTA-AAAAA
1 TAATATAT-ACACTATAAAAA
*
2237468 TAATATATATACTATAAAAA
1 TAATATATACACTATAAAAA
2237488 T-ATATA
1 TAATATA
2237494 AATATATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (20 bp):
TAATATATACACTATAAAAA
Found at i:2237498 original size:21 final size:19
Alignment explanation
Indices: 2237459--2237504 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
2237449 AATATATAAC
*
2237459 ACTAAAAAATAATATATAT
1 ACTAAAAAATAATAAATAT
2237478 ACTATAAAAATATATAAATAT
1 ACTA-AAAAATA-ATAAATAT
*
2237499 ATTAAA
1 ACTAAA
2237505 TTTATATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.17
20 9 0.39
21 10 0.43
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
ACTAAAAAATAATAAATAT
Found at i:2237552 original size:14 final size:14
Alignment explanation
Indices: 2237533--2237590 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
2237523 TATTGGAAGT
*
2237533 ATTTATGTATTTTA
1 ATTTATATATTTTA
2237547 ATTTATATATTATTAA
1 ATTTATATATT-TT-A
2237563 ATTTA-ATATTTTA
1 ATTTATATATTTTA
2237576 ATTT-TCATATTTTA
1 ATTTAT-ATATTTTA
2237590 A
1 A
2237591 AAATTATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
13 5 0.13
14 21 0.54
15 7 0.18
16 6 0.15
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTTATATATTTTA
Found at i:2237628 original size:19 final size:19
Alignment explanation
Indices: 2237604--2237661 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
2237594 TTATAATAAA
*
2237604 TAAAAAATAATTAATATGT
1 TAAAAAATAATTAATATAT
* *
2237623 TAAAAATTATTTAA-ATAT
1 TAAAAAATAATTAATATAT
2237641 TAATAAAAT-ATTAATATAT
1 TAA-AAAATAATTAATATAT
2237660 TA
1 TA
2237662 TTAAATTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 10 0.31
19 22 0.69
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
TAAAAAATAATTAATATAT
Found at i:2237643 original size:18 final size:19
Alignment explanation
Indices: 2237582--2237661 Score: 62
Period size: 19 Copynumber: 4.4 Consensus size: 19
2237572 TTTAATTTTC
*
2237582 ATATTTTAAAAATTA--TA
1 ATATATTAAAAATTATTTA
* * *
2237599 ATA-AATAAAAAATAATTA
1 ATATATTAAAAATTATTTA
*
2237617 ATATGTTAAAAATTATTTA
1 ATATATTAAAAATTATTTA
*
2237636 A-ATATTAATAAAATA-TTA
1 ATATATTAA-AAATTATTTA
2237654 ATATATTA
1 ATATATTA
2237662 TTAAATTTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
16 8 0.16
17 3 0.06
18 15 0.31
19 23 0.47
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (19 bp):
ATATATTAAAAATTATTTA
Found at i:2237667 original size:18 final size:18
Alignment explanation
Indices: 2237633--2237688 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
2237623 TAAAAATTAT
2237633 TTAAATATTAATAAAATA
1 TTAAATATTAATAAAATA
* *
2237651 TTAATATATT-ATTAAATT
1 TTAA-ATATTAATAAAATA
*
2237669 TTAAATTTTATATAAAATA
1 TTAAATATTA-ATAAAATA
2237688 T
1 T
2237689 ATTTAAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
17 4 0.13
18 14 0.47
19 12 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAAATATTAATAAAATA
Found at i:2237808 original size:17 final size:19
Alignment explanation
Indices: 2237774--2237810 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2237764 TAAATAATTT
2237774 TTTAATATTATTAATTTTTA
1 TTTAATATTATT-ATTTTTA
2237794 TTTAATA-TATT-TTTTTA
1 TTTAATATTATTATTTTTA
2237811 AATATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.35
19 4 0.24
20 7 0.41
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTAATATTATTATTTTTA
Found at i:2237823 original size:33 final size:32
Alignment explanation
Indices: 2237760--2237829 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 32
2237750 ATTTTATTAA
**
2237760 TATTTAAATAATTTTTTAATATTATTAATTTT
1 TATTTAAATAATTTTTTAATATTAAAAATTTT
*
2237792 TATTTAATATATTTTTTTAA-ATATAAAAATTTT
1 TATTTAA-ATAATTTTTTAATAT-TAAAAATTTT
*
2237825 AATTT
1 TATTT
2237830 TAATTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 9 0.28
33 23 0.72
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
TATTTAAATAATTTTTTAATATTAAAAATTTT
Found at i:2238345 original size:31 final size:32
Alignment explanation
Indices: 2238310--2238374 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
2238300 TATGAATTGG
2238310 ATTTAAATAATAAAAATTA-TTTATT-TTTAAA
1 ATTT-AATAATAAAAATTATTTTATTATTTAAA
* **
2238341 ATTTAGTTTTAAAAATTATTTTATTATTTAAA
1 ATTTAATAATAAAAATTATTTTATTATTTAAA
2238373 AT
1 AT
2238375 ATATTAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 11 0.38
31 10 0.34
32 8 0.28
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (32 bp):
ATTTAATAATAAAAATTATTTTATTATTTAAA
Found at i:2240673 original size:2 final size:2
Alignment explanation
Indices: 2240661--2240690 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
2240651 ATTCAATGAG
2240661 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT A
2240691 GTAATGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2240866 original size:21 final size:21
Alignment explanation
Indices: 2240819--2240867 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2240809 TATATAGATT
2240819 ATAAATTTTTAATTATATTAA
1 ATAAATTTTTAATTATATTAA
* *
2240840 AAAAATTTTATTATT-TATTAA
1 ATAAATTTT-TAATTATATTAA
*
2240861 TTAAATT
1 ATAAATT
2240868 ACTTACATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATAAATTTTTAATTATATTAA
Found at i:2241013 original size:14 final size:14
Alignment explanation
Indices: 2240990--2241050 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
2240980 TATTTTAAAT
*
2240990 AAATTTTTTAATTA
1 AAATTATTTAATTA
2241004 AAATTATTTAA-TA
1 AAATTATTTAATTA
*
2241017 AAATTAATATAATT-
1 AAATT-ATTTAATTA
2241031 AAATTAATTT-ATTA
1 AAATT-ATTTAATTA
*
2241045 ATATTA
1 AAATTA
2241051 AAATTTTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
13 11 0.28
14 28 0.70
15 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AAATTATTTAATTA
Found at i:2241029 original size:28 final size:28
Alignment explanation
Indices: 2240998--2241051 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
2240988 ATAAATTTTT
2240998 TAATTAAAATT-ATTTAATAAAATTAATA
1 TAATT-AAATTAATTTAATAAAATTAATA
* *
2241026 TAATTAAATTAATTTATTAATATTAA
1 TAATTAAATTAATTTAATAAAATTAA
2241052 AATTTTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TAATTAAATTAATTTAATAAAATTAATA
Found at i:2241071 original size:15 final size:15
Alignment explanation
Indices: 2241038--2241084 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
2241028 ATTAAATTAA
2241038 TTTATTAATATTAAAAT
1 TTTA-TAATATT-AAAT
2241055 TTTATAATATTAAAT
1 TTTATAATATTAAAT
* *
2241070 TTAATAATTTTAAAT
1 TTTATAATATTAAAT
2241085 ATAAATTACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 17 0.61
16 7 0.25
17 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTATAATATTAAAT
Found at i:2241091 original size:21 final size:22
Alignment explanation
Indices: 2241040--2241091 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
2241030 TAAATTAATT
2241040 TATT-AATATTAAAATTTTATAA
1 TATTAAAT-TTAAAATTTTATAA
2241062 TATTAAATTTAATAATTTTA-AA
1 TATTAAATTTAA-AATTTTATAA
2241084 TA-TAAATT
1 TATTAAATT
2241092 ACCCTGTGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 6 0.21
22 12 0.43
23 10 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TATTAAATTTAAAATTTTATAA
Found at i:2241413 original size:8 final size:8
Alignment explanation
Indices: 2241379--2241440 Score: 56
Period size: 8 Copynumber: 7.6 Consensus size: 8
2241369 ATTTAATTTA
2241379 ATTTTAAT
1 ATTTTAAT
* *
2241387 A-TTAAAA
1 ATTTTAAT
2241394 ATATTT-AT
1 AT-TTTAAT
2241402 ATTTTAAT
1 ATTTTAAT
2241410 ATTTTAATT
1 ATTTTAA-T
2241419 ATTTTAAT
1 ATTTTAAT
*
2241427 ATATTTAAA
1 AT-TTTAAT
2241436 ATTTT
1 ATTTT
2241441 TTTAAAAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
7 8 0.18
8 19 0.43
9 17 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
ATTTTAAT
Found at i:2241421 original size:17 final size:18
Alignment explanation
Indices: 2241401--2241434 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2241391 AAAATATTTA
2241401 TATTTTAATAT-TTTAAT
1 TATTTTAATATATTTAAT
2241418 TATTTTAATATATTTAA
1 TATTTTAATATATTTAA
2241435 AATTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTTAATATATTTAAT
Found at i:2241421 original size:23 final size:23
Alignment explanation
Indices: 2241374--2241440 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 23
2241364 ATTTGATTTA
**
2241374 ATTTA-ATTTTAATATTAAAAAT
1 ATTTATATTTTAATATTTTAAAT
*
2241396 ATTTATATTTTAATATTTTAATT
1 ATTTATATTTTAATATTTTAAAT
*
2241419 ATTTTAATATATTTAAAATTTT
1 A-TTT-ATAT-TTTAATATTTT
2241441 TTTAAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.14
23 15 0.41
24 3 0.08
25 4 0.11
26 10 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTATATTTTAATATTTTAAAT
Found at i:2241439 original size:17 final size:17
Alignment explanation
Indices: 2241402--2241440 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2241392 AAATATTTAT
*
2241402 ATTTTAATATTTTAATT
1 ATTTTAATATTTTAATA
2241419 ATTTTAATATATTTAA-A
1 ATTTTAATAT-TTTAATA
2241436 ATTTT
1 ATTTT
2241441 TTTAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTAATATTTTAATA
Found at i:2243410 original size:17 final size:15
Alignment explanation
Indices: 2243376--2243427 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
2243366 GTCATAATTA
*
2243376 AATATATTTTTA-TT
1 AATATATATTTATTT
2243390 AATATATATTCGTATTT
1 AATATATATT--TATTT
*
2243407 AATATTTATTTATTT
1 AATATATATTTATTT
2243422 AA-ATAT
1 AATATAT
2243428 TAAGTAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 12 0.38
15 7 0.22
16 2 0.06
17 11 0.34
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (15 bp):
AATATATATTTATTT
Found at i:2244132 original size:12 final size:12
Alignment explanation
Indices: 2244115--2244139 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2244105 CGTTCAAAAA
2244115 TATTATATTTTT
1 TATTATATTTTT
2244127 TATTATATTTTT
1 TATTATATTTTT
2244139 T
1 T
2244140 GACATACTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTATATTTTT
Found at i:2245213 original size:91 final size:91
Alignment explanation
Indices: 2245058--2245229 Score: 292
Period size: 91 Copynumber: 1.9 Consensus size: 91
2245048 AAATACAACG
*
2245058 TATGAAAAGATGTTTATAATTTTTCTGTCATGACCTCCTCTACATTTAGAGTATTTAGGGGAGAA
1 TATGAAAAGATGTTTATAATTTTTCCGTCATGACCTCCTCTACATTTAGAGTATTTAGGGGAGAA
*
2245123 AGTAAAATTAATTTTTTATTTATATA
66 AATAAAATTAATTTTTTATTTATATA
**
2245149 TATGAAAAGATGTTTATAATTTTTCCGTCATGACCTACC-CTTGATTTAGAGTATTTAGGGGAGA
1 TATGAAAAGATGTTTATAATTTTTCCGTCATGACCT-CCTCTACATTTAGAGTATTTAGGGGAGA
2245213 AAATAAAATTAATTTTT
65 AAATAAAATTAATTTTT
2245230 GTTCATACAT
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
91 74 0.97
92 2 0.03
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.41
Consensus pattern (91 bp):
TATGAAAAGATGTTTATAATTTTTCCGTCATGACCTCCTCTACATTTAGAGTATTTAGGGGAGAA
AATAAAATTAATTTTTTATTTATATA
Found at i:2246035 original size:16 final size:16
Alignment explanation
Indices: 2246015--2246086 Score: 69
Period size: 16 Copynumber: 4.4 Consensus size: 16
2246005 TTATGTATAA
2246015 TTATATTTA-AAATAT
1 TTATATTTATAAATAT
*
2246030 TATATATTTATAAAAAT
1 T-TATATTTATAAATAT
2246047 TTATATTATATAAAT-T
1 TTATATT-TATAAATAT
*
2246063 TTAATATATT-TATATAT
1 TT-ATAT-TTATAAATAT
2246080 TTATATT
1 TTATATT
2246087 ATGTTTGTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
15 2 0.04
16 25 0.52
17 20 0.42
18 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATTTATAAATAT
Found at i:2246069 original size:17 final size:15
Alignment explanation
Indices: 2246015--2246063 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
2246005 TTATGTATAA
2246015 TTATATT-TAAAATAT
1 TTATATTATAAAA-AT
2246030 TATATATTTATAAAAAT
1 T-TATA-TTATAAAAAT
*
2246047 TTATATTATATAAAT
1 TTATATTATAAAAAT
2246062 TT
1 TT
2246064 TAATATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 12 0.40
16 8 0.27
17 5 0.17
18 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATATTATAAAAAT
Found at i:2246123 original size:35 final size:35
Alignment explanation
Indices: 2245995--2246137 Score: 91
Period size: 35 Copynumber: 4.1 Consensus size: 35
2245985 AAAAACTAAA
* * * * *
2245995 TTTATATATTT-TATGTATA-ATTATATTTAAAAT
1 TTTATATATTTATATATTTATATTATGTTTATATT
* * * *
2246028 ATTATATATTTATAAAAATTTATATTA--TATAAATT
1 TTTATATATTTAT--ATATTTATATTATGTTTATATT
* *
2246063 TTAATATATTTATATATTTATATTATGTTTGTATT
1 TTTATATATTTATATATTTATATTATGTTTATATT
*
2246098 TTTATAT-TTTATTATATTT-TAATTATTTTTATATT
1 TTTATATATTTA-TATATTTAT-ATTATGTTTATATT
2246133 ATTTA
1 -TTTA
2246138 ATTATAATCA
Statistics
Matches: 86, Mismatches: 15, Indels: 15
0.74 0.13 0.13
Matches are distributed among these distances:
33 21 0.24
34 6 0.07
35 47 0.55
36 8 0.09
37 4 0.05
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (35 bp):
TTTATATATTTATATATTTATATTATGTTTATATT
Found at i:2246137 original size:19 final size:17
Alignment explanation
Indices: 2246060--2246142 Score: 64
Period size: 19 Copynumber: 4.6 Consensus size: 17
2246050 TATTATATAA
*
2246060 ATTTTAA-TATATTTAT
1 ATTTTAATTATTTTTAT
2246076 ATATTTATATTATGTTTGTAT
1 AT-TTTA-ATTAT-TTT-TAT
*
2246097 -TTTTATATT-TTATTAT
1 ATTTTA-ATTATTTTTAT
2246113 ATTTTAATTATTTTTAT
1 ATTTTAATTATTTTTAT
2246130 ATTATTTAATTAT
1 A-T-TTTAATTAT
2246143 AATCATATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
16 8 0.15
17 18 0.33
18 3 0.05
19 20 0.36
20 3 0.05
21 3 0.05
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.66
Consensus pattern (17 bp):
ATTTTAATTATTTTTAT
Found at i:2246153 original size:27 final size:27
Alignment explanation
Indices: 2246046--2246145 Score: 77
Period size: 27 Copynumber: 3.9 Consensus size: 27
2246036 TTTATAAAAA
* *
2246046 TTTATATTATA-TAAATTTTAATATATT
1 TTTATATTATATTATATTATAAT-TATT
* * *
2246073 TATATATTTATATTATGTT-T--GTATT
1 TTTATA-TTATATTATATTATAATTATT
* *
2246098 TTTATATTTTATTATATTTTAATTATT
1 TTTATATTATATTATATTATAATTATT
2246125 TTTATATTAT-TTA-ATTATAAT
1 TTTATATTATATTATATTATAAT
2246146 CATATTTTCT
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
24 10 0.17
25 17 0.29
26 3 0.05
27 18 0.31
28 6 0.10
29 4 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (27 bp):
TTTATATTATATTATATTATAATTATT
Found at i:2248097 original size:23 final size:23
Alignment explanation
Indices: 2248043--2248097 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
2248033 TATAAATATA
*
2248043 AATATAAATA-AATTTGTTTTAT
1 AATATTAATATAATTTGTTTTAT
* *
2248065 -ATATTTATATAATTTTTTTTAT
1 AATATTAATATAATTTGTTTTAT
2248087 AATATTAATAT
1 AATATTAATAT
2248098 TTTAATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 7 0.26
22 11 0.41
23 9 0.33
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
AATATTAATATAATTTGTTTTAT
Found at i:2248837 original size:2 final size:2
Alignment explanation
Indices: 2248830--2248855 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2248820 ATTGACTATG
2248830 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
2248856 TAAGATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2249573 original size:27 final size:28
Alignment explanation
Indices: 2249528--2249637 Score: 93
Period size: 27 Copynumber: 3.8 Consensus size: 28
2249518 TCGTGCATGA
* *
2249528 TTTATATATTTATATTATATTATAATAAT
1 TTTAAATATATAT-TTATATTATAATAAT
2249557 ATTTAAA-ATAT-TTTATATT-TATATAATT
1 -TTTAAATATATATTTATATTATA-ATAA-T
*
2249585 TTTAATATATAAATAATTTATTTTATAA-AAT
1 TTTAA-ATAT--AT-ATTTATATTATAATAAT
2249616 TTTAAATATATATTTATATTAT
1 TTTAAATATATATTTATATTAT
2249638 TTTATACATA
Statistics
Matches: 67, Mismatches: 4, Indels: 21
0.73 0.04 0.23
Matches are distributed among these distances:
26 2 0.03
27 26 0.39
28 5 0.07
29 5 0.07
30 9 0.13
31 8 0.12
32 2 0.03
33 8 0.12
34 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTAAATATATATTTATATTATAATAAT
Found at i:2249574 original size:16 final size:17
Alignment explanation
Indices: 2249555--2249619 Score: 68
Period size: 16 Copynumber: 4.1 Consensus size: 17
2249545 TATTATAATA
2249555 ATATTTA-AAATATTTT
1 ATATTTATAAATATTTT
2249571 ATATTTATATAAT-TTTT
1 ATATTTATA-AATATTTT
* *
2249588 A-ATATATAAATAATTT
1 ATATTTATAAATATTTT
2249604 AT-TTTATAAA-ATTTT
1 ATATTTATAAATATTTT
2249619 A
1 A
2249620 AATATATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
15 8 0.20
16 24 0.59
17 6 0.15
18 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATTTATAAATATTTT
Found at i:2249638 original size:32 final size:31
Alignment explanation
Indices: 2249530--2249643 Score: 105
Period size: 32 Copynumber: 3.7 Consensus size: 31
2249520 GTGCATGATT
*
2249530 TATATATTTATATTATATTATAATAATATTTAA
1 TATATATTTATATTATTTTATAA-AAT-TTTAA
*
2249563 -A-ATATTT-TA-TA-TTTATATAATTTTTAA
1 TATATATTTATATTATTTTATA-AAATTTTAA
**
2249590 TATATAAATA-ATTTATTTTATAAAATTTTAAA
1 TATATATTTATA-TTATTTTATAAAATTTT-AA
2249622 TATATATTTATATTATTTTATA
1 TATATATTTATATTATTTTATA
2249644 CATATTAAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
27 5 0.08
28 8 0.12
29 8 0.12
30 2 0.03
31 14 0.22
32 27 0.42
33 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
TATATATTTATATTATTTTATAAAATTTTAA
Found at i:2250493 original size:16 final size:17
Alignment explanation
Indices: 2250450--2250514 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 17
2250440 GTATTATATT
*
2250450 TATTATAATTATAAATA
1 TATTATAATAATAAATA
2250467 TAATTATTAATAATAAATA
1 T-ATTA-TAATAATAAATA
*
2250486 T-TTATAATAAAAAATAA
1 TATTATAATAATAAAT-A
*
2250503 AATTATAA-AATA
1 TATTATAATAATA
2250515 TGAATAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.25
17 8 0.20
18 10 0.25
19 12 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TATTATAATAATAAATA
Found at i:2261024 original size:44 final size:45
Alignment explanation
Indices: 2260976--2261062 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 45
2260966 TGATTTTAGT
2260976 TCATTTATGT-TT-ATAAATAAATTTATTTATTA-TTCATTTAAAAC
1 TCATTTAT-TATTCATAAA-AAATTTATTTATTAGTTCATTTAAAAC
** *
2261020 TCATTTATTATTCATTTAAAATTTATTTATTAGTTTATTTAAA
1 TCATTTATTATTCATAAAAAATTTATTTATTAGTTCATTTAAA
2261063 GTTAATTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
43 1 0.03
44 24 0.65
45 12 0.32
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (45 bp):
TCATTTATTATTCATAAAAAATTTATTTATTAGTTCATTTAAAAC
Found at i:2261070 original size:23 final size:22
Alignment explanation
Indices: 2260994--2261071 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
2260984 GTTTATAAAT
*
2260994 AAATTTATTTATTATTCATTTA
1 AAATTAATTTATTATTCATTTA
* *
2261016 AAACTCATTTATTATTCATTTA
1 AAATTAATTTATTATTCATTTA
* *
2261038 AAATTTATTTATTAGTTTATTTA
1 AAATTAATTTATTA-TTCATTTA
*
2261061 AAGTTAATTTA
1 AAATTAATTTA
2261072 AAGCTTGTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 32 0.67
23 16 0.33
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (22 bp):
AAATTAATTTATTATTCATTTA
Found at i:2261884 original size:11 final size:11
Alignment explanation
Indices: 2261868--2262022 Score: 62
Period size: 11 Copynumber: 14.5 Consensus size: 11
2261858 ATAATTTATG
2261868 TATTTATATTA
1 TATTTATATTA
2261879 TATTTATA-TA
1 TATTTATATTA
*
2261889 TTTTATTATATTA
1 -TAT-TTATATTA
*
2261902 TAATTATATTTA
1 TATTTATA-TTA
*
2261914 AATTT-T-TTA
1 TATTTATATTA
* *
2261923 TATTTAAATAA
1 TATTTATATTA
* *
2261934 AATTTTTA-TA
1 TATTTATATTA
2261944 TA-TTA-A-TA
1 TATTTATATTA
*
2261952 -ATTTATTTTA
1 TATTTATATTA
*
2261962 TATTAATATTA
1 TATTTATATTA
2261973 TTTATTTATATTA
1 --TATTTATATTA
*
2261986 TA-CT-TATTA
1 TATTTATATTA
2261995 TATTT-TAATTA
1 TATTTAT-ATTA
* *
2262006 TTTTTTATATTT
1 -TATTTATATTA
2262018 TATTT
1 TATTT
2262023 TTATGGTAAT
Statistics
Matches: 105, Mismatches: 23, Indels: 32
0.66 0.14 0.20
Matches are distributed among these distances:
7 1 0.01
8 6 0.06
9 16 0.15
10 9 0.09
11 41 0.39
12 19 0.18
13 13 0.12
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTTATATTA
Found at i:2261939 original size:19 final size:20
Alignment explanation
Indices: 2261912--2261949 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2261902 TAATTATATT
*
2261912 TAAATTTTTTATAT-TTAAA
1 TAAAATTTTTATATATTAAA
2261931 TAAAATTTTTATATATTAA
1 TAAAATTTTTATATATTAA
2261950 TAATTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAAAATTTTTATATATTAAA
Found at i:2261951 original size:19 final size:19
Alignment explanation
Indices: 2261912--2261969 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
2261902 TAATTATATT
*
2261912 TAAATTTTTTATAT-TTAAA
1 TAAAATTTTTATATATT-AA
2261931 TAAAATTTTTATATATTAA
1 TAAAATTTTTATATATTAA
*
2261950 T--AATTTATTTTATATTAA
1 TAAAATTT-TTATATATTAA
2261968 TA
1 TA
2261970 TTATTTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 5 0.15
18 11 0.32
19 16 0.47
20 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TAAAATTTTTATATATTAA
Found at i:2261975 original size:20 final size:20
Alignment explanation
Indices: 2261942--2262005 Score: 75
Period size: 18 Copynumber: 3.4 Consensus size: 20
2261932 AAAATTTTTA
2261942 TATATTAATA--ATTTATTT
1 TATATTAATATTATTTATTT
2261960 TATATTAATATTATTTA-TT
1 TATATTAATATTATTTATTT
2261979 TATATT-ATACTTATTATATTT
1 TATATTAATA-TTATT-TATTT
2262000 TA-ATTA
1 TATATTA
2262006 TTTTTTATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
18 13 0.32
19 13 0.32
20 10 0.25
21 4 0.10
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TATATTAATATTATTTATTT
Found at i:2262583 original size:12 final size:12
Alignment explanation
Indices: 2262563--2262601 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
2262553 TTTATATTAA
*
2262563 TATATTTTTATT
1 TATAATTTTATT
2262575 TATAATTTTA-T
1 TATAATTTTATT
2262586 TATAAATTTTATT
1 TAT-AATTTTATT
2262599 TAT
1 TAT
2262602 GTATTCATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 4 0.17
12 16 0.67
13 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATAATTTTATT
Found at i:2263350 original size:26 final size:28
Alignment explanation
Indices: 2263299--2263360 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 28
2263289 GAGTTTTTTT
*
2263299 TTTTCTTTTAAAAAATTACAAATATT-A
1 TTTTATTTTAAAAAATTACAAATATTAA
*
2263326 TTTTATTTT-AAAAATTA-ATATTATTAA
1 TTTTATTTTAAAAAATTACA-AATATTAA
2263353 TTATTATT
1 TT-TTATT
2263361 ATATATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 1 0.03
26 13 0.43
27 11 0.37
28 5 0.17
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (28 bp):
TTTTATTTTAAAAAATTACAAATATTAA
Found at i:2264125 original size:26 final size:26
Alignment explanation
Indices: 2264094--2264144 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
2264084 ATATATTTTG
** *
2264094 TATTTTTCTTTATTTTCTTTTTTAAA
1 TATTTTTAATTATTTTCTTTATTAAA
2264120 TATTTTTAATTATTTTCTTTATTAA
1 TATTTTTAATTATTTTCTTTATTAA
2264145 TGAATTTTTT
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:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (26 bp):
TATTTTTAATTATTTTCTTTATTAAA
Found at i:2264152 original size:26 final size:26
Alignment explanation
Indices: 2264103--2264152 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2264093 GTATTTTTCT
* *
2264103 TTATTTTCTTTTTTAAATATTTTTAA
1 TTATTTTCTTTATTAAATAATTTTAA
2264129 TTATTTTCTTTATT-AATGAATTTT
1 TTATTTTCTTTATTAAAT-AATTTT
2264153 TTAAATGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (26 bp):
TTATTTTCTTTATTAAATAATTTTAA
Found at i:2264920 original size:19 final size:19
Alignment explanation
Indices: 2264893--2264971 Score: 56
Period size: 17 Copynumber: 4.0 Consensus size: 19
2264883 TTAATAATTA
*
2264893 TTATTTTTTATTTATTTAT
1 TTATATTTTATTTATTTAT
* *
2264912 TTATA-TTT-TTAATATAT
1 TTATATTTTATTTATTTAT
2264929 TTATATTTTCATATTATATTTAT
1 TTATA-TTT--TATT-TATTTAT
2264952 ATTATATTTTAATTT-TTTAT
1 -TTATATTTT-ATTTATTTAT
2264972 ATCTATTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 15
0.70 0.07 0.22
Matches are distributed among these distances:
17 12 0.26
18 3 0.06
19 6 0.13
20 5 0.11
21 3 0.06
22 5 0.11
23 8 0.17
24 5 0.11
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATATTTTATTTATTTAT
Found at i:2264931 original size:17 final size:18
Alignment explanation
Indices: 2264909--2264954 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
2264899 TTTATTTATT
2264909 TATTTATATTTT-TAATA
1 TATTTATATTTTATAATA
*
2264926 TATTTATATTTTCATATTA
1 TATTTATATTTT-ATAATA
2264945 TATTTATATT
1 TATTTATATT
2264955 ATATTTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 12 0.46
19 14 0.54
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTTATATTTTATAATA
Found at i:2264955 original size:11 final size:11
Alignment explanation
Indices: 2264891--2264960 Score: 62
Period size: 11 Copynumber: 6.9 Consensus size: 11
2264881 AATTAATAAT
*
2264891 TATTAT-TTTT
1 TATTATATTTA
2264901 TATT-TATTTA
1 TATTATATTTA
*
2264911 T-TTATATTTT
1 TATTATATTTA
*
2264921 TAATATATTTA
1 TATTATATTTA
*
2264932 TA-T-T-TTCA
1 TATTATATTTA
2264940 TATTATATTTA
1 TATTATATTTA
2264951 TATTATATTT
1 TATTATATTT
2264961 TAATTTTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
8 5 0.10
9 5 0.10
10 16 0.33
11 22 0.46
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (11 bp):
TATTATATTTA
Found at i:2265167 original size:29 final size:27
Alignment explanation
Indices: 2265125--2265186 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 27
2265115 TATTTTTATC
2265125 ATTTAAAATATTATAAATTTATATAAT
1 ATTTAAAATATTATAAATTTATATAAT
* *
2265152 ATTTATAAATATTTATATATTTATATCAT
1 ATTTA-AAATA-TTATAAATTTATATAAT
2265181 ATTTAA
1 ATTTAA
2265187 TTTTTATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 5 0.16
28 6 0.19
29 20 0.65
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTTAAAATATTATAAATTTATATAAT
Found at i:2265185 original size:11 final size:11
Alignment explanation
Indices: 2265136--2265170 Score: 56
Period size: 10 Copynumber: 3.4 Consensus size: 11
2265126 TTTAAAATAT
2265136 TATAA-ATTTA
1 TATAATATTTA
2265146 TATAATATTTA
1 TATAATATTTA
2265157 TA-AATATTTA
1 TATAATATTTA
2265167 TATA
1 TATA
2265171 TTTATATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 15 0.65
11 8 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TATAATATTTA
Found at i:2265195 original size:18 final size:18
Alignment explanation
Indices: 2265160--2265207 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
2265150 ATATTTATAA
*
2265160 ATATTTATATATTTATATC
1 ATATTTA-ATTTTTATATC
*
2265179 ATATTTAATTTTTATATT
1 ATATTTAATTTTTATATC
2265197 ATATTTTAATT
1 ATA-TTTAATT
2265208 AATTTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTTAATTTTTATATC
Found at i:2266370 original size:2 final size:2
Alignment explanation
Indices: 2266363--2266390 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2266353 CTCAAGTCGT
2266363 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2266391 AGTGTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2267060 original size:3 final size:3
Alignment explanation
Indices: 2267045--2267079 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2267035 TTAGTGGTCT
*
2267045 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2267080 CTTTATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2273287 original size:35 final size:35
Alignment explanation
Indices: 2273241--2273358 Score: 191
Period size: 35 Copynumber: 3.4 Consensus size: 35
2273231 CACGTTAAGC
** * *
2273241 ATGCAAGCATCTGCCTAATTTCCTAGACATCCTTA
1 ATGCAAGCATCTGAGTAATTTCTTGGACATCCTTA
*
2273276 ATGCAAGCATCTGAGTGATTTCTTGGACATCCTTA
1 ATGCAAGCATCTGAGTAATTTCTTGGACATCCTTA
2273311 ATGCAAGCATCTGAGTAATTTCTTGGACATCCTTA
1 ATGCAAGCATCTGAGTAATTTCTTGGACATCCTTA
2273346 ATGCAAGCATCTG
1 ATGCAAGCATCTG
2273359 TATGTTTTAA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 77 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (35 bp):
ATGCAAGCATCTGAGTAATTTCTTGGACATCCTTA
Found at i:2275610 original size:2 final size:2
Alignment explanation
Indices: 2275560--2275591 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2275550 CTTAGTTCAC
2275560 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
2275592 TAATGATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2275735 original size:10 final size:10
Alignment explanation
Indices: 2275720--2275744 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2275710 ATAATAATTC
2275720 ATATTTTTTT
1 ATATTTTTTT
2275730 ATATTTTTTT
1 ATATTTTTTT
2275740 ATATT
1 ATATT
2275745 AAAATTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
ATATTTTTTT
Found at i:2275785 original size:14 final size:14
Alignment explanation
Indices: 2275768--2275817 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
2275758 AAATATTATA
2275768 TAATATATAAATTT
1 TAATATATAAATTT
2275782 TAATATATTAATATTTT
1 TAATATA-TAA-A-TTT
*
2275799 TATTATATAAATTT
1 TAATATATAAATTT
2275813 TAATA
1 TAATA
2275818 ATTTTATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 14 0.45
15 4 0.13
16 4 0.13
17 9 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TAATATATAAATTT
Found at i:2275832 original size:22 final size:23
Alignment explanation
Indices: 2275789--2275833 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2275779 TTTTAATATA
* *
2275789 TTAATATTTTTATTATATAAATT
1 TTAATAATTTTATTATAAAAATT
2275812 TTAATAATTTTA-TATAAAAATT
1 TTAATAATTTTATTATAAAAATT
2275834 ATATTTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTAATAATTTTATTATAAAAATT
Found at i:2275845 original size:24 final size:24
Alignment explanation
Indices: 2275818--2275867 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
2275808 AATTTTAATA
2275818 ATTTTATATAAAAATTATATTTAT
1 ATTTTATATAAAAATTATATTTAT
* * *
2275842 ATTTTATATTATAATTATTTTTAT
1 ATTTTATATAAAAATTATATTTAT
2275866 AT
1 AT
2275868 CATATTACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTTTATATAAAAATTATATTTAT
Found at i:2276488 original size:22 final size:22
Alignment explanation
Indices: 2276453--2276494 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2276443 CTAAAATTTT
*
2276453 TTTATATTAAATATGTTTAATA
1 TTTATATTAAATATGATTAATA
**
2276475 TTTATATTTGATATGATTAA
1 TTTATATTAAATATGATTAA
2276495 ATATAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (22 bp):
TTTATATTAAATATGATTAATA
Found at i:2276696 original size:20 final size:20
Alignment explanation
Indices: 2276673--2276834 Score: 63
Period size: 20 Copynumber: 8.6 Consensus size: 20
2276663 GTACATACAA
2276673 TATTAATATATAATATAAAT
1 TATTAATATATAATATAAAT
2276693 TATTAA-A-AT-AT-TAAA-
1 TATTAATATATAATATAAAT
*
2276708 -ATTTATATA-AATATTAAAT
1 TATTAATATATAATA-TAAAT
* *
2276727 ATTTTAA-ACATAAT-T--AT
1 -TATTAATATATAATATAAAT
* *
2276744 TATAAAT-TA-AAT-TATAT
1 TATTAATATATAATATAAAT
*
2276761 CTAATAATAT-TAA-ATATAAT
1 -TATTAATATATAATATA-AAT
2276781 TATATAA-ATATAATACATATAA-
1 TAT-TAATATATAAT--ATA-AAT
2276803 TATTAATATATAATATAAAT
1 TATTAATATATAATATAAAT
*
2276823 TATTAAAATATA
1 TATTAATATATA
2276835 TAAAAATATA
Statistics
Matches: 106, Mismatches: 12, Indels: 48
0.64 0.07 0.29
Matches are distributed among these distances:
14 4 0.04
15 5 0.05
16 12 0.11
17 6 0.06
18 11 0.10
19 13 0.12
20 30 0.28
21 9 0.08
22 10 0.09
23 6 0.06
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TATTAATATATAATATAAAT
Found at i:2276801 original size:15 final size:14
Alignment explanation
Indices: 2276762--2276820 Score: 61
Period size: 14 Copynumber: 4.2 Consensus size: 14
2276752 AAATTATATC
2276762 TAATAATATTAAATA
1 TAATAATA-TAAATA
*
2276777 TAATTATATAAATA
1 TAATAATATAAATA
2276791 TAATACATAT-AATA
1 TAATA-ATATAAATA
2276805 T--TAATATATAATA
1 TAATAATATA-AATA
2276818 TAA
1 TAA
2276821 ATTATTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
11 4 0.11
12 2 0.05
13 5 0.14
14 15 0.41
15 11 0.30
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATAATATAAATA
Found at i:2276836 original size:35 final size:35
Alignment explanation
Indices: 2276764--2276837 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
2276754 ATTATATCTA
*
2276764 ATAATATTAAATATAATTATATAAATATAATACAT
1 ATAATATTAAATATAATTATATAAATATAAAACAT
* *
2276799 ATAATATTAATATATAA-TATA-AATTATTAAAATAT
1 ATAATATTAA-ATATAATTATATAAATA-TAAAACAT
2276834 ATAA
1 ATAA
2276838 AAATATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 4 0.12
35 24 0.71
36 6 0.18
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (35 bp):
ATAATATTAAATATAATTATATAAATATAAAACAT
Found at i:2276843 original size:8 final size:9
Alignment explanation
Indices: 2276815--2276860 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
2276805 TTAATATATA
*
2276815 ATATAAATT
1 ATATAAAAT
2276824 AT-TAAAAT
1 ATATAAAAT
2276832 ATATAAAA-
1 ATATAAAAT
2276840 ATATAAAAT
1 ATATAAAAT
* *
2276849 ATTTTAAAT
1 ATATAAAAT
2276858 ATA
1 ATA
2276861 CTTGTTATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
8 15 0.48
9 16 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
ATATAAAAT
Found at i:2276882 original size:122 final size:127
Alignment explanation
Indices: 2276649--2276882 Score: 343
Period size: 130 Copynumber: 1.9 Consensus size: 127
2276639 CATAAACATG
*
2276649 ATTATATAAATATAGTACATACAATATTAATATATAATATAAATTATTAAAATATTAAAATTTAT
1 ATTATATAAATATAATACATACAATATTAATATATAATATAAATTATTAAAATATT--AA-TTAT
* *
2276714 ATAAATATTAAATATTTTAAACATAATTATTATAAATTAAATTATATCTAATAATATTAAATATA
63 ATAAATATAAAATATTTTAAACATAATTATTATAAATTAAAATATATCTAATAATATTAAATATA
*
2276779 ATTATATAAATATAATACATATAATATTAATATATAATATAAATTATTAAAATA-T-A-TA-A-A
1 ATTATATAAATATAATACATACAATATTAATATATAATATAAATTATTAAAATATTAATTATATA
* * *
2276839 AATATAAAATATTTTAAATATACTTGTTATAAATTAAAATATAT
66 AATATAAAATATTTTAAACATAATTATTATAAATTAAAATATAT
2276883 AAATATTAAA
Statistics
Matches: 97, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
122 40 0.41
123 1 0.01
124 2 0.02
126 1 0.01
129 1 0.01
130 52 0.54
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (127 bp):
ATTATATAAATATAATACATACAATATTAATATATAATATAAATTATTAAAATATTAATTATATA
AATATAAAATATTTTAAACATAATTATTATAAATTAAAATATATCTAATAATATTAAATATA
Found at i:2277271 original size:30 final size:31
Alignment explanation
Indices: 2277222--2277297 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 31
2277212 TATTATTTTT
*
2277222 ATATAAAAAAT-TTATAATTTAAAA-ATATAA
1 ATATAATAAATATTATAATTTAAAATA-ATAA
* *
2277252 ATATCATAAATATTA-AATTTTAAATAATAA
1 ATATAATAAATATTATAATTTAAAATAATAA
*
2277282 ATTTAATAAATATTAT
1 ATATAATAAATATTAT
2277298 TTTTTTAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
30 34 0.89
31 4 0.11
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (31 bp):
ATATAATAAATATTATAATTTAAAATAATAA
Found at i:2277277 original size:14 final size:15
Alignment explanation
Indices: 2277237--2277296 Score: 61
Period size: 14 Copynumber: 4.0 Consensus size: 15
2277227 AAAAATTTAT
*
2277237 AATTTAAAAATA-TA
1 AATTTATAAATATTA
*
2277251 AATATCATAAATATTA
1 AAT-TTATAAATATTA
*
2277267 AATTT-TAAATAATA
1 AATTTATAAATATTA
2277281 AATTTAATAAATATTA
1 AATTT-ATAAATATTA
2277297 TTTTTTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
14 16 0.43
15 8 0.22
16 13 0.35
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
AATTTATAAATATTA
Found at i:2278626 original size:25 final size:24
Alignment explanation
Indices: 2278595--2278644 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2278585 TTTTTCCAAA
2278595 TTTTATCCATTTAAAATTTATAAAT
1 TTTTAT-CATTTAAAATTTATAAAT
** *
2278620 TTTTATCATTTTCAATTTATTAAT
1 TTTTATCATTTAAAATTTATAAAT
2278644 T
1 T
2278645 AATTTTTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTATCATTTAAAATTTATAAAT
Found at i:2285503 original size:10 final size:10
Alignment explanation
Indices: 2285490--2285588 Score: 53
Period size: 10 Copynumber: 9.9 Consensus size: 10
2285480 TATAAACTAG
2285490 TTTAAATAAA
1 TTTAAATAAA
*
2285500 TTTAAAT-TA
1 TTTAAATAAA
*
2285509 TTTATTTATAAA
1 TTTA--AATAAA
*
2285521 TATAAATAAA
1 TTTAAATAAA
2285531 -TTAAATAAAA
1 TTTAAAT-AAA
**
2285541 TTTAAGATTTA
1 TTTAA-ATAAA
* *
2285552 -TT-ATTTAA
1 TTTAAATAAA
*
2285560 TTTAATTAAA
1 TTTAAATAAA
2285570 TTTAAATAAA
1 TTTAAATAAA
*
2285580 TATAAATAA
1 TTTAAATAA
2285589 TATTAATATT
Statistics
Matches: 68, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
8 3 0.04
9 13 0.19
10 39 0.57
11 7 0.10
12 6 0.09
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (10 bp):
TTTAAATAAA
Found at i:2285593 original size:39 final size:41
Alignment explanation
Indices: 2285490--2285593 Score: 101
Period size: 39 Copynumber: 2.6 Consensus size: 41
2285480 TATAAACTAG
2285490 TTTAAATAAATTTAAAT-TATTTATTTATAAATATAAATAAA
1 TTTAAATAAATTTAAATATA-TTATTTATAAATATAAATAAA
* * *
2285531 -TTAAATAAAATTTAAGATTTATTA-TT-T-AATTTAATTAAA
1 TTTAAAT-AAATTTAA-ATATATTATTTATAAATATAAATAAA
*
2285570 TTTAAATAAATATAAATAATATTA
1 TTTAAATAAATTTAAAT-ATATTA
2285594 ATATTTAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
38 2 0.04
39 22 0.41
40 13 0.24
41 10 0.19
42 5 0.09
43 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (41 bp):
TTTAAATAAATTTAAATATATTATTTATAAATATAAATAAA
Found at i:2286307 original size:38 final size:38
Alignment explanation
Indices: 2286256--2286331 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 38
2286246 TCAAATTTTT
*
2286256 ATATTTAATTAATTAT-TTTTATAAAATTTTAAAAAATA
1 ATATTTAATTAATTATATTTT-CAAAATTTTAAAAAATA
*
2286294 ATATTATAA-TAATTATATTTTCAAAATTTTAATAAATA
1 ATATT-TAATTAATTATATTTTCAAAATTTTAAAAAATA
2286332 TTTAATAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 27 0.79
39 7 0.21
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (38 bp):
ATATTTAATTAATTATATTTTCAAAATTTTAAAAAATA
Found at i:2292649 original size:34 final size:33
Alignment explanation
Indices: 2292564--2292649 Score: 83
Period size: 34 Copynumber: 2.6 Consensus size: 33
2292554 CATATTTATT
*
2292564 TATATTTAAATATAAAT-A-TAATGATCTAAAAA
1 TATATTTAAATATAAATAATTAA-GATCAAAAAA
*
2292596 TAT-TTTATATA-AAATTAATTAA-ATCAAATAAAA
1 TATATTTAAATATAAA-TAATTAAGATC-AA-AAAA
2292629 TATATTTAAATATAAATAATT
1 TATATTTAAATATAAATAATT
2292650 TACATTAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
30 3 0.07
31 11 0.25
32 5 0.11
33 10 0.23
34 12 0.27
35 3 0.07
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (33 bp):
TATATTTAAATATAAATAATTAAGATCAAAAAA
Found at i:2292650 original size:15 final size:15
Alignment explanation
Indices: 2292621--2292671 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
2292611 TAATTAAATC
2292621 AAATA-AAATATATTT
1 AAATATAAATA-ATTT
2292636 AAATATAAATAATTT
1 AAATATAAATAATTT
* * *
2292651 ACAT-TAAATTATAT
1 AAATATAAATAATTT
2292665 AAATATA
1 AAATATA
2292672 TACAAATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 11 0.37
15 14 0.47
16 5 0.17
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATATAAATAATTT
Found at i:2292681 original size:23 final size:22
Alignment explanation
Indices: 2292638--2292690 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
2292628 ATATATTTAA
* *
2292638 ATATAAATAATTTACATTAAATT
1 ATATAAATAATATACAATAAA-T
2292661 ATATAAAT-ATATACAAATAAAT
1 ATATAAATAATATAC-AATAAAT
*
2292683 AAATAAAT
1 ATATAAAT
2292691 TTATTTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATAAATAATATACAATAAAT
Found at i:2299966 original size:30 final size:30
Alignment explanation
Indices: 2299927--2299991 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
2299917 GGCAAATACG
2299927 TGAA-GGCTTAAACAGAATTTCAAATATAT
1 TGAAGGGCTTAAACAGAATTTCAAATATAT
2299956 TGAAGGGCTTAAACAGAATTTCAAATATAT
1 TGAAGGGCTTAAACAGAATTTCAAATATAT
2299986 TGAAGG
1 TGAAGG
2299992 ATATACTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 4 0.11
30 31 0.89
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.29
Consensus pattern (30 bp):
TGAAGGGCTTAAACAGAATTTCAAATATAT
Found at i:2301893 original size:7 final size:7
Alignment explanation
Indices: 2301881--2301910 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2301871 ATTCTAAAGG
2301881 TAATTAA
1 TAATTAA
2301888 TAATTAA
1 TAATTAA
*
2301895 TAATTAG
1 TAATTAA
2301902 TAATTAA
1 TAATTAA
2301909 TA
1 TA
2301911 GTGGTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (7 bp):
TAATTAA
Found at i:2302016 original size:19 final size:21
Alignment explanation
Indices: 2301992--2302042 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
2301982 ATATTATATT
2301992 ATTTTATTTATT-AT-AAATA
1 ATTTTATTTATTAATAAAATA
2302011 ATTTTATTT-TTAATAAAATA
1 ATTTTATTTATTAATAAAATA
2302031 ATTTTATATTAT
1 ATTTTAT-TTAT
2302043 CTGTTAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.07
19 11 0.39
20 12 0.43
21 2 0.07
22 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTTATTTATTAATAAAATA
Found at i:2304430 original size:2 final size:2
Alignment explanation
Indices: 2304423--2304453 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2304413 GTGCACTAAC
2304423 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2304454 CTTATTAGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2304876 original size:19 final size:19
Alignment explanation
Indices: 2304838--2304876 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2304828 TATTATTAAA
*
2304838 ATATTTTATATAAATATTT
1 ATATTTTAAATAAATATTT
2304857 ATATTTTAAAATAAAT-TTT
1 ATATTTT-AAATAAATATTT
2304876 A
1 A
2304877 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTTTAAATAAATATTT
Found at i:2304882 original size:31 final size:30
Alignment explanation
Indices: 2304823--2304895 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
2304813 TTTTATCTTT
* *
2304823 TATTATATTATTAAAATATTTTATATAAATA
1 TATTATATT-TTAAAATATTTTAAATAAAAA
2304854 T-TTATATTTTAAAATAAATTTTAAATAAAAA
1 TATTATATTTTAAAAT--ATTTTAAATAAAAA
2304885 TATTAT-TTTTA
1 TATTATATTTTA
2304896 TTATTAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
29 7 0.19
30 7 0.19
31 19 0.51
32 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TATTATATTTTAAAATATTTTAAATAAAAA
Found at i:2304996 original size:16 final size:16
Alignment explanation
Indices: 2304975--2305011 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2304965 AAACTTACGA
*
2304975 AATAATTCGACTTATG
1 AATAATTCGAATTATG
*
2304991 AATAATTCTAATTATG
1 AATAATTCGAATTATG
2305007 AATAA
1 AATAA
2305012 CGATGACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (16 bp):
AATAATTCGAATTATG
Found at i:2305203 original size:16 final size:18
Alignment explanation
Indices: 2305173--2305206 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
2305163 TTTTTTTATA
2305173 ATTTTATATATAATTAAT
1 ATTTTATATATAATTAAT
2305191 ATTTTA-ATA-AATTAAT
1 ATTTTATATATAATTAAT
2305207 TATCGAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 3 0.19
18 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTATATATAATTAAT
Found at i:2305349 original size:28 final size:29
Alignment explanation
Indices: 2305291--2305358 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
2305281 AATTAAAAAT
*
2305291 ATTATTTTTAATAAAATATAATGGCTAAA
1 ATTATTTTTAATAAAATATAATAGCTAAA
* *
2305320 ATTATTTTTATATATAATA-AATAG-TTAA
1 ATTATTTTTA-ATAAAATATAATAGCTAAA
2305348 A-TATTTTTAAT
1 ATTATTTTTAAT
2305359 TAACTTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 2 0.06
27 8 0.23
28 4 0.11
29 14 0.40
30 7 0.20
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (29 bp):
ATTATTTTTAATAAAATATAATAGCTAAA
Found at i:2305766 original size:2 final size:2
Alignment explanation
Indices: 2305759--2305809 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2305749 CTAAATCATG
2305759 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
2305801 AT AT AT AT A
1 AT AT AT AT A
2305810 GAGTTACATC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2305995 original size:15 final size:15
Alignment explanation
Indices: 2305955--2305996 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
2305945 TATAAAATAT
2305955 ATAAATATTAATAAA
1 ATAAATATTAATAAA
* *
2305970 A-ATATTTTTAATAAA
1 ATA-AATATTAATAAA
2305985 ATAAATATTAAT
1 ATAAATATTAAT
2305997 TGAAACTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAATATTAATAAA
Found at i:2308887 original size:12 final size:12
Alignment explanation
Indices: 2308870--2308907 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
2308860 ATATTTAATA
2308870 AATTTTAATATG
1 AATTTTAATATG
2308882 AATTTTAACT-T-
1 AATTTTAA-TATG
2308893 AATTTTAATATG
1 AATTTTAATATG
2308905 AAT
1 AAT
2308908 CTTTTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 1 0.04
11 9 0.39
12 12 0.52
13 1 0.04
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (12 bp):
AATTTTAATATG
Found at i:2310614 original size:17 final size:18
Alignment explanation
Indices: 2310589--2310622 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2310579 AGTTATAGAA
2310589 AATAAAATT-AATGATAT
1 AATAAAATTAAATGATAT
*
2310606 AATATAATTAAATGATA
1 AATAAAATTAAATGATA
2310623 ATTATTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (18 bp):
AATAAAATTAAATGATAT
Found at i:2311560 original size:2 final size:2
Alignment explanation
Indices: 2311553--2311578 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2311543 GAAAACTATC
2311553 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
2311579 GTATGTATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2315910 original size:15 final size:16
Alignment explanation
Indices: 2315882--2315913 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2315872 TTTTTGTGTA
2315882 ATATAAATTATATAAT
1 ATATAAATTATATAAT
2315898 ATATAAA-TATATAAT
1 ATATAAATTATATAAT
2315913 A
1 A
2315914 ATTATATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATAAATTATATAAT
Found at i:2315999 original size:17 final size:15
Alignment explanation
Indices: 2315979--2316037 Score: 75
Period size: 17 Copynumber: 3.7 Consensus size: 15
2315969 TTTAGCTCAT
2315979 TTTTTTAATAAATTTA
1 TTTTTT-ATAAATTTA
2315995 TTTTTTATTTAAATTTA
1 TTTTTTA--TAAATTTA
2316012 TTTTTTA-AAATTTA
1 TTTTTTATAAATTTA
2316026 TTTATTTATAAA
1 TTT-TTTATAAA
2316038 CATAAATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
14 10 0.26
15 5 0.13
16 9 0.23
17 15 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTTTATAAATTTA
Found at i:2316053 original size:45 final size:46
Alignment explanation
Indices: 2316003--2316094 Score: 109
Period size: 46 Copynumber: 2.0 Consensus size: 46
2315993 TATTTTTTAT
* * *
2316003 TTAAATTTATTTT-TTAAAATT-TATTTATTT-ATAAACATAAATAAA
1 TTAAATATATTTTATTAAAATTCAATTCATTTAAT-AA-ATAAATAAA
*
2316048 TTAAATATATTTTATTCAAATTCAATTCATTTAATAAATAAATAAA
1 TTAAATATATTTTATTAAAATTCAATTCATTTAATAAATAAATAAA
2316094 T
1 T
2316095 ATTAAAACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
45 12 0.30
46 17 0.43
47 9 0.22
48 2 0.05
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (46 bp):
TTAAATATATTTTATTAAAATTCAATTCATTTAATAAATAAATAAA
Found at i:2316589 original size:50 final size:53
Alignment explanation
Indices: 2316510--2316608 Score: 136
Period size: 50 Copynumber: 1.9 Consensus size: 53
2316500 TTCCGATCAA
2316510 ATAAATATTAAATAATTAAAAAATA-TTTTTATTTAAATTTAATTATAAAATAT
1 ATAAATATTAAATAATTAAAAAATATTTTTTATTTAAA-TTAATTATAAAATAT
*
2316563 ATAAATATT-AAT-A-T-AAAAATAATTTTTTATTTATATTAATTATAAA
1 ATAAATATTAAATAATTAAAAAAT-ATTTTTTATTTAAATTAATTATAAA
2316609 TAGTAATATG
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
49 6 0.14
50 13 0.30
51 12 0.28
52 3 0.07
53 9 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (53 bp):
ATAAATATTAAATAATTAAAAAATATTTTTTATTTAAATTAATTATAAAATAT
Found at i:2316625 original size:50 final size:51
Alignment explanation
Indices: 2316520--2316629 Score: 124
Period size: 50 Copynumber: 2.2 Consensus size: 51
2316510 ATAAATATTA
2316520 AATAAT-T-AAAAAATATTTTTATTTAAATTTAATTATAAAATATATAAAT
1 AATAATATAAAAAAATATTTTTATTTAAATTTAATTATAAAATATATAAAT
* * *
2316569 ATTAATATAAAAATAAT-TTTTTATTTATA-TTAATTAT-AAATAGTA-ATAT
1 AATAATATAAAAA-AATATTTTTATTTAAATTTAATTATAAAATA-TATAAAT
2316618 GAATAATATAAA
1 -AATAATATAAA
2316630 TCAATGGACC
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
49 13 0.25
50 21 0.40
51 15 0.29
52 3 0.06
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (51 bp):
AATAATATAAAAAAATATTTTTATTTAAATTTAATTATAAAATATATAAAT
Found at i:2317216 original size:14 final size:15
Alignment explanation
Indices: 2317197--2317231 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
2317187 TATTGTGTTA
2317197 ATAAAATTAA-AATT
1 ATAAAATTAATAATT
2317211 ATAAAATTAATAATT
1 ATAAAATTAATAATT
*
2317226 TTAAAA
1 ATAAAA
2317232 ATTTAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAAAATTAATAATT
Found at i:2317967 original size:12 final size:12
Alignment explanation
Indices: 2317950--2317974 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2317940 TGCTAATGTG
2317950 TTTATTTCTTCA
1 TTTATTTCTTCA
2317962 TTTATTTCTTCA
1 TTTATTTCTTCA
2317974 T
1 T
2317975 CCAGCTGCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTTCTTCA
Found at i:2318517 original size:21 final size:21
Alignment explanation
Indices: 2318468--2318513 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
2318458 TATGAAAATT
2318468 TTTTAA-ATTTTTTTTATATA
1 TTTTAATATTTTTTTTATATA
2318488 TTTTAATATTTTTTTTATA-A
1 TTTTAATATTTTTTTTATATA
2318508 TTTTAA
1 TTTTAA
2318514 ATATGTGCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTAATATTTTTTTTATATA
Found at i:2320557 original size:23 final size:21
Alignment explanation
Indices: 2320526--2320572 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
2320516 TTAATATAAT
*
2320526 TATATATTTAAGAATTATAAAAA
1 TATAAATTTAA-AATT-TAAAAA
*
2320549 TATAAATTTTAAATTTAAAAA
1 TATAAATTTAAAATTTAAAAA
2320570 TAT
1 TAT
2320573 CTAAATAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 4 0.18
23 9 0.41
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TATAAATTTAAAATTTAAAAA
Found at i:2322300 original size:21 final size:22
Alignment explanation
Indices: 2322275--2322315 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2322265 TCAATTATTT
*
2322275 TTATTTGTTA-TCAATATTTAA
1 TTATTTGTTAGTCAAAATTTAA
*
2322296 TTATTTTTTAGTCAAAATTT
1 TTATTTGTTAGTCAAAATTT
2322316 CGGTGTCCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (22 bp):
TTATTTGTTAGTCAAAATTTAA
Found at i:2322461 original size:2 final size:2
Alignment explanation
Indices: 2322454--2322493 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2322444 AATCAAACTC
2322454 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
2322494 TAAATAGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2323044 original size:21 final size:22
Alignment explanation
Indices: 2323019--2323059 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2323009 AAATAATATA
2323019 ATTAAATAAATA-TATATTTTT
1 ATTAAATAAATATTATATTTTT
* *
2323040 ATTAATTAATTATTATATTT
1 ATTAAATAAATATTATATTT
2323060 AATATGATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTAAATAAATATTATATTTTT
Found at i:2323699 original size:11 final size:10
Alignment explanation
Indices: 2323671--2323703 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
2323661 TTTAAGTTTA
2323671 ATTATAAAAT
1 ATTATAAAAT
2323681 A-TATAAAAT
1 ATTATAAAAT
2323690 ATTAATAAAAT
1 ATT-ATAAAAT
2323701 ATT
1 ATT
2323704 TTTTTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
10 2 0.10
11 10 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATTATAAAAT
Done.