Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167982.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_24, whole genome shotgun sequence
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: 18142777
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 63000 characters in sequence are not A, C, G, or T
File 18 of 84
Found at i:3329490 original size:12 final size:12
Alignment explanation
Indices: 3329474--3329503 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3329464 TTTAAAAATG
3329474 ATTTAATAAAAA
1 ATTTAATAAAAA
*
3329486 TTTTAATAAAAA
1 ATTTAATAAAAA
3329498 ATTTAA
1 ATTTAA
3329504 ATTGATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTTAATAAAAA
Found at i:3329637 original size:35 final size:34
Alignment explanation
Indices: 3329598--3329665 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 34
3329588 CTATACTTAT
* *
3329598 TTAA-TAAAAATTCTATCAATACTTTATTAAAAATA
1 TTAACTAAAAA-TATATCAA-AATTTATTAAAAATA
3329633 TTAATCTAAAAATATATCAAAATTTATTAAAAA
1 TTAA-CTAAAAATATATCAAAATTTATTAAAAA
3329666 ATTTTTCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 16 0.55
36 7 0.24
37 6 0.21
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.38
Consensus pattern (34 bp):
TTAACTAAAAATATATCAAAATTTATTAAAAATA
Found at i:3331195 original size:30 final size:30
Alignment explanation
Indices: 3331159--3331215 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
3331149 TTAAAAAGTG
*
3331159 TTCTGTTTTCTTTTCTTAACTCATTTTGTA
1 TTCTGTTTTCCTTTCTTAACTCATTTTGTA
*
3331189 TTCTGTTTTCCTTTCTTAACTTATTTT
1 TTCTGTTTTCCTTTCTTAACTCATTTT
3331216 ATATCTTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.12, C:0.18, G:0.05, T:0.65
Consensus pattern (30 bp):
TTCTGTTTTCCTTTCTTAACTCATTTTGTA
Found at i:3332041 original size:16 final size:16
Alignment explanation
Indices: 3332020--3332051 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3332010 GGCCCTTCAA
3332020 TTCCTTTTCTTATAAT
1 TTCCTTTTCTTATAAT
3332036 TTCCTTTTCTTATAAT
1 TTCCTTTTCTTATAAT
3332052 GTTAAGTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (16 bp):
TTCCTTTTCTTATAAT
Found at i:3334053 original size:20 final size:21
Alignment explanation
Indices: 3334015--3334053 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3334005 TTTCTCTTGA
*
3334015 TTTTTCTAATTGATTCTTAAT
1 TTTTTCTAATTGATACTTAAT
*
3334036 TTTTTTTAATTGA-ACTTA
1 TTTTTCTAATTGATACTTA
3334054 GTGGGGGTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTTTCTAATTGATACTTAAT
Found at i:3336029 original size:15 final size:15
Alignment explanation
Indices: 3336009--3336038 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3335999 ACTCTGCTAA
3336009 TCCTTTTTGCAAGTT
1 TCCTTTTTGCAAGTT
3336024 TCCTTTTTGCAAGTT
1 TCCTTTTTGCAAGTT
3336039 AGTTGTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.13, T:0.53
Consensus pattern (15 bp):
TCCTTTTTGCAAGTT
Found at i:3338822 original size:21 final size:21
Alignment explanation
Indices: 3338797--3338838 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3338787 AAATATTCAT
3338797 TTAAAAATA-TATCAAAATTTA
1 TTAAAAA-AGTATCAAAATTTA
*
3338818 TTAAAAAAGTATCAATATTTA
1 TTAAAAAAGTATCAAAATTTA
3338839 CATATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (21 bp):
TTAAAAAAGTATCAAAATTTA
Found at i:3340209 original size:19 final size:19
Alignment explanation
Indices: 3340185--3340222 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3340175 CATAGTCCAA
3340185 CTTATAATTTCAATCTTTT
1 CTTATAATTTCAATCTTTT
*
3340204 CTTATAATTTCGATCTTTT
1 CTTATAATTTCAATCTTTT
3340223 TAATCAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.03, T:0.58
Consensus pattern (19 bp):
CTTATAATTTCAATCTTTT
Found at i:3340552 original size:26 final size:28
Alignment explanation
Indices: 3340523--3340579 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
3340513 TTTTTATTCC
*
3340523 TTTTTTTAC-TTTGAATT-TTTAAAAAA
1 TTTTTTCACATTTGAATTGTTTAAAAAA
* *
3340549 -TTTTTCACATTTTAATTGTTTAAAATA
1 TTTTTTCACATTTGAATTGTTTAAAAAA
3340576 TTTT
1 TTTT
3340580 AGATTTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
25 7 0.28
26 7 0.28
27 8 0.32
28 3 0.12
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (28 bp):
TTTTTTCACATTTGAATTGTTTAAAAAA
Found at i:3341820 original size:15 final size:17
Alignment explanation
Indices: 3341800--3341833 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3341790 CTCTTCTATG
3341800 TTTTA-TTTT-ATTTTT
1 TTTTATTTTTAATTTTT
3341815 TTTTATTTTTAATTTTT
1 TTTTATTTTTAATTTTT
3341832 TT
1 TT
3341834 AAAAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 4 0.24
17 8 0.47
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTATTTTTAATTTTT
Found at i:3341830 original size:16 final size:15
Alignment explanation
Indices: 3341800--3341833 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3341790 CTCTTCTATG
*
3341800 TTTTATTTTATTTTT
1 TTTTATTTTAATTTT
3341815 TTTTATTTTTAATTTT
1 TTTTA-TTTTAATTTT
3341831 TTT
1 TTT
3341834 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTATTTTAATTTT
Found at i:3346692 original size:27 final size:26
Alignment explanation
Indices: 3346657--3346720 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
3346647 CTTTGAATTT
* *
3346657 TTTTTAAAAAAATTTCATATTTAAATA
1 TTTTTAAAAAAATTTAAAATTTAAA-A
*
3346684 TTTTT-AAAAATTTTAAAATTTAAAA
1 TTTTTAAAAAAATTTAAAATTTAAAA
*
3346709 TTTTAAAAAAAA
1 TTTTTAAAAAAA
3346721 ATTTTAGATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 5 0.16
26 21 0.68
27 5 0.16
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
TTTTTAAAAAAATTTAAAATTTAAAA
Found at i:3346693 original size:26 final size:25
Alignment explanation
Indices: 3346657--3346764 Score: 91
Period size: 25 Copynumber: 4.4 Consensus size: 25
3346647 CTTTGAATTT
* *
3346657 TTTTTAAAAAAATTTCATATTTAAATA
1 TTTTT-AAAAAATTTAAAATTTAAA-A
*
3346684 TTTTTAAAAATTTTAAAATTTAAAA
1 TTTTTAAAAAATTTAAAATTTAAAA
* *
3346709 -TTTT-AAAAA---AAAATTTTAGA
1 TTTTTAAAAAATTTAAAATTTAAAA
* *
3346729 TTTTTAAAAATTTTAAATTTTAAAA
1 TTTTTAAAAAATTTAAAATTTAAAA
*
3346754 TTTTAAAAAAA
1 TTTTTAAAAAA
3346765 AATTTTAGAT
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
20 9 0.14
21 4 0.06
22 4 0.06
23 4 0.06
24 4 0.06
25 18 0.28
26 16 0.25
27 5 0.08
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (25 bp):
TTTTTAAAAAATTTAAAATTTAAAA
Found at i:3346707 original size:7 final size:8
Alignment explanation
Indices: 3346685--3346761 Score: 74
Period size: 8 Copynumber: 10.0 Consensus size: 8
3346675 ATTTAAATAT
3346685 TTTTAAAAA
1 TTTT-AAAA
3346694 TTTTAAAA
1 TTTTAAAA
3346702 -TTTAAAA
1 TTTTAAAA
3346709 TTTTAAAA
1 TTTTAAAA
*
3346717 ---AAAAA
1 TTTTAAAA
* *
3346722 TTTTAGAT
1 TTTTAAAA
3346730 TTTTAAAAA
1 TTTT-AAAA
3346739 TTTT-AAA
1 TTTTAAAA
3346746 TTTTAAAA
1 TTTTAAAA
3346754 TTTTAAAA
1 TTTTAAAA
3346762 AAAAATTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
5 4 0.07
7 14 0.25
8 28 0.50
9 10 0.18
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (8 bp):
TTTTAAAA
Found at i:3346733 original size:21 final size:21
Alignment explanation
Indices: 3346709--3346783 Score: 96
Period size: 21 Copynumber: 3.4 Consensus size: 21
3346699 AAATTTAAAA
3346709 TTTTAAAAAAAAATTTTAGAT
1 TTTTAAAAAAAAATTTTAGAT
* * *
3346730 TTTTAAAAATTTTAAATTTTAAAA
1 TTTTAAAAA---AAAATTTTAGAT
3346754 TTTTAAAAAAAAATTTTAGAT
1 TTTTAAAAAAAAATTTTAGAT
3346775 TTTTAAAAA
1 TTTTAAAAA
3346784 GTTTAATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
21 27 0.60
24 18 0.40
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
TTTTAAAAAAAAATTTTAGAT
Found at i:3346737 original size:17 final size:16
Alignment explanation
Indices: 3346717--3346795 Score: 76
Period size: 17 Copynumber: 5.1 Consensus size: 16
3346707 AATTTTAAAA
3346717 AAAAATTTTAGATTTTT
1 AAAAATTTTA-ATTTTT
*
3346734 AAAAATTTTAAATTTT
1 AAAAATTTTAATTTTT
**
3346750 -AAAATTTTAA---AA
1 AAAAATTTTAATTTTT
3346762 AAAAATTTTAGATTTTT
1 AAAAATTTTA-ATTTTT
*
3346779 AAAAAGTTTAATTTTT
1 AAAAATTTTAATTTTT
3346795 A
1 A
3346796 TTTTTTTAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
13 9 0.18
14 1 0.02
15 10 0.20
16 12 0.24
17 19 0.37
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (16 bp):
AAAAATTTTAATTTTT
Found at i:3346795 original size:45 final size:45
Alignment explanation
Indices: 3346683--3346795 Score: 199
Period size: 45 Copynumber: 2.5 Consensus size: 45
3346673 ATATTTAAAT
*
3346683 ATTTTTAAAAATTTTAAAATTTAAAATTTTAAAAAAAAATTTTAG
1 ATTTTTAAAAATTTTAAATTTTAAAATTTTAAAAAAAAATTTTAG
3346728 ATTTTTAAAAATTTTAAATTTTAAAATTTTAAAAAAAAATTTTAG
1 ATTTTTAAAAATTTTAAATTTTAAAATTTTAAAAAAAAATTTTAG
* *
3346773 ATTTTTAAAAAGTTTAATTTTTA
1 ATTTTTAAAAATTTTAAATTTTA
3346796 TTTTTTTAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 65 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.48
Consensus pattern (45 bp):
ATTTTTAAAAATTTTAAATTTTAAAATTTTAAAAAAAAATTTTAG
Found at i:3350290 original size:3 final size:3
Alignment explanation
Indices: 3350284--3350512 Score: 120
Period size: 3 Copynumber: 78.7 Consensus size: 3
3350274 TTTTTTTTAA
* * * * * * *
3350284 AAT AAT AAT AAT AAT AAT AAT AAT GAT GAT GAT GAT GAT GAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * *
3350332 GAT AGT AGT AAT AAT AAT AAT AAT AAT ACT AAC AA- ACT -AT GTAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
3350376 AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * *
3350423 ACT -AT AAT ATAT CACT -CT ATT AAT ATT CTAT ACT -CT AAT -AT AAT
1 AAT AAT AAT A-AT -AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
* *
3350467 AAT AAT -AT AA- AAT AAT ACT AAT AAT -AT AAT -AT AAT AAT ACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3350511 AA
1 AA
3350513 AAATGGCTCT
Statistics
Matches: 182, Mismatches: 29, Indels: 30
0.76 0.12 0.12
Matches are distributed among these distances:
2 19 0.10
3 157 0.86
4 5 0.03
5 1 0.01
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:3350490 original size:19 final size:19
Alignment explanation
Indices: 3350462--3350516 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
3350452 ATACTCTAAT
3350462 ATAATAATAATATAAAATA
1 ATAATAATAATATAAAATA
* *
3350481 ATACTAATAATATAATATA
1 ATAATAATAATATAAAATA
*
3350500 ATAATACTAATA-AAAAT
1 ATAATAATAATATAAAAT
3350517 GGCTCTATTG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
18 4 0.13
19 27 0.87
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAATAATAATATAAAATA
Found at i:3351395 original size:20 final size:21
Alignment explanation
Indices: 3351370--3351410 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3351360 ACACGCTCTC
3351370 TCTTGATT-CTTTTAATTGAT
1 TCTTGATTGCTTTTAATTGAT
*
3351390 TCTTGATTGTTTTTAATTGAT
1 TCTTGATTGCTTTTAATTGAT
3351411 CTTAGTGGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.20, C:0.07, G:0.12, T:0.61
Consensus pattern (21 bp):
TCTTGATTGCTTTTAATTGAT
Found at i:3353937 original size:21 final size:21
Alignment explanation
Indices: 3353912--3353952 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3353902 AATATTCATC
3353912 TAAAAATATATCAAAATTTAT
1 TAAAAATATATCAAAATTTAT
* *
3353933 TAAAAATTTATCAATATTTA
1 TAAAAATATATCAAAATTTA
3353953 CACATTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAAATATATCAAAATTTAT
Found at i:3354191 original size:34 final size:34
Alignment explanation
Indices: 3354152--3354221 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
3354142 TACAAGGTAC
*
3354152 ATATAGATATCTCAAATAAAAAATTAGATTTTAA
1 ATATAGATATCTCAAATAAAAAACTAGATTTTAA
*
3354186 ATATAGATATCTCAAATAAAAGACTAGATTTTAA
1 ATATAGATATCTCAAATAAAAAACTAGATTTTAA
3354220 AT
1 AT
3354222 TTTATAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.34
Consensus pattern (34 bp):
ATATAGATATCTCAAATAAAAAACTAGATTTTAA
Found at i:3357688 original size:153 final size:153
Alignment explanation
Indices: 3357411--3357718 Score: 442
Period size: 153 Copynumber: 2.0 Consensus size: 153
3357401 AAGTATGAAC
* * * *
3357411 TCTAAAAGTATTAATAGTGAACGACATAAATACCCTTATAAATTTAAGAAATAACAAATTTACTT
1 TCTAAAAGTATTAAAAATGAACAACATAAATACCCTTATAAATTTAAAAAATAACAAATTTACTT
*
3357476 TTAAATTTCTAGCATTATTTATTTATTTAATAATGATTATTTGTCATTAAATATATAGC-TTTTA
66 TTAAATTTCTAGCATTATTTATTTATTTAATAATGATTATTTGTCATTAAAAATATAGCTTTTTA
3357540 TTAGTTAGTTATTTAAATTTAAA
131 TTAGTTAGTTATTTAAATTTAAA
* ** *
3357563 TCTAAAAGTGTTAAAAATGAACAACATAAATGTCTTTATAAATTTTAAAAAATAACAAATTTA-T
1 TCTAAAAGTATTAAAAATGAACAACATAAATACCCTTATAAA-TTTAAAAAATAACAAATTTACT
* * *
3357627 ATTTCAATTTCTTGCATTTTTTATTTATTTAATAAAT-ATTATTTGTCATTAAAAATATAGCTTT
65 -TTTAAATTTCTAGCATTATTTATTTATTTAAT-AATGATTATTTGTCATTAAAAATATAGCTTT
* *
3357691 TTATTTGTTGGTTATTTAAATTTAAA
128 TTATTAGTTAGTTATTTAAATTTAAA
3357717 TC
1 TC
3357719 AACTAAAAAT
Statistics
Matches: 138, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
152 36 0.26
153 71 0.51
154 31 0.22
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (153 bp):
TCTAAAAGTATTAAAAATGAACAACATAAATACCCTTATAAATTTAAAAAATAACAAATTTACTT
TTAAATTTCTAGCATTATTTATTTATTTAATAATGATTATTTGTCATTAAAAATATAGCTTTTTA
TTAGTTAGTTATTTAAATTTAAA
Found at i:3360365 original size:22 final size:22
Alignment explanation
Indices: 3360340--3360599 Score: 120
Period size: 22 Copynumber: 11.9 Consensus size: 22
3360330 TATATTATGG
*
3360340 ATAACTTAATAATAAATAAATA
1 ATAACTTAATAGTAAATAAATA
* * *
3360362 ATAATTTAATAGTAAATAATTG
1 ATAACTTAATAGTAAATAAATA
** * **** *
3360384 ATAAGATAATTGTATGCCAATG
1 ATAACTTAATAGTAAATAAATA
* * *
3360406 ATAACATAATAATAAATACATA
1 ATAACTTAATAGTAAATAAATA
*
3360428 ATAA-TATAGTAGTAAATAACA-A
1 ATAACT-TAATAGTAAATAA-ATA
* * * *
3360450 ATAACTTAATGGTAAATTATTT
1 ATAACTTAATAGTAAATAAATA
* * *
3360472 AT-ACATAATTGTAAATATATA
1 ATAACTTAATAGTAAATAAATA
* **
3360493 ATAA-TATAATAGTAAATTAAGG
1 ATAACT-TAATAGTAAATAAATA
* * * *
3360515 ATAATTTAATA-AAAATAAGTG
1 ATAACTTAATAGTAAATAAATA
*
3360536 ATAACTTAATCA-TAAAGT-AATG
1 ATAACTTAAT-AGTAAA-TAAATA
* *
3360558 ATAACTTAGTAGTAAATTAATA
1 ATAACTTAATAGTAAATAAATA
*
3360580 ATAATTTAATAGTAAATAAA
1 ATAACTTAATAGTAAATAAA
3360600 CTTCAATTTA
Statistics
Matches: 173, Mismatches: 54, Indels: 22
0.69 0.22 0.09
Matches are distributed among these distances:
21 32 0.18
22 137 0.79
23 4 0.02
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.34
Consensus pattern (22 bp):
ATAACTTAATAGTAAATAAATA
Found at i:3361059 original size:22 final size:22
Alignment explanation
Indices: 3361029--3361288 Score: 183
Period size: 22 Copynumber: 11.8 Consensus size: 22
3361019 TAAATTAGTG
* *
3361029 ATAACTTAATAATACATCAATA
1 ATAACTTAATAGTAAATCAATA
* *
3361051 ATAATTTAATAGTAAAT-AATTG
1 ATAACTTAATAGTAAATCAA-TA
3361073 ATAACTTAATAGTAAATCAATA
1 ATAACTTAATAGTAAATCAATA
3361095 ATAA-TATAATAGTAAATGC-ATA
1 ATAACT-TAATAGTAAAT-CAATA
* *
3361117 ATAACTCAATAGTAAATCAATT
1 ATAACTTAATAGTAAATCAATA
*
3361139 ATAACATAA-ATGTAAATGC-ATA
1 ATAACTTAATA-GTAAAT-CAATA
* * * *
3361161 ATAGCATAGTAGTAAATCAATG
1 ATAACTTAATAGTAAATCAATA
** * *
3361183 ATAACTTAATAAACAAATAAATG
1 ATAACTTAAT-AGTAAATCAATA
* * *
3361206 ATAACTTAATAGTTAATCATTG
1 ATAACTTAATAGTAAATCAATA
*
3361228 ATAATTTAATAGTAAATCAATGA
1 ATAACTTAATAGTAAATCAAT-A
* * * * *
3361251 A-AATTTAGTAATAAATTACA-G
1 ATAACTTAATAGTAAATCA-ATA
3361272 ATAACTTAATAGTAAAT
1 ATAACTTAATAGTAAAT
3361289 ATGTTTTAGT
Statistics
Matches: 188, Mismatches: 36, Indels: 28
0.75 0.14 0.11
Matches are distributed among these distances:
21 7 0.04
22 154 0.82
23 27 0.14
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.33
Consensus pattern (22 bp):
ATAACTTAATAGTAAATCAATA
Found at i:3361118 original size:66 final size:66
Alignment explanation
Indices: 3361035--3361288 Score: 221
Period size: 66 Copynumber: 3.8 Consensus size: 66
3361025 AGTGATAACT
* * * *
3361035 TAATAATACATCAATAATAATTTAATAGTAAATAATTGATAACTTAATAGTAAATCAATAATAAT
1 TAATAGTAAATCAATAATAACTTAATAATAAATAATTGATAACTTAATAGTAAATCAATAATAAT
3361100 A
66 A
* * *
3361101 TAATAGTAAATGC-ATAATAACTCAATAGTAAATCAATT-ATAACATAA-ATGTAAATGC-ATAA
1 TAATAGTAAAT-CAATAATAACTTAATAATAAAT-AATTGATAACTTAATA-GTAAAT-CAATAA
**
3361162 TAGCA
62 TAATA
* * * * * * *
3361167 TAGTAGTAAATCAATGATAACTTAATAAACAAATAAATGATAACTTAATAGTTAATCATTGATAA
1 TAATAGTAAATCAATAATAACTTAAT-AATAAATAATTGATAACTTAATAGTAAATCAATAATAA
*
3361232 TT
65 TA
* * * **
3361234 TAATAGTAAATCAATGAA-AATTTAGTAATAAATTACAGATAACTTAATAGTAAAT
1 TAATAGTAAATCAAT-AATAACTTAATAATAAATAATTGATAACTTAATAGTAAAT
3361289 ATGTTTTAGT
Statistics
Matches: 149, Mismatches: 29, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
65 2 0.01
66 97 0.65
67 48 0.32
68 2 0.01
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.33
Consensus pattern (66 bp):
TAATAGTAAATCAATAATAACTTAATAATAAATAATTGATAACTTAATAGTAAATCAATAATAAT
A
Found at i:3361380 original size:22 final size:22
Alignment explanation
Indices: 3361350--3361458 Score: 89
Period size: 22 Copynumber: 5.0 Consensus size: 22
3361340 TAACTTAGTA
3361350 TATAGTAAATCATTGATAATTT
1 TATAGTAAATCATTGATAATTT
* **
3361372 TATAATAAATTTTTGATAA-TT
1 TATAGTAAATCATTGATAATTT
* * *
3361393 TAGTAGTAAATCACTAATAATGT
1 TA-TAGTAAATCATTGATAATTT
* *
3361416 TATAGT-AATTATTGATAA-CT
1 TATAGTAAATCATTGATAATTT
* *
3361436 TAGTTGTAAATCAGTGATAATTT
1 TA-TAGTAAATCATTGATAATTT
3361459 AGTATAAATT
Statistics
Matches: 65, Mismatches: 17, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
20 3 0.05
21 16 0.25
22 42 0.65
23 4 0.06
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (22 bp):
TATAGTAAATCATTGATAATTT
Found at i:3361445 original size:43 final size:44
Alignment explanation
Indices: 3361352--3361469 Score: 125
Period size: 43 Copynumber: 2.7 Consensus size: 44
3361342 ACTTAGTATA
* * * * *
3361352 TAGTAAATCATTGATAATTTTATAATAAATTTTTGATAATTTAG
1 TAGTAAATCACTAATAATGTTATAATAAATTATTGATAACTTAG
*
3361396 TAGTAAATCACTAATAATGTTATAGT-AATTATTGATAACTTAG
1 TAGTAAATCACTAATAATGTTATAATAAATTATTGATAACTTAG
* * *
3361439 TTGTAAATCAGTGATAAT-TTAGT-ATAAATTA
1 TAGTAAATCACTAATAATGTTA-TAATAAATTA
3361470 ATAATGATTT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
42 4 0.06
43 36 0.58
44 22 0.35
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (44 bp):
TAGTAAATCACTAATAATGTTATAATAAATTATTGATAACTTAG
Found at i:3361460 original size:22 final size:22
Alignment explanation
Indices: 3361385--3361489 Score: 72
Period size: 22 Copynumber: 4.9 Consensus size: 22
3361375 AATAAATTTT
* *
3361385 TGATAATTTAGTAGTAAATCAC
1 TGATAATTTAGTTGTAAATCAA
* * * *
3361407 TAATAATGTTA-TAGT-AATTAT
1 TGATAAT-TTAGTTGTAAATCAA
* *
3361428 TGATAACTTAGTTGTAAATCAG
1 TGATAATTTAGTTGTAAATCAA
* *
3361450 TGATAATTTAG-TATAAATTAA
1 TGATAATTTAGTTGTAAATCAA
* *
3361471 TAATGATTTAGTTGTAAAT
1 TGATAATTTAGTTGTAAAT
3361490 TAGTTAATTA
Statistics
Matches: 64, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
20 3 0.05
21 28 0.44
22 30 0.47
23 3 0.05
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.42
Consensus pattern (22 bp):
TGATAATTTAGTTGTAAATCAA
Found at i:3361549 original size:22 final size:21
Alignment explanation
Indices: 3361490--3361567 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 21
3361480 AGTTGTAAAT
* *
3361490 TAGTTAATTATTAACAAC-TTA
1 TAGTAAATTA-TAATAACTTTA
*
3361511 TTAGTAAATCATCAATAACTTTA
1 -TAGTAAATTAT-AATAACTTTA
*
3361534 TAGTAAATTAGTAATAATTTTA
1 TAGTAAATTA-TAATAACTTTA
*
3361556 TAATAAATTATA
1 TAGTAAATTATA
3361568 GTAAATTAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
21 3 0.06
22 40 0.85
23 4 0.09
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.42
Consensus pattern (21 bp):
TAGTAAATTATAATAACTTTA
Found at i:3361561 original size:11 final size:10
Alignment explanation
Indices: 3361531--3361598 Score: 64
Period size: 11 Copynumber: 6.4 Consensus size: 10
3361521 ATCAATAACT
*
3361531 TTATAGTAAA
1 TTATAATAAA
*
3361541 TTAGTAATAATT
1 TTA-TAATAA-A
3361553 TTATAATAAA
1 TTATAATAAA
*
3361563 TTATAGTAAA
1 TTATAATAAA
*
3361573 TTAGTAATAACT
1 TTA-TAATAA-A
3361585 TTATAATAAA
1 TTATAATAAA
3361595 TTAT
1 TTAT
3361599 CTATAACTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
10 19 0.40
11 22 0.47
12 6 0.13
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (10 bp):
TTATAATAAA
Found at i:3361570 original size:32 final size:32
Alignment explanation
Indices: 3361531--3361598 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
3361521 ATCAATAACT
*
3361531 TTATAGTAAATTAGTAATAATTTTATAATAAA
1 TTATAGTAAATTAGTAATAACTTTATAATAAA
3361563 TTATAGTAAATTAGTAATAACTTTATAATAAA
1 TTATAGTAAATTAGTAATAACTTTATAATAAA
3361595 TTAT
1 TTAT
3361599 CTATAACTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (32 bp):
TTATAGTAAATTAGTAATAACTTTATAATAAA
Found at i:3361588 original size:22 final size:22
Alignment explanation
Indices: 3361563--3361639 Score: 86
Period size: 22 Copynumber: 3.5 Consensus size: 22
3361553 TTATAATAAA
3361563 TTATAGTAAATTAGT-AATAACT
1 TTATAGTAAATTA-TCAATAACT
* *
3361585 TTATAATAAATTATCTATAACT
1 TTATAGTAAATTATCAATAACT
* *
3361607 TAATAGTAAATTATCACTAA-T
1 TTATAGTAAATTATCAATAACT
3361628 TTAGTAGTAAAT
1 TTA-TAGTAAAT
3361640 CTTTATACTT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
21 4 0.09
22 42 0.91
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (22 bp):
TTATAGTAAATTATCAATAACT
Found at i:3361639 original size:76 final size:75
Alignment explanation
Indices: 3361463--3361639 Score: 182
Period size: 76 Copynumber: 2.4 Consensus size: 75
3361453 TAATTTAGTA
* * * * * *
3361463 TAAATTAATAATGATTTAGTTGTAAA-TTAGTTAATTATTAACAACTTATTAGTAAATCATCAAT
1 TAAATTAGTAATAATTTAGTAGTAAATTTAGTAAATTAGTAACAACTTATTAATAAATCATCAAT
*
3361527 AACTTTATAG
66 AACTTAATAG
* * *
3361537 TAAATTAGTAATAATTTTA-TAATAAATTATAGTAAATTAGTAATAACTT-TATAATAAATTATC
1 TAAATTAGTAATAA-TTTAGTAGTAAATT-TAGTAAATTAGTAACAACTTAT-TAATAAATCATC
*
3361600 TATAACTTAATAG
63 AATAACTTAATAG
*
3361613 TAAATTA-TCACTAATTTAGTAGTAAAT
1 TAAATTAGT-AATAATTTAGTAGTAAAT
3361640 CTTTATACTT
Statistics
Matches: 84, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
74 17 0.20
75 11 0.13
76 56 0.67
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.42
Consensus pattern (75 bp):
TAAATTAGTAATAATTTAGTAGTAAATTTAGTAAATTAGTAACAACTTATTAATAAATCATCAAT
AACTTAATAG
Found at i:3361673 original size:22 final size:22
Alignment explanation
Indices: 3361579--3361681 Score: 79
Period size: 22 Copynumber: 4.8 Consensus size: 22
3361569 TAAATTAGTA
*
3361579 ATAACTTTA-TAATAAATTATCT
1 ATAAC-TTAGTAATAAATCATCT
* * *
3361601 ATAACTTAATAGTAAATTATC-
1 ATAACTTAGTAATAAATCATCT
* * *
3361622 ACTAATTTAGTAGTAAATC-TTT
1 A-TAACTTAGTAATAAATCATCT
*
3361644 AT-ACTTAGCAATAAATCATCT
1 ATAACTTAGTAATAAATCATCT
*
3361665 ATAACTTAGTGATAAAT
1 ATAACTTAGTAATAAAT
3361682 TAATGATAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
20 12 0.18
21 10 0.15
22 43 0.66
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.40
Consensus pattern (22 bp):
ATAACTTAGTAATAAATCATCT
Found at i:3362373 original size:22 final size:22
Alignment explanation
Indices: 3362348--3362448 Score: 96
Period size: 22 Copynumber: 4.5 Consensus size: 22
3362338 CTCATATATT
* *
3362348 GTAATTTATTGATAAATTAATA
1 GTAATTTATTAATAACTTAATA
* * *
3362370 GTAAATCATAAATAACTTAATA
1 GTAATTTATTAATAACTTAATA
* *
3362392 GTAATTTAATTGATAATTTAATA
1 GTAATTT-ATTAATAACTTAATA
* *
3362415 GTAAATAATTAATAACTTAATA
1 GTAATTTATTAATAACTTAATA
3362437 GCTAA-TTATTAA
1 G-TAATTTATTAA
3362449 AAAGTTAGTA
Statistics
Matches: 62, Mismatches: 15, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
22 42 0.68
23 20 0.32
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.41
Consensus pattern (22 bp):
GTAATTTATTAATAACTTAATA
Found at i:3362413 original size:45 final size:44
Alignment explanation
Indices: 3362348--3362443 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 44
3362338 CTCATATATT
*
3362348 GTAATTTATTGATAAATTAATAGTAAATCATAAATAACTTAATA
1 GTAATTTATTGATAAATTAATAGTAAATAATAAATAACTTAATA
* *
3362392 GTAATTTAATTGATAATTTAATAGTAAATAATTAATAACTTAATA
1 GTAATTT-ATTGATAAATTAATAGTAAATAATAAATAACTTAATA
3362437 GCTAATT
1 G-TAATT
3362444 ATTAAAAAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 7 0.15
45 35 0.74
46 5 0.11
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (44 bp):
GTAATTTATTGATAAATTAATAGTAAATAATAAATAACTTAATA
Found at i:3362688 original size:66 final size:66
Alignment explanation
Indices: 3362613--3362740 Score: 170
Period size: 66 Copynumber: 1.9 Consensus size: 66
3362603 GATAATTTTA
* * * *
3362613 TAGTAAATCATTTATAACTTCATAGAAAATTAGTT-ATAACTTT-ATAATAAATTATCAATAACT
1 TAGTAAATCATTCATAACTTAATAGAAAATCA-TTGATAA-TTTAATAATAAATCATCAATAACT
3362676 TAG
64 TAG
* *
3362679 TAGTAAATCATTCATAACTTAATAGTAAATCATTGATAATTTAATAATAAATCATTAATAAC
1 TAGTAAATCATTCATAACTTAATAGAAAATCATTGATAATTTAATAATAAATCATCAATAAC
3362741 ATAATAATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
65 5 0.09
66 49 0.91
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.38
Consensus pattern (66 bp):
TAGTAAATCATTCATAACTTAATAGAAAATCATTGATAATTTAATAATAAATCATCAATAACTTA
G
Found at i:3362761 original size:22 final size:22
Alignment explanation
Indices: 3362596--3362752 Score: 129
Period size: 22 Copynumber: 7.1 Consensus size: 22
3362586 TAAATTTGTT
* * * *
3362596 AATCATTGATAATTTTATAGTA
1 AATCATTAATAACTTAATAATA
* *
3362618 AATCATTTATAACTTCATAGA-A
1 AATCATTAATAACTTAATA-ATA
* *
3362640 AATTAGTT-ATAACTTTATAATA
1 AATCA-TTAATAACTTAATAATA
* * * *
3362662 AATTATCAATAACTTAGTAGTA
1 AATCATTAATAACTTAATAATA
* *
3362684 AATCATTCATAACTTAATAGTA
1 AATCATTAATAACTTAATAATA
* *
3362706 AATCATTGATAATTTAATAATA
1 AATCATTAATAACTTAATAATA
*
3362728 AATCATTAATAACATAATAATA
1 AATCATTAATAACTTAATAATA
3362750 AAT
1 AAT
3362753 TAGTTATAAT
Statistics
Matches: 111, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
21 2 0.02
22 107 0.96
23 2 0.02
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (22 bp):
AATCATTAATAACTTAATAATA
Found at i:3362763 original size:17 final size:17
Alignment explanation
Indices: 3362741--3362773 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3362731 CATTAATAAC
3362741 ATAATAATAAATTAGTT
1 ATAATAATAAATTAGTT
*
3362758 ATAATAATATATTAGT
1 ATAATAATAAATTAGT
3362774 ATTAACTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
ATAATAATAAATTAGTT
Found at i:3362822 original size:22 final size:21
Alignment explanation
Indices: 3362795--3362845 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
3362785 CGTAATTTTT
3362795 TGATAACTTAATG-ATAAATCAG
1 TGATAA-TTAA-GCATAAATCAG
*
3362817 TTATAATTAAGCTATAAATCAG
1 TGATAATTAAGC-ATAAATCAG
3362839 TGATAAT
1 TGATAAT
3362846 AATAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.04
21 4 0.16
22 20 0.80
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (21 bp):
TGATAATTAAGCATAAATCAG
Found at i:3365903 original size:35 final size:35
Alignment explanation
Indices: 3365857--3365925 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
3365847 GGTTTTACTG
3365857 GCATACAGATAGGAAGAAGAAAGTGTT-GAAGCCAA
1 GCATACAGATAGGAAGAAGAAAGT-TTAGAAGCCAA
* *
3365892 GCATACAGATAGGAGGGAGAAAGTTTAGAAGCCA
1 GCATACAGATAGGAAGAAGAAAGTTTAGAAGCCA
3365926 GAAAGTGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 2 0.06
35 29 0.94
ACGTcount: A:0.43, C:0.12, G:0.30, T:0.14
Consensus pattern (35 bp):
GCATACAGATAGGAAGAAGAAAGTTTAGAAGCCAA
Found at i:3371462 original size:22 final size:21
Alignment explanation
Indices: 3371432--3371490 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
3371422 AATAAATATT
*
3371432 AAAATATTTTTAAAATGT-AGAA
1 AAAAAATTTTTAAAAT-TCA-AA
*
3371454 AAAAAATTTTTACAATTCAAA
1 AAAAAATTTTTAAAATTCAAA
*
3371475 ATATAAATTTTTAAAA
1 A-AAAAATTTTTAAAA
3371491 AAGTAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (21 bp):
AAAAAATTTTTAAAATTCAAA
Found at i:3371498 original size:23 final size:24
Alignment explanation
Indices: 3371472--3371516 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3371462 TTTACAATTC
*
3371472 AAAATAT-AAATTTTTAAAAAAGT
1 AAAATATGAAATTTCTAAAAAAGT
*
3371495 AAAATATGGAATTTCTAAAAAA
1 AAAATATGAAATTTCTAAAAAA
3371517 AAATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (24 bp):
AAAATATGAAATTTCTAAAAAAGT
Found at i:3375916 original size:27 final size:27
Alignment explanation
Indices: 3375884--3375993 Score: 220
Period size: 27 Copynumber: 4.1 Consensus size: 27
3375874 GAGATATGCT
3375884 AATAGAACCAACTTACTAGAAATGCCA
1 AATAGAACCAACTTACTAGAAATGCCA
3375911 AATAGAACCAACTTACTAGAAATGCCA
1 AATAGAACCAACTTACTAGAAATGCCA
3375938 AATAGAACCAACTTACTAGAAATGCCA
1 AATAGAACCAACTTACTAGAAATGCCA
3375965 AATAGAACCAACTTACTAGAAATGCCA
1 AATAGAACCAACTTACTAGAAATGCCA
3375992 AA
1 AA
3375994 AAGAGTTAAC
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 83 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (27 bp):
AATAGAACCAACTTACTAGAAATGCCA
Found at i:3376208 original size:74 final size:74
Alignment explanation
Indices: 3376087--3376227 Score: 264
Period size: 74 Copynumber: 1.9 Consensus size: 74
3376077 AGGCCCCCGC
*
3376087 TGCCAAAAAGAGTTAACCTTTAGGGCTATATTGTTTAAGTATGAGATATGCTAATAGAACCAACT
1 TGCCAAAAAGAGTTAACCTTTAGGGCTATATTGTTTAAGTATGAGATATGCCAATAGAACCAACT
3376152 TACTAGAAA
66 TACTAGAAA
*
3376161 TGCCAAAAAGAGTTAACCTTTAGGGCTATATTGTTTAAGTGTGAGATATGCCAATAGAACCAACT
1 TGCCAAAAAGAGTTAACCTTTAGGGCTATATTGTTTAAGTATGAGATATGCCAATAGAACCAACT
3376226 TA
66 TA
3376228 AGACTTCTTT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 65 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (74 bp):
TGCCAAAAAGAGTTAACCTTTAGGGCTATATTGTTTAAGTATGAGATATGCCAATAGAACCAACT
TACTAGAAA
Found at i:3376361 original size:27 final size:27
Alignment explanation
Indices: 3376329--3376384 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
3376319 GAGATATGCT
3376329 AATAGAACCAACTTACTAGAAATGCCA
1 AATAGAACCAACTTACTAGAAATGCCA
*
3376356 AATAGAACCAACTTATTAGAAATGCCA
1 AATAGAACCAACTTACTAGAAATGCCA
3376383 AA
1 AA
3376385 AGGAGTTAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.50, C:0.20, G:0.11, T:0.20
Consensus pattern (27 bp):
AATAGAACCAACTTACTAGAAATGCCA
Found at i:3378694 original size:17 final size:16
Alignment explanation
Indices: 3378663--3378696 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3378653 ACTAATTCGC
*
3378663 AAATCTGATTTTTTAT
1 AAATCTGAATTTTTAT
3378679 AAATCATGAATTTTTAT
1 AAATC-TGAATTTTTAT
3378696 A
1 A
3378697 TGACTTATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (16 bp):
AAATCTGAATTTTTAT
Found at i:3384662 original size:12 final size:12
Alignment explanation
Indices: 3384645--3384669 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3384635 TAATCATATT
3384645 TATCTAATATAA
1 TATCTAATATAA
3384657 TATCTAATATAA
1 TATCTAATATAA
3384669 T
1 T
3384670 TTTGAGAATG
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TATCTAATATAA
Found at i:3388275 original size:63 final size:63
Alignment explanation
Indices: 3388187--3388311 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 63
3388177 AGATTAAGTG
* * * ** * *
3388187 TAGTATCTATTTTTATCAGTTTAATATCTGATATGTGGGTCATTGACCCACATGGTATTAAAT
1 TAGTATCTATTCTTATAAATTTAATATCTGATATGTGCATCATTCACCCACACGGTATTAAAT
*
3388250 TAGTATCTGTTCTTATAAATTTAATATCTGATATGTGCATCATTCACCCACACGGTATTAAA
1 TAGTATCTATTCTTATAAATTTAATATCTGATATGTGCATCATTCACCCACACGGTATTAAA
3388312 GTAATTTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (63 bp):
TAGTATCTATTCTTATAAATTTAATATCTGATATGTGCATCATTCACCCACACGGTATTAAAT
Found at i:3388538 original size:35 final size:35
Alignment explanation
Indices: 3388492--3388561 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
3388482 AGGTTTTACT
3388492 AGCATACAGATAGGAAGAAGAAAGTGTT-GAAGCCA
1 AGCATACAGATAGGAAGAAGAAAGT-TTAGAAGCCA
* *
3388527 AGCATACAGATAGGAGGGAGAAAGTTTAGAAGCCA
1 AGCATACAGATAGGAAGAAGAAAGTTTAGAAGCCA
3388562 GAAAGTGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 2 0.06
35 30 0.94
ACGTcount: A:0.44, C:0.11, G:0.30, T:0.14
Consensus pattern (35 bp):
AGCATACAGATAGGAAGAAGAAAGTTTAGAAGCCA
Found at i:3391551 original size:3 final size:3
Alignment explanation
Indices: 3391543--3391580 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3391533 AAACACCATT
3391543 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 TT
3391581 TATTTAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3392395 original size:26 final size:26
Alignment explanation
Indices: 3392359--3392452 Score: 179
Period size: 26 Copynumber: 3.6 Consensus size: 26
3392349 CGCTCAGAAC
3392359 CAAAACGACGTCGTTTCATTAAAGGT
1 CAAAACGACGTCGTTTCATTAAAGGT
3392385 CAAAACGACGTCGTTTCATTAAAGGT
1 CAAAACGACGTCGTTTCATTAAAGGT
*
3392411 CAAAATGACGTCGTTTCATTAAAGGT
1 CAAAACGACGTCGTTTCATTAAAGGT
3392437 CAAAACGACGTCGTTT
1 CAAAACGACGTCGTTT
3392453 TAACCGCTGA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 66 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (26 bp):
CAAAACGACGTCGTTTCATTAAAGGT
Found at i:3394196 original size:14 final size:14
Alignment explanation
Indices: 3394177--3394224 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
3394167 GGTCAAAAAC
*
3394177 AAAAAAAAAAATTA
1 AAAAAAAAAAATCA
*
3394191 AAAAAAACAAATC-
1 AAAAAAAAAAATCA
* *
3394204 AAAAATAAAAAGCA
1 AAAAAAAAAAATCA
3394218 AAAAAAA
1 AAAAAAA
3394225 TTCACATACA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.83, C:0.06, G:0.02, T:0.08
Consensus pattern (14 bp):
AAAAAAAAAAATCA
Found at i:3405389 original size:46 final size:46
Alignment explanation
Indices: 3405278--3405889 Score: 670
Period size: 46 Copynumber: 12.8 Consensus size: 46
3405268 AACATATGAG
*
3405278 ATTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGCCTTTTTCAAGAAGAGA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTC---AAGAGA
3405328 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGA
* * **
3405374 ATTTTAAAATTGTTGAGCCTCTGCTGAGATGAGCACTTTCAAGAGA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGA
* * * *
3405420 TTTTTTAAAAGTTGTTGAGCCTCTACTGAGATGAGCCCTTTTCAAGAGA
1 -ATTTT-AAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAAGAGA
* * * * *
3405469 ATTTAAAAGTTATTGAACCTCCGCTGATAGGAGCTTTTTCAAGATGAA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGA-G-A
* * * * *
3405517 ATTTTAAAGTTTTTGAGCATTTGCTGAGAGAAGC-ATTTCTAAGAGA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC-AAGAGA
* * * * *
3405563 TTTTTTAAAGTTGTTGAGCTTTTGCTGAGAGGAGCCCTTTCCAAGATGAA
1 -ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAAGA-G-A
* *
3405613 ATTTTAAAG-TGTTGAGCCTCTGCTGAGAGGAGCATTTCCAAGAGA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGA
* *
3405658 ATTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTTCAAAATGA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGA-GA
*
3405705 GATTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGCTTTTTCAAGATGGAA
1 -ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGA--G-A
* * **
3405755 ATTTTAAAGTTGTTAAGCCTTTGCTGAGAAAAGCTTTTTTCAAGAAGAGA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTTTC---AAGAGA
3405805 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGA
* * * *
3405851 ATTTTAAAGTTATTGAGCCTTTGCTAAGAGGAGCCTTTT
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTT
3405890 AAACTTTCAA
Statistics
Matches: 483, Mismatches: 59, Indels: 44
0.82 0.10 0.08
Matches are distributed among these distances:
45 10 0.02
46 131 0.27
47 73 0.15
48 127 0.26
49 66 0.14
50 71 0.15
51 1 0.00
53 4 0.01
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (46 bp):
ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGA
Found at i:3405449 original size:48 final size:47
Alignment explanation
Indices: 3405278--3405889 Score: 687
Period size: 48 Copynumber: 12.8 Consensus size: 47
3405268 AACATATGAG
*
3405278 ATTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGCCTTTTTCAAGAAGAGA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAAG-AGA-A
3405328 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAG-A
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGAA
* * ** *
3405374 ATTTTAAAATTGTTGAGCCTCTGCTGAGATGAGCACTTTCAAGAGAT
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGAA
* * * *
3405421 TTTTTAAAAGTTGTTGAGCCTCTACTGAGATGAGCCCTTTTCAAGAG-A
1 ATTTT-AAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAAGAGAA
* * * * *
3405469 ATTTAAAAGTTATTGAACCTCCGCTGATAGGAGCTTTTTCAAGATGAA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGA-GAA
* * * * * *
3405517 ATTTTAAAGTTTTTGAGCATTTGCTGAGAGAAGC-ATTTCTAAGAGAT
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTC-AAGAGAA
* * * * *
3405564 TTTTTAAAGTTGTTGAGCTTTTGCTGAGAGGAGCCCTTTCCAAGATGAA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAAGA-GAA
* *
3405613 ATTTTAAAG-TGTTGAGCCTCTGCTGAGAGGAGCATTTCCAAGAG-A
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGAA
* * *
3405658 ATTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTTCAAAATGAG
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGA-GAA
*
3405706 ATTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGCTTTTTCAAGATGGAA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGA--GAA
* * **
3405755 ATTTTAAAGTTGTTAAGCCTTTGCTGAGAAAAGCTTTTTTCAAGAAGAGA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTTTCAAG-AGA-A
3405805 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAG-A
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGAA
* * * *
3405851 ATTTTAAAGTTATTGAGCCTTTGCTAAGAGGAGCCTTTT
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTT
3405890 AAACTTTCAA
Statistics
Matches: 481, Mismatches: 65, Indels: 36
0.83 0.11 0.06
Matches are distributed among these distances:
45 10 0.02
46 119 0.25
47 73 0.15
48 131 0.27
49 75 0.16
50 72 0.15
51 1 0.00
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (47 bp):
ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAGAA
Found at i:3405509 original size:95 final size:94
Alignment explanation
Indices: 3405278--3405889 Score: 726
Period size: 95 Copynumber: 6.4 Consensus size: 94
3405268 AACATATGAG
* *
3405278 ATTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGCCTTTTTCAAGAAGAGAATTTTAAAGTTGTTG
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAAGATGA-AATTTTAAAGTTGTTG
3405343 AGCCTCTGCTGAGAGGAGCTTTTTCAAGAGA
64 AGCCTCTGCTGAGAGGAGCTTTTTCAAGAGA
* * ** **
3405374 ATTTTAAAATTGTTGAGCCTCTGCTGAGATGAGCACTTTCAAGA-GATTTTTTAAAAGTTGTTGA
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATGAAATTTT-AAAGTTGTTGA
* * *
3405438 GCCTCTACTGAGATGAGCCCTTTTCAAGAGA
65 GCCTCTGCTGAGAGGAG-CTTTTTCAAGAGA
* * * * * *
3405469 ATTTAAAAGTTATTGAACCTCCGCTGATAGGAGCTTTTTCAAGATGAAATTTTAAAGTTTTTGAG
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATGAAATTTTAAAGTTGTTGAG
* * * *
3405534 CATTTGCTGAGAGAAGC-ATTTCTAAGAGA
66 CCTCTGCTGAGAGGAGCTTTTTC-AAGAGA
* * * * *
3405563 TTTTTTAAAGTTGTTGAGCTTTTGCTGAGAGGAGCCCTTTCCAAGATGAAATTTTAAAG-TGTTG
1 -ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAAGATGAAATTTTAAAGTTGTTG
* *
3405627 AGCCTCTGCTGAGAGGAGCATTTCCAAGAGA
64 AGCCTCTGCTGAGAGGAGCTTTTTCAAGAGA
* * *
3405658 ATTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTTCAAAATGAGATTTTAAAGTTGTTGAG
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATGAAATTTTAAAGTTGTTGAG
*
3405723 CCTCTGCTAAGAGGAGCTTTTTCAAGATGGAA
66 CCTCTGCTGAGAGGAGCTTTTTCAAGA--G-A
* * ** *
3405755 ATTTTAAAGTTGTTAAGCCTTTGCTGAGAAAAGCTTTTTTCAAGAAGAGAATTTTAAAGTTGTTG
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTTTCAAGATGA-AATTTTAAAGTTGTTG
3405820 AGCCTCTGCTGAGAGGAGCTTTTTCAAGAGA
64 AGCCTCTGCTGAGAGGAGCTTTTTCAAGAGA
* * * *
3405851 ATTTTAAAGTTATTGAGCCTTTGCTAAGAGGAGCCTTTT
1 ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTT
3405890 AAACTTTCAA
Statistics
Matches: 433, Mismatches: 70, Indels: 27
0.82 0.13 0.05
Matches are distributed among these distances:
93 28 0.06
94 95 0.22
95 133 0.31
96 92 0.21
97 31 0.07
98 11 0.03
99 43 0.10
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (94 bp):
ATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATGAAATTTTAAAGTTGTTGAG
CCTCTGCTGAGAGGAGCTTTTTCAAGAGA
Found at i:3406109 original size:6 final size:6
Alignment explanation
Indices: 3406098--3406137 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
3406088 TATTTAATTT
* *
3406098 TTTTTC TTTTTC TCTTTC TTTTTC TTCTTC TTTTTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT
3406138 CTTCCCATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:3406117 original size:12 final size:11
Alignment explanation
Indices: 3406095--3406140 Score: 67
Period size: 12 Copynumber: 4.1 Consensus size: 11
3406085 ATTTATTTAA
3406095 TTTT-TTTTCT
1 TTTTCTTTTCT
3406105 TTTTCTCTTTCT
1 TTTTCT-TTTCT
3406117 TTTTCTTCTTCT
1 TTTTCTT-TTCT
3406129 TTTTCTTTTCT
1 TTTTCTTTTCT
3406140 T
1 T
3406141 CCCATTTCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.12
11 7 0.21
12 22 0.67
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:3410636 original size:24 final size:24
Alignment explanation
Indices: 3410588--3410633 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3410578 TTGAAAATTT
* *
3410588 AAAAATTTTTTTTTTAGATTTTTA
1 AAAAAATTTATTTTTAGATTTTTA
3410612 AAAAAATTTATTTTTA-ATTTTT
1 AAAAAATTTATTTTTAGATTTTT
3410634 TAATTATGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAAAAATTTATTTTTAGATTTTTA
Found at i:3414164 original size:2 final size:2
Alignment explanation
Indices: 3414157--3414194 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3414147 ACATACATAC
*
3414157 AT AT AT AT AA 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
3414195 TCCAACGCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3415351 original size:28 final size:28
Alignment explanation
Indices: 3415311--3415367 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
3415301 CATGATTATC
*
3415311 GATGACACATGATTATTATGTGACAATA
1 GATGACACATGATTATCATGTGACAATA
3415339 GATGACACATGATTATCATGTGACAATA
1 GATGACACATGATTATCATGTGACAATA
3415367 G
1 G
3415368 CATTTATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (28 bp):
GATGACACATGATTATCATGTGACAATA
Found at i:3415433 original size:22 final size:21
Alignment explanation
Indices: 3415403--3415461 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
3415393 AATAAATATT
*
3415403 AAAATATTTTTAAAATGT-AGAA
1 AAAAAATTTTTAAAAT-TCA-AA
*
3415425 AAAAAATTTTTACAATTCAAA
1 AAAAAATTTTTAAAATTCAAA
*
3415446 ATATAAATTTTTAAAA
1 A-AAAAATTTTTAAAA
3415462 AAGTAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (21 bp):
AAAAAATTTTTAAAATTCAAA
Found at i:3415469 original size:23 final size:24
Alignment explanation
Indices: 3415443--3415487 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3415433 TTTACAATTC
*
3415443 AAAATAT-AAATTTTTAAAAAAGT
1 AAAATATGAAATTTCTAAAAAAGT
*
3415466 AAAATATGGAATTTCTAAAAAA
1 AAAATATGAAATTTCTAAAAAA
3415488 AATTTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (24 bp):
AAAATATGAAATTTCTAAAAAAGT
Found at i:3416020 original size:19 final size:19
Alignment explanation
Indices: 3415996--3416038 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
3415986 GAATTAGTAG
3415996 GGATGTGTCACAGACCTAA
1 GGATGTGTCACAGACCTAA
**
3416015 GGATGTGTCATGGACCTAA
1 GGATGTGTCACAGACCTAA
*
3416034 AGATG
1 GGATG
3416039 AGTCCTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.23
Consensus pattern (19 bp):
GGATGTGTCACAGACCTAA
Found at i:3427492 original size:64 final size:63
Alignment explanation
Indices: 3427405--3427533 Score: 177
Period size: 64 Copynumber: 2.0 Consensus size: 63
3427395 AGATTAAGTG
* * * ** * *
3427405 TAGTATCTATTTTTATCAGTTTAATATCTGATATGTTGGGTCATTGACTCACATGGTATTAAAT
1 TAGTATCTATTCTTATAAATTTAATATCTGATATG-TGCATCATTCACCCACATGGTATTAAAT
*
3427469 TAGTATCTGTTCTTATAAATTTAATATCTGATATGTGCATCATTCACCCACATGGTATTAAAT
1 TAGTATCTATTCTTATAAATTTAATATCTGATATGTGCATCATTCACCCACATGGTATTAAAT
3427532 TA
1 TA
3427534 ATTTTTTTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 26 0.46
64 31 0.54
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (63 bp):
TAGTATCTATTCTTATAAATTTAATATCTGATATGTGCATCATTCACCCACATGGTATTAAAT
Found at i:3427757 original size:35 final size:35
Alignment explanation
Indices: 3427711--3427780 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
3427701 AGGTTTTACT
3427711 AGCATACAGATAGGAAGAAGAAAGTGTT-GAAGCCA
1 AGCATACAGATAGGAAGAAGAAAGT-TTAGAAGCCA
* *
3427746 AGCATACAGATAGGAGGGAGAAAGTTTAGAAGCCA
1 AGCATACAGATAGGAAGAAGAAAGTTTAGAAGCCA
3427781 GAAAGTGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 2 0.06
35 30 0.94
ACGTcount: A:0.44, C:0.11, G:0.30, T:0.14
Consensus pattern (35 bp):
AGCATACAGATAGGAAGAAGAAAGTTTAGAAGCCA
Found at i:3428475 original size:30 final size:30
Alignment explanation
Indices: 3428437--3428510 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
3428427 ATTAATTTTT
* *
3428437 TAAT-TTTTTATTTATATATATTTATATAA
1 TAATATTTTTATTTATATATATTTAAAAAA
* ** *
3428466 TGATATTTTTAAATATTTATATTTAAAAAA
1 TAATATTTTTATTTATATATATTTAAAAAA
3428496 TAATATTTTATATTT
1 TAATATTTT-TATTT
3428511 TAAAAAATAA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
29 3 0.09
30 28 0.82
31 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (30 bp):
TAATATTTTTATTTATATATATTTAAAAAA
Found at i:3428507 original size:21 final size:22
Alignment explanation
Indices: 3428477--3428528 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
3428467 GATATTTTTA
3428477 AATA-TTTATA-TTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
3428497 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
3428519 AATATTTTAT
1 AATATTTTAT
3428529 TAATTTCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 20 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:3428842 original size:18 final size:18
Alignment explanation
Indices: 3428796--3428844 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
3428786 AATTTTCATA
3428796 TTCTAATTTTTAAAAAAT
1 TTCTAATTTTTAAAAAAT
*
3428814 TTCTAGA-TTTTAAAATGAT
1 TTCTA-ATTTTTAAAA-AAT
3428833 TT-TAATTTTTAA
1 TTCTAATTTTTAA
3428845 TTTTCTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 1 0.04
18 21 0.78
19 5 0.19
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (18 bp):
TTCTAATTTTTAAAAAAT
Found at i:3433427 original size:58 final size:59
Alignment explanation
Indices: 3433358--3433861 Score: 575
Period size: 59 Copynumber: 8.6 Consensus size: 59
3433348 AGTTTTTTTT
* *
3433358 TTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTTC-AAAAAATA
1 TTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAGTTTTCAAAAAAATA
* ** *
3433416 TTTTTGGGAAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAA-TTTTCAAAAAAAAA
1 TTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAGTTTTCAAAAAAATA
*
3433474 TTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTCGAAAATAGATGTTTTC-AAAAAATA
1 TTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATA-AAGTTTTCAAAAAAATA
*
3433533 TTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAA-TGTTTCCAAAAAATA
1 TTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAGT-TTTCAAAAAAATA
* ** *
3433592 TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTTCAAAAAAAAAAGTTT
1 TTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAGTTTTC---AAAAAAA--TA
* * * *
3433655 TTTTTGAGG-GAAAGTTGAAAGTATCAATTTCCCTTGAAATTAAAGTTTTTCCAAAAAAATA
1 TTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAG-TTTT-CAAAAAAATA
* * *
3433716 TTTTTGGGAAAAAGTTGAAAGTATCAATTTTCTTCGAAATTAAAG-TTTC-AAAAGATA
1 TTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAGTTTTCAAAAAAATA
* * * * * *
3433773 -TTTTGAGG-AAAAGTTGAAAATATCGATTTTCCTCGAGATTAAA-ATTTCTAAAAAATA
1 TTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAGTTTTCAAAAAAATA
*
3433830 -TTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 TTTTTGGGAAAAAGTTGAAAGTATCAATTTTCC
3433862 CTGCACCAAA
Statistics
Matches: 391, Mismatches: 34, Indels: 43
0.84 0.07 0.09
Matches are distributed among these distances:
56 42 0.11
57 49 0.13
58 94 0.24
59 102 0.26
60 7 0.02
61 45 0.12
63 45 0.12
64 2 0.01
65 4 0.01
66 1 0.00
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (59 bp):
TTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAAGTTTTCAAAAAAATA
Found at i:3434948 original size:107 final size:107
Alignment explanation
Indices: 3434762--3434969 Score: 398
Period size: 107 Copynumber: 1.9 Consensus size: 107
3434752 TTTCTACCCA
* *
3434762 ATGATAGATATAGCTTGAAATTAGGACACAAAAAGGGTGTTTATCTAATCATTTTGATTGTTTAA
1 ATGATAGATATACCCTGAAATTAGGACACAAAAAGGGTGTTTATCTAATCATTTTGATTGTTTAA
3434827 CTTTATGCATCATTTTCATTATCATATGTAACATTAGGACAT
66 CTTTATGCATCATTTTCATTATCATATGTAACATTAGGACAT
3434869 ATGATAGATATACCCTGAAATTAGGACACAAAAAGGGTGTTTATCTAATCATTTTGATTGTTTAA
1 ATGATAGATATACCCTGAAATTAGGACACAAAAAGGGTGTTTATCTAATCATTTTGATTGTTTAA
3434934 CTTTATGCATCATTTTCATTATCATATGTAACATTA
66 CTTTATGCATCATTTTCATTATCATATGTAACATTA
3434970 TGCATCAGCA
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 99 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (107 bp):
ATGATAGATATACCCTGAAATTAGGACACAAAAAGGGTGTTTATCTAATCATTTTGATTGTTTAA
CTTTATGCATCATTTTCATTATCATATGTAACATTAGGACAT
Found at i:3437606 original size:14 final size:13
Alignment explanation
Indices: 3437587--3437645 Score: 59
Period size: 12 Copynumber: 4.5 Consensus size: 13
3437577 TGAAAAATGA
3437587 AAAAAAAAAGATGACG
1 AAAAAAAAA-A-GA-G
3437603 AAAAAAAAAAGAG
1 AAAAAAAAAAGAG
3437616 AAAAAAAAAAG-G
1 AAAAAAAAAAGAG
* *
3437628 AAAGAAAGAAG-G
1 AAAAAAAAAAGAG
3437640 AAAAAA
1 AAAAAA
3437646 TGAAAAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
12 16 0.40
13 12 0.30
14 2 0.05
15 1 0.03
16 9 0.22
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.02
Consensus pattern (13 bp):
AAAAAAAAAAGAG
Found at i:3437607 original size:17 final size:15
Alignment explanation
Indices: 3437585--3437625 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
3437575 GATGAAAAAT
3437585 GAAAAAAAAAAGATGA
1 GAAAAAAAAAAGA-GA
3437601 CGAAAAAAAAAAGAGA
1 -GAAAAAAAAAAGAGA
3437617 -AAAAAAAAA
1 GAAAAAAAAA
3437626 GGAAAGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.38
16 2 0.08
17 13 0.54
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (15 bp):
GAAAAAAAAAAGAGA
Found at i:3438950 original size:41 final size:42
Alignment explanation
Indices: 3438886--3439036 Score: 272
Period size: 41 Copynumber: 3.7 Consensus size: 42
3438876 TGATTGTCAG
*
3438886 GGAGTAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
3438928 GGAGCAATTTAC-TTTTCAAAGTCGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
3438969 GGAGCAATTTAC--TTTCAAAGTCGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
3439009 GGAGCAATTTACTTTTTCAAAGTCGTGG
1 GGAGCAATTTACTTTTTCAAAGTCGTGG
3439037 AGCAATTTAC
Statistics
Matches: 106, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
40 40 0.38
41 41 0.39
42 25 0.24
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.37
Consensus pattern (42 bp):
GGAGCAATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
Found at i:3439045 original size:26 final size:26
Alignment explanation
Indices: 3439009--3439062 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
3438999 TCTGTTTAGA
3439009 GGAGCAATTTACTTTTTCAAAGTCGT
1 GGAGCAATTTACTTTTTCAAAGTCGT
*
3439035 GGAGCAATTTACTTTTTCAAAGTTGT
1 GGAGCAATTTACTTTTTCAAAGTCGT
3439061 GG
1 GG
3439063 TGCCTCTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (26 bp):
GGAGCAATTTACTTTTTCAAAGTCGT
Found at i:3439076 original size:68 final size:65
Alignment explanation
Indices: 3438969--3439103 Score: 216
Period size: 68 Copynumber: 2.0 Consensus size: 65
3438959 TCTGTTTAGA
*
3438969 GGAGCAATTTACTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTTCAAAGTCG
1 GGAGCAATTTACTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTAC-TTTACAAAGTCG
3439034 T
65 T
* *
3439035 GGAGCAATTTACTTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGTAATTTACTTTACAAAGTC
1 GGAGCAATTTAC--TTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTACAAAGTC
3439100 GT
64 GT
3439102 GG
1 GG
3439104 TGCCTCTGTT
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
66 12 0.19
67 14 0.22
68 38 0.59
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (65 bp):
GGAGCAATTTACTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTACAAAGTCGT
Found at i:3439104 original size:41 final size:41
Alignment explanation
Indices: 3439035--3439367 Score: 467
Period size: 41 Copynumber: 8.1 Consensus size: 41
3439025 TCAAAGTCGT
*
3439035 GGAGCAATTTACTTTTTCAAAGTTGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTAC-TTTTCAAAGTCGTGGTGCCTCTGTTTAGA
* *
3439077 GGAGTAATTTACTTTACAAAGTCGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
* * *
3439118 -GAGCAACTTACTTTTCAAAGTCGTAGTGCCTCTATTTAGA
1 GGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
3439158 GGAGC-ATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTAC-TTTTCAAAGTCGTGGTGCCTCTGTTTAGA
* *
3439199 AGAGCAATTTACTTTCCAAAGTTTCGT--TGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAG--TCGTGGTGCCTCTGTTTAGA
*
3439240 GGAGTAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
* *
3439281 GGAGCAATTTACTTTCCAAAGTCATGGTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
* * * *
3439322 GGAGCAAGTTACTTTCCAAAGTCGTTGAGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
3439363 GGAGC
1 GGAGC
3439368 TTTGATAAAA
Statistics
Matches: 261, Mismatches: 23, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
39 4 0.02
40 40 0.15
41 196 0.75
42 17 0.07
43 4 0.02
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (41 bp):
GGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
Found at i:3439122 original size:108 final size:106
Alignment explanation
Indices: 3438928--3439141 Score: 367
Period size: 108 Copynumber: 2.0 Consensus size: 106
3438918 TCTGTTTAGA
3438928 GGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCAAAGTCGT
1 GGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCAAAGTCGT
*
3438993 GGTGCCTCTGTTTAGAGGAGCAATTTACTTTTTCAAAGTCGT
66 GGTGCCTCTGTTTAGAGGAGCAACTTAC-TTTTCAAAGTCGT
* *
3439035 GGAGCAATTTACTTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGTAATTTACTTTACAAAGTC
1 GGAGCAATTTAC-TTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTT-CAAAGTC
3439100 GTGGTGCCTCTGTTTAGA-GAGCAACTTACTTTTCAAAGTCGT
64 GTGGTGCCTCTGTTTAGAGGAGCAACTTACTTTTCAAAGTCGT
3439142 AGTGCCTCTA
Statistics
Matches: 102, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
107 25 0.25
108 52 0.51
109 25 0.25
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (106 bp):
GGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCAAAGTCGT
GGTGCCTCTGTTTAGAGGAGCAACTTACTTTTCAAAGTCGT
Found at i:3439387 original size:10 final size:10
Alignment explanation
Indices: 3439372--3439400 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
3439362 AGGAGCTTTG
3439372 ATAAAAAAAA
1 ATAAAAAAAA
3439382 AT-AAAAAAA
1 ATAAAAAAAA
3439391 ATAAAAAAAA
1 ATAAAAAAAA
3439401 GTTGCCTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (10 bp):
ATAAAAAAAA
Found at i:3439389 original size:9 final size:9
Alignment explanation
Indices: 3439375--3439400 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3439365 AGCTTTGATA
3439375 AAAAAAAAT
1 AAAAAAAAT
3439384 AAAAAAAAT
1 AAAAAAAAT
3439393 AAAAAAAA
1 AAAAAAAA
3439401 GTTGCCTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:3439528 original size:123 final size:124
Alignment explanation
Indices: 3439384--3439642 Score: 346
Period size: 123 Copynumber: 2.1 Consensus size: 124
3439374 AAAAAAAAAT
* * *
3439384 AAAAAAAATAAAAAAAAGTTGCCTCTATTTAAAGGAGCTTTGTTTATGCTTT-TCAAAGCCATTT
1 AAAAAAAATAAAAAAAAGTTGCCTCTATTTAAAGGAGCTTTATTTATG-TTTCTCAAAACCATTG
* *
3439448 AGCCTCTGCTCAAAGGAGCTTTGATC-A-TTTTAAAAAAAAAAGCAAAAAAAAAT-GGACA
65 AGCCTCTGCTCAAAGAAGCTTTGATCAATTTTTAAAAAAAAAAGCAAAAAAAAATCCG-CA
* *
3439506 AAAAAAAATAAAAAAAGAGTTGCCTCTATTTAGAGGAGCTTTATTTATGTTTCTCAAAATCATTG
1 AAAAAAAATAAAAAAA-AGTTGCCTCTATTTAAAGGAGCTTTATTTATGTTTCTCAAAACCATTG
* * *
3439571 AGCCTCTGCTTAGAGAAGCTTTGATCAAAATTTTTTAAAAAAAAAAGCAAGAAAAAATCCGCA
65 AGCCTCTGCTCAAAGAAGCTTTGATC--AA-TTTTTAAAAAAAAAAGCAAAAAAAAATCCGCA
3439634 AAAAAAAAT
1 AAAAAAAAT
3439643 CAGTTGAGTC
Statistics
Matches: 119, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
122 19 0.16
123 62 0.52
126 1 0.01
128 36 0.30
129 1 0.01
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.28
Consensus pattern (124 bp):
AAAAAAAATAAAAAAAAGTTGCCTCTATTTAAAGGAGCTTTATTTATGTTTCTCAAAACCATTGA
GCCTCTGCTCAAAGAAGCTTTGATCAATTTTTAAAAAAAAAAGCAAAAAAAAATCCGCA
Found at i:3439819 original size:22 final size:24
Alignment explanation
Indices: 3439783--3439841 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
3439773 CAGTTGTAGG
* *
3439783 GATTTTTATTCATTTTTAT-TTTA-
1 GATTTTT-TTTATTTTCATATTTAT
3439806 GATTTTTTTTA-TTTCATATTTAT
1 GATTTTTTTTATTTTCATATTTAT
*
3439829 CATTTTTTTTATT
1 GATTTTTTTTATT
3439842 ATCTAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 5 0.17
22 7 0.23
23 17 0.57
24 1 0.03
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.71
Consensus pattern (24 bp):
GATTTTTTTTATTTTCATATTTAT
Found at i:3446050 original size:28 final size:28
Alignment explanation
Indices: 3446010--3446066 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
3446000 TAGTAGGAGT
3446010 AACTTTGTTTTTCTGTCATTCAGTTGGG
1 AACTTTGTTTTTCTGTCATTCAGTTGGG
3446038 AACTTTGTTTTTCTGTCATTCAGTTGGG
1 AACTTTGTTTTTCTGTCATTCAGTTGGG
3446066 A
1 A
3446067 GGGAGCTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.16, C:0.14, G:0.21, T:0.49
Consensus pattern (28 bp):
AACTTTGTTTTTCTGTCATTCAGTTGGG
Found at i:3447381 original size:74 final size:72
Alignment explanation
Indices: 3447259--3447399 Score: 203
Period size: 74 Copynumber: 1.9 Consensus size: 72
3447249 AATACTAGGT
* * *
3447259 AATGCCAAAAAGAGTACATTTAGGGCTATATTGTTCAAGTATATGATATGCCAATAGAACCTACT
1 AATGCCAAAAAGAGTACATTTAGGGCAATATTGTTCAAGTATATGATATGCCAACAGAACCAACT
3447324 TACTAGA
66 TACTAGA
* *
3447331 AATGCCAAAAAGAGTTAACCTTTAGGGCAATATTGTTTAAGTATGA-GATATGCCAACAGAACCA
1 AATGCCAAAAAGAG-T-ACATTTAGGGCAATATTGTTCAAGTAT-ATGATATGCCAACAGAACCA
3447395 ACTTA
63 ACTTA
3447400 AGACTTCTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
72 14 0.23
73 1 0.02
74 45 0.74
75 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.28
Consensus pattern (72 bp):
AATGCCAAAAAGAGTACATTTAGGGCAATATTGTTCAAGTATATGATATGCCAACAGAACCAACT
TACTAGA
Found at i:3457912 original size:7 final size:7
Alignment explanation
Indices: 3457902--3457930 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
3457892 TTACATATTA
3457902 TTAAAAT
1 TTAAAAT
3457909 TTAAAAT
1 TTAAAAT
3457916 TTAAAAT
1 TTAAAAT
3457923 TTAAAAT
1 TTAAAAT
3457930 T
1 T
3457931 ATTGAATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TTAAAAT
Found at i:3463704 original size:122 final size:122
Alignment explanation
Indices: 3463521--3463881 Score: 668
Period size: 122 Copynumber: 3.0 Consensus size: 122
3463511 ACGTAGATGA
* * * *
3463521 TTTCTTTACCGTTCGGTTCGTTCAGACAGTCGGTAGAGGGGCCCAGTGATATAACGGCTTGCTGA
1 TTTCTTTACCGTTCGGTTCGTTCAGACAGTGGGTCGTGGGGCCCAGTGATATAACGACTTGCTGA
*
3463586 CCGCGAAACATTTGTTTTTCTTTTAATTTTTAATAAATTTTATTAATTTAAAAATGG
66 CCACGAAACATTTGTTTTTCTTTTAATTTTTAATAAATTTTATTAATTTAAAAATGG
3463643 TTTCTTTACCGTTCGGTTCGTTCAGACAGTGGGTCGTGGGGCCCAGTGATATAACGACTTGCTGA
1 TTTCTTTACCGTTCGGTTCGTTCAGACAGTGGGTCGTGGGGCCCAGTGATATAACGACTTGCTGA
3463708 CCACGAAACATTTGTTTTTCTTTTAATTTTTAATAAATTTTATTAATTTAAAAATGG
66 CCACGAAACATTTGTTTTTCTTTTAATTTTTAATAAATTTTATTAATTTAAAAATGG
3463765 TTTCTTTACCGTTCGGTTCGTTCAGACAGTGGGTCGTGGGGCCCAGTGATATAACGACTTGCTGA
1 TTTCTTTACCGTTCGGTTCGTTCAGACAGTGGGTCGTGGGGCCCAGTGATATAACGACTTGCTGA
*
3463830 CCACGAAACATTTGTTTTTCTTTTAATTTTTAATAAATTTTATTATTTTAAA
66 CCACGAAACATTTGTTTTTCTTTTAATTTTTAATAAATTTTATTAATTTAAA
3463882 TACAATATAA
Statistics
Matches: 233, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
122 233 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (122 bp):
TTTCTTTACCGTTCGGTTCGTTCAGACAGTGGGTCGTGGGGCCCAGTGATATAACGACTTGCTGA
CCACGAAACATTTGTTTTTCTTTTAATTTTTAATAAATTTTATTAATTTAAAAATGG
Found at i:3463911 original size:16 final size:17
Alignment explanation
Indices: 3463888--3463934 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
3463878 TAAATACAAT
3463888 ATAATAATATAAAATAA
1 ATAATAATATAAAATAA
*
3463905 A-AATAATA-CAAATAA
1 ATAATAATATAAAATAA
*
3463920 ATAATAATTTAAAAT
1 ATAATAATATAAAAT
3463935 TTTAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 7 0.28
16 13 0.52
17 5 0.20
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAATAATATAAAATAA
Found at i:3463980 original size:23 final size:22
Alignment explanation
Indices: 3463915--3463972 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
3463905 AAATAATACA
**
3463915 AATAAATAATAATTTAAAATTTT
1 AATAAA-AATAAAATAAAATTTT
* *
3463938 AATAAAAATTATATACAAATTTT
1 AATAAAAATAAAATA-AAATTTT
3463961 -ATAAAAATAAAA
1 AATAAAAATAAAA
3463973 GCTAAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
AATAAAAATAAAATAAAATTTT
Found at i:3471293 original size:24 final size:24
Alignment explanation
Indices: 3471265--3471314 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
3471255 ATCCATCAAC
3471265 AATCAAACCCAAAGAAGATCAAAG
1 AATCAAACCCAAAGAAGATCAAAG
3471289 AATCAAACCCAAAGAAGATCAAAG
1 AATCAAACCCAAAGAAGATCAAAG
3471313 AA
1 AA
3471315 GTGCTTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.60, C:0.20, G:0.12, T:0.08
Consensus pattern (24 bp):
AATCAAACCCAAAGAAGATCAAAG
Found at i:3475850 original size:36 final size:35
Alignment explanation
Indices: 3475804--3475881 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
3475794 TTGAAAAATT
*
3475804 AATATTATCAAATACTT-TTATAATAATAATTTTTTTA
1 AATA-TATCAAAT--TTATTATAATAACAATTTTTTTA
* *
3475841 AATATATCAAATTTATTATTATTACAATTTTTTTA
1 AATATATCAAATTTATTATAATAACAATTTTTTTA
3475876 AATATA
1 AATATA
3475882 AAAATAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 2 0.05
35 23 0.62
36 8 0.22
37 4 0.11
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (35 bp):
AATATATCAAATTTATTATAATAACAATTTTTTTA
Found at i:3481030 original size:4 final size:4
Alignment explanation
Indices: 3481023--3481053 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3481013 ATATATATAT
3481023 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
3481054 TAGATATGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:3491591 original size:21 final size:21
Alignment explanation
Indices: 3491566--3491609 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3491556 TCATATTTAA
3491566 TTTATATAAAATATAAA-AAAT
1 TTTATATAAAATA-AAATAAAT
*
3491587 TTTATATCAAATAAAATAAAT
1 TTTATATAAAATAAAATAAAT
3491608 TT
1 TT
3491610 CTTTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTATATAAAATAAAATAAAT
Found at i:3496161 original size:10 final size:10
Alignment explanation
Indices: 3496141--3496173 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
3496131 TTTGATATAA
3496141 AATAA-TTTT
1 AATAATTTTT
3496150 AATAATTTTT
1 AATAATTTTT
3496160 AATAATTTATT
1 AATAATTT-TT
3496171 AAT
1 AAT
3496174 TTAAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 5 0.23
10 12 0.55
11 5 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
AATAATTTTT
Found at i:3498653 original size:2 final size:2
Alignment explanation
Indices: 3498646--3498692 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
3498636 CTTGGCTGTA
* * *
3498646 AT AT AT AT -T TT AC AT AT CT 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
3498687 AT AT AT
1 AT AT AT
3498693 TTAATATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3499563 original size:2 final size:2
Alignment explanation
Indices: 3499556--3499586 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3499546 TGTGATTGTA
3499556 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
3499587 GAGAGAGAGA
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:3499591 original size:2 final size:2
Alignment explanation
Indices: 3499586--3499623 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3499576 ATATATATAT
3499586 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3499624 GCAATGAACG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3505502 original size:3 final size:3
Alignment explanation
Indices: 3505487--3505516 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3505477 ACAGGGACAC
*
3505487 GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
3505517 ATCAAAGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3513308 original size:29 final size:30
Alignment explanation
Indices: 3513267--3513345 Score: 99
Period size: 29 Copynumber: 2.6 Consensus size: 30
3513257 TAATAAAATA
*
3513267 TTTAATATGATATTTAAATT-TAAAATTT-T
1 TTTAATATAATATTTAAATTAT-AAATTTAT
3513296 TTTAATATAATATTTAAATTATAAATTTAT
1 TTTAATATAATATTTAAATTATAAATTTAT
*
3513326 TAATTAATACAATATTTAAA
1 T--TTAATATAATATTTAAA
3513346 AAATTATTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
29 25 0.57
30 3 0.07
32 16 0.36
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (30 bp):
TTTAATATAATATTTAAATTATAAATTTAT
Found at i:3513406 original size:18 final size:19
Alignment explanation
Indices: 3513383--3513424 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
3513373 ATTAAAATTA
3513383 ATTATATTAA-AAATAAAT
1 ATTATATTAATAAATAAAT
*
3513401 ATTATATTAATTAATAAAT
1 ATTATATTAATAAATAAAT
3513420 -TTATA
1 ATTATA
3513425 ATTCAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTATATTAATAAATAAAT
Found at i:3514713 original size:2 final size:2
Alignment explanation
Indices: 3514708--3514740 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3514698 CTTTTTTGTT
3514708 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3514741 TTATTGGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3515556 original size:18 final size:20
Alignment explanation
Indices: 3515533--3515572 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
3515523 GTGTTGGTGA
3515533 TTCAATC-AAAATTTT-TTT
1 TTCAATCTAAAATTTTCTTT
*
3515551 TTCAATCTAAAGTTTTCTTT
1 TTCAATCTAAAATTTTCTTT
3515571 TT
1 TT
3515573 GTGGATCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 7 0.37
20 5 0.26
ACGTcount: A:0.28, C:0.12, G:0.03, T:0.57
Consensus pattern (20 bp):
TTCAATCTAAAATTTTCTTT
Found at i:3515571 original size:19 final size:18
Alignment explanation
Indices: 3515533--3515571 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
3515523 GTGTTGGTGA
*
3515533 TTCAATCAAAATTTTTTT
1 TTCAATCAAAATTTTCTT
*
3515551 TTCAATCTAAAGTTTTCTT
1 TTCAATC-AAAATTTTCTT
3515570 TT
1 TT
3515572 TGTGGATCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.28, C:0.13, G:0.03, T:0.56
Consensus pattern (18 bp):
TTCAATCAAAATTTTCTT
Found at i:3527678 original size:2 final size:2
Alignment explanation
Indices: 3527671--3527697 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3527661 GAGGTGATCA
3527671 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
3527698 TGGCTTTTTA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3537804 original size:64 final size:64
Alignment explanation
Indices: 3537703--3537972 Score: 477
Period size: 64 Copynumber: 4.2 Consensus size: 64
3537693 TGCATGGTAA
3537703 TACTCGTAGTTATGTGTTATGGTTTTAGTACTTGTTAGTTTTAATGTTACAAGAAATGTGCTTG
1 TACTCGTAGTTATGTGTTATGGTTTTAGTACTTGTTAGTTTTAATGTTACAAGAAATGTGCTTG
3537767 TACTCGTAGTTATGTGTTATGGTTTTAGTACTTGTTAGTTTTAATGTTACAAGAAATGTGCTTG
1 TACTCGTAGTTATGTGTTATGGTTTTAGTACTTGTTAGTTTTAATGTTACAAGAAATGTGCTTG
* * *
3537831 TATTCGTAGTTATGTGTTATGGTTTTAGTGCTTGTTAGTTTTAATGTTACAAGAAATGCGCTTG
1 TACTCGTAGTTATGTGTTATGGTTTTAGTACTTGTTAGTTTTAATGTTACAAGAAATGTGCTTG
* * * *
3537895 TATTCGTAGTTATGTGTTATGGTTTTAGTGCTTGTTAGTTTTAATGTGACAAGAAATATGCTTG
1 TACTCGTAGTTATGTGTTATGGTTTTAGTACTTGTTAGTTTTAATGTTACAAGAAATGTGCTTG
3537959 TACTCGTAGTTATG
1 TACTCGTAGTTATG
3537973 AGCATGGCCA
Statistics
Matches: 199, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 199 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.47
Consensus pattern (64 bp):
TACTCGTAGTTATGTGTTATGGTTTTAGTACTTGTTAGTTTTAATGTTACAAGAAATGTGCTTG
Found at i:3537849 original size:34 final size:34
Alignment explanation
Indices: 3537811--3537913 Score: 81
Period size: 34 Copynumber: 3.1 Consensus size: 34
3537801 TTAGTTTTAA
3537811 TGTTACAAGAAATGTGCTTGTATTCGTAGTTATG
1 TGTTACAAGAAATGTGCTTGTATTCGTAGTTATG
** *** * * *
3537845 TGTTA-TGGTTTTAGTGCTTG--TTAGT-TTTA-A
1 TGTTACAAGAAAT-GTGCTTGTATTCGTAGTTATG
*
3537875 TGTTACAAGAAATGCGCTTGTATTCGTAGTTATG
1 TGTTACAAGAAATGTGCTTGTATTCGTAGTTATG
3537909 TGTTA
1 TGTTA
3537914 TGGTTTTAGT
Statistics
Matches: 46, Mismatches: 17, Indels: 12
0.61 0.23 0.16
Matches are distributed among these distances:
30 11 0.24
31 5 0.11
32 8 0.17
33 5 0.11
34 17 0.37
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (34 bp):
TGTTACAAGAAATGTGCTTGTATTCGTAGTTATG
Found at i:3537928 original size:34 final size:34
Alignment explanation
Indices: 3537824--3537929 Score: 87
Period size: 34 Copynumber: 3.2 Consensus size: 34
3537814 TACAAGAAAT
3537824 GTGCTTGTATTCGTAGTTATGTGTTATGGTTTTA
1 GTGCTTGTATTCGTAGTTATGTGTTATGGTTTTA
* * * ** ***
3537858 GTGCTTG--TTAGT-TTTA-ATGTTACAAGAAAT-
1 GTGCTTGTATTCGTAGTTATGTGTTA-TGGTTTTA
*
3537888 GCGCTTGTATTCGTAGTTATGTGTTATGGTTTTA
1 GTGCTTGTATTCGTAGTTATGTGTTATGGTTTTA
3537922 GTGCTTGT
1 GTGCTTGT
3537930 TAGTTTTAAT
Statistics
Matches: 48, Mismatches: 18, Indels: 12
0.62 0.23 0.15
Matches are distributed among these distances:
30 11 0.23
31 5 0.10
32 8 0.17
33 5 0.10
34 19 0.40
ACGTcount: A:0.18, C:0.08, G:0.25, T:0.49
Consensus pattern (34 bp):
GTGCTTGTATTCGTAGTTATGTGTTATGGTTTTA
Found at i:3538092 original size:33 final size:33
Alignment explanation
Indices: 3538050--3538117 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
3538040 GTGTGTGAAT
*
3538050 GGATTGTAATTAGGTGTTAATTTTTAAAATTAA
1 GGATTGTAATTAGGTGTTAATTATTAAAATTAA
3538083 GGATTGTAATTAGGTGTTAATTATTAAAATTAA
1 GGATTGTAATTAGGTGTTAATTATTAAAATTAA
3538116 GG
1 GG
3538118 GGAACTTGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.43
Consensus pattern (33 bp):
GGATTGTAATTAGGTGTTAATTATTAAAATTAA
Found at i:3547562 original size:36 final size:35
Alignment explanation
Indices: 3547494--3547572 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 35
3547484 ATTTTGACAC
* * *
3547494 ATAATTTTTTTTAACAATTGAATATGTGTTATTTT
1 ATAATTTTATTTAACAATTGAAAATGTGTTATTGT
* *
3547529 ATTAATTTTATTTATACAATTTAAAAT-TTTTATTGT
1 A-TAATTTTATTTA-ACAATTGAAAATGTGTTATTGT
3547565 ATAATTTT
1 ATAATTTT
3547573 TCTTTTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
35 8 0.22
36 19 0.51
37 10 0.27
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (35 bp):
ATAATTTTATTTAACAATTGAAAATGTGTTATTGT
Found at i:3547929 original size:14 final size:15
Alignment explanation
Indices: 3547910--3547943 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3547900 ATATTTTTTC
3547910 AAAAATTATTTAAT-
1 AAAAATTATTTAATG
*
3547924 AAAAATTTTTTAATG
1 AAAAATTATTTAATG
3547939 AAAAA
1 AAAAA
3547944 AAAAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
AAAAATTATTTAATG
Found at i:3547952 original size:19 final size:19
Alignment explanation
Indices: 3547924--3547964 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
3547914 ATTATTTAAT
*
3547924 AAAAATTTTTTAATGAAAAA
1 AAAAATTTTTAAAT-AAAAA
3547944 AAAAATTTTTAAATAAAAA
1 AAAAATTTTTAAATAAAAA
3547963 AA
1 AA
3547965 TAAGAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAAATTTTTAAATAAAAA
Found at i:3552434 original size:23 final size:24
Alignment explanation
Indices: 3552360--3552425 Score: 105
Period size: 25 Copynumber: 2.7 Consensus size: 24
3552350 AAATGCTCGG
3552360 ATATATGATATTTTTTAATATATAA
1 ATATATGAT-TTTTTTAATATATAA
*
3552385 ATATATGTTTTTTTTTAATATATAA
1 ATATATG-ATTTTTTTAATATATAA
3552410 ATATATGATTTTTTTA
1 ATATATGATTTTTTTA
3552426 TACAAAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 8 0.21
25 29 0.76
26 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (24 bp):
ATATATGATTTTTTTAATATATAA
Found at i:3552439 original size:23 final size:24
Alignment explanation
Indices: 3552360--3552439 Score: 81
Period size: 25 Copynumber: 3.3 Consensus size: 24
3552350 AAATGCTCGG
* *
3552360 ATATATGATATTTTTTAATATATAA
1 ATATATGAT-TTTTTTAATACAAAA
* * *
3552385 ATATATGTTTTTTTTTAATATATAA
1 ATATATG-ATTTTTTTAATACAAAA
3552410 ATATATGATTTTTTT-ATACAAAA
1 ATATATGATTTTTTTAATACAAAA
*
3552433 ATTTATG
1 ATATATG
3552440 TATGAACTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
23 12 0.24
24 7 0.14
25 29 0.59
26 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (24 bp):
ATATATGATTTTTTTAATACAAAA
Found at i:3561009 original size:30 final size:30
Alignment explanation
Indices: 3560905--3561009 Score: 115
Period size: 30 Copynumber: 3.5 Consensus size: 30
3560895 TTGTCCAATA
*
3560905 AAAAATTTAATTGAA-TAAAAATAAATATTT
1 AAAAATTTAATT-AATTCAAAATAAATATTT
* * *
3560935 AAAAATTAAATTAAATGAAAA-AAATATTT
1 AAAAATTTAATTAATTCAAAATAAATATTT
* *
3560964 AAAAATTTAACTAATTCAAAATAAAAATTT
1 AAAAATTTAATTAATTCAAAATAAATATTT
* *
3560994 TAAAATTTGATTAATT
1 AAAAATTTAATTAATT
3561010 ATATTAATGT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
29 27 0.43
30 36 0.57
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAAATTTAATTAATTCAAAATAAATATTT
Found at i:3566273 original size:31 final size:29
Alignment explanation
Indices: 3566237--3566313 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 29
3566227 TAATAAGACT
*
3566237 TGGAAAAATAATAATTTCTTCTTTTTTAAGAA
1 TGGAAAAA-AATAATTT-TTATTTTTTAA-AA
3566269 -GGAAAAACAATAA-TTTTATTTTTTAAAA
1 TGGAAAAA-AATAATTTTTATTTTTTAAAA
*
3566297 TAGAAAAAAATAATTTT
1 TGGAAAAAAATAATTTT
3566314 AGAGTAGCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 7 0.17
29 19 0.47
30 2 0.05
31 12 0.30
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (29 bp):
TGGAAAAAAATAATTTTTATTTTTTAAAA
Found at i:3568079 original size:28 final size:29
Alignment explanation
Indices: 3568005--3568080 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
3567995 AATAAGACTT
*
3568005 GGAAAAACAATAATTTATTCTTTTTTAAAGAA
1 GGAAAAACAATAA---ATTATTTTTTAAAGAA
3568037 GGAAAAA-AATAAAATTATTTTTTAAA-ATA
1 GGAAAAACAAT-AAATTATTTTTTAAAGA-A
3568066 -GAAAAACAATAAATT
1 GGAAAAACAATAAATT
3568081 TAGGGTTGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
28 12 0.30
29 16 0.40
31 3 0.08
32 9 0.22
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.33
Consensus pattern (29 bp):
GGAAAAACAATAAATTATTTTTTAAAGAA
Found at i:3581031 original size:2 final size:2
Alignment explanation
Indices: 3581024--3581048 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3581014 CCATGCAATC
3581024 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
3581049 GCAAGAGACA
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:3590352 original size:45 final size:45
Alignment explanation
Indices: 3590270--3590357 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
3590260 CTTAGCTGTA
*
3590270 ACTTTTAATAAGACAATAACTTGTACTAGGACATTCTTATTAGTC
1 ACTTTTAATAAGACAATAACTTGTACAAGGACATTCTTATTAGTC
* * *
3590315 ACTTTTAGTAAGACAATAACTTGTACCAATG-CTTTCTTATTAG
1 ACTTTTAATAAGACAATAACTTGTA-CAAGGACATTCTTATTAG
3590358 GCAAGACTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 35 0.92
46 3 0.08
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (45 bp):
ACTTTTAATAAGACAATAACTTGTACAAGGACATTCTTATTAGTC
Found at i:3628294 original size:2 final size:2
Alignment explanation
Indices: 3628287--3628337 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
3628277 CTTATAGGTT
3628287 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3628329 TC TC TC TC T
1 TC TC TC TC T
3628338 ACTTTATCCT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3632265 original size:15 final size:16
Alignment explanation
Indices: 3632237--3632279 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
3632227 TTCCATTTTC
*
3632237 TTTTTTCTACATTTCTT
1 TTTTTTCTA-TTTTCTT
3632254 TTTTTTCTATTTTCTT
1 TTTTTTCTATTTTCTT
*
3632270 ATGTTTTCTA
1 -TTTTTTCTA
3632280 CGGAACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.12, C:0.14, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTTTTCTATTTTCTT
Done.