Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 177 of 190
Found at i:29654985 original size:6 final size:6
Alignment explanation
Indices: 29654974--29654998 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29654964 TTAAAAATTT
29654974 AATTAA AATTAA AATTAA AATTAA A
1 AATTAA AATTAA AATTAA AATTAA A
29654999 TTATATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATTAA
Found at i:29657486 original size:16 final size:16
Alignment explanation
Indices: 29657462--29657503 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
29657452 CAAATTAAAA
29657462 AATTAAAATTC-AATCG
1 AATTAAAA-TCGAATCG
*
29657478 AATTCAAATCGAATCG
1 AATTAAAATCGAATCG
29657494 AATTTAAAAT
1 AA-TTAAAAT
29657504 TTAAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 2 0.09
16 14 0.64
17 6 0.27
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.31
Consensus pattern (16 bp):
AATTAAAATCGAATCG
Found at i:29657861 original size:40 final size:39
Alignment explanation
Indices: 29657781--29657878 Score: 98
Period size: 40 Copynumber: 2.6 Consensus size: 39
29657771 ATTTATTATA
* *
29657781 TTATTAATTA-AA-TTTA-AAATTTAATTTTAATAAAAT
1 TTATTAATTATAATTTTATTAATTTAATTATAATAAAAT
*
29657817 TTATTTATTATAAGTTTT-TTAATTATAATTATAATAATAA-
1 TTATTAATTATAA-TTTTATTAATT-TAATTATAATAA-AAT
*
29657857 TTATTAATTTTAATTTTATTAA
1 TTATTAATTATAATTTTATTAA
29657879 AATTAATCTC
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
36 9 0.18
37 2 0.04
39 11 0.22
40 26 0.52
41 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (39 bp):
TTATTAATTATAATTTTATTAATTTAATTATAATAAAAT
Found at i:29663279 original size:13 final size:13
Alignment explanation
Indices: 29663248--29663317 Score: 69
Period size: 13 Copynumber: 5.8 Consensus size: 13
29663238 GCAGAGAAAG
*
29663248 ATAATTTAA-AAT
1 ATAATATAATAAT
29663260 ATAATATAATAAT
1 ATAATATAATAAT
*
29663273 ATGATAT-A-AAT
1 ATAATATAATAAT
*
29663284 ATAATATAAAAAT
1 ATAATATAATAAT
*
29663297 AAAATATAA-AA-
1 ATAATATAATAAT
29663308 ATAATATAAT
1 ATAATATAAT
29663318 TTAAAATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
11 17 0.35
12 12 0.24
13 20 0.41
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (13 bp):
ATAATATAATAAT
Found at i:29663287 original size:24 final size:24
Alignment explanation
Indices: 29663256--29663317 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
29663246 AGATAATTTA
**
29663256 AAATATAATATAATAATATGATAT
1 AAATATAATATAATAATAAAATAT
*
29663280 AAATATAATATAAAAATAAAATAT
1 AAATATAATATAATAATAAAATAT
*
29663304 AAAAATAATATAAT
1 AAATATAATATAAT
29663318 TTAAAATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (24 bp):
AAATATAATATAATAATAAAATAT
Found at i:29663290 original size:11 final size:11
Alignment explanation
Indices: 29663256--29663316 Score: 59
Period size: 11 Copynumber: 5.2 Consensus size: 11
29663246 AGATAATTTA
29663256 AAATATAATAT
1 AAATATAATAT
*
29663267 AATAATATGATAT
1 -A-AATATAATAT
29663280 AAATATAATAT
1 AAATATAATAT
*
29663291 AAAAATAAAATAT
1 --AAATATAATAT
*
29663304 AAAAATAATAT
1 AAATATAATAT
29663315 AA
1 AA
29663317 TTTAAAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
11 20 0.49
12 2 0.05
13 19 0.46
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
AAATATAATAT
Found at i:29665710 original size:1 final size:1
Alignment explanation
Indices: 29665704--29665728 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
29665694 ATACAAATGC
29665704 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
29665729 CAAAGGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29668496 original size:42 final size:42
Alignment explanation
Indices: 29668444--29668538 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
29668434 ACTTACACCC
* *
29668444 CTCCACCATCTCTTCCAACAGAACCA-CAGAATACTCCTCCAT
1 CTCCACCATCTCCTCCAACA-AAACATCAGAATACTCCTCCAT
* * * *
29668486 CTCCAGCATCTCCTCCTACAAAATATCAGAATCCTCCTCCAT
1 CTCCACCATCTCCTCCAACAAAACATCAGAATACTCCTCCAT
*
29668528 CCCCACCATCT
1 CTCCACCATCT
29668539 TCGCCCCCTC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 3 0.07
42 41 0.93
ACGTcount: A:0.28, C:0.44, G:0.04, T:0.23
Consensus pattern (42 bp):
CTCCACCATCTCCTCCAACAAAACATCAGAATACTCCTCCAT
Found at i:29668606 original size:42 final size:42
Alignment explanation
Indices: 29668468--29668618 Score: 142
Period size: 42 Copynumber: 3.6 Consensus size: 42
29668458 CCAACAGAAC
* * * *
29668468 CACAGAATACTCCTCCATCTCCAGCATCTCCTCCTACAAAAT
1 CACAGAATCCTCCTCCATCTCCAACATCTCCACCCACAAAAT
* * * * * ** *
29668510 -ATCAGAATCCTCCTCCATCCCCACCATCTTCGCCCCCTCAGT
1 CA-CAGAATCCTCCTCCATCTCCAACATCTCCACCCACAAAAT
*
29668552 CACATAATCCTCCTCCATCTCCAACATCTCCACCCACAAAAT
1 CACAGAATCCTCCTCCATCTCCAACATCTCCACCCACAAAAT
* * *
29668594 CAGAGAACCCTCCTCCACCTCCAAC
1 CACAGAATCCTCCTCCATCTCCAAC
29668619 TCCCACATAT
Statistics
Matches: 84, Mismatches: 23, Indels: 4
0.76 0.21 0.04
Matches are distributed among these distances:
41 1 0.01
42 82 0.98
43 1 0.01
ACGTcount: A:0.28, C:0.46, G:0.05, T:0.21
Consensus pattern (42 bp):
CACAGAATCCTCCTCCATCTCCAACATCTCCACCCACAAAAT
Found at i:29670251 original size:15 final size:16
Alignment explanation
Indices: 29670226--29670255 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29670216 TAAATCTAGT
29670226 TTTTGTTTTACTTTTA
1 TTTTGTTTTACTTTTA
29670242 TTTT-TTTTACTTTT
1 TTTTGTTTTACTTTT
29670256 TACAATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (16 bp):
TTTTGTTTTACTTTTA
Found at i:29670639 original size:15 final size:13
Alignment explanation
Indices: 29670614--29670656 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
29670604 ATAAATAATT
29670614 TTTTATATATTATTAA
1 TTTT-TATATTA--AA
29670630 TTTTTATATTAAA
1 TTTTTATATTAAA
29670643 TTTTT-TATTAAA
1 TTTTTATATTAAA
29670655 TT
1 TT
29670657 ATTTTTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 9 0.33
13 7 0.26
15 7 0.26
16 4 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTTTATATTAAA
Found at i:29670654 original size:12 final size:12
Alignment explanation
Indices: 29670623--29670666 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
29670613 TTTTTATATA
29670623 TTATT-AATTTT
1 TTATTAAATTTT
29670634 TATATTAAATTTT
1 T-TATTAAATTTT
29670647 TTATTAAATTATT
1 TTATTAAATT-TT
29670660 TT-TTAAA
1 TTATTAAA
29670667 AAATTTTCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.03
12 18 0.60
13 11 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTATTAAATTTT
Found at i:29675405 original size:20 final size:21
Alignment explanation
Indices: 29675360--29675405 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
29675350 TATCTCTTTC
*
29675360 TAAATATGAAAAACAAATGTT
1 TAAATATGAAAAACAAATCTT
* *
29675381 AAAATATTAAAAA-AAATCTT
1 TAAATATGAAAAACAAATCTT
29675401 TAAAT
1 TAAAT
29675406 TATTTCATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.30
Consensus pattern (21 bp):
TAAATATGAAAAACAAATCTT
Found at i:29675593 original size:30 final size:30
Alignment explanation
Indices: 29675521--29675636 Score: 121
Period size: 30 Copynumber: 4.0 Consensus size: 30
29675511 TAAAAGCTTC
* *
29675521 TTTAAATATTATTTAAAATTTAAAAA-TTA
1 TTTAAATATAAATTAAAATTTAAAAATTTA
* * *
29675550 TTTGAATACAAATTAAATTTTAAAAATTTA
1 TTTAAATATAAATTAAAATTTAAAAATTTA
* *
29675580 TTTAAATATAAATTAAAAATTAAAAATGTA
1 TTTAAATATAAATTAAAATTTAAAAATTTA
* * *
29675610 TTTGAATGT-AA-TAAAATATAAAAATTT
1 TTTAAATATAAATTAAAATTTAAAAATTT
29675637 GTCGAAGTAG
Statistics
Matches: 71, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
28 13 0.18
29 23 0.32
30 35 0.49
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.42
Consensus pattern (30 bp):
TTTAAATATAAATTAAAATTTAAAAATTTA
Found at i:29677656 original size:36 final size:37
Alignment explanation
Indices: 29677586--29677658 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 37
29677576 CTTTCAGAAC
*
29677586 AAATTTTATATGTAATAATATTAAATAAATATATTTT
1 AAATTTTATATGTAATAATATTAAATAAAAATATTTT
* * *
29677623 AAATTTTATCTGTAA-ATTATTAAGTAAAAATATTTT
1 AAATTTTATATGTAATAATATTAAATAAAAATATTTT
29677659 GTTTTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 18 0.56
37 14 0.44
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (37 bp):
AAATTTTATATGTAATAATATTAAATAAAAATATTTT
Found at i:29677831 original size:40 final size:40
Alignment explanation
Indices: 29677782--29677868 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
29677772 AAATATTTTT
* * *
29677782 TTAT-TTTTAAACAAAGACTATGTTTTTATCTTAGAAACA
1 TTATCTTTTAAACAAAAAATATGTTTTTATCTTAAAAACA
* * *
29677821 TTATCTTTTAAACAAAAAATGTGTTTTTATTTTAAAAATA
1 TTATCTTTTAAACAAAAAATATGTTTTTATCTTAAAAACA
*
29677861 TCATCTTT
1 TTATCTTT
29677869 ATTAAATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 4 0.10
40 36 0.90
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (40 bp):
TTATCTTTTAAACAAAAAATATGTTTTTATCTTAAAAACA
Found at i:29683846 original size:61 final size:61
Alignment explanation
Indices: 29683735--29683929 Score: 144
Period size: 64 Copynumber: 3.1 Consensus size: 61
29683725 TGCTTCAATG
* * * *
29683735 TTTTTGTTAATAGATTATTCAAGGCATATTTT-GC-CAAAATGCCTTAAATAATCCTATTTAAT
1 TTTTTG-T-ATAGGTTATTAAAGGCAT-TTTTAGCAAAAAATACCTTAAATAATCCTATTTAAT
* * *** * * *
29683797 TTTTTGTAT-GGATTATTAAAGGTATTTTTTGTTGAAAATACCTTTAATAATTCTTCTTTAAAAT
1 TTTTTGTATAGG-TTATTAAAGGCATTTTTAGCAAAAAATACCTTAAATAA-TCCTATTT--AAT
** * * * *
29683861 TTTTTAAATAGGTTATTATAGGCGTTTTTAGCAAAAAATACCTTCAATAATCCCATTTAAT
1 TTTTTGTATAGGTTATTAAAGGCATTTTTAGCAAAAAATACCTTAAATAATCCTATTTAAT
29683922 TTTTTGTA
1 TTTTTGTA
29683930 AGCCAATAGT
Statistics
Matches: 102, Mismatches: 24, Indels: 15
0.72 0.17 0.11
Matches are distributed among these distances:
59 5 0.05
60 14 0.14
61 24 0.24
62 12 0.12
63 5 0.05
64 40 0.39
65 2 0.02
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (61 bp):
TTTTTGTATAGGTTATTAAAGGCATTTTTAGCAAAAAATACCTTAAATAATCCTATTTAAT
Found at i:29684813 original size:18 final size:18
Alignment explanation
Indices: 29684770--29684813 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
29684760 AAAAAAAATC
29684770 TTAAATATCATATTTTTT
1 TTAAATATCATATTTTTT
* *
29684788 TCAAAAATCATATATTTTTT
1 TTAAATATC--ATATTTTTT
29684808 TTAAAT
1 TTAAAT
29684814 TTAAAATTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
18 7 0.35
20 13 0.65
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAAATATCATATTTTTT
Found at i:29685396 original size:12 final size:12
Alignment explanation
Indices: 29685379--29685403 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29685369 TGCTGCTTCT
29685379 TGTAACCATGGC
1 TGTAACCATGGC
29685391 TGTAACCATGGC
1 TGTAACCATGGC
29685403 T
1 T
29685404 AGGACAAGGC
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:0.24, G:0.24, T:0.28
Consensus pattern (12 bp):
TGTAACCATGGC
Found at i:29687191 original size:29 final size:30
Alignment explanation
Indices: 29687158--29687221 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
29687148 GTAACCTTCA
*
29687158 TATTGAAATATTAAAATA-TTTTATAT-TTT
1 TATTGAAATATT-AAATAGTTTAATATGTTT
29687187 TATTGAAATATTAAATAGTTTAATATGTTT
1 TATTGAAATATTAAATAGTTTAATATGTTT
29687217 TATTG
1 TATTG
29687222 GTTTTACTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 5 0.16
29 19 0.59
30 8 0.25
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (30 bp):
TATTGAAATATTAAATAGTTTAATATGTTT
Found at i:29688210 original size:12 final size:12
Alignment explanation
Indices: 29688193--29688218 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29688183 ATTTAAATTA
29688193 TAAATAATTTTT
1 TAAATAATTTTT
29688205 TAAATAATTTTT
1 TAAATAATTTTT
29688217 TA
1 TA
29688219 TATATTATCT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TAAATAATTTTT
Found at i:29688482 original size:26 final size:27
Alignment explanation
Indices: 29688453--29688509 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
29688443 AAGAATAATT
29688453 TTAAACATGAT-ATAAAAATA-ATAAAC
1 TTAAA-ATGATAATAAAAATATATAAAC
** *
29688479 TTAAAATTTTAATAAAAATATATAAAT
1 TTAAAATGATAATAAAAATATATAAAC
29688506 TTAA
1 TTAA
29688510 TAAAATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 3 0.12
26 14 0.54
27 9 0.35
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (27 bp):
TTAAAATGATAATAAAAATATATAAAC
Found at i:29692720 original size:21 final size:22
Alignment explanation
Indices: 29692694--29692764 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 22
29692684 TTAATAATAT
29692694 ATATTTTAATATA-AAATATAA
1 ATATTTTAATATATAAATATAA
*
29692715 ATATTTTAATA-ATAAATATTA
1 ATATTTTAATATATAAATATAA
*
29692736 TTATTTTAATATTAATAAA-ATAA
1 ATATTTTAATA-T-ATAAATATAA
*
29692759 AAATTT
1 ATATTT
29692765 AAGAATAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
20 1 0.02
21 28 0.68
23 7 0.17
24 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATTTTAATATATAAATATAA
Found at i:29692964 original size:20 final size:21
Alignment explanation
Indices: 29692934--29692973 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
29692924 TATACATTAA
*
29692934 TAATAAATTATTTTAATATTT
1 TAATAAATTATATTAATATTT
29692955 TAAT-AATTATATTAATATT
1 TAATAAATTATATTAATATT
29692974 AATTGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TAATAAATTATATTAATATTT
Found at i:29694546 original size:3 final size:3
Alignment explanation
Indices: 29694538--29694563 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29694528 GTGGAAACCG
29694538 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
29694564 GCATGCAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:29695940 original size:12 final size:12
Alignment explanation
Indices: 29695923--29695948 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29695913 ATATCTTAAG
29695923 AAAAAACCACAA
1 AAAAAACCACAA
29695935 AAAAAACCACAA
1 AAAAAACCACAA
29695947 AA
1 AA
29695949 TGGTGAATCA
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:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAACCACAA
Found at i:29698901 original size:3 final size:3
Alignment explanation
Indices: 29698893--29698946 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
29698883 CTGAACACCT
** * * * *
29698893 GCA GCA GCA GTT GCA GCA GGA GCA GCA GGA GCA GCA GCA CCA GCA GCT
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
29698941 GCA GCA
1 GCA GCA
29698947 TCTTTTCTCG
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.30, C:0.30, G:0.35, T:0.06
Consensus pattern (3 bp):
GCA
Found at i:29698918 original size:18 final size:18
Alignment explanation
Indices: 29698893--29698946 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
29698883 CTGAACACCT
*
29698893 GCAGCAGCAGTTGCAGCA
1 GCAGCAGCAGCTGCAGCA
* **
29698911 GGAGCAGCAGGAGCAGCA
1 GCAGCAGCAGCTGCAGCA
*
29698929 GCACCAGCAGCTGCAGCA
1 GCAGCAGCAGCTGCAGCA
29698947 TCTTTTCTCG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.30, C:0.30, G:0.35, T:0.06
Consensus pattern (18 bp):
GCAGCAGCAGCTGCAGCA
Found at i:29702377 original size:2 final size:2
Alignment explanation
Indices: 29702370--29702401 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29702360 TGTTCTGCTG
29702370 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
29702402 CCCTTATCAT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:29702595 original size:22 final size:22
Alignment explanation
Indices: 29702553--29702596 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29702543 TTTAACAGAA
*
29702553 AACTGACTGGTCAACGGAAAAT
1 AACTGACTGGTCAACGAAAAAT
* *
29702575 AACTTACTGGTCAATGAAAAAT
1 AACTGACTGGTCAACGAAAAAT
29702597 CAAACCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (22 bp):
AACTGACTGGTCAACGAAAAAT
Found at i:29702734 original size:18 final size:18
Alignment explanation
Indices: 29702711--29702943 Score: 118
Period size: 18 Copynumber: 12.8 Consensus size: 18
29702701 AATTTTACTT
29702711 ATAAATAATATTATATAA
1 ATAAATAATATTATATAA
*
29702729 ATAAATAAATATTATATTA
1 ATAAAT-AATATTATATAA
*
29702748 ATAAATAATA-TACTATTA
1 ATAAATAATATTA-TATAA
29702766 AT--ATAATA-TAT-T-A
1 ATAAATAATATTATATAA
29702779 ATAAA-AATATTAATATAGA
1 ATAAATAATATT-ATATA-A
* *
29702798 ATATTATAATATATTCATAAATA
1 ATA-AAT-A-ATATT-ATATA-A
* *
29702821 ATAAATAATATAATATTA
1 ATAAATAATATTATATAA
29702839 ATAAATAATATTATAGT-A
1 ATAAATAATATTATA-TAA
**
29702857 ATATTGTAATA-TAT-T-A
1 ATA-AATAATATTATATAA
29702873 ATAAATAATATTA-A-AA
1 ATAAATAATATTATATAA
29702889 ATAATATTAAT-TTA-ATAAA
1 ATAA-A-TAATATTATAT-AA
* *
29702908 TATTATAATAATATAATATTA
1 -A-TA-AATAATATTATATAA
29702929 ATAAATAATATTATA
1 ATAAATAATATTATA
29702944 ATATATTAAT
Statistics
Matches: 171, Mismatches: 17, Indels: 54
0.71 0.07 0.22
Matches are distributed among these distances:
13 3 0.02
14 5 0.03
15 8 0.05
16 22 0.13
17 8 0.05
18 54 0.32
19 34 0.20
20 11 0.06
21 7 0.04
22 6 0.04
23 13 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (18 bp):
ATAAATAATATTATATAA
Found at i:29702750 original size:15 final size:15
Alignment explanation
Indices: 29702732--29702963 Score: 122
Period size: 15 Copynumber: 14.9 Consensus size: 15
29702722 TATATAAATA
*
29702732 AATAAATATTATATT
1 AATAAATAATATATT
*
29702747 AATAAATAATATACT
1 AATAAATAATATATT
*
29702762 ATTAATATAATATATT
1 AATAA-ATAATATATT
29702778 AATAAA-AATATTAATAT
1 AATAAATAATA-T-AT-T
*
29702795 AGAATATTATAATATATT
1 --AATA-AATAATATATT
* *
29702813 CATAAATAATA-AAT
1 AATAAATAATATATT
29702827 AAT--AT-A-ATATT
1 AATAAATAATATATT
29702838 AATAAATAATATTATAGT
1 AATAAATAATA-TAT--T
**
29702856 AATATTGTAATATATT
1 AATA-AATAATATATT
29702872 AATAAAT-A-ATATT
1 AATAAATAATATATT
29702885 AA-AAATAATATTAATTT
1 AATAAATAATA-T-A-TT
* *
29702902 AATAAATATTATAAT
1 AATAAATAATATATT
* *
29702917 AATATAATATTAATAAAT
1 AATA-AATAAT-AT-ATT
*
29702935 AATATTATAATATATT
1 AATA-AATAATATATT
29702951 AATAAATAATATA
1 AATAAATAATATA
29702964 GAGAATAATA
Statistics
Matches: 170, Mismatches: 21, Indels: 52
0.70 0.09 0.21
Matches are distributed among these distances:
10 1 0.01
11 6 0.04
12 6 0.04
13 10 0.06
14 11 0.06
15 41 0.24
16 40 0.24
17 10 0.06
18 28 0.16
19 11 0.06
20 2 0.01
21 4 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (15 bp):
AATAAATAATATATT
Found at i:29702827 original size:73 final size:68
Alignment explanation
Indices: 29702711--29702977 Score: 223
Period size: 64 Copynumber: 3.9 Consensus size: 68
29702701 AATTTTACTT
* *
29702711 ATAAATAATATTATATAAATAAATAAATATTATATTAATAAATAATATACTATTAATATAAT-AT
1 ATAAATAATATTATATAAATAAATAAATATTATAATAATAAATAATATAATATTAATA-AATAAT
29702775 ATTA
65 ATTA
*
29702779 ATAAA-AATATTAATATAGAATATTATAATATATTCATAAATAATAAATAATATAATATTAATAA
1 ATAAATAATATT-ATATA-AATA-AATAA-ATATT-AT-AATAATAAATAATATAATATTAATAA
29702843 ATAATATT-
60 ATAATATTA
* * * * * *
29702851 AT-AGTAATATTGTAATATATTAATAAATA--ATATTAA-AAATAATATTAAT-TTAATAAATAT
1 ATAAATAATATTAT-ATAAATAAATAAATATTATAATAATAAATAATA-TAATATTAATAAATAA
29702911 TA-TA
64 TATTA
* * * * *
29702915 ATAATATAATATTA-ATAAAT-AATATTATAATATATTAATAAATAATATAGAGAATAATAAATA
1 ATAA-ATAATATTATATAAATAAATA-AATATTATAATAATAAATAATATA-ATATTAATAAATA
29702978 GTTTTATTTT
Statistics
Matches: 164, Mismatches: 16, Indels: 38
0.75 0.07 0.17
Matches are distributed among these distances:
63 5 0.03
64 30 0.18
65 9 0.05
66 18 0.11
67 15 0.09
68 19 0.12
69 7 0.04
70 8 0.05
71 9 0.05
72 16 0.10
73 28 0.17
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.40
Consensus pattern (68 bp):
ATAAATAATATTATATAAATAAATAAATATTATAATAATAAATAATATAATATTAATAAATAATA
TTA
Found at i:29702867 original size:59 final size:60
Alignment explanation
Indices: 29702741--29702959 Score: 188
Period size: 59 Copynumber: 3.7 Consensus size: 60
29702731 AAATAAATAT
** * * * *
29702741 TATATTAATAAATAATATACTATTAATATAATATATTAATAAAAATATTAATATAGAATATTATA
1 TATATTAATAAATAATATAAAAATAATAT--TA-ATTAA-ATAAATATT-ATA-ATAATATTGTA
29702806 A
60 A
* *
29702807 TATATTCATAAATAATA-AATAATATAATATTAA-TAAAT-AATATTATAGTAATATTGTAA
1 TATATTAATAAATAATATAA-AA-ATAATATTAATTAAATAAATATTATAATAATATTGTAA
*
29702866 TATATTAATAAATAATATTAAAAATAATATTAATTTAATAAATATTATAATAATA---T-A
1 TATATTAATAAATAATA-TAAAAATAATATTAATTAAATAAATATTATAATAATATTGTAA
* *
29702923 -ATATTAATAAATAATATTATAAT-ATATTAA-TAAATAA
1 TATATTAATAAATAATATAAAAATAATATTAATTAAATAA
29702960 TATAGAGAAT
Statistics
Matches: 133, Mismatches: 14, Indels: 25
0.77 0.08 0.15
Matches are distributed among these distances:
53 6 0.05
54 7 0.05
55 5 0.04
56 16 0.12
57 1 0.01
58 1 0.01
59 35 0.26
60 9 0.07
61 22 0.17
62 1 0.01
63 3 0.02
64 1 0.01
65 3 0.02
66 17 0.13
67 6 0.05
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (60 bp):
TATATTAATAAATAATATAAAAATAATATTAATTAAATAAATATTATAATAATATTGTAA
Found at i:29702906 original size:64 final size:60
Alignment explanation
Indices: 29702741--29702954 Score: 182
Period size: 61 Copynumber: 3.5 Consensus size: 60
29702731 AAATAAATAT
* * *
29702741 TATATTAATAAATAATATACTATTAATATAATATATTAATAAAAATATTAATATAGAATATTATA
1 TATATTAATAAATAATATA-AAATAATATTA-ATATTAATAAAAATATT-ATAT--AATATT-TA
29702806 A
60 A
*
29702807 TATATTCATAAAT-A-AT-AAATAATA-TAATATTAATAAATAATATTATAGTAATATTGTAA
1 TATATTAATAAATAATATAAAATAATATTAATATTAATAAA-AATATTATA-TAATATT-TAA
29702866 TATATTAATAAATAATATTAAAAATAATATTAAT-TTAAT--AAATATTATAATAATA--T-A
1 TATATTAATAAATAATA-T-AAAATAATATTAATATTAATAAAAATATTAT-ATAATATTTAA
*
29702923 -ATATTAATAAATAATATTATAAT-ATATTAATA
1 TATATTAATAAATAATA-TAAAATAATATTAATA
29702955 AATAATATAG
Statistics
Matches: 131, Mismatches: 7, Indels: 31
0.78 0.04 0.18
Matches are distributed among these distances:
54 8 0.06
55 4 0.03
56 18 0.14
57 1 0.01
58 1 0.01
59 21 0.16
60 15 0.11
61 22 0.17
62 9 0.07
64 15 0.11
65 5 0.04
66 12 0.09
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (60 bp):
TATATTAATAAATAATATAAAATAATATTAATATTAATAAAAATATTATATAATATTTAA
Found at i:29702977 original size:23 final size:23
Alignment explanation
Indices: 29702923--29702977 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
29702913 TAATAATATA
* * *
29702923 ATATTAATAAATAATATTATAAT
1 ATATAAATAAATAATATGAGAAT
*
29702946 ATATTAATAAATAATATAGAGAAT
1 ATATAAATAAATAATAT-GAGAAT
29702970 A-ATAAATA
1 ATATAAATA
29702978 GTTTTATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAAATAAATAATATGAGAAT
Found at i:29703000 original size:16 final size:16
Alignment explanation
Indices: 29702979--29703068 Score: 58
Period size: 15 Copynumber: 5.6 Consensus size: 16
29702969 TAATAAATAG
* *
29702979 TTTTATTTTAAGTATT
1 TTTTATATTAAATATT
29702995 TTTTATATTAAATA-T
1 TTTTATATTAAATATT
* *
29703010 TATTATAATATAATTATT
1 TTTTAT-AT-TAAATATT
* *
29703028 TTTAATATT-AATAAT
1 TTTTATATTAAATATT
* *
29703043 TTTAATAATAAATAATT
1 TTTTATATTAAAT-ATT
*
29703060 TTTAATATT
1 TTTTATATT
29703069 TTAATAGTTA
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
15 18 0.31
16 18 0.31
17 17 0.29
18 5 0.09
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (16 bp):
TTTTATATTAAATATT
Found at i:29703029 original size:33 final size:32
Alignment explanation
Indices: 29702991--29703068 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 32
29702981 TTATTTTAAG
*
29702991 TATTTTTTATATTAA-ATATTATT-ATAATATAAT
1 TATTTTTAATATTAATA-ATT-TTAATAATA-AAT
29703024 TATTTTTAATATTAATAATTTTAATAATAAAT
1 TATTTTTAATATTAATAATTTTAATAATAAAT
*
29703056 AATTTTTAATATT
1 TATTTTTAATATT
29703069 TTAATAGTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
32 17 0.41
33 23 0.56
34 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
TATTTTTAATATTAATAATTTTAATAATAAAT
Found at i:29703061 original size:32 final size:33
Alignment explanation
Indices: 29702992--29703068 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 33
29702982 TATTTTAAGT
* *
29702992 ATTTTTTATATTAAATATTATTATAATATAATT
1 ATTTTTAATATTAAATATTATTATAATATAATA
29703025 ATTTTTAATATT-AATAATT-TTAATAATA-AATA
1 ATTTTTAATATTAAAT-ATTATT-ATAATATAATA
29703057 ATTTTTAATATT
1 ATTTTTAATATT
29703069 TTAATAGTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
32 20 0.50
33 20 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
ATTTTTAATATTAAATATTATTATAATATAATA
Found at i:29706643 original size:12 final size:12
Alignment explanation
Indices: 29706626--29706671 Score: 83
Period size: 12 Copynumber: 3.8 Consensus size: 12
29706616 ATTTCAAATC
29706626 TCAAATTTAAAA
1 TCAAATTTAAAA
29706638 TCAAATTTAAAA
1 TCAAATTTAAAA
*
29706650 TCAAATTTAAAT
1 TCAAATTTAAAA
29706662 TCAAATTTAA
1 TCAAATTTAA
29706672 TATTATATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (12 bp):
TCAAATTTAAAA
Found at i:29706658 original size:24 final size:25
Alignment explanation
Indices: 29706600--29706671 Score: 85
Period size: 24 Copynumber: 2.9 Consensus size: 25
29706590 AAAAAATTTG
* *
29706600 ATCAAATTT-GAATTAAATTTCAAAT
1 ATCAAATTTAAAATCAAATTT-AAAT
*
29706625 CTCAAATTTAAAATCAAATTTAAA-
1 ATCAAATTTAAAATCAAATTTAAAT
*
29706649 ATCAAATTTAAATTCAAATTTAA
1 ATCAAATTTAAAATCAAATTTAA
29706672 TATTATATTG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
24 21 0.51
25 11 0.27
26 9 0.22
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.38
Consensus pattern (25 bp):
ATCAAATTTAAAATCAAATTTAAAT
Found at i:29710408 original size:15 final size:15
Alignment explanation
Indices: 29710387--29710424 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
29710377 ACCACCCCAT
29710387 CCACCTCCGCCTCCA
1 CCACCTCCGCCTCCA
*
29710402 CCGCCTCCGCCTCCA
1 CCACCTCCGCCTCCA
29710417 CCACCTCC
1 CCACCTCC
29710425 ATGTAAGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.68, G:0.08, T:0.13
Consensus pattern (15 bp):
CCACCTCCGCCTCCA
Found at i:29712564 original size:17 final size:17
Alignment explanation
Indices: 29712544--29712585 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
29712534 AAATAAAATA
*
29712544 TATTTTATAATTTTTAT
1 TATTTAATAATTTTTAT
*
29712561 TATTTAATTATTTTTA-
1 TATTTAATAATTTTTAT
29712577 -ATTTAATAA
1 TATTTAATAA
29712586 AAATAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 8 0.36
17 14 0.64
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTTAATAATTTTTAT
Found at i:29723316 original size:29 final size:30
Alignment explanation
Indices: 29723284--29723344 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
29723274 TTATTAAAAT
*
29723284 TTTAAATCGTATTACAT-TTATATT-TTATA
1 TTTAAATCATATT-CATATTATATTATTATA
* *
29723313 TTTATATCATATTCGTATTATATTATTATA
1 TTTAAATCATATTCATATTATATTATTATA
29723343 TT
1 TT
29723345 ATATTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 2 0.07
29 18 0.67
30 7 0.26
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (30 bp):
TTTAAATCATATTCATATTATATTATTATA
Found at i:29728406 original size:47 final size:44
Alignment explanation
Indices: 29728320--29728411 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 44
29728310 AGTTTGATTG
*
29728320 TTTAATTATATTATAATTTATTAATTGATTATTCAATGATTGTAA
1 TTTAATTATATTATAATTTATTAATTAATTATTCAATGA-TGTAA
29728365 TTTAATTATATATAATAATTTATT-ATTAATTGATT-ATATGATGTAA
1 TTTAATTATAT-T-ATAATTTATTAATTAATT-ATTCA-ATGATGTAA
29728411 T
1 T
29728412 ATTTTATTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
45 11 0.26
46 14 0.33
47 17 0.40
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.53
Consensus pattern (44 bp):
TTTAATTATATTATAATTTATTAATTAATTATTCAATGATGTAA
Found at i:29729471 original size:24 final size:22
Alignment explanation
Indices: 29729435--29729486 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 22
29729425 ATGATATGAA
29729435 AATAATATAATTTAAAAATTTAAT
1 AATAATATAATTT--AAATTTAAT
29729459 AATAAT-TATATTTAAATTTAAT
1 AATAATATA-ATTTAAATTTAAT
29729481 AA-AATA
1 AATAATA
29729487 AAAAATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 3 0.12
22 11 0.42
23 2 0.08
24 10 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATAATATAATTTAAATTTAAT
Found at i:29729487 original size:24 final size:25
Alignment explanation
Indices: 29729433--29729487 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
29729423 ATATGATATG
29729433 AAAATAATATAATTTAAAAATTTAAT
1 AAAATAATATAATTT-AAAATTTAAT
29729459 --AATAAT-TATATTT-AAATTTAAT
1 AAAATAATATA-ATTTAAAATTTAAT
29729481 AAAATAA
1 AAAATAA
29729488 AAAATATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
22 9 0.35
23 2 0.08
24 15 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAATAATATAATTTAAAATTTAAT
Found at i:29729561 original size:20 final size:19
Alignment explanation
Indices: 29729531--29729581 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
29729521 TTATAATATA
29729531 TAAT-TTTTATATAAAATT
1 TAATATTTTATATAAAATT
*
29729549 TAATATTTATATATAAATTT
1 TAATATTT-TATATAAAATT
29729569 TAATATTTTATAT
1 TAATATTTTATAT
29729582 TATACGAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 4 0.13
19 8 0.27
20 18 0.60
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TAATATTTTATATAAAATT
Found at i:29731559 original size:128 final size:121
Alignment explanation
Indices: 29731313--29731562 Score: 338
Period size: 128 Copynumber: 2.0 Consensus size: 121
29731303 TCAACATTTT
* * **
29731313 CTTTCCCATGATCTGGCAGCAGCTTTTTCGTTAACTTGATATCGCCCGGAAGGTTAGACACCGGA
1 CTTTCACATGATCTGACAGCAGCTTTTTCGTTAACTTGATATCGCCCGGAAGGTTAGACACCACA
* *
29731378 AATTCTTCATATTCAGACTCAAGTTTCTTGTGCGGCTCGTAGAGTATCATGCACTC
66 AATTCTTCAGATTCAGACTCAAGTTTCTTGTGCGGCTCGTACAGTATCATGCACTC
* * *
29731434 CTTTCACATGATCTGATAGCAGCTTTTTCGTTAACTTGATTTCGCCTGGAAGGTTAGGCAATGGG
1 CTTTCACATGATCTGACAGCAGCTTTTTCGTTAACTTGATATCGCCCGGAAGGTTA-G--A----
* *
29731499 CACCACAAATTCTTCAGATTCAGACTCAAGTTTCTTGTGTGGCTCGTACAGTGTCATGCACTC
59 CACCACAAATTCTTCAGATTCAGACTCAAGTTTCTTGTGCGGCTCGTACAGTATCATGCACTC
29731562 C
1 C
29731563 ATTGTGCAGG
Statistics
Matches: 111, Mismatches: 11, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
121 51 0.46
122 1 0.01
124 1 0.01
128 58 0.52
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (121 bp):
CTTTCACATGATCTGACAGCAGCTTTTTCGTTAACTTGATATCGCCCGGAAGGTTAGACACCACA
AATTCTTCAGATTCAGACTCAAGTTTCTTGTGCGGCTCGTACAGTATCATGCACTC
Found at i:29747335 original size:13 final size:14
Alignment explanation
Indices: 29747317--29747345 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
29747307 TTTTACTATC
29747317 TTTTCTTTT-CTTT
1 TTTTCTTTTCCTTT
29747330 TTTTCTTTTCCTTT
1 TTTTCTTTTCCTTT
29747344 TT
1 TT
29747346 GTTAATGACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTCTTTTCCTTT
Found at i:29748105 original size:24 final size:22
Alignment explanation
Indices: 29748062--29748106 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
29748052 AACACAAAAA
**
29748062 TATTAAATATATATTTTTATTT
1 TATTAAATATATATAATTATTT
29748084 TATTAAATTCATATATAATTATT
1 TATTAAA-T-ATATATAATTATT
29748107 ATTAAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 1 0.05
24 11 0.58
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTAAATATATATAATTATTT
Found at i:29751548 original size:2 final size:2
Alignment explanation
Indices: 29751537--29751568 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
29751527 CCACCTCATG
29751537 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29751569 GAAACACAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29756652 original size:21 final size:20
Alignment explanation
Indices: 29756606--29756677 Score: 90
Period size: 21 Copynumber: 3.5 Consensus size: 20
29756596 TTATTTAATT
*
29756606 TTATATTTACATTAAAAAATA
1 TTAT-TTTATATTAAAAAATA
*
29756627 ATATTTTATATTAAAAATATA
1 TTATTTTATATTAAAAA-ATA
*
29756648 TTATTTATATTTTAAAAAATA
1 TTATTT-TATATTAAAAAATA
29756669 TTATTTTAT
1 TTATTTTAT
29756678 TAAATTTAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
20 15 0.33
21 20 0.44
22 10 0.22
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATTTTATATTAAAAAATA
Found at i:29759330 original size:16 final size:16
Alignment explanation
Indices: 29759281--29759330 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
29759271 CCTTCTTTTG
29759281 ATAATTTAAAAT-ATA
1 ATAATTTAAAATAATA
29759296 AT-A--TAAATATAAT-
1 ATAATTTAAA-ATAATA
29759309 ATAATTTAAAATAATA
1 ATAATTTAAAATAATA
29759325 ATAATT
1 ATAATT
29759331 ATTATTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
12 4 0.14
13 4 0.14
14 4 0.14
15 7 0.24
16 10 0.34
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAATTTAAAATAATA
Found at i:29768638 original size:21 final size:21
Alignment explanation
Indices: 29768592--29768640 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
29768582 AAAAAAATCA
29768592 TAAAAAATAATTTTAAACTA-
1 TAAAAAATAATTTTAAACTAT
*
29768612 TAAAAAAGTAATTTTAGA-TATT
1 TAAAAAA-TAATTTTAAACTA-T
29768634 TAAAAAA
1 TAAAAAA
29768641 ATAAATAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 9 0.36
21 9 0.36
22 7 0.28
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (21 bp):
TAAAAAATAATTTTAAACTAT
Found at i:29778673 original size:44 final size:46
Alignment explanation
Indices: 29778594--29778684 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
29778584 GCCCTCTATA
*
29778594 TATATATATATATACGTTTTTGTTTTGATTCTCAGTAACGGCATTG
1 TATATATATATATACGTTTTTGTTTTGATTATCAGTAACGGCATTG
29778640 TATATATATATATACGTTTTT-TTTT-ATTATCAGTAACGGCATTG
1 TATATATATATATACGTTTTTGTTTTGATTATCAGTAACGGCATTG
29778684 T
1 T
29778685 CTTATGATTG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 19 0.43
45 4 0.09
46 21 0.48
ACGTcount: A:0.27, C:0.10, G:0.13, T:0.49
Consensus pattern (46 bp):
TATATATATATATACGTTTTTGTTTTGATTATCAGTAACGGCATTG
Found at i:29779747 original size:15 final size:15
Alignment explanation
Indices: 29779727--29779765 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
29779717 ACAAACTCTC
29779727 CAAAAGCTACAAAAA
1 CAAAAGCTACAAAAA
29779742 CAAAAGCTACAAAAA
1 CAAAAGCTACAAAAA
29779757 CAAAAGCTA
1 CAAAAGCTA
29779766 GAGAGACTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.64, C:0.21, G:0.08, T:0.08
Consensus pattern (15 bp):
CAAAAGCTACAAAAA
Found at i:29781706 original size:10 final size:10
Alignment explanation
Indices: 29781693--29781738 Score: 56
Period size: 10 Copynumber: 4.3 Consensus size: 10
29781683 TATTATATAT
29781693 AAATATATTA
1 AAATATATTA
29781703 AAATATATTAA
1 AAATATATT-A
*
29781714 AAATTTATTA
1 AAATATATTA
29781724 AAATAATATATA
1 AAAT-ATAT-TA
29781736 AAA
1 AAA
29781739 AACTTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 14 0.45
11 12 0.39
12 5 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
AAATATATTA
Found at i:29781717 original size:21 final size:23
Alignment explanation
Indices: 29781686--29781739 Score: 76
Period size: 21 Copynumber: 2.4 Consensus size: 23
29781676 TAATTACTAT
*
29781686 TATATATAAATATATTAAAAT-A
1 TATATAAAAATATATTAAAATAA
*
29781708 TAT-TAAAAATTTATTAAAATAA
1 TATATAAAAATATATTAAAATAA
29781730 TATATAAAAA
1 TATATAAAAA
29781740 ACTTTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 15 0.54
22 7 0.25
23 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
TATATAAAAATATATTAAAATAA
Found at i:29781746 original size:22 final size:21
Alignment explanation
Indices: 29781698--29781748 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
29781688 TATATAAATA
**
29781698 TATTAAAATATATTAAAAATT
1 TATTAAAATATATTAAAAAAC
29781719 TATTAAAATAATATATAAAAAAC
1 TATTAAAAT-ATAT-TAAAAAAC
29781742 T-TTAAAA
1 TATTAAAA
29781749 ATCAGTGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 9 0.35
22 10 0.38
23 7 0.27
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
TATTAAAATATATTAAAAAAC
Found at i:29781919 original size:17 final size:17
Alignment explanation
Indices: 29781897--29781932 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
29781887 GATTTGAACC
29781897 ATTATCACCCTTATAAT
1 ATTATCACCCTTATAAT
29781914 ATTATCACCCTTATAAT
1 ATTATCACCCTTATAAT
29781931 AT
1 AT
29781933 GGACATCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTATCACCCTTATAAT
Found at i:29785463 original size:17 final size:18
Alignment explanation
Indices: 29785441--29785482 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
29785431 TTGTGTTTTA
*
29785441 TATTTTTTAACAAAT-AT
1 TATTTTTTAAAAAATAAT
*
29785458 TATTTTTAAAAAAATAAT
1 TATTTTTTAAAAAATAAT
29785476 T-TTTTTT
1 TATTTTTT
29785483 TCTTTTTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTTTTAAAAAATAAT
Found at i:29786212 original size:58 final size:58
Alignment explanation
Indices: 29786082--29786221 Score: 156
Period size: 58 Copynumber: 2.4 Consensus size: 58
29786072 TGATAGAGTG
* ** *
29786082 CAAGGTTGTGTGCTATAATTGAGTTCAAGCTTGAAAGTCATTAAAACAACCTAAACAG
1 CAAGATTGTGTGCTATAATTGAGTTCAAGCTTGAAACACATTAAAACAACCTAAACAA
* * * * * **
29786140 CAA-AGTTGTATGCTATAATTGAGTTCAAGTTTGAGACACATTAAGATAACCTAGGCAA
1 CAAGA-TTGTGTGCTATAATTGAGTTCAAGCTTGAAACACATTAAAACAACCTAAACAA
*
29786198 CAAGATTGTGTGCTATGATTGAGT
1 CAAGATTGTGTGCTATAATTGAGT
29786222 AAACTTGAGA
Statistics
Matches: 67, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
58 66 0.99
59 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.30
Consensus pattern (58 bp):
CAAGATTGTGTGCTATAATTGAGTTCAAGCTTGAAACACATTAAAACAACCTAAACAA
Found at i:29788034 original size:21 final size:20
Alignment explanation
Indices: 29788010--29788079 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 20
29788000 ATTTTATAAA
29788010 ATAAAAATAATTATTTAATAT
1 ATAAAAAT-ATTATTTAATAT
29788031 AT--AAATA-TATTTAAATAT
1 ATAAAAATATTATTT-AATAT
*
29788049 ATCAAAAATTTTATTAAGTAATAT
1 AT-AAAAATATTATT---TAATAT
29788073 ATAAAAA
1 ATAAAAA
29788080 AATTTAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
17 5 0.12
18 8 0.20
19 4 0.10
21 6 0.15
22 4 0.10
23 5 0.12
24 7 0.17
25 1 0.03
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (20 bp):
ATAAAAATATTATTTAATAT
Found at i:29788093 original size:23 final size:24
Alignment explanation
Indices: 29788044--29788094 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
29788034 AATATATTTA
* * *
29788044 AATATATCAAAAATTTTATTAAGT
1 AATATATAAAAAAATTTATAAAGT
*
29788068 AATATATAAAAAAATTTA-AAATT
1 AATATATAAAAAAATTTATAAAGT
29788091 AATA
1 AATA
29788095 AATTAATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (24 bp):
AATATATAAAAAAATTTATAAAGT
Found at i:29788975 original size:26 final size:25
Alignment explanation
Indices: 29788927--29788987 Score: 81
Period size: 26 Copynumber: 2.5 Consensus size: 25
29788917 TATTCAATAA
**
29788927 TAAAAA-ATTTATTAATATTTTTAT
1 TAAAAATATTTATTAATAAATTTAT
29788951 TAAAAATATTTATTTAATAAATTTAT
1 TAAAAATATTTA-TTAATAAATTTAT
29788977 TAAAAAT-TTTA
1 TAAAAATATTTA
29788988 AATTTTATGC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 6 0.18
25 9 0.27
26 18 0.55
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TAAAAATATTTATTAATAAATTTAT
Found at i:29788987 original size:12 final size:12
Alignment explanation
Indices: 29788927--29788987 Score: 61
Period size: 12 Copynumber: 4.9 Consensus size: 12
29788917 TATTCAATAA
*
29788927 TAAAAAATTTAT
1 TAAAAATTTTAT
* *
29788939 TAATATTTTTAT
1 TAAAAATTTTAT
29788951 TAAAAATATTTATT
1 TAAAAAT-TTTA-T
29788965 TAATAAA-TTTAT
1 TAA-AAATTTTAT
29788977 TAAAAATTTTA
1 TAAAAATTTTA
29788988 AATTTTATGC
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
11 3 0.08
12 22 0.55
13 8 0.20
14 4 0.10
15 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TAAAAATTTTAT
Found at i:29789817 original size:23 final size:23
Alignment explanation
Indices: 29789791--29789836 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
29789781 ACCAAATTTT
29789791 AGAA-AAAAAAAACAAAATAAAAG
1 AGAAGAAAAAAAA-AAAATAAAAG
* *
29789814 AGAAGAAAATAAAAAAATTAAAG
1 AGAAGAAAAAAAAAAAATAAAAG
29789837 TGGTACGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.78, C:0.02, G:0.11, T:0.09
Consensus pattern (23 bp):
AGAAGAAAAAAAAAAAATAAAAG
Found at i:29794272 original size:53 final size:53
Alignment explanation
Indices: 29794180--29794285 Score: 149
Period size: 53 Copynumber: 2.0 Consensus size: 53
29794170 TTTAAATAAT
* * * *
29794180 TCTCGTATTTAAATATGTAAGGATTATTTAAGATATTTTTCAAATAAAAATGC
1 TCTCGTATTTAAATATATAAGAATTATTTAAGACATTTTTCAAACAAAAATGC
* * *
29794233 TCTCGTATTTAAATATATAAGAATTATTTAAGGCGTTTTTCATACAAAAATGC
1 TCTCGTATTTAAATATATAAGAATTATTTAAGACATTTTTCAAACAAAAATGC
29794286 CTTAAATAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (53 bp):
TCTCGTATTTAAATATATAAGAATTATTTAAGACATTTTTCAAACAAAAATGC
Found at i:29794323 original size:64 final size:64
Alignment explanation
Indices: 29794255--29794428 Score: 171
Period size: 63 Copynumber: 2.7 Consensus size: 64
29794245 ATATATAAGA
*
29794255 ATTATTTAAGGCGTTTTTCATACAAAAATGCCTTAAATAATTATTTTTATAAAAATAT-GAAAAG
1 ATTATTTAAGGCATTTTTCATACAAAAATGCCTTAAATAATTATTTTTATAAAAATATAG-AAAG
* * * * **
29794319 ATTATTTAAGACATTTTT-GTACAGAAAA--CATTTTAA-AA-TATCTTCTTATTTAAATATAGA
1 ATTATTTAAGGCATTTTTCATACA-AAAATGC-CTTAAATAATTAT-TT-TTATAAAAATATAGA
*
29794379 ATG
62 AAG
* *
29794382 ATTATTTAAGGCATTTTTCACACAAAAATGCCTTAAATAATCATTTT
1 ATTATTTAAGGCATTTTTCATACAAAAATGCCTTAAATAATTATTTT
29794429 AAAAAACTGC
Statistics
Matches: 86, Mismatches: 14, Indels: 20
0.72 0.12 0.17
Matches are distributed among these distances:
61 3 0.03
62 5 0.06
63 42 0.49
64 29 0.34
65 5 0.06
66 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (64 bp):
ATTATTTAAGGCATTTTTCATACAAAAATGCCTTAAATAATTATTTTTATAAAAATATAGAAAG
Found at i:29796447 original size:21 final size:21
Alignment explanation
Indices: 29796403--29796447 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
29796393 ATTCACTTAA
* *
29796403 TATTTATTTGTATTTTATATT
1 TATTGATTTGTATTTTATACT
29796424 TATTGATTTG-ATTTTAATACT
1 TATTGATTTGTATTTT-ATACT
29796445 TAT
1 TAT
29796448 ATTTCATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (21 bp):
TATTGATTTGTATTTTATACT
Found at i:29798742 original size:310 final size:310
Alignment explanation
Indices: 29798172--29798792 Score: 1080
Period size: 310 Copynumber: 2.0 Consensus size: 310
29798162 CTTCTATCTG
* *
29798172 TATTCTTGACTTCTGTCTAAAAGTAAACTGAAATACCCTTAATCATTTTCATAGCTTTATCATAT
1 TATTCTCGACTTCTGTCTAAAAGTAAACTGAAATACCCTTAATCATATTCATAGCTTTATCATAT
* * *
29798237 GAAGCACCAATATTGCCAATCTAAAGCACCAATTCAACGATTGGTCCATCCTCTTTCCTAGAATG
66 GAAGCACCAATATTGCCAATCTAAAGCACCAATTCAACAATTGATCCATCCTCATTCCTAGAATG
* *
29798302 CTTTTTGCCTGAGAACGTCGTCCTAACATTGCTCGAAGCTGCAGAACCAATTTCTTCTTCATCTT
131 CTTTTTGCCTGAGAACGTCATCCTAACATTGCTAGAAGCTGCAGAACCAATTTCTTCTTCATCTT
* *
29798367 TTCCTCTCTTCACATTTCTTTTGACATTGATATCAAACTTAGGAGAGAAGTAAGCATCCTCATTA
196 TTCCTCTCTCCACATTTCTTTTGACATTGATATCAAACTTAGGAGAAAAGTAAGCATCCTCATTA
*
29798432 GCATTCAATGATTCAATAGCATTTGTTGTTGGTTTGGCTCATTGCTTGGT
261 GCATTCAATGATTCAATAGCATTTGTTGTTGGTTTGGCTCATTGATTGGT
29798482 TATTCTCGACTTCTGTCTAAAAGTAAACTGAAATACCCTTAATCATATTCATAGCTTTATCATAT
1 TATTCTCGACTTCTGTCTAAAAGTAAACTGAAATACCCTTAATCATATTCATAGCTTTATCATAT
* * * * *
29798547 GAAGCACCAATATTGTCAATTTGATGCACCAATTCAACAATTGATCCTTCCTCATTCCTAGAATG
66 GAAGCACCAATATTGCCAATCTAAAGCACCAATTCAACAATTGATCCATCCTCATTCCTAGAATG
*
29798612 CTTTTTGCCTGAGAATGTCATCCTAACATTGCTAGAAGCTGCAGAACCAATTTCTTCTTCATCTT
131 CTTTTTGCCTGAGAACGTCATCCTAACATTGCTAGAAGCTGCAGAACCAATTTCTTCTTCATCTT
*
29798677 TTCCTCTCTCCACATTTCTTTTGACATTGATATCAAACTTAGGAGAAAAGTAAGCATCTTCATTA
196 TTCCTCTCTCCACATTTCTTTTGACATTGATATCAAACTTAGGAGAAAAGTAAGCATCCTCATTA
*
29798742 GCATTCAATGATTCAATAGCATTTGTTGTTGTTTTGGCTCATTGATTGGT
261 GCATTCAATGATTCAATAGCATTTGTTGTTGGTTTGGCTCATTGATTGGT
29798792 T
1 T
29798793 GTTCCATCAG
Statistics
Matches: 293, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
310 293 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.37
Consensus pattern (310 bp):
TATTCTCGACTTCTGTCTAAAAGTAAACTGAAATACCCTTAATCATATTCATAGCTTTATCATAT
GAAGCACCAATATTGCCAATCTAAAGCACCAATTCAACAATTGATCCATCCTCATTCCTAGAATG
CTTTTTGCCTGAGAACGTCATCCTAACATTGCTAGAAGCTGCAGAACCAATTTCTTCTTCATCTT
TTCCTCTCTCCACATTTCTTTTGACATTGATATCAAACTTAGGAGAAAAGTAAGCATCCTCATTA
GCATTCAATGATTCAATAGCATTTGTTGTTGGTTTGGCTCATTGATTGGT
Found at i:29804479 original size:2 final size:2
Alignment explanation
Indices: 29804468--29804506 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
29804458 AGTGTCCACT
29804468 TA TA -A TA TA TA 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 TA TA TA TA TA TA
29804507 GATAGATAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29812927 original size:69 final size:70
Alignment explanation
Indices: 29812791--29812997 Score: 328
Period size: 70 Copynumber: 3.0 Consensus size: 70
29812781 ATCCGAAAGG
* * * * * *
29812791 TGTGGTTTGTTCGGTAGTGACAATGTCTG-TTTGGCGGCGATGGATCCAAATAGGCCCAGGGTAA
1 TGTGGTTTGTTCGATAGTGATAGTGTCTGCTTTGGTGGAGATGGGTCCAAATAGGCCCAGGGTAA
29812855 AAAAA
66 AAAAA
29812860 TGTGGTTTGTTCGATAGTGATAGTGTCTGCTTTGGTGGAGATGGGTCCAAATAGGCCCAGGGTAA
1 TGTGGTTTGTTCGATAGTGATAGTGTCTGCTTTGGTGGAGATGGGTCCAAATAGGCCCAGGGTAA
29812925 AAAAA
66 AAAAA
**
29812930 TGTGGTTTGTTCGATAGTGATAGTGTCTGC-TTGGTGGAGATGGGTCCAAATAGGCCCAGCATAA
1 TGTGGTTTGTTCGATAGTGATAGTGTCTGCTTTGGTGGAGATGGGTCCAAATAGGCCCAGGGTAA
29812994 AAAA
66 AAAA
29812998 TATTCGTTAT
Statistics
Matches: 129, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
69 62 0.48
70 67 0.52
ACGTcount: A:0.26, C:0.13, G:0.32, T:0.29
Consensus pattern (70 bp):
TGTGGTTTGTTCGATAGTGATAGTGTCTGCTTTGGTGGAGATGGGTCCAAATAGGCCCAGGGTAA
AAAAA
Found at i:29826929 original size:19 final size:19
Alignment explanation
Indices: 29826904--29826951 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
29826894 GATACGAATA
29826904 AATATGAATAAA-ACGGA-T
1 AATATGAATAAACAC-GATT
29826922 ATATATGAATAAACACGATT
1 A-ATATGAATAAACACGATT
29826942 AATATGAATA
1 AATATGAATA
29826952 TATATGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 1 0.04
19 22 0.81
20 4 0.15
ACGTcount: A:0.54, C:0.06, G:0.12, T:0.27
Consensus pattern (19 bp):
AATATGAATAAACACGATT
Found at i:29827617 original size:11 final size:13
Alignment explanation
Indices: 29827598--29827636 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
29827588 TATGTAAATT
29827598 TTATTATATTAT-
1 TTATTATATTATA
29827610 TT-TTATATTATA
1 TTATTATATTATA
*
29827622 TTATTATATCATA
1 TTATTATATTATA
29827635 TT
1 TT
29827637 TAAAATTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 9 0.38
12 4 0.17
13 11 0.46
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTATATTATA
Found at i:29833747 original size:24 final size:24
Alignment explanation
Indices: 29833715--29833760 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
29833705 ACATGAATTT
*
29833715 TGAACGATTTGAGTGGACCCCACA
1 TGAACGATTGGAGTGGACCCCACA
* *
29833739 TGAATGATTGGGGTGGACCCCA
1 TGAACGATTGGAGTGGACCCCA
29833761 ATAATTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (24 bp):
TGAACGATTGGAGTGGACCCCACA
Found at i:29835197 original size:28 final size:29
Alignment explanation
Indices: 29835164--29835227 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 29
29835154 ATTTATTGAA
*
29835164 TTATTTTAAATATAT-AATTTATAAT-TA-T
1 TTATTTTAAAT-TATCAA-ATATAATATATT
29835192 TTATTTTAAATTATCAAATATAATATATT
1 TTATTTTAAATTATCAAATATAATATATT
29835221 TTATTTT
1 TTATTTT
29835228 GATTTAAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 9 0.28
28 15 0.47
29 8 0.25
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (29 bp):
TTATTTTAAATTATCAAATATAATATATT
Found at i:29835203 original size:14 final size:14
Alignment explanation
Indices: 29835164--29835205 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
29835154 ATTTATTGAA
29835164 TTATTTTAAA-TAT
1 TTATTTTAAATTAT
* *
29835177 ATAATTTATAATTAT
1 TTATTTTA-AATTAT
29835192 TTATTTTAAATTAT
1 TTATTTTAAATTAT
29835206 CAAATATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 6 0.26
14 8 0.35
15 9 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATTTTAAATTAT
Found at i:29835839 original size:31 final size:31
Alignment explanation
Indices: 29835754--29835844 Score: 78
Period size: 31 Copynumber: 2.9 Consensus size: 31
29835744 CAATCGATTT
** *
29835754 AATTAATTTAAT-TTTAAAAAATTAATAATTA
1 AATTAA-TTAATATTTATTAAATAAATAATTA
* * *
29835785 ATTTAATTAATTTTTATTTAATAAATAATTA
1 AATTAATTAATATTTATTAAATAAATAATTA
* *
29835816 AATTGATTAAATATTT-TTAAATAATTAAT
1 AATTAATT-AATATTTATTAAATAAATAAT
29835845 CATAATCGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
30 5 0.10
31 37 0.77
32 6 0.12
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
AATTAATTAATATTTATTAAATAAATAATTA
Found at i:29835938 original size:29 final size:27
Alignment explanation
Indices: 29835876--29835938 Score: 63
Period size: 29 Copynumber: 2.2 Consensus size: 27
29835866 CGATTTAATT
*
29835876 AATTTGATTAAAAAATTAATTAATTATT
1 AATTT-ATTAAAAAATTAATTAATTATA
** *
29835904 TTTTTATTATAAATAATTATTTAATTATA
1 AATTTATTA-AAA-AATTAATTAATTATA
29835933 AATTTA
1 AATTTA
29835939 ATTTAATAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
27 4 0.15
28 6 0.22
29 17 0.63
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
AATTTATTAAAAAATTAATTAATTATA
Found at i:29835959 original size:16 final size:17
Alignment explanation
Indices: 29835909--29835960 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 17
29835899 TTATTTTTTT
29835909 ATTATAAATAATT-ATTTA
1 ATTATAAAT--TTAATTTA
29835927 ATTATAAATTTAATTTA
1 ATTATAAATTTAATTTA
29835944 A-TA-AAATTTAAATTTA
1 ATTATAAATTT-AATTTA
29835960 A
1 A
29835961 ATATCATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 6 0.19
16 11 0.34
17 6 0.19
18 9 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTATAAATTTAATTTA
Found at i:29836111 original size:18 final size:18
Alignment explanation
Indices: 29836069--29836115 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
29836059 TTTTAAAAAT
*
29836069 AAAAATTTGATTGAATTA
1 AAAAATTTAATTGAATTA
** *
29836087 ATTAATTTAATTGATTTA
1 AAAAATTTAATTGAATTA
29836105 AAAAA-TTAATT
1 AAAAATTTAATT
29836116 ATAATCATAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (18 bp):
AAAAATTTAATTGAATTA
Found at i:29843198 original size:11 final size:10
Alignment explanation
Indices: 29843177--29843209 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
29843167 TTTTAATATC
29843177 AAAAA-ATAA
1 AAAAATATAA
29843186 AAAAATCATAA
1 AAAAAT-ATAA
29843197 AAAAATATAA
1 AAAAATATAA
29843207 AAA
1 AAA
29843210 TATAAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.23
10 7 0.32
11 10 0.45
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAATATAA
Found at i:29843201 original size:19 final size:18
Alignment explanation
Indices: 29843171--29843216 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
29843161 TATGATTTTT
*
29843171 AATATCAAAAAATAAAAA
1 AATATAAAAAAATAAAAA
*
29843189 AATCATAAAAAAATATAAA
1 AAT-ATAAAAAAATAAAAA
29843208 AATATAAAA
1 AATATAAAA
29843217 TTTTCTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (18 bp):
AATATAAAAAAATAAAAA
Found at i:29846912 original size:30 final size:30
Alignment explanation
Indices: 29846878--29846948 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
29846868 TGATTTAACT
*
29846878 TAAAAT-TAATAAAATATTATTTTTTACATA
1 TAAAATATAATAAAATATTA-TTTTTAAATA
* **
29846908 TAAAATATTATTTAATATTATTTTTAAATA
1 TAAAATATAATAAAATATTATTTTTAAATA
29846938 TAAATATATAA
1 TAAA-ATATAA
29846949 AAATTTAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 19 0.56
31 15 0.44
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (30 bp):
TAAAATATAATAAAATATTATTTTTAAATA
Found at i:29851288 original size:19 final size:20
Alignment explanation
Indices: 29851250--29851289 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
29851240 TCGATTAGTG
*
29851250 AAATATTTAATTTTTTTAAA
1 AAATATTTAATTTATTTAAA
*
29851270 AAATTTTTAA-TTATTTAAA
1 AAATATTTAATTTATTTAAA
29851289 A
1 A
29851290 TCATAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATATTTAATTTATTTAAA
Found at i:29859552 original size:18 final size:20
Alignment explanation
Indices: 29859524--29859606 Score: 73
Period size: 19 Copynumber: 4.0 Consensus size: 20
29859514 GACTCGAAAT
29859524 TATATAAATATT-TTTAAAA
1 TATATAAATATTATTTAAAA
*
29859543 TATA-AAATATTATTTAAAT
1 TATATAAATATTATTTAAAA
29859562 TAATATAAATATATATTATAATAAA
1 T-ATATAAATAT-TATT-T-A-AAA
*
29859587 TATATATAATAATA-TTAAAA
1 TATATA-AATATTATTTAAAA
29859607 AATAATTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
18 7 0.13
19 11 0.21
20 6 0.11
21 7 0.13
22 5 0.09
23 2 0.04
24 8 0.15
25 7 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TATATAAATATTATTTAAAA
Found at i:29859578 original size:22 final size:20
Alignment explanation
Indices: 29859520--29859578 Score: 77
Period size: 19 Copynumber: 3.0 Consensus size: 20
29859510 ATTTGACTCG
29859520 AAATTATATAAATATT-TTT
1 AAATTATATAAATATTATTT
*
29859539 AAAATATA-AAATATTATTT
1 AAATTATATAAATATTATTT
29859558 AAATTAATATAAATATATATT
1 AAATT-ATATAAATAT-TATT
29859579 ATAATAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 7 0.21
19 14 0.41
20 3 0.09
21 6 0.18
22 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATTATATAAATATTATTT
Found at i:29859585 original size:16 final size:16
Alignment explanation
Indices: 29859562--29859600 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
29859552 TTATTTAAAT
29859562 TAAT-ATAAATATATA
1 TAATAATAAATATATA
*
29859577 TTATAATAAATATATA
1 TAATAATAAATATATA
29859593 TAATAATA
1 TAATAATA
29859601 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAAATATATA
Found at i:29859588 original size:22 final size:22
Alignment explanation
Indices: 29859540--29859590 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
29859530 AATATTTTTA
29859540 AAATATAAAATATTATTTAAAT
1 AAATATAAAATATTATTTAAAT
*
29859562 TAATAT-AAATA-TATATTATAAT
1 AAATATAAAATATTAT-TTA-AAT
29859584 AAATATA
1 AAATATA
29859591 TATAATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 3 0.12
21 8 0.33
22 13 0.54
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATATAAAATATTATTTAAAT
Found at i:29859609 original size:22 final size:24
Alignment explanation
Indices: 29859564--29859610 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
29859554 ATTTAAATTA
29859564 ATATAAATATATATTATAATAAAT
1 ATATAAATATATATTATAATAAAT
29859588 ATATATAATA-ATATTA-AA-AAAT
1 ATATA-AATATATATTATAATAAAT
29859610 A
1 A
29859611 ATTTTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 2 0.09
24 11 0.50
25 4 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATAAATATATATTATAATAAAT
Found at i:29860728 original size:23 final size:23
Alignment explanation
Indices: 29860702--29860759 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
29860692 TTATATTTAT
29860702 GTAAAATTTTTTTGTCGCTAAAA
1 GTAAAATTTTTTTGTCGCTAAAA
** *
29860725 GTAAGTTTTTTTTGTTGCTAAAA
1 GTAAAATTTTTTTGTCGCTAAAA
29860748 --AAAAGTTTTTTT
1 GTAAAA-TTTTTTT
29860760 TTTATTTGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 2 0.07
22 7 0.24
23 20 0.69
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.50
Consensus pattern (23 bp):
GTAAAATTTTTTTGTCGCTAAAA
Found at i:29860760 original size:23 final size:23
Alignment explanation
Indices: 29860708--29860760 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
29860698 TTATGTAAAA
**
29860708 TTTTTTTGTCGCTAAAAGTAAGT
1 TTTTTTTGTCGCTAAAAAAAAGT
*
29860731 TTTTTTTGTTGCTAAAAAAAAGT
1 TTTTTTTGTCGCTAAAAAAAAGT
29860754 TTTTTTT
1 TTTTTTT
29860761 TTATTTGACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (23 bp):
TTTTTTTGTCGCTAAAAAAAAGT
Found at i:29863617 original size:24 final size:25
Alignment explanation
Indices: 29863585--29863641 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
29863575 ACCAATAAGA
29863585 TATGGAATTTATA-TCTTTCTT-TTG
1 TATGGAATTTA-AGTCTTTCTTCTTG
*
29863609 TATGGAATTTAAGTCTTTTTTCTTG
1 TATGGAATTTAAGTCTTTCTTCTTG
*
29863634 TTTGGAAT
1 TATGGAAT
29863642 ACCAATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 1 0.03
24 18 0.62
25 10 0.34
ACGTcount: A:0.21, C:0.07, G:0.16, T:0.56
Consensus pattern (25 bp):
TATGGAATTTAAGTCTTTCTTCTTG
Found at i:29864769 original size:52 final size:52
Alignment explanation
Indices: 29864691--29864817 Score: 175
Period size: 52 Copynumber: 2.4 Consensus size: 52
29864681 TGGACAAGAA
* *
29864691 GACTTGCAAAAGAAGAATT-TCAAAAGAAAGAGGACTCTTAATAAGTAAGTTT
1 GACTTGCAAAAGAAGAATTCT-AAAAGAAAAAGGACTCTTAATAAGCAAGTTT
* *
29864743 GACTTGCAAAAGAAGAATTCTAAAAGAAAAAGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAAAGAAGAATTCTAAAAGAAAAAGGACTCTTAATAAGCAAGTTT
* **
29864795 GACTTACAGGAGAAGAATTCTAA
1 GACTTGCAAAAGAAGAATTCTAA
29864818 GAGGAGAAGG
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
52 66 0.99
53 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (52 bp):
GACTTGCAAAAGAAGAATTCTAAAAGAAAAAGGACTCTTAATAAGCAAGTTT
Found at i:29864828 original size:52 final size:52
Alignment explanation
Indices: 29864691--29864833 Score: 171
Period size: 52 Copynumber: 2.8 Consensus size: 52
29864681 TGGACAAGAA
* * * *
29864691 GACTTGCAAAAGAAGAATT-TCAAAAGAAAGAGGACTCTTAATAAGTAAGTTT
1 GACTTACAAAAGAAGAATTCT-AAAAGAAAAAGGATTCTTAATAAGCAAGTTT
* *
29864743 GACTTGCAAAAGAAGAATTCTAAAAGAAAAAGGATTCTTAATAGGCAAGTTT
1 GACTTACAAAAGAAGAATTCTAAAAGAAAAAGGATTCTTAATAAGCAAGTTT
** * * *
29864795 GACTTACAGGAGAAGAATTCTAAGAGGAGAAGGATTCTT
1 GACTTACAAAAGAAGAATTCTAAAAGAAAAAGGATTCTT
29864834 TAAATAGGTA
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
52 79 0.99
53 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (52 bp):
GACTTACAAAAGAAGAATTCTAAAAGAAAAAGGATTCTTAATAAGCAAGTTT
Found at i:29865391 original size:25 final size:25
Alignment explanation
Indices: 29865357--29865431 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
29865347 AAGTGGTATC
*
29865357 AAAGCTAAAGGTTCGAAACGT-AAGA
1 AAAGTTAAAGGTTCGAAACGTGAA-A
* *
29865382 AAAGTTAAAGATTC-AAAGTGTGAAA
1 AAAGTTAAAGGTTCGAAA-CGTGAAA
* *
29865407 AAAGTCAAAGGTTCGAGACGTGAAA
1 AAAGTTAAAGGTTCGAAACGTGAAA
29865432 GAGCTGAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
24 3 0.08
25 33 0.82
26 4 0.10
ACGTcount: A:0.48, C:0.09, G:0.24, T:0.19
Consensus pattern (25 bp):
AAAGTTAAAGGTTCGAAACGTGAAA
Found at i:29865441 original size:25 final size:25
Alignment explanation
Indices: 29865413--29865473 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
29865403 GAAAAAAGTC
29865413 AAAGGTTCGAGACGTGA-AAGAGCT
1 AAAGGTTCGAGACGTGAGAAGAGCT
*
29865437 GAAA-GTTCGAGATGTGAGAAGAGCT
1 -AAAGGTTCGAGACGTGAGAAGAGCT
*
29865462 AAAGGTTTGAGA
1 AAAGGTTCGAGA
29865474 AGTGCATGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 15 0.47
25 17 0.53
ACGTcount: A:0.38, C:0.08, G:0.34, T:0.20
Consensus pattern (25 bp):
AAAGGTTCGAGACGTGAGAAGAGCT
Found at i:29865453 original size:24 final size:24
Alignment explanation
Indices: 29865417--29865465 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
29865407 AAAGTCAAAG
29865417 GTTCGAGACGTGA-AAGAGCTGAAA
1 GTTCGAGACGTGAGAAGAGCT-AAA
*
29865441 GTTCGAGATGTGAGAAGAGCTAAA
1 GTTCGAGACGTGAGAAGAGCTAAA
29865465 G
1 G
29865466 GTTTGAGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (24 bp):
GTTCGAGACGTGAGAAGAGCTAAA
Found at i:29865733 original size:11 final size:11
Alignment explanation
Indices: 29865717--29865747 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
29865707 AATCACATAA
29865717 GAGATTTGTTT
1 GAGATTTGTTT
29865728 GAGATTTGTTT
1 GAGATTTGTTT
29865739 GAGATTTGT
1 GAGATTTGT
29865748 CAGATATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:29865850 original size:52 final size:52
Alignment explanation
Indices: 29865772--29865928 Score: 183
Period size: 52 Copynumber: 3.0 Consensus size: 52
29865762 TGGACAAGAA
*
29865772 GACTTGCAAAAGAAGAATT-TCAAAAGAAAGAGGATTCTTAATAAGTAAGTTT
1 GACTTGCAAAAGAAGAATTCT-AAAAGAAAGAGGATTCTTAATAAGCAAGTTT
* * *
29865824 GACTTGCAAAAGAAGAATTCTAAAAGAAAAAAGATTCTTAATAGGCAAGTTT
1 GACTTGCAAAAGAAGAATTCTAAAAGAAAGAGGATTCTTAATAAGCAAGTTT
* ** * * **
29865876 GACTTACAGGAGAAGAATTCTAAGAG-GAGAGGGATTCTTAATGGGCAAGTTT
1 GACTTGCAAAAGAAGAATTCTAAAAGAAAGA-GGATTCTTAATAAGCAAGTTT
29865928 G
1 G
29865929 TATGGTTATA
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
51 2 0.02
52 88 0.97
53 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.25
Consensus pattern (52 bp):
GACTTGCAAAAGAAGAATTCTAAAAGAAAGAGGATTCTTAATAAGCAAGTTT
Found at i:29870627 original size:15 final size:15
Alignment explanation
Indices: 29870604--29870654 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
29870594 ATTTATAAAT
*
29870604 AATATTATATTAATA
1 AATAATATATTAATA
29870619 AATAATATATTAATA
1 AATAATATATTAATA
29870634 AAT-AT-TATTAATA
1 AATAATATATTAATA
29870647 AATAATAT
1 AATAATAT
29870655 TATAATATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
13 11 0.33
14 4 0.12
15 18 0.55
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATAATATATTAATA
Found at i:29870646 original size:28 final size:25
Alignment explanation
Indices: 29870609--29870678 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 25
29870599 TAAATAATAT
29870609 TATATTAATAAATAATATATTAATAAA
1 TATATTAATAAATAATATATT-AT-AA
29870636 TATTATTAATAAAT-A-ATATTATAA
1 TA-TATTAATAAATAATATATTATAA
*
29870660 TATGTTAATAAATAATATA
1 TATATTAATAAATAATATA
29870679 AAGAATAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
23 10 0.26
24 5 0.13
25 5 0.13
26 5 0.13
27 3 0.08
28 11 0.28
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (25 bp):
TATATTAATAAATAATATATTATAA
Found at i:29870679 original size:28 final size:26
Alignment explanation
Indices: 29870610--29870679 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 26
29870600 AAATAATATT
29870610 ATATTAATAAATAATAT-ATTAATAA
1 ATATTAATAAATAATATAATTAATAA
* *
29870635 ATATT-ATTAATAA-ATAATATTATAA
1 ATATTAATAAATAATATAAT-TAATAA
*
29870660 TATGTTAATAAATAATATAA
1 -ATATTAATAAATAATATAA
29870680 AGAATAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
23 2 0.06
24 9 0.25
25 10 0.28
26 4 0.11
27 7 0.19
28 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (26 bp):
ATATTAATAAATAATATAATTAATAA
Found at i:29870737 original size:19 final size:19
Alignment explanation
Indices: 29870713--29870750 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
29870703 AAGTATTTTT
29870713 TATTAACATAATATT-TTAA
1 TATTAA-ATAATATTATTAA
*
29870732 TATTAAATATTATTATTAA
1 TATTAAATAATATTATTAA
29870751 AATATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTAAATAATATTATTAA
Found at i:29870791 original size:16 final size:16
Alignment explanation
Indices: 29870759--29870800 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
29870749 AAAATATAAT
**
29870759 TAATTTTAAT-ATTAA
1 TAATTTTAATAACAAA
29870774 TAATTTTAATAACAAA
1 TAATTTTAATAACAAA
*
29870790 TAATTTCAATA
1 TAATTTTAATA
29870801 TATTTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATTTTAATAACAAA
Found at i:29870793 original size:25 final size:24
Alignment explanation
Indices: 29870765--29870834 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 24
29870755 TAATTAATTT
29870765 TAATATTAATAATTTTAATAACAAA
1 TAAT-TTAATAATTTTAATAACAAA
*
29870790 TAATTTCAATATATTTTAATAATAAA
1 TAATTT-AATA-ATTTTAATAACAAA
29870816 TAATTTTTAAT-ATTTTAAT
1 TAA--TTTAATAATTTTAAT
29870835 TATTATATTG
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 16 0.40
27 3 0.08
28 3 0.08
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATTTAATAATTTTAATAACAAA
Found at i:29870809 original size:26 final size:26
Alignment explanation
Indices: 29870772--29870834 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
29870762 TTTTAATATT
29870772 AATA-ATTTTAATAACAAATAATTTC
1 AATATATTTTAATAACAAATAATTTC
* *
29870797 AATATATTTTAATAATAAATAATTTT
1 AATATATTTTAATAACAAATAATTTC
*
29870823 TA-ATATTTTAAT
1 AATATATTTTAAT
29870835 TATTATATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 14 0.41
26 20 0.59
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (26 bp):
AATATATTTTAATAACAAATAATTTC
Found at i:29870821 original size:16 final size:16
Alignment explanation
Indices: 29870725--29870827 Score: 60
Period size: 15 Copynumber: 6.6 Consensus size: 16
29870715 TTAACATAAT
*
29870725 ATTTTAATATTAAATA
1 ATTTTAATAATAAATA
29870741 TTATTATTAA-AATATAATTA
1 --ATT-TTAATAATA-AA-TA
*
29870761 ATTTTAAT-ATTAATA
1 ATTTTAATAATAAATA
*
29870776 ATTTTAATAACAAATA
1 ATTTTAATAATAAATA
*
29870792 A-TTT--CAAT--AT-
1 ATTTTAATAATAAATA
29870802 ATTTTAATAATAAATA
1 ATTTTAATAATAAATA
29870818 ATTTTTAATA
1 A-TTTTAATA
29870828 TTTTAATTAT
Statistics
Matches: 66, Mismatches: 7, Indels: 25
0.67 0.07 0.26
Matches are distributed among these distances:
10 1 0.02
11 5 0.08
13 5 0.08
15 15 0.23
16 9 0.14
17 14 0.21
18 9 0.14
19 6 0.09
20 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTTAATAATAAATA
Found at i:29870874 original size:16 final size:16
Alignment explanation
Indices: 29870849--29870879 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29870839 ATATTGATAT
*
29870849 ATTTTTAAAAAATAAA
1 ATTTTCAAAAAATAAA
29870865 ATTTTCAAAAAATAA
1 ATTTTCAAAAAATAA
29870880 TCAAACAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTTTCAAAAAATAAA
Found at i:29871362 original size:27 final size:28
Alignment explanation
Indices: 29871315--29871390 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 28
29871305 TATGACATAA
29871315 AAATATTATAAATAAT-ATAAAAA-TAGTAT
1 AAAT-TTA-AAATAATAATAAAAATTA-TAT
**
29871344 -AATTTAAAATTTTAATAAAAATTATAT
1 AAATTTAAAATAATAATAAAAATTATAT
29871371 AAATTTAAAATAATAATAAA
1 AAATTTAAAATAATAATAAA
29871391 TTGTTGTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 5 0.12
27 13 0.32
28 22 0.55
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (28 bp):
AAATTTAAAATAATAATAAAAATTATAT
Found at i:29871656 original size:16 final size:17
Alignment explanation
Indices: 29871622--29871656 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
29871612 TATTTCACTT
29871622 TTATGAAAGAAAAAAAA
1 TTATGAAAGAAAAAAAA
*
29871639 TTATGAAA-AAACAAAA
1 TTATGAAAGAAAAAAAA
29871655 TT
1 TT
29871657 TCTTTCACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.66, C:0.03, G:0.09, T:0.23
Consensus pattern (17 bp):
TTATGAAAGAAAAAAAA
Found at i:29876602 original size:140 final size:140
Alignment explanation
Indices: 29876350--29876634 Score: 570
Period size: 140 Copynumber: 2.0 Consensus size: 140
29876340 AATGCGGGCA
29876350 TTTTTCACTCTGCTATTTTTATGTTCGTCATTGCTGTGATAAAATTCATATCTTCAGCATTTTAT
1 TTTTTCACTCTGCTATTTTTATGTTCGTCATTGCTGTGATAAAATTCATATCTTCAGCATTTTAT
29876415 TTTAGTGTTGCAAGTTAAGGAATTGACCTTTTCTAATTGTTGACCGAGATCTAGGAAAGTTATTG
66 TTTAGTGTTGCAAGTTAAGGAATTGACCTTTTCTAATTGTTGACCGAGATCTAGGAAAGTTATTG
29876480 CTTGCAAGTT
131 CTTGCAAGTT
29876490 TTTTTCACTCTGCTATTTTTATGTTCGTCATTGCTGTGATAAAATTCATATCTTCAGCATTTTAT
1 TTTTTCACTCTGCTATTTTTATGTTCGTCATTGCTGTGATAAAATTCATATCTTCAGCATTTTAT
29876555 TTTAGTGTTGCAAGTTAAGGAATTGACCTTTTCTAATTGTTGACCGAGATCTAGGAAAGTTATTG
66 TTTAGTGTTGCAAGTTAAGGAATTGACCTTTTCTAATTGTTGACCGAGATCTAGGAAAGTTATTG
29876620 CTTGCAAGTT
131 CTTGCAAGTT
29876630 TTTTT
1 TTTTT
29876635 TTTTTTTTTT
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 145 1.00
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (140 bp):
TTTTTCACTCTGCTATTTTTATGTTCGTCATTGCTGTGATAAAATTCATATCTTCAGCATTTTAT
TTTAGTGTTGCAAGTTAAGGAATTGACCTTTTCTAATTGTTGACCGAGATCTAGGAAAGTTATTG
CTTGCAAGTT
Found at i:29879608 original size:19 final size:18
Alignment explanation
Indices: 29879584--29879652 Score: 79
Period size: 19 Copynumber: 3.8 Consensus size: 18
29879574 TTCCTTTGTA
29879584 ATTAATAATATATAATTTT
1 ATTAAT-ATATATAATTTT
*
29879603 ATTAATATATTATTATTTT
1 ATTAATATA-TATAATTTT
29879622 ATTAAT-TAATATAATTTT
1 ATTAATAT-ATATAATTTT
*
29879640 ATTTATATA-ATAA
1 ATTAATATATATAA
29879653 AATATTATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
17 4 0.09
18 18 0.41
19 22 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTAATATATATAATTTT
Found at i:29879629 original size:23 final size:24
Alignment explanation
Indices: 29879603--29879673 Score: 80
Period size: 23 Copynumber: 3.1 Consensus size: 24
29879593 ATATAATTTT
29879603 ATTAATATATTATTATTTTAT-TA
1 ATTAATATATTATTATTTTATATA
29879626 ATTAATATAATT-TTA-TTTATATA
1 ATTAATAT-ATTATTATTTTATATA
*
29879649 A-TAAAATATTATT-TTTTAATATA
1 ATTAATATATTATTATTTT-ATATA
29879672 AT
1 AT
29879674 AATTGTAACA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
21 3 0.07
22 15 0.37
23 20 0.49
24 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTAATATATTATTATTTTATATA
Found at i:29879661 original size:37 final size:37
Alignment explanation
Indices: 29879584--29879673 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 37
29879574 TTCCTTTGTA
* * ** *
29879584 ATTAATAATATATAATTTTATTAATATATTATTATTTT
1 ATTAATTA-ATATAATTTTATTAATATAATAAAATATT
*
29879622 ATTAATTAATATAATTTTATTTATATAATAAAATATT
1 ATTAATTAATATAATTTTATTAATATAATAAAATATT
**
29879659 ATTTTTTAATATAAT
1 ATTAATTAATATAAT
29879674 AATTGTAACA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
37 37 0.84
38 7 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (37 bp):
ATTAATTAATATAATTTTATTAATATAATAAAATATT
Found at i:29880105 original size:6 final size:7
Alignment explanation
Indices: 29880082--29880122 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
29880072 GAAAAAAAAT
29880082 AAAAACG
1 AAAAACG
*
29880089 AAAGACG
1 AAAAACG
*
29880096 AAAAACA
1 AAAAACG
29880103 AAAAAC-
1 AAAAACG
29880109 AAAAAC-
1 AAAAACG
29880115 AAAAACG
1 AAAAACG
29880122 A
1 A
29880123 TAACATTAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.76, C:0.15, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAACG
Found at i:29880112 original size:13 final size:13
Alignment explanation
Indices: 29880075--29880119 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
29880065 ATAAAAAGAA
*
29880075 AAAAAATAAAAAC
1 AAAAAACAAAAAC
* *
29880088 GAAAGACGAAAAAC
1 AAAAAAC-AAAAAC
29880102 AAAAAACAAAAAC
1 AAAAAACAAAAAC
29880115 AAAAA
1 AAAAA
29880120 CGATAACATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.80, C:0.11, G:0.07, T:0.02
Consensus pattern (13 bp):
AAAAAACAAAAAC
Found at i:29881639 original size:45 final size:45
Alignment explanation
Indices: 29881589--29881681 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 45
29881579 TGGCAATTTA
*
29881589 ACAACATCACCAGCACTAGCAACAGGAACGGCTACAGCAACAGCG
1 ACAACACCACCAGCACTAGCAACAGGAACGGCTACAGCAACAGCG
* *
29881634 ACAACACCACCAGCACTAGCAACAGGAACGGCTACAGCGACAGTG
1 ACAACACCACCAGCACTAGCAACAGGAACGGCTACAGCAACAGCG
29881679 ACA
1 ACA
29881682 GCTGCAGTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.40, C:0.33, G:0.20, T:0.06
Consensus pattern (45 bp):
ACAACACCACCAGCACTAGCAACAGGAACGGCTACAGCAACAGCG
Done.