Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008737.1 Hibiscus syriacus cultivar Beakdansim tig00111812_pilon, 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: 2791265
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 14
Found at i:931171 original size:32 final size:32
Alignment explanation
Indices: 931019--931159 Score: 85
Period size: 33 Copynumber: 4.4 Consensus size: 32
931009 AACTTTTGAA
* *
931019 AAAATTATTTAATCAAAAT-AAAAATGTATAAC
1 AAAATTATTTAGTCACAATAAAAAAT-TATAAC
* ** *
931051 AAATATTAATTT-TTCATTATAAAAAATTGA-GAC
1 AAA-ATT-ATTTAGTCACAATAAAAAATT-ATAAC
* ** * * *
931084 AAATAATATTTTTTCATAATAACAAATTGTAAC
1 AAA-ATTATTTAGTCACAATAAAAAATTATAAC
*
931117 AAAATTATTTAGTCACAGTAAAAAATTATAA-
1 AAAATTATTTAGTCACAATAAAAAATTATAAC
931148 AAAA-TATTTAGT
1 AAAATTATTTAGT
931160 GACGAAATAA
Statistics
Matches: 87, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
30 8 0.09
31 4 0.05
32 28 0.32
33 36 0.41
34 11 0.13
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.36
Consensus pattern (32 bp):
AAAATTATTTAGTCACAATAAAAAATTATAAC
Found at i:932208 original size:2 final size:2
Alignment explanation
Indices: 932201--932278 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
932191 GGAAAGGAGG
932201 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
932243 -A GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
932279 GGGGGGGGAG
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 74 0.99
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:933181 original size:3 final size:3
Alignment explanation
Indices: 933173--933250 Score: 104
Period size: 3 Copynumber: 25.7 Consensus size: 3
933163 ATAACAAAAG
* *
933173 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT GAT AAT AATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
*
933222 AA- AAT AAT AAT GAT AAT AATT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AA
933251 ACAATTAAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.03
3 58 0.88
4 6 0.09
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:935280 original size:20 final size:20
Alignment explanation
Indices: 935255--935530 Score: 218
Period size: 20 Copynumber: 13.7 Consensus size: 20
935245 AATTTTCCAG
** *
935255 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
**
935275 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATC-CGTA
* * *
935295 AATCGCAACGAGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* * *
935314 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATCCGT-A
*
935336 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
935356 AATCGCAACGAC-AATACGTA
1 AATCGCAACG-CGAATCCGTA
* *
935376 AATTCGCAACGTGTATCCGTA
1 AA-TCGCAACGCGAATCCGTA
* *
935397 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
935417 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATCCGTA
** **
935437 AATCGCAACGATAAAACGTA
1 AATCGCAACGCGAATCCGTA
* *
935457 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
935477 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
*
935498 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
935518 AATCGCAACGCGA
1 AATCGCAACGCGA
935531 TCGATAATTC
Statistics
Matches: 203, Mismatches: 42, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
19 1 0.00
20 149 0.73
21 52 0.26
22 1 0.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:935338 original size:61 final size:62
Alignment explanation
Indices: 935273--935530 Score: 232
Period size: 61 Copynumber: 4.2 Consensus size: 62
935263 CGCGAATATG
** * * * *
935273 AAAATCGCAACGCGAACATATAAATCGCAACGA-GATTC-TGACTATCGCAACGAGTATCCGT
1 AAAATCGCAACGCGAACACGTAAATCGCAACGACAATACGTAAAT-TCGCAACGAGTATCCGT
* *
935334 AAAATCGCAACGCGTATC-CGTAAATCGCAACGACAATACGTAAATTCGCAACGTGTATCCGT
1 AAAATCGCAACGCG-AACACGTAAATCGCAACGACAATACGTAAATTCGCAACGAGTATCCGT
* * * **
935396 -AAATCGCAACGAGAATACGTAAATCGCAACG-C-GTATCTGTAAA-TCGCAACGA-TAAAACGT
1 AAAATCGCAACGCGAACACGTAAATCGCAACGACAATA-C-GTAAATTCGCAACGAGT-ATCCGT
* * * *
935456 -AAATCGCAATGCGTATC-CGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGT
1 AAAATCGCAACGCG-AACACGTAAATCGCAACGACAATACGTAAATTCGCAACGAGTATCCGT
935517 -AAATCGCAACGCGA
1 AAAATCGCAACGCGA
935531 TCGATAATTC
Statistics
Matches: 161, Mismatches: 24, Indels: 25
0.77 0.11 0.12
Matches are distributed among these distances:
59 3 0.02
60 46 0.29
61 85 0.53
62 24 0.15
63 3 0.02
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (62 bp):
AAAATCGCAACGCGAACACGTAAATCGCAACGACAATACGTAAATTCGCAACGAGTATCCGT
Found at i:935361 original size:41 final size:41
Alignment explanation
Indices: 935316--935527 Score: 320
Period size: 41 Copynumber: 5.2 Consensus size: 41
935306 GATTCTGACT
** *
935316 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
* *
935357 ATCGCAACGACAATACGTAAATTCGCAACGTGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
* *
935398 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
935438 ATCGCAACGATAAAACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
935478 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
935519 ATCGCAACG
1 ATCGCAACG
935528 CGATCGATAA
Statistics
Matches: 154, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 71 0.46
41 83 0.54
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:935666 original size:20 final size:20
Alignment explanation
Indices: 935641--935708 Score: 111
Period size: 20 Copynumber: 3.4 Consensus size: 20
935631 TTTTCCTAAT
*
935641 TCGCAATGCTAATACGTAAA
1 TCGCAATGCGAATACGTAAA
935661 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
935681 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
935701 TCGCAATG
1 TCGCAATG
935709 AGATTCTGAC
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 1 0.02
20 45 0.98
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:935716 original size:20 final size:20
Alignment explanation
Indices: 935656--935716 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
935646 ATGCTAATAC
*
935656 GTAAATCGCAATGCGAATAC-
1 GTAAATCGCAATGCG-ATTCT
*
935676 GTAAATCGCAATGCGAATCT
1 GTAAATCGCAATGCGATTCT
*
935696 GTAAATCGCAATGAGATTCT
1 GTAAATCGCAATGCGATTCT
935716 G
1 G
935717 ACTATCGCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
19 2 0.06
20 34 0.94
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (20 bp):
GTAAATCGCAATGCGATTCT
Found at i:936618 original size:24 final size:24
Alignment explanation
Indices: 936561--936620 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
936551 TAGTCAGTAT
936561 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* * *
936585 CCGGACTTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
*
936609 TCGAATTTTGAT
1 TCGAAATTTGAT
936621 GATTTTTCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:940594 original size:2 final size:2
Alignment explanation
Indices: 940587--940611 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
940577 GTGTAATGAG
940587 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
940612 AAACTCAAGA
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:952087 original size:23 final size:21
Alignment explanation
Indices: 952061--952116 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 21
952051 TTTTATATAC
952061 TATAAATATAAAATTAATTAAAT
1 TATAAATATAAAATT--TTAAAT
*
952084 TAT-AATAT-TAA-TTTAAAT
1 TATAAATATAAAATTTTAAAT
952102 TATAATATATAAAAT
1 TATAA-ATATAAAAT
952117 GTCTAACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
18 9 0.33
19 1 0.04
20 5 0.19
21 4 0.15
22 5 0.19
23 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATAAATATAAAATTTTAAAT
Found at i:952101 original size:18 final size:17
Alignment explanation
Indices: 952063--952109 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 17
952053 TTATATACTA
*
952063 TAAA-TATAAAATTAAT
1 TAAATTATAATATTAAT
952079 TAAATTATAATATTAATT
1 TAAATTATAATATTAA-T
952097 TAAATTATAATAT
1 TAAATTATAATAT
952110 ATAAAATGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 4 0.14
17 10 0.36
18 14 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATTATAATATTAAT
Found at i:961076 original size:90 final size:90
Alignment explanation
Indices: 960954--961131 Score: 277
Period size: 90 Copynumber: 2.0 Consensus size: 90
960944 TAATCCCGAA
* * * * *
960954 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAAT-AAAACCACTAATATGA
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAAAC-CTAATATAA
961018 TTAGGGTAACTTAGACATAAAAGGAT
65 TTAGGGTAACTTAGACATAAAAGGAT
961044 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAAACCTAATATAAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAAACCTAATATAAT
* *
961109 TAGGGTAACTTGGATATAAAAGG
66 TAGGGTAACTTAGACATAAAAGG
961132 GTGTGTTGGG
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
90 75 0.94
91 5 0.06
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.36
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAAACCTAATATAAT
TAGGGTAACTTAGACATAAAAGGAT
Found at i:964471 original size:24 final size:20
Alignment explanation
Indices: 964422--964462 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
964412 ATCACGACTC
964422 AAGTTATAAATAAATACGTG
1 AAGTTATAAATAAATACGTG
964442 AAGTTATAAATAAATACGTG
1 AAGTTATAAATAAATACGTG
964462 A
1 A
964463 TTTAAGTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (20 bp):
AAGTTATAAATAAATACGTG
Found at i:964698 original size:16 final size:16
Alignment explanation
Indices: 964677--964711 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
964667 TCTCGTGGAG
964677 ATTTGATAAATATTTT
1 ATTTGATAAATATTTT
*
964693 ATTTGATTAATATTTT
1 ATTTGATAAATATTTT
964709 ATT
1 ATT
964712 ATTAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTTGATAAATATTTT
Found at i:964721 original size:18 final size:16
Alignment explanation
Indices: 964685--964723 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
964675 AGATTTGATA
*
964685 AATATTTTATTTGATT
1 AATATTTTATTTAATT
964701 AATATTTTATTATTAATT
1 AATATTTTA-T-TTAATT
964719 AATAT
1 AATAT
964724 GTGTTACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 1 0.05
18 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
AATATTTTATTTAATT
Found at i:965854 original size:20 final size:21
Alignment explanation
Indices: 965813--965854 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
965803 TTTCTATTTC
*
965813 TTTTACTTTAGTTTTATTTTA
1 TTTTACTTTAGTTTGATTTTA
965834 TTTTA-TTTA-TTTGATTATTA
1 TTTTACTTTAGTTTGATT-TTA
965854 T
1 T
965855 AAACCCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 6 0.32
20 8 0.42
21 5 0.26
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.71
Consensus pattern (21 bp):
TTTTACTTTAGTTTGATTTTA
Found at i:968624 original size:26 final size:26
Alignment explanation
Indices: 968595--968670 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
968585 TCTTGACGAA
* *
968595 TAAATAATAGGAACATTAATAAATTT
1 TAAATGATATGAACATTAATAAATTT
* * **
968621 TAAATGATATTATCATTAATATTTTT
1 TAAATGATATGAACATTAATAAATTT
*
968647 TAAATGATATGAATATTAATAAAT
1 TAAATGATATGAACATTAATAAAT
968671 ATAATAATTC
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.42
Consensus pattern (26 bp):
TAAATGATATGAACATTAATAAATTT
Found at i:975648 original size:2 final size:2
Alignment explanation
Indices: 975641--975671 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
975631 AATAATTAAA
975641 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
975672 TACAATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:976248 original size:60 final size:60
Alignment explanation
Indices: 976120--976249 Score: 154
Period size: 60 Copynumber: 2.2 Consensus size: 60
976110 AATAGTTCGG
* * * * * *
976120 TGACCATTTTGTAACTTTTAATAGTCGATGGACTTAATAAAACAACACTCTATAGTCAAA
1 TGACCATTTTATAACTTTTAACAGTCAATAGAATTAATAAAACAACACCCTATAGTCAAA
* * * *
976180 TGATCATTTTATAACTTTTAACAGTCAATAGAATTAATAAAGCAATACCCTATAGTCGAGA
1 TGACCATTTTATAACTTTTAACAGTCAATAGAATTAATAAAACAACACCCTATAGTC-AAA
976241 -GACCATTTT
1 TGACCATTTT
976250 TGTATTTTAC
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 56 0.97
61 2 0.03
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (60 bp):
TGACCATTTTATAACTTTTAACAGTCAATAGAATTAATAAAACAACACCCTATAGTCAAA
Found at i:979955 original size:18 final size:18
Alignment explanation
Indices: 979932--979970 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
979922 GGAAGATCGA
979932 AAGAAATTAAGGATTGAG
1 AAGAAATTAAGGATTGAG
*
979950 AAGAAATTAGGGATTGAG
1 AAGAAATTAAGGATTGAG
979968 AAG
1 AAG
979971 TTACCTGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.31, T:0.21
Consensus pattern (18 bp):
AAGAAATTAAGGATTGAG
Found at i:985155 original size:18 final size:18
Alignment explanation
Indices: 985129--985167 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
985119 GGAGGATCGA
985129 AAGAAATTAGGGATTGAG
1 AAGAAATTAGGGATTGAG
*
985147 AAGAGATTAGGGATTGAG
1 AAGAAATTAGGGATTGAG
985165 AAG
1 AAG
985168 TTACCTGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.21
Consensus pattern (18 bp):
AAGAAATTAGGGATTGAG
Found at i:986253 original size:20 final size:20
Alignment explanation
Indices: 986228--986279 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
986218 GCGTCTAATT
*
986228 TTTTATTTTATTTTATATAA
1 TTTTATTTTATTTTAAATAA
*
986248 TTTTATTTTATGTTAAATAA
1 TTTTATTTTATTTTAAATAA
*
986268 TTGTATTTTATT
1 TTTTATTTTATT
986280 CTATCTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTTATTTTATTTTAAATAA
Found at i:990265 original size:13 final size:14
Alignment explanation
Indices: 990236--990265 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
990226 AACCATGCAA
990236 GTGATATGAACTAT
1 GTGATATGAACTAT
990250 GTGATATGAA-TAT
1 GTGATATGAACTAT
990263 GTG
1 GTG
990266 GAATATGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (14 bp):
GTGATATGAACTAT
Found at i:990484 original size:23 final size:20
Alignment explanation
Indices: 990431--990489 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 20
990421 GAGGGTCTAC
990431 GTGGTCATTCGGGACATATA
1 GTGGTCATTCGGGACATATA
* * *
990451 GTGATCCTTCGGGATATTTCATA
1 GTGGTCATTCGGGACA--T-ATA
990474 GTGGTCATTCGGGACA
1 GTGGTCATTCGGGACA
990490 AATTTCATAG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 13 0.43
22 1 0.03
23 16 0.53
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (20 bp):
GTGGTCATTCGGGACATATA
Found at i:991905 original size:14 final size:14
Alignment explanation
Indices: 991882--991917 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
991872 GAAATAAATG
*
991882 AAAAATACTTTAAT
1 AAAAAAACTTTAAT
991896 AAAAAAACTTTAAT
1 AAAAAAACTTTAAT
991910 AATAAAAA
1 AA-AAAAA
991918 AAAGATCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAAAACTTTAAT
Found at i:991911 original size:33 final size:34
Alignment explanation
Indices: 991891--991955 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 34
991881 GAAAAATACT
991891 TTAATAAAAAAACTTTAAT-AATAAAAAAAAGATC
1 TTAAT-AAAAAACTTTAATAAATAAAAAAAAGATC
*
991925 TTAATAAAAAACTTTAATAAA-AATAAAAAGA
1 TTAATAAAAAACTTTAATAAATAAAAAAAAGA
991956 CATTATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 22 0.76
34 7 0.24
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (34 bp):
TTAATAAAAAACTTTAATAAATAAAAAAAAGATC
Found at i:992956 original size:21 final size:21
Alignment explanation
Indices: 992930--993171 Score: 246
Period size: 21 Copynumber: 11.6 Consensus size: 21
992920 GTTTCCAGAT
992930 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
992951 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
992972 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* **
992992 TCGCAATGCGATA-GTCAACTA
1 TCGCAATGCGA-ACTTGGACTA
*
993013 TTGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
993034 TCGCAATGCGAAACTTGGACTA
1 TCGCAATGCG-AACTTGGACTA
*
993056 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
* *
993077 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
* * *
993098 TCGCAATGTGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* * *
993118 TCGCAATGCGATA-GTCGACAA
1 TCGCAATGCGA-ACTTGGACTA
993139 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
993160 TCGCAATGCGAA
1 TCGCAATGCGAA
993172 TATGTAAATC
Statistics
Matches: 186, Mismatches: 25, Indels: 20
0.81 0.11 0.09
Matches are distributed among these distances:
20 31 0.17
21 133 0.72
22 22 0.12
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:992996 original size:62 final size:62
Alignment explanation
Indices: 992946--993192 Score: 338
Period size: 62 Copynumber: 4.0 Consensus size: 62
992936 TGCGAACTTG
992946 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
* * * * *
993008 AACTATTGCAATGCGAACTTGGACTATCGCAATGCGAA-ACTTGGACTATCGCAATGCGA-ACTT
1 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATA--TGTA-AATCGCAATGCGATA-GT
993071 C
62 C
* * *
993072 GACTATCGCAATGCGATA-GTCGACTATCGCAATGTGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGA-ACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
* *
993134 GACAATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGTGATA
1 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATA
993193 AGAATTTTCT
Statistics
Matches: 159, Mismatches: 18, Indels: 16
0.82 0.09 0.08
Matches are distributed among these distances:
61 2 0.01
62 102 0.64
63 8 0.05
64 45 0.28
65 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (62 bp):
GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
Found at i:993087 original size:126 final size:126
Alignment explanation
Indices: 992930--993171 Score: 405
Period size: 126 Copynumber: 1.9 Consensus size: 126
992920 GTTTCCAGAT
* * *
992930 TCGCAATGCGAACTTGGACTATCGCAATGCGA-ACTTGGACTATCGCAATGCGAATATGTAAATC
1 TCGCAATGCGAACTTCGACTATCGCAATGCGATA-GTCGACTATCGCAATGCGAATATGTAAATC
* *
992994 GCAATGCGATAGTCAACTATTGCAATGCGAACTTGGACTATCGCAATGCGAAACTTGGACTA
65 GCAATGCGATAGTCAACAATCGCAATGCGAACTTGGACTATCGCAATGCGAAACTTGGACTA
*
993056 TCGCAATGCGAACTTCGACTATCGCAATGCGATAGTCGACTATCGCAATGTGAATATGTAAATCG
1 TCGCAATGCGAACTTCGACTATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAAATCG
*
993121 CAATGCGATAGTCGACAATCGCAATGCGAACTTGGACTATCGCAATGCGAA
66 CAATGCGATAGTCAACAATCGCAATGCGAACTTGGACTATCGCAATGCGAA
993172 TATGTAAATC
Statistics
Matches: 108, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
126 107 0.99
127 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (126 bp):
TCGCAATGCGAACTTCGACTATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAAATCG
CAATGCGATAGTCAACAATCGCAATGCGAACTTGGACTATCGCAATGCGAAACTTGGACTA
Found at i:993257 original size:6 final size:6
Alignment explanation
Indices: 993246--993335 Score: 87
Period size: 6 Copynumber: 15.5 Consensus size: 6
993236 GACACGTATT
* * * * *
993246 ACCACG ACCACG AGCACG AGCACG AGCACG AGCACG AGCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* * *
993294 ACCACA ACCAAG ACCCCG ACCACG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
993336 CGAGACGAGA
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
5 15 0.20
6 61 0.80
ACGTcount: A:0.32, C:0.47, G:0.21, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:993326 original size:5 final size:5
Alignment explanation
Indices: 993308--993338 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
993298 CAACCAAGAC
993308 CCCGA CCACGA CCCGA CCCGA CCCGA CCCGA
1 CCCGA CC-CGA CCCGA CCCGA CCCGA CCCGA
993339 GACGAGACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
CCCGA
Found at i:993863 original size:6 final size:6
Alignment explanation
Indices: 993842--993890 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
993832 TCTCGTCTCG
*
993842 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT AGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
993888 GGT
1 GGT
993891 AATACGTGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
5 10 0.24
6 31 0.76
ACGTcount: A:0.02, C:0.16, G:0.51, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:994254 original size:177 final size:177
Alignment explanation
Indices: 993954--994341 Score: 526
Period size: 177 Copynumber: 2.2 Consensus size: 177
993944 AACAGAAAAG
* * * *
993954 TTGAAAACATCCAGCACTGAAGGTCTTATGGATGGCCCAAAGGACTTATAAATCAAGAAACCCCC
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCAAAGGACGTACAAATCAAGAAACCCCC
* * * * * *
994019 GAAGGCTTAGTTTCTTAGTTGTTAATGAACCCCTTTTTTAGGCTTATCTTCTTTTAACAACTCTT
66 GAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGACTTAGCTTCCTTTAACAACTCTT
* **
994084 TTGAGATAATTAGTAAACC-CTTGAAGGATTGGTTTCTAAAATCTCAA
131 TTGAAATAATTAGTAAACCAC-CAAAGGATTGGTTTCTAAAATCTCAA
*** * *
994131 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCTGTAGGACGTACGAATCAAGAAACCCTC
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCAAAGGACGTACAAATCAAGAAACCCCC
** **
994196 GAAGGCTTAGTTTCTTAGTTGTCAAGGAACTTCTTTGTTAGACTTAGCTTCCTTTAACAGTTCTT
66 GAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGACTTAGCTTCCTTTAACAACTCTT
* *
994261 TTGAAATAATTAGTAAACCACCAAAGGCTTGGTTTCTAAAATCTCAT
131 TTGAAATAATTAGTAAACCACCAAAGGATTGGTTTCTAAAATCTCAA
* *
994308 TTAAAAACATCATGCACTGAAGGTCTTATGGATG
1 TTGAAAACATCCTGCACTGAAGGTCTTATGGATG
994342 GCCCGGAGGT
Statistics
Matches: 184, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
177 183 0.99
178 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (177 bp):
TTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCAAAGGACGTACAAATCAAGAAACCCCC
GAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGACTTAGCTTCCTTTAACAACTCTT
TTGAAATAATTAGTAAACCACCAAAGGATTGGTTTCTAAAATCTCAA
Found at i:994588 original size:223 final size:223
Alignment explanation
Indices: 994200--994798 Score: 934
Period size: 223 Copynumber: 2.7 Consensus size: 223
994190 ACCCTCGAAG
* ** * *
994200 GCTTAGTTTCTTAGTTGTCAAGGAACTTCTTTGTTAGACTTAGCTTCCTTTAACAGTTCTTTTGA
1 GCTTAGTTTCTTGGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAGCTCTTTTGA
* * * *
994265 AATAATTAGTAAACCACCAAAGGCTTGGTTTCTAAAATCTCATTTAAAAACATCATGCACTGAAG
66 GATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACATCATGCACTGAAG
* *
994330 GTCTTATGGATGGCCCGGAGGTCTTATCATCTTGCTCAGAAGGCTTACAGATGACCCGAAGGATT
131 GTCTTATGGATGGCCCGGAGGTCTTATAATCTTGCTCAGAAGGCTTACAGATAACCCGAAGGATT
994395 TAAACATCAAGAAACTCTTGAAAATCAA
196 TAAACATCAAGAAACTCTTGAAAATCAA
994423 GCTTAGTTTCTTGGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAGCTCTTTTGA
1 GCTTAGTTTCTTGGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAGCTCTTTTGA
*
994488 GATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAG
66 GATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACATCATGCACTGAAG
* * * *
994553 GTCTCATGGATGACCCGGATGTCTTATAATCTTGCTCAGAAGGCTTACAGATAACCCGTAGGATT
131 GTCTTATGGATGGCCCGGAGGTCTTATAATCTTGCTCAGAAGGCTTACAGATAACCCGAAGGATT
994618 TAAACATCAAGAAACTCTTGAAAATCAA
196 TAAACATCAAGAAACTCTTGAAAATCAA
* * *** * * *
994646 GCTTAGTTTCTTGGTTGTTAAAGAA-CCC-TTAAAAGGCTTAACTTCCTTTAAAAACTCTTTTGA
1 GCTTAGTTTCTTGGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAGCTCTTTTGA
* *
994709 GATAATTAGTAAACACCTGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACATCATGC-CTGAAG
66 GATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACATCATGCACTGAAG
*
994773 GTCTTATGGATGGCCCAGAGGTCTTA
131 GTCTTATGGATGGCCCGGAGGTCTTA
994799 CAAATTCGGG
Statistics
Matches: 345, Mismatches: 31, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
220 28 0.08
221 84 0.24
222 3 0.01
223 230 0.67
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (223 bp):
GCTTAGTTTCTTGGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAGCTCTTTTGA
GATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTTGAAAACATCATGCACTGAAG
GTCTTATGGATGGCCCGGAGGTCTTATAATCTTGCTCAGAAGGCTTACAGATAACCCGAAGGATT
TAAACATCAAGAAACTCTTGAAAATCAA
Found at i:995516 original size:22 final size:22
Alignment explanation
Indices: 995429--995511 Score: 141
Period size: 22 Copynumber: 3.8 Consensus size: 22
995419 AAATCCAATA
*
995429 AATCTTTCATCTTTGAAAAGAG
1 AATCTATCATCTTTGAAAAGAG
995451 AATCTATCATCTTTGAAAAGAG
1 AATCTATCATCTTTGAAAAGAG
995473 AATCTATCATCTTTGAAAA-ATG
1 AATCTATCATCTTTGAAAAGA-G
995495 AATCTATCATCTTTGAA
1 AATCTATCATCTTTGAA
995512 GAATGTAGAT
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
21 1 0.02
22 58 0.98
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (22 bp):
AATCTATCATCTTTGAAAAGAG
Found at i:995946 original size:54 final size:54
Alignment explanation
Indices: 995880--996203 Score: 461
Period size: 54 Copynumber: 6.0 Consensus size: 54
995870 ATAATCACTG
* *
995880 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGTTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
*
995934 GTCCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
* ** *
995988 GTTCGTAAAACATTTGACAACATATTCATCCGTTCCTGTGGCTTCTACCCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
* * * *
996042 GTTCGTAAAACATTTGACAATACATTCATCCTTTCTTGTGGCTTCTGCCCATAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
* * * * * *
996096 ATTCGTAAAACATTTGACAATATATTCATCATTTCTTGTGACTTCTGCGCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
* *
996150 GCTT-GTAAAACATTTGACAACACATTCATCTTTTCCTGTGACTTCTGCCCAGAT
1 G-TTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
996204 TTCTCATCAG
Statistics
Matches: 243, Mismatches: 26, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
54 241 0.99
55 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
Found at i:996784 original size:42 final size:42
Alignment explanation
Indices: 996734--996871 Score: 120
Period size: 42 Copynumber: 3.3 Consensus size: 42
996724 ATTGTTGTGA
*
996734 GCCTTCAAAATGCCCCATATGGATCATTTTTGTTTGAATTAG
1 GCCTTCAAAATGCCCCATATGGATCATTTATGTTTGAATTAG
* * * * * * *
996776 GCATTCAAAATGGCCC-TA--CATTCTATTTCTGGTTGAAATGG
1 GCCTTCAAAATGCCCCATATGGA-TC-ATTTATGTTTGAATTAG
* * * * *
996817 GCCTTCAAGATGTCCTACATGGATCATTTATGTCTGAATTAG
1 GCCTTCAAAATGCCCCATATGGATCATTTATGTTTGAATTAG
996859 GCCTTCAAAATGC
1 GCCTTCAAAATGC
996872 TCCAACATTC
Statistics
Matches: 71, Mismatches: 20, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
39 1 0.01
40 2 0.03
41 27 0.38
42 38 0.54
43 2 0.03
44 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (42 bp):
GCCTTCAAAATGCCCCATATGGATCATTTATGTTTGAATTAG
Found at i:998253 original size:7 final size:7
Alignment explanation
Indices: 998241--998331 Score: 71
Period size: 7 Copynumber: 12.4 Consensus size: 7
998231 CTTAATTCAA
998241 TTTCTTT
1 TTTCTTT
998248 TTTCTTCT
1 TTTCTT-T
998256 TTTCTTT
1 TTTCTTT
*
998263 TTTATTTT
1 TTT-CTTT
998271 TTTCTATT
1 TTTCT-TT
998279 TTT-TTCT
1 TTTCTT-T
998286 TTAT-TTT
1 TT-TCTTT
998293 TTTCTTT
1 TTTCTTT
998300 ATTT-TTT
1 -TTTCTTT
*
998307 CCTTCTTT
1 -TTTCTTT
*
998315 TCTCTTT
1 TTTCTTT
998322 TTTCTTT
1 TTTCTTT
998329 TTT
1 TTT
998332 TTCTCTGATG
Statistics
Matches: 69, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
6 2 0.03
7 40 0.58
8 27 0.39
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTCTTT
Found at i:998272 original size:9 final size:10
Alignment explanation
Indices: 998241--998335 Score: 65
Period size: 10 Copynumber: 9.5 Consensus size: 10
998231 CTTAATTCAA
998241 TTTCT-TTTT
1 TTTCTATTTT
998250 TCTTCT-TTTCT
1 T-TTCTATTT-T
*
998261 TTTTTATTTT
1 TTTCTATTTT
998271 TTTCTATTTT
1 TTTCTATTTT
998281 TTTCTTTATTTT
1 TTTC--TATTTT
*
998293 TTTCTTTATTT
1 TTTCTAT-TTT
* *
998304 TTTC-CTTCT
1 TTTCTATTTT
*
998313 TTTCT-CTTT
1 TTTCTATTTT
998322 TTTCT-TTTT
1 TTTCTATTTT
998331 TTTCT
1 TTTCT
998336 CTGATGGATC
Statistics
Matches: 71, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
9 22 0.31
10 27 0.38
11 12 0.17
12 10 0.14
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTCTATTTT
Found at i:998280 original size:22 final size:20
Alignment explanation
Indices: 998246--998330 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 20
998236 TTCAATTTCT
*
998246 TTTTTCTTCTTTTCTTTTTTA
1 TTTTT-TTCTTTTTTTTTTTA
998267 TTTTTTTCTATTTTTTTCTTTA
1 TTTTTTTCT-TTTTTTT-TTTA
* **
998289 TTTTTTTCTTTATTTTTTCC
1 TTTTTTTCTTTTTTTTTTTA
998309 TTCTTTTCTCTTTTTTCTTTTT
1 TT-TTTT-TCTTTTTT-TTTTT
998331 TTTCTCTGAT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
20 8 0.15
21 21 0.40
22 20 0.38
23 4 0.08
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTTTCTTTTTTTTTTTA
Found at i:998282 original size:12 final size:12
Alignment explanation
Indices: 998267--998333 Score: 50
Period size: 12 Copynumber: 5.4 Consensus size: 12
998257 TTCTTTTTTA
998267 TTTTTTTCTATT
1 TTTTTTTCTATT
998279 TTTTTCTT-TATT
1 TTTTT-TTCTATT
998291 TTTTTCTT-TATT
1 TTTTT-TTCTATT
* *
998303 TTTTCCTTCTTTT
1 TTTT-TTTCTATT
998316 CTCTTTTTTCT-TT
1 -T-TTTTTTCTATT
998329 TTTTT
1 TTTTT
998334 CTCTGATGGA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
11 4 0.09
12 28 0.60
13 7 0.15
14 5 0.11
15 3 0.06
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTTCTATT
Found at i:998324 original size:18 final size:18
Alignment explanation
Indices: 998301--998337 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
998291 TTTTTCTTTA
998301 TTTTTTCCTTCTTTTCTC
1 TTTTTTCCTTCTTTTCTC
* *
998319 TTTTTTCTTTTTTTTCTC
1 TTTTTTCCTTCTTTTCTC
998337 T
1 T
998338 GATGGATCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTCCTTCTTTTCTC
Found at i:998335 original size:23 final size:24
Alignment explanation
Indices: 998243--998335 Score: 77
Period size: 23 Copynumber: 3.8 Consensus size: 24
998233 TAATTCAATT
998243 TCTTTTTTCTTCTTTTCTT-TTTTA
1 TCTTTTTTCTT-TTTTCTTCTTTTA
*
998267 T-TTTTTTCTATTTTT-TTCTTTATT
1 TCTTTTTTCT-TTTTTCTTCTTT-TA
* * *
998291 TTTTTCTTTATTTTTTCCTTCTTTTC
1 TCTTT-TTTCTTTTTT-CTTCTTTTA
998317 TCTTTTTTCTTTTTT-TTCT
1 TCTTTTTTCTTTTTTCTTCT
998336 CTGATGGATC
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
22 2 0.04
23 19 0.33
24 4 0.07
25 17 0.30
26 9 0.16
27 6 0.11
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (24 bp):
TCTTTTTTCTTTTTTCTTCTTTTA
Found at i:999653 original size:20 final size:21
Alignment explanation
Indices: 999628--999671 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
999618 AGCGGGTTTG
999628 GTGCACTTTCGT-GTCTTGGT
1 GTGCACTTTCGTGGTCTTGGT
999648 GTGCACTTTCGTGGTCTTGGT
1 GTGCACTTTCGTGGTCTTGGT
999669 GTG
1 GTG
999672 ATGTATTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.05, C:0.18, G:0.34, T:0.43
Consensus pattern (21 bp):
GTGCACTTTCGTGGTCTTGGT
Found at i:1003165 original size:26 final size:25
Alignment explanation
Indices: 1003134--1003182 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
1003124 ATAAAATAAT
1003134 AAAGAAT-AAAGAATTGAAATAAATCA
1 AAAGAATCAAA-AATT-AAATAAATCA
*
1003160 AAAGAATCATAAATTAAATAAAT
1 AAAGAATCAAAAATTAAATAAAT
1003183 ATGATTCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 8 0.38
26 11 0.52
27 2 0.10
ACGTcount: A:0.65, C:0.04, G:0.08, T:0.22
Consensus pattern (25 bp):
AAAGAATCAAAAATTAAATAAATCA
Found at i:1005470 original size:3 final size:3
Alignment explanation
Indices: 1005462--1005528 Score: 82
Period size: 3 Copynumber: 22.7 Consensus size: 3
1005452 TTTGGGTATG
* * * *
1005462 TAA TAA TAA TAA TTA TAT TAA TAA TAA TAA TAA TAT TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1005510 TAA TAT TAA TAA -AA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
1005529 TTATTATTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1005483 original size:9 final size:9
Alignment explanation
Indices: 1005462--1005540 Score: 79
Period size: 9 Copynumber: 8.9 Consensus size: 9
1005452 TTTGGGTATG
*
1005462 TAATAATAA
1 TAATAATAT
*
1005471 TAATTATAT
1 TAATAATAT
*
1005480 TAATAATAA
1 TAATAATAT
1005489 TAATAATAT
1 TAATAATAT
* *
1005498 TAATAACAA
1 TAATAATAT
1005507 TAATAATAT
1 TAATAATAT
*
1005516 TAATAA-AA
1 TAATAATAT
*
1005524 TAATATTAT
1 TAATAATAT
*
1005533 TATTAATA
1 TAATAATA
1005541 ACAATGAAAA
Statistics
Matches: 55, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
8 6 0.11
9 49 0.89
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (9 bp):
TAATAATAT
Found at i:1005485 original size:18 final size:18
Alignment explanation
Indices: 1005462--1005541 Score: 117
Period size: 18 Copynumber: 4.5 Consensus size: 18
1005452 TTTGGGTATG
*
1005462 TAATAATAATAATTATAT
1 TAATAATAATAATAATAT
1005480 TAATAATAATAATAATAT
1 TAATAATAATAATAATAT
*
1005498 TAATAACAATAATAATAT
1 TAATAATAATAATAATAT
*
1005516 TAATAA-AATAATATTAT
1 TAATAATAATAATAATAT
*
1005533 TATTAATAA
1 TAATAATAA
1005542 CAATGAAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
17 15 0.26
18 42 0.74
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATAATAATAATAATAT
Found at i:1014560 original size:17 final size:17
Alignment explanation
Indices: 1014535--1014570 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1014525 TGTTGGAAGA
1014535 AATCATTGTTAAAAGTG
1 AATCATTGTTAAAAGTG
*
1014552 AATCTTTGTTAAAAGTG
1 AATCATTGTTAAAAGTG
1014569 AA
1 AA
1014571 GGTTATGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.36
Consensus pattern (17 bp):
AATCATTGTTAAAAGTG
Found at i:1016435 original size:15 final size:15
Alignment explanation
Indices: 1016415--1016445 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1016405 ATAAAAAAAA
1016415 AGTAAAATCAGTATC
1 AGTAAAATCAGTATC
1016430 AGTAAAATCAGTATC
1 AGTAAAATCAGTATC
1016445 A
1 A
1016446 TTAACTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (15 bp):
AGTAAAATCAGTATC
Found at i:1017629 original size:21 final size:21
Alignment explanation
Indices: 1017548--1017631 Score: 89
Period size: 21 Copynumber: 3.9 Consensus size: 21
1017538 CATCTTGTTT
1017548 TTCTTCATCTTGTTCATCTTC
1 TTCTTCATCTTGTTCATCTTC
*
1017569 TAT-TTCAACTTGTTCATCTTATAC
1 T-TCTTCATCTTGTTCATC-T-T-C
*
1017593 TTCTTCATTTTGTTCATCTTC
1 TTCTTCATCTTGTTCATCTTC
* *
1017614 TTCTGCATCTTTTTCATC
1 TTCTTCATCTTGTTCATC
1017632 CTCAGCTGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
21 31 0.60
22 3 0.06
23 3 0.06
24 15 0.29
ACGTcount: A:0.14, C:0.25, G:0.05, T:0.56
Consensus pattern (21 bp):
TTCTTCATCTTGTTCATCTTC
Found at i:1022603 original size:9 final size:9
Alignment explanation
Indices: 1022589--1022622 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
1022579 TTTTCAGATG
1022589 TTATTTTGT
1 TTATTTTGT
1022598 TTATTTTGTT
1 TTATTTTG-T
1022608 TTGATTTTGT
1 TT-ATTTTGT
1022618 TTATT
1 TTATT
1022623 GAATGAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 11 0.48
10 6 0.26
11 6 0.26
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (9 bp):
TTATTTTGT
Found at i:1029330 original size:11 final size:12
Alignment explanation
Indices: 1029293--1029336 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
1029283 AATAAAATCT
*
1029293 TATTTTTCTCTC
1 TATTTTTCTCTA
*
1029305 TAGTTTTCTCTA
1 TATTTTTCTCTA
1029317 TATTTTTCTC-A
1 TATTTTTCTCTA
1029328 TATTTTTCT
1 TATTTTTCT
1029337 ATTATGCTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 10 0.34
12 19 0.66
ACGTcount: A:0.14, C:0.18, G:0.02, T:0.66
Consensus pattern (12 bp):
TATTTTTCTCTA
Found at i:1029815 original size:18 final size:15
Alignment explanation
Indices: 1029780--1029819 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 15
1029770 AATTTATTTA
1029780 TTTATTTATTTTTCT
1 TTTATTTATTTTTCT
1029795 TTTATTTAATTCTTATCT
1 TTTATTT-ATT-TT-TCT
1029813 TTTATTT
1 TTTATTT
1029820 TAAAGACAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.32
16 3 0.14
17 2 0.09
18 10 0.45
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTATTTATTTTTCT
Found at i:1030377 original size:23 final size:23
Alignment explanation
Indices: 1030351--1030397 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1030341 TTCTTAGTGG
1030351 CGGGACTCCGTTTCAATTAAAGA
1 CGGGACTCCGTTTCAATTAAAGA
1030374 CGGGACTCCGTTTCAATTAAAGA
1 CGGGACTCCGTTTCAATTAAAGA
1030397 C
1 C
1030398 ATGACTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (23 bp):
CGGGACTCCGTTTCAATTAAAGA
Found at i:1030403 original size:23 final size:23
Alignment explanation
Indices: 1030353--1030404 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
1030343 CTTAGTGGCG
*
1030353 GGACTCCGTTTCAATTAAAGACG
1 GGACTCCGTTTCAATTAAAGACA
1030376 GGACTCCGTTTCAATTAAAGACA
1 GGACTCCGTTTCAATTAAAGACA
*
1030399 TGACTC
1 GGACTC
1030405 ATTTATCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (23 bp):
GGACTCCGTTTCAATTAAAGACA
Found at i:1032746 original size:16 final size:16
Alignment explanation
Indices: 1032725--1032770 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
1032715 GGAGGTAACC
*
1032725 CATTTCGTTTTATTTT
1 CATTTCATTTTATTTT
1032741 CATTTCATTTTA-TTT
1 CATTTCATTTTATTTT
*
1032756 -ATTTTATTTTATTTT
1 CATTTCATTTTATTTT
1032771 ATTAGATGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 10 0.37
15 6 0.22
16 11 0.41
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (16 bp):
CATTTCATTTTATTTT
Found at i:1032758 original size:4 final size:5
Alignment explanation
Indices: 1032732--1032797 Score: 62
Period size: 5 Copynumber: 12.8 Consensus size: 5
1032722 ACCCATTTCG
* ** *
1032732 TTTTA TTTTCA TTTCA TTTTA -TTTA TTTTA TTTTA TTTTA TTAGA TGCTTAA
1 TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T--TTTA
1032784 TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTT
1032798 TCTCTGAACA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
4 4 0.08
5 39 0.78
6 4 0.08
7 3 0.06
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (5 bp):
TTTTA
Found at i:1034615 original size:65 final size:64
Alignment explanation
Indices: 1034468--1034623 Score: 181
Period size: 65 Copynumber: 2.4 Consensus size: 64
1034458 TATTATTTTT
*
1034468 ATATTTTATCTTTTTTTTAGGTATTTTAGTTGAAATAGGTTTTAGTGTTTTAATTAAGATTTAGA
1 ATATTTTA-CTTTTTTTTAGGTATTTTAGTTGAAATAGGTTTTAGCGTTTTAATTAAGATTTAGA
* * * *
1034533 ATATTATATTATTTTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGCGTTTTAATTAGGATTTTA
1 ATATTTTACT-TTTTTTTAGGTATTTTAGTTGAAATAGGTTTT-AGCGTTTTAATTAAGA-TTTA
1034597 G-
63 GA
* * *
1034598 ATGTTTTAGCTTGTTTTTAGGAATTT
1 ATATTTTA-CTTTTTTTTAGGTATTT
1034624 GAAGGCTATA
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
64 6 0.08
65 65 0.84
66 6 0.08
ACGTcount: A:0.27, C:0.02, G:0.15, T:0.56
Consensus pattern (64 bp):
ATATTTTACTTTTTTTTAGGTATTTTAGTTGAAATAGGTTTTAGCGTTTTAATTAAGATTTAGA
Found at i:1035282 original size:16 final size:15
Alignment explanation
Indices: 1035261--1035300 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
1035251 TCTCCATTTT
1035261 ATATTTATTACTATTA
1 ATATTTATTACTA-TA
*
1035277 ATATTTATTATTATA
1 ATATTTATTACTATA
*
1035292 TTATTTATT
1 ATATTTATT
1035301 TATTTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATTTATTACTATA
Found at i:1035289 original size:19 final size:19
Alignment explanation
Indices: 1035265--1035304 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1035255 CATTTTATAT
1035265 TTATTACTATTA-ATATTTA
1 TTATTA-TATTATATATTTA
*
1035284 TTATTATATTATTTATTTA
1 TTATTATATTATATATTTA
1035303 TT
1 TT
1035305 TATTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTATATTATATATTTA
Found at i:1036076 original size:16 final size:15
Alignment explanation
Indices: 1036055--1036124 Score: 77
Period size: 16 Copynumber: 4.5 Consensus size: 15
1036045 AGAGTCTCTA
1036055 AATCATTCAACATTT
1 AATCATTCAACATTT
* *
1036070 GAATCATTCAGCGTTT
1 -AATCATTCAACATTT
**
1036086 AATCATTCAGTATTT
1 AATCATTCAACATTT
*
1036101 AAATCATTCAACACTT
1 -AATCATTCAACATTT
1036117 AATCATTC
1 AATCATTC
1036125 TGAAGTAAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
15 21 0.46
16 25 0.54
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.39
Consensus pattern (15 bp):
AATCATTCAACATTT
Found at i:1036091 original size:31 final size:31
Alignment explanation
Indices: 1036055--1036124 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
1036045 AGAGTCTCTA
* * **
1036055 AATCATTCAACATTTGAATCATTCAGCGTTT
1 AATCATTCAACATTTAAATCATTCAACACTT
**
1036086 AATCATTCAGTATTTAAATCATTCAACACTT
1 AATCATTCAACATTTAAATCATTCAACACTT
1036117 AATCATTC
1 AATCATTC
1036125 TGAAGTAAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.39
Consensus pattern (31 bp):
AATCATTCAACATTTAAATCATTCAACACTT
Found at i:1039171 original size:7 final size:7
Alignment explanation
Indices: 1039159--1039185 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1039149 ATATATTGAA
1039159 CATCATC
1 CATCATC
1039166 CATCATC
1 CATCATC
1039173 CATCATC
1 CATCATC
1039180 CATCAT
1 CATCAT
1039186 GAAAGCATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.41, G:0.00, T:0.30
Consensus pattern (7 bp):
CATCATC
Found at i:1040456 original size:89 final size:91
Alignment explanation
Indices: 1040269--1040572 Score: 312
Period size: 89 Copynumber: 3.4 Consensus size: 91
1040259 CATTATGCAT
* ** * * * * * *
1040269 TTTCATTTATGACATTCTTTCATGCCAATAATGCACCCA-TATGCATTTAAATTATGACATCCTT
1 TTTCATTTATGACATCCTTTCATGCCTTTTATACA-CTATTATACATTTCAGTTATGACATCCTT
** * * ** *
1040333 TCATG-CCGATAATGCACCCATATGCA
65 TCATGCCCTTTTATACACTAATATACA
* *
1040359 TTTCATTTATGGCATCCTTTCATGCCTTTTATACACTATTATACATTTC-GTTATTACATCCTTT
1 TTTCATTTATGACATCCTTTCATGCCTTTTATACACTATTATACATTTCAGTTATGACATCCTTT
* *
1040423 CATG-CCTTTTGTACACTATTATACA
66 CATGCCCTTTTATACACTAATATACA
* * **
1040448 TTTCATTTATGACATCCTTTCATGCTTTTTATACACTATTATACATTTCATTTATGGTATCCTTT
1 TTTCATTTATGACATCCTTTCATGCCTTTTATACACTATTATACATTTCAGTTATGACATCCTTT
*
1040513 CATGCCCTTTTATATACTAATATACA
66 CATGCCCTTTTATACACTAATATACA
* *
1040539 TTTCA-TTATTGACATCCATTCATGCCATTTATAC
1 TTTCATTTA-TGACATCCTTTCATGCCTTTTATAC
1040573 CACGTTACAC
Statistics
Matches: 178, Mismatches: 32, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
89 78 0.44
90 55 0.31
91 45 0.25
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.44
Consensus pattern (91 bp):
TTTCATTTATGACATCCTTTCATGCCTTTTATACACTATTATACATTTCAGTTATGACATCCTTT
CATGCCCTTTTATACACTAATATACA
Found at i:1040466 original size:134 final size:136
Alignment explanation
Indices: 1040320--1040564 Score: 352
Period size: 134 Copynumber: 1.8 Consensus size: 136
1040310 TGCATTTAAA
* *
1040320 TTATGACATCCTTTCATGCCGATAATGCACCCA-TATGCATTTCATTTATGGCATCCTTTCATG-
1 TTATGACATCCTTTCATGCCGATAATACA-CCATTATACATTTCATTTATGGCATCCTTTCATGC
* * *
1040383 CCTTTTATACACTATTATACATTTCGTTATT-ACATCCTTTCATGCCTTTTGTACACTATTATAC
65 CCTTTTATACACTAATATACATTTCATTATTGACATCCATTCATGCCTTTTGTACACTATTATAC
1040447 ATTTCAT
130 ATTTCAT
*** * * *
1040454 TTATGACATCCTTTCATGCTTTTTATACACTATTATACATTTCATTTATGGTATCCTTTCATGCC
1 TTATGACATCCTTTCATGCCGATAATACACCATTATACATTTCATTTATGGCATCCTTTCATGCC
*
1040519 CTTTTATATACTAATATACATTTCATTATTGACATCCATTCATGCC
66 CTTTTATACACTAATATACATTTCATTATTGACATCCATTCATGCC
1040565 ATTTATACCA
Statistics
Matches: 96, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
133 2 0.02
134 52 0.54
135 28 0.29
136 14 0.15
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.44
Consensus pattern (136 bp):
TTATGACATCCTTTCATGCCGATAATACACCATTATACATTTCATTTATGGCATCCTTTCATGCC
CTTTTATACACTAATATACATTTCATTATTGACATCCATTCATGCCTTTTGTACACTATTATACA
TTTCAT
Found at i:1040483 original size:45 final size:45
Alignment explanation
Indices: 1040260--1040572 Score: 310
Period size: 45 Copynumber: 6.9 Consensus size: 45
1040250 ATAATGCACC
* * ** * * *
1040260 ATTATGCATTTTCATTTATGACATTCTTTCATGCCAATAATGCACCC
1 ATTATACA-TTTCATTTATGACATCCTTTCATGCCTTTTATACA-CT
* * * ** * * *
1040307 A-TATGCATTTAAATTATGACATCCTTTCATGCCGATAATGCACCC
1 ATTATACATTTCATTTATGACATCCTTTCATGCCTTTTATACA-CT
* *
1040352 A-TATGCATTTCATTTATGGCATCCTTTCATGCCTTTTATACACT
1 ATTATACATTTCATTTATGACATCCTTTCATGCCTTTTATACACT
* * *
1040396 ATTATACATTTC-GTTATTACATCCTTTCATGCCTTTTGTACACT
1 ATTATACATTTCATTTATGACATCCTTTCATGCCTTTTATACACT
*
1040440 ATTATACATTTCATTTATGACATCCTTTCATGCTTTTTATACACT
1 ATTATACATTTCATTTATGACATCCTTTCATGCCTTTTATACACT
** *
1040485 ATTATACATTTCATTTATGGTATCCTTTCATGCCCTTTTATATACT
1 ATTATACATTTCATTTATGACATCCTTTCATG-CCTTTTATACACT
* * *
1040531 AATATACATTTCA-TTATTGACATCCATTCATGCCATTTATAC
1 ATTATACATTTCATTTA-TGACATCCTTTCATGCCTTTTATAC
1040573 CACGTTACAC
Statistics
Matches: 231, Mismatches: 31, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
44 42 0.18
45 147 0.64
46 41 0.18
47 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.44
Consensus pattern (45 bp):
ATTATACATTTCATTTATGACATCCTTTCATGCCTTTTATACACT
Found at i:1040796 original size:68 final size:68
Alignment explanation
Indices: 1040687--1041149 Score: 624
Period size: 68 Copynumber: 6.8 Consensus size: 68
1040677 TTATCTTTTA
* * * * *
1040687 CTCAAAGGTATTTAACCTTTCATCTAACTGGCAAAATTGACACCTTTCTGTCACATGCACAACTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTA
*
1040752 TGC
66 GGC
* * *
1040755 CTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTCTCAAATGCACAGCTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTA
1040820 GGC
66 GGC
* * * *
1040823 CTCAAAGGCACATAACCTTTCATCTATCT-GCATAATTGACACATTTCTGTCAAATGCACAACTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTA
1040887 GGC
66 GGC
* * *
1040890 CTCAAAGGCACTTAGCCTTTCATCT-ACATGGCATAATTGACATCTTTCTGTCAAATGCATAGCT
1 CTCAAAGGCACTTAGCCTTTCATCTAAC-TGGCATAATTGACACCTTTCTGTCAAATGCACAACT
**
1040954 ACAC
65 AGGC
* * * *
1040958 CTCAAAGGCATTTAGTCTTTCATCTAACTGGCATAATTGACACCTTTATGTCAAATGCACAGCTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTA
*
1041023 GGT
66 GGC
* * * *
1041026 CTCAAAGGCATTTAGTCTTTCATCTAATTGGCATAATTAACACCTTTCTGTCAAATGCACAACTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTA
1041091 GGC
66 GGC
* * **
1041094 CTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTGATATTTTTCTGTCAAAT
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAAT
1041150 TGTAACAACC
Statistics
Matches: 346, Mismatches: 46, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
66 1 0.00
67 58 0.17
68 285 0.82
69 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.31
Consensus pattern (68 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTA
GGC
Found at i:1041887 original size:9 final size:9
Alignment explanation
Indices: 1041873--1041985 Score: 73
Period size: 10 Copynumber: 11.8 Consensus size: 9
1041863 GGCTGCTGGA
1041873 AACCGGTTT
1 AACCGGTTT
1041882 AACCGGTTTT
1 AACCGG-TTT
1041892 CAACCGGTTCT
1 -AACCGGTT-T
*
1041903 GACCGGTTT
1 AACCGGTTT
*
1041912 GACCGGTTT
1 AACCGGTTT
*
1041921 CAACCGGTTCG
1 -AACCGGTT-T
1041932 AACCGGTTT
1 AACCGGTTT
* *
1041941 GACCGGTCT
1 AACCGGTTT
*
1041950 GACTCGGTTT
1 AAC-CGGTTT
* *
1041960 GACCGGTCTG
1 AACCGGT-TT
*
1041970 AGCCGGTTT
1 AACCGGTTT
*
1041979 GACCGGT
1 AACCGGT
1041986 CTGACCCGAC
Statistics
Matches: 84, Mismatches: 13, Indels: 14
0.76 0.12 0.13
Matches are distributed among these distances:
9 36 0.43
10 41 0.49
11 7 0.08
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:1041918 original size:19 final size:18
Alignment explanation
Indices: 1041894--1041991 Score: 117
Period size: 19 Copynumber: 5.2 Consensus size: 18
1041884 CCGGTTTTCA
*
1041894 ACCGGTTCTGACCGGTTTG
1 ACCGGTT-TGACCGGTCTG
*
1041913 ACCGGTTTCAACCGGT-TCG
1 ACCGGTTT-GACCGGTCT-G
1041932 AACCGGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTCTG
1041951 ACTCGGTTTGACCGGTCTG
1 AC-CGGTTTGACCGGTCTG
1041970 AGCCGGTTTGACCGGTCTG
1 A-CCGGTTTGACCGGTCTG
1041989 ACC
1 ACC
1041992 CGACCCGACT
Statistics
Matches: 71, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
18 6 0.08
19 55 0.77
20 10 0.14
ACGTcount: A:0.13, C:0.29, G:0.31, T:0.28
Consensus pattern (18 bp):
ACCGGTTTGACCGGTCTG
Found at i:1041936 original size:29 final size:30
Alignment explanation
Indices: 1041873--1041947 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
1041863 GGCTGCTGGA
*
1041873 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
1041904 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
1041932 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
1041948 CTGACTCGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:1041957 original size:29 final size:27
Alignment explanation
Indices: 1041874--1041985 Score: 107
Period size: 29 Copynumber: 3.9 Consensus size: 27
1041864 GCTGCTGGAA
* *
1041874 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTT-GACCGGTTC-G
*
1041904 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTT-GACCGGTTCG
* *
1041932 AACCGGTTTGACCGGTCTGACTCGGTTTG
1 -ACCGGTTTGACCGGTTTGAC-CGGTTCG
*
1041961 ACCGGTCTGAGCCGGTTTGACCGGT
1 ACCGGTTTGA-CCGGTTTGACCGGT
1041986 CTGACCCGAC
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
28 16 0.22
29 44 0.60
30 13 0.18
ACGTcount: A:0.14, C:0.27, G:0.29, T:0.29
Consensus pattern (27 bp):
ACCGGTTTGACCGGTTTGACCGGTTCG
Found at i:1041965 original size:38 final size:37
Alignment explanation
Indices: 1041874--1041991 Score: 141
Period size: 38 Copynumber: 3.1 Consensus size: 37
1041864 GCTGCTGGAA
*
1041874 ACCGGTTTAACCGGTTTTC-AACCGGTTCTGACCGGTTTG
1 ACCGGTTTAACCGG--TTCGAACCGGTT-TGACCGGTCTG
1041913 ACCGGTTTCAACCGGTTCGAACCGGTTTGACCGGTCTG
1 ACCGGTTT-AACCGGTTCGAACCGGTTTGACCGGTCTG
* *
1041951 ACTCGGTTTGACCGG-TCTGAGCCGGTTTGACCGGTCTG
1 AC-CGGTTTAACCGGTTC-GAACCGGTTTGACCGGTCTG
1041989 ACC
1 ACC
1041992 CGACCCGACT
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
37 3 0.04
38 41 0.57
39 22 0.31
40 6 0.08
ACGTcount: A:0.14, C:0.28, G:0.29, T:0.29
Consensus pattern (37 bp):
ACCGGTTTAACCGGTTCGAACCGGTTTGACCGGTCTG
Found at i:1042013 original size:5 final size:5
Alignment explanation
Indices: 1042005--1042045 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
1041995 CCCGACTGTT
*
1042005 GACCC GACCC GACCC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC
1042046 GTTGACCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.20, C:0.54, G:0.22, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:1042016 original size:22 final size:22
Alignment explanation
Indices: 1041988--1042052 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
1041978 TGACCGGTCT
*
1041988 GACCCGACCCGACTGTTGACCC
1 GACCCGACCCGACCGTTGACCC
1042010 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
1042032 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
1042053 GTTGACCGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.11
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:1042054 original size:7 final size:7
Alignment explanation
Indices: 1042042--1042086 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
1042032 GACCCGACCC
1042042 GACCGTT
1 GACCGTT
1042049 GACCGTT
1 GACCGTT
1042056 GACCGTT
1 GACCGTT
1042063 GACCGTT
1 GACCGTT
1042070 GACCGTT
1 GACCGTT
1042077 GACCGTT
1 GACCGTT
1042084 GAC
1 GAC
1042087 TTTCTTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.27
Consensus pattern (7 bp):
GACCGTT
Found at i:1043024 original size:63 final size:63
Alignment explanation
Indices: 1042956--1043079 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
1042946 CTAATGTGAC
* ** * *
1042956 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
1043019 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
1043080 TCCCTTAGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 50 0.96
64 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:1049293 original size:10 final size:9
Alignment explanation
Indices: 1049258--1049374 Score: 101
Period size: 10 Copynumber: 12.3 Consensus size: 9
1049248 GCTGCTGGAA
*
1049258 ACCGGTTTA
1 ACCGGTTTG
*
1049267 ACCGGTTTTCA
1 ACCGG-TTT-G
1049278 ACCGGTTCTG
1 ACCGGTT-TG
1049288 ACCGGTTTG
1 ACCGGTTTG
*
1049297 ACCGGTTTCA
1 ACCGGTTT-G
*
1049307 ACCGGTTCG
1 ACCGGTTTG
1049316 AACCGGTTTG
1 -ACCGGTTTG
*
1049326 ACCGGTCTG
1 ACCGGTTTG
1049335 ACTCGGTTTG
1 AC-CGGTTTG
*
1049345 ACCGGTCTG
1 ACCGGTTTG
1049354 AGCCGGTTTG
1 A-CCGGTTTG
*
1049364 A-CGGTCTG
1 ACCGGTTTG
1049372 ACC
1 ACC
1049375 CGACCCGACT
Statistics
Matches: 90, Mismatches: 10, Indels: 16
0.78 0.09 0.14
Matches are distributed among these distances:
8 7 0.08
9 33 0.37
10 43 0.48
11 7 0.08
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1049302 original size:19 final size:18
Alignment explanation
Indices: 1049278--1049374 Score: 108
Period size: 19 Copynumber: 5.2 Consensus size: 18
1049268 CCGGTTTTCA
*
1049278 ACCGGTTCTGACCGGTTTG
1 ACCGGTT-TGACCGGTCTG
*
1049297 ACCGGTTTCAACCGGT-TCG
1 ACCGGTTT-GACCGGTCT-G
1049316 AACCGGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTCTG
1049335 ACTCGGTTTGACCGGTCTG
1 AC-CGGTTTGACCGGTCTG
1049354 AGCCGGTTTGA-CGGTCTG
1 A-CCGGTTTGACCGGTCTG
1049372 ACC
1 ACC
1049375 CGACCCGACT
Statistics
Matches: 70, Mismatches: 2, Indels: 14
0.81 0.02 0.16
Matches are distributed among these distances:
17 2 0.03
18 12 0.17
19 46 0.66
20 10 0.14
ACGTcount: A:0.13, C:0.28, G:0.31, T:0.28
Consensus pattern (18 bp):
ACCGGTTTGACCGGTCTG
Found at i:1049320 original size:29 final size:30
Alignment explanation
Indices: 1049257--1049331 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
1049247 GGCTGCTGGA
*
1049257 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
1049288 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
1049316 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
1049332 CTGACTCGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:1049341 original size:29 final size:27
Alignment explanation
Indices: 1049258--1049365 Score: 99
Period size: 29 Copynumber: 3.7 Consensus size: 27
1049248 GCTGCTGGAA
* *
1049258 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTT-GACCGGTTC-G
*
1049288 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTT-GACCGGTTCG
* *
1049316 AACCGGTTTGACCGGTCTGACTCGGTTTG
1 -ACCGGTTTGACCGGTTTGAC-CGGTTCG
*
1049345 ACCGGTCTGAGCCGGTTTGAC
1 ACCGGTTTGA-CCGGTTTGAC
1049366 GGTCTGACCC
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
28 12 0.17
29 44 0.64
30 13 0.19
ACGTcount: A:0.15, C:0.27, G:0.29, T:0.30
Consensus pattern (27 bp):
ACCGGTTTGACCGGTTTGACCGGTTCG
Found at i:1049423 original size:22 final size:22
Alignment explanation
Indices: 1049371--1049434 Score: 112
Period size: 21 Copynumber: 3.0 Consensus size: 22
1049361 TTGACGGTCT
*
1049371 GACCCGACCCGACTGTTGACCC
1 GACCCGACCCGACCGTTGACCC
1049393 GA-CCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
1049414 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
1049435 GTTGACCGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 20 0.50
22 20 0.50
ACGTcount: A:0.19, C:0.47, G:0.23, T:0.11
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:1049436 original size:7 final size:7
Alignment explanation
Indices: 1049424--1049468 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
1049414 GACCCGACCC
1049424 GACCGTT
1 GACCGTT
1049431 GACCGTT
1 GACCGTT
1049438 GACCGTT
1 GACCGTT
*
1049445 GGCCGTT
1 GACCGTT
1049452 GACCGTT
1 GACCGTT
1049459 GACCGTT
1 GACCGTT
1049466 GAC
1 GAC
1049469 TTTCTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.13, C:0.29, G:0.31, T:0.27
Consensus pattern (7 bp):
GACCGTT
Found at i:1050404 original size:62 final size:62
Alignment explanation
Indices: 1050338--1050460 Score: 151
Period size: 62 Copynumber: 2.0 Consensus size: 62
1050328 CTAATGTGAC
* ** * *
1050338 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTG
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTG
* *
1050400 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
1050461 TCCCTTAGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
61 1 0.02
62 50 0.96
63 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.25
Consensus pattern (62 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTG
Found at i:1050409 original size:31 final size:31
Alignment explanation
Indices: 1050338--1050413 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
1050328 CTAATGTGAC
* *
1050338 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
** *
1050369 TCTCGGGTAGGCCCTGCGGCCCTAAGAT-GT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
1050399 GTCTTAGGTAGGCCC
1 -TCTTAGGTAGGCCC
1050414 CACGGCCCCG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
30 1 0.03
31 36 0.97
ACGTcount: A:0.14, C:0.28, G:0.32, T:0.26
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
Found at i:1050420 original size:31 final size:31
Alignment explanation
Indices: 1050374--1050460 Score: 79
Period size: 31 Copynumber: 2.8 Consensus size: 31
1050364 ATCATTCTCG
** *
1050374 GGTAGGCCCTGCGGCCCTAAGATGTGTCTTA
1 GGTAGGCCCCACGGCCCTAAGATGTATCTTA
* * *
1050405 GGTAGGCCCCACGGCCCCGAA-ATCTATCTTG
1 GGTAGGCCCCACGG-CCCTAAGATGTATCTTA
*
1050436 GGTAGGCTCTCA-GGCCCTAAGATGT
1 GGTAGGC-CCCACGGCCCTAAGATGT
1050461 TCCCTTAGTG
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
30 5 0.11
31 31 0.70
32 8 0.18
ACGTcount: A:0.18, C:0.29, G:0.30, T:0.23
Consensus pattern (31 bp):
GGTAGGCCCCACGGCCCTAAGATGTATCTTA
Found at i:1051366 original size:57 final size:57
Alignment explanation
Indices: 1051305--1051475 Score: 229
Period size: 57 Copynumber: 3.0 Consensus size: 57
1051295 TAAAGTTCTT
* *
1051305 ATACGAAAATTCGTAAACAAATTATGAGTTTCTTAACTTTTTGTACACTCAGTGCCC
1 ATACGAAAATTCATAAACAAATTATGAGTTTCTTAACTTTTTGCACACTCAGTGCCC
* * **
1051362 ATACGAAAATTCATAAACCAATTATG-GATTTCGTAACTTTTTGCACACAAAGTGCCC
1 ATACGAAAATTCATAAACAAATTATGAG-TTTCTTAACTTTTTGCACACTCAGTGCCC
* *
1051419 ATACGAATATTCATAAACAAATTATGAATTTTCTTAAC-TTTTGACACACTCAGTGCC
1 ATACGAAAATTCATAAACAAATTATG-AGTTTCTTAACTTTTTG-CACACTCAGTGCC
1051476 ATTATGTAAT
Statistics
Matches: 98, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
56 1 0.01
57 78 0.80
58 19 0.19
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (57 bp):
ATACGAAAATTCATAAACAAATTATGAGTTTCTTAACTTTTTGCACACTCAGTGCCC
Found at i:1051841 original size:22 final size:19
Alignment explanation
Indices: 1051809--1051862 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
1051799 TACCCCTACC
1051809 ATGGTATCGATACTACTATACT
1 ATGGTATCGATACT-CTA-A-T
*
1051831 ATGGTACCGATACTCTAAT
1 ATGGTATCGATACTCTAAT
1051850 ATGGTATCGATAC
1 ATGGTATCGATAC
1051863 CATTTTTGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 13 0.43
20 1 0.03
21 3 0.10
22 13 0.43
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (19 bp):
ATGGTATCGATACTCTAAT
Found at i:1055191 original size:22 final size:20
Alignment explanation
Indices: 1055143--1055194 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
1055133 ATGCCAAATT
*
1055143 AGTATCGATA-CCTTGAGTA
1 AGTATCGATACCCTTGAGAA
*
1055162 GGTATCGATACCCTTGAAGGAA
1 AGTATCGATACCCTTG-A-GAA
1055184 AGTATCGATAC
1 AGTATCGATAC
1055195 TGTAGGGGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 9 0.33
20 5 0.19
21 1 0.04
22 12 0.44
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (20 bp):
AGTATCGATACCCTTGAGAA
Found at i:1056016 original size:21 final size:23
Alignment explanation
Indices: 1055982--1056041 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 23
1055972 GTCGAGGGTT
1055982 TTATGTGGTC-CTTCAGG-AC-AA
1 TTATGTGG-CACTTCAGGTACAAA
*
1056003 TTATGTGGCACTTC-GGTGCAAA
1 TTATGTGGCACTTCAGGTACAAA
1056025 TCTATGTGGCACTTCAG
1 T-TATGTGGCACTTCAG
1056042 TGTAAACCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 3 0.09
21 13 0.39
22 3 0.09
23 13 0.39
24 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (23 bp):
TTATGTGGCACTTCAGGTACAAA
Found at i:1056031 original size:23 final size:23
Alignment explanation
Indices: 1056004--1056056 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1055994 TCAGGACAAT
* *
1056004 TATGTGGCACTTCGGTGCAAATC
1 TATGTGGCACTTCAGTGCAAACC
*
1056027 TATGTGGCACTTCAGTGTAAACC
1 TATGTGGCACTTCAGTGCAAACC
1056050 TATGTGG
1 TATGTGG
1056057 TTATTTGGGA
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:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (23 bp):
TATGTGGCACTTCAGTGCAAACC
Found at i:1064275 original size:22 final size:22
Alignment explanation
Indices: 1064250--1064321 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
1064240 ATGCATTTCA
*
1064250 TTTATGACATCATTGCATGCCT
1 TTTATGACATCATTACATGCCT
** *
1064272 TTTAT-ACA-CTATTATACATTTCA
1 TTTATGACATC-A-T-TACATGCCT
*
1064295 TTTATGACATCATTTCATGCCT
1 TTTATGACATCATTACATGCCT
1064317 TTTAT
1 TTTAT
1064322 ACACTATTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
20 1 0.03
21 4 0.11
22 16 0.43
23 11 0.30
24 4 0.11
25 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.47
Consensus pattern (22 bp):
TTTATGACATCATTACATGCCT
Found at i:1064292 original size:45 final size:45
Alignment explanation
Indices: 1064243--1064431 Score: 297
Period size: 45 Copynumber: 4.2 Consensus size: 45
1064233 CACCCATATG
*
1064243 CATTTCATTTATGACATCATTGCATGCCTTTTATACACTATTATA
1 CATTTCATTTATGACATCATTTCATGCCTTTTATACACTATTATA
1064288 CATTTCATTTATGACATCATTTCATGCCTTTTATACACTATTATA
1 CATTTCATTTATGACATCATTTCATGCCTTTTATACACTATTATA
* * * *
1064333 TATTTCATTTATGGCATCCTTTCATGCCTTATATACACTATTATA
1 CATTTCATTTATGACATCATTTCATGCCTTTTATACACTATTATA
* *
1064378 CATTTCATTTATGGCATCCTTTCATGCCCTTTTATACACTATTATA
1 CATTTCATTTATGACATCATTTCATG-CCTTTTATACACTATTATA
*
1064424 AATTTCAT
1 CATTTCAT
1064432 CATTGTCTTC
Statistics
Matches: 135, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
45 110 0.81
46 25 0.19
ACGTcount: A:0.28, C:0.21, G:0.06, T:0.46
Consensus pattern (45 bp):
CATTTCATTTATGACATCATTTCATGCCTTTTATACACTATTATA
Found at i:1064305 original size:90 final size:90
Alignment explanation
Indices: 1064198--1064402 Score: 241
Period size: 90 Copynumber: 2.3 Consensus size: 90
1064188 CACCCATATG
* * * * *
1064198 CATTTCAATTATAACATCATTTCATATCGATAATGCACCCA-TATGCATTTCATTTATGACATCA
1 CATTTCATTTATGACATCATTTCATACCGATAATACA-CCATTATACATTTCATTTATGACATCA
*
1064262 TTGCATGCCTTTTATACACTATTATA
65 TTGCATGCCTTATATACACTATTATA
* ** * * * * *
1064288 CATTTCATTTATGACATCATTTCATGCCTTTTATACACTATTATATATTTCATTTATGGCATCCT
1 CATTTCATTTATGACATCATTTCATACCGATAATACACCATTATACATTTCATTTATGACATCAT
*
1064353 TTCATGCCTTATATACACTATTATA
66 TGCATGCCTTATATACACTATTATA
* *
1064378 CATTTCATTTATGGCATCCTTTCAT
1 CATTTCATTTATGACATCATTTCAT
1064403 GCCCTTTTAT
Statistics
Matches: 97, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
89 2 0.02
90 95 0.98
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (90 bp):
CATTTCATTTATGACATCATTTCATACCGATAATACACCATTATACATTTCATTTATGACATCAT
TGCATGCCTTATATACACTATTATA
Found at i:1064472 original size:91 final size:90
Alignment explanation
Indices: 1064244--1064459 Score: 274
Period size: 90 Copynumber: 2.4 Consensus size: 90
1064234 ACCCATATGC
* * * * *
1064244 ATTTCATTTATGACATCATTGCATGCCTTTTATACACTATTATACATTTCATTTATGACATCATT
1 ATTTCATATATGGCATCATTTCAAGCCTTATATACACTATTATACATTTCATTTATGACATCATT
*
1064309 TCATGCCTTTTATACACTATTATAT
66 TCATGCCTTTTATACACTATTATAA
* * * * *
1064334 ATTTCATTTATGGCATCCTTTCATGCCTTATATACACTATTATACATTTCATTTATGGCATCCTT
1 ATTTCATATATGGCATCATTTCAAGCCTTATATACACTATTATACATTTCATTTATGACATCATT
1064399 TCATGCCCTTTTATACACTATTATAA
66 TCATG-CCTTTTATACACTATTATAA
* *
1064425 ATTTCATCAT-TGTCTTCATTTCAAGCCATT-TATAC
1 ATTTCAT-ATATGGCATCATTTCAAGCC-TTATATAC
1064460 TACGTTCTAC
Statistics
Matches: 111, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
90 64 0.58
91 44 0.40
92 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.46
Consensus pattern (90 bp):
ATTTCATATATGGCATCATTTCAAGCCTTATATACACTATTATACATTTCATTTATGACATCATT
TCATGCCTTTTATACACTATTATAA
Found at i:1064598 original size:81 final size:83
Alignment explanation
Indices: 1064486--1064641 Score: 262
Period size: 82 Copynumber: 1.9 Consensus size: 83
1064476 ATACATCTAG
* * *
1064486 TCTTTTAGTCAAAGGCATTTTAACCTTTCATCTAACTGGCATGATTG-ACACCTTTTTGTCAAAT
1 TCTTTTACTCAAAGGCATTTTAACCTTTCATCTAACTGGCATAATTGAACACCTTTCTGTCAAAT
1064550 GCACAGCTAGGCCATTTA
66 GCACAGCTAGGCCATTTA
*
1064568 TCTTTTACTCAAAGGTA-TTTAACCTTTCATCTAACTGGCATAATTGAACACCTTTCTGTCAAAT
1 TCTTTTACTCAAAGGCATTTTAACCTTTCATCTAACTGGCATAATTGAACACCTTTCTGTCAAAT
1064632 GCACAGCTAG
66 GCACAGCTAG
1064642 ACCTCAAAGG
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
81 28 0.41
82 41 0.59
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.36
Consensus pattern (83 bp):
TCTTTTACTCAAAGGCATTTTAACCTTTCATCTAACTGGCATAATTGAACACCTTTCTGTCAAAT
GCACAGCTAGGCCATTTA
Found at i:1064720 original size:68 final size:68
Alignment explanation
Indices: 1064575--1064993 Score: 570
Period size: 68 Copynumber: 6.2 Consensus size: 68
1064565 TTATCTTTTA
* * * *
1064575 CTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGAACACCTTTCTGTCAAATGCACAGCT
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTG-ACACCTTTCTGTCAAATGCACAGCT
*
1064640 AGAC
65 AGGC
* * * * *
1064644 CTCAAAGGCACTTAGCATTTCATCTATCTGTCATAATTGGCACATTTCTGTCAAATGCACAGCTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGCTA
1064709 GGC
66 GGC
* * * *
1064712 CTCGAAGGCACTTAGCCTTTTATCTAACTGACATAATTGACACATTTCTGTCAAATGCACAGCTT
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGCTA
1064777 GGC
66 GGC
* * * * *
1064780 CTCAAAGTCACTTAGCATTTCATCTAACTGGCATAATTAACACCTTTCTGTCAAATGCACATCTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGCTA
1064845 GGC
66 GGC
* * * *
1064848 CTCAAAGGAACTAAGCCTTTCATCTAACTG-CATGATTGACACCTTTCTGTCAAATGCACAACTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGCTA
1064912 GGC
66 GGC
* * * *
1064915 GTCAAAGACACTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTTTCAAATGCACAACTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGCTA
1064980 GGC
66 GGC
*
1064983 CTCAAATGCAC
1 CTCAAAGGCAC
1064994 AACTAGGCCT
Statistics
Matches: 308, Mismatches: 41, Indels: 3
0.88 0.12 0.01
Matches are distributed among these distances:
67 60 0.19
68 215 0.70
69 33 0.11
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.30
Consensus pattern (68 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGCTA
GGC
Found at i:1064941 original size:135 final size:135
Alignment explanation
Indices: 1064575--1065196 Score: 679
Period size: 136 Copynumber: 4.4 Consensus size: 135
1064565 TTATCTTTTA
* * * *
1064575 CTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGAACACCTTTCTGTCAAATGCACAGCT
1 CTCAAAGGAACTTAGCCTTTCATCTAACT-GCATAATTG-ACACCTTTCTGTCAAATGCACAACT
* * * * *
1064640 AGACCTCAAAGGCACTTAGCATTTCATCTATCTGTCATAATTGGCACATTTCTGTCAAATGCACA
64 AGGCCTCAAAGGCACTTAGCATTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACA
1064705 GCTAGGC
129 GCTAGGC
* * * * * *
1064712 CTCGAAGGCACTTAGCCTTTTATCTAACTGACATAATTGACACATTTCTGTCAAATGCACAGCTT
1 CTCAAAGGAACTTAGCCTTTCATCTAACTG-CATAATTGACACCTTTCTGTCAAATGCACAACTA
* * *
1064777 GGCCTCAAAGTCACTTAGCATTTCATCTAACTGGCATAATTAACACCTTTCTGTCAAATGCACAT
65 GGCCTCAAAGGCACTTAGCATTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAG
1064842 CTAGGC
130 CTAGGC
* *
1064848 CTCAAAGGAACTAAGCCTTTCATCTAACTGCATGATTGACACCTTTCTGTCAAATGCACAACTAG
1 CTCAAAGGAACTTAGCCTTTCATCTAACTGCATAATTGACACCTTTCTGTCAAATGCACAACTAG
* * * * * *
1064913 GCGTCAAAGACACTTAGCCTTTCATCTAACTGACATAATTGACACCTTTCTTTCAAATGCACAAC
66 GCCTCAAAGGCACTTAGCATTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGC
1064978 TAGGCC
131 TAGG-C
**
1064984 TCAAATGCACAACTAGGCCTCGAAGGCACTTAGCCTTTCATCTAACTGCATAATTGACATATTTC
1 -C---T---CAA--A-G----G-A---ACTTAGCCTTTCATCTAACTGCATAATTGACACCTTTC
* * * * * * *
1065049 TCTCAAATGCAAAACTTGGCATCAAAGGCACTTAGCCTTTCATCTAACTAGCATAATTGACACTT
48 TGTCAAATGCACAACTAGGCCTCAAAGGCACTTAGCATTTCATCTAACTGGCATAATTGACACCT
* *
1065114 TTCTTTCAAATGCATAGCTAGGC
113 TTCTGTCAAATGCACAGCTAGGC
* *
1065137 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACTCCTTTCTGTC-AATGCACA
1 CTCAAAGGAACTTAGCCTTTCATCTAACT-GCATAATTGACACCTTTCTGTCAAATGCACA
1065197 GTTAGATGTT
Statistics
Matches: 414, Mismatches: 50, Indels: 44
0.81 0.10 0.09
Matches are distributed among these distances:
135 120 0.29
136 133 0.32
137 33 0.08
139 1 0.00
140 1 0.00
143 4 0.01
144 1 0.00
145 1 0.00
146 4 0.01
149 1 0.00
150 1 0.00
151 1 0.00
152 1 0.00
153 1 0.00
154 111 0.27
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (135 bp):
CTCAAAGGAACTTAGCCTTTCATCTAACTGCATAATTGACACCTTTCTGTCAAATGCACAACTAG
GCCTCAAAGGCACTTAGCATTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGC
TAGGC
Found at i:1064989 original size:19 final size:19
Alignment explanation
Indices: 1064965--1065004 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1064955 CACCTTTCTT
1064965 TCAAATGCACAACTAGGCC
1 TCAAATGCACAACTAGGCC
1064984 TCAAATGCACAACTAGGCC
1 TCAAATGCACAACTAGGCC
1065003 TC
1 TC
1065005 GAAGGCACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.33, G:0.15, T:0.17
Consensus pattern (19 bp):
TCAAATGCACAACTAGGCC
Found at i:1065012 original size:19 final size:19
Alignment explanation
Indices: 1064965--1065012 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1064955 CACCTTTCTT
*
1064965 TCAAATGCACAACTAGGCC
1 TCAAAGGCACAACTAGGCC
*
1064984 TCAAATGCACAACTAGGCC
1 TCAAAGGCACAACTAGGCC
*
1065003 TCGAAGGCAC
1 TCAAAGGCAC
1065013 TTAGCCTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.35, C:0.31, G:0.19, T:0.15
Consensus pattern (19 bp):
TCAAAGGCACAACTAGGCC
Found at i:1065058 original size:154 final size:154
Alignment explanation
Indices: 1064830--1065147 Score: 476
Period size: 154 Copynumber: 2.1 Consensus size: 154
1064820 CACCTTTCTG
* * *
1064830 TCAAATGCACATCTAGGCCTCAAAGGAACTAAGCCTTTCATCTAACTGCATGATTGACACCTTTC
1 TCAAATGCACAACTAGGCCTCAAAGGAACTAAGCCTTTCATCTAACTGCATAATTGACACATTTC
* * *
1064895 TGTCAAATGCACAACTAGGCGTCAAAGACACTTAGCCTTTCATCTAACT-GACATAATTGACACC
66 TCTCAAATGCAAAACTAGGCATCAAAGACACTTAGCCTTTCATCTAACTAG-CATAATTGACACC
1064959 TTTCTTTCAAATGCACAACTAGGCC
130 TTTCTTTCAAATGCACAACTAGGCC
* * * *
1064984 TCAAATGCACAACTAGGCCTCGAAGGCACTTAGCCTTTCATCTAACTGCATAATTGACATATTTC
1 TCAAATGCACAACTAGGCCTCAAAGGAACTAAGCCTTTCATCTAACTGCATAATTGACACATTTC
* * *
1065049 TCTCAAATGCAAAACTTGGCATCAAAGGCACTTAGCCTTTCATCTAACTAGCATAATTGACACTT
66 TCTCAAATGCAAAACTAGGCATCAAAGACACTTAGCCTTTCATCTAACTAGCATAATTGACACCT
* *
1065114 TTCTTTCAAATGCATAGCTAGGCC
131 TTCTTTCAAATGCACAACTAGGCC
*
1065138 TCAAAGGCAC
1 TCAAATGCAC
1065148 TTAGCCTTTC
Statistics
Matches: 147, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
154 146 0.99
155 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (154 bp):
TCAAATGCACAACTAGGCCTCAAAGGAACTAAGCCTTTCATCTAACTGCATAATTGACACATTTC
TCTCAAATGCAAAACTAGGCATCAAAGACACTTAGCCTTTCATCTAACTAGCATAATTGACACCT
TTCTTTCAAATGCACAACTAGGCC
Found at i:1065091 original size:67 final size:68
Alignment explanation
Indices: 1064983--1065194 Score: 295
Period size: 68 Copynumber: 3.1 Consensus size: 68
1064973 ACAACTAGGC
* *
1064983 CTCAAATGCACAACTAGGCCTCGAAGGCACTTAGCCTTTCATCTAACT-GCATAATTGACA-TAT
1 CTCAAATGCAAAACTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTAGCATAATTGACACT-T
1065046 TTCT
65 TTCT
* *
1065050 CTCAAATGCAAAACTTGGCATCAAAGGCACTTAGCCTTTCATCTAACTAGCATAATTGACACTTT
1 CTCAAATGCAAAACTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTAGCATAATTGACACTTT
1065115 TCT
66 TCT
* * * * * *
1065118 TTCAAATGCATAGCTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACTCCTT
1 CTCAAATGCAAAACTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTAGCATAATTGACACTTT
1065183 TCT
66 TCT
*
1065186 GTC-AATGCA
1 CTCAAATGCA
1065195 CAGTTAGATG
Statistics
Matches: 130, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
67 50 0.38
68 79 0.61
69 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.31
Consensus pattern (68 bp):
CTCAAATGCAAAACTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTAGCATAATTGACACTTT
TCT
Found at i:1065578 original size:57 final size:57
Alignment explanation
Indices: 1065416--1065579 Score: 202
Period size: 57 Copynumber: 2.9 Consensus size: 57
1065406 TCTTATATGG
* * ** * * * *
1065416 AAATTCGTAAACAAATTATGAATTTCTTATCTTTTTTAACACTCAGTTCCCATACGG
1 AAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACTAAGTGCCCATAAGA
* * * *
1065473 AAATTCATAAACCAATTATGGATTTCTTAACTTTTTGCACACAAAGTGCCTATAAGA
1 AAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACTAAGTGCCCATAAGA
* *
1065530 AAATTCATAAACAAATTATGAATTTCTTAGCTTTTTGCACACTTAGTGCC
1 AAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACTAAGTGCC
1065580 GTTATGTAAT
Statistics
Matches: 90, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
57 90 1.00
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (57 bp):
AAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACTAAGTGCCCATAAGA
Found at i:1069063 original size:16 final size:16
Alignment explanation
Indices: 1068996--1069064 Score: 106
Period size: 16 Copynumber: 4.4 Consensus size: 16
1068986 CGTTCATTTA
1068996 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
*
1069010 ATAAAAGAACACGAAC
1 ATAAATGAACACGAAC
*
1069026 ATAAACGAACACGAAC
1 ATAAATGAACACGAAC
1069042 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
1069058 ATAAATG
1 ATAAATG
1069065 TTGGAGACCC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 43 0.86
ACGTcount: A:0.59, C:0.17, G:0.12, T:0.12
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:1069259 original size:16 final size:16
Alignment explanation
Indices: 1069228--1069259 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1069218 ATTGAAACTC
*
1069228 GACTCGAACTCGAAAA
1 GACTCGAACTCAAAAA
1069244 GACTCGAACTCAAAAA
1 GACTCGAACTCAAAAA
1069260 AAAAATTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.25, G:0.16, T:0.12
Consensus pattern (16 bp):
GACTCGAACTCAAAAA
Found at i:1070225 original size:14 final size:14
Alignment explanation
Indices: 1070208--1070239 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1070198 AATGAACATA
1070208 AACGAACATAACCG
1 AACGAACATAACCG
1070222 AACGAACATAACCG
1 AACGAACATAACCG
1070236 AACG
1 AACG
1070240 TTCACGAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.28, G:0.16, T:0.06
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1077337 original size:105 final size:104
Alignment explanation
Indices: 1077180--1077404 Score: 281
Period size: 105 Copynumber: 2.2 Consensus size: 104
1077170 CCATCTATTC
* * ** **
1077180 GACACAATTATCAATATAAATTATGATGACTTATTTCACACTAAAAATATATTTTGTGATTATTA
1 GACACTATTATCAATAGAAATTATGATGACTTATTTCACACTAAAAATATATTTTGTGACCACCA
* *
1077245 ATATTGTTACACTAAGTATTTTTTAGTGACCAAATGTTT
66 ATATTGTCACAATAAGTATTTTTTAGTGACCAAATGTTT
* * * * *
1077284 GATACTATTATCAATAGAAATTGTGAT-ACATTTATTTGACACTGAAAGTATATTTTGTGACCAC
1 GACACTATTATCAATAGAAATTATGATGAC--TTATTTCACACTAAAAATATATTTTGTGACCAC
* *
1077348 CAATGTTGTCACAATAAGTGTTTTTTAGTGACCAAATGTTT
64 CAATATTGTCACAATAAGTATTTTTTAGTGACCAAATGTTT
*
1077389 GACACTATTAACAATA
1 GACACTATTATCAATA
1077405 ACTCTGTCAC
Statistics
Matches: 102, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
103 2 0.02
104 23 0.23
105 77 0.75
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (104 bp):
GACACTATTATCAATAGAAATTATGATGACTTATTTCACACTAAAAATATATTTTGTGACCACCA
ATATTGTCACAATAAGTATTTTTTAGTGACCAAATGTTT
Found at i:1081481 original size:2 final size:2
Alignment explanation
Indices: 1081474--1081503 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1081464 TGAAACATGC
1081474 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1081504 TAATGGGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1082710 original size:18 final size:18
Alignment explanation
Indices: 1082683--1082733 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
1082673 CTTGAGCTCC
1082683 AATTTCTTCTAATTAGAT
1 AATTTCTTCTAATTAGAT
* *
1082701 AATTTATTCTAATCAGAT
1 AATTTCTTCTAATTAGAT
* *
1082719 GATTTCTTCTTATTA
1 AATTTCTTCTAATTA
1082734 TGAACTCTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (18 bp):
AATTTCTTCTAATTAGAT
Found at i:1082934 original size:17 final size:17
Alignment explanation
Indices: 1082912--1082956 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
1082902 AAAGTTGAAC
1082912 AAGTTCTTCTCATTATG
1 AAGTTCTTCTCATTATG
1082929 AAGTTCTTCTCATTATG
1 AAGTTCTTCTCATTATG
*
1082946 AACTTCTTCTC
1 AAGTTCTTCTC
1082957 CCTCGTCAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.47
Consensus pattern (17 bp):
AAGTTCTTCTCATTATG
Found at i:1083292 original size:138 final size:139
Alignment explanation
Indices: 1082929--1083564 Score: 997
Period size: 140 Copynumber: 4.6 Consensus size: 139
1082919 TCTCATTATG
* * * * *
1082929 AAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCAGATGAGTTCTTATCATTATGAACTATCCC
1 AAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCA
* * * * *
1082994 CTTGGAAATGTTGATCCCTCGAGTGAGGTGTTGCTTATTCGAGTCCATATGCGATGAATCGAGTT
66 C-TGGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGCT
1083059 AAGGTTGAAC
130 AAGGTTGAAC
* *
1083069 AAGTTCTTCTCATTATGAAATTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCTA
1 AAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCA
* * * *
1083134 CTAGAAATGTTAATCTCTCGAGTGAGGTGTTGTTGATTCAACTCCATATGTGATGAATCGAGCTA
66 CTGGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGCTA
1083199 AGGTTGAAC
131 AGGTTGAAC
* *
1083208 AAGTTCTT-TCATTATAAACTTCTTCTGCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCA
1 AAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCA
1083272 CTGGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGCTA
66 CTGGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGCTA
1083337 AGGTTGAAC
131 AGGTTGAAC
* *
1083346 AAGTTCTTCTCACTATGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTCTCTC
1 AAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTC-C
** * *
1083411 ACTATAAATATTGATCCCTTGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGCT
65 ACTGGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGCT
1083476 AAGGTTGAAC
130 AAGGTTGAAC
* *
1083486 AAGTTCTTCTCATTTTGAACTTCTTCTCCCTCATCGAATGAGTTCTTCTCATTATGAACTCTCCA
1 AAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCA
1083551 -TCGGAAATGTTGAT
66 CT-GGAAATGTTGAT
1083565 TGGTTTACCC
Statistics
Matches: 454, Mismatches: 39, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
138 131 0.29
139 133 0.29
140 190 0.42
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (139 bp):
AAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCA
CTGGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCGAGCTA
AGGTTGAAC
Found at i:1086711 original size:7 final size:7
Alignment explanation
Indices: 1086694--1086822 Score: 61
Period size: 7 Copynumber: 17.9 Consensus size: 7
1086684 ATTTGATCGG
1086694 TTTTCTTC
1 TTTT-TTC
1086702 TTTTTTC
1 TTTTTTC
1086709 --TTTTC
1 TTTTTTC
1086714 TTTTTTC
1 TTTTTTC
*
1086721 TTTTTCC
1 TTTTTTC
*
1086728 TCTTTT-
1 TTTTTTC
*
1086734 TTTGTT-
1 TTTTTTC
*
1086740 ATTTTTC
1 TTTTTTC
*
1086747 TATTTGTTA
1 T-TTT-TTC
* *
1086756 TTTGTTA
1 TTTTTTC
*
1086763 TTTTTTAT
1 TTTTTT-C
1086771 TTTTTTC
1 TTTTTTC
1086778 AATTTTTTC
1 --TTTTTTC
1086787 TTTATTT-
1 TTT-TTTC
*
1086794 TTTCTTC
1 TTTTTTC
1086801 TTTTTTC
1 TTTTTTC
1086808 ATTTTTTC
1 -TTTTTTC
1086816 TCTTTTT
1 T-TTTTT
1086823 TCTCCTATTT
Statistics
Matches: 94, Mismatches: 15, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
5 5 0.05
6 10 0.11
7 39 0.41
8 30 0.32
9 10 0.11
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.78
Consensus pattern (7 bp):
TTTTTTC
Found at i:1086716 original size:12 final size:12
Alignment explanation
Indices: 1086699--1086724 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1086689 ATCGGTTTTC
1086699 TTCTTTTTTCTT
1 TTCTTTTTTCTT
1086711 TTCTTTTTTCTT
1 TTCTTTTTTCTT
1086723 TT
1 TT
1086725 TCCTCTTTTT
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:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:1086794 original size:10 final size:9
Alignment explanation
Indices: 1086694--1086870 Score: 65
Period size: 10 Copynumber: 18.3 Consensus size: 9
1086684 ATTTGATCGG
1086694 TTTTCTTCTT
1 TTTTCTT-TT
1086704 TTTTCTTTT
1 TTTTCTTTT
1086713 CTTTT-TTCTT
1 -TTTTCTT-TT
*
1086723 TTTCCTCTTT
1 TTTTCT-TTT
* *
1086733 TTTTGTTAT
1 TTTTCTTTT
1086742 TTTTCTATTT
1 TTTTCT-TTT
1086752 GTTATT-TGTTAT
1 -TT-TTCT-TT-T
1086764 TTTT-TATTT
1 TTTTCT-TTT
**
1086773 TTTTCAATT
1 TTTTCTTTT
1086782 TTTTCTTTATT
1 TTTTC-TT-TT
1086793 TTTTCTTCTT
1 TTTTCTT-TT
1086803 TTTTCATTTT
1 TTTTC-TTTT
*
1086813 TTCTCTTTT
1 TTTTCTTTT
* *
1086822 TTCTCCTATT
1 TT-TTCTTTT
1086832 TTTTC-TTT
1 TTTTCTTTT
* *
1086840 CTCTCTTTT
1 TTTTCTTTT
* * *
1086849 CTATATTTT
1 TTTTCTTTT
1086858 TCTTTCTTTT
1 T-TTTCTTTT
1086868 TTT
1 TTT
1086871 GTTATATTTT
Statistics
Matches: 126, Mismatches: 26, Indels: 31
0.69 0.14 0.17
Matches are distributed among these distances:
8 5 0.04
9 46 0.37
10 55 0.44
11 17 0.13
12 3 0.02
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.77
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:1086806 original size:23 final size:23
Alignment explanation
Indices: 1086780--1086885 Score: 77
Period size: 23 Copynumber: 4.9 Consensus size: 23
1086770 TTTTTTTCAA
*
1086780 TTTTTTCTTTATTTTTTCTTC--
1 TTTTTTCTATATTTTTTCTTCTT
1086801 TTTTTTC---ATTTTTTC-TCTT
1 TTTTTTCTATATTTTTTCTTCTT
* * *
1086820 TTTTCTC-CTATTTTTTCTTTCTC
1 TTTTTTCTATATTTTTTC-TTCTT
*
1086843 TCTTTTCTATA-TTTTTCTTTCTT
1 TTTTTTCTATATTTTTTC-TTCTT
1086866 TTTTTGT-TATATTTTTTCTT
1 TTTTT-TCTATATTTTTTCTT
1086886 TCTCTCGGTG
Statistics
Matches: 69, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
17 2 0.03
18 8 0.12
19 6 0.09
21 15 0.22
23 29 0.42
24 9 0.13
ACGTcount: A:0.07, C:0.16, G:0.01, T:0.76
Consensus pattern (23 bp):
TTTTTTCTATATTTTTTCTTCTT
Found at i:1086806 original size:39 final size:39
Alignment explanation
Indices: 1086763--1086838 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
1086753 TTATTTGTTA
*
1086763 TTTTTT-ATTTTTT-TCAATTTTTTCT-TTATTTTTTCTTC
1 TTTTTTCATTTTTTCTC--TTTTTTCTCCTATTTTTTCTTC
1086801 TTTTTTCATTTTTTCTCTTTTTTCTCCTATTTTTTCTT
1 TTTTTTCATTTTTTCTCTTTTTTCTCCTATTTTTTCTT
1086839 TCTCTCTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
38 14 0.41
39 18 0.53
40 2 0.06
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (39 bp):
TTTTTTCATTTTTTCTCTTTTTTCTCCTATTTTTTCTTC
Found at i:1086819 original size:17 final size:18
Alignment explanation
Indices: 1086790--1086824 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1086780 TTTTTTCTTT
1086790 ATTTTTTCTTCTTTTTTC
1 ATTTTTTCTTCTTTTTTC
1086808 ATTTTTTC-TCTTTTTTC
1 ATTTTTTCTTCTTTTTTC
1086825 TCCTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (18 bp):
ATTTTTTCTTCTTTTTTC
Found at i:1086881 original size:24 final size:24
Alignment explanation
Indices: 1086812--1086891 Score: 92
Period size: 23 Copynumber: 3.3 Consensus size: 24
1086802 TTTTTCATTT
* *
1086812 TTTCTCTTTTTTCTCCTATTTTTTC
1 TTTCTCTCTTTTCT-ATATTTTTTC
1086837 TTTCTCTCTTTTCTATA-TTTTTC
1 TTTCTCTCTTTTCTATATTTTTTC
* *
1086860 TTTCT-TTTTTTGTTATATTTTTTC
1 TTTCTCTCTTTT-CTATATTTTTTC
1086884 TTTCTCTC
1 TTTCTCTC
1086892 GGTGTTATCA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
22 5 0.11
23 15 0.32
24 13 0.28
25 14 0.30
ACGTcount: A:0.06, C:0.20, G:0.01, T:0.72
Consensus pattern (24 bp):
TTTCTCTCTTTTCTATATTTTTTC
Found at i:1100019 original size:2 final size:2
Alignment explanation
Indices: 1100012--1100068 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
1100002 ACACTCATCA
1100012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1100054 AT TT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT
1100069 TCATGGGACT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Done.