Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009643.1 Hibiscus syriacus cultivar Beakdansim tig00117056_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: 8859806
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 41
Found at i:1054503 original size:3 final size:3
Alignment explanation
Indices: 1054497--1054581 Score: 120
Period size: 3 Copynumber: 28.7 Consensus size: 3
1054487 TTTTTATCCA
* *
1054497 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAC TAC TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1054543 TAT ATAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1054582 AATATATATT
Statistics
Matches: 76, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
2 4 0.05
3 69 0.91
4 3 0.04
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1054593 original size:11 final size:11
Alignment explanation
Indices: 1054577--1054608 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
1054567 TTATTATTAT
1054577 TATTAAATATA
1 TATTAAATATA
1054588 TATTAAATATA
1 TATTAAATATA
1054599 TATATAAATA
1 TAT-TAAATA
1054609 ATTAATTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAATATA
Found at i:1056934 original size:21 final size:21
Alignment explanation
Indices: 1056910--1056949 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1056900 TTGGTTTTCC
1056910 GGAAAATGAATTACTGGAACT
1 GGAAAATGAATTACTGGAACT
1056931 GGAAAATGAATTACTGGAA
1 GGAAAATGAATTACTGGAA
1056950 TTTAAATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.25, T:0.23
Consensus pattern (21 bp):
GGAAAATGAATTACTGGAACT
Found at i:1056969 original size:14 final size:15
Alignment explanation
Indices: 1056928--1056973 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1056918 AATTACTGGA
*
1056928 ACTGGAAAATGAATT
1 ACTGGAAAATAAATT
**
1056943 ACTGGAATTTAAATT
1 ACTGGAAAATAAATT
1056958 -CTGGAAAATAAATT
1 ACTGGAAAATAAATT
1056972 AC
1 AC
1056974 ATTTCTGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (15 bp):
ACTGGAAAATAAATT
Found at i:1057348 original size:23 final size:22
Alignment explanation
Indices: 1057310--1057364 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
1057300 TTTATATTTT
**
1057310 TTTTAAATA-TTAATTAGTATA
1 TTTTAAATATTTAATTAAAATA
*
1057331 TTTTAAATATCTTTATTAAAATA
1 TTTTAAATAT-TTAATTAAAATA
1057354 TTTTAACATAT
1 TTTTAA-ATAT
1057365 AAATAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.32
23 15 0.54
24 4 0.14
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTAAATATTTAATTAAAATA
Found at i:1057392 original size:26 final size:27
Alignment explanation
Indices: 1057351--1057485 Score: 88
Period size: 26 Copynumber: 5.1 Consensus size: 27
1057341 CTTTATTAAA
1057351 ATATT-TTAACATATAAATAATAATATT
1 ATATTATTAA-ATATAAATAATAATATT
**
1057378 CA-A-TATTAAATATAAA-AATTTTATT
1 -ATATTATTAAATATAAATAATAATATT
*
1057403 ATATTATTAAATAAAAAT-ATAATATCTT
1 ATATTATTAAATATAAATAATAATA--TT
* * * * *
1057431 ATATTATTATA-ATAATTGATTATTTT
1 ATATTATTAAATATAAATAATAATATT
*
1057457 ATATATATTAAA-A-AAATAATATTATT
1 ATAT-TATTAAATATAAATAATAATATT
1057483 ATA
1 ATA
1057486 AATATAATAA
Statistics
Matches: 83, Mismatches: 16, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
24 1 0.01
25 8 0.10
26 41 0.49
27 16 0.19
28 17 0.20
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (27 bp):
ATATTATTAAATATAAATAATAATATT
Found at i:1057492 original size:17 final size:18
Alignment explanation
Indices: 1057457--1057499 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1057447 TGATTATTTT
1057457 ATATATATTAAAAAAATA
1 ATATATATTAAAAAAATA
* *
1057475 ATAT-TATTATAAATATA
1 ATATATATTAAAAAAATA
*
1057492 ATAAATAT
1 ATATATAT
1057500 AATGATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATATATTAAAAAAATA
Found at i:1057501 original size:26 final size:25
Alignment explanation
Indices: 1057352--1057502 Score: 71
Period size: 26 Copynumber: 5.9 Consensus size: 25
1057342 TTTATTAAAA
* *
1057352 TATTTTAACATATAAATA-ATAATAT
1 TATTATAA-ATATAAAAATATAATAT
* * *
1057377 TCAATATTAAATATAAAAATTTTAT-T
1 T-ATTA-TAAATATAAAAATATAATAT
*
1057403 ATATTATTAA-ATAAAAATATAATAT
1 -TATTATAAATATAAAAATATAATAT
* * * *
1057428 CT-TATATTATTATAATAAT-TGATTAT
1 -TAT-TATAAATATAAAAATAT-AATAT
* *
1057454 T-TTATATATATTAAAAAAATAATAT
1 TATTATAAATA-TAAAAATATAATAT
1057479 TATTATAAATATAATAAATATAAT
1 TATTATAAATATAA-AAATATAAT
1057503 GATATTTTGA
Statistics
Matches: 93, Mismatches: 21, Indels: 23
0.68 0.15 0.17
Matches are distributed among these distances:
24 17 0.18
25 27 0.29
26 42 0.45
27 7 0.08
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (25 bp):
TATTATAAATATAAAAATATAATAT
Found at i:1057732 original size:42 final size:42
Alignment explanation
Indices: 1057681--1057795 Score: 153
Period size: 42 Copynumber: 2.8 Consensus size: 42
1057671 ATCAATTACA
*
1057681 TTCCGGAAAATCAATTACGTAAAACAAACACGGGAAAACATT
1 TTCCGGAAAATCAATTACGTGAAACAAACACGGGAAAACATT
* * *
1057723 TTCCGGAAAA-CGAACTACATGAAACAAATACGGGAAAACATT
1 TTCCGGAAAATC-AATTACGTGAAACAAACACGGGAAAACATT
* *
1057765 TTCC-AAAAATGAATTACGTGAAACAAACACG
1 TTCCGGAAAATCAATTACGTGAAACAAACACG
1057796 AAAATTTGAG
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
41 22 0.35
42 40 0.65
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.18
Consensus pattern (42 bp):
TTCCGGAAAATCAATTACGTGAAACAAACACGGGAAAACATT
Found at i:1066688 original size:2 final size:2
Alignment explanation
Indices: 1066681--1066737 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
1066671 ATTTGTTTTA
1066681 AT AT AT AT AT AT AT AT AT AT A- 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
1066722 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1066738 CTTACTAATT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1068105 original size:10 final size:10
Alignment explanation
Indices: 1068092--1068117 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1068082 ATAACTTGTG
1068092 ATAAGGCAGC
1 ATAAGGCAGC
1068102 ATAAGGCAGC
1 ATAAGGCAGC
1068112 ATAAGG
1 ATAAGG
1068118 GTTAGAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.15, G:0.31, T:0.12
Consensus pattern (10 bp):
ATAAGGCAGC
Found at i:1069615 original size:3 final size:3
Alignment explanation
Indices: 1069607--1069634 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1069597 GCTAATGAAT
1069607 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1069635 GTATGGCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1073029 original size:44 final size:44
Alignment explanation
Indices: 1072979--1073063 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
1072969 ACTCAAGATT
* * *
1072979 TGACATATCATATTTCTTTTTTATGTCGTCGATAAATAATGATA
1 TGACATATCATATTTATTCTTTATGTCGTCAATAAATAATGATA
* * *
1073023 TGACATATCATGTTTATTCTTTATGTGGTCAATAAGTAATG
1 TGACATATCATATTTATTCTTTATGTCGTCAATAAATAATG
1073064 GTCTATAGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.45
Consensus pattern (44 bp):
TGACATATCATATTTATTCTTTATGTCGTCAATAAATAATGATA
Found at i:1075231 original size:26 final size:25
Alignment explanation
Indices: 1075184--1075235 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
1075174 TTAGGAGTGA
*
1075184 ACTTATACAATTTTAAGAAGATATAT
1 ACTTATAAAATTTTAAGAAGAT-TAT
* *
1075210 ACTTATAAAATTTTAGGGAGATTAT
1 ACTTATAAAATTTTAAGAAGATTAT
1075235 A
1 A
1075236 ATAGATGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (25 bp):
ACTTATAAAATTTTAAGAAGATTAT
Found at i:1078576 original size:21 final size:21
Alignment explanation
Indices: 1078537--1078577 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1078527 AAATATAAAC
* *
1078537 AATTTTAAATTTTATTTTTAG
1 AATTTTAAATTTAAATTTTAG
*
1078558 AATTTTTAATTTAAATTTTA
1 AATTTTAAATTTAAATTTTA
1078578 AATAATTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
AATTTTAAATTTAAATTTTAG
Found at i:1079439 original size:15 final size:17
Alignment explanation
Indices: 1079419--1079455 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
1079409 CTACTTATGA
1079419 TATAATA-TAATTT-TT
1 TATAATATTAATTTATT
*
1079434 TATAATATTTATTTATT
1 TATAATATTAATTTATT
1079451 TATAA
1 TATAA
1079456 AAAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 5 0.26
17 7 0.37
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATAATATTAATTTATT
Found at i:1079476 original size:27 final size:26
Alignment explanation
Indices: 1079440--1079528 Score: 83
Period size: 28 Copynumber: 3.3 Consensus size: 26
1079430 TTTTTATAAT
1079440 ATTTATTTATTTATAAAAAAATTAAA
1 ATTTATTTATTTATAAAAAAATTAAA
*
1079466 ATTTATATTATTTTATAAATAAATATCATAA
1 ATTTAT-TTA-TTTATAAA-AAA-ATTA-AA
* *
1079497 ATTTATTT-TTTA-AAACAAATTAAT
1 ATTTATTTATTTATAAAAAAATTAAA
*
1079521 ATTGATTT
1 ATTTATTT
1079529 TATAAAATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
24 8 0.15
25 3 0.06
26 8 0.15
27 6 0.11
28 12 0.23
29 3 0.06
30 5 0.09
31 8 0.15
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (26 bp):
ATTTATTTATTTATAAAAAAATTAAA
Found at i:1079489 original size:22 final size:22
Alignment explanation
Indices: 1079464--1079534 Score: 52
Period size: 26 Copynumber: 3.0 Consensus size: 22
1079454 AAAAAAATTA
*
1079464 AAATTTATATTATTTTATAAAT
1 AAATTTATATTATTTTATAAAC
* *
1079486 AAATATCATAAATTTATTTTTTAAAAC
1 AAAT-T--TATA-TTATTTTAT-AAAC
*
1079513 AAATTAATATTGATTTTATAAA
1 AAATTTATATT-ATTTTATAAA
1079535 ATATATAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
22 4 0.11
23 6 0.16
24 8 0.22
25 3 0.08
26 9 0.24
27 7 0.19
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (22 bp):
AAATTTATATTATTTTATAAAC
Found at i:1079545 original size:24 final size:23
Alignment explanation
Indices: 1079470--1079552 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 23
1079460 ATTAAAATTT
1079470 ATATTATTTTATAAATAAATATCATAA
1 ATATTATTTTAT--A-AAATAT-ATAA
* * * *
1079497 AT-TTATTTTTTAAAACAAATTA
1 ATATTATTTTATAAAATATATAA
1079519 ATATTGATTTTATAAAATATATAA
1 ATATT-ATTTTATAAAATATATAA
1079543 ATAATTATTT
1 AT-ATTATTT
1079553 GATTATTTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
22 5 0.11
23 6 0.13
24 21 0.47
25 3 0.07
26 8 0.18
27 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (23 bp):
ATATTATTTTATAAAATATATAA
Found at i:1082711 original size:24 final size:23
Alignment explanation
Indices: 1082667--1082733 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
1082657 TCAAATAATC
* * *
1082667 AAAAAACGTGTCA-AAATACATAA
1 AAAAAACATATCATAAAGACAT-A
1082690 AAAAAACATATCATAAAGACATA
1 AAAAAACATATCATAAAGACATA
* * *
1082713 TAAAATCATATCATACAGACA
1 AAAAAACATATCATAAAGACA
1082734 AAGTAAATAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
23 30 0.81
24 7 0.19
ACGTcount: A:0.60, C:0.15, G:0.06, T:0.19
Consensus pattern (23 bp):
AAAAAACATATCATAAAGACATA
Found at i:1082741 original size:23 final size:23
Alignment explanation
Indices: 1082691--1082740 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1082681 AATACATAAA
* *
1082691 AAAAACATATCATAAAGACATAT
1 AAAATCATATCATAAAGACAAAT
*
1082714 AAAATCATATCATACAGACAAAGT
1 AAAATCATATCATAAAGACAAA-T
1082738 AAA
1 AAA
1082741 TACAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.06, T:0.20
Consensus pattern (23 bp):
AAAATCATATCATAAAGACAAAT
Found at i:1084000 original size:60 final size:60
Alignment explanation
Indices: 1083899--1084089 Score: 160
Period size: 60 Copynumber: 3.2 Consensus size: 60
1083889 CATTACATGA
* * ** *
1083899 CCTCAAAGTATAA-CTCTCATTTTAAATT-GATCCATAAACTTTTAAATATTCCAATTGT-AT
1 CCTCAAACTATAACCT-TCATTCTAAATTAG-TCCCCAAACTTTTAAATATTACAATT-TCAT
* * ** * **
1083959 CC-CTAAACTATAA-TTATCATTCTAAATTAGTCCTCAAACTTTTGGACATTTTAATTTCAT
1 CCTC-AAACTATAACCT-TCATTCTAAATTAGTCCCCAAACTTTTAAATATTACAATTTCAT
* *
1084019 CCTCAAACTATAACCTTCATTCTAAATTGGTCCCCAAACTTTTTAAATATTACAATTTCTT
1 CCTCAAACTATAACCTTCATTCTAAATTAGTCCCCAAAC-TTTTAAATATTACAATTTCAT
1084080 CC-CAAACTAT
1 CCTCAAACTAT
1084090 TCATATGTAC
Statistics
Matches: 105, Mismatches: 20, Indels: 12
0.77 0.15 0.09
Matches are distributed among these distances:
59 2 0.02
60 83 0.79
61 20 0.19
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (60 bp):
CCTCAAACTATAACCTTCATTCTAAATTAGTCCCCAAACTTTTAAATATTACAATTTCAT
Found at i:1084317 original size:15 final size:15
Alignment explanation
Indices: 1084297--1084325 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1084287 TGGCCGACCG
1084297 AACCGAATTAACCAT
1 AACCGAATTAACCAT
1084312 AACCGAATTAACCA
1 AACCGAATTAACCA
1084326 AACTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.28, G:0.07, T:0.17
Consensus pattern (15 bp):
AACCGAATTAACCAT
Found at i:1084604 original size:131 final size:127
Alignment explanation
Indices: 1084469--1084730 Score: 321
Period size: 127 Copynumber: 2.0 Consensus size: 127
1084459 AATTAAATAT
* * *
1084469 TTTTAATTCAAAAAAGTTTA-TAATTAA-TTTAAATATTAAATAATTATAAAATAAAAATTTTAG
1 TTTTAAAT-AAAAAAGTTTAGCAA-TAATTTTAAATAATAAATAATTAT-AAA-AAAAA-TTTAG
*
1084532 ATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAATTATTAATT
61 AT-AAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAAATATTAATT
1084597 GGG
125 GGG
****** * * * * *
1084600 TTTTAAATGGTTTGGTTTAGCCATAATTTTAAATAATATATAATTATAAAAACAATTTATATAAT
1 TTTTAAATAAAAAAGTTTAGCAATAATTTTAAATAATAAATAATTATAAAAAAAATTTAGATAAA
1084665 TTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAAATATTAATTGGG
66 TTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAAATATTAATTGGG
1084727 TTTT
1 TTTT
1084731 TAATGATTTG
Statistics
Matches: 114, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
127 67 0.59
128 6 0.05
129 4 0.04
130 11 0.10
131 26 0.23
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (127 bp):
TTTTAAATAAAAAAGTTTAGCAATAATTTTAAATAATAAATAATTATAAAAAAAATTTAGATAAA
TTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAAAATATTAATTGGG
Found at i:1084693 original size:127 final size:131
Alignment explanation
Indices: 1084496--1084741 Score: 392
Period size: 127 Copynumber: 1.9 Consensus size: 131
1084486 TTATAATTAA
*
1084496 TTTAAATATTAAATAATTATAAAATAAAAATTTTAGATAAAATTTTTAATTAATTAATATTGATT
1 TTTAAATAATAAATAATTATAAAATAAAAATTTTAGATAAAATTTTTAATTAATTAATATTGATT
* *
1084561 TAAGTTTAAAAGTTATTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGTTTAGCCATAA
66 TAAGTTTAAAAGTTATTGGATCTTAAAATATTAATTGGGTTTTAAATGATTTGGTTTAGCCATAA
1084626 T
131 T
* * * *
1084627 TTTAAATAATATATAATTAT-AAA-AACAA-TTTATAT-AATTTTTTAATTAATTAATATTGATT
1 TTTAAATAATAAATAATTATAAAATAAAAATTTTAGATAAAATTTTTAATTAATTAATATTGATT
*
1084688 TAAGTTTAAAAGTTATTGGATCTTAAAATATTAATTGGGTTTTTAATGATTTGG
66 TAAGTTTAAAAGTTATTGGATCTTAAAATATTAATTGGGTTTTAAATGATTTGG
1084742 GTTGAGCTCA
Statistics
Matches: 107, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
127 76 0.71
128 6 0.06
129 4 0.04
130 3 0.03
131 18 0.17
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (131 bp):
TTTAAATAATAAATAATTATAAAATAAAAATTTTAGATAAAATTTTTAATTAATTAATATTGATT
TAAGTTTAAAAGTTATTGGATCTTAAAATATTAATTGGGTTTTAAATGATTTGGTTTAGCCATAA
T
Found at i:1086939 original size:31 final size:31
Alignment explanation
Indices: 1086901--1086965 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1086891 GATGCAAAGA
1086901 AAATACAAGAGATCGGGATTCCT-TTTTCGGG
1 AAATACAAGAGATCGGGATTCCTCTTTT-GGG
* *
1086932 AAATACAAGTGATCGGTATTCCTCTTTTGGG
1 AAATACAAGAGATCGGGATTCCTCTTTTGGG
1086963 AAA
1 AAA
1086966 CTAAGTAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (31 bp):
AAATACAAGAGATCGGGATTCCTCTTTTGGG
Found at i:1093380 original size:23 final size:23
Alignment explanation
Indices: 1093350--1093395 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1093340 CCAGGGATGG
1093350 GGGAGTTATGGATATTATCACGA
1 GGGAGTTATGGATATTATCACGA
1093373 GGGAGTTATGGATATTATCACGA
1 GGGAGTTATGGATATTATCACGA
1093396 CCATTGTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.30
Consensus pattern (23 bp):
GGGAGTTATGGATATTATCACGA
Found at i:1103359 original size:27 final size:29
Alignment explanation
Indices: 1103275--1103370 Score: 133
Period size: 27 Copynumber: 3.3 Consensus size: 29
1103265 AACAATGTAA
* *
1103275 TGTTCATGTTTATTTATTTATTTTGGAAGG
1 TGTTCATGTTTATTTATTTGTTTT-TAAGG
* *
1103305 TGTTCATGTTTGTTTGTTTGTTTTTAAGG
1 TGTTCATGTTTATTTATTTGTTTTTAAGG
1103334 TGTTCATG-TT-TTTATTTGTTTTTAAGG
1 TGTTCATGTTTATTTATTTGTTTTTAAGG
1103361 TGTTCATGTT
1 TGTTCATGTT
1103371 CTTGTTTGGT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
27 24 0.40
28 3 0.05
29 12 0.20
30 21 0.35
ACGTcount: A:0.15, C:0.04, G:0.21, T:0.60
Consensus pattern (29 bp):
TGTTCATGTTTATTTATTTGTTTTTAAGG
Found at i:1103378 original size:27 final size:27
Alignment explanation
Indices: 1103301--1103378 Score: 120
Period size: 27 Copynumber: 2.8 Consensus size: 27
1103291 TTTATTTTGG
1103301 AAGGTGTTCATGTTTGTTTGTTTGTTTTT
1 AAGGTGTTCATG-TT-TTTGTTTGTTTTT
*
1103330 AAGGTGTTCATGTTTTTATTTGTTTTT
1 AAGGTGTTCATGTTTTTGTTTGTTTTT
*
1103357 AAGGTGTTCATGTTCTTGTTTG
1 AAGGTGTTCATGTTTTTGTTTG
1103379 GTTTGTGTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 32 0.70
28 2 0.04
29 12 0.26
ACGTcount: A:0.13, C:0.05, G:0.23, T:0.59
Consensus pattern (27 bp):
AAGGTGTTCATGTTTTTGTTTGTTTTT
Found at i:1103617 original size:23 final size:23
Alignment explanation
Indices: 1103516--1103616 Score: 116
Period size: 23 Copynumber: 4.4 Consensus size: 23
1103506 TGTTCGTGAT
* * **
1103516 TGTTTATTTATTGTTCGCGAACA
1 TGTTTGTTTAATGTTCATGAACA
1103539 T-TTTGTTTAATGTTCATGAACA
1 TGTTTGTTTAATGTTCATGAACA
*
1103561 TGTTTGTTTAATGTTCATGAACT
1 TGTTTGTTTAATGTTCATGAACA
**
1103584 TGTTCATTTAGA-GTTCATGAACA
1 TGTTTGTTTA-ATGTTCATGAACA
1103607 TGTTTGTTTA
1 TGTTTGTTTA
1103617 GTATTCATTT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
22 18 0.27
23 47 0.71
24 1 0.02
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.50
Consensus pattern (23 bp):
TGTTTGTTTAATGTTCATGAACA
Found at i:1103623 original size:23 final size:23
Alignment explanation
Indices: 1103534--1103640 Score: 96
Period size: 23 Copynumber: 4.7 Consensus size: 23
1103524 TATTGTTCGC
* *
1103534 GAACAT-TTTGTTTAATGTTCAT
1 GAACATGTTTGTTTAGTATTCAT
* *
1103556 GAACATGTTTGTTTAATGTTCAT
1 GAACATGTTTGTTTAGTATTCAT
* **
1103579 GAACTTGTTCATTTAG-AGTTCAT
1 GAACATGTTTGTTTAGTA-TTCAT
1103602 GAACATGTTTGTTTAGTATTCATT
1 GAACATGTTTGTTTAGTATTCA-T
*
1103626 TAA-A-GTTTGTTTAGT
1 GAACATGTTTGTTTAGT
1103641 GTATGTCTAG
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
22 17 0.24
23 51 0.71
24 4 0.06
ACGTcount: A:0.26, C:0.08, G:0.17, T:0.49
Consensus pattern (23 bp):
GAACATGTTTGTTTAGTATTCAT
Found at i:1106397 original size:10 final size:11
Alignment explanation
Indices: 1106378--1106414 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1106368 TTTAAGTTTA
1106378 TAATATTTTTT
1 TAATATTTTTT
1106389 TAATA-TTTTT
1 TAATATTTTTT
1106399 TAA-ATTATTTT
1 TAATATT-TTTT
1106410 TAATA
1 TAATA
1106415 GAATATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 1 0.04
10 9 0.39
11 12 0.52
12 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TAATATTTTTT
Found at i:1108263 original size:21 final size:23
Alignment explanation
Indices: 1108224--1108267 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
1108214 TTATTTAATT
1108224 ATTACAAGGTAGTACCGATACTC
1 ATTACAAGGTAGTACCGATACTC
*
1108247 ATTA-AAGG-AGTATCGATACTC
1 ATTACAAGGTAGTACCGATACTC
1108268 CCTATTTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 4 0.20
23 4 0.20
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (23 bp):
ATTACAAGGTAGTACCGATACTC
Found at i:1120160 original size:3 final size:3
Alignment explanation
Indices: 1120152--1120186 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
1120142 ATCTCCATCC
1120152 TCT TCT TCT TCTT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT T
1120187 TTGTGTCGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:1121656 original size:27 final size:27
Alignment explanation
Indices: 1121618--1121678 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
1121608 ACGCAGAATA
*
1121618 TCACTTCTTCTATAGGAAAGTGGATTG
1 TCACATCTTCTATAGGAAAGTGGATTG
1121645 TCACATCTTCTATAGGAAAGTGGATTG
1 TCACATCTTCTATAGGAAAGTGGATTG
*
1121672 CCACATC
1 TCACATC
1121679 ATATGAACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (27 bp):
TCACATCTTCTATAGGAAAGTGGATTG
Found at i:1123955 original size:16 final size:16
Alignment explanation
Indices: 1123934--1123967 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1123924 TTACTATTCA
*
1123934 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
1123950 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
1123966 CG
1 CG
1123968 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:1136548 original size:21 final size:21
Alignment explanation
Indices: 1136524--1136563 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1136514 TTTATTTTAT
*
1136524 AACTTTATTTCAGTTATCGTA
1 AACTTTATTTCAATTATCGTA
*
1136545 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
1136564 AACTTGAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:1136611 original size:33 final size:33
Alignment explanation
Indices: 1136558--1136656 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1136548 TTTGTTTCAA
1136558 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1136590 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
1136623 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1136656 T
1 T
1136657 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:1136685 original size:13 final size:13
Alignment explanation
Indices: 1136642--1136696 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1136632 TTGGAAGTAT
1136642 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
1136655 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
1136669 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
1136682 TTAAGTATTTGAA
1 TTAAGTATTTCAA
1136695 TT
1 TT
1136697 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:1137117 original size:15 final size:15
Alignment explanation
Indices: 1137092--1137147 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
1137082 ATCTGGAATA
*
1137092 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
1137107 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
1137122 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
1137139 TTAAAACCG
1 TTAAAACCG
1137148 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:1137156 original size:21 final size:18
Alignment explanation
Indices: 1137111--1137144 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1137101 GTTTTTTTAT
1137111 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
1137128 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
1137145 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:1137264 original size:15 final size:17
Alignment explanation
Indices: 1137238--1137269 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1137228 TTCTACGGGA
1137238 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
1137254 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
1137270 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:1140330 original size:103 final size:103
Alignment explanation
Indices: 1140151--1140473 Score: 576
Period size: 103 Copynumber: 3.1 Consensus size: 103
1140141 GGTATACGCA
*
1140151 GTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
1 GTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
1140216 CTTGGTATATGTATATGATTCTTAAGGAATGATATGTG
66 CTTGGTATATGTATATGATTCTTAAGGAATGATATGTG
1140254 GTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
1 GTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
1140319 CTTGGTATATGTATATGATTCTTAAGGAATGATATGTG
66 CTTGGTATATGTATATGATTCTTAAGGAATGATATGTG
*
1140357 GTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
1 GTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
* * * *
1140422 CCTAGTATATATATATGATTCTTAAGGAATGATATGTA
66 CTTGGTATATGTATATGATTCTTAAGGAATGATATGTG
1140460 GTCCTT-ATGGACAT
1 GTCCTTCA-GGACAT
1140474 TATTATATGG
Statistics
Matches: 212, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
103 212 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
GTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
CTTGGTATATGTATATGATTCTTAAGGAATGATATGTG
Found at i:1140517 original size:23 final size:23
Alignment explanation
Indices: 1140482--1140549 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1140472 ATTATTATAT
*
1140482 GGCACTACAGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1140505 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
1140528 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
1140550 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1142388 original size:83 final size:83
Alignment explanation
Indices: 1142275--1142450 Score: 212
Period size: 83 Copynumber: 2.1 Consensus size: 83
1142265 TCTACCCATC
* * * *
1142275 ATCCAACCATTTGAAACTCTCGTCATCATCAAGAAT-TTATGCCAT-CTCACTCTATTAAATCGT
1 ATCCAACCATTTGAAACTCTCGCCATCATCAA-AATATTATACCATGCT-ACTCTACTAAATCAT
*
1142338 ACTTGAATCATCTAAAATTT
64 ACTTGAATCACCTAAAATTT
* * * * *
1142358 ATCCAACTATTTGAAGCTCTTGCCATCATCAAAATATTATACCATGCTGCTCTACTAAATTATAC
1 ATCCAACCATTTGAAACTCTCGCCATCATCAAAATATTATACCATGCTACTCTACTAAATCATAC
1142423 TTGAATCACCTAAAATTT
66 TTGAATCACCTAAAATTT
* *
1142441 GTCTAACCAT
1 ATCCAACCAT
1142451 CATCCAAGAA
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
82 3 0.04
83 73 0.94
84 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.35
Consensus pattern (83 bp):
ATCCAACCATTTGAAACTCTCGCCATCATCAAAATATTATACCATGCTACTCTACTAAATCATAC
TTGAATCACCTAAAATTT
Found at i:1155966 original size:73 final size:73
Alignment explanation
Indices: 1155874--1156021 Score: 199
Period size: 73 Copynumber: 2.0 Consensus size: 73
1155864 GTATTTTTTA
* * *
1155874 TAACATTCTATATACCATTTAGGTTTAATAATACTATTGTCTTTTTACT-AAAAGAAAATCAATT
1 TAACATTCGATATAACATTTAGGTTTAATAATACTATTGTCTTTTTACTGAAAA-AAAATCAACT
1155938 AAACTCTTT
65 AAACTCTTT
* * * * **
1155947 TAACATTCGGTATAACATTTAGGTTTGATAATATTGTTGTCTTTTTACTGGGAAAAAATCAACTA
1 TAACATTCGATATAACATTTAGGTTTAATAATACTATTGTCTTTTTACTGAAAAAAAATCAACTA
1156012 AACTCTTT
66 AACTCTTT
1156020 TA
1 TA
1156022 TATATATATA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
73 63 0.97
74 2 0.03
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (73 bp):
TAACATTCGATATAACATTTAGGTTTAATAATACTATTGTCTTTTTACTGAAAAAAAATCAACTA
AACTCTTT
Found at i:1170847 original size:14 final size:14
Alignment explanation
Indices: 1170825--1170868 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
1170815 CCTCTCTTTT
*
1170825 TTTTA-TATGATCA
1 TTTTACTATGAGCA
1170838 TTTTACTATGAGCA
1 TTTTACTATGAGCA
1170852 TTTTACTATGAGCA
1 TTTTACTATGAGCA
1170866 TTT
1 TTT
1170869 GCTTTATGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 5 0.17
14 24 0.83
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.50
Consensus pattern (14 bp):
TTTTACTATGAGCA
Found at i:1172758 original size:22 final size:21
Alignment explanation
Indices: 1172711--1172770 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
1172701 ATAGTTCGCT
1172711 AATAATAATA-TCTTTTCTAAA
1 AATAA-AATATTCTTTTCTAAA
* **
1172732 CATAAGGTATTCTTTCTCTAAA
1 AATAAAATATTCTTT-TCTAAA
1172754 AATAAAATATTCTTTTC
1 AATAAAATATTCTTTTC
1172771 CTAATAATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
20 2 0.06
21 11 0.35
22 18 0.58
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.43
Consensus pattern (21 bp):
AATAAAATATTCTTTTCTAAA
Found at i:1178409 original size:205 final size:209
Alignment explanation
Indices: 1177994--1178537 Score: 679
Period size: 205 Copynumber: 2.5 Consensus size: 209
1177984 CGAGTTGAGC
* * * * *
1177994 GAAACTTTATTTTGGTCTGGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGTGTCGGG-T
1 GAAACTTTATTTTGTTCGGGTCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTCGGGTTGGGTT
*
1178058 CAGGTTCAGTTTTAGGGTGAAAAAAACTAGACCGACCCGAAAATATATATAATTCAGGTCGGTCG
65 C-GG----G-TTTAGGGTGAAAAAAACTGGACCGACCCGAAAATATATATAATTCAGGTCGGTCG
***
1178123 GATTAAGTCAATGTTTTTATTAAATAAAAATATTTTTTTATTATTTTGAGTCGGGTCGGGTTGGA
124 GATTAAGTCAATGTTTTTATTAAAT---AATATTTTTTTATTA-TTT--GTCGGGTCGGGTCAAA
*
1178188 TTTCTAATTCATATATTCGGTTCGGAT
183 TTTCTAATTCATATATTCGGGTCGGAT
*
1178215 GAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTAATATTCGGGTCGGGTTGGGTTC
1 GAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTTGGGTTC
*
1178280 GGGTTTAGGGTGAAAAAAAACTGGACCGACCCGAAAATATATATAATTCGGGTCGGGTCGGATTA
66 GGGTTTAGGGTG-AAAAAAACTGGACCGACCCGAAAATATATATAATTCAGGTC-GGTCGGATTA
* *
1178345 AGTCACTGTTTTTATTAAAT-A-A-TTTTTT-TTA-TT-TCGGGTCGGGTCAAATTTCTAATTTA
129 AGTCAATGTTTTTATTAAATAATATTTTTTTATTATTTGTCGGGTCGGGTCAAATTTCTAATTCA
1178404 TATATTCGGGTCGGAT
194 TATATTCGGGTCGGAT
**
1178420 GAAACTTTATTTTGTTCGGGTCGGGTCATGTTTTTTAAGTGTGATATTCGGGTCAGGTCGGTTCG
1 GAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTC--G--GGTT-G
* * *
1178485 GGTTCGGGTTTAGGATGAAAAAAACCGGACCGACCCAAAAAATATATATAATT
61 GGTTCGGGTTTAGGGTGAAAAAAACTGGACCGACCC-GAAAATATATATAATT
1178538 TTACCTTATA
Statistics
Matches: 294, Mismatches: 20, Indels: 29
0.86 0.06 0.08
Matches are distributed among these distances:
205 88 0.30
207 1 0.00
208 2 0.01
209 22 0.07
210 35 0.12
211 6 0.02
212 1 0.00
213 1 0.00
215 9 0.03
216 40 0.14
217 29 0.10
220 31 0.11
221 29 0.10
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.37
Consensus pattern (209 bp):
GAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTTGGGTTC
GGGTTTAGGGTGAAAAAAACTGGACCGACCCGAAAATATATATAATTCAGGTCGGTCGGATTAAG
TCAATGTTTTTATTAAATAATATTTTTTTATTATTTGTCGGGTCGGGTCAAATTTCTAATTCATA
TATTCGGGTCGGAT
Found at i:1179435 original size:2 final size:2
Alignment explanation
Indices: 1179428--1179477 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
1179418 ATCATTTACC
1179428 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
1179470 AT AT -T AT A
1 AT AT AT AT A
1179478 CAGAGTTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1185864 original size:12 final size:12
Alignment explanation
Indices: 1185847--1185871 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1185837 ACATCCTTAC
1185847 TTCTCGGCGATA
1 TTCTCGGCGATA
1185859 TTCTCGGCGATA
1 TTCTCGGCGATA
1185871 T
1 T
1185872 ATAAATGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (12 bp):
TTCTCGGCGATA
Found at i:1189082 original size:27 final size:27
Alignment explanation
Indices: 1189050--1189103 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1189040 TTGAATCTTC
1189050 CATCACTTTACCAAATAATACAAAAAG
1 CATCACTTTACCAAATAATACAAAAAG
1189077 CATCACTTTACCAAATAATACAAAAAG
1 CATCACTTTACCAAATAATACAAAAAG
1189104 AATACTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.52, C:0.22, G:0.04, T:0.22
Consensus pattern (27 bp):
CATCACTTTACCAAATAATACAAAAAG
Found at i:1192055 original size:2 final size:2
Alignment explanation
Indices: 1192048--1192082 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1192038 GACTAAAAAG
1192048 TA TA TA TA 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 TA T
1192083 TTCATCCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1192414 original size:21 final size:21
Alignment explanation
Indices: 1192372--1192486 Score: 133
Period size: 21 Copynumber: 5.5 Consensus size: 21
1192362 ATTCTGACTA
* *
1192372 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTTCCTAAT
** *
1192393 TCGTGTTGTGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
1192414 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
* *
1192435 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTTCCTAAT
* *
1192455 TCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCCTAAT
*
1192476 TCGCAATGCGA
1 TCGCATTGCGA
1192487 ATACGTAAAT
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 17 0.22
21 61 0.78
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:1192416 original size:62 final size:62
Alignment explanation
Indices: 1192350--1192486 Score: 152
Period size: 62 Copynumber: 2.2 Consensus size: 62
1192340 CAGTTTCCAG
* * * * *
1192350 ATTCGCAACGCGATTCTGACT-A-TCGCATTGCGATTTCCCAAATTCGTGTTGTGATTTTCCTA
1 ATTCGCAATGCGATT-TGACTAATTCGCATTGCGATTT-ACAAATTCGCGTTGCGATTTTCATA
* ** **
1192412 ATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCATA
1 ATTCGCAATGCGATTTGACTAATTCGCATTGCGATTTACAAATTCGCGTTGCGATTTTCATA
1192474 ATTCGCAATGCGA
1 ATTCGCAATGCGA
1192487 ATACGTAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
61 3 0.05
62 45 0.73
63 14 0.23
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (62 bp):
ATTCGCAATGCGATTTGACTAATTCGCATTGCGATTTACAAATTCGCGTTGCGATTTTCATA
Found at i:1192519 original size:21 final size:20
Alignment explanation
Indices: 1192476--1192522 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
1192466 TTTTCATAAT
* *
1192476 TCGCAATGCGAATACGTAAA
1 TCGCAATGCAAATACGAAAA
*
1192496 TCGCAATGCAAATTAGGAAAA
1 TCGCAATGCAAA-TACGAAAA
1192517 TCGCAA
1 TCGCAA
1192523 ACGTAAATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAATGCAAATACGAAAA
Found at i:1193155 original size:19 final size:19
Alignment explanation
Indices: 1193113--1193183 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
1193103 TAGTTTCGAG
1193113 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
** *
1193133 AATGACTATCGTAACGCGA
1 AATGAAAATCGCAACGCGA
1193152 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
**
1193171 AACCAAAATCGCA
1 AATGAAAATCGCA
1193184 TTGCGATTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.67
20 14 0.33
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.13
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:1193201 original size:19 final size:19
Alignment explanation
Indices: 1193179--1193218 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1193169 GAAACCAAAA
1193179 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1193198 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1193217 TC
1 TC
1193219 AACCAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.23, G:0.17, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1195083 original size:94 final size:93
Alignment explanation
Indices: 1194893--1195268 Score: 616
Period size: 94 Copynumber: 4.1 Consensus size: 93
1194883 TAGATTGCTT
* *
1194893 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1194954 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
*
1194983 AGTAAATTTATTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1195048 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* *
1195077 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACGGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1195142 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
1195171 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1195236 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
1195264 AGTAA
1 AGTAA
1195269 TGCAATCCAT
Statistics
Matches: 271, Mismatches: 10, Indels: 7
0.94 0.03 0.02
Matches are distributed among these distances:
90 34 0.13
92 3 0.01
93 28 0.10
94 206 0.76
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:1195430 original size:19 final size:19
Alignment explanation
Indices: 1195365--1195421 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
1195355 GGTTGAAATA
* *
1195365 AAAATCGCAACGAGAGAATG
1 AAAATCGCAACGCGA-AACG
1195385 AAAATCGCAACGCGAAACG
1 AAAATCGCAACGCGAAACG
1195404 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
1195422 TATAATCGCG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 21 0.60
20 14 0.40
ACGTcount: A:0.49, C:0.23, G:0.21, T:0.07
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACG
Found at i:1195487 original size:33 final size:33
Alignment explanation
Indices: 1195430--1195524 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
1195420 ACTATAATCG
* * *
1195430 CGTTGCGATTTTTGGTTTCGCGTTGCGATTTTGT
1 CGTTGCGA-TTTTCGTTTCGCGTTGCGATTCTCT
*
1195464 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCGTTTCGCGTTGCGATTCTCT
1195497 CGTTGCGATTTTCGTTTCGCGTTGCGAT
1 CGTTGCGATTTTCGTTTCGCGTTGCGAT
1195525 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 48 0.86
34 8 0.14
ACGTcount: A:0.07, C:0.20, G:0.26, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCGTTTCGCGTTGCGATTCTCT
Found at i:1195488 original size:19 final size:18
Alignment explanation
Indices: 1195427--1195524 Score: 77
Period size: 19 Copynumber: 5.7 Consensus size: 18
1195417 GAAACTATAA
*
1195427 TCGCGTTGCGATTTTTGGTT
1 TCGCGTTGCGA-TTTT-CTT
*
1195447 TCGCGTTGCGA-TTT-TG
1 TCGCGTTGCGATTTTCTT
1195463 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
1195480 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCTT
*
1195494 TCTCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTC-TT
1195513 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1195525 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 21
0.72 0.04 0.24
Matches are distributed among these distances:
14 18 0.28
15 3 0.05
16 5 0.08
17 5 0.08
18 3 0.05
19 19 0.30
20 11 0.17
ACGTcount: A:0.07, C:0.20, G:0.27, T:0.46
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCTT
Found at i:1196037 original size:42 final size:41
Alignment explanation
Indices: 1195945--1196037 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 41
1195935 GCCCGACTCG
* * * * *
1195945 CCTGTCATCCCTCAAGAGTCTACTCCTATCGTTGAAGAGGC
1 CCTGTCATTCCTCAAGAGTCCACTCCCACCGTTCAAGAGGC
* * *
1195986 CCATATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGC
1 CC-TGTCATTCCTCAAGAGTCCACTCCCACCGTTCAAGAGGC
1196028 CACTGTCATT
1 C-CTGTCATT
1196038 GTAACACCCC
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
41 2 0.05
42 38 0.93
43 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.17, T:0.26
Consensus pattern (41 bp):
CCTGTCATTCCTCAAGAGTCCACTCCCACCGTTCAAGAGGC
Found at i:1196771 original size:30 final size:30
Alignment explanation
Indices: 1196737--1196803 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
1196727 CCCGAAGGAC
* *
1196737 CTATCTAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1196767 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAA
*
1196797 CTGTCCA
1 CTATCCA
1196804 TATGTTCCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCAGTAA
Found at i:1196834 original size:31 final size:31
Alignment explanation
Indices: 1196795--1196891 Score: 124
Period size: 31 Copynumber: 3.1 Consensus size: 31
1196785 GATCCTCAGT
*
1196795 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
* * *
1196826 TACTGTCCATATGTCTCGAAAG-ACATAGGTAA
1 AACTGTCCATATGT-TCCATAGAACATAGGT-A
*
1196858 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
1196889 AAC
1 AAC
1196892 CCTTGACTCT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
31 29 0.53
32 26 0.47
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.29
Consensus pattern (31 bp):
AACTGTCCATATGTTCCATAGAACATAGGTA
Found at i:1198419 original size:21 final size:21
Alignment explanation
Indices: 1198387--1198428 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1198377 ATGTTGTTCG
* *
1198387 TTTGAAGAGGTATCGGTTCCC
1 TTTGAAGAGGTACCGATTCCC
1198408 TTTGAATG-GGTACCGATTCCC
1 TTTGAA-GAGGTACCGATTCCC
1198429 CTTGCCCAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.33
Consensus pattern (21 bp):
TTTGAAGAGGTACCGATTCCC
Found at i:1201749 original size:30 final size:30
Alignment explanation
Indices: 1201715--1201781 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
1201705 CCCGAATGAC
*
1201715 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATACTCGGTAA
1201745 CTATCCAGAGGTCATAAAGATACTCGGTAA
1 CTATCCAGAGGTCATAAAGATACTCGGTAA
*
1201775 CTGTCCA
1 CTATCCA
1201782 TATGTTCCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATACTCGGTAA
Found at i:1201812 original size:31 final size:30
Alignment explanation
Indices: 1201770--1201867 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 30
1201760 AAAGATACTC
*
1201770 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCATAGAACATA
* *
1201800 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCATAGAACATA
*
1201831 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCATAGAACATA
1201863 GGTAA
1 GGTAA
1201868 ACCCTCGACT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
30 6 0.11
31 25 0.44
32 25 0.44
33 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCATAGAACATA
Found at i:1203402 original size:21 final size:21
Alignment explanation
Indices: 1203378--1203419 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1203368 ATGTTGTTCG
*
1203378 TTTGAAGGGGTATCGGTTCCC
1 TTTGAAGGGGTATCGATTCCC
*
1203399 TTTGAATGGGTATCGATTCCC
1 TTTGAAGGGGTATCGATTCCC
1203420 CTTGCCCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.36
Consensus pattern (21 bp):
TTTGAAGGGGTATCGATTCCC
Found at i:1205611 original size:19 final size:19
Alignment explanation
Indices: 1205589--1205654 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
1205579 AAAAATGACT
*
1205589 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1205608 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
1205622 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1205641 ACCGCAACGCGAAA
1 ATCGCAACGCGAAA
1205655 CTAAATTCGC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 23 0.59
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.09
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1205708 original size:33 final size:33
Alignment explanation
Indices: 1205664--1205757 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
1205654 ACTAAATTCG
* *
1205664 CGTTGCAATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* *
1205697 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1205730 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1205758 AGTCATTTCC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:1205756 original size:19 final size:19
Alignment explanation
Indices: 1205699--1205777 Score: 69
Period size: 19 Copynumber: 4.4 Consensus size: 19
1205689 GATTCCCTCG
1205699 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
1205718 TTGTGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1205732 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
1205751 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
1205771 TTGCGAT
1 TTGCGAT
1205778 AGACATTAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
14 5 0.11
16 7 0.15
17 7 0.15
19 18 0.38
20 10 0.21
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1205776 original size:20 final size:20
Alignment explanation
Indices: 1205730--1205823 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
1205720 GTGATTCTCT
**
1205730 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
1205749 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
1205769 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
1205788 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
1205810 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
1205824 AATGAATGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1207111 original size:24 final size:24
Alignment explanation
Indices: 1207077--1207144 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
1207067 TCTGAAAAAT
1207077 ATCAAAATCCGAATATTGACCAAG
1 ATCAAAATCCGAATATTGACCAAG
* **
1207101 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAATATTGACCAAG
* * *
1207125 ATCAAATTTCGAATACTGAC
1 ATCAAAATCCGAATATTGAC
1207145 TAGTACTCAC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAATATTGACCAAG
Found at i:1208017 original size:21 final size:21
Alignment explanation
Indices: 1207993--1208059 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
1207983 AGAATCTCGT
1207993 TGCGAATTAGGAAAATCGCAA
1 TGCGAATTAGGAAAATCGCAA
* * *
1208014 TGCG-ATTACGTAAATTG-AA
1 TGCGAATTAGGAAAATCGCAA
1208033 GTGCGAATTAGGAAAATCGCAA
1 -TGCGAATTAGGAAAATCGCAA
1208055 TGCGA
1 TGCGA
1208060 TTACGTGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 14 0.38
21 19 0.51
22 2 0.05
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.22
Consensus pattern (21 bp):
TGCGAATTAGGAAAATCGCAA
Found at i:1208028 original size:20 final size:20
Alignment explanation
Indices: 1208005--1208065 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
1207995 CGAATTAGGA
1208005 AAATCGCAATGCGATTACGT
1 AAATCGCAATGCGATTACGT
* * *
1208025 AAATTG-AAGTGCGAATTAGGA
1 AAATCGCAA-TGCG-ATTACGT
1208046 AAATCGCAATGCGATTACGT
1 AAATCGCAATGCGATTACGT
1208066 GCGATTACGG
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
19 2 0.06
20 14 0.44
21 14 0.44
22 2 0.06
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.25
Consensus pattern (20 bp):
AAATCGCAATGCGATTACGT
Found at i:1213315 original size:5 final size:5
Alignment explanation
Indices: 1213305--1213329 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1213295 AAGCTATATC
1213305 GTTTT GTTTT GTTTT GTTTT GTTTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT
1213330 CAGATTAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
GTTTT
Found at i:1216845 original size:14 final size:16
Alignment explanation
Indices: 1216801--1216843 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
1216791 CCATATACAC
* *
1216801 TAAACTAATAAATTAG
1 TAAAATAATATATTAG
1216817 TAAAATAATATATTAG
1 TAAAATAATATATTAG
*
1216833 TAAATTAATAT
1 TAAAATAATAT
1216844 TAATTTGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (16 bp):
TAAAATAATATATTAG
Found at i:1220687 original size:6 final size:6
Alignment explanation
Indices: 1220676--1220732 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
1220666 GACACGTATT
1220676 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1220724 ACCACG ACC
1 ACCACG ACC
1220733 CGAGACGGAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1221374 original size:20 final size:20
Alignment explanation
Indices: 1221349--1221445 Score: 122
Period size: 20 Copynumber: 4.8 Consensus size: 20
1221339 ACTGTAGACT
1221349 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
1221369 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
1221390 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
*
1221410 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
1221430 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
1221446 CAACGCGAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 49 0.77
21 15 0.23
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1232162 original size:20 final size:20
Alignment explanation
Indices: 1232135--1232184 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
1232125 ATTAACCAAA
1232135 ATAT-TAAATATTTA-ATAT
1 ATATATAAATATTTATATAT
1232153 ATTATATAAATA-TTATATAT
1 A-TATATAAATATTTATATAT
*
1232173 ATATATACATAT
1 ATATATAAATAT
1232185 ATATTAAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 1 0.04
19 15 0.56
20 11 0.41
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATATAAATATTTATATAT
Found at i:1232185 original size:27 final size:27
Alignment explanation
Indices: 1232133--1232187 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1232123 GAATTAACCA
* *
1232133 AAATATTAAATATTTAATATATTATAT
1 AAATATTAAATATATAATATAATATAT
*
1232160 AAATATTATATATAT-ATATACATATAT
1 AAATATTAAATATATAATATA-ATATAT
1232187 A
1 A
1232188 TTAAGATTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
AAATATTAAATATATAATATAATATAT
Found at i:1232899 original size:40 final size:40
Alignment explanation
Indices: 1232839--1232920 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
1232829 TGCAAGTTAC
* *
1232839 ATCCACGTTATCATAGTAATTATTGGTTGGAGATTCATTA
1 ATCCACGTCATCATAATAATTATTGGTTGGAGATTCATTA
* *
1232879 ATCCACGTCATCATAATAATTATTGTTTGGGGATTCATTA
1 ATCCACGTCATCATAATAATTATTGGTTGGAGATTCATTA
1232919 AT
1 AT
1232921 GAACTAAGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.40
Consensus pattern (40 bp):
ATCCACGTCATCATAATAATTATTGGTTGGAGATTCATTA
Found at i:1239854 original size:14 final size:14
Alignment explanation
Indices: 1239835--1239864 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1239825 CATTTAAATG
1239835 ATAAACGAACACAA
1 ATAAACGAACACAA
*
1239849 ATAAACGAACATAA
1 ATAAACGAACACAA
1239863 AT
1 AT
1239865 GAACTGATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.17, G:0.07, T:0.13
Consensus pattern (14 bp):
ATAAACGAACACAA
Found at i:1240229 original size:21 final size:21
Alignment explanation
Indices: 1240203--1240271 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
1240193 CATATTCACA
*
1240203 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
1240224 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
* *
1240245 TTGCGATAGTTGATGTTCGCG
1 TTGCGATAGTCGAAGTTCGCG
1240266 TTGCGA
1 TTGCGA
1240272 ATCTGGAAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.17, C:0.19, G:0.32, T:0.32
Consensus pattern (21 bp):
TTGCGATAGTCGAAGTTCGCG
Found at i:1241497 original size:21 final size:22
Alignment explanation
Indices: 1241476--1241518 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
1241466 TTTTATTTAA
1241476 ATTAA-ATTATAAAATATATAAAT
1 ATTAATATTA-AAAATATAT-AAT
1241499 ATTAATATTAAAAATATATA
1 ATTAATATTAAAAATATATA
1241519 TTAAATGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 1 0.05
23 14 0.74
24 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTAATATTAAAAATATATAAT
Found at i:1242166 original size:34 final size:32
Alignment explanation
Indices: 1242128--1242216 Score: 99
Period size: 33 Copynumber: 2.7 Consensus size: 32
1242118 AAATGAAAGG
1242128 AAAAATAATAAAGAAAA-AATAAGAGAAAAAAATT
1 AAAAATAATAAA-AAAATAA-AA-AGAAAAAAATT
* *
1242162 AAAAATATTAAAAAAATAAAAAGGAAAAAATT
1 AAAAATAATAAAAAAATAAAAAGAAAAAAATT
* *
1242194 AAAAAAAAGTAAAAAATTAAAAA
1 AAAAATAA-TAAAAAAATAAAAA
1242217 ATGAAATGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
32 16 0.33
33 19 0.40
34 13 0.27
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.16
Consensus pattern (32 bp):
AAAAATAATAAAAAAATAAAAAGAAAAAAATT
Found at i:1242171 original size:9 final size:9
Alignment explanation
Indices: 1242153--1242217 Score: 50
Period size: 9 Copynumber: 7.7 Consensus size: 9
1242143 AAAATAAGAG
1242153 AAAAAAATT
1 AAAAAAATT
*
1242162 AAAAATATT
1 AAAAAAATT
1242171 AAAAAAA-T
1 AAAAAAATT
*
1242179 --AAAAA-G
1 AAAAAAATT
*
1242185 GAAAAAATT
1 AAAAAAATT
*
1242194 AAAAAAAAGT
1 -AAAAAAATT
1242204 -AAAAAATT
1 AAAAAAATT
1242212 AAAAAA
1 AAAAAA
1242218 TGAAATGAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
6 5 0.11
8 13 0.30
9 19 0.43
10 7 0.16
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (9 bp):
AAAAAAATT
Found at i:1242200 original size:18 final size:18
Alignment explanation
Indices: 1242179--1242217 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1242169 TTAAAAAAAT
1242179 AAAAAGGAAAAAATTAAA
1 AAAAAGGAAAAAATTAAA
*
1242197 AAAAAGTAAAAAATTAAA
1 AAAAAGGAAAAAATTAAA
1242215 AAA
1 AAA
1242218 TGAAATGAAA
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:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (18 bp):
AAAAAGGAAAAAATTAAA
Found at i:1242218 original size:8 final size:8
Alignment explanation
Indices: 1242154--1242218 Score: 60
Period size: 8 Copynumber: 7.9 Consensus size: 8
1242144 AAATAAGAGA
1242154 AAAAAATT
1 AAAAAATT
1242162 AAAAATATT
1 AAAAA-ATT
*
1242171 AAAAAAAT
1 AAAAAATT
**
1242179 -AAAAAGG
1 AAAAAATT
1242186 AAAAAATT
1 AAAAAATT
*
1242194 AAAAAAAAGT
1 --AAAAAATT
1242204 AAAAAATT
1 AAAAAATT
1242212 AAAAAAT
1 AAAAAAT
1242219 GAAATGAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
7 5 0.11
8 26 0.57
9 8 0.17
10 7 0.15
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (8 bp):
AAAAAATT
Found at i:1242233 original size:41 final size:42
Alignment explanation
Indices: 1242128--1242231 Score: 113
Period size: 40 Copynumber: 2.5 Consensus size: 42
1242118 AAATGAAAGG
** *
1242128 AAAAATAATAAAGAAAAAATAAGAGAAAAAAATTAAAAATATTAA
1 AAAAATAA-AAAGAAAAAA-ATTA-AAAAAAAGTAAAAATATTAA
*
1242173 AAAAATAAAAAGGAAAAAATTAAAAAAAAGTAAAAA-ATT-A
1 AAAAATAAAAAGAAAAAAATTAAAAAAAAGTAAAAATATTAA
* *
1242213 AAAAATGAAATGAAAAAAA
1 AAAAATAAAAAGAAAAAAA
1242232 ATGTTAAATT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
40 17 0.33
41 3 0.06
42 13 0.25
43 2 0.04
44 9 0.17
45 8 0.15
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (42 bp):
AAAAATAAAAAGAAAAAAATTAAAAAAAAGTAAAAATATTAA
Found at i:1242305 original size:16 final size:15
Alignment explanation
Indices: 1242272--1242322 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
1242262 AATAAGAAGC
*
1242272 AAAAAATAAATAAA-T
1 AAAAAAT-ACTAAATT
1242287 AAAAACATACTAAATT
1 AAAAA-ATACTAAATT
*
1242303 AAAAAATGCTAAAATT
1 AAAAAATACT-AAATT
1242319 AAAA
1 AAAA
1242323 TGAAAATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 14 0.45
16 17 0.55
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.22
Consensus pattern (15 bp):
AAAAAATACTAAATT
Found at i:1243228 original size:40 final size:41
Alignment explanation
Indices: 1243116--1243264 Score: 136
Period size: 41 Copynumber: 3.7 Consensus size: 41
1243106 ATAATAATAA
*
1243116 ATATATTTACAAATA-TTTT-AAAACTATATATTATATATATAT
1 ATATATTCA-AAATAGTTTTAAAAAC-A-ATATTATATATATAT
* * *
1243158 ATATATTTTAAAAAAGTTTTCAAAAC--TA-TATAT-TATAT
1 ATATA-TTCAAAATAGTTTTAAAAACAATATTATATATATAT
1243196 AGT-T-TTCAAAAT-GTTTTAAAAACAATATTATATATATAT
1 A-TATATTCAAAATAGTTTTAAAAACAATATTATATATATAT
* *
1243235 ATATATTCAAAATATTTTTAAAAACCATAT
1 ATATATTCAAAATAGTTTTAAAAACAATAT
1243265 ATTTTCAAAA
Statistics
Matches: 90, Mismatches: 6, Indels: 23
0.76 0.05 0.19
Matches are distributed among these distances:
35 10 0.11
36 6 0.07
37 2 0.02
38 13 0.14
39 13 0.14
40 10 0.11
41 14 0.16
42 9 0.10
43 8 0.09
44 5 0.06
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (41 bp):
ATATATTCAAAATAGTTTTAAAAACAATATTATATATATAT
Found at i:1243273 original size:28 final size:28
Alignment explanation
Indices: 1243233--1243295 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
1243223 TTATATATAT
*
1243233 ATATATATTCAAAATATTTTTAAAAACC
1 ATATATTTTCAAAATATTTTTAAAAACC
*
1243261 ATATATTTTCAAAATGTTTTTAAAAACC
1 ATATATTTTCAAAATATTTTTAAAAACC
1243289 ATATATT
1 ATATATT
1243296 ATATAAGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.43
Consensus pattern (28 bp):
ATATATTTTCAAAATATTTTTAAAAACC
Found at i:1243280 original size:79 final size:78
Alignment explanation
Indices: 1243126--1243267 Score: 191
Period size: 76 Copynumber: 1.8 Consensus size: 78
1243116 ATATATTTAC
* * *
1243126 AAATATTTTAAAACTATATATTATATATATATATATATTTTAAAAAAGTTTTCAAAACTATATAT
1 AAATATTTTAAAACTATATATTATATATATATATATATTTCAAAAAAGTTTTAAAAACCATATAT
*
1243191 TATATAGTTTTCA
66 TATAAAGTTTTCA
* * *
1243204 AAATGTTTTAAAAAC-A-ATATTATATATATATATATA-TTCAAAATATTTTTAAAAACCATATA
1 AAATATTTT-AAAACTATATATTATATATATATATATATTTCAAAAAAGTTTTAAAAACCATATA
1243266 TT
65 TT
1243268 TTCAAAATGT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
76 23 0.40
77 20 0.35
78 9 0.16
79 5 0.09
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (78 bp):
AAATATTTTAAAACTATATATTATATATATATATATATTTCAAAAAAGTTTTAAAAACCATATAT
TATAAAGTTTTCA
Found at i:1243316 original size:37 final size:36
Alignment explanation
Indices: 1243261--1243521 Score: 181
Period size: 37 Copynumber: 7.4 Consensus size: 36
1243251 TTTAAAAACC
1243261 ATAT-ATTTTCAAAATGTTTTTAAAAACCATATATT
1 ATATAATTTTCAAAATGTTTTTAAAAACCATATATT
*
1243296 ATATAAGTTTTCAAAATGTTTTTAAAAACCATGTATT
1 ATATAA-TTTTCAAAATGTTTTTAAAAACCATATATT
** * * *
1243333 ATATAAGTTTTCAAAAACTATGT----A--TTATA-T
1 ATATAA-TTTTCAAAATGTTTTTAAAAACCATATATT
* * * * *
1243363 ATAT-GTTTTTAAAATATTTTCAAAAACTATATATT
1 ATATAATTTTCAAAATGTTTTTAAAAACCATATATT
* *
1243398 ATATATATTTTCAAAATGTTTTCAAAAACTATATATT
1 ATATA-ATTTTCAAAATGTTTTTAAAAACCATATATT
* *
1243435 ATAT-ATTTTCAAAAATAG-TTTTCAAAA-C-TATAAT
1 ATATAATTTTC-AAAAT-GTTTTTAAAAACCATATATT
** * *
1243469 ATATATATTTTCAAAAATCATTTTCAAAACCATATAAT
1 ATATA-ATTTTC-AAAATGTTTTTAAAAACCATATATT
1243507 ATAT-ATATTTCAAAA
1 ATATAAT-TTTCAAAA
1243522 ATCATTTGTA
Statistics
Matches: 184, Mismatches: 23, Indels: 37
0.75 0.09 0.15
Matches are distributed among these distances:
28 10 0.05
30 5 0.03
31 3 0.02
32 1 0.01
33 1 0.01
34 13 0.07
35 15 0.08
36 40 0.22
37 86 0.47
38 10 0.05
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (36 bp):
ATATAATTTTCAAAATGTTTTTAAAAACCATATATT
Found at i:1243320 original size:65 final size:66
Alignment explanation
Indices: 1243192--1243397 Score: 224
Period size: 65 Copynumber: 3.1 Consensus size: 66
1243182 ACTATATATT
1243192 ATATAGTTTTCAAAATG-TTTTAAAAACAATATTATATATATATA-TATATTCAAAATATTTTTA
1 ATATA-TTTTCAAAATGTTTTTAAAAACAATA-TAT-TATATATAGT-T-TTCAAAATATTTTTA
1243255 AAAACC
61 AAAACC
* *
1243261 ATATATTTTCAAAATGTTTTTAAAAACCATATATTATATA-AGTTTTCAAAATGTTTTTAAAAAC
1 ATATATTTTCAAAATGTTTTTAAAAACAATATATTATATATAGTTTTCAAAATATTTTTAAAAAC
1243325 C
66 C
* * * * * * * *
1243326 ATGTATTAT-ATAA-GTTTTCAAAAACTATGTATTATATATATGTTTTTAAAATATTTTCAAAAA
1 ATATATTTTCAAAATGTTTTTAAAAACAATATATTATATATA-GTTTTCAAAATATTTTTAAAAA
*
1243389 CT
65 CC
1243391 ATATATT
1 ATATATT
1243398 ATATATATTT
Statistics
Matches: 120, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
63 22 0.18
64 4 0.03
65 53 0.44
66 2 0.02
67 7 0.06
68 14 0.12
69 18 0.15
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (66 bp):
ATATATTTTCAAAATGTTTTTAAAAACAATATATTATATATAGTTTTCAAAATATTTTTAAAAAC
C
Found at i:1243376 original size:28 final size:27
Alignment explanation
Indices: 1243310--1243376 Score: 100
Period size: 26 Copynumber: 2.5 Consensus size: 27
1243300 AAGTTTTCAA
1243310 AATGTTTTTAAAAACCATGTATTATAT
1 AATGTTTTTAAAAACCATGTATTATAT
* *
1243337 AA-GTTTTCAAAAACTATGTATTATAT
1 AATGTTTTTAAAAACCATGTATTATAT
1243363 ATATGTTTTTAAAA
1 A-ATGTTTTTAAAA
1243377 TATTTTCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 23 0.66
27 3 0.09
28 9 0.26
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (27 bp):
AATGTTTTTAAAAACCATGTATTATAT
Found at i:1243388 original size:102 final size:99
Alignment explanation
Indices: 1243143--1243451 Score: 324
Period size: 102 Copynumber: 3.0 Consensus size: 99
1243133 TTAAAACTAT
*
1243143 ATATTATATATATATATATATTTTAAAAAAGTTTTC-AAAACTATATATTATAT-AGTTTTCAAA
1 ATATTAT-TATATATATAT-TTTTAAAATA-TTTTCAAAAACTATATATTATATAAGTTTTCAAA
1243206 ATG-TTTTAAAAACAATATTATATATATATATATATTC-AAA
63 ATGTTTTTAAAAACAATA-TAT-TATATA-AT-T-TTCAAAA
* * * * * * *
1243246 ATATTTTTAAAAACCATATATTTTCAAAATGTTTTTAAAAACCATATATTATATAAGTTTTCAAA
1 ATATTATT--ATA-TATATATTTTTAAAATATTTTCAAAAACTATATATTATATAAGTTTTCAAA
* *
1243311 ATGTTTTTAAAAACCATGTATTATATAAGTTTTCAAAA
63 ATGTTTTTAAAAACAATATATTATATAA-TTTTCAAAA
*
1243349 ACTATGTATTATATATATGTTTTTAAAATATTTTCAAAAACTATATATTATATATA-TTTTCAAA
1 A-TAT-TATTATATATATATTTTTAAAATATTTTCAAAAACTATATATTATATA-AGTTTTCAAA
* *
1243413 ATGTTTTCAAAAACTATATATTATAT-ATTTTCAAAA
63 ATGTTTTTAAAAACAATATATTATATAATTTTCAAAA
1243449 ATA
1 ATA
1243452 GTTTTCAAAA
Statistics
Matches: 174, Mismatches: 21, Indels: 26
0.79 0.10 0.12
Matches are distributed among these distances:
99 2 0.01
100 10 0.06
101 1 0.01
102 70 0.40
103 19 0.11
104 35 0.20
105 25 0.14
106 12 0.07
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (99 bp):
ATATTATTATATATATATTTTTAAAATATTTTCAAAAACTATATATTATATAAGTTTTCAAAATG
TTTTTAAAAACAATATATTATATAATTTTCAAAA
Found at i:1243462 original size:36 final size:38
Alignment explanation
Indices: 1243338--1243523 Score: 228
Period size: 36 Copynumber: 5.0 Consensus size: 38
1243328 GTATTATATA
* **
1243338 AGTTTTCAAAAACTATGTATTATATATATGTTTTTAAAAT
1 AGTTTTCAAAAACTATATA-TATATATAT-TTTCAAAAAT
1243378 A-TTTTCAAAAACTATATATTATATATATTTTC-AAAAT
1 AGTTTTCAAAAACTATATA-TATATATATTTTCAAAAAT
1243415 -GTTTTCAAAAACTATATAT-TATATATTTTCAAAAAT
1 AGTTTTCAAAAACTATATATATATATATTTTCAAAAAT
1243451 AGTTTTC-AAAACTATA-ATATATATATTTTCAAAAAT
1 AGTTTTCAAAAACTATATATATATATATTTTCAAAAAT
*
1243487 CA-TTTTC-AAAACCATATA-ATATATATATTTCAAAAAT
1 -AGTTTTCAAAAACTATATATATATATAT-TTTCAAAAAT
1243524 CATTTGTAAA
Statistics
Matches: 136, Mismatches: 3, Indels: 17
0.87 0.02 0.11
Matches are distributed among these distances:
35 13 0.10
36 53 0.39
37 40 0.29
38 3 0.02
39 26 0.19
40 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (38 bp):
AGTTTTCAAAAACTATATATATATATATTTTCAAAAAT
Found at i:1243527 original size:37 final size:36
Alignment explanation
Indices: 1243359--1243548 Score: 180
Period size: 37 Copynumber: 5.3 Consensus size: 36
1243349 ACTATGTATT
* ** *
1243359 ATATATATGTTTTTAAAATATTTTCAAAAACTATATA
1 ATATATATATTTCAAAAATATTTTC-AAAACCATATA
* * *
1243396 TTATATATATTTTC-AAAATGTTTTCAAAAACTATATA
1 ATATATATA-TTTCAAAAATATTTTC-AAAACCATATA
*
1243433 TTATATAT-TTTCAAAAATAGTTTTCAAAA-C-TATA
1 ATATATATATTTCAAAAATA-TTTTCAAAACCATATA
1243467 ATATATATATTTTCAAAAATCATTTTCAAAACCATATA
1 ATATATATA-TTTCAAAAAT-ATTTTCAAAACCATATA
1243505 ATATATATATTTCAAAAATCATTTGT--AAA-C-TATA
1 ATATATATATTTCAAAAAT-ATTT-TCAAAACCATATA
1243539 ATATATATAT
1 ATATATATAT
1243549 ATATAATAAA
Statistics
Matches: 137, Mismatches: 7, Indels: 21
0.83 0.04 0.13
Matches are distributed among these distances:
34 25 0.18
35 5 0.04
36 31 0.23
37 59 0.43
38 17 0.12
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (36 bp):
ATATATATATTTCAAAAATATTTTCAAAACCATATA
Found at i:1243545 original size:36 final size:35
Alignment explanation
Indices: 1243358--1243550 Score: 166
Period size: 36 Copynumber: 5.3 Consensus size: 35
1243348 AACTATGTAT
* **
1243358 TATATATATGTTTTTAAAAT-ATTTTCAAAAACTATA
1 TATATATATATTTCAAAAATCATTTT--AAAACTATA
*
1243394 TATTATATATATTTTC-AAAAT-GTTTTCAAAAACTATA
1 TA-TATATATA-TTTCAAAAATCATTTT--AAAACTATA
1243431 TAT-TATATATTTTCAAAAAT-AGTTTTCAAAACTATA
1 TATATATATA-TTTCAAAAATCA-TTTT-AAAACTATA
*
1243467 -ATATATATATTTTCAAAAATCATTTTCAAAACCATA
1 TATATATATA-TTTCAAAAATCATTTT-AAAACTATA
1243503 TAATATATATATTTCAAAAATCATTTGT-AAACTATAA
1 T-ATATATATATTTCAAAAATCATTT-TAAAACTAT-A
1243540 TATATATATAT
1 TATATATATAT
1243551 ATAATAAAAT
Statistics
Matches: 140, Mismatches: 7, Indels: 20
0.84 0.04 0.12
Matches are distributed among these distances:
35 13 0.09
36 63 0.45
37 51 0.36
38 13 0.09
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (35 bp):
TATATATATATTTCAAAAATCATTTTAAAACTATA
Found at i:1244522 original size:137 final size:135
Alignment explanation
Indices: 1244381--1244848 Score: 488
Period size: 137 Copynumber: 3.4 Consensus size: 135
1244371 GAACTAAGTT
*
1244381 TGAAATTGAACCTGAAATGGAGGCTTTAATTATTAACCTAATTAATTTTAACCAATTATTTGATT
1 TGAAATT-AACCT-AAATGGAGGCTATAATTATTAACCTAATTAATTTTAACCAATTATTTGATT
*
1244446 CAAATAGA-TAAAATGGAACATCGAGCAAAAGCGATGACCAAATTAA-AGATTCTCTAAATTTAA
64 CAAATA-ATTAAAATGGAAC-TCGAGCAAAAGCGATGACCAAATTAAGA-ATTCCCTAAATTTAA
*
1244509 GGACTAG-TG
126 GGACTAGATA
1244518 TGAAATTAAGCCTAAAATGGAGGCTATAATTATTAACCTAATTAATTTTAACCAATTATTTGATT
1 TGAAATTAA-CCT-AAATGGAGGCTATAATTATTAACCTAATTAATTTTAACCAATTATTTGATT
* * * *
1244583 -AGAATAATTAAAATGCAGCCTCGAGCAAAGGCGA-GTACCAAATTAAGAATTCCCTAAATTTTA
64 CA-AATAATTAAAATGGA-ACTCGAGCAAAAGCGATG-ACCAAATTAAGAATTCCCTAAATTTAA
1244646 GGACTAGATA
126 GGACTAGATA
* * * * * * **
1244656 TGAAATTAAACCTAAAGTGAATGCTCTAA-TATTAGTCATAATTAATTTTAATCAATTATCCGAT
1 TGAAATT-AACCTAAA-TGGAGGCTATAATTATTA-ACCTAATTAATTTTAACCAATTATTTGAT
* * * * *
1244720 TCAAATAATTAAAGTGGAACCCGAGCAAAAGAGATAATCAAATTAAGAATTCACCTAAATTTAAG
63 TCAAATAATTAAAATGGAACTCGAGCAAAAGCGATGACCAAATTAAGAATTC-CCTAAATTTAAG
* * *
1244785 GACCAAATT
127 GACTAGATA
* * *
1244794 TGAAATTATGCCTAAA---AGGATATAA-TATTAATCCTAATTAATTTTAATCAATTAT
1 TGAAATTA-ACCTAAATGGAGGCTATAATTATTAA-CCTAATTAATTTTAACCAATTAT
1244849 GATTTGAATC
Statistics
Matches: 282, Mismatches: 34, Indels: 33
0.81 0.10 0.09
Matches are distributed among these distances:
134 33 0.12
136 5 0.02
137 151 0.54
138 90 0.32
139 3 0.01
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (135 bp):
TGAAATTAACCTAAATGGAGGCTATAATTATTAACCTAATTAATTTTAACCAATTATTTGATTCA
AATAATTAAAATGGAACTCGAGCAAAAGCGATGACCAAATTAAGAATTCCCTAAATTTAAGGACT
AGATA
Found at i:1246168 original size:27 final size:29
Alignment explanation
Indices: 1246130--1246188 Score: 95
Period size: 27 Copynumber: 2.1 Consensus size: 29
1246120 ATTCGAGTAC
1246130 TTAAATTAAATTAATAATA-TATTAAT-T
1 TTAAATTAAATTAATAATATTATTAATAT
*
1246157 TTAAATTAAATTATTAATATTATTAATAT
1 TTAAATTAAATTAATAATATTATTAATAT
1246186 TTA
1 TTA
1246189 TATATTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 18 0.62
28 7 0.24
29 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TTAAATTAAATTAATAATATTATTAATAT
Found at i:1248691 original size:24 final size:24
Alignment explanation
Indices: 1248663--1248708 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1248653 GTTTAAGATA
*
1248663 TATTTTATTATATTTAA-TATTTTG
1 TATTTAATT-TATTTAAGTATTTTG
1248687 TATTTAATTTATTTAAGTATTT
1 TATTTAATTTATTTAAGTATTT
1248709 AAATTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
TATTTAATTTATTTAAGTATTTTG
Found at i:1248708 original size:17 final size:17
Alignment explanation
Indices: 1248686--1248719 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1248676 TTAATATTTT
*
1248686 GTATTTAATTTATTTAA
1 GTATTTAAATTATTTAA
1248703 GTATTTAAATTATTTAA
1 GTATTTAAATTATTTAA
1248720 CATTGTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
GTATTTAAATTATTTAA
Found at i:1248727 original size:21 final size:19
Alignment explanation
Indices: 1248684--1248731 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 19
1248674 ATTTAATATT
*
1248684 TTGTATTTAATTTATTTAA
1 TTGTATTTAAATTATTTAA
1248703 --GTATTTAAATTATTTAACA
1 TTGTATTTAAATTATTT-A-A
1248722 TTGTATTTAA
1 TTGTATTTAA
1248732 TTAATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 14 0.58
18 1 0.04
19 1 0.04
21 8 0.33
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.56
Consensus pattern (19 bp):
TTGTATTTAAATTATTTAA
Found at i:1250029 original size:23 final size:23
Alignment explanation
Indices: 1250003--1250048 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1249993 CACCACAGCT
*
1250003 CGTATAAACGCACCGAAGTGCCA
1 CGTAGAAACGCACCGAAGTGCCA
** *
1250026 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAACGCACCGAAGTGCCA
1250049 TATAAGATTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.17
Consensus pattern (23 bp):
CGTAGAAACGCACCGAAGTGCCA
Found at i:1250400 original size:25 final size:24
Alignment explanation
Indices: 1250366--1250433 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 24
1250356 ATGTCACTTA
* *
1250366 ATGTAT-ATAATATGAATTCATATC
1 ATGTATCATAATATGAATGC-GATC
1250390 ATGTATCATAATATGAAATGCGATC
1 ATGTATCATAATATG-AATGCGATC
*
1250415 ATGTATCAAAATATTGAAT
1 ATGTATCATAATA-TGAAT
1250434 CTAGACTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
24 6 0.16
25 26 0.68
26 6 0.16
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.37
Consensus pattern (24 bp):
ATGTATCATAATATGAATGCGATC
Found at i:1251315 original size:3 final size:3
Alignment explanation
Indices: 1251307--1251339 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
1251297 GTCTCACGGG
1251307 GAA GAA GAAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA GA
1251340 GAAATCTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1252490 original size:351 final size:351
Alignment explanation
Indices: 1251845--1252535 Score: 1188
Period size: 351 Copynumber: 2.0 Consensus size: 351
1251835 CATGAGCTAC
* * *
1251845 CTGATGATTTAGAAAAAATGAGGGTGCTAATTGATCAGAAGGCTGGCACACATGTATGCCTTTTA
1 CTGATGATTTAGAAAAAATGAGCGTGCTAATCGATCAGAAGGCTGGCACACAGGTATGCCTTTTA
1251910 ATGTTTAAAAATCAATTTTAGATTATAGTTGTATAATTAGATTATTATTTTGATAAAAACTATAT
66 ATGTTTAAAAATCAATTTTAGATTATAGTTGTATAATTAGATTATTATTTTGATAAAAACTATAT
* *
1251975 ATATTTGTTTTAGTTTGAATGAGTGTCATATTCTAATGATGATGTGAGGATGGTGATCCCACTTG
131 ATATTTGTTTTAGTTTGAATGAGTGTCATATTCTAATGATGATGTGAGGATGGTGATCCAACCTG
1252040 AGTTGAGGGGCCCATTAGATGTTTGGATGGCGATGGTCCCTTTGATATGTTATGCGATCGTCGAG
196 AGTTGAGGGGCCCATTAGATGTTTGGATGGCGATGGTCCCTTTGATATGTTATGCGATCGTCGAG
* *
1252105 TGGCACTCCACTGATCGTGTGCTTCGACAATTTGGTTGTTTTCAACCAATTCCGAAAGCACCTTG
261 TGGCACTCCACTGATCGCGTGCTTCGACAATTTGGTTGTTTTCAACCAATTCCGAAAGCACCTCG
1252170 CAATATGGACGAGTTGAATAGCACAA
326 CAATATGGACGAGTTGAATAGCACAA
*
1252196 CTGATGATTTAGAAAAAATGAGCGTGCTAATCGATCAGAAGGTTGGCACACAGGTATGCCTTTTA
1 CTGATGATTTAGAAAAAATGAGCGTGCTAATCGATCAGAAGGCTGGCACACAGGTATGCCTTTTA
* *
1252261 ATGTTTAAAAATCGATTTTAGATTATAGTTGTATAATTAGATTATTATTTTGATAAAAATTATAT
66 ATGTTTAAAAATCAATTTTAGATTATAGTTGTATAATTAGATTATTATTTTGATAAAAACTATAT
*
1252326 ATATTTGTTTTAGTTTGAAT-AGGTGTCATATTCTAATGATGATGTGAGGATGTTGATCCAACCT
131 ATATTTGTTTTAGTTTGAATGA-GTGTCATATTCTAATGATGATGTGAGGATGGTGATCCAACCT
** * *
1252390 GAGTTTTGGGGCCCATTAGATGTTTGGATGGCGATGGTCCCTTTGATTTGTTATGCGATCGTCTA
195 GAGTTGAGGGGCCCATTAGATGTTTGGATGGCGATGGTCCCTTTGATATGTTATGCGATCGTCGA
* *
1252455 GTGGCACTCCACTGATCGCGTGC-TCTGATAATTTGGTTGTTTTCAACCAATTCCGAAAGTACCT
260 GTGGCACTCCACTGATCGCGTGCTTC-GACAATTTGGTTGTTTTCAACCAATTCCGAAAGCACCT
*
1252519 CGTAATATGGACGAGTT
324 CGCAATATGGACGAGTT
1252536 ACATAGTACA
Statistics
Matches: 320, Mismatches: 18, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
350 3 0.01
351 317 0.99
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.36
Consensus pattern (351 bp):
CTGATGATTTAGAAAAAATGAGCGTGCTAATCGATCAGAAGGCTGGCACACAGGTATGCCTTTTA
ATGTTTAAAAATCAATTTTAGATTATAGTTGTATAATTAGATTATTATTTTGATAAAAACTATAT
ATATTTGTTTTAGTTTGAATGAGTGTCATATTCTAATGATGATGTGAGGATGGTGATCCAACCTG
AGTTGAGGGGCCCATTAGATGTTTGGATGGCGATGGTCCCTTTGATATGTTATGCGATCGTCGAG
TGGCACTCCACTGATCGCGTGCTTCGACAATTTGGTTGTTTTCAACCAATTCCGAAAGCACCTCG
CAATATGGACGAGTTGAATAGCACAA
Found at i:1252680 original size:10 final size:10
Alignment explanation
Indices: 1252665--1252697 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
1252655 CCTCTTGATA
1252665 GTTGCTGACG
1 GTTGCTGACG
1252675 GTTGCTGACG
1 GTTGCTGACG
1252685 GTTGCTGACG
1 GTTGCTGACG
1252695 GTT
1 GTT
1252698 ATTACGAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.09, C:0.18, G:0.39, T:0.33
Consensus pattern (10 bp):
GTTGCTGACG
Found at i:1252991 original size:24 final size:24
Alignment explanation
Indices: 1252945--1252995 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1252935 CCTTTACCCG
* *
1252945 ATGCCGCCACCGTCACCTGGTTTT
1 ATGCCGCCACCGCCACCAGGTTTT
1252969 ATGCCGCCACCGCCA-CAGAGTTTT
1 ATGCCGCCACCGCCACCAG-GTTTT
1252993 ATG
1 ATG
1252996 ACCCCTCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.18, C:0.35, G:0.22, T:0.25
Consensus pattern (24 bp):
ATGCCGCCACCGCCACCAGGTTTT
Found at i:1256699 original size:185 final size:185
Alignment explanation
Indices: 1256386--1256759 Score: 649
Period size: 185 Copynumber: 2.0 Consensus size: 185
1256376 ACTCTTTATT
1256386 CTTATAGAGTGTAGCCAATGGTGTAAGTAGCTTTAAAACAAGCCGAATAAATTTCATTGATCTAG
1 CTTATAGAGTGTAGCCAATGGTGTAAGTAGCTTTAAAACAAGCCGAATAAATTTCATTGATCTAG
* * * *
1256451 TTGGCTTAGAGCGACAAAAGTTAAATGGTGCAACAGGAGAGCGCTTAAAGGAGGCATGCAATATT
66 CTGGCTCAGAGCAACAAAAGTTAAATGGTGCAACAGGAGAGCGCTTAAAGGAGGCAGGCAATATT
*
1256516 AATCGTTCACTCTCACAGCTTGGGTATGCTCTTTTATCTTTTATTTCTTGTCATC
131 AATCGTTCACTCTCACAACTTGGGTATGCTCTTTTATCTTTTATTTCTTGTCATC
* * *
1256571 CTTATAGAGTGTAGCCGATGGTGTAAGTAGCTTTAAAATAAGCCGAATAAATTTCGTTGATCTAG
1 CTTATAGAGTGTAGCCAATGGTGTAAGTAGCTTTAAAACAAGCCGAATAAATTTCATTGATCTAG
* *
1256636 CTGGCTCAGAGCAACAAAAGTTAACTGGTGCAGCAGGAGAGCGCTTAAAGGAGGCAGGCAATATT
66 CTGGCTCAGAGCAACAAAAGTTAAATGGTGCAACAGGAGAGCGCTTAAAGGAGGCAGGCAATATT
*
1256701 AATCGTTCACTCTCACAACTTGGGTATGCTCTTTTATCTTTTCTTTCTTGTCATC
131 AATCGTTCACTCTCACAACTTGGGTATGCTCTTTTATCTTTTATTTCTTGTCATC
1256756 CTTA
1 CTTA
1256760 ACTCTATACT
Statistics
Matches: 178, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
185 178 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (185 bp):
CTTATAGAGTGTAGCCAATGGTGTAAGTAGCTTTAAAACAAGCCGAATAAATTTCATTGATCTAG
CTGGCTCAGAGCAACAAAAGTTAAATGGTGCAACAGGAGAGCGCTTAAAGGAGGCAGGCAATATT
AATCGTTCACTCTCACAACTTGGGTATGCTCTTTTATCTTTTATTTCTTGTCATC
Found at i:1259927 original size:108 final size:103
Alignment explanation
Indices: 1259751--1259947 Score: 256
Period size: 108 Copynumber: 1.9 Consensus size: 103
1259741 TTTCGTGTAC
*
1259751 TTTAACTTCATTGCTTGATATTATGATTGGTGTTACATATTAAGTTTTCAGTTTTGAACTTAAAG
1 TTTAACTTCACTGCTTGATATTATGATTGGTGTTACATATTAAGTTTTCAGTTTTGAACTTAAAG
*
1259816 CCAAAATTGGTAGCTATA-GTAGTTATGTTTTTGTACAG
66 CCAAAATCGGTAGCTA-AGGTAGTTATGTTTTTGTACAG
*
1259854 TTTAACTTCACTGCTTGATTATTATTG-TTGTTGTTACATATTAATTAAGTTTATC-GTTTTGAA
1 TTTAACTTCACTGCTTGA-TATTA-TGATTGGTGTTAC--A-T-ATTAAGTTT-TCAGTTTTGAA
**
1259917 CTTAGGGCCAAAATCGGTAGCTAAGGTAGTT
59 CTTAAAGCCAAAATCGGTAGCTAAGGTAGTT
1259948 TTTTGTTATT
Statistics
Matches: 81, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
103 17 0.21
104 14 0.17
105 2 0.02
106 1 0.01
107 2 0.02
108 43 0.53
109 2 0.02
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (103 bp):
TTTAACTTCACTGCTTGATATTATGATTGGTGTTACATATTAAGTTTTCAGTTTTGAACTTAAAG
CCAAAATCGGTAGCTAAGGTAGTTATGTTTTTGTACAG
Found at i:1260924 original size:291 final size:288
Alignment explanation
Indices: 1260396--1260978 Score: 875
Period size: 291 Copynumber: 2.0 Consensus size: 288
1260386 ACTCTTAACG
* *
1260396 AGCTGCTTGCAGAATCGATTCTGCCTAAAGATGCAATACCACCTTATGACAAGTTTGATATTCCC
1 AGCTGCTTGCAGAATCGAGTCTGCCTAAAGATGCAATACCACCTTATAACAAGTTTGATATTCCC
* * *
1260461 AAATATGATGCAAGTGAGATCCACGATGCCAGTGATCAGCGTTGGTGAGAAGAATTTGAACCATT
66 AAATATGATGCAAGCGAGATCCACGATGCCAGTGATCAGCGATGGCGAGAAGAATTTGAACCATT
* * *
1260526 CTATAACGGTGAGGATGGCGAATTATCATCGAAACTTGCAGGAAATTCATCATGGTTCTTTGGTT
131 CTATAACAGTGAGGATGGCAAATTATCATCGAAACTTGCAGGAAATTCATCATGGTTCTTTAGTT
*
1260591 ATGATCTTTGCAATATATAGATCAACTTTAACTGGAGCAACA-GCGTGTG-TGTATGTACTATTA
196 ATGATCATTGCAATATATAGATCAACTTTAACTGGAGCAACAGGCGTGTGATGTATGTACTATTA
* *
1260654 CTTATAGTTTCTGTGACATAGTTTATTCAT
261 CATATAGGTTCTGT--CATAGTTTATTCAT
*
1260684 AGCTGCTTGCAGAATCGCGTCTGCCTAAAGATGCAATACCATCTTCTTATAACAAGTTTGATATT
1 AGCTGCTTGCAGAATCGAGTCTGCCTAAAGATGCAATACCA-C--CTTATAACAAGTTTGATATT
* * *
1260749 CCCAAATATGATGCAAGCGAGGTCCATGATGCCATTGATCAGCGATGGCGAGAAGAATTTGAACC
63 CCCAAATATGATGCAAGCGAGATCCACGATGCCAGTGATCAGCGATGGCGAGAAGAATTTGAACC
* * * *
1260814 ATTCTTTAACAGTGAGGATTGCAAATTATCATCGATACTTGCA-GAAATTTCGTCATGGTTCTTT
128 ATTCTATAACAGTGAGGATGGCAAATTATCATCGAAACTTGCAGGAAA-TTCATCATGGTTCTTT
* *
1260878 AGTTATGATCATTGCAATATATAGATCAACTTTAACTGGTGCAACAGTGTGTGTGTATGTATGTA
192 AGTTATGATCATTGCAATATATAGATCAACTTTAACTGGAGCAACAG-GCGTGTG-ATGTATGTA
*
1260943 CTATTACATATAGGTTCTGTCGTAGTTTATTCAT
255 CTATTACATATAGGTTCTGTCATAGTTTATTCAT
1260977 AG
1 AG
1260979 TTGTTTTTTG
Statistics
Matches: 265, Mismatches: 22, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
288 39 0.15
289 1 0.00
290 4 0.02
291 174 0.66
293 21 0.08
295 26 0.10
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (288 bp):
AGCTGCTTGCAGAATCGAGTCTGCCTAAAGATGCAATACCACCTTATAACAAGTTTGATATTCCC
AAATATGATGCAAGCGAGATCCACGATGCCAGTGATCAGCGATGGCGAGAAGAATTTGAACCATT
CTATAACAGTGAGGATGGCAAATTATCATCGAAACTTGCAGGAAATTCATCATGGTTCTTTAGTT
ATGATCATTGCAATATATAGATCAACTTTAACTGGAGCAACAGGCGTGTGATGTATGTACTATTA
CATATAGGTTCTGTCATAGTTTATTCAT
Found at i:1265236 original size:27 final size:27
Alignment explanation
Indices: 1265198--1265263 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
1265188 TATTTATAAT
1265198 ATCATATCTCTATAGGAATGGTAACAA
1 ATCATATCTCTATAGGAATGGTAACAA
1265225 ATCATATCTCTATAGGAATGGTAACAA
1 ATCATATCTCTATAGGAATGGTAACAA
1265252 ATC--ATCTCTATA
1 ATCATATCTCTATA
1265264 ATTCCTACAC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.23
27 30 0.77
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (27 bp):
ATCATATCTCTATAGGAATGGTAACAA
Found at i:1265773 original size:7 final size:7
Alignment explanation
Indices: 1265761--1265792 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
1265751 ATCTTAACAG
1265761 TTCTGTC
1 TTCTGTC
1265768 TTCTGTC
1 TTCTGTC
1265775 TTCTGTC
1 TTCTGTC
1265782 TTCTGTC
1 TTCTGTC
1265789 TTCT
1 TTCT
1265793 TAAACATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.00, C:0.28, G:0.12, T:0.59
Consensus pattern (7 bp):
TTCTGTC
Found at i:1271987 original size:64 final size:66
Alignment explanation
Indices: 1271889--1272013 Score: 202
Period size: 64 Copynumber: 1.9 Consensus size: 66
1271879 TAATGAAGGT
*
1271889 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTTAATGGG
1 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAATGGG
1271953 G
66 G
*
1271954 ATGCATCGATGCACT-C-CTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAA
1 ATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAA
1272014 ATTCATGCAT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
63 1 0.02
64 30 0.54
65 25 0.45
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (66 bp):
ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAATGGG
G
Found at i:1272042 original size:64 final size:63
Alignment explanation
Indices: 1271889--1272049 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 63
1271879 TAATGAAGGT
* * *
1271889 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTACA-TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGC
* * *
1271954 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT-TC
1 ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGC
* * *
1272018 ATGCATCGATGCACTGCATGTGCATCAATGCA
1 ATGCATCGATGCACTACATATGCATCGATGCA
1272050 CCTTAAACAA
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 57 0.68
65 24 0.29
66 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGC
Done.