Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_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: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 47 of 78
Found at i:9377785 original size:42 final size:42
Alignment explanation
Indices: 9377726--9377906 Score: 211
Period size: 42 Copynumber: 4.3 Consensus size: 42
9377716 CCAAAATTTA
9377726 TAAATCCTTCGGGTCATCAATAAGTC-TTCTGAGCATGATGCT
1 TAAATCCTTCGGGTCATCAATAAGTCTTTC-GAGCATGATGCT
* * *
9377768 TAAATCCTCCGGGTCATCAGTAAGTCTTTCGAGCATAATGCT
1 TAAATCCTTCGGGTCATCAATAAGTCTTTCGAGCATGATGCT
* * * *
9377810 TAAATCCTTCGGATCATCAGTAAGTCTTCCGAGCATGATGGT
1 TAAATCCTTCGGGTCATCAATAAGTCTTTCGAGCATGATGCT
** * * * *
9377852 TAAATATTTTGGGTCATCTATAAGCCTTTCGAGCATGATGAT
1 TAAATCCTTCGGGTCATCAATAAGTCTTTCGAGCATGATGCT
* *
9377894 TAAGTCCTCCGGG
1 TAAATCCTTCGGG
9377907 CAATCTAAAG
Statistics
Matches: 116, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
42 113 0.97
43 3 0.03
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (42 bp):
TAAATCCTTCGGGTCATCAATAAGTCTTTCGAGCATGATGCT
Found at i:9377955 original size:37 final size:37
Alignment explanation
Indices: 9377908--9377980 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
9377898 TCCTCCGGGC
**
9377908 AATCTAAAGCCTTCACCGAAGAGTAGTGAAGAAAATA
1 AATCTAAAGCCTTCACAAAAGAGTAGTGAAGAAAATA
* * *
9377945 AATCTTAAGCCTTCATAAAAGAGTAGTGAAGCAAAT
1 AATCTAAAGCCTTCACAAAAGAGTAGTGAAGAAAAT
9377981 TCAGATATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (37 bp):
AATCTAAAGCCTTCACAAAAGAGTAGTGAAGAAAATA
Found at i:9378182 original size:111 final size:111
Alignment explanation
Indices: 9377982--9378783 Score: 1178
Period size: 111 Copynumber: 7.2 Consensus size: 111
9377972 GAAGCAAATT
* * *
9377982 CAGATATGATATTCCCTCAGAGGAAGCGGAACAGATCCCTCTT-TTTCAAGATTTGATATTCCCT
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAAATCTCT-TTCTTTCAAGATTTGATATTCCCT
* *
9378046 GAGTGACAGCGAAACAAATCTACCCCGATTCAATGGATCAACTCTCT
65 GAGTGACAGCGGAACAAATCTACCCCGATTCAATGGATCAACTCTCC
*
9378093 CAGCTCTGATATTCCCTCAGAGGAAGCGGAACAAATCTCTTTCTTTCAAGATTTGATATTCCCTG
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAAATCTCTTTCTTTCAAGATTTGATATTCCCTG
* *
9378158 AGTGACAGCGGAACAAATCTACCCCGATTAAATGGATCAACACTCC
66 AGTGACAGCGGAACAAATCTACCCCGATTCAATGGATCAACTCTCC
* * * *
9378204 CAGATCTGTCGATCTGATATTCCCTCAGAAGAAGCGGGACATATCTCTCTCTTTCAAGATTTGAT
1 C--A------GATCTGATATTCCCTCAGAGGAAGCGGAACAAATCTCTTTCTTTCAAGATTTGAT
* * *
9378269 ATTCCCTGAGTGATAGCGGAACAAATCTGCCCTGATTCAATGGATCAACTCTCC
58 ATTCCCTGAGTGACAGCGGAACAAATCTACCCCGATTCAATGGATCAACTCTCC
* * * *
9378323 TAGATTTGATACTCCCTCAGAGGAAGCGGAACAAATCTCTTTCTTTCAAGATTTGATATTCCCTA
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAAATCTCTTTCTTTCAAGATTTGATATTCCCTG
* * *
9378388 AGTGACAACAGAACAAATCTGCCCCGATTCAATGGATCAACTCTCC
66 AGTGACAGCGGAACAAATCTACCCCGATTCAATGGATCAACTCTCC
* * *
9378434 CAGATCTGATATTCCCTCAGAGGAAGCGGAATAGATCTCTCTCTTTCAAGATTTGATATTCCCTG
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAAATCTCTTTCTTTCAAGATTTGATATTCCCTG
*
9378499 AGTGACAGCGGAACAAATCTGCCCCGATTCAATGGATCAACTCTCC
66 AGTGACAGCGGAACAAATCTACCCCGATTCAATGGATCAACTCTCC
* *
9378545 CAGATCTGATATTTCCTCAGAGGAAGCGGAA-AAGATCTCTCTCTTTCAAGATTTGATATTCCCT
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAA-ATCTCTTTCTTTCAAGATTTGATATTCCCT
9378609 GAGTGACAGCGGAACAAATCTACCCCGATTCAATGGATCAACTCTCC
65 GAGTGACAGCGGAACAAATCTACCCCGATTCAATGGATCAACTCTCC
* *
9378656 CAGATCTGATATTCCCTCAGAGGAAGCGGAACATATCTCTTTTTTTCAAGATTTGATATTCCCTG
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAAATCTCTTTCTTTCAAGATTTGATATTCCCTG
* * *
9378721 AGTGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACATCT-C
66 AGTGACAGCGGAACAAATCTACCCCGATTCAATGGATCAAC-TCTCC
*
9378767 CATATCTGATATTCCCT
1 CAGATCTGATATTCCCT
9378784 GAGTGACAGC
Statistics
Matches: 629, Mismatches: 50, Indels: 24
0.89 0.07 0.03
Matches are distributed among these distances:
110 3 0.00
111 521 0.83
112 4 0.01
113 1 0.00
117 1 0.00
119 99 0.16
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (111 bp):
CAGATCTGATATTCCCTCAGAGGAAGCGGAACAAATCTCTTTCTTTCAAGATTTGATATTCCCTG
AGTGACAGCGGAACAAATCTACCCCGATTCAATGGATCAACTCTCC
Found at i:9378953 original size:3 final size:3
Alignment explanation
Indices: 9378941--9378989 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
9378931 CGTCTTTTAA
* *
9378941 TAT T-T TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
9378986 TAT T
1 TAT T
9378990 GTATTTTACA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.90
4 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:9380861 original size:2 final size:2
Alignment explanation
Indices: 9380854--9380911 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
9380844 TTGCATATTA
9380854 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
9380896 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
9380912 GTTATAATGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9385080 original size:27 final size:28
Alignment explanation
Indices: 9385050--9385105 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
9385040 CTTTTAAACA
*
9385050 TTAATA-TTTTCTT-ATTTATTGTTTATT
1 TTAATATTTTTCTTAATTT-TTCTTTATT
9385077 TTAATATTTTTCTTAATTTTTCTTTATT
1 TTAATATTTTTCTTAATTTTTCTTTATT
9385105 T
1 T
9385106 CTCTTGTGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 6 0.23
28 16 0.62
29 4 0.15
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (28 bp):
TTAATATTTTTCTTAATTTTTCTTTATT
Found at i:9390822 original size:236 final size:236
Alignment explanation
Indices: 9390399--9390873 Score: 851
Period size: 236 Copynumber: 2.0 Consensus size: 236
9390389 ACTAGAAGAA
* * *
9390399 TGGCTCAATAGCAAGTGTTATCAGAATCTGGCATTGTGTTTATGAGCCAAAAGATGATAAAACAA
1 TGGCTCAATAGCAAGTGTTATCAGAATATGGCATTGTGTTTATGAGCCAAAAGACGATAAAAAAA
* *
9390464 GGAATGCCATAATAGATTCTCTAGTAAGACGGGCATCAGATGATTATGAGTCCCTAGGTTTTAAT
66 GGAATGACATAATAGATTCTCTAGTAAGACGGGCATCAGATGATTACGAGTCCCTAGGTTTTAAT
*
9390529 TTGTTTAGATGAGGATTTATTTTGAATCTTTAATGAAGAATAAATTAAAGCAGGTGACGAATCCT
131 TTGTTTAGATGAGGATTTATTTTGAATCTTTAATGAAGAATAAATTAAAGAAGGTGACGAATCCT
* *
9390594 GGAAGTTATAATGGGGTATCCAATGCTTTGGGATGAGAATT
196 GGAAGCTATAATGGGGCATCCAATGCTTTGGGATGAGAATT
* * *
9390635 TGGCTCGATAGCAAGTGTTATCATAATATGGCATTGTGTTTGTGAGCCAAAAGACGATAAAAAAA
1 TGGCTCAATAGCAAGTGTTATCAGAATATGGCATTGTGTTTATGAGCCAAAAGACGATAAAAAAA
9390700 GGAATGACATAATAGATTCTCTAGTAAGACGGGCATCAGATGATTACGAGTCCCTAGGTTTTAAT
66 GGAATGACATAATAGATTCTCTAGTAAGACGGGCATCAGATGATTACGAGTCCCTAGGTTTTAAT
9390765 TTGTTTAGATGAGGATTTATTTTGAATCTTTAATGAAGAATAAATTAAAGAAGGTGACGAATCCT
131 TTGTTTAGATGAGGATTTATTTTGAATCTTTAATGAAGAATAAATTAAAGAAGGTGACGAATCCT
9390830 GGAAGCTATAATGGGGCATCCAATGCTTTGGGATGAGAATT
196 GGAAGCTATAATGGGGCATCCAATGCTTTGGGATGAGAATT
9390871 TGG
1 TGG
9390874 GGCAGTGGTG
Statistics
Matches: 228, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
236 228 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (236 bp):
TGGCTCAATAGCAAGTGTTATCAGAATATGGCATTGTGTTTATGAGCCAAAAGACGATAAAAAAA
GGAATGACATAATAGATTCTCTAGTAAGACGGGCATCAGATGATTACGAGTCCCTAGGTTTTAAT
TTGTTTAGATGAGGATTTATTTTGAATCTTTAATGAAGAATAAATTAAAGAAGGTGACGAATCCT
GGAAGCTATAATGGGGCATCCAATGCTTTGGGATGAGAATT
Found at i:9391432 original size:5 final size:5
Alignment explanation
Indices: 9391399--9391615 Score: 88
Period size: 5 Copynumber: 40.6 Consensus size: 5
9391389 GAATTACACC
* * * *
9391399 AAAGA AAATA AAACA AAACA AAACAA AAAGAA AAAGA AAAGA AAAGA AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAA-GA AAAG-A AAAGA AAAGA AAAGA AAAGA
* * * *
9391451 AAA-A AGA-A AAAGA AGAGA AAATA AAAGAA AAAGGAA AAAGA AAAAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAG-A AAA-G-A AAAGA AAAGA
* *
9391497 AGAAGAA AAAAA TAAAGA AAAAA TAAAGGAA AAAGA AATA-A AAAGAA AAAGA
1 A-AAG-A AAAGA -AAAGA AAAGA -AAA-G-A AAAGA AA-AGA AAAG-A AAAGA
*
9391549 GAGAAGA AATA-A AAAGAA AAAGA GAGAATA AATA-A AAAGA AGAA-A AAAGA
1 -A-AAGA AA-AGA AAAG-A AAAGA -A-AAGA AA-AGA AAAGA A-AAGA AAAGA
*
9391599 AAAGA GAA-A AAAGA AAA
1 AAAGA AAAGA AAAGA AAA
9391616 CTAAAAGGAG
Statistics
Matches: 167, Mismatches: 19, Indels: 52
0.70 0.08 0.22
Matches are distributed among these distances:
4 14 0.08
5 89 0.53
6 45 0.27
7 18 0.11
8 1 0.01
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:9391438 original size:22 final size:22
Alignment explanation
Indices: 9391408--9391615 Score: 86
Period size: 22 Copynumber: 9.1 Consensus size: 22
9391398 CAAAGAAAAT
*
9391408 AAAACAAAACAAAACAAAAAG-A
1 AAAAGAAAACAAAA-AAAAAGAA
* *
9391430 AAAAGAAAAGAAAAGAAAAGAA
1 AAAAGAAAACAAAAAAAAAGAA
*
9391452 AAAAGAAAAAGAAGAGAAAATAAAAGAA
1 AAAAG---AA-AACA-AAAA-AAAAGAA
* *
9391480 AAAGGAAAA-AGAAAAAAAGAA
1 AAAAGAAAACAAAAAAAAAGAA
* * * *
9391501 GAAA-AAAATAAAGAAAAA-AT
1 AAAAGAAAACAAAAAAAAAGAA
* * *
9391521 AAAGGAAAAAGAAATAAAAAGAA
1 AAAAG-AAAACAAAAAAAAAGAA
* * *
9391544 AAAGAGAGAAGAAATAAAAAGAA
1 AAA-AGAAAACAAAAAAAAAGAA
9391567 AAAGAGAGAATA-AATAAAAAGAAGAA
1 AAA-AGA-AA-ACAA-AAAAA-AAGAA
* *
9391593 AAAAGAAAA-GAGAAAAAAGAA
1 AAAAGAAAACAAAAAAAAAGAA
9391614 AA
1 AA
9391616 CTAAAAGGAG
Statistics
Matches: 148, Mismatches: 22, Indels: 33
0.73 0.11 0.16
Matches are distributed among these distances:
20 7 0.05
21 28 0.19
22 37 0.25
23 30 0.20
24 8 0.05
25 12 0.08
26 12 0.08
27 3 0.02
28 11 0.07
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.03
Consensus pattern (22 bp):
AAAAGAAAACAAAAAAAAAGAA
Found at i:9391461 original size:23 final size:22
Alignment explanation
Indices: 9391423--9391615 Score: 134
Period size: 23 Copynumber: 8.5 Consensus size: 22
9391413 AAAACAAAAC
9391423 AAAAAG-AAAAAG-AAAAGAAA
1 AAAAAGAAAAAAGAAAAAGAAA
*
9391443 AGAAAAGAAAAAAGAAAAAGAAG
1 A-AAAAGAAAAAAGAAAAAGAAA
* *
9391466 AGAAA-ATAAAAGAAAAAGGAAA
1 AAAAAGAAAAAAGAAAAA-GAAA
9391488 AAGAAA-AAAAGAAGAAAAA-AATA
1 AA-AAAGAAAA-AAGAAAAAGAA-A
9391511 AAGAAA-AAATAAAGGAAAAAGAAA
1 AA-AAAGAAA-AAA-GAAAAAGAAA
*
9391535 TAAAAAG-AAAAAGAGAGAAGAAA
1 -AAAAAGAAAAAAGA-AAAAGAAA
9391558 TAAAAAGAAAAAGAGAGAATAA-ATAA
1 -AAAAAGAAAAA-AGA-AA-AAGA-AA
*
9391584 AAAGAAGAAAAAAG-AAAAGAGA
1 AAA-AAGAAAAAAGAAAAAGAAA
9391606 AAAAAGAAAA
1 AAAAAGAAAA
9391616 CTAAAAGGAG
Statistics
Matches: 145, Mismatches: 9, Indels: 37
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.01
21 23 0.16
22 23 0.16
23 46 0.32
24 25 0.17
25 15 0.10
26 12 0.08
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (22 bp):
AAAAAGAAAAAAGAAAAAGAAA
Found at i:9391477 original size:33 final size:33
Alignment explanation
Indices: 9391401--9391606 Score: 122
Period size: 34 Copynumber: 6.0 Consensus size: 33
9391391 ATTACACCAA
* *
9391401 AGAAAATAAAACAAAACAAAACAA-AAAGAA-AA-
1 AGAAAATAAAAGAAAAGAAAA-AAGAAA-AAGAAG
*
9391433 AGAAAAGAAAAGAAAAGAAAAAAGAAAAAGAAG
1 AGAAAATAAAAGAAAAGAAAAAAGAAAAAGAAG
*
9391466 AGAAAATAAAAGAAAAAGGAAAAAGAAAAA-AAG
1 AGAAAATAAAAG-AAAAGAAAAAAGAAAAAGAAG
* *
9391499 AAGAAAAAAATAAAGAAAA-AATAAAGGAAAAAGAA-
1 -AG-AAAATA-AAAGAAAAGAA-AAAAGAAAAAGAAG
* *
9391534 ATAAAAAGAAAAAGAGAGAAGAAATAAAAAGAAAAAG-AG
1 A-GAAAA-TAAAAGA-A-AAG--A-AAAAAGAAAAAGAAG
*
9391573 AGAATAAATAAAA-AGAAGAAAAAAGAAAAGAGAA
1 AG-A-AAATAAAAGAAAAGAAAAAAGAAAA-AGAA
9391607 AAAAGAAAAC
Statistics
Matches: 139, Mismatches: 13, Indels: 41
0.72 0.07 0.21
Matches are distributed among these distances:
31 4 0.03
32 23 0.17
33 24 0.17
34 32 0.23
35 22 0.16
36 11 0.08
38 2 0.01
39 17 0.12
40 4 0.03
ACGTcount: A:0.78, C:0.01, G:0.17, T:0.04
Consensus pattern (33 bp):
AGAAAATAAAAGAAAAGAAAAAAGAAAAAGAAG
Found at i:9391507 original size:46 final size:44
Alignment explanation
Indices: 9391429--9391615 Score: 158
Period size: 41 Copynumber: 4.2 Consensus size: 44
9391419 AAACAAAAAG
9391429 AAAAAG-AAAA-G-AAAAGAAAAGAAAA-AAGAAAAAGAAGAGAAA
1 AAAAAGAAAAAGGAAAAAG-AAA-AAAAGAAGAAAAAGAAGAGAAA
* *
9391471 ATAAAAGAAAAAGGAAAAAGAAAAAAAGAAGAAAAA-AATA-AAG
1 A-AAAAGAAAAAGGAAAAAGAAAAAAAGAAGAAAAAGAAGAGAAA
* *
9391514 AAAAA-ATAAAGGAAAAAGAAATAAA-AAGAAAAAGAGAGAAGAAA
1 AAAAAGAAAAAGGAAAAAGAAAAAAAGAAGAAAAAGA-AG-AGAAA
* * *
9391558 TAAAAAGAAAAAGAGAGAATAA-ATAAAAAGAAGAAAAAAGAAAAGAGA
1 -AAAAAGAAAAAG-GA-AA-AAGAAAAAAAGAAG-AAAAAGAAGAGAAA
9391606 AAAAAGAAAA
1 AAAAAGAAAA
9391616 CTAAAAGGAG
Statistics
Matches: 118, Mismatches: 11, Indels: 27
0.76 0.07 0.17
Matches are distributed among these distances:
40 8 0.07
41 19 0.16
42 6 0.05
43 9 0.08
44 13 0.11
45 17 0.14
46 10 0.08
47 12 0.10
48 11 0.09
49 6 0.05
50 7 0.06
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (44 bp):
AAAAAGAAAAAGGAAAAAGAAAAAAAGAAGAAAAAGAAGAGAAA
Found at i:9391518 original size:11 final size:10
Alignment explanation
Indices: 9391399--9391601 Score: 113
Period size: 10 Copynumber: 18.8 Consensus size: 10
9391389 GAATTACACC
*
9391399 AAAGAAAATA
1 AAAGAAAAAA
*
9391409 AAACAAAACAA
1 AAAGAAAA-AA
9391420 AACA-AAAAGAA
1 AA-AGAAAA-AA
*
9391431 AAAGAAAAGA
1 AAAGAAAAAA
9391441 AAAGAAAAGAAA
1 AAAG-AAA-AAA
9391453 AAAGAAAAAGA
1 AAAGAAAAA-A
* *
9391464 AGAGAAAATA
1 AAAGAAAAAA
9391474 AAAGAAAAAGGAA
1 AAAG-AAAA--AA
9391487 AAAGAAAAAA
1 AAAGAAAAAA
9391497 AGAAGAAAAAA
1 A-AAGAAAAAA
* *
9391508 ATA-AAGAAA
1 AAAGAAAAAA
* *
9391517 AAATAAAGGAA
1 AAAGAAA-AAA
*
9391528 AAAGAAATAA
1 AAAGAAAAAA
9391538 AAAGAAAAAGA
1 AAAGAAAAA-A
*
9391549 GAGAAGAAATAA
1 -A-AAGAAAAAA
9391561 AAAGAAAAAGA
1 AAAGAAAAA-A
* *
9391572 GAGAATAAATAA
1 -A-AAGAAAAAA
*
9391584 AAAGAAGAAA
1 AAAGAAAAAA
9391594 AAAGAAAA
1 AAAGAAAA
9391602 GAGAAAAAAG
Statistics
Matches: 150, Mismatches: 25, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
9 7 0.05
10 55 0.37
11 55 0.37
12 15 0.10
13 18 0.12
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.04
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:9393700 original size:66 final size:65
Alignment explanation
Indices: 9393625--9393798 Score: 165
Period size: 66 Copynumber: 2.7 Consensus size: 65
9393615 CTTGGGAAAG
* *
9393625 TTTCCCTTAAAACATAAATTTTGAAATTGTTTCACTCGAATCAAATTTTTATCTCACATGAGATA
1 TTTCCCTTAAAACACAAATTTTGAAATTGTTTCACTCGAA-CAAATTTTTATCTCACATGAGACA
*
9393690 T
65 A
* * * * * * * * *
9393691 TTTCTCTTAAAATACGAATTATGAAATTATTTCATTC--A-AAATTTTTTTCTTACTTGAGACAA
1 TTTCCCTTAAAACACAAATTTTGAAATTGTTTCACTCGAACAAATTTTTATCTCACATGAGACAA
* * *
9393753 GTTCCCTTTGAAACACAAATTTTAAAATTGTTTCACTCGAAACAAA
1 TTTCCC-TTAAAACACAAATTTTGAAATTGTTTCACTCG-AACAAA
9393799 ATTGATCTTA
Statistics
Matches: 82, Mismatches: 21, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
62 23 0.28
63 24 0.29
64 1 0.01
66 31 0.38
67 3 0.04
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.40
Consensus pattern (65 bp):
TTTCCCTTAAAACACAAATTTTGAAATTGTTTCACTCGAACAAATTTTTATCTCACATGAGACAA
Found at i:9393887 original size:103 final size:102
Alignment explanation
Indices: 9393742--9394021 Score: 303
Period size: 103 Copynumber: 2.7 Consensus size: 102
9393732 TTTTTTTCTT
* * * * *
9393742 ACTTGAGACAA-GTTCCCTTTGAAACACAAATTTTAAAATTGTTTCACTCGAAACAAAATTGATC
1 ACTTGAGACAATTTTCCC-TTGAAACACAAAATTTGAAATTGTTTCACTCGAAACCAAATTAATC
* * * *
9393806 TTACTTTAGATTATTTTTGTCAAAACCAATTTTATCTC
65 TCACTTGAGATTATTTTTCTCAAAACCAATTTCATCTC
* * * * *
9393844 GCTTGAGATAGTTTTCCCTTGAAACACAAAATTTGGAATTTGTTTCACTTGAAACCAAATTAATC
1 ACTTGAGACAATTTTCCCTTGAAACACAAAATTT-GAAATTGTTTCACTCGAAACCAAATTAATC
* * *
9393909 TCACTTGAGATTGTTTTTCTTAAAATCAATTTCATCTC
65 TCACTTGAGATTATTTTTCTCAAAACCAATTTCATCTC
* * * * * *
9393947 ACTTGAGACAATTTTCTCTTGGAATATAAAACTTGAAATTG-TTCACTCGAAACCAAATTTTATC
1 ACTTGAGACAATTTTCCCTTGAAACACAAAATTTGAAATTGTTTCACTCGAAACCAAA-TTAATC
*
9394011 TCACCTGAGAT
65 TCACTTGAGAT
9394022 AGCTTCTCTT
Statistics
Matches: 146, Mismatches: 29, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
101 15 0.10
102 44 0.30
103 87 0.60
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (102 bp):
ACTTGAGACAATTTTCCCTTGAAACACAAAATTTGAAATTGTTTCACTCGAAACCAAATTAATCT
CACTTGAGATTATTTTTCTCAAAACCAATTTCATCTC
Found at i:9394785 original size:117 final size:115
Alignment explanation
Indices: 9394641--9394888 Score: 311
Period size: 116 Copynumber: 2.1 Consensus size: 115
9394631 TGTTCCTTTT
* *
9394641 AAATCCATCACAGAAGGAGATGGATCATCATTCCCAAT-GAAGAGTTCATAATGAGAAAAACTCA
1 AAATCCATCACAGAAGAAGATGGATCATCATTCCCAATAAAAG-GTTCATAATGAGAAAAACTCA
* * * *
9394705 TTCAAAGAGGGAGAAGAAGTTCATAATGA-CAGAACTTGTTCAACCTTTTGCTA
65 TTCAAA-A-AG-GAAGAAGTTCATAATGAGAAGAACTTGGTCAACCTTTTACTA
* *** *
9394758 AAATCCATTACAGAAGAAGATGGATCATCATTTTTAATAAAATGGTTCATAATGAGAAGAACTCA
1 AAATCCATCACAGAAGAAGATGGATCATCATTCCCAATAAAA-GGTTCATAATGAGAAAAACTCA
* * *
9394823 TTCAAAAAGGAAGAAGTTTATAATGAGAAGAACTTGGTCGACCTTTTACTC
65 TTCAAAAAGGAAGAAGTTCATAATGAGAAGAACTTGGTCAACCTTTTACTA
9394874 AAATCCATCACAGAA
1 AAATCCATCACAGAA
9394889 TAAAGTGGAT
Statistics
Matches: 113, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
115 16 0.14
116 34 0.30
117 34 0.30
118 28 0.25
119 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (115 bp):
AAATCCATCACAGAAGAAGATGGATCATCATTCCCAATAAAAGGTTCATAATGAGAAAAACTCAT
TCAAAAAGGAAGAAGTTCATAATGAGAAGAACTTGGTCAACCTTTTACTA
Found at i:9394838 original size:118 final size:115
Alignment explanation
Indices: 9394417--9394888 Score: 320
Period size: 105 Copynumber: 4.2 Consensus size: 115
9394407 AACATCAATA
* * * * * * *** *
9394417 TTTTACTCAAATCCATCACAAAATAAGGTGGATCGTCATTTCCAACGGAGAGTTCAAAATGAGAA
1 TTTTACTAAAATCCATCACAGAAGAAGATGGATCATCATTCCCAATAAAGAGTTCATAATGAGAA
* ** * ** *
9394482 GATTTCATCCAAATAAGGGGAAGAAGTTCATAATGAGAATTACTT-GT--TCC
66 AAACTCATTCAAA-AA--GGAAGAAGTTCATAATGAGAAGAACTTGGTCAACC
* * * *
9394532 -TTT-C--AAATCCATCACAGAAGGAGATGGACCAAT-ATTTCC-A-GAAGAGTTCATAATGAGA
1 TTTTACTAAAATCCATCACAGAAGAAGATGGATC-ATCATTCCCAATAAAGAGTTCATAATGAGA
* ** ** * * *
9394590 AGAACTC-GCCCCAAAGG-AGAAAGTTCATAATGAGAATATCTT-GT--TCC
65 AAAACTCATTCAAAAAGGAAG-AAGTTCATAATGAGAAGAACTTGGTCAACC
* *
9394637 -TTT--T-AAATCCATCACAGAAGGAGATGGATCATCATTCCCAATGAAGAGTTCATAATGAGAA
1 TTTTACTAAAATCCATCACAGAAGAAGATGGATCATCATTCCCAATAAAGAGTTCATAATGAGAA
* * *
9394698 AAACTCATTCAAAGAGGGAGAAGAAGTTCATAATGA-CAGAACTTGTTCAACC
66 AAACTCATTCAAA-A-AG-GAAGAAGTTCATAATGAGAAGAACTTGGTCAACC
* * ***
9394750 TTTTGCTAAAATCCATTACAGAAGAAGATGGATCATCATTTTTAATAAA-ATGGTTCATAATGAG
1 TTTTACTAAAATCCATCACAGAAGAAGATGGATCATCATTCCCAATAAAGA--GTTCATAATGAG
* * *
9394814 AAGAACTCATTCAAAAAGGAAGAAGTTTATAATGAGAAGAACTTGGTCGACC
64 AAAAACTCATTCAAAAAGGAAGAAGTTCATAATGAGAAGAACTTGGTCAACC
*
9394866 TTTTACTCAAATCCATCACAGAA
1 TTTTACTAAAATCCATCACAGAA
9394889 TAAAGTGGAT
Statistics
Matches: 293, Mismatches: 43, Indels: 41
0.78 0.11 0.11
Matches are distributed among these distances:
104 4 0.01
105 60 0.20
106 1 0.00
107 26 0.09
108 5 0.02
109 22 0.08
110 7 0.02
111 42 0.14
112 3 0.01
113 3 0.01
114 6 0.02
115 16 0.05
116 36 0.12
117 36 0.12
118 26 0.09
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (115 bp):
TTTTACTAAAATCCATCACAGAAGAAGATGGATCATCATTCCCAATAAAGAGTTCATAATGAGAA
AAACTCATTCAAAAAGGAAGAAGTTCATAATGAGAAGAACTTGGTCAACC
Found at i:9395868 original size:14 final size:14
Alignment explanation
Indices: 9395849--9395881 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
9395839 TTTTTTATTC
9395849 AATTTCAATC-CTTT
1 AATTTC-ATCACTTT
9395863 AATTTCATCACTTT
1 AATTTCATCACTTT
9395877 AATTT
1 AATTT
9395882 TCTATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (14 bp):
AATTTCATCACTTT
Found at i:9397945 original size:20 final size:22
Alignment explanation
Indices: 9397907--9397953 Score: 80
Period size: 20 Copynumber: 2.2 Consensus size: 22
9397897 GTAAACAACC
9397907 CTAACAAATCTTAGACAGCTCA
1 CTAACAAATCTTAGACAGCTCA
9397929 CTAAC-AATCTT-GACAGCTCA
1 CTAACAAATCTTAGACAGCTCA
9397949 CTAAC
1 CTAAC
9397954 GAACCTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 14 0.56
21 6 0.24
22 5 0.20
ACGTcount: A:0.38, C:0.30, G:0.09, T:0.23
Consensus pattern (22 bp):
CTAACAAATCTTAGACAGCTCA
Found at i:9407440 original size:24 final size:24
Alignment explanation
Indices: 9407408--9407457 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
9407398 AATATGTTAG
*
9407408 TTTGGTGTATTTATGGATTATTAC
1 TTTGGTGTATTTATAGATTATTAC
*
9407432 TTTGGTGTATTTATAGATTGTTAC
1 TTTGGTGTATTTATAGATTATTAC
9407456 TT
1 TT
9407458 ATGAGTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.04, G:0.20, T:0.56
Consensus pattern (24 bp):
TTTGGTGTATTTATAGATTATTAC
Found at i:9408111 original size:282 final size:285
Alignment explanation
Indices: 9407547--9408113 Score: 876
Period size: 285 Copynumber: 2.0 Consensus size: 285
9407537 TTAACCTTTG
* * *
9407547 TATTGTATTATTAAATTTTACATATATATTTTTTTAAATAAGAATAAAGATCTGGTCAGTGGCGG
1 TATTGAATTATTAAATTTTACATATATATTTTTTTAAATAAGAATAAAGATCTGATAAGTGGCGG
*
9407612 AACACAATTGAGGCTAATGAGAACAACGTCCCCCAGAATTTGAAAAATTATAATTTAAACATTTA
66 AACACAATGGAGGCTAATGAGAACAACGTCCCCCAGAATTTGAAAAATTATAATTTAAACATTTA
* * *
9407677 AAATTTATAAAATATTTAATTTGGCCTCCATAAATTTTTTAAAAATTCATATTATTCTTTAATTT
131 AAATTTATAAAATATTTAATTTGGCCTCCATAAAATATTTAAAAATTCATATTAATCTTTAATTT
*
9407742 TTTTTGAATATCCTTAATTAAACCCCTCCCATAATTTTTAAAAATTCTCGTTAAGTCTCTTAAAA
196 TTTTTGAATATCCTTAATTAAACCCCTCCCATAATTTTTAAAAATTCTCATTAAGTCTCTTAAAA
*
9407807 TTTAAAAAATTTAAATTAGACCCTA
261 TTTAAAAAAATTAAATTAGACCCTA
* * * *
9407832 TATTGAATTATTAAATTTTACATATATGTTTTTTTTAAATAAGATTAAAGTTTTGATAAGTGGCG
1 TATTGAATTATTAAATTTTACATATAT-ATTTTTTTAAATAAGAATAAAGATCTGATAAGTGGCG
* * * * *
9407897 GAACACAATGGAGGGTAGTGGGAACCACGT-CCCCA-AATTTTACAAAATTATAATTTAAACATT
65 GAACACAATGGAGGCTAATGAGAACAACGTCCCCCAGAATTTGA-AAAATTATAATTTAAACATT
* *
9407960 TAAAATTTATAAAATATTTAATTTGGCC-CCATAAAATATTTAGATATTCATATTAATCTTTAA-
129 TAAAATTTATAAAATATTTAATTTGGCCTCCATAAAATATTTAAAAATTCATATTAATCTTTAAT
*
9408023 TTTTTTT-AATATCCTTAATTAAACCCCTCCCATAATTTTTGAAAATTCTCATTAAGTCTCTTAA
194 TTTTTTTGAATATCCTTAATTAAACCCCTCCCATAATTTTTAAAAATTCTCATTAAGTCTCTTAA
9408087 AATTTAAAAAAAATT-AATTAGACCCTA
259 AATTT-AAAAAAATTAAATTAGACCCTA
9408114 ATCTTTTTGG
Statistics
Matches: 258, Mismatches: 21, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
282 72 0.28
283 15 0.06
284 36 0.14
285 79 0.31
286 56 0.22
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.40
Consensus pattern (285 bp):
TATTGAATTATTAAATTTTACATATATATTTTTTTAAATAAGAATAAAGATCTGATAAGTGGCGG
AACACAATGGAGGCTAATGAGAACAACGTCCCCCAGAATTTGAAAAATTATAATTTAAACATTTA
AAATTTATAAAATATTTAATTTGGCCTCCATAAAATATTTAAAAATTCATATTAATCTTTAATTT
TTTTTGAATATCCTTAATTAAACCCCTCCCATAATTTTTAAAAATTCTCATTAAGTCTCTTAAAA
TTTAAAAAAATTAAATTAGACCCTA
Found at i:9409901 original size:30 final size:31
Alignment explanation
Indices: 9409861--9409918 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
9409851 GTAATATGAA
*
9409861 TTTTTAAAAATTT-AGGGGTATAAATTAATT
1 TTTTTAAAAATTTGAAGGGTATAAATTAATT
* *
9409891 TTTTTGAAAATTTGAAGGGTCTAAATTA
1 TTTTTAAAAATTTGAAGGGTATAAATTA
9409919 TAATATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.45
Consensus pattern (31 bp):
TTTTTAAAAATTTGAAGGGTATAAATTAATT
Found at i:9412070 original size:10 final size:11
Alignment explanation
Indices: 9412037--9412072 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
9412027 CACTTTTCAC
*
9412037 TTTATTATTTT
1 TTTATTAATTT
9412048 TTTATTAATTT
1 TTTATTAATTT
9412059 TTTATTAATTT
1 TTTATTAATTT
9412070 TTT
1 TTT
9412073 TGATAAGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTATTAATTT
Found at i:9412501 original size:2 final size:2
Alignment explanation
Indices: 9412494--9412520 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9412484 TAAAATTTTC
9412494 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9412521 GTGCAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9414445 original size:17 final size:17
Alignment explanation
Indices: 9414392--9414440 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
9414382 TTGGACCCTT
* *
9414392 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
9414410 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
9414428 AGTGCATTCGATG
1 AGTGCA-TCGATG
9414441 TTCAAAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:9414607 original size:65 final size:62
Alignment explanation
Indices: 9414412--9414616 Score: 202
Period size: 65 Copynumber: 3.2 Consensus size: 62
9414402 TGCACTAAGA
* * ** * *
9414412 GTGCATCGATGCATCAAGTGCATTCGATGTTCAAAAT-AGCCAGAGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTCAATATAATTCAGTGCATCGATGCATGGTTG
* * *
9414473 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCTCAGTGTATCGGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG--TTCAATATAAT--TCAGTGCATCGATGCATGGT-
9414537 T-
61 TG
* *
9414538 GTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCATGGTGCATCGATGCATGGATTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTCAATATAATTCA--GTGCATCGATGCATGG-TTG
*
9414603 GTGCAT-GGTGCATC
1 GTGCATCGATGCATC
9414617 GATGCATGGA
Statistics
Matches: 117, Mismatches: 16, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
61 28 0.24
62 5 0.04
63 7 0.06
64 26 0.22
65 50 0.43
66 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (62 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTCAATATAATTCAGTGCATCGATGCATGGTTG
Found at i:9414609 original size:27 final size:27
Alignment explanation
Indices: 9414579--9414643 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
9414569 CAATTTAATT
9414579 CATGGTGCATCGATGCATGGATTGGTG
1 CATGGTGCATCGATGCATGGATTGGTG
9414606 CATGGTGCATCGATGCATGGATTGGTG
1 CATGGTGCATCGATGCATGGATTGGTG
9414633 CATGGTGCATC
1 CATGGTGCATC
9414644 ACTCTGAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.18, C:0.17, G:0.35, T:0.29
Consensus pattern (27 bp):
CATGGTGCATCGATGCATGGATTGGTG
Found at i:9414624 original size:15 final size:15
Alignment explanation
Indices: 9414579--9414625 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
9414569 CAATTTAATT
9414579 CATGGTGCATCGATG
1 CATGGTGCATCGATG
* *
9414594 CAT-G-G-ATTGGTG
1 CATGGTGCATCGATG
9414606 CATGGTGCATCGATG
1 CATGGTGCATCGATG
9414621 CATGG
1 CATGG
9414626 ATTGGTGCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
12 8 0.32
13 2 0.08
14 2 0.08
15 13 0.52
ACGTcount: A:0.19, C:0.17, G:0.36, T:0.28
Consensus pattern (15 bp):
CATGGTGCATCGATG
Found at i:9414963 original size:39 final size:39
Alignment explanation
Indices: 9414915--9415000 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
9414905 TTTCAATTTA
*
9414915 GAAAA-ATTACTCCCCCTTACTATAACATTTCTCCCTTT
1 GAAAACATTACTCCCCCTTACTATAACACTTCTCCCTTT
*
9414953 GAAAACATTACTCCCCCTTACTATAATACTTCTCCCTTT
1 GAAAACATTACTCCCCCTTACTATAACACTTCTCCCTTT
9414992 GAAAACATT
1 GAAAACATT
9415001 TTAACACACT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 5 0.11
39 40 0.89
ACGTcount: A:0.31, C:0.30, G:0.03, T:0.35
Consensus pattern (39 bp):
GAAAACATTACTCCCCCTTACTATAACACTTCTCCCTTT
Found at i:9415656 original size:21 final size:21
Alignment explanation
Indices: 9415632--9415675 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
9415622 GAGCTGGAGG
* *
9415632 AGGAGGAGCACGAGAGGAGCT
1 AGGAGCAGCACGAGAGGAACT
* *
9415653 AGGAGCAGCTCGTGAGGAACT
1 AGGAGCAGCACGAGAGGAACT
9415674 AG
1 AG
9415676 CTATCGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.43, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAGGAACT
Found at i:9420940 original size:22 final size:21
Alignment explanation
Indices: 9420898--9420937 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
9420888 GAGTTTATTT
*
9420898 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
9420919 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
9420938 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:9422897 original size:18 final size:17
Alignment explanation
Indices: 9422843--9422891 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
9422833 TTGGACCCTT
* *
9422843 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
9422861 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
9422879 AGTGCATTCGATG
1 AGTGCA-TCGATG
9422892 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:9422932 original size:19 final size:19
Alignment explanation
Indices: 9422908--9422959 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
9422898 AATAGCCAGA
9422908 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
9422927 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
9422946 GTGCATCGATGCAT
1 GTGCATCGATGCAT
9422960 CAAATGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.17, C:0.21, G:0.35, T:0.27
Consensus pattern (19 bp):
GTGCATCGATGCATGGCTG
Found at i:9423019 original size:83 final size:83
Alignment explanation
Indices: 9422863--9423020 Score: 205
Period size: 83 Copynumber: 1.9 Consensus size: 83
9422853 TGCACTAAGA
* * ***
9422863 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCAAA
9422928 TGCATCGATGCATGGCTG
66 TGCATCGATGCATGGCTG
* *
9422946 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCAT-G-A
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGGCA
9423008 AATGCATTCGATG
64 AATGCA-TCGATG
9423021 TTCAATTTAA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
82 4 0.06
83 35 0.54
84 23 0.35
85 3 0.05
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (83 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCAAA
TGCATCGATGCATGGCTG
Found at i:9426651 original size:26 final size:26
Alignment explanation
Indices: 9426615--9426690 Score: 125
Period size: 26 Copynumber: 2.9 Consensus size: 26
9426605 TTCTTTAACA
*
9426615 TTAATCTAACCGAAATTATTTGACCG
1 TTAATCGAACCGAAATTATTTGACCG
*
9426641 TTAATGGAACCGAAATTATTTGACCG
1 TTAATCGAACCGAAATTATTTGACCG
9426667 TTAATCGAACCGAAATTTATTTGA
1 TTAATCGAACCGAAA-TTATTTGA
9426691 AAATTATTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
26 38 0.83
27 8 0.17
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (26 bp):
TTAATCGAACCGAAATTATTTGACCG
Found at i:9426652 original size:94 final size:95
Alignment explanation
Indices: 9426448--9426786 Score: 387
Period size: 95 Copynumber: 3.5 Consensus size: 95
9426438 TTTTTCTTTA
* *
9426448 ACCGTTAATCGAACTGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAAATTTTTTT
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAAACAAATTAACCGAAATTTTTTT
9426513 CTTTAACATTAATCGAACCGAAATTATTTG
66 CTTTAACATTAATCGAACCGAAATTATTTG
* *
9426543 ACCGTTAATCAAACCGAAATTTATTTGAAAATTATTAACCGAAACAAATTAACCG-ATTTTTTTT
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAAACAAATTAACCGAAATTTTTTT
*
9426607 CTTTAACATTAATCTAACCGAAATTATTTG
66 CTTTAACATTAATCGAACCGAAATTATTTG
* *** * *
9426637 ACCGTTAATGGAACCGAAA-TTATTTGACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAA
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATT-AT-TAACCG--A---A----ACAA--ATTAA
*
9426701 CC-AAATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTG
53 CCGAAATTTTTTTCTTTAA-CATTAATCGAACCGAAATTATTTG
* * * *
9426744 ACCATTAATCAAACCCAAATTTATTTGAAAATTATTCACCGAA
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAA
9426787 TAAAATAAAT
Statistics
Matches: 204, Mismatches: 24, Indels: 26
0.80 0.09 0.10
Matches are distributed among these distances:
93 10 0.05
94 56 0.27
95 57 0.28
97 1 0.00
100 1 0.00
101 1 0.00
104 4 0.02
106 25 0.12
107 39 0.19
108 10 0.05
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.36
Consensus pattern (95 bp):
ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAAACAAATTAACCGAAATTTTTTT
CTTTAACATTAATCGAACCGAAATTATTTG
Found at i:9426748 original size:26 final size:26
Alignment explanation
Indices: 9426613--9426771 Score: 115
Period size: 26 Copynumber: 6.0 Consensus size: 26
9426603 TTTTCTTTAA
* *
9426613 CATTAATCTAACCGAAATTATTTGAC
1 CATTAATCGAACCAAAATTATTTGAC
* * *
9426639 CGTTAATGGAACCGAAATTATTTGAC
1 CATTAATCGAACCAAAATTATTTGAC
* * *
9426665 CGTTAATCGAACCGAAATTTATTTGAA
1 CATTAATCGAACC-AAAATTATTTGAC
* * * * *
9426692 AATT-AT-TAACCAAATTTTTTTCTTTAAC
1 CATTAATCGAACCAAA----ATTATTTGAC
9426720 CATTAATCGAACCAAAATTATTTGAC
1 CATTAATCGAACCAAAATTATTTGAC
* *
9426746 CATTAATCAAACCCAAATTTATTTGA
1 CATTAATCGAA-CCAAAATTATTTGA
9426772 AAATTATTCA
Statistics
Matches: 105, Mismatches: 20, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
24 3 0.03
25 4 0.04
26 54 0.51
27 25 0.24
28 10 0.10
29 2 0.02
30 7 0.07
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (26 bp):
CATTAATCGAACCAAAATTATTTGAC
Found at i:9426777 original size:27 final size:26
Alignment explanation
Indices: 9426721--9426777 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
9426711 TTCTTTAACC
* **
9426721 ATTAATCGAACCAAAATTATTTGACC
1 ATTAATCAAACCAAAATTATTTGAAA
*
9426747 ATTAATCAAACCCAAATTTATTTGAAA
1 ATTAATCAAA-CCAAAATTATTTGAAA
9426774 ATTA
1 ATTA
9426778 TTCACCGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.33
Consensus pattern (26 bp):
ATTAATCAAACCAAAATTATTTGAAA
Found at i:9426829 original size:65 final size:66
Alignment explanation
Indices: 9426744--9426903 Score: 209
Period size: 65 Copynumber: 2.4 Consensus size: 66
9426734 AAATTATTTG
* * * *
9426744 ACCATTAATCAAACCCAAATTTATTTGAAAATTATTCACCGAATAAAAT-AA-ATTATTTTTCTT
1 ACCATTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACAAAATCAACATT-TTTTTCTT
9426807 TA
65 TA
* * *
9426809 ACCGTTAATCGAGCCGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGATTTTTTTCT
1 ACCATTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACAAAATCAA-C-ATTTTTTTCT
9426874 TTA
64 TTA
9426877 ACCATTAATCGAACCGAAA-TTATTTGA
1 ACCATTAATCGAACCGAAATTTATTTGA
9426904 CCGTTAATCT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
65 42 0.51
66 2 0.02
67 8 0.10
68 27 0.33
69 3 0.04
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.36
Consensus pattern (66 bp):
ACCATTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACAAAATCAACATTTTTTTCTTT
A
Found at i:9426882 original size:159 final size:159
Alignment explanation
Indices: 9426705--9427064 Score: 578
Period size: 159 Copynumber: 2.3 Consensus size: 159
9426695 TATTAACCAA
*
9426705 ATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCATTAATCAAACCCAAATTTATTT
1 ATTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCATTAATCAAACCCAAATTTATTT
* * *
9426770 GAAAATTATTCACCGAATAAAATAAATTA-TTTTTCTTTAACCGTTAATCGAGCCGAAATTTATT
66 GAAAATTATTAACCGAATAAAATAAATTATTTTTTCCTTAACCGTTAATCGAACCGAAA-TTATT
*
9426834 TGAAAATTATTAACCGAACCAAATCAACCG
130 TGAAAATTATTAACCGAACAAAATCAACCG
* * * *
9426864 ATTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCGTTAATCTAATCGAAATTTATTT
1 ATTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCATTAATCAAACCCAAATTTATTT
*
9426929 GAAAATTATTAACCGAATAAAATAAATTATTTTTTCCTTAACCGTTAATCGAACTGAAATTATTT
66 GAAAATTATTAACCGAATAAAATAAATTATTTTTTCCTTAACCGTTAATCGAACCGAAATTATTT
9426994 GAAAATTATTAACCGAACAAAATCAACCG
131 GAAAATTATTAACCGAACAAAATCAACCG
* *
9427023 ATTTTTTTTTCCTTAACCATTAATCGTACCGAAATTATTTGA
1 A--TTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGA
9427065 TCGTTAATGG
Statistics
Matches: 186, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
159 123 0.66
160 26 0.14
161 37 0.20
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.38
Consensus pattern (159 bp):
ATTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCATTAATCAAACCCAAATTTATTT
GAAAATTATTAACCGAATAAAATAAATTATTTTTTCCTTAACCGTTAATCGAACCGAAATTATTT
GAAAATTATTAACCGAACAAAATCAACCG
Found at i:9426909 original size:94 final size:92
Alignment explanation
Indices: 9426809--9426995 Score: 257
Period size: 94 Copynumber: 2.0 Consensus size: 92
9426799 TTTTTCTTTA
* * * *
9426809 ACCGTTAATCGAGCCGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGATTTTTTTCT
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACAAAAT-AAACGA-TTTTTTCC
9426874 TTAACCATTAATCGAACCGAAATTATTTG
64 TTAACCATTAATCGAACCGAAATTATTTG
* * * **
9426903 ACCGTTAATCTAATCGAAATTTATTTGAAAATTATTAACCGAATAAAATAAATTATTTTTTCCTT
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACAAAATAAACGATTTTTTCCTT
* *
9426968 AACCGTTAATCGAACTGAAATTATTTG
66 AACCATTAATCGAACCGAAATTATTTG
9426995 A
1 A
9426996 AAATTATTAA
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
92 35 0.43
93 3 0.04
94 44 0.54
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (92 bp):
ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACAAAATAAACGATTTTTTCCTT
AACCATTAATCGAACCGAAATTATTTG
Found at i:9427003 original size:65 final size:67
Alignment explanation
Indices: 9426903--9427064 Score: 213
Period size: 69 Copynumber: 2.4 Consensus size: 67
9426893 AAATTATTTG
* *
9426903 ACCGTTAATCTAA-TCGAAATTTATTTGAAAATTATTAACCGAATAAAAT-AA-ATTATTTTTTC
1 ACCGTTAATCGAACT-GAAA-TTATTTGAAAATTATTAACCGAACAAAATCAACATTATTTTTTC
9426965 CTTA
64 CTTA
*
9426969 ACCGTTAATCGAACTGAAATTATTTGAAAATTATTAACCGAACAAAATCAACCGATTTTTTTTTC
1 ACCGTTAATCGAACTGAAATTATTTGAAAATTATTAACCGAACAAAATCAA-C-ATTATTTTTTC
9427034 CTTA
64 CTTA
* * *
9427038 ACCATTAATCGTACCGAAATTATTTGA
1 ACCGTTAATCGAACTGAAATTATTTGA
9427065 TCGTTAATGG
Statistics
Matches: 85, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
65 28 0.33
66 18 0.21
67 1 0.01
69 38 0.45
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (67 bp):
ACCGTTAATCGAACTGAAATTATTTGAAAATTATTAACCGAACAAAATCAACATTATTTTTTCCT
TA
Found at i:9427081 original size:26 final size:26
Alignment explanation
Indices: 9427042--9427117 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
9427032 TCCTTAACCA
* * *
9427042 TTAATCGTACCGAAATTATTTGATCG
1 TTAATCGAATCGAAATTATTTGACCG
* *
9427068 TTAATGGAATCGAAATTATTTCACCG
1 TTAATCGAATCGAAATTATTTGACCG
*
9427094 TTAATCGAATCGAGATTTATTTGA
1 TTAATCGAATCGA-AATTATTTGA
9427118 ATATTATTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 33 0.80
27 8 0.20
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (26 bp):
TTAATCGAATCGAAATTATTTGACCG
Found at i:9430234 original size:13 final size:14
Alignment explanation
Indices: 9430211--9430240 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
9430201 TTCCCATTAC
9430211 AGACGTGCATATGA
1 AGACGTGCATATGA
9430225 AGAC-TGCATATGA
1 AGACGTGCATATGA
9430238 AGA
1 AGA
9430241 TTGTTCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AGACGTGCATATGA
Found at i:9431765 original size:28 final size:30
Alignment explanation
Indices: 9431734--9431795 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 30
9431724 TTATAAATTT
* *
9431734 TTCAAGGACCAAATTG-AA-TTTGATTTAA
1 TTCAAGGACCAAAGTGAAATTTTGATTAAA
*
9431762 TTCAAGGACTAAAGTGAAATTTTGATTAAA
1 TTCAAGGACCAAAGTGAAATTTTGATTAAA
9431792 TTCA
1 TTCA
9431796 TATCCAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 14 0.48
29 2 0.07
30 13 0.45
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (30 bp):
TTCAAGGACCAAAGTGAAATTTTGATTAAA
Found at i:9432319 original size:17 final size:17
Alignment explanation
Indices: 9432297--9432338 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
9432287 ACTTTGAAAA
*
9432297 AAAAGTCAAAAATTTTG
1 AAAAGTCAAAAATTTCG
9432314 AAAAGTCAAAAATTTCG
1 AAAAGTCAAAAATTTCG
9432331 AAAAGTCA
1 AAAAGTCA
9432339 TCTTTTATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.24
Consensus pattern (17 bp):
AAAAGTCAAAAATTTCG
Found at i:9433639 original size:39 final size:39
Alignment explanation
Indices: 9433503--9433679 Score: 144
Period size: 39 Copynumber: 4.5 Consensus size: 39
9433493 TTACCGCTTT
* * *
9433503 CCGCATGCTCCTC-GACTTTGTGCTTATGGTAAGTCCTTA
1 CCGCAGGCTCCTCTG-CTTTGTGCTCAAGGTAAGTCCTTA
* * * * *
9433542 CCGTAGGTTCCTCGGCTTTATGCTCAGGGTAAGTCCTTA
1 CCGCAGGCTCCTCTGCTTTGTGCTCAAGGTAAGTCCTTA
* * * *
9433581 CTGCATGTTCAT-TGACTTTGTGCTCAAGGTAAGTCCTTA
1 CCGCAGGCTCCTCTG-CTTTGTGCTCAAGGTAAGTCCTTA
* * * * *
9433620 CTGCAGGCTCCTATGCTTTGTGCAC-AGGATAAGACTTTA
1 CCGCAGGCTCCTCTGCTTTGTGCTCAAGG-TAAGTCCTTA
*
9433659 CCACAGGCTCCTCTGCTTTGT
1 CCGCAGGCTCCTCTGCTTTGT
9433680 ACACATTCTG
Statistics
Matches: 112, Mismatches: 22, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
38 4 0.04
39 105 0.94
40 3 0.03
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (39 bp):
CCGCAGGCTCCTCTGCTTTGTGCTCAAGGTAAGTCCTTA
Found at i:9436450 original size:20 final size:20
Alignment explanation
Indices: 9436425--9436477 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
9436415 ATCTTCTTGT
9436425 CCAAAGGTCTTATAGATGAC
1 CCAAAGGTCTTATAGATGAC
*
9436445 CCAAAGGTCTTATAGATGGC
1 CCAAAGGTCTTATAGATGAC
*
9436465 CCAAAGGACTTAT
1 CCAAAGGTCTTAT
9436478 CATCTTGCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (20 bp):
CCAAAGGTCTTATAGATGAC
Found at i:9436794 original size:42 final size:41
Alignment explanation
Indices: 9436715--9436818 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 41
9436705 CAAAGGAGTT
* * *
9436715 ATAGATGGCACGAAGGACTTATCATCTTGCTCGAAAGACTG
1 ATAGATGGCCCGAAGGACTTATCATCATGCTCAAAAGACTG
* * *
9436756 ATAGATGACCCGAAGGATTTAATCATCATGCTCAAAAGACTT
1 ATAGATGGCCCGAAGGACTT-ATCATCATGCTCAAAAGACTG
9436798 ACT-GATGGCCCGAAGGACTTA
1 A-TAGATGGCCCGAAGGACTTA
9436819 CCAATTTTGG
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 18 0.34
42 34 0.64
43 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (41 bp):
ATAGATGGCCCGAAGGACTTATCATCATGCTCAAAAGACTG
Found at i:9436906 original size:259 final size:259
Alignment explanation
Indices: 9436445--9436944 Score: 795
Period size: 259 Copynumber: 1.9 Consensus size: 259
9436435 TATAGATGAC
* * * *
9436445 CCAAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGATCTGA
1 CCAAAGGACTTATAGATGGCACAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGA
* ** * * *
9436510 ATGATTTAATCATCATGCTTGAAATATTTATTGATGGCCCGAAGGACTTACCAATTTTGGAAATA
66 AGGATTTAATCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATA
* *
9436575 GTTTACTACGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTTCAAAATTTCATTTTCTGAAAAT
131 GTTTACTACGTAAGAAACTTTGGAAATCGCTTCCTTACTTTTTCAAAATTTCATTTTCTAAAAAT
** *
9436640 ACTAAATGAGAAACTTTGAAAATTGCCTTCTCATTTTTCAAATTATCATATGAAAGCATCTTAT
196 ACTAAATGAGAAACTTTGAAAATCACCTTCTCATTTTTAAAATTATCATATGAAAGCATCTTAT
* * *
9436704 CCAAAGGAGTTATAGATGGCACGAAGGACTTATCATCTTGCTCGAAAGACTGATAGATGACCCGA
1 CCAAAGGACTTATAGATGGCACAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGA
9436769 AGGATTTAATCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATA
66 AGGATTTAATCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATA
*
9436834 GTTTACTATGTAAGAAACTTTGGAAATCGCTTCCTTAC-TTTTCAAAAATTTCATTTTCTAAAAA
131 GTTTACTACGTAAGAAACTTTGGAAATCGCTTCCTTACTTTTTC-AAAATTTCATTTTCTAAAAA
* *
9436898 TTCTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTAAAATTAT
195 TACTAAATGAGAAACTTTGAAAATCACCTTCTCATTTTTAAAATTAT
9436945 ATAAAAACAA
Statistics
Matches: 219, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
258 5 0.02
259 214 0.98
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (259 bp):
CCAAAGGACTTATAGATGGCACAAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGA
AGGATTTAATCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATA
GTTTACTACGTAAGAAACTTTGGAAATCGCTTCCTTACTTTTTCAAAATTTCATTTTCTAAAAAT
ACTAAATGAGAAACTTTGAAAATCACCTTCTCATTTTTAAAATTATCATATGAAAGCATCTTAT
Found at i:9439069 original size:27 final size:26
Alignment explanation
Indices: 9439039--9439158 Score: 106
Period size: 27 Copynumber: 4.6 Consensus size: 26
9439029 ACTTGATATG
*
9439039 TTTTCTTTCTTCTTTTTCTTCTTCTCA
1 TTTTCTTT-TTCTTTTTCTTCTTCTTA
9439066 TTTT-TTCTTCTCTTTTTCTTCTTCTTA
1 TTTTCTT-TT-TCTTTTTCTTCTTCTTA
* * *
9439093 TTTTATGTTTCTTTTTTCTT-TTCTTT
1 TTTTCTTTTTC-TTTTTCTTCTTCTTA
*
9439119 TCTTTCTTTTTCTTTTTCTTATT-TT-
1 T-TTTCTTTTTCTTTTTCTTCTTCTTA
*
9439144 TTCTC-TTTTCTTTTT
1 TTTTCTTTTTCTTTTT
9439159 TTATCTTAAA
Statistics
Matches: 81, Mismatches: 6, Indels: 16
0.79 0.06 0.16
Matches are distributed among these distances:
23 10 0.12
24 3 0.04
25 1 0.01
26 21 0.26
27 45 0.56
28 1 0.01
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (26 bp):
TTTTCTTTTTCTTTTTCTTCTTCTTA
Found at i:9439114 original size:5 final size:5
Alignment explanation
Indices: 9439106--9439157 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
9439096 TATGTTTCTT
*
9439106 TTTTC TTTTC TTTTC -TTTC TTTTTC TTTTTC TTATTT TTTCTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC -TTTTC -TTTTC TT-TTC TTT-TC TTTTC
9439154 TTTT
1 TTTT
9439158 TTTATCTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 4 0.10
5 19 0.46
6 18 0.44
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:9439118 original size:38 final size:38
Alignment explanation
Indices: 9439039--9439158 Score: 113
Period size: 38 Copynumber: 3.1 Consensus size: 38
9439029 ACTTGATATG
* *
9439039 TTTTCTTTCTTCTT-TTTCTTCTTCTCATTTTTTCTTCTCT
1 TTTTCTTTCTTCTTATTT-TTCTTAT--TTTTTTCTTTTCT
*
9439079 TTTTC-TTCTTCTTATTTTATGTT-TCTTTTTTCTTTTC-
1 TTTTCTTTCTTCTTATTTT-TCTTAT-TTTTTTCTTTTCT
* *
9439116 TTTTCTTTCTTTTTCTTTTTCTTATTTTTTCTCTTTTCT
1 TTTTCTTTCTTCTTATTTTTCTTATTTTTT-TCTTTTCT
9439155 TTTT
1 TTTT
9439159 TTATCTTAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
37 13 0.19
38 30 0.44
39 14 0.21
40 11 0.16
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (38 bp):
TTTTCTTTCTTCTTATTTTTCTTATTTTTTTCTTTTCT
Found at i:9439137 original size:33 final size:34
Alignment explanation
Indices: 9439039--9439165 Score: 88
Period size: 33 Copynumber: 3.6 Consensus size: 34
9439029 ACTTGATATG
*
9439039 TTTTC-TTTC-TTCTTTTTCTTCTTCTCATTTTTTC
1 TTTTCTTTTCTTTCTTTTTCTT-TTATC-TTTTTTC
*
9439073 TTCTCTTTTTCTTCTTCTTATTT-TATGTT-TCTTTTTTC
1 TTTTC-TTTTC-T-TTCTT-TTTCT-T-TTATCTTTTTTC
9439111 TTTTCTTTTCTTTCTTTTTCTTTT-TCTTATTTT-
1 TTTTCTTTTCTTTCTTTTTCTTTTATCTT-TTTTC
*
9439144 TTCTCTTTTCTTT-TTTTATCTT
1 TTTTCTTTTCTTTCTTTT-TCTT
9439166 AAATATGAAT
Statistics
Matches: 79, Mismatches: 4, Indels: 21
0.76 0.04 0.20
Matches are distributed among these distances:
32 4 0.05
33 22 0.28
34 12 0.15
35 6 0.08
36 5 0.06
37 5 0.06
38 11 0.14
39 8 0.10
40 6 0.08
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (34 bp):
TTTTCTTTTCTTTCTTTTTCTTTTATCTTTTTTC
Found at i:9439147 original size:43 final size:46
Alignment explanation
Indices: 9439066--9439165 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 46
9439056 CTTCTTCTCA
*
9439066 TTTTTTCTTCTCTTTTTCTTCTTCTTATTTTATGTTTCTTTTTTCTT
1 TTTTTTCTTCTCTTTTTCTTCTTCTTA-TTTATGTTTCTCTTTTCTT
*
9439113 TTCTTTTCTT-TCTTTTTCTTTTTCTTA-TT-T-TTTCTCTTTTCTT
1 TT-TTTTCTTCTCTTTTTCTTCTTCTTATTTATGTTTCTCTTTTCTT
9439156 TTTTTATCTT
1 TTTTT-TCTT
9439166 AAATATGAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
42 3 0.06
43 18 0.37
44 1 0.02
45 2 0.04
47 18 0.37
48 7 0.14
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.78
Consensus pattern (46 bp):
TTTTTTCTTCTCTTTTTCTTCTTCTTATTTATGTTTCTCTTTTCTT
Found at i:9446875 original size:3 final size:3
Alignment explanation
Indices: 9446852--9446888 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
9446842 GGCCTGCAAA
9446852 AAT AAT AA- AAT AA- AAT AAAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
9446889 ACCCAGGCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.13
3 24 0.77
4 3 0.10
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:9448610 original size:172 final size:172
Alignment explanation
Indices: 9448304--9448648 Score: 584
Period size: 172 Copynumber: 2.0 Consensus size: 172
9448294 TTATTTTTAA
*
9448304 GACATTATTGGTTAATTAAAATAGTTAACATATTTAATTATTCTAGTAAAAAATGATAAAGGAAA
1 GACATCATTGGTTAATTAAAATAGTTAACATATTTAATTATTCTAGTAAAAAATGATAAAGGAAA
* * *
9448369 CAAAAATACTAAATCGGAAAATTCCTGTTGGGAGACTCATTCATTAAAATCAGGTGTGTGACACA
66 CAAAAATACTAAATCGGAAAATTCCTGTTGGGAGACTCATTCACTAAAATCAGATATGTGACACA
* *
9448434 AGTCGGTCTGGATTAGTTAGGGTGAAACCCTTAAATCAGGAG
131 AGTCGGTCTGGATTAGTCAGGGCGAAACCCTTAAATCAGGAG
9448476 GACATCATTGGTTAATTAAAATAGTTAACATCA-TTAATTATTCTAGTAAAAAATGATAAAGGAA
1 GACATCATTGGTTAATTAAAATAGTTAACAT-ATTTAATTATTCTAGTAAAAAATGATAAAGGAA
* **
9448540 GCAAAAATACTAAATCGGAAAATTCCTGTTGGGAGACTCATTCACTAAAATCAGATATGTGATGC
65 ACAAAAATACTAAATCGGAAAATTCCTGTTGGGAGACTCATTCACTAAAATCAGATATGTGACAC
*
9448605 AAGTCGGTCTGGATTAGTCAGGGCGAAACCCTTAAATCGGGAG
130 AAGTCGGTCTGGATTAGTCAGGGCGAAACCCTTAAATCAGGAG
9448648 G
1 G
9448649 GCACAAAAAA
Statistics
Matches: 162, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
172 161 0.99
173 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (172 bp):
GACATCATTGGTTAATTAAAATAGTTAACATATTTAATTATTCTAGTAAAAAATGATAAAGGAAA
CAAAAATACTAAATCGGAAAATTCCTGTTGGGAGACTCATTCACTAAAATCAGATATGTGACACA
AGTCGGTCTGGATTAGTCAGGGCGAAACCCTTAAATCAGGAG
Found at i:9449339 original size:3 final size:3
Alignment explanation
Indices: 9449326--9449407 Score: 128
Period size: 3 Copynumber: 27.0 Consensus size: 3
9449316 ATTTGTATTC
9449326 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
9449372 AAT AAT AAT AAC AAT AAC AAT AAC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9449408 GAGGTACAAT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
3 69 0.96
4 3 0.04
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:9450058 original size:18 final size:20
Alignment explanation
Indices: 9450016--9450053 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9450006 ATAATAATGC
*
9450016 AGCTGAGTACAACTGATTGT
1 AGCTGACTACAACTGATTGT
9450036 AGCTGACTACAACTGATT
1 AGCTGACTACAACTGATT
9450054 AGCTGTAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (20 bp):
AGCTGACTACAACTGATTGT
Found at i:9453575 original size:28 final size:27
Alignment explanation
Indices: 9453543--9453605 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
9453533 AGAAAATCAG
*
9453543 AAAAGAAATTGAAGCACTCCAAAAGAA-A
1 AAAAGAAA-TCAAGCACT-CAAAAGAAGA
* *
9453571 GAAAGAAATCCAGCACTCAAAAGAAGA
1 AAAAGAAATCAAGCACTCAAAAGAAGA
9453598 AAAAGAAA
1 AAAAGAAA
9453606 AGAAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 8 0.27
27 15 0.50
28 7 0.23
ACGTcount: A:0.62, C:0.14, G:0.16, T:0.08
Consensus pattern (27 bp):
AAAAGAAATCAAGCACTCAAAAGAAGA
Found at i:9453608 original size:14 final size:14
Alignment explanation
Indices: 9453589--9453623 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
9453579 TCCAGCACTC
9453589 AAAAGAAGAAAAAG
1 AAAAGAAGAAAAAG
*
9453603 AAAAGAAAAAAAAG
1 AAAAGAAGAAAAAG
9453617 -AAAGAAG
1 AAAAGAAG
9453624 TTGAAGCACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAAAAG
Found at i:9454865 original size:24 final size:21
Alignment explanation
Indices: 9454831--9454873 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
9454821 TCCACAAGAT
*
9454831 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
9454853 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
9454874 ATAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:9458131 original size:15 final size:15
Alignment explanation
Indices: 9458113--9458168 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
9458103 AATTATGCTC
**
9458113 ATAATTCTTTGTCTA
1 ATAATTCTGCGTCTA
*
9458128 ATAATTATGCGTCTA
1 ATAATTCTGCGTCTA
9458143 ATAATTCTGC-TC--
1 ATAATTCTGCGTCTA
*
9458155 ATAATTCTGTGTCT
1 ATAATTCTGCGTCT
9458169 TCAATAAGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
12 9 0.26
13 2 0.06
14 2 0.06
15 21 0.62
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (15 bp):
ATAATTCTGCGTCTA
Found at i:9459385 original size:24 final size:24
Alignment explanation
Indices: 9459358--9459407 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
9459348 CACAATGTAC
9459358 CTTCATAACAACCATCCACATCAT
1 CTTCATAACAACCATCCACATCAT
** * *
9459382 CTTCATCTCATCCATCTACATCAT
1 CTTCATAACAACCATCCACATCAT
9459406 CT
1 CT
9459408 ACATCACTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.38, G:0.00, T:0.32
Consensus pattern (24 bp):
CTTCATAACAACCATCCACATCAT
Found at i:9459447 original size:27 final size:27
Alignment explanation
Indices: 9459428--9459490 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
9459418 CACTATCCCT
*
9459428 ATCTCTATCATCAACATCACTACCACC
1 ATCTCCATCATCAACATCACTACCACC
9459455 ATCTCCATCATCAACATCACTACCACC
1 ATCTCCATCATCAACATCACTACCACC
9459482 ATCTCCATC
1 ATCTCCATC
9459491 TCTATCATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.32, C:0.43, G:0.00, T:0.25
Consensus pattern (27 bp):
ATCTCCATCATCAACATCACTACCACC
Found at i:9459490 original size:33 final size:30
Alignment explanation
Indices: 9459393--9459498 Score: 92
Period size: 33 Copynumber: 3.4 Consensus size: 30
9459383 TTCATCTCAT
* * *
9459393 CCATCTACATCATCTACATCACTGTCACTATC
1 CCATCTCCATCATCAACATCAC--TCACCATC
*
9459425 CCTATCTCTATCATCAACATCACT-ACCA--
1 CC-ATCTCCATCATCAACATCACTCACCATC
9459453 CCATCTCCATCATCAACATCACTACCACCATC
1 CCATCTCCATCATCAACATCACT--CACCATC
*
9459485 TCCATCTCTATCAT
1 -CCATCTCCATCAT
9459499 TTTCATCTCC
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
27 20 0.33
28 2 0.03
30 7 0.11
31 1 0.02
32 2 0.03
33 29 0.48
ACGTcount: A:0.29, C:0.41, G:0.01, T:0.29
Consensus pattern (30 bp):
CCATCTCCATCATCAACATCACTCACCATC
Found at i:9459507 original size:15 final size:15
Alignment explanation
Indices: 9459481--9459524 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
9459471 TCACTACCAC
* *
9459481 CATCTCCATCTCTAT
1 CATCTTCATCTCCAT
*
9459496 CATTTTCATCTCCAT
1 CATCTTCATCTCCAT
*
9459511 TATCTTCATCTCCA
1 CATCTTCATCTCCA
9459525 CCATTACCAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.20, C:0.36, G:0.00, T:0.43
Consensus pattern (15 bp):
CATCTTCATCTCCAT
Found at i:9462186 original size:29 final size:30
Alignment explanation
Indices: 9462144--9462201 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
9462134 TAATTTTTAG
9462144 ATAAGAAGAGGTTAAATAAAAAAATAAAAA
1 ATAAGAAGAGGTTAAATAAAAAAATAAAAA
* * *
9462174 ATAA-AAGATGTTAAATTAAAAATTAAAA
1 ATAAGAAGAGGTTAAATAAAAAAATAAAA
9462202 TGAATTATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.22
Consensus pattern (30 bp):
ATAAGAAGAGGTTAAATAAAAAAATAAAAA
Found at i:9463339 original size:5 final size:5
Alignment explanation
Indices: 9463329--9463700 Score: 286
Period size: 5 Copynumber: 73.8 Consensus size: 5
9463319 GACTTCGACC
9463329 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
9463379 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
* * * * * *
9463429 TAT-G TATAA CATATA TATTA TATAA AAT-A TATGA TATAA TAT-A TATTA
1 TATAA TATAA TATA-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA
*** * * *
9463477 TACCG TAT-A TTTATA TATAC TATAA TATGA TAT-A TAT-A TATATA TATATA
1 TATAA TATAA TATA-A TATAA TATAA TATAA TATAA TATAA TATA-A TATA-A
* * *
9463527 TATATA TATAC TATAA TA-GA TA-ACA TATAA TATTA TACTATA TATAA
1 TATA-A TATAA TATAA TATAA TATA-A TATAA TATAA TA-TA-A TATAA
* *
9463574 TATAA AATAA TACT-A TACTATA TATAATA TATAA TATAA TATTA TAATAA
1 TATAA TATAA TA-TAA TA-TA-A TAT-A-A TATAA TATAA TATAA T-ATAA
* * *
9463624 CA-AA TATACA AATATA TATAC TATAA TAT-A TATAA TAT-A TACT-A
1 TATAA TATA-A TATA-A TATAA TATAA TATAA TATAA TATAA TA-TAA
* * *
9463668 TATAA TGT-A TATTA TATAA TATAG TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATA
9463701 TACTATCCCG
Statistics
Matches: 303, Mismatches: 41, Indels: 46
0.78 0.11 0.12
Matches are distributed among these distances:
4 37 0.12
5 212 0.70
6 42 0.14
7 12 0.04
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:9479088 original size:56 final size:56
Alignment explanation
Indices: 9479008--9479507 Score: 600
Period size: 56 Copynumber: 9.0 Consensus size: 56
9478998 GGTGTGCACG
* * * *
9479008 TAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCATGGGTTTTTCACACT
1 TAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGTTTTGCACACT
* ** * * *
9479064 TATTGATGATATGGTCGTTTATAAACATATTATGAATTACGTGGG--TTGCACACT
1 TAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGTTTTGCACACT
* *
9479118 TAGTGCCAATACGGTCGTTCATAAACATATTATGAATTTTGTGGGTTTTGCACACT
1 TAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGTTTTGCACACT
* *
9479174 TAGTGCCGATATGGTCGTTCATAAACATATTATGAATTTCAT-GGTTTTGCACACT
1 TAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGTTTTGCACACT
* ** * *
9479229 TAGTGTCGATACATTCATTCAAAAACATATTATGAATTTCGTGGG--TTGCACACT
1 TAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGTTTTGCACACT
* * * * **
9479283 TAGTGTCGATATGGTCATTCATAAACATATTATGAATTAT-ATGGGTTTAACACACT
1 TAGTGCCGATACGGTCGTTCATAAACATATTATGAATT-TCGTGGGTTTTGCACACT
* * * * *
9479339 TAGGGCCTATACAGTCGTTCATAAACATATTATGAATTACGTGGGTTTTACACACT
1 TAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGTTTTGCACACT
* * * *
9479395 TAGTACCGATATGGTTGTTCATAAACATATTATGAATTTCGTGGTTTTTGCACACT
1 TAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGTTTTGCACACT
* * * *
9479451 TAGTGCCGATACAGTAGTTCATAAACATATTATGAATTTCAT-GGTTTTACACACT
1 TAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGTTTTGCACACT
9479506 TA
1 TA
9479508 TGGTCGATAG
Statistics
Matches: 378, Mismatches: 59, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
54 92 0.24
55 62 0.16
56 224 0.59
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (56 bp):
TAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGTTTTGCACACT
Found at i:9479395 original size:221 final size:219
Alignment explanation
Indices: 9479008--9479516 Score: 691
Period size: 221 Copynumber: 2.3 Consensus size: 219
9478998 GGTGTGCACG
* * * *
9479008 TAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCATGGGTTTTTCACACTTATTGAT-G
1 TAGTGTCGATACAGTCATTCATAAACATATTATGAATTTCATGGG--TTACACACTTA-TG-TCG
* * * * * *
9479072 ATATGGTCGTTTATAAACATATTATGAATTACGTGGGTTGCACACTTAGTGCCAATACGGTCGTT
62 ATATGGTCATTCATAAACATATTATGAATTACATGGGTTACACACTTAGGGCCAATACAGTCGTT
** * *
9479137 CATAAACATATTATGAATTTTGTGGGTTTTGCACACTTAGTGCCGATATGGTCGTTCATAAACAT
127 CATAAACATATTATGAATTACGTGGGTTTTACACACTTAGTACCGATATGGTCGTTCATAAACAT
9479202 ATTATGAATTTCATGG-TTTTGCACACT
192 ATTATGAATTTCATGGTTTTTGCACACT
* * * *
9479229 TAGTGTCGATACATTCATTCAAAAACATATTATGAATTTCGTGGGTTGCACACTTAGTGTCGATA
1 TAGTGTCGATACAGTCATTCATAAACATATTATGAATTTCATGGGTTACACACTTA-TGTCGATA
* *
9479294 TGGTCATTCATAAACATATTATGAATTATATGGGTTTAACACACTTAGGGCCTATACAGTCGTTC
65 TGGTCATTCATAAACATATTATGAATTACATGGG-TT-ACACACTTAGGGCCAATACAGTCGTTC
*
9479359 ATAAACATATTATGAATTACGTGGGTTTTACACACTTAGTACCGATATGGTTGTTCATAAACATA
128 ATAAACATATTATGAATTACGTGGGTTTTACACACTTAGTACCGATATGGTCGTTCATAAACATA
*
9479424 TTATGAATTTCGTGGTTTTTGCACACT
193 TTATGAATTTCATGGTTTTTGCACACT
* *
9479451 TAGTGCCGATACAGT-AGTTCATAAACATATTATGAATTTCATGGTTTTACACACTTATGGTCGA
1 TAGTGTCGATACAGTCA-TTCATAAACATATTATGAATTTCATGG-GTTACACACTTAT-GTCGA
9479515 TA
63 TA
9479517 GTACACATAG
Statistics
Matches: 253, Mismatches: 28, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
218 1 0.00
219 46 0.18
220 2 0.01
221 137 0.54
222 50 0.20
223 17 0.07
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.37
Consensus pattern (219 bp):
TAGTGTCGATACAGTCATTCATAAACATATTATGAATTTCATGGGTTACACACTTATGTCGATAT
GGTCATTCATAAACATATTATGAATTACATGGGTTACACACTTAGGGCCAATACAGTCGTTCATA
AACATATTATGAATTACGTGGGTTTTACACACTTAGTACCGATATGGTCGTTCATAAACATATTA
TGAATTTCATGGTTTTTGCACACT
Found at i:9479998 original size:21 final size:19
Alignment explanation
Indices: 9479972--9480011 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
9479962 TCCCACAGCA
9479972 GTATCGATACTAATTGCATCG
1 GTATCGATACT-ATT-CATCG
9479993 GTATCGATACTATTCATCG
1 GTATCGATACTATTCATCG
9480012 TAATTCTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 3 0.16
21 11 0.58
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (19 bp):
GTATCGATACTATTCATCG
Found at i:9486202 original size:75 final size:73
Alignment explanation
Indices: 9486112--9486394 Score: 205
Period size: 64 Copynumber: 4.1 Consensus size: 73
9486102 TTAAACTCAA
*
9486112 ATTTAGGATAATATTTTAAACATTATATTTATCTTT-GTATTTTAGTTTAAATAGGTTTTTAGTA
1 ATTTAGGATATTATTTT-AACATTATATTTAT-TTTAGTATTTTAGTTTAAATAGG-TTTTAGTA
9486176 TTTTAATTAAG
63 TTTTAATTAAG
* *** * *
9486187 TTTTAGGATATTATTTTATTTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATT
1 ATTTAGGATATTATTTTAACATTATATTTATTTTA-GTATTTTAGTTTAAATAGGTTTTAGTATT
*
9486252 TTAATTAGG
65 TTAATTAAG
* * *
9486261 ATTTA-GA-A-TA--TT-ATATTAT-TTT-TTATAAT-TTTTAGGTATT--ATAGGTTTTAGTAT
1 ATTTAGGATATTATTTTAACATTATATTTATTTTAGTATTTTA-GT-TTAAATAGGTTTTAGTAT
*
9486315 TTTAATTAGG
64 TTTAATTAAG
* *
9486325 ATTTA-GA-A-TA--TT-ATA-T-TATTT-TTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGT
1 ATTTAGGATATTATTTTAACATTATATTTATTTTA-GTATTTTAGTTTAAATAGGTTTT-AGTAT
*
9486380 TTTAATTAGG
64 TTTAATTAAG
9486390 ATTTA
1 ATTTA
9486395 AGATGTTTTA
Statistics
Matches: 182, Mismatches: 16, Indels: 30
0.80 0.07 0.13
Matches are distributed among these distances:
62 1 0.01
63 10 0.05
64 52 0.29
65 30 0.16
66 6 0.03
67 3 0.02
68 5 0.03
69 2 0.01
71 2 0.01
72 1 0.01
73 5 0.03
74 31 0.17
75 34 0.19
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (73 bp):
ATTTAGGATATTATTTTAACATTATATTTATTTTAGTATTTTAGTTTAAATAGGTTTTAGTATTT
TAATTAAG
Found at i:9486260 original size:19 final size:19
Alignment explanation
Indices: 9486232--9486330 Score: 56
Period size: 19 Copynumber: 4.8 Consensus size: 19
9486222 GGTATTTTAG
*
9486232 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
9486251 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
9486270 ATTATATTATTTTTTA-TAATT
1 TTTA-ATTAGGTTTTAGT-A-T
9486291 TTTAGGTATTATAGGTTTTAGTAT
1 TTTA---A-T-TAGGTTTTAGTAT
*
9486315 TTTAATTAGGATTTAG
1 TTTAATTAGGTTTTAG
9486331 AATATTATAT
Statistics
Matches: 60, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
19 28 0.47
20 10 0.17
21 5 0.08
23 2 0.03
24 6 0.10
25 8 0.13
26 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:9486387 original size:65 final size:65
Alignment explanation
Indices: 9486217--9486394 Score: 267
Period size: 64 Copynumber: 2.8 Consensus size: 65
9486207 TTTATCTTTG
9486217 TTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATATTATTT
1 TTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATATTATTT
*
9486282 TTTATA-AT-TTTTAGGTATT--ATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATATTA
1 TTT-TAGGTATTTTA-GT-TTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATATTA
9486343 TTT
63 TTT
*
9486346 TTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTA
1 TTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGGATTTA
9486395 AGATGTTTTA
Statistics
Matches: 102, Mismatches: 3, Indels: 16
0.84 0.02 0.13
Matches are distributed among these distances:
63 4 0.04
64 61 0.60
65 33 0.32
66 4 0.04
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (65 bp):
TTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATATTATTT
Found at i:9487022 original size:18 final size:19
Alignment explanation
Indices: 9486979--9487023 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
9486969 TCTTTAACTT
* *
9486979 GTTTATTTAATTATTTTTC
1 GTTTATTTAATTACTTATC
*
9486998 TTTTATTTAATT-CTTATC
1 GTTTATTTAATTACTTATC
9487016 GTTTATTT
1 GTTTATTT
9487024 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.69
Consensus pattern (19 bp):
GTTTATTTAATTACTTATC
Found at i:9490014 original size:5 final size:5
Alignment explanation
Indices: 9490006--9490103 Score: 60
Period size: 5 Copynumber: 19.8 Consensus size: 5
9489996 ATATTTTTGT
* ** * **
9490006 TTTTA TTTTTG TTTTA TTTCG TTTTA TTTTTA TTTTA -TTT- TTTTA GTGAA
1 TTTTA -TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA
* * *
9490056 CTTTA TTTCA TTATA -TTTA TTTTA TTTTGA -TTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTT
9490104 TCTCTGAACA
Statistics
Matches: 69, Mismatches: 17, Indels: 13
0.70 0.17 0.13
Matches are distributed among these distances:
4 10 0.14
5 49 0.71
6 10 0.14
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:9490020 original size:11 final size:11
Alignment explanation
Indices: 9489997--9490047 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
9489987 CATTTCGTTA
9489997 TATTTTTGTTTT
1 TATTTTTG-TTT
9490009 TATTTTTGTTT
1 TATTTTTGTTT
*
9490020 TA-TTTCGTTT
1 TATTTTTGTTT
*
9490030 TATTTTTATTT
1 TATTTTTGTTT
9490041 TATTTTT
1 TATTTTT
9490048 TTAGTGAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
10 9 0.26
11 18 0.51
12 8 0.23
ACGTcount: A:0.12, C:0.02, G:0.06, T:0.80
Consensus pattern (11 bp):
TATTTTTGTTT
Found at i:9490032 original size:21 final size:21
Alignment explanation
Indices: 9490006--9490102 Score: 71
Period size: 21 Copynumber: 4.9 Consensus size: 21
9489996 ATATTTTTGT
*
9490006 TTTTATTTTTGTTTTATTTCG
1 TTTTATTTTTATTTTATTTCG
9490027 TTTTATTTTTATTTTATTT--
1 TTTTATTTTTATTTTATTTCG
* ** *
9490046 TTTTA-GTGAACTTTATTTC-
1 TTTTATTTTTATTTTATTTCG
* * *
9490065 -ATTATATTTATTTTATTTTG
1 TTTTATTTTTATTTTATTTCG
*
9490085 ATTTA-TTTTATTTTATTT
1 TTTTATTTTTATTTTATTT
9490103 TTCTCTGAAC
Statistics
Matches: 59, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
18 12 0.20
19 14 0.24
20 12 0.20
21 21 0.36
ACGTcount: A:0.19, C:0.03, G:0.05, T:0.73
Consensus pattern (21 bp):
TTTTATTTTTATTTTATTTCG
Found at i:9490060 original size:29 final size:25
Alignment explanation
Indices: 9490028--9490104 Score: 75
Period size: 29 Copynumber: 2.8 Consensus size: 25
9490018 TTTATTTCGT
9490028 TTTATTTTTATTTTATTTTTTTAGTGAA
1 TTTATTTTTATTTTATTTTTTT--TG-A
9490056 CTTTATTTCATTATATTTATTTTATTTTGA
1 -TTTATTT--TTAT-TTTATTTT-TTTTGA
9490086 TTTA-TTTTATTTTATTTTT
1 TTTATTTTTATTTTATTTTT
9490105 CTCTGAACAT
Statistics
Matches: 44, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
24 1 0.02
25 8 0.18
26 4 0.09
28 2 0.05
29 11 0.25
30 1 0.02
31 6 0.14
32 8 0.18
33 3 0.07
ACGTcount: A:0.21, C:0.03, G:0.04, T:0.73
Consensus pattern (25 bp):
TTTATTTTTATTTTATTTTTTTTGA
Found at i:9490090 original size:15 final size:14
Alignment explanation
Indices: 9490028--9490102 Score: 71
Period size: 15 Copynumber: 5.2 Consensus size: 14
9490018 TTTATTTCGT
9490028 TTTATTTTTATTTTA
1 TTTA-TTTTATTTTA
* **
9490043 TTT-TTTTAGTGAA
1 TTTATTTTATTTTA
* *
9490056 CTTTATTTCATTATA
1 -TTTATTTTATTTTA
9490071 TTTATTTTATTTTGA
1 TTTATTTTATTTT-A
9490086 TTTATTTTATTTTA
1 TTTATTTTATTTTA
9490100 TTT
1 TTT
9490103 TTCTCTGAAC
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
13 7 0.15
14 18 0.38
15 23 0.48
ACGTcount: A:0.21, C:0.03, G:0.04, T:0.72
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:9492084 original size:74 final size:75
Alignment explanation
Indices: 9491903--9492114 Score: 311
Period size: 74 Copynumber: 2.8 Consensus size: 75
9491893 TTTTATCTTT
* * * * * *
9491903 GTATTTTAGTTTAAATATGTTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTATTTTTTGT
1 GTATTTTAGTTTAAATA-GGTTTTAGTATTTTAATTAGGATTTAGAATATTATATTATTTTTTAT
9491968 CTTTGTTTTAG
65 CTTTGTTTTAG
*
9491979 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTGGGATTTAGAATATTATATTATTTTTTAT-
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATATTATTTTTTATC
9492043 TATT-TTTTAG
66 T-TTGTTTTAG
* *
9492053 GTATTTTAATTTAAATAGGTTTTAGTTTTTTAATTAGGATTTAGAATATTATATTATTTTTT
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATATTATTTTTT
9492115 TAGGTATTTT
Statistics
Matches: 125, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
74 66 0.53
75 42 0.34
76 17 0.14
ACGTcount: A:0.27, C:0.00, G:0.13, T:0.59
Consensus pattern (75 bp):
GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATATTATTTTTTATC
TTTGTTTTAG
Found at i:9492115 original size:65 final size:64
Alignment explanation
Indices: 9492040--9492160 Score: 190
Period size: 65 Copynumber: 1.9 Consensus size: 64
9492030 TATTATTTTT
**
9492040 TATTATTTTTTAGGTATTTTAATTTAAATAGGTTTT-AGTTTTTTAATTAGGATTTAGAATATTA
1 TATTATTTTTTAGGTATTTTAATTTAAATA-GTTTTAAGTGATTTAATTAGGATTTAGAATATTA
*
9492104 TATTATTTTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTGATTTAATTAGGATTTA
1 TATTA-TTTTTTAGGTATTTTAATTTAAATAGTTTTAAGTGATTTAATTAGGATTTA
9492161 AGATGTTTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
64 10 0.19
65 42 0.81
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (64 bp):
TATTATTTTTTAGGTATTTTAATTTAAATAGTTTTAAGTGATTTAATTAGGATTTAGAATATTA
Found at i:9492125 original size:74 final size:72
Alignment explanation
Indices: 9491903--9492160 Score: 282
Period size: 74 Copynumber: 3.6 Consensus size: 72
9491893 TTTTATCTTT
* * * * *
9491903 GTATTTTAGTTTAAATATGTTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTATTTTTTGT
1 GTATTTTAGTTTAAATA-GGTTTTAGTATTTTAATTAGGATTTAGAATATTATATTA-TTTTT-T
* *
9491968 CTTTGTTTTAG
63 -TATATTTTAG
*
9491979 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTGGGATTTAGAATATTATATTATTTTTTATT
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATATTA-TTTTT-TT
*
9492044 ATTTTTTAG
64 ATATTTTAG
* *
9492053 GTATTTTAATTTAAATAGGTTTTAGTTTTTTAATTAGGATTTAGAATATTATATTA-----TT-T
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATATTATTTTTTTAT
9492112 -TTTTAG
66 ATTTTAG
9492118 GTATTTTAGTTTAAATA-GTTTTAAGTGA-TTTAATTAGGATTTA
1 GTATTTTAGTTTAAATAGGTTTT-AGT-ATTTTAATTAGGATTTA
9492161 AGATGTTTTA
Statistics
Matches: 166, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
64 5 0.03
65 40 0.24
66 1 0.01
67 2 0.01
74 61 0.37
75 40 0.24
76 17 0.10
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (72 bp):
GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATATTATTTTTTTAT
ATTTTAG
Found at i:9492785 original size:18 final size:19
Alignment explanation
Indices: 9492746--9492789 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
9492736 CTTTAATTTG
* *
9492746 TTTATTTAATTATTTTTCT
1 TTTATTTAATTACTTATCT
9492765 TTTATTTAATT-CTTATCT
1 TTTATTTAATTACTTATCT
9492783 TTTATTT
1 TTTATTT
9492790 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATTTAATTACTTATCT
Found at i:9493183 original size:56 final size:55
Alignment explanation
Indices: 9493108--9493785 Score: 769
Period size: 55 Copynumber: 12.3 Consensus size: 55
9493098 TTCTTTGAGG
* * *
9493108 TGCACACGTAGTGCCGATACAGTCGTTCATAAACATATTATGAATTATGTGGGTTT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCTGT-GGTTT
* * * * *
9493164 TGAACACTTAGTGTCGATACGATC-TATCATAAACATATTATGAATTCCGTGG-GT
1 TGCACACTTAGTGCCGATACGGTCGT-TCATAAACATATTATGAATTCTGTGGTTT
* * * * * **
9493218 TGTACACTTAATGTCGATACTGTCATTTGTAAACATATTATGAATTCTGTGGTTT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCTGTGGTTT
* * *
9493273 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATAAATTCCGTGG-GT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCTGTGGTTT
* * * **
9493327 TGCACACTTAGTACCGAAATGGTCGTTCATAAACATATTATGAATTCCATGGTTT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCTGTGGTTT
* * *
9493382 TTCACACTTAGTGTC-ATACGGTC-TTCATAAATATATTATGAATT-TCGTGGGTTT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCT-GT-GGTTT
* * * * **
9493436 TGCACACTTAGTGCTGATACGGTTGTTCATAAACATATAACGAATTCCATGGTTT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCTGTGGTTT
* *
9493491 TGCACACTTAGTGCCGATACAGTCGTTCATAAACATATTATGAATTCTGTGG-GT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCTGTGGTTT
* ** * **
9493545 TGCACACTTTGTATCGATACGATCGTTCATAAACATATTATGAATTCCATGGTTT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCTGTGGTTT
* * * *
9493600 TACACACTTAGTGCCAATACAGTCGTTCATAAACATATTATGAATTATGTGGGTTT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCTGT-GGTTT
* * * *
9493656 TACAAACTTAGTGCCGATACGGTCGTTTATAAACATATTATGAATTCAGTGGTGTT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCTGTGGT-TT
* *
9493712 TGCATACTTAGTGCCGATACAGTCGTTCATAAACATATTATGAATT-TCGTGGTTT
1 TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCT-GTGGTTT
* *
9493767 TTCACACTTAGTGTCGATA
1 TGCACACTTAGTGCCGATA
9493786 GTACACATAG
Statistics
Matches: 520, Mismatches: 89, Indels: 27
0.82 0.14 0.04
Matches are distributed among these distances:
53 21 0.04
54 161 0.31
55 180 0.35
56 158 0.30
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (55 bp):
TGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCTGTGGTTT
Found at i:9493310 original size:109 final size:109
Alignment explanation
Indices: 9493108--9493785 Score: 801
Period size: 109 Copynumber: 6.2 Consensus size: 109
9493098 TTCTTTGAGG
* * * *** *
9493108 TGCACACGTAGTGCCGATACAGTCGTTCATAAACATATTATGAATTATGTGGGTTTTGAACACTT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCAT-GGTTTTGCACACTT
*
9493173 AGTGTCGATAC-GATC-TATCATAAACATATTATGAATTCCGTGGGT
65 AGTGCCGATACAG-TCGT-TCATAAACATATTATGAATTCCGTGGGT
* * * * ** **
9493218 TGTACACTTAATGTCGATACTGTCATTTGTAAACATATTATGAATTCTGTGGTTTTGCACACTTA
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCATGGTTTTGCACACTTA
* *
9493283 GTGCCGATACGGTCGTTCATAAACATATTATAAATTCCGTGGGT
66 GTGCCGATACAGTCGTTCATAAACATATTATGAATTCCGTGGGT
** * * *
9493327 TGCACACTTAGTACCGAAATGGTCGTTCATAAACATATTATGAATTCCATGGTTTTTCACACTTA
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCATGGTTTTGCACACTTA
* * * *
9493392 GTGTC-ATACGGTC-TTCATAAATATATTATGAATTTCGTGGGTTT
66 GTGCCGATACAGTCGTTCATAAACATATTATGAATTCCGTGGG--T
* * *
9493436 TGCACACTTAGTG-CTGATACGGTTGTTCATAAACATATAACGAATTCCATGGTTTTGCACACTT
1 TGCACACTTAGTGTC-GATACGGTCGTTCATAAACATATTATGAATTCCATGGTTTTGCACACTT
*
9493500 AGTGCCGATACAGTCGTTCATAAACATATTATGAATTCTGTGGGT
65 AGTGCCGATACAGTCGTTCATAAACATATTATGAATTCCGTGGGT
* * * *
9493545 TGCACACTTTGTATCGATACGATCGTTCATAAACATATTATGAATTCCATGGTTTTACACACTTA
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCATGGTTTTGCACACTTA
* **
9493610 GTGCCAATACAGTCGTTCATAAACATATTATGAATTATGTGGGTTT
66 GTGCCGATACAGTCGTTCATAAACATATTATGAATTCCGTGGG--T
* * * * *
9493656 TACAAACTTAGTGCCGATACGGTCGTTTATAAACATATTATGAATT-CAGTGGTGTTTGCATACT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCA-TGGT-TTTGCACACT
* *
9493720 TAGTGCCGATACAGTCGTTCATAAACATATTATGAATTTCGTGGTTT
64 TAGTGCCGATACAGTCGTTCATAAACATATTATGAATTCCGTGG-GT
*
9493767 TTCACACTTAGTGTCGATA
1 TGCACACTTAGTGTCGATA
9493786 GTACACATAG
Statistics
Matches: 489, Mismatches: 66, Indels: 25
0.84 0.11 0.04
Matches are distributed among these distances:
107 25 0.05
108 9 0.02
109 267 0.55
110 53 0.11
111 86 0.18
112 49 0.10
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (109 bp):
TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCATGGTTTTGCACACTTA
GTGCCGATACAGTCGTTCATAAACATATTATGAATTCCGTGGGT
Found at i:9504037 original size:105 final size:105
Alignment explanation
Indices: 9503855--9504049 Score: 356
Period size: 105 Copynumber: 1.9 Consensus size: 105
9503845 ACATTTATCG
*
9503855 TGACGTTTTCCTCGCCAACTCTCATGGTGAATTCTCCCTTTTCACAATCTATTAAAATTCTCCTG
1 TGACGCTTTCCTCGCCAACTCTCATGGTGAATTCTCCCTTTTCACAATCTATTAAAATTCTCCTG
9503920 GTGGCTAAGAATGGGCGTCCCAAAACCAAAAACTTGATCA
66 GTGGCTAAGAATGGGCGTCCCAAAACCAAAAACTTGATCA
*
9503960 TGACGCTTTGCTCGCCAACTCTCATGGTGAATTCTCCCTTTTCACAATCTATTAAAATTCT-CTC
1 TGACGCTTTCCTCGCCAACTCTCATGGTGAATTCTCCCTTTTCACAATCTATTAAAATTCTCCT-
9504024 GGTGGCTAAGAATGGGCGTCCCAAAA
65 GGTGGCTAAGAATGGGCGTCCCAAAA
9504050 TGGTTGGTGC
Statistics
Matches: 87, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
104 2 0.02
105 85 0.98
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (105 bp):
TGACGCTTTCCTCGCCAACTCTCATGGTGAATTCTCCCTTTTCACAATCTATTAAAATTCTCCTG
GTGGCTAAGAATGGGCGTCCCAAAACCAAAAACTTGATCA
Found at i:9514811 original size:15 final size:15
Alignment explanation
Indices: 9514791--9514820 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
9514781 TAAAAAACTT
9514791 TAGGTATTGATACCA
1 TAGGTATTGATACCA
9514806 TAGGTATTGATACCA
1 TAGGTATTGATACCA
9514821 AACATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (15 bp):
TAGGTATTGATACCA
Found at i:9517828 original size:13 final size:13
Alignment explanation
Indices: 9517810--9517837 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
9517800 TTTCTAAACC
9517810 ATTGTATGACTTT
1 ATTGTATGACTTT
9517823 ATTGTATGACTTT
1 ATTGTATGACTTT
9517836 AT
1 AT
9517838 GTGATGCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.54
Consensus pattern (13 bp):
ATTGTATGACTTT
Found at i:9518157 original size:193 final size:193
Alignment explanation
Indices: 9517823--9518180 Score: 608
Period size: 193 Copynumber: 1.9 Consensus size: 193
9517813 GTATGACTTT
* * *
9517823 ATTGTATGACTTTATGTGATGCATTAAACTTTGTATTGTGGACTAAATTATATGATTACTTTGGT
1 ATTGAATGACTTTATGTGATGCATTAAACTTTGTATTATGAACTAAATTATATGATTACTTTGGT
9517888 TGATAATTAGCATGTTTCTGATTACACATATGATCCATGGTTAAGCATGCCTTTATGTTATCCGT
66 TGATAATTAGCATGTTTCTGATTACACATATGATCCATGGTTAAGCATGCCTTTATGTTATCCGT
* * *
9517953 TAAATATTGAAAATATCTATTATGCCTGAAATATGTTTTAAGCGTTGATAACATTTCTAAACC
131 TAAAAATTGAAAAGATCTATTATGCCTAAAATATGTTTTAAGCGTTGATAACATTTCTAAACC
* * *
9518016 ATTGAATGACTTTATTTGATGTATTGAACTTTGTATTATGAACTAAATTATATGATTACTTTGGT
1 ATTGAATGACTTTATGTGATGCATTAAACTTTGTATTATGAACTAAATTATATGATTACTTTGGT
* * *
9518081 TGATAATTAGCATGTTTCTGATTACACATATGATTCATGGTTAAGCATGCCTTTGTGTTATCTGT
66 TGATAATTAGCATGTTTCTGATTACACATATGATCCATGGTTAAGCATGCCTTTATGTTATCCGT
9518146 TAAAAATTGAAAAGATCTATTATGCCTAAAATATG
131 TAAAAATTGAAAAGATCTATTATGCCTAAAATATG
9518181 ACTTTATCTG
Statistics
Matches: 153, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
193 153 1.00
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (193 bp):
ATTGAATGACTTTATGTGATGCATTAAACTTTGTATTATGAACTAAATTATATGATTACTTTGGT
TGATAATTAGCATGTTTCTGATTACACATATGATCCATGGTTAAGCATGCCTTTATGTTATCCGT
TAAAAATTGAAAAGATCTATTATGCCTAAAATATGTTTTAAGCGTTGATAACATTTCTAAACC
Found at i:9518312 original size:157 final size:157
Alignment explanation
Indices: 9518021--9518316 Score: 511
Period size: 157 Copynumber: 1.9 Consensus size: 157
9518011 AAACCATTGA
*
9518021 ATGACTTTATTTGATGTATTGAACTTTGTATTATGAACTAAATTATATGATTACTTTGGTTGATA
1 ATGACTTTATCTGATGTATTGAACTTTGTATTATGAACTAAATTATATGATTACTTTGGTTGATA
* * *
9518086 ATTAGCATGTTTCTGATTACACATATGATTCATGGTTAAGCATGCCTTTGTGTTATCTGTTAAAA
66 ATTAGCATGTTTCTGATTACACATATGATCCATGGTTAAGCATGCCTTCGTGTTAACTGTTAAAA
9518151 ATTGAAAAGATCTATTATGCCTAAAAT
131 ATTGAAAAGATCTATTATGCCTAAAAT
* * * *
9518178 ATGACTTTATCTGATGTATTGAACTTTTTATTATGGACTAAATTATATGATTATTTTGGTTTATA
1 ATGACTTTATCTGATGTATTGAACTTTGTATTATGAACTAAATTATATGATTACTTTGGTTGATA
*
9518243 ATTAGCATGTTTCTGATTACACATATGATCCATGGTTAAGCATGCCTTCGTGTTAACTGTTAAAT
66 ATTAGCATGTTTCTGATTACACATATGATCCATGGTTAAGCATGCCTTCGTGTTAACTGTTAAAA
9518308 ATTGAAAAG
131 ATTGAAAAG
9518317 CATGTTTCTA
Statistics
Matches: 130, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
157 130 1.00
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (157 bp):
ATGACTTTATCTGATGTATTGAACTTTGTATTATGAACTAAATTATATGATTACTTTGGTTGATA
ATTAGCATGTTTCTGATTACACATATGATCCATGGTTAAGCATGCCTTCGTGTTAACTGTTAAAA
ATTGAAAAGATCTATTATGCCTAAAAT
Found at i:9519377 original size:40 final size:41
Alignment explanation
Indices: 9519269--9519401 Score: 134
Period size: 40 Copynumber: 3.3 Consensus size: 41
9519259 TTTTTTCGAT
* * * *
9519269 AAACGCCACAACAAAGTAGTACTTTAGCAGCG-TTTTTATAC
1 AAACGCCGCAATAAATTAGTACTTTAG-TGCGTTTTTTATAC
* * *
9519310 AAACGCCGCAATAGATCTA-T-CTATAGTGGCGTTTTTTA-AT
1 AAACGCCGCAATAAAT-TAGTACTTTAGT-GCGTTTTTTATAC
9519350 AAAC-CCGCAATAAATTAGTACTTTAGTGC-TTTTTTATAC
1 AAACGCCGCAATAAATTAGTACTTTAGTGCGTTTTTTATAC
9519389 AAACGCCGCAATA
1 AAACGCCGCAATA
9519402 GGGTTCACCT
Statistics
Matches: 75, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
38 9 0.12
39 18 0.24
40 27 0.36
41 19 0.25
42 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (41 bp):
AAACGCCGCAATAAATTAGTACTTTAGTGCGTTTTTTATAC
Found at i:9519425 original size:79 final size:81
Alignment explanation
Indices: 9519258--9519485 Score: 214
Period size: 80 Copynumber: 2.8 Consensus size: 81
9519248 CTTTAGCAGT
*
9519258 GTTTTTTCGATAAACGCCACAACAAAGTAGTACTTTAGCAGCGTTTTTATACAAACGCCGCAATA
1 GTTTTTT-AATAAACGCCACAACAAAGTAGTACTTTAGCAGCGTTTTTATACAAACGCCGCAATA
* *
9519323 GATCTATCTATAGTGGC
65 GATCTACCTATAGTGAC
* * * * *
9519340 GTTTTTTAATAAAC-CCGCAATAAATTAGTACTTTAG-TGCTTTTTTATACAAACGCCGCAATAG
1 GTTTTTTAATAAACGCCACAACAAAGTAGTACTTTAGCAGCGTTTTTATACAAACGCCGCAATA-
*
9519403 GGT-TCACCTATAGTGAC
65 GATCT-ACCTATAGTGAC
* * * ** * * *
9519420 GTTTTTCTTATGAACGTCGTAA-AAGTGTAGTGA-TTTAGCGGCGTTTTTATACAAACGACGCAA
1 GTTTTT-TAATAAACGCCACAACAA-AGTAGT-ACTTTAGCAGCGTTTTTATACAAACGCCGCAA
9519483 TAG
63 TAG
9519486 GTTTCATTTG
Statistics
Matches: 121, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
79 25 0.21
80 37 0.31
81 14 0.12
82 21 0.17
83 24 0.20
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (81 bp):
GTTTTTTAATAAACGCCACAACAAAGTAGTACTTTAGCAGCGTTTTTATACAAACGCCGCAATAG
ATCTACCTATAGTGAC
Found at i:9520038 original size:26 final size:26
Alignment explanation
Indices: 9519991--9520040 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
9519981 CTACTCACAG
* **
9519991 TTTACTGTTCGGACACTTTAAAAAAA
1 TTTACTGTTCAGACACCATAAAAAAA
9520017 TTTACTGTTCAGACACCATAAAAA
1 TTTACTGTTCAGACACCATAAAAA
9520041 TCGCAGACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (26 bp):
TTTACTGTTCAGACACCATAAAAAAA
Found at i:9521675 original size:14 final size:14
Alignment explanation
Indices: 9521646--9521688 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 14
9521636 CATGATATTT
9521646 AATTTTAATGTTTATA
1 AATTTTAA--TTTATA
9521662 AATTTTAATTTATA
1 AATTTTAATTTATA
9521676 AATTTTAATTTAT
1 AATTTTAATTTAT
9521689 TTTGTTGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 19 0.70
16 8 0.30
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
AATTTTAATTTATA
Found at i:9521915 original size:43 final size:43
Alignment explanation
Indices: 9521840--9522105 Score: 227
Period size: 43 Copynumber: 6.2 Consensus size: 43
9521830 AAGGTAATTA
* * * *
9521840 GCGGCGTTTGTATCAAAAAACGACGCTATAGATTTGACCTTTT
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTT
* * * * *
9521883 GTGGTGTTTATATCCAAAAATGCCGCTATAGATCAGATCTTTT
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTT
* *
9521926 GCGGCGTTTGT-TCCAAAACTACCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTT
* *
9521968 GCGGCATTTGTATCC-AAAATAGCCGCTATAGATCTGACTTTTT
1 GCGGCGTTTGTATCCAAAAAT-GCCGCTATAGATCTGACCTTTT
* ** * * * * *
9522011 TCTACGTTTGT-TACAAAAACGCCACTATAGATATCAACCTTTT
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCT-GACCTTTT
** * **
9522054 GCAACGTTTAT-TCCAAAAGCGCCGCTATAGATATCT-ACCTTTT
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAG--ATCTGACCTTTT
9522097 GCGGCGTTT
1 GCGGCGTTT
9522106 TTGGATATTT
Statistics
Matches: 178, Mismatches: 39, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
42 55 0.31
43 120 0.67
45 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTT
Found at i:9521984 original size:85 final size:85
Alignment explanation
Indices: 9521840--9522009 Score: 220
Period size: 85 Copynumber: 2.0 Consensus size: 85
9521830 AAGGTAATTA
* * **
9521840 GCGGCGTTTGTATCAAAAAACGACGCTATAGATTTGACCTTTTGTGGTGTTTATATCCAAAA-AT
1 GCGGCGTTTGTATCAAAAAACGACGCTATAGATCTGACCTTTTGCGGCATTTATATCCAAAATA-
9521904 GCCGCTATAGATCAGATCTTTT
65 GCCGCTATAGATCAGA-CTTTT
* * *
9521926 GCGGCGTTTGT-TC-CAAAACTACCGCTATAGATCTGACCTTTTGCGGCATTTGTATCCAAAATA
1 GCGGCGTTTGTATCAAAAAACGA-CGCTATAGATCTGACCTTTTGCGGCATTTATATCCAAAATA
*
9521989 GCCGCTATAGATCTGACTTTT
65 GCCGCTATAGATCAGACTTTT
9522010 TTCTACGTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
84 11 0.15
85 51 0.69
86 12 0.16
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (85 bp):
GCGGCGTTTGTATCAAAAAACGACGCTATAGATCTGACCTTTTGCGGCATTTATATCCAAAATAG
CCGCTATAGATCAGACTTTT
Found at i:9522019 original size:85 final size:85
Alignment explanation
Indices: 9521863--9522085 Score: 211
Period size: 85 Copynumber: 2.6 Consensus size: 85
9521853 CAAAAAACGA
* * **
9521863 CGCTATAGATTTGACCTTTTGTGGTGTTTATATCCAAAAATGCCGCTATAGATCAGATCTTTTGC
1 CGCTATAGATCTGACCTTTTGCGGCATTTATATCCAAAAATGCCGCTATAGATCAGATCTTTTGC
* *
9521928 GGCGTTTGTTCCAAAACTAC
66 GACGTTTGTTACAAAACTAC
* *
9521948 CGCTATAGATCTGACCTTTTGCGGCATTTGTATCC-AAAATAGCCGCTATAGATCTGA-CTTTTT
1 CGCTATAGATCTGACCTTTTGCGGCATTTATATCCAAAAAT-GCCGCTATAGATCAGATC-TTTT
* * *
9522011 TCTACGTTTGTTACAAAAAC-GC
64 GCGACGTTTGTTAC-AAAACTAC
* * * ** * **
9522033 CACTATAGATATCAACCTTTTGCAACGTTTAT-TCCAAAAGCGCCGCTATAGAT
1 CGCTATAGATCT-GACCTTTTGCGGCATTTATATCCAAAAATGCCGCTATAGAT
9522086 ATCTACCTTT
Statistics
Matches: 113, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
84 6 0.05
85 85 0.75
86 22 0.19
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.35
Consensus pattern (85 bp):
CGCTATAGATCTGACCTTTTGCGGCATTTATATCCAAAAATGCCGCTATAGATCAGATCTTTTGC
GACGTTTGTTACAAAACTAC
Found at i:9522119 original size:26 final size:26
Alignment explanation
Indices: 9522083--9522133 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
9522073 CGCCGCTATA
* *
9522083 GATATCTACCTTTTGCGGCGTTTTTG
1 GATATCTACCTATTGCAGCGTTTTTG
* *
9522109 GATATTTACCTATTGCAGTGTTTTT
1 GATATCTACCTATTGCAGCGTTTTT
9522134 TGTTCTCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.49
Consensus pattern (26 bp):
GATATCTACCTATTGCAGCGTTTTTG
Found at i:9527822 original size:134 final size:134
Alignment explanation
Indices: 9527257--9528091 Score: 1067
Period size: 134 Copynumber: 6.2 Consensus size: 134
9527247 CAAATGAATC
* * * * * *
9527257 GATTTGCTTCACTACTCTTCAGGGAATACTAAATTTGAAAGAAGAAGAATATGCTCCACTACTCT
1 GATTTGCTTCGCTGCTCTTCA-GGAAGACCAAATCTGAAAGAAGAAGAATTTGCTCCACTACTCT
* * *
9527322 TTATGGGAGATCAGACTTGAGAAAACTTTGATCCACTTAACTGCTCTTCAGGGAAGATTGAATCA
65 TTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCA
**
9527387 AATGT
130 AACAT
* * * *
9527392 GATTTCCTTCGCTACTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTT-CTTCACTACTGT
1 GATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAAT-TTGCTCCACTACTCT
*
9527456 TTA-GGGAGATCAGACTCGAGAAATA-TTTGATCCACTTCACTG-TCTTCAGGGAAGATTGAATG
65 TTAGGGGAGATCAGACTCGAGAAA-ACTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATC
*
9527518 AAACGT
129 AAACAT
* * *
9527524 GATTTGCTTCTCTTG-TCTTCAAGAAGACCAAATCTGAAAGAAGAAGAATATGCTCCACTACTCT
1 GATTTGCTTCGC-TGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATTTGCTCCACTACTCT
* * * *
9527588 TTAGGGGATATCAGACTCGAGAAAACTTT-ATCCACTTCATTGGTCTTCAGGGAAGATTGAATCG
65 TTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCA
9527652 AACAT
130 AACAT
* * * * * * *
9527657 GATTTGCTTTGTTGCTCTTCAGGAATACCAAATATGAAATAAGAAGAATTTGATCCACTACTTTT
1 GATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATTTGCTCCACTACTCTT
* * *
9527722 TAGGGGAGATCAGACTCGAGAAAACTTTGATCCATTTCACTTCTCTTCATGGAAGATTGAATCAA
66 TAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCAA
9527787 ACAT
131 ACAT
* *
9527791 GATTTGCTTCGCTGCTCTTCAGGAAGACCAAATTTTAAAGAAGAAGAATTTGCTCCACTACTCTT
1 GATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATTTGCTCCACTACTCTT
* * * *
9527856 TAGGGGAGATCAGACTTGAGAAATA-TTTGATACACTTCACTGCTCTTCAGGGAAGATTTAATCG
66 TAGGGGAGATCAGACTCGAGAAA-ACTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCA
*
9527920 AGCAT
130 AACAT
* * * * *
9527925 GATTTGCTTCACTGTTCTTCAAGAAGACCAAATCTAAAAGCAGAAGAATCTT-CTCCACTACTCT
1 GATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAAT-TTGCTCCACTACTCT
* *
9527989 TTAGGGGAGATCAGACTCGAGAAATCTTTGATCCACTTCACTGCTCTTCAGTGAAGATTGAATCA
65 TTAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCA
*
9528054 AACGT
130 AACAT
* * * *
9528059 GATTTGTTTCTCTTG-TCTTCAAGAAGACAAAAT
1 GATTTGCTTCGC-TGCTCTTCAGGAAGACCAAAT
9528092 ATAGAAATCA
Statistics
Matches: 613, Mismatches: 74, Indels: 27
0.86 0.10 0.04
Matches are distributed among these distances:
131 1 0.00
132 95 0.15
133 160 0.26
134 332 0.54
135 25 0.04
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (134 bp):
GATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATTTGCTCCACTACTCTT
TAGGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCAA
ACAT
Found at i:9528744 original size:51 final size:50
Alignment explanation
Indices: 9528669--9528801 Score: 135
Period size: 50 Copynumber: 2.6 Consensus size: 50
9528659 AACATTACAG
* ** * * *
9528669 AAAGATTGACTTCTCTATAAGAGAAAGTCACGTTGAGGAACGATA-CTACTTA
1 AAAGATTGACTACTCTCCACGAGAAAGTCAAGTTGA-GAACGAAATC-AC-TA
* * *
9528721 AAAG-TTGACTCCTCTCCACGAGAATGTCAAGTTGAGAATGAAATCACTA
1 AAAGATTGACTACTCTCCACGAGAAAGTCAAGTTGAGAACGAAATCACTA
*
9528770 AAAGATTGACTACTCTTCACGAGAAAGTCAAG
1 AAAGATTGACTACTCTCCACGAGAAAGTCAAG
9528802 AATAACAATA
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
49 6 0.09
50 32 0.47
51 26 0.38
52 4 0.06
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (50 bp):
AAAGATTGACTACTCTCCACGAGAAAGTCAAGTTGAGAACGAAATCACTA
Found at i:9528817 original size:45 final size:44
Alignment explanation
Indices: 9528766--9528929 Score: 127
Period size: 45 Copynumber: 3.7 Consensus size: 44
9528756 GAATGAAATC
*
9528766 ACTAAAAGATTGACTACTCTTCACGAGAAAGTCAAGAATAACAAT
1 ACTAAAAGATTGAATACTCTTCACGAGAAAGTCAAGAAT-ACAAT
* * * * * * * *
9528811 AATAAAATAATGAATCCTCGTCACAAGAAAGTCAAGGAAGACAAC
1 ACTAAAAGATTGAATACTCTTCACGAGAAAGTCAA-GAATACAAT
** * * *
9528856 ACCGAAAGATTGAATCCTATTCGCGAGAAAGTCAAGAAT--AAT
1 ACTAAAAGATTGAATACTCTTCACGAGAAAGTCAAGAATACAAT
* * *
9528898 ACTGAATGATTGACA-CCTCTTCACGAGAAAGT
1 ACTAAAAGATTGA-ATACTCTTCACGAGAAAGT
9528930 AATGTCATGG
Statistics
Matches: 93, Mismatches: 24, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
42 28 0.30
43 1 0.01
44 3 0.03
45 58 0.62
46 3 0.03
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.21
Consensus pattern (44 bp):
ACTAAAAGATTGAATACTCTTCACGAGAAAGTCAAGAATACAAT
Found at i:9543194 original size:6 final size:6
Alignment explanation
Indices: 9543183--9543212 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
9543173 CAGATTCTTG
9543183 GTCAAA GTCAAA GTCAAA GTCAAA GTCAAA
1 GTCAAA GTCAAA GTCAAA GTCAAA GTCAAA
9543213 ATTTCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
GTCAAA
Found at i:9543347 original size:5 final size:5
Alignment explanation
Indices: 9543337--9543407 Score: 65
Period size: 5 Copynumber: 13.8 Consensus size: 5
9543327 AACGGTCAAC
* * *
9543337 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG AGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
9543386 GGTCG GGTC- GGTC- GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTC
9543408 AGACCGGTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
4 8 0.15
5 39 0.71
7 8 0.15
ACGTcount: A:0.07, C:0.23, G:0.51, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:9543355 original size:22 final size:22
Alignment explanation
Indices: 9543330--9543396 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
9543320 GAAAGTCAAC
9543330 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
9543352 GGTCAACGGTCGGGTCGAGTCG
1 GGTCAACGGTCGGGTCGGGTCG
9543374 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
9543396 G
1 G
9543397 TCGGTCGGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.10, C:0.22, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:9543433 original size:10 final size:10
Alignment explanation
Indices: 9543418--9543512 Score: 51
Period size: 10 Copynumber: 9.8 Consensus size: 10
9543408 AGACCGGTCA
9543418 AACCGGTTCG
1 AACCGGTTCG
9543428 AACCGGTT--
1 AACCGGTTCG
*
9543436 --TCGGTTCG
1 AACCGGTTCG
9543444 AACCGGTCGGTCG
1 AACCGGT---TCG
*
9543457 AAACCGG-TCA
1 -AACCGGTTCG
*
9543467 AACCGGTTAG
1 AACCGGTTCG
*
9543477 AATCGGTT-G
1 AACCGGTTCG
*
9543486 AACCGGTTAG
1 AACCGGTTCG
*
9543496 AATCGGTT-G
1 AACCGGTTCG
9543505 AACCGGTT
1 AACCGGTT
9543513 TCCAGCAGCC
Statistics
Matches: 66, Mismatches: 9, Indels: 21
0.69 0.09 0.22
Matches are distributed among these distances:
6 5 0.08
9 22 0.33
10 30 0.45
13 3 0.05
14 6 0.09
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (10 bp):
AACCGGTTCG
Found at i:9543483 original size:19 final size:19
Alignment explanation
Indices: 9543467--9543512 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
9543457 AAACCGGTCA
9543467 AACCGGTTAGAATCGGTTG
1 AACCGGTTAGAATCGGTTG
9543486 AACCGGTTAGAATCGGTTG
1 AACCGGTTAGAATCGGTTG
9543505 AACCGGTT
1 AACCGGTT
9543513 TCCAGCAGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (19 bp):
AACCGGTTAGAATCGGTTG
Found at i:9543492 original size:9 final size:10
Alignment explanation
Indices: 9543458--9543512 Score: 62
Period size: 9 Copynumber: 5.8 Consensus size: 10
9543448 GGTCGGTCGA
*
9543458 AACCGGTCA-
1 AACCGGTTAG
9543467 AACCGGTTAG
1 AACCGGTTAG
*
9543477 AATCGGTT-G
1 AACCGGTTAG
9543486 AACCGGTTAG
1 AACCGGTTAG
*
9543496 AATCGGTT-G
1 AACCGGTTAG
9543505 AACCGGTT
1 AACCGGTT
9543513 TCCAGCAGCC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
9 24 0.62
10 15 0.38
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (10 bp):
AACCGGTTAG
Found at i:9543988 original size:22 final size:22
Alignment explanation
Indices: 9543963--9544015 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
9543953 ACGATCGGAT
*
9543963 GTCGGGTCGGGTCAACGGTCGG
1 GTCGGGTCGGGTCAACAGTCGG
9543985 GTCGGGTCGGGTCAACAGTCGG
1 GTCGGGTCGGGTCAACAGTCGG
9544007 GTC-GGTCGG
1 GTCGGGTCGG
9544016 TCGGTCGGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GTCGGGTCGGGTCAACAGTCGG
Found at i:9544047 original size:19 final size:19
Alignment explanation
Indices: 9544020--9544064 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
9544010 GGTCGGTCGG
*
9544020 TCGGGTCAGACCGATCAAA
1 TCGGTTCAGACCGATCAAA
*
9544039 TCGGTTCAGACCGGTCAAA
1 TCGGTTCAGACCGATCAAA
*
9544058 CCGGTTC
1 TCGGTTC
9544065 GAACCGGTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (19 bp):
TCGGTTCAGACCGATCAAA
Found at i:9544070 original size:19 final size:19
Alignment explanation
Indices: 9544025--9544078 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
9544015 GTCGGTCGGG
* *
9544025 TCAGACCGATCAAATCGGT
1 TCAGACCGGTCAAACCGGT
9544044 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
9544063 TC-GAACCGGTCGAAAC
1 TCAG-ACCGGTC-AAAC
9544079 TGGTCTCCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 1 0.03
19 26 0.84
20 4 0.13
ACGTcount: A:0.30, C:0.30, G:0.24, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:9548398 original size:23 final size:24
Alignment explanation
Indices: 9548358--9548407 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
9548348 CTCTCTCTCT
9548358 TTTTTCGAACAACATATTTTTTTC
1 TTTTTCGAACAACATATTTTTTTC
**
9548382 TTTTTCGAACTGC-TATTTTTTTC
1 TTTTTCGAACAACATATTTTTTTC
9548405 TTT
1 TTT
9548408 ATTTTTTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.18, C:0.16, G:0.06, T:0.60
Consensus pattern (24 bp):
TTTTTCGAACAACATATTTTTTTC
Found at i:9563892 original size:24 final size:25
Alignment explanation
Indices: 9563865--9563919 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
9563855 TACCACACTC
* *
9563865 AAAAAAAAGAAAAATAAAA-AAATA
1 AAAAAAAAGAAAAAGAAAATAAAGA
* *
9563889 AAAAAAAGGGAAAAGAAAATAAAGA
1 AAAAAAAAGAAAAAGAAAATAAAGA
9563914 AAAAAA
1 AAAAAA
9563920 GGAAAAAAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 16 0.62
25 10 0.38
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (25 bp):
AAAAAAAAGAAAAAGAAAATAAAGA
Found at i:9563920 original size:8 final size:8
Alignment explanation
Indices: 9563866--9563928 Score: 51
Period size: 8 Copynumber: 8.0 Consensus size: 8
9563856 ACCACACTCA
9563866 AAAAAAAG
1 AAAAAAAG
9563874 AAAAATAA-
1 AAAAA-AAG
*
9563882 AAAAATA-
1 AAAAAAAG
9563889 AAAAAAAG
1 AAAAAAAG
**
9563897 -GGAAAAG
1 AAAAAAAG
9563904 AAAATAAAG
1 AAAA-AAAG
9563913 AAAAAAAG
1 AAAAAAAG
*
9563921 GAAAAAAG
1 AAAAAAAG
9563929 GGAAAGAGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
7 12 0.27
8 22 0.50
9 10 0.23
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (8 bp):
AAAAAAAG
Found at i:9563926 original size:33 final size:32
Alignment explanation
Indices: 9563870--9563947 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
9563860 CACTCAAAAA
*
9563870 AAAGA-AAAATAA-AAAAATA-AAAAAAAGGG
1 AAAGAGAAAATAAGAAAAAAAGAAAAAAAGGG
*
9563899 AAA-AGAAAATAAAGAAAAAAAGGAAAAAAGGG
1 AAAGAGAAAAT-AAGAAAAAAAGAAAAAAAGGG
*
9563931 AAAGAGAAAGTAAGAAA
1 AAAGAGAAAATAAGAAA
9563948 GGATATATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 1 0.02
29 8 0.20
30 2 0.05
31 6 0.15
32 18 0.44
33 6 0.15
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (32 bp):
AAAGAGAAAATAAGAAAAAAAGAAAAAAAGGG
Found at i:9568907 original size:22 final size:24
Alignment explanation
Indices: 9568882--9568925 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
9568872 ATAATGATAA
9568882 ACTCTT-AATA-TTTTAATATATT
1 ACTCTTGAATATTTTTAATATATT
*
9568904 ACTCTTGATTATTTTTAATATA
1 ACTCTTGAATATTTTTAATATA
9568926 ACATATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 3 0.16
24 10 0.53
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (24 bp):
ACTCTTGAATATTTTTAATATATT
Found at i:9574874 original size:20 final size:21
Alignment explanation
Indices: 9574849--9574900 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
9574839 TTTTCCCAAT
*
9574849 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
9574869 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
9574890 TCGCAATGCGA
1 TCGCAATGCGA
9574901 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:9574933 original size:61 final size:61
Alignment explanation
Indices: 9574886--9575002 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
9574876 GCGAATTGGG
* * * *
9574886 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATAATGACTATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
* * *
9574947 AAAATCGCAACGAGATAATGACTTTCGCAATGCGATTCTGACTTTCGCAATGCGAT
1 AAAATCGCAACGAGATAATGACTATCGCAATGCGATACTGACTATCGCAATGCGAT
9575003 TTTCAAAGCG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (61 bp):
AAAATCGCAACGAGATAATGACTATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
Found at i:9575003 original size:20 final size:20
Alignment explanation
Indices: 9574889--9575002 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
9574879 AATTGGGAAA
9574889 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
9574909 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
9574929 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* * *
9574950 ATCGCAACGAGATAATGACT
1 ATCGCAATGCGATACTGACT
* *
9574970 TTCGCAATGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
*
9574990 TTCGCAATGCGAT
1 ATCGCAATGCGAT
9575003 TTTCAAAGCG
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.77
21 14 0.17
22 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Done.