Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007957.1 Hibiscus syriacus cultivar Beakdansim tig00110384_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: 8646418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 43
Found at i:2408771 original size:32 final size:32
Alignment explanation
Indices: 2408714--2408803 Score: 153
Period size: 32 Copynumber: 2.8 Consensus size: 32
2408704 CCTGGAGACA
*
2408714 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACA-AAAAAACCTTTGAAAAT
2408747 GTTTCTCTTGAAACAAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACAAAAAAACCTTTGAAAAT
*
2408779 GTTTCTCTTGAAACAAAAAGACCTT
1 GTTTCTCTTGAAACAAAAAAACCTT
2408804 GAGTTTGACT
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 40 0.73
33 15 0.27
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (32 bp):
GTTTCTCTTGAAACAAAAAAACCTTTGAAAAT
Found at i:2408948 original size:80 final size:81
Alignment explanation
Indices: 2408795--2409023 Score: 297
Period size: 80 Copynumber: 2.9 Consensus size: 81
2408785 CTTGAAACAA
* * * * * *
2408795 AAAGA-CCTTGAGTTTGACTACACTCAGCTTCGAGGGCACATCATTTGCAACATAACTCAAGGCT
1 AAAGACCCTCGAGTTCGATTACATTCAGCTTCAAGGGCACATCATTTGCAGCATAACTCAAGGCT
2408859 AGAAGGGTTATCTGCC
66 AGAAGGGTTATCTGCC
2408875 AAAGACCCTCGAGTTCGATTACATTCAGCTTCAAGGGCACATCATTTGCAGC-TAACTCAAGGCT
1 AAAGACCCTCGAGTTCGATTACATTCAGCTTCAAGGGCACATCATTTGCAGCATAACTCAAGGCT
*
2408939 AGAAGGGTTATCTTCC
66 AGAAGGGTTATCTGCC
* * * ** * *
2408955 AAAAACCTTCGAGTTCGATTCCATTCAGC-TCAA-GGCACA-CATTCACAGCATAGCTCAAGGCA
1 AAAGACCCTCGAGTTCGATTACATTCAGCTTCAAGGGCACATCATTTGCAGCATAACTCAAGGCT
2409017 AGAAGGG
66 AGAAGGG
2409024 CTATATGTCA
Statistics
Matches: 133, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
77 8 0.06
78 23 0.17
79 4 0.03
80 58 0.44
81 40 0.30
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (81 bp):
AAAGACCCTCGAGTTCGATTACATTCAGCTTCAAGGGCACATCATTTGCAGCATAACTCAAGGCT
AGAAGGGTTATCTGCC
Found at i:2410291 original size:8 final size:8
Alignment explanation
Indices: 2410280--2410404 Score: 76
Period size: 8 Copynumber: 15.6 Consensus size: 8
2410270 CCTTTTATCT
2410280 TTTTTTTA
1 TTTTTTTA
2410288 TTTTTTT-
1 TTTTTTTA
2410295 TATTTTTTA
1 T-TTTTTTA
2410304 TTTTTTTA
1 TTTTTTTA
***
2410312 TTTATACGA
1 TTT-TTTTA
* *
2410321 -TATTATA
1 TTTTTTTA
* * *
2410328 TATATATA
1 TTTTTTTA
2410336 TATTTTTTA
1 T-TTTTTTA
2410345 TTTTTTTA
1 TTTTTTTA
**
2410353 TCCTTTTA
1 TTTTTTTA
2410361 TTTTTTTA
1 TTTTTTTA
*
2410369 TTTGTTTA
1 TTTTTTTA
*
2410377 TTTTATTA
1 TTTTTTTA
*
2410385 TTATTTTA
1 TTTTTTTA
*
2410393 TTTCTTT-
1 TTTTTTTA
2410400 TTTTT
1 TTTTT
2410405 CTACTACTTT
Statistics
Matches: 87, Mismatches: 25, Indels: 11
0.71 0.20 0.09
Matches are distributed among these distances:
7 7 0.08
8 72 0.83
9 8 0.09
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (8 bp):
TTTTTTTA
Found at i:2410507 original size:5 final size:5
Alignment explanation
Indices: 2410497--2410536 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
2410487 TTTTTATTTA
2410497 TTAAT TTAAT TTAAT TTAAT TT-AT TTAAT TT-AT TTAAT TT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TT
2410537 TTTATTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 8 0.24
5 25 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TTAAT
Found at i:2410524 original size:9 final size:9
Alignment explanation
Indices: 2410489--2410540 Score: 72
Period size: 9 Copynumber: 5.9 Consensus size: 9
2410479 ATATACTCTT
2410489 TTTATTT-A
1 TTTATTTAA
*
2410497 TTAATTTAA
1 TTTATTTAA
2410506 TTTAATTTAA
1 TTT-ATTTAA
2410516 TTTATTTAA
1 TTTATTTAA
2410525 TTTATTTAA
1 TTTATTTAA
2410534 TTT-TTTA
1 TTTATTTA
2410541 TTTTTATTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
8 10 0.25
9 21 0.52
10 9 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTATTTAA
Found at i:2410531 original size:23 final size:23
Alignment explanation
Indices: 2410489--2410543 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
2410479 ATATACTCTT
2410489 TTTATTTA-TTAATTTAATTTAA
1 TTTATTTATTTAATTTAATTTAA
2410511 TTTAATTTATTTAATTT-ATTTAA
1 TTT-ATTTATTTAATTTAATTTAA
2410534 TTT-TTTATTT
1 TTTATTTATTT
2410544 TTATTGTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.23
22 3 0.10
23 14 0.45
24 7 0.23
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTATTTATTTAATTTAATTTAA
Found at i:2410546 original size:18 final size:17
Alignment explanation
Indices: 2410487--2410597 Score: 59
Period size: 18 Copynumber: 6.3 Consensus size: 17
2410477 TTATATACTC
*
2410487 TTTTTATTTATTAATTTA
1 TTTTTATTTATT-TTTTA
* *
2410505 ATTTAATTTAATTTATTTA
1 TTTTTATTT-ATTT-TTTA
*
2410524 -ATTTATTTAATTTTTTA
1 TTTTTATTT-ATTTTTTA
2410541 TTTTTATTGTA-TTTTT-
1 TTTTTATT-TATTTTTTA
* * *
2410557 TTCTT-TCTAGTTTTTA
1 TTTTTATTTATTTTTTA
2410573 TTTATTATTTATATATTTTA
1 TTT-TTATTTAT-T-TTTTA
2410593 TTTTT
1 TTTTT
2410598 TCCCTTGTTC
Statistics
Matches: 72, Mismatches: 11, Indels: 19
0.71 0.11 0.19
Matches are distributed among these distances:
14 2 0.03
15 6 0.08
16 6 0.08
17 11 0.15
18 28 0.39
19 11 0.15
20 8 0.11
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTTTATTTATTTTTTA
Found at i:2410546 original size:23 final size:23
Alignment explanation
Indices: 2410487--2410554 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 23
2410477 TTATATACTC
2410487 TTTTTATTTATTAATTTAATTTAAT
1 TTTTTATTT-TTAATTT-ATTTAAT
2410512 TTAATTTA--TTTAATTTATTTAAT
1 TT--TTTATTTTTAATTTATTTAAT
2410535 TTTTTATTTTT-ATTGTATTT
1 TTTTTATTTTTAATT-TATTT
2410555 TTTTCTTTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
21 4 0.11
22 3 0.08
23 17 0.45
24 7 0.18
25 3 0.08
27 4 0.11
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (23 bp):
TTTTTATTTTTAATTTATTTAAT
Found at i:2410682 original size:40 final size:37
Alignment explanation
Indices: 2410638--2410718 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 37
2410628 TTTATTATAT
*
2410638 TTATCCTATTTAACTTCATTTTATT-TTTATTTTCTTTATC
1 TTATCCTATTT-ACTTCATTTT-TTAATTA-TTT-TTTATC
* *
2410678 TTATCTTATTTATTTCATTTTTTAATTATTTTTTATC
1 TTATCCTATTTACTTCATTTTTTAATTATTTTTTATC
2410715 TTAT
1 TTAT
2410719 TTATTTCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
37 10 0.27
38 5 0.14
39 12 0.32
40 10 0.27
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (37 bp):
TTATCCTATTTACTTCATTTTTTAATTATTTTTTATC
Found at i:2410722 original size:16 final size:17
Alignment explanation
Indices: 2410672--2410724 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
2410662 TTTTATTTTC
2410672 TTTATCTTATCTTATTTA
1 TTTAT-TTATCTTATTTA
*
2410690 TTTCATTT-T-TTAATTA
1 TTT-ATTTATCTTATTTA
2410706 TTT-TTTATCTTATTTA
1 TTTATTTATCTTATTTA
2410722 TTT
1 TTT
2410725 CATTACTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 3 0.10
15 1 0.03
16 18 0.60
17 1 0.03
18 5 0.17
19 2 0.07
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATTTATCTTATTTA
Found at i:2412334 original size:19 final size:19
Alignment explanation
Indices: 2412310--2412354 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2412300 CGTGTTGCGA
2412310 CTGTTGCGACTGTCGCGGT
1 CTGTTGCGACTGTCGCGGT
*
2412329 CTGTTGCGGCTGTCGCGGT
1 CTGTTGCGACTGTCGCGGT
*
2412348 CGGTTGC
1 CTGTTGC
2412355 ATTGCTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.02, C:0.27, G:0.40, T:0.31
Consensus pattern (19 bp):
CTGTTGCGACTGTCGCGGT
Found at i:2421181 original size:30 final size:30
Alignment explanation
Indices: 2421138--2421214 Score: 113
Period size: 29 Copynumber: 2.6 Consensus size: 30
2421128 TTTGGTTCGT
* * *
2421138 TTAATCGAGCCAAAATTTATTTGAAAATTA
1 TTAACCGAACCAAAATTAATTTGAAAATTA
2421168 TTAACCGAACC-AAATTAATTTGAAAATTA
1 TTAACCGAACCAAAATTAATTTGAAAATTA
2421197 TTAACCGAACC-AAATTAA
1 TTAACCGAACCAAAATTAA
2421215 CCGAATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 35 0.80
30 9 0.20
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (30 bp):
TTAACCGAACCAAAATTAATTTGAAAATTA
Found at i:2421182 original size:29 final size:29
Alignment explanation
Indices: 2421150--2421214 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
2421140 AATCGAGCCA
*
2421150 AAATTTATTTGAAAATTATTAACCGAACC
1 AAATTAATTTGAAAATTATTAACCGAACC
2421179 AAATTAATTTGAAAATTATTAACCGAACC
1 AAATTAATTTGAAAATTATTAACCGAACC
2421208 AAATTAA
1 AAATTAA
2421215 CCGAATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.32
Consensus pattern (29 bp):
AAATTAATTTGAAAATTATTAACCGAACC
Found at i:2421715 original size:22 final size:22
Alignment explanation
Indices: 2421680--2421736 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
2421670 AAATTGATAG
* * *
2421680 AATATGTAAATATTAAGGACCA
1 AATATATAATTATTAAAGACCA
2421702 AATATATAATTATTAAAGACCA
1 AATATATAATTATTAAAGACCA
2421724 AATATATAATTAT
1 AATATATAATTAT
2421737 GCCAATTAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (22 bp):
AATATATAATTATTAAAGACCA
Found at i:2431399 original size:20 final size:20
Alignment explanation
Indices: 2431346--2431400 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
2431336 TTGTTAAGGA
* *
2431346 ATGTATCGATACACTATAGT
1 ATGTACCGATACATTATAGT
2431366 ATGTACCGATACATTATAGT
1 ATGTACCGATACATTATAGT
2431386 ATGTACCGATACATT
1 ATGTACCGATACATT
2431401 TAAAAGGGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (20 bp):
ATGTACCGATACATTATAGT
Found at i:2436652 original size:21 final size:22
Alignment explanation
Indices: 2436627--2436671 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
2436617 TTTAATTAAA
*
2436627 TAATAGTATTCATTTATT-TTT
1 TAATAGTATTCAATTATTATTT
*
2436648 TAATAGTATTTAATTATTATTT
1 TAATAGTATTCAATTATTATTT
2436670 TA
1 TA
2436672 TTTCATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (22 bp):
TAATAGTATTCAATTATTATTT
Found at i:2436660 original size:70 final size:70
Alignment explanation
Indices: 2436580--2436722 Score: 286
Period size: 70 Copynumber: 2.0 Consensus size: 70
2436570 TATTTTAAAT
2436580 ATAGTATTTAATTATTATTTTATTTCATATGAAAATATTTAATTAAATAATAGTATTCATTTATT
1 ATAGTATTTAATTATTATTTTATTTCATATGAAAATATTTAATTAAATAATAGTATTCATTTATT
2436645 TTTTA
66 TTTTA
2436650 ATAGTATTTAATTATTATTTTATTTCATATGAAAATATTTAATTAAATAATAGTATTCATTTATT
1 ATAGTATTTAATTATTATTTTATTTCATATGAAAATATTTAATTAAATAATAGTATTCATTTATT
2436715 TTTTA
66 TTTTA
2436720 ATA
1 ATA
2436723 TCAAAAAATG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (70 bp):
ATAGTATTTAATTATTATTTTATTTCATATGAAAATATTTAATTAAATAATAGTATTCATTTATT
TTTTA
Found at i:2438177 original size:51 final size:51
Alignment explanation
Indices: 2438117--2438220 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
2438107 CATTAATTGT
2438117 TTTTCTTTTATTGTATTTTTTTATCTTTCAATAAAGTTTCAAATTTGAAAG
1 TTTTCTTTTATTGTATTTTTTTATCTTTCAATAAAGTTTCAAATTTGAAAG
2438168 TTTTCTTTTATTGTATTTTTTTATCTTTCAATAAAGTTTCAAATTTGAAAG
1 TTTTCTTTTATTGTATTTTTTTATCTTTCAATAAAGTTTCAAATTTGAAAG
2438219 TT
1 TT
2438221 GAAACTGTAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.58
Consensus pattern (51 bp):
TTTTCTTTTATTGTATTTTTTTATCTTTCAATAAAGTTTCAAATTTGAAAG
Found at i:2439164 original size:2 final size:2
Alignment explanation
Indices: 2439157--2439208 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2439147 TTAATGCACG
2439157 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2439199 TA TA TA TA TA
1 TA TA TA TA TA
2439209 ATACGTTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2440153 original size:164 final size:164
Alignment explanation
Indices: 2439899--2440288 Score: 669
Period size: 164 Copynumber: 2.4 Consensus size: 164
2439889 TAGTTGTCTC
*
2439899 AATTCATAATTGAGACATTCTTTCTCTTCAATTAGAAATGACAGAATATCAACTTTTTCTTTTTA
1 AATTCATAATTGAGACATTCTTTCTCTTCAATTAGAAATGACAGAATATCATCTTTTTCTTTTTA
2439964 GAATATTGTCTTAATAAAATATCATTCTTAAATATGGAATTCCTTAATAGAAAATTATGAAATTC
66 GAATATTGTCTTAATAAAATATCATTCTTAAATATGGAATTCCTTAATAGAAAATTATGAAATTC
*
2440029 AATCGTTTCAGTTGACAAGAGAAATAATCGTTTA
131 AATCGTTTCAGTTGACAAGAGAAATAATCGATTA
2440063 AATTCATAATTGAGACATTCTTTCTCTTCAATTAGAAATGACAGAATATCATCTTTTTCTTTTTA
1 AATTCATAATTGAGACATTCTTTCTCTTCAATTAGAAATGACAGAATATCATCTTTTTCTTTTTA
2440128 GAATATTGTCTTAATAAAATATCATTCTTAAATATGGAATTCCTTAATAGAAAATTATGAAATTC
66 GAATATTGTCTTAATAAAATATCATTCTTAAATATGGAATTCCTTAATAGAAAATTATGAAATTC
2440193 AATCGTTTCAGTTGACAAGAGAAATAATCGATTA
131 AATCGTTTCAGTTGACAAGAGAAATAATCGATTA
* ** * * * *
2440227 AATTCAT-GTTGAGAGGTTCTTTCTCTTCTATTACAAATGA-TGAAATATC-TATTTTTCTTTTT
1 AATTCATAATTGAGACATTCTTTCTCTTCAATTAGAAATGACAG-AATATCATCTTTTTCTTTTT
2440289 TTAGATTTTT
Statistics
Matches: 216, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
162 13 0.06
163 34 0.16
164 169 0.78
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (164 bp):
AATTCATAATTGAGACATTCTTTCTCTTCAATTAGAAATGACAGAATATCATCTTTTTCTTTTTA
GAATATTGTCTTAATAAAATATCATTCTTAAATATGGAATTCCTTAATAGAAAATTATGAAATTC
AATCGTTTCAGTTGACAAGAGAAATAATCGATTA
Found at i:2445886 original size:2 final size:2
Alignment explanation
Indices: 2445879--2445903 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2445869 ACATTCCCTA
2445879 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2445904 TCACATGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2447921 original size:111 final size:111
Alignment explanation
Indices: 2447751--2448298 Score: 596
Period size: 111 Copynumber: 4.9 Consensus size: 111
2447741 GCTCTCTGAT
* * *
2447751 CCCAAGAATCTTGTAACTAATCCCATGGCTAAAGTTGCATCCTCGGAGACGAGTGTTACCATTCC
1 CCCAAGAATCTTGTAACTTAT-CC-T-GCTAAAGTTGCATCTTCAGAGACGAGTGTTACCATTCC
* * * *
2447816 AATAGATACGAACTTAGACCATGTAAAGGATACAGGTTTGTCCTCCAAC
63 AGTAGATACGAACTTAGACCATGTAAAAGATAAAGATTTGTCCTCCAAC
** * * * * *
2447865 CCTGAGAATCCTGTAACTTATCCTGCTGAAGTTGCATCTTCCGAGATGAGTGTTACCATTTCAGT
1 CCCAAGAATCTTGTAACTTATCCTGCTAAAGTTGCATCTTCAGAGACGAGTGTTACCATTCCAGT
* *
2447930 AGATACGAACTTATACCATGTAAAAGATAAAGATTTTTCCTCCAAC
66 AGATACGAACTTAGACCATGTAAAAGATAAAGATTTGTCCTCCAAC
* * * * *
2447976 CCCAAGAATCTTCTAACTTATCCGGCTAATGTTGCATCTTCAGAGACAAGTGTTACTATTCCAGT
1 CCCAAGAATCTTGTAACTTATCCTGCTAAAGTTGCATCTTCAGAGACGAGTGTTACCATTCCAGT
* * *
2448041 TGATACGAACTTAGACAATGTAAAAGA-AACAGATCTGTCCTCCAAC
66 AGATACGAACTTAGACCATGTAAAAGATAA-AGATTTGTCCTCCAAC
* * * *
2448087 CCCAAGAATCATGTAACTTATCCAGCTAAAGTTGCATCTTCAGAGACGAGTGTTTCCATTCCGGT
1 CCCAAGAATCTTGTAACTTATCCTGCTAAAGTTGCATCTTCAGAGACGAGTGTTACCATTCCAGT
* * * **
2448152 TGATACAAATTTAGACCATGTAAAAGATAAAGATTTGTCCTTGAAC
66 AGATACGAACTTAGACCATGTAAAAGATAAAGATTTGTCCTCCAAC
* * * * *** * * **
2448198 CTCAAGAATTCAT-TAACTTATCCCATGTTTGAAGTCAAATCCTCAGAGGCGAGTAATACCATTC
1 CCCAAGAA-TCTTGTAACTTAT-CC-TG-CTAAAGTTGCATCTTCAGAGACGAGTGTTACCATTC
* *
2448262 CAGTAGATATGAACTTAGACAATGTAAAAGATAAAGA
62 CAGTAGATACGAACTTAGACCATGTAAAAGATAAAGA
2448299 CTCCCATACC
Statistics
Matches: 364, Mismatches: 64, Indels: 12
0.83 0.15 0.03
Matches are distributed among these distances:
110 2 0.01
111 276 0.76
112 9 0.02
113 3 0.01
114 74 0.20
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (111 bp):
CCCAAGAATCTTGTAACTTATCCTGCTAAAGTTGCATCTTCAGAGACGAGTGTTACCATTCCAGT
AGATACGAACTTAGACCATGTAAAAGATAAAGATTTGTCCTCCAAC
Found at i:2452477 original size:3 final size:3
Alignment explanation
Indices: 2452469--2452500 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2452459 CTGGATCTTT
2452469 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2452501 TAATATACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2457761 original size:37 final size:36
Alignment explanation
Indices: 2457666--2457769 Score: 104
Period size: 37 Copynumber: 2.9 Consensus size: 36
2457656 TTTCACTCGG
* * * * *
2457666 AACAAAGTGTTGTCTCGCTAGATACAGTTTTCTGAAA
1 AACAAA-TTTTGTCTCGCTTGAGACAATTTTCTCAAA
**
2457703 AACAAATTTTGTCTCATTTGAGACAATTTATCTCAAA
1 AACAAATTTTGTCTCGCTTGAGACAATTT-TCTCAAA
2457740 AACAAATTTCT-TCTCGCTTGAGAC-ATTTTC
1 AACAAATTT-TGTCTCGCTTGAGACAATTTTC
2457770 CTTTGAGATG
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
35 2 0.04
36 21 0.38
37 32 0.57
38 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (36 bp):
AACAAATTTTGTCTCGCTTGAGACAATTTTCTCAAA
Found at i:2457958 original size:30 final size:30
Alignment explanation
Indices: 2457922--2458112 Score: 107
Period size: 30 Copynumber: 5.9 Consensus size: 30
2457912 AATTGATAAA
*
2457922 CTTTGAGATTGTTTCTCTTGAAACAAAAAT
1 CTTTGAGATTGTTTCCCTTGAAACAAAAAT
* * * **
2457952 CTTTGAGATCGCTTCCCTTGAAATAAAGTTTTGTCT
1 CTTTGAGATTGTTTCCCTTGAAACAAA------AAT
* *
2457988 CTCTTGAGATAGTTTCTCTTGAAACAAAAAT
1 CT-TTGAGATTGTTTCCCTTGAAACAAAAAT
* *
2458019 CTTTGAG-TCTGGTTCCCTTGAAACAAAGTTTTGTAT
1 CTTTGAGAT-TGTTTCCCTTGAAACAAA------AAT
** *
2458055 CTATTGAGAGAGTTTCTCTTGAAACAAAAAT
1 CT-TTGAGATTGTTTCCCTTGAAACAAAAAT
2458086 CTTTGAG-TCTGTTTCCCTTGAAACAAA
1 CTTTGAGAT-TGTTTCCCTTGAAACAAA
2458113 TTTTGTCTCG
Statistics
Matches: 120, Mismatches: 24, Indels: 34
0.67 0.13 0.19
Matches are distributed among these distances:
29 1 0.01
30 64 0.53
31 7 0.06
36 7 0.06
37 41 0.34
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (30 bp):
CTTTGAGATTGTTTCCCTTGAAACAAAAAT
Found at i:2457995 original size:67 final size:67
Alignment explanation
Indices: 2457924--2458148 Score: 337
Period size: 67 Copynumber: 3.4 Consensus size: 67
2457914 TTGATAAACT
* *
2457924 TTGAGATTGTTTCTCTTGAAACAAAAATCTTTGAGATC-GCTTCCCTTGAAATAAAGTTTTGTCT
1 TTGAGATAGTTTCTCTTGAAACAAAAATCTTTGAG-TCTGCTTCCCTTGAAACAAAGTTTTGTCT
2457988 CTC
65 CTC
* *
2457991 TTGAGATAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGGTTCCCTTGAAACAAAGTTTTGTATC
1 TTGAGATAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGCTTCCCTTGAAACAAAGTTTTGTCTC
*
2458056 TA
66 TC
* *
2458058 TTGAGAGAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAACAAA-TTTTGTCTC
1 TTGAGATAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGCTTCCCTTGAAACAAAGTTTTGTCTC
*
2458122 GC
66 TC
**
2458124 TTGAGACCGTTTCTCTTGAAACAAA
1 TTGAGATAGTTTCTCTTGAAACAAA
2458149 TTACCCCTAA
Statistics
Matches: 145, Mismatches: 12, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
66 33 0.23
67 112 0.77
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.38
Consensus pattern (67 bp):
TTGAGATAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGCTTCCCTTGAAACAAAGTTTTGTCTC
TC
Found at i:2458438 original size:137 final size:137
Alignment explanation
Indices: 2458166--2458472 Score: 377
Period size: 137 Copynumber: 2.2 Consensus size: 137
2458156 TAAAGATGGT
* * * * *
2458166 CAGCCGTCCTCATCACGTAGGAACTGTGTTATCACCATTTATCCCTAATGATTGTAGTTGTCCTC
1 CAGCTGTCCTCATCACGTAGGAACTGTGTTATCACCATTTATCCCTAAAGATGGCAGTTGCCCTC
* *
2458231 ATCATGTAGGAATCATGTCATCCACCGACCAGATCTCCTCATCATGTAAGAGCCACATCAACCTT
66 ATCACGTAGGAATCATGTCATCCACCGACCAGATCTCCTCATCACGTAAGAGCCACATCAACCTT
2458296 AGATAAC
131 AGATAAC
*
2458303 CAGCTGTCCTCATCACGTATGAACTGTGTTATCACCATTTATCCCTAAAGATGGCCAGTTGCCCT
1 CAGCTGTCCTCATCACGTAGGAACTGTGTTATCACCATTTATCCCTAAAGATGG-CAGTTGCCCT
* * ** * **
2458368 CATCACGTAGGAATCGT-TCATCCACCGACCA-ATTCTCCTTATCACGTTGGAG-CAGCGTCGCC
65 CATCACGTAGGAATCATGTCATCCACCGACCAGA-TCTCCTCATCACGTAAGAGCCA-CATCAAC
*
2458430 CTTTGATAAC
128 CTTAGATAAC
* * ** *
2458440 CAGATTTCCTCATCATATAGGAACCGTGTTATC
1 CAGCTGTCCTCATCACGTAGGAACTGTGTTATC
2458473 CCTAAATTTA
Statistics
Matches: 145, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
136 3 0.02
137 119 0.82
138 23 0.16
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (137 bp):
CAGCTGTCCTCATCACGTAGGAACTGTGTTATCACCATTTATCCCTAAAGATGGCAGTTGCCCTC
ATCACGTAGGAATCATGTCATCCACCGACCAGATCTCCTCATCACGTAAGAGCCACATCAACCTT
AGATAAC
Found at i:2462784 original size:16 final size:16
Alignment explanation
Indices: 2462763--2462796 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2462753 TTACTATTCA
*
2462763 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
2462779 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
2462795 CG
1 CG
2462797 GTCGACGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:2470071 original size:30 final size:30
Alignment explanation
Indices: 2470035--2470095 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2470025 AGTCGAGGGT
* *
2470035 TACCTATGTCCTTCGGGACATATGGATAGG
1 TACCTATATCCTTCGGGACATATGGACAGG
2470065 TACCTATATCCTTCGGGACATATGGACAGG
1 TACCTATATCCTTCGGGACATATGGACAGG
2470095 T
1 T
2470096 CCTTCAGGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
TACCTATATCCTTCGGGACATATGGACAGG
Found at i:2475175 original size:30 final size:30
Alignment explanation
Indices: 2475139--2475199 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
2475129 AGTCGAGGGT
* *
2475139 TACCTATGTCTTTCGGGACAAATGGATAGG
1 TACCTATGTCCTTCGGGACAAATGGACAGG
*
2475169 TACCTATGTCCTTCGGGACATATGGACAGG
1 TACCTATGTCCTTCGGGACAAATGGACAGG
2475199 T
1 T
2475200 TCTTCGGGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.30
Consensus pattern (30 bp):
TACCTATGTCCTTCGGGACAAATGGACAGG
Found at i:2475493 original size:4 final size:4
Alignment explanation
Indices: 2475484--2476437 Score: 1644
Period size: 4 Copynumber: 242.8 Consensus size: 4
2475474 TAAATGATGA
2475484 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2475532 TATG TATG TATG TATG TATG TATG TATG TATG TAT- TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2475579 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2475627 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2475675 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2475723 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
2475771 TATG TATG TATG TGTA TGTG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
2475819 TATG TATG TATG TAT- TATG TATG TATG TATG TATG TGTA TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2475866 TATG TATG T-TG TATG TATG T-TG TATG TATG TATG TATG T-TG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
2475911 TATG TATG TATG TATG TATG TATG TATG TATG TATT TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2475959 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2476007 TATG TATG TATG TATG TATG T-TG TATG TATG T-TG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2476053 TATG TATG TATG TATG TAGTG TATG TATG TATG TATG T-TG TATG TATG
1 TATG TATG TATG TATG TA-TG TATG TATG TATG TATG TATG TATG TATG
2476101 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T-TG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2476148 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2476196 TATG --TG TATG TATG TATG TATG TATG TA-G TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2476241 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
2476289 TATG TATG TATG --TG TATG TATG TGTTG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG T-ATG TATG TATG TATG TATG TATG
2476336 TATG T-TG TATG TATG TATG TATG TATG TATGG TATGG TATG T-TG TATG
1 TATG TATG TATG TATG TATG TATG TATG TAT-G TAT-G TATG TATG TATG
* *
2476384 TATG TATG --TG TATG TATG TATG TATG T-TG T-TG TTTG TATA T-TG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2476427 TATG TATG TAT
1 TATG TATG TAT
2476438 TTGTTACATG
Statistics
Matches: 912, Mismatches: 15, Indels: 46
0.94 0.02 0.05
Matches are distributed among these distances:
2 6 0.01
3 44 0.05
4 846 0.93
5 16 0.02
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:2487879 original size:20 final size:21
Alignment explanation
Indices: 2487841--2487879 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2487831 CATCAAGGTC
*
2487841 TTTGTTGAGGCCATGAAATCT
1 TTTGTCGAGGCCATGAAATCT
2487862 TTTGTCGAGGCCAT-AAAT
1 TTTGTCGAGGCCATGAAAT
2487880 TCCTGCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (21 bp):
TTTGTCGAGGCCATGAAATCT
Found at i:2491829 original size:22 final size:22
Alignment explanation
Indices: 2491739--2491830 Score: 71
Period size: 23 Copynumber: 4.1 Consensus size: 22
2491729 GGTTCTACAC
* *
2491739 GGTCCTTCAGGAAAATTCTATGT
1 GGTCCTTC-GGGACATTCTATGT
* * *
2491762 GGTCATTCGGGATATTTCTACGCT
1 GGTCCTTCGGGACA-TTCTATG-T
* *
2491786 -GTCCTTCGAGACAATACT-TGT
1 GGTCCTTCGGGAC-ATTCTATGT
2491807 GGTCCTTCGGGACATTCTATGT
1 GGTCCTTCGGGACATTCTATGT
2491829 GG
1 GG
2491831 CACTGCGGTG
Statistics
Matches: 53, Mismatches: 11, Indels: 11
0.71 0.15 0.15
Matches are distributed among these distances:
21 5 0.09
22 21 0.40
23 25 0.47
24 2 0.04
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.35
Consensus pattern (22 bp):
GGTCCTTCGGGACATTCTATGT
Found at i:2498837 original size:23 final size:23
Alignment explanation
Indices: 2498805--2498913 Score: 132
Period size: 23 Copynumber: 4.8 Consensus size: 23
2498795 GAGTCGAGGG
2498805 TTCTATGTGGTCCTTCGGGACAA
1 TTCTATGTGGTCCTTCGGGACAA
* * *
2498828 TTCTACGTGGTCCTTTGGGACAT
1 TTCTATGTGGTCCTTCGGGACAA
* *
2498851 TTCTATATGGTCCTTCAGGACAA
1 TTCTATGTGGTCCTTCGGGACAA
* *
2498874 TACTATATGGTCCTTCGGGAC-A
1 TTCTATGTGGTCCTTCGGGACAA
2498896 TTCTATGTGG-CACTTCGG
1 TTCTATGTGGTC-CTTCGG
2498914 TGCAATTTAT
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
21 1 0.01
22 15 0.21
23 57 0.78
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCGGGACAA
Found at i:2501916 original size:2 final size:2
Alignment explanation
Indices: 2501909--2501942 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2501899 TATATTTTCA
2501909 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
2501943 TCTAATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2503202 original size:20 final size:21
Alignment explanation
Indices: 2503155--2503230 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 21
2503145 ATTTCTTTAA
2503155 ATATATTTCGTTTATTATTAT-T
1 ATATATTT--TTTATTATTATAT
*
2503177 ACATATTTTTTATTATTATAT
1 ATATATTTTTTATTATTATAT
*
2503198 -TATATTTATTATATATATATAT
1 ATATATTTTTTAT-TAT-TATAT
*
2503220 ATATATATTTT
1 ATATATTTTTT
2503231 CATATATATG
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 21 0.47
21 4 0.09
22 12 0.27
23 8 0.18
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (21 bp):
ATATATTTTTTATTATTATAT
Found at i:2503205 original size:17 final size:19
Alignment explanation
Indices: 2503185--2503245 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 19
2503175 TTACATATTT
2503185 TTTATTAT-TATAT-TATA
1 TTTATTATATATATATATA
2503202 TTTATTATATATATATATA
1 TTTATTATATATATATATA
* *
2503221 TATATATTTTCATATATATGTA
1 T-T-TATTAT-ATATATATATA
2503243 TTT
1 TTT
2503246 TTCACAATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
17 8 0.22
18 5 0.14
19 5 0.14
20 2 0.05
21 6 0.16
22 11 0.30
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTATTATATATATATATA
Found at i:2503235 original size:16 final size:16
Alignment explanation
Indices: 2503216--2503246 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2503206 TTATATATAT
2503216 ATATATATATATTTTC
1 ATATATATATATTTTC
*
2503232 ATATATATGTATTTT
1 ATATATATATATTTT
2503247 TCACAATCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (16 bp):
ATATATATATATTTTC
Found at i:2503237 original size:18 final size:17
Alignment explanation
Indices: 2503214--2503249 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
2503204 TATTATATAT
2503214 ATATATATATATATTTTC
1 ATATATATATAT-TTTTC
*
2503232 ATATATATGTATTTTTC
1 ATATATATATATTTTTC
2503249 A
1 A
2503250 CAATCTAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (17 bp):
ATATATATATATTTTTC
Found at i:2514476 original size:106 final size:106
Alignment explanation
Indices: 2514286--2514767 Score: 741
Period size: 106 Copynumber: 4.5 Consensus size: 106
2514276 TTGTCAATAG
* *
2514286 CAATCTCGGAGCCGATATT-AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
1 CAATTTCGGAGCCAAT-TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
2514350 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC
65 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC
* * * * *
2514392 CAATTTCGGAGCCAATTTTAACTTCATAGCGAAGGATATGGGATTCCAGACAACGCAAGTTCAAC
1 CAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
* *
2514457 TTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACCTCC
66 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC
* *
2514498 CAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
1 CAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
*
2514563 TTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCC
66 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC
* * * **
2514604 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGTTAACGCAAGTTCAAC
1 CAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
* * *
2514669 TTCACGACGAAGGGTCCGCTGGTTGTCAACGAACAATTTCC
66 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC
* * *
2514710 CAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGCCTCGAAACAACGCAA
1 CAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
2514768 CTTACATTGG
Statistics
Matches: 342, Mismatches: 33, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
105 2 0.01
106 340 0.99
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (106 bp):
CAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC
Found at i:2515068 original size:133 final size:132
Alignment explanation
Indices: 2514830--2515113 Score: 471
Period size: 133 Copynumber: 2.1 Consensus size: 132
2514820 ACAGATAGAC
* *
2514830 TCAACTTCACGACGAAGGAGTCATCTGTAACACCACAACTCCAAAGTCTTCAAGTTAAGTTTCAC
1 TCAACTTCGCAACGAAGGAGTCATCTGTAACACCACAACTCCAAAGTCTTCAAGTTAAGTTTCAC
****
2514895 CTTCGCGACGAAATATCTTGAGCCAGAAGACGATTCAGAGGCCACTTG-CTTTGGCTTTGAGCTC
66 CTTCGCGACGAAATATCTTGAGCCAGAAGACGATTCAGAGG-C-CTTGCCAAAAGCTTTGAGCTC
2514959 GTTT
129 GTTT
2514963 TCAACTTCGCAACGAAGGAGTCATCTGTAACACCACAACTCCAAAGTCTTCAAGTTAAGTTTCAC
1 TCAACTTCGCAACGAAGGAGTCATCTGTAACACCACAACTCCAAAGTCTTCAAGTTAAGTTTCAC
*
2515028 CTTCGCGATGAAATATCTTGAGCCAGAAGACGATTCAGAGGCCTTGCCAAAAGCTTTGAGCTCGT
66 CTTCGCGACGAAATATCTTGAGCCAGAAGACGATTCAGAGGCCTTGCCAAAAGCTTTGAGCTCGT
2515093 TT
131 TT
*
2515095 TCAACATCGCAACGAAGGA
1 TCAACTTCGCAACGAAGGA
2515114 TTCCGTGCTC
Statistics
Matches: 142, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
131 4 0.03
132 35 0.25
133 103 0.73
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (132 bp):
TCAACTTCGCAACGAAGGAGTCATCTGTAACACCACAACTCCAAAGTCTTCAAGTTAAGTTTCAC
CTTCGCGACGAAATATCTTGAGCCAGAAGACGATTCAGAGGCCTTGCCAAAAGCTTTGAGCTCGT
TT
Found at i:2516409 original size:25 final size:24
Alignment explanation
Indices: 2516380--2516427 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
2516370 TTCTTTAAAT
2516380 ATATTTCGTTTATTATTATTATTAC
1 ATATTTCGTTTATTATTA-TATTAC
**
2516405 ATATTTTTTTTATTATTATATTA
1 ATATTTCGTTTATTATTATATTA
2516428 TATTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (24 bp):
ATATTTCGTTTATTATTATATTAC
Found at i:2516433 original size:17 final size:19
Alignment explanation
Indices: 2516413--2516449 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
2516403 ACATATTTTT
2516413 TTTATTAT-TATAT-TATA
1 TTTATTATATATATATATA
2516430 TTTATTATATATATATATA
1 TTTATTATATATATATATA
2516449 T
1 T
2516450 ATATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 5 0.28
19 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATTATATATATATATA
Found at i:2516464 original size:15 final size:15
Alignment explanation
Indices: 2516446--2516476 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2516436 ATATATATAT
2516446 ATATATATATTTTTC
1 ATATATATATTTTTC
*
2516461 ATATATGTATTTTTC
1 ATATATATATTTTTC
2516476 A
1 A
2516477 CAATCTAACG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (15 bp):
ATATATATATTTTTC
Found at i:2519622 original size:15 final size:17
Alignment explanation
Indices: 2519597--2519628 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2519587 ATTAGATTTG
2519597 ATCCGAAAATTT-GGAT
1 ATCCGAAAATTTAGGAT
2519613 ATCC-AAAATTTAGGAT
1 ATCCGAAAATTTAGGAT
2519629 TGCTAAACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (17 bp):
ATCCGAAAATTTAGGAT
Found at i:2520503 original size:9 final size:9
Alignment explanation
Indices: 2520491--2520542 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
2520481 TAATATTTTG
2520491 TATTTAATT
1 TATTTAATT
*
2520500 TATTTAA-G
1 TATTTAATT
2520508 TATTTAATT
1 TATTTAATT
2520517 TATTTAA--
1 TATTTAATT
* *
2520524 TATTTTACT
1 TATTTAATT
2520533 TATTTAATT
1 TATTTAATT
2520542 T
1 T
2520543 TTTTGCAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:2520512 original size:17 final size:17
Alignment explanation
Indices: 2520490--2520539 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
2520480 TTAATATTTT
2520490 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
2520507 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
2520524 -TATTTTACTTATTTAA
1 GTATTTAATTTATTTAA
2520540 TTTTTTTGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:2520535 original size:16 final size:16
Alignment explanation
Indices: 2520499--2520544 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
2520489 TGTATTTAAT
* *
2520499 TTATTTAAGTATTTAAT
1 TTATTTAA-TATTTTAC
2520516 TTATTTAATATTTTAC
1 TTATTTAATATTTTAC
2520532 TTATTTAAT-TTTT
1 TTATTTAATATTTT
2520545 TTGCAGATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTTAATATTTTAC
Found at i:2530534 original size:96 final size:96
Alignment explanation
Indices: 2530370--2530563 Score: 388
Period size: 96 Copynumber: 2.0 Consensus size: 96
2530360 ACATCCTTCT
2530370 CGACAACGAATTCCAACCCTACATTTCTGATTTCGGCCTCAACAAACTCATCACCCTCACCAGCA
1 CGACAACGAATTCCAACCCTACATTTCTGATTTCGGCCTCAACAAACTCATCACCCTCACCAGCA
2530435 CCGGTTCCTCTTTTTCCGGCGGATTCATCGG
66 CCGGTTCCTCTTTTTCCGGCGGATTCATCGG
2530466 CGACAACGAATTCCAACCCTACATTTCTGATTTCGGCCTCAACAAACTCATCACCCTCACCAGCA
1 CGACAACGAATTCCAACCCTACATTTCTGATTTCGGCCTCAACAAACTCATCACCCTCACCAGCA
2530531 CCGGTTCCTCTTTTTCCGGCGGATTCATCGG
66 CCGGTTCCTCTTTTTCCGGCGGATTCATCGG
2530562 CG
1 CG
2530564 GACTTCCTTA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.23, C:0.37, G:0.15, T:0.26
Consensus pattern (96 bp):
CGACAACGAATTCCAACCCTACATTTCTGATTTCGGCCTCAACAAACTCATCACCCTCACCAGCA
CCGGTTCCTCTTTTTCCGGCGGATTCATCGG
Found at i:2532722 original size:3 final size:3
Alignment explanation
Indices: 2532714--2532760 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
2532704 TTCTACATTT
2532714 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2532761 CAATTACATT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2536767 original size:36 final size:35
Alignment explanation
Indices: 2536711--2536836 Score: 110
Period size: 36 Copynumber: 3.7 Consensus size: 35
2536701 GAAACACAAA
*
2536711 CTTTGAGATCATTTTC-CTTGAAACGAATTTTGTCT
1 CTTTGAGATCAGTTTCTCTTGAAAC-AATTTTGTCT
2536746 CTATTGAGA-CAGTTTCTCTTGAAAC-A-----TCAT
1 CT-TTGAGATCAGTTTCTCTTGAAACAATTTTGTC-T
*
2536776 CTTTGAGATC-GTTTCCCTTGAAACAAATTTTGTCT
1 CTTTGAGATCAGTTTCTCTTGAAAC-AATTTTGTCT
*
2536811 CTCTAGAGA-CAGTTTCTCTTGAAACA
1 CT-TTGAGATCAGTTTCTCTTGAAACA
2536837 TCACCTTTAA
Statistics
Matches: 74, Mismatches: 4, Indels: 26
0.71 0.04 0.25
Matches are distributed among these distances:
29 21 0.28
30 4 0.05
31 1 0.01
34 1 0.01
35 13 0.18
36 34 0.46
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (35 bp):
CTTTGAGATCAGTTTCTCTTGAAACAATTTTGTCT
Found at i:2536783 original size:65 final size:64
Alignment explanation
Indices: 2536693--2536909 Score: 255
Period size: 65 Copynumber: 3.4 Consensus size: 64
2536683 TTGGAAATTA
* * *
2536693 TTTCACTTGAAACA-CAAACTTTGAGATCATTTTCCTTGAAACGAATTTTGTCTCTATTGAGACA
1 TTTCTCTTGAAACATC-ATCTTTGAGATC-TTTTCCTTGAAACGAATTTTGTCTCTCTTGAGACA
2536757 G
64 G
* * *
2536758 TTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCTCTAGAGACAG
1 TTTCTCTTGAAACATCATCTTTGAGATC-TTTTCCTTGAAACGAATTTTGTCTCTCTTGAGACAG
* * * * *
2536823 TTTCTCTTGAAACATCACCTTTAAGATCGTTTCTCTTAAAACG-ATTTT-TCCTCTCTTGAGGCA
1 TTTCTCTTGAAACATCATCTTTGAGATCTTTTC-CTTGAAACGAATTTTGT-CTCTCTTGAGACA
2536886 -
64 G
2536886 TTTCTCTTG-AACATCATCTTTGAG
1 TTTCTCTTGAAACATCATCTTTGAG
2536910 TTGAAACAAT
Statistics
Matches: 132, Mismatches: 17, Indels: 9
0.84 0.11 0.06
Matches are distributed among these distances:
62 13 0.10
63 10 0.08
64 19 0.14
65 89 0.67
66 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (64 bp):
TTTCTCTTGAAACATCATCTTTGAGATCTTTTCCTTGAAACGAATTTTGTCTCTCTTGAGACAG
Found at i:2537208 original size:133 final size:132
Alignment explanation
Indices: 2536955--2537216 Score: 303
Period size: 133 Copynumber: 2.0 Consensus size: 132
2536945 TGAAACTATT
* * * * **
2536955 ATCCCTAAAGATGGCCATCCGTCTTCATCACCTAGAACCGTGTCATCCACTGACCATATCTCCTC
1 ATCCCTAAAGATGGCAATCCATCCTCATCACCTAGAACCGAGTCATCCACCAACCATATCTCCTC
* ** * * *
2537020 ATCACGTAGAGTTGCATCAACCTTTGATAACCAGCCGTCCTCATCGCGTAGGAACCATGTTATCA
66 ATAACGTAGAGCCGCATCAACCTTAGATAACCAGACGTCCTCATCACGTAGGAACCATGTTATCA
2537085 TC
131 TC
*
2537087 ATCCCTAAAGATGGTCAAT-CATCCTCATCACGTAGGAACCGAGTCATCCACCAACCATATCTCC
1 ATCCCTAAAGATGG-CAATCCATCCTCATCACCTA-GAACCGAGTCATCCACCAACCATATCTCC
** * * * * *
2537151 TCATAACGTAGGAGCCGTGTCACCCTTAGATAGCCAGACTTCCTCA-CATGTATGAACCATGTTA
64 TCATAACGTA-GAGCCGCATCAACCTTAGATAACCAGACGTCCTCATCACGTAGGAACCATGTTA
2537215 TC
128 TC
2537217 TCCAAATTTA
Statistics
Matches: 107, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
132 26 0.24
133 55 0.51
134 26 0.24
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.26
Consensus pattern (132 bp):
ATCCCTAAAGATGGCAATCCATCCTCATCACCTAGAACCGAGTCATCCACCAACCATATCTCCTC
ATAACGTAGAGCCGCATCAACCTTAGATAACCAGACGTCCTCATCACGTAGGAACCATGTTATCA
TC
Found at i:2537415 original size:3 final size:3
Alignment explanation
Indices: 2537407--2537441 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2537397 GGGCTCTACA
2537407 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2537442 CATTACAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2542130 original size:17 final size:18
Alignment explanation
Indices: 2542097--2542130 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2542087 GAATTTGTCC
*
2542097 CGAATGACCACTATATCT
1 CGAAGGACCACTATATCT
2542115 CGAAGGACCA-TATATC
1 CGAAGGACCACTATATC
2542131 ACATATGTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (18 bp):
CGAAGGACCACTATATCT
Found at i:2542157 original size:18 final size:18
Alignment explanation
Indices: 2542134--2542169 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2542124 ATATATCACA
2542134 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
2542152 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
2542170 ATAGAACCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.17
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:2551022 original size:44 final size:44
Alignment explanation
Indices: 2550959--2551065 Score: 151
Period size: 44 Copynumber: 2.4 Consensus size: 44
2550949 TTTTGTTCAC
* *
2550959 TATGCATCAATACACTATGAAAGTGTAACGATGCATCCCTTAAA
1 TATGCATCGATACACTATGAAAGTGCAACGATGCATCCCTTAAA
* * * *
2551003 TATGCATCGATACACTATGAAGGTGCACCGATGCATGCCTTGAA
1 TATGCATCGATACACTATGAAAGTGCAACGATGCATCCCTTAAA
*
2551047 TGTGCATCGATACACTATG
1 TATGCATCGATACACTATG
2551066 CAGTGCATTG
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (44 bp):
TATGCATCGATACACTATGAAAGTGCAACGATGCATCCCTTAAA
Found at i:2551597 original size:13 final size:13
Alignment explanation
Indices: 2551568--2551604 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2551558 CATACTATGA
*
2551568 TTTTTCAAACATTG
1 TTTTTCAAA-ATAG
2551582 TTTTTCAAAATAG
1 TTTTTCAAAATAG
2551595 TTTTTCAAAA
1 TTTTTCAAAA
2551605 ATTTGCCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (13 bp):
TTTTTCAAAATAG
Found at i:2553414 original size:12 final size:14
Alignment explanation
Indices: 2553387--2553421 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
2553377 AGGGGAAGTA
2553387 ATTTTCAAAAATTG
1 ATTTTCAAAAATTG
2553401 A-TTTCAAAAA-TG
1 ATTTTCAAAAATTG
2553413 ATTTTCAAA
1 ATTTTCAAA
2553422 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 16 0.80
14 1 0.05
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (14 bp):
ATTTTCAAAAATTG
Found at i:2553907 original size:65 final size:64
Alignment explanation
Indices: 2553755--2553910 Score: 201
Period size: 65 Copynumber: 2.4 Consensus size: 64
2553745 ACACCCTAAT
* * *
2553755 TCGAATGCATTTTGTGTACCAATGCACAACCATGCATCGATGCACTCCTGATTTTATTGAAACA
1 TCGAATGCATTTAGTGTACCGATGCACAACCATGCATCGATGCACTCCTGATCTTATTGAAACA
* * *
2553819 TCGAATCCATTTTA-TGTATCGATGCACAGACCATGCATCGATGCACTCCTGGCTCTT-TTGAAA
1 TCGAATGCA-TTTAGTGTACCGATGCACA-ACCATGCATCGATGCACTCCT-GATCTTATTGAAA
2553882 CA
63 CA
2553884 TCGAATGTCA-TTAGTGTACCGATGCAC
1 TCGAATG-CATTTAGTGTACCGATGCAC
2553911 CCCAAGTGTA
Statistics
Matches: 79, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
64 23 0.29
65 50 0.63
66 6 0.08
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (64 bp):
TCGAATGCATTTAGTGTACCGATGCACAACCATGCATCGATGCACTCCTGATCTTATTGAAACA
Found at i:2556433 original size:21 final size:19
Alignment explanation
Indices: 2556370--2556440 Score: 106
Period size: 19 Copynumber: 3.6 Consensus size: 19
2556360 CGGCCAAGAG
2556370 CATGTATCTTCATTAAAAT
1 CATGTATCTTCATTAAAAT
2556389 CATGTATCTTCATTAAAAT
1 CATGTATCTTCATTAAAAT
*
2556408 CATGTATTTTCATTTAAAAGT
1 CATGTATCTTCA-TTAAAA-T
*
2556429 CATGTATTTTCA
1 CATGTATCTTCA
2556441 AAGGGGTTTC
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 30 0.61
20 6 0.12
21 13 0.27
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (19 bp):
CATGTATCTTCATTAAAAT
Found at i:2557166 original size:14 final size:12
Alignment explanation
Indices: 2557143--2557207 Score: 69
Period size: 14 Copynumber: 5.0 Consensus size: 12
2557133 GTACAAAAAG
2557143 AAAGAAAAGACAA
1 AAAGAAAAGA-AA
2557156 AAAGAAAA-AGAA
1 AAAGAAAAGA-AA
2557168 AAAGAAAAGAAGAA
1 AAAGAAAAG-A-AA
2557182 AAAGAAAAGAAGA
1 AAAGAAAAGAA-A
2557195 AAAGAAAAAGAAA
1 AAAG-AAAAGAAA
2557208 TTCAAAAAGA
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
12 12 0.26
13 15 0.32
14 20 0.43
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:2557167 original size:19 final size:18
Alignment explanation
Indices: 2557143--2557207 Score: 94
Period size: 19 Copynumber: 3.4 Consensus size: 18
2557133 GTACAAAAAG
2557143 AAAGAAAAGACAAAAAGAA
1 AAAGAAAAGA-AAAAAGAA
2557162 AAAGAAAAAGAAAAGAAGAA
1 AAAG-AAAAGAAAA-AAGAA
2557182 AAAGAAAAGAAGAAAAGAA
1 AAAGAAAAGAA-AAAAGAA
2557201 AAAGAAA
1 AAAGAAA
2557208 TTCAAAAAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
19 26 0.60
20 17 0.40
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAGAAAAGAAAAAAGAA
Found at i:2560621 original size:21 final size:19
Alignment explanation
Indices: 2560558--2560628 Score: 106
Period size: 19 Copynumber: 3.6 Consensus size: 19
2560548 CGGCCAAGAG
2560558 CATGTATCTTCATTAAAAT
1 CATGTATCTTCATTAAAAT
2560577 CATGTATCTTCATTAAAAT
1 CATGTATCTTCATTAAAAT
*
2560596 CATGTATTTTCATTTAAAAGT
1 CATGTATCTTCA-TTAAAA-T
*
2560617 CATGTATTTTCA
1 CATGTATCTTCA
2560629 AAGGGGTTTC
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 30 0.61
20 6 0.12
21 13 0.27
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (19 bp):
CATGTATCTTCATTAAAAT
Found at i:2567024 original size:3 final size:3
Alignment explanation
Indices: 2567016--2567080 Score: 58
Period size: 3 Copynumber: 21.0 Consensus size: 3
2567006 TTTTTTCATT
** * * *
2567016 TTA TTA TTA TTA TTA AAA TTA TCA TTA TTA TTA ATA TTA TACA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
*
2567062 TATC TTA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA TTA
2567081 AATAATTACA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
3 44 0.92
4 4 0.08
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:2571745 original size:8 final size:7
Alignment explanation
Indices: 2571721--2571774 Score: 65
Period size: 7 Copynumber: 7.6 Consensus size: 7
2571711 TTTTCATACA
2571721 TGCA-TT
1 TGCATTT
2571727 TGCATTT
1 TGCATTT
2571734 TGCATCTT
1 TGCAT-TT
2571742 TGCATTT
1 TGCATTT
2571749 TGCATCTT
1 TGCAT-TT
2571757 TGCATTT
1 TGCATTT
**
2571764 TTTATTT
1 TGCATTT
2571771 TGCA
1 TGCA
2571775 ATTATACTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
6 4 0.10
7 23 0.56
8 14 0.34
ACGTcount: A:0.15, C:0.17, G:0.13, T:0.56
Consensus pattern (7 bp):
TGCATTT
Found at i:2571745 original size:15 final size:15
Alignment explanation
Indices: 2571725--2571764 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
2571715 CATACATGCA
2571725 TTTGCATTTTGCATC
1 TTTGCATTTTGCATC
2571740 TTTGCATTTTGCATC
1 TTTGCATTTTGCATC
2571755 TTTGCATTTT
1 TTTGCATTTT
2571765 TTATTTTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.12, C:0.17, G:0.12, T:0.57
Consensus pattern (15 bp):
TTTGCATTTTGCATC
Found at i:2571753 original size:22 final size:22
Alignment explanation
Indices: 2571725--2571774 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2571715 CATACATGCA
2571725 TTTGCATTTTGCATCTTTGCAT
1 TTTGCATTTTGCATCTTTGCAT
**
2571747 TTTGCATCTTTGCAT-TTTTTAT
1 TTTGCAT-TTTGCATCTTTGCAT
2571769 TTTGCA
1 TTTGCA
2571775 ATTATACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.14, C:0.16, G:0.12, T:0.58
Consensus pattern (22 bp):
TTTGCATTTTGCATCTTTGCAT
Found at i:2576132 original size:114 final size:114
Alignment explanation
Indices: 2575931--2576154 Score: 367
Period size: 114 Copynumber: 2.0 Consensus size: 114
2575921 GTGCCACGTT
*
2575931 CTCATAGTAGAAATAAAGAGACCCAATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATG
1 CTCATAGTAGAAATAAAGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATG
* * *
2575996 GTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTG
66 GTTCGGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTG
* * *
2576045 CTCATAGTAGAAATAAGGAGACCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAAGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATG
* *
2576110 GTTCGGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 GTTCGGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAA
2576155 CTGCATGATC
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (114 bp):
CTCATAGTAGAAATAAAGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATG
GTTCGGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTG
Found at i:2578769 original size:23 final size:22
Alignment explanation
Indices: 2578710--2578787 Score: 120
Period size: 22 Copynumber: 3.5 Consensus size: 22
2578700 ATCTACACTC
* *
2578710 TTCAAAGATGATATATTATCTT
1 TTCAAAGATGATAGATTCTCTT
*
2578732 TTCAAATATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
2578754 TTCAAAAGATGATAGATTCTCTT
1 TTC-AAAGATGATAGATTCTCTT
2578777 TTCAAAGATGA
1 TTCAAAGATGA
2578788 AAGCTTTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 30 0.59
23 21 0.41
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:2579791 original size:73 final size:73
Alignment explanation
Indices: 2579669--2580314 Score: 1195
Period size: 73 Copynumber: 8.8 Consensus size: 73
2579659 GTTTTCAAAT
*
2579669 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTATCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
2579734 CTCGAAAC
66 CTCGAAAC
2579742 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
2579807 CTCGAAAC
66 CTCGAAAC
2579815 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
2579880 CTCGAAAC
66 CTCGAAAC
*
2579888 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACATAATTTGTCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
2579953 CTCGAAAC
66 CTCGAAAC
2579961 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
2580026 CTCGAAAC
66 CTCGAAAC
* *
2580034 ATAACTTTATCTCACTTGAGATTGTTTTTCTTAAAA-AAAAATTGTCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
2580098 CTCGAAAC
66 CTCGAAAC
2580106 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
2580171 CTCGAAAC
66 CTCGAAAC
*
2580179 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTTGTCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
*
2580244 CTTGAAAC
66 CTCGAAAC
* * *
2580252 AAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAGATTTGTCTCGCTTAAGACAGTT
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-ATTTGTCTCGCTTGAGACAGTT
2580315 ATTTCGAGTT
Statistics
Matches: 558, Mismatches: 13, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
72 70 0.13
73 468 0.84
74 20 0.04
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.38
Consensus pattern (73 bp):
AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
CTCGAAAC
Found at i:2580194 original size:291 final size:292
Alignment explanation
Indices: 2579669--2580314 Score: 1197
Period size: 291 Copynumber: 2.2 Consensus size: 292
2579659 GTTTTCAAAT
*
2579669 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTATCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
*
2579734 CTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGA
66 CTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAAATTGTCTCGCTTGAGA
2579799 CAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTC
131 CAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTC
2579864 GCTTGAGACAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACATAA
196 GCTTGAGACAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACA-AA
2579929 -TTTGTCTCGCTTGAGACAGTTTCACTCGAAAC
260 TTTTGTCTCGCTTGAGACAGTTTCACTCGAAAC
2579961 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
*
2580026 CTCGAAACATAACTTTATCTCACTTGAGATTGTTTTTCTTAAAA-AAAAATTGTCTCGCTTGAGA
66 CTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAAATTGTCTCGCTTGAGA
2580090 CAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTC
131 CAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTC
2580155 GCTTGAGACAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAT
196 GCTTGAGACAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAT
*
2580220 TTTGTCTCGCTTGAGACAGTTTCACTTGAAAC
261 TTTGTCTCGCTTGAGACAGTTTCACTCGAAAC
* * *
2580252 AAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAGATTTGTCTCGCTTAAGACAGTT
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-ATTTGTCTCGCTTGAGACAGTT
2580315 ATTTCGAGTT
Statistics
Matches: 345, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
290 2 0.01
291 215 0.62
292 128 0.37
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.38
Consensus pattern (292 bp):
AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
CTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAAATTGTCTCGCTTGAGA
CAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTC
GCTTGAGACAGTTTCACTCGAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAT
TTTGTCTCGCTTGAGACAGTTTCACTCGAAAC
Found at i:2580720 original size:3 final size:3
Alignment explanation
Indices: 2580714--2580778 Score: 58
Period size: 3 Copynumber: 21.0 Consensus size: 3
2580704 TTTTTTCATT
** * * *
2580714 TTA TTA TTA TTA TTA AAA TTA TCA TTA TTA TTA ATA TTA TACA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
*
2580760 TATC TTA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA TTA
2580779 AATAATTACA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
3 44 0.92
4 4 0.08
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:2583602 original size:2 final size:2
Alignment explanation
Indices: 2583595--2583622 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2583585 AAATATGAAG
2583595 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
2583623 GAATTGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2596223 original size:23 final size:24
Alignment explanation
Indices: 2596179--2596228 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
2596169 TTGTTCCTGT
* *
2596179 AAAAAATTTAAATTATTATATTTA
1 AAAAAAATTAAATTATTATATTGA
2596203 AAAAAAATTAATATT-TT-TATTGA
1 AAAAAAATTAA-ATTATTATATTGA
2596226 AAA
1 AAA
2596229 TTTATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 8 0.35
24 12 0.52
25 3 0.13
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
AAAAAAATTAAATTATTATATTGA
Found at i:2597407 original size:2 final size:2
Alignment explanation
Indices: 2597400--2597436 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2597390 ATGCTTAGGT
2597400 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2597437 CGTCTATAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2597762 original size:23 final size:23
Alignment explanation
Indices: 2597719--2597768 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
2597709 TATGTGTTTG
*
2597719 TTGATATATTTTTTATATTAATT
1 TTGATATATTTTTTATATTAATA
2597742 TTGATATATTTTTTATATTAATA
1 TTGATATATTTTTTATATTAATA
2597765 TTGA
1 TTGA
2597769 AATGGTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (23 bp):
TTGATATATTTTTTATATTAATA
Found at i:2598451 original size:36 final size:37
Alignment explanation
Indices: 2598377--2598676 Score: 214
Period size: 38 Copynumber: 8.3 Consensus size: 37
2598367 TCCAGAGTTT
* * *
2598377 TATTTTTAAAACATTTTTCAAAAAAATATATAATATA
1 TATTTTTGAAACATTTTTTAAAAATATATATAATATA
2598414 TAATTTTTGAAACATTTTTTAAAAATATATATAATATA
1 T-ATTTTTGAAACATTTTTTAAAAATATATATAATATA
* *
2598452 TAGTTTTTGAAATATTTTTTGAAAATATATATAATATA
1 TA-TTTTTGAAACATTTTTTAAAAATATATATAATATA
2598490 TATTTTTG------------AAAATATATATAATATA
1 TATTTTTGAAACATTTTTTAAAAATATATATAATATA
* ** * * ** *
2598515 TAGTTTCAAAAAATATTTTTCGAAAACGTAAATAATATA
1 TATTTTTGAAACAT-TTTTT-AAAAATATATATAATATA
*
2598554 TAGTTTTAGAAAACATTTTTTAAAAATATATATAATATA
1 TA-TTTTTG-AAACATTTTTTAAAAATATATATAATATA
* *** *
2598593 TAGTTTTGAAA-ACGCTTTGAAAATATATATAATATA
1 TATTTTTGAAACATTTTTTAAAAATATATATAATATA
* * * * *
2598629 TAGTTTAGAAAACA-TTTTTGAAAACATACATAATATA
1 TATTTTTG-AAACATTTTTTAAAAATATATATAATATA
*
2598666 TAGTTTTGAAA
1 TATTTTTGAAA
2598677 ATATATAATA
Statistics
Matches: 212, Mismatches: 31, Indels: 41
0.75 0.11 0.14
Matches are distributed among these distances:
25 22 0.10
36 31 0.15
37 40 0.19
38 74 0.35
39 32 0.15
40 8 0.04
41 5 0.02
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (37 bp):
TATTTTTGAAACATTTTTTAAAAATATATATAATATA
Found at i:2598500 original size:25 final size:25
Alignment explanation
Indices: 2598463--2598516 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
2598453 AGTTTTTGAA
2598463 ATAT-TTTTTGAAAATATATATAAT
1 ATATATTTTTGAAAATATATATAAT
2598487 ATATATTTTTGAAAATATATATAAT
1 ATATATTTTTGAAAATATATATAAT
2598512 ATATA
1 ATATA
2598517 GTTTCAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.14
25 25 0.86
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (25 bp):
ATATATTTTTGAAAATATATATAAT
Found at i:2598526 original size:25 final size:25
Alignment explanation
Indices: 2598473--2598530 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
2598463 ATATTTTTTG
* **
2598473 AAAATATATATAATATATATTTTTG
1 AAAATATATATAATATATAGTTTCA
2598498 AAAATATATATAATATATAGTTTCA
1 AAAATATATATAATATATAGTTTCA
2598523 AAAA-ATAT
1 AAAATATAT
2598531 TTTTCGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (25 bp):
AAAATATATATAATATATAGTTTCA
Found at i:2598677 original size:37 final size:37
Alignment explanation
Indices: 2598491--2598677 Score: 223
Period size: 39 Copynumber: 5.0 Consensus size: 37
2598481 TATAATATAT
** *
2598491 ATTTTTGAAAATATATATAATATATAGTTTCAAAAAAT
1 ATTTTTGAAAATATATATAATATATAGTTT-TGAAAAC
** *
2598529 ATTTTTCGAAAACGTAAATAATATATAGTTTTAGAAAAC
1 ATTTTT-GAAAATATATATAATATATAGTTTT-GAAAAC
*
2598568 ATTTTTTAAAAATATATATAATATATAGTTTTGAAAAC
1 A-TTTTTGAAAATATATATAATATATAGTTTTGAAAAC
** *
2598606 -GCTTTGAAAATATATATAATATATAGTTTAGAAAAC
1 ATTTTTGAAAATATATATAATATATAGTTTTGAAAAC
* *
2598642 ATTTTTGAAAACATACATAATATATAGTTTTGAAAA
1 ATTTTTGAAAATATATATAATATATAGTTTTGAAAA
2598678 TATATAATAT
Statistics
Matches: 126, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
36 32 0.25
37 30 0.24
38 12 0.10
39 47 0.37
40 5 0.04
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.40
Consensus pattern (37 bp):
ATTTTTGAAAATATATATAATATATAGTTTTGAAAAC
Found at i:2598688 original size:23 final size:23
Alignment explanation
Indices: 2598644--2598700 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
2598634 TAGAAAACAT
*
2598644 TTTTGAAAACATACATAATATATAG
1 TTTTG-AAA-ATACATAATATATAA
*
2598669 TTTTGAAAATATATAATATATAA
1 TTTTGAAAATACATAATATATAA
*
2598692 TTTAGAAAA
1 TTTTGAAAA
2598701 CATTTTTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 21 0.72
24 3 0.10
25 5 0.17
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.39
Consensus pattern (23 bp):
TTTTGAAAATACATAATATATAA
Found at i:2598703 original size:60 final size:60
Alignment explanation
Indices: 2598608--2598737 Score: 199
Period size: 60 Copynumber: 2.1 Consensus size: 60
2598598 TTGAAAACGC
*
2598608 TTTGAAAATATATATAATATATAGTTTAGAAAACATTTTTGAAAACATACATAATATAT-AGT
1 TTTG-AAA-ATATATAATATATAATTTAGAAAACATTTTTGAAAACATACATAATATATGA-T
* *
2598670 TTTGAAAATATATAATATATAATTTAGAAAACATTTTTGAAAATATATATAATATATGAT
1 TTTGAAAATATATAATATATAATTTAGAAAACATTTTTGAAAACATACATAATATATGAT
2598730 TTTGAAAA
1 TTTGAAAA
2598738 CATTTTTCAA
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
60 56 0.88
61 4 0.06
62 4 0.06
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.40
Consensus pattern (60 bp):
TTTGAAAATATATAATATATAATTTAGAAAACATTTTTGAAAACATACATAATATATGAT
Found at i:2598737 original size:37 final size:36
Alignment explanation
Indices: 2598669--2598762 Score: 127
Period size: 37 Copynumber: 2.6 Consensus size: 36
2598659 TAATATATAG
2598669 TTTTG-AAAATATATAATATATAATTTAGAAAACAT
1 TTTTGAAAAATATATAATATATAATTTAGAAAACAT
* *
2598704 TTTTGAAAATATATATAATATATGATTTTGAAAACAT
1 TTTTGAAAA-ATATATAATATATAATTTAGAAAACAT
*
2598741 TTTTCAAAAAAATATATAATAT
1 TTTT--GAAAAATATATAATAT
2598763 TAGTTTTTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
35 5 0.10
36 3 0.06
37 29 0.56
38 11 0.21
39 4 0.08
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.41
Consensus pattern (36 bp):
TTTTGAAAAATATATAATATATAATTTAGAAAACAT
Found at i:2600012 original size:13 final size:13
Alignment explanation
Indices: 2599978--2600040 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 13
2599968 ATAAATTTTA
2599978 ATTTATTTTAATTT
1 ATTT-TTTTAATTT
2599992 GATCTTTTTT-ATTT
1 -AT-TTTTTTAATTT
**
2600006 ATTTTTTTGGTTT
1 ATTTTTTTAATTT
2600019 AATTTTTTTAATTT
1 -ATTTTTTTAATTT
*
2600033 CTTTTTTT
1 ATTTTTTT
2600041 CAAAAACATT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
12 6 0.15
13 12 0.29
14 15 0.37
15 6 0.15
16 2 0.05
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (13 bp):
ATTTTTTTAATTT
Found at i:2600134 original size:19 final size:20
Alignment explanation
Indices: 2600072--2600136 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 20
2600062 GCATTTTTCT
* *
2600072 TATTTTTTATCTTTCTTTAA
1 TATTTTTTACCTTTTTTTAA
* * * *
2600092 -ATTTTTTCCCCTTTATTATG
1 TATTTTTTACCTTTTTTTA-A
2600112 TATTTTTT-CCTTTTTTTAA
1 TATTTTTTACCTTTTTTTAA
2600131 TATTTT
1 TATTTT
2600137 AAAATTTTTC
Statistics
Matches: 34, Mismatches: 9, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
19 19 0.56
20 8 0.24
21 7 0.21
ACGTcount: A:0.17, C:0.12, G:0.02, T:0.69
Consensus pattern (20 bp):
TATTTTTTACCTTTTTTTAA
Found at i:2607308 original size:2 final size:2
Alignment explanation
Indices: 2607301--2607404 Score: 201
Period size: 2 Copynumber: 52.5 Consensus size: 2
2607291 AACATTTTTA
2607301 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
2607343 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
2607385 AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
2607405 GTTTTGGAAA
Statistics
Matches: 101, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 100 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2607543 original size:39 final size:38
Alignment explanation
Indices: 2607387--2607598 Score: 283
Period size: 38 Copynumber: 5.6 Consensus size: 38
2607377 ATATATATAT
*
2607387 ATATATATATATAATATAGTTTTGG-AAACATTTTTTTTAAAA
1 ATATATATA-AT-ATATAGTTTTGGAAAACA---TTTTTGAAA
*
2607429 ATATATATAATATATAGTTTTTG-AAACATTTTTTGAAA
1 ATATATATAATATATAGTTTTGGAAAACA-TTTTTGAAA
2607467 ATATATATAATATATAGTTTT-GAAAACATTTTTGAAA
1 ATATATATAATATATAGTTTTGGAAAACATTTTTGAAA
2607504 ATATATATAATATATAGTTTTGGAAAACATTTTTCGAAA
1 ATATATATAATATATAGTTTTGGAAAACATTTTT-GAAA
**
2607543 ACGTATATAATATATAGTTTTGGAAAACATTTTTG-AA
1 ATATATATAATATATAGTTTTGGAAAACATTTTTGAAA
2607580 A-ATATATAATAT-TAGTTTT
1 ATATATATAATATATAGTTTT
2607599 TAAAAAATAT
Statistics
Matches: 162, Mismatches: 5, Indels: 13
0.90 0.03 0.07
Matches are distributed among these distances:
35 7 0.04
36 10 0.06
37 34 0.21
38 48 0.30
39 36 0.22
40 16 0.10
41 2 0.01
42 9 0.06
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (38 bp):
ATATATATAATATATAGTTTTGGAAAACATTTTTGAAA
Found at i:2607658 original size:28 final size:28
Alignment explanation
Indices: 2607627--2607681 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
2607617 TTACATTATA
2607627 TTTATTT-TTTATTTAATTATTC-ATTTTG
1 TTTATTTCTTTATTT--TTATTCTATTTTG
2607655 TTTATTTCTTTATTTTTATTCTATTTT
1 TTTATTTCTTTATTTTTATTCTATTTT
2607682 TTCTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 6 0.24
28 12 0.48
29 7 0.28
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (28 bp):
TTTATTTCTTTATTTTTATTCTATTTTG
Found at i:2608982 original size:28 final size:28
Alignment explanation
Indices: 2608930--2608987 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
2608920 CACTTTAGAA
* *
2608930 TTTTTCCTTTTTTTCTCTTTCTTTAATT
1 TTTTTCCTTTTATTATCTTTCTTTAATT
* *
2608958 TTTTTCCTTTTATTATGTTTTTTTAATT
1 TTTTTCCTTTTATTATCTTTCTTTAATT
2608986 TT
1 TT
2608988 ACCTTTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (28 bp):
TTTTTCCTTTTATTATCTTTCTTTAATT
Found at i:2610713 original size:2 final size:2
Alignment explanation
Indices: 2610706--2610753 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
2610696 GTCAGCTAAT
2610706 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2610747 TA T- TA TA
1 TA TA TA TA
2610754 AAATGTCTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2610734 original size:21 final size:21
Alignment explanation
Indices: 2610708--2610753 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
2610698 CAGCTAATTA
2610708 TATATATATATATATATATAT
1 TATATATATATATATATATAT
2610729 TATATATATATATATATATAT
1 TATATATATATATATATATAT
2610750 TATA
1 TATA
2610754 AAATGTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATATATATATATATATATAT
Found at i:2612842 original size:22 final size:21
Alignment explanation
Indices: 2612791--2612842 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
2612781 TTTTTTAGAT
* * *
2612791 TAAACTAAAATAGTATTTATTT
1 TAAA-TAAAAAAGTATTAATTA
2612813 TAATATAAAAAAGTATTAATTAA
1 TAA-ATAAAAAAGTATTAATT-A
2612836 TAAATAA
1 TAAATAA
2612843 TGATCCGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (21 bp):
TAAATAAAAAAGTATTAATTA
Found at i:2613537 original size:26 final size:26
Alignment explanation
Indices: 2613506--2613638 Score: 99
Period size: 26 Copynumber: 5.0 Consensus size: 26
2613496 TTTTCTTTAA
*
2613506 CATTAATCGAACCAAAATTATTTGAC
1 CATTAATCGAACCAAATTTATTTGAC
* * * *
2613532 CATTAATAGAGCCGGAATTTATTTGAA
1 CATTAATCGAACC-AAATTTATTTGAC
* * * *
2613559 AATT-AT-TAACCGAAATTTTTTCTTTAAC
1 CATTAATCGAACC-AAA---TTTATTTGAC
* *
2613587 CATTAATCGAACCAAAATTATTTTAC
1 CATTAATCGAACCAAATTTATTTGAC
2613613 CATTAATCGAACCCAAATTTATTTGA
1 CATTAATCGAA-CCAAATTTATTTGA
2613639 AAAATATTAA
Statistics
Matches: 81, Mismatches: 19, Indels: 13
0.72 0.17 0.12
Matches are distributed among these distances:
25 6 0.07
26 31 0.38
27 25 0.31
28 10 0.12
29 5 0.06
30 4 0.05
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (26 bp):
CATTAATCGAACCAAATTTATTTGAC
Found at i:2613554 original size:93 final size:94
Alignment explanation
Indices: 2613347--2613653 Score: 349
Period size: 93 Copynumber: 3.4 Consensus size: 94
2613337 TTTTTAACCG
* * *
2613347 TTAATCGAACCAAAATTTATATGAAAATTATTAATCGAACCAAATCAACAGATTTTTTTTCTTTA
1 TTAATAGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATCAACAGATTTTTTTTCTTTA
* *
2613412 ACATTAATCGAACCGAAATTATTTGACCG
66 ACATTAATCGAACCAAAATTATTTGACCA
* * *
2613441 TTAATCGAACCAAAATTTATTTGGAAATTATTAACCGAACCAAATTAACCA-A-TTTTTTTCTTT
1 TTAATAGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATCAA-CAGATTTTTTTTCTTT
2613504 AACATTAATCGAACCAAAATTATTTGACCA
65 AACATTAATCGAACCAAAATTATTTGACCA
* **
2613534 TTAATAGAGCCGGAATTTATTTGAAAATTATTAACCG----------A-A-A--TTTTTTCTTTA
1 TTAATAGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATCAACAGATTTTTTTTCTTTA
*
2613585 ACCATTAATCGAACCAAAATTATTTTACCA
66 A-CATTAATCGAACCAAAATTATTTGACCA
* * *
2613615 TTAATCGAACCCAAATTTATTTGAAAAATATTAACCGAA
1 TTAATAGAACCAAAATTTATTTGAAAATTATTAACCGAA
2613654 TTAACTGAAT
Statistics
Matches: 192, Mismatches: 17, Indels: 19
0.84 0.07 0.08
Matches are distributed among these distances:
80 12 0.06
81 61 0.32
83 1 0.01
93 71 0.37
94 45 0.23
95 2 0.01
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.36
Consensus pattern (94 bp):
TTAATAGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATCAACAGATTTTTTTTCTTTA
ACATTAATCGAACCAAAATTATTTGACCA
Found at i:2613604 original size:81 final size:80
Alignment explanation
Indices: 2613484--2613653 Score: 261
Period size: 81 Copynumber: 2.1 Consensus size: 80
2613474 ACCGAACCAA
* * **
2613484 ATTAACC-AATTTTTTTCTTTAACATTAATCGAACCAAAATTATTTGACCATTAATAGAGCCGGA
1 ATTAACCGAAATTTTTTCTTTAACATTAATCGAACCAAAATTATTTGACCATTAATAGAACCCAA
*
2613548 ATTTATTTGAAAATT
66 ATTTATTTGAAAAAT
* *
2613563 ATTAACCGAAATTTTTTCTTTAACCATTAATCGAACCAAAATTATTTTACCATTAATCGAACCCA
1 ATTAACCGAAATTTTTTCTTTAA-CATTAATCGAACCAAAATTATTTGACCATTAATAGAACCCA
2613628 AATTTATTTGAAAAAT
65 AATTTATTTGAAAAAT
2613644 ATTAACCGAA
1 ATTAACCGAA
2613654 TTAACTGAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
79 7 0.09
80 14 0.17
81 61 0.74
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (80 bp):
ATTAACCGAAATTTTTTCTTTAACATTAATCGAACCAAAATTATTTGACCATTAATAGAACCCAA
ATTTATTTGAAAAAT
Found at i:2613794 original size:167 final size:167
Alignment explanation
Indices: 2613573--2614266 Score: 947
Period size: 167 Copynumber: 4.2 Consensus size: 167
2613563 ATTAACCGAA
*
2613573 ATTTTTTCTTTAACCATTAATCGAACCAAAATTATTTTACCATTAATCGAACCCAAATTTATTTG
1 ATTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCATTAATCGAACCCAAATTTATTTG
* * * *
2613638 AAAAATATTAACCGAATTAACTGAATAAAATAAATTATTTTTCTTTAACC-TCTAATTGAACCGA
66 AAAATTATTAACCGAATTAACCGAATAAAATAAATTATTTTTCTTTAACCGT-TAATCGAACCAA
2613702 AATTTATTTGAAAATTATTAACCGAACCAAATCAACCG
130 AATTTATTTGAAAATTATTAACCGAACCAAATCAACCG
* * * *
2613740 ATTTTTTCTTTAACCATTAATCAAACCAAAATTATTTGACCGTTAATTGAACCCAAATTTATTTC
1 ATTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCATTAATCGAACCCAAATTTATTTG
*
2613805 AAAATTATTAACCGAATTAACCGAATAAAATAAACTATTTTTCTTTAACCGTTAATCGAACCAAA
66 AAAATTATTAACCGAATTAACCGAATAAAATAAATTATTTTTCTTTAACCGTTAATCGAACCAAA
* *
2613870 ATTTATTTGAAAATTATTAATCGAACCAAATCAATCG
131 ATTTATTTGAAAATTATTAACCGAACCAAATCAACCG
* * *
2613907 ATTTTTTATTTAACCATTAATCGAACCGAAATTATTTGA-C------CG-TCCCAAATTTATTTG
1 ATTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCATTAATCGAACCCAAATTTATTTG
* * *
2613964 AAAATTATTAACCGAATTAA-CGAA-ATAAATAAATTATTTTTCATTAACCGTTAATCTAACCGA
66 AAAATTATTAACCGAATTAACCGAATA-AAATAAATTATTTTTCTTTAACCGTTAATCGAACCAA
*
2614027 AATTTATTTGAAAATTATTAACCGAACCCAATCAACCG
130 AATTTATTTGAAAATTATTAACCGAACCAAATCAACCG
* *
2614065 ATTTTTTTCTTTTACCATTAATCGAACCGAAATTATTTGACCATTAATCGAA---AAATTTATTT
1 A-TTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCATTAATCGAACCCAAATTTATTT
* * * *
2614127 GAAATTTATTAACCG----AACCGAGTAAAATAAATTATTTTTTCTTTAACCATTAATCCAACCA
65 GAAAATTATTAACCGAATTAACCGAATAAAATAAATTA-TTTTTCTTTAACCGTTAATCGAACCA
* * *
2614188 AAATTTATTTGAAAATTATTATCCGAATCAAATTAACCG
129 AAATTTATTTGAAAATTATTAACCGAACCAAATCAACCG
2614227 AATTTTTTTCTTTAACCATTAATCGAACCAAAATTTATTT
1 -A-TTTTTTCTTTAACCATTAATCGAACCAAAA-TTATTT
2614267 AAACAAATAA
Statistics
Matches: 471, Mismatches: 40, Indels: 35
0.86 0.07 0.06
Matches are distributed among these distances:
157 1 0.00
158 73 0.15
159 69 0.15
160 4 0.01
161 13 0.03
162 58 0.12
163 30 0.06
164 30 0.06
166 3 0.01
167 189 0.40
168 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.37
Consensus pattern (167 bp):
ATTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCATTAATCGAACCCAAATTTATTTG
AAAATTATTAACCGAATTAACCGAATAAAATAAATTATTTTTCTTTAACCGTTAATCGAACCAAA
ATTTATTTGAAAATTATTAACCGAACCAAATCAACCG
Found at i:2616688 original size:12 final size:11
Alignment explanation
Indices: 2616665--2616711 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
2616655 TATATGTATA
*
2616665 TTGTTATTTTT
1 TTGTTTTTTTT
2616676 TTGATTTTTTTT
1 TTG-TTTTTTTT
2616688 TTGTTTTTTTT
1 TTGTTTTTTTT
* *
2616699 TTCTTTTTCTT
1 TTGTTTTTTTT
2616710 TT
1 TT
2616712 ATTATTTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.04, C:0.04, G:0.06, T:0.85
Consensus pattern (11 bp):
TTGTTTTTTTT
Found at i:2616706 original size:23 final size:25
Alignment explanation
Indices: 2616663--2616720 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
2616653 TATATATGTA
* *
2616663 TATTGTTATTTTTTTGATTTT-TTT
1 TATTGTTTTTTTTTTCATTTTCTTT
*
2616687 T-TTGTTTTTTTTTTCTTTTTCTTT
1 TATTGTTTTTTTTTTCATTTTCTTT
*
2616711 TATTATTTTT
1 TATTGTTTTT
2616721 CTTTATGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 16 0.57
24 5 0.18
25 7 0.25
ACGTcount: A:0.09, C:0.03, G:0.05, T:0.83
Consensus pattern (25 bp):
TATTGTTTTTTTTTTCATTTTCTTT
Found at i:2616734 original size:14 final size:14
Alignment explanation
Indices: 2616702--2616735 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2616692 TTTTTTTTTC
2616702 TTTTTCTTTTATTA
1 TTTTTCTTTTATTA
*
2616716 TTTTTCTTTATGTTA
1 TTTTTCTTT-TATTA
2616731 TTTTT
1 TTTTT
2616736 ATGTATATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.79
Consensus pattern (14 bp):
TTTTTCTTTTATTA
Found at i:2622876 original size:17 final size:17
Alignment explanation
Indices: 2622854--2622892 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2622844 ATATATTTAT
2622854 TAATATTTCTAATAATA
1 TAATATTTCTAATAATA
* *
2622871 TAATATTTTTAATATTA
1 TAATATTTCTAATAATA
2622888 TAATA
1 TAATA
2622893 AAATAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATATTTCTAATAATA
Found at i:2622928 original size:23 final size:23
Alignment explanation
Indices: 2622863--2622932 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
2622853 TTAATATTTC
* *
2622863 TAATAATATAATATTTTTAATATTA
1 TAATAATATAACA-TATT-ATATTA
*
2622888 TAATAAAATAATCA-ATTATATTA
1 TAATAATATAA-CATATTATATTA
*
2622911 TAATAATATAAGATATTATATT
1 TAATAATATAACATATTATATT
2622933 TTTATTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 1 0.03
23 24 0.63
24 2 0.05
25 10 0.26
26 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (23 bp):
TAATAATATAACATATTATATTA
Found at i:2623041 original size:27 final size:29
Alignment explanation
Indices: 2622994--2623063 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 29
2622984 AATCTCATAG
2622994 AAATAATATTA-TTAAATTA-TTAATAAT
1 AAATAATATTATTTAAATTATTTAATAAT
* *
2623021 GAATAATATTATTTATA-TATTTAATAAT
1 AAATAATATTATTTAAATTATTTAATAAT
*
2623049 AATATAATAATATTT
1 AA-ATAATATTATTT
2623064 TAATAAAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 12 0.33
28 13 0.36
29 11 0.31
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (29 bp):
AAATAATATTATTTAAATTATTTAATAAT
Found at i:2623090 original size:23 final size:22
Alignment explanation
Indices: 2623064--2623107 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2623054 AATAATATTT
2623064 TAATAAAGATATTAAAAATATAC
1 TAATAAAGAT-TTAAAAATATAC
* * *
2623087 TAATTAATATTTTAAAATATA
1 TAATAAAGATTTAAAAATATA
2623108 ATATAACACT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
TAATAAAGATTTAAAAATATAC
Found at i:2623470 original size:14 final size:14
Alignment explanation
Indices: 2623451--2623509 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
2623441 CCATAAATGT
2623451 AATTCATTTTCCAG
1 AATTCATTTTCCAG
* *
2623465 AATTCAATTTCTAG
1 AATTCATTTTCCAG
*
2623479 TAATTCATTTTACAG
1 -AATTCATTTTCCAG
2623494 AATTCAATTTT-CAG
1 AATTC-ATTTTCCAG
2623508 AA
1 AA
2623510 AACCAATTAC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
14 22 0.58
15 16 0.42
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (14 bp):
AATTCATTTTCCAG
Found at i:2634870 original size:20 final size:21
Alignment explanation
Indices: 2634845--2634883 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2634835 TTTTGGTGCA
*
2634845 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
2634865 GAGGGAACCGATTCCCCCC
1 GAGGGAACCGATTCCCCCC
2634884 ACAGGGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:2643420 original size:17 final size:17
Alignment explanation
Indices: 2643382--2643420 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2643372 GTATATACAT
**
2643382 AAAAA-TAAAATATTAA
1 AAAAACTAAAATAGAAA
2643398 AAAAACTAAAATAGAAA
1 AAAAACTAAAATAGAAA
2643415 AAAAAC
1 AAAAAC
2643421 CCAAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (17 bp):
AAAAACTAAAATAGAAA
Found at i:2644561 original size:2 final size:2
Alignment explanation
Indices: 2644550--2644592 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2644540 TAATAATACT
2644550 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2644591 TA
1 TA
2644593 ATTTATAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2648461 original size:21 final size:21
Alignment explanation
Indices: 2648436--2648490 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
2648426 ATACTCATAG
* * *
2648436 GAGTATCAATACTTGACCCTA
1 GAGTATCGATACTTAACCCCA
2648457 GAGTATCGATACTTAACCCCA
1 GAGTATCGATACTTAACCCCA
*
2648478 AAGTATCGATACT
1 GAGTATCGATACT
2648491 ACTAGTAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.27
Consensus pattern (21 bp):
GAGTATCGATACTTAACCCCA
Found at i:2648746 original size:13 final size:13
Alignment explanation
Indices: 2648728--2648754 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2648718 CGATCATTGC
2648728 GTAGGGTGTACCA
1 GTAGGGTGTACCA
2648741 GTAGGGTGTACCA
1 GTAGGGTGTACCA
2648754 G
1 G
2648755 AAAGTGGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.41, T:0.22
Consensus pattern (13 bp):
GTAGGGTGTACCA
Found at i:2649647 original size:32 final size:32
Alignment explanation
Indices: 2649549--2649706 Score: 118
Period size: 32 Copynumber: 4.9 Consensus size: 32
2649539 GTTACACAAT
* * * *
2649549 AGAGTCAGTATTGCATTCAAATAATGCACAGT
1 AGAGTCAATATAGCATTCAAATAATGCATAGC
* ** * **
2649581 ATAGTCAATATTCCTTTCAGGTAATGCATAGC
1 AGAGTCAATATAGCATTCAAATAATGCATAGC
* *
2649613 AGAGTCAATATAGCATTCAAATAATACATTGC
1 AGAGTCAATATAGCATTCAAATAATGCATAGC
* * * * *
2649645 AGAATTAGTATTGCATTCATATAATGCATAGC
1 AGAGTCAATATAGCATTCAAATAATGCATAGC
* * * * *
2649677 AAAGTCAATATTGTATTTAGATAATGCATA
1 AGAGTCAATATAGCATTCAAATAATGCATA
2649707 AACAGAGCTA
Statistics
Matches: 96, Mismatches: 30, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
32 96 1.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (32 bp):
AGAGTCAATATAGCATTCAAATAATGCATAGC
Found at i:2650953 original size:2 final size:2
Alignment explanation
Indices: 2650946--2650977 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2650936 ATTAAAGTTA
2650946 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
2650978 TTGAATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2651239 original size:23 final size:24
Alignment explanation
Indices: 2651194--2651239 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
2651184 ATGGATCCTC
* *
2651194 CAAAATACTTGAAATTAATATTTA
1 CAAAATACTTCAAATTAACATTTA
*
2651218 CAAAATA-TTCAAATTTACATTT
1 CAAAATACTTCAAATTAACATTT
2651240 TAACCTGACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (24 bp):
CAAAATACTTCAAATTAACATTTA
Found at i:2657387 original size:16 final size:17
Alignment explanation
Indices: 2657357--2657391 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2657347 TTATGATGAA
*
2657357 ATTTTATTAGGGATTTT
1 ATTTTATTAGAGATTTT
2657374 ATTTT-TTAGAGATTTT
1 ATTTTATTAGAGATTTT
2657390 AT
1 AT
2657392 AAGGTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (17 bp):
ATTTTATTAGAGATTTT
Found at i:2660384 original size:18 final size:18
Alignment explanation
Indices: 2660342--2660384 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2660332 GATTTGAACT
* * *
2660342 CTGACCCCGTCCTCTAGA
1 CTGACCGCGTCCCCAAGA
2660360 CTGACCGCGTCCCCAAGA
1 CTGACCGCGTCCCCAAGA
2660378 CTGACCG
1 CTGACCG
2660385 GTCAGGGATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.44, G:0.21, T:0.16
Consensus pattern (18 bp):
CTGACCGCGTCCCCAAGA
Found at i:2670242 original size:10 final size:10
Alignment explanation
Indices: 2670227--2670325 Score: 53
Period size: 10 Copynumber: 9.8 Consensus size: 10
2670217 TATTTTATAT
2670227 ATATATTAAA
1 ATATATTAAA
*
2670237 ATATATTATTTA
1 ATATATTA--AA
2670249 AT-TATT-AA
1 ATATATTAAA
*
2670257 ATATAATAAA
1 ATATATTAAA
*
2670267 ATATAATAAA
1 ATATATTAAA
* *
2670277 ATAGATTAAT
1 ATATATTAAA
* *
2670287 TTAATAGTTTAA
1 AT-ATA-TTAAA
*
2670299 ATATAAT-AA
1 ATATATTAAA
2670308 ATA-ATTAGAA
1 ATATATTA-AA
2670318 ATATATTA
1 ATATATTA
2670326 TTTTAATTAT
Statistics
Matches: 67, Mismatches: 13, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
8 5 0.07
9 8 0.12
10 34 0.51
11 13 0.19
12 7 0.10
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (10 bp):
ATATATTAAA
Found at i:2670251 original size:37 final size:36
Alignment explanation
Indices: 2670172--2670251 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 36
2670162 CCCAATTCGG
*
2670172 TTAATTTTTATTTATATATATTATAATTAATATTTTA
1 TTAATTTTTATTTATATATATTATAA-TAATATATTA
*
2670209 ATAATTTTTATTT-TATATATATATTAA-AATATATTA
1 TTAATTTTTATTTATATATAT-TA-TAATAATATATTA
2670245 TTTAATT
1 -TTAATT
2670252 ATTAAATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
36 15 0.41
37 19 0.51
38 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (36 bp):
TTAATTTTTATTTATATATATTATAATAATATATTA
Found at i:2670310 original size:41 final size:41
Alignment explanation
Indices: 2670227--2670336 Score: 138
Period size: 41 Copynumber: 2.7 Consensus size: 41
2670217 TATTTTATAT
2670227 ATATATTAAAATATATT-ATTTAATTATTAAATATAATAAA
1 ATATATTAAAATATATTAATTTAATTATTAAATATAATAAA
* *
2670267 ATATAATAAAATAGATTAATTTAA-TAGTTTAAATATAAT-AA
1 ATATATTAAAATATATTAATTTAATTA--TTAAATATAATAAA
*
2670308 ATA-ATTAGAAATATATTATTTTAATTATT
1 ATATATTA-AAATATATTAATTTAATTATT
2670337 TTTAAAAATA
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
40 22 0.37
41 25 0.42
42 13 0.22
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (41 bp):
ATATATTAAAATATATTAATTTAATTATTAAATATAATAAA
Found at i:2672653 original size:23 final size:23
Alignment explanation
Indices: 2672622--2672733 Score: 152
Period size: 23 Copynumber: 4.9 Consensus size: 23
2672612 TTGAATGATT
* * *
2672622 CAGTGCTGACTGATTCAGTAAAA
1 CAGTGCTGAATGATTAAGCAAAA
*
2672645 TAGTGCTGAATGATTAAGCAAAA
1 CAGTGCTGAATGATTAAGCAAAA
*
2672668 CAGTGATGAATGATTAAGCAAAA
1 CAGTGCTGAATGATTAAGCAAAA
*
2672691 CAGTGTTGAATGATTAAGCAAAA
1 CAGTGCTGAATGATTAAGCAAAA
* *
2672714 CAGTGTTGAATGATTCAGCA
1 CAGTGCTGAATGATTAAGCA
2672734 CAAAAGTATA
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 81 1.00
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (23 bp):
CAGTGCTGAATGATTAAGCAAAA
Found at i:2675727 original size:51 final size:51
Alignment explanation
Indices: 2675665--2675778 Score: 124
Period size: 51 Copynumber: 2.2 Consensus size: 51
2675655 AAAATAACAA
* * *
2675665 TGACTAAAATGCAAGAAAATAAAGGT-TAGTAGCCAAATCAGAAA-TAAATAG
1 TGACCAAAATGCAA-AAAATAAA-ATATAGTAGCCAAATCAGAAATTAAAAAG
* * *
2675716 TGGCCAAAATGCAAAAATTAAAATAATAGTAGCTAAATCAGAAATTAAAAAG
1 TGACCAAAATGCAAAAAATAAAAT-ATAGTAGCCAAATCAGAAATTAAAAAG
*
2675768 TGACTAAAATG
1 TGACCAAAATG
2675779 AATAAATTGC
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
49 1 0.02
50 7 0.13
51 29 0.56
52 15 0.29
ACGTcount: A:0.54, C:0.10, G:0.16, T:0.21
Consensus pattern (51 bp):
TGACCAAAATGCAAAAAATAAAATATAGTAGCCAAATCAGAAATTAAAAAG
Done.