Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_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: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 31
Found at i:3031011 original size:14 final size:16
Alignment explanation
Indices: 3030991--3031055 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 16
3030981 ATAATATATG
*
3030991 TTATATAATT-TTTTTA
1 TTATAT-ATTATTTATA
3031007 TTATATATTATTTATA
1 TTATATATTATTTATA
*
3031023 TTAT-TA-TATATTATT
1 TTATATATTAT-TTATA
3031038 TTATAT-TTATTTAT-
1 TTATATATTATTTATA
3031052 TTAT
1 TTAT
3031056 TTAATTTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
14 7 0.16
15 17 0.40
16 19 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATATATTATTTATA
Found at i:3031028 original size:19 final size:20
Alignment explanation
Indices: 3031003--3031062 Score: 83
Period size: 19 Copynumber: 3.1 Consensus size: 20
3030993 ATATAATTTT
3031003 TTTATTATATATTATTTATA
1 TTTATTATATATTATTTATA
3031023 -TTATTATATATTATTTTATA
1 TTTATTATATATTA-TTTATA
3031043 TTTATT-TAT-TTATTTA-A
1 TTTATTATATATTATTTATA
3031060 TTT
1 TTT
3031063 TATTTTTCAG
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.11
18 4 0.11
19 16 0.42
20 9 0.24
21 5 0.13
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTATTATATATTATTTATA
Found at i:3031032 original size:10 final size:9
Alignment explanation
Indices: 3030991--3031058 Score: 68
Period size: 10 Copynumber: 7.3 Consensus size: 9
3030981 ATAATATATG
*
3030991 TTATATAAT
1 TTATATTAT
*
3031000 TT-TTTTAT
1 TTATATTAT
3031008 TATATATTAT
1 T-TATATTAT
3031018 TTATATTAT
1 TTATATTAT
3031027 TATATATTATT
1 T-TATATTA-T
3031038 TTATATTTAT
1 TTATA-TTAT
3031048 TTAT-TTAT
1 TTATATTAT
3031056 TTA
1 TTA
3031059 ATTTTATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
8 12 0.24
9 12 0.24
10 22 0.43
11 5 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTATATTAT
Found at i:3031050 original size:4 final size:4
Alignment explanation
Indices: 3030998--3031058 Score: 52
Period size: 4 Copynumber: 14.2 Consensus size: 4
3030988 ATGTTATATA
* *
3030998 ATTT TTTT ATTAT ATATT ATTT ATATT ATTAT ATATT ATTT -TAT ATTT
1 ATTT ATTT ATT-T AT-TT ATTT AT-TT ATT-T AT-TT ATTT ATTT ATTT
3031046 ATTT ATTT ATTT A
1 ATTT ATTT ATTT A
3031059 ATTTTATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
3 2 0.04
4 27 0.57
5 16 0.34
6 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (4 bp):
ATTT
Found at i:3031064 original size:6 final size:5
Alignment explanation
Indices: 3031002--3031068 Score: 50
Period size: 5 Copynumber: 13.8 Consensus size: 5
3030992 TATATAATTT
* * * * *
3031002 TTTTA TTATA TATTA -TTTA TATTA TTATA TATTA TTTTA TATTTA -TTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA
*
3031051 -TTTA TTTAA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTT
3031069 TCAGGTCCAA
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
4 11 0.23
5 32 0.68
6 4 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (5 bp):
TTTTA
Found at i:3031065 original size:29 final size:31
Alignment explanation
Indices: 3030991--3031068 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 31
3030981 ATAATATATG
* *
3030991 TTATATAATTTTTTTATTATATATTATTTATA
1 TTATTTAATTTTATT-TTATATATTATTTATA
*
3031023 TTA-TTATATATTATTTTATAT-TTATTTAT-
1 TTATTTA-ATTTTATTTTATATATTATTTATA
3031052 TTATTTAATTTTATTTT
1 TTATTTAATTTTATTTT
3031069 TCAGGTCCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 12 0.30
30 11 0.28
31 8 0.20
32 9 0.22
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (31 bp):
TTATTTAATTTTATTTTATATATTATTTATA
Found at i:3034627 original size:22 final size:22
Alignment explanation
Indices: 3034575--3034627 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
3034565 AACAATCGAA
*
3034575 AAACATG-CTAAAAGACATAGAT
1 AAACATGTC-AAAAGACAAAGAT
*
3034597 AAACGTGTCAAAAGACAAAGA-
1 AAACATGTCAAAAGACAAAGAT
3034618 AAATCATGTC
1 AAA-CATGTC
3034628 CATAAAGCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 3 0.12
22 22 0.85
23 1 0.04
ACGTcount: A:0.53, C:0.15, G:0.15, T:0.17
Consensus pattern (22 bp):
AAACATGTCAAAAGACAAAGAT
Found at i:3045367 original size:7 final size:7
Alignment explanation
Indices: 3045355--3045379 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3045345 AATGGCCTCC
3045355 ACTTCAA
1 ACTTCAA
3045362 ACTTCAA
1 ACTTCAA
3045369 ACTTCAA
1 ACTTCAA
3045376 ACTT
1 ACTT
3045380 TGAATTCGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (7 bp):
ACTTCAA
Found at i:3050903 original size:12 final size:12
Alignment explanation
Indices: 3050877--3050910 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
3050867 GTATCATAAT
3050877 TTTTCAAACATTA
1 TTTTCAAA-ATTA
3050890 TTTTCAAAATTA
1 TTTTCAAAATTA
3050902 TTTTCAAAA
1 TTTTCAAAA
3050911 ATTGCCCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (12 bp):
TTTTCAAAATTA
Found at i:3052594 original size:13 final size:13
Alignment explanation
Indices: 3052572--3052605 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3052562 AGTAATTTTC
*
3052572 ATTTTCAAAATTG
1 ATTTTCAAAAATG
3052585 A-TTTCAAAAATG
1 ATTTTCAAAAATG
3052597 ATTTTCAAA
1 ATTTTCAAA
3052606 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:3055343 original size:3 final size:3
Alignment explanation
Indices: 3055335--3055386 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
3055325 TTAATCCGAG
3055335 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3055383 ATA A
1 ATA A
3055387 ATATTATTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3055825 original size:21 final size:22
Alignment explanation
Indices: 3055779--3055875 Score: 64
Period size: 21 Copynumber: 4.5 Consensus size: 22
3055769 AAGGTTAAGA
*
3055779 CCTTTCGATGAAAGGACTTAAT
1 CCTTTCAATGAAAGGACTTAAT
*
3055801 -CTTTCAATTAAAGGACTT-AT
1 CCTTTCAATGAAAGGACTTAAT
*
3055821 CCTTTTC-ATGAAA-AATGCTTAA-
1 CC-TTTCAATGAAAGGA--CTTAAT
*
3055843 CCTTTTC-ATGAAAGGATTTAAT
1 CC-TTTCAATGAAAGGACTTAAT
*
3055865 CTTTTC-ATGAA
1 CCTTTCAATGAA
3055876 GAGAATTGTT
Statistics
Matches: 61, Mismatches: 7, Indels: 15
0.73 0.08 0.18
Matches are distributed among these distances:
20 3 0.05
21 35 0.57
22 21 0.34
23 2 0.03
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (22 bp):
CCTTTCAATGAAAGGACTTAAT
Found at i:3056391 original size:30 final size:30
Alignment explanation
Indices: 3056328--3056393 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 30
3056318 TACACCACTG
3056328 TTACTATTGTGTTCATCCCATTGTAAGGTACT
1 TTACTATTGTGTTCATCCCATTGT-A-GTACT
3056360 TTACTATTGTGTTCATCCCATTGCT-GTACT
1 TTACTATTGTGTTCATCCCATTG-TAGTACT
3056390 TTAC
1 TTAC
3056394 GAGATAGTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 9 0.27
32 23 0.70
33 1 0.03
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (30 bp):
TTACTATTGTGTTCATCCCATTGTAGTACT
Found at i:3062326 original size:22 final size:25
Alignment explanation
Indices: 3062271--3062326 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
3062261 ATCTTTGTGG
*
3062271 CACGTTTTCTTCTATCTTTTATGAT
1 CACGTTTTCTTATATCTTTTATGAT
3062296 -ACGTTTT-TCTATAT-TTTTATG-T
1 CACGTTTTCT-TATATCTTTTATGAT
3062318 CACGTTTTC
1 CACGTTTTC
3062327 GGTTGTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 1 0.04
23 15 0.56
24 11 0.41
ACGTcount: A:0.16, C:0.18, G:0.09, T:0.57
Consensus pattern (25 bp):
CACGTTTTCTTATATCTTTTATGAT
Found at i:3068820 original size:11 final size:11
Alignment explanation
Indices: 3068806--3068834 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3068796 TATTATGCCC
3068806 TTATATTTATT
1 TTATATTTATT
3068817 TTATATTTATT
1 TTATATTTATT
3068828 TTA-ATTT
1 TTATATTT
3068835 TGGTTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATATTTATT
Found at i:3074282 original size:39 final size:38
Alignment explanation
Indices: 3073961--3074777 Score: 842
Period size: 36 Copynumber: 21.9 Consensus size: 38
3073951 TTTCGTCTTC
* * ** *
3073961 CTTGAGACAGTTTCTCTTGAAACAAAG-TTTCGTCTCC
1 CTTGAGATAGTTTCCCTTGAAACAAAGATTTTATCTCG
* * *
3073998 CTTGAG-TCAGTTTCCCTGGAAAC-AA-ATTTTGTCTCC
1 CTTGAGAT-AGTTTCCCTTGAAACAAAGATTTTATCTCG
* * ** * *
3074034 CTTGAGACAGTTTCTCTTGAAAC-AA-ATTTCGTTTCC
1 CTTGAGATAGTTTCCCTTGAAACAAAGATTTTATCTCG
* * * * * * *
3074070 CTTGAGACAGTTTCTCTTGGAATAAGGCATTGTCT-TC-
1 CTTGAGATAGTTTCCCTTGAAACAAAG-ATTTTATCTCG
* ** *
3074107 CTTGAGACAGTTTCCCTTGAAAC-AA-ATTTCGTCTCC
1 CTTGAGATAGTTTCCCTTGAAACAAAGATTTTATCTCG
* * * *
3074143 CTTGAGACATTTTCTCTTGAAAC--ATATTTTATCTCG
1 CTTGAGATAGTTTCCCTTGAAACAAAGATTTTATCTCG
*
3074179 CTTGAGATAGTTTCCCTTGAAAC--AGATTTTATATCG
1 CTTGAGATAGTTTCCCTTGAAACAAAGATTTTATCTCG
3074215 CTTGAGATAGTTT-CCTTGAAACAGAAGATTTTATCTCG
1 CTTGAGATAGTTTCCCTTGAAACA-AAGATTTTATCTCG
*
3074253 CTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCT
1 CTTGAGATAGTTTCCCTTGAAACA-AAGATTTTATCTCG
*
3074292 CTTGAGATAGTTTCCCTTGAAAC--AGATTTTATCTTG
1 CTTGAGATAGTTTCCCTTGAAACAAAGATTTTATCTCG
* *
3074328 CTTTAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCA
1 CTTGAGATAGTTTCCCTTGAAACA-AAGATTTTATCTCG
3074367 CTTGAGATAGTTTCCCTTGAAAC-AA-ATTTTATCTCG
1 CTTGAGATAGTTTCCCTTGAAACAAAGATTTTATCTCG
* *
3074403 CTTGAGATAGTTTCCCTCGAAATAGAAGATTTTATCTCG
1 CTTGAGATAGTTTCCCTTGAAACA-AAGATTTTATCTCG
* *
3074442 CTTGAGATAGTTTCCCTTG-AA-ATAGATTTTTATCACG
1 CTTGAGATAGTTTCCCTTGAAACAAAGA-TTTTATCTCG
*
3074479 CTTGAGATAGTTTCCCTTGAAAC--ATATTTTATCTCG
1 CTTGAGATAGTTTCCCTTGAAACAAAGATTTTATCTCG
* *
3074515 CTTGAGATAGTTTCCCTTGAAACATAAGATTTTTTCTCA
1 CTTGAGATAGTTTCCCTTGAAACA-AAGATTTTATCTCG
* * * *
3074554 CTTGAGATAATTTCCCTCGAAACAGAAAATTTTATCTCT
1 CTTGAGATAGTTTCCCTTGAAACA-AAGATTTTATCTCG
* * **
3074593 TTTGAGATAGTTTCTCTTGAAAC--AGATTTTATCTAT
1 CTTGAGATAGTTTCCCTTGAAACAAAGATTTTATCTCG
*
3074629 CTTGAGATATTTTCCCTTGAAAC--AGATTTTATCTCG
1 CTTGAGATAGTTTCCCTTGAAACAAAGATTTTATCTCG
3074665 CTTGAGATAGTTTCCCTTGAAACAAAAGATTTTATCTCG
1 CTTGAGATAGTTTCCCTTGAAAC-AAAGATTTTATCTCG
* *
3074704 ATTGAGATAATTTCCCTTGAAACAGAAGATTTTATCTCG
1 CTTGAGATAGTTTCCCTTGAAACA-AAGATTTTATCTCG
* **
3074743 CTTGAGATAGTTTCACTCCAAACAAAAGATTTTAT
1 CTTGAGATAGTTTCCCTTGAAAC-AAAGATTTTAT
3074778 AAAAAAACTA
Statistics
Matches: 674, Mismatches: 76, Indels: 58
0.83 0.09 0.07
Matches are distributed among these distances:
34 4 0.01
35 12 0.02
36 299 0.44
37 73 0.11
38 34 0.05
39 251 0.37
40 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (38 bp):
CTTGAGATAGTTTCCCTTGAAACAAAGATTTTATCTCG
Found at i:3074352 original size:75 final size:75
Alignment explanation
Indices: 3073961--3074756 Score: 844
Period size: 75 Copynumber: 10.7 Consensus size: 75
3073951 TTTCGTCTTC
* * ** * * *
3073961 CTTGAGACAGTTTCTCTTGAAACA-AAG-TTTCGTCTCCCTTGAG-TCAGTTTCCCTGGAAACAA
1 CTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGAT-AGTTTCCCTTGAAACAG
* *
3074023 ATTTTGTCTCC
65 ATTTTATCTCG
* * ** * * * *
3074034 CTTGAGACAGTTTCTCTTGAAAC--AA-ATTTCGTTTCCCTTGAGACAGTTTCTCTTGGAATA-A
1 CTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTT-GAA-ACA
* *
3074095 GGCATTGTCT-TC-
64 -G-ATTTTATCTCG
* ** * * * * *
3074107 CTTGAGACAGTTTCCCTTGAAAC--AA-ATTTCGTCTCCCTTGAGACATTTTCTCTTGAAACATA
1 CTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAGA
3074169 TTTTATCTCG
66 TTTTATCTCG
*
3074179 CTTGAGATAGTTTCCCTTGAAAC---AGATTTTATATCGCTTGAGATAGTTT-CCTTGAAACAGA
1 CTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC---
3074240 AGATTTTATCTCG
63 AGATTTTATCTCG
*
3074253 CTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAGA
1 CTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAGA
*
3074318 TTTTATCTTG
66 TTTTATCTCG
* * *
3074328 CTTTAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCACTTGAGATAGTTTCCCTTGAAACAAA
1 CTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAGA
3074393 TTTTATCTCG
66 TTTTATCTCG
* * *
3074403 CTTGAGATAGTTTCCCTCGAAATAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAATAGA
1 CTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAGA
*
3074468 TTTTTATCACG
66 -TTTTATCTCG
*
3074479 CTTGAGATAGTTTCCCTTGAAAC---ATATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACATA
1 CTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC---
* *
3074541 AGATTTTTTCTCA
63 AGATTTTATCTCG
* * * ** *
3074554 CTTGAGATAATTTCCCTCGAAACAGAAAATTTTATCTCTTTTGAGATAGTTTCTCTTGAAACAGA
1 CTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAGA
**
3074619 TTTTATCTAT
66 TTTTATCTCG
*
3074629 CTTGAGATATTTTCCCTTGAAAC---AGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAA
1 CTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC---
3074691 AGATTTTATCTCG
63 AGATTTTATCTCG
* *
3074704 ATTGAGATAATTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTC
1 CTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTC
3074757 ACTCCAAACA
Statistics
Matches: 631, Mismatches: 62, Indels: 55
0.84 0.08 0.07
Matches are distributed among these distances:
70 5 0.01
71 12 0.02
72 101 0.16
73 112 0.18
74 38 0.06
75 238 0.38
76 33 0.05
77 24 0.04
78 68 0.11
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (75 bp):
CTTGAGATAGTTTCCCTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAGA
TTTTATCTCG
Found at i:3075056 original size:97 final size:98
Alignment explanation
Indices: 3074780--3075199 Score: 478
Period size: 94 Copynumber: 4.3 Consensus size: 98
3074770 GATTTTATAA
** * *
3074780 AAAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGAAAATTTTCAATGAATTTATAAAAGGAAGC
1 AAAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATGATTTTCAATGAGTTTTTAAAAGGAAGC
* * *
3074845 TAAACCTAATTTTTAGGGGTTTCTTGACAACTT
66 TAAGCCTAATTTTTAGGGGTTCCTAGACAACTT
* * ** *
3074878 AGAAACAAAGTTTGATTTTTAGGGGTTTCTTGATGAT--TTTT-AATGAGTTTTTAAAAGGAAGC
1 AAAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATGATTTTCAATGAGTTTTTAAAAGGAAGC
3074940 TAAGCCTAATTTTTA-GGGTTCCTAGACAACTT
66 TAAGCCTAATTTTTAGGGGTTCCTAGACAACTT
* * * *
3074972 AGAAACTAAGCCTGATTTTCAGGCGTTTCTTGATGATGATTTTCAATGCGTTTTTCAAAGGAAGC
1 AAAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATGATTTTCAATGAGTTTTTAAAAGGAAGC
* * * *
3075037 TAAGCCT-ATTTTTAGGGGTTCTTTGATAATTT
66 TAAGCCTAATTTTTAGGGGTTCCTAGACAACTT
* * *
3075069 AAAAACTAAGCCTGATTTTTAGGGGTTTCTT-A--ATGATTTTCAAGGAGTTTTTAAGAGGAAGC
1 AAAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATGATTTTCAATGAGTTTTTAAAAGGAAGC
* ** * ** *
3075131 CAAGTTTAATTTATAGGGGTTATTTGATGACAACTA
66 TAAGCCTAATTTTTAGGGGTT-CCT-A-GACAACTT
*
3075167 AAAAACTAAGCTTGATTTTCAGGGGTTTCTTGA
1 AAAAACTAAGCCTGATTTTCAGGGGTTTCTTGA
3075200 CGATTATCTC
Statistics
Matches: 273, Mismatches: 40, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
94 77 0.28
95 45 0.16
96 18 0.07
97 67 0.25
98 65 0.24
99 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (98 bp):
AAAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATGATTTTCAATGAGTTTTTAAAAGGAAGC
TAAGCCTAATTTTTAGGGGTTCCTAGACAACTT
Found at i:3075130 original size:191 final size:196
Alignment explanation
Indices: 3074779--3075199 Score: 548
Period size: 191 Copynumber: 2.2 Consensus size: 196
3074769 AGATTTTATA
3074779 AAAAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGAAAATTTTCAATGAATTTATAAAAGGAAG
1 AAAAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGAAAATTTTCAATGAATTTATAAAAGGAAG
* **
3074844 CTAAACCTAATTTTTAGGGGTTTCTTGACAACTTAGAAACAAAGTTTGATTTTTAGGGGTTTCTT
66 CTAAACCTAATTTTTAGGGGTTTCTTGACAACTTAAAAACAAAGCCTGATTTTTAGGGGTTTCTT
* * * * *
3074909 GATGATTTTTAATGAGTTTTTAAAAGGAAGCTAAGCCTAATTTTTA-GGGTT-CCT-A-GACAAC
131 AATGATTTTCAAGGAGTTTTTAAAAGGAAGCCAAGCCTAATTTATAGGGGTTACCTGATGACAAC
3074970 T
196 T
* * * ** ** * *
3074971 TAGAAACTAAGCCTGATTTTCAGGCGTTTCTTGATGATGATTTTCAATGCGTTTTTCAAAGGAAG
1 AAAAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGAAAATTTTCAATGAATTTATAAAAGGAAG
* * * *
3075036 CTAAGCCT-ATTTTTAGGGG-TTCTTTGATAATTTAAAAACTAAGCCTGATTTTTAGGGGTTTCT
66 CTAAACCTAATTTTTAGGGGTTTC-TTGACAACTTAAAAACAAAGCCTGATTTTTAGGGGTTTCT
* ** **
3075099 TAATGATTTTCAAGGAGTTTTTAAGAGGAAGCCAAGTTTAATTTATAGGGGTTATTTGATGACAA
130 TAATGATTTTCAAGGAGTTTTTAAAAGGAAGCCAAGCCTAATTTATAGGGGTTACCTGATGACAA
3075164 CT
195 CT
*
3075166 AAAAAACTAAGCTTGATTTTCAGGGGTTTCTTGA
1 AAAAAACTAAGCCTGATTTTCAGGGGTTTCTTGA
3075200 CGATTATCTC
Statistics
Matches: 194, Mismatches: 30, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
190 3 0.02
191 84 0.43
192 68 0.35
193 1 0.01
194 1 0.01
195 37 0.19
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (196 bp):
AAAAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGAAAATTTTCAATGAATTTATAAAAGGAAG
CTAAACCTAATTTTTAGGGGTTTCTTGACAACTTAAAAACAAAGCCTGATTTTTAGGGGTTTCTT
AATGATTTTCAAGGAGTTTTTAAAAGGAAGCCAAGCCTAATTTATAGGGGTTACCTGATGACAAC
T
Found at i:3075360 original size:36 final size:37
Alignment explanation
Indices: 3075319--3075399 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
3075309 TGTTTCTTTG
**
3075319 GAAACAAAG-TTTGTCTCCCTTGAGACAGTTTTTCTT
1 GAAACAAAGTTTTGTCTCCCTTGAGACAGTTTCCCTT
*
3075355 GAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTT
1 GAAACAAAGTTTTGTCTCCCTTGAGACAGTTTCCCTT
3075392 GAAACAAA
1 GAAACAAA
3075400 ATCTTTGATA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 9 0.22
37 32 0.78
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.35
Consensus pattern (37 bp):
GAAACAAAGTTTTGTCTCCCTTGAGACAGTTTCCCTT
Found at i:3075485 original size:66 final size:65
Alignment explanation
Indices: 3075355--3075527 Score: 204
Period size: 66 Copynumber: 2.6 Consensus size: 65
3075345 AGTTTTTCTT
* * *
3075355 GAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGATATCCTTTCCCT
1 GAAACAAA-TTGTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAGATCCTTTCCCT
3075420 C
65 C
* * * *
3075421 GAAACGAATTGTGTCTCCCTTGAGACAGTTTCTCTTGAAATACAAATCTTTGAGATCGTTTCCCT
1 GAAACAAATTGTGTCTCCCTTGAGACAGTTTCCCTTGAAACA-AAATCTTTGAGATCCTTTCCCT
*
3075486 T
65 C
* * **
3075487 GAAACAAATTTTGTC-CTTCTACAGACAGTTTCCCTTGAAAC
1 GAAACAAATTGTGTCTC-CCTTGAGACAGTTTCCCTTGAAAC
3075528 GAATTTTGTC
Statistics
Matches: 90, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
65 31 0.34
66 59 0.66
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (65 bp):
GAAACAAATTGTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAGATCCTTTCCCTC
Found at i:3075525 original size:36 final size:36
Alignment explanation
Indices: 3075478--3075565 Score: 140
Period size: 36 Copynumber: 2.4 Consensus size: 36
3075468 CTTTGAGATC
*
3075478 GTTTCCCTTGAAACAAATTTTGTCCTTCTACAGACA
1 GTTTCCCTTGAAACAAATTTTGTCCCTCTACAGACA
* **
3075514 GTTTCCCTTGAAACGAATTTTGTCCCTCTGGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCCCTCTACAGACA
3075550 GTTTCCCTTGAAACAA
1 GTTTCCCTTGAAACAA
3075566 GAAATTTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCCCTCTACAGACA
Found at i:3075661 original size:73 final size:74
Alignment explanation
Indices: 3075545--3075732 Score: 263
Period size: 73 Copynumber: 2.5 Consensus size: 74
3075535 GTCCCTCTGG
*
3075545 AGACAG-TTTCCCTTGAAACAAGAAATTTTATCTCACTCGAGATGGTTTTTCTTAAAACCAACTT
1 AGACAGTTTTCCCTTGAAAC-A-AAATTGTATCTCACTCGAGATGGTTTTTCTTAAAACCAACTT
*
3075609 TGTCTCGCTTA
64 TATCTCGCTTA
* *
3075620 AGACAGTTTTCCCTTGAAACAAAA-TGTATCTTACTCGAGATGGTTTTTCTTGAAACCAACTTTA
1 AGACAGTTTTCCCTTGAAACAAAATTGTATCTCACTCGAGATGGTTTTTCTTAAAACCAACTTTA
*
3075684 TCTCGCTTG
66 TCTCGCTTA
*
3075693 AGACAGTTTTCCCTTGAAACAAGAAAATTTTATCTCACTC
1 AGACAGTTTTCCCTTGAAAC---AAAATTGTATCTCACTC
3075733 AAGAGAAGTT
Statistics
Matches: 101, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
73 64 0.63
74 3 0.03
75 7 0.07
76 17 0.17
77 10 0.10
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (74 bp):
AGACAGTTTTCCCTTGAAACAAAATTGTATCTCACTCGAGATGGTTTTTCTTAAAACCAACTTTA
TCTCGCTTA
Found at i:3075702 original size:36 final size:37
Alignment explanation
Indices: 3075509--3075712 Score: 128
Period size: 36 Copynumber: 5.5 Consensus size: 37
3075499 GTCCTTCTAC
* * * * * *
3075509 AGACAG-TTTCCCTTGAAACGAATTTTGTCCCTCTGG
1 AGACAGTTTTCCCTTGAAACCAACTTTATCTCACTCG
* *
3075545 AGACAG-TTTCCCTTGAAACAAGAAATTTTATCTCACTCG
1 AGACAGTTTTCCCTTGAAAC---CAACTTTATCTCACTCG
** * * * * **
3075584 AGATGGTTTT-TCTTAAAACCAACTTTGTCTCGCTTA
1 AGACAGTTTTCCCTTGAAACCAACTTTATCTCACTCG
* * * *
3075620 AGACAGTTTTCCCTTGAAACAAAATGTATCTTACTCG
1 AGACAGTTTTCCCTTGAAACCAACTTTATCTCACTCG
** * * *
3075657 AGATGGTTTT-TCTTGAAACCAACTTTATCTCGCTTG
1 AGACAGTTTTCCCTTGAAACCAACTTTATCTCACTCG
3075693 AGACAGTTTTCCCTTGAAAC
1 AGACAGTTTTCCCTTGAAAC
3075713 AAGAAAATTT
Statistics
Matches: 123, Mismatches: 39, Indels: 11
0.71 0.23 0.06
Matches are distributed among these distances:
36 65 0.53
37 32 0.26
39 23 0.19
40 3 0.02
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.35
Consensus pattern (37 bp):
AGACAGTTTTCCCTTGAAACCAACTTTATCTCACTCG
Found at i:3076228 original size:136 final size:136
Alignment explanation
Indices: 3076012--3076458 Score: 524
Period size: 136 Copynumber: 3.3 Consensus size: 136
3076002 TGAATTGGTC
* *
3076012 AACATTTCAAAAGGAAAGTTCATAATGAGAAGAACTCATCCGAA-AGAGGGAGAACAAGTTCATA
1 AACATTTCAAATGGAAAGTTCATAATGAGAAGAACTCATCC-AACAGAGGGAGAACAAGTTTATA
* * *
3076076 ATGAAAAGAGCTTGTTCGACCTATCACTCGATTCACGATATTTCAAATCAGTGAAACCTCACTTG
65 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCAAATCAGTGAAACCTCACTTG
3076141 AGGGATT
130 AGGGATT
* * * * *
3076148 GACATTTCAAATGCAAAGTTCATATTGAGAAGAACTCATCCAACAGAGGGAGAATACGTTTATAA
1 AACATTTCAAATGGAAAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAACAAGTTTATAA
* * ** *
3076213 TGAGAAGAGTTTGTTCGACCTATCACTCGATTCATAACATTTTGAATCAGTGAAACCTCGCTTGA
66 TGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCAAATCAGTGAAACCTCACTTGA
*
3076278 GGGATC
131 GGGATT
* * * * * * *
3076284 AACATTTCCAGTGGAGAGGTCATAATGAGAAGAACTCCTCCGACAGAGGGAGAAGAAGTTCT-TA
1 AACATTTCAAATGGAAAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAACAAGTT-TATA
* * * *** * *
3076348 ATGAGAAGAACTTGTTTGACCTTTTGTTCGATTCATGACATTTCAAATCAG-CAACACCTCACTC
65 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCAAATCAGTGAA-ACCTCACTT
3076412 GAGGGATT
129 GAGGGATT
* * *
3076420 AACATTTCTAGTGGAGAA-TTCATAATGAAAAGAACTCAT
1 AACATTTCAAATGGA-AAGTTCATAATGAGAAGAACTCAT
3076459 TCGTTAAGGG
Statistics
Matches: 261, Mismatches: 46, Indels: 8
0.83 0.15 0.03
Matches are distributed among these distances:
135 4 0.02
136 255 0.98
137 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (136 bp):
AACATTTCAAATGGAAAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAACAAGTTTATAA
TGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCAAATCAGTGAAACCTCACTTGA
GGGATT
Found at i:3076590 original size:40 final size:40
Alignment explanation
Indices: 3076513--3076625 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 40
3076503 TTAGCTTGTT
* * * * *
3076513 TCCATCGCATAAGGAGTTGGAACATCACCGACTTTTCTC-A
1 TCCATCACATAAGGAGTTGGATCAGCATC-ACATTTCTCTA
*
3076553 TCCATCACATAAGGAGTTGGATCAGCATCATCATTTCTCTTG
1 TCCATCACATAAGGAGTTGGATCAGCATCA-CATTTCTC-TA
3076595 TCCATCACATAAGGAGTTGGATCAGCATCAC
1 TCCATCACATAAGGAGTTGGATCAGCATCAC
3076626 CTTGGCTCAA
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
39 1 0.02
40 32 0.50
41 1 0.02
42 30 0.47
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (40 bp):
TCCATCACATAAGGAGTTGGATCAGCATCACATTTCTCTA
Found at i:3076953 original size:21 final size:18
Alignment explanation
Indices: 3076913--3076949 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3076903 ACTCGGTAGG
3076913 CCACCGATTTCTCCACTA
1 CCACCGATTTCTCCACTA
3076931 CCACCGATTTCTCCACTA
1 CCACCGATTTCTCCACTA
3076949 C
1 C
3076950 TACCTCTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.46, G:0.05, T:0.27
Consensus pattern (18 bp):
CCACCGATTTCTCCACTA
Found at i:3082853 original size:11 final size:12
Alignment explanation
Indices: 3082830--3082856 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3082820 TCGTTTGCAA
3082830 TTTTTGGATTTT
1 TTTTTGGATTTT
3082842 TTTTTGGATTTT
1 TTTTTGGATTTT
3082854 TTT
1 TTT
3082857 ACTTTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.00, G:0.15, T:0.78
Consensus pattern (12 bp):
TTTTTGGATTTT
Found at i:3082880 original size:18 final size:19
Alignment explanation
Indices: 3082839--3082880 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
3082829 ATTTTTGGAT
*
3082839 TTTTTTTTGGATTTTTTTA
1 TTTTTTTTGGATTTTTATA
*
3082858 CTTTTTTT-GATTTTTATA
1 TTTTTTTTGGATTTTTATA
3082876 TTTTT
1 TTTTT
3082881 GATGTACAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.12, C:0.02, G:0.07, T:0.79
Consensus pattern (19 bp):
TTTTTTTTGGATTTTTATA
Found at i:3082938 original size:10 final size:9
Alignment explanation
Indices: 3082899--3082937 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
3082889 ATAGCAAACT
3082899 AAAA-AGAA
1 AAAATAGAA
* *
3082907 GAAATTGAA
1 AAAATAGAA
3082916 AAAATAGAA
1 AAAATAGAA
3082925 AAAATAGAA
1 AAAATAGAA
3082934 AAAA
1 AAAA
3082938 AATGAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
8 3 0.12
9 23 0.88
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (9 bp):
AAAATAGAA
Found at i:3085961 original size:23 final size:23
Alignment explanation
Indices: 3085917--3085961 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3085907 ATGGCACTAC
*
3085917 GGTACAAATCTACGCGGTACTTT
1 GGTACAAATCTACGCGGAACTTT
* *
3085940 GGTACAATTCTACGTGGAACTT
1 GGTACAAATCTACGCGGAACTT
3085962 CCGTGCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (23 bp):
GGTACAAATCTACGCGGAACTTT
Found at i:3092308 original size:45 final size:47
Alignment explanation
Indices: 3092207--3092310 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 47
3092197 CCATTCAATA
* *
3092207 GGTATCGATACCCTCTCAAACGAAAAAGAATCACAGAATGTCATGAG
1 GGTATCGATACCCTCTCAAACGAAAAAGAATAACAGAATGTCATAAG
* ** *
3092254 GGTACCGATACCCTCTTGAAC-AAAAA-ACTAACAGAATG-CAGTAAG
1 GGTATCGATACCCTCTCAAACGAAAAAGAATAACAGAATGTCA-TAAG
3092299 GGTATCGATACC
1 GGTATCGATACC
3092311 TCAAAGGGTG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
44 2 0.04
45 24 0.49
46 5 0.10
47 18 0.37
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.19
Consensus pattern (47 bp):
GGTATCGATACCCTCTCAAACGAAAAAGAATAACAGAATGTCATAAG
Found at i:3092972 original size:23 final size:23
Alignment explanation
Indices: 3092938--3092995 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
3092928 CATCTTATAT
*
3092938 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* *
3092961 GGCACTTTGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
3092984 GGCACTTCGGTG
1 GGCACTTCGGTG
3092996 TATTTATATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:3095314 original size:10 final size:10
Alignment explanation
Indices: 3095299--3095323 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3095289 CAAATATAAC
3095299 CTAAATGCAA
1 CTAAATGCAA
3095309 CTAAATGCAA
1 CTAAATGCAA
3095319 CTAAA
1 CTAAA
3095324 GTGATGTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (10 bp):
CTAAATGCAA
Found at i:3096653 original size:46 final size:46
Alignment explanation
Indices: 3096586--3096677 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
3096576 CTTTGAGCTC
* * * * *
3096586 TTTGAGCTGTTTTAGGGACTGGTGTTGCTTGATGGATAGGGGACTG
1 TTTGAGCTATTTCAGGGACTGGCGTTGCTTGACGGACAGGGGACTG
*
3096632 TTTGAGCTATTTCAGGGACTGGCGTTGCTTGACGGACGGGGGACTG
1 TTTGAGCTATTTCAGGGACTGGCGTTGCTTGACGGACAGGGGACTG
3096678 CACTGGAGCT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.15, C:0.13, G:0.39, T:0.33
Consensus pattern (46 bp):
TTTGAGCTATTTCAGGGACTGGCGTTGCTTGACGGACAGGGGACTG
Found at i:3105465 original size:10 final size:10
Alignment explanation
Indices: 3105450--3105484 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
3105440 CAAATATAAC
*
3105450 CTAAATAAAA
1 CTAAATACAA
*
3105460 CTAAATGCAA
1 CTAAATACAA
3105470 CTAAATACAA
1 CTAAATACAA
3105480 CTAAA
1 CTAAA
3105485 GTGATGTGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.60, C:0.17, G:0.03, T:0.20
Consensus pattern (10 bp):
CTAAATACAA
Found at i:3118926 original size:2 final size:2
Alignment explanation
Indices: 3118914--3118960 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
3118904 TGAAATGAAC
* * *
3118914 AT AT AT TT AT AT AT AT AT TT AT AC A- 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
3118955 AT AT AT
1 AT AT AT
3118961 TGTATAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3118966 original size:23 final size:23
Alignment explanation
Indices: 3118916--3118959 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3118906 AAATGAACAT
* *
3118916 ATATTTATATATATATTTATACA
1 ATATATATATATATATATATACA
3118939 ATATATATATATATATATATA
1 ATATATATATATATATATATA
3118960 TTGTATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATATATATATATATATATACA
Found at i:3120079 original size:2 final size:2
Alignment explanation
Indices: 3120072--3120107 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3120062 GTATTATTAA
3120072 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
3120108 TCTAATGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3120133 original size:15 final size:15
Alignment explanation
Indices: 3120105--3120135 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3120095 TATATATATA
3120105 TATTCTAATGTTTTT
1 TATTCTAATGTTTTT
3120120 TATT-TAATGTTTTT
1 TATTCTAATGTTTTT
3120134 TA
1 TA
3120136 AAGTTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.68
Consensus pattern (15 bp):
TATTCTAATGTTTTT
Found at i:3120523 original size:12 final size:13
Alignment explanation
Indices: 3120497--3120532 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
3120487 TTTTTCGCTT
*
3120497 TTTTATGTATTTG
1 TTTTATGTTTTTG
3120510 TTTT-TGTTTTTG
1 TTTTATGTTTTTG
3120522 TTTTATGTTTT
1 TTTTATGTTTT
3120533 CATATTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.08, C:0.00, G:0.14, T:0.78
Consensus pattern (13 bp):
TTTTATGTTTTTG
Found at i:3130344 original size:75 final size:76
Alignment explanation
Indices: 3130231--3130370 Score: 185
Period size: 75 Copynumber: 1.9 Consensus size: 76
3130221 AGTACTTCGC
* * * *
3130231 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTT-AAAAAAAAGAGAAAA-AGAAAAAGGAAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTAAAAAAAAAG-GAAAAGAGAAAAAAGAAAAAA
3130294 ATAAAAAATCAT
65 ATAAAAAATCAT
* * * *
3130306 TTAGGGTGAAAACCTGAAAGGGCGCCCTAAATTGAAAAAAAAGGAAAAGGGAAAAAAGAAAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTAAAAAAAAAGGAAAAGAGAAAAAAGAAAAAAA
3130371 AACAAAAGAA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
75 33 0.59
76 23 0.41
ACGTcount: A:0.56, C:0.09, G:0.22, T:0.12
Consensus pattern (76 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTAAAAAAAAAGGAAAAGAGAAAAAAGAAAAAAA
TAAAAAATCAT
Found at i:3130382 original size:11 final size:11
Alignment explanation
Indices: 3130358--3130393 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
3130348 GGAAAAGGGA
3130358 AAAAAGAAAA-
1 AAAAAGAAAAG
*
3130368 AAAAACAAAAG
1 AAAAAGAAAAG
3130379 AAAAAGAAAAG
1 AAAAAGAAAAG
3130390 AAAA
1 AAAA
3130394 TAAGGTGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:3131203 original size:101 final size:102
Alignment explanation
Indices: 3130936--3131241 Score: 360
Period size: 101 Copynumber: 3.0 Consensus size: 102
3130926 ACGAAGGGGC
* * *
3130936 TTCCCAATGTCATAACCAATTTCAACTTCATAGCGAAGGATATTGGACCCAAGACAACACAAGCT
1 TTCCCAATTTCATATCCAATTTCAACTTCACAGCGAAGGATATTGGA-CCAAGACAACACAAGCT
* * *
3131001 CAACTTCACGATGAAGGGGCGGCTGATTGTCAACAAACA
65 CAACTTCACGGTGAAGGGGC-GCTGACTGTCAACAAAAA
* * * *
3131040 ---GC--TTTCAGAGT-CAATTTCAACTTCACAACGAAGGATA-TGGACTCAAGACAGCACAAGC
1 TTCCCAATTTCATA-TCCAATTTCAACTTCACAGCGAAGGATATTGGAC-CAAGACAACACAAGC
* *
3131098 TCAACTTCACGGCGAAGGGGCG-TGACTCTCAACAAATAA
64 TCAACTTCACGGTGAAGGGGCGCTGACTGTCAACAAA-AA
3131137 TTCCCAATTTCATATCCAATTTCAACTTCACAGC-AAGGATATTGGACCAAGACAACACAAGCTC
1 TTCCCAATTTCATATCCAATTTCAACTTCACAGCGAAGGATATTGGACCAAGACAACACAAGCTC
* *
3131201 AACTTCACAGTGAAGGGGTGGCTGACTGTCAACAAACAA
66 AACTTCACGGTGAAGGGG-CGCTGACTGTCAACAAA-AA
3131240 TT
1 TT
3131242 TTCTAGTTCC
Statistics
Matches: 169, Mismatches: 21, Indels: 25
0.79 0.10 0.12
Matches are distributed among these distances:
96 12 0.07
97 3 0.02
98 37 0.22
99 29 0.17
100 1 0.01
101 41 0.24
102 29 0.17
103 17 0.10
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (102 bp):
TTCCCAATTTCATATCCAATTTCAACTTCACAGCGAAGGATATTGGACCAAGACAACACAAGCTC
AACTTCACGGTGAAGGGGCGCTGACTGTCAACAAAAA
Found at i:3132040 original size:2 final size:2
Alignment explanation
Indices: 3132033--3132068 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
3132023 GAACATATTT
*
3132033 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3132069 GTTATAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3132051 original size:21 final size:21
Alignment explanation
Indices: 3132027--3132068 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3132017 TGAAATGAAC
* *
3132027 ATATTTTATATATATATATAT
1 ATATATTATATATATAAATAT
3132048 ATATATTATATATATAAATAT
1 ATATATTATATATATAAATAT
3132069 GTTATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATATATTATATATATAAATAT
Found at i:3132057 original size:17 final size:17
Alignment explanation
Indices: 3132033--3132079 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
3132023 GAACATATTT
*
3132033 TATA-TATATATATATA
1 TATATTATATATATAAA
3132049 TATATTATATATATAAA
1 TATATTATATATATAAA
* *
3132066 TATGTTATAAATAT
1 TATATTATATATAT
3132080 GTTTTACATC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 4 0.15
17 23 0.85
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
TATATTATATATATAAA
Found at i:3132074 original size:15 final size:15
Alignment explanation
Indices: 3132034--3132068 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3132024 AACATATTTT
*
3132034 ATATATATATATATAT
1 ATAT-TATATATATAA
3132050 ATATTATATATATAA
1 ATATTATATATATAA
3132065 ATAT
1 ATAT
3132069 GTTATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATTATATATATAA
Found at i:3133272 original size:16 final size:16
Alignment explanation
Indices: 3133251--3133286 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3133241 ATATTAATTA
3133251 TTTTTATTCTAATATT
1 TTTTTATTCTAATATT
* *
3133267 TTTTTATTTTAATGTT
1 TTTTTATTCTAATATT
3133283 TTTT
1 TTTT
3133287 AAAGTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTTTATTCTAATATT
Found at i:3133300 original size:2 final size:2
Alignment explanation
Indices: 3133295--3133326 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3133285 TTAAAGTTAT
*
3133295 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3133327 ACTATTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3134613 original size:18 final size:20
Alignment explanation
Indices: 3134585--3134621 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3134575 AATATTAAAA
3134585 AAAATTAATG-TTTAGGTAG
1 AAAATTAATGTTTTAGGTAG
3134604 AAAA-TAATGTTTTAGGTA
1 AAAATTAATGTTTTAGGTA
3134622 ATTGTTTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (20 bp):
AAAATTAATGTTTTAGGTAG
Found at i:3134773 original size:25 final size:25
Alignment explanation
Indices: 3134745--3134793 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
3134735 TAATGATAAG
* *
3134745 GTTATCTAAGTTTTTAAATCTTGTT
1 GTTATCTAACTATTTAAATCTTGTT
3134770 GTTATCTAACTATTTAAATCTTGT
1 GTTATCTAACTATTTAAATCTTGT
3134794 CAATTAAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.53
Consensus pattern (25 bp):
GTTATCTAACTATTTAAATCTTGTT
Found at i:3135627 original size:29 final size:30
Alignment explanation
Indices: 3135558--3135629 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
3135548 TAATGTGACA
*
3135558 CTTAGGTAGGCTCTGCGGCCCTGAGATCATT
1 CTTAGGTAGGC-CTGCGGCCCTAAGATCATT
** *
3135589 CTCGGGTAGGCCTGCGGCCCTAAGAT-GTT
1 CTTAGGTAGGCCTGCGGCCCTAAGATCATT
3135618 CTTAGGTAGGCC
1 CTTAGGTAGGCC
3135630 CCACGGCCCC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 12 0.34
30 14 0.40
31 9 0.26
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.26
Consensus pattern (30 bp):
CTTAGGTAGGCCTGCGGCCCTAAGATCATT
Found at i:3135637 original size:30 final size:31
Alignment explanation
Indices: 3135603--3135679 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
3135593 GGTAGGCCTG
3135603 CGGCCCTAAGATGTTCTTAGGTAGGC-CCCA
1 CGGCCCTAAGATGTTCTTAGGTAGGCTCCCA
* * * *
3135633 CGGCCCCGAA-ATCTATCTTGGGTAGGCTCTCA
1 CGG-CCCTAAGATGT-TCTTAGGTAGGCTCCCA
3135665 -GGCCCTAAGATGTTC
1 CGGCCCTAAGATGTTC
3135680 CCTTAGGTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
30 13 0.35
31 21 0.57
32 3 0.08
ACGTcount: A:0.19, C:0.30, G:0.26, T:0.25
Consensus pattern (31 bp):
CGGCCCTAAGATGTTCTTAGGTAGGCTCCCA
Found at i:3137684 original size:13 final size:13
Alignment explanation
Indices: 3137666--3137714 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
3137656 TCATAACCCG
3137666 ACCCGACCCGTTT
1 ACCCGACCCGTTT
3137679 ACCCGACCCGTTT
1 ACCCGACCCGTTT
* *
3137692 ACCCGACCAGTTG
1 ACCCGACCCGTTT
3137705 ACCCGACCCG
1 ACCCGACCCG
3137715 ACCCGTTGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.18, C:0.47, G:0.18, T:0.16
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:3137732 original size:7 final size:7
Alignment explanation
Indices: 3137717--3137754 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
3137707 CCGACCCGAC
3137717 CCGTTGA
1 CCGTTGA
*
3137724 CCTTTGA
1 CCGTTGA
3137731 CCGTTGA
1 CCGTTGA
3137738 CCCGTTGA
1 -CCGTTGA
3137746 CCGTTGA
1 CCGTTGA
3137753 CC
1 CC
3137755 CAGTTGACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 21 0.75
8 7 0.25
ACGTcount: A:0.13, C:0.34, G:0.24, T:0.29
Consensus pattern (7 bp):
CCGTTGA
Found at i:3137741 original size:22 final size:24
Alignment explanation
Indices: 3137714--3137763 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 24
3137704 GACCCGACCC
*
3137714 GACCCGTTGACCTTTGA-CC-GTT
1 GACCCGTTGACCGTTGACCCAGTT
3137736 GACCCGTTGACCGTTGACCCAGTT
1 GACCCGTTGACCGTTGACCCAGTT
3137760 GACC
1 GACC
3137764 AGTGTTGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 16 0.64
23 2 0.08
24 7 0.28
ACGTcount: A:0.16, C:0.34, G:0.24, T:0.26
Consensus pattern (24 bp):
GACCCGTTGACCGTTGACCCAGTT
Found at i:3137745 original size:15 final size:15
Alignment explanation
Indices: 3137717--3137763 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
3137707 CCGACCCGAC
*
3137717 CCGTTGA-CCTTTGA
1 CCGTTGACCCGTTGA
3137731 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
3137746 CCGTTGACCCAGTTGA
1 CCGTTGACCC-GTTGA
3137762 CC
1 CC
3137764 AGTGTTGACC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 7 0.23
15 16 0.53
16 7 0.23
ACGTcount: A:0.15, C:0.34, G:0.23, T:0.28
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:3139066 original size:18 final size:18
Alignment explanation
Indices: 3139040--3139074 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3139030 TCGAAAGGAC
*
3139040 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
3139058 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
3139075 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:3140656 original size:31 final size:30
Alignment explanation
Indices: 3140586--3140659 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
3140576 TAATGTGACA
*
3140586 CTTAGGTAGGCTCTGCGGCCCTGAGATCATT
1 CTTAGGTAGGC-CTGCGGCCCTAAGATCATT
** **
3140617 CTCGGGTAGGCCTGCGGCCCTAAGATGTGTT
1 CTTAGGTAGGCCTGCGGCCCTAAGAT-CATT
3140648 CTTAGGTAGGCC
1 CTTAGGTAGGCC
3140660 CCACGGCCCC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 14 0.40
31 21 0.60
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.27
Consensus pattern (30 bp):
CTTAGGTAGGCCTGCGGCCCTAAGATCATT
Found at i:3142781 original size:18 final size:18
Alignment explanation
Indices: 3142758--3142811 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
3142748 ACCGGTCATA
*
3142758 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
3142776 ACCCGA-CC-A---GTTG
1 ACCCGACCCGACCCGTTG
3142789 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
3142807 ACCCG
1 ACCCG
3142812 TTGACCGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
13 9 0.30
14 2 0.07
15 1 0.03
16 1 0.03
17 2 0.07
18 15 0.50
ACGTcount: A:0.19, C:0.48, G:0.20, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:3142809 original size:8 final size:8
Alignment explanation
Indices: 3142798--3142840 Score: 72
Period size: 8 Copynumber: 5.6 Consensus size: 8
3142788 GACCCGACCC
3142798 GACCCGTT
1 GACCCGTT
3142806 GACCCGTT
1 GACCCGTT
3142814 GA-CCGTT
1 GACCCGTT
3142821 GACCCGTT
1 GACCCGTT
3142829 GA-CCGTT
1 GACCCGTT
3142836 GACCC
1 GACCC
3142841 ACGTTGACCA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.42
8 19 0.58
ACGTcount: A:0.14, C:0.37, G:0.26, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:3142811 original size:13 final size:13
Alignment explanation
Indices: 3142762--3142798 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
3142752 GTCATAACCC
3142762 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
3142775 TACCCGACCAGTT
1 GACCCGACCCGTT
3142788 GACCCGACCCG
1 GACCCGACCCG
3142799 ACCCGTTGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.46, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:3142821 original size:7 final size:7
Alignment explanation
Indices: 3142801--3142839 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
3142791 CCGACCCGAC
3142801 CCGTTGA
1 CCGTTGA
3142808 CCCGTTGA
1 -CCGTTGA
3142816 CCGTTGA
1 CCGTTGA
3142823 CCCGTTGA
1 -CCGTTGA
3142831 CCGTTGA
1 CCGTTGA
3142838 CC
1 CC
3142840 CACGTTGACC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.13, C:0.36, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:3142821 original size:15 final size:15
Alignment explanation
Indices: 3142801--3142840 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
3142791 CCGACCCGAC
3142801 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
3142816 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
3142831 CCGTTGACCC
1 CCGTTGACCC
3142841 ACGTTGACCA
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:0.38, G:0.25, T:0.25
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:3144155 original size:18 final size:18
Alignment explanation
Indices: 3144129--3144163 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3144119 TCGAAAGGAC
*
3144129 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
3144147 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
3144164 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:3145739 original size:31 final size:30
Alignment explanation
Indices: 3145669--3145742 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
3145659 TAATGTGACA
*
3145669 CTTAGGTAGGCTCTGCGGCCCTGAGATCATT
1 CTTAGGTAGGC-CTGCGGCCCTAAGATCATT
** **
3145700 CTCGGGTAGGCCTGCGGCCCTAAGATGTGTT
1 CTTAGGTAGGCCTGCGGCCCTAAGAT-CATT
3145731 CTTAGGTAGGCC
1 CTTAGGTAGGCC
3145743 CCACGGCCCC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 14 0.40
31 21 0.60
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.27
Consensus pattern (30 bp):
CTTAGGTAGGCCTGCGGCCCTAAGATCATT
Found at i:3146590 original size:11 final size:10
Alignment explanation
Indices: 3146568--3146606 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
3146558 TGAAATGAAC
3146568 ATATATTTAT
1 ATATATTTAT
3146578 ATATATATTAT
1 ATATAT-TTAT
3146589 ATATATTGTAT
1 ATATATT-TAT
*
3146600 AAATATT
1 ATATATT
3146607 GTTATAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 7 0.27
11 19 0.73
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (10 bp):
ATATATTTAT
Found at i:3146607 original size:11 final size:12
Alignment explanation
Indices: 3146585--3146617 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
3146575 TATATATATA
*
3146585 TTATATATATTG
1 TTATAAATATTG
3146597 -TATAAATATTG
1 TTATAAATATTG
3146608 TTATAAATAT
1 TTATAAATAT
3146618 GTTTTACATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (12 bp):
TTATAAATATTG
Found at i:3147851 original size:16 final size:15
Alignment explanation
Indices: 3147818--3147853 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3147808 ATATTAATTA
3147818 TTTTTATTCTAATAT
1 TTTTTATTCTAATAT
* *
3147833 TTTTTATTTTAATGT
1 TTTTTATTCTAATAT
3147848 TTTTTA
1 TTTTTA
3147854 AAGTTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (15 bp):
TTTTTATTCTAATAT
Found at i:3147985 original size:10 final size:10
Alignment explanation
Indices: 3147970--3147997 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3147960 ATGTATATTC
3147970 TTTATTGTAT
1 TTTATTGTAT
3147980 TTTATTGTAT
1 TTTATTGTAT
3147990 TTTATTGT
1 TTTATTGT
3147998 TGTACCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.71
Consensus pattern (10 bp):
TTTATTGTAT
Found at i:3150022 original size:3 final size:3
Alignment explanation
Indices: 3150014--3150099 Score: 55
Period size: 3 Copynumber: 25.7 Consensus size: 3
3150004 TGTCCGTTTA
*
3150014 TAT TAT TAT TAT ATAT TAT TAAT TAT ATAT GTTT TAT TAT ATACGT TAT
1 TAT TAT TAT TAT -TAT TAT T-AT TAT -TAT -TAT TAT TAT -TA--T TAT
* * *
3150063 TAT TAT ATAT TAT ATAT TAA TAA TAT TAG TAT TAT TA
1 TAT TAT -TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA
3150100 AATAATATTA
Statistics
Matches: 68, Mismatches: 7, Indels: 16
0.75 0.08 0.18
Matches are distributed among these distances:
3 46 0.68
4 19 0.28
5 2 0.03
6 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:3150032 original size:7 final size:7
Alignment explanation
Indices: 3150012--3150081 Score: 67
Period size: 7 Copynumber: 10.0 Consensus size: 7
3150002 TTTGTCCGTT
3150012 TATATTA
1 TATATTA
3150019 T-TATTA
1 TATATTA
3150025 TATATTA
1 TATATTA
3150032 T-TAATTA
1 TAT-ATTA
3150039 TATATGT-
1 TATAT-TA
*
3150046 TTTATTA
1 TATATTA
3150053 TATACGTTA
1 TATA--TTA
3150062 T-TATTA
1 TATATTA
3150068 TATATTA
1 TATATTA
3150075 TATATTA
1 TATATTA
3150082 ATAATATTAG
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
6 12 0.23
7 33 0.62
8 4 0.08
9 4 0.08
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (7 bp):
TATATTA
Found at i:3150054 original size:12 final size:14
Alignment explanation
Indices: 3150012--3150081 Score: 76
Period size: 14 Copynumber: 5.0 Consensus size: 14
3150002 TTTGTCCGTT
3150012 TATA-TTATTATTA
1 TATAGTTATTATTA
3150025 TATA-TTATTAATTA
1 TATAGTTATT-ATTA
3150039 TATATGTT-TTATTA
1 TATA-GTTATTATTA
3150053 TATACGTTATTATTA
1 TATA-GTTATTATTA
3150068 TATA-TTATATATTA
1 TATAGTTAT-TATTA
3150082 ATAATATTAG
Statistics
Matches: 51, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
13 13 0.25
14 24 0.47
15 12 0.24
16 2 0.04
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (14 bp):
TATAGTTATTATTA
Found at i:3150095 original size:22 final size:19
Alignment explanation
Indices: 3150069--3150109 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3150059 TTATTATTAT
3150069 ATATTA-TA-TATT-AATA
1 ATATTAGTATTATTAAATA
3150085 ATATTAGTATTATTAAATA
1 ATATTAGTATTATTAAATA
3150104 ATATTA
1 ATATTA
3150110 CAAAATACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.27
17 2 0.09
18 4 0.18
19 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATTAGTATTATTAAATA
Found at i:3151511 original size:15 final size:14
Alignment explanation
Indices: 3151493--3151535 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
3151483 TTATAACAAC
3151493 ATTAATATAATTTAT
1 ATTAATATAATTT-T
*
3151508 ATTAAGATAATTTT
1 ATTAATATAATTTT
*
3151522 A-TAATATAGTTTT
1 ATTAATATAATTTT
3151535 A
1 A
3151536 ATATTATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.44
14 2 0.08
15 12 0.48
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (14 bp):
ATTAATATAATTTT
Found at i:3152067 original size:10 final size:11
Alignment explanation
Indices: 3152036--3152067 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3152026 TTGCAGTAAA
*
3152036 TAATAATTTTT
1 TAATTATTTTT
3152047 TAATTATTTTT
1 TAATTATTTTT
3152058 TAATTATTTT
1 TAATTATTTT
3152068 ACTAACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TAATTATTTTT
Found at i:3158651 original size:41 final size:41
Alignment explanation
Indices: 3158602--3158691 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 41
3158592 CATGAATTTG
* * * * *
3158602 TAAATCCTTTGGGTCATCTGTAAGTCTTTTGAGCATGATGT
1 TAAATCCTTCGGGTCATATGTAAGTCTTTCGAGCAAGATGA
*
3158643 TAAATCCTTCGGGTCATATGTTAGTCTTTCGAGCAAGATGA
1 TAAATCCTTCGGGTCATATGTAAGTCTTTCGAGCAAGATGA
*
3158684 TAAGTCCT
1 TAAATCCT
3158692 AAGGTCCATC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (41 bp):
TAAATCCTTCGGGTCATATGTAAGTCTTTCGAGCAAGATGA
Found at i:3158879 original size:20 final size:20
Alignment explanation
Indices: 3158856--3158919 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
3158846 TTGTAAATCC
3158856 TTCGGGTCATCTGTAAGTCT
1 TTCGGGTCATCTGTAAGTCT
* * * *
3158876 TTCGAG-CATGATGTTAAATCC
1 TTCGGGTCAT-CTG-TAAGTCT
*
3158897 TTCGGGTCATCTGTTAGTCT
1 TTCGGGTCATCTGTAAGTCT
3158917 TTC
1 TTC
3158920 AAGCAAGATG
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
19 3 0.09
20 14 0.44
21 12 0.38
22 3 0.09
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (20 bp):
TTCGGGTCATCTGTAAGTCT
Found at i:3158906 original size:41 final size:41
Alignment explanation
Indices: 3158849--3158947 Score: 144
Period size: 41 Copynumber: 2.4 Consensus size: 41
3158839 CACAAATTTG
* * *
3158849 TAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGT
1 TAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGA
*
3158890 TAAATCCTTCGGGTCATCTGTTAGTCTTTCAAGCAAGATGA
1 TAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGA
* *
3158931 TAAGTCCTTAGGGTCAT
1 TAAATCCTTCGGGTCAT
3158948 TCGTCAAACC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (41 bp):
TAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGA
Found at i:3158911 original size:21 final size:21
Alignment explanation
Indices: 3158849--3158912 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
3158839 CACAAATTTG
3158849 TAAATCCTTCGGGTCATCTG-
1 TAAATCCTTCGGGTCATCTGT
* * * *
3158869 TAAGTCTTTCGAG-CATGATGT
1 TAAATCCTTCGGGTCAT-CTGT
3158890 TAAATCCTTCGGGTCATCTGT
1 TAAATCCTTCGGGTCATCTGT
3158911 TA
1 TA
3158913 GTCTTTCAAG
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
19 3 0.09
20 12 0.36
21 15 0.45
22 3 0.09
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (21 bp):
TAAATCCTTCGGGTCATCTGT
Found at i:3159142 original size:247 final size:248
Alignment explanation
Indices: 3158565--3159221 Score: 980
Period size: 247 Copynumber: 2.7 Consensus size: 248
3158555 GCGATTTTCA
* * * * * *
3158565 AAGTTTCTTACCCACTAAATTATTTCCCATGAATTTGTAAATCCTTTGGGTCATCTGTAAGTCTT
1 AAGTCTCTTACCCAATAAAATATTTCTCACGAATTTGTAAATCCTTCGGGTCATCTGTAAGTCTT
*
3158630 TTGAGCATGATGTTAAATCCTTCGGGTCATATGTTAGTCTTTCGAGCAAGATGATAAGTCC-TAA
66 TCGAGCATGATGTTAAATCCTTCGGGTCATATGTTAGTCTTTCGAGCAAGATGATAAGTCCTTAA
* *
3158694 GGTCCATCCGTCAAACCTTTGGGTAGGATGTTTACATATGATTTTCTCATGAAAATGAGATAGCA
131 GGT-CATCCGTCAAACCTTTGGGTAAGATGTTTACATATGATTTTCGCATGAAAATGAGATAGCA
*
3158759 ATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATCAAATTTTTGAAAAGTAAG
195 ATTTTCAAAGTTTCCCATTTAATGTTCTAGAAAATCAAATTTTTGAAAAGTAAG
* *
3158813 AAGTCTCTTA-CCAGTAAAATATTTCTCACAAATTTGTAAATCCTTCGGGTCATCTGTAAGTCTT
1 AAGTCTCTTACCCAATAAAATATTTCTCACGAATTTGTAAATCCTTCGGGTCATCTGTAAGTCTT
* * *
3158877 TCGAGCATGATGTTAAATCCTTCGGGTCATCTGTTAGTCTTTCAAGCAAGATGATAAGTCCTTAG
66 TCGAGCATGATGTTAAATCCTTCGGGTCATATGTTAGTCTTTCGAGCAAGATGATAAGTCCTTAA
* * * **
3158942 GGTCATTCGTCAAACCTTTGGGTATGATGTTTACATATGATTTTCGCATGAAAATTAGATAG-TT
131 GGTCATCCGTCAAACCTTTGGGTAAGATGTTTACATATGATTTTCGCATGAAAATGAGATAGCAA
*
3159006 TTTTCAAAGTTTCCCATTTAATGTTCTAGAAAAT-AATTTTTTGAAAAGTAAG
196 TTTTCAAAGTTTCCCATTTAATGTTCTAGAAAATCAAATTTTTGAAAAGTAAG
* *
3159058 AAGTCTCTTACCCAATAAAATATTTCTCACGAATTTTTAAATCCTTCGGGTCATCTGTAAGTCCT
1 AAGTCTCTTACCCAATAAAATATTTCTCACGAATTTGTAAATCCTTCGGGTCATCTGTAAGTCTT
* * * ** *
3159123 TCGAGCATGATGTTTAAATCCTTCAGGTTATTTGCCAGTCTTTCGAGCAAAATGATAAGTCCTTA
66 TCGAGCATGATG-TTAAATCCTTCGGGTCATATGTTAGTCTTTCGAGCAAGATGATAAGTCCTTA
* * *
3159188 AGGCCATCCGTCAGACCTTTGGGCAAGATGTTTA
130 AGGTCATCCGTCAAACCTTTGGGTAAGATGTTTA
3159222 TAATTTTTAA
Statistics
Matches: 370, Mismatches: 36, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
245 27 0.07
246 95 0.26
247 234 0.63
248 14 0.04
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (248 bp):
AAGTCTCTTACCCAATAAAATATTTCTCACGAATTTGTAAATCCTTCGGGTCATCTGTAAGTCTT
TCGAGCATGATGTTAAATCCTTCGGGTCATATGTTAGTCTTTCGAGCAAGATGATAAGTCCTTAA
GGTCATCCGTCAAACCTTTGGGTAAGATGTTTACATATGATTTTCGCATGAAAATGAGATAGCAA
TTTTCAAAGTTTCCCATTTAATGTTCTAGAAAATCAAATTTTTGAAAAGTAAG
Found at i:3159477 original size:3 final size:3
Alignment explanation
Indices: 3159386--3159459 Score: 58
Period size: 3 Copynumber: 21.7 Consensus size: 3
3159376 TTTCCGTTTA
*
3159386 TAT TAT TAT TAT TAT TAT ATAT TAT TAAT TAT ATAT GTTT TAT TAT ATACGT
1 TAT TAT TAT TAT TAT TAT -TAT TAT T-AT TAT -TAT -TAT TAT TAT -TA--T
3159438 TAT TAT TAT ATAT TAT ATAT TA
1 TAT TAT TAT -TAT TAT -TAT TA
3159460 ATAATATAAG
Statistics
Matches: 60, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
3 38 0.63
4 19 0.32
5 2 0.03
6 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:3181957 original size:21 final size:21
Alignment explanation
Indices: 3181924--3181963 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3181914 AAATAGTCGT
3181924 AACAGCGCCCGCTACGGCCGC
1 AACAGCGCCCGCTACGGCCGC
* * *
3181945 AACAGTGCTCGCTATGGCC
1 AACAGCGCCCGCTACGGCC
3181964 ACAATCGCAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.40, G:0.28, T:0.12
Consensus pattern (21 bp):
AACAGCGCCCGCTACGGCCGC
Found at i:3190796 original size:17 final size:17
Alignment explanation
Indices: 3190769--3190802 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
3190759 CCATTCGAAC
3190769 AAAAAACAAC-AAGAAA
1 AAAAAACAACAAAGAAA
3190785 AAAAAACAAACAAAGAAA
1 AAAAAAC-AACAAAGAAA
3190803 CGGAGAGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 3 0.19
18 6 0.38
ACGTcount: A:0.82, C:0.12, G:0.06, T:0.00
Consensus pattern (17 bp):
AAAAAACAACAAAGAAA
Found at i:3197165 original size:98 final size:99
Alignment explanation
Indices: 3196991--3197192 Score: 327
Period size: 98 Copynumber: 2.1 Consensus size: 99
3196981 ATATAATATT
* * *
3196991 ATATGTATACAATAAAGCTTGAATTGTCCCTCTAGAGCAATTGGTTAAATGCCCCGTCTTTATGG
1 ATATATATACAATAAAGCTTGAATTGTCCCTCTAAAGCAATTGGTTAAATGCCCCGGCTTTATGG
3197056 ATAAGATTCAACTAGCCTGAT-AAGGTGATTATA
66 ATAAGATTCAACTAGCCTGATAAAGGTGATTATA
* * *
3197089 ATATATATACAATAAAGCTTGAGTTGTCCCTCTAAATCAATTGGTTAAACT-CCTCGGCTTTATG
1 ATATATATACAATAAAGCTTGAATTGTCCCTCTAAAGCAATTGGTTAAA-TGCCCCGGCTTTATG
3197153 GATAAGATTCAACTAGCCTGATAAAGGTGATTATA
65 GATAAGATTCAACTAGCCTGATAAAGGTGATTATA
3197188 ATATA
1 ATATA
3197193 CAATAAAGTT
Statistics
Matches: 96, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
98 78 0.81
99 18 0.19
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (99 bp):
ATATATATACAATAAAGCTTGAATTGTCCCTCTAAAGCAATTGGTTAAATGCCCCGGCTTTATGG
ATAAGATTCAACTAGCCTGATAAAGGTGATTATA
Found at i:3200132 original size:249 final size:250
Alignment explanation
Indices: 3199694--3202693 Score: 3744
Period size: 250 Copynumber: 12.0 Consensus size: 250
3199684 TAAGTTGTTT
* * * * * *
3199694 TGAAAATAAGAAAGCGATGATCAAAGTTTCTCGTTTAATCTTTT-ATGAAAATGAAATTTTTGAA
1 TGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCA-GAAAATGAAATTCTTGAA
*
3199758 AAGTAAGAAAGCGATTACTAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAGTCCTTC
65 AAGTAAGAAAGCGATTACCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAGTCCTTC
* * * * *
3199823 AGGCCATCAGTAAGTCTTTCGAGTATGATGCTTAAATCCTTCGAGCCATCTATAAGTCTTTCGAG
130 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAG
* *
3199888 CAAGATGATAAGTCCTTCGGGCTATCCGTAAGACATTC-GGTAGGATGTTTTCACA
195 CAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACA
* * *
3199943 TGAAAATGAGAAAGCGATTACCAAAGTTTCTTATTTAATGTTTTCAAAAAATGAAATTTTTGAAA
1 TGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTCTTGAAA
* * *
3200008 AGTAA-AAATGAGATTACTAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAGTCATTC
66 AGTAAGAAA-GCGATTACCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAGTCCTTC
* * * ** *
3200072 GGGTCATCAATAAGTCTTTTGAGCATGATGCTTAAATCCTTTAGGTCATCTGTAAGTCTTTCAAG
130 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAG
3200137 CAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACA
195 CAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACA
* *
3200193 TGAAAATGAGAAAGTGATTA-CAAAGTTTCTCATTTAATGTTTTCAGAAAGTGAAATTCTTGAAA
1 TGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTCTTGAAA
* * *
3200257 AGTAAGAAAACGATTACCGAAGTTTCTTA-CCTGTAAATTATTTCCAAAATTTGTAAGTCCTTCG
66 AGTAAGAAAGCGATTACCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAGTCCTTCG
* *
3200321 AGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTTGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGC
* * *
3200386 AAGATGATAAGTCCTTTGGGCTATCCGTAAGACCTTCGGGTAGAATGTTTTCACA
196 AAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACA
3200441 TGAAAA--AGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTCTTGAAA
1 TGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTCTTGAAA
* * * * *
3200504 AGTAAGAAATCGATTACCAAAGTTTCTTACCTAGTAAATTATTCCCAAAATTTGTCAGTCCTTCA
66 AGTAAGAAAGCGATTACCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAGTCCTTCG
* * * *
3200569 GGCCATCAGAAACTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAAC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGC
* * * *
3200634 AAGATGATAACTCCTTCGGGCCATACGTAAGAGCTTCGGGTAGGATGTTTTCATA
196 AAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACA
* * * *
3200689 TGAAAATGAGAAAGTGATTACCAAAGTATATCAATTAATGTTTTCAGAAAATGAAATTCTTGAAA
1 TGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTCTTGAAA
* * *
3200754 AGTAAGAAAGTGATTACCAAAGTTTCTTACCCAGTAAATTATTTCCCAAAATTTGAAAGTGCTTC
66 AGTAAGAAAGCGATTACCAAAGTTTCTTACCCAGTAAATTATTT-CCAAAATTTGTAAGTCCTTC
* * *
3200819 GGGTCATCAATAAGTCTTTC-ATGCATGATCCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGA
130 GGGCCATCAGTAAGTCTTTCGA-GCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGA
*
3200883 GCAAGATGATAAGTCCTTCGGGCCATCCGTAAGATCTTCGAGCCATCCGTAAGATCTTCGGGTAA
194 GCAAGATGATAAGTCCTTCGGGCCATCCGT---A------AG--A--C-------CTTCGGGTAG
*
3200948 GATGTTTTCACT
239 GATGTTTTCACA
* * *
3200960 TGAAAATGAGAAAACGATTACCAAAGTTTCTCATTTAATGTTTTTAGAAAGTGAAATTCTTGAAA
1 TGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTCTTGAAA
* * * * *
3201025 AGCAAGAAAGCAATTACCAACGTTTCTTACCCAATAAATTATTTCCAAAATTTGTAACTCCTTCG
66 AGTAAGAAAGCGATTACCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAGTCCTTCG
* *
3201090 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCACCTGTAAGTCTTTCGAGT
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGC
* ** * * * * *
3201155 AAGATGATAAGTCTTTCAAGCTATCTGTAAGACCTTCGCGTAGGATTTTTTCATA
196 AAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACA
* *
3201210 TGAAAATGAGAAAGCGATTACCAAAGTATCTCATTTAATGTTTTCAAAAAATGAAATTCTTGAAA
1 TGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTCTTGAAA
3201275 AGTAAGAAA-CGATTACCAAAGTTTCTTACCCAGTAAATTATTTCTCAAAATTTGTAAGTCCTTC
66 AGTAAGAAAGCGATTACCAAAGTTTCTTACCCAGTAAATTATTTC-CAAAATTTGTAAGTCCTTC
* * *
3201339 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTTATCTGTAAGTCTTTTGAG
130 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAG
* *
3201404 CAAGATGATAAGTCTTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTTTACA
195 CAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATG-TTTTCACA
* *
3201461 TGAAAATGAGAAAGCGATTACCAAATTTTCTCATTTAATGTTTTTAGAAAATGAAATAT-TTGAA
1 TGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAAT-TCTTGAA
* * * * *
3201525 AAGTAAAAAATCGATTACCATAGTTTCTTACCGACTAAATTATTTCACAAAATTTGTAAG-CCTT
65 AAGTAAGAAAGCGATTACCAAAGTTTCTTACCCAGTAAATTATTTC-CAAAATTTGTAAGTCC-T
* * * * *
3201589 TCGGGCAATCAGTAAGTCTTT-TAGTATGATGATTAAATCTTTCGGGTCATCTGTAAGTCTTTCG
128 TCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCG
* * ** * * * *
3201653 AGCAAAACGATAAGTCCTTTAGGCCGTCTGTAACACCTTCAGGTAGGATGTTTTCACA
193 AGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACA
* * *
3201711 TGAAAATGAGAAAGTGATTACCAAAGTTTCTCTTTTAATGTTTTCAGAAAAGGAAAATT-TTGAA
1 TGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATG-AAATTCTTGAA
* * *
3201775 AAGTAAGAAAGTGATTATCAAAGTTTCTCACCCAGTAAATTATTTCCCAAAA----T---T-CTT
65 AAGTAAGAAAGCGATTACCAAAGTTTCTTACCCAGTAAATTATTT-CCAAAATTTGTAAGTCCTT
* *
3201832 CGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAATTCTTTCGA
129 CGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGA
* * *
3201897 GCAAGATGATAAGTCCTTCAGGACAT-CGATAACACCTTCGGGTAGGATGTTTTCACA
194 GCAAGATGATAAGTCCTTCGGGCCATCCG-TAAGACCTTCGGGTAGGATGTTTTCACA
3201954 TGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAAATT-TTGAA
1 TGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATG-AAATTCTTGAA
* *
3202018 AAGTAAAAAAGCGATTACCAAAAG--T-TT---C-------T-TTTCTAAAATTTGTAAGTCCTT
65 AAGTAAGAAAGCGATTACC-AAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAGTCCTT
* * * * *
3202069 TGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCAGGTCATCTATAAGTCTTTCGA
129 CGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGA
* * * * *
3202134 TCAAGATGGTAAGTCTTTCGGGCCATCTGTAAGACCTTCGGGTAGGATTTTTTCACA
194 GCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACA
* * *
3202191 TGAAAA-AAGAAAGTGATTACCAAAGTTTCTCATTTAATGTTTTTAGAAAATGAAATTCTTGAAA
1 TGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTCTTGAAA
* * * * * *
3202255 AGTAAGAAATCGATTACCAAAATTTCATACCTAGTAAATTATTTCC-AAATTTGTAAGTCATTTG
66 AGTAAGAAAGCGATTACCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAGTCCTTCG
* * * *
3202319 GGCGATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGC
131 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGC
* * ** *
3202384 AAGATGATAAGTCCTTCGGGTCATCTGTAAGACCTTCGGACAAGATGTTTTCAACTGA
196 AAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTC-AC--A
* *** *** * * *
3202442 TTTTTTTAAAATGAGAAAATTATTTTTAATTACTTT-T-ATTTAATATTTTTAGAAAATGAAATT
1 -----TGAAAATGAGAAAGCGATTACCAA--AGTTTCTCATTTAATGTTTTCAGAAAATGAAATT
* * * * * *
3202505 TTTGAAAAGTATGAAAGCGATTTCCAGAGTTTCTTACCTAGTAAACTATTTCCAAAATTTGTAAG
59 CTTGAAAAGTAAGAAAGCGATTACCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAG
* * * * * *
3202570 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCCTAATGATTAAATCCTTTGGGTCATCTCTCAGTCT
124 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCT
* * * * *
3202635 TTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAAACTT-TGGTAGGATATTTTCA
189 TTCGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCA
3202694 TTCTTTGTTA
Statistics
Matches: 2397, Mismatches: 276, Indels: 149
0.85 0.10 0.05
Matches are distributed among these distances:
229 5 0.00
230 3 0.00
231 1 0.00
233 1 0.00
235 8 0.00
236 66 0.03
237 117 0.05
238 3 0.00
241 1 0.00
242 23 0.01
243 166 0.07
244 4 0.00
246 12 0.01
247 70 0.03
248 415 0.17
249 303 0.13
250 442 0.18
251 257 0.11
252 67 0.03
254 1 0.00
256 6 0.00
257 92 0.04
258 107 0.04
259 5 0.00
260 2 0.00
261 2 0.00
262 1 0.00
267 1 0.00
270 99 0.04
271 117 0.05
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (250 bp):
TGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTCTTGAAA
AGTAAGAAAGCGATTACCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTTGTAAGTCCTTCG
GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGC
AAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACA
Found at i:3200921 original size:20 final size:20
Alignment explanation
Indices: 3200898--3200944 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3200888 ATGATAAGTC
3200898 CTTCGGGCCATCCGTAAGAT
1 CTTCGGGCCATCCGTAAGAT
*
3200918 CTTCGAGCCATCCGTAAGAT
1 CTTCGGGCCATCCGTAAGAT
3200938 CTTCGGG
1 CTTCGGG
3200945 TAAGATGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.19, C:0.30, G:0.26, T:0.26
Consensus pattern (20 bp):
CTTCGGGCCATCCGTAAGAT
Found at i:3201218 original size:521 final size:509
Alignment explanation
Indices: 3200412--3202666 Score: 2629
Period size: 521 Copynumber: 4.5 Consensus size: 509
3200402 TGGGCTATCC
3200412 GTAAGACCTTCGGGTAGAATGTTTTCACATGAAAA--AGAAAGCGATTACCAAAGTTTCTCATTT
1 GTAAGACCTTCGGGT-G-ATGTTTTCACATGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTT
* * *
3200475 AATGTTTTCAGAAAATGAAATTCTTGAAAAGTAAGAAATCGATTACCAAAGTTTCTTACCTAGTA
64 AATGTTTTTAGAAAATGAAATT-TTGAAAAGTAAGAAAGCGATTACC-AAGTTTCTTACCCAGTA
* * * * * *
3200540 AATTATTCCCAAAATTTGTCAGTCCTTCAGGCCATCAGAAACTCTTTCGAGCATGATGCTTAAAT
127 AATTATTTCCAAAATTTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAAT
* * * * * *
3200605 CCTTCGGGTCATCTGTAAGTCTTTCAAACAAGATGATAACTCCTTCGGGCCATAC-GTAAGAGCT
192 CCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCTTTCAGGCCAT-CTGTAAGACCT
* * *
3200669 TCGGGTAGGATGTTTTCATATGAAAATGAGAAAGTGATTACCAAAGTATATCAATTAATGTTTTC
256 TCGGGTAGGATGTTTTCACATGAAAATGAGAAAGTGATTACCAAAGTATCTCATTTAATGTTTTC
3200734 AGAAAATGAAATTCTTGAAAAGTAAGAAAGTGATTACCAAAGTTTCTTACCCAGTAAATTATTTC
321 AGAAAATGAAATTCTTGAAAAGTAAGAAA-TGATTACCAAAGTTTCTTACCCAGTAAATTATTTC
* * * **
3200799 CCAAAATTTGAAAGTGCTTCGGGTCATCAATAAGTCTTTC-ATGCATGATCCTTAAATCCTTCGG
385 CCAAAATTTGTAAGT-CTTCGGGCCATCAGTAAGTCTTTCGA-GCATGATGATTAAATCCTTCGG
*
3200863 GTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGATCTTCGAGCCA
448 GTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCG-G--A
* * *
3200928 TCCGTAAGATCTTCGGGTAAGATGTTTTCACTTGAAAATGAGAAAACGATTACCAAAGTTTCTCA
1 ---GTAAGACCTTCGGGT--GATGTTTTCACATGAAAATGAGAAAGCGATTACCAAAGTTTCTCA
* * *
3200993 TTTAATGTTTTTAGAAAGTGAAATTCTTGAAAAGCAAGAAAGCAATTACCAACGTTTCTTACCCA
61 TTTAATGTTTTTAGAAAATGAAATT-TTGAAAAGTAAGAAAGCGATTACCAA-GTTTCTTACCCA
* * *
3201058 ATAAATTATTTCCAAAATTTGTAACTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTA
124 GTAAATTATTTCCAAAATTTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTA
* * * *
3201123 AATCCTTCGGGTCACCTGTAAGTCTTTCGAGTAAGATGATAAGTCTTTCAAGCTATCTGTAAGAC
189 AATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCTTTCAGGCCATCTGTAAGAC
* * * *
3201188 CTTCGCGTAGGATTTTTTCATATGAAAATGAGAAAGCGATTACCAAAGTATCTCATTTAATGTTT
254 CTTCGGGTAGGATGTTTTCACATGAAAATGAGAAAGTGATTACCAAAGTATCTCATTTAATGTTT
* *
3201253 TCAAAAAATGAAATTCTTGAAAAGTAAGAAACGATTACCAAAGTTTCTTACCCAGTAAATTATTT
319 TCAGAAAATGAAATTCTTGAAAAGTAAGAAATGATTACCAAAGTTTCTTACCCAGTAAATTATTT
* * *
3201318 CTCAAAATTTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAG
384 CCCAAAATTTGTAAGT-CTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
* * *
3201383 GTTATCTGTAAGTCTTTTGAGCAAGATGATAAGTCTTTCGGGCCATCCGTAAGACCTTCGG-
448 GTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGA
* *
3201444 GTAGGA---T---GT--T-TTTT-ACATGAAAATGAGAAAGCGATTACCAAATTTTCTCATTTAA
1 GTAAGACCTTCGGGTGATGTTTTCACATGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAA
* * * *
3201499 TGTTTTTAGAAAATGAAATATTTGAAAAGTAAAAAATCGATTACCATAGTTTCTTACCGACTAAA
66 TGTTTTTAGAAAATGAAAT-TTTGAAAAGTAAGAAAGCGATTACCA-AGTTTCTTACCCAGTAAA
* * *
3201564 TTATTTCACAAAATTTGTAAG-CCTTTCGGGCAATCAGTAAGTCTTT-TAGTATGATGATTAAAT
129 TTATTTC-CAAAATTTGTAAGTCC-TTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAAT
* * * * *
3201627 CTTTCGGGTCATCTGTAAGTCTTTCGAGCAAAACGATAAGTCCTTT-AGGCCGTCTGTAACACCT
192 CCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGT-CTTTCAGGCCATCTGTAAGACCT
* * *
3201691 TCAGGTAGGATGTTTTCACATGAAAATGAGAAAGTGATTACCAAAGTTTCTCTTTTAATGTTTTC
256 TCGGGTAGGATGTTTTCACATGAAAATGAGAAAGTGATTACCAAAGTATCTCATTTAATGTTTTC
* * *
3201756 AGAAAAGGAAAATT-TTGAAAAGTAAGAAAGTGATTATCAAAGTTTCTCACCCAGTAAATTATTT
321 AGAAAATG-AAATTCTTGAAAAGTAAGAAA-TGATTACCAAAGTTTCTTACCCAGTAAATTATTT
3201820 CCCAAAA----T---TCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG
384 CCCAAAATTTGTAAGTCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG
* * * *
3201878 TCATCTGTAATTCTTTCGAGCAAGATGATAAGTCCTTCAGGACAT-CGATAACACCTTCGG-
449 TCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCG-TAAGACCTTCGGA
3201938 GT---A-------G-GATGTTTTCACATGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAA
1 GTAAGACCTTCGGGTGATGTTTTCACATGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAA
* *
3201992 TGTTTTCAGAAAATGAAAATTTTGAAAAGTAAAAAAGCGATTACCAA-------A---AGT---T
66 TGTTTTTAGAAAATG-AAATTTTGAAAAGTAAGAAAGCGATTACCAAGTTTCTTACCCAGTAAAT
* * * *
3202044 TCTTTTCTAAAATTTGTAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCA
130 T-ATTTCCAAAATTTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCC
* * * * *
3202109 TTCAGGTCATCTATAAGTCTTTCGATCAAGATGGTAAGTCTTTCGGGCCATCTGTAAGACCTTCG
194 TTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCTTTCAGGCCATCTGTAAGACCTTCG
* * * *
3202174 GGTAGGATTTTTTCACATGAAAA-AAGAAAGTGATTACCAAAGTTTCTCATTTAATGTTTTTAGA
259 GGTAGGATGTTTTCACATGAAAATGAGAAAGTGATTACCAAAGTATCTCATTTAATGTTTTCAGA
* * *
3202238 AAATGAAATTCTTGAAAAGTAAGAAATCGATTACCAAAATTTCATACCTAGTAAATTATTT-CC-
324 AAATGAAATTCTTGAAAAGTAAGAAAT-GATTACCAAAGTTTCTTACCCAGTAAATTATTTCCCA
* * *
3202301 AAATTTGTAAGTCATTTGGGCGATTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCA
388 AAATTTGTAAGTC-TTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCA
* * *
3202366 TCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGTCATCTGTAAGACCTTCGGA
452 TCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGA
* ** *** * *** *** *
3202424 -CAAGATGTTTTCAACTGAT-TTTT----TTAAAATGAGAAAATTATTTTTAATTACTTT-T-AT
1 GTAAGA--CCTTCGGGTGATGTTTTCACATGAAAATGAGAAAGCGATTACCAA--AGTTTCTCAT
* * * *
3202481 TTAATATTTTTAGAAAATGAAATTTTTGAAAAGTATGAAAGCGATTTCCAGAGTTTCTTACCTAG
62 TTAATGTTTTTAGAAAATGAAA-TTTTGAAAAGTAAGAAAGCGATTACCA-AGTTTCTTACCCAG
* * *
3202546 TAAACTATTTCCAAAATTTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCCTAATGATTAA
125 TAAATTATTTCCAAAATTTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAA
* * * * *
3202611 ATCCTTTGGGTCATCTCTCAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATC
190 ATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCTTTCAGGCCATC
3202667 CATAAAAACT
Statistics
Matches: 1511, Mismatches: 160, Indels: 143
0.83 0.09 0.08
Matches are distributed among these distances:
477 3 0.00
478 8 0.01
479 123 0.08
480 94 0.06
481 1 0.00
482 2 0.00
484 2 0.00
485 98 0.06
486 1 0.00
488 1 0.00
490 1 0.00
491 2 0.00
492 8 0.01
493 141 0.09
494 105 0.07
495 5 0.00
497 4 0.00
498 4 0.00
501 245 0.16
502 85 0.06
503 1 0.00
504 3 0.00
506 102 0.07
507 3 0.00
510 1 0.00
513 5 0.00
519 31 0.02
520 150 0.10
521 282 0.19
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (509 bp):
GTAAGACCTTCGGGTGATGTTTTCACATGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAA
TGTTTTTAGAAAATGAAATTTTGAAAAGTAAGAAAGCGATTACCAAGTTTCTTACCCAGTAAATT
ATTTCCAAAATTTGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT
CGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCTTTCAGGCCATCTGTAAGACCTTCGGG
TAGGATGTTTTCACATGAAAATGAGAAAGTGATTACCAAAGTATCTCATTTAATGTTTTCAGAAA
ATGAAATTCTTGAAAAGTAAGAAATGATTACCAAAGTTTCTTACCCAGTAAATTATTTCCCAAAA
TTTGTAAGTCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTG
TAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGA
Found at i:3201380 original size:42 final size:41
Alignment explanation
Indices: 3201333--3201435 Score: 107
Period size: 42 Copynumber: 2.5 Consensus size: 41
3201323 AATTTGTAAG
* *
3201333 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATG-ATAAA
* ** * * *
3201375 TCCTTCAGGTTATCTGTAAGTCTTTTGAGCAAGATGATAAG
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATGATAAA
* *
3201416 TCTTTCGGGCCATCCGTAAG
1 TCCTTCGGGCCATCAGTAAG
3201436 ACCTTCGGGT
Statistics
Matches: 48, Mismatches: 13, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
41 18 0.38
42 30 0.62
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.33
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATGATAAA
Found at i:3201893 original size:42 final size:41
Alignment explanation
Indices: 3201824--3201915 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 41
3201814 TTATTTCCCA
* *
3201824 AAATTCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATT
1 AAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATGA-T
* * *
3201866 AAATCCTTCGGGTCATCTGTAATTCTTTCGAGCAAGATGAT
1 AAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATGAT
*
3201907 AAGTCCTTC
1 AAATCCTTC
3201916 AGGACATCGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 9 0.20
42 35 0.80
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (41 bp):
AAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATGAT
Found at i:3202411 original size:41 final size:42
Alignment explanation
Indices: 3202330--3202411 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 42
3202320 GCGATTAGTA
*
3202330 AGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTC
1 AGTCTTTCGAGCAAGATGATTAAATCCTTCGGGTCATCTGTC
*
3202372 AGTCTTTCGAGCAAGATGA-TAAGTCCTTCGGGTCATCTGT
1 AGTCTTTCGAGCAAGATGATTAAATCCTTCGGGTCATCTGT
3202412 AAGACCTTCG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 20 0.53
42 18 0.47
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (42 bp):
AGTCTTTCGAGCAAGATGATTAAATCCTTCGGGTCATCTGTC
Found at i:3202428 original size:41 final size:42
Alignment explanation
Indices: 3202335--3202430 Score: 124
Period size: 41 Copynumber: 2.3 Consensus size: 42
3202325 TAGTAAGTCT
* * * *
3202335 TTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCT
1 TTCGAGCAAGATGATTAAATCCTTCGGGTCATCTGTAAGACC
*
3202377 TTCGAGCAAGATGA-TAAGTCCTTCGGGTCATCTGTAAGACC
1 TTCGAGCAAGATGATTAAATCCTTCGGGTCATCTGTAAGACC
3202418 TTCG-GACAAGATG
1 TTCGAG-CAAGATG
3202431 TTTTCAACTG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
40 1 0.02
41 34 0.71
42 13 0.27
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (42 bp):
TTCGAGCAAGATGATTAAATCCTTCGGGTCATCTGTAAGACC
Found at i:3202649 original size:42 final size:41
Alignment explanation
Indices: 3202570--3202666 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 41
3202560 AATTTGTAAG
** * *
3202570 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCCTAATGATTAAA
1 TCCTTCGGGCCATCTCTCAGTCTTTCGAGCCAAATGA-TAAA
* * *
3202612 TCCTTTGGGTCATCTCTCAGTCTTTCGAG-CAAGATGATAAG
1 TCCTTCGGGCCATCTCTCAGTCTTTCGAGCCAA-ATGATAAA
3202653 TCCTTCGGGCCATC
1 TCCTTCGGGCCATC
3202667 CATAAAAACT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 17 0.38
42 28 0.62
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.32
Consensus pattern (41 bp):
TCCTTCGGGCCATCTCTCAGTCTTTCGAGCCAAATGATAAA
Found at i:3202873 original size:62 final size:62
Alignment explanation
Indices: 3202707--3202960 Score: 296
Period size: 62 Copynumber: 4.1 Consensus size: 62
3202697 TTTGTTATTC
* * * * * *
3202707 TTGACTTCCTTATGAAGAGAAATAAACATTTGTTATTCCTGACTCCCCAGTAGAGTCAATCA
1 TTGACTTCCTCATGAAGAGAAGTCAACTTTTATTATTCATGACTCCCCAGTAGAGTCAATCA
* ** *
3202769 TTAACTTCCTCAT-AAGAGAAGTCAACTTTTATTATTTC-TGACTCATCAGTAGAGTTAATCA
1 TTGACTTCCTCATGAAGAGAAGTCAACTTTTATTA-TTCATGACTCCCCAGTAGAGTCAATCA
* * *
3202830 TTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTCATGACTCCCCAGTAGAGTCAATCT
1 TTGACTTCCTCATGAAGAGAAGTCAACTTTTATTATTCATGACTCCCCAGTAGAGTCAATCA
** * * * * **
3202892 TTGACTTCCTTGTGAAAAGACGTCAACTTTTGTTATTTATGACTCCCCAGTAGAGTCAATTT
1 TTGACTTCCTCATGAAGAGAAGTCAACTTTTATTATTCATGACTCCCCAGTAGAGTCAATCA
3202954 TTGACTT
1 TTGACTT
3202961 TCTCTCGTAG
Statistics
Matches: 166, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
61 51 0.31
62 115 0.69
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (62 bp):
TTGACTTCCTCATGAAGAGAAGTCAACTTTTATTATTCATGACTCCCCAGTAGAGTCAATCA
Found at i:3203049 original size:91 final size:91
Alignment explanation
Indices: 3202882--3203051 Score: 241
Period size: 91 Copynumber: 1.9 Consensus size: 91
3202872 CTCCCCAGTA
* * * * *
3202882 GAGTCAATCTTTGACTTCCTTGTGAAAAGACGTCAACTTTTGTTATTTATGACTCCCCAGTAGAG
1 GAGTCAATCCTTAACTTCCTCGTGAAAAGAAGTCAACCTTTGTTATTTATGACTCCCCAGTAGAG
**
3202947 TCAATTTTTGACTTTCTCTCGTAGAT
66 TCAATCCTTGACTTTCTCTCGTAGAT
* * *
3202973 GAGTCAATCCTTAACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCTCCAGTAGAG
1 GAGTCAATCCTTAACTTCCTCGTGAAAAGAAGTCAACCTTTGTTATTTATGACTCCCCAGTAGAG
*
3203038 TCGATCCTTGACTT
66 TCAATCCTTGACTT
3203052 CCTCGTGAAG
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
91 68 1.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (91 bp):
GAGTCAATCCTTAACTTCCTCGTGAAAAGAAGTCAACCTTTGTTATTTATGACTCCCCAGTAGAG
TCAATCCTTGACTTTCTCTCGTAGAT
Found at i:3203238 original size:89 final size:89
Alignment explanation
Indices: 3203100--3203296 Score: 200
Period size: 89 Copynumber: 2.2 Consensus size: 89
3203090 CTGAAGAACC
* * * * * **
3203100 AGTGAATCAAATTAATCTCGAGTCTGATCTCCCCGGAAGAGTAGAGGAACAAATTCACC-ATATT
1 AGTGAAGCAAATCAATCTCGAGTATCATCTCCACGGAAGAACAGAGGAAC-AATTCACCTA-ATT
* * * *
3203164 TCATAT-TTGGTCTCCATGGAAGAGT
64 TCAGATATTGGCCTCCACGAAAGAGT
* * * ** *
3203189 AGTGAAGCAAATCAATTTCGAGTATCATCTCTACGGAAGAACAGTGGAACAATTCTTCTAATTTT
1 AGTGAAGCAAATCAATCTCGAGTATCATCTCCACGGAAGAACAGAGGAACAATTCACCTAATTTC
*
3203254 AGATATTGGCCTTCACGAAAGAGT
66 AGATATTGGCCTCCACGAAAGAGT
3203278 AGTGAAGCAAATCAATCTC
1 AGTGAAGCAAATCAATCTC
3203297 AGAGGTCAAG
Statistics
Matches: 87, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
88 13 0.15
89 74 0.85
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (89 bp):
AGTGAAGCAAATCAATCTCGAGTATCATCTCCACGGAAGAACAGAGGAACAATTCACCTAATTTC
AGATATTGGCCTCCACGAAAGAGT
Found at i:3203572 original size:3 final size:3
Alignment explanation
Indices: 3203564--3203623 Score: 95
Period size: 3 Copynumber: 20.0 Consensus size: 3
3203554 TTTGTCCCAT
*
3203564 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3203612 TTAA TT- TTA TTA
1 TT-A TTA TTA TTA
3203624 CATGCCATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3206344 original size:3 final size:3
Alignment explanation
Indices: 3206338--3206379 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
3206328 AATATTATCC
3206338 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3206380 TTATTATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3206384 original size:3 final size:3
Alignment explanation
Indices: 3206378--3206411 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
3206368 ATAATAATAA
* *
3206378 TAT TAT TAT TAT TAT TAT CAT CAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3206412 GAAGTAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:3208548 original size:17 final size:17
Alignment explanation
Indices: 3208514--3208547 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3208504 AGATTAACTT
*
3208514 ATAAAATTCTAATAAAA
1 ATAAAATTATAATAAAA
3208531 ATAAAATTAT-ATAAAA
1 ATAAAATTATAATAAAA
3208547 A
1 A
3208548 AATATCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATTATAATAAAA
Found at i:3209376 original size:19 final size:19
Alignment explanation
Indices: 3209352--3209389 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3209342 AATAACACCC
3209352 TATAATTAGGAGACCATCT
1 TATAATTAGGAGACCATCT
3209371 TATAATTAGGAGACCATCT
1 TATAATTAGGAGACCATCT
3209390 GTGTACTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
TATAATTAGGAGACCATCT
Found at i:3213883 original size:54 final size:54
Alignment explanation
Indices: 3213798--3214194 Score: 537
Period size: 54 Copynumber: 7.4 Consensus size: 54
3213788 CTATGTGTAC
* * *
3213798 TATAGGTACTAAGTGTGCAACCCACAGAATTCAACATATGTTGATGAATGACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * *
3213852 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATAAATGACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * * *
3213906 TATAGGAACTAAGTGTGCAACCAACAAAATTCATCATATGTTGATGAACGACCA
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
** **
3213960 TATAGAAACTAAGTGTGCAACCCATTGAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * *
3214014 TATATGCACTAAGTGTGCAACCCATAGAATTCATCATATGTTGATGAATGACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * *
3214068 TATAGGCACTAAGTGTGCAACCCACAGAATTCATAATGTGTTTATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * * *
3214122 TATAGGCACTAAGTGTGCAACCCA-TGAAATTCATAACATGTTTATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACGACCG
*
3214176 TATCA-GCACTATGTGTGCA
1 TAT-AGGCACTAAGTGTGCA
3214195 TCTCAAAGAA
Statistics
Matches: 311, Mismatches: 30, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
53 1 0.00
54 309 0.99
55 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
Found at i:3215098 original size:31 final size:31
Alignment explanation
Indices: 3215062--3215134 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
3215052 GGGTCTGGGA
*
3215062 GCCTACCCAAGAAAGTTCTCGGGGCCACGGG
1 GCCTACCCAAGAAAGTTCTCGGGGCCAAGGG
*
3215093 GCCTACCTAAGAAAGTTCTCGGGGCCAAGGG
1 GCCTACCCAAGAAAGTTCTCGGGGCCAAGGG
3215124 GCCTACCCAAG
1 GCCTACCCAAG
3215135 GGTCGTCTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.25, C:0.32, G:0.30, T:0.14
Consensus pattern (31 bp):
GCCTACCCAAGAAAGTTCTCGGGGCCAAGGG
Found at i:3215281 original size:66 final size:66
Alignment explanation
Indices: 3215155--3215282 Score: 175
Period size: 66 Copynumber: 1.9 Consensus size: 66
3215145 GGTCCATAAG
* * * * *
3215155 GAATTACCAGTCGATGTTGAACCTATAAAAGGAATTACCAGCAGCGACTAAACCTGCCAGAGATA
1 GAATTACCAATCGATGTAGAACCTATAAAAGGAATTAACAACAGCGACTAAACCTACCAGAGATA
3215220 T
66 T
* * **
3215221 GAATTACCAATCGATGTAGAACCTATACAAGGAATTAACAACAGGGACTGCACCTACCAGAG
1 GAATTACCAATCGATGTAGAACCTATAAAAGGAATTAACAACAGCGACTAAACCTACCAGAG
3215283 TCTTCATACA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (66 bp):
GAATTACCAATCGATGTAGAACCTATAAAAGGAATTAACAACAGCGACTAAACCTACCAGAGATA
T
Found at i:3217112 original size:22 final size:22
Alignment explanation
Indices: 3217087--3217129 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3217077 ACGATCAACG
*
3217087 GTCAATGACCTGACCGGTCAAA
1 GTCAACGACCTGACCGGTCAAA
**
3217109 GTCAACGGTCTGACCGGTCAA
1 GTCAACGACCTGACCGGTCAA
3217130 CGGTTAACTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
GTCAACGACCTGACCGGTCAAA
Found at i:3218446 original size:23 final size:23
Alignment explanation
Indices: 3218420--3218476 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
3218410 CTCATATAAA
*
3218420 TGCACCGAAGTGCAACGTAGAAT
1 TGCACCGAAGTGCAACATAGAAT
* **
3218443 TGCATCGAAGTGCCGCATAGAAT
1 TGCACCGAAGTGCAACATAGAAT
3218466 TGCACCGAAGT
1 TGCACCGAAGT
3218477 TTCATATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCAACATAGAAT
Found at i:3220056 original size:20 final size:20
Alignment explanation
Indices: 3220031--3220068 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3220021 TCCCCTTTGA
3220031 AGTGCATCGATACATTCTAC
1 AGTGCATCGATACATTCTAC
*
3220051 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
3220069 TTAACATGTG
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:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:3223526 original size:23 final size:23
Alignment explanation
Indices: 3223500--3223576 Score: 136
Period size: 23 Copynumber: 3.3 Consensus size: 23
3223490 AAATGCATCA
*
3223500 AAGTGCCATGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTGCACCG
3223523 AAGTGCCACGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTGCACCG
3223546 AAGTGCCACGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTGCACCG
*
3223569 AAATGCCA
1 AAGTGCCA
3223577 TATAAAATGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (23 bp):
AAGTGCCACGTAGAATTGCACCG
Found at i:3226799 original size:23 final size:21
Alignment explanation
Indices: 3226750--3226831 Score: 69
Period size: 21 Copynumber: 3.9 Consensus size: 21
3226740 CAGAACCCGT
* *
3226750 GGGGGTATCAATTCCC-TCAA
1 GGGGGAATCAGTTCCCTTCAA
*
3226770 GAGGGAATCAGTTCCCATTCAAA
1 GGGGGAATCAGTTCCC-TTC-AA
* *
3226793 GGGGGAATCGGTTCTCTTCAA
1 GGGGGAATCAGTTCCCTTCAA
*
3226814 GGGGGTATC-GATTCCCTT
1 GGGGGAATCAG-TTCCCTT
3226832 TGCACTAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
20 14 0.28
21 16 0.32
22 5 0.10
23 15 0.30
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (21 bp):
GGGGGAATCAGTTCCCTTCAA
Found at i:3235897 original size:64 final size:64
Alignment explanation
Indices: 3235814--3235958 Score: 197
Period size: 64 Copynumber: 2.3 Consensus size: 64
3235804 GACTTTAATT
3235814 TTTTTCTTTG-TTTTTCTCCCCTCAAAAATCTCTTATTATT-TTTAGACCTGGTTCGAATC-AAA
1 TTTTT-TTTGTTTTTTCTCCCCTCAAAAATCTCTTATT-TTGTTTAGACCTGGTTCGAATCGAAA
3235876 C
64 C
* * *
3235877 TTTTTTTTGTTTTTTGCTCCCCTCAAAAATCTCTTCTTTTGTTTAGATCTGGTTCGAATCGAACC
1 TTTTTTTTGTTTTTT-CTCCCCTCAAAAATCTCTTATTTTGTTTAGACCTGGTTCGAATCGAAAC
* *
3235942 TTTTTTCTATTTTTTCT
1 TTTTTTTTGTTTTTTCT
3235959 TTTCTTCCTC
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
62 4 0.05
63 12 0.16
64 41 0.56
65 16 0.22
ACGTcount: A:0.18, C:0.21, G:0.09, T:0.52
Consensus pattern (64 bp):
TTTTTTTTGTTTTTTCTCCCCTCAAAAATCTCTTATTTTGTTTAGACCTGGTTCGAATCGAAAC
Found at i:3236518 original size:4 final size:4
Alignment explanation
Indices: 3236495--3236540 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
3236485 AATAATAATA
* *
3236495 AAAT AACAT AAAT AAA- AAAT AAAT AAA- ATAG AAAT AAAT AAAT AAA
1 AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
3236541 AGGACCGGGC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
3 5 0.14
4 27 0.75
5 4 0.11
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:3236529 original size:11 final size:10
Alignment explanation
Indices: 3236483--3236541 Score: 52
Period size: 11 Copynumber: 5.9 Consensus size: 10
3236473 TAAACCTACC
3236483 AAAATAATAAT
1 AAAATAA-AAT
*
3236494 AAAATAACAT
1 AAAATAAAAT
*
3236504 -AAATAAAAA
1 AAAATAAAAT
3236513 ATAAATAAAAT
1 A-AAATAAAAT
3236524 AGAAAT-AAAT
1 A-AAATAAAAT
3236534 -AAATAAAA
1 AAAATAAAA
3236542 GGACCGGGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
8 4 0.10
9 10 0.25
10 6 0.15
11 20 0.50
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:3238732 original size:6 final size:6
Alignment explanation
Indices: 3238721--3238766 Score: 55
Period size: 5 Copynumber: 8.3 Consensus size: 6
3238711 ATAAGGATGT
*
3238721 GTTAGG GTTAGG GTT-GG GTT-GG GTTA-G GTTA-G GTTAGG GTTTGG
1 GTTAGG GTTAGG GTTAGG GTTAGG GTTAGG GTTAGG GTTAGG GTTAGG
3238765 GT
1 GT
3238767 CTGAGTATGG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
5 20 0.54
6 17 0.46
ACGTcount: A:0.11, C:0.00, G:0.50, T:0.39
Consensus pattern (6 bp):
GTTAGG
Found at i:3238746 original size:16 final size:17
Alignment explanation
Indices: 3238721--3238766 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
3238711 ATAAGGATGT
*
3238721 GTTAGGGTTAGGGTTGG
1 GTTAGGGTTAGGGTTAG
3238738 GTT-GGGTTA-GGTTAG
1 GTTAGGGTTAGGGTTAG
*
3238753 GTTAGGGTTTGGGT
1 GTTAGGGTTAGGGT
3238767 CTGAGTATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 8 0.32
16 11 0.44
17 6 0.24
ACGTcount: A:0.11, C:0.00, G:0.50, T:0.39
Consensus pattern (17 bp):
GTTAGGGTTAGGGTTAG
Found at i:3238873 original size:27 final size:28
Alignment explanation
Indices: 3238843--3238899 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
3238833 TGGGTTTGGG
*
3238843 TATTTTGTAATAATA-AATAAATAATAA
1 TATTTTATAATAATATAATAAATAATAA
* *
3238870 TATTTTATAATAATATTATTAATAATAA
1 TATTTTATAATAATATAATAAATAATAA
3238898 TA
1 TA
3238900 ATATATAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
TATTTTATAATAATATAATAAATAATAA
Found at i:3238881 original size:13 final size:15
Alignment explanation
Indices: 3238862--3238899 Score: 62
Period size: 13 Copynumber: 2.7 Consensus size: 15
3238852 ATAATAAATA
3238862 AATAATAATATT-TT
1 AATAATAATATTATT
3238876 -ATAATAATATTATT
1 AATAATAATATTATT
3238890 AATAATAATA
1 AATAATAATA
3238900 ATATATAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.50
14 2 0.09
15 9 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAATAATATTATT
Found at i:3240544 original size:103 final size:101
Alignment explanation
Indices: 3240350--3240537 Score: 261
Period size: 103 Copynumber: 1.8 Consensus size: 101
3240340 TTTATTTATT
*
3240350 TTATTAATTTTTGAATCATTAGACGACCTTGTGGTGACCCGATTCAGGGTATGATCCACATTATT
1 TTATTAATTTTTGAATCATTAGACGACCTTGTAGTGACCCGATTCAGGGTATGATCCACATTATT
* * *
3240415 ATGGTTCATACTCTATTAACTCCTAACGGTTATTTC
66 ATGGTCCAGAATCTATTAACTCCTAACGGTTATTTC
* * * *
3240451 TTATTAATTTGATTGAATTATTATATGACCTTGTAGTGACCCGA-TCCGGGATATGATCCACATT
1 TTATTAATTT--TTGAATCATTAGACGACCTTGTAGTGACCCGATTCAGGG-TATGATCCACATT
*
3240515 ATTATGGTCCAGAATCTGTTAAC
63 ATTATGGTCCAGAATCTATTAAC
3240538 ATCTAACCGC
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
101 10 0.13
102 5 0.07
103 60 0.80
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (101 bp):
TTATTAATTTTTGAATCATTAGACGACCTTGTAGTGACCCGATTCAGGGTATGATCCACATTATT
ATGGTCCAGAATCTATTAACTCCTAACGGTTATTTC
Found at i:3247443 original size:76 final size:75
Alignment explanation
Indices: 3247340--3247587 Score: 279
Period size: 76 Copynumber: 3.3 Consensus size: 75
3247330 GATATAAGCC
* *
3247340 TTCAGCATGCCCCAACA-TTGCTAATACAGACGTTCAAAATGAGCCAACATTCCTGA-TTCTGAT
1 TTCAGCATGCCCCAACATTTGCTAATACAAACGTTCAAAATGAGTCAACATTCCT-ATTTCTGAT
*
3247403 TAAAATGGGCT
65 TGAAATGGGCT
* ** * *
3247414 TTCAGCATACCCCCAACATTTGCTAATACAAACGTTCAAAACAAATC-ACATTTCTATTTCTGA-
1 TTCAGCAT-GCCCCAACATTTGCTAATACAAACGTTCAAAATGAGTCAACATTCCTATTTCTGAT
3247477 TGAAATGGGCCT
65 TGAAATGGG-CT
* * * * * * *
3247489 TTCAGCGTGCCCCAACATTTGCTGATACAAACATTCAAAATGTGTTTAATATTCATATTTCTGAT
1 TTCAGCATGCCCCAACATTTGCTAATACAAACGTTCAAAATGAG-TCAACATTCCTATTTCTGAT
3247554 TGAAATGGGCT
65 TGAAATGGGCT
* *
3247565 TTCAGCATTCCTCAACATTTGCT
1 TTCAGCATGCCCCAACATTTGCT
3247588 TCTTGTGATG
Statistics
Matches: 144, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
74 46 0.32
75 31 0.22
76 58 0.40
77 9 0.06
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (75 bp):
TTCAGCATGCCCCAACATTTGCTAATACAAACGTTCAAAATGAGTCAACATTCCTATTTCTGATT
GAAATGGGCT
Found at i:3247510 original size:74 final size:75
Alignment explanation
Indices: 3247340--3247528 Score: 224
Period size: 74 Copynumber: 2.5 Consensus size: 75
3247330 GATATAAGCC
* ** *
3247340 TTCAGCATGCCCCAACA-TTGCTAATACAGACGTTCAAAATGAGCCAACATTCCTGATTCTGATT
1 TTCAGCATGCCCCAACATTTGCTAATACAAACGTTCAAAACAAACCAACATTCCTGATTCTGATT
3247404 AAAATGGGCT
66 AAAATGGGCT
* * *
3247414 TTCAGCATACCCCCAACATTTGCTAATACAAACGTTCAAAACAAATC-ACATTTCT-ATTTCTGA
1 TTCAGCAT-GCCCCAACATTTGCTAATACAAACGTTCAAAACAAACCAACATTCCTGA-TTCTGA
*
3247477 -TGAAATGGGCCT
64 TTAAAATGGG-CT
* * *
3247489 TTCAGCGTGCCCCAACATTTGCTGATACAAACATTCAAAA
1 TTCAGCATGCCCCAACATTTGCTAATACAAACGTTCAAAA
3247529 TGTGTTTAAT
Statistics
Matches: 99, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
74 46 0.46
75 30 0.30
76 23 0.23
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (75 bp):
TTCAGCATGCCCCAACATTTGCTAATACAAACGTTCAAAACAAACCAACATTCCTGATTCTGATT
AAAATGGGCT
Done.