Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007838.1 Hibiscus syriacus cultivar Beakdansim tig00110187_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: 3429202
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 13
Found at i:1785431 original size:32 final size:29
Alignment explanation
Indices: 1785390--1785451 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 29
1785380 CATAAGTTAA
1785390 AAATAATTATA-AAATAATAATATTAATATTG
1 AAATAATTATATAAA-AAT-ATA-TAATATTG
1785421 AAATAAATTATATAAAAATATATAATATTG
1 AAAT-AATTATATAAAAATATATAATATTG
1785451 A
1 A
1785452 TAATTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
30 9 0.31
31 7 0.24
32 10 0.34
33 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (29 bp):
AAATAATTATATAAAAATATATAATATTG
Found at i:1790046 original size:17 final size:16
Alignment explanation
Indices: 1790024--1790062 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1790014 TATATTATCA
1790024 ATAAATAGAATTTTTAT
1 ATAAATA-AATTTTTAT
1790041 ATAAAT-AATTTTTAT
1 ATAAATAAATTTTTAT
*
1790056 TTAAATA
1 ATAAATA
1790063 TTTAGAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 14 0.70
17 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
ATAAATAAATTTTTAT
Found at i:1790827 original size:29 final size:31
Alignment explanation
Indices: 1790769--1790831 Score: 103
Period size: 29 Copynumber: 2.1 Consensus size: 31
1790759 GATAACATGG
*
1790769 TTGATGGGCTTAATTGATTCTTTTAGAAAGT
1 TTGATGGGCTTAATTGATTATTTTAGAAAGT
1790800 TTGA-GGGCTTAATT-ATTATTTTAGAAAGT
1 TTGATGGGCTTAATTGATTATTTTAGAAAGT
1790829 TTG
1 TTG
1790832 CGAAAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 17 0.55
30 10 0.32
31 4 0.13
ACGTcount: A:0.27, C:0.05, G:0.22, T:0.46
Consensus pattern (31 bp):
TTGATGGGCTTAATTGATTATTTTAGAAAGT
Found at i:1791778 original size:12 final size:12
Alignment explanation
Indices: 1791756--1791806 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
1791746 TTATATGAAA
1791756 ATATCCTAATTAT
1 ATAT-CTAATTAT
1791769 ATATCTAATT-T
1 ATATCTAATTAT
*
1791780 ATAATTATAATTAT
1 AT-A-TCTAATTAT
*
1791794 ACATCTAATTAT
1 ATATCTAATTAT
1791806 A
1 A
1791807 ATTATGAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 3 0.09
12 16 0.50
13 11 0.34
14 2 0.06
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATCTAATTAT
Found at i:1791799 original size:25 final size:24
Alignment explanation
Indices: 1791762--1791811 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
1791752 GAAAATATCC
*
1791762 TAATTATATATCTAATTTATAATTA
1 TAATTATACATCTAA-TTATAATTA
1791787 TAATTATACATCTAATTATAATTA
1 TAATTATACATCTAATTATAATTA
1791811 T
1 T
1791812 GAATATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (24 bp):
TAATTATACATCTAATTATAATTA
Found at i:1794530 original size:66 final size:66
Alignment explanation
Indices: 1794280--1794603 Score: 532
Period size: 66 Copynumber: 5.0 Consensus size: 66
1794270 CAGTTTTTTT
* *
1794280 AAGCAAAACAAGGATATGATTGAGGAACAAGGTAATGAAGAAAATGGTGAATTTGTTGATGAAAC
1 AAGCAAAACAAGGTTATGATTGAGGAACAAGGTAAAGAAGAAAATGGTGAATTTGTTGATGAAAC
1794345 G
66 G
1794346 AAGCAAAACAAGGTTATGATTGAGGAACAAGGT--A-AAGAAAATGGTGAATTTGTTGATGAAAC
1 AAGCAAAACAAGGTTATGATTGAGGAACAAGGTAAAGAAGAAAATGGTGAATTTGTTGATGAAAC
1794408 G
66 G
1794409 AAGCAAAAC-AGGTTATGATTGAGGAACAAGGTAAAGAAGAAAATGGTGAATTTGTTGATGAAAC
1 AAGCAAAACAAGGTTATGATTGAGGAACAAGGTAAAGAAGAAAATGGTGAATTTGTTGATGAAAC
1794473 G
66 G
* * *
1794474 AAGCAAAACAAGGTTATGATTGAGGAACAAGGTAAAGAAGAAAATGGGGAAGTTGTTGACGAAAC
1 AAGCAAAACAAGGTTATGATTGAGGAACAAGGTAAAGAAGAAAATGGTGAATTTGTTGATGAAAC
1794539 G
66 G
* * * *
1794540 AATCAAAACAAGGTTATGATTGAGGAACAAGGTGAAGAAG-AAATGGTGAATCTGTTGACGAAAC
1 AAGCAAAACAAGGTTATGATTGAGGAACAAGGTAAAGAAGAAAATGGTGAATTTGTTGATGAAAC
1794604 CGGGGATCTG
Statistics
Matches: 244, Mismatches: 10, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
62 23 0.09
63 38 0.16
64 1 0.00
65 59 0.24
66 123 0.50
ACGTcount: A:0.45, C:0.07, G:0.28, T:0.20
Consensus pattern (66 bp):
AAGCAAAACAAGGTTATGATTGAGGAACAAGGTAAAGAAGAAAATGGTGAATTTGTTGATGAAAC
G
Found at i:1801655 original size:3 final size:3
Alignment explanation
Indices: 1801649--1801687 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
1801639 CTCTTCTTCT
* *
1801649 TCC TCC TCC TCT TCC TCC TCC TCC TCC TCC TCT TCC TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
1801688 AAATCACCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (3 bp):
TCC
Found at i:1813247 original size:15 final size:16
Alignment explanation
Indices: 1813213--1813251 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
1813203 CATGAACACA
1813213 CATAATATATATATAT
1 CATAATATATATATAT
1813229 -ATAATATATATA-AT
1 CATAATATATATATAT
1813243 CATAA-ATAT
1 CATAATATAT
1813252 TTATTGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (16 bp):
CATAATATATATATAT
Found at i:1813702 original size:21 final size:21
Alignment explanation
Indices: 1813651--1813703 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1813641 ATTATGAATA
1813651 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
1813672 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
1813693 TCGCAATGCGA
1 TCGCAATGCGA
1813704 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1813718 original size:20 final size:21
Alignment explanation
Indices: 1813693--1813744 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1813683 TTTTCCCAAT
*
1813693 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1813713 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1813734 TCGCAATGCGA
1 TCGCAATGCGA
1813745 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1813757 original size:41 final size:41
Alignment explanation
Indices: 1813730--1813867 Score: 145
Period size: 41 Copynumber: 3.4 Consensus size: 41
1813720 GCGAATTGGG
* *
1813730 AAAATCGCAATGCGATACTGACTATCGCAACGTGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
1813771 AAAATTGCAACGCGATACTGACTTTCGCAACGCGATACTTAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATA-ATAC
** * * *
1813813 --TTTCGCAACGCGATACTGACTTTCGTAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
1813852 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
1813868 TTTCAAAGCG
Statistics
Matches: 80, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.04
40 30 0.38
41 44 0.55
42 3 0.04
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1813758 original size:20 final size:20
Alignment explanation
Indices: 1813733--1813847 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
1813723 AATTGGGAAA
*
1813733 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1813753 ATCGCAACGTGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1813774 ATTGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1813794 TTCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1813814 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1813834 TTCGTAACGAGATA
1 ATCGCAACGCGATA
1813848 ATACATAATC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.03
20 61 0.78
21 13 0.17
22 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1814059 original size:22 final size:22
Alignment explanation
Indices: 1814031--1814074 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1814021 CACTCTCTCA
1814031 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1814053 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1814075 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1814350 original size:20 final size:20
Alignment explanation
Indices: 1814301--1814359 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1814291 TTTATTCTCT
* **
1814301 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
1814321 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
1814341 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
1814360 AGAAACTATC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:1816264 original size:20 final size:19
Alignment explanation
Indices: 1816230--1816293 Score: 76
Period size: 20 Copynumber: 3.4 Consensus size: 19
1816220 ATAGTTACTT
1816230 TCGCAACACGAAATGACTA
1 TCGCAACACGAAATGACTA
*
1816249 TCGCAACACGGAAATGGCTA
1 TCGCAACAC-GAAATGACTA
** *
1816269 TCGCAATGCGAAATGA-AA
1 TCGCAACACGAAATGACTA
1816287 TCGCAAC
1 TCGCAAC
1816294 GACAAAATCG
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 7 0.18
19 15 0.39
20 16 0.42
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (19 bp):
TCGCAACACGAAATGACTA
Found at i:1816303 original size:14 final size:14
Alignment explanation
Indices: 1816284--1816341 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 14
1816274 ATGCGAAATG
1816284 AAATCGCAACGACA
1 AAATCGCAACGACA
*
1816298 AAATCGCAATGCGAAATGA
1 AAATCGCAA--CG--A-CA
1816317 AAATCGCAACGACA
1 AAATCGCAACGACA
1816331 AAATCGCAACG
1 AAATCGCAACG
1816342 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 21 0.57
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.27
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:1816326 original size:33 final size:32
Alignment explanation
Indices: 1816268--1816357 Score: 162
Period size: 33 Copynumber: 2.8 Consensus size: 32
1816258 GGAAATGGCT
1816268 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1816300 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
*
1816333 ATCGCAACGCGAAATGAAATCGCAA
1 ATCGCAATGCGAAATGAAATCGCAA
1816358 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 25 0.45
33 31 0.55
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGACAAA
Found at i:1816403 original size:19 final size:19
Alignment explanation
Indices: 1816387--1816486 Score: 68
Period size: 20 Copynumber: 5.4 Consensus size: 19
1816377 TGCGATTTGT
1816387 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* * *
1816406 CATTGAGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
1816420 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
***
1816439 CGTTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
*
1816459 CGTTGCGATAGTT-ATTTTCG
1 CGTTGCGAT-TTTCA-TTTCG
1816479 CGTTGCGA
1 CGTTGCGA
1816487 AAGTAAGTTT
Statistics
Matches: 61, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
14 6 0.10
15 3 0.05
16 2 0.03
17 2 0.03
18 3 0.05
19 20 0.33
20 22 0.36
21 3 0.05
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1816424 original size:33 final size:32
Alignment explanation
Indices: 1816369--1816439 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 32
1816359 GCGATTTGTG
*
1816369 TTTCGCATTGCGATTTGTCGTTGCGATTTTCA
1 TTTCGCATTGAGATTTGTCGTTGCGATTTTCA
1816401 TTTCGCATTGAGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGAGA-TTTGTCGTTGCGATTTTCA
1816434 TTTCGC
1 TTTCGC
1816440 GTTGCGATAG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 12 0.32
33 25 0.68
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (32 bp):
TTTCGCATTGAGATTTGTCGTTGCGATTTTCA
Found at i:1816497 original size:20 final size:19
Alignment explanation
Indices: 1816433--1816512 Score: 79
Period size: 20 Copynumber: 4.1 Consensus size: 19
1816423 TGCGATTTTC
* **
1816433 ATTTCGCGTTGCGATAGCC
1 ATTTCGCGTTGCGAAAGTA
*
1816452 ATTTCCGCGTTGCGATAGTTA
1 ATTT-CGCGTTGCGAAAG-TA
*
1816473 TTTTCGCGTTGCGAAAGTA
1 ATTTCGCGTTGCGAAAGTA
*
1816492 AGTTTCGTGTTGCGAAAGTA
1 A-TTTCGCGTTGCGAAAGTA
1816512 A
1 A
1816513 ACTATTATTC
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
19 6 0.12
20 43 0.83
21 3 0.06
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.35
Consensus pattern (19 bp):
ATTTCGCGTTGCGAAAGTA
Found at i:1816927 original size:41 final size:41
Alignment explanation
Indices: 1816852--1816966 Score: 117
Period size: 41 Copynumber: 2.8 Consensus size: 41
1816842 GACTCACCTG
* * *
1816852 TCATCCCTC-A-AGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTA
*
1816892 TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
** * * * *
1816933 TCATCGTTGAAGAGTCCCTCCCACCATTCCAGAG
1 TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAG
1816967 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
40 9 0.14
41 47 0.75
42 7 0.11
ACGTcount: A:0.23, C:0.41, G:0.16, T:0.21
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
Found at i:1818253 original size:18 final size:18
Alignment explanation
Indices: 1818230--1818293 Score: 82
Period size: 18 Copynumber: 3.7 Consensus size: 18
1818220 GCAACGAGAG
1818230 AATCGCAATGCGAAATGA
1 AATCGCAATGCGAAATGA
1818248 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATG-A
*
1818267 AATCGCAA--CGAGA--A
1 AATCGCAATGCGAAATGA
1818281 AATCGCAATGCGA
1 AATCGCAATGCGA
1818294 TTTTCATTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
14 9 0.21
16 3 0.07
17 4 0.10
18 17 0.40
19 9 0.21
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (18 bp):
AATCGCAATGCGAAATGA
Found at i:1818337 original size:20 final size:19
Alignment explanation
Indices: 1818312--1818367 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1818302 TCGCATTGCG
1818312 ATTTTCTCGTTGCGATAGCC
1 ATTTTC-CGTTGCGATAGCC
*
1818332 ATTTTCCGGTTGCGATAGTC
1 ATTTTCC-GTTGCGATAGCC
1818352 ATTTTCGCGTTGCGAT
1 ATTTTC-CGTTGCGAT
1818368 TTCCCCGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.21, G:0.23, T:0.41
Consensus pattern (19 bp):
ATTTTCCGTTGCGATAGCC
Found at i:1819019 original size:21 final size:21
Alignment explanation
Indices: 1818993--1819048 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
1818983 CGAAAGTTAG
1818993 TATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATTTTGTAT
1819014 TATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATTTTGTAT
1819035 TATCGCGTTGCGAT
1 TATCGCGTTGCGAT
1819049 AGTCAGTATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.14, C:0.16, G:0.25, T:0.45
Consensus pattern (21 bp):
TATCGCGTTGCGATTTTGTAT
Found at i:1819060 original size:20 final size:20
Alignment explanation
Indices: 1818913--1819068 Score: 118
Period size: 20 Copynumber: 7.7 Consensus size: 20
1818903 AATTATGTAT
* *
1818913 TATCTCGTTGCGATACTCAG
1 TATCGCGTTGCGATAGTCAG
* *
1818933 AATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * * *
1818953 AATCTCGTTACGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
1818973 AATCGCGTTGCGAAAGTTAG
1 TATCGCGTTGCGATAGTCAG
* *
1818993 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
* *
1819014 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
1819035 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
1819055 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
1819069 TTTCCAAATT
Statistics
Matches: 119, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
19 3 0.03
20 79 0.66
21 35 0.29
22 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:1819087 original size:62 final size:62
Alignment explanation
Indices: 1818974--1819091 Score: 157
Period size: 62 Copynumber: 1.9 Consensus size: 62
1818964 GAAAGTCAGA
* * ** * *
1818974 ATCGCGTTGCGAAAGTTAGTATCGCGTTGCGATTTTGTATTATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTCAAATATCGCATTGCGATTTTGTATT
*
1819036 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT-TCGCATTGCGATTT
1 ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTT-CAAATATCGCATTGCGATTT
1819092 ACTTATTCGC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
62 46 0.96
63 2 0.04
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (62 bp):
ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTCAAATATCGCATTGCGATTTTGTATT
Found at i:1819101 original size:20 final size:21
Alignment explanation
Indices: 1819057--1819108 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1819047 ATAGTCAGTA
*
1819057 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1819078 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1819098 TCGCATTGCGA
1 TCGCATTGCGA
1819109 ATTGAGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1819150 original size:21 final size:22
Alignment explanation
Indices: 1819098--1819150 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1819088 ATTTACTTAT
1819098 TCGCATTGCG-AATTGAGAAAA
1 TCGCATTGCGAAATTGAGAAAA
**
1819119 TCGCAACGCGAAATTG-GAAAA
1 TCGCATTGCGAAATTGAGAAAA
1819140 TCGCATTGCGA
1 TCGCATTGCGA
1819151 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGAGAAAA
Found at i:1822295 original size:21 final size:22
Alignment explanation
Indices: 1822269--1822309 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
1822259 TCACTACTAA
1822269 GAAATGCCGCA-TTTCCATTTT
1 GAAATGCCGCATTTTCCATTTT
1822290 GAAATGCCGCATTTTCCATT
1 GAAATGCCGCATTTTCCATT
1822310 ATTTTCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (22 bp):
GAAATGCCGCATTTTCCATTTT
Found at i:1824090 original size:21 final size:21
Alignment explanation
Indices: 1824057--1824097 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1824047 TTCTGGGCAA
* *
1824057 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
1824078 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
1824098 ACGAACAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:1825841 original size:23 final size:22
Alignment explanation
Indices: 1825754--1825833 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
1825744 ATCATTATAT
*
1825754 GGCACTACGGTGC-ATTCTACG
1 GGCACTTCGGTGCAATTCTACG
1825775 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
1825797 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
1825820 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
1825834 TTTATACGAG
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
21 12 0.21
22 29 0.52
23 15 0.27
ACGTcount: A:0.17, C:0.28, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:1828523 original size:163 final size:163
Alignment explanation
Indices: 1828201--1828526 Score: 636
Period size: 163 Copynumber: 2.0 Consensus size: 163
1828191 TATGTTCTTA
1828201 CTAAGATGTTCAGTGAAAATTCGAGGGCGAATTTTCTTATAAGGAGGGGAGATTTGTAACATCCC
1 CTAAGATGTTCAGTGAAAATTCGAGGGCGAATTTTCTTATAAGGAGGGGAGATTTGTAACATCCC
1828266 CAAAAGCCGGATCAGTGACTAAAATGTAAATTTTGGAACTGTGTGCTCAATTTTGAAATAAGTTA
66 CAAAAGCCGGATCAGTGACTAAAATGTAAATTTTGGAACTGTGTGCTCAATTTTGAAATAAGTTA
1828331 AAAGTGTTGGGATTTAAGTAAAGGAATTTTGAT
131 AAAGTGTTGGGATTTAAGTAAAGGAATTTTGAT
1828364 CTAAGATGTTCAGTGAAAATTCGAGGGCGAATTTTCTTATAAGGAGGGGAGATTTGTAACATCCC
1 CTAAGATGTTCAGTGAAAATTCGAGGGCGAATTTTCTTATAAGGAGGGGAGATTTGTAACATCCC
1828429 CAAAAGCCGGATCAGTGACTAAAATGTAAATTTTGGAAACTGTGTGCTCAATTTTGAAATAAGTT
66 CAAAAGCCGGATCAGTGACTAAAATGTAAATTTTGG-AACTGTGTGCTCAATTTTGAAATAAGTT
1828494 AAAAGTGTTGGGATTTAAGTAAA-GAATTTTGAT
130 AAAAGTGTTGGGATTTAAGTAAAGGAATTTTGAT
1828527 GATGGATTGA
Statistics
Matches: 162, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
163 111 0.69
164 51 0.31
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (163 bp):
CTAAGATGTTCAGTGAAAATTCGAGGGCGAATTTTCTTATAAGGAGGGGAGATTTGTAACATCCC
CAAAAGCCGGATCAGTGACTAAAATGTAAATTTTGGAACTGTGTGCTCAATTTTGAAATAAGTTA
AAAGTGTTGGGATTTAAGTAAAGGAATTTTGAT
Found at i:1830799 original size:22 final size:22
Alignment explanation
Indices: 1830713--1830791 Score: 126
Period size: 22 Copynumber: 3.6 Consensus size: 22
1830703 ATCATTATAT
*
1830713 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
1830735 GGCACTTCGGTGCAATTCTAC-
1 GGCACTTCGGTGCAATTCTACG
1830756 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
1830779 GGCAC-TCGGTGCA
1 GGCACTTCGGTGCA
1830792 TTTATACGAG
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
21 21 0.39
22 28 0.52
23 5 0.09
ACGTcount: A:0.19, C:0.28, G:0.29, T:0.24
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:1833233 original size:57 final size:57
Alignment explanation
Indices: 1833141--1833256 Score: 214
Period size: 57 Copynumber: 2.0 Consensus size: 57
1833131 ATTACCTGAA
*
1833141 GGATCTTCACAAGATCTTGGACTAGGATCAGATTCTTGGTTTTACTGCAGAGGTGTT
1 GGATCTTCACAAGATCTTGGACTAGGATCAAATTCTTGGTTTTACTGCAGAGGTGTT
*
1833198 GGATCTTCACAAGATCTTGGACTAGGATCAAATTCTTGGTTTTGCTGCAGAGGTGTT
1 GGATCTTCACAAGATCTTGGACTAGGATCAAATTCTTGGTTTTACTGCAGAGGTGTT
1833255 GG
1 GG
1833257 TGGTTCCATC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (57 bp):
GGATCTTCACAAGATCTTGGACTAGGATCAAATTCTTGGTTTTACTGCAGAGGTGTT
Found at i:1843575 original size:3 final size:3
Alignment explanation
Indices: 1843567--1843592 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1843557 AGTATAGTAT
1843567 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1843593 TAAAAATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1848516 original size:11 final size:11
Alignment explanation
Indices: 1848500--1848604 Score: 51
Period size: 11 Copynumber: 9.8 Consensus size: 11
1848490 CAGTTTACGG
1848500 TTAATTTGAAT
1 TTAATTTGAAT
1848511 TTAATTTG-AT
1 TTAATTTGAAT
* *
1848521 TAAAATTT--AG
1 T-TAATTTGAAT
*
1848531 TTAATATTTAAT
1 TTAAT-TTGAAT
1848543 TTAATTTG-AT
1 TTAATTTGAAT
* **
1848553 TTGATTAAAAT
1 TTAATTTGAAT
* *
1848564 TT-AGTTAATAT
1 TTAATTTGA-AT
1848575 TTAATTT-AAT
1 TTAATTTGAAT
*
1848585 TTAATTTAAAT
1 TTAATTTGAAT
*
1848596 TTGATTTGA
1 TTAATTTGA
1848605 TATCTTAACA
Statistics
Matches: 73, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
9 3 0.04
10 27 0.37
11 34 0.47
12 9 0.12
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (11 bp):
TTAATTTGAAT
Found at i:1848546 original size:5 final size:5
Alignment explanation
Indices: 1848500--1848593 Score: 62
Period size: 5 Copynumber: 17.8 Consensus size: 5
1848490 CAGTTTACGG
* * * *
1848500 TTAAT TTGAAT TTAAT TTGAT TAAAAT TTAGT TAATAT TTAAT TTAAT
1 TTAAT TT-AAT TTAAT TTAAT T-TAAT TTAAT TTA-AT TTAAT TTAAT
* * * * *
1848548 TTGAT TTGAT TAAAAT TTAGT TAATAT TTAAT TTAAT TTAAT TTAA
1 TTAAT TTAAT T-TAAT TTAAT TTA-AT TTAAT TTAAT TTAAT TTAA
1848594 ATTTGATTTG
Statistics
Matches: 68, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
5 51 0.75
6 17 0.25
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.54
Consensus pattern (5 bp):
TTAAT
Found at i:1848555 original size:37 final size:37
Alignment explanation
Indices: 1848500--1848591 Score: 166
Period size: 37 Copynumber: 2.5 Consensus size: 37
1848490 CAGTTTACGG
1848500 TTAATTTGAATTTAATTTGATTAAAATTTAGTTAATAT
1 TTAATTT-AATTTAATTTGATTAAAATTTAGTTAATAT
*
1848538 TTAATTTAATTTGATTTGATTAAAATTTAGTTAATAT
1 TTAATTTAATTTAATTTGATTAAAATTTAGTTAATAT
1848575 TTAATTTAATTTAATTT
1 TTAATTTAATTTAATTT
1848592 AAATTTGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
37 45 0.87
38 7 0.13
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (37 bp):
TTAATTTAATTTAATTTGATTAAAATTTAGTTAATAT
Found at i:1849026 original size:28 final size:28
Alignment explanation
Indices: 1848995--1849096 Score: 107
Period size: 28 Copynumber: 3.4 Consensus size: 28
1848985 TGTTGAATTC
1848995 TTTTTGAAAATATATATATAATATATAG
1 TTTTTGAAAATATATATATAATATATAG
1849023 TTTTTGAAAACATTTTGAAAATATATATAATATATAG
1 TTTTTG-AAA-A---T----ATATATATAATATATAG
*
1849060 TTTTTGAAAACATATATATAATATATAG
1 TTTTTGAAAATATATATATAATATATAG
1849088 -TTTTGAAAA
1 TTTTTGAAAA
1849097 CATTTTGAAG
Statistics
Matches: 64, Mismatches: 1, Indels: 19
0.76 0.01 0.23
Matches are distributed among these distances:
27 9 0.14
28 23 0.36
29 3 0.05
30 1 0.02
33 1 0.02
35 1 0.02
36 3 0.05
37 23 0.36
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (28 bp):
TTTTTGAAAATATATATATAATATATAG
Found at i:1849047 original size:37 final size:39
Alignment explanation
Indices: 1848973--1849072 Score: 150
Period size: 37 Copynumber: 2.6 Consensus size: 39
1848963 ATATATTAAA
* ** *
1848973 ATAATATATAGTTGTTGAATTCTTTTTGAAAATATATAT
1 ATAATATATAGTTTTTGAAAACATTTTGAAAATATATAT
1849012 ATAATATATAGTTTTTGAAAACATTTTG-AAA-ATATAT
1 ATAATATATAGTTTTTGAAAACATTTTGAAAATATATAT
1849049 ATAATATATAGTTTTTGAAAACAT
1 ATAATATATAGTTTTTGAAAACAT
1849073 ATATATAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
37 30 0.53
38 3 0.05
39 24 0.42
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (39 bp):
ATAATATATAGTTTTTGAAAACATTTTGAAAATATATAT
Found at i:1849083 original size:37 final size:37
Alignment explanation
Indices: 1848973--1849086 Score: 131
Period size: 37 Copynumber: 3.0 Consensus size: 37
1848963 ATATATTAAA
* ** * *
1848973 ATAATATATAGTTGTTGAATTCTTTTTGAAAATATATAT
1 ATAATATATAGTTTTTGAAAACATTATG-AAA-ATATAT
*
1849012 ATAATATATAGTTTTTGAAAACATTTTGAAAATATAT
1 ATAATATATAGTTTTTGAAAACATTATGAAAATATAT
*
1849049 ATAATATATAGTTTTTGAAAACATATAT-ATAATATAT
1 ATAATATATAGTTTTTGAAAACAT-TATGAAAATATAT
1849086 A
1 A
1849087 GTTTTGAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
37 39 0.57
38 5 0.07
39 24 0.35
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (37 bp):
ATAATATATAGTTTTTGAAAACATTATGAAAATATAT
Found at i:1849133 original size:65 final size:63
Alignment explanation
Indices: 1848999--1849179 Score: 186
Period size: 65 Copynumber: 2.8 Consensus size: 63
1848989 GAATTCTTTT
* * ** *
1848999 TGAAAATATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAGTTTT
1 TGAAAA-ATATATATAATATATAG-TTTTGAAAACATTTTGAAAATATATATAATAGAAACATTC
** *
1849064 TGAAAACATATATATAATATATAGTTTTGAAAACATTTTGAAGACATATAT-TTTTGGAAACATT
1 TGAAAA-ATATATATAATATATAGTTTTGAAAACATTTTGAA-A-ATATATATAATAGAAACATT
1849128 C
63 C
* * * *
1849129 TG-AAAATATATATAATATATGGTTTTAAAAATATTTTTGAAAATAAATATA
1 TGAAAAATATATATAATATATAGTTTTGAAAACA-TTTTGAAAATATATATA
1849180 TTTTAAAATA
Statistics
Matches: 98, Mismatches: 14, Indels: 10
0.80 0.11 0.08
Matches are distributed among these distances:
62 5 0.05
63 27 0.28
64 28 0.29
65 32 0.33
66 6 0.06
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.41
Consensus pattern (63 bp):
TGAAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAATATATATAATAGAAACATTC
Found at i:1849139 original size:27 final size:27
Alignment explanation
Indices: 1849035--1849141 Score: 94
Period size: 27 Copynumber: 4.0 Consensus size: 27
1849025 TTTGAAAACA
* *
1849035 TTTTGAAAATA-TAT-ATAATATATAGT
1 TTTTGAAAACATTATGAAAATATATA-T
* *
1849061 TTTTGAAAACATATAT-ATAATATATAG
1 TTTTGAAAACAT-TATGAAAATATATAT
* * *
1849088 TTTTGAAAACATTTTGAAGACATATAT
1 TTTTGAAAACATTATGAAAATATATAT
* *
1849115 TTTTGGAAACATTCTGAAAATATATAT
1 TTTTGAAAACATTATGAAAATATATAT
1849142 AATATATGGT
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
26 12 0.18
27 42 0.63
28 13 0.19
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (27 bp):
TTTTGAAAACATTATGAAAATATATAT
Found at i:1849180 original size:18 final size:17
Alignment explanation
Indices: 1849154--1849203 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
1849144 TATATGGTTT
*
1849154 TAAAAATATTTTTGAAAA
1 TAAATATATTTTT-AAAA
1849172 TAAATATA-TTTTAAAA
1 TAAATATATTTTTAAAA
1849188 T-AATATACTTTTTAAA
1 TAAATATA-TTTTTAAA
1849204 TTATTTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 6 0.21
16 5 0.17
17 11 0.38
18 7 0.24
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATATATTTTTAAAA
Found at i:1849204 original size:16 final size:16
Alignment explanation
Indices: 1849157--1849204 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
1849147 ATGGTTTTAA
1849157 AAATAT-TTTTGAAAAT
1 AAATATATTTT-AAAAT
1849173 AAATATATTTTAAAAT
1 AAATATATTTTAAAAT
*
1849189 -AATATACTTTTTAAAT
1 AAATATA-TTTTAAAAT
1849205 TATTTATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 6 0.21
16 19 0.66
17 4 0.14
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (16 bp):
AAATATATTTTAAAAT
Found at i:1857023 original size:6 final size:6
Alignment explanation
Indices: 1857012--1857045 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1857002 TTCAGGTTCG
*
1857012 ATTATA ATTATA ACTATA ATTATA ATTATA ATTA
1 ATTATA ATTATA ATTATA ATTATA ATTATA ATTA
1857046 ATATGTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (6 bp):
ATTATA
Found at i:1857375 original size:20 final size:20
Alignment explanation
Indices: 1857330--1857371 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1857320 TTTTTGATTT
*
1857330 AATTTGATTTAGAATTTTATA
1 AATTTGATTTA-AATTTTAAA
1857351 AATTTGATTT-AATTTTAAA
1 AATTTGATTTAAATTTTAAA
1857370 AA
1 AA
1857372 ATTTAAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
21 10 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (20 bp):
AATTTGATTTAAATTTTAAA
Found at i:1857929 original size:21 final size:21
Alignment explanation
Indices: 1857905--1857973 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
1857895 AAGGGTTAAG
*
1857905 ACCTTTAGATGAAATGACTTA
1 ACCTTTAGATGAAAGGACTTA
* *
1857926 ACCTTTTGATTAAAGGACTTA
1 ACCTTTAGATGAAAGGACTTA
* *
1857947 TCCTTTTA-ATGAAAGGGCTTA
1 ACC-TTTAGATGAAAGGACTTA
*
1857968 ATCTTT
1 ACCTTT
1857974 TCATAAAGAA
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
20 3 0.08
21 32 0.84
22 3 0.08
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (21 bp):
ACCTTTAGATGAAAGGACTTA
Found at i:1868673 original size:15 final size:15
Alignment explanation
Indices: 1868650--1868705 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
1868640 AAACAACTCA
1868650 TGAAACAGGAGACTT
1 TGAAACAGGAGACTT
* * *
1868665 TGAATCAGGTGGACTCA
1 TGAAACAGG-AGACT-T
1868682 TGAAACAGGAGACTT
1 TGAAACAGGAGACTT
*
1868697 TGAATCAGG
1 TGAAACAGG
1868706 TGGGCTTAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 16 0.50
16 8 0.25
17 8 0.25
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (15 bp):
TGAAACAGGAGACTT
Found at i:1868682 original size:32 final size:32
Alignment explanation
Indices: 1868645--1868708 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1868635 TGGTAAAACA
1868645 ACTCATGAAACAGGAGACTTTGAATCAGGTGG
1 ACTCATGAAACAGGAGACTTTGAATCAGGTGG
1868677 ACTCATGAAACAGGAGACTTTGAATCAGGTGG
1 ACTCATGAAACAGGAGACTTTGAATCAGGTGG
1868709 GCTTAATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (32 bp):
ACTCATGAAACAGGAGACTTTGAATCAGGTGG
Found at i:1868695 original size:16 final size:16
Alignment explanation
Indices: 1868645--1868695 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1868635 TGGTAAAACA
1868645 ACTCATGAAACAGGAG
1 ACTCATGAAACAGGAG
* * *
1868661 ACT-TTGAATCAGGTGG
1 ACTCATGAAACAGG-AG
1868677 ACTCATGAAACAGGAG
1 ACTCATGAAACAGGAG
1868693 ACT
1 ACT
1868696 TTGAATCAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
15 8 0.30
16 11 0.41
17 8 0.30
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (16 bp):
ACTCATGAAACAGGAG
Found at i:1869459 original size:50 final size:50
Alignment explanation
Indices: 1869401--1869562 Score: 141
Period size: 50 Copynumber: 3.2 Consensus size: 50
1869391 GTCATTATGA
1869401 AAAATAAAATATTTTAAGTACTATTTTAATAAAAGAAAAATAGTAGTATC
1 AAAATAAAATATTTTAAGTACTATTTTAATAAAAGAAAAATAGTAGTATC
* * * * * * ** * ** * *
1869451 CAAATAAAATTATTGATAATTA--ATTAT-GTGACTGAAATGAGCGTCATTATGA
1 AAAATAAAA-TATT-TTAAGTACTATTTTAATAAAAGAAA-AATAGT-AGTAT-C
1869503 AAAATAAAATATTTTAAGTACTATTTTAATAAAAGAAAAATAGTAGTATC
1 AAAATAAAATATTTTAAGTACTATTTTAATAAAAGAAAAATAGTAGTATC
1869553 AAAATAAAAT
1 AAAATAAAAT
1869563 TTAGATGTTT
Statistics
Matches: 78, Mismatches: 26, Indels: 16
0.65 0.22 0.13
Matches are distributed among these distances:
49 6 0.08
50 30 0.38
51 16 0.21
52 20 0.26
53 6 0.08
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.33
Consensus pattern (50 bp):
AAAATAAAATATTTTAAGTACTATTTTAATAAAAGAAAAATAGTAGTATC
Found at i:1869548 original size:102 final size:102
Alignment explanation
Indices: 1869372--1869563 Score: 366
Period size: 102 Copynumber: 1.9 Consensus size: 102
1869362 TATCTTTATT
*
1869372 TTATGTGACTGAAATGAGTGTCATTATGAAAAATAAAATATTTTAAGTACTATTTTAATAAAAGA
1 TTATGTGACTGAAATGAGCGTCATTATGAAAAATAAAATATTTTAAGTACTATTTTAATAAAAGA
*
1869437 AAAATAGTAGTATCCAAATAAAATTATTGATAATTAA
66 AAAATAGTAGTATCAAAATAAAATTATTGATAATTAA
1869474 TTATGTGACTGAAATGAGCGTCATTATGAAAAATAAAATATTTTAAGTACTATTTTAATAAAAGA
1 TTATGTGACTGAAATGAGCGTCATTATGAAAAATAAAATATTTTAAGTACTATTTTAATAAAAGA
1869539 AAAATAGTAGTATCAAAATAAAATT
66 AAAATAGTAGTATCAAAATAAAATT
1869564 TAGATGTTTT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 88 1.00
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.34
Consensus pattern (102 bp):
TTATGTGACTGAAATGAGCGTCATTATGAAAAATAAAATATTTTAAGTACTATTTTAATAAAAGA
AAAATAGTAGTATCAAAATAAAATTATTGATAATTAA
Found at i:1885603 original size:37 final size:37
Alignment explanation
Indices: 1885551--1885627 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
1885541 GCATTATAGA
* *
1885551 GATAAACACTCCGAAAGCAACAATTACTTAGCTGATT
1 GATAAACACTCCGAAAGCAACAACTACTTAGCCGATT
*
1885588 GATAAACACTGCGAAAGCAACAACTACTTAGCCGATT
1 GATAAACACTCCGAAAGCAACAACTACTTAGCCGATT
1885625 GAT
1 GAT
1885628 CCTTTAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (37 bp):
GATAAACACTCCGAAAGCAACAACTACTTAGCCGATT
Found at i:1886983 original size:37 final size:37
Alignment explanation
Indices: 1886932--1887040 Score: 200
Period size: 37 Copynumber: 2.9 Consensus size: 37
1886922 AATTAGTTTC
*
1886932 AAATATGTACGCATATGATTTGAATCATGGAATAATT
1 AAATATGTATGCATATGATTTGAATCATGGAATAATT
1886969 AAATATGTATGCATATGATTTGAATCATGGAATAATT
1 AAATATGTATGCATATGATTTGAATCATGGAATAATT
*
1887006 AAATATGTATGCATATGATTTGAATCTTGGAATAA
1 AAATATGTATGCATATGATTTGAATCATGGAATAA
1887041 GGATGAAAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (37 bp):
AAATATGTATGCATATGATTTGAATCATGGAATAATT
Found at i:1908597 original size:181 final size:181
Alignment explanation
Indices: 1908294--1908654 Score: 706
Period size: 181 Copynumber: 2.0 Consensus size: 181
1908284 ATGAAAACGG
1908294 TCGTTTCAGATTCTTCAGATCACACAAACAAGATGAAAGAGAACTCTTTTCTTGCCCCTGATGTT
1 TCGTTTCAGATTCTTCAGATCACACAAACAAGATGAAAGAGAACTCTTTTCTTGCCCCTGATGTT
1908359 AGCCTTCAAGAACTTGGTATGTTTATTAGTAATATATGATTCTGGGATGCACGTTCTTCACTGCT
66 AGCCTTCAAGAACTTGGTATGTTTATTAGTAATATATGATTCTGGGATGCACGTTCTTCACTGCT
1908424 TTGAAATCGTTATCAATT-AAAGTAGAAGTTAATTTCATTTATTCCACTCC
131 TTGAAATCGTTATCAATTAAAAGTAGAAGTTAATTTCATTTATTCCACTCC
1908474 TCGTTTCAGATTCTTCAGATCCACACAAACAAGATGAAAGAGAACTCTTTTCTTGCCCCTGATGT
1 TCGTTTCAGATTCTTCAGAT-CACACAAACAAGATGAAAGAGAACTCTTTTCTTGCCCCTGATGT
1908539 TAGCCTTCAAGAACTTGGTATGTTTATTAGTAATATATGATTCTGGGATGCACGTTCTTCACTGC
65 TAGCCTTCAAGAACTTGGTATGTTTATTAGTAATATATGATTCTGGGATGCACGTTCTTCACTGC
1908604 TTTGAAATCGTTATCAATTAAAAGTAGAAGTTAATTTCATTTATTCCACTC
130 TTTGAAATCGTTATCAATTAAAAGTAGAAGTTAATTTCATTTATTCCACTC
1908655 TCCATCCTCT
Statistics
Matches: 179, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
180 20 0.11
181 128 0.72
182 31 0.17
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.37
Consensus pattern (181 bp):
TCGTTTCAGATTCTTCAGATCACACAAACAAGATGAAAGAGAACTCTTTTCTTGCCCCTGATGTT
AGCCTTCAAGAACTTGGTATGTTTATTAGTAATATATGATTCTGGGATGCACGTTCTTCACTGCT
TTGAAATCGTTATCAATTAAAAGTAGAAGTTAATTTCATTTATTCCACTCC
Found at i:1914910 original size:36 final size:36
Alignment explanation
Indices: 1914863--1914936 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
1914853 ATGCTTTCTC
1914863 TGTCACCTACCATATTCCTACATTGAAGACAGCTGA
1 TGTCACCTACCATATTCCTACATTGAAGACAGCTGA
1914899 TGTCACCTACCATATTCCTACATTGAAGACAGCTGA
1 TGTCACCTACCATATTCCTACATTGAAGACAGCTGA
1914935 TG
1 TG
1914937 CAAAGAAGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (36 bp):
TGTCACCTACCATATTCCTACATTGAAGACAGCTGA
Found at i:1917547 original size:13 final size:13
Alignment explanation
Indices: 1917529--1917560 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1917519 ATATTTAAAA
*
1917529 TTTAATTATATTT
1 TTTAATTATACTT
1917542 TTTAATTATACTT
1 TTTAATTATACTT
1917555 TTTAAT
1 TTTAAT
1917561 AAGTTTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTAATTATACTT
Found at i:1923075 original size:2 final size:2
Alignment explanation
Indices: 1923068--1923095 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1923058 TTTGACATAA
1923068 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
1923096 TATTTTTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1926360 original size:13 final size:13
Alignment explanation
Indices: 1926341--1926389 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
1926331 ATATATATAT
1926341 ATATATTATATAAA
1 ATATATT-TATAAA
1926355 AT-TATTTA-AATA
1 ATATATTTATAA-A
1926367 ATATATTTATAAA
1 ATATATTTATAAA
1926380 ATATATTTAT
1 ATATATTTAT
1926390 TATTATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 2 0.06
12 5 0.16
13 21 0.66
14 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATATATTTATAAA
Found at i:1936464 original size:99 final size:102
Alignment explanation
Indices: 1936290--1936492 Score: 367
Period size: 99 Copynumber: 2.0 Consensus size: 102
1936280 AGCTCATATT
1936290 TCTAGGTTTCTGCTGCATCATCAATCGCTAGCATGCATTGTCACAGTAAACTGAGAACTTTCGCT
1 TCTAGGTTTCTGCTG-A-CATCAATCGCTAGCATGCATTGTCACAGTAAACTGAGAACTTTCGCT
1936355 GTCATTTTTGCAGACG-C-CAGTAAAGCTAACATGCAAG
64 GTCATTTTTGCAGACGCCACAGTAAAGCTAACATGCAAG
1936392 TCTAGGTTTCTGCTG-CATCAATCGCTAGCATGCATTGTCACAGTAAACTGAGAACTTTCGCTGT
1 TCTAGGTTTCTGCTGACATCAATCGCTAGCATGCATTGTCACAGTAAACTGAGAACTTTCGCTGT
1936456 CATTTTTGCAGACGCCACAGTAAAGCTAACATGCAAG
66 CATTTTTGCAGACGCCACAGTAAAGCTAACATGCAAG
1936493 AACACCAAGT
Statistics
Matches: 99, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
99 63 0.64
100 1 0.01
101 20 0.20
102 15 0.15
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (102 bp):
TCTAGGTTTCTGCTGACATCAATCGCTAGCATGCATTGTCACAGTAAACTGAGAACTTTCGCTGT
CATTTTTGCAGACGCCACAGTAAAGCTAACATGCAAG
Found at i:1937570 original size:47 final size:47
Alignment explanation
Indices: 1937501--1937602 Score: 195
Period size: 47 Copynumber: 2.2 Consensus size: 47
1937491 AGATCATTTT
1937501 ATAAATTTTAATAATCGAAAAGTTCAACAATACAACGTCTTATAATC
1 ATAAATTTTAATAATCGAAAAGTTCAACAATACAACGTCTTATAATC
*
1937548 ATAAATTTTAATAATCGAAAAGTTCAACAATGCAACGTCTTATAATC
1 ATAAATTTTAATAATCGAAAAGTTCAACAATACAACGTCTTATAATC
1937595 ATAAATTT
1 ATAAATTT
1937603 AATTATAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (47 bp):
ATAAATTTTAATAATCGAAAAGTTCAACAATACAACGTCTTATAATC
Found at i:1943524 original size:29 final size:30
Alignment explanation
Indices: 1943467--1943537 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
1943457 ACTAAATGAT
1943467 GAACATGAACACTATAAAAAATAAATAAAC
1 GAACATGAACACTATAAAAAATAAATAAAC
* *
1943497 G-ACATGAACACTATATCAAAA-AATTAAAC
1 GAACATGAACACTATA-AAAAATAAATAAAC
*
1943526 GAAAATGAACAC
1 GAACATGAACAC
1943538 ATTTAAAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 22 0.61
30 14 0.39
ACGTcount: A:0.59, C:0.15, G:0.08, T:0.17
Consensus pattern (30 bp):
GAACATGAACACTATAAAAAATAAATAAAC
Found at i:1944130 original size:16 final size:17
Alignment explanation
Indices: 1944109--1944140 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1944099 ATAAGGATTA
1944109 TTTAAAA-TTAATTATT
1 TTTAAAATTTAATTATT
1944125 TTTAAAATTTAATTAT
1 TTTAAAATTTAATTAT
1944141 AATTTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAAAATTTAATTATT
Found at i:1944166 original size:28 final size:28
Alignment explanation
Indices: 1944130--1944191 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1944120 TTATTTTTAA
* * *
1944130 AATTTAATTATAATTTTAATAGAATTAT
1 AATTAAATTATAATTTTAATAAAATAAT
* *
1944158 AATTAAATTATATTTTTATTAAAATAAT
1 AATTAAATTATAATTTTAATAAAATAAT
1944186 AATTAA
1 AATTAA
1944192 TTAAAGTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
AATTAAATTATAATTTTAATAAAATAAT
Found at i:1944921 original size:26 final size:28
Alignment explanation
Indices: 1944868--1944932 Score: 79
Period size: 26 Copynumber: 2.5 Consensus size: 28
1944858 AAACTACTTA
*
1944868 AATTAATTATAA--TTTAATAGAATTAT
1 AATTAATTATAATTTTTAATAGAATAAT
1944894 AATTAATTATAATTTTTAA-A-AATAAT
1 AATTAATTATAATTTTTAATAGAATAAT
1944920 AATTAA--ATAATTT
1 AATTAATTATAATTT
1944933 AATTTGTTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
24 7 0.19
26 23 0.64
27 1 0.03
28 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
AATTAATTATAATTTTTAATAGAATAAT
Found at i:1944995 original size:17 final size:16
Alignment explanation
Indices: 1944966--1945003 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
1944956 AGTTATATAA
1944966 TTAAAAATAATTAATT
1 TTAAAAATAATTAATT
*
1944982 TTAATAAATGATTAATT
1 TTAA-AAATAATTAATT
1944999 TTAAA
1 TTAAA
1945004 TAGATTCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TTAAAAATAATTAATT
Found at i:1945483 original size:60 final size:59
Alignment explanation
Indices: 1945384--1945529 Score: 143
Period size: 60 Copynumber: 2.4 Consensus size: 59
1945374 ATAGTTTGGG
** * * *
1945384 ATGAAATTGGAATGTTCAGAAAGTTTATAGACCAATTAGAATGA-AGGCCATAATTTAGGG
1 ATGAAATTAAAATGTTTA-AAAGTTTATAGACCAATTAGAATGATA-GCCATAATTTAAGA
* * * *
1945444 ATGAAGTTAAAATGTTTAAAAGTTTA-AGGACTAATTTAGAATGATAGTCATACTTTAAGA
1 ATGAAATTAAAATGTTTAAAAGTTTATA-GACCAA-TTAGAATGATAGCCATAATTTAAGA
* *
1945504 ATGAAATTGAAATATTTAAAAGTTTA
1 ATGAAATTAAAATGTTTAAAAGTTTA
1945530 GGAATCAATT
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
58 1 0.01
59 13 0.18
60 56 0.79
61 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.33
Consensus pattern (59 bp):
ATGAAATTAAAATGTTTAAAAGTTTATAGACCAATTAGAATGATAGCCATAATTTAAGA
Found at i:1945540 original size:60 final size:60
Alignment explanation
Indices: 1945444--1945563 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 60
1945434 TAATTTAGGG
* * * * *
1945444 ATGAAGTTAAAATGTTTAAAAGTTTAAGGACTAATTTAGAATGATAGTCATACTTT-AAGA
1 ATGAAATTAAAATATTTAAAAGTTTAAGGAATAATTTA-AATAAGAGTCATACTTTGAAGA
*
1945504 ATGAAATTGAAATATTTAAAAGTTT-AGGAATCAATTTAAATAAGAGTCATACTTTGAAGA
1 ATGAAATTAAAATATTTAAAAGTTTAAGGAAT-AATTTAAATAAGAGTCATACTTTGAAGA
1945564 TATACGATGC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 20 0.38
60 32 0.62
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (60 bp):
ATGAAATTAAAATATTTAAAAGTTTAAGGAATAATTTAAATAAGAGTCATACTTTGAAGA
Found at i:1949416 original size:41 final size:42
Alignment explanation
Indices: 1949359--1949441 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 42
1949349 GTTGGCTGCT
1949359 ACATTCATTTTCATGGGACGTGTTGT-TATAGGTGTTTGAAG
1 ACATTCATTTTCATGGGACGTGTTGTATATAGGTGTTTGAAG
1949400 ACATTCATTTTCATGGGACGTGTTGTATATAGGTGTTTGAAG
1 ACATTCATTTTCATGGGACGTGTTGTATATAGGTGTTTGAAG
1949442 GCAAATACTT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 26 0.63
42 15 0.37
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.41
Consensus pattern (42 bp):
ACATTCATTTTCATGGGACGTGTTGTATATAGGTGTTTGAAG
Found at i:1951365 original size:21 final size:21
Alignment explanation
Indices: 1951314--1951365 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1951304 ACTTATATAT
* *
1951314 ATATTATTTTTAATTAAATTA
1 ATATTATTTTTAATAAAAATA
*
1951335 TTATTATTTTTGAATAAAAATA
1 ATATTATTTTT-AATAAAAATA
1951357 ATATT-TTTT
1 ATATTATTTT
1951366 ATTATTTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATATTATTTTTAATAAAAATA
Found at i:1954647 original size:182 final size:180
Alignment explanation
Indices: 1954441--1954907 Score: 638
Period size: 182 Copynumber: 2.6 Consensus size: 180
1954431 GATCCAAATT
* * * **
1954441 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAAGTAAAA-TATGATAAAACCGGTATCAAAATGATA
* * * * *
1954506 AAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
65 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTC
* **
1954571 GTGAATTTAAAAGAGAAGCAATTTTAAATCCTATAAAGTGTCGATACTTTTA
129 GTGAATTTAAAAGAGAAGCAATTTTAAAGCCTATAAAGTGTCGATACTTAAA
* *
1954623 AAAAATGTATCGATCCAAAACGATATACCATGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAAGT-AAAATATGATAAAACCGGTATCAAAATGATA
* * * *
1954688 AAATCGGTAAAACGTTACCAGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTTG
65 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCG
* ** *
1954753 TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTAAA
130 TGAATTTAAAAGAGAAGCAATTTTAAAGCCTATAAAGTGTCGATACTTAAA
* * *
1954804 AAAAATATATCGATCCACAACG--ATAACAAGTAAAATATGATAAAACCGGTACCAAAATGAT-A
1 AAAAATGTATCGATCCAAAACGATATAACAAGTAAAATATGATAAAACCGGTATCAAAATGATAA
1954866 AACC--TAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
66 AACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
1954908 CGTAAGTACG
Statistics
Matches: 255, Mismatches: 29, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
175 36 0.14
177 4 0.02
178 29 0.11
179 7 0.03
181 83 0.33
182 92 0.36
183 4 0.02
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.27
Consensus pattern (180 bp):
AAAAATGTATCGATCCAAAACGATATAACAAGTAAAATATGATAAAACCGGTATCAAAATGATAA
AACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCGT
GAATTTAAAAGAGAAGCAATTTTAAAGCCTATAAAGTGTCGATACTTAAA
Found at i:1957131 original size:21 final size:21
Alignment explanation
Indices: 1957101--1957165 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
1957091 AAGACAATCA
* *
1957101 AGAGTTGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
1957122 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
1957143 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1957164 AG
1 AG
1957166 GCATAAGGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.42, C:0.09, G:0.31, T:0.18
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1957260 original size:32 final size:33
Alignment explanation
Indices: 1957199--1957263 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1957189 AAATAGATGG
*
1957199 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*
1957232 AGTGGTGAAAGAAGTTG-GGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1957264 TATTAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1958964 original size:19 final size:19
Alignment explanation
Indices: 1958942--1958990 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1958932 AATGTAGGGT
1958942 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1958961 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1958980 TAATTTTGTAT
1 TAATTTTGTAT
1958991 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1960568 original size:598 final size:600
Alignment explanation
Indices: 1959224--1960785 Score: 2752
Period size: 598 Copynumber: 2.6 Consensus size: 600
1959214 AATTTACAAT
* * *
1959224 ATGGTAAACAGGATGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
1959289 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
1959354 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTATAGTTTGTGTCGATATTTTTGGTCCAG
* *
1959419 AATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAGAGTGTCGATCCGATA
196 AATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
* * *
1959484 AACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGATACAAGTATACCG
261 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCG
* *
1959549 GTTTTATGAGAGAATATGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGG
326 GTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCAATATTTTTGG
* * *
1959614 TCCAGAATGAATGGCAAACAGGGTGTAATAATAAAGTGTCGATTCATATATAAAAAGTGTCGATC
391 TCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATTCACATATAAAAAGTGTCGATC
1959679 CCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTA
456 CCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTA
*
1959744 TACCGATTTTATGAGAGAATAGGTCTAAATAATGTGTCGATACTTTTGTAGTTTGTGTCGATATT
521 TACCGATTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATT
1959809 TTTGGTCCAGAATGA
586 TTTGGTCCAGAATGA
*
1959824 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
1959889 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGATTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * * *
1959954 ATGAGAGAATAGGTCTAAATAATGTTTCAACACTTTTTTAGTTTGTGTTGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTATAGTTTGTGTCGATATTTTTGGTCCAG
*
1960019 AATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
196 AATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
*
1960084 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATATCG
261 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCG
*
1960149 GTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCAATATTTTTGG
326 GTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCAATATTTTTGG
1960214 TCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGA-TC-CATATAAAAAGTGTCGATC
391 TCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATTCACATATAAAAAGTGTCGATC
* *
1960277 CGATAAATATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTA
456 CCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTA
*
1960342 TACCTG-TTTTATGAGAGAATAGGTCTAAATAATGTTTCGACACTTTTGTAGTTTGTGTCGATAT
521 TACC-GATTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATAT
1960406 TTTTGGTCCAGAATGA
585 TTTTGGTCCAGAATGA
* *
1960422 ATGGCAAACAGGGTGCAACAATAAACTGTCAATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
1960487 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACTGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
1960552 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTATAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTATAGTTTGTGTCGATATTTTTGGTCCAG
* *
1960617 ATTGAATGGCAAATAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
196 AATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
* * *
1960682 AACATCTAAACCCATAAGTATAATGTATTAGGTAATTTTTCAATCTAACCAGTACAAGTATACCG
261 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCG
1960747 GTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACT
326 GTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACT
1960786 GTTTAATGTT
Statistics
Matches: 916, Mismatches: 45, Indels: 4
0.95 0.05 0.00
Matches are distributed among these distances:
598 504 0.55
599 3 0.00
600 409 0.45
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (600 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTATAGTTTGTGTCGATATTTTTGGTCCAG
AATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCG
GTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCAATATTTTTGG
TCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATTCACATATAAAAAGTGTCGATC
CCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTA
TACCGATTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATT
TTTGGTCCAGAATGA
Found at i:1960804 original size:200 final size:200
Alignment explanation
Indices: 1959224--1960785 Score: 2732
Period size: 200 Copynumber: 7.8 Consensus size: 200
1959214 AATTTACAAT
* * *
1959224 ATGGTAAACAGGATGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
1959289 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
1959354 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1959419 AATGA
196 AATGA
* * *
1959424 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAGAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * *
1959489 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGATACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
1959554 ATGAGAGAATATGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1959619 AATGA
196 AATGA
* * *
1959624 ATGGCAAACAGGGTGTAATAATAAAGTGTCGATTCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
1959689 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGATTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
1959754 ATGAGAGAATAGGTCTAAATAATGTGTCGATACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1959819 AATGA
196 AATGA
*
1959824 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
1959889 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGATTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * * *
1959954 ATGAGAGAATAGGTCTAAATAATGTTTCAACACTTTTTTAGTTTGTGTTGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1960019 AATGA
196 AATGA
1960024 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
1960089 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATATCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
1960154 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCAATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1960219 AATGA
196 AATGA
* *
1960224 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCGATAAATAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
1960287 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCTGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
1960352 ATGAGAGAATAGGTCTAAATAATGTTTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
1960417 AATGA
196 AATGA
* *
1960422 ATGGCAAACAGGGTGCAACAATAAACTGTCAATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
1960487 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACTGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
1960552 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTATAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
*
1960617 ATTGA
196 AATGA
* *
1960622 ATGGCAAATAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * *
1960687 CTAAACCCATAAGTATAATGTATTAGGTAATTTTTCAATCTAACCAGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
1960752 ATGAGAGAATAGGTCTAAATAATGTATCGACACT
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACT
1960786 GTTTAATGTT
Statistics
Matches: 1300, Mismatches: 60, Indels: 4
0.95 0.04 0.00
Matches are distributed among these distances:
198 190 0.15
200 1110 0.85
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:1963911 original size:182 final size:183
Alignment explanation
Indices: 1963544--1963942 Score: 743
Period size: 182 Copynumber: 2.2 Consensus size: 183
1963534 AAGTTTTCAT
1963544 ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCA
1 ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCA
1963609 AAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAA
66 AAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAA
1963674 CCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGAC
131 CCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGAC
* *
1963727 ACTTTTTAATATTGTGTCGGTACTTTATATCCAGAATGGAATAAAAATGTGTCGATACCTTGTCA
1 ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCA
1963792 AAAAGTGTCGACATTTACACATCGGAA-CCAGAATTATAATGTAATAGATAATTTTGTAATATAA
66 AAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAA
*
1963856 CTGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGAC
131 CCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGAC
1963909 ACTTTTTAAT-TT-TGTCGGTAC-TTATGTCCAGAAT
1 ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAAT
1963943 TATAATGTAC
Statistics
Matches: 212, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
179 12 0.06
180 9 0.04
181 2 0.01
182 99 0.47
183 90 0.42
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (183 bp):
ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCA
AAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAA
CCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGAC
Found at i:1964025 original size:117 final size:120
Alignment explanation
Indices: 1963819--1964062 Score: 424
Period size: 117 Copynumber: 2.1 Consensus size: 120
1963809 CACATCGGAA
*
1963819 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACTGGTATAAATATACCGGTTTTATGAGC
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
1963884 GAATAGGTCTACAACCTATATCGACACTTTTTAAT-TT-TGTCGGTAC-TTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
* *
1963936 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTG-G
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTA-TGAG
1964000 CGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
65 CGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
1964056 CCAGAAT
1 CCAGAAT
1964063 GGAAGAAAAA
Statistics
Matches: 120, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
117 94 0.78
118 4 0.03
119 9 0.08
120 13 0.11
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (120 bp):
CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
Found at i:1965156 original size:13 final size:13
Alignment explanation
Indices: 1965138--1965164 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1965128 AAGTAATCCG
1965138 CTTTCAACTCGTT
1 CTTTCAACTCGTT
1965151 CTTTCAACTCGTT
1 CTTTCAACTCGTT
1965164 C
1 C
1965165 ATACGCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.07, T:0.44
Consensus pattern (13 bp):
CTTTCAACTCGTT
Found at i:1967005 original size:23 final size:23
Alignment explanation
Indices: 1966974--1967046 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
1966964 ATAGGTGAAA
*
1966974 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
1966997 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1967020 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1967043 ATAT
1 ATAT
1967047 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1967492 original size:23 final size:23
Alignment explanation
Indices: 1967461--1967533 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
1967451 ATAGGTAAAA
*
1967461 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
1967484 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1967507 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1967530 ATAT
1 ATAT
1967534 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1967722 original size:489 final size:488
Alignment explanation
Indices: 1966787--1968420 Score: 2915
Period size: 489 Copynumber: 3.4 Consensus size: 488
1966777 GACCCAAATT
1966787 AATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTA
1 AATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTA
1966852 ATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAATTGAAACATAAATTACATAACTTT-
66 ATATTGTAGGTGGAAAACATGAAACACTATT--AAAAAAATTGAAACATAAATTACATAACTTTA
* *
1966916 AAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTGAATATAATAGGTGAAAATATGAT
129 AAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGAT
1966981 GTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATA
194 GTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATA
1967046 TTGTAAAGTATCTATCC-TTTTAT-AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTT
259 TTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATAC-TTTTTCACTGTGGAAAACATTAATTT
1967109 AAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATT
323 AAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATT
1967174 TTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATT
388 TTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATT
* *
1967239 ATTATCTTTGGTTAATATTGTTAAATTTAAAATCTA
453 ATTATATTTGGTTAATATTGTTAAATTTAAATTCTA
*
1967275 AATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTA
1 AATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTA
1967340 ATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAA
66 ATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAA
1967405 AAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGT
131 AAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGT
1967470 AATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATT
196 AATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATT
* *
1967535 GTAAAGTATTTATCCTTTTTATAAAAGTGTCCATACTTTCTTCACTATGGAAAACATTAATTTAA
261 GTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTT-TTCACTGTGGAAAACATTAATTTAA
1967600 GGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTT
325 GGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTT
* *
1967665 TTACGTTACGATATATATTATTATTAAATTAAAAACAGTAAACATATATATTACATATTTATTAT
390 TTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTAT
1967730 TATATTTGGTTAATATTGTTAAATTTAAATTCTA
455 TATATTTGGTTAATATTGTTAAATTTAAATTCTA
*
1967764 AATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGGAAATGAAATTATTAAATTA
1 AATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTA
1967829 ATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAA
66 ATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAA
* **
1967894 AAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGACAT
131 AAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGT
1967959 AATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATT
196 AATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATT
* ** *
1968024 GTAAAATATCTATCCTTTTTATAAAAGTGTTTATACTTATTTAACTGTGGAAAACATTAATTTAA
261 GTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTT-TTTCACTGTGGAAAACATTAATTTAA
* * **
1968089 GGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAATTATATGTATCTAATGATTTATTTT
325 GGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTT
* *
1968154 TTATGTTACGGTATATATTATCATTAAATTAAAAACAATAAAC--ATATA-TA-ATATTTATTAT
390 TTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTAT
1968215 TATATTTGGTTAATATTGTTAAATTTAAATTCTA
455 TATATTTGGTTAATATTGTTAAATTTAAATTCTA
*
1968249 AATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTA
1 AATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTA
* *
1968314 ATATTGTAGGTAGAAAACATGAAACACTATT-AAAAAATTAAAACATAAATTACATAACTTTAAA
66 ATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAA
*
1968378 AAAAGTATCGATCCTTTTTATAAAAAAGTATGGACACTTTCAA
131 AAAAGTATCGATCATTTTTAT-AAAAAGTATGGACACTTTCAA
1968421 CATATTATAA
Statistics
Matches: 1109, Mismatches: 31, Indels: 15
0.96 0.03 0.01
Matches are distributed among these distances:
484 53 0.05
485 160 0.14
486 33 0.03
487 149 0.13
488 104 0.09
489 609 0.55
490 1 0.00
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.39
Consensus pattern (488 bp):
AATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTA
ATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAA
AAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGT
AATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATT
GTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAG
GTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTT
TACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATT
ATATTTGGTTAATATTGTTAAATTTAAATTCTA
Found at i:1967984 original size:23 final size:23
Alignment explanation
Indices: 1967958--1968022 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
1967948 AAATATGACA
1967958 TAATAGGTAGCGCTTATATAATG
1 TAATAGGTAGCGCTTATATAATG
*
1967981 TAATAGGTAGCGTTTATATAATG
1 TAATAGGTAGCGCTTATATAATG
*
1968004 TAATAGGTAGTGCTTATAT
1 TAATAGGTAGCGCTTATAT
1968023 TGTAAAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (23 bp):
TAATAGGTAGCGCTTATATAATG
Found at i:1972006 original size:22 final size:22
Alignment explanation
Indices: 1971981--1972022 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1971971 AATAAAAATA
1971981 ATGAATATTTA-AAAAAAATTGT
1 ATGAAT-TTTATAAAAAAATTGT
*
1972003 ATGAATTTTATTAAAAAATT
1 ATGAATTTTATAAAAAAATT
1972023 TAATAGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (22 bp):
ATGAATTTTATAAAAAAATTGT
Found at i:1972905 original size:13 final size:13
Alignment explanation
Indices: 1972887--1972916 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1972877 GTCATAACCC
1972887 GACCCGACCCGTT
1 GACCCGACCCGTT
1972900 GACCCGACCCGTT
1 GACCCGACCCGTT
1972913 GACC
1 GACC
1972917 GTTAACCGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1975421 original size:24 final size:24
Alignment explanation
Indices: 1975393--1975457 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
1975383 TTTCTATTAT
* *
1975393 AATACCTGACCCGGATTCTGATCG
1 AATACTTGACCTGGATTCTGATCG
* * *
1975417 GATACTTGACCTGGATTTTGATTG
1 AATACTTGACCTGGATTCTGATCG
1975441 AATACTTGACCTGGATT
1 AATACTTGACCTGGATT
1975458 ATGTTATGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.34
Consensus pattern (24 bp):
AATACTTGACCTGGATTCTGATCG
Found at i:1975676 original size:2 final size:2
Alignment explanation
Indices: 1975669--1975737 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
1975659 TGGGGGTATT
1975669 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1975711 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1975738 GTTTTAAAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1980132 original size:24 final size:24
Alignment explanation
Indices: 1980105--1980195 Score: 110
Period size: 24 Copynumber: 3.8 Consensus size: 24
1980095 TTTGATTATA
*
1980105 ATACCTGACCTGGATTCTGATCGG
1 ATACCTGACCTGGATTATGATCGG
* *
1980129 ATACCTGACCTGGATTATGATTGA
1 ATACCTGACCTGGATTATGATCGG
* * * *
1980153 ATACTTGACCTGAATTTTGATCTG
1 ATACCTGACCTGGATTATGATCGG
*
1980177 ATACTTGACCTGGATTATG
1 ATACCTGACCTGGATTATG
1980196 TTATGATTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (24 bp):
ATACCTGACCTGGATTATGATCGG
Found at i:1980162 original size:48 final size:48
Alignment explanation
Indices: 1980104--1980195 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
1980094 ATTTGATTAT
*
1980104 AATACCTGACCTGGATTCTGATCGGATACCTGACCTGGATTATGATTG
1 AATACCTGACCTGAATTCTGATCGGATACCTGACCTGGATTATGATTG
* * * *
1980152 AATACTTGACCTGAATTTTGATCTGATACTTGACCTGGATTATG
1 AATACCTGACCTGAATTCTGATCGGATACCTGACCTGGATTATG
1980196 TTATGATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (48 bp):
AATACCTGACCTGAATTCTGATCGGATACCTGACCTGGATTATGATTG
Found at i:1985863 original size:2 final size:2
Alignment explanation
Indices: 1985856--1985880 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1985846 TCTCTAGCTT
1985856 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1985881 TTAGGTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1986918 original size:32 final size:31
Alignment explanation
Indices: 1986882--1986957 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
1986872 GGGGCCGTGA
*
1986882 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** **
1986914 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
1986945 AGCCTACCTAAGA
1 GGCCTACCTAAGA
1986958 GTCACATTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.14
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:1986940 original size:63 final size:63
Alignment explanation
Indices: 1986834--1986957 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
1986824 CCCTAAGGGA
* * *
1986834 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTACCTAAGAAC
* *
1986897 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
1986958 GTCACATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 2 0.04
63 49 0.92
64 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:1987839 original size:7 final size:7
Alignment explanation
Indices: 1987827--1987869 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
1987817 GTCAAAGAAA
1987827 GTCAACG
1 GTCAACG
1987834 GTCAACG
1 GTCAACG
1987841 GTC-ACG
1 GTCAACG
1987847 GTCAACG
1 GTCAACG
1987854 GTC-ACG
1 GTCAACG
1987860 GTCAACG
1 GTCAACG
1987867 GTC
1 GTC
1987870 GGGTCGGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.35
7 22 0.65
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:1987849 original size:13 final size:13
Alignment explanation
Indices: 1987831--1987869 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1987821 AAGAAAGTCA
1987831 ACGGTCAACGGTC
1 ACGGTCAACGGTC
1987844 ACGGTCAACGGTC
1 ACGGTCAACGGTC
1987857 ACGGTCAACGGTC
1 ACGGTCAACGGTC
1987870 GGGTCGGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:1987852 original size:20 final size:20
Alignment explanation
Indices: 1987827--1987869 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
1987817 GTCAAAGAAA
1987827 GTCAACGGTCAACGGTCACG
1 GTCAACGGTCAACGGTCACG
1987847 GTCAACGGTC-ACGGTCAACG
1 GTCAACGGTCAACGGTC-ACG
1987867 GTC
1 GTC
1987870 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.16
Consensus pattern (20 bp):
GTCAACGGTCAACGGTCACG
Found at i:1987881 original size:17 final size:17
Alignment explanation
Indices: 1987859--1987899 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1987849 CAACGGTCAC
*
1987859 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1987876 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1987893 GGTCAAC
1 GGTCAAC
1987900 CCGGTTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:1987917 original size:19 final size:20
Alignment explanation
Indices: 1987893--1987960 Score: 95
Period size: 19 Copynumber: 3.5 Consensus size: 20
1987883 AGTCGGGTCG
*
1987893 GGTCAACCCGGTTCAG-ACC
1 GGTCAAACCGGTTCAGAACC
1987912 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAGAACC
* *
1987931 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTCAGAACC
1987951 GGTCAAACCG
1 GGTCAAACCG
1987961 ATTTTCCAGC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
18 1 0.02
19 30 0.68
20 13 0.30
ACGTcount: A:0.28, C:0.31, G:0.25, T:0.16
Consensus pattern (20 bp):
GGTCAAACCGGTTCAGAACC
Found at i:1987930 original size:10 final size:10
Alignment explanation
Indices: 1987895--1987960 Score: 66
Period size: 9 Copynumber: 6.8 Consensus size: 10
1987885 TCGGGTCGGG
*
1987895 TCAACCCGGT
1 TCAAACCGGT
*
1987905 TCAGACCGG-
1 TCAAACCGGT
1987914 TCAAACCGGT
1 TCAAACCGGT
*
1987924 TCGAACCGG-
1 TCAAACCGGT
1987933 TCAAACCGGT
1 TCAAACCGGT
*
1987943 TCAAAACTGG-
1 TC-AAACCGGT
1987953 TCAAACCG
1 TCAAACCG
1987961 ATTTTCCAGC
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
9 21 0.46
10 19 0.41
11 6 0.13
ACGTcount: A:0.29, C:0.32, G:0.23, T:0.17
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1991954 original size:849 final size:849
Alignment explanation
Indices: 1990317--1992017 Score: 3402
Period size: 849 Copynumber: 2.0 Consensus size: 849
1990307 AATATATATG
1990317 TATTCATCAGTTGATCTGTACTCCGAAAAGGGTAACACTTTTCTGTTTTACATTACGACCTGATT
1 TATTCATCAGTTGATCTGTACTCCGAAAAGGGTAACACTTTTCTGTTTTACATTACGACCTGATT
1990382 CAAATCCATCTACAGCTTTATCTTCATTCAACTTACTACAAGTCTTACTGTAATTCTTCCCCCTC
66 CAAATCCATCTACAGCTTTATCTTCATTCAACTTACTACAAGTCTTACTGTAATTCTTCCCCCTC
1990447 AAACTCAGCTCCAAGTCCACTGCCAAATCATCCACTCCAGACGTATTAGTCCCATTCTTATTGCC
131 AAACTCAGCTCCAAGTCCACTGCCAAATCATCCACTCCAGACGTATTAGTCCCATTCTTATTGCC
1990512 CTCGTTGATGCAACAGCTTTCACCACTCACATCGATGAGGAAGAAACTTCTGCCATTTTGATTCC
196 CTCGTTGATGCAACAGCTTTCACCACTCACATCGATGAGGAAGAAACTTCTGCCATTTTGATTCC
1990577 CACCAGGGCACTCACACATGTAAAATGTCAAGGTATCTTTCTCACCAAGTTTCTTCTCCTTCACG
261 CACCAGGGCACTCACACATGTAAAATGTCAAGGTATCTTTCTCACCAAGTTTCTTCTCCTTCACG
1990642 AAACGGCTCCATCCCCTAGTGAAAACAAAGCTTTGGCTACTCCTCCAATAACAGTAACGAAATTT
326 AAACGGCTCCATCCCCTAGTGAAAACAAAGCTTTGGCTACTCCTCCAATAACAGTAACGAAATTT
1990707 CCATCTCACCATTAACTTGTCGTAGAAGACAAGTTCAATGTCTTCGACACCACCGCCGACCGAAC
391 CCATCTCACCATTAACTTGTCGTAGAAGACAAGTTCAATGTCTTCGACACCACCGCCGACCGAAC
1990772 TAATGTGAGGGAAGTGTTTAACGGCGTATTTTTTAGGGATCACGAGCCTGTTAAGCTTTCCGACA
456 TAATGTGAGGGAAGTGTTTAACGGCGTATTTTTTAGGGATCACGAGCCTGTTAAGCTTTCCGACA
1990837 TCGCTCGGTGTTAATTCCTTTTGAAAAAGTTGCATGCATGAGAACTGTGTATCACCATGCACAAG
521 TCGCTCGGTGTTAATTCCTTTTGAAAAAGTTGCATGCATGAGAACTGTGTATCACCATGCACAAG
1990902 CTTCTTGTTTAGATAAGTGGTCAATTTCCCATCATTTCTAGACAAGATCTTGACGAATTCTTCCA
586 CTTCTTGTTTAGATAAGTGGTCAATTTCCCATCATTTCTAGACAAGATCTTGACGAATTCTTCCA
1990967 GCTTGGCTTGATACGAACCGTCCCTGATCATGTTCAGTACATCCTCGGTCGAATAAAGGTGTTGA
651 GCTTGGCTTGATACGAACCGTCCCTGATCATGTTCAGTACATCCTCGGTCGAATAAAGGTGTTGA
1991032 AAGTCCAGTTCTTGGATGTTGAGATCGGTCCACGGGAAGTTCCTATGAGTTTCGCCGCCACCGCT
716 AAGTCCAGTTCTTGGATGTTGAGATCGGTCCACGGGAAGTTCCTATGAGTTTCGCCGCCACCGCT
1991097 ACGTAGCTTGATGGCGGAGCTGTCGTAAGCCATGGCGGCTTCTCTCTTGGACTTGAACGTCCCAA
781 ACGTAGCTTGATGGCGGAGCTGTCGTAAGCCATGGCGGCTTCTCTCTTGGACTTGAACGTCCCAA
1991162 GCCA
846 GCCA
1991166 TATTCATCAGTTGATCTGTACTCCGAAAAGGGTAACACTTTTCTGTTTTACATTACGACCTGATT
1 TATTCATCAGTTGATCTGTACTCCGAAAAGGGTAACACTTTTCTGTTTTACATTACGACCTGATT
1991231 CAAATCCATCTACAGCTTTATCTTCATTCAACTTACTACAAGTCTTACTGTAATTCTTCCCCCTC
66 CAAATCCATCTACAGCTTTATCTTCATTCAACTTACTACAAGTCTTACTGTAATTCTTCCCCCTC
1991296 AAACTCAGCTCCAAGTCCACTGCCAAATCATCCACTCCAGACGTATTAGTCCCATTCTTATTGCC
131 AAACTCAGCTCCAAGTCCACTGCCAAATCATCCACTCCAGACGTATTAGTCCCATTCTTATTGCC
1991361 CTCGTTGATGCAACAGCTTTCACCACTCACATCGATGAGGAAGAAACTTCTGCCATTTTGATTCC
196 CTCGTTGATGCAACAGCTTTCACCACTCACATCGATGAGGAAGAAACTTCTGCCATTTTGATTCC
1991426 CACCAGGGCACTCACACATGTAAAATGTCAAGGTATCTTTCTCACCAAGTTTCTTCTCCTTCACG
261 CACCAGGGCACTCACACATGTAAAATGTCAAGGTATCTTTCTCACCAAGTTTCTTCTCCTTCACG
1991491 AAACGGCTCCATCCCCTAGTGAAAACAAAGCTTTGGCTACTCCTCCAATAACAGTAACGAAATTT
326 AAACGGCTCCATCCCCTAGTGAAAACAAAGCTTTGGCTACTCCTCCAATAACAGTAACGAAATTT
1991556 CCATCTCACCATTAACTTGTCGTAGAAGACAAGTTCAATGTCTTCGACACCACCGCCGACCGAAC
391 CCATCTCACCATTAACTTGTCGTAGAAGACAAGTTCAATGTCTTCGACACCACCGCCGACCGAAC
1991621 TAATGTGAGGGAAGTGTTTAACGGCGTATTTTTTAGGGATCACGAGCCTGTTAAGCTTTCCGACA
456 TAATGTGAGGGAAGTGTTTAACGGCGTATTTTTTAGGGATCACGAGCCTGTTAAGCTTTCCGACA
1991686 TCGCTCGGTGTTAATTCCTTTTGAAAAAGTTGCATGCATGAGAACTGTGTATCACCATGCACAAG
521 TCGCTCGGTGTTAATTCCTTTTGAAAAAGTTGCATGCATGAGAACTGTGTATCACCATGCACAAG
1991751 CTTCTTGTTTAGATAAGTGGTCAATTTCCCATCATTTCTAGACAAGATCTTGACGAATTCTTCCA
586 CTTCTTGTTTAGATAAGTGGTCAATTTCCCATCATTTCTAGACAAGATCTTGACGAATTCTTCCA
1991816 GCTTGGCTTGATACGAACCGTCCCTGATCATGTTCAGTACATCCTCGGTCGAATAAAGGTGTTGA
651 GCTTGGCTTGATACGAACCGTCCCTGATCATGTTCAGTACATCCTCGGTCGAATAAAGGTGTTGA
1991881 AAGTCCAGTTCTTGGATGTTGAGATCGGTCCACGGGAAGTTCCTATGAGTTTCGCCGCCACCGCT
716 AAGTCCAGTTCTTGGATGTTGAGATCGGTCCACGGGAAGTTCCTATGAGTTTCGCCGCCACCGCT
1991946 ACGTAGCTTGATGGCGGAGCTGTCGTAAGCCATGGCGGCTTCTCTCTTGGACTTGAACGTCCCAA
781 ACGTAGCTTGATGGCGGAGCTGTCGTAAGCCATGGCGGCTTCTCTCTTGGACTTGAACGTCCCAA
1992011 GCCA
846 GCCA
1992015 TAT
1 TAT
1992018 CCGGTGATGG
Statistics
Matches: 852, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
849 852 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (849 bp):
TATTCATCAGTTGATCTGTACTCCGAAAAGGGTAACACTTTTCTGTTTTACATTACGACCTGATT
CAAATCCATCTACAGCTTTATCTTCATTCAACTTACTACAAGTCTTACTGTAATTCTTCCCCCTC
AAACTCAGCTCCAAGTCCACTGCCAAATCATCCACTCCAGACGTATTAGTCCCATTCTTATTGCC
CTCGTTGATGCAACAGCTTTCACCACTCACATCGATGAGGAAGAAACTTCTGCCATTTTGATTCC
CACCAGGGCACTCACACATGTAAAATGTCAAGGTATCTTTCTCACCAAGTTTCTTCTCCTTCACG
AAACGGCTCCATCCCCTAGTGAAAACAAAGCTTTGGCTACTCCTCCAATAACAGTAACGAAATTT
CCATCTCACCATTAACTTGTCGTAGAAGACAAGTTCAATGTCTTCGACACCACCGCCGACCGAAC
TAATGTGAGGGAAGTGTTTAACGGCGTATTTTTTAGGGATCACGAGCCTGTTAAGCTTTCCGACA
TCGCTCGGTGTTAATTCCTTTTGAAAAAGTTGCATGCATGAGAACTGTGTATCACCATGCACAAG
CTTCTTGTTTAGATAAGTGGTCAATTTCCCATCATTTCTAGACAAGATCTTGACGAATTCTTCCA
GCTTGGCTTGATACGAACCGTCCCTGATCATGTTCAGTACATCCTCGGTCGAATAAAGGTGTTGA
AAGTCCAGTTCTTGGATGTTGAGATCGGTCCACGGGAAGTTCCTATGAGTTTCGCCGCCACCGCT
ACGTAGCTTGATGGCGGAGCTGTCGTAAGCCATGGCGGCTTCTCTCTTGGACTTGAACGTCCCAA
GCCA
Found at i:1994535 original size:38 final size:36
Alignment explanation
Indices: 1994491--1994568 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 36
1994481 AAATTGTATC
* *
1994491 TAATTTTTTCATTTATTTTGATTTTGATTACTCATCGT
1 TAATTTTTT--TTTATTCTGATTTTAATTACTCATCGT
1994529 TAA---TTTTTTATTCTGATTTTAATTACTCATCGT
1 TAATTTTTTTTTATTCTGATTTTAATTACTCATCGT
1994562 TAATTTT
1 TAATTTT
1994569 GACCGTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
33 28 0.80
35 3 0.09
36 1 0.03
38 3 0.09
ACGTcount: A:0.23, C:0.10, G:0.06, T:0.60
Consensus pattern (36 bp):
TAATTTTTTTTTATTCTGATTTTAATTACTCATCGT
Found at i:1994546 original size:33 final size:33
Alignment explanation
Indices: 1994502--1994568 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
1994492 AATTTTTTCA
* *
1994502 TTTATTTTGATTTTGATTACTCATCGTTAATTT
1 TTTATTCTGATTTTAATTACTCATCGTTAATTT
1994535 TTTATTCTGATTTTAATTACTCATCGTTAATTT
1 TTTATTCTGATTTTAATTACTCATCGTTAATTT
1994568 T
1 T
1994569 GACCGTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.22, C:0.10, G:0.07, T:0.60
Consensus pattern (33 bp):
TTTATTCTGATTTTAATTACTCATCGTTAATTT
Found at i:2003854 original size:20 final size:20
Alignment explanation
Indices: 2003826--2003927 Score: 96
Period size: 20 Copynumber: 5.1 Consensus size: 20
2003816 GTAAAACCGT
* * *
2003826 AACGCGTATCCATAAATCAC
1 AACGTGTATCCGTAAATCGC
*
2003846 AACGTGTATCCGTAAATCGT
1 AACGTGTATCCGTAAATCGC
* * *
2003866 AACGAGAATACGTAAATCGC
1 AACGTGTATCCGTAAATCGC
* *
2003886 AACGTGTATCTGTAAATCGT
1 AACGTGTATCCGTAAATCGC
* * *
2003906 AACGAGAATACGTAAATCGC
1 AACGTGTATCCGTAAATCGC
2003926 AA
1 AA
2003928 TAATGTCCAT
Statistics
Matches: 64, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.23
Consensus pattern (20 bp):
AACGTGTATCCGTAAATCGC
Found at i:2003924 original size:40 final size:40
Alignment explanation
Indices: 2003800--2003927 Score: 168
Period size: 40 Copynumber: 3.2 Consensus size: 40
2003790 GATTCTGACT
* * * * *
2003800 ATCGCAAC-TAGTATCTGTAAAACCGTAACGCGTATCCATAA
1 ATCGCAACGT-GTATCTGT-AAATCGTAACGAGAATACGTAA
* *
2003841 ATCACAACGTGTATCCGTAAATCGTAACGAGAATACGTAA
1 ATCGCAACGTGTATCTGTAAATCGTAACGAGAATACGTAA
2003881 ATCGCAACGTGTATCTGTAAATCGTAACGAGAATACGTAA
1 ATCGCAACGTGTATCTGTAAATCGTAACGAGAATACGTAA
2003921 ATCGCAA
1 ATCGCAA
2003928 TAATGTCCAT
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
40 62 0.81
41 14 0.18
42 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (40 bp):
ATCGCAACGTGTATCTGTAAATCGTAACGAGAATACGTAA
Found at i:2004191 original size:14 final size:14
Alignment explanation
Indices: 2004174--2004209 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2004164 TTGTTTTAAT
2004174 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2004188 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2004202 TGATTTGT
1 TGATTTGT
2004210 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2004332 original size:19 final size:17
Alignment explanation
Indices: 2004316--2004366 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
2004306 AAAAATGATT
2004316 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
2004335 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
2004349 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
2004366 A
1 A
2004367 AACGCGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.30
16 5 0.19
17 7 0.26
19 7 0.26
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:2004375 original size:13 final size:13
Alignment explanation
Indices: 2004357--2004381 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2004347 GAATCGCAAT
2004357 GCGAAATGAAAAC
1 GCGAAATGAAAAC
2004370 GCGAAATGAAAA
1 GCGAAATGAAAA
2004382 TCGCAACGCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.12, G:0.24, T:0.08
Consensus pattern (13 bp):
GCGAAATGAAAAC
Found at i:2004444 original size:19 final size:19
Alignment explanation
Indices: 2004406--2004478 Score: 57
Period size: 19 Copynumber: 4.1 Consensus size: 19
2004396 TAGTTTCGCG
* *
2004406 TTTTGATTTTGTCGTTGCGA
1 TTTTCATTTTG-CATTGCGA
2004426 TTTTCATTTTGCATTGCGA
1 TTTTCATTTTGCATTGCGA
* *
2004445 --TTC--TCT-CGTTGCGA
1 TTTTCATTTTGCATTGCGA
*
2004459 TTTTCATTTCGCATTGCGA
1 TTTTCATTTTGCATTGCGA
2004478 T
1 T
2004479 AGTCATTTCC
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
14 7 0.17
15 2 0.05
16 3 0.07
17 3 0.07
18 1 0.02
19 15 0.37
20 10 0.24
ACGTcount: A:0.12, C:0.18, G:0.19, T:0.51
Consensus pattern (19 bp):
TTTTCATTTTGCATTGCGA
Found at i:2004459 original size:33 final size:33
Alignment explanation
Indices: 2004417--2004565 Score: 154
Period size: 33 Copynumber: 4.3 Consensus size: 33
2004407 TTTGATTTTG
*
2004417 TCGTTGCGATTTTCATTTTGCATTGCGATTCTC
1 TCGTTGCGATTTTCATTTCGCATTGCGATTCTC
2004450 TCGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCC
1 TCGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-C
* * * * * *
2004489 GCGGTGCGATATTCATATTCGCGTTGTGATTTTC
1 TCGTTGCGATTTTCAT-TTCGCATTGCGATTCTC
* *
2004523 ACGTTGCGATTTTCATTTCGCATTGCGATTATC
1 TCGTTGCGATTTTCATTTCGCATTGCGATTCTC
2004556 TCGTTGCGAT
1 TCGTTGCGAT
2004566 AGACATTAAG
Statistics
Matches: 95, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
33 51 0.54
34 14 0.15
35 3 0.03
38 2 0.02
39 14 0.15
40 11 0.12
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.44
Consensus pattern (33 bp):
TCGTTGCGATTTTCATTTCGCATTGCGATTCTC
Found at i:2004511 original size:20 final size:19
Alignment explanation
Indices: 2004454--2004511 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
2004444 ATTCTCTCGT
* **
2004454 TGCGATTTTCATTTCGCAT
1 TGCGATATTCATTTCGCGG
*
2004473 TGCGATAGTCATTTCCGCGG
1 TGCGATATTCATTT-CGCGG
2004493 TGCGATATTCATATTCGCG
1 TGCGATATTCAT-TTCGCG
2004512 TTGTGATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
19 12 0.38
20 18 0.56
21 2 0.06
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
TGCGATATTCATTTCGCGG
Found at i:2004548 original size:19 final size:19
Alignment explanation
Indices: 2004420--2004552 Score: 97
Period size: 19 Copynumber: 7.4 Consensus size: 19
2004410 GATTTTGTCG
*
2004420 TTGCGATTTTCATTTTGCA
1 TTGCGATTTTCATTTCGCA
*
2004439 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2004453 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
2004472 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
* * *
2004492 GTGCGATATTCATATTCGCG
1 TTGCGATTTTCAT-TTCGCA
*
2004512 TTGTGATTTTCA---CG--
1 TTGCGATTTTCATTTCGCA
2004526 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2004545 TTGCGATT
1 TTGCGATT
2004553 ATCTCGTTGC
Statistics
Matches: 90, Mismatches: 12, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
14 17 0.19
16 8 0.09
17 9 0.10
19 27 0.30
20 27 0.30
21 2 0.02
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2004757 original size:20 final size:20
Alignment explanation
Indices: 2004728--2004774 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2004718 AATACAACGT
*
2004728 TTGC-ATTTACGTATTCACA
1 TTGCGATTTACGTAATCACA
* *
2004747 TTGCGATTTACGTAATCGCG
1 TTGCGATTTACGTAATCACA
2004767 TTGCGATT
1 TTGCGATT
2004775 AGGAAAATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACGTAATCACA
Found at i:2004792 original size:20 final size:19
Alignment explanation
Indices: 2004769--2004813 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
2004759 TAATCGCGTT
2004769 GCGATTAGGAAAATCGCAAC
1 GCGATT-GGAAAATCGCAAC
* *
2004789 GCGAATTGGGAAATCGCAAT
1 GCG-ATTGGAAAATCGCAAC
2004809 GCGAT
1 GCGAT
2004814 AGTCAGAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 17 0.77
21 3 0.14
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.18
Consensus pattern (19 bp):
GCGATTGGAAAATCGCAAC
Found at i:2005231 original size:13 final size:13
Alignment explanation
Indices: 2005213--2005237 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2005203 AATTTCTTTT
2005213 TTTATTATTAAAG
1 TTTATTATTAAAG
2005226 TTTATTATTAAA
1 TTTATTATTAAA
2005238 TTTTTTTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TTTATTATTAAAG
Found at i:2008217 original size:29 final size:29
Alignment explanation
Indices: 2008174--2008256 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
2008164 CTCACCTAAA
2008174 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
2008204 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
2008233 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
2008257 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:2017294 original size:2 final size:2
Alignment explanation
Indices: 2017287--2017324 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2017277 TTCCTCTCGA
2017287 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2017325 GTTTCCGAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2017765 original size:2 final size:2
Alignment explanation
Indices: 2017754--2017792 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2017744 TATGTAATTT
2017754 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2017793 ATTGTTTATC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2019003 original size:21 final size:21
Alignment explanation
Indices: 2018977--2019090 Score: 119
Period size: 21 Copynumber: 5.4 Consensus size: 21
2018967 TTTTCAAATT
2018977 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCGAAGTTCG
* * *
2018998 CGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCGAAGTTCG
2019019 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCGAAGTTCG
* *
2019040 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCGAAGTTCG
2019061 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCGAAGTTCG
2019082 CGTTGCGAT
1 CGTTGCGAT
2019091 TTATTCCAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
19 17 0.23
21 41 0.55
23 17 0.23
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.34
Consensus pattern (21 bp):
CGTTGCGATAGTCGAAGTTCG
Found at i:2019029 original size:42 final size:42
Alignment explanation
Indices: 2018939--2019115 Score: 295
Period size: 42 Copynumber: 4.3 Consensus size: 42
2018929 GACTATCGCA
* * *
2018939 TTGCGATAGTCCAAGTTTGCGTTACGATTT-TT-CAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
2018979 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
2019021 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
2019063 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
2019105 TTGTGATAGTC
1 TTGCGATAGTC
2019116 CAAAATCGCA
Statistics
Matches: 129, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
40 27 0.21
41 2 0.02
42 100 0.78
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:2019106 original size:21 final size:21
Alignment explanation
Indices: 2018948--2019107 Score: 102
Period size: 21 Copynumber: 7.6 Consensus size: 21
2018938 ATTGCGATAG
*
2018948 TCCAAGTTTGCGTTACGATTT-T
1 TCCAAG-TT-CGTTGCGATTTAT
* *
2018970 T-CAAATTCGTTGCGA--TAG
1 TCCAAGTTCGTTGCGATTTAT
*
2018988 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGATTTAT
* *
2019011 TCCAAATTCGTTGCGA--TAG
1 TCCAAGTTCGTTGCGATTTAT
*
2019030 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGATTTAT
*
2019053 TCCAAGTTCGTTGCGA--TAG
1 TCCAAGTTCGTTGCGATTTAT
*
2019072 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGATTTAT
*
2019095 TCCAAATTCGTTG
1 TCCAAGTTCGTTG
2019108 TGATAGTCCA
Statistics
Matches: 106, Mismatches: 18, Indels: 29
0.69 0.12 0.19
Matches are distributed among these distances:
17 1 0.01
18 1 0.01
19 28 0.26
20 2 0.02
21 48 0.45
22 1 0.01
23 25 0.24
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (21 bp):
TCCAAGTTCGTTGCGATTTAT
Done.