Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 139 of 210
Found at i:42359397 original size:25 final size:25
Alignment explanation
Indices: 42359295--42359404 Score: 80
Period size: 25 Copynumber: 4.4 Consensus size: 25
42359285 TTGCTCTCCG
* * **
42359295 GAGCTACCCGATAT-TGGCTCACAT
1 GAGCTTCCCGTTATATGGCTCGGAT
* * **
42359319 GAGCTTCCCGTTACATGACTCACAT
1 GAGCTTCCCGTTATATGGCTCGGAT
* *
42359344 GAGCTTCCGGTTATATGGCTCGGAA
1 GAGCTTCCCGTTATATGGCTCGGAT
**
42359369 GAGCTTCCCGTT-TATGTGCTCTTAT
1 GAGCTTCCCGTTATATG-GCTCGGAT
42359394 GAGCATTCCCG
1 GAGC-TTCCCG
42359405 AATATGAATT
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
24 15 0.22
25 48 0.70
26 6 0.09
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGCTCGGAT
Found at i:42361229 original size:24 final size:24
Alignment explanation
Indices: 42361193--42361240 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
42361183 GACACACCAC
* *
42361193 AGCTCGCAAGAGCATCCCGTTATT
1 AGCTCCCAAGAGCATCCCGATATT
* *
42361217 AGCTCCCATGAGCATTCCGATATT
1 AGCTCCCAAGAGCATCCCGATATT
42361241 GGCTTTCTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (24 bp):
AGCTCCCAAGAGCATCCCGATATT
Found at i:42361433 original size:24 final size:24
Alignment explanation
Indices: 42361361--42361440 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 24
42361351 CTTATAAGTG
42361361 TCCCGATATATGGCTCACACGAGCT
1 TCCCGATAT-TGGCTCACACGAGCT
* *
42361386 TCCTGATTAATT-GCTCTC-CGGAGCT
1 TCCCGA-T-ATTGGCTCACAC-GAGCT
* *
42361411 ACCCGATATTGGCTCACATGAGCT
1 TCCCGATATTGGCTCACACGAGCT
42361435 TCCCGA
1 TCCCGA
42361441 ATATGAATTC
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
23 3 0.07
24 17 0.40
25 19 0.44
26 2 0.05
27 2 0.05
ACGTcount: A:0.21, C:0.31, G:0.20, T:0.28
Consensus pattern (24 bp):
TCCCGATATTGGCTCACACGAGCT
Found at i:42369306 original size:8 final size:8
Alignment explanation
Indices: 42369293--42369357 Score: 76
Period size: 8 Copynumber: 7.4 Consensus size: 8
42369283 AGTAAAACGA
42369293 AAATAAAG
1 AAATAAAG
42369301 AAATAAAG
1 AAATAAAG
42369309 AAATAAAG
1 AAATAAAG
42369317 AAATAAAG
1 AAATAAAG
42369325 AAAGAATAAAG
1 --A-AATAAAG
42369336 AAATAAAG
1 AAATAAAG
42369344 TAAAAATAAAG
1 ---AAATAAAG
42369355 AAA
1 AAA
42369358 GAATGGAGGA
Statistics
Matches: 51, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
8 34 0.67
9 1 0.02
10 1 0.02
11 15 0.29
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAATAAAG
Found at i:42369312 original size:16 final size:17
Alignment explanation
Indices: 42369291--42369357 Score: 91
Period size: 19 Copynumber: 3.8 Consensus size: 17
42369281 AAAGTAAAAC
42369291 GAAAATAAAGAAATAAA
1 GAAAATAAAGAAATAAA
42369308 G-AAATAAAGAAATAAA
1 GAAAATAAAGAAATAAA
42369324 GAAAGAATAAAGAAATAAA
1 G-AA-AATAAAGAAATAAA
42369343 GTAAAAATAAAGAAA
1 G--AAAATAAAGAAA
42369358 GAATGGAGGA
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
16 16 0.35
17 1 0.02
18 1 0.02
19 25 0.54
20 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.12
Consensus pattern (17 bp):
GAAAATAAAGAAATAAA
Found at i:42369330 original size:4 final size:4
Alignment explanation
Indices: 42369297--42369360 Score: 51
Period size: 4 Copynumber: 16.5 Consensus size: 4
42369287 AAACGAAAAT
* * * * *
42369297 AAAG AAAT AAAG AAAT AAAG AAAT AAAG AAAG -AAT AAAG AAAT AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
* *
42369344 TAA- AAAT AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AA
42369361 TGGAGGAATG
Statistics
Matches: 45, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
3 4 0.09
4 41 0.91
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (4 bp):
AAAG
Found at i:42370835 original size:31 final size:29
Alignment explanation
Indices: 42370800--42370894 Score: 77
Period size: 31 Copynumber: 3.1 Consensus size: 29
42370790 ACGTTTTAGC
42370800 CACTTACGTTAACATGTTATAACATTTTAAT
1 CACTTACGTTAA-ATGTT-TAACATTTTAAT
*
42370831 CACTTATGTTTGAAATG-TT-ACATTTTAAT
1 CACTTACG-TT-AAATGTTTAACATTTTAAT
* * * *
42370860 TACTTACATTAATATGTTGTATCATTTTAGT
1 CACTTACGTTAA-ATGTT-TAACATTTTAAT
42370891 CACT
1 CACT
42370895 ATGCTGTTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
27 2 0.04
28 5 0.10
29 16 0.31
30 2 0.04
31 19 0.37
32 5 0.10
33 2 0.04
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (29 bp):
CACTTACGTTAAATGTTTAACATTTTAAT
Found at i:42370859 original size:29 final size:29
Alignment explanation
Indices: 42370777--42370865 Score: 83
Period size: 29 Copynumber: 3.0 Consensus size: 29
42370767 CACTTTTGTT
* **
42370777 TGTTTGAAATGTTACGTTTTAGCCACTTA
1 TGTTTGAAATGTTACATTTTAATCACTTA
*
42370806 CG-TT-AACATGTTATAACATTTTAATCACTTA
1 TGTTTGAA-ATG-T-T-ACATTTTAATCACTTA
*
42370837 TGTTTGAAATGTTACATTTTAATTACTTA
1 TGTTTGAAATGTTACATTTTAATCACTTA
42370866 CATTAATATG
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
27 2 0.04
28 5 0.10
29 17 0.35
30 2 0.04
31 15 0.31
32 5 0.10
33 2 0.04
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.46
Consensus pattern (29 bp):
TGTTTGAAATGTTACATTTTAATCACTTA
Found at i:42370865 original size:60 final size:60
Alignment explanation
Indices: 42370777--42370894 Score: 155
Period size: 60 Copynumber: 2.0 Consensus size: 60
42370767 CACTTTTGTT
* * *
42370777 TGTTTGAAATGTTACGTTTTAGCCACTTACGTTAACATGTTATAACATTTTAATCACTTA
1 TGTTTGAAATGTTACATTTTAACCACTTACATTAACATGTTATAACATTTTAATCACTTA
** * * * *
42370837 TGTTTGAAATGTTACATTTTAATTACTTACATTAATATGTTGTATCATTTTAGTCACT
1 TGTTTGAAATGTTACATTTTAACCACTTACATTAACATGTTATAACATTTTAATCACT
42370895 ATGCTGTTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.47
Consensus pattern (60 bp):
TGTTTGAAATGTTACATTTTAACCACTTACATTAACATGTTATAACATTTTAATCACTTA
Found at i:42371492 original size:14 final size:14
Alignment explanation
Indices: 42371447--42371494 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
42371437 AATTAAATAG
42371447 TAAACAAAATTATTA
1 TAAA-AAAATTATTA
* **
42371462 TAAAAAATTTAAAA
1 TAAAAAAATTATTA
42371476 TAAAAAAATTATTA
1 TAAAAAAATTATTA
42371490 TAAAA
1 TAAAA
42371495 TTAAGGGGGA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
14 23 0.85
15 4 0.15
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAAAAAATTATTA
Found at i:42371498 original size:25 final size:29
Alignment explanation
Indices: 42371422--42371498 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 29
42371412 TGTAAAACTG
42371422 AATTAATTGATAATAAATTAAATAGTAAACAA
1 AATT-ATT-ATAA-AAATTAAATAGTAAACAA
42371454 AATTATTATAAAAAATTTAAA-A-TAAA-AA
1 AATTATTAT-AAAAA-TTAAATAGTAAACAA
42371482 AATTATTAT-AAAATTAA
1 AATTATTATAAAAATTAA
42371499 GGGGGAAAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
25 4 0.09
26 4 0.09
28 11 0.26
29 4 0.09
30 6 0.14
31 10 0.23
32 4 0.09
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (29 bp):
AATTATTATAAAAATTAAATAGTAAACAA
Found at i:42374655 original size:19 final size:17
Alignment explanation
Indices: 42374631--42374694 Score: 74
Period size: 19 Copynumber: 3.5 Consensus size: 17
42374621 CCTATTAATC
42374631 AAAATTTACAATAATTTCT
1 AAAATTT-CAA-AATTTCT
42374650 AAAATTTCTAAAATTTCT
1 AAAATTTC-AAAATTTCT
*
42374668 AAAATTTTTTAAAATTTCT
1 AAAA--TTTCAAAATTTCT
42374687 AAAATTTC
1 AAAATTTC
42374695 GACATGGCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 3 0.08
18 12 0.30
19 22 0.55
20 3 0.08
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATTTCAAAATTTCT
Found at i:42374657 original size:9 final size:9
Alignment explanation
Indices: 42374643--42374694 Score: 86
Period size: 9 Copynumber: 5.7 Consensus size: 9
42374633 AATTTACAAT
42374643 AATTTCTAA
1 AATTTCTAA
42374652 AATTTCTAA
1 AATTTCTAA
42374661 AATTTCTAA
1 AATTTCTAA
*
42374670 AATTTTTTAA
1 AA-TTTCTAA
42374680 AATTTCTAA
1 AATTTCTAA
42374689 AATTTC
1 AATTTC
42374695 GACATGGCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
9 32 0.80
10 8 0.20
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (9 bp):
AATTTCTAA
Found at i:42375288 original size:76 final size:76
Alignment explanation
Indices: 42375154--42375297 Score: 182
Period size: 76 Copynumber: 1.9 Consensus size: 76
42375144 ATATATTTAA
* * * *
42375154 TAAATATTTAAGAGTCCAATTTACGGGAATAGAGTCTCAGGAATGTACTTTCCAACACCCCTGAC
1 TAAATATTTAAGAGTCCAATTTACAGGAACAGAGTCTCAGGAATGCACTTTCCAACACCCCTAAC
42375219 TATTTGGTCGT
66 TATTTGGTCGT
* * * ***
42375230 TAAATATTTACGAGTCTAATTTACAGGAACGGAGTCTC-GAGAATGCACTTTTTGACACCCCTAA
1 TAAATATTTAAGAGTCCAATTTACAGGAACAGAGTCTCAG-GAATGCACTTTCCAACACCCCTAA
42375294 CTAT
65 CTAT
42375298 CGAGTCGTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
75 1 0.02
76 56 0.98
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (76 bp):
TAAATATTTAAGAGTCCAATTTACAGGAACAGAGTCTCAGGAATGCACTTTCCAACACCCCTAAC
TATTTGGTCGT
Found at i:42380591 original size:5 final size:5
Alignment explanation
Indices: 42380577--42380623 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
42380567 ACACACATAT
* * *
42380577 ATTCA TTTCA ATTCA ATTCA ATTCA A-TCA ACTTTA AATCA ATTCA AT
1 ATTCA ATTCA ATTCA ATTCA ATTCA ATTCA A-TTCA ATTCA ATTCA AT
42380624 AATCAAAGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 4 0.12
5 27 0.79
6 3 0.09
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTCA
Found at i:42382587 original size:24 final size:26
Alignment explanation
Indices: 42382553--42382604 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
42382543 GATTCCAGTC
42382553 AAAAACTCTAAA-TTTAAAAATATTA
1 AAAAACTCTAAATTTTAAAAATATTA
*
42382578 AAAAAC-CTAAATTTTAAAAATTTTA
1 AAAAACTCTAAATTTTAAAAATATTA
42382603 AA
1 AA
42382605 CCTAGAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.33
Consensus pattern (26 bp):
AAAAACTCTAAATTTTAAAAATATTA
Found at i:42387590 original size:24 final size:24
Alignment explanation
Indices: 42387563--42387614 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
42387553 AATCAAAGTC
*
42387563 AAATATATTATACTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
42387587 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
42387611 AAAT
1 AAAT
42387615 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:42395118 original size:22 final size:24
Alignment explanation
Indices: 42395047--42395113 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 24
42395037 TGTTATTTAT
42395047 TTATTTATTTTAAACCTATTTCTCATATA
1 TTATTTATTTTAAA--TATTT-T-AT-TA
42395076 TTATTTATTTTAAATTATTTTATTA
1 TTATTTATTTTAAA-TATTTTATTA
42395101 TTATTTATTTTAA
1 TTATTTATTTTAA
42395114 GTTTTCCACA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
25 15 0.41
26 2 0.05
27 1 0.03
28 5 0.14
29 14 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (24 bp):
TTATTTATTTTAAATATTTTATTA
Found at i:42395230 original size:26 final size:26
Alignment explanation
Indices: 42395047--42395448 Score: 241
Period size: 26 Copynumber: 15.2 Consensus size: 26
42395037 TGTTATTTAT
* *
42395047 TTATTTATTTTAAACCTATTTCTCATATA
1 TTATTTATTTTAAA-TTGTTT-T-ATATA
*
42395076 TTATTTATTTTAAATTATTTTAT-TA
1 TTATTTATTTTAAATTGTTTTATATA
* ** *
42395101 TTATTTATTTTAAGTT-TTCCACATA
1 TTATTTATTTTAAATTGTTTTATATA
* * * * * *
42395126 TAATGTATTTTAAACTATTTCAAACTA
1 TTATTTATTTTAAATTGTTTTATA-TA
**
42395153 TTATCCATTTTAAATT-TTTTATATA
1 TTATTTATTTTAAATTGTTTTATATA
* **
42395178 TTATTTATTTTTAAACTGTCATATATA
1 TTATTTA-TTTTAAATTGTTTTATATA
*
42395205 TTATTTATTTTGAATTGTTTTTTATATA
1 TTATTTATTTTAAATTG--TTTTATATA
* *
42395233 TATCATTTATTTTTTTAAAAACT-TTTTAGTACA
1 T-T-ATTTA---TTTT--AAATTGTTTTA-TATA
* *
42395266 TTATTTATTTTAAACTTCTTTTTACATA
1 TTATTTATTTTAAA-TT-GTTTTATATA
*
42395294 TTATTTATTTTAAA--CTTTT-TATA
1 TTATTTATTTTAAATTGTTTTATATA
* *
42395317 -TA-TTATTTTAAATTGTCTTATATG
1 TTATTTATTTTAAATTGTTTTATATA
* * *
42395341 TTATTTATTTTAAATTGCTTTGTCTA
1 TTATTTATTTTAAATTGTTTTATATA
* *
42395367 TTATTTATTTTAATTTGTTTTACATA
1 TTATTTATTTTAAATTGTTTTATATA
* *
42395393 TTAGTTACTTTAAATTG-TTT-TATA
1 TTATTTATTTTAAATTGTTTTATATA
* * * *
42395417 CTATTTACTTCAAATTGTTCTATATA
1 TTATTTATTTTAAATTGTTTTATATA
42395443 TTATTT
1 TTATTT
42395449 TGTTTCGTTT
Statistics
Matches: 292, Mismatches: 56, Indels: 53
0.73 0.14 0.13
Matches are distributed among these distances:
21 10 0.03
22 2 0.01
23 6 0.02
24 27 0.09
25 45 0.15
26 92 0.32
27 30 0.10
28 33 0.11
29 20 0.07
30 5 0.02
31 5 0.02
32 6 0.02
33 8 0.03
35 3 0.01
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.59
Consensus pattern (26 bp):
TTATTTATTTTAAATTGTTTTATATA
Found at i:42395276 original size:28 final size:27
Alignment explanation
Indices: 42395239--42395324 Score: 97
Period size: 28 Copynumber: 3.2 Consensus size: 27
42395229 TATATATCAT
*
42395239 TTATTT-TTTTAAAAACTTTTTAGTACA
1 TTATTTATTTTAAAAACTTTTTA-TATA
** *
42395266 TTATTTATTTTAAACTTCTTTTTACATA
1 TTATTTATTTTAAA-AACTTTTTATATA
42395294 TTATTTATTTT--AAACTTTTTATATA
1 TTATTTATTTTAAAAACTTTTTATATA
42395319 TTATTT
1 TTATTT
42395325 TAAATTGTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
25 16 0.32
26 1 0.02
27 6 0.12
28 20 0.40
29 7 0.14
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.62
Consensus pattern (27 bp):
TTATTTATTTTAAAAACTTTTTATATA
Found at i:42395431 original size:24 final size:23
Alignment explanation
Indices: 42395397--42395444 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
42395387 TACATATTAG
* *
42395397 TTACTTTAAATTGTTTTATACTAT
1 TTACTTCAAATTGTTCTATA-TAT
42395421 TTACTTCAAATTGTTCTATATAT
1 TTACTTCAAATTGTTCTATATAT
42395444 T
1 T
42395445 ATTTTGTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.56
Consensus pattern (23 bp):
TTACTTCAAATTGTTCTATATAT
Found at i:42405241 original size:19 final size:20
Alignment explanation
Indices: 42405199--42405234 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
42405189 GTTTTCAAAT
42405199 AATT-ATAAAAATATATTAA
1 AATTAATAAAAATATATTAA
42405218 AATTAATAAAAAT-TATT
1 AATTAATAAAAATATATT
42405235 CGAATTACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTAATAAAAATATATTAA
Found at i:42410649 original size:33 final size:33
Alignment explanation
Indices: 42410607--42410673 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
42410597 ATAAAAGTAA
42410607 AAAGGAAGGAAACAACCTATTTGCTTTTAAGCG
1 AAAGGAAGGAAACAACCTATTTGCTTTTAAGCG
42410640 AAAGGAAGGAAACAACCTATTTGCTTTTAAGCG
1 AAAGGAAGGAAACAACCTATTTGCTTTTAAGCG
42410673 A
1 A
42410674 CGCCGTAGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (33 bp):
AAAGGAAGGAAACAACCTATTTGCTTTTAAGCG
Found at i:42423435 original size:44 final size:44
Alignment explanation
Indices: 42423357--42423784 Score: 271
Period size: 44 Copynumber: 9.9 Consensus size: 44
42423347 AAAAATGGCA
* *
42423357 AATCTTATCTTCCTGAAGTTGCAGCAGAGCAGATTAAAGCCGAC
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGAC
* * * * * *
42423401 AATCCTATCTCTCTGAAGTTGCAGTGGAGAAGATTAAAACC-TC
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGAC
* * *
42423444 AGATCTTATCTCTCTGAAGTTGTAG-AGAGCAGA-T--CG-C-ATC
1 A-ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGA-C
* * * **
42423484 TAGTCTTATTTCCCTGAAGTTGCAGT-GAGGCAGACTAAAGATGGTA-
1 -AATCTTATCTCCCTGAAGTTGCAGTAGA-GCAGATTAAAG-CCG-AC
* **
42423530 AATCTTATCTTCCTGAAGTTGCAGCGGAGCAGATTAAAGCCGAC
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGAC
* ** * *
42423574 AATCCTATCTCCCTGAAGTTGCAGTAGAGTGGATTAAAACC-TC
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGAC
* ** *
42423617 AGATCTTATCTCTCTGAAGTTATAG-AGAGCAGA-T--CG-C-ATC
1 A-ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGA-C
* * * ** *
42423657 TAGTCTTATTTCCCTGAAGTTGCAGT-GAGGCAGACTAAAGATGGC
1 -AATCTTATCTCCCTGAAGTTGCAGTAGA-GCAGATTAAAGCCGAC
**
42423702 AAATCTTATCTCCCTGAAGTTGCAGCGGAGCAGATTAAAGCCGAC
1 -AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGAC
* * *
42423747 AAT-TCTATCTCCCTGAAGTTGCAATGGAGCGGATTAAA
1 AATCT-TATCTCCCTGAAGTTGCAGTAGAGCAGATTAAA
42423785 ATCTTAGATC
Statistics
Matches: 294, Mismatches: 64, Indels: 52
0.72 0.16 0.13
Matches are distributed among these distances:
39 2 0.01
40 43 0.15
41 12 0.04
42 4 0.01
43 18 0.06
44 144 0.49
45 66 0.22
46 4 0.01
48 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGAC
Found at i:42423611 original size:173 final size:173
Alignment explanation
Indices: 42423323--42423838 Score: 854
Period size: 173 Copynumber: 3.0 Consensus size: 173
42423313 GTCTTATCCT
* * *
42423323 CCTGAAGTTGCAGTGGGGCAGACTAAAAATGGCAAATCTTATCTTCCTGAAGTTGCAGCAGAGCA
1 CCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTTCCTGAAGTTGCAGCGGAGCA
* *
42423388 GATTAAAGCCGACAATCCTATCTCTCTGAAGTTGCAGTGGAGAAGATTAAAACCTCAGATCTTAT
66 GATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGAGGATTAAAACCTCAGATCTTAT
42423453 CTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATTTC
131 CTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATTTC
*
42423496 CCTGAAGTTGCAGTGAGGCAGACTAAAGATGGTAAATCTTATCTTCCTGAAGTTGCAGCGGAGCA
1 CCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTTCCTGAAGTTGCAGCGGAGCA
* *
42423561 GATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTAGAGTGGATTAAAACCTCAGATCTTAT
66 GATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGAGGATTAAAACCTCAGATCTTAT
*
42423626 CTCTCTGAAGTTATAGAGAGCAGATCGCATCTAGTCTTATTTC
131 CTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATTTC
*
42423669 CCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGCGGAGCA
1 CCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTTCCTGAAGTTGCAGCGGAGCA
* * * * *
42423734 GATTAAAGCCGACAATTCTATCTCCCTGAAGTTGCAATGGAGCGGATTAAAATCTTAGATCTTAT
66 GATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGAGGATTAAAACCTCAGATCTTAT
* * *
42423799 CTTTCTGAAATTGCAGAGAGCAGATCGCGA-CTAGTCTTAT
131 CTCTCTGAAGTTGTAGAGAGCAGATCGC-ATCTAGTCTTAT
42423839 CTCCTTAAAG
Statistics
Matches: 321, Mismatches: 21, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
173 320 1.00
174 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (173 bp):
CCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTTCCTGAAGTTGCAGCGGAGCA
GATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGAGGATTAAAACCTCAGATCTTAT
CTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATTTC
Found at i:42423756 original size:129 final size:128
Alignment explanation
Indices: 42423532--42423766 Score: 280
Period size: 129 Copynumber: 1.8 Consensus size: 128
42423522 AGATGGTAAA
* *
42423532 TCTTATCTTCCTGAAGTTGCAGCGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTTCCTGAAGTTGCAGCGGAGCAGACTAAAGACGACAATCCTATCTCCCTGAAGTTGCA
* ** * *
42423597 GTAGAGTGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTATAGAGAGCAGATCGCATCTAG
66 GCAGAGCAGATTAAAACCACAGATCTTATCTCCCTGAAGTTATAGAGAGCAGATCGCATCTAG
* * * *
42423660 TCTTAT-TTCCCTGAAGTTGCAG-TGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTT
1 TCTTATCTT-CCTGAAGTTGCAGCGGA-GCAGACTAAAGACGAC-AATCCTATCTCCCTGAAGTT
* *
42423723 GCAGCGGAGCAGATTAAAGCCGACA-AT-TCTATCTCCCTGAAGTT
63 GCAGCAGAGCAGATTAAAACC-ACAGATCT-TATCTCCCTGAAGTT
42423767 GCAATGGAGC
Statistics
Matches: 89, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
127 4 0.04
128 32 0.36
129 51 0.57
130 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (128 bp):
TCTTATCTTCCTGAAGTTGCAGCGGAGCAGACTAAAGACGACAATCCTATCTCCCTGAAGTTGCA
GCAGAGCAGATTAAAACCACAGATCTTATCTCCCTGAAGTTATAGAGAGCAGATCGCATCTAG
Found at i:42423800 original size:44 final size:44
Alignment explanation
Indices: 42423314--42423823 Score: 233
Period size: 44 Copynumber: 11.7 Consensus size: 44
42423304 ACAGATCGAG
* * *** *
42423314 TCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTAAAAATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGAGCAGA-TTAAAATCTTAGA
* ** * ** *
42423359 TCTTATCTTCCTGAAGTTGCAGCAGAGCAGATT-AAAGCCGACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTTA-GA
* * * * *
42423403 TCCTATCTCTCTGAAGTTGCAGTGGAGAAGATTAAAACCTCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTTAGA
* * * ***
42423447 TCTTATCTCTCTGAAGTTGTAG-AGAGCAGA-TCGCATC-TAG-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTTAGA
* * ** *
42423487 TCTTATTTCCCTGAAGTTGCAGT-GAGGCAGACTAAAGATGGTAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGA-GCAGATTAAA-ATCTTAGA
* * * ** *
42423532 TCTTATCTTCCTGAAGTTGCAGCGGAGCAGATT-AAAGCCGACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTTA-GA
* * ** * *
42423576 TCCTATCTCCCTGAAGTTGCAGTAGAGTGGATTAAAACCTCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTTAGA
* ** * ***
42423620 TCTTATCTCTCTGAAGTTATAG-AGAGCAGA-TCGCATC-TAG-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTTAGA
* * *** *
42423660 TCTTATTTCCCTGAAGTTGCAGT-GAGGCAGACTAAAGATGGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGA-GCAGATTAAA-ATCTTAGA
* * ** *
42423705 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGATT-AAAGCCGACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTTA-GA
* *
42423749 T-TCTATCTCCCTGAAGTTGCAATGGAGCGGATTAAAATCTTAGA
1 TCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTTAGA
** * *
42423793 TCTTATCTTTCTGAAATTGCAG-AGAGCAGAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
42423824 CGCGACTAGT
Statistics
Matches: 347, Mismatches: 95, Indels: 48
0.71 0.19 0.10
Matches are distributed among these distances:
40 41 0.12
41 14 0.04
42 8 0.02
43 32 0.09
44 153 0.44
45 95 0.27
46 4 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCTTAGA
Found at i:42424129 original size:45 final size:43
Alignment explanation
Indices: 42424010--42424129 Score: 102
Period size: 45 Copynumber: 2.7 Consensus size: 43
42424000 AGATTGTAAG
* ** *
42424010 TCTTATTTCCCTGAAGTTGCAGTGGAATAGACTAGTGAAACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAGTG-AACAAA
* * *
42424054 TCTTATACT-CTTGAAGTGGCAGT-GAGGCAGACTGAAGATG-GCAAA
1 TCTTAT-CTCCCTGAAGTTGCAGTGGA-GCAGACT--AG-TGAACAAA
42424099 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
42424130 TTAAAGCCGA
Statistics
Matches: 60, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
43 2 0.03
44 25 0.42
45 27 0.45
46 4 0.07
47 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (43 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAGTGAACAAA
Found at i:42424175 original size:44 final size:44
Alignment explanation
Indices: 42424097--42424180 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 44
42424087 GAAGATGGCA
* * * *
42424097 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
1 AATCTTATCTCCCTAAAGTTACAATGAAGCAGATTAAAGCCGAT
* * *
42424141 AATCTTATCTCCTTAAAGTTACAATGAAGTAGATTGAAGC
1 AATCTTATCTCCCTAAAGTTACAATGAAGCAGATTAAAGC
42424181 ACTAATTCCT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
44 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTAAAGTTACAATGAAGCAGATTAAAGCCGAT
Found at i:42426432 original size:98 final size:98
Alignment explanation
Indices: 42426312--42426508 Score: 367
Period size: 98 Copynumber: 2.0 Consensus size: 98
42426302 TTTAAAATAA
*
42426312 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
42426377 TTAAATCTTGGATAAGTGGATGTTCTCTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTCTTAAAG
*
42426410 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
42426475 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTCTTAAAG
42426508 T
1 T
42426509 TTTATTGCAG
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTCTTAAAG
Found at i:42429653 original size:18 final size:17
Alignment explanation
Indices: 42429625--42429659 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42429615 ATTATTAAGA
*
42429625 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
42429642 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
42429660 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:42429916 original size:16 final size:16
Alignment explanation
Indices: 42429895--42429946 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
42429885 GATTTGCTAT
42429895 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
42429911 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
42429927 TACACCTCTAAACCAA
1 TACACCTCTAATCCAA
42429943 TACA
1 TACA
42429947 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.23
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:42430257 original size:2 final size:2
Alignment explanation
Indices: 42430250--42430277 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42430240 ACTATTAAGA
42430250 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
42430278 TTTTAATTAG
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:42435609 original size:6 final size:6
Alignment explanation
Indices: 42435598--42435628 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
42435588 AATTATGAAC
42435598 AATTAA AATTAA AATTAA AATTAA AATTAA A
1 AATTAA AATTAA AATTAA AATTAA AATTAA A
42435629 CATAAATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATTAA
Found at i:42442440 original size:2 final size:2
Alignment explanation
Indices: 42442377--42442421 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
42442367 TAAGTATAAG
*
42442377 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42442419 AT A
1 AT A
42442422 AGGTTCGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42442882 original size:41 final size:41
Alignment explanation
Indices: 42442825--42442992 Score: 164
Period size: 41 Copynumber: 4.1 Consensus size: 41
42442815 TTAAAGTGAT
*
42442825 TGAAATAATTCAGACTTTACGTCTAGCAGGCTTGATGCCGG
1 TGAAATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGG
42442866 TGAAATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGG
1 TGAAATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGG
* * * *
42442907 TG--ATACATATCGGACTATATGTCTAGCAGGC-TAAGTGCTGG
1 TGAAATA-AT-TCAGACTTTACGTCTAGCAGGCTTAA-TGCCGG
* * * * * * *
42442948 TGTATTGAA-TCAGGCTTTAAGCCTAGCAGGCTAAATACCGG
1 TGAAAT-AATTCAGACTTTACGTCTAGCAGGCTTAATGCCGG
42442989 TGAA
1 TGAA
42442993 TCTGTTTTTA
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
39 3 0.03
40 5 0.05
41 92 0.88
42 2 0.02
43 2 0.02
44 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (41 bp):
TGAAATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGG
Found at i:42445813 original size:43 final size:42
Alignment explanation
Indices: 42445744--42445830 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 42
42445734 AAGCGTTGCA
* * *
42445744 AAAGATCATGTTCTGTAGCAACGTTTGTAGTAAAAGCGCCACT
1 AAAGATCATGTTCTATAGCAACGTTTGTAGGAAAA-CACCACT
***
42445787 AAAGATCATGTTCTATAGCGGTGTTTGTAGGAAAACACCACT
1 AAAGATCATGTTCTATAGCAACGTTTGTAGGAAAACACCACT
42445829 AA
1 AA
42445831 CATTAACAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
42 8 0.21
43 30 0.79
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (42 bp):
AAAGATCATGTTCTATAGCAACGTTTGTAGGAAAACACCACT
Found at i:42450019 original size:25 final size:25
Alignment explanation
Indices: 42449989--42450043 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
42449979 GGATGGGAAA
*
42449989 GAAAAAAATAAGTTAGGGAATTGGG
1 GAAAAAAATAAGTTAGAGAATTGGG
* *
42450014 GAAAAAACTAAGTTAGAGATTTGGG
1 GAAAAAAATAAGTTAGAGAATTGGG
42450039 GAAAA
1 GAAAA
42450044 TGATTTTGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.49, C:0.02, G:0.29, T:0.20
Consensus pattern (25 bp):
GAAAAAAATAAGTTAGAGAATTGGG
Found at i:42450267 original size:83 final size:83
Alignment explanation
Indices: 42450120--42450280 Score: 191
Period size: 83 Copynumber: 1.9 Consensus size: 83
42450110 ATATTCGCGA
* * * *
42450120 CGTTTATGAGAAAAACACTACTATCGTTTTTAACCTTTTGCGGTATTTATGCAAAAACGTCACTA
1 CGTTTATGAGAAAAACACTACTATCGTTATTAACCTTTAGCGGCATTTATGCAAAAACGCCACTA
42450185 TTGT-TTTACCTTTTGCAG
66 TT-TCTTTACCTTTTGCAG
* * * * * **
42450203 CGTTTATGCGAAAAATACTGCTATTGTTATTATACCTTTAGCGGCGTTTA-GGGAAAACGCCACT
1 CGTTTATGAGAAAAACACTACTATCGTTATTA-ACCTTTAGCGGCATTTATGCAAAAACGCCACT
42450267 ATTTCTTTACCTTT
65 ATTTCTTTACCTTT
42450281 CACGGCGCTT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
82 1 0.02
83 50 0.77
84 14 0.22
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (83 bp):
CGTTTATGAGAAAAACACTACTATCGTTATTAACCTTTAGCGGCATTTATGCAAAAACGCCACTA
TTTCTTTACCTTTTGCAG
Found at i:42455186 original size:19 final size:19
Alignment explanation
Indices: 42455133--42455187 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
42455123 AAGCAAATTA
* *
42455133 AATAAAATAAG-AAATGAT
1 AATAAAAGAAGTAAATAAT
**
42455151 AAGCAAAGAGAGT-AATAAT
1 AATAAAAGA-AGTAAATAAT
42455170 AATAAAAGAAGTAAATAA
1 AATAAAAGAAGTAAATAA
42455188 AAAATAAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.65, C:0.02, G:0.15, T:0.18
Consensus pattern (19 bp):
AATAAAAGAAGTAAATAAT
Found at i:42455205 original size:16 final size:16
Alignment explanation
Indices: 42455186--42455216 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42455176 AGAAGTAAAT
*
42455186 AAAAAATAAATAAAAG
1 AAAAAATAAAGAAAAG
42455202 AAAAAATAAAGAAAA
1 AAAAAATAAAGAAAA
42455217 AAGGGAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAAAATAAAGAAAAG
Found at i:42461606 original size:22 final size:25
Alignment explanation
Indices: 42461580--42461633 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
42461570 TTATAAATTC
42461580 AATTTAAAAG-ATA-TAAT-ACAAT
1 AATTTAAAAGCATATTAATAACAAT
*
42461602 AATTT-CAAGCATATTTAATAACAAT
1 AATTTAAAAGCATA-TTAATAACAAT
42461627 AATTTAA
1 AATTTAA
42461634 TTATAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.12
22 8 0.32
24 4 0.16
25 10 0.40
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (25 bp):
AATTTAAAAGCATATTAATAACAAT
Found at i:42467995 original size:4 final size:4
Alignment explanation
Indices: 42467986--42468022 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
42467976 TATTATTAAA
*
42467986 TTAT TTAT TTAT TTAT TTAT TTAT TTGT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
42468023 ATCATTAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:42468217 original size:3 final size:3
Alignment explanation
Indices: 42468209--42468302 Score: 145
Period size: 3 Copynumber: 31.3 Consensus size: 3
42468199 TTTAGATTTC
42468209 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
42468257 TAT TAT TAT TAT T-T TCAT CAT TAT TAT TAT TAA TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42468302 T
1 T
42468303 CTTAAATTGT
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
2 2 0.02
3 81 0.96
4 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:42468331 original size:4 final size:4
Alignment explanation
Indices: 42468322--42468350 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
42468312 TTTTATACAA
42468322 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
42468351 CTCTAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:42474418 original size:44 final size:44
Alignment explanation
Indices: 42474222--42474485 Score: 198
Period size: 44 Copynumber: 6.0 Consensus size: 44
42474212 TCATGATGAA
* * **
42474222 TCTTATCTCCCTAAAGTTGTAGTGGAACAGATTAAAGCCACTAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGATAC-AAG
* * ** * *
42474266 TCTTA-CCCCCTTGAAGTTGTAGTGGGGCAGGTTGAAA-TTACAAG
1 TCTTATCTCCC-TGAAGTTGCAGTGGAACAGATT-AAAGATACAAG
* * * *
42474310 TCTTATCTCCTTAAAGTTGCAGTGGAACAGACTAAAGATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGATA-CAAG
* * * *
42474355 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGATACAAG
* * *
42474399 TCTTATCTCCCTGAAGTTGCAGTAGG--CAGACTAAAGACAGTGAA-
1 TCTTATCTCCCTGAAGTTGCAGT-GGAACAGATTAAAGATA--CAAG
* ** *
42474443 TCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGATACAA
42474486 ATTATTGCGG
Statistics
Matches: 171, Mismatches: 38, Indels: 23
0.74 0.16 0.10
Matches are distributed among these distances:
43 22 0.13
44 93 0.54
45 56 0.33
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGATACAAG
Found at i:42474485 original size:88 final size:88
Alignment explanation
Indices: 42474222--42474485 Score: 239
Period size: 88 Copynumber: 3.0 Consensus size: 88
42474212 TCATGATGAA
* * * * * *
42474222 TCTTATCTCCCTAAAGTTGTAGTGGAACAGATTAAAGCCA-CTAATCTTA-CCCCCTTGAAGTTG
1 TCTTATCTCCCTAAAGTTGCAGTGG-ACAGACTAAAGACAGCAAACCTTATCTCCC-TGAAGTTG
* ** * *
42474285 TAGTGGGGCAGGTTGAAA-TTACAAG
64 CAGTGGAACAGATT-AAAGATACAAG
* *
42474310 TCTTATCTCCTTAAAGTTGCAGTGGAACAGACTAAAGATAGCAAACCTTATCTCCCTGAAGTTGC
1 TCTTATCTCCCTAAAGTTGCAGTGG-ACAGACTAAAGACAGCAAACCTTATCTCCCTGAAGTTGC
* * *
42474375 AGTGGAGCAGGTTGAAGATACAAG
65 AGTGGAACAGATTAAAGATACAAG
* ** * * **
42474399 TCTTATCTCCCTGAAGTTGCAGTAGG-CAGACTAAAGACAGTGAATCTTATTTCCCTGGCGTTGC
1 TCTTATCTCCCTAAAGTTGCAGT-GGACAGACTAAAGACAGCAAACCTTATCTCCCTGAAGTTGC
*
42474463 AGTGGAACAGATTAAAGCTACAA
65 AGTGGAACAGATTAAAGATACAA
42474486 ATTATTGCGG
Statistics
Matches: 147, Mismatches: 25, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
88 87 0.59
89 54 0.37
90 6 0.04
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (88 bp):
TCTTATCTCCCTAAAGTTGCAGTGGACAGACTAAAGACAGCAAACCTTATCTCCCTGAAGTTGCA
GTGGAACAGATTAAAGATACAAG
Found at i:42474621 original size:143 final size:143
Alignment explanation
Indices: 42474356--42474954 Score: 699
Period size: 143 Copynumber: 4.2 Consensus size: 143
42474346 GATAGCAAAC
* * ** * *
42474356 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAG
1 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAG
* *
42474421 TAG-GCAGACTAAAGACAGTGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACA
66 CAGAGCAGACTAAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACA
*
42474485 AATTATTGCGGAT
131 AATTATTGCAGAT
* * * * *
42474498 CTTATCTTCCCGAAGTTGTAGTAGAGCAGATTGAAGCCACCAGTCTTATCTCTCTGAAGTTGCAG
1 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAG
* *
42474563 CAGAGCAAACTAAAGACAGCGAATCTTATTTCCCTAGCGTTGCAGTGGAACAGATTAAAGCTACA
66 CAGAGCAGACTAAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACA
** *
42474628 AA-TGGTGGAGAAT
131 AATTATTGCAG-AT
* * * * *
42474641 CTTATCATCCTAAAGTTACAGTGGAGCAGGTTGAAGCCACCAGCCTTATCTCTCTGAAGTTGCAG
1 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAG
* * * * * * * * *
42474706 CGGAGCAGACTGAATATAGCGAACCTTATTTCTCTGGTGTTGCAGTGGAATAAATTAAAGCTACA
66 CAGAGCAGACTAAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACA
42474771 AATTA-TGACAGAT
131 AATTATTG-CAGAT
* * *
42474784 CTTATCTTCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACCAACCTCATCTCCCTGAAGTTGCAG
1 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAG
* * * ** * * * *
42474849 CAGAGCAGACTGAAGATAGCGAATCTTATATCCCTGAAGTTGCAGTGGAATAGATTGACGCTA-T
66 CAGAGCAGACTAAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACA
*
42474913 AA--ACTGCAGAT
131 AATTATTGCAGAT
*
42474924 CTTAT-TTCTCTGAAGTTGCAGTAGAGCAGAT
1 CTTATCTTC-CTGAAGTTGCAGTGGAGCAGAT
42474955 CATATTAAAC
Statistics
Matches: 392, Mismatches: 59, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
139 3 0.01
140 31 0.08
141 2 0.01
142 64 0.16
143 289 0.74
144 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (143 bp):
CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAG
CAGAGCAGACTAAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACA
AATTATTGCAGAT
Found at i:42475061 original size:45 final size:45
Alignment explanation
Indices: 42475005--42475170 Score: 165
Period size: 45 Copynumber: 3.7 Consensus size: 45
42474995 TCGAAGTTAT
* *
42475005 AAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAAGACAGC
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACAAC
* * * * *
42475050 TAGTCTTATCTCCCTCAAGTTGCAGTGAAGCAGACTGAAGATAAC
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACAAC
* * * * * *
42475095 AAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAG-CCAC
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACAAC
* * *
42475139 AAATCTAATCTCCCTGAA-TATGTAGTGGAGCA
1 AAGTCTTATCTCCCTGAAGT-TGCAGTGGAGCA
42475171 AATTGTAGAT
Statistics
Matches: 100, Mismatches: 20, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
43 1 0.01
44 28 0.28
45 71 0.71
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (45 bp):
AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACAAC
Found at i:42476710 original size:64 final size:65
Alignment explanation
Indices: 42476633--42476754 Score: 144
Period size: 64 Copynumber: 1.9 Consensus size: 65
42476623 TTATTAAATT
* *
42476633 AATTAATTAATTAATATCA-TTAGTATTATTATTTTTCC-T-TTTATTTATTTACTTATTATTAC
1 AATTAATTAATTAAT-T-AGTTAGCATTATTATATTTCCTTATTTATTTATTTACTTATTATTAC
42476695 TA
64 TA
* *
42476697 AATT-ATTATATTAATTAGTTTTGCATTATTATATTTCCTTATTTATTTATTTATTTAT
1 AATTAATTA-ATTAATTAG-TTAGCATTATTATATTTCCTTATTTATTTATTTACTTAT
42476755 CTAAATATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
62 1 0.02
63 5 0.10
64 26 0.53
65 1 0.02
66 16 0.33
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (65 bp):
AATTAATTAATTAATTAGTTAGCATTATTATATTTCCTTATTTATTTATTTACTTATTATTACTA
Found at i:42476844 original size:3 final size:3
Alignment explanation
Indices: 42476836--42476929 Score: 116
Period size: 3 Copynumber: 31.3 Consensus size: 3
42476826 TTTAGATTTC
42476836 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * *
42476884 TAT TAT CAT CAT CAT CAT CAT TAT TAT TAT TAA TAC TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
42476930 CTTAATTTGT
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:42478867 original size:19 final size:18
Alignment explanation
Indices: 42478839--42478878 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
42478829 TTAGAAAATA
* *
42478839 TATATTTTTAATAATTTT
1 TATATTTTTAAAAATGTT
42478857 TATAGTTTTTAAAAATGTT
1 TATA-TTTTTAAAAATGTT
42478876 TAT
1 TAT
42478879 TAAAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
TATATTTTTAAAAATGTT
Found at i:42480610 original size:9 final size:9
Alignment explanation
Indices: 42480593--42480623 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
42480583 TCGAGTTGAT
42480593 TCGAATAAC
1 TCGAATAAC
*
42480602 TCGATTAAC
1 TCGAATAAC
42480611 TCGAATAAC
1 TCGAATAAC
42480620 TCGA
1 TCGA
42480624 TTCATTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:42484122 original size:6 final size:6
Alignment explanation
Indices: 42484111--42484141 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
42484101 AGTTTTCTTC
42484111 AAAATG AAAATG AAAATG AAAATG AAAATG A
1 AAAATG AAAATG AAAATG AAAATG AAAATG A
42484142 CCTAGAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:42486647 original size:92 final size:92
Alignment explanation
Indices: 42486485--42486661 Score: 275
Period size: 92 Copynumber: 1.9 Consensus size: 92
42486475 AAGCAGGTAG
* *
42486485 AAAAGATAGAGAGGATTGAGAATAGGAGAGAATAAAGAAGGAAGTTGTATTAACCAAAATTGATA
1 AAAAGATAGAGAGGATTGAGAAGAGGAGAGAATAAAGAAGGAAATTGTATTAACCAAAATTGATA
* *
42486550 GTTGTTTCCTCTCTCAACAGTAGAGAA
66 ATTGTTTCCCCTCTCAACAGTAGAGAA
* * *
42486577 AAAAGATATA-AGGAATTGAGAAGAGGATAGAATAATGAAGGAAATTGTATTAACCAAAATTGAT
1 AAAAGATAGAGAGG-ATTGAGAAGAGGAGAGAATAAAGAAGGAAATTGTATTAACCAAAATTGAT
42486641 AATTGTTTCCCCTCTCAACAG
65 AATTGTTTCCCCTCTCAACAG
42486662 CAGGTTAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
91 3 0.04
92 74 0.96
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (92 bp):
AAAAGATAGAGAGGATTGAGAAGAGGAGAGAATAAAGAAGGAAATTGTATTAACCAAAATTGATA
ATTGTTTCCCCTCTCAACAGTAGAGAA
Found at i:42489238 original size:24 final size:24
Alignment explanation
Indices: 42489174--42489238 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
42489164 ATTCTTTGTC
42489174 ATTTGTCCTTTTTTTAAAGTTTTTT
1 ATTTGTCCTTTTTTT-AAGTTTTTT
*
42489199 ATTTAT--TTACTTTTTAAGTTTTTT
1 ATTTGTCCTT--TTTTTAAGTTTTTT
*
42489223 ATTTGTCCTTTATTTA
1 ATTTGTCCTTTTTTTA
42489239 TTTTACTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
23 2 0.06
24 19 0.58
25 10 0.30
26 2 0.06
ACGTcount: A:0.18, C:0.08, G:0.06, T:0.68
Consensus pattern (24 bp):
ATTTGTCCTTTTTTTAAGTTTTTT
Found at i:42489242 original size:22 final size:21
Alignment explanation
Indices: 42489217--42489262 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
42489207 ACTTTTTAAG
42489217 TTTT-TTATTTGTCCTTTATTTA
1 TTTTATTATTTGT--TTTATTTA
42489239 TTTTACTTATTTGTTTTATTTA
1 TTTTA-TTATTTGTTTTATTTA
42489261 TT
1 TT
42489263 GGTTTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 14 0.64
24 8 0.36
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (21 bp):
TTTTATTATTTGTTTTATTTA
Found at i:42492730 original size:30 final size:30
Alignment explanation
Indices: 42492694--42492796 Score: 154
Period size: 30 Copynumber: 3.4 Consensus size: 30
42492684 CCTATGGCCA
*
42492694 GGTGATATGAACTTGAATCGCCCATGTCTG
1 GGTGATATGAACTCGAATCGCCCATGTCTG
* *
42492724 GGTGATATGAACTCAAATCGCCCATGTCCG
1 GGTGATATGAACTCGAATCGCCCATGTCTG
*
42492754 GGTGATATGAACTCGTA-CTGCCCATGTCTG
1 GGTGATATGAACTCGAATC-GCCCATGTCTG
42492784 GGTGATATGAACT
1 GGTGATATGAACT
42492797 GCTCTGCGAC
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 1 0.02
30 65 0.98
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.28
Consensus pattern (30 bp):
GGTGATATGAACTCGAATCGCCCATGTCTG
Found at i:42492758 original size:60 final size:60
Alignment explanation
Indices: 42492660--42492796 Score: 186
Period size: 60 Copynumber: 2.3 Consensus size: 60
42492650 TGGTTGTTGC
* * * *
42492660 TCTGGGTGAAATAAACTCAAACCGCCTATGGCCAGGTGATATGAACTTGAA-TCGCCCATG
1 TCTGGGTGATATGAACTCAAACCGCCCATGGCCAGGTGATATGAACTCGAACT-GCCCATG
* * * *
42492720 TCTGGGTGATATGAACTCAAATCGCCCATGTCCGGGTGATATGAACTCGTACTGCCCATG
1 TCTGGGTGATATGAACTCAAACCGCCCATGGCCAGGTGATATGAACTCGAACTGCCCATG
42492780 TCTGGGTGATATGAACT
1 TCTGGGTGATATGAACT
42492797 GCTCTGCGAC
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 67 0.99
61 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (60 bp):
TCTGGGTGATATGAACTCAAACCGCCCATGGCCAGGTGATATGAACTCGAACTGCCCATG
Found at i:42495452 original size:19 final size:21
Alignment explanation
Indices: 42495409--42495465 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
42495399 TGACCAGTTA
*
42495409 TAATATATATTTTTAATTTTC
1 TAATATATAATTTTAATTTTC
*
42495430 TAATATA-AATTTTACTTTT-
1 TAATATATAATTTTAATTTTC
42495449 TAATATATATATTTTAA
1 TAATATATA-ATTTTAA
42495466 AAAAGCCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 7 0.23
20 11 0.35
21 13 0.42
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (21 bp):
TAATATATAATTTTAATTTTC
Found at i:42495508 original size:24 final size:24
Alignment explanation
Indices: 42495480--42495531 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
42495470 GCCATAATTC
42495480 TTTTTAAC-AAATAAAATCCTTTTT
1 TTTTTAACTAAAT-AAATCCTTTTT
42495504 TTTTTAACTAAATAAATCCTTTTT
1 TTTTTAACTAAATAAATCCTTTTT
42495528 TTTT
1 TTTT
42495532 ATTTTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTTTAACTAAATAAATCCTTTTT
Found at i:42495606 original size:23 final size:24
Alignment explanation
Indices: 42495580--42495624 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
42495570 ATAAAATATT
42495580 ATTTTTT-AAAATTTTTAAATAGA
1 ATTTTTTAAAAATTTTTAAATAGA
*
42495603 ATTTTTTAAAAATTTTTGAATA
1 ATTTTTTAAAAATTTTTAAATA
42495625 TCATTAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (24 bp):
ATTTTTTAAAAATTTTTAAATAGA
Found at i:42495655 original size:14 final size:14
Alignment explanation
Indices: 42495636--42495671 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
42495626 CATTAAAAGC
42495636 AATTTAAAAATCAT
1 AATTTAAAAATCAT
*
42495650 AATTTAAAAATTAT
1 AATTTAAAAATCAT
42495664 -ATTTAAAA
1 AATTTAAAA
42495672 TTAAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTAAAAATCAT
Found at i:42495701 original size:21 final size:20
Alignment explanation
Indices: 42495677--42495720 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
42495667 TAAAATTAAA
*
42495677 TAAATATATATTTAAAAATTT
1 TAAATATACATTT-AAAATTT
42495698 TAAAATATACATTTAAAATTT
1 T-AAATATACATTTAAAATTT
42495719 TA
1 TA
42495721 TAAAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 9 0.43
22 11 0.52
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATATACATTTAAAATTT
Found at i:42495735 original size:24 final size:22
Alignment explanation
Indices: 42495652--42495739 Score: 65
Period size: 24 Copynumber: 3.9 Consensus size: 22
42495642 AAAATCATAA
* *
42495652 TTTAAAAATTATATTT-AAAA-
1 TTTAAAAAATAAATTTAAAAAT
42495672 -TTAAATAAATATATATTTAAAAAT
1 TTTAAA-AAATA-A-ATTTAAAAAT
* * *
42495696 TTTAAAATATACATTTAAAATT
1 TTTAAAAAATAAATTTAAAAAT
42495718 TTATAAAAAAATAAATTTAAAA
1 TT-T-AAAAAATAAATTTAAAA
42495740 GGTCATATCT
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
19 5 0.09
20 4 0.08
22 15 0.28
23 5 0.09
24 19 0.36
25 5 0.09
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTAAAAAATAAATTTAAAAAT
Found at i:42495803 original size:16 final size:17
Alignment explanation
Indices: 42495782--42495815 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
42495772 GTTTTATATT
42495782 ATTAAAAA-ATATTTAA
1 ATTAAAAATATATTTAA
42495798 ATTAAAAATATATTTAA
1 ATTAAAAATATATTTAA
42495815 A
1 A
42495816 ATTTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTAAAAATATATTTAA
Found at i:42495959 original size:24 final size:24
Alignment explanation
Indices: 42495905--42495965 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
42495895 TAAATAAAGG
*
42495905 AAAAATAAAAAAACTTAAAAAGTAA
1 AAAAAT-AAAAAACTTAAAAAGAAA
* *
42495930 ATAAATAAAAAACTTAAAACGAAA
1 AAAAATAAAAAACTTAAAAAGAAA
*
42495954 AAAAATGAAAAA
1 AAAAATAAAAAA
42495966 GGACAAAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (24 bp):
AAAAATAAAAAACTTAAAAAGAAA
Found at i:42501075 original size:35 final size:34
Alignment explanation
Indices: 42501034--42501099 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
42501024 ATGTATATAT
*
42501034 ATGTATATGTTATAATAATAAATAA-AATGAATCTA
1 ATGTATATATTATAAT-AT-AATAATAATGAATCTA
42501069 ATGTATATATTATAATATAATAATAATGAAT
1 ATGTATATATTATAATATAATAATAATGAAT
42501100 GAAATTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 5 0.17
34 9 0.31
35 15 0.52
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.39
Consensus pattern (34 bp):
ATGTATATATTATAATATAATAATAATGAATCTA
Found at i:42502331 original size:19 final size:20
Alignment explanation
Indices: 42502302--42502345 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
42502292 CAAAGATTAA
42502302 AAATG-AATATGAGA-TGA-G
1 AAATGAAATATGA-ATTGATG
42502320 AAATGAAATATGAATTGATG
1 AAATGAAATATGAATTGATG
42502340 AAATGA
1 AAATGA
42502346 GATGTGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.26
19 10 0.43
20 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.25
Consensus pattern (20 bp):
AAATGAAATATGAATTGATG
Found at i:42512261 original size:19 final size:19
Alignment explanation
Indices: 42512237--42512278 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
42512227 ATATATACAA
42512237 AATAAAATAATAATAAAAT
1 AATAAAATAATAATAAAAT
* * *
42512256 AATAAAATATTAGTAAACT
1 AATAAAATAATAATAAAAT
42512275 AATA
1 AATA
42512279 TTTATTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
AATAAAATAATAATAAAAT
Found at i:42517795 original size:30 final size:30
Alignment explanation
Indices: 42517755--42517812 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
42517745 AGCTTAGGGA
*
42517755 CAAAAGTGTAAATATTCAAAAGTTTGGGGG
1 CAAAAGTGTAAATATTCAAAAATTTGGGGG
* * *
42517785 CAAAATTGTAATTTTTCAAAAATTTGGG
1 CAAAAGTGTAAATATTCAAAAATTTGGG
42517813 TGGAGGACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.33
Consensus pattern (30 bp):
CAAAAGTGTAAATATTCAAAAATTTGGGGG
Found at i:42518208 original size:33 final size:33
Alignment explanation
Indices: 42518144--42518468 Score: 163
Period size: 33 Copynumber: 9.4 Consensus size: 33
42518134 ATATAAAGGG
*
42518144 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
42518171 GGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
42518204 GGTTGCTAAGTGCTTATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG---GT
*
42518246 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
42518279 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---GGT
42518321 GGTTGCTAAGTGCTGATTCCCC----CGA--GG-
1 GGTTGCTAAGTGCTGATTCCCCGATTC-ATTGGT
* *
42518348 GGTTCCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
42518381 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG---GT
* *
42518423 GGTTGCTAAGTGCTGATTCCCCAACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
42518456 AGTTGCTAAGTGC
1 GGTTGCTAAGTGC
42518469 AGAATCCACC
Statistics
Matches: 231, Mismatches: 26, Indels: 76
0.69 0.08 0.23
Matches are distributed among these distances:
27 42 0.18
28 2 0.01
30 1 0.00
31 3 0.01
32 4 0.02
33 70 0.30
34 10 0.04
35 3 0.01
36 4 0.02
37 8 0.03
38 8 0.03
39 5 0.02
40 2 0.01
41 7 0.03
42 62 0.27
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:42518265 original size:42 final size:41
Alignment explanation
Indices: 42518204--42518340 Score: 173
Period size: 42 Copynumber: 3.5 Consensus size: 41
42518194 ATTCATTGGT
*
42518204 GGTTGCTAAGTGCTTATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG-AAGG
* *
42518246 GGTTGCTAAGTGCTGATTCC-CCG-A-C-T-CAT-TG--GT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGG
42518279 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAA-GG
42518321 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
42518341 CCCGAGGGGT
Statistics
Matches: 81, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
33 21 0.26
34 3 0.04
35 1 0.01
36 3 0.04
37 3 0.04
38 3 0.04
39 3 0.04
40 1 0.01
41 3 0.04
42 40 0.49
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGG
Found at i:42518290 original size:75 final size:75
Alignment explanation
Indices: 42518167--42518342 Score: 316
Period size: 75 Copynumber: 2.3 Consensus size: 75
42518157 TGATTCCCCC
* * *
42518167 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTTATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
42518232 TTAAATGTGA
66 TTAAATGTGA
42518242 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
42518307 TTAAATGTGA
66 TTAAATGTGA
*
42518317 AGGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGTTGCTAAGTGCTGATTCCCC
42518343 CGAGGGGTTC
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 97 1.00
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.33
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:42518349 original size:102 final size:102
Alignment explanation
Indices: 42518243--42518444 Score: 368
Period size: 102 Copynumber: 2.0 Consensus size: 102
42518233 TAAATGTGAA
* * *
42518243 AGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
1 AGGGGTTCCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
*
42518308 TAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCG
42518345 AGGGGTTCCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
1 AGGGGTTCCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
42518410 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
42518445 AACTCATTGG
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 96 1.00
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (102 bp):
AGGGGTTCCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:42518435 original size:177 final size:177
Alignment explanation
Indices: 42518139--42518479 Score: 592
Period size: 177 Copynumber: 1.9 Consensus size: 177
42518129 ATTGAATATA
* * *
42518139 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTCCTAAGTGCTGATTCCCCGAATCATTGGT
* * *
42518204 GGTTGCTAAGTGCTTATTCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCG
66 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCA
* * *
42518269 ACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
131 ACTCATTGGTAGTTGCTAAGTGCAGAATCCACCGTATCTTAAATGTG
*
42518316 AAGGGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTCCTAAGTGCTGATTCCCCGAATCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTCCTAAGTGCTGATTCCCCGAATCATTGGT
42518381 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCA
66 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCA
42518446 ACTCATTGGTAGTTGCTAAGTGCAGAATCCACCG
131 ACTCATTGGTAGTTGCTAAGTGCAGAATCCACCG
42518480 ATAAAGGATA
Statistics
Matches: 154, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
177 154 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (177 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTCCTAAGTGCTGATTCCCCGAATCATTGGT
GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCA
ACTCATTGGTAGTTGCTAAGTGCAGAATCCACCGTATCTTAAATGTG
Found at i:42519907 original size:45 final size:47
Alignment explanation
Indices: 42519856--42519966 Score: 163
Period size: 49 Copynumber: 2.4 Consensus size: 47
42519846 TCCATATAGA
* *
42519856 ATTACACTTCTTTTATTT-TATT-TTAGAATAAGGTTTTTCAACCTT
1 ATTACACTTCTTCTATTTATATTATTAGAATAAGGTATTTCAACCTT
*
42519901 ATTACACTTCATCTATTTGATATTAATTAGAATAAGGTATTTCAACCTT
1 ATTACACTTCTTCTATTT-ATATT-ATTAGAATAAGGTATTTCAACCTT
42519950 ATTACACTTCTTCTATT
1 ATTACACTTCTTCTATT
42519967 AGAATATGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
45 16 0.28
47 4 0.07
49 38 0.66
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.49
Consensus pattern (47 bp):
ATTACACTTCTTCTATTTATATTATTAGAATAAGGTATTTCAACCTT
Found at i:42525029 original size:100 final size:100
Alignment explanation
Indices: 42524840--42525028 Score: 303
Period size: 100 Copynumber: 1.9 Consensus size: 100
42524830 AAAAAACCAT
42524840 ATAGTACACTAGTGGCGCCATTCTATATGGCTAACCAAATAAAATATTATTTCTTTAAAAATTTA
1 ATAGTACACTAGTGGCGCCATTCTATATGGCTAACCAAATAAAATATTATTTCTTTAAAAATTTA
42524905 AAATAAAAAATAACACATTTAAAAATATATTATAC
66 AAATAAAAAATAACACATTTAAAAATATATTATAC
* * *
42524940 ATAGTATACTGGTGGCGCCATTCTATATGGCTCTACCAAATAAAATA-TATTT-TTTAAAAATTT
1 ATAGTACACTAGTGGCGCCATTCTATATGGCT-AACCAAATAAAATATTATTTCTTTAAAAA-TT
*
42525003 TAAATTAAAAAA-AACACATTTAAAAA
64 TAAAATAAAAAATAACACATTTAAAAA
42525029 AACCCTAATA
Statistics
Matches: 83, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
99 22 0.27
100 48 0.58
101 13 0.16
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (100 bp):
ATAGTACACTAGTGGCGCCATTCTATATGGCTAACCAAATAAAATATTATTTCTTTAAAAATTTA
AAATAAAAAATAACACATTTAAAAATATATTATAC
Found at i:42526287 original size:15 final size:16
Alignment explanation
Indices: 42526267--42526296 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
42526257 CTTTAAAAAT
42526267 TATTAAAAT-ATAAAC
1 TATTAAAATAATAAAC
42526282 TATTAAAATAATAAA
1 TATTAAAATAATAAA
42526297 ATTGTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
TATTAAAATAATAAAC
Found at i:42528524 original size:28 final size:25
Alignment explanation
Indices: 42528444--42528610 Score: 69
Period size: 28 Copynumber: 6.5 Consensus size: 25
42528434 AAAGGTTGAT
42528444 AATTTAAATG-AAATGAGAA-AAAAA
1 AATTTAAATGAAAATGA-AAGAAAAA
*** * *
42528468 AATTTGTTTG-AAATGAAATGGTACAA
1 AATTTAAATGAAAATGAAA--GAAAAA
42528494 AATTTAAATGAAAATTGAAAGAAAGATA
1 AATTTAAATGAAAA-TGAAAGAAA-A-A
* *
42528522 AATTTAAAT-TAAATG--AGTAAAA
1 AATTTAAATGAAAATGAAAGAAAAA
* * *
42528544 ATTTTCATTG-AAATGAAATGAGAAAA
1 AATTTAAATGAAAATGAAA-GA-AAAA
* * *
42528570 AAATTAAATTAAATTTGAAAGAAAGATA
1 AATTTAAATGAAA-ATGAAAGAAA-A-A
42528598 AATTTAAATGAAA
1 AATTTAAATGAAA
42528611 TGAGAGGCAC
Statistics
Matches: 103, Mismatches: 24, Indels: 28
0.66 0.15 0.18
Matches are distributed among these distances:
22 12 0.12
23 3 0.03
24 18 0.17
25 1 0.01
26 25 0.24
27 12 0.12
28 32 0.31
ACGTcount: A:0.57, C:0.01, G:0.13, T:0.29
Consensus pattern (25 bp):
AATTTAAATGAAAATGAAAGAAAAA
Found at i:42528577 original size:76 final size:76
Alignment explanation
Indices: 42528444--42528655 Score: 230
Period size: 76 Copynumber: 2.8 Consensus size: 76
42528434 AAAGGTTGAT
* * ** * *
42528444 AATTTAAATGAAATGAGAAAAAAAAATTTGTTTGAAATGAAATG-GTACAAAATTTAAATGAAAA
1 AATTTAAATGAAATGAG--AGAAAATTTTAATTGAAATGAAATGAG-AAAAAAATTAAATGAAAA
42528508 TTGAAAGAAAGATA
63 TTGAAAGAAAGATA
* * * *
42528522 AATTTAAATTAAATGAGTA-AAAATTTTCATTGAAATGAAATGAGAAAAAAATTAAATTAAATTT
1 AATTTAAATGAAATGAG-AGAAAATTTTAATTGAAATGAAATGAGAAAAAAATTAAATGAAAATT
42528586 GAAAGAAAGATA
65 GAAAGAAAGATA
** * * * *
42528598 AATTTAAATGAAATGAGAGGCACTTTTAATTTAAATAAAATGAGAAAAAAATTTAATG
1 AATTTAAATGAAATGAGAGAAAATTTTAATTGAAATGAAATGAGAAAAAAATTAAATG
42528656 GAAAGATAGA
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
75 1 0.01
76 95 0.83
77 2 0.02
78 16 0.14
ACGTcount: A:0.55, C:0.02, G:0.14, T:0.29
Consensus pattern (76 bp):
AATTTAAATGAAATGAGAGAAAATTTTAATTGAAATGAAATGAGAAAAAAATTAAATGAAAATTG
AAAGAAAGATA
Found at i:42528652 original size:27 final size:27
Alignment explanation
Indices: 42528443--42528654 Score: 81
Period size: 27 Copynumber: 8.1 Consensus size: 27
42528433 GAAAGGTTGA
42528443 TAATTTAAATGAAATGAGAAAAAAAAATT
1 TAATTTAAATGAAATGAG--AAAAAAATT
* * *
42528472 T-GTTTGAAATGAAATG-GTACAAAATT
1 TAATTT-AAATGAAATGAGAAAAAAATT
* * * *
42528498 TAA-ATGAA--AATTGA-AAGAAAGA-T
1 TAATTTAAATGAAATGAGAA-AAAAATT
* * * *
42528521 AAATTTAAATTAAATGAGTAAAAATTT
1 TAATTTAAATGAAATGAGAAAAAAATT
* *
42528548 TCATTGAAATGAAATGAGAAAAAAA-T
1 TAATTTAAATGAAATGAGAAAAAAATT
* * *
42528574 TAAATTAAAT---TTGA-AAGAAAGA-T
1 TAATTTAAATGAAATGAGAA-AAAAATT
* *** **
42528597 AAATTTAAATGAAATGAGAGGCACTTT
1 TAATTTAAATGAAATGAGAAAAAAATT
*
42528624 TAATTTAAATAAAATGAGAAAAAAATT
1 TAATTTAAATGAAATGAGAAAAAAATT
42528651 TAAT
1 TAAT
42528655 GGAAAGATAG
Statistics
Matches: 125, Mismatches: 43, Indels: 32
0.62 0.22 0.16
Matches are distributed among these distances:
22 2 0.02
23 24 0.19
24 6 0.05
25 2 0.02
26 29 0.23
27 47 0.38
28 4 0.03
29 11 0.09
ACGTcount: A:0.55, C:0.02, G:0.13, T:0.30
Consensus pattern (27 bp):
TAATTTAAATGAAATGAGAAAAAAATT
Found at i:42528758 original size:48 final size:47
Alignment explanation
Indices: 42528624--42528820 Score: 162
Period size: 48 Copynumber: 4.3 Consensus size: 47
42528614 GAGGCACTTT
* * *
42528624 TAATTTAAATAAAATGAG--AAAA--AAATTT-AATGGAAAGATAGA
1 TAATTTAAATGAAATGAGAAAAAATTAAATTTAAATTGAAAAATAGA
* * ***
42528666 TAATTTAAAAGAAATGACAAAAAAAATTAAATTTGCGTTGAAAAATAGA
1 TAATTTAAATGAAATG--AGAAAAAATTAAATTTAAATTGAAAAATAGA
* *
42528715 AAATTTAAATGAAATGAGGAAAAAATTAAATTTAAATTTAAAAATA-A
1 TAATTTAAATGAAATGA-GAAAAAATTAAATTTAAATTGAAAAATAGA
* * * *
42528762 T-A--TATATGAATTGAGAAAAAAATAAATTTAAATTGAAAAA-ATA
1 TAATTTAAATGAAATGAGAAAAAATTAAATTTAAATTGAAAAATAGA
*
42528805 TAATTTAAGTGAAATG
1 TAATTTAAATGAAATG
42528821 GAATTGAAAT
Statistics
Matches: 121, Mismatches: 22, Indels: 20
0.74 0.13 0.12
Matches are distributed among these distances:
42 15 0.12
43 26 0.21
44 12 0.10
46 13 0.11
47 2 0.02
48 29 0.24
49 24 0.20
ACGTcount: A:0.58, C:0.01, G:0.12, T:0.29
Consensus pattern (47 bp):
TAATTTAAATGAAATGAGAAAAAATTAAATTTAAATTGAAAAATAGA
Found at i:42528780 original size:22 final size:22
Alignment explanation
Indices: 42528733--42528804 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 22
42528723 ATGAAATGAG
*
42528733 GAAAAAAT--TAAATTTAAATT
1 GAAAAAATAATAAATATAAATT
* * *
42528753 -TAAAAATAATATATATGAATT
1 GAAAAAATAATAAATATAAATT
*
42528774 GAGAAAAA-AATAAATTTAAATT
1 GA-AAAAATAATAAATATAAATT
42528796 GAAAAAATA
1 GAAAAAATA
42528805 TAATTTAAGT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
19 6 0.15
21 14 0.36
22 14 0.36
23 5 0.13
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (22 bp):
GAAAAAATAATAAATATAAATT
Found at i:42528817 original size:19 final size:19
Alignment explanation
Indices: 42528778--42528818 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
42528768 TGAATTGAGA
*
42528778 AAAAAATAAATTTAAATTG
1 AAAAAATAAATTTAAAGTG
42528797 AAAAAATATAATTT-AAGTG
1 AAAAAATA-AATTTAAAGTG
42528816 AAA
1 AAA
42528819 TGGAATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (19 bp):
AAAAAATAAATTTAAAGTG
Found at i:42528837 original size:12 final size:12
Alignment explanation
Indices: 42528814--42528843 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
42528804 ATAATTTAAG
42528814 TGAAAT-GGAAT
1 TGAAATGGGAAT
42528825 TGAAATGGGAAT
1 TGAAATGGGAAT
42528837 TGAAATG
1 TGAAATG
42528844 AAATTGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (12 bp):
TGAAATGGGAAT
Found at i:42528847 original size:5 final size:5
Alignment explanation
Indices: 42528814--42528892 Score: 50
Period size: 5 Copynumber: 14.6 Consensus size: 5
42528804 ATAATTTAAG
* * * *
42528814 TGAAA TGGAAT TGAAA TGGGAAT TGAAA TGAAA TTGGAA TGAAA TAAAA
1 TGAAA T-GAAA TGAAA T--GAAA TGAAA TGAAA -TGAAA TGAAA TGAAA
* *
42528863 TTAAAA TGAAA TGAAAA TGAAA AGAAA TGA
1 -TGAAA TGAAA TG-AAA TGAAA TGAAA TGA
42528893 CTAATCTGCA
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
5 36 0.62
6 18 0.31
7 4 0.07
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.23
Consensus pattern (5 bp):
TGAAA
Found at i:42528855 original size:11 final size:11
Alignment explanation
Indices: 42528814--42528890 Score: 66
Period size: 11 Copynumber: 7.0 Consensus size: 11
42528804 ATAATTTAAG
*
42528814 TGAAATGGAAT
1 TGAAATGAAAT
*
42528825 TGAAATGGGAAT
1 TGAAAT-GAAAT
42528837 TGAAATGAAAT
1 TGAAATGAAAT
*
42528848 TGGAATGAAA-
1 TGAAATGAAAT
* * *
42528858 TAAAATTAAAA
1 TGAAATGAAAT
*
42528869 TGAAATGAAAA
1 TGAAATGAAAT
*
42528880 TGAAAAGAAAT
1 TGAAATGAAAT
42528891 GACTAATCTG
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
10 7 0.13
11 37 0.67
12 11 0.20
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (11 bp):
TGAAATGAAAT
Found at i:42528858 original size:16 final size:16
Alignment explanation
Indices: 42528814--42528892 Score: 68
Period size: 16 Copynumber: 4.8 Consensus size: 16
42528804 ATAATTTAAG
*
42528814 TGAAATGGAATTGAAAT
1 TGAAAT-GAAATGAAAT
* *
42528831 GGGAATTGAAATGAAAT
1 -TGAAATGAAATGAAAT
* *
42528848 TGGAATGAAATAAAAT
1 TGAAATGAAATGAAAT
* *
42528864 TAAAATGAAATGAAAA
1 TGAAATGAAATGAAAT
*
42528880 TGAAAAGAAATGA
1 TGAAATGAAATGA
42528893 CTAATCTGCA
Statistics
Matches: 48, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
16 35 0.73
17 9 0.19
18 4 0.08
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.23
Consensus pattern (16 bp):
TGAAATGAAATGAAAT
Found at i:42531057 original size:49 final size:53
Alignment explanation
Indices: 42530962--42531075 Score: 146
Period size: 53 Copynumber: 2.2 Consensus size: 53
42530952 TCAAAAAAAT
* * * * *
42530962 TTGACAGGTCAGCATAAAAAAAAATTAATTTATTTTTGTACTTGGT-GTGGCTA
1 TTGACAGGCCAACACAAAAAAAAATTAA-TTATCTTTGTACTTGGTGGTGGCCA
42531015 TTGACAGGCCAACACAAAAAAAAATTAA-T-TCTTT-TACTTGGTGGTGGCCA
1 TTGACAGGCCAACACAAAAAAAAATTAATTATCTTTGTACTTGGTGGTGGCCA
42531065 TTGACAGGCCA
1 TTGACAGGCCA
42531076 GCATCAATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
49 8 0.15
50 21 0.38
51 1 0.02
53 25 0.45
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (53 bp):
TTGACAGGCCAACACAAAAAAAAATTAATTATCTTTGTACTTGGTGGTGGCCA
Found at i:42534197 original size:32 final size:32
Alignment explanation
Indices: 42534160--42534226 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
42534150 TATATTTATA
42534160 TAATTTGATTTATTCTTTTATTGAAAGTAAAT
1 TAATTTGATTTATTCTTTTATTGAAAGTAAAT
42534192 TAATTTGATTTATTCTTTTATTGAAAGTAAAT
1 TAATTTGATTTATTCTTTTATTGAAAGTAAAT
42534224 TAA
1 TAA
42534227 AAAATTTCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (32 bp):
TAATTTGATTTATTCTTTTATTGAAAGTAAAT
Found at i:42534333 original size:22 final size:23
Alignment explanation
Indices: 42534284--42534333 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
42534274 TAAGCTCTCA
*
42534284 TAAATTTTTAAAAAATTATAAAT
1 TAAATTGTTAAAAAATTATAAAT
42534307 T-AATTGTT-AAAAATT-TAGAAT
1 TAAATTGTTAAAAAATTATA-AAT
42534328 TAAATT
1 TAAATT
42534334 TTTTTATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.08
21 11 0.46
22 10 0.42
23 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
TAAATTGTTAAAAAATTATAAAT
Found at i:42534485 original size:20 final size:19
Alignment explanation
Indices: 42534451--42534503 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
42534441 TATAAAAAAT
* *
42534451 TAATTTTTGTAATTTGTTTA
1 TAATTTTTATAATTT-TTAA
*
42534471 TAATTTTTATGATTTTTAA
1 TAATTTTTATAATTTTTAA
42534490 T-ATTTTTA-AATTTT
1 TAATTTTTATAATTTT
42534504 AAAAGTGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 5 0.17
18 7 0.24
19 4 0.14
20 13 0.45
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (19 bp):
TAATTTTTATAATTTTTAA
Found at i:42535069 original size:31 final size:31
Alignment explanation
Indices: 42535034--42535097 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
42535024 CCACGTAAAA
*
42535034 ATATATGGTACACTATTTTTAGAAAAAGTAT
1 ATATATGGTACACTATTTTTAGAAAAAATAT
42535065 ATATATGGTACACTATTTTTAGAAAAAATAT
1 ATATATGGTACACTATTTTTAGAAAAAATAT
42535096 AT
1 AT
42535098 GATAATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (31 bp):
ATATATGGTACACTATTTTTAGAAAAAATAT
Found at i:42539020 original size:3 final size:3
Alignment explanation
Indices: 42539012--42539050 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
42539002 AATTGAAACA
42539012 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42539051 CGTCAATGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:42540862 original size:4 final size:4
Alignment explanation
Indices: 42540853--42540889 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
42540843 AATAGTATAT
*
42540853 TATG TATG TATG TATG TATG TATA TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
42540890 GTAATGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:42542565 original size:3 final size:3
Alignment explanation
Indices: 42542557--42542582 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
42542547 CCATGTACAT
42542557 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
42542583 GTCTCTCTTA
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:42542685 original size:22 final size:22
Alignment explanation
Indices: 42542657--42542733 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
42542647 TTTCTTTTAA
42542657 TTAGGAGATTAGATGCTAAAGT
1 TTAGGAGATTAGATGCTAAAGT
** * *
42542679 TTAGGAGATAATATTTTGGTTTAA--
1 TTAGGAGAT--TA-GAT-GCTAAAGT
42542703 TTAGGAGATTAGATGCTAAAGT
1 TTAGGAGATTAGATGCTAAAGT
42542725 TTAGGAGAT
1 TTAGGAGAT
42542734 AATATTTTGG
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 4 0.10
21 1 0.02
22 20 0.49
24 11 0.27
25 1 0.02
26 4 0.10
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (22 bp):
TTAGGAGATTAGATGCTAAAGT
Found at i:42542706 original size:46 final size:46
Alignment explanation
Indices: 42542652--42542746 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
42542642 TCTCTTTTCT
42542652 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
42542698 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
42542744 TTT
1 TTT
42542747 CTATATTTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.41
Consensus pattern (46 bp):
TTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
Found at i:42543888 original size:2 final size:2
Alignment explanation
Indices: 42543881--42543918 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
42543871 AGAAGTAAAG
42543881 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
42543919 GAAAAATAGG
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):
TA
Found at i:42544240 original size:2 final size:2
Alignment explanation
Indices: 42544233--42544257 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42544223 TAATAAGGTA
42544233 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
42544258 ATAGGTAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42546104 original size:44 final size:43
Alignment explanation
Indices: 42546055--42546297 Score: 245
Period size: 44 Copynumber: 5.5 Consensus size: 43
42546045 TCGACCTACA
* * * *
42546055 GCAACTTCAGAGG-CATAGGATTCATCATTTTAATCCGCTCCACT
1 GCAACTTCAG-GGAGATAGGATT-ATAACTTTAATCTGCTCCACT
*
42546099 GCAACTTCAGGGAGATAGGATTTGTAACTTTAATCTGCTCCACT
1 GCAACTTCAGGGAGATAGGA-TTATAACTTTAATCTGCTCCACT
* * * * *
42546143 GCAACTTTAGGGAGATAAGATTCACTATCTTCAATCTACTCCACT
1 GCAACTTCAGGGAGATAGGATT-A-TAACTTTAATCTGCTCCACT
* * * *
42546188 GCAACTTCAGGGAGATAAGACTTGTAACTTCAATCCGCTCCACT
1 GCAACTTCAGGGAGATAGGA-TTATAACTTTAATCTGCTCCACT
** *
42546232 GCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTACTCCACT
1 GCAACTTCAGGGAGATAGGATTA-TAACTTTAATCTGCTCCACT
* *
42546276 GCAACTTCAGAGAGATAAGATT
1 GCAACTTCAGGGAGATAGGATT
42546298 CGCCAGGATC
Statistics
Matches: 168, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
43 6 0.04
44 122 0.73
45 38 0.23
46 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (43 bp):
GCAACTTCAGGGAGATAGGATTATAACTTTAATCTGCTCCACT
Found at i:42546238 original size:133 final size:131
Alignment explanation
Indices: 42546086--42546596 Score: 450
Period size: 133 Copynumber: 3.8 Consensus size: 131
42546076 TCATCATTTT
* *
42546086 AATCCGCTCCACTGCAACTTCAGGGAGATAGGATT-TGTAACTTTAATCTGCTCCACTGCAACTT
1 AATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAT-TAACTTTAATCTACTCCACTACAACTT
*
42546150 TAGGGAGATAAGATTCACTATCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTAA
65 CAGGGAGATAAGATTCACT-TCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGACTTGT-A
42546215 CTTC
128 CTTC
** *
42546219 AATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTACTCCACTGCAACTTC
1 AATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTAACTTTAATCTACTCCACTACAACTTC
* * *** * * *
42546284 AGAGAGATAAGATTCGC--C-AGGATCTACTCTACTGCAACTTTAGAGAGATAAGA-TTCG--C-
66 AGGGAGATAAGATTCACTTCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGACTT-GTACT
42546342 -C
130 TC
** * * * **
42546343 AGGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGTTCCAC
1 A--ATCCGCTCCACTGCAACTTCAGGGAGATAGGA--T-T-A-TTA-A-CTTTAATCTACTCCAC
* * * ** *
42546408 CACAACTTTAGGGAAATAAGATTTGCTATCTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAG
57 TACAACTTCAGGGAGATAAGATTCACT-TCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAG
* *
42546473 ACTT-CATTTC
121 ACTTGTACTTC
* * * ** *
42546483 GATCCGCT-CATTGCAACTTCAGGGAGATAGTATTATTGGCTTTAATCTACTCTACTACAACTTC
1 AATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTAACTTTAATCTACTCCACTACAACTTC
* *
42546547 AGGGAGATAAGATTTGTCATCTTCTTCAATCTATTCCACTGCCACTTCAG
66 AGGGAGATAAGA--T-TCA-CTTCTTCAATCTACTCCACTGCAACTTCAG
42546597 TGGTATAGGA
Statistics
Matches: 298, Mismatches: 56, Indels: 48
0.74 0.14 0.12
Matches are distributed among these distances:
124 2 0.01
126 28 0.09
128 3 0.01
129 31 0.10
130 33 0.11
131 2 0.01
132 3 0.01
133 135 0.45
134 4 0.01
135 1 0.00
136 1 0.00
137 47 0.16
138 7 0.02
140 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (131 bp):
AATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTAACTTTAATCTACTCCACTACAACTTC
AGGGAGATAAGATTCACTTCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTACTT
C
Found at i:42546321 original size:41 final size:41
Alignment explanation
Indices: 42546264--42546378 Score: 212
Period size: 41 Copynumber: 2.8 Consensus size: 41
42546254 ATTGGCTTTA
*
42546264 ATCTACTCCACTGCAACTTCAGAGAGATAAGATTCGCCAGG
1 ATCTACTCTACTGCAACTTCAGAGAGATAAGATTCGCCAGG
*
42546305 ATCTACTCTACTGCAACTTTAGAGAGATAAGATTCGCCAGG
1 ATCTACTCTACTGCAACTTCAGAGAGATAAGATTCGCCAGG
42546346 ATCTACTCTACTGCAACTTCAGAGAGATAAGAT
1 ATCTACTCTACTGCAACTTCAGAGAGATAAGAT
42546379 CTGTGATTTA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (41 bp):
ATCTACTCTACTGCAACTTCAGAGAGATAAGATTCGCCAGG
Found at i:42562867 original size:20 final size:19
Alignment explanation
Indices: 42562844--42563050 Score: 85
Period size: 20 Copynumber: 10.4 Consensus size: 19
42562834 ATGCACATTA
42562844 GTGCCCCTGTTTGCACTTT
1 GTGCCCCTGTTTGCACTTT
* ***
42562863 GGTGCCCTTAAATGCACATTT
1 -GTGCCCCTGTTTGCAC-TTT
****
42562884 GTGCCCCTGAACACACATTT
1 GTGCCCCTGTTTGCAC-TTT
*
42562904 GTGCCCCTGTTCGCACTTT
1 GTGCCCCTGTTTGCACTTT
* * *
42562923 GGTACCCCTGTATACACTTT
1 -GTGCCCCTGTTTGCACTTT
* *
42562943 AGTGTCCCTGCTTGCACGTTT
1 -GTGCCCCTGTTTGCAC-TTT
* * **
42562964 GTGCTCCTGTTCGCACTACG
1 GTGCCCCTGTTTGCACT-TT
* * * * *
42562984 GTGCCCTTGTATACAATTCG
1 GTGCCCCTGTTTGCACTT-T
42563004 GTGTCCCC-GTTTGCACGTTT
1 GTG-CCCCTGTTTGCAC-TTT
*
42563024 GTG-CCCTGTTCGCACTTT
1 GTGCCCCTGTTTGCACTTT
42563042 AGTGCCCCT
1 -GTGCCCCT
42563051 ATTCTGTATA
Statistics
Matches: 137, Mismatches: 40, Indels: 20
0.70 0.20 0.10
Matches are distributed among these distances:
18 6 0.04
19 14 0.10
20 106 0.77
21 11 0.08
ACGTcount: A:0.13, C:0.31, G:0.21, T:0.35
Consensus pattern (19 bp):
GTGCCCCTGTTTGCACTTT
Found at i:42562908 original size:40 final size:40
Alignment explanation
Indices: 42562832--42562909 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
42562822 AGTGTTCCTG
****
42562832 AAATGCACATTAGTGCCCCTGTTTGCACTTTGGTGCCCTT
1 AAATGCACATTAGTGCCCCTGAACACACTTTGGTGCCCTT
*
42562872 AAATGCACATTTGTGCCCCTGAACACACATTT-GTGCCC
1 AAATGCACATTAGTGCCCCTGAACACAC-TTTGGTGCCC
42562910 CTGTTCGCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 29 0.91
41 3 0.09
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (40 bp):
AAATGCACATTAGTGCCCCTGAACACACTTTGGTGCCCTT
Found at i:42562952 original size:60 final size:60
Alignment explanation
Indices: 42562837--42562998 Score: 164
Period size: 60 Copynumber: 2.7 Consensus size: 60
42562827 TCCTGAAATG
* * ** *
42562837 CACATTAGTGCCCCTGTTTGCACTTTGGTGCCCTTAAATGCACATTTGTGCCCCTGAACA
1 CACATTTGTGCCCCTGTTCGCACTTTGGTGCCCTTGTATACACATTTGTGCCCCTGAACA
* * * ****
42562897 CACATTTGTGCCCCTGTTCGCACTTTGGTACCCCTGTATACAC-TTTAGTGTCCCTGCTTG
1 CACATTTGTGCCCCTGTTCGCACTTTGGTGCCCTTGTATACACATTT-GTGCCCCTGAACA
* * **
42562957 CACGTTTGTGCTCCTGTTCGCACTACGGTGCCCTTGTATACA
1 CACATTTGTGCCCCTGTTCGCACTTTGGTGCCCTTGTATACA
42562999 ATTCGGTGTC
Statistics
Matches: 83, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
59 3 0.04
60 80 0.96
ACGTcount: A:0.16, C:0.31, G:0.19, T:0.34
Consensus pattern (60 bp):
CACATTTGTGCCCCTGTTCGCACTTTGGTGCCCTTGTATACACATTTGTGCCCCTGAACA
Found at i:42563008 original size:60 final size:59
Alignment explanation
Indices: 42562901--42563039 Score: 179
Period size: 60 Copynumber: 2.3 Consensus size: 59
42562891 TGAACACACA
** * * *
42562901 TTTGTGCCCCTGTTCGCACTTTGGTACCCCTGTATACACTTTAGTGTCCCTGCTTGCACG
1 TTTGTG-CCCTGTTCGCACTACGGTACCCCTGTATACAATTCAGTGTCCCCGCTTGCACG
* * * *
42562961 TTTGTGCTCCTGTTCGCACTACGGTGCCCTTGTATACAATTCGGTGTCCCCGTTTGCACG
1 TTTGTGC-CCTGTTCGCACTACGGTACCCCTGTATACAATTCAGTGTCCCCGCTTGCACG
42563021 TTTGTGCCCTGTTCGCACT
1 TTTGTGCCCTGTTCGCACT
42563040 TTAGTGCCCC
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
59 13 0.19
60 56 0.81
ACGTcount: A:0.11, C:0.31, G:0.22, T:0.37
Consensus pattern (59 bp):
TTTGTGCCCTGTTCGCACTACGGTACCCCTGTATACAATTCAGTGTCCCCGCTTGCACG
Found at i:42565104 original size:44 final size:42
Alignment explanation
Indices: 42565035--42565129 Score: 102
Period size: 44 Copynumber: 2.2 Consensus size: 42
42565025 TGTGACATCG
* * * *
42565035 TGTAAGACCACGTCTTGGACGTTGGCCTCGATTTGAGATTTGCA
1 TGTAAGACCACGTCTTGGACATTGGCCTC-ATATAAGA-TTACA
* *
42565079 TGTAAGACCATGTC-TGAGACATTGGCGTCATATAAGATTACA
1 TGTAAGACCACGTCTTG-GACATTGGCCTCATATAAGATTACA
42565121 TGTAAGACC
1 TGTAAGACC
42565130 CTGTTTGGGA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
42 13 0.30
43 8 0.18
44 23 0.52
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.29
Consensus pattern (42 bp):
TGTAAGACCACGTCTTGGACATTGGCCTCATATAAGATTACA
Found at i:42570328 original size:8 final size:8
Alignment explanation
Indices: 42570315--42570339 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
42570305 TTTTTAATGA
42570315 TATTTTAT
1 TATTTTAT
42570323 TATTTTAT
1 TATTTTAT
42570331 TATTTTAT
1 TATTTTAT
42570339 T
1 T
42570340 TAGCATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:42575384 original size:7 final size:7
Alignment explanation
Indices: 42575372--42575396 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
42575362 TAATAAATTA
42575372 GTTTAGG
1 GTTTAGG
42575379 GTTTAGG
1 GTTTAGG
42575386 GTTTAGG
1 GTTTAGG
42575393 GTTT
1 GTTT
42575397 TTAAGTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (7 bp):
GTTTAGG
Found at i:42575692 original size:125 final size:126
Alignment explanation
Indices: 42575469--42575753 Score: 412
Period size: 125 Copynumber: 2.3 Consensus size: 126
42575459 TAATTTAAAG
* * * * *
42575469 AAGCTCCGACATGAACGCGCTTTTGCTACAGTGGCTCCTGAGAAAATAATTTCGAGTAGACGTTT
1 AAGCTCCCACATGGACGCTCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
* * *
42575534 CTGAGCAAACAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGTAGAAGTACTGAAAA
66 CTGAGCAAACAATGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
* * *
42575595 AAGCTCCCACGTGGACGCTCTTTTGTTACAGTAGCTCCT-AAAAAATAATTTTGAGTAGACGTTT
1 AAGCTCCCACATGGACGCTCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
42575659 CTGAGCAAACAATGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
66 CTGAGCAAACAATGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
* * * *
42575720 AATCTTCCACTTGGAC-ATGCTTTTGCTACAGTAG
1 AAGCTCCCACATGGACGCT-CTTTTGCTACAGTAG
42575754 TTGAACGTTA
Statistics
Matches: 142, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
124 1 0.01
125 108 0.76
126 33 0.23
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (126 bp):
AAGCTCCCACATGGACGCTCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
CTGAGCAAACAATGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
Found at i:42576164 original size:21 final size:21
Alignment explanation
Indices: 42576119--42576166 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
42576109 TTTGTCCAGT
* * * *
42576119 CTCCGGCGGGGGTTGTGGTTG
1 CTCCGGCGGGGATTCTAGTTC
42576140 CTCCGGCGGGGATTCTAGTTC
1 CTCCGGCGGGGATTCTAGTTC
42576161 CTCCGG
1 CTCCGG
42576167 TATGGTATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.04, C:0.27, G:0.42, T:0.27
Consensus pattern (21 bp):
CTCCGGCGGGGATTCTAGTTC
Found at i:42578313 original size:11 final size:10
Alignment explanation
Indices: 42578299--42578401 Score: 61
Period size: 11 Copynumber: 9.9 Consensus size: 10
42578289 AAATAGGGAT
42578299 TTGAGAGAAA
1 TTGAGAGAAA
*
42578309 TTTGAAAGGAAA
1 -TTGAGA-GAAA
42578321 TTGAGAGCAAA
1 TTGAGAG-AAA
*
42578332 TTGAGATTAAA
1 TTGAGA-GAAA
* *
42578343 -T-AG-GGAT
1 TTGAGAGAAA
42578350 TTGAGAGAAA
1 TTGAGAGAAA
*
42578360 TTTGAAAGCAAA
1 -TTGAGAG-AAA
42578372 TTGAGAGCAAA
1 TTGAGAG-AAA
42578383 TTGAGAGGAAA
1 TTGAGA-GAAA
42578394 TT-AGAGAA
1 TTGAGAGAA
42578402 GGAATGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
7 1 0.01
8 1 0.01
9 7 0.10
10 7 0.10
11 49 0.67
12 8 0.11
ACGTcount: A:0.47, C:0.03, G:0.27, T:0.23
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:42578327 original size:22 final size:22
Alignment explanation
Indices: 42578299--42578401 Score: 75
Period size: 22 Copynumber: 4.4 Consensus size: 22
42578289 AAATAGGGAT
42578299 TTGAGAGAAATTTGAAAGGAAA
1 TTGAGAGAAATTTGAAAGGAAA
* * *
42578321 TTGAGAGCAAATTGAGATTAAATAGGGAT
1 TTGAGAG-AAA-T----TTGAA-AGGAAA
*
42578350 TTGAGAGAAATTTGAAAGCAAA
1 TTGAGAGAAATTTGAAAGGAAA
*
42578372 TTGAGAGCAAA-TTGAGAGGAAA
1 TTGAGAG-AAATTTGAAAGGAAA
42578394 TT-AGAGAA
1 TTGAGAGAA
42578402 GGAATGATTT
Statistics
Matches: 64, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
20 2 0.03
21 4 0.06
22 28 0.44
23 10 0.16
24 1 0.02
27 1 0.02
28 7 0.11
29 11 0.17
ACGTcount: A:0.47, C:0.03, G:0.27, T:0.23
Consensus pattern (22 bp):
TTGAGAGAAATTTGAAAGGAAA
Found at i:42578342 original size:51 final size:51
Alignment explanation
Indices: 42578287--42578388 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
42578277 TAAAGCTCTT
*
42578287 TTAAATAGGGATTTGAGAGAAATTTGAAAGGAAATTGAGAGCAAATTGAGA
1 TTAAATAGGGATTTGAGAGAAATTTGAAAGCAAATTGAGAGCAAATTGAGA
42578338 TTAAATAGGGATTTGAGAGAAATTTGAAAGCAAATTGAGAGCAAATTGAGA
1 TTAAATAGGGATTTGAGAGAAATTTGAAAGCAAATTGAGAGCAAATTGAGA
42578389 GGAAATTAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.45, C:0.03, G:0.26, T:0.25
Consensus pattern (51 bp):
TTAAATAGGGATTTGAGAGAAATTTGAAAGCAAATTGAGAGCAAATTGAGA
Found at i:42578833 original size:9 final size:9
Alignment explanation
Indices: 42578807--42578857 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
42578797 TAAAAATTTT
42578807 ATTTTTATA
1 ATTTTTATA
42578816 ATTTGTTTATA
1 A-TT-TTTATA
*
42578827 ATTTTTATG
1 ATTTTTATA
42578836 ATTTTTA-A
1 ATTTTTATA
42578844 TATTTTTA-A
1 -ATTTTTATA
42578853 ATTTT
1 ATTTT
42578858 AAAAGCGTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
8 5 0.14
9 21 0.57
10 4 0.11
11 7 0.19
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (9 bp):
ATTTTTATA
Found at i:42578848 original size:18 final size:19
Alignment explanation
Indices: 42578806--42578856 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
42578796 ATAAAAATTT
*
42578806 TATTTTTATAATTTGTTTA
1 TATTTTTATAATTTGTTAA
*
42578825 TAATTTTTATGATTT-TTAA
1 T-ATTTTTATAATTTGTTAA
42578844 TATTTTTA-AATTT
1 TATTTTTATAATTT
42578857 TAAAAGCGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 4 0.14
18 7 0.25
19 5 0.18
20 12 0.43
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
TATTTTTATAATTTGTTAA
Found at i:42584052 original size:28 final size:28
Alignment explanation
Indices: 42584015--42584073 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
42584005 ATATGCTTAG
42584015 AATCCCTAATGAGTCTATTTTCTGAAGA
1 AATCCCTAATGAGTCTATTTTCTGAAGA
42584043 AATCCCTAATGAGTCTATTTTCTGAAGA
1 AATCCCTAATGAGTCTATTTTCTGAAGA
42584071 AAT
1 AAT
42584074 AAAGGAAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.36
Consensus pattern (28 bp):
AATCCCTAATGAGTCTATTTTCTGAAGA
Found at i:42595588 original size:62 final size:62
Alignment explanation
Indices: 42595512--42595638 Score: 227
Period size: 62 Copynumber: 2.0 Consensus size: 62
42595502 TATTCTAAAT
* * *
42595512 TTTAATTACTATCTTATCTATGATGTTTCCTACAAAGTTCAAAATTATGGGGTATGGGTCGA
1 TTTAATTACAATCTTATCTATGATGTTTCATACAAAGTTCAAAATTATAGGGTATGGGTCGA
42595574 TTTAATTACAATCTTATCTATGATGTTTCATACAAAGTTCAAAATTATAGGGTATGGGTCGA
1 TTTAATTACAATCTTATCTATGATGTTTCATACAAAGTTCAAAATTATAGGGTATGGGTCGA
42595636 TTT
1 TTT
42595639 CACGTCACAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.41
Consensus pattern (62 bp):
TTTAATTACAATCTTATCTATGATGTTTCATACAAAGTTCAAAATTATAGGGTATGGGTCGA
Done.