Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007832.1 Hibiscus syriacus cultivar Beakdansim tig00110174_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: 4020056
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 21
Found at i:306061 original size:20 final size:21
Alignment explanation
Indices: 306038--306078 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
306028 TATTATATAT
**
306038 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
306058 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
306079 GAAAAATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:307493 original size:11 final size:11
Alignment explanation
Indices: 307470--307501 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
307460 TGTAATTAAT
307470 TATTTATATATA
1 TATTTA-ATATA
307482 TATTTAATATA
1 TATTTAATATA
307493 TATTTAATA
1 TATTTAATA
307502 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:307505 original size:3 final size:3
Alignment explanation
Indices: 307497--307629 Score: 216
Period size: 3 Copynumber: 44.7 Consensus size: 3
307487 AATATATATT
*
307497 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
307545 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
307593 TAA TAA T-A TAA TAA T-A TGGA TAA AAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TA
307630 TGGATAAAAA
Statistics
Matches: 122, Mismatches: 5, Indels: 6
0.92 0.04 0.05
Matches are distributed among these distances:
2 4 0.03
3 116 0.95
4 2 0.02
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:312252 original size:18 final size:18
Alignment explanation
Indices: 312213--312252 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
312203 AAATATTTTT
* *
312213 ATTATTATTATCATCATT
1 ATTATTATTATCAGCATA
*
312231 ATTATTATTATTAGCATA
1 ATTATTATTATCAGCATA
312249 ATTA
1 ATTA
312253 CACTTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTATTATTATCAGCATA
Found at i:313747 original size:30 final size:30
Alignment explanation
Indices: 313712--313826 Score: 101
Period size: 30 Copynumber: 3.8 Consensus size: 30
313702 TTATTTTCTA
313712 TTTAGTCCCTTAAGTTTCTATTTTTGTTAT
1 TTTAGTCCCTTAAGTTTCTATTTTTGTTAT
** * * *
313742 TTTAGTCATTTAA--ATATATTTATT-TTCT
1 TTTAGTCCCTTAAGTTTCTATTT-TTGTTAT
* * * *
313770 ATTTAGTCCCTTTAGTTTTTGTTTTTGATAT
1 -TTTAGTCCCTTAAGTTTCTATTTTTGTTAT
313801 TTTAGTCCCTTAAGTTTCTAGTTTTT
1 TTTAGTCCCTTAAGTTTCTA-TTTTT
313827 CAATTTTTTC
Statistics
Matches: 63, Mismatches: 16, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
28 9 0.14
29 12 0.19
30 30 0.48
31 12 0.19
ACGTcount: A:0.19, C:0.11, G:0.10, T:0.60
Consensus pattern (30 bp):
TTTAGTCCCTTAAGTTTCTATTTTTGTTAT
Found at i:317554 original size:26 final size:26
Alignment explanation
Indices: 317521--317628 Score: 87
Period size: 26 Copynumber: 4.2 Consensus size: 26
317511 AGATCAAATC
*
317521 AAAACAAAGAGAAAATAAGCAAAGAA
1 AAAACAAAGAGAAAAGAAGCAAAGAA
* * * *
317547 AGAGCAAAGGGAAAAGAAGTAAAGAA
1 AAAACAAAGAGAAAAGAAGCAAAGAA
*
317573 AAAACAAAGAGCAAAACAA--AAGAGAA
1 AAAACAAAGAG-AAAAGAAGCAA-AGAA
* * *
317599 AAGAAAAAAGAAAAAAGAA-AAAAGAA
1 AA-AACAAAGAGAAAAGAAGCAAAGAA
317625 AAAA
1 AAAA
317629 AAATCAAAAG
Statistics
Matches: 66, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
25 4 0.06
26 47 0.71
27 15 0.23
ACGTcount: A:0.74, C:0.06, G:0.19, T:0.02
Consensus pattern (26 bp):
AAAACAAAGAGAAAAGAAGCAAAGAA
Found at i:317600 original size:7 final size:7
Alignment explanation
Indices: 317590--317648 Score: 75
Period size: 7 Copynumber: 8.3 Consensus size: 7
317580 AGAGCAAAAC
*
317590 AAAAGAG
1 AAAAGAA
317597 AAAAGAA
1 AAAAGAA
317604 AAAAGAA
1 AAAAGAA
317611 AAAAGAA
1 AAAAGAA
317618 AAAAGAA
1 AAAAGAA
*
317625 AAAAAAA
1 AAAAGAA
317632 TCAAAAGAA
1 --AAAAGAA
317641 AAAA-AA
1 AAAAGAA
317647 AA
1 AA
317649 CAAATAAAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
6 4 0.09
7 37 0.79
9 6 0.13
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:317605 original size:31 final size:31
Alignment explanation
Indices: 317520--317607 Score: 88
Period size: 33 Copynumber: 2.8 Consensus size: 31
317510 AAGATCAAAT
* * *
317520 CAAAAC-AAAGAGAAAATAAGCAAAGAAAGAG
1 CAAAACAAAAGAGAAAAGAA-AAAACAAAGAG
** *
317551 CAAAGGGAAAAGAAGTAAAGAAAAAACAAAGAG
1 CAAA-ACAAAAG-AGAAAAGAAAAAACAAAGAG
317584 CAAAACAAAAGAGAAAAGAAAAAA
1 CAAAACAAAAGAGAAAAGAAAAAA
317608 GAAAAAAGAA
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
31 16 0.36
32 5 0.11
33 17 0.38
34 7 0.16
ACGTcount: A:0.70, C:0.08, G:0.19, T:0.02
Consensus pattern (31 bp):
CAAAACAAAAGAGAAAAGAAAAAACAAAGAG
Found at i:317607 original size:14 final size:13
Alignment explanation
Indices: 317569--317648 Score: 72
Period size: 14 Copynumber: 5.9 Consensus size: 13
317559 AAAGAAGTAA
*
317569 AGAAAAAACAAAG
1 AGAAAAAAAAAAG
* *
317582 AGCAAAACAAAAG
1 AGAAAAAAAAAAG
317595 AGAAAAGAAAAAAG
1 AGAAAA-AAAAAAG
*
317609 AAAAAAGAAAAAAG
1 AGAAAA-AAAAAAG
*
317623 A-AAAAAAAATCAAA
1 AGAAAAAAAA--AAG
317637 AGAAAAAAAAAA
1 AGAAAAAAAAAA
317649 CAAATAAAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
12 4 0.07
13 21 0.38
14 23 0.41
15 8 0.14
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.01
Consensus pattern (13 bp):
AGAAAAAAAAAAG
Found at i:317619 original size:12 final size:12
Alignment explanation
Indices: 317557--317648 Score: 64
Period size: 12 Copynumber: 7.4 Consensus size: 12
317547 AGAGCAAAGG
*
317557 GAAAAGAAGTAAA
1 GAAAAGAA-AAAA
317570 GAAAA-AACAAAGA
1 GAAAAGAA-AAA-A
* *
317583 GCAAAACAAAAGA
1 G-AAAAGAAAAAA
317596 GAAAAGAAAAAA
1 GAAAAGAAAAAA
317608 GAAAAAAGAAAAAA
1 G--AAAAGAAAAAA
*
317622 GAAAA-AAAAAT
1 GAAAAGAAAAAA
*
317633 CAAAAGAAAAAA
1 GAAAAGAAAAAA
317645 -AAAA
1 GAAAA
317649 CAAATAAAAG
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
11 13 0.20
12 23 0.35
13 9 0.14
14 18 0.28
15 2 0.03
ACGTcount: A:0.79, C:0.04, G:0.14, T:0.02
Consensus pattern (12 bp):
GAAAAGAAAAAA
Found at i:317647 original size:16 final size:15
Alignment explanation
Indices: 317585--317652 Score: 77
Period size: 14 Copynumber: 4.5 Consensus size: 15
317575 AACAAAGAGC
*
317585 AAAACAAAAGAGAAA
1 AAAACAAAAGAAAAA
*
317600 AGAA-AAAAGAAAAA
1 AAAACAAAAGAAAAA
*
317614 AGAA-AAAAGAAAAA
1 AAAACAAAAGAAAAA
317628 AAAATCAAAAGAAAAAA
1 AAAA-CAAAAG-AAAAA
317645 AAAACAAA
1 AAAACAAA
317653 TAAAAGGGGA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
14 26 0.55
15 3 0.06
16 9 0.19
17 9 0.19
ACGTcount: A:0.84, C:0.04, G:0.10, T:0.01
Consensus pattern (15 bp):
AAAACAAAAGAAAAA
Found at i:318985 original size:65 final size:62
Alignment explanation
Indices: 318897--319122 Score: 200
Period size: 65 Copynumber: 3.5 Consensus size: 62
318887 AATTTCTATC
* * ** *
318897 AAAACAAATTTCGTCTCACTTGAGACATTTTTCTTTGAAACACAAATATTTGAGTTTGTTTCCCT
1 AAAA-AAATTT-GTCTCCCTTGAGACA-TTTTCTAT-AAACAC-AACCTTTGAGATTGTTTCCCT
318962 TG
61 TG
* * * * *
318964 AAAAAAATTTGTCTCCCTTGAGATAGTTTCCCATAAAACACAACCTGTGAGATTGTTTCCCTTT
1 AAAAAAATTTGTCTCCCTTGAGACA-TTTTCTAT-AAACACAACCTTTGAGATTGTTTCCCTTG
* * * *
319028 AAACAAATTTTGTCTCCCTTGAGATAATTTCTCATAAACATTAACCTTTGAGATTGTTTCCCTTG
1 AAA-AAAATTTGTCTCCCTTGAGACATTTTCT-ATAAACA-CAACCTTTGAGATTGTTTCCCTTG
* ** *
319093 AAACAGTTTTGTCTCCCTTGAGACAGTTTC
1 AAAAAAATTTGTCTCCCTTGAGACATTTTC
319123 CCATGAAACA
Statistics
Matches: 133, Mismatches: 23, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
64 52 0.39
65 71 0.53
66 6 0.05
67 4 0.03
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.38
Consensus pattern (62 bp):
AAAAAAATTTGTCTCCCTTGAGACATTTTCTATAAACACAACCTTTGAGATTGTTTCCCTTG
Found at i:319109 original size:20 final size:20
Alignment explanation
Indices: 319081--319121 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
319071 ACCTTTGAGA
*
319081 TTGTTTCCCTTGAAACAGTT
1 TTGTCTCCCTTGAAACAGTT
*
319101 TTGTCTCCCTTGAGACAGTT
1 TTGTCTCCCTTGAAACAGTT
319121 T
1 T
319122 CCCATGAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (20 bp):
TTGTCTCCCTTGAAACAGTT
Found at i:319132 original size:65 final size:63
Alignment explanation
Indices: 318945--319175 Score: 261
Period size: 65 Copynumber: 3.6 Consensus size: 63
318935 AACACAAATA
* * *
318945 TTTGAGTTTGTTTCCCTTGAAAAAAATTTGTCTCCCTTGAGATAGTTTCCCATAAAACACAACC
1 TTTGAGATTGTTTCCCTTGAAACAATTTTGTCTCCCTTGAGATAGTTTCCCAT-AAACACAACC
* * * * *
319009 TGTGAGATTGTTTCCCTTTAAACAAATTTTGTCTCCCTTGAGATAATTTCTCATAAACATTAACC
1 TTTGAGATTGTTTCCCTTGAAAC-AATTTTGTCTCCCTTGAGATAGTTTCCCATAAACA-CAACC
* * * *
319074 TTTGAGATTGTTTCCCTTGAAACAGTTTTGTCTCCCTTGAGACAGTTTCCCATGAAACACCCATC
1 TTTGAGATTGTTTCCCTTGAAACAATTTTGTCTCCCTTGAGATAGTTTCCCAT-AAACA-CAACC
* *
319139 TTTGAGATCG-TT-CCTTG-AACGAATTTTGTCTCTCTTG
1 TTTGAGATTGTTTCCCTTGAAAC-AATTTTGTCTCCCTTG
319176 CGACAGCTTC
Statistics
Matches: 142, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
62 3 0.02
63 19 0.13
64 52 0.37
65 68 0.48
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.39
Consensus pattern (63 bp):
TTTGAGATTGTTTCCCTTGAAACAATTTTGTCTCCCTTGAGATAGTTTCCCATAAACACAACC
Found at i:319466 original size:130 final size:130
Alignment explanation
Indices: 319228--319468 Score: 315
Period size: 130 Copynumber: 1.9 Consensus size: 130
319218 TGAAACCAAA
* *
319228 ATCCCTAAAGTGGTATATCATCCTCATCGCGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTC
1 ATCCCTAAAGTGGTATATCATCCTCATCACATAGGAACCGTGTCATCCCCCGACCAGACCTCCTC
* ** ** **
319293 ATCACGTAGGAGCTTTGTCACCCCTAGATAATTAGTCGACCTCATCACATAGGAACCATGTTATC
66 ATCACATAGGAGCCGTGTCACCCCTAGATAACCAACCGACCTCATCACATAGGAACCATGTTATC
* * *
319358 ATCCCTAAAGATGGCT-TATCGTCCTCATCACATAGGAACTGTGTCAT-CCCCGACCAGACCTTC
1 ATCCCTAAAG-TGG-TATATCATCCTCATCACATAGGAACCGTGTCATCCCCCGACCAGACCTCC
** *
319421 TCATCACATAGGAGCCGTGTCACCTTTAGATAACCAACCGTCCTCATC
64 TCATCACATAGGAGCCGTGTCACCCCTAGATAACCAACCGACCTCATC
319469 CCGAACCATG
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
130 63 0.67
131 30 0.32
132 1 0.01
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.25
Consensus pattern (130 bp):
ATCCCTAAAGTGGTATATCATCCTCATCACATAGGAACCGTGTCATCCCCCGACCAGACCTCCTC
ATCACATAGGAGCCGTGTCACCCCTAGATAACCAACCGACCTCATCACATAGGAACCATGTTATC
Found at i:321499 original size:12 final size:12
Alignment explanation
Indices: 321484--321534 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
321474 CCGGTTTTAT
321484 TTATAATTATTA
1 TTATAATTATTA
321496 TTAT-ATTATTTA
1 TTATAATTA-TTA
* *
321508 TTATATTTTTTA
1 TTATAATTATTA
*
321520 TTTTAA-TATTA
1 TTATAATTATTA
321531 TTAT
1 TTAT
321535 TACAACCAGG
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
11 11 0.35
12 18 0.58
13 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATAATTATTA
Found at i:321504 original size:21 final size:20
Alignment explanation
Indices: 321480--321536 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 20
321470 TGTCCCGGTT
321480 TTATTTATAATTATTATTATA
1 TTATTTAT-ATTATTATTATA
*
321501 TTATTTAT-TATATT-TTTTA
1 TTATTTATAT-TATTATTATA
*
321520 TT-TTAATATTATTATTA
1 TTATTTATATTATTATTA
321537 CAACCAGGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
18 8 0.27
19 10 0.33
20 4 0.13
21 8 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTATATTATTATTATA
Found at i:323649 original size:33 final size:31
Alignment explanation
Indices: 323612--323672 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
323602 ATTAAAATTT
* *
323612 CATATTTAATTTATAATTTTTTATATATATATA
1 CATA-TTAATTTAT-AGTATTTATATATATATA
*
323645 CATATTATTTTATAGTATTTATATATAT
1 CATATTAATTTATAGTATTTATATATAT
323673 TATTAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 13 0.52
32 8 0.32
33 4 0.16
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (31 bp):
CATATTAATTTATAGTATTTATATATATATA
Found at i:323655 original size:23 final size:24
Alignment explanation
Indices: 323629--323676 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
323619 AATTTATAAT
323629 TTTTTATA-TATATATACATATTA
1 TTTTTATAGTATATATACATATTA
* *
323652 -TTTTATAGTATTTATATATATTA
1 TTTTTATAGTATATATACATATTA
323675 TT
1 TT
323677 AATATTTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
22 7 0.33
23 13 0.62
24 1 0.05
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTTTATAGTATATATACATATTA
Found at i:332192 original size:7 final size:7
Alignment explanation
Indices: 332171--332229 Score: 63
Period size: 7 Copynumber: 9.0 Consensus size: 7
332161 ATTATGCTTG
*
332171 AAGAAGA
1 AAGAAAA
332178 AA-AAAA
1 AAGAAAA
332184 AAGAAAA
1 AAGAAAA
332191 AAGAAAA
1 AAGAAAA
332198 AAG--AA
1 AAGAAAA
332203 AAGAAAA
1 AAGAAAA
*
332210 AAGAGAA
1 AAGAAAA
332217 AA-AAAA
1 AAGAAAA
*
332223 AGGAAAA
1 AAGAAAA
332230 GGGGAGGTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 5 0.11
6 9 0.20
7 30 0.68
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:332197 original size:12 final size:12
Alignment explanation
Indices: 332174--332230 Score: 64
Period size: 12 Copynumber: 4.7 Consensus size: 12
332164 ATGCTTGAAG
332174 AAGAAAA-AAAA
1 AAGAAAAGAAAA
*
332185 AGAAAAAAGAAAA
1 A-AGAAAAGAAAA
332198 AAGAAAAGAAAA
1 AAGAAAAGAAAA
332210 AAGAGAAA-AAAA
1 AAGA-AAAGAAAA
332222 AAGGAAAAG
1 AA-GAAAAG
332231 GGGAGGTCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 1 0.03
12 28 0.72
13 10 0.26
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAGAAAAGAAAA
Found at i:332204 original size:19 final size:18
Alignment explanation
Indices: 332177--332229 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 18
332167 CTTGAAGAAG
332177 AAAAAAAAAGAAAAAAGA
1 AAAAAAAAAGAAAAAAGA
332195 AAAAAGAAAAGAAAAAAGA
1 AAAAA-AAAAGAAAAAAGA
332214 GAAAAAAAAAGGAAAA
1 -AAAAAAAAA-GAAAA
332230 GGGGAGGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.16
19 17 0.53
20 10 0.31
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGAAAAAAGA
Found at i:333509 original size:83 final size:83
Alignment explanation
Indices: 333370--333885 Score: 962
Period size: 83 Copynumber: 6.2 Consensus size: 83
333360 TAACTGGAAT
*
333370 AGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AGATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
333434 ACCAATCATTGAATTTGGA
65 ACCAATCATTGAATTTGGA
* *
333453 AGATGAATGTGCTAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
1 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
333518 CCAATCATTGAATTTGGA
66 CCAATCATTGAATTTGGA
333536 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
1 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
333601 CCAATCATTGAATTTGGA
66 CCAATCATTGAATTTGGA
333619 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
1 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
333684 CCAATCATTGAATTTGGA
66 CCAATCATTGAATTTGGA
333702 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
1 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
333767 CCAATCATTGAATTTGGA
66 CCAATCATTGAATTTGGA
* *
333785 AGATGAATGTGCTCATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGCAGAA
1 AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
333850 CCAATCATTGAATTTGGA
66 CCAATCATTGAATTTGGA
*
333868 AGATGAATTTGCTCATAG
1 AGATGAATGTGCTCATAG
333886 TAGAAATAAG
Statistics
Matches: 424, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
83 424 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (83 bp):
AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
CCAATCATTGAATTTGGA
Found at i:334888 original size:113 final size:113
Alignment explanation
Indices: 334704--335563 Score: 1431
Period size: 113 Copynumber: 7.6 Consensus size: 113
334694 TGGATTGACA
334704 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
334769 AGAATTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCT
66 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
334817 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
334882 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
66 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
334930 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
334995 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
66 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
335043 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
335108 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
66 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
*
335156 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * *
335221 AGAACTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATCAGCC
66 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
* *
335269 TTTCCAGAAAAAGTTCATAATGAAAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * *
335334 AGAATTTGTTCAAACTTTTG-CTCAAATCTATCACTTGATAGATTAGCT
66 AGAATTTGTTCAACCTTTTGCCTGAATTC-ATCACTTGATGGATCAGCT
**** * *
335382 TTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * *
335447 AGAATTTGTTCAGA-TTTTTG-CTCAAATCCATCACTTGATGGATCAACT
66 AGAATTTGTTCA-ACCTTTTGCCT-GAATTCATCACTTGATGGATCAGCT
* *
335495 TTTCTAGAGAAAGTTCATAATGAGAAGAACTCATC-GAAAGAAGGATGAAGAAGTTCATAATGAG
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG-AAGAAGGAAGAAGAAGTTCATAATGAG
335559 AAGAA
65 AAGAA
335564 CTCATCAAGA
Statistics
Matches: 705, Mismatches: 38, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
112 7 0.01
113 694 0.98
114 4 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
Found at i:335834 original size:3 final size:3
Alignment explanation
Indices: 335828--335877 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
335818 ATTTATAATA
* *
335828 ATT ATT ATT A-T ATT ATTT ATT A-T ATT -TT TTT ATT ATT AAT ATT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
335871 ATT ATT A
1 ATT ATT A
335878 CAACCAGGCC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
2 6 0.15
3 31 0.77
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:335847 original size:12 final size:12
Alignment explanation
Indices: 335816--335875 Score: 54
Period size: 12 Copynumber: 4.9 Consensus size: 12
335806 TGTCCCGGTT
*
335816 TTATTTATAATAA
1 TTATTTATTAT-A
335829 TTA-TTATTATA
1 TTATTTATTATA
335840 TTATTTATTATA
1 TTATTTATTATA
335852 TT-TTT-TTATTA
1 TTATTTATTA-TA
335863 TTAATATTATTAT
1 TT-AT-TTATTAT
335876 TACAACCAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
10 3 0.08
11 11 0.28
12 16 0.40
13 4 0.10
14 3 0.08
15 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTATTTATTATA
Found at i:335853 original size:20 final size:19
Alignment explanation
Indices: 335816--335876 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 19
335806 TGTCCCGGTT
*
335816 TTATTTA-TAATAATTATTA
1 TTATTTATTATTAA-TATTA
335835 TTATATTATTTATT-ATATT-
1 TTAT-TTA-TTATTAATATTA
335854 TT-TTTATTATTAATATTA
1 TTATTTATTATTAATATTA
335872 TTATT
1 TTATT
335877 ACAACCAGGC
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
16 5 0.14
17 8 0.23
18 3 0.09
19 8 0.23
20 7 0.20
21 1 0.03
22 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTTATTATTAATATTA
Found at i:336356 original size:17 final size:18
Alignment explanation
Indices: 336321--336366 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
336311 AAAAAAACGG
336321 AGAGACAGAGAACACAAC
1 AGAGACAGAGAACACAAC
336339 AGAGAC-GAGGAA-ACAAC
1 AGAGACAGA-GAACACAAC
*
336356 AGAAACAGAGA
1 AGAGACAGAGA
336367 GAGATACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.57, C:0.17, G:0.26, T:0.00
Consensus pattern (18 bp):
AGAGACAGAGAACACAAC
Found at i:337995 original size:30 final size:29
Alignment explanation
Indices: 337952--338080 Score: 129
Period size: 30 Copynumber: 4.4 Consensus size: 29
337942 ATTATTTTTA
337952 TTTTCTA-TTTAGTCCCTTAAGTTTCTAT
1 TTTTCTATTTTAGTCCCTTAAGTTTCTAT
* * * *
337980 TTTTGTTATTTTAGTCCTTTAAATGTATGTA-
1 TTTT-CTATTTTAGTCCCTT-AA-GTTTCTAT
*
338011 TTTTCTA-TTTAGTCCCTTTAGTTTCTAT
1 TTTTCTATTTTAGTCCCTTAAGTTTCTAT
* *
338039 TTTTGCTATTTTAGTCTCTTAAGTTTCTGTT
1 TTTT-CTATTTTAGTCCCTTAAGTTTCT-AT
338070 TTTTCTATTTT
1 TTTTCTATTTT
338081 GGACCTTTAA
Statistics
Matches: 81, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
27 5 0.06
28 9 0.11
29 15 0.19
30 36 0.44
31 11 0.14
32 5 0.06
ACGTcount: A:0.16, C:0.13, G:0.09, T:0.61
Consensus pattern (29 bp):
TTTTCTATTTTAGTCCCTTAAGTTTCTAT
Found at i:338130 original size:30 final size:29
Alignment explanation
Indices: 338026--338130 Score: 79
Period size: 30 Copynumber: 3.6 Consensus size: 29
338016 TATTTAGTCC
* * *
338026 CTTT-AGTTTCTATTTTTGCTATTTT-AGT
1 CTTTAAGTTTCTGTTTGTACTATTTTGA-T
* * *
338054 CTCTTAAGTTTCTGTTTTTTCTATTTTGGAC
1 CT-TTAAGTTTCTGTTTGTACTATTTT-GAT
* *
338085 CTTTAAATTCCTGTTTGTACTATTTTGATT
1 CTTTAAGTTTCTGTTTGTACTATTTTGA-T
*
338115 CTTTAAGTTTTTGTTT
1 CTTTAAGTTTCTGTTT
338131 TTCCCATTCT
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
28 2 0.03
29 4 0.07
30 52 0.85
31 2 0.03
32 1 0.02
ACGTcount: A:0.15, C:0.12, G:0.11, T:0.61
Consensus pattern (29 bp):
CTTTAAGTTTCTGTTTGTACTATTTTGAT
Found at i:342261 original size:39 final size:39
Alignment explanation
Indices: 342218--342322 Score: 108
Period size: 39 Copynumber: 2.7 Consensus size: 39
342208 TTTAAAAAAT
*
342218 AATTTAGAATGTTAATGTAAAATAATTTAATAAATTAAG
1 AATTTAGAATGTTAATGTAAAATAATTTAAGAAATTAAG
* * *
342257 AATTTAAAATGTT-ATGGTATTAA-AATTTAAGAAATTAGG
1 AATTTAGAATGTTAAT-GTA-AAATAATTTAAGAAATTAAG
* *
342296 AATTTTGAATGTTAGA-GTGAAATAATT
1 AATTTAGAATGTTA-ATGTAAAATAATT
342323 GAGAATTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
38 4 0.08
39 46 0.87
40 2 0.04
41 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (39 bp):
AATTTAGAATGTTAATGTAAAATAATTTAAGAAATTAAG
Found at i:350408 original size:21 final size:21
Alignment explanation
Indices: 350384--350423 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
350374 TTTATGTATG
*
350384 ATATAACTTAAACTAACAAGA
1 ATATAAATTAAACTAACAAGA
350405 ATATAAATTAAACTAACAA
1 ATATAAATTAAACTAACAA
350424 ACTAATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.03, T:0.25
Consensus pattern (21 bp):
ATATAAATTAAACTAACAAGA
Found at i:350437 original size:21 final size:21
Alignment explanation
Indices: 350387--350437 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
350377 ATGTATGATA
350387 TAACTTAAACTAACAAGAATAT
1 TAAC-TAAACTAACAAGAATAT
* * *
350409 AAATTAAACTAACAA-ACTAAT
1 TAACTAAACTAACAAGAAT-AT
350430 TAACTAAA
1 TAACTAAA
350438 ATTTTGTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 2 0.09
21 19 0.83
22 2 0.09
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (21 bp):
TAACTAAACTAACAAGAATAT
Found at i:350481 original size:21 final size:19
Alignment explanation
Indices: 350452--350507 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 19
350442 TGTTTTACCC
*
350452 TAAACTAAAAAACTAATTATT
1 TAAAATAAAAAACTAA-T-TT
350473 TAAAATAAAAAAACTAATTT
1 TAAAAT-AAAAAACTAATTT
*
350493 AAATAATAAAAAACT
1 TAA-AATAAAAAACT
350508 TAACTCGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 12 0.39
21 9 0.29
22 10 0.32
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAAATAAAAAACTAATTT
Found at i:350504 original size:22 final size:22
Alignment explanation
Indices: 350458--350505 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
350448 ACCCTAAACT
*
350458 AAAAAACTAATTATTTAAAATA
1 AAAAAACTAATTATTAAAAATA
350480 AAAAAACTAA-T-TTAAATAATA
1 AAAAAACTAATTATTAAA-AATA
350501 AAAAA
1 AAAAA
350506 CTTAACTCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 10 0.42
22 10 0.42
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAAAACTAATTATTAAAAATA
Found at i:350567 original size:15 final size:15
Alignment explanation
Indices: 350543--350577 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
350533 CTTCTTCTTC
*
350543 CTCTTTTCCCTTTCT
1 CTCTTCTCCCTTTCT
350558 CTCTTCTCCCTTTCT
1 CTCTTCTCCCTTTCT
*
350573 TTCTT
1 CTCTT
350578 TTATCATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (15 bp):
CTCTTCTCCCTTTCT
Found at i:350699 original size:12 final size:12
Alignment explanation
Indices: 350682--350724 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
350672 GATAATACAA
350682 CAATAATTGCTG
1 CAATAATTGCTG
*
350694 CAATAA-TGCAG
1 CAATAATTGCTG
*
350705 CAATAAGTGCTG
1 CAATAATTGCTG
350717 CAAATAAT
1 C-AATAAT
350725 GTTGAATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 10 0.38
12 11 0.42
13 5 0.19
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (12 bp):
CAATAATTGCTG
Found at i:350708 original size:23 final size:24
Alignment explanation
Indices: 350673--350725 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
350663 CAGTGCCGCG
* *
350673 ATAATACAACAATAATTGCTGC-A
1 ATAATGCAACAATAAGTGCTGCAA
*
350696 ATAATGCAGCAATAAGTGCTGCAA
1 ATAATGCAACAATAAGTGCTGCAA
350720 ATAATG
1 ATAATG
350726 TTGAATTCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (24 bp):
ATAATGCAACAATAAGTGCTGCAA
Found at i:358290 original size:22 final size:20
Alignment explanation
Indices: 358260--358299 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
358250 TCCATTTTTA
358260 TTTTTTAAATACAAAAATATG
1 TTTTTTAAA-ACAAAAATATG
*
358281 TTTTTATAAAATAAAAATA
1 TTTTT-TAAAACAAAAATA
358300 ATTAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
TTTTTTAAAACAAAAATATG
Found at i:362897 original size:2 final size:2
Alignment explanation
Indices: 362890--362915 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
362880 AAATACCTAC
362890 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
362916 ACTAAATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:363318 original size:54 final size:55
Alignment explanation
Indices: 363195--363323 Score: 163
Period size: 55 Copynumber: 2.4 Consensus size: 55
363185 GGAATATAGA
* * * * *
363195 ACTCGAATAATCTTTAACAATCGTGTTTGCTCCCTATTTGTTCAGAGAGTATGAG
1 ACTCGAACAATCTTCAATAATCGTGTTTGCTCCCTATTCGTTCAGAGAGTATAAG
* * *
363250 ACACGAACAATCTTCAATAATC-TTTTCTGCTCTCTATTCGTTCA-AGAGTATAAG
1 ACTCGAACAATCTTCAATAATCGTGTT-TGCTCCCTATTCGTTCAGAGAGTATAAG
363304 ACTCGAACAATCTTCAATAA
1 ACTCGAACAATCTTCAATAA
363324 ACAGGTTCGC
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
54 31 0.48
55 33 0.52
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (55 bp):
ACTCGAACAATCTTCAATAATCGTGTTTGCTCCCTATTCGTTCAGAGAGTATAAG
Found at i:363366 original size:54 final size:51
Alignment explanation
Indices: 363295--364007 Score: 810
Period size: 54 Copynumber: 13.5 Consensus size: 51
363285 ATTCGTTCAA
*
363295 GAGTATA-AGACTCGAACAATCTTCAATAAACAGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATAGA-ACTCGAAC-ATCTTC---AAACGGGTTCGCTCCCTCTTTCTCTAGG
363350 GAGTATAGAACT-GAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
** * *
363400 GAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGTTCCCTCTTTATCTAGG
1 GAGTATAGAACTCGAACA---TCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
*
363454 GAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAGG
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGG
* * * *
363505 GAGTATAAAACTCGAATATCTTCTTCAAACGGGTTCGCTCCCTCTTT-TCCAAG
1 GAGTATAGAACTCG-A-A-CATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
*
363558 GAGTATGGAACT-GAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* * *
363608 GAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTGTTTCAGG
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGG
* * *
363660 AAGTATAGAACTCGAATAATCTTCTGCAAACGGATTCGCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAA-CATC-T-T-CAAACGGGTTCGCTCCCTCTTTCTCTAGG
* ** * *
363715 GAGTATTGAACTCGAACATCTTCTTCTTACGGGTTCGTTCCCTCTTTATCTAGG
1 GAGTATAGAACTCGAACA---TCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
*
363769 GAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAGG
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGG
* *
363820 GAGAATAGAACTCGAATATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCG-A-ACA-TCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* *
363874 GAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTTCAGG
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGG
* * ** * *
363926 AAGTATAGAACTCGAATAATCTTCTGCAAATAGGTTCTCTCCCT-TTTCTTTAGG
1 GAGTATAGAACTCGAA-CATC-T-T-CAAACGGGTTCGCTCCCTCTTTCTCTAGG
*
363980 GAGTATAGAACTCGAAAATCTTCAAACG
1 GAGTATAGAACTCGAACATCTTCAAACG
364008 TGTCTGCTCC
Statistics
Matches: 571, Mismatches: 57, Indels: 65
0.82 0.08 0.09
Matches are distributed among these distances:
49 27 0.05
50 62 0.11
51 147 0.26
52 40 0.07
53 33 0.06
54 182 0.32
55 38 0.07
56 40 0.07
57 2 0.00
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (51 bp):
GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:363488 original size:105 final size:106
Alignment explanation
Indices: 363295--364037 Score: 924
Period size: 105 Copynumber: 7.1 Consensus size: 106
363285 ATTCGTTCAA
* * *
363295 GAGTATA-AGACTCGAACAATCTTCAAT-AAACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATAG
1 GAGTATAGA-ACTCGAAC-ATCTTC-TTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGG
363358 AACT-GAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGG
63 AACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTCAGG
** * *
363400 GAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGTTCCCTCTTTATCTAGGGAGTATGGAAC
1 GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAAC
363465 TCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAGG
66 TCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTCAGG
* * * *
363505 GAGTATAAAACTCGAATATCTTCTTCAAACGGGTTCGCTCCCTCTTT-TCCAAGGAGTATGGAAC
1 GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAAC
363569 T-GAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGG
66 TCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTCAGG
* * * * *
363608 GAGTATGGAACTCGAACA---TCTTCAAACGGGTTCGCTCCCTCTTTGTTTCAGGAAGTATAGAA
1 GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGAA
* *
363670 CTCGAATAATCTTCTGCAAACGGATTCGCTCCCTCTTTCTCT-AGG
65 CTCGAA-CATC-T-T-CAAACGGGTTCGCTCCCTCTTTCTCTCAGG
* ** * *
363715 GAGTATTGAACTCGAACATCTTCTTCTTACGGGTTCGTTCCCTCTTTATCTAGGGAGTATGGAAC
1 GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAAC
363780 TCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAGG
66 TCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTCAGG
* * *
363820 GAGAATAGAACTCGAATATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAAC
1 GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAAC
*
363885 TCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTTCAGG
66 TCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTCAGG
* * * ** * * *
363926 AAGTATAGAACTCGAATAATCTTCTGCAAATAGGTTCTCTCCCT-TTTCTTTAGGGAGTATAGAA
1 GAGTATAGAACTCGAA-CATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAA
* * * * *
363990 CTCGAAAATCTTCAAACGTG-TCTGCTCCTTATTTCT-TCAGA
65 CTCGAACATCTTCAAACGGGTTC-GCTCCCTCTTTCTCTCAGG
364031 GAGTATA
1 GAGTATA
364038 AGACCCACAA
Statistics
Matches: 561, Mismatches: 58, Indels: 38
0.85 0.09 0.06
Matches are distributed among these distances:
100 26 0.05
101 1 0.00
102 12 0.02
103 55 0.10
104 62 0.11
105 224 0.40
106 69 0.12
107 67 0.12
108 3 0.01
109 17 0.03
110 25 0.04
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (106 bp):
GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAAC
TCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTCAGG
Found at i:363834 original size:315 final size:315
Alignment explanation
Indices: 363296--364002 Score: 1088
Period size: 315 Copynumber: 2.2 Consensus size: 315
363286 TTCGTTCAAG
*
363296 AGTATA-AGACTCGAACAATCTTCAATAAACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAA
1 AGTATAGA-ACTCGAAC-ATCTTC---AAACAGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAA
* *
363360 CT-GAACATC-T-TCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTT
61 CTCGAAAATCTTCTCAAACGGATTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTT
363422 CTTCTTACGGGTTCGTTCCCTCTTTATCTAGGGAGTATGGAACTCGAACATCTTCAAACGGGTTC
126 CTTCTTACGGGTTCGTTCCCTCTTTATCTAGGGAGTATGGAACTCGAACATCTTCAAACGGGTTC
* *
363487 GCTCCCTCTTTCTTCAGGGAGTATAAAACTCGAATATCTTCTTCAAACGGGTTCGCTCCCTCTTT
191 GCTCCCTCTTTCTTCAGGGAGAATAAAACTCGAATATATTCTTCAAACGGGTTCGCTCCCTCTTT
*
363552 -TCCAAGGAGTATGGAACT-GAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGG
256 CTCCAAGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTCAGGA
* * * *
363609 AGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTGTTTCAGGAAGTATAGAACTCG
1 AGTATAGAACTCGAACATCTTCAAACAGGTTCGCTCCCTCTTTCTTT-AGGGAGTATAGAACTCG
*
363674 AATAATCTTCTGCAAACGGATTCGCTCCCTCTTTCTCTAGGGAGTATTGAACTCGAACATCTTCT
65 AA-AATCTTCT-CAAACGGATTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCT
363739 TCTTACGGGTTCGTTCCCTCTTTATCTAGGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGC
128 TCTTACGGGTTCGTTCCCTCTTTATCTAGGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGC
*
363804 TCCCTCTTTCTTCAGGGAGAATAGAACTCGAATATATTCTTCAAACGGGTTCGCTCCCTCTTTCT
193 TCCCTCTTTCTTCAGGGAGAATAAAACTCGAATATATTCTTCAAACGGGTTCGCTCCCTCTTTCT
* * *
363869 CTAGGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTTCAGGA
258 CCAAGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTCAGGA
* * *
363927 AGTATAGAACTCGAATAATCTTCTGCAAATAGGTTCTCTCCCT-TTTCTTTAGGGAGTATAGAAC
1 AGTATAGAACTCGAA-CATC-T-T-CAAACAGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAAC
363991 TCGAAAATCTTC
62 TCGAAAATCTTC
364003 AAACGTGTCT
Statistics
Matches: 358, Mismatches: 22, Indels: 22
0.89 0.05 0.05
Matches are distributed among these distances:
309 22 0.06
310 14 0.04
311 3 0.01
312 9 0.03
313 14 0.04
314 2 0.01
315 176 0.49
316 16 0.04
317 34 0.09
318 17 0.05
319 10 0.03
320 19 0.05
321 7 0.02
322 15 0.04
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (315 bp):
AGTATAGAACTCGAACATCTTCAAACAGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGA
AAATCTTCTCAAACGGATTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCT
TACGGGTTCGTTCCCTCTTTATCTAGGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCC
CTCTTTCTTCAGGGAGAATAAAACTCGAATATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCCA
AGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTCAGGA
Found at i:375414 original size:16 final size:16
Alignment explanation
Indices: 375393--375424 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
375383 ACCTTATTCG
375393 CATGGTATCTACCCAA
1 CATGGTATCTACCCAA
*
375409 CATGGTATCTATCCAA
1 CATGGTATCTACCCAA
375425 TTATGCTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.28
Consensus pattern (16 bp):
CATGGTATCTACCCAA
Found at i:378664 original size:2 final size:2
Alignment explanation
Indices: 378657--378700 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
378647 ATACCTACTG
378657 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
378699 TA
1 TA
378701 ATAACTAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:385998 original size:20 final size:20
Alignment explanation
Indices: 385973--386015 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
385963 TCAAAACCGT
*
385973 TTTTCAAAATTTC-ATTTTGC
1 TTTTCAAAA-TCCGATTTTGC
385993 TTTTCAAAATCCGATTTTGC
1 TTTTCAAAATCCGATTTTGC
386013 TTT
1 TTT
386016 CAAGAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.23, C:0.16, G:0.07, T:0.53
Consensus pattern (20 bp):
TTTTCAAAATCCGATTTTGC
Found at i:392687 original size:30 final size:30
Alignment explanation
Indices: 392603--392676 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
392593 TAGGTAAATT
* * * *
392603 ATATTATACTTTTAGAAAGATATAT-GAAAG
1 ATATAATATTTTTAAAAAGATTTATAG-AAG
392633 ATATAATATTTTTAAAAAGATTTATAGAAG
1 ATATAATATTTTTAAAAAGATTTATAGAAG
*
392663 ATGTAATATCTTTT
1 ATATAATAT-TTTT
392677 CTAAAATTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 32 0.86
31 5 0.14
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.42
Consensus pattern (30 bp):
ATATAATATTTTTAAAAAGATTTATAGAAG
Found at i:396644 original size:23 final size:22
Alignment explanation
Indices: 396594--396642 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
396584 GTGTTTTTCT
396594 GCTTTCGAATAGAAAAATAATA
1 GCTTTCGAATAGAAAAATAATA
* *
396616 GCTTTCGACTAGGAAAATAATA
1 GCTTTCGAATAGAAAAATAATA
396638 GCTTT
1 GCTTT
396643 TCAAAACGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (22 bp):
GCTTTCGAATAGAAAAATAATA
Found at i:410582 original size:21 final size:21
Alignment explanation
Indices: 410556--410595 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
410546 AACAGATCTT
*
410556 TAGTGGCGTTTTTTAGTTCTA
1 TAGTGGCGTTTTTAAGTTCTA
410577 TAGTGGCGTTTTTAAGTTC
1 TAGTGGCGTTTTTAAGTTC
410596 CACTAGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.10, G:0.25, T:0.50
Consensus pattern (21 bp):
TAGTGGCGTTTTTAAGTTCTA
Found at i:411812 original size:36 final size:36
Alignment explanation
Indices: 411733--411819 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 36
411723 TTATCCCATT
*
411733 ATCATTTTTC-AACAAACATCTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATCTACCAAACTTTGAAA
* *
411768 AACTATTTTTCAAAGAAACATTTACCAAACTTTGAAA
1 ATC-ATTTTTCAAAGAAACATCTACCAAACTTTGAAA
411805 ATCATTTTTTCAAAG
1 ATCA-TTTTTCAAAG
411820 TTGGTTGCCA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
35 2 0.04
36 8 0.18
37 35 0.78
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (36 bp):
ATCATTTTTCAAAGAAACATCTACCAAACTTTGAAA
Found at i:416186 original size:31 final size:31
Alignment explanation
Indices: 416144--416225 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 31
416134 AATTTATAGG
***
416144 TGTT-GGGGACCATATTGCAAATGGACTAAA
1 TGTTGGGGGACCATATTGCAAACAAACTAAA
416174 TGTTGGGGGACCATATTGCAAACAAACTAAA
1 TGTTGGGGGACCATATTGCAAACAAACTAAA
* **
416205 TGTTGGGAGACTGTATTGCAA
1 TGTTGGGGGACCATATTGCAA
416226 TTTTTAAAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
30 4 0.09
31 41 0.91
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (31 bp):
TGTTGGGGGACCATATTGCAAACAAACTAAA
Found at i:417250 original size:31 final size:30
Alignment explanation
Indices: 417212--417292 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 30
417202 CTTTTAAAAC
* *
417212 TTGCAATATAGTCTCCCAATATTTAGTCCT-T
1 TTGCAATATGGTC-CCCAACATTTAGT-CTGT
*
417243 TTGCAATATGGTCCCCTAACATTTAGTTTGT
1 TTGCAATATGGTCCCC-AACATTTAGTCTGT
417274 TTGCAATATGGTCCCCAAC
1 TTGCAATATGGTCCCCAAC
417293 GTAACTGTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
30 7 0.16
31 38 0.84
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (30 bp):
TTGCAATATGGTCCCCAACATTTAGTCTGT
Found at i:418538 original size:32 final size:32
Alignment explanation
Indices: 418497--418561 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
418487 TGAAGTATGA
*
418497 TGGTGGTACACGTTGATGGCTAACGTGCATGC
1 TGGTGGTACACGCTGATGGCTAACGTGCATGC
418529 TGGTGGTACACGCTGATGGCTAACGTGCATGC
1 TGGTGGTACACGCTGATGGCTAACGTGCATGC
418561 T
1 T
418562 AGTTTGAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.18, C:0.20, G:0.34, T:0.28
Consensus pattern (32 bp):
TGGTGGTACACGCTGATGGCTAACGTGCATGC
Found at i:426337 original size:20 final size:20
Alignment explanation
Indices: 426312--426368 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
426302 ATAAGGGTAT
426312 TATCGATACTCTTGAACCAA
1 TATCGATACTCTTGAACCAA
* *
426332 TATCGATACTTTTGAACCAG
1 TATCGATACTCTTGAACCAA
* *
426352 TATTGATACTCATGAAC
1 TATCGATACTCTTGAAC
426369 TAGGGTATCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
TATCGATACTCTTGAACCAA
Found at i:430200 original size:20 final size:20
Alignment explanation
Indices: 430162--430200 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
430152 TGCTTAAGTG
* *
430162 GTATTGATACTCGGGGCCTA
1 GTATCGATACTCGGAGCCTA
*
430182 GTATCGATACTTGGAGCCT
1 GTATCGATACTCGGAGCCT
430201 TGATCAGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (20 bp):
GTATCGATACTCGGAGCCTA
Found at i:441590 original size:18 final size:18
Alignment explanation
Indices: 441567--441602 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
441557 ATTATCGGTT
441567 TTTCGAGCATCATCACCA
1 TTTCGAGCATCATCACCA
*
441585 TTTCGAGCATCATTACCA
1 TTTCGAGCATCATCACCA
441603 ATTAAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.31
Consensus pattern (18 bp):
TTTCGAGCATCATCACCA
Found at i:443970 original size:39 final size:39
Alignment explanation
Indices: 443916--443990 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
443906 CACTCACAAA
*
443916 CACAAATTTCAACTACAAAATAAAGTGTATAGAAAAGAG
1 CACAAATTTCAACTACAAAACAAAGTGTATAGAAAAGAG
*
443955 CACAAATTTCAACTACAAAACAAAGTGTGTAGAAAA
1 CACAAATTTCAACTACAAAACAAAGTGTATAGAAAA
443991 ATCAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.53, C:0.15, G:0.12, T:0.20
Consensus pattern (39 bp):
CACAAATTTCAACTACAAAACAAAGTGTATAGAAAAGAG
Found at i:446067 original size:23 final size:24
Alignment explanation
Indices: 446034--446085 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
446024 AGCACCAGAT
* *
446034 CAAACATTTGC-CTTTTAAATTGA
1 CAAACACTTGCACTTGTAAATTGA
*
446057 CAAACACTTGCAGGTTGTAAATTGA
1 CAAACACTTGCA-CTTGTAAATTGA
446082 CAAA
1 CAAA
446086 AAGTGACAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 10 0.42
25 14 0.58
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.31
Consensus pattern (24 bp):
CAAACACTTGCACTTGTAAATTGA
Found at i:447516 original size:216 final size:214
Alignment explanation
Indices: 447244--447650 Score: 760
Period size: 216 Copynumber: 1.9 Consensus size: 214
447234 GGTTAACGAC
447244 ATGGATAACTAGTATGACTGTAACATTTGTTCACGAAAAAGCAAAACAACAAACATGATTGTGAT
1 ATGGATAACTAGTATGACTGTAACATTTGTTCACGAAAAAGCAAAACAACAAACATGATTGTGAT
447309 AACTAGTATGACTGTAAAATTTTAAAATTGCAATGTAACTCCATTGCAACACACAGAAACAGAAA
66 AACTAGTATGACTGTAAAATTTTAAAATTGCAATGTAACTCCATTGCAACACACAGAAACAGAAA
* *
447374 ATATTGATACACACACATACGAAAACCTATCCGCATACATACATAGATGCAGACATGAATACACC
131 ATATTGATACACACA-A-ACGAAAACCTATCCGAATACATACATAGATGCAGACATAAATACACC
447439 CAGGACTCAAGTCACACAGAA
194 CAGGACTCAAGTCACACAGAA
447460 ATGGATAACTAGTATGACTGTAACATTTGTTCACGAAAAAGCAAAACAACAAACATGATTGTGAT
1 ATGGATAACTAGTATGACTGTAACATTTGTTCACGAAAAAGCAAAACAACAAACATGATTGTGAT
*
447525 AACTAGTATGACTGTAAAATTTTAAAATTGCAATGTAACTCCATTGCCACACACAGAAACAGAAA
66 AACTAGTATGACTGTAAAATTTTAAAATTGCAATGTAACTCCATTGCAACACACAGAAACAGAAA
*
447590 ATATTGATACACACAAACGAAAACCTATCCGAATACATACATAGATGCAGGCATAAATACA
131 ATATTGATACACACAAACGAAAACCTATCCGAATACATACATAGATGCAGACATAAATACA
447651 TCCTTTTAAT
Statistics
Matches: 187, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
214 42 0.22
215 1 0.01
216 144 0.77
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (214 bp):
ATGGATAACTAGTATGACTGTAACATTTGTTCACGAAAAAGCAAAACAACAAACATGATTGTGAT
AACTAGTATGACTGTAAAATTTTAAAATTGCAATGTAACTCCATTGCAACACACAGAAACAGAAA
ATATTGATACACACAAACGAAAACCTATCCGAATACATACATAGATGCAGACATAAATACACCCA
GGACTCAAGTCACACAGAA
Found at i:450170 original size:15 final size:15
Alignment explanation
Indices: 450152--450184 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
450142 TTCATTTTTA
*
450152 TTAATATTTAATTAT
1 TTAATATTTAATGAT
450167 TTAATATTTAATGAT
1 TTAATATTTAATGAT
450182 TTA
1 TTA
450185 GTAATGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TTAATATTTAATGAT
Found at i:450177 original size:22 final size:22
Alignment explanation
Indices: 450131--450184 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
450121 GTTTTTTAAA
*
450131 TAATATTTAAGTTCATTTTTAT
1 TAATATTTAAGTTCATTTATAT
450153 TAATATTTAA-TT-ATTTAATATT
1 TAATATTTAAGTTCATTT-ATA-T
450175 TAATGATTTA
1 TAAT-ATTTA
450185 GTAATGATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.14
21 4 0.14
22 15 0.54
23 5 0.18
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (22 bp):
TAATATTTAAGTTCATTTATAT
Found at i:452277 original size:22 final size:22
Alignment explanation
Indices: 452251--452312 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 22
452241 TTTTGATATT
452251 TTAAAAAATAAAAATATTTTTA
1 TTAAAAAATAAAAATATTTTTA
*
452273 TTAAAAAATAAATATATATTTTTT
1 TTAAAAAATAAA-A-ATATTTTTA
452297 TTAAAAATTATAAAAA
1 TTAAAAA--ATAAAAA
452313 AAAAATCCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
22 12 0.34
23 1 0.03
24 16 0.46
25 1 0.03
26 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAAAAATAAAAATATTTTTA
Found at i:453310 original size:53 final size:53
Alignment explanation
Indices: 453230--453336 Score: 169
Period size: 53 Copynumber: 2.0 Consensus size: 53
453220 TCAAAAGTGA
* *
453230 AAATCCCTTGATTTTTTCCTTTGACTTTCTCAACTTGATTTTAGATCCTTATC
1 AAATCCCTTGATTTTCTCCTTTGACTTTCTCAACTTGATTGTAGATCCTTATC
* * *
453283 AAATCCCTTGATTTTCTCCTTTGACTTTCTTAATTTGATTGTATATCCTTATC
1 AAATCCCTTGATTTTCTCCTTTGACTTTCTCAACTTGATTGTAGATCCTTATC
453336 A
1 A
453337 TGCCCCAACA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (53 bp):
AAATCCCTTGATTTTCTCCTTTGACTTTCTCAACTTGATTGTAGATCCTTATC
Found at i:457662 original size:53 final size:53
Alignment explanation
Indices: 457582--457685 Score: 199
Period size: 53 Copynumber: 2.0 Consensus size: 53
457572 TCAAAAGTGA
457582 AAATCCCTTGATTTTCTCCTTTGACTTTCTCAACTTGATTGTATATCCTTATC
1 AAATCCCTTGATTTTCTCCTTTGACTTTCTCAACTTGATTGTATATCCTTATC
*
457635 AAATCCCTTGATTTTCTCCTTTGACTTTCTCAATTTGATTGTATATCCTTA
1 AAATCCCTTGATTTTCTCCTTTGACTTTCTCAACTTGATTGTATATCCTTA
457686 CCGTCATCCT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.21, C:0.23, G:0.08, T:0.48
Consensus pattern (53 bp):
AAATCCCTTGATTTTCTCCTTTGACTTTCTCAACTTGATTGTATATCCTTATC
Found at i:463336 original size:85 final size:85
Alignment explanation
Indices: 463187--463352 Score: 201
Period size: 85 Copynumber: 2.0 Consensus size: 85
463177 ATACAATCAC
* * * * * *
463187 GACACACGAATGTGTGTTATCTTTTTTAATGACGTGTGCTTCAATGACACGCAATGTGAGTCATA
1 GACACACAAATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATGCGAGTCATA
* * *
463252 TATGCGTGTCATAAATTTAT
66 AATACGCGTCATAAATTTAT
* *
463272 GACACACAAATGTGTGTCATCTTCATTT-ATGACGGGGGCTTCAATGACGCTCAATGCGCA-TCA
1 GACACACAAATGTGTGTCATCTT-ATTTAATGACGGGGGCTTCAATGACACGCAATGCG-AGTCA
463335 TAAATACGCGTCATAAAT
64 TAAATACGCGTCATAAAT
463353 GTGAGTCATA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
85 64 0.94
86 4 0.06
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATGCGAGTCATA
AATACGCGTCATAAATTTAT
Found at i:466674 original size:2 final size:2
Alignment explanation
Indices: 466656--466715 Score: 83
Period size: 2 Copynumber: 32.0 Consensus size: 2
466646 TAAAATAATA
*
466656 AT AT AT A- AT TT AT -T AT AT A- AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
466694 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
466716 CATAATTTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
1 4 0.08
2 48 0.92
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:466682 original size:10 final size:10
Alignment explanation
Indices: 466650--466721 Score: 58
Period size: 12 Copynumber: 6.8 Consensus size: 10
466640 TGGTCCTAAA
466650 ATAATAATAT
1 ATAATAATAT
*
466660 ATAATTTATTAT
1 ATAA--TAATAT
466672 ATAATAATAT
1 ATAATAATAT
466682 AT-AT-ATAT
1 ATAATAATAT
466690 ATATATATATAT
1 ATA-ATA-ATAT
466702 ATATATATATAT
1 ATA-ATA-ATAT
*
466714 ATCATAAT
1 ATAATAAT
466722 TTAAACGGAC
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
8 6 0.11
9 2 0.04
10 15 0.28
11 3 0.06
12 27 0.51
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (10 bp):
ATAATAATAT
Found at i:466684 original size:12 final size:12
Alignment explanation
Indices: 466649--466714 Score: 62
Period size: 14 Copynumber: 5.1 Consensus size: 12
466639 TTGGTCCTAA
466649 AATAATAATATAT
1 AATAAT-ATATAT
*
466662 AAT-TTATTATAT
1 AATAATA-TATAT
466674 AATAATATATAT
1 AATAATATATAT
466686 ATATATATATATAT
1 A-ATA-ATATATAT
466700 ATATATATATATAT
1 A-ATA-ATATATAT
466714 A
1 A
466715 TCATAATTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
11 1 0.02
12 15 0.32
13 8 0.17
14 23 0.49
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AATAATATATAT
Found at i:467358 original size:68 final size:66
Alignment explanation
Indices: 467238--467417 Score: 184
Period size: 66 Copynumber: 2.7 Consensus size: 66
467228 ACAGAATTCA
* ** ** *
467238 TTTCAAGGGAAACGATCTCAAAGATATTTGTTGTTTCTTGAGAAACGATCTCAATGGAAACAAAA
1 TTTCAAGAGAAAAAATCTCAAAGAT-TTTG-TGTTTCAAGAGAAACGATCTCAAGGGAAACAAAA
467303 TCTT
64 T-TT
* * * *
467307 GTTTTAAGGGAAATAAAT-TCAAAGATTTTGTGTTTCAAGAGAAACTG-TCTCAAGGGAGACACA
1 -TTTCAAGAGAAA-AAATCTCAAAGATTTTGTGTTTCAAGAGAAAC-GATCTCAAGGGAAACAAA
467370 ATTT
63 ATTT
* *
467374 TTTCAAGAGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAAAC
1 TTTCAAGAGAAAAAATCTCAAAGATTTTGTGTTTCAAGAGAAAC
467418 ATTTTCAAAG
Statistics
Matches: 95, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
65 3 0.03
66 36 0.38
67 2 0.02
68 28 0.29
69 5 0.05
70 19 0.20
71 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (66 bp):
TTTCAAGAGAAAAAATCTCAAAGATTTTGTGTTTCAAGAGAAACGATCTCAAGGGAAACAAAATT
T
Found at i:467440 original size:33 final size:33
Alignment explanation
Indices: 467374--467486 Score: 167
Period size: 33 Copynumber: 3.4 Consensus size: 33
467364 GACACAATTT
*
467374 TTTCAAGAGAAACAATCTCAAAGG--TTTTGTG
1 TTTCAAGAGAAACAATTTCAAAGGTTTTTTGTG
*
467405 TTTCAAGAGAAACATTTTCAAAGGTTTTTTGTG
1 TTTCAAGAGAAACAATTTCAAAGGTTTTTTGTG
467438 TTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTGTG
1 TTTCAAGAGAAACAATTTCAAAGG--T-TTTTTGTG
467474 TTTCAAGAGAAAC
1 TTTCAAGAGAAAC
467487 TGTCTCAAGG
Statistics
Matches: 74, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
31 22 0.30
33 30 0.41
35 1 0.01
36 21 0.28
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (33 bp):
TTTCAAGAGAAACAATTTCAAAGGTTTTTTGTG
Found at i:467591 original size:37 final size:36
Alignment explanation
Indices: 467540--467624 Score: 143
Period size: 37 Copynumber: 2.3 Consensus size: 36
467530 CAAAGATCGG
467540 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
467577 TGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
467613 TGTTTCAAGAGA
1 TGTTTCAAGAGA
467625 GACTAAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
36 13 0.29
37 32 0.71
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:467622 original size:21 final size:21
Alignment explanation
Indices: 467596--467645 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
467586 GGAAACTGTC
467596 TCAAGAGAGACTAAATTTGTT
1 TCAAGAGAGACTAAATTTGTT
467617 TCAAGAGAGACTAAATTTGTT
1 TCAAGAGAGACTAAATTTGTT
467638 TCAAGAGA
1 TCAAGAGA
467646 AACTGTCTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (21 bp):
TCAAGAGAGACTAAATTTGTT
Found at i:468296 original size:110 final size:110
Alignment explanation
Indices: 468150--468584 Score: 638
Period size: 110 Copynumber: 4.0 Consensus size: 110
468140 CAAGTATGTA
* * * * ** *
468150 TTGTTTCAAGTCAAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAATTGGGAAGTTG
1 TTGTCTCAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTA
* *
468215 TTTGTTGACAGCCAGTCGCCCATTCGCTGTGAAGTTGAGCTTGTG
66 TTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTG
* * *
468260 TTGTCCCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTA
1 TTGTCTCAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTA
*
468325 TTTGTTAACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTG
66 TTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTG
* * *
468370 TTCTCTCAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTG
1 TTGTCTCAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTA
* * *
468435 TTTGTTGACAGTCAATCACCCCTTTGCTGTGAAGTTGAGCTTGTG
66 TTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTG
* * *
468480 TTGTATCAAGT-CAATATCCTTCGTTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTA
1 TTGTCTCAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTA
* * *
468544 TTTGTTGACAATCAGTCTCCCCTTCGCTGTAAAGTTGAGCT
66 TTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCT
468585 ACAACCATCA
Statistics
Matches: 293, Mismatches: 32, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
109 87 0.30
110 206 0.70
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (110 bp):
TTGTCTCAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTA
TTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTG
Found at i:472502 original size:35 final size:35
Alignment explanation
Indices: 472462--472532 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
472452 AAATTTTGAA
* *
472462 AAAAAGTAAATGGTAAGTGTTGAATAAAAGTAAAT
1 AAAAAGTAAATGGTAAGTGCTGAATAAAAGGAAAT
*
472497 AAAAAGTAAATGGTAAGTGCTGAATGAAAGGAAAT
1 AAAAAGTAAATGGTAAGTGCTGAATAAAAGGAAAT
472532 A
1 A
472533 TATAAAACGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.54, C:0.01, G:0.23, T:0.23
Consensus pattern (35 bp):
AAAAAGTAAATGGTAAGTGCTGAATAAAAGGAAAT
Found at i:472503 original size:24 final size:24
Alignment explanation
Indices: 472457--472503 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
472447 ACATTAAATT
***
472457 TTGAAAAAAAGTAAATGGTAAGTG
1 TTGAAAAAAAGTAAATAAAAAGTG
*
472481 TTGAATAAAAGTAAATAAAAAGT
1 TTGAAAAAAAGTAAATAAAAAGT
472504 AAATGGTAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.19, T:0.26
Consensus pattern (24 bp):
TTGAAAAAAAGTAAATAAAAAGTG
Found at i:473766 original size:20 final size:21
Alignment explanation
Indices: 473730--473789 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
473720 TGGTCCTGAA
473730 ATAATAATATATAATTTATTAT
1 ATAATAATATATAATTTA-TAT
473752 ATAATAATAT-T-ATTTATAT
1 ATAATAATATATAATTTATAT
473771 ATATATAAT-TCATAATTTA
1 ATA-ATAATAT-ATAATTTA
473790 AACGAACGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
19 7 0.21
20 10 0.29
21 2 0.06
22 15 0.44
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAATAATATATAATTTATAT
Found at i:474421 original size:32 final size:33
Alignment explanation
Indices: 474363--474427 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
474353 GCAATACGTT
*
474363 GACGAATCACCTAGCGGCTAGCGAGACAGGGTG
1 GACGAATCACCTAGCGACTAGCGAGACAGGGTG
474396 GACGAATCACC-AGCGACTAGCGAGACAGGGTG
1 GACGAATCACCTAGCGACTAGCGAGACAGGGTG
474428 TAGGCTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 20 0.65
33 11 0.35
ACGTcount: A:0.29, C:0.25, G:0.35, T:0.11
Consensus pattern (33 bp):
GACGAATCACCTAGCGACTAGCGAGACAGGGTG
Found at i:478823 original size:23 final size:23
Alignment explanation
Indices: 478762--478815 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
478752 ACAATCTTAT
478762 ATGGCACTACGGTGCAATTCTAC
1 ATGGCACTACGGTGCAATTCTAC
**
478785 GCGGCACTACGGTGCAATTCTAC
1 ATGGCACTACGGTGCAATTCTAC
478808 ATGGCACT
1 ATGGCACT
478816 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (23 bp):
ATGGCACTACGGTGCAATTCTAC
Found at i:478944 original size:2 final size:2
Alignment explanation
Indices: 478933--478980 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
478923 GAATACAACG
478933 TA 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 TA
478974 TA TA TA T
1 TA TA TA T
478981 GTGTAATATG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:483898 original size:23 final size:23
Alignment explanation
Indices: 483807--483890 Score: 134
Period size: 23 Copynumber: 3.7 Consensus size: 23
483797 CAATCTTATA
*
483807 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
483830 CGGCA-TTACGGTGCAATTCTACG
1 TGGCACTT-CGGTGCAATTCTACG
483853 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
483876 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
483891 TTTATACGAG
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
22 1 0.02
23 53 0.95
24 2 0.04
ACGTcount: A:0.19, C:0.26, G:0.27, T:0.27
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:487912 original size:54 final size:54
Alignment explanation
Indices: 487869--488153 Score: 401
Period size: 54 Copynumber: 5.3 Consensus size: 54
487859 TTCCATGCTT
* * *
487869 TGCACACCTAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTCTGTGGAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGGAA
* ** *
487923 TGCACTCTTAGTGCCGAAATAGTTATTCATCCACATAGGATGAATTCCATGGAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGGAA
* * * *
487977 TGCACACTTAGTGTCGAAACGGTTATTCATCCACATAAGATAAATTCTGTGGAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGGAA
* *
488031 TGCACACTTAGTGCCAAAACGGTTATTCATCCACATAGGATAAATTCCGTGGAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGGAA
* * *
488085 TGCACACTTAGTGCC-AGAACGGTTATTCATCCATATATGATGAATTCCGTGGAT
1 TGCACACTTAGTGCCGA-AACGGTTATTCATCCACATAGGATGAATTCCGTGGAA
*
488139 TGCACATTTAGTGCC
1 TGCACACTTAGTGCC
488154 TATTGGGTAT
Statistics
Matches: 206, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
53 1 0.00
54 205 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGGAA
Found at i:488618 original size:95 final size:97
Alignment explanation
Indices: 488472--488672 Score: 257
Period size: 95 Copynumber: 2.1 Consensus size: 97
488462 GGCCCTTCAA
* * *
488472 TATCGATA-TCTCTACCATGGTATCGATACTACCCTACTATGGTATCGATACCCCT-TTACGGTA
1 TATCGATACCCTCTACCATGGTATCGATACTACCCTACTAAGGTACCGATACCCCTCTTACGGTA
*
488535 TCGATACCAAAATTAGCTTCGATGTGTCTT-GG
66 TCGATACCAAAATTAGCTTCGATGT-TATTAGG
* ** * * *
488567 TATCGATACCCTC-ACCATGGTATTGATACTACTTTGCTAAGGTACCTATACCCCTCTTCCGGTA
1 TATCGATACCCTCTACCATGGTATCGATACTACCCTACTAAGGTACCGATACCCCTCTTACGGTA
* *
488631 TCGATTCCAAAATTAGGTTCGATGTTATTAGG
66 TCGATACCAAAATTAGCTTCGATGTTATTAGG
488663 TATCGATACC
1 TATCGATACC
488673 ACTTCGCTAG
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
95 46 0.51
96 45 0.49
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.34
Consensus pattern (97 bp):
TATCGATACCCTCTACCATGGTATCGATACTACCCTACTAAGGTACCGATACCCCTCTTACGGTA
TCGATACCAAAATTAGCTTCGATGTTATTAGG
Found at i:494992 original size:108 final size:108
Alignment explanation
Indices: 494826--495048 Score: 306
Period size: 108 Copynumber: 2.1 Consensus size: 108
494816 TTTGCACTCC
* **
494826 TAGTGCCGAAACGATTATTCATCTACATAGGATAAATTCCGTAGAATGCACTCTTAGTGTTGAAA
1 TAGTGCCGAAACGATTATTCATCTACATAGGATAAATTCCGTAGAATGCACACTTAGTGCCGAAA
* * *
494891 CGGTTATTCATCTACATAAGATGAATTTCA-TGGAATACACACT
66 CAGTTATTCATCCACATAAGACGAA-TTCATTGGAATACACACT
* * *
494934 TAGTGCCGAAACGGTTATTCATGC-ACATAGGATAAATTTCGTGGAATGCACACTTAGTGCCGAA
1 TAGTGCCGAAACGATTATTCAT-CTACATAGGATAAATTCCGTAGAATGCACACTTAGTGCCGAA
* * *
494998 ACAGTTATTCATCCACATAAGACGAATTCATTGGATTGCACATT
65 ACAGTTATTCATCCACATAAGACGAATTCATTGGAATACACACT
495042 TAGTGCC
1 TAGTGCC
495049 TATTGGGTAA
Statistics
Matches: 101, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
107 4 0.04
108 96 0.95
109 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (108 bp):
TAGTGCCGAAACGATTATTCATCTACATAGGATAAATTCCGTAGAATGCACACTTAGTGCCGAAA
CAGTTATTCATCCACATAAGACGAATTCATTGGAATACACACT
Found at i:495038 original size:54 final size:55
Alignment explanation
Indices: 494826--495048 Score: 247
Period size: 54 Copynumber: 4.1 Consensus size: 55
494816 TTTGCACTCC
* * * * * *
494826 TAGTGCCGAAACGATTATTCATCTACATAGGATAAA-TTCCGTAGAATGCACTCT
1 TAGTGCCGAAACGGTTATTCATCCACATAAGATAAATTTCAGTGGAATGCACACT
** * * *
494880 TAGTGTTGAAACGGTTATTCATCTACATAAGATGAATTTCA-TGGAATACACACT
1 TAGTGCCGAAACGGTTATTCATCCACATAAGATAAATTTCAGTGGAATGCACACT
* *
494934 TAGTGCCGAAACGGTTATTCATGCACATAGGATAAATTTC-GTGGAATGCACACT
1 TAGTGCCGAAACGGTTATTCATCCACATAAGATAAATTTCAGTGGAATGCACACT
* ** * * *
494988 TAGTGCCGAAACAGTTATTCATCCACATAAGACGAA-TTCATTGGATTGCACATT
1 TAGTGCCGAAACGGTTATTCATCCACATAAGATAAATTTCAGTGGAATGCACACT
495042 TAGTGCC
1 TAGTGCC
495049 TATTGGGTAA
Statistics
Matches: 142, Mismatches: 24, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
53 3 0.02
54 136 0.96
55 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (55 bp):
TAGTGCCGAAACGGTTATTCATCCACATAAGATAAATTTCAGTGGAATGCACACT
Found at i:495399 original size:20 final size:20
Alignment explanation
Indices: 495371--495425 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
495361 TTGCCCTTCA
* *
495371 GTATTGATACCTCTACCATG
1 GTATCGATACCCCTACCATG
*
495391 GTATCGATACTACCCTACTATG
1 GTATCGATAC--CCCTACCATG
495413 GTATCGATACCCC
1 GTATCGATACCCC
495426 CTTACGGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.40
22 18 0.60
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (20 bp):
GTATCGATACCCCTACCATG
Found at i:495413 original size:22 final size:23
Alignment explanation
Indices: 495378--495422 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
495368 TCAGTATTGA
495378 TACCTCTACCATGGTATCGATAC
1 TACCTCTACCATGGTATCGATAC
*
495401 TACC-CTACTATGGTATCGATAC
1 TACCTCTACCATGGTATCGATAC
495423 CCCCTTACGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (23 bp):
TACCTCTACCATGGTATCGATAC
Found at i:495564 original size:95 final size:95
Alignment explanation
Indices: 495386--495590 Score: 238
Period size: 95 Copynumber: 2.2 Consensus size: 95
495376 GATACCTCTA
* * * * *
495386 CCATGGTATCGATACTACCCTACTATGGTATCGATACCCCCTTACGGTATCGATACCAAATTTGG
1 CCATGATATCGATACTACCATACTAAGGTACCGATACCCCCTTACGGTATCGATACCAAATTAGG
** *
495451 CTTCGATGTGTCTTGGTATCGATACCCTCG
66 CTTCGATGTGTCCGGGTATCAATACCCTCG
* *
495481 CCATGATATTGATACTACTATACTAAGGTACCGATACCCCCTT-CAGGTATCGATACCAAAATTA
1 CCATGATATCGATACTACCATACTAAGGTACCGATACCCCCTTAC-GGTATCGATACC-AAATTA
*
495545 GG-TTCGATGT-TACCGGGTATCAATTCCCTC-
64 GGCTTCGATGTGT-CCGGGTATCAATACCCTCG
*
495575 CCTATGGTATCGATAC
1 CC-ATGATATCGATAC
495591 CACTTCGCTA
Statistics
Matches: 93, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
94 4 0.04
95 82 0.88
96 7 0.08
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (95 bp):
CCATGATATCGATACTACCATACTAAGGTACCGATACCCCCTTACGGTATCGATACCAAATTAGG
CTTCGATGTGTCCGGGTATCAATACCCTCG
Found at i:498485 original size:33 final size:33
Alignment explanation
Indices: 498448--498512 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
498438 TTTGAACCAA
*
498448 ACTGATTTTTCTGA-ATTGTTCGAACCAAACTAC
1 ACTGATTTTTCT-ACACTGTTCGAACCAAACTAC
*
498481 ACTGATTTTTCTACACTGTTTGAACCAAACTA
1 ACTGATTTTTCTACACTGTTCGAACCAAACTA
498513 TATTGTTCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 28 0.97
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.37
Consensus pattern (33 bp):
ACTGATTTTTCTACACTGTTCGAACCAAACTAC
Found at i:501337 original size:23 final size:21
Alignment explanation
Indices: 501299--501341 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
501289 ATAATTATTT
501299 AAAAAATTAAATAAAAATATA
1 AAAAAATTAAATAAAAATATA
*
501320 AAAAATATTTAATAAAAA-ATA
1 AAAAA-ATTAAATAAAAATATA
501341 A
1 A
501342 TTTTTATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATA
Found at i:504348 original size:23 final size:23
Alignment explanation
Indices: 504321--504411 Score: 146
Period size: 23 Copynumber: 4.0 Consensus size: 23
504311 ATGCCAAATA
504321 TTTGTCCCGAAGGACCACATAGT
1 TTTGTCCCGAAGGACCACATAGT
*
504344 TTTGTCTCGAAGGACCACATAGT
1 TTTGTCCCGAAGGACCACATAGT
*
504367 TTTGTCTCGAAGGACCACATAGT
1 TTTGTCCCGAAGGACCACATAGT
* *
504390 TTTGTCCCGAATGACCATATAG
1 TTTGTCCCGAAGGACCACATAG
504412 AACCCTCGAC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (23 bp):
TTTGTCCCGAAGGACCACATAGT
Found at i:511295 original size:21 final size:22
Alignment explanation
Indices: 511250--511344 Score: 79
Period size: 23 Copynumber: 4.3 Consensus size: 22
511240 CACCATAACT
511250 CACATAATTTG-CACTGAAGTG-C
1 CACATAATTTGTC-CTGAAG-GAC
511272 CACA-AATTTGTCCTGAAGGAC
1 CACATAATTTGTCCTGAAGGAC
* *
511293 CACATAGTTTTGTCCTGAATGAC
1 CACATA-ATTTGTCCTGAAGGAC
* * * *
511316 CACATAGTTTTGTCCCGAAGAAT
1 CACATA-ATTTGTCCTGAAGGAC
511339 CACATA
1 CACATA
511345 GAACCCTCGA
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
20 1 0.02
21 17 0.27
22 6 0.10
23 39 0.62
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (22 bp):
CACATAATTTGTCCTGAAGGAC
Found at i:511308 original size:23 final size:23
Alignment explanation
Indices: 511278--511345 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
511268 GTGCCACAAA
511278 TTTGTCCTGAAGGACCACATAGT
1 TTTGTCCTGAAGGACCACATAGT
*
511301 TTTGTCCTGAATGACCACATAGT
1 TTTGTCCTGAAGGACCACATAGT
* * *
511324 TTTGTCCCGAAGAATCACATAG
1 TTTGTCCTGAAGGACCACATAG
511346 AACCCTCGAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (23 bp):
TTTGTCCTGAAGGACCACATAGT
Found at i:513372 original size:22 final size:22
Alignment explanation
Indices: 513329--513372 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
513319 TAAATTGTAC
*
513329 TTTTCTATTTCATATCACATCA
1 TTTTCTATTTCATATCAAATCA
*
513351 TTTTCATATTTTAT-TCAAATCA
1 TTTTC-TATTTCATATCAAATCA
513373 CATATTTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTCTATTTCATATCAAATCA
Found at i:513544 original size:2 final size:2
Alignment explanation
Indices: 513537--513572 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
513527 AGGCCACATC
513537 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
513573 TGTCAAACAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:519167 original size:15 final size:17
Alignment explanation
Indices: 519135--519173 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
519125 TGTTAAGAGA
519135 TAAAGAAAATAAAGATT
1 TAAAGAAAATAAAGATT
*
519152 TAAAGAAAA-CAA-ATT
1 TAAAGAAAATAAAGATT
519167 TAAAGAA
1 TAAAGAA
519174 TATGAAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
16 2 0.10
17 9 0.43
ACGTcount: A:0.67, C:0.03, G:0.10, T:0.21
Consensus pattern (17 bp):
TAAAGAAAATAAAGATT
Found at i:524970 original size:22 final size:21
Alignment explanation
Indices: 524945--524987 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
524935 TAGGTTGTTT
524945 TTAAAATATAAACATATAAATA
1 TTAAAATATAAACATA-AAATA
* * *
524967 TTAAGATTTAAACCTAAAATA
1 TTAAAATATAAACATAAAATA
524988 ATACCAAGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (21 bp):
TTAAAATATAAACATAAAATA
Found at i:526522 original size:2 final size:2
Alignment explanation
Indices: 526517--526542 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
526507 TTCTCTCCTT
526517 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
526543 GCGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:526550 original size:2 final size:2
Alignment explanation
Indices: 526545--526578 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
526535 TATATATAGC
526545 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
526579 TCATCATTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:528320 original size:42 final size:41
Alignment explanation
Indices: 528255--528342 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 41
528245 TTTATAGTAG
*
528255 CATTTTTTCACAAATGCTACTAATTCTCTT-TTCTTTAGTGA
1 CATTTTTTCACAAATGCTACTAATTCTATTATT-TTTAGTGA
* *
528296 CATTTTTTCCACAAATGAC-GCTAATTCTATTATTTTTAGTGG
1 CATTTTTT-CACAAATG-CTACTAATTCTATTATTTTTAGTGA
528338 CATTT
1 CATTT
528343 GTAATTCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
41 8 0.20
42 30 0.73
43 3 0.07
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.48
Consensus pattern (41 bp):
CATTTTTTCACAAATGCTACTAATTCTATTATTTTTAGTGA
Found at i:534821 original size:12 final size:12
Alignment explanation
Indices: 534804--534841 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
534794 ATGCTTGACG
*
534804 AAACAAAAACAA
1 AAACAAAAATAA
534816 AAACAAAAATAA
1 AAACAAAAATAA
*
534828 AAATAAAAATAA
1 AAACAAAAATAA
534840 AA
1 AA
534842 TAAAAGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
AAACAAAAATAA
Found at i:534842 original size:5 final size:6
Alignment explanation
Indices: 534808--534846 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
534798 TTGACGAAAC
* *
534808 AAAAAC AAAAAC AAAAAT AAAAAT AAAAAT -AAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
534847 GTATAGCAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (6 bp):
AAAAAT
Found at i:540373 original size:18 final size:19
Alignment explanation
Indices: 540352--540393 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
540342 GGTAAAAAAT
*
540352 ATTAAAATAA-TAAAAGCG
1 ATTAAAATAAGTAAAAGCA
540370 ATT-AAATAAGTAAAAGCA
1 ATTAAAATAAGTAAAAGCA
540388 ATTAAA
1 ATTAAA
540394 GTAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 13 0.62
19 2 0.10
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (19 bp):
ATTAAAATAAGTAAAAGCA
Found at i:543120 original size:81 final size:82
Alignment explanation
Indices: 542950--543206 Score: 234
Period size: 83 Copynumber: 3.1 Consensus size: 82
542940 GGTGTTTTTT
* * * * * * * * * *
542950 TTTGTATAAAAACAACACTAAAGTACAACTCTGTCGCGGC-GTTCTTGAAAAAAGCCACTATGAA
1 TTTGTATAAAAAGACCACTAAAATACTACTATGTTGCGACATTTGTTGAAAAAAGCCACTATGGA
* *
543014 TGAACCCTATTGCAACA
66 TGAACCCTATTGCAGCG
* * * *
543031 TTTCTATAAAAAG-CCATTAAAATACTACTATGTTGTTG-CGTTTGTTGAAAAAAGCCACTATGG
1 TTTGTATAAAAAGACCACTAAAATACTACTATGTTG-CGACATTTGTTGAAAAAAGCCACTATGG
* *
543094 ATGAACCCTATTACAGTG
65 ATGAACCCTATTGCAGCG
* * * *
543112 TTTGTATAAAATGCACCGCTAAAATACTACTTTGTTGCGACATTTGTT-AAAAAACACCACTATG
1 TTTGTATAAAAAG-ACCACTAAAATACTACTATGTTGCGACATTTGTTGAAAAAA-GCCACTATG
* *
543176 GATGAAACCTATTGCGGCG
64 GATGAACCCTATTGCAGCG
*
543195 TTCGTATAAAAA
1 TTTGTATAAAAA
543207 CGCTACTAAA
Statistics
Matches: 140, Mismatches: 30, Indels: 10
0.78 0.17 0.06
Matches are distributed among these distances:
80 17 0.12
81 57 0.41
82 7 0.05
83 59 0.42
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (82 bp):
TTTGTATAAAAAGACCACTAAAATACTACTATGTTGCGACATTTGTTGAAAAAAGCCACTATGGA
TGAACCCTATTGCAGCG
Found at i:548777 original size:183 final size:181
Alignment explanation
Indices: 548456--548819 Score: 568
Period size: 183 Copynumber: 2.0 Consensus size: 181
548446 ATATTACCAT
** *
548456 AAATAGTAAAAAAAAATAAAACTAGTGATTCGGAGGGGAAAACGTTAGAATTTGAGATCGAAAAA
1 AAATAGTAAAAAAAAATAAAACTAGTGATTCGGAGGGGAAAACGGCAGAATTTGAGATAGAAAAA
*
548521 AAGTCCACATGGAGACATGAATGTGGACAGCATGCGCGTCGAAAGGGGCTTTCCGAATTAGGGTC
66 AAGGCCACATGGAGACATGAATGTGGACAGCATGCGCGTCGAAAGGGGCTTTCCGAATTAGGGTC
*
548586 TTATGCGCGATTCCGACACCCGTAGCCAAAGTTATG-GTCAAAAGACTAAAAC
131 TTATGCGCGATTCCGAAACCCGTAGCCAAA-TTA-GAGTCAAAAGACTAAAAC
* * * *
548638 AAATAGTAAAAAATAAATAAAACTGGTTATTCGGAGGGGAAAATGGCAGAATTTGAGGTAGAAAA
1 AAATAGTAAAAAA-AAATAAAACTAGTGATTCGGAGGGGAAAACGGCAGAATTTGAGATAGAAAA
* * * *
548703 AAAGGCCACATGGAGCCATGAATGTGGACAGCGTGCGCGTCGAAAGGGGCTTTCTGAATTGGGGT
65 AAAGGCCACATGGAGACATGAATGTGGACAGCATGCGCGTCGAAAGGGGCTTTCCGAATTAGGGT
*
548768 CTTATGCGCGATTCCGAAACCCGTAGCCAAATTAGAGTCAAAAGACTGAAAC
130 CTTATGCGCGATTCCGAAACCCGTAGCCAAATTAGAGTCAAAAGACTAAAAC
548820 GCACTCAAAA
Statistics
Matches: 166, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
181 1 0.01
182 31 0.19
183 134 0.81
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.20
Consensus pattern (181 bp):
AAATAGTAAAAAAAAATAAAACTAGTGATTCGGAGGGGAAAACGGCAGAATTTGAGATAGAAAAA
AAGGCCACATGGAGACATGAATGTGGACAGCATGCGCGTCGAAAGGGGCTTTCCGAATTAGGGTC
TTATGCGCGATTCCGAAACCCGTAGCCAAATTAGAGTCAAAAGACTAAAAC
Found at i:551953 original size:22 final size:22
Alignment explanation
Indices: 551925--551969 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
551915 CAAAATAGAG
551925 AAAGGTGTAAAGATGATTTCTC
1 AAAGGTGTAAAGATGATTTCTC
551947 AAAGGTGTAAAGATGATTTCTC
1 AAAGGTGTAAAGATGATTTCTC
551969 A
1 A
551970 GACTCACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (22 bp):
AAAGGTGTAAAGATGATTTCTC
Found at i:554460 original size:4 final size:4
Alignment explanation
Indices: 554440--554484 Score: 58
Period size: 4 Copynumber: 11.2 Consensus size: 4
554430 TAAGAATAAT
554440 AATA ATATA AATAA AATA AATA AAT- AA-A AATA AATA AATA AATA A
1 AATA A-ATA AAT-A AATA AATA AATA AATA AATA AATA AATA AATA A
554485 GATTGAGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
3 4 0.11
4 25 0.68
5 8 0.22
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:554469 original size:14 final size:14
Alignment explanation
Indices: 554434--554481 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
554424 ACATAATAAG
*
554434 AATAATAATAATATA
1 AATAAAAATAA-ATA
554449 AAT-AAAATAAATA
1 AATAAAAATAAATA
554462 AATAAAAATAAATA
1 AATAAAAATAAATA
554476 AATAAA
1 AATAAA
554482 TAAGATTGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
13 6 0.19
14 22 0.71
15 3 0.10
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
AATAAAAATAAATA
Found at i:554474 original size:18 final size:19
Alignment explanation
Indices: 554443--554484 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
554433 GAATAATAAT
*
554443 AATATAAATAAAATAAATA
1 AATAAAAATAAAATAAATA
554462 AATAAAAAT-AAATAAATA
1 AATAAAAATAAAATAAATA
554480 AATAA
1 AATAA
554485 GATTGAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AATAAAAATAAAATAAATA
Found at i:555537 original size:3 final size:3
Alignment explanation
Indices: 555505--555580 Score: 72
Period size: 3 Copynumber: 26.0 Consensus size: 3
555495 GCCTGCAAAA
* *
555505 AAT AAT TAT AAT ATAT AA- ATT AAT -AT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
555549 AAT AAAT AAT -AT AAAT AAT AAT -AT AAT -AT AAT
1 AAT -AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
555581 GTTTTGTAGA
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
2 9 0.15
3 44 0.72
4 8 0.13
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:555574 original size:12 final size:12
Alignment explanation
Indices: 555512--555580 Score: 57
Period size: 10 Copynumber: 6.4 Consensus size: 12
555502 AAAAATAATT
555512 ATAAT-ATATAA
1 ATAATAATATAA
555523 AT--TAATAT-A
1 ATAATAATATAA
555532 ATAAT-A-AT-A
1 ATAATAATATAA
*
555541 ATAATAATA-AT
1 ATAATAATATAA
555552 A-AATAATATAA
1 ATAATAATATAA
555563 ATAATAATATAA
1 ATAATAATATAA
555575 TATAAT
1 -ATAAT
555581 GTTTTGTAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
9 12 0.26
10 13 0.28
11 7 0.15
12 10 0.21
13 5 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
ATAATAATATAA
Found at i:555975 original size:124 final size:124
Alignment explanation
Indices: 555752--556336 Score: 580
Period size: 124 Copynumber: 4.7 Consensus size: 124
555742 AGCACAATAT
* * * *
555752 CCTTCTTCGTGAAGTTGAAATCGTGGACGACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
* * * *
555817 TCATTCGTCGTGAAGTTGAAATCCATTCTGAAGATGAATGTTGCTGGTGGGCACGATTC
66 TCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACGATTC
* *
555876 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTAAATTTGATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
* *
555941 TCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGAGCACGTTTC
66 TCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACGATTC
* *
556000 CTTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATA
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
* * *
556065 TTCTTCATCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCT--TCGAGTC-CAATAT-
66 TCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGT-GAG-CACGAT-TC
* ** * * * *
556123 CATTCACCTTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCTTCGCTGTGAAGTTGAGC
1 CCTTCGTCGTGAAGTTGAAA----C-C-G--TG-GA-T-GG--CCCCTTCGTTGTGAAGTTGAGC
* * *
556188 TTTGAATTGGATATCATTCGTCGTGAAGTTGAAATCCAATCT----A-G-A----G-T--AG-GC
53 CTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGC
556239 ACGATAT-
118 ACGAT-TC
* * * * *
556246 CCTTCGTCGTGAAGTTGAAATCGTGGATGGACCCTTCATTGTGAAGTTGATCCTTGACTT-GATT
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGA-T
556310 ATCCTTCGTCGTGAAGTTGAAATCCAA
65 ATCCTTCGTCGTGAAGTTGAAATCCAA
556337 GCTTGTATTG
Statistics
Matches: 395, Mismatches: 48, Indels: 50
0.80 0.10 0.10
Matches are distributed among these distances:
109 2 0.01
110 51 0.13
112 2 0.01
113 1 0.00
114 1 0.00
115 2 0.01
117 1 0.00
118 1 0.00
122 2 0.01
123 43 0.11
124 218 0.55
125 1 0.00
126 1 0.00
127 1 0.00
128 1 0.00
129 1 0.00
130 1 0.00
131 3 0.01
132 2 0.01
133 1 0.00
134 2 0.01
136 57 0.14
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (124 bp):
CCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATA
TCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGAGCACGATTC
Found at i:556324 original size:246 final size:240
Alignment explanation
Indices: 556002--556459 Score: 661
Period size: 246 Copynumber: 1.9 Consensus size: 240
555992 CACGTTTCCT
* *
556002 TTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATT
1 TTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCATTGTGAAGTTGAGCCTTGAATTGGATATC
* * *
556067 CTTCATCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTTCGAGTCCAATATCATTCACCT
66 CTTCATCGTGAAGTTGAAATCCAAGCT-----TG--TATTGCTTCGAGTCCAATATCATTCACCG
* *
556132 TGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAG-CCCTTCGCTGTGAAGTTGAGCTTTGAATT
124 TGAAGTTGAAATTGGCTCTGAATGAAAATGGGAAGCCCCTTCGCCGTGAAGTTGAGCTTTGAATT
*
556196 GGATATCATTCGTCGTGAAGTTGAAATCCAATCTAGAGTAGGCACGATATCC
189 GGATATCATTCGCCGTGAAGTTGAAATCCAATCTAGAGTAGGCACGATATCC
* * *
556248 TTCGTCGTGAAGTTGAAATCGTGGATGGACCC-TTCATTGTGAAGTTGATCCTTGACTT-GATTA
1 TTCGTCGTGAAGTTGAAACCGTGGATGG-CCCATTCATTGTGAAGTTGAGCCTTGAATTGGA-TA
* * * *
556311 TCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTCGCCGTGAAG
64 TCCTTCATCGTGAAGTTGAAATCCAAGCTTGTATTGCTTCGAGTCCAATATCATTCACCGTGAAG
556376 TTGAAATTGGCTCTGAATGAAAATGGGAAGCCCCTTCGCCGTGAAGTTGAGCTTTGAATTGGATA
129 TTGAAATTGGCTCTGAATGAAAATGGGAAGCCCCTTCGCCGTGAAGTTGAGCTTTGAATTGGATA
* *
556441 TCCTTTGCCGTGAAGTTGA
194 TCATTCGCCGTGAAGTTGA
556460 GCTTTGAATT
Statistics
Matches: 192, Mismatches: 17, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
239 58 0.30
240 49 0.26
241 2 0.01
245 2 0.01
246 78 0.41
247 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (240 bp):
TTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCATTGTGAAGTTGAGCCTTGAATTGGATATC
CTTCATCGTGAAGTTGAAATCCAAGCTTGTATTGCTTCGAGTCCAATATCATTCACCGTGAAGTT
GAAATTGGCTCTGAATGAAAATGGGAAGCCCCTTCGCCGTGAAGTTGAGCTTTGAATTGGATATC
ATTCGCCGTGAAGTTGAAATCCAATCTAGAGTAGGCACGATATCC
Found at i:556456 original size:34 final size:34
Alignment explanation
Indices: 556408--556493 Score: 145
Period size: 34 Copynumber: 2.5 Consensus size: 34
556398 ATGGGAAGCC
556408 CCTTCGCCGTGAAGTTGAGCTTTGAATTGGATAT
1 CCTTCGCCGTGAAGTTGAGCTTTGAATTGGATAT
*
556442 CCTTTGCCGTGAAGTTGAGCTTTGAATTGGATAT
1 CCTTCGCCGTGAAGTTGAGCTTTGAATTGGATAT
**
556476 CCTTCATCGTGAAGTTGA
1 CCTTCGCCGTGAAGTTGA
556494 AATCCAATCT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (34 bp):
CCTTCGCCGTGAAGTTGAGCTTTGAATTGGATAT
Found at i:557894 original size:95 final size:94
Alignment explanation
Indices: 557699--557959 Score: 355
Period size: 95 Copynumber: 2.7 Consensus size: 94
557689 GGCTAGCTGA
* * *
557699 ATCCATAAAGCTGGGACGTTTAACCAATTGCTCTAGAGGGACAGCTTAATATCATTGTATAG-AT
1 ATCCATAAAGC-GGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAA-A-C-TT-TATTGTAT
*
557763 ATTTTAATCACCTTTATCAGGCTAGCTGAATATT
61 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
* *
557797 ATCCATAAAGTCGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAACTTTATTGTATATTA
1 ATCCATAAAG-CGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAAACTTTATTGTATATTA
* *
557862 TAATCACCTTTATCAGGCTAGTTGAATCTT
65 TAATCACCTTTATCAGGCTAGCTGAATATT
* *
557892 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGACAGCTCAAGCTTTATTGTATA-TA
1 ATCCATAAAG-CGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAAACTTTATTGTATATTA
557956 TAAT
65 TAAT
557960 ATTATAATCT
Statistics
Matches: 148, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
94 10 0.07
95 92 0.62
96 1 0.01
97 1 0.01
98 43 0.29
99 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (94 bp):
ATCCATAAAGCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAAACTTTATTGTATATTAT
AATCACCTTTATCAGGCTAGCTGAATATT
Found at i:560564 original size:18 final size:18
Alignment explanation
Indices: 560507--560575 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 18
560497 TTAGATTGTA
* *
560507 AAATAAAAAAAAAATATT
1 AAATAAAAATAAAATAAT
*
560525 AACATAATAATAATAATAAT
1 AA-ATAAAAATAA-AATAAT
*
560545 AAA-ATAAATAAAATAGAT
1 AAATAAAAATAAAATA-AT
560563 AAATAAAAATAAA
1 AAATAAAAATAAA
560576 TAAGATTGAG
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
17 4 0.10
18 13 0.32
19 17 0.41
20 7 0.17
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.23
Consensus pattern (18 bp):
AAATAAAAATAAAATAAT
Found at i:562394 original size:14 final size:14
Alignment explanation
Indices: 562375--562403 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
562365 TTATTTTTCT
562375 TAATATTTTAATTC
1 TAATATTTTAATTC
562389 TAATATTTTAATTC
1 TAATATTTTAATTC
562403 T
1 T
562404 TATTAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATATTTTAATTC
Found at i:564544 original size:47 final size:47
Alignment explanation
Indices: 564493--564616 Score: 115
Period size: 47 Copynumber: 2.6 Consensus size: 47
564483 TTGGACACTA
* * **
564493 AATGTGTCATATTATTACTGGCAATTTATACTACATATTGGGCACCG
1 AATGTGTCATACTATTACTGGCAATTTATACTACATACTAAGCACCG
* * * * * * *
564540 AATGT-TCCCTACTGTTATTGGTAGTTTATACTGCATACTAAGCACTG
1 AATGTGT-CATACTATTACTGGCAATTTATACTACATACTAAGCACCG
* *
564587 AATGGGTCATACTATTACTGACAATTTATA
1 AATGTGTCATACTATTACTGGCAATTTATA
564617 TTGTATACTA
Statistics
Matches: 57, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
46 1 0.02
47 55 0.96
48 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (47 bp):
AATGTGTCATACTATTACTGGCAATTTATACTACATACTAAGCACCG
Found at i:565394 original size:76 final size:75
Alignment explanation
Indices: 565303--565467 Score: 233
Period size: 76 Copynumber: 2.2 Consensus size: 75
565293 TTAAACTCAA
* *
565303 ATTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATATGTTTTTAAT
1 ATTTAGGATATTATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATA-GGTTTTAAT
565367 ATTTTAATTAAG
64 ATTTTAATTAAG
* * * * *
565379 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAATAT
565444 TTTAATTAAG
66 TTTAATTAAG
*
565454 ATTTAGAATATTAT
1 ATTTAGGATATTAT
565468 ATTATTTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 38 0.48
76 41 0.52
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAATAT
TTTAATTAAG
Found at i:566638 original size:21 final size:21
Alignment explanation
Indices: 566614--566667 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
566604 TATCGCAAAT
566614 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
566635 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
566656 TCGCGTTGCGAT
1 TCGCGTTGCGAT
566668 TTTCCATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Done.