Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003498.1 Hibiscus syriacus cultivar Beakdansim tig00007396_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: 386253
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:7423 original size:94 final size:87
Alignment explanation
Indices: 7307--7503 Score: 286
Period size: 94 Copynumber: 2.2 Consensus size: 87
7297 CCATAAATAA
7307 TAAAAATTATTTTTATTCAATAAAAACAATGATTTAATTGGAAAAAATAATATATAGAGAGATAT
1 TAAAAATTATTTTTATTCAATAAAAACAATGATTTAATT-GAAAAAA-AATATATAGAG-GATAT
7372 TATTTTGATTATTCATAAATATATAAGG
63 TA-TTTGATTATTCAT-AA-ATATAAGG
* * *
7400 TAAAAATTTGTTTTTATTCAATAAAAATAATGATTTAATTGAAAAAAAATATATAGAGGGTATTA
1 TAAAAA-TTATTTTTATTCAATAAAAACAATGATTTAATTGAAAAAAAATATATAGAGGATATTA
7465 TTTGATTATTCATAAATATAAGG
65 TTTGATTATTCATAAATATAAGG
*
7488 TAAAATTATATTTTTA
1 TAAAAAT-TATTTTTA
7504 GGATCGGGTA
Statistics
Matches: 97, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
87 1 0.01
88 20 0.21
89 2 0.02
90 13 0.13
91 6 0.06
92 11 0.11
93 13 0.13
94 31 0.32
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.41
Consensus pattern (87 bp):
TAAAAATTATTTTTATTCAATAAAAACAATGATTTAATTGAAAAAAAATATATAGAGGATATTAT
TTGATTATTCATAAATATAAGG
Found at i:12545 original size:15 final size:15
Alignment explanation
Indices: 12519--12588 Score: 86
Period size: 15 Copynumber: 4.5 Consensus size: 15
12509 CGGGTGTTAT
*
12519 GGGTACCTGGTAATC
1 GGGTACCCGGTAATC
*
12534 GGGTATCCGGTAATC
1 GGGTACCCGGTAATC
**
12549 GGGTACCCGGATGTTAC
1 GGGTACCCGG-TAAT-C
12566 GGGTACCCGGTAATC
1 GGGTACCCGGTAATC
12581 GGGTACCC
1 GGGTACCC
12589 AGATTTTATG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
15 31 0.67
16 4 0.09
17 11 0.24
ACGTcount: A:0.19, C:0.24, G:0.34, T:0.23
Consensus pattern (15 bp):
GGGTACCCGGTAATC
Found at i:12576 original size:32 final size:32
Alignment explanation
Indices: 12533--12603 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
12523 ACCTGGTAAT
* *
12533 CGGGTATCCGGTAATCGGGTACCCGGATGTTA
1 CGGGTACCCGGTAATCGGGTACCCAGATGTTA
*
12565 CGGGTACCCGGTAATCGGGTACCCAGATTTTA
1 CGGGTACCCGGTAATCGGGTACCCAGATGTTA
*
12597 TGGGTAC
1 CGGGTAC
12604 TTGATTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.25
Consensus pattern (32 bp):
CGGGTACCCGGTAATCGGGTACCCAGATGTTA
Found at i:12857 original size:28 final size:28
Alignment explanation
Indices: 12824--12879 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
12814 CGGGTCCTAT
*
12824 CGGGAAATGTCGGGCCGGGTATCCGACC
1 CGGGAAATGTCGGGCCGGGTACCCGACC
*
12852 CGGGAAATGTCGGGTCGGGTACCCGACC
1 CGGGAAATGTCGGGCCGGGTACCCGACC
12880 TTGCCGGGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.18, C:0.29, G:0.39, T:0.14
Consensus pattern (28 bp):
CGGGAAATGTCGGGCCGGGTACCCGACC
Found at i:22270 original size:28 final size:26
Alignment explanation
Indices: 22248--22301 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
22238 AATTGATGCG
22248 AAAAT-ACGATAGAGGTGAAATTGAT
1 AAAATGACGATAGAGGTGAAATTGAT
* *
22273 AAATTGATGATAGAGGTGAAATTGAT
1 AAAATGACGATAGAGGTGAAATTGAT
22299 AAA
1 AAA
22302 TTGATCTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.48, C:0.02, G:0.24, T:0.26
Consensus pattern (26 bp):
AAAATGACGATAGAGGTGAAATTGAT
Found at i:22288 original size:26 final size:26
Alignment explanation
Indices: 22255--22306 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
22245 GCGAAAATAC
22255 GATAGAGGTGAAATTGATAAATTGAT
1 GATAGAGGTGAAATTGATAAATTGAT
22281 GATAGAGGTGAAATTGATAAATTGAT
1 GATAGAGGTGAAATTGATAAATTGAT
22307 CTACTAAGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (26 bp):
GATAGAGGTGAAATTGATAAATTGAT
Found at i:27481 original size:60 final size:60
Alignment explanation
Indices: 27380--27493 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
27370 ATTTTGTAAC
* ** * *
27380 TTTTAATAGTCAATGGACTCAACAAAGCAACTCCTTGTAGTCGGGGGACTATTTTACAAT
1 TTTTAATAGTCAATAGACTCAACAAAGCAACTCCTCATAGTCGGAGGACCATTTTACAAT
27440 TTTTAATAGTCAATAGACTCAACAAAAG-AATCTCC-CATAGTCGGAGGACCATTT
1 TTTTAATAGTCAATAGACTCAAC-AAAGCAA-CTCCTCATAGTCGGAGGACCATTT
27494 ATGTACTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 39 0.83
61 8 0.17
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (60 bp):
TTTTAATAGTCAATAGACTCAACAAAGCAACTCCTCATAGTCGGAGGACCATTTTACAAT
Found at i:33290 original size:31 final size:31
Alignment explanation
Indices: 33182--33290 Score: 105
Period size: 31 Copynumber: 3.5 Consensus size: 31
33172 TTTACTTATC
* * * *
33182 TAAAA-TATTTGTTTAATCAAAATAAGTATT
1 TAAAAGTATTTTTTTTATCAAAATAAATATA
* * * *
33212 TAAAATTATTTTTTTGATCGAAATACATACTA
1 TAAAAGTATTTTTTTTATCAAAATAAATA-TA
*
33244 TAAAAGTATTTTTTTTATAAAAATAAATATA
1 TAAAAGTATTTTTTTTATCAAAATAAATATA
33275 TAAAA-TATTTATTTTT
1 TAAAAGTATTT-TTTTT
33291 TCATCGAAGT
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
30 10 0.15
31 30 0.46
32 25 0.38
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.47
Consensus pattern (31 bp):
TAAAAGTATTTTTTTTATCAAAATAAATATA
Found at i:34460 original size:18 final size:19
Alignment explanation
Indices: 34422--34460 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
34412 TTGTTTTTTT
*
34422 ATAATTTTAATAATATGAC
1 ATAATTTTAATAATATCAC
34441 ATAATTTTAA-AATATCAC
1 ATAATTTTAATAATATCAC
34459 AT
1 AT
34461 CATTAGAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (19 bp):
ATAATTTTAATAATATCAC
Found at i:35076 original size:21 final size:20
Alignment explanation
Indices: 35050--35094 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
35040 CTTAGAAAAA
*
35050 AATATTTATGTAACAA-TCTAC
1 AATATTGATGT-ACAATTC-AC
35071 AATATTGATGTACAATTCAC
1 AATATTGATGTACAATTCAC
35091 AATA
1 AATA
35095 CTATTGTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (20 bp):
AATATTGATGTACAATTCAC
Found at i:35092 original size:20 final size:21
Alignment explanation
Indices: 35050--35094 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
35040 CTTAGAAAAA
*
35050 AATATTTATGTAACAATCTAC
1 AATATTGATGTAACAATCTAC
35071 AATATTGATGT-ACAAT-TCAC
1 AATATTGATGTAACAATCT-AC
35091 AATA
1 AATA
35095 CTATTGTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.50
21 10 0.45
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (21 bp):
AATATTGATGTAACAATCTAC
Found at i:36073 original size:39 final size:39
Alignment explanation
Indices: 36029--36126 Score: 119
Period size: 38 Copynumber: 2.5 Consensus size: 39
36019 GAAGTTTAGT
* * *
36029 TTTTTTTTTCATTTTAGTACTCCACTATTAAAA-ACTTTAG
1 TTTTTATTTCATTTTAGTACTCCACCATTAAAATA--TTAA
* *
36069 TTTTTATTTCATTTTAATA-TTCACCATTAAAATATTAA
1 TTTTTATTTCATTTTAGTACTCCACCATTAAAATATTAA
36107 TTTTTATTTCATTTTAGTAC
1 TTTTTATTTCATTTTAGTAC
36127 CCCATTCAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
38 21 0.42
39 11 0.22
40 18 0.36
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (39 bp):
TTTTTATTTCATTTTAGTACTCCACCATTAAAATATTAA
Found at i:39497 original size:21 final size:21
Alignment explanation
Indices: 39473--39514 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
39463 CATTATAGTA
39473 TTGATATGACAGTTCATGATG
1 TTGATATGACAGTTCATGATG
*
39494 TTGATGTGACAGTTCATGATG
1 TTGATATGACAGTTCATGATG
39515 GTGACGTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (21 bp):
TTGATATGACAGTTCATGATG
Found at i:39528 original size:21 final size:21
Alignment explanation
Indices: 39479--39522 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
39469 AGTATTGATA
* *
39479 TGACAGTTCATGATGTTGATG
1 TGACAGTTCATGATGGTGACG
39500 TGACAGTTCATGATGGTGACG
1 TGACAGTTCATGATGGTGACG
39521 TG
1 TG
39523 GTAGTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.11, G:0.32, T:0.34
Consensus pattern (21 bp):
TGACAGTTCATGATGGTGACG
Found at i:40614 original size:2 final size:2
Alignment explanation
Indices: 40607--40658 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
40597 GTGTAAATGG
40607 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40649 AT AT AT AT AT
1 AT AT AT AT AT
40659 TGTGTAAAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40837 original size:2 final size:2
Alignment explanation
Indices: 40830--40864 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
40820 GATGTAAAAC
40830 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40865 TATTTGGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41307 original size:35 final size:35
Alignment explanation
Indices: 41261--41333 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
41251 ATCTATTAAT
41261 CGATTAATCCAGATCGAAAACTGCAGAGGCAAAGA
1 CGATTAATCCAGATCGAAAACTGCAGAGGCAAAGA
41296 CGATTAATCCAGATCGAAAACTGCAGAGGCAAAGA
1 CGATTAATCCAGATCGAAAACTGCAGAGGCAAAGA
41331 CGA
1 CGA
41334 CCCTCCCAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (35 bp):
CGATTAATCCAGATCGAAAACTGCAGAGGCAAAGA
Found at i:42283 original size:22 final size:21
Alignment explanation
Indices: 42220--42301 Score: 71
Period size: 22 Copynumber: 4.0 Consensus size: 21
42210 AAAAATTAAA
*
42220 TTAAAATTA-AATTATAAAAT
1 TTAAAATTATAATGATAAAAT
* * *
42240 TTATAATTA-ACT-CTAAAAT
1 TTAAAATTATAATGATAAAAT
* *
42259 TTAATATTATAATTATATAAAT
1 TTAAAATTATAATGATA-AAAT
*
42281 TTAAAATTTTAATGATAAAAT
1 TTAAAATTATAATGATAAAAT
42302 AAAGTGATTC
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
19 13 0.27
20 12 0.24
21 6 0.12
22 18 0.37
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (21 bp):
TTAAAATTATAATGATAAAAT
Found at i:42514 original size:17 final size:17
Alignment explanation
Indices: 42455--42515 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
42445 AAATAAATAC
*
42455 AAGACAATATATATTTA
1 AAGATAATATATATTTA
* **
42472 AATATAATATGAGTAAGTA
1 AAGATAATAT-A-TATTTA
42491 TAAGATAATATATATTTA
1 -AAGATAATATATATTTA
42509 AAGATAA
1 AAGATAA
42516 ACTCTCAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
17 15 0.44
18 5 0.15
19 5 0.15
20 9 0.26
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (17 bp):
AAGATAATATATATTTA
Found at i:42567 original size:23 final size:23
Alignment explanation
Indices: 42530--42592 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
42520 TCAATTTTTC
*
42530 GACAT-TAAATGCTCATA-CCCCT
1 GACATCTAAATCCTCA-AGCCCCT
42552 GACATCTAAATCCTCAAGCCCCT
1 GACATCTAAATCCTCAAGCCCCT
42575 GACATCTAAATCCTCAAG
1 GACATCTAAATCCTCAAG
42593 AAATAATAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
22 6 0.16
23 32 0.84
ACGTcount: A:0.33, C:0.33, G:0.10, T:0.24
Consensus pattern (23 bp):
GACATCTAAATCCTCAAGCCCCT
Found at i:53697 original size:3 final size:3
Alignment explanation
Indices: 53689--53735 Score: 69
Period size: 3 Copynumber: 15.3 Consensus size: 3
53679 AATATTTTTA
53689 ATT ATT ATT ATT -TT AATT ATT ATT ATT ATT AATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
53735 A
1 A
53736 ACAATATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.05
3 34 0.83
4 5 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:53702 original size:16 final size:16
Alignment explanation
Indices: 53681--53736 Score: 96
Period size: 16 Copynumber: 3.6 Consensus size: 16
53671 GTCTTAAAAA
*
53681 TATTTTTAATTATTAT
1 TATTATTAATTATTAT
53697 TATT-TTAATTATTAT
1 TATTATTAATTATTAT
53712 TATTATTAATTATTAT
1 TATTATTAATTATTAT
53728 TATTATTAA
1 TATTATTAA
53737 CAATATTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.38
16 24 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTATTAATTATTAT
Found at i:55226 original size:15 final size:16
Alignment explanation
Indices: 55190--55227 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
55180 TTTGTGCTTC
55190 ATTATTT-ATCCTTTT
1 ATTATTTAATCCTTTT
*
55205 ATGATTTAATCC-TTT
1 ATTATTTAATCCTTTT
55220 ATTATTTA
1 ATTATTTA
55228 GTTTCATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.26, C:0.11, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTATTTAATCCTTTT
Found at i:62368 original size:26 final size:27
Alignment explanation
Indices: 62339--62397 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 27
62329 ATATCCTTTT
*
62339 TTATTTGA-TCAAAATATATACTTAAA
1 TTATTTGAGTCAAAATAGATACTTAAA
* * *
62365 TTATTTTATGTGAAAATAGATATTTAAA
1 TTATTTGA-GTCAAAATAGATACTTAAA
62393 TTATT
1 TTATT
62398 CAATCATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 7 0.26
28 20 0.74
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (27 bp):
TTATTTGAGTCAAAATAGATACTTAAA
Found at i:62615 original size:27 final size:29
Alignment explanation
Indices: 62565--62622 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
62555 GTATCATTTT
*
62565 TTTTTTGTCAAAATAGGTACCTT-AAGTA
1 TTTTTGGTCAAAATAGGTACCTTAAAGTA
*
62593 TTTTTGGTCAAAATATGTA-CTTAAAGTA
1 TTTTTGGTCAAAATAGGTACCTTAAAGTA
62621 TT
1 TT
62623 CAGTTTCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 3 0.11
28 24 0.89
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.45
Consensus pattern (29 bp):
TTTTTGGTCAAAATAGGTACCTTAAAGTA
Found at i:62785 original size:30 final size:30
Alignment explanation
Indices: 62740--62796 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
62730 ATAAAATATT
*
62740 TTAGGTATCTATTTTGACCAAAAAATACCC
1 TTAGATATCTATTTTGACCAAAAAATACCC
* *
62770 TTAGATATTTATTTTGATCAAAAAATA
1 TTAGATATCTATTTTGACCAAAAAATA
62797 TTTTAGGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (30 bp):
TTAGATATCTATTTTGACCAAAAAATACCC
Found at i:63205 original size:32 final size:30
Alignment explanation
Indices: 63129--63201 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
63119 GAAGTTTAAA
* *
63129 TTTTTTAATTTAATTACTTAATTTTCAAAT
1 TTTTTTAATTTAATCACTTAACTTTCAAAT
** *
63159 TATTCCTAATTTAATCACTCTAACTTTCATAT
1 T-TTTTTAATTTAATCACT-TAACTTTCAAAT
63191 TTTTTTAATTT
1 TTTTTTAATTT
63202 TAATTATATA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
30 1 0.03
31 22 0.65
32 11 0.32
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (30 bp):
TTTTTTAATTTAATCACTTAACTTTCAAAT
Found at i:63476 original size:21 final size:22
Alignment explanation
Indices: 63431--63476 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
63421 TACGATTTTA
*
63431 AAAAATTAAAAATTTAATTACT
1 AAAAATTAAAAATTTAAGTACT
* *
63453 AAAAA-TAATAATTTAAGTATT
1 AAAAATTAAAAATTTAAGTACT
63474 AAA
1 AAA
63477 TACATAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
AAAAATTAAAAATTTAAGTACT
Found at i:66841 original size:60 final size:60
Alignment explanation
Indices: 66715--66841 Score: 132
Period size: 60 Copynumber: 2.1 Consensus size: 60
66705 AATAGTCCCT
* * * *
66715 TGACTATAGAGTATTACTTTGTAGAGTCTCATGACTATTAAAAGTAATAAAATGGCCCTC
1 TGACTATAGAGTATTACTTTGTAGAGTCTCATGACTATTAAAAATAACAAAATGACCATC
* * * * * *
66775 TAACTATAGGGTGTTGA-TTTGTTGAGTCTC-TCGACTATTAAAAATTACAAAATGATCATC
1 TGACTATAGAGTATT-ACTTTGTAGAGTCTCAT-GACTATTAAAAATAACAAAATGACCATC
66835 TGACTAT
1 TGACTAT
66842 TCATATGTTT
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
59 1 0.02
60 52 0.96
61 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (60 bp):
TGACTATAGAGTATTACTTTGTAGAGTCTCATGACTATTAAAAATAACAAAATGACCATC
Found at i:67553 original size:29 final size:29
Alignment explanation
Indices: 67484--67566 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 29
67474 TTTAGATACC
* *
67484 TATTTTGACATAAAAT-ACTTTAAGTACA
1 TATTTTGATAAAAAATAACTTTAAGTACA
**
67512 TATTTTGATTAAAAAATAACTTTAAGTATT
1 TATTTTGA-TAAAAAATAACTTTAAGTACA
*
67542 TATTTTGATAAAAAAAATACTTTAA
1 TATTTTGATAAAAAATA-ACTTTAA
67567 ATAATTAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
28 8 0.17
29 14 0.30
30 25 0.53
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (29 bp):
TATTTTGATAAAAAATAACTTTAAGTACA
Found at i:81194 original size:2 final size:2
Alignment explanation
Indices: 81187--81215 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
81177 TATGCATGTG
81187 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
81216 TCCTCTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:82703 original size:30 final size:29
Alignment explanation
Indices: 82627--82706 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 29
82617 AATTAATACC
*
82627 CATTTTATAATAATTTGATAAAATTTAATGA
1 CATTTTATAAT-ATTT-AAAAAATTTAATGA
** *
82658 CCGTTTATGATTATTTAAAAAATTTAATGA
1 CATTTTAT-AATATTTAAAAAATTTAATGA
82688 TCATTTTATAATATTTAAA
1 -CATTTTATAATATTTAAA
82707 TTCTCATTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
30 22 0.55
31 16 0.40
32 2 0.05
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.46
Consensus pattern (29 bp):
CATTTTATAATATTTAAAAAATTTAATGA
Found at i:82954 original size:35 final size:35
Alignment explanation
Indices: 82908--82977 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
82898 TTTCATATAA
*
82908 TTTAAAATAA-TTC-TATAAATTTAATATTTTGAAAT
1 TTTAAAATAATTTCTTA-AAATTT-ATATTTTAAAAT
*
82943 TTTAATATAATTTCTTAAAATTTATATTTTAAAAT
1 TTTAAAATAATTTCTTAAAATTTATATTTTAAAAT
82978 ATAAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 20 0.65
36 9 0.29
37 2 0.06
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (35 bp):
TTTAAAATAATTTCTTAAAATTTATATTTTAAAAT
Found at i:87440 original size:20 final size:22
Alignment explanation
Indices: 87390--87440 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
87380 AATTTAGATA
*
87390 AAAATAAA-AAGTTTAAGTACT
1 AAAATAAATAAGTTTAAATACT
*
87411 AAAATTAATAA-TTTAAATACT
1 AAAATAAATAAGTTTAAATACT
87432 -AAATAAATA
1 AAAATAAATA
87441 CATATTTTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 8 0.31
21 16 0.62
22 2 0.08
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (22 bp):
AAAATAAATAAGTTTAAATACT
Found at i:87717 original size:343 final size:343
Alignment explanation
Indices: 87152--87838 Score: 1313
Period size: 343 Copynumber: 2.0 Consensus size: 343
87142 GAATTTAGTA
87152 CTTAAATTATTAGTTTTAGTTTGTTTTAGTACCTAAACTTTCAGTTTTTCAAAACCATACCTAAT
1 CTTAAATTATTAGTTTTAGTTTGTTTTAGTACCTAAACTTTCAGTTTTTCAAAACCATACCTAAT
*
87217 GTTTAATTTTCTAATACCTATACTATCAATTTTGGTTCATTTTAGTACCTAAACTTTTAGTTTTT
66 GTTTAATTTTCTAATACCTATACTATCAATTTTGGTTCATTTTAGTACCTAAACTTTTAGATTTT
87282 TCAAAACTTAATATTAACTTTTGAACGGGATACTAATATAAAAAAACTAAAGTTTTTAATAGTGG
131 TCAAAACTTAATATTAACTTTTGAACGGGATACTAATATAAAAAAACTAAAGTTTTTAATAGTGG
87347 GATATTAAAATAAAACAAAAAATTAAAAACTAAAATTTAGATAAAAATAAAAAGTTTAAGTACTA
196 GATATTAAAATAAAACAAAAAATTAAAAACTAAAATTTAGATAAAAATAAAAAGTTTAAGTACTA
*
87412 AAATTAATAATTTAAATACTAAATAAATACATATTTTACCCTATGATATAGCATATAATAATATA
261 AAATTAATAATTTAAATACTAAATAAATACATATTTTACCCTATGATATAGCATATAATAATAAA
87477 AAATATATAATAAAACCC
326 AAATATATAATAAAACCC
*
87495 CTTAAATTATTAGTTTTAGTTTGTTTTAGTATCTAAACTTTCAGTTTTTCAAAACCATACCTAAT
1 CTTAAATTATTAGTTTTAGTTTGTTTTAGTACCTAAACTTTCAGTTTTTCAAAACCATACCTAAT
* *
87560 GTTTAATTTTCTAGTACCTATACTATCAGTTTTGGTTCATTTTAGTACCTAAACTTTTA-ATTTT
66 GTTTAATTTTCTAATACCTATACTATCAATTTTGGTTCATTTTAGTACCTAAACTTTTAGATTTT
87624 TCAAAACTTAATATTAACTTTTGAACGGGATACTAATATAAAAAAAACTAAAGTTTTTAATAGTG
131 TCAAAACTTAATATTAACTTTTGAACGGGATACTAATAT-AAAAAAACTAAAGTTTTTAATAGTG
87689 GGATATTAAAATAAAACAAAAAATTAAAAACTAAAATTTAGATAAAAATAAAAAGTTTAAGTACT
195 GGATATTAAAATAAAACAAAAAATTAAAAACTAAAATTTAGATAAAAATAAAAAGTTTAAGTACT
87754 AAAATTAATAATTTAAATACTAAATAAATACATATTTTACCCTATGATATAGCATATAATAATAA
260 AAAATTAATAATTTAAATACTAAATAAATACATATTTTACCCTATGATATAGCATATAATAATAA
87819 AAAATATATAATAAAACCC
325 AAAATATATAATAAAACCC
87838 C
1 C
87839 ATAATTCTGT
Statistics
Matches: 338, Mismatches: 5, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
342 43 0.13
343 295 0.87
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (343 bp):
CTTAAATTATTAGTTTTAGTTTGTTTTAGTACCTAAACTTTCAGTTTTTCAAAACCATACCTAAT
GTTTAATTTTCTAATACCTATACTATCAATTTTGGTTCATTTTAGTACCTAAACTTTTAGATTTT
TCAAAACTTAATATTAACTTTTGAACGGGATACTAATATAAAAAAACTAAAGTTTTTAATAGTGG
GATATTAAAATAAAACAAAAAATTAAAAACTAAAATTTAGATAAAAATAAAAAGTTTAAGTACTA
AAATTAATAATTTAAATACTAAATAAATACATATTTTACCCTATGATATAGCATATAATAATAAA
AAATATATAATAAAACCC
Found at i:87783 original size:20 final size:22
Alignment explanation
Indices: 87733--87783 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
87723 AATTTAGATA
*
87733 AAAATAAA-AAGTTTAAGTACT
1 AAAATAAATAAGTTTAAATACT
*
87754 AAAATTAATAA-TTTAAATACT
1 AAAATAAATAAGTTTAAATACT
87775 -AAATAAATA
1 AAAATAAATA
87784 CATATTTTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 8 0.31
21 16 0.62
22 2 0.08
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (22 bp):
AAAATAAATAAGTTTAAATACT
Found at i:89409 original size:20 final size:20
Alignment explanation
Indices: 89384--89502 Score: 154
Period size: 20 Copynumber: 5.9 Consensus size: 20
89374 TAATTGAAAA
*
89384 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
89404 TCGCGTTGCGATTTT-CAGT
1 TCGCGTTGCGATTTTCCAGT
89423 TCGCGTTGCGATTTTCC-GTT
1 TCGCGTTGCGATTTTCCAG-T
89443 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* *
89463 TCGCGTTGCGATAATCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
89485 T-GTCGTTGCGATTTTCCA
1 TCG-CGTTGCGATTTTCCA
89503 AATTCGTTGC
Statistics
Matches: 88, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
19 19 0.22
20 51 0.58
21 2 0.02
22 16 0.18
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:89438 original size:39 final size:40
Alignment explanation
Indices: 89384--89474 Score: 166
Period size: 39 Copynumber: 2.3 Consensus size: 40
89374 TAATTGAAAA
89384 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTT-CAGT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGT
*
89423 TCGCGTTGCGATTTTCCGTTTCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGT
89463 TCGCGTTGCGAT
1 TCGCGTTGCGAT
89475 AATCTACAGT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 34 0.68
40 16 0.32
ACGTcount: A:0.09, C:0.24, G:0.25, T:0.42
Consensus pattern (40 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGT
Found at i:89455 original size:59 final size:61
Alignment explanation
Indices: 89384--89501 Score: 179
Period size: 59 Copynumber: 2.0 Consensus size: 61
89374 TAATTGAAAA
* *
89384 TCGCGTTGCGATTTTCCATTTCGCGTTGCGAT-T-TTCAGTTCG-CGTTGCGATTTTCCGTT
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATATCTACAGTT-GTCGTTGCGATTTTCCGTT
89443 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAATCTACAGTTGTCGTTGCGATTTTCC
1 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGAT-ATCTACAGTTGTCGTTGCGATTTTCC
89502 AAATTCGTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
59 31 0.58
61 2 0.04
62 20 0.38
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.42
Consensus pattern (61 bp):
TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATATCTACAGTTGTCGTTGCGATTTTCCGTT
Found at i:89491 original size:22 final size:21
Alignment explanation
Indices: 89466--89537 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 21
89456 TTCCAGTTCG
89466 CGTTGCGATAATCTACAGTTGT
1 CGTTGCGAT-ATCTACAGTTGT
* * **
89488 CGTTGCGAT-TTTCCAAAT-T
1 CGTTGCGATATCTACAGTTGT
89507 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATA-TCTACAGTTGT
89529 CGTTGCGAT
1 CGTTGCGAT
89538 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (21 bp):
CGTTGCGATATCTACAGTTGT
Found at i:89511 original size:19 final size:19
Alignment explanation
Indices: 89487--89555 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
89477 TCTACAGTTG
89487 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
89506 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
89527 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
89547 TCGTTGCGA
1 TCGTTGCGA
89556 AAATCGCGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 19 0.49
20 5 0.13
21 5 0.13
22 10 0.26
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:89522 original size:41 final size:41
Alignment explanation
Indices: 89446--89560 Score: 178
Period size: 41 Copynumber: 2.8 Consensus size: 41
89436 TTCCGTTTCG
*
89446 CGTTGCGATTTTCC-AGTTCGCGTTGCGATAATCTACAGTTGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAATCTACAGTTGT
*
89488 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAATCTACAGTTGT
*
89529 CGTTGCGATTTTCCAAATTCGTTGCGAAAATC
1 CGTTGCGATTTTCCAAATTCGTTGCGATAATC
89561 GCGTTGCGAT
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
41 51 0.75
42 14 0.21
43 3 0.04
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAATCTACAGTTGT
Found at i:89611 original size:96 final size:94
Alignment explanation
Indices: 89489--89674 Score: 284
Period size: 96 Copynumber: 2.0 Consensus size: 94
89479 TACAGTTGTC
*
89489 GTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGC
1 GTTGCGATTTTCCAAATTCGCTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGC
89554 GAAAATCGCGTTGCGATAGTTGAAAATCGT
66 GAAAAT-GCGTTGCGATAGTTGAAAATCGT
* *
89584 GTTGCGATTTTCC-AGTTCGCGCTGCGATAGTCTATAGTTGTCGTTGCGATTTTCCAAATTCGTT
1 GTTGCGATTTTCCAAATT--CGCTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTT
* * *
89648 GCGAAAATTCGTTGTGATAGTTTAAAA
64 GCGAAAATGCGTTGCGATAGTTGAAAA
89675 AAAAAAGATT
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
94 3 0.04
95 29 0.35
96 51 0.61
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (94 bp):
GTTGCGATTTTCCAAATTCGCTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGC
GAAAATGCGTTGCGATAGTTGAAAATCGT
Found at i:90268 original size:6 final size:6
Alignment explanation
Indices: 90259--90298 Score: 62
Period size: 6 Copynumber: 6.3 Consensus size: 6
90249 CCGTCTCGTC
90259 TCGTGG TCGTGTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
1 TCGTGG TC--GTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
90299 ATACGTGTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 26 0.81
8 6 0.19
ACGTcount: A:0.00, C:0.17, G:0.47, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:90424 original size:21 final size:19
Alignment explanation
Indices: 90372--90427 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 19
90362 ATCTTTTTTT
90372 TTTA-ACTATCGCAACGAA
1 TTTAGACTATCGCAACGAA
* **
90390 TTTGGAAAATCGCAACGACA
1 TTTAGACTATCGCAACGA-A
90410 TTGTAGACTATCGCAACG
1 TT-TAGACTATCGCAACG
90428 CAAAATGAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 3 0.10
19 11 0.38
20 3 0.10
21 12 0.41
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (19 bp):
TTTAGACTATCGCAACGAA
Found at i:90461 original size:41 final size:41
Alignment explanation
Indices: 90370--90510 Score: 171
Period size: 41 Copynumber: 3.5 Consensus size: 41
90360 AAATCTTTTT
* **
90370 TTTTTAACTATCGCAACG-AATTTGGAAAATCGCAACGAC-A
1 TTTTCAACTATCGCAACGCAAAATGGAAAATCGCAACG-CGA
* *
90410 TTGT-AGACTATCGCAACGCAAAATGAAAAATCGCAACGCGA
1 TTTTCA-ACTATCGCAACGCAAAATGGAAAATCGCAACGCGA
* * *
90451 TTTTCAACTATAGCAACTCGAAATGGAAAATCGCAACGCGA
1 TTTTCAACTATCGCAACGCAAAATGGAAAATCGCAACGCGA
90492 TTTTCAACTATCGCAACGC
1 TTTTCAACTATCGCAACGC
90511 GAATTTGCGA
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
39 1 0.01
40 16 0.19
41 68 0.79
42 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (41 bp):
TTTTCAACTATCGCAACGCAAAATGGAAAATCGCAACGCGA
Found at i:90505 original size:21 final size:21
Alignment explanation
Indices: 90439--90512 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
90429 AAAATGAAAA
90439 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* * ** ** *
90460 ATAGCAACTCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
90480 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
90501 ATCGCAACGCGA
1 ATCGCAACGCGA
90513 ATTTGCGATT
Statistics
Matches: 38, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 13 0.34
21 25 0.66
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:94413 original size:30 final size:30
Alignment explanation
Indices: 94377--94436 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
94367 GTTGGCCTAG
* *
94377 TATCCAACGAATAATGCCCTTCAGGTTCCT
1 TATCCAACGAATAATGCCCTCCAAGTTCCT
94407 TATCCAACGAATAATGCCCTCCAAGTTCCT
1 TATCCAACGAATAATGCCCTCCAAGTTCCT
94437 AATCTTATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.32, G:0.12, T:0.28
Consensus pattern (30 bp):
TATCCAACGAATAATGCCCTCCAAGTTCCT
Found at i:102400 original size:46 final size:46
Alignment explanation
Indices: 102333--102429 Score: 185
Period size: 46 Copynumber: 2.1 Consensus size: 46
102323 ATGCATTGTA
*
102333 TCTATTGGTACATCTTTTTCCAACATTTTATGTATGGATAATATTC
1 TCTATTGATACATCTTTTTCCAACATTTTATGTATGGATAATATTC
102379 TCTATTGATACATCTTTTTCCAACATTTTATGTATGGATAATATTC
1 TCTATTGATACATCTTTTTCCAACATTTTATGTATGGATAATATTC
102425 TCTAT
1 TCTAT
102430 GCTCAAAATG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.48
Consensus pattern (46 bp):
TCTATTGATACATCTTTTTCCAACATTTTATGTATGGATAATATTC
Found at i:113006 original size:20 final size:20
Alignment explanation
Indices: 112967--113006 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
112957 TTTATTTGGA
* * *
112967 GAAAAAAACTAACAATTATT
1 GAAAAAAAATAAAAAATATT
112987 GAAAAAAAATAAAAAATATT
1 GAAAAAAAATAAAAAATATT
113007 TTAAAAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (20 bp):
GAAAAAAAATAAAAAATATT
Found at i:121937 original size:16 final size:16
Alignment explanation
Indices: 121916--121958 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
121906 ATTTATTTAT
*
121916 TTTATTTTTATGATTA
1 TTTATTTTTATGAATA
***
121932 TTTATTTACGTGAATA
1 TTTATTTTTATGAATA
121948 TTTATTTTTAT
1 TTTATTTTTAT
121959 CCTTAAGATA
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.65
Consensus pattern (16 bp):
TTTATTTTTATGAATA
Found at i:124815 original size:2 final size:2
Alignment explanation
Indices: 124808--124837 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
124798 TCCAGATCAG
124808 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
124838 ATCCAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:131649 original size:29 final size:29
Alignment explanation
Indices: 131615--131671 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
131605 TTGTTGAGTC
131615 CATTGACTATCAAATA-TTACAAAATGATT
1 CATTGACTATCAAA-AGTTACAAAATGATT
* * *
131644 CATTGATTATTAAAAGTTATAAAATGAT
1 CATTGACTATCAAAAGTTACAAAATGAT
131672 CACCTAACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (29 bp):
CATTGACTATCAAAAGTTACAAAATGATT
Found at i:135153 original size:22 final size:21
Alignment explanation
Indices: 135123--135170 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
135113 GCGTTTAATG
135123 TTAAAAGATTA-AGAATTATAT
1 TTAAAAGA-TACAGAATTATAT
*
135144 TTAAACAGATACCGAATTATAT
1 TTAAA-AGATACAGAATTATAT
135166 TTAAA
1 TTAAA
135171 GAGAATGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.35
Consensus pattern (21 bp):
TTAAAAGATACAGAATTATAT
Found at i:138885 original size:18 final size:18
Alignment explanation
Indices: 138857--138898 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
138847 TTGTCGATAC
* *
138857 TTTTTATTATTCTTTTATT
1 TTTTTATTATT-ATATATT
138876 TTTTTA-TATTATATATT
1 TTTTTATTATTATATATT
138893 TTTTTA
1 TTTTTA
138899 ATTTTAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 11 0.52
18 4 0.19
19 6 0.29
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTATTATTATATATT
Found at i:139421 original size:13 final size:14
Alignment explanation
Indices: 139396--139425 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
139386 TTTGTATATA
139396 TTTTTATTCAAGTT
1 TTTTTATTCAAGTT
139410 TTTTTATT-AAGTT
1 TTTTTATTCAAGTT
139423 TTT
1 TTT
139426 AATCTTTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (14 bp):
TTTTTATTCAAGTT
Found at i:140710 original size:3 final size:3
Alignment explanation
Indices: 140704--140738 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
140694 ACTCAGAAGA
140704 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
140739 CTCAAAATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:141944 original size:12 final size:12
Alignment explanation
Indices: 141927--141951 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
141917 TGTCGGTGTC
141927 GCTCTCGTCGCT
1 GCTCTCGTCGCT
141939 GCTCTCGTCGCT
1 GCTCTCGTCGCT
141951 G
1 G
141952 AAGGAATCCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.40, G:0.28, T:0.32
Consensus pattern (12 bp):
GCTCTCGTCGCT
Found at i:143989 original size:44 final size:44
Alignment explanation
Indices: 143921--144024 Score: 181
Period size: 44 Copynumber: 2.4 Consensus size: 44
143911 AATAAGTGAT
143921 TAAATTGGGTTGGGAGAGTCGAAACTTGACATTTACGAACGAAA
1 TAAATTGGGTTGGGAGAGTCGAAACTTGACATTTACGAACGAAA
*
143965 TAAATTGGGTTGGGAGAGTTGAAACTTGACATTTACGAACGAAA
1 TAAATTGGGTTGGGAGAGTCGAAACTTGACATTTACGAACGAAA
* *
144009 CAAATTGAGTTGGGAG
1 TAAATTGGGTTGGGAG
144025 GGTCACCCTC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.36, C:0.10, G:0.29, T:0.26
Consensus pattern (44 bp):
TAAATTGGGTTGGGAGAGTCGAAACTTGACATTTACGAACGAAA
Found at i:153787 original size:24 final size:24
Alignment explanation
Indices: 153742--153815 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
153732 TTTCCTTGTG
* * *
153742 ACACGTTTTTCTCTGTTTTTGTGGC
1 ACACG-TTCTCTCTGATCTTGTGGC
* *
153767 ACACGTTCTCTCTTATCTTGTGAC
1 ACACGTTCTCTCTGATCTTGTGGC
* * *
153791 ACGCGTTTTCTCTGCTCTTGTGGC
1 ACACGTTCTCTCTGATCTTGTGGC
153815 A
1 A
153816 TGTTCTTTAT
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
24 34 0.87
25 5 0.13
ACGTcount: A:0.11, C:0.26, G:0.19, T:0.45
Consensus pattern (24 bp):
ACACGTTCTCTCTGATCTTGTGGC
Found at i:155792 original size:6 final size:6
Alignment explanation
Indices: 155766--155822 Score: 78
Period size: 6 Copynumber: 9.5 Consensus size: 6
155756 CAAAAGAATC
* * * *
155766 ACCTAC ACCTAC ACCTAT ACCTGT ACCTGT ACCTAT ACCTAT ACCTAT
1 ACCTAT ACCTAT ACCTAT ACCTAT ACCTAT ACCTAT ACCTAT ACCTAT
155814 ACCTAT ACC
1 ACCTAT ACC
155823 CTAATACCCT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.30, C:0.39, G:0.04, T:0.28
Consensus pattern (6 bp):
ACCTAT
Found at i:158621 original size:62 final size:62
Alignment explanation
Indices: 158524--158647 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
158514 AAACCATTAA
*
158524 GCCTTAACCCATAACAAAGAATTATGGTTCACTACTCAAAACCACACAGTGAAACGATCATT
1 GCCTTAACCCATAACAAAGAATAATGGTTCACTACTCAAAACCACACAGTGAAACGATCATT
158586 GCCTTAACCCATAACAAAGAATAATGGTTCACTACTCAAAACCACACAGTGAAACGATCATT
1 GCCTTAACCCATAACAAAGAATAATGGTTCACTACTCAAAACCACACAGTGAAACGATCATT
158648 ATTCATCTTT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.41, C:0.26, G:0.11, T:0.22
Consensus pattern (62 bp):
GCCTTAACCCATAACAAAGAATAATGGTTCACTACTCAAAACCACACAGTGAAACGATCATT
Found at i:160377 original size:49 final size:49
Alignment explanation
Indices: 160323--160426 Score: 190
Period size: 49 Copynumber: 2.1 Consensus size: 49
160313 AAATGAAACA
160323 AAAACTAAATGTTAGGTATGATTTTAAAAAAAATAAAAGTTTAAGTACT
1 AAAACTAAATGTTAGGTATGATTTTAAAAAAAATAAAAGTTTAAGTACT
* *
160372 AAAACTAAATGTTATGTATGATTTTTAAAAAAATAAAAGTTTAAGTACT
1 AAAACTAAATGTTAGGTATGATTTTAAAAAAAATAAAAGTTTAAGTACT
160421 AAAACT
1 AAAACT
160427 GATGTTTAGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.34
Consensus pattern (49 bp):
AAAACTAAATGTTAGGTATGATTTTAAAAAAAATAAAAGTTTAAGTACT
Found at i:164580 original size:13 final size:13
Alignment explanation
Indices: 164562--164589 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
164552 AAAAATTGAC
164562 GGTTGTATAAGAT
1 GGTTGTATAAGAT
164575 GGTTGTATAAGAT
1 GGTTGTATAAGAT
164588 GG
1 GG
164590 ATATTAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.36, T:0.36
Consensus pattern (13 bp):
GGTTGTATAAGAT
Found at i:164846 original size:60 final size:60
Alignment explanation
Indices: 164740--164914 Score: 235
Period size: 60 Copynumber: 2.9 Consensus size: 60
164730 ATAGCCGGGT
* * * * * * * * *
164740 AATCATTTTGTAACTTTCAGTAGTCAAGAGACTCAACAAAACAACACCCTATAATAGAAG
1 AATCATTTTATAATTTTTAATAGTTAAGATACTTAATAAAACAACACCCTATAACAGAAG
*
164800 AATCATTTTATAATTTTTAATAGTTAAGATACTTAATAAAATAACACCCTATAACAGAAG
1 AATCATTTTATAATTTTTAATAGTTAAGATACTTAATAAAACAACACCCTATAACAGAAG
*
164860 AA-CTATTTTATAATTTTTAATAATTAAGATACTTAATAAAACAACACCCTATAAC
1 AATC-ATTTTATAATTTTTAATAGTTAAGATACTTAATAAAACAACACCCTATAAC
164915 GAATACCATT
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
59 1 0.01
60 101 0.99
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (60 bp):
AATCATTTTATAATTTTTAATAGTTAAGATACTTAATAAAACAACACCCTATAACAGAAG
Found at i:171778 original size:60 final size:61
Alignment explanation
Indices: 171678--171818 Score: 243
Period size: 60 Copynumber: 2.4 Consensus size: 61
171668 ATAGTCAAGT
*
171678 GATCA-TTT-TAACTTTTAATATTCAAAGGGACTCAACAAAGCAACTCCCTATGGTCGAGG
1 GATCATTTTGTAACTTTTAATATTCAAAGGGACTCAACAAAGCAACTCCCTATGGTCGAGA
171737 GATCATTTTGTAACTTTTAATATTC-AAGGGACTCAACAAAGCAACTCCCTATGGTCGAGA
1 GATCATTTTGTAACTTTTAATATTCAAAGGGACTCAACAAAGCAACTCCCTATGGTCGAGA
*
171797 GACCATTTTGTAACTTTTAATA
1 GATCATTTTGTAACTTTTAATA
171819 GTCCATTTAT
Statistics
Matches: 78, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
59 5 0.06
60 58 0.74
61 15 0.19
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (61 bp):
GATCATTTTGTAACTTTTAATATTCAAAGGGACTCAACAAAGCAACTCCCTATGGTCGAGA
Found at i:178534 original size:17 final size:16
Alignment explanation
Indices: 178509--178560 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
178499 TTTATTCATG
178509 TTATTTTAAAATTAAA
1 TTATTTTAAAATTAAA
178525 TTATTTTTAAAATTAAA
1 TTA-TTTTAAAATTAAA
* *
178542 TTAATTTAAATTTAAA
1 TTATTTTAAAATTAAA
178558 TTA
1 TTA
178561 AATATTTCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
16 17 0.52
17 16 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATTTTAAAATTAAA
Found at i:181908 original size:243 final size:243
Alignment explanation
Indices: 181474--181969 Score: 739
Period size: 243 Copynumber: 2.0 Consensus size: 243
181464 TTGGTTTATG
* * * *
181474 TCCATTATAATATAAGGTTGAAGCTAAGACACATGCAAAGCAAAAGTTCACAATAGTTATAAATG
1 TCCATTATAATATAAGGTTGAAGCTAAGACACATGCAAAACAAAAGTGCACAAGAGTTAGAAATG
* * *
181539 GGTTTTAATCCAATTAATCTTAAGAATTTTTTTGAAGAATAGGATCTACTAAATGCATGGATTAA
66 GGTTTTAATCCAATTAATCTTAAGAATATTTTTGAAGAAGAGGATATACTAAATGCATGGATTAA
* *
181604 GGAAAGAAATAATACTACGCTTGATAGTGAACAAAATTTATCATAGCTGTCTGAGGAGTTACTTA
131 GGAAAGAAATAATACTACACTTGATAATGAACAAAATTTATCATAGCTGTCTGAGGAGTTACTTA
* *
181669 ATGAAATTGATGAAGAAAGTAAGGTAAAGATATGAATAGTTCA-CTTGC
196 ATGAAATTGATGAAGAAACTAAGGTAAAGATATGAATAGTTAATC-TGC
* *
181717 TCCATTATAATATGAGGTTGAAGCTAAGAGACATGCAAAACAAAAGTGCACAAGAGTTAGAAATG
1 TCCATTATAATATAAGGTTGAAGCTAAGACACATGCAAAACAAAAGTGCACAAGAGTTAGAAATG
* *
181782 GGTTTTAATCCAATTAATCTTGAGAATATTTTTGAAGAAGATGATATACTAAATGCATGGATTGA
66 GGTTTTAATCCAATTAATCTTAAGAATATTTTTGAAGAAGAGGATATACTAAATGCATGGATT-A
* * * * * * *
181847 A-GAAAGAGATGATGCTACACTTGATAATGAACAAAATTTCTCATGGTTG-CATGATGAGTTACT
130 AGGAAAGAAATAATACTACACTTGATAATGAACAAAATTTATCATAGCTGTC-TGAGGAGTTACT
181910 TAATGAAATTGATGAAGAAACTAAGGTAAAGATATGAATAGTTAATCTGC
194 TAATGAAATTGATGAAGAAACTAAGGTAAAGATATGAATAGTTAATCTGC
181960 TCCA-TATAAT
1 TCCATTATAAT
181970 GAGGAAAATG
Statistics
Matches: 228, Mismatches: 22, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
242 7 0.03
243 218 0.96
244 3 0.01
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (243 bp):
TCCATTATAATATAAGGTTGAAGCTAAGACACATGCAAAACAAAAGTGCACAAGAGTTAGAAATG
GGTTTTAATCCAATTAATCTTAAGAATATTTTTGAAGAAGAGGATATACTAAATGCATGGATTAA
GGAAAGAAATAATACTACACTTGATAATGAACAAAATTTATCATAGCTGTCTGAGGAGTTACTTA
ATGAAATTGATGAAGAAACTAAGGTAAAGATATGAATAGTTAATCTGC
Found at i:182634 original size:12 final size:12
Alignment explanation
Indices: 182617--182644 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
182607 ACTTGTATGG
182617 TTTATATTTGTT
1 TTTATATTTGTT
182629 TTTATATTTGTT
1 TTTATATTTGTT
182641 TTTA
1 TTTA
182645 ATAAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.75
Consensus pattern (12 bp):
TTTATATTTGTT
Found at i:184202 original size:41 final size:41
Alignment explanation
Indices: 184135--184243 Score: 114
Period size: 41 Copynumber: 2.7 Consensus size: 41
184125 GTTCAAAACC
* *
184135 CTAAAGTACGAGTCTATAG-TGACGTTTATATAAAAACGCCA
1 CTAAAGTACGAGTCTTTAGCAG-CGTTTATATAAAAACGCCA
* * * *
184176 CTAAAGTACGAGCCTTTAGCAGCGTTTGTATATAATCGCCA
1 CTAAAGTACGAGTCTTTAGCAGCGTTTATATAAAAACGCCA
* *
184217 -TGAAAGTACAAGTCTTTAGCGGCGTTT
1 CT-AAAGTACGAGTCTTTAGCAGCGTTT
184244 TTGCTTAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
40 1 0.02
41 55 0.96
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (41 bp):
CTAAAGTACGAGTCTTTAGCAGCGTTTATATAAAAACGCCA
Found at i:184960 original size:29 final size:29
Alignment explanation
Indices: 184926--185012 Score: 138
Period size: 29 Copynumber: 3.0 Consensus size: 29
184916 ATGTTCTCTT
** *
184926 GTAGGTCGCCGGGAAGACATGGCGACCTA
1 GTAGGTCGCCCAGAAGGCATGGCGACCTA
*
184955 TTAGGTCGCCCAGAAGGCATGGCGACCTA
1 GTAGGTCGCCCAGAAGGCATGGCGACCTA
184984 GTAGGTCGCCCAGAAGGCATGGCGACCTA
1 GTAGGTCGCCCAGAAGGCATGGCGACCTA
185013 CGGCCAACAC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.24, C:0.26, G:0.34, T:0.15
Consensus pattern (29 bp):
GTAGGTCGCCCAGAAGGCATGGCGACCTA
Found at i:187275 original size:2 final size:2
Alignment explanation
Indices: 187268--187297 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
187258 TTTAATTTTG
187268 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
187298 ACCTGGTCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:187801 original size:2 final size:2
Alignment explanation
Indices: 187794--187861 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
187784 CAATAATGCT
187794 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
187836 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
187862 GCATATGTAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:190936 original size:31 final size:31
Alignment explanation
Indices: 190901--190991 Score: 110
Period size: 31 Copynumber: 2.9 Consensus size: 31
190891 TCATACCTAG
* *
190901 TGTTTAGTTTTTGTTTCATTTTAGTACTCAT
1 TGTTTACTTTTTGTTTCATTTTAGTACCCAT
** *
190932 TGTTTACTTTTTGTTTCGCTTTAGTACCCCTT
1 TGTTTACTTTTTGTTTCATTTTAGTA-CCCAT
* *
190964 TGTTAACTTTTTATTTCATTTTAGTACC
1 TGTTTACTTTTTGTTTCATTTTAGTACC
190992 TAAAATTTCA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 25 0.50
32 25 0.50
ACGTcount: A:0.15, C:0.15, G:0.11, T:0.58
Consensus pattern (31 bp):
TGTTTACTTTTTGTTTCATTTTAGTACCCAT
Found at i:190973 original size:32 final size:32
Alignment explanation
Indices: 190908--190991 Score: 107
Period size: 32 Copynumber: 2.7 Consensus size: 32
190898 TAGTGTTTAG
* *
190908 TTTTTGTTTCATTTTAGTA-CTCATTGTTTAC
1 TTTTTGTTTCATTTTAGTACCCCATTGTTAAC
** *
190939 TTTTTGTTTCGCTTTAGTACCCCTTTGTTAAC
1 TTTTTGTTTCATTTTAGTACCCCATTGTTAAC
*
190971 TTTTTATTTCATTTTAGTACC
1 TTTTTGTTTCATTTTAGTACC
190992 TAAAATTTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 17 0.39
32 27 0.61
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.58
Consensus pattern (32 bp):
TTTTTGTTTCATTTTAGTACCCCATTGTTAAC
Found at i:191794 original size:6 final size:6
Alignment explanation
Indices: 191775--191820 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
191765 AGTTTTTCAA
*
191775 CCCTTT CCCCTT CCCTTT CCCTTT CCCTTT CCCTTT CCCTTT CCCT
1 CCCTTT CCCTTT CCCTTT CCCTTT CCCTTT CCCTTT CCCTTT CCCT
191821 ATAAGCTACC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (6 bp):
CCCTTT
Found at i:194149 original size:24 final size:24
Alignment explanation
Indices: 194094--194163 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
194084 TTTACCCTTT
**
194094 ATTTTT-ACTAATTTACCATTA-A
1 ATTTTTAACTAATTTATAATTATA
194116 ATTTTTAACTAATTTATAATTATA
1 ATTTTTAACTAATTTATAATTATA
*
194140 GTTTTTAACTAATTTATAATTATA
1 ATTTTTAACTAATTTATAATTATA
194164 CGTGCAATAC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
22 6 0.14
23 13 0.30
24 24 0.56
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (24 bp):
ATTTTTAACTAATTTATAATTATA
Found at i:195002 original size:2 final size:2
Alignment explanation
Indices: 194995--195037 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
194985 TCCTCATTAC
194995 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
195037 T
1 T
195038 CATAAACCCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:199045 original size:15 final size:15
Alignment explanation
Indices: 199025--199074 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
199015 ACTCCTTTTA
*
199025 AAATTTTATAAATTT
1 AAATTTTATGAATTT
* *
199040 AAA-TTTATGACTTG
1 AAATTTTATGAATTT
199054 AAATTTTATGAATTT
1 AAATTTTATGAATTT
199069 AAATTT
1 AAATTT
199075 ACTCCCTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (15 bp):
AAATTTTATGAATTT
Found at i:209297 original size:36 final size:34
Alignment explanation
Indices: 209233--209302 Score: 86
Period size: 36 Copynumber: 2.0 Consensus size: 34
209223 AACATCTACC
* *
209233 AAACTTTATCAAAATTTGAAAAATATTTTTCAAAG
1 AAACTTTACCAAAATTTGAAAAACA-TTTTCAAAG
* *
209268 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
1 AAAC-TTTACCAAAATTTGAAAAACATTTTCAAAG
209303 TTGGTTGCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 13 0.43
36 17 0.57
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (34 bp):
AAACTTTACCAAAATTTGAAAAACATTTTCAAAG
Found at i:212903 original size:17 final size:17
Alignment explanation
Indices: 212881--212921 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
212871 GGGTTGTGAT
212881 TGTGTTGAGTTCATTTA
1 TGTGTTGAGTTCATTTA
212898 TGTGTTGAGTTCATTTA
1 TGTGTTGAGTTCATTTA
*
212915 GGTGTTG
1 TGTGTTG
212922 TGCCATCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.15, C:0.05, G:0.29, T:0.51
Consensus pattern (17 bp):
TGTGTTGAGTTCATTTA
Found at i:213875 original size:35 final size:35
Alignment explanation
Indices: 213807--213921 Score: 187
Period size: 35 Copynumber: 3.3 Consensus size: 35
213797 ACCCATTCCT
* * *
213807 ATTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 ATTTTCAAAGAAACATTTACCAAACTTTGAAAACC
213841 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAACC
213877 ATTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 ATTTTCAAAGAAACATTTACCAAACTTTGAAAACC
213912 ATTTTCAAAG
1 ATTTTCAAAG
213922 TTGGTTGCCA
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
34 1 0.01
35 49 0.64
36 26 0.34
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (35 bp):
ATTTTCAAAGAAACATTTACCAAACTTTGAAAACC
Found at i:213879 original size:21 final size:21
Alignment explanation
Indices: 213855--213915 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
213845 TTCAAAGAAA
213855 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
213876 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
213890 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
213911 CATTT
1 CATTT
213916 TCAAAGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:214759 original size:60 final size:61
Alignment explanation
Indices: 214692--214808 Score: 200
Period size: 60 Copynumber: 1.9 Consensus size: 61
214682 TGTGATTTTA
** *
214692 TTAAATTAACTGATAATTGATTGAGTTAAAGTCAA-TTTTTAATTCTTTAACTCAATCTTT
1 TTAAATTAACTGATAATTGATCAAGTTAAAGTCAATTTTTTAACTCTTTAACTCAATCTTT
214752 TTAAATTAACTGATAATTGATCAAGTTAAAGTCAATTTTTTAACTCTTTAACTCAAT
1 TTAAATTAACTGATAATTGATCAAGTTAAAGTCAATTTTTTAACTCTTTAACTCAAT
214809 TTTGTTAGAT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
60 33 0.62
61 20 0.38
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (61 bp):
TTAAATTAACTGATAATTGATCAAGTTAAAGTCAATTTTTTAACTCTTTAACTCAATCTTT
Found at i:216359 original size:12 final size:13
Alignment explanation
Indices: 216340--216371 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
216330 TGAAAATCCA
216340 TCTTTTCCTCCCT
1 TCTTTTCCTCCCT
216353 T-TTTTCCTCCCT
1 TCTTTTCCTCCCT
216365 TCTTTTC
1 TCTTTTC
216372 ACGTCAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (13 bp):
TCTTTTCCTCCCT
Found at i:217555 original size:21 final size:23
Alignment explanation
Indices: 217529--217580 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
217519 TCGAAAATTT
217529 AAAATTATTA-AATATTTAA-AA
1 AAAATTATTATAATATTTAATAA
* *
217550 AAAATTA-TATATTTTTTAATAA
1 AAAATTATTATAATATTTAATAA
217572 AAAATTATT
1 AAAATTATT
217581 TTTTTCTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 2 0.08
21 14 0.54
22 9 0.35
23 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAATTATTATAATATTTAATAA
Found at i:217592 original size:20 final size:21
Alignment explanation
Indices: 217569--217612 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
217559 TATTTTTTAA
*
217569 TAAAAAATTATTT-TTTTCTC
1 TAAAAAATTATTTCGTTTCTC
**
217589 TAAAATTTTATTTCGTTTCTC
1 TAAAAAATTATTTCGTTTCTC
217610 TAA
1 TAA
217613 GTTTAAACTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.32, C:0.11, G:0.02, T:0.55
Consensus pattern (21 bp):
TAAAAAATTATTTCGTTTCTC
Found at i:217765 original size:19 final size:19
Alignment explanation
Indices: 217743--217788 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
217733 AATAGATGAT
217743 TAAAATTAATAACAAAAAG
1 TAAAATTAATAACAAAAAG
* * *
217762 TAAAATATACTTATAAAAAG
1 TAAAAT-TAATAACAAAAAG
217782 TAAAATT
1 TAAAATT
217789 TTAATCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (19 bp):
TAAAATTAATAACAAAAAG
Found at i:221107 original size:19 final size:19
Alignment explanation
Indices: 221085--221129 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
221075 TAAATATTCT
*
221085 TGATTTTTATAGTAAACTG
1 TGATATTTATAGTAAACTG
*
221104 TGATATTTATAGTAAATTG
1 TGATATTTATAGTAAACTG
221123 TGATATT
1 TGATATT
221130 GACTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (19 bp):
TGATATTTATAGTAAACTG
Found at i:224869 original size:22 final size:22
Alignment explanation
Indices: 224844--224889 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
224834 CCCTTAAAAG
* *
224844 ATAAA-AAATGTAAATAAATAAA
1 ATAAAGAAA-GTAAAAAAAGAAA
224866 ATAAAGAAAGTAAAAAAAGAAA
1 ATAAAGAAAGTAAAAAAAGAAA
224888 AT
1 AT
224890 TTATGGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (22 bp):
ATAAAGAAAGTAAAAAAAGAAA
Found at i:225924 original size:2 final size:2
Alignment explanation
Indices: 225913--225970 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
225903 AAAATTAATA
225913 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
225954 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
225971 ATACAATAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:226615 original size:36 final size:36
Alignment explanation
Indices: 226568--226795 Score: 359
Period size: 36 Copynumber: 6.3 Consensus size: 36
226558 TTAAAGGTTG
226568 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
226604 TGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
226640 TGTTTCAAGGGCAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
** * *
226677 ACTTT-AAGGGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
226712 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
226748 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
226784 TGTTTCAAGGGA
1 TGTTTCAAGGGA
226796 GACGAAATTT
Statistics
Matches: 172, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
35 5 0.03
36 163 0.95
37 4 0.02
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:226648 original size:21 final size:19
Alignment explanation
Indices: 226579--226873 Score: 81
Period size: 21 Copynumber: 16.2 Consensus size: 19
226569 GTTTCAAGGG
226579 AAACTGTCTCAAGAGAGAC
1 AAACTGTCTCAAGAGAGAC
* *
226598 AAAATTTGTTTCAAG-G-G--
1 -AAA-CTGTCTCAAGAGAGAC
226615 AAACTGTCTCAAGAGAGAC
1 AAACTGTCTCAAGAGAGAC
*
226634 TAAACTTGTTTCAAG-G-G-C
1 -AAAC-TGTCTCAAGAGAGAC
226652 -AACTGTCTCAAGAGAGAC
1 AAACTGTCTCAAGAGAGAC
*
226670 AAAACT-TACTTTAAG-G-G--
1 -AAACTGT-C-TCAAGAGAGAC
*
226687 AAACTGTCTCAAGGGAGAC
1 AAACTGTCTCAAGAGAGAC
* *
226706 GAAATTTGTTTC-A-AGAG--
1 -AAA-CTGTCTCAAGAGAGAC
226723 AAACTGTCTCAAGAGAGAC
1 AAACTGTCTCAAGAGAGAC
* *
226742 AAAATATGTTTCAAG-G-G--
1 -AAA-CTGTCTCAAGAGAGAC
226759 AAACTGTCTCAAGAGAGAC
1 AAACTGTCTCAAGAGAGAC
* * *
226778 AAAATTTGTTTCAAGGGAGAC
1 -AAA-CTGTCTCAAGAGAGAC
* *
226799 GAAATTTGTTTCAAG-G-G--
1 -AAA-CTGTCTCAAGAGAGAC
*
226816 AAACTGTCTCAAGGGAGAC
1 AAACTGTCTCAAGAGAGAC
* *
226835 GAAATTTGTTTCAAG-G-G--
1 -AAA-CTGTCTCAAGAGAGAC
226852 AAACTGTCTCAAGAGAGAC
1 AAACTGTCTCAAGAGAGAC
226871 AAA
1 AAA
226874 AATTTGTTTC
Statistics
Matches: 205, Mismatches: 27, Indels: 87
0.64 0.08 0.27
Matches are distributed among these distances:
15 49 0.24
16 31 0.15
17 11 0.05
18 2 0.01
19 13 0.06
20 31 0.15
21 68 0.33
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (19 bp):
AAACTGTCTCAAGAGAGAC
Found at i:226798 original size:129 final size:130
Alignment explanation
Indices: 226659--226923 Score: 426
Period size: 129 Copynumber: 2.0 Consensus size: 130
226649 GGCAACTGTC
226659 TCAAGAGAGACAAAACTTACTTT-AAGGGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGAG
1 TCAAGAGAGACAAAA-TTACTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGAG
*
226723 AAACTGTCTCAAGAGAGAC-AAAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
65 AAACTGTCTCAAGAGAGACAAAAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTAT
226787 T
130 T
* * ** *
226788 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGA
1 TCAAGAGAGACAAAATTACTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGAGA
* * *
226853 AACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAATTTTATT
66 AACTGTCTCAAGAGAGACAAAAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATT
226918 TCAAGA
1 TCAAGA
226924 AAAACAATCT
Statistics
Matches: 124, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
128 5 0.04
129 72 0.58
130 47 0.38
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.25
Consensus pattern (130 bp):
TCAAGAGAGACAAAATTACTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGAGA
AACTGTCTCAAGAGAGACAAAAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATT
Found at i:226828 original size:36 final size:36
Alignment explanation
Indices: 226788--226922 Score: 200
Period size: 36 Copynumber: 3.7 Consensus size: 36
226778 AAAATTTGTT
*
226788 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACTGTC
1 TCAAGAGAGACGAAATTTGTTTCAAGGGAAACTGTC
*
226824 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACTGTC
1 TCAAGAGAGACGAAATTTGTTTCAAGGGAAACTGTC
* *
226860 TCAAGAGAGACAAAAATTTGTTTCAAGGGAAATTGTC
1 TCAAGAGAGAC-GAAATTTGTTTCAAGGGAAACTGTC
*
226897 TCAAGAGAGAC-AAATTTTATTTCAAG
1 TCAAGAGAGACGAAA-TTTGTTTCAAG
226923 AAAAACAATC
Statistics
Matches: 93, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
35 3 0.03
36 56 0.60
37 34 0.37
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.27
Consensus pattern (36 bp):
TCAAGAGAGACGAAATTTGTTTCAAGGGAAACTGTC
Found at i:226850 original size:57 final size:57
Alignment explanation
Indices: 226731--226852 Score: 199
Period size: 57 Copynumber: 2.1 Consensus size: 57
226721 AGAAACTGTC
*
226731 TCAAGAGAGACAAAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
* * * *
226788 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTGTT
1 TCAAGGGAGACAAAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
226845 TCAAGGGA
1 TCAAGGGA
226853 AACTGTCTCA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (57 bp):
TCAAGGGAGACAAAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
Found at i:226870 original size:93 final size:94
Alignment explanation
Indices: 226695--226889 Score: 347
Period size: 93 Copynumber: 2.1 Consensus size: 94
226685 GGAAACTGTC
226695 TCAAGGGAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATATGTTTCAAGGGA
1 TCAAGGGAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATATGTTTCAAGGGA
226760 AACTGTCTCAAGAGAGAC-AAAATTTGTT
66 AACTGTCTCAAGAGAGACAAAAATTTGTT
* * * *
226788 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGA
1 TCAAGGGAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATATGTTTCAAGGGA
226853 AACTGTCTCAAGAGAGACAAAAATTTGTT
66 AACTGTCTCAAGAGAGACAAAAATTTGTT
226882 TCAAGGGA
1 TCAAGGGA
226890 AATTGTCTCA
Statistics
Matches: 97, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
93 79 0.81
94 18 0.19
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.25
Consensus pattern (94 bp):
TCAAGGGAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATATGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAAATTTGTT
Found at i:226886 original size:37 final size:37
Alignment explanation
Indices: 226800--226910 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
226790 AAGGGAGACG
* *
226800 AAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGAC-G
1 AAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
226836 AAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 AAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
226873 AAATTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAA
1 AAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
226910 A
1 A
226911 TTTTATTTCA
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 34 0.48
37 37 0.52
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.25
Consensus pattern (37 bp):
AAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
Found at i:226935 original size:73 final size:73
Alignment explanation
Indices: 226800--226936 Score: 195
Period size: 73 Copynumber: 1.9 Consensus size: 73
226790 AAGGGAGACG
* * ** **
226800 AAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACTGTCTCAAG
1 AAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTATTTCAAGAAAAACAATCTCAAG
226865 AGAGACAA
66 AGAGACAA
*
226873 AAATTTGTTTCAAGGGAAATTGTCTCAAGAGAGAC-AAATTTTATTTCAAGAAAAACAATCTCAA
1 AAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA-TTTATTTCAAGAAAAACAATCTCAA
226937 AGGTTTTTGT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 3 0.05
73 53 0.95
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (73 bp):
AAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTATTTCAAGAAAAACAATCTCAAG
AGAGACAA
Found at i:227088 original size:81 final size:80
Alignment explanation
Indices: 226953--227127 Score: 251
Period size: 81 Copynumber: 2.2 Consensus size: 80
226943 TTGTTGACAA
* * * * * * *
226953 ATAACTCCTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGGAGCTGAGTGTAATCGAACT
1 ATAAC-CCTCTCGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACT
227018 CGGGGGTCGTTGGCAG
65 CGGGGGTCGTTGGCAG
227034 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAACCC-TCTCGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACT
*
227099 CGGGGGTCTTTGGCAG
65 CGGGGGTCGTTGGCAG
*
227115 ATAGCCCTCTCGA
1 ATAACCCTCTCGA
227128 GTTGGATATC
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
80 8 0.10
81 76 0.90
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (80 bp):
ATAACCCTCTCGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTC
GGGGGTCGTTGGCAG
Found at i:227343 original size:106 final size:106
Alignment explanation
Indices: 227153--228584 Score: 2289
Period size: 106 Copynumber: 13.4 Consensus size: 106
227143 TCGTGAAGTT
* *
227153 GAAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAATC
1 GAAA-TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
* * * * *
227218 CAATATCCTTTGCTATGAAGTTGAAATTGACTCTGAAATTGG
65 CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
* *
227260 GAAATTGTTTATTGACAACCAGTGGTCCCTTCGTCGTTAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* *
227325 AATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGA
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
* * * *
227366 GAAGTTGTTTGTTGACAACCAGCGGTCCCTCCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
*
227431 AATATCCTTCGTTGTGATGTTGAAATTGGCTCTGAAATTGA
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
* *
227472 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * *
227537 AATATCCTTCATTGTGAAGTTGAAATTGACTCTGAAATTGG
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
* *
227578 GAAGTTGTTTATTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
227643 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
* * *
227684 GAAGTTGTTTGTTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* *
227749 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
227790 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* *
227855 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGCTCT
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-G---A
* *
227900 GAAATTGGGAAGTTATTTATTGACAACCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGTGTTGTC
1 GAAATT-----G---TTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
227965 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
58 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
* * * * *
228014 GAAGTTATTTATTGACAACCAACGGTCCATTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
*
228079 AATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
* *
228120 GAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAATCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
228184 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
228225 GAAA-TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* *
228289 AATATCCTTCATTGTGAAGTTGAAATTGGATCTGAAATTGA
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
* *
228330 GAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAATCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* *
228394 AATACCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
228435 GAAA-TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
228499 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
*
228540 GAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
228585 ATCCGCTCTC
Statistics
Matches: 1246, Mismatches: 67, Indels: 26
0.93 0.05 0.02
Matches are distributed among these distances:
105 439 0.35
106 695 0.56
107 5 0.00
110 6 0.00
114 5 0.00
115 1 0.00
117 1 0.00
118 94 0.08
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
Found at i:227892 original size:12 final size:12
Alignment explanation
Indices: 227875--227907 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
227865 GCTGTGAAGT
227875 TGAAATTGGCTC
1 TGAAATTGGCTC
227887 TGAAATTGGCTC
1 TGAAATTGGCTC
227899 TGAAATTGG
1 TGAAATTGG
227908 GAAGTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.33
Consensus pattern (12 bp):
TGAAATTGGCTC
Found at i:230556 original size:27 final size:26
Alignment explanation
Indices: 230505--230557 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
230495 TGAGACATGT
* *
230505 GAATGTAAAAAAAGGAAAAATAATGC
1 GAATGTAAAAAAAGAAAAAAAAATGC
230531 GAATGTAAAAAAA-AAATAACAAAATGC
1 GAATGTAAAAAAAGAAA-AA-AAAATGC
230558 ACAATATGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 2 0.09
26 15 0.65
27 6 0.26
ACGTcount: A:0.64, C:0.06, G:0.15, T:0.15
Consensus pattern (26 bp):
GAATGTAAAAAAAGAAAAAAAAATGC
Found at i:232272 original size:22 final size:22
Alignment explanation
Indices: 232241--232292 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
232231 TTGTACCCTT
* *
232241 AAGAAGATAAA-AAATGTAAATA
1 AAGAAAATAAAGAAA-GTAAAAA
*
232263 AATAAAATAAAGAAAGTAAAAA
1 AAGAAAATAAAGAAAGTAAAAA
232285 AAGAAAAT
1 AAGAAAAT
232293 TTATGGAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (22 bp):
AAGAAAATAAAGAAAGTAAAAA
Found at i:232322 original size:2 final size:2
Alignment explanation
Indices: 232315--232349 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
232305 GAAATTAAAC
232315 AT AT AT AT AT 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 AT AT AT AT AT A
232350 ATAAGGGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:233610 original size:13 final size:13
Alignment explanation
Indices: 233589--233649 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
233579 ATTTTGTTAG
233589 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
233602 TATTGTA-TTATT
1 TATTTTATTTAAT
233614 TGATTTT-TTTAAT
1 T-ATTTTATTTAAT
*
233627 TATTTTATTTAAA
1 TATTTTATTTAAT
233640 TATTTTATTT
1 TATTTTATTT
233650 TTTTTGCAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 10 0.25
13 30 0.75
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:233644 original size:25 final size:25
Alignment explanation
Indices: 233589--233649 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
233579 ATTTTGTTAG
**
233589 TATTTTATTTAATTATTGTATTATT
1 TATTTTATTTAATTATTGTATTAAA
*
233614 TGATTTT-TTTAATTATTTTATTTAAA
1 T-ATTTTATTTAATTATTGTA-TTAAA
233640 TATTTTATTT
1 TATTTTATTT
233650 TTTTTGCAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 18 0.60
26 12 0.40
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (25 bp):
TATTTTATTTAATTATTGTATTAAA
Found at i:237188 original size:11 final size:11
Alignment explanation
Indices: 237163--237232 Score: 69
Period size: 11 Copynumber: 6.8 Consensus size: 11
237153 ATTATATTGA
*
237163 TTAATAAAT-T
1 TTAATAATTAT
237173 TTAATAATTAT
1 TTAATAATTAT
237184 TTAATAA--AT
1 TTAATAATTAT
*
237193 TTAATGATTAT
1 TTAATAATTAT
237204 TTAATAA--AT
1 TTAATAATTAT
*
237213 TTAATGATTAT
1 TTAATAATTAT
*
237224 TTTATAATT
1 TTAATAATT
237233 TATGTAAGTA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
9 16 0.33
10 8 0.16
11 25 0.51
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
TTAATAATTAT
Found at i:237197 original size:20 final size:20
Alignment explanation
Indices: 237163--237234 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
237153 ATTATATTGA
*
237163 TTAATAAATTTTAATAATTAT
1 TTAATAAA-TTTAATGATTAT
237184 TTAATAAATTTAATGATTAT
1 TTAATAAATTTAATGATTAT
237204 TTAATAAATTTAATGATTAT
1 TTAATAAATTTAATGATTAT
*
237224 TTTAT-AATTTA
1 TTAATAAATTTA
237235 TGTAAGTATA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.12
20 35 0.71
21 8 0.16
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TTAATAAATTTAATGATTAT
Found at i:237660 original size:19 final size:20
Alignment explanation
Indices: 237638--237679 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
237628 TGCTCAGTAG
*
237638 TTTTCTCATTGCT-TTTTTC
1 TTTTCTCATTCCTGTTTTTC
* *
237657 TTTTGTCTTTCCTGTTTTTC
1 TTTTCTCATTCCTGTTTTTC
237677 TTT
1 TTT
237680 AGGATTCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.02, C:0.19, G:0.07, T:0.71
Consensus pattern (20 bp):
TTTTCTCATTCCTGTTTTTC
Found at i:250283 original size:30 final size:29
Alignment explanation
Indices: 250215--250286 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
250205 TTATCAAACA
* *
250215 CGTCCCCATTTAGCATAAACGGTTTTCCC
1 CGTCCCCGTTTAACATAAACGGTTTTCCC
* * * *
250244 CATCTCCGTTTAACATAAACGATTTTTCTC
1 CGTCCCCGTTTAACATAAACG-GTTTTCCC
250274 CGTCCCCGTTTAA
1 CGTCCCCGTTTAA
250287 TTCGATTTTC
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 17 0.50
30 17 0.50
ACGTcount: A:0.22, C:0.32, G:0.11, T:0.35
Consensus pattern (29 bp):
CGTCCCCGTTTAACATAAACGGTTTTCCC
Found at i:251390 original size:98 final size:100
Alignment explanation
Indices: 251282--251479 Score: 337
Period size: 98 Copynumber: 2.0 Consensus size: 100
251272 ACAAATTCAA
* * * * *
251282 ATATAATATTTTATTTAAATGATATCAAATTATTTATTATTTAAATTCATTCGTCGGTTAATCTC
1 ATATAATATTTTACTTAAATGATATCAAATTACTTATCACTTAAATTCATTCGTAGGTTAATCTC
251347 TGCATCTTTAAACATTCTAATAACC-CC-AAAAAT
66 TGCATCTTTAAACATTCTAATAACCTCCTAAAAAT
251380 ATATAATATTTTACTTAAATGATATCAAATTACTTATCACTTAAATTCATTCGTAGGTTAATCTC
1 ATATAATATTTTACTTAAATGATATCAAATTACTTATCACTTAAATTCATTCGTAGGTTAATCTC
251445 TGCATCTTTAAACATTCTAATAACCTCCTAAAAAT
66 TGCATCTTTAAACATTCTAATAACCTCCTAAAAAT
251480 CATTTACCTA
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
98 85 0.91
99 2 0.02
100 6 0.06
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (100 bp):
ATATAATATTTTACTTAAATGATATCAAATTACTTATCACTTAAATTCATTCGTAGGTTAATCTC
TGCATCTTTAAACATTCTAATAACCTCCTAAAAAT
Found at i:253855 original size:26 final size:27
Alignment explanation
Indices: 253821--253872 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
253811 TTATAAAATG
*
253821 ATTTATCAGTATACAAA-AGTAAAACAT
1 ATTTATCAGAAT-CAAATAGTAAAACAT
*
253848 ATTT-TCAGAATCAAATATTAAAACA
1 ATTTATCAGAATCAAATAGTAAAACA
253873 AAATACAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 4 0.18
26 14 0.64
27 4 0.18
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.31
Consensus pattern (27 bp):
ATTTATCAGAATCAAATAGTAAAACAT
Found at i:254465 original size:24 final size:24
Alignment explanation
Indices: 254438--254509 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
254428 AAACGGAGAT
*
254438 ATCATAAATCAAAACAGAATTCAG
1 ATCATAAATCAGAACAGAATTCAG
* * *
254462 ATCAGT-TATCAGAACAGAATCCAA
1 ATCA-TAAATCAGAACAGAATTCAG
* *
254486 ATCAGAAATCAGAACATAATTCAG
1 ATCATAAATCAGAACAGAATTCAG
254510 GTAAAGTATC
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
24 36 0.97
25 1 0.03
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.21
Consensus pattern (24 bp):
ATCATAAATCAGAACAGAATTCAG
Found at i:254544 original size:24 final size:24
Alignment explanation
Indices: 254439--254546 Score: 71
Period size: 24 Copynumber: 4.5 Consensus size: 24
254429 AACGGAGATA
*
254439 TCATAAATCAAAACAGAATTC-AG
1 TCATAAATCAGAACAGAATTCAAG
* * *
254462 ATCAGT-TATCAGAACAGAATCCAAA
1 -TCA-TAAATCAGAACAGAATTCAAG
* * *
254487 TCAGAAATCAGAACATAATTCAGG
1 TCATAAATCAGAACAGAATTCAAG
* *
254511 T-A-AAGTATCATAACATAATTCAAG
1 TCATAA--ATCAGAACAGAATTCAAG
254535 TCATAAATCAGA
1 TCATAAATCAGA
254547 TAAAATATTT
Statistics
Matches: 64, Mismatches: 13, Indels: 14
0.70 0.14 0.15
Matches are distributed among these distances:
22 2 0.03
23 1 0.02
24 56 0.88
25 3 0.05
26 2 0.03
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.23
Consensus pattern (24 bp):
TCATAAATCAGAACAGAATTCAAG
Found at i:263549 original size:2 final size:2
Alignment explanation
Indices: 263544--263569 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
263534 ACTTTTTTTA
263544 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
263570 TAATTTGGGA
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):
AT
Found at i:264497 original size:41 final size:38
Alignment explanation
Indices: 264434--264509 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 38
264424 TAATGTTAAA
*
264434 TTTTAAATGGGGTACTAAAATGAAATAAAAATTAAATTT
1 TTTTAAATGGGGTACTAAAATG-AACAAAAATTAAATTT
* *
264473 TTTTATATGAGGGTTACTAGAATGAACAAAAATTAAA
1 TTTTAAATG-GGG-TACTAAAATGAACAAAAATTAAA
264510 CTTTAAGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 8 0.25
40 15 0.47
41 9 0.28
ACGTcount: A:0.47, C:0.04, G:0.14, T:0.34
Consensus pattern (38 bp):
TTTTAAATGGGGTACTAAAATGAACAAAAATTAAATTT
Found at i:274295 original size:16 final size:18
Alignment explanation
Indices: 274274--274319 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
274264 AACATTCCTA
274274 GTAATCTTATTC-C-CTG
1 GTAATCTTATTCTCACTG
274290 GTAATCTTATATTCTCACTG
1 GTAATC-T-TATTCTCACTG
274310 GTAATCTTAT
1 GTAATCTTAT
274320 ATTTCAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.23
17 1 0.04
18 8 0.31
19 2 0.08
20 9 0.35
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.46
Consensus pattern (18 bp):
GTAATCTTATTCTCACTG
Found at i:274312 original size:20 final size:21
Alignment explanation
Indices: 274287--274343 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
274277 ATCTTATTCC
274287 CTGGTAATCTTATATTCTC-A
1 CTGGTAATCTTATATTCTCAA
274307 CTGGTAATCTTATATT-TCAA
1 CTGGTAATCTTATATTCTCAA
* *
274327 TTGATAATCTTATATTC
1 CTGGTAATCTTATATTC
274344 CGTGAACCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (21 bp):
CTGGTAATCTTATATTCTCAA
Found at i:275172 original size:14 final size:14
Alignment explanation
Indices: 275155--275183 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
275145 CAATTTAAGT
275155 GAGACCATTTTAAA
1 GAGACCATTTTAAA
275169 GAGACCATTTTAAA
1 GAGACCATTTTAAA
275183 G
1 G
275184 CACAAAATAG
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:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (14 bp):
GAGACCATTTTAAA
Done.