Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, 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: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 21 of 131
Found at i:5153685 original size:5 final size:5
Alignment explanation
Indices: 5153672--5153703 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
5153662 AGCGGCTTGG
*
5153672 GGCTT GGCTC GGCTC GGCTC GGCTC GGCTC GG
1 GGCTC GGCTC GGCTC GGCTC GGCTC GGCTC GG
5153704 AGGGGCTGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.44, T:0.22
Consensus pattern (5 bp):
GGCTC
Found at i:5153942 original size:19 final size:18
Alignment explanation
Indices: 5153918--5153962 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
5153908 AACACCGGTG
*
5153918 CGCGGATTCTGGAAATTCT
1 CGCGGAATCTGGAAATT-T
5153937 CGCGGAATCTGGAAATTT
1 CGCGGAATCTGGAAATTT
5153955 CGCCGGAA
1 CG-CGGAA
5153963 GTTGGCCGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (18 bp):
CGCGGAATCTGGAAATTT
Found at i:5154144 original size:26 final size:26
Alignment explanation
Indices: 5154097--5154152 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
5154087 AATCTGGAAA
*
5154097 TTTCCCAGAAATTTCCAGAAAAAATT
1 TTTCCCAAAAATTTCCAGAAAAAATT
* *
5154123 TTTCGCCAAAAATTTCTA-AAAAATTT
1 TTTC-CCAAAAATTTCCAGAAAAAATT
5154149 TTTC
1 TTTC
5154153 TCACTCCCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.38
Consensus pattern (26 bp):
TTTCCCAAAAATTTCCAGAAAAAATT
Found at i:5154470 original size:41 final size:43
Alignment explanation
Indices: 5154410--5154516 Score: 107
Period size: 42 Copynumber: 2.5 Consensus size: 43
5154400 CTCCAAAATC
* *
5154410 AAAAATAAAAAACTAGATAATAATAGATAATCA-AA-AGATATTT
1 AAAAA-AAAAAACTAGATAATAA-AGAAAATCAGAACAGATAATT
* * *
5154453 AAAAAAAAAATCT-GATAATCAGGAAAATCAGAACAGATAATT
1 AAAAAAAAAAACTAGATAATAAAGAAAATCAGAACAGATAATT
5154495 AAAAAAAAATAA-TA-ATAATAAA
1 AAAAAAAAA-AACTAGATAATAAA
5154517 TAATAAAATA
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
40 7 0.13
41 9 0.17
42 30 0.58
43 6 0.12
ACGTcount: A:0.65, C:0.06, G:0.07, T:0.21
Consensus pattern (43 bp):
AAAAAAAAAAACTAGATAATAAAGAAAATCAGAACAGATAATT
Found at i:5154513 original size:42 final size:39
Alignment explanation
Indices: 5154416--5154514 Score: 94
Period size: 41 Copynumber: 2.5 Consensus size: 39
5154406 AATCAAAAAT
* * *
5154416 AAAAAACTAGATAATAATAGATAATCAAAAGATATTTAAA
1 AAAAAAATAGATAATAATAGAAAATCAAAAGATAATT-AA
* * *
5154456 AAAAAAATCTGATAATCA-GGAAAATCAGAACAGATAATTAA
1 AAAAAAAT-AGATAATAATAGAAAATCA-AA-AGATAATTAA
5154497 AAAAAAATA-ATAATAATA
1 AAAAAAATAGATAATAATA
5154515 AATAATAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
39 6 0.13
40 14 0.30
41 19 0.41
42 7 0.15
ACGTcount: A:0.64, C:0.06, G:0.08, T:0.22
Consensus pattern (39 bp):
AAAAAAATAGATAATAATAGAAAATCAAAAGATAATTAA
Found at i:5154561 original size:3 final size:3
Alignment explanation
Indices: 5154555--5154657 Score: 56
Period size: 3 Copynumber: 32.7 Consensus size: 3
5154545 TACAAAAAAA
5154555 AAT AAT AAT AAT AAT AAT AAT AAT AAAT ATAT AAT ATAT ACAT -AT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AAT A-AT A-AT AAT AAT
*
5154602 ATCT AAT -AT AAAT AAT AAAT AA- ATAT ACAT AAAT AAT AAT AAT -AT
1 A-AT AAT AAT -AAT AAT -AAT AAT A-AT A-AT -AAT AAT AAT AAT AAT
5154647 AA- AAT ACAT AA
1 AAT AAT A-AT AA
5154658 ATACAAAAGA
Statistics
Matches: 81, Mismatches: 4, Indels: 30
0.70 0.03 0.26
Matches are distributed among these distances:
2 10 0.12
3 45 0.56
4 25 0.31
5 1 0.01
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5154634 original size:32 final size:33
Alignment explanation
Indices: 5154572--5154662 Score: 82
Period size: 32 Copynumber: 2.8 Consensus size: 33
5154562 ATAATAATAA
* *
5154572 TAATAATAAATATATAATATATACATATAAATC
1 TAATAATAAATATATAATAAATACACATAAATC
*
5154605 TAAT-ATAAATA-ATAAATAAATATACATAAA--
1 TAATAATAAATATAT-AATAAATACACATAAATC
*
5154635 TAATAATAATATAAAATACATAAATACA
1 TAATAATAA-AT-ATATA-ATAAATACA
5154663 AAAGAAGAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
30 4 0.08
31 6 0.12
32 22 0.46
33 6 0.12
34 10 0.21
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (33 bp):
TAATAATAAATATATAATAAATACACATAAATC
Found at i:5154635 original size:10 final size:10
Alignment explanation
Indices: 5154576--5154649 Score: 53
Period size: 11 Copynumber: 7.2 Consensus size: 10
5154566 TAATAATAAT
5154576 AATAAATATA
1 AATAAATATA
* *
5154586 TAATATATACA
1 -AATAAATATA
* *
5154597 TATAAATCTA
1 AATAAATATA
5154607 ATATAAATAATA
1 A-ATAAAT-ATA
5154619 AATAAATATA
1 AATAAATATA
*
5154629 CATAAATA-A
1 AATAAATATA
5154638 TAAT-AATATA
1 -AATAAATATA
5154648 AA
1 AA
5154650 ATACATAAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
9 7 0.14
10 19 0.39
11 20 0.41
12 3 0.06
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (10 bp):
AATAAATATA
Found at i:5154641 original size:24 final size:25
Alignment explanation
Indices: 5154558--5154660 Score: 99
Period size: 24 Copynumber: 4.2 Consensus size: 25
5154548 AAAAAAAAAT
*
5154558 AATAATAATAATA-ATAATAATAAATA
1 AATAATAATAATATA-AAT-ATACATA
* *
5154584 TATAATATATACATATAAATCTA-ATA
1 AATAATA-ATA-ATATAAATATACATA
*
5154610 TA-AATAATAA-ATAAATATACATA
1 AATAATAATAATATAAATATACATA
5154633 AATAATAATAATATAAA-ATACATA
1 AATAATAATAATATAAATATACATA
5154657 AATA
1 AATA
5154661 CAAAAGAAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
22 8 0.12
23 5 0.07
24 22 0.33
25 9 0.13
26 11 0.16
27 5 0.07
28 6 0.09
29 1 0.01
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (25 bp):
AATAATAATAATATAAATATACATA
Found at i:5154845 original size:1 final size:1
Alignment explanation
Indices: 5154835--5154937 Score: 134
Period size: 1 Copynumber: 103.0 Consensus size: 1
5154825 CAACTCAACA
* ** * * *
5154835 TTTTTATTTTTTTGATTTTTTTTTTTTTTTTTTTTTGTTTTTTTTGTTTTTTTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
5154900 TTTTTGTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5154938 GCCGAAGCTC
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 87 1.00
ACGTcount: A:0.02, C:0.00, G:0.06, T:0.92
Consensus pattern (1 bp):
T
Found at i:5154868 original size:24 final size:23
Alignment explanation
Indices: 5154835--5154937 Score: 170
Period size: 23 Copynumber: 4.4 Consensus size: 23
5154825 CAACTCAACA
* *
5154835 TTTTTATTTTTTTGATTTTTTTT
1 TTTTTTTTTTTTTGTTTTTTTTT
*
5154858 TTTTTTTTTTTTTGTTTTTTTTG
1 TTTTTTTTTTTTTGTTTTTTTTT
5154881 TTTTTTTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTGTTTTTTTTT
5154904 TGTTTTTTTTTTTTGTTTTTTTTT
1 T-TTTTTTTTTTTTGTTTTTTTTT
5154928 TTTTTTTTTT
1 TTTTTTTTTT
5154938 GCCGAAGCTC
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
23 52 0.69
24 23 0.31
ACGTcount: A:0.02, C:0.00, G:0.06, T:0.92
Consensus pattern (23 bp):
TTTTTTTTTTTTTGTTTTTTTTT
Found at i:5155078 original size:80 final size:80
Alignment explanation
Indices: 5154944--5155460 Score: 863
Period size: 80 Copynumber: 6.5 Consensus size: 80
5154934 TTTTGCCGAA
* * *
5154944 GCTCCTCTAAACAGAGACTCAACGACTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCAACGAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAC
5155008 TTTG-AAAGTAAATT
66 TTTGAAAAGTAAATT
*
5155022 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGG-CAACG
5155087 ACTTTGAAAAGTAAATT
64 ACTTTGAAAAGTAAATT
5155104 GCTCCTCTAAACAGAGGCA--ACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACG
5155167 ACTTTGAAAAGTAAATT
64 ACTTTGAAAAGTAAATT
5155184 GCTCCTCTAAACAGAGG---CACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAC
5155246 TTTGAAAAGTAAATT
66 TTTGAAAAGTAAATT
5155261 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACACGA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-ACGA
*
5155326 CTTTGAAAAATAAATT
65 CTTTGAAAAGTAAATT
5155342 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAC
*
5155407 TTTGAAAAATAAATT
66 TTTGAAAAGTAAATT
5155422 GCTCCTCTAAACAGAGGCA--ACGAACTTTGAAAAGTAAAT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGAAAAGTAAAT
5155461 ACTCCTAGAC
Statistics
Matches: 421, Mismatches: 6, Indels: 23
0.94 0.01 0.05
Matches are distributed among these distances:
77 37 0.09
78 30 0.07
79 85 0.20
80 151 0.36
81 89 0.21
82 29 0.07
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (80 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAC
TTTGAAAAGTAAATT
Found at i:5155176 original size:120 final size:119
Alignment explanation
Indices: 5154944--5155460 Score: 891
Period size: 120 Copynumber: 4.3 Consensus size: 119
5154934 TTTTGCCGAA
*
5154944 GCTCCTCTAAACAGAGACTCAACGACTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCAACGAC
1 GCTCCTCTAAACAGAGGC-C-ACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAC
5155008 TTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
64 TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
5155064 GCTCCTCTAAACAGAGGACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACT
1 GCTCCTCTAAACAGAGG-CCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACT
5155129 TTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
65 TTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
5155184 GCTCCTCTAAACAGAGG-CACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTT
1 GCTCCTCTAAACAGAGGCCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTT
5155248 TGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
66 TGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
5155302 GCTCCTCTAAACAGAGGCACACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGA
1 GCTCCTCTAAACAGAGGC-CACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACGA
*
5155367 CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACGACTTTGAAAAATAAATT
63 CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
5155422 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAAT
1 GCTCCTCTAAACAGAGGCCACG-ACTTTGAAAAGTAAAT
5155461 ACTCCTAGAC
Statistics
Matches: 384, Mismatches: 5, Indels: 16
0.95 0.01 0.04
Matches are distributed among these distances:
118 118 0.31
119 12 0.03
120 175 0.46
121 40 0.10
122 39 0.10
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (119 bp):
GCTCCTCTAAACAGAGGCCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTT
TGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:5155408 original size:238 final size:238
Alignment explanation
Indices: 5154944--5155460 Score: 900
Period size: 238 Copynumber: 2.2 Consensus size: 238
5154934 TTTTGCCGAA
*
5154944 GCTCCTCTAAACAGAGACTCAACGACTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCAACGAC
1 GCTCCTCTAAACAGAG--GCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAC
5155008 TTTGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTA
64 TTTGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTA
*
5155073 AACAGAGGACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTTTGAAAAGT
129 AACAGAGGACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGACTTTGAAAAGT
*
5155138 AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
194 AAATTGCTCCTCTAAACAGAGGCA-CACGACTTTGAAAAATAAATT
5155184 GCTCCTCTAAACAGAGGC-ACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTT
1 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTT
5155248 TGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCTCTAA
66 TG-AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAA
5155312 ACAGAGG-CACACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAA
130 ACAGAGGAC-CACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCA--ACGACTTTGAAAA
5155376 GTAAATTGCTCCTCTAAACAGAGGCA-ACGACTTTGAAAAATAAATT
192 GTAAATTGCTCCTCTAAACAGAGGCACACGACTTTGAAAAATAAATT
5155422 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAAT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGAAAAGTAAAT
5155461 ACTCCTAGAC
Statistics
Matches: 267, Mismatches: 3, Indels: 14
0.94 0.01 0.05
Matches are distributed among these distances:
237 10 0.04
238 144 0.54
239 42 0.16
240 71 0.27
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (238 bp):
GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTT
TGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAA
CAGAGGACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAA
ATTGCTCCTCTAAACAGAGGCACACGACTTTGAAAAATAAATT
Found at i:5156497 original size:10 final size:9
Alignment explanation
Indices: 5156472--5156571 Score: 84
Period size: 9 Copynumber: 11.2 Consensus size: 9
5156462 TCCTTTTTCA
*
5156472 TTCACTTTT
1 TTCATTTTT
5156481 TTC-TTTTT
1 TTCATTTTT
5156489 TTCCATTTTT
1 TT-CATTTTT
*
5156499 TCCATTTTT
1 TTCATTTTT
5156508 TT--TTCATTT
1 TTCATT--TTT
*
5156517 TTCATCATTT
1 TTCAT-TTTT
5156527 TTCATTTTT
1 TTCATTTTT
*
5156536 TCCA-TTTT
1 TTCATTTTT
5156544 TTCATTTTT
1 TTCATTTTT
*
5156553 TTTATTTTT
1 TTCATTTTT
5156562 TT-ATTTTT
1 TTCATTTTT
5156570 TT
1 TT
5156572 TGTATTTTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
7 2 0.03
8 21 0.28
9 37 0.49
10 14 0.19
11 1 0.01
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (9 bp):
TTCATTTTT
Found at i:5156499 original size:17 final size:18
Alignment explanation
Indices: 5156472--5156570 Score: 84
Period size: 17 Copynumber: 5.6 Consensus size: 18
5156462 TCCTTTTTCA
5156472 TTCACTTTTTT-C-TTTTT
1 TTCA-TTTTTTCCATTTTT
5156489 TTCCATTTTTTCCATTTTTTT
1 TT-CATTTTTTCCA--TTTTT
*
5156510 TTCA-TTTTT-CATCATTT
1 TTCATTTTTTCCAT-TTTT
5156527 TTCATTTTTTCCA-TTTT
1 TTCATTTTTTCCATTTTT
**
5156544 TTCATTTTTTTTATTTTT
1 TTCATTTTTTCCATTTTT
5156562 TT-ATTTTTT
1 TTCATTTTTT
5156571 TTGTATTTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
16 1 0.01
17 36 0.52
18 16 0.23
19 7 0.10
20 2 0.03
21 7 0.10
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (18 bp):
TTCATTTTTTCCATTTTT
Found at i:5156571 original size:9 final size:9
Alignment explanation
Indices: 5156540--5156582 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
5156530 ATTTTTTCCA
*
5156540 TTTTTTCAT
1 TTTTTTTAT
5156549 TTTTTTTA-
1 TTTTTTTAT
5156557 TTTTTTTAT
1 TTTTTTTAT
*
5156566 TTTTTTTGT
1 TTTTTTTAT
5156575 ATTTTTTT
1 -TTTTTTT
5156583 CAAGCATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
8 8 0.27
9 15 0.50
10 7 0.23
ACGTcount: A:0.09, C:0.02, G:0.02, T:0.86
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:5156579 original size:17 final size:18
Alignment explanation
Indices: 5156523--5156580 Score: 66
Period size: 17 Copynumber: 3.3 Consensus size: 18
5156513 ATTTTTCATC
**
5156523 ATTTTTCATTTTTTCCAT
1 ATTTTTCATTTTTTTTAT
5156541 -TTTTTCATTTTTTTTAT
1 ATTTTTCATTTTTTTTAT
* *
5156558 -TTTTTTATTTTTTTTGT
1 ATTTTTCATTTTTTTTAT
5156575 ATTTTT
1 ATTTTT
5156581 TTCAAGCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 30 0.86
18 5 0.14
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (18 bp):
ATTTTTCATTTTTTTTAT
Found at i:5163823 original size:15 final size:15
Alignment explanation
Indices: 5163803--5163849 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
5163793 TTGTAAGTGT
5163803 AATGAATGAGAATGC
1 AATGAATGAGAATGC
* *
5163818 AATGAATAAGAATGT
1 AATGAATGAGAATGC
5163833 AATGAATGAGAAATGC
1 AATGAATGAG-AATGC
5163849 A
1 A
5163850 TGTATGCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 22 0.81
16 5 0.19
ACGTcount: A:0.51, C:0.04, G:0.23, T:0.21
Consensus pattern (15 bp):
AATGAATGAGAATGC
Found at i:5167168 original size:59 final size:59
Alignment explanation
Indices: 5166998--5167642 Score: 787
Period size: 59 Copynumber: 10.9 Consensus size: 59
5166988 TTTTGTTAAG
* * *
5166998 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTCTTGAAATTTTAATTTC-GA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTT-ATTTCTAA
*
5167056 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTATTTTTTTTTTTTGAAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA--TA----TTTTTTTTGAAAATTTATTTCTAA
*
5167121 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTCCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTCTAA
* *
5167180 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA--TTTTTTGGAAATTTGGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTT--ATTTCT-AA
* *** *
5167239 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA-CCCTTTTTTG-AAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTCTAA
* * *
5167296 GGAAAATTGATACTTTCGACTTTTCCCCAAAAATA-TTTTTTGGAAATTTTGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTT-ATTTCT-AA
* * * * *
5167355 GGAAAATTGGTACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGAAATTTTGTTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTTTGAAAATTTATTTCTAA
* * *
5167416 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT-GTTTTTTTG-GAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTCTAA
* *
5167473 GGAAAATTGATACTCTCAACTTTTCCCTAAAAATATTTTTTTTGAAAATTTTAATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAA-TTT-ATTTCT-AA
*
5167534 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTCTAA
*
5167591 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAAATTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTTGAAAATTT
5167643 TTATTTTTAT
Statistics
Matches: 518, Mismatches: 38, Indels: 60
0.84 0.06 0.10
Matches are distributed among these distances:
57 139 0.27
58 59 0.11
59 150 0.29
60 26 0.05
61 76 0.15
62 15 0.03
63 2 0.00
64 5 0.01
65 46 0.09
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (59 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTCTAA
Found at i:5167532 original size:295 final size:295
Alignment explanation
Indices: 5166993--5167631 Score: 966
Period size: 295 Copynumber: 2.2 Consensus size: 295
5166983 TTTTTTTTTG
*
5166993 TTAAGGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTCTTGAAATTTTAATTTCGAGG
1 TTAA-GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTT-TTGAAATTTTAATTTCAAGG
5167058 AAAATTGATACTTTCAACTTTTCCTCAAAAATTTATTTTTTTTTTTTGAAAATTTATTTCTAAGG
64 AAAATTGATACTTTCAACTTTTCCTCAAAAA-TTA-TTTTTTTTTTTGAAAATTTATTTCTAAGG
*
5167123 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAAATTTATTTCCAAGGAAAATT
127 AAAATTGATACTTTCAACTTTTCCCCAAAAATAGTTTTTTTGAAAATTTATTTCCAAGGAAAATT
* * *
5167188 GATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTGGATTTTCAAGGAAAATTGATACT
192 GATACTCTCAACTTTTCCCTAAAAATATTTTTTGAAAATTTGAATTTTCAAGGAAAATTGATACT
* *
5167253 TTCAACTTTTCCTCAAAAACCCTTTTTT-GAAATTTATTT
257 TTCAACTTTTCCCCAAAAA-CATTTTTTGGAAATTTATTT
* *
5167292 TTAAGGAAAATTGATACTTTCGACTTTTCCCCAAAAATATTTTTTGGAAATTTTGATTTTCAAGG
1 TTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT-GAAATTTT-AATTTCAAGG
* * * *
5167357 AAAATTGGTACTTTCAACTTTTCC-CTAAAAA-TA-TTTTTTTTTTGAAATTTTGTTTTTAAGGA
64 AAAATTGATACTTTCAACTTTTCCTC-AAAAATTATTTTTTTTTTTGAAAATTTATTTCTAAGGA
* **
5167419 AAATTGATACTTTCAACTTTTCCCCAAAAAT-GTTTTTTTG-GAATTTATTTTTAAGGAAAATTG
128 AAATTGATACTTTCAACTTTTCCCCAAAAATAGTTTTTTTGAAAATTTATTTCCAAGGAAAATTG
*
5167482 ATACTCTCAACTTTTCCCTAAAAATATTTTTTTTGAAAATTTTAATTTTCAAGGAAAATTGATAC
193 ATACTCTCAACTTTTCCCTAAAAATA--TTTTTTGAAAATTTGAATTTTCAAGGAAAATTGATAC
*
5167547 TTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTT
256 TTTCAACTTTTCCCCAAAAACATTTTTTGGAAATTTATTT
* *
5167587 CTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT
1 TTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
5167632 TTTGAAAATT
Statistics
Matches: 313, Mismatches: 21, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
293 45 0.14
294 14 0.04
295 163 0.52
297 4 0.01
298 47 0.15
299 40 0.13
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (295 bp):
TTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAATTTTAATTTCAAGGAA
AATTGATACTTTCAACTTTTCCTCAAAAATTATTTTTTTTTTTGAAAATTTATTTCTAAGGAAAA
TTGATACTTTCAACTTTTCCCCAAAAATAGTTTTTTTGAAAATTTATTTCCAAGGAAAATTGATA
CTCTCAACTTTTCCCTAAAAATATTTTTTGAAAATTTGAATTTTCAAGGAAAATTGATACTTTCA
ACTTTTCCCCAAAAACATTTTTTGGAAATTTATTT
Found at i:5167793 original size:5 final size:5
Alignment explanation
Indices: 5167780--5167811 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
5167770 GCGGCTTGGT
*
5167780 GGCTT GGCTC GGCTC GGCTC GGCTC GGCTC GG
1 GGCTC GGCTC GGCTC GGCTC GGCTC GGCTC GG
5167812 AGGGGCTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.44, T:0.22
Consensus pattern (5 bp):
GGCTC
Found at i:5168071 original size:20 final size:20
Alignment explanation
Indices: 5168036--5168087 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
5168026 CACCGGTGGG
* *
5168036 ATTTCGTCGGATTCTGG-AA
1 ATTTCGCCGGAATCTGGAAA
5168055 ATTCTCGCCGGAATCTGGAAA
1 ATT-TCGCCGGAATCTGGAAA
5168076 ATTTCGCCGGAA
1 ATTTCGCCGGAA
5168088 GTTCGCCGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 3 0.10
20 21 0.72
21 5 0.17
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (20 bp):
ATTTCGCCGGAATCTGGAAA
Found at i:5168157 original size:19 final size:20
Alignment explanation
Indices: 5168121--5168161 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
5168111 TCACCGGTTT
5168121 CTGGGATTCTTCGCCGGAAA
1 CTGGGATTCTTCGCCGGAAA
*
5168141 CTGGGATTGTT-GCCGGAAA
1 CTGGGATTCTTCGCCGGAAA
5168160 CT
1 CT
5168162 TCAAGTTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.20, C:0.22, G:0.32, T:0.27
Consensus pattern (20 bp):
CTGGGATTCTTCGCCGGAAA
Found at i:5168277 original size:25 final size:25
Alignment explanation
Indices: 5168230--5168283 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
5168220 AATCTGGAAA
*
5168230 TTTCCCAGAAATTTCCAGAAAATTT
1 TTTCCCAAAAATTTCCAGAAAATTT
*
5168255 TTTCGCCAAAAATTTCTAG-AAATTT
1 TTTC-CCAAAAATTTCCAGAAAATTT
5168280 TTTC
1 TTTC
5168284 TCACTCCCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (25 bp):
TTTCCCAAAAATTTCCAGAAAATTT
Found at i:5168647 original size:3 final size:3
Alignment explanation
Indices: 5168639--5168735 Score: 69
Period size: 3 Copynumber: 32.7 Consensus size: 3
5168629 GATAATTAAA
* **
5168639 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA- GAT AA- ACCC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * *
5168682 AAGT ATAT ATT ACA- AA- AAA AAA AAT AAT AAT AAT AAT AAT AAT AAT
1 AA-T A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5168728 AAT AAT AA
1 AAT AAT AA
5168736 ATATATAACT
Statistics
Matches: 78, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
2 7 0.09
3 66 0.85
4 4 0.05
5 1 0.01
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:5169787 original size:3 final size:3
Alignment explanation
Indices: 5169779--5169811 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5169769 TAAAATTTTT
5169779 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5169812 TTATTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5169816 original size:3 final size:3
Alignment explanation
Indices: 5169810--5169843 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
5169800 ATAATAATAA
5169810 TAT TAT TAT TAT TAT TAT TAT TAT TAT TCAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
5169844 GAATAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:5171090 original size:19 final size:19
Alignment explanation
Indices: 5171028--5171091 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
5171018 TTATATGCAA
* *
5171028 TATATATTAAAATATCATAT
1 TATATTTTAAAAT-TTATAT
*
5171048 TA-ATATTTAAAATTTA-AA
1 TATAT-TTTAAAATTTATAT
*
5171066 TATATTTTATAATTTATAT
1 TATATTTTAAAATTTATAT
5171085 TATATTT
1 TATATTT
5171092 AAGTATTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
18 13 0.36
19 14 0.39
20 9 0.25
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATTTTAAAATTTATAT
Found at i:5171092 original size:18 final size:18
Alignment explanation
Indices: 5171028--5171093 Score: 62
Period size: 18 Copynumber: 3.5 Consensus size: 18
5171018 TTATATGCAA
*
5171028 TATATATTAAAATATCATAT
1 TATAT-TTAAAAT-TTATAT
*
5171048 TAATATTTAAAATTTA-AA
1 T-ATATTTAAAATTTATAT
*
5171066 TATATTTTATAATTTATAT
1 TATA-TTTAAAATTTATAT
5171085 TATATTTAA
1 TATATTTAA
5171094 GTATTAATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
17 3 0.08
18 16 0.42
19 7 0.18
20 8 0.21
21 4 0.11
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TATATTTAAAATTTATAT
Found at i:5175250 original size:22 final size:22
Alignment explanation
Indices: 5175222--5175266 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
5175212 ATAATTGTTC
*
5175222 TGTGAAAAAGTTATTACGTGAA
1 TGTGAAAAAGTCATTACGTGAA
*
5175244 TGTGAAAAAGTCATTATGTGAA
1 TGTGAAAAAGTCATTACGTGAA
5175266 T
1 T
5175267 AGTTATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.33
Consensus pattern (22 bp):
TGTGAAAAAGTCATTACGTGAA
Found at i:5178651 original size:22 final size:23
Alignment explanation
Indices: 5178604--5178658 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
5178594 AAGACAATTT
5178604 TTTAAA-AT-TATTTTTTTAATAA
1 TTTAAATATATATTTTTTTAAT-A
*
5178626 TTTAGATATATATTTTTTTAAT-
1 TTTAAATATATATTTTTTTAATA
5178648 TTTAAATATAT
1 TTTAAATATAT
5178659 CAAATATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 15 0.52
23 2 0.07
24 12 0.41
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTAAATATATATTTTTTTAATA
Found at i:5179710 original size:34 final size:36
Alignment explanation
Indices: 5179637--5179711 Score: 84
Period size: 34 Copynumber: 2.1 Consensus size: 36
5179627 CTATTTATAT
**
5179637 ATATATTATTAAAATGTTAAAATTTTATAATATTAA
1 ATATATTATTAAAATGTTAAAATTAAATAATATTAA
* *
5179673 ATATATT-TT-AAAT-TTAAAATTAAAATAATTTTTA
1 ATATATTATTAAAATGTTAAAATT-AAATAATATTAA
5179707 ATATA
1 ATATA
5179712 ATAATATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
33 8 0.24
34 17 0.50
35 2 0.06
36 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (36 bp):
ATATATTATTAAAATGTTAAAATTAAATAATATTAA
Found at i:5179736 original size:40 final size:42
Alignment explanation
Indices: 5179657--5179737 Score: 96
Period size: 40 Copynumber: 2.0 Consensus size: 42
5179647 AAAATGTTAA
*
5179657 AATTTTATAATATTAAATATATTTTAAATTTAAAATTAAAAT
1 AATTTTATAATATTAAATATATTTTAAATCTAAAATTAAAAT
* * *
5179699 AATTTT-TAATA-T-AATAATATTTTGAATCTATACTTAAAA
1 AATTTTATAATATTAAAT-ATATTTTAAATCTAAAATTAAAA
5179738 AGTAATGCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
39 3 0.09
40 20 0.59
41 5 0.15
42 6 0.18
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (42 bp):
AATTTTATAATATTAAATATATTTTAAATCTAAAATTAAAAT
Found at i:5181706 original size:2 final size:2
Alignment explanation
Indices: 5181699--5181733 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5181689 TCAATTTGAA
5181699 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
5181734 AAAGGAGTAT
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:5181938 original size:2 final size:2
Alignment explanation
Indices: 5181931--5181970 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5181921 TAAGGTTGTT
5181931 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
5181971 GATAAGAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5182105 original size:2 final size:2
Alignment explanation
Indices: 5182098--5182132 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5182088 TCAATTTGAA
5182098 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
5182133 AGAGTATAGC
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:5183016 original size:88 final size:88
Alignment explanation
Indices: 5182855--5183017 Score: 240
Period size: 88 Copynumber: 1.9 Consensus size: 88
5182845 ATATTGTTCC
* * *
5182855 AAAATATAAAATTATTTCATTTTGGAACATTTCAAAATAAAATACGCACAAAGAAAATGAAAAAA
1 AAAATAGAAAATTATTTCATTTTGAAACATTTCAAAATAAAATACGCACAAACAAAATGAAAAAA
*
5182920 AAGTAGTAATCAATAGTTTTCAA
66 AAGAAGTAATCAATAGTTTTCAA
* *
5182943 AAAATAGAAAATTATTTCATTTTGAAAC-TTTCCAAGAATAAAATATGGACAAACAAAATGAAAA
1 AAAATAGAAAATTATTTCATTTTGAAACATTT-CAA-AATAAAATACGCACAAACAAAATGAAAA
5183007 AAAA-AAGTAAT
64 AAAAGAAGTAAT
5183018 ATTATTACAG
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
87 3 0.04
88 35 0.52
89 29 0.43
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.27
Consensus pattern (88 bp):
AAAATAGAAAATTATTTCATTTTGAAACATTTCAAAATAAAATACGCACAAACAAAATGAAAAAA
AAGAAGTAATCAATAGTTTTCAA
Found at i:5183265 original size:2 final size:2
Alignment explanation
Indices: 5183258--5183284 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5183248 TCAATTTGAA
5183258 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 A
5183285 AAGAGTATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5183692 original size:772 final size:778
Alignment explanation
Indices: 5182154--5183691 Score: 2015
Period size: 789 Copynumber: 2.0 Consensus size: 778
5182144 AATAATGTTC
* * *
5182154 AAAAATATAAAATTATTTCATTTTGAAAAATTCCAAAAATAAAATATGGACTAAGAAAATGAAAA
1 AAAAATAGAAAATTATTTCATTTTGAAAAATTCCAAAAATAAAATATGGACAAACAAAATGAAAA
* *
5182219 AAAAAGTATTACTATTAAAGTAAGTTAACAAATTTGATCAACATTTAAATACTATGTGTCATTTT
66 AAAAAGTAATACTATTAAAGTAAGTTAACAAATTTGATCAACATTTAAATACTATGTATCATTTT
* * *
5182284 TTTTAGCTTCCTTTCAAAAATAGGAGGATTATATTTATAAGGTTGTTTTTTATACAAGAGTTAAG
131 TTTTAGCTTCCTTTCAAAAACAAGAAGATTATATTTATAAGGTTGTTTTTTATACAAGAGTTAAG
* * ** * *
5182349 AAAGTAGATAAAAATGTTATTTTTAATAAAAATGAATGGTGTAAAAAATTTCAAAATTATAATCT
196 AAAGCAAATAAAAATGTTATTTTTAATAAAAATGAATGGTACAAAAAAATTCAAAATTACAATCT
* *
5182414 AAAATGATTTTTTTTTTTGCCTTTTATACAATCGACCTTAGATCAATTTAAAATATAAAAAAATA
261 AAAATAATTTTTTTTTTTGCCTTTTATACAATCGACCTTAAATCAATTTAAAATAT-AAAAAATA
* * * ** * *
5182479 AGAATATAGTTAATAGTGTTCAAAAATAGAATATTATTTCATTTTGAAACATTCCAAAAATAAAA
325 AGAATATAG-TAATAGTGAT-AAAAATAGAATATTAGTTAATAGTG----AGTCAAAAAATAAAA
*
5182544 TACACACAAAGAAAATGAAAAAAGAAAGTATTACTATTAAAGTAAGTTAACAAATTTGATCAATA
384 TACACACAAAGAAAATGAAAAAAGAAAGTATTACTATTAAAGTAAGTTAACAAATTTGATCAACA
* *
5182609 TTTAAATACTATGTATCAATTTTTTTAGCTTCATTTTGAAAAATAGGAAGATTATTTTTATAAAA
449 TTTAAATACTATGTATCAATTTTTTTAGCTTCACTTTCAAAAATAGGAAGATTATTTTTATAAAA
* *
5182674 TTATTTTTTTATACAAGAGCTAAGAAAAGTAGATGAAAAGATTGTTTTTAACAAAAATAAGTGAT
514 TTAGTTTTTTATACAAGAGCTAAGAAAAGTAGATGAAAAGATTGTTTTTAACAAAAATAAGTGAC
* * *
5182739 ATAAGAAAATTCAAAATTATAACTTAACATGATTTTTTTTTTTTTTTTGCCTTTTATATAGTCGA
579 ATAAAAAAATTCAAAATTACAACTTAACATGA---TTTTTTTTTTTTTGCCTTTTATATAGTCAA
* * * * * * *
5182804 CCTTCGATCAATTTGAAATAATAAAAAAAAGGGTATAGTCAATATTGTTCCAAAATATAAAATTA
641 CCTTAGATCAATTTGAAATAAAAAAAAAAAGAGAATAGTCAATAGTGTTCAAAAATAGAAAATTA
* *
5182869 TTTCATTTTGGAACATTTCAAAATAAAATACGCACAAAGAAAATGAAAAAAAAGTAGTAATCAAT
706 TTTCATTTTGAAACATTCCAAAATAAAATACGCACAAAGAAAATGAAAAAAAAGTAGTAATCAAT
5182934 AGTTTTCA
771 AGTTTTCA
** *
5182942 AAAAATAGAAAATTATTTCATTTTGAAACTTTCCAAGAATAAAATATGGACAAACAAAATGAAAA
1 AAAAATAGAAAATTATTTCATTTTGAAAAATTCCAAAAATAAAATATGGACAAACAAAATG-AAA
* *
5183007 AAAAAAGTAATATTATTACAGTAAGTTAACAAATTTGATCAACATTTAAATACTATGTATCATTT
65 AAAAAAGTAATACTATTAAAGTAAGTTAACAAATTTGATCAACATTTAAATACTATGTATCATTT
* * * * *
5183072 TTTTTAGCTTCCTTTCAAAAACAAGAAGATTATTTTTATAAGGTTATTTTTTTGTTCGAGAGTTA
130 TTTTTAGCTTCCTTTCAAAAACAAGAAGATTATATTTATAAGGTT-GTTTTTTATACAAGAGTTA
* * * *
5183137 AGAAAGCAAATGAAAATTTTGTTTTTAATAAAAATGAGTGGTACAAAAAAATTCAAAATTACAAT
194 AGAAAGCAAATAAAAATGTTATTTTTAATAAAAATGAATGGTACAAAAAAATTCAAAATTACAAT
* * * * * *
5183202 CTAACATAATATTTTATTTTTTGCGTTTTATACAGTCGACCTTAAATCAATTTGAAATAT-ATAT
259 CTAAAATAAT-TTTT-TTTTTTGCCTTTTATACAATCGACCTTAAATCAATTTAAAATATAAAAA
* * * *
5183266 AT-A-TATATA-T-ATA-T-AT-ATAA-AGAGTA-TAGTTAATAGTG-GT-AAAAAATAAAATAT
322 ATAAGAATATAGTAATAGTGATAAAAATAGAATATTAGTTAATAGTGAGTCAAAAAATAAAATAC
** *
5183320 GGACAAAGAAAATGAAAAAA-AAAGTATTACTATTAAAGTAAGTTAACAAATTTGATTAACATTT
387 ACACAAAGAAAATGAAAAAAGAAAGTATTACTATTAAAGTAAGTTAACAAATTTGATCAACATTT
*
5183384 AAATACTATGTAT-AATTTTTTTTTAGCTTC-CTTTCAAAAATAGGAAGATTATTTTTATAAGAT
452 AAATACTATGTATCAA--TTTTTTTAGCTTCACTTTCAAAAATAGGAAGATTATTTTTATAAAAT
* * *
5183447 T-GTTTTTTATACAAGAGTTAA-AAAAGTAGATG-AAA-A-TGTTTTTAACAAAAATGAGTGACG
515 TAGTTTTTTATACAAGAGCTAAGAAAAGTAGATGAAAAGATTGTTTTTAACAAAAATAAGTGACA
*
5183507 TAAAAAAATTCAAAATTACAA-TCTAATATGA-TTTTTTTTTTTTGCCTTTTATATAGTCAA-CT
580 TAAAAAAATTCAAAATTACAACT-TAACATGATTTTTTTTTTTTTGCCTTTTATATAGTCAACCT
*
5183569 CTAGATCAATTTGAAATATAAAAAAAAAATAAGAGAATAGTTAATAGTGTTCAAAAATAGAAAAT
644 -TAGATCAATTTG-AA-AT-AAAAAAAAA-AAGAGAATAGTCAATAGTGTTCAAAAATAGAAAAT
* *
5183634 TATTTCATTTTGAAATATTCCAAAAATAAAATAACGGTACAAAGAAAATGAAAAAAAA
704 TATTTCATTTTGAAACATTCC-AAAATAAAAT-AC-GCACAAAGAAAATGAAAAAAAA
5183692 AGTATTACCA
Statistics
Matches: 660, Mismatches: 75, Indels: 48
0.84 0.10 0.06
Matches are distributed among these distances:
762 2 0.00
763 39 0.06
764 2 0.00
765 2 0.00
766 9 0.01
767 94 0.14
768 11 0.02
769 5 0.01
770 32 0.05
771 20 0.03
772 86 0.13
773 43 0.07
774 1 0.00
779 8 0.01
780 5 0.01
781 3 0.00
783 1 0.00
784 1 0.00
785 3 0.00
786 1 0.00
788 60 0.09
789 106 0.16
790 82 0.12
791 4 0.01
792 40 0.06
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.36
Consensus pattern (778 bp):
AAAAATAGAAAATTATTTCATTTTGAAAAATTCCAAAAATAAAATATGGACAAACAAAATGAAAA
AAAAAGTAATACTATTAAAGTAAGTTAACAAATTTGATCAACATTTAAATACTATGTATCATTTT
TTTTAGCTTCCTTTCAAAAACAAGAAGATTATATTTATAAGGTTGTTTTTTATACAAGAGTTAAG
AAAGCAAATAAAAATGTTATTTTTAATAAAAATGAATGGTACAAAAAAATTCAAAATTACAATCT
AAAATAATTTTTTTTTTTGCCTTTTATACAATCGACCTTAAATCAATTTAAAATATAAAAAATAA
GAATATAGTAATAGTGATAAAAATAGAATATTAGTTAATAGTGAGTCAAAAAATAAAATACACAC
AAAGAAAATGAAAAAAGAAAGTATTACTATTAAAGTAAGTTAACAAATTTGATCAACATTTAAAT
ACTATGTATCAATTTTTTTAGCTTCACTTTCAAAAATAGGAAGATTATTTTTATAAAATTAGTTT
TTTATACAAGAGCTAAGAAAAGTAGATGAAAAGATTGTTTTTAACAAAAATAAGTGACATAAAAA
AATTCAAAATTACAACTTAACATGATTTTTTTTTTTTTGCCTTTTATATAGTCAACCTTAGATCA
ATTTGAAATAAAAAAAAAAAGAGAATAGTCAATAGTGTTCAAAAATAGAAAATTATTTCATTTTG
AAACATTCCAAAATAAAATACGCACAAAGAAAATGAAAAAAAAGTAGTAATCAATAGTTTTCA
Found at i:5184041 original size:350 final size:351
Alignment explanation
Indices: 5183485--5184587 Score: 1328
Period size: 350 Copynumber: 3.2 Consensus size: 351
5183475 GATGAAAATG
* * * * * *
5183485 TTTTTAACAAAAATGAGTGACGTAAAAAAATTCAAAATTACAATCTAATATGA---TTTTTTTTT
1 TTTTTAACAAAAATGAATGGCGCAAAAAAATTTAAAATTACAACCTAACATGATTTTTTTTTTTT
* *
5183547 TTTGCCTTTTATATAGTCAA-CTCTAGATCAATTTGAAATATAAAAAAAAAATAAGAGAATAGTT
66 TTTGCCTTTTATATAGTCAACCT-TAGATCAATTTGAAATAT-ATAAAAAAATAAGAG-ATAGTC
* *
5183611 AATAGTGTTCAAAAATAGAAAATTATTTCATTTTGAAATATTCCAAAAATAAAATAACGGTACAA
128 AATAGTGTTCAAAAAAAGAAAATTATTTCATTTTGAAACATTCCAAAAATAAAAT-ACGG-ACAA
* *
5183676 AGAAAATGAAAAAAAAAGTATTACCATTAAAGTAAGTTAACAAATTTGATCAACATTTAAATTCT
191 AGAAAATGAAAAAAAAAGTATTACTATTAAAGTAAGTTAACAAATTTGATCAACATTTAAATACT
* * ** * *
5183741 AAGTATGA-TTTTTTTTAGCTTTATTTCAAAAGCAAAAAGATTATTTTAATAAGGTCGTTTTTTA
256 ATGTATAATTTTTTTTTAGCTTCCTTTCAAAAACAAAAAGATTATTTTTATAAGGTCGTTTTTTA
*
5183805 TACAAAAGTTAAGAAAATATACGAAAATGTT
321 TACAAAAGTTAAGAAAATAGACGAAAATGTT
* *
5183836 ATTTTTAACAAAAATGAGTGGCGCAAAAAAATTTAAAATTACAGCCTAACATGATTTTTTTTTTT
1 -TTTTTAACAAAAATGAATGGCGCAAAAAAATTTAAAATTACAACCTAACATGATTTTTTTTTTT
*
5183901 TTTTGCCTTTTATATAGTCAACCTTAGATCAATTTGAAATATATTAAAAAAA-AAGAGTATCGTC
65 TTTTGCCTTTTATATAGTCAACCTTAGATCAATTTGAAATATA-TAAAAAAATAAGAG-ATAGTC
* * * *
5183965 AATAGTGTTCAAAAAAAGAAAATTATTTAATTTTCAAACATTTCAAAAATAAAATATGGACAAA-
128 AATAGTGTTCAAAAAAAGAAAATTATTTCATTTTGAAACATTCCAAAAATAAAATACGGACAAAG
* * *
5184029 AAAATGAAAAAAAAAGTATTACTATTAAAGTAAGTAAACAAATTTGATCAACATTTGAATACTCT
193 AAAATGAAAAAAAAAGTATTACTATTAAAGTAAGTTAACAAATTTGATCAACATTTAAATACTAT
* * * * ** *
5184094 TTATCA--TTTTTTTAGCTTCCTTTCAAATATAGGAAGATTATTTTTATAAGG-CTATTTTTTAT
258 GTATAATTTTTTTTTAGCTTCCTTTCAAAAACAAAAAGATTATTTTTATAAGGTC-GTTTTTTAT
* * * * *
5184156 ATAAAAATTAAGAAAGTAGCCGAAAAGGTT
322 ACAAAAGTTAAGAAAATAGACGAAAATGTT
* * * * *
5184186 GGTTTTAACAAAAATGAATGGCCCAAGAAAATTTAAAATTACAACCTAAGATGATCTTTTTTTTT
1 -TTTTTAACAAAAATGAATGGCGCAAAAAAATTTAAAATTACAACCTAACATGATTTTTTTTTTT
*
5184251 TTTTGCC-----T-T-G---ACCTAAGATCAATTT-AAA-ATATAAAAAAATAAGA-ATAGTCAA
65 TTTTGCCTTTTATATAGTCAACCTTAGATCAATTTGAAATATATAAAAAAATAAGAGATAGTCAA
5184303 TAGTGTTCAAAAATAA-AAAATTATTTCATTTTGAAACATTCCAAAAATAAAATACGGACAAAGA
130 TAGTGTTCAAAAA-AAGAAAATTATTTCATTTTGAAACATTCCAAAAATAAAATACGGACAAAGA
*
5184367 AAATG-AAAAAAAAGTATTACTATTAAAGTAAGTTAACAAATTTGATCAACATTTAAATATTATG
194 AAATGAAAAAAAAAGTATTACTATTAAAGTAAGTTAACAAATTTGATCAACATTTAAATACTATG
*
5184431 TATAATTTTTTTTTAGCTTCCTTTCAAAAACAAAAA-AGTTATTTTTATAAGGTTGTTTTTTTAT
259 TATAATTTTTTTTTAGCTTCCTTTCAAAAACAAAAAGA-TTATTTTTATAAGGTCG-TTTTTTAT
* * * * * *
5184495 ACAAGAGTTAAAAAAATAAATGAAACGTTTTT
322 ACAAAAGTTAAGAAAATAGACGAAA--ATGTT
* * * *
5184527 TTTTTAAC-AAAATGAAT--AGCATAAAAAATTTAAAATTACGACTTAACATAATTTTTTTTTT
1 TTTTTAACAAAAATGAATGGCGCA-AAAAAATTTAAAATTACAACCTAACATGATTTTTTTTTT
5184588 ACCTTTTACA
Statistics
Matches: 649, Mismatches: 85, Indels: 48
0.83 0.11 0.06
Matches are distributed among these distances:
336 120 0.18
337 19 0.03
338 79 0.12
339 37 0.06
340 21 0.03
341 2 0.00
343 1 0.00
344 1 0.00
345 1 0.00
349 1 0.00
350 133 0.20
351 63 0.10
352 52 0.08
353 3 0.00
354 60 0.09
355 54 0.08
356 2 0.00
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (351 bp):
TTTTTAACAAAAATGAATGGCGCAAAAAAATTTAAAATTACAACCTAACATGATTTTTTTTTTTT
TTTGCCTTTTATATAGTCAACCTTAGATCAATTTGAAATATATAAAAAAATAAGAGATAGTCAAT
AGTGTTCAAAAAAAGAAAATTATTTCATTTTGAAACATTCCAAAAATAAAATACGGACAAAGAAA
ATGAAAAAAAAAGTATTACTATTAAAGTAAGTTAACAAATTTGATCAACATTTAAATACTATGTA
TAATTTTTTTTTAGCTTCCTTTCAAAAACAAAAAGATTATTTTTATAAGGTCGTTTTTTATACAA
AAGTTAAGAAAATAGACGAAAATGTT
Found at i:5190949 original size:31 final size:33
Alignment explanation
Indices: 5190914--5190975 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
5190904 TTATGATACA
5190914 TAAATT-TT-ATATCAAATATAATATGAATATC
1 TAAATTATTAATATCAAATATAATATGAATATC
***
5190945 TAAATTATTAATATTTTATATAATATGAATA
1 TAAATTATTAATATCAAATATAATATGAATA
5190976 CTTTATGACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 6 0.23
32 2 0.08
33 18 0.69
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (33 bp):
TAAATTATTAATATCAAATATAATATGAATATC
Found at i:5191229 original size:16 final size:16
Alignment explanation
Indices: 5191199--5191229 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5191189 TATTAATTAA
*
5191199 ACAAAAAATATAAAAT
1 ACAAAAAATAAAAAAT
5191215 ACAAAAAATAAAAAA
1 ACAAAAAATAAAAAA
5191230 AAATAAAAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (16 bp):
ACAAAAAATAAAAAAT
Found at i:5195624 original size:15 final size:16
Alignment explanation
Indices: 5195598--5195627 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5195588 TAAAGTTGTT
5195598 GAGCATTTTTCAAGAG
1 GAGCATTTTTCAAGAG
5195614 GAGCA-TTTTCAAGA
1 GAGCATTTTTCAAGA
5195628 TGAGGTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.30
Consensus pattern (16 bp):
GAGCATTTTTCAAGAG
Found at i:5195747 original size:57 final size:56
Alignment explanation
Indices: 5195633--5195748 Score: 139
Period size: 57 Copynumber: 2.1 Consensus size: 56
5195623 CAAGATGAGG
* *
5195633 TTTTTTTTTAAGTTGTTGAACCTCTACCTAGAAGAGCCTTTTTTTAAGCTGAGATTT
1 TTTTTTTTTAAGTTGTTGAACCTCTACCTAAAAGAGCCTTTTTTCAA-CTGAGATTT
* *
5195690 TTTTTTTTTAAGTTGTT-AAGCCTTTACC-AAAATGAGCCTTTTTTCATA-TGAGAATT
1 TTTTTTTTTAAGTTGTTGAA-CCTCTACCTAAAA-GAGCCTTTTTTCA-ACTGAGATTT
5195746 TTT
1 TTT
5195749 AAGTTGTTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
56 15 0.29
57 36 0.69
58 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.14, T:0.49
Consensus pattern (56 bp):
TTTTTTTTTAAGTTGTTGAACCTCTACCTAAAAGAGCCTTTTTTCAACTGAGATTT
Found at i:5195882 original size:49 final size:51
Alignment explanation
Indices: 5195786--5195934 Score: 142
Period size: 52 Copynumber: 2.9 Consensus size: 51
5195776 CTTTTTTTTT
* * * *
5195786 TCAAGATGAGAATTTTTTAAAGTTGTTGAGCCTCAACCA-AAAGGAGCC-TTA
1 TCAAGATGA-AATATTTTAAAGTTGTTGAGCCTCTA-CATAGATGAGCCTTTA
* * *
5195837 TCCAGATGAAA-ATTTTAAAGTTATTGAGCCTCTACATAGATGAGCCTTTT
1 TCAAGATGAAATATTTTAAAGTTGTTGAGCCTCTACATAGATGAGCCTTTA
* * * * *
5195887 TCAAGATGAAATTTTTTTTAAGTTGTTAAGCCACTACCTAGATGAGCC
1 TCAAGATGAAA-TATTTTAAAGTTGTTGAGCCTCTACATAGATGAGCC
5195935 ATTTTAAGTT
Statistics
Matches: 80, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
48 2 0.03
49 27 0.34
50 14 0.17
51 8 0.10
52 29 0.36
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (51 bp):
TCAAGATGAAATATTTTAAAGTTGTTGAGCCTCTACATAGATGAGCCTTTA
Found at i:5195933 original size:52 final size:52
Alignment explanation
Indices: 5195619--5195939 Score: 194
Period size: 50 Copynumber: 6.1 Consensus size: 52
5195609 AAGAGGAGCA
** *
5195619 TTTTCAAGATGAGGTTTTTTTTTAAGTTGTTGAA-CCTCTACCTAGAAGAGCCTT
1 TTTTCAAGATGA-GAATTTTTTTAAGTTGTT-AAGCCTCTACCTAGATGAGCC-T
* * * * * *
5195673 TTTTTAAGCTGAGATTTTTTTTTTTTAAGTTGTTAAGCCTTTACCAAAATGAGCCTT
1 TTTTCAAGATGAGA----ATTTTTTTAAGTTGTTAAGCCTCTACCTAGATGAGCC-T
* * *
5195730 TTTTC-ATATGAGAA--TTTTTAAGTTGTTAAGCCTCTA-CTGAGA-GAAACTTTTTT
1 TTTTCAAGATGAGAATTTTTTTAAGTTGTTAAGCCTCTACCT-AGATG-AGC----CT
* * * * * *
5195783 TTTTCAAGATGAGAATTTTTTAAAGTTGTTGAGCCTCAACCAAAAGGAGCC-
1 TTTTCAAGATGAGAATTTTTTTAAGTTGTTAAGCCTCTACCTAGATGAGCCT
* * * * * * *
5195834 TTATCCAGATGA-AA-ATTTTAAAGTTATTGAGCCTCTACATAGATGAGCCT
1 TTTTCAAGATGAGAATTTTTTTAAGTTGTTAAGCCTCTACCTAGATGAGCCT
* *
5195884 TTTTCAAGATGA-AATTTTTTTTAAGTTGTTAAGCCACTACCTAGATGAGCCA
1 TTTTCAAGATGAGAA-TTTTTTTAAGTTGTTAAGCCTCTACCTAGATGAGCCT
5195936 TTTT
1 TTTT
5195940 AAGTTTTCAA
Statistics
Matches: 206, Mismatches: 42, Indels: 40
0.72 0.15 0.14
Matches are distributed among these distances:
49 30 0.15
50 39 0.19
51 10 0.05
52 33 0.16
53 7 0.03
54 18 0.09
56 31 0.15
57 38 0.18
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (52 bp):
TTTTCAAGATGAGAATTTTTTTAAGTTGTTAAGCCTCTACCTAGATGAGCCT
Found at i:5197894 original size:212 final size:215
Alignment explanation
Indices: 5197625--5198128 Score: 576
Period size: 212 Copynumber: 2.3 Consensus size: 215
5197615 TTTTTAGGTG
* * * * * * * * *
5197625 AGAATATTTTTTAAAGATACTCCCAGTGTATTGAAATATTTTTAAAGAGTTTTCAATACAACAAA
1 AGAAT-TTTTTTAAAAATATTACCAGTATATTGAAGTATTTATAAAAAATTTTCAATATAA-AAA
5197690 AAATTT-T-TTTCCCT-ATAAAATAGTAAATGAAAATTAACTAATTTGTTAAAAATAAAAGTGAT
64 AAATTTCTCTTTCCCTCA-AAAAT-GTAAATGAAAATTAACTAATTTGTTAAAAATAAAA-TGAT
* * *
5197752 AAAATAAAAAT-GAG-AAAA-AAAATTTTA-TCTGATGACATG-ATTCTAAAAGTATTTCGAGTA
126 AAAATAAAAATAAAGAAAAATAAAATTTTATTC-GATGACA-GAATTCCAAAAGTATTTCGAATA
**
5197812 GTGATGTTTTACGAAATCCCTAAAT-A
189 GTGATACTTTACGAAATCCCTAAATGA
* * * *
5197838 AGAATTTTTTTAAAAATATTACCAGTATATTGGAGTATTTATAAAAAATCTTCAATATGATAAAA
1 AGAATTTTTTTAAAAATATTACCAGTATATTGAAGTATTTATAAAAAATTTTCAATATAAAAAAA
* *** * *
5197903 GTTTCTCTTTTTTTCAAAAATTTAAATGAAAATTAACTAATTTGTTAAAAGTAAAATGATAAAAT
66 ATTTCTCTTTCCCTCAAAAATGTAAATGAAAATTAACTAATTTGTTAAAAATAAAATGATAAAAT
*
5197968 AAAAATAAAGAAAAATAAAATTTTATTCGATGATAGAATTCCAAAAGTATTTCGAATAGTGATAC
131 AAAAATAAAGAAAAATAAAATTTTATTCGATGACAGAATTCCAAAAGTATTTCGAATAGTGATAC
* *
5198033 TTTATGAAATTCCTAAATGA
196 TTTACGAAATCCCTAAATGA
* * * * *
5198053 AAAGATTTTTTTAAAAATATTACCAATAAATTAAAGTATTTATAAAAAATTTTCAATATAATAAA
1 AGA-ATTTTTTTAAAAATATTACCAGTATATTGAAGTATTTATAAAAAATTTTCAATATAAAAAA
*
5198118 AATTTATCTTT
65 AATTTCTCTTT
5198129 TGTTCAAAAA
Statistics
Matches: 245, Mismatches: 36, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
211 22 0.09
212 79 0.32
213 19 0.08
214 56 0.23
215 5 0.02
216 64 0.26
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.37
Consensus pattern (215 bp):
AGAATTTTTTTAAAAATATTACCAGTATATTGAAGTATTTATAAAAAATTTTCAATATAAAAAAA
ATTTCTCTTTCCCTCAAAAATGTAAATGAAAATTAACTAATTTGTTAAAAATAAAATGATAAAAT
AAAAATAAAGAAAAATAAAATTTTATTCGATGACAGAATTCCAAAAGTATTTCGAATAGTGATAC
TTTACGAAATCCCTAAATGA
Found at i:5198110 original size:216 final size:212
Alignment explanation
Indices: 5197713--5198145 Score: 611
Period size: 216 Copynumber: 2.0 Consensus size: 212
5197703 TATAAAATAG
*
5197713 TAAATGAAAATTAACTAATTTGTTAAAAATAAAAGTGATAAAATAAAAATGAGAAAAAAAATTTT
1 TAAATGAAAATTAACTAATTTGTTAAAAATAAAAGTGATAAAATAAAAATAAGAAAAAAAATTTT
* * ** *
5197778 ATCTGATGACATGATTCTAAAAGTATTTCGAGTAGTGATGTTTTACGAAATCCCTAAATAAGAAT
66 ATCTGATGACATGATTCCAAAAGTATTTCGAATAGTGATACTTTACGAAATCCCTAAATAAAAAT
* * ** * * *
5197843 TTTTTTAAAAATATTACCAGTATATTGGAGTATTTATAAAAAATCTTCAATATGATAAAAGTTTC
131 TTTTTTAAAAATATTACCAATAAATTAAAGTATTTATAAAAAATCTTCAATATAATAAAAATTTA
*
5197908 TCTTTTTTTCAAAAATT
196 TCTTTTGTTCAAAAATT
*
5197925 TAAATGAAAATTAACTAATTTGTTAAAAGTAAAA-TGATAAAATAAAAATAAAGAAAAATAAAAT
1 TAAATGAAAATTAACTAATTTGTTAAAAATAAAAGTGATAAAATAAAAAT-AAG-AAAA-AAAAT
* * *
5197989 TTTAT-TCGATGATA-GAATTCCAAAAGTATTTCGAATAGTGATACTTTATGAAATTCCTAAATG
63 TTTATCT-GATGACATG-ATTCCAAAAGTATTTCGAATAGTGATACTTTACGAAATCCCTAAAT-
*
5198052 AAAAGATTTTTTTAAAAATATTACCAATAAATTAAAGTATTTATAAAAAATTTTCAATATAATAA
125 AAAA-ATTTTTTTAAAAATATTACCAATAAATTAAAGTATTTATAAAAAATCTTCAATATAATAA
5198117 AAATTTATCTTTTGTTCAAAAATT
189 AAATTTATCTTTTGTTCAAAAATT
5198141 TAAAT
1 TAAAT
5198146 AATAATTCAA
Statistics
Matches: 195, Mismatches: 19, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
211 15 0.08
212 35 0.18
213 6 0.03
214 56 0.29
215 3 0.02
216 80 0.41
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (212 bp):
TAAATGAAAATTAACTAATTTGTTAAAAATAAAAGTGATAAAATAAAAATAAGAAAAAAAATTTT
ATCTGATGACATGATTCCAAAAGTATTTCGAATAGTGATACTTTACGAAATCCCTAAATAAAAAT
TTTTTTAAAAATATTACCAATAAATTAAAGTATTTATAAAAAATCTTCAATATAATAAAAATTTA
TCTTTTGTTCAAAAATT
Found at i:5198765 original size:16 final size:16
Alignment explanation
Indices: 5198741--5198774 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5198731 TTAATAGCTA
*
5198741 TTATATATTTTTTGTT
1 TTATATATTTTTTATT
*
5198757 TTATTTATTTTTTATT
1 TTATATATTTTTTATT
5198773 TT
1 TT
5198775 TAAATTCATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (16 bp):
TTATATATTTTTTATT
Found at i:5199354 original size:13 final size:14
Alignment explanation
Indices: 5199346--5199379 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5199336 GATATTTGAA
5199346 TATTTTA-TTAAAT
1 TATTTTATTTAAAT
*
5199359 TATTTTATTTAATT
1 TATTTTATTTAAAT
5199373 TATTTTA
1 TATTTTA
5199380 AATATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTATTTAAAT
Found at i:5199544 original size:16 final size:16
Alignment explanation
Indices: 5199523--5199561 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
5199513 AATAAAAAAT
5199523 AATTAATTCAATTTAA-
1 AATTAATT-AATTTAAG
5199539 AATTAATTAATTTAAG
1 AATTAATTAATTTAAG
5199555 AATTAAT
1 AATTAAT
5199562 ATTTTGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (16 bp):
AATTAATTAATTTAAG
Found at i:5199746 original size:23 final size:22
Alignment explanation
Indices: 5199701--5199746 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
5199691 TTTCATCATT
5199701 TAAAATTAATTACATTAAAAAA
1 TAAAATTAATTACATTAAAAAA
*
5199723 TAAAATTTATATTA-ATTAATAAA
1 TAAAA-TTA-ATTACATTAAAAAA
5199746 T
1 T
5199747 TTATAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 12 0.57
24 4 0.19
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAAATTAATTACATTAAAAAA
Found at i:5199797 original size:29 final size:28
Alignment explanation
Indices: 5199731--5199798 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
5199721 AATAAAATTT
*
5199731 ATATTAATTAATAAATTTATAATTTAAA
1 ATATTAATTAATAAATTTATAAATTAAA
* *
5199759 A-ATCAGATTAA-AAATTTTTAAAATTAAA
1 ATATTA-ATTAATAAATTTAT-AAATTAAA
5199787 ATATTATATTAA
1 ATATTA-ATTAA
5199799 CATTTTATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
27 10 0.31
28 14 0.44
29 8 0.25
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (28 bp):
ATATTAATTAATAAATTTATAAATTAAA
Found at i:5203868 original size:19 final size:17
Alignment explanation
Indices: 5203841--5203879 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
5203831 ATGACAATTT
*
5203841 AAAACATGATAATAAAATA
1 AAAAAATGAT-AT-AAATA
5203860 AAAAAATGATATAAATA
1 AAAAAATGATATAAATA
5203877 AAA
1 AAA
5203880 TGTATAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 2 0.11
19 9 0.47
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAAAATGATATAAATA
Found at i:5204162 original size:32 final size:31
Alignment explanation
Indices: 5204120--5204222 Score: 104
Period size: 32 Copynumber: 3.3 Consensus size: 31
5204110 AATACAATGA
*
5204120 ATAATTTTTAAATTATTAATAAAGTATTTAAT
1 ATAATATTTAAATTATTAATAAA-TATTTAAT
5204152 ATAATATTTAAATT-TTAA-ATAAT-TTTAAT
1 ATAATATTTAAATTATTAATA-AATATTTAAT
* * * * *
5204181 GTGATATTTAAATTATGAATATATTAATTAAT
1 ATAATATTTAAATTATTAATA-AATATTTAAT
5204213 ATAATATTTA
1 ATAATATTTA
5204223 TTTTTAATAT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
29 18 0.31
30 5 0.08
31 10 0.17
32 26 0.44
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.50
Consensus pattern (31 bp):
ATAATATTTAAATTATTAATAAATATTTAAT
Found at i:5207233 original size:2 final size:2
Alignment explanation
Indices: 5207228--5207255 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5207218 GTGTGTGTGT
5207228 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
5207256 CAGACAGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5209299 original size:37 final size:37
Alignment explanation
Indices: 5209243--5209314 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
5209233 TAAATGCAAG
* * * *
5209243 ATTAATTAGACAGCGTACATGTTTCATTTTTTTTTTT
1 ATTAATTAGACAACATACATGTTTCACTCTTTTTTTT
5209280 ATTAATTAGACAACATACATGTTTCACTCTTTTTT
1 ATTAATTAGACAACATACATGTTTCACTCTTTTTT
5209315 GGTACAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.28, C:0.14, G:0.08, T:0.50
Consensus pattern (37 bp):
ATTAATTAGACAACATACATGTTTCACTCTTTTTTTT
Found at i:5216897 original size:2 final size:2
Alignment explanation
Indices: 5216890--5216924 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5216880 AGATTTAATA
5216890 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
5216925 AAGTTTGAAA
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:5217577 original size:19 final size:17
Alignment explanation
Indices: 5217533--5217602 Score: 59
Period size: 17 Copynumber: 3.8 Consensus size: 17
5217523 TTTTTTTAAT
5217533 AAAATTATAAATATAAA
1 AAAATTATAAATATAAA
*
5217550 AAAATTATAATTATAATCA
1 AAAATTATAAATATAA--A
* *
5217569 AATATTATATCTATATATAA
1 AAAATTATA--AATATA-AA
5217589 AAAATTATTAAATA
1 AAAATTA-TAAATA
5217603 ATCAACGAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
17 15 0.37
19 12 0.29
20 7 0.17
21 6 0.15
22 1 0.02
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAATTATAAATATAAA
Found at i:5220165 original size:7 final size:8
Alignment explanation
Indices: 5220149--5220180 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
5220139 TTTAAGACCC
5220149 TTTTATTT
1 TTTTATTT
5220157 TTTTATTT
1 TTTTATTT
5220165 TTTTA-TT
1 TTTTATTT
5220172 TTTTATTT
1 TTTTATTT
5220180 T
1 T
5220181 CTGTTTGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTATTT
Found at i:5220173 original size:15 final size:16
Alignment explanation
Indices: 5220149--5220180 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
5220139 TTTAAGACCC
5220149 TTTTATTTTTTTATTT
1 TTTTATTTTTTTATTT
5220165 TTTTA-TTTTTTATTT
1 TTTTATTTTTTTATTT
5220180 T
1 T
5220181 CTGTTTGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTATTTTTTTATTT
Found at i:5229377 original size:16 final size:16
Alignment explanation
Indices: 5229339--5229377 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5229329 CTTTATCTAG
5229339 AAAAATAAAAATAAAT
1 AAAAATAAAAATAAAT
** *
5229355 AGTAATAATAATAAAT
1 AAAAATAAAAATAAAT
5229371 AAAAATA
1 AAAAATA
5229378 CCCTAAAAAA
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
AAAAATAAAAATAAAT
Found at i:5231460 original size:7 final size:7
Alignment explanation
Indices: 5231448--5231481 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
5231438 TGATATTAAC
5231448 AAATTTA
1 AAATTTA
5231455 AAATTTA
1 AAATTTA
5231462 AAATTTA
1 AAATTTA
5231469 ACAA-TTA
1 A-AATTTA
5231476 AAATTT
1 AAATTT
5231482 TTTTCTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 2 0.08
7 21 0.84
8 2 0.08
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATTTA
Found at i:5236573 original size:32 final size:30
Alignment explanation
Indices: 5236537--5236643 Score: 94
Period size: 32 Copynumber: 3.5 Consensus size: 30
5236527 ATAACATTTA
5236537 TTTATATATAGTTTCTATTAAAATTTTAAAAT
1 TTTATATATA-TTTCT-TTAAAATTTTAAAAT
*** *
5236569 TTTATAT-TATTT-TTTAGTTTTTGTCAAA-
1 TTTATATATATTTCTTTAAAATTT-TAAAAT
*
5236597 TTTATATATAATTTTTGTTAAAATTTTAAAAT
1 TTTATATAT-ATTTCT-TTAAAATTTTAAAAT
5236629 TTTATATTATATTTC
1 TTTATA-TATATTTC
5236644 GGTGTGGCTT
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
28 13 0.22
29 6 0.10
30 7 0.12
31 7 0.12
32 23 0.39
33 3 0.05
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.59
Consensus pattern (30 bp):
TTTATATATATTTCTTTAAAATTTTAAAAT
Found at i:5236576 original size:60 final size:58
Alignment explanation
Indices: 5236509--5236635 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 58
5236499 AAATAAGAAA
5236509 TATATATTTTTAATTTTTAT-AACATTTATTTATATATAGTTTCTATTAAAATTTTAAAATTT
1 TATATATTTTTAATTTTTATCAA-ATTTA--TATATA-A-TTTCTATTAAAATTTTAAAATTT
* * * *
5236571 TATATTATTTTTTAGTTTTTGTCAAATTTATATATAATTTTTGTTAAAATTTTAAAATTT
1 TATA-TA-TTTTTAATTTTTATCAAATTTATATATAATTTCTATTAAAATTTTAAAATTT
5236631 TATAT
1 TATAT
5236636 TATATTTCGG
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
59 1 0.02
60 25 0.43
61 1 0.02
62 10 0.17
63 2 0.03
64 17 0.29
65 2 0.03
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.59
Consensus pattern (58 bp):
TATATATTTTTAATTTTTATCAAATTTATATATAATTTCTATTAAAATTTTAAAATTT
Found at i:5236635 original size:30 final size:30
Alignment explanation
Indices: 5236536--5236635 Score: 89
Period size: 30 Copynumber: 3.3 Consensus size: 30
5236526 TATAACATTT
* *
5236536 ATTTATATATAGTTTCTATTAAAATTTTAAA
1 ATTTATATATAATTT-TTTTAAAATTTTAAA
* *** *
5236567 ATTT-TATATTA-TTTTTTAGTTTTTGTCAA
1 ATTTATATATAATTTTTTTAAAATTT-TAAA
5236596 ATTTATATATAATTTTTGTTAAAATTTTAAA
1 ATTTATATATAATTTTT-TTAAAATTTTAAA
5236627 ATTT-TATAT
1 ATTTATATAT
5236636 TATATTTCGG
Statistics
Matches: 53, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
28 7 0.13
29 9 0.17
30 16 0.30
31 15 0.28
32 6 0.11
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (30 bp):
ATTTATATATAATTTTTTTAAAATTTTAAA
Found at i:5237011 original size:26 final size:26
Alignment explanation
Indices: 5236975--5237025 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
5236965 GTAAAATAAT
5236975 TTTATTAATTTAATATAATAAATAAAA
1 TTTATTAATTTAATAT-ATAAATAAAA
*
5237002 TTTATT-ATTTAATATATTAATAAA
1 TTTATTAATTTAATATATAAATAAA
5237026 TAATTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.35
26 9 0.39
27 6 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TTTATTAATTTAATATATAAATAAAA
Found at i:5237049 original size:13 final size:14
Alignment explanation
Indices: 5237033--5237066 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
5237023 AAATAATTTG
5237033 AATAAATTTTAT-T
1 AATAAATTTTATAT
*
5237046 AATAAAATTTATAT
1 AATAAATTTTATAT
5237060 AATAAAT
1 AATAAAT
5237067 AAATCTTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATAAATTTTATAT
Found at i:5240824 original size:21 final size:21
Alignment explanation
Indices: 5240762--5240824 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
5240752 ATACAAACAA
* * *
5240762 ATATAAGTAT-ATTTTTTAAA
1 ATATAAATATAATTTTTTTAT
* **
5240782 ATATAGATTATAATTTAATTAT
1 ATATA-AATATAATTTTTTTAT
5240804 ATATAAATATAATTTTTTTAT
1 ATATAAATATAATTTTTTTAT
5240825 TAAATTAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
20 5 0.15
21 17 0.52
22 11 0.33
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (21 bp):
ATATAAATATAATTTTTTTAT
Found at i:5240831 original size:29 final size:29
Alignment explanation
Indices: 5240798--5240879 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 29
5240788 ATTATAATTT
*
5240798 AATTATATATAAATATAATTTTTTTATTA
1 AATTATATATAAATATAATTTTTTTACTA
* * *
5240827 AATTAAATTATTAA-ATAATATTTTTACTA
1 AATTATA-TATAAATATAATTTTTTTACTA
5240856 ATATAATATATATAAATATGAATT
1 A-AT--TATATATAAATAT-AATT
5240880 AAATAAATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
29 20 0.50
30 7 0.17
31 5 0.12
32 5 0.12
33 3 0.08
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (29 bp):
AATTATATATAAATATAATTTTTTTACTA
Found at i:5242202 original size:10 final size:10
Alignment explanation
Indices: 5242179--5242221 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
5242169 AATATCCTTT
*
5242179 ATTTTTATTA
1 ATTTTGATTA
*
5242189 ATTTTGATTG
1 ATTTTGATTA
*
5242199 ATTTTGATAA
1 ATTTTGATTA
*
5242209 ATTTTGATAA
1 ATTTTGATTA
5242219 ATT
1 ATT
5242222 AATTTATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (10 bp):
ATTTTGATTA
Found at i:5242283 original size:15 final size:16
Alignment explanation
Indices: 5242265--5242307 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
5242255 TATTTTATAA
*
5242265 TTTATAATTT-ATTTT
1 TTTATAATTTGATTAT
5242280 TTTATAATTTGATTAT
1 TTTATAATTTGATTAT
5242296 TTT-TAATTTGAT
1 TTTATAATTTGAT
5242308 AAAAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 19 0.73
16 7 0.27
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (16 bp):
TTTATAATTTGATTAT
Found at i:5244127 original size:6 final size:6
Alignment explanation
Indices: 5244110--5244148 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
5244100 AACAACTTGC
* * *
5244110 CTTTGT CCTTGT CTTTGT CTTTGC CTTTGT CTTAGT CTT
1 CTTTGT CTTTGT CTTTGT CTTTGT CTTTGT CTTTGT CTT
5244149 ACGCTCTCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.03, C:0.23, G:0.15, T:0.59
Consensus pattern (6 bp):
CTTTGT
Found at i:5244141 original size:12 final size:12
Alignment explanation
Indices: 5244106--5244142 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
5244096 CATGAACAAC
*
5244106 TTGCCTTTGTCC
1 TTGCCTTTGTCT
*
5244118 TTGTCTTTGTCT
1 TTGCCTTTGTCT
5244130 TTGCCTTTGTCT
1 TTGCCTTTGTCT
5244142 T
1 T
5244143 AGTCTTACGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.24, G:0.16, T:0.59
Consensus pattern (12 bp):
TTGCCTTTGTCT
Found at i:5244672 original size:17 final size:17
Alignment explanation
Indices: 5244636--5244749 Score: 117
Period size: 17 Copynumber: 6.7 Consensus size: 17
5244626 AAACCCCTCC
*
5244636 CATGGTTTGC-A-AGCA
1 CATGGTTTGCAACAGAA
5244651 CATGGTTTGCAACAGAA
1 CATGGTTTGCAACAGAA
*
5244668 CATGGTTT-CGAACAGCA
1 CATGGTTTGC-AACAGAA
*
5244685 CATGGTTTGCAATAGAA
1 CATGGTTTGCAACAGAA
* *
5244702 CATGGTTTCGAAAACAGCA
1 CATGGTTT-G-CAACAGAA
* *
5244721 CATGGTTTGTAACAAAA
1 CATGGTTTGCAACAGAA
5244738 CATGGTTTGCAA
1 CATGGTTTGCAA
5244750 GTTGCAACAG
Statistics
Matches: 82, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
15 10 0.12
16 2 0.02
17 54 0.66
18 3 0.04
19 13 0.16
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (17 bp):
CATGGTTTGCAACAGAA
Found at i:5244688 original size:34 final size:35
Alignment explanation
Indices: 5244647--5244745 Score: 155
Period size: 34 Copynumber: 2.8 Consensus size: 35
5244637 ATGGTTTGCA
5244647 AGCACATGGTTTGCAACAGAACATGGTTTCG-AAC
1 AGCACATGGTTTGCAACAGAACATGGTTTCGAAAC
*
5244681 AGCACATGGTTTGCAATAGAACATGGTTTCGAAAAC
1 AGCACATGGTTTGCAACAGAACATGGTTTCG-AAAC
* *
5244717 AGCACATGGTTTGTAACAAAACATGGTTT
1 AGCACATGGTTTGCAACAGAACATGGTTT
5244746 GCAAGTTGCA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
34 30 0.51
36 29 0.49
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.26
Consensus pattern (35 bp):
AGCACATGGTTTGCAACAGAACATGGTTTCGAAAC
Found at i:5244726 original size:53 final size:50
Alignment explanation
Indices: 5244636--5244749 Score: 133
Period size: 53 Copynumber: 2.2 Consensus size: 50
5244626 AAACCCCTCC
* * **
5244636 CATGGTTTGC-AAGCACATGGTTTGCAACAGAACATGGTTTCG-AACAGCA
1 CATGGTTTGCAAAGAACATGGTTTGAAACAGAACATGGTTT-GTAACAAAA
*
5244685 CATGGTTTGCAATAGAACATGGTTTCGAAAACAGCACATGGTTTGTAACAAAA
1 CATGGTTTGCAA-AGAACATGGTTT-G-AAACAGAACATGGTTTGTAACAAAA
5244738 CATGGTTTGCAA
1 CATGGTTTGCAA
5244750 GTTGCAACAG
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
49 10 0.18
50 1 0.02
51 11 0.20
52 2 0.04
53 31 0.56
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (50 bp):
CATGGTTTGCAAAGAACATGGTTTGAAACAGAACATGGTTTGTAACAAAA
Found at i:5247097 original size:21 final size:23
Alignment explanation
Indices: 5247071--5247116 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
5247061 TGGTCGACGA
*
5247071 AGGGGC-TGGA-TTTTTAGAGAG
1 AGGGGCTTGGATTTTTTAGAAAG
*
5247092 AGGGGCTTTGATTTTTTAGAAAG
1 AGGGGCTTGGATTTTTTAGAAAG
5247115 AG
1 AG
5247117 AAGGGAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 3 0.14
23 12 0.57
ACGTcount: A:0.26, C:0.04, G:0.37, T:0.33
Consensus pattern (23 bp):
AGGGGCTTGGATTTTTTAGAAAG
Found at i:5247280 original size:19 final size:19
Alignment explanation
Indices: 5247253--5247302 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
5247243 GTATGTAAGT
* *
5247253 TTTTCTTTTTTTATTTTCC
1 TTTTATTTTTTTATTTTCA
* *
5247272 TTTTATTTTTTGATTTTGA
1 TTTTATTTTTTTATTTTCA
5247291 TTTTATTTTTTT
1 TTTTATTTTTTT
5247303 TGTTTAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.10, C:0.06, G:0.04, T:0.80
Consensus pattern (19 bp):
TTTTATTTTTTTATTTTCA
Found at i:5247797 original size:6 final size:7
Alignment explanation
Indices: 5247778--5247804 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5247768 TATTAAAACC
5247778 ATAAAAA
1 ATAAAAA
5247785 ATAAAAA
1 ATAAAAA
5247792 ATAAAAA
1 ATAAAAA
5247799 ATAAAA
1 ATAAAA
5247805 GTGTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
ATAAAAA
Found at i:5248204 original size:51 final size:51
Alignment explanation
Indices: 5248089--5248218 Score: 140
Period size: 51 Copynumber: 2.6 Consensus size: 51
5248079 ACAGAAAGTT
* * *
5248089 GAGATGATTCTAAAATCTATTTAA-AATTTTTAAGATTTCGTAAAAGAGTC
1 GAGATGATTCTAAAATTTATTTAATAAATTTTAAGACTTCGTAAAAGAGTC
* * *
5248139 GGGATAATTCTAAAATTTATTTAATAAATTTTAAGAACTT-GTCAAAGAGTC
1 GAGATGATTCTAAAATTTATTTAATAAATTTTAAG-ACTTCGTAAAAGAGTC
* * *
5248190 GAGATGCTTTTAAAA-TCATTTTAATAAAT
1 GAGATGATTCTAAAATTTA-TTTAATAAAT
5248219 AAATAAATAA
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
50 23 0.35
51 40 0.61
52 3 0.05
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (51 bp):
GAGATGATTCTAAAATTTATTTAATAAATTTTAAGACTTCGTAAAAGAGTC
Found at i:5251814 original size:33 final size:32
Alignment explanation
Indices: 5251743--5251808 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
5251733 TACGCATGAG
*
5251743 CAAATGATTAGGTTTCAACAAAAGCTGATAAAA
1 CAAATGATTAGGTTTCAACAAAAACTGA-AAAA
*
5251776 CAAATGATTAGGTTTCAAGAAGAAACTCGAAAA
1 CAAATGATTAGGTTTCAACAA-AAACT-GAAAA
5251809 GAAATGGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 20 0.69
34 7 0.24
35 2 0.07
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.23
Consensus pattern (32 bp):
CAAATGATTAGGTTTCAACAAAAACTGAAAAA
Found at i:5260403 original size:40 final size:40
Alignment explanation
Indices: 5260314--5260563 Score: 213
Period size: 40 Copynumber: 6.2 Consensus size: 40
5260304 TTCTCTCAGA
* * * *
5260314 TTTTTAATTTAAAATTTCATAGCCTCTGGT--TAGAAGAGC
1 TTTTAAATTTAAAGTTTCGTAGCCTCTGGTCAGAGAAGA-C
*
5260353 TTTTAAAATTTAAAGTTTCGTTA-CCTTTGGTCAGAGAAGAC
1 TTTT-AAATTTAAAGTTTCG-TAGCCTCTGGTCAGAGAAGAC
* * *
5260394 TTTTGAATTTAAAGTTTTGTAGCCTCTGGTCAGAGCA-AC
1 TTTTAAATTTAAAGTTTCGTAGCCTCTGGTCAGAGAAGAC
* ** *
5260433 TTTTTAAATTTAAAGTTTCATAGCCTCTAATCAGAGAAGTC
1 -TTTTAAATTTAAAGTTTCGTAGCCTCTGGTCAGAGAAGAC
* ** * * **
5260474 TTTTAAATTTAAAGTTTCATAGTTTCTAGTCAAATG-AGTT
1 TTTTAAATTTAAAGTTTCGTAGCCTCTGGTCAGA-GAAGAC
* * * *
5260514 TTTTAAATTTAAAGTTTCATAGCCTCTGGTTAGAGGAGTC
1 TTTTAAATTTAAAGTTTCGTAGCCTCTGGTCAGAGAAGAC
5260554 TTTTAAATTT
1 TTTTAAATTT
5260564 TTAGGAGTTA
Statistics
Matches: 175, Mismatches: 27, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
39 9 0.05
40 151 0.86
41 9 0.05
42 6 0.03
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (40 bp):
TTTTAAATTTAAAGTTTCGTAGCCTCTGGTCAGAGAAGAC
Found at i:5260442 original size:80 final size:80
Alignment explanation
Indices: 5260314--5260563 Score: 236
Period size: 80 Copynumber: 3.1 Consensus size: 80
5260304 TTCTCTCAGA
* * * * *
5260314 TTTTTAATTTAAAATTTCATAGCCTCTGGTTAGAAGAGCTTTTAAAATTTAAAGTTTCGTTA-CC
1 TTTTAAATTTAAAGTTTCATAGCCTCTGGTCAGAAGAACTTTTAAAATTTAAAGTTTC-ATAGCC
* **
5260378 TTTGGTCAGAGAAGAC
65 TCTAATCAGAGAAGAC
* ** *
5260394 TTTTGAATTTAAAGTTTTGTAGCCTCTGGTCAG-AGCAACTTTTTAAATTTAAAGTTTCATAGCC
1 TTTTAAATTTAAAGTTTCATAGCCTCTGGTCAGAAG-AACTTTTAAAATTTAAAGTTTCATAGCC
*
5260458 TCTAATCAGAGAAGTC
65 TCTAATCAGAGAAGAC
** * ** *
5260474 TTTTAAATTTAAAGTTTCATAGTTTCTAGTCA-AATGAGTTTTTTAAATTTAAAGTTTCATAGCC
1 TTTTAAATTTAAAGTTTCATAGCCTCTGGTCAGAA-GAACTTTTAAAATTTAAAGTTTCATAGCC
** * * *
5260538 TCTGGTTAGAGGAGTC
65 TCTAATCAGAGAAGAC
5260554 TTTTAAATTT
1 TTTTAAATTT
5260564 TTAGGAGTTA
Statistics
Matches: 142, Mismatches: 24, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
79 4 0.03
80 137 0.96
81 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (80 bp):
TTTTAAATTTAAAGTTTCATAGCCTCTGGTCAGAAGAACTTTTAAAATTTAAAGTTTCATAGCCT
CTAATCAGAGAAGAC
Found at i:5260620 original size:83 final size:83
Alignment explanation
Indices: 5260513--5260732 Score: 354
Period size: 83 Copynumber: 2.6 Consensus size: 83
5260503 TCAAATGAGT
* *
5260513 TTTTTAAATTTAAAGTTTCATAGCCTCTGGTTAGAGGAGTCTTTTAAATTTTTAGGAGTTATTGA
1 TTTTAAAATTTAAAGTTTCATAGCCTCTGGTTAGAGGAGTCTTTTAAATTTTCAGGAGTTATTGA
5260578 ACCTTTATTTAGCGAAGC
66 ACCTTTATTTAGCGAAGC
5260596 TTTTAAAATTTAAAGTTTCATAGCCTCTGGTTAGAGGAGTCTTTTAAATTTTCAGGAGTTATTGA
1 TTTTAAAATTTAAAGTTTCATAGCCTCTGGTTAGAGGAGTCTTTTAAATTTTCAGGAGTTATTGA
5260661 ACCTTTATTTAGCGAAGC
66 ACCTTTATTTAGCGAAGC
* *
5260679 TTTTAAAATTTCAAAAGTTGTCA-AGCCTCTGCTTAGAGGAG-CTTTCCAAATTTT
1 TTTTAAAATTT--AAAGTT-TCATAGCCTCTGGTTAGAGGAGTCTTT-TAAATTTT
5260733 AAAAAAACAA
Statistics
Matches: 129, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
83 92 0.71
84 4 0.03
85 30 0.23
86 3 0.02
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (83 bp):
TTTTAAAATTTAAAGTTTCATAGCCTCTGGTTAGAGGAGTCTTTTAAATTTTCAGGAGTTATTGA
ACCTTTATTTAGCGAAGC
Found at i:5260684 original size:42 final size:42
Alignment explanation
Indices: 5260553--5260691 Score: 133
Period size: 42 Copynumber: 3.3 Consensus size: 42
5260543 TTAGAGGAGT
* *
5260553 CTTTTAAATTTTTAGGAGTTATTGAACCTTTATTTAGCGAAG
1 CTTTTAAAATTTCAGGAGTTATTGAACCTTTATTTAGCGAAG
* * * ** * *
5260595 CTTTTAAAATTT-A-AAGTT-TCAT-AGCCTCTGGTTAGAGGAG
1 CTTTTAAAATTTCAGGAGTTAT--TGAACCTTTATTTAGCGAAG
*
5260635 TCTTTTAAATTTTCAGGAGTTATTGAACCTTTATTTAGCGAAG
1 -CTTTTAAAATTTCAGGAGTTATTGAACCTTTATTTAGCGAAG
5260678 CTTTTAAAATTTCA
1 CTTTTAAAATTTCA
5260692 AAAGTTGTCA
Statistics
Matches: 73, Mismatches: 17, Indels: 14
0.70 0.16 0.13
Matches are distributed among these distances:
39 1 0.01
40 16 0.22
41 13 0.18
42 26 0.36
43 16 0.22
44 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (42 bp):
CTTTTAAAATTTCAGGAGTTATTGAACCTTTATTTAGCGAAG
Found at i:5260722 original size:42 final size:41
Alignment explanation
Indices: 5260593--5260723 Score: 106
Period size: 42 Copynumber: 3.1 Consensus size: 41
5260583 TATTTAGCGA
*
5260593 AGCTTTTAAAATTT--AAAGTTTCATAGCCTCTGGTTAGAGG
1 AGCTTTTAAAATTTCAAAAGTTTCA-AGCCTCTGCTTAGAGG
* ** * * ** * *
5260633 AGTCTTTTAAATTTTCAGGAGTTATTGAA-CCTTTATTTAGCGA
1 AG-CTTTTAAAATTTCAAAAG-T-TTCAAGCCTCTGCTTAGAGG
5260676 AGCTTTTAAAATTTCAAAAGTTGTCAAGCCTCTGCTTAGAGG
1 AGCTTTTAAAATTTCAAAAGTT-TCAAGCCTCTGCTTAGAGG
5260718 AGCTTT
1 AGCTTT
5260724 CCAAATTTTA
Statistics
Matches: 66, Mismatches: 18, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
40 3 0.05
41 15 0.23
42 30 0.45
43 13 0.20
44 2 0.03
45 3 0.05
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (41 bp):
AGCTTTTAAAATTTCAAAAGTTTCAAGCCTCTGCTTAGAGG
Found at i:5261757 original size:8 final size:8
Alignment explanation
Indices: 5261746--5261835 Score: 134
Period size: 8 Copynumber: 11.5 Consensus size: 8
5261736 TTCCATTTTA
5261746 TTTTGATT
1 TTTTGATT
5261754 TTTTGATT
1 TTTTGATT
5261762 TTTTGATT
1 TTTTGATT
5261770 TTTTGATT
1 TTTTGATT
5261778 TTTTGATT
1 TTTTGATT
5261786 TTTTGATT
1 TTTTGATT
5261794 TTTTGA--
1 TTTTGATT
5261800 TTTTGATT
1 TTTTGATT
5261808 TGATTTGATT
1 T--TTTGATT
5261818 TTTT-A-T
1 TTTTGATT
5261824 TTTTGATT
1 TTTTGATT
5261832 TTTT
1 TTTT
5261836 TTTTACAATT
Statistics
Matches: 76, Mismatches: 0, Indels: 12
0.86 0.00 0.14
Matches are distributed among these distances:
6 11 0.14
7 2 0.03
8 55 0.72
10 8 0.11
ACGTcount: A:0.13, C:0.00, G:0.12, T:0.74
Consensus pattern (8 bp):
TTTTGATT
Found at i:5266969 original size:16 final size:15
Alignment explanation
Indices: 5266948--5266977 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5266938 AAAATAAAAG
5266948 TTTAAATATAATTTAA
1 TTTAAATAT-ATTTAA
5266964 TTTAAATATATTTA
1 TTTAAATATATTTA
5266978 TTATTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAAATATATTTAA
Found at i:5267106 original size:15 final size:15
Alignment explanation
Indices: 5267088--5267124 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
5267078 AATAAAATAA
*
5267088 TTTAATTAATTTAAT
1 TTTAAATAATTTAAT
5267103 TTTAAATAATTTAAT
1 TTTAAATAATTTAAT
*
5267118 TTAAAAT
1 TTTAAAT
5267125 TAATCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTAAATAATTTAAT
Found at i:5267136 original size:20 final size:20
Alignment explanation
Indices: 5267091--5267137 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
5267081 AAAATAATTT
**
5267091 AATTAATTTAATTTTAAATA
1 AATTAATTTAAAATTAAATA
*
5267111 ATTTAATTTAAAATT-AATCA
1 AATTAATTTAAAATTAAAT-A
5267131 AATTAAT
1 AATTAAT
5267138 CGAATAAACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTAATTTAAAATTAAATA
Found at i:5268846 original size:34 final size:33
Alignment explanation
Indices: 5268780--5268850 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 33
5268770 TTTTTATCAT
**
5268780 AAAATGCCGTTAAATTTAGCGGCATTTATAGTA
1 AAAATGCCACTAAATTTAGCGGCATTTATAGTA
* ** *
5268813 GAAAATGCCACTAAATTTAGTGGTGTTTGTAGTA
1 -AAAATGCCACTAAATTTAGCGGCATTTATAGTA
5268847 AAAA
1 AAAA
5268851 GAGCTATTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
33 4 0.13
34 27 0.87
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (33 bp):
AAAATGCCACTAAATTTAGCGGCATTTATAGTA
Found at i:5270089 original size:34 final size:34
Alignment explanation
Indices: 5270051--5270121 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
5270041 AGCAGAAACA
* *
5270051 TAACAAATCCA-ATAGAAAGTTTAGGGATTTGACC
1 TAACAAAT-CAGATAAAAAGTTTAAGGATTTGACC
5270085 TAACAAATCAGATAAAAAGTTTAAGGATTTGACC
1 TAACAAATCAGATAAAAAGTTTAAGGATTTGACC
5270119 TAA
1 TAA
5270122 AATGCAAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 2 0.06
34 32 0.94
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (34 bp):
TAACAAATCAGATAAAAAGTTTAAGGATTTGACC
Found at i:5270423 original size:58 final size:60
Alignment explanation
Indices: 5270326--5270442 Score: 143
Period size: 59 Copynumber: 2.0 Consensus size: 60
5270316 AAGAAAGTGT
* * * *
5270326 GATTATTTAAAGCGTTTTTGGCTAAAAATATCTTCAATAA-TCCCTTCC-ATTTTTTTTAA
1 GATTATTTAAAGCGTTTCTAGCTAAAAATACCTTAAATAATTCCC-TCCAATTTTTTTTAA
*
5270385 GATTA-TTAAACGCGTTTCTAGC-AAAAATGCCTTAAATAATTCCCTCCAATTTTTTTTA
1 GATTATTTAAA-GCGTTTCTAGCTAAAAATACCTTAAATAATTCCCTCCAATTTTTTTTA
5270443 TTTTTTTAGG
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
58 22 0.44
59 28 0.56
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.43
Consensus pattern (60 bp):
GATTATTTAAAGCGTTTCTAGCTAAAAATACCTTAAATAATTCCCTCCAATTTTTTTTAA
Found at i:5270600 original size:59 final size:60
Alignment explanation
Indices: 5270515--5270680 Score: 157
Period size: 59 Copynumber: 2.8 Consensus size: 60
5270505 GAATTGAATG
**
5270515 AGGTTATTCAAGGC-ACTTCTAGCCAAAAATGCCTTGAATAATCCTCTTC-CATTTTTTTA
1 AGGTTATTCAAGGCGTTTTCTAGCCAAAAAT-CCTTGAATAATCCTCTTCTCATTTTTTTA
* * *
5270574 AGGTTATTCAAGGCGTTTTCTA-CCAAAACA-CCTTTAATAATCC-ATTCTCATTTTTTTT
1 AGGTTATTCAAGGCGTTTTCTAGCCAAAA-ATCCTTGAATAATCCTCTTCTCATTTTTTTA
* * * *
5270632 GGGATTATTCAAAGTGTTTT-TAGTCAGAAAATACCTTGAATAA-CCTCTT
1 AGG-TTATTCAAGGCGTTTTCTAGCCA-AAAAT-CCTTGAATAATCCTCTT
5270681 ACAAAAAATT
Statistics
Matches: 87, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
57 3 0.03
58 25 0.29
59 37 0.43
60 11 0.13
61 11 0.13
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (60 bp):
AGGTTATTCAAGGCGTTTTCTAGCCAAAAATCCTTGAATAATCCTCTTCTCATTTTTTTA
Found at i:5270788 original size:65 final size:62
Alignment explanation
Indices: 5270632--5270791 Score: 155
Period size: 65 Copynumber: 2.5 Consensus size: 62
5270622 CATTTTTTTT
* * *
5270632 GGGATTATTCAAAGTGTTTTTAGTCAGAAAATACCTTGAATAACCTCTTACAAAAAATTGAAT
1 GGGATTATTCAAGGTGTTTTTAGTCA-AAAACACCTTGAATAACCTCTTACAAAAAATTGAAG
** * * *
5270695 GAAATTATTCAAGATGTTTTT-GACCAAAAACACCTTGAATAATCC-CTTTCAATTAAAAATT-A
1 GGGATTATTCAAGGTGTTTTTAG-TCAAAAACACCTTGAATAA-CCTCTTAC-A--AAAAATTGA
5270757 GAG
61 -AG
*
5270760 GGGATTATTCAAGGTATTTTTAGTCAAAAACA
1 GGGATTATTCAAGGTGTTTTTAGTCAAAAACA
5270792 TTTTTAATAA
Statistics
Matches: 77, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
62 20 0.26
63 22 0.29
64 1 0.01
65 33 0.43
66 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (62 bp):
GGGATTATTCAAGGTGTTTTTAGTCAAAAACACCTTGAATAACCTCTTACAAAAAATTGAAG
Found at i:5270905 original size:149 final size:148
Alignment explanation
Indices: 5270667--5270938 Score: 325
Period size: 149 Copynumber: 1.8 Consensus size: 148
5270657 AGAAAATACC
* *
5270667 TTGAATAACCTCTTACAAAAAATTGAATGAAATTATTCAAGATGTTTTTGACCAAAAACACCTTG
1 TTGAATAACCTCTTACAAAAAATTGAATGAAATTATTCAAGA-GTTTTTGACAAAAAACACCTTC
** *
5270732 AATAATCCCTTTCAATTAAAAATTAGAGGGGATTATTCAAGGTATTTTTAGTCAAAAACATTTTT
65 AATAATCCCTTTCAATTAAAAATTAGAGAAGATTATTCAAGGCATTTTTAGTCAAAAACATTTTT
5270797 AATAATCTCCTCTAATTTT
130 AATAATCTCCTCTAATTTT
** * *
5270816 TTGAATAATCC-CTTACAAAAAATTGAATTG-GGTTATTCAATGCA-TTTTTGACAAAAAATACT
1 TTGAATAA-CCTCTTACAAAAAATTGAA-TGAAATTATTCAA-G-AGTTTTTGACAAAAAACACC
* * *** * * *
5270878 TTCAATAATCTCTTTTAATTTTTAATTAGATAAGATTATTCAAGGCGTTTTTGGTCAAAAA
62 TTCAATAATCCCTTTCAATTAAAAATTAGAGAAGATTATTCAAGGCATTTTTAGTCAAAAA
5270939 GGTCATCAAT
Statistics
Matches: 102, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
149 96 0.94
150 5 0.05
151 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (148 bp):
TTGAATAACCTCTTACAAAAAATTGAATGAAATTATTCAAGAGTTTTTGACAAAAAACACCTTCA
ATAATCCCTTTCAATTAAAAATTAGAGAAGATTATTCAAGGCATTTTTAGTCAAAAACATTTTTA
ATAATCTCCTCTAATTTT
Found at i:5271763 original size:13 final size:14
Alignment explanation
Indices: 5271745--5271773 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5271735 GCATTTGTTT
5271745 AAAAAC-GCCATTA
1 AAAAACAGCCATTA
5271758 AAAAACAGCCATTA
1 AAAAACAGCCATTA
5271772 AA
1 AA
5271774 TCTCCATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.59, C:0.21, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAAACAGCCATTA
Found at i:5282623 original size:14 final size:15
Alignment explanation
Indices: 5282604--5282632 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5282594 TACCCAAAAT
5282604 TTTTA-TTTTTATTA
1 TTTTATTTTTTATTA
5282618 TTTTATTTTTTATTA
1 TTTTATTTTTTATTA
5282633 AATTAAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTATTTTTTATTA
Found at i:5283469 original size:3 final size:3
Alignment explanation
Indices: 5283461--5283513 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
5283451 AAATCAATCA
*
5283461 AAT AAT AAT AAT AAT AA- AAT AAAT AAT AAT -AT AAT AGT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT -AAT AAT
*
5283506 AAA AAT AA
1 AAT AAT AA
5283514 ATAAGAAACA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 4 0.10
3 33 0.79
4 5 0.12
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:5283477 original size:26 final size:23
Alignment explanation
Indices: 5283461--5283517 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
5283451 AAATCAATCA
5283461 AATAATAATAATAATAAAATAAAT
1 AATAAT-ATAATAATAAAATAAAT
*
5283485 AATAATATAATAGT-AAAT-AAT
1 AATAATATAATAATAAAATAAAT
*
5283506 AAAAATA-AATAA
1 AATAATATAATAA
5283518 GAAACAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 4 0.13
21 9 0.30
22 4 0.13
23 7 0.23
24 6 0.20
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AATAATATAATAATAAAATAAAT
Found at i:5283487 original size:18 final size:18
Alignment explanation
Indices: 5283460--5283514 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
5283450 AAAATCAATC
5283460 AAAT-AATAATAATAATA
1 AAATAAATAATAATAATA
5283477 AAATAAATAATAAT-ATA
1 AAATAAATAATAATAATA
* *
5283494 ATAGTAAATAATAAAAATA
1 A-AATAAATAATAATAATA
5283513 AA
1 AA
5283515 TAAGAAACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
17 8 0.24
18 21 0.64
19 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
AAATAAATAATAATAATA
Found at i:5283540 original size:18 final size:20
Alignment explanation
Indices: 5283506--5283553 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
5283496 AGTAAATAAT
5283506 AAAAATAAATAAGAAACAAA
1 AAAAATAAATAAGAAACAAA
5283526 AAAAATAAA-AA-AAACAAA
1 AAAAATAAATAAGAAACAAA
5283544 ATAAAA-AAAT
1 A-AAAATAAAT
5283554 GAGCCCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 11 0.42
19 6 0.23
20 9 0.35
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.10
Consensus pattern (20 bp):
AAAAATAAATAAGAAACAAA
Found at i:5283551 original size:16 final size:17
Alignment explanation
Indices: 5283506--5283552 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
5283496 AGTAAATAAT
* *
5283506 AAAAATAAATAAGAAAC
1 AAAAATAAAAAAAAAAC
*
5283523 AAAAAAAATAAAAAAAAC
1 AAAAATAA-AAAAAAAAC
5283541 -AAAATAAAAAAA
1 AAAAATAAAAAAA
5283553 TGAGCCCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 5 0.20
17 13 0.52
18 7 0.28
ACGTcount: A:0.85, C:0.04, G:0.02, T:0.09
Consensus pattern (17 bp):
AAAAATAAAAAAAAAAC
Found at i:5283802 original size:45 final size:44
Alignment explanation
Indices: 5283736--5283901 Score: 122
Period size: 44 Copynumber: 3.8 Consensus size: 44
5283726 AATCTTGATC
* * * *
5283736 AAAGCTCCTCTAATCAGAGGCTCAATGACTTTTAAAAAAATAAA
1 AAAGCTCATCTAAACAAAGGCTCAACGACTTTTAAAAAAATAAA
* * * * **
5283780 CAAGCCTCATCTAAATAAAGGCTTAACAAC-TTTGGAAAAATAAA
1 AAAG-CTCATCTAAACAAAGGCTCAACGACTTTTAAAAAAATAAA
* * * * *
5283824 TAAGGCTCTTCTAAACATAGGCTCGATGA-TTTTGAAAAAAA-AAA
1 -AAAGCTCATCTAAACAAAGGCTCAACGACTTTT-AAAAAAATAAA
* *
5283868 TAAAGCTCATCTAAACAGAGGCTTAACGACTTTT
1 -AAAGCTCATCTAAACAAAGGCTCAACGACTTTT
5283902 GGAAAGTAAA
Statistics
Matches: 90, Mismatches: 27, Indels: 9
0.71 0.21 0.07
Matches are distributed among these distances:
44 61 0.68
45 29 0.32
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (44 bp):
AAAGCTCATCTAAACAAAGGCTCAACGACTTTTAAAAAAATAAA
Found at i:5283837 original size:44 final size:44
Alignment explanation
Indices: 5283771--5283906 Score: 137
Period size: 44 Copynumber: 3.1 Consensus size: 44
5283761 TGACTTTTAA
* * * *
5283771 AAAAATAAACAAGCCTCATCTAAATAAAGGCTTAACAACTTTGG
1 AAAAATAAATAAGGCTCATCTAAACAAAGGCTTAACGACTTTGG
* * ** * * *
5283815 AAAAATAAATAAGGCTCTTCTAAACATAGGCTCGATGATTTTGA
1 AAAAATAAATAAGGCTCATCTAAACAAAGGCTTAACGACTTTGG
* * *
5283859 AAAAAAAAATAAAGCTCATCTAAACAGAGGCTTAACGACTTTTGG
1 AAAAATAAATAAGGCTCATCTAAACAAAGGCTTAACGAC-TTTGG
5283904 AAA
1 AAA
5283907 GTAAATTCCT
Statistics
Matches: 71, Mismatches: 20, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
44 64 0.90
45 7 0.10
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.24
Consensus pattern (44 bp):
AAAAATAAATAAGGCTCATCTAAACAAAGGCTTAACGACTTTGG
Found at i:5283894 original size:88 final size:90
Alignment explanation
Indices: 5283739--5283906 Score: 218
Period size: 89 Copynumber: 1.9 Consensus size: 90
5283729 CTTGATCAAA
* * *
5283739 GCTCCTCTAATCAGAGGCTCAATGACTTTTAAAAAAATAAACAAGCCTCATCTAAATAAAGGCTT
1 GCTCCTCTAAACAGAGGCTCAATGACTTTTAAAAAAATAAAAAAGCCTCATCTAAACAAAGGCTT
5283804 AACAAC-TTTGGAAAAATAAATAAG
66 AACAACTTTTGGAAAAATAAATAAG
* * * *
5283828 GCTCTTCTAAACATAGGCTCGATGA-TTTTGAAAAAAA-AAATAAAG-CTCATCTAAACAGAGGC
1 GCTCCTCTAAACAGAGGCTCAATGACTTTT-AAAAAAATAAA-AAAGCCTCATCTAAACAAAGGC
*
5283890 TTAACGACTTTTGGAAA
64 TTAACAACTTTTGGAAA
5283907 GTAAATTCCT
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
88 29 0.43
89 39 0.57
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (90 bp):
GCTCCTCTAAACAGAGGCTCAATGACTTTTAAAAAAATAAAAAAGCCTCATCTAAACAAAGGCTT
AACAACTTTTGGAAAAATAAATAAG
Found at i:5283990 original size:44 final size:43
Alignment explanation
Indices: 5283937--5284057 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 43
5283927 GAGGCACCAC
* * *
5283937 AACAGAGGCAACCATGACTTTGGAAAAAATAAATTGCTCTTTTA
1 AACAGAGGCAACCACGACTTT-GAAAAAATAAATTGCTCCTCTA
* * * *
5283981 AACAAAGGCAATCGCGACTTTTAAAAAAATAAATTGCTCCTCTA
1 AACAGAGGCAACCACGAC-TTTGAAAAAATAAATTGCTCCTCTA
*
5284025 AATAGAGGCAACCACGACTTTGAAAAAATAAAT
1 AACAGAGGCAACCACGACTTTGAAAAAATAAAT
5284058 AAAGCTCTTT
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
43 14 0.22
44 47 0.73
45 3 0.05
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (43 bp):
AACAGAGGCAACCACGACTTTGAAAAAATAAATTGCTCCTCTA
Found at i:5285778 original size:19 final size:19
Alignment explanation
Indices: 5285756--5285793 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5285746 CATTTTCTCT
5285756 CATTTTCAT-ATTTTTTTTC
1 CATTTT-ATCATTTTTTTTC
*
5285775 CATTTTTTCATTTTTTTTC
1 CATTTTATCATTTTTTTTC
5285794 TTTTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (19 bp):
CATTTTATCATTTTTTTTC
Found at i:5285788 original size:18 final size:17
Alignment explanation
Indices: 5285767--5285809 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
5285757 ATTTTCATAT
5285767 TTTTTTTCCATTTTTTC
1 TTTTTTTCCATTTTTTC
* *
5285784 ATTTTTTTTCTTTTTTTC
1 -TTTTTTTCCATTTTTTC
5285802 TTTTTTTC
1 TTTTTTTC
5285810 TTTTTCATCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTTCCATTTTTTC
Found at i:5285797 original size:7 final size:8
Alignment explanation
Indices: 5285767--5285814 Score: 60
Period size: 8 Copynumber: 5.6 Consensus size: 8
5285757 ATTTTCATAT
5285767 TTTTTTTCC
1 TTTTTTT-C
*
5285776 ATTTTTTC
1 TTTTTTTC
5285784 ATTTTTTTTC
1 --TTTTTTTC
5285794 TTTTTTTC
1 TTTTTTTC
5285802 TTTTTTTC
1 TTTTTTTC
5285810 TTTTT
1 TTTTT
5285815 CATCCATTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
8 22 0.63
9 6 0.17
10 7 0.20
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:5290813 original size:17 final size:17
Alignment explanation
Indices: 5290786--5290834 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 17
5290776 TAATGTGAAC
5290786 ATGAGAATGATGCATATG
1 ATGA-AATGATGCATATG
5290804 ATGAAATGATG-ATATG
1 ATGAAATGATGCATATG
*
5290820 --GAAATGTTGCATATG
1 ATGAAATGATGCATATG
5290835 CATAGAATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 8 0.28
15 5 0.17
16 5 0.17
17 7 0.24
18 4 0.14
ACGTcount: A:0.39, C:0.04, G:0.27, T:0.31
Consensus pattern (17 bp):
ATGAAATGATGCATATG
Found at i:5290825 original size:14 final size:16
Alignment explanation
Indices: 5290786--5290834 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
5290776 TAATGTGAAC
5290786 ATGAG-AATGATGCAT
1 ATGAGAAATGATGCAT
5290801 ATGATGAAATGATG-AT
1 ATGA-GAAATGATGCAT
*
5290817 ATG-GAAATGTTGCAT
1 ATGAGAAATGATGCAT
5290832 ATG
1 ATG
5290835 CATAGAATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 8 0.27
15 9 0.30
16 6 0.20
17 7 0.23
ACGTcount: A:0.39, C:0.04, G:0.27, T:0.31
Consensus pattern (16 bp):
ATGAGAAATGATGCAT
Found at i:5292333 original size:16 final size:17
Alignment explanation
Indices: 5292307--5292338 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5292297 TAATTCTAAA
5292307 ATTTTTATATTTTTTTC
1 ATTTTTATATTTTTTTC
5292324 ATTTTT-TATTTTTTT
1 ATTTTTATATTTTTTT
5292339 GTTTGAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (17 bp):
ATTTTTATATTTTTTTC
Found at i:5292519 original size:15 final size:15
Alignment explanation
Indices: 5292503--5292531 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5292493 TTCTTAAAAT
5292503 TTTTATT-TTTATTA
1 TTTTATTATTTATTA
5292517 TTTTATTATTTATTA
1 TTTTATTATTTATTA
5292532 AATTAAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATTATTTATTA
Found at i:5292862 original size:19 final size:19
Alignment explanation
Indices: 5292840--5292877 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5292830 TCCTTCAGAT
*
5292840 TTTTCTTCCTTCTTCTCTC
1 TTTTCTCCCTTCTTCTCTC
*
5292859 TTTTCTCCCTTTTTCTCTC
1 TTTTCTCCCTTCTTCTCTC
5292878 CTCTTTCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTCTCCCTTCTTCTCTC
Found at i:5293366 original size:12 final size:12
Alignment explanation
Indices: 5293349--5293373 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5293339 ATCAAAAAAT
5293349 AATAATAATATA
1 AATAATAATATA
5293361 AATAATAATATA
1 AATAATAATATA
5293373 A
1 A
5293374 TACTGAATGG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATAATAATATA
Found at i:5293411 original size:11 final size:12
Alignment explanation
Indices: 5293349--5293417 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 12
5293339 ATCAAAAAAT
*
5293349 AATAATAATATA
1 AATAATAATAAA
*
5293361 AATAATAAT-AT
1 AATAATAATAAA
*
5293372 AATACTGAATGGAAAA
1 AATAAT-AAT---AAA
5293388 AATAAATAATAAA
1 AAT-AATAATAAA
5293401 AATAA-AATAAA
1 AATAATAATAAA
5293412 AATAAT
1 AATAAT
5293418 TTTAAAAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
11 16 0.36
12 14 0.31
13 6 0.13
16 7 0.16
17 2 0.04
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.26
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:5297950 original size:201 final size:200
Alignment explanation
Indices: 5297600--5298295 Score: 792
Period size: 207 Copynumber: 3.4 Consensus size: 200
5297590 TTCAATTCTA
* * * * *
5297600 AAAAAATTAGCATTAAATT-CATTCCGCACAAGTACAAAAAATTCTCCAAAGTCGCACCTAAATT
1 AAAAAATTAGCTTTAAATTCCA-TCCACATAAGTAC-AAAAATTCTCCAAAGTCACACCTAAACT
* * * * * *
5297664 CAGTTGATAGATTAGTTC-TTTTGAAATTTATGATTTTGACCTATTTATGGTTTTTGGATCAGTT
64 CAATTGACAGATTAGTTCTTTTTGAAATTCATGGTTTTGACTTCTTTATGGTTTTTGGATCAGTT
* * * *
5297728 CTTGATGAATTCTAACTTGTTTTGAGCCAAAAGTTTTATGTTAGATTCTTAACTCATATATCTTT
129 CTTGATGAATTCTAGCTTGTTTTGAGCCAAAATTTTTTTGTTAGATTCTTAACTCATAGATCTTT
5297793 AATCTTG
194 AATCTTG
* *
5297800 AAAAAATTAGCTTCAAATTCCATCCACATAAGTACATAAAATTTTCCAGAA-TCACACCTAAACT
1 AAAAAATTAGCTTTAAATTCCATCCACATAAGTACA-AAAATTCTCCA-AAGTCACACCTAAACT
* * * *
5297864 TATTTGATAGATTAGTTCTTTTTGAAATTCATGGTTTTGACTTCTTTGTGGTTTTTGGATCAGTT
64 CAATTGACAGATTAGTTCTTTTTGAAATTCATGGTTTTGACTTCTTTATGGTTTTTGGATCAGTT
*
5297929 CTTGATGAATTCTAGCTTGTTTTGAGCAAAAAAAAATTTTTTTTGTTAGATTCTTAACTCATAGA
129 CTTGATGAATTCTAGCTTGTTTTGAGC----CAAAA-TTTTTTTGTTAGATTCTTAACTCATAGA
**
5297994 TCTTTAATTCTAA
189 TCTTTAA-TCTTG
* * ** *
5298007 AAAAAATTAGCTTTAAATTCCATCCACATAAGTAC-AAAATTCTTTTCAAAATCATGCTTAAACT
1 AAAAAATTAGCTTTAAATTCCATCCACATAAGTACAAAAATTC--TCCAAAGTCACACCTAAACT
* * *
5298071 CAATTGACAGATTAGTTCCTTTTGAAATTCATAGTTTTGACTTCTTTATGGTTTTTTGGATTAGT
64 CAATTGACAGATTAGTTCTTTTTGAAATTCATGGTTTTGACTTCTTTATGG-TTTTTGGATCAGT
* * * * * *
5298136 TTTTAATGAATTCTAGCTTGTTTTGAGCCAAAAATTTTTTTGTTAGAATCCTAACTTATAGATAT
128 TCTTGATGAATTCTAGCTTGTTTTGAGCC-AAAATTTTTTTGTTAGATTCTTAACTCATAGATCT
5298201 TTAAT-TATG
192 TTAATCT-TG
* * * * *
5298210 AAAAAAAATTAGCTTTAAATTGCAT-AAAAAAAGTATAGAAAATTCTCCAAAGTCACACCTAAAC
1 --AAAAAATTAGCTTTAAATTCCATCCACATAAGTACA-AAAATTCTCCAAAGTCACACCTAAAC
*
5298274 TCAATTGACAAATTAGTTCTTT
63 TCAATTGACAGATTAGTTCTTT
5298296 GCATGAGTGA
Statistics
Matches: 421, Mismatches: 55, Indels: 36
0.82 0.11 0.07
Matches are distributed among these distances:
199 1 0.00
200 65 0.15
201 71 0.17
202 1 0.00
203 1 0.00
204 72 0.17
205 36 0.09
206 41 0.10
207 95 0.23
208 38 0.09
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (200 bp):
AAAAAATTAGCTTTAAATTCCATCCACATAAGTACAAAAATTCTCCAAAGTCACACCTAAACTCA
ATTGACAGATTAGTTCTTTTTGAAATTCATGGTTTTGACTTCTTTATGGTTTTTGGATCAGTTCT
TGATGAATTCTAGCTTGTTTTGAGCCAAAATTTTTTTGTTAGATTCTTAACTCATAGATCTTTAA
TCTTG
Done.