Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008504.1 Hibiscus syriacus cultivar Beakdansim tig00111356_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2056749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 10
Found at i:947401 original size:22 final size:22
Alignment explanation
Indices: 947391--947435 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 22
947381 TTAAAAAATG
947391 AATAATAATAATAATAATAATA
1 AATAATAATAATAATAATAATA
947413 AATAATAATAAATAATAATAATA
1 AATAATAAT-AATAATAATAATA
947436 TATATATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AATAATAATAATAATAATAATA
Found at i:947418 original size:10 final size:10
Alignment explanation
Indices: 947394--947433 Score: 73
Period size: 10 Copynumber: 4.1 Consensus size: 10
947384 AAAAATGAAT
947394 AATAATAAT-
1 AATAATAATA
947403 AATAATAATA
1 AATAATAATA
947413 AATAATAATA
1 AATAATAATA
947423 AATAATAATA
1 AATAATAATA
947433 A
1 A
947434 TATATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 9 0.30
10 21 0.70
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
AATAATAATA
Found at i:947505 original size:38 final size:35
Alignment explanation
Indices: 947458--947710 Score: 169
Period size: 38 Copynumber: 7.0 Consensus size: 35
947448 AATATTTTCA
947458 AAAACATATAATATATAAATTTTCAAAATGTTTTTTT
1 AAAACATATAATATATAAATTTTCAAAATG--TTTTT
* * * * *
947495 TAAACTATATAATATACGAATGTTTTCAACATGTTTTC
1 AAAAC-ATATAATATA-TAA-ATTTTCAAAATGTTTTT
* * *
947533 AAAA-ATAT--TATATAAGTTTTCAAAAACGTTTTA
1 AAAACATATAATATATAAATTTTC-AAAATGTTTTT
*
947566 AAAACTATATAATATATAAATGTTTTCAAAATGTTTTC
1 AAAAC-ATATAATATATAAA--TTTTCAAAATGTTTTT
*** *
947604 AAAAC-TATAATATATGTGTTTTCAAAAATGTTTTC
1 AAAACATATAATATATAAATTTTC-AAAATGTTTTT
* *
947639 AAAA-AT-TATATATATAAGTTTTCAAAATGATTTT
1 AAAACATATA-ATATATAAATTTTCAAAATGTTTTT
* *
947673 AAAA-ATTATATATTATATATATTTTTTAAAATGTTTTT
1 AAAACA-TATA-A-TATATA-AATTTTCAAAATGTTTTT
947711 TTTTAAAAAC
Statistics
Matches: 176, Mismatches: 23, Indels: 33
0.76 0.10 0.14
Matches are distributed among these distances:
32 6 0.03
33 14 0.08
34 25 0.14
35 33 0.19
36 18 0.10
37 17 0.10
38 46 0.26
39 7 0.04
40 10 0.06
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (35 bp):
AAAACATATAATATATAAATTTTCAAAATGTTTTT
Found at i:947570 original size:108 final size:107
Alignment explanation
Indices: 947451--947713 Score: 304
Period size: 108 Copynumber: 2.4 Consensus size: 107
947441 ATACATAAAT
947451 ATTTTCAAAAACATATAATATATAAATTTTCAAAATGTTTTTTTTAAACTATATAATATACGAAT
1 ATTTT-AAAAACATATAATATATAAATTTTCAAAATGTTTTTTTTAAAC--TATAATATACG--T
*
947516 GTTTTC-AACATGTTTTCAAAAA-TAT-TATATAAGTTTTCAAAAACG
61 GTTTTCAAAAATGTTTTCAAAAATTATATATATAAGTTTTC-AAAACG
** *
947561 -TTTTAAAAACTATATAATATATAAATGTTTTCAAAATG--TTTTCAAAACTATAATATATGTGT
1 ATTTTAAAAAC-ATATAATATATAAA--TTTTCAAAATGTTTTTTTTAAACTATAATATACGTGT
*
947623 TTTCAAAAATGTTTTCAAAAATTATATATATAAGTTTTCAAAATG
63 TTTCAAAAATGTTTTCAAAAATTATATATATAAGTTTTCAAAACG
* * * *
947668 ATTTTAAAAATTATATATTATATATATTTTTTAAAATGTTTTTTTT
1 ATTTTAAAAA-CATATAATATATA-AATTTTCAAAATGTTTTTTTT
947714 TAAAAACTAT
Statistics
Matches: 131, Mismatches: 11, Indels: 23
0.79 0.07 0.14
Matches are distributed among these distances:
105 7 0.05
106 15 0.11
107 28 0.21
108 39 0.30
109 31 0.24
111 11 0.08
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (107 bp):
ATTTTAAAAACATATAATATATAAATTTTCAAAATGTTTTTTTTAAACTATAATATACGTGTTTT
CAAAAATGTTTTCAAAAATTATATATATAAGTTTTCAAAACG
Found at i:947578 original size:71 final size:73
Alignment explanation
Indices: 947447--947685 Score: 219
Period size: 71 Copynumber: 3.3 Consensus size: 73
947437 ATATATACAT
* * * ***
947447 AAATATTTTCAAAAACATATAATATATAAATTTTC-AAAATGTTTTTTTTAAACTATATAATATA
1 AAATGTTTTC-AAAAC--ATAATATATAAGTTTTCAAAAACG-TTTTCAAAAACTATATAATATA
*
947511 CGAATGTTTTCA
62 CAAATGTTTTCA
* * *
947523 ACATGTTTTCAAAA-ATATTATATAAGTTTTCAAAAACGTTTT-AAAAACTATATAATATATAAA
1 AAATGTTTTCAAAACATAATATATAAGTTTTCAAAAACGTTTTCAAAAACTATATAATATACAAA
947586 TGTTTTCA
66 TGTTTTCA
** * *
947594 AAATGTTTTCAAAACTATAATATATGTGTTTTCAAAAATGTTTTCAAAAA-T-TAT-ATATA-TA
1 AAATGTTTTCAAAAC-ATAATATATAAGTTTTCAAAAACGTTTTCAAAAACTATATAATATACAA
947655 A-GTTTTCA
65 ATGTTTTCA
*
947663 AAATGATTTT-AAAA-ATTATATAT
1 AAATG-TTTTCAAAACATAATATAT
947686 TATATATATT
Statistics
Matches: 142, Mismatches: 16, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
67 8 0.06
69 16 0.11
70 6 0.04
71 43 0.30
72 22 0.15
73 30 0.21
74 5 0.04
75 4 0.03
76 8 0.06
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (73 bp):
AAATGTTTTCAAAACATAATATATAAGTTTTCAAAAACGTTTTCAAAAACTATATAATATACAAA
TGTTTTCA
Found at i:947599 original size:11 final size:11
Alignment explanation
Indices: 947583--947607 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
947573 TATAATATAT
947583 AAATGTTTTCA
1 AAATGTTTTCA
947594 AAATGTTTTCA
1 AAATGTTTTCA
947605 AAA
1 AAA
947608 CTATAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:947637 original size:12 final size:12
Alignment explanation
Indices: 947620--947644 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
947610 ATAATATATG
947620 TGTTTTCAAAAA
1 TGTTTTCAAAAA
947632 TGTTTTCAAAAA
1 TGTTTTCAAAAA
947644 T
1 T
947645 TATATATATA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TGTTTTCAAAAA
Found at i:947815 original size:20 final size:20
Alignment explanation
Indices: 947778--947816 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
947768 CGTAGTTTTA
*
947778 AAATATGTATATATATATAT
1 AAATATGTATATACATATAT
*
947798 AAATATGTATGTACATATA
1 AAATATGTATATACATATA
947817 AAGGAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (20 bp):
AAATATGTATATACATATAT
Found at i:951522 original size:23 final size:23
Alignment explanation
Indices: 951492--951536 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
951482 CATTTTATAT
951492 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
951515 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
951537 AGTTGTGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.29, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:954749 original size:36 final size:36
Alignment explanation
Indices: 954709--954801 Score: 141
Period size: 36 Copynumber: 2.6 Consensus size: 36
954699 GTTGTTGAAC
* *
954709 TTGATCTGCAGTAGTTACAACTGTATGTTGCTGCAT
1 TTGATCTGCAGCAGTTTCAACTGTATGTTGCTGCAT
* *
954745 TTGATCTGCAGCAGTTTCAACTGTGTGTTGTTGCAT
1 TTGATCTGCAGCAGTTTCAACTGTATGTTGCTGCAT
*
954781 TTGATTTGCAGCAGTTTCAAC
1 TTGATCTGCAGCAGTTTCAAC
954802 CTCCTCCTCA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (36 bp):
TTGATCTGCAGCAGTTTCAACTGTATGTTGCTGCAT
Found at i:963302 original size:162 final size:162
Alignment explanation
Indices: 963035--963360 Score: 652
Period size: 162 Copynumber: 2.0 Consensus size: 162
963025 CCGGATACAC
963035 CATAGTAAGTGTGCGAGGCACTTTGACGACTAATTTGGGCGCAAGGCCTAACACTCGCGAGGGGT
1 CATAGTAAGTGTGCGAGGCACTTTGACGACTAATTTGGGCGCAAGGCCTAACACTCGCGAGGGGT
963100 GGGTTAGTCGAATGTGATATACACAGTTGCTAGTGCTTGATGGCTTTATGAGACCAAATACTAGT
66 GGGTTAGTCGAATGTGATATACACAGTTGCTAGTGCTTGATGGCTTTATGAGACCAAATACTAGT
963165 TAGTATTGCATATAGAAAATGCACAACAGAGT
131 TAGTATTGCATATAGAAAATGCACAACAGAGT
963197 CATAGTAAGTGTGCGAGGCACTTTGACGACTAATTTGGGCGCAAGGCCTAACACTCGCGAGGGGT
1 CATAGTAAGTGTGCGAGGCACTTTGACGACTAATTTGGGCGCAAGGCCTAACACTCGCGAGGGGT
963262 GGGTTAGTCGAATGTGATATACACAGTTGCTAGTGCTTGATGGCTTTATGAGACCAAATACTAGT
66 GGGTTAGTCGAATGTGATATACACAGTTGCTAGTGCTTGATGGCTTTATGAGACCAAATACTAGT
963327 TAGTATTGCATATAGAAAATGCACAACAGAGT
131 TAGTATTGCATATAGAAAATGCACAACAGAGT
963359 CA
1 CA
963361 GAGTCATTTA
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
162 164 1.00
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (162 bp):
CATAGTAAGTGTGCGAGGCACTTTGACGACTAATTTGGGCGCAAGGCCTAACACTCGCGAGGGGT
GGGTTAGTCGAATGTGATATACACAGTTGCTAGTGCTTGATGGCTTTATGAGACCAAATACTAGT
TAGTATTGCATATAGAAAATGCACAACAGAGT
Found at i:966316 original size:176 final size:176
Alignment explanation
Indices: 966109--966425 Score: 530
Period size: 176 Copynumber: 1.8 Consensus size: 176
966099 TTTCCCTAAA
*
966109 AATGTACCTTTTTATTTAATCCTTTAACTTTGCATTTTATTCAATTTAATCTTTTGACTACAATT
1 AATGTACCTTTTTATTTAATCCTTCAACTTTGCATTTTATTCAATTTAATCTTTTGACTACAATT
* *
966174 GTTTACAAATTCTTTCTTCCCATTAATTCCTTGACTCTTTTATACTCTCATCAATTAC-TTCAAA
66 GTTTACAAACTCTTTCTTCCCATCAATTCCTTGACTCTTTTATACTCTCATCAATT-CTTTCAAA
966238 ATATAATATTAAATAACATTATAATGTGGAAAGAATATGATATATAT
130 ATATAATATTAAATAACATTATAATGTGGAAAGAATATGATATATAT
* *
966285 AATGTACCTTTTTATTTAATTCC-TCAACTTTGCATTTTATTCAATTTAGTCTTTTGATTACAAT
1 AATGTACCTTTTTATTTAA-TCCTTCAACTTTGCATTTTATTCAATTTAATCTTTTGACTACAAT
* * *
966349 TGTTTACAAACTCTTTTTTCCTATCAATTCCTTGACTCTTTTATACTTTCATCAATTCTTTCAAA
65 TGTTTACAAACTCTTTCTTCCCATCAATTCCTTGACTCTTTTATACTCTCATCAATTCTTTCAAA
966414 ATATAATATTAA
130 ATATAATATTAA
966426 TATGTACCAT
Statistics
Matches: 131, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
175 1 0.01
176 127 0.97
177 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.05, T:0.47
Consensus pattern (176 bp):
AATGTACCTTTTTATTTAATCCTTCAACTTTGCATTTTATTCAATTTAATCTTTTGACTACAATT
GTTTACAAACTCTTTCTTCCCATCAATTCCTTGACTCTTTTATACTCTCATCAATTCTTTCAAAA
TATAATATTAAATAACATTATAATGTGGAAAGAATATGATATATAT
Found at i:966819 original size:15 final size:15
Alignment explanation
Indices: 966801--966856 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
966791 TAACCGGTTT
966801 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
966816 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
966833 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
966848 CGATTTTAA
1 CGGTTTTAA
966857 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:966829 original size:17 final size:17
Alignment explanation
Indices: 966804--966854 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
966794 CCGGTTTCGG
966804 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
966821 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
966836 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
966853 TT
1 TT
966855 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:967274 original size:13 final size:13
Alignment explanation
Indices: 967253--967307 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
967243 AAGTTCGATA
*
967253 AATTCAAATACTT
1 AATTGAAATACTT
967266 AATTGAAATACTT
1 AATTGAAATACTT
* *
967279 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
967293 AATTGAAATACTT
1 AATTGAAATACTT
967306 AA
1 AA
967308 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:967389 original size:32 final size:33
Alignment explanation
Indices: 967293--967391 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
967283 AACTCAACAT
* * *
967293 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
967326 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
967359 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
967391 A
1 A
967392 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:967410 original size:21 final size:21
Alignment explanation
Indices: 967386--967425 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
967376 ACTTCAAGTT
967386 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
967407 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
967426 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:969726 original size:12 final size:12
Alignment explanation
Indices: 969709--969755 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
969699 TTCGGATAAA
969709 AACCGGTTTTTT
1 AACCGGTTTTTT
969721 AACCGGTTTTTTT
1 AACCGG-TTTTTT
969734 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
969748 ATCCGGTT
1 AACCGGTT
969756 AAAAAACCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 13 0.42
13 6 0.19
14 6 0.19
15 6 0.19
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:969739 original size:15 final size:14
Alignment explanation
Indices: 969708--969747 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
969698 TTTCGGATAA
969708 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
969721 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
969734 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
969748 ATCCGGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:970385 original size:46 final size:46
Alignment explanation
Indices: 970318--970411 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 46
970308 AGAGCACTGC
* * * *
970318 AAGCCGAGCGGAGAATAAGGTTCGAACCCTTCTGGGCTCGACTAGT
1 AAGCCGAGCGGAGAACAAGGTTCAAACCCTTCCGGGCTCAACTAGT
* *
970364 AAGCCGAGCGGAGCACGAGGTTCAAACCCTTCCGGGCTCAACTAGT
1 AAGCCGAGCGGAGAACAAGGTTCAAACCCTTCCGGGCTCAACTAGT
970410 AA
1 AA
970412 ACAATGGATA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.28, C:0.27, G:0.29, T:0.17
Consensus pattern (46 bp):
AAGCCGAGCGGAGAACAAGGTTCAAACCCTTCCGGGCTCAACTAGT
Found at i:974112 original size:2 final size:2
Alignment explanation
Indices: 974105--974129 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
974095 ATAATATTTA
974105 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
974130 AGAAGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:977370 original size:21 final size:21
Alignment explanation
Indices: 977344--977399 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
977334 AGGCTGATAT
977344 GGATCTTATGAAATAGAATAA
1 GGATCTTATGAAATAGAATAA
977365 GGATCTTATGAAATAGAATAA
1 GGATCTTATGAAATAGAATAA
977386 GGATCTTATGAAAT
1 GGATCTTATGAAAT
977400 TGAAAGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (21 bp):
GGATCTTATGAAATAGAATAA
Found at i:981623 original size:3 final size:3
Alignment explanation
Indices: 981610--981672 Score: 63
Period size: 3 Copynumber: 20.7 Consensus size: 3
981600 GTAATTATTT
* * * *
981610 ATA ATTA ATA ATA ATA ATA AGA ATA AGA ATA TTA AAA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
981656 TTT ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
981673 GGGAAAATTA
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:981907 original size:39 final size:39
Alignment explanation
Indices: 981846--982290 Score: 613
Period size: 39 Copynumber: 11.4 Consensus size: 39
981836 GAATAATTTT
* * * * *
981846 TTCAGACTATGAACTTCTTCTTCCTCTTTAGATGAGTTC
1 TTCAGATTATGAACTCCTTTTTCCTCTTCAGACGAGTTC
* * * *
981885 TTCATAATATGAACCCCTTCTTCCTCTTCAGACGAGTTC
1 TTCAGATTATGAACTCCTTTTTCCTCTTCAGACGAGTTC
* * *
981924 TTCTGATTATGAACTCCTTTTTCCTCTTCAAATGAGTTC
1 TTCAGATTATGAACTCCTTTTTCCTCTTCAGACGAGTTC
* *
981963 TTCAGATTATGAACTCCTTATTCCTCTTCAGATGAGTTC
1 TTCAGATTATGAACTCCTTTTTCCTCTTCAGACGAGTTC
* **
982002 TTCAGATTATGAACT-CTTTTGTTCTCTTTGGACGAGTTC
1 TTCAGATTATGAACTCCTTTT-TCCTCTTCAGACGAGTTC
* *
982041 TTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAGTTC
1 TTCAGATTATGAACTCCTTTTTCCTCTTCAGACGAGTTC
*
982080 TTCAGATTATGAAATCCTTTTTCCTCTTCAGACGAGTTC
1 TTCAGATTATGAACTCCTTTTTCCTCTTCAGACGAGTTC
* * *
982119 TTCAGATTATGAACTCATTCTTCCTCTTCAGATGAGTTC
1 TTCAGATTATGAACTCCTTTTTCCTCTTCAGACGAGTTC
*
982158 TTCAGATTATGAACTCCTTTTTTCTCTTCAGACGAGTTC
1 TTCAGATTATGAACTCCTTTTTCCTCTTCAGACGAGTTC
*
982197 TTCAGATTATGAACTCCTTTTTCCTCTTCAGATGAGTTC
1 TTCAGATTATGAACTCCTTTTTCCTCTTCAGACGAGTTC
* * *
982236 ATCAGTTTATGAACTCCTTTTTCCTCTTTAGACGAGTTC
1 TTCAGATTATGAACTCCTTTTTCCTCTTCAGACGAGTTC
*
982275 TTCGGATTATGAACTC
1 TTCAGATTATGAACTC
982291 TTTCTGGAAA
Statistics
Matches: 358, Mismatches: 46, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
38 4 0.01
39 350 0.98
40 4 0.01
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (39 bp):
TTCAGATTATGAACTCCTTTTTCCTCTTCAGACGAGTTC
Found at i:982506 original size:45 final size:45
Alignment explanation
Indices: 982354--983409 Score: 1224
Period size: 45 Copynumber: 23.4 Consensus size: 45
982344 CAAATATTCG
* ** * *
982354 GCACTGAAGGTATTATGGATGGCCCGAAGGACTTTTTGAAAACATCCT
1 GCACTGAAGGTCTTACAGATGACCCGAAGG---TTTTGAAAACATCAT
* ** *
982402 GCACTGTAGGTCTTATGGATGACCCGAAGGCTTTTTG-AAACATCCT
1 GCACTGAAGGTCTTACAGATGACCCGAAGG--TTTTGAAAACATCAT
** *
982448 GCACTGTAA-GTCTTATGGATGACCCGAAGGCTTTGAAAACATCAT
1 GCACTG-AAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAT
* *
982493 GCACTGAAGGTCTTACAGATGACTCGAAGGCTTTGAAAACATCAT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAT
* * *
982538 GCACT-AGAGATCTTACAGATGACCTGAAAGTTTTGAAAACATCAT
1 GCACTGA-AGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAT
* * *
982583 GCACTGAAGGTCTTACAGATGTCTCGAAGTTTTTGAAAACATCAT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAT
* *
982628 GAACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAATATCAT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAT
*
982673 GCACTGAAGGTCTTACAGATGACCCGAAAGTTTTGAAAACATCAT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAT
* * *
982718 GCACTGAAGGTCTTACAGATGGCTCGAAGGTTTTAAAAACATCAT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAT
* *
982763 GCACTGTAGGTCTTACAGATTACCCGAAGGTTTTGAAAACATCAT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAT
* * * * *
982808 GCATTGTAGGTCTTACAGATTACCCGAA-GTCTTTGAAAGCATCCT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGT-TTTGAAAACATCAT
* * *
982853 ACACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCCT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAT
* * ** *
982898 GTACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCCT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAT
* * *
982943 GCACTGTAGGTCTTATAGATGACCCGAA-GTATTTGAAAACATCCT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGT-TTTGAAAACATCAT
* ** * *
982988 GCACTGTAGGTCTTATGGATGACCCAAAGGTTTTGAAAACATCCT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAT
* * * *
983033 GCACTAAAGGTCTTACATATGACCCGAAGGCTTTGAAAACATCCT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAT
* ** * * *
983078 GCACTGTAGGTCTTATGGATGACTCAAAGGTTTTGAAAACATCTT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAT
** * * ** * *
983123 AAATTGTAGGTCTTATGGATGACCCGAAGGCTTTGAAAACATCCT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAT
* * ** *
983168 ACACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCCT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAT
* * *
983213 GCACTGTAGGTCTTATAGATAACCCGAAGGTTTTGAAAACATCAT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAT
* * *
983258 GCACTGTAGGTCTTACAGATGACCC-AAAGTCTTTGAAAACATCCT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGT-TTTGAAAACATCAT
* ** * *
983303 GCACTGTAGGTCTTATGGATGACCAGAAGGTTTTGAAAATATCAT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAT
*
983348 GCACTGAAGGTCTTACAGATAACCCGAAGGTTTTGAAAACATCAT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAT
983393 GCACTGAAGGTCTTACA
1 GCACTGAAGGTCTTACA
983410 AATGTGGGAA
Statistics
Matches: 895, Mismatches: 102, Indels: 25
0.88 0.10 0.02
Matches are distributed among these distances:
44 15 0.02
45 801 0.89
46 44 0.05
47 8 0.01
48 27 0.03
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (45 bp):
GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAT
Found at i:989989 original size:16 final size:17
Alignment explanation
Indices: 989957--989991 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
989947 TAGGGGAATG
989957 TAGGTTACAATTTTTTT
1 TAGGTTACAATTTTTTT
989974 TAGGTTACAATTTTTTT
1 TAGGTTACAATTTTTTT
989991 T
1 T
989992 CATATTAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (17 bp):
TAGGTTACAATTTTTTT
Found at i:998104 original size:24 final size:21
Alignment explanation
Indices: 998069--998111 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
998059 GGCACATTCT
*
998069 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATATCAA-AGG-ACATCC
998092 TTTGAAATATCAAAGGACAT
1 TTTG-AATATCAAAGGACAT
998112 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (21 bp):
TTTGAATATCAAAGGACATCC
Found at i:999246 original size:23 final size:24
Alignment explanation
Indices: 999197--999249 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
999187 TTTTTTGCTT
*
999197 TTTC-TTCGTTTGAGTGCTGCATT
1 TTTCTTTCGTTTGAGTGCTGCATC
* *
999220 TTTCTTTCTTTTGAGTGCTTCA-C
1 TTTCTTTCGTTTGAGTGCTGCATC
999243 TTTCTTT
1 TTTCTTT
999250 TCTGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.08, C:0.19, G:0.15, T:0.58
Consensus pattern (24 bp):
TTTCTTTCGTTTGAGTGCTGCATC
Found at i:999375 original size:23 final size:24
Alignment explanation
Indices: 999337--999384 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
999327 TCCACCAAAA
*
999337 CTCTGATTACCGCTTGATGTAAGG
1 CTCTGATTACCACTTGATGTAAGG
999361 CTCTGA-TACCACTTGATGTAAGG
1 CTCTGATTACCACTTGATGTAAGG
999384 C
1 C
999385 ATTTGTACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (24 bp):
CTCTGATTACCACTTGATGTAAGG
Found at i:1003416 original size:13 final size:13
Alignment explanation
Indices: 1003398--1003431 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1003388 TTGCATTTCT
*
1003398 CAATTTTTATAAA
1 CAATTTTCATAAA
1003411 CAATTTGTCATAAA
1 CAATTT-TCATAAA
1003425 CAATTTT
1 CAATTTT
1003432 AAAGCATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (13 bp):
CAATTTTCATAAA
Found at i:1003784 original size:2 final size:2
Alignment explanation
Indices: 1003777--1003809 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1003767 CGTTCTTCAA
1003777 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 A
1003810 ATAACGTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1004083 original size:18 final size:18
Alignment explanation
Indices: 1004062--1004096 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1004052 AAGTATACAC
*
1004062 TTAGTGAGGCATATAAAG
1 TTAGTAAGGCATATAAAG
*
1004080 TTAGTAAGGCATTTAAA
1 TTAGTAAGGCATATAAA
1004097 ACATAGGTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (18 bp):
TTAGTAAGGCATATAAAG
Found at i:1007404 original size:13 final size:13
Alignment explanation
Indices: 1007388--1007438 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
1007378 ACTGATTACG
1007388 TACATTGAAGCAA
1 TACATTGAAGCAA
*
1007401 TACATTGAATCAA
1 TACATTGAAGCAA
* **
1007414 AATTTTGAAGCAA
1 TACATTGAAGCAA
*
1007427 TTCATTGAAGCA
1 TACATTGAAGCA
1007439 GTACTTCTCA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (13 bp):
TACATTGAAGCAA
Found at i:1008569 original size:23 final size:23
Alignment explanation
Indices: 1008543--1008589 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1008533 CGATTCACGA
1008543 AATCCAGTGACGGATGCACGTTC
1 AATCCAGTGACGGATGCACGTTC
1008566 AATCCAGTGACGGATGCACGTTC
1 AATCCAGTGACGGATGCACGTTC
1008589 A
1 A
1008590 CTTTAACGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
AATCCAGTGACGGATGCACGTTC
Found at i:1008786 original size:18 final size:17
Alignment explanation
Indices: 1008763--1008796 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1008753 AGAATTTGAA
*
1008763 AAATTATATTTATAAAAT
1 AAATTAAATTTA-AAAAT
1008781 AAATTAAATTTAAAAA
1 AAATTAAATTTAAAAA
1008797 CATATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTAAATTTAAAAAT
Found at i:1009090 original size:26 final size:26
Alignment explanation
Indices: 1009022--1009090 Score: 79
Period size: 27 Copynumber: 2.7 Consensus size: 26
1009012 TATATAAACT
* *
1009022 ATTAAATATAGTTTA-T-TTTATTGA
1 ATTAAAAATATTTTATTATTTATTGA
* *
1009046 AATAAAAATATATTAATTATTTATTGA
1 ATTAAAAATAT-TTTATTATTTATTGA
1009073 ATTAAAAATATTTTATTA
1 ATTAAAAATATTTTATTA
1009091 GTAAATAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
24 8 0.22
25 3 0.08
26 7 0.19
27 18 0.50
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (26 bp):
ATTAAAAATATTTTATTATTTATTGA
Found at i:1009567 original size:49 final size:49
Alignment explanation
Indices: 1009495--1009594 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
1009485 AGAATATTAT
*
1009495 ATATATATATATATCAGCCGGAGATTCCATGGCGGCAGATAGGGCAGGA
1 ATATATATATATATCAGCCGGAGATTCCATAGCGGCAGATAGGGCAGGA
*
1009544 ATATATATATATATCAGCCGGAGATTCCGTAGCGGCAGATAGGGCAGGA
1 ATATATATATATATCAGCCGGAGATTCCATAGCGGCAGATAGGGCAGGA
1009593 AT
1 AT
1009595 TGCAGTTTCC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (49 bp):
ATATATATATATATCAGCCGGAGATTCCATAGCGGCAGATAGGGCAGGA
Found at i:1014621 original size:15 final size:15
Alignment explanation
Indices: 1014601--1014636 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1014591 GTTAGTTGGG
1014601 TTTAATAAGGATGGA
1 TTTAATAAGGATGGA
*
1014616 TTTAATAAGGATGGG
1 TTTAATAAGGATGGA
1014631 TTTAAT
1 TTTAAT
1014637 GGTATTGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.25, T:0.39
Consensus pattern (15 bp):
TTTAATAAGGATGGA
Found at i:1015768 original size:54 final size:54
Alignment explanation
Indices: 1015651--1015768 Score: 130
Period size: 54 Copynumber: 2.2 Consensus size: 54
1015641 AACGGTGCAT
* **
1015651 TTTCAGCAATAAATGTGCAACCCATGGCATTCATAATGTGTTTATGAATGACCA
1 TTTCAGCACTAAATGTGCAACCCATGGCATTCATAATAAGTTTATGAATGACCA
* * * * * **
1015705 TGTT-GGCACTATATGTGCAATCCATGGGATTCATAATAAGTTTGTGAATTTCCA
1 T-TTCAGCACTAAATGTGCAACCCATGGCATTCATAATAAGTTTATGAATGACCA
1015759 TTTCAGCACT
1 TTTCAGCACT
1015769 TTGGTGCATT
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
53 2 0.04
54 47 0.92
55 2 0.04
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (54 bp):
TTTCAGCACTAAATGTGCAACCCATGGCATTCATAATAAGTTTATGAATGACCA
Found at i:1024409 original size:40 final size:40
Alignment explanation
Indices: 1024365--1024486 Score: 217
Period size: 40 Copynumber: 3.0 Consensus size: 40
1024355 ACCGTAGTGC
1024365 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
1024405 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
1024445 TACACATAAGGTCATGCCCACCATATACACCGAAGTATAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1024485 TA
1 TA
1024487 TAAACCTACA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1028313 original size:22 final size:21
Alignment explanation
Indices: 1028267--1028306 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1028257 CATATTCTTG
*
1028267 AAAAAGGATTGACCCCTTTGC
1 AAAAAGGATAGACCCCTTTGC
*
1028288 AAAAAGGATAGATCCCTTT
1 AAAAAGGATAGACCCCTTT
1028307 TTCAAAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (21 bp):
AAAAAGGATAGACCCCTTTGC
Found at i:1030316 original size:25 final size:25
Alignment explanation
Indices: 1030286--1030376 Score: 119
Period size: 25 Copynumber: 3.6 Consensus size: 25
1030276 GTATTAAATA
*
1030286 AGCATTGCATGTTATTAGTTCATGT
1 AGCATTGCATGTTATTAATTCATGT
*
1030311 AACATTGCATGTTATTAATTCATGT
1 AGCATTGCATGTTATTAATTCATGT
* * **
1030336 GGCATGGCATGTTACCAATTCATGT
1 AGCATTGCATGTTATTAATTCATGT
*
1030361 TGCATTGCATGTTATT
1 AGCATTGCATGTTATT
1030377 CATGTTGCAT
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 55 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (25 bp):
AGCATTGCATGTTATTAATTCATGT
Found at i:1034392 original size:8 final size:8
Alignment explanation
Indices: 1034379--1034408 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
1034369 CATGGGGTAT
1034379 TAATTAAA
1 TAATTAAA
1034387 TAATTAAA
1 TAATTAAA
1034395 TAATTAAA
1 TAATTAAA
1034403 TAATTA
1 TAATTA
1034409 TGGTGGGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TAATTAAA
Found at i:1035404 original size:32 final size:32
Alignment explanation
Indices: 1035363--1035521 Score: 264
Period size: 32 Copynumber: 5.0 Consensus size: 32
1035353 CCAAGAGTCA
*
1035363 AGGATTACCTATGTCTTTCGGGACATATAGAC
1 AGGATTACCTATGTCTTTCGGGACATATGGAC
1035395 AGGATTACCTATGTCTTTCGGGACATATGGAC
1 AGGATTACCTATGTCTTTCGGGACATATGGAC
1035427 AGGATTACCTATGTCTTTCGGGACATATGGAC
1 AGGATTACCTATGTCTTTCGGGACATATGGAC
* * ** *
1035459 ATGATTACCTATGTCTTTTGGGACATATCTAT
1 AGGATTACCTATGTCTTTCGGGACATATGGAC
1035491 AGGATTACCTATGTCTTTCGGGACATATGGA
1 AGGATTACCTATGTCTTTCGGGACATATGGA
1035522 AAGTTACGTA
Statistics
Matches: 117, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 117 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.34
Consensus pattern (32 bp):
AGGATTACCTATGTCTTTCGGGACATATGGAC
Found at i:1038023 original size:21 final size:21
Alignment explanation
Indices: 1037994--1038065 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
1037984 AATAAGTTTG
* *
1037994 GGATTGATCCCTTGAGGAAAA
1 GGATCGATCCCTTGACGAAAA
* *
1038015 GGATCGATCCCTTCACCAAAA
1 GGATCGATCCCTTGACGAAAA
* * *
1038036 GGATTGATCCCTCGATGAAAA
1 GGATCGATCCCTTGACGAAAA
1038057 GGATCGATC
1 GGATCGATC
1038066 TCTTCCCTTA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (21 bp):
GGATCGATCCCTTGACGAAAA
Found at i:1039398 original size:27 final size:27
Alignment explanation
Indices: 1039359--1039445 Score: 95
Period size: 27 Copynumber: 3.2 Consensus size: 27
1039349 CGAATTGCAT
* *
1039359 CGTTGGTCATTGATTGTTGACTTTGAC
1 CGTTGATCGTTGATTGTTGACTTTGAC
* * *
1039386 CGTTGATTGTTGATCGTTGACTTTAAC
1 CGTTGATCGTTGATTGTTGACTTTGAC
* *
1039413 CATTGATCGTTGATTGTTG-CTTTTGAT
1 CGTTGATCGTTGATTGTTGAC-TTTGAC
1039440 CGTTGA
1 CGTTGA
1039446 CTTTTTCTAT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
26 1 0.02
27 47 0.98
ACGTcount: A:0.16, C:0.14, G:0.24, T:0.46
Consensus pattern (27 bp):
CGTTGATCGTTGATTGTTGACTTTGAC
Found at i:1039458 original size:20 final size:20
Alignment explanation
Indices: 1039395--1039458 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
1039385 CCGTTGATTG
* *
1039395 TTGATCGTTGACTTTAACCA
1 TTGATCGTTGACTTTTACTA
* *
1039415 TTGATCGTTGA-TTGTTGCTT
1 TTGATCGTTGACTT-TTACTA
*
1039435 TTGATCGTTGACTTTTTCTA
1 TTGATCGTTGACTTTTACTA
1039455 TTGA
1 TTGA
1039459 CTATTTTCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 2 0.06
20 32 0.89
21 2 0.06
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (20 bp):
TTGATCGTTGACTTTTACTA
Found at i:1039762 original size:32 final size:32
Alignment explanation
Indices: 1039721--1039784 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1039711 GCATAAGTGT
1039721 TATTTAGTGACTTTATAGTAAATTTCAATTTA
1 TATTTAGTGACTTTATAGTAAATTTCAATTTA
*
1039753 TATTTAGTGATTTTATAGTAAATTTCAATTTA
1 TATTTAGTGACTTTATAGTAAATTTCAATTTA
1039785 GATATATGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (32 bp):
TATTTAGTGACTTTATAGTAAATTTCAATTTA
Found at i:1040165 original size:29 final size:29
Alignment explanation
Indices: 1040069--1040199 Score: 131
Period size: 29 Copynumber: 4.5 Consensus size: 29
1040059 TTTTATTTTG
* *
1040069 CATGAGATTATAT-CCCGTCGTGATTCTA
1 CATGGGATTATATCCCCGTCCTGATTCTA
* *
1040097 CATGGCATTATATCCCTTGTCCTGATTCTA
1 CATGGGATTATATCCC-CGTCCTGATTCTA
* * *
1040127 CACGGAATTATATCCCCATCCTGATTCTGA
1 CATGGGATTATATCCCCGTCCTGATTCT-A
* * *
1040157 -ATGGGATTATATTCACGTCCTAATTCTA
1 CATGGGATTATATCCCCGTCCTGATTCTA
*
1040185 CATGAGATTATATCC
1 CATGGGATTATATCC
1040200 TTATCCTATT
Statistics
Matches: 83, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
28 12 0.14
29 45 0.54
30 26 0.31
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.36
Consensus pattern (29 bp):
CATGGGATTATATCCCCGTCCTGATTCTA
Found at i:1040732 original size:19 final size:19
Alignment explanation
Indices: 1040708--1040746 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1040698 ATTGTTTTTC
1040708 TGAAAATGATGTTATAATA
1 TGAAAATGATGTTATAATA
1040727 TGAAAATGATGTTATAATA
1 TGAAAATGATGTTATAATA
1040746 T
1 T
1040747 TGTAGCTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (19 bp):
TGAAAATGATGTTATAATA
Found at i:1041466 original size:23 final size:23
Alignment explanation
Indices: 1041436--1041486 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1041426 CACCTTTTTG
*
1041436 ATAAGGAGGTAGAATAAAGGAGA
1 ATAAGGAGGTAAAATAAAGGAGA
*
1041459 ATAAGGAGGTAAAATAGAGGAGA
1 ATAAGGAGGTAAAATAAAGGAGA
*
1041482 GTAAG
1 ATAAG
1041487 AGTGAGGTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.35, T:0.14
Consensus pattern (23 bp):
ATAAGGAGGTAAAATAAAGGAGA
Found at i:1051002 original size:60 final size:59
Alignment explanation
Indices: 1050864--1051037 Score: 165
Period size: 60 Copynumber: 2.9 Consensus size: 59
1050854 ATATATATAT
* * ** *
1050864 ATAGTTTGGGATGAAATTGAAATGTTAAAAAGGTTTGGTGACCAATTTAGAATGAAGGTC
1 ATAGTTTGGGATAAAATTGAAATATTAAAAA-GTTTGAAGACTAATTTAGAATGAAGGTC
* **
1050924 ATAGTTTTGGAATAAAATTGAAATATGCAAAAGTTTGAAGACTAATTTAGAATGATA-GTC
1 ATAG-TTTGGGATAAAATTGAAATATTAAAAAGTTTGAAGACTAATTTAGAATGA-AGGTC
* * * *
1050984 ATAGTTTAGGGATTAAATT-AGAATATTTAAAAGTTT-AGGGACTAATTTAAAATG
1 ATAGTTT-GGGATAAAATTGA-AATATTAAAAAGTTTGA-AGACTAATTTAGAATG
1051038 GGGTCATTCT
Statistics
Matches: 95, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
59 5 0.05
60 67 0.71
61 23 0.24
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34
Consensus pattern (59 bp):
ATAGTTTGGGATAAAATTGAAATATTAAAAAGTTTGAAGACTAATTTAGAATGAAGGTC
Found at i:1061017 original size:117 final size:118
Alignment explanation
Indices: 1060863--1061193 Score: 418
Period size: 117 Copynumber: 2.8 Consensus size: 118
1060853 GCTGATCCAA
* * *
1060863 CTCCTTATGTGATGGAATCGAGTAAGGGTTGAACAAGTTCCTT-TCATTATGAACTTATTCTCCC
1 CTCCTTTTGTAATGGAATCGAGTAAGGGTTGAACAAGTT-CTTATCATTATGAACTTCTTCTCCC
1060927 TCATCGAATGAGTTATTCTCATTATGAACTCTCAACTG-AAAATGTTAAACCAC
65 TCATCGAATGAGTTATTCTCATTATGAACTCTCAACTGAAAAATGTTAAACCAC
* * *
1060980 CTCCTTTTGTAATGGAATCAAATAAGGGTTGAACAAGTTCTTATCATTATGAACTTCTTCTCTCT
1 CTCCTTTTGTAATGGAATCGAGTAAGGGTTGAACAAGTTCTTATCATTATGAACTTCTTCTCCCT
* * * * *
1061045 CATCGGATGAGTTGTTCTAATTATGAACTCTCCACTGAAAAATGTTAATCCAC
66 CATCGAATGAGTTATTCTCATTATGAACTCTCAACTGAAAAATGTTAAACCAC
* * * * * * *
1061098 CT--TATTCTACGATGCAATCGAGTAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTCC
1 CTCCTTTTGTA--ATGGAATCGAGTAAGGGTTGAACAAGTTCTTATCATTATGAACTTCTTCTCC
* * *
1061161 TTCAACGAATGAGTTCTTCTCATTATGAACTCT
64 CTCATCGAATGAGTTATTCTCATTATGAACTCT
1061194 TTTTTGGGAA
Statistics
Matches: 184, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
116 8 0.04
117 88 0.48
118 88 0.48
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.36
Consensus pattern (118 bp):
CTCCTTTTGTAATGGAATCGAGTAAGGGTTGAACAAGTTCTTATCATTATGAACTTCTTCTCCCT
CATCGAATGAGTTATTCTCATTATGAACTCTCAACTGAAAAATGTTAAACCAC
Found at i:1061155 original size:118 final size:115
Alignment explanation
Indices: 1060873--1061193 Score: 403
Period size: 118 Copynumber: 2.7 Consensus size: 115
1060863 CTCCTTATGT
*
1060873 GATGGAATCGAGTAAGGGTTGAACAAGTTCCTTTCATTATGAACTTATTCTCCCTCATCGAATGA
1 GATGGAATCGAGTAAGGGTTGAACAAGTT-CTTTCATTATGAACTTCTTCT-CCTCATCGAATGA
* *
1060938 GTTATTCTCATTATGAACTCTCAACTGAAAATGTTAAACCACCTCCTTTTGTA
64 GTTATTCTCATTATGAACTCTCAACTGAAAATGTTAAACCACCT-CTATTCTA
* * *
1060991 -ATGGAATCAAATAAGGGTTGAACAAGTTCTTATCATTATGAACTTCTTCTCTCTCATCGGATGA
1 GATGGAATCGAGTAAGGGTTGAACAAGTTCTT-TCATTATGAACTTCTTCTC-CTCATCGAATGA
* * * *
1061055 GTTGTTCTAATTATGAACTCTCCACTGAAAAATGTTAATCCACCT-TATTCTA
64 GTTATTCTCATTATGAACTCTCAACTG-AAAATGTTAAACCACCTCTATTCTA
* * * * *
1061107 CGATGCAATCGAGTAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTCCTTCAACGAATG
1 -GATGGAATCGAGTAAGGGTTGAACAAGTTCTT-TCATTATGAACTTCTTCTCC-TCATCGAATG
*
1061172 AGTTCTTCTCATTATGAACTCT
63 AGTTATTCTCATTATGAACTCT
1061194 TTTTTGGGAA
Statistics
Matches: 176, Mismatches: 21, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
116 9 0.05
117 79 0.45
118 88 0.50
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36
Consensus pattern (115 bp):
GATGGAATCGAGTAAGGGTTGAACAAGTTCTTTCATTATGAACTTCTTCTCCTCATCGAATGAGT
TATTCTCATTATGAACTCTCAACTGAAAATGTTAAACCACCTCTATTCTA
Found at i:1062306 original size:15 final size:14
Alignment explanation
Indices: 1062237--1062329 Score: 66
Period size: 14 Copynumber: 6.5 Consensus size: 14
1062227 TCTTGAACCC
1062237 TTATTTTCACTTTTATT
1 TTATTTT-A-TTTT-TT
*
1062254 TTATTTT-TTCTTT
1 TTATTTTATTTTTT
**
1062267 TTA-TTTATCTCCTT
1 TTATTTTAT-TTTTT
1062281 TTATTTTATTTTATT
1 TTATTTTATTTT-TT
*
1062296 TTATTTTATTTTCT
1 TTATTTTATTTTTT
*
1062310 TTATTTT-TTGTTT
1 TTATTTTATTTTTT
*
1062323 TTCTTTT
1 TTATTTT
1062330 CTTCTTAAGT
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
12 3 0.05
13 16 0.25
14 19 0.30
15 19 0.30
17 7 0.11
ACGTcount: A:0.13, C:0.09, G:0.01, T:0.77
Consensus pattern (14 bp):
TTATTTTATTTTTT
Found at i:1062332 original size:5 final size:5
Alignment explanation
Indices: 1062237--1062316 Score: 69
Period size: 5 Copynumber: 16.4 Consensus size: 5
1062227 TCTTGAACCC
* * **
1062237 TTATT TTCACTT TTATT TTATT TT-TT CT-TT TTA-T TTATC TCCTT TTATT
1 TTATT TT-A-TT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT
*
1062286 TTATT TTATT TTATT TTATT TT-CT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TT
1062317 TTGTTTTTCT
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
4 13 0.22
5 41 0.68
6 2 0.03
7 4 0.07
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:1065825 original size:9 final size:9
Alignment explanation
Indices: 1065811--1065847 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1065801 CCCAAAGTTT
1065811 ATGTAAAAA
1 ATGTAAAAA
1065820 ATGTAAAAA
1 ATGTAAAAA
*
1065829 ATGTAAAGA
1 ATGTAAAAA
1065838 ATGTAAAAA
1 ATGTAAAAA
1065847 A
1 A
1065848 ATATTGCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.14, T:0.22
Consensus pattern (9 bp):
ATGTAAAAA
Found at i:1092639 original size:13 final size:13
Alignment explanation
Indices: 1092621--1092650 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1092611 AGTTACAACT
1092621 ATATAATACTCTA
1 ATATAATACTCTA
1092634 ATATAATACTCTA
1 ATATAATACTCTA
1092647 ATAT
1 ATAT
1092651 TCTCCCGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATAATACTCTA
Found at i:1101834 original size:6 final size:7
Alignment explanation
Indices: 1101808--1101837 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1101798 TTACTTTTCA
1101808 AATTTTT
1 AATTTTT
1101815 AATTTTT
1 AATTTTT
1101822 AATTTTT
1 AATTTTT
*
1101829 ATTTTTT
1 AATTTTT
1101836 AA
1 AA
1101838 CTCTCAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
AATTTTT
Found at i:1103562 original size:57 final size:58
Alignment explanation
Indices: 1103481--1103591 Score: 134
Period size: 57 Copynumber: 1.9 Consensus size: 58
1103471 GACGCGTATT
* **
1103481 TATGACGCTCATTACACGTCATTGAAGCCCCCGTCA-TAAATGAAGATGACACACATG
1 TATGACGCTCATTACACGTCATTGAAGCCCACGTCATTAAAAAAAGATGACACACATG
* ** * **
1103538 TATGACGCTCATTGCGTGTTATTGAAGTTCACGTCATTAAAAAAAGATGACACA
1 TATGACGCTCATTACACGTCATTGAAGCCCACGTCATTAAAAAAAGATGACACA
1103592 TATTCTTGTG
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
57 29 0.66
58 15 0.34
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (58 bp):
TATGACGCTCATTACACGTCATTGAAGCCCACGTCATTAAAAAAAGATGACACACATG
Found at i:1105186 original size:2 final size:2
Alignment explanation
Indices: 1105174--1105238 Score: 121
Period size: 2 Copynumber: 32.0 Consensus size: 2
1105164 TATTTGGTGC
1105174 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1105217 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
1105239 CTCCGCCAAG
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 60 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1110072 original size:47 final size:46
Alignment explanation
Indices: 1109961--1110073 Score: 129
Period size: 47 Copynumber: 2.4 Consensus size: 46
1109951 GACTTGAGAG
** *
1109961 ACTGTTACTGGCAGTTTATACTGCATACTGGCATTAAATGTGCCAT
1 ACTGTTACTGGCAGTTTATACAACATACAGGCATTAAATGTGCCAT
* * *
1110007 ACTGATT-CTAGTAGTTTATACAACATACCAGGCATTGAATGTGCCAT
1 ACTG-TTACTGGCAGTTTATACAACATA-CAGGCATTAAATGTGCCAT
* *
1110054 ACTGTTATTGGCAATTTATA
1 ACTGTTACTGGCAGTTTATA
1110074 GTGTATACTG
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
46 22 0.41
47 32 0.59
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (46 bp):
ACTGTTACTGGCAGTTTATACAACATACAGGCATTAAATGTGCCAT
Found at i:1110327 original size:17 final size:17
Alignment explanation
Indices: 1110307--1110401 Score: 75
Period size: 17 Copynumber: 5.6 Consensus size: 17
1110297 AGTAACAATG
1110307 CAATAAAAGATATAGTA
1 CAATAAAAGATATAGTA
* * *
1110324 CAATAAAAGATACAATG
1 CAATAAAAGATATAGTA
** * *
1110341 CGGTAAAAGATATAATG
1 CAATAAAAGATATAGTA
* * *
1110358 CAATAAATGAAACAGTA
1 CAATAAAAGATATAGTA
1110375 CAATAAAAGA-ATCAGTA
1 CAATAAAAGATAT-AGTA
*
1110392 TAATAAAAGA
1 CAATAAAAGA
1110402 AACAATATAG
Statistics
Matches: 61, Mismatches: 16, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
16 1 0.02
17 60 0.98
ACGTcount: A:0.58, C:0.08, G:0.14, T:0.20
Consensus pattern (17 bp):
CAATAAAAGATATAGTA
Found at i:1110339 original size:34 final size:34
Alignment explanation
Indices: 1110280--1110407 Score: 125
Period size: 34 Copynumber: 3.8 Consensus size: 34
1110270 ATGAAACTAG
* * *
1110280 AAGAAATAGTACGA-AAAAGTAACAATGCAATAA
1 AAGATATAGTACAATAAAAGAAACAATGCAATAA
* **
1110313 AAGATATAGTACAATAAAAGATACAATGCGGTAA
1 AAGATATAGTACAATAAAAGAAACAATGCAATAA
* * * * *
1110347 AAGATATAATGCAATAAATGAAACAGTACAATAA
1 AAGATATAGTACAATAAAAGAAACAATGCAATAA
*
1110381 AAGA-ATCAGTATAATAAAAGAAACAAT
1 AAGATAT-AGTACAATAAAAGAAACAAT
1110408 ATAGAAAGAA
Statistics
Matches: 74, Mismatches: 19, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
33 14 0.19
34 60 0.81
ACGTcount: A:0.59, C:0.09, G:0.14, T:0.19
Consensus pattern (34 bp):
AAGATATAGTACAATAAAAGAAACAATGCAATAA
Found at i:1110402 original size:17 final size:17
Alignment explanation
Indices: 1110280--1110405 Score: 74
Period size: 17 Copynumber: 7.5 Consensus size: 17
1110270 ATGAAACTAG
* *
1110280 AAGAAATAGTACGA-AA
1 AAGAAACAGTACAATAA
* * *
1110296 AAGTAACAATGCAATAA
1 AAGAAACAGTACAATAA
* *
1110313 AAGATATAGTACAATAA
1 AAGAAACAGTACAATAA
* * * **
1110330 AAGATACAATGCGGTAA
1 AAGAAACAGTACAATAA
* * * *
1110347 AAGATATAATGCAATAA
1 AAGAAACAGTACAATAA
*
1110364 ATGAAACAGTACAATAA
1 AAGAAACAGTACAATAA
* *
1110381 AAGAATCAGTATAATAA
1 AAGAAACAGTACAATAA
1110398 AAGAAACA
1 AAGAAACA
1110406 ATATAGAAAG
Statistics
Matches: 82, Mismatches: 27, Indels: 1
0.75 0.25 0.01
Matches are distributed among these distances:
16 9 0.11
17 73 0.89
ACGTcount: A:0.59, C:0.09, G:0.14, T:0.18
Consensus pattern (17 bp):
AAGAAACAGTACAATAA
Found at i:1113246 original size:44 final size:44
Alignment explanation
Indices: 1113197--1113324 Score: 120
Period size: 44 Copynumber: 3.2 Consensus size: 44
1113187 TTTAAACATT
1113197 ATATTTTATCTTTATTTTAGGTATTTTAGTTTAAATAGGTTTTA
1 ATATTTTATCTTTATTTTAGGTATTTTAGTTTAAATAGGTTTTA
* *
1113241 ATATTTTA-ATTAAGTTTTAGG-A---TA--TT--AT---TTTT-
1 ATATTTTATCTTTA-TTTTAGGTATTTTAGTTTAAATAGGTTTTA
*
1113273 ATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTA
1 ATATTTTATCTTTATTTTAGGTATTTTAGTTTAAATAGGTTTTA
*
1113317 GTATTTTA
1 ATATTTTA
1113325 ATTAGGATTT
Statistics
Matches: 64, Mismatches: 6, Indels: 28
0.65 0.06 0.29
Matches are distributed among these distances:
32 15 0.23
33 7 0.11
36 4 0.06
38 4 0.06
40 4 0.06
43 8 0.12
44 22 0.34
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.59
Consensus pattern (44 bp):
ATATTTTATCTTTATTTTAGGTATTTTAGTTTAAATAGGTTTTA
Found at i:1113399 original size:75 final size:77
Alignment explanation
Indices: 1113202--1113410 Score: 300
Period size: 76 Copynumber: 2.8 Consensus size: 77
1113192 ACATTATATT
* * * *
1113202 TTATCTTTATTTTAGGTATTTTAGTTTAAATAGGTTTTAA-TATTTTAATTAAGTTTTAGGATAT
1 TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAAGTATTTTAATTAGGATTTAGAATAT
* *
1113266 TATTTTTATATT
66 TATTTTTAAATA
1113278 TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGGATTTAGAATAT
1 TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAAGTATTTTAATTAGGATTTAGAATAT
1113342 TA-TTTTAAATA
66 TATTTTTAAATA
* * * *
1113353 TTATTTTTGTTTTAGGAATTTTAGTTTAAATA-TTTTTAAGTGTTTTAATTAGGATTTA
1 TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAAGTATTTTAATTAGGATTTA
1113411 AGATGTTTTA
Statistics
Matches: 121, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
74 4 0.03
75 57 0.47
76 60 0.50
ACGTcount: A:0.29, C:0.01, G:0.12, T:0.57
Consensus pattern (77 bp):
TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAAGTATTTTAATTAGGATTTAGAATAT
TATTTTTAAATA
Found at i:1114050 original size:17 final size:18
Alignment explanation
Indices: 1114028--1114069 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
1114018 CTTTCAATTA
1114028 TTTATTTAATTATT-TCT
1 TTTATTTAATTATTATCT
*
1114045 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
1114063 TTTATTT
1 TTTATTT
1114070 TAAAAATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:1114123 original size:27 final size:25
Alignment explanation
Indices: 1114093--1114158 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 25
1114083 TAAAACCCCC
1114093 ATTTTTATTTTACTACTATTATTTATT
1 ATTTTTATTTT-CT-CTATTATTTATT
*
1114120 ATTTTATTATTTTCTCTTTTATTTATT
1 A-TTT-TTATTTTCTCTATTATTTATT
*
1114147 ATTATCTATTTT
1 ATT-TTTATTTT
1114159 TTATGCATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
26 8 0.24
27 14 0.41
28 5 0.15
29 7 0.21
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.70
Consensus pattern (25 bp):
ATTTTTATTTTCTCTATTATTTATT
Found at i:1114158 original size:19 final size:18
Alignment explanation
Indices: 1114109--1114160 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
1114099 ATTTTACTAC
* *
1114109 TATTATTTATTATTTTAT
1 TATTATCTATTTTTTTAT
* *
1114127 TATTTTCTCTTTTATTTAT
1 TATTATCTATTTT-TTTAT
1114146 TATTATCTATTTTTT
1 TATTATCTATTTTTT
1114161 ATGCATTTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (18 bp):
TATTATCTATTTTTTTAT
Found at i:1115781 original size:108 final size:109
Alignment explanation
Indices: 1115586--1115799 Score: 376
Period size: 108 Copynumber: 2.0 Consensus size: 109
1115576 CATATTAGAC
*
1115586 AAACCCTATGAATGCAAAACTACTTACCAAGGGATTTATCTCTCAAGATCTTTCATGAGCACATT
1 AAACCCTATGAATGCAAAACTACTTACCAAGGGATTTATCACTCAAGATCTTTCATGAGCACATT
*
1115651 GCTTATATGGGTATAATGTCATTTAAGGATATTTAATTTTTGAG
66 GCTTATATAGGTATAATGTCATTTAAGGATATTTAATTTTTGAG
* * *
1115695 AAACTCTATGAATGCAAAATTACTTACCAAGGGA-TTATCACTCAAGGTCTTTCATGAGCACATT
1 AAACCCTATGAATGCAAAACTACTTACCAAGGGATTTATCACTCAAGATCTTTCATGAGCACATT
1115759 GCTTATATAGGTATAATGTCATTTAAGGATATTTAATTTTT
66 GCTTATATAGGTATAATGTCATTTAAGGATATTTAATTTTT
1115800 TAAGAAGTTT
Statistics
Matches: 100, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
108 68 0.68
109 32 0.32
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (109 bp):
AAACCCTATGAATGCAAAACTACTTACCAAGGGATTTATCACTCAAGATCTTTCATGAGCACATT
GCTTATATAGGTATAATGTCATTTAAGGATATTTAATTTTTGAG
Found at i:1116182 original size:21 final size:21
Alignment explanation
Indices: 1116145--1116220 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
1116135 TCTTCCGATG
* *
1116145 AAAAGGATCAATTCCTTCACC
1 AAAAGGATCGATCCCTTCACC
* **
1116166 AAAAGGATCGATCCCTTGATG
1 AAAAGGATCGATCCCTTCACC
* *
1116187 AAAATGATTGATCCCTTC-CC
1 AAAAGGATCGATCCCTTCACC
*
1116207 TTAAAGGATCGATC
1 -AAAAGGATCGATC
1116221 TCTTTCTTGC
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (21 bp):
AAAAGGATCGATCCCTTCACC
Found at i:1116204 original size:42 final size:41
Alignment explanation
Indices: 1116108--1116220 Score: 108
Period size: 42 Copynumber: 2.7 Consensus size: 41
1116098 CAATAGCATT
1116108 GGATTGATCCCTTCACCAAAGGAAT-GAT-CTTCCGATGAAAA
1 GGATTGATCCCTTCACCAAAGG-ATCGATCCTT-CGATGAAAA
** *
1116149 GGATCAATTCCTTCACCAAAAGGATCGATCCCTT-GATGAAAA
1 GGATTGATCCCTTCACC-AAAGGATCGAT-CCTTCGATGAAAA
*
1116191 TGATTGATCCCTTC-CCTTAAAGGATCGATC
1 GGATTGATCCCTTCACC--AAAGGATCGATC
1116221 TCTTTCTTGC
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
41 19 0.32
42 37 0.63
44 3 0.05
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (41 bp):
GGATTGATCCCTTCACCAAAGGATCGATCCTTCGATGAAAA
Found at i:1118775 original size:30 final size:30
Alignment explanation
Indices: 1118739--1118803 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
1118729 GAGAATCGGT
* *
1118739 GGTTCACACCGGTTTTGCCGGTTTTCAGCC
1 GGTTCACACCGATTTTGCCGGTTCTCAGCC
* * *
1118769 GGTTCACCCCGATTTTGTCGGTTCTCAGTC
1 GGTTCACACCGATTTTGCCGGTTCTCAGCC
1118799 GGTTC
1 GGTTC
1118804 TTCCAGTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.09, C:0.29, G:0.26, T:0.35
Consensus pattern (30 bp):
GGTTCACACCGATTTTGCCGGTTCTCAGCC
Found at i:1118898 original size:41 final size:41
Alignment explanation
Indices: 1118848--1118940 Score: 177
Period size: 41 Copynumber: 2.2 Consensus size: 41
1118838 TTTGGGAGTT
1118848 AACCGGACCGGACAGGCCACCGGTTGACGGTTAAACCGATTG
1 AACC-GACCGGACAGGCCACCGGTTGACGGTTAAACCGATTG
1118890 AACCGACCGGACAGGCCACCGGTTGACGGTTAAACCGATTG
1 AACCGACCGGACAGGCCACCGGTTGACGGTTAAACCGATTG
1118931 AACCGACCGG
1 AACCGACCGG
1118941 TCCGGTCCGA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 47 0.92
42 4 0.08
ACGTcount: A:0.27, C:0.30, G:0.30, T:0.13
Consensus pattern (41 bp):
AACCGACCGGACAGGCCACCGGTTGACGGTTAAACCGATTG
Found at i:1119802 original size:48 final size:48
Alignment explanation
Indices: 1119758--1119864 Score: 164
Period size: 48 Copynumber: 2.3 Consensus size: 48
1119748 ATATTTATAC
1119758 ATTCT-ATCA-ATTTGGTCATAAATTTAATTTAATTTAATAAATTTAA
1 ATTCTAATCAGATTTGGTCATAAATTTAATTTAATTTAATAAATTTAA
* *
1119804 TTTCTAATTAGATTTGGTCATAAATTTAATTTAATTTAATAAATTTAA
1 ATTCTAATCAGATTTGGTCATAAATTTAATTTAATTTAATAAATTTAA
* *
1119852 TTTCTAATTAGAT
1 ATTCTAATCAGAT
1119865 GGTGACACAT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
46 4 0.07
47 3 0.05
48 50 0.88
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (48 bp):
ATTCTAATCAGATTTGGTCATAAATTTAATTTAATTTAATAAATTTAA
Found at i:1120676 original size:20 final size:20
Alignment explanation
Indices: 1120661--1120746 Score: 154
Period size: 20 Copynumber: 4.3 Consensus size: 20
1120651 CTATCGCATT
*
1120661 GCGAATACGTAAATCGCAAT
1 GCGAATACGTAAATCGCAAC
*
1120681 ACGAATACGTAAATCGCAAC
1 GCGAATACGTAAATCGCAAC
1120701 GCGAATACGTAAATCGCAAC
1 GCGAATACGTAAATCGCAAC
1120721 GCGAATACGTAAATCGCAAC
1 GCGAATACGTAAATCGCAAC
1120741 GCGAAT
1 GCGAAT
1120747 CTGACTATCG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
GCGAATACGTAAATCGCAAC
Found at i:1120965 original size:22 final size:22
Alignment explanation
Indices: 1120940--1121005 Score: 114
Period size: 22 Copynumber: 3.0 Consensus size: 22
1120930 GGCGACATTC
1120940 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
1120962 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
*
1120984 GTCTCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
1121006 TTCACGGTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.26, C:0.39, G:0.14, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:1121408 original size:20 final size:20
Alignment explanation
Indices: 1121341--1121410 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
1121331 CGATTCTGTC
*
1121341 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
** *
1121360 GTTGCGATAGTAATTTTCGT
1 GTTGCGATTTTCATTTTCGT
1121380 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
1121400 GTTGCGATTTT
1 GTTGCGATTTT
1121411 AAGTTTCAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 10 0.23
20 33 0.77
ACGTcount: A:0.13, C:0.14, G:0.23, T:0.50
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:1123315 original size:20 final size:20
Alignment explanation
Indices: 1123290--1123426 Score: 95
Period size: 20 Copynumber: 7.5 Consensus size: 20
1123280 AGAATAGTTT
1123290 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1123310 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
1123326 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
1123343 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
1123359 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1123377 ACTATCGCAATGCAAAAATG
1 ACTATCGCAATGCGAAAATG
* **
1123397 ACTATCGCAATACGAATTTG
1 ACTATCGCAATGCGAAAATG
1123417 ACTATCGCAA
1 ACTATCGCAA
1123427 ACAAAACAGG
Statistics
Matches: 95, Mismatches: 8, Indels: 28
0.73 0.06 0.21
Matches are distributed among these distances:
14 14 0.15
16 10 0.11
17 8 0.08
18 5 0.05
19 7 0.07
20 51 0.54
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1123336 original size:34 final size:34
Alignment explanation
Indices: 1123293--1123386 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
1123283 ATAGTTTACT
* * *
1123293 ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACAACAAA
**
1123327 ATCGCAATGCG-AAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAAATGACTATCGCAACAACAAA
*
1123360 ATCGCAACGCGAAAATGACTATCGCAA
1 ATCGCAATGCGAAAATGACTATCGCAA
1123387 TGCAAAAATG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 27 0.53
34 24 0.47
ACGTcount: A:0.45, C:0.22, G:0.19, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACAACAAA
Found at i:1123395 original size:34 final size:34
Alignment explanation
Indices: 1123293--1123395 Score: 106
Period size: 34 Copynumber: 3.1 Consensus size: 34
1123283 ATAGTTTACT
* *
1123293 ATCGCAATGCGAAAATGACTATCGCAA-CGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAAGC-ACAAA
**
1123327 ATCGCAATGCG-AAATGAAAATCGCAA-CAACAAA
1 ATCGCAATGCGAAAATGACTATCGCAAGC-ACAAA
*
1123360 ATCGCAACGCGAAAATGACTATCGCAATGCA-AAA
1 ATCGCAATGCGAAAATGACTATCGCAA-GCACAAA
1123394 AT
1 AT
1123396 GACTATCGCA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
33 27 0.47
34 29 0.50
35 1 0.02
36 1 0.02
ACGTcount: A:0.46, C:0.21, G:0.18, T:0.15
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAAGCACAAA
Found at i:1125213 original size:19 final size:19
Alignment explanation
Indices: 1125189--1125228 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1125179 ATTCAAACAT
1125189 TTACTAATGTCATGGCATA
1 TTACTAATGTCATGGCATA
1125208 TTACTAATGTCATGGCATA
1 TTACTAATGTCATGGCATA
1125227 TT
1 TT
1125229 TATTTTACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (19 bp):
TTACTAATGTCATGGCATA
Found at i:1132426 original size:44 final size:43
Alignment explanation
Indices: 1132344--1132436 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 43
1132334 ATTACAAGAG
* *
1132344 AAATAAATAAAAATGAAAAAATGTTAAATTCCAAAAGAAATTTA
1 AAATAAATAAAAATGAAAAAATATTAAATTCCAAAAGAAA-TAA
** *
1132388 AAATAAATAAAAATGAAGAAAATATT-AATTTTAGAAGAAATAA
1 AAATAAATAAAAATGAA-AAAATATTAAATTCCAAAAGAAATAA
1132431 AAATAA
1 AAATAA
1132437 CAAATTTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
43 8 0.19
44 28 0.65
45 7 0.16
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.25
Consensus pattern (43 bp):
AAATAAATAAAAATGAAAAAATATTAAATTCCAAAAGAAATAA
Found at i:1136881 original size:31 final size:32
Alignment explanation
Indices: 1136823--1136883 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
1136813 TTAAATGTTG
* *
1136823 ATGTAAAATTTTAATATATTTTTAAATTAATT
1 ATGTAAAATTTTAATATATATTAAAATTAATT
1136855 ATGT-AAATTTTAATAT-TAATTAAAATTAA
1 ATGTAAAATTTTAATATAT-ATTAAAATTAA
1136884 AATAATACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 1 0.04
31 21 0.81
32 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (32 bp):
ATGTAAAATTTTAATATATATTAAAATTAATT
Found at i:1136955 original size:15 final size:15
Alignment explanation
Indices: 1136935--1136965 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1136925 CAACAAATAG
1136935 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1136950 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1136965 A
1 A
1136966 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1137347 original size:3 final size:3
Alignment explanation
Indices: 1137339--1137433 Score: 98
Period size: 3 Copynumber: 33.7 Consensus size: 3
1137329 TAAAAAGAAT
*
1137339 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA -AA TAA -AA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1137384 TAA T-A TAA T-A TAA T-A TAA T-A TAA T-A TAA TATA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
1137425 CTAA TAA TA
1 -TAA TAA TA
1137434 TGTTTTCAAA
Statistics
Matches: 78, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
2 16 0.21
3 57 0.73
4 5 0.06
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1137359 original size:15 final size:15
Alignment explanation
Indices: 1137339--1137433 Score: 98
Period size: 13 Copynumber: 6.7 Consensus size: 15
1137329 TAAAAAGAAT
1137339 TAATAATAATAATAA
1 TAATAATAATAATAA
1137354 TAATAATAATAAT-A
1 TAATAATAATAATAA
1137368 TAA-AATAA-AATAA
1 TAATAATAATAATAA
*
1137381 AAATAAT-ATAAT-A
1 TAATAATAATAATAA
1137394 TAAT-ATAAT-ATAA
1 TAATAATAATAATAA
1137407 T-ATAATATATAATAA
1 TAATAATA-ATAATAA
*
1137422 AAACTAATAATA
1 TAA-TAATAATA
1137434 TGTTTTCAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 19
0.75 0.03 0.21
Matches are distributed among these distances:
12 9 0.13
13 20 0.30
14 12 0.18
15 17 0.25
16 4 0.06
17 5 0.07
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (15 bp):
TAATAATAATAATAA
Found at i:1137375 original size:5 final size:5
Alignment explanation
Indices: 1137343--1137423 Score: 54
Period size: 5 Copynumber: 15.4 Consensus size: 5
1137333 AAGAATTAAT
* *
1137343 AATAA TAATAA TAATAA TAATAA TATAA AATAA AATAAA AATAA TATAA
1 AATAA -AATAA -AATAA -AATAA AATAA AATAA AAT-AA AATAA AATAA
* * * * * *
1137392 TATAA TATAA TATAA TATAA TATAT AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AA
1137424 ACTAATAATA
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
5 46 0.68
6 22 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (5 bp):
AATAA
Found at i:1137429 original size:17 final size:17
Alignment explanation
Indices: 1137340--1137430 Score: 75
Period size: 16 Copynumber: 5.4 Consensus size: 17
1137330 AAAAAGAATT
1137340 AATAATA-ATAATAATAA
1 AATAATATATAAT-ATAA
*
1137357 TAATAATAATATAAAATAA
1 -AATAAT-ATATAATATAA
*
1137376 AATAA-AAATAATATAA
1 AATAATATATAATATAA
*
1137392 TAT-A-ATATAATATAA
1 AATAATATATAATATAA
*
1137407 TATAATATATAATA-AA
1 AATAATATATAATATAA
1137423 AACTAATA
1 AA-TAATA
1137431 ATATGTTTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
15 14 0.23
16 15 0.24
17 13 0.21
18 11 0.18
19 5 0.08
20 4 0.06
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAATATATAATATAA
Found at i:1137521 original size:36 final size:38
Alignment explanation
Indices: 1137480--1137598 Score: 107
Period size: 40 Copynumber: 3.1 Consensus size: 38
1137470 AGAAAAAAAG
* *
1137480 AAAAATCATTTTTAAAACTATAT-AT-TATATGGTTTC
1 AAAAATCATTTTCAAAACTATATAATATATATGCTTTC
** * *
1137516 AAAAATTGTTTTCGAAATTATATAATATATATGCTTTC
1 AAAAATCATTTTCAAAACTATATAATATATATGCTTTC
** * * *
1137554 AAAAAAAATGTTTTCGAAACTATACAATATATATGTTTTC
1 AAAAATCA--TTTTCAAAACTATATAATATATATGCTTTC
1137594 AAAAA
1 AAAAA
1137599 CTATATATTA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
36 18 0.27
37 2 0.03
38 15 0.22
40 32 0.48
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (38 bp):
AAAAATCATTTTCAAAACTATATAATATATATGCTTTC
Found at i:1137556 original size:38 final size:38
Alignment explanation
Indices: 1137494--1137598 Score: 133
Period size: 40 Copynumber: 2.8 Consensus size: 38
1137484 ATCATTTTTA
* *
1137494 AAACTATAT-AT-TATATGGTTTCAAAAATTGTTTTCG
1 AAACTATATAATATATATGCTTTCAAAAAATGTTTTCG
*
1137530 AAATTATATAATATATATGCTTTCAAAAAAAATGTTTTCG
1 AAACTATATAATATATATGCTTTC--AAAAAATGTTTTCG
* *
1137570 AAACTATACAATATATATGTTTTCAAAAA
1 AAACTATATAATATATATGCTTTCAAAAA
1137599 CTATATATTA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
36 8 0.14
37 2 0.03
38 15 0.25
40 34 0.58
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.40
Consensus pattern (38 bp):
AAACTATATAATATATATGCTTTCAAAAAATGTTTTCG
Found at i:1137603 original size:26 final size:24
Alignment explanation
Indices: 1137561--1137622 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
1137551 TTCAAAAAAA
*
1137561 ATGTTTTC-GAAACTATACAATATAT
1 ATGTTTTCAAAAACTATA-AAT-TAT
*
1137586 ATGTTTTCAAAAACTATATATTAT
1 ATGTTTTCAAAAACTATAAATTAT
*
1137610 ACGTTTTCAAAAA
1 ATGTTTTCAAAAA
1137623 TGTGTTTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 15 0.45
25 10 0.30
26 8 0.24
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.40
Consensus pattern (24 bp):
ATGTTTTCAAAAACTATAAATTAT
Found at i:1137642 original size:37 final size:37
Alignment explanation
Indices: 1137584--1137690 Score: 178
Period size: 37 Copynumber: 2.9 Consensus size: 37
1137574 TATACAATAT
*
1137584 ATATGTTTTCAAAAACTATATATTATACGTTTTCAAAA
1 ATATGTTTTC-AAAACTATATAATATACGTTTTCAAAA
*
1137622 ATGTGTTTTCAAAACTATATAATATACGTTTTCAAAA
1 ATATGTTTTCAAAACTATATAATATACGTTTTCAAAA
*
1137659 ATATGTTTTCAAAACTATATAATATATGTTTT
1 ATATGTTTTCAAAACTATATAATATACGTTTT
1137691 TAAATCGTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
37 56 0.86
38 9 0.14
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (37 bp):
ATATGTTTTCAAAACTATATAATATACGTTTTCAAAA
Found at i:1138401 original size:6 final size:6
Alignment explanation
Indices: 1138384--1138437 Score: 99
Period size: 6 Copynumber: 9.0 Consensus size: 6
1138374 AAAATCCGGT
*
1138384 CTCTCA CACTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA
1 CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA CTCTCA
1138432 CTCTCA
1 CTCTCA
1138438 GACGGGGAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.19, C:0.50, G:0.00, T:0.31
Consensus pattern (6 bp):
CTCTCA
Found at i:1141953 original size:21 final size:22
Alignment explanation
Indices: 1141906--1141954 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1141896 CGTTGACCAT
* *
1141906 TACGATACTGACATGACACTTC
1 TACGGTACTGACATGACACGTC
1141928 T-CGGTACTGACATGACA-GTC
1 TACGGTACTGACATGACACGTC
1141948 TACGGTA
1 TACGGTA
1141955 GTTGTGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 20 0.83
22 1 0.04
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (22 bp):
TACGGTACTGACATGACACGTC
Found at i:1147303 original size:21 final size:22
Alignment explanation
Indices: 1147277--1147332 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
1147267 AAATATTCAA
*
1147277 AAAAATTAAATA-TAAAATACC
1 AAAAATTAAAAATTAAAATACC
* *
1147298 AAAAA-TAAAAATTAAATTACT
1 AAAAATTAAAAATTAAAATACC
1147319 ATAAAATTAAAAAT
1 A-AAAATTAAAAAT
1147333 ATATCTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 5 0.17
21 13 0.45
22 4 0.14
23 7 0.24
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAAATTAAAAATTAAAATACC
Found at i:1148151 original size:26 final size:26
Alignment explanation
Indices: 1148114--1148166 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1148104 ACTTTAGAAT
1148114 CTCACAAAACTTACCTATAACGTTAA
1 CTCACAAAACTTACCTATAACGTTAA
* *
1148140 CTCACAACACTTATCTATAACGTTAA
1 CTCACAAAACTTACCTATAACGTTAA
1148166 C
1 C
1148167 ATGTCATCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.28, G:0.04, T:0.28
Consensus pattern (26 bp):
CTCACAAAACTTACCTATAACGTTAA
Found at i:1150591 original size:14 final size:15
Alignment explanation
Indices: 1150572--1150610 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
1150562 TATAAGGTAA
1150572 TTTTATTATA-ATAT
1 TTTTATTATACATAT
*
1150586 TTTTATTATACTTAT
1 TTTTATTATACATAT
1150601 TGTTTATTAT
1 T-TTTATTAT
1150611 GATTATTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.45
15 4 0.18
16 8 0.36
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTATTATACATAT
Found at i:1150616 original size:16 final size:14
Alignment explanation
Indices: 1150572--1150618 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 14
1150562 TATAAGGTAA
*
1150572 TTTTATTATAATAT
1 TTTTATTATATTAT
1150586 TTTTATTATACTTAT
1 TTTTATTATA-TTAT
1150601 TGTTTATTATGATTAT
1 T-TTTATTAT-ATTAT
1150617 TT
1 TT
1150619 GAAAAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 10 0.34
15 5 0.17
16 13 0.45
17 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (14 bp):
TTTTATTATATTAT
Found at i:1154030 original size:35 final size:34
Alignment explanation
Indices: 1153945--1154031 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 34
1153935 AATATAATTT
*
1153945 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
*
1153979 TAAATGATAA-ACAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACA-AAATTACAATAA--G-TATTAAATGG
1154017 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
1154032 ACCAAATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
34 6 0.13
35 22 0.49
36 2 0.04
37 4 0.09
38 11 0.24
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:1154060 original size:34 final size:33
Alignment explanation
Indices: 1154022--1154099 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 33
1154012 AATGGTAATA
* *
1154022 AACAAAATTAACCAAAT-ATATTAACAA-AAAGTTC
1 AACAAAATTAACAAAATAAT-TTAA-AATAAA-TCC
*
1154056 AACAAATTTAACAAAATAATTTAAAATAAATCC
1 AACAAAATTAACAAAATAATTTAAAATAAATCC
1154089 AACAAAATTAA
1 AACAAAATTAA
1154100 TGAAATAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
33 14 0.37
34 22 0.58
35 2 0.05
ACGTcount: A:0.62, C:0.13, G:0.01, T:0.24
Consensus pattern (33 bp):
AACAAAATTAACAAAATAATTTAAAATAAATCC
Found at i:1156420 original size:17 final size:18
Alignment explanation
Indices: 1156391--1156438 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
1156381 CAAAAAAAAA
*
1156391 TTAATTAAA-TAAAATA-
1 TTAAATAAATTAAAATAC
*
1156407 TTAAA-AAATTTAAATAC
1 TTAAATAAATTAAAATAC
1156424 TTAAATAAATTAAAA
1 TTAAATAAATTAAAA
1156439 ACAAAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.12
16 10 0.38
17 5 0.19
18 8 0.31
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
TTAAATAAATTAAAATAC
Found at i:1160411 original size:23 final size:23
Alignment explanation
Indices: 1160385--1160437 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1160375 AAAACTACCA
* *
1160385 AAAGACAGAGATAAACGTGTCAT
1 AAAGACAAAGATAAACGTGTCAC
*
1160408 AAAGACAAAGATAAATGTGTCAC
1 AAAGACAAAGATAAACGTGTCAC
1160431 AAAGACA
1 AAAGACA
1160438 TAATTATTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.53, C:0.13, G:0.19, T:0.15
Consensus pattern (23 bp):
AAAGACAAAGATAAACGTGTCAC
Found at i:1163145 original size:2 final size:2
Alignment explanation
Indices: 1163138--1163167 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1163128 TAAATCAAAT
1163138 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
1163168 AAATAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1165966 original size:2 final size:2
Alignment explanation
Indices: 1165961--1166016 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1165951 AAATATATCG
1165961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1166003 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1166017 TCCATACTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1171738 original size:14 final size:14
Alignment explanation
Indices: 1171719--1171748 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1171709 AGGCGTTACC
1171719 TAATATGTTGATAA
1 TAATATGTTGATAA
1171733 TAATATGTTGATAA
1 TAATATGTTGATAA
1171747 TA
1 TA
1171749 CTAATAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
TAATATGTTGATAA
Found at i:1171902 original size:117 final size:118
Alignment explanation
Indices: 1171763--1172023 Score: 375
Period size: 118 Copynumber: 2.2 Consensus size: 118
1171753 TAACAAATTA
* * *
1171763 AGTAATTAACCTATTTTGTTATCGTCAGATTTTCAAAGCCCCATCAAC-TTAAAAATGT-GCTAC
1 AGTAATTAACCGATTATGTTATCGTCAGATTTCCAAAGCCCCATCAACTTTAAAAA-GTCGCTAC
*
1171826 CTATTACGTTATATAAGCACTACCTAATATTTTATTATGCTTGATAATGTTTCT-
65 CTATTACGTTATATAAGCACTACCTAATATGTTATTATGCTTGATAAT-TTTCTC
* * * *
1171880 AGTAATTAATCGATTATGTTATCGTAAGATTTCCAAAGCTCCATCAGCTTTAAAAAGTCGCTACC
1 AGTAATTAACCGATTATGTTATCGTCAGATTTCCAAAGCCCCATCAACTTTAAAAAGTCGCTACC
** * *
1171945 TATTACGTTATATAAGTGCTACCTAATATGTTATTGTGCTTGATAATTTTTTC
66 TATTACGTTATATAAGCACTACCTAATATGTTATTATGCTTGATAATTTTCTC
1171998 AGTAATTAACCGATTATGTTATCGTC
1 AGTAATTAACCGATTATGTTATCGTC
1172024 TATATTTTTT
Statistics
Matches: 127, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
117 47 0.37
118 80 0.63
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (118 bp):
AGTAATTAACCGATTATGTTATCGTCAGATTTCCAAAGCCCCATCAACTTTAAAAAGTCGCTACC
TATTACGTTATATAAGCACTACCTAATATGTTATTATGCTTGATAATTTTCTC
Found at i:1171965 original size:23 final size:24
Alignment explanation
Indices: 1171934--1171978 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1171924 CAGCTTTAAA
*
1171934 AAGTCGCTACCTATTACGTTATAT
1 AAGTCGCTACCTAATACGTTATAT
*
1171958 AAGT-GCTACCTAATATGTTAT
1 AAGTCGCTACCTAATACGTTAT
1171979 TGTGCTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (24 bp):
AAGTCGCTACCTAATACGTTATAT
Found at i:1172158 original size:16 final size:16
Alignment explanation
Indices: 1172137--1172188 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
1172127 CGGTATCAAT
*
1172137 TTTAACCAGTCACTTG
1 TTTAACCAATCACTTG
1172153 TTTAACCAATCACTTG
1 TTTAACCAATCACTTG
*
1172169 CTTAACCAATCACGTTG
1 TTTAACCAATCAC-TTG
1172186 TTT
1 TTT
1172189 TTTAGCCGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
16 27 0.84
17 5 0.16
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (16 bp):
TTTAACCAATCACTTG
Found at i:1174161 original size:21 final size:21
Alignment explanation
Indices: 1174111--1174191 Score: 126
Period size: 21 Copynumber: 3.8 Consensus size: 21
1174101 GTTATGGAAT
*
1174111 GGGAGTATCGATACTCATCAA
1 GGGAGTATCGATACTCACCAA
*
1174132 GGAGAGTATCGGTACTCACCAA
1 GG-GAGTATCGATACTCACCAA
1174154 GGGAGTATCGATACTCACCAA
1 GGGAGTATCGATACTCACCAA
*
1174175 GGGAGTATCGGTACTCA
1 GGGAGTATCGATACTCA
1174192 TAGGAATAGT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
21 36 0.65
22 19 0.35
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (21 bp):
GGGAGTATCGATACTCACCAA
Found at i:1174176 original size:43 final size:42
Alignment explanation
Indices: 1174111--1174191 Score: 144
Period size: 43 Copynumber: 1.9 Consensus size: 42
1174101 GTTATGGAAT
*
1174111 GGGAGTATCGATACTCATCAAGGAGAGTATCGGTACTCACCAA
1 GGGAGTATCGATACTCACCAAGG-GAGTATCGGTACTCACCAA
1174154 GGGAGTATCGATACTCACCAAGGGAGTATCGGTACTCA
1 GGGAGTATCGATACTCACCAAGGGAGTATCGGTACTCA
1174192 TAGGAATAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
42 15 0.41
43 22 0.59
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (42 bp):
GGGAGTATCGATACTCACCAAGGGAGTATCGGTACTCACCAA
Found at i:1175995 original size:21 final size:21
Alignment explanation
Indices: 1175969--1176011 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1175959 TTGATCTTAA
1175969 AAGTTTTGTCTACATTCCAAG
1 AAGTTTTGTCTACATTCCAAG
*
1175990 AAGTTTTGTCTACCTTCCAAG
1 AAGTTTTGTCTACATTCCAAG
1176011 A
1 A
1176012 TTTGAGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (21 bp):
AAGTTTTGTCTACATTCCAAG
Found at i:1177367 original size:74 final size:74
Alignment explanation
Indices: 1177247--1177413 Score: 266
Period size: 74 Copynumber: 2.3 Consensus size: 74
1177237 TTAAATGACT
1177247 AAGGGTATCAGTACCTAT-AGGGGGTATCGGTACCTATTGGGCATTCTGTTTTTCTCGGAGCCAA
1 AAGGGTATCAGTACCTATGAGGGGGTATCGGTACCTATTGGGCATTCTGTTTTTCTCGGAGCCAA
*
1177311 AATTAACAC
66 AATCAACAC
*
1177320 AAGGGTATCAGTACCCTATGA-GGGGTATCGGTACCTATTTGGCATTCTGTTTTTCTCGGAGCCA
1 AAGGGTATCAGTA-CCTATGAGGGGGTATCGGTACCTATTGGGCATTCTGTTTTTCTCGGAGCCA
*
1177384 AAATCAACAT
65 AAATCAACAC
* *
1177394 AAAGGTATCGGTACCTATGA
1 AAGGGTATCAGTACCTATGA
1177414 CTTAGGTATC
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
73 20 0.23
74 66 0.76
75 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (74 bp):
AAGGGTATCAGTACCTATGAGGGGGTATCGGTACCTATTGGGCATTCTGTTTTTCTCGGAGCCAA
AATCAACAC
Found at i:1177749 original size:14 final size:14
Alignment explanation
Indices: 1177730--1177764 Score: 63
Period size: 13 Copynumber: 2.6 Consensus size: 14
1177720 GATTTTCTTA
1177730 TTGAAAATCATTTT
1 TTGAAAATCATTTT
1177744 TTG-AAATCATTTT
1 TTGAAAATCATTTT
1177757 TTGAAAAT
1 TTGAAAAT
1177765 TACTCCCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (14 bp):
TTGAAAATCATTTT
Found at i:1178091 original size:14 final size:16
Alignment explanation
Indices: 1178072--1178103 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1178062 TCAATCATCC
1178072 ATATC-ATCCAAA-AT
1 ATATCAATCCAAACAT
1178086 ATATCAATCCAAACAT
1 ATATCAATCCAAACAT
1178102 AT
1 AT
1178104 CCAAAATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 7 0.44
16 4 0.25
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (16 bp):
ATATCAATCCAAACAT
Found at i:1181506 original size:18 final size:18
Alignment explanation
Indices: 1181483--1181548 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
1181473 AGGGATTATC
*
1181483 AGTGGTCCTTCGAGACAT
1 AGTGGTCATTCGAGACAT
*
1181501 AGTGGTCATTCGAGAAAT
1 AGTGGTCATTCGAGACAT
* *
1181519 ATTGGTCATTC-AGGACTT
1 AGTGGTCATTCGA-GACAT
*
1181537 AGTGGTCCTTCG
1 AGTGGTCATTCG
1181549 TGAAAAATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
17 1 0.03
18 38 0.97
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (18 bp):
AGTGGTCATTCGAGACAT
Found at i:1182231 original size:21 final size:21
Alignment explanation
Indices: 1182205--1182277 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
1182195 CAAAGAGGGC
1182205 ATCGATACACGTTAAAGGAGT
1 ATCGATACACGTTAAAGGAGT
*
1182226 ATCGATAC-C--TAGCAAGGGATT
1 ATCGATACACGTTA--AA-GGAGT
* **
1182247 ATCGATACATGTTTTAGGAGT
1 ATCGATACACGTTAAAGGAGT
1182268 ATCGATACAC
1 ATCGATACAC
1182278 TGTGCACAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
18 2 0.05
20 3 0.08
21 33 0.82
22 1 0.03
24 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (21 bp):
ATCGATACACGTTAAAGGAGT
Found at i:1192540 original size:21 final size:21
Alignment explanation
Indices: 1192516--1192569 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1192506 TGCTCATAGA
* * *
1192516 AGTATTGATACTTGATCCTAG
1 AGTATCGATACTTGACCCCAG
*
1192537 AGTATCGATACTTTACCCCAG
1 AGTATCGATACTTGACCCCAG
1192558 AGTATCGATACT
1 AGTATCGATACT
1192570 ACCCATCTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (21 bp):
AGTATCGATACTTGACCCCAG
Found at i:1192652 original size:20 final size:20
Alignment explanation
Indices: 1192629--1192667 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1192619 GGGATGGTCT
*
1192629 GTAAGGATAGAACTTAGTCC
1 GTAAGGATAAAACTTAGTCC
1192649 GTAAGGATAAAACTTAGTC
1 GTAAGGATAAAACTTAGTC
1192668 TGTGAGGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (20 bp):
GTAAGGATAAAACTTAGTCC
Done.