Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 188 of 218
Found at i:55937015 original size:15 final size:15
Alignment explanation
Indices: 55936966--55937015 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
55936956 GAATAGGTGA
*
55936966 AGAACTTGTTCGTTG
1 AGAATTTGTTCGTTG
* *
55936981 AGAGTTTG--CGATG
1 AGAATTTGTTCGTTG
55936994 AAGAATTTGTTCGTTG
1 -AGAATTTGTTCGTTG
55937010 AGAATT
1 AGAATT
55937016 CGTGTCAAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
13 4 0.15
14 7 0.26
15 12 0.44
16 4 0.15
ACGTcount: A:0.26, C:0.08, G:0.28, T:0.38
Consensus pattern (15 bp):
AGAATTTGTTCGTTG
Found at i:55939013 original size:20 final size:20
Alignment explanation
Indices: 55938988--55939025 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
55938978 TTTTCGTGTC
55938988 AGAATCAGATATCAGTATTT
1 AGAATCAGATATCAGTATTT
55939008 AGAATCAGATATCAGTAT
1 AGAATCAGATATCAGTAT
55939026 ATGAAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (20 bp):
AGAATCAGATATCAGTATTT
Found at i:55939320 original size:109 final size:105
Alignment explanation
Indices: 55939035--55939342 Score: 429
Period size: 107 Copynumber: 2.9 Consensus size: 105
55939025 TATGAAAAAA
* * *
55939035 GTATACTGATATTTGATTCTTACAAGAAAAAAAAATGAA-TTTTTTTAAATTATACTGGGTGCCG
1 GTATACTGATATCTGATTCTAAC-A-AAAAAAAAA-GAATTTTTTTTAAATTGTACTGGGTGCCG
*
55939099 GCCATTGACAGGCCAGCACCCATAATTTTTTTTTTACTTTTTTC
63 GCCATTGACAGACCAGCACCCA-AATTTTTTTTTTACTTTTTTC
* * * *
55939143 GTATACTGATATCTGATTTTGACACAAAAAAAAAGAATTTTTTTTAAATTGTACTGGATGCCGAC
1 GTATACTGATATCTGATTCTAACA-AAAAAAAAAGAATTTTTTTTAAATTGTACTGGGTGCCGGC
*
55939208 CATTGACAGACCAGCACCCAAATTTTTTTTTTATTTTTTTC
65 CATTGACAGACCAGCACCCAAATTTTTTTTTTACTTTTTTC
55939249 GTATACTGATATCTGATTCTAACAATTAAAAAAAAGAAATTTTTTTTAAAATTGTACTGGGTGCC
1 GTATACTGATATCTGATTCTAACAA--AAAAAAAAG-AATTTTTTTT-AAATTGTACTGGGTGCC
**
55939314 GGCCATTGACAGACCAATACCCAAATTTT
62 GGCCATTGACAGACCAGCACCCAAATTTT
55939343 GTTTCCCTTT
Statistics
Matches: 180, Mismatches: 15, Indels: 9
0.88 0.07 0.04
Matches are distributed among these distances:
105 1 0.01
106 45 0.25
107 62 0.34
108 30 0.17
109 42 0.23
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (105 bp):
GTATACTGATATCTGATTCTAACAAAAAAAAAAGAATTTTTTTTAAATTGTACTGGGTGCCGGCC
ATTGACAGACCAGCACCCAAATTTTTTTTTTACTTTTTTC
Found at i:55941333 original size:14 final size:14
Alignment explanation
Indices: 55941316--55941345 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55941306 CGGTGTTGTT
55941316 TTGTTATTATATTA
1 TTGTTATTATATTA
*
55941330 TTGTTATTTTATTA
1 TTGTTATTATATTA
55941344 TT
1 TT
55941346 ATTGTTTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (14 bp):
TTGTTATTATATTA
Found at i:55945289 original size:3 final size:3
Alignment explanation
Indices: 55945281--55945307 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
55945271 AGGTAGCAAG
55945281 CAC CAC CAC CAC CAC CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC
55945308 TCATTTTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:55947132 original size:61 final size:61
Alignment explanation
Indices: 55947067--55947205 Score: 183
Period size: 60 Copynumber: 2.3 Consensus size: 61
55947057 ACCAAAAATT
* ** *
55947067 AATTTATTGAATTTTTTAGAATT-AGAACTAAATTGACAAACTTTGTAAATGTTGAAGGTTA
1 AATTTATTGAATTTTTTAGAATTCA-AACTAAAATGACAAACTTTGTAAACATTGAAGGCTA
* *
55947128 AATTTATTG-ATTTTTTAGAATTCAAACTAAAATGACAAATTTTGTAAACATTGATGGCTA
1 AATTTATTGAATTTTTTAGAATTCAAACTAAAATGACAAACTTTGTAAACATTGAAGGCTA
* *
55947188 AATTTGTTGAATATTTTA
1 AATTTATTGAATTTTTTA
55947206 TATTTAGGAT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
60 51 0.75
61 17 0.25
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (61 bp):
AATTTATTGAATTTTTTAGAATTCAAACTAAAATGACAAACTTTGTAAACATTGAAGGCTA
Found at i:55971916 original size:44 final size:44
Alignment explanation
Indices: 55971853--55972009 Score: 251
Period size: 44 Copynumber: 3.6 Consensus size: 44
55971843 TTTGAGTACT
* * *
55971853 TCTGATCAGTAACAAGTGATTAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGTTACACTTA
55971897 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGTTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGTTACACTTA
*
55971941 TCTAATCAGTGACAAGTGATAAGTGGTAGCTTTAGTTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGTTACACTTA
* * *
55971985 TCTTATCAGTGACAAATGACAAGTG
1 TCTGATCAGTGACAAGTGATAAGTG
55972010 TTGTGATATG
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 106 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGTTACACTTA
Found at i:55972084 original size:47 final size:48
Alignment explanation
Indices: 55972011--55972109 Score: 130
Period size: 47 Copynumber: 2.1 Consensus size: 48
55972001 TGACAAGTGT
** *
55972011 TGTGATATGTGATTTTCGTGTAAGACCATATCTAGGATATGGCATT-GG
1 TGTGATATGTGATTCCCGTGTAAGACCATAGCTAGGATATGGC-TTCGG
* *
55972059 TGTGATATGTG-TTCCCGTGTAAGACCATAGCTGGGCTATGGCTTCGG
1 TGTGATATGTGATTCCCGTGTAAGACCATAGCTAGGATATGGCTTCGG
55972106 TGTG
1 TGTG
55972110 TGATATAAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
46 2 0.04
47 32 0.71
48 11 0.24
ACGTcount: A:0.20, C:0.14, G:0.30, T:0.35
Consensus pattern (48 bp):
TGTGATATGTGATTCCCGTGTAAGACCATAGCTAGGATATGGCTTCGG
Found at i:55975725 original size:21 final size:21
Alignment explanation
Indices: 55975700--55975751 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
55975690 TTTTTTTAAG
55975700 TTTTTTTTTTATG-TAAGTTT
1 TTTTTTTTTTATGTTAAGTTT
**
55975720 TCTTTTAATTTATGTTTTAAGTTT
1 T-TTTTTTTTTATG--TTAAGTTT
55975744 TTTTTTTT
1 TTTTTTTT
55975752 AACTCTAGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
20 1 0.04
21 10 0.42
23 5 0.21
24 8 0.33
ACGTcount: A:0.15, C:0.02, G:0.08, T:0.75
Consensus pattern (21 bp):
TTTTTTTTTTATGTTAAGTTT
Found at i:55986585 original size:26 final size:26
Alignment explanation
Indices: 55986556--55986606 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
55986546 CCCAAATCTT
*
55986556 TGTTAAAGAAAATACAGTGGTAAAAG
1 TGTTAAAGAAAATACAATGGTAAAAG
55986582 TGTTAAAGAAAATACAATGGTAAAA
1 TGTTAAAGAAAATACAATGGTAAAA
55986607 CTAGGGGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.24
Consensus pattern (26 bp):
TGTTAAAGAAAATACAATGGTAAAAG
Found at i:55986898 original size:20 final size:23
Alignment explanation
Indices: 55986864--55986909 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
55986854 AAGTAAGTTA
55986864 AAAATATTTTAATTAT-TATTTG
1 AAAATATTTTAATTATATATTTG
55986886 AAAAT-TTTT-ATTATAATATTTG
1 AAAATATTTTAATTAT-ATATTTG
55986908 AA
1 AA
55986910 TTTTTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.23
21 4 0.18
22 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
AAAATATTTTAATTATATATTTG
Found at i:55989520 original size:20 final size:20
Alignment explanation
Indices: 55989495--55989535 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
55989485 TGAGACTATG
55989495 TTATCTTGATTCTTACATTA
1 TTATCTTGATTCTTACATTA
55989515 TTATCTTGATTCTTACATTA
1 TTATCTTGATTCTTACATTA
55989535 T
1 T
55989536 GTACCATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.05, T:0.56
Consensus pattern (20 bp):
TTATCTTGATTCTTACATTA
Found at i:55997566 original size:9 final size:9
Alignment explanation
Indices: 55997549--55997585 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
55997539 TATAGTTTGA
55997549 TATTCGAAT
1 TATTCGAAT
*
55997558 TATTTGAAT
1 TATTCGAAT
*
55997567 TATTCGAGT
1 TATTCGAAT
55997576 TATTCGAAT
1 TATTCGAAT
55997585 T
1 T
55997586 GGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:55999323 original size:40 final size:39
Alignment explanation
Indices: 55999268--55999345 Score: 147
Period size: 40 Copynumber: 2.0 Consensus size: 39
55999258 TAAACTTAAT
55999268 CACTTTAATATTAAATTAATAAAATATTTATCAAGATAAC
1 CACTTTAATATTAAATTAATAAAATA-TTATCAAGATAAC
55999308 CACTTTAATATTAAATTAATAAAATATTATCAAGATAA
1 CACTTTAATATTAAATTAATAAAATATTATCAAGATAA
55999346 GTATTAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
39 12 0.32
40 26 0.68
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (39 bp):
CACTTTAATATTAAATTAATAAAATATTATCAAGATAAC
Found at i:56002792 original size:3 final size:3
Alignment explanation
Indices: 56002784--56002888 Score: 51
Period size: 3 Copynumber: 35.3 Consensus size: 3
56002774 TTTAACACTT
* * * *
56002784 TTA TTA TTA TT- TT- TTC TTCA TTA TT- TTA ATG TTA TTA TCTT TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA T-TA TTA
* * *
56002828 TTA TTA TGA TTA TTA TT- TCTA TTA TTA TT- TATA TCA TTT TTA TTCA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA TTA TT-A
*
56002874 TCA -TA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
56002889 ATGATAGTTT
Statistics
Matches: 77, Mismatches: 15, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
2 9 0.12
3 60 0.78
4 8 0.10
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:56003068 original size:2 final size:2
Alignment explanation
Indices: 56003061--56003097 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
56003051 GTACATATTT
*
56003061 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56003098 TCTTTATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:56003106 original size:37 final size:37
Alignment explanation
Indices: 56003059--56003142 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 37
56003049 ATGTACATAT
* *
56003059 TTTATATATATATATATATATATATATATATTTATATATTC
1 TTTATAT-TATA-AAATATAT-TATATAT-TTTATATATAC
*
56003100 TTTATATTTTAAAATATATTATATATTTTATATATAC
1 TTTATATTATAAAATATATTATATATTTTATATATAC
56003137 TTTATA
1 TTTATA
56003143 ATTCTAACAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
37 16 0.40
38 7 0.17
39 7 0.17
40 3 0.08
41 7 0.17
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (37 bp):
TTTATATTATAAAATATATTATATATTTTATATATAC
Found at i:56003308 original size:18 final size:18
Alignment explanation
Indices: 56003261--56003304 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
56003251 CTTAAAGTGC
* *
56003261 TTTAATTTTATTTGTTTA
1 TTTACTTTTATTTGTTGA
56003279 TTTACTTTTATTTGTTGA
1 TTTACTTTTATTTGTTGA
56003297 TTT-CTTTT
1 TTTACTTTT
56003305 TATTATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.73
Consensus pattern (18 bp):
TTTACTTTTATTTGTTGA
Found at i:56009041 original size:20 final size:20
Alignment explanation
Indices: 56009018--56009061 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
56009008 GTATGGTTAA
56009018 AAGTGGGCTTGTATCGATAG
1 AAGTGGGCTTGTATCGATAG
* *
56009038 AAGTGGGCTTGTATTGGTAG
1 AAGTGGGCTTGTATCGATAG
56009058 AAGT
1 AAGT
56009062 CCCCCTGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.25, C:0.07, G:0.36, T:0.32
Consensus pattern (20 bp):
AAGTGGGCTTGTATCGATAG
Found at i:56010049 original size:14 final size:16
Alignment explanation
Indices: 56010028--56010063 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
56010018 GAAATTGATT
56010028 AAAA-TATT-AAT-TA
1 AAAATTATTAAATATA
56010041 AAAATTATTAAATATA
1 AAAATTATTAAATATA
56010057 AAAATTA
1 AAAATTA
56010064 AATATAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 4 0.20
15 3 0.15
16 9 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATTATTAAATATA
Found at i:56010062 original size:23 final size:23
Alignment explanation
Indices: 56010019--56010065 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
56010009 AACGAAAAAG
**
56010019 AAATTGATTAAAATATTAATTAA
1 AAATTGATTAAAATAAAAATTAA
56010042 AAATT-ATTAAATATAAAAATTAA
1 AAATTGATTAAA-ATAAAAATTAA
56010065 A
1 A
56010066 TATAATGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AAATTGATTAAAATAAAAATTAA
Found at i:56025375 original size:109 final size:109
Alignment explanation
Indices: 56025184--56025398 Score: 412
Period size: 109 Copynumber: 2.0 Consensus size: 109
56025174 ATAGAGAACA
* *
56025184 TAAATGATCAATATTGGACATTACGTGCAGAGGAGGTAAGGCTCTTTGTCCTCCAAACGTGTCCC
1 TAAATGATCAATAGTGGACATTACGTGCAGAGGAGGTAAGGCTCTTTGTCCTCCAAACATGTCCC
56025249 AATTTGTATTTATACAGTATACCAATCTTAATTCTTGTAAAATG
66 AATTTGTATTTATACAGTATACCAATCTTAATTCTTGTAAAATG
56025293 TAAATGATCAATAGTGGACATTACGTGCAGAGGAGGTAAGGCTCTTTGTCCTCCAAACATGTCCC
1 TAAATGATCAATAGTGGACATTACGTGCAGAGGAGGTAAGGCTCTTTGTCCTCCAAACATGTCCC
56025358 AATTTGTATTTATACAGTATACCAATCTTAATTCTTGTAAA
66 AATTTGTATTTATACAGTATACCAATCTTAATTCTTGTAAA
56025399 TTTTACATTC
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 104 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (109 bp):
TAAATGATCAATAGTGGACATTACGTGCAGAGGAGGTAAGGCTCTTTGTCCTCCAAACATGTCCC
AATTTGTATTTATACAGTATACCAATCTTAATTCTTGTAAAATG
Found at i:56029614 original size:23 final size:24
Alignment explanation
Indices: 56029588--56029634 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
56029578 TATAATAGTT
* *
56029588 TAGGTATTTAAGTGAG-GAAAAAA
1 TAGGTACTGAAGTGAGTGAAAAAA
*
56029611 TAGGTACTGCAGTGAGTGAAAAAA
1 TAGGTACTGAAGTGAGTGAAAAAA
56029635 ACCTATATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.45, C:0.04, G:0.28, T:0.23
Consensus pattern (24 bp):
TAGGTACTGAAGTGAGTGAAAAAA
Found at i:56034195 original size:21 final size:22
Alignment explanation
Indices: 56034155--56034195 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
56034145 TTAAATAGAC
* *
56034155 TTAAGACAAATTAAAGCATACA
1 TTAAAACAAATTAAAACATACA
56034177 TTAAAACAAA-TAAAACATA
1 TTAAAACAAATTAAAACATA
56034196 TTTATCATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.61, C:0.12, G:0.05, T:0.22
Consensus pattern (22 bp):
TTAAAACAAATTAAAACATACA
Found at i:56035926 original size:15 final size:16
Alignment explanation
Indices: 56035901--56035932 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
56035891 TATCTCACAC
56035901 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
56035917 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
56035932 T
1 T
56035933 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:56036981 original size:12 final size:11
Alignment explanation
Indices: 56036952--56037001 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 11
56036942 ATACAAACTT
*
56036952 TTTTTTTTGAA
1 TTTTTTTCGAA
56036963 TTGTTTTTCGAAA
1 TT-TTTTTCG-AA
56036976 TTTTTTTC-AA
1 TTTTTTTCGAA
56036986 TTTTTTT-G-A
1 TTTTTTTCGAA
56036995 TTTTTTT
1 TTTTTTT
56037002 ACAATACCGT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
9 8 0.23
10 9 0.26
11 2 0.06
12 12 0.34
13 4 0.11
ACGTcount: A:0.16, C:0.04, G:0.08, T:0.72
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:56039618 original size:24 final size:24
Alignment explanation
Indices: 56039591--56039637 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
56039581 CTCTTTTTTA
56039591 TTTGGGCTTGTAATAT-TTTTTTGT
1 TTTGGGC-TGTAATATATTTTTTGT
* *
56039615 TTTGGTCTGTAATTTATTTTTTG
1 TTTGGGCTGTAATATATTTTTTG
56039638 CTTATTTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.13, C:0.04, G:0.19, T:0.64
Consensus pattern (24 bp):
TTTGGGCTGTAATATATTTTTTGT
Found at i:56043405 original size:28 final size:28
Alignment explanation
Indices: 56043362--56043416 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
56043352 ATGATGTTCA
*
56043362 TATTTGTACATTTTTCGCTCATTATTTT
1 TATTTGTACATCTTTCGCTCATTATTTT
* *
56043390 TATTTGTTCATCTTTCGCTCGTTATTT
1 TATTTGTACATCTTTCGCTCATTATTT
56043417 ATACATATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.15, C:0.16, G:0.09, T:0.60
Consensus pattern (28 bp):
TATTTGTACATCTTTCGCTCATTATTTT
Found at i:56045117 original size:14 final size:14
Alignment explanation
Indices: 56045098--56045131 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
56045088 CAAGGTTTTT
*
56045098 GTTTGGGGTTACGA
1 GTTTGGGGTTACAA
56045112 GTTTGGGGTTACAA
1 GTTTGGGGTTACAA
56045126 GTTTGG
1 GTTTGG
56045132 ATTCAAAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.15, C:0.06, G:0.41, T:0.38
Consensus pattern (14 bp):
GTTTGGGGTTACAA
Found at i:56047021 original size:6 final size:6
Alignment explanation
Indices: 56047012--56047048 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
56047002 TCTATTTCTA
56047012 AAAAAT AAAAAAT AAAAAGT AAAAAT AAAAAT AAAAA
1 AAAAAT -AAAAAT AAAAA-T AAAAAT AAAAAT AAAAA
56047049 ATATTTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 17 0.59
7 12 0.41
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:56047022 original size:7 final size:7
Alignment explanation
Indices: 56047010--56047051 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
56047000 TTTCTATTTC
56047010 TAAAAAA
1 TAAAAAA
56047017 TAAAAAA
1 TAAAAAA
*
56047024 TAAAAAG
1 TAAAAAA
56047031 T-AAAAA
1 TAAAAAA
56047037 T-AAAAA
1 TAAAAAA
56047043 TAAAAAA
1 TAAAAAA
56047050 TA
1 TA
56047052 TTTTCAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 11 0.34
7 21 0.66
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (7 bp):
TAAAAAA
Found at i:56047049 original size:13 final size:13
Alignment explanation
Indices: 56047012--56047051 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
56047002 TCTATTTCTA
56047012 AAAAATAAAAAAT
1 AAAAATAAAAAAT
56047025 AAAAAGT-AAAAAT
1 AAAAA-TAAAAAAT
56047038 AAAAATAAAAAAT
1 AAAAATAAAAAAT
56047051 A
1 A
56047052 TTTTCAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.04
13 23 0.92
14 1 0.04
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:56049461 original size:3 final size:3
Alignment explanation
Indices: 56049455--56049498 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
56049445 AAAATAAAAC
56049455 AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA
56049499 AACGTAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:56049467 original size:20 final size:21
Alignment explanation
Indices: 56049438--56049495 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
56049428 ATTCTAAAAG
*
56049438 AATAAAAAAAATAA-AACAAT
1 AATAATAAAAATAATAACAAT
*
56049458 AATAAT-AAAATAATAATAAT
1 AATAATAAAAATAATAACAAT
56049478 AATAATAAATAATAATAA
1 AATAATAAA-AATAATAA
56049496 TAAAACGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.21
20 16 0.48
21 2 0.06
22 8 0.24
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
AATAATAAAAATAATAACAAT
Found at i:56049487 original size:19 final size:20
Alignment explanation
Indices: 56049445--56049498 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
56049435 AAGAATAAAA
*
56049445 AAAATAA-AACAATAATAAT
1 AAAATAATAATAATAATAAT
56049464 AAAATAATAATAATAATAAT
1 AAAATAATAATAATAATAAT
56049484 -AAATAATAATAATAA
1 AAAATAATAATAATAA
56049499 AACGTAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 22 0.67
20 11 0.33
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAATAATAATAATAATAAT
Found at i:56049509 original size:33 final size:33
Alignment explanation
Indices: 56049445--56049518 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 33
56049435 AAGAATAAAA
*
56049445 AAAATAAAACAATAATAATAAAATAATAATAA-T
1 AAAAT-AAATAATAATAATAAAATAATAATAAGT
56049478 AATAATAAATAATAATAATAAAACGT-A-AATAAGT
1 AA-AATAAATAATAATAATAAAA--TAATAATAAGT
56049512 AAAATAA
1 AAAATAA
56049519 GTTAAGAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
33 28 0.78
34 7 0.19
35 1 0.03
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (33 bp):
AAAATAAATAATAATAATAAAATAATAATAAGT
Found at i:56049684 original size:3 final size:3
Alignment explanation
Indices: 56049678--56049759 Score: 67
Period size: 3 Copynumber: 26.7 Consensus size: 3
56049668 TAATAGCAGA
* * * * * *
56049678 AAT AAT AAT AAT AAT ACT ACT ACT ACT ACT ACT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
56049726 AAT AAT AAT AAGGT AAT AATT AAT TA- AAT AAT AA
1 AAT AAT AAT AA--T AAT AA-T AAT AAT AAT AAT AA
56049760 AATTGCTAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
2 1 0.01
3 64 0.90
4 3 0.04
5 3 0.04
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:56049744 original size:23 final size:23
Alignment explanation
Indices: 56049716--56049759 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
56049706 CTACTAATAA
56049716 TAATAA-TAATAATAATAATAAGG
1 TAATAATTAATAA-AATAATAAGG
*
56049739 TAATAATTAATTAAATAATAA
1 TAATAATTAATAAAATAATAA
56049760 AATTGCTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (23 bp):
TAATAATTAATAAAATAATAAGG
Found at i:56050464 original size:15 final size:16
Alignment explanation
Indices: 56050426--56050465 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
56050416 TATTTTTTCG
56050426 AAATAAAAAAAATCAA
1 AAATAAAAAAAATCAA
* *
56050442 GAAGAAAAAAAA-CAA
1 AAATAAAAAAAATCAA
56050457 AAATAAAAA
1 AAATAAAAA
56050466 TAAGAAAGCA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.82, C:0.05, G:0.05, T:0.07
Consensus pattern (16 bp):
AAATAAAAAAAATCAA
Found at i:56051188 original size:88 final size:91
Alignment explanation
Indices: 56051121--56051293 Score: 226
Period size: 91 Copynumber: 1.9 Consensus size: 91
56051111 CTTCTTTGTA
* * *
56051121 GCAACTTCAGGGGGACGAGATTCG-TG-G-TTTTAGTCTACTCCACTGCAACGTTAGTGAGATAA
1 GCAACTTCAGGGGGACAAGATTCGATGTGATTTTAGTCTACTCCACTGCAACGTCAGGGAGATAA
* *
56051183 GACTTGTAACTTCAACCTGCCCCACT
66 GACTTGTAGCTTCAATCTGCCCCACT
* * * *
56051209 GCGACTTCAGGGGGATAAGATTGGATGTGATTTTAGTTTACTCCACTGCAACGTCAGGGAGATAA
1 GCAACTTCAGGGGGACAAGATTCGATGTGATTTTAGTCTACTCCACTGCAACGTCAGGGAGATAA
* *
56051274 GACTTGTGGCTTAAATCTGC
66 GACTTGTAGCTTCAATCTGC
56051294 TTCCTACTAT
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
88 20 0.28
89 2 0.03
90 1 0.01
91 48 0.68
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.28
Consensus pattern (91 bp):
GCAACTTCAGGGGGACAAGATTCGATGTGATTTTAGTCTACTCCACTGCAACGTCAGGGAGATAA
GACTTGTAGCTTCAATCTGCCCCACT
Found at i:56051541 original size:87 final size:87
Alignment explanation
Indices: 56051439--56053203 Score: 2323
Period size: 87 Copynumber: 20.2 Consensus size: 87
56051429 CTGCCAAATA
* * *
56051439 CAGGAAGACAAGATCTGTTATCTTTAACCAACTCCACTGCAACCGATGGAGGCAAGGCTTTGTTT
1 CAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTT
56051504 TCGATCTGCTTCGCTGTTAATG
66 TCGATCTGCTTCGCTGTTAATG
* *
56051526 CATGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTT
1 CAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTT
*
56051591 TCGATCTGCTTCGCTGTTAACG
66 TCGATCTGCTTCGCTGTTAATG
** *
56051613 CAGGAAGGCAAGATCTACTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTT
1 CAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTT
* * *
56051678 TCGATCTGCTTTGATGCTAATG
66 TCGATCTGCTTCGCTGTTAATG
** * *
56051700 CAGGAAGGCAAGATCTGCGATATTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTT
1 CAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTT
*
56051765 TCGATATGCTTCGCTGTTAATG
66 TCGATCTGCTTCGCTGTTAATG
* *
56051787 CATGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTT
1 CAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTT
*
56051852 TCGATCTGCTTCGCTGTTAACG
66 TCGATCTGCTTCGCTGTTAATG
* * *
56051874 CAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTT
1 CAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTT
* *
56051939 TCGATCTGCTTTGCTGTTAACG
66 TCGATCTGCTTCGCTGTTAATG
** *
56051961 CAGGAAGGCAAGATCTGCGATATTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTT
1 CAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTT
56052026 TCGATCTGCTTCGCTGTTAATG
66 TCGATCTGCTTCGCTGTTAATG
*
56052048 CATGAAGGCAAGATCTGCTT-TCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTT
1 CAGGAAGGCAAGATCTG-TTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTT
*
56052112 TTCGATCTGCTTCGTTGTTAATG
65 TTCGATCTGCTTCGCTGTTAATG
*
56052135 CATGAAGGCAAGATCTGCTT-TCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTT
1 CAGGAAGGCAAGATCTG-TTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTT
56052199 TTCGATCTGCTTCGCTGTTAATG
65 TTCGATCTGCTTCGCTGTTAATG
* * *
56052222 CAGGAAGGCAAGATTTGCTT-TCTTTAACCAGCTCCACTGCAACCGATGAAGGCAAGGCTTTGTT
1 CAGGAAGGCAAGATCTG-TTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTT
* *
56052286 TTCGATCTGCTTGGATGTTAATG
65 TTCGATCTGCTTCGCTGTTAATG
* * *
56052309 CAGGAAGGCAAGACCTGCT-TCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGACTTTGTTT
1 CAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTT
56052373 TCGATCTGCTTCGCT-TTCAATG
66 TCGATCTGCTTCGCTGTT-AATG
* * * * *
56052395 CATGAAGGCAAGATCTACTT-TTTTTAACCAGCTCCACTACAACCGATAGAGGCAAGGCTTTGCT
1 CAGGAAGGCAAGATCT-GTTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTT
56052459 TTCGATCTGCTTCGCTGTTAATG
65 TTCGATCTGCTTCGCTGTTAATG
* *
56052482 CAGGAAGGCAAGATCTGCTT-TCTTTAACCAGCTCCACTACAACCTATGGAGGCAAGCCTTTGTT
1 CAGGAAGGCAAGATCTG-TTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTT
56052546 TTCGATCTGCTTCGCTGTTAATG
65 TTCGATCTGCTTCGCTGTTAATG
* * * **
56052569 CAGGAATGCAAGATATGCT-TCTTTAACCAGCTCCACTACAACCGATGGAGGTGAGGCTTTGTTT
1 CAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTT
*
56052633 TCGATCTGCTTCGCTGTTAATA
66 TCGATCTGCTTCGCTGTTAATG
* * * *
56052655 CATGAAGGCAAGATCTGCTT-TATTTAACCAGCTCCACCACAACCGAGGGAGGCAAGG-TTTGTG
1 CAGGAAGGCAAGATCTG-TTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGT-
* *
56052718 TCTTCGATCTGCTTCACTGTCAATG
64 T-TTCGATCTGCTTCGCTGTTAATG
* * * * *
56052743 TAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATTACAACTGA-GAGAGGCAAGG-TTTGTG
1 CAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTACAACCGATG-GAGGCAAGGCTTTGT-
* * *
56052806 TCTCCGACCTGCTTCGCTGTCAATG
64 T-TTCGATCTGCTTCGCTGTTAATG
* * *
56052831 CAGGAAGGCAAGATCTTTTATCTTCAACCAGCTTCA-TCACAACCGA-GAGAGGCAAGG-TTTGT
1 CAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACT-ACAACCGATG-GAGGCAAGGCTTTGT
*
56052893 GTCTTCGATCTGCTTCGCTGTCAATG
64 -T-TTCGATCTGCTTCGCTGTTAATG
* * * *
56052919 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCA-TCATAACCGA-GAGAGGTAAGG-TTTGT
1 CAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACT-ACAACCGATG-GAGGCAAGGCTTTGT
* *
56052981 GTCTTCGACCTGCTTCGCTGTCAATG
64 -T-TTCGATCTGCTTCGCTGTTAATG
* * * * * *
56053007 CAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCACCACAGCCGAGGGAGGCAAGG-TTTGTGT
1 CAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGT-T
*
56053071 CTTCGATCTGCTTCGCTGTCAATG
65 -TTCGATCTGCTTCGCTGTTAATG
** * *
56053095 CAGGAATACAAGATCTGTTGTCTTCAACCAGCTCCA-TCACAACCGA-GAGAGGCAAGG-TTTGT
1 CAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACT-ACAACCGATG-GAGGCAAGGCTTTGT
* * * *
56053157 GTCTTTGAACTGCTTCGCTGTCAAGG
64 -T-TTCGATCTGCTTCGCTGTTAATG
56053183 CAGGAAGGCAAGATCTGTTAT
1 CAGGAAGGCAAGATCTGTTAT
56053204 ATTCACTGAT
Statistics
Matches: 1534, Mismatches: 129, Indels: 29
0.91 0.08 0.02
Matches are distributed among these distances:
85 2 0.00
86 156 0.10
87 945 0.62
88 430 0.28
89 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (87 bp):
CAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTT
TCGATCTGCTTCGCTGTTAATG
Found at i:56052275 original size:44 final size:44
Alignment explanation
Indices: 56052049--56052277 Score: 114
Period size: 44 Copynumber: 5.2 Consensus size: 44
56052039 CTGTTAATGC
* *
56052049 ATGAAGGCAAGATCTGCTTTCTTTAACCAGCTCCACTACAACCG
1 ATGAAGGCAAGATTTGCTTTCTTTAACCAGCTCCACTGCAACCG
* * ** * * * ** * *
56052093 ATGGAGGCAAGGCTTTG--TT-TTCGATCTGCTTCGTTGTTAA-TG
1 ATGAAGGCAA-GATTTGCTTTCTTTAACCAGCTCCACTG-CAACCG
* *
56052135 CATGAAGGCAAGATCTGCTTTCTTTAACCAGCTCCACTACAACCG
1 -ATGAAGGCAAGATTTGCTTTCTTTAACCAGCTCCACTGCAACCG
* * ** * * * * * *
56052180 ATGGAGGCAAGGCTTTG--TT-TTCGATCTGCTTCGCTGTTAA-TG
1 ATGAAGGCAA-GATTTGCTTTCTTTAACCAGCTCCACTG-CAACCG
*
56052222 CAGGAAGGCAAGATTTGCTTTCTTTAACCAGCTCCACTGCAACCG
1 -ATGAAGGCAAGATTTGCTTTCTTTAACCAGCTCCACTGCAACCG
56052267 ATGAAGGCAAG
1 ATGAAGGCAAG
56052278 GCTTTGTTTT
Statistics
Matches: 121, Mismatches: 50, Indels: 28
0.61 0.25 0.14
Matches are distributed among these distances:
42 30 0.25
43 25 0.21
44 36 0.30
45 30 0.25
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (44 bp):
ATGAAGGCAAGATTTGCTTTCTTTAACCAGCTCCACTGCAACCG
Found at i:56054467 original size:23 final size:24
Alignment explanation
Indices: 56054428--56054472 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
56054418 ATTTTTACTC
56054428 TTTCATTTTTTCATTTT-TTTTCA
1 TTTCATTTTTTCATTTTGTTTTCA
**
56054451 TTTCATTTTTTTGTTTTGTTTT
1 TTTCATTTTTTCATTTTGTTTT
56054473 GTTTTTTTTT
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:0.09, C:0.09, G:0.04, T:0.78
Consensus pattern (24 bp):
TTTCATTTTTTCATTTTGTTTTCA
Found at i:56055300 original size:24 final size:23
Alignment explanation
Indices: 56055273--56055317 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
56055263 TTTTTCTCCT
56055273 ATTTTTTGACTTTGATTTTTTTGG
1 ATTTTTT-ACTTTGATTTTTTTGG
* *
56055297 ATTTTTTATTTTTATTTTTTT
1 ATTTTTTACTTTGATTTTTTT
56055318 TGAGTTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.13, C:0.02, G:0.09, T:0.76
Consensus pattern (23 bp):
ATTTTTTACTTTGATTTTTTTGG
Found at i:56056598 original size:15 final size:15
Alignment explanation
Indices: 56056578--56056607 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
56056568 AATATTCTCT
*
56056578 AATGCATGTAATGCG
1 AATGCATGAAATGCG
56056593 AATGCATGAAATGCG
1 AATGCATGAAATGCG
56056608 TGCCTACAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.23
Consensus pattern (15 bp):
AATGCATGAAATGCG
Found at i:56058526 original size:3 final size:3
Alignment explanation
Indices: 56058518--56058543 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
56058508 TAAATAAAAC
56058518 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
56058544 AACTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:56058819 original size:26 final size:24
Alignment explanation
Indices: 56058770--56058819 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
56058760 GGGACTAAAT
*
56058770 CGAAATAAAAATAAAAAAATGAGG
1 CGAAATAAAAATAAAAAAAGGAGG
*
56058794 CGAAATCAAAATAATAAAAAAGGAGG
1 CGAAATAAAAAT-A-AAAAAAGGAGG
56058820 GATTGATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.50
25 1 0.05
26 10 0.45
ACGTcount: A:0.64, C:0.06, G:0.18, T:0.12
Consensus pattern (24 bp):
CGAAATAAAAATAAAAAAAGGAGG
Found at i:56059462 original size:15 final size:15
Alignment explanation
Indices: 56059425--56059463 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
56059415 TATTGTTTCG
*
56059425 AAATAAAAAAATCAA
1 AAATAAAAAAAACAA
* *
56059440 GAAGAAAAAAAACAA
1 AAATAAAAAAAACAA
56059455 AAATAAAAA
1 AAATAAAAA
56059464 TAAGAAAGCA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.82, C:0.05, G:0.05, T:0.08
Consensus pattern (15 bp):
AAATAAAAAAAACAA
Found at i:56061187 original size:6 final size:6
Alignment explanation
Indices: 56061178--56061214 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
56061168 TCTATTTCTA
56061178 AAAAAT AAAAAAT AAAAAGT AAAAAT AAAAAT AAAAA
1 AAAAAT -AAAAAT AAAAA-T AAAAAT AAAAAT AAAAA
56061215 ATATTTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 17 0.59
7 12 0.41
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:56061188 original size:7 final size:7
Alignment explanation
Indices: 56061176--56061217 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
56061166 TTTCTATTTC
56061176 TAAAAAA
1 TAAAAAA
56061183 TAAAAAA
1 TAAAAAA
*
56061190 TAAAAAG
1 TAAAAAA
56061197 T-AAAAA
1 TAAAAAA
56061203 T-AAAAA
1 TAAAAAA
56061209 TAAAAAA
1 TAAAAAA
56061216 TA
1 TA
56061218 TTTTCAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 11 0.34
7 21 0.66
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (7 bp):
TAAAAAA
Found at i:56061215 original size:13 final size:13
Alignment explanation
Indices: 56061178--56061217 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
56061168 TCTATTTCTA
56061178 AAAAATAAAAAAT
1 AAAAATAAAAAAT
56061191 AAAAAGT-AAAAAT
1 AAAAA-TAAAAAAT
56061204 AAAAATAAAAAAT
1 AAAAATAAAAAAT
56061217 A
1 A
56061218 TTTTCAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.04
13 23 0.92
14 1 0.04
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:56064860 original size:27 final size:28
Alignment explanation
Indices: 56064830--56064888 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
56064820 TTTTTGTCAA
*
56064830 AATTCACACTTTAATTA-TAAAATAATT
1 AATTCACACTTAAATTATTAAAATAATT
** * *
56064857 AATTTGCACTTAAATTATTAACATATTT
1 AATTCACACTTAAATTATTAAAATAATT
56064885 AATT
1 AATT
56064889 TTAATTATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (28 bp):
AATTCACACTTAAATTATTAAAATAATT
Found at i:56067068 original size:13 final size:13
Alignment explanation
Indices: 56067050--56067074 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56067040 GAGATGATGA
56067050 TTTTTTCTAAATT
1 TTTTTTCTAAATT
56067063 TTTTTTCTAAAT
1 TTTTTTCTAAAT
56067075 AAGGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTTCTAAATT
Found at i:56068907 original size:19 final size:19
Alignment explanation
Indices: 56068883--56068929 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
56068873 CAATGTCTCT
*
56068883 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTGCAT-CA
56068902 TTTGCATTACATTGCATCA
1 TTTGCATTACATTGCATCA
*
56068921 TATGCATTA
1 TTTGCATTA
56068930 GATTTTCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTGCATCA
Found at i:56071792 original size:17 final size:17
Alignment explanation
Indices: 56071767--56071869 Score: 63
Period size: 17 Copynumber: 5.8 Consensus size: 17
56071757 AAAAAATGTT
56071767 AAGAA-AAAAAGAGAGAA
1 AAGAAGAAAAAGA-AGAA
56071784 AA-AAGAAAAAGAAGGAA
1 AAGAAGAAAAAGAA-GAA
56071801 ATAGAAGAAAAAAGAAAGAA
1 A-AGAAG-AAAAAG-AAGAA
56071821 TAAGAAG-AAAAGAA-AA
1 -AAGAAGAAAAAGAAGAA
* *
56071837 AGAAAAGGAAAAGAA-AA
1 A-AGAAGAAAAAGAAGAA
*
56071854 AGTAAAAGAAAAAGAA
1 A--AGAAGAAAAAGAA
56071870 AATGAGAGGC
Statistics
Matches: 73, Mismatches: 3, Indels: 19
0.77 0.03 0.20
Matches are distributed among these distances:
15 1 0.01
16 9 0.12
17 25 0.34
18 18 0.25
19 3 0.04
20 14 0.19
21 3 0.04
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (17 bp):
AAGAAGAAAAAGAAGAA
Found at i:56071794 original size:6 final size:6
Alignment explanation
Indices: 56071783--56071871 Score: 67
Period size: 6 Copynumber: 14.7 Consensus size: 6
56071773 AAAAGAGAGA
* * * *
56071783 AAAAAG AAAAAG AAGGAAA- TAGAAG AAAAA- AGAAAG AATAAG AAGAAAAG
1 AAAAAG AAAAAG AA--AAAG AAAAAG AAAAAG AAAAAG AAAAAG -A-AAAAG
* *
56071833 AAAAAG -AAAAG GAAAAG AAAAAG TAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
56071872 TGAGAGGCCA
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
5 11 0.17
6 44 0.68
7 3 0.05
8 7 0.11
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:56071812 original size:20 final size:20
Alignment explanation
Indices: 56071771--56071840 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
56071761 AATGTTAAGA
*
56071771 AAAAAAGAGAGAA-AA-AAG
1 AAAAAAGAAAGAATAAGAAG
*
56071789 -AAAAAGAAGGAA-ATAGAAG
1 AAAAAAGAAAGAATA-AGAAG
56071808 AAAAAAGAAAGAATAAGAAG
1 AAAAAAGAAAGAATAAGAAG
56071828 AAAAGAA-AAAGAA
1 AAAA-AAGAAAGAA
56071841 AAGGAAAAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
17 11 0.25
18 1 0.02
19 3 0.07
20 26 0.59
21 3 0.07
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (20 bp):
AAAAAAGAAAGAATAAGAAG
Found at i:56071839 original size:11 final size:11
Alignment explanation
Indices: 56071784--56071871 Score: 71
Period size: 10 Copynumber: 8.4 Consensus size: 11
56071774 AAAGAGAGAA
56071784 AAAAGAAAAAG
1 AAAAGAAAAAG
* *
56071795 -AAGGAAATAG
1 AAAAGAAAAAG
*
56071805 AAGA-AAAAAG
1 AAAAGAAAAAG
*
56071815 -AAAGAATAAG
1 AAAAGAAAAAG
56071825 --AAG-AAAAG
1 AAAAGAAAAAG
*
56071833 AAAAAGAAAAGG
1 -AAAAGAAAAAG
56071845 AAAAGAAAAAG
1 AAAAGAAAAAG
56071856 TAAAAGAAAAAG
1 -AAAAGAAAAAG
56071868 AAAA
1 AAAA
56071872 TGAGAGGCCA
Statistics
Matches: 60, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
8 4 0.07
9 5 0.08
10 18 0.30
11 18 0.30
12 15 0.25
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.03
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:56071871 original size:17 final size:16
Alignment explanation
Indices: 56071767--56071871 Score: 80
Period size: 14 Copynumber: 6.8 Consensus size: 16
56071757 AAAAAATGTT
* *
56071767 AAGAAAA-AAAGAGAG
1 AAGAAAAGAAAAAGAA
56071782 AA-AAAAGAAAAAG-A
1 AAGAAAAGAAAAAGAA
* *
56071796 AGGAAATAGAAGAA-AA
1 AAGAAA-AGAAAAAGAA
*
56071812 AAG-AAAGAATAAG--
1 AAGAAAAGAAAAAGAA
56071825 AAGAAAAGAAAAAGAA
1 AAGAAAAGAAAAAGAA
56071841 AAGGAAAAGAAAAAGTAA
1 AA-GAAAAGAAAAAG-AA
56071859 AAGAAAAAGAAAA
1 AAG-AAAAGAAAA
56071872 TGAGAGGCCA
Statistics
Matches: 72, Mismatches: 7, Indels: 19
0.73 0.07 0.19
Matches are distributed among these distances:
13 3 0.04
14 20 0.28
15 12 0.17
16 11 0.15
17 13 0.18
18 13 0.18
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (16 bp):
AAGAAAAGAAAAAGAA
Found at i:56074085 original size:89 final size:89
Alignment explanation
Indices: 56073175--56074073 Score: 1080
Period size: 89 Copynumber: 10.1 Consensus size: 89
56073165 CCCTGAAATT
* * * * * * *
56073175 ACAGTGGAGTAGACTAAAAATAACAGATCTTGCCTTCCTGTACTGACGGCAAAGCAGAAT-GAAG
1 ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAG-ATCGAAG
* *
56073239 ACATCAGCCTTGCCTTCGTGTACTG
65 ACACCAGCCTTGCCTTCCTGTACTG
* * * *
56073264 ACAGCGGAGCAGACTGAAGATAGCAGATATTGCCTTCTTGTACTGACGGTGAAGCAGATCGAAGA
1 ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
*
56073329 CACTAGCCTTGCCTTCCTGTACTG
66 CACCAGCCTTGCCTTCCTGTACTG
** *
56073353 ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGATGGCGAAGCAGATTGAAGA
1 ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
* * *
56073418 CACTAACCTTGCCTTCCTATACTG
66 CACCAGCCTTGCCTTCCTGTACTG
* * ** *
56073442 ACAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCATGTACAAACAGAGAAGCAGATCGAAGA
1 ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
56073507 CACCAGCCTTGCCTTCCTGTACTG
66 CACCAGCCTTGCCTTCCTGTACTG
* * *
56073531 ACAGCGAAGCAGACTGAAGATAACAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGA
1 ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
* *
56073596 CACCAGTCTTGCATTCCTGTACTG
66 CACCAGCCTTGCCTTCCTGTACTG
* * * * *
56073620 ACAGCGGAGCAGGCTGAAGATAGAAGATCTTGCCTTCTTGTACTGACGGTGAAGCAGATCGAAGA
1 ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
*
56073685 CACCAGCCTTGCCTTCCTGTACCG
66 CACCAGCCTTGCCTTCCTGTACTG
* * * *
56073709 ACAGCGGAGTAGACTGAAGATAGCAGATCTTGCATTCCTGTACTGACAGAGAAGTAGATCGAAGA
1 ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
**
56073774 CACCAGTTTTGCCTTCCTGTACTG
66 CACCAGCCTTGCCTTCCTGTACTG
* * ** * *
56073798 ACAGCGAAGCAGACTGAAGATAGTAGATCTTGTTTTCCTATACTGACAGCGAAGCAGATCAAAGA
1 ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
** * ** *
56073863 CACCAGTTTTTCCTTTTTGTACTA
66 CACCAGCCTTGCCTTCCTGTACTG
* * * * * * * *
56073887 ACAACGGAGCAGACTAAAGATAGTAGATCTTGCCTTCTTATACTGACGGCGAAACAGATCAAAGA
1 ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
* * * *
56073952 CACCAGCCTTGCATTCTTTTACAG
66 CACCAGCCTTGCCTTCCTGTACTG
* * * * * *** *
56073976 ACGGCGGAACAGACTGAAGATAGCAGATCTTGCCTTCCTATACCGACAGTGAATTGGATCGAAAA
1 ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
* *
56074041 CACCGGCCTTGCCTTCTTGTACTG
66 CACCAGCCTTGCCTTCCTGTACTG
*
56074065 ACAGTGGAG
1 ACAGCGGAG
56074074 TAGGTTGAAG
Statistics
Matches: 697, Mismatches: 112, Indels: 2
0.86 0.14 0.00
Matches are distributed among these distances:
88 2 0.00
89 695 1.00
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (89 bp):
ACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
CACCAGCCTTGCCTTCCTGTACTG
Found at i:56074233 original size:132 final size:132
Alignment explanation
Indices: 56074067--56074550 Score: 765
Period size: 132 Copynumber: 3.7 Consensus size: 132
56074057 TTGTACTGAC
*
56074067 AGTGGAGTAGGTTGAAGATTGCAAATTCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
1 AGTGGAGTAGGTTGAAGATTGCAGATTCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
*
56074132 TGAATCTTATCTTCCCAAGATAGTGGAGAAGTAGATTTAAGCCATTAGTCCTATCTCCCTAAGCA
66 TGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCA
56074197 GT
131 GT
* * *
56074199 AGTGGAGTAGGTTGAAAATTGCAGATTTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAG
1 AGTGGAGTAGGTTGAAGATTGCAGATTCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
* * *
56074264 TGAATCTTATCTTCTCAAGATAGTAGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTAAGTA
66 TGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCA
56074329 GT
131 GT
*
56074331 AGTGGAGTAGGTTGAAGATTGCA-ATTCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAAATGG
1 AGTGGAGTAGGTTGAAGATTGCAGATTCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
* ** *
56074395 TGAATCTTATCTTCTCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGTTATATCTCCCTGAGCA
66 TGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCA
*
56074460 GC
131 GT
* * * **
56074462 AGTGGAGTAAGTTGAAGATTGCAGA-TCTTGTCTCCTTAAGCAGTATTGGAGCAGATAAAAGATG
1 AGTGGAGTAGGTTGAAGATTGCAGATTC-TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATG
*
56074526 GTGAATCTTATCTTCCCAAGGTAGT
65 GTGAATCTTATCTTCCCAAGATAGT
56074551 AGGGAAGTAA
Statistics
Matches: 324, Mismatches: 26, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
131 123 0.38
132 201 0.62
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (132 bp):
AGTGGAGTAGGTTGAAGATTGCAGATTCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
TGAATCTTATCTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCA
GT
Found at i:56074774 original size:88 final size:88
Alignment explanation
Indices: 56074675--56074861 Score: 304
Period size: 88 Copynumber: 2.1 Consensus size: 88
56074665 TCTAATCTCC
*
56074675 CTGAAGTTGCAGTGGAGCAGACTAAAACCACAAATCTTTTCCCCCTAAAGTTGTTACGAAGAAGA
1 CTGAAGTTGCAGTGGAGCAGACTAAAACCACAAATCTCTTCCCCCTAAAGTTGTTACGAAGAAGA
56074740 TTGAAGTTACAAGTCATATCTAT
66 TTGAAGTTACAAGTCATATCTAT
* * * *
56074763 CTGAAGTTGCAGTGGAGCAGGCTAAAACCACAAATCTCTTCCCCTTGAAGTTGTTGCGAAGAAGA
1 CTGAAGTTGCAGTGGAGCAGACTAAAACCACAAATCTCTTCCCCCTAAAGTTGTTACGAAGAAGA
*
56074828 TTGCAGTTACAAGTCATATCTAT
66 TTGAAGTTACAAGTCATATCTAT
*
56074851 TTGAAG-TGCAG
1 CTGAAGTTGCAG
56074862 AAGAGTGGAT
Statistics
Matches: 92, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
87 5 0.05
88 87 0.95
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (88 bp):
CTGAAGTTGCAGTGGAGCAGACTAAAACCACAAATCTCTTCCCCCTAAAGTTGTTACGAAGAAGA
TTGAAGTTACAAGTCATATCTAT
Found at i:56080046 original size:14 final size:14
Alignment explanation
Indices: 56080029--56080058 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56080019 ACTTGAGCCA
*
56080029 CAAGCCTTGTGGGC
1 CAAGCCGTGTGGGC
56080043 CAAGCCGTGTGGGC
1 CAAGCCGTGTGGGC
56080057 CA
1 CA
56080059 CACGGGTCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.30, G:0.37, T:0.17
Consensus pattern (14 bp):
CAAGCCGTGTGGGC
Found at i:56082854 original size:29 final size:30
Alignment explanation
Indices: 56082820--56082881 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
56082810 GTTTCACGTG
56082820 TATAATT-ATACCAAATTAAAATTCATATA
1 TATAATTAATACCAAATTAAAATTCATATA
** *
56082849 TATAATTACATATTAAATTAAAGTTCATATA
1 TATAATTA-ATACCAAATTAAAATTCATATA
56082880 TA
1 TA
56082882 ATTTTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 7 0.25
31 21 0.75
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (30 bp):
TATAATTAATACCAAATTAAAATTCATATA
Found at i:56091986 original size:21 final size:22
Alignment explanation
Indices: 56091941--56091987 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
56091931 TAACATGTTT
56091941 AATTTTAATTAATTTTATAATA
1 AATTTTAATTAATTTTATAATA
* * *
56091963 AATTTTGATTTATTTT-TGATA
1 AATTTTAATTAATTTTATAATA
56091984 AATT
1 AATT
56091988 CACACAAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (22 bp):
AATTTTAATTAATTTTATAATA
Found at i:56094551 original size:27 final size:27
Alignment explanation
Indices: 56094511--56094563 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
56094501 AAATGTTTAT
*
56094511 TTTAAGTCATTTTATGTTAGTGTCTCG
1 TTTAAGTCAATTTATGTTAGTGTCTCG
*
56094538 TTTAAGTCAATTTATGTTCGTGTCTC
1 TTTAAGTCAATTTATGTTAGTGTCTC
56094564 AAAACATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.13, G:0.17, T:0.51
Consensus pattern (27 bp):
TTTAAGTCAATTTATGTTAGTGTCTCG
Found at i:56097738 original size:20 final size:21
Alignment explanation
Indices: 56097715--56097753 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
56097705 TTTATTTTTT
*
56097715 GCTTTTTTTAA-TTTTTTTAA
1 GCTTATTTTAAGTTTTTTTAA
56097735 GCTTATTTTAAGTTTTTTT
1 GCTTATTTTAAGTTTTTTT
56097754 TTCCTCTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.18, C:0.05, G:0.08, T:0.69
Consensus pattern (21 bp):
GCTTATTTTAAGTTTTTTTAA
Found at i:56100277 original size:22 final size:25
Alignment explanation
Indices: 56100249--56100301 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 25
56100239 AAATGTTAAT
56100249 AAAAATATTA-TATTAAAA-ATA-A
1 AAAAATATTATTATTAAAATATATA
*
56100271 AAAAATATTATTTTTAAAATATATA
1 AAAAATATTATTATTAAAATATATA
56100296 AAAAAT
1 AAAAAT
56100302 TAATAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 10 0.37
23 7 0.26
24 3 0.11
25 7 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
AAAAATATTATTATTAAAATATATA
Found at i:56104929 original size:42 final size:42
Alignment explanation
Indices: 56104883--56104974 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
56104873 GACTTGTCTG
** *
56104883 ATGATGCAATTATGTG-CTTGTATATTTGCTTCGGTTCATCCA
1 ATGATGCAATTATGTGTC-AATATATTTGCTTCGATTCATCCA
* *
56104925 ATGATGCATTTATGTGTCAATATATTTGCTTCGATTTATCCA
1 ATGATGCAATTATGTGTCAATATATTTGCTTCGATTCATCCA
56104967 ATGATGCA
1 ATGATGCA
56104975 CTTCGGTGCC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 43 0.98
43 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (42 bp):
ATGATGCAATTATGTGTCAATATATTTGCTTCGATTCATCCA
Found at i:56107923 original size:50 final size:50
Alignment explanation
Indices: 56107808--56108056 Score: 282
Period size: 50 Copynumber: 4.8 Consensus size: 50
56107798 GATAATAACA
* * ** *
56107808 TGCCAAAGCCATGTCTCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTTGG
* * * *
56107859 TGCCCATGCCATGTCCCAGACATGGTCTTATAAGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
* *
56107909 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
* * * *
56107959 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGAGCTCTCATGATCTTAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-C-CTC-TCATC-T--TGG
* *
56108015 TGCCAATGCCATGTCCCAGACATGTTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
56108057 TTACCCAAAT
Statistics
Matches: 167, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
50 87 0.52
51 33 0.20
52 3 0.02
53 4 0.02
54 4 0.02
56 36 0.22
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
Found at i:56108001 original size:100 final size:103
Alignment explanation
Indices: 56107807--56108056 Score: 317
Period size: 100 Copynumber: 2.4 Consensus size: 103
56107797 TGATAATAAC
* ** *
56107807 ATGCCAAAGCCATGTCTCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTTGGTGCCCATGCCATG
*
56107872 TCCCAGACATGGTCTTATAAGGGACCTCTC-ATC-T-CG
65 TCCCAGACATGGTCTTACAAGGGACCTCTCAATCTTACG
* * *
56107908 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTTGGTGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTGCCCATGCCATGT
* * *
56107973 CCCAGACATGGTCTTACAGGGGAGCTCTCATGATCTTAATG
66 CCCAGACATGGTCTTACAAGGGACCTCTCA--ATCTT-ACG
* * *
56108014 ATGCCAATGCCATGTCCCAGACATGTTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
56108057 TTACCCAAAT
Statistics
Matches: 128, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
100 49 0.38
101 35 0.27
103 3 0.02
104 1 0.01
106 40 0.31
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (103 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAAGGGACCTCTCAATCTTACG
Found at i:56108172 original size:13 final size:13
Alignment explanation
Indices: 56108151--56108182 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
56108141 GCTTGGATCA
*
56108151 TCATCAAATAAAT
1 TCATAAAATAAAT
56108164 TCATAAAATAAAT
1 TCATAAAATAAAT
56108177 TCATAA
1 TCATAA
56108183 TTACTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:56108426 original size:29 final size:30
Alignment explanation
Indices: 56108394--56108450 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
56108384 CCTTGACTCT
56108394 AACTTTT-CAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
56108423 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
56108451 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.40
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:56111640 original size:14 final size:14
Alignment explanation
Indices: 56111621--56111647 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
56111611 CATGAGTTAG
56111621 TCACTGACCATGCA
1 TCACTGACCATGCA
56111635 TCACTGACCATGC
1 TCACTGACCATGC
56111648 GTATGCAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.37, G:0.15, T:0.22
Consensus pattern (14 bp):
TCACTGACCATGCA
Found at i:56112721 original size:37 final size:38
Alignment explanation
Indices: 56112670--56112777 Score: 104
Period size: 37 Copynumber: 2.9 Consensus size: 38
56112660 TTATTCTAAA
*
56112670 AAATATTATTTTAATAGTTTAATATTAAATTTAAT-TT
1 AAATATTATCTTAATAGTTTAATATTAAATTTAATATT
* *
56112707 -AATACTTATCTTAATAGTATT-TTACT-AATTTAATATT
1 AAATA-TTATCTTAATAGT-TTAATATTAAATTTAATATT
56112744 AAAGTGATTATCTTAATA--TTAA-ATTAAATTTAAT
1 AAA-T-ATTATCTTAATAGTTTAATATTAAATTTAAT
56112778 GTTTATCTTG
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
36 16 0.28
37 25 0.43
38 4 0.07
39 12 0.21
40 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (38 bp):
AAATATTATCTTAATAGTTTAATATTAAATTTAATATT
Found at i:56112838 original size:17 final size:17
Alignment explanation
Indices: 56112816--56112872 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
56112806 TTTTGATGAG
56112816 ATTTAATATTTA-ATTTA
1 ATTTAATATTTATA-TTA
*
56112833 ATTTAATATTTATCTTA
1 ATTTAATATTTATATTA
*
56112850 A-TAAATA-TTATATTA
1 ATTTAATATTTATATTA
56112865 ATTTAATA
1 ATTTAATA
56112873 CCAAAGTGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
15 8 0.24
16 10 0.29
17 16 0.47
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTAATATTTATATTA
Found at i:56117185 original size:18 final size:17
Alignment explanation
Indices: 56117152--56117190 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
56117142 TTTTATAAAT
56117152 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
56117170 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
56117187 TGTG
1 TGTG
56117191 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:56117443 original size:23 final size:23
Alignment explanation
Indices: 56117416--56117513 Score: 124
Period size: 23 Copynumber: 4.3 Consensus size: 23
56117406 AGTGTTATTG
*
56117416 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
56117439 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
56117462 TTCAATGGTAGCTACAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
56117485 ATCAGTGGTAGTTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
56117508 ATCAGT
1 ATCAGT
56117514 ATGGCACTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:56123623 original size:22 final size:22
Alignment explanation
Indices: 56123597--56123643 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
56123587 TTCGAATCCT
56123597 TAGGGATGAAAGAATAAAACGA
1 TAGGGATGAAAGAATAAAACGA
56123619 TAGGGATGAAAGAATAAAACGA
1 TAGGGATGAAAGAATAAAACGA
56123641 TAG
1 TAG
56123644 CTTTATCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.53, C:0.04, G:0.28, T:0.15
Consensus pattern (22 bp):
TAGGGATGAAAGAATAAAACGA
Found at i:56124615 original size:16 final size:16
Alignment explanation
Indices: 56124594--56124624 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56124584 TTCACTATTA
*
56124594 TATCTTTTGTATTTTC
1 TATCTTTTATATTTTC
56124610 TATCTTTTATATTTT
1 TATCTTTTATATTTT
56124625 GCATGCATAG
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:0.16, C:0.10, G:0.03, T:0.71
Consensus pattern (16 bp):
TATCTTTTATATTTTC
Found at i:56127275 original size:12 final size:11
Alignment explanation
Indices: 56127228--56127272 Score: 63
Period size: 11 Copynumber: 3.8 Consensus size: 11
56127218 ATTTAAGATA
56127228 TTTTAAAAATAT
1 TTTTAAAAAT-T
56127240 TTTTAAAATACTT
1 TTTTAAAA-A-TT
56127253 TTTTAAAAATT
1 TTTTAAAAATT
56127264 TTTTAAAAA
1 TTTTAAAAA
56127273 ATTGGTGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.35
12 9 0.29
13 10 0.32
14 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (11 bp):
TTTTAAAAATT
Found at i:56133108 original size:5 final size:5
Alignment explanation
Indices: 56133100--56133128 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
56133090 TTCATTTAAT
56133100 TTGAC TTGAC TTGAC TTGAC TTGAC TTGA
1 TTGAC TTGAC TTGAC TTGAC TTGAC TTGA
56133129 TTTAAGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (5 bp):
TTGAC
Found at i:56158414 original size:23 final size:23
Alignment explanation
Indices: 56158361--56158414 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
56158351 TTTGTATTTT
*
56158361 ATTATTTCCAATTATTTCACTAC
1 ATTATTTCCAATTATTTCACTAA
* *
56158384 ATTTTTTCCAATTATTTGTA-TAA
1 ATTATTTCCAATTATTT-CACTAA
56158407 ATTATTTC
1 ATTATTTC
56158415 TGAATTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.30, C:0.15, G:0.02, T:0.54
Consensus pattern (23 bp):
ATTATTTCCAATTATTTCACTAA
Found at i:56158894 original size:19 final size:19
Alignment explanation
Indices: 56158859--56158896 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
56158849 TTTAAACACA
56158859 CAAATATTACAAAAAAATT
1 CAAATATTACAAAAAAATT
*
56158878 CAAAT-TTATAAATAAAATT
1 CAAATATTACAAA-AAAATT
56158897 ACCTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
CAAATATTACAAAAAAATT
Found at i:56158941 original size:18 final size:18
Alignment explanation
Indices: 56158918--56159021 Score: 61
Period size: 18 Copynumber: 5.4 Consensus size: 18
56158908 CATTTCTTCC
56158918 CTCTTCTTCTTCTTTTTT
1 CTCTTCTTCTTCTTTTTT
*
56158936 CTCTTCTCCTTTCCCTTTCTTT
1 CTCTTCTTC-TT--CTTT-TTT
56158958 C-CTTCTTTCTTTCTTTTTT
1 CTCTTC-TTC-TTCTTTTTT
* *
56158977 AT-TCTCTTCTCCTTTTCTT
1 CTCT-TCTTCTTCTTTT-TT
*
56158996 CTTCTTTCTT-TCCTTTTTT
1 C-TC-TTCTTCTTCTTTTTT
56159015 CTCTTCT
1 CTCTTCT
56159022 CCTTTCCTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 23
0.71 0.05 0.23
Matches are distributed among these distances:
17 4 0.06
18 16 0.23
19 14 0.20
20 14 0.20
21 12 0.17
22 10 0.14
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (18 bp):
CTCTTCTTCTTCTTTTTT
Found at i:56158942 original size:12 final size:12
Alignment explanation
Indices: 56158925--56159079 Score: 69
Period size: 12 Copynumber: 13.0 Consensus size: 12
56158915 TCCCTCTTCT
56158925 TCTTCTTTTTTC
1 TCTTCTTTTTTC
**
56158937 TCTTCTCCTTTC
1 TCTTCTTTTTTC
56158949 -C--CTTTCTTTC
1 TCTTCTTT-TTTC
56158959 -CTTCTTTCTTTC
1 TCTTCTTT-TTTC
*
56158971 T-TT-TTTATTC
1 TCTTCTTTTTTC
**
56158981 TCTTCTCCTTT-
1 TCTTCTTTTTTC
*
56158992 TCTTCTTCTTTC
1 TCTTCTTTTTTC
56159004 T-TTCCTTTTTTC
1 TCTT-CTTTTTTC
* *
56159016 TCTTCTCCTTTCC
1 TCTTCT-TTTTTC
*
56159029 TTTTCTTTCTTTCC
1 TCTTCTTT-TTT-C
*
56159043 TCTCCTTTCTTTC
1 TCTTCTTT-TTTC
56159056 T-TTCTTTCTTTC
1 TCTTCTTT-TTTC
56159068 T-TTCTTTCTTTC
1 TCTTCTTT-TTTC
56159080 CCTCCTTCTG
Statistics
Matches: 113, Mismatches: 18, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
9 2 0.02
10 9 0.08
11 18 0.16
12 58 0.51
13 15 0.13
14 11 0.10
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.68
Consensus pattern (12 bp):
TCTTCTTTTTTC
Found at i:56158967 original size:4 final size:4
Alignment explanation
Indices: 56158950--56159079 Score: 99
Period size: 4 Copynumber: 31.2 Consensus size: 4
56158940 TCTCCTTTCC
* *
56158950 CTTT CTTT CCTT CTTT CTTT CTTT -TTT ATTCT CTTCT CCTTT -TCTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT-T CTT-T -CTTT CT-TT
*
56158996 C-TT CTTT CTTT CCTTT -TTT CTCTT C-TC CTTT CCTTTT CTTT CTTT
1 CTTT CTTT CTTT -CTTT CTTT CT-TT CTTT CTTT -C-TTT CTTT CTTT
*
56159041 CCTCTC CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
1 -CT-TT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
56159080 CCTCCTTCTG
Statistics
Matches: 105, Mismatches: 7, Indels: 28
0.75 0.05 0.20
Matches are distributed among these distances:
3 12 0.11
4 67 0.64
5 19 0.18
6 7 0.07
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:56158987 original size:44 final size:42
Alignment explanation
Indices: 56158904--56159058 Score: 144
Period size: 41 Copynumber: 3.7 Consensus size: 42
56158894 ATTACCTTTT
*
56158904 TTTTCATTTC-TTCCCTC-TTC-TTCTTCTTTTTTCTCTTCTCC
1 TTTTC-TTTCTTTCCTTCTTTCTTTCTT-TTTTTTCTCTTCTCC
*
56158945 TTTCCCTTTCTTTCCTTCTTTCTTTCTTTTTTATTCTCTTCTCC
1 TTT-TCTTTCTTTCCTTCTTTCTTTCTTTTTT-TTCTCTTCTCC
* * *
56158989 TTTTC-TTC-TTCTTTCTTTCCTTT-TTTCTCTTCTCCTT-TCC
1 TTTTCTTTCTTTCCTTCTTT-CTTTCTTTTTTTTCT-CTTCTCC
56159029 TTTTCTTTCTTTCCTCTCCTTTCTTTCTTT
1 TTTTCTTTCTTTCCT-T-CTTTCTTTCTTT
56159059 CTTTCTTTCT
Statistics
Matches: 95, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
40 12 0.13
41 26 0.27
42 18 0.19
43 13 0.14
44 26 0.27
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.66
Consensus pattern (42 bp):
TTTTCTTTCTTTCCTTCTTTCTTTCTTTTTTTTCTCTTCTCC
Found at i:56158997 original size:34 final size:35
Alignment explanation
Indices: 56158954--56159078 Score: 113
Period size: 34 Copynumber: 3.7 Consensus size: 35
56158944 CTTTCCCTTT
*
56158954 CTTTCCTTCTTTCTTTCTTT-TTTATTCTCTTCTC
1 CTTTTCTTCTTTCTTTCTTTCTTTATTCTCTTCTC
*
56158988 CTTTTCTTC-TTCTTTCTTTCCTTTTTTCTCTTCTC
1 CTTTTCTTCTTTCTTTCTTT-CTTTATTCTCTTCTC
* **
56159023 C-TTTCCT-TTTCTTTCTTTCCTCTCCTT-TCTT-T-
1 CTTTTCTTCTTTCTTTCTTT-CT-TTATTCTCTTCTC
56159055 C-TTTCTTTCTTTCTTTCTTTCTTT
1 CTTTTC-TTCTTTCTTTCTTTCTTT
56159079 CCCTCCTTCT
Statistics
Matches: 78, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
32 6 0.08
33 14 0.18
34 41 0.53
35 17 0.22
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (35 bp):
CTTTTCTTCTTTCTTTCTTTCTTTATTCTCTTCTC
Found at i:56159000 original size:37 final size:35
Alignment explanation
Indices: 56158954--56159080 Score: 136
Period size: 35 Copynumber: 3.6 Consensus size: 35
56158944 CTTTCCCTTT
*
56158954 CTTTCCTTCTTTCTTTCTTT--TTTATTCTCTTCTC
1 CTTTCCTTC-TTCTTTCTTTCCTTTTTTCTCTTCTC
*
56158988 CTTTTCTTCTTCTTTCTTTCCTTTTTTCTCTTCTC
1 CTTTCCTTCTTCTTTCTTTCCTTTTTTCTCTTCTC
* *
56159023 CTTTCCTT-TTCTTTCTTTCCTCTCCTTTCT-TTCTTT
1 CTTTCCTTCTTCTTTCTTTCCT-T-TTTTCTCTTC-TC
*
56159059 CTTTCTTTCTTTCTTTCTTTCC
1 CTTTCCTTC-TTCTTTCTTTCC
56159081 CTCCTTCTGC
Statistics
Matches: 80, Mismatches: 6, Indels: 10
0.83 0.06 0.10
Matches are distributed among these distances:
33 10 0.12
34 21 0.26
35 24 0.30
36 13 0.16
38 12 0.15
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (35 bp):
CTTTCCTTCTTCTTTCTTTCCTTTTTTCTCTTCTC
Found at i:56159153 original size:27 final size:27
Alignment explanation
Indices: 56159122--56159196 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
56159112 AACACCAACC
56159122 GGTGCCGCCAATGGCATTGGCACCATT
1 GGTGCCGCCAATGGCATTGGCACCATT
** *
56159149 GGTGCCGCCAATGGTTTTGGCACCTTT
1 GGTGCCGCCAATGGCATTGGCACCATT
**
56159176 GGTGCCGCCAATACCATTGGC
1 GGTGCCGCCAATGGCATTGGC
56159197 GTGATCAGTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.25
Consensus pattern (27 bp):
GGTGCCGCCAATGGCATTGGCACCATT
Found at i:56159302 original size:28 final size:28
Alignment explanation
Indices: 56159273--56159340 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
56159263 TTTTTTTTAT
56159273 ATATTTTGGTAAAT-AAAAAAAGTT-TA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
56159299 ATATTTTGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
56159327 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
56159341 TTTTATTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 14 0.35
27 10 0.25
28 16 0.40
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTGTA
Found at i:56166264 original size:12 final size:12
Alignment explanation
Indices: 56166247--56166271 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56166237 TTATTCTTAA
56166247 CAACATATTTAC
1 CAACATATTTAC
56166259 CAACATATTTAC
1 CAACATATTTAC
56166271 C
1 C
56166272 TGACTTAACA
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:0.28, G:0.00, T:0.32
Consensus pattern (12 bp):
CAACATATTTAC
Found at i:56170142 original size:31 final size:29
Alignment explanation
Indices: 56170073--56170146 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
56170063 ATAAAATAAT
**
56170073 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATGGCA
*
56170102 AACATAAGTGACTAAAATGTAACCTGAGGCA
1 AACATAAGTGACTAAAATGTAACAT--GGCA
*
56170133 AACAAAAGTGACTA
1 AACATAAGTGACTA
56170147 TTTTTATAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.22
Consensus pattern (29 bp):
AACATAAGTGACTAAAATGTAACATGGCA
Found at i:56170984 original size:9 final size:9
Alignment explanation
Indices: 56170955--56170991 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
56170945 TGAGTTTTCG
56170955 AATTCGAAT
1 AATTCGAAT
*
56170964 AACTCGAAT
1 AATTCGAAT
56170973 AATTCGAAT
1 AATTCGAAT
*
56170982 AATTCAAAT
1 AATTCGAAT
56170991 A
1 A
56170992 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:56171408 original size:18 final size:17
Alignment explanation
Indices: 56171360--56171414 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
56171350 TATTTACTTT
56171360 CCCTCAAACTTTTATT-C
1 CCCT-AAACTTTTATTCC
*
56171377 CCCAAAACTTTTTATTTCC
1 CCCTAAAC-TTTTA-TTCC
56171396 CCCTAAACTTTTACTTCC
1 CCCTAAACTTTTA-TTCC
56171414 C
1 C
56171415 ACCCTTTACT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 4 0.12
17 8 0.25
18 12 0.38
19 8 0.25
ACGTcount: A:0.24, C:0.36, G:0.00, T:0.40
Consensus pattern (17 bp):
CCCTAAACTTTTATTCC
Found at i:56171925 original size:5 final size:5
Alignment explanation
Indices: 56171915--56171940 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
56171905 GAATAAATAT
56171915 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
56171941 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:56172956 original size:81 final size:81
Alignment explanation
Indices: 56172860--56173021 Score: 288
Period size: 81 Copynumber: 2.0 Consensus size: 81
56172850 TTACATACAT
* *
56172860 AATAAAGAAAGAAAGGGTTAAAAGTAAAAGCTATATACCTGCCATTATTAGAGAATGTGGTGCTA
1 AATAAAGAAAGAAAGGGTTAAAAGTAAAAGCTATATACCTGCCATTATGAGAGAATGTAGTGCTA
56172925 CCTGCAATGCAGAAAC
66 CCTGCAATGCAGAAAC
* *
56172941 AATAAAGAAAGAAAGGGTTATAAGTAGAAGCTATATACCTGCCATTATGAGAGAATGTAGTGCTA
1 AATAAAGAAAGAAAGGGTTAAAAGTAAAAGCTATATACCTGCCATTATGAGAGAATGTAGTGCTA
56173006 CCTGCAATGCAGAAAC
66 CCTGCAATGCAGAAAC
56173022 GTGGAGGGGA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.22
Consensus pattern (81 bp):
AATAAAGAAAGAAAGGGTTAAAAGTAAAAGCTATATACCTGCCATTATGAGAGAATGTAGTGCTA
CCTGCAATGCAGAAAC
Found at i:56173380 original size:29 final size:31
Alignment explanation
Indices: 56173348--56173429 Score: 71
Period size: 29 Copynumber: 2.7 Consensus size: 31
56173338 AAGAAAATGC
56173348 AAATAACA-AATCAATTAAGCCCCTGT-ATT
1 AAATAACACAATCAATTAAGCCCCTGTCATT
* ** * *
56173377 AAAT-TCACACCCAATTAAGCTCCTGTCGTT
1 AAATAACACAATCAATTAAGCCCCTGTCATT
* * *
56173407 AACTAAAATAATCAATTAAGCCC
1 AAATAACACAATCAATTAAGCCC
56173430 TTCCGTTAAC
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
28 2 0.05
29 19 0.50
30 5 0.13
31 12 0.32
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.27
Consensus pattern (31 bp):
AAATAACACAATCAATTAAGCCCCTGTCATT
Found at i:56173554 original size:17 final size:17
Alignment explanation
Indices: 56173532--56173564 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
56173522 TTTTTCCCTT
56173532 AAAAATCATAAAAATAA
1 AAAAATCATAAAAATAA
*
56173549 AAAAATTATAAAAATA
1 AAAAATCATAAAAATA
56173565 TTTAAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAATCATAAAAATAA
Found at i:56174198 original size:21 final size:21
Alignment explanation
Indices: 56174151--56174244 Score: 60
Period size: 21 Copynumber: 4.7 Consensus size: 21
56174141 ATGGTTCATG
* *
56174151 ATTTTTTTAGTATTTTAATAC
1 ATTTTTATAATATTTTAATAC
*
56174172 ATTTTTATAATATTTTAA-AT
1 ATTTTTATAATATTTTAATAC
* *
56174192 ATGTTTTATTA-ATTAT-ATA-
1 AT-TTTTATAATATTTTAATAC
56174211 ATTTATTAT-A-ATTTT--TAC
1 ATTT-TTATAATATTTTAATAC
56174229 ATCTTTTATAATATTT
1 AT-TTTTATAATATTT
56174245 ATATTTTTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
17 2 0.03
18 13 0.22
19 10 0.17
20 12 0.20
21 23 0.38
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTTTTATAATATTTTAATAC
Found at i:56174253 original size:18 final size:18
Alignment explanation
Indices: 56174173--56174254 Score: 58
Period size: 18 Copynumber: 4.3 Consensus size: 18
56174163 TTTTAATACA
56174173 TTTTTATAATATTTTAAATAT
1 TTTTTATAATA-TTT--ATAT
* *
56174194 GTTTTATTAAT-TATATAAT
1 TTTTTA-TAATATTTAT-AT
* * *
56174213 TTATTATAATTTTTACAT
1 TTTTTATAATATTTATAT
*
56174231 CTTTTATAATATTTATAT
1 TTTTTATAATATTTATAT
56174249 TTTTTA
1 TTTTTA
56174255 AGTTTATATC
Statistics
Matches: 47, Mismatches: 11, Indels: 9
0.70 0.16 0.13
Matches are distributed among these distances:
18 27 0.57
19 9 0.19
20 2 0.04
21 5 0.11
22 4 0.09
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (18 bp):
TTTTTATAATATTTATAT
Found at i:56185950 original size:49 final size:50
Alignment explanation
Indices: 56185894--56185990 Score: 124
Period size: 49 Copynumber: 2.0 Consensus size: 50
56185884 TTTATTTTTT
* * * *
56185894 CGATGCCATAGTCAAACTATGGTATTACATGTAGTCACAT-ATCACATAC
1 CGATGCCATAGCCAAACTATGGTATTACACGGAATCACATAATCACATAC
* * *
56185943 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCACAT
1 CGATGCCATAGCCAAACTATGGTATTACACGGAATCACATAATCACAT
56185991 TTTCACATGT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
49 33 0.82
50 7 0.17
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (50 bp):
CGATGCCATAGCCAAACTATGGTATTACACGGAATCACATAATCACATAC
Found at i:56204661 original size:27 final size:29
Alignment explanation
Indices: 56204612--56204675 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 29
56204602 TTTTTCATCT
* **
56204612 GAAGAAGATGAAGAGGTAACTTCTTCTGAG
1 GAAGAAGAAGAAGAGGT-ACTTCAACTGAG
56204642 GAAGAAGAAGAAG-GGT-CTTCAACTGAG
1 GAAGAAGAAGAAGAGGTACTTCAACTGAG
56204669 GAAGAAG
1 GAAGAAG
56204676 GTGAGGAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 16 0.52
29 3 0.10
30 12 0.39
ACGTcount: A:0.41, C:0.09, G:0.33, T:0.17
Consensus pattern (29 bp):
GAAGAAGAAGAAGAGGTACTTCAACTGAG
Found at i:56210536 original size:10 final size:10
Alignment explanation
Indices: 56210523--56210590 Score: 54
Period size: 10 Copynumber: 7.1 Consensus size: 10
56210513 ATCATAAAAA
56210523 ATAAAAAATT
1 ATAAAAAATT
56210533 ATAAAAAGA-T
1 ATAAAAA-ATT
* *
56210543 ATTAAAATTT
1 ATAAAAAATT
* *
56210553 ATATAAACTT
1 ATAAAAAATT
*
56210563 AT-AAATATT
1 ATAAAAAATT
56210572 AT-AAAAA-T
1 ATAAAAAATT
56210580 ATAAAAAATT
1 ATAAAAAATT
56210590 A
1 A
56210591 ATGAAACCTA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
8 3 0.07
9 15 0.33
10 26 0.58
11 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:56213414 original size:18 final size:18
Alignment explanation
Indices: 56213371--56213414 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
56213361 AAATATAATA
*
56213371 AAAAG-AAATCAACAAAT
1 AAAAGTAAATAAACAAAT
56213388 AAAAGTAAATAAACAAAT
1 AAAAGTAAATAAACAAAT
*
56213406 AAAATTAAA
1 AAAAGTAAA
56213415 GCACTTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.16
Consensus pattern (18 bp):
AAAAGTAAATAAACAAAT
Found at i:56213608 original size:21 final size:21
Alignment explanation
Indices: 56213531--56213600 Score: 53
Period size: 19 Copynumber: 3.6 Consensus size: 21
56213521 ATGTTAGAAT
*
56213531 TATAAAGTATATAT-AATATA
1 TATAAAGAATATATAAATATA
* * *
56213551 TAT-AA-TATATTTTAA-A-A
1 TATAAAGAATATATAAATATA
56213568 TATAAAGAATATATAAATATA
1 TATAAAGAATATATAAATATA
56213589 TATATAA-AATAT
1 TATA-AAGAATAT
56213601 GTACATATGC
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
17 4 0.10
18 9 0.22
19 11 0.28
20 4 0.10
21 10 0.25
22 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
TATAAAGAATATATAAATATA
Found at i:56213775 original size:3 final size:3
Alignment explanation
Indices: 56213767--56213877 Score: 63
Period size: 3 Copynumber: 37.3 Consensus size: 3
56213757 AAACTATCAT
* * *
56213767 ATA ATA ATA AT- ATG ATGA ATA AAA ATG AT- ATAA ATA ATA ATA GA-A
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA AT-A ATA ATA ATA -ATA
* * * * *
56213812 ATA ATA ATC ATA ATA ATA AAA GATA ATA ACA TTA A-A ATA ATGA AGA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA AT-A ATA
56213858 A-A A-A ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
56213878 AAGTGTTAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
2 11 0.13
3 65 0.76
4 9 0.11
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:56214524 original size:14 final size:14
Alignment explanation
Indices: 56214501--56214531 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
56214491 AAATAGTTCG
56214501 AAAGAAAAAAAAAT
1 AAAGAAAAAAAAAT
*
56214515 AAAGAGAAAAAAAT
1 AAAGAAAAAAAAAT
56214529 AAA
1 AAA
56214532 AATAGAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (14 bp):
AAAGAAAAAAAAAT
Found at i:56214524 original size:16 final size:16
Alignment explanation
Indices: 56214503--56214540 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
56214493 ATAGTTCGAA
56214503 AGAAAAAAA-AATAAAG
1 AGAAAAAAATAA-AAAG
*
56214519 AGAAAAAAATAAAAAT
1 AGAAAAAAATAAAAAG
56214535 AGAAAA
1 AGAAAA
56214541 GGAAAATAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.08
Consensus pattern (16 bp):
AGAAAAAAATAAAAAG
Found at i:56215120 original size:22 final size:24
Alignment explanation
Indices: 56215095--56215139 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
56215085 TAATACATAA
*
56215095 AGATAAATA-AA-TGATTTATCTT
1 AGATAAATAGAAGTAATTTATCTT
56215117 AGATAAATAGAAGTAATTTATCT
1 AGATAAATAGAAGTAATTTATCT
56215140 CCTATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 2 0.10
24 9 0.45
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (24 bp):
AGATAAATAGAAGTAATTTATCTT
Found at i:56215584 original size:16 final size:15
Alignment explanation
Indices: 56215567--56215599 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
56215557 TATATATATA
*
56215567 TATAT-ATAAAAACT
1 TATATCATAAAAAAT
56215581 TATATCATAAAAAAT
1 TATATCATAAAAAAT
56215596 TATA
1 TATA
56215600 ATAAGATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (15 bp):
TATATCATAAAAAAT
Found at i:56220281 original size:21 final size:21
Alignment explanation
Indices: 56220255--56220295 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
56220245 AGACGAGCAA
* *
56220255 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
56220276 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
56220296 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:56223858 original size:20 final size:19
Alignment explanation
Indices: 56223820--56223893 Score: 64
Period size: 20 Copynumber: 3.9 Consensus size: 19
56223810 CTTAAAAATC
*
56223820 ATAAAAA-ATA-AAAAATT
1 ATAAAAACATATAAAATTT
*
56223837 ATAAAAAGATATTAAAATTT
1 ATAAAAACATA-TAAAATTT
*
56223857 ATATAAACATAT-AAATATT
1 ATAAAAACATATAAAAT-TT
* *
56223876 ATAAAAATATAAAAAATT
1 ATAAAAACATATAAAATT
56223894 AACGAAACCT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
17 7 0.15
18 7 0.15
19 13 0.28
20 19 0.41
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (19 bp):
ATAAAAACATATAAAATTT
Found at i:56223946 original size:21 final size:20
Alignment explanation
Indices: 56223920--56223958 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
56223910 AATAAAATAT
*
56223920 ATATTAGAATTATTTAAAAAA
1 ATATTAAAATTA-TTAAAAAA
56223941 ATATTAAAATTATTAAAA
1 ATATTAAAATTATTAAAA
56223959 TTGTATAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
ATATTAAAATTATTAAAAAA
Found at i:56225812 original size:22 final size:24
Alignment explanation
Indices: 56225787--56225831 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
56225777 TAATACATAA
*
56225787 AGATAAATA-AA-TGATTTATCTT
1 AGATAAATAGAAGTAATTTATCTT
56225809 AGATAAATAGAAGTAATTTATCT
1 AGATAAATAGAAGTAATTTATCT
56225832 CCTATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 2 0.10
24 9 0.45
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (24 bp):
AGATAAATAGAAGTAATTTATCTT
Found at i:56229164 original size:20 final size:20
Alignment explanation
Indices: 56229139--56229194 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
56229129 ATCATAAAAA
*
56229139 ATTAAAAATTATAAAAAGAT
1 ATTAAAAATTATAAAAACAT
* * *
56229159 ATTAAAATTTATATAAACTT
1 ATTAAAAATTATAAAAACAT
*
56229179 A-TAAATATTATAAAAA
1 ATTAAAAATTATAAAAA
56229195 TATAAAATAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
ATTAAAAATTATAAAAACAT
Found at i:56229266 original size:9 final size:9
Alignment explanation
Indices: 56229254--56229307 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
56229244 CTTTAAAAAA
56229254 ATTAAAATT
1 ATTAAAATT
56229263 ATTAAAATT
1 ATTAAAATT
56229272 ATTAAAATT
1 ATTAAAATT
* *
56229281 GTATAAACTT
1 AT-TAAAATT
56229291 A-TAAATATT
1 ATTAAA-ATT
*
56229300 ATAAAAAT
1 ATTAAAAT
56229308 ATAAAAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
8 4 0.11
9 24 0.65
10 9 0.24
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (9 bp):
ATTAAAATT
Found at i:56229269 original size:18 final size:18
Alignment explanation
Indices: 56229246--56229280 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56229236 TTAGAATTCT
56229246 TTAAAAAAATTAAAATTA
1 TTAAAAAAATTAAAATTA
**
56229264 TTAAAATTATTAAAATT
1 TTAAAAAAATTAAAATT
56229281 GTATAAACTT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAAAAAATTAAAATTA
Found at i:56229362 original size:22 final size:21
Alignment explanation
Indices: 56229336--56229384 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
56229326 CTATTTAAAA
* *
56229336 TAAAATACATATTAGAATTCTT
1 TAAAATACATATTAAAATT-AT
* *
56229358 TAAAAAATATATTAAAATTAT
1 TAAAATACATATTAAAATTAT
56229379 TAAAAT
1 TAAAAT
56229385 TGTATAAACT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (21 bp):
TAAAATACATATTAAAATTAT
Done.