Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009617.1 Hibiscus syriacus cultivar Beakdansim tig00117005_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: 3386631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 16
Found at i:2332107 original size:198 final size:197
Alignment explanation
Indices: 2331634--2332325 Score: 800
Period size: 200 Copynumber: 3.5 Consensus size: 197
2331624 TATTGACCCA
* * * *
2331634 AAAAACATCAAAACCAATAATTATAATGGAATAGGTAAATTAACAATGTAACCGGTATAAATATA
1 AAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATA
* * * * **
2331699 CC-GATTAATTAGAAAACAGGTCAACATAATGTATCGACACTTGTGGAATTTGTGTCGATACTTA
66 CCGGTTTTATGAGAAAATAGGTC-ACATAATGTATCGACACTTGTTAAATTTGTGTCGATACTT-
* * * *
2331763 TTGTCCAGAATGAATGCCCAAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAA-AGTAT
129 TTTTCCAGAATGAATGTCC-AACGAGGTGCAAGCATAAAGTGTCGATACATTTA--AAATTGTAT
2331827 CGATCCC
191 CGATCCC
* * *
2331834 AAAAACATCAAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAATCGATATAAATATA
1 AAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATA
* *
2331899 CCGATTTTATGAGAAAATAGGTCAGCATAAAGTATCGACACTTGTTAAATTTGTGTCGATACATT
66 CCGGTTTTATGAGAAAATAGGTCA-CATAATGTATCGACACTTGTTAAATTTGTGTCGATAC-TT
* * *
2331964 TTTTCCATAATGAATGTCCAACGAGGTACAAGAATAAAGTGTCGATACATTTAAAATTGTATCGA
129 TTTTCCAGAATGAATGTCCAACGAGGTGCAAGCATAAAGTGTCGATACATTTAAAATTGTATCGA
2332029 TCCC
194 TCCC
* * * * * * * *
2332033 ATAAACACCGAAA-CAAAAATTACAATGTGATAGGTAAATTTACAATGTACCCAGTATAAATATA
1 AAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATA
* * * * * * *
2332097 CCGGTTTTATGAGAAAATATGTTTAAATAATGTATCAACACATT-TTTAGTTTGTGTCGATATTT
66 CCGGTTTTATGAGAAAATA-GGTCACATAATGTATCGACAC-TTGTTAAATTTGTGTCGATACTT
2332161 TTTTCCAGAATGAAATATGAATACCCAACGAGGTGCAAGCATAAAGTGTCGATACATTTAAAATT
129 TTTTCCAGAATG--A-ATG--T--CCAACGAGGTGCAAGCATAAAGTGTCGATACATTTAAAATT
* *
2332226 TTATCGATCCA
187 GTATCGATCCC
* * *
2332237 AAAAATATCGAAACCGATAATTATAATGTAATAGGTAAATTTGCAATGTTACCGGTATAAATATA
1 AAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATA
**
2332302 CCGG-TTTACTTCGAAAATAGGTCA
66 CCGGTTTTA-TGAGAAAATAGGTCA
2332326 ATATAAGCGC
Statistics
Matches: 417, Mismatches: 60, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
197 13 0.03
198 92 0.22
199 27 0.06
200 97 0.23
201 65 0.16
202 3 0.01
204 65 0.16
205 55 0.13
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.30
Consensus pattern (197 bp):
AAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATA
CCGGTTTTATGAGAAAATAGGTCACATAATGTATCGACACTTGTTAAATTTGTGTCGATACTTTT
TTCCAGAATGAATGTCCAACGAGGTGCAAGCATAAAGTGTCGATACATTTAAAATTGTATCGATC
CC
Found at i:2332429 original size:87 final size:87
Alignment explanation
Indices: 2332328--2332488 Score: 277
Period size: 87 Copynumber: 1.9 Consensus size: 87
2332318 ATAGGTCAAT
* *
2332328 ATAAGCGCTACCTATTTCATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCC
1 ATAAGCGCTACCTATTACATTAAATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCC
2332393 GGCTAAATGCCTATTTTATTAA
66 GGCTAAATGCCTATTTTATTAA
* *
2332415 ATAAGCGCTACCTATTACATTAAATAAGCGCTACCTAATATGTTTTTGTACTTGATAATATTTCC
1 ATAAGCGCTACCTATTACATTAAATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCC
*
2332480 GGTTAAATG
66 GGCTAAATG
2332489 ATATAACATA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (87 bp):
ATAAGCGCTACCTATTACATTAAATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCC
GGCTAAATGCCTATTTTATTAA
Found at i:2336350 original size:5 final size:5
Alignment explanation
Indices: 2336340--2336365 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2336330 TGTTCTAAAA
2336340 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
2336366 GGTGTTCTTA
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:2342950 original size:38 final size:37
Alignment explanation
Indices: 2342900--2343334 Score: 461
Period size: 36 Copynumber: 11.8 Consensus size: 37
2342890 AAAAATCGGG
* *
2342900 TTTTAAAAATATATAT--TATATAGCTTTGAAAATGAT
1 TTTTAAAAATATATATAATATATAGTTTTGAAAA-CAT
* * **
2342936 TTTTGAAAATATATATATTATATAG-TTTGTAAATGAT
1 TTTTAAAAATATATATAATATATAGTTTTG-AAAACAT
2342973 TTTTGAAAAAATATATATAATATATAGTTTTTGAAAACA-
1 TTTT--AAAAATATATATAATATATAG-TTTTGAAAACAT
*
2343012 TTTTGAAAATATATATAATATATAGTTTTTTGAAAACA-
1 TTTTAAAAATATATATAATATATAG--TTTTGAAAACAT
* *
2343050 TTTTGAAAATATATATAATATATAGTTTTTAAAA-AT
1 TTTTAAAAATATATATAATATATAGTTTTGAAAACAT
2343086 ATTTTAAAAACT-TATATAATATATAGTTTTGAAAACA-
1 -TTTTAAAAA-TATATATAATATATAGTTTTGAAAACAT
*
2343123 TTTTAAAAACT-TATATAATATATAGTTTTGAAATCA-
1 TTTTAAAAA-TATATATAATATATAGTTTTGAAAACAT
*
2343159 TTTTAAAAACT-TATATAATATATAGTTTTGAAATCA-
1 TTTTAAAAA-TATATATAATATATAGTTTTGAAAACAT
2343195 TTTTAAAAACT-TATATAATATATAGTTTT-AAAACAT
1 TTTTAAAAA-TATATATAATATATAGTTTTGAAAACAT
* *
2343231 TTTTCAAAA-CTATATAATATATAGTTTTGAAAACAT
1 TTTTAAAAATATATATAATATATAGTTTTGAAAACAT
**
2343267 TTTTAAAAAATATATATATAATATATAGTTTT-AAAATGT
1 TTTT--AAAA-ATATATATAATATATAGTTTTGAAAACAT
* * *
2343306 TTTTGAAAATATATATATTATATGGTTTT
1 TTTTAAAAATATATATAATATATAGTTTT
2343335 TTGAAATATT
Statistics
Matches: 360, Mismatches: 20, Indels: 38
0.86 0.05 0.09
Matches are distributed among these distances:
35 24 0.07
36 161 0.45
37 64 0.18
38 52 0.14
39 33 0.09
40 22 0.06
41 4 0.01
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (37 bp):
TTTTAAAAATATATATAATATATAGTTTTGAAAACAT
Found at i:2343119 original size:73 final size:72
Alignment explanation
Indices: 2342900--2343302 Score: 439
Period size: 75 Copynumber: 5.5 Consensus size: 72
2342890 AAAAATCGGG
* * * *
2342900 TTTTAAAAATATATAT--TATATAGCTTTGAAAATGATTTTTGAAAA-TATATATATTATATAG-
1 TTTTAAAAATATATATAATATATAGTTTTAAAAAT-A-TTTTAAAAACT-TATATAATATATAGT
**
2342961 TTTGTAAATGA
63 TTTG-AAAACA
* * *
2342972 TTTTTGAAAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAA-TATATATAATATATA
1 -TTTT--AAAAATATATATAATATATAG-TTTTAAAAATATTTTAAAAACT-TATATAATATATA
2343036 GTTTTTTGAAAACA
61 G--TTTTGAAAACA
*
2343050 TTTTGAAAATATATATAATATATAGTTTTTAAAAATATTTTAAAAACTTATATAATATATAGTTT
1 TTTTAAAAATATATATAATATATAG-TTTTAAAAATATTTTAAAAACTTATATAATATATAGTTT
2343115 TGAAAACA
65 TGAAAACA
*
2343123 TTTTAAAAACT-TATATAATATATAGTTTT-GAAATCATTTTAAAAACTTATATAATATATAGTT
1 TTTTAAAAA-TATATATAATATATAGTTTTAAAAAT-ATTTTAAAAACTTATATAATATATAGTT
*
2343186 TTGAAATCA
64 TTGAAAACA
*
2343195 TTTTAAAAACT-TATATAATATATAGTTTTAAAACAT-TTTTCAAAAC-TATATAATATATAGTT
1 TTTTAAAAA-TATATATAATATATAGTTTTAAAA-ATATTTTAAAAACTTATATAATATATAGTT
2343257 TTGAAAACA
64 TTGAAAACA
2343266 TTTTTAAAAAATATATATATAATATATAGTTTTAAAA
1 -TTTT--AAAA-ATATATATAATATATAGTTTTAAAA
2343303 TGTTTTTGAA
Statistics
Matches: 297, Mismatches: 15, Indels: 34
0.86 0.04 0.10
Matches are distributed among these distances:
71 28 0.09
72 82 0.28
73 39 0.13
74 8 0.03
75 87 0.29
76 25 0.08
77 12 0.04
78 12 0.04
79 4 0.01
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.44
Consensus pattern (72 bp):
TTTTAAAAATATATATAATATATAGTTTTAAAAATATTTTAAAAACTTATATAATATATAGTTTT
GAAAACA
Found at i:2343367 original size:3 final size:3
Alignment explanation
Indices: 2343359--2343416 Score: 73
Period size: 3 Copynumber: 19.0 Consensus size: 3
2343349 ATATATAAAA
*
2343359 TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAGT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
*
2343404 TTT TATT TAT TAT
1 TAT TA-T TAT TAT
2343417 ATTTTTTCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.04
3 41 0.85
4 5 0.10
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:2344680 original size:28 final size:28
Alignment explanation
Indices: 2344640--2344698 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
2344630 AAATCTAACA
*
2344640 TTTTTATCATTTTT-ATTTTATTTCATTAT
1 TTTTTATCATTTTTGA-TTTATTTAATT-T
*
2344669 TTTTTCTC-TTTTTGATTTATTTAATTT
1 TTTTTATCATTTTTGATTTATTTAATTT
2344696 TTT
1 TTT
2344699 AATTTTCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 4 0.15
28 15 0.56
29 8 0.30
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.75
Consensus pattern (28 bp):
TTTTTATCATTTTTGATTTATTTAATTT
Found at i:2344755 original size:4 final size:4
Alignment explanation
Indices: 2344746--2344779 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
2344736 TTTTCCTTTC
2344746 ATTT ATTT A-TT ATTT ATTT ATTT ATTT A-TT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
2344780 CTTATCTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 22 0.79
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:2351908 original size:21 final size:21
Alignment explanation
Indices: 2351882--2351928 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2351872 GAGGTAAATT
2351882 TTTTTAGTAATTTAAATTTTA
1 TTTTTAGTAATTTAAATTTTA
* * *
2351903 TTTTTAGTATTTTTATTTTTA
1 TTTTTAGTAATTTAAATTTTA
2351924 TTTTT
1 TTTTT
2351929 TATATTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (21 bp):
TTTTTAGTAATTTAAATTTTA
Found at i:2351916 original size:15 final size:13
Alignment explanation
Indices: 2351898--2351937 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 13
2351888 GTAATTTAAA
2351898 TTTTATTTTTAGTAT
1 TTTTATTTTTA-T-T
2351913 TTTTATTTTTATT
1 TTTTATTTTTATT
2351926 TTTTATATTTTA
1 TTTTAT-TTTTA
2351938 AATATTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.29
14 6 0.25
15 11 0.46
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:2356926 original size:13 final size:13
Alignment explanation
Indices: 2356904--2356937 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2356894 GCACAATCAT
2356904 AGACACAACTTTG
1 AGACACAACTTTG
*
2356917 AGAGACAACTTTG
1 AGACACAACTTTG
2356930 AGACACAA
1 AGACACAA
2356938 TACACAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (13 bp):
AGACACAACTTTG
Found at i:2364871 original size:204 final size:204
Alignment explanation
Indices: 2364521--2364919 Score: 735
Period size: 204 Copynumber: 2.0 Consensus size: 204
2364511 GATATACATA
2364521 TGAATTTAATTATCCCGAATATAGTAAGTAAGCATTAAAAGAATGTAATTTAGATTACAACTCTT
1 TGAATTTAATTATCCCGAATATAGTAAGTAAGCATTAAAAGAATGTAATTTAGATTACAACTCTT
2364586 TTAATTGATATATATAATTCGAAATAATTAAATAAGTTTTTAAATAAACATTAAATATTATAATT
66 TTAATTGATATATATAATTCGAAATAATTAAATAAGTTTTTAAATAAACATTAAATATTATAATT
*
2364651 CTTATTATAAGTCTTTAATCTATATTTAATTTGAATTAATTAAATAATATTTTATTTATTAATTC
131 CTGATTATAAGTCTTTAATCTATATTTAATTTGAATTAATTAAATAATATTTTATTTATTAATTC
2364716 CGATCAATT
196 CGATCAATT
*
2364725 TGAATTTAATTATCCTGAATATAGTAAGTAAGCATTAAAAGAATGTAATTTAGATTACAACTCTT
1 TGAATTTAATTATCCCGAATATAGTAAGTAAGCATTAAAAGAATGTAATTTAGATTACAACTCTT
* *
2364790 TTAATTGATATATATAATTCGGAATAATTAAATAAGTTTTTAAATAAACATTAAATATTGTAATT
66 TTAATTGATATATATAATTCGAAATAATTAAATAAGTTTTTAAATAAACATTAAATATTATAATT
* * *
2364855 CTGATTATAAGTCTTTAATGTTTTTTTAATTTGAATTAATTAAATAATATTTTATTTATTAATTC
131 CTGATTATAAGTCTTTAATCTATATTTAATTTGAATTAATTAAATAATATTTTATTTATTAATTC
2364920 GAAACAACTT
Statistics
Matches: 188, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
204 188 1.00
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (204 bp):
TGAATTTAATTATCCCGAATATAGTAAGTAAGCATTAAAAGAATGTAATTTAGATTACAACTCTT
TTAATTGATATATATAATTCGAAATAATTAAATAAGTTTTTAAATAAACATTAAATATTATAATT
CTGATTATAAGTCTTTAATCTATATTTAATTTGAATTAATTAAATAATATTTTATTTATTAATTC
CGATCAATT
Found at i:2373764 original size:21 final size:21
Alignment explanation
Indices: 2373726--2373766 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2373716 AAAAAAATAC
*
2373726 TTAATCTAAAATATTATAAAA
1 TTAATCTAAAATAGTATAAAA
* *
2373747 TTAATTTAAAATGGTATAAA
1 TTAATCTAAAATAGTATAAA
2373767 TAACATACTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
TTAATCTAAAATAGTATAAAA
Found at i:2374491 original size:17 final size:17
Alignment explanation
Indices: 2374469--2374501 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2374459 CGAGATTATA
*
2374469 ATATTATTTTTTATATT
1 ATATTATATTTTATATT
2374486 ATATTATATTTTATAT
1 ATATTATATTTTATAT
2374502 AAATTAATAT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:2384310 original size:28 final size:30
Alignment explanation
Indices: 2384254--2384310 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2384244 TAAACTTTAC
*
2384254 TCTCTCTTATTTCACTCATTGTAATTTAAA
1 TCTCTCTTATTTCACTCATTGTAAATTAAA
2384284 TCTCT-TTAATTTC-CTCATTG-AAATTAA
1 TCTCTCTT-ATTTCACTCATTGTAAATTAA
2384311 TATAATGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 6 0.24
29 9 0.36
30 10 0.40
ACGTcount: A:0.28, C:0.19, G:0.04, T:0.49
Consensus pattern (30 bp):
TCTCTCTTATTTCACTCATTGTAAATTAAA
Found at i:2394414 original size:14 final size:14
Alignment explanation
Indices: 2394390--2394429 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2394380 CTTGAGGAGG
*
2394390 AAGAAGAAGAGAGA
1 AAGATGAAGAGAGA
*
2394404 AAGATGGAGAGAGA
1 AAGATGAAGAGAGA
*
2394418 ATGATGAAGAGA
1 AAGATGAAGAGA
2394430 AGAGGAAGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.38, T:0.07
Consensus pattern (14 bp):
AAGATGAAGAGAGA
Found at i:2396690 original size:27 final size:26
Alignment explanation
Indices: 2396660--2396710 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
2396650 ATGTATGATC
*
2396660 ATAATTCAAAAGTATTTTTAATAAAAA
1 ATAATTCAAAAGCA-TTTTAATAAAAA
2396687 ATAATTCAAAAGCATTTTAATAAA
1 ATAATTCAAAAGCATTTTAATAAA
2396711 TTAAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (26 bp):
ATAATTCAAAAGCATTTTAATAAAAA
Found at i:2400012 original size:21 final size:21
Alignment explanation
Indices: 2399986--2400026 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2399976 TATGGGCAAA
*
2399986 GTGTATCGATGCACATTCAAT
1 GTGTATCAATGCACATTCAAT
*
2400007 GTGTATCAATGCACTTTCAA
1 GTGTATCAATGCACATTCAA
2400027 ATAAATGAAC
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:0.20, G:0.17, T:0.34
Consensus pattern (21 bp):
GTGTATCAATGCACATTCAAT
Found at i:2400167 original size:24 final size:20
Alignment explanation
Indices: 2400135--2400190 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
2400125 GCACAGGTAG
2400135 TGCATCGATGCACATGTTAAGGAA
1 TGCATCGATGCAC-TG-T-A-GAA
* *
2400159 TGCATCGATACACTGTAGAG
1 TGCATCGATGCACTGTAGAA
2400179 TGCATCGATGCA
1 TGCATCGATGCA
2400191 TACCTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 13 0.45
21 1 0.03
22 1 0.03
23 2 0.07
24 12 0.41
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:2401671 original size:23 final size:23
Alignment explanation
Indices: 2401615--2401681 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
2401605 ATTTTATATA
*
2401615 GCACTTCGGTGCAATTCTACGCG
1 GCACTTCGGTGCAATTATACGCG
* * * *
2401638 GCAATTTGGTGAAATTATACGTG
1 GCACTTCGGTGCAATTATACGCG
*
2401661 GCACTTCGGTGCATTTATACG
1 GCACTTCGGTGCAATTATACG
2401682 AGCTGTGGTG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.31
Consensus pattern (23 bp):
GCACTTCGGTGCAATTATACGCG
Found at i:2404094 original size:20 final size:20
Alignment explanation
Indices: 2404069--2404139 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
2404059 AAACTGAAAT
*
2404069 AGTATCGATACTGACTCATC
1 AGTATCGATATTGACTCATC
*
2404089 AGTATCGATATTAACTCATC
1 AGTATCGATATTGACTCATC
* * * *
2404109 AGTATCAATATTGGCTTAGC
1 AGTATCGATATTGACTCATC
2404129 AGTATCGATAT
1 AGTATCGATAT
2404140 ATTTCCCCGA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (20 bp):
AGTATCGATATTGACTCATC
Found at i:2406564 original size:17 final size:17
Alignment explanation
Indices: 2406542--2406589 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 17
2406532 ATTTAGAATC
2406542 ATAAAAATAAATTTAAT
1 ATAAAAATAAATTTAAT
2406559 ATAAAAATATTGAATTTAAT
1 ATAAAAATA---AATTTAAT
2406579 -TAAAATATAAA
1 ATAAAA-ATAAA
2406590 AATAATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 11 0.41
19 5 0.19
20 11 0.41
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
ATAAAAATAAATTTAAT
Found at i:2406566 original size:45 final size:45
Alignment explanation
Indices: 2406510--2406599 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
2406500 TAGAAATATA
*
2406510 AATATGAAAAATATTGAATTTAATTTAGAATCATAAAAATAA-ATTT
1 AATATGAAAAATATTGAATTTAA-TTAAAAT-ATAAAAATAATATTT
2406556 AATAT-AAAAATATTGAATTTAATTAAAATATAAAAATAATATTT
1 AATATGAAAAATATTGAATTTAATTAAAATATAAAAATAATATTT
2406600 TTTTTAATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
43 10 0.24
44 10 0.24
45 17 0.40
46 5 0.12
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (45 bp):
AATATGAAAAATATTGAATTTAATTAAAATATAAAAATAATATTT
Found at i:2408511 original size:2 final size:2
Alignment explanation
Indices: 2408506--2408559 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
2408496 TATATATATA
* * * *
2408506 TG TG TG TG TG TG TG TG TG TG TG TT TG TG TG CG TT TG TG TG CG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2408548 TG TG TG TG TG TG
1 TG TG TG TG TG TG
2408560 AACATAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.04, G:0.46, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2409544 original size:23 final size:23
Alignment explanation
Indices: 2409511--2409578 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
2409501 AACTTTATAT
2409511 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
2409534 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* *
2409557 GGCACTTCGATGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
2409579 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:2410575 original size:67 final size:69
Alignment explanation
Indices: 2410494--2410623 Score: 219
Period size: 67 Copynumber: 1.9 Consensus size: 69
2410484 TCAAATGCCT
*
2410494 TTTTATAGTAAGATATGAAGTTACCTTGCC-TTTCAATTATTTTT-TAGGCATTCTTTTATTTAA
1 TTTTATAGTAAGATAAGAAGTTACCTTGCCTTTTCAATTATTTTTGTAGGCATTCTTTTATTTAA
2410557 TTTC
66 TTTC
* *
2410561 TTTTATAGTTAGATAAGAAGTTATCTTGCCTTTTCAATTATTTTTGTAGGCATTCTTTTATTT
1 TTTTATAGTAAGATAAGAAGTTACCTTGCCTTTTCAATTATTTTTGTAGGCATTCTTTTATTT
2410624 CATTGAAATG
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
67 27 0.47
68 14 0.24
69 17 0.29
ACGTcount: A:0.25, C:0.11, G:0.12, T:0.53
Consensus pattern (69 bp):
TTTTATAGTAAGATAAGAAGTTACCTTGCCTTTTCAATTATTTTTGTAGGCATTCTTTTATTTAA
TTTC
Found at i:2429495 original size:18 final size:18
Alignment explanation
Indices: 2429472--2429507 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2429462 AAAGTTCAAA
2429472 TCGTGAACTATGAAATAT
1 TCGTGAACTATGAAATAT
2429490 TCGTGAACTATGAAATAT
1 TCGTGAACTATGAAATAT
2429508 CCCAAAGCCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (18 bp):
TCGTGAACTATGAAATAT
Found at i:2435083 original size:2 final size:2
Alignment explanation
Indices: 2435078--2435125 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2435068 TGTGTGTGTG
2435078 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2435120 TA TA TA
1 TA TA TA
2435126 GCCGATTCTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2435480 original size:31 final size:31
Alignment explanation
Indices: 2435432--2435505 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
2435422 AGTTACGTCG
* *
2435432 GGGACCATATTGCAAACGGACTAAATGTTGA
1 GGGATCATATTGAAAACGGACTAAATGTTGA
* *
2435463 GGGATCATATTGAAAACGGACTAAGTGTTGG
1 GGGATCATATTGAAAACGGACTAAATGTTGA
*
2435494 GGGATTATATTG
1 GGGATCATATTG
2435506 CAAGTTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (31 bp):
GGGATCATATTGAAAACGGACTAAATGTTGA
Found at i:2437244 original size:42 final size:42
Alignment explanation
Indices: 2437139--2437233 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 42
2437129 AGACGTAACT
* *
2437139 TAAAATATTATAAAAAATTAACATTTTCGGTTGAGTGTGACC
1 TAAAATATTATAAAATATTAATATTTTCGGTTGAGTGTGACC
2437181 TAAAATATTATAAAATATTAATATTTTCGGTTGAGTGTTG-CC
1 TAAAATATTATAAAATATTAATATTTTCGGTTGAGTG-TGACC
*
2437223 TAAAATGTTAT
1 TAAAATATTAT
2437234 TTTTTCTTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
42 47 0.96
43 2 0.04
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (42 bp):
TAAAATATTATAAAATATTAATATTTTCGGTTGAGTGTGACC
Found at i:2439750 original size:21 final size:21
Alignment explanation
Indices: 2439726--2439804 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
2439716 ATCGTAGCCG
*
2439726 TTTCAGATGGCACCACAACCA
1 TTTCAGATGCCACCACAACCA
* ** *
2439747 TTTCAGATGCCATCACAGTCG
1 TTTCAGATGCCACCACAACCA
* *
2439768 GTTCAGACGCCACCACAACCAA
1 TTTCAGATGCCACCACAACC-A
2439790 TTT-AGATGCCACCAC
1 TTTCAGATGCCACCAC
2439805 CGTAGGGTTT
Statistics
Matches: 44, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
21 42 0.95
22 2 0.05
ACGTcount: A:0.30, C:0.34, G:0.15, T:0.20
Consensus pattern (21 bp):
TTTCAGATGCCACCACAACCA
Found at i:2440244 original size:14 final size:15
Alignment explanation
Indices: 2440226--2440266 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
2440216 ATTAATTTAG
2440226 TTGTTTGAATTGTAA
1 TTGTTTGAATTGTAA
*
2440241 -TGTTTGTATT-TAA
1 TTGTTTGAATTGTAA
*
2440254 TTGTTTTAATTGT
1 TTGTTTGAATTGT
2440267 TTTTACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
13 3 0.14
14 17 0.81
15 1 0.05
ACGTcount: A:0.22, C:0.00, G:0.17, T:0.61
Consensus pattern (15 bp):
TTGTTTGAATTGTAA
Found at i:2441606 original size:14 final size:14
Alignment explanation
Indices: 2441573--2441606 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
2441563 ACATTATCCG
*
2441573 GCCCGCATCCGCCT
1 GCCCACATCCGCCT
2441587 GCCCCACATCCGCCT
1 G-CCCACATCCGCCT
2441602 GCCCA
1 GCCCA
2441607 GCTAAATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.12, C:0.59, G:0.18, T:0.12
Consensus pattern (14 bp):
GCCCACATCCGCCT
Found at i:2442545 original size:21 final size:21
Alignment explanation
Indices: 2442497--2442545 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
2442487 CCGAAATAAT
* * * *
2442497 AAAAAAATATTATTTTTATTT
1 AAAAAAATAGTAATTTAATTG
2442518 AATAAAAATAGTAATTTAATTG
1 AA-AAAAATAGTAATTTAATTG
2442540 AAAAAA
1 AAAAAA
2442546 CAATATGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (21 bp):
AAAAAAATAGTAATTTAATTG
Found at i:2446438 original size:27 final size:27
Alignment explanation
Indices: 2446403--2446461 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
2446393 TTGGTTTAAG
*
2446403 TTGTGTTTT-GGTATCAATTTGTGTTAT
1 TTGTTTTTTAGGTA-CAATTTGTGTTAT
* *
2446430 TTGTTTTTTATGTAGAATTTGTGTTAT
1 TTGTTTTTTAGGTACAATTTGTGTTAT
2446457 TTGTT
1 TTGTT
2446462 AAATGAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 25 0.89
28 3 0.11
ACGTcount: A:0.15, C:0.02, G:0.20, T:0.63
Consensus pattern (27 bp):
TTGTTTTTTAGGTACAATTTGTGTTAT
Found at i:2446494 original size:45 final size:44
Alignment explanation
Indices: 2446445--2446537 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 44
2446435 TTTTATGTAG
** *
2446445 AATTTGTGTTATTTGTTAAATGAAATTAAGTTGTGTTTTGGTATT
1 AATTTGTGCCATTTGTTAAATGAAATTAAGTAGTG-TTTGGTATT
*
2446490 AATTTGTGCCATTTGTTGAATGAAATTAAGTAGTGTTTGGTATT
1 AATTTGTGCCATTTGTTAAATGAAATTAAGTAGTGTTTGGTATT
2446534 AATT
1 AATT
2446538 AAGTGCCGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 13 0.30
45 31 0.70
ACGTcount: A:0.28, C:0.02, G:0.20, T:0.49
Consensus pattern (44 bp):
AATTTGTGCCATTTGTTAAATGAAATTAAGTAGTGTTTGGTATT
Found at i:2466384 original size:45 final size:45
Alignment explanation
Indices: 2466334--2466562 Score: 392
Period size: 45 Copynumber: 5.2 Consensus size: 45
2466324 ATGTAGGATT
2466334 TGGCCTGGGAGTTTGATTCAGCAATCCTTGTTGTTGCACAGCCTG
1 TGGCCTGGGAGTTTGATTCAGCAATCCTTGTTGTTGCACAGCCTG
*
2466379 TGGCCTGGGAGTTTGATTCAGCAATCCTTGTTGTTGCACAGTCTG
1 TGGCCTGGGAGTTTGATTCAGCAATCCTTGTTGTTGCACAGCCTG
* *
2466424 TGGCCTGGGAGTGTGATTCAGCAATCC---TTGTTGCACAGTCTG
1 TGGCCTGGGAGTTTGATTCAGCAATCCTTGTTGTTGCACAGCCTG
*
2466466 TGGCCTGGGAGTGTGATTCAGCAATCCTTGTTGTTGCACAGCCTG
1 TGGCCTGGGAGTTTGATTCAGCAATCCTTGTTGTTGCACAGCCTG
*
2466511 TGGCCTGGGAGTTTGATTCAGCAGTCCTTGTTGTTGCACAGCCTG
1 TGGCCTGGGAGTTTGATTCAGCAATCCTTGTTGTTGCACAGCCTG
2466556 TGGCCTG
1 TGGCCTG
2466563 TACGTACAAG
Statistics
Matches: 176, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
42 42 0.24
45 134 0.76
ACGTcount: A:0.15, C:0.22, G:0.31, T:0.33
Consensus pattern (45 bp):
TGGCCTGGGAGTTTGATTCAGCAATCCTTGTTGTTGCACAGCCTG
Found at i:2466484 original size:87 final size:88
Alignment explanation
Indices: 2466334--2466562 Score: 370
Period size: 87 Copynumber: 2.6 Consensus size: 88
2466324 ATGTAGGATT
*
2466334 TGGCCTGGGAGTTTGATTCAGCAATCCTTGTTGTTGCACAGCCTGTGGCCTGGGAGTTTGATTCA
1 TGGCCTGGGAGTTTGATTCAGCAATCC-T-TTGTTGCACAGCCTGTGGCCTGGGAGTGTGATTCA
*
2466399 GCAATCCTTGTTGTTGCACAGTCTG
64 GCAATCCTTGTTGTTGCACAGCCTG
* *
2466424 TGGCCTGGGAGTGTGATTCAGCAATCC-TTGTTGCACAGTCTGTGGCCTGGGAGTGTGATTCAGC
1 TGGCCTGGGAGTTTGATTCAGCAATCCTTTGTTGCACAGCCTGTGGCCTGGGAGTGTGATTCAGC
2466488 AATCCTTGTTGTTGCACAGCCTG
66 AATCCTTGTTGTTGCACAGCCTG
*
2466511 TGGCCTGGGAGTTTGATTCAGCAGTCCTTGTTGTTGCACAGCCTGTGGCCTG
1 TGGCCTGGGAGTTTGATTCAGCAATCC-T-TTGTTGCACAGCCTGTGGCCTG
2466563 TACGTACAAG
Statistics
Matches: 129, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
87 82 0.64
90 47 0.36
ACGTcount: A:0.15, C:0.22, G:0.31, T:0.33
Consensus pattern (88 bp):
TGGCCTGGGAGTTTGATTCAGCAATCCTTTGTTGCACAGCCTGTGGCCTGGGAGTGTGATTCAGC
AATCCTTGTTGTTGCACAGCCTG
Found at i:2471653 original size:59 final size:59
Alignment explanation
Indices: 2471557--2471671 Score: 194
Period size: 59 Copynumber: 1.9 Consensus size: 59
2471547 AGACAATCTG
* *
2471557 AACAATTAAAAAATTAGTATGAGCCACTCGATGGTAACTTATATACACTTCTATAATTT
1 AACAATTAAAAAATTAGTATGAGCCACTCGATCGTAACTTATATACACTCCTATAATTT
* *
2471616 AACAATTAAAAAATTAGTATGAGCCATTCGATCGTAACTTATGTACACTCCTATAA
1 AACAATTAAAAAATTAGTATGAGCCACTCGATCGTAACTTATATACACTCCTATAA
2471672 CATTGCTATA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (59 bp):
AACAATTAAAAAATTAGTATGAGCCACTCGATCGTAACTTATATACACTCCTATAATTT
Found at i:2479282 original size:23 final size:23
Alignment explanation
Indices: 2479256--2479301 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2479246 TATTTTTTAA
2479256 GTTTAAAA-TAATAATCCAATTTT
1 GTTTAAAAGT-ATAATCCAATTTT
*
2479279 GTTTAAAAGTATAATTCAATTTT
1 GTTTAAAAGTATAATCCAATTTT
2479302 CTGTACGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.46
Consensus pattern (23 bp):
GTTTAAAAGTATAATCCAATTTT
Found at i:2479838 original size:2 final size:2
Alignment explanation
Indices: 2479831--2479868 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2479821 CGACCATCTT
2479831 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2479869 TTAAATTATC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2480466 original size:107 final size:107
Alignment explanation
Indices: 2480283--2480486 Score: 376
Period size: 107 Copynumber: 1.9 Consensus size: 107
2480273 CAAAAATGGT
2480283 TTGCATATGCCCAACTTAGATTTACCGGGAAATAAAAAGCTTTTACAATGAATCCCAATCCTTAA
1 TTGCATATGCCCAACTTAGATTTACCGGGAAATAAAAAGCTTTTACAATGAATCCCAATCCTTAA
2480348 AATTAAAAGAAAAAAGAAAAAAAT-GGTACGATGTTCGTGTGG
66 AATTAAAAGAAAAAA-AAAAAAATGGGTACGATGTTCGTGTGG
2480390 TTGCATATGCCCAACTTAGATTTACCGGGAAATAAAAAGCTTTTTACAATGAAT-CCAATCCTTA
1 TTGCATATGCCCAACTTAGATTTACCGGGAAATAAAAAGC-TTTTACAATGAATCCCAATCCTTA
2480454 AAATTAAAAGAAAAAAAAAAAAATGGGTACGAT
65 AAATTAAAAGAAAAAAAAAAAAATGGGTACGAT
2480487 TCGTGAGTTG
Statistics
Matches: 95, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
106 8 0.08
107 74 0.78
108 13 0.14
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (107 bp):
TTGCATATGCCCAACTTAGATTTACCGGGAAATAAAAAGCTTTTACAATGAATCCCAATCCTTAA
AATTAAAAGAAAAAAAAAAAAATGGGTACGATGTTCGTGTGG
Found at i:2480564 original size:119 final size:124
Alignment explanation
Indices: 2480425--2480672 Score: 418
Period size: 124 Copynumber: 2.0 Consensus size: 124
2480415 CGGGAAATAA
*
2480425 AAAGCTTTTTACAATGAAT-CCAATCCTTAAAATT-AA-AAGAA-AAAAAAAAAAATGGGTACGA
1 AAAGCTTTTTACAATGAATCCCAATCCTTAAAATTAAAGAAAAAGAAAAAAAAAAAT-GGTACGA
2480486 -TTCGTGAGTTGGACAATAATTAATTGGATTACAGGAGAAATGATTATGGACTTATGGCT
65 GTTCGTGAGTTGGACAATAATTAATTGGATTACAGGAGAAATGATTATGGACTTATGGCT
2480545 AAAGC-TTTTACAATGAATCCCAATCCTTAAAATTAAAGAAAAAGAAAAAAAAAAATGGTACGAT
1 AAAGCTTTTTACAATGAATCCCAATCCTTAAAATTAAAGAAAAAGAAAAAAAAAAATGGTACGA-
*
2480609 GTTCGTGAGTTGGACAATAATTAATTGGATTTCAGGAGAAATGATTATGGACTTATGGCT
65 GTTCGTGAGTTGGACAATAATTAATTGGATTACAGGAGAAATGATTATGGACTTATGGCT
2480669 AAAG
1 AAAG
2480673 TAAAACCTTG
Statistics
Matches: 120, Mismatches: 2, Indels: 8
0.92 0.02 0.06
Matches are distributed among these distances:
119 13 0.11
120 20 0.17
121 2 0.02
122 11 0.09
123 12 0.10
124 62 0.52
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.28
Consensus pattern (124 bp):
AAAGCTTTTTACAATGAATCCCAATCCTTAAAATTAAAGAAAAAGAAAAAAAAAAATGGTACGAG
TTCGTGAGTTGGACAATAATTAATTGGATTACAGGAGAAATGATTATGGACTTATGGCT
Found at i:2485544 original size:28 final size:31
Alignment explanation
Indices: 2485486--2485553 Score: 106
Period size: 32 Copynumber: 2.3 Consensus size: 31
2485476 ACGTTCAATA
2485486 ATTCGTTCGTTTATGTTCATTTTATCATTTAT
1 ATTCGTTCGTTTATGTTCATTTTAT-ATTTAT
2485518 ATTCGTTCGTTTATGTT-ATTTT-T-TTTAT
1 ATTCGTTCGTTTATGTTCATTTTATATTTAT
2485546 ATTCGTTC
1 ATTCGTTC
2485554 ATATTCTCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
28 13 0.36
30 1 0.03
31 5 0.14
32 17 0.47
ACGTcount: A:0.16, C:0.12, G:0.10, T:0.62
Consensus pattern (31 bp):
ATTCGTTCGTTTATGTTCATTTTATATTTAT
Found at i:2490346 original size:2 final size:2
Alignment explanation
Indices: 2490339--2490369 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2490329 TTTGCTAATT
2490339 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2490370 CATGGAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2491571 original size:24 final size:21
Alignment explanation
Indices: 2491524--2491574 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
2491514 TTATCAACTC
*
2491524 AATTTAAAAATCTTTTATTTT
1 AATTTAAAAATATTTTATTTT
2491545 AATTTAAAAATATATATATATTTT
1 AATTTAAAAATAT-T-T-TATTTT
2491569 AATTTA
1 AATTTA
2491575 TTAAAATAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
22 1 0.04
23 1 0.04
24 12 0.46
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
AATTTAAAAATATTTTATTTT
Found at i:2498915 original size:28 final size:28
Alignment explanation
Indices: 2498872--2498936 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
2498862 TCAGTTCTAT
* * *
2498872 TATATGGTTGGCTCTACCGCGTGATTGA
1 TATATGGTCGGCTCTACCGCATGAATGA
*
2498900 TATATGGTCGGTTCTACCGCATGAATGA
1 TATATGGTCGGCTCTACCGCATGAATGA
2498928 TATATGGTC
1 TATATGGTC
2498937 AGCCTTGCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (28 bp):
TATATGGTCGGCTCTACCGCATGAATGA
Found at i:2501564 original size:24 final size:24
Alignment explanation
Indices: 2501537--2501582 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2501527 TTATCGTTAA
2501537 CAGTTAACA-AATTTGGTGATGTGG
1 CAGTTAA-ATAATTTGGTGATGTGG
*
2501561 CAGTTAAATATTTTGGTGATGT
1 CAGTTAAATAATTTGGTGATGT
2501583 ATCACCCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.28, C:0.07, G:0.26, T:0.39
Consensus pattern (24 bp):
CAGTTAAATAATTTGGTGATGTGG
Found at i:2502951 original size:7 final size:7
Alignment explanation
Indices: 2502939--2502963 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2502929 GAAGTTTTCC
2502939 TTTCCTT
1 TTTCCTT
2502946 TTTCCTT
1 TTTCCTT
2502953 TTTCCTT
1 TTTCCTT
2502960 TTTC
1 TTTC
2502964 ATGTAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTCCTT
Found at i:2505132 original size:24 final size:27
Alignment explanation
Indices: 2505105--2505157 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 27
2505095 TTAATTTAGG
*
2505105 AATTTTATT-TTAA-TATTTTTA-TTA
1 AATTTGATTCTTAACTATTTTTAGTTA
*
2505129 AATTTGATTCTTAACTTTTTTTAGTTA
1 AATTTGATTCTTAACTATTTTTAGTTA
2505156 AA
1 AA
2505158 CTAATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.33
25 4 0.17
26 7 0.29
27 5 0.21
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (27 bp):
AATTTGATTCTTAACTATTTTTAGTTA
Found at i:2506243 original size:23 final size:23
Alignment explanation
Indices: 2506217--2506261 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
2506207 ACGCAAAGAA
2506217 AAACATGCCACAAAGACAGAGAT
1 AAACATGCCACAAAGACAGAGAT
* * * *
2506240 AAACGTGTCATAAAGGCAGAGA
1 AAACATGCCACAAAGACAGAGA
2506262 ACATGTCACA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.49, C:0.18, G:0.22, T:0.11
Consensus pattern (23 bp):
AAACATGCCACAAAGACAGAGAT
Found at i:2508270 original size:18 final size:18
Alignment explanation
Indices: 2508247--2508284 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2508237 CGAGGGATTT
2508247 ATAGTGGTCCTTCGAGAC
1 ATAGTGGTCCTTCGAGAC
2508265 ATAGTGGTCCTTCGAGAC
1 ATAGTGGTCCTTCGAGAC
2508283 AT
1 AT
2508285 TTCATAGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (18 bp):
ATAGTGGTCCTTCGAGAC
Found at i:2508294 original size:23 final size:23
Alignment explanation
Indices: 2508243--2508316 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
2508233 GAGTCGAGGG
2508243 ATTT-ATAGTGGTCCTTCGAG--
1 ATTTCATAGTGGTCCTTCGAGAC
2508263 A---CATAGTGGTCCTTCGAGAC
1 ATTTCATAGTGGTCCTTCGAGAC
2508283 ATTTCATAGTGGTCCTTCGAGAC
1 ATTTCATAGTGGTCCTTCGAGAC
2508306 AAATTTCATAG
1 --ATTTCATAG
2508317 CCCATAGTGG
Statistics
Matches: 46, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
18 16 0.35
20 2 0.04
23 19 0.41
25 9 0.20
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.34
Consensus pattern (23 bp):
ATTTCATAGTGGTCCTTCGAGAC
Found at i:2514446 original size:21 final size:21
Alignment explanation
Indices: 2514420--2514682 Score: 215
Period size: 21 Copynumber: 12.6 Consensus size: 21
2514410 CTTGGAATAA
2514420 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
2514441 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTCGACT
2514460 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* *
2514483 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTCGACT
2514502 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* *
2514525 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTCGACT
* *
2514544 AAATCGCAACACGAATTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* *
2514567 ATCGCAA--CGAA-TTTGAAAT
1 ATCGCAACGCGAACTTCG-ACT
2514586 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* * **
2514609 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
*
2514628 ACCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
2514649 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
2514670 ATCGCAATGCGAA
1 ATCGCAACGCGAA
2514683 TATGTAAATC
Statistics
Matches: 193, Mismatches: 29, Indels: 40
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.02
19 50 0.26
21 102 0.53
23 35 0.18
24 3 0.02
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:2514453 original size:42 final size:42
Alignment explanation
Indices: 2514388--2514667 Score: 447
Period size: 42 Copynumber: 6.7 Consensus size: 42
2514378 TACGATTTTG
* * *
2514388 GAACTTGGACTATCACAATGAACTTGGAATAAATCGCAACGC
1 GAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGC
2514430 GAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGC
1 GAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGC
2514472 GAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGC
1 GAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGC
*
2514514 GAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACAC
1 GAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGC
* * *
2514556 GAATTTCGACTATCGCAACGAATTTGAAATAAATCGCAACGC
1 GAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGC
* *
2514598 GAACTTCGACTATCGCAACGAATTTGG-A-AAACCGCAACGC
1 GAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGC
2514638 GAACTTCGACTATCGCAACGCGAACTTGGA
1 GAACTTCGACTATCGCAA--CGAACTTGGA
2514668 CTATCGCAAT
Statistics
Matches: 223, Mismatches: 12, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
40 29 0.13
41 1 0.00
42 193 0.87
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (42 bp):
GAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGC
Found at i:2527132 original size:2 final size:2
Alignment explanation
Indices: 2527127--2527187 Score: 92
Period size: 2 Copynumber: 32.0 Consensus size: 2
2527117 TAAAAAAAAT
2527127 TA TA TA T- TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2527167 GA TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
2527188 ACCCTAATTT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
1 3 0.06
2 51 0.94
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2527147 original size:15 final size:14
Alignment explanation
Indices: 2527127--2527187 Score: 92
Period size: 13 Copynumber: 4.6 Consensus size: 14
2527117 TAAAAAAAAT
2527127 TATATAT-TATATA
1 TATATATATATATA
2527140 TATATATAT-TATA
1 TATATATATATATA
2527153 TATATATATATATA
1 TATATATATATATA
*
2527167 GATATAT-TATATA
1 TATATATATATATA
2527180 TATATATA
1 TATATATA
2527188 ACCCTAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
13 32 0.74
14 11 0.26
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
TATATATATATATA
Found at i:2532843 original size:202 final size:199
Alignment explanation
Indices: 2532501--2532902 Score: 743
Period size: 202 Copynumber: 2.0 Consensus size: 199
2532491 CTATTGTACC
2532501 ACTTGTATAGGACTGCTAGAGGTAATCTACAGAGGCTCCCACCAAAGAGATTAGGATTGTGAAGT
1 ACTTGTATAGGACTGCTAGAGGTAATCTACAGAGGCTCCCACCAAAGAGATTAGGATTGTGAAGT
2532566 ATCTTCTTACGATTGAGGATCCAGAGCGACTGTGTGCCTTAAATGATGCGTTTACACACGGAAAA
66 ATCTTCTTACGATTGAGGATCCAGAGCGACTGTGTGCCTTAAATGATGCGTTTACACACGGAAAA
2532631 GAACTTGAAGGGGTGGATTTGGACAACCTTCACACGTATGTCTGTTGCTCTGACTTAA-TTTTGT
131 GAACTTGAAGGGGTGGATTTGGACAACCTTCACACGTATGTCTGTTGCTCTGACTTAATTTTTGT
2532695 CAAA
196 CAAA
* *
2532699 ACTTGTATATGACTGCTAGAGGTAATCTACAGAGGCTCCCACCAAAAGAGATTAGGATTGTGTAG
1 ACTTGTATAGGACTGCTAGAGGTAATCTACAGAGGCTCCCACC-AAAGAGATTAGGATTGTGAAG
2532764 TATCTTCTTACGATTGAGGATCCCGAGGAGCGACTGTGTGCCTTAAATGATGCGTTTACACACGG
65 TATCTTCTTACGATTGAGGAT-CC-A-GAGCGACTGTGTGCCTTAAATGATGCGTTTACACACGG
2532829 AAAAGAACTTGAAGGGGTGGATTTGGACAACCTTCACACGTATGTCTGTTGCTCTGACTTAATTT
127 AAAAGAACTTGAAGGGGTGGATTTGGACAACCTTCACACGTATGTCTGTTGCTCTGACTTAATTT
2532894 TTGTCAAA
192 TTGTCAAA
2532902 A
1 A
2532903 TTTAGTACCA
Statistics
Matches: 197, Mismatches: 2, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
198 42 0.21
199 41 0.21
200 2 0.01
201 1 0.01
202 100 0.51
203 11 0.06
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (199 bp):
ACTTGTATAGGACTGCTAGAGGTAATCTACAGAGGCTCCCACCAAAGAGATTAGGATTGTGAAGT
ATCTTCTTACGATTGAGGATCCAGAGCGACTGTGTGCCTTAAATGATGCGTTTACACACGGAAAA
GAACTTGAAGGGGTGGATTTGGACAACCTTCACACGTATGTCTGTTGCTCTGACTTAATTTTTGT
CAAA
Found at i:2535415 original size:29 final size:29
Alignment explanation
Indices: 2535383--2535511 Score: 133
Period size: 29 Copynumber: 4.4 Consensus size: 29
2535373 TTTTTTTAAA
*
2535383 TAATTACCAAAATAGCACCATTTTCGAAT
1 TAATTCCCAAAATAGCACCATTTTCGAAT
* *
2535412 TAATTCACAAAAT---ATCATTTCTCGAAT
1 TAATTCCCAAAATAGCACCATTT-TCGAAT
2535439 TAAATTCCCAAAATAGCA-CATTTTCGAAT
1 T-AATTCCCAAAATAGCACCATTTTCGAAT
* *
2535468 TAAATTTCCAAAAATAGCACCCA-TTTCGTAT
1 T-AA-TTCCCAAAATAGCA-CCATTTTCGAAT
2535499 TAATTCCCAAAAT
1 TAATTCCCAAAAT
2535512 GTCACGCGTG
Statistics
Matches: 85, Mismatches: 7, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
26 6 0.07
27 7 0.08
28 11 0.13
29 30 0.35
30 20 0.24
31 9 0.11
32 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (29 bp):
TAATTCCCAAAATAGCACCATTTTCGAAT
Found at i:2535509 original size:30 final size:30
Alignment explanation
Indices: 2535391--2535510 Score: 119
Period size: 30 Copynumber: 4.1 Consensus size: 30
2535381 AATAATTACC
*
2535391 AAAATAGCACCATTTTCGAATT-AATTCAC-
1 AAAATAGCA-CATTTTCGAATTAAATTCCCA
*
2535420 AAAATA--TCATTTCTCGAATTAAATTCCC-
1 AAAATAGCACATTT-TCGAATTAAATTCCCA
*
2535448 AAAATAGCACATTTTCGAATTAAATTTCCA
1 AAAATAGCACATTTTCGAATTAAATTCCCA
*
2535478 AAAATAGCACCCA-TTTCGTATT-AATTCCCA
1 AAAATAGCA--CATTTTCGAATTAAATTCCCA
2535508 AAA
1 AAA
2535511 TGTCACGCGT
Statistics
Matches: 78, Mismatches: 6, Indels: 13
0.80 0.06 0.13
Matches are distributed among these distances:
26 5 0.06
27 7 0.09
28 12 0.15
29 20 0.26
30 24 0.31
31 8 0.10
32 2 0.03
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.32
Consensus pattern (30 bp):
AAAATAGCACATTTTCGAATTAAATTCCCA
Found at i:2540398 original size:40 final size:40
Alignment explanation
Indices: 2540343--2540425 Score: 139
Period size: 40 Copynumber: 2.1 Consensus size: 40
2540333 TATTACCCTG
*
2540343 CTCCAGATCCTGAAACTCCTGACGTCGCTCCTGCAAGTAT
1 CTCCAGATCCTGAAACTCCTGACGTCACTCCTGCAAGTAT
* *
2540383 CTCCAGATCCTGAAACTCTTGACGTCACTCTTGCAAGTAT
1 CTCCAGATCCTGAAACTCCTGACGTCACTCCTGCAAGTAT
2540423 CTC
1 CTC
2540426 TCTCCGATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.28
Consensus pattern (40 bp):
CTCCAGATCCTGAAACTCCTGACGTCACTCCTGCAAGTAT
Found at i:2542612 original size:29 final size:29
Alignment explanation
Indices: 2542573--2542731 Score: 113
Period size: 29 Copynumber: 5.4 Consensus size: 29
2542563 CATTTTACAG
*
2542573 AAATATCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTTAAAATAATTACCA
* ** *
2542602 AAATAGTACCCTTTTCGAAATAATTCCCA
1 AAATAGCACCCTTTTTAAAATAATTACCA
* * *
2542631 AAATAGCACCTTTTTTTCAAATTAAATTCCCA
1 AAATAGCACC-CTTTTT-AAAAT-AATTACCA
* * * *
2542663 AAATAGCA-CATTTTCAAATTAAATTCCCA
1 AAATAGCACCCTTTTTAAAAT-AATTACCA
* ** * *
2542692 AAATAGCACCCATTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTTAAAATAATTACCA
*
2542721 AAATATCACCC
1 AAATAGCACCC
2542732 GGTCAACGGT
Statistics
Matches: 110, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
29 73 0.66
30 17 0.15
31 4 0.04
32 16 0.15
ACGTcount: A:0.41, C:0.24, G:0.04, T:0.31
Consensus pattern (29 bp):
AAATAGCACCCTTTTTAAAATAATTACCA
Found at i:2547544 original size:29 final size:29
Alignment explanation
Indices: 2547493--2547616 Score: 112
Period size: 29 Copynumber: 4.4 Consensus size: 29
2547483 CATTTTACAG
** * *
2547493 AAATAGCA-CCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTCGAATTAATTCCCA
* *
2547521 AAATAGCACCCTTTTCGAGTTAATTCCTA
1 AAATAGCACCCTTTTCGAATTAATTCCCA
* *
2547550 CAATAGCA-CTTTTTCGAATTAAATTCCCA
1 AAATAGCACCCTTTTCGAATT-AATTCCCA
* *
2547579 AAATA--ACACATTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTCGAATTAATTCCCA
*
2547606 AAATATCACCC
1 AAATAGCACCC
2547617 GGTCAACAGT
Statistics
Matches: 76, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
27 14 0.18
28 27 0.36
29 35 0.46
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (29 bp):
AAATAGCACCCTTTTCGAATTAATTCCCA
Found at i:2547608 original size:27 final size:28
Alignment explanation
Indices: 2547533--2547610 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
2547523 ATAGCACCCT
* * * * *
2547533 TTTCGAGTTAATTCCTACAATAGCACTT
1 TTTCGAATTAATTCCCAAAATAACACTA
2547561 TTTCGAATTAAATTCCCAAAATAACAC-A
1 TTTCGAATT-AATTCCCAAAATAACACTA
2547589 TTTCGAATTAATTCCCAAAATA
1 TTTCGAATTAATTCCCAAAATA
2547611 TCACCCGGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
27 13 0.30
28 17 0.39
29 14 0.32
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (28 bp):
TTTCGAATTAATTCCCAAAATAACACTA
Found at i:2553395 original size:138 final size:137
Alignment explanation
Indices: 2553209--2553473 Score: 377
Period size: 138 Copynumber: 1.9 Consensus size: 137
2553199 TTTTGTCGTT
** * * * * * *
2553209 AATCTTTAATTTATGCCTCATTTTATTTTTGTCATCAGTATTTTAATTTAGTGTAAAATATTATT
1 AATCTTTAATTTACACCTCATTTTATTTTTGCCATCAATATTTCAATTTAGTGTAAAACATCACT
* * *
2553274 TAACTATTTAATTTGTTCAATTAGATCATTTATCGTTAATATTTGACAAAAATATTAACATGGAA
66 TAACTATTTAATTTATTCAATCAGATCATTTATCGTTAATATTCGACAAAAATATTAACATGGAA
2553339 GTTTATC
131 GTTTATC
* *
2553346 AATCTTTCAATTTACACCTCATTTTATTTTTGCCATCAATCTTTCAATTTAGTGTGAAACATCAC
1 AATCTTT-AATTTACACCTCATTTTATTTTTGCCATCAATATTTCAATTTAGTGTAAAACATCAC
* * *
2553411 TTAACTATTTAATTTATTCAATCAGATCATTTATCGTTAATATTCGATAGAAATATTGACATG
65 TTAACTATTTAATTTATTCAATCAGATCATTTATCGTTAATATTCGACAAAAATATTAACATG
2553474 ACAGTTAAAA
Statistics
Matches: 111, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
137 7 0.06
138 104 0.94
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (137 bp):
AATCTTTAATTTACACCTCATTTTATTTTTGCCATCAATATTTCAATTTAGTGTAAAACATCACT
TAACTATTTAATTTATTCAATCAGATCATTTATCGTTAATATTCGACAAAAATATTAACATGGAA
GTTTATC
Found at i:2556957 original size:13 final size:13
Alignment explanation
Indices: 2556939--2556967 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2556929 ACCAGAAGGA
2556939 TCATCGAGAGCCC
1 TCATCGAGAGCCC
2556952 TCATCGAGAGCCC
1 TCATCGAGAGCCC
2556965 TCA
1 TCA
2556968 AAAGTCGTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.38, G:0.21, T:0.17
Consensus pattern (13 bp):
TCATCGAGAGCCC
Found at i:2557889 original size:36 final size:30
Alignment explanation
Indices: 2557809--2557874 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
2557799 ATAAGAGTTG
2557809 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
2557839 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
2557869 ATTTGT
1 ATTTGT
2557875 GCTTGTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTCTT
Found at i:2558049 original size:20 final size:20
Alignment explanation
Indices: 2558024--2558302 Score: 207
Period size: 20 Copynumber: 14.8 Consensus size: 20
2558014 GCGATTTTCT
*
2558024 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
2558044 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
2558064 CGTTGCGAT--T---A-TCT
1 CGTTGCGATAGTCAAATTCG
*
2558078 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
* *
2558098 CGTTGCGATAGTTAAATTTG
1 CGTTGCGATAGTCAAATTCG
**
2558118 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
**
2558138 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
2558158 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* *
2558172 CATTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
* **
2558192 CGTTGTGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
2558212 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* *
2558226 CGTTGCGATATTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
* *
2558246 CATTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* *
2558266 CGTTGCGATAGTCATATTCA
1 CGTTGCGATAGTCAAATTCG
2558286 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
2558303 GAATGTGTAA
Statistics
Matches: 207, Mismatches: 34, Indels: 36
0.75 0.12 0.13
Matches are distributed among these distances:
14 32 0.15
15 1 0.00
16 3 0.01
18 3 0.01
19 3 0.01
20 165 0.80
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2558070 original size:54 final size:54
Alignment explanation
Indices: 2557985--2558126 Score: 194
Period size: 54 Copynumber: 2.6 Consensus size: 54
2557975 TCTGCATCAT
* * * * * *
2557985 ATTCGCGTTGCGATAGTCTAATACACTTTGCGATTTTCTCGTTGCGATAGTCAA
1 ATTCACGTTGCGATAGTCAAATTCGCGTTGCGATTATCTCGTTGCGATAGTCAA
* *
2558039 ATTCCCGTTGCGATAATCAAATTCGCGTTGCGATTATCTCGTTGCGATAGTCAA
1 ATTCACGTTGCGATAGTCAAATTCGCGTTGCGATTATCTCGTTGCGATAGTCAA
* *
2558093 ATTCACGTTGCGATAGTTAAATTTGCGTTGCGAT
1 ATTCACGTTGCGATAGTCAAATTCGCGTTGCGAT
2558127 AGTCATTTTC
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 77 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (54 bp):
ATTCACGTTGCGATAGTCAAATTCGCGTTGCGATTATCTCGTTGCGATAGTCAA
Found at i:2558106 original size:74 final size:74
Alignment explanation
Indices: 2558026--2558294 Score: 294
Period size: 74 Copynumber: 3.6 Consensus size: 74
2558016 GATTTTCTCG
* * *
2558026 TTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCGCGTTGCGATTATCTCGTTGCGATAGTC
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCGTTGCGATTATCTCGTTGCGATAGTC
*
2558091 AAATTCACG
66 AAATTCACA
* * * * *
2558100 TTGCGATAGTTAAATTTGCGTTGCGATAGTCATTTTCGCGTTGCGA-TAGTCAT--TTTCGCATT
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCGTTGCGATTA-TC-TCGTTGCG-ATA
* * *
2558162 G-CGATTATCCCA
63 GTCAAAT-TCACA
* * * * * *
2558174 TTGCGATAGTCAAATTTGCGTTGTGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATATTC
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCGTTGCGATTATCTCGTTGCGATAGTC
2558239 AAATTCACA
66 AAATTCACA
* *
2558248 TTGCGATAGTCATATTCGCGTTGCGATAGTCATATTCACGTTGCGAT
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCGTTGCGAT
2558295 AGTCAAATGA
Statistics
Matches: 159, Mismatches: 28, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
73 9 0.06
74 140 0.88
75 10 0.06
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (74 bp):
TTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCGTTGCGATTATCTCGTTGCGATAGTC
AAATTCACA
Found at i:2558179 original size:54 final size:54
Alignment explanation
Indices: 2558120--2558274 Score: 213
Period size: 54 Copynumber: 2.9 Consensus size: 54
2558110 TAAATTTGCG
*
2558120 TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCA
1 TTGCGATAGTCAATTTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCA
* *
2558174 TTGCGATAGTCAAATTT-GCGTTGTGATAGTCATTTTCGCATTGCGATTATCCCG
1 TTGCGATAGTC-AATTTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCA
* * * * * *
2558228 TTGCGATATTCAAATTCACATTGCGATAGTCATATTCGCGTTGCGAT
1 TTGCGATAGTCAATTTCGCGTTGCGATAGTCATTTTCGCATTGCGAT
2558275 AGTCATATTC
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
53 4 0.04
54 81 0.91
55 4 0.04
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (54 bp):
TTGCGATAGTCAATTTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCA
Found at i:2558500 original size:18 final size:18
Alignment explanation
Indices: 2558477--2558511 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2558467 AAGCCGGTTG
*
2558477 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
2558495 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
2558512 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:2560793 original size:24 final size:24
Alignment explanation
Indices: 2560759--2560812 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2560749 CTGAAACATC
2560759 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2560783 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2560807 ATCAAA
1 ATCAAA
2560813 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2561661 original size:20 final size:20
Alignment explanation
Indices: 2561633--2561780 Score: 156
Period size: 20 Copynumber: 7.3 Consensus size: 20
2561623 AATTCAGTGA
*
2561633 TGCGTTAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
2561653 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
**
2561673 TGCGATCACGT-ATTATCGCGT
1 TGCGAT-A-GTCAGAATCGCGT
**
2561694 TGCGATAGTCAGAATATCGT
1 TGCGATAGTCAGAATCGCGT
*
2561714 TGCGATAGTCAGAATCACGT
1 TGCGATAGTCAGAATCGCGT
**
2561734 TGCGATCACGT-ATTATCGCGT
1 TGCGAT-A-GTCAGAATCGCGT
* *
2561755 TGCGATAGTCAGAATCACAT
1 TGCGATAGTCAGAATCGCGT
2561775 TGCGAT
1 TGCGAT
2561781 CACGTGTTAT
Statistics
Matches: 106, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
19 4 0.04
20 69 0.65
21 29 0.27
22 4 0.04
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGT
Found at i:2561703 original size:61 final size:61
Alignment explanation
Indices: 2561633--2561780 Score: 244
Period size: 61 Copynumber: 2.4 Consensus size: 61
2561623 AATTCAGTGA
* * *
2561633 TGCGTTAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGT
1 TGCGATAGTCAGAATCACGTTGCGATAGTCAGAATCACGTTGCGATCACGTATTATCGCGT
2561694 TGCGATAGTCAGAAT-ATCGTTGCGATAGTCAGAATCACGTTGCGATCACGTATTATCGCGT
1 TGCGATAGTCAGAATCA-CGTTGCGATAGTCAGAATCACGTTGCGATCACGTATTATCGCGT
*
2561755 TGCGATAGTCAGAATCACATTGCGAT
1 TGCGATAGTCAGAATCACGTTGCGAT
2561781 CACGTGTTAT
Statistics
Matches: 81, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
61 80 0.99
62 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (61 bp):
TGCGATAGTCAGAATCACGTTGCGATAGTCAGAATCACGTTGCGATCACGTATTATCGCGT
Found at i:2561817 original size:41 final size:41
Alignment explanation
Indices: 2561711--2561801 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
2561701 GTCAGAATAT
*
2561711 CGTTGCGATAGTCAGAATCACGTTGCGATCACGTATTATCG
1 CGTTGCGATAGTCAGAATCACATTGCGATCACGTATTATCG
*
2561752 CGTTGCGATAGTCAGAATCACATTGCGATCACGTGTTATCG
1 CGTTGCGATAGTCAGAATCACATTGCGATCACGTATTATCG
2561793 CGTTGCGAT
1 CGTTGCGAT
2561802 TTACATATTC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (41 bp):
CGTTGCGATAGTCAGAATCACATTGCGATCACGTATTATCG
Found at i:2561822 original size:20 final size:20
Alignment explanation
Indices: 2561790--2561842 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2561780 TCACGTGTTA
*
2561790 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
2561810 TCGCATTGTGATTTACATAT
1 TCGCATTGCGATTTACATAT
2561830 TCGCATTGCGATT
1 TCGCATTGCGATT
2561843 ATCTAAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:2561940 original size:20 final size:19
Alignment explanation
Indices: 2561916--2561962 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2561906 TGGAAACTGA
*
2561916 ATTGCGATAATGGAGATCGC
1 ATTGCGAT-ATAGAGATCGC
* *
2561936 GTTGCGATTTAGAGATCGC
1 ATTGCGATATAGAGATCGC
2561955 ATTGCGAT
1 ATTGCGAT
2561963 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (19 bp):
ATTGCGATATAGAGATCGC
Found at i:2561952 original size:19 final size:19
Alignment explanation
Indices: 2561928--2561964 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2561918 TGCGATAATG
*
2561928 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
2561947 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
2561965 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:2570687 original size:23 final size:23
Alignment explanation
Indices: 2570651--2570704 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
2570641 TAACTTAATA
*
2570651 AATAAT-ATATAATTTAATCTTTT-
1 AATAATAAT-TAA-TTAATATTTTG
*
2570674 AATTATAATTAATTAATATTTTG
1 AATAATAATTAATTAATATTTTG
2570697 AATAATAA
1 AATAATAA
2570705 CTTTTTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 9 0.35
23 15 0.58
24 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
AATAATAATTAATTAATATTTTG
Found at i:2570740 original size:18 final size:19
Alignment explanation
Indices: 2570697--2570741 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
2570687 TAATATTTTG
2570697 AATA-ATAACTTTTTAAAA
1 AATATATAACTTTTTAAAA
* *
2570715 AATTTATAATTTTTTAAAA
1 AATATATAACTTTTTAAAA
2570734 AA-ATATAA
1 AATATATAA
2570742 AGATATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
AATATATAACTTTTTAAAA
Found at i:2570761 original size:22 final size:19
Alignment explanation
Indices: 2570732--2570790 Score: 55
Period size: 22 Copynumber: 2.9 Consensus size: 19
2570722 AATTTTTTAA
2570732 AAAAATATAAAGATATTTTT
1 AAAAATATAAA-ATATTTTT
** *
2570752 AAAATTATATTATTATAATTTT
1 AAAA--ATA-TAAAATATTTTT
2570774 AAAAATATAAAATATTT
1 AAAAATATAAAATATTT
2570791 AATTTATTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 7 0.23
20 7 0.23
22 14 0.47
23 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
AAAAATATAAAATATTTTT
Found at i:2570785 original size:30 final size:29
Alignment explanation
Indices: 2570751--2570815 Score: 89
Period size: 28 Copynumber: 2.2 Consensus size: 29
2570741 AAGATATTTT
2570751 TAAAATTATATT-ATTATAATTTTAAAAATA
1 TAAAATTAT-TTAATT-TAATTTTAAAAATA
*
2570781 TAAAA-TATTTAATTTATTTTTAAAAATA
1 TAAAATTATTTAATTTAATTTTAAAAATA
2570809 TAAAATT
1 TAAAATT
2570816 CATAATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
28 20 0.62
29 7 0.22
30 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TAAAATTATTTAATTTAATTTTAAAAATA
Found at i:2570821 original size:28 final size:27
Alignment explanation
Indices: 2570770--2570827 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
2570760 ATTATTATAA
*
2570770 TTTTAAAAATATAAAATATTTAATTTAT
1 TTTTAAAAATATAAAATATATAATTT-T
2570798 TTTTAAAAATATAAAAT-TCATAATTTT
1 TTTTAAAAATATAAAATAT-ATAATTTT
2570825 TTT
1 TTT
2570828 AAATTATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
TTTTAAAAATATAAAATATATAATTTT
Found at i:2573781 original size:22 final size:21
Alignment explanation
Indices: 2573756--2573796 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2573746 TATAAAAAAT
2573756 TATTTTTATTAAATATTTTTTG
1 TATTTTTATTAAAT-TTTTTTG
*
2573778 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
2573797 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTTG
Found at i:2574006 original size:35 final size:35
Alignment explanation
Indices: 2573967--2574036 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
2573957 CTCCAATATT
2573967 TCTCTCCCACTTTTTCCCTCCAGGAAAGCTGCGAA
1 TCTCTCCCACTTTTTCCCTCCAGGAAAGCTGCGAA
2574002 TCTCTCCCACTTTTTCCCTCCAGGAAAGCTGCGAA
1 TCTCTCCCACTTTTTCCCTCCAGGAAAGCTGCGAA
2574037 GAAAAGAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.20, C:0.37, G:0.14, T:0.29
Consensus pattern (35 bp):
TCTCTCCCACTTTTTCCCTCCAGGAAAGCTGCGAA
Found at i:2576300 original size:15 final size:15
Alignment explanation
Indices: 2576280--2576314 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2576270 CCGTAGGACC
2576280 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
*
2576295 ACTACGTCCCGAATG
1 ACTACGTCCCGAAGG
2576310 ACTAC
1 ACTAC
2576315 AATACCCTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:2585794 original size:25 final size:24
Alignment explanation
Indices: 2585762--2585824 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
2585752 AAAATAAAGC
* *
2585762 AAAGAGAAAATAAAAAAGAGCAACAAA
1 AAAGAAAAAAGAAAAAA-AG-AAC-AA
2585789 AAAGAAACAAAGAAAAAAAGAACAA
1 AAAGAAA-AAAGAAAAAAAGAACAA
2585814 AAAGAAAAAAG
1 AAAGAAAAAAG
2585825 GGATGAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
24 4 0.12
25 9 0.27
26 3 0.09
27 8 0.24
28 9 0.27
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.02
Consensus pattern (24 bp):
AAAGAAAAAAGAAAAAAAGAACAA
Found at i:2585802 original size:8 final size:8
Alignment explanation
Indices: 2585786--2585823 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
2585776 AAAGAGCAAC
2585786 AAAAAAGA
1 AAAAAAGA
*
2585794 AACAAAGA
1 AAAAAAGA
2585802 AAAAAAGA
1 AAAAAAGA
2585810 ACAAAAAGA
1 A-AAAAAGA
2585819 AAAAA
1 AAAAA
2585824 GGGATGAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 19 0.70
9 8 0.30
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:2585807 original size:16 final size:17
Alignment explanation
Indices: 2585786--2585823 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2585776 AAAGAGCAAC
*
2585786 AAAAAAGAA-ACAAAGA
1 AAAAAAGAACAAAAAGA
2585802 AAAAAAGAACAAAAAGA
1 AAAAAAGAACAAAAAGA
2585819 AAAAA
1 AAAAA
2585824 GGGATGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAAAGAACAAAAAGA
Found at i:2587651 original size:66 final size:63
Alignment explanation
Indices: 2587562--2587718 Score: 167
Period size: 66 Copynumber: 2.5 Consensus size: 63
2587552 CAAAACAAAA
* * * *
2587562 ATCTTTGAGATCATTTC-CTTTGAAACGAATTTGGTCTCTCTTGAGTCAACTTCTCTTGAAA-CA
1 ATCTTTGAGATCGTTTCTC-TTGAAACAAATTT--TCTCTCTTGAGACAACTTAT-TTGAAAGCA
2587625 CTC
62 -TC
* * ** *
2587628 ATCTATGAGATCGTTTCTCTTGAAACAAATTTTGTCTCTTGAGACATTTTATTTGAAAGGATC
1 ATCTTTGAGATCGTTTCTCTTGAAACAAATTTTCTCTCTTGAGACAACTTATTTGAAAGCATC
2587691 ATCTTTGAG-TCGTTTCTCTTGAAACAAA
1 ATCTTTGAGATCGTTTCTCTTGAAACAAA
2587719 AGGTTTGTGA
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
62 19 0.24
63 16 0.20
64 16 0.20
66 27 0.34
67 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (63 bp):
ATCTTTGAGATCGTTTCTCTTGAAACAAATTTTCTCTCTTGAGACAACTTATTTGAAAGCATC
Found at i:2589829 original size:13 final size:14
Alignment explanation
Indices: 2589792--2589838 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
2589782 ATGTATCAAT
*
2589792 TACACGATAACATA
1 TACATGATAACATA
*
2589806 TATGATGATAACATA
1 TA-CATGATAACATA
*
2589821 TACAT-ATAACACA
1 TACATGATAACATA
2589834 TACAT
1 TACAT
2589839 TCTCATGTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
13 12 0.43
14 4 0.14
15 12 0.43
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (14 bp):
TACATGATAACATA
Found at i:2596705 original size:18 final size:18
Alignment explanation
Indices: 2596682--2596754 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
2596672 ACTGAATATT
2596682 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
2596700 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* * *
2596719 TTATTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
2596738 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
2596755 GTTAATCCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 31 0.66
19 2 0.04
20 14 0.30
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:2598615 original size:2 final size:2
Alignment explanation
Indices: 2598608--2598641 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2598598 TTAAACATTA
2598608 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
2598642 TCTTTTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2598753 original size:2 final size:2
Alignment explanation
Indices: 2598746--2598792 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2598736 TTGTTAATGT
2598746 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2598788 TA TA T
1 TA TA T
2598793 TTTTTCCCTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2599208 original size:17 final size:17
Alignment explanation
Indices: 2599178--2599211 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2599168 AACAATATAT
**
2599178 AAATTATATTAAAAATA
1 AAATTATAAAAAAAATA
2599195 AAATTATAAAAAAAATA
1 AAATTATAAAAAAAATA
2599212 TTAGAAAATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATTATAAAAAAAATA
Found at i:2599227 original size:29 final size:26
Alignment explanation
Indices: 2599183--2599238 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 26
2599173 TATATAAATT
* *
2599183 ATATTAAAAATAAAATTATAAAAAAA
1 ATATTAAAAATAAAATCACAAAAAAA
2599209 ATATTAGAAAATCCAAAATCACAAAAAAA
1 ATATTA-AAAAT--AAAATCACAAAAAAA
2599238 A
1 A
2599239 ACTTAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.24
27 5 0.20
29 14 0.56
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.21
Consensus pattern (26 bp):
ATATTAAAAATAAAATCACAAAAAAA
Found at i:2599499 original size:2 final size:2
Alignment explanation
Indices: 2599492--2599521 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2599482 TGCCATTAAC
2599492 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
2599522 TATTTATTTT
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):
AT
Found at i:2599528 original size:126 final size:131
Alignment explanation
Indices: 2599398--2599647 Score: 375
Period size: 134 Copynumber: 1.9 Consensus size: 131
2599388 TATATTCATT
*
2599398 TTTATTTTTAAACCTTTCATTAACTACAA-T-T-TA-A-TATATATGAAATATAATTTGTTTGCG
1 TTTATTTTTAAACCTTTCATTAACTACAATTATATATACTATATATGAAATATAATTTGTTTACG
* *
2599458 AAATTTGTTTCAATGATTTATTTATGCCATTAACATATATATATATATATATATATATATATATT
66 AAATTTGTTTCAATGATTTATTTATGCCATTAACAAATATATATATATACATATATATATATATT
2599523 A
131 A
*
2599524 TTTATTTTTAAATCTTTCATTAACTACAATTTAATATATACCTATATATGAAATATAATTTGTTT
1 TTTATTTTTAAACCTTTCATTAACTACAA-TT-ATATATA-CTATATATGAAATATAATTTGTTT
* * *
2599589 ATGAATTTTGTTTCGATGATTTATTTATGCCATTAACAAATATATATATATACATATAT
63 ACGAAATTTGTTTCAATGATTTATTTATGCCATTAACAAATATATATATATACATATAT
2599648 TATTCGTTTT
Statistics
Matches: 109, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
126 28 0.26
128 1 0.01
130 1 0.01
131 2 0.02
132 1 0.01
134 76 0.70
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (131 bp):
TTTATTTTTAAACCTTTCATTAACTACAATTATATATACTATATATGAAATATAATTTGTTTACG
AAATTTGTTTCAATGATTTATTTATGCCATTAACAAATATATATATATACATATATATATATATT
A
Found at i:2602049 original size:35 final size:35
Alignment explanation
Indices: 2602001--2602077 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
2601991 TATAAACCCT
*
2602001 AAATTGAAGTATTTTAGAATTTTGGGTTTAAAATG
1 AAATTGAAGTATTTTAGAATTTGGGGTTTAAAATG
* * * *
2602036 TAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAAGTATTTTAGAATTTGGGGTTTAAAATG
2602071 AAATTGA
1 AAATTGA
2602078 GGATTGTGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (35 bp):
AAATTGAAGTATTTTAGAATTTGGGGTTTAAAATG
Found at i:2608693 original size:27 final size:27
Alignment explanation
Indices: 2608664--2608714 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
2608654 TATTTTCCTT
*
2608664 TTTTTTTACT-TAAAAACATAAATAGC
1 TTTTTATACTATAAAAACATAAATAGC
2608690 TTTTTATACTATAAAAACATAAATA
1 TTTTTATACTATAAAAACATAAATA
2608715 ATGATCAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (27 bp):
TTTTTATACTATAAAAACATAAATAGC
Found at i:2611019 original size:31 final size:32
Alignment explanation
Indices: 2610944--2611021 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 32
2610934 TTTTTTATTT
* * * *
2610944 AAGTACCTAAAGTATTTTTTTTTGGTGAAAAC
1 AAGTACCTAAAGTATATCTTTCTGGTCAAAAC
* *
2610976 AAGTACCCAAAGT-TATCTTTCTGGTCAAAAT
1 AAGTACCTAAAGTATATCTTTCTGGTCAAAAC
*
2611007 AGGTACCTAAAGTAT
1 AAGTACCTAAAGTAT
2611022 TTTAATTTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (32 bp):
AAGTACCTAAAGTATATCTTTCTGGTCAAAAC
Found at i:2613205 original size:17 final size:17
Alignment explanation
Indices: 2613183--2613219 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2613173 GTTGAAGTGT
2613183 GAATAAGTGGTCTATAA
1 GAATAAGTGGTCTATAA
*
2613200 GAATAAGTGGTGTATAA
1 GAATAAGTGGTCTATAA
2613217 GAA
1 GAA
2613220 AAAAGGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.43, C:0.03, G:0.27, T:0.27
Consensus pattern (17 bp):
GAATAAGTGGTCTATAA
Found at i:2615875 original size:60 final size:60
Alignment explanation
Indices: 2615811--2615960 Score: 187
Period size: 60 Copynumber: 2.5 Consensus size: 60
2615801 GTAACACAGA
2615811 AGTCAAATTCGCAACGCGATAGTCAAATTCACAACACAAAAGTCAAATTCGCAACGCGAC
1 AGTCAAATTCGCAACGCGATAGTCAAATTCACAACACAAAAGTCAAATTCGCAACGCGAC
* ** * *
2615871 AGTCAAATTCGCAACGCGAATTTGT-AAA-TCGTAACACATAAGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCG-A-TAGTCAAATTCACAACACAAAAGTCAAATTCGCAACGCGAC
* * * *
2615931 AGTCAAATTCGTAACACAAAAGTCAAATTC
1 AGTCAAATTCGCAACGCGATAGTCAAATTC
2615961 GCAATGCGGA
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
58 2 0.03
59 4 0.05
60 63 0.83
61 4 0.05
62 3 0.04
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (60 bp):
AGTCAAATTCGCAACGCGATAGTCAAATTCACAACACAAAAGTCAAATTCGCAACGCGAC
Found at i:2615993 original size:19 final size:19
Alignment explanation
Indices: 2615953--2616005 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
2615943 AACACAAAAG
2615953 TCAAATTCGCAATGCGGAATT
1 TCAAATTCGCAA--CGGAATT
*
2615974 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACGGAATT
2615993 TCAAATTCGCAAC
1 TCAAATTCGCAAC
2616006 ACGAATTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 19 0.61
21 12 0.39
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (19 bp):
TCAAATTCGCAACGGAATT
Found at i:2615993 original size:100 final size:100
Alignment explanation
Indices: 2615754--2615986 Score: 346
Period size: 100 Copynumber: 2.3 Consensus size: 100
2615744 TGCGATTTTC
* *
2615754 CAAATTCGCAACGCGAATCTGT-AAA-TCGTAACGCGAATTTGTAAATCGTAACACAGAAGTCAA
1 CAAATTCGCAACGCG-A-CAGTCAAATTCGCAACGCGAATTTGTAAATCGTAACACAGAAGTCAA
2615817 ATTCGCAACGCGATAGTCAAATTCACAACACAAAAGT
64 ATTCGCAACGCGATAGTCAAATTCACAACACAAAAGT
*
2615854 CAAATTCGCAACGCGACAGTCAAATTCGCAACGCGAATTTGTAAATCGTAACACATAAGTCAAAT
1 CAAATTCGCAACGCGACAGTCAAATTCGCAACGCGAATTTGTAAATCGTAACACAGAAGTCAAAT
**
2615919 TCGCAACGCGATAGTCAAATTCGTAACACAAAAGT
66 TCGCAACGCGATAGTCAAATTCACAACACAAAAGT
* *
2615954 CAAATTCGCAATGCGGA-ATTTCAAATTCGCAAC
1 CAAATTCGCAACGC-GACA-GTCAAATTCGCAAC
2615987 TGAATTTCAA
Statistics
Matches: 122, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
98 3 0.02
99 4 0.03
100 100 0.82
101 15 0.12
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (100 bp):
CAAATTCGCAACGCGACAGTCAAATTCGCAACGCGAATTTGTAAATCGTAACACAGAAGTCAAAT
TCGCAACGCGATAGTCAAATTCACAACACAAAAGT
Found at i:2616013 original size:20 final size:20
Alignment explanation
Indices: 2615754--2616011 Score: 153
Period size: 20 Copynumber: 12.9 Consensus size: 20
2615744 TGCGATTTTC
2615754 CAAATTCGCAACGCGAATCTGT
1 CAAATTCGCAACGCGAA--TGT
*
2615776 -AAA-TCGTAACGCGAATTTGT
1 CAAATTCGCAACGCGAA--TGT
* *
2615796 -AAA-TCGTAACACAGAA-GT
1 CAAATTCGCAACGC-GAATGT
2615814 CAAATTCGCAACGCG-ATAGT
1 CAAATTCGCAACGCGAAT-GT
* * * *
2615834 CAAATTCACAACACAAAAGT
1 CAAATTCGCAACGCGAATGT
2615854 CAAATTCGCAACGCGACA-GT
1 CAAATTCGCAACGCGA-ATGT
2615874 CAAATTCGCAACGCGAATTTGT
1 CAAATTCGCAACGCGAA--TGT
* * *
2615896 -AAA-TCGTAACAC-ATAAGT
1 CAAATTCGCAACGCGA-ATGT
2615914 CAAATTCGCAACGCG-ATAGT
1 CAAATTCGCAACGCGAAT-GT
* * * *
2615934 CAAATTCGTAACACAAAAGT
1 CAAATTCGCAACGCGAATGT
* *
2615954 CAAATTCGCAATGCGGAATTT
1 CAAATTCGCAACGC-GAATGT
* *
2615975 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATGT
*
2615994 CAAATTCGCAACACGAAT
1 CAAATTCGCAACGCGAAT
2616012 TTAGTTTCGT
Statistics
Matches: 187, Mismatches: 31, Indels: 38
0.73 0.12 0.15
Matches are distributed among these distances:
18 5 0.03
19 28 0.15
20 126 0.67
21 26 0.14
22 2 0.01
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATGT
Found at i:2616883 original size:24 final size:24
Alignment explanation
Indices: 2616856--2616911 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
2616846 CAGTATTCGA
2616856 ACTTTGATCTTGGTCAATACCCGG
1 ACTTTGATCTTGGTCAATACCCGG
*
2616880 ACTTTGATCTTGGTCAATACTCGG
1 ACTTTGATCTTGGTCAATACCCGG
*
2616904 ATTTTGAT
1 ACTTTGAT
2616912 GATGTGATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (24 bp):
ACTTTGATCTTGGTCAATACCCGG
Found at i:2619371 original size:20 final size:20
Alignment explanation
Indices: 2619348--2619393 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
2619338 TTGTGTTTGA
2619348 TTGCTTGGATAGTTGTTCTC
1 TTGCTTGGATAGTTGTTCTC
2619368 TTGCTTGGATAGTTGTTCTC
1 TTGCTTGGATAGTTGTTCTC
2619388 TTGCTT
1 TTGCTT
2619394 CTTCAAGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.09, C:0.15, G:0.24, T:0.52
Consensus pattern (20 bp):
TTGCTTGGATAGTTGTTCTC
Found at i:2621184 original size:21 final size:21
Alignment explanation
Indices: 2621160--2621258 Score: 78
Period size: 21 Copynumber: 4.7 Consensus size: 21
2621150 GCGGGCGGGA
*
2621160 CCTCTTGAATGATGACAGGGG
1 CCTCTTGAATGATGAGAGGGG
* * *
2621181 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGAGAGGGG
* *
2621202 CTTATTCG-ATGATGAGAGGGG
1 CCTCTT-GAATGATGAGAGGGG
* *
2621223 CCTTTTGAACT-AT-AGGAGGAG
1 CCTCTTGAA-TGATGA-GAGGGG
2621244 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
2621259 TAGGTGCATC
Statistics
Matches: 59, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
20 3 0.05
21 53 0.90
22 3 0.05
ACGTcount: A:0.23, C:0.16, G:0.34, T:0.26
Consensus pattern (21 bp):
CCTCTTGAATGATGAGAGGGG
Found at i:2621256 original size:42 final size:42
Alignment explanation
Indices: 2621160--2621258 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 42
2621150 GCGGGCGGGA
* * *
2621160 CCTCTTGAATGATGACAGGGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGAG
* * * * *
2621202 CTTATTCG-ATGATGAGAGGGGCCTTTTGAACTATAGGAGGAG
1 CCTCTT-GAATGATGACAGGGGCCTCTTGAACGATAGGAGGAG
2621244 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
2621259 TAGGTGCATC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
41 1 0.02
42 43 0.96
43 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.34, T:0.26
Consensus pattern (42 bp):
CCTCTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGAG
Found at i:2627484 original size:32 final size:32
Alignment explanation
Indices: 2627435--2627505 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
2627425 ATGTTAGTTT
*
2627435 AACCAA-TAAAGTAAATTGGAAATTCAGAATC
1 AACCAATTAAAGTAAATTGGAAATTCAGAAGC
* *
2627466 AACCAATTAAAGTGAATTGTAAATTCAGAAGC
1 AACCAATTAAAGTAAATTGGAAATTCAGAAGC
*
2627498 AAACAATT
1 AACCAATT
2627506 TTCCAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
31 6 0.17
32 29 0.83
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.24
Consensus pattern (32 bp):
AACCAATTAAAGTAAATTGGAAATTCAGAAGC
Found at i:2630283 original size:47 final size:48
Alignment explanation
Indices: 2630212--2630311 Score: 127
Period size: 47 Copynumber: 2.1 Consensus size: 48
2630202 AAAATTATAT
* *
2630212 TATAATAAATAATATAATAGTAATAAGTA-AT-AATAGTAATTATT-AAA
1 TATAATAAATAATAAAATAGTAATAA-TATATAAATA-TAATAATTAAAA
2630259 TATAATAAATAATTAAAATA-TAATAATATATAAATATAATAATTAAAA
1 TATAATAAATAA-TAAAATAGTAATAATATATAAATATAATAATTAAAA
2630307 TATAA
1 TATAA
2630312 ATTTTATAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
46 2 0.04
47 27 0.57
48 18 0.38
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (48 bp):
TATAATAAATAATAAAATAGTAATAATATATAAATATAATAATTAAAA
Found at i:2630295 original size:16 final size:16
Alignment explanation
Indices: 2630255--2630311 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
2630245 TAGTAATTAT
2630255 TAAATATAATAA-ATAA
1 TAAATATAATAATAT-A
2630271 TTAAAATATAATAATATA
1 -T-AAATATAATAATATA
2630289 TAAATATAATAAT-TA
1 TAAATATAATAATATA
2630304 -AAATATAA
1 TAAATATAA
2630312 ATTTTATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 8 0.21
15 2 0.05
16 12 0.32
17 2 0.05
18 12 0.32
19 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAATATAATAATATA
Found at i:2630301 original size:30 final size:31
Alignment explanation
Indices: 2630212--2630311 Score: 107
Period size: 30 Copynumber: 3.2 Consensus size: 31
2630202 AAAATTATAT
*
2630212 TATAATAA-ATAATATAATAGTAATAAGTAATAA
1 TATAATAATAT-ATATAATA-TAATAATTAA-AA
* *
2630245 TAGTAATTATTAAATATAATA-AATAATTAAAA
1 TA-TAA-TAATATATATAATATAATAATTAAAA
2630277 TATAATAATATATA-AATATAATAATTAAAA
1 TATAATAATATATATAATATAATAATTAAAA
2630307 TATAA
1 TATAA
2630312 ATTTTATAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
29 4 0.07
30 23 0.40
31 3 0.05
32 4 0.07
33 10 0.17
34 3 0.05
35 10 0.17
36 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (31 bp):
TATAATAATATATATAATATAATAATTAAAA
Found at i:2630320 original size:20 final size:19
Alignment explanation
Indices: 2630277--2630324 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
2630267 ATAATTAAAA
*
2630277 TATAATAATATATAAATAT
1 TATAATAAAATATAAATAT
* *
2630296 AATAATTAAAATATAAATTT
1 TATAA-TAAAATATAAATAT
2630316 TATAA-AAAA
1 TATAATAAAA
2630325 AAATTATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 16 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TATAATAAAATATAAATAT
Found at i:2630382 original size:4 final size:4
Alignment explanation
Indices: 2630373--2630445 Score: 51
Period size: 4 Copynumber: 18.0 Consensus size: 4
2630363 ATTATATTAT
* * * *
2630373 AATA AATA AATA AATA AAT- AAGA AAT- AATA ATATT AATT ATTA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA AATA AATA
* *
2630420 TAATA AATA ATTAA AATA TATA AATA
1 -AATA AATA AAT-A AATA AATA AATA
2630446 TAGTAATTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
3 5 0.09
4 39 0.72
5 10 0.19
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (4 bp):
AATA
Found at i:2630473 original size:151 final size:151
Alignment explanation
Indices: 2630201--2630646 Score: 573
Period size: 151 Copynumber: 2.9 Consensus size: 151
2630191 TTTATGATCC
* * *
2630201 AAAAATTATATTATAATAAAT-AATATAATAGTAATAAGTAATAATAGTAATTATTAAATATAAT
1 AAAAATTATATTATAATAAATAAATA-AATAATAATAAATAATAATATTAATTATTAAATATAAT
* * *
2630265 AAATAATTAAAATATAATAATATATAAATATAATAATTAAAATATAAATTTTATAAAAAAAAATT
65 --A-AA-T--AAT-TAATAATATATAAATAT-ATAATTAAAATAGATATTTTATAAAAAATAATT
2630330 ATAATATATTTTTTAAAACTTGAAATAAT-
122 ATAATATATTTTTTAAAACTTGAAATAATG
*
2630359 AAAAATTATATTATAATAAATAAATAAATAAATAAGAAATAATAATATTAATTATTAAATATAAT
1 AAAAATTATATTATAATAAATAAATAAAT-AATAATAAATAATAATATTAATTATTAAATATAAT
2630424 AAATAATTAA-AATATATAAATATAGTAATTAAAATAGATATTTTAT-AAAAATAATTATAATAT
65 AAATAATTAATAATATATAAATATA-TAATTAAAATAGATATTTTATAAAAAATAATTATAATAT
* * * *
2630487 ACTTTGTAAAATTTTAAATAATG
129 ATTTTTTAAAACTTGAAATAATG
* *
2630510 AAAAATTATATTATAATATATAAAT--ATAATAATAATTAATAATATTAATTATTAAATATAATA
1 AAAAATTATATTATAATAAATAAATAAATAATAATAAATAATAATATTAATTATTAAATATAATA
2630573 AATAATTAAATTGAATAATATACAAATATATAATTAAAATAGATATTTTATAAAAAATAATTATA
66 AATAATT-AA-T-AAT-ATAT--AAATATATAATTAAAATAGATATTTTATAAAAAATAATTATA
2630638 ATAT-TTTTT
125 ATATATTTTT
2630647 GAAATTTGAA
Statistics
Matches: 260, Mismatches: 16, Indels: 28
0.86 0.05 0.09
Matches are distributed among these distances:
148 41 0.16
149 4 0.02
150 35 0.13
151 56 0.22
152 6 0.02
153 7 0.03
154 24 0.09
155 25 0.10
156 2 0.01
157 1 0.00
158 24 0.09
159 35 0.13
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (151 bp):
AAAAATTATATTATAATAAATAAATAAATAATAATAAATAATAATATTAATTATTAAATATAATA
AATAATTAATAATATATAAATATATAATTAAAATAGATATTTTATAAAAAATAATTATAATATAT
TTTTTAAAACTTGAAATAATG
Found at i:2630541 original size:16 final size:16
Alignment explanation
Indices: 2630517--2630606 Score: 64
Period size: 16 Copynumber: 5.6 Consensus size: 16
2630507 ATGAAAAATT
*
2630517 ATATTATAATATATAA
1 ATATAATAATATATAA
*
2630533 ATATAATAATA-ATTA
1 ATATAATAATATATAA
*
2630548 ATAATATTAAT-TATTAA
1 AT-ATAATAATATA-TAA
2630565 ATATAATAA-ATAATTAA
1 ATATAATAATAT-A-TAA
*
2630582 AT-TGAATAATATACAA
1 ATAT-AATAATATATAA
2630598 ATAT-ATAAT
1 ATATAATAAT
2630607 TAAAATAGAT
Statistics
Matches: 60, Mismatches: 6, Indels: 17
0.72 0.07 0.20
Matches are distributed among these distances:
15 10 0.17
16 30 0.50
17 18 0.30
18 2 0.03
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (16 bp):
ATATAATAATATATAA
Found at i:2632074 original size:21 final size:21
Alignment explanation
Indices: 2632050--2632096 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
2632040 TAGGGACGCC
*
2632050 CAATTGCAAAGAAGAGATGCT
1 CAATTGCAAAGAAAAGATGCT
*
2632071 CAATTGGAAAGAAAAGATGCT
1 CAATTGCAAAGAAAAGATGCT
2632092 CAATT
1 CAATT
2632097 ATTAATAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (21 bp):
CAATTGCAAAGAAAAGATGCT
Done.