Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008736.1 Hibiscus syriacus cultivar Beakdansim tig00111810_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: 2478687
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 13
Found at i:1067512 original size:16 final size:15
Alignment explanation
Indices: 1067482--1067528 Score: 67
Period size: 16 Copynumber: 3.0 Consensus size: 15
1067472 TTTTAACATT
1067482 TTATTAATTTTTTTTA
1 TTATT-ATTTTTTTTA
*
1067498 TTTTTATTATTTTTTA
1 TTATTATT-TTTTTTA
1067514 TTATTATTTTTTTTA
1 TTATTATTTTTTTTA
1067529 CGTGTTTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTATTATTTTTTTTA
Found at i:1067517 original size:10 final size:10
Alignment explanation
Indices: 1067480--1067523 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
1067470 TTTTTTAACA
1067480 TTTTATTAATT
1 TTTTATT-ATT
1067491 TTTT-TTA-T
1 TTTTATTATT
1067499 TTTTATTATT
1 TTTTATTATT
1067509 TTTTATTATT
1 TTTTATTATT
1067519 ATTTT
1 -TTTT
1067524 TTTTACGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 5 0.17
9 4 0.13
10 13 0.43
11 8 0.27
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTATTATT
Found at i:1070617 original size:14 final size:13
Alignment explanation
Indices: 1070597--1070637 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
1070587 ACAAAAAGAG
1070597 AAAAAAGAGAAAA
1 AAAAAAGAGAAAA
1070610 AAACAAAGAGAAAA
1 AAA-AAAGAGAAAA
*
1070624 TAAAAAGAGAAAA
1 AAAAAAGAGAAAA
1070637 A
1 A
1070638 CAAAGGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (13 bp):
AAAAAAGAGAAAA
Found at i:1070628 original size:16 final size:14
Alignment explanation
Indices: 1070600--1070637 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1070590 AAAAGAGAAA
1070600 AAAGAGAAAAAAAC
1 AAAGAGAAAAAAAC
*
1070614 AAAGAGAAAATAA-
1 AAAGAGAAAAAAAC
1070627 AAAGAGAAAAA
1 AAAGAGAAAAA
1070638 CAAAGGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.03
Consensus pattern (14 bp):
AAAGAGAAAAAAAC
Found at i:1070630 original size:13 final size:13
Alignment explanation
Indices: 1070598--1070648 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
1070588 CAAAAAGAGA
*
1070598 AAAAAGAGAAAAA
1 AAAAAGAGAAAAT
1070611 AACAAAGAGAAAAT
1 AA-AAAGAGAAAAT
1070625 AAAAAGAGAAAA-
1 AAAAAGAGAAAAT
*
1070637 ACAAAG-GAAAAT
1 AAAAAGAGAAAAT
1070649 TGAAGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 5 0.15
12 5 0.15
13 12 0.35
14 12 0.35
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (13 bp):
AAAAAGAGAAAAT
Found at i:1070642 original size:25 final size:25
Alignment explanation
Indices: 1070584--1070648 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
1070574 AGATTCAATC
* *
1070584 AAAACAAAAAGAGAAA-AAAGAGAAA
1 AAAACAAAGAGA-AAATAAAAAGAAA
*
1070609 AAAACAAAGAGAAAATAAAAAGAGA
1 AAAACAAAGAGAAAATAAAAAGAAA
1070634 AAAACAAAG-GAAAAT
1 AAAACAAAGAGAAAAT
1070649 TGAAGAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.25
25 27 0.75
ACGTcount: A:0.77, C:0.05, G:0.15, T:0.03
Consensus pattern (25 bp):
AAAACAAAGAGAAAATAAAAAGAAA
Found at i:1072290 original size:36 final size:36
Alignment explanation
Indices: 1072206--1072431 Score: 200
Period size: 36 Copynumber: 6.4 Consensus size: 36
1072196 ATTGAAAACA
* * *
1072206 TTTCCCTTGAAAAAAAATTCGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* *
1072242 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
** *
1072278 TTTCTCTTGAAACAAA-----T-T-AATTGA-ATATG
1 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
* * * *
1072307 TTT-TATTTGAAACAAATTTCATCTCCCTTGAGATAG
1 TTTCT-CTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * * *
1072343 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
*
1072380 TTTCTCTTAAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
1072416 TTTCCCTTGAAACAAA
1 TTTCTCTTGAAACAAA
1072432 ATCTTTGAAT
Statistics
Matches: 155, Mismatches: 23, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
28 3 0.02
29 18 0.12
30 1 0.01
31 1 0.01
34 1 0.01
35 1 0.01
36 98 0.63
37 32 0.21
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:1072291 original size:101 final size:101
Alignment explanation
Indices: 1072153--1072396 Score: 276
Period size: 101 Copynumber: 2.4 Consensus size: 101
1072143 ATTTCTAATA
* * * *
1072153 TAAATATTGTCTCCCTTGAGACAGTTTCTATTGAAACATAA-ACATTGAAAACATTTCCCTTGAA
1 TAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AATA-ATTGAAAACATTTCACTTGAA
* *
1072217 AAAAAATTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
64 AAAAAATTCATCTCCCTTGAGACAGTTTCCCTTGAAAC
* ** * *
1072255 -AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTAATTGAATATGTTTTATTTGAAA
1 TAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA-TAATTGAAAACATTTCACTTGAAA
* * * ** *
1072319 CAAATTTCATCTCCCTTGAGATAGTTTCTTTTGGAAC
65 AAAAATTCATCTCCCTTGAGACAGTTTCCCTTGAAAC
* *
1072356 TAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAAT
1 TAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAT
1072397 TTCGTCTCTC
Statistics
Matches: 120, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
100 2 0.02
101 80 0.67
102 38 0.32
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.39
Consensus pattern (101 bp):
TAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATAATTGAAAACATTTCACTTGAAAA
AAAATTCATCTCCCTTGAGACAGTTTCCCTTGAAAC
Found at i:1072393 original size:102 final size:101
Alignment explanation
Indices: 1072212--1072397 Score: 273
Period size: 102 Copynumber: 1.8 Consensus size: 101
1072202 AACATTTCCC
* *
1072212 TTGAAAAAAAATTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 TTGAAAAAAAATTCATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
1072277 GTTTCTCTTGAAACAAATTAATTGAATATGTTTTAT
66 GTTTCTCTTAAAACAAATTAATTGAATATGTTTTAT
* * * ** * *
1072313 TTGAAACAAATTTCATCTCCCTTGAGATAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
1 TTGAAAAAAAATTCATCTCCCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGAC
1072378 AGTTTCTCTTAAAACAAATT
65 AGTTTCTCTTAAAACAAATT
1072398 TCGTCTCTCT
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
101 35 0.47
102 39 0.53
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (101 bp):
TTGAAAAAAAATTCATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
GTTTCTCTTAAAACAAATTAATTGAATATGTTTTAT
Found at i:1072476 original size:138 final size:138
Alignment explanation
Indices: 1072226--1072485 Score: 358
Period size: 138 Copynumber: 1.9 Consensus size: 138
1072216 AAAAAAATTC
* * *
1072226 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * * ** * * *
1072291 AAATTAATTGAATATGTTTTATTTGAAACAAATTTCATCTCCCTTGAGATAGTTTCTTTTGGAAC
66 AAAATAATTGAATATATTTCACCTAAAACAAATTTCATCTCCATTGAGACAGTTTCTTTTGGAAC
1072356 TAAGTTTT
131 TAAGTTTT
*
1072364 GTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
** * * **
1072429 AAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCATTGAGACAGTTTCT
66 AAAATAATTGAATATATTTCACCTAAAACAAATTTCATCTCCATTGAGACAGTTTCT
1072486 CTTGAAACAC
Statistics
Matches: 104, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
138 104 1.00
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (138 bp):
GTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC
AAAATAATTGAATATATTTCACCTAAAACAAATTTCATCTCCATTGAGACAGTTTCTTTTGGAAC
TAAGTTTT
Found at i:1072559 original size:67 final size:67
Alignment explanation
Indices: 1072380--1072561 Score: 235
Period size: 65 Copynumber: 2.7 Consensus size: 67
1072370 CTTGAGACAG
* * * * **
1072380 TTTCTCTTAAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
1072443 TA
66 TA
* *
1072445 TTTCCCCTAAAACAAATTTTGTCTCCATTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
1072510 TA
66 TA
* * *
1072512 TTTCCCTTAAAACAAAATTTTGTTTCCCTTGAGACCGTTT-TCATGAAACA
1 TTTCCCTTAAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1072562 ACATATATCT
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
65 39 0.39
66 2 0.02
67 37 0.37
68 23 0.23
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (67 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
TA
Found at i:1073494 original size:106 final size:102
Alignment explanation
Indices: 1073268--1073536 Score: 274
Period size: 106 Copynumber: 2.5 Consensus size: 102
1073258 ACGAAGGGGC
* * * * * *
1073268 TTCCTAGTTTCAGAGCCAATTTTAACTTCATAGCGAGGGATATTGGACTCAAGACAACACAAGCT
1 TTCCCAGTTCCAGAGCCAATTTCAACTTCACAG-GAAGGATATTGGACTCGAGACAACACAAGCT
1073333 CAACTTCACAACGAAGGGGCGATTATCAACAAACAACT
65 CAACTTCACAACGAAGGGGCGATTATCAACAAACAACT
* * *
1073371 TT-TCAGTTTCATTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGAACTCGAGACAACACA
1 TTCCCAG-TTC---CAGAGCCAATTTCAACTTCACAG-GAAGGATATTGGACTCGAGACAACACA
* * * * *
1073435 AGCTCAACTTCATAGCGAAGGGGCGGCTGGCTGTCAACAAATAA-T
61 AGCTCAACTTCACAACGAAGGGGC-GAT---TATCAACAAACAACT
*
1073480 TTCCCAGTTCCAGAGCCAATTTCAACTTCACGACGG-AGGATATTGGACTCGAAACAA
1 TTCCCAGTTCCAGAGCCAATTTCAACTTCAC-A-GGAAGGATATTGGACTCGAGACAA
1073537 TACTACCCAC
Statistics
Matches: 136, Mismatches: 19, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
102 2 0.01
103 4 0.03
106 105 0.77
107 4 0.03
108 1 0.01
109 6 0.04
110 14 0.10
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (102 bp):
TTCCCAGTTCCAGAGCCAATTTCAACTTCACAGGAAGGATATTGGACTCGAGACAACACAAGCTC
AACTTCACAACGAAGGGGCGATTATCAACAAACAACT
Found at i:1074922 original size:14 final size:14
Alignment explanation
Indices: 1074899--1074931 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1074889 ATTCCTCTTT
1074899 TTAT-TTATTTTTA
1 TTATATTATTTTTA
1074912 TTATATTATTTTTA
1 TTATATTATTTTTA
1074926 TTATAT
1 TTATAT
1074932 ATATCTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATATTATTTTTA
Found at i:1074924 original size:25 final size:24
Alignment explanation
Indices: 1074856--1074924 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 24
1074846 CCTATATATA
*
1074856 TATTTTTAAATA-TATTTTTTATT
1 TATTTTTATATATTATTTTTTATT
*
1074879 TA--TTTACTATATTCCTCTTTTTATT
1 TATTTTTA-TATATT-AT-TTTTTATT
1074904 TATTTTTATTATATTATTTTT
1 TATTTTTA-TATATTATTTTT
1074925 ATTATATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
21 4 0.11
22 3 0.08
23 3 0.08
24 1 0.03
25 14 0.39
26 1 0.03
27 10 0.28
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.70
Consensus pattern (24 bp):
TATTTTTATATATTATTTTTTATT
Found at i:1074934 original size:2 final size:2
Alignment explanation
Indices: 1074927--1074967 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
1074917 TTATTTTTAT
*
1074927 TA TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
1074968 GATGTATTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
1 2 0.06
2 31 0.89
3 2 0.06
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1075076 original size:32 final size:36
Alignment explanation
Indices: 1074997--1075094 Score: 107
Period size: 37 Copynumber: 2.8 Consensus size: 36
1074987 ATTTACTATG
*
1074997 TATATATTTTTTCTTAATATTATATTTTATACGTTTT
1 TATATATATTTTCTTAATATTATATTTTATA-GTTTT
*
1075034 TATATATATTTTCTTAATATTCTATTTT-T-GTTTT
1 TATATATATTTTCTTAATATTATATTTTATAGTTTT
*
1075068 TAT-T-TATTTAT-ATATATATTATATTTT
1 TATATATATTT-TCTTA-ATATTATATTTT
1075095 TACTTTATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
32 7 0.13
33 13 0.24
34 8 0.15
36 1 0.02
37 26 0.47
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (36 bp):
TATATATATTTTCTTAATATTATATTTTATAGTTTT
Found at i:1075357 original size:22 final size:22
Alignment explanation
Indices: 1075332--1075392 Score: 59
Period size: 25 Copynumber: 2.6 Consensus size: 22
1075322 ATTTTGTTTA
1075332 TTTTGTTTATTATTTTTACGTG
1 TTTTGTTTATTATTTTTACGTG
* * *
1075354 TTTTGTTATTTTTCATTTTTTCTTG
1 TTTTG-T-TTATT-ATTTTTACGTG
*
1075379 TTTTATTTATTATT
1 TTTTGTTTATTATT
1075393 CTCACGTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
22 8 0.26
23 5 0.16
24 5 0.16
25 13 0.42
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (22 bp):
TTTTGTTTATTATTTTTACGTG
Found at i:1077597 original size:2 final size:2
Alignment explanation
Indices: 1077590--1077616 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1077580 TGCTAATGAG
1077590 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1077617 AAAGTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1083738 original size:23 final size:23
Alignment explanation
Indices: 1083708--1083771 Score: 119
Period size: 23 Copynumber: 2.8 Consensus size: 23
1083698 CAATACACTA
1083708 TGAATGTGTACCGATACATTCCT
1 TGAATGTGTACCGATACATTCCT
1083731 TGAATGTGTACCGATACATTCCT
1 TGAATGTGTACCGATACATTCCT
*
1083754 TGAATGTGTATCGATACA
1 TGAATGTGTACCGATACA
1083772 CTCACAAGTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (23 bp):
TGAATGTGTACCGATACATTCCT
Found at i:1085704 original size:24 final size:25
Alignment explanation
Indices: 1085654--1085710 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
1085644 TGTTAAAACA
1085654 TTTTGAATGTTTTTGGATTTGTGTG
1 TTTTGAATGTTTTTGGATTTGTGTG
* * *
1085679 TTTTGGATG-TTTTGGATTTTTTTG
1 TTTTGAATGTTTTTGGATTTGTGTG
1085703 -TTTGAATG
1 TTTTGAATG
1085711 GTTTGAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 7 0.25
24 13 0.46
25 8 0.29
ACGTcount: A:0.12, C:0.00, G:0.26, T:0.61
Consensus pattern (25 bp):
TTTTGAATGTTTTTGGATTTGTGTG
Found at i:1090000 original size:14 final size:14
Alignment explanation
Indices: 1089981--1090017 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1089971 TGTTTATATG
1089981 CAGAGATTTTTAGA
1 CAGAGATTTTTAGA
*
1089995 CAGAGATTTTTAGG
1 CAGAGATTTTTAGA
*
1090009 CAGGGATTT
1 CAGAGATTT
1090018 ATGTGCAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.35
Consensus pattern (14 bp):
CAGAGATTTTTAGA
Found at i:1092167 original size:23 final size:23
Alignment explanation
Indices: 1092136--1092197 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
1092126 AAAACTATCA
*
1092136 AAAGGCAGAGAAAAACGTGCCAC
1 AAAGGCAGAGATAAACGTGCCAC
* * *
1092159 AAAGACAGAGATAAACGTGTCAT
1 AAAGGCAGAGATAAACGTGCCAC
1092182 AAAGGCAGAGATAAAC
1 AAAGGCAGAGATAAAC
1092198 ATATCAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.50, C:0.16, G:0.24, T:0.10
Consensus pattern (23 bp):
AAAGGCAGAGATAAACGTGCCAC
Found at i:1092208 original size:23 final size:22
Alignment explanation
Indices: 1092127--1092208 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
1092117 AAACGATTGA
*
1092127 AAAC-TATCAAAAGGCAGAGAA
1 AAACGTATCAAAAGGCAGAGAT
** *
1092148 AAACGTGCCACAAAGACAGAGAT
1 AAACGTATCA-AAAGGCAGAGAT
*
1092171 AAACGTGTCATAAAGGCAGAGAT
1 AAACGTATCA-AAAGGCAGAGAT
*
1092194 AAACATATCAGAAAG
1 AAACGTATCA-AAAG
1092209 AGAAAATTAT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
21 4 0.08
22 3 0.06
23 42 0.86
ACGTcount: A:0.51, C:0.16, G:0.21, T:0.12
Consensus pattern (22 bp):
AAACGTATCAAAAGGCAGAGAT
Found at i:1095255 original size:18 final size:20
Alignment explanation
Indices: 1095236--1095272 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
1095226 GATATTATTA
*
1095236 TTATTTTA-CTATAAAATAT
1 TTATTTTAGATATAAAATAT
1095255 TTATTTTAGATATAAAAT
1 TTATTTTAGATATAAAAT
1095273 TATAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (20 bp):
TTATTTTAGATATAAAATAT
Found at i:1095617 original size:20 final size:20
Alignment explanation
Indices: 1095589--1095627 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1095579 GTAAAATTAA
1095589 TTTAAATA-TATAAAGTATAT
1 TTTAAATATTA-AAAGTATAT
*
1095609 TTTAGATATTAAAAGTATA
1 TTTAAATATTAAAAGTATA
1095628 ATATGAACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (20 bp):
TTTAAATATTAAAAGTATAT
Found at i:1098856 original size:16 final size:16
Alignment explanation
Indices: 1098837--1098927 Score: 67
Period size: 16 Copynumber: 5.7 Consensus size: 16
1098827 CTTTTGATTT
*
1098837 GGGTTAATTTCGGTTC
1 GGGTTAATTTCAGTTC
* *
1098853 GGGTTACTTTCGGTTTC
1 GGGTTAATTTCAG-TTC
* *
1098870 GAGTTATTTTCAGTTC
1 GGGTTAATTTCAGTTC
* * *
1098886 GGATT-ACTTCAATTC
1 GGGTTAATTTCAGTTC
*
1098901 GGGTTAATTTCAGCTC
1 GGGTTAATTTCAGTTC
**
1098917 AAGTTAATTTC
1 GGGTTAATTTC
1098928 GTTTCAGATT
Statistics
Matches: 58, Mismatches: 15, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
15 11 0.19
16 34 0.59
17 13 0.22
ACGTcount: A:0.19, C:0.15, G:0.22, T:0.44
Consensus pattern (16 bp):
GGGTTAATTTCAGTTC
Found at i:1105988 original size:29 final size:29
Alignment explanation
Indices: 1105941--1106123 Score: 178
Period size: 29 Copynumber: 6.4 Consensus size: 29
1105931 ATCGTTGATC
* * * *
1105941 GGGTGATATTTTAGAAATTAATTCGAAAT
1 GGGTGCTATTTTGGGAATTAATTCGAAAA
1105970 GGGTGCTATTTTGGGAATTTAATTCGAAAA
1 GGGTGCTATTTTGGGAA-TTAATTCGAAAA
*
1106000 -GGTGTTATTTTGGGAATTAAATTC-AAAA
1 GGGTGCTATTTTGGGAATT-AATTCGAAAA
** *
1106028 AAGTGTTATTTTGGGAATTTAATTC-AAAA
1 GGGTGCTATTTTGGGAA-TTAATTCGAAAA
*
1106057 --GTGCTATTTAGGGAATTAATTCGAAAA
1 GGGTGCTATTTTGGGAATTAATTCGAAAA
* * * **
1106084 GGGTTCTATTTTGGTAATTATTTTAAAAA
1 GGGTGCTATTTTGGGAATTAATTCGAAAA
1106113 GGGTGCTATTT
1 GGGTGCTATTT
1106124 CTGTAAAATG
Statistics
Matches: 132, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
26 7 0.05
27 17 0.13
28 6 0.05
29 89 0.67
30 13 0.10
ACGTcount: A:0.33, C:0.05, G:0.22, T:0.40
Consensus pattern (29 bp):
GGGTGCTATTTTGGGAATTAATTCGAAAA
Found at i:1113319 original size:58 final size:58
Alignment explanation
Indices: 1113220--1113352 Score: 191
Period size: 58 Copynumber: 2.3 Consensus size: 58
1113210 CCGTTAATCG
* * *
1113220 GGTGATATTTTGAGAA-TTAATTCGAAATGGGTGCTATTTTGGGAATTTAATTCGAAAAA
1 GGTGCTATTTTGGGAATTTAATTCGAAA-GAGTGCTATTTTGGGAATTTAATTCG-AAAA
1113279 GGTGCTATTTTGGGAATTTAATTCGAAA-AGTGCTATTTTGGGAATTTAATTCGAAAA
1 GGTGCTATTTTGGGAATTTAATTCGAAAGAGTGCTATTTTGGGAATTTAATTCGAAAA
*
1113336 -GTGCTATTTTGGTAATT
1 GGTGCTATTTTGGGAATT
1113353 ATTTTAAAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
56 16 0.23
57 4 0.06
58 24 0.35
59 14 0.20
60 11 0.16
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (58 bp):
GGTGCTATTTTGGGAATTTAATTCGAAAGAGTGCTATTTTGGGAATTTAATTCGAAAA
Found at i:1113320 original size:28 final size:28
Alignment explanation
Indices: 1113225--1113352 Score: 186
Period size: 28 Copynumber: 4.5 Consensus size: 28
1113215 AATCGGGTGA
* *
1113225 TATTTTGAGAA-TTAATTCGAAATGGGTGC
1 TATTTTGGGAATTTAATTCGAAA--AGTGC
1113254 TATTTTGGGAATTTAATTCGAAAAAGGTGC
1 TATTTTGGGAATTTAATTCG-AAAA-GTGC
1113284 TATTTTGGGAATTTAATTCGAAAAGTGC
1 TATTTTGGGAATTTAATTCGAAAAGTGC
1113312 TATTTTGGGAATTTAATTCGAAAAGTGC
1 TATTTTGGGAATTTAATTCGAAAAGTGC
*
1113340 TATTTTGGTAATT
1 TATTTTGGGAATT
1113353 ATTTTAAAAA
Statistics
Matches: 93, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
28 44 0.47
29 14 0.15
30 32 0.34
31 3 0.03
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.41
Consensus pattern (28 bp):
TATTTTGGGAATTTAATTCGAAAAGTGC
Found at i:1115974 original size:21 final size:21
Alignment explanation
Indices: 1115958--1116002 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1115948 TATTTAGTGT
1115958 TTTA-GATTTAAGTTTTAAGG
1 TTTATGATTTAAGTTTTAAGG
*
1115978 TTTATGATTTAAGTTTTGAGG
1 TTTATGATTTAAGTTTTAAGG
1115999 TTTA
1 TTTA
1116003 GGGTAGGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (21 bp):
TTTATGATTTAAGTTTTAAGG
Found at i:1118465 original size:46 final size:43
Alignment explanation
Indices: 1118414--1118522 Score: 132
Period size: 46 Copynumber: 2.5 Consensus size: 43
1118404 TCTATATATG
1118414 TATATATATTTTTAATATTTTATTTATGTAC-TATATTTTATCATTA
1 TATATATATTTTTAATATTTTATTTA--TACGTATA--TTATCATTA
* * *
1118460 TATATATACTTTTAATATTTTATTTATACGTCTATTATTATTA
1 TATATATATTTTTAATATTTTATTTATACGTATATTATCATTA
1118503 TATATAT-TTTTTAATCATTT
1 TATATATATTTTTAAT-ATTT
1118523 GATTATTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
42 7 0.12
43 19 0.33
44 3 0.05
45 3 0.05
46 25 0.44
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.61
Consensus pattern (43 bp):
TATATATATTTTTAATATTTTATTTATACGTATATTATCATTA
Found at i:1118547 original size:20 final size:19
Alignment explanation
Indices: 1118499--1118548 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
1118489 GTCTATTATT
1118499 ATTATATATATTTTTTAATC
1 ATTATAT-TATTTTTTAATC
*
1118519 ATT-TGATTATTTTTTATTGC
1 ATTAT-ATTATTTTTTAAT-C
1118539 ATTATATTAT
1 ATTATATTAT
1118549 ATATATGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 11 0.42
20 14 0.54
21 1 0.04
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (19 bp):
ATTATATTATTTTTTAATC
Found at i:1118621 original size:16 final size:17
Alignment explanation
Indices: 1118562--1118641 Score: 60
Period size: 17 Copynumber: 4.6 Consensus size: 17
1118552 TATGTATATG
1118562 TTTTC-ATTTTTACTTTA
1 TTTTCTATTTTTAC-TTA
* *
1118579 TTTATTTATTTTTAAATCTTT
1 TTT-TCTATTTTT--A-CTTA
1118600 TTTTCTATTTTTA-TTA
1 TTTTCTATTTTTACTTA
1118616 TTTTCT-TTTTTACTTTA
1 TTTTCTATTTTTAC-TTA
1118633 TTTT-TATTT
1 TTTTCTATTT
1118642 CCTTGTTGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
15 6 0.12
16 9 0.18
17 13 0.25
18 2 0.04
19 6 0.12
20 8 0.16
21 6 0.12
22 1 0.02
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTCTATTTTTACTTA
Found at i:1118636 original size:26 final size:25
Alignment explanation
Indices: 1118562--1118641 Score: 74
Period size: 26 Copynumber: 3.0 Consensus size: 25
1118552 TATGTATATG
*
1118562 TTTTCATTTTTACTTTATTTATTTATT
1 TTTTCTTTTTTACTTTA-TT-TTTATT
*
1118589 TTTAAATCTTTTTT--TCTATTTTTATT
1 TTT---TCTTTTTTACTTTATTTTTATT
1118615 ATTTTCTTTTTTACTTTATTTTTATT
1 -TTTTCTTTTTTACTTTATTTTTATT
1118641 T
1 T
1118642 CCTTGTTGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
24 8 0.18
25 1 0.02
26 17 0.39
27 8 0.18
28 3 0.07
30 7 0.16
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTTCTTTTTTACTTTATTTTTATT
Found at i:1118742 original size:14 final size:13
Alignment explanation
Indices: 1118707--1118771 Score: 55
Period size: 14 Copynumber: 4.8 Consensus size: 13
1118697 AGATTATTAC
1118707 TATTTTCTTTA-TT
1 TATTTT-TTTATTT
*
1118720 TA-TTATTTATTAT
1 TATTTTTTTATT-T
1118733 TATTTTTTTATTT
1 TATTTTTTTATTT
1118746 CTATTTTTTCT-TTT
1 -TATTTTTT-TATTT
1118760 TATTTTCTTTAT
1 TATTTT-TTTAT
1118772 CTTTTTATCT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
11 4 0.09
12 3 0.07
13 13 0.30
14 22 0.51
15 1 0.02
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (13 bp):
TATTTTTTTATTT
Found at i:1118750 original size:17 final size:17
Alignment explanation
Indices: 1118730--1118802 Score: 58
Period size: 19 Copynumber: 4.0 Consensus size: 17
1118720 TATTATTTAT
1118730 TATTATTTTTTTATTTC
1 TATTATTTTTTTATTTC
*
1118747 TATTTTTTCTTTTTATTTTC
1 TA-TTATT-TTTTTA-TTTC
*
1118767 T-TTATCTTTTTATCTTC
1 TATTATTTTTTTAT-TTC
*
1118784 ATGTTATTTTCTTTATTTC
1 -TATTATTTT-TTTATTTC
1118803 CTTTGTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
16 1 0.02
17 11 0.24
18 8 0.18
19 15 0.33
20 10 0.22
ACGTcount: A:0.14, C:0.11, G:0.01, T:0.74
Consensus pattern (17 bp):
TATTATTTTTTTATTTC
Found at i:1119266 original size:2 final size:2
Alignment explanation
Indices: 1119259--1119283 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1119249 ATAGCGATAC
1119259 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 T
1119284 GGTAATTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1121601 original size:2 final size:2
Alignment explanation
Indices: 1121594--1121638 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1121584 TTATACATCC
1121594 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
1121636 TA T
1 TA T
1121639 TGCATTGCAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1126163 original size:10 final size:9
Alignment explanation
Indices: 1126130--1126179 Score: 55
Period size: 10 Copynumber: 5.2 Consensus size: 9
1126120 ACCGGTTTAG
1126130 ACCGGTCAA
1 ACCGGTCAA
* *
1126139 ACTGGTTCCA
1 ACCGG-TCAA
1126149 ACCGGTCGAA
1 ACCGGTC-AA
1126159 ACCGGTCAAA
1 ACCGGTC-AA
1126169 ACCGGTCAA
1 ACCGGTCAA
1126178 AC
1 AC
1126180 TGATTTTCAG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 10 0.29
10 24 0.71
ACGTcount: A:0.32, C:0.32, G:0.22, T:0.14
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:1131404 original size:21 final size:21
Alignment explanation
Indices: 1131380--1131430 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
1131370 CTAAGATTAG
1131380 GTAGCTGAACCAGCTCAAA-GA
1 GTAGCTGAACCAGCT-AAATGA
* * *
1131401 GTAGTTAAACTAGCTAAATGA
1 GTAGCTGAACCAGCTAAATGA
1131422 G-AGCTGAAC
1 GTAGCTGAAC
1131431 TTAGCTTGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.20
Consensus pattern (21 bp):
GTAGCTGAACCAGCTAAATGA
Found at i:1138517 original size:8 final size:8
Alignment explanation
Indices: 1138504--1138535 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
1138494 TCAGTCCCTA
1138504 TATGTTTT
1 TATGTTTT
1138512 TATGTTTT
1 TATGTTTT
*
1138520 TAGGTTTT
1 TATGTTTT
1138528 TATGTTTT
1 TATGTTTT
1138536 AACATTTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.12, C:0.00, G:0.16, T:0.72
Consensus pattern (8 bp):
TATGTTTT
Found at i:1139558 original size:40 final size:40
Alignment explanation
Indices: 1139489--1139597 Score: 114
Period size: 40 Copynumber: 2.8 Consensus size: 40
1139479 TGAAATTGTG
* * * * * *
1139489 ATTTGGCGTCCTTTACATAAAGGATCAAGATTATTCCCTA
1 ATTTGGCGTCCTTTAGAGAAAAGAGCAAGATCATTCCCCA
*
1139529 ATTTGGCGTCCTTTAGAGAAAAGAGCAAGATCGTTCCCCA
1 ATTTGGCGTCCTTTAGAGAAAAGAGCAAGATCATTCCCCA
* *
1139569 ATTTGATC-TCCTTCAGAGAAAAGAG-AAGA
1 ATTTG-GCGTCCTTTAGAGAAAAGAGCAAGA
1139598 ATTTTCATTA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.07
40 54 0.92
41 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (40 bp):
ATTTGGCGTCCTTTAGAGAAAAGAGCAAGATCATTCCCCA
Found at i:1139725 original size:40 final size:42
Alignment explanation
Indices: 1139602--1139735 Score: 112
Period size: 40 Copynumber: 3.2 Consensus size: 42
1139592 AGAAGAATTT
* *
1139602 TCATTAATTATGACTTGGTGTCCTTTAGAGAAATGAGCAAATCAA
1 TCATT-ATCATGACTTGGCGTCCTTTAGAGAAATGAGC-AA-CAA
* * * * *
1139647 TCATTGATCATGACTTGACATCCTTAAAAGAAAGGAGCAA-AA
1 TCATT-ATCATGACTTGGCGTCCTTTAGAGAAATGAGCAACAA
* * * *
1139689 TCGTT-TCTTGATTTGGCGTCCTTTAGAGAAATGAGCAA-GA
1 TCATTATCATGACTTGGCGTCCTTTAGAGAAATGAGCAACAA
1139729 TCATTAT
1 TCATTAT
1139736 TCCACTTGAC
Statistics
Matches: 70, Mismatches: 18, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
40 31 0.44
41 1 0.01
42 6 0.09
44 2 0.03
45 30 0.43
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (42 bp):
TCATTATCATGACTTGGCGTCCTTTAGAGAAATGAGCAACAA
Found at i:1140316 original size:45 final size:45
Alignment explanation
Indices: 1140230--1140330 Score: 103
Period size: 45 Copynumber: 2.2 Consensus size: 45
1140220 CATTTTTCAG
* *** *
1140230 AGAAAAGAGCAGATCAATCATTGATTATGTCTTGGATTCCTTAAA
1 AGAAAAGAGCAGATCAACCATTGATTACAACTTGGAGTCCTTAAA
* * * * *
1140275 AGAAAGGAGCATATCAACCATTGATTACAACTTGGCGTCCTTTAG
1 AGAAAAGAGCAGATCAACCATTGATTACAACTTGGAGTCCTTAAA
*
1140320 AGAAATGAGCA
1 AGAAAAGAGCA
1140331 AGATTATTCT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (45 bp):
AGAAAAGAGCAGATCAACCATTGATTACAACTTGGAGTCCTTAAA
Found at i:1141362 original size:17 final size:18
Alignment explanation
Indices: 1141321--1141367 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
1141311 TGTTTATGAG
* *
1141321 GGAATTAGAATCTGTGAA
1 GGAATTGGAATCTGTCAA
1141339 GGAATTGGAATCTGTCAA
1 GGAATTGGAATCTGTCAA
1141357 -GAATTGGAATC
1 GGAATTGGAATC
1141368 CAATTCCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTCAA
Found at i:1142094 original size:270 final size:258
Alignment explanation
Indices: 1141731--1142516 Score: 1031
Period size: 270 Copynumber: 3.0 Consensus size: 258
1141721 ACCCGACTTG
* *
1141731 ACCAAAATAAAGTTTCACCCGACTCAACCCGAATATATGAATT----ACCCGACCCGAAATAAT-
1 ACCAAAATAAAGTTT---CCGACCCGACCCGAATATATGAATTAGAAACCCGACCCGAAATAATA
* *
1141791 TAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATTATATATAGAGGGGTAT
63 AAAAAATTATTTTTATTCAATAAAAATAGTGACTTAATTGAAAAAAATTATATATAGAGGGGTAT
* * *
1141856 TATTGTAATTATTCCTAAAAATATAAGGTAAAATTATATATTTTTTCGGGACAGGTCGGGTCAGG
128 TATTGTAATTATTTCTAAATATATAAGGTAAAATTATATATTTTTTCGGG-C-GGTCGGGTCGGG
* *
1141921 TATTTTTCACCATAAACCCAAACTCGACCCGACCCGAATATCACACTTAAAAAAAACTGACCCGA
191 TATTTTTCACCATAAACTCGAACTCGACCCGACCCGAATATCACACTTAAAAAAAAC-GACCCGA
1141986 CCCA
255 CCCA
1141990 ACCAAAATAAAGTTT-C-ACCCGACCCGAATATATGAATTAGAAACCCGATCCGACTCAACCCGA
1 ACCAAAATAAAGTTTCCGACCCGACCCGAATATATGAATTAGAAA--C---CCG-----ACCCGA
1142053 AATAATAAAAAAAATTATTTTTATTCAATAAAAATAGTGACTTAATTGAAAAAAATTATATATAG
56 AATAAT-AAAAAAATTATTTTTATTCAATAAAAATAGTGACTTAATTGAAAAAAATTATATATAG
1142118 AGGGGTATTATTGTAATTATTTCTAAATATATAAGGTAAAATTATATATTTTTT-GGGTCGGGTC
120 AGGGGTATTATTGTAATTATTTCTAAATATATAAGGTAAAATTATATATTTTTTCGGG-C-GGTC
* *
1142182 GAGTCGGGTATTTTTCACCATAAACTCGAACCCGACCCGACCCGAATATCACACTT-AAAAAAAC
183 GGGTCGGGTATTTTTCACCATAAACTCGAACTCGACCCGACCCGAATATCACACTTAAAAAAAAC
* * **
1142246 CAACCGACCTG
248 GACCCGACCCA
*
1142257 ACCAAATTAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGACCCGAAATAATA
1 ACCAAAATAAAGTTT---CCGACCCGACCCGAATATATGAATTAGAAACCCGACCCGAAATAATA
* * *
1142322 AAAAAATTATTTGTATTCAATAAAAAATAGTAACTTAATTG-AAAAAATTATATATAGATGGGTA
63 AAAAAATTATTTTTATTCAAT-AAAAATAGTGACTTAATTGAAAAAAATTATATATAGAGGGGTA
1142386 TTATTGTAATTATTTCTAAATATATAAGGTAAAATTATATATATATTTTC--G-GGTCGGGTCGG
127 TTATTGTAATTATTTCTAAATATATAAGGTAAAATTATATAT-T-TTTTCGGGCGGTCGGGTCGG
* * ** *
1142448 GTATTTTTCACCCTAAACTCGAACTCGACTCGACCCGAATATCACTTTTAAAAAAACCCGACCCG
190 GTATTTTTCACCATAAACTCGAACTCGACCCGACCCGAATATCACACTTAAAAAAA-ACGACCCG
1142513 ACCC
254 ACCC
1142517 GAATTTTTAA
Statistics
Matches: 469, Mismatches: 31, Indels: 52
0.85 0.06 0.09
Matches are distributed among these distances:
254 20 0.04
255 1 0.00
258 1 0.00
259 69 0.15
260 7 0.01
261 93 0.20
262 32 0.07
263 7 0.01
267 24 0.05
268 20 0.04
269 59 0.13
270 108 0.23
271 1 0.00
272 27 0.06
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.29
Consensus pattern (258 bp):
ACCAAAATAAAGTTTCCGACCCGACCCGAATATATGAATTAGAAACCCGACCCGAAATAATAAAA
AAATTATTTTTATTCAATAAAAATAGTGACTTAATTGAAAAAAATTATATATAGAGGGGTATTAT
TGTAATTATTTCTAAATATATAAGGTAAAATTATATATTTTTTCGGGCGGTCGGGTCGGGTATTT
TTCACCATAAACTCGAACTCGACCCGACCCGAATATCACACTTAAAAAAAACGACCCGACCCA
Found at i:1145986 original size:2 final size:2
Alignment explanation
Indices: 1145979--1146006 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1145969 ATAAAAGTGA
1145979 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
1146007 CTTTTAGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1150275 original size:29 final size:29
Alignment explanation
Indices: 1150241--1150299 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1150231 CCTAAATTAA
1150241 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1150270 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1150299 T
1 T
1150300 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1154964 original size:29 final size:29
Alignment explanation
Indices: 1154930--1154988 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1154920 CCTAAATTAA
1154930 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1154959 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1154988 T
1 T
1154989 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1165602 original size:21 final size:22
Alignment explanation
Indices: 1165578--1165658 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 22
1165568 TTTAGTGAGA
*
1165578 GGGAATCGATACCCC-TTGAAG
1 GGGAATCGATACCCCTTTAAAG
* *
1165599 GGGAACCGATTCCCCCTTTAAAG
1 GGGAATCGA-TACCCCTTTAAAG
* ***
1165622 GGGAATCGATTCCCCCCCACAA-
1 GGGAATCGATACCCCTTTA-AAG
1165644 GGGAATCGATACCCC
1 GGGAATCGATACCCC
1165659 CTGAGGGTTA
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
21 8 0.17
22 25 0.52
23 15 0.31
ACGTcount: A:0.27, C:0.32, G:0.23, T:0.17
Consensus pattern (22 bp):
GGGAATCGATACCCCTTTAAAG
Found at i:1165645 original size:23 final size:23
Alignment explanation
Indices: 1165596--1165660 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
1165586 ATACCCCTTG
* **
1165596 AAGGGGAACCGATTCCCCCTTTA
1 AAGGGGAATCGATTCCCCCTCCA
1165619 AAGGGGAATCGATTCCCCC-CCA
1 AAGGGGAATCGATTCCCCCTCCA
*
1165641 CAA-GGGAATCGATACCCCCT
1 -AAGGGGAATCGATTCCCCCT
1165661 GAGGGTTATG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 16 0.44
23 20 0.56
ACGTcount: A:0.28, C:0.34, G:0.22, T:0.17
Consensus pattern (23 bp):
AAGGGGAATCGATTCCCCCTCCA
Found at i:1170410 original size:31 final size:31
Alignment explanation
Indices: 1170375--1170439 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1170365 TTAATTGTTA
* *
1170375 AGGGATTAAAATCTAAC-TGATCGATAACGTT
1 AGGGACTAAAATCAAACGT-ATCGATAACGTT
1170406 AGGGACTAAAATCAAACGTATCGATAACGTT
1 AGGGACTAAAATCAAACGTATCGATAACGTT
1170437 AGG
1 AGG
1170440 ACCATGTACC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.25
Consensus pattern (31 bp):
AGGGACTAAAATCAAACGTATCGATAACGTT
Found at i:1188951 original size:104 final size:104
Alignment explanation
Indices: 1188771--1188978 Score: 416
Period size: 104 Copynumber: 2.0 Consensus size: 104
1188761 TTATCTTTTG
1188771 ATTCTTCAATGGAATATACGACATAATCAAACTTTGGTGTCAGCGAACGCAATATCTTTTTAACA
1 ATTCTTCAATGGAATATACGACATAATCAAACTTTGGTGTCAGCGAACGCAATATCTTTTTAACA
1188836 ATGGTGACATCTTCCATCTTCTCACTATGAAAGTGCATT
66 ATGGTGACATCTTCCATCTTCTCACTATGAAAGTGCATT
1188875 ATTCTTCAATGGAATATACGACATAATCAAACTTTGGTGTCAGCGAACGCAATATCTTTTTAACA
1 ATTCTTCAATGGAATATACGACATAATCAAACTTTGGTGTCAGCGAACGCAATATCTTTTTAACA
1188940 ATGGTGACATCTTCCATCTTCTCACTATGAAAGTGCATT
66 ATGGTGACATCTTCCATCTTCTCACTATGAAAGTGCATT
1188979 TTGTTACTAT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (104 bp):
ATTCTTCAATGGAATATACGACATAATCAAACTTTGGTGTCAGCGAACGCAATATCTTTTTAACA
ATGGTGACATCTTCCATCTTCTCACTATGAAAGTGCATT
Found at i:1197597 original size:24 final size:25
Alignment explanation
Indices: 1197556--1197602 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1197546 CTCAAAAAAA
1197556 AAAATTAGAAGCTCGATTGAAGTCT
1 AAAATTAGAAGCTCGATTGAAGTCT
* *
1197581 AAAATTCG-AGCTTGATTGAAGT
1 AAAATTAGAAGCTCGATTGAAGT
1197603 GAAATAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (25 bp):
AAAATTAGAAGCTCGATTGAAGTCT
Found at i:1197963 original size:69 final size:69
Alignment explanation
Indices: 1197890--1198029 Score: 271
Period size: 69 Copynumber: 2.0 Consensus size: 69
1197880 ATTTAATATA
*
1197890 TTTTACCTTAAATATTATGTTGTAGTTAATTTGAATCATTTTGTTTCACTTGGTTTTATGGTTTT
1 TTTTAACTTAAATATTATGTTGTAGTTAATTTGAATCATTTTGTTTCACTTGGTTTTATGGTTTT
1197955 TAAC
66 TAAC
1197959 TTTTAACTTAAATATTATGTTGTAGTTAATTTGAATCATTTTGTTTCACTTGGTTTTATGGTTTT
1 TTTTAACTTAAATATTATGTTGTAGTTAATTTGAATCATTTTGTTTCACTTGGTTTTATGGTTTT
1198024 TAAC
66 TAAC
1198028 TT
1 TT
1198030 ATATATGTTA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.24, C:0.08, G:0.13, T:0.56
Consensus pattern (69 bp):
TTTTAACTTAAATATTATGTTGTAGTTAATTTGAATCATTTTGTTTCACTTGGTTTTATGGTTTT
TAAC
Found at i:1198670 original size:21 final size:21
Alignment explanation
Indices: 1198640--1198717 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 21
1198630 GATTTACATA
*
1198640 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
1198661 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
1198682 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
1198703 TT--CGTTGCGATAGTC
1 TTCGCGTTGCGATAGTC
1198718 GACGACCACG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
19 11 0.22
21 38 0.78
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.33
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:1198730 original size:6 final size:6
Alignment explanation
Indices: 1198719--1198746 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1198709 GCGATAGTCG
1198719 ACGACC ACGACC ACGACC ACGACC ACGA
1 ACGACC ACGACC ACGACC ACGACC ACGA
1198747 GACGAGACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.46, G:0.18, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:1199365 original size:21 final size:21
Alignment explanation
Indices: 1199339--1199534 Score: 201
Period size: 21 Copynumber: 9.4 Consensus size: 21
1199329 ATTTTGGACT
1199339 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
1199360 ATCGCAACGCGAACTTAGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
1199381 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
1199402 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
1199423 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
1199444 ATCGCAATGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
1199465 ATCGCAACGAATTTGG-A-AA
1 ATCGCAACGAATTTGGAATAA
* *
1199484 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAATTTGGAATAA
1199505 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
1199526 ATCGCAACG
1 ATCGCAACG
1199535 CGAACTTCGA
Statistics
Matches: 145, Mismatches: 16, Indels: 28
0.77 0.08 0.15
Matches are distributed among these distances:
19 34 0.23
21 93 0.64
23 18 0.12
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:1199382 original size:42 final size:42
Alignment explanation
Indices: 1199335--1199595 Score: 390
Period size: 42 Copynumber: 6.3 Consensus size: 42
1199325 TGCGATTTTG
*
1199335 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
1199377 GACTATCGCAACGAACTTGGAATAAATCGCAA--CGAATTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
1199417 GAATAAATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTC
1 GACT--ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1199461 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1199501 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1199543 GACTATTGCAACGAATTT-GAA-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1199583 GACTATCGCAACG
1 GACTATCGCAACG
1199596 CGAACTTGGA
Statistics
Matches: 200, Mismatches: 13, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
40 77 0.38
41 5 0.03
42 109 0.55
44 9 0.05
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:1199538 original size:82 final size:82
Alignment explanation
Indices: 1199332--1199595 Score: 406
Period size: 82 Copynumber: 3.2 Consensus size: 82
1199322 AAATGCGATT
* *
1199332 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTAGACTATCGCAACGAACTTGG
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGG
*
1199397 AATAAATCGCAA--CGAAT
66 -A-AAATCGCAACGCGAAC
* *
1199414 TTGGAATAAATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGACTATCGCAACGAATTT
1 TTGGACT--ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTT
1199479 GGAAAATCGCAACGCGAAC
64 GGAAAATCGCAACGCGAAC
* *
1199498 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATTGCAACGAATTTGA
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGG
1199563 AAAATCGCAACGCGAAC
66 AAAATCGCAACGCGAAC
*
1199580 TTCGACTATCGCAACG
1 TTGGACTATCGCAACG
1199596 CGAACTTGGA
Statistics
Matches: 168, Mismatches: 10, Indels: 8
0.90 0.05 0.04
Matches are distributed among these distances:
82 102 0.61
83 1 0.01
84 65 0.39
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (82 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGG
AAAATCGCAACGCGAAC
Found at i:1199553 original size:21 final size:21
Alignment explanation
Indices: 1199332--1199620 Score: 183
Period size: 21 Copynumber: 14.0 Consensus size: 21
1199322 AAATGCGATT
*
1199332 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
1199351 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
1199374 TTAGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
* *
1199393 TTGGAATAAATCGCAA--CGAAT
1 TTGGACT--ATCGCAACGCGAAC
* *
1199414 TTGGAATAAATCGCAA--CGAAT
1 TTGGACT--ATCGCAACGCGAAC
* *
1199435 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
1199458 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
**
1199477 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
1199498 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
1199517 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* * *
1199540 TTCGACTATTGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* **
1199559 TTGAAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
1199580 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
1199601 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAACGCGAA
1199621 TATGTAAATC
Statistics
Matches: 218, Mismatches: 36, Indels: 30
0.77 0.13 0.11
Matches are distributed among these distances:
19 54 0.25
21 137 0.63
23 27 0.12
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:1204504 original size:20 final size:20
Alignment explanation
Indices: 1204466--1204543 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
1204456 AATTGTCCAA
*
1204466 GGGGTACAGATTCTTCCCCAG
1 GGGGTACAGATTC-CCCCCAG
*
1204487 GGGGTACAGATTCCCCCCAA
1 GGGGTACAGATTCCCCCCAG
* * *
1204507 GGGGAATAGATTCCCCCTAG
1 GGGGTACAGATTCCCCCCAG
*
1204527 GGGGTACTGATTCCCCC
1 GGGGTACAGATTCCCCC
1204544 TGTCTAACGG
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
20 35 0.73
21 13 0.27
ACGTcount: A:0.21, C:0.31, G:0.28, T:0.21
Consensus pattern (20 bp):
GGGGTACAGATTCCCCCCAG
Found at i:1204539 original size:40 final size:40
Alignment explanation
Indices: 1204462--1204543 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
1204452 ATCAAATTGT
*
1204462 CCAAGGGGTACAGATTCTTCCCCAGGGGGTACAGATTCCCC
1 CCAAGGGGAACAGATTC-TCCCCAGGGGGTACAGATTCCCC
* *
1204503 CCAAGGGGAATAGATTC-CCCCTAGGGGGTACTGATTCCCC
1 CCAAGGGGAACAGATTCTCCCC-AGGGGGTACAGATTCCCC
1204543 C
1 C
1204544 TGTCTAACGG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 4 0.11
40 18 0.49
41 15 0.41
ACGTcount: A:0.22, C:0.32, G:0.27, T:0.20
Consensus pattern (40 bp):
CCAAGGGGAACAGATTCTCCCCAGGGGGTACAGATTCCCC
Found at i:1206479 original size:17 final size:17
Alignment explanation
Indices: 1206457--1206497 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
1206447 ATATTGCATA
1206457 AAGTATTTTAGACTTGG
1 AAGTATTTTAGACTTGG
1206474 AAGTATTTTAGACTTGG
1 AAGTATTTTAGACTTGG
1206491 AAGTATT
1 AAGTATT
1206498 GAATTTCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (17 bp):
AAGTATTTTAGACTTGG
Found at i:1209527 original size:14 final size:14
Alignment explanation
Indices: 1209508--1209539 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1209498 CTATTCAAAC
*
1209508 CGGGTTGACCGGTT
1 CGGGTTGACCAGTT
1209522 CGGGTTGACCAGTT
1 CGGGTTGACCAGTT
1209536 CGGG
1 CGGG
1209540 CTAGTCCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.22, G:0.44, T:0.25
Consensus pattern (14 bp):
CGGGTTGACCAGTT
Found at i:1221419 original size:39 final size:39
Alignment explanation
Indices: 1221373--1221457 Score: 170
Period size: 39 Copynumber: 2.2 Consensus size: 39
1221363 CCCCACTAAA
1221373 GAGCCTACCTATGCTTTTTCCCCTTAGCTAACCACTTTT
1 GAGCCTACCTATGCTTTTTCCCCTTAGCTAACCACTTTT
1221412 GAGCCTACCTATGCTTTTTCCCCTTAGCTAACCACTTTT
1 GAGCCTACCTATGCTTTTTCCCCTTAGCTAACCACTTTT
1221451 GAGCCTA
1 GAGCCTA
1221458 TTCTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.19, C:0.33, G:0.12, T:0.36
Consensus pattern (39 bp):
GAGCCTACCTATGCTTTTTCCCCTTAGCTAACCACTTTT
Found at i:1221449 original size:21 final size:21
Alignment explanation
Indices: 1221386--1221450 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1221376 CCTACCTATG
1221386 CTTTTTCCCCTTAGCTAACCA
1 CTTTTTCCCCTTAGCTAACCA
*** * **
1221407 CTTTTGAGCC-TACCT-A-TG
1 CTTTTTCCCCTTAGCTAACCA
1221425 CTTTTTCCCCTTAGCTAACCA
1 CTTTTTCCCCTTAGCTAACCA
1221446 CTTTT
1 CTTTT
1221451 GAGCCTATTC
Statistics
Matches: 29, Mismatches: 12, Indels: 6
0.62 0.26 0.13
Matches are distributed among these distances:
18 7 0.24
19 5 0.17
20 5 0.17
21 12 0.41
ACGTcount: A:0.17, C:0.34, G:0.08, T:0.42
Consensus pattern (21 bp):
CTTTTTCCCCTTAGCTAACCA
Found at i:1221619 original size:17 final size:17
Alignment explanation
Indices: 1221595--1221641 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
1221585 AAAGGAAGAA
1221595 GAAAAAAAACAGCA-GTTC
1 GAAAAAAAA-AG-ATGTTC
1221613 GAAAAAAAAAGATGTTC
1 GAAAAAAAAAGATGTTC
*
1221630 GAAAGAAAAAGA
1 GAAAAAAAAAGA
1221642 AAGAGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 1 0.04
17 17 0.63
18 9 0.33
ACGTcount: A:0.62, C:0.09, G:0.19, T:0.11
Consensus pattern (17 bp):
GAAAAAAAAAGATGTTC
Found at i:1224292 original size:18 final size:18
Alignment explanation
Indices: 1224266--1224308 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1224256 TGACTTTTTC
*
1224266 GGTCAAAGTCAATGAGTCG
1 GGTC-AAGTCAACGAGTCG
*
1224285 GGTCAAGTCAACGGGTCG
1 GGTCAAGTCAACGAGTCG
1224303 GGTCAA
1 GGTCAA
1224309 AGGGGTTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.28, C:0.19, G:0.35, T:0.19
Consensus pattern (18 bp):
GGTCAAGTCAACGAGTCG
Found at i:1226219 original size:21 final size:21
Alignment explanation
Indices: 1226193--1226237 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1226183 GGATTTTCAA
1226193 TATCGAAACATTTCCATCCAG
1 TATCGAAACATTTCCATCCAG
*
1226214 TATCGAAACATTTCCATCCGG
1 TATCGAAACATTTCCATCCAG
1226235 TAT
1 TAT
1226238 TGAGACCGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (21 bp):
TATCGAAACATTTCCATCCAG
Found at i:1229455 original size:14 final size:14
Alignment explanation
Indices: 1229436--1229489 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
1229426 TAACCGGTTT
1229436 CGGTTTTAAAAAAC
1 CGGTTTTAAAAAAC
*
1229450 CGGTTTTTTTAAAAAAT
1 CGG---TTTTAAAAAAC
*
1229467 CGGTTATAAAAAAC
1 CGGTTTTAAAAAAC
*
1229481 CGATTTTAA
1 CGGTTTTAA
1229490 TATTATTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 19 0.59
17 13 0.41
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (14 bp):
CGGTTTTAAAAAAC
Found at i:1229461 original size:17 final size:17
Alignment explanation
Indices: 1229439--1229471 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1229429 CCGGTTTCGG
1229439 TTTTAAAAAACCGGTTT
1 TTTTAAAAAACCGGTTT
*
1229456 TTTTAAAAAATCGGTT
1 TTTTAAAAAACCGGTT
1229472 ATAAAAAACC
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:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (17 bp):
TTTTAAAAAACCGGTTT
Found at i:1229871 original size:65 final size:65
Alignment explanation
Indices: 1229767--1229897 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
1229757 GGTGACCAAA
1229767 ATGTAACGTTAAGTATGATTTTGAAACAAAAAATAGTTGGACGACCAAAACGAAATAAAAGTGAT
1 ATGTAACGTTAAGTATGATTTTGAAACAAAAAATAGTTGGACGACCAAAACGAAATAAAAGTGAT
1229832 ATGTAACGTTAAGTATGATTTTGAAACAAAAAATAGTTGGACGACCAAAACGAAATAAAAGTGAT
1 ATGTAACGTTAAGTATGATTTTGAAACAAAAAATAGTTGGACGACCAAAACGAAATAAAAGTGAT
1229897 A
1 A
1229898 ATTGGGTACT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.24
Consensus pattern (65 bp):
ATGTAACGTTAAGTATGATTTTGAAACAAAAAATAGTTGGACGACCAAAACGAAATAAAAGTGAT
Found at i:1244993 original size:33 final size:33
Alignment explanation
Indices: 1244928--1245017 Score: 107
Period size: 33 Copynumber: 2.8 Consensus size: 33
1244918 ATATATCACA
* **
1244928 AAATTGAAGTGATATATCA-TTGAAAATATCAT
1 AAATTGAAGTGATATAACACTAAAAAATATCAT
1244960 AGAATTGAAGTGATATAACACTAAAAAAT-TCAT
1 A-AATTGAAGTGATATAACACTAAAAAATATCAT
1244993 AAA-TGAAGTGAT-TGAACACTAAAAA
1 AAATTGAAGTGATAT-AACACTAAAAA
1245018 GATTTTGTCA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
30 1 0.02
31 20 0.38
32 3 0.06
33 22 0.42
34 6 0.12
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.28
Consensus pattern (33 bp):
AAATTGAAGTGATATAACACTAAAAAATATCAT
Found at i:1249917 original size:35 final size:35
Alignment explanation
Indices: 1249876--1249955 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
1249866 AACACAATCA
*
1249876 TCAATTACATTTTAAACCCCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
* *
1249911 TCAATTACATTCTAAACCTCAAATTCTAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
1249946 TCAATTACAT
1 TCAATTACAT
1249956 GCCCAACTCC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.34
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAATACT
Found at i:1262204 original size:35 final size:35
Alignment explanation
Indices: 1262094--1262282 Score: 175
Period size: 35 Copynumber: 5.3 Consensus size: 35
1262084 AAATATAGTA
* * *
1262094 TTTG-AAATATATAATATATAGTTTTTGGAAACTTACT
1 TTTGAAAACATATAATATATAGTTTTT-AAAAC--AAT
* *
1262131 TTT-AAAAAATGTATAATATATAGTTTTTAAAACCAT
1 TTTGAAAACA--TATAATATATAGTTTTTAAAACAAT
* * * *
1262167 TTTGAAAACATATATTAAATAGTTTTTAAGATAAT
1 TTTGAAAACATATAATATATAGTTTTTAAAACAAT
* *
1262202 TTTGAAAACGTATAATATATAGTTTTTAAAACAGT
1 TTTGAAAACATATAATATATAGTTTTTAAAACAAT
* * * **
1262237 TTTGAAAACGTATAATATATAATTTTTAAATCGGT
1 TTTGAAAACATATAATATATAGTTTTTAAAACAAT
1262272 TTTGAAAACAT
1 TTTGAAAACAT
1262283 TTTTTAAAAA
Statistics
Matches: 128, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
35 91 0.71
36 4 0.03
37 12 0.09
38 4 0.03
39 17 0.13
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (35 bp):
TTTGAAAACATATAATATATAGTTTTTAAAACAAT
Found at i:1262386 original size:16 final size:16
Alignment explanation
Indices: 1262356--1262394 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1262346 AGTAAAATAT
*
1262356 ATTTT-TTTCTTTTTC
1 ATTTTATTTCTATTTC
*
1262371 TTTTTATTTCTATTTC
1 ATTTTATTTCTATTTC
1262387 ATTTTATT
1 ATTTTATT
1262395 ATTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTTTATTTCTATTTC
Found at i:1262412 original size:16 final size:13
Alignment explanation
Indices: 1262381--1262432 Score: 52
Period size: 13 Copynumber: 3.7 Consensus size: 13
1262371 TTTTTATTTC
1262381 TATTTCATT-TTAT
1 TATTT-ATTATTAT
1262394 TATTTATATATTAGGT
1 TATTTAT-TATTA--T
1262410 TATATTATTATTAT
1 TAT-TTATTATTAT
1262424 TATTTATTA
1 TATTTATTA
1262433 CTTAATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 2 0.06
13 12 0.35
14 7 0.21
16 9 0.26
17 4 0.12
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (13 bp):
TATTTATTATTAT
Found at i:1263597 original size:10 final size:11
Alignment explanation
Indices: 1263572--1263597 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1263562 ATCCTTTAAA
1263572 TTTTTTATTTC
1 TTTTTTATTTC
1263583 TTTTTTATTTC
1 TTTTTTATTTC
1263594 TTTT
1 TTTT
1263598 AAAATTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTATTTC
Found at i:1264163 original size:13 final size:13
Alignment explanation
Indices: 1264145--1264170 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1264135 GTAGTGAAAT
1264145 TAACTTAAATGAC
1 TAACTTAAATGAC
1264158 TAACTTAAATGAC
1 TAACTTAAATGAC
1264171 ATCCTAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TAACTTAAATGAC
Found at i:1264629 original size:23 final size:24
Alignment explanation
Indices: 1264584--1264629 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1264574 GTTCATGAAT
1264584 ATGTTCGTGAACATATAAACGAAC
1 ATGTTCGTGAACATATAAACGAAC
1264608 ATGTTCGCT-AACAT-TAAACGAA
1 ATGTTCG-TGAACATATAAACGAA
1264630 TGCTAAACGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.26
Consensus pattern (24 bp):
ATGTTCGTGAACATATAAACGAAC
Found at i:1268490 original size:35 final size:35
Alignment explanation
Indices: 1268444--1268555 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
1268434 AAAATAGTCC
* * *
1268444 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCAAAATTCCAAAATAAT
*
1268479 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCAAAATTCCAAAATAAT
** * *
1268514 TCAATTAAATTCTAAACCCAAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCAAAATTCCAAAATAAT
1268549 TCAATTT
1 TCAATTT
1268556 AAGGTTTAGA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCAAAATTCCAAAATAAT
Found at i:1270364 original size:35 final size:35
Alignment explanation
Indices: 1270324--1270435 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
1270314 TCTAAACCTT
* * * *
1270324 AAATTGAAGTATTTTAGAATTTGGGGTTTATAATT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATA
* *
1270359 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATA
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATA
* *
1270394 AAATTGAATTATTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATA
1270429 AAATTGA
1 AAATTGA
1270436 GGACTATTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAGAATA
Found at i:1270786 original size:22 final size:22
Alignment explanation
Indices: 1270761--1270830 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
1270751 ATAAACATCA
*
1270761 AATACAATAAATAATATTATTT
1 AATAAAATAAATAATATTATTT
* *
1270783 AATAAAAATTAATAATAAT-TTT
1 AAT-AAAATAAATAATATTATTT
*
1270805 AA-AATATTAGAATAAT-TTATTT
1 AATAA-AATA-AATAATATTATTT
1270827 AATA
1 AATA
1270831 TTATTTATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
20 2 0.05
21 3 0.08
22 19 0.51
23 13 0.35
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (22 bp):
AATAAAATAAATAATATTATTT
Found at i:1271058 original size:22 final size:22
Alignment explanation
Indices: 1271009--1271089 Score: 112
Period size: 22 Copynumber: 3.7 Consensus size: 22
1270999 AGTTTCCAAA
* *
1271009 TTCGCAACACATAATTTG-GAA-
1 TTCGCAACAC-GAATTTGACAAT
*
1271030 TTCGCAACTCGAATTTGACAAT
1 TTCGCAACACGAATTTGACAAT
1271052 TTCGCAACACGAATTTGACAAT
1 TTCGCAACACGAATTTGACAAT
1271074 TTCGCAACACGAATTT
1 TTCGCAACACGAATTT
1271090 CTTTTTCGCA
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
20 6 0.11
21 11 0.20
22 37 0.69
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (22 bp):
TTCGCAACACGAATTTGACAAT
Found at i:1271129 original size:40 final size:40
Alignment explanation
Indices: 1271051--1271160 Score: 123
Period size: 40 Copynumber: 2.7 Consensus size: 40
1271041 AATTTGACAA
* * * *
1271051 TTTCGCAACACGAATTTGACAATTTCGCAACACGAATTTCTT
1 TTTCGCAACACGATTTTTA-AA-TTCGCAACACAAATTTCCT
* *
1271093 TTTCGCAACTCGATTTTTAAATTCGCAATACAAATTTCCT
1 TTTCGCAACACGATTTTTAAATTCGCAACACAAATTTCCT
*
1271133 TTTCGCAACAAGATTTTCT-AATTCGCAA
1 TTTCGCAACACGATTTT-TAAATTCGCAA
1271161 AGCGCGTTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
40 40 0.68
41 3 0.05
42 16 0.27
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (40 bp):
TTTCGCAACACGATTTTTAAATTCGCAACACAAATTTCCT
Found at i:1271190 original size:20 final size:20
Alignment explanation
Indices: 1271030--1271236 Score: 78
Period size: 20 Copynumber: 10.2 Consensus size: 20
1271020 TAATTTGGAA
* *
1271030 TTCGCAACTCGAATTTGACAAT
1 TTCGCAACGCGAATTT--TAAT
* *
1271052 TTCGCAACACGAATTTGACAAT
1 TTCGCAACGCGAATTT--TAAT
* *
1271074 TTCGCAACACGAATTTCT-TT
1 TTCGCAACGCGAATTT-TAAT
* * *
1271094 TTCGCAACTCGATTTTTAAA
1 TTCGCAACGCGAATTTTAAT
** * ***
1271114 TTCGCAATACAAATTTCCTT
1 TTCGCAACGCGAATTTTAAT
** *
1271134 TTCGCAACAAGATTTTCTAA-
1 TTCGCAACGCGAATTT-TAAT
* **
1271154 TTCGCAAAGCGCGTTTTAAT
1 TTCGCAACGCGAATTTTAAT
* *
1271174 TTCGTAACGCGAATTTTATT
1 TTCGCAACGCGAATTTTAAT
* * *
1271194 TTTGCAACTCGAATTTCGAA-
1 TTCGCAACGCGAATTT-TAAT
* *
1271214 TTCGCAAGGCGAATTTAAAT
1 TTCGCAACGCGAATTTTAAT
1271234 TTC
1 TTC
1271237 AAAAACCAGC
Statistics
Matches: 138, Mismatches: 42, Indels: 12
0.72 0.22 0.06
Matches are distributed among these distances:
19 6 0.04
20 94 0.68
21 1 0.01
22 37 0.27
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (20 bp):
TTCGCAACGCGAATTTTAAT
Found at i:1271373 original size:22 final size:22
Alignment explanation
Indices: 1271348--1271402 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1271338 TCTCTCACTC
1271348 TCTCCGGCGACATCCGTCCCCA
1 TCTCCGGCGACATCCGTCCCCA
* *
1271370 TCTCTGACGACATCCGTCCCCA
1 TCTCCGGCGACATCCGTCCCCA
* *
1271392 TATTCGGCGAC
1 TCTCCGGCGAC
1271403 CCCCTCCATC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.16, C:0.44, G:0.18, T:0.22
Consensus pattern (22 bp):
TCTCCGGCGACATCCGTCCCCA
Found at i:1271781 original size:20 final size:20
Alignment explanation
Indices: 1271753--1271792 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1271743 TTTGCAACAC
1271753 GAAAATCGCAA-ATCGAAAAT
1 GAAAATCGCAACA-CGAAAAT
*
1271773 GAAATTCGCAACACGAAAAT
1 GAAAATCGCAACACGAAAAT
1271793 CACAACTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.53, C:0.17, G:0.15, T:0.15
Consensus pattern (20 bp):
GAAAATCGCAACACGAAAAT
Found at i:1271784 original size:34 final size:34
Alignment explanation
Indices: 1271740--1271814 Score: 123
Period size: 34 Copynumber: 2.2 Consensus size: 34
1271730 CATAAAACTT
* *
1271740 AAATTTGCAACACGAAAATCGCAAATCGAAAATG
1 AAATTCGCAACACGAAAATCACAAATCGAAAATG
*
1271774 AAATTCGCAACACGAAAATCACAACTCGAAAATG
1 AAATTCGCAACACGAAAATCACAAATCGAAAATG
1271808 AAATTCG
1 AAATTCG
1271815 AGTTGTGAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.49, C:0.20, G:0.13, T:0.17
Consensus pattern (34 bp):
AAATTCGCAACACGAAAATCACAAATCGAAAATG
Found at i:1271833 original size:20 final size:20
Alignment explanation
Indices: 1271808--1271845 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1271798 CTCGAAAATG
* *
1271808 AAATTCGAGTTGTGAATTCA
1 AAATTCGACTTGCGAATTCA
1271828 AAATTCGACTTGCGAATT
1 AAATTCGACTTGCGAATT
1271846 TCATTTTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (20 bp):
AAATTCGACTTGCGAATTCA
Found at i:1271860 original size:20 final size:20
Alignment explanation
Indices: 1271837--1271901 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
1271827 AAAATTCGAC
1271837 TTGCGAATTTCATTTTTGAG
1 TTGCGAATTTCATTTTTGAG
*
1271857 TTGCGATTTTCA----T--G
1 TTGCGAATTTCATTTTTGAG
*
1271871 TTGTGAATTTCATTTTTGAG
1 TTGCGAATTTCATTTTTGAG
*
1271891 TTGCGATTTTC
1 TTGCGAATTTC
1271902 GTGTTGCGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 12
0.67 0.10 0.24
Matches are distributed among these distances:
14 11 0.32
16 1 0.03
18 1 0.03
20 21 0.62
ACGTcount: A:0.17, C:0.11, G:0.20, T:0.52
Consensus pattern (20 bp):
TTGCGAATTTCATTTTTGAG
Found at i:1271884 original size:34 final size:34
Alignment explanation
Indices: 1271837--1271914 Score: 138
Period size: 34 Copynumber: 2.3 Consensus size: 34
1271827 AAAATTCGAC
1271837 TTGCGAATTTCATTTTTGAGTTGCGATTTTCATG
1 TTGCGAATTTCATTTTTGAGTTGCGATTTTCATG
* *
1271871 TTGTGAATTTCATTTTTGAGTTGCGATTTTCGTG
1 TTGCGAATTTCATTTTTGAGTTGCGATTTTCATG
1271905 TTGCGAATTT
1 TTGCGAATTT
1271915 AAGTTTCAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.17, C:0.10, G:0.22, T:0.51
Consensus pattern (34 bp):
TTGCGAATTTCATTTTTGAGTTGCGATTTTCATG
Found at i:1273369 original size:42 final size:42
Alignment explanation
Indices: 1273310--1273475 Score: 205
Period size: 42 Copynumber: 4.0 Consensus size: 42
1273300 CCCCACTTTT
*
1273310 TCATCGAGTCGATTCTCCACTTCGACACCGAGATCCATCACC
1 TCATCGAGTCGATTCTACACTTCGACACCGAGATCCATCACC
* *
1273352 TCATCGAGTCGATTCTCCACTTTGACACCGAGATCCATCACC
1 TCATCGAGTCGATTCTACACTTCGACACCGAGATCCATCACC
* * * * *
1273394 CCTTTGAGCCGATTCTACACATCGACACCGAGATCCATCACC
1 TCATCGAGTCGATTCTACACTTCGACACCGAGATCCATCACC
* *
1273436 TC-T--AG-CTGACTCTACACCTCGACACCGAGATCCATCACC
1 TCATCGAGTC-GATTCTACACTTCGACACCGAGATCCATCACC
1273475 T
1 T
1273476 ATTACATCAC
Statistics
Matches: 112, Mismatches: 11, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
38 1 0.01
39 33 0.29
41 1 0.01
42 77 0.69
ACGTcount: A:0.25, C:0.38, G:0.14, T:0.23
Consensus pattern (42 bp):
TCATCGAGTCGATTCTACACTTCGACACCGAGATCCATCACC
Found at i:1273749 original size:21 final size:21
Alignment explanation
Indices: 1273575--1273765 Score: 115
Period size: 21 Copynumber: 9.1 Consensus size: 21
1273565 ACCTCCACGG
*
1273575 GATGAGTTAGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
1273596 GATGAGGTCA-GTGCTTTACGT
1 GATGAGGT-AGGTGCTTTACGT
*
1273617 GATGAGGTTGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
** **
1273638 GATGA-CAATGGTGCATGGA-GT
1 GATGAGGTA-GGTGC-TTTACGT
*
1273659 GATAAGGTAGG-GTCTTTACGT
1 GATGAGGTAGGTG-CTTTACGT
* * **
1273680 GGTG-GTATATCTGCTTTACGT
1 GATGAG-GTAGGTGCTTTACGT
** *
1273701 GATGA-CAATGTTGCTTTACGT
1 GATGAGGTA-GGTGCTTTACGT
* *
1273722 GGTGAGGTAGCTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
* * *
1273743 GATGAGGCAAGTGCTCTACGT
1 GATGAGGTAGGTGCTTTACGT
1273764 GA
1 GA
1273766 GATTGTTTCA
Statistics
Matches: 127, Mismatches: 31, Indels: 24
0.70 0.17 0.13
Matches are distributed among these distances:
20 5 0.04
21 116 0.91
22 6 0.05
ACGTcount: A:0.20, C:0.13, G:0.34, T:0.34
Consensus pattern (21 bp):
GATGAGGTAGGTGCTTTACGT
Found at i:1273763 original size:63 final size:62
Alignment explanation
Indices: 1273584--1273765 Score: 181
Period size: 63 Copynumber: 2.9 Consensus size: 62
1273574 GGATGAGTTA
**
1273584 GGTGCTTTACGTGATGAGGTCAGTGCTTTACGTGATGAGGTTGGTGCTTTACGTGATGACAAT
1 GGTGCTTTACGTGATGAGGT-AGTGCTTTACGTGATGAGGTAAGTGCTTTACGTGATGACAAT
** * * * *
1273647 GGTGCATGGA-GTGATAAGGTAGGGTCTTTACGTG--GTGGTATATCTGCTTTACGTGATGACAA
1 GGTGC-TTTACGTGATGAGGTAGTG-CTTTACGTGATGAGGTA-A-GTGCTTTACGTGATGACAA
1273709 T
62 T
* * * *
1273710 GTTGCTTTACGTGGTGAGGTAGCTGCTTTACGTGATGAGGCAAGTGCTCTACGTGA
1 GGTGCTTTACGTGATGAGGTAG-TGCTTTACGTGATGAGGTAAGTGCTTTACGTGA
1273766 GATTGTTTCA
Statistics
Matches: 93, Mismatches: 18, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
61 4 0.04
62 5 0.05
63 76 0.82
64 4 0.04
65 4 0.04
ACGTcount: A:0.20, C:0.13, G:0.34, T:0.34
Consensus pattern (62 bp):
GGTGCTTTACGTGATGAGGTAGTGCTTTACGTGATGAGGTAAGTGCTTTACGTGATGACAAT
Found at i:1274131 original size:21 final size:21
Alignment explanation
Indices: 1274101--1274250 Score: 149
Period size: 21 Copynumber: 7.0 Consensus size: 21
1274091 AAGCTTGATT
*
1274101 CACCTACCATTGTTCAGGATC
1 CACCTCCCATTGTTCAGGATC
1274122 CACCTCCCATTGTTCAGGATC
1 CACCTCCCATTGTTCAGGATC
*
1274143 CACCTCCCATTGTTCAGGATT
1 CACCTCCCATTGTTCAGGATC
* * *
1274164 CACCTCTCATCGTTCAAGATGCC
1 CACCTCCCATTGTTCAGGAT--C
* * *
1274187 CACCCCTCCCATTATTCAAGAGGC
1 CA--CCTCCCATTGTTCAGGA-TC
**
1274211 C-CCTCCCATCATTCAGGATC
1 CACCTCCCATTGTTCAGGATC
*
1274231 CACCTCCCATCGTTCAGGAT
1 CACCTCCCATTGTTCAGGAT
1274251 TCACATTCTA
Statistics
Matches: 109, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
20 2 0.02
21 89 0.82
23 2 0.02
24 2 0.02
25 14 0.13
ACGTcount: A:0.21, C:0.39, G:0.13, T:0.27
Consensus pattern (21 bp):
CACCTCCCATTGTTCAGGATC
Found at i:1276150 original size:20 final size:20
Alignment explanation
Indices: 1276127--1276178 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1276117 TACCTTTAAG
*
1276127 AAAATCAAATTTGCAACT-CA
1 AAAATCAAATTCGCAA-TACA
* *
1276147 AAAATCGAATTCGCAATACG
1 AAAATCAAATTCGCAATACA
1276167 AAAATCAAATTC
1 AAAATCAAATTC
1276179 ACAACATGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (20 bp):
AAAATCAAATTCGCAATACA
Found at i:1276189 original size:20 final size:20
Alignment explanation
Indices: 1276126--1276191 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
1276116 CTACCTTTAA
** *
1276126 GAAAATCAAATTTGCAACTC
1 GAAAATCAAATTCACAACAC
* * * *
1276146 AAAAATCGAATTCGCAATAC
1 GAAAATCAAATTCACAACAC
*
1276166 GAAAATCAAATTCACAACAT
1 GAAAATCAAATTCACAACAC
1276186 GAAAAT
1 GAAAAT
1276192 TGCAACTCGA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.52, C:0.18, G:0.09, T:0.21
Consensus pattern (20 bp):
GAAAATCAAATTCACAACAC
Found at i:1276218 original size:20 final size:20
Alignment explanation
Indices: 1276188--1276245 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1276178 CACAACATGA
* *
1276188 AAATT-GCAACTCGATATTC
1 AAATTCGCAACTCGAAAATC
1276207 AAATTCGCAACTCGAAAATC
1 AAATTCGCAACTCGAAAATC
* *
1276227 GAATTCGCAACGCGAAAAT
1 AAATTCGCAACTCGAAAAT
1276246 GAAAATCGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 5 0.15
20 29 0.85
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.22
Consensus pattern (20 bp):
AAATTCGCAACTCGAAAATC
Found at i:1276412 original size:20 final size:20
Alignment explanation
Indices: 1276261--1276413 Score: 131
Period size: 20 Copynumber: 8.0 Consensus size: 20
1276251 TCGAAATCGA
* * *
1276261 TTTCAAGTTACGAATTTCAT
1 TTTCGAGTTGCGAATTTGAT
1276281 TTTCGAGTTGCGAATTAT-AT
1 TTTCGAGTTGCGAATT-TGAT
* * *
1276301 TTTCGACTTGCGAATTTTAA
1 TTTCGAGTTGCGAATTTGAT
*
1276321 TATCGAGTTGC------GAT
1 TTTCGAGTTGCGAATTTGAT
* * *
1276335 TTTAGTGTTGCGAATTTGAG
1 TTTCGAGTTGCGAATTTGAT
* *
1276355 TTTCGAATTGCGAATTCGAT
1 TTTCGAGTTGCGAATTTGAT
*
1276375 TTCCGAGTTGCGAATTTGAT
1 TTTCGAGTTGCGAATTTGAT
1276395 TTTCGAGTTGCGAATTTGA
1 TTTCGAGTTGCGAATTTGA
1276414 ACTAGGCAAA
Statistics
Matches: 104, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
14 9 0.09
19 1 0.01
20 93 0.89
21 1 0.01
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (20 bp):
TTTCGAGTTGCGAATTTGAT
Found at i:1276664 original size:11 final size:11
Alignment explanation
Indices: 1276646--1276694 Score: 80
Period size: 11 Copynumber: 4.5 Consensus size: 11
1276636 GTATACATCC
1276646 ACACATAAAAT
1 ACACATAAAAT
*
1276657 ATACATAAAAT
1 ACACATAAAAT
*
1276668 ACACATAAAAC
1 ACACATAAAAT
1276679 ACACATAAAAT
1 ACACATAAAAT
1276690 ACACA
1 ACACA
1276695 CAAAGTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.63, C:0.20, G:0.00, T:0.16
Consensus pattern (11 bp):
ACACATAAAAT
Found at i:1276846 original size:18 final size:18
Alignment explanation
Indices: 1276823--1276863 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1276813 AGGTGAAGGC
1276823 GATTTTGATTGAGATTTT
1 GATTTTGATTGAGATTTT
*
1276841 GATTTTGATTGCGATTTT
1 GATTTTGATTGAGATTTT
1276859 GATTT
1 GATTT
1276864 CCCTTTGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.02, G:0.22, T:0.56
Consensus pattern (18 bp):
GATTTTGATTGAGATTTT
Found at i:1278976 original size:24 final size:24
Alignment explanation
Indices: 1278916--1278976 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
1278906 ATCATTAAAA
* *
1278916 TCCGAGTATTGACCAAGATCAAAG
1 TCCGAATACTGACCAAGATCAAAG
** * *
1278940 TCCGGTTATTGACCAAGATCAAAT
1 TCCGAATACTGACCAAGATCAAAG
*
1278964 TTCGAATACTGAC
1 TCCGAATACTGAC
1278977 TAGTACTCAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (24 bp):
TCCGAATACTGACCAAGATCAAAG
Found at i:1279922 original size:20 final size:20
Alignment explanation
Indices: 1279872--1279927 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
1279862 TACCCAAAAT
1279872 ATTTGTGTTG-TGAAATTAAA
1 ATTTGTGTTGCT-AAATTAAA
** *
1279892 AGCTGTTTTGCTAAATTAAA
1 ATTTGTGTTGCTAAATTAAA
1279912 ATTTGTGTTGC-AAATT
1 ATTTGTGTTGCTAAATT
1279928 CGAAAATCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 5 0.17
20 23 0.79
21 1 0.03
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (20 bp):
ATTTGTGTTGCTAAATTAAA
Found at i:1280034 original size:40 final size:41
Alignment explanation
Indices: 1279998--1280087 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 41
1279988 AGAAAATCTT
*
1279998 GTTGCGAAAAGGAAACTT-GTGTTGC-AAATTTAAAAATCGA
1 GTTGCGAAAAAGAAA-TTCGTGTTGCGAAATTTAAAAATCGA
* * *
1280038 GTTGCGAAAAAGAAATTCGTGTTGCGAAATTGTCATATTCGA
1 GTTGCGAAAAAGAAATTCGTGTTGCGAAATT-TAAAAATCGA
1280080 GTTGCGAA
1 GTTGCGAA
1280088 TTTGACTTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 2 0.05
40 21 0.49
41 5 0.12
42 15 0.35
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (41 bp):
GTTGCGAAAAAGAAATTCGTGTTGCGAAATTTAAAAATCGA
Found at i:1280061 original size:20 final size:20
Alignment explanation
Indices: 1279938--1280066 Score: 63
Period size: 20 Copynumber: 6.5 Consensus size: 20
1279928 CGAAAATCGA
*
1279938 GTTGCGAAAATA-AAATTCGC
1 GTTGCGAAAA-AGAAATTCGT
** **
1279958 GTTGCGAAATTGAAACGCGCT
1 GTTGCGAAAAAGAAATTCG-T
** * *
1279979 -TTGCGAATTAGAAAATCTT
1 GTTGCGAAAAAGAAATTCGT
*
1279998 GTTGCGAAAAGGAAACTT-GT
1 GTTGCGAAAAAGAAA-TTCGT
*
1280018 GTTGC-AAATTTAA-AAA-TCGA
1 GTTGCGAAA---AAGAAATTCGT
1280038 GTTGCGAAAAAGAAATTCGT
1 GTTGCGAAAAAGAAATTCGT
1280058 GTTGCGAAA
1 GTTGCGAAA
1280067 TTGTCATATT
Statistics
Matches: 80, Mismatches: 18, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
18 2 0.03
19 8 0.10
20 62 0.77
21 7 0.09
22 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.27
Consensus pattern (20 bp):
GTTGCGAAAAAGAAATTCGT
Found at i:1280441 original size:15 final size:17
Alignment explanation
Indices: 1280421--1280453 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1280411 CAATATTATT
1280421 AAAATA-TAAAA-AATA
1 AAAATATTAAAATAATA
1280436 AAAATATTAAAATAATA
1 AAAATATTAAAATAATA
1280453 A
1 A
1280454 TATTATGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 5 0.31
17 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATATTAAAATAATA
Found at i:1280455 original size:14 final size:13
Alignment explanation
Indices: 1280400--1280458 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 13
1280390 ATTAATTACT
1280400 TATTAAAATAACAA
1 TATTAAAATAA-AA
*
1280414 TATT--ATTAAAA
1 TATTAAAATAAAA
*
1280425 TATAAAAAATAAAAA
1 TAT-TAAAAT-AAAA
1280440 TATTAAAATAATAA
1 TATTAAAATAA-AA
1280454 TATTA
1 TATTA
1280459 TGTTATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
11 5 0.14
12 4 0.11
13 2 0.06
14 18 0.50
15 7 0.19
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (13 bp):
TATTAAAATAAAA
Found at i:1280621 original size:39 final size:37
Alignment explanation
Indices: 1280578--1280681 Score: 99
Period size: 39 Copynumber: 2.8 Consensus size: 37
1280568 ACAATAGTAT
1280578 AATATTATATATTATTAATAATATAATTATAACAATAAA
1 AATATTATATATTATTAATAATATAATTAT--CAATAAA
* *
1280617 AATATTATATAATATT-AT--TAAAATTATCAATAAA
1 AATATTATATATTATTAATAATATAATTATCAATAAA
* *
1280651 TATAATTATATTTTTATTAA-AATAATAATTA
1 AAT-ATTATA-TATTATTAATAAT-ATAATTA
1280682 AATAGTTTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
34 9 0.17
35 6 0.11
36 13 0.25
37 1 0.02
38 3 0.06
39 21 0.40
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (37 bp):
AATATTATATATTATTAATAATATAATTATCAATAAA
Found at i:1283550 original size:18 final size:18
Alignment explanation
Indices: 1283519--1283554 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1283509 GCATTATATA
*
1283519 TGGTTGTTTGATATATTT
1 TGGTTCTTTGATATATTT
*
1283537 TGGTTCTTTTATATATTT
1 TGGTTCTTTGATATATTT
1283555 CTATGTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.64
Consensus pattern (18 bp):
TGGTTCTTTGATATATTT
Found at i:1294665 original size:22 final size:22
Alignment explanation
Indices: 1294628--1294686 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
1294618 GTATGAACAG
**
1294628 TGAACAGTACTATGAACAATAA
1 TGAACAGTACCGTGAACAATAA
* *
1294650 TGAACATTACCGTGAACATTAA
1 TGAACAGTACCGTGAACAATAA
*
1294672 TGAACAGTATCGTGA
1 TGAACAGTACCGTGA
1294687 GAAGTACCCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (22 bp):
TGAACAGTACCGTGAACAATAA
Found at i:1294768 original size:21 final size:22
Alignment explanation
Indices: 1294727--1294768 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1294717 TATCAAAGGG
*
1294727 GAACCGATTCTCCTACTACAGA
1 GAACCGATACTCCTACTACAGA
*
1294749 GAACCGATAC-CCTGCTACAG
1 GAACCGATACTCCTACTACAG
1294769 TTCTGCTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.19
Consensus pattern (22 bp):
GAACCGATACTCCTACTACAGA
Found at i:1295526 original size:31 final size:31
Alignment explanation
Indices: 1295491--1295602 Score: 179
Period size: 31 Copynumber: 3.6 Consensus size: 31
1295481 TCCATAGATT
* *
1295491 CCGAAGAACCTAGGTAATCAATCCATATGTC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
*
1295522 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
* *
1295553 CTGATGAACATAGGTAAACAATCCATATGTC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
1295584 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
1295603 CCTCGACCCT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 73 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAATCCATATGTC
Found at i:1296284 original size:22 final size:22
Alignment explanation
Indices: 1296242--1296284 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1296232 TTTTTTCTTT
*
1296242 AGGGGGGAATCGATACTCCCTC
1 AGGGGGGAATCGATACCCCCTC
1296264 AGGGGGGAATCTG-TACCCCCT
1 AGGGGGGAATC-GATACCCCCT
1296285 GCACAATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.21, C:0.28, G:0.33, T:0.19
Consensus pattern (22 bp):
AGGGGGGAATCGATACCCCCTC
Found at i:1299009 original size:2 final size:2
Alignment explanation
Indices: 1299002--1299049 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1298992 CAAACTATTC
1299002 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1299044 AT AT AT
1 AT AT AT
1299050 TCTTTCCAGT
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):
AT
Found at i:1300563 original size:21 final size:20
Alignment explanation
Indices: 1300527--1300581 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
1300517 ATATATGTTT
*
1300527 TATGAATAGTAA-AATATGG
1 TATGAATAGTAACAATATCG
*
1300546 TATGAACAGTGAACAATATCG
1 TATGAATAGT-AACAATATCG
1300567 TATGAATAGTAACAA
1 TATGAATAGTAACAA
1300582 ACATTACTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.29
20 7 0.23
21 15 0.48
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.27
Consensus pattern (20 bp):
TATGAATAGTAACAATATCG
Found at i:1300695 original size:21 final size:22
Alignment explanation
Indices: 1300654--1300696 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1300644 ATTTTCAAAG
*
1300654 GGGAACCGATTCCCCTACTACA
1 GGGAACCGATTACCCTACTACA
*
1300676 GGGAACCGA-TACCCTGCTACA
1 GGGAACCGATTACCCTACTACA
1300697 ATATTGCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.28, C:0.35, G:0.21, T:0.16
Consensus pattern (22 bp):
GGGAACCGATTACCCTACTACA
Found at i:1301042 original size:11 final size:11
Alignment explanation
Indices: 1301026--1301050 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1301016 CACGCTAAGT
1301026 TGATGACTTAG
1 TGATGACTTAG
1301037 TGATGACTTAG
1 TGATGACTTAG
1301048 TGA
1 TGA
1301051 GACATATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (11 bp):
TGATGACTTAG
Found at i:1301502 original size:31 final size:31
Alignment explanation
Indices: 1301442--1301550 Score: 161
Period size: 31 Copynumber: 3.6 Consensus size: 31
1301432 TCCATAGATT
* *
1301442 CCGAAGAACCTAGGTAATCAG--T-TATGTC
1 CCGAAGAACATAGGTAAACAGTCTATATGTC
1301470 CCGAAGAACATAGGTAAACAGTCTATATGTC
1 CCGAAGAACATAGGTAAACAGTCTATATGTC
* *
1301501 CCGAAGAACATAGGTAAACAATCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCTATATGTC
1301532 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
1301551 CCTCGACCCT
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
28 19 0.26
30 1 0.01
31 54 0.73
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.20
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCTATATGTC
Done.