Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008639.1 Hibiscus syriacus cultivar Beakdansim tig00111614_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: 1076872
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:950653 original size:38 final size:37
Alignment explanation
Indices: 950569--950656 Score: 92
Period size: 36 Copynumber: 2.4 Consensus size: 37
950559 AATAGTAAGT
* * *
950569 AAAATAAATATAAAAATATAAAAATAAAGAAAAAGAAG
1 AAAAT-AATATATAAATAAAAAAATAAAGAAAAAGAAA
950607 AAAA-AATATATAAATAAAACAAATAAA-AAAATTA-AAA
1 AAAATAATATATAAATAAAA-AAATAAAGAAAA--AGAAA
950644 AAAATAATATATA
1 AAAATAATATATA
950657 TATATATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
36 17 0.40
37 13 0.30
38 13 0.30
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.19
Consensus pattern (37 bp):
AAAATAATATATAAATAAAAAAATAAAGAAAAAGAAA
Found at i:950685 original size:42 final size:45
Alignment explanation
Indices: 950639--950760 Score: 119
Period size: 46 Copynumber: 2.7 Consensus size: 45
950629 ATAAAAAAAT
* *
950639 TAAAAAAAATAATATATATATATATATATATAA-AATAATA-A-A
1 TAAAAAAAATAAAATATATATATATATATATAATAATAAAACAGA
* *
950681 TAAAAACATAA-AAAATAGTAAATATATGTATA-AATTAATAAAACAGA
1 TAAAAA-A-AATAAAATA-TATATATATATATATAA-TAATAAAACAGA
*
950728 TAATAAAAAATAACATATATATATATATATATA
1 TAA-AAAAAATAAAATATATATATATATATATA
950761 TATGTAATCT
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
42 6 0.10
43 8 0.13
44 14 0.22
45 6 0.10
46 15 0.24
47 11 0.17
48 3 0.05
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (45 bp):
TAAAAAAAATAAAATATATATATATATATATAATAATAAAACAGA
Found at i:950747 original size:2 final size:2
Alignment explanation
Indices: 950742--950793 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
950732 AAAAAATAAC
* *
950742 AT AT AT AT AT AT AT AT AT AT AT GT A- AT CT 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
950783 AT AT AT AT AT A
1 AT AT AT AT AT A
950794 CTAAAGTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:951372 original size:37 final size:37
Alignment explanation
Indices: 951322--951392 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
951312 TTGTGGATCA
*
951322 TATTTTTAGGAGTTTGAATCCTAGTAGAACTCTATCC
1 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCC
951359 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
1 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
951393 ACGATATGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCC
Found at i:951973 original size:35 final size:36
Alignment explanation
Indices: 951901--951985 Score: 136
Period size: 36 Copynumber: 2.4 Consensus size: 36
951891 AAGGTCTTAG
* *
951901 GTTTCAAGAGAAACATTTTCAAAGGTTTTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGT
951937 GTTTCAAGAGAAACAATTTCAAAGG-TTTTTTGTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGT
*
951972 GTTTTAAGAGAAAC
1 GTTTCAAGAGAAAC
951986 TTTCCCAAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 22 0.48
36 24 0.52
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (36 bp):
GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGT
Found at i:952122 original size:36 final size:36
Alignment explanation
Indices: 952038--952370 Score: 323
Period size: 36 Copynumber: 9.3 Consensus size: 36
952028 CAAAGATTGA
* *
952038 TGTTTCAAGAGAAACTGTGTCAAGAGAGAC--ACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
952072 TGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
952108 TATTTCAATAGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
952144 TATTTCAAGAGAAACTGTCACAAGAGAGACAAAGGCAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAG----A--CAAAATT
952186 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
952223 AGTTTCAAAAGAAACAGTCT-AAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
952258 TGTTT-AATGTA-AAACATAT-TC-----A-A-AAATTT
1 TGTTTCAA-G-AGAAAC-TGTCTCAAGAGAGACAAAATT
*
952287 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* **
952323 TGTTTCAAGGGAAACTGTCTCAAGAGAGGTAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
952359 TGTTTCAAGAGA
1 TGTTTCAAGAGA
952371 GACAACTTTG
Statistics
Matches: 249, Mismatches: 27, Indels: 44
0.78 0.08 0.14
Matches are distributed among these distances:
28 2 0.01
29 17 0.07
30 3 0.01
31 1 0.00
34 30 0.12
35 12 0.05
36 130 0.52
37 19 0.08
38 1 0.00
40 1 0.00
42 33 0.13
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:952207 original size:78 final size:75
Alignment explanation
Indices: 952038--952254 Score: 239
Period size: 78 Copynumber: 2.9 Consensus size: 75
952028 CAAAGATTGA
* * * * *
952038 TGTTTCAAGAGAAACTGTGTCAAGAGAGAC--ACTTTGTTTTAAGGGAAACTGTCTCAAGAGAG-
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTC-CAAGAGAGA
952100 ---ACAAAATT
65 CAAACAAAATT
* *
952108 TATTTCAATAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCACAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTC-CAAGAGAGA
952173 CAAAGGCAAAATT
65 CAAA--CAAAATT
* * * * *
952186 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTTCAAAAGAAACAGTCTAAGGGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTA-TTTCAAGAGAAACTGTCCAAGAGAGA
952251 CAAA
65 CAAA
952255 ATTTGTTTAA
Statistics
Matches: 123, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
70 27 0.22
72 27 0.22
76 1 0.01
78 53 0.43
79 15 0.12
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.24
Consensus pattern (75 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCCAAGAGAGAC
AAACAAAATT
Found at i:952357 original size:101 final size:100
Alignment explanation
Indices: 952180--952363 Score: 271
Period size: 101 Copynumber: 1.8 Consensus size: 100
952170 AGACAAAGGC
952180 AAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTTCAAAAGAAACAGTCTAA
1 AAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTTCAAAAGAAACAGTCTAA
*
952245 GGGAGACAAAATTTGTTTAATGTAAAACATATTCA
66 GAGAGACAAAATTTGTTTAATGTAAAACATATTCA
* * ** *
952280 AAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTC
1 AAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTTCAAAAGAAACAGTCT-
**
952344 AAGAGAGGTAAAATTTGTTT
64 AAGAGAGACAAAATTTGTTT
952364 CAAGAGAGAC
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
100 22 0.30
101 52 0.70
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.29
Consensus pattern (100 bp):
AAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTTCAAAAGAAACAGTCTAA
GAGAGACAAAATTTGTTTAATGTAAAACATATTCA
Found at i:952688 original size:116 final size:116
Alignment explanation
Indices: 952472--952701 Score: 347
Period size: 116 Copynumber: 2.0 Consensus size: 116
952462 CCTGAAGATA
* * * *
952472 AATGCTGCTGGTGGGTACGATTCCCTTCGTCGTGAAGTTGAAACCATGGATGGCCCATTCGTTGT
1 AATGCTGCTGGTGAGCACGATTCCCTTCGCCGTGAAATTGAAACCATGGATGGCCCATTCGTTGT
952537 GAACTTGAGCCTTGAATTAGATATCCTTCACCGTGAAGTTGAAATCCAATG
66 GAACTTGAGCCTTGAATTAGATATCCTTCACCGTGAAGTTGAAATCCAATG
*
952588 AATGTTGCTGGTGAGCACGATTCCCTTCGCCGTGAAATTGAAACCATGGATGGCCCATTCGTTGT
1 AATGCTGCTGGTGAGCACGATTCCCTTCGCCGTGAAATTGAAACCATGGATGGCCCATTCGTTGT
* * * *
952653 GAAGTTGAGCCTT-AACTT-GAATATCCTTTATCGTGAAGTTTAAATCCAA
66 GAACTTGAGCCTTGAA-TTAG-ATATCCTTCACCGTGAAGTTGAAATCCAA
952702 GCTTATATTG
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
115 3 0.03
116 100 0.97
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (116 bp):
AATGCTGCTGGTGAGCACGATTCCCTTCGCCGTGAAATTGAAACCATGGATGGCCCATTCGTTGT
GAACTTGAGCCTTGAATTAGATATCCTTCACCGTGAAGTTGAAATCCAATG
Found at i:954405 original size:10 final size:9
Alignment explanation
Indices: 954376--954453 Score: 50
Period size: 10 Copynumber: 8.0 Consensus size: 9
954366 GCGTCTTGTC
954376 TTCTTTTTT
1 TTCTTTTTT
**
954385 CTTCACTTTT
1 -TTCTTTTTT
954395 TTCTTTGTTT
1 TTCTTT-TTT
*
954405 TTGTTTCTCTT
1 TTCTTT-T-TT
954416 TT-TTATTTT
1 TTCTT-TTTT
*
954425 CTCTTTTTT
1 TTCTTTTTT
954434 CTTCTTTTTT
1 -TTCTTTTTT
954444 TCTCTTTTTT
1 T-TCTTTTTT
954454 ATTTTTGTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 12 0.22
10 37 0.69
11 5 0.09
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.78
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:954417 original size:12 final size:11
Alignment explanation
Indices: 954377--954453 Score: 59
Period size: 12 Copynumber: 6.7 Consensus size: 11
954367 CGTCTTGTCT
954377 TCTTTTTTCTTC
1 TCTTTTTT-TTC
*
954389 ACTTTTTTCTT-
1 TCTTTTTT-TTC
*
954400 TGTTTTTGTTTC
1 TCTTTTT-TTTC
*
954412 TCTTTTTTATTT
1 TCTTTTTT-TTC
*
954424 TCTCTTTTTTC
1 TCTTTTTTTTC
954435 T-TCTTTTTTTC
1 TCT-TTTTTTTC
954446 TCTTTTTT
1 TCTTTTTT
954454 ATTTTTGTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
10 1 0.02
11 24 0.46
12 27 0.52
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.78
Consensus pattern (11 bp):
TCTTTTTTTTC
Found at i:954418 original size:24 final size:24
Alignment explanation
Indices: 954377--954446 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
954367 CGTCTTGTCT
* *
954377 TCTTTTTTCTTCACTTTTTTCTTTG
1 TCTTTTTTCTTC-TTTTTTTCTTTC
*
954402 TTTTTGTTTC-TCTTTTTTAT-TTTC
1 TCTTT-TTTCTTCTTTTTT-TCTTTC
954426 TCTTTTTTCTTCTTTTTTTCT
1 TCTTTTTTCTTCTTTTTTTCT
954447 CTTTTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
23 5 0.14
24 21 0.57
25 7 0.19
26 4 0.11
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (24 bp):
TCTTTTTTCTTCTTTTTTTCTTTC
Found at i:954459 original size:18 final size:19
Alignment explanation
Indices: 954416--954464 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
954406 TGTTTCTCTT
*
954416 TTTTATTTTCTCTTTTTTCT
1 TTTT-TTTTCTCTTTTTTCA
954436 TCTTTTTTTCTCTTTTTT-A
1 T-TTTTTTTCTCTTTTTTCA
*
954455 TTTTTGTTCT
1 TTTTTTTTCT
954465 GATTGGATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 8 0.31
19 1 0.04
20 14 0.54
21 3 0.12
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTTTTCTCTTTTTTCA
Found at i:957641 original size:17 final size:19
Alignment explanation
Indices: 957613--957661 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
957603 TATTTTGAAA
957613 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
957631 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
957650 CACCGATGCACT
1 CATCGATGCACT
957662 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:963348 original size:24 final size:24
Alignment explanation
Indices: 963321--963401 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
963311 ACACTTAACA
963321 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
963345 GTGCATCGATTCAT-CATGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
*
963367 -TGCACCGATGCA-CGCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
963389 GTGCATCGATGCA
1 GTGCATCGATGCA
963402 CAGGGTCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
20 3 0.07
21 11 0.24
22 1 0.02
23 14 0.31
24 16 0.36
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:964988 original size:21 final size:21
Alignment explanation
Indices: 964946--964989 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
964936 ACTCCGGGAG
* *
964946 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
964967 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
964988 CT
1 CT
964990 CCGGCTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:965859 original size:21 final size:23
Alignment explanation
Indices: 965835--965876 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
965825 AAATTAGTTT
965835 AAATGAATTT-TAAG-ATTTTAC
1 AAATGAATTTCTAAGTATTTTAC
*
965856 AAATGATTTTCTAAGTATTTT
1 AAATGAATTTCTAAGTATTTT
965877 CGATTCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 4 0.22
23 5 0.28
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.48
Consensus pattern (23 bp):
AAATGAATTTCTAAGTATTTTAC
Found at i:966240 original size:17 final size:19
Alignment explanation
Indices: 966212--966260 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
966202 TATTTTGAAA
966212 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
966230 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
966249 CACCGATGCACT
1 CATCGATGCACT
966261 AAGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:967402 original size:13 final size:13
Alignment explanation
Indices: 967384--967416 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
967374 AAAAATATAT
967384 ATAAATAAAACAA
1 ATAAATAAAACAA
*
967397 ATAAATAAAATAA
1 ATAAATAAAACAA
967410 A-AAATAA
1 ATAAATAA
967417 TAAAGTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (13 bp):
ATAAATAAAACAA
Found at i:967406 original size:29 final size:31
Alignment explanation
Indices: 967333--967464 Score: 84
Period size: 29 Copynumber: 4.5 Consensus size: 31
967323 ATAGTAAGTA
*
967333 AAATAAATAAAAATATATATATAAAAATAAAG
1 AAATAAAT-AAAATATATATATAAAAATAAAC
* * *
967365 AAAAAGAAGAAAA-ATATATATAAATA-AAAC
1 AAATA-AATAAAATATATATATAAAAATAAAC
* *
967395 AAATAAATAAAATA-A-A-A-AATAATAAAG
1 AAATAAATAAAATATATATATAAAAATAAAC
* * * *
967422 TAA-AAATAATATATATATAT-ATAATAAAA
1 AAATAAATAAAATATATATATAAAAATAAAC
967451 AAATATAA-AAAATA
1 AAATA-AATAAAATA
967465 GGAATATATG
Statistics
Matches: 77, Mismatches: 14, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
26 12 0.16
27 7 0.09
28 2 0.03
29 18 0.23
30 14 0.18
31 14 0.18
32 8 0.10
33 2 0.03
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (31 bp):
AAATAAATAAAATATATATATAAAAATAAAC
Found at i:967428 original size:14 final size:15
Alignment explanation
Indices: 967374--967432 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 15
967364 GAAAAAGAAG
967374 AAAAATATATATAAATAA
1 AAAAATA-ATA-AAAT-A
967392 AACAAATAAATAAAATA
1 AA-AAAT-AATAAAATA
*
967409 AAAAATAATAAAGT-
1 AAAAATAATAAAATA
967423 AAAAATAATA
1 AAAAATAATA
967433 TATATATATA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 10 0.26
15 7 0.18
16 4 0.11
17 3 0.08
18 6 0.16
19 7 0.18
20 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (15 bp):
AAAAATAATAAAATA
Found at i:967471 original size:38 final size:40
Alignment explanation
Indices: 967411--967524 Score: 117
Period size: 38 Copynumber: 2.8 Consensus size: 40
967401 ATAAAATAAA
*
967411 AAATAATAAAGTAAA-AATAATATATATATATATAATAAAA-
1 AAATAATAAA--AAATAACAATATATATATATATAATAAAAC
** * *
967451 AAAT-ATAAAAAATAGGAATATATGTATAAATTAATAAAAC
1 AAATAATAAAAAATAACAATATATATATATA-TAATAAAAC
*
967491 AGATAATAAAAAATAACATATATATATATATATA
1 AAATAATAAAAAATAACA-ATATATATATATATA
967525 TATATATGTA
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
37 3 0.05
38 13 0.22
39 13 0.22
40 7 0.12
41 13 0.22
42 11 0.18
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (40 bp):
AAATAATAAAAAATAACAATATATATATATATAATAAAAC
Found at i:968125 original size:37 final size:37
Alignment explanation
Indices: 968075--968182 Score: 180
Period size: 37 Copynumber: 2.9 Consensus size: 37
968065 TTGTGGATCT
* *
968075 TATTTTTAAGAGTTTGAATCATAGTAGAACTCTATCC
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCC
* *
968112 TATTTTTAGGAGTTTGAATCCTAGTAAAACTATATCC
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCC
968149 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTA
968183 ACGTTATGTT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCC
Found at i:969092 original size:15 final size:14
Alignment explanation
Indices: 969072--969128 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 14
969062 AACCGGGTAT
969072 CGGGTACCCGATTCC
1 CGGGTACCCGATT-C
*
969087 CGGGTACCCGCAAAATC
1 CGGGTACCCG---ATTC
969104 CGGGTACCCGATTAC
1 CGGGTACCCGATT-C
969119 CGGGTACCCG
1 CGGGTACCCG
969129 TAACATCCGG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 2 0.06
15 21 0.58
17 11 0.31
18 2 0.06
ACGTcount: A:0.19, C:0.37, G:0.28, T:0.16
Consensus pattern (14 bp):
CGGGTACCCGATTC
Found at i:969108 original size:17 final size:16
Alignment explanation
Indices: 969086--969140 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 16
969076 TACCCGATTC
969086 CCGGGTACCCGCAAAAT
1 CCGGGTACCCG-AAAAT
**
969103 CCGGGTACCCGATTA-
1 CCGGGTACCCGAAAAT
*
969118 CCGGGTACCCGTAACAT
1 CCGGGTACCCG-AAAAT
969135 CCGGGT
1 CCGGGT
969141 CGGGACACGG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 11 0.34
16 4 0.12
17 17 0.53
ACGTcount: A:0.22, C:0.35, G:0.27, T:0.16
Consensus pattern (16 bp):
CCGGGTACCCGAAAAT
Found at i:969113 original size:32 final size:32
Alignment explanation
Indices: 969072--969140 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
969062 AACCGGGTAT
*
969072 CGGGTACCCGATTCCCGGGTACCCGCAAAATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
* *
969104 CGGGTACCCGATTACCGGGTACCCGTAACATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
969136 CGGGT
1 CGGGT
969141 CGGGACACGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.17
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGGTACCCGCAAAATC
Found at i:970824 original size:2 final size:2
Alignment explanation
Indices: 970817--970864 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
970807 CTTTAACTTA
970817 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
970859 AT AT AT
1 AT AT AT
970865 TTAGAAGTTT
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:973138 original size:16 final size:16
Alignment explanation
Indices: 973087--973139 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
973077 TGTATGTGAT
973087 ATATGTATATGATGTGTG
1 ATATG-ATAT-ATGTGTG
* * **
973105 ATATGATGTGTGCATG
1 ATATGATATATGTGTG
973121 ATATGATATATGTGTG
1 ATATGATATATGTGTG
973137 ATA
1 ATA
973140 GGGGTTATGG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.42
Consensus pattern (16 bp):
ATATGATATATGTGTG
Found at i:977903 original size:103 final size:103
Alignment explanation
Indices: 977683--977895 Score: 390
Period size: 103 Copynumber: 2.1 Consensus size: 103
977673 GGGTCTACGC
977683 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
977748 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
*
977786 GGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
977851 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
977889 GGTCCTT
1 GGTCCTT
977896 ATGGACATTA
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:977951 original size:23 final size:23
Alignment explanation
Indices: 977919--977979 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
977909 TATGGAACTA
*
977919 CGGTGCAATTCTACGCGGTACTC
1 CGGTGCAATTCTACGCGGCACTC
* * *
977942 CGGTGAAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGCGGCACTC
*
977965 CGGTGCAATTATACG
1 CGGTGCAATTCTACG
977980 AGCTGTGGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTC
Found at i:991737 original size:33 final size:35
Alignment explanation
Indices: 991673--991739 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
991663 ATTTCAAATG
* * *
991673 TGATTGCACTTTGTGTGCATATTATGATTCTGATA
1 TGATAGCACTGTGTGTGCATAATATGATTCTGATA
991708 TGATAGCACTGTGTGTGC-TAATATG-TTCTGAT
1 TGATAGCACTGTGTGTGCATAATATGATTCTGAT
991740 TGAGATGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 7 0.24
34 6 0.21
35 16 0.55
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.43
Consensus pattern (35 bp):
TGATAGCACTGTGTGTGCATAATATGATTCTGATA
Found at i:994180 original size:103 final size:102
Alignment explanation
Indices: 993992--994194 Score: 302
Period size: 103 Copynumber: 2.0 Consensus size: 102
993982 GTGGAGTGAT
* * * * *
993992 TGATATAATGTGGTGTTATCGGTGGGTATACTAGTATATTTCGATATTATTGCACTTTGTGTGCA
1 TGATATAATGTGGTGTTACCGGTAGGTACACTAGTATATTTAGATATGATTGCACTTTGTGTGCA
*
994057 TATTATGATTTCGATGTGATAGCACTGTGTGTGCTTA
66 TATTATGATTTCGATATGATAGCACTGTGTGTGCTTA
*
994094 TGATATACA-GTGGTGTTACCGGTAGGTACACTAGTATATTTAAGATGTGATTGCACTTTGTGTG
1 TGATATA-ATGTGGTGTTACCGGTAGGTACACTAGTATATTT-AGATATGATTGCACTTTGTGTG
994158 CATATTATGA-TTCTGATATGATAGCACTGTGTGTGCT
64 CATATTATGATTTC-GATATGATAGCACTGTGTGTGCT
994195 AATATGTTCT
Statistics
Matches: 91, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
102 39 0.43
103 52 0.57
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.41
Consensus pattern (102 bp):
TGATATAATGTGGTGTTACCGGTAGGTACACTAGTATATTTAGATATGATTGCACTTTGTGTGCA
TATTATGATTTCGATATGATAGCACTGTGTGTGCTTA
Found at i:1000511 original size:22 final size:22
Alignment explanation
Indices: 1000486--1000532 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1000476 CTAATAATAT
1000486 ATAAAGTTTAATTCATATTTTC
1 ATAAAGTTTAATTCATATTTTC
1000508 ATAAAGTTTAATTCATATTTTC
1 ATAAAGTTTAATTCATATTTTC
1000530 ATA
1 ATA
1000533 TCCAGGCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (22 bp):
ATAAAGTTTAATTCATATTTTC
Found at i:1001767 original size:32 final size:31
Alignment explanation
Indices: 1001721--1001795 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 31
1001711 TAATAATATA
1001721 TTTCGATAAATTTAAGGACTATTATATAATAG
1 TTTCGATAAATTTAAGGA-TATTATATAATAG
* * * * *
1001753 TTTCTATAGATTTAATGATATTTTATAATAA
1 TTTCGATAAATTTAAGGATATTATATAATAG
*
1001784 TTT-AATAAATTT
1 TTTCGATAAATTT
1001796 TAATAACATT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 7 0.19
31 14 0.39
32 15 0.42
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (31 bp):
TTTCGATAAATTTAAGGATATTATATAATAG
Found at i:1001879 original size:2 final size:2
Alignment explanation
Indices: 1001872--1001896 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1001862 ACATACAAAT
1001872 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
1001897 CTTTAAAAAG
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:1003406 original size:29 final size:29
Alignment explanation
Indices: 1003374--1003465 Score: 89
Period size: 29 Copynumber: 3.1 Consensus size: 29
1003364 AATCAATCTT
1003374 TAAACTTTTGAATATTCTAAATTCATCCC
1 TAAACTTTTGAATATTCTAAATTCATCCC
* * *
1003403 TAAAC-TATGACTCTATCTAAATT-AGTCCCC
1 TAAACTTTTGAATAT-TCTAAATTCA-T-CCC
* * *
1003433 CAAACTTTTGAAAATTCTAATTTCATCCC
1 TAAACTTTTGAATATTCTAAATTCATCCC
1003462 TAAA
1 TAAA
1003466 TACATTTAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
28 7 0.15
29 20 0.42
30 15 0.31
31 6 0.12
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (29 bp):
TAAACTTTTGAATATTCTAAATTCATCCC
Found at i:1003698 original size:60 final size:60
Alignment explanation
Indices: 1003584--1003722 Score: 199
Period size: 60 Copynumber: 2.3 Consensus size: 60
1003574 GTATATACGT
* * *
1003584 ATAGTTTGGGATGAAATTGGAATGTTCAAAATGTTTTAGGACTAATTTAGAATGAAAGTC
1 ATAGTTTGGGATGAAATTGAAATGTTCAAAACGTTTGAGGACTAATTTAGAATGAAAGTC
* * *
1003644 ATAGTTTGGAGATGAAATTGAAATGTTC-AAACGTTTGAGGACTAGTTTATAATGATAGTC
1 ATAGTTTGG-GATGAAATTGAAATGTTCAAAACGTTTGAGGACTAATTTAGAATGAAAGTC
1003704 ATAGTTTAGGGATGAAATT
1 ATAGTTT-GGGATGAAATT
1003723 AAAACATTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
60 52 0.73
61 19 0.27
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (60 bp):
ATAGTTTGGGATGAAATTGAAATGTTCAAAACGTTTGAGGACTAATTTAGAATGAAAGTC
Found at i:1003758 original size:60 final size:60
Alignment explanation
Indices: 1003584--1003758 Score: 164
Period size: 60 Copynumber: 2.9 Consensus size: 60
1003574 GTATATACGT
** * *
1003584 ATAGTTTGG-GATGAAATTGGAATGTTCAAAATGTTTTA-GGACTAATTTAGAATGAAAGTC
1 ATAGTTTGGAGATGAAATTAAAATGTTC-AAACG-TTTAGGGACTAATTTAAAATGAAAGTC
* * * *
1003644 ATAGTTTGGAGATGAAATTGAAATGTTCAAACGTTT-GAGGACTAGTTTATAATGATAGTC
1 ATAGTTTGGAGATGAAATTAAAATGTTCAAACGTTTAG-GGACTAATTTAAAATGAAAGTC
* *
1003704 ATAGTTTAGG-GATGAAATTAAAACAT-TTTAAA-GTTTAGGGACCAATTTAAAATGA
1 ATAGTTT-GGAGATGAAATT-AAA-ATGTTCAAACGTTTAGGGACTAATTTAAAATGA
1003759 GTGGCATACT
Statistics
Matches: 98, Mismatches: 10, Indels: 14
0.80 0.08 0.11
Matches are distributed among these distances:
59 3 0.03
60 66 0.67
61 27 0.28
62 2 0.02
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (60 bp):
ATAGTTTGGAGATGAAATTAAAATGTTCAAACGTTTAGGGACTAATTTAAAATGAAAGTC
Found at i:1006256 original size:20 final size:20
Alignment explanation
Indices: 1006231--1006269 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1006221 CCGTTTTTCA
1006231 TCGGGAATTCAACTACTTCG
1 TCGGGAATTCAACTACTTCG
1006251 TCGGGAATTCAACTACTTC
1 TCGGGAATTCAACTACTTC
1006270 ATGCTTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (20 bp):
TCGGGAATTCAACTACTTCG
Found at i:1011275 original size:26 final size:27
Alignment explanation
Indices: 1011231--1011283 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 27
1011221 TCCATTTTAT
1011231 ATATGTAAAAAAATTAA-TTAAATAAA
1 ATATGTAAAAAAATTAATTTAAATAAA
*
1011257 ATAT-TAAAAAATTTAAATTTAAATAAA
1 ATATGTAAAAAAATT-AATTTAAATAAA
1011284 TTACTAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 9 0.38
26 6 0.25
27 9 0.38
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (27 bp):
ATATGTAAAAAAATTAATTTAAATAAA
Found at i:1015139 original size:24 final size:24
Alignment explanation
Indices: 1015067--1015175 Score: 95
Period size: 24 Copynumber: 4.7 Consensus size: 24
1015057 TGGCCTTGTA
1015067 CATCGATGCACATTC-AA-GGAGTG
1 CATCGATGCACATTCAAAGGGA-TG
* *
1015090 CATCGGTGCATC-TTC--A-TGATG
1 CATCGATGCA-CATTCAAAGGGATG
* * *
1015111 TATCGATGAACATTCAAATGGATG
1 CATCGATGCACATTCAAAGGGATG
*
1015135 CATCGATGCACTTTCAAAGGGATG
1 CATCGATGCACATTCAAAGGGATG
1015159 CATCGATGCACTATTCA
1 CATCGATGCAC-ATTCA
1015176 GTGTATCGAT
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
20 1 0.01
21 12 0.17
22 3 0.04
23 13 0.19
24 36 0.52
25 4 0.06
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (24 bp):
CATCGATGCACATTCAAAGGGATG
Found at i:1021109 original size:19 final size:19
Alignment explanation
Indices: 1021085--1021135 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
1021075 TATTTGTTCA
1021085 AGAGTGCATCGATGCATAG
1 AGAGTGCATCGATGCATAG
1021104 AGAGTGCATCGATGCATAG
1 AGAGTGCATCGATGCATAG
1021123 AGAGTGCATCGAT
1 AGAGTGCATCGAT
1021136 ACACTTAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.22
Consensus pattern (19 bp):
AGAGTGCATCGATGCATAG
Found at i:1026887 original size:24 final size:24
Alignment explanation
Indices: 1026860--1026910 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1026850 CATAATTTTG
* *
1026860 AAAA-AAATTAAAAGTTTATATATT
1 AAAATAAATTAAAA-TTAATAAATT
*
1026884 AAAATGAATTAAAATTAATAAATT
1 AAAATAAATTAAAATTAATAAATT
1026908 AAA
1 AAA
1026911 TACTAGATGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
AAAATAAATTAAAATTAATAAATT
Found at i:1028407 original size:19 final size:19
Alignment explanation
Indices: 1028383--1028422 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1028373 TCCGTCCCGG
*
1028383 TTATCGACTTCGGTCTCGA
1 TTATCGACTTCGATCTCGA
*
1028402 TTATCGACTTTGATCTCGA
1 TTATCGACTTCGATCTCGA
1028421 TT
1 TT
1028423 TAGGTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (19 bp):
TTATCGACTTCGATCTCGA
Found at i:1028634 original size:25 final size:25
Alignment explanation
Indices: 1028603--1028658 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
1028593 AGGATGTTGA
*
1028603 ATTTTAATAATTTA-TTGTTTTAAAC
1 ATTTTAAT-ATTTATTTATTTTAAAC
*
1028628 ATTTTAATATTTATTTATTTTTAAC
1 ATTTTAATATTTATTTATTTTAAAC
1028653 ATTTTA
1 ATTTTA
1028659 GAATAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 5 0.18
25 23 0.82
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (25 bp):
ATTTTAATATTTATTTATTTTAAAC
Found at i:1036704 original size:2 final size:2
Alignment explanation
Indices: 1036697--1036746 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1036687 GGAAGGTAAT
1036697 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1036739 GA GA GA GA
1 GA GA GA GA
1036747 AAGTGGTGGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1037105 original size:60 final size:61
Alignment explanation
Indices: 1037041--1037165 Score: 173
Period size: 60 Copynumber: 2.1 Consensus size: 61
1037031 TTGAAGGATG
* * * *
1037041 AAATTGAAATGTTCAAAAATTTAAGGACTAATTTAAAATGATAG-TCATAGTTTAAGAATA-
1 AAATTGAAATGTTCAAAAAATTAAAGACCAATTTAAAAT-AAAGTTCATAGTTTAAGAATAT
* *
1037101 AAATTGAAATGTTCAAAAAATTAAAGACCAATTTAAAATAAAGTTTATAGTTTGAGAATAT
1 AAATTGAAATGTTCAAAAAATTAAAGACCAATTTAAAATAAAGTTCATAGTTTAAGAATAT
1037162 AAAT
1 AAAT
1037166 ATTCAAACTC
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 3 0.05
60 50 0.88
61 4 0.07
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.33
Consensus pattern (61 bp):
AAATTGAAATGTTCAAAAAATTAAAGACCAATTTAAAATAAAGTTCATAGTTTAAGAATAT
Found at i:1038686 original size:29 final size:29
Alignment explanation
Indices: 1038652--1038710 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1038642 CCTAAATTAA
*
1038652 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
1038681 TTTGATGTCATTACTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
1038710 T
1 T
1038711 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTACTTACATCAATTTAGT
Found at i:1043371 original size:29 final size:29
Alignment explanation
Indices: 1043337--1043395 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1043327 CCTAAATTAA
1043337 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1043366 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1043395 T
1 T
1043396 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:1051860 original size:20 final size:21
Alignment explanation
Indices: 1051835--1051878 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
1051825 GTCAAAGAAA
1051835 GTCAACGGTCAACGGTC-ACG
1 GTCAACGGTCAACGGTCAACG
1051855 GTCAACGGTCAACGGTCAACG
1 GTCAACGGTCAACGGTCAACG
1051876 GTC
1 GTC
1051879 GGGTCGGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.16
Consensus pattern (21 bp):
GTCAACGGTCAACGGTCAACG
Found at i:1051890 original size:17 final size:17
Alignment explanation
Indices: 1051868--1051942 Score: 141
Period size: 17 Copynumber: 4.4 Consensus size: 17
1051858 AACGGTCAAC
1051868 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1051885 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1051902 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
1051919 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1051936 GGTCAAC
1 GGTCAAC
1051943 CCGGTTCAGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 57 1.00
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:1051895 original size:7 final size:7
Alignment explanation
Indices: 1051835--1051878 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
1051825 GTCAAAGAAA
1051835 GTCAACG
1 GTCAACG
1051842 GTCAACG
1 GTCAACG
1051849 GTC-ACG
1 GTCAACG
1051855 GTCAACG
1 GTCAACG
1051862 GTCAACG
1 GTCAACG
1051869 GTCAACG
1 GTCAACG
1051876 GTC
1 GTC
1051879 GGGTCGGGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.17
7 30 0.83
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:1051970 original size:10 final size:10
Alignment explanation
Indices: 1051938--1051987 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
1051928 TCGGGTCGGG
*
1051938 TCAACCCGGT
1 TCAAACCGGT
*
1051948 TCAGACCGG-
1 TCAAACCGGT
1051957 TCAAACCGGT
1 TCAAACCGGT
*
1051967 TCAAAACTGG-
1 TC-AAACCGGT
1051977 TCAAACCGGT
1 TCAAACCGGT
1051987 T
1 T
1051988 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 14 0.44
10 12 0.38
11 6 0.19
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1051978 original size:20 final size:19
Alignment explanation
Indices: 1051936--1051987 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
1051926 AGTCGGGTCG
* *
1051936 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAAACC
*
1051955 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AAACC
1051975 GGTCAAACCGGTT
1 GGTCAAACCGGTT
1051988 TTCCAGCAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:1058266 original size:32 final size:31
Alignment explanation
Indices: 1058183--1058304 Score: 93
Period size: 31 Copynumber: 3.9 Consensus size: 31
1058173 ACCCTAAGGG
* * *
1058183 AACATCTTAGGGCCTG-AGAGCCTACCCAAGA
1 AACATCTCAGGGCC-GCAGGGCCTACCTAAGA
* * * * *
1058214 TAGATTTCGGGGCCGTAGGGCCTACCTAAGA
1 AACATCTCAGGGCCGCAGGGCCTACCTAAGA
* **
1058245 ACACATCTTAGGGCCGCAGGGCCTACCCGAGA
1 A-ACATCTCAGGGCCGCAGGGCCTACCTAAGA
** *
1058277 ATGATCTCAGGGCCGCAGAGCCTACCTA
1 AACATCTCAGGGCCGCAGGGCCTACCTA
1058305 TGAGTCACAT
Statistics
Matches: 68, Mismatches: 21, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
30 1 0.01
31 43 0.63
32 24 0.35
ACGTcount: A:0.26, C:0.30, G:0.27, T:0.17
Consensus pattern (31 bp):
AACATCTCAGGGCCGCAGGGCCTACCTAAGA
Found at i:1058290 original size:63 final size:63
Alignment explanation
Indices: 1058184--1058304 Score: 156
Period size: 63 Copynumber: 1.9 Consensus size: 63
1058174 CCCTAAGGGA
* * * *
1058184 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTAGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
1058247 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTA
1058305 TGAGTCACAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
62 2 0.04
63 48 0.96
ACGTcount: A:0.26, C:0.30, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:1059199 original size:13 final size:13
Alignment explanation
Indices: 1059181--1059243 Score: 78
Period size: 13 Copynumber: 5.0 Consensus size: 13
1059171 AAGAAAGTCA
1059181 ACGGTCAACGGTC
1 ACGGTCAACGGTC
1059194 ACGGTCAACGGTC
1 ACGGTCAACGGTC
*
1059207 ACGGTCAACAGTC
1 ACGGTCAACGGTC
1059220 AACGGTC-A-GGTC
1 -ACGGTCAACGGTC
*
1059232 -GGGTCAACGGTC
1 ACGGTCAACGGTC
1059244 GGGTCGGGTC
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
10 4 0.09
11 1 0.02
12 7 0.16
13 26 0.59
14 6 0.14
ACGTcount: A:0.24, C:0.29, G:0.32, T:0.16
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:1059202 original size:20 final size:19
Alignment explanation
Indices: 1059177--1059243 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 19
1059167 GTCAAAGAAA
1059177 GTCAACGGTCAACGGTCACG
1 GTCAACGGTC-ACGGTCACG
*
1059197 GTCAACGGTCACGGTCAACA
1 GTCAACGGTCACGGTC-ACG
*
1059217 GTCAACGGTCA-GGTC-GG
1 GTCAACGGTCACGGTCACG
1059234 GTCAACGGTC
1 GTCAACGGTC
1059244 GGGTCGGGTC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
17 10 0.23
19 10 0.23
20 23 0.53
ACGTcount: A:0.24, C:0.28, G:0.31, T:0.16
Consensus pattern (19 bp):
GTCAACGGTCACGGTCACG
Found at i:1059239 original size:17 final size:17
Alignment explanation
Indices: 1059217--1059290 Score: 121
Period size: 17 Copynumber: 4.4 Consensus size: 17
1059207 ACGGTCAACA
* *
1059217 GTCAACGGTCAGGTCGG
1 GTCAACAGTCGGGTCGG
*
1059234 GTCAACGGTCGGGTCGG
1 GTCAACAGTCGGGTCGG
1059251 GTCAACAGTCGGGTCGG
1 GTCAACAGTCGGGTCGG
1059268 GTCAACAGTCGGGTCGG
1 GTCAACAGTCGGGTCGG
1059285 GTCAAC
1 GTCAAC
1059291 CCAGTTCAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 55 1.00
ACGTcount: A:0.18, C:0.24, G:0.41, T:0.18
Consensus pattern (17 bp):
GTCAACAGTCGGGTCGG
Found at i:1059243 original size:7 final size:7
Alignment explanation
Indices: 1059177--1059227 Score: 79
Period size: 7 Copynumber: 7.6 Consensus size: 7
1059167 GTCAAAGAAA
1059177 GTCAACG
1 GTCAACG
1059184 GTCAACG
1 GTCAACG
1059191 GTC-ACG
1 GTCAACG
1059197 GTCAACG
1 GTCAACG
1059204 GTC-ACG
1 GTCAACG
*
1059210 GTCAACA
1 GTCAACG
1059217 GTCAACG
1 GTCAACG
1059224 GTCA
1 GTCA
1059228 GGTCGGGTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 12 0.30
7 28 0.70
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:1059330 original size:20 final size:20
Alignment explanation
Indices: 1059307--1059344 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1059297 CAGACCGGTC
1059307 AAACCGGTCAAACCGGTTCA
1 AAACCGGTCAAACCGGTTCA
*
1059327 AAACTGGTCAAACCGGTT
1 AAACCGGTCAAACCGGTT
1059345 TTCCAGCAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.18
Consensus pattern (20 bp):
AAACCGGTCAAACCGGTTCA
Found at i:1059337 original size:10 final size:9
Alignment explanation
Indices: 1059300--1059343 Score: 61
Period size: 9 Copynumber: 4.7 Consensus size: 9
1059290 CCCAGTTCAG
1059300 ACCGGTCAA
1 ACCGGTCAA
1059309 ACCGGTCAA
1 ACCGGTCAA
1059318 ACCGGTTCAAA
1 ACCGG-TC-AA
*
1059329 ACTGGTCAA
1 ACCGGTCAA
1059338 ACCGGT
1 ACCGGT
1059344 TTTCCAGCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 21 0.68
10 4 0.13
11 6 0.19
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:1063612 original size:3 final size:3
Alignment explanation
Indices: 1063606--1063632 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1063596 CAAAAAAATG
1063606 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1063633 AAGACCTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1064097 original size:28 final size:27
Alignment explanation
Indices: 1064065--1064124 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
1064055 TAAAAAATTT
**
1064065 AAATAATTTAGGTATCTACTTTAACATA
1 AAATAATTTAAATATCTACTTTAAC-TA
* *
1064093 AAATATTTTAAATATCTATTTTAACTA
1 AAATAATTTAAATATCTACTTTAACTA
1064120 AAATA
1 AAATA
1064125 TAATTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (27 bp):
AAATAATTTAAATATCTACTTTAACTA
Found at i:1064723 original size:59 final size:60
Alignment explanation
Indices: 1064654--1064785 Score: 187
Period size: 59 Copynumber: 2.2 Consensus size: 60
1064644 TAACTACAAC
*
1064654 TCTAAATTAGTCCTCAAACTTTTGAACATTCTATTTTCATCC-CTAACTATGACTC-TCAT
1 TCTAAATTAGTCCTCAAACTTTTGAACATTCTACTTTCATCCTCTAACTATGAC-CATCAT
* ** *
1064713 TCTAAGTTAGTCCTCAAACTTTTGAATGTTCTACTTTCATCCTCTAGCTATGACCATCAT
1 TCTAAATTAGTCCTCAAACTTTTGAACATTCTACTTTCATCCTCTAACTATGACCATCAT
*
1064773 TCTAAATTGGTCC
1 TCTAAATTAGTCC
1064786 CAATTTTTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
59 39 0.61
60 25 0.39
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (60 bp):
TCTAAATTAGTCCTCAAACTTTTGAACATTCTACTTTCATCCTCTAACTATGACCATCAT
Found at i:1066683 original size:2 final size:2
Alignment explanation
Indices: 1066676--1066702 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1066666 GAAAAAGGAA
1066676 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
1066703 CATCAAAGTA
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:1067126 original size:18 final size:17
Alignment explanation
Indices: 1067105--1067147 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1067095 ATATATACAT
1067105 ATAATAATAATAACATAA
1 ATAATAATAATAA-ATAA
* *
1067123 ATAATAAAAATAAATGA
1 ATAATAATAATAAATAA
1067140 ATAA-AATA
1 ATAATAATA
1067148 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:1067144 original size:14 final size:13
Alignment explanation
Indices: 1067107--1067145 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
1067097 ATATACATAT
1067107 AATAATAATAACATA
1 AATAATAA-AA-ATA
1067122 AATAATAAAAATA
1 AATAATAAAAATA
1067135 AATGAATAAAA
1 AAT-AATAAAA
1067146 TATCCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (13 bp):
AATAATAAAAATA
Found at i:1068488 original size:105 final size:105
Alignment explanation
Indices: 1068305--1068859 Score: 850
Period size: 105 Copynumber: 5.3 Consensus size: 105
1068295 GCATTGTTCA
* * **
1068305 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
1068365 CAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1068405 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
1068470 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
1068510 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
* *
1068575 CAGTGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1068615 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGAAAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
1068680 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1068720 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
1068785 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1068825 GAGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 GAGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
1068860 CGCGGATGGC
Statistics
Matches: 419, Mismatches: 28, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
100 35 0.08
101 1 0.00
102 2 0.00
103 2 0.00
104 2 0.00
105 352 0.84
106 3 0.01
108 22 0.05
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1069594 original size:67 final size:65
Alignment explanation
Indices: 1069461--1069914 Score: 284
Period size: 65 Copynumber: 6.7 Consensus size: 65
1069451 AATATATATG
* * * **
1069461 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA-
1069526 TT
64 TT
* * *
1069528 TGTGTTTCAAGAGTAATTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
1069593 T
65 T
* ** * * *
1069594 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-AT
* *
1069659 ACAAA-ACT
57 TCAAAGATT
* * * * * * * * * * *
1069667 TAGTTCCAAAAGCAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* * * * * * *
1069732 TTGTTTCAAGGGAAATTGTCTTAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-AT
*
1069797 ACAAA-ATT
57 TCAAAGATT
* * * * * * *** *
1069805 TTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-TT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
1069869 TATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAA
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAA
1069915 AAAAGCAATC
Statistics
Matches: 298, Mismatches: 67, Indels: 46
0.73 0.16 0.11
Matches are distributed among these distances:
64 11 0.04
65 121 0.41
66 4 0.01
67 24 0.08
68 32 0.11
70 1 0.00
72 2 0.01
73 93 0.31
74 10 0.03
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:1069645 original size:36 final size:36
Alignment explanation
Indices: 1069593--1069855 Score: 245
Period size: 36 Copynumber: 7.4 Consensus size: 36
1069583 ATTCAAAGAT
* *
1069593 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
1069629 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * * *
1069665 CTTAGTTCCAAAAGCAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * * *
1069702 TTTGTTTCAAAGAAAACATAT-TC-----A-A-ATAT
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
* *
1069731 TTTGTTTCAAGGGAAATTGTCTTAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
1069767 TTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
1069803 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
1069840 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGGGAAA
1069856 TGTTTTCAAT
Statistics
Matches: 182, Mismatches: 34, Indels: 22
0.76 0.14 0.09
Matches are distributed among these distances:
28 2 0.01
29 16 0.09
30 1 0.01
31 1 0.01
34 1 0.01
35 1 0.01
36 96 0.53
37 64 0.35
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:1069725 original size:138 final size:138
Alignment explanation
Indices: 1069545--1069914 Score: 463
Period size: 138 Copynumber: 2.7 Consensus size: 138
1069535 CAAGAGTAAT
* * * *
1069545 TGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGAAAC
* *
1069610 TGTCTCAAGATAGACGAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCA
66 TGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCA
*
1069675 AAAGCAAC
131 AAAGAAAC
* * * * *
1069683 TGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGAAAT
1 TGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGAAAC
* * * * * * *
1069748 TGTCTTAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCA
66 TGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCA
**
1069813 AGGGAAAC
131 AAAGAAAC
* * * * * * *
1069821 TATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-TTTATGTTTCAAGAGAAA
1 TGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTT-TGTTTCAAGGGAAA
*
1069885 CTGTCTCAAGGGAGACAAAATTTGTTTTAA
65 CTGTCTCAAGAGAGACAAAATTTGTTTTAA
1069915 AAAAGCAATC
Statistics
Matches: 194, Mismatches: 37, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
137 3 0.02
138 191 0.98
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (138 bp):
TGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGAAAC
TGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCA
AAAGAAAC
Found at i:1069762 original size:102 final size:102
Alignment explanation
Indices: 1069629--1069813 Score: 255
Period size: 102 Copynumber: 1.8 Consensus size: 102
1069619 ATAGACGAAA
* * *
1069629 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGCAACTGTCTCAAGGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAG
*
1069694 AGACGAAA-TTTGTTTCAAAGAAAACATATTCAAATAT
65 AGACAAAATTTTGTTTCAAAGAAAACATATTCAAATAT
* * * * * **
1069731 TTTGTTTCAAGGGAAATTGTCTTAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGA
1069796 GACAAAATTTTGTTTCAA
66 GACAAAATTTTGTTTCAA
1069814 GGGAAACTAT
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
101 26 0.37
102 45 0.63
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (102 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGA
GACAAAATTTTGTTTCAAAGAAAACATATTCAAATAT
Found at i:1070304 original size:18 final size:18
Alignment explanation
Indices: 1070277--1070312 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1070267 TGTTGAATCC
* *
1070277 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
1070295 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1070313 TTGATGTTGA
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:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:1070734 original size:22 final size:22
Alignment explanation
Indices: 1070706--1070760 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1070696 ATGTGTTTGG
1070706 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1070728 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
1070750 TCAAATGTTTG
1 TCAAAGGTTTG
1070761 ATGGGATAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1071397 original size:13 final size:12
Alignment explanation
Indices: 1071380--1071432 Score: 61
Period size: 13 Copynumber: 4.2 Consensus size: 12
1071370 TTTTTGTCCC
1071380 TTTTTCTTTTTT
1 TTTTTCTTTTTT
* *
1071392 CTTTTTGTTCTTT
1 -TTTTTCTTTTTT
*
1071405 TTTTGCTTTTTT
1 TTTTTCTTTTTT
1071417 TTTTTGCTTTTTT
1 TTTTT-CTTTTTT
1071430 TTT
1 TTT
1071433 CTTTTGCCCT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
12 13 0.39
13 20 0.61
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:1071399 original size:23 final size:25
Alignment explanation
Indices: 1071369--1071422 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
1071359 TTTGCATGTG
1071369 CTTTTTG-TCCCTTTTT-CTTTTTT
1 CTTTTTGTTCCCTTTTTGCTTTTTT
**
1071392 CTTTTTGTTCTTTTTTTGCTTTTTT
1 CTTTTTGTTCCCTTTTTGCTTTTTT
1071417 -TTTTTG
1 CTTTTTG
1071423 CTTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 7 0.26
24 13 0.48
25 7 0.26
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (25 bp):
CTTTTTGTTCCCTTTTTGCTTTTTT
Found at i:1071402 original size:9 final size:8
Alignment explanation
Indices: 1071380--1071437 Score: 59
Period size: 8 Copynumber: 7.2 Consensus size: 8
1071370 TTTTTGTCCC
1071380 TTTTTC-T
1 TTTTTCTT
1071387 TTTTTCTT
1 TTTTTCTT
1071395 TTTGTTCTT
1 TTT-TTCTT
1071404 TTTTTGCTT
1 TTTTT-CTT
1071413 TTTTT-TT
1 TTTTTCTT
*
1071420 TTGCTT-TT
1 TT-TTTCTT
1071428 TTTTTCTT
1 TTTTTCTT
1071436 TT
1 TT
1071438 GCCCTTTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
7 12 0.27
8 16 0.36
9 16 0.36
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.84
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1071409 original size:11 final size:10
Alignment explanation
Indices: 1071386--1071437 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 10
1071376 TCCCTTTTTC
1071386 TTTTTTC-TT
1 TTTTTTCTTT
*
1071395 TTTGTTCTTT
1 TTTTTTCTTT
1071405 TTTTGCTT-TTT
1 TTTT--TTCTTT
1071416 TTTTTTGCTTT
1 TTTTTT-CTTT
1071427 TTTTTTCTTT
1 TTTTTTCTTT
1071437 T
1 T
1071438 GCCCTTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
9 8 0.22
10 10 0.28
11 16 0.44
12 2 0.06
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.85
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:1071445 original size:16 final size:16
Alignment explanation
Indices: 1071410--1071451 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1071400 TCTTTTTTTG
*
1071410 CTTTTTTT-TTTTGCT
1 CTTTTTTTCTTTTGCC
*
1071425 TTTTTTTTCTTTTGCC
1 CTTTTTTTCTTTTGCC
1071441 CTTTTTATTCT
1 CTTTTT-TTCT
1071452 GATTAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 7 0.32
16 11 0.50
17 4 0.18
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.76
Consensus pattern (16 bp):
CTTTTTTTCTTTTGCC
Found at i:1071445 original size:31 final size:33
Alignment explanation
Indices: 1071371--1071446 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 33
1071361 TGCATGTGCT
*
1071371 TTTTGTCCCTTTTTCTTTTTTCTTTTTGTTCTTT
1 TTTTG-CCCTTTTTCTTTTTTCTTTTTGTTCTTC
1071405 TTTTG--CTTTTT-TTTTTTGCTTTTT-TT-TTC
1 TTTTGCCCTTTTTCTTTTTT-CTTTTTGTTCTTC
1071434 TTTTGCCCTTTTT
1 TTTTGCCCTTTTT
1071447 ATTCTGATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
29 7 0.18
30 8 0.21
31 18 0.47
34 5 0.13
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.78
Consensus pattern (33 bp):
TTTTGCCCTTTTTCTTTTTTCTTTTTGTTCTTC
Found at i:1071446 original size:18 final size:15
Alignment explanation
Indices: 1071380--1071439 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 15
1071370 TTTTTGTCCC
*
1071380 TTTTTCTTTTTT-CTT
1 TTTTTTTTTTTTGC-T
1071395 TTTGTTCTTTTTTTGC-
1 TTT-TT-TTTTTTTGCT
1071411 -TTTTTTTTTTTGCT
1 TTTTTTTTTTTTGCT
1071425 TTTTTTTTCTTTTGC
1 TTTTTTTT-TTTTGC
1071440 CCTTTTTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
13 9 0.24
14 2 0.05
15 12 0.32
16 8 0.21
17 6 0.16
18 1 0.03
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTTTTGCT
Found at i:1072629 original size:8 final size:8
Alignment explanation
Indices: 1072613--1072651 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1072603 ATTGTAGATG
1072613 AAAATGCA
1 AAAATGCA
*
1072621 AAAAGGCA
1 AAAATGCA
1072629 AAAATGC-
1 AAAATGCA
1072636 AAAATGCA
1 AAAATGCA
*
1072644 AGAATGCA
1 AAAATGCA
1072652 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:1072639 original size:15 final size:15
Alignment explanation
Indices: 1072613--1072651 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1072603 ATTGTAGATG
1072613 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
1072629 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
1072644 AGAATGCA
1 AAAATGCA
1072652 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:1074044 original size:14 final size:14
Alignment explanation
Indices: 1074025--1074051 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1074015 CAAGTGATGA
1074025 AAATAAAATAAAAT
1 AAATAAAATAAAAT
1074039 AAATAAAATAAAA
1 AAATAAAATAAAA
1074052 GATGAAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:1075167 original size:9 final size:9
Alignment explanation
Indices: 1075153--1075186 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1075143 GAAAAGGGAA
1075153 AAATAAAAT
1 AAATAAAAT
1075162 AAATAAAAT
1 AAATAAAAT
1075171 AAAT-AAAT
1 AAATAAAAT
1075179 AAGATAAA
1 AA-ATAAA
1075187 GGAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1075174 original size:13 final size:13
Alignment explanation
Indices: 1075152--1075186 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1075142 GGAAAAGGGA
1075152 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
1075166 AAAATAAATAAAT
1 AAAATAAATAAAT
*
1075179 AAGATAAA
1 AAAATAAA
1075187 GGAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:1075243 original size:2 final size:2
Alignment explanation
Indices: 1075236--1075262 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1075226 GAAAAAGGAA
1075236 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
1075263 CATCAAAGTA
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:1075502 original size:25 final size:23
Alignment explanation
Indices: 1075458--1075503 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
1075448 AAATAATATA
* *
1075458 TATAATATATATATATATAAAGT
1 TATAAGATATATATAAATAAAGT
1075481 TATAAGATATATTACTAAATAAA
1 TATAAGATATA-TA-TAAATAAA
1075504 AAATAATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 2 0.11
25 7 0.37
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.39
Consensus pattern (23 bp):
TATAAGATATATATAAATAAAGT
Found at i:1076853 original size:2 final size:2
Alignment explanation
Indices: 1076846--1076870 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1076836 TCACATATGA
1076846 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 A
1076871 GA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.