Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008245.1 Hibiscus syriacus cultivar Beakdansim tig00110895_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: 6601124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 33
Found at i:1370897 original size:12 final size:12
Alignment explanation
Indices: 1370880--1370904 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1370870 TCTTCGGGGA
1370880 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1370892 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1370904 C
1 C
1370905 AGGATTACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1371711 original size:12 final size:12
Alignment explanation
Indices: 1371686--1371718 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1371676 TTGCCGGATG
*
1371686 AGGAA-GGATGT
1 AGGAACGGATAT
1371697 AGGAACGGATAT
1 AGGAACGGATAT
1371709 AGGAACGGAT
1 AGGAACGGAT
1371719 GTCGCTGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.39, C:0.06, G:0.39, T:0.15
Consensus pattern (12 bp):
AGGAACGGATAT
Found at i:1371942 original size:20 final size:21
Alignment explanation
Indices: 1371917--1371968 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1371907 TTTTCCTAAT
*
1371917 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
1371937 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1371958 TCGCAATGCGA
1 TCGCAATGCGA
1371969 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1371999 original size:41 final size:40
Alignment explanation
Indices: 1371954--1372045 Score: 121
Period size: 41 Copynumber: 2.3 Consensus size: 40
1371944 GCGAATTTGG
*
1371954 AAAATCGCAATGCGATACTGACTATCGCAACGAGATTATAC
1 AAAATCGCAATGAGATACTGACTATCGCAACGAGATTAT-C
* * * * *
1371995 AAAATCGCAACGAGATTCTGACTTTCGCAACGAGATTCTG
1 AAAATCGCAATGAGATACTGACTATCGCAACGAGATTATC
1372035 AAAATCGCAAT
1 AAAATCGCAAT
1372046 CATCTTCAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 10 0.23
41 34 0.77
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (40 bp):
AAAATCGCAATGAGATACTGACTATCGCAACGAGATTATC
Found at i:1372042 original size:20 final size:20
Alignment explanation
Indices: 1371953--1372044 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
1371943 TGCGAATTTG
* * *
1371953 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATTCT
** *
1371973 GACTATCGCAACGAGATTAT
1 GAAAATCGCAACGAGATTCT
*
1371993 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATTCT
***
1372014 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATTCT
1372034 GAAAATCGCAA
1 GAAAATCGCAA
1372045 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 38 0.70
21 16 0.30
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
GAAAATCGCAACGAGATTCT
Found at i:1372353 original size:20 final size:20
Alignment explanation
Indices: 1372258--1372345 Score: 97
Period size: 20 Copynumber: 4.4 Consensus size: 20
1372248 CAACAGGGAA
*
1372258 ATCGCAATGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1372278 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
1372298 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
*
1372318 ATTGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1372338 ATCGCAAC
1 ATCGCAAC
1372346 TAGAAAATCG
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
19 5 0.09
20 43 0.81
21 5 0.09
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:1374044 original size:43 final size:42
Alignment explanation
Indices: 1373997--1374089 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
1373987 CCTCTTCAAC
* * * *
1373997 GATGACAGTGTCCTCTTGAACGGTGGGGGGGGGACTCTTGAGG
1 GATGACAGAGGCCTCTTGAACGAT-GGGAGGGGACTCTTGAGG
* * *
1374040 GATGATAGAGGCCTCTTGAACGATTGGAGGGGACTCTTTAGG
1 GATGACAGAGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
*
1374082 AATGACAG
1 GATGACAG
1374090 GTGAGTCGGG
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
42 21 0.51
43 20 0.49
ACGTcount: A:0.23, C:0.15, G:0.39, T:0.24
Consensus pattern (42 bp):
GATGACAGAGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
Found at i:1374458 original size:20 final size:20
Alignment explanation
Indices: 1374433--1374518 Score: 111
Period size: 20 Copynumber: 4.3 Consensus size: 20
1374423 TAGTTTACTT
* *
1374433 TCGCAACGAGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
1374453 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1374473 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1374493 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1374512 TCGCAAC
1 TCGCAAC
1374519 TACAAAATCG
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 13 0.22
20 45 0.78
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1374488 original size:40 final size:39
Alignment explanation
Indices: 1374433--1374559 Score: 113
Period size: 33 Copynumber: 3.4 Consensus size: 39
1374423 TAGTTTACTT
**
1374433 TCGCAACGAGAAAATGACTATCGCAACGCGGAAATGACTA
1 TCGCAACGAGAAAATGACTATCGCAACGC-GAAATGAAAA
* * * *
1374473 TCGCAACGCGGAAATGGCTATCGCAATGCGAAATGAAAA
1 TCGCAACGAGAAAATGACTATCGCAACGCGAAATGAAAA
* * *
1374512 TCGCAAC--TACAA--A--ATCGCAATGCGAAATGAAAA
1 TCGCAACGAGAAAATGACTATCGCAACGCGAAATGAAAA
*
1374545 TCGCAACGACAAAAT
1 TCGCAACGAGAAAAT
1374560 CGCAACGCGA
Statistics
Matches: 72, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
33 27 0.38
35 3 0.04
37 2 0.03
39 15 0.21
40 25 0.35
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.15
Consensus pattern (39 bp):
TCGCAACGAGAAAATGACTATCGCAACGCGAAATGAAAA
Found at i:1374514 original size:19 final size:19
Alignment explanation
Indices: 1374492--1374550 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
1374482 GGAAATGGCT
1374492 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1374511 ATCGCAA--C--TA-CAAA
1 ATCGCAATGCGAAATGAAA
1374525 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1374544 ATCGCAA
1 ATCGCAA
1374551 CGACAAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 10 0.32
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 17 0.55
ACGTcount: A:0.47, C:0.20, G:0.17, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1374560 original size:14 final size:14
Alignment explanation
Indices: 1374508--1374566 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
1374498 ATGCGAAATG
*
1374508 AAAATCGCAACTAC
1 AAAATCGCAACGAC
*
1374522 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
1374541 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1374555 AAAATCGCAACG
1 AAAATCGCAACG
1374567 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 22 0.59
15 1 0.03
16 1 0.03
17 2 0.05
18 1 0.03
19 10 0.27
ACGTcount: A:0.49, C:0.24, G:0.15, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1374582 original size:33 final size:33
Alignment explanation
Indices: 1374492--1374571 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
1374482 GGAAATGGCT
*
1374492 ATCGCAATGCGAAATGAAAATCGCAACTACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1374525 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1374558 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1374572 CACAAATCGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1374600 original size:19 final size:19
Alignment explanation
Indices: 1374578--1374707 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
1374568 GAAACACAAA
1374578 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1374597 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1374613 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1374630 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1374646 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1374663 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1374679 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1374696 TCGCATTGCGAT
1 TCGCATTGCGAT
1374708 AGCCATTTCC
Statistics
Matches: 89, Mismatches: 7, Indels: 30
0.71 0.06 0.24
Matches are distributed among these distances:
14 18 0.20
15 9 0.10
16 12 0.13
17 12 0.13
18 9 0.10
19 29 0.33
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1374619 original size:14 final size:14
Alignment explanation
Indices: 1374600--1374691 Score: 76
Period size: 14 Copynumber: 5.9 Consensus size: 14
1374590 TTTCATTTCG
1374600 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1374614 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
1374631 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1374647 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
1374664 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1374680 CGTTGCGATTTT
1 CGTTGCGATTTT
1374692 CATTTCGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 20
0.73 0.05 0.23
Matches are distributed among these distances:
14 24 0.38
15 6 0.09
16 8 0.12
17 8 0.12
18 6 0.09
19 12 0.19
ACGTcount: A:0.11, C:0.17, G:0.23, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1374625 original size:33 final size:33
Alignment explanation
Indices: 1374583--1374707 Score: 241
Period size: 33 Copynumber: 3.8 Consensus size: 33
1374573 ACAAATCGCA
*
1374583 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1374616 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1374649 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1374682 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1374708 AGCCATTTCC
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 91 1.00
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1374714 original size:19 final size:20
Alignment explanation
Indices: 1374692--1374735 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1374682 TTGCGATTTT
*
1374692 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTACGATAGC
* *
1374711 CATTTCCGCGTTACGATAGT
1 CATTTCCGCATTACGATAGC
1374731 CATTT
1 CATTT
1374736 TCATGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTACGATAGC
Found at i:1375310 original size:18 final size:18
Alignment explanation
Indices: 1375287--1375334 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1375277 CGGGTCGATC
1375287 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
1375305 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
1375323 AGGTGATGGCTC
1 AGGTGATGGCTC
1375335 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:1376689 original size:20 final size:20
Alignment explanation
Indices: 1376666--1376705 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1376656 AATCTCAATA
1376666 CGAAAATGACAATCGCAACG
1 CGAAAATGACAATCGCAACG
** *
1376686 CGAATTTGACTATCGCAACG
1 CGAAAATGACAATCGCAACG
1376706 AGAGAATAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (20 bp):
CGAAAATGACAATCGCAACG
Found at i:1376996 original size:22 final size:22
Alignment explanation
Indices: 1376968--1377011 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1376958 GATGGTGATA
1376968 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1376990 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1377012 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1377297 original size:41 final size:41
Alignment explanation
Indices: 1377178--1377315 Score: 161
Period size: 41 Copynumber: 3.4 Consensus size: 41
1377168 CGCTTTGAAA
* * *
1377178 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* * ** * * *
1377219 ATTGAGTTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
1377259 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
1377300 ACCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
1377316 CCAAATTCGC
Statistics
Matches: 77, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 32 0.42
41 45 0.58
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:1377312 original size:20 final size:20
Alignment explanation
Indices: 1377198--1377311 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
1377188 GATTATGTAT
*
1377198 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * * *
1377218 TATTGAGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
1377238 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
1377258 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
1377279 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1377299 TACCGCGTTGCGA
1 TATCGCGTTGCGA
1377312 TTTTCCAAAT
Statistics
Matches: 76, Mismatches: 15, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
19 3 0.04
20 57 0.75
21 14 0.18
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1377332 original size:21 final size:21
Alignment explanation
Indices: 1377306--1377436 Score: 228
Period size: 21 Copynumber: 6.3 Consensus size: 21
1377296 CAGTACCGCG
1377306 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
1377327 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
1377348 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
1377369 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
1377390 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
* **
1377411 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCAAATTCGCA
1377431 TTGCGA
1 TTGCGA
1377437 ATTGGGAAAA
Statistics
Matches: 107, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
20 17 0.16
21 90 0.84
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCA
Found at i:1377478 original size:21 final size:22
Alignment explanation
Indices: 1377426--1377478 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
1377416 ATTTACTTAT
1377426 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
1377447 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
*
1377468 TCGCGTTGCGA
1 TCGCATTGCGA
1377479 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:1378693 original size:50 final size:50
Alignment explanation
Indices: 1378595--1378699 Score: 165
Period size: 50 Copynumber: 2.1 Consensus size: 50
1378585 GACTCGTTAA
* * ** *
1378595 ATTATTAATACCTAATTAAATTTTAACCTAAATTAAAATATTTTTATTAT
1 ATTAATAATACCTAATTAAATTTTAACCTAAATTAAAAAAAATCTATTAT
1378645 ATTAATAATACCTAATTAAATTTTAACCTAAATTAAAAAAAATCTATTAT
1 ATTAATAATACCTAATTAAATTTTAACCTAAATTAAAAAAAATCTATTAT
1378695 ATTAA
1 ATTAA
1378700 AATTAATTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (50 bp):
ATTAATAATACCTAATTAAATTTTAACCTAAATTAAAAAAAATCTATTAT
Found at i:1381526 original size:28 final size:22
Alignment explanation
Indices: 1381445--1381512 Score: 118
Period size: 22 Copynumber: 3.0 Consensus size: 22
1381435 TTGCCCAAAA
*
1381445 AAATCACAAAAAATAATTTATT
1 AAATCATAAAAAATAATTTATT
1381467 AAATCATAAAAAATAATTTATT
1 AAATCATAAAAAATAATTTATT
1381489 AAATCATAAAAAAGTAATTTATT
1 AAATCATAAAAAA-TAATTTATT
1381512 A
1 A
1381513 TACTATTCTA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 34 0.77
23 10 0.23
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.34
Consensus pattern (22 bp):
AAATCATAAAAAATAATTTATT
Found at i:1385367 original size:10 final size:10
Alignment explanation
Indices: 1385354--1385433 Score: 51
Period size: 10 Copynumber: 8.1 Consensus size: 10
1385344 TGGTTTTCTG
1385354 ATATATGTAT
1 ATATATGTAT
*
1385364 ATATATGTGTT
1 ATATATGT-AT
*
1385375 TTATATGGT-T
1 ATATAT-GTAT
1385385 -T-TATG-AT
1 ATATATGTAT
*
1385392 ATATATATAT
1 ATATATGTAT
*
1385402 ATATATATAT
1 ATATATGTAT
*
1385412 ATATATTTAT
1 ATATATGTAT
*
1385422 ATTTATCGTAT
1 ATATAT-GTAT
1385433 A
1 A
1385434 AACATTTCTT
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
7 2 0.04
8 4 0.07
9 4 0.07
10 35 0.61
11 10 0.18
12 2 0.04
ACGTcount: A:0.36, C:0.01, G:0.09, T:0.54
Consensus pattern (10 bp):
ATATATGTAT
Found at i:1385380 original size:36 final size:36
Alignment explanation
Indices: 1385335--1385405 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
1385325 ACCAGTATTT
* *
1385335 TGTTTTATATGGTTTTCTGATATATGTATATATATG
1 TGTTTTATATGGTTTTATGATATATATATATATATG
1385371 TGTTTTATATGGTTTTATGATATATATATATATAT
1 TGTTTTATATGGTTTTATGATATATATATATATAT
1385406 ATATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.01, G:0.14, T:0.56
Consensus pattern (36 bp):
TGTTTTATATGGTTTTATGATATATATATATATATG
Found at i:1385397 original size:2 final size:2
Alignment explanation
Indices: 1385390--1385423 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1385380 TGGTTTTATG
*
1385390 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1385424 TTATCGTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1385563 original size:2 final size:2
Alignment explanation
Indices: 1385556--1385580 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1385546 TAAAAGGGGT
1385556 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
1385581 GTAAGGCGGC
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:1385911 original size:3 final size:3
Alignment explanation
Indices: 1385891--1385971 Score: 87
Period size: 3 Copynumber: 27.7 Consensus size: 3
1385881 TTTTTCATTT
* *
1385891 TTA TT- TTA TT- TATA TTA TTA TTA TTA TAA TTA TTA TTA TTA TAA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1385935 TTA TAA TTA TAA TTA TTA TTA TTA TTA ATA -TA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1385972 TAATATTACA
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
2 5 0.08
3 59 0.91
4 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1385911 original size:12 final size:12
Alignment explanation
Indices: 1385887--1385979 Score: 54
Period size: 12 Copynumber: 7.8 Consensus size: 12
1385877 ATTTTTTTTC
*
1385887 ATTTTTATT-TT
1 ATTTATATTATT
1385898 ATTTATATTATT
1 ATTTATATTATT
*
1385910 A-TTATTATAATT
1 ATTTA-TATTATT
1385922 A-TTATTATTA-T
1 ATTTA-TATTATT
*
1385933 AATTATAATTA-T
1 ATTTAT-ATTATT
*
1385945 AATTATTATTATT
1 ATTTA-TATTATT
*
1385958 ATTAATA-TATT
1 ATTTATATTATT
1385969 ATTTAATATTA
1 ATTT-ATATTA
1385980 CAAGCCCAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
11 21 0.31
12 40 0.59
13 7 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTTATATTATT
Found at i:1386461 original size:15 final size:15
Alignment explanation
Indices: 1386441--1386482 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1386431 ACAACTCAGC
1386441 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
1386456 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
1386471 AAAGAAGAGAAA
1 AAAGAAAAGAAA
1386483 CTTATTGTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:1386466 original size:20 final size:20
Alignment explanation
Indices: 1386441--1386482 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1386431 ACAACTCAGC
*
1386441 AAAGAAACAGAAAAGAA-AGA
1 AAAGAAAAAG-AAAGAAGAGA
1386461 AAAGAAAAAGAAAGAAGAGA
1 AAAGAAAAAGAAAGAAGAGA
1386481 AA
1 AA
1386483 CTTATTGTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAGAGA
Found at i:1387560 original size:109 final size:107
Alignment explanation
Indices: 1387365--1387581 Score: 251
Period size: 109 Copynumber: 2.0 Consensus size: 107
1387355 ATATAATAAA
* * * *
1387365 TAATAATTAATTTTTTTAAATAAATTATTTTAATATTTATTTTTCAATATCGAAGAAAAGGACAG
1 TAATAATTAATTTTTTAAAATAAATTAATTTAATATTTATTTATCAATATCAAAGAAAAGGACAG
* * * *
1387430 TCTTAATACAACTGGATGTCCTATTCTGGTATTTTAAA-ATT
66 TCTTAAGACAACTAGAAGTCCTATTCTGATATTTTAAATATT
*
1387471 TAATAATTAATTTTTTAAAATATTATTTAATTTAA-ATTAATATTTATCAATATCAAAGAAAA-G
1 TAATAATTAATTTTTTAAAATA--AATTAATTTAATATT--TATTTATCAATATCAAAGAAAAGG
* * * *
1387534 AGCTGTCTTAAGGCACCTAGAAGTCCTTTTCTGATATTTTAAATATT
62 A-CAGTCTTAAGACAACTAGAAGTCCTATTCTGATATTTTAAATATT
1387581 T
1 T
1387582 TTTATAAATT
Statistics
Matches: 92, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
106 21 0.23
107 3 0.03
108 11 0.12
109 53 0.58
110 4 0.04
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.44
Consensus pattern (107 bp):
TAATAATTAATTTTTTAAAATAAATTAATTTAATATTTATTTATCAATATCAAAGAAAAGGACAG
TCTTAAGACAACTAGAAGTCCTATTCTGATATTTTAAATATT
Found at i:1391413 original size:15 final size:15
Alignment explanation
Indices: 1391393--1391424 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1391383 ATCAATACCT
1391393 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
1391408 TTTTGCATACATTCA
1 TTTTGCATACATGCA
1391423 TT
1 TT
1391425 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:1398769 original size:9 final size:9
Alignment explanation
Indices: 1398755--1398796 Score: 66
Period size: 9 Copynumber: 4.6 Consensus size: 9
1398745 TGCTTGAAGA
1398755 AAAAAAAAG
1 AAAAAAAAG
1398764 AAAAAAAAG
1 AAAAAAAAG
*
1398773 AAAAAAGAG
1 AAAAAAAAG
1398782 AAAAAAGAAG
1 AAAAAA-AAG
1398792 AAAAA
1 AAAAA
1398797 GGGGGGACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
9 23 0.77
10 7 0.23
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:1398775 original size:19 final size:20
Alignment explanation
Indices: 1398750--1398796 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 20
1398740 TATTATGCTT
1398750 GAAGAAAAAAAAAGAAAAAA
1 GAAGAAAAAAAAAGAAAAAA
*
1398770 -AAG-AAAAAAGAGAAAAAA
1 GAAGAAAAAAAAAGAAAAAA
1398788 GAAGAAAAA
1 GAAGAAAAA
1398797 GGGGGGACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 14 0.58
19 6 0.25
20 4 0.17
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (20 bp):
GAAGAAAAAAAAAGAAAAAA
Found at i:1398778 original size:16 final size:16
Alignment explanation
Indices: 1398757--1398795 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1398747 CTTGAAGAAA
1398757 AAAAAAGAAAAAAAAG
1 AAAAAAGAAAAAAAAG
*
1398773 AAAAAAGAGAAAAAAG
1 AAAAAAGAAAAAAAAG
1398789 AAGAAAA
1 AA-AAAA
1398796 AGGGGGGACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAG
Found at i:1399135 original size:16 final size:16
Alignment explanation
Indices: 1399109--1399153 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1399099 TTTGAATACA
*
1399109 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
1399126 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
1399141 ATTCAATTTATTT
1 ATTCAATTTATTT
1399154 TCGAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:1400121 original size:83 final size:83
Alignment explanation
Indices: 1399922--1400121 Score: 337
Period size: 83 Copynumber: 2.4 Consensus size: 83
1399912 ATCCCAGTCT
* *
1399922 AATCATTGAATTTGAAAGATGAATGTGCTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 AATCATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTA
* *
1399987 ATCTGGTTTGGTAGAACC
66 ATCTGGTTTGGCAAAACC
1400005 AATCATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTA
1 AATCATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTA
1400070 ATCTGGTTTGGCAAAACC
66 ATCTGGTTTGGCAAAACC
* * *
1400088 AATCATTGGATTTAAAAGATGAATTTGCTCATAG
1 AATCATTGAATTTGAAAGATGAATGTGCTCATAG
1400122 TAAAAATAAA
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 110 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.36
Consensus pattern (83 bp):
AATCATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTA
ATCTGGTTTGGCAAAACC
Found at i:1401118 original size:113 final size:113
Alignment explanation
Indices: 1400931--1401597 Score: 1084
Period size: 113 Copynumber: 5.9 Consensus size: 113
1400921 TCAATAGTGT
*
1400931 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAATAAGGATGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
* *
1400996 TTTGTTCAACCTTTTGATCAAATCCATCACTTGATGGATCAACTTTTC
66 TTTGTTCAACCTTTTGATCAAATCCATCACTTGATAGATCATCTTTTC
1401044 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
* *
1401109 TTTGTTCAACCTTTTGATCAAATCTATCACTTGATAGATTATCTTTTC
66 TTTGTTCAACCTTTTGATCAAATCCATCACTTGATAGATCATCTTTTC
1401157 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
* * * *
1401222 TTTATTCAACCTTTTGATCTAATCCATCACTTGATGGATCAACTTTTC
66 TTTGTTCAACCTTTTGATCAAATCCATCACTTGATAGATCATCTTTTC
1401270 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
* * *
1401335 TTTATTCAACCTTTTGATCAAATCTATCACTTGATAGATTATCTTTTC
66 TTTGTTCAACCTTTTGATCAAATCCATCACTTGATAGATCATCTTTTC
* *
1401383 CAGTTCGAGTTCATAATGAGAAGAACTTATCTGAAGAAATAGATGAAGAAGTTCATAATGAGAAG
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG-AA-GGATGAAGAAGTTCATAATGAGAAG
* * *
1401448 AATTTGTTCAACCTTCTGCTCAAA-CCTATCACTTGATAGATTATCTTTTC
64 AATTTGTTCAACCTTTTGATCAAATCC-ATCACTTGATAGATCATCTTTTC
* * *
1401498 TAGTTCGAGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
* * * *
1401563 TTTGTTCAGCTTTTTGCTCAAATCCATTACTTGAT
66 TTTGTTCAACCTTTTGATCAAATCCATCACTTGAT
1401598 GGGTCAGTTT
Statistics
Matches: 519, Mismatches: 31, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
113 411 0.79
114 7 0.01
115 101 0.19
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (113 bp):
CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
TTTGTTCAACCTTTTGATCAAATCCATCACTTGATAGATCATCTTTTC
Found at i:1401597 original size:341 final size:339
Alignment explanation
Indices: 1400931--1401613 Score: 1141
Period size: 341 Copynumber: 2.0 Consensus size: 339
1400921 TCAATAGTGT
*
1400931 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAATAAGGATGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
* *
1400996 TTTGTTCAACCTTTTGATCAAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAAT
66 TTTATTCAACCTTTTGATCAAATCCATCACTTGATAGATCAACTTTTCCAGTTCGAGTTCATAAT
* *
1401061 GAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGA
131 GAGAAGAACTCATCTGAAGAAAGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTCTGA
* *
1401126 TCAAATCTATCACTTGATAGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
196 TCAAACCTATCACTTGATAGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACCCATCTGA
* *
1401191 AGAAGGATGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGATCTAATCCATCACTTGA
261 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGATCAAATCCATCACTTGA
1401256 TGGATCAACTTTTC
326 TGGATCAACTTTTC
1401270 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
1 CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
* * *
1401335 TTTATTCAACCTTTTGATCAAATCTATCACTTGATAGATTATCTTTTCCAGTTCGAGTTCATAAT
66 TTTATTCAACCTTTTGATCAAATCCATCACTTGATAGATCAACTTTTCCAGTTCGAGTTCATAAT
*
1401400 GAGAAGAACTTATCTGAAGAAATAGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTCT
131 GAGAAGAACTCATCTGAAG-AA-AGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTCT
* *
1401465 GCTCAAACCTATCACTTGATAGATTATCTTTTCTAGTTCGAGTTCATAATGAGAAGAACCCATCT
194 GATCAAACCTATCACTTGATAGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACCCATCT
* * * * *
1401530 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAGCTTTTTGCTCAAATCCATTACTT
259 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGATCAAATCCATCACTT
* **
1401595 GATGGGTCAGTTTTTC
324 GATGGATCAACTTTTC
1401611 CAG
1 CAG
1401614 AGAAGAACTT
Statistics
Matches: 319, Mismatches: 23, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
339 142 0.45
340 2 0.01
341 175 0.55
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (339 bp):
CAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAA
TTTATTCAACCTTTTGATCAAATCCATCACTTGATAGATCAACTTTTCCAGTTCGAGTTCATAAT
GAGAAGAACTCATCTGAAGAAAGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTCTGA
TCAAACCTATCACTTGATAGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACCCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGATCAAATCCATCACTTGA
TGGATCAACTTTTC
Found at i:1401874 original size:3 final size:3
Alignment explanation
Indices: 1401854--1401934 Score: 87
Period size: 3 Copynumber: 27.7 Consensus size: 3
1401844 TTTTTCATTT
* *
1401854 TTA TT- TTA TT- TATA TTA TTA TTA TTA TAA TTA TTA TTA TTA TAA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1401898 TTA TAA TTA TAA TTA TTA TTA TTA TTA ATA -TA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1401935 TAATATTACA
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
2 5 0.08
3 59 0.91
4 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1401874 original size:12 final size:12
Alignment explanation
Indices: 1401850--1401942 Score: 54
Period size: 12 Copynumber: 7.8 Consensus size: 12
1401840 CATTTTTTTC
*
1401850 ATTTTTATT-TT
1 ATTTATATTATT
1401861 ATTTATATTATT
1 ATTTATATTATT
*
1401873 A-TTATTATAATT
1 ATTTA-TATTATT
1401885 A-TTATTATTA-T
1 ATTTA-TATTATT
*
1401896 AATTATAATTA-T
1 ATTTAT-ATTATT
*
1401908 AATTATTATTATT
1 ATTTA-TATTATT
*
1401921 ATTAATA-TATT
1 ATTTATATTATT
1401932 ATTTAATATTA
1 ATTT-ATATTA
1401943 CAAGCACAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
11 21 0.31
12 40 0.59
13 7 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTTATATTATT
Found at i:1402425 original size:15 final size:15
Alignment explanation
Indices: 1402405--1402446 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1402395 ACAACTCAGC
1402405 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
1402420 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
1402435 AAAGAAGAGAAA
1 AAAGAAAAGAAA
1402447 CTTACTGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:1402430 original size:20 final size:20
Alignment explanation
Indices: 1402405--1402446 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1402395 ACAACTCAGC
*
1402405 AAAGAAACAGAAAAGAA-AGA
1 AAAGAAAAAG-AAAGAAGAGA
1402425 AAAGAAAAAGAAAGAAGAGA
1 AAAGAAAAAGAAAGAAGAGA
1402445 AA
1 AA
1402447 CTTACTGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAGAGA
Found at i:1403525 original size:109 final size:107
Alignment explanation
Indices: 1403324--1403540 Score: 242
Period size: 109 Copynumber: 2.0 Consensus size: 107
1403314 ATATAATAAA
* * * *
1403324 TAATAATTAATTTTTTTAAATAAATTATTTTAATATTTATTTTTCAATATCGAAGAAAATGACAG
1 TAATAATTAATTTTTTAAAATAAATTAATTTAATATTTATTTATCAATATCAAAGAAAATGACAG
* * * *
1403389 TCTTAATACAACTGGATGTCCTATTCTGGTATTTTAAA-ATT
66 TCTTAAGACAACTAGAAGTCCTATTCTGATATTTTAAATATT
*
1403430 TAATAATTAATTTTTTAAAATATTATTTAATTTAA-ATTAATATTTATCAATATCAAAGAAAA-G
1 TAATAATTAATTTTTTAAAATA--AATTAATTTAATATT--TATTTATCAATATCAAAGAAAATG
* * * * *
1403493 AGCTGTCTTAAGGCACCTAGAAGTCTTTTTCTGATATTTTAAATATT
62 A-CAGTCTTAAGACAACTAGAAGTCCTATTCTGATATTTTAAATATT
1403540 T
1 T
1403541 TTTATAAATT
Statistics
Matches: 91, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
106 21 0.23
107 3 0.03
108 11 0.12
109 52 0.57
110 4 0.04
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (107 bp):
TAATAATTAATTTTTTAAAATAAATTAATTTAATATTTATTTATCAATATCAAAGAAAATGACAG
TCTTAAGACAACTAGAAGTCCTATTCTGATATTTTAAATATT
Found at i:1412117 original size:6 final size:6
Alignment explanation
Indices: 1412100--1412160 Score: 68
Period size: 6 Copynumber: 9.5 Consensus size: 6
1412090 GATCAATATT
* *
1412100 TTTGCA TATGCA TTTGCATA TTTGCA TTTGCA TATGCA TTTGCATA TTTGCA
1 TTTGCA TTTGCA TTTGC--A TTTGCA TTTGCA TTTGCA TTTGC--A TTTGCA
1412152 TTTGCA TTT
1 TTTGCA TTT
1412161 ACCTTTACAC
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
6 35 0.74
8 12 0.26
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49
Consensus pattern (6 bp):
TTTGCA
Found at i:1412129 original size:26 final size:26
Alignment explanation
Indices: 1412100--1412158 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
1412090 GATCAATATT
1412100 TTTGCATATGCATTTGCATATTTGCA
1 TTTGCATATGCATTTGCATATTTGCA
1412126 TTTGCATATGCATTTGCATATTTGCA
1 TTTGCATATGCATTTGCATATTTGCA
1412152 TTTGCAT
1 TTTGCAT
1412159 TTACCTTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.47
Consensus pattern (26 bp):
TTTGCATATGCATTTGCATATTTGCA
Found at i:1412160 original size:20 final size:20
Alignment explanation
Indices: 1412100--1412158 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
1412090 GATCAATATT
*
1412100 TTTGCATATGCATTTGCATA
1 TTTGCATTTGCATTTGCATA
*
1412120 TTTGCATTTGCATATGC--A
1 TTTGCATTTGCATTTGCATA
1412138 TTTGCATATTTGCATTTGCAT
1 TTTGC--ATTTGCATTTGCAT
1412159 TTACCTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 6 0.19
20 26 0.81
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.47
Consensus pattern (20 bp):
TTTGCATTTGCATTTGCATA
Found at i:1415288 original size:17 final size:17
Alignment explanation
Indices: 1415266--1415314 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
1415256 AAAAACACAC
*
1415266 ACAAAAAGAAAGTAAAA
1 ACAAAAAGAAAGAAAAA
*
1415283 ACAAAAAAAAAGAAAAA
1 ACAAAAAGAAAGAAAAA
*
1415300 AAAAAAAGAAA-AAAA
1 ACAAAAAGAAAGAAAA
1415315 GAAAGAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 4 0.14
17 24 0.86
ACGTcount: A:0.86, C:0.04, G:0.08, T:0.02
Consensus pattern (17 bp):
ACAAAAAGAAAGAAAAA
Found at i:1415294 original size:21 final size:22
Alignment explanation
Indices: 1415268--1415365 Score: 85
Period size: 21 Copynumber: 4.4 Consensus size: 22
1415258 AAACACACAC
* *
1415268 AAAAAGAAAGTAAAAACAA-AA
1 AAAAAGAAAGAAAAAAAAAGAA
1415289 AAAAAGAAA-AAAAAAAAAGAA
1 AAAAAGAAAGAAAAAAAAAGAA
* **
1415310 AAAAAGAAAGAGAAAACGAGAA
1 AAAAAGAAAGAAAAAAAAAGAA
*
1415332 AAAGA-AAAGAAGAAAAAAAAGAA
1 AAAAAGAAAG-A-AAAAAAAAGAA
1415355 GAAAGAAGAAA
1 -AAA-AAGAAA
1415366 ATAGACAGAT
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
20 7 0.12
21 24 0.40
22 14 0.23
23 8 0.13
24 3 0.05
25 1 0.02
26 3 0.05
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.01
Consensus pattern (22 bp):
AAAAAGAAAGAAAAAAAAAGAA
Found at i:1415298 original size:8 final size:8
Alignment explanation
Indices: 1415269--1415366 Score: 65
Period size: 8 Copynumber: 11.5 Consensus size: 8
1415259 AACACACACA
1415269 AAAAGAAAG
1 AAAA-AAAG
1415278 TAAAAACAA-
1 -AAAAA-AAG
1415287 AAAAAAAG
1 AAAAAAAG
1415295 AAAAAAA-
1 AAAAAAAG
*
1415302 AAAAAGAAA
1 AAAAA-AAG
1415311 AAAAGAAAG
1 AAAA-AAAG
* *
1415320 AGAAAACG
1 AAAAAAAG
*
1415328 AGAAAAAG
1 AAAAAAAG
*
1415336 AAAAGAAG
1 AAAAAAAG
1415344 AAAAAAAAG
1 -AAAAAAAG
1415353 AAGAAAGAAG
1 AA-AAA-AAG
1415363 AAAA
1 AAAA
1415367 TAGACAGATC
Statistics
Matches: 73, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
7 7 0.10
8 32 0.44
9 22 0.30
10 12 0.16
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.01
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1415304 original size:14 final size:14
Alignment explanation
Indices: 1415280--1415350 Score: 63
Period size: 14 Copynumber: 4.9 Consensus size: 14
1415270 AAAGAAAGTA
1415280 AAAACAAAAAAAAAG
1 AAAA-AAAAAAAAAG
1415295 -AAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
* *
1415308 AAAAAAAGAAAGAG
1 AAAAAAAAAAAAAG
** *
1415322 AAAACGAGAAAAAG
1 AAAAAAAAAAAAAG
1415336 AAAAGAAGAAAAAAA
1 AAAA-AA-AAAAAAA
1415351 AGAAGAAAGA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
13 10 0.22
14 29 0.64
16 6 0.13
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:1415365 original size:33 final size:34
Alignment explanation
Indices: 1415268--1415366 Score: 93
Period size: 33 Copynumber: 3.0 Consensus size: 34
1415258 AAACACACAC
*
1415268 AAAAAGAAAGTAAAAACAAA-AAAAAAGAA-AAAAA
1 AAAAAG-AAG-AAAAACAAAGAAGAAAGAAGAAAAA
*
1415302 AAAAAGAA-AAAAAGAAAG-AGAAA-ACGAGAAAAA
1 AAAAAGAAGAAAAACAAAGAAGAAAGA--AGAAAAA
*
1415335 GAAAAGAAGAAAAA-AAAGAAGAAAGAAGAAAA
1 AAAAAGAAGAAAAACAAAGAAGAAAGAAGAAAA
1415367 TAGACAGATC
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
30 1 0.02
31 12 0.22
32 1 0.02
33 24 0.44
34 16 0.29
35 1 0.02
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.01
Consensus pattern (34 bp):
AAAAAGAAGAAAAACAAAGAAGAAAGAAGAAAAA
Found at i:1417490 original size:43 final size:43
Alignment explanation
Indices: 1417443--1418184 Score: 698
Period size: 43 Copynumber: 17.3 Consensus size: 43
1417433 ATTTTCAACA
** *
1417443 TTTCTTGATGACAAGCTTGAGAAACCATCATGATATGTAGGGG
1 TTTCTTGATGACAAGCTTGAGGGACCATCGTGATATGTAGGGG
* *
1417486 TTTCTTGAGGACAAGTTTGAGGGACCATCGTGATATGTAGGGG
1 TTTCTTGATGACAAGCTTGAGGGACCATCGTGATATGTAGGGG
* * * *
1417529 TTCCTTGAAGAAAAGCTTGAGAGACCATCGTGATATGTAGGGGG
1 TTTCTTGATGACAAGCTTGAGGGACCATCGTGATATGTA-GGGG
* * *
1417573 TTT-TTGAGGACAAGTTTGAGGGACCATTGTGATATGTA-GGG
1 TTTCTTGATGACAAGCTTGAGGGACCATCGTGATATGTAGGGG
* * *
1417614 TTCCTTGATGACACA-CATGAGGGACCAACGTGATATGTAGGGG
1 TTTCTTGATGACA-AGCTTGAGGGACCATCGTGATATGTAGGGG
* * * ** * * * *
1417657 TTCCTTGGTGACAA--TTAAGAAACTAAGCCTGAT-TTTCAGGGG
1 TTTCTTGATGACAAGCTTGAGGGAC-CATCGTGATATGT-AGGGG
**
1417699 TTTCTTGATGACAAGCTTGAGAAACCATCGTGATATGTAGGGG
1 TTTCTTGATGACAAGCTTGAGGGACCATCGTGATATGTAGGGG
* * *
1417742 TTTCTTGAGGATAAGTTTGAGGGACCATCGTGATATGTAGGGG
1 TTTCTTGATGACAAGCTTGAGGGACCATCGTGATATGTAGGGG
* * * * *
1417785 -TTCTTTGAAGAAAAACTTGAGAGACTATCGTGATATGTAGGGG
1 TTTC-TTGATGACAAGCTTGAGGGACCATCGTGATATGTAGGGG
* * * *
1417828 GTTCTTGAGGACAAGTTTGAGGGACCATCGTGATATTTAGGGG
1 TTTCTTGATGACAAGCTTGAGGGACCATCGTGATATGTAGGGG
* *
1417871 TTCCTTGATGACAAACTTGAGGGACCAAT-GTGATATGTAGGGG
1 TTTCTTGATGACAAGCTTGAGGGACC-ATCGTGATATGTAGGGG
* * * * ** * * * * *
1417914 TTCCTTGGTGA-AA-ATTAAGAAACTAAGCCTGATTTTTAGGGG
1 TTTCTTGATGACAAGCTTGAGGGAC-CATCGTGATATGTAGGGG
**
1417956 TTTCTTGATGACAAGCTTGAGAAACCATCGTGATATGTAGGGG
1 TTTCTTGATGACAAGCTTGAGGGACCATCGTGATATGTAGGGG
* * * *
1417999 TTTCTTGAGGAAAAGTTTGAGGGACCGTCGTGATATGTAGGGG
1 TTTCTTGATGACAAGCTTGAGGGACCATCGTGATATGTAGGGG
* * * * * *
1418042 TTCCTTAAAGAAAAGCTTGAGAGACTATCGTGATATGTAGGGG
1 TTTCTTGATGACAAGCTTGAGGGACCATCGTGATATGTAGGGG
* * *
1418085 TTTCTTGAGGACAAGTTTGAGGGACCATCGTGATATATAGGGG
1 TTTCTTGATGACAAGCTTGAGGGACCATCGTGATATGTAGGGG
*
1418128 -TTCTTTGATGACACA-CTTGAGGGACCAACGTGATATGTAGGGG
1 TTTC-TTGATGACA-AGCTTGAGGGACCATCGTGATATGTAGGGG
* *
1418171 TTCCTTGGTGACAA
1 TTTCTTGATGACAA
1418185 CTAAGAAAGT
Statistics
Matches: 572, Mismatches: 108, Indels: 39
0.80 0.15 0.05
Matches are distributed among these distances:
41 19 0.03
42 81 0.14
43 440 0.77
44 32 0.06
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (43 bp):
TTTCTTGATGACAAGCTTGAGGGACCATCGTGATATGTAGGGG
Found at i:1417591 original size:86 final size:86
Alignment explanation
Indices: 1417446--1418177 Score: 815
Period size: 86 Copynumber: 8.5 Consensus size: 86
1417436 TTCAACATTT
* * *
1417446 CTTGATGACAAGCTTGAGAAACCATCATGATATGTAGGGGTTTCTTGAGGACAAGTTTGAGGGAC
1 CTTGATGAAAAGCTTGAGAGACCATCGTGATATGTAGGGGTTTCTTGAGGACAAGTTTGAGGGAC
1417511 CATCGTGATATGTAGGGGTTC
66 CATCGTGATATGTAGGGGTTC
*
1417532 CTTGAAGAAAAGCTTGAGAGACCATCGTGATATGTAGGGGGTTT-TTGAGGACAAGTTTGAGGGA
1 CTTGATGAAAAGCTTGAGAGACCATCGTGATATGTA-GGGGTTTCTTGAGGACAAGTTTGAGGGA
*
1417596 CCATTGTGATATGTA-GGGTTC
65 CCATCGTGATATGTAGGGGTTC
* * * * * * **
1417617 CTTGATGACACA-CATGAGGGACCAACGTGATATGTAGGGGTTCCTTG-GTGACAA--TTAAGAA
1 CTTGATGA-AAAGCTTGAGAGACCATCGTGATATGTAGGGGTTTCTTGAG-GACAAGTTTGAGGG
* * * * *
1417678 ACTAAGCCTGAT-TTTCAGGGGTTT
64 AC-CATCGTGATATGT-AGGGGTTC
* * *
1417702 CTTGATGACAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGAGGATAAGTTTGAGGGAC
1 CTTGATGAAAAGCTTGAGAGACCATCGTGATATGTAGGGGTTTCTTGAGGACAAGTTTGAGGGAC
1417767 CATCGTGATATGTAGGGGTTC
66 CATCGTGATATGTAGGGGTTC
* * * * *
1417788 TTTGAAGAAAAACTTGAGAGACTATCGTGATATGTAGGGGGTTCTTGAGGACAAGTTTGAGGGAC
1 CTTGATGAAAAGCTTGAGAGACCATCGTGATATGTAGGGGTTTCTTGAGGACAAGTTTGAGGGAC
*
1417853 CATCGTGATATTTAGGGGTTC
66 CATCGTGATATGTAGGGGTTC
* * * * *
1417874 CTTGATGACAAA-CTTGAGGGACCAAT-GTGATATGTAGGGGTTCCTTG-GTGA-AA-ATTAAGA
1 CTTGATGA-AAAGCTTGAGAGACC-ATCGTGATATGTAGGGGTTTCTTGAG-GACAAGTTTGAGG
* * * * * * *
1417934 AACTAAGCCTGATTTTTAGGGGTTT
63 GAC-CATCGTGATATGTAGGGGTTC
* * *
1417959 CTTGATGACAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGAGGAAAAGTTTGAGGGAC
1 CTTGATGAAAAGCTTGAGAGACCATCGTGATATGTAGGGGTTTCTTGAGGACAAGTTTGAGGGAC
*
1418024 CGTCGTGATATGTAGGGGTTC
66 CATCGTGATATGTAGGGGTTC
* * *
1418045 CTTAAAGAAAAGCTTGAGAGACTATCGTGATATGTAGGGGTTTCTTGAGGACAAGTTTGAGGGAC
1 CTTGATGAAAAGCTTGAGAGACCATCGTGATATGTAGGGGTTTCTTGAGGACAAGTTTGAGGGAC
*
1418110 CATCGTGATATATAGGGGTTC
66 CATCGTGATATGTAGGGGTTC
* * * * *
1418131 TTTGATGACACA-CTTGAGGGACCAACGTGATATGTAGGGGTTCCTTG
1 CTTGATGA-AAAGCTTGAGAGACCATCGTGATATGTAGGGGTTTCTTG
1418178 GTGACAACTA
Statistics
Matches: 533, Mismatches: 91, Indels: 44
0.80 0.14 0.07
Matches are distributed among these distances:
83 8 0.02
84 24 0.05
85 147 0.28
86 326 0.61
87 28 0.05
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (86 bp):
CTTGATGAAAAGCTTGAGAGACCATCGTGATATGTAGGGGTTTCTTGAGGACAAGTTTGAGGGAC
CATCGTGATATGTAGGGGTTC
Found at i:1418003 original size:257 final size:257
Alignment explanation
Indices: 1417335--1418223 Score: 1433
Period size: 257 Copynumber: 3.5 Consensus size: 257
1417325 GACAAACTGA
* * * * *
1417335 AGGGACCATCATGATATGTAGGGGTTCCTTGATGACACACTTGAGGAACCAATGTGGTATGCAGG
1 AGGGACCATCGTGATATGTAGGGGTTCCTTGATGACACACTTGAGGGACCAACGTGATATGTAGG
* ***
1417400 GGTTCCTTGGT-AACAATTAAGAAACTAAACCTGATTTTCA-ACATTTCTTGATGACAAGCTTGA
66 GGTTCCTTGGTGAA-AATTAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGACAAGCTTGA
* *
1417463 GAAACCATCATGATATGTAGGGGTTTCTTGAGGACAAGTTTGAGGGACCATCGTGATATGTAGGG
130 GAAACCATCGTGATATGTAGGGGTTTCTTGAGGAAAAGTTTGAGGGACCATCGTGATATGTAGGG
* *
1417528 GTTCCTTGAAGAAAAGCTTGAGAGACCATCGTGATATGTAGGGGGTTTTTGAGGACAAGTTTG
195 GTTCCTTGAAGAAAAGCTTGAGAGACTATCGTGATATGTAGGGGGTTCTTGAGGACAAGTTTG
* *
1417591 AGGGACCATTGTGATATGTA-GGGTTCCTTGATGACACACATGAGGGACCAACGTGATATGTAGG
1 AGGGACCATCGTGATATGTAGGGGTTCCTTGATGACACACTTGAGGGACCAACGTGATATGTAGG
*
1417655 GGTTCCTTGGTGACAATTAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGACAAGCTTGAG
66 GGTTCCTTGGTGAAAATTAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGACAAGCTTGAG
*
1417720 AAACCATCGTGATATGTAGGGGTTTCTTGAGGATAAGTTTGAGGGACCATCGTGATATGTAGGGG
131 AAACCATCGTGATATGTAGGGGTTTCTTGAGGAAAAGTTTGAGGGACCATCGTGATATGTAGGGG
* *
1417785 TTCTTTGAAGAAAAACTTGAGAGACTATCGTGATATGTAGGGGGTTCTTGAGGACAAGTTTG
196 TTCCTTGAAGAAAAGCTTGAGAGACTATCGTGATATGTAGGGGGTTCTTGAGGACAAGTTTG
* * *
1417847 AGGGACCATCGTGATATTTAGGGGTTCCTTGATGACAAACTTGAGGGACCAATGTGATATGTAGG
1 AGGGACCATCGTGATATGTAGGGGTTCCTTGATGACACACTTGAGGGACCAACGTGATATGTAGG
*
1417912 GGTTCCTTGGTGAAAATTAAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGACAAGCTTGAG
66 GGTTCCTTGGTGAAAATTAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGACAAGCTTGAG
*
1417977 AAACCATCGTGATATGTAGGGGTTTCTTGAGGAAAAGTTTGAGGGACCGTCGTGATATGTAGGGG
131 AAACCATCGTGATATGTAGGGGTTTCTTGAGGAAAAGTTTGAGGGACCATCGTGATATGTAGGGG
* *
1418042 TTCCTTAAAGAAAAGCTTGAGAGACTATCGTGATATGTAGGGGTTTCTTGAGGACAAGTTTG
196 TTCCTTGAAGAAAAGCTTGAGAGACTATCGTGATATGTAGGGGGTTCTTGAGGACAAGTTTG
* *
1418104 AGGGACCATCGTGATATATAGGGGTTCTTTGATGACACACTTGAGGGACCAACGTGATATGTAGG
1 AGGGACCATCGTGATATGTAGGGGTTCCTTGATGACACACTTGAGGGACCAACGTGATATGTAGG
* * * * * * *
1418169 GGTTCCTTGGTGACAACTAAGAAAGTGAGCTTGATTTTCAAGAGTTTCTTGATGA
66 GGTTCCTTGGTGAAAATTAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGA
1418224 GTAAGTCCTT
Statistics
Matches: 587, Mismatches: 43, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
255 75 0.13
256 179 0.30
257 333 0.57
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (257 bp):
AGGGACCATCGTGATATGTAGGGGTTCCTTGATGACACACTTGAGGGACCAACGTGATATGTAGG
GGTTCCTTGGTGAAAATTAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGACAAGCTTGAG
AAACCATCGTGATATGTAGGGGTTTCTTGAGGAAAAGTTTGAGGGACCATCGTGATATGTAGGGG
TTCCTTGAAGAAAAGCTTGAGAGACTATCGTGATATGTAGGGGGTTCTTGAGGACAAGTTTG
Found at i:1418463 original size:91 final size:90
Alignment explanation
Indices: 1418308--1418558 Score: 387
Period size: 91 Copynumber: 2.8 Consensus size: 90
1418298 AGCAAGATGA
* *
1418308 TAAGTCCTTTGGGCCATCCATAAGATCTTCAGTGCAAGATGTTTTCAAATGAGATTTTAGAAACT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAAGATGTTTTCAAATGAGATTTTAGAAACT
*
1418373 AAGCCTTCGGGGGGTTTCTTGATTTT
66 AAGCCTTC-GGGGGTTTCTTGATTTG
* * * * *
1418399 TAAGTCATTCGGGCTATCCGTAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTGTAGAAACT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAAGATGTTTTCAAATGAGATTTTAGAAACT
1418464 AAGCCTTCGGGGGTTTCTTGATTTG
66 AAGCCTTCGGGGGTTTCTTGATTTG
* * *
1418489 TAAGTCCTTCTGGCCATCCATAAGACCTTC-GGGCAAGATGTTTTCAAATGAGTTTTTAGAAACT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAAGATGTTTTCAAATGAGATTTTAGAAACT
1418553 AAGCCT
66 AAGCCT
1418559 CATTTTCAGG
Statistics
Matches: 144, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
89 36 0.25
90 42 0.29
91 66 0.46
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (90 bp):
TAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAAGATGTTTTCAAATGAGATTTTAGAAACT
AAGCCTTCGGGGGTTTCTTGATTTG
Found at i:1418784 original size:41 final size:41
Alignment explanation
Indices: 1418704--1418789 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 41
1418694 AGGCTATCAG
* ** * *
1418704 TAAGTCTTTCGAGCATGATGTGTAAGTCCTTCGGGCATCTA
1 TAAGTCTTTCGAGCAAGATGAATAAGTCATTCGGCCATCTA
*
1418745 TAAGTCTTTCGAGCAAGAT-AATAAGTCATTTGAGCCATCTA
1 TAAGTCTTTCGAGCAAGATGAATAAGTCATTCG-GCCATCTA
1418786 TAAG
1 TAAG
1418790 ACCTTCGGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 9 0.24
41 29 0.76
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (41 bp):
TAAGTCTTTCGAGCAAGATGAATAAGTCATTCGGCCATCTA
Found at i:1419007 original size:21 final size:21
Alignment explanation
Indices: 1418983--1419044 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
1418973 TTCTAAAAAA
1418983 ACAAATTTTGTCTCACTTGAG
1 ACAAATTTTGTCTCACTTGAG
*
1419004 AC-AA-TTT-T-T-ACTTGAA
1 ACAAATTTTGTCTCACTTGAG
* *
1419020 ACAAGTTTTGTCTCCCTTGAG
1 ACAAATTTTGTCTCACTTGAG
1419041 ACAA
1 ACAA
1419045 TTTCCCTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 8 0.25
17 2 0.06
18 4 0.12
19 4 0.12
20 3 0.09
21 11 0.34
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (21 bp):
ACAAATTTTGTCTCACTTGAG
Found at i:1419058 original size:73 final size:72
Alignment explanation
Indices: 1418981--1419131 Score: 205
Period size: 73 Copynumber: 2.1 Consensus size: 72
1418971 TTTTCTAAAA
** *
1418981 AAACAAATTTTGTCTCACTTGAGACAATTTTTACTTGAAACA-AGTTTTGTCTCCCTTGAGACAA
1 AAACAAATTTCATCTCACTTGAGACAATTTCT-CTTGAAACATA-TTTTGTCTCCCTTGAGACAA
1419045 TTTCCCTTG
64 TTTCCCTTG
* * * *
1419054 AAACAAAATTTCATCTCCCTTGAGACAGTTTCTCTTGAAACATATTTTGTCTCCTTTGAGACAGT
1 AAAC-AAATTTCATCTCACTTGAGACAATTTCTCTTGAAACATATTTTGTCTCCCTTGAGACAAT
1419119 TTCCCTTG
65 TTCCCTTG
1419127 AAACA
1 AAACA
1419132 TCAATCTTTA
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
72 1 0.01
73 44 0.64
74 24 0.35
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (72 bp):
AAACAAATTTCATCTCACTTGAGACAATTTCTCTTGAAACATATTTTGTCTCCCTTGAGACAATT
TCCCTTG
Found at i:1419132 original size:36 final size:36
Alignment explanation
Indices: 1418981--1419131 Score: 185
Period size: 37 Copynumber: 4.1 Consensus size: 36
1418971 TTTTCTAAAA
* * **
1418981 AAACAAATTTTGTCTCACTTGAGACAATTTTTACTTG
1 AAACAAATTTTGTCTCCCTTGAGAC-AGTTTCCCTTG
* *
1419018 AAACAAGTTTTGTCTCCCTTGAGACAATTTCCCTTG
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTG
** *
1419054 AAACAAAATTTCATCTCCCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCCCTTGAGACAGTTTCCCTTG
* *
1419091 AAACATATTTTGTCTCCTTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTG
1419127 AAACA
1 AAACA
1419132 TCAATCTTTA
Statistics
Matches: 98, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
36 44 0.45
37 54 0.55
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (36 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTG
Found at i:1430938 original size:65 final size:65
Alignment explanation
Indices: 1430820--1430961 Score: 159
Period size: 65 Copynumber: 2.2 Consensus size: 65
1430810 GGACCCTTAG
* * *
1430820 TGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGATGTATGTCTTGTACATCGATGCAT-CAA
1 TGCATTCGATGTTTTCAAAATAGCCCGAGTGCATCGATGCATGTCATGTACATCGATGCATAC-A
1430883 A
65 A
* *
1430884 TGCATTCGATGTTTTCATAGAA-A-CCCGAGTGCATCGATGCATGAT-ATGTGCATCGATGTATA
1 TGCATTCGATGTTTTCA-A-AATAGCCCGAGTGCATCGATGCATG-TCATGTACATCGATGCATA
1430946 CAA
63 CAA
*
1430949 TGCATTCAATGTT
1 TGCATTCGATGTT
1430962 CAATTTATTC
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
64 11 0.16
65 50 0.75
66 4 0.06
67 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (65 bp):
TGCATTCGATGTTTTCAAAATAGCCCGAGTGCATCGATGCATGTCATGTACATCGATGCATACAA
Found at i:1432069 original size:20 final size:20
Alignment explanation
Indices: 1432000--1432098 Score: 110
Period size: 20 Copynumber: 4.8 Consensus size: 20
1431990 AGGGTGTCAA
* * *
1432000 AGTGCATCTATGCACTCCTAC
1 AGTGCATCCATGCAC-CATGC
1432021 AGTGCATCCATGCACC-TGCCAC
1 AGTGCATCCATGCACCATG---C
*
1432043 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCATGC
1432064 AGTGCATCCATGCACCATGC
1 AGTGCATCCATGCACCATGC
1432084 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
1432099 TCCATTTCGA
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.01
20 35 0.51
21 15 0.22
22 1 0.01
23 15 0.22
24 2 0.03
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCATGC
Found at i:1434635 original size:21 final size:21
Alignment explanation
Indices: 1434609--1434648 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1434599 AAACAATTGG
1434609 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
*
1434630 TAACAATTGATATCTTTTT
1 TAACAATTGATATCATTTT
1434649 CATTAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:1434896 original size:21 final size:21
Alignment explanation
Indices: 1434870--1435013 Score: 159
Period size: 21 Copynumber: 6.7 Consensus size: 21
1434860 AGGGTGTCAA
* *
1434870 AGTGCATCCATACACTCCTGC
1 AGTGCATCCATGCACCCCTGC
1434891 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
1434912 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
1434933 AGTGCATCCATGCACCTGCC-AC
1 AGTGCATCCATGCACC--CCTGC
* *
1434955 TAGTGCATCGATGCA-CCATGC
1 -AGTGCATCCATGCACCCCTGC
*
1434976 AGTGCATCCATGCACCTGCC-AC
1 AGTGCATCCATGCACC--CCTGC
1434998 TAGTGCATCCATGCAC
1 -AGTGCATCCATGCAC
1435014 TCCATTTTGA
Statistics
Matches: 106, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
20 14 0.13
21 58 0.55
22 3 0.03
23 31 0.29
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:1434990 original size:43 final size:43
Alignment explanation
Indices: 1434870--1435013 Score: 204
Period size: 43 Copynumber: 3.3 Consensus size: 43
1434860 AGGGTGTCAA
* *
1434870 AGTGCATCCATACACTCCTGCAGTGCATCCATGCACC--CCTGC-
1 AGTGCATCCATGCAC-CCTGCAGTGCATCCATGCACCTGCC-ACT
1434912 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCACCTGCCACT
1 AGTGCATCCATGCA-CCCTGCAGTGCATCCATGCACCTGCCACT
* *
1434956 AGTGCATCGATGCACCATGCAGTGCATCCATGCACCTGCCACT
1 AGTGCATCCATGCACCCTGCAGTGCATCCATGCACCTGCCACT
1434999 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
1435014 TCCATTTTGA
Statistics
Matches: 93, Mismatches: 5, Indels: 7
0.89 0.05 0.07
Matches are distributed among these distances:
42 34 0.37
43 44 0.47
44 15 0.16
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.21
Consensus pattern (43 bp):
AGTGCATCCATGCACCCTGCAGTGCATCCATGCACCTGCCACT
Found at i:1454948 original size:16 final size:17
Alignment explanation
Indices: 1454919--1454952 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
1454909 AAGAAATAAA
1454919 AGAGAAAATGAGAAAATG
1 AGAGAAAA-GAGAAAATG
1454937 AGAGAAAA-AGAAAATG
1 AGAGAAAAGAGAAAATG
1454953 TTGAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (17 bp):
AGAGAAAAGAGAAAATG
Found at i:1455016 original size:6 final size:7
Alignment explanation
Indices: 1454999--1455032 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
1454989 AAAGGGAAGA
1454999 AAAAATG
1 AAAAATG
1455006 AAAAATG
1 AAAAATG
*
1455013 AAAAAGAG
1 AAAAA-TG
1455021 AAAAATG
1 AAAAATG
1455028 AAAAA
1 AAAAA
1455033 AAGAGAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (7 bp):
AAAAATG
Found at i:1455041 original size:15 final size:15
Alignment explanation
Indices: 1454997--1455045 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
1454987 GAAAAGGGAA
*
1454997 GAAAAAATGAAAAAT
1 GAAAAAAAGAAAAAT
*
1455012 GAAAAAGAGAAAAAT
1 GAAAAAAAGAAAAAT
*
1455027 GAAAAAAAGAGAAAT
1 GAAAAAAAGAAAAAT
1455042 -AAAA
1 GAAAA
1455046 GGAGGGTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 4 0.13
15 26 0.87
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (15 bp):
GAAAAAAAGAAAAAT
Found at i:1455761 original size:177 final size:174
Alignment explanation
Indices: 1455468--1455819 Score: 652
Period size: 177 Copynumber: 2.0 Consensus size: 174
1455458 AAGACGCCTA
1455468 CTCTTTTGTTCTTTTATTTTCCAGTTAAAAGTTTGCCATGTAGTTACCTGAAAATTCTCGACATT
1 CTCTTTTGTTCTTTTATTTTCCAGTTAAAAGTTTGCCATGTAGTTACCTGAAAATTCTCGACATT
1455533 TATAAATAAAGAGATGTATTTCCTTGTTCGTTTCCCTCTTGTAAACATCTTATTTTGAAAGGTTA
66 TATAAATAAAGAGATGTATTTCCTTGTTCGTTTCCCTCTTGTAAACATCTTATTTTGAAAGGTTA
1455598 AAACATATAGCTTAACTTGAAGTACAT-GATCATTTTGTATTAT
131 AAACATATAGCTTAACTTGAAGTACATAGATCATTTTGTATTAT
1455641 CTCTTTTGTTCTTTTATTGTTTCCAGTTAAAAGTTTGCCATGTAGTTACCTGAAAATTCTCGACA
1 CTCTTTTGTTCTTTTA-T-TTTCCAGTTAAAAGTTTGCCATGTAGTTACCTGAAAATTCTCGACA
1455706 TTTATATAAATAAAGAGATGTATTTCCTTGTTCGTTTCCCTCTTGTAAACATCTTATTTTGAAAG
64 -TT-TATAAATAAAGAGATGTATTTCCTTGTTCGTTTCCCTCTTGTAAACATCTTATTTTGAAAG
1455771 GTTAAAACATATAGCTTAACTTGAAGTACATGAGATCATTTTGTATTAT
127 GTTAAAACATATAGCTTAACTTGAAGTACAT-AGATCATTTTGTATTAT
1455820 TGTGCAAAAG
Statistics
Matches: 173, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
173 16 0.09
174 1 0.01
175 46 0.27
176 2 0.01
177 92 0.53
179 16 0.09
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (174 bp):
CTCTTTTGTTCTTTTATTTTCCAGTTAAAAGTTTGCCATGTAGTTACCTGAAAATTCTCGACATT
TATAAATAAAGAGATGTATTTCCTTGTTCGTTTCCCTCTTGTAAACATCTTATTTTGAAAGGTTA
AAACATATAGCTTAACTTGAAGTACATAGATCATTTTGTATTAT
Found at i:1456578 original size:36 final size:37
Alignment explanation
Indices: 1456489--1456599 Score: 170
Period size: 36 Copynumber: 3.0 Consensus size: 37
1456479 TCAAAACAGG
* * * *
1456489 TCAATCTTAAGCCTTCATGAAAGAGCAGTGAAGCAAT
1 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
*
1456526 TCAAACTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
1456563 TC-ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
1456599 T
1 T
1456600 TCGTTTGTTG
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
36 34 0.50
37 34 0.50
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.23
Consensus pattern (37 bp):
TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
Found at i:1456680 original size:55 final size:54
Alignment explanation
Indices: 1456616--1457035 Score: 393
Period size: 55 Copynumber: 7.6 Consensus size: 54
1456606 GTTGAAGATT
* * **
1456616 GAGTCCTATACTCTCTGAAGGAATAGGGAGAGGACAAATTCGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACACGTT-GTTGAAGATTGTTC
*
1456671 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGAC-CTGTT-TCATGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACAC-GTTGT--TGAAGATTGTTC
* * * * *
1456726 GAGTTCTATACTCTCTGAAGGAGTAGAGAGCGAACACGTTTTATGAAGATTGATC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTGT-TGAAGATTGTTC
* * *
1456781 GAGTTCTATACTCCCTGAACGAATAGGGAGCGGAC-CTGTTTATTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACAC-G-TTGTTGAAGATTGTTC
* * * *
1456836 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTGT-TGAAGATTGTTC
* * *
1456891 GAG-TCTTATACTCCCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTT
1 GAGTTC-TATACTCTCTGAAGGAATAGGGAGCGGACACG-TTGTTGAAGATTGTTC
* ** ** ** *
1456946 GAG-TCTTATACTCCCTGAATAAATAGGGAGCAAACACGTTTGCCGAAGATTGTCC
1 GAGTTC-TATACTCTCTGAAGGAATAGGGAGCGGACACG-TTGTTGAAGATTGTTC
* * * *
1457001 GAG-TCTTATACTCCCTAAAAGAATAGGGAGTGGAC
1 GAGTTC-TATACTCTCTGAAGGAATAGGGAGCGGAC
1457036 CCATCATTTG
Statistics
Matches: 314, Mismatches: 40, Indels: 22
0.84 0.11 0.06
Matches are distributed among these distances:
53 1 0.00
54 5 0.02
55 299 0.95
56 9 0.03
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (54 bp):
GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTGTTGAAGATTGTTC
Found at i:1456814 original size:110 final size:109
Alignment explanation
Indices: 1456616--1457036 Score: 465
Period size: 110 Copynumber: 3.8 Consensus size: 109
1456606 GTTGAAGATT
* * * * ** *
1456616 GAGTCCTATACTCTCTGAAGGAATAGGGAGAGGACAAATTCGT-TGAAGATTGTTCGAGT-TCTA
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACACGTT-TTATGAAGATTGTTCGAGTCT-TA
* *
1456679 TACTCTCTGAAGGAATAGAGAGCGGACCTGTTTCATGAAGATTGTTC
64 TACTCCCTGAAGGAATAGGGAGCGGACCTGTTT-ATGAAGATTGTTC
* *
1456726 GAGTTCTATACTCTCTGAAGGAGTAGAGAGCGAACACGTTTTATGAAGATTGATCGAGT-TCTAT
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACACGTTTTATGAAGATTGTTCGAGTCT-TAT
*
1456790 ACTCCCTGAACGAATAGGGAGCGGACCTGTTTATTGAAGATTGTTC
65 ACTCCCTGAAGGAATAGGGAGCGGACCTGTTTA-TGAAGATTGTTC
* * *
1456836 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTCTTATA
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACACGTTTTATGAAGATTGTTCGAGTCTTATA
* * *
1456901 CTCCCTGAAGGAATAGGGAGCAGACAC-GTTTGTTGAAGATTGTTT
66 CTCCCTGAAGGAATAGGGAGCGGAC-CTGTTT-ATGAAGATTGTTC
* ** * * *** *
1456946 GAG-TCTTATACTCCCTGAATAAATAGGGAGCAAACACGTTTGCCGAAGATTGTCCGAGTCTTAT
1 GAGTTC-TATACTCTCTGAAGGAATAGAGAGCGAACACGTTTTATGAAGATTGTTCGAGTCTTAT
* * *
1457010 ACTCCCTAAAAGAATAGGGAGTGGACC
65 ACTCCCTGAAGGAATAGGGAGCGGACC
1457037 CATCATTTGA
Statistics
Matches: 268, Mismatches: 37, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
109 4 0.01
110 262 0.98
111 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (109 bp):
GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACACGTTTTATGAAGATTGTTCGAGTCTTATA
CTCCCTGAAGGAATAGGGAGCGGACCTGTTTATGAAGATTGTTC
Found at i:1456893 original size:165 final size:165
Alignment explanation
Indices: 1456601--1456976 Score: 489
Period size: 165 Copynumber: 2.3 Consensus size: 165
1456591 GAAGCAAATT
* * * * *
1456601 CGTTTGTTGAAGA-T--T-GAGTCCTATACTCTCTGAAGGAATAGGGAGAGGACAAATTCGTTGA
1 CGTTTGTTGAAGATTGATCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACAAATTCATTGA
* *
1456662 AGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCTGTTTCATGAAGATTGTTCG
66 AGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTGTTCG
* *
1456727 AGT-TCTATACTCTCTGAAGGAGTAGAGAGC-GAACA
131 AGTCT-TATACTCCCTGAAGGAATAGAGAGCAG-ACA
*** *
1456762 CGTTT-TATGAAGATTGATCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCTGTTTATTG
1 CGTTTGT-TGAAGATTGATCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACAAATTCATTG
*
1456826 AAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTC
65 AAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTGTTC
*
1456891 GAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACA
130 GAGTCTTATACTCCCTGAAGGAATAGAGAGCAGACA
* * **
1456927 CGTTTGTTGAAGATTGTTTGAG-TCTTATACTCCCTGAATAAATAGGGAGC
1 CGTTTGTTGAAGATTGATCGAGTTC-TATACTCCCTGAACGAATAGGGAGC
1456977 AAACACGTTT
Statistics
Matches: 187, Mismatches: 19, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
160 1 0.01
161 11 0.06
162 1 0.01
164 3 0.02
165 168 0.90
166 3 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (165 bp):
CGTTTGTTGAAGATTGATCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACAAATTCATTGA
AGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTGTTCG
AGTCTTATACTCCCTGAAGGAATAGAGAGCAGACA
Found at i:1456996 original size:165 final size:165
Alignment explanation
Indices: 1456660--1457037 Score: 478
Period size: 165 Copynumber: 2.3 Consensus size: 165
1456650 CAAATTCGTT
* *
1456660 GAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCTGTTTCATGAAGATTGTT
1 GAAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTGTT
* *
1456725 CGAGTTCTATACTCTCTGAAGGAGTAGAGAGCGAACACGTTTTATGAAGATTGATCGAGTTCTAT
66 CGAGTTCTATACTCCCTGAAGGAATAGAGAGCGAACACGTTTTATGAAGATTGATCGAGTTCTAT
* ** **
1456790 ACTCCCTGAACGAATAGGGAGCGGACCTGTTTATT
131 ACTCCCTGAACAAATAGGGAGCAAACCTGTTTACC
*
1456825 GAAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTT
1 GAAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTGTT
* * *
1456890 CGAG-TCTTATACTCCCTGAAGGAATAGGGAGC-AGACACGTTTGT-TGAAGATTGTTTGAG-TC
66 CGAGTTC-TATACTCCCTGAAGGAATAGAGAGCGA-ACACGTTT-TATGAAGATTGATCGAGTTC
* *
1456951 TTATACTCCCTGAATAAATAGGGAGCAAACAC-GTTTGCC
128 -TATACTCCCTGAACAAATAGGGAGCAAAC-CTGTTTACC
* * * * * * *
1456990 GAAGATTGTCCGAGTCTTATACTCCCTAAAAGAATAGGGAGTGGACCC
1 GAAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCC
1457038 ATCATTTGAA
Statistics
Matches: 186, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
164 5 0.03
165 179 0.96
166 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (165 bp):
GAAGATTGTTCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTGTT
CGAGTTCTATACTCCCTGAAGGAATAGAGAGCGAACACGTTTTATGAAGATTGATCGAGTTCTAT
ACTCCCTGAACAAATAGGGAGCAAACCTGTTTACC
Found at i:1460614 original size:7 final size:7
Alignment explanation
Indices: 1460528--1460659 Score: 63
Period size: 7 Copynumber: 18.1 Consensus size: 7
1460518 AAAGTGTTAG
1460528 ATAAAAA
1 ATAAAAA
**
1460535 ATATTAA
1 ATAAAAA
1460542 ATAAATTAA
1 ATAAA--AA
*
1460551 A-AAAAC
1 ATAAAAA
1460557 ATAAAAA
1 ATAAAAA
1460564 ATGAAAATA
1 AT-AAAA-A
*
1460573 ATAAATA
1 ATAAAAA
1460580 ATAAAAAA
1 AT-AAAAA
*
1460588 ATAATAA
1 ATAAAAA
* *
1460595 ATCACAA
1 ATAAAAA
**
1460602 GGAAAAA
1 ATAAAAA
1460609 ATAAAAA
1 ATAAAAA
*
1460616 ATAAGAA
1 ATAAAAA
1460623 ATAAAAA
1 ATAAAAA
*
1460630 CA-AATAA
1 -ATAAAAA
*
1460637 A-AACAA
1 ATAAAAA
1460643 ATAAAACAA
1 AT-AAA-AA
1460652 ATAAAAA
1 ATAAAAA
1460659 A
1 A
1460660 ATACTCAAAC
Statistics
Matches: 93, Mismatches: 22, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
6 8 0.09
7 53 0.57
8 22 0.24
9 10 0.11
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.17
Consensus pattern (7 bp):
ATAAAAA
Found at i:1460636 original size:10 final size:10
Alignment explanation
Indices: 1460621--1460658 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
1460611 AAAAAATAAG
1460621 AAATAAAAAC
1 AAATAAAAAC
1460631 AAATAAAAAC
1 AAATAAAAAC
1460641 AAAT-AAAAC
1 AAATAAAAAC
1460650 AAATAAAAA
1 AAATAAAAA
1460659 AATACTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.33
10 18 0.67
ACGTcount: A:0.82, C:0.08, G:0.00, T:0.11
Consensus pattern (10 bp):
AAATAAAAAC
Found at i:1460650 original size:19 final size:20
Alignment explanation
Indices: 1460621--1460658 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1460611 AAAAAATAAG
1460621 AAATAAAAACAAATAAAAAC
1 AAATAAAAACAAATAAAAAC
1460641 AAAT-AAAACAAATAAAAA
1 AAATAAAAACAAATAAAAA
1460659 AATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.82, C:0.08, G:0.00, T:0.11
Consensus pattern (20 bp):
AAATAAAAACAAATAAAAAC
Found at i:1460654 original size:43 final size:46
Alignment explanation
Indices: 1460559--1460659 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 46
1460549 AAAAAAACAT
* * *
1460559 AAAAAAT-GAAAATAATAAATAATAAAAAAATAATAAATCACAAGG
1 AAAAAATAAAAAATAAGAAATAATAAAAAAATAATAAATCACAAGA
* *
1460604 AAAAAATAAAAAATAAGAAATAA-AAACAAATAA-AAA-CA-AATA
1 AAAAAATAAAAAATAAGAAATAATAAAAAAATAATAAATCACAAGA
1460646 AAACAAATAAAAAA
1 AAA-AAATAAAAAA
1460660 ATACTCAAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
42 5 0.10
43 12 0.24
44 3 0.06
45 16 0.33
46 13 0.27
ACGTcount: A:0.77, C:0.05, G:0.04, T:0.14
Consensus pattern (46 bp):
AAAAAATAAAAAATAAGAAATAATAAAAAAATAATAAATCACAAGA
Found at i:1463014 original size:17 final size:18
Alignment explanation
Indices: 1462981--1463033 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
1462971 TATGTAAAGT
*
1462981 AGTATCGGTACCCCTTTG
1 AGTATCGGTACCCTTTTG
*
1462999 AGTATAGGTACCCTTTTG
1 AGTATCGGTACCCTTTTG
* *
1463017 AATATCGGTACCATTTT
1 AGTATCGGTACCCTTTT
1463034 TGCATTATGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (18 bp):
AGTATCGGTACCCTTTTG
Found at i:1465295 original size:24 final size:24
Alignment explanation
Indices: 1465253--1465299 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1465243 TAATCCGTTC
*
1465253 GTTCATTTATGTCCATGTATGTTT
1 GTTCATTTATCTCCATGTATGTTT
**
1465277 GTTCATTTATCTCTGTGTATGTT
1 GTTCATTTATCTCCATGTATGTT
1465300 CGTTTGTCCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.17, T:0.55
Consensus pattern (24 bp):
GTTCATTTATCTCCATGTATGTTT
Found at i:1465565 original size:23 final size:23
Alignment explanation
Indices: 1465518--1465565 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1465508 GTTGTTTACA
* *
1465518 TTCGTTTACGTTCATTTATTGTG
1 TTCGATTACGTTCATTTATTATG
* *
1465541 TTCGATTATGTTCATTTGTTATG
1 TTCGATTACGTTCATTTATTATG
1465564 TT
1 TT
1465566 TGTGCAGCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.15, C:0.10, G:0.17, T:0.58
Consensus pattern (23 bp):
TTCGATTACGTTCATTTATTATG
Found at i:1465628 original size:14 final size:14
Alignment explanation
Indices: 1465609--1465642 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1465599 CATTTATGTC
1465609 CGTTTACATT-CGTT
1 CGTTTAC-TTCCGTT
1465623 CGTTTACTTCCGTT
1 CGTTTACTTCCGTT
1465637 CGTTTA
1 CGTTTA
1465643 TGTTTGTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 17 0.89
ACGTcount: A:0.12, C:0.24, G:0.15, T:0.50
Consensus pattern (14 bp):
CGTTTACTTCCGTT
Found at i:1476599 original size:13 final size:13
Alignment explanation
Indices: 1476581--1476610 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1476571 ACGTTCAGAT
1476581 TTTTAAAAAAATA
1 TTTTAAAAAAATA
1476594 TTTT-AAAAAATA
1 TTTTAAAAAAATA
1476606 TTTTA
1 TTTTA
1476611 CTTTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TTTTAAAAAAATA
Found at i:1479189 original size:42 final size:42
Alignment explanation
Indices: 1479098--1479303 Score: 252
Period size: 42 Copynumber: 4.8 Consensus size: 42
1479088 CTATACACCA
* * * *
1479098 GTAAGGCTTAACTTGTGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTTACCTT-TGCACACAGCAAAGGGA-CCT-GGGAAACT
* * * *
1479142 GTAAGGTTTATCTTTGCACACAACAAATGGACCTGGGAAACT
1 GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACT
* *
1479184 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACT
* *
1479226 GTAAGGCTTACCTTCGCACACAGCAAAGGGACTTGGGAAACT
1 GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACT
*
1479268 GTAAGGCTTACCTTAGCACACAGCAAAAGGGACCTG
1 GTAAGGCTTACCTTTGCACACAGC-AAAGGGACCTG
1479304 ATAATACTTC
Statistics
Matches: 142, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
42 104 0.73
43 23 0.16
44 15 0.11
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (42 bp):
GTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACT
Found at i:1479921 original size:22 final size:22
Alignment explanation
Indices: 1479893--1479944 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
1479883 GAATTTCGGG
*
1479893 TCAGAATTTGACAAAACGGACT
1 TCAGAATCTGACAAAACGGACT
1479915 TCAGAATCTGACAAAACGGACT
1 TCAGAATCTGACAAAACGGACT
1479937 TCAGAATC
1 TCAGAATC
1479945 AGATTCAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.21
Consensus pattern (22 bp):
TCAGAATCTGACAAAACGGACT
Found at i:1480215 original size:29 final size:29
Alignment explanation
Indices: 1480179--1480413 Score: 237
Period size: 29 Copynumber: 8.1 Consensus size: 29
1480169 CATTTTACAG
** * *
1480179 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTCGAATTAATTCCCA
* *
1480208 AAATAGCA-CTTTTTCGAATTAAATTCCTA
1 AAATAGCACCCTTTTCGAATT-AATTCCCA
* * *
1480237 AAATAGCAGCTTTTTTGAATTAAATTCCCA
1 AAATAGCACCCTTTTCGAATT-AATTCCCA
*
1480267 AAATAGCA--CTTTTCGAATTAAATTCTCA
1 AAATAGCACCCTTTTCGAATT-AATTCCCA
*
1480295 AAATATCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTCGAATTAATTCCCA
* *** *
1480324 AAATAGTACCAAGTTCAAATTAATTCCCA
1 AAATAGCACCCTTTTCGAATTAATTCCCA
*
1480353 AAATAGCA-CCATTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTCGAATTAATTCCCA
*
1480381 AAATAGCA-CCTATTTCGAATTAATTCTCA
1 AAATAGCACCCT-TTTCGAATTAATTCCCA
1480410 AAAT
1 AAAT
1480414 GTCACTCGGT
Statistics
Matches: 176, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
28 59 0.34
29 79 0.45
30 38 0.22
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.33
Consensus pattern (29 bp):
AAATAGCACCCTTTTCGAATTAATTCCCA
Found at i:1480462 original size:13 final size:13
Alignment explanation
Indices: 1480444--1480477 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1480434 CGGTCGAGTA
*
1480444 GGGTCAAAGGGTT
1 GGGTCAAAGGGTC
*
1480457 GGGTCAACGGGTC
1 GGGTCAAAGGGTC
1480470 GGGTCAAA
1 GGGTCAAA
1480478 ACCGATCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.24, C:0.15, G:0.44, T:0.18
Consensus pattern (13 bp):
GGGTCAAAGGGTC
Found at i:1484804 original size:17 final size:17
Alignment explanation
Indices: 1484782--1484829 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1484772 AATATATCAC
1484782 ATTTAATGTTTTATATA
1 ATTTAATGTTTTATATA
*
1484799 ATTTAATGATTTT-TCTA
1 ATTTAATG-TTTTATATA
* *
1484816 ATATATTGTTTTAT
1 ATTTAATGTTTTAT
1484830 CTTATAGACT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 4 0.15
17 18 0.69
18 4 0.15
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.60
Consensus pattern (17 bp):
ATTTAATGTTTTATATA
Found at i:1487562 original size:152 final size:152
Alignment explanation
Indices: 1487286--1487589 Score: 608
Period size: 152 Copynumber: 2.0 Consensus size: 152
1487276 TTTGCAAAGT
1487286 TTGTATTTTTCTCTTTGAGAAGAGAGTGTCTCAAGAATTTGGGGTATAATTCTTGAGGGAGTTGC
1 TTGTATTTTTCTCTTTGAGAAGAGAGTGTCTCAAGAATTTGGGGTATAATTCTTGAGGGAGTTGC
1487351 AAGGTTAATCTTTATCCTCAAAAGAAAGACAAATTAGTAAATTTGTGGAAAATCCTTAGTGTGGA
66 AAGGTTAATCTTTATCCTCAAAAGAAAGACAAATTAGTAAATTTGTGGAAAATCCTTAGTGTGGA
1487416 TAGCTAAGGTGGTGGAAGTAGA
131 TAGCTAAGGTGGTGGAAGTAGA
1487438 TTGTATTTTTCTCTTTGAGAAGAGAGTGTCTCAAGAATTTGGGGTATAATTCTTGAGGGAGTTGC
1 TTGTATTTTTCTCTTTGAGAAGAGAGTGTCTCAAGAATTTGGGGTATAATTCTTGAGGGAGTTGC
1487503 AAGGTTAATCTTTATCCTCAAAAGAAAGACAAATTAGTAAATTTGTGGAAAATCCTTAGTGTGGA
66 AAGGTTAATCTTTATCCTCAAAAGAAAGACAAATTAGTAAATTTGTGGAAAATCCTTAGTGTGGA
1487568 TAGCTAAGGTGGTGGAAGTAGA
131 TAGCTAAGGTGGTGGAAGTAGA
1487590 CTTTGGTTGA
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
152 152 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.34
Consensus pattern (152 bp):
TTGTATTTTTCTCTTTGAGAAGAGAGTGTCTCAAGAATTTGGGGTATAATTCTTGAGGGAGTTGC
AAGGTTAATCTTTATCCTCAAAAGAAAGACAAATTAGTAAATTTGTGGAAAATCCTTAGTGTGGA
TAGCTAAGGTGGTGGAAGTAGA
Found at i:1494099 original size:40 final size:40
Alignment explanation
Indices: 1494055--1494134 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
1494045 AGTCAAGTCT
1494055 AGTGCGAGTGTTTTAGATTATCACGAACGCTTTCTTCATC
1 AGTGCGAGTGTTTTAGATTATCACGAACGCTTTCTTCATC
1494095 AGTGCGAGTGTTTTAGATTATCACGAACGCTTTCTTCATC
1 AGTGCGAGTGTTTTAGATTATCACGAACGCTTTCTTCATC
1494135 TTATGATCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (40 bp):
AGTGCGAGTGTTTTAGATTATCACGAACGCTTTCTTCATC
Found at i:1495880 original size:54 final size:54
Alignment explanation
Indices: 1495736--1495914 Score: 209
Period size: 54 Copynumber: 3.3 Consensus size: 54
1495726 TTTTATGATT
* * * * * * *
1495736 TTGCACACGTAGTGTCGATACGGTAATTCACAAACTCATTATGAATTAC--AAGGGG
1 TTGCACACATAGTGCCAATACAGAAATTCACAAACTTATTATGAATTTCTTAA---G
* *
1495791 TTGCACACATAGTTCCAATACGGAAATTCACAAACTTATTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACAGAAATTCACAAACTTATTATGAATTTCTTAAG
* * *
1495845 TTGTACACACAGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACAGAAATTCACAAACTTATTATGAATTTCTTAAG
1495899 TTGCACACATAGTGCC
1 TTGCACACATAGTGCC
1495915 CATTCGATAA
Statistics
Matches: 108, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
54 64 0.59
55 42 0.39
57 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (54 bp):
TTGCACACATAGTGCCAATACAGAAATTCACAAACTTATTATGAATTTCTTAAG
Found at i:1504601 original size:21 final size:22
Alignment explanation
Indices: 1504577--1504623 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
1504567 CAGATTACAA
* *
1504577 ACAGGGAATCGATT-CCCTGCT
1 ACAGGGAACCGATTCCCCTACT
*
1504598 ACAGGGTACCGATTCCCCTACT
1 ACAGGGAACCGATTCCCCTACT
1504620 ACAG
1 ACAG
1504624 TACTGCTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.21
Consensus pattern (22 bp):
ACAGGGAACCGATTCCCCTACT
Found at i:1505223 original size:22 final size:22
Alignment explanation
Indices: 1505193--1505258 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
1505183 GGGGCACTAA
*
1505193 ATATTTGTCCCGAAGGACCACT
1 ATATATGTCCCGAAGGACCACT
*
1505215 ATATATGTCCCGAAGGACCAAT
1 ATATATGTCCCGAAGGACCACT
* * *
1505237 GTGTATGTCCTGAAGGACCACT
1 ATATATGTCCCGAAGGACCACT
1505259 CCTTAAGAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (22 bp):
ATATATGTCCCGAAGGACCACT
Found at i:1508834 original size:55 final size:54
Alignment explanation
Indices: 1508775--1508927 Score: 173
Period size: 54 Copynumber: 2.8 Consensus size: 54
1508765 CTGATACAGT
* * ** * * *
1508775 AATTCACAAACTCATTATGAATTACGTGGGGTTGCACACATAGTGTCAATACGGA
1 AATTCATAAACTTATTATGAATTAC-TGAAGTTGCACACACAGTGGCAATACGAA
* * *
1508830 AATTCATACACTTATTATGAATTTCTTAAGTTGCACACACAGTGGCAATACGAA
1 AATTCATAAACTTATTATGAATTACTGAAGTTGCACACACAGTGGCAATACGAA
* *
1508884 AATTCATAAACTTATTATAAATTTCAT-AAGTTGCACACACAGTG
1 AATTCATAAACTTATTATGAATTAC-TGAAGTTGCACACACAGTG
1508928 CCCATTCGGT
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
54 63 0.74
55 22 0.26
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (54 bp):
AATTCATAAACTTATTATGAATTACTGAAGTTGCACACACAGTGGCAATACGAA
Found at i:1508880 original size:54 final size:54
Alignment explanation
Indices: 1508805--1508927 Score: 192
Period size: 54 Copynumber: 2.3 Consensus size: 54
1508795 ATTACGTGGG
* * * * * *
1508805 GTTGCACACATAGTGTCAATACGGAAATTCATACACTTATTATGAATTTCTTAA
1 GTTGCACACACAGTGGCAATACGAAAATTCATAAACTTATTATAAATTTCATAA
1508859 GTTGCACACACAGTGGCAATACGAAAATTCATAAACTTATTATAAATTTCATAA
1 GTTGCACACACAGTGGCAATACGAAAATTCATAAACTTATTATAAATTTCATAA
1508913 GTTGCACACACAGTG
1 GTTGCACACACAGTG
1508928 CCCATTCGGT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (54 bp):
GTTGCACACACAGTGGCAATACGAAAATTCATAAACTTATTATAAATTTCATAA
Found at i:1510592 original size:25 final size:25
Alignment explanation
Indices: 1510564--1510624 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 25
1510554 TTGAAAATAT
*
1510564 TTTTAAAAATATATATAATATATAG
1 TTTTAAAAATATACATAATATATAG
* *
1510589 TTTTGAAAACATTTACATATTATATAG
1 TTTT-AAAA-ATATACATAATATATAG
*
1510616 TTTTTAAAA
1 TTTTAAAAA
1510625 CATTTTGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 5 0.17
26 7 0.23
27 18 0.60
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (25 bp):
TTTTAAAAATATACATAATATATAG
Found at i:1510613 original size:29 final size:27
Alignment explanation
Indices: 1510578--1510629 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1510568 AAAAATATAT
1510578 ATAATATATAGTTTTGAAAACATTTAC
1 ATAATATATAGTTTTGAAAACATTTAC
* *
1510605 ATATTATATAGTTTTTAAAACATTT
1 ATAATATATAGTTTTGAAAACATTT
1510630 TGAAAACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (27 bp):
ATAATATATAGTTTTGAAAACATTTAC
Found at i:1510649 original size:36 final size:36
Alignment explanation
Indices: 1510589--1510810 Score: 213
Period size: 38 Copynumber: 6.1 Consensus size: 36
1510579 TAATATATAG
* *
1510589 TTTTGAAAACATTTACATATTATATAGTTTTTAAAACA
1 TTTTGAAAAC--TTATATAATATATAGTTTTTAAAACA
* *
1510627 TTTTGAAAACTTATATAGTATATAATTTTTTAAAACAA
1 TTTTGAAAACTTATATAATATAT-AGTTTTTAAAAC-A
* * *
1510665 TTTTGAAAAATTATATAATATATAATTTTAAAAACA
1 TTTTGAAAACTTATATAATATATAGTTTTTAAAACA
* *
1510701 TTTTTGGAAAAATTATATAATATATAGTTTTAAAAACA
1 -TTTT-GAAAACTTATATAATATATAGTTTTTAAAACA
1510739 TTTTTTGAAAAC-T-TAT-ATA-ATA-TTTTTAAAACA
1 --TTTTGAAAACTTATATAATATATAGTTTTTAAAACA
* * * *
1510772 ATTTGAAAAC-TATATAATAAATAGTTTTGAAAACT
1 TTTTGAAAACTTATATAATATATAGTTTTTAAAACA
1510807 TTTT
1 TTTT
1510811 TAAATATAAT
Statistics
Matches: 161, Mismatches: 14, Indels: 21
0.82 0.07 0.11
Matches are distributed among these distances:
31 10 0.06
32 3 0.02
33 13 0.08
34 6 0.04
35 15 0.09
36 15 0.09
37 26 0.16
38 68 0.42
39 5 0.03
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.44
Consensus pattern (36 bp):
TTTTGAAAACTTATATAATATATAGTTTTTAAAACA
Found at i:1510910 original size:14 final size:15
Alignment explanation
Indices: 1510884--1510917 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1510874 ATTATTATTA
1510884 TTTATTCATTTTCCT
1 TTTATTCATTTTCCT
*
1510899 TTTATT-ATTTTCTT
1 TTTATTCATTTTCCT
1510913 TTTAT
1 TTTAT
1510918 GTTTGTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATTCATTTTCCT
Found at i:1515196 original size:95 final size:94
Alignment explanation
Indices: 1515013--1515208 Score: 234
Period size: 95 Copynumber: 2.1 Consensus size: 94
1515003 ATATATTATA
* * * * *
1515013 TATATATACAATAAAGCTTGAGTTATCACTCTAGAGCAATTGGTTAAACGCCCTGGTTTTATGGA
1 TATATATACAATAAAGCTTGAGCTATCACTCAAGAGCAATTGGTTAAACACCCTAGCTTTATGGA
* * * *
1515078 TAATATTCGGCTAGCCTGGTAAAGGCGAT
66 TAAGATTCAGCTAACCTGATAAAGGCGAT
* *
1515107 TATACTATACAATAAAGCTTGAGCTGTCCCTCCAAG-GCAATTGGTTAAACACCAC-AGCTTTAT
1 TATA-TATACAATAAAGCTTGAGCTATCACT-CAAGAGCAATTGGTTAAACACC-CTAGCTTTAT
* *
1515170 GGATAAGATTCAGCTAACCTGATAAAGGTGTT
63 GGATAAGATTCAGCTAACCTGATAAAGGCGAT
1515202 TATATAT
1 TATATAT
1515209 TGAGTTGTCC
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
94 7 0.08
95 75 0.87
96 4 0.05
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGCTATCACTCAAGAGCAATTGGTTAAACACCCTAGCTTTATGGA
TAAGATTCAGCTAACCTGATAAAGGCGAT
Found at i:1516287 original size:110 final size:110
Alignment explanation
Indices: 1516101--1516571 Score: 626
Period size: 110 Copynumber: 4.3 Consensus size: 110
1516091 TACAGCTTTT
* * *
1516101 AGAGTCAATTTCAACTTCACATCGAATGATATTGGACTCGAGACAACAAAAGCTCAACTTCACAG
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAG
* * *
1516166 CCAAGGAGCGACTGACTGTCAACAAACAACTTTTTAGTTTCATTA
66 CGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTA
* *
1516211 AGAGTCAATTTCAACTTCACAACTAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAG
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAG
* *
1516276 CGAAGGGGCGACTGACTGTCAACAAACAACTTTTCATTTTCATTC
66 CGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTA
** * * *
1516321 AGAGTCAATTTCAACTTCACAGCGAAATATACTAGACTCGAGACAACACAAGCTCAGCTTCACAG
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAG
* * *
1516386 CGAAGGGGCGACTGACTATCAACAAACAACTTTTCAGTTTTATTC
66 CGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTA
* * * * * *
1516431 AGAGTCAATTTCAACTTCACAGCAAATGATATTGAACTCGAGATAGCACAAGCTCAACTTAACAG
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAG
* * * ** *
1516496 TGAAGGGGGGGCTGGTTGTCAACAAACAACTTTCCAGTTTC---A
66 CGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTA
* *
1516538 A-AGTCAATTTCAATTTCACGGCGAAGGATATTGG
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
1516572 GCTCAAAACA
Statistics
Matches: 318, Mismatches: 43, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
106 28 0.09
107 1 0.00
110 289 0.91
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.25
Consensus pattern (110 bp):
AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAG
CGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTA
Found at i:1516822 original size:84 final size:84
Alignment explanation
Indices: 1516689--1517112 Score: 463
Period size: 84 Copynumber: 5.0 Consensus size: 84
1516679 AAGGGAATCA
* * * ** *
1516689 TGCCCACCAAAAACCTTCGAGTTCAACTACGCTCAGCTCCAAGTTACATCATTTACAGCATAACT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCT
*
1516754 TAAGTCGAGAAGGGTTATC
66 TAAGTCGAGAAGGGCTATC
* * * *
1516773 TGCCAACCAAAGACTTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAACATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCT
*
1516838 TAAGTCGAGAAGGGCTATA
66 TAAGTCGAGAAGGGCTATC
* * * * * * ** * *
1516857 TGCCAACCTAAGACCCTCAAGTTCAATTACACTCAGCTTTGAGGGCACATCATTTACAGCATAAC
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACAGCATAGC
* * * * *
1516922 TCAAGGCTAAAAGGGTTATC
65 TTAAGTCGAGAAGGGCTATC
* * * *
1516942 TGTC-ACCAAAATACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAGC
1 TGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGC
1517006 TTAAGTCGAGAAGGGCTATC
65 TTAAGTCGAGAAGGGCTATC
* * * * *
1517026 TGCCAACCGAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAGC
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACAGCATAGC
* * *
1517091 TCAAGGCAAGAAGGGCTATC
65 TTAAGTCGAGAAGGGCTATC
1517111 TG
1 TG
1517113 TCAATAAAAT
Statistics
Matches: 274, Mismatches: 62, Indels: 7
0.80 0.18 0.02
Matches are distributed among these distances:
84 169 0.62
85 105 0.38
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (84 bp):
TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCT
TAAGTCGAGAAGGGCTATC
Found at i:1517013 original size:169 final size:167
Alignment explanation
Indices: 1516734--1517115 Score: 566
Period size: 169 Copynumber: 2.3 Consensus size: 167
1516724 GCTCCAAGTT
* * * * *
1516734 ACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACTTTCGAGTTCGA
1 ACATCATTTACAGCATAACTCAAGGC-AAAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGA
1516799 CTACGCTCAGCTCAAAGGCACATCATTTGCAACATAGCTTAAGTCGAGAAGGGCTATATGCCAAC
64 CTACGCTCAGCTCAAAGGCACATCATTTGCAACATAGCTTAAGTCGAGAAGGGCTATATGCCAAC
* *
1516864 CTAAGACCCTCAAGTTCAATTACACTCAGCTTTGAGGGC
129 CGAAGACCCTCAAGTTCAATTACACTCAGCTTCGAGGGC
*
1516903 ACATCATTTACAGCATAACTCAAGGCTAAAAGGGTTATCTGTCACCAAAATACCTTCGAGTTCGA
1 ACATCATTTACAGCATAACTCAAGGC-AAAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGA
* * * *
1516968 CTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAC
64 CTACGCTCAGCTCAAAGGCACATCATTTGCAACATAGCTTAAGTCGAGAAGGGCTATATGCCAAC
* * *
1517033 CGAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGC
129 CGAAGACCCTCAAGTTCAATTACACTCAGCTTCGAGGGC
* *
1517072 ACATCATTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCA
1 ACATCATTTACAGCATAACTCAAGGCAA-AAGGGTTATCTGTCA
1517116 ATAAAATTGT
Statistics
Matches: 193, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
168 5 0.03
169 188 0.97
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (167 bp):
ACATCATTTACAGCATAACTCAAGGCAAAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCAAAGGCACATCATTTGCAACATAGCTTAAGTCGAGAAGGGCTATATGCCAACCG
AAGACCCTCAAGTTCAATTACACTCAGCTTCGAGGGC
Found at i:1517318 original size:15 final size:15
Alignment explanation
Indices: 1517298--1517327 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1517288 AAGACCCTTC
1517298 GAGCTCGATTCCATT
1 GAGCTCGATTCCATT
1517313 GAGCTCGATTCCATT
1 GAGCTCGATTCCATT
1517328 CATATCGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (15 bp):
GAGCTCGATTCCATT
Found at i:1517932 original size:36 final size:36
Alignment explanation
Indices: 1517770--1518128 Score: 331
Period size: 38 Copynumber: 9.8 Consensus size: 36
1517760 TTTTGACAAA
* * *
1517770 ATATAATATATAATTTTCAGAAAACGATTTTCG-AAAGTT
1 ATATAATATATAGTTTT--TAAAAC-ATTTT-GAAAAATT
* * * * *
1517809 GTATATTATATGGTTTTTGAAAATATTTTTAAAATATAT
1 ATATAATATATAGTTTTT-AAAACATTTTGAAAA-AT-T
*
1517848 ATATAATATATAGTTTTAAAAACATTTTGAAAAAAATT
1 ATATAATATATAGTTTTTAAAACATTTTG--AAAAATT
* *
1517886 ATATATTATATAGTTTTTAAAACATTTTGAAAACTT
1 ATATAATATATAGTTTTTAAAACATTTTGAAAAATT
*
1517922 ATATAATATATAGTTTTTAAAACATTTTGAAAACTT
1 ATATAATATATAGTTTTTAAAACATTTTGAAAAATT
*
1517958 ATA-AATATATAATTTTTTAAAACATTTTTGAAAAATT
1 ATATAATATAT-AGTTTTTAAAACA-TTTTGAAAAATT
* *
1517995 ATATAATATATAATTTTAAAAACATTTTTAGAAAAATT
1 ATATAATATATAGTTTTTAAAACA-TTTT-GAAAAATT
* *
1518033 ATATAATATATAGTTTTAAAAACATTTTTTG-AAAACT
1 ATATAATATATAGTTTTTAAAACA--TTTTGAAAAATT
*
1518070 -TAT-ATA-ATA-TTTTTAAAACGA-TTTG-AAAACT
1 ATATAATATATAGTTTTTAAAAC-ATTTTGAAAAATT
* *
1518101 ATATAATATATAGTTTTGAAAACTTTTT
1 ATATAATATATAGTTTTTAAAACATTTT
1518129 TTAAATATAA
Statistics
Matches: 276, Mismatches: 27, Indels: 38
0.81 0.08 0.11
Matches are distributed among these distances:
31 10 0.04
32 3 0.01
33 12 0.04
34 7 0.03
35 22 0.08
36 59 0.21
37 43 0.16
38 81 0.29
39 35 0.13
40 4 0.01
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (36 bp):
ATATAATATATAGTTTTTAAAACATTTTGAAAAATT
Found at i:1518171 original size:34 final size:33
Alignment explanation
Indices: 1517846--1518171 Score: 119
Period size: 38 Copynumber: 9.2 Consensus size: 33
1517836 TTTAAAATAT
***
1517846 ATATATAATATATAGTTTTAAAAACATTTTGAAAAAA
1 ATATATAATATATAGTTTTAAAAA-ATTTT---TTGA
* * ***
1517883 ATTATATATTATATAGTTTTTAAAACATTTTGAAA
1 A-TATATAATATATAG-TTTTAAAAAATTTTTTGA
*
1517918 ACTTATATAATATATAGTTTTTAAAACA--TTTTGA
1 A--TATATAATATATAG-TTTTAAAAAATTTTTTGA
* * *
1517952 AAACTTATAAATATATAATTTTTTAAAACA-TTTTTGAAAA
1 ATA--TAT-AATATAT-A-GTTTTAAAAAATTTTTTG---A
* *
1517992 ATTATATAATATATAATTTTAAAAACATTTTTAGAAAA
1 A-TATATAATATATAGTTTTAAAAA-ATTTTTTG---A
1518030 ATTATATAATATATAGTTTTAAAAACATTTTTTGA
1 A-TATATAATATATAGTTTTAAAAA-ATTTTTTGA
* * * ***
1518065 A-A-ACTTATATAATATTTTTAAAACGA-TTTGAAA
1 ATATA-TAATAT-ATAGTTTTAAAA-AATTTTTTGA
* * *
1518098 ACTATATAATATATAGTTTTGAAAACTTTTTTTA
1 A-TATATAATATATAGTTTTAAAAAATTTTTTGA
1518132 A-ATATAATATATAG-TTTAAAAAATATTTTTGA
1 ATATATAATATATAGTTTTAAAAAAT-TTTTTGA
1518164 AGTATATA
1 A-TATATA
1518172 TATTAGATAA
Statistics
Matches: 232, Mismatches: 32, Indels: 53
0.73 0.10 0.17
Matches are distributed among these distances:
31 8 0.03
32 22 0.09
33 11 0.05
34 39 0.17
35 19 0.08
36 45 0.19
37 8 0.03
38 66 0.28
39 11 0.05
40 2 0.01
41 1 0.00
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (33 bp):
ATATATAATATATAGTTTTAAAAAATTTTTTGA
Found at i:1518173 original size:68 final size:69
Alignment explanation
Indices: 1517848--1518164 Score: 238
Period size: 68 Copynumber: 4.5 Consensus size: 69
1517838 TAAAATATAT
* * * *
1517848 ATATAATATATAGTTTTAAAAACA-TTTTGAAAAAAATTATATATTATATAGTTTTTAAAACATT
1 ATATAATATATAATTTTAAAAACATTTTTG---AAAACTATATAATATATAGTTTTAAAAACATT
***
1517912 TTGAAAA
63 TTTTGAA
* * * *
1517919 CTTATATAATATATAGTTTTTAAAACA-TTTTGAAAACT-TATAAATATATAATTTTTTAAAACA
1 ---ATATAATATATAATTTTAAAAACATTTTTGAAAACTATAT-AATATAT-AGTTTTAAAAACA
1517982 -TTTTTGAAAAA
61 TTTTTTG---AA
*
1517993 TTATATAATATATAATTTTAAAAACATTTTTAGAAAAATTATATAATATATAGTTTTAAAAACAT
1 --ATATAATATATAATTTTAAAAACATTTTT-G-AAAACTATATAATATATAGTTTTAAAAACAT
1518058 TTTTTGAA
62 TTTTTGAA
* * *
1518066 A-ACTTATATA-ATATTTTTAAAACGA--TTTGAAAACTATATAATATATAGTTTTGAAAAC-TT
1 ATA-TAATATATA-ATTTTAAAAAC-ATTTTTGAAAACTATATAATATATAGTTTTAAAAACATT
*
1518126 TTTTTAA
63 TTTTGAA
* * *
1518133 ATATAATATATAGTTTAAAAAATATTTTTGAA
1 ATATAATATATAATTTTAAAAACATTTTTGAA
1518165 GTATATATAT
Statistics
Matches: 204, Mismatches: 22, Indels: 40
0.77 0.08 0.15
Matches are distributed among these distances:
66 1 0.00
67 22 0.11
68 35 0.17
69 1 0.00
70 8 0.04
71 31 0.15
72 13 0.06
73 26 0.13
74 34 0.17
75 12 0.06
76 18 0.09
77 3 0.01
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (69 bp):
ATATAATATATAATTTTAAAAACATTTTTGAAAACTATATAATATATAGTTTTAAAAACATTTTT
TGAA
Found at i:1520954 original size:22 final size:23
Alignment explanation
Indices: 1520923--1520965 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1520913 GATTTTAGGT
*
1520923 ATTTATATTATTGATTTATTACA
1 ATTTATATTATTAATTTATTACA
1520946 ATTTA-ATTATTAATTTATTA
1 ATTTATATTATTAATTTATTA
1520966 AATAAAGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
ATTTATATTATTAATTTATTACA
Found at i:1521550 original size:67 final size:68
Alignment explanation
Indices: 1521439--1521580 Score: 250
Period size: 67 Copynumber: 2.1 Consensus size: 68
1521429 CAGACGATAT
1521439 TGTTACTACTACATAATGATTGTTGTTGTGGTTGCAAACCATTTTTTAAGTAGTTGTTCCTAATA
1 TGTTACTACTACATAATGA-T-TTGTTGTGGTTGCAAACCATTTTTTAAGTAGTTGTTCCTAATA
1521504 ACAAA
64 ACAAA
*
1521509 TGTTACTACTACATAATGA-TTGTTGTGGTTGCAAACCATTTTTTAAGTGGTTGTTCCTAATAAC
1 TGTTACTACTACATAATGATTTGTTGTGGTTGCAAACCATTTTTTAAGTAGTTGTTCCTAATAAC
1521573 AAA
66 AAA
1521576 TGTTA
1 TGTTA
1521581 AAAAAATAAA
Statistics
Matches: 71, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
67 52 0.73
70 19 0.27
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.42
Consensus pattern (68 bp):
TGTTACTACTACATAATGATTTGTTGTGGTTGCAAACCATTTTTTAAGTAGTTGTTCCTAATAAC
AAA
Found at i:1521843 original size:30 final size:30
Alignment explanation
Indices: 1521783--1521874 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 30
1521773 TTAAAAGTAT
* *
1521783 GCCCCTAATAAAAAAATATTGAAGAAATTGG
1 GCCCCTAAT-AAAAAATATTAAAAAAATTGG
* *
1521814 GCCCCTAATAACAAGTATTAAAAAAATTGG
1 GCCCCTAATAAAAAATATTAAAAAAATTGG
* * *
1521844 ACCCTTAATAATAAATATTAAAAAATATTGG
1 GCCCCTAATAAAAAATATTAAAAAA-ATTGG
1521875 TAAAAAATTA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 38 0.73
31 14 0.27
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.26
Consensus pattern (30 bp):
GCCCCTAATAAAAAATATTAAAAAAATTGG
Found at i:1526537 original size:23 final size:23
Alignment explanation
Indices: 1526511--1526555 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1526501 AAAATCCTGT
1526511 TTACCAAAACCGGAAAACTCTGC
1 TTACCAAAACCGGAAAACTCTGC
* *
1526534 TTACCAGAGCCGGAAAACTCTG
1 TTACCAAAACCGGAAAACTCTG
1526556 TTTCTAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.29, G:0.18, T:0.18
Consensus pattern (23 bp):
TTACCAAAACCGGAAAACTCTGC
Found at i:1531558 original size:22 final size:23
Alignment explanation
Indices: 1531533--1531576 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1531523 TTAATTTCAT
1531533 AATC-AAAAACCCTATTTACCAA
1 AATCGAAAAACCCTATTTACCAA
* * *
1531555 AATCGGAAAACTCTTTTTACCA
1 AATCGAAAAACCCTATTTACCA
1531577 GAGCCGGGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.43, C:0.25, G:0.05, T:0.27
Consensus pattern (23 bp):
AATCGAAAAACCCTATTTACCAA
Found at i:1531564 original size:23 final size:23
Alignment explanation
Indices: 1531538--1531612 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 23
1531528 TTCATAATCA
* *
1531538 AAAACCCTATTTACCAAAATCGG
1 AAAACTCTATTTACCAAAACCGG
* * *
1531561 AAAACTCTTTTTACCAGAGCCGG
1 AAAACTCTATTTACCAAAACCGG
* * *
1531584 GAAACTCTATTTACCAGAGCCGG
1 AAAACTCTATTTACCAAAACCGG
1531607 AAAACT
1 AAAACT
1531613 TTGTTTCTAC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (23 bp):
AAAACTCTATTTACCAAAACCGG
Found at i:1542564 original size:288 final size:288
Alignment explanation
Indices: 1542048--1542748 Score: 1244
Period size: 288 Copynumber: 2.4 Consensus size: 288
1542038 TTAGCGGCGT
* *
1542048 TTGCTAAACTTTAAAATTTACCTCACCCTTTTCTCATGTTTTCCCCTTCACATATTTTTTTCATT
1 TTGCTAAACTTTAAAATTTACCGCACCTTTTTCTCATGTTTTCCCCTTCACATATTTTTTTCATT
*
1542113 CCCGCTCCCTCCCTTTTTGAAAAATCAAAATGTTTAGTGGTGTTAGTATGAAAACGCCGCGAAAG
66 CCCGCTCCCTCCCTTTTTGAAAAATCAAAATGTTTAGTGGTGTTAGTATGAAAACACCGCGAAAG
**
1542178 ACTCTTACTTTAGAGGCGTTTGTATGCAAACGCCGCTATAGACTGCTACATTAGTGGTGTTTTTC
131 ACTCTTACTTTAGAGGCGTTTGTATGCAAACGCCGCTATAGACTGCTACATTAGTGGCATTTTTC
1542243 AATAAATGCCACAATATATTAGTACTTTAGCAGCATTTTTATAAAAAAAGCCACTATATACTCGT
196 AATAAATGCCACAATATATTAGTACTTTAGCAGCATTTTTATAAAAAAAGCCACTATATACTCGT
*
1542308 ATTTTAGTGGTATTTTTAAACACAAACG
261 ATTTTAGTGGCATTTTTAAACACAAACG
*
1542336 TTGCTAAACTTTAAAATTTACCGCACATTTTTCTCATGTTTTCCCCTTCACATATTTTTTTCATT
1 TTGCTAAACTTTAAAATTTACCGCACCTTTTTCTCATGTTTTCCCCTTCACATATTTTTTTCATT
*
1542401 CCCGCTCCCTCCCTTTTTGAAAAATCAAAATGTTTAGTGGTGTTAGTATGAAAACACCGTGAAAG
66 CCCGCTCCCTCCCTTTTTGAAAAATCAAAATGTTTAGTGGTGTTAGTATGAAAACACCGCGAAAG
1542466 ACTCTTACTTTAGAGGCGTTTGTATGCAAACGCCGCTATAGACTGCTACATTAGTGGCATTTTTC
131 ACTCTTACTTTAGAGGCGTTTGTATGCAAACGCCGCTATAGACTGCTACATTAGTGGCATTTTTC
*
1542531 AATAAATGCCACAATATATTAGTACTTTAGCAGCGTTTTTATAAAAAAAGCCACTATATACTCGT
196 AATAAATGCCACAATATATTAGTACTTTAGCAGCATTTTTATAAAAAAAGCCACTATATACTCGT
1542596 ATTTTAGTGGCATTTTTAAACACAAACG
261 ATTTTAGTGGCATTTTTAAACACAAACG
1542624 TTGCTAAACTTTAAAATTTACCGCACCTTTTTCTCATGTTTTCCCCTTCACATATTTTTTTCATT
1 TTGCTAAACTTTAAAATTTACCGCACCTTTTTCTCATGTTTTCCCCTTCACATATTTTTTTCATT
* * *
1542689 CCCACTCCCTCCCTCCTTTTCTAAAAA--ATAAATGTTTAGTGGTGTTTGTATGAAAACACC
66 CCCGCTCCCTCCCT--TTTT-GAAAAATCA-AAATGTTTAGTGGTGTTAGTATGAAAACACC
1542749 ACTATAAACT
Statistics
Matches: 396, Mismatches: 13, Indels: 6
0.95 0.03 0.01
Matches are distributed among these distances:
288 356 0.90
289 1 0.00
290 34 0.09
291 5 0.01
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.38
Consensus pattern (288 bp):
TTGCTAAACTTTAAAATTTACCGCACCTTTTTCTCATGTTTTCCCCTTCACATATTTTTTTCATT
CCCGCTCCCTCCCTTTTTGAAAAATCAAAATGTTTAGTGGTGTTAGTATGAAAACACCGCGAAAG
ACTCTTACTTTAGAGGCGTTTGTATGCAAACGCCGCTATAGACTGCTACATTAGTGGCATTTTTC
AATAAATGCCACAATATATTAGTACTTTAGCAGCATTTTTATAAAAAAAGCCACTATATACTCGT
ATTTTAGTGGCATTTTTAAACACAAACG
Found at i:1542612 original size:42 final size:42
Alignment explanation
Indices: 1542516--1542613 Score: 99
Period size: 42 Copynumber: 2.4 Consensus size: 42
1542506 GACTGCTACA
* * *
1542516 TTAGTGGCATTTTT-CAATAAATGCCACAATATATTAGTACT
1 TTAGTGGCATTTTTACAAAAAAAGCCACAATATACTAGTACT
** * * * * *
1542557 TTAGCAGCGTTTTTATAAAAAAAGCCACTATATACTCGTATT
1 TTAGTGGCATTTTTACAAAAAAAGCCACAATATACTAGTACT
1542599 TTAGTGGCATTTTTA
1 TTAGTGGCATTTTTA
1542614 AACACAAACG
Statistics
Matches: 43, Mismatches: 13, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
41 11 0.26
42 32 0.74
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (42 bp):
TTAGTGGCATTTTTACAAAAAAAGCCACAATATACTAGTACT
Found at i:1544453 original size:21 final size:21
Alignment explanation
Indices: 1544429--1544497 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
1544419 AGCCAAAAAT
1544429 GAAGCAAG-GGAAGCAGAGAGA
1 GAAGC-AGCGGAAGCAGAGAGA
* *
1544450 GAAGCAGCAGAAGCAAAGAGA
1 GAAGCAGCGGAAGCAGAGAGA
1544471 GAAGCAGCGGAAGCAGAGAGA
1 GAAGCAGCGGAAGCAGAGAGA
1544492 GAAGCA
1 GAAGCA
1544498 ACATATCAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 2 0.05
21 41 0.95
ACGTcount: A:0.48, C:0.13, G:0.39, T:0.00
Consensus pattern (21 bp):
GAAGCAGCGGAAGCAGAGAGA
Found at i:1544455 original size:12 final size:11
Alignment explanation
Indices: 1544429--1544498 Score: 53
Period size: 9 Copynumber: 6.6 Consensus size: 11
1544419 AGCCAAAAAT
1544429 GAAGCAAG-G-
1 GAAGCAAGAGA
1544438 GAAGCAGAGAGA
1 GAAGCA-AGAGA
*
1544450 GAAGC-AG-CA
1 GAAGCAAGAGA
1544459 GAAGCAAAGAGA
1 GAAGC-AAGAGA
*
1544471 GAAGC-AGCG-
1 GAAGCAAGAGA
1544480 GAAGCAGAGAGA
1 GAAGCA-AGAGA
1544492 GAAGCAA
1 GAAGCAA
1544499 CATATCAACA
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
9 17 0.35
10 7 0.15
11 7 0.15
12 17 0.35
ACGTcount: A:0.49, C:0.13, G:0.39, T:0.00
Consensus pattern (11 bp):
GAAGCAAGAGA
Done.