Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 112 of 175
Found at i:35251987 original size:35 final size:36
Alignment explanation
Indices: 35251911--35252070 Score: 123
Period size: 36 Copynumber: 4.4 Consensus size: 36
35251901 AAAAAACTAA
* * * *
35251911 TCGTGTTTC-AAAAATTTTCATGTTTCCAAAAAATTC
1 TCGTGTTTCTAAAAATTTCCGTGTTTTC-AAAAATTT
*
35251947 CCGTGTTT-TAAAAATTTCCGTGTTTTCAAAAATTT
1 TCGTGTTTCTAAAAATTTCCGTGTTTTCAAAAATTT
* ** * *
35251982 TCGTGTTTCAAAAAAAATCCTTGTGTTTTTAAGAATTT
1 TCGTGTTTCTAAAAATTTCC--GTGTTTTCAAAAATTT
*
35252020 TCGTGTTTCT-AAAA-TCCTCGTGTTTT-AAAAATTTT
1 TCGTGTTTCTAAAAATTTC-CGTGTTTTCAAAAA-TTT
*
35252055 TCGTGTTCTCAAAAAA
1 TCGTGTT-TCTAAAAA
35252071 ATAATTATTT
Statistics
Matches: 100, Mismatches: 16, Indels: 15
0.76 0.12 0.11
Matches are distributed among these distances:
34 4 0.04
35 31 0.31
36 33 0.33
37 9 0.09
38 23 0.23
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (36 bp):
TCGTGTTTCTAAAAATTTCCGTGTTTTCAAAAATTT
Found at i:35251996 original size:18 final size:18
Alignment explanation
Indices: 35251911--35252070 Score: 105
Period size: 18 Copynumber: 8.8 Consensus size: 18
35251901 AAAAAACTAA
35251911 TCGTGTTTC-AAAAATTT
1 TCGTGTTTCAAAAAATTT
* *
35251928 TCATGTTTCCAAAAAATTC
1 TCGTGTTT-CAAAAAATTT
* *
35251947 CCGTGTTT-TAAAAATTT
1 TCGTGTTTCAAAAAATTT
*
35251964 CCGTGTTTTC-AAAAATTT
1 TCGTG-TTTCAAAAAATTT
*
35251982 TCGTGTTTCAAAAAAAATCCT
1 TCGTGTTTC--AAAAAAT-TT
** *
35252003 T-GTGTTTTTAAGAATTT
1 TCGTGTTTCAAAAAATTT
* **
35252020 TCGTGTTTC-TAAAATCC
1 TCGTGTTTCAAAAAATTT
* *
35252037 TCGTGTTTTAAAAATTTT
1 TCGTGTTTCAAAAAATTT
35252055 TCGTGTTCTCAAAAAA
1 TCGTGTT-TCAAAAAA
35252071 ATAATTATTT
Statistics
Matches: 108, Mismatches: 24, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
17 37 0.34
18 38 0.35
19 19 0.18
20 12 0.11
21 2 0.02
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (18 bp):
TCGTGTTTCAAAAAATTT
Found at i:35252008 original size:55 final size:54
Alignment explanation
Indices: 35251912--35252050 Score: 163
Period size: 54 Copynumber: 2.6 Consensus size: 54
35251902 AAAAACTAAT
* * *
35251912 CGTGTTTCAAAAATTTTCATGTTTCCAAAAAATTCCCGTG-TTTTAAAAATTTC
1 CGTGTTTCAAAAATTTTCGTGTTTCAAAAAAAATCCCGTGTTTTTAAAAATTTC
* * *
35251965 CGTGTTTTCAAAAATTTTCGTGTTTCAAAAAAAATCCTTGTGTTTTTAAGAATTTT
1 CGTG-TTTCAAAAATTTTCGTGTTTCAAAAAAAATCC-CGTGTTTTTAAAAATTTC
* ** *
35252021 CGTGTTTCTAAAATCCTCGTGTTTTAAAAA
1 CGTGTTTCAAAAATTTTCGTGTTTCAAAAA
35252051 TTTTTCGTGT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
53 4 0.05
54 29 0.40
55 25 0.34
56 15 0.21
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (54 bp):
CGTGTTTCAAAAATTTTCGTGTTTCAAAAAAAATCCCGTGTTTTTAAAAATTTC
Found at i:35252050 original size:17 final size:17
Alignment explanation
Indices: 35251939--35252051 Score: 61
Period size: 17 Copynumber: 6.4 Consensus size: 17
35251929 CATGTTTCCA
35251939 AAAAATTCC-CGTGTTTT
1 AAAAA-TCCTCGTGTTTT
*
35251956 AAAAAT-TTCCGTGTTTT
1 AAAAATCCT-CGTGTTTT
** *
35251973 CAAAAATTTTCGTGTTTCAAA
1 -AAAAATCCTCGTGTTT---T
*
35251994 AAAAATCCTTGTGTTTTT
1 AAAAATCCTCGTG-TTTT
* **
35252012 AAGAATTTTCGTGTTTCT
1 AAAAATCCTCGTGTTT-T
35252030 -AAAATCCTCGTGTTTT
1 AAAAATCCTCGTGTTTT
35252046 AAAAAT
1 AAAAAT
35252052 TTTTCGTGTT
Statistics
Matches: 73, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
16 2 0.03
17 33 0.45
18 23 0.32
19 2 0.03
20 10 0.14
21 3 0.04
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (17 bp):
AAAAATCCTCGTGTTTT
Found at i:35252103 original size:18 final size:18
Alignment explanation
Indices: 35251956--35252110 Score: 54
Period size: 18 Copynumber: 8.7 Consensus size: 18
35251946 CCCGTGTTTT
**
35251956 AAAAAT-TTCCGTGTTTTC
1 AAAAATCTT-CGTGTTTAA
*
35251974 AAAAATTTTCGTGTTTCAAA
1 AAAAATCTTCGTGTTT--AA
**
35251994 AAAAATCCTT-GTGTTTTT
1 AAAAAT-CTTCGTGTTTAA
* * *
35252012 AAGAATTTTCGTGTTT-C
1 AAAAATCTTCGTGTTTAA
* * *
35252029 TAAAATCCTCGTGTTTTA
1 AAAAATCTTCGTGTTTAA
* *
35252047 AAAATTTTTCGTGTTCTCAA
1 AAAAATCTTCGTGTT-T-AA
** * *
35252067 AAAAATAAT--TATTT-C
1 AAAAATCTTCGTGTTTAA
35252082 AAAAATCTTCGTGTTTAA
1 AAAAATCTTCGTGTTTAA
35252100 AAAAAT-TTCGT
1 AAAAATCTTCGT
35252111 ATTTTGATCG
Statistics
Matches: 99, Mismatches: 27, Indels: 23
0.66 0.18 0.15
Matches are distributed among these distances:
15 7 0.07
17 24 0.24
18 44 0.44
19 3 0.03
20 19 0.19
21 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43
Consensus pattern (18 bp):
AAAAATCTTCGTGTTTAA
Found at i:35256767 original size:2 final size:2
Alignment explanation
Indices: 35256760--35256786 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35256750 AAAAGAAACA
35256760 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
35256787 AGAACCTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35259445 original size:33 final size:33
Alignment explanation
Indices: 35259408--35259478 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
35259398 ACCTGTATCT
*
35259408 CAGTCACATAGGT-CTCCTTAACCTGCCCCACTA
1 CAGTCACATAGGTCCT-CTTAACCTGCCCCACAA
* *
35259441 CAGTCACATATGTCCTCTTCACCTGCCCCACAA
1 CAGTCACATAGGTCCTCTTAACCTGCCCCACAA
35259474 CAGTC
1 CAGTC
35259479 CTCCATCATG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 32 0.94
34 2 0.06
ACGTcount: A:0.24, C:0.41, G:0.11, T:0.24
Consensus pattern (33 bp):
CAGTCACATAGGTCCTCTTAACCTGCCCCACAA
Found at i:35261211 original size:19 final size:19
Alignment explanation
Indices: 35261180--35261247 Score: 52
Period size: 19 Copynumber: 3.5 Consensus size: 19
35261170 GGAATGTTAG
*
35261180 AGTAGTTAGTAAAGCTGTT
1 AGTAGTTAGTAAAACTGTT
35261199 AGTAGTT-GTTAAAACTGTT
1 AGTAGTTAG-TAAAACTGTT
* *
35261218 -GTACGGTTAGT-CAACAGTT
1 AGTA--GTTAGTAAAACTGTT
35261237 GAGTAGTTAGT
1 -AGTAGTTAGT
35261248 TATGCTTACG
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
18 4 0.10
19 28 0.70
20 4 0.10
21 4 0.10
ACGTcount: A:0.29, C:0.07, G:0.26, T:0.37
Consensus pattern (19 bp):
AGTAGTTAGTAAAACTGTT
Found at i:35268087 original size:30 final size:30
Alignment explanation
Indices: 35268051--35268143 Score: 159
Period size: 30 Copynumber: 3.1 Consensus size: 30
35268041 ACTTAACAAG
*
35268051 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
35268081 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
* *
35268111 CAAATGTCTTTAAAATTATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
35268141 CAA
1 CAA
35268144 TAAAATAAGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.56, C:0.14, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAACAAAATTAA
Found at i:35273770 original size:19 final size:19
Alignment explanation
Indices: 35273743--35273779 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
35273733 AATACGAGCA
35273743 AAAACAAATAAAAACAAAAT
1 AAAACAAAT-AAAACAAAAT
35273763 AAAA-AAATAAAACAAAA
1 AAAACAAATAAAACAAAA
35273780 CAATTATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 4 0.24
20 4 0.24
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (19 bp):
AAAACAAATAAAACAAAAT
Found at i:35276133 original size:44 final size:44
Alignment explanation
Indices: 35276085--35276188 Score: 129
Period size: 44 Copynumber: 2.4 Consensus size: 44
35276075 CGCTTCAATA
* * *
35276085 CAACTTTAGGGAGATAGG-ATTAGTAGCTTCAGCCTGCTCCACTG
1 CAACTTTAGAGAGATAGGAATTA-TAGCTTCAACCTGCCCCACTG
* *
35276129 CAACTTCAGAGAGATAGGAATTATATCTTCAACCTGCCCCACTG
1 CAACTTTAGAGAGATAGGAATTATAGCTTCAACCTGCCCCACTG
* *
35276173 CAATTTTAGAGGGATA
1 CAACTTTAGAGAGATA
35276189 AGGTTTGTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 47 0.92
45 4 0.08
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (44 bp):
CAACTTTAGAGAGATAGGAATTATAGCTTCAACCTGCCCCACTG
Found at i:35277671 original size:6 final size:6
Alignment explanation
Indices: 35277660--35277726 Score: 74
Period size: 6 Copynumber: 11.8 Consensus size: 6
35277650 TTGGCCTCTA
35277660 CTTTTT CTTTTT C-TTTT CTTTTT CTTCTTT -TCTTTT C-TTTT C-TTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTT-TTT CT-TTTT CTTTTT CTTTTT
35277706 C-TTTT C-TTTT CTTTTT CTTTT
1 CTTTTT CTTTTT CTTTTT CTTTT
35277727 ATTTTTTTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
5 25 0.45
6 27 0.48
7 4 0.07
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:35277676 original size:5 final size:5
Alignment explanation
Indices: 35277662--35277745 Score: 100
Period size: 5 Copynumber: 16.8 Consensus size: 5
35277652 GGCCTCTACT
*
35277662 TTTTC TTTTTC TTTTC TTTT- TCTTC TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
* * *
35277712 TTTTC TTTTTC TTTTA TTTTT TTTTG TTTT- TTTT
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
35277746 AACATTCTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
4 7 0.10
5 54 0.76
6 10 0.14
ACGTcount: A:0.01, C:0.14, G:0.01, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:35284282 original size:9 final size:9
Alignment explanation
Indices: 35284265--35284295 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
35284255 TCAAGTTGAT
35284265 TCGAATAAC
1 TCGAATAAC
*
35284274 TCGATTAAC
1 TCGAATAAC
35284283 TCGAATAAC
1 TCGAATAAC
35284292 TCGA
1 TCGA
35284296 TTCATTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:35288393 original size:106 final size:106
Alignment explanation
Indices: 35288201--35288402 Score: 275
Period size: 106 Copynumber: 1.9 Consensus size: 106
35288191 AAGGAAAATT
* *
35288201 TTTCAAATTAAGGCAATATTTTGCGTTGGAAAATTCGAGAAAACGTGCCCTAACGTACTGAGTCT
1 TTTCAAAGTAAGGCAATATTTTGCGTTAGAAAATTCGAGAAAACGTGCCCTAACGTACTGAGTCT
*
35288266 CGATTTCTCGTCTGATCAAATAGCCGAATATGCTTTCGAAA
66 CGATTTCTCGTCTGATCAAATAGCCAAATATGCTTTCGAAA
* * * * * *
35288307 TTTCAAAGTGAGGCAATATTTTGCATTTAG-AAATTCGAGAGAACGTGCCCTAACGTGCTGGGTT
1 TTTCAAAGTAAGGCAATATTTTGC-GTTAGAAAATTCGAGAAAACGTGCCCTAACGTACTGAGTC
35288371 TCGATTTCTCGT-TCGA-CTAAATAGCCAAATAT
65 TCGATTTCTCGTCT-GATC-AAATAGCCAAATAT
35288403 CCTCTTAAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
105 2 0.02
106 79 0.94
107 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (106 bp):
TTTCAAAGTAAGGCAATATTTTGCGTTAGAAAATTCGAGAAAACGTGCCCTAACGTACTGAGTCT
CGATTTCTCGTCTGATCAAATAGCCAAATATGCTTTCGAAA
Found at i:35290353 original size:69 final size:69
Alignment explanation
Indices: 35290119--35290363 Score: 264
Period size: 69 Copynumber: 3.6 Consensus size: 69
35290109 AGTATGTTAC
* * * *
35290119 ACTTAAAAACAGTAGCAAAATCTTAGATATTTAAGAACATATGGCAAACCAACACTCAACTAAAA
1 ACTTAAAAACAGTAGCAAAATATTAGATATTTAAGAACATATGACAAACTAACACTTAACTAAAA
35290184 CAAG
66 CAAG
* * * * * *** * ** *
35290188 ACTTAGAAACAGTAGCAAAACATTAGATATTTGAGAACATAAGA-AAATTTTGACATATGTTACA
1 ACTTAAAAACAGTAGCAAAATATTAGATATTTAAGAACATATGACAAACTAACACTTA-ACTAAA
35290252 AC-AG
65 ACAAG
* * *
35290256 -TTTACAAACAGTAGCCAAAA-AGTAGATATTTAAGAACATATGACAAACTAACACTTAACTAAA
1 ACTTAAAAACAGTAG-CAAAATATTAGATATTTAAGAACATATGACAAACTAACACTTAACTAAA
35290319 ACAAG
65 ACAAG
*
35290324 ACTTAAAAACAATAGCAAAATATTAGATATTTAAGAACAT
1 ACTTAAAAACAGTAGCAAAATATTAGATATTTAAGAACAT
35290364 GTGAAATTTT
Statistics
Matches: 137, Mismatches: 33, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
67 37 0.27
68 28 0.20
69 72 0.53
ACGTcount: A:0.51, C:0.15, G:0.11, T:0.24
Consensus pattern (69 bp):
ACTTAAAAACAGTAGCAAAATATTAGATATTTAAGAACATATGACAAACTAACACTTAACTAAAA
CAAG
Found at i:35290375 original size:136 final size:136
Alignment explanation
Indices: 35290125--35290387 Score: 393
Period size: 136 Copynumber: 1.9 Consensus size: 136
35290115 TTACACTTAA
** *
35290125 AAACAGTAGCAAAATCTTAGATATTTAAGAACATATGGCAAACCAACACTCAACTAAAACAAGAC
1 AAACAGTAGCAAAATAGTAGATATTTAAGAACATATGACAAACCAACACTCAACTAAAACAAGAC
* * *
35290190 TTAGAAACAGTAGCAAAACATTAGATATTTGAGAACATAAGAAAATTTTGACATATGTTACAACA
66 TTAAAAACAATAGCAAAACATTAGATATTTAAGAACATAAGAAAATTTTGACATATGTTACAACA
35290255 GTTTAC
131 GTTTAC
* *
35290261 AAACAGTAGCCAAAA-AGTAGATATTTAAGAACATATGACAAACTAACACTTAACTAAAACAAGA
1 AAACAGTAG-CAAAATAGTAGATATTTAAGAACATATGACAAACCAACACTCAACTAAAACAAGA
* ** * *
35290325 CTTAAAAACAATAGCAAAATATTAGATATTTAAGAACATGTGAAATTTTTGGCATATGTTACA
65 CTTAAAAACAATAGCAAAACATTAGATATTTAAGAACATAAGAAAATTTTGACATATGTTACA
35290388 CTTTAAAACA
Statistics
Matches: 113, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
136 108 0.96
137 5 0.04
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (136 bp):
AAACAGTAGCAAAATAGTAGATATTTAAGAACATATGACAAACCAACACTCAACTAAAACAAGAC
TTAAAAACAATAGCAAAACATTAGATATTTAAGAACATAAGAAAATTTTGACATATGTTACAACA
GTTTAC
Found at i:35290514 original size:39 final size:39
Alignment explanation
Indices: 35290471--35290548 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
35290461 AACTACACTT
* * **
35290471 AAAAACAGTAGTAAAACATTAGATATTTAAGAACATATG
1 AAAAAAAGTAGCAAAACATTAGATAAGTAAGAACATATG
* *
35290510 AAAAAAAGTAGCAAATCATTATATAAGTAAGAACATATG
1 AAAAAAAGTAGCAAAACATTAGATAAGTAAGAACATATG
35290549 GCAAACCAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.55, C:0.08, G:0.13, T:0.24
Consensus pattern (39 bp):
AAAAAAAGTAGCAAAACATTAGATAAGTAAGAACATATG
Found at i:35296769 original size:20 final size:21
Alignment explanation
Indices: 35296730--35296769 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
35296720 TTTCTTCCCT
*
35296730 CAAAAACACCACTTTCTCCTA
1 CAAAAACACCACTTTATCCTA
*
35296751 CAAAAACA-CATTTTATCCT
1 CAAAAACACCACTTTATCCT
35296770 GAAACTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.40, C:0.33, G:0.00, T:0.28
Consensus pattern (21 bp):
CAAAAACACCACTTTATCCTA
Found at i:35304819 original size:3 final size:3
Alignment explanation
Indices: 35304811--35304842 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
35304801 TTGCTTTTCC
35304811 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
35304843 TATAACTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:35314198 original size:6 final size:6
Alignment explanation
Indices: 35314187--35314212 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
35314177 CTGGTACAAG
35314187 TTTGAA TTTGAA TTTGAA TTTGAA TT
1 TTTGAA TTTGAA TTTGAA TTTGAA TT
35314213 GGGACTGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (6 bp):
TTTGAA
Found at i:35314442 original size:21 final size:20
Alignment explanation
Indices: 35314418--35314461 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
35314408 TCCTAATGCC
35314418 ATAT-TAAAAATGCTAACCAAA
1 ATATCTAAAAATG-TAA-CAAA
35314439 ATATCCTAAAAATGTAACAAA
1 ATAT-CTAAAAATGTAACAAA
35314460 AT
1 AT
35314462 TTACTTAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 10 0.48
22 3 0.14
23 8 0.38
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.25
Consensus pattern (20 bp):
ATATCTAAAAATGTAACAAA
Found at i:35325925 original size:59 final size:59
Alignment explanation
Indices: 35325858--35325971 Score: 192
Period size: 59 Copynumber: 1.9 Consensus size: 59
35325848 GTGTAGAGTG
35325858 CCCTTTTTTGCCCTCTCATCACAACAAGAACCCTACGAGAAACTCTTAAGCCATTACTA
1 CCCTTTTTTGCCCTCTCATCACAACAAGAACCCTACGAGAAACTCTTAAGCCATTACTA
* * * *
35325917 CCCTTTTTTGTCCTCTCATTACAACAAGAACCCTATGAGAAACTTTTAAGCCATT
1 CCCTTTTTTGCCCTCTCATCACAACAAGAACCCTACGAGAAACTCTTAAGCCATT
35325972 TGACTCAATG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.30, C:0.31, G:0.09, T:0.31
Consensus pattern (59 bp):
CCCTTTTTTGCCCTCTCATCACAACAAGAACCCTACGAGAAACTCTTAAGCCATTACTA
Found at i:35328535 original size:27 final size:28
Alignment explanation
Indices: 35328475--35328529 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
35328465 AAAACTAATT
*
35328475 AAAATTAAATATGTTAATAATTTAAGTG
1 AAAATTAAATATGTTAATAATTAAAGTG
* *
35328503 AAAATTAATTAT-TTTATAATTAAAGTG
1 AAAATTAAATATGTTAATAATTAAAGTG
35328530 TGAATTTCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (28 bp):
AAAATTAAATATGTTAATAATTAAAGTG
Found at i:35331813 original size:67 final size:66
Alignment explanation
Indices: 35331688--35331911 Score: 213
Period size: 67 Copynumber: 3.3 Consensus size: 66
35331678 CCTCAAAAAA
* * * * *
35331688 GGTTCAAGGTGTAAGACCTTAGCTTGGCTAAT-GCAACCAATAAAGTCCGCAAGGATGTTAAACA
1 GGTTCAAGGTGTAAGACCAT-GCTTAGCT-ATGGCAACCAATAGAGTCAGCAATGATGTTAAACA
35331752 TGG
64 TGG
* *
35331755 GGTTACAAGGTGTAAGACCATGCTTAGCTATGGTAACCAATAGAGTCAG-ACATGATGTTAAATA
1 GGTT-CAAGGTGTAAGACCATGCTTAGCTATGGCAACCAATAGAGTCAGCA-ATGATGTTAAACA
35331819 TGG
64 TGG
** * * * *
35331822 GGTTACAAGGTGTAAGACCACAAC-TCGACTATGGCAACCAATAGAGTCTGCTATGAGGTTAAAC
1 GGTT-CAAGGTGTAAGACCA-TGCTTAG-CTATGGCAACCAATAGAGTCAGCAATGATGTTAAAC
35331886 AT-G
63 ATGG
*
35331889 GGTTCAGACTGTGTAAGACCATG
1 GGTTCA-A-GGTGTAAGACCATG
35331912 GCTCGGCTAT
Statistics
Matches: 131, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
66 5 0.04
67 67 0.51
68 59 0.45
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (66 bp):
GGTTCAAGGTGTAAGACCATGCTTAGCTATGGCAACCAATAGAGTCAGCAATGATGTTAAACATG
G
Found at i:35331922 original size:68 final size:67
Alignment explanation
Indices: 35331688--35331923 Score: 239
Period size: 68 Copynumber: 3.5 Consensus size: 67
35331678 CCTCAAAAAA
* * * * *
35331688 GGTT-CAAGGTGTAAGACCTTAGCTTGGCTAAT-GCAACCAATAAAGTCCGCAAGGATGTTAAAC
1 GGTTACAAGGTGTAAGACCATAGCTCGGCT-ATGGCAACCAATAGAGTCAGC-ATGATGTTAAAC
35331751 ATGG
64 ATGG
** * *
35331755 GGTTACAAGGTGTAAGACCAT-GCTTAGCTATGGTAACCAATAGAGTCAGACATGATGTTAAATA
1 GGTTACAAGGTGTAAGACCATAGCTCGGCTATGGCAACCAATAGAGTCAG-CATGATGTTAAACA
35331819 TGG
65 TGG
* * * * *
35331822 GGTTACAAGGTGTAAGACCACAACTCGACTATGGCAACCAATAGAGTCTGCTATGAGGTTAAACA
1 GGTTACAAGGTGTAAGACCATAGCTCGGCTATGGCAACCAATAGAGTCAGC-ATGATGTTAAACA
35331887 T-G
65 TGG
* *
35331889 GGTT-CAGACTGTGTAAGACCATGGCTCGGCTATGG
1 GGTTACA-A-GGTGTAAGACCATAGCTCGGCTATGG
35331924 TGTCAGGTAA
Statistics
Matches: 141, Mismatches: 21, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
66 4 0.03
67 66 0.47
68 71 0.50
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (67 bp):
GGTTACAAGGTGTAAGACCATAGCTCGGCTATGGCAACCAATAGAGTCAGCATGATGTTAAACAT
GG
Found at i:35336526 original size:10 final size:10
Alignment explanation
Indices: 35336511--35336601 Score: 50
Period size: 10 Copynumber: 9.0 Consensus size: 10
35336501 ATTTAAAATA
35336511 TATATTATAT
1 TATATTATAT
35336521 TATATT-TACT
1 TATATTATA-T
35336531 TA-ATTA-AT
1 TATATTATAT
* *
35336539 AAGTATGT-TTT
1 TA-TAT-TATAT
35336550 TATATTATAT
1 TATATTATAT
35336560 TATTATTA-A-
1 TA-TATTATAT
*
35336569 TATATTATAC
1 TATATTATAT
35336579 TATATTATTAT
1 TATATTA-TAT
35336590 ATATATATATAT
1 -TATAT-TATAT
35336602 AACAAAAGAA
Statistics
Matches: 63, Mismatches: 5, Indels: 24
0.68 0.05 0.26
Matches are distributed among these distances:
8 7 0.11
9 10 0.16
10 26 0.41
11 10 0.16
12 8 0.13
13 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (10 bp):
TATATTATAT
Found at i:35336576 original size:24 final size:26
Alignment explanation
Indices: 35336549--35336599 Score: 79
Period size: 24 Copynumber: 2.0 Consensus size: 26
35336539 AAGTATGTTT
*
35336549 TTATATTATATTATTAT-TA-ATATA
1 TTATACTATATTATTATATATATATA
35336573 TTATACTATATTATTATATATATATA
1 TTATACTATATTATTATATATATATA
35336599 T
1 T
35336600 ATAACAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 2 0.08
26 6 0.25
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
TTATACTATATTATTATATATATATA
Found at i:35336667 original size:35 final size:34
Alignment explanation
Indices: 35336622--35336688 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 34
35336612 AGAATAGAAA
*
35336622 TGAGAAAGAAAGAA-ACAAAGAAGCAAAACGAAATT
1 TGAGAAAGAAA-AAGACAAAGAAG-AAAAAGAAATT
*
35336657 TGAGAAAGAAAAAGAGAAAGAAGAAAAAGAAA
1 TGAGAAAGAAAAAGACAAAGAAGAAAAAGAAA
35336689 GAGAACCACG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 10 0.34
35 19 0.66
ACGTcount: A:0.67, C:0.04, G:0.22, T:0.06
Consensus pattern (34 bp):
TGAGAAAGAAAAAGACAAAGAAGAAAAAGAAATT
Found at i:35337492 original size:22 final size:22
Alignment explanation
Indices: 35337443--35337493 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
35337433 ATTAAATGAT
35337443 ATTGAAT-TATTTGTGAATTGA
1 ATTGAATATATTTGTGAATTGA
* *
35337464 AAT-AATATATGTTTTGAATTG-
1 ATTGAATATAT-TTGTGAATTGA
35337485 ATTGAATAT
1 ATTGAATAT
35337494 TTGAAATTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
20 3 0.12
21 7 0.29
22 14 0.58
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (22 bp):
ATTGAATATATTTGTGAATTGA
Found at i:35343323 original size:20 final size:20
Alignment explanation
Indices: 35343298--35343402 Score: 129
Period size: 20 Copynumber: 5.2 Consensus size: 20
35343288 TATTGCTGAA
35343298 CAGAGGCACCGAAGTGCAAT
1 CAGAGGCACCGAAGTGCAAT
* *
35343318 CAGAGGCAGCGAAGTACAAT
1 CAGAGGCACCGAAGTGCAAT
* *
35343338 CAAAGGCATCGAAGTGCAAT
1 CAGAGGCACCGAAGTGCAAT
** *
35343358 CAGAGGCGTCGAAGTACAAT
1 CAGAGGCACCGAAGTGCAAT
* *
35343378 CAAAGGCACCAAAGTGCAAT
1 CAGAGGCACCGAAGTGCAAT
35343398 CAGAG
1 CAGAG
35343403 AGTACATAAA
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.39, C:0.22, G:0.28, T:0.11
Consensus pattern (20 bp):
CAGAGGCACCGAAGTGCAAT
Found at i:35343356 original size:40 final size:40
Alignment explanation
Indices: 35343301--35343402 Score: 170
Period size: 40 Copynumber: 2.5 Consensus size: 40
35343291 TGCTGAACAG
35343301 AGGCACCGAAGTGCAATCAGAGGCAG-CGAAGTACAATCAA
1 AGGCACCGAAGTGCAATCAGAGGC-GTCGAAGTACAATCAA
*
35343341 AGGCATCGAAGTGCAATCAGAGGCGTCGAAGTACAATCAA
1 AGGCACCGAAGTGCAATCAGAGGCGTCGAAGTACAATCAA
*
35343381 AGGCACCAAAGTGCAATCAGAG
1 AGGCACCGAAGTGCAATCAGAG
35343403 AGTACATAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 1 0.02
40 57 0.98
ACGTcount: A:0.39, C:0.22, G:0.27, T:0.12
Consensus pattern (40 bp):
AGGCACCGAAGTGCAATCAGAGGCGTCGAAGTACAATCAA
Found at i:35343445 original size:22 final size:22
Alignment explanation
Indices: 35343383--35343513 Score: 85
Period size: 22 Copynumber: 6.0 Consensus size: 22
35343373 ACAATCAAAG
* *
35343383 GCACCAAAGTGC-AATCAGAGA
1 GCACAAAAGTGCAAATTAGAGA
*
35343404 GTACATAAA-TGCTAAA-TAGAGA
1 GCACA-AAAGTGC-AAATTAGAGA
35343426 GCACAAAAGTGCAAATTAGAGA
1 GCACAAAAGTGCAAATTAGAGA
* *
35343448 GC-CTAGAAGTG-ATAATTAGAAA
1 GCAC-AAAAGTGCA-AATTAGAGA
*
35343470 GCATAAAAGTGCTAAA-TAGAGA
1 GCACAAAAGTGC-AAATTAGAGA
** * *
35343492 GCACTGAAGTGCTAATCAGAGA
1 GCACAAAAGTGCAAATTAGAGA
35343514 TCCAATTTCA
Statistics
Matches: 85, Mismatches: 14, Indels: 21
0.71 0.12 0.17
Matches are distributed among these distances:
21 16 0.19
22 64 0.75
23 4 0.05
24 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.23, T:0.18
Consensus pattern (22 bp):
GCACAAAAGTGCAAATTAGAGA
Found at i:35343478 original size:44 final size:44
Alignment explanation
Indices: 35343420--35343507 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
35343410 AAATGCTAAA
*
35343420 TAGAGAGCACAAAAGTGC-AAATTAGAGAGC-CTAGAAGTGATAAT
1 TAGAAAGCACAAAAGTGCTAAA-TAGAGAGCACT-GAAGTGATAAT
* *
35343464 TAGAAAGCATAAAAGTGCTAAATAGAGAGCACTGAAGTGCTAAT
1 TAGAAAGCACAAAAGTGCTAAATAGAGAGCACTGAAGTGATAAT
35343508 CAGAGATCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
44 34 0.87
45 5 0.13
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.19
Consensus pattern (44 bp):
TAGAAAGCACAAAAGTGCTAAATAGAGAGCACTGAAGTGATAAT
Found at i:35344708 original size:23 final size:23
Alignment explanation
Indices: 35344664--35344708 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
35344654 TTAAAAAGTA
*
35344664 GTTAATTTCCACTTTAAACCTTG
1 GTTAATTTCCACTATAAACCTTG
*
35344687 GTTAATTTACCA-TATAAGCCTT
1 GTTAATTT-CCACTATAAACCTT
35344709 TTAACTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.42
Consensus pattern (23 bp):
GTTAATTTCCACTATAAACCTTG
Found at i:35350432 original size:13 final size:14
Alignment explanation
Indices: 35350404--35350433 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
35350394 GAAAAATACA
35350404 AAAATTAAATTCTT
1 AAAATTAAATTCTT
35350418 AAAATTAAATT-TT
1 AAAATTAAATTCTT
35350431 AAA
1 AAA
35350434 TCTATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAATTAAATTCTT
Found at i:35351714 original size:4 final size:4
Alignment explanation
Indices: 35351705--35351732 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
35351695 TCAACCACTG
35351705 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
35351733 TAGAATTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:35355955 original size:22 final size:21
Alignment explanation
Indices: 35355899--35355969 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 21
35355889 ATACAGTGTG
35355899 GATAAACCACTAATTA-GTATA
1 GATAAACCACTAA-TACGTATA
* *
35355920 GATAAAAACTACTAATACGCTATG
1 GAT--AAACCACTAATACG-TATA
35355944 GATAAACCACTAAT-CGTATA
1 GATAAACCACTAATACGTATA
35355964 GATAAA
1 GATAAA
35355970 ATCTGCTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
20 9 0.21
21 5 0.12
22 12 0.29
23 10 0.24
24 6 0.14
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.25
Consensus pattern (21 bp):
GATAAACCACTAATACGTATA
Found at i:35355979 original size:44 final size:45
Alignment explanation
Indices: 35355874--35356000 Score: 161
Period size: 44 Copynumber: 2.8 Consensus size: 45
35355864 TAAATGTTGC
*
35355874 AGATAAAAGCTGCTAATACAG-TGTGGATAAACCACTAATTAGTAT
1 AGATAAAAACTGCTAATAC-GCTGTGGATAAACCACTAATTAGTAT
* * *
35355919 AGATAAAAACTACTAATACGCTATGGATAAACCACTAA-TCGTAT
1 AGATAAAAACTGCTAATACGCTGTGGATAAACCACTAATTAGTAT
* *
35355963 AGATAAAATCTGCTAATACGAC-GTGGATTAACCACTAA
1 AGATAAAAACTGCTAATACG-CTGTGGATAAACCACTAA
35356001 ACGGTGAAGA
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
44 38 0.53
45 34 0.47
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (45 bp):
AGATAAAAACTGCTAATACGCTGTGGATAAACCACTAATTAGTAT
Found at i:35372555 original size:123 final size:124
Alignment explanation
Indices: 35372399--35372625 Score: 341
Period size: 123 Copynumber: 1.8 Consensus size: 124
35372389 TCTTCGTAGC
35372399 AAACATACATTCGGATAACATATATATAATTCATACAATTAAATTCAACTTAT-AGAACTCAAAA
1 AAACATACATTCGGATAACATATATATAATTCATACAATTAAATTCAACTTATCA-AACTCAAAA
* * *
35372463 CATACATTCGGCTAACATATATATATAATTTATACAATTAGTTTCAACTCATAGAACTCA
65 CATACATTCAGCTAACATATATATATAATTCATAAAATTAGTTTCAACTCATAGAACTCA
* * ** * *
35372523 AAACATACATT-GGCTAACATATTTATAATTCATACAATTAGTTTCAACTTATCAAACTTAAAGC
1 AAACATACATTCGGATAACATATATATAATTCATACAATTAAATTCAACTTATCAAACTCAAAAC
*
35372587 ATACATTCAGCTAACATATTTATATAATTCATAAAATTA
66 ATACATTCAGCTAACATATATATATAATTCATAAAATTA
35372626 AATTCAGCTT
Statistics
Matches: 92, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
123 80 0.87
124 12 0.13
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.34
Consensus pattern (124 bp):
AAACATACATTCGGATAACATATATATAATTCATACAATTAAATTCAACTTATCAAACTCAAAAC
ATACATTCAGCTAACATATATATATAATTCATAAAATTAGTTTCAACTCATAGAACTCA
Found at i:35372590 original size:60 final size:62
Alignment explanation
Indices: 35372399--35372642 Score: 325
Period size: 63 Copynumber: 4.0 Consensus size: 62
35372389 TCTTCGTAGC
* **
35372399 AAACATACATTCGGATAACATA-TATATAATTCATACAATTAAATTCAACTTATAGAACTCA
1 AAACATACATTCGGCTAACATATTATATAATTCATACAATTAGTTTCAACTTATAGAACTCA
* *
35372460 AAACATACATTCGGCTAACATATATATATAATTTATACAATTAGTTTCAACTCATAGAACTCA
1 AAACATACATTCGGCTAACATAT-TATATAATTCATACAATTAGTTTCAACTTATAGAACTCA
*
35372523 AAACATACATT-GGCTAACATATT-TATAATTCATACAATTAGTTTCAACTTATCA-AACTTA
1 AAACATACATTCGGCTAACATATTATATAATTCATACAATTAGTTTCAACTTAT-AGAACTCA
* * * ** *
35372583 AAGCATACATTCAGCTAACATATTTATATAATTCATAAAATTAAATTCAGCTTATAGAAC
1 AAACATACATTCGGCTAACATA-TTATATAATTCATACAATTAGTTTCAACTTATAGAAC
35372643 ATATATATAT
Statistics
Matches: 162, Mismatches: 14, Indels: 12
0.86 0.07 0.06
Matches are distributed among these distances:
60 42 0.26
61 32 0.20
62 14 0.09
63 74 0.46
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (62 bp):
AAACATACATTCGGCTAACATATTATATAATTCATACAATTAGTTTCAACTTATAGAACTCA
Found at i:35380137 original size:40 final size:40
Alignment explanation
Indices: 35380093--35380320 Score: 259
Period size: 40 Copynumber: 5.8 Consensus size: 40
35380083 AATTATTGTA
* *
35380093 TGAATGCACATATGTGCCTTTGTTTGTACTTCGATACCCC
1 TGAATGCACATACGTGCCCTTGTTTGTACTTCGATACCCC
*
35380133 TGAATGCACATGCGTG-CCTCTGTTTGTACTT-GAGTACCCC
1 TGAATGCACATACGTGCCCT-TGTTTGTACTTCGA-TACCCC
* * * * *
35380173 TGAATGGACATACGTGCCCATG-TTGTACTTTGGTATCCC
1 TGAATGCACATACGTGCCCTTGTTTGTACTTCGATACCCC
* * *
35380212 TGAATGCACATGCGTGCCCTTATTTGTACTTCGGTACCCC
1 TGAATGCACATACGTGCCCTTGTTTGTACTTCGATACCCC
*
35380252 TGAATGCACATACGTGCCCTTGTTTGTACTTCCG-TACCCT
1 TGAATGCACATACGTGCCCTTGTTTGTACTT-CGATACCCC
* * *
35380292 TGAATGCACTTATGTG-CCTTGTTTATACT
1 TGAATGCACATACGTGCCCTTGTTTGTACT
35380321 CCGGTAACTC
Statistics
Matches: 162, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
39 47 0.29
40 111 0.69
41 4 0.02
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.36
Consensus pattern (40 bp):
TGAATGCACATACGTGCCCTTGTTTGTACTTCGATACCCC
Found at i:35380216 original size:79 final size:79
Alignment explanation
Indices: 35380093--35380300 Score: 278
Period size: 79 Copynumber: 2.6 Consensus size: 79
35380083 AATTATTGTA
* * * *
35380093 TGAATGCACATATGTGCCTTTGTTTGTACTTCGATACCCCTGAATGCACATGCGTG-CCTCTGTT
1 TGAATGCACATACGTGCCCTTGTTTGTACTTCGGTA-CCCTGAATGCACATGCGTGCCCT-TATT
35380157 TGTACTT-GAGTACCCC
64 TGTACTTCG-GTACCCC
* * *
35380173 TGAATGGACATACGTGCCCATG-TTGTACTTTGGTATCCCTGAATGCACATGCGTGCCCTTATTT
1 TGAATGCACATACGTGCCCTTGTTTGTACTTCGGTA-CCCTGAATGCACATGCGTGCCCTTATTT
35380237 GTACTTCGGTACCCC
65 GTACTTCGGTACCCC
*
35380252 TGAATGCACATACGTGCCCTTGTTTGTACTTCCGTACCCTTGAATGCAC
1 TGAATGCACATACGTGCCCTTGTTTGTACTTCGGTACCC-TGAATGCAC
35380301 TTATGTGCCT
Statistics
Matches: 112, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
79 70 0.62
80 42 0.38
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.34
Consensus pattern (79 bp):
TGAATGCACATACGTGCCCTTGTTTGTACTTCGGTACCCTGAATGCACATGCGTGCCCTTATTTG
TACTTCGGTACCCC
Found at i:35380302 original size:20 final size:20
Alignment explanation
Indices: 35380239--35380302 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 20
35380229 CCTTATTTGT
* *
35380239 ACTTCGGTACCCCTGAATGC
1 ACTTCCGTACCCTTGAATGC
* * * ** *
35380259 ACATACGTGCCCTTGTTTGT
1 ACTTCCGTACCCTTGAATGC
35380279 ACTTCCGTACCCTTGAATGC
1 ACTTCCGTACCCTTGAATGC
35380299 ACTT
1 ACTT
35380303 ATGTGCCTTG
Statistics
Matches: 30, Mismatches: 14, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (20 bp):
ACTTCCGTACCCTTGAATGC
Found at i:35380309 original size:119 final size:119
Alignment explanation
Indices: 35380093--35380309 Score: 310
Period size: 119 Copynumber: 1.8 Consensus size: 119
35380083 AATTATTGTA
* * * *
35380093 TGAATGCACATATGTGCCTTTGTTTGTACTTCGATACCCCTGAATGCACATGCGTGCCTCTGTTT
1 TGAATGCACATACGTGCCCTTATTTGTACTTCGATACCCCTGAATGCACATACGTGCCTCTGTTT
* *
35380158 GTACTTGAGTACCCCTGAATGGACATACGTGCCCATGTTGTACTTTGGTATCCC
66 GTACTTCAGTACCCCTGAATGCACATACGTGCCCATGTTGTACTTTGGTATCCC
* *
35380212 TGAATGCACATGCGTGCCCTTATTTGTACTTCGGTACCCCTGAATGCACATACGTGCC-CTTGTT
1 TGAATGCACATACGTGCCCTTATTTGTACTTCGATACCCCTGAATGCACATACGTGCCTC-TGTT
* * * *
35380276 TGTACTTCCGTACCCTTGAATGCACTTATGTGCC
65 TGTACTTCAGTACCCCTGAATGCACATACGTGCC
35380310 TTGTTTATAC
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
118 1 0.01
119 84 0.99
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.34
Consensus pattern (119 bp):
TGAATGCACATACGTGCCCTTATTTGTACTTCGATACCCCTGAATGCACATACGTGCCTCTGTTT
GTACTTCAGTACCCCTGAATGCACATACGTGCCCATGTTGTACTTTGGTATCCC
Found at i:35380326 original size:79 final size:76
Alignment explanation
Indices: 35380093--35380335 Score: 263
Period size: 79 Copynumber: 3.1 Consensus size: 76
35380083 AATTATTGTA
* *
35380093 TGAATGCACATATGTGCCTTTGTTTGTACTTCGATACCCCTGAATGCACATGCGTGCCTCTGTTT
1 TGAATGCACATACGTGCCCTTGTTTGTACTTCG-TA-CCCTGAATGCACATGCGTGCCT-TGTTT
*
35380158 GTACTTGAGTACCCC
63 GTACTCG-GTACCCC
* * * *
35380173 TGAATGGACATACGTGCCCATG-TTGTACTTTGGTATCCCTGAATGCACATGCGTGCCCTTATTT
1 TGAATGCACATACGTGCCCTTGTTTGTAC-TTCGTA-CCCTGAATGCACATGCGTG-CCTTGTTT
35380237 GTACTTCGGTACCCC
63 GTAC-TCGGTACCCC
* ** *
35380252 TGAATGCACATACGTGCCCTTGTTTGTACTTCCGTACCCTTGAATGCACTTATGTGCCTTGTTTA
1 TGAATGCACATACGTGCCCTTGTTTGTACTT-CGTACCC-TGAATGCACATGCGTGCCTTGTTTG
* *
35380317 TACTCCGGTAACTC
64 TACT-CGGTACCCC
35380331 TGAAT
1 TGAAT
35380336 TATGTAGTAT
Statistics
Matches: 138, Mismatches: 18, Indels: 15
0.81 0.11 0.09
Matches are distributed among these distances:
78 1 0.01
79 89 0.64
80 48 0.35
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (76 bp):
TGAATGCACATACGTGCCCTTGTTTGTACTTCGTACCCTGAATGCACATGCGTGCCTTGTTTGTA
CTCGGTACCCC
Found at i:35380334 original size:119 final size:119
Alignment explanation
Indices: 35380093--35380335 Score: 292
Period size: 119 Copynumber: 2.0 Consensus size: 119
35380083 AATTATTGTA
* * * *
35380093 TGAATGCACATATGTGCCTTTGTTTGTACTTCGATACCCCTGAATGCACATGCGTGCCTCTGTTT
1 TGAATGCACATACGTGCCCTTATTTGTACTTCGATACCCCTGAATGCACATACGTGCCTCTGTTT
* * * ** *
35380158 GTACTTGAGTACCCCTGAATGGACATACGTGCCCATGTTGTACTTTGGTATCCC
66 GTACTTCAGTACCCCTGAATGCACATACGTGCCCATGTTATACTCCGGTAACCC
* *
35380212 TGAATGCACATGCGTGCCCTTATTTGTACTTCGGTACCCCTGAATGCACATACGTGCC-CTTGTT
1 TGAATGCACATACGTGCCCTTATTTGTACTTCGATACCCCTGAATGCACATACGTGCCTC-TGTT
* * * * * *
35380276 TGTACTTCCGTACCCTTGAATGCACTTATGTG-CCTTGTTTATACTCCGGTAACTC
65 TGTACTTCAGTACCCCTGAATGCACATACGTGCCCATG-TTATACTCCGGTAACCC
35380331 TGAAT
1 TGAAT
35380336 TATGTAGTAT
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
118 5 0.05
119 99 0.95
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (119 bp):
TGAATGCACATACGTGCCCTTATTTGTACTTCGATACCCCTGAATGCACATACGTGCCTCTGTTT
GTACTTCAGTACCCCTGAATGCACATACGTGCCCATGTTATACTCCGGTAACCC
Found at i:35381533 original size:39 final size:40
Alignment explanation
Indices: 35381416--35381577 Score: 227
Period size: 40 Copynumber: 4.1 Consensus size: 40
35381406 AATTATTGTA
* *
35381416 TGAATGCACATGCGTACCCCTGTTTGTACTTCGGTACCCC
1 TGAATGCACATGCGTGCCCCTGTTTGTACTTCAGTACCCC
* *
35381456 TAAAGGCACATGCGTGCCCCTGTTTGTACTTCAGTACCCC
1 TGAATGCACATGCGTGCCCCTGTTTGTACTTCAGTACCCC
*
35381496 TGAATGCACATACGTGCCCCTG-TTGTACTTCAGTACCCC
1 TGAATGCACATGCGTGCCCCTGTTTGTACTTCAGTACCCC
* * * * *
35381535 TGAATGCACATGCATGCCCTTGTTTCTACTTCGGTACCTC
1 TGAATGCACATGCGTGCCCCTGTTTGTACTTCAGTACCCC
35381575 TGA
1 TGA
35381578 CTACTCTTAC
Statistics
Matches: 108, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
39 36 0.33
40 72 0.67
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.30
Consensus pattern (40 bp):
TGAATGCACATGCGTGCCCCTGTTTGTACTTCAGTACCCC
Found at i:35381536 original size:19 final size:20
Alignment explanation
Indices: 35381472--35381537 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
35381462 CACATGCGTG
*
35381472 CCCCTGTTTGTACTTCAGTA
1 CCCCTGATTGTACTTCAGTA
* * * *
35381492 CCCCTGAATGCACAT-ACGTG
1 CCCCTGATTGTACTTCA-GTA
35381512 CCCCTG-TTGTACTTCAGTA
1 CCCCTGATTGTACTTCAGTA
35381531 CCCCTGA
1 CCCCTGA
35381538 ATGCACATGC
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
19 14 0.41
20 20 0.59
ACGTcount: A:0.18, C:0.35, G:0.17, T:0.30
Consensus pattern (20 bp):
CCCCTGATTGTACTTCAGTA
Found at i:35381553 original size:79 final size:80
Alignment explanation
Indices: 35381416--35381577 Score: 227
Period size: 79 Copynumber: 2.0 Consensus size: 80
35381406 AATTATTGTA
* * *
35381416 TGAATGCACATGCGTACCCCTGTTTGTACTTCGGTACCCCTAAAGGCACATGCGTGCCCCTGTTT
1 TGAATGCACATACGTACCCCTGTTTGTACTTCAGTACCCCTAAAGGCACATGCATGCCCCTGTTT
*
35381481 GTACTTCAGTACCCC
66 CTACTTCAGTACCCC
* * * *
35381496 TGAATGCACATACGTGCCCCTG-TTGTACTTCAGTACCCCTGAATGCACATGCATGCCCTTGTTT
1 TGAATGCACATACGTACCCCTGTTTGTACTTCAGTACCCCTAAAGGCACATGCATGCCCCTGTTT
* *
35381560 CTACTTCGGTACCTC
66 CTACTTCAGTACCCC
35381575 TGA
1 TGA
35381578 CTACTCTTAC
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 52 0.72
80 20 0.28
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.30
Consensus pattern (80 bp):
TGAATGCACATACGTACCCCTGTTTGTACTTCAGTACCCCTAAAGGCACATGCATGCCCCTGTTT
CTACTTCAGTACCCC
Found at i:35400518 original size:20 final size:20
Alignment explanation
Indices: 35400482--35400519 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35400472 AATCAAAAAT
*
35400482 AAATTAAAATTTAATTACAA
1 AAATTAAAATATAATTACAA
35400502 AAATTAAAA-ATATATTAC
1 AAATTAAAATATA-ATTAC
35400520 TTAAAAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATTAAAATATAATTACAA
Found at i:35402601 original size:13 final size:13
Alignment explanation
Indices: 35402579--35402627 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
35402569 TTAGAAAGCT
35402579 ATTTTGTTATATAA
1 ATTTT-TTATATAA
*
35402593 ATTTTTTATATAT
1 ATTTTTTATATAA
* *
35402606 ATTTTTTCTAGATA
1 ATTTTTTATATA-A
35402620 ATTTTTTA
1 ATTTTTTA
35402628 GAATCATGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (13 bp):
ATTTTTTATATAA
Found at i:35403193 original size:20 final size:18
Alignment explanation
Indices: 35403170--35403213 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 18
35403160 TCTTTTTGAA
35403170 TTTTTATGAACTTTTTATATT
1 TTTTTATGAA--TTTTA-ATT
35403191 TTTTT-TGAATTTTAATT
1 TTTTTATGAATTTTAATT
35403208 TTTTTA
1 TTTTTA
35403214 AATTAACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 8 0.36
18 5 0.23
20 4 0.18
21 5 0.23
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTTTATGAATTTTAATT
Found at i:35405393 original size:24 final size:22
Alignment explanation
Indices: 35405364--35405407 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
35405354 TTGCAATTTA
35405364 TATAATTTCTTATAGTTTTTTTTT
1 TATAATTT-TTATA-TTTTTTTTT
35405388 TATAATTTTTATATTTTTTT
1 TATAATTTTTATATTTTTTT
35405408 ATAATGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 5 0.25
24 8 0.40
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (22 bp):
TATAATTTTTATATTTTTTTTT
Found at i:35406834 original size:14 final size:15
Alignment explanation
Indices: 35406800--35406843 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
35406790 ATATGATAAT
35406800 ATGCGAACCCTATAC
1 ATGCGAACCCTATAC
* *
35406815 ATGCGAACCC-CTAG
1 ATGCGAACCCTATAC
35406829 ATGCGAACCTCTATA
1 ATGCGAACC-CTATA
35406844 TATGTGTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 11 0.46
15 11 0.46
16 2 0.08
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (15 bp):
ATGCGAACCCTATAC
Found at i:35407289 original size:45 final size:46
Alignment explanation
Indices: 35407192--35407288 Score: 135
Period size: 46 Copynumber: 2.1 Consensus size: 46
35407182 GATGGTAATT
* *
35407192 TAAAAAGCCATTAAAACTGGGTCGACCGGGATGATAGTTATTGTAG
1 TAAAAAGCCATCAAAACTGGGTCAACCGGGATGATAGTTATTGTAG
*
35407238 TAAAAAGCCATCAAAA-TCGGG-CAACCGGGATGGTAAGTTATTGTAG
1 TAAAAAGCCATCAAAACT-GGGTCAACCGGGATGAT-AGTTATTGTAG
35407284 TAAAA
1 TAAAA
35407289 GTCATCGTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
45 12 0.26
46 34 0.74
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (46 bp):
TAAAAAGCCATCAAAACTGGGTCAACCGGGATGATAGTTATTGTAG
Found at i:35412834 original size:16 final size:16
Alignment explanation
Indices: 35412795--35412837 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
35412785 CAAGAATCAT
35412795 CAATTGTAAT-GTTTCA
1 CAATT-TAATAGTTTCA
*
35412811 AAACTTTAATAGTTTCA
1 CAA-TTTAATAGTTTCA
35412828 CAATTTAATA
1 CAATTTAATA
35412838 CCCGAGCTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.42
Consensus pattern (16 bp):
CAATTTAATAGTTTCA
Found at i:35418781 original size:11 final size:11
Alignment explanation
Indices: 35418745--35418792 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
35418735 TAAATCCTTT
*
35418745 CTCTC-AATTT
1 CTCTCAAATTC
35418755 CTCTCCAATATT-
1 CTCT-CAA-ATTC
35418767 CTCTCAAATTC
1 CTCTCAAATTC
35418778 CTCTCAAATTC
1 CTCTCAAATTC
35418789 CTCT
1 CTCT
35418793 TAAAAAAAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
10 7 0.21
11 19 0.56
12 5 0.15
13 3 0.09
ACGTcount: A:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:35424549 original size:126 final size:126
Alignment explanation
Indices: 35424262--35424550 Score: 382
Period size: 126 Copynumber: 2.3 Consensus size: 126
35424252 GGCCAAACAT
* * * *
35424262 GAGCTACTGTAGCAAAAGCGCATCCAC-TTAGAAGCTTTTTTCAGTACTTTTGCTGATAAAGCAT
1 GAGCTACTGTAGCAAAAACGCATCCACGTGAG-AGCTTCTTTCAGTACTTTTGCTGACAAAGCAT
* * * *
35424326 CCTGTTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAA
65 CCTGCTTAAAGCGTCTTTGACACTATTTGCTCAGAAACATCTACTCGAAATTATTTTTGCAA
* * * * **
35424388 GAGCTACTGTAACAAAAACGCGTCCATGTGGGAGCTTCTTTCAGTACTTTTTTTGACAAAGCATC
1 GAGCTACTGTAGCAAAAACGCATCCACGTGAGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
* * * *
35424453 CTGCTTAAAGCGTCTTTGACACTATTTGCTCAGGAATATCTATTCGAAATTATTTTTGCAG
66 CTGCTTAAAGCGTCTTTGACACTATTTGCTCAGAAACATCTACTCGAAATTATTTTTGCAA
* *
35424514 GAGCTACTGTAGCAAAACCACATCCACGTGAGAGCTT
1 GAGCTACTGTAGCAAAAACGCATCCACGTGAGAGCTT
35424551 TTTTAAATTA
Statistics
Matches: 138, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
126 136 0.99
127 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (126 bp):
GAGCTACTGTAGCAAAAACGCATCCACGTGAGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
CTGCTTAAAGCGTCTTTGACACTATTTGCTCAGAAACATCTACTCGAAATTATTTTTGCAA
Found at i:35426668 original size:15 final size:17
Alignment explanation
Indices: 35426632--35426668 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
35426622 TTTGGTTTCG
*
35426632 GTTTTTGATAATTTTAT
1 GTTTTTGATAATTGTAT
35426649 GTTTTTGAT-ATTGT-T
1 GTTTTTGATAATTGTAT
35426664 GTTTT
1 GTTTT
35426669 GTGTACTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 4 0.21
17 9 0.47
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (17 bp):
GTTTTTGATAATTGTAT
Found at i:35427980 original size:41 final size:41
Alignment explanation
Indices: 35427919--35427999 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
35427909 CAAGCTTAAA
** *
35427919 GTCCAGCAAGCTTAAGGCCGGTGATGTAATTCGGACTTTAT
1 GTCCAGCAAGCTTAAGGCCGGTGAAATAATTCAGACTTTAT
* *
35427960 GTCCAGCATGCTTAATGCCGGTGAAATAATTCAGACTTTA
1 GTCCAGCAAGCTTAAGGCCGGTGAAATAATTCAGACTTTA
35428000 AGTCTAACAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (41 bp):
GTCCAGCAAGCTTAAGGCCGGTGAAATAATTCAGACTTTAT
Found at i:35428020 original size:41 final size:41
Alignment explanation
Indices: 35427917--35428025 Score: 112
Period size: 41 Copynumber: 2.7 Consensus size: 41
35427907 TTCAAGCTTA
* * * ** *
35427917 AAGTCCAGCAAGCTTAAGGCCGGTGATGTAATTCGGACTTT
1 AAGTCCAACAGGCTTAATGCCGGTGAAATAATTCAGACTTT
* * *
35427958 ATGTCCAGCATGCTTAATGCCGGTGAAATAATTCAGACTTT
1 AAGTCCAACAGGCTTAATGCCGGTGAAATAATTCAGACTTT
*
35427999 AAGTCTAACAGGC-TAATTGCCGGTGAA
1 AAGTCCAACAGGCTTAA-TGCCGGTGAA
35428026 CTGAATAAGG
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 3 0.05
41 54 0.95
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (41 bp):
AAGTCCAACAGGCTTAATGCCGGTGAAATAATTCAGACTTT
Found at i:35440886 original size:6 final size:6
Alignment explanation
Indices: 35440875--35440913 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
35440865 GAAAAGCCAT
35440875 GAGCAG GAGCAG GAGCAG GAGCAG GAGCAG GAGCAG GAG
1 GAGCAG GAGCAG GAGCAG GAGCAG GAGCAG GAGCAG GAG
35440914 ATTCCTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.51, T:0.00
Consensus pattern (6 bp):
GAGCAG
Found at i:35447617 original size:12 final size:13
Alignment explanation
Indices: 35447593--35447621 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
35447583 GGGCTATAAC
35447593 TATTGCATTTATT
1 TATTGCATTTATT
35447606 TATTGC-TTTATT
1 TATTGCATTTATT
35447618 TATT
1 TATT
35447622 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:35461814 original size:31 final size:32
Alignment explanation
Indices: 35461778--35461842 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
35461768 CTTAGATAAT
35461778 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
35461809 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
35461841 TT
1 TT
35461843 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:35469719 original size:21 final size:21
Alignment explanation
Indices: 35469647--35469785 Score: 98
Period size: 21 Copynumber: 6.5 Consensus size: 21
35469637 TAGCTCTCAC
*
35469647 GAGCTTCTGTTTAACTCATAT
1 GAGCTTCTGTTTAACTCTTAT
* ** * * *
35469668 GAGTTTCCATTCAGCTCTCTTTT
1 GAGCTTCTGTTTA--ACTCTTAT
*
35469691 GGGCTTCTGTTTAACTCTTAT
1 GAGCTTCTGTTTAACTCTTAT
* *
35469712 GAGTTTCTGTTTAGCTCTTAT
1 GAGCTTCTGTTTAACTCTTAT
* * *
35469733 GAGCTTCCGTTCAACCCTTAT
1 GAGCTTCTGTTTAACTCTTAT
* * * *
35469754 GGGTTTCTGTTTAGCACTTAT
1 GAGCTTCTGTTTAACTCTTAT
*
35469775 GTGCTTCTGTT
1 GAGCTTCTGTT
35469786 CAGCCGTCGG
Statistics
Matches: 86, Mismatches: 30, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
21 73 0.85
23 13 0.15
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (21 bp):
GAGCTTCTGTTTAACTCTTAT
Found at i:35469753 original size:42 final size:42
Alignment explanation
Indices: 35469629--35469787 Score: 156
Period size: 42 Copynumber: 3.7 Consensus size: 42
35469619 TCGTGTTTAC
* * * *
35469629 TTTCCGTTTAGCTCTCACGAGCTTCTGTTTAACTCATATGAG
1 TTTCCGTTTAGCTCTTATGAGCTTCTGTTCAACTCTTATGAG
* * * * *
35469671 TTTCCATTCAGCTCTCTTTTGGGCTTCTGTTTAACTCTTATGAG
1 TTTCCGTTTAG--CTCTTATGAGCTTCTGTTCAACTCTTATGAG
* * * *
35469715 TTTCTGTTTAGCTCTTATGAGCTTCCGTTCAACCCTTATGGG
1 TTTCCGTTTAGCTCTTATGAGCTTCTGTTCAACTCTTATGAG
* * *
35469757 TTTCTGTTTAGCACTTATGTGCTTCTGTTCA
1 TTTCCGTTTAGCTCTTATGAGCTTCTGTTCA
35469788 GCCGTCGGGC
Statistics
Matches: 96, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
42 62 0.65
44 34 0.35
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (42 bp):
TTTCCGTTTAGCTCTTATGAGCTTCTGTTCAACTCTTATGAG
Found at i:35472316 original size:26 final size:26
Alignment explanation
Indices: 35472237--35472323 Score: 88
Period size: 26 Copynumber: 3.4 Consensus size: 26
35472227 GAGTCATATT
* *
35472237 GGGAAGCTC-CAGAGAGCCATTAATT
1 GGGAAGCTCACAAAGAGCCATTAATC
* * * *
35472262 AGGAAGCTTAGAAAGAGCCTTTAATC
1 GGGAAGCTCACAAAGAGCCATTAATC
35472288 GGGAAGCTCACAAAGAGCCATATAA-C
1 GGGAAGCTCACAAAGAGCCAT-TAATC
*
35472314 GGGACGCTCA
1 GGGAAGCTCA
35472324 TAAGAGCTGT
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
25 7 0.14
26 39 0.80
27 3 0.06
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (26 bp):
GGGAAGCTCACAAAGAGCCATTAATC
Found at i:35472775 original size:10 final size:10
Alignment explanation
Indices: 35472760--35472814 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
35472750 CTATACGAGT
*
35472760 AATTTAACTC
1 AATTTAATTC
*
35472770 AATTTAATAC
1 AATTTAATTC
35472780 AATTTATATTC
1 AATTTA-ATTC
*
35472791 AATTCAATTC
1 AATTTAATTC
* *
35472801 AATTCAAATC
1 AATTTAATTC
35472811 AATT
1 AATT
35472815 CACATCTTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
10 31 0.79
11 8 0.21
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (10 bp):
AATTTAATTC
Found at i:35472794 original size:21 final size:20
Alignment explanation
Indices: 35472760--35472816 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
35472750 CTATACGAGT
*
35472760 AATTTAACTCAATTTAATAC
1 AATTTAACTCAATTCAATAC
* *
35472780 AATTTATATTCAATTCAATTC
1 AATTTA-ACTCAATTCAATAC
* *
35472801 AATTCAAATCAATTCA
1 AATTTAACTCAATTCA
35472817 CATCTTAGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTTAACTCAATTCAATAC
Found at i:35472797 original size:5 final size:5
Alignment explanation
Indices: 35472768--35472816 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
35472758 GTAATTTAAC
* * * *
35472768 TCAAT TTAAT ACAAT TTATAT TCAAT TCAAT TCAAT TCAAA TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCAAT TCAAT TCA
35472817 CATCTTAGGA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
5 31 0.89
6 4 0.11
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (5 bp):
TCAAT
Found at i:35473321 original size:13 final size:13
Alignment explanation
Indices: 35473303--35473329 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35473293 TTTTCTTTTA
35473303 TTATTTATCATCT
1 TTATTTATCATCT
35473316 TTATTTATCATCT
1 TTATTTATCATCT
35473329 T
1 T
35473330 GCCAATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATTTATCATCT
Found at i:35477748 original size:18 final size:18
Alignment explanation
Indices: 35477734--35477768 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35477724 GTTCTTTTCT
35477734 CCTTTAATTTTCTTTATG
1 CCTTTAATTTTCTTTATG
*
35477752 CCTTTATTTTTCTTTAT
1 CCTTTAATTTTCTTTAT
35477769 AGATTTTCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.17, G:0.03, T:0.66
Consensus pattern (18 bp):
CCTTTAATTTTCTTTATG
Found at i:35486703 original size:13 final size:13
Alignment explanation
Indices: 35486685--35486714 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35486675 TCCAGCAACT
35486685 ATGAATTTATTTC
1 ATGAATTTATTTC
*
35486698 ATGAATTTATTTG
1 ATGAATTTATTTC
35486711 ATGA
1 ATGA
35486715 TGGTCCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:35486884 original size:50 final size:50
Alignment explanation
Indices: 35486809--35487051 Score: 351
Period size: 50 Copynumber: 4.8 Consensus size: 50
35486799 ATTTGGGTAA
* * *
35486809 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGAATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
35486859 AGAGGTCCCACGTAAGACCATGTCTGGGACATGTCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
35486909 AGAGGTCCCATGTAAGACCATGCCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
35486959 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
35487009 AGAACATCCCATGTAAGACCATGTCTGGGGCATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
35487052 TGTTATTATC
Statistics
Matches: 172, Mismatches: 20, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 139 0.81
51 33 0.19
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:35487606 original size:12 final size:12
Alignment explanation
Indices: 35487589--35487625 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
35487579 TTTGATGATG
35487589 AATGGTTATTAA
1 AATGGTTATTAA
35487601 AATGGTTA--AA
1 AATGGTTATTAA
*
35487611 TATGGTTATTAA
1 AATGGTTATTAA
35487623 AAT
1 AAT
35487626 TGGCTGAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 9 0.43
12 12 0.57
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (12 bp):
AATGGTTATTAA
Found at i:35496330 original size:18 final size:18
Alignment explanation
Indices: 35496309--35496347 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
35496299 AAAGGAAGAC
35496309 AGAAAAAG-AAATCGAAAA
1 AGAAAAAGCAAA-CGAAAA
*
35496327 AGAAAAAGCGAACGAAAA
1 AGAAAAAGCAAACGAAAA
35496345 AGA
1 AGA
35496348 GCAAAAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.69, C:0.08, G:0.21, T:0.03
Consensus pattern (18 bp):
AGAAAAAGCAAACGAAAA
Found at i:35497211 original size:30 final size:30
Alignment explanation
Indices: 35497163--35497421 Score: 263
Period size: 30 Copynumber: 8.6 Consensus size: 30
35497153 TTGACAATAT
*
35497163 ATATGTATACAT-TACAAATCAATTCGGCA
1 ATATATATACATATACAAATCAATTCGGCA
35497192 ATATATATACATATACAAATCAATTCGGCA
1 ATATATATACATATACAAATCAATTCGGCA
* *
35497222 ATGTATAT-CTATATATAAATCAATTCGGCA
1 ATATATATAC-ATATACAAATCAATTCGGCA
* * * * *
35497252 ATGTATATCCATATATAAATCAATTCGACT
1 ATATATATACATATACAAATCAATTCGGCA
* * *
35497282 ATGTATATCCATATACAAATCAATTCGGTA
1 ATATATATACATATACAAATCAATTCGGCA
* * * *
35497312 ATGTATATCCATATACAAATCAATTCGTCT
1 ATATATATACATATACAAATCAATTCGGCA
* *
35497342 ATATATAT-CTATATATAAATCAATTCGACA
1 ATATATATAC-ATATACAAATCAATTCGGCA
* **
35497372 ATATATATATCCATATACAAATTAATTTAGCA
1 ATATATATA--CATATACAAATCAATTCGGCA
*
35497404 ATATATAAAACATATACA
1 ATATAT-ATACATATACA
35497422 TTTGAATTCA
Statistics
Matches: 200, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
29 13 0.06
30 154 0.77
31 9 0.05
32 21 0.10
33 3 0.01
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (30 bp):
ATATATATACATATACAAATCAATTCGGCA
Found at i:35497250 original size:60 final size:60
Alignment explanation
Indices: 35497178--35497398 Score: 298
Period size: 60 Copynumber: 3.6 Consensus size: 60
35497168 TATACATTAC
* *
35497178 AAATCAATTCGGCAATATATATACATATACAAATCAATTCGGCAATGTATATCTATATAT
1 AAATCAATTCGGCAATATATATACATATACAAATCAATTCGACTATGTATATCTATATAT
* * * * *
35497238 AAATCAATTCGGCAATGTATATCCATATATAAATCAATTCGACTATGTATATCCATATAC
1 AAATCAATTCGGCAATATATATACATATACAAATCAATTCGACTATGTATATCTATATAT
* * * * *
35497298 AAATCAATTCGGTAATGTATATCCATATACAAATCAATTCGTCTATATATATCTATATAT
1 AAATCAATTCGGCAATATATATACATATACAAATCAATTCGACTATGTATATCTATATAT
* *
35497358 AAATCAATTCGACAATATATATATCCATATACAAATTAATT
1 AAATCAATTCGGCAATATATATA--CATATACAAATCAATT
35497399 TAGCAATATA
Statistics
Matches: 141, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
60 126 0.89
62 15 0.11
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.35
Consensus pattern (60 bp):
AAATCAATTCGGCAATATATATACATATACAAATCAATTCGACTATGTATATCTATATAT
Found at i:35497302 original size:90 final size:90
Alignment explanation
Indices: 35497178--35497398 Score: 316
Period size: 90 Copynumber: 2.4 Consensus size: 90
35497168 TATACATTAC
* * * * *
35497178 AAATCAATTCGGCAATATATATACATATACAAATCAATTCGGCAATGTATATCTATATATAAATC
1 AAATCAATTCGACTATATATATCCATATACAAATCAATTCGGCAATGTATATCCATATACAAATC
*
35497243 AATTCGGCAATGTATATCCATATAT
66 AATTCGGCAATATATATCCATATAT
* *
35497268 AAATCAATTCGACTATGTATATCCATATACAAATCAATTCGGTAATGTATATCCATATACAAATC
1 AAATCAATTCGACTATATATATCCATATACAAATCAATTCGGCAATGTATATCCATATACAAATC
* * *
35497333 AATTCGTCTATATATATCTATATAT
66 AATTCGGCAATATATATCCATATAT
*
35497358 AAATCAATTCGACAATATATATATCCATATACAAATTAATT
1 AAATCAATTCGAC--TATATATATCCATATACAAATCAATT
35497399 TAGCAATATA
Statistics
Matches: 116, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
90 92 0.79
92 24 0.21
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.35
Consensus pattern (90 bp):
AAATCAATTCGACTATATATATCCATATACAAATCAATTCGGCAATGTATATCCATATACAAATC
AATTCGGCAATATATATCCATATAT
Found at i:35499405 original size:41 final size:41
Alignment explanation
Indices: 35499355--35499433 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
35499345 ATATTTTATT
35499355 TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTCCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTCCC
*
35499396 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTT
1 TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTT
35499434 TCCCAATTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTCCC
Found at i:35503149 original size:19 final size:19
Alignment explanation
Indices: 35503125--35503165 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
35503115 TATTTTAAAG
35503125 TTATTTAGGTAGATAAAAC
1 TTATTTAGGTAGATAAAAC
*
35503144 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAAAC
35503163 TTA
1 TTA
35503166 GAATAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (19 bp):
TTATTTAGGTAGATAAAAC
Found at i:35503249 original size:41 final size:41
Alignment explanation
Indices: 35503203--35503283 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
35503193 ATATTTTATT
*
35503203 TTATCTTTTAGTAGTTTATTAGAATAAGGGAACTATTTTCC
1 TTATCTTTTAGTAGTTTATTAGAACAAGGGAACTATTTTCC
*
35503244 TTATCTTTTAGTAGTTTATTAGAACAAGGGAATTATTTTC
1 TTATCTTTTAGTAGTTTATTAGAACAAGGGAACTATTTTC
35503284 TCAATTAGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.47
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTTATTAGAACAAGGGAACTATTTTCC
Found at i:35505910 original size:18 final size:18
Alignment explanation
Indices: 35505887--35505922 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
35505877 TTTGTTGAAA
*
35505887 CAAATCGAATTGGCCAAC
1 CAAATCGAATCGGCCAAC
35505905 CAAATCGAATCGGCCAAC
1 CAAATCGAATCGGCCAAC
35505923 AACCCTCCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.31, G:0.17, T:0.14
Consensus pattern (18 bp):
CAAATCGAATCGGCCAAC
Found at i:35513318 original size:69 final size:69
Alignment explanation
Indices: 35513202--35513360 Score: 160
Period size: 69 Copynumber: 2.3 Consensus size: 69
35513192 GGTTAGCTTG
* * * * * *
35513202 GCTATGAAAACCAATAGAGTCTATTGGGACAGTAAATACGAATATTTCAAGGTGTAAGACCATAG
1 GCTATGACAACCAATAGAGTCTATTAGGACAGTAAATACGAAGATTTCAAGATGTAAAAACATAG
35513267 CTCA
66 CTCA
* * * * *
35513271 GCTATGACAACCAATAGAGTTTGTTAGGATAGTAAACATA-G-AGATTTCAATATTTAAAAACAT
1 GCTATGACAACCAATAGAGTCTATTAGGACAGT-AA-ATACGAAGATTTCAAGATGTAAAAACAT
*
35513334 AGCTCG
64 AGCTCA
* *
35513340 GCTTTGGCAACCAATAGAGTC
1 GCTATGACAACCAATAGAGTC
35513361 CATCTGGACA
Statistics
Matches: 73, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
69 67 0.92
70 3 0.04
71 3 0.04
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.26
Consensus pattern (69 bp):
GCTATGACAACCAATAGAGTCTATTAGGACAGTAAATACGAAGATTTCAAGATGTAAAAACATAG
CTCA
Found at i:35516446 original size:13 final size:13
Alignment explanation
Indices: 35516428--35516457 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35516418 TCCAGCAACT
35516428 ATGAATTTATTTC
1 ATGAATTTATTTC
*
35516441 ATGAATTTATTTG
1 ATGAATTTATTTC
35516454 ATGA
1 ATGA
35516458 TGGTCCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:35516630 original size:50 final size:50
Alignment explanation
Indices: 35516552--35516694 Score: 178
Period size: 50 Copynumber: 2.8 Consensus size: 50
35516542 ATTTGGGTAA
* * * *
35516552 AGAGGTCCCATGTAAGACCAAGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGACATG
** *
35516602 AGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGACATG
** * *
35516652 AGAACATCCCATGTAAGACCATGTTTGGGGCATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCA
35516695 TGTTATTATC
Statistics
Matches: 78, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 45 0.58
51 33 0.42
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGACATG
Found at i:35519331 original size:120 final size:120
Alignment explanation
Indices: 35519197--35519532 Score: 593
Period size: 120 Copynumber: 2.8 Consensus size: 120
35519187 TTAATCATAT
*
35519197 TTTAACATATTTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
35519262 AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATACAA
35519317 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
**
35519382 AAATATTCTTATATGAATTTTCCT-TTATCATAATATATAATACTATAAAATACAA
66 AAATATTCTTATATGAATTTT-CTAAAATCATAATATATAATACTATAAAATACAA
*
35519437 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATACAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
**
35519502 AAATATTCTTATATGAATTTAATAAAATCAT
66 AAATATTCTTATATGAATTTTCTAAAATCAT
35519533 GTAAAAAGAA
Statistics
Matches: 205, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
119 1 0.00
120 202 0.99
121 2 0.01
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATACAA
Found at i:35524160 original size:21 final size:21
Alignment explanation
Indices: 35524126--35524177 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
35524116 CAGATCTTCT
35524126 AAGATTGC--ATATCATATCC
1 AAGATTGCATATATCATATCC
*
35524145 AAGATTGCATATATCATATCT
1 AAGATTGCATATATCATATCC
35524166 AAGATTGCATAT
1 AAGATTGCATAT
35524178 CCTTGAAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 8 0.27
21 22 0.73
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (21 bp):
AAGATTGCATATATCATATCC
Found at i:35525085 original size:50 final size:50
Alignment explanation
Indices: 35524988--35525085 Score: 119
Period size: 51 Copynumber: 2.0 Consensus size: 50
35524978 AAATAAAAAT
* *
35524988 TTATTAATTAAAAGATGAATTAAAAACAAAAAAACTTGAAAATAATATAA
1 TTATTAATTAAAACATGAATTAAAAACAAAAAAACTTGAAAACAATATAA
* * *
35525038 TTATTGATTAAAAACATTAATTAAAATA-AAAAAAGCTTG-AAACAATAT
1 TTATTAATT-AAAACATGAATTAAAA-ACAAAAAAACTTGAAAACAATAT
35525086 GAAATAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
50 16 0.39
51 24 0.59
52 1 0.02
ACGTcount: A:0.59, C:0.05, G:0.06, T:0.30
Consensus pattern (50 bp):
TTATTAATTAAAACATGAATTAAAAACAAAAAAACTTGAAAACAATATAA
Found at i:35526062 original size:13 final size:13
Alignment explanation
Indices: 35526021--35526071 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
35526011 GTTAATCATA
35526021 TAATATATTA--T
1 TAATATATTATTT
* *
35526032 TAATATGATTAATA
1 TAATAT-ATTATTT
35526046 TAATATATTATTT
1 TAATATATTATTT
*
35526059 TAATAAATTATTT
1 TAATATATTATTT
35526072 AATTTTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 6 0.18
12 4 0.12
13 17 0.52
14 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (13 bp):
TAATATATTATTT
Found at i:35526118 original size:15 final size:16
Alignment explanation
Indices: 35526091--35526120 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35526081 ATTTTATATT
35526091 AATAATAAATTTTAAC
1 AATAATAAATTTTAAC
35526107 AATAAT-AATTTTAA
1 AATAATAAATTTTAA
35526121 AGTTTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAATAAATTTTAAC
Found at i:35526231 original size:23 final size:23
Alignment explanation
Indices: 35526205--35526257 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
35526195 TTTAATAATA
35526205 AATATTTTATAGTATA-AAATATG
1 AATATTTTA-AGTATATAAATATG
*
35526228 AATATTTTAATTATATAAATATG
1 AATATTTTAAGTATATAAATATG
*
35526251 AGTATTT
1 AATATTT
35526258 GTTTAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 5 0.19
23 22 0.81
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (23 bp):
AATATTTTAAGTATATAAATATG
Found at i:35532170 original size:16 final size:18
Alignment explanation
Indices: 35532133--35532172 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
35532123 GGCTTTTAAC
35532133 GTTGTGATGAGCAATCGAT
1 GTTGTGATGAGCAA-CGAT
35532152 GTTGTGATGA-CAA-GAT
1 GTTGTGATGAGCAACGAT
35532168 GTTGT
1 GTTGT
35532173 AGTCATGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
18 3 0.14
19 10 0.48
ACGTcount: A:0.25, C:0.07, G:0.33, T:0.35
Consensus pattern (18 bp):
GTTGTGATGAGCAACGAT
Found at i:35535661 original size:25 final size:25
Alignment explanation
Indices: 35535633--35535832 Score: 110
Period size: 25 Copynumber: 8.1 Consensus size: 25
35535623 TCCTCTCTCA
* *
35535633 AGCCATATAATGGGAAGCTCATATG
1 AGCCATATAACGGGAAGCTCATAAG
* * * *
35535658 AGCCATGTAACGAGAAGCTTATCCAG
1 AGCCATATAACGGGAAGCTCAT-AAG
** **
35535684 -GCTGTATAACGGGAAGCTCATGCG
1 AGCCATATAACGGGAAGCTCATAAG
*
35535708 AGCCA-ATAACGGGTAGCTC-TGAAG
1 AGCCATATAACGGGAAGCTCAT-AAG
* *
35535732 AGCCAT-TAACGGGAAGCTC-TGGAT
1 AGCCATATAACGGGAAGCTCAT-AAG
* * *
35535756 AGCCATATATCGGGAAGTTCA-AGCG
1 AGCCATATAACGGGAAGCTCATA-AG
* * *
35535781 ATCCATAT--TGGGAAGCTCACAAAG
1 AGCCATATAACGGGAAGCTCA-TAAG
* *
35535805 AGCCATATAATGGGATGCTCATAAG
1 AGCCATATAACGGGAAGCTCATAAG
35535830 AGC
1 AGC
35535833 TGCAGTGTGC
Statistics
Matches: 131, Mismatches: 33, Indels: 22
0.70 0.18 0.12
Matches are distributed among these distances:
23 10 0.08
24 49 0.37
25 61 0.47
26 11 0.08
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (25 bp):
AGCCATATAACGGGAAGCTCATAAG
Found at i:35535719 original size:24 final size:24
Alignment explanation
Indices: 35535689--35535772 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 24
35535679 TCCAGGCTGT
*
35535689 ATAACGGGAAGCTCATG-CGAGCCA
1 ATAACGGGAAGCTC-TGAAGAGCCA
*
35535713 ATAACGGGTAGCTCTGAAGAGCCA
1 ATAACGGGAAGCTCTGAAGAGCCA
* * *
35535737 TTAACGGGAAGCTCTGGATAGCCA
1 ATAACGGGAAGCTCTGAAGAGCCA
*
35535761 TATATCGGGAAG
1 -ATAACGGGAAG
35535773 TTCAAGCGAT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
23 2 0.04
24 39 0.78
25 9 0.18
ACGTcount: A:0.32, C:0.20, G:0.30, T:0.18
Consensus pattern (24 bp):
ATAACGGGAAGCTCTGAAGAGCCA
Found at i:35543457 original size:24 final size:24
Alignment explanation
Indices: 35543367--35543457 Score: 71
Period size: 24 Copynumber: 3.8 Consensus size: 24
35543357 TGTATAACGT
35543367 GAAGCTCAT-AAGAGCCA-TAATCAG
1 GAAGCTC-TGAAGAGCCATTAA-CAG
* *
35543391 GAAGATCATG-AGAGCCAATAACAG
1 GAAGCTC-TGAAGAGCCATTAACAG
* * *
35543415 GTAGCTCTGAAGAGTCATTAACGG
1 GAAGCTCTGAAGAGCCATTAACAG
* *
35543439 GAAGCTCTGGATAGCCATT
1 GAAGCTCTGAAGAGCCATT
35543458 TATTGGGAAG
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
23 2 0.04
24 49 0.91
25 3 0.06
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (24 bp):
GAAGCTCTGAAGAGCCATTAACAG
Found at i:35543521 original size:26 final size:26
Alignment explanation
Indices: 35543479--35543546 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
35543469 TCAAGCTAGC
*
35543479 TATATTGGGAAGCTCACAAAGAGCC-
1 TATAATGGGAAGCTCACAAAGAGCCA
* *
35543504 TTTAATCGGGAAGCTCACGAAGAGCCA
1 TATAAT-GGGAAGCTCACAAAGAGCCA
*
35543531 TATAATGGGATGCTCA
1 TATAATGGGAAGCTCA
35543547 TAAGAGCTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
25 4 0.11
26 27 0.75
27 5 0.14
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (26 bp):
TATAATGGGAAGCTCACAAAGAGCCA
Found at i:35543646 original size:25 final size:25
Alignment explanation
Indices: 35543618--35543673 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
35543608 GCTATTAAAA
*
35543618 GGAAGCACGCAAGAACCATACAACG
1 GGAAGCACGCAAGAACCACACAACG
** *
35543643 GGAAGCTTGCAAGAACCACATAACG
1 GGAAGCACGCAAGAACCACACAACG
35543668 GGAAGC
1 GGAAGC
35543674 TTGAGAGGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.41, C:0.25, G:0.27, T:0.07
Consensus pattern (25 bp):
GGAAGCACGCAAGAACCACACAACG
Found at i:35543674 original size:25 final size:25
Alignment explanation
Indices: 35543626--35543676 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
35543616 AAGGAAGCAC
*
35543626 GCAAGAACCATACAACGGGAAGCTT
1 GCAAGAACCACACAACGGGAAGCTT
*
35543651 GCAAGAACCACATAACGGGAAGCTT
1 GCAAGAACCACACAACGGGAAGCTT
35543676 G
1 G
35543677 AGAGGGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.24, G:0.25, T:0.12
Consensus pattern (25 bp):
GCAAGAACCACACAACGGGAAGCTT
Found at i:35543985 original size:5 final size:5
Alignment explanation
Indices: 35543975--35544018 Score: 70
Period size: 5 Copynumber: 8.8 Consensus size: 5
35543965 TACAATTCCT
* *
35543975 ATTCA ATTCA ATTCA ATTCA ATCCT ATTCA ATTCA ATTCA ATTC
1 ATTCA ATTCA ATTCA ATTCA ATTCA ATTCA ATTCA ATTCA ATTC
35544019 TCATCCTAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTCA
Found at i:35544002 original size:25 final size:25
Alignment explanation
Indices: 35543971--35544018 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
35543961 TTAGTACAAT
35543971 TCCTATTCAATTCAATTCAATTCAA
1 TCCTATTCAATTCAATTCAATTCAA
35543996 TCCTATTCAATTCAATTCAATTC
1 TCCTATTCAATTCAATTCAATTC
35544019 TCATCCTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (25 bp):
TCCTATTCAATTCAATTCAATTCAA
Found at i:35548985 original size:30 final size:30
Alignment explanation
Indices: 35548951--35549019 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 30
35548941 AAAAAATATC
* *
35548951 AATTTAACTCTTTTGAAAGGTTGATGGTCA
1 AATTTAACTCTTTTAAAAGGTTGATGGACA
**
35548981 AATTTGATTTCTTTTAAAAGGTTGATGGACA
1 AATTT-AACTCTTTTAAAAGGTTGATGGACA
35549012 AATTTAAC
1 AATTTAAC
35549020 AAAAAAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 6 0.19
31 26 0.81
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (30 bp):
AATTTAACTCTTTTAAAAGGTTGATGGACA
Found at i:35550492 original size:14 final size:14
Alignment explanation
Indices: 35550473--35550500 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35550463 TAAAAGACAA
35550473 TGATTACTTAATGG
1 TGATTACTTAATGG
35550487 TGATTACTTAATGG
1 TGATTACTTAATGG
35550501 GGTTCTCCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (14 bp):
TGATTACTTAATGG
Found at i:35550626 original size:27 final size:27
Alignment explanation
Indices: 35550587--35550900 Score: 344
Period size: 27 Copynumber: 11.6 Consensus size: 27
35550577 CACGACAGAT
* *
35550587 AAGAATAGCCTTTATGGCGTAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* *
35550614 AAGAAAAGTCTTTGTGGCGTAATATGT
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* * * *
35550641 AAGAAAATCATTTGTGGCATAATATGT
1 AAGAAAAGCCTTTGTGGCGTAATATGA
*
35550668 AAGAAAAGCATTTGTGGCGTAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* * *
35550695 AATAATAGCCTTTGTGACGTAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* * *
35550722 AAGAAAAACCTTTGTGGCATAATATGT
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* * *
35550749 ATGAAAAGCCTTTGTGACATAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* *
35550776 AATAATAA-CCTTTGTAGCGTAATATGA
1 AAGAA-AAGCCTTTGTGGCGTAATATGA
*
35550803 AAGAAAAGCCTTTGTAGCGTAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* * **
35550830 AATAATAGCCTTTGTGATGTAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
* **
35550857 AAGAATAGCCTTTGTGGCAAAATATGA
1 AAGAAAAGCCTTTGTGGCGTAATATGA
35550884 AATG-AAAGCCTTTGTGG
1 AA-GAAAAGCCTTTGTGG
35550901 AAAACCATGA
Statistics
Matches: 242, Mismatches: 42, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
26 2 0.01
27 237 0.98
28 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.31
Consensus pattern (27 bp):
AAGAAAAGCCTTTGTGGCGTAATATGA
Found at i:35550672 original size:54 final size:54
Alignment explanation
Indices: 35550587--35550956 Score: 347
Period size: 54 Copynumber: 6.9 Consensus size: 54
35550577 CACGACAGAT
* * * * *
35550587 AAGAATAGCCTTTATGGCGTAATATGAAAGAAAAGTCTTTGTGGCGTAATATGT
1 AAGAAAAGCCTTTGTGGCATAATATGAAAGAAAAGCCTTTGTGGCGTAATATGA
* * * *
35550641 AAGAAAATCATTTGTGGCATAATATGTAAGAAAAGCATTTGTGGCGTAATATGA
1 AAGAAAAGCCTTTGTGGCATAATATGAAAGAAAAGCCTTTGTGGCGTAATATGA
* * * * * * *
35550695 AATAATAGCCTTTGTGACGTAATATGAAAGAAAAACCTTTGTGGCATAATATGT
1 AAGAAAAGCCTTTGTGGCATAATATGAAAGAAAAGCCTTTGTGGCGTAATATGA
* * * *
35550749 ATGAAAAGCCTTTGTGACATAATATGAAATAATAA-CCTTTGTAGCGTAATATGA
1 AAGAAAAGCCTTTGTGGCATAATATGAAAGAA-AAGCCTTTGTGGCGTAATATGA
* * * * **
35550803 AAGAAAAGCCTTTGTAGCGTAATATGAAATAATAGCCTTTGTGATGTAATATGA
1 AAGAAAAGCCTTTGTGGCATAATATGAAAGAAAAGCCTTTGTGGCGTAATATGA
* * ** *
35550857 AAGAATAGCCTTTGTGGCAAAATATGAAATG-AAAGCCTTTGTGG-AAAACCATGA
1 AAGAAAAGCCTTTGTGGCATAATATGAAA-GAAAAGCCTTTGTGGCGTAA-TATGA
* *
35550911 AA-AGAAAGTCTTTGTGGCA-AATCACGAAACG-AAAGCCTTTGTGGCG
1 AAGA-AAAGCCTTTGTGGCATAAT-ATGAAA-GAAAAGCCTTTGTGGCG
35550957 ATCTCCCTTG
Statistics
Matches: 258, Mismatches: 51, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
53 7 0.03
54 249 0.97
55 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (54 bp):
AAGAAAAGCCTTTGTGGCATAATATGAAAGAAAAGCCTTTGTGGCGTAATATGA
Found at i:35550955 original size:27 final size:26
Alignment explanation
Indices: 35550587--35550955 Score: 159
Period size: 27 Copynumber: 13.7 Consensus size: 26
35550577 CACGACAGAT
* *
35550587 AAGAATAGCCTTTATGGCGTAAT-ATGA
1 AAGAA-AGCCTTTGTGGC-AAATCATGA
* * *
35550614 AAGAAAAGTCTTTGTGGCGTAAT-ATGT
1 AAG-AAAGCCTTTGTGGC-AAATCATGA
* * *
35550641 AAGAAAATCATTTGTGGCATAAT-ATGT
1 AAG-AAAGCCTTTGTGGCA-AATCATGA
* *
35550668 AAGAAAAGCATTTGTGGCGTAAT-ATGA
1 AAG-AAAGCCTTTGTGGC-AAATCATGA
* * *
35550695 AATAATAGCCTTTGTGACGTAAT-ATGA
1 AAGAA-AGCCTTTGTGGC-AAATCATGA
* *
35550722 AAGAAAAACCTTTGTGGCATAAT-ATGT
1 AAG-AAAGCCTTTGTGGCA-AATCATGA
* *
35550749 ATGAAAAGCCTTTGTGACATAAT-ATGA
1 AAG-AAAGCCTTTGTGGCA-AATCATGA
* * * *
35550776 AATAATAACCTTTGTAGCGTAAT-ATGA
1 AAGAA-AGCCTTTGTGGC-AAATCATGA
* *
35550803 AAGAAAAGCCTTTGTAGCGTAAT-ATGA
1 AAG-AAAGCCTTTGTGGC-AAATCATGA
* *
35550830 AATAATAGCCTTTGTGATG-TAAT-ATGA
1 AAGAA-AGCCTTTGTG--GCAAATCATGA
35550857 AAGAATAGCCTTTGTGGCAAAAT-ATGA
1 AAGAA-AGCCTTTGTGGC-AAATCATGA
* *
35550884 AATGAAAGCCTTTGTGGAAAACCATGAA
1 AA-GAAAGCCTTTGTGGCAAATCATG-A
* *
35550912 AAGAAAGTCTTTGTGGCAAATCACGA
1 AAGAAAGCCTTTGTGGCAAATCATGA
35550938 AACGAAAGCCTTTGTGGC
1 AA-GAAAGCCTTTGTGGC
35550956 GATCTCCCTT
Statistics
Matches: 283, Mismatches: 41, Indels: 36
0.79 0.11 0.10
Matches are distributed among these distances:
25 1 0.00
26 12 0.04
27 257 0.91
28 12 0.04
29 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (26 bp):
AAGAAAGCCTTTGTGGCAAATCATGA
Found at i:35552978 original size:21 final size:21
Alignment explanation
Indices: 35552954--35553019 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
35552944 TACTTCAGTA
35552954 CCCCTAGATTGCACATACGTG
1 CCCCTAGATTGCACATACGTG
* * * *
35552975 CCCCT-GTTTGTAC-TTCGGTA
1 CCCCTAGATTGCACATAC-GTG
* *
35552995 CCCTTAAATTGCACATACGTG
1 CCCCTAGATTGCACATACGTG
35553016 CCCC
1 CCCC
35553020 CGTTTGTACT
Statistics
Matches: 31, Mismatches: 11, Indels: 6
0.65 0.23 0.12
Matches are distributed among these distances:
19 2 0.06
20 12 0.39
21 15 0.48
22 2 0.06
ACGTcount: A:0.20, C:0.35, G:0.17, T:0.29
Consensus pattern (21 bp):
CCCCTAGATTGCACATACGTG
Found at i:35553072 original size:41 final size:40
Alignment explanation
Indices: 35552858--35553079 Score: 282
Period size: 41 Copynumber: 5.4 Consensus size: 40
35552848 CTTTAATTAT
* *
35552858 TTTGTACTTTGGTACCCCATAATTGCACATACGTGCCCCTA
1 TTTGTACTTCGGTACCCC-TAATTGCACATACGTGCCCCTG
* * * * *
35552899 TTTGTACTTTGATACCCATGAATTGCACATACATGCCCTTG
1 TTTGTACTTCGGTACCCCT-AATTGCACATACGTGCCCCTG
*
35552940 TTTGTACTTCAGTACCCCTAGATTGCACATACGTGCCCCTG
1 TTTGTACTTCGGTACCCCTA-ATTGCACATACGTGCCCCTG
* *
35552981 TTTGTACTTCGGTACCCTTAAATTGCACATACGTGCCCCCG
1 TTTGTACTTCGGTACCCCT-AATTGCACATACGTGCCCCTG
*
35553022 TTTGTACTTCGGTACCCCTGAATTGCACATACGTGCCTCTG
1 TTTGTACTTCGGTACCCCT-AATTGCACATACGTGCCCCTG
* *
35553063 TTTATACTTCAGTACCC
1 TTTGTACTTCGGTACCC
35553080 TTGGATGTAC
Statistics
Matches: 158, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
40 2 0.01
41 155 0.98
42 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (40 bp):
TTTGTACTTCGGTACCCCTAATTGCACATACGTGCCCCTG
Found at i:35553077 original size:123 final size:123
Alignment explanation
Indices: 35552858--35553079 Score: 331
Period size: 123 Copynumber: 1.8 Consensus size: 123
35552848 CTTTAATTAT
* * *
35552858 TTTGTACTTTGGTACCCCATAATTGCACATACGTGCCCCTATTTGTACTTTGATACCCATGAATT
1 TTTGTACTTCGGTACCCCATAATTGCACATACGTGCCCCCATTTGTACTTCGATACCCATGAATT
*
35552923 GCACATACATGCCCTTGTTTGTACTTCAGTACCCCTAGATTGCACATACGTGCCCCTG
66 GCACATACATGCCCTTGTTTATACTTCAGTACCCCTAGATTGCACATACGTGCCCCTG
* * * *
35552981 TTTGTACTTCGGTA-CCCTTAAATTGCACATACGTGCCCCCGTTTGTACTTCGGTACCCCTGAAT
1 TTTGTACTTCGGTACCCCAT-AATTGCACATACGTGCCCCCATTTGTACTTCGATACCCATGAAT
*
35553045 TGCACATACGTG-CCTCTGTTTATACTTCAGTACCC
65 TGCACATACATGCCCT-TGTTTATACTTCAGTACCC
35553080 TTGGATGTAC
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
122 7 0.08
123 81 0.92
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (123 bp):
TTTGTACTTCGGTACCCCATAATTGCACATACGTGCCCCCATTTGTACTTCGATACCCATGAATT
GCACATACATGCCCTTGTTTATACTTCAGTACCCCTAGATTGCACATACGTGCCCCTG
Found at i:35557928 original size:36 final size:36
Alignment explanation
Indices: 35557887--35557955 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
35557877 AGAAGTTATG
*
35557887 ATAATTACACATTTAAAAATAATCACAATTTAATTA
1 ATAATTACACATTTAAAAATAATCAAAATTTAATTA
* * *
35557923 ATAATTATACATTTATAAATAATTAAAATTTAA
1 ATAATTACACATTTAAAAATAATCAAAATTTAA
35557956 ATTACAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (36 bp):
ATAATTACACATTTAAAAATAATCAAAATTTAATTA
Found at i:35557943 original size:18 final size:18
Alignment explanation
Indices: 35557887--35557947 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
35557877 AGAAGTTATG
*
35557887 ATAATTACACATTTAAAA
1 ATAATTACACATTTATAA
* *
35557905 ATAATCACA-ATTTAATTA
1 ATAATTACACATTT-ATAA
*
35557923 ATAATTATACATTTATAA
1 ATAATTACACATTTATAA
35557941 ATAATTA
1 ATAATTA
35557948 AAATTTAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 4 0.11
18 27 0.77
19 4 0.11
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATTACACATTTATAA
Found at i:35557965 original size:36 final size:36
Alignment explanation
Indices: 35557889--35557966 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
35557879 AAGTTATGAT
* * *
35557889 AATTACACATTTAAAAATAATCACAATTTAATTAAT
1 AATTATACATTTAAAAATAATCAAAATTTAATTAAC
* *
35557925 AATTATACATTTATAAATAATTAAAATTTAAATT-AC
1 AATTATACATTTAAAAATAATCAAAATTT-AATTAAC
35557961 AATTAT
1 AATTAT
35557967 TCCTTAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
36 32 0.89
37 4 0.11
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.40
Consensus pattern (36 bp):
AATTATACATTTAAAAATAATCAAAATTTAATTAAC
Found at i:35569023 original size:28 final size:29
Alignment explanation
Indices: 35568979--35569051 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
35568969 TTTAAAAAAA
* *
35568979 TAATTTTTATATTTTTATAC-CTTTTTTAT
1 TAATTTTTATAATTTTAAACAC-TTTTTAT
35569008 TAATTTTTA-AATTTTAAACACTTTTTAT
1 TAATTTTTATAATTTTAAACACTTTTTAT
*
35569036 AAATTTTT-TGAATTTT
1 TAATTTTTAT-AATTTT
35569052 TAAATTTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 22 0.58
29 16 0.42
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.63
Consensus pattern (29 bp):
TAATTTTTATAATTTTAAACACTTTTTAT
Found at i:35571524 original size:21 final size:21
Alignment explanation
Indices: 35571498--35571539 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
35571488 CTCAACGGGA
* *
35571498 TAGCTGAGGTGGCCAGTTAAC
1 TAGCTGAGGTAGCCAATTAAC
*
35571519 TAGCTGATGTAGCCAATTAAC
1 TAGCTGAGGTAGCCAATTAAC
35571540 GTTAACTTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (21 bp):
TAGCTGAGGTAGCCAATTAAC
Found at i:35572948 original size:10 final size:10
Alignment explanation
Indices: 35572933--35572959 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
35572923 TCGACGAGGA
35572933 AGTTTCGTTC
1 AGTTTCGTTC
35572943 AGTTTCGTTC
1 AGTTTCGTTC
35572953 AGTTTCG
1 AGTTTCG
35572960 AAAATGGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (10 bp):
AGTTTCGTTC
Found at i:35575071 original size:24 final size:24
Alignment explanation
Indices: 35575025--35575073 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
35575015 ACATTTTTTT
**
35575025 ATTTGATTGAATTTTGCTATTAAA
1 ATTTGATTGAATTTTAATATTAAA
* *
35575049 ATTTGATTTAATTTTAATTTTAAA
1 ATTTGATTGAATTTTAATATTAAA
35575073 A
1 A
35575074 AAATGAAGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (24 bp):
ATTTGATTGAATTTTAATATTAAA
Found at i:35580679 original size:87 final size:87
Alignment explanation
Indices: 35580532--35580728 Score: 243
Period size: 87 Copynumber: 2.3 Consensus size: 87
35580522 CTCTAATTTG
* * * * * *
35580532 TGGATGAACCACCAGTGTTTGCAGATGAACTGCCAGTAGGTTATGGATGCACAACATATTTGCAA
1 TGGATAAACCATCAGTGTTTGCAAATAAACTGCCAGTAGGTTATGAATACACAACATATTTGCAA
* * * *
35580597 ATAAGAGCTGGC-AATAAGTTTA
66 ATAAAAGAT-GCTAATAAATTCA
* * *
35580619 TGGATAAACCATCAGTGTTTGCAAATAAACTGCCAGTAGGTTATGAATACACAACGTATTTGTAG
1 TGGATAAACCATCAGTGTTTGCAAATAAACTGCCAGTAGGTTATGAATACACAACATATTTGCAA
* *
35580684 ATAAAAGATGCTAGTAAATTCG
66 ATAAAAGATGCTAATAAATTCA
35580706 TGGATAAACCATCAGTGTTTGCA
1 TGGATAAACCATCAGTGTTTGCA
35580729 GATTATTAAA
Statistics
Matches: 94, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
86 2 0.02
87 92 0.98
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (87 bp):
TGGATAAACCATCAGTGTTTGCAAATAAACTGCCAGTAGGTTATGAATACACAACATATTTGCAA
ATAAAAGATGCTAATAAATTCA
Found at i:35584075 original size:53 final size:53
Alignment explanation
Indices: 35584005--35584135 Score: 190
Period size: 53 Copynumber: 2.5 Consensus size: 53
35583995 TGAAGAATCT
* * *
35584005 TATCGTGTAAGACCGTAATTGGTGGGTTATGACATCATATGGAAAGAAGACCA
1 TATCGTGTAAAACCGTAACTGGTGGGTTATGACATCATATGGAAAGAAAACCA
*
35584058 TATCGTGTAAAACCGTAACTGGTGGGTTATGACATCATATGGAAAGAAAATCA
1 TATCGTGTAAAACCGTAACTGGTGGGTTATGACATCATATGGAAAGAAAACCA
* * **
35584111 TATCATGTAAGATTGTAACTGGTGG
1 TATCGTGTAAAACCGTAACTGGTGG
35584136 TTTTTGGGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 70 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.28
Consensus pattern (53 bp):
TATCGTGTAAAACCGTAACTGGTGGGTTATGACATCATATGGAAAGAAAACCA
Found at i:35584353 original size:61 final size:61
Alignment explanation
Indices: 35584261--35584423 Score: 245
Period size: 61 Copynumber: 2.7 Consensus size: 61
35584251 ACCAAGAAAG
* *
35584261 GAAAGCCTTTTTGGCGAGTACTGAATGTAAATGAATGCCTTTGTAACAAAACTCTAGACAA
1 GAAAGCCTTTCTGGCGAGTACTAAATGTAAATGAATGCCTTTGTAACAAAACTCTAGACAA
* * * * * *
35584322 GAAAGCCTTTGTGGAGAGTACTAAATGTAAATGAACGCCTTTGTAGCAAAACTCTGGACAT
1 GAAAGCCTTTCTGGCGAGTACTAAATGTAAATGAATGCCTTTGTAACAAAACTCTAGACAA
*
35584383 GAAAGCTTTTCTGGCGAGTACTAAATGTAAATGAATGCCTT
1 GAAAGCCTTTCTGGCGAGTACTAAATGTAAATGAATGCCTT
35584424 CGTGGCGCAA
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 91 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (61 bp):
GAAAGCCTTTCTGGCGAGTACTAAATGTAAATGAATGCCTTTGTAACAAAACTCTAGACAA
Done.