Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 15 of 259
Found at i:4325092 original size:21 final size:22
Alignment explanation
Indices: 4325062--4325119 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 22
4325052 AATGAGTATA
*
4325062 TCATAACATATCATGTGCAT-C
1 TCATAGCATATCATGTGCATAC
4325083 TCATAGCATATCATGTGCATAC
1 TCATAGCATATCATGTGCATAC
4325105 -CAT-GTCATATCATGT
1 TCATAG-CATATCATGT
4325120 ATAACAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATAGCATATCATGTGCATAC
Found at i:4342943 original size:24 final size:24
Alignment explanation
Indices: 4342910--4342957 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
4342900 TTGGATATAG
*
4342910 AACAATCATATAGTGATATATGGT
1 AACAACCATATAGTGATATATGGT
4342934 AACAACCATATAGTGATATATGGT
1 AACAACCATATAGTGATATATGGT
4342958 GCGCCATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (24 bp):
AACAACCATATAGTGATATATGGT
Found at i:4346950 original size:25 final size:25
Alignment explanation
Indices: 4346922--4346973 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
4346912 AAAGGGTGAT
4346922 ATAGTTAACTTAATAATAAGTAGAA
1 ATAGTTAACTTAATAATAAGTAGAA
* *
4346947 ATAGTTACCTTAATAATAAGTGGAA
1 ATAGTTAACTTAATAATAAGTAGAA
4346972 AT
1 AT
4346974 TTTGAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.33
Consensus pattern (25 bp):
ATAGTTAACTTAATAATAAGTAGAA
Found at i:4350448 original size:18 final size:18
Alignment explanation
Indices: 4350425--4350461 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4350415 TAGCACATTA
4350425 TGATGTTGTTTGAGGATG
1 TGATGTTGTTTGAGGATG
4350443 TGATGTTGTTTGAGGATG
1 TGATGTTGTTTGAGGATG
4350461 T
1 T
4350462 TTTTAAGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.38, T:0.46
Consensus pattern (18 bp):
TGATGTTGTTTGAGGATG
Found at i:4350650 original size:13 final size:14
Alignment explanation
Indices: 4350623--4350651 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4350613 CTCAAAAATT
4350623 GGTTAGTAGAATCG
1 GGTTAGTAGAATCG
4350637 GGTTAGTA-AATCG
1 GGTTAGTAGAATCG
4350650 GG
1 GG
4350652 AGTTAGTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.28, C:0.07, G:0.38, T:0.28
Consensus pattern (14 bp):
GGTTAGTAGAATCG
Found at i:4359434 original size:13 final size:13
Alignment explanation
Indices: 4359416--4359449 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
4359406 AGCACAAGGG
4359416 CGTGTGACATGGT
1 CGTGTGACATGGT
4359429 CGTGTGACATGGT
1 CGTGTGACATGGT
4359442 CGTGTGAC
1 CGTGTGAC
4359450 CTTACTCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.15, C:0.18, G:0.38, T:0.29
Consensus pattern (13 bp):
CGTGTGACATGGT
Found at i:4363463 original size:46 final size:46
Alignment explanation
Indices: 4363393--4363483 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
4363383 GGGTTTTTGT
*
4363393 TACACACTTGATATGGATTCGACGTAATGATAATACTCTAAAATGG
1 TACACACTTGATATGGATTCGACGTAACGATAATACTCTAAAATGG
*
4363439 TACACACTTGATATGGATTTGACGTAACGATAATACTCTAAAATG
1 TACACACTTGATATGGATTCGACGTAACGATAATACTCTAAAATG
4363484 ACATACTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (46 bp):
TACACACTTGATATGGATTCGACGTAACGATAATACTCTAAAATGG
Found at i:4367315 original size:19 final size:18
Alignment explanation
Indices: 4367285--4367321 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
4367275 AGGCAACCCA
4367285 ATTTTATCTTTATTTTCT
1 ATTTTATCTTTATTTTCT
4367303 ATTTTATTCTTTATTTTCT
1 ATTTTA-TCTTTATTTTCT
4367322 TGCATGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTTATCTTTATTTTCT
Found at i:4368227 original size:102 final size:102
Alignment explanation
Indices: 4368101--4368297 Score: 299
Period size: 102 Copynumber: 1.9 Consensus size: 102
4368091 GAATTAAATA
4368101 ATAATAATAAATAAGAGTGTGTTGGGCTAAGTAATCGGGGTGGGGTGCTTGGGTTGTCATCCCAC
1 ATAATAATAAATAAGAGTGTGTTGGGCTAAGTAATCGGGGTGGGGTGCTTGGGTTGTCATCCCAC
*
4368166 TTCATGTCAAAAGGG-AAAACATTCTTAACCAAAAAC
66 TTCACGTCAAAAGGGCAAAACATTCTTAACCAAAAAC
* *
4368202 ATAATAATAAAATATA-AGTGTGTTGGGCTGAGTAATTGGGGTGGGGTGCTTGGGTTGTCATCCC
1 ATAATAAT-AAATA-AGAGTGTGTTGGGCTAAGTAATCGGGGTGGGGTGCTTGGGTTGTCATCCC
* * *
4368266 TCTTCGCGTCAAAAGGGCCAATACATTCTTAA
64 ACTTCACGTCAAAAGGG-CAAAACATTCTTAA
4368298 GAAAAAAAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
101 8 0.09
102 65 0.76
103 1 0.01
104 12 0.14
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (102 bp):
ATAATAATAAATAAGAGTGTGTTGGGCTAAGTAATCGGGGTGGGGTGCTTGGGTTGTCATCCCAC
TTCACGTCAAAAGGGCAAAACATTCTTAACCAAAAAC
Found at i:4370330 original size:9 final size:8
Alignment explanation
Indices: 4370301--4370339 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
4370291 AATGATAGGC
4370301 AAAAAGAA
1 AAAAAGAA
*
4370309 AAGAAAGTA
1 AA-AAAGAA
4370318 AAAAAGAA
1 AAAAAGAA
4370326 GAAAAAGAA
1 -AAAAAGAA
4370335 AAAAA
1 AAAAA
4370340 AACAGTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 12 0.44
9 15 0.56
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (8 bp):
AAAAAGAA
Found at i:4370339 original size:17 final size:17
Alignment explanation
Indices: 4370301--4370339 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
4370291 AATGATAGGC
*
4370301 AAAAAGAAAAGAAAGTA
1 AAAAAGAAAAGAAAGAA
4370318 AAAAAGAAGAA-AAAGAA
1 AAAAAGAA-AAGAAAGAA
4370335 AAAAA
1 AAAAA
4370340 AACAGTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (17 bp):
AAAAAGAAAAGAAAGAA
Found at i:4377544 original size:27 final size:27
Alignment explanation
Indices: 4377497--4377549 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
4377487 GTCACAGTTA
*
4377497 TTATTATTTATTTATTCATTATTATTG
1 TTATTATTTATTTAATCATTATTATTG
*
4377524 TTATTA-TTATTTACATGATTATTATT
1 TTATTATTTATTTA-ATCATTATTATT
4377550 TTTTTACGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (27 bp):
TTATTATTTATTTAATCATTATTATTG
Found at i:4377548 original size:30 final size:30
Alignment explanation
Indices: 4377493--4377549 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
4377483 TATTGTCACA
* *
4377493 GTTATTATTATTTATTTATTCATTATTATT
1 GTTATTATTATTTAATGATTCATTATTATT
4377523 GTTATTATTATTTACATGATT-ATTATT
1 GTTATTATTATTTA-ATGATTCATTATT
4377550 TTTTTACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.28, C:0.04, G:0.05, T:0.63
Consensus pattern (30 bp):
GTTATTATTATTTAATGATTCATTATTATT
Found at i:4377625 original size:22 final size:21
Alignment explanation
Indices: 4377594--4377639 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
4377584 ATTTCTATCT
4377594 TTACTTTTATCATTAACATTA
1 TTACTTTTATCATTAACATTA
* **
4377615 TTACTATTTATTATTATTATTA
1 TTACT-TTTATCATTAACATTA
4377637 TTA
1 TTA
4377640 TTTACACATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.59
Consensus pattern (21 bp):
TTACTTTTATCATTAACATTA
Found at i:4377751 original size:3 final size:3
Alignment explanation
Indices: 4377743--4377873 Score: 60
Period size: 3 Copynumber: 44.7 Consensus size: 3
4377733 TTTATAATAC
* * * * *
4377743 TAT TAT TAT AAT CTCAT T-T TAT TAT TAT CAT TCT TAT TAA TA- CAT
1 TAT TAT TAT TAT -T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
4377788 TAT TAT TAT T-T TAC CA- TAT TGT TAT T-T TAT ATAT TAT TAC TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* * *
4377831 TAT TAA CA- TAT TAT TAT TAT TA- TATT TAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TA
4377874 GTACTAGTAT
Statistics
Matches: 94, Mismatches: 23, Indels: 22
0.68 0.17 0.16
Matches are distributed among these distances:
2 11 0.12
3 75 0.80
4 6 0.06
5 2 0.02
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:4377773 original size:14 final size:15
Alignment explanation
Indices: 4377756--4377797 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
4377746 TATTATAATC
4377756 TCATT-TTATTATTA
1 TCATTATTATTATTA
* *
4377770 TCATTCTTATTAATA
1 TCATTATTATTATTA
4377785 -CATTATTATTATT
1 TCATTATTATTATT
4377798 TTACCATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.60
Consensus pattern (15 bp):
TCATTATTATTATTA
Found at i:4377861 original size:38 final size:35
Alignment explanation
Indices: 4377786--4377873 Score: 97
Period size: 38 Copynumber: 2.5 Consensus size: 35
4377776 TTATTAATAC
* * *
4377786 ATTATTATTATT-TTACCATATTGTTATTTTATAT
1 ATTATTAATATTATTAACATATTATTATTTTATAT
* *
4377820 ATTATTACTGTTATTAACATATTATTATTATTATATTT
1 ATTATTAATATTATTAACATATTATTATT-TTATA--T
4377858 ATTATTAATATTATTA
1 ATTATTAATATTATTA
4377874 GTACTAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
34 10 0.23
35 14 0.32
36 5 0.11
38 15 0.34
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (35 bp):
ATTATTAATATTATTAACATATTATTATTTTATAT
Found at i:4377870 original size:35 final size:34
Alignment explanation
Indices: 4377786--4377870 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 34
4377776 TTATTAATAC
* * *
4377786 ATTATTATTATTTTACCATATTGTTATTTTATAT
1 ATTATTATTATATTAACATATTATTATTTTATAT
4377820 ATTATTACTGT-TATTAACATATTATTATTATTATAT
1 ATTATTA-T-TATATTAACATATTATTATT-TTATAT
4377856 -TTATTATTAATATTA
1 ATTATTATT-ATATTA
4377871 TTAGTACTAG
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
33 1 0.02
34 8 0.19
35 27 0.63
36 7 0.16
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (34 bp):
ATTATTATTATATTAACATATTATTATTTTATAT
Found at i:4378015 original size:25 final size:24
Alignment explanation
Indices: 4377987--4378066 Score: 76
Period size: 24 Copynumber: 3.3 Consensus size: 24
4377977 ATTGTATATG
4377987 TTTATATATATATCATGTATATTTT
1 TTTATATAT-TATCATGTATATTTT
*
4378012 TTTA-ATATTATTA-GTTATATATTT
1 TTTATATATTATCATG-TATAT-TTT
* *
4378036 TTTATACTATT-TCATATATATATT
1 TTTATA-TATTATCATGTATATTTT
4378060 TTTATAT
1 TTTATAT
4378067 TATCCTTGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
22 1 0.02
23 10 0.22
24 19 0.41
25 12 0.26
26 4 0.09
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.61
Consensus pattern (24 bp):
TTTATATATTATCATGTATATTTT
Found at i:4378046 original size:23 final size:23
Alignment explanation
Indices: 4378004--4378065 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
4377994 ATATATCATG
* **
4378004 TATAT-TTTTTTAATATTATTAGT
1 TATATATTTTTT-ATACTATTACA
*
4378027 TATATATTTTTTATACTATTTCA
1 TATATATTTTTTATACTATTACA
4378050 TATATATATTTTTATA
1 TATATAT-TTTTTATA
4378066 TTATCCTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 19 0.58
24 14 0.42
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (23 bp):
TATATATTTTTTATACTATTACA
Found at i:4378119 original size:21 final size:20
Alignment explanation
Indices: 4378087--4378127 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
4378077 ATTATTATTG
* *
4378087 GTATATGTTTTATTATATAT
1 GTATATATTTTAATATATAT
4378107 GTATATATCTTTAATATATAT
1 GTATATAT-TTTAATATATAT
4378128 TTATGTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.56
Consensus pattern (20 bp):
GTATATATTTTAATATATAT
Found at i:4378226 original size:22 final size:21
Alignment explanation
Indices: 4378177--4378227 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
4378167 TTCTAATATG
*
4378177 TATATATTATGTAATATTTAA
1 TATATATTATGTAACATTTAA
**
4378198 TACTATATTATGTATACATTTTT
1 TA-TATATTATGTA-ACATTTAA
4378221 TATATAT
1 TATATAT
4378228 ATTACGTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 16 0.64
23 7 0.28
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (21 bp):
TATATATTATGTAACATTTAA
Found at i:4378228 original size:24 final size:23
Alignment explanation
Indices: 4378177--4378242 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 23
4378167 TTCTAATATG
4378177 TATATATTATG--TAATATTTAA
1 TATATATTATGTATAATATTTAA
* *
4378198 TACTATATTATGTATACATTTTTTA
1 TA-TATATTATGTATA-ATATTTAA
*
4378223 TATATATTACGTATATATAT
1 TATATATTATGTATA-ATAT
4378243 CTTTTTAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
21 2 0.06
22 9 0.25
24 17 0.47
25 8 0.22
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (23 bp):
TATATATTATGTATAATATTTAA
Found at i:4378344 original size:25 final size:25
Alignment explanation
Indices: 4378316--4378389 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
4378306 ACATATTATC
4378316 TTATGTATATATTTTAATAACTATA
1 TTATGTATATATTTTAATAACTATA
* * *
4378341 TTATATATGTATTTT--TAACGCCATA
1 TTATGTATATATTTTAATAA--CTATA
*
4378366 TTATGTACATATTTTTAAT-ACTAT
1 TTATGTATATA-TTTTAATAACTAT
4378390 GCATACACAT
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
23 3 0.08
25 28 0.76
26 4 0.11
27 1 0.03
28 1 0.03
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.51
Consensus pattern (25 bp):
TTATGTATATATTTTAATAACTATA
Found at i:4378773 original size:8 final size:8
Alignment explanation
Indices: 4378760--4378790 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
4378750 TTTCTTTTAC
4378760 TTTTATTT
1 TTTTATTT
4378768 TTTTATTT
1 TTTTATTT
4378776 TTTTATTT
1 TTTTATTT
4378784 TATTTAT
1 T-TTTAT
4378791 CTAGAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.77
9 5 0.23
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTATTT
Found at i:4387165 original size:23 final size:24
Alignment explanation
Indices: 4387130--4387174 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
4387120 TTATTCAACA
4387130 GAAAAACAAG-TTTA-TGTTTTCT
1 GAAAAACAAGTTTTAGTGTTTTCT
*
4387152 GAAACAACATGTTTTAGTGTTTT
1 GAAA-AACAAGTTTTAGTGTTTT
4387175 TAAGCTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 5 0.26
24 4 0.21
25 6 0.32
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (24 bp):
GAAAAACAAGTTTTAGTGTTTTCT
Found at i:4394259 original size:18 final size:18
Alignment explanation
Indices: 4394236--4394307 Score: 56
Period size: 18 Copynumber: 3.7 Consensus size: 18
4394226 GAAATAACCA
4394236 AGATGAGAAATGAATATG
1 AGATGAGAAATGAATATG
4394254 AGATGAGAATTATTGAAT-TGG
1 AGATGAGAA--A-TGAATAT-G
*
4394275 CAAATATGAGAAATGAATATG
1 ---AGATGAGAAATGAATATG
*
4394296 AGATGACAAATG
1 AGATGAGAAATG
4394308 TGATATGAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
18 19 0.44
20 2 0.05
21 12 0.28
22 2 0.05
24 8 0.19
ACGTcount: A:0.47, C:0.03, G:0.25, T:0.25
Consensus pattern (18 bp):
AGATGAGAAATGAATATG
Found at i:4394269 original size:42 final size:42
Alignment explanation
Indices: 4394222--4394301 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
4394212 TTATAGTTGA
*
4394222 TATTGAAATAACCAAGATGAGAAATGAATATGAGATGAGAAT
1 TATTGAAATAACAAAGATGAGAAATGAATATGAGATGAGAAT
* ** *
4394264 TATTGAATTGGCAAATATGAGAAATGAATATGAGATGA
1 TATTGAAATAACAAAGATGAGAAATGAATATGAGATGA
4394302 CAAATGTGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.47, C:0.04, G:0.23, T:0.26
Consensus pattern (42 bp):
TATTGAAATAACAAAGATGAGAAATGAATATGAGATGAGAAT
Found at i:4394612 original size:123 final size:123
Alignment explanation
Indices: 4394474--4394707 Score: 450
Period size: 123 Copynumber: 1.9 Consensus size: 123
4394464 TGTAATAAAG
4394474 AATGAAAAAAAATTGTATCATTGATTTGAAACATAAGTGCATAATATTTCTTGTTGCATTCTCAC
1 AATGAAAAAAAATTGTATCATTGATTTGAAACATAAGTGCATAATATTTCTTGTTGCATTCTCAC
*
4394539 ATTTTGATTACTTATATTAAGTTAGATTGTTCGGATTATAGAAATAACGCTGAGTTAT
66 ATTTTGATTACTTATATTAAGTTAAATTGTTCGGATTATAGAAATAACGCTGAGTTAT
*
4394597 AATGGAAAAAAATTGTATCATTGATTTGAAACATAAGTGCATAATATTTCTTGTTGCATTCTCAC
1 AATGAAAAAAAATTGTATCATTGATTTGAAACATAAGTGCATAATATTTCTTGTTGCATTCTCAC
4394662 ATTTTGATTACTTATATTAAGTTAAATTGTTCGGATTATAGAAATA
66 ATTTTGATTACTTATATTAAGTTAAATTGTTCGGATTATAGAAATA
4394708 CCATTGAGTT
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 109 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.40
Consensus pattern (123 bp):
AATGAAAAAAAATTGTATCATTGATTTGAAACATAAGTGCATAATATTTCTTGTTGCATTCTCAC
ATTTTGATTACTTATATTAAGTTAAATTGTTCGGATTATAGAAATAACGCTGAGTTAT
Found at i:4395368 original size:42 final size:43
Alignment explanation
Indices: 4395301--4395408 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 43
4395291 CACACACGAG
* *
4395301 CGTGTGACC-CAAGTTAGT-AAGTTACACGGGCTGAGAAACGGC
1 CGTGTG-CCTCAAGTCAGTGAAGTTACACGGGCTAAGAAACGGC
* * *
4395343 CGTGTGCCTCAAGTCAGTGAA-TTACATGGGCTAAGACATGGC
1 CGTGTGCCTCAAGTCAGTGAAGTTACACGGGCTAAGAAACGGC
** *
4395385 TATGTGTCTCAAGTCAGTG-AGTTA
1 CGTGTGCCTCAAGTCAGTGAAGTTA
4395409 TAAGGGCAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
41 3 0.05
42 50 0.91
43 2 0.04
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (43 bp):
CGTGTGCCTCAAGTCAGTGAAGTTACACGGGCTAAGAAACGGC
Found at i:4399301 original size:20 final size:20
Alignment explanation
Indices: 4399276--4399313 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4399266 GACCATTTCA
*
4399276 AAAAAAATCAAAAAAATTTG
1 AAAAAAATAAAAAAAATTTG
*
4399296 AAAAAAGTAAAAAAAATT
1 AAAAAAATAAAAAAAATT
4399314 AGGAAATAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (20 bp):
AAAAAAATAAAAAAAATTTG
Found at i:4400163 original size:6 final size:6
Alignment explanation
Indices: 4400152--4400178 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4400142 ATATGCTTAC
4400152 ATATTT ATATTT ATATTT ATATTT ATA
1 ATATTT ATATTT ATATTT ATATTT ATA
4400179 AGCCAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
ATATTT
Found at i:4401174 original size:45 final size:45
Alignment explanation
Indices: 4401119--4401275 Score: 217
Period size: 45 Copynumber: 3.5 Consensus size: 45
4401109 TTACCATAGT
* * *
4401119 GTCTTTCAACTATGGTCTTACTCGTTTGATTCGTTATGCCATAAT
1 GTCTTTCAACTATGGTCTTACTCGATTGAATCGTTATGCCATAAC
* *
4401164 GTCTGTCAACTATGGTCTTACTCGATTGAATCG-TATGTCATAAC
1 GTCTTTCAACTATGGTCTTACTCGATTGAATCGTTATGCCATAAC
* ** * *
4401208 ATCTTTCAGTTATGGTCTTACTCGATGGAATCGTGATGCCATAAC
1 GTCTTTCAACTATGGTCTTACTCGATTGAATCGTTATGCCATAAC
4401253 GTCTTTCAACTATGGTCTTACTC
1 GTCTTTCAACTATGGTCTTACTC
4401276 ATTTCTGGTA
Statistics
Matches: 96, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
44 37 0.39
45 59 0.61
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.39
Consensus pattern (45 bp):
GTCTTTCAACTATGGTCTTACTCGATTGAATCGTTATGCCATAAC
Found at i:4401302 original size:45 final size:45
Alignment explanation
Indices: 4401253--4401369 Score: 164
Period size: 44 Copynumber: 2.6 Consensus size: 45
4401243 ATGCCATAAC
* * *
4401253 GTCTTTCAACTATGGTCTTACTCATTTCTGGTATGGTGTTATAGT
1 GTCTTTCAACTATGGTCTTAATCATTTCTGGTATAGTGTCATAGT
* *
4401298 GTC-TTCAACTATGGTCTTATTTATTTCTGGTATAGTGTCATAGT
1 GTCTTTCAACTATGGTCTTAATCATTTCTGGTATAGTGTCATAGT
* *
4401342 GTTTTTCAACTATGGTTTTAATCATTTC
1 GTCTTTCAACTATGGTCTTAATCATTTC
4401370 CTTCAAGCCA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 39 0.62
45 24 0.38
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.49
Consensus pattern (45 bp):
GTCTTTCAACTATGGTCTTAATCATTTCTGGTATAGTGTCATAGT
Found at i:4401316 original size:89 final size:89
Alignment explanation
Indices: 4401113--4401275 Score: 227
Period size: 89 Copynumber: 1.8 Consensus size: 89
4401103 GTCGTGTTAC
* * * * *
4401113 CATAGTGTCTTTCAACTATGGTCTTACTCGTTTGATTCGTTATGCCATAATGTCTGTCAACTATG
1 CATAGTGTCTTTCAACTATGGTCTTACTCGATGGAATCGTGATGCCATAACGTCTGTCAACTATG
4401178 GTCTTACTCGATTGAATCGTATGT
66 GTCTTACTCGATTGAATCGTATGT
*** ** *
4401202 CATAACATCTTTCAGTTATGGTCTTACTCGATGGAATCGTGATGCCATAACGTCTTTCAACTATG
1 CATAGTGTCTTTCAACTATGGTCTTACTCGATGGAATCGTGATGCCATAACGTCTGTCAACTATG
4401267 GTCTTACTC
66 GTCTTACTC
4401276 ATTTCTGGTA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
89 63 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (89 bp):
CATAGTGTCTTTCAACTATGGTCTTACTCGATGGAATCGTGATGCCATAACGTCTGTCAACTATG
GTCTTACTCGATTGAATCGTATGT
Found at i:4406580 original size:34 final size:34
Alignment explanation
Indices: 4406508--4406580 Score: 78
Period size: 34 Copynumber: 2.1 Consensus size: 34
4406498 CATGGTACTT
* **
4406508 TTAATTAGTGAAAATCATTGTATTGTATTACATG
1 TTAATTAGTGAAAATCATTGTATTGGATTACAAA
*
4406542 TTAATTAGTGAAAATC-TTTTAATTGGAGTTA-AAA
1 TTAATTAGTGAAAATCATTGT-ATTGGA-TTACAAA
4406576 TTAAT
1 TTAAT
4406581 GTTATATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
33 3 0.09
34 27 0.82
35 3 0.09
ACGTcount: A:0.38, C:0.04, G:0.14, T:0.44
Consensus pattern (34 bp):
TTAATTAGTGAAAATCATTGTATTGGATTACAAA
Found at i:4407613 original size:62 final size:62
Alignment explanation
Indices: 4407516--4407640 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
4407506 CTCGAAAGAA
4407516 TAAACTGCTCCCAAACTTCTTGTGCCTTACAACAATCCCGAAGCACGCGAGTGGTGGATTCT
1 TAAACTGCTCCCAAACTTCTTGTGCCTTACAACAATCCCGAAGCACGCGAGTGGTGGATTCT
4407578 TAAACTGCTCCCAAACTTCTTGTGCCTTACAACAATCCCGAAGCACGCGAGTGGTGGATTCT
1 TAAACTGCTCCCAAACTTCTTGTGCCTTACAACAATCCCGAAGCACGCGAGTGGTGGATTCT
4407640 T
1 T
4407641 CAGCACAGTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (62 bp):
TAAACTGCTCCCAAACTTCTTGTGCCTTACAACAATCCCGAAGCACGCGAGTGGTGGATTCT
Found at i:4416699 original size:3 final size:3
Alignment explanation
Indices: 4416685--4416719 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
4416675 CCCCATTTCT
*
4416685 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4416720 TTCTCCTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4422428 original size:19 final size:20
Alignment explanation
Indices: 4422393--4422437 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
4422383 TATTTTTTTA
4422393 TTTTTCCCAATTGTCCTTTC
1 TTTTTCCCAATTGTCCTTTC
* *
4422413 TTTTTCCCAGTT-TCCTTTT
1 TTTTTCCCAATTGTCCTTTC
4422432 TTTTTC
1 TTTTTC
4422438 TTCTTCCCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.07, C:0.27, G:0.04, T:0.62
Consensus pattern (20 bp):
TTTTTCCCAATTGTCCTTTC
Found at i:4424825 original size:11 final size:13
Alignment explanation
Indices: 4424799--4424893 Score: 52
Period size: 12 Copynumber: 8.1 Consensus size: 13
4424789 ATAGGGTCTC
4424799 CAAATTCACATTT
1 CAAATTCACATTT
4424812 CAAA-TCAC-TTT
1 CAAATTCACATTT
4424823 C-AATGTCA-ATTT
1 CAAAT-TCACATTT
**
4424835 CACTTTCA-A-TT
1 CAAATTCACATTT
*
4424846 CAAATTCACAATT
1 CAAATTCACATTT
4424859 C-AATTCA-ATTCT
1 CAAATTCACATT-T
*
4424871 C--ATT--CAGTT
1 CAAATTCACATTT
4424880 CAAATTCACATTT
1 CAAATTCACATTT
4424893 C
1 C
4424894 CATTTTCTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 24
0.67 0.07 0.26
Matches are distributed among these distances:
9 2 0.03
10 4 0.06
11 20 0.32
12 24 0.38
13 13 0.21
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (13 bp):
CAAATTCACATTT
Found at i:4424837 original size:18 final size:17
Alignment explanation
Indices: 4424816--4424868 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 17
4424806 ACATTTCAAA
4424816 TCACTTTCAATGTCAATT
1 TCACTTTCAAT-TCAATT
*
4424834 TCACTTTCAATTCAAAT
1 TCACTTTCAATTCAATT
*
4424851 TCACAATTCAATTCAATT
1 TCAC-TTTCAATTCAATT
4424869 CTCATTCAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
17 9 0.29
18 22 0.71
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.42
Consensus pattern (17 bp):
TCACTTTCAATTCAATT
Found at i:4424848 original size:34 final size:34
Alignment explanation
Indices: 4424810--4424893 Score: 102
Period size: 34 Copynumber: 2.5 Consensus size: 34
4424800 AAATTCACAT
4424810 TTCAAA-TCAC-TTTCAATGTCAATT-TCACTTTCAA
1 TTCAAATTCACATTTCAAT-TCAATTCTCA--TTCAA
* *
4424844 TTCAAATTCACAATTCAATTCAATTCTCATTCAG
1 TTCAAATTCACATTTCAATTCAATTCTCATTCAA
4424878 TTCAAATTCACATTTC
1 TTCAAATTCACATTTC
4424894 CATTTTCTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
34 25 0.57
35 10 0.23
36 9 0.20
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.40
Consensus pattern (34 bp):
TTCAAATTCACATTTCAATTCAATTCTCATTCAA
Found at i:4424869 original size:17 final size:17
Alignment explanation
Indices: 4424810--4424891 Score: 87
Period size: 17 Copynumber: 4.8 Consensus size: 17
4424800 AAATTCACAT
*
4424810 TTCAAA-TCACTTTCAA
1 TTCAAATTCACATTCAA
* *
4424826 TGTCAATTTCACTTTCAA
1 T-TCAAATTCACATTCAA
4424844 TTCAAATTCACAATTCAA
1 TTCAAATTCAC-ATTCAA
* *
4424862 TTC-AATTCTCATTCAG
1 TTCAAATTCACATTCAA
4424878 TTCAAATTCACATT
1 TTCAAATTCACATT
4424892 TCCATTTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
16 9 0.16
17 28 0.50
18 19 0.34
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.40
Consensus pattern (17 bp):
TTCAAATTCACATTCAA
Found at i:4425042 original size:15 final size:16
Alignment explanation
Indices: 4425022--4425054 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4425012 ATTCTTAAAC
4425022 TAATTC-ATTTTTATT
1 TAATTCAATTTTTATT
4425037 TAATTCATATTTTTATT
1 TAATTCA-ATTTTTATT
4425054 T
1 T
4425055 CATTTTCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (16 bp):
TAATTCAATTTTTATT
Found at i:4430437 original size:20 final size:20
Alignment explanation
Indices: 4430385--4430431 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
4430375 GTGTTTAGCA
* *
4430385 AAAAAAAAAGG-AAATTGGG
1 AAAAAGAAAGGAAAATTAGG
*
4430404 AAGAAGAAAGGAAAATTAGG
1 AAAAAGAAAGGAAAATTAGG
4430424 AAAAAGAA
1 AAAAAGAA
4430432 GAGAAACAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.66, C:0.00, G:0.26, T:0.09
Consensus pattern (20 bp):
AAAAAGAAAGGAAAATTAGG
Found at i:4433115 original size:21 final size:22
Alignment explanation
Indices: 4433091--4433135 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
4433081 TACGGTTTTG
4433091 TTGTTCCA-TATGAGGGTTCTT
1 TTGTTCCATTATGAGGGTTCTT
*
4433112 TTGTTCCATTATGAGGTTTCTT
1 TTGTTCCATTATGAGGGTTCTT
4433134 TT
1 TT
4433136 CTTATTTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.13, C:0.13, G:0.20, T:0.53
Consensus pattern (22 bp):
TTGTTCCATTATGAGGGTTCTT
Found at i:4436741 original size:31 final size:31
Alignment explanation
Indices: 4436706--4436773 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
4436696 TTTTTTGAAC
**
4436706 TTTTTTTCTTTTCTTTTGTCTT-TTCTTTCTT
1 TTTTTTTCTTTT-TTTTGAATTATTCTTTCTT
*
4436737 TTTTTTTCTTTTTTTTGAATTATTTTTTCTT
1 TTTTTTTCTTTTTTTTGAATTATTCTTTCTT
4436768 TTTTTT
1 TTTTTT
4436774 GTGTGCTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 7 0.21
31 26 0.79
ACGTcount: A:0.04, C:0.10, G:0.03, T:0.82
Consensus pattern (31 bp):
TTTTTTTCTTTTTTTTGAATTATTCTTTCTT
Found at i:4436750 original size:21 final size:21
Alignment explanation
Indices: 4436686--4436743 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
4436676 ATCAAACTTT
* *
4436686 TTTTCTTT-TTTTTTTTGAAC
1 TTTTCTTTCTTTTTTTTTATC
* *
4436706 TTTT-TTTCTTTTCTTTTGTC
1 TTTTCTTTCTTTTTTTTTATC
4436726 TTTTCTTTCTTTTTTTTT
1 TTTTCTTTCTTTTTTTTT
4436744 CTTTTTTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 3 0.10
20 16 0.52
21 12 0.39
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.81
Consensus pattern (21 bp):
TTTTCTTTCTTTTTTTTTATC
Found at i:4436800 original size:51 final size:50
Alignment explanation
Indices: 4436691--4436807 Score: 139
Period size: 51 Copynumber: 2.3 Consensus size: 50
4436681 ACTTTTTTTC
* *
4436691 TTTTTTTTTTTGAACTTTTTTTCTTTTCTTTTGTCTTTTCTTTCTTTTTT
1 TTTTTTTTTTTGAACTTTTTTTCTTTTCTTTTGTCTTTTCTTTCTTCTCT
* *
4436741 TTTCTTTTTTTTGAATTATTTTTTCTTTTTTTTGTGTGCTTTT-TTTC-TCTCT
1 TTT-TTTTTTTTGAACT-TTTTTTCTTTTCTTT-TGT-CTTTTCTTTCTTCTCT
*
4436793 TTTTTTTTGTTGAAC
1 TTTTTTTTTTTGAAC
4436808 ATGATCTCAC
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
50 3 0.05
51 22 0.39
52 20 0.35
53 7 0.12
54 5 0.09
ACGTcount: A:0.06, C:0.11, G:0.07, T:0.76
Consensus pattern (50 bp):
TTTTTTTTTTTGAACTTTTTTTCTTTTCTTTTGTCTTTTCTTTCTTCTCT
Found at i:4443908 original size:16 final size:16
Alignment explanation
Indices: 4443887--4443921 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4443877 ACATAAAATA
* *
4443887 AAATAAAGTAAAGTAG
1 AAATAAAATAAAGAAG
4443903 AAATAAAATAAAGAAG
1 AAATAAAATAAAGAAG
4443919 AAA
1 AAA
4443922 ATTTTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (16 bp):
AAATAAAATAAAGAAG
Found at i:4444225 original size:35 final size:35
Alignment explanation
Indices: 4444186--4444252 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
4444176 GTGCCCAGCA
*
4444186 TCGTGCCCACGACTCCAGCCGTGACAGAATAAGCG
1 TCGTGCCCACGACTCCAACCGTGACAGAATAAGCG
*
4444221 TCGTGCCCACGACTCCAACTGTGACAGAATAA
1 TCGTGCCCACGACTCCAACCGTGACAGAATAA
4444253 AAAGAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.16
Consensus pattern (35 bp):
TCGTGCCCACGACTCCAACCGTGACAGAATAAGCG
Found at i:4447955 original size:18 final size:18
Alignment explanation
Indices: 4447932--4447967 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4447922 GACCATTTAT
4447932 GGCACTATTCACGTATAC
1 GGCACTATTCACGTATAC
* *
4447950 GGCACTGTTCATGTATAC
1 GGCACTATTCACGTATAC
4447968 AGTAATTGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (18 bp):
GGCACTATTCACGTATAC
Found at i:4453603 original size:25 final size:25
Alignment explanation
Indices: 4453557--4453604 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
4453547 AATAATTTAA
* *
4453557 AATTATAAAAATATTCACAAAAAAC
1 AATTATAAAAATATCCAAAAAAAAC
4453582 AATTATAAAAA-ATCCAAAAAAAA
1 AATTATAAAAATATCCAAAAAAAA
4453605 GTAAGTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (25 bp):
AATTATAAAAATATCCAAAAAAAAC
Found at i:4454922 original size:26 final size:28
Alignment explanation
Indices: 4454893--4454955 Score: 87
Period size: 26 Copynumber: 2.3 Consensus size: 28
4454883 TTATTCAAGA
*
4454893 TTTAGGGTTC-ATGGTTC-GGGTTTG-AG
1 TTTAGGGTTCAAT-GTTCAAGGTTTGTAG
4454919 TTTAGGGTTCAATGTTCAAGGTTTGTAG
1 TTTAGGGTTCAATGTTCAAGGTTTGTAG
4454947 TTTAGGGTT
1 TTTAGGGTT
4454956 TAAGGTTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
26 14 0.42
27 8 0.24
28 11 0.33
ACGTcount: A:0.16, C:0.06, G:0.33, T:0.44
Consensus pattern (28 bp):
TTTAGGGTTCAATGTTCAAGGTTTGTAG
Found at i:4463620 original size:24 final size:24
Alignment explanation
Indices: 4463593--4463639 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
4463583 TTCAGAATAA
4463593 CATAGTTTAATTTTAATAAAAATT
1 CATAGTTTAATTTTAATAAAAATT
4463617 CATAGTTTAATTTTAATAAAAAT
1 CATAGTTTAATTTTAATAAAAAT
4463640 ATCTAGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (24 bp):
CATAGTTTAATTTTAATAAAAATT
Found at i:4483006 original size:51 final size:52
Alignment explanation
Indices: 4482915--4483034 Score: 142
Period size: 51 Copynumber: 2.4 Consensus size: 52
4482905 TCTTATTAAT
*
4482915 TTAAATTAATTAAGAGATAAATATTAAAAATTTATATTATCATTAATTAAAA
1 TTAAAATAATTAAGAGATAAATATTAAAAATTTATATTATCATTAATTAAAA
* * * *
4482967 TTAAAATAATTAAGTGAT-AATATTAAATGA-TTATTTTATCTTTAATT--AA
1 TTAAAATAATTAAGAGATAAATATTAAA-AATTTATATTATCATTAATTAAAA
*
4483016 TTAAATTAA-TAAGAGATAA
1 TTAAAATAATTAAGAGATAA
4483035 GTTGTAAAGC
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
48 7 0.12
49 11 0.19
51 24 0.41
52 17 0.29
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.42
Consensus pattern (52 bp):
TTAAAATAATTAAGAGATAAATATTAAAAATTTATATTATCATTAATTAAAA
Found at i:4484507 original size:33 final size:33
Alignment explanation
Indices: 4484465--4484530 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
4484455 TTCATGTGAT
4484465 TGGATCAAATAGAGTAGTTAAATTCTACAAGAA
1 TGGATCAAATAGAGTAGTTAAATTCTACAAGAA
4484498 TGGATCAAATAGAGTAGTTAAATTCTACAAGAA
1 TGGATCAAATAGAGTAGTTAAATTCTACAAGAA
4484531 CTCTATTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.27
Consensus pattern (33 bp):
TGGATCAAATAGAGTAGTTAAATTCTACAAGAA
Found at i:4490772 original size:17 final size:16
Alignment explanation
Indices: 4490739--4490769 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4490729 AAAATAATTT
*
4490739 AAAACTTTAAATTTTG
1 AAAACTTAAAATTTTG
4490755 AAAACTTAAAATTTT
1 AAAACTTAAAATTTT
4490770 TGAGAAACGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (16 bp):
AAAACTTAAAATTTTG
Found at i:4491038 original size:23 final size:23
Alignment explanation
Indices: 4490997--4491055 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
4490987 CTATTGATGT
* *
4490997 GCCAGAGAAT-CTTACTGTTCT-T
1 GCCAGAGAATATTTACTGTT-TAC
*
4491019 GCCAGGGAATATTTACTGTTTAC
1 GCCAGAGAATATTTACTGTTTAC
4491042 GCCAGAGAATATTT
1 GCCAGAGAATATTT
4491056 CTTGTTCACT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 10 0.32
23 21 0.68
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (23 bp):
GCCAGAGAATATTTACTGTTTAC
Found at i:4500379 original size:28 final size:29
Alignment explanation
Indices: 4500347--4500405 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
4500337 ACTAAGAATG
*
4500347 AACAA-AATGTACTAAAAACATGCAAATT
1 AACAATAATGTACTAAAAACAGGCAAATT
**
4500375 AACAATCTTGTACTAAAAACAGGCAAATT
1 AACAATAATGTACTAAAAACAGGCAAATT
4500404 AA
1 AA
4500406 AAACCTATCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.22
Consensus pattern (29 bp):
AACAATAATGTACTAAAAACAGGCAAATT
Found at i:4500419 original size:28 final size:29
Alignment explanation
Indices: 4500356--4500419 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
4500346 GAACAAAATG
* * * *
4500356 TACTAAAAACATGCAAATTAACAATCTTG
1 TACTAAAAACAGGCAAATTAACAAACCTA
4500385 TACTAAAAACAGGCAAATTAA-AAACCTA
1 TACTAAAAACAGGCAAATTAACAAACCTA
*
4500413 TCCTAAA
1 TACTAAA
4500420 CTCTAAAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 10 0.33
29 20 0.67
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.23
Consensus pattern (29 bp):
TACTAAAAACAGGCAAATTAACAAACCTA
Found at i:4500657 original size:8 final size:8
Alignment explanation
Indices: 4500644--4500673 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
4500634 TTCCAGTGTG
4500644 AAAAAAAT
1 AAAAAAAT
4500652 AAAAAAAT
1 AAAAAAAT
4500660 AAAAAAAT
1 AAAAAAAT
4500668 AAAAAA
1 AAAAAA
4500674 CACACAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:4507269 original size:23 final size:23
Alignment explanation
Indices: 4507243--4507287 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
4507233 TGGAAATGTG
*
4507243 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
4507266 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
4507288 TTGAATTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:4509360 original size:18 final size:19
Alignment explanation
Indices: 4509337--4509380 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
4509327 CTAAATATTT
4509337 ATTTTAATATTT-TTAT-AC
1 ATTTTAAT-TTTATTATCAC
4509355 ATTTTAATTTTATTATGCAC
1 ATTTTAATTTTATTAT-CAC
4509375 ATTTTA
1 ATTTTA
4509381 TTACCTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
20 8 0.35
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTTTAATTTTATTATCAC
Found at i:4525344 original size:44 final size:46
Alignment explanation
Indices: 4525230--4525344 Score: 137
Period size: 46 Copynumber: 2.5 Consensus size: 46
4525220 ATACAGGTCT
* * *
4525230 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATGTCAGATCC
* *
4525276 TATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-ATAGT-A-ATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAAT-GTCAGATCC
* *
4525320 TATCTCCTTGAGATTACAATGGAGC
1 TATCTCCCTGAGATTACAGTGGAGC
4525345 GGATTAAAAG
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 25 0.42
45 3 0.05
46 32 0.53
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (46 bp):
TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAATGTCAGATCC
Found at i:4525447 original size:44 final size:43
Alignment explanation
Indices: 4525270--4525606 Score: 190
Period size: 44 Copynumber: 8.0 Consensus size: 43
4525260 AAAGAATTTC
* * *
4525270 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-T
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACA
* * * ** * *
4525312 AGTAATCCTATCTCCTTGAGATTACAATGGAGCGGAT--TA-A-A
1 AG--ATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACA
* * * * * * *
4525353 AGATCTTATCTCTCTGAAGTTACAGCAGAGTAGACCGCA-TC-
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACA
* * * *
4525394 AGGTCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACA
*
4525437 GAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA
1 -AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACA
** * * * * * * *
4525481 CTATCCTATCTCCCTGAAGTTACAGTGGAGCGGAT-TAAAATAA
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGA-CA
* * * * *
4525524 AGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCA-TCA
1 A-GATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACA
* * * * *
4525567 AG-TCCTATCTCCCTGAAGTTGCAGTGGAGCAGATAGAAGA
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGA
4525607 AACCAATCCT
Statistics
Matches: 215, Mismatches: 68, Indels: 24
0.70 0.22 0.08
Matches are distributed among these distances:
39 22 0.10
41 61 0.28
42 8 0.04
43 31 0.14
44 92 0.43
45 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (43 bp):
AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACA
Found at i:4525566 original size:172 final size:168
Alignment explanation
Indices: 4525270--4525605 Score: 496
Period size: 172 Copynumber: 2.0 Consensus size: 168
4525260 AAAGAATTTC
* * *
4525270 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATT
* *
4525335 ACAATGGAGCGGATTAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGACCGCATCAGGTCT
66 ACAATGGAGCGGATTAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGACCGCATCAAGTCC
* *
4525400 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
131 TATCTCCCTGAAGTTACAGTGGAGCAGATAGAAGCCAG
*
4525438 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCTGA-AGT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGA-T
* * *
4525501 TACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATC
65 TACAATGGAGCGGATT---A-AAA-GATCTTATCTCTCTGAAGTTACAGCAGAGTAGACCGCATC
*
4525566 AAGTCCTATCTCCCTGAAGTTGCAGTGGAGCAGATAGAAG
125 AAGTCCTATCTCCCTGAAGTTACAGTGGAGCAGATAGAAG
4525606 AAACCAATCC
Statistics
Matches: 150, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
166 1 0.01
167 30 0.20
168 42 0.28
170 1 0.01
171 3 0.02
172 73 0.49
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (168 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATT
ACAATGGAGCGGATTAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGTAGACCGCATCAAGTCC
TATCTCCCTGAAGTTACAGTGGAGCAGATAGAAGCCAG
Found at i:4525618 original size:44 final size:44
Alignment explanation
Indices: 4525569--4525688 Score: 154
Period size: 44 Copynumber: 2.7 Consensus size: 44
4525559 TCGCATCAAG
* *
4525569 TCCTATCTCCCTGAAGTTGCAGTGGAGCAGATAGAAGAAAC-CA-A
1 TCCTATCTCTCTGAAGTTGCAGTAGAGCAGAT-GAA-AAACACAGA
* * *
4525613 TCCTATCTCTCTGAAGTTGCAGTAGAGCGGATTAAAATCACAGA
1 TCCTATCTCTCTGAAGTTGCAGTAGAGCAGATGAAAAACACAGA
*
4525657 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 TCCTATCTCTCTGAAGTTGCAGTAGAGCAGAT
4525689 CGCATCAAGT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.04
43 4 0.06
44 60 0.90
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (44 bp):
TCCTATCTCTCTGAAGTTGCAGTAGAGCAGATGAAAAACACAGA
Found at i:4525620 original size:85 final size:84
Alignment explanation
Indices: 4525351--4525626 Score: 295
Period size: 85 Copynumber: 3.2 Consensus size: 84
4525341 GAGCGGATTA
* * * * *
4525351 AAAG-ATCTTATCTCTCTGAAGTTACAGCAGAGTAGACCGCATCAGGTCTTATCTCCCTGAGGTT
1 AAAGAATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATCAAGTCCTATCTCCCTGAAGTT
*
4525415 ACAGTGGAGCAGATTGAAG
66 ACAGTGGAGCAGATAGAAG
** * * * * * *
4525434 CCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTA-TCCTATCTCCCTGA
1 AAAGA-ATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCA-TCA--AGTCCTATCTCCCTGA
* * *
4525498 AGTTACAGTGGAGCGGATTAAAAT
62 AGTTACAGTGGAGCAGA-TAGAAG
*
4525522 AAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATCAAGTCCTATCTCCCTGAAGTT
1 AAAGAATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATCAAGTCCTATCTCCCTGAAGTT
*
4525587 GCAGTGGAGCAGATAGAAG
66 ACAGTGGAGCAGATAGAAG
* *
4525606 AAACCAATCCTATCTCTCTGA
1 AAA-GAATCTTATCTCTCTGA
4525627 AGTTGCAGTA
Statistics
Matches: 152, Mismatches: 33, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
83 2 0.01
84 8 0.05
85 73 0.48
86 4 0.03
87 60 0.39
88 5 0.03
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (84 bp):
AAAGAATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATCAAGTCCTATCTCCCTGAAGTT
ACAGTGGAGCAGATAGAAG
Found at i:4525643 original size:129 final size:128
Alignment explanation
Indices: 4525444--4525707 Score: 354
Period size: 129 Copynumber: 2.1 Consensus size: 128
4525434 CCAGAGATCT
* * * *
4525444 TATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAGTGG
1 TATCTCCCTGAGATTACAGCGGAGCAGATAGAAGAAACAATCCTATCTCCCTGAAGTTACAGTAG
* *
4525509 AGCGGATTAAAAT-AAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATCAAGTCC
66 AGCGGATTAAAATCAAA-GATCTTATCTCTCTGAAGTTACAGCAGAGCAGATCGCATCAAGTCC
* * * *
4525572 TATCTCCCTGA-AGTTGCAGTGGAGCAGATAGAAGAAACCAATCCTATCTCTCTGAAGTTGCAGT
1 TATCTCCCTGAGA-TTACAGCGGAGCAGATAGAAGAAA-CAATCCTATCTCCCTGAAGTTACAGT
* * * *
4525636 AGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCT
64 AGAGCGGATTAAAATCAAAGATCTTATCTCTCTGAAGTTACAGCAGAGCAGATCGCATCAAGTCC
4525701 TAT-TCCC
1 TATCTCCC
4525708 CCGAAGTACA
Statistics
Matches: 119, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
127 1 0.01
128 35 0.29
129 81 0.68
130 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.26
Consensus pattern (128 bp):
TATCTCCCTGAGATTACAGCGGAGCAGATAGAAGAAACAATCCTATCTCCCTGAAGTTACAGTAG
AGCGGATTAAAATCAAAGATCTTATCTCTCTGAAGTTACAGCAGAGCAGATCGCATCAAGTCC
Found at i:4525924 original size:15 final size:15
Alignment explanation
Indices: 4525906--4525959 Score: 108
Period size: 15 Copynumber: 3.6 Consensus size: 15
4525896 CACTAACAAA
4525906 AAACCCAATACCCAC
1 AAACCCAATACCCAC
4525921 AAACCCAATACCCAC
1 AAACCCAATACCCAC
4525936 AAACCCAATACCCAC
1 AAACCCAATACCCAC
4525951 AAACCCAAT
1 AAACCCAAT
4525960 TACCATGCCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.48, C:0.44, G:0.00, T:0.07
Consensus pattern (15 bp):
AAACCCAATACCCAC
Found at i:4525941 original size:8 final size:7
Alignment explanation
Indices: 4525905--4525958 Score: 54
Period size: 7 Copynumber: 7.3 Consensus size: 7
4525895 CCACTAACAA
4525905 AAAACCC
1 AAAACCC
*
4525912 AATACCC
1 AAAACCC
4525919 ACAAACCC
1 A-AAACCC
*
4525927 AATACCC
1 AAAACCC
4525934 ACAAACCC
1 A-AAACCC
*
4525942 AATACCC
1 AAAACCC
4525949 ACAAACCC
1 A-AAACCC
4525957 AA
1 AA
4525959 TTACCATGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
7 20 0.53
8 18 0.47
ACGTcount: A:0.50, C:0.44, G:0.00, T:0.06
Consensus pattern (7 bp):
AAAACCC
Found at i:4526983 original size:31 final size:29
Alignment explanation
Indices: 4526912--4526983 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 29
4526902 TTTGTTTATA
*
4526912 CTTAT-TATGTAAATTTTATATATATATG
1 CTTATATATGTATATTTTATATATATATG
*
4526940 CTT-CATAT-TATATTATTAT-TATATAATTG
1 CTTATATATGTATATT-TTATATATAT-A-TG
4526969 CTTATATATGTATAT
1 CTTATATATGTATAT
4526984 AGGTATATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
27 10 0.29
28 11 0.31
29 5 0.14
30 4 0.11
31 5 0.14
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.54
Consensus pattern (29 bp):
CTTATATATGTATATTTTATATATATATG
Found at i:4554097 original size:13 final size:13
Alignment explanation
Indices: 4554079--4554104 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4554069 ACCTGATTCA
4554079 TCATAAACCAGAT
1 TCATAAACCAGAT
4554092 TCATAAACCAGAT
1 TCATAAACCAGAT
4554105 GTCTTCTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
TCATAAACCAGAT
Found at i:4556403 original size:22 final size:22
Alignment explanation
Indices: 4556375--4556418 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4556365 CAATGTGTGC
*
4556375 CATGCATCTCATATGAAGATAT
1 CATGCATCTCATATGAAAATAT
4556397 CATGCATCTCATATGAAAATAT
1 CATGCATCTCATATGAAAATAT
4556419 TTACCATTTT
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:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (22 bp):
CATGCATCTCATATGAAAATAT
Found at i:4557325 original size:19 final size:20
Alignment explanation
Indices: 4557285--4557327 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
4557275 ATTTTGCAAG
4557285 AAAAAAATTATATAATAAATT
1 AAAAAAATTATATAAT-AATT
4557306 AAAATAAATT-TATAAT-ATT
1 AAAA-AAATTATATAATAATT
4557325 AAA
1 AAA
4557328 CATATTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.29
21 10 0.48
22 5 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAAAATTATATAATAATT
Found at i:4558122 original size:6 final size:6
Alignment explanation
Indices: 4558111--4558188 Score: 70
Period size: 6 Copynumber: 12.7 Consensus size: 6
4558101 AATAAATTAT
* * *
4558111 AAAACC AAAACC AAAACC AAAACC AAAA-C AAAAGC AATAGCA ATATTAACC
1 AAAACC AAAACC AAAACC AAAACC AAAACC AAAACC AA-AACC A-A--AACC
*
4558162 AAAACC AAAATC AAAACC AAAA-C AAAA
1 AAAACC AAAACC AAAACC AAAACC AAAA
4558189 GCAATAGCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
5 10 0.16
6 43 0.70
7 2 0.03
8 2 0.03
9 4 0.07
ACGTcount: A:0.67, C:0.24, G:0.03, T:0.06
Consensus pattern (6 bp):
AAAACC
Found at i:4558177 original size:39 final size:39
Alignment explanation
Indices: 4558119--4558194 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
4558109 ATAAAACCAA
*
4558119 AACCAAAACCAAAACCAAAA-CAAAAGCAATAGCAATATT
1 AACCAAAACCAAAACCAAAACCAAAA-CAAAAGCAATATT
*
4558158 AACCAAAACCAAAATCAAAACCAAAACAAAAGCAATA
1 AACCAAAACCAAAACCAAAACCAAAACAAAAGCAATA
4558195 GCAATATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 29 0.85
40 5 0.15
ACGTcount: A:0.64, C:0.24, G:0.04, T:0.08
Consensus pattern (39 bp):
AACCAAAACCAAAACCAAAACCAAAACAAAAGCAATATT
Found at i:4558177 original size:45 final size:45
Alignment explanation
Indices: 4558113--4558204 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
4558103 TAAATTATAA
4558113 AACCAAAACCAAAACCAAAACCAAAACAAAAGCAATAGCAATATT
1 AACCAAAACCAAAACCAAAACCAAAACAAAAGCAATAGCAATATT
*
4558158 AACCAAAACCAAAATCAAAACCAAAACAAAAGCAATAGCAATATT
1 AACCAAAACCAAAACCAAAACCAAAACAAAAGCAATAGCAATATT
4558203 AA
1 AA
4558205 GTTGTTAACC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.63, C:0.23, G:0.04, T:0.10
Consensus pattern (45 bp):
AACCAAAACCAAAACCAAAACCAAAACAAAAGCAATAGCAATATT
Found at i:4558711 original size:28 final size:28
Alignment explanation
Indices: 4558671--4558725 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
4558661 ATCCATCATA
4558671 AACCAGATGTCTTCTTAAAGAACAAATT
1 AACCAGATGTCTTCTTAAAGAACAAATT
* *
4558699 AACCAGATGTCTTCTTGAAGAATAAAT
1 AACCAGATGTCTTCTTAAAGAACAAAT
4558726 CATCATAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (28 bp):
AACCAGATGTCTTCTTAAAGAACAAATT
Found at i:4559367 original size:15 final size:15
Alignment explanation
Indices: 4559334--4559374 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
4559324 TCTGTTGTGT
4559334 TTTTTAGTTTT-GGA
1 TTTTTAGTTTTAGGA
*
4559348 CTTTTAGTTTTAGGA
1 TTTTTAGTTTTAGGA
*
4559363 TTTTTATTTTTA
1 TTTTTAGTTTTA
4559375 TTTATTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.66
Consensus pattern (15 bp):
TTTTTAGTTTTAGGA
Found at i:4569371 original size:25 final size:25
Alignment explanation
Indices: 4569343--4569404 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
4569333 TATCTCATAT
*
4569343 GAGCTTACTGTTATTCAGCTTGGAG
1 GAGCTTACTGTTATTCAGCTCGGAG
4569368 GAGCTTACTGTTATTCAGCTCGGAG
1 GAGCTTACTGTTATTCAGCTCGGAG
*
4569393 GATCTTACTGTT
1 GAGCTTACTGTT
4569405 TATAGCTCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (25 bp):
GAGCTTACTGTTATTCAGCTCGGAG
Found at i:4571818 original size:16 final size:15
Alignment explanation
Indices: 4571797--4571828 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
4571787 ATGGCGTCGG
4571797 AGAAAAATGGCGATA
1 AGAAAAATGGCGATA
4571812 AGAAAAATGGCGATA
1 AGAAAAATGGCGATA
4571827 AG
1 AG
4571829 GGTATATTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.28, T:0.12
Consensus pattern (15 bp):
AGAAAAATGGCGATA
Found at i:4576151 original size:36 final size:36
Alignment explanation
Indices: 4576092--4576164 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 36
4576082 CTTCAAGGTA
* * *
4576092 TAAGTTTTTTAAGTAAAAAC-TTTTAGGTATTAATT
1 TAAGTTTTTGAAATAAAAACTTTTTAGGTATAAATT
4576127 TAAGTTTTTGAAATACAAAACTTTTTAGGTATAAATT
1 TAAGTTTTTGAAATA-AAAACTTTTTAGGTATAAATT
4576164 T
1 T
4576165 TTGAAAAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 13 0.39
36 5 0.15
37 15 0.45
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (36 bp):
TAAGTTTTTGAAATAAAAACTTTTTAGGTATAAATT
Found at i:4581630 original size:21 final size:20
Alignment explanation
Indices: 4581583--4581630 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
4581573 ATAAAATACC
4581583 TAATAT-GTAAAAGAATTTA
1 TAATATAGTAAAAGAATTTA
* *
4581602 TATTTATAGTAAAATAATTATA
1 TA-ATATAGTAAAAGAATT-TA
4581624 TAATATA
1 TAATATA
4581631 TATGAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.09
20 3 0.13
21 14 0.61
22 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (20 bp):
TAATATAGTAAAAGAATTTA
Found at i:4581983 original size:17 final size:17
Alignment explanation
Indices: 4581946--4582003 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
4581936 AAAAATATAG
*
4581946 ATAATAATGTA-AAATA
1 ATAATAATTTATAAATA
*
4581962 ATAATAATTTATAAAAA
1 ATAATAATTTATAAATA
*
4581979 ATAATACA-TAATAAATA
1 ATAATA-ATTTATAAATA
4581996 ATAATAAT
1 ATAATAAT
4582004 ATGAAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 11 0.31
17 23 0.66
18 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
ATAATAATTTATAAATA
Found at i:4587049 original size:11 final size:11
Alignment explanation
Indices: 4587020--4587061 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
4587010 TAGAATATAC
* *
4587020 CCCATACATTG
1 CCCATACCTTA
*
4587031 CCCATACCTTT
1 CCCATACCTTA
4587042 CCCATACC-TA
1 CCCATACCTTA
4587052 CCCATACCTT
1 CCCATACCTT
4587062 GGAAAGGTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (11 bp):
CCCATACCTTA
Found at i:4587621 original size:18 final size:18
Alignment explanation
Indices: 4587594--4587668 Score: 78
Period size: 18 Copynumber: 4.2 Consensus size: 18
4587584 TACGACCGTT
*
4587594 TACGGTACTATTCACGTA
1 TACGGCACTATTCACGTA
* * *
4587612 TACGACACTATTTACATA
1 TACGGCACTATTCACGTA
* * *
4587630 TATGGCACTATTTATGTA
1 TACGGCACTATTCACGTA
*
4587648 TACGGTACTATTCACGTA
1 TACGGCACTATTCACGTA
4587666 TAC
1 TAC
4587669 AGTAGTTGGG
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (18 bp):
TACGGCACTATTCACGTA
Found at i:4591659 original size:11 final size:11
Alignment explanation
Indices: 4591643--4591685 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
4591633 TAGAATATAC
4591643 CCCATACCTTG
1 CCCATACCTTG
*
4591654 CCCATACCTTT
1 CCCATACCTTG
*
4591665 CCCATACC-TA
1 CCCATACCTTG
4591675 CCCATACCTTG
1 CCCATACCTTG
4591686 GAAAGGTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.21, C:0.47, G:0.05, T:0.28
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:4591680 original size:21 final size:22
Alignment explanation
Indices: 4591643--4591684 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
4591633 TAGAATATAC
*
4591643 CCCATACCTTGCCCATACCTTT
1 CCCATACCTTACCCATACCTTT
4591665 CCCATACC-TACCCATACCTT
1 CCCATACCTTACCCATACCTT
4591685 GGAAAGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.21, C:0.48, G:0.02, T:0.29
Consensus pattern (22 bp):
CCCATACCTTACCCATACCTTT
Found at i:4593745 original size:43 final size:43
Alignment explanation
Indices: 4593697--4593835 Score: 170
Period size: 43 Copynumber: 3.2 Consensus size: 43
4593687 CGAAAAAAAT
*
4593697 GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTGGCAAAC
1 GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTGACAAAC
* * *
4593740 GCCGCTAAAGACCACGACTTTTAGCGGCGCTTTTTTCACAAAC
1 GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTGACAAAC
* * * * * * *
4593783 GCCGCTAAAGATCATAAACTTTAGCGCCACTTTTTCGCCAAAC
1 GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTGACAAAC
*
4593826 GCCACTAAAG
1 GCCGCTAAAG
4593836 GTCATGAAAT
Statistics
Matches: 81, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 81 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.24
Consensus pattern (43 bp):
GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTTGACAAAC
Found at i:4594049 original size:6 final size:6
Alignment explanation
Indices: 4594038--4594114 Score: 57
Period size: 6 Copynumber: 12.5 Consensus size: 6
4594028 ATTAAATATT
* *
4594038 AAAATA AAAATA AAAATA TAAAATCA AAACT- AAAATA AATAATA AAAATT
1 AAAATA AAAATA AAAATA -AAAAT-A AAAATA AAAATA AA-AATA AAAATA
* * * * *
4594088 AGATTA AATATA AAGATA TAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
4594115 TACAGCAAGT
Statistics
Matches: 54, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
5 4 0.07
6 34 0.63
7 15 0.28
8 1 0.02
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (6 bp):
AAAATA
Found at i:4594056 original size:20 final size:20
Alignment explanation
Indices: 4594031--4594072 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
4594021 TCAAGTTATT
4594031 AAATATTAAAAT-AAAAATAA
1 AAATA-TAAAATCAAAAATAA
*
4594051 AAATATAAAATCAAAACTAA
1 AAATATAAAATCAAAAATAA
4594071 AA
1 AA
4594073 TAAATAATAA
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:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (20 bp):
AAATATAAAATCAAAAATAA
Found at i:4594061 original size:19 final size:19
Alignment explanation
Indices: 4594031--4594114 Score: 64
Period size: 19 Copynumber: 4.1 Consensus size: 19
4594021 TCAAGTTATT
4594031 AAATATTAAAATAAAAATAA
1 AAATA-TAAAATAAAAATAA
*
4594051 AAATATAAAATCAAAACT-A
1 AAATATAAAAT-AAAAATAA
4594070 AAATA-AATAATAAAAATTAGA
1 AAATATAA-AATAAAAA-TA-A
*
4594091 TTAAATATAAAGATATAAATAA
1 --AAATATAAA-ATAAAAATAA
4594113 AA
1 AA
4594115 TACAGCAAGT
Statistics
Matches: 52, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
18 6 0.12
19 16 0.31
20 12 0.23
21 1 0.02
22 1 0.02
23 8 0.15
24 8 0.15
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (19 bp):
AAATATAAAATAAAAATAA
Found at i:4598886 original size:14 final size:15
Alignment explanation
Indices: 4598850--4598886 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
4598840 AACCATTAAA
4598850 CTTAAACCATAGAAC
1 CTTAAACCATAGAAC
*
4598865 CCTAAACCATAG-AC
1 CTTAAACCATAGAAC
4598879 CTTAAACC
1 CTTAAACC
4598887 TTAAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.43, C:0.32, G:0.05, T:0.19
Consensus pattern (15 bp):
CTTAAACCATAGAAC
Found at i:4599065 original size:16 final size:17
Alignment explanation
Indices: 4599044--4599077 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
4599034 AAAGTTATAG
4599044 TTTAAGGTTTAG-GGTT
1 TTTAAGGTTTAGAGGTT
4599060 TTTAAGGTTTAGAGGTT
1 TTTAAGGTTTAGAGGTT
4599077 T
1 T
4599078 AGTGCATTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (17 bp):
TTTAAGGTTTAGAGGTT
Found at i:4599204 original size:41 final size:41
Alignment explanation
Indices: 4599147--4599288 Score: 257
Period size: 41 Copynumber: 3.5 Consensus size: 41
4599137 GTTATATGAC
4599147 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
* * *
4599188 TTTTAGCGGCGTTTTACAGAAAGCGACGCTAATTCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
4599229 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
4599270 TTTTAGCGGCGTTTTACCG
1 TTTTAGCGGCGTTTTACCG
4599289 CTATTGCTCT
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 95 1.00
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.34
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
Found at i:4635786 original size:17 final size:17
Alignment explanation
Indices: 4635764--4635804 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
4635754 AAAACTACCT
4635764 ACCCAAATA-ACCCCAAA
1 ACCCAAATAGA-CCCAAA
*
4635781 ACCCAATTAGACCCAAA
1 ACCCAAATAGACCCAAA
4635798 ACCCAAA
1 ACCCAAA
4635805 CCTTAGCTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.51, C:0.39, G:0.02, T:0.07
Consensus pattern (17 bp):
ACCCAAATAGACCCAAA
Found at i:4636959 original size:22 final size:22
Alignment explanation
Indices: 4636921--4637001 Score: 60
Period size: 22 Copynumber: 3.7 Consensus size: 22
4636911 ATATTTTTGC
*
4636921 TATTATCTATTATTATCATATT
1 TATTATCTATTATTATCATATA
* *
4636943 TATTAT-TATTTTCTATCCTATA
1 TATTATCTATTAT-TATCATATA
* * *
4636965 TATTTTCTTTTTAGTATCA-ATCA
1 TATTATC-TATTATTATCATAT-A
4636988 TATTAT-TATTATTA
1 TATTATCTATTATTA
4637002 CTTTCCTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 9
0.69 0.17 0.14
Matches are distributed among these distances:
21 11 0.25
22 20 0.45
23 10 0.23
24 3 0.07
ACGTcount: A:0.30, C:0.10, G:0.01, T:0.59
Consensus pattern (22 bp):
TATTATCTATTATTATCATATA
Found at i:4637204 original size:18 final size:17
Alignment explanation
Indices: 4637175--4637209 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
4637165 ATTTGTTTTT
4637175 GTATTTTATTATTATTA
1 GTATTTTATTATTATTA
4637192 GTATTTCTATTATTATTA
1 GTATTT-TATTATTATTA
4637210 TTGTTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.63
Consensus pattern (17 bp):
GTATTTTATTATTATTA
Found at i:4637538 original size:3 final size:3
Alignment explanation
Indices: 4637530--4637682 Score: 55
Period size: 3 Copynumber: 50.7 Consensus size: 3
4637520 CCCTCATCAC
* * *
4637530 TAT TAT TAT CTA- TACT TTAT TAT TGT TACT TAT TAT T-T TAC TAT TGT
1 TAT TAT TAT -TAT TA-T T-AT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
* * * * * *
4637577 TAT CTAT TA- TAT CAT CAT TAT CAT TAT TTT TAT T-T TAC TAT TGT
1 TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * *
4637621 AACT TAA TA- TAT TAG CAT TGT TAT TTT TAT TGT TGT TAT TAT TAT
1 TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
4637666 TAT TAT CAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
4637683 CCATCTTATT
Statistics
Matches: 108, Mismatches: 31, Indels: 22
0.67 0.19 0.14
Matches are distributed among these distances:
2 10 0.09
3 84 0.78
4 13 0.12
5 1 0.01
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:4637569 original size:21 final size:21
Alignment explanation
Indices: 4637528--4637586 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
4637518 TACCCTCATC
* *
4637528 ACTATTATTATCTA-TACTTT
1 ACTATTGTTATCTATTATTTT
*
4637548 ATTATTGTTA-CTTATTATTTT
1 ACTATTGTTATC-TATTATTTT
4637569 ACTATTGTTATCTATTAT
1 ACTATTGTTATCTATTAT
4637587 ATCATCATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 1 0.03
20 10 0.31
21 20 0.62
22 1 0.03
ACGTcount: A:0.27, C:0.10, G:0.03, T:0.59
Consensus pattern (21 bp):
ACTATTGTTATCTATTATTTT
Found at i:4637592 original size:65 final size:65
Alignment explanation
Indices: 4637523--4637644 Score: 147
Period size: 65 Copynumber: 1.9 Consensus size: 65
4637513 GTTATTACCC
* * * * *
4637523 TCATCACTATTATTATCTATACTTTATTATTGTTACTTATTATTTTA-CTATTGTTATCTATTAT
1 TCATCACTATCATTATCTATACTTTACTATTGTAACTTAATATATTAGC-ATTGTTATCTATTAT
4637587 A
65 A
* * * *
4637588 TCATCATTATCATTATTTTTATTTTACTATTGTAACTTAATATATTAGCATTGTTAT
1 TCATCACTATCATTATCTATACTTTACTATTGTAACTTAATATATTAGCATTGTTAT
4637645 TTTTATTGTT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
65 46 0.98
66 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.04, T:0.56
Consensus pattern (65 bp):
TCATCACTATCATTATCTATACTTTACTATTGTAACTTAATATATTAGCATTGTTATCTATTATA
Found at i:4637702 original size:3 final size:3
Alignment explanation
Indices: 4637546--4637682 Score: 57
Period size: 3 Copynumber: 46.0 Consensus size: 3
4637536 TATCTATACT
* * * *
4637546 TTA TTA TTG TTA CTTA TTA TT- TTA CTA TTG TTA TCTA TTA -TA TCA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
* * * * * * *
4637591 TCA TTA TCA TTA TTT TTA TT- TTA CTA TTG TAA CTTA ATA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
** * * * * *
4637635 GCA TTG TTA TTT TTA TTG TTG TTA TTA TTA TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4637683 CCATCTTATT
Statistics
Matches: 96, Mismatches: 31, Indels: 14
0.68 0.22 0.10
Matches are distributed among these distances:
2 8 0.08
3 80 0.83
4 8 0.08
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:4642668 original size:66 final size:66
Alignment explanation
Indices: 4642538--4642761 Score: 213
Period size: 66 Copynumber: 3.4 Consensus size: 66
4642528 GTCAATAGCC
* * * * **
4642538 TCACACGGCTTAGCACATGAGTGTGTGG-TTGGCTGTGTGACACAAGAT-AGTATACCTAGTATT
1 TCACACGGCCTAGCACACGAGCGTGTGGCTTGGCCGTGTGACACAAG-TCAGTATACCTACCATT
4642601 TT
65 TT
* * *
4642603 TCACACGGCCTAGCACACGGGCGTGTGGCTTGGCCGTGTGTCACAAGTCAGTAT-GCTCACCATT
1 TCACACGGCCTAGCACACGAGCGTGTGGCTTGGCCGTGTGACACAAGTCAGTATACCT-ACCATT
4642667 TT
65 TT
* * * * * *
4642669 TC-CCCTGGCCTAGCACACGAGCGTGTGGCTTGACCGTGTGACCCAAGTCAGTAAACTTACTATT
1 TCACAC-GGCCTAGCACACGAGCGTGTGGCTTGGCCGTGTGACACAAGTCAGTATACCTACCATT
4642733 TT
65 TT
*** * *
4642735 GGGCACGGGCTAGGACACGAGCGTGTG
1 TCACACGGCCTAGCACACGAGCGTGTG
4642762 TCCCCATTTT
Statistics
Matches: 130, Mismatches: 23, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
65 29 0.22
66 98 0.75
67 3 0.02
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (66 bp):
TCACACGGCCTAGCACACGAGCGTGTGGCTTGGCCGTGTGACACAAGTCAGTATACCTACCATTT
T
Found at i:4651705 original size:43 final size:43
Alignment explanation
Indices: 4651639--4651784 Score: 147
Period size: 43 Copynumber: 3.4 Consensus size: 43
4651629 CCGAGATGTA
* *
4651639 ATTATATGTAAGACCATGTCTGGGATATTGGCATTGTATTGTG
1 ATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGTG
* *
4651682 ATTACATGTAAGACCATGTCTGGGACATTGGCATCAT-TAAT-CG
1 ATTACATGTAAGACCATGTCTGGGACATTGGCAT--TGTATTGTG
* * * *
4651725 ATTA-AGTGTAAGGCCCTGTCTGGGACAGTGGCATCG-ATATGTG
1 ATTACA-TGTAAGACCATGTCTGGGACATTGGCATTGTAT-TGTG
*
4651768 ATAACATGTAAGACCAT
1 ATTACATGTAAGACCAT
4651785 AAATGGGATA
Statistics
Matches: 83, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 75 0.90
44 4 0.05
45 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.32
Consensus pattern (43 bp):
ATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGTG
Found at i:4660113 original size:27 final size:30
Alignment explanation
Indices: 4660050--4660108 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
4660040 ATCTCAAAAC
*
4660050 TATACATGAATTTTAATTTAATGTGTAATTG
1 TATACATGAATTTTAATTT-AGGTGTAATTG
4660081 TATACATGAACTTTT-ATTT-GGTGTAATT
1 TATACATGAA-TTTTAATTTAGGTGTAATT
4660109 ATACACGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 8 0.31
31 14 0.54
32 4 0.15
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (30 bp):
TATACATGAATTTTAATTTAGGTGTAATTG
Found at i:4660685 original size:31 final size:29
Alignment explanation
Indices: 4660606--4660685 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
4660596 AAATTGTATC
*
4660606 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATC-AAAGTTCATGTATAAAATTGCACA
* * *
4660636 AAATCAAAGTTTACGTATATAATTGCACA
1 AAATCAAAGTTCATGTATAAAATTGCACA
*
4660665 TTAAATCATAGTTCATGTATA
1 --AAATCAAAGTTCATGTATA
4660686 GTTTTGGGAT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 20 0.49
30 5 0.12
31 16 0.39
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (29 bp):
AAATCAAAGTTCATGTATAAAATTGCACA
Found at i:4661337 original size:70 final size:67
Alignment explanation
Indices: 4661217--4661349 Score: 176
Period size: 70 Copynumber: 1.9 Consensus size: 67
4661207 ATAAACAATA
* *
4661217 TAATGATTTTGCCTTTTAACTTAATAAGTAAACATTTATCAAAACAACGTAGATTTGCCTTTTAA
1 TAATGATTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAACAACGTAGATTTGCCTTTTAA
4661282 CT
66 CT
* ** * *
4661284 TAATGGTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATCAAAATGACGTAGTTTTTCCTTT
1 TAATGATTTTGACTTTTAAC-TTA-AAAA-GTAAACATTTATCAAAACAACGTAGATTTGCCTTT
4661349 T
63 T
4661350 CTTATTCAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
67 18 0.32
68 3 0.05
69 3 0.05
70 32 0.57
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (67 bp):
TAATGATTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAACAACGTAGATTTGCCTTTTAA
CT
Found at i:4662729 original size:18 final size:17
Alignment explanation
Indices: 4662702--4662748 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 17
4662692 CGATGACCGG
4662702 CCCCTTGGCCGAATTTT
1 CCCCTTGGCCGAATTTT
4662719 CCCCGTTGGCCGAATTTT
1 CCCC-TTGGCCGAATTTT
4662737 CCCCCTTGGCCG
1 -CCCCTTGGCCG
4662749 GAGCTCCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.14
18 20 0.71
19 4 0.14
ACGTcount: A:0.09, C:0.40, G:0.21, T:0.30
Consensus pattern (17 bp):
CCCCTTGGCCGAATTTT
Found at i:4663519 original size:21 final size:19
Alignment explanation
Indices: 4663483--4663531 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 19
4663473 TCTTCTGTAC
4663483 TATTATATATATTTTCTAA
1 TATTATATATATTTTCTAA
4663502 TATTACTATATATATTTCTAA
1 TATTA-TATATAT-TTTCTAA
4663523 TA-TATATAT
1 TATTATATAT
4663532 TAAAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.36
20 9 0.32
21 9 0.32
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTATATATATTTTCTAA
Found at i:4663724 original size:22 final size:24
Alignment explanation
Indices: 4663673--4663733 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 24
4663663 TTTTGCTATT
*
4663673 TCATATATATTTTTAAATACCATAA
1 TCATTTATATTTTT-AATACCATAA
*
4663698 T-ATTTATATTTTT-ATACCAT-C
1 TCATTTATATTTTTAATACCATAA
4663719 TCATTTATATGTTTT
1 TCATTTATAT-TTTT
4663734 TATGTTATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 1 0.03
22 15 0.47
23 4 0.12
24 11 0.34
25 1 0.03
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.54
Consensus pattern (24 bp):
TCATTTATATTTTTAATACCATAA
Found at i:4667738 original size:44 final size:44
Alignment explanation
Indices: 4667675--4667764 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
4667665 AAATTGTACT
* * * * *
4667675 TTAAATTCTAATTATTTTTAAATGTGTAGTTATCACAACTTCTA
1 TTAAATTATAAATATTTTTAAACGTATAATTATCACAACTTCTA
4667719 TTAAATTATAAATATTTTTAAACGTATAATTATCACAACTTCTA
1 TTAAATTATAAATATTTTTAAACGTATAATTATCACAACTTCTA
4667763 TT
1 TT
4667765 TTATTTTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (44 bp):
TTAAATTATAAATATTTTTAAACGTATAATTATCACAACTTCTA
Found at i:4669971 original size:32 final size:32
Alignment explanation
Indices: 4669935--4669999 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
4669925 TGTATGCATT
4669935 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
4669967 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
4669999 T
1 T
4670000 GGTAAGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATGGGCA
Found at i:4671509 original size:26 final size:26
Alignment explanation
Indices: 4671480--4671532 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
4671470 TTTACAGTTT
4671480 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
4671506 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
4671532 T
1 T
4671533 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:4685651 original size:35 final size:35
Alignment explanation
Indices: 4685583--4685653 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
4685573 CGTCGTGCCC
4685583 AGCGTCGTGCCCACGACTCCAGCCGCGACAGAATA
1 AGCGTCGTGCCCACGACTCCAGCCGCGACAGAATA
*
4685618 AGCGTCGTGCCCACGACTCCAGCCGTGACAGAATA
1 AGCGTCGTGCCCACGACTCCAGCCGCGACAGAATA
4685653 A
1 A
4685654 AAAGAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.27, C:0.35, G:0.25, T:0.13
Consensus pattern (35 bp):
AGCGTCGTGCCCACGACTCCAGCCGCGACAGAATA
Found at i:4686391 original size:8 final size:8
Alignment explanation
Indices: 4686387--4686492 Score: 72
Period size: 8 Copynumber: 12.5 Consensus size: 8
4686377 AACTTTTTTA
*
4686387 TTTTTATT
1 TTTTTCTT
*
4686395 TTTTAACTT
1 TTTT-TCTT
4686404 TTTTTCTCT
1 TTTTTCT-T
*
4686413 CTTTTCTT
1 TTTTTCTT
4686421 TTTTTCTT
1 TTTTTCTT
4686429 TTTTTCTTT
1 TTTTTC-TT
4686438 TTTTTCGAATT
1 TTTTTC---TT
4686449 ATTTCTTCTT
1 -TTT-TTCTT
*
4686459 TTTTT-TG
1 TTTTTCTT
4686466 TTTTT-TT
1 TTTTTCTT
*
4686473 TTTTGCTT
1 TTTTTCTT
*
4686481 TTTTTGTT
1 TTTTTCTT
4686489 TTTT
1 TTTT
4686493 GTTTTGCTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
7 11 0.14
8 34 0.43
9 24 0.30
10 2 0.03
11 2 0.03
12 3 0.04
13 3 0.04
ACGTcount: A:0.06, C:0.10, G:0.04, T:0.80
Consensus pattern (8 bp):
TTTTTCTT
Found at i:4686436 original size:21 final size:20
Alignment explanation
Indices: 4686401--4686527 Score: 85
Period size: 21 Copynumber: 6.0 Consensus size: 20
4686391 TATTTTTTAA
* *
4686401 CTTTTTTTCTCTCTTTTCTTT
1 CTTTTTTTTTTTCTTTT-TTT
4686422 -TTTTCTTTTTTTCTTTTTTTT
1 CTTTT-TTTTTTTC-TTTTTTT
** * *
4686443 CGAATTATTTCTTCTTTTTTTT
1 C-TTTTTTTTTTTC-TTTTTTT
*
4686465 GTTTTTTTTTTTGCTTTTTTT
1 CTTTTTTTTTTT-CTTTTTTT
* *
4686486 GTTTTTTGTTTTGCTTTTTTGT
1 CTTTTTT-TTTTTCTTTTTT-T
*
4686508 CTTTTTTTTTGTCTTTTTTT
1 CTTTTTTTTTTTCTTTTTTT
4686528 TGTGGAACAT
Statistics
Matches: 84, Mismatches: 15, Indels: 15
0.74 0.13 0.13
Matches are distributed among these distances:
20 5 0.06
21 47 0.56
22 30 0.36
23 2 0.02
ACGTcount: A:0.02, C:0.11, G:0.06, T:0.80
Consensus pattern (20 bp):
CTTTTTTTTTTTCTTTTTTT
Found at i:4686474 original size:12 final size:12
Alignment explanation
Indices: 4686457--4686528 Score: 72
Period size: 12 Copynumber: 5.6 Consensus size: 12
4686447 TTATTTCTTC
4686457 TTTTTTTTGTTT
1 TTTTTTTTGTTT
4686469 TTTTTTTTGCTTTTT
1 TTTTTTTTG---TTT
4686484 TTGTTTTTTGTTT
1 TT-TTTTTTGTTT
* *
4686497 TGCTTTTTTGTCT
1 T-TTTTTTTGTTT
*
4686510 TTTTTTTTGTCT
1 TTTTTTTTGTTT
4686522 TTTTTTT
1 TTTTTTT
4686529 GTGGAACATG
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
12 26 0.50
13 14 0.27
15 5 0.10
16 7 0.13
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.85
Consensus pattern (12 bp):
TTTTTTTTGTTT
Found at i:4693883 original size:35 final size:35
Alignment explanation
Indices: 4693844--4693914 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
4693834 CGTCGTGCCC
* *
4693844 AGCGTTGTGCCCACGACTCCAGCCGCGACAGAATA
1 AGCGTCGTGCCCACAACTCCAGCCGCGACAGAATA
*
4693879 AGCGTCGTGCCCACAACTCCAGCCGTGACAGAATA
1 AGCGTCGTGCCCACAACTCCAGCCGCGACAGAATA
4693914 A
1 A
4693915 AAAGAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.28, C:0.34, G:0.24, T:0.14
Consensus pattern (35 bp):
AGCGTCGTGCCCACAACTCCAGCCGCGACAGAATA
Done.