Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 4 of 211
Found at i:1274536 original size:23 final size:23
Alignment explanation
Indices: 1274445--1274539 Score: 75
Period size: 23 Copynumber: 4.1 Consensus size: 23
1274435 GTAAAAATGT
* *
1274445 TGCTCAATTTGGTACGTATATGC
1 TGCTAAATTTGGTATGTATATGC
** * *
1274468 TGC-CCATTTGTTGTGTATATGC
1 TGCTAAATTTGGTATGTATATGC
* * ** *
1274490 TGTTAAATTTTGGTGTAAAAATGC
1 TGCTAAA-TTTGGTATGTATATGC
1274514 TGCTAAATTTGGTATGTATATGC
1 TGCTAAATTTGGTATGTATATGC
1274537 TGC
1 TGC
1274540 CCATTTGTTG
Statistics
Matches: 54, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
22 17 0.31
23 19 0.35
24 18 0.33
ACGTcount: A:0.23, C:0.13, G:0.22, T:0.42
Consensus pattern (23 bp):
TGCTAAATTTGGTATGTATATGC
Found at i:1274555 original size:22 final size:22
Alignment explanation
Indices: 1274404--1274578 Score: 71
Period size: 24 Copynumber: 7.5 Consensus size: 22
1274394 GTACTAACCC
* *
1274404 ATTTGTTGTATATATGCTGTTAA
1 ATTTGGTGTATATATGCTG-CAA
* * * *
1274427 ATTTTGGTGTAAAAATGTTGCTCA
1 A-TTTGGTGTATATATGCTGC-AA
*** **
1274451 ATTTGGTACGTATATGCTGCCC
1 ATTTGGTGTATATATGCTGCAA
* * *
1274473 ATTTGTTGTGTATATGCTGTTAA
1 ATTTGGTGTATATATGCTG-CAA
* *
1274496 ATTTTGGTGTAAAAATGCTGCTAA
1 A-TTTGGTGTATATATGCTGC-AA
* * **
1274520 ATTTGGTATGTATATGCTGCCC
1 ATTTGGTGTATATATGCTGCAA
* *
1274542 ATTTGTTGTATATAAGCTGTCCAA
1 ATTTGGTGTATATATGCTG--CAA
1274566 ATTTTGGTGTATA
1 A-TTTGGTGTATA
1274579 AATGTTGTTT
Statistics
Matches: 107, Mismatches: 37, Indels: 14
0.68 0.23 0.09
Matches are distributed among these distances:
22 32 0.30
23 30 0.28
24 35 0.33
25 10 0.09
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (22 bp):
ATTTGGTGTATATATGCTGCAA
Found at i:1274624 original size:23 final size:22
Alignment explanation
Indices: 1274548--1274635 Score: 68
Period size: 23 Copynumber: 3.7 Consensus size: 22
1274538 GCCCATTTGT
1274548 TGTATATAAGCTGTCCAAATTTTGG
1 TGTATA-AAGCTGTCCAAA--TTGG
* ** *
1274573 TGTATAAATGTTGTTTAATTTGG
1 TGTATAAA-GCTGTCCAAATTGG
* *
1274596 TATATAAATGCTGTCCAAATTGA
1 TGTATAAA-GCTGTCCAAATTGG
1274619 TGTATAAGAGCTGTCCA
1 TGTATAA-AGCTGTCCA
1274636 GACAAGGTAG
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
23 35 0.70
24 3 0.06
25 12 0.24
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (22 bp):
TGTATAAAGCTGTCCAAATTGG
Found at i:1288988 original size:15 final size:15
Alignment explanation
Indices: 1288968--1288998 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1288958 ATATATTATT
1288968 AAATTTTAGTACTAA
1 AAATTTTAGTACTAA
*
1288983 AAATTTTAGTATTAA
1 AAATTTTAGTACTAA
1288998 A
1 A
1288999 TTTTAGCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (15 bp):
AAATTTTAGTACTAA
Found at i:1288996 original size:28 final size:28
Alignment explanation
Indices: 1288963--1289029 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
1288953 GTAATATATA
1288963 TTATTAAATTTTAG-TACTAAA-AATTT
1 TTATTAAATTTTAGCTACTAAATAATTT
**
1288989 TAGTATTAAATTTTAGCTTTTAAATAATTT
1 T--TATTAAATTTTAGCTACTAAATAATTT
1289019 TTATTAAATTT
1 TTATTAAATTT
1289030 AATAATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 1 0.03
28 23 0.66
29 5 0.14
30 6 0.17
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (28 bp):
TTATTAAATTTTAGCTACTAAATAATTT
Found at i:1289013 original size:14 final size:13
Alignment explanation
Indices: 1288964--1289004 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
1288954 TAATATATAT
1288964 TATTAAATTTTAG
1 TATTAAATTTTAG
*
1288977 TACTAAAAATTTTAG
1 TA-T-TAAATTTTAG
1288992 TATTAAATTTTAG
1 TATTAAATTTTAG
1289005 CTTTTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 11 0.46
14 2 0.08
15 11 0.46
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (13 bp):
TATTAAATTTTAG
Found at i:1290572 original size:18 final size:19
Alignment explanation
Indices: 1290546--1290585 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1290536 TAATATATAT
1290546 AATACATATTTGATTAAAA
1 AATACATATTTGATTAAAA
*
1290565 ATATATATATTTGATTAAAA
1 A-ATACATATTTGATTAAAA
1290585 A
1 A
1290586 TAAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (19 bp):
AATACATATTTGATTAAAA
Found at i:1290594 original size:20 final size:20
Alignment explanation
Indices: 1290551--1290594 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1290541 TATATAATAC
* *
1290551 ATATTTGATTAAAAATATAT
1 ATATTTGATTAAAAATAAAA
1290571 ATATTTGATTAAAAATAAAA
1 ATATTTGATTAAAAATAAAA
1290591 ATAT
1 ATAT
1290595 ATATATTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
ATATTTGATTAAAAATAAAA
Found at i:1290596 original size:26 final size:26
Alignment explanation
Indices: 1290560--1290636 Score: 120
Period size: 26 Copynumber: 3.0 Consensus size: 26
1290550 CATATTTGAT
1290560 TAAAAATATATATATTTGATTAAAAA
1 TAAAAATATATATATTTGATTAAAAA
*
1290586 TAAAAATATATATATTTGATTAAGAA
1 TAAAAATATATATATTTGATTAAAAA
*
1290612 TAAAAA-ATATATATTTAATATAAAA
1 TAAAAATATATATATTTGAT-TAAAA
1290637 TTCGAGCCGG
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
25 12 0.26
26 35 0.74
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (26 bp):
TAAAAATATATATATTTGATTAAAAA
Found at i:1293360 original size:25 final size:23
Alignment explanation
Indices: 1293331--1293384 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
1293321 TTTAAAGATT
1293331 TAAAAGAAGAAAATAATTTATATAG
1 TAAAA-AAGAAAA-AATTTATATAG
**
1293356 TAAAAAAGCCAAAATTTATAT-G
1 TAAAAAAGAAAAAATTTATATAG
1293378 ATAAAAA
1 -TAAAAA
1293385 TCACCTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 1 0.04
23 15 0.58
24 5 0.19
25 5 0.19
ACGTcount: A:0.61, C:0.04, G:0.09, T:0.26
Consensus pattern (23 bp):
TAAAAAAGAAAAAATTTATATAG
Found at i:1298517 original size:19 final size:21
Alignment explanation
Indices: 1298488--1298531 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
1298478 TTTATTAAAC
1298488 TAAAAACAATTAATA-AAATT
1 TAAAAACAATTAATATAAATT
*
1298508 TAAAAA-AATTCATATAAATT
1 TAAAAACAATTAATATAAATT
1298528 TAAA
1 TAAA
1298532 TTATGTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (21 bp):
TAAAAACAATTAATATAAATT
Found at i:1300204 original size:2 final size:2
Alignment explanation
Indices: 1300197--1300223 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1300187 GGGTCTGCCC
1300197 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1300224 AGGGTGTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1300518 original size:18 final size:17
Alignment explanation
Indices: 1300497--1300531 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1300487 TTATTATTAA
*
1300497 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
1300515 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
1300532 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:1300585 original size:157 final size:158
Alignment explanation
Indices: 1300384--1300697 Score: 515
Period size: 157 Copynumber: 2.0 Consensus size: 158
1300374 TAGAATATTT
* *
1300384 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAAATTATTA
1 TTAGCAGAAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAAATTATTA
* * * * *
1300449 TTATCAATAATAAATAATTT-AATCAT-ATTTAAACATAATTATTATTAAATATATTTTAATTAA
66 ATATCAACAATAAATAATTTAAAACATAATTT-AACATAATTATTATTAAATATAATTTAATAAA
1300512 AATATATAATTTAATAAAATTCTTAATAA
130 AATATATAATTTAATAAAATTCTTAATAA
* *
1300541 TTAGCAGAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAAATTATTA
*
1300606 ATATCAACAATAAATAATTTAAAAGATAATTTAACATAATTATTATTAAATATAATTTAATAAAA
66 ATATCAACAATAAATAATTTAAAACATAATTTAACATAATTATTATTAAATATAATTTAATAAAA
1300671 ATATATAATTTAATAAAATTCTTAATA
131 ATATATAATTTAATAAAATTCTTAATA
1300698 TTAAATATTC
Statistics
Matches: 145, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
157 79 0.54
158 62 0.43
159 4 0.03
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (158 bp):
TTAGCAGAAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAAATTATTA
ATATCAACAATAAATAATTTAAAACATAATTTAACATAATTATTATTAAATATAATTTAATAAAA
ATATATAATTTAATAAAATTCTTAATAA
Found at i:1300730 original size:19 final size:18
Alignment explanation
Indices: 1300655--1300810 Score: 77
Period size: 18 Copynumber: 8.0 Consensus size: 18
1300645 TTATTATTAA
*
1300655 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAATT
1300673 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAATT
* ***
1300691 CT-TAATATTAAATATTCTT
1 ATATAAT-TT-AATAAAATT
1300710 ATATGAATTTAATAAAATT
1 ATAT-AATTTAATAAAATT
* *
1300729 ATA-ATATATAATACTATAA-A
1 ATATA-ATTTAATA--A-AATT
1300749 ATATAATTTAAAATAATTATTATT
1 ATATAATTT--AATAA--A--ATT
1300773 AAATATAATTTAATAGAAA-T
1 --ATATAATTTAATA-AAATT
1300793 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAATT
1300811 CTTAATATTT
Statistics
Matches: 106, Mismatches: 13, Indels: 38
0.68 0.08 0.24
Matches are distributed among these distances:
17 8 0.08
18 41 0.39
19 16 0.15
20 12 0.11
21 9 0.08
22 4 0.04
23 2 0.02
24 4 0.04
25 1 0.01
26 9 0.08
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (18 bp):
ATATAATTTAATAAAATT
Found at i:1300757 original size:120 final size:120
Alignment explanation
Indices: 1300625--1301165 Score: 917
Period size: 120 Copynumber: 4.5 Consensus size: 120
1300615 ATAAATAATT
* *
1300625 TAAAAGATAATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
1 TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
* * *
1300690 TCTTAATATTAAATATTCTTATATGAATTTAATAAAATTATAATATATAATACTA
66 TCTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTA
*
1300745 TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAGAAATATATAATTTAATAAAAT
1 TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
1300810 TCTTAATATTTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTA
66 TCTTAATA-TTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTA
1300866 TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
1 TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
*
1300931 TTTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTA
66 TCTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTA
* *
1300986 TAAAATATAATTTAAAATAATTATTATTAAAAATATAATTTAGTAAAAATATTTAATTTAATAAA
1 TAAAATATAATTTAAAATAATTATTATT--AAATATAATTTAATAAAAATATATAATTTAATAAA
*
1301051 ATTATTTAATATTAAATATTCTT--A-GAATTTACTAAAATCATAATATATAATACTA
64 ATT-CTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTA
* *
1301106 TAAAATATAATTTAAATTAATTATTTTTAAATATAATTTAATAAAAATATATAATTTAAT
1 TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAAT
1301166 CAAACCATTA
Statistics
Matches: 403, Mismatches: 14, Indels: 10
0.94 0.03 0.02
Matches are distributed among these distances:
118 30 0.07
120 202 0.50
121 116 0.29
122 36 0.09
123 19 0.05
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (120 bp):
TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
TCTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTA
Found at i:1300763 original size:22 final size:23
Alignment explanation
Indices: 1300721--1300763 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1300711 TATGAATTTA
*
1300721 ATAAAATTATAATATATAATACT
1 ATAAAATTATAATATAAAATACT
*
1300744 ATAAAA-TATAATTTAAAATA
1 ATAAAATTATAATATAAAATA
1300764 ATTATTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
ATAAAATTATAATATAAAATACT
Found at i:1300895 original size:241 final size:239
Alignment explanation
Indices: 1300625--1301165 Score: 915
Period size: 241 Copynumber: 2.3 Consensus size: 239
1300615 ATAAATAATT
* *
1300625 TAAAAGATAATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
1 TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
* *
1300690 TCTTAATATTAAATATTCTTATATGAATTTAATAAAATTATAATATATAATACTATAAAATATAA
66 TCTTAATATTAAATATTCTTAAATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
*
1300755 TTTAAAATAATTATTATT-AAATATAATTTAATAGAAATATATAATTTAATAAAATT-CTTAATA
131 TTTAAAATAATTATTATTAAAATATAATTTAATAAAAATATATAATTTAATAAAATTACTTAATA
1300818 TTTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTA
196 -TTAAATATTCTT--A-GAATTTACTAAAATCATAATATATAATACTA
1300866 TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
1 TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
* *
1300931 TTTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 TCTTAATATTAAATATTCTTAAATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
* * *
1300996 TTTAAAATAATTATTATTAAAAATATAATTTAGTAAAAATATTTAATTTAATAAAATTATTTAAT
131 TTTAAAATAATTATTATT-AAAATATAATTTAATAAAAATATATAATTTAATAAAATTACTTAAT
1301061 ATTAAATATTCTTAGAATTTACTAAAATCATAATATATAATACTA
195 ATTAAATATTCTTAGAATTTACTAAAATCATAATATATAATACTA
* *
1301106 TAAAATATAATTTAAATTAATTATTTTTAAATATAATTTAATAAAAATATATAATTTAAT
1 TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAAT
1301166 CAAACCATTA
Statistics
Matches: 285, Mismatches: 12, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
240 89 0.31
241 143 0.50
243 47 0.16
244 6 0.02
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (239 bp):
TAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
TCTTAATATTAAATATTCTTAAATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
TTTAAAATAATTATTATTAAAATATAATTTAATAAAAATATATAATTTAATAAAATTACTTAATA
TTAAATATTCTTAGAATTTACTAAAATCATAATATATAATACTA
Found at i:1300998 original size:66 final size:64
Alignment explanation
Indices: 1300923--1301151 Score: 187
Period size: 64 Copynumber: 3.7 Consensus size: 64
1300913 TATATAATTT
1300923 AATAAAATTTTTAATATTAAATATTCTTAAAT-GAATTTACTAAAATCATAATATATAATACTAT
1 AATAAAA--TTTAA-ATTAAATATTCTTAAATAGAATTTACTAAAATCATAATATATAATACTAT
1300987 AA
63 AA
* * * * * * *
1300989 AATATAATTTAAAATAATTATTATTAAAAATATAATTTAGTAAAA--AT-AT-T-TAAT-TTAAT
1 AATAAAATTTAAATTAAATATTCTT--AAATAGAATTTACTAAAATCATAATATATAATACT-AT
1301048 AA
63 AA
*
1301050 AAT--TATTTAATATTAAATATTC-T---TAGAATTTACTAAAATCATAATATATAATACTATAA
1 AATAAAATTTAA-ATTAAATATTCTTAAATAGAATTTACTAAAATCATAATATATAATACTATAA
* * * * *
1301109 AATATAATTTAAATTAATTATTTTTAAATATAATTTAATAAAA
1 AATAAAATTTAAATTAAATATTCTTAAATAGAATTTACTAAAA
1301152 ATATATAATT
Statistics
Matches: 127, Mismatches: 19, Indels: 36
0.70 0.10 0.20
Matches are distributed among these distances:
54 13 0.10
56 2 0.02
57 2 0.02
58 1 0.01
59 18 0.14
60 19 0.15
61 18 0.14
62 1 0.01
63 12 0.09
64 20 0.16
65 4 0.03
66 17 0.13
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (64 bp):
AATAAAATTTAAATTAAATATTCTTAAATAGAATTTACTAAAATCATAATATATAATACTATAA
Found at i:1301056 original size:18 final size:18
Alignment explanation
Indices: 1301013--1301065 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
1301003 TAATTATTAT
*
1301013 TAAAAATA--TAATTTAG
1 TAAAAATATTTAATTTAA
1301029 TAAAAATATTTAATTTAA
1 TAAAAATATTTAATTTAA
*
1301047 TAAAATTATTTAATATTAA
1 TAAAAATATTTAAT-TTAA
1301066 ATATTCTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
16 8 0.25
18 20 0.62
19 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TAAAAATATTTAATTTAA
Found at i:1304921 original size:4 final size:4
Alignment explanation
Indices: 1304912--1304937 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1304902 TGAAAATATA
1304912 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
1304938 TTACAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:1311644 original size:31 final size:32
Alignment explanation
Indices: 1311609--1311673 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
1311599 TATTGCTTGG
*
1311609 TTGGTACCTGAT-TTTAATTTTAATGTTC-ATT
1 TTGGTACCTG-TGATTAATTTTAATGTTCAATT
* *
1311640 TTGGTATCTGTGATTAGTTTTAATGTTCAATT
1 TTGGTACCTGTGATTAATTTTAATGTTCAATT
1311672 TT
1 TT
1311674 CGTTTTCCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 1 0.03
31 23 0.79
32 5 0.17
ACGTcount: A:0.22, C:0.08, G:0.15, T:0.55
Consensus pattern (32 bp):
TTGGTACCTGTGATTAATTTTAATGTTCAATT
Found at i:1311850 original size:22 final size:22
Alignment explanation
Indices: 1311816--1311857 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1311806 AATTTAAACA
* *
1311816 AAAAAAATTAAATATCAAATTG
1 AAAAAAATCAAATACCAAATTG
*
1311838 AAAAAACTCAAATACCAAAT
1 AAAAAAATCAAATACCAAAT
1311858 CTAATATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAAAAATCAAATACCAAATTG
Found at i:1311898 original size:31 final size:31
Alignment explanation
Indices: 1311841--1311907 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
1311831 CAAATTGAAA
* *
1311841 AAACTCAAATACCAAATCTAATATT-AAATC
1 AAACTAAAATACCAAATCTAACATTAAAATC
*
1311871 TAAACTAAAATACTAAAT-TAAACATTAAAATC
1 -AAACTAAAATACCAAATCT-AACATTAAAATC
1311903 AAACT
1 AAACT
1311908 CTTAAAATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 1 0.03
31 25 0.81
32 5 0.16
ACGTcount: A:0.57, C:0.16, G:0.00, T:0.27
Consensus pattern (31 bp):
AAACTAAAATACCAAATCTAACATTAAAATC
Found at i:1319169 original size:17 final size:17
Alignment explanation
Indices: 1319127--1319161 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1319117 AAATATTATG
1319127 AAATAAAAAAAGTTTAA
1 AAATAAAAAAAGTTTAA
*
1319144 AAATAAAAATAGTTTAA
1 AAATAAAAAAAGTTTAA
1319161 A
1 A
1319162 TCTAAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (17 bp):
AAATAAAAAAAGTTTAA
Found at i:1322663 original size:17 final size:17
Alignment explanation
Indices: 1322633--1322670 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1322623 ATTTGATTTG
1322633 TTAT-TATCGCATAGAA
1 TTATATATCGCATAGAA
*
1322649 TTATATATCGTATAGAA
1 TTATATATCGCATAGAA
1322666 TTATA
1 TTATA
1322671 CAAAGTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (17 bp):
TTATATATCGCATAGAA
Found at i:1333767 original size:16 final size:15
Alignment explanation
Indices: 1333748--1333778 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1333738 ATAATATAAT
1333748 ATATATATATATGTGC
1 ATATATAT-TATGTGC
1333764 ATATATATTATGTGC
1 ATATATATTATGTGC
1333779 TCTTATTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (15 bp):
ATATATATTATGTGC
Found at i:1351561 original size:13 final size:13
Alignment explanation
Indices: 1351543--1351568 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1351533 TGACTTTGCA
1351543 CGCTGAAATAGAC
1 CGCTGAAATAGAC
1351556 CGCTGAAATAGAC
1 CGCTGAAATAGAC
1351569 AATCCCAACC
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:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (13 bp):
CGCTGAAATAGAC
Found at i:1357832 original size:19 final size:18
Alignment explanation
Indices: 1357808--1357847 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
1357798 TAAATGGTAG
1357808 CAAAACAGTGAGAAAAT-AA
1 CAAAACAGT-A-AAAATCAA
1357827 CAAAACAGTAAAAATCAA
1 CAAAACAGTAAAAATCAA
1357845 CAA
1 CAA
1357848 GAAAACAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 6 0.30
19 9 0.45
ACGTcount: A:0.65, C:0.15, G:0.10, T:0.10
Consensus pattern (18 bp):
CAAAACAGTAAAAATCAA
Found at i:1358163 original size:36 final size:36
Alignment explanation
Indices: 1358123--1358195 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
1358113 GACTTATAGG
1358123 TCAACGAAAAATAAGCTTTTTTCCTTGTAAAATGAC
1 TCAACGAAAAATAAGCTTTTTTCCTTGTAAAATGAC
*
1358159 TCAACGAAAAATAAGCTTTTTTCTTTGTAAAATGAC
1 TCAACGAAAAATAAGCTTTTTTCCTTGTAAAATGAC
1358195 T
1 T
1358196 TACTCTTTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (36 bp):
TCAACGAAAAATAAGCTTTTTTCCTTGTAAAATGAC
Found at i:1360161 original size:29 final size:31
Alignment explanation
Indices: 1360119--1360192 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 31
1360109 ACAAAACGAT
* *
1360119 AACATAAGCGACTAAAACGTAATAT-A-TCA
1 AACATAAGTGACTAAAACGAAATATAAGTCA
* *
1360148 AACATAAGTGACTAAAATGAAATCTAAGTCA
1 AACATAAGTGACTAAAACGAAATATAAGTCA
*
1360179 AACAAAAGTGACTA
1 AACATAAGTGACTA
1360193 TTTTTATAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 21 0.55
30 1 0.03
31 16 0.42
ACGTcount: A:0.53, C:0.15, G:0.12, T:0.20
Consensus pattern (31 bp):
AACATAAGTGACTAAAACGAAATATAAGTCA
Found at i:1361292 original size:350 final size:350
Alignment explanation
Indices: 1360646--1361324 Score: 1180
Period size: 350 Copynumber: 1.9 Consensus size: 350
1360636 TTTATAGGGG
1360646 TTTCATTTTTTCTATAATTTATTTTTGAGAAATATGTAAAATGTGGCTTCAAATTTGAAGTTTGG
1 TTTCATTTTTTCTATAATTTATTTTTGAGAAATATGTAAAATGTGGCTTCAAATTTGAAGTTTGG
* *
1360711 GGTAGAATGTATCTTTTTTTAGAGCTACAAAGTTACGTATTTTGGGTTTTTGGTAAGGTAAAAAG
66 GGTAGAATGTATCTTTTTATAGAGCTACAAAGTTACGCATTTTGGGTTTTTGGTAAGGTAAAAAG
1360776 ATGGAAAGTTTTGATGGGTTCATTTCATATTAATTTGGGTCTTTGAGGAATTTCTTCATACATTT
131 ATGGAAAGTTTTGATGGGTTCATTTCATATTAATTTGGGTCTTTGAGGAATTTCTTCATACATTT
*
1360841 ATCGAGCAACACTTTTTAACCACAGTTTGACCGCTTTAGTTCATCTCCTTGACTTCAATTTTGTG
196 ATCGAGCAACACTTTTTAACCACAGTTTGACCGCTTTAGTTCATCTCCTTGACTTCAAGTTTGTG
* * *
1360906 AATTAAATATTTTCTTAAAGCAGAATGTGTGTTATTATGTATGTTTTGAGTAAGTCCCTGATTCA
261 AATTAAATATGTTCTTAAAGCACAATGTGAGTTATTATGTATGTTTTGAGTAAGTCCCTGATTCA
1360971 TTTTGCCTGTATGTTTAAGGTTTCT
326 TTTTGCCTGTATGTTTAAGGTTTCT
* * *
1360996 TTTCATTTTTTCTGTAATTTATTTTTGGGAAATATGTAAAATGTGGCTTCATATTTGAAGTTTGG
1 TTTCATTTTTTCTATAATTTATTTTTGAGAAATATGTAAAATGTGGCTTCAAATTTGAAGTTTGG
* * *
1361061 GGTGGAATGTAT-TTTTTCATAGAGCTACAAAGTTAGGCATTTTGGGTTTTTGGTAAGGTAAAGA
66 GGTAGAATGTATCTTTTT-ATAGAGCTACAAAGTTACGCATTTTGGGTTTTTGGTAAGGTAAAAA
1361125 GATGGAAAGTTTTGATGGGTTCATTTCATATTAATTTGGGTCTTTGAGGAATTTCTTCATACATT
130 GATGGAAAGTTTTGATGGGTTCATTTCATATTAATTTGGGTCTTTGAGGAATTTCTTCATACATT
* * * * * *
1361190 TATCGTGCAACATTTTTTTACCACAGTTTGACTGCTTTAGTTCATTTTCTTGACTTCAAGTTTGT
195 TATCGAGCAACACTTTTTAACCACAGTTTGACCGCTTTAGTTCATCTCCTTGACTTCAAGTTTGT
1361255 GAATTAAATATGTTCTTAAAGCACAATGTGAGTTATTATGTATGTTTTGAGTAAGTCCCTGATTC
260 GAATTAAATATGTTCTTAAAGCACAATGTGAGTTATTATGTATGTTTTGAGTAAGTCCCTGATTC
1361320 ATTTT
325 ATTTT
1361325 TGCTTTCTGC
Statistics
Matches: 310, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
349 5 0.02
350 305 0.98
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (350 bp):
TTTCATTTTTTCTATAATTTATTTTTGAGAAATATGTAAAATGTGGCTTCAAATTTGAAGTTTGG
GGTAGAATGTATCTTTTTATAGAGCTACAAAGTTACGCATTTTGGGTTTTTGGTAAGGTAAAAAG
ATGGAAAGTTTTGATGGGTTCATTTCATATTAATTTGGGTCTTTGAGGAATTTCTTCATACATTT
ATCGAGCAACACTTTTTAACCACAGTTTGACCGCTTTAGTTCATCTCCTTGACTTCAAGTTTGTG
AATTAAATATGTTCTTAAAGCACAATGTGAGTTATTATGTATGTTTTGAGTAAGTCCCTGATTCA
TTTTGCCTGTATGTTTAAGGTTTCT
Found at i:1380479 original size:43 final size:43
Alignment explanation
Indices: 1380414--1380500 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
1380404 TCATCACCTA
* *
1380414 TTTGGTTTAAAGAATTTGTTTTTAATGATTTTTTTTATAATTTT
1 TTTGGTTTAAAGAATTTATTTTTAATGATTCTTTTTAT-ATTTT
*
1380458 TTTGG-TTAAAGAATTTATTTTTAATGGTTCTTTTTATATTTT
1 TTTGGTTTAAAGAATTTATTTTTAATGATTCTTTTTATATTTT
1380500 T
1 T
1380501 AAAATTTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 6 0.15
43 29 0.73
44 5 0.12
ACGTcount: A:0.24, C:0.01, G:0.11, T:0.63
Consensus pattern (43 bp):
TTTGGTTTAAAGAATTTATTTTTAATGATTCTTTTTATATTTT
Found at i:1385208 original size:17 final size:16
Alignment explanation
Indices: 1385182--1385219 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1385172 AAATTTTCAT
*
1385182 ATAATCTTTTTATAAAA
1 ATAAT-TTTTTTTAAAA
1385199 ATAATTTTTTTTAAAA
1 ATAATTTTTTTTAAAA
1385215 A-AATT
1 ATAATT
1385220 AGCCCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 11 0.55
17 5 0.25
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
ATAATTTTTTTTAAAA
Found at i:1385449 original size:20 final size:20
Alignment explanation
Indices: 1385426--1385603 Score: 80
Period size: 20 Copynumber: 8.9 Consensus size: 20
1385416 TAAAGTATTT
1385426 AAAAATATATAAAAATTGTA
1 AAAAATATATAAAAATTGTA
* *
1385446 AAAAATA-AT-TAAATTATA
1 AAAAATATATAAAAATTGTA
* * *
1385464 AAAAA-A-ATCAAATACTGTT
1 AAAAATATAT-AAAAATTGTA
* * * * *
1385483 AACAGTATTTTAAATTTGTA
1 AAAAATATATAAAAATTGTA
*
1385503 AAAAATATTATTAAAAATTATA
1 AAAAATA-TA-TAAAAATTGTA
* * **
1385525 AAACATTATTTAAATTTTGTA
1 AAA-AATATATAAAAATTGTA
* *
1385546 AAAATTAT-TAAAAATTGCA
1 AAAAATATATAAAAATTGTA
* *
1385565 AATAAT-TATTAAAAGTTGTA
1 AAAAATATA-TAAAAATTGTA
* *
1385585 AAAATTATTTAAAAATTGT
1 AAAAATATATAAAAATTGT
1385604 GAACCAATAG
Statistics
Matches: 111, Mismatches: 37, Indels: 20
0.66 0.22 0.12
Matches are distributed among these distances:
17 3 0.03
18 13 0.12
19 21 0.19
20 45 0.41
21 14 0.13
22 12 0.11
23 3 0.03
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (20 bp):
AAAAATATATAAAAATTGTA
Found at i:1385476 original size:17 final size:18
Alignment explanation
Indices: 1385438--1385476 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1385428 AAATATATAA
* *
1385438 AAATTGTAAAAAATAATT
1 AAATTATAAAAAATAATC
1385456 AAATTATAAAAAA-AATC
1 AAATTATAAAAAATAATC
1385473 AAAT
1 AAAT
1385477 ACTGTTAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (18 bp):
AAATTATAAAAAATAATC
Found at i:1385538 original size:12 final size:10
Alignment explanation
Indices: 1385504--1385601 Score: 69
Period size: 10 Copynumber: 9.7 Consensus size: 10
1385494 AAATTTGTAA
1385504 AAAATATTATT
1 AAAA-ATTATT
1385515 AAAAATTA-T
1 AAAAATTATT
1385524 AAAACATTATT
1 AAAA-ATTATT
* *
1385535 -TAAATTTTGT
1 AAAAATTAT-T
1385545 AAAAATTATT
1 AAAAATTATT
**
1385555 AAAAATT-GC
1 AAAAATTATT
1385564 AAATAATTATT
1 AAA-AATTATT
* *
1385575 AAAAGTT-GT
1 AAAAATTATT
1385584 AAAAATTATTT
1 AAAAATTA-TT
1385595 AAAAATT
1 AAAAATT
1385602 GTGAACCAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 16
0.71 0.13 0.17
Matches are distributed among these distances:
9 19 0.28
10 26 0.39
11 22 0.33
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (10 bp):
AAAAATTATT
Found at i:1385573 original size:40 final size:39
Alignment explanation
Indices: 1385491--1385602 Score: 127
Period size: 40 Copynumber: 2.7 Consensus size: 39
1385481 TTAACAGTAT
**
1385491 TTTAAATTTGTAAAAAATATTATTAAAAATTATAAAACATTA
1 TTTAAATTTGT--AAAA-ATTATTAAAAATTGCAAAACATTA
1385533 TTTAAATTTTGTAAAAATTATTAAAAATTGCAAATA-ATTA
1 TTTAAA-TTTGTAAAAATTATTAAAAATTGCAAA-ACATTA
* *
1385573 TTAAAAGTTGTAAAAATTATTTAAAAATTG
1 TTTAAATTTGTAAAAATTA-TTAAAAATTG
1385603 TGAACCAATA
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
39 12 0.19
40 35 0.56
41 5 0.08
42 6 0.10
43 5 0.08
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (39 bp):
TTTAAATTTGTAAAAATTATTAAAAATTGCAAAACATTA
Found at i:1385819 original size:10 final size:10
Alignment explanation
Indices: 1385804--1385881 Score: 59
Period size: 10 Copynumber: 7.7 Consensus size: 10
1385794 TGATTATTTC
1385804 TAATTTTTAA
1 TAATTTTTAA
1385814 TAATTTTTAA
1 TAATTTTTAA
* ** *
1385824 CAAAAATTAAA
1 -TAATTTTTAA
*
1385835 TAATGTTTAA
1 TAATTTTTAA
*
1385845 TGATTTTTAA
1 TAATTTTTAA
1385855 TAACTTTTTAA
1 TAA-TTTTTAA
* *
1385866 AAATTTTAAA
1 TAATTTTTAA
1385876 T-ATTTT
1 TAATTTT
1385882 AAACAATATT
Statistics
Matches: 52, Mismatches: 14, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
9 5 0.10
10 32 0.62
11 15 0.29
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:1385871 original size:21 final size:20
Alignment explanation
Indices: 1385805--1385913 Score: 69
Period size: 21 Copynumber: 5.3 Consensus size: 20
1385795 GATTATTTCT
*
1385805 AATTTTTAATAATTTTTAACA
1 AATTTTAAATAATTTTTAA-A
** * *
1385826 AAAATTAAATAATGTTTAAT
1 AATTTTAAATAATTTTTAAA
* *
1385846 GATTTTTAATAACTTTTTAAA
1 AATTTTAAATAA-TTTTTAAA
*
1385867 AATTTTAAAT-ATTTTAAACA
1 AATTTTAAATAATTTTTAA-A
* *
1385887 ATATTTTATA-AATTATTTATA
1 A-ATTTTAAATAATT-TTTAAA
1385908 AATTTT
1 AATTTT
1385914 CTCCTTTTTT
Statistics
Matches: 66, Mismatches: 17, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
19 6 0.09
20 16 0.24
21 41 0.62
22 3 0.05
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (20 bp):
AATTTTAAATAATTTTTAAA
Found at i:1393661 original size:18 final size:18
Alignment explanation
Indices: 1393638--1393672 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1393628 TTTATAGTAG
1393638 TAAATATATGAAAAATTA
1 TAAATATATGAAAAATTA
* *
1393656 TAAATATTTGAATAATT
1 TAAATATATGAAAAATT
1393673 TTAGTGAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
TAAATATATGAAAAATTA
Found at i:1399138 original size:3 final size:3
Alignment explanation
Indices: 1399130--1399184 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
1399120 CCATATACTC
1399130 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1399178 CTT CTT C
1 CTT CTT C
1399185 AGAAGCTTTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:1403950 original size:28 final size:28
Alignment explanation
Indices: 1403902--1403968 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 28
1403892 GTCCTTGTAT
*
1403902 TATTTGTAACTTGTGTATTTAGTC-ATTG
1 TATTT-TAACTTGTGTATTTAGTCAAATG
*
1403930 TATTTTAACTTG-GTCATTTTATTCAAATG
1 TATTTTAACTTGTGT-A-TTTAGTCAAATG
*
1403959 TATTGTAACT
1 TATTTTAACT
1403969 ATTGAATTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 2 0.06
27 8 0.24
28 11 0.33
29 12 0.36
ACGTcount: A:0.25, C:0.09, G:0.13, T:0.52
Consensus pattern (28 bp):
TATTTTAACTTGTGTATTTAGTCAAATG
Found at i:1405087 original size:27 final size:27
Alignment explanation
Indices: 1405057--1405111 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
1405047 CCATATTATT
1405057 TTTTATTTTTT-TATAATAAAAATTTTA
1 TTTTATTTTTTAT-TAATAAAAATTTTA
* *
1405084 TTTTATTTTTTATTTATTAAAATTTTA
1 TTTTATTTTTTATTAATAAAAATTTTA
1405111 T
1 T
1405112 ATACATGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTATTTTTTATTAATAAAAATTTTA
Found at i:1405200 original size:5 final size:5
Alignment explanation
Indices: 1405190--1405251 Score: 124
Period size: 5 Copynumber: 12.4 Consensus size: 5
1405180 ATGTGTTATA
1405190 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1405240 AATAT AATAT AA
1 AATAT AATAT AA
1405252 ACTTAGAGAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 57 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:1421910 original size:6 final size:6
Alignment explanation
Indices: 1421899--1421932 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1421889 TTTACAAATG
*
1421899 AATTTT AATTTT AATTTT AATTTT -ATTAT AATTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTT
1421933 GAACTCAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
AATTTT
Found at i:1427702 original size:7 final size:7
Alignment explanation
Indices: 1427690--1427714 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1427680 TTTAATTTCC
1427690 TTTTAAA
1 TTTTAAA
1427697 TTTTAAA
1 TTTTAAA
1427704 TTTTAAA
1 TTTTAAA
1427711 TTTT
1 TTTT
1427715 CATTTTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:1430156 original size:31 final size:32
Alignment explanation
Indices: 1430096--1430156 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
1430086 TGAAAAATGA
*
1430096 TTATATTAATTATATATGTTAAATAATTAATT
1 TTATATTAATTATATATATTAAATAATTAATT
* * *
1430128 TTATATTTA-TATTTATATTAAATCATTAA
1 TTATATTAATTATATATATTAAATAATTAA
1430157 CCCAATAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (32 bp):
TTATATTAATTATATATATTAAATAATTAATT
Found at i:1430965 original size:24 final size:24
Alignment explanation
Indices: 1430933--1430978 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1430923 ATTAGAAAGA
1430933 GAGAGAACTCTAGAAGGCAATGAT
1 GAGAGAACTCTAGAAGGCAATGAT
1430957 GAGAGAACTCTAGAAGGCAATG
1 GAGAGAACTCTAGAAGGCAATG
1430979 TTGATATTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.13, G:0.30, T:0.15
Consensus pattern (24 bp):
GAGAGAACTCTAGAAGGCAATGAT
Found at i:1433104 original size:33 final size:32
Alignment explanation
Indices: 1433059--1433217 Score: 104
Period size: 33 Copynumber: 4.8 Consensus size: 32
1433049 CAGTGTTTAT
1433059 ATGTAAGACCATAGTTGGGCTATGGCATTCTG
1 ATGTAAGACCATAGTTGGGCTATGGCATTCTG
** * * * *
1433091 ATGATAAGACCATAACTGAGTTATGGCACTATG
1 ATG-TAAGACCATAGTTGGGCTATGGCATTCTG
* * * * * * *
1433124 AACGTAAGACCATGGTTGGACCATGACAGTGTTTAT
1 -ATGTAAGACCATAGTTGGGCTATGGCA-T-TCT-G
* *
1433160 ATGTAAGACCGTAGTTGGGCTATGGCATTCTA
1 ATGTAAGACCATAGTTGGGCTATGGCATTCTG
*
1433192 ATGATAAGACCAT-GATTGGGTTATGG
1 ATG-TAAGACCATAG-TTGGGCTATGG
1433218 TACTCCGAAT
Statistics
Matches: 92, Mismatches: 28, Indels: 13
0.69 0.21 0.10
Matches are distributed among these distances:
32 7 0.08
33 59 0.64
34 3 0.03
35 23 0.25
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (32 bp):
ATGTAAGACCATAGTTGGGCTATGGCATTCTG
Found at i:1433215 original size:101 final size:101
Alignment explanation
Indices: 1432992--1433217 Score: 344
Period size: 101 Copynumber: 2.2 Consensus size: 101
1432982 TGAATTGACG
* * * * * *
1432992 GATAATACCATAACTAGGTTATGACACTATGAACATAAGACCATGGTTTGATCATGGCAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAACATAAGACCATGGTTGGACCATGACAGTGTTT
*
1433057 ATATGTAAGACCATAGTTGGGCTATGGCATTCTGAT
66 ATATGTAAGACCATAGTTGGGCTATGGCATTCTAAT
* *
1433093 GATAAGACCATAACTGAGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGACAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAACATAAGACCATGGTTGGACCATGACAGTGTTT
*
1433158 ATATGTAAGACCGTAGTTGGGCTATGGCATTCTAAT
66 ATATGTAAGACCATAGTTGGGCTATGGCATTCTAAT
* *
1433194 GATAAGACCATGATTGGGTTATGG
1 GATAAGACCATAACTGGGTTATGG
1433218 TACTCCGAAT
Statistics
Matches: 112, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 112 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (101 bp):
GATAAGACCATAACTGGGTTATGGCACTATGAACATAAGACCATGGTTGGACCATGACAGTGTTT
ATATGTAAGACCATAGTTGGGCTATGGCATTCTAAT
Found at i:1433275 original size:24 final size:24
Alignment explanation
Indices: 1433225--1433275 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1433215 TGGTACTCCG
*
1433225 AATGTAAAGGATGAATTGATGGAA
1 AATGTAAAGGATGAATTGATCGAA
*
1433249 AATGTAAATGATGAATTGA-CGACA
1 AATGTAAAGGATGAATTGATCGA-A
1433273 AAT
1 AAT
1433276 TACCCAAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.47, C:0.04, G:0.24, T:0.25
Consensus pattern (24 bp):
AATGTAAAGGATGAATTGATCGAA
Found at i:1435805 original size:22 final size:22
Alignment explanation
Indices: 1435770--1435819 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1435760 ATATCCAAAC
1435770 AATAATAATAAAAT-AGTAACAA
1 AATAATAATAAAATGA-TAACAA
* * *
1435792 TATAATAGTGAAATGATAACAA
1 AATAATAATAAAATGATAACAA
1435814 AATAAT
1 AATAAT
1435820 GAAAAACAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.26
Consensus pattern (22 bp):
AATAATAATAAAATGATAACAA
Found at i:1437405 original size:17 final size:15
Alignment explanation
Indices: 1437372--1437414 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
1437362 ATTTACCAAA
1437372 TAATTTTTCATAAAT
1 TAATTTTTCATAAAT
1437387 TAATTTTTCAATAAAAT
1 TAATTTTTC-AT-AAAT
*
1437404 T-ATTATTCATA
1 TAATTTTTCATA
1437415 GATATGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 1 0.04
15 11 0.44
16 8 0.32
17 5 0.20
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (15 bp):
TAATTTTTCATAAAT
Found at i:1439606 original size:13 final size:13
Alignment explanation
Indices: 1439588--1439616 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1439578 AATATTCGAT
1439588 AATTAAACACAAC
1 AATTAAACACAAC
1439601 AATTAAACACAAC
1 AATTAAACACAAC
1439614 AAT
1 AAT
1439617 CAAAAATTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.17
Consensus pattern (13 bp):
AATTAAACACAAC
Found at i:1441040 original size:3 final size:3
Alignment explanation
Indices: 1441032--1441072 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
1441022 CTATAATTTG
*
1441032 AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1441073 AGAACCTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1444273 original size:18 final size:19
Alignment explanation
Indices: 1444246--1444284 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
1444236 AAAAAATAAT
1444246 TTAATCT-AAATATAATTAA
1 TTAATCTAAAAT-TAATTAA
1444265 TTAAT-TAAAATTAATTAA
1 TTAATCTAAAATTAATTAA
1444283 TT
1 TT
1444285 GATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAATCTAAAATTAATTAA
Found at i:1444292 original size:18 final size:19
Alignment explanation
Indices: 1444253--1444294 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
1444243 AATTTAATCT
*
1444253 AAATATAATTAATTAATTA
1 AAATATAATTAATTAATAA
*
1444272 AAAT-TAATTAATTGATAA
1 AAATATAATTAATTAATAA
1444290 AAATA
1 AAATA
1444295 GTAGCAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AAATATAATTAATTAATAA
Found at i:1452039 original size:3 final size:3
Alignment explanation
Indices: 1452033--1452063 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1452023 CATCATCATC
1452033 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1452064 CTACTACTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1453642 original size:4 final size:4
Alignment explanation
Indices: 1453633--1453663 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1453623 ATTAGACCTA
1453633 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1453664 GAATAGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1457470 original size:15 final size:16
Alignment explanation
Indices: 1457445--1457475 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1457435 TAAATTTTTA
1457445 AAAATATTCAAAAAAT
1 AAAATATTCAAAAAAT
1457461 AAAA-ATTCAAAAAAT
1 AAAATATTCAAAAAAT
1457476 TAGTATAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATATTCAAAAAAT
Found at i:1485110 original size:19 final size:18
Alignment explanation
Indices: 1485077--1485113 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1485067 TGTTCATATA
1485077 ATAAAAATTAAAATTAAT
1 ATAAAAATTAAAATTAAT
*
1485095 ATAAAAACTTAGAATTAAT
1 ATAAAAA-TTAAAATTAAT
1485114 TATATATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (18 bp):
ATAAAAATTAAAATTAAT
Found at i:1485940 original size:34 final size:35
Alignment explanation
Indices: 1485884--1485950 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
1485874 CAAACACCAA
* *
1485884 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGAAAATCATTTTACAGAAAAGT
*
1485919 AAAACATTTTCCA-AAAATCATTTTAGAGAAAA
1 AAAACATTTTCCAGAAAATCATTTTACAGAAAA
1485951 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGAAAATCATTTTACAGAAAAGT
Found at i:1494260 original size:23 final size:23
Alignment explanation
Indices: 1494229--1494282 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1494219 CTCCTATATA
*
1494229 TGCTCACTGAGTTCCTAATAATT
1 TGCTTACTGAGTTCCTAATAATT
* *
1494252 TGCTTACTGATTTCGTAATAATT
1 TGCTTACTGAGTTCCTAATAATT
*
1494275 TACTTACT
1 TGCTTACT
1494283 CTGCTCATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (23 bp):
TGCTTACTGAGTTCCTAATAATT
Found at i:1494416 original size:2 final size:2
Alignment explanation
Indices: 1494409--1494447 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1494399 TAAATCGAAA
1494409 AG AG AG AG AG AG 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 AG AG AG AG AG AG A
1494448 CAAGATTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1496358 original size:22 final size:24
Alignment explanation
Indices: 1496317--1496362 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
1496307 CTCTTTATAA
1496317 AAAATAATAATATTAATTTAAATT
1 AAAATAATAATATTAATTTAAATT
*
1496341 AAAA-AATAA-ATTATTTTAAATT
1 AAAATAATAATATTAATTTAAATT
1496363 GAGATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.57
23 5 0.24
24 4 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AAAATAATAATATTAATTTAAATT
Found at i:1508431 original size:21 final size:18
Alignment explanation
Indices: 1508406--1508448 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
1508396 TATATTTTTA
1508406 ATATTTATATTCGTGTTAAAT
1 ATATTT-TATTC-T-TTAAAT
1508427 ATA-TTTATTCTTTAAAT
1 ATATTTTATTCTTTAAAT
1508444 ATATT
1 ATATT
1508449 AAATATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 9 0.43
18 2 0.10
19 5 0.24
20 2 0.10
21 3 0.14
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56
Consensus pattern (18 bp):
ATATTTTATTCTTTAAAT
Found at i:1508530 original size:5 final size:5
Alignment explanation
Indices: 1508520--1508545 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1508510 TTTTTTTAAA
1508520 ATATT ATATT ATATT ATATT ATATT A
1 ATATT ATATT ATATT ATATT ATATT A
1508546 AATGTCTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:1514306 original size:27 final size:28
Alignment explanation
Indices: 1514250--1514311 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 28
1514240 AATTCTAAAC
* * *
1514250 TTTGGGTTCGATGTTCAAGGTTTAATG-
1 TTTGGGTTCGAAGTTCAAGGTTCAAAGT
*
1514277 TTTGGGTTC-AAGATTCAATGTTCAAAGT
1 TTTGGGTTCGAAG-TTCAAGGTTCAAAGT
1514305 TTTGGGT
1 TTTGGGT
1514312 ATGGGGTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 2 0.07
27 20 0.69
28 7 0.24
ACGTcount: A:0.21, C:0.08, G:0.27, T:0.44
Consensus pattern (28 bp):
TTTGGGTTCGAAGTTCAAGGTTCAAAGT
Found at i:1515977 original size:35 final size:34
Alignment explanation
Indices: 1515936--1516015 Score: 126
Period size: 35 Copynumber: 2.3 Consensus size: 34
1515926 TTTTTAGGGT
*
1515936 TTTTTTTATAATCTTTGATGGGTTTCTTTTATT-
1 TTTTTTTATAATCTTCGATGGGTTTCTTTTATTC
1515969 TATCTTTTTATAATCTTCGATGGGTTTCTTTTATTC
1 T-T-TTTTTATAATCTTCGATGGGTTTCTTTTATTC
1516005 TTTTTTTATAA
1 TTTTTTTATAA
1516016 ATATTGGTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
33 1 0.02
34 10 0.23
35 31 0.72
36 1 0.02
ACGTcount: A:0.17, C:0.09, G:0.10, T:0.64
Consensus pattern (34 bp):
TTTTTTTATAATCTTCGATGGGTTTCTTTTATTC
Found at i:1524457 original size:28 final size:28
Alignment explanation
Indices: 1524417--1524473 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1524407 GACCATACTC
1524417 ACATTATAGACAACCTCAAGAGAAAAAT
1 ACATTATAGACAACCTCAAGAGAAAAAT
1524445 ACATTATAGACAACCTCAAGAGAAAAAT
1 ACATTATAGACAACCTCAAGAGAAAAAT
1524473 A
1 A
1524474 AACACAACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.54, C:0.18, G:0.11, T:0.18
Consensus pattern (28 bp):
ACATTATAGACAACCTCAAGAGAAAAAT
Found at i:1527184 original size:20 final size:20
Alignment explanation
Indices: 1527157--1527203 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1527147 AATTTTAACA
1527157 TTATTAATAATTT-TAAT-TT
1 TTATTAAT-ATTTCTAATATT
1527176 TTAATTAATATTTCTAATATT
1 TT-ATTAATATTTCTAATATT
1527197 TTATTAA
1 TTATTAA
1527204 AAATGGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.24
20 15 0.60
21 4 0.16
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATTAATATTTCTAATATT
Found at i:1527293 original size:23 final size:25
Alignment explanation
Indices: 1527261--1527307 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
1527251 TATTAAGTAA
*
1527261 TTAATGTTTTA-TAATA-TAATATG
1 TTAATATTTTAGTAATATTAATATG
1527284 TTAATATTTTAGTAATATTAATAT
1 TTAATATTTTAGTAATATTAATAT
1527308 AAATATCAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 5 0.24
25 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (25 bp):
TTAATATTTTAGTAATATTAATATG
Found at i:1532311 original size:27 final size:27
Alignment explanation
Indices: 1532276--1532330 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1532266 CAAATAAGTC
1532276 TGGTTCACAAAGTCGGGAGCATCATGG
1 TGGTTCACAAAGTCGGGAGCATCATGG
*
1532303 TGGTTCACAAAGTCGGGAGCATCGTGG
1 TGGTTCACAAAGTCGGGAGCATCATGG
1532330 T
1 T
1532331 TGATGGACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.24
Consensus pattern (27 bp):
TGGTTCACAAAGTCGGGAGCATCATGG
Found at i:1534668 original size:56 final size:54
Alignment explanation
Indices: 1534558--1534668 Score: 136
Period size: 56 Copynumber: 2.0 Consensus size: 54
1534548 ATTTTTGTAT
* *
1534558 AATTTTAAAAAATATATAATACATTAAAATAAATATTTTTCAAAAAATTAAAAATA
1 AATTTTAAAAAATATAGAAT--ATTAAAATAAATATTTTTCAAAAAATAAAAAATA
1534614 AATTTTAAAAAATATAGAAT-TTAACAAGTAAATATTTTT-AAAATAATAATAAAAT
1 AATTTTAAAAAATATAGAATATTAA-AA-TAAATATTTTTCAAAA-AATAA-AAAAT
1534669 TAATAAATGT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
53 4 0.08
54 6 0.12
55 15 0.31
56 24 0.49
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (54 bp):
AATTTTAAAAAATATAGAATATTAAAATAAATATTTTTCAAAAAATAAAAAATA
Found at i:1534696 original size:11 final size:11
Alignment explanation
Indices: 1534682--1534786 Score: 54
Period size: 11 Copynumber: 9.5 Consensus size: 11
1534672 TAAATGTCTT
1534682 TAAAATAATAA
1 TAAAATAATAA
1534693 TAAAATTAATAA
1 TAAAA-TAATAA
1534705 TAAAATAA-AA
1 TAAAATAATAA
* * * *
1534715 TTTATAGAATAT
1 -TAAAATAATAA
*
1534727 TTAAATAAT-A
1 TAAAATAATAA
*
1534737 TCAACAA-AATGA
1 T-AA-AATAATAA
* *
1534749 TAATATAATAG
1 TAAAATAATAA
*
1534760 TAAAATAGTAA
1 TAAAATAATAA
* *
1534771 TAAAATTATAC
1 TAAAATAATAA
1534782 TAAAA
1 TAAAA
1534787 AGTAAATTGT
Statistics
Matches: 70, Mismatches: 17, Indels: 14
0.69 0.17 0.14
Matches are distributed among these distances:
10 4 0.06
11 50 0.71
12 16 0.23
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:1534704 original size:12 final size:12
Alignment explanation
Indices: 1534682--1534710 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1534672 TAAATGTCTT
1534682 TAAAA-TAATAA
1 TAAAATTAATAA
1534693 TAAAATTAATAA
1 TAAAATTAATAA
1534705 TAAAAT
1 TAAAAT
1534711 AAAATTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTAATAA
Found at i:1534711 original size:17 final size:17
Alignment explanation
Indices: 1534681--1534716 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1534671 ATAAATGTCT
1534681 TTAAAATAATAATAAAA
1 TTAAAATAATAATAAAA
1534698 TTAATAATAA-AATAAAA
1 TTAA-AATAATAATAAAA
1534715 TT
1 TT
1534717 TATAGAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAATAATAATAAAA
Found at i:1534773 original size:22 final size:21
Alignment explanation
Indices: 1534748--1534791 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1534738 CAACAAAATG
* *
1534748 ATAATATAATAGTAAAATAGTA
1 ATAAAATAATACTAAAA-AGTA
*
1534770 ATAAAATTATACTAAAAAGTA
1 ATAAAATAATACTAAAAAGTA
1534791 A
1 A
1534792 ATTGTTTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (21 bp):
ATAAAATAATACTAAAAAGTA
Found at i:1538113 original size:39 final size:39
Alignment explanation
Indices: 1538059--1538139 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
1538049 GAACACCGAG
1538059 ATAGAAGAAGAAATGTTGCTCGAGTTGCACGATCATGGC
1 ATAGAAGAAGAAATGTTGCTCGAGTTGCACGATCATGGC
1538098 ATAGAAGAAGAAATGTTGCTCGAGTTGCACGATCATGGC
1 ATAGAAGAAGAAATGTTGCTCGAGTTGCACGATCATGGC
1538137 ATA
1 ATA
1538140 AGGGACGCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (39 bp):
ATAGAAGAAGAAATGTTGCTCGAGTTGCACGATCATGGC
Found at i:1544076 original size:15 final size:15
Alignment explanation
Indices: 1544044--1544083 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1544034 TCAATCTCTT
**
1544044 AATAAATAATTTTTA
1 AATAAATAATTTACA
1544059 AATAAATAATTTACA
1 AATAAATAATTTACA
1544074 AATATAATAA
1 AATA-AATAA
1544084 ATATATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
AATAAATAATTTACA
Found at i:1544911 original size:16 final size:15
Alignment explanation
Indices: 1544878--1544925 Score: 64
Period size: 16 Copynumber: 3.3 Consensus size: 15
1544868 TGTTGTTTGC
1544878 TTTTTCTCTT-TT-T
1 TTTTTCTCTTATTGT
1544891 TTTTTCTCTTATTGAT
1 TTTTTCTCTTATTG-T
*
1544907 TTTTTCTTTTATTGT
1 TTTTTCTCTTATTGT
1544922 TTTT
1 TTTT
1544926 GTCATTCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 10 0.32
14 2 0.06
15 5 0.16
16 14 0.45
ACGTcount: A:0.06, C:0.10, G:0.04, T:0.79
Consensus pattern (15 bp):
TTTTTCTCTTATTGT
Found at i:1549531 original size:16 final size:16
Alignment explanation
Indices: 1549510--1549541 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1549500 AGATGATGAT
1549510 GCCTATTGTTGTTGAA
1 GCCTATTGTTGTTGAA
1549526 GCCTATTGTTGTTGAA
1 GCCTATTGTTGTTGAA
1549542 ACTCCACTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.44
Consensus pattern (16 bp):
GCCTATTGTTGTTGAA
Found at i:1551106 original size:17 final size:19
Alignment explanation
Indices: 1551067--1551118 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
1551057 CGCCATTATT
*
1551067 TATAAAAATAATACAAAAAAA
1 TATAAAAAT-AT-CAAAATAA
*
1551088 TAAAAAAAATATCAAAATAA
1 T-ATAAAAATATCAAAATAA
1551108 TATAAAAATAT
1 TATAAAAATAT
1551119 TTTTATTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 9 0.33
20 8 0.30
21 3 0.11
22 7 0.26
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (19 bp):
TATAAAAATATCAAAATAA
Found at i:1551116 original size:11 final size:11
Alignment explanation
Indices: 1551067--1551117 Score: 63
Period size: 11 Copynumber: 4.9 Consensus size: 11
1551057 CGCCATTATT
1551067 TATAAAAATAA
1 TATAAAAATAA
*
1551078 TACAAAAA-AA
1 TATAAAAATAA
1551088 TA-AAAAA-AA
1 TATAAAAATAA
*
1551097 TATCAAAATAA
1 TATAAAAATAA
1551108 TATAAAAATA
1 TATAAAAATA
1551118 TTTTTATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 9 0.26
10 8 0.23
11 18 0.51
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.22
Consensus pattern (11 bp):
TATAAAAATAA
Found at i:1551118 original size:19 final size:20
Alignment explanation
Indices: 1551067--1551118 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
1551057 CGCCATTATT
1551067 TATAAAAATAATACAAAAAAA
1 TATAAAAAT-ATACAAAAAAA
* *
1551088 TA-AAAAAAATATCAAAATAA
1 TATAAAAATATA-CAAAAAAA
1551108 TATAAAAATAT
1 TATAAAAATAT
1551119 TTTTATTTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 3 0.12
20 14 0.54
21 9 0.35
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (20 bp):
TATAAAAATATACAAAAAAA
Found at i:1551453 original size:153 final size:154
Alignment explanation
Indices: 1551227--1551730 Score: 723
Period size: 157 Copynumber: 3.3 Consensus size: 154
1551217 GCGGCACCAA
* * * * *
1551227 TTGTTTGTATTTTTTTCTCGGATTTTATTAATTT-TA-AAAAATATATTATTTT-TTATTTTTTT
1 TTGTTCGTATTTTTTTCTCGAATTTTATTAATTTCAATAAAAATATATTATTTTCGTA-TTTTAT
* *
1551289 TATTTTACATTATTTTAGTACATTAGGTTTGAAATGTATTAATTTAGTGTG-TTTTTAAATAAAT
65 TATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAAT
*
1551353 TAAAAAAAAACCTTATTTCAACCCT
130 TAAAAAAAAACCTTATTTCGACCCT
*
1551378 TTGTTCGTATTTTTTTCTTGAATTTTATTAATTTCAATAAAAATATATTATTTTCGTATTTTATT
1 TTGTTCGTATTTTTTTCTCGAATTTTATTAATTTCAATAAAAATATATTATTTTCGTATTTTATT
** * *
1551443 CGTTTACATTATTTTAATATATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAATT
66 ATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAA--
** *
1551508 TTTAAAAAAAGCCCTTATTTCGACCAT
129 -TTAAAAAAAAACCTTATTTCGACCCT
* *
1551535 TTGTTCGTATTTTTTTCTCGGATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATT
1 TTGTTCGTATTTTTTTCTCGAATTTTATTAATTTCAATAAAAATATATTATTTTCGTATTTTATT
*
1551600 ATTTTACATTATTTTAGTACATTTTGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAATT
66 ATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAATT
*
1551665 --AAAAAAACTCTTATTTCGGCCCT
131 AAAAAAAAAC-CTTATTTCGACCCT
* *
1551688 TTGTTCGTATTTTTTTCCCGAATTTTATTACTTTCAATAAAAA
1 TTGTTCGTATTTTTTTCTCGAATTTTATTAATTTCAATAAAAA
1551731 ACAGACTAAA
Statistics
Matches: 315, Mismatches: 30, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
151 31 0.10
152 7 0.02
153 119 0.38
154 16 0.05
157 142 0.45
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.53
Consensus pattern (154 bp):
TTGTTCGTATTTTTTTCTCGAATTTTATTAATTTCAATAAAAATATATTATTTTCGTATTTTATT
ATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAATT
AAAAAAAAACCTTATTTCGACCCT
Found at i:1553419 original size:3 final size:3
Alignment explanation
Indices: 1553411--1553444 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1553401 ACATGCTTAT
1553411 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1553445 AGAAACCACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1561207 original size:27 final size:27
Alignment explanation
Indices: 1561175--1561230 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1561165 AGAATAAGCA
1561175 TCTCTAGCATATTAAAGAAAATGTCAT
1 TCTCTAGCATATTAAAGAAAATGTCAT
1561202 TCTCTAGCATATTAAAGAAAATGTCAT
1 TCTCTAGCATATTAAAGAAAATGTCAT
1561229 TC
1 TC
1561231 ATACCTGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (27 bp):
TCTCTAGCATATTAAAGAAAATGTCAT
Found at i:1566973 original size:86 final size:85
Alignment explanation
Indices: 1566870--1567045 Score: 257
Period size: 86 Copynumber: 2.1 Consensus size: 85
1566860 CTGTTATAGA
* *
1566870 AAAGTGGTTAAAAACATATAAGAGCTGCATGAATTATTGTTTTTATGCAA-ATTTTTGTTTTACA
1 AAAGTGGTTAAAAACATATAAAAGCTGCATGAATTATTGTTTTTATGCAATA-TTTTATTTTACA
*
1566934 TAT-TTCCACACGATTAATTAT
65 T-TCTTCCACACAATTAATTAT
* *
1566955 AAAGTGGTTAAAAAACATATAAAAGCTGCATGAATTATTGTTTTTATGCATTATTTTATTTTGCA
1 AAAGTGGTT-AAAAACATATAAAAGCTGCATGAATTATTGTTTTTATGCAATATTTTATTTTACA
*
1567020 TTCTTTCACACAATTAATTAT
65 TTCTTCCACACAATTAATTAT
1567041 AAAGT
1 AAAGT
1567046 TCATAAGTTT
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
85 10 0.12
86 71 0.87
87 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.41
Consensus pattern (85 bp):
AAAGTGGTTAAAAACATATAAAAGCTGCATGAATTATTGTTTTTATGCAATATTTTATTTTACAT
TCTTCCACACAATTAATTAT
Found at i:1568813 original size:167 final size:167
Alignment explanation
Indices: 1568536--1568875 Score: 488
Period size: 167 Copynumber: 2.0 Consensus size: 167
1568526 GAATTGGGTT
*
1568536 TGGGTAAAACTAGACCTGTCCATAAGGCGGATCACTCGACCCGAAAGCCTACCCAAAAAGTAAGA
1 TGGGTAAAACTAGACCTGTCCATAAGGCGGATCACCCGACCCGAAAGCCTACCCAAAAAGTAAGA
* * * **
1568601 GGGTTTGGATAAAATATAGGCCCGAAAAATGAGATTTGAGCAAAAAATAAGGTTCGTTTGAAAAA
66 GGGTTTAGATAAAATATAGGCCCAAAAAATGAGATTGGAGCAAAAAATAAGGCCCGTTTGAAAAA
*
1568666 CGGGTCAAGTAT-TGGGTAAGACTTTTTTGGTCTTGAG
131 CGGGTCAAGCATCT-GGTAAGACTTTTTTGGTCTTGAG
** * * **
1568703 TGGGTAAAACTAGACCTGTCCATGGGGCGGGTCACCCGACCCGAAAG-CT-CGCCTGAAAAGTGG
1 TGGGTAAAACTAGACCTGTCCATAAGGCGGATCACCCGACCCGAAAGCCTAC-CC-AAAAAGTAA
* *
1568766 GAGGGTTTAGATAAAATATAGGCCCAAAAAATGAGCTTGGGGCAAAAAATAAGGCCCGTTTGAAA
64 GAGGGTTTAGATAAAATATAGGCCCAAAAAATGAGATTGGAGCAAAAAATAAGGCCCGTTTGAAA
*
1568831 AACGGGTCAAGCATCTTGTAAGACTTTTTTGGTCTTGAG
129 AACGGGTCAAGCATCTGGTAAGACTTTTTTGGTCTTGAG
1568870 TGGGTA
1 TGGGTA
1568876 TGACCCGCCC
Statistics
Matches: 154, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
165 1 0.01
166 4 0.03
167 148 0.96
168 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (167 bp):
TGGGTAAAACTAGACCTGTCCATAAGGCGGATCACCCGACCCGAAAGCCTACCCAAAAAGTAAGA
GGGTTTAGATAAAATATAGGCCCAAAAAATGAGATTGGAGCAAAAAATAAGGCCCGTTTGAAAAA
CGGGTCAAGCATCTGGTAAGACTTTTTTGGTCTTGAG
Found at i:1568911 original size:141 final size:142
Alignment explanation
Indices: 1568736--1569010 Score: 464
Period size: 141 Copynumber: 1.9 Consensus size: 142
1568726 GGGGCGGGTC
*
1568736 ACCCGACCCGAAAGCTCGCCTGAAAAGTGGGAGGGTTTAGATAAAATATAGGCCCAAAAAATGAG
1 ACCCGACCCGAAAGCTCGCCTGAAAAGTGAGAGGGTTTAGATAAAATATAGGCCCAAAAAATGAG
*
1568801 CTTGGGGCAAAAAATAAGGCCCGTTTGAAAAACGGGTCAAGCATCTTGTAAGACTTTTTTGGTCT
66 CTTGGGGCAAAAAATAAGGCCCGTTTGAAAAACGGGTCAAGCATCGTGTAAGACTTTTTTGGTCT
1568866 TGAGTGGGTATG
131 TGAGTGGGTATG
* * *
1568878 ACCCG-CCCGAAAGCTCG-CTTAGAAAGTGAGAGGGTTTGGATAAAATATAGGCCCGAAAAATGA
1 ACCCGACCCGAAAGCTCGCCTGA-AAAGTGAGAGGGTTTAGATAAAATATAGGCCCAAAAAATGA
* *
1568941 GCTTGGGGCAAAAAATAAGGTCCGTTTGAAAAACGGGTCAAGCATCGTGTAAGACTTTTTTGGTT
65 GCTTGGGGCAAAAAATAAGGCCCGTTTGAAAAACGGGTCAAGCATCGTGTAAGACTTTTTTGGTC
1569006 TTGAG
130 TTGAG
1569011 CCCAACTCGG
Statistics
Matches: 125, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
140 3 0.02
141 117 0.94
142 5 0.04
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (142 bp):
ACCCGACCCGAAAGCTCGCCTGAAAAGTGAGAGGGTTTAGATAAAATATAGGCCCAAAAAATGAG
CTTGGGGCAAAAAATAAGGCCCGTTTGAAAAACGGGTCAAGCATCGTGTAAGACTTTTTTGGTCT
TGAGTGGGTATG
Found at i:1572069 original size:16 final size:16
Alignment explanation
Indices: 1572028--1572062 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1572018 ACGAGATTGT
*
1572028 AACCTCTTCAACTAAC
1 AACCACTTCAACTAAC
1572044 AACCACTTCAACTAAC
1 AACCACTTCAACTAAC
1572060 AAC
1 AAC
1572063 TAGTTCACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (16 bp):
AACCACTTCAACTAAC
Found at i:1572740 original size:10 final size:11
Alignment explanation
Indices: 1572699--1572743 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
1572689 ATATCCAAAC
*
1572699 AATAATAACAA
1 AATAATAGCAA
1572710 AATAATAGCAA
1 AATAATAGCAA
*
1572721 TATAATAGCAA
1 AATAATAGCAA
1572732 AAT-ATAGCAA
1 AATAATAGCAA
1572742 AA
1 AA
1572744 AAATGAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
10 9 0.29
11 22 0.71
ACGTcount: A:0.64, C:0.09, G:0.07, T:0.20
Consensus pattern (11 bp):
AATAATAGCAA
Found at i:1583347 original size:5 final size:5
Alignment explanation
Indices: 1583337--1583367 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
1583327 GTCATTTTCA
1583337 ATAAT ATAAT ATAAT ATAAT ATTAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT
1583368 GATTCCTTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATAAT
Found at i:1583827 original size:18 final size:18
Alignment explanation
Indices: 1583791--1583835 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
1583781 AGCTTTTAAG
*
1583791 AAATACTTTTGGGACAAA
1 AAATACTTTTGAGACAAA
* *
1583809 AAATGCTTTTGAGA-GAA
1 AAATACTTTTGAGACAAA
1583826 AAATACTTTT
1 AAATACTTTT
1583836 CAAACACCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (18 bp):
AAATACTTTTGAGACAAA
Found at i:1586246 original size:123 final size:123
Alignment explanation
Indices: 1586026--1586393 Score: 576
Period size: 123 Copynumber: 3.0 Consensus size: 123
1586016 TTTTAGGTAT
** * *
1586026 TGGAAGAAATAATTTCGAGTTGACGTTTCTGATCAAATAGTATAAAATCGCTTCTAGCAGGATGC
1 TGGAAGAAATAATTT--TTTTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGC
* * *
1586091 TATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTAGACGCGCTTTTGCTACAGTAGGTCA
64 TATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGATGCGCTTTTGCTACAGTAGGTCA
1586151 TGGAAGAAATAATTTTTTTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTA
1 TGGAAGAAATAATTTTTTTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTA
* * *
1586216 TTTGAGAAGAATTTGTAAAATTGCGTCCTCGTGGATGCGCTTTTGCTACAGTCGGTCA
66 TTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGATGCGCTTTTGCTACAGTAGGTCA
*
1586274 TGGAAGAAATAATTTTTTTGACGATTT-TGAGCAAATAATATAAAATCGCTTTTAGCAGGATGCT
1 TGGAAGAAATAATTTTTTTGACG-TTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCT
* *
1586338 ATTTGAGAAGAATTTTTGAAAATCGCGCCCTCGTGGATGCGCTTTTGCTATAGTAG
65 ATTTGAGAAGAATTTGT-AAAATCGCGCCCTCGTGGATGCGCTTTTGCTACAGTAG
1586394 CATGTTTGGG
Statistics
Matches: 225, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
123 173 0.77
124 37 0.16
125 15 0.07
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (123 bp):
TGGAAGAAATAATTTTTTTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTA
TTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGATGCGCTTTTGCTACAGTAGGTCA
Found at i:1589614 original size:116 final size:116
Alignment explanation
Indices: 1589405--1589644 Score: 392
Period size: 116 Copynumber: 2.1 Consensus size: 116
1589395 TTTGTGAAAT
* *
1589405 TATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTTTCAAATTATATAAAATTATTAATTGT
1 TATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAATTGT
** * *
1589470 TAGTACCAGTCAAAACATTTTTCTAAATCTAACATTATGTGAATGTAAAAC
66 TAGTACCAGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTAAAAC
1589521 TATTAATTGATAAATTGTATTAATGATTAGT-AAAATTATCAAATTATATAAAATTATTAATTGT
1 TATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAATTGT
* *
1589585 TAGTACCAGGAAAAAATATTTTTCCAAATCTAACATTATGTGAAAGTAAAAT
66 TAGTACCA-GAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTAAAAC
1589637 TATTAATT
1 TATTAATT
1589645 TAGTTTAGGG
Statistics
Matches: 115, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
115 40 0.35
116 75 0.65
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (116 bp):
TATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAATTGT
TAGTACCAGAAAAAACATTTTTCCAAATCTAACATTATGTGAAAGTAAAAC
Found at i:1589698 original size:28 final size:23
Alignment explanation
Indices: 1589638--1589771 Score: 114
Period size: 23 Copynumber: 5.9 Consensus size: 23
1589628 AAGTAAAATT
* *
1589638 ATTAATTTAGTTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
1589661 ATTAAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
* *
1589684 ATTTAAGTAGGTTAGGGTTTTTAA
1 ATTAAATTAGGTTAGGGTTTTT-A
***
1589708 ATT-AAGGGGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
* * *
1589730 AGT---TTAGGGTTTAAGATTTTTA
1 ATTAAATTA-GG-TTAGGGTTTTTA
*
1589752 ATTTAATTAGGTTAGGGTTT
1 ATTAAATTAGGTTAGGGTTT
1589772 AAAAATTTTT
Statistics
Matches: 90, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
21 2 0.02
22 15 0.17
23 64 0.71
24 6 0.07
25 3 0.03
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.49
Consensus pattern (23 bp):
ATTAAATTAGGTTAGGGTTTTTA
Found at i:1589702 original size:46 final size:44
Alignment explanation
Indices: 1589647--1589771 Score: 137
Period size: 46 Copynumber: 2.8 Consensus size: 44
1589637 TATTAATTTA
1589647 GTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-TTTAAGTAG
1 GTTTAGGGTTTTTAATT-AATTAGGTTAGGGTTTTTAAGTTT-AG--G
***
1589694 G-TTAGGGTTTTTAAATTAAGGGGGTTAGGGTTTTTAAGTTTAGG
1 GTTTAGGGTTTTT-AATTAATTAGGTTAGGGTTTTTAAGTTTAGG
* *
1589738 GTTTAAGATTTTTAATTTAATTAGGTTAGGGTTT
1 GTTTAGGGTTTTTAA-TTAATTAGGTTAGGGTTT
1589772 AAAAATTTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 10
0.79 0.10 0.12
Matches are distributed among these distances:
44 4 0.06
45 24 0.36
46 30 0.45
47 8 0.12
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (44 bp):
GTTTAGGGTTTTTAATTAATTAGGTTAGGGTTTTTAAGTTTAGG
Found at i:1589836 original size:29 final size:29
Alignment explanation
Indices: 1589782--1589867 Score: 138
Period size: 30 Copynumber: 3.0 Consensus size: 29
1589772 AAAAATTTTT
*
1589782 AAAAATTAAAAAAAGTATTTTAAAAATAA
1 AAAAATTAAAAAAAATATTTTAAAAATAA
1589811 ACAAAATTAAAAAAAATATTTTAAAAATAA
1 A-AAAATTAAAAAAAATATTTTAAAAATAA
*
1589841 AAAAATT-AAAAAAATAATTTAAAAATA
1 AAAAATTAAAAAAAATATTTTAAAAATA
1589868 TTTTAAAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
28 19 0.35
29 7 0.13
30 28 0.52
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.27
Consensus pattern (29 bp):
AAAAATTAAAAAAAATATTTTAAAAATAA
Found at i:1589876 original size:30 final size:29
Alignment explanation
Indices: 1589769--1589877 Score: 112
Period size: 30 Copynumber: 3.7 Consensus size: 29
1589759 TAGGTTAGGG
* *
1589769 TTTAAAAATTTTTAAAAATTAAAAAAAGTAT
1 TTTAAAAATATAT-AAAATTAAAAAAA-TAT
* *
1589800 TTTAAAAATAAACAAAATTAAAAAAAATAT
1 TTTAAAAATATATAAAATT-AAAAAAATAT
* *
1589830 TTTAAAAATA-AAAAAATTAAAAAAATAA
1 TTTAAAAATATATAAAATTAAAAAAATAT
*
1589858 TTTAAAAATATTTTAAAATT
1 TTTAAAAATA-TATAAAATT
1589878 TTAAAATTAA
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
28 19 0.28
29 7 0.10
30 25 0.37
31 16 0.24
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (29 bp):
TTTAAAAATATATAAAATTAAAAAAATAT
Found at i:1589903 original size:38 final size:39
Alignment explanation
Indices: 1589821--1589908 Score: 101
Period size: 38 Copynumber: 2.3 Consensus size: 39
1589811 ACAAAATTAA
1589821 AAAAAATATTTTAAAAATAAAAAAATTAAAAAAATAATTT
1 AAAAAATATTTTAAAAATAAAAAAATTAAAAAAAT-ATTT
*** *
1589861 -AAAAATATTTT-AAAATTTTAAAATTAAAAAAGT-TTGT
1 AAAAAATATTTTAAAAATAAAAAAATTAAAAAAATATT-T
1589898 AAAAAATATTT
1 AAAAAATATTT
1589909 CGGGCCTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
36 2 0.05
37 1 0.02
38 28 0.67
39 11 0.26
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (39 bp):
AAAAAATATTTTAAAAATAAAAAAATTAAAAAAATATTT
Found at i:1590259 original size:24 final size:22
Alignment explanation
Indices: 1590223--1590266 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
1590213 ATTTTTACGG
1590223 TTTAAAAAAATTTTTAAAAAAAAA
1 TTTAAAAAAA--TTTAAAAAAAAA
*
1590247 TTTAAAAATATTTAAAAAAA
1 TTTAAAAAAATTTAAAAAAA
1590267 GAGAGTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
24 9 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TTTAAAAAAATTTAAAAAAAAA
Found at i:1590265 original size:12 final size:12
Alignment explanation
Indices: 1590223--1590266 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1590213 ATTTTTACGG
*
1590223 TTTAAAAAAATT
1 TTTAAAAAAATA
*
1590235 TTTAAAAAAAAA
1 TTTAAAAAAATA
1590247 TTT--AAAAATA
1 TTTAAAAAAATA
1590257 TTTAAAAAAA
1 TTTAAAAAAA
1590267 GAGAGTTAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 9 0.33
12 18 0.67
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TTTAAAAAAATA
Found at i:1590288 original size:11 final size:11
Alignment explanation
Indices: 1590272--1590313 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
1590262 AAAAAGAGAG
1590272 TTAAGAGAAAC
1 TTAAGAGAAAC
*
1590283 TTAAGAGGAAC
1 TTAAGAGAAAC
1590294 TTAAGAGAAAC
1 TTAAGAGAAAC
1590305 TTAAGAGAA
1 TTAAGAGAA
1590314 TTTTTGAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.19
Consensus pattern (11 bp):
TTAAGAGAAAC
Found at i:1590337 original size:11 final size:11
Alignment explanation
Indices: 1590317--1590356 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
1590307 AAGAGAATTT
1590317 TTGA-AGGAAA
1 TTGAGAGGAAA
1590327 TTGAGAGGAAA
1 TTGAGAGGAAA
1590338 TTGAGAGGAAA
1 TTGAGAGGAAA
1590349 TTTGAGAG
1 -TTGAGAG
1590357 ACGATTAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 4 0.14
11 17 0.61
12 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:1591165 original size:14 final size:14
Alignment explanation
Indices: 1591140--1591167 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1591130 CACTATTATA
1591140 TTGTTATTATTTTG
1 TTGTTATTATTTTG
1591154 TTGTTATTATTTTG
1 TTGTTATTATTTTG
1591168 ATATTGTATA
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:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (14 bp):
TTGTTATTATTTTG
Found at i:1592739 original size:14 final size:14
Alignment explanation
Indices: 1592720--1592750 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1592710 TGTGCTTCAG
1592720 CATACTCAAACTCA
1 CATACTCAAACTCA
*
1592734 CATACTCGAACTCA
1 CATACTCAAACTCA
1592748 CAT
1 CAT
1592751 CCTCCTACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.35, G:0.03, T:0.23
Consensus pattern (14 bp):
CATACTCAAACTCA
Found at i:1600784 original size:40 final size:40
Alignment explanation
Indices: 1600740--1600829 Score: 121
Period size: 39 Copynumber: 2.3 Consensus size: 40
1600730 TCCACGTAAG
* *
1600740 CGCGATTTGCTT-CCACGTTAGCAAATCGCGCTTACGTGGA
1 CGCGATTTGCTTGCCACGTAAG-AAATCGCGCTGACGTGGA
* *
1600780 CGCGATTTG-TTGCCACGTAAGTAATCGCGCTGGCGTGGA
1 CGCGATTTGCTTGCCACGTAAGAAATCGCGCTGACGTGGA
1600819 CGCGATTTGCT
1 CGCGATTTGCT
1600830 GACACGTCCC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
39 26 0.59
40 18 0.41
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.28
Consensus pattern (40 bp):
CGCGATTTGCTTGCCACGTAAGAAATCGCGCTGACGTGGA
Found at i:1605954 original size:18 final size:18
Alignment explanation
Indices: 1605931--1605967 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1605921 TTGAGAGCTT
*
1605931 TGTCCCTCTTAATGACAG
1 TGTCCCTCGTAATGACAG
*
1605949 TGTCCCTCGTAATTACAG
1 TGTCCCTCGTAATGACAG
1605967 T
1 T
1605968 AGCCCCATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.35
Consensus pattern (18 bp):
TGTCCCTCGTAATGACAG
Found at i:1610768 original size:109 final size:109
Alignment explanation
Indices: 1610577--1610797 Score: 365
Period size: 109 Copynumber: 2.0 Consensus size: 109
1610567 GAGTTTAATA
1610577 TGTATGTGGACCAAATTTATATAATTTGTAAATATGGAGGGTTAATTTTATTAAATTGTTAAGAA
1 TGTATGTGGACCAAATTTATATAATTTGTAAATATGGAGGGTTAATTTTATTAAATTGTTAAGAA
1610642 CTAGGACCAAAATGATAAAATGTGTAAGTGTCGATGACTAAATG
66 CTAGGACCAAAATGATAAAATGTGTAAGTGTCGATGACTAAATG
*
1610686 TGTATGTGGACCAAATTTATATAATTTGTAAATGA-GGAGGGTTAATTTTATTAGATTGTTAAGA
1 TGTATGTGGACCAAATTTATATAATTTGTAAAT-ATGGAGGGTTAATTTTATTAAATTGTTAAGA
* * * *
1610750 ATTTA-GACTAAACTGATAAAATGTGTAAGTGTTGATGACTAAATG
65 A-CTAGGACCAAAATGATAAAATGTGTAAGTGTCGATGACTAAATG
1610795 TGT
1 TGT
1610798 TAATATATCA
Statistics
Matches: 105, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
109 102 0.97
110 3 0.03
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (109 bp):
TGTATGTGGACCAAATTTATATAATTTGTAAATATGGAGGGTTAATTTTATTAAATTGTTAAGAA
CTAGGACCAAAATGATAAAATGTGTAAGTGTCGATGACTAAATG
Found at i:1620993 original size:27 final size:27
Alignment explanation
Indices: 1620955--1621008 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1620945 ATCTTAAGTT
1620955 CAATCGAAAATTCGGGTTTTTGGCTAA
1 CAATCGAAAATTCGGGTTTTTGGCTAA
1620982 CAATCGAAAATTCGGGTTTTTGGCTAA
1 CAATCGAAAATTCGGGTTTTTGGCTAA
1621009 TAACGCTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (27 bp):
CAATCGAAAATTCGGGTTTTTGGCTAA
Found at i:1627130 original size:44 final size:44
Alignment explanation
Indices: 1627044--1627297 Score: 222
Period size: 44 Copynumber: 5.6 Consensus size: 44
1627034 AATTCTCTAC
* ** * * *
1627044 CCCTGAAGTTGCAATGGAAAAAGATTGAAGTTACAAAACTTATCT
1 CCCTGAAGTTGCAGTGG-AGCAGATTAAAGCTACAAATCTTATCT
* *
1627089 CCTTGAAGTTGCAGTGGAGTAGATTAAAGCCT-CAAATCTTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTAAAG-CTACAAATCTTATCT
* ** * *
1627133 TCCTGAAGTTGCAGTGGAATAGATTGAAGATAGCAAATCTTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-CAAATCTTATCT
* * * * *
1627178 CTCTGAAATTGCAGTAGAGCAAATTAAAGCTACAAATCTTATTT
1 CCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCT
* * *
1627222 CCCTAAAGTTGCAGTGGAACATATTAAAGCTACAAATTACAAATCTTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTAAAG---C----TACAAATCTTATCT
1627273 CCCTGAAGTTGCAGTGGAGCAGATT
1 CCCTGAAGTTGCAGTGGAGCAGATT
1627298 GAAACATAAG
Statistics
Matches: 167, Mismatches: 32, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
43 1 0.01
44 79 0.47
45 51 0.31
47 1 0.01
51 35 0.21
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (44 bp):
CCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCT
Found at i:1627190 original size:89 final size:88
Alignment explanation
Indices: 1627044--1627240 Score: 247
Period size: 89 Copynumber: 2.2 Consensus size: 88
1627034 AATTCTCTAC
* * * * *
1627044 CCCTGAAGTTGCAATGGAAAAAGATTGAAGTTACAAAACTTATCTCCTTGAAGTTGCAGTGGAGT
1 CCCTGAAGTTGCAGTGG-AAAAGATTGAAGATACAAAACTTATCTCCTTGAAATTGCAGTAGAGC
*
1627109 AGATTAAAGCCT-CAAATCTTATCTT
65 AAATTAAAG-CTACAAATCTTAT-TT
* *
1627134 -CCTGAAGTTGCAGTGGAATAGATTGAAGATAGCAAATCTTATCT-CTCTGAAATTGCAGTAGAG
1 CCCTGAAGTTGCAGTGGAAAAGATTGAAGATA-CAAAACTTATCTCCT-TGAAATTGCAGTAGAG
1627197 CAAATTAAAGCTACAAATCTTATTT
64 CAAATTAAAGCTACAAATCTTATTT
*
1627222 CCCTAAAGTTGCAGTGGAA
1 CCCTGAAGTTGCAGTGGAA
1627241 CATATTAAAG
Statistics
Matches: 94, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
88 19 0.20
89 75 0.80
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (88 bp):
CCCTGAAGTTGCAGTGGAAAAGATTGAAGATACAAAACTTATCTCCTTGAAATTGCAGTAGAGCA
AATTAAAGCTACAAATCTTATTT
Found at i:1628958 original size:12 final size:12
Alignment explanation
Indices: 1628943--1628982 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1628933 TATGTTATGT
*
1628943 TTTATTTATTTA
1 TTTATTTATTCA
*
1628955 TTTATTCATTCA
1 TTTATTTATTCA
1628967 TTTATTTAATTCA
1 TTTATTT-ATTCA
1628980 TTT
1 TTT
1628983 TTTTGTGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTTATTCA
Found at i:1633467 original size:6 final size:6
Alignment explanation
Indices: 1633456--1633484 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1633446 TGGAGGATGG
1633456 TATATT TATATT TATATT TATATT TATAT
1 TATATT TATATT TATATT TATATT TATAT
1633485 ATGATTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:1640474 original size:113 final size:114
Alignment explanation
Indices: 1640250--1640508 Score: 387
Period size: 113 Copynumber: 2.3 Consensus size: 114
1640240 ACTGATTCCC
1640250 ATTAATGGAAGAATTGGTTTGGTTTGATTTGATAATATACTATTGGTTTTTATGTTATTAGGTAA
1 ATTAATGGAAGAATTGGTTTGGTTTGATTTGATAATATACTATTGGTTTTTATGTTATTAGGTAA
* * * *
1640315 TGTTTTTAGAACCGGATCAATAGTCGTACCAGTCATGTCATCAATTTCA
66 TGTCTTCAAAACCGGATCAATAGTCGAACCAGTCATGTCATCAATTTCA
**
1640364 ATTAATGGAAGAATTGGTTTGGTTTGATTTGATAATATTTTATTGG-TTTTATGTTATTAGGTAA
1 ATTAATGGAAGAATTGGTTTGGTTTGATTTGATAATATACTATTGGTTTTTATGTTATTAGGTAA
* * *
1640428 TGTCTTCAAAACTGGATTAATAGTCGAACCAGTTATGTCATCAATTTCA
66 TGTCTTCAAAACCGGATCAATAGTCGAACCAGTCATGTCATCAATTTCA
* **
1640477 ATTAAT-GACAGAATTGTTTTGACTTGATTTGA
1 ATTAATGGA-AGAATTGGTTTGGTTTGATTTGA
1640509 ATCAAAGTTT
Statistics
Matches: 132, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
112 2 0.02
113 86 0.65
114 44 0.33
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.43
Consensus pattern (114 bp):
ATTAATGGAAGAATTGGTTTGGTTTGATTTGATAATATACTATTGGTTTTTATGTTATTAGGTAA
TGTCTTCAAAACCGGATCAATAGTCGAACCAGTCATGTCATCAATTTCA
Found at i:1648194 original size:4 final size:4
Alignment explanation
Indices: 1648185--1648213 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1648175 ACAAATTATG
1648185 ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
1648214 CTAAGTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:1651396 original size:27 final size:27
Alignment explanation
Indices: 1651366--1651449 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 27
1651356 ATTGGTTCTT
1651366 TGAAACTGCACAAGTCCATCTATGACC
1 TGAAACTGCACAAGTCCATCTATGACC
* * * * * *
1651393 TGAAACAAGCGCCA--CAAGCT-TG-GC
1 TGAAAC-TGCACAAGTCCATCTATGACC
1651417 TGAAACTGCACAAGTCCATCTATGACC
1 TGAAACTGCACAAGTCCATCTATGACC
1651444 TGAAAC
1 TGAAAC
1651450 AAGCACCACA
Statistics
Matches: 40, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
23 4 0.10
24 7 0.17
25 6 0.15
26 6 0.15
27 13 0.32
28 4 0.10
ACGTcount: A:0.35, C:0.29, G:0.18, T:0.19
Consensus pattern (27 bp):
TGAAACTGCACAAGTCCATCTATGACC
Done.