Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 191 of 216
Found at i:59610709 original size:27 final size:27
Alignment explanation
Indices: 59610642--59610713 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
59610632 TTTATTATCA
*
59610642 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
59610670 ATAAT-TATTATTTAATATATTTAATT
1 AAAATATATAATTTAATATATTTAAAC
59610696 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
59610714 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
26 12 0.33
27 20 0.56
28 4 0.11
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:59610851 original size:18 final size:17
Alignment explanation
Indices: 59610830--59610864 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
59610820 TTATTATTAA
*
59610830 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
59610848 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
59610865 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:59610876 original size:147 final size:148
Alignment explanation
Indices: 59610603--59610876 Score: 489
Period size: 147 Copynumber: 1.9 Consensus size: 148
59610593 ATGATTATTG
*
59610603 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
*
59610668 ACATAATTATTATTTAATATATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCA
66 ACATAATTATTATTAAATATATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCA
59610733 GAAATTTGTTTTGGTAAA
131 GAAATTTGTTTTGGTAAA
* *
59610751 TTATT-TTATTTAAATTTTAATAAGATTA-TTAATATCAATAATAAATAATTTACTCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
59610814 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ACATAATTATTATTAAATATA-TTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
59610877 ATATTCTTAT
Statistics
Matches: 121, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
146 52 0.43
147 64 0.53
148 5 0.04
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (148 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
ACATAATTATTATTAAATATATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCA
GAAATTTGTTTTGGTAAA
Found at i:59610972 original size:18 final size:17
Alignment explanation
Indices: 59610932--59610984 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
59610922 AAATATAAAT
59610932 TAAAATA-ATAA-TT-A
1 TAAAATATATAATTTAA
*
59610946 TTAAATATAT--TTTAA
1 TAAAATATATAATTTAA
59610961 TTAAAATATATAATTTAA
1 -TAAAATATATAATTTAA
59610979 TAAAAT
1 TAAAAT
59610985 TCTAATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.26
15 3 0.10
16 9 0.29
17 6 0.19
18 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATATATAATTTAA
Found at i:59611042 original size:60 final size:59
Alignment explanation
Indices: 59610858--59611044 Score: 157
Period size: 60 Copynumber: 3.1 Consensus size: 59
59610848 ATATAATTTA
*
59610858 ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTC-TAATAA-TAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
* * ** * * * ** * * * *
59610919 GTAAAATAT-AAATTAA-AATAATAATTAT-TAAATATATTTTAATTAAAATATATAAT-TT
1 ATAAAAT-TCTAA-TAATAAT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT
59610977 AATAAAATTCTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTAATAAT-AATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
59611038 ATAAAAT
1 ATAAAAT
59611045 ATAATTTGAA
Statistics
Matches: 91, Mismatches: 26, Indels: 19
0.67 0.19 0.14
Matches are distributed among these distances:
58 5 0.05
59 37 0.41
60 38 0.42
61 10 0.11
62 1 0.01
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (59 bp):
ATAAAATTCTAATAATAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
Found at i:59611043 original size:119 final size:120
Alignment explanation
Indices: 59610810--59611104 Score: 495
Period size: 119 Copynumber: 2.5 Consensus size: 120
59610800 TTACTCATAT
*
59610810 TTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTAAA-ATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* * *
59610875 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
65 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
59610931 TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC-TAATAATC
1 TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATC
*
59610995 AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAT
66 AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
* *
59611050 TTGAAATAATTAA-TATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 TTAAAATAA-TAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
59611105 TAAAATAATT
Statistics
Matches: 166, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
119 108 0.65
120 53 0.32
121 5 0.03
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (120 bp):
TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATC
AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
Found at i:59614386 original size:20 final size:20
Alignment explanation
Indices: 59614361--59614412 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
59614351 GCACATTCAC
**
59614361 TATAATTTATAAATTTTAAT
1 TATAATTTATAAATAATAAT
*
59614381 TATAA-TAATAATATAATAAT
1 TATAATTTATAA-ATAATAAT
59614401 TATAATTT-TAAA
1 TATAATTTATAAA
59614413 GTTGATATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 6 0.23
20 19 0.73
21 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATAATTTATAAATAATAAT
Found at i:59615100 original size:27 final size:27
Alignment explanation
Indices: 59615060--59615126 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
59615050 AAAATAATAG
*
59615060 AAAAACTATAAATATTATTAA-ATATT
1 AAAAAATATAAATATTATTAATATATT
*
59615086 AAAAAATATAGAATATTATTAATATGTT
1 AAAAAATATA-AATATTATTAATATATT
59615114 ATGAAAAATATAA
1 A--AAAAATATAA
59615127 TAATATATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 9 0.26
27 11 0.31
28 5 0.14
29 1 0.03
30 9 0.26
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.36
Consensus pattern (27 bp):
AAAAAATATAAATATTATTAATATATT
Found at i:59615121 original size:30 final size:27
Alignment explanation
Indices: 59615051--59615145 Score: 97
Period size: 28 Copynumber: 3.4 Consensus size: 27
59615041 GAAAATATAA
*
59615051 AAATAATAGAAAAACTATAAATATTATT
1 AAATATTAGAAAAA-TATAAATATTATT
59615079 AAATATTA-AAAAATATAGAATATTATT
1 AAATATTAGAAAAATATA-AATATTATT
* *
59615106 AATATGTTATGAAAAATAT-AATAATATAT
1 AA-ATATTA-GAAAAATATAAATATTAT-T
59615135 AAAT-TTAGAAA
1 AAATATTAGAAA
59615146 TTATAGAAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
26 8 0.14
27 19 0.32
28 21 0.36
29 3 0.05
30 8 0.14
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.35
Consensus pattern (27 bp):
AAATATTAGAAAAATATAAATATTATT
Found at i:59615160 original size:21 final size:19
Alignment explanation
Indices: 59615135--59615214 Score: 56
Period size: 20 Copynumber: 4.1 Consensus size: 19
59615125 AATAATATAT
59615135 AAATTTAGAAATTATAGAAA
1 AAATTTAGAAATTATA-AAA
*
59615155 ACAATTTA-AAAATATAAAA
1 A-AATTTAGAAATTATAAAA
* *
59615174 AAGTTATAGAAA-TATATATA
1 AAATT-TAGAAATTATA-AAA
* *
59615194 AATTTATAAAAATTATAAAA
1 AAATT-TAGAAATTATAAAA
59615214 A
1 A
59615215 CTTATTAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
18 3 0.06
19 10 0.20
20 26 0.53
21 10 0.20
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.31
Consensus pattern (19 bp):
AAATTTAGAAATTATAAAA
Found at i:59615186 original size:19 final size:19
Alignment explanation
Indices: 59615161--59615251 Score: 67
Period size: 20 Copynumber: 4.6 Consensus size: 19
59615151 GAAAACAATT
59615161 TAAAAATATAAAAAAGTTA
1 TAAAAATATAAAAAAGTTA
* * *
59615180 TAGAAATATATATAAATTTA
1 TAAAAATATA-AAAAAGTTA
*
59615200 TAAAAAT-TATAAAAACTTA
1 TAAAAATATA-AAAAAGTTA
* * *
59615219 TTAATAGTATTAAAAAGTTA
1 -TAAAAATATAAAAAAGTTA
*
59615239 TATAAATTATAAA
1 TA-AAAATATAAA
59615252 TATATATAAG
Statistics
Matches: 55, Mismatches: 13, Indels: 7
0.73 0.17 0.09
Matches are distributed among these distances:
19 21 0.38
20 33 0.60
21 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.35
Consensus pattern (19 bp):
TAAAAATATAAAAAAGTTA
Found at i:59615191 original size:10 final size:9
Alignment explanation
Indices: 59615157--59615251 Score: 59
Period size: 10 Copynumber: 10.0 Consensus size: 9
59615147 TATAGAAAAC
59615157 AATT-TAAA
1 AATTATAAA
59615165 AA-TATAAAA
1 AATTAT-AAA
*
59615174 AAGTTATAGA
1 AA-TTATAAA
59615184 AATATATATAA
1 AAT-TATA-AA
*
59615195 ATTTATAAA
1 AATTATAAA
59615204 AATTATAAA
1 AATTATAAA
*
59615213 AACTTATTAA
1 AA-TTATAAA
* *
59615223 TAGTATTAAA
1 AATTA-TAAA
*
59615233 AAGTTATATA
1 AA-TTATAAA
59615243 AATTATAAA
1 AATTATAAA
59615252 TATATATAAG
Statistics
Matches: 66, Mismatches: 12, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
7 1 0.02
8 3 0.05
9 26 0.39
10 28 0.42
11 8 0.12
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (9 bp):
AATTATAAA
Found at i:59615210 original size:60 final size:60
Alignment explanation
Indices: 59615129--59615275 Score: 144
Period size: 59 Copynumber: 2.5 Consensus size: 60
59615119 AAATATAATA
*
59615129 ATATATAAA-TT-TAGAAATTATAGAAAACA-ATTTAAAAATATAAAAAAGTTATAGAAAT
1 ATATATAAATTTATAAAAATTATAGAAAACATA-TTAAAAATATAAAAAAGTTATAGAAAT
* * * * *
59615187 ATATATAAATTTATAAAAATTATA-AAAACTTATTAATAGTATTAAAAAGTTATATAAAT
1 ATATATAAATTTATAAAAATTATAGAAAACATATTAAAAATATAAAAAAGTTATAGAAAT
* *
59615246 -TATA-AATATATATAAGAAAAATATAGAAAA
1 ATATATAA-ATTTAT-A-AAAATTATAGAAAA
59615276 ATTTTGTTAT
Statistics
Matches: 74, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
57 2 0.03
58 18 0.24
59 31 0.42
60 19 0.26
61 4 0.05
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.33
Consensus pattern (60 bp):
ATATATAAATTTATAAAAATTATAGAAAACATATTAAAAATATAAAAAAGTTATAGAAAT
Found at i:59615539 original size:20 final size:20
Alignment explanation
Indices: 59615514--59615578 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 20
59615504 TATTAATTTT
*
59615514 TTAAAA-ACTATTAGAAATTA
1 TTAAAATACTA-TAAAAATTA
*
59615534 TTAAAATATTATAAAAATTA
1 TTAAAATACTATAAAAATTA
59615554 TT-AAAT-CTTATAAAAATT-
1 TTAAAATAC-TATAAAAATTA
59615572 TTAAAAT
1 TTAAAAT
59615579 TACTGCTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 2 0.05
19 18 0.46
20 16 0.41
21 3 0.08
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (20 bp):
TTAAAATACTATAAAAATTA
Found at i:59615564 original size:19 final size:19
Alignment explanation
Indices: 59615528--59615580 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
59615518 AAACTATTAG
59615528 AAATTATTAAAATATTATAA
1 AAATTATT-AAATATTATAA
*
59615548 AAATTATTAAATCTTATAA
1 AAATTATTAAATATTATAA
59615567 AAATT-TTAAA-ATTA
1 AAATTATTAAATATTA
59615581 CTGCTATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 3 0.10
18 5 0.16
19 15 0.48
20 8 0.26
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTATTAAATATTATAA
Found at i:59617698 original size:20 final size:20
Alignment explanation
Indices: 59617673--59617733 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
59617663 TTGTTTTTTT
59617673 TTTTTAATTTTTAATTAATA
1 TTTTTAATTTTTAATTAATA
* *
59617693 TTTTTAATTTATAAGTATATTA
1 TTTTTAATTTTTAA-T-TAATA
*
59617715 TTTTGAAGTTTTTAATTAA
1 TTTTTAA-TTTTTAATTAA
59617734 AAAACATGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
20 13 0.39
21 3 0.09
22 11 0.33
23 6 0.18
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTTTAATTTTTAATTAATA
Found at i:59618268 original size:69 final size:70
Alignment explanation
Indices: 59618183--59618322 Score: 194
Period size: 72 Copynumber: 2.0 Consensus size: 70
59618173 TTTTACATAT
* *
59618183 AAAAATAATGATATTTGAAATAATTACTT-TTTT-TAATATTAGAATTTACCATACCCACAATGT
1 AAAAATAATGATATTTGAAATAATTACTTATTTTATAATATTAGAATCTACCATACCCACAATGA
59618246 AGGTG
66 AGGTG
* * * *
59618251 AAAACATATTGATATTTGTAATAATTATTTAATTTTATAATATTAGAATCTATCATACCCACAAT
1 AAAA-ATAATGATATTTGAAATAATTACTT-ATTTTATAATATTAGAATCTACCATACCCACAAT
59618316 GAAGGTG
64 GAAGGTG
59618323 GAACAAAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
68 4 0.06
69 22 0.35
71 4 0.06
72 32 0.52
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (70 bp):
AAAAATAATGATATTTGAAATAATTACTTATTTTATAATATTAGAATCTACCATACCCACAATGA
AGGTG
Found at i:59624729 original size:16 final size:17
Alignment explanation
Indices: 59624708--59624739 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
59624698 TATGTGAATG
59624708 TTAAGGG-TTAGGGTTT
1 TTAAGGGTTTAGGGTTT
59624724 TTAAGGGTTTAGGGTT
1 TTAAGGGTTTAGGGTT
59624740 AGGGTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.44
Consensus pattern (17 bp):
TTAAGGGTTTAGGGTTT
Found at i:59624762 original size:23 final size:23
Alignment explanation
Indices: 59624736--59625585 Score: 873
Period size: 23 Copynumber: 36.5 Consensus size: 23
59624726 AAGGGTTTAG
59624736 GGTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
*
59624759 GGTTAAGG--TTTAAGGTTTAATTA
1 GGTTAGGGTTTTTAA--TTTAATTA
*
59624782 GGTTAGGGTTTTCT-TTTTAATTA
1 GGTTAGGGTTTT-TAATTTAATTA
59624805 GGTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
* *
59624828 GGTTAAGGTTTTCAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
* *
59624851 GGTTATGGTTTTTAATTTAATTT
1 GGTTAGGGTTTTTAATTTAATTA
****
59624874 GGTTAGGGTTTAGGGTTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
**
59624897 GGTTAGTATTTTTAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
59624920 GGTTAGGGTTTTTCAATTTAATTA
1 GGTTAGGGTTTTT-AATTTAATTA
*
59624944 GGTAAGGGTTTTCTTTTCAATTTAATTA
1 GGTTAGGG---T-TTTT-AATTTAATTA
****
59624972 GGTTAGGGTTTAGGGTTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
*
59624995 GGTTAGAGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
59625018 GGTTAGGG--TTTAAGGTTTAATTA
1 GGTTAGGGTTTTTAA--TTTAATTA
*
59625041 GGTTAGGGTTTTCAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
59625064 GGTTAGGG--TTTAAGGTTTAATTA
1 GGTTAGGGTTTTTAA--TTTAATTA
*
59625087 GGTTAGGGTTTTCAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
59625110 GGTTAGGG--TTTAAGGTTTAATTA
1 GGTTAGGGTTTTTAA--TTTAATTA
*
59625133 GGTTAGGGTTTTCAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
****
59625156 GGTTAGGGTTTAGGGTTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
** *
59625179 GGTTAGAATTTTTAGTTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
59625202 GGTTAGGGTTTTTCAATTTAATTA
1 GGTTAGGGTTTTT-AATTTAATTA
59625226 GGTTAGGGTTTTTCAATTTAATTA
1 GGTTAGGGTTTTT-AATTTAATTA
****
59625250 GGTTAGGGTTTAGGGTTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
59625273 GGTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
****
59625296 GGTTAGGGTTTAGGGTTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
* *
59625319 GGTTAGGATTTTCAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
****
59625342 GGTTAGGGTTTAGGGTTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
*
59625365 GGTTAGGGTTTTCAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
* **
59625388 GG--A--GTTTATGGTTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
59625407 GGTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
* *
59625430 GGTTAGGGTTTTTCAATTCAATAA
1 GGTTAGGGTTTTT-AATTTAATTA
59625454 GGTTAGGGTTTTCTTTTCAATTTAATTA
1 GGTTAGGG---T-TTTT-AATTTAATTA
* ****
59625482 GGTTAGAGTTTAGGGTTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
* *
59625505 AGTTAGGGTTTTCT-TTTTAATTA
1 GGTTAGGGTTTT-TAATTTAATTA
*
59625528 GGTTAAGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
59625551 GGTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAATTTAATTA
*
59625574 GATTAGGGTTTT
1 GGTTAGGGTTTT
59625586 CTTTTCAATT
Statistics
Matches: 688, Mismatches: 104, Indels: 70
0.80 0.12 0.08
Matches are distributed among these distances:
19 14 0.02
21 20 0.03
22 2 0.00
23 510 0.74
24 81 0.12
25 16 0.02
26 1 0.00
27 2 0.00
28 42 0.06
ACGTcount: A:0.25, C:0.02, G:0.24, T:0.49
Consensus pattern (23 bp):
GGTTAGGGTTTTTAATTTAATTA
Found at i:59625603 original size:46 final size:46
Alignment explanation
Indices: 59624736--59625584 Score: 987
Period size: 46 Copynumber: 18.2 Consensus size: 46
59624726 AAGGGTTTAG
* ** *
59624736 GGTTAGGGTTTTTAATTTAATTAGGTTAAGG--TTTAAGGTTTAATTA
1 GGTTAGGGTTTATGGTTTAATTAGGTTAGGGTTTTTAA--TTTAATTA
**
59624782 GGTTAGGGTTT-TCTTTTTAATTAGGTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTAT-GGTTTAATTAGGTTAGGGTTTTTAATTTAATTA
* ** * *
59624828 GGTTAAGGTTT-TCAATTTAATTAGGTTATGGTTTTTAATTTAATTT
1 GGTTAGGGTTTAT-GGTTTAATTAGGTTAGGGTTTTTAATTTAATTA
* **
59624874 GGTTAGGGTTTAGGGTTTAATTAGGTTAGTATTTTTAATTTAATTA
1 GGTTAGGGTTTATGGTTTAATTAGGTTAGGGTTTTTAATTTAATTA
* ** *
59624920 GGTTAGGGTTTTTCAATTTAATTAGGTAAGGGTTTTCTTTTCAATTTAATTA
1 GGTTAGGGTTTAT-GGTTTAATTAGGTTAGGG---T-TTTT-AATTTAATTA
* *
59624972 GGTTAGGGTTTAGGGTTTAATTAGGTTAGAGTTTTTAATTTAATTA
1 GGTTAGGGTTTATGGTTTAATTAGGTTAGGGTTTTTAATTTAATTA
* *
59625018 GGTTAGGGTTTAAGGTTTAATTAGGTTAGGGTTTTCAATTTAATTA
1 GGTTAGGGTTTATGGTTTAATTAGGTTAGGGTTTTTAATTTAATTA
* *
59625064 GGTTAGGGTTTAAGGTTTAATTAGGTTAGGGTTTTCAATTTAATTA
1 GGTTAGGGTTTATGGTTTAATTAGGTTAGGGTTTTTAATTTAATTA
* *
59625110 GGTTAGGGTTTAAGGTTTAATTAGGTTAGGGTTTTCAATTTAATTA
1 GGTTAGGGTTTATGGTTTAATTAGGTTAGGGTTTTTAATTTAATTA
* ** *
59625156 GGTTAGGGTTTAGGGTTTAATTAGGTTAGAATTTTTAGTTTAATTA
1 GGTTAGGGTTTATGGTTTAATTAGGTTAGGGTTTTTAATTTAATTA
* **
59625202 GGTTAGGGTTTTTCAATTTAATTAGGTTAGGGTTTTTCAATTTAATTA
1 GGTTAGGGTTTAT-GGTTTAATTAGGTTAGGGTTTTT-AATTTAATTA
*
59625250 GGTTAGGGTTTAGGGTTTAATTAGGTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTATGGTTTAATTAGGTTAGGGTTTTTAATTTAATTA
* * *
59625296 GGTTAGGGTTTAGGGTTTAATTAGGTTAGGATTTTCAATTTAATTA
1 GGTTAGGGTTTATGGTTTAATTAGGTTAGGGTTTTTAATTTAATTA
* *
59625342 GGTTAGGGTTTAGGGTTTAATTAGGTTAGGGTTTTCAATTTAATTA
1 GGTTAGGGTTTATGGTTTAATTAGGTTAGGGTTTTTAATTTAATTA
59625388 GG--A--GTTTATGGTTTAATTAGGTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTATGGTTTAATTAGGTTAGGGTTTTTAATTTAATTA
* ** * *
59625430 GGTTAGGGTTTTTCAATTCAATAAGGTTAGGGTTTTCTTTTCAATTTAATTA
1 GGTTAGGGTTTAT-GGTTTAATTAGGTTAGGG---T-TTTT-AATTTAATTA
* * * *
59625482 GGTTAGAGTTTAGGGTTTAATTAAGTTAGGGTTTTCT-TTTTAATTA
1 GGTTAGGGTTTATGGTTTAATTAGGTTAGGGTTTT-TAATTTAATTA
* * **
59625528 GGTTAAGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTATGGTTTAATTAGGTTAGGGTTTTTAATTTAATTA
*
59625574 GATTAGGGTTT
1 GGTTAGGGTTT
59625585 TCTTTTCAAT
Statistics
Matches: 702, Mismatches: 77, Indels: 48
0.85 0.09 0.06
Matches are distributed among these distances:
42 39 0.06
44 2 0.00
45 2 0.00
46 479 0.68
47 74 0.11
48 28 0.04
50 2 0.00
51 35 0.05
52 41 0.06
ACGTcount: A:0.25, C:0.02, G:0.24, T:0.49
Consensus pattern (46 bp):
GGTTAGGGTTTATGGTTTAATTAGGTTAGGGTTTTTAATTTAATTA
Found at i:59625681 original size:25 final size:25
Alignment explanation
Indices: 59625652--59625700 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
59625642 ATTCAAAAAT
59625652 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
59625677 TTCTATTTTATTACATCAAATAAA
1 TTCTATTTTATTACATCAAATAAA
59625701 TTTCAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (25 bp):
TTCTATTTTATTACATCAAATAAAC
Found at i:59626144 original size:18 final size:18
Alignment explanation
Indices: 59626108--59626145 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
59626098 CTCAGAAAAT
*
59626108 GATACATATAAGAGTTAG
1 GATACATATAAGAGCTAG
*
59626126 GATACATATAAGGGCTAG
1 GATACATATAAGAGCTAG
59626144 GA
1 GA
59626146 AACGCACCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.08, G:0.26, T:0.24
Consensus pattern (18 bp):
GATACATATAAGAGCTAG
Found at i:59627027 original size:20 final size:20
Alignment explanation
Indices: 59626990--59627027 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
59626980 TTTATTTTTA
*
59626990 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
59627010 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
59627028 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:59628020 original size:22 final size:22
Alignment explanation
Indices: 59627995--59628069 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
59627985 AAATATGAAT
59627995 TTGAGAGAATTTTAGAAGGAAA
1 TTGAGAGAATTTTAGAAGGAAA
* *
59628017 TTGAGAGAATTTTGGAAAGAAA
1 TTGAGAGAATTTTAGAAGGAAA
* *
59628039 TTGAGAGGAAATTGAG-AGGAAA
1 TTGAGA-GAATTTTAGAAGGAAA
59628061 TATGAGAGA
1 T-TGAGAGA
59628070 GGATTAGTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
22 34 0.76
23 11 0.24
ACGTcount: A:0.45, C:0.00, G:0.31, T:0.24
Consensus pattern (22 bp):
TTGAGAGAATTTTAGAAGGAAA
Found at i:59628068 original size:12 final size:11
Alignment explanation
Indices: 59628035--59628068 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
59628025 ATTTTGGAAA
59628035 GAAATTGAGAG
1 GAAATTGAGAG
59628046 GAAATTGAGAG
1 GAAATTGAGAG
59628057 GAAATATGAGAG
1 GAAAT-TGAGAG
59628069 AGGATTAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.35, T:0.18
Consensus pattern (11 bp):
GAAATTGAGAG
Found at i:59631102 original size:92 final size:92
Alignment explanation
Indices: 59630850--59631159 Score: 327
Period size: 107 Copynumber: 3.1 Consensus size: 92
59630840 AAAAAGAAAA
59630850 ACGAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCTGCACCCAGTACAATTTTTTTTAAAAA
1 ACGAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCC-GCACCCAGTACAA-----TTT-AAAA
59630915 AAGTTCTTTTTTTTGTGTCAGAATCAGATATAAATAT
59 AA--T-TTTTTTTTGTGTCAGAATCAGATATAAATAT
*
59630952 ACGAAAAAAATAAAAAAATTTGGGTGCTGGCCTGTTAATGGCCGGCACCCAGTACAATTT-AAAA
1 ACG----AAA-AAAAAAATTTGGGTGCTGGCCTGTCAATGGCC-GCACCCAGTACAATTTAAAAA
59631016 A-TTTTTTTTGTGTCAGAATCAGATATAAATAT
60 ATTTTTTTTTGTGTCAGAATCAGATATAAATAT
* *
59631048 ATGAAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGACACCTAGTACAATTTTTAAAAAAA
1 ACGAAAAAAAAAA-TTTGGGTGCTGGCCTGTCAATGGCCG-CACCCAGTACAA--TTT---AAAA
* *
59631113 AATTCTTTTTTTTCATGTCTGAATCAGATATAAATAT
59 AA-T-TTTTTTTT-GTGTCAGAATCAGATATAAATAT
59631150 ACGAAAAAAA
1 ACGAAAAAAA
59631160 TAAACATAAT
Statistics
Matches: 183, Mismatches: 8, Indels: 34
0.81 0.04 0.15
Matches are distributed among these distances:
91 8 0.04
92 38 0.21
94 3 0.02
96 33 0.18
98 5 0.03
100 5 0.03
101 8 0.04
102 36 0.20
106 3 0.02
107 44 0.24
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (92 bp):
ACGAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGCACCCAGTACAATTTAAAAAATTTTT
TTTTGTGTCAGAATCAGATATAAATAT
Found at i:59633991 original size:103 final size:102
Alignment explanation
Indices: 59633641--59634323 Score: 881
Period size: 104 Copynumber: 6.6 Consensus size: 102
59633631 ATAACCGACC
*
59633641 AAAAAAGAATTTTTTTTAATATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACTCAAATTTTT
1 AAAAAAGAA-TTTTTTTAA-ATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTT
* * *
59633706 TTTTTATTTTTTCGTATATTTATATATGATTCTGACAC-G
64 TTTAT-TTTTTTCGTATATTTATATCTGATTCTGACACAA
* *
59633745 AAAAAA-AA--TTTTAAAATTGTACTGGGTGCCGGCCATTGAAAGGCCAGCACCCAAATTTTTTT
1 AAAAAAGAATTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAA-TTTTTT
* *
59633807 TTATTTTTTT-GTATATTTATATCTTATTCTGACACGA
65 TTATTTTTTTCGTATATTTATATCTGATTCTGACACAA
*
59633844 AAAAAA-AA-----TTAAATTGTACTGGGTGCCGGCCATTGACAGACCAGCACCCAAATTTTTTT
1 AAAAAAGAATTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTT
59633903 TATTTTTTTCGTATATTTATATCTGATTCTGACACAAA
66 TATTTTTTTCGTATATTTATATCTGATTCTGACAC-AA
*
59633941 AAAAAAGAATTTTTTTAAATTGTACTGGGTGCCGGCCATTGATAGGCCAGCACCCAAAATTTTTT
1 AAAAAAGAATTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC-AAATTTTTT
* *
59634006 TTATTTTTTTCGTATACTGATATCTGATTCTGACACGAA
65 TTATTTTTTTCGTATATTTATATCTGATTCTGACAC-AA
* * * *
59634045 AAGAAAGAAATTTTTTTTAATATTGTACTGGGTGCCAGCCATTGACAGGCCAACA-CTAAATTTT
1 AAAAAAG-AA-TTTTTTTAA-ATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTT
59634109 TTTTA-TTTTTTCGTATATTTATATCTGATTCTGACACGAA
63 TTTTATTTTTTTCGTATATTTATATCTGATTCTGACAC-AA
* *
59634149 AAAAAAGAATTTTTTTTAAAATTGTATTGGGTGCCGGCCATTGACAAGCCAGCA-CCAAATTTTT
1 AAAAAAGAA-TTTTTTT-AAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAA-TTTT
*
59634213 TTTTATTTTTTTCGTATATTTATATCTGATTATGACACAA
63 TTTTATTTTTTTCGTATATTTATATCTGATTCTGACACAA
** ** *
59634253 AAAAAAGAAAAAAAATTTAAAAATTGTACTGGGTGCCAGCCATTGACAGGCCAGCACCCAAAATT
1 AAAAAAG----AATTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC-AAATT
59634318 TTTTTT
61 TTTTTT
59634324 TTTCGTTTTT
Statistics
Matches: 518, Mismatches: 38, Indels: 43
0.86 0.06 0.07
Matches are distributed among these distances:
95 16 0.03
96 65 0.13
97 7 0.01
98 25 0.05
99 52 0.10
100 15 0.03
103 85 0.16
104 116 0.22
105 45 0.09
106 43 0.08
107 44 0.08
108 5 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (102 bp):
AAAAAAGAATTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTT
TATTTTTTTCGTATATTTATATCTGATTCTGACACAA
Found at i:59634340 original size:15 final size:14
Alignment explanation
Indices: 59634316--59634349 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
59634306 GCACCCAAAA
*
59634316 TTTTTTTTTTTCGT
1 TTTTTTTTTTTCCT
59634330 TTTTCTTTTTTTCCT
1 TTTT-TTTTTTTCCT
59634345 TTTTT
1 TTTTT
59634350 CGTATATCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (14 bp):
TTTTTTTTTTTCCT
Found at i:59640801 original size:11 final size:11
Alignment explanation
Indices: 59640787--59640830 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
59640777 AGATAAATAT
59640787 TATTTTATTAA
1 TATTTTATTAA
*
59640798 TATTTTAATAAAA
1 TATTTT-AT-TAA
59640811 TATTTTATTAA
1 TATTTTATTAA
59640822 TATTTTATT
1 TATTTTATT
59640831 TAGTATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 17 0.59
12 4 0.14
13 8 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:59642895 original size:101 final size:100
Alignment explanation
Indices: 59642720--59643014 Score: 324
Period size: 101 Copynumber: 3.0 Consensus size: 100
59642710 AATTGACGAA
* * * * * * * * * *
59642720 TAAGACCATGGTTAGACCATGGAAATGTTTAAATGTAAGACCATGGTTGAGCTGTGGCATTTTAA
1 TAAGACCATGGTTGGACCATGG-AGTGTTTATATGTAAGACCATAGCTGGGCTATGACATTCTGA
* * *
59642785 TGAAAAGACCATAACTGGGTTATGACACTATGAACG
65 TGATAAGACCATAATTGGGTTATGGCACTATGAACG
59642821 TAAGACCATGGTTGGACCATGAGAGTGTTTATATGTAAGACCATAGCTGGGCTATGACATTCTGA
1 TAAGACCATGGTTGGACCATG-GAGTGTTTATATGTAAGACCATAGCTGGGCTATGACATTCTGA
*
59642886 TGATAAGACCATAATTGGGCTATGGCACTATGAACG
65 TGATAAGACCATAATTGGGTTATGGCACTATGAACG
* *
59642922 TAAGACCA----TGG----T--AGTTTTTATATGTAAGACCATAGCTAGGCTAT-ATCATTCTGA
1 TAAGACCATGGTTGGACCATGGAGTGTTTATATGTAAGACCATAGCTGGGCTATGA-CATTCTGA
* *
59642976 TGATAAGACCATAATTGGGTTATGGCACTACGAATG
65 TGATAAGACCATAATTGGGTTATGGCACTATGAACG
59643012 TAA
1 TAA
59643015 AGGATGAATT
Statistics
Matches: 173, Mismatches: 19, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
89 1 0.01
90 74 0.43
93 1 0.01
97 3 0.02
101 93 0.54
102 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (100 bp):
TAAGACCATGGTTGGACCATGGAGTGTTTATATGTAAGACCATAGCTGGGCTATGACATTCTGAT
GATAAGACCATAATTGGGTTATGGCACTATGAACG
Found at i:59642988 original size:90 final size:90
Alignment explanation
Indices: 59642835--59643014 Score: 283
Period size: 90 Copynumber: 2.0 Consensus size: 90
59642825 ACCATGGTTG
*
59642835 GACCATGAGAGTGTTTATATGTAAGACCATAGCTGGGCTATGACATTCTGATGATAAGACCATAA
1 GACCATGAGAGTGTTTATATGTAAGACCATAGCTAGGCTATGACATTCTGATGATAAGACCATAA
*
59642900 TTGGGCTATGGCACTATGAACGTAA
66 TTGGGCTATGGCACTACGAACGTAA
*
59642925 GACCATG-GTAGTTTTTATATGTAAGACCATAGCTAGGCTAT-ATCATTCTGATGATAAGACCAT
1 GACCATGAG-AGTGTTTATATGTAAGACCATAGCTAGGCTATGA-CATTCTGATGATAAGACCAT
* *
59642988 AATTGGGTTATGGCACTACGAATGTAA
64 AATTGGGCTATGGCACTACGAACGTAA
59643015 AGGATGAATT
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
89 2 0.02
90 81 0.98
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (90 bp):
GACCATGAGAGTGTTTATATGTAAGACCATAGCTAGGCTATGACATTCTGATGATAAGACCATAA
TTGGGCTATGGCACTACGAACGTAA
Found at i:59643037 original size:90 final size:90
Alignment explanation
Indices: 59642853--59643038 Score: 214
Period size: 90 Copynumber: 2.1 Consensus size: 90
59642843 GAGTGTTTAT
* *
59642853 ATGTAAGACCATAGCTGGGCTATGACATTCTGATGATAAGACCATAATTGGGCTATGGCACTATG
1 ATGTAAGACCATAGCTAGGCTATGACATTCTGATGATAAGACCATAATTGGGCTATGGCACTACG
* ***** *
59642918 AACGTAAGACCATGGTAGTTTTTAT
66 AACGTAAGACCATGATAGACGGAAA
*
59642943 ATGTAAGACCATAGCTAGGCTAT-ATCATTCTGATGATAAGACCATAATTGGGTTATGGCACTAC
1 ATGTAAGACCATAGCTAGGCTATGA-CATTCTGATGATAAGACCATAATTGGGCTATGGCACTAC
* ** *
59643007 GAATGTAA-AGGATGAATTGACGGAAA
65 GAACGTAAGACCATG-ATAGACGGAAA
59643033 ATGTAA
1 ATGTAA
59643039 AGGATGATAT
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
89 5 0.06
90 75 0.94
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (90 bp):
ATGTAAGACCATAGCTAGGCTATGACATTCTGATGATAAGACCATAATTGGGCTATGGCACTACG
AACGTAAGACCATGATAGACGGAAA
Found at i:59643063 original size:25 final size:25
Alignment explanation
Indices: 59643008--59643073 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
59642998 TGGCACTACG
*
59643008 AATGTAAAGGATGA-ATTGACGGAA
1 AATGTAAAGGATGATATTGACAGAA
59643032 AATGTAAAGGATGATATATGA-AGAA
1 AATGTAAAGGATGATAT-TGACAGAA
*
59643057 ACA-GTAAAAGATGATAT
1 A-ATGTAAAGGATGATAT
59643074 GTATCATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
24 14 0.38
25 19 0.51
26 4 0.11
ACGTcount: A:0.50, C:0.03, G:0.24, T:0.23
Consensus pattern (25 bp):
AATGTAAAGGATGATATTGACAGAA
Found at i:59645441 original size:21 final size:22
Alignment explanation
Indices: 59645420--59645509 Score: 64
Period size: 21 Copynumber: 4.3 Consensus size: 22
59645410 AGGGTTGAAC
59645420 GAAAGCTCATAAGAGCTAAACG
1 GAAAGCTCATAAGAGCTAAACG
* * *
59645442 GAAA-CCCA-ATAGGGTTAAAC-
1 GAAAGCTCATA-AGAGCTAAACG
* * * * *
59645462 TAAAACTCATATGAG-TTAACT
1 GAAAGCTCATAAGAGCTAAACG
59645483 G-AAGCTCATAAGAGCTAAACG
1 GAAAGCTCATAAGAGCTAAACG
59645504 GAAAGC
1 GAAAGC
59645510 AAACACGAAA
Statistics
Matches: 49, Mismatches: 13, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
20 19 0.39
21 21 0.43
22 9 0.18
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (22 bp):
GAAAGCTCATAAGAGCTAAACG
Found at i:59645456 original size:42 final size:42
Alignment explanation
Indices: 59645380--59645472 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
59645370 GGCTGCACAG
* * * *
59645380 AAGCACATAAGTGCTAAACAGAAACCCGTAAGGGTTGAACGA
1 AAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTAAACGA
* *
59645422 AAGCTCATAAGAGCTAAACGGAAACCCA-ATAGGGTTAAACTA
1 AAGCTCATAAGAGCTAAACAGAAACCCATA-AGGGTTAAACGA
*
59645464 AAACTCATA
1 AAGCTCATA
59645473 TGAGTTAACT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 1 0.02
42 42 0.98
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.16
Consensus pattern (42 bp):
AAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTAAACGA
Found at i:59655117 original size:8 final size:8
Alignment explanation
Indices: 59655106--59655152 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
59655096 TGATTTTTTA
59655106 TATATTTG
1 TATATTTG
59655114 TATATTTG
1 TATATTTG
*
59655122 TATATATG
1 TATATTTG
* *
59655130 TACATGTG
1 TATATTTG
59655138 TATATATT-
1 TATAT-TTG
59655146 TATATTT
1 TATATTT
59655153 TTTAACGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
7 2 0.06
8 30 0.91
9 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (8 bp):
TATATTTG
Found at i:59655131 original size:16 final size:16
Alignment explanation
Indices: 59655106--59655152 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
59655096 TGATTTTTTA
*
59655106 TATATTTGTATATTTG
1 TATATATGTATATTTG
* *
59655122 TATATATGTACATGTG
1 TATATATGTATATTTG
*
59655138 TATATATTTATATTT
1 TATATATGTATATTT
59655153 TTTAACGAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (16 bp):
TATATATGTATATTTG
Found at i:59659449 original size:21 final size:21
Alignment explanation
Indices: 59659424--59659471 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
59659414 TTAGTATGAT
59659424 TTTAAAATATAAAATATATTA
1 TTTAAAATATAAAATATATTA
* * * *
59659445 TTTAAATTGTTAATTATATTA
1 TTTAAAATATAAAATATATTA
59659466 TTTAAA
1 TTTAAA
59659472 TGCATTATAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTAAAATATAAAATATATTA
Found at i:59668767 original size:73 final size:73
Alignment explanation
Indices: 59668648--59668794 Score: 267
Period size: 73 Copynumber: 2.0 Consensus size: 73
59668638 AGCAGTCCTA
59668648 CCCATTGAAGTCGAAATTCCTTCTCTCCGAGTATTGGCTGAATTAAAATTCGATGAGGCTGAATG
1 CCCATTGAAGTCGAAATTCCTTCTCTCCGAGTATTGGCTGAATTAAAATTCGATGAGGCTGAATG
59668713 GCTCCAAT
66 GCTCCAAT
* * *
59668721 CCCATTGAAGTCGAAATTCTTTCTCTCTGGGTATTGGCTGAATTAAAATTCGATGAGGCTGAATG
1 CCCATTGAAGTCGAAATTCCTTCTCTCCGAGTATTGGCTGAATTAAAATTCGATGAGGCTGAATG
59668786 GCTCCAAT
66 GCTCCAAT
59668794 C
1 C
59668795 TCGGTATGAT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (73 bp):
CCCATTGAAGTCGAAATTCCTTCTCTCCGAGTATTGGCTGAATTAAAATTCGATGAGGCTGAATG
GCTCCAAT
Found at i:59670481 original size:133 final size:133
Alignment explanation
Indices: 59670243--59671238 Score: 1380
Period size: 133 Copynumber: 7.5 Consensus size: 133
59670233 CATGATTCAC
* * *
59670243 AGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGACCGAAGATGCAGATCTTGTCTTCC
1 AGATAACAGATCTTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
* * * *
59670308 CATACTAGTGGCAAATTAGAACGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
66 CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
59670373 CGA
131 CGA
* *
59670376 AGATAACAGATCTTGTCTTCCTATATTGGTACCGAAGTGGATCGAAGATGCAGATATTGTCTTCC
1 AGATAACAGATCTTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
*
59670441 CATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
66 CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
59670506 CGA
131 CGA
* * *
59670509 AGATAACAGATCCTGTCTTTCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTGGTCTTCC
1 AGATAACAGATCTTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
*
59670574 CATACTGGTGGCGAAGTGGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
66 CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
59670639 CGA
131 CGA
*
59670642 AGATAACAGAT-TCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTC
1 AGATAACAGATCT-TGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTC
* *
59670706 CCATACTAGTGGCAAAGTAGAAT-GAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAG
65 CCATACTGGTGGCGAAGTAG-ATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAG
59670770 ATCGA
129 ATCGA
*
59670775 AGATAACAGATCTTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATATTGTCTTCC
1 AGATAACAGATCTTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
* *
59670840 CATACTGGTGGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
66 CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
59670905 CGA
131 CGA
* * *
59670908 AGATAACAGATCTTGTCTTTCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTGGTCTTCC
1 AGATAACAGATCTTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
* * * *
59670973 CATACTGGTGGCGAAGTGGATCGAAGAAAGCAGATCTTGTCTTCCCATACTAGTGGC--AAAGTA
66 CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT--CAT-GTATTGGCGTGAAGTA
59671036 GATCGA
128 GATCGA
* * * * *
59671042 AGA-AAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTGGATCGAAGATAACAGATCTTGTCTT
1 AGATAA-CAGATCTTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGAT-GCAGATCTTGTCTT
* * * * * * *** * *
59671105 CCTATATTGGTAGCGAAGTGGATCGAAG-ATGCAGATCTTATCTTCCCATATTGGTGGCGAAGTA
64 CCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTA
59671169 GATCGA
128 GATCGA
* * * * ** * *
59671175 AGA-AAGTAGATCTTGTCTTCATGTATTGG-CGTAAAGTGGATCGAAAATAGCAGATCCTGTCTT
1 AGATAA-CAGATCTTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGAT-GCAGATCTTGTCTT
59671238 C
64 C
59671239 TTATATTGGC
Statistics
Matches: 789, Mismatches: 62, Indels: 24
0.90 0.07 0.03
Matches are distributed among these distances:
130 5 0.01
131 1 0.00
132 2 0.00
133 698 0.88
134 74 0.09
135 3 0.00
136 6 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (133 bp):
AGATAACAGATCTTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
CGA
Found at i:59671217 original size:44 final size:44
Alignment explanation
Indices: 59670247--59671253 Score: 777
Period size: 44 Copynumber: 22.7 Consensus size: 44
59670237 ATTCACAGAT
* * * * *
59670247 AGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGACCGAAG-A
1 AGCAGATCTTGTCTTCATATATTGG-CGTGAAGTGGATCGAAGAA
* * * * * *
59670291 TGCAGATCTTGTCTTCCCATACTAGTGGC--AAATTAGAACGAAGAA
1 AGCAGATCTTGTCTT--CATA-TATTGGCGTGAAGTGGATCGAAGAA
* *
59670336 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATA
1 AGCAGATCTTGTCTTCATATATTGGCGTGAAGTGGATCGAAGA-A
* *
59670381 A-CAGATCTTGTCTTCCTATATTGGTAC-CGAAGTGGATCGAAG-A
1 AGCAGATCTTGTCTTCATATATTGG--CGTGAAGTGGATCGAAGAA
* * ** * * *
59670424 TGCAGATATTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATATATTGG-CGTGAAGTGGATCGAAGAA
* *
59670469 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATA
1 AGCAGATCTTGTCTTCATATATTGGCGTGAAGTGGATCGAAGA-A
* * *
59670514 A-CAGATCCTGTCTTTC-TATATTGGTAGCGAAGTGGATCGAAG-A
1 AGCAGATCTTGTC-TTCATATATTGG-CGTGAAGTGGATCGAAGAA
* * ** * * *
59670557 TGCAGATCTGGTCTTCCCATACTGGTGGCGAAGTGGATCGAAGAA
1 AGCAGATCTTGTCTTCATATATTGG-CGTGAAGTGGATCGAAGAA
* *
59670602 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATA
1 AGCAGATCTTGTCTTCATATATTGGCGTGAAGTGGATCGAAGA-A
* *
59670647 A-CAGAT-TCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAG-A
1 AGCAGATCT-TGTCTTCATATATTGG-CGTGAAGTGGATCGAAGAA
* * * *
59670690 TGCAGATCTTGTCTTCCCATACTAGTGGC--AAAGTAGAAT-GAAGAA
1 AGCAGATCTTGTCTT--CATA-TATTGGCGTGAAGT-GGATCGAAGAA
* *
59670735 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATA
1 AGCAGATCTTGTCTTCATATATTGGCGTGAAGTGGATCGAAGA-A
* * *
59670780 A-CAGATCTTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAG-A
1 AGCAGATCTTGTCTTCATATATTGG-CGTGAAGTGGATCGAAGAA
* * ** * * * *
59670823 TGCAGATATTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAA
1 AGCAGATCTTGTCTTCATATATTGG-CGTGAAGTGGATCGAAGAA
* *
59670868 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATA
1 AGCAGATCTTGTCTTCATATATTGGCGTGAAGTGGATCGAAGA-A
*
59670913 A-CAGATCTTGTCTTTC-TATATTGGTAGTGAAGTGGATCGAAG-A
1 AGCAGATCTTGTC-TTCATATATTGG-CGTGAAGTGGATCGAAGAA
* * ** * * *
59670956 TGCAGATCTGGTCTTCCCATACTGGTGGCGAAGTGGATCGAAGAA
1 AGCAGATCTTGTCTTCATATATTGG-CGTGAAGTGGATCGAAGAA
* * *
59671001 AGCAGATCTTGTCTTCCCATACTAGTGGC--AAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTT--CATA-TATTGGCGTGAAGTGGATCGAAGAA
*
59671046 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTGGATCGAAGATA
1 AGCAGATCTTGTCTTCATATATTGGCGTGAAGTGGATCGAAGA-A
* * *
59671091 A-CAGATCTTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAG-A
1 AGCAGATCTTGTCTTCATATATTGG-CGTGAAGTGGATCGAAGAA
* * ** * * *
59671134 TGCAGATCTTATCTTCCCATATTGGTGGCGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATATATTGG-CGTGAAGTGGATCGAAGAA
* * *
59671179 AGTAGATCTTGTCTTCATGTATTGGCGTAAAGTGGATCGAA-AA
1 AGCAGATCTTGTCTTCATATATTGGCGTGAAGTGGATCGAAGAA
* *
59671222 TAGCAGATCCTGTCTTCTTATATTGGCAGTGA
1 -AGCAGATCTTGTCTTCATATATTGGC-GTGA
59671254 CGCAGACTGA
Statistics
Matches: 775, Mismatches: 136, Indels: 103
0.76 0.13 0.10
Matches are distributed among these distances:
42 18 0.02
43 26 0.03
44 443 0.57
45 264 0.34
46 7 0.01
47 12 0.02
48 5 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.30
Consensus pattern (44 bp):
AGCAGATCTTGTCTTCATATATTGGCGTGAAGTGGATCGAAGAA
Found at i:59674534 original size:30 final size:31
Alignment explanation
Indices: 59674483--59674556 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 31
59674473 TCACTAAATT
* ** *
59674483 TTTATTAAAA-TGATATTTCAGTTATTAA-A
1 TTTATAAAAAGTGATAAATCAGTCATTAACA
*
59674512 TTTATAAAAAGTGATAAATCAGTCATTAACG
1 TTTATAAAAAGTGATAAATCAGTCATTAACA
*
59674543 TTTATGAAAAGTGA
1 TTTATAAAAAGTGA
59674557 CAAAGCAATC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 9 0.24
30 15 0.41
31 13 0.35
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.39
Consensus pattern (31 bp):
TTTATAAAAAGTGATAAATCAGTCATTAACA
Found at i:59677650 original size:57 final size:56
Alignment explanation
Indices: 59677556--59677670 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 56
59677546 CTTTTACTTT
*
59677556 TGGTGGATAGAATTCCCTTAACAGTTCTCATAAATTGAGAATTCATTTGTGTTTGA
1 TGGTGGATAGAATTCCCTTAACAGTTCTCATAAATTGAGAATTCACTTGTGTTTGA
**
59677612 TGGTGGATAGAATTCCCTTTAACTTTTCTCATAAATTGAGAATTCACTTGTGTTTGA
1 TGGTGGATAGAATTCCC-TTAACAGTTCTCATAAATTGAGAATTCACTTGTGTTTGA
59677669 TG
1 TG
59677671 ATATGAAATT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 17 0.31
57 38 0.69
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (56 bp):
TGGTGGATAGAATTCCCTTAACAGTTCTCATAAATTGAGAATTCACTTGTGTTTGA
Found at i:59686645 original size:5 final size:5
Alignment explanation
Indices: 59686635--59686680 Score: 83
Period size: 5 Copynumber: 9.2 Consensus size: 5
59686625 CATTGCTTTC
*
59686635 TCTAG TCTAG TCTAG TCTAG TCTAG TCTAG TCTAG TCTTG TCTAG T
1 TCTAG TCTAG TCTAG TCTAG TCTAG TCTAG TCTAG TCTAG TCTAG T
59686681 GTAGGTCTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.43
Consensus pattern (5 bp):
TCTAG
Found at i:59716068 original size:21 final size:21
Alignment explanation
Indices: 59716044--59716132 Score: 56
Period size: 21 Copynumber: 4.2 Consensus size: 21
59716034 ACTCGTATGA
59716044 GTTTCAGATTAACCCTTCTGG
1 GTTTCAGATTAACCCTTCTGG
* * * *
59716065 GTTTCAG-TTCAGCTCTTTTGA
1 GTTTCAGATT-AACCCTTCTGG
* * * *
59716086 GCTTCAGTTTAGCTCTTCTGAG
1 GTTTCAGATTAACCCTTCTG-G
* *
59716108 CTTT-AGATTAACCCTTATGG
1 GTTTCAGATTAACCCTTCTGG
59716128 GTTTC
1 GTTTC
59716133 CATTCAGCTC
Statistics
Matches: 50, Mismatches: 14, Indels: 8
0.69 0.19 0.11
Matches are distributed among these distances:
20 6 0.12
21 40 0.80
22 4 0.08
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (21 bp):
GTTTCAGATTAACCCTTCTGG
Found at i:59716168 original size:21 final size:21
Alignment explanation
Indices: 59716117--59716168 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
59716107 GCTTTAGATT
* *
59716117 AACCCTTATGGGTTTCCATTC
1 AACCCTTATGAGCTTCCATTC
* *
59716138 AGCTCC-TATGAGCTTCCGTTC
1 AAC-CCTTATGAGCTTCCATTC
59716159 AACCCTTATG
1 AACCCTTATG
59716169 GATTTTCGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.19, C:0.31, G:0.15, T:0.35
Consensus pattern (21 bp):
AACCCTTATGAGCTTCCATTC
Found at i:59722963 original size:19 final size:19
Alignment explanation
Indices: 59722933--59722972 Score: 64
Period size: 18 Copynumber: 2.1 Consensus size: 19
59722923 TTCTTCATAA
59722933 TTTGTATATTTTAAATATTT
1 TTTGTATATTTT-AATATTT
59722953 TTTGT-TATTTTAATATTT
1 TTTGTATATTTTAATATTT
59722971 TT
1 TT
59722973 CAATTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 9 0.45
19 6 0.30
20 5 0.25
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTGTATATTTTAATATTT
Found at i:59722969 original size:18 final size:20
Alignment explanation
Indices: 59722933--59723005 Score: 68
Period size: 19 Copynumber: 3.9 Consensus size: 20
59722923 TTCTTCATAA
59722933 TTTGTATATTTTAAATATTT
1 TTTGTATATTTTAAATATTT
59722953 TTTGT-TATTTT-AATA-TT
1 TTTGTATATTTTAAATATTT
* *
59722970 TTT-CA-ATTTTAAAATAATT
1 TTTGTATATTTT-AAATATTT
*
59722989 TTTATA-ATTTTAAATAT
1 TTTGTATATTTTAAATAT
59723006 AAAATATTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
16 5 0.11
17 5 0.11
18 8 0.18
19 16 0.36
20 11 0.24
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTGTATATTTTAAATATTT
Found at i:59722989 original size:19 final size:21
Alignment explanation
Indices: 59722967--59723007 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
59722957 TTATTTTAAT
59722967 ATTTTT-CAATTTTAAA-ATA
1 ATTTTTACAATTTTAAATATA
*
59722986 ATTTTTATAATTTTAAATATA
1 ATTTTTACAATTTTAAATATA
59723007 A
1 A
59723008 AATATTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 9 0.47
21 4 0.21
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTTACAATTTTAAATATA
Found at i:59723220 original size:16 final size:16
Alignment explanation
Indices: 59723199--59723253 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
59723189 GTTTGGTTCA
59723199 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
59723215 CTGTAAAT-GAATAGAG
1 CTGT-AATGGAATAGAG
*
59723231 CTGTAATGGAATAAAG
1 CTGTAATGGAATAGAG
*
59723247 TTGTAAT
1 CTGTAAT
59723254 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 3 0.09
16 29 0.83
17 3 0.09
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.29
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:59726401 original size:44 final size:43
Alignment explanation
Indices: 59726351--59727786 Score: 784
Period size: 44 Copynumber: 32.4 Consensus size: 43
59726341 GCCAATACAT
* * **
59726351 GAAGACAAGGTCTATTTTTTCGATCTGTTTCGCAACCAGTATGG
1 GAAGACAAGATCTGTTTTTTCGATCTACTTCGC-ACCAGTATGG
* * ***
59726395 GAAGACAAGATCTGTTATCTTT-GATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGTT-T-TTTCGATCTACTTCGCACCAGTATGG
*
59726439 GAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAATATGG
1 GAAGACAAGATCTGTTTT-TTCGATCTACTTCG-CACCAGTATGG
** * ***
59726484 GAAGACAAGATCTGGTATCGTT-GATCTACTTCACACCAGTACAT
1 GAAGACAAGATCT-GT-TTTTTCGATCTACTTCGCACCAGTATGG
*
59726528 GAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCATCAGTATGG
1 GAAGACAAGATCTGTTTT-TTCGATCTACTTCG-CACCAGTATGG
* * * * ***
59726573 TAAGACAAGATCTGTTATCTTT-GATCTACTCCACGCCAGTACAT
1 GAAGACAAGATCTGTT-T-TTTCGATCTACTTCGCACCAGTATGG
* * *
59726617 GAAGACAAGATCTACTTTCTTCGATTTACTTCGCCACCAGTATGG
1 GAAGACAAGATCT-GTTTTTTCGATCTACTTCG-CACCAGTATGG
* * ** * ***
59726662 GAAAACAAGATCTGGTATCTTT-GATCTACTTTACGCCAGTACAT
1 GAAGACAAGATCT-GT-TTTTTCGATCTACTTCGCACCAGTATGG
* *
59726706 GAAGACAAGATCTGCTTTCTTCAATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTG-TTTTTTCGATCTACTTCG-CACCAGTATGG
* * ***
59726751 GAAGACAAGATCTGTTATCTTT-GATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGTT-T-TTTCGATCTACTTCGCACCAGTATGG
* * *** ***
59726795 GAAGACAAAATCTGGTATCTTT-GATCTACTTCATGCCAGTACAT
1 GAAGACAAGATCT-GT-TTTTTCGATCTACTTCGCACCAGTATGG
* * *
59726839 AAAGATAAGATCTGCTTTCTTT-GATCTACTTCGCCAGCAGTATGG
1 GAAGACAAGATCTG-TTT-TTTCGATCTACTTCG-CACCAGTATGG
* * * ***
59726884 GAAGATAAGATCTGTTATCTTT-GATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGTT-T-TTTCGATCTACTTCGCACCAGTATGG
59726928 GAAGACAAGATCTGCTTTCTTT-GATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTG-TTT-TTTCGATCTACTTCG-CACCAGTATGG
* * * * * ***
59726973 GAAGATAAGATTTGTTATTTTTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGTT-TTTTCGATCTACTTCGCACCAGTATGG
* *
59727017 GAAGACAAGATCTGATTTCTTCGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTG-TTTTTTCGATCTACTTCG-CACCAGTATGG
* * * * * * * ***
59727062 GAAGGCAAGATCTGGTATCTCTAATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGTTTTTTC-GATCTACTTCGCACCAGTATGG
* **
59727106 GAAGACAAGATCTGCTTTCTTCGATCTGTTTCGTCACCAGTATGG
1 GAAGACAAGATCTG-TTTTTTCGATCTACTTCG-CACCAGTATGG
* * * * ***
59727151 GAAGACAAGATCTGTTATTTTTGATCTACTCCACGCCAGTACAT
1 GAAGACAAGATCTGTT-TTTTCGATCTACTTCGCACCAGTATGG
* * * ***
59727195 GAAGACAAGATCTGGTATCTTT-GATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCT-GT-TTTTTCGATCTACTTCGCACCAGTATGG
* * *
59727239 GAAGACAAGATTTGCTTTCTTCGATCTACTTCACCACCAGTATGG
1 GAAGACAAGATCTG-TTTTTTCGATCTACTTC-GCACCAGTATGG
* ** * ***
59727284 GAAGACAAGATCTGGTATCTTT-GATCTACTTTACGCCAGTACAT
1 GAAGACAAGATCT-GT-TTTTTCGATCTACTTCGCACCAGTATGG
* * *
59727328 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATAG
1 GAAGACAAGATCTG-TTTTTTCGATCTACTTC-GCACCAGTATGG
* * ** ***
59727373 GAAGACAAGATCTGTTATCTTT-GATCTATTTCACGTCAGTACAT
1 GAAGACAAGATCTGTT-T-TTTCGATCTACTTCGCACCAGTATGG
* * * * ***
59727417 GAAGACAAAATCTGGTATCTTT-GATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCT-GT-TTTTTCGATCTACTTCGCACCAGTATGG
* *
59727461 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATAT--
1 GAAGACAAGATCTG-TTTTTTCGATCTACTTCG-CACCAGTATGG
* *
59727504 GAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTG-TTTTTTCGATCTACTTCG-CACCAGTATGG
* * * * * * * ***
59727549 GAAGGCAAGATATAG-TATCTCTGATCTACTTCACGCCGGTACAT
1 GAAGACAAGATCT-GTTTTTTC-GATCTACTTCGCACCAGTATGG
* **
59727593 GAAGACAAGATCTGCTTTCTTCGATCTGTTTCGTCACCAGTATGG
1 GAAGACAAGATCTG-TTTTTTCGATCTACTTCG-CACCAGTATGG
* * ***
59727638 GAAGACAAGATCTGTTATCTTT-GATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTGTT-T-TTTCGATCTACTTCGCACCAGTATGG
* *
59727682 GAAGACAAGATCTATTGTCTTT-GATCTACTTCACCACCAGTATGG
1 GAAGACAAGATCTGTT-T-TTTCGATCTACTTC-GCACCAGTATGG
* * * * * * * ***
59727727 GAAGGCAAGATTTGGTTTCTCTGATCTACCTCACGCCAGTACAT
1 GAAGACAAGATCTGTTTTTTC-GATCTACTTCGCACCAGTATGG
59727771 GAAGACAAGATCTGTT
1 GAAGACAAGATCTGTT
59727787 ATCTTTCAAC
Statistics
Matches: 1071, Mismatches: 255, Indels: 132
0.73 0.17 0.09
Matches are distributed among these distances:
42 2 0.00
43 71 0.07
44 553 0.52
45 416 0.39
46 27 0.03
47 2 0.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (43 bp):
GAAGACAAGATCTGTTTTTTCGATCTACTTCGCACCAGTATGG
Found at i:59726494 original size:89 final size:89
Alignment explanation
Indices: 59726314--59727791 Score: 1445
Period size: 89 Copynumber: 16.7 Consensus size: 89
59726304 CAGAGTAATG
* * * * * *
59726314 AGATCTGCTATGC-TTGATCTATTTCATGCCAATACATGAAGACAAGGTCTATTTT-TTCGATCT
1 AGATCTGTTAT-CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCT
** *
59726377 GTTTCGCAACCAGTATGGGAAGACA
65 ACTTCGCCACCAGTATGGGAAGACA
59726402 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTA
1 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTA
*
59726467 CTTCGCCACCAATATGGGAAGACA
66 CTTCGCCACCAGTATGGGAAGACA
* * *
59726491 AGATCTGGTATCGTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTA
1 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTA
* *
59726556 CTTCGCCATCAGTATGGTAAGACA
66 CTTCGCCACCAGTATGGGAAGACA
* ** *
59726580 AGATCTGTTATCTTTGATCTACTCCACGCCAGTACATGAAGACAAGATCTACTTTCTTCGATTTA
1 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTA
*
59726645 CTTCGCCACCAGTATGGGAAAACA
66 CTTCGCCACCAGTATGGGAAGACA
* * * *
59726669 AGATCTGGTATCTTTGATCTACTTTACGCCAGTACATGAAGACAAGATCTGCTTTCTTCAATCTA
1 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTA
59726734 CTTCGCCACCAGTATGGGAAGACA
66 CTTCGCCACCAGTATGGGAAGACA
* * * *
59726758 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAAATCTGGTATCTTTGATCTA
1 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTA
*** **** *
59726823 CTTC-ATGCCAGTACATAAAGATA
66 CTTCGCCACCAGTATGGGAAGACA
* * * * *
59726846 AGATCTGCTT-TCTTTGATCTACTT--CGCCAGCAGTATGGGAAGATAAGATCTGTTATCTTTGA
1 AGATCTG-TTATCTTTGATCTACTTCACGCCAGTA-CAT--GAAGACAAGATCTGTTTTCTTCGA
* * ***
59726908 TCTACTTC-ACGCCAGTACATGAAGACA
62 TCTACTTCGCCACCAGTATGGGAAGACA
* * *** * * *
59726935 AGATCTGCTT-TCTTTGATCTACTTCGCCACCAGTATGGGAAGATAAGATTTGTTATT-TTTGAT
1 AGATCTG-TTATCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGTT-TTCTTCGAT
* * ***
59726998 CTACTTC-ACGCCAGTACATGAAGACA
63 CTACTTCGCCACCAGTATGGGAAGACA
* * * * *** * * * *
59727024 AGATCTGATT-TCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATC-TCTAAT
1 AGATCTG-TTATCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGTTTTCTTC-GAT
* * ***
59727087 CTACTTC-ACGCCAGTACATGAAGACA
63 CTACTTCGCCACCAGTATGGGAAGACA
* ** * * *** *
59727113 AGATCTGCTT-TCTTCGATCTGTTTCGTCACCAGTATGGGAAGACAAGATCTGTTATT-TTTGAT
1 AGATCTG-TTATCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGTT-TTCTTCGAT
* ***
59727176 CTAC-TC-CACGCCAGTACATGAAGACA
63 CTACTTCGC-CACCAGTATGGGAAGACA
* * *
59727202 AGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATTTGCTTTCTTCGATCTA
1 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTA
*
59727267 CTTCACCACCAGTATGGGAAGACA
66 CTTCGCCACCAGTATGGGAAGACA
* * *
59727291 AGATCTGGTATCTTTGATCTACTTTACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTA
1 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTA
* *
59727356 CTTCACCACCAGTATAGGAAGACA
66 CTTCGCCACCAGTATGGGAAGACA
* * * * * *
59727380 AGATCTGTTATCTTTGATCTATTTCACGTCAGTACATGAAGACAAAATCTGGTATCTTTGATCTA
1 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTA
* * ***
59727445 CTTC-ACGCCAGTACATGAAGACA
66 CTTCGCCACCAGTATGGGAAGACA
* ** * *
59727468 AGATCTGCTT-TCTTCGATCTACTT--CGCCACCAATATGAAGACAAGATCTGCTTTCTTCGATC
1 AGATCTG-TTATCTTTGATCTACTTCACGCCA-GTACATGAAGACAAGATCTGTTTTCTTCGATC
* *
59727530 TGCTTCGCCACCAGTATGGGAAGGCA
64 TACTTCGCCACCAGTATGGGAAGACA
* * * *
59727556 AGATATAG-TATCTCTGATCTACTTCACGCCGGTACATGAAGACAAGATCTGCTTTCTTCGATCT
1 AGATCT-GTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCT
** *
59727620 GTTTCGTCACCAGTATGGGAAGACA
65 ACTTCGCCACCAGTATGGGAAGACA
* * *
59727645 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTGTCTTTGATCTA
1 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTA
* *
59727710 CTTCACCACCAGTATGGGAAGGCA
66 CTTCGCCACCAGTATGGGAAGACA
* * * *
59727734 AGATTTGGTT-TCTCTGATCTACCTCACGCCAGTACATGAAGACAAGATCTGTTATCTT
1 AGATCT-GTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
59727792 TCAACCTGCT
Statistics
Matches: 1206, Mismatches: 156, Indels: 55
0.85 0.11 0.04
Matches are distributed among these distances:
86 11 0.01
87 36 0.03
88 179 0.15
89 962 0.80
90 11 0.01
91 1 0.00
92 6 0.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (89 bp):
AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTA
CTTCGCCACCAGTATGGGAAGACA
Found at i:59726819 original size:222 final size:221
Alignment explanation
Indices: 59726314--59727792 Score: 1267
Period size: 222 Copynumber: 6.7 Consensus size: 221
59726304 CAGAGTAATG
* * * * * * *
59726314 AGATCTGCTATGC-TTGATCTATTTCATGCCAATACATGAAGACAAGGTCT-ATTTTTTCGATCT
1 AGATCTGTTAT-CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCT
** ** * * * ***
59726377 GTTTCGCA-ACCAGTATGGGAAGACAAGATCTG-TTATCTTTGATCTACTTC-ACGCCAGTACAT
65 -ACTC-CACACCAGTATATGAAGACAAGATCTGCTT-TCTTCGATCTACTTCGCCACCAGTATGG
* * * * * * *** * * *
59726439 GAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGGTATCG
127 GAAGACAAGATCTGCTATCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTTTCT
* *
59726504 TTGATCTACTTCACACCAGTACATGAAGACA
191 TTGATCTACTTCCCACCAGTACAGGAAGACA
* * * *
59726535 AGATCTGTTTTCTTCGATCTACTT--CGCCA-TCAGTATGGTAAGACAAGATCTG-TTATCTTTG
1 AGATCTGTTATCTTTGATCTACTTCACGCCAGT-A-CAT-G-AAGACAAGATCTGCTT-TCTTCG
* * * *
59726596 ATCTACTCCACGCCAGTACATGAAGACAAGATCTACTTTCTTCGATTTACTTCGCCACCAGTATG
61 ATCTACTCCACACCAGTATATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATG
* * *
59726661 GGAAAACAAGATCTGGTATCTTTGATCTACTTTACGCCAGTACATGAAGACAAGATCTGCTTTCT
126 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCT
** **
59726726 TCAATCTACTTCGCCACCAGTATGGGAAGACA
191 TTGATCTACTTC-CCACCAGTACAGGAAGACA
* * * *
59726758 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAAATCTGGTATCTTTGATCTA
1 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTA
* ** * * * * *
59726823 CTTCATGCCAGTACATAAAGATAAGATCTGCTTTCTTTGATCTACTTCGCCAGCAGTATGGGAAG
66 CTCCACACCAGTATATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAG
* *
59726888 ATAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGAT
131 ACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGAT
** *
59726953 CTACTTCGCCACCAGTATGGGAAGATA
196 CTACTTC-CCACCAGTACAGGAAGACA
* * * *
59726980 AGATTTGTTATTTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGATTTCTTCGATCTG
1 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTA
** * * * * * * ***
59727045 CTTCGC-CACCAGTATGGGAAGGCAAGATCTGGTATC-TCTAATCTACTTC-ACGCCAGTACATG
66 C-TC-CACACCAGTATATGAAGACAAGATCTGCTTTCTTC-GATCTACTTCGCCACCAGTATGGG
* * ** * * *** *
59727107 AAGACAAGATCTGCTTTCTTCGATCTGTTTCGTCACCAGTATGGGAAGACAAGATCTG-TTATTT
128 AAGACAAGATCTGCTATCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTT-TCT
* *
59727171 TTGATCTAC-TCCACGCCAGTACATGAAGACA
191 TTGATCTACTTCC-CACCAGTACAGGAAGACA
* *
59727202 AGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATTTGCTTTCTTCGATCTA
1 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTA
* ** * * * ** * ***
59727267 CTTCACCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTT-TACGCCAGTACATGAA
66 CTCCA-CACCAGTATATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAA
* * * * *
59727331 GACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATAGGAAGACAAGATCTG-TTATCTTT
130 GACAAGATCTGCTATCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGCTT-TCTTT
* * ** *
59727395 GATCTATTTCACGTCAGTACATGAAGACA
193 GATCTACTTCCCACCAGTACAGGAAGACA
* *
59727424 AAATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTA
1 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTA
*
59727489 CTTCGC-CACCA--ATATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGA
66 C-TC-CACACCAGTATATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGA
* * * * *
59727551 AGGCAAGATATAG-TATCTCTGATCTACTTCACGCCGGTACATGAAGACAAGATCTGCTTTCTTC
129 AGACAAGATCT-GCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTT
** * **
59727615 GATCTGTTTCGTCACCAGTATGGGAAGACA
193 GATCTACTTC-CCACCAGTACAGGAAGACA
* *
59727645 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCT-ATTGTCTTTGATCT
1 AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT-TCTTCGATCT
* ** * * * * * * ***
59727709 ACTTCACCACCAGTATGGGAAGGCAAGATTTGGTTTC-TCTGATCTACCTC-ACGCCAGTACATG
65 ACTCCA-CACCAGTATATGAAGACAAGATCTGCTTTCTTC-GATCTACTTCGCCACCAGTATGGG
*
59727772 AAGACAAGATCTGTTATCTTT
128 AAGACAAGATCTGCTATCTTT
59727793 CAACCTGCTC
Statistics
Matches: 1042, Mismatches: 176, Indels: 79
0.80 0.14 0.06
Matches are distributed among these distances:
218 1 0.00
219 6 0.01
220 70 0.07
221 136 0.13
222 643 0.62
223 175 0.17
224 4 0.00
225 6 0.01
226 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (221 bp):
AGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTA
CTCCACACCAGTATATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAG
ACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGAT
CTACTTCCCACCAGTACAGGAAGACA
Found at i:59727091 original size:400 final size:399
Alignment explanation
Indices: 59726395--59727792 Score: 1833
Period size: 400 Copynumber: 3.5 Consensus size: 399
59726385 ACCAGTATGG
* *
59726395 GAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* * *
59726460 CGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGGTATCGTTGATCTACTTCACACCAGTA
66 CGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTA
* * *
59726525 CATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCATCAGTATGGTAAGACAAGATCTGTTA
131 CATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTA
* *
59726590 TCTTTGATCTACTCCACGCCAGTACATGAAGACAAGATCT-ACTTTCTTCGATTTACTTCGCCAC
196 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGA-TTTCTTCGATCTACTTCGCCAC
*
59726654 CAGTATGGGAAAACAAGATCTGGTATCTTTGATCTACTTTACGCCAGTACATGAAGACAAGATCT
260 CAGTATGGGAAGACAAGATCTGGTATC-TTGATCTACTTTACGCCAGTACATGAAGACAAGATCT
* *
59726719 GCTTTCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCA
324 GCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCA
59726784 CGCCAGTACAT
389 CGCCAGTACAT
* * * *
59726795 GAAGACAAAATCTGGTATCTTTGATCTACTTCATGCCAGTACATAAAGATAAGATCTGCTTTCTT
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* * * *
59726860 TGATCTACTTCGCCAGCAGTATGGGAAGATAAGATCTGTTATCTTTGATCTACTTCACGCCAGTA
66 CGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTA
* * *
59726925 CATGAAGACAAGATCTGCTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGATAAGATTTGTTA
131 CATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTA
* *
59726990 TTTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGATTTCTTCGATCTGCTTCGCCACC
196 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGATTTCTTCGATCTACTTCGCCACC
* * *
59727055 AGTATGGGAAGGCAAGATCTGGTATCTCTAATCTACTTCACGCCAGTACATGAAGACAAGATCTG
261 AGTATGGGAAGACAAGATCTGGTATCT-TGATCTACTTTACGCCAGTACATGAAGACAAGATCTG
* * * *
59727120 CTTTCTTCGATCTGTTTCGTCACCAGTATGGGAAGACAAGATCTGTTATTTTTGATCTACTCCAC
325 CTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCAC
59727185 GCCAGTACAT
390 GCCAGTACAT
*
59727195 GAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATTTGCTTTCTT
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
* *
59727260 CGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTTACGCCAGTA
66 CGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTA
* *
59727325 CATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATAGGAAGACAAGATCTGTTA
131 CATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTA
* * * * * * * *
59727390 TCTTTGATCTATTTCACGTCAGTACATGAAGACAAAATCTGGTATCTTTGATCTACTTC-ACGCC
196 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGATTTCTTCGATCTACTTCGCCACC
*** * * ** *
59727454 AGTACATGAAGACAAGATCTGCTTTCTTCGATCTAC-TT-CGCCACCAATATGAAGACAAGATCT
261 AGTATGGGAAGACAAGATCTGGTATCTT-GATCTACTTTACGCCA-GTACATGAAGACAAGATCT
* * *
59727517 GCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATATAG-TATCTCTGATCTACTTC
324 GCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCT-GTTATCTTTGATCTACTTC
*
59727581 ACGCCGGTACAT
388 ACGCCAGTACAT
* * * ** * * ***
59727593 GAAGACAAGATCTGCTTTCTTCGATCTGTTTCGTCACCAGTATGGGAAGACAAGATCTG-TTATC
1 GAAGACAAGATCTGGTATCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTT-TC
* * * *** ** * *
59727657 TTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTATTGTCTTTGATCTACTTCACCACCA
64 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCA-CGCCA
*** * * * * * * ***
59727721 GTATGGGAAGGCAAGATTTGGTTTC-TCTGATCTACCTC-ACGCCAGTACATGAAGACAAGATCT
128 GTACATGAAGACAAGATCTGCTTTCTTC-GATCTACTTCGCCACCAGTATGGGAAGACAAGATCT
59727784 GTTATCTTT
192 GTTATCTTT
59727793 CAACCTGCTC
Statistics
Matches: 878, Mismatches: 111, Indels: 20
0.87 0.11 0.02
Matches are distributed among these distances:
397 5 0.01
398 181 0.21
399 98 0.11
400 593 0.68
401 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (399 bp):
GAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTT
CGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTA
CATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTA
TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGATTTCTTCGATCTACTTCGCCACC
AGTATGGGAAGACAAGATCTGGTATCTTGATCTACTTTACGCCAGTACATGAAGACAAGATCTGC
TTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACG
CCAGTACAT
Found at i:59745179 original size:18 final size:20
Alignment explanation
Indices: 59745137--59745179 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
59745127 AAATATAAAA
*
59745137 ATAAATATAAGTATGTACAT
1 ATAAATATAAGTATATACAT
*
59745157 ATAAATAT-A-TATATACTT
1 ATAAATATAAGTATATACAT
59745175 ATAAA
1 ATAAA
59745180 AATTTAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 12 0.57
19 1 0.05
20 8 0.38
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (20 bp):
ATAAATATAAGTATATACAT
Found at i:59745225 original size:14 final size:14
Alignment explanation
Indices: 59745207--59745244 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
59745197 TATAGCTATG
*
59745207 AATATATGAA-TAT
1 AATATATAAATTAT
59745220 ATATATATAAATTAT
1 A-ATATATAAATTAT
59745235 AATATATAAA
1 AATATATAAA
59745245 ATAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 17 0.77
15 4 0.18
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (14 bp):
AATATATAAATTAT
Found at i:59745479 original size:3 final size:3
Alignment explanation
Indices: 59745407--59745464 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
59745397 AAAATAAAAC
* * *
59745407 TAA TAA TAA TAAA TAG TAA TAA TAG TAA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
59745453 TAA TAA TAA TAA
1 TAA TAA TAA TAA
59745465 ATGTAATGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:59746195 original size:18 final size:17
Alignment explanation
Indices: 59746171--59746215 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
59746161 TTGTATTTCG
*
59746171 AAATAAAAAATAAAAAA
1 AAATAAAAAAGAAAAAA
* *
59746188 ACAATAAAAACGAAACAA
1 A-AATAAAAAAGAAAAAA
59746206 AAATAAAAAA
1 AAATAAAAAA
59746216 AGAGTGACCT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.82, C:0.07, G:0.02, T:0.09
Consensus pattern (17 bp):
AAATAAAAAAGAAAAAA
Found at i:59747952 original size:16 final size:15
Alignment explanation
Indices: 59747929--59747969 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
59747919 CAAAACATCT
*
59747929 TAAAAATAAATGGTA
1 TAAAAATAAATAGTA
59747944 TATAAAATAAATAGTA
1 TA-AAAATAAATAGTA
59747960 TAAAAA-AAAT
1 TAAAAATAAAT
59747970 TTGCAATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 6 0.25
16 14 0.58
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (15 bp):
TAAAAATAAATAGTA
Found at i:59748571 original size:22 final size:21
Alignment explanation
Indices: 59748536--59748600 Score: 53
Period size: 22 Copynumber: 3.1 Consensus size: 21
59748526 AAAGGGTATC
* * *
59748536 TACAAATTAAATCTCTAATAT
1 TACAAATCATATCTCTAAGAT
59748557 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
59748580 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
59748599 TA
1 TA
59748601 TATATCCTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
19 9 0.25
21 3 0.08
22 15 0.42
23 9 0.25
ACGTcount: A:0.43, C:0.15, G:0.05, T:0.37
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:59748931 original size:13 final size:13
Alignment explanation
Indices: 59748913--59748939 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59748903 TTGTAATAAT
59748913 AAATTTGTTTAGC
1 AAATTTGTTTAGC
59748926 AAATTTGTTTAGC
1 AAATTTGTTTAGC
59748939 A
1 A
59748940 TAGATGATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (13 bp):
AAATTTGTTTAGC
Found at i:59770009 original size:32 final size:32
Alignment explanation
Indices: 59769968--59770030 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
59769958 AACTGAAGTG
59769968 GTGTTTCTTAACAAGTTGAGCCTGTATGAGTA
1 GTGTTTCTTAACAAGTTGAGCCTGTATGAGTA
**
59770000 GTGTTTCTTAATGAGTTGAGCCTGTATGAGT
1 GTGTTTCTTAACAAGTTGAGCCTGTATGAGT
59770031 GACCCAGCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.22, C:0.11, G:0.27, T:0.40
Consensus pattern (32 bp):
GTGTTTCTTAACAAGTTGAGCCTGTATGAGTA
Found at i:59787852 original size:16 final size:16
Alignment explanation
Indices: 59787831--59787863 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
59787821 ATTCGTTGAG
59787831 ATTATCTTCATATTGT
1 ATTATCTTCATATTGT
59787847 ATTATCTTCATATTGT
1 ATTATCTTCATATTGT
59787863 A
1 A
59787864 CTCTTTCTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.55
Consensus pattern (16 bp):
ATTATCTTCATATTGT
Found at i:59789522 original size:20 final size:21
Alignment explanation
Indices: 59789483--59789524 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
59789473 AGACTAAATC
* *
59789483 GAAAACATTTGAAAAGTTTAG
1 GAAAAAATTTGAAAAATTTAG
59789504 GAAAAAATTT-AAAAATTTAG
1 GAAAAAATTTGAAAAATTTAG
59789524 G
1 G
59789525 CTGCAGGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.52, C:0.02, G:0.17, T:0.29
Consensus pattern (21 bp):
GAAAAAATTTGAAAAATTTAG
Found at i:59789955 original size:13 final size:13
Alignment explanation
Indices: 59789937--59789961 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59789927 TCATATAGGC
59789937 ACATTAAACATAT
1 ACATTAAACATAT
59789950 ACATTAAACATA
1 ACATTAAACATA
59789962 CCTAAACATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (13 bp):
ACATTAAACATAT
Found at i:59795117 original size:42 final size:42
Alignment explanation
Indices: 59794999--59795157 Score: 158
Period size: 42 Copynumber: 3.8 Consensus size: 42
59794989 TTAACTTATA
* * * ***
59794999 TGAGTTTCAGTTTAACCATAATGGGTTTCCATTCAGCT-TTT
1 TGAGCTTCAGTTTAACCCTTATGGGTTTTTGTTCAGCTCTTT
* ** *
59795040 TAGAGCTTCAGTTTAACCCTAATGGGTTTCCGTTCAGTTCTTT
1 T-GAGCTTCAGTTTAACCCTTATGGGTTTTTGTTCAGCTCTTT
* *
59795083 TGAGCTTCAATTTAACCCTTATGGGTTTTTGTTCAGCTCTTA
1 TGAGCTTCAGTTTAACCCTTATGGGTTTTTGTTCAGCTCTTT
* ** *
59795125 CGAGCTTTTGTTCAACCCTTATGGGTTTTTGTT
1 TGAGCTTCAGTTTAACCCTTATGGGTTTTTGTT
59795158 TAACACTTAT
Statistics
Matches: 101, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
41 1 0.01
42 96 0.95
43 4 0.04
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.45
Consensus pattern (42 bp):
TGAGCTTCAGTTTAACCCTTATGGGTTTTTGTTCAGCTCTTT
Found at i:59795154 original size:21 final size:21
Alignment explanation
Indices: 59795096--59795168 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 21
59795086 GCTTCAATTT
59795096 AACCCTTATGGGTTTTTGTTC
1 AACCCTTATGGGTTTTTGTTC
* * * * *
59795117 AGCTCTTACGAGCTTTTGTTC
1 AACCCTTATGGGTTTTTGTTC
*
59795138 AACCCTTATGGGTTTTTGTTT
1 AACCCTTATGGGTTTTTGTTC
*
59795159 AACACTTATG
1 AACCCTTATG
59795169 TGCTTCTGTG
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.45
Consensus pattern (21 bp):
AACCCTTATGGGTTTTTGTTC
Found at i:59799686 original size:45 final size:44
Alignment explanation
Indices: 59799501--59799688 Score: 133
Period size: 45 Copynumber: 4.2 Consensus size: 44
59799491 ATACTCGGAT
* * *
59799501 AATCACATATATCGAAAAATGCCAACGTCCCAGACGTGGTCTTACATG
1 AATCACATATATCG----ATGCCATCGTCCCAGGCGTGGTCTTACACG
* *
59799549 CTATCTC--ATATCGATGCCA-CTGTCCC-GGACAG-GGTCTTACACG
1 -AATCACATATATCGATGCCATC-GTCCCAGG-C-GTGGTCTTACACG
* * *
59799592 AATCA-A-ATA-CGATGCCAAT-GTCCTAGACATGGTCTTACACG
1 AATCACATATATCGATGCC-ATCGTCCCAGGCGTGGTCTTACACG
59799633 TAATCACATATATCGATGCCATCGTCCCAGGCGTGGTCTTACACG
1 -AATCACATATATCGATGCCATCGTCCCAGGCGTGGTCTTACACG
*
59799678 AGAACACATAT
1 A-ATCACATAT
59799689 CGAAAATCCT
Statistics
Matches: 112, Mismatches: 13, Indels: 32
0.71 0.08 0.20
Matches are distributed among these distances:
41 23 0.21
42 15 0.13
43 23 0.21
44 7 0.06
45 34 0.30
47 6 0.05
49 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (44 bp):
AATCACATATATCGATGCCATCGTCCCAGGCGTGGTCTTACACG
Found at i:59808925 original size:46 final size:46
Alignment explanation
Indices: 59808851--59808989 Score: 199
Period size: 46 Copynumber: 3.0 Consensus size: 46
59808841 CATGGCAAAG
* *
59808851 TGTGGAACGTAGGCATGGTAATTT-AGTAAAGAAAACCATACTGAGT
1 TGTGAAACGTAGGTATGGT-ATTTCAGTAAAGAAAACCATACTGAGT
* *
59808897 TGTGAAACGTAGGTATGGTATTTCAGTAACGAAAACTATACTGAGT
1 TGTGAAACGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGT
* * *
59808943 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAATCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGT
59808989 T
1 T
59808990 ATAGCATTGT
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 4 0.05
46 79 0.95
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.29
Consensus pattern (46 bp):
TGTGAAACGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGT
Found at i:59809200 original size:13 final size:14
Alignment explanation
Indices: 59809177--59809205 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
59809167 TGGCAGGAAA
59809177 TGTTGTATTATAAT
1 TGTTGTATTATAAT
59809191 TGTT-TATTATAAT
1 TGTTGTATTATAAT
59809204 TG
1 TG
59809206 ATAGTGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (14 bp):
TGTTGTATTATAAT
Found at i:59820898 original size:19 final size:19
Alignment explanation
Indices: 59820856--59820898 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
59820846 CTTAGCCATC
* **
59820856 AAATTAAAAAAAAAATGTT
1 AAATGAAAAAAAAAAACTT
59820875 AAATGAAAAAAAAAAACTT
1 AAATGAAAAAAAAAAACTT
*
59820894 CAATG
1 AAATG
59820899 TTAAATTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (19 bp):
AAATGAAAAAAAAAAACTT
Found at i:59826042 original size:16 final size:16
Alignment explanation
Indices: 59826000--59826041 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
59825990 CAGCATTTAA
59826000 TTAATTTTTTAAAATT
1 TTAATTTTTTAAAATT
*
59826016 TAAATTTTTTAATAATT
1 TTAATTTTTTAA-AATT
59826033 TTAATTTTT
1 TTAATTTTT
59826042 AGAAGTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTAATTTTTTAAAATT
Found at i:59828087 original size:58 final size:58
Alignment explanation
Indices: 59827985--59828102 Score: 137
Period size: 58 Copynumber: 2.0 Consensus size: 58
59827975 AAGGGACTCA
* * * * *
59827985 AATAATGAAGATATGCCTCACCTCTATTGACAGCATAAAGGGTTCAAAGAGGGGCCCG
1 AATAATAAAGATATGCCTCACCTCCATCGACAGCACAAAAGGTTCAAAGAGGGGCCCG
* * * ** *
59828043 AATAATAAAGATATGTCTCACCTCCATCGAGAGCCCAAAAGGTTCATGGATGGGCCCG
1 AATAATAAAGATATGCCTCACCTCCATCGACAGCACAAAAGGTTCAAAGAGGGGCCCG
59828101 AA
1 AA
59828103 ATGAAGATAA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (58 bp):
AATAATAAAGATATGCCTCACCTCCATCGACAGCACAAAAGGTTCAAAGAGGGGCCCG
Found at i:59828438 original size:50 final size:50
Alignment explanation
Indices: 59828259--59828529 Score: 158
Period size: 50 Copynumber: 5.4 Consensus size: 50
59828249 ATAGAAGGTG
* * * *
59828259 GTAATAATGATTTTGCTCCTAAACGCATGGGAGAAGACTTAC-GGAAGATT
1 GTAATAATGATCTTGCTCCTAAACGCATGGGAGGAGACTTACAGAAAG-TA
* * * * * *
59828309 GTAATAGATG-TCATGCTCCCAAACGCATGGGGGGATG-CTCACAAAAAGTG
1 GTAATA-ATGATCTTGCTCCTAAACGCATGGGAGGA-GACTTACAGAAAGTA
* * * * * * ** **
59828359 GTAATAATGGTCTTACTCTTAGACACATGGGAGGAGGCTTATGGAATTTA
1 GTAATAATGATCTTGCTCCTAAACGCATGGGAGGAGACTTACAGAAAGTA
* * *
59828409 GTAATAATGATCTTGCTCCCAAACGCAT-GGAGGGAGACTTATAGAAGGTA
1 GTAATAATGATCTTGCTCCTAAACGCATGGGA-GGAGACTTACAGAAAGTA
* * ** * *
59828459 GTAATAAAGA-CTCTACTCCTAAACGCATGGTCGGA-AGCTTACAGAAGGTG
1 GTAATAATGATCT-TGCTCCTAAACGCATGGGAGGAGA-CTTACAGAAAGTA
* * *
59828509 GTAACAATGGTCCTGCTCCTA
1 GTAATAATGATCTTGCTCCTA
59828530 GACATATAAG
Statistics
Matches: 166, Mismatches: 45, Indels: 20
0.72 0.19 0.09
Matches are distributed among these distances:
49 10 0.06
50 147 0.89
51 9 0.05
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (50 bp):
GTAATAATGATCTTGCTCCTAAACGCATGGGAGGAGACTTACAGAAAGTA
Found at i:59828463 original size:100 final size:100
Alignment explanation
Indices: 59828245--59828488 Score: 253
Period size: 100 Copynumber: 2.4 Consensus size: 100
59828235 CACAAGGAAG
* * *
59828245 GCTTATAGAAGGTGGTAATAATGATTTTGCTCCTAAACGCATGGGAGAAGACTTACGGAAGATTG
1 GCTTATAGAAGGTGGTAATAATGATCTTACTCCTAAACACATGGGAGAAGACTTACGGAAGATTG
*
59828310 TAATAGATGTCATGCTCCCAAACGCATGGGGGGAT
66 TAATAGATGTCATGCTCCCAAACGCATGGAGGGAT
* * * * * * * * * * *
59828345 GCTCACAAAAAGTGGTAATAATGGTCTTACTCTTAGACACATGGGAGGAGGCTTATGGAA-TTTA
1 GCTTATAGAAGGTGGTAATAATGATCTTACTCCTAAACACATGGGAGAAGACTTACGGAAGATT-
*
59828409 GTAATA-ATGATCTTGCTCCCAAACGCATGGAGGGA-
65 GTAATAGATG-TCATGCTCCCAAACGCATGGAGGGAT
* * *
59828444 GACTTATAGAAGGTAGTAATAAAGA-CTCTACTCCTAAACGCATGG
1 G-CTTATAGAAGGTGGTAATAATGATCT-TACTCCTAAACACATGG
59828489 TCGGAAGCTT
Statistics
Matches: 114, Mismatches: 26, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
99 8 0.07
100 106 0.93
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (100 bp):
GCTTATAGAAGGTGGTAATAATGATCTTACTCCTAAACACATGGGAGAAGACTTACGGAAGATTG
TAATAGATGTCATGCTCCCAAACGCATGGAGGGAT
Found at i:59828532 original size:150 final size:150
Alignment explanation
Indices: 59828259--59828533 Score: 322
Period size: 150 Copynumber: 1.8 Consensus size: 150
59828249 ATAGAAGGTG
* * * * * *
59828259 GTAATAATGATTTTGCTCCTAAACGCATGGGAGAAGACTTACGGAAGATTGTAATAGATGTCATG
1 GTAATAATGATCTTGCTCCCAAACGCATGGGAGAAGACTTACAGAAGATAGTAATAGATCTCATA
* * * * *
59828324 CTCCCAAACGCATGGGGGGATGCTCACAAAAAGTGGTAATAATGGTCTTACTCTTAGACACATGG
66 CTCCCAAACGCATGGGCGGAAGCTCACAAAAAGTGGTAACAATGGTCCTACTCCTAGACACATGG
59828389 GAGGAGGCTTATGGAATTTA
131 GAGGAGGCTTATGGAATTTA
* * *
59828409 GTAATAATGATCTTGCTCCCAAACGCAT-GGAGGGAGACTTATAGAAGGTAGTAATAAAGA-CTC
1 GTAATAATGATCTTGCTCCCAAACGCATGGGA-GAAGACTTACAGAAGATAGTAAT--AGATCTC
* * * * * *
59828472 -TACTCCTAAACGCATGGTCGGAAGCTTACAGAAGGTGGTAACAATGGTCCTGCTCCTAGACA
63 ATACTCCCAAACGCATGGGCGGAAGCTCACAAAAAGTGGTAACAATGGTCCTACTCCTAGACA
59828534 TATAAGGGAA
Statistics
Matches: 102, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
149 3 0.03
150 94 0.92
151 2 0.02
152 3 0.03
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (150 bp):
GTAATAATGATCTTGCTCCCAAACGCATGGGAGAAGACTTACAGAAGATAGTAATAGATCTCATA
CTCCCAAACGCATGGGCGGAAGCTCACAAAAAGTGGTAACAATGGTCCTACTCCTAGACACATGG
GAGGAGGCTTATGGAATTTA
Found at i:59828600 original size:50 final size:50
Alignment explanation
Indices: 59828493--59828636 Score: 141
Period size: 50 Copynumber: 2.9 Consensus size: 50
59828483 GCATGGTCGG
* * * * * * * *
59828493 AAGCTTACAGAAGGTGGTAACAATGGTCCTGCTCCTAGACATATAAGGGA
1 AAGCTTATAGAAAGTGGTAATAATAGCCCTGCTCCAAGACACATAAGAGA
59828543 AAGCTTATAGAATA-TGGTAATAA-AGGCCCTGCTCCAAGACACATAAAGAGA
1 AAGCTTATAGAA-AGTGGTAATAATA-GCCCTGCTCCAAGACACAT-AAGAGA
* * *
59828594 AA-CTTATCGAAAGTGGTAATAATAGCCCTACTCCCAGACACAT
1 AAGCTTATAGAAAGTGGTAATAATAGCCCTGCTCCAAGACACAT
59828637 GGGGGAGCCT
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
49 1 0.01
50 69 0.88
51 8 0.10
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (50 bp):
AAGCTTATAGAAAGTGGTAATAATAGCCCTGCTCCAAGACACATAAGAGA
Found at i:59829985 original size:22 final size:22
Alignment explanation
Indices: 59829958--59830034 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
59829948 TTTCTTTTTA
59829958 TTAGGAGATTAGATGCTAAAGT
1 TTAGGAGATTAGATGCTAAAGT
* * ** ****
59829980 TTAGGAGATAATATTTTGGTTTT
1 TTAGGAGATTAGATGCT-AAAGT
59830003 ATTAGGAGATTAGATGCTAAAGT
1 -TTAGGAGATTAGATGCTAAAGT
59830026 TTAGGAGAT
1 TTAGGAGAT
59830035 AATATTTTGG
Statistics
Matches: 37, Mismatches: 16, Indels: 4
0.65 0.28 0.07
Matches are distributed among these distances:
22 22 0.59
23 2 0.05
24 13 0.35
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.38
Consensus pattern (22 bp):
TTAGGAGATTAGATGCTAAAGT
Found at i:59830003 original size:46 final size:46
Alignment explanation
Indices: 59829953--59830047 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
59829943 TCTATTTTCT
59829953 TTTTATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTTATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
59829999 TTTTATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
1 TTTTATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
59830045 TTT
1 TTT
59830048 CTATCTTTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.32, C:0.02, G:0.23, T:0.43
Consensus pattern (46 bp):
TTTTATTAGGAGATTAGATGCTAAAGTTTAGGAGATAATATTTTGG
Found at i:59841227 original size:23 final size:23
Alignment explanation
Indices: 59841200--59842207 Score: 941
Period size: 23 Copynumber: 40.9 Consensus size: 23
59841190 AATAGGTTAG
59841200 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
59841223 GGTTA-GGTTAGGGATTTCAATTAAATTA
1 GGTTAGGGTT-----TTT-AATTAAATTA
59841251 GGTTAGGGTTAGGGTTTGTAATTAAATTAAATTA
1 GGTTAGGG-T----TTT-TAATT--A--A-ATTA
* *
59841285 GCTTAGGGTTTTTAATTAAGTTA
1 GGTTAGGGTTTTTAATTAAATTA
*
59841308 TGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
59841331 GGTTAGGGTTTTTAATTAAATTAGGTTA
1 GGTTAGGGTTTTTAATT-AA--A--TTA
*
59841359 GGGTTAGGGTTTTTAATT-AAGTA
1 -GGTTAGGGTTTTTAATTAAATTA
59841382 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
*
59841405 TGTTAGGGTTTTTAATTTAATTAAGTTA
1 GGTTAGGGTTTTTAA-TT-A--AA-TTA
*
59841433 GGTTAGGGTTTTTAATTAAGTTA
1 GGTTAGGGTTTTTAATTAAATTA
*
59841456 TGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
59841479 GGTTAGGGTTTTTAATTAAATTAGGTTA
1 GGTTAGGGTTTTTAATT-AA--A--TTA
*
59841507 GGGTTAGGGTTTTTAATT-AAGTA
1 -GGTTAGGGTTTTTAATTAAATTA
59841530 GGGTTAGGGTTTTTAATTTAATTAAGTTA
1 -GGTTAGGGTTTTTAA-TT-A--AA-TTA
* *
59841559 GGTTAGGTTTTTTAATTAAGTTA
1 GGTTAGGGTTTTTAATTAAATTA
*
59841582 TGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
* * **
59841605 GGTTAGGGTTAGTGTTTTTATTTAAGAA
1 GGTTA-GG---GT-TTTTAATTAAATTA
*
59841633 GGGTTAGGGTTTTTAATTAAGTTA
1 -GGTTAGGGTTTTTAATTAAATTA
* * *
59841657 TGTTCGGGTTTTGAATATAATTAAGTTA
1 GGTTAGGG-TTT---T-TAATTAAATTA
* *
59841685 GGTTAGGTTTTTTAATTAAGTTA
1 GGTTAGGGTTTTTAATTAAATTA
*
59841708 TGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
59841731 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
*
59841754 GGTTAGGGTTTTTAATT-AAGTA
1 GGTTAGGGTTTTTAATTAAATTA
*
59841776 GGGTTAGGGTTTTTAATTAAGTTA
1 -GGTTAGGGTTTTTAATTAAATTA
*
59841800 TGTTAGGGTTTTTAATTTAATTAAGTTA
1 GGTTAGGGTTTTTAA-TT-A--AA-TTA
* *
59841828 GGTTAGGTTTTTTAATTAAGTTA
1 GGTTAGGGTTTTTAATTAAATTA
*
59841851 TGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
59841874 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
*
59841897 GGTTAGGGTTTTTAATT-AAGTA
1 GGTTAGGGTTTTTAATTAAATTA
*
59841919 GGTTA-GGTTTTTAATTAAGTTA
1 GGTTAGGGTTTTTAATTAAATTA
*
59841941 TGTTAGGGTTTTTAATTTAATTAAGTTA
1 GGTTAGGGTTTTTAA-TT-A--AA-TTA
*
59841969 GGTTAGGTTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
59841992 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
*
59842015 GGTTAGGGTTTTTAATTAAGTTA
1 GGTTAGGGTTTTTAATTAAATTA
*
59842038 TGTTAGGGTTTTTAATTTAATTAAGTTA
1 GGTTAGGGTTTTTAA-TT-A--AA-TTA
* *
59842066 GGTTAGGTTTTTTAATTAAGTTA
1 GGTTAGGGTTTTTAATTAAATTA
*
59842089 TGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
59842112 GGTTAGGGTTTTTAATTAAATTAGGTTA
1 GGTTAGGGTTTTTAATT-AA--A--TTA
*
59842140 GGGTTAGGGTTTTTAATT-AAGTA
1 -GGTTAGGGTTTTTAATTAAATTA
*
59842163 GGGTTAGGATTTTTAATTAAATTA
1 -GGTTAGGGTTTTTAATTAAATTA
*
59842187 GGTTAGGGTTTTTAATCAAAT
1 GGTTAGGGTTTTTAATTAAAT
59842208 AATGTCAAAA
Statistics
Matches: 831, Mismatches: 75, Indels: 158
0.78 0.07 0.15
Matches are distributed among these distances:
21 11 0.01
22 41 0.05
23 465 0.56
24 45 0.05
25 9 0.01
26 9 0.01
27 27 0.03
28 138 0.17
29 69 0.08
30 2 0.00
31 1 0.00
33 2 0.00
34 12 0.01
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.48
Consensus pattern (23 bp):
GGTTAGGGTTTTTAATTAAATTA
Found at i:59841387 original size:74 final size:75
Alignment explanation
Indices: 59841131--59842207 Score: 955
Period size: 74 Copynumber: 14.4 Consensus size: 75
59841121 TTTTTAATTA
* * * * * *
59841131 AATTAGGTTAGGGTTAGGGATTTTAATTAAAATAGGTTAGGGTTAGGGTTTTCATGTAAAATAGG
1 AATTAAGTTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGG-T----TTTTAAT-TAAATTAAG
59841196 TTAGGGTTAGGGTTTTT
59 TTAGGGTTAGGGTTTTT
* *
59841213 AATTAAATTAGGTTAGGTTAGGGATTTCAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAAAT
1 AATT--A--A-GTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGG-T----TTT-TAATTAAAT
* *
59841278 TAAATTA-GCTTAGGGTTTTT
55 TAAGTTAGGGTTAGGGTTTTT
* *
59841298 AATTAAGTTATGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGT
1 AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGT
59841363 TAGGGTTTTT
66 TAGGGTTTTT
* *
59841373 AATTAAG-TAGGTTAGGGTTTTTAATTAAATTATGTTAGGGTTTTTAATTTAATTAAGTTA-GGT
1 AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGT
59841436 TAGGGTTTTT
66 TAGGGTTTTT
* *
59841446 AATTAAGTTATGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGT
1 AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGT
59841511 TAGGGTTTTT
66 TAGGGTTTTT
* * *
59841521 AATTAAG-TAGGGTTAGGGTTTTTAATTTAATTAAGTTA-GGTTAGGTTT--TTTAATTAAGTTA
1 AATTAAGTTA-GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT---TTTAATTAAATTAAGTTA
*
59841582 -TGTTAGGGTTTTT
62 GGGTTAGGGTTTTT
* * * ** * *
59841595 AATTAAATTAGGTTAGGGTTAGTGTTTTTATTTAAGAAGGGTTAGGGTTTTTAATTAAGTTATGT
1 AATTAAGTTAGGTTA-GG---GT-TTTTAATTAAATTA-GGTTAGGGTTTTTAATTAAATTAAGT
* ** ** *
59841660 TCGGGTT-TTGAATAT
60 TAGGGTTAGGGTTTTT
* * *
59841675 AATTAAGTTAGGTTAGGTTTTTTAATTAAGTTATGTTAGGGTTTTTAATT--A--AA-TTA-GGT
1 AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGT
59841734 TAGGGTTTTT
66 TAGGGTTTTT
* * * *
59841744 AATTAAATTAGGTTAGGGTTTTTAATT-AAGTAGGGTTAGGGTTTTTAATTAAGTTATGTTAGGG
1 AATTAAGTTAGGTTAGGGTTTTTAATTAAATTA-GGTTAGGGTTTTTAATTAAATTAAGTTAGGG
*
59841808 TT---TTTAATTT
65 TTAGGGTT--TTT
* * *
59841818 AATTAAGTTAGGTTAGGTTTTTTAATTAAGTTATGTTAGGGTTTTTAATT--A--AA-TTA-GGT
1 AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGT
59841877 TAGGGTTTTT
66 TAGGGTTTTT
* * * *
59841887 AATTAAATTAGGTTAGGGTTTTTAATT-AAGTAGGTTA-GGTTTTTAATTAAGTTATGTTAGGGT
1 AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGT
*
59841950 T---TTTAATTT
66 TAGGGTT--TTT
*
59841959 AATTAAGTTAGGTTAGGTTTTTTAATTAAATTAGGTTAGGGTTTTTAATT--A--AA-TTA-GGT
1 AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGT
59842018 TAGGGTTTTT
66 TAGGGTTTTT
* * * *
59842028 AATTAAGTTATGTTAGGGTTTTTAATTTAATTAAGTTA-GGTTAGGTTT--TTTAATTAAGTTA-
1 AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT---TTTAATTAAATTAAGTTAG
*
59842089 TGTTAGGGTTTTT
63 GGTTAGGGTTTTT
*
59842102 AATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTT--TT-AATTAAG-TA
1 AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT----TTTAATTAAATTAAGTTA
*
59842163 GGGTTAGGATTTTT
62 GGGTTAGGGTTTTT
* *
59842177 AATTAAATTAGGTTAGGGTTTTTAATCAAAT
1 AATTAAGTTAGGTTAGGGTTTTTAATTAAAT
59842208 AATGTCAAAA
Statistics
Matches: 831, Mismatches: 102, Indels: 131
0.78 0.10 0.12
Matches are distributed among these distances:
67 11 0.01
68 26 0.03
69 119 0.14
70 5 0.01
71 9 0.01
72 33 0.04
73 36 0.04
74 266 0.32
75 150 0.18
76 8 0.01
77 3 0.00
78 5 0.01
79 14 0.02
80 62 0.07
81 8 0.01
82 4 0.00
83 1 0.00
84 1 0.00
85 16 0.02
86 47 0.06
87 7 0.01
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (75 bp):
AATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGGT
TAGGGTTTTT
Found at i:59844527 original size:28 final size:28
Alignment explanation
Indices: 59844464--59844520 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
59844454 TTGAAAATAT
59844464 TAAAAA-TTTTAAAATTATTTAAAAAAA
1 TAAAAATTTTTAAAATTATTTAAAAAAA
*
59844491 TAAAAATTTTTAAAATTTTCTTAAAAAAA
1 TAAAAATTTTTAAAATTAT-TTAAAAAAA
59844520 T
1 T
59844521 GAAATTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 6 0.22
28 11 0.41
29 10 0.37
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (28 bp):
TAAAAATTTTTAAAATTATTTAAAAAAA
Found at i:59844592 original size:22 final size:22
Alignment explanation
Indices: 59844562--59844603 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
59844552 ATTTGGAGAT
*
59844562 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
59844584 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
59844604 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:59844611 original size:30 final size:30
Alignment explanation
Indices: 59844575--59844633 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
59844565 TTGAAGGAAA
* *
59844575 TTGAGAGGATTTTGGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTGGAAGGAAATTGAGAGT
59844605 TTGAGAGAATTTTGGAAGGAAATTGAGAG
1 TTGAGAGAATTTTGGAAGGAAATTGAGAG
59844634 AAATTTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.31
Consensus pattern (30 bp):
TTGAGAGAATTTTGGAAGGAAATTGAGAGT
Found at i:59844624 original size:52 final size:51
Alignment explanation
Indices: 59844553--59844655 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 51
59844543 TTAATATGGA
* * *
59844553 TTTGGAGATTTTTTGAAGGAAATTGAGAG-GATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTT-GAAGGGAA-TTGAGAG
59844604 TTTGAGAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
59844656 AATTTTTGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
51 4 0.09
52 33 0.72
53 9 0.20
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.32
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
Found at i:59844630 original size:22 final size:22
Alignment explanation
Indices: 59844605--59844696 Score: 125
Period size: 22 Copynumber: 4.2 Consensus size: 22
59844595 ATTTGAGAGT
59844605 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
*
59844627 TTGAGAGAAATTTT-GAAGGGAA
1 TTGAGAG-AATTTTGGAAGGAAA
*
59844649 TTGAGAGAATTTTTGAAAGG-AA
1 TTGAGAGAA-TTTTGGAAGGAAA
*
59844671 TTGAGAGAATTTTTGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
59844693 TTGA
1 TTGA
59844697 TATTGAATTT
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
21 10 0.16
22 42 0.68
23 10 0.16
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.30
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:59844654 original size:44 final size:44
Alignment explanation
Indices: 59844605--59844696 Score: 141
Period size: 44 Copynumber: 2.1 Consensus size: 44
59844595 ATTTGAGAGT
* *
59844605 TTGAGAGAA-TTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAA
1 TTGAGAGAATTTTTGAAAGG-AATTGAGAGAAATTTTGAAGGAAA
*
59844649 TTGAGAGAATTTTTGAAAGGAATTGAGAGAATTTTTGAAGGAAA
1 TTGAGAGAATTTTTGAAAGGAATTGAGAGAAATTTTGAAGGAAA
59844693 TTGA
1 TTGA
59844697 TATTGAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 35 0.80
45 9 0.20
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.30
Consensus pattern (44 bp):
TTGAGAGAATTTTTGAAAGGAATTGAGAGAAATTTTGAAGGAAA
Found at i:59845840 original size:29 final size:29
Alignment explanation
Indices: 59845797--59845853 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
59845787 GCAAGACAAT
* * *
59845797 TTTCAATTAGGTGTTTATCTACGTTATTA
1 TTTCAAATAGATGTTTATCTAAGTTATTA
59845826 TTTCAAATAGATGTTTATCTAAGTTATT
1 TTTCAAATAGATGTTTATCTAAGTTATT
59845854 TATAAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.51
Consensus pattern (29 bp):
TTTCAAATAGATGTTTATCTAAGTTATTA
Found at i:59851365 original size:20 final size:20
Alignment explanation
Indices: 59851342--59851397 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
59851332 ATCATATGAA
*
59851342 AAAAAAATTAAAAATATTTT
1 AAAAAAATTAAAAATATTAT
*
59851362 AAAAAATTGTAAAAA-ATTAT
1 AAAAAAAT-TAAAAATATTAT
*
59851382 AAAAAATATTAGAAAT
1 AAAAAA-ATTAAAAAT
59851398 TCTAAAAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
20 22 0.76
21 7 0.24
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (20 bp):
AAAAAAATTAAAAATATTAT
Found at i:59851367 original size:19 final size:18
Alignment explanation
Indices: 59851343--59851444 Score: 78
Period size: 19 Copynumber: 5.3 Consensus size: 18
59851333 TCATATGAAA
59851343 AAAAAATTAAAAATATTTT
1 AAAAAATTAAAAA-ATTTT
*
59851362 AAAAAATTGTAAAAAATTAT
1 AAAAAA-T-TAAAAAATTTT
* * *
59851382 AAAAAATATTAGAAATTCT
1 AAAAAAT-TAAAAAATTTT
*
59851401 AAAAGATTATAAAAATTATT
1 AAAAAATTA-AAAAATT-TT
* *
59851421 AAAAATTTTAAAAAATATT
1 AAAAA-ATTAAAAAATTTT
59851440 AAAAA
1 AAAAA
59851445 TTATTGTATC
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
18 1 0.02
19 34 0.52
20 22 0.33
21 9 0.14
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (18 bp):
AAAAAATTAAAAAATTTT
Found at i:59851446 original size:29 final size:29
Alignment explanation
Indices: 59851343--59851449 Score: 121
Period size: 29 Copynumber: 3.7 Consensus size: 29
59851333 TCATATGAAA
*
59851343 AAAAAATTA-AAAATATT-TTAAAAAATTGT
1 AAAAAATTATAAAA-ATTATT-AAAAATTCT
* *
59851372 AAAAAATTATAAAAAATATTAGAAATTCT
1 AAAAAATTATAAAAATTATTAAAAATTCT
* *
59851401 AAAAGATTATAAAAATTATTAAAAATTTT
1 AAAAAATTATAAAAATTATTAAAAATTCT
59851430 AAAAAA-TATTAAAAATTATT
1 AAAAAATTA-TAAAAATTATT
59851450 GTATCTTGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.03
29 59 0.88
30 6 0.09
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAAAATTATAAAAATTATTAAAAATTCT
Found at i:59851449 original size:10 final size:10
Alignment explanation
Indices: 59851348--59851449 Score: 86
Period size: 10 Copynumber: 10.3 Consensus size: 10
59851338 TGAAAAAAAA
59851348 ATTAAAAATAT
1 ATTAAAAAT-T
*
59851359 TTTAAAAAATT
1 ATT-AAAAATT
* *
59851370 GTAAAAAATT
1 ATTAAAAATT
*
59851380 A-TAAAAAAT
1 ATTAAAAATT
*
59851389 ATTAGAAATT
1 ATTAAAAATT
*
59851399 -CTAAAAGATT
1 ATTAAAA-ATT
59851409 A-TAAAAATT
1 ATTAAAAATT
59851418 ATTAAAAATT
1 ATTAAAAATT
*
59851428 -TTAAAAAAT
1 ATTAAAAATT
59851437 ATTAAAAATT
1 ATTAAAAATT
59851447 ATT
1 ATT
59851450 GTATCTTGAA
Statistics
Matches: 73, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
9 23 0.32
10 40 0.55
11 4 0.05
12 6 0.08
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:59855566 original size:28 final size:28
Alignment explanation
Indices: 59855526--59855585 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
59855516 ACAAACAAGC
59855526 AGCCTTTCAATTACCGGACTACACGCAA
1 AGCCTTTCAATTACCGGACTACACGCAA
* *
59855554 AGCCTTTCAATTATCGGACTACACGCAG
1 AGCCTTTCAATTACCGGACTACACGCAA
59855582 AGCC
1 AGCC
59855586 GTGTCCCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.22
Consensus pattern (28 bp):
AGCCTTTCAATTACCGGACTACACGCAA
Found at i:59855841 original size:7 final size:7
Alignment explanation
Indices: 59855829--59855856 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
59855819 TAACCCCAAA
59855829 GAGCTAC
1 GAGCTAC
59855836 GAGCTAC
1 GAGCTAC
59855843 GAGCTAC
1 GAGCTAC
59855850 GAGCTAC
1 GAGCTAC
59855857 CTCTATCCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (7 bp):
GAGCTAC
Found at i:59859246 original size:17 final size:17
Alignment explanation
Indices: 59859220--59859257 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
59859210 AAATATGAAT
59859220 AAAT-AAATCTAGACTA
1 AAATAAAATCTAGACTA
*
59859236 AAATAAAATCTAGATTA
1 AAATAAAATCTAGACTA
59859253 AAATA
1 AAATA
59859258 TGCATTCAGC
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:0.61, C:0.08, G:0.05, T:0.26
Consensus pattern (17 bp):
AAATAAAATCTAGACTA
Found at i:59862709 original size:11 final size:11
Alignment explanation
Indices: 59862693--59862719 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
59862683 AACAGGGGTG
59862693 GCACGATATCA
1 GCACGATATCA
59862704 GCACGATATCA
1 GCACGATATCA
59862715 GCACG
1 GCACG
59862720 TTACGGGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.30, G:0.22, T:0.15
Consensus pattern (11 bp):
GCACGATATCA
Found at i:59867049 original size:21 final size:20
Alignment explanation
Indices: 59867013--59867053 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
59867003 AAATTTCAAA
59867013 TTTATGTCTCGAGACAAGGTC
1 TTTATGTCTCGAGAC-AGGTC
* *
59867034 TTTATGTCTTGGGACAGGTC
1 TTTATGTCTCGAGACAGGTC
59867054 ATAAATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.37
Consensus pattern (20 bp):
TTTATGTCTCGAGACAGGTC
Found at i:59875957 original size:41 final size:40
Alignment explanation
Indices: 59875911--59876020 Score: 118
Period size: 41 Copynumber: 2.8 Consensus size: 40
59875901 GACTTCGAGT
*
59875911 TGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAAT
1 TGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAAC
* * * * *
59875951 TCGATGAGGCACTGGGTGCCAA--T-TTACTTTGGTTTAGC
1 T-GATGAGACACTGGGTGTCAATTTATTACTTCGGATTAAC
* *
59875989 TGATGAGATACTGAGTGTCAATTTATTACTTC
1 TGATGAGACACTGGGTGTCAATTTATTACTTC
59876021 AAATTATCCA
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
37 16 0.29
38 12 0.22
39 2 0.04
40 7 0.13
41 18 0.33
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.37
Consensus pattern (40 bp):
TGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAAC
Found at i:59876940 original size:41 final size:42
Alignment explanation
Indices: 59876878--59876957 Score: 119
Period size: 41 Copynumber: 1.9 Consensus size: 42
59876868 ATTTTGAGTC
59876878 CACACGGCCAGACACACGGGCGTGTGA-TTGGACCGTGTGAGA
1 CACACGGCCAGACACACGGGCGTGTGATTTGG-CCGTGTGAGA
* *
59876920 CACACGGCTA-ACACATGGGCGTGTGATTTGGCCGTGTG
1 CACACGGCCAGACACACGGGCGTGTGATTTGGCCGTGTG
59876958 TCCCCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
41 22 0.63
42 13 0.37
ACGTcount: A:0.21, C:0.25, G:0.35, T:0.19
Consensus pattern (42 bp):
CACACGGCCAGACACACGGGCGTGTGATTTGGCCGTGTGAGA
Found at i:59878510 original size:11 final size:11
Alignment explanation
Indices: 59878474--59878511 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
59878464 CCCAAGCCTA
59878474 TTTATATTATT
1 TTTATATTATT
*
59878485 TTTA-ATATATA
1 TTTATAT-TATT
59878496 TTTATATTATT
1 TTTATATTATT
59878507 TTTAT
1 TTTAT
59878512 TTAATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 2 0.09
11 19 0.83
12 2 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTATATTATT
Found at i:59878518 original size:22 final size:23
Alignment explanation
Indices: 59878472--59878535 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 23
59878462 AACCCAAGCC
*
59878472 TATTTATATTATTTTTA-ATATA
1 TATTTATATTATTTTTATTTATA
59878494 TATTTATATTATTTTTATTTA-A
1 TATTTATATTATTTTTATTTATA
*
59878516 TATTTA-A-TAATTTTATTTAT
1 TATTTATATTATTTTTATTTAT
59878536 TAAATTGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
20 11 0.29
21 1 0.03
22 24 0.63
23 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTTATATTATTTTTATTTATA
Found at i:59884802 original size:19 final size:21
Alignment explanation
Indices: 59884780--59884822 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
59884770 ATGTAAAATG
59884780 ATCCAGAAAATTCT-TAA-AA
1 ATCCAGAAAATTCTATAACAA
*
59884799 ATCCAGAAGATTCTATAACAA
1 ATCCAGAAAATTCTATAACAA
59884820 ATC
1 ATC
59884823 GAAAAGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.62
20 3 0.14
21 5 0.24
ACGTcount: A:0.49, C:0.19, G:0.07, T:0.26
Consensus pattern (21 bp):
ATCCAGAAAATTCTATAACAA
Found at i:59886054 original size:63 final size:64
Alignment explanation
Indices: 59885978--59886099 Score: 183
Period size: 63 Copynumber: 1.9 Consensus size: 64
59885968 AAATAAAACG
59885978 ATTGCTCTCAATCTCATACATAAATAATAAACAA-ATATTTTTTAAATAAACGTTAAAAAAATA
1 ATTGCTCTCAATCTCATACATAAATAATAAACAAGATATTTTTTAAATAAACGTTAAAAAAATA
* * * * *
59886041 ATTGCTCTTAATCTCGTACATAAATATTAAACAAGTCTTTTTTTTAAATAAACGTTAAA
1 ATTGCTCTCAATCTCATACATAAATAATAAACAAG-ATATTTTTTAAATAAACGTTAAA
59886100 GTCTTGTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
63 31 0.60
65 21 0.40
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (64 bp):
ATTGCTCTCAATCTCATACATAAATAATAAACAAGATATTTTTTAAATAAACGTTAAAAAAATA
Found at i:59891147 original size:46 final size:46
Alignment explanation
Indices: 59891080--59891264 Score: 316
Period size: 46 Copynumber: 4.0 Consensus size: 46
59891070 ACATTGCTAT
* * *
59891080 AACTCAGTATGATTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
* *
59891126 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAT
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
*
59891172 AACTCAGTATGGTTTTCTTCGCCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
59891218 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
59891264 A
1 A
59891265 CTTTGCCATG
Statistics
Matches: 131, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 131 1.00
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.34
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
Found at i:59896452 original size:65 final size:65
Alignment explanation
Indices: 59896378--59896508 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
59896368 TCTATATGTG
59896378 AGAGGTGTCCAATTGTTATGAAATTTTAAATTGGAGGTCTTTATATGGTAATTAGACCATTGGTT
1 AGAGGTGTCCAATTGTTATGAAATTTTAAATTGGAGGTCTTTATATGGTAATTAGACCATTGGTT
59896443 AGAGGTGTCCAATTGTTATGAAATTTTAAATTGGAGGTCTTTATATGGTAATTAGACCATTGGTT
1 AGAGGTGTCCAATTGTTATGAAATTTTAAATTGGAGGTCTTTATATGGTAATTAGACCATTGGTT
59896508 A
1 A
59896509 AGTTGGTGGA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.40
Consensus pattern (65 bp):
AGAGGTGTCCAATTGTTATGAAATTTTAAATTGGAGGTCTTTATATGGTAATTAGACCATTGGTT
Found at i:59897555 original size:44 final size:45
Alignment explanation
Indices: 59897469--59897555 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
59897459 TGTGAACTGA
* * *
59897469 ACATCATTGATTAGTAAGGTGGTTGCTATGTGTTGATTCCACCAG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCAG
59897514 ACATCATTGATTAATAAGGTGG-TGCTATGTGCTGAATCCACC
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACC
59897556 GAGTATTTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 18 0.46
45 21 0.54
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.33
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCAG
Found at i:59897627 original size:23 final size:22
Alignment explanation
Indices: 59897601--59897644 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
59897591 AATTGACTAA
59897601 GTGT-AATTGAATAATGAATATAG
1 GTGTGAATTGAAT--TGAATATAG
59897624 GTGTGGAATTGAATTGAATAT
1 GTGT-GAATTGAATTGAATAT
59897645 CGACTTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (22 bp):
GTGTGAATTGAATTGAATATAG
Found at i:59901101 original size:12 final size:12
Alignment explanation
Indices: 59901086--59901125 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
59901076 AGTAAATAAA
59901086 TAAATAAAATAT
1 TAAATAAAATAT
*
59901098 TAAATGAAATAT
1 TAAATAAAATAT
*
59901110 TAAATAAAATAG
1 TAAATAAAATAT
59901122 TAAA
1 TAAA
59901126 AAATGATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (12 bp):
TAAATAAAATAT
Found at i:59903139 original size:45 final size:45
Alignment explanation
Indices: 59902986--59903284 Score: 269
Period size: 45 Copynumber: 6.7 Consensus size: 45
59902976 GGTGTCTTTG
* * * * * *
59902986 ATCTGCTTCGCTGTCAGTACAGTAAGGCAAAATCTGCTATCTTCA
1 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
* * * ** ** * * * * * *
59903031 GTCTGCTCCGCTGTAAACCCAGGGAGGCAAGA-CTGGTGTCGTCG
1 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
* * *
59903075 ATCTATTTCGCTGCCAATACAGGAAGATAAAATCTGCTATCTTCA
1 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
** * *
59903120 ATCTACTTTACTGCCAATACAGAAAGACAAGATCTGCTAAT-TTCG
1 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCT-ATCTTCA
* ** **
59903165 ATCTACTTTGCTGCCAATACAAAAAGACAAGATCTGCTAAATTCA
1 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
*
59903210 ATCTACTTCGCTGCCGATACAGGAAGACAAGATCTGCTATCTTCA
1 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
* *
59903255 ATCTACTTCGCTGCCAATGCCGGAAGACAA
1 ATCTACTTCGCTGCCAATACAGGAAGACAA
59903285 TGTCGAAACA
Statistics
Matches: 202, Mismatches: 49, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
44 29 0.14
45 171 0.85
46 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (45 bp):
ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
Found at i:59906063 original size:45 final size:45
Alignment explanation
Indices: 59906006--59906141 Score: 209
Period size: 45 Copynumber: 3.0 Consensus size: 45
59905996 TGGTTATTAC
*
59906006 AGACAATATCTGTTATCTTTGATCTACTTCGCTGCCAATACAGGA
1 AGACAAAATCTGTTATCTTTGATCTACTTCGCTGCCAATACAGGA
59906051 AGACAAAATCTGTTATCTTTGATCTACTTCGCTGCCAATACAGGA
1 AGACAAAATCTGTTATCTTTGATCTACTTCGCTGCCAATACAGGA
* * * * **
59906096 AAACAAGATCTGCTATCTTCGATCTACTTTACTGCCAATACAGGA
1 AGACAAAATCTGTTATCTTTGATCTACTTCGCTGCCAATACAGGA
59906141 A
1 A
59906142 TATAAGATCT
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 84 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Consensus pattern (45 bp):
AGACAAAATCTGTTATCTTTGATCTACTTCGCTGCCAATACAGGA
Found at i:59906149 original size:45 final size:45
Alignment explanation
Indices: 59906008--59906156 Score: 208
Period size: 45 Copynumber: 3.3 Consensus size: 45
59905998 GTTATTACAG
* * *
59906008 ACAATATCTGTTATCTTTGATCTACTTCGCTGCCAATACAGGAAG
1 ACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAATACAGGAAA
* *
59906053 ACAAAATCTGTTATCTTTGATCTACTTCGCTGCCAATACAGGAAA
1 ACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAATACAGGAAA
* ** *
59906098 ACAAGATCTGCTATCTTCGATCTACTTTACTGCCAATACAGGAAT
1 ACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAATACAGGAAA
*
59906143 ATAAGATCTGCTAT
1 ACAAGATCTGCTAT
59906157 TTTCAACCTA
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 95 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (45 bp):
ACAAGATCTGCTATCTTTGATCTACTTCGCTGCCAATACAGGAAA
Found at i:59906175 original size:45 final size:45
Alignment explanation
Indices: 59906037--59906175 Score: 125
Period size: 45 Copynumber: 3.1 Consensus size: 45
59906027 ATCTACTTCG
* * * ** * * * *
59906037 CTGCCAATACAGGAAGACAAAATCTGTTATCTTTGATCTACTTCG
1 CTGCCAATACAGGAAAACAAGATCTGCTATCTTCAACCTAATCCA
* * * **
59906082 CTGCCAATACAGGAAAACAAGATCTGCTATCTTCGATCTACTTTA
1 CTGCCAATACAGGAAAACAAGATCTGCTATCTTCAACCTAATCCA
* * *
59906127 CTGCCAATACAGGAATATAAGATCTGCTATTTTCAACCTAATCCA
1 CTGCCAATACAGGAAAACAAGATCTGCTATCTTCAACCTAATCCA
59906172 CTGC
1 CTGC
59906176 TGCTCAGGGA
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 80 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.29
Consensus pattern (45 bp):
CTGCCAATACAGGAAAACAAGATCTGCTATCTTCAACCTAATCCA
Found at i:59915772 original size:16 final size:16
Alignment explanation
Indices: 59915751--59915784 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
59915741 TTTTAGAATG
* *
59915751 AAATGCTATGCAGTCA
1 AAATGCCATGCAATCA
59915767 AAATGCCATGCAATCA
1 AAATGCCATGCAATCA
59915783 AA
1 AA
59915785 GCAAAACACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (16 bp):
AAATGCCATGCAATCA
Found at i:59919218 original size:50 final size:50
Alignment explanation
Indices: 59919103--59919351 Score: 336
Period size: 50 Copynumber: 4.8 Consensus size: 50
59919093 GATCATAACA
* ** *
59919103 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * *
59919154 TGCCCAGGCCATGTCCCAGATATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
59919204 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
59919254 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* *
59919309 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
59919352 TTACCCAAAT
Statistics
Matches: 177, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
50 97 0.55
51 33 0.19
53 5 0.03
55 2 0.01
56 40 0.23
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:59919467 original size:13 final size:13
Alignment explanation
Indices: 59919446--59919477 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
59919436 GCTTGGATCA
*
59919446 TCATCAAATAAAT
1 TCATAAAATAAAT
59919459 TCATAAAATAAAT
1 TCATAAAATAAAT
59919472 TCATAA
1 TCATAA
59919478 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:59921516 original size:12 final size:11
Alignment explanation
Indices: 59921499--59921533 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
59921489 AACAAATCCT
59921499 CTCTCATATTTC
1 CTCTCA-ATTTC
59921511 CTCTCAA-TTC
1 CTCTCAATTTC
59921521 CTCTCAATTTC
1 CTCTCAATTTC
59921532 CT
1 CT
59921534 TCCAAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.17, C:0.37, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:59921581 original size:51 final size:51
Alignment explanation
Indices: 59921514--59921637 Score: 207
Period size: 51 Copynumber: 2.5 Consensus size: 51
59921504 ATATTTCCTC
*
59921514 TCAA-TTCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATG
59921564 TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATG
1 TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATG
*
59921615 TCAATTTGCTC-CAAATTTCCTTC
1 TCAATTTCCTCTC-AATTTCCTTC
59921638 TTTAAAATAA
Statistics
Matches: 70, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
50 5 0.07
51 65 0.93
ACGTcount: A:0.28, C:0.28, G:0.02, T:0.42
Consensus pattern (51 bp):
TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATG
Found at i:59923946 original size:25 final size:25
Alignment explanation
Indices: 59923918--59924000 Score: 112
Period size: 25 Copynumber: 3.3 Consensus size: 25
59923908 TATTTTGATA
59923918 TTATTCGATGTAATAAAATAGAAGT
1 TTATTCGATGTAATAAAATAGAAGT
** *
59923943 TTATTTTATGTAATAAAATAGATGT
1 TTATTCGATGTAATAAAATAGAAGT
* *
59923968 TTATTTGATGTAATAAAATAGAAAT
1 TTATTCGATGTAATAAAATAGAAGT
*
59923993 TTTTTCGA
1 TTATTCGA
59924001 GTTATTTTGA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.43
Consensus pattern (25 bp):
TTATTCGATGTAATAAAATAGAAGT
Found at i:59924071 original size:29 final size:29
Alignment explanation
Indices: 59924025--59924318 Score: 495
Period size: 29 Copynumber: 10.2 Consensus size: 29
59924015 ATTTGATGTA
*
59924025 ATTAAAAACCCTACCCCTAACCTAATTTG
1 ATTAAAAACCCTAACCCTAACCTAATTTG
59924054 ATTAAAAACCCTAACCCTAACCTAATTTG
1 ATTAAAAACCCTAACCCTAACCTAATTTG
*
59924083 ATTAAAAACCCT-AGCCTAACCTAATTTG
1 ATTAAAAACCCTAACCCTAACCTAATTTG
*
59924111 ATTAAAAACCCCAACCCTAACCTAATTTG
1 ATTAAAAACCCTAACCCTAACCTAATTTG
*
59924140 ATTAAAAACCCTAACCCTAACTTAATTTG
1 ATTAAAAACCCTAACCCTAACCTAATTTG
59924169 ATTAAAAACCCTAACCCTAACCTAATTTG
1 ATTAAAAACCCTAACCCTAACCTAATTTG
*
59924198 ATTAAAAACCCTAACCTTAACCTAATTTG
1 ATTAAAAACCCTAACCCTAACCTAATTTG
* *
59924227 ATTAAAAACCCTAACCTTAACCTAATTTA
1 ATTAAAAACCCTAACCCTAACCTAATTTG
59924256 ATTAAAAACCCTAA-CCTAACCTAATTTG
1 ATTAAAAACCCTAACCCTAACCTAATTTG
*
59924284 AATAAAAACCCTAA-CCTAACCTAATTTG
1 ATTAAAAACCCTAACCCTAACCTAATTTG
59924312 ATTAAAA
1 ATTAAAA
59924319 TCCCAGTCAT
Statistics
Matches: 251, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
28 71 0.28
29 180 0.72
ACGTcount: A:0.43, C:0.26, G:0.03, T:0.28
Consensus pattern (29 bp):
ATTAAAAACCCTAACCCTAACCTAATTTG
Found at i:59924166 original size:86 final size:86
Alignment explanation
Indices: 59924025--59924318 Score: 500
Period size: 86 Copynumber: 3.4 Consensus size: 86
59924015 ATTTGATGTA
*
59924025 ATTAAAAACCCTACCCCTAACCTAATTTGATTAAAAACCCTAACCCTAACCTAATTTGATTAAAA
1 ATTAAAAACCCTAACCCTAACCTAATTTGATTAAAAACCCTAACCCTAACCTAATTTGATTAAAA
*
59924090 ACCCTAGCCTAACCTAATTTG
66 ACCCTAACCTAACCTAATTTG
* *
59924111 ATTAAAAACCCCAACCCTAACCTAATTTGATTAAAAACCCTAACCCTAACTTAATTTGATTAAAA
1 ATTAAAAACCCTAACCCTAACCTAATTTGATTAAAAACCCTAACCCTAACCTAATTTGATTAAAA
59924176 ACCCTAACCCTAACCTAATTTG
66 ACCCTAA-CCTAACCTAATTTG
* * *
59924198 ATTAAAAACCCTAACCTTAACCTAATTTGATTAAAAACCCTAACCTTAACCTAATTTAATTAAAA
1 ATTAAAAACCCTAACCCTAACCTAATTTGATTAAAAACCCTAACCCTAACCTAATTTGATTAAAA
59924263 ACCCTAACCTAACCTAATTTG
66 ACCCTAACCTAACCTAATTTG
*
59924284 AATAAAAACCCTAA-CCTAACCTAATTTGATTAAAA
1 ATTAAAAACCCTAACCCTAACCTAATTTGATTAAAA
59924319 TCCCAGTCAT
Statistics
Matches: 196, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
85 20 0.10
86 95 0.48
87 81 0.41
ACGTcount: A:0.43, C:0.26, G:0.03, T:0.28
Consensus pattern (86 bp):
ATTAAAAACCCTAACCCTAACCTAATTTGATTAAAAACCCTAACCCTAACCTAATTTGATTAAAA
ACCCTAACCTAACCTAATTTG
Done.