Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold109
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: 1855911
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.34
Warning! 69956 characters in sequence are not A, C, G, or T
File 11 of 13
Found at i:1507830 original size:6 final size:6
Alignment explanation
Indices: 1507819--1507847 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1507809 AATAACATTC
1507819 TTTATA TTTATA TTTATA TTTATA TTTAT
1 TTTATA TTTATA TTTATA TTTATA TTTAT
1507848 GAATAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTATA
Found at i:1508142 original size:35 final size:36
Alignment explanation
Indices: 1508103--1508183 Score: 100
Period size: 35 Copynumber: 2.3 Consensus size: 36
1508093 TACTCATACT
1508103 ATATTTATATAATATTATTTATA-T-TAT-ATCATATC
1 ATATTTATA-AATATT-TTTATATTATATAATCATATC
*
1508138 ATATTT-TAATTATTTTTATATTATATAATCATATC
1 ATATTTATAAATATTTTTATATTATATAATCATATC
1508173 ATATTTA-AAAT
1 ATATTTATAAAT
1508184 TTAAAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
32 6 0.15
33 6 0.15
34 5 0.12
35 23 0.57
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (36 bp):
ATATTTATAAATATTTTTATATTATATAATCATATC
Found at i:1508680 original size:23 final size:25
Alignment explanation
Indices: 1508627--1508680 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
1508617 AAAATATATT
*
1508627 TATAAT-TATTAAAAATTAAATAAA
1 TATAATATATTAAAAAATAAATAAA
*
1508651 AAT-ATAT-TTAAAAAATAAA-AAA
1 TATAATATATTAAAAAATAAATAAA
1508673 TATAATAT
1 TATAATAT
1508681 GAACTAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 5 0.20
23 17 0.68
24 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
TATAATATATTAAAAAATAAATAAA
Found at i:1510085 original size:28 final size:29
Alignment explanation
Indices: 1510051--1510107 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
1510041 TTATGTTAAC
1510051 GTGATTAGA-GGATAGCTGTCAATAACAA
1 GTGATTAGAGGGATAGCTGTCAATAACAA
1510079 GTGATTAGAGGGATAGCTGTCAATAACAA
1 GTGATTAGAGGGATAGCTGTCAATAACAA
1510108 AATTATAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.25
Consensus pattern (29 bp):
GTGATTAGAGGGATAGCTGTCAATAACAA
Found at i:1510122 original size:29 final size:29
Alignment explanation
Indices: 1510052--1510122 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 29
1510042 TATGTTAACG
* *
1510052 TGATTAGAG-GATAGCTGTCAATAACAAG
1 TGATAAGAGAGATAGCTGTCAATAACAAA
* *
1510080 TGATTAGAGGGATAGCTGTCAATAACAAAA
1 TGATAAGAGAGATAGCTGTCAATAAC-AAA
*
1510110 TTATAAGA-AGATA
1 TGATAAGAGAGATA
1510123 AATTTAGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 9 0.24
29 20 0.54
30 8 0.22
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.25
Consensus pattern (29 bp):
TGATAAGAGAGATAGCTGTCAATAACAAA
Found at i:1514703 original size:29 final size:29
Alignment explanation
Indices: 1514667--1514724 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1514657 GAGTGTTAAC
**
1514667 GTGATTAGAGGGATAGCTGTCAATAACAA
1 GTGATTAGAGGGATAGCTACCAATAACAA
1514696 GTGATTAGAGGGATAGCTACCAATAACAA
1 GTGATTAGAGGGATAGCTACCAATAACAA
1514725 AATTATAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.22
Consensus pattern (29 bp):
GTGATTAGAGGGATAGCTACCAATAACAA
Found at i:1521336 original size:2 final size:2
Alignment explanation
Indices: 1521324--1521378 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
1521314 TTCTTTCCAT
*
1521324 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1521366 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1521379 TGTTTGACAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1522508 original size:15 final size:15
Alignment explanation
Indices: 1522488--1522516 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1522478 TATAATCTCA
1522488 AAAAAAAATTACCTC
1 AAAAAAAATTACCTC
1522503 AAAAAAAATTACCT
1 AAAAAAAATTACCT
1522517 ACTTAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.17, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAAAAATTACCTC
Found at i:1523080 original size:15 final size:15
Alignment explanation
Indices: 1523053--1523096 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1523043 TCTTTTAATA
1523053 ATAATATAATAATA-T
1 ATAATA-AATAATAGT
1523068 CATAATAAATAATAGT
1 -ATAATAAATAATAGT
*
1523084 GTAATAAATAATA
1 ATAATAAATAATA
1523097 ACAAAGTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 19 0.73
16 7 0.27
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (15 bp):
ATAATAAATAATAGT
Found at i:1524384 original size:17 final size:19
Alignment explanation
Indices: 1524364--1524399 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
1524354 AAGTATTATT
1524364 ATTTAAATT-T-ATATTTA
1 ATTTAAATTATAATATTTA
1524381 ATTTAAATTATAATATTTA
1 ATTTAAATTATAATATTTA
1524400 TTAGATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 1 0.06
19 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTAAATTATAATATTTA
Found at i:1524417 original size:17 final size:18
Alignment explanation
Indices: 1524383--1524424 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
1524373 TATATTTAAT
1524383 TTAAAT-TATAATATTTA
1 TTAAATATATAATATTTA
*
1524400 TTAGATATATAA-ATTTA
1 TTAAATATATAATATTTA
1524417 TTAAATAT
1 TTAAATAT
1524425 CAAATTCATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TTAAATATATAATATTTA
Found at i:1524740 original size:10 final size:10
Alignment explanation
Indices: 1524725--1524750 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1524715 ATTTAAAAAT
1524725 AAATAATTAA
1 AAATAATTAA
1524735 AAATAATTAA
1 AAATAATTAA
1524745 AAATAA
1 AAATAA
1524751 AATATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAATAATTAA
Found at i:1525347 original size:19 final size:20
Alignment explanation
Indices: 1525323--1525369 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
1525313 TAATTTATTT
1525323 TATATTTTATAAATTTTA-A
1 TATATTTTATAAATTTTATA
* *
1525342 TATA-TTAATAATTTTTATA
1 TATATTTTATAAATTTTATA
*
1525361 TAAATTTTA
1 TATATTTTA
1525370 AAAAATTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 11 0.50
19 8 0.36
20 3 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATATTTTATAAATTTTATA
Found at i:1525412 original size:22 final size:23
Alignment explanation
Indices: 1525386--1525443 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
1525376 TAATACATTA
*
1525386 ATATTATATTT-TAATTATTTTT
1 ATATTATATTTATAATTATTATT
*
1525408 ATATTATATTTATTATTATTATT
1 ATATTATATTTATAATTATTATT
*
1525431 AAATT-TATTTATA
1 ATATTATATTTATA
1525444 TCATATTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 18 0.58
23 13 0.42
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
ATATTATATTTATAATTATTATT
Found at i:1525466 original size:27 final size:27
Alignment explanation
Indices: 1525436--1525503 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
1525426 TTATTAAATT
* * *
1525436 TATTTATATCATATTTATATTTTTATA
1 TATTTATATCAAATTTAAAATTTTATA
*
1525463 TA-TTATAATTAAATTTAAAATTTTATA
1 TATTTAT-ATCAAATTTAAAATTTTATA
1525490 T-TTTATAT-AAATTT
1 TATTTATATCAAATTT
1525504 TATTATATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
25 6 0.17
26 6 0.17
27 23 0.66
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (27 bp):
TATTTATATCAAATTTAAAATTTTATA
Found at i:1525478 original size:21 final size:21
Alignment explanation
Indices: 1525416--1525478 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
1525406 TTATATTATA
*
1525416 TTTAT-TATTATTATTAAATT
1 TTTATATATTATAATTAAATT
* * *
1525436 TATT-TATATCATATTTATATT
1 T-TTATATATTATAATTAAATT
1525457 TTTATATATTATAATTAAATT
1 TTTATATATTATAATTAAATT
1525478 T
1 T
1525479 AAAATTTTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATATATTATAATTAAATT
Found at i:1528154 original size:16 final size:18
Alignment explanation
Indices: 1528117--1528154 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
1528107 ATATTTATGT
*
1528117 ATAAATTATTTATAAAAT
1 ATAAATTATTTATAAAAA
1528135 ATAAA-TATTT-TAAAAA
1 ATAAATTATTTATAAAAA
1528151 ATAA
1 ATAA
1528155 GCGTTAGGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 5 0.26
18 5 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAAATTATTTATAAAAA
Found at i:1530938 original size:13 final size:14
Alignment explanation
Indices: 1530914--1530942 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1530904 ATAAAATTAG
1530914 ATTTAGTTATCTAT
1 ATTTAGTTATCTAT
1530928 ATTTA-TTATCTAT
1 ATTTAGTTATCTAT
1530941 AT
1 AT
1530943 AAATAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.31, C:0.07, G:0.03, T:0.59
Consensus pattern (14 bp):
ATTTAGTTATCTAT
Found at i:1531169 original size:19 final size:18
Alignment explanation
Indices: 1531147--1531188 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1531137 AATATATTAT
1531147 TTAAAAATAAAATAAAAAA
1 TTAAAAAT-AAATAAAAAA
* *
1531166 TTAAAAGTAATTAAAAAA
1 TTAAAAATAAATAAAAAA
1531184 -TAAAA
1 TTAAAA
1531189 TATTTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 9 0.43
19 7 0.33
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
TTAAAAATAAATAAAAAA
Found at i:1531795 original size:16 final size:16
Alignment explanation
Indices: 1531774--1531805 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1531764 CTGATTACCT
1531774 ATGGAAGAAAGAACTA
1 ATGGAAGAAAGAACTA
*
1531790 ATGGAAGAAAGGACTA
1 ATGGAAGAAAGAACTA
1531806 TCGAAGGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.28, T:0.12
Consensus pattern (16 bp):
ATGGAAGAAAGAACTA
Found at i:1537227 original size:28 final size:28
Alignment explanation
Indices: 1537195--1537295 Score: 82
Period size: 28 Copynumber: 3.4 Consensus size: 28
1537185 ATATATTTAT
1537195 ATTTTCATATATTATAATTAAA-TTTAAA
1 ATTTT-ATATATTATAATTAAATTTTAAA
* *
1537223 ATTTTATATATT-TTATATAAATTTTAAT
1 ATTTTATATATTATAAT-TAAATTTTAAA
*
1537251 ATATTA-ATAATTATATTATTTAAATTTTATAA
1 ATTTTATAT-ATTATA--A-TTAAATTTTA-AA
1537283 ATTTTTATATATT
1 A-TTTTATATATT
1537296 TTATATAACT
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
26 3 0.05
27 13 0.23
28 18 0.32
29 1 0.02
31 10 0.18
32 3 0.05
33 7 0.12
34 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTTATATATTATAATTAAATTTTAAA
Found at i:1537237 original size:9 final size:9
Alignment explanation
Indices: 1537223--1537338 Score: 59
Period size: 9 Copynumber: 13.0 Consensus size: 9
1537213 TAAATTTAAA
1537223 ATTTTATAT
1 ATTTTATAT
1537232 ATTTTATAT
1 ATTTTATAT
1537241 AAATTTTA-AT
1 --ATTTTATAT
*
1537251 ATATTA-AT
1 ATTTTATAT
*
1537259 A-ATTATAT
1 ATTTTATAT
1537267 -TATTTA-A-
1 AT-TTTATAT
*
1537274 ATTTTATAA
1 ATTTTATAT
1537283 ATTTTTATAT
1 A-TTTTATAT
1537293 ATTTTATAT
1 ATTTTATAT
1537302 AACTTTTA-AT
1 -A-TTTTATAT
* *
1537312 ACTTATATAA
1 A-TTTTATAT
*
1537322 ATTTTA-AA
1 ATTTTATAT
1537330 ATTTTATAT
1 ATTTTATAT
1537339 TAATTAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 26
0.73 0.06 0.22
Matches are distributed among these distances:
7 8 0.09
8 21 0.24
9 32 0.37
10 15 0.17
11 11 0.13
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTTTATAT
Found at i:1537241 original size:52 final size:55
Alignment explanation
Indices: 1537185--1537301 Score: 133
Period size: 52 Copynumber: 2.2 Consensus size: 55
1537175 TATTTACATC
* *
1537185 ATATATTTATATTTTCATATATT-ATAATTA-A-ATTTAAAATTTTATATA-TTTT
1 ATATATTTATATTTTAATATATTAATAATTATATATTT-AAATTTTATAAATTTTT
1537237 ATATA---A-ATTTTAATATATTAATAATTATATTATTTAAATTTTATAAATTTTT
1 ATATATTTATATTTTAATATATTAATAATTATA-TATTTAAATTTTATAAATTTTT
1537289 ATATATTTTATAT
1 ATATA-TTTATAT
1537302 AACTTTTAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
48 12 0.23
49 8 0.15
50 1 0.02
51 11 0.21
52 18 0.34
56 1 0.02
57 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (55 bp):
ATATATTTATATTTTAATATATTAATAATTATATATTTAAATTTTATAAATTTTT
Found at i:1537338 original size:19 final size:19
Alignment explanation
Indices: 1537221--1537364 Score: 109
Period size: 19 Copynumber: 7.5 Consensus size: 19
1537211 ATTAAATTTA
1537221 AAATTTTATATATTTTATAT
1 AAATTTTA-ATATTTTATAT
*
1537241 AAATTTTAATATATTAATAATT
1 AAATTTTAATAT-TTTAT-A-T
*
1537263 ATATTATTTAA-ATTTTATA-
1 A-AAT-TTTAATATTTTATAT
*
1537282 AATTTTTATATATTTTATAT
1 AAATTTTA-ATATTTTATAT
* *
1537302 AACTTTTAATA-CTTATAT
1 AAATTTTAATATTTTATAT
*
1537320 AAATTTTAAAATTTTATAT
1 AAATTTTAATATTTTATAT
* * *
1537339 TAA--TTAATATATTATCT
1 AAATTTTAATATTTTATAT
1537356 AAATTTTAA
1 AAATTTTAA
1537365 CATATTTTCC
Statistics
Matches: 100, Mismatches: 13, Indels: 23
0.74 0.10 0.17
Matches are distributed among these distances:
17 17 0.17
18 19 0.19
19 28 0.28
20 19 0.19
21 2 0.02
22 6 0.06
23 4 0.04
24 5 0.05
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
AAATTTTAATATTTTATAT
Found at i:1539867 original size:17 final size:17
Alignment explanation
Indices: 1539847--1539886 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
1539837 TATAAATATA
*
1539847 TTTAATTTTTAAAATTT
1 TTTAATATTTAAAATTT
*
1539864 TTTATATATTTAAATTTT
1 TTTA-ATATTTAAAATTT
1539882 TTTAA
1 TTTAA
1539887 ATAATTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTAATATTTAAAATTT
Found at i:1539898 original size:18 final size:18
Alignment explanation
Indices: 1539855--1539900 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
1539845 TATTTAATTT
* * *
1539855 TTAAAATTTTTTATATAT
1 TTAAATTTTTTTAAATAA
1539873 TTAAATTTTTTTAAATAA
1 TTAAATTTTTTTAAATAA
*
1539891 TTATATTTTT
1 TTAAATTTTT
1539901 ATATTTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTAAATTTTTTTAAATAA
Found at i:1541880 original size:13 final size:14
Alignment explanation
Indices: 1541855--1541888 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1541845 TAATAGAGAG
1541855 AGTTTAGGATTTTA
1 AGTTTAGGATTTTA
1541869 AGTTTA-GATTTTA
1 AGTTTAGGATTTTA
1541882 AGCTTTA
1 AG-TTTA
1541889 ACTCGTACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (14 bp):
AGTTTAGGATTTTA
Found at i:1543633 original size:137 final size:137
Alignment explanation
Indices: 1543387--1543662 Score: 525
Period size: 137 Copynumber: 2.0 Consensus size: 137
1543377 GCCTAATCAA
*
1543387 TTTTCATAAAAATTGCCACGTTTCACATTCACATAGGAGATTTCTTATCAAAAATATCCTGTAAT
1 TTTTCATAAAAATTACCACGTTTCACATTCACATAGGAGATTTCTTATCAAAAATATCCTGTAAT
*
1543452 ACCCCATTTGATTTCATTAAGTTATAAGAATCATTAAAAATATAACTTAACACCTTTGCAGGCAG
66 ACCCCATTTGATTTCATTAAATTATAAGAATCATTAAAAATATAACTTAACACCTTTGCAGGCAG
1543517 TACTGAT
131 TACTGAT
1543524 TTTTCATAAAAATTACCACGTTTCACATTCACATAGGAGATTTCTTATCAAAAATATCCTGTAAT
1 TTTTCATAAAAATTACCACGTTTCACATTCACATAGGAGATTTCTTATCAAAAATATCCTGTAAT
*
1543589 ACCCCATTTGATTTCATTAAATTATAAGAATCATTAAAAGTATAACTTAACACCTTTGCAGGCAG
66 ACCCCATTTGATTTCATTAAATTATAAGAATCATTAAAAATATAACTTAACACCTTTGCAGGCAG
1543654 TACTGAT
131 TACTGAT
1543661 TT
1 TT
1543663 ATCAAAAGAA
Statistics
Matches: 136, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
137 136 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (137 bp):
TTTTCATAAAAATTACCACGTTTCACATTCACATAGGAGATTTCTTATCAAAAATATCCTGTAAT
ACCCCATTTGATTTCATTAAATTATAAGAATCATTAAAAATATAACTTAACACCTTTGCAGGCAG
TACTGAT
Found at i:1547628 original size:3 final size:3
Alignment explanation
Indices: 1547620--1547659 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1547610 ATCATTCAAT
1547620 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1547660 AGATTTCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1550332 original size:45 final size:38
Alignment explanation
Indices: 1550266--1550374 Score: 103
Period size: 37 Copynumber: 2.7 Consensus size: 38
1550256 CTGAGCTATC
* *
1550266 AATAAATTTTATGATTATTATAAATTTGATAATTTATATATT
1 AATATATTTTAT-ATTTTTATAAATTT-ATAA-TTATAT-TT
1550308 CATATCATATTTTTATATTTTTATAAA-TTATAATTATATTT
1 -A-AT-ATA-TTTTATATTTTTATAAATTTATAATTATATTT
* *
1550349 AATATATTATATATTTATATAAATTT
1 AATATATTTTATATTTTTATAAATTT
1550375 TTTATGTTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 13
0.77 0.05 0.17
Matches are distributed among these distances:
37 15 0.26
38 5 0.09
39 2 0.03
40 1 0.02
41 2 0.03
42 6 0.10
43 5 0.09
44 4 0.07
45 12 0.21
46 6 0.10
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (38 bp):
AATATATTTTATATTTTTATAAATTTATAATTATATTT
Found at i:1550359 original size:20 final size:21
Alignment explanation
Indices: 1550320--1550368 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
1550310 TATCATATTT
*
1550320 TTATATTTTTATAAATTATAA
1 TTATATTTTAATAAATTATAA
*
1550341 TTATA-TTTAATATATTATATA
1 TTATATTTTAATAAATTATA-A
1550362 TTTATAT
1 -TTATAT
1550369 AAATTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 12 0.52
21 6 0.26
22 5 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATATTTTAATAAATTATAA
Found at i:1550492 original size:25 final size:29
Alignment explanation
Indices: 1550442--1550494 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1550432 CTGAATTATT
1550442 TTTTATATCATATTATATATATTTATTTC
1 TTTTATATCATATTATATATATTTATTTC
1550471 TTTTATAT-A-ATTATAT-TA-TTATTT
1 TTTTATATCATATTATATATATTTATTT
1550495 AAAATTATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 6 0.25
26 2 0.08
27 7 0.29
28 1 0.04
29 8 0.33
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTTATATCATATTATATATATTTATTTC
Found at i:1551652 original size:2 final size:2
Alignment explanation
Indices: 1551645--1551673 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1551635 GTAATGTGAA
1551645 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1551674 GAAATATAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1553447 original size:11 final size:14
Alignment explanation
Indices: 1553417--1553462 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
1553407 ATCTAACTTA
*
1553417 TTTTATCATAAAATT
1 TTTTAT-ATATAATT
1553432 ATTTTAT-TAT-ATT
1 -TTTTATATATAATT
1553445 TTTTATATATAATT
1 TTTTATATATAATT
1553459 TTTT
1 TTTT
1553463 TAATATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 6 0.22
13 6 0.22
14 9 0.33
16 6 0.22
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTATATATAATT
Found at i:1553458 original size:27 final size:28
Alignment explanation
Indices: 1553417--1553470 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
1553407 ATCTAACTTA
*
1553417 TTTTATCATAAAATTATTTTATTATATT
1 TTTTATCATAAAATTATTTTAATATATT
* *
1553445 TTTTAT-ATATAATTTTTTTAATATAT
1 TTTTATCATAAAATTATTTTAATATAT
1553471 ATGATAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTTATCATAAAATTATTTTAATATATT
Found at i:1553561 original size:20 final size:18
Alignment explanation
Indices: 1553533--1553573 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1553523 ATTTAATTTC
1553533 TTTTATAT-TTATATAAAT
1 TTTTATATATTA-ATAAAT
*
1553551 TTTTATATATTAATAACT
1 TTTTATATATTAATAAAT
1553569 TTTTA
1 TTTTA
1553574 AATAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTATATATTAATAAAT
Found at i:1553614 original size:13 final size:13
Alignment explanation
Indices: 1553598--1553647 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
1553588 TATTAATTTA
1553598 TTAATATTATATT
1 TTAATATTATATT
*
1553611 TTAAT-TT-TTTT
1 TTAATATTATATT
1553622 TTAATATTATA-T
1 TTAATATTATATT
1553634 TTAATAATTATATT
1 TTAAT-ATTATATT
1553648 ATATTTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 8 0.26
12 10 0.32
13 12 0.39
14 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTAATATTATATT
Found at i:1553633 original size:5 final size:5
Alignment explanation
Indices: 1553625--1553672 Score: 50
Period size: 5 Copynumber: 10.4 Consensus size: 5
1553615 TTTTTTTTTA
* *
1553625 ATATT ATATT -TAAT A-ATT ATATT ATATT -TAAT A-ATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1553671 AT
1 AT
1553673 CTAAATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
4 12 0.34
5 23 0.66
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:1553646 original size:18 final size:18
Alignment explanation
Indices: 1553625--1553670 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
1553615 TTTTTTTTTA
1553625 ATATTATATTTAATAATT
1 ATATTATATTTAATAATT
1553643 ATATTATATTTAATAATT
1 ATATTATATTTAATAATT
1553661 ATATTATATT
1 ATATTATATT
1553671 ATCTAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATTATATTTAATAATT
Found at i:1556160 original size:37 final size:40
Alignment explanation
Indices: 1556108--1556201 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 40
1556098 ATATAAATAT
1556108 ATATTTGATATAAATATATT-TAATTTTT-TA-TATATTTAAAA
1 ATATTT-AT-TAAATATATTAT-ATTTTTATATTATA-TTAAAA
1556149 A-ATTT-TTAAATA-ATTATATTTTTATATTATATTAAAA
1 ATATTTATTAAATATATTATATTTTTATATTATATTAAAA
*
1556186 ATATTTATAAAATATA
1 ATATTTATTAAATATA
1556202 ATATTAAATA
Statistics
Matches: 46, Mismatches: 1, Indels: 13
0.77 0.02 0.22
Matches are distributed among these distances:
36 9 0.20
37 16 0.35
38 9 0.20
39 6 0.13
40 5 0.11
41 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (40 bp):
ATATTTATTAAATATATTATATTTTTATATTATATTAAAA
Found at i:1556206 original size:38 final size:35
Alignment explanation
Indices: 1556128--1556206 Score: 90
Period size: 38 Copynumber: 2.2 Consensus size: 35
1556118 TAAATATATT
*
1556128 TAAT-TTTTTATATATTTAAAAAATTTTTAAATAA
1 TAATATTTTTATATATTTAAAAAATTTTAAAATAA
*
1556162 TTATATTTTTATATTATATTAAAAATATTTATAAAAT-A
1 TAATATTTTTATA-TAT-TTAAAAA-ATTT-TAAAATAA
1556200 TAATATT
1 TAATATT
1556207 AAATATAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
34 3 0.08
35 8 0.22
36 3 0.08
37 7 0.19
38 11 0.30
39 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (35 bp):
TAATATTTTTATATATTTAAAAAATTTTAAAATAA
Found at i:1557131 original size:24 final size:23
Alignment explanation
Indices: 1557094--1557140 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1557084 TTATTAAATA
**
1557094 AAAAATATAATAAATGTAAATTT
1 AAAAATATAATAAAAATAAATTT
*
1557117 AAAAATAATAGTAAAAATAAATTT
1 AAAAAT-ATAATAAAAATAAATTT
1557141 TCGTAAACCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (23 bp):
AAAAATATAATAAAAATAAATTT
Found at i:1558682 original size:18 final size:19
Alignment explanation
Indices: 1558659--1558694 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1558649 TATCTAATGG
1558659 TAATAT-TTAATGCTAAAA
1 TAATATATTAATGCTAAAA
*
1558677 TAATATATTAATGTTAAA
1 TAATATATTAATGCTAAA
1558695 TACTTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (19 bp):
TAATATATTAATGCTAAAA
Found at i:1558821 original size:33 final size:32
Alignment explanation
Indices: 1558732--1558821 Score: 87
Period size: 31 Copynumber: 2.8 Consensus size: 32
1558722 AAACATAATT
*
1558732 ATATAAATATTTAAAATATTATAAATATTATTAAA
1 ATATAAATA-TTAAAA-ATTAT-AATACTATTAAA
* *
1558767 ATAAAAATATGT--ATATT-TAATACTATTCAAA
1 ATATAAATAT-TAAAAATTATAATACTATT-AAA
1558798 ATATAAATATTAAAAATTATAATA
1 ATATAAATATTAAAAATTATAATA
1558822 TTAAAATAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
30 9 0.20
31 13 0.29
32 7 0.16
33 6 0.13
34 1 0.02
35 9 0.20
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (32 bp):
ATATAAATATTAAAAATTATAATACTATTAAA
Found at i:1562892 original size:100 final size:99
Alignment explanation
Indices: 1562732--1563035 Score: 385
Period size: 100 Copynumber: 3.0 Consensus size: 99
1562722 ACCAAGGTTC
* * *
1562732 TTTTTCTGAGAAATTATATCATTCATCATATCTTAAGATTTTAGATTTTAGGAGCGGAGTTAACA
1 TTTTTATGAGAAATTATATCATTCATCATATGTGAAGATTTTAGATTTTAGGAGC-GAGTTAACA
* * *
1562797 TGGTAAAACATGTACCTTGAGATATATTTAAATTA
65 TGGTGAAACATATATCTTGAGATATATTTAAATTA
* * *
1562832 TTTTTATGAAAAATTATATCATTCATC-TCGTGTGAAGATTTTAGATTTTAGGAGCAGAGTTAGC
1 TTTTTATGAGAAATTATATCATTCATCAT-ATGTGAAGATTTTAGATTTTAGGAGC-GAGTTAAC
* *
1562896 ATGGTGAAACATATATCTGGATATATATATATAAATTA
64 ATGGTGAAACATATATCTTGAGATATAT-T-TAAATTA
* * * *
1562934 ATTTTATGAGAAATTATACCATTCATCATATGTGAAGATTTTAGATTTTAGAAACGAAGTTAACA
1 TTTTTATGAGAAATTATATCATTCATCATATGTGAAGATTTTAGATTTTAGGAGCG-AGTTAACA
* * *
1562999 TGGTGAATCATATATATTGAGATATATTTAAAATA
65 TGGTGAAACATATATCTTGAGATATATTTAAATTA
1563034 TT
1 TT
1563036 AAAAATAATT
Statistics
Matches: 174, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
99 1 0.01
100 85 0.49
101 3 0.02
102 84 0.48
103 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.39
Consensus pattern (99 bp):
TTTTTATGAGAAATTATATCATTCATCATATGTGAAGATTTTAGATTTTAGGAGCGAGTTAACAT
GGTGAAACATATATCTTGAGATATATTTAAATTA
Found at i:1562971 original size:102 final size:99
Alignment explanation
Indices: 1562733--1563030 Score: 373
Period size: 102 Copynumber: 3.0 Consensus size: 99
1562723 CCAAGGTTCT
* * *
1562733 TTTTCTGAGAAATTATATCATTCATCATATCTTAAGATTTTAGATTTTAGGAGCGGAGTTAACAT
1 TTTTATGAGAAATTATATCATTCATCATATGTGAAGATTTTAGATTTTAGGAGC-GAGTTAACAT
* * * * *
1562798 GGTAAAACATGTACCTTGAGATATATTTAAATTAT
65 GGTGAAACATATATCTGGAGATATATTTAAATTAA
* * *
1562833 TTTTATGAAAAATTATATCATTCATC-TCGTGTGAAGATTTTAGATTTTAGGAGCAGAGTTAGCA
1 TTTTATGAGAAATTATATCATTCATCAT-ATGTGAAGATTTTAGATTTTAGGAGC-GAGTTAACA
*
1562897 TGGTGAAACATATATCTGGATATATATATATAAATTAA
64 TGGTGAAACATATATCTGGAGATATAT-T-TAAATTAA
* * *
1562935 TTTTATGAGAAATTATACCATTCATCATATGTGAAGATTTTAGATTTTAGAAACGAAGTTAACAT
1 TTTTATGAGAAATTATATCATTCATCATATGTGAAGATTTTAGATTTTAGGAGCG-AGTTAACAT
* * *
1563000 GGTGAATCATATATATTGAGATATATTTAAA
65 GGTGAAACATATATCTGGAGATATATTTAAA
1563031 ATATTAAAAA
Statistics
Matches: 170, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
99 1 0.01
100 81 0.48
101 3 0.02
102 84 0.49
103 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.39
Consensus pattern (99 bp):
TTTTATGAGAAATTATATCATTCATCATATGTGAAGATTTTAGATTTTAGGAGCGAGTTAACATG
GTGAAACATATATCTGGAGATATATTTAAATTAA
Found at i:1565054 original size:17 final size:18
Alignment explanation
Indices: 1565022--1565056 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
1565012 TAAATATAAT
1565022 ATTTATAATTATTTTTTAA
1 ATTTATAA-TATTTTTTAA
1565041 ATTTATAA-ATTTTTTA
1 ATTTATAATATTTTTTA
1565057 TGAACGTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTATAATATTTTTTAA
Found at i:1565684 original size:9 final size:9
Alignment explanation
Indices: 1565609--1565688 Score: 59
Period size: 9 Copynumber: 9.4 Consensus size: 9
1565599 GATATATACA
1565609 ATATACATAT
1 ATATA-ATAT
1565619 ATAT-ATAT
1 ATATAATAT
1565627 ATATAATAT
1 ATATAATAT
1565636 ACTA-AA-AGT
1 A-TATAATA-T
*
1565645 ATATAAAAT
1 ATATAATAT
1565654 AT-TAATAT
1 ATATAATAT
1565662 ATATAAT-T
1 ATATAATAT
1565670 -T-T-ATAT
1 ATATAATAT
*
1565676 ATCTAATAT
1 ATATAATAT
1565685 ATAT
1 ATAT
1565689 TTAAAAATTA
Statistics
Matches: 58, Mismatches: 2, Indels: 21
0.72 0.02 0.26
Matches are distributed among these distances:
5 2 0.03
6 2 0.03
7 2 0.03
8 20 0.34
9 25 0.43
10 7 0.12
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (9 bp):
ATATAATAT
Found at i:1565899 original size:17 final size:16
Alignment explanation
Indices: 1565868--1565903 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1565858 ATCATGAAAT
*
1565868 TTAATATTTTATTATA
1 TTAATATTATATTATA
1565884 TTAATAATTATATTATA
1 TTAAT-ATTATATTATA
1565901 TTA
1 TTA
1565904 TCTAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTAATATTATATTATA
Found at i:1567942 original size:25 final size:23
Alignment explanation
Indices: 1567889--1567942 Score: 54
Period size: 25 Copynumber: 2.3 Consensus size: 23
1567879 CGATCGATCA
* *
1567889 AAATTTTTAATTTTTTTAATTAT
1 AAATATTTAATTTTTTTAAATAT
**
1567912 TGATATTTAATTTATATTTAAATAT
1 AAATATTTAATTT-T-TTTAAATAT
1567937 AAATAT
1 AAATAT
1567943 AAAAATATAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
23 10 0.43
24 1 0.04
25 12 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
AAATATTTAATTTTTTTAAATAT
Found at i:1568434 original size:22 final size:22
Alignment explanation
Indices: 1568384--1568435 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1568374 TAATAAAAAT
*
1568384 TTAATTAATATTAAAATAATCT
1 TTAATTAATATTAAAATAATCA
* *
1568406 TTAATTACTATTAAATTAAATCA
1 TTAATTAATATTAAAAT-AATCA
1568429 TT-ATTAA
1 TTAATTAA
1568436 GTTATATTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAATTAATATTAAAATAATCA
Found at i:1569517 original size:2 final size:2
Alignment explanation
Indices: 1569510--1569534 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1569500 GAATGCAATC
1569510 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1569535 ATTTGTAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1569655 original size:23 final size:24
Alignment explanation
Indices: 1569628--1569675 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1569618 CATCACTAAA
1569628 TAAAAAT-ATAAT-AAATATAAATT
1 TAAAAATAATAATAAAAT-TAAATT
*
1569651 TAAAAATAATAGTAAAATTAAATT
1 TAAAAATAATAATAAAATTAAATT
1569675 T
1 T
1569676 TCGTAAACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 11 0.50
25 4 0.18
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
TAAAAATAATAATAAAATTAAATT
Found at i:1573157 original size:5 final size:5
Alignment explanation
Indices: 1573147--1573180 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
1573137 TCAACTCTAT
1573147 TTTTC TTTTC TTTT- TTTATC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTT-TC TTTTC TTTTC TTTT
1573181 TCCTCTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 3 0.11
5 21 0.78
6 3 0.11
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:1573170 original size:15 final size:14
Alignment explanation
Indices: 1573146--1573207 Score: 54
Period size: 14 Copynumber: 4.2 Consensus size: 14
1573136 ATCAACTCTA
1573146 TTTTTCTTTTCTTT
1 TTTTTCTTTTCTTT
1573160 TTTTATCTTTTCTTTT
1 TTTT-TCTTTTC-TTT
* *
1573176 CTTTTTCCTCTCTTT
1 -TTTTTCTTTTCTTT
*
1573191 TTTGTTC-TATCTTT
1 TTT-TTCTTTTCTTT
1573205 TTT
1 TTT
1573208 ACTACTATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
14 16 0.39
15 13 0.32
16 8 0.20
17 4 0.10
ACGTcount: A:0.03, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTTTCTTTTCTTT
Found at i:1573915 original size:21 final size:21
Alignment explanation
Indices: 1573860--1573936 Score: 86
Period size: 21 Copynumber: 3.8 Consensus size: 21
1573850 AAAACTTGAC
*
1573860 ATTGTATCAATACAATCA--T
1 ATTGTATCAATACAATCAGCA
* * *
1573879 ATTGAATTAATGCAATCAGCA
1 ATTGTATCAATACAATCAGCA
*
1573900 ATTGTATCAATACAATAAGCA
1 ATTGTATCAATACAATCAGCA
*
1573921 ATTGTACCAATACAAT
1 ATTGTATCAATACAAT
1573937 GCATTCATAG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.32
21 32 0.68
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (21 bp):
ATTGTATCAATACAATCAGCA
Found at i:1574589 original size:20 final size:20
Alignment explanation
Indices: 1574553--1574595 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1574543 TTTAATCTAA
*
1574553 AAAATGAACATAAAATTACAT
1 AAAATGAACACAAAATTA-AT
1574574 AAAATGAA-ACAAAATTAAT
1 AAAATGAACACAAAATTAAT
1574593 AAA
1 AAA
1574596 CAGAACCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 8 0.38
21 8 0.38
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAATGAACACAAAATTAAT
Found at i:1577573 original size:49 final size:49
Alignment explanation
Indices: 1577449--1577939 Score: 782
Period size: 49 Copynumber: 10.0 Consensus size: 49
1577439 TCTTTTTTCC
* * * *
1577449 TTTATTT-ATTCTATCATGCTCCCTTTTATTATTTATGCTTTTTCTTTT
1 TTTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTT
1577497 TATTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTT
1 T-TTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTT
*
1577547 TTTATTTCATTCCATCATGCTTCATTTTATTATTCATGCTTTTTCTTTT
1 TTTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTT
1577596 TTT-TTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTT
1 TTTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTT
1577644 TTTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTTTT
1 TTTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTC--TTTT
*
1577695 TTTATTTCATTCCATCATGCTTCATTTTATTATTCATGCTTTTT-TTTT
1 TTTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTT
1577743 TATTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTC---T
1 T-TTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTT
*
1577790 TTT-TTT-ATTCCATCATGCTACATTTTATTATTCATGTTTTTTCTTTTTT
1 TTTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTC--TTTT
*
1577839 TCTTATTTCATTCCATCATGCTACGTTTTATTATTCATGCTTTTTCTTTT
1 T-TTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTT
*
1577889 TTTATTTCATTCCATCATGCTTCATTTTATTATTCATGCTTTTTCTTTT
1 TTTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTT
1577938 TT
1 TT
1577940 ATTATTATTA
Statistics
Matches: 415, Mismatches: 13, Indels: 29
0.91 0.03 0.06
Matches are distributed among these distances:
44 36 0.09
45 3 0.01
46 2 0.00
47 2 0.00
48 53 0.13
49 189 0.46
50 45 0.11
51 50 0.12
52 35 0.08
ACGTcount: A:0.17, C:0.18, G:0.04, T:0.61
Consensus pattern (49 bp):
TTTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTT
Found at i:1577722 original size:100 final size:98
Alignment explanation
Indices: 1577449--1577939 Score: 782
Period size: 97 Copynumber: 5.0 Consensus size: 98
1577439 TCTTTTTTCC
* * * *
1577449 TTTATTT-ATTCTATCATGCTCCCTTTTATTATTTATGCTTTTTCTTTTTATTATTTCATTCCAT
1 TTTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTTT-TTATTTCATTCCAT
1577513 CATGCTACATTTTATTATTCATGCTTTTTCTTTT
65 CATGCTACATTTTATTATTCATGCTTTTTCTTTT
*
1577547 TTTATTTCATTCCATCATGCTTCATTTTATTATTCATGCTTTTTCTTTTTTT-TTTCATTCCATC
1 TTTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTTTTTATTTCATTCCATC
1577611 ATGCTACATTTTATTATTCATGCTTTTTCTTTT
66 ATGCTACATTTTATTATTCATGCTTTTTCTTTT
1577644 TTTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTTTTTTTATTTCATTCCA
1 TTTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTC--TTTTTTTATTTCATTCCA
*
1577709 TCATGCTTCATTTTATTATTCATGCTTTTT-TTTT
64 TCATGCTACATTTTATTATTCATGCTTTTTCTTTT
1577743 TATTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTC---TTTT-TTT-ATTCCAT
1 T-TTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTTTTTATTTCATTCCAT
*
1577803 CATGCTACATTTTATTATTCATGTTTTTTCTTTTTT
65 CATGCTACATTTTATTATTCATGCTTTTTC--TTTT
*
1577839 TCTTATTTCATTCCATCATGCTACGTTTTATTATTCATGCTTTTTCTTTTTTTATTTCATTCCAT
1 T-TTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTTTTTATTTCATTCCAT
*
1577904 CATGCTTCATTTTATTATTCATGCTTTTTCTTTT
65 CATGCTACATTTTATTATTCATGCTTTTTCTTTT
1577938 TT
1 TT
1577940 ATTATTATTA
Statistics
Matches: 368, Mismatches: 12, Indels: 26
0.91 0.03 0.06
Matches are distributed among these distances:
93 34 0.09
94 3 0.01
95 4 0.01
96 48 0.13
97 89 0.24
98 10 0.03
99 59 0.16
100 86 0.23
101 35 0.10
ACGTcount: A:0.17, C:0.18, G:0.04, T:0.61
Consensus pattern (98 bp):
TTTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTTTTTATTTCATTCCATC
ATGCTACATTTTATTATTCATGCTTTTTCTTTT
Found at i:1577975 original size:145 final size:145
Alignment explanation
Indices: 1577449--1577976 Score: 589
Period size: 145 Copynumber: 3.6 Consensus size: 145
1577439 TCTTTTTTCC
* * * * *
1577449 TTTATTT-ATTCTATCATGCTCCCTTTTATTATTTATGCTTTTTCTTTTTATTATT-TCATTCCA
1 TTTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTTT-TTATTATCATTACA
** * * *
1577512 TCATGCTACATTTTATTATTCATGCTTTTTC--TTTTTTTATTTCATTCCATCATGCTTCATTTT
65 TTTTGAT-TA-TTT-TT-TT-ATGTTTTTTCTTTTTTTTTATTTCATTCCATCATGCTTCATTTT
1577575 ATTATTCATGCTTTTTCTTTT
125 ATTATTCATGCTTTTTCTTTT
*
1577596 TTT-TTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTTTTTATT-TCATTCCAT
1 TTTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTTTTTATTATCATTACAT
** * * *
1577659 CATGCTACATTTTATTATTCATGCTTTTTCTTTTTTTTTATTTCATTCCATCATGCTTCATTTTA
66 TTTGAT-TA-TTT-TT-TT-ATGTTTTTTCTTTTTTTTTATTTCATTCCATCATGCTTCATTTTA
1577724 TTATTCATGCTTTTT-TTTT
126 TTATTCATGCTTTTTCTTTT
1577743 TATTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTTTTTATTCCATCATGC
1 T-TTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTTTTTATT--ATCAT--
* * *
1577808 TACATTTT-ATTA----TTCATGTTTTTTCTTTTTTTCTTATTTCATTCCATCATGCTACGTTTT
61 TACATTTTGATTATTTTTTTATGTTTTTTCTTTTTTT-TTATTTCATTCCATCATGCTTCATTTT
1577868 ATTATTCATGCTTTTTCTTTT
125 ATTATTCATGCTTTTTCTTTT
* * **
1577889 TTTATTTCATTCCATCATGCTTCATTTTATTATTCATGCTTTTTC-TTTTTTATTATTATTATTT
1 TTTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTTTTTATTATCATTACAT
1577953 TTTGATTGATTTTTTTAT-TTTTTT
66 TTTGATT-ATTTTTTTATGTTTTTT
1577977 AAATTTCTTG
Statistics
Matches: 345, Mismatches: 18, Indels: 38
0.86 0.04 0.09
Matches are distributed among these distances:
140 6 0.02
141 3 0.01
142 5 0.01
144 25 0.07
145 91 0.26
146 57 0.17
147 46 0.13
148 50 0.14
149 51 0.15
152 5 0.01
153 1 0.00
154 5 0.01
ACGTcount: A:0.17, C:0.16, G:0.04, T:0.62
Consensus pattern (145 bp):
TTTATTTCATTCCATCATGCTACATTTTATTATTCATGCTTTTTCTTTTTTTATTATCATTACAT
TTTGATTATTTTTTTATGTTTTTTCTTTTTTTTTATTTCATTCCATCATGCTTCATTTTATTATT
CATGCTTTTTCTTTT
Found at i:1578043 original size:50 final size:46
Alignment explanation
Indices: 1577934--1578044 Score: 107
Period size: 47 Copynumber: 2.3 Consensus size: 46
1577924 ATGCTTTTTC
*
1577934 TTTTTTATTATTATTATTTTTTGATTGATTTTTTTATTTTTTTAAAT
1 TTTTTTATT-TTATTATTTATTGATTGATTTTTTTATTTTTTTAAAT
* * * *
1577981 TTCTTGATTTTTATTATTATATTGAATATTATTATTTTTAATTTTTTT-GAT
1 TTTTTTA-TTTTATTATT-TATTG-AT-TGATT-TTTTT-ATTTTTTTAAAT
1578032 TTTTTTATTTTAT
1 TTTTTTATTTTAT
1578045 ACCAAAAAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
47 13 0.25
48 6 0.12
49 2 0.04
50 10 0.20
51 12 0.24
52 8 0.16
ACGTcount: A:0.23, C:0.01, G:0.05, T:0.72
Consensus pattern (46 bp):
TTTTTTATTTTATTATTTATTGATTGATTTTTTTATTTTTTTAAAT
Found at i:1578398 original size:15 final size:17
Alignment explanation
Indices: 1578367--1578398 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1578357 CAAGAAGAAT
1578367 AAAACAAGAATGCAGGA
1 AAAACAAGAATGCAGGA
1578384 AAAACAA-AA-GCAGGA
1 AAAACAAGAATGCAGGA
1578399 CCACACAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.62, C:0.12, G:0.22, T:0.03
Consensus pattern (17 bp):
AAAACAAGAATGCAGGA
Found at i:1578575 original size:42 final size:42
Alignment explanation
Indices: 1578497--1579671 Score: 917
Period size: 42 Copynumber: 27.4 Consensus size: 42
1578487 AAAACCAACG
* * *
1578497 GGCAGACTTAGGGAAAGAAAAGTCTCCAGGGACAAAGCTGACA
1 GGCAGACTGAGGG-AAGAAAAGTCTCCAGGGTCAAAGCCGACA
*
1578540 GGCAGACTGAGAGAA-AGAAAGTCTCCAGGGTCAAAGCCGACA
1 GGCAGACTGAGGGAAGA-AAAGTCTCCAGGGTCAAAGCCGACA
* * * *
1578582 GGCAGACTAAAGGAAGGAAAGTCTCCAGGGTCAAAGCCGATA
1 GGCAGACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACA
** * *
1578624 GGCAGACTGAGGGTTGAAAAGTCTCCACGGTCAAAGCCGATA
1 GGCAGACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACA
**
1578666 GGCAGACTGAGGGTCGAAAAGTCTCCAGGGTCAAAGCCGACA
1 GGCAGACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACA
* * *
1578708 GGCAGACTGCGGGAA-AGAAAGTCTCCAGGGACGAAGCCGACA
1 GGCAGACTGAGGGAAGA-AAAGTCTCCAGGGTCAAAGCCGACA
* **
1578750 GGTAGACTGAAGGGTTGAAAAGTCTCCAGGGTCAAAGCCGACA
1 GGCAGACTG-AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACA
* * ** * * *
1578793 GGCAGACTAAGGGAAAAAAAGTCTTTAGGGACGAAGCTGACA
1 GGCAGACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACA
* * * *
1578835 TGCAGACTGCGAGAA-ATAAAGTCTCCAGGGAT-GAAGCCGACA
1 GGCAGACTGAGGGAAGA-AAAGTCTCCAGGG-TCAAAGCCGACA
* ** * *
1578877 GGTAGACTGAAGGGTTGAAAAGTCTCTAGGGTCAAAGCTGACA
1 GGCAGACTG-AGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACA
* *
1578920 GGCAGACTGAAGGAAGAAAAGTCTCTAGGGTCAAAGCCGACA
1 GGCAGACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACA
* ** * * **
1578962 GGCAGACTAAGGGAAGAAACCGACAGGTAAACTGAAGGGTTGAAAAGTCTCCA
1 GGCAGACTGAGGGAAG-AA---A-A-GT---CTCCAGGG-T-CAAAGCCGACA
* ** * ** * * *
1579015 GG--GTCAAAGCCGACAG-GCAGACT-GAGGGATAAAAAGTCTCCAGAGTCAA
1 GGCAGACTGAG-GGA-AGAAAAGTCTCCAGGG-T-CAAAG---CC-GA--C-A
* * * * ** *** ** * ** *
1579064 AGCCGAC-AAGCAGATTGAGGGAAG--AAAAGTCTCAAGGGTCAAAGCT
1 GGCAGACTGAG-GGA---AGAAAAGTCTCCAGGGTCAA-AG-CCGA-CA
* *
1579110 GACAGGCAGACTGAGGGAAGAAAAGTCTCAAGGGTCAAAGCTGACA
1 G----GCAGACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACA
* * *
1579156 GGCAGACTAAAGGAAGAAAAGTCTCCAGGGTCAAAACCGACA
1 GGCAGACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACA
*
1579198 GGCAGACTAAGGGATAGAAAAGTCTCCAGGGTCAAAGCCGACA
1 GGCAGACTGAGGGA-AGAAAAGTCTCCAGGGTCAAAGCCGACA
* *
1579241 GGCAGACTAAGGGATGAAAAGTCTCCAGGGTCAAAGCCGACA
1 GGCAGACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACA
*
1579283 AGCAGACT-ACGGGAA-AGAAAGTCTCCAGGGTCAAAG-C--C-
1 GGCAGACTGA-GGGAAGA-AAAGTCTCCAGGGTCAAAGCCGACA
* * *
1579321 GGTAGACTGAGGGATGAAAAATCTCCAGGGTCAAAGCCGACA
1 GGCAGACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACA
** *
1579363 GGCAGACTGAGGGTTGAAAAGTCTCCAGGGTTAAAGCCGACA
1 GGCAGACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACA
* *
1579405 GGCAAACTGAGGGATGAAAAGTCTCCAGGGTCAAAGCCGACA
1 GGCAGACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACA
** * **
1579447 GGCAGACTGAGGGTTGAAAAGTCTCCAGGGTTAAAGCTAACA
1 GGCAGACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACA
* *
1579489 GGCAGACTGAGGGATGAAAAGTCTCCAGGGTCAAAGCCGATA
1 GGCAGACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACA
* * *
1579531 GGCAGACTAAGGGATGAAAAGTCTCCAGGGTCAAAGCTGACA
1 GGCAGACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACA
* * *
1579573 GGCAGATTGAGGGATGAAAAGTCTTCAGGGTCAAAGCCGACA
1 GGCAGACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACA
* * *
1579615 GGCAGACTGAGGGATGAAAAGTCTCCAGGGTCAAAACCGATA
1 GGCAGACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACA
*
1579657 GGCAGACTAAGGGAA
1 GGCAGACTGAGGGAA
1579672 AACAAAAAAG
Statistics
Matches: 925, Mismatches: 154, Indels: 107
0.78 0.13 0.09
Matches are distributed among these distances:
38 28 0.03
39 4 0.00
41 7 0.01
42 681 0.74
43 119 0.13
44 2 0.00
45 1 0.00
46 4 0.00
47 10 0.01
48 5 0.01
49 11 0.01
50 15 0.02
51 17 0.02
52 7 0.01
53 14 0.02
ACGTcount: A:0.36, C:0.19, G:0.31, T:0.13
Consensus pattern (42 bp):
GGCAGACTGAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACA
Found at i:1578841 original size:127 final size:127
Alignment explanation
Indices: 1578513--1578969 Score: 603
Period size: 127 Copynumber: 3.6 Consensus size: 127
1578503 CTTAGGGAAA
* * * * *
1578513 GAAAAGTCTCCAGGGACAAAGCTGACAGGCAGACTGAGAGAAAGAAAGTCTCCAGGGTCAAAGCC
1 GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAAAAAGTCTCCAGGGTCAAAGCC
*** * * * * *
1578578 GACAGGCAGACTAAAGGAAGGAAAGTCTCCAGGGTCAAAGCCGATAGGCAGACTG-AGGGTT
66 GACAGGCAGACTGCGGGAAAGAAAGTCTCCAGGGACGAAGCCGACAGGTAGACTGAAGGGTT
* * * ***
1578639 GAAAAGTCTCCACGGTCAAAGCCGATAGGCAGACTGAGGGTCGAAAAGTCTCCAGGGTCAAAGCC
1 GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAAAAAGTCTCCAGGGTCAAAGCC
1578704 GACAGGCAGACTGCGGGAAAGAAAGTCTCCAGGGACGAAGCCGACAGGTAGACTGAAGGGTT
66 GACAGGCAGACTGCGGGAAAGAAAGTCTCCAGGGACGAAGCCGACAGGTAGACTGAAGGGTT
** * * *
1578766 GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAAAAAGTCTTTAGGGACGAAGCT
1 GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAAAAAGTCTCCAGGGTCAAAGCC
* * * *
1578831 GACATGCAGACTGCGAGAAATAAAGTCTCCAGGGATGAAGCCGACAGGTAGACTGAAGGGTT
66 GACAGGCAGACTGCGGGAAAGAAAGTCTCCAGGGACGAAGCCGACAGGTAGACTGAAGGGTT
* * * *
1578893 GAAAAGTCTCTAGGGTCAAAGCTGACAGGCAGACTGAA-GGAAGAAAAGTCTCTAGGGTCAAAGC
1 GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACT-AAGGGAAAAAAAGTCTCCAGGGTCAAAGC
1578957 CGACAGGCAGACT
65 CGACAGGCAGACT
1578970 AAGGGAAGAA
Statistics
Matches: 289, Mismatches: 40, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
126 103 0.36
127 184 0.64
128 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.32, T:0.13
Consensus pattern (127 bp):
GAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGAAAAAAAGTCTCCAGGGTCAAAGCC
GACAGGCAGACTGCGGGAAAGAAAGTCTCCAGGGACGAAGCCGACAGGTAGACTGAAGGGTT
Found at i:1579054 original size:110 final size:110
Alignment explanation
Indices: 1578861--1579217 Score: 351
Period size: 110 Copynumber: 3.1 Consensus size: 110
1578851 TAAAGTCTCC
* * * * *
1578861 AGGGATGAAGCCGACAGGTAGACTGAAGGGTTGAAAAGTCTCTAGGGTCAAAGCTGACAGGCAGA
1 AGGGAAGAAACCGACAGGTAAACTGAAGGGTTGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGA
* * *
1578926 CTGAAGGAAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTA
66 CTGAAGGAAGAAAAGTCTCCAGAGTCAAAGCCGACAAGCAGACTA
1578971 AGGGAAGAAACCGACAGGTAAACTGAAGGGTTGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGA
1 AGGGAAGAAACCGACAGGTAAACTGAAGGGTTGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGA
* * *
1579036 CTGAGGGATA-AAAAGTCTCCAGAGTCAAAGCCGACAAGCAGATTG
66 CTGAAGGA-AGAAAAGTCTCCAGAGTCAAAGCCGACAAGCAGACTA
* *
1579081 AGGGAAGAAAAGTCTC-A-AGGGTCAAAGCTGACAGGCAGACTGAGGGAAGAAAAGTCTCAAGGG
1 AGGGAAG-AAA--C-CGACA-GGT-AAA-CTGA-AGG--G--T------TGAAAAGTCTCCAGGG
* * * * *
1579144 TCAAAGCTGACAGGCAGACTAAAGGAAGAAAAGTCTCCAGGGTCAAAACCGACAGGCAGACTA
48 TCAAAGCCGACAGGCAGACTGAAGGAAGAAAAGTCTCCAGAGTCAAAGCCGACAAGCAGACTA
1579207 AGGGATAGAAA
1 AGGGA-AGAAA
1579218 AGTCTCCAGG
Statistics
Matches: 205, Mismatches: 21, Indels: 26
0.81 0.08 0.10
Matches are distributed among these distances:
110 104 0.51
111 4 0.02
112 1 0.00
113 5 0.02
114 4 0.02
115 4 0.02
116 3 0.01
118 1 0.00
120 1 0.00
125 1 0.00
126 75 0.37
127 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.31, T:0.13
Consensus pattern (110 bp):
AGGGAAGAAACCGACAGGTAAACTGAAGGGTTGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGA
CTGAAGGAAGAAAAGTCTCCAGAGTCAAAGCCGACAAGCAGACTA
Found at i:1582253 original size:122 final size:123
Alignment explanation
Indices: 1581934--1582254 Score: 444
Period size: 122 Copynumber: 2.6 Consensus size: 123
1581924 TGTTATTTTT
* * *
1581934 AATAAAAATAATATTTAATTAACTTTAAAGAAATTTATATGAACAAATTAAAATATT-A--ATTA
1 AATAAAAATAATATTTAATTAAGTTT-AA-AAATTTACATTAACAAATTAAAATATTAATTATTA
*
1581996 T-TTTTTAAAAATAA-AAAATTAAATAAAAATAAAATGAGTTTATTATTATTTTTTAATAA
64 TGTTTTTAAAAA-AATAAAATAAAATAAAAATAAAATGAGTTTATTATTATTTTTTAATAA
* *
1582055 AATTAAAAATAATATTTAATTAAGTTTAAAAAATTACAATAACAAATTAAAAT-TTAATTATTAT
1 AA-TAAAAATAATATTTAATTAAGTTTAAAAATTTACATTAACAAATTAAAATATTAATTATTAT
* *
1582119 GTTTTTATAAAAATAAAA-AAAATAAAAATAAAA-G-GTTTTTTATTATAATTTTTAATAA
65 GTTTTTAAAAAAATAAAATAAAATAAAAATAAAATGAGTTTATTATTAT--TTTTTAATAA
*
1582177 AATAAAAATAATATTTAATTAAGTTTAAAAATTTACATTAAAAAATTAAAATATTAATTATTATG
1 AATAAAAATAATATTTAATTAAGTTTAAAAATTTACATTAACAAATTAAAATATTAATTATTATG
1582242 TTTTTAAAAAAAT
66 TTTTTAAAAAAAT
1582255 TTAAATTAAA
Statistics
Matches: 179, Mismatches: 12, Indels: 17
0.86 0.06 0.08
Matches are distributed among these distances:
119 2 0.01
120 32 0.18
121 52 0.29
122 80 0.45
123 13 0.07
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (123 bp):
AATAAAAATAATATTTAATTAAGTTTAAAAATTTACATTAACAAATTAAAATATTAATTATTATG
TTTTTAAAAAAATAAAATAAAATAAAAATAAAATGAGTTTATTATTATTTTTTAATAA
Found at i:1582294 original size:48 final size:46
Alignment explanation
Indices: 1582203--1582297 Score: 109
Period size: 48 Copynumber: 2.0 Consensus size: 46
1582193 AATTAAGTTT
* * *
1582203 AAAAATTTACATTAAAAAATTAAAATATTAATTATTATGTTTTTAA
1 AAAAATTTAAATTAAAAAATTAAAATAATAATTATTATATTTTTAA
** * *
1582249 AAAAATTTAAATTAAAAAAATTTATTATAATAATTTTTTTATTTTTAA
1 AAAAATTTAAATT-AAAAAA-TTAAAATAATAATTATTATATTTTTAA
1582297 A
1 A
1582298 TATATTTTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 12 0.30
47 6 0.15
48 22 0.55
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (46 bp):
AAAAATTTAAATTAAAAAATTAAAATAATAATTATTATATTTTTAA
Found at i:1582751 original size:111 final size:113
Alignment explanation
Indices: 1582597--1582877 Score: 367
Period size: 111 Copynumber: 2.5 Consensus size: 113
1582587 AATGTTATTT
*
1582597 TTTTAATTTGTTAATGTAAAATTTTTTAAAATTTAATTAAATATTATTTTTTATTTTATTAAAAA
1 TTTTAATTTGTTAATGT--AATTTTTTTAAATTTAATTAAATATTATTTTTTATTTTATTAAAAA
*
1582662 ATAATAATAATAAA-TACTT-TTT-ATTTTTA-TAAAAACATATAATTAATA
64 ATAAAAATAATAAACTACTTATTTAATTTTTATTAAAAA-A-ATAATTAATA
*
1582710 TTTTAATTTGTTAATGTAATTTTTTTAAATTTAATTAAATATTATTTTTAATTTTATTAAAAAAT
1 TTTTAATTTGTTAATGTAATTTTTTTAAATTTAATTAAATATTATTTTTTATTTTATTAAAAAAT
** *
1582775 AAAAATAATAAACCCTTTTTAATTTAATTTTTATTTTAAAAAATAATTAATA
66 AAAAATAATAAA--CTACTT-ATTTAATTTTTA-TTAAAAAAATAATTAATA
* * *
1582827 TTTTAATTTATTAATGTAAATTTTTT-AAGTTAATT-AATATTATTTTTTATT
1 TTTTAATTTGTTAATGTAATTTTTTTAAATTTAATTAAATATTATTTTTTATT
1582878 AAAAATAATA
Statistics
Matches: 150, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
111 57 0.38
113 17 0.11
114 3 0.02
115 15 0.10
116 11 0.07
117 41 0.27
118 1 0.01
119 5 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (113 bp):
TTTTAATTTGTTAATGTAATTTTTTTAAATTTAATTAAATATTATTTTTTATTTTATTAAAAAAT
AAAAATAATAAACTACTTATTTAATTTTTATTAAAAAAATAATTAATA
Found at i:1582925 original size:65 final size:67
Alignment explanation
Indices: 1582793--1582933 Score: 182
Period size: 68 Copynumber: 2.1 Consensus size: 67
1582783 TAAACCCTTT
* * * *
1582793 TTAATTTAATTTTTATTTTAAAAAATAATTAATATTTTAATTTATTAATGTAAATTTTTTAAGTT
1 TTAATTTATTTTTTATTTAAAAAAATAATTAATATATTAATTTATTAATGTAAATTTTTAAAGTT
1582858 AA
66 AA
* *
1582860 TTAATATTATTTTTTA-TTAAAAATAATAATTAATATATT-A-TTATTTAT-TAAATTTTTAAAT
1 TTAAT-TTATTTTTTATTTAAAAA-AATAATTAATATATTAATTTATTAATGTAAATTTTTAAAG
1582921 TTAA
64 TTAA
1582925 TTAATTTAT
1 TTAATTTAT
1582934 AAAAAAATTA
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
64 4 0.06
65 20 0.30
66 7 0.11
67 12 0.18
68 23 0.35
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (67 bp):
TTAATTTATTTTTTATTTAAAAAAATAATTAATATATTAATTTATTAATGTAAATTTTTAAAGTT
AA
Found at i:1586405 original size:20 final size:19
Alignment explanation
Indices: 1586380--1586422 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1586370 TAGATCATGA
1586380 AAAATG-ACGAAAATGATATT
1 AAAATGCACG-AAATGATA-T
*
1586400 AAAATGCATGAAATGATAT
1 AAAATGCACGAAATGATAT
1586419 AAAA
1 AAAA
1586423 GTCCTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 14 0.67
21 2 0.10
ACGTcount: A:0.58, C:0.05, G:0.14, T:0.23
Consensus pattern (19 bp):
AAAATGCACGAAATGATAT
Found at i:1586470 original size:58 final size:58
Alignment explanation
Indices: 1586380--1586596 Score: 201
Period size: 58 Copynumber: 3.7 Consensus size: 58
1586370 TAGATCATGA
* * * * * * *
1586380 AAAATGACGAAAATGATATTAAAATGCATGAAATGATATAAAAGTCCTTAAATTATAG
1 AAAATAACTAAAATGATATAAAAATACATGAAATGATATAAAAATCCTTAAGTCATAG
* * * *
1586438 AAAATAACTAAAATGACATAAAAATACATGAAA-CATCATAAAAATCTTTAGGTCATAG
1 AAAATAACTAAAATGATATAAAAATACATGAAATGAT-ATAAAAATCCTTAAGTCATAG
* * * * *
1586496 AAAATAACTAAAATGAAATAAAAATAGATAAAATGTTACAAAAATTCC-TAAGTCAT-G
1 AAAATAACTAAAATGATATAAAAATACATGAAATGATATAAAAA-TCCTTAAGTCATAG
*
1586553 AAAAATGAA-TAAAATGATATAAAAATACACTG-AATGACATAAAA
1 -AAAAT-AACTAAAATGATATAAAAATACA-TGAAATGATATAAAA
1586597 CTCCCTAGTT
Statistics
Matches: 128, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
57 3 0.02
58 119 0.93
59 6 0.05
ACGTcount: A:0.57, C:0.09, G:0.10, T:0.24
Consensus pattern (58 bp):
AAAATAACTAAAATGATATAAAAATACATGAAATGATATAAAAATCCTTAAGTCATAG
Found at i:1586610 original size:58 final size:56
Alignment explanation
Indices: 1586368--1586623 Score: 157
Period size: 58 Copynumber: 4.4 Consensus size: 56
1586358 GCTCCAAGTT
* ** * * *
1586368 CCTAGATCATGAAAAATGACGAAAATGATATTAAAATGCATGAAATGATATAAAAGTC
1 CCTAGTTCATGAAAAATGAATAAAATGATATAAAAATACATG-AATGACATAAAA-TC
* * * **
1586426 CTTAAATT-AT-AGAAAAT-AACTAAAATGACATAAAAATACATGAAACATCATAAAAATC
1 CCT-AGTTCATGA-AAAATGAA-TAAAATGATATAAAAATACATGAATGA-CAT-AAAATC
** * * * * *
1586484 TTTAGGTCAT-AGAAAAT-AACTAAAATGAAATAAAAATAGATAAAATGTTACA-AAAATT
1 CCTAGTTCATGA-AAAATGAA-TAAAATGATATAAAAATACAT-GAATG--ACATAAAATC
1586542 CCTAAG-TCATGAAAAATGAATAAAATGATATAAAAATACACTGAATGACATAAAACTC
1 CCT-AGTTCATGAAAAATGAATAAAATGATATAAAAATACA-TGAATGACATAAAA-TC
*
1586600 CCTAGTTCATGAAAAATGACTAAA
1 CCTAGTTCATGAAAAATGAATAAA
1586624 TTGACAAAAA
Statistics
Matches: 155, Mismatches: 27, Indels: 32
0.72 0.13 0.15
Matches are distributed among these distances:
56 3 0.02
57 13 0.08
58 122 0.79
59 14 0.09
60 2 0.01
61 1 0.01
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.25
Consensus pattern (56 bp):
CCTAGTTCATGAAAAATGAATAAAATGATATAAAAATACATGAATGACATAAAATC
Found at i:1587975 original size:11 final size:11
Alignment explanation
Indices: 1587957--1587993 Score: 60
Period size: 10 Copynumber: 3.5 Consensus size: 11
1587947 AAGCTATCAT
1587957 TCTTTTTTT-C
1 TCTTTTTTTGC
1587967 TCTTTTTTTGC
1 TCTTTTTTTGC
1587978 TCTTTTTTTGC
1 TCTTTTTTTGC
1587989 T-TTTT
1 TCTTTT
1587994 AAAATTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 13 0.50
11 13 0.50
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (11 bp):
TCTTTTTTTGC
Found at i:1589996 original size:20 final size:20
Alignment explanation
Indices: 1589968--1590042 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1589958 TCATACCCTG
1589968 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1589988 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1590008 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1590028 ATGTATCGATACATT
1 ATGTATCGATACATT
1590043 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1590035 original size:40 final size:39
Alignment explanation
Indices: 1589968--1590045 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1589958 TCATACCCTG
* *
1589968 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1590008 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1590046 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1594425 original size:19 final size:20
Alignment explanation
Indices: 1594401--1594444 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1594391 AAAGCCACCT
1594401 ATTTAT-AAAAT-AAAAAAA
1 ATTTATCAAAATCAAAAAAA
*
1594419 CATTTATCAAAATCAAATAAA
1 -ATTTATCAAAATCAAAAAAA
1594440 ATTTA
1 ATTTA
1594445 ATAGTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 10 0.45
21 6 0.27
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (20 bp):
ATTTATCAAAATCAAAAAAA
Found at i:1598485 original size:13 final size:13
Alignment explanation
Indices: 1598467--1598505 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1598457 ATTAACTTTT
*
1598467 CTATTATATAATG
1 CTATTATATAATA
*
1598480 CTATTATCTAATA
1 CTATTATATAATA
1598493 CTATTATATAATA
1 CTATTATATAATA
1598506 TTAGAATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (13 bp):
CTATTATATAATA
Found at i:1602706 original size:47 final size:46
Alignment explanation
Indices: 1602612--1602712 Score: 148
Period size: 47 Copynumber: 2.2 Consensus size: 46
1602602 ATTTTTAAAA
* * * *
1602612 TGATGCTTACTTTATCTTTTTGTTTTGATTAAATTATTGATCGAAT
1 TGATGCTTACTCTATCTTTTTATTTTGATTAAATTATAGATCAAAT
1602658 TGATGCTTACTCTATCTTCTTTATTTTGATTAAATTATAGATCAAAT
1 TGATGCTTACTCTATCTT-TTTATTTTGATTAAATTATAGATCAAAT
*
1602705 TGGTGCTT
1 TGATGCTT
1602713 TAAAAACCTA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 17 0.35
47 32 0.65
ACGTcount: A:0.25, C:0.11, G:0.13, T:0.51
Consensus pattern (46 bp):
TGATGCTTACTCTATCTTTTTATTTTGATTAAATTATAGATCAAAT
Found at i:1603704 original size:66 final size:64
Alignment explanation
Indices: 1603564--1603714 Score: 196
Period size: 66 Copynumber: 2.3 Consensus size: 64
1603554 ATTACTATGT
** * *
1603564 AAATACATCAAAACATACCAAATTACTAAATAAAAAGATGATATCAAATTTACTTCAAAGACAA
1 AAATACATCAAAAGGTACTAAATTACTAAATAAAAAAATGATATCAAATTTACTTCAAAGACAA
* * *
1603628 AAATACATCAAAAGGTACTAAATTACTACATAAAATAAAATGATATTAAATTTACTT-AGAAGAT
1 AAATACATCAAAAGGTACTAAATTACTAAAT-AAA-AAAATGATATCAAATTTACTTCA-AAGAC
1603692 AA
63 AA
*
1603694 AAATATATCAAAAGGTACTAA
1 AAATACATCAAAAGGTACTAA
1603715 GTTTACAACT
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
64 27 0.36
65 4 0.05
66 45 0.59
ACGTcount: A:0.56, C:0.12, G:0.07, T:0.26
Consensus pattern (64 bp):
AAATACATCAAAAGGTACTAAATTACTAAATAAAAAAATGATATCAAATTTACTTCAAAGACAA
Found at i:1604319 original size:16 final size:17
Alignment explanation
Indices: 1604295--1604331 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1604285 AAAGTATTAA
*
1604295 TTAATTAATTTATTTTT
1 TTAATTAATATATTTTT
1604312 TTAA-TAATATATTTTT
1 TTAATTAATATATTTTT
1604328 TTAA
1 TTAA
1604332 AAAAAATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTAATTAATATATTTTT
Found at i:1604922 original size:13 final size:13
Alignment explanation
Indices: 1604904--1604935 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1604894 TTTTACAATA
1604904 TATTAATAAAAAT
1 TATTAATAAAAAT
1604917 TATTAATAAAAAT
1 TATTAATAAAAAT
1604930 TATTAA
1 TATTAA
1604936 CAATTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TATTAATAAAAAT
Found at i:1606369 original size:24 final size:23
Alignment explanation
Indices: 1606342--1606400 Score: 55
Period size: 24 Copynumber: 2.4 Consensus size: 23
1606332 AAAAGATACC
*
1606342 AAATTTACTTGACAAAATTATCAA
1 AAATTTACTTG-CAAAATCATCAA
** *
1606366 AAATAAAATATGCAAAATCATCAA
1 AAATTTACT-TGCAAAATCATCAA
1606390 AAATTCTACTT
1 AAATT-TACTT
1606401 AGATATTGAA
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.31
Consensus pattern (23 bp):
AAATTTACTTGCAAAATCATCAA
Found at i:1606566 original size:12 final size:13
Alignment explanation
Indices: 1606541--1606571 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
1606531 TTTTATTAAA
1606541 AATAAAATTTTTT
1 AATAAAATTTTTT
1606554 AATAAAA-TTTTT
1 AATAAAATTTTTT
1606566 AATAAA
1 AATAAA
1606572 TTGATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATAAAATTTTTT
Found at i:1612302 original size:138 final size:138
Alignment explanation
Indices: 1612054--1612331 Score: 538
Period size: 138 Copynumber: 2.0 Consensus size: 138
1612044 AAACTGACAC
1612054 CTTGTGCTGACACAATTTCTCATTCATCTGCAATCAACAACCAAGAAACAAAGGTTGTTCAGTCT
1 CTTGTGCTGACACAATTTCTCATTCATCTGCAATCAACAACCAAGAAACAAAGGTTGTTCAGTCT
*
1612119 GAGGGAAGACCAAGTACTTTATCAGGATCAACCAGCAATCTAGCTCGTAAAGGTGTAGAAAATGC
66 GAGGGAAGACCAAGTACTTTATCAAGATCAACCAGCAATCTAGCTCGTAAAGGTGTAGAAAATGC
1612184 AGTTACTT
131 AGTTACTT
*
1612192 CTTGTGCTGACACAATTTCTCATTCATCTGCAATCAACAGCCAAGAAACAAAGGTTGTTCAGTCT
1 CTTGTGCTGACACAATTTCTCATTCATCTGCAATCAACAACCAAGAAACAAAGGTTGTTCAGTCT
1612257 GAGGGAAGACCAAGTACTTTATCAAGATCAACCAGCAATCTAGCTCGTAAAGGTGTAGAAAATGC
66 GAGGGAAGACCAAGTACTTTATCAAGATCAACCAGCAATCTAGCTCGTAAAGGTGTAGAAAATGC
1612322 AGTTACTT
131 AGTTACTT
1612330 CT
1 CT
1612332 GGTATGATGT
Statistics
Matches: 138, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 138 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (138 bp):
CTTGTGCTGACACAATTTCTCATTCATCTGCAATCAACAACCAAGAAACAAAGGTTGTTCAGTCT
GAGGGAAGACCAAGTACTTTATCAAGATCAACCAGCAATCTAGCTCGTAAAGGTGTAGAAAATGC
AGTTACTT
Found at i:1613566 original size:18 final size:18
Alignment explanation
Indices: 1613543--1613580 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1613533 TCCCTGTTCA
1613543 CTCCCCCTCCCCCTTTTT
1 CTCCCCCTCCCCCTTTTT
*
1613561 CTCCCCCTCCCTCTTTTT
1 CTCCCCCTCCCCCTTTTT
1613579 CT
1 CT
1613581 TTTTTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (18 bp):
CTCCCCCTCCCCCTTTTT
Found at i:1618996 original size:14 final size:15
Alignment explanation
Indices: 1618972--1619013 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
1618962 TAAAATGGTT
1618972 TGAGCTTAAAAAAAA
1 TGAGCTTAAAAAAAA
1618987 TGAG-TTAAAAAAAA
1 TGAGCTTAAAAAAAA
*
1619001 TTGAACTTAAAAA
1 -TGAGCTTAAAAA
1619014 TACTCAATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 10 0.42
15 7 0.29
16 7 0.29
ACGTcount: A:0.60, C:0.05, G:0.12, T:0.24
Consensus pattern (15 bp):
TGAGCTTAAAAAAAA
Found at i:1620958 original size:11 final size:11
Alignment explanation
Indices: 1620942--1620983 Score: 59
Period size: 12 Copynumber: 3.8 Consensus size: 11
1620932 ATTGTAATTA
1620942 AATATATTTTT
1 AATATATTTTT
1620953 AATATATTTTTT
1 AATATA-TTTTT
*
1620965 AATATATTATT
1 AATATATTTTT
1620976 -ATATATTT
1 AATATATTT
1620984 AAAATCTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 7 0.25
11 10 0.36
12 11 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
AATATATTTTT
Found at i:1621503 original size:12 final size:11
Alignment explanation
Indices: 1621472--1621506 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1621462 ATAATAAACT
1621472 ATTTTTAAATA
1 ATTTTTAAATA
*
1621483 AGTTTTAAATA
1 ATTTTTAAATA
1621494 ATTTTATAAATA
1 ATTTT-TAAATA
1621506 A
1 A
1621507 ATTATAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (11 bp):
ATTTTTAAATA
Found at i:1621511 original size:11 final size:11
Alignment explanation
Indices: 1621477--1621543 Score: 55
Period size: 11 Copynumber: 6.0 Consensus size: 11
1621467 AAACTATTTT
* *
1621477 TAAATAAGTTT
1 TAAATAAATTA
*
1621488 TAAATAATTTTA
1 TAAATAA-ATTA
1621500 TAAATAAATTA
1 TAAATAAATTA
*
1621511 TAAACAAATTTA
1 TAAATAAA-TTA
**
1621523 TTTATAAA-TA
1 TAAATAAATTA
1621533 TAAATAAATTA
1 TAAATAAATTA
1621544 AATCACTTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
10 8 0.18
11 19 0.43
12 17 0.39
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (11 bp):
TAAATAAATTA
Found at i:1621514 original size:23 final size:23
Alignment explanation
Indices: 1621472--1621539 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
1621462 ATAATAAACT
* *
1621472 ATTTT-TAAATAAGTTTTAAATA
1 ATTTTATAAATAAATTATAAATA
*
1621494 ATTTTATAAATAAATTATAAACA
1 ATTTTATAAATAAATTATAAATA
* **
1621517 AATTTATTTATAAA-TATAAATA
1 ATTTTATAAATAAATTATAAATA
1621539 A
1 A
1621540 ATTAAATCAC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 13 0.34
23 25 0.66
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (23 bp):
ATTTTATAAATAAATTATAAATA
Found at i:1626274 original size:5 final size:5
Alignment explanation
Indices: 1626241--1626324 Score: 59
Period size: 5 Copynumber: 17.0 Consensus size: 5
1626231 CGTGTATTAA
* * *
1626241 ATATA ATATT A-ATT ATATT -TAAAT ATATT ATATT TTATT -TATT ATATT
1 ATATT ATATT ATATT ATATT AT-ATT ATATT ATATT ATATT ATATT ATATT
* * *
1626289 ATTTTT TTATT -TATT AAATT ATATTT ATATT ATATT
1 A-TATT ATATT ATATT ATATT ATA-TT ATATT ATATT
1626325 TTTAAATCGT
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
4 13 0.21
5 41 0.65
6 9 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATATT
Found at i:1626281 original size:20 final size:19
Alignment explanation
Indices: 1626246--1626324 Score: 79
Period size: 20 Copynumber: 4.0 Consensus size: 19
1626236 ATTAAATATA
* *
1626246 ATATTA-ATTATATTTAAAT
1 ATATTATATTTTATTT-ATT
1626265 ATATTATATTTTATTTATT
1 ATATTATATTTTATTTATT
*
1626284 ATATTATTTTTTTATTTATT
1 ATATTA-TATTTTATTTATT
*
1626304 AAATTATATTTATATTATATT
1 ATATTATATTT-TATT-TATT
1626325 TTTAAATCGT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
19 18 0.35
20 29 0.57
21 4 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATATTATATTTTATTTATT
Found at i:1628584 original size:2 final size:2
Alignment explanation
Indices: 1628577--1628618 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1628567 TCATTATTAA
1628577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1628619 TTGTGAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1630082 original size:14 final size:15
Alignment explanation
Indices: 1630058--1630089 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1630048 CATGTTTCTC
1630058 TTAATTTTATTAAAT
1 TTAATTTTATTAAAT
1630073 TTAA-TTTATTAAAT
1 TTAATTTTATTAAAT
1630087 TTA
1 TTA
1630090 TTATAATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTAATTTTATTAAAT
Found at i:1630112 original size:21 final size:20
Alignment explanation
Indices: 1630074--1630150 Score: 81
Period size: 21 Copynumber: 4.0 Consensus size: 20
1630064 TTATTAAATT
*
1630074 TAATTTATTAA-ATTTATTA
1 TAATGTATTAATATTTATTA
*
1630093 TAATGATATTAATTTTTATT-
1 TAATG-TATTAATATTTATTA
*
1630113 T-A-GGATTAATATTTATTA
1 TAATGTATTAATATTTATTA
1630131 TAATGTTATTAATATTTATT
1 TAATG-TATTAATATTTATT
1630151 TATATTATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
17 12 0.26
18 2 0.04
19 6 0.13
20 8 0.17
21 19 0.40
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
TAATGTATTAATATTTATTA
Found at i:1630114 original size:34 final size:35
Alignment explanation
Indices: 1630065--1630153 Score: 108
Period size: 38 Copynumber: 2.5 Consensus size: 35
1630055 CTCTTAATTT
* *
1630065 TATTAAATTTAATTTATTAA-ATTTATTATAATGA
1 TATTAATTTTTATTTATTAATATTTATTATAATGA
*
1630099 TATTAATTTTTATTTAGGATTAATATTTATTATAATGT
1 TATTAATTTTTATTT---ATTAATATTTATTATAATGA
*
1630137 TATTAATATTTATTTAT
1 TATTAATTTTTATTTAT
1630154 ATTATTATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
34 13 0.28
35 2 0.04
37 5 0.11
38 27 0.57
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (35 bp):
TATTAATTTTTATTTATTAATATTTATTATAATGA
Found at i:1630133 original size:38 final size:37
Alignment explanation
Indices: 1630080--1630152 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 37
1630070 AATTTAATTT
*
1630080 ATTAAATTTATTATAATGATATTAATTTTTATTTAGG
1 ATTAAATTTATTATAATGATATTAATATTTATTTAGG
*
1630117 ATTAATATTTATTATAATGTTATTAATATTTATTTA
1 ATTAA-ATTTATTATAATGATATTAATATTTATTTA
1630153 TATTATTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 5 0.15
38 28 0.85
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (37 bp):
ATTAAATTTATTATAATGATATTAATATTTATTTAGG
Found at i:1630234 original size:21 final size:21
Alignment explanation
Indices: 1630205--1630254 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1630195 GACTACTGCT
*
1630205 ATTTTTTATTTATG-TTATTAA
1 ATTTATTA-TTATGTTTATTAA
*
1630226 ATTTATTATTATGTTTTTTAA
1 ATTTATTATTATGTTTATTAA
*
1630247 ATTAATTA
1 ATTTATTA
1630255 AAAATTAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (21 bp):
ATTTATTATTATGTTTATTAA
Found at i:1630289 original size:19 final size:20
Alignment explanation
Indices: 1630247--1630289 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1630237 TGTTTTTTAA
*
1630247 ATTAATTAAAAATTAGGATT
1 ATTAATTAAAAATTAGGATC
1630267 ATTAA-TAAAAGATTA-GATC
1 ATTAATTAAAA-ATTAGGATC
1630286 ATTA
1 ATTA
1630290 TATATAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.37
Consensus pattern (20 bp):
ATTAATTAAAAATTAGGATC
Found at i:1632509 original size:2 final size:2
Alignment explanation
Indices: 1632502--1632531 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1632492 AAACAAATAC
1632502 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1632532 AAGAAAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1633534 original size:2 final size:2
Alignment explanation
Indices: 1633527--1633558 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1633517 ACCCCAAGTT
1633527 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1633559 ATTTTAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1634036 original size:18 final size:18
Alignment explanation
Indices: 1634013--1634048 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1634003 TTAATTATAA
1634013 AATAATATATATTAATAT
1 AATAATATATATTAATAT
* *
1634031 AATAATATTTTTTAATAT
1 AATAATATATATTAATAT
1634049 TTTATTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATAATATATATTAATAT
Found at i:1634359 original size:2 final size:2
Alignment explanation
Indices: 1634352--1634388 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1634342 TGAATGATCG
1634352 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1634389 CTGTGTTGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1635715 original size:68 final size:67
Alignment explanation
Indices: 1635631--1635798 Score: 157
Period size: 58 Copynumber: 2.6 Consensus size: 67
1635621 TAAGAACAAA
1635631 TAAA-AAAAAAG-AACAAAATTGAGTGATTATGAAATAATTTTATAATCACTATTAAATTCAATT
1 TAAATAAAAAAGAAACAAAATTGAGTGATTATGAAATAATTTT-TAA-CACTATTAAATTCAATT
1635694 AGAG
64 AGAG
* * * *
1635698 T-ATTAAAAAAGAAAC-AAA-T-A-TAAATTAT----T--TTTGTTTAGACTATTAAATTCAATT
1 TAAATAAAAAAGAAACAAAATTGAGT-GATTATGAAATAATTT-TTAACACTATTAAATTCAATT
1635752 AGAG
64 AGAG
1635756 TAAATAAAAAA-AGAACAAAATTGAGTGATTATGAAATAATTTT
1 TAAATAAAAAAGA-AACAAAATTGAGTGATTATGAAATAATTTT
1635799 CTTATTTCAA
Statistics
Matches: 79, Mismatches: 6, Indels: 32
0.68 0.05 0.27
Matches are distributed among these distances:
58 22 0.28
59 16 0.20
60 4 0.05
61 2 0.03
62 6 0.08
63 1 0.01
64 1 0.01
65 6 0.08
66 3 0.04
67 12 0.15
68 6 0.08
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.33
Consensus pattern (67 bp):
TAAATAAAAAAGAAACAAAATTGAGTGATTATGAAATAATTTTTAACACTATTAAATTCAATTAG
AG
Found at i:1636307 original size:15 final size:15
Alignment explanation
Indices: 1636284--1636315 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1636274 GTAGATTCAC
*
1636284 ATCTTATAAAATCTT
1 ATCTCATAAAATCTT
1636299 ATCTCATAAAATCTT
1 ATCTCATAAAATCTT
1636314 AT
1 AT
1636316 ATCTTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.44
Consensus pattern (15 bp):
ATCTCATAAAATCTT
Found at i:1636324 original size:17 final size:17
Alignment explanation
Indices: 1636284--1636333 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
1636274 GTAGATTCAC
1636284 ATCTTATAAAATC-T-T
1 ATCTTATAAAATCTTAT
*
1636299 ATCTCATAAAATCTTAT
1 ATCTTATAAAATCTTAT
*
1636316 ATCTTATAAAATTTTAT
1 ATCTTATAAAATCTTAT
1636333 A
1 A
1636334 AAATAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 17 0.57
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (17 bp):
ATCTTATAAAATCTTAT
Found at i:1636749 original size:2 final size:2
Alignment explanation
Indices: 1636706--1636730 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1636696 TTAAACTATC
1636706 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1636731 AATTTTAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1637936 original size:2 final size:2
Alignment explanation
Indices: 1637923--1637961 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1637913 ATAACTTTAA
*
1637923 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1637962 AAAGTTAGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1639183 original size:4 final size:4
Alignment explanation
Indices: 1639174--1639200 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1639164 GTTTGTAATG
1639174 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1639201 GAGATTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1639575 original size:8 final size:8
Alignment explanation
Indices: 1639559--1639591 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
1639549 CACTTATTTC
1639559 AAAAA-AT
1 AAAAATAT
1639566 AAAAATAT
1 AAAAATAT
1639574 AAAAATAT
1 AAAAATAT
1639582 AAAAATAT
1 AAAAATAT
1639590 AA
1 AA
1639592 TTCTTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.20
8 20 0.80
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAATAT
Found at i:1639901 original size:15 final size:15
Alignment explanation
Indices: 1639864--1639910 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1639854 TTGGGGAAAT
* *
1639864 TATTTTT-ATTTTTA
1 TATTTTTAAATTTAA
*
1639878 TATTATTAAATTTAA
1 TATTTTTAAATTTAA
1639893 TATTTTTAAATTATAA
1 TATTTTTAAATT-TAA
1639909 TA
1 TA
1639911 AATAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 6 0.22
15 16 0.59
16 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTTTTAAATTTAA
Found at i:1639940 original size:23 final size:24
Alignment explanation
Indices: 1639895--1639943 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1639885 AAATTTAATA
*
1639895 TTTTTAAATTATAATAAATAAAAT
1 TTTTTAAATAATAATAAATAAAAT
* *
1639919 TTTTTTAATAATATTAAA-AAAAT
1 TTTTTAAATAATAATAAATAAAAT
1639942 TT
1 TT
1639944 AAATTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTTTTAAATAATAATAAATAAAAT
Found at i:1645905 original size:2 final size:2
Alignment explanation
Indices: 1645900--1645929 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1645890 ATCTCTCTTC
*
1645900 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1645930 AACAATACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1646415 original size:2 final size:2
Alignment explanation
Indices: 1646408--1646457 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
1646398 AACCCAACTC
1646408 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1646449 AT AT TT AT A
1 AT AT AT AT A
1646458 AATAATATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1646645 original size:10 final size:11
Alignment explanation
Indices: 1646625--1646661 Score: 58
Period size: 10 Copynumber: 3.4 Consensus size: 11
1646615 TTTAATTTAA
1646625 TAAATTTAAAT
1 TAAATTTAAAT
1646636 TAAA-TTAAAT
1 TAAATTTAAAT
1646646 TAAATTTAAAT
1 TAAATTTAAAT
1646657 ATAAA
1 -TAAA
1646662 ATTTGATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.42
11 10 0.42
12 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAT
Found at i:1647484 original size:26 final size:26
Alignment explanation
Indices: 1647455--1647511 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
1647445 AGAATATATC
*
1647455 AATATAGATATAAAAATAAATTTTTT
1 AATATAAATATAAAAATAAATTTTTT
*
1647481 AATATAAATATAAAAATAATTTTTTT
1 AATATAAATATAAAAATAAATTTTTT
1647507 AATAT
1 AATAT
1647512 TTTAATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
AATATAAATATAAAAATAAATTTTTT
Found at i:1651976 original size:13 final size:14
Alignment explanation
Indices: 1651941--1652009 Score: 54
Period size: 13 Copynumber: 4.9 Consensus size: 14
1651931 TTAAAAAATC
*
1651941 TTTAA-TAAGTAGA
1 TTTAATTAATTAGA
1651954 TTTAATTAATTAGA
1 TTTAATTAATTAGA
*
1651968 -TTAATTAATT-GT
1 TTTAATTAATTAGA
*
1651980 TTATAGATACCAATTAGA
1 TT-TA-AT--TAATTAGA
1651998 TTTAATTAATTA
1 TTTAATTAATTA
1652010 TTATATAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
12 1 0.02
13 16 0.36
14 14 0.32
15 2 0.05
16 2 0.05
17 6 0.14
18 3 0.07
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (14 bp):
TTTAATTAATTAGA
Found at i:1652222 original size:24 final size:24
Alignment explanation
Indices: 1652166--1652229 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
1652156 TTCAATCTTC
*
1652166 TTTAAATTTATT-TATTTATTTATT
1 TTTAATTTTATTCT-TTTATTTATT
** *
1652190 TTTCCTTTTATTCTTTTATTTTTT
1 TTTAATTTTATTCTTTTATTTATT
1652214 TTTAATTTTATGTCTT
1 TTTAATTTTAT-TCTT
1652230 CCTACTGTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
24 27 0.84
25 5 0.16
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTAATTTTATTCTTTTATTTATT
Found at i:1652582 original size:66 final size:62
Alignment explanation
Indices: 1652474--1652598 Score: 164
Period size: 66 Copynumber: 2.0 Consensus size: 62
1652464 TTATATATTA
*
1652474 AATATATAAAAATAATTAAAATAATTAATTTTATTATTTATAAAATTAAAA-ATTTTATAGTT
1 AATATATAAAAATAATTAAAATAATTAAATTTATTATTTAT-AAATTAAAACATTTTATAGTT
*
1652536 AATATATTAAAAATAAACTTATAAACT-ATTAAATTTATTATTTATAAGTTAAAACATTTTATA
1 AATATA-TAAAAAT-AA-TTA-AAA-TAATTAAATTTATTATTTATAAATTAAAACATTTTATA
1652599 ATAGATTTTA
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
62 6 0.11
63 7 0.13
64 2 0.04
65 11 0.20
66 28 0.51
67 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (62 bp):
AATATATAAAAATAATTAAAATAATTAAATTTATTATTTATAAATTAAAACATTTTATAGTT
Found at i:1652768 original size:4 final size:4
Alignment explanation
Indices: 1652759--1652784 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1652749 ATAAAATAAC
1652759 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
1652785 CCAAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Done.