Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1
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: 8764944
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 632878 characters in sequence are not A, C, G, or T
File 8 of 52
Found at i:1288067 original size:13 final size:13
Alignment explanation
Indices: 1288049--1288073 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1288039 ATTACTCAAA
1288049 TGTATCGATACAT
1 TGTATCGATACAT
1288062 TGTATCGATACA
1 TGTATCGATACA
1288074 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1292283 original size:21 final size:21
Alignment explanation
Indices: 1292223--1292284 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
1292213 TGGACATGTT
*
1292223 AAAATGCATGGTACATAGCTC
1 AAAATGCATGGTACATGGCTC
1292244 AAAATGCATGGTACATGGCTC
1 AAAATGCATGGTACATGGCTC
1292265 AAAATGCATGG-ACATTGGCT
1 AAAATGCATGGTACA-TGGCT
1292285 GTTTAGATGA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 3 0.08
21 36 0.92
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (21 bp):
AAAATGCATGGTACATGGCTC
Found at i:1293179 original size:20 final size:20
Alignment explanation
Indices: 1293154--1293224 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
1293144 AATGAACTAT
*
1293154 ATGTATCGATATATTGAAAA
1 ATGTATCGATACATTGAAAA
* * * *
1293174 ATGTATTGATACATTCATAC
1 ATGTATCGATACATTGAAAA
*
1293194 ATGTATTGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
*
1293214 ATCTATCGATA
1 ATGTATCGATA
1293225 TATCTGGGTA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:1297704 original size:19 final size:20
Alignment explanation
Indices: 1297660--1297712 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
1297650 TGCCAGTTTA
* **
1297660 ATGTATTAATACAATTGAGT
1 ATGTATCAATACAATTGAAC
1297680 ATGTATCAATACAA-TGAAC
1 ATGTATCAATACAATTGAAC
*
1297699 ATGTATCGATACAA
1 ATGTATCAATACAA
1297713 AGCATTATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.32
Consensus pattern (20 bp):
ATGTATCAATACAATTGAAC
Found at i:1298293 original size:21 final size:21
Alignment explanation
Indices: 1298253--1298293 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1298243 TCGAAGGATA
*
1298253 TTTCTCCCCCTTAATTAAATT
1 TTTCTCCCCCTTAATAAAATT
* *
1298274 TTTCTCTCCCTTGATAAAAT
1 TTTCTCCCCCTTAATAAAAT
1298294 AATTAAAGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.02, T:0.46
Consensus pattern (21 bp):
TTTCTCCCCCTTAATAAAATT
Found at i:1300119 original size:6 final size:6
Alignment explanation
Indices: 1300108--1300141 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
1300098 CAAATTCATC
1300108 AACAAA AACAAA AA-AAA AATCAAA AACAAA AACA
1 AACAAA AACAAA AACAAA AA-CAAA AACAAA AACA
1300142 CAAGATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 16 0.62
7 5 0.19
ACGTcount: A:0.82, C:0.15, G:0.00, T:0.03
Consensus pattern (6 bp):
AACAAA
Found at i:1306187 original size:19 final size:20
Alignment explanation
Indices: 1306144--1306195 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
1306134 GCTAGTTTCT
**
1306144 TGTATCGATACAATTGAGTA
1 TGTATCGATACAATTGAACA
1306164 TGTATCGATACAA-TGAACA
1 TGTATCGATACAATTGAACA
1306183 TGTATCGATACAA
1 TGTATCGATACAA
1306196 ACCATTATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.31
Consensus pattern (20 bp):
TGTATCGATACAATTGAACA
Found at i:1306444 original size:20 final size:21
Alignment explanation
Indices: 1306407--1306445 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1306397 TTAAAAGAAT
1306407 AAAACTTGTTTACGGTTTTTC
1 AAAACTTGTTTACGGTTTTTC
*
1306428 AAAACTT-TTTTCGGTTTT
1 AAAACTTGTTTACGGTTTT
1306446 ATCCATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (21 bp):
AAAACTTGTTTACGGTTTTTC
Found at i:1314459 original size:20 final size:20
Alignment explanation
Indices: 1314434--1314487 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1314424 TAGCTTGAAT
1314434 TGTATCGATACAAAAAAATA
1 TGTATCGATACAAAAAAATA
* ***
1314454 TGTATCGATACAACACTTTA
1 TGTATCGATACAAAAAAATA
1314474 TGTATCGATACAAA
1 TGTATCGATACAAA
1314488 TCGTTGAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (20 bp):
TGTATCGATACAAAAAAATA
Found at i:1315498 original size:49 final size:48
Alignment explanation
Indices: 1315334--1315709 Score: 349
Period size: 49 Copynumber: 7.8 Consensus size: 48
1315324 AAAAGGATGT
* * * * * *
1315334 CAATGTGCTGATTTAAGGTCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGA---AGAA-GTGC
1315386 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-AAG--GTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGTGC
* *
1315429 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAG-TGC
* * *
1315478 CAATATGTTGATTCAAGGCCAGCGATATTGGACTTGAAGAAGAAGTTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAG-TGC
* *
1315527 CAATATGCGGATTCAAGGCCAGCGATATTGGACTT---GAAG--GTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGTGC
* * * *
1315570 CAATGTGCTGATTCAAGGCCAGCTACATTGGACATAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAA-GTGC
* * *
1315619 CAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAGAGAAAGGATGT
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-GA-AG-AA-G-TGC
* * *
1315674 CAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
1315710 GAAGGGTTGC
Statistics
Matches: 277, Mismatches: 29, Indels: 34
0.81 0.09 0.10
Matches are distributed among these distances:
43 70 0.25
44 1 0.00
45 1 0.00
46 11 0.04
48 1 0.00
49 115 0.42
50 3 0.01
51 1 0.00
52 32 0.12
53 1 0.00
54 5 0.02
55 36 0.13
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (48 bp):
CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGTGC
Found at i:1315509 original size:92 final size:93
Alignment explanation
Indices: 1315325--1315714 Score: 328
Period size: 92 Copynumber: 4.1 Consensus size: 93
1315315 AAGATGAGAA
* * * * * * *
1315325 AAAGGATGTCAATGTGCTGATTTAAGGTCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA--GAGAA-GTGCCAAT
*
1315390 ATGCTGATTCAAGGCCAGCTATATTGGACTT
63 ATGCTGATTCAAGGCCAGCGATATTGGACTT
* *
1315421 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGTTGCCAATAT
1 AAAGGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAGAGAAG-TGCCAATAT
*
1315484 GTTGATTCAAGGCCAGCGATATTGGACTT
65 GCTGATTCAAGGCCAGCGATATTGGACTT
* * *
1315513 GAAGAAGAAGTTGCCAATATGCGGATTCAAGGCCAGCGATATTGGACTT---GA-AG--GTGCCA
1 --A-AAG--GATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAGAGAAGTGCCA
* * * *
1315572 ATGTGCTGATTCAAGGCCAGCTACATTGGACAT
61 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
* *
1315605 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAGAGAAAGG
1 AAAG--G-A--TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AA-A-GAGAG-AA-G
* * *
1315670 ATGTCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT
56 -TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1315709 AGAAGG
1 A-AAGG
1315715 GTTGCCACTG
Statistics
Matches: 246, Mismatches: 25, Indels: 39
0.79 0.08 0.13
Matches are distributed among these distances:
89 5 0.02
90 1 0.00
91 1 0.00
92 108 0.44
93 1 0.00
94 1 0.00
95 46 0.19
96 5 0.02
97 1 0.00
98 36 0.15
99 2 0.01
103 2 0.01
104 34 0.14
105 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (93 bp):
AAAGGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAGAGAAGTGCCAATATG
CTGATTCAAGGCCAGCGATATTGGACTT
Found at i:1315637 original size:141 final size:145
Alignment explanation
Indices: 1315334--1315714 Score: 497
Period size: 141 Copynumber: 2.6 Consensus size: 145
1315324 AAAAGGATGT
* * * * * *
1315334 CAATGTGCTGATTTAAGGTCAGCTACATTGAACTTA-AAGATG-GAAAAGG-TGCCAATATGCTG
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAAGA-GAG-AAAGGATGCCAATATGCTG
* *
1315396 ATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
64 ATTCAAGGCCAGCGATATTGGACTTGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
* *
1315461 CTTAAAGAAGAAGTTGC
129 CATAAAGAAGAAGGTGC
* * *
1315478 CAATATGTTGATTCAAGGCCAGCGATATTGGACTT-GAAGA-AG-AA-GTTGCCAATATGCGGAT
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAAGAGAGAAAGGATGCCAATATGCTGAT
1315539 TCAAGGCCAGCGATATTGGACTTGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACA
66 TCAAGGCCAGCGATATTGGACTTGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACA
*
1315604 TAAAGATGAAGGTGC
131 TAAAGAAGAAGGTGC
* * * *
1315619 CAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAGAGAAAGGATGTCAATGTGCTG
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT--AGAAGAGAGAAAGGATGCCAATATGCTG
*
1315684 ATTCAAGGCCAGCGATATTGGGCTTAGAAGG
64 ATTCAAGGCCAGCGATATTGGACTT-GAAGG
1315715 GTTGCCACTG
Statistics
Matches: 206, Mismatches: 21, Indels: 16
0.85 0.09 0.07
Matches are distributed among these distances:
140 1 0.00
141 124 0.60
143 1 0.00
144 36 0.17
145 2 0.01
146 2 0.01
147 35 0.17
148 5 0.02
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (145 bp):
CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAAGAGAGAAAGGATGCCAATATGCTGAT
TCAAGGCCAGCGATATTGGACTTGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACA
TAAAGAAGAAGGTGC
Found at i:1315708 original size:55 final size:49
Alignment explanation
Indices: 1315276--1315709 Score: 334
Period size: 49 Copynumber: 8.8 Consensus size: 49
1315266 GTGATAAAGA
* * * * *
1315276 TGCCAATATGTTGATTCACGGCCAACGATATCGGGCTTAAAGATGAGAAAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGAT--G---AAGG
* * * * * **
1315330 ATGTCAATGTGCTGATTTAAGGTCAGCTACATTGAACTTAAAGATGGAAAAGG
1 -TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGAT-G--AAGG
* * *
1315383 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAAGG
* * * * *
1315426 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGT
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAAGG
* * * * * *
1315475 TGCCAATATGTTGATTCAAGGCCAGCGATATTGGACTTGAAGAAGAAGT
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAAGG
* * *
1315524 TGCCAATATGCGGATTCAAGGCCAGCGATATTGGAC-T-----TGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAAGG
* * * *
1315567 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACATAAAGATGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAAGG
*
1315616 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAGAGAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGAT----G-AAGG
*
1315670 ATGTCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTA
1 -TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTA
1315710 GAAGGGTTGC
Statistics
Matches: 319, Mismatches: 42, Indels: 36
0.80 0.11 0.09
Matches are distributed among these distances:
43 76 0.24
44 1 0.00
47 1 0.00
48 2 0.01
49 126 0.39
52 32 0.10
53 7 0.02
54 5 0.02
55 69 0.22
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.25
Consensus pattern (49 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATGAAGG
Found at i:1315750 original size:32 final size:31
Alignment explanation
Indices: 1315702--1315795 Score: 120
Period size: 32 Copynumber: 3.0 Consensus size: 31
1315692 CCAGCGATAT
1315702 TGGGC-TTAGAAGGGTTGCCACTGACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACTGACTTGTG
*
1315732 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGA-AGGGTTGCCACTGACTTGTG
* *
1315764 TGGGCTTTTGAAAAGGG-TGCCACTAACTTGTG
1 TGGGC-TTT-AGAAGGGTTGCCACTGACTTGTG
1315796 GGCTTAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
30 5 0.09
31 5 0.09
32 37 0.66
33 7 0.12
34 2 0.04
ACGTcount: A:0.18, C:0.17, G:0.35, T:0.30
Consensus pattern (31 bp):
TGGGCTTTAGAAGGGTTGCCACTGACTTGTG
Found at i:1315861 original size:35 final size:34
Alignment explanation
Indices: 1315774--1315864 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 34
1315764 TGGGCTTTTG
* * *
1315774 AAAAGGGTGCCACTA-ACTTGTGGGCTTAAAAAGA
1 AAAAGAGTGCCAC-AGAGTTGTGAGCTTAAAAAGA
* *
1315808 AAAAGAGTGCTATAGAGTTGTGAGCTTACAAAAGA
1 AAAAGAGTGCCACAGAGTTGTGAGCTTA-AAAAGA
*
1315843 AAAAGAGTGCCACGGAGTTGTG
1 AAAAGAGTGCCACAGAGTTGTG
1315865 GACTTTGGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
33 1 0.02
34 21 0.45
35 25 0.53
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (34 bp):
AAAAGAGTGCCACAGAGTTGTGAGCTTAAAAAGA
Found at i:1315892 original size:29 final size:29
Alignment explanation
Indices: 1315841--1316130 Score: 309
Period size: 30 Copynumber: 10.0 Consensus size: 29
1315831 GCTTACAAAA
* * *
1315841 GAAAAAGAGTGCCACGGAGTTGTGGACTTT
1 GAAAAAGA-TGCCACTGACTTGTGGGCTTT
* * *
1315871 GGAAAAGATGCCACCGACTTGTGGGCTTCG
1 GAAAAAGATGCCACTGACTTGTGGGCTT-T
* * *
1315901 GAAAAGGGTGCCACTGATTTGTGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
* *
1315930 G--AAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAAGATGCCACTGACTTGTGGGC-TTT
*
1315958 GAAAAAAATGCCACTGACTTGTGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
*
1315987 GAAAAAGATGCCACTAACTTGTGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
* * *
1316016 -TAAAGGTTGCCACTGACTTGTGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
*
1316044 GAAAAAAGATGCCACTAACTTGTGGGCTTT
1 G-AAAAAGATGCCACTGACTTGTGGGCTTT
* * * *
1316074 -TAAAGGTTGCCACTAACTTGTGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
* *
1316102 GAAAAATATGCCACTGACTTGTGGACTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
1316131 TGAAGGGTGA
Statistics
Matches: 218, Mismatches: 35, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
27 21 0.10
28 53 0.24
29 70 0.32
30 74 0.34
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (29 bp):
GAAAAAGATGCCACTGACTTGTGGGCTTT
Found at i:1315962 original size:57 final size:58
Alignment explanation
Indices: 1315843--1316134 Score: 324
Period size: 57 Copynumber: 5.0 Consensus size: 58
1315833 TTACAAAAGA
* * * * * **
1315843 AAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGG
1 AAAAGGGTGCCACTGACTTGTGGGCTTT-GAAAAGATGCCACTGACTTGTGGGCTTTTG
* * *
1315902 AAAAGGGTGCCACTGATTTGTGGGCTTTG-AAGGTTGCCACTGACTTGTGGGCTTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTTG
*** *
1315959 AAAAAAATGCCACTGACTTGTGGGCTTTGAAAAAGATGCCACTAACTTGTGGGCTTTT-
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAAGATGCCACTGACTTGTGGGCTTTTG
* *
1316017 -AAAGGTTGCCACTGACTTGTGGGCTTTGAAAAAAGATGCCACTAACTTGTGGGCTTTT-
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG--AAAAGATGCCACTGACTTGTGGGCTTTTG
* * * *
1316075 -AAAGGTTGCCACTAACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGACTTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAAGATGCCACTGACTTGTGGGCTTTTG
1316133 AA
1 AA
1316135 GGGTGAGGAA
Statistics
Matches: 205, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
57 99 0.48
58 57 0.28
59 49 0.24
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (58 bp):
AAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTTG
Found at i:1316024 original size:87 final size:86
Alignment explanation
Indices: 1315850--1316130 Score: 341
Period size: 87 Copynumber: 3.2 Consensus size: 86
1315840 AGAAAAAGAG
* * * * * * *
1315850 TGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCAC
1 TGCCACTGACTTGTGGACTTTGAAAAAAATGCCACTGACTTGTGGGCTT-TGAAAAGGATGCCAC
* * *
1315915 TGATTTGTGGGC-TTTGAAGGT
65 TAACTTGTGGGCTTTTAAAGGT
* *
1315936 TGCCACTGACTTGTGGGCTTTTGAAAAAAATGCCACTGACTTGTGGGCTTTGAAAAAGATGCCAC
1 TGCCACTGACTTGTGGAC-TTTGAAAAAAATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCAC
1316001 TAACTTGTGGGCTTTTAAAGGT
65 TAACTTGTGGGCTTTTAAAGGT
* * * *
1316023 TGCCACTGACTTGTGGGCTTTGAAAAAAGATGCCACTAACTTGTGGGCTTT-TAAAGGTTGCCAC
1 TGCCACTGACTTGTGGACTTTGAAAAAA-ATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCAC
* **
1316087 TAACTTGTGGGCTTTGAAAAAT
65 TAACTTGTGGGCTTTTAAAGGT
1316109 ATGCCACTGACTTGTGGACTTT
1 -TGCCACTGACTTGTGGACTTT
1316131 TGAAGGGTGA
Statistics
Matches: 171, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
86 76 0.44
87 95 0.56
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (86 bp):
TGCCACTGACTTGTGGACTTTGAAAAAAATGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACT
AACTTGTGGGCTTTTAAAGGT
Found at i:1320335 original size:7 final size:7
Alignment explanation
Indices: 1320319--1320357 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
1320309 CATCTGAGAT
1320319 AAAAATA
1 AAAAATA
*
1320326 AAAAACA
1 AAAAATA
1320333 AAAAAT-
1 AAAAATA
1320339 AAAAATA
1 AAAAATA
1320346 AAAAATA
1 AAAAATA
1320353 AAAAA
1 AAAAA
1320358 ATGGATGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (7 bp):
AAAAATA
Found at i:1320340 original size:20 final size:20
Alignment explanation
Indices: 1320317--1320357 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1320307 GGCATCTGAG
1320317 ATAAAAATAAAAAACAAAAA
1 ATAAAAATAAAAAACAAAAA
*
1320337 ATAAAAATAAAAAATAAAAA
1 ATAAAAATAAAAAACAAAAA
1320357 A
1 A
1320358 ATGGATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.85, C:0.02, G:0.00, T:0.12
Consensus pattern (20 bp):
ATAAAAATAAAAAACAAAAA
Found at i:1320342 original size:13 final size:13
Alignment explanation
Indices: 1320319--1320356 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
1320309 CATCTGAGAT
1320319 AAAAATAAAAAACA
1 AAAAAT-AAAAACA
*
1320333 AAAAATAAAAATA
1 AAAAATAAAAACA
1320346 AAAAATAAAAA
1 AAAAATAAAAA
1320357 AATGGATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.11
Consensus pattern (13 bp):
AAAAATAAAAACA
Found at i:1320691 original size:36 final size:36
Alignment explanation
Indices: 1320644--1320716 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
1320634 TTATCTCTAT
1320644 TGAAAAATCATTATTGCATCTTATCCCTAAATTGTA
1 TGAAAAATCATTATTGCATCTTATCCCTAAATTGTA
** *
1320680 TGAAAAATCATTATTTTATCTTATCCCTATATTGTA
1 TGAAAAATCATTATTGCATCTTATCCCTAAATTGTA
1320716 T
1 T
1320717 CTATTTTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (36 bp):
TGAAAAATCATTATTGCATCTTATCCCTAAATTGTA
Found at i:1322505 original size:28 final size:27
Alignment explanation
Indices: 1322425--1322513 Score: 106
Period size: 29 Copynumber: 3.2 Consensus size: 27
1322415 ACATTCCTCA
*
1322425 ACCTTTAAAAGCCCACAAGTCAGTGGC
1 ACCTTCAAAAGCCCACAAGTCAGTGGC
* *
1322452 ACCATTCTCAAAGCCCACAAATCAGTGGC
1 ACC-TTC-AAAAGCCCACAAGTCAGTGGC
* *
1322481 AACCTTCAAAAACCCATAAGTCAGTGGC
1 -ACCTTCAAAAGCCCACAAGTCAGTGGC
1322509 ACCTT
1 ACCTT
1322514 TTTCTTTTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
27 8 0.15
28 19 0.37
29 22 0.42
30 3 0.06
ACGTcount: A:0.35, C:0.31, G:0.15, T:0.19
Consensus pattern (27 bp):
ACCTTCAAAAGCCCACAAGTCAGTGGC
Found at i:1322562 original size:34 final size:33
Alignment explanation
Indices: 1322504--1322614 Score: 117
Period size: 34 Copynumber: 3.5 Consensus size: 33
1322494 CCATAAGTCA
* * *
1322504 GTGGCACCTTTTTCTTTTTAAGTCCACAACTCC
1 GTGGCACCTTTCTCCTTCTAAGTCCACAACTCC
1322537 GTGGCACTCTTTCTCCTTCTAAGTCCACAACTCC
1 GTGGCAC-CTTTCTCCTTCTAAGTCCACAACTCC
* *
1322571 GTGGCACC---CT--TT-TACGTCCACAGCTCC
1 GTGGCACCTTTCTCCTTCTAAGTCCACAACTCC
*
1322598 GTGGCATCTTTCTCCTT
1 GTGGCACCTTTCTCCTT
1322615 TTTCAAAGCC
Statistics
Matches: 66, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
27 20 0.30
28 2 0.03
30 4 0.06
32 2 0.03
33 8 0.12
34 30 0.45
ACGTcount: A:0.15, C:0.35, G:0.14, T:0.35
Consensus pattern (33 bp):
GTGGCACCTTTCTCCTTCTAAGTCCACAACTCC
Found at i:1322581 original size:27 final size:27
Alignment explanation
Indices: 1322551--1322603 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1322541 CACTCTTTCT
1322551 CCTTCTAAGTCCACAACTCCGTGGCAC
1 CCTTCTAAGTCCACAACTCCGTGGCAC
* * *
1322578 CCTTTTACGTCCACAGCTCCGTGGCA
1 CCTTCTAAGTCCACAACTCCGTGGCA
1322604 TCTTTCTCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.40, G:0.17, T:0.25
Consensus pattern (27 bp):
CCTTCTAAGTCCACAACTCCGTGGCAC
Found at i:1322648 original size:32 final size:32
Alignment explanation
Indices: 1322611--1322805 Score: 275
Period size: 33 Copynumber: 6.0 Consensus size: 32
1322601 GCATCTTTCT
*
1322611 CCTTTTTCAAAGCCCACACAAGTCGATGGCAA
1 CCTTTTTCAAAGCCCACACAAGTCGGTGGCAA
1322643 CCTTTTTCCAAAGCCCACACAAGTCGGTGGCAA
1 CCTTTTT-CAAAGCCCACACAAGTCGGTGGCAA
* *
1322676 CCATTCTCAAAGCCCACACAAGTCGGTGGCAA
1 CCTTTTTCAAAGCCCACACAAGTCGGTGGCAA
*
1322708 CCTTTTTCTAAAGCCCACACAAGTTGGTGGCAA
1 CCTTTTTC-AAAGCCCACACAAGTCGGTGGCAA
** *
1322741 TCCCCTCT-AAAGCCCACACAAGTCGGTGGCAA
1 -CCTTTTTCAAAGCCCACACAAGTCGGTGGCAA
*
1322773 CCTTTTTCTAAAGCCCACACAAGTTGGTGGCAA
1 CCTTTTTC-AAAGCCCACACAAGTCGGTGGCAA
1322806 TCCCCTCAAA
Statistics
Matches: 144, Mismatches: 14, Indels: 9
0.86 0.08 0.05
Matches are distributed among these distances:
31 4 0.03
32 61 0.42
33 75 0.52
34 4 0.03
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.22
Consensus pattern (32 bp):
CCTTTTTCAAAGCCCACACAAGTCGGTGGCAA
Found at i:1322686 original size:65 final size:66
Alignment explanation
Indices: 1322617--1322817 Score: 329
Period size: 65 Copynumber: 3.1 Consensus size: 66
1322607 TTCTCCTTTT
* * * *
1322617 TCAAAGCCCACACAAGTCGATGGCAACCTTTTTCCAAAGCCCACACAAGTCGGTGGCAA-CCATT
1 TCAAAGCCCACACAAGTCGGTGGCAACCTTTTTCTAAAGCCCACACAAGTTGGTGGCAATCCACT
1322681 C
66 C
*
1322682 TCAAAGCCCACACAAGTCGGTGGCAACCTTTTTCTAAAGCCCACACAAGTTGGTGGCAATCCCCT
1 TCAAAGCCCACACAAGTCGGTGGCAACCTTTTTCTAAAGCCCACACAAGTTGGTGGCAATCCACT
1322747 C
66 C
1322748 T-AAAGCCCACACAAGTCGGTGGCAACCTTTTTCTAAAGCCCACACAAGTTGGTGGCAATCC-C-
1 TCAAAGCCCACACAAGTCGGTGGCAACCTTTTTCTAAAGCCCACACAAGTTGGTGGCAATCCACT
1322810 C
66 C
1322811 TCAAAGC
1 TCAAAGC
1322818 TCGAATGGTG
Statistics
Matches: 129, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
63 2 0.02
64 6 0.05
65 116 0.90
66 5 0.04
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (66 bp):
TCAAAGCCCACACAAGTCGGTGGCAACCTTTTTCTAAAGCCCACACAAGTTGGTGGCAATCCACT
C
Found at i:1323070 original size:19 final size:20
Alignment explanation
Indices: 1323027--1323079 Score: 90
Period size: 19 Copynumber: 2.7 Consensus size: 20
1323017 ATTTCAACGA
1323027 TTTGTATCGATACATAAAGT
1 TTTGTATCGATACATAAAGT
*
1323047 GTTGTATCGATACAT-AAGT
1 TTTGTATCGATACATAAAGT
1323066 TTTGTATCGATACA
1 TTTGTATCGATACA
1323080 ATTTAAGCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (20 bp):
TTTGTATCGATACATAAAGT
Found at i:1323119 original size:21 final size:21
Alignment explanation
Indices: 1323094--1323152 Score: 118
Period size: 21 Copynumber: 2.8 Consensus size: 21
1323084 AAGCTCCAAA
1323094 AAATGTATCGATACATTACTC
1 AAATGTATCGATACATTACTC
1323115 AAATGTATCGATACATTACTC
1 AAATGTATCGATACATTACTC
1323136 AAATGTATCGATACATT
1 AAATGTATCGATACATT
1323153 GTATCGATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (21 bp):
AAATGTATCGATACATTACTC
Found at i:1323157 original size:13 final size:13
Alignment explanation
Indices: 1323139--1323163 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1323129 ATTACTCAAA
1323139 TGTATCGATACAT
1 TGTATCGATACAT
1323152 TGTATCGATACA
1 TGTATCGATACA
1323164 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1323216 original size:52 final size:52
Alignment explanation
Indices: 1323172--1323300 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
1323162 CACTGATCTT
*
1323172 TGTATCGATACATGCAGGCAACTTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
1323224 TGTATCGATACATGGAAGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1323276 TGTATCGATACATGCAGGCGAATTT
1 TGTATCGATACATGCAGGCAAATTT
1323301 TCATATTTCG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1326703 original size:13 final size:13
Alignment explanation
Indices: 1326685--1326711 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1326675 ACATTATGCT
1326685 TTGTATCGATACA
1 TTGTATCGATACA
1326698 TTGTATCGATACA
1 TTGTATCGATACA
1326711 T
1 T
1326712 GTTCATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1326741 original size:20 final size:19
Alignment explanation
Indices: 1326695--1326751 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1326685 TTGTATCGAT
*
1326695 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGC
* *
1326714 TCATTGTATCTATACATGC
1 ACATTGTATCGATACATGC
1326733 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1326752 AAACTAGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:1328410 original size:20 final size:19
Alignment explanation
Indices: 1328385--1328424 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1328375 TTCCGTGTAA
*
1328385 ATGTATCGATACAATTTTTG
1 ATGTATCGATA-AATATTTG
1328405 ATGTATCGATAAATATTTG
1 ATGTATCGATAAATATTTG
1328424 A
1 A
1328425 AAACATAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (19 bp):
ATGTATCGATAAATATTTG
Found at i:1329250 original size:21 final size:21
Alignment explanation
Indices: 1329209--1329252 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1329199 CTCCCCTTTA
* *
1329209 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1329230 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1329251 TC
1 TC
1329253 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1336311 original size:40 final size:40
Alignment explanation
Indices: 1336262--1336354 Score: 125
Period size: 40 Copynumber: 2.3 Consensus size: 40
1336252 TGCCAATTTC
**
1336262 ATGTATCGATACAATTTATCCATGTATCGATACAT-TGAGT
1 ATGTATCGATACAAGGTA-CCATGTATCGATACATCTGAGT
* *
1336302 ATGTATCGATACAAGGTAGCATGTATCGATACATCTGGGT
1 ATGTATCGATACAAGGTACCATGTATCGATACATCTGAGT
*
1336342 GTGTATCGATACA
1 ATGTATCGATACA
1336355 TTCAAGGGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 15 0.32
40 32 0.68
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (40 bp):
ATGTATCGATACAAGGTACCATGTATCGATACATCTGAGT
Found at i:1336327 original size:20 final size:20
Alignment explanation
Indices: 1336261--1336334 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
1336251 CTGCCAATTT
* *
1336261 CATGTATCGATACAATTTATC
1 CATGTATCGATACAATGTA-G
*
1336282 CATGTATCGATACATTG-AG
1 CATGTATCGATACAATGTAG
* *
1336301 TATGTATCGATACAAGGTAG
1 CATGTATCGATACAATGTAG
1336321 CATGTATCGATACA
1 CATGTATCGATACA
1336335 TCTGGGTGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
19 14 0.31
20 16 0.36
21 15 0.33
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATGTAG
Found at i:1336762 original size:22 final size:21
Alignment explanation
Indices: 1336727--1336776 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1336717 TTTGTTGATG
*
1336727 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
1336747 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
1336768 AATTTGAAG
1 ATTTTGAAG
1336777 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:1336773 original size:21 final size:22
Alignment explanation
Indices: 1336734--1336776 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1336724 ATGATTTTGA
* *
1336734 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1336756 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1336777 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:1349033 original size:13 final size:13
Alignment explanation
Indices: 1349015--1349041 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1349005 CAATTTTTTT
1349015 TTGTATCGATACA
1 TTGTATCGATACA
1349028 TTGTATCGATACA
1 TTGTATCGATACA
1349041 T
1 T
1349042 ACTTTGTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1351165 original size:21 final size:20
Alignment explanation
Indices: 1351136--1351178 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1351126 GACTAGTGTG
*
1351136 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGTGACCT
*
1351157 GGGAGTGCCGGTCGTGACCT
1 GGGACTGCCGGTCGTGACCT
1351177 GG
1 GG
1351179 TGGTGCTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.26, G:0.44, T:0.21
Consensus pattern (20 bp):
GGGACTGCCGGTCGTGACCT
Found at i:1351646 original size:20 final size:20
Alignment explanation
Indices: 1351610--1351687 Score: 59
Period size: 20 Copynumber: 3.6 Consensus size: 20
1351600 ATAATCCCCC
* *
1351610 TGTATCGATAGAAAGAAAAA
1 TGTATCGATACATAGAAAAA
*
1351630 TGTATCGATACATAGAATTTCCAGA
1 TGTATCGATACATAGAA-----AAA
*
1351655 TGTATCGATACACA-AAAACA
1 TGTATCGATACATAGAAAA-A
1351675 TGTATCGATACAT
1 TGTATCGATACAT
1351688 TTTGGACATT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
19 1 0.02
20 28 0.61
24 2 0.04
25 15 0.33
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (20 bp):
TGTATCGATACATAGAAAAA
Found at i:1353722 original size:15 final size:15
Alignment explanation
Indices: 1353702--1353732 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1353692 ATTTCGTTTG
*
1353702 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1353717 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1353732 G
1 G
1353733 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1361931 original size:13 final size:13
Alignment explanation
Indices: 1361913--1361937 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1361903 AAATTCTTAA
1361913 GAGATTGTAACCC
1 GAGATTGTAACCC
1361926 GAGATTGTAACC
1 GAGATTGTAACC
1361938 TAAGGTTGAA
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:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (13 bp):
GAGATTGTAACCC
Found at i:1365993 original size:16 final size:16
Alignment explanation
Indices: 1365961--1366006 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1365951 ATTTATATAT
1365961 TATTTATTCATAT-ACA
1 TATTTATTCAT-TCACA
1365977 TATTTATTCATTCACA
1 TATTTATTCATTCACA
*
1365993 TGTATTA-TCATTCA
1 TAT-TTATTCATTCA
1366007 TTAAATACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 1 0.04
16 23 0.85
17 3 0.11
ACGTcount: A:0.33, C:0.15, G:0.02, T:0.50
Consensus pattern (16 bp):
TATTTATTCATTCACA
Found at i:1367467 original size:16 final size:17
Alignment explanation
Indices: 1367446--1367477 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1367436 TGACATGATA
1367446 ACCTTATAT-TTATAAT
1 ACCTTATATCTTATAAT
1367462 ACCTTATATCTTATAA
1 ACCTTATATCTTATAA
1367478 GAATTGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (17 bp):
ACCTTATATCTTATAAT
Found at i:1374327 original size:23 final size:22
Alignment explanation
Indices: 1374292--1374343 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
1374282 TTTTTTCCAA
* *
1374292 TTTTCTCTCTTTTTCTTTCTTTT
1 TTTTCT-TTTTTTTCTCTCTTTT
1374315 TCTTTCTTTTTTTTCTCTCTTTT
1 T-TTTCTTTTTTTTCTCTCTTTT
1374338 TTTTCT
1 TTTTCT
1374344 CCATGTGCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 5 0.19
23 16 0.62
24 5 0.19
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTCTTTTTTTTCTCTCTTTT
Found at i:1374329 original size:13 final size:13
Alignment explanation
Indices: 1374303--1374343 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
1374293 TTTCTCTCTT
1374303 TTTCTTTCTTTTTC
1 TTTCTTT-TTTTTC
1374317 TTTCTTTTTTTTC
1 TTTCTTTTTTTTC
*
1374330 TCTCTTTTTTTTC
1 TTTCTTTTTTTTC
1374343 T
1 T
1374344 CCATGTGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 19 0.73
14 7 0.27
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTCTTTTTTTTC
Found at i:1374338 original size:10 final size:10
Alignment explanation
Indices: 1374292--1374330 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
1374282 TTTTTTCCAA
*
1374292 TTTTCTCTCT
1 TTTTCTTTCT
1374302 TTTTCTTTCT
1 TTTTCTTTCT
1374312 TTTTCTTTCT
1 TTTTCTTTCT
1374322 TTTT-TTTCT
1 TTTTCTTTCT
1374331 CTCTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
9 5 0.18
10 23 0.82
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:1375297 original size:167 final size:166
Alignment explanation
Indices: 1374828--1375299 Score: 454
Period size: 167 Copynumber: 2.8 Consensus size: 166
1374818 AATATATATT
* * * * * * * *
1374828 AAAAAAATTAAAAACTCA-AAAAATAAATTGAATTTCTGAAAACTAATTTAATAGGAGTTCAATG
1 AAAAAAATGAAAAACTCATAAAAATAAA-GGAATTTTTCAAAACTAATTTAATATGAATTAAATA
* * * * *
1374892 ACAAAATCAGATGTATTATAAAAATTTTAAACCGAAG-AAAACCCCCCAAAAAACATTTATGGGA
65 ATAATATCTGATGAATTTTAAAAATTTTAAACC-AAGAAAAACCCCCC-AAAAACATTTATGGGA
* * * * *
1374956 TAGAAAATTCAGTTTTTTGGAAACATGGGCATTTCAAGA
128 TAGAAAACTCAGTTTTTTGGAAACAAGAGCAATCCAAGA
* * *
1374995 AAAAAAATGAAAAATTCATAAAAATAAATGAATTTTTCAAAACTAATTTAATATGAATTAAATGA
1 AAAAAAATGAAAAACTCATAAAAATAAAGGAATTTTTCAAAACTAATTTAATATGAATTAAATAA
* * * * * *
1375060 TGATATCTGATGAATTTTAAAAATTTTGAACCTAGAAAAACCCTCACAAAAACTTTTATGGAATA
66 TAATATCTGATGAATTTTAAAAATTTTAAACCAAGAAAAACCC-CCCAAAAACATTTATGGGATA
* *
1375125 GAAAACTCAGTTTTTTGGAAATAAGAG-AATCCAAGG
130 GAAAACTCAGTTTTTTGGAAACAAGAGCAATCCAAGA
* * ** * * * *
1375161 AAAAAAATGAAAAACTCAT-GAAATAAAAGGATTTTTTTTGAAACTGATTTATTGTGAGTTAAAT
1 AAAAAAATGAAAAACTCATAAAAAT-AAAGGA-ATTTTTCAAAACTAATTTAATATGAATTAAAT
* *
1375225 AATAATATTTGATGAATTTT-AAAATTTATAAACCAAGAAAAATCCCCCCAAATAA-ATTTACAG
64 AATAATATCTGATGAATTTTAAAAATTT-TAAACCAAGAAAAA-CCCCCCAAA-AACATTTA-TG
1375288 GGA-AGAAAACTC
125 GGATAGAAAACTC
1375300 CATATTTCGA
Statistics
Matches: 252, Mismatches: 44, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
165 4 0.02
166 38 0.15
167 191 0.76
168 19 0.08
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.29
Consensus pattern (166 bp):
AAAAAAATGAAAAACTCATAAAAATAAAGGAATTTTTCAAAACTAATTTAATATGAATTAAATAA
TAATATCTGATGAATTTTAAAAATTTTAAACCAAGAAAAACCCCCCAAAAACATTTATGGGATAG
AAAACTCAGTTTTTTGGAAACAAGAGCAATCCAAGA
Found at i:1377139 original size:13 final size:13
Alignment explanation
Indices: 1377121--1377162 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1377111 GATACTATTC
1377121 ACACTGTATCGAT
1 ACACTGTATCGAT
*
1377134 ACACTGCATCGAT
1 ACACTGTATCGAT
* *
1377147 ATAATGTATCGAT
1 ACACTGTATCGAT
1377160 ACA
1 ACA
1377163 TGAATAGTGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (13 bp):
ACACTGTATCGAT
Found at i:1377265 original size:10 final size:10
Alignment explanation
Indices: 1377236--1377266 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1377226 GTATCGATAC
*
1377236 ATGAACAGTA
1 ATGAACAGTG
1377246 ATGAACAGTG
1 ATGAACAGTG
1377256 ATGAACAGTG
1 ATGAACAGTG
1377266 A
1 A
1377267 AAATGAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.26, T:0.19
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:1379754 original size:24 final size:25
Alignment explanation
Indices: 1379727--1379792 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 25
1379717 CGATACATCT
1379727 TGTATCGATACAT-TACATCTTGTA
1 TGTATCGATACATATACATCTTGTA
1379751 TGTATCGATACATTATCGATACATCTTGTA
1 TGTATCGATAC---AT--ATACATCTTGTA
1379781 TGTATCGATACA
1 TGTATCGATACA
1379793 AACAGTTAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
24 11 0.31
27 3 0.08
30 22 0.61
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (25 bp):
TGTATCGATACATATACATCTTGTA
Found at i:1379870 original size:20 final size:21
Alignment explanation
Indices: 1379823--1379875 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1379813 GCCAATCAAC
*
1379823 TGTATCGATACATTCTTTGCA
1 TGTATCGATACATTCTGTGCA
*
1379844 AGTATCGATACATT-TG-GTCA
1 TGTATCGATACATTCTGTG-CA
1379864 TGTATCGATACA
1 TGTATCGATACA
1379876 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTGCA
Found at i:1379881 original size:13 final size:13
Alignment explanation
Indices: 1379863--1379887 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1379853 ACATTTGGTC
1379863 ATGTATCGATACA
1 ATGTATCGATACA
1379876 ATGTATCGATAC
1 ATGTATCGATAC
1379888 TGTGCATTAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1380016 original size:111 final size:111
Alignment explanation
Indices: 1379876--1380110 Score: 461
Period size: 111 Copynumber: 2.1 Consensus size: 111
1379866 TATCGATACA
1379876 ATGTATCGATACTGTGCATTATGTATCGATACAGCTAAAGGTGTATCAATACATTTGAGGGTTTT
1 ATGTATCGATACTGTGCATTATGTATCGATACAGCTAAAGGTGTATCAATACATTTGAGGGTTTT
1379941 GACCTTTGTAGCCTTAGTCAACCTTAATGTATCGATACAAATACCT
66 GACCTTTGTAGCCTTAGTCAACCTTAATGTATCGATACAAATACCT
*
1379987 ATGTATCGATACTGTGCATTATGTATCGATACATCTAAAGGTGTATCAATACATTTGAGGGTTTT
1 ATGTATCGATACTGTGCATTATGTATCGATACAGCTAAAGGTGTATCAATACATTTGAGGGTTTT
1380052 GACCTTTGTAGCCTTAGTCAACCTTAATGTATCGATACAAATACCT
66 GACCTTTGTAGCCTTAGTCAACCTTAATGTATCGATACAAATACCT
1380098 ATGTATCGATACT
1 ATGTATCGATACT
1380111 TTGATTTATT
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 123 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (111 bp):
ATGTATCGATACTGTGCATTATGTATCGATACAGCTAAAGGTGTATCAATACATTTGAGGGTTTT
GACCTTTGTAGCCTTAGTCAACCTTAATGTATCGATACAAATACCT
Found at i:1392248 original size:20 final size:20
Alignment explanation
Indices: 1392202--1392274 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
1392192 TTCCAATGAC
***
1392202 ATGTATCGATACATTTTTTT
1 ATGTATCGATACATTGAATT
1392222 CATGTATCGATACATTGCAA-T
1 -ATGTATCGATACATTG-AATT
*
1392243 ATGTATCGATACTTTGAATT
1 ATGTATCGATACATTGAATT
*
1392263 GTGTATCGATAC
1 ATGTATCGATAC
1392275 TTTTAAGGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 27 0.60
21 16 0.36
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTGAATT
Found at i:1398629 original size:21 final size:21
Alignment explanation
Indices: 1398600--1398644 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1398590 AAGTTTTTAT
*
1398600 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1398620 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1398642 TTT
1 TTT
1398645 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1400562 original size:32 final size:30
Alignment explanation
Indices: 1400526--1400584 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
1400516 GAAATCAAAT
1400526 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
1400558 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
1400585 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:1400887 original size:34 final size:32
Alignment explanation
Indices: 1400844--1400906 Score: 108
Period size: 34 Copynumber: 1.9 Consensus size: 32
1400834 TACAAGCCAA
1400844 TGTATCGATACATATTTTATGTGTATCGATACAT
1 TGTATCGATACATA-TTT-TGTGTATCGATACAT
1400878 TGTATCGATACATATTTTGTGTATCGATA
1 TGTATCGATACATATTTTGTGTATCGATA
1400907 TAAGTTTGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 12 0.41
33 3 0.10
34 14 0.48
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (32 bp):
TGTATCGATACATATTTTGTGTATCGATACAT
Found at i:1400902 original size:19 final size:19
Alignment explanation
Indices: 1400844--1400906 Score: 66
Period size: 13 Copynumber: 3.5 Consensus size: 19
1400834 TACAAGCCAA
1400844 TGTATCGATACATATTTTATG
1 TGTATCGATACATA-TTT-TG
1400865 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
1400878 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
1400897 TGTATCGATA
1 TGTATCGATA
1400907 TAAGTTTGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
13 11 0.31
14 1 0.03
15 1 0.03
18 1 0.03
19 11 0.31
21 11 0.31
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:1403449 original size:166 final size:161
Alignment explanation
Indices: 1403078--1403672 Score: 635
Period size: 166 Copynumber: 3.6 Consensus size: 161
1403068 TCTCCATAAT
* * * * ** *
1403078 TTTTTTTGGGAGGATTTTTCTTAATTTTTAATTTTTAAAATTCATCAAATATTTTTATTTATTTA
1 TTTTTTTGAG-GGATTTTTCTTAGTTTTCAATTTTTAAAATTCATCAAACATCATTATTTATTTC
* *
1403143 ATATTAATTCAATTTTCCAAAATTCATTCATTTTCATAAGCTTTTGATTTTTTTCCTTG-AATT-
65 ATATTAATTCAATTTTCAAAAATTCATTCATTTTCATTAGCTTTTGA-TTTTTTCCTTGAAATTC
* * *
1403206 TTTTTTCGAAATACAGTG-TTTTCTACTCTGTAAA
129 TTTTTT-TAAATAC-GGGATTTTCTATTCTGTAAA
** * * * *
1403240 TTTTTTCAAACGGATTTTTCATGGTTTTCAATTTTTAAAATTCATCAAACATTATCT-TTTATTT
1 TTTTTT-TGAGGGATTTTTCTTAGTTTTCAATTTTTAAAATTCATCAAACATCAT-TATTTATTT
*
1403304 CATATTAATTCAATTTTCAAAACTTCATTCATTTTCATTAGCTTTTGATTTTTTCCTTGAAACTT
64 CATATTAATTCAATTTTCAAAAATTCATTCATTTTCATTAGCTTTTGATTTTTTCCTTGAAA-TT
1403369 CTTTTCTTTAAAATACGGGATTTTCTATTCTGTAAA
128 CTTTT-TTT-AAATACGGGATTTTCTATTCTGTAAA
* * *
1403405 TTTGTTTTGAGGGAATTTTTCTTGGTTTTCAATTTTTAAAATTCATAAAACATCATAATTTATTT
1 TTT-TTTTGAGGG-ATTTTTCTTAGTTTTCAATTTTTAAAATTCATCAAACATCATTATTTATTT
* * * * *
1403470 TATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATTCA-TTTTTTATTTTTTCTTTGAAAAT
64 CATATTAATTCAATTTTCAAAAATTCATTCATTTTCATT-AGCTTTTGATTTTTTCCTTG-AAAT
* * * *
1403534 CCCTTTTTTCCTAAATACCGTATTTTCTATTCCGTAAA
127 -TCTTTTTT--TAAATACGGGATTTTCTATTCTGTAAA
* * * * *
1403572 TTTTTCTGAGGGGATATTTCTCAGTTTTCAATTTTTAGAATTCATCAAACATCATTGTTTGA-TT
1 TTTTTTTGA-GGGATTTTTCTTAGTTTTCAATTTTTAAAATTCATCAAACATCATTATTT-ATTT
* * *
1403636 CATATTAATTCAGTTTTAAAAAATTAATTCATTTTCA
64 CATATTAATTCAATTTTCAAAAATTCATTCATTTTCA
1403673 AGAGTTTGGG
Statistics
Matches: 370, Mismatches: 45, Indels: 32
0.83 0.10 0.07
Matches are distributed among these distances:
161 11 0.03
162 97 0.26
163 3 0.01
164 6 0.02
165 29 0.08
166 184 0.50
167 39 0.11
168 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.07, T:0.52
Consensus pattern (161 bp):
TTTTTTTGAGGGATTTTTCTTAGTTTTCAATTTTTAAAATTCATCAAACATCATTATTTATTTCA
TATTAATTCAATTTTCAAAAATTCATTCATTTTCATTAGCTTTTGATTTTTTCCTTGAAATTCTT
TTTTTAAATACGGGATTTTCTATTCTGTAAA
Found at i:1403775 original size:332 final size:327
Alignment explanation
Indices: 1403107--1403777 Score: 686
Period size: 332 Copynumber: 2.0 Consensus size: 327
1403097 CTTAATTTTT
* * ** * *
1403107 AATTTTTAAAATTCATCAAATATTTTTATTTATTTAATATTAATTCAATTTTCCAAAATTCATTC
1 AATTTTTAAAATTCATAAAACATCATAATTTATTTAATATTAATTCAATTTTCAAAAATTCATTC
* * *
1403172 ATTTTCATAAGCTTTTGATTTTTTTCCTTGAATTTTTTTTCGAAATACAGTGTTTTCTACTCTGT
66 ATTTTCATAAGCTTTTGATTTTTTTCCTTGAATTTTTTTCCGAAATACAGTATTTTCTACTCCGT
*
1403237 AAATTTTTTCAAACGGATTTTTCATGGTTTTCAATTTTTAAAATTCATCAAACATTATCTTTTAT
131 AAATTTTTTCAAACGGATTTTTCA-GGTTTTCAATTTTTAAAATTCATCAAACATCATCTTTTAT
* * * ** * *
1403302 TTCATATTAATTCAATTTTCAAAACTTCATTCATTTTCATTAGCTTTTGATTTTTTCCTTGAAAC
195 TTCATATTAATTCAATTTTAAAAAATTAATTCATTTTCAAGAGCTTTGGATTTTTTCATTGAAAC
* * * *
1403367 TTCTTTTCTTTAAAATACGGGATTTTCTATTCTGTAAATTTGTTTTGAGGGAATTTTTCTTGGTT
260 TTCTTTTCTTTAAAATACGAGATTTTCTATCCTGTAAATATGTTTTGAGGGAATTTTTCTTGGTC
***
1403432 TTC
325 AAA
* *
1403435 AATTTTTAAAATTCATAAAACATCATAATTTATTTTATATTAATTCAGTTTTCAAAAATTCATTC
1 AATTTTTAAAATTCATAAAACATCATAATTTATTTAATATTAATTCAATTTTCAAAAATTCATTC
* * * * * *
1403500 ATTTTCATTCA-TTTTTTA-TTTTTTCTTTGAAAATCCCTTTTTTCCTAAATACCGTATTTTCTA
66 ATTTTCA-TAAGCTTTTGATTTTTTTCCTTG--AAT---TTTTTTCCGAAATACAGTATTTTCTA
* * ** *
1403563 TTCCGTAAA-TTTTTCTGAGGGGATATTTCTCA-GTTTTCAATTTTTAGAATTCATCAAACATCA
125 CTCCGTAAATTTTTTC-AAACGGAT-TTT-TCAGGTTTTCAATTTTTAAAATTCATCAAACATCA
*
1403626 T-TGTTTGA-TTCATATTAATTCAGTTTTAAAAAATTAATTCATTTTCAAGAG-TTTGGGATTTT
187 TCT-TTT-ATTTCATATTAATTCAATTTTAAAAAATTAATTCATTTTCAAGAGCTTT-GGATTTT
* * *
1403688 TTTATTGAAA-TTCTCCTTT-TTTGAGAAA-CCGAG-TTTTCT-TCCTCGTAAATAT-TTTTGGG
249 TTCATTGAAACTTCT--TTTCTTT-A-AAATACGAGATTTTCTATCCT-GTAAATATGTTTTGAG
*
1403747 GGGA-TTTTCTTCGGTCAAA
309 GGAATTTTTCTT-GGTCAAA
1403766 AATTTTTTAAAA
1 AA-TTTTTAAAA
1403778 AGCATCTAAT
Statistics
Matches: 282, Mismatches: 42, Indels: 34
0.79 0.12 0.09
Matches are distributed among these distances:
327 10 0.04
328 69 0.24
329 5 0.02
330 7 0.02
331 31 0.11
332 143 0.51
333 11 0.04
334 6 0.02
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (327 bp):
AATTTTTAAAATTCATAAAACATCATAATTTATTTAATATTAATTCAATTTTCAAAAATTCATTC
ATTTTCATAAGCTTTTGATTTTTTTCCTTGAATTTTTTTCCGAAATACAGTATTTTCTACTCCGT
AAATTTTTTCAAACGGATTTTTCAGGTTTTCAATTTTTAAAATTCATCAAACATCATCTTTTATT
TCATATTAATTCAATTTTAAAAAATTAATTCATTTTCAAGAGCTTTGGATTTTTTCATTGAAACT
TCTTTTCTTTAAAATACGAGATTTTCTATCCTGTAAATATGTTTTGAGGGAATTTTTCTTGGTCA
AA
Found at i:1404398 original size:11 final size:10
Alignment explanation
Indices: 1404330--1404389 Score: 66
Period size: 11 Copynumber: 5.6 Consensus size: 10
1404320 ACTCAGCTGA
*
1404330 AAAAAAGAAGC
1 AAAAAA-AAGG
1404341 AAAAAAAAGG
1 AAAAAAAAGG
*
1404351 ACAAAAAAAGA
1 A-AAAAAAAGG
1404362 AAGAAAAAAGAG
1 AA-AAAAAAG-G
1404374 AAAAAAAAGG
1 AAAAAAAAGG
1404384 AAAAAA
1 AAAAAA
1404390 TAGTGAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
10 12 0.28
11 29 0.67
12 2 0.05
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGG
Found at i:1409857 original size:51 final size:51
Alignment explanation
Indices: 1409781--1409909 Score: 177
Period size: 51 Copynumber: 2.5 Consensus size: 51
1409771 AACTAGATGT
* * **
1409781 ATCGATAAATTGCAAAATGTATCGATACATCTGGGTAAAAAGACAAAATGC
1 ATCGATACATTGAAAAATGTATCGATACATCTACGTAAAAAGACAAAATGC
* * * *
1409832 ATCGATACATTGAAAAATGTATCGATATATCTACGTAAAAAGATAGAATGT
1 ATCGATACATTGAAAAATGTATCGATACATCTACGTAAAAAGACAAAATGC
*
1409883 ATCGATACATTGAAAAATATATCGATA
1 ATCGATACATTGAAAAATGTATCGATA
1409910 AATTCATACA
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 69 1.00
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.27
Consensus pattern (51 bp):
ATCGATACATTGAAAAATGTATCGATACATCTACGTAAAAAGACAAAATGC
Found at i:1410962 original size:28 final size:28
Alignment explanation
Indices: 1410928--1411393 Score: 540
Period size: 28 Copynumber: 16.5 Consensus size: 28
1410918 CATCGACTTG
1410928 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* ** *
1410956 TGTGGGCTTTGAAAAGAAACCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* * *
1410984 TGTGGGCTCTAAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* * * *
1411012 CGTGGGCTCTAAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* ***
1411040 CGTGGGCTCAAAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
*
1411068 TGTGGGCTTTGAAAGGATGCCATTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* * * * *
1411096 CGTGGGCTTTGAAATGATGCCATTGATT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
*
1411124 TGTCGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* * *
1411152 TGTGGCCTTTGAAAAGGGATGCCAATGACT
1 TGTGGGCTTTG-AAA-GGATGCCACTAACT
** * *
1411182 CATGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
1411210 TGTGGGCTTTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTTG-AAAGGATGCCACTAACT
* *
1411238 TGTGGGCTTTAAAAAGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
*
1411266 TGTGGGCTTTGAAAGAATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
*
1411294 TGTGGGCTTTGAAAGAATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* * *
1411322 TATGGGCTTTAAAAAGGGATGCCACTGACT
1 TGTGGGCTTT-GAAA-GGATGCCACTAACT
1411352 TGTGGGCTTTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTTG-AAAGGATGCCACTAACT
1411380 TGTGGGCTTTGAAA
1 TGTGGGCTTTGAAA
1411394 AGGTCTCGTA
Statistics
Matches: 379, Mismatches: 52, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
27 7 0.02
28 313 0.83
29 15 0.04
30 44 0.12
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTAACT
Found at i:1411236 original size:170 final size:168
Alignment explanation
Indices: 1410929--1411397 Score: 629
Period size: 170 Copynumber: 2.8 Consensus size: 168
1410919 ATCGACTTGT
* ** * *
1410929 GTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGAAACCACTGACTTGTGGGCTCT
1 GTGGGCTTTGAAA-GATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTT
* * **
1410994 AAAA-GGATGCCACTGACTCGTGGGCTCT-AAAAGGATGCCACTGACTCGTGGGC-TCAAAAAGG
65 AAAAGGGATGCCACTGACTCGTGGGCTTTGAAAA-GATGCCACTGACTTGTGGGCTTTGAAAAGG
* * *
1411056 ATGCCACTAACTTGTGGGCTTTGAAAGGATGCCATTAACTC
129 -TGCCACTAACTTGTGGGCTTTAAAAAGATGCCACTAACTC
* * * * *
1411097 GTGGGCTTTGAAATGATGCCATTGATTTGTCGGCTTTGAAAGGATGCCACTAACTTGTGGCCTTT
1 GTGGGCTTTGAAA-GATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTT
* *
1411162 GAAAAGGGATGCCAATGACTCATGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGG
65 -AAAAGGGATGCCACTGACTCGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGG
*
1411227 TGCCACTAACTTGTGGGCTTTAAAAAGATGCCACTAACTT
129 TGCCACTAACTTGTGGGCTTTAAAAAGATGCCACTAACTC
* *
1411267 GTGGGCTTTGAAAGAATGCCACTAACTTGTGGGCTTTGAAAGAATGCCACTAACTTATGGGCTTT
1 GTGGGCTTTGAAAG-ATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTT
* * *
1411332 AAAAAGGGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTAACTTGTGGGCTTTGAAAAGG
65 -AAAAGGGATGCCACTGACTCGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGG
1411397 T
129 T
1411398 CTCGTATTGA
Statistics
Matches: 262, Mismatches: 34, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
168 54 0.21
169 5 0.02
170 192 0.73
171 11 0.04
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (168 bp):
GTGGGCTTTGAAAGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTA
AAAGGGATGCCACTGACTCGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGTG
CCACTAACTTGTGGGCTTTAAAAAGATGCCACTAACTC
Found at i:1413526 original size:13 final size:13
Alignment explanation
Indices: 1413486--1413534 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
1413476 CCGTTAGAAG
1413486 CAATGTATCGATA
1 CAATGTATCGATA
1413499 CAA--T-TC-AT-
1 CAATGTATCGATA
1413507 C-ATGTATCGATA
1 CAATGTATCGATA
1413519 CAATGTATCGATA
1 CAATGTATCGATA
1413532 CAA
1 CAA
1413535 AGCATAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.10
10 4 0.13
11 3 0.10
12 1 0.03
13 17 0.57
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1413528 original size:33 final size:33
Alignment explanation
Indices: 1413486--1413550 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1413476 CCGTTAGAAG
** *
1413486 CAATGTATCGATACAATTCATCATGTATCGATA
1 CAATGTATCGATACAAAGCATAATGTATCGATA
1413519 CAATGTATCGATACAAAGCATAATGTATCGAT
1 CAATGTATCGATACAAAGCATAATGTATCGAT
1413551 GCATCTTGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (33 bp):
CAATGTATCGATACAAAGCATAATGTATCGATA
Found at i:1425363 original size:51 final size:51
Alignment explanation
Indices: 1425304--1425447 Score: 225
Period size: 51 Copynumber: 2.8 Consensus size: 51
1425294 TAACTAGATG
* * * *
1425304 TATCGATACATTGCAAAATGTATCGATACATCTAGGTAAAAGGATAGAATA
1 TATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAAAATA
*
1425355 TATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAAAATG
1 TATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAAAATA
* *
1425406 TAGCGATACATTGAAAAATGTATTGATACATCTGGGTAAAAA
1 TATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
1425448 TATGACCTTT
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 86 1.00
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (51 bp):
TATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAAAATA
Found at i:1426542 original size:13 final size:13
Alignment explanation
Indices: 1426524--1426549 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1426514 TACAGCAAGT
1426524 ATGTATCGATACA
1 ATGTATCGATACA
1426537 ATGTATCGATACA
1 ATGTATCGATACA
1426550 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1428799 original size:21 final size:21
Alignment explanation
Indices: 1428766--1428810 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1428756 TTGCAAGTTG
*
1428766 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1428788 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1428808 AAA
1 AAA
1428811 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1430630 original size:15 final size:15
Alignment explanation
Indices: 1430610--1430640 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1430600 TAAAAATGTC
*
1430610 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1430625 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1430640 C
1 C
1430641 CAAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1434603 original size:30 final size:30
Alignment explanation
Indices: 1434569--1434628 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1434559 ACAATTATTT
1434569 CATTAAGGGGGAGAATGTACAAATTTGTTA
1 CATTAAGGGGGAGAATGTACAAATTTGTTA
1434599 CATTAAGGGGGAGAATGTACAAATTTGTTA
1 CATTAAGGGGGAGAATGTACAAATTTGTTA
1434629 AATTTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.30
Consensus pattern (30 bp):
CATTAAGGGGGAGAATGTACAAATTTGTTA
Found at i:1435288 original size:13 final size:13
Alignment explanation
Indices: 1435270--1435295 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1435260 TACAGCAAGT
1435270 ATGTATCGATACA
1 ATGTATCGATACA
1435283 ATGTATCGATACA
1 ATGTATCGATACA
1435296 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1438362 original size:19 final size:21
Alignment explanation
Indices: 1438316--1438369 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
1438306 TTTCAACAAT
1438316 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAACAGTAA
* *
1438337 CTGTATCGATACAAA-AGT-G
1 TTGTATCGATACAAACAGTAA
1438356 TTGTATCGATACAA
1 TTGTATCGATACAA
1438370 TGTATCACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TTGTATCGATACAAACAGTAA
Found at i:1438423 original size:20 final size:20
Alignment explanation
Indices: 1438398--1438466 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
1438388 CTGCCAAGGA
1438398 AATGTATCGATACATTACTC
1 AATGTATCGATACATTACTC
*
1438418 AATGTATTGATAC---A-T-
1 AATGTATCGATACATTACTC
1438433 --TGTATCGATACATTACTC
1 AATGTATCGATACATTACTC
*
1438451 AATGTATTGATACATT
1 AATGTATCGATACATT
1438467 GTATCGATAC
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
13 10 0.26
16 2 0.05
17 2 0.05
20 25 0.64
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTACTC
Found at i:1438442 original size:13 final size:13
Alignment explanation
Indices: 1438420--1438480 Score: 53
Period size: 13 Copynumber: 5.2 Consensus size: 13
1438410 CATTACTCAA
*
1438420 TGTATTGATACAT
1 TGTATCGATACAT
1438433 TGTATCGATACA-
1 TGTATCGATACAT
*
1438445 T-TA-C--T-CAA
1 TGTATCGATACAT
*
1438453 TGTATTGATACAT
1 TGTATCGATACAT
1438466 TGTATCGATACAT
1 TGTATCGATACAT
1438479 TG
1 TG
1438481 ATCTTTATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
7 2 0.05
8 2 0.05
9 2 0.05
10 1 0.03
11 2 0.05
12 2 0.05
13 27 0.71
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1438498 original size:33 final size:33
Alignment explanation
Indices: 1438400--1438479 Score: 160
Period size: 33 Copynumber: 2.4 Consensus size: 33
1438390 GCCAAGGAAA
1438400 TGTATCGATACATTACTCAATGTATTGATACAT
1 TGTATCGATACATTACTCAATGTATTGATACAT
1438433 TGTATCGATACATTACTCAATGTATTGATACAT
1 TGTATCGATACATTACTCAATGTATTGATACAT
1438466 TGTATCGATACATT
1 TGTATCGATACATT
1438480 GATCTTTATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATTACTCAATGTATTGATACAT
Found at i:1447831 original size:27 final size:27
Alignment explanation
Indices: 1447787--1447845 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
1447777 GCATCTTTTT
* * *
1447787 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTGAAGCCCACAACTCCATGGCAC
*
1447814 CCTTTGAAGCCCATAACTCCATGGCAC
1 CCTTTGAAGCCCACAACTCCATGGCAC
*
1447841 TCTTT
1 CCTTT
1447846 TTCTTTTAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.36, G:0.14, T:0.29
Consensus pattern (27 bp):
CCTTTGAAGCCCACAACTCCATGGCAC
Found at i:1447871 original size:60 final size:61
Alignment explanation
Indices: 1447755--1448367 Score: 702
Period size: 60 Copynumber: 10.1 Consensus size: 61
1447745 TCATGTCATG
* * *
1447755 CTTTTAAGTCCACAACTTCGTGGCA-TCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTGAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
* * * * *
1447815 CTTTGAAGCCCATAACTCCATGGCACTCTTTTT-CTTTTAAGTCTATAACTCTGTGGCACC
1 CTTTGAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
* ** * ** *
1447875 CTTTTAAATCCACAAGCTCTGTGGCACT-TTTGCCCCTTTTAAAGCCCACAACTCCGTGGCACC
1 CTTTGAAGCCCACAA-CTCCGTGGCACTCTTT-TTCCTTTT-AAGTCCACAACTCCGTGGCACC
* * * * *
1447938 CTTTTAAGTCCACAACTCCATGGCA-TCTTTTTCCTTTTATGTCCACAACTCTGTGGCACC
1 CTTTGAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
* *
1447998 CTTTGAAGCCAACAACTCTGTGGCA-TCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTGAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
* * * * *
1448058 CTTTGAAGCCTATAACTCCATGGCACTCTTTTT-CTTTTAAGTCTACAACTCTGTGGCACC
1 CTTTGAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
* * * *** *
1448118 CTTTTAAGTCCACAAGCTCTGTGGCAC-CTTGCCCCTTTTAAAGCCCACAACTCCGTGGCACC
1 CTTTGAAGCCCACAA-CTCCGTGGCACTCTTTTTCCTTTT-AAGTCCACAACTCCGTGGCACC
* * *
1448180 CTTTTAAGTCCACAACTCCGTGGCA-TCTTTTTCCTTTTATGTCCACAACTCCGTGGCACC
1 CTTTGAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
* *
1448240 CTTTGAAGCCCACAACTCTGTGGCATTCTTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTGAAGCCCACAACTCCGTGGCACTC-TTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
* * * * * *
1448302 CTTTGAAGCTCACAACTCCGTGGCACTCTTTTTTCTTTTAAGCCCACACCTCTGCGGCATCC
1 CTTTGAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA-CC
1448364 CTTT
1 CTTT
1448368 TTCCTTTAAG
Statistics
Matches: 468, Mismatches: 71, Indels: 26
0.83 0.13 0.05
Matches are distributed among these distances:
60 232 0.50
61 91 0.19
62 113 0.24
63 32 0.07
ACGTcount: A:0.20, C:0.32, G:0.14, T:0.33
Consensus pattern (61 bp):
CTTTGAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1447955 original size:27 final size:27
Alignment explanation
Indices: 1447908--1448333 Score: 264
Period size: 27 Copynumber: 14.3 Consensus size: 27
1447898 GCACTTTTGC
*
1447908 CCCTTTTAAAGCCCACAACTCCGTGGCA
1 CCCTTTT-AAGTCCACAACTCCGTGGCA
*
1447936 CCCTTTTAAGTCCACAACTCCATGGCA
1 CCCTTTTAAGTCCACAACTCCGTGGCA
* *
1447963 TCTTTTTCCTTTTATGTCCACAACTCTGTGGCA
1 -C-----CCTTTTAAGTCCACAACTCCGTGGCA
* *
1447996 CCCTTTGAAG-CCAACAACTCTGTGGCA
1 CCCTTTTAAGTCC-ACAACTCCGTGGCA
1448023 TCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA
1 -C-----CCTTTTAAGTCCACAACTCCGTGGCA
* * *
1448056 CCCTTTGAAG-CCTATAACTCCATGGCA
1 CCCTTTTAAGTCC-ACAACTCCGTGGCA
* *
1448083 CTCTTTTTCTTTTAAGTCTACAACTCTGTGGCA
1 C-C-----CTTTTAAGTCCACAACTCCGTGGCA
*
1448116 CCCTTTTAAGTCCACAAGCTCTGTGGCA
1 CCCTTTTAAGTCCACAA-CTCCGTGGCA
*
1448144 CCTTGCCCCTTTTAAAGCCCACAACTCCGTGGCA
1 ------CCCTTTT-AAGTCCACAACTCCGTGGCA
1448178 CCCTTTTAAGTCCACAACTCCGTGGCA
1 CCCTTTTAAGTCCACAACTCCGTGGCA
*
1448205 TCTTTTTCCTTTTATGTCCACAACTCCGTGGCA
1 -C-----CCTTTTAAGTCCACAACTCCGTGGCA
* * *
1448238 CCCTTTGAAGCCCACAACTCTGTGGCA
1 CCCTTTTAAGTCCACAACTCCGTGGCA
1448265 TTCTTTTTTCCTTTTAAGTCCACAACTCCGTGGCA
1 --C------CCTTTTAAGTCCACAACTCCGTGGCA
*
1448300 CCCTTTGAAG-CTCACAACTCCGTGGCA
1 CCCTTTTAAGTC-CACAACTCCGTGGCA
*
1448327 CTCTTTT
1 CCCTTTT
1448334 TTCTTTTAAG
Statistics
Matches: 321, Mismatches: 32, Indels: 91
0.72 0.07 0.20
Matches are distributed among these distances:
26 5 0.02
27 143 0.45
28 28 0.09
29 1 0.00
32 4 0.01
33 89 0.28
34 19 0.06
35 32 0.10
ACGTcount: A:0.20, C:0.33, G:0.14, T:0.32
Consensus pattern (27 bp):
CCCTTTTAAGTCCACAACTCCGTGGCA
Found at i:1448177 original size:95 final size:91
Alignment explanation
Indices: 1447910--1448394 Score: 321
Period size: 95 Copynumber: 5.3 Consensus size: 91
1447900 ACTTTTGCCC
* * * *
1447910 CTTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCATGGCATCTTTTTCCTTT
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-C-CTTCCCTTT
* * *
1447975 TATGTCCACAACTCTGTGGCAC-C-----
63 TAAGCCCACAACTCCGTGGCACTCTTTTT
* *
1447998 CTTTGAAG-CCAACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA----CC
1 CTTTTAAGTCC-ACAACTCCGTGGCA-C-----CCTTTTAAGTCCACAACTCCGTGGCACCTTCC
* * * *
1448058 CTTTGAAGCCTATAACTCCATGGCACTCTTTTT
59 CTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
* * *
1448091 CTTTTAAGTCTACAACTCTGTGGCACCCTTTTAAGTCCACAAGCTCTGTGGCACCTTGCCCCTTT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAA-CTCCGTGGCACCTT--CCCTTT
1448156 TAAAGCCCACAACTCCGTGGCAC-C-----
63 T-AAGCCCACAACTCCGTGGCACTCTTTTT
*
1448180 CTTTTAAGTCCACAACTCCGTGGCATCTTTTTCCTTTTATGTCCACAACTCCGTGGCA----CCC
1 CTTTTAAGTCCACAACTCCGTGGCA-C-----CCTTTTAAGTCCACAACTCCGTGGCACCTTCCC
* * *
1448241 TTTGAAGCCCACAACTCTGTGGCATTCTTTTTT
60 TTTTAAGCCCACAACTCCGTGGCACTC-TTTTT
* **
1448274 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTGAAG-CTCACAACTCCGTGGCACTCTTTTTTCT
1 -CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC-CACAACTCCGTGGCAC-C--TTCCCT
* * * *
1448338 TTTAAGCCCACACCTCTGCGGCATCCCTTTTT
61 TTTAAGCCCACAACTCCGTGGCA-CTCTTTTT
*
1448370 CCTTTAAGTCCACAACTCCGTGGCA
1 CTTTTAAGTCCACAACTCCGTGGCA
1448395 TCTTTAAAAC
Statistics
Matches: 317, Mismatches: 35, Indels: 83
0.73 0.08 0.19
Matches are distributed among these distances:
86 2 0.01
87 71 0.22
88 23 0.07
89 45 0.14
90 1 0.00
92 1 0.00
93 46 0.15
94 18 0.06
95 82 0.26
96 27 0.09
97 1 0.00
ACGTcount: A:0.20, C:0.33, G:0.14, T:0.33
Consensus pattern (91 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTCCCTTTTAA
GCCCACAACTCCGTGGCACTCTTTTT
Found at i:1448272 original size:243 final size:243
Alignment explanation
Indices: 1447755--1448368 Score: 1018
Period size: 243 Copynumber: 2.5 Consensus size: 243
1447745 TCATGTCATG
* *
1447755 CTTTTAAGTCCACAACT-TCGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTT
1 CTTTGAAGCCCACAACTCT-GTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTT
* *
1447819 GAAGCCCATAACTCCATGGCACTCTTTTTCTTTTAAGTCTATAACTCTGTGGCACCCTTTTAAAT
65 GAAGCCTATAACTCCATGGCACTCTTTTTCTTTTAAGTCTACAACTCTGTGGCACCCTTTTAAAT
*
1447884 CCACAAGCTCTGTGGCACTTTTGCCCCTTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCC
130 CCACAAGCTCTGTGGCACTCTTGCCCCTTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCC
*
1447949 ACAACTCCATGGCATCTTTTTCCTTTTATGTCCACAACTCTGTGGCACC
195 ACAACTCCATGGCATCTTTTTCCTTTTATGTCCACAACTCCGTGGCACC
*
1447998 CTTTGAAGCCAACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTG
1 CTTTGAAGCCCACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTG
*
1448063 AAGCCTATAACTCCATGGCACTCTTTTTCTTTTAAGTCTACAACTCTGTGGCACCCTTTTAAGTC
66 AAGCCTATAACTCCATGGCACTCTTTTTCTTTTAAGTCTACAACTCTGTGGCACCCTTTTAAATC
1448128 CACAAGCTCTGTGGCAC-CTTGCCCCTTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCCA
131 CACAAGCTCTGTGGCACTCTTGCCCCTTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCCA
*
1448192 CAACTCCGTGGCATCTTTTTCCTTTTATGTCCACAACTCCGTGGCACC
196 CAACTCCATGGCATCTTTTTCCTTTTATGTCCACAACTCCGTGGCACC
1448240 CTTTGAAGCCCACAACTCTGTGGCATTCTTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTT
1 CTTTGAAGCCCACAACTCTGTGGCA-TC-TTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTT
* * * * * *
1448305 TGAAG-CTCACAACTCCGTGGCACTCTTTTTTCTTTTAAGCCCACACCTCTGCGGCATCCCTTTT
64 TGAAGCCT-ATAACTCCATGGCACTC-TTTTTCTTTTAAGTCTACAACTCTGTGGCA-CCCTTTT
1448369 TCCTTTAAGT
Statistics
Matches: 349, Mismatches: 16, Indels: 9
0.93 0.04 0.02
Matches are distributed among these distances:
242 116 0.33
243 143 0.41
244 57 0.16
245 26 0.07
246 7 0.02
ACGTcount: A:0.20, C:0.32, G:0.14, T:0.34
Consensus pattern (243 bp):
CTTTGAAGCCCACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTG
AAGCCTATAACTCCATGGCACTCTTTTTCTTTTAAGTCTACAACTCTGTGGCACCCTTTTAAATC
CACAAGCTCTGTGGCACTCTTGCCCCTTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCCA
CAACTCCATGGCATCTTTTTCCTTTTATGTCCACAACTCCGTGGCACC
Found at i:1448288 original size:35 final size:34
Alignment explanation
Indices: 1448239--1448399 Score: 142
Period size: 34 Copynumber: 4.9 Consensus size: 34
1448229 TCCGTGGCAC
* *
1448239 CCTTTGAAGCCCACAACTCTGTGGCATTCTTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCA-TCTTTTTT
*
1448274 CCTTTTAAGTCCACAACTCCGTGGCA-C------
1 CCTTTTAAGCCCACAACTCCGTGGCATCTTTTTT
* *
1448301 CCTTTGAAGCTCACAACTCCGTGGCACTCTTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCA-TCTTTTTT
* * * *
1448336 -CTTTTAAGCCCACACCTCTGCGGCATCCCTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCAT-CTTTTTT
*
1448370 CC-TTTAAGTCCACAACTCCGTGGCATCTTT
1 CCTTTTAAGCCCACAACTCCGTGGCATCTTT
1448400 AAAACCAATG
Statistics
Matches: 99, Mismatches: 17, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
27 23 0.23
29 1 0.01
33 5 0.05
34 46 0.46
35 24 0.24
ACGTcount: A:0.18, C:0.34, G:0.14, T:0.35
Consensus pattern (34 bp):
CCTTTTAAGCCCACAACTCCGTGGCATCTTTTTT
Found at i:1448555 original size:39 final size:39
Alignment explanation
Indices: 1448501--1448831 Score: 239
Period size: 39 Copynumber: 7.8 Consensus size: 39
1448491 GTCTTTAAGA
* *
1448501 CCAATGTCGCTGGCCTTGAATCAGCACATTATCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGTCACAAGC
* *
1448540 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGA
1 CCAATATCGCTGGCCTTGAATCAGC--A----CA--TTGTCAC-AAGC
* *
1448588 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGTCACAAGC
* *
1448627 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGA
1 CCAATATCGCTGGCCTTGAATCAGC--A----CA--TTGTCAC-AAGC
* *
1448675 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGTCACAAGC
* *
1448714 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGA
1 CCAATATCGCTGGCCTTGAATCAGC--A----CA--TTGTCAC-AAGC
** * * *
1448762 TTAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGTCACAAGC
* * *
1448801 CCAATATCGCTGGCCTTTAATTAGCATATTG
1 CCAATATCGCTGGCCTTGAATCAGCACATTG
1448832 GCACCTTGTC
Statistics
Matches: 232, Mismatches: 33, Indels: 54
0.73 0.10 0.17
Matches are distributed among these distances:
39 106 0.46
40 14 0.06
41 3 0.01
42 6 0.03
45 6 0.03
46 3 0.01
47 15 0.06
48 79 0.34
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (39 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGTCACAAGC
Found at i:1448599 original size:87 final size:87
Alignment explanation
Indices: 1448453--1448883 Score: 763
Period size: 87 Copynumber: 5.0 Consensus size: 87
1448443 ATCTTTAAGA
* *
1448453 CCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTGGCCTT
**
1448518 GAATCAGCACATTATCACAAGC
66 GAATCAGCACATTGGCACAAGC
1448540 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTGGCCTT
1448605 GAATCAGCACATTGGCACAAGC
66 GAATCAGCACATTGGCACAAGC
1448627 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTGGCCTT
1448692 GAATCAGCACATTGGCACAAGC
66 GAATCAGCACATTGGCACAAGC
**
1448714 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGATTAATGTCGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTGGCCTT
*
1448779 GAATCAGCACATTGGCATAAGC
66 GAATCAGCACATTGGCACAAGC
* * **
1448801 CCAATATCGCTGGCCTTTAATTAGCATATTGGCACCTTGTCTCTGTGACCAATGTCGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTGGCCTT
1448866 GAATCAGCACATTGGCAC
66 GAATCAGCACATTGGCAC
1448884 CTTCATCTTT
Statistics
Matches: 330, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 330 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (87 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTGGCCTT
GAATCAGCACATTGGCACAAGC
Found at i:1448962 original size:52 final size:49
Alignment explanation
Indices: 1448801--1449028 Score: 199
Period size: 49 Copynumber: 4.6 Consensus size: 49
1448791 TGGCATAAGC
* * * * * * ***
1448801 CCAATATCGCTGGCCTTTAATTAGCATATTGGCACCTT-GTCTCTGTGA
1 CCAATGTCACTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAAA
* * **
1448849 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
1 CCAATGTCACTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAAA
* *
1448898 CCAATATCACTGGCCTTGAATCAACATATTGGCGA-CTTCGTTATCTTTAAAA
1 CCAATGTCACTGGCCTTGAATCAGCATATTGGC-ACCTTC---ATCTTTAAAA
* * **
1448950 CCAATGTCACTGGCCTTGAATCAGTATATTGGCACCTTCATCCTTAAGT
1 CCAATGTCACTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAAA
* ** *
1448999 CCAATATCGTTGGCCTTGAATCAGCGTATT
1 CCAATGTCACTGGCCTTGAATCAGCATATT
1449029 AGCATCTTTA
Statistics
Matches: 148, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
48 34 0.23
49 70 0.47
50 1 0.01
51 1 0.01
52 42 0.28
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (49 bp):
CCAATGTCACTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAAA
Found at i:1449065 original size:101 final size:100
Alignment explanation
Indices: 1448848--1449123 Score: 274
Period size: 101 Copynumber: 2.8 Consensus size: 100
1448838 TGTCTCTGTG
*
1448848 ACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCACTGGCC
1 ACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCCTTAAGTCCAATATCACTGGCC
* *
1448913 TTGAATCAACATATTGGCGACTTCGTTATCTTTAAA
66 TTGAATCAACATATTAGCGAC-TCGTTAACTTTAAA
* * * **
1448949 ACCAATGTCACTGGCCTTGAATCAGTATATTGGCACCTTCATCCTTAAGTCCAATATCGTTGGCC
1 ACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCCTTAAGTCCAATATCACTGGCC
* * * *
1449014 TTGAATCAGCGTATTAGC-A-TCTTTAACATTCCTAAG
66 TTGAATCAACATATTAGCGACTCGTTAAC-TT--TAAA
* * * ** * * * *
1449050 CCCAATGTTGTTGGCCTTGTCTCAGCACATTGGCA--TTC-TTCTTCAAGTCTAATGTCGCTGGC
1 ACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCCTT-AAGTCCAATATCACTGGC
*
1449112 CATGAATCAACA
65 CTTGAATCAACA
1449124 CATTGTCATT
Statistics
Matches: 144, Mismatches: 27, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
98 10 0.07
99 29 0.20
100 1 0.01
101 104 0.72
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (100 bp):
ACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCCTTAAGTCCAATATCACTGGCC
TTGAATCAACATATTAGCGACTCGTTAACTTTAAA
Found at i:1453537 original size:16 final size:15
Alignment explanation
Indices: 1453507--1453540 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1453497 GATGAAAAGA
1453507 ATTTTTTATTATTTT
1 ATTTTTTATTATTTT
*
1453522 ATTTTGTTATTTTTTT
1 ATTTT-TTATTATTTT
1453538 ATT
1 ATT
1453541 ATATTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (15 bp):
ATTTTTTATTATTTT
Found at i:1454459 original size:21 final size:22
Alignment explanation
Indices: 1454434--1454498 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 22
1454424 AGAGGCTCGA
* *
1454434 GCTGCTACCGTGTTTGTGGATGCT
1 GCTGCTACCATGTTCGTGGA--CT
1454458 GCTGCTACCATGTTCGTGGA-T
1 GCTGCTACCATGTTCGTGGACT
* * *
1454479 GCTGCTGCTATGTTCATGGA
1 GCTGCTACCATGTTCGTGGA
1454499 AGCTGGAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 18 0.50
24 18 0.50
ACGTcount: A:0.12, C:0.22, G:0.31, T:0.35
Consensus pattern (22 bp):
GCTGCTACCATGTTCGTGGACT
Found at i:1454463 original size:24 final size:24
Alignment explanation
Indices: 1454434--1454488 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
1454424 AGAGGCTCGA
* *
1454434 GCTGCTACCGTGTTTGTGGATGCT
1 GCTGCTACCATGTTCGTGGATGCT
1454458 GCTGCTACCATGTTCGTGGATGCT
1 GCTGCTACCATGTTCGTGGATGCT
1454482 GCTGCTA
1 GCTGCTA
1454489 TGTTCATGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.11, C:0.24, G:0.31, T:0.35
Consensus pattern (24 bp):
GCTGCTACCATGTTCGTGGATGCT
Found at i:1454503 original size:21 final size:21
Alignment explanation
Indices: 1454458--1454503 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1454448 TGTGGATGCT
* *
1454458 GCTGCTACCATGTTCGTGGAT
1 GCTGCTACCATGTTCATGGAA
* *
1454479 GCTGCTGCTATGTTCATGGAA
1 GCTGCTACCATGTTCATGGAA
1454500 GCTG
1 GCTG
1454504 GAAGAGGCTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.15, C:0.22, G:0.30, T:0.33
Consensus pattern (21 bp):
GCTGCTACCATGTTCATGGAA
Found at i:1454566 original size:31 final size:31
Alignment explanation
Indices: 1454493--1454582 Score: 110
Period size: 31 Copynumber: 2.9 Consensus size: 31
1454483 CTGCTATGTT
* * *
1454493 CATGGAAGCTGGAAGAGGCTCGAGC-ATTTC
1 CATGGAAGCTGGAAGAAGCTCGAGCTACTGC
* *
1454523 CGTGGAAGCTGGAAGAAGCTCGAGCTACTGG
1 CATGGAAGCTGGAAGAAGCTCGAGCTACTGC
* *
1454554 CATGAAAGCTGGAAGTAGCTCGAGCTACT
1 CATGGAAGCTGGAAGAAGCTCGAGCTACT
1454583 AGTTTCAGGT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 23 0.45
31 28 0.55
ACGTcount: A:0.28, C:0.20, G:0.33, T:0.19
Consensus pattern (31 bp):
CATGGAAGCTGGAAGAAGCTCGAGCTACTGC
Found at i:1457861 original size:20 final size:20
Alignment explanation
Indices: 1457806--1457861 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1457796 AAATTCCCCA
**
1457806 AATGTATCGATACAAAGATC
1 AATGTATCGATACATTGATC
*
1457826 AATGTATCGATTCATTGAAT-
1 AATGTATCGATACATTG-ATC
1457846 AATGTATCGATACATT
1 AATGTATCGATACATT
1457862 TTCTCGGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACATTGATC
Found at i:1457901 original size:13 final size:13
Alignment explanation
Indices: 1457883--1457934 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
1457873 AGCTTCGTAG
1457883 CGATACATTGTAT
1 CGATACATTGTAT
1457896 CGATACAACACTTATGTAT
1 CGAT---ACA-TT--GTAT
1457915 CGATACATTGTAT
1 CGATACATTGTAT
1457928 CGATACA
1 CGATACA
1457935 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 15 0.45
15 2 0.06
16 6 0.18
17 2 0.06
19 8 0.24
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1457915 original size:19 final size:19
Alignment explanation
Indices: 1457891--1457953 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
1457881 AGCGATACAT
1457891 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1457910 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1457923 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1457942 TGTATCGATACA
1 TGTATCGATACA
1457954 GTTACTGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 6 0.16
18 1 0.03
19 21 0.55
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1457924 original size:32 final size:32
Alignment explanation
Indices: 1457883--1457953 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
1457873 AGCTTCGTAG
1457883 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1457915 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1457947 CGATACA
1 CGATACA
1457954 GTTACTGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:1458816 original size:34 final size:35
Alignment explanation
Indices: 1458778--1458844 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1458768 CCTTACAACA
1458778 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1458812 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1458845 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:1459320 original size:13 final size:13
Alignment explanation
Indices: 1459302--1459327 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1459292 CAATTTTTTG
1459302 TGTATCGATACAT
1 TGTATCGATACAT
1459315 TGTATCGATACAT
1 TGTATCGATACAT
1459328 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1459392 original size:21 final size:21
Alignment explanation
Indices: 1459366--1459441 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1459356 CTGCCAAGAA
*
1459366 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1459387 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1459407 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1459428 ATGTATCGATACAT
1 ATGTATCGATACAT
1459442 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1459412 original size:20 final size:20
Alignment explanation
Indices: 1459387--1459459 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1459377 CATCTTTTTT
1459387 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1459407 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1459428 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1459448 ATGTATCGATAC
1 ATGTATCGATAC
1459460 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1459423 original size:41 final size:41
Alignment explanation
Indices: 1459366--1459459 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1459356 CTGCCAAGAA
*
1459366 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1459407 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1459448 ATGTATCGATAC
1 ATGTATCGATAC
1459460 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1460119 original size:21 final size:21
Alignment explanation
Indices: 1460095--1460136 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1460085 ATCTCCCCCT
1460095 TAATCAAGTAATTCACAACAA
1 TAATCAAGTAATTCACAACAA
1460116 TAATCAAGTAATTCACAACAA
1 TAATCAAGTAATTCACAACAA
1460137 AAATTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.19, G:0.05, T:0.24
Consensus pattern (21 bp):
TAATCAAGTAATTCACAACAA
Found at i:1461285 original size:13 final size:13
Alignment explanation
Indices: 1461267--1461291 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1461257 ACTGAAGCAA
1461267 TGTATCGATACAT
1 TGTATCGATACAT
1461280 TGTATCGATACA
1 TGTATCGATACA
1461292 ATTTGGAAAA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1461898 original size:23 final size:24
Alignment explanation
Indices: 1461853--1461899 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1461843 CAAAGAATTG
*
1461853 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
1461877 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
1461900 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:1462938 original size:84 final size:84
Alignment explanation
Indices: 1462783--1462942 Score: 200
Period size: 84 Copynumber: 1.9 Consensus size: 84
1462773 CATTTTCCAC
* * * * *
1462783 TTGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTCTTTTTAGAAGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTACAAGAATTATTCTCTAAAC
1462848 TCATTGATTTACATTCATT
66 TCATTGATTTACATTCATT
*
1462867 TTGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCTA
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTCTTTTTACAAGAAT-T-ATTCTCTA
* *
1462929 TACTTATTGATTTA
63 AACTCATTGATTTA
1462943 TTTTCTTCTT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
82 6 0.09
83 9 0.14
84 50 0.77
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.51
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTACAAGAATTATTCTCTAAAC
TCATTGATTTACATTCATT
Found at i:1464511 original size:34 final size:35
Alignment explanation
Indices: 1464473--1464539 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1464463 CCTTACAACA
1464473 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1464507 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1464540 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:1465011 original size:13 final size:13
Alignment explanation
Indices: 1464993--1465018 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1464983 CAATTTTTTG
1464993 TGTATCGATACAT
1 TGTATCGATACAT
1465006 TGTATCGATACAT
1 TGTATCGATACAT
1465019 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1465083 original size:21 final size:21
Alignment explanation
Indices: 1465057--1465132 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1465047 CTGCCAAGAA
*
1465057 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1465078 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1465098 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1465119 ATGTATCGATACAT
1 ATGTATCGATACAT
1465133 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1465103 original size:20 final size:20
Alignment explanation
Indices: 1465078--1465150 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1465068 CATCTTTTTT
1465078 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1465098 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1465119 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1465139 ATGTATCGATAC
1 ATGTATCGATAC
1465151 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1465114 original size:41 final size:41
Alignment explanation
Indices: 1465057--1465150 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1465047 CTGCCAAGAA
*
1465057 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1465098 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1465139 ATGTATCGATAC
1 ATGTATCGATAC
1465151 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1465967 original size:101 final size:98
Alignment explanation
Indices: 1465722--1466232 Score: 557
Period size: 101 Copynumber: 5.4 Consensus size: 98
1465712 ATATTAAAGA
* * * * *
1465722 TGCCAATACGCTGATTCAAGGCCAACAATATTGGACTTAAGGATGAAGGTGCTAATGTGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATT
* * *
1465787 TAAGGCCAGCAACATTGGT-TTTAAAGACAAAG
66 TAAGGCCAGCGACATTGGTCTTAAAAGACAAGG
**
1465819 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTTTTAAAGATGAAGGTGCCAATGTGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATT
*
1465884 TAAGGCCAGTGACATTGGTCTTAAAGATGACGAAGG
66 TAAGGCCAGCGACATTGGTCTTAAA-A-GAC-AAGG
* *
1465920 TGCCAATATGCTGATTCAAGGCTAGCGATATTGAACTTAAAGATGAAGGTGCCAATGTGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATT
* * *
1465985 CAAGGTCAGCGACATTGGACTTAAATATGACAAAGG
66 TAAGGCCAGCGACATTGGTCTTAAA-A-GAC-AAGG
*
1466021 CT-CCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T----GTGCCAATGTGCTAAT
1 -TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAT
*
1466075 TTAAGGCGAGCGACATTGGTCTT-AAAGACAAGG
65 TTAAGGCCAGCGACATTGGTCTTAAAAGACAAGG
* * *
1466108 TGTCAATAAGCTGATTCAAGGCCAGCGATATTGGGC-T-----T--A--TGCCAATGTGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATT
* *
1466163 CAAGGCCAACGACATTGGTCTT-AAAGACAAGG
66 TAAGGCCAGCGACATTGGTCTTAAAAGACAAGG
* * *
1466195 TGCCAATATGTTGATTAAAGGCCAACGATATTGGACTT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1466233 TGAAGAAGAC
Statistics
Matches: 365, Mismatches: 41, Indels: 25
0.85 0.10 0.06
Matches are distributed among these distances:
86 1 0.00
87 111 0.30
88 4 0.01
89 1 0.00
90 2 0.01
91 34 0.09
95 1 0.00
97 75 0.21
98 4 0.01
99 1 0.00
100 4 0.01
101 126 0.35
102 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (98 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATT
TAAGGCCAGCGACATTGGTCTTAAAAGACAAGG
Found at i:1466055 original size:52 final size:49
Alignment explanation
Indices: 1465722--1466232 Score: 395
Period size: 49 Copynumber: 10.8 Consensus size: 49
1465712 ATATTAAAGA
* * * *
1465722 TGCCAATACGCTGATTCAAGGCCAACAATATTGGACTTAAGGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * * ** * *
1465771 TGCTAATGTGCTGATTTAAGGCCAGCAACATTGGTTTTAAAGA-CAAAG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
**
1465819 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTTTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * *
1465868 TGCCAATGTGCTGATTTAAGGCCAGTGACATTGGTCTTAAAGATGACGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT---GAAGG
* *
1465920 TGCCAATATGCTGATTCAAGGCTAGCGATATTGAACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * *
1465969 TGCCAATGTGCTGATTCAAGGTCAGCGACATTGGACTTAAATATGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGG
1466021 CT-CCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T----G
1 -TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * * * *
1466060 TGCCAATGTGCTAATTTAAGGCGAGCGACATTGGTCTTAAAGA-CAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * *
1466108 TGTCAATAAGCTGATTCAAGGCCAGCGATATTGGGC-T-----T--A--
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * *
1466147 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGA-CAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * *
1466195 TGCCAATATGTTGATTAAAGGCCAACGATATTGGACTT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1466233 TGAAGAAGAC
Statistics
Matches: 368, Mismatches: 64, Indels: 61
0.75 0.13 0.12
Matches are distributed among these distances:
38 1 0.00
39 59 0.16
40 2 0.01
41 1 0.00
46 2 0.01
47 1 0.00
48 103 0.28
49 120 0.33
51 1 0.00
52 77 0.21
53 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
Found at i:1466141 original size:87 final size:86
Alignment explanation
Indices: 1465968--1466232 Score: 352
Period size: 87 Copynumber: 3.0 Consensus size: 86
1465958 AAAGATGAAG
*
1465968 GTGCCAATGTGCTGATTCAAGGTCAGCGACATTGGACTTAAATATGACAAAGGCT-CCAATATGC
1 GTGCCAATGTGCTGATTCAAGG-CAGCGACATTGGTCTT-AA-A-GAC-AAGG-TGCCAATATGC
1466032 TGATTCAAGGCCAGCGATATTGGACTT
60 TGATTCAAGGCCAGCGATATTGGACTT
* * * *
1466059 GTGCCAATGTGCTAATTTAAGGCGAGCGACATTGGTCTTAAAGACAAGGTGTCAATAAGCTGATT
1 GTGCCAATGTGCTGATTCAAGGC-AGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
*
1466124 CAAGGCCAGCGATATTGGGCTT
65 CAAGGCCAGCGATATTGGACTT
* * *
1466146 ATGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAATATGTTGATT
1 GTGCCAATGTGCTGATTCAAGG-CAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
* *
1466211 AAAGGCCAACGATATTGGACTT
65 CAAGGCCAGCGATATTGGACTT
1466233 TGAAGAAGAC
Statistics
Matches: 155, Mismatches: 16, Indels: 10
0.86 0.09 0.06
Matches are distributed among these distances:
86 1 0.01
87 112 0.72
88 4 0.03
89 1 0.01
90 3 0.02
91 34 0.22
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (86 bp):
GTGCCAATGTGCTGATTCAAGGCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
AAGGCCAGCGATATTGGACTT
Found at i:1466380 original size:34 final size:32
Alignment explanation
Indices: 1466342--1466422 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 32
1466332 GCCACCAACT
1466342 TGTGGGCTTACAGGAAA-AAAAGATGCCACAGATG
1 TGTGGGCTTA-A--AAAGAAAAGATGCCACAGATG
*
1466376 TGTGGGCTTAAAAAGAAAAGGTGCCACAGA-G
1 TGTGGGCTTAAAAAGAAAAGATGCCACAGATG
*
1466407 TTGTGGACTTAAAAAG
1 -TGTGGGCTTAAAAAG
1466423 GTGCCACGGA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
31 4 0.09
32 28 0.65
33 1 0.02
34 10 0.23
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.20
Consensus pattern (32 bp):
TGTGGGCTTAAAAAGAAAAGATGCCACAGATG
Found at i:1466401 original size:32 final size:32
Alignment explanation
Indices: 1466341--1466555 Score: 141
Period size: 27 Copynumber: 6.8 Consensus size: 32
1466331 TGCCACCAAC
1466341 TTGTGGGCTTACAGGAAA-AAAAGATGCCACAGA-
1 TTGTGGGCTTA-A--AAAGAAAAGATGCCACAGAG
*
1466374 TGTGTGGGCTTAAAAAGAAAAGGTGCCACAGAG
1 T-TGTGGGCTTAAAAAGAAAAGATGCCACAGAG
* *
1466407 TTGTGGACTTAAAAAG----G-TGCCACGGAG
1 TTGTGGGCTTAAAAAGAAAAGATGCCACAGAG
* * *
1466434 TTGTGGACTTAAAGGAATAAAAG-TGCCACGGAG
1 TTGTGGGCTTAAA--AAGAAAAGATGCCACAGAG
* *
1466467 TTGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAG
1 TTGTGGGCTTAAAAAG-AAAAGA-TGCCACAGAG
* **
1466501 TTGTGGACTT-AAAAG---AG-TGCCATGGAG
1 TTGTGGGCTTAAAAAGAAAAGATGCCACAGAG
* *
1466528 TTGTGGACTTAAAAGGAAAAAGATGCCA
1 TTGTGGGCTTAAAAAG-AAAAGATGCCA
1466556 TGGACTTGTG
Statistics
Matches: 153, Mismatches: 11, Indels: 36
0.76 0.05 0.18
Matches are distributed among these distances:
27 41 0.27
28 5 0.03
29 4 0.03
31 4 0.03
32 35 0.23
33 35 0.23
34 29 0.19
ACGTcount: A:0.36, C:0.13, G:0.31, T:0.20
Consensus pattern (32 bp):
TTGTGGGCTTAAAAAGAAAAGATGCCACAGAG
Found at i:1466460 original size:33 final size:32
Alignment explanation
Indices: 1466341--1466565 Score: 163
Period size: 33 Copynumber: 7.2 Consensus size: 32
1466331 TGCCACCAAC
* * *
1466341 TTGTGGGCTTACAGGAAAAAAAGATGCCACAGA-
1 TTGTGGACTTAAAGG-AAAAAAG-TGCCACGGAG
* *
1466374 TGTGTGGGCTTAAA--AAGAAAAGGTGCCACAGAG
1 T-TGTGGACTTAAAGGAA-AAAA-GTGCCACGGAG
*
1466407 TTGTGGACTT-----AAAAAGGTGCCACGGAG
1 TTGTGGACTTAAAGGAAAAAAGTGCCACGGAG
1466434 TTGTGGACTTAAAGGAATAAAAGTGCCACGGAG
1 TTGTGGACTTAAAGGAA-AAAAGTGCCACGGAG
*
1466467 TTGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAG
1 TTGTGGACTT-AAAGGAAAAA-AGTGCCACGGAG
* *
1466501 TTGTGGACTT-----AAAAGAGTGCCATGGAG
1 TTGTGGACTTAAAGGAAAAAAGTGCCACGGAG
* *
1466528 TTGTGGACTTAAAAGG-AAAAAGATGCCATGGAC
1 TTGTGGACTT-AAAGGAAAAAAG-TGCCACGGAG
1466561 TTGTG
1 TTGTG
1466566 TGCTTTTGAA
Statistics
Matches: 162, Mismatches: 11, Indels: 38
0.77 0.05 0.18
Matches are distributed among these distances:
27 41 0.25
28 7 0.04
29 2 0.01
31 2 0.01
32 28 0.17
33 43 0.27
34 39 0.24
ACGTcount: A:0.35, C:0.12, G:0.32, T:0.21
Consensus pattern (32 bp):
TTGTGGACTTAAAGGAAAAAAGTGCCACGGAG
Found at i:1466482 original size:34 final size:33
Alignment explanation
Indices: 1466417--1466565 Score: 170
Period size: 33 Copynumber: 4.7 Consensus size: 33
1466407 TTGTGGACTT
*
1466417 AAAAAGGTGCCACGGAGTTGTGGACTT-AAAGG
1 AAAAAAGTGCCACGGAGTTGTGGACTTAAAAGG
*
1466449 AATAAAAGTGCCACGGAGTTGTGGGCTTAAAAGG
1 AA-AAAAGTGCCACGGAGTTGTGGACTTAAAAGG
1466483 AAAAAGAGTGCCACGGAGTTGTGGACTTAAAA-G
1 AAAAA-AGTGCCACGGAGTTGTGGACTTAAAAGG
*
1466516 -----AGTGCCATGGAGTTGTGGACTTAAAAGG
1 AAAAAAGTGCCACGGAGTTGTGGACTTAAAAGG
* *
1466544 -AAAAAGATGCCATGGACTTGTG
1 AAAAAAG-TGCCACGGAGTTGTG
1466566 TGCTTTTGAA
Statistics
Matches: 103, Mismatches: 5, Indels: 17
0.82 0.04 0.14
Matches are distributed among these distances:
27 25 0.24
28 1 0.01
32 4 0.04
33 41 0.40
34 32 0.31
ACGTcount: A:0.35, C:0.12, G:0.32, T:0.21
Consensus pattern (33 bp):
AAAAAAGTGCCACGGAGTTGTGGACTTAAAAGG
Found at i:1466522 original size:94 final size:91
Alignment explanation
Indices: 1466341--1466570 Score: 286
Period size: 94 Copynumber: 2.5 Consensus size: 91
1466331 TGCCACCAAC
* * *
1466341 TTGTGGGCTTACAGGAAAAAAAGATGCCACAGATGTGTGGGCTTAAAAAGAAAAGGTGCCACAGA
1 TTGTGGACTTAAAGG-AAAAAAGATGCCACGGAT-TGTGGGCTTAAAAAGAAAAGGTGCCACAGA
1466406 GTTGTGGACTTAAAAAGGTGCCACGGAG
64 GTTGTGGACTTAAAAAGGTGCCACGGAG
* *
1466434 TTGTGGACTTAAAGGAATAAAAG-TGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACG
1 TTGTGGACTTAAAGGAA-AAAAGATGCCACGGA-TTGTGGGCTTAAAAAG-AAAAG-GTGCCACA
*
1466498 GAGTTGTGGACTT-AAAAGAGTGCCATGGAG
62 GAGTTGTGGACTTAAAAAG-GTGCCACGGAG
* *
1466528 TTGTGGACTTAAAAGG-AAAAAGATGCCATGGACTTGTGTGCTT
1 TTGTGGACTT-AAAGGAAAAAAGATGCCACGGA-TTGTGGGCTT
1466571 TTGAAGGTTG
Statistics
Matches: 121, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
92 24 0.20
93 34 0.28
94 58 0.48
95 5 0.04
ACGTcount: A:0.34, C:0.13, G:0.31, T:0.22
Consensus pattern (91 bp):
TTGTGGACTTAAAGGAAAAAAGATGCCACGGATTGTGGGCTTAAAAAGAAAAGGTGCCACAGAGT
TGTGGACTTAAAAAGGTGCCACGGAG
Done.