Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold139
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: 1720190
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 4798 characters in sequence are not A, C, G, or T
File 9 of 11
Found at i:1265771 original size:28 final size:28
Alignment explanation
Indices: 1265702--1266248 Score: 380
Period size: 28 Copynumber: 19.4 Consensus size: 28
1265692 CATCAACTTG
* * * *
1265702 TGTGGGCTTTGAAAGGATACCACTAAC-
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* * *
1265729 TATGGGCTTTGAAAAGATGCCACTAACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* * *
1265757 TGTGGGTTTTAAAAAGATACTACTGACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* *
1265785 TGTGGGCTTTGAAAAAG-TGCCATTAACT
1 TGTGGGCTTT-AAAAAGATGCCACTGACT
* * * *
1265813 TGTGGGCTTTGAAAAGGGTTGTCTCTGACT
1 TGTGGGCTTT-AAAA-AGATGCCACTGACT
* * *
1265843 TATGGGCTTTGAAAAGATGCCACTAACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* *
1265871 TGTGGGCTTTGAGAAAG-TGTCACTGACT
1 TGTGGGCTTT-AAAAAGATGCCACTGACT
** ** **
1265899 TGTAAGCTTCGAAAAGGCGCCACTGACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* *
1265927 TGTGGGCTTTGAAAAGGGTTGCCACTGACT
1 TGTGGGCTTT-AAAA-AGATGCCACTGACT
* ** * * * *
1265957 TATGGGCTTCGAAAGGAAGCCATTAACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* ** * * * *
1265985 TATGGGCTTCGAAAGGAAGCCATTAACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* * *
1266013 TATGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* * *
1266041 TGTGGGCTTTAAAAGGGTGCCACTAACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* * *
1266069 TATGAGCTTTAAAAAGATGCCATTGACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
** *
1266097 TGTGGGCTTTAAATGGGTGCCACTGACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
*
1266125 TGTGGGCTTTAAAAAGATACCACTGACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* * * * * *
1266153 TGTAGGTTTTGAAAAGGTGCCATTAACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
* * *
1266181 TATGGGCTTTGAAAAGGTGCCACTGACT
1 TGTGGGCTTTAAAAAGATGCCACTGACT
** * *
1266209 TGTGGGCTTTGAGAAGGGTTGCCACTGATT
1 TGTGGGCTTT-A-AAAAGATGCCACTGACT
1266239 TGTGGGCTTT
1 TGTGGGCTTT
1266249 GAAAGGATTG
Statistics
Matches: 416, Mismatches: 94, Indels: 17
0.79 0.18 0.03
Matches are distributed among these distances:
27 28 0.07
28 310 0.75
29 20 0.05
30 58 0.14
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTAAAAAGATGCCACTGACT
Found at i:1265799 original size:56 final size:56
Alignment explanation
Indices: 1265702--1266252 Score: 455
Period size: 56 Copynumber: 9.8 Consensus size: 56
1265692 CATCAACTTG
* * * * * *
1265702 TGTGGGCTTTGAAAGGATACCACTAAC-TATGGGCTTTGAAAAGATGCCACTAACT
1 TGTGGGTTTTAAAAGGGTGCCACTGACTTATGGGCTTTGAAAAGATGCCACTGACT
* * * * * * *
1265757 TGTGGGTTTTAAAAAGATACTACTGACTTGTGGGCTTTGAAAA-AGTGCCATTAACT
1 TGTGGGTTTTAAAAGGGTGCCACTGACTTATGGGCTTTGAAAAGA-TGCCACTGACT
* * * *
1265813 TGTGGGCTTTGAAAAGGGTTGTCTCTGACTTATGGGCTTTGAAAAGATGCCACTAACT
1 TGTGGG-TTTTAAAAGGG-TGCCACTGACTTATGGGCTTTGAAAAGATGCCACTGACT
* * * ** * **
1265871 TGTGGGCTTTGAGAAA--GTGTCACTGACTTGTAAGCTTCGAAAAGGCGCCACTGACT
1 TGTGGG-TTTTA-AAAGGGTGCCACTGACTTATGGGCTTTGAAAAGATGCCACTGACT
* * * * * *
1265927 TGTGGGCTTTGAAAAGGGTTGCCACTGACTTATGGGCTTCGAAAGGAAGCCATTAACT
1 TGTGGG-TTTTAAAAGGG-TGCCACTGACTTATGGGCTTTGAAAAGATGCCACTGACT
* * ** ** * * *
1265985 TATGGGCTTCGAAAGGAAGCCATTAACTTATGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGTTTTAAAAGGGTGCCACTGACTTATGGGCTTTGAAAAGATGCCACTGACT
* * * * *
1266041 TGTGGGCTTTAAAAGGGTGCCACTAACTTATGAGCTTTAAAAAGATGCCATTGACT
1 TGTGGGTTTTAAAAGGGTGCCACTGACTTATGGGCTTTGAAAAGATGCCACTGACT
* * * * *
1266097 TGTGGGCTTTAAATGGGTGCCACTGACTTGTGGGCTTTAAAAAGATACCACTGACT
1 TGTGGGTTTTAAAAGGGTGCCACTGACTTATGGGCTTTGAAAAGATGCCACTGACT
* * * *
1266153 TGTAGGTTTTGAAAA-GGTGCCATTAACTTATGGGCTTTGAAAAGGTGCCACTGACT
1 TGTGGGTTTT-AAAAGGGTGCCACTGACTTATGGGCTTTGAAAAGATGCCACTGACT
* * * *
1266209 TGTGGGCTTTGAGAAGGGTTGCCACTGATTTGTGGGCTTTGAAA
1 TGTGGG-TTTTAAAAGGG-TGCCACTGACTTATGGGCTTTGAAA
1266253 GGATTGTGGG
Statistics
Matches: 406, Mismatches: 77, Indels: 23
0.80 0.15 0.05
Matches are distributed among these distances:
55 26 0.06
56 252 0.62
57 25 0.06
58 99 0.24
59 4 0.01
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (56 bp):
TGTGGGTTTTAAAAGGGTGCCACTGACTTATGGGCTTTGAAAAGATGCCACTGACT
Found at i:1268057 original size:18 final size:18
Alignment explanation
Indices: 1268034--1268070 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1268024 AAGAGAAAGG
1268034 ATCCCAACTTCAATTGGC
1 ATCCCAACTTCAATTGGC
1268052 ATCCCAACTTCAATTGGC
1 ATCCCAACTTCAATTGGC
1268070 A
1 A
1268071 ATACGACTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.32, G:0.11, T:0.27
Consensus pattern (18 bp):
ATCCCAACTTCAATTGGC
Found at i:1280545 original size:2 final size:2
Alignment explanation
Indices: 1280538--1280568 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1280528 GAGATTTTCG
*
1280538 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1280569 AATAAAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1280983 original size:20 final size:20
Alignment explanation
Indices: 1280960--1281005 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1280950 TTTTTCTTTT
1280960 TTTCTTTTTCTTCTTCTTCC
1 TTTCTTTTTCTTCTTCTTCC
1280980 TTTCTTTTTCTTCTTCTTCC
1 TTTCTTTTTCTTCTTCTTCC
1281000 -TTCTTT
1 TTTCTTT
1281006 CCCACCCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTCTTTTTCTTCTTCTTCC
Found at i:1286723 original size:51 final size:51
Alignment explanation
Indices: 1286629--1286746 Score: 168
Period size: 52 Copynumber: 2.3 Consensus size: 51
1286619 TCTGAAAAAA
*
1286629 AAATGTATCGATACATTTTTATTGTATCGATACATTCTAGG-TTTTGAC-C
1 AAATGTATCGATACATTTTTATTGTATCAATACATTCTAGGTTTTTGACTC
* * *
1286678 TGAATGTATCGATACGTTTTTCATTGTATCAATACATTCTTGGTTTTTGACTC
1 -AAATGTATCGATACATTTTT-ATTGTATCAATACATTCTAGGTTTTTGACTC
1286731 AAATGTATCGATACAT
1 AAATGTATCGATACAT
1286747 CTATTTAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
50 18 0.31
51 19 0.32
52 21 0.36
53 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.43
Consensus pattern (51 bp):
AAATGTATCGATACATTTTTATTGTATCAATACATTCTAGGTTTTTGACTC
Found at i:1288390 original size:46 final size:46
Alignment explanation
Indices: 1288321--1288501 Score: 157
Period size: 50 Copynumber: 3.7 Consensus size: 46
1288311 TTTCACAATT
* *
1288321 TGTATCGATACATCTTTCTTTATATCGATACATTTTGGG-ACCCAAA
1 TGTATCGATACA-CTTTCATTATATCGATACATTCTGGGTACCCAAA
* *
1288367 TGTATTGATACACTATTCATTATATCGATACATTCTGGGTTTTACCCCAA
1 TGTATCGATACACT-TTCATTATATCGATACATTCTGGG---TACCCAAA
* * *
1288417 TGTATCGATACATTTTTCATTGTATCGATACATTCTGGGTTTTAACCCAGA
1 TGTATCGATACA-CTTTCATTATATCGATACATTCTGGG---T-ACCCAAA
* * * *
1288468 TGTATCCATACATTTCTCAATGTATCGATACATT
1 TGTATCGATACACTT-TCATTATATCGATACATT
1288502 TAGACATTTT
Statistics
Matches: 116, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
45 2 0.02
46 33 0.28
50 47 0.41
51 34 0.29
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (46 bp):
TGTATCGATACACTTTCATTATATCGATACATTCTGGGTACCCAAA
Found at i:1288436 original size:50 final size:50
Alignment explanation
Indices: 1288360--1288501 Score: 194
Period size: 50 Copynumber: 2.8 Consensus size: 50
1288350 ACATTTTGGG
* * * * *
1288360 ACCCAAATGTATTGATACACTATTCATTATATCGATACATTCTGGGTTTT
1 ACCCCAATGTATCGATACATTTTTCATTGTATCGATACATTCTGGGTTTT
1288410 ACCCCAATGTATCGATACATTTTTCATTGTATCGATACATTCTGGGTTTT
1 ACCCCAATGTATCGATACATTTTTCATTGTATCGATACATTCTGGGTTTT
* * * *
1288460 AACCCAGATGTATCCATACATTTCTCAATGTATCGATACATT
1 ACCCCA-ATGTATCGATACATTTTTCATTGTATCGATACATT
1288502 TAGACATTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 50 0.61
51 32 0.39
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (50 bp):
ACCCCAATGTATCGATACATTTTTCATTGTATCGATACATTCTGGGTTTT
Found at i:1288492 original size:51 final size:50
Alignment explanation
Indices: 1288389--1288501 Score: 181
Period size: 51 Copynumber: 2.2 Consensus size: 50
1288379 CTATTCATTA
* * * *
1288389 TATCGATACATTCTGGGTTTTACCCCAATGTATCGATACATTTTTCATTG
1 TATCGATACATTCTGGGTTTTAACCCAATGTATCCATACATTTCTCAATG
1288439 TATCGATACATTCTGGGTTTTAACCCAGATGTATCCATACATTTCTCAATG
1 TATCGATACATTCTGGGTTTTAACCCA-ATGTATCCATACATTTCTCAATG
1288490 TATCGATACATT
1 TATCGATACATT
1288502 TAGACATTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 26 0.45
51 32 0.55
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (50 bp):
TATCGATACATTCTGGGTTTTAACCCAATGTATCCATACATTTCTCAATG
Found at i:1290973 original size:79 final size:77
Alignment explanation
Indices: 1290840--1291079 Score: 252
Period size: 79 Copynumber: 3.1 Consensus size: 77
1290830 TCATTCATGT
* * * *
1290840 TTTTA-TTTCTAAAATACCAATTTTCCACCATCGAGGATACTCCAACCTTGTTATTTTCGAGGGG
1 TTTTATTTTC-AAAACATCAATTTTCTA-CATCGAGGATACTCCAACCCTGTTATTTTCGAGGGG
1290904 ATACTCCAACCTCGG
64 ATACTCCAA-CTCGG
* * ** * *
1290919 TTTTATTTTCAAAACATCAATTTTTCATA-ATTGGGGATACTCCAACCCCATTATTTTCAACAGG
1 TTTTATTTTCAAAACATCAA-TTTTC-TACATCGAGGATACTCCAACCCTGTTATTTTCGA-GGG
1290983 G-TACTCCAAACTCGG
63 GATACTCC-AACTCGG
* * * *
1290998 TTTTATTTTTAAAACATCAATTTTCTACTATCGAGGATATTCCAATCCTGTTATTTCCGAGGGGA
1 TTTTATTTTCAAAACATCAATTTTCTAC-ATCGAGGATACTCCAACCCTGTTATTTTCGAGGGGA
*
1291063 TACTCCAACTCCG
65 TACTCCAACTCGG
1291076 TTTT
1 TTTT
1291080 TATCTCCAAA
Statistics
Matches: 132, Mismatches: 21, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
77 2 0.02
78 18 0.14
79 97 0.73
80 14 0.11
81 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (77 bp):
TTTTATTTTCAAAACATCAATTTTCTACATCGAGGATACTCCAACCCTGTTATTTTCGAGGGGAT
ACTCCAACTCGG
Found at i:1297111 original size:11 final size:11
Alignment explanation
Indices: 1297095--1297132 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1297085 TTAAATAAAA
1297095 TTTTTTCACTT
1 TTTTTTCACTT
*
1297106 TTTTTTCA-AT
1 TTTTTTCACTT
*
1297116 TTTTTTCTCTT
1 TTTTTTCACTT
1297127 TTTTTT
1 TTTTTT
1297133 TCTTTTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTCACTT
Found at i:1297138 original size:20 final size:20
Alignment explanation
Indices: 1297095--1297180 Score: 77
Period size: 21 Copynumber: 4.2 Consensus size: 20
1297085 TTAAATAAAA
* *
1297095 TTTTTTCACTTTTTTTTCAAT
1 TTTTTTCTCTTTTTTTT-TAT
*
1297116 TTTTTTCTCTTTTTTTTT-C
1 TTTTTTCTCTTTTTTTTTAT
**
1297135 TTTTTTCT-TTCTAATTTTAT
1 TTTTTTCTCTT-TTTTTTTAT
1297155 TTTTTTCTTCCTTTTTTTTTAT
1 TTTTTTC-T-CTTTTTTTTTAT
1297177 TTTT
1 TTTT
1297181 CATTTTCTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
18 2 0.04
19 13 0.25
20 7 0.13
21 17 0.33
22 11 0.21
23 2 0.04
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTCTCTTTTTTTTTAT
Found at i:1297181 original size:20 final size:20
Alignment explanation
Indices: 1297103--1297181 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 20
1297093 AATTTTTTCA
*
1297103 CTTTTTTTTCAATTTTT-TTC
1 CTTTTTTTT-TATTTTTCTTC
* *
1297123 TCTTTTTTTTTCTTTTTTCTTT
1 -CTTTTTTTTT-ATTTTTCTTC
* *
1297145 CTAATTTTATT-TTTTTCTTC
1 CT-TTTTTTTTATTTTTCTTC
1297165 CTTTTTTTTTATTTTTC
1 CTTTTTTTTTATTTTTC
1297182 ATTTTCTTCA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
19 6 0.13
20 16 0.35
21 16 0.35
22 8 0.17
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (20 bp):
CTTTTTTTTTATTTTTCTTC
Found at i:1298260 original size:41 final size:41
Alignment explanation
Indices: 1298203--1298291 Score: 133
Period size: 41 Copynumber: 2.2 Consensus size: 41
1298193 TATGGCGTCG
*
1298203 GCACGCTAAGAAAACAGAAGCTCTCATTTGATAAGGTATGA
1 GCACGCTAAGAAAACAGAAACTCTCATTTGATAAGGTATGA
* * * *
1298244 GCACGTTAATAAAACAGAAACTCTCATTTGATAAGGTGTGG
1 GCACGCTAAGAAAACAGAAACTCTCATTTGATAAGGTATGA
1298285 GCACGCT
1 GCACGCT
1298292 CTATGAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (41 bp):
GCACGCTAAGAAAACAGAAACTCTCATTTGATAAGGTATGA
Found at i:1298807 original size:42 final size:42
Alignment explanation
Indices: 1298748--1298835 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 42
1298738 TCTCTCTAAC
* *
1298748 AGTATTGGGGCAGAATGTATAGTATCATCCTCTTCCAAGTCA
1 AGTATTAGGGCAAAATGTATAGTATCATCCTCTTCCAAGTCA
*
1298790 AGTATTAGGGCAAAATGTATAGTATCATCCTCTTCCATGTCA
1 AGTATTAGGGCAAAATGTATAGTATCATCCTCTTCCAAGTCA
1298832 AGTA
1 AGTA
1298836 CATAGAAATC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (42 bp):
AGTATTAGGGCAAAATGTATAGTATCATCCTCTTCCAAGTCA
Found at i:1301921 original size:22 final size:22
Alignment explanation
Indices: 1301896--1301937 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1301886 TTAAGTTGTC
1301896 TGCCTCTA-GACCGTGCCCACCT
1 TGCCTC-AGGACCGTGCCCACCT
*
1301918 TGCCTCAGGAGCGTGCCCAC
1 TGCCTCAGGACCGTGCCCAC
1301938 GGTCTATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.14, C:0.43, G:0.24, T:0.19
Consensus pattern (22 bp):
TGCCTCAGGACCGTGCCCACCT
Found at i:1302817 original size:10 final size:10
Alignment explanation
Indices: 1302788--1302828 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
1302778 TTGTTTTCAC
*
1302788 TTTTTTTTCG
1 TTTTTTTTCT
*
1302798 ATTTTTTTCT
1 TTTTTTTTCT
1302808 TTTTTTTTCT
1 TTTTTTTTCT
1302818 TTTTTCTTTCT
1 TTTTT-TTTCT
1302829 AATTTTAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 22 0.81
11 5 0.19
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.83
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:1302820 original size:17 final size:17
Alignment explanation
Indices: 1302800--1302869 Score: 68
Period size: 17 Copynumber: 3.8 Consensus size: 17
1302790 TTTTTTCGAT
1302800 TTTTTTCTTTTTTTTTC
1 TTTTTTCTTTTTTTTTC
*
1302817 TTTTTTCTTTCTAATTTTAAC
1 TTTTTTCTTT-T--TTTT-TC
*
1302838 TTTTTTCCTTTTTTTTC
1 TTTTTTCTTTTTTTTTC
*
1302855 ATTTTTCATTTTTTT
1 TTTTTTC-TTTTTTT
1302870 CAAGGAATCA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
17 17 0.40
18 11 0.26
20 5 0.12
21 10 0.23
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTCTTTTTTTTTC
Found at i:1307213 original size:32 final size:34
Alignment explanation
Indices: 1307168--1307258 Score: 109
Period size: 36 Copynumber: 2.7 Consensus size: 34
1307158 CAACACTATC
1307168 TTTC-AAGGCTAAGATAGAAACCTC-C-CTATC-T
1 TTTCAAAGGCTAAGATAG-AACCTCTCTCTATCTT
**
1307199 TTTCACGGGCTAAGATAGAACCTTTCTCTCTATCTT
1 TTTCAAAGGCTAAGATAGAACC--TCTCTCTATCTT
1307235 TTTCAAAGGCTAAGATAGAACCTC
1 TTTCAAAGGCTAAGATAGAACCTC
1307259 ACAATCACTT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
31 8 0.16
32 11 0.22
33 2 0.04
34 3 0.06
35 5 0.10
36 21 0.42
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (34 bp):
TTTCAAAGGCTAAGATAGAACCTCTCTCTATCTT
Found at i:1307740 original size:19 final size:20
Alignment explanation
Indices: 1307697--1307740 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1307687 TCGTTGGACT
**
1307697 CAATGTATCGATACTATTCA
1 CAATGTATCGATACTATGAA
1307717 CAATGTATCGATAC-ATGAA
1 CAATGTATCGATACTATGAA
1307736 CAATG
1 CAATG
1307741 ATGAACAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (20 bp):
CAATGTATCGATACTATGAA
Found at i:1307805 original size:56 final size:54
Alignment explanation
Indices: 1307719--1307831 Score: 163
Period size: 56 Copynumber: 2.1 Consensus size: 54
1307709 ACTATTCACA
* *
1307719 ATGTATCGATACATGAACAATGATGAACAGTAATGAATAGTGATGCATGAACAGTG
1 ATGTATCGATACATGAACAATGATGAACAGTAATGAAT--CGATACATGAACAGTG
* * *
1307775 ATGTATCGATACATGAATAGTGATGAACAGTGATGAATCGATACATGAACAGTG
1 ATGTATCGATACATGAACAATGATGAACAGTAATGAATCGATACATGAACAGTG
1307829 ATG
1 ATG
1307832 AATAGTGATG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 17 0.33
56 35 0.67
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.26
Consensus pattern (54 bp):
ATGTATCGATACATGAACAATGATGAACAGTAATGAATCGATACATGAACAGTG
Found at i:1307806 original size:10 final size:10
Alignment explanation
Indices: 1307787--1307845 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
1307777 GTATCGATAC
*
1307787 ATGAATAGTG
1 ATGAACAGTG
1307797 ATGAACAGTG
1 ATGAACAGTG
*
1307807 ATGAATC-GATAC
1 ATGAA-CAG-T-G
1307819 ATGAACAGTG
1 ATGAACAGTG
*
1307829 ATGAATAGTG
1 ATGAACAGTG
1307839 ATGAACA
1 ATGAACA
1307846 ACGATGAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
10 30 0.75
11 4 0.10
12 6 0.15
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.24
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:1307806 original size:32 final size:32
Alignment explanation
Indices: 1307765--1307843 Score: 131
Period size: 32 Copynumber: 2.5 Consensus size: 32
1307755 ATAGTGATGC
* *
1307765 ATGAACAGTGATGTATCGATACATGAATAGTG
1 ATGAACAGTGATGAATCGATACATGAACAGTG
1307797 ATGAACAGTGATGAATCGATACATGAACAGTG
1 ATGAACAGTGATGAATCGATACATGAACAGTG
*
1307829 ATGAATAGTGATGAA
1 ATGAACAGTGATGAA
1307844 CAACGATGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.41, C:0.09, G:0.25, T:0.25
Consensus pattern (32 bp):
ATGAACAGTGATGAATCGATACATGAACAGTG
Found at i:1307894 original size:13 final size:13
Alignment explanation
Indices: 1307878--1307902 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1307868 TATCAGTTTT
1307878 ATGTATCGATACA
1 ATGTATCGATACA
1307891 ATGTATCGATAC
1 ATGTATCGATAC
1307903 TAAGCAAAAT
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:1309729 original size:23 final size:24
Alignment explanation
Indices: 1309702--1309746 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1309692 ATGCTTAAAT
*
1309702 AAATTTTTTTC-ACTTTTTTTTAA
1 AAATTTTTCTCTACTTTTTTTTAA
*
1309725 AAATTTTTCTCTTCTTTTTTTT
1 AAATTTTTCTCTACTTTTTTTT
1309747 CTTTTTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (24 bp):
AAATTTTTCTCTACTTTTTTTTAA
Found at i:1309772 original size:29 final size:27
Alignment explanation
Indices: 1309739--1309803 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 27
1309729 TTTTCTCTTC
1309739 TTTTTTTTCTTTTTTCTTTCTAATTTTAA
1 TTTTTTTTCTTTTTT-TTTC-AATTTTAA
* *
1309768 TTTTTTTTCTTTTTTTTTCATTTTTCA
1 TTTTTTTTCTTTTTTTTTCAATTTTAA
*
1309795 TATTTTTTC
1 TTTTTTTTC
1309804 AAAGAATCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 14 0.42
28 4 0.12
29 15 0.45
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (27 bp):
TTTTTTTTCTTTTTTTTTCAATTTTAA
Found at i:1312354 original size:14 final size:15
Alignment explanation
Indices: 1312323--1312397 Score: 66
Period size: 14 Copynumber: 5.1 Consensus size: 15
1312313 ATTTATATTT
1312323 TTAAATTTAATAAAAA
1 TTAAA-TTAATAAAAA
1312339 TTAAATTAAT-AAAA
1 TTAAATTAATAAAAA
*
1312353 TTAAATT-TTAAAAA
1 TTAAATTAATAAAAA
* **
1312367 TATATATTTTTAAAAA
1 T-TAAATTAATAAAAA
*
1312383 ATAAATT-ATAAAAA
1 TTAAATTAATAAAAA
1312397 T
1 T
1312398 ATAATTTGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
13 1 0.02
14 22 0.44
15 15 0.30
16 12 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAAATTAATAAAAA
Found at i:1312388 original size:30 final size:31
Alignment explanation
Indices: 1312344--1312404 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
1312334 AAAAATTAAA
*
1312344 TTAATAAAATTAAATTTTAAAAATATATATTT
1 TTAATAAAATTAAATTATAAAAATATA-ATTT
1312376 TTAA-AAAA-TAAATTATAAAAATATAATTT
1 TTAATAAAATTAAATTATAAAAATATAATTT
1312405 GAATAGATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 4 0.14
30 16 0.57
31 4 0.14
32 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (31 bp):
TTAATAAAATTAAATTATAAAAATATAATTT
Found at i:1312401 original size:15 final size:15
Alignment explanation
Indices: 1312332--1312401 Score: 67
Period size: 14 Copynumber: 4.8 Consensus size: 15
1312322 TTTAAATTTA
1312332 ATAAAAAT-TAAATT
1 ATAAAAATATAAATT
1312346 A-ATAAAAT-TAAATT
1 ATA-AAAATATAAATT
* *
1312360 TTAAAAATATATATTT
1 ATAAAAATATA-AATT
*
1312376 TTAAAAA-ATAAATT
1 ATAAAAATATAAATT
1312390 ATAAAAATATAA
1 ATAAAAATATAA
1312402 TTTGAATAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
13 1 0.02
14 26 0.55
15 10 0.21
16 10 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAAAAATATAAATT
Found at i:1312924 original size:15 final size:15
Alignment explanation
Indices: 1312904--1312935 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1312894 GAAGTTTTTA
*
1312904 TAAAAAAATAAGAAT
1 TAAAAAAATAAAAAT
1312919 TAAAAAAATAAAAAT
1 TAAAAAAATAAAAAT
1312934 TA
1 TA
1312936 TTTGATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (15 bp):
TAAAAAAATAAAAAT
Found at i:1313708 original size:16 final size:16
Alignment explanation
Indices: 1313678--1313752 Score: 100
Period size: 16 Copynumber: 4.8 Consensus size: 16
1313668 TAAGTTCATC
1313678 TAAA-TTAAAATTAATT
1 TAAATTTAAAA-TAATT
*
1313694 TGAATTTAAAATAATT
1 TAAATTTAAAATAATT
*
1313710 TAAATTCAAAA-AATT
1 TAAATTTAAAATAATT
*
1313725 TATATTTAAAATAATT
1 TAAATTTAAAATAATT
1313741 TAAATTTAAAAT
1 TAAATTTAAAAT
1313753 TATTAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
15 13 0.25
16 32 0.63
17 6 0.12
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (16 bp):
TAAATTTAAAATAATT
Found at i:1313776 original size:25 final size:24
Alignment explanation
Indices: 1313729--1313783 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
1313719 AAAATTTATA
* **
1313729 TTTAAAATAATTTAAATTTAAAAT
1 TTTAAAAAAATTTAAATAAAAAAT
*
1313753 TATTAAAAAAATTTAAGTAAAAAAT
1 T-TTAAAAAAATTTAAATAAAAAAT
1313778 TTTAAA
1 TTTAAA
1313784 TTAAAAATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
TTTAAAAAAATTTAAATAAAAAAT
Found at i:1313789 original size:14 final size:14
Alignment explanation
Indices: 1313708--1313801 Score: 61
Period size: 14 Copynumber: 6.7 Consensus size: 14
1313698 TTTAAAATAA
*
1313708 TTTAAATTCAAAAAA
1 TTTAAATT-AAAAAT
* *
1313723 TTTATATTTAAAATAA
1 TTTA-AATTAAAA-AT
*
1313739 TTTAAATTTAAAAT
1 TTTAAATTAAAAAT
1313753 TATT-AA--AAAAA-
1 T-TTAAATTAAAAAT
* *
1313764 TTTAAGTAAAAAAT
1 TTTAAATTAAAAAT
1313778 TTTAAATTAAAAAT
1 TTTAAATTAAAAAT
*
1313792 GTTAAATTAA
1 TTTAAATTAA
1313802 GATGATCTAC
Statistics
Matches: 63, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
10 2 0.03
11 2 0.03
12 4 0.06
13 5 0.08
14 25 0.40
15 16 0.25
16 9 0.14
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.40
Consensus pattern (14 bp):
TTTAAATTAAAAAT
Found at i:1315787 original size:38 final size:38
Alignment explanation
Indices: 1315745--1315820 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
1315735 GATGCTGCAA
*
1315745 GAGATCCACCCATTGTAGTGAATAGCAACATGTCAGTT
1 GAGATCCACCCATTGTAGTGAATAGCAACACGTCAGTT
* *
1315783 GAGATCCATCTATTGTAGTGAATAGCAACACGTCAGTT
1 GAGATCCACCCATTGTAGTGAATAGCAACACGTCAGTT
1315821 TGTACTGGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (38 bp):
GAGATCCACCCATTGTAGTGAATAGCAACACGTCAGTT
Found at i:1319447 original size:16 final size:16
Alignment explanation
Indices: 1319422--1319455 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1319412 TTATTCTATC
*
1319422 ATAAATTATTTATTTT
1 ATAAAGTATTTATTTT
1319438 ATAAAGTATTTATTTT
1 ATAAAGTATTTATTTT
1319454 AT
1 AT
1319456 TATACCGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
ATAAAGTATTTATTTT
Found at i:1321977 original size:20 final size:20
Alignment explanation
Indices: 1321952--1322006 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
1321942 TTTTCACAAT
*
1321952 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTATTCA
1321972 TTGTATCGATACATTATTCA
1 TTGTATCGATACATTATTCA
1321992 TTGTATCGATACATT
1 TTGTATCGATACATT
1322007 CTGGGTTTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (20 bp):
TTGTATCGATACATTATTCA
Found at i:1324488 original size:51 final size:52
Alignment explanation
Indices: 1324412--1324634 Score: 288
Period size: 51 Copynumber: 4.3 Consensus size: 52
1324402 TTATTTTCGA
* * ***
1324412 GGGGATACTCCAACCCCAGCTTTATTTCTAAAATATTGAT-TTCTCACAATC
1 GGGGATACTCCAACCCCAACTTTATTTCTAAAACACCAATCTTCTCACAATC
* *
1324463 GGGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATCTTTTCACAATC
1 GGGGATACTCCAACCCCAACTTTATTTCTAAAACACCAATCTTCTCACAATC
* ** * ***
1324515 GGGGATACTCCAAGCCCGGCTTTATTTCTAAAATATTGAT-TTCTCACAATC
1 GGGGATACTCCAACCCCAACTTTATTTCTAAAACACCAATCTTCTCACAATC
* *
1324566 GGGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATCTTTTCACAATC
1 GGGGATACTCCAACCCCAACTTTATTTCTAAAACACCAATCTTCTCACAATC
1324618 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
1324635 GTCATTTTCA
Statistics
Matches: 145, Mismatches: 25, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
51 76 0.52
52 69 0.48
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (52 bp):
GGGGATACTCCAACCCCAACTTTATTTCTAAAACACCAATCTTCTCACAATC
Found at i:1324591 original size:103 final size:103
Alignment explanation
Indices: 1324412--1324635 Score: 430
Period size: 103 Copynumber: 2.2 Consensus size: 103
1324402 TTATTTTCGA
*
1324412 GGGGATACTCCAACCCCAGCTTTATTTCTAAAATATTGATTTCTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTCTCACAATCGGGGATACTCCAAC
1324477 CCCAATTTTATTTCTAAAACACCAATCTTTTCACAATC
66 CCCAATTTTATTTCTAAAACACCAATCTTTTCACAATC
*
1324515 GGGGATACTCCAAGCCCGGCTTTATTTCTAAAATATTGATTTCTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTCTCACAATCGGGGATACTCCAAC
1324580 CCCAATTTTATTTCTAAAACACCAATCTTTTCACAATC
66 CCCAATTTTATTTCTAAAACACCAATCTTTTCACAATC
1324618 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1324636 TCATTTTCAA
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 118 1.00
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (103 bp):
GGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTCTCACAATCGGGGATACTCCAAC
CCCAATTTTATTTCTAAAACACCAATCTTTTCACAATC
Found at i:1324698 original size:79 final size:80
Alignment explanation
Indices: 1324566--1324795 Score: 277
Period size: 79 Copynumber: 2.9 Consensus size: 80
1324556 TCTCACAATC
* * * *
1324566 GGGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATCTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCAGTTTTATTTCTAGAACACCGATTTTTTCACAATCGGGGATACTCCAA
1324631 CCCCGTCATTTTCAA
66 CCCCGTCATTTTCAA
* * *
1324646 -GGGATACTCTAACCCCAGTTTTATTTCCAGAACACCGATTTTTTCACAATCGGGGATACTCTAA
1 GGGGATACTCCAACCCCAGTTTTATTTCTAGAACACCGATTTTTTCACAATCGGGGATACTCCAA
*
1324710 CCCCGTTATTTTCAA
66 CCCCGTCATTTTCAA
* * * * * * *
1324725 GGGGATACTCCGA-CCCTGATTTTATTTCTAGTACATCGA-TTTTCCATAGTCAGGGGATACTCC
1 GGGGATACTCCAACCCCAG-TTTTATTTCTAGAACACCGATTTTTTCACAATC-GGGGATACTCC
*
1324788 AGCCCCGT
64 AACCCCGT
1324796 TGTCATCTCC
Statistics
Matches: 128, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
79 84 0.66
80 44 0.34
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (80 bp):
GGGGATACTCCAACCCCAGTTTTATTTCTAGAACACCGATTTTTTCACAATCGGGGATACTCCAA
CCCCGTCATTTTCAA
Found at i:1327861 original size:13 final size:13
Alignment explanation
Indices: 1327843--1327868 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1327833 CAATTTTTTG
1327843 TGTATCGATACAT
1 TGTATCGATACAT
1327856 TGTATCGATACAT
1 TGTATCGATACAT
1327869 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:1330420 original size:13 final size:13
Alignment explanation
Indices: 1330402--1330440 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1330392 ATAATCACCT
*
1330402 TGTATCGATACAG
1 TGTATCGATACAA
1330415 TGTATCGATACAA
1 TGTATCGATACAA
1330428 TGTATCGATACAA
1 TGTATCGATACAA
1330441 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1330451 original size:20 final size:20
Alignment explanation
Indices: 1330426--1330504 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
1330416 GTATCGATAC
1330426 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1330446 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
1330471 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
1330491 CATGTATCGATACA
1 AATGTATCGATACA
1330505 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1332547 original size:15 final size:15
Alignment explanation
Indices: 1332511--1332548 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1332501 TTCATCAATT
* *
1332511 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
1332526 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
1332541 TCATTTTG
1 TCATTTTG
1332549 GACATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:1334381 original size:21 final size:21
Alignment explanation
Indices: 1334352--1334396 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1334342 AAGTTTTCAT
*
1334352 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1334372 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1334394 TTT
1 TTT
1334397 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:1336632 original size:13 final size:13
Alignment explanation
Indices: 1336614--1336639 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1336604 CAATTTTTTG
1336614 TGTATCGATACAT
1 TGTATCGATACAT
1336627 TGTATCGATACAT
1 TGTATCGATACAT
1336640 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:1342467 original size:155 final size:157
Alignment explanation
Indices: 1342130--1342498 Score: 387
Period size: 155 Copynumber: 2.4 Consensus size: 157
1342120 AAGTTCAAAG
** * ** *
1342130 AAAATTACAAAAATACCCTTAAGGGATACCTTCAATGTAAAAGTACCC-A-AGTCCTCTAAAGGA
1 AAAATTACAAAAATACCCTTAAGGGATATTTTCGACATAAAAGTACCCGATA-TCC-CTAAAAGA
** * *
1342193 CTTA-AAA--AGGACAATAGATGAGACGAACCTATCCTAAATACCCAACTTTCAGCATAAAAGCT
64 CTTACAAACGATTACAA-A-ATGGGATGAACCTATCCTAAATACCCAACTTTCAGCATAAAAGCT
* * * *
1342255 GACCCGGTAATAACCTAAGACTCGATTTTAT
127 GACCCAGTAACAACCTAAGACTCGATTCTAA
* * * *
1342286 AAAATTACAAAAATACCCTTAGGGGATATTTTCGACGTCAAAGTGCCCGATATCCCTAAAAGACT
1 AAAATTACAAAAATACCCTTAAGGGATATTTTCGACATAAAAGTACCCGATATCCCTAAAAGACT
* *
1342351 TACAAACGATTACAAAATGGGATGAACCTATTCTAAATACCCAAC-TTCGGCAT-AAAGC-GAAC
66 TACAAACGATTACAAAATGGGATGAACCTATCCTAAATACCCAACTTTCAGCATAAAAGCTG-AC
* * * * *
1342413 CTAGTGACAACCTAGGACTTGGTTCTAA
130 CCAGTAACAACCTAAGACTCGATTCTAA
*
1342441 AAAATTACGAAAATACTCC-TAAGGGATATTTTCGACATAAAAGTACCCGATATCCCTA
1 AAAATTACAAAAATAC-CCTTAAGGGATATTTTCGACATAAAAGTACCCGATATCCCTA
1342499 GTGGACACTA
Statistics
Matches: 178, Mismatches: 28, Indels: 15
0.81 0.13 0.07
Matches are distributed among these distances:
154 1 0.01
155 76 0.43
156 61 0.34
157 33 0.19
158 2 0.01
159 5 0.03
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (157 bp):
AAAATTACAAAAATACCCTTAAGGGATATTTTCGACATAAAAGTACCCGATATCCCTAAAAGACT
TACAAACGATTACAAAATGGGATGAACCTATCCTAAATACCCAACTTTCAGCATAAAAGCTGACC
CAGTAACAACCTAAGACTCGATTCTAA
Found at i:1344442 original size:20 final size:21
Alignment explanation
Indices: 1344389--1344445 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
1344379 CTATTGGAGT
*
1344389 TTGCTAGAGTTGCTGCTGGTG
1 TTGCTAGAGCTGCTGCTGGTG
* * *
1344410 TTCACTGGAGCTGCTGCTTG-G
1 TT-GCTAGAGCTGCTGCTGGTG
1344431 TTGCTAGAGCTGCTG
1 TTGCTAGAGCTGCTG
1344446 TTTTGTGTCT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 11 0.38
21 5 0.17
22 13 0.45
ACGTcount: A:0.11, C:0.19, G:0.35, T:0.35
Consensus pattern (21 bp):
TTGCTAGAGCTGCTGCTGGTG
Found at i:1348053 original size:20 final size:20
Alignment explanation
Indices: 1348028--1348079 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1348018 CATATTTTTG
1348028 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1348048 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1348068 ATGTATCGATAC
1 ATGTATCGATAC
1348080 TTTTAAGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1357837 original size:1 final size:1
Alignment explanation
Indices: 1357827--1357915 Score: 70
Period size: 1 Copynumber: 89.0 Consensus size: 1
1357817 TGGCAATTGG
* * * ** * * * **
1357827 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAACAAAACAAAAAAAAAGGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
1357892 AAGAAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAA
1357916 GTGAAGATTT
Statistics
Matches: 68, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.87, C:0.06, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:1357866 original size:17 final size:17
Alignment explanation
Indices: 1357846--1357903 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
1357836 AAAACAAAAC
1357846 AAAAAAAAGGAAAAAGA
1 AAAAAAAAGGAAAAAGA
*
1357863 AAAAAAAA--ACAAAACA
1 AAAAAAAAGGA-AAAAGA
1357879 AAAAAAAAGGAAAAAGA
1 AAAAAAAAGGAAAAAGA
1357896 AAAAAAAA
1 AAAAAAAA
1357904 AACAAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
15 1 0.03
16 13 0.36
17 21 0.58
18 1 0.03
ACGTcount: A:0.86, C:0.03, G:0.10, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGGAAAAAGA
Found at i:1357883 original size:33 final size:34
Alignment explanation
Indices: 1357828--1357915 Score: 146
Period size: 33 Copynumber: 2.6 Consensus size: 34
1357818 GGCAATTGGA
1357828 AAAAGAAAAAAACAAAAC-AAAAAAAAGGAAAAAG
1 AAAA-AAAAAAACAAAACAAAAAAAAAGGAAAAAG
1357862 -AAAAAAAAAACAAAACAAAAAAAAAGGAAAAAG
1 AAAAAAAAAAACAAAACAAAAAAAAAGGAAAAAG
1357895 AAAAAAAAAAACAAAA-AAAAA
1 AAAAAAAAAAACAAAACAAAAA
1357916 GTGAAGATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
32 13 0.25
33 24 0.46
34 15 0.29
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (34 bp):
AAAAAAAAAAACAAAACAAAAAAAAAGGAAAAAG
Found at i:1357915 original size:29 final size:30
Alignment explanation
Indices: 1357825--1357916 Score: 143
Period size: 29 Copynumber: 3.0 Consensus size: 30
1357815 CATGGCAATT
1357825 GGAAAAAGAAAAAAACAAAAC-AAAAAAAA
1 GGAAAAAGAAAAAAACAAAACAAAAAAAAA
1357854 GGAAAAAGAAAAAAAAAACAAAACAAAAAAAAA
1 GGAAAAAG---AAAAAAACAAAACAAAAAAAAA
1357887 GGAAAAAGAAAAAAA-AAAACAAAAAAAAA
1 GGAAAAAGAAAAAAACAAAACAAAAAAAAA
1357916 G
1 G
1357917 TGAAGATTTG
Statistics
Matches: 59, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
29 23 0.39
30 7 0.12
32 13 0.22
33 16 0.27
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (30 bp):
GGAAAAAGAAAAAAACAAAACAAAAAAAAA
Found at i:1360911 original size:13 final size:13
Alignment explanation
Indices: 1360893--1360931 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1360883 ATAATCCCCC
*
1360893 TGTATCGATACAG
1 TGTATCGATACAA
1360906 TGTATCGATACAA
1 TGTATCGATACAA
1360919 TGTATCGATACAA
1 TGTATCGATACAA
1360932 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1367146 original size:33 final size:33
Alignment explanation
Indices: 1367087--1367151 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
1367077 TACAAGCCAA
* *
1367087 TGTATCGATACAATTTTTTGTATATCGATACAT
1 TGTATCGATACAATCTTTGGTATATCGATACAT
*
1367120 TGTATCGATAC-ATACTTTGGTGTATCGATACA
1 TGTATCGATACAAT-CTTTGGTATATCGATACA
1367152 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATCTTTGGTATATCGATACAT
Found at i:1368727 original size:20 final size:20
Alignment explanation
Indices: 1368698--1368775 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
1368688 GTAAAAAAAC
1368698 AGAATGTATCGATACATTAT
1 AGAATGTATCGATACATTAT
*
1368718 AGAATATATCGATACATTCAT
1 AGAATGTATCGATACATT-AT
* * *
1368739 A-CATGTATCGATTCATTAA
1 AGAATGTATCGATACATTAT
*
1368758 AAAATGTATCGATACATT
1 AGAATGTATCGATACATT
1368776 TAGGTAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
19 2 0.04
20 44 0.90
21 3 0.06
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (20 bp):
AGAATGTATCGATACATTAT
Found at i:1369923 original size:79 final size:77
Alignment explanation
Indices: 1369794--1370044 Score: 297
Period size: 79 Copynumber: 3.2 Consensus size: 77
1369784 AACAGGGCCT
* *
1369794 GAGTATCCCCCGATTATGGAAAATCGGTATTCTAGAAATAAAACCGGGGTTGGAGTATCCCCTTA
1 GAGTAT-CCCCGATTAT-GAAAATCGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCC-TA
*
1369859 GAAATAACAGGGTTG
63 GAAATAACGGGGTTG
* * *
1369874 GAGTATCCCTGATTATAGAAAATCGGTATTTT-GAAAATAAAATCAGGGTTGGAGTATCCCCTCG
1 GAGTATCCCCGATTAT-GAAAATCGGTATTTTAG-AAATAAAATCGGGGTTGGAGTATCCCCTAG
1369938 AAAATAACGGGGTTG
64 -AAATAACGGGGTTG
* * ** * * *
1369953 GAGTATCCCCAATTATGAAAAATCGATGCTTTAGAAATAAAGTTGGGGTTGGAGTATCCCCGATG
1 GAGTATCCCCGATTATG-AAAATCGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTA-G
*
1370018 GAATAACGGGGTTG
64 AAATAACGGGGTTG
1370032 GAGTATCCCCGAT
1 GAGTATCCCCGAT
1370045 GGAATAACGG
Statistics
Matches: 147, Mismatches: 19, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
78 4 0.03
79 135 0.92
80 8 0.05
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (77 bp):
GAGTATCCCCGATTATGAAAATCGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTAGAA
ATAACGGGGTTG
Found at i:1370031 original size:28 final size:28
Alignment explanation
Indices: 1369997--1370068 Score: 144
Period size: 28 Copynumber: 2.6 Consensus size: 28
1369987 AAATAAAGTT
1369997 GGGGTTGGAGTATCCCCGATGGAATAAC
1 GGGGTTGGAGTATCCCCGATGGAATAAC
1370025 GGGGTTGGAGTATCCCCGATGGAATAAC
1 GGGGTTGGAGTATCCCCGATGGAATAAC
1370053 GGGGTTGGAGTATCCC
1 GGGGTTGGAGTATCCC
1370069 GGATTATGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.22
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGATGGAATAAC
Found at i:1370038 original size:107 final size:106
Alignment explanation
Indices: 1369919--1370123 Score: 270
Period size: 107 Copynumber: 1.9 Consensus size: 106
1369909 AATAAAATCA
1369919 GGGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCGATG-C
1 GGGTTGGAGTAT-CCC-CGAGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCGATGTC
* * ** *
1369982 TTTAGAAATAAAGTTGGGGTTGGAGTATCCCCGATGGAATAACG
64 TTGA-AAATAAAATCAGAGTTGGAGTATCCCCGATGGAATAACG
* ** *
1370026 GGGTTGGAGTATCCCCGATGGAATAACGGGGTTGGAGTATCCCGGATTATGAAAAATTGATGTCT
1 GGGTTGGAGTATCCCCGA-GAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCGATGTCT
*
1370091 TGAAAATAAAATCAGAGTTGGAGTATCTCCGAT
65 TGAAAATAAAATCAGAGTTGGAGTATCCCCGAT
1370124 TGTGGAAAAT
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
105 3 0.04
106 3 0.04
107 75 0.88
108 4 0.05
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (106 bp):
GGGTTGGAGTATCCCCGAGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCGATGTCTT
GAAAATAAAATCAGAGTTGGAGTATCCCCGATGGAATAACG
Found at i:1370133 original size:51 final size:51
Alignment explanation
Indices: 1370055--1370170 Score: 148
Period size: 51 Copynumber: 2.3 Consensus size: 51
1370045 GGAATAACGG
1370055 GGTTGGAGTATCCCGGATTATGAAAAATTGATGTCTTGA-AAATAAAATCAGA
1 GGTTGGAGTATCCCGGATTATGAAAAATTGATGT-TTGAGAAATAAAA-CAGA
* * * *
1370107 -GTTGGAGTATCTCC-GATTGTGGAAAATTGATGTTTTAGAAATAAAACCGA
1 GGTTGGAGTATC-CCGGATTATGAAAAATTGATGTTTGAGAAATAAAACAGA
1370157 GGTTGGAGTATCCC
1 GGTTGGAGTATCCC
1370171 TTTGGAAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
50 8 0.14
51 47 0.82
52 2 0.04
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCGGATTATGAAAAATTGATGTTTGAGAAATAAAACAGA
Found at i:1372652 original size:48 final size:49
Alignment explanation
Indices: 1372581--1372712 Score: 185
Period size: 50 Copynumber: 2.7 Consensus size: 49
1372571 AAAATGCCTG
* * **
1372581 AATGTATCGATACATTGCAAAATGTATCGATACATCTGGGT-AACCCAA
1 AATGTATCGATACAATGAAAAATGTATCGATACATCTAAGTAAACCCAA
* *
1372629 AATGTATCGATACAATGAAAAATGTATCGATATATCTAAGTAAAACCCAG
1 AATGTATCGATACAATGAAAAATGTATCGATACATCTAAGT-AAACCCAA
*
1372679 AATGTATCGATACAATGAACAATGTATCGATACA
1 AATGTATCGATACAATGAAAAATGTATCGATACA
1372713 AATTGTGAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
48 36 0.49
50 38 0.51
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (49 bp):
AATGTATCGATACAATGAAAAATGTATCGATACATCTAAGTAAACCCAA
Found at i:1373888 original size:42 final size:41
Alignment explanation
Indices: 1373842--1373964 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1373832 AAGAGAAAGG
* * **
1373842 AGTCTCTCGGGTCTAAGTTGATGGGCAAATAAAGGGTAACTA
1 AGTCTCTCGGGTC-AAGTTGATGGGCAGATAAAAGGTAAAAA
** * * *
1373884 AGTCTCTTAGGTCAAAGTCGACGGGTAGATAAAAGGTAAAAA
1 AGTCTCTCGGGTC-AAGTTGATGGGCAGATAAAAGGTAAAAA
*
1373926 AGTCT-TCTGGGTCAAGGTTGATGGGCAGATAAATGGTAA
1 AGTCTCTC-GGGTCAA-GTTGATGGGCAGATAAAAGGTAA
1373965 TGAAGTCCCC
Statistics
Matches: 63, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
41 3 0.05
42 60 0.95
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.25
Consensus pattern (41 bp):
AGTCTCTCGGGTCAAGTTGATGGGCAGATAAAAGGTAAAAA
Found at i:1373971 original size:84 final size:84
Alignment explanation
Indices: 1373842--1374056 Score: 210
Period size: 84 Copynumber: 2.5 Consensus size: 84
1373832 AAGAGAAAGG
* **
1373842 AGTCTCTCGGGTCTAAGTTGATGGGCAAATAAAGGGTAACT-AAGTCTCTTA-GGTCAAAG-TCG
1 AGTCTCTCGGGTC-AAGTTGATGGGCAGATAAA-GGTAA-TGAAGTCTCCCATGGTCAAAGCT-G
**
1373904 ACGGGTAGATAAAAGGTAAA-AA
62 ACAAGTAGATAAAAGGTAAAGAA
*
1373926 AGTCT-TCTGGGTCAAGGTTGATGGGCAGATAAATGGTAATGAAGTC-CCCATGGTTAAAGCTGA
1 AGTCTCTC-GGGTCAA-GTTGATGGGCAGATAAA-GGTAATGAAGTCTCCCATGGTCAAAGCTGA
1373989 CAAGTAGATAAAAGGTAAAGAA
63 CAAGTAGATAAAAGGTAAAGAA
* * * *
1374011 A-TCTCTCGGGTCAAAGCTGATAGGTAGACTAAAGGTAAAGAAGTCT
1 AGTCTCTCGGGTC-AAGTTGATGGGCAGA-TAAAGGTAATGAAGTCT
1374057 ATAAGGTTAA
Statistics
Matches: 110, Mismatches: 11, Indels: 19
0.79 0.08 0.14
Matches are distributed among these distances:
83 7 0.06
84 91 0.83
85 12 0.11
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (84 bp):
AGTCTCTCGGGTCAAGTTGATGGGCAGATAAAGGTAATGAAGTCTCCCATGGTCAAAGCTGACAA
GTAGATAAAAGGTAAAGAA
Found at i:1374027 original size:42 final size:43
Alignment explanation
Indices: 1373981--1374234 Score: 188
Period size: 42 Copynumber: 6.1 Consensus size: 43
1373971 CCCCATGGTT
* * **
1373981 AAAGCTGACAAGTAGA-TAAAAGGTAAAGAAATCTCTCGGGTC
1 AAAGCTGACAGGTAGACTAAAAGGTAAAGAAATCTATAAGGTC
* * *
1374023 AAAGCTGATAGGTAGACT-AAAGGTAAAGAAGTCTATAAGGTT
1 AAAGCTGACAGGTAGACTAAAAGGTAAAGAAATCTATAAGGTC
* * *
1374065 AAAGCTGACAGGCAGACTAAAA-GTAAAGAAGTAT-TCAAGGTC
1 AAAGCTGACAGGTAGACTAAAAGGTAAAGAAATCTAT-AAGGTC
* ** * *
1374107 AAAGCCGACAGACAGACT-AAAGGTAAAGAAGTCTACAAGGTC
1 AAAGCTGACAGGTAGACTAAAAGGTAAAGAAATCTATAAGGTC
* * * * * *
1374149 AAGGTTGACAGGCAGACT-AAAGGTAAAGAAGTCTTTAGGGTC
1 AAAGCTGACAGGTAGACTAAAAGGTAAAGAAATCTATAAGGTC
* * * *
1374191 -AAGACCGACA--T-G-CAAAAAGGTAAAGAAGTCTCTAAGGTC
1 AAAG-CTGACAGGTAGACTAAAAGGTAAAGAAATCTATAAGGTC
1374230 AAAGC
1 AAAGC
1374235 AAATAGACAA
Statistics
Matches: 175, Mismatches: 29, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
38 1 0.01
39 24 0.14
40 3 0.02
41 6 0.03
42 137 0.78
43 4 0.02
ACGTcount: A:0.43, C:0.14, G:0.25, T:0.18
Consensus pattern (43 bp):
AAAGCTGACAGGTAGACTAAAAGGTAAAGAAATCTATAAGGTC
Found at i:1374065 original size:84 final size:85
Alignment explanation
Indices: 1373913--1374192 Score: 284
Period size: 84 Copynumber: 3.3 Consensus size: 85
1373903 GACGGGTAGA
* * * * * **
1373913 TAAAAGGTAAA-AAAGTCTTCTGGGTCAAGGTTGATGGGCAGA-TAAATGGTAATGAAGTCCCCA
1 TAAAAGGTAAAGAAA-TCTTCAGGGTCAAAGCTGATAGGCAGACTAAA-GGTAAAGAAGTCTACA
* * *
1373976 TGGTTAAAGCTGACAAGTAGA-
64 AGGTTAAAGCTGACAGGCAGAC
* *
1373997 TAAAAGGTAAAGAAATCTCTC-GGGTCAAAGCTGATAGGTAGACTAAAGGTAAAGAAGTCTATAA
1 TAAAAGGTAAAGAAATCT-TCAGGGTCAAAGCTGATAGGCAGACTAAAGGTAAAGAAGTCTACAA
1374061 GGTTAAAGCTGACAGGCAGAC
65 GGTTAAAGCTGACAGGCAGAC
* * * * * *
1374082 TAAAA-GTAAAGAAGTATTCAAGGTCAAAGCCGACAGACAGACTAAAGGTAAAGAAGTCTACAAG
1 TAAAAGGTAAAGAAATCTTCAGGGTCAAAGCTGATAGGCAGACTAAAGGTAAAGAAGTCTACAAG
* * *
1374146 GTCAAGGTTGACAGGCAGAC
66 GTTAAAGCTGACAGGCAGAC
* *
1374166 T-AAAGGTAAAGAAGTCTTTAGGGTCAA
1 TAAAAGGTAAAGAAATCTTCAGGGTCAA
1374193 GACCGACATG
Statistics
Matches: 165, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
83 5 0.03
84 146 0.88
85 14 0.08
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.20
Consensus pattern (85 bp):
TAAAAGGTAAAGAAATCTTCAGGGTCAAAGCTGATAGGCAGACTAAAGGTAAAGAAGTCTACAAG
GTTAAAGCTGACAGGCAGAC
Found at i:1374199 original size:84 final size:84
Alignment explanation
Indices: 1374036--1374234 Score: 257
Period size: 84 Copynumber: 2.4 Consensus size: 84
1374026 GCTGATAGGT
* *
1374036 AGACTAAAGGTAAAGAAGTCTATAAGGTTAAAGCTGACAGGCAGACTAAAAGTAAAGAAGTATTC
1 AGACTAAAGGTAAAGAAGTCTACAAGGTCAAAGCTGACAGGCAGACTAAAAGTAAAGAAGTATTC
1374101 AAGGTCAAAGCCGACA-GAC
66 AAGGTCAAAGCCGACATG-C
* * * * *
1374120 AGACTAAAGGTAAAGAAGTCTACAAGGTCAAGGTTGACAGGCAGACTAAAGGTAAAGAAGTCTTT
1 AGACTAAAGGTAAAGAAGTCTACAAGGTCAAAGCTGACAGGCAGACTAAAAGTAAAGAAGTATTC
*
1374185 AGGGTC-AAGACCGACATGC
66 AAGGTCAAAG-CCGACATGC
1374204 A-A--AAAGGTAAAGAAGTCT-CTAAGGTCAAAGC
1 AGACTAAAGGTAAAGAAGTCTAC-AAGGTCAAAGC
1374235 AAATAGACAA
Statistics
Matches: 102, Mismatches: 10, Indels: 9
0.84 0.08 0.07
Matches are distributed among these distances:
80 1 0.01
81 25 0.25
83 4 0.04
84 71 0.70
85 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.25, T:0.17
Consensus pattern (84 bp):
AGACTAAAGGTAAAGAAGTCTACAAGGTCAAAGCTGACAGGCAGACTAAAAGTAAAGAAGTATTC
AAGGTCAAAGCCGACATGC
Found at i:1374336 original size:42 final size:42
Alignment explanation
Indices: 1374272--1375567 Score: 614
Period size: 42 Copynumber: 30.8 Consensus size: 42
1374262 TCTCCATGGT
* * * *
1374272 AGACAAAAGGTAAATAAGTCTCTAGGGTCAAAGTTGGCAAGC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
* * *
1374314 AG-CTTAAAGGTAAAGAAGTCTCTAGGGTCAAAGCTGATAGGT
1 AGAC-TAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
* * *
1374356 AGACTAAAGGTAAAGAAGTCTCTAAGATCAAAGTCGACAGGC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
** *
1374398 AGACTAAAGGTAAAGAAGTCT-TCAGGGTCAAAGCCGACAAGC
1 AGACTAAAGGTAAAGAAGTCTCT-AGGGTCAAAGTTGACAGGC
* * * * ** * *
1374440 AAACTAAAGGATATAGAAGTCTGC-AAGATCAAAGCCGAGAGGT
1 AGACTAAAGG-TAAAGAAGTCT-CTAGGGTCAAAGTTGACAGGC
* * * ** *
1374483 AGACTAAAAGTAAAGAAGTCTCCAAGGTCAAAGCCGATAGGC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
* * * * * ** *
1374525 AGAC-AAAGATAAAAAAAATCTCTCGAGTCAAAGCCGACAGGA
1 AGACTAAAGGT-AAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
* * * ** *
1374567 AGACTAAAAGTAAAGAAGTCTCCAAGGTCAAAGTCAACAGGT
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
*** *
1374609 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGCCAACAAGC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
* * * ** * * *
1374651 AGAC-AAAGATAAAAAAATCTCCCGGGTCAAAGTTGATAAGT
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
* * *
1374692 AGACTTAAAGGTAAAGAAGTCTCTATAGGGTTAAAGTTGACAAGA
1 AGAC-TAAAGGTAAAGAAGTCTC--TAGGGTCAAAGTTGACAGGC
* * * * **
1374737 AGACTAAAGGTAAAGAAGTCTCCAAGGTTAAAGCTGACAAAC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
* * * ** * ** *
1374779 AGACTAAAAGTAAAGAAGTTTCCAGGGTTGAGGTCAACAAGC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
* * * * * * **
1374821 AGGCTAAAAGTAAAGAAATCTCCAAGGTCAAGGCCGACAGGC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
** *
1374863 AGACTAAAGGTAAAGAAGTCTCTAGGACCAAA-TTCGATAGGC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTT-GACAGGC
* * * * ** *
1374905 AGACTAAAGGTAAAGAAGTTTCCAAGGTCAAAATCAACAAGC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
** * * * ** **
1374947 AGACTAAAGGATGTAGAAGTCTCCAAGGTTAAAGCCGACATAC
1 AGACTAAAGG-TAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
* * * * ** *
1374990 AAACTAAATGTAAAGAAGTCTCTAAGGTCATAGCCGATAGGC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
* * * * * * *
1375032 AGACTAAAGGATATAGAAGTGTCGAAGGTCAAAGTGGATAGGT
1 AGACTAAAGG-TAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
* * * ** * *
1375075 AGACTAAAGGTAAAAAAGTCTCCAGGGTTAAAGCCGATAGGT
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
* * * **
1375117 AAACTAAAAGTAAAGAAGTCTCTAGGGTCAAAGCTGATTGGC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
** * * *** **
1375159 A-AAAAAAGGGTAAAGAAGTTTCTAGGTTCAAAACCGACAGAT
1 AGACTAAA-GGTAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
* * * *
1375201 AAACTAATGGATATAA-AAGTCTCTTGGGTCAAAGCTGACAGGC
1 AGACTAAAGG-TA-AAGAAGTCTCTAGGGTCAAAGTTGACAGGC
* * * *** *
1375244 AAACTAAAGGTAAAGAAGTCTCCAAGGTCAAAGCCAACAGGA
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
* ** * * * *
1375286 AAAC-AAAAATAAAAAAAGTCTCCCA-AGTCAAAGCTGACAGGC
1 AGACTAAAGGT-AAAGAAGTCT-CTAGGGTCAAAGTTGACAGGC
* * * * *
1375328 TGACTAAAGATAAAGAAATCTC-AAGGTCAAAGTCGACAGGC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
* * * *** *
1375369 AAACTAAAGGCAAAAAAGTCTCTAGGGTCAAAGCCAATTA-GC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGA-CAGGC
* * * * * * *
1375411 AAACTAAAGTTAAAGAAGTCTCAAAGGTCAGAGCTGACAAGC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
* * * *
1375453 AAAC-AAAGATAAAGAAATCTCCT-GGGTCACAGTTGAC-GAGC
1 AGACTAAAGGTAAAGAAGTCT-CTAGGGTCAAAGTTGACAG-GC
* * * * * * * *
1375494 AAACAAAAGGTGAAGAAATCT-TCCGGGTTAAAGCTGA-TGAGC
1 AGACTAAAGGTAAAGAAGTCTCT-AGGGTCAAAGTTGACAG-GC
*
1375536 AGAC-AAAGATAAAGAAGTCTCTTA-GGTCAAAG
1 AGACTAAAGGTAAAGAAGTCTC-TAGGGTCAAAG
1375568 CTGATGGGTA
Statistics
Matches: 975, Mismatches: 242, Indels: 75
0.75 0.19 0.06
Matches are distributed among these distances:
40 2 0.00
41 131 0.13
42 641 0.66
43 162 0.17
44 20 0.02
45 19 0.02
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.18
Consensus pattern (42 bp):
AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTTGACAGGC
Found at i:1374410 original size:84 final size:84
Alignment explanation
Indices: 1374272--1375567 Score: 834
Period size: 84 Copynumber: 15.4 Consensus size: 84
1374262 TCTCCATGGT
* * * * *
1374272 AGACAAAAGGTAAATAAGTCTCTAGGGTCAAAGTTGGCAAGCAG-CTTAAAGGTAAAGAAGTCTC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTCGACAGGCAGAC-TAAAGGTAAAGAAGTCTC
* * * * *
1374336 TAGGGTCAAAGCTGATAGGT
65 CAAGGTCAAAGCCGACAGGC
* * *
1374356 AGACTAAAGGTAAAGAAGTCTCTAAGATCAAAGTCGACAGGCAGACTAAAGGTAAAGAAGTCTTC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTCGACAGGCAGACTAAAGGTAAAGAAGTCTCC
* *
1374421 AGGGTCAAAGCCGACAAGC
66 AAGGTCAAAGCCGACAGGC
* * * * * * * *
1374440 AAACTAAAGGATATAGAAGTCTGC-AAGATCAAAGCCGAGAGGTAGACTAAAAGTAAAGAAGTCT
1 AGACTAAAGG-TAAAGAAGTCT-CTAGGGTCAAAGTCGACAGGCAGACTAAAGGTAAAGAAGTCT
*
1374504 CCAAGGTCAAAGCCGATAGGC
64 CCAAGGTCAAAGCCGACAGGC
* * * * * * * *
1374525 AGAC-AAAGATAAAAAAAATCTCTCGAGTCAAAGCCGACAGGAAGACTAAAAGTAAAGAAGTCTC
1 AGACTAAAGGT-AAAGAAGTCTCTAGGGTCAAAGTCGACAGGCAGACTAAAGGTAAAGAAGTCTC
* * *
1374589 CAAGGTCAAAGTCAACAGGT
65 CAAGGTCAAAGCCGACAGGC
* * * * * *
1374609 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGCCAACAAGCAGAC-AAAGATAAAAAAATCTCC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTCGACAGGCAGACTAAAGGTAAAGAAGTCTCC
** ** * * *
1374673 CGGGTCAAAGTTGATAAGT
66 AAGGTCAAAGCCGACAGGC
* * * *
1374692 AGACTTAAAGGTAAAGAAGTCTCTATAGGGTTAAAGTTGACAAGAAGACTAAAGGTAAAGAAGTC
1 AGAC-TAAAGGTAAAGAAGTCTC--TAGGGTCAAAGTCGACAGGCAGACTAAAGGTAAAGAAGTC
* * **
1374757 TCCAAGGTTAAAGCTGACAAAC
63 TCCAAGGTCAAAGCCGACAGGC
* * * ** * * * * * *
1374779 AGACTAAAAGTAAAGAAGTTTCCAGGGTTGAGGTCAACAAGCAGGCTAAAAGTAAAGAAATCTCC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTCGACAGGCAGACTAAAGGTAAAGAAGTCTCC
*
1374844 AAGGTCAAGGCCGACAGGC
66 AAGGTCAAAGCCGACAGGC
** * * *
1374863 AGACTAAAGGTAAAGAAGTCTCTAGGACCAAATTCGATAGGCAGACTAAAGGTAAAGAAGTTTCC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTCGACAGGCAGACTAAAGGTAAAGAAGTCTCC
** * *
1374928 AAGGTCAAAATCAACAAGC
66 AAGGTCAAAGCCGACAGGC
** * * * * ** * *
1374947 AGACTAAAGGATGTAGAAGTCTCCAAGGTTAAAGCCGACATACAAACTAAATGTAAAGAAGTCTC
1 AGACTAAAGG-TAAAGAAGTCTCTAGGGTCAAAGTCGACAGGCAGACTAAAGGTAAAGAAGTCTC
* * *
1375012 TAAGGTCATAGCCGATAGGC
65 CAAGGTCAAAGCCGACAGGC
* * * * * * * *
1375032 AGACTAAAGGATATAGAAGTGTCGAAGGTCAAAGTGGATAGGTAGACTAAAGGTAAAAAAGTCTC
1 AGACTAAAGG-TAAAGAAGTCTCTAGGGTCAAAGTCGACAGGCAGACTAAAGGTAAAGAAGTCTC
* * * *
1375097 CAGGGTTAAAGCCGATAGGT
65 CAAGGTCAAAGCCGACAGGC
* * ** **
1375117 AAACTAAAAGTAAAGAAGTCTCTAGGGTCAAAG-CTGATTGGCA-AAAAAAGGGTAAAGAAGT-T
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTC-GACAGGCAGACTAAA-GGTAAAGAAGTCT
* * * **
1375179 TCTAGGTTCAAAACCGACAGAT
64 CCAAGG-TCAAAGCCGACAGGC
* * * *
1375201 AAACTAATGGATATAA-AAGTCTCTTGGGTCAAAG-CTGACAGGCAAACTAAAGGTAAAGAAGTC
1 AGACTAAAGG-TA-AAGAAGTCTCTAGGGTCAAAGTC-GACAGGCAGACTAAAGGTAAAGAAGTC
* *
1375264 TCCAAGGTCAAAGCCAACAGGA
63 TCCAAGGTCAAAGCCGACAGGC
* ** * * * * * *
1375286 AAAC-AAAAATAAAAAAAGTCTCCCA-AGTCAAAG-CTGACAGGCTGACTAAAGATAAAGAAATC
1 AGACTAAAGGT-AAAGAAGTCT-CTAGGGTCAAAGTC-GACAGGCAGACTAAAGGTAAAGAAGTC
*
1375348 T-CAAGGTCAAAGTCGACAGGC
63 TCCAAGGTCAAAGCCGACAGGC
* * * * * * * *
1375369 AAACTAAAGGCAAAAAAGTCTCTAGGGTCAAAGCCAATTA-GCAAACTAAAGTTAAAGAAGTCTC
1 AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTCGA-CAGGCAGACTAAAGGTAAAGAAGTCTC
* * * *
1375433 AAAGGTCAGAGCTGACAAGC
65 CAAGGTCAAAGCCGACAGGC
* * * * * * * * *
1375453 AAAC-AAAGATAAAGAAATCTCCT-GGGTCACAGTTGAC-GAGCAAACAAAAGGTGAAGAAATCT
1 AGACTAAAGGTAAAGAAGTCT-CTAGGGTCAAAGTCGACAG-GCAGACTAAAGGTAAAGAAGTC-
* * * *
1375515 TCC-GGGTTAAAGCTGA-TGAGC
63 TCCAAGGTCAAAGCCGACAG-GC
*
1375536 AGAC-AAAGATAAAGAAGTCTCTTA-GGTCAAAG
1 AGACTAAAGGTAAAGAAGTCTC-TAGGGTCAAAG
1375568 CTGATGGGTA
Statistics
Matches: 948, Mismatches: 231, Indels: 67
0.76 0.19 0.05
Matches are distributed among these distances:
82 3 0.00
83 179 0.19
84 435 0.46
85 253 0.27
86 47 0.05
87 31 0.03
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.18
Consensus pattern (84 bp):
AGACTAAAGGTAAAGAAGTCTCTAGGGTCAAAGTCGACAGGCAGACTAAAGGTAAAGAAGTCTCC
AAGGTCAAAGCCGACAGGC
Found at i:1375126 original size:296 final size:294
Alignment explanation
Indices: 1374318--1375150 Score: 768
Period size: 296 Copynumber: 2.8 Consensus size: 294
1374308 GCAAGCAGCT
* * * ** * * * *
1374318 TAAAGGTAAAGAAGTCTCTAGGGTCAAAGCTGATAGGTAGACTAAAGG-TAAAGAAGTCTCTAAG
1 TAAAGGTAAAGAAGTCTCCAAGGTCAAAACCAACAAGCAGACTAAAGGATAAAGAAGTCTCCAAG
* * * *
1374382 ATCAAAGTCGACAGGCAGACTAAAGGTAAAGAAGTCT-TCAGGGTCAAAGCCGACAAGCAAACTA
66 GTCAAAGTCGACA-ACAGACTAAAGGTAAAGAAGTCTCT-AAGGTCAAAGCCGACAAGCAGACTA
* * * *
1374446 AAGGATATAGAAGTCT-GCAAGATCAAAGCCGAGAGGTAGACTAAAAGTAAAGAAGTCTCCAAGG
129 AAGGATATAGAAGTCTCG-AAGGTCAAAG-TGACAGGTAGACTAAAAGTAAAGAAGTCTCCAGGG
* * *
1374510 TCAAAGCCGATAGGCAGAC--AAAGATAAAAAAAATCTCTCGA-GTCAAAGCCGACAGGAAGACT
192 TTAAAGCCGATAGGCAGACTAAAAG-T-AAAGAAATCTC-CAAGGTCAAAGCCGACAGGAAGACT
* *
1374572 AAAAGTAAAGAAGTCTCCAAGGTCAAAGTCAACAGGTAGAC
254 AAAAGTAAAGAAGTCTCCAAGGCCAAAGTCAACAGGCAGAC
* * * * * **
1374613 TAAAGGTAAAGAAGTCTCTAGGGTCAAAGCCAACAAGCAGAC-AAA-GATAAAAAAATCTCCCGG
1 TAAAGGTAAAGAAGTCTCCAAGGTCAAAACCAACAAGCAGACTAAAGGATAAAGAAGTCTCCAAG
* * * * ** *
1374676 GTCAAAGTTGATAAGTAGACTTAAAGGTAAAGAAGTCTCTATAGGGTTAAAGTTGACAAGAAGAC
66 GTCAAAGTCGACAA-CAGAC-TAAAGGTAAAGAAGTCTCTA-A-GGTCAAAGCCGACAAGCAGAC
* * * *** *
1374741 TAAAGG-TAAAGAAGTCTCCAAGGTTAAAGCTGACAAACAGACTAAAAGTAAAGAAGTTTCCAGG
127 TAAAGGATATAGAAGTCTCGAAGGTCAAAG-TGACAGGTAGACTAAAAGTAAAGAAGTCTCCAGG
* * * * * * * * *
1374805 GTTGAGGTCAACAAGCAGGCTAAAAGTAAAGAAATCTCCAAGGTCAAGGCCGACAGGCAGACTAA
191 GTTAAAGCCGATAGGCAGACTAAAAGTAAAGAAATCTCCAAGGTCAAAGCCGACAGGAAGACTAA
* * * * *
1374870 AGGTAAAGAAGTCT-CTAGGACCAAATTCGATAGGCAGAC
256 AAGTAAAGAAGTCTCCAAGG-CCAAAGTCAACAGGCAGAC
* * **
1374909 TAAAGGTAAAGAAGTTTCCAAGGTCAAAATCAACAAGCAGACTAAAGGATGTAGAAGTCTCCAAG
1 TAAAGGTAAAGAAGTCTCCAAGGTCAAAACCAACAAGCAGACTAAAGGATAAAGAAGTCTCCAAG
* * * * * * *
1374974 GTTAAAGCCGACATACAAACTAAATGTAAAGAAGTCTCTAAGGTCATAGCCGATAGGCAGACTAA
66 GTCAAAGTCGACA-ACAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAAGCAGACTAA
* * * *
1375039 AGGATATAGAAGTGTCGAAGGTCAAAGTGGATAGGTAGACTAAAGGTAAAAAAGTCTCCAGGGTT
130 AGGATATAGAAGTCTCGAAGGTCAAAGT-GACAGGTAGACTAAAAGTAAAGAAGTCTCCAGGGTT
* * * * *
1375104 AAAGCCGATAGGTAAACTAAAAGTAAAGAAGTCTCTAGGGTCAAAGC
194 AAAGCCGATAGGCAGACTAAAAGTAAAGAAATCTCCAAGGTCAAAGC
1375151 TGATTGGCAA
Statistics
Matches: 422, Mismatches: 100, Indels: 31
0.76 0.18 0.06
Matches are distributed among these distances:
293 1 0.00
294 28 0.07
295 82 0.19
296 237 0.56
297 45 0.11
298 28 0.07
299 1 0.00
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.18
Consensus pattern (294 bp):
TAAAGGTAAAGAAGTCTCCAAGGTCAAAACCAACAAGCAGACTAAAGGATAAAGAAGTCTCCAAG
GTCAAAGTCGACAACAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAAGCAGACTAAA
GGATATAGAAGTCTCGAAGGTCAAAGTGACAGGTAGACTAAAAGTAAAGAAGTCTCCAGGGTTAA
AGCCGATAGGCAGACTAAAAGTAAAGAAATCTCCAAGGTCAAAGCCGACAGGAAGACTAAAAGTA
AAGAAGTCTCCAAGGCCAAAGTCAACAGGCAGAC
Found at i:1375179 original size:254 final size:253
Alignment explanation
Indices: 1374318--1375567 Score: 830
Period size: 254 Copynumber: 4.9 Consensus size: 253
1374308 GCAAGCAGCT
* * * * * * *
1374318 TAAAGGTAAAGAAGTCTCTAGGGTCAAAGCTGATAGGTAGACTAAAGGTAAAGAAGTCTCTAAGA
1 TAAAAGTAAAAAAGTCTCCAAGGTCAAAGCCGACAGGTAGACTAAAGGTAAAGAAGTCTCTAGGA
* * *
1374383 TCAAAG-TCGACAGGCAGACTAAAGGTAAAGAAGTCTTCAGGGTCAAAGCCGACAAGCAAACTAA
66 TCAAAGCTCGACAGGCAGAATAAAGGTAAAGAAGT-TTCAAGGTCAAAACCGACAAGCAAACTAA
* * * ** * *
1374447 AGGATATAGAAGTCTGCAAGATCAAAGCCGAGAGGTAGACTAAAAGTAAAGAAGTCTCCAAGGTC
130 AGGATATAGAAGTCTCCAAGGTCAAAGCCGACAGACAAACTAAAGGTAAAGAAGTCTCCAAGGTC
* * *
1374512 AAAGCCGATAGGCAGAC-AAAGATAAAAAAAATCTCTCG-A-GTCAAAGCCGACAGGAAGAC
195 AAAGCCGATAGGCAGACTAAAGAT--AAAGAA-GTCTCGAAGGTCAAAGTCGACAGGAAGAC
* * * *
1374571 TAAAAGTAAAGAAGTCTCCAAGGTCAAAGTCAACAGGTAGACTAAAGGTAAAGAAGTCTCTAGGG
1 TAAAAGTAAAAAAGTCTCCAAGGTCAAAGCCGACAGGTAGACTAAAGGTAAAGAAGTCTCTAGGA
* * * * * * * ** *** * * *
1374636 TCAAAGC-CAACAAGCAG-ACAAAGATAAAAAAATCTCCCGGGTCAAAGTTGATAAGTAGACTTA
66 TCAAAGCTCGACAGGCAGAATAAAGGTAAAGAAGT-TTCAAGGTCAAAACCGACAAGCAAAC-TA
* * * ** *
1374699 AAGG-TAAAGAAGTCTCTATAGGGTTAAAGTTGACAAGA-AGACTAAAGGTAAAGAAGTCTCCAA
129 AAGGATATAGAAGTCTCCA-A-GGTCAAAGCCGAC-AGACAAACTAAAGGTAAAGAAGTCTCCAA
* * * ** * * * ** * * * * *
1374762 GGTTAAAGCTGACAAACAGACTAAA-AGTAAAGAAGTTTCCAGGGTTGAGGTCAACAAGCAGGC
191 GGTCAAAGCCGATAGGCAGACTAAAGA-TAAAGAAGTCTCGAAGGTCAAAGTCGACAGGAAGAC
* *
1374825 TAAAAGTAAAGAAA-TCTCCAAGGTCAAGGCCGACAGGCAGACTAAAGGTAAAGAAGTCTCTAGG
1 TAAAAGTAAA-AAAGTCTCCAAGGTCAAAGCCGACAGGTAGACTAAAGGTAAAGAAGTCTCTAGG
* * * * * * *
1374889 ACCAAA-TTCGATAGGCAGACTAAAGGTAAAGAAGTTTCCAAGGTCAAAATCAACAAGCAGACTA
65 ATCAAAGCTCGACAGGCAGAATAAAGGTAAAGAAGTTT-CAAGGTCAAAACCGACAAGCAAACTA
* * * * *
1374953 AAGGATGTAGAAGTCTCCAAGGTTAAAGCCGACATACAAACTAAATGTAAAGAAGTCTCTAAGGT
129 AAGGATATAGAAGTCTCCAAGGTCAAAGCCGACAGACAAACTAAAGGTAAAGAAGTCTCCAAGGT
* * * * * *
1375018 CATAGCCGATAGGCAGACTAAAGGATATAGAAGTGTCGAAGGTCAAAGTGGATAGGTAGAC
194 CAAAGCCGATAGGCAGACTAAA-GATAAAGAAGTCTCGAAGGTCAAAGTCGACAGGAAGAC
* * * * * * *
1375079 TAAAGGTAAAAAAGTCTCCAGGGTTAAAGCCGATAGGTAAACTAAAAGTAAAGAAGTCTCTAGGG
1 TAAAAGTAAAAAAGTCTCCAAGGTCAAAGCCGACAGGTAGACTAAAGGTAAAGAAGTCTCTAGGA
** * * *
1375144 TCAAAGCT-GATTGGCA-AAAAAAGGGTAAAGAAGTTTCTAGGTTCAAAACCGAC-AGATAAACT
66 TCAAAGCTCGACAGGCAGAATAAA-GGTAAAGAAGTTTCAAGG-TCAAAACCGACAAG-CAAACT
* * *** * *
1375206 AATGGATATAAAAGTCTCTTGGGTCAAAGCTGACAGGCAAACTAAAGGTAAAGAAGTCTCCAAGG
128 AAAGGATATAGAAGTCTCCAAGGTCAAAGCCGACAGACAAACTAAAGGTAAAGAAGTCTCCAAGG
* * * * * * * **
1375271 TCAAAGCCAACAGGAAAAC-AAAAATAAAAAAAGTCTCCCAA-GTCAAAG-CTGACAGGCTGAC
193 TCAAAGCCGATAGGCAGACTAAAGAT-AAAGAAGTCT-CGAAGGTCAAAGTC-GACAGGAAGAC
* * * * *
1375332 T-AAAGATAAAGAAA-TCT-CAAGGTCAAAGTCGACAGGCAAACTAAAGGCAAAAAAGTCTCTAG
1 TAAAAG-TAAA-AAAGTCTCCAAGGTCAAAGCCGACAGGTAGACTAAAGGTAAAGAAGTCTCTAG
* * * * * * * *
1375394 GGTCAAAGC-CAATTA-GCA-AACTAAAGTTAAAGAAGTCTCAAAGGTCAGAGCTGACAAGCAAA
64 GATCAAAGCTCGA-CAGGCAGAA-TAAAGGTAAAGAAGTTTC-AAGGTCAAAACCGACAAGCAAA
* * ** * ** * * *
1375456 C-AAA-GATAAAGAAATCTCCTGGGTCACAGTTGAC-GAGCAAACAAAAGGTGAAGAAATCTTCC
126 CTAAAGGATATAGAAGTCTCCAAGGTCAAAGCCGACAGA-CAAACTAAAGGTAAAGAAGTC-TCC
* * * **
1375518 -GGGTTAAAGCTGAT-GAGCAGAC-AAAGATAAAGAAGTCTCTTAGGTCAAAG
189 AAGGTCAAAGCCGATAG-GCAGACTAAAGATAAAGAAGTCTCGAAGGTCAAAG
1375568 CTGATGGGTA
Statistics
Matches: 772, Mismatches: 189, Indels: 76
0.74 0.18 0.07
Matches are distributed among these distances:
248 2 0.00
249 18 0.02
250 60 0.08
251 5 0.01
252 128 0.17
253 189 0.24
254 321 0.42
255 49 0.06
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.18
Consensus pattern (253 bp):
TAAAAGTAAAAAAGTCTCCAAGGTCAAAGCCGACAGGTAGACTAAAGGTAAAGAAGTCTCTAGGA
TCAAAGCTCGACAGGCAGAATAAAGGTAAAGAAGTTTCAAGGTCAAAACCGACAAGCAAACTAAA
GGATATAGAAGTCTCCAAGGTCAAAGCCGACAGACAAACTAAAGGTAAAGAAGTCTCCAAGGTCA
AAGCCGATAGGCAGACTAAAGATAAAGAAGTCTCGAAGGTCAAAGTCGACAGGAAGAC
Found at i:1375449 original size:125 final size:124
Alignment explanation
Indices: 1375227--1375473 Score: 302
Period size: 125 Copynumber: 2.0 Consensus size: 124
1375217 AAGTCTCTTG
* *
1375227 GGTCAAAGCTGACAGGCAAACTAAAGGTAAAGAAGTCTCCAAGGTCAAAGCCAACAGGAAAACAA
1 GGTCAAAGCTGACAGGCAAACTAAAGGCAAAAAAGTCTCCAAGGTCAAAGCCAACAGGAAAACAA
* * **
1375292 AAATAAAAAAAGTCTCCCAAGTCAAAGCTGACAGGCTGACTAAAGATAAAGAAATCTCAA
66 AAATAAAAAAAGTCTCCAAAGTCAAAGCTGACAAGCAAAC-AAAGATAAAGAAATCTCAA
* * * *
1375352 GGTCAAAG-TCGACAGGCAAACTAAAGGCAAAAAAGTCTCTAGGGTCAAAGCCAATTA-GCAAAC
1 GGTCAAAGCT-GACAGGCAAACTAAAGGCAAAAAAGTCTCCAAGGTCAAAGCCAA-CAGGAAAAC
* * * * *
1375415 TAAAGTTAAAGAAGTCT-CAAAGGTCAGAGCTGACAAGCAAACAAAGATAAAGAAATCTC
64 AAAAATAAAAAAAGTCTCCAAA-GTCAAAGCTGACAAGCAAACAAAGATAAAGAAATCTC
1375474 CTGGGTCACA
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
124 21 0.20
125 82 0.79
126 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.15
Consensus pattern (124 bp):
GGTCAAAGCTGACAGGCAAACTAAAGGCAAAAAAGTCTCCAAGGTCAAAGCCAACAGGAAAACAA
AAATAAAAAAAGTCTCCAAAGTCAAAGCTGACAAGCAAACAAAGATAAAGAAATCTCAA
Found at i:1375481 original size:125 final size:126
Alignment explanation
Indices: 1375220--1375503 Score: 301
Period size: 125 Copynumber: 2.3 Consensus size: 126
1375210 GATATAAAAG
* * *
1375220 TCTCTTGGGTCAAAG-CTGACAGGCAAACTAAAGGTAAAGAAGTCTCCAAGGTCAAAGCCAACAG
1 TCTCCTGGGTCAAAGTC-GACAGGCAAACTAAAGGCAAAAAAGTCTCCAAGGTCAAAGCCAACAG
* * **
1375284 GAAAACAAAAATAAAAAAAGTCTCCCAAGTCAAAGCTGACAGGCTGACTAAAGATAAAGAAA
65 GAAAACAAAAATAAAAAAAGTCTCCAAAGTCAAAGCTGACAAGCAAACTAAAGATAAAGAAA
** * * *
1375346 TCT-CAAGGTCAAAGTCGACAGGCAAACTAAAGGCAAAAAAGTCTCTAGGGTCAAAGCCAATTA-
1 TCTCCTGGGTCAAAGTCGACAGGCAAACTAAAGGCAAAAAAGTCTCCAAGGTCAAAGCCAA-CAG
* * * * * *
1375409 GCAAACTAAAGTTAAAGAAGTCT-CAAAGGTCAGAGCTGACAAGCAAAC-AAAGATAAAGAAA
65 GAAAACAAAAATAAAAAAAGTCTCCAAA-GTCAAAGCTGACAAGCAAACTAAAGATAAAGAAA
* * *
1375470 TCTCCTGGGTCACAGTTGAC-GAGCAAACAAAAGG
1 TCTCCTGGGTCAAAGTCGACAG-GCAAACTAAAGG
1375504 TGAAGAAATC
Statistics
Matches: 130, Mismatches: 23, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
124 20 0.15
125 105 0.81
126 5 0.04
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (126 bp):
TCTCCTGGGTCAAAGTCGACAGGCAAACTAAAGGCAAAAAAGTCTCCAAGGTCAAAGCCAACAGG
AAAACAAAAATAAAAAAAGTCTCCAAAGTCAAAGCTGACAAGCAAACTAAAGATAAAGAAA
Found at i:1375617 original size:36 final size:38
Alignment explanation
Indices: 1375559--1375632 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 38
1375549 GAAGTCTCTT
* ***
1375559 AGGTCAAAGCTGATGGGTAGAC-AAAAAAAGT-TTCCA
1 AGGTCAAAGCTAATGAACAGACAAAAAAAAGTCTTCCA
1375595 AGGTCAAAGCTAATGAACAGACAAAAAAAAGTCTTCCA
1 AGGTCAAAGCTAATGAACAGACAAAAAAAAGTCTTCCA
1375633 GGTTTGAGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 18 0.56
37 9 0.28
38 5 0.16
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.18
Consensus pattern (38 bp):
AGGTCAAAGCTAATGAACAGACAAAAAAAAGTCTTCCA
Found at i:1375928 original size:88 final size:87
Alignment explanation
Indices: 1375822--1376109 Score: 351
Period size: 88 Copynumber: 3.3 Consensus size: 87
1375812 ATGCAAATTG
* * * *
1375822 TTTGACCAGGGTGGTAACCATATGTCAAATCGGAATGAAAAGAATTTGACAAGGGTGGTAACCAT
1 TTTGACCAAGGTGGTAACCATACGTCAAATCGAAATGAAAAGAATCTGAC-AGGGTGGTAACCAT
1375887 ACGTCAGACAAGAAAGAGGCAAA
65 ACGTCAGACAAGAAAGAGGCAAA
* * * * **
1375910 TTTGACCAAGGTGATAACCATACGTCAAATCAAAATGAAAAGAATCTGATCGGGGTAGTAATAAT
1 TTTGACCAAGGTGGTAACCATACGTCAAATCGAAATGAAAAGAATCTGA-CAGGGTGGTAACCAT
* * *
1375975 ATGTCAGACAAGAAGGAGGCGAA
65 ACGTCAGACAAGAAAGAGGCAAA
* * *
1375998 TTTGACTAAGGTGGTAACCATACGTCAAATCGAAATGAAAAAAATCTGACCAGGGTGATAACCAT
1 TTTGACCAAGGTGGTAACCATACGTCAAATCGAAATGAAAAGAATCTGA-CAGGGTGGTAACCAT
* * * *
1376063 ACATCAGATAGGAAAGAGGCAGA
65 ACGTCAGACAAGAAAGAGGCAAA
* *
1376086 TTTAACCAGGGTGGTAACCATACG
1 TTTGACCAAGGTGGTAACCATACG
1376110 CTAGACAAGA
Statistics
Matches: 166, Mismatches: 33, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
88 165 0.99
89 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.20
Consensus pattern (87 bp):
TTTGACCAAGGTGGTAACCATACGTCAAATCGAAATGAAAAGAATCTGACAGGGTGGTAACCATA
CGTCAGACAAGAAAGAGGCAAA
Found at i:1376116 original size:132 final size:132
Alignment explanation
Indices: 1375980--1376239 Score: 337
Period size: 132 Copynumber: 2.0 Consensus size: 132
1375970 ATAATATGTC
* *
1375980 AGACAAGAAGGAGGC-GAATTTGACTAAGGTGGTAACCATACGTCAAATC-GAAATGAAAAAAAT
1 AGACAAGAAGAAGGCAG-ATTTGACTAAGGTGGTAACCATACGTCAAATCAG-AACGAAAAAAAT
* *
1376043 CTGACCAGGGT-GATAACCATACATCAGATAGGAAAGAGGCAGATTTAACCAGGGTGGTAACCAT
64 CTGACCAGGGTCG-TAACCATACATCAGACAAGAAAGAGGCAGATTTAACCAGGGTGGTAACCAT
1376107 ACGCT
128 ACGCT
* * * * *
1376112 AGACAAGAAGAATGCAGATTTGATTAGGGTGGTAACTATACGTCAAATCAGAACGAAAAGAATCT
1 AGACAAGAAGAAGGCAGATTTGACTAAGGTGGTAACCATACGTCAAATCAGAACGAAAAAAATCT
* * * * * *
1376177 GACTAGGGTCGTAACCATACGTCAGACAAGAGAGAGGTAGATTTGACCAGGGTGGTAATCATA
66 GACCAGGGTCGTAACCATACATCAGACAAGAAAGAGGCAGATTTAACCAGGGTGGTAACCATA
1376240 TGTCAAATCA
Statistics
Matches: 110, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
132 107 0.97
133 3 0.03
ACGTcount: A:0.39, C:0.15, G:0.26, T:0.20
Consensus pattern (132 bp):
AGACAAGAAGAAGGCAGATTTGACTAAGGTGGTAACCATACGTCAAATCAGAACGAAAAAAATCT
GACCAGGGTCGTAACCATACATCAGACAAGAAAGAGGCAGATTTAACCAGGGTGGTAACCATACG
CT
Found at i:1376185 original size:88 final size:88
Alignment explanation
Indices: 1376090--1376372 Score: 279
Period size: 88 Copynumber: 3.2 Consensus size: 88
1376080 GGCAGATTTA
* **
1376090 ACCAGGGTGGTAACCATACG-CTAGACAAGA-AGAATGCAGATTTGATTAGGGTGGTAA-CTATA
1 ACCAGGGTGGTAACCATACGTC-AGACAAGAGAG-AGGCAGATTTGACCAGGGTGGTAATC-ATA
*
1376152 CGTCAAATCAGAACGAAAAGAATCTG
63 CGTCAAATCAGAACGAAAAGAATCAG
* * * *
1376178 ACTAGGGTCGTAACCATACGTCAGACAAGAGAGAGGTAGATTTGACCAGGGTGGTAATCATATGT
1 ACCAGGGTGGTAACCATACGTCAGACAAGAGAGAGGCAGATTTGACCAGGGTGGTAATCATACGT
* * *
1376243 CAAATCATAATGAAAAGAGTCAG
66 CAAATCAGAACGAAAAGAATCAG
** * * ** * * * *
1376266 ACCAGGGTGGTAACTGTACATCAGACAAGAGAGAGGTAGATTTTCCCAAGGCGGTAACCATACAT
1 ACCAGGGTGGTAACCATACGTCAGACAAGAGAGAGGCAGATTTGACCAGGGTGGTAATCATACGT
*
1376331 CAAATC-GAAATGAAAAGAATCTA-
66 CAAATCAG-AACGAAAAGAATC-AG
*
1376354 ACAAGGGTGGTAACCATAC
1 ACCAGGGTGGTAACCATAC
1376373 ATTAGATAGG
Statistics
Matches: 162, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
88 157 0.97
89 5 0.03
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.20
Consensus pattern (88 bp):
ACCAGGGTGGTAACCATACGTCAGACAAGAGAGAGGCAGATTTGACCAGGGTGGTAATCATACGT
CAAATCAGAACGAAAAGAATCAG
Found at i:1376229 original size:44 final size:43
Alignment explanation
Indices: 1375822--1376244 Score: 209
Period size: 44 Copynumber: 9.6 Consensus size: 43
1375812 ATGCAAATTG
* * *
1375822 TTTGACCAGGGTGGTAACCATATGTCAAATCGGAATGAA-AAG-A-A
1 TTTGACCAGGGTGGTAACCATACGTCAGA-C--AA-GAAGAGGCAGA
* *
1375866 TTTGACAAGGGTGGTAACCATACGTCAGACAAGAAAGAGGCAAA
1 TTTGACCAGGGTGGTAACCATACGTCAGACAAG-AAGAGGCAGA
* * * **
1375910 TTTGACCAAGGTGATAACCATACGTCAAATCAA-AATGA-AAAGAA
1 TTTGACCAGGGTGGTAACCATACGTCAGA-CAAGAA-GAGGCAG-A
* * * * ** *
1375954 TCTGATCGGGGTAGTAATAATATGTCAGACAAGAAGGAGGC-GAA
1 TTTGACCAGGGTGGTAACCATACGTCAGACAAGAA-GAGGCAG-A
* * * * *** *
1375998 TTTGACTAAGGTGGTAACCATACGTCAAATCGAA-ATGAAAAAAA
1 TTTGACCAGGGTGGTAACCATACGTCAGA-C-AAGAAGAGGCAGA
* * * * *
1376042 TCTGACCAGGGTGATAACCATACATCAGATAGGAAAGAGGCAGA
1 TTTGACCAGGGTGGTAACCATACGTCAGACAAG-AAGAGGCAGA
* *
1376086 TTTAACCAGGGTGGTAACCATACG-CTAGACAAGAAGAATGCAGA
1 TTTGACCAGGGTGGTAACCATACGTC-AGACAAGAAG-AGGCAGA
** * * **
1376130 TTTGATTAGGGTGGTAACTATACGTCAAATC-AGAACGA-AAAGAA
1 TTTGACCAGGGTGGTAACCATACGTCAGA-CAAGAA-GAGGCAG-A
* * * *
1376174 TCTGACTAGGGTCGTAACCATACGTCAGACAAGAGAGAGGTAGA
1 TTTGACCAGGGTGGTAACCATACGTCAGACAAGA-AGAGGCAGA
* *
1376218 TTTGACCAGGGTGGTAATCATATGTCA
1 TTTGACCAGGGTGGTAACCATACGTCA
1376245 AATCATAATG
Statistics
Matches: 278, Mismatches: 78, Indels: 46
0.69 0.19 0.11
Matches are distributed among these distances:
40 1 0.00
41 4 0.01
42 3 0.01
43 15 0.05
44 242 0.87
45 11 0.04
46 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (43 bp):
TTTGACCAGGGTGGTAACCATACGTCAGACAAGAAGAGGCAGA
Found at i:1376460 original size:39 final size:39
Alignment explanation
Indices: 1376401--1376480 Score: 124
Period size: 39 Copynumber: 2.1 Consensus size: 39
1376391 GAGTTTGACT
* *
1376401 AGGCCCTAACACCAATACAATCAAATAAGGGATGGAAAA
1 AGGCCCTAACACCAATACAATCAAATAAGAGATGAAAAA
* *
1376440 AGGCTCTAACACCAATACAATCAAATGAGAGATGAAAAA
1 AGGCCCTAACACCAATACAATCAAATAAGAGATGAAAAA
1376479 AG
1 AG
1376481 TTTGACTAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.50, C:0.19, G:0.17, T:0.14
Consensus pattern (39 bp):
AGGCCCTAACACCAATACAATCAAATAAGAGATGAAAAA
Found at i:1376513 original size:36 final size:36
Alignment explanation
Indices: 1376454--1376525 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
1376444 TCTAACACCA
* *
1376454 ATACAATCAAATGAGAGATGAAAAAAGTTTGACTAG
1 ATACAATCAAACGAGAGAAGAAAAAAGTTTGACTAG
*
1376490 ATACAATCAAACGAG-GAAAGAAAAGAGTTTGACTAG
1 ATACAATCAAACGAGAG-AAGAAAAAAGTTTGACTAG
1376526 GCCTTAACAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 1 0.03
36 31 0.97
ACGTcount: A:0.50, C:0.10, G:0.21, T:0.19
Consensus pattern (36 bp):
ATACAATCAAACGAGAGAAGAAAAAAGTTTGACTAG
Found at i:1378626 original size:15 final size:15
Alignment explanation
Indices: 1378602--1378631 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1378592 CATTCCGTTT
*
1378602 TTTCTTTTTTTTTTC
1 TTTCTCTTTTTTTTC
1378617 TTTCTCTTTTTTTTC
1 TTTCTCTTTTTTTTC
1378632 ACGCTCCTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTCTCTTTTTTTTC
Found at i:1383450 original size:32 final size:31
Alignment explanation
Indices: 1383414--1383476 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1383404 AATTTTTATG
*
1383414 ATAGTTTTTATTGGAAGAAAAGGAATTTATTT
1 ATAG-TTTTATTAGAAGAAAAGGAATTTATTT
* *
1383446 ATAGTTTTGTTAGAAGAAAATGAATTTATTT
1 ATAGTTTTATTAGAAGAAAAGGAATTTATTT
1383477 GTTATTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.44
Consensus pattern (31 bp):
ATAGTTTTATTAGAAGAAAAGGAATTTATTT
Found at i:1385338 original size:34 final size:34
Alignment explanation
Indices: 1385300--1385408 Score: 104
Period size: 28 Copynumber: 3.3 Consensus size: 34
1385290 TTTTTTTCTT
1385300 TTGCTGTTTCAATTCTATTTTTTTCTTCCTCCTC
1 TTGCTGTTTCAATTCTATTTTTTTCTTCCTCCTC
* * **
1385334 TTGCTGTTTCGATT-TCTTCCTTT-TT--T--TC
1 TTGCTGTTTCAATTCTATTTTTTTCTTCCTCCTC
1385362 TTGCTGTTTCAATTCTATTTTTTCTTCCTTCCTCCTC
1 TTGCTGTTTCAATTCTA-TTTTT-TT-CTTCCTCCTC
*
1385399 TTGTTGTTTC
1 TTGCTGTTTC
1385409 TATTTCTTCA
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
28 15 0.26
29 1 0.02
30 4 0.07
31 2 0.04
32 2 0.04
33 8 0.14
34 13 0.23
35 1 0.02
37 11 0.19
ACGTcount: A:0.06, C:0.25, G:0.08, T:0.61
Consensus pattern (34 bp):
TTGCTGTTTCAATTCTATTTTTTTCTTCCTCCTC
Found at i:1385374 original size:62 final size:62
Alignment explanation
Indices: 1385290--1385454 Score: 213
Period size: 65 Copynumber: 2.6 Consensus size: 62
1385280 TTTGTTTTCT
*
1385290 TTTTTTTCTTTTGCTGTTTCAATTCTATTTTTTTCTTCCTCCTCTTGCTGTTTCGATTTCTTCC
1 TTTTTTTC--TTGCTGTTTCAATTCTATTTTTTTCTTCCTCCTCTTGCTGTTTCGATTTCTTCA
* *
1385354 TTTTTTTCTTGCTGTTTCAATTCTATTTTTTCTTCCTTCCTCCTCTTGTTGTTTCTATTTCTTCA
1 TTTTTTTCTTGCTGTTTCAATTCTA-TTTTT-TT-CTTCCTCCTCTTGCTGTTTCGATTTCTTCA
* * * * *
1385419 TTTTTCTCTTGTTCTTTCGATTCTGTTTTTTTCTTC
1 TTTTTTTCTTGCTGTTTCAATTCTATTTTTTTCTTC
1385455 TTGTTGTTTC
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
62 21 0.23
63 7 0.08
64 15 0.17
65 47 0.52
ACGTcount: A:0.06, C:0.22, G:0.07, T:0.64
Consensus pattern (62 bp):
TTTTTTTCTTGCTGTTTCAATTCTATTTTTTTCTTCCTCCTCTTGCTGTTTCGATTTCTTCA
Found at i:1385436 original size:28 final size:27
Alignment explanation
Indices: 1385396--1385472 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 27
1385386 TTCCTTCCTC
*
1385396 CTCTTGTTGTTTCTATTTCTTCATTTTT
1 CTCTTGTTGTTTCAATTTCTT-ATTTTT
* * *
1385424 CTCTTGTTCTTTCGA-TTCTGTTTTTTT
1 CTCTTGTTGTTTCAATTTCT-TATTTTT
1385451 CTTCTTGTTGTTTCAATTTCTT
1 C-TCTTGTTGTTTCAATTTCTT
1385473 TCTTAATTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
27 10 0.24
28 27 0.66
29 4 0.10
ACGTcount: A:0.06, C:0.18, G:0.09, T:0.66
Consensus pattern (27 bp):
CTCTTGTTGTTTCAATTTCTTATTTTT
Found at i:1385933 original size:33 final size:33
Alignment explanation
Indices: 1385873--1385951 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 33
1385863 ATGAAAGCAT
* * * *
1385873 GCATGAAATGCCACCTAATTGATTTAGGTGGCA
1 GCATGAAATGCCACCAAAATCAATTAGGTGGCA
*
1385906 GCATGCAATGCCACCAAAATCAATTAGGT-G--
1 GCATGAAATGCCACCAAAATCAATTAGGTGGCA
1385936 GC-TGAAATGCCACCAA
1 GCATGAAATGCCACCAA
1385952 TTCGAATGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 13 0.32
30 2 0.05
32 1 0.03
33 24 0.60
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.22
Consensus pattern (33 bp):
GCATGAAATGCCACCAAAATCAATTAGGTGGCA
Found at i:1396241 original size:23 final size:23
Alignment explanation
Indices: 1396165--1396247 Score: 58
Period size: 23 Copynumber: 3.4 Consensus size: 23
1396155 TTCCAACCCG
* *
1396165 TTTTTATTTCCAAAATATTAAAA
1 TTTTTATCTCCAAAATATTAAAT
* * * *
1396188 TTTTTATCTTCGAGATACTTCAACCCCT
1 TTTTTATCTCCAAAATA-TT-AA---AT
1396216 TTTTTATCTCCAAAATATTAAAT
1 TTTTTATCTCCAAAATATTAAAT
*
1396239 TTTTCATCT
1 TTTTTATCT
1396248 GAAAATGTAC
Statistics
Matches: 44, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
23 22 0.50
24 2 0.05
25 2 0.05
26 2 0.05
27 2 0.05
28 14 0.32
ACGTcount: A:0.31, C:0.18, G:0.02, T:0.48
Consensus pattern (23 bp):
TTTTTATCTCCAAAATATTAAAT
Found at i:1403592 original size:19 final size:18
Alignment explanation
Indices: 1403568--1403630 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
1403558 AGTGATACAT
1403568 TGTATCGATACAACATTTA
1 TGTATCGATACAACA-TTA
1403587 TGTATCGAT---ACA-T-
1 TGTATCGATACAACATTA
*
1403600 TGTATTGATACAACACTTA
1 TGTATCGATACAACA-TTA
1403619 TGTATCGATACA
1 TGTATCGATACA
1403631 TTTATTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 8 0.22
14 1 0.03
16 6 0.17
18 1 0.03
19 20 0.56
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (18 bp):
TGTATCGATACAACATTA
Found at i:1403599 original size:16 final size:16
Alignment explanation
Indices: 1403580--1403635 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
1403570 TATCGATACA
1403580 ACATTTATGTATCGAT
1 ACATTTATGTATCGAT
1403596 ACATTGTAT-TGATAC-A-
1 ACATT-TATGT-AT-CGAT
*
1403612 ACACTTATGTATCGAT
1 ACATTTATGTATCGAT
1403628 ACATTTAT
1 ACATTTAT
1403636 TGTTTGTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
14 1 0.03
15 6 0.19
16 18 0.56
17 6 0.19
18 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (16 bp):
ACATTTATGTATCGAT
Found at i:1403602 original size:32 final size:32
Alignment explanation
Indices: 1403561--1403632 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
1403551 GCTTTGTAGT
*
1403561 GATACATTGTATCGATACAACATTTATGTATC
1 GATACATTGTATCGATACAACACTTATGTATC
*
1403593 GATACATTGTATTGATACAACACTTATGTATC
1 GATACATTGTATCGATACAACACTTATGTATC
1403625 GATACATT
1 GATACATT
1403633 TATTGTTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (32 bp):
GATACATTGTATCGATACAACACTTATGTATC
Found at i:1404027 original size:20 final size:20
Alignment explanation
Indices: 1404004--1404042 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1403994 TTCCTCCCCC
*
1404004 TTAATAAAATTTCT-TCCCTT
1 TTAA-AAAATATCTCTCCCTT
1404024 TTAAAAAATATCTCTCCCT
1 TTAAAAAATATCTCTCCCT
1404043 CTTTTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAAAAAATATCTCTCCCTT
Found at i:1409763 original size:15 final size:14
Alignment explanation
Indices: 1409736--1409771 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
1409726 TTCTAGTTCG
1409736 ACAATTTATTTTCA
1 ACAATTTATTTTCA
*
1409750 AGAATTTCATTTTCA
1 ACAATTT-ATTTTCA
1409765 ACAATTT
1 ACAATTT
1409772 TTTATTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (14 bp):
ACAATTTATTTTCA
Found at i:1411268 original size:13 final size:13
Alignment explanation
Indices: 1411250--1411274 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1411240 ACTGTTCATG
1411250 TATCGATACAGTA
1 TATCGATACAGTA
1411263 TATCGATACAGT
1 TATCGATACAGT
1411275 GTGAATAGTA
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):
TATCGATACAGTA
Found at i:1414526 original size:20 final size:20
Alignment explanation
Indices: 1414501--1414542 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1414491 CATTACAAGC
* *
1414501 ATGTATCAATATATTCACTT
1 ATGTATCAATACATTAACTT
*
1414521 ATGTATCGATACATTAACTT
1 ATGTATCAATACATTAACTT
1414541 AT
1 AT
1414543 TGTGTTATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (20 bp):
ATGTATCAATACATTAACTT
Found at i:1416618 original size:24 final size:22
Alignment explanation
Indices: 1416579--1416627 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
1416569 TATCTTTCTC
1416579 AAAAAATTGAATAAAAATATTT
1 AAAAAATTGAATAAAAATATTT
* *
1416601 AAAAAATTTTAATGAAAAATTTTT
1 AAAAAA-TTGAAT-AAAAATATTT
1416625 AAA
1 AAA
1416628 GACATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 6 0.26
23 5 0.22
24 12 0.52
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (22 bp):
AAAAAATTGAATAAAAATATTT
Found at i:1419755 original size:22 final size:21
Alignment explanation
Indices: 1419722--1419764 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1419712 TTCTTACTAT
1419722 TTTTTGTCTTTAGAT-TTTTTA
1 TTTTTGTCTTTA-ATATTTTTA
*
1419743 TTTTTGATTTTTAATATTTTTA
1 TTTTTG-TCTTTAATATTTTTA
1419765 CCGATTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.72
Consensus pattern (21 bp):
TTTTTGTCTTTAATATTTTTA
Found at i:1421786 original size:23 final size:25
Alignment explanation
Indices: 1421746--1421795 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
1421736 TTTATTTATG
*
1421746 TTTAATTAAAAAGATA-TTAAAATT
1 TTTAAATAAAAAGATATTTAAAATT
*
1421770 TTTAAATAAAAAG-TATTTAATATT
1 TTTAAATAAAAAGATATTTAAAATT
1421794 TT
1 TT
1421796 AATTTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
TTTAAATAAAAAGATATTTAAAATT
Found at i:1422473 original size:25 final size:24
Alignment explanation
Indices: 1422425--1422473 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1422415 TGGTTACCTC
1422425 CTTATTCTCAAATCAACTTAAACA
1 CTTATTCTCAAATCAACTTAAACA
*
1422449 CTTATTC-CAAACTCACATTTAAACA
1 CTTATTCTCAAA-TCA-ACTTAAACA
1422474 GTAAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.18
24 10 0.45
25 8 0.36
ACGTcount: A:0.41, C:0.27, G:0.00, T:0.33
Consensus pattern (24 bp):
CTTATTCTCAAATCAACTTAAACA
Found at i:1428395 original size:2 final size:2
Alignment explanation
Indices: 1428388--1428422 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1428378 TGATGCTTAA
1428388 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1428423 CACACACACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1429047 original size:2 final size:2
Alignment explanation
Indices: 1429040--1429066 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1429030 TATGACTATG
1429040 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1429067 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1430547 original size:14 final size:14
Alignment explanation
Indices: 1430530--1430568 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1430520 ATGCATAATT
1430530 TTTAATTTTTATAA
1 TTTAATTTTTATAA
* *
1430544 TTTAATTCTTCTAA
1 TTTAATTTTTATAA
1430558 -TTAATTTTTAT
1 TTTAATTTTTAT
1430569 GGTATTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTAATTTTTATAA
Found at i:1431567 original size:20 final size:21
Alignment explanation
Indices: 1431529--1431569 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1431519 AAAATTAGAA
1431529 TTACTAAATTGTAAAAAAAAG
1 TTACTAAATTGTAAAAAAAAG
*
1431550 TTACTAAGTTGTAAAAAAAA
1 TTACTAAATTGTAAAAAAAA
1431570 AAATTGTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.29
Consensus pattern (21 bp):
TTACTAAATTGTAAAAAAAAG
Found at i:1431889 original size:163 final size:163
Alignment explanation
Indices: 1431697--1432364 Score: 657
Period size: 163 Copynumber: 4.1 Consensus size: 163
1431687 TTTTGTAATT
* *
1431697 TTTA-AAAGTTTAGGGATTTAGTTGTAAATATTAGAAAAA-TTTGTTCCAAGGCCAAAGGTAATT
1 TTTAGAAAGTTTAGGG-TTTAGTTGTAAATATTAGAAAAATTTTGTTCCAAGGCCAAAGATGATT
* * * * *
1431760 GGTCGAACCTTCCTT-TAATTTTTGGATTTGATTTTGTATTGGTTTTGATATAATTGATGCTTAA
65 GGTCGAATCTTTCTTGTAACTTTTGGATTTGATTTT-TATTAGTTTTGATATATTTGATGCTTAA
* *
1431824 TTTTGTGTTTTAATTGTGTAATGACCAATTTACAAA
129 TTTTGTGTTTTAATTATGTAA-GACCAATTTGCAAA
*
1431860 TTTAGAAA-TTTAGGGTTTTA-TTAGTAAATATT-GAAAAATTTTGTTCTAAGGCCAAAGATGAT
1 TTTAGAAAGTTTAGGG-TTTAGTT-GTAAATATTAGAAAAATTTTGTTCCAAGGCCAAAGATGAT
* * * * * * *
1431922 AGGTAGAATCTTTCTTGTAACTTTCGGATGTGATTTTTGTGTTGGTTTTAATATATTTGATGCTT
64 TGGTCGAATCTTTCTTGTAACTTTTGGATTTGA-TTTT-TATTAGTTTTGATATATTTGATGCTT
* * * * * *
1431987 AATTTTATATCTTAATTCTATAAGAACGAATTTGCAAA
127 AATTTTGTGTTTTAATTATGTAAG-ACCAATTTGCAAA
* * *
1432025 TTTAGAAAGTTTAAAGGTTTAGTTGTAAATATTA-CAAAATTTTGTTCAAAGGCCAAAGATGATT
1 TTTAGAAAGTTT-AGGGTTTAGTTGTAAATATTAGAAAAATTTTGTTCCAAGGCCAAAGATGATT
* * * * * * *
1432089 AG-CTAAATCTTTCTTGTGACTTGT-GATCTT-ATTTTTGTCAATTTTGATATATTTGATGCTTA
65 GGTC-GAATCTTTCTTGTAACTTTTGGAT-TTGATTTTTATTAGTTTTGATATATTTGATGCTTA
*
1432151 ATTTTGTGTTTTAATTATGTAAAGACCAACTTGCAAA
128 ATTTTGTGTTTTAATTATGT-AAGACCAATTTGCAAA
** * * *
1432188 TTTAGAAAGTTTAAAG----GTTGTAAATATTA-AAAAATTTTGTTTCAAGGTCAAAGGTGATTG
1 TTTAGAAAGTTTAGGGTTTAGTTGTAAATATTAGAAAAATTTTGTTCCAAGGCCAAAGATGATTG
* * * * * *
1432248 GTTG-ATATTTCTGGTGACTTTTGGATCTGATTTTTATGTTAGTTTTGATATATTTGATGTTTAA
66 GTCGAATCTTTCTTGTAACTTTTGGATTTGATTTTTA--TTAGTTTTGATATATTTGATGCTTAA
*
1432312 TTTTGTGTTTTAATTATGTAAGGACTAATTTGCAAA
129 TTTTGTGTTTTAATTATGTAA-GACCAATTTGCAAA
*
1432348 CTTAGAAAAGTTTAGGG
1 TTTAG-AAAGTTTAGGG
1432365 ACCATTAGGT
Statistics
Matches: 420, Mismatches: 65, Indels: 42
0.80 0.12 0.08
Matches are distributed among these distances:
157 16 0.04
158 48 0.11
159 2 0.00
160 58 0.14
161 9 0.02
162 11 0.03
163 117 0.28
164 24 0.06
165 69 0.16
166 61 0.15
167 5 0.01
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (163 bp):
TTTAGAAAGTTTAGGGTTTAGTTGTAAATATTAGAAAAATTTTGTTCCAAGGCCAAAGATGATTG
GTCGAATCTTTCTTGTAACTTTTGGATTTGATTTTTATTAGTTTTGATATATTTGATGCTTAATT
TTGTGTTTTAATTATGTAAGACCAATTTGCAAA
Found at i:1434006 original size:202 final size:200
Alignment explanation
Indices: 1433605--1434156 Score: 664
Period size: 202 Copynumber: 2.7 Consensus size: 200
1433595 CCTCAGAGAT
* * * *
1433605 AAAATTATGAAAATATTTAGAAACAAAAGAGAAGATTTGAGTTCTTTTTATGAAGAACGCGGTTG
1 AAAATTTTGAAAATATTTAGGAACAAAAGA-AA-ATTTGAG-T-TTTTTATGAAGAACGAGGTTA
* * * * *
1433670 GAGTATCTCTTTACAGTAAT-GAGTTAGAGTATCCTTAAAGATAAAATTATATGAAGAGAAAATT
62 GAGTATCCCCTTAGAGTAATGGAGTTAGAGTTTCCCTAAAGATAAAATTATATGAAGAGAAAATT
* * * * *
1433734 TGAGTTTTTTTTTTAAGAACGGACTTGAAATATCCCTTTGGAGTAGTGGGGTTAGAGTTCCCCCC
127 TGAGTTTTTTTTTTAAGAACGGACTTGAAATAGCCCCTTAGAGTAGTGGGGTTAGAATTCCCCAC
1433799 AAAGTC-AA
192 AAAGTCAAA
* * * *
1433807 AAATTTTTGAAAATATTTAGGAACATGAAGAAAATTTGAGTTTTTTATGAAGAACAAGGTTTGAG
1 AAAATTTTGAAAATATTTAGGAACA-AAAGAAAATTTGAGTTTTTTATGAAGAACGAGGTTAGAG
* * * * *
1433872 TATCCCCTTGGAGTAGTGGAATTGGAGTTTCCCTAAAAATAAAATTATATGAAGAGAAAATTTGA
65 TATCCCCTTAGAGTAATGGAGTTAGAGTTTCCCTAAAGATAAAATTATATGAAGAGAAAATTTGA
* ** * *
1433937 GTTTTTTTTTATAAAGAATGGGGTT-AGAGT-GCCCACTTAGAGTAGTGGGGTTAGAATTTCCCA
130 GTTTTTTTTT-T-AAGAACGGACTTGA-AATAGCCC-CTTAGAGTAGTGGGGTTAGAATTCCCCA
1434000 CAAAGTCAAA
191 CAAAGTCAAA
*
1434010 AAAATTTT-AAAATATTTAGGAACAAAGAGAAAATTTGAGTTTTTTATGAAGAACGGGGTTAGAG
1 AAAATTTTGAAAATATTTAGGAACAAA-AGAAAATTTGAGTTTTTTATGAAGAACGAGGTTAGAG
* * * *
1434074 TATTCCCTTAGAGTAATGGAGTTAGAGTTTTCCTAAAGATAAAATTATATGAAGAGAATATTTAA
65 TATCCCCTTAGAGTAATGGAGTTAGAGTTTCCCTAAAGATAAAATTATATGAAGAGAAAATTTGA
* *
1434139 GTTTTTTTATGAAGAACG
130 GTTTTTTTTTTAAGAACG
1434157 AGGTTGGAGT
Statistics
Matches: 298, Mismatches: 44, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
199 33 0.11
200 59 0.20
201 13 0.04
202 180 0.60
203 13 0.04
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.33
Consensus pattern (200 bp):
AAAATTTTGAAAATATTTAGGAACAAAAGAAAATTTGAGTTTTTTATGAAGAACGAGGTTAGAGT
ATCCCCTTAGAGTAATGGAGTTAGAGTTTCCCTAAAGATAAAATTATATGAAGAGAAAATTTGAG
TTTTTTTTTTAAGAACGGACTTGAAATAGCCCCTTAGAGTAGTGGGGTTAGAATTCCCCACAAAG
TCAAA
Found at i:1434262 original size:90 final size:92
Alignment explanation
Indices: 1434033--1434293 Score: 329
Period size: 92 Copynumber: 2.9 Consensus size: 92
1434023 ATTTAGGAAC
* * * * * *
1434033 AAAGAGAAAATTTGAGTTTTTTATGAAGAACGGGGTTAGAGTATTCCCT-TAGAGTAATGGAGTT
1 AAAGAGAAAATTTGAGTTTTTTATGAAGAACGGAGTTGGAGTATCCCCTCGA-AGTAGTGGGGTT
1434097 AGAGTTTTCCTAAAGATAAAATTATATG
65 AGAGTTTTCCTAAAGATAAAATTATATG
* *
1434125 -AAGAGAATATTTAAGTTTTTTTATGAAGAAC-GAGGTTGGAGTATCCCCTCGAAGTAGTGGGGT
1 AAAGAGAAAATTTGAG-TTTTTTATGAAGAACGGA-GTTGGAGTATCCCCTCGAAGTAGTGGGGT
1434188 TAGAGTTTCTCC-AAAGATAAAATTATA-G
64 TAGAGTTT-TCCTAAAGATAAAATTATATG
* *
1434216 AAAGA-AAAATTTGAGTTCTTTATGAAGAACGGAGTTGG-GATATCCCCTCGGAGTAGTGGGGTT
1 AAAGAGAAAATTTGAGTTTTTTATGAAGAACGGAGTTGGAG-TATCCCCTCGAAGTAGTGGGGTT
*
1434279 AGAGTTTACCTAAAG
65 AGAGTTTTCCTAAAG
1434294 TCAAAAAAAT
Statistics
Matches: 148, Mismatches: 13, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
89 3 0.02
90 52 0.35
91 25 0.17
92 64 0.43
93 4 0.03
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.31
Consensus pattern (92 bp):
AAAGAGAAAATTTGAGTTTTTTATGAAGAACGGAGTTGGAGTATCCCCTCGAAGTAGTGGGGTTA
GAGTTTTCCTAAAGATAAAATTATATG
Found at i:1437628 original size:73 final size:73
Alignment explanation
Indices: 1437355--1438165 Score: 567
Period size: 73 Copynumber: 11.0 Consensus size: 73
1437345 CCCAGATGAA
* ** * ** * *
1437355 TGCCACTAGATTGTGT-GGCTTTGAAGTAGGTAAGAAAAATGTCTTGCTCTTTGAAGACTAGAGG
1 TGCCACTAGCTTGTGTGGGCTTTGTGGTAAGTAAGAAAAACATCATGCTCTTTGAGGACTAGAGG
1437419 TAGATAGG
66 TAGATAGG
* * * * ** *
1437427 TGCCA-TCAGCGTGTGTAGGCTTTGTGAT-AGATGAGAAAAAGCGCCATACTCTTTGAGGACTAG
1 TGCCACT-AGCTTGTGTGGGCTTTGTGGTAAG-TAAGAAAAA-CATCATGCTCTTTGAGGACTAG
* *
1437490 AGGCAGATAGA
63 AGGTAGATAGG
* * * * * * * *
1437501 TGCTACCAACTTCTGCGAGCTTTGTGGTTAGTAAGAAAAACGACCTAT--TCTTTGAGGACTAGA
1 TGCCACTAGCTTGTGTGGGCTTTGTGGTAAGTAAGAAAAAC-ATC-ATGCTCTTTGAGGACTAGA
*
1437564 GGCAGATAGG
64 GGTAGATAGG
* ** * * * *
1437574 TGCCACTAGCTTGTGTGGGCTTTGTGGTAATTAAGAAAAACATTTTTCTTTTTGAGGACTGGAGA
1 TGCCACTAGCTTGTGTGGGCTTTGTGGTAAGTAAGAAAAACATCATGCTCTTTGAGGACTAGAGG
1437639 TAGATAGG
66 TAGATAGG
* * * * * * *
1437647 TGCCACTAGCTTGTGTGGGCTTTATGGTAGGTAAAAAAAACATCCTGCTCTTTAAAGACTGGAGG
1 TGCCACTAGCTTGTGTGGGCTTTGTGGTAAGTAAGAAAAACATCATGCTCTTTGAGGACTAGAGG
1437712 TAGATAGG
66 TAGATAGG
* * * *** * * * **
1437720 TGCCACTAGCTTATATGAGCTTTGAAATAGGTACGAAAAACATCTTGCTCTTTGAGGACT-GAAA
1 TGCCACTAGCTTGTGTGGGCTTTGTGGTAAGTAAGAAAAACATCATGCTCTTTGAGGACTAGAGG
1437784 TAGATAGG
66 TAGATAGG
* ** * * ** * * *
1437792 TGCCACCAATTTGTGTGGGTTTTTTGGTAAGTAAGAAAAAGTGTCATGCTTTTTTAGAACTAGAG
1 TGCCACTAGCTTGTGTGGGCTTTGTGGTAAGTAAGAAAAA-CATCATGCTCTTTGAGGACTAGAG
1437857 GTAGATAGG
65 GTAGATAGG
* * *** *
1437866 TGCCA-TGAGCTTGTGTGGGCTTTATGGTAGGTAAGAAAAGTGTCATGCTATTTGAGGACTAGAG
1 TGCCACT-AGCTTGTGTGGGCTTTGTGGTAAGTAAGAAAAACATCATGCTCTTTGAGGACTAGAG
*
1437930 ATAGATAGG
65 GTAGATAGG
* * * * * * * * *
1437939 TGCCACTAGCTTATGTGGGTTTTGTGGTAAGTAAGGAATACATCATGTTTTTTAATGACTAAAGG
1 TGCCACTAGCTTGTGTGGGCTTTGTGGTAAGTAAGAAAAACATCATGCTCTTTGAGGACTAGAGG
1438004 TAGATAGG
66 TAGATAGG
* * * * * * * * * *
1438012 TGTCACCAGCTTGTGTGAGCTTTATAGTAGGTAAGAAAAGCGTCCTGCTCTTTGAGGTCTTAAGG
1 TGCCACTAGCTTGTGTGGGCTTTGTGGTAAGTAAGAAAAACATCATGCTCTTTGAGGAC-T-A-G
*
1438077 ACTAGCGATGGATAGG
63 ---AG-G-TAGATAGG
* * * * * *
1438093 TGCCACCAGCTTGTGTGAGTTTTGTGGT-AGATAAGAAAAAGCGTCTTACTCTTTGAGGACTAGA
1 TGCCACTAGCTTGTGTGGGCTTTGTGGTAAG-TAAGAAAAA-CATCATGCTCTTTGAGGACTAGA
1438157 GGTAGATAG
64 GGTAGATAG
1438166 AGGCCATCAA
Statistics
Matches: 572, Mismatches: 143, Indels: 46
0.75 0.19 0.06
Matches are distributed among these distances:
71 2 0.00
72 51 0.09
73 345 0.60
74 104 0.18
75 6 0.01
76 2 0.00
79 3 0.01
80 3 0.01
81 40 0.07
82 16 0.03
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (73 bp):
TGCCACTAGCTTGTGTGGGCTTTGTGGTAAGTAAGAAAAACATCATGCTCTTTGAGGACTAGAGG
TAGATAGG
Found at i:1439444 original size:16 final size:15
Alignment explanation
Indices: 1439423--1439474 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
1439413 TCTCACTCTT
1439423 TTTTTTTTTGGTTGTG
1 TTTTTTTTTGGTT-TG
**
1439439 TTTTTTTCTTTTTTTG
1 TTTTTTT-TTGGTTTG
1439455 -TTTTTTTTGGTTT-
1 TTTTTTTTTGGTTTG
1439468 TTTTTTT
1 TTTTTTT
1439475 GTTTTATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 11 0.37
15 6 0.20
16 9 0.30
17 4 0.13
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (15 bp):
TTTTTTTTTGGTTTG
Found at i:1439444 original size:18 final size:15
Alignment explanation
Indices: 1439421--1439489 Score: 59
Period size: 16 Copynumber: 4.5 Consensus size: 15
1439411 GTTCTCACTC
*
1439421 TTTTTTTTTTTGGTT
1 TTTTTTTTTTTTGTT
*
1439436 GTGTTTTTTTCTTT-TT
1 -T-TTTTTTTTTTTGTT
* *
1439452 TTGTTTTTTTTGGTT
1 TTTTTTTTTTTTGTT
*
1439467 TTTTTTTTGTTTTATT
1 TTTTTTTT-TTTTGTT
1439483 TTTTTTT
1 TTTTTTT
1439490 CGAAGGGTGA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
14 8 0.19
15 10 0.24
16 15 0.36
17 9 0.21
ACGTcount: A:0.01, C:0.01, G:0.12, T:0.86
Consensus pattern (15 bp):
TTTTTTTTTTTTGTT
Found at i:1439471 original size:21 final size:19
Alignment explanation
Indices: 1439421--1439489 Score: 75
Period size: 21 Copynumber: 3.4 Consensus size: 19
1439411 GTTCTCACTC
*
1439421 TTTTTTTTTTTGGTTGTGTTT
1 TTTTTTTTTTTTGTT-T-TTT
*
1439442 TTTTCTTTTTTTGTTTTTT
1 TTTTTTTTTTTTGTTTTTT
1439461 TTGGTTTTTTTTTTGTTTTATT
1 TT--TTTTTTTTTTGTTTT-TT
1439483 TTTTTTT
1 TTTTTTT
1439490 CGAAGGGTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 5 0.12
20 6 0.14
21 27 0.64
22 4 0.10
ACGTcount: A:0.01, C:0.01, G:0.12, T:0.86
Consensus pattern (19 bp):
TTTTTTTTTTTTGTTTTTT
Found at i:1439485 original size:17 final size:16
Alignment explanation
Indices: 1439439--1439489 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
1439429 TTTGGTTGTG
*
1439439 TTTTTTTCTTTTTTTGT
1 TTTTTTTATTTTTTT-T
*
1439456 TTTTTTTGGTTTTTTTT
1 TTTTTTT-ATTTTTTTT
*
1439473 TTGTTTTATTTTTTTT
1 TTTTTTTATTTTTTTT
1439489 T
1 T
1439490 CGAAGGGTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 9 0.30
17 14 0.47
18 7 0.23
ACGTcount: A:0.02, C:0.02, G:0.08, T:0.88
Consensus pattern (16 bp):
TTTTTTTATTTTTTTT
Found at i:1439486 original size:26 final size:26
Alignment explanation
Indices: 1439419--1439488 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
1439409 TGGTTCTCAC
**
1439419 TCTTTTTTT-TTTTGGTTGTGTTTTTT
1 TCTTTTTTTATTTTTTTTG-GTTTTTT
*
1439445 TCTTTTTTTGTTTTTTTTGGTTTTTT
1 TCTTTTTTTATTTTTTTTGGTTTTTT
1439471 T-TTTGTTTTATTTTTTTT
1 TCTTT-TTTTATTTTTTTT
1439489 TCGAAGGGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
25 3 0.08
26 29 0.74
27 7 0.18
ACGTcount: A:0.01, C:0.03, G:0.11, T:0.84
Consensus pattern (26 bp):
TCTTTTTTTATTTTTTTTGGTTTTTT
Found at i:1451813 original size:21 final size:20
Alignment explanation
Indices: 1451789--1451827 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
1451779 TTTCTACAAT
1451789 ATGTATCAATACAATAAGTTA
1 ATGTATCAATAC-ATAAGTTA
1451810 ATGTATCAATACATAAGT
1 ATGTATCAATACATAAGT
1451828 GAATTTATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGTATCAATACATAAGTTA
Found at i:1453058 original size:237 final size:237
Alignment explanation
Indices: 1452643--1453357 Score: 1288
Period size: 237 Copynumber: 3.0 Consensus size: 237
1452633 CAAGCAAACT
* *
1452643 AGAATCCAAAGTGTTTTTGGTATATTTTCTCACCTATTTATGCTCATTTTCTATTTTTCAGCAAT
1 AGAATCCAAAGTGTTGTTGGTATATTTTCTCACCTATCTATGCTCATTTTCTATTTTTCAGCAAT
*
1452708 GTGATCATTTTAGTGAGCCAAAATCTGAAATCCCATAGCTCTATCTCTAGCCATTGAAAGAATTC
66 GTGATCATTTTAGTGAGCCAAAATCTGAAATCCCATAGCTCTATCTCTAGCCATTGAAAGAACTC
*
1452773 ATAAACACCCATCATCCCATCAAAATATCACTCTAGAACTCATTTCAATTAACACTAGCACCAAA
131 ATAAACACCCATCATCCCATCAAAATATCACTCTAGAACTCATTTCAATTAACACCAGCACCAAA
1452838 AGGCCTTTATTTCCTCCCTTTTTTCTTACTAATCATTAGCAA
196 AGGCCTTTATTTCCTCCCTTTTTTCTTACTAATCATTAGCAA
* *
1452880 AGAATCCAAAGTGTTGTTGGTATATTTTCTCACCTATCTGTGCTCATTTTCTATCTTTCAGCAAT
1 AGAATCCAAAGTGTTGTTGGTATATTTTCTCACCTATCTATGCTCATTTTCTATTTTTCAGCAAT
* *
1452945 GTGATCATTTTAGTGAGCTAAAATCTAAAATCCCATAGCTCTATCTCTAGCCATTGAAAGAACTC
66 GTGATCATTTTAGTGAGCCAAAATCTGAAATCCCATAGCTCTATCTCTAGCCATTGAAAGAACTC
1453010 ATAAACACCCATCATCCCATCAAAATATCACTCTAGAACTCATTTCAATTAACACCAGCACCAAA
131 ATAAACACCCATCATCCCATCAAAATATCACTCTAGAACTCATTTCAATTAACACCAGCACCAAA
1453075 AGGCCTTTATTTCCT-CCTTTATTTCTTACTAATCATTAGCAA
196 AGGCCTTTATTTCCTCCCTTT-TTTCTTACTAATCATTAGCAA
*
1453117 AGAATCCAAAGTGTTGTTGGTATATTTTCTCACCTATCCATGCTCATTTTCTATTTTTCAGCAAT
1 AGAATCCAAAGTGTTGTTGGTATATTTTCTCACCTATCTATGCTCATTTTCTATTTTTCAGCAAT
*
1453182 GTGATCATTTTAGTGAGCCAAAATCTGAAATCCCATAGCTCTATCTCTAGCCATTAAAAGAACTC
66 GTGATCATTTTAGTGAGCCAAAATCTGAAATCCCATAGCTCTATCTCTAGCCATTGAAAGAACTC
* * *
1453247 ATAAACACCCATAATCCCATCAAAATATCACTCTAGAACTCACTTCCATTAACACCAGCACCAAA
131 ATAAACACCCATCATCCCATCAAAATATCACTCTAGAACTCATTTCAATTAACACCAGCACCAAA
*
1453312 AGGCCTTTATTTCCTCCCTTATTTCTTACTAATCATTAGCAA
196 AGGCCTTTATTTCCTCCCTTTTTTCTTACTAATCATTAGCAA
1453354 AGAA
1 AGAA
1453358 AGGGAAAAAG
Statistics
Matches: 458, Mismatches: 18, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
236 5 0.01
237 449 0.98
238 4 0.01
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (237 bp):
AGAATCCAAAGTGTTGTTGGTATATTTTCTCACCTATCTATGCTCATTTTCTATTTTTCAGCAAT
GTGATCATTTTAGTGAGCCAAAATCTGAAATCCCATAGCTCTATCTCTAGCCATTGAAAGAACTC
ATAAACACCCATCATCCCATCAAAATATCACTCTAGAACTCATTTCAATTAACACCAGCACCAAA
AGGCCTTTATTTCCTCCCTTTTTTCTTACTAATCATTAGCAA
Found at i:1454405 original size:54 final size:54
Alignment explanation
Indices: 1454323--1454429 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
1454313 CTAAGCTATC
*
1454323 CAAAACCCTTGGAAAACTAGCAAGATGTATTCTGGTTGGGCCATTTAGGCCCAT
1 CAAAACCCTTGGAAAACTAGCAAGATGTATTCTGGTTAGGCCATTTAGGCCCAT
1454377 CAAAACCCTTGGAAAACTAGCAAGATGTATTCTGGTTAGGCCATTTAGGCCCA
1 CAAAACCCTTGGAAAACTAGCAAGATGTATTCTGGTTAGGCCATTTAGGCCCA
1454430 CTAGATGATT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (54 bp):
CAAAACCCTTGGAAAACTAGCAAGATGTATTCTGGTTAGGCCATTTAGGCCCAT
Found at i:1455583 original size:14 final size:14
Alignment explanation
Indices: 1455559--1455598 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1455549 TTTTTAAAAA
1455559 TAAAA-TAAAATTT
1 TAAAATTAAAATTT
*
1455572 TAAAATTAAAATAT
1 TAAAATTAAAATTT
1455586 TAAAATTAAAATT
1 TAAAATTAAAATT
1455599 AATAATCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAATTAAAATTT
Found at i:1457297 original size:39 final size:39
Alignment explanation
Indices: 1457243--1457321 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
1457233 TCCCCTACTT
1457243 TTGGTTATTGCCAAAATTGGTTTATTTTCCTGGATTCCA
1 TTGGTTATTGCCAAAATTGGTTTATTTTCCTGGATTCCA
1457282 TTGGTTATTGCCAAAATTGGTTTATTTTCCTGGATTCCA
1 TTGGTTATTGCCAAAATTGGTTTATTTTCCTGGATTCCA
1457321 T
1 T
1457322 CCTGAGACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.20, C:0.15, G:0.18, T:0.47
Consensus pattern (39 bp):
TTGGTTATTGCCAAAATTGGTTTATTTTCCTGGATTCCA
Found at i:1459817 original size:33 final size:33
Alignment explanation
Indices: 1459775--1459839 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1459765 TTTGAAGCAA
*
1459775 TGTATCGATACAAT-TCATCATGTATCAATACAT
1 TGTATCGATACAATAT-ACCATGTATCAATACAT
*
1459808 TGTATCGATACAATATACCATGTATCGATACA
1 TGTATCGATACAATATACCATGTATCAATACA
1459840 AATTGTGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAATATACCATGTATCAATACAT
Found at i:1459902 original size:20 final size:20
Alignment explanation
Indices: 1459877--1459926 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
1459867 TTCATATATT
*
1459877 GATACAATTGTCCATGTATC
1 GATACAATTGTACATGTATC
*
1459897 GATACAA-TGAACATGTATC
1 GATACAATTGTACATGTATC
*
1459916 GCTAC-ATTGTA
1 GATACAATTGTA
1459927 TCGATACAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 1 0.04
19 17 0.68
20 7 0.28
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (20 bp):
GATACAATTGTACATGTATC
Found at i:1460573 original size:17 final size:17
Alignment explanation
Indices: 1460551--1460584 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1460541 TGATAATCGG
*
1460551 TTAAAAGGATTTACTCC
1 TTAAAAAGATTTACTCC
*
1460568 TTAAAAAGATTTTCTCC
1 TTAAAAAGATTTACTCC
1460585 CCCTTGATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (17 bp):
TTAAAAAGATTTACTCC
Found at i:1460766 original size:17 final size:18
Alignment explanation
Indices: 1460744--1460781 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1460734 TTATAAACAC
*
1460744 AAAGTCA-AATTATAAGA
1 AAAGTCACAATAATAAGA
*
1460761 AAAGTCACAATAATAATA
1 AAAGTCACAATAATAAGA
1460779 AAA
1 AAA
1460782 AACAAGTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.21
Consensus pattern (18 bp):
AAAGTCACAATAATAAGA
Found at i:1461412 original size:22 final size:21
Alignment explanation
Indices: 1461372--1461426 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
1461362 CCGTTTTTGT
1461372 TGAAGATTTTG-A-TGAAAAA
1 TGAAGATTTTGAAGTGAAAAA
1461391 TGAAGTATTTTGAAGTGAAAAA
1 TGAAG-ATTTTGAAGTGAAAAA
*
1461413 T-AAGAAATTTGAAG
1 TGAAG-ATTTTGAAG
1461427 AAGATTTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.16
20 6 0.19
21 12 0.39
22 8 0.26
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.31
Consensus pattern (21 bp):
TGAAGATTTTGAAGTGAAAAA
Found at i:1474189 original size:20 final size:20
Alignment explanation
Indices: 1474164--1474351 Score: 98
Period size: 20 Copynumber: 8.8 Consensus size: 20
1474154 AAAAAAAGAC
1474164 AGAATGTATCGATACATTAA
1 AGAATGTATCGATACATTAA
*
1474184 AGAATGTATCGATACACTAA
1 AGAATGTATCGATACATTAA
*
1474204 AAAATGTATCGATACATCTGAGTAAAAAAA
1 AGAATGTATCGATACA--T---T-----AA
* *
1474234 TAGAATATATCGATACATGAA
1 -AGAATGTATCGATACATTAA
* *
1474255 AGAATATATCGATATATT--
1 AGAATGTATCGATACATTAA
* * *
1474273 CGTACATGTATCGAAACATTGA
1 AG-A-ATGTATCGATACATTAA
*
1474295 AGAATATATCGATACATT--
1 AGAATGTATCGATACATTAA
*
1474313 CGTACATGTATCGATACATTGAA
1 AG-A-ATGTATCGATACATT-AA
1474336 A-AATGTATCGATACAT
1 AGAATGTATCGATACAT
1474352 CTAGGTAAAA
Statistics
Matches: 130, Mismatches: 18, Indels: 40
0.69 0.10 0.21
Matches are distributed among these distances:
18 2 0.02
19 2 0.02
20 103 0.79
21 4 0.03
22 1 0.01
25 1 0.01
29 1 0.01
30 2 0.02
31 14 0.11
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.29
Consensus pattern (20 bp):
AGAATGTATCGATACATTAA
Done.