Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008721.1 Hibiscus syriacus cultivar Beakdansim tig00111779_pilon, whole genome shotgun sequence
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: 2464137
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 12
Found at i:951593 original size:33 final size:33
Alignment explanation
Indices: 951498--951617 Score: 138
Period size: 33 Copynumber: 3.5 Consensus size: 33
951488 TCTTTTGGTT
*
951498 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
951539 GAAATGAAAATCGCAAC--GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
951570 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
951603 GAAATG-AAATCGCAA
1 GAAATGAAAATCGCAA
951618 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 1, Indels: 13
0.84 0.01 0.14
Matches are distributed among these distances:
31 18 0.24
32 9 0.12
33 27 0.36
36 1 0.01
38 1 0.01
39 3 0.04
41 17 0.22
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:951653 original size:14 final size:14
Alignment explanation
Indices: 951634--951690 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
951624 TTTGGTTTCG
951634 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
951648 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
951667 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
951681 CGTTGCGATT
1 CGTTGCGATT
951691 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:951666 original size:33 final size:33
Alignment explanation
Indices: 951618--951697 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
951608 GAAATCGCAA
**
951618 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
951651 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
951684 TGCGATTTTCATTT
1 TGCGATTTTCATTT
951698 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:951703 original size:21 final size:21
Alignment explanation
Indices: 951678--951750 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
951668 GTTGCGATTC
951678 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
951699 TCTCGTTGCAGATAGTCA--TT
1 TCTCGTTGC-GATTTTCATTTT
* *
951719 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
951740 TCTCGTTGCGA
1 TCTCGTTGCGA
951751 ATCTTCTGCA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 6 0.14
20 10 0.24
21 20 0.48
22 6 0.14
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:951872 original size:33 final size:33
Alignment explanation
Indices: 951830--951900 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
951820 AATACTAACT
951830 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
951863 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
951896 TGAAA
1 TGAAA
951901 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:952304 original size:20 final size:20
Alignment explanation
Indices: 952279--952433 Score: 240
Period size: 20 Copynumber: 7.7 Consensus size: 20
952269 CTTTAAAAAT
952279 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
952299 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
952319 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
952340 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
952360 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
952380 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
952400 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
952420 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
952434 TTTGTTCGCG
Statistics
Matches: 122, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
20 105 0.86
21 17 0.14
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:952443 original size:20 final size:20
Alignment explanation
Indices: 952420--952471 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
952410 TTTACGGATA
* *
952420 CGCGTTGCGATTTAT-TTGTT
1 CGCGTTGCGATTT-TCATATT
952440 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
952460 CGCGTTGCGATT
1 CGCGTTGCGATT
952472 CTTGAAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.12, C:0.19, G:0.25, T:0.44
Consensus pattern (20 bp):
CGCGTTGCGATTTTCATATT
Found at i:952446 original size:40 final size:40
Alignment explanation
Indices: 952278--952471 Score: 239
Period size: 40 Copynumber: 4.8 Consensus size: 40
952268 GCTTTAAAAA
*
952278 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTACGGAT
*
952319 T-GTCGTTGCGATTTACGGATACGCGTTGCGATATACGGAT
1 TCG-CGTTGCGATTTACGGATACGCGTTGCGATTTACGGAT
* *
952359 ACGCATTGCGATTTACGGATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGAT
* * **
952399 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATTTG-T
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTA-CGGAT
* ** *
952439 TCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATT
952472 CTTGAAAATC
Statistics
Matches: 135, Mismatches: 15, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
40 104 0.77
41 31 0.23
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.36
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGAT
Found at i:952466 original size:60 final size:60
Alignment explanation
Indices: 952279--952471 Score: 230
Period size: 60 Copynumber: 3.2 Consensus size: 60
952269 CTTTAAAAAT
*
952279 CGCGTTGCGATTTACGGATACGCGTTGCGATTT-TACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATACGT-TCG-CGTTGCGATTTACGGATA
* * *
952340 CGCGTTGCGATATACGGATACGCATTGCGA-TT-TACGGATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATAC-G-TTCGCGTTGCGATTTACGGATA
* ** * ** *
952400 CACGTTGCGATTTACGGATACGCGTTGCGATTTATTTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATACGTTCGCGTTGCGATTTACGGATA
952460 CGCGTTGCGATT
1 CGCGTTGCGATT
952472 CTTGAAAATC
Statistics
Matches: 113, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
60 78 0.69
61 33 0.29
62 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATACGTTCGCGTTGCGATTTACGGATA
Found at i:952524 original size:21 final size:20
Alignment explanation
Indices: 952439--952536 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
952429 ATTTATTTGT
* *
952439 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
952459 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
952480 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
952501 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
952522 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
952537 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:952532 original size:42 final size:43
Alignment explanation
Indices: 952439--952537 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
952429 ATTTATTTGT
* *
952439 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
952480 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
952522 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
952538 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:953678 original size:16 final size:15
Alignment explanation
Indices: 953657--953691 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
953647 CAATCAGATC
*
953657 TGTTTGTATTTATTTT
1 TGTTTGAATTT-TTTT
953673 TGTTTGAATTTTTTT
1 TGTTTGAATTTTTTT
953688 TGTT
1 TGTT
953692 AGATTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.11, C:0.00, G:0.14, T:0.74
Consensus pattern (15 bp):
TGTTTGAATTTTTTT
Found at i:959971 original size:20 final size:20
Alignment explanation
Indices: 959946--960005 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
959936 TAATTGAAAA
959946 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* *
959966 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
959988 T-GTCGTTGCGATTTTCCA
1 TCG-CGTTGCGATTTTCCA
960006 AATTCGTTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 16 0.48
21 1 0.03
22 16 0.48
ACGTcount: A:0.13, C:0.23, G:0.25, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:959994 original size:22 final size:22
Alignment explanation
Indices: 959969--960040 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
959959 TTCCAGTTCG
959969 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
959991 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
960010 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
960032 CGTTGCGAT
1 CGTTGCGAT
960041 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:960014 original size:41 final size:41
Alignment explanation
Indices: 959949--960056 Score: 173
Period size: 41 Copynumber: 2.6 Consensus size: 41
959939 TTGAAAATCG
*
959949 CGTTGCGATTTTCC-AGTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
959991 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
*
960032 CGTTGCGATTTTCCAAATTTGTTGC
1 CGTTGCGATTTTCCAAATTCGTTGC
960057 AAAAATCACG
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
41 46 0.73
42 14 0.22
43 3 0.05
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
Found at i:960053 original size:22 final size:21
Alignment explanation
Indices: 959987--960050 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 21
959977 TAGTCTACAG
959987 TTGTCGTTGCGATTTTCCAAA
1 TTGTCGTTGCGATTTTCCAAA
** * *
960008 -T-TCGTTGCGATAGTCTACAG
1 TTGTCGTTGCGATTTTCCA-AA
960028 TTGTCGTTGCGATTTTCCAAA
1 TTGTCGTTGCGATTTTCCAAA
960049 TT
1 TT
960051 TGTTGCAAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 13 0.41
20 2 0.06
21 4 0.12
22 13 0.41
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (21 bp):
TTGTCGTTGCGATTTTCCAAA
Found at i:960090 original size:20 final size:20
Alignment explanation
Indices: 960062--960141 Score: 88
Period size: 20 Copynumber: 3.9 Consensus size: 20
960052 GTTGCAAAAA
*
960062 TCACGTTGCGATTTTCCATT
1 TCACGTTGCGATTTTCCAGT
*
960082 TCGCGTTGCGATTTTCCAGT
1 TCACGTTGCGATTTTCCAGT
* *
960102 TCACGTTGCGATAGTCTACAGT
1 TCACGTTGCGAT--TTTCCAGT
**
960124 TGTCGTTGCGATTTTCCA
1 TCACGTTGCGATTTTCCA
960142 AATTCGTTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
20 33 0.67
22 16 0.33
ACGTcount: A:0.15, C:0.24, G:0.21, T:0.40
Consensus pattern (20 bp):
TCACGTTGCGATTTTCCAGT
Found at i:960273 original size:6 final size:6
Alignment explanation
Indices: 960263--960327 Score: 103
Period size: 6 Copynumber: 10.8 Consensus size: 6
960253 ACACGTATTA
* * *
960263 CCACGA CCACGA CCACGA CCACGG CCACGG CCACGG CCACGG CCACGG
1 CCACGG CCACGG CCACGG CCACGG CCACGG CCACGG CCACGG CCACGG
960311 CCACGG CCACGG CCACG
1 CCACGG CCACGG CCACG
960328 ACCCGAGACG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.22, C:0.51, G:0.28, T:0.00
Consensus pattern (6 bp):
CCACGG
Found at i:961025 original size:22 final size:22
Alignment explanation
Indices: 960995--961042 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
960985 TGGAAAATCA
* *
960995 CAACGACAACTGTAGACTTTCG
1 CAACAACAACTGTAGACTATCG
961017 CAACAACAACTGTAGACTATCG
1 CAACAACAACTGTAGACTATCG
961039 CAAC
1 CAAC
961043 GAATTTAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.29, G:0.15, T:0.19
Consensus pattern (22 bp):
CAACAACAACTGTAGACTATCG
Found at i:961127 original size:41 final size:41
Alignment explanation
Indices: 961070--961173 Score: 154
Period size: 41 Copynumber: 2.5 Consensus size: 41
961060 ACGACATTGT
961070 ACGCGAAATGGAAAATCGCAACACGATTTTCAACTATAGCA
1 ACGCGAAATGGAAAATCGCAACACGATTTTCAACTATAGCA
**** *
961111 ACGCGAAATGGAAAATCGCGTTGCGATTTTCAACTATCGCA
1 ACGCGAAATGGAAAATCGCAACACGATTTTCAACTATAGCA
*
961152 ACGCGAAATGAAAAATCGCAAC
1 ACGCGAAATGGAAAATCGCAAC
961174 GCGAAATGGA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.19
Consensus pattern (41 bp):
ACGCGAAATGGAAAATCGCAACACGATTTTCAACTATAGCA
Found at i:961171 original size:20 final size:20
Alignment explanation
Indices: 961146--961197 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
961136 ATTTTCAACT
961146 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
*
961166 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
961186 ATCGCAACGCGA
1 ATCGCAACGCGA
961198 TTTTCAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:961180 original size:61 final size:61
Alignment explanation
Indices: 961108--961222 Score: 203
Period size: 61 Copynumber: 1.9 Consensus size: 61
961098 TTCAACTATA
***
961108 GCAACGCGAAATGGAAAATCGCGTTGCGATTTTCAACTATCGCAACGCGAAATGAAAAATC
1 GCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGAAAAATC
961169 GCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
1 GCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
961223 CAACGCGAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (61 bp):
GCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGAAAAATC
Found at i:963424 original size:29 final size:29
Alignment explanation
Indices: 963382--963456 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
963372 AACCCAACCA
**
963382 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
963411 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
963440 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
963457 GGGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:963462 original size:29 final size:29
Alignment explanation
Indices: 963383--963470 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
963373 ACCCAACCAT
* * ****
963383 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
963412 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
963441 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
963470 A
1 A
963471 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:963704 original size:29 final size:29
Alignment explanation
Indices: 963669--963755 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
963659 GTTGGCTGGT
*
963669 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* ***
963698 AGGTCGCTGGGCGTGCATGGCGACCTGGT
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
*
963727 AGGTCGCCGGGCGTGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
963756 CCCGGTACTG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.16
Consensus pattern (29 bp):
AGGTCGCAGGGCGTGCATGGCGACCTACC
Found at i:964428 original size:15 final size:15
Alignment explanation
Indices: 964395--964432 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
964385 GACATTGAGG
* *
964395 ATTTAATAAATTATT
1 ATTTAAAAAAATATT
964410 -TTTAAAAAAATATT
1 ATTTAAAAAAATATT
964424 ATTTAAAAA
1 ATTTAAAAA
964433 TAAATATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTAAAAAAATATT
Found at i:965212 original size:29 final size:28
Alignment explanation
Indices: 965164--965218 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
965154 TTTTCACTAA
965164 TAAATTTTTAATATTCTAAAATAATTAT
1 TAAATTTTTAATATTCTAAAATAATTAT
*
965192 TAAATTTATTAA-ATTGTTAAAATAATT
1 TAAATTT-TTAATATT-CTAAAATAATT
965219 TATGTGGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (28 bp):
TAAATTTTTAATATTCTAAAATAATTAT
Found at i:965506 original size:28 final size:28
Alignment explanation
Indices: 965474--965529 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
965464 AACTTTCACA
*
965474 ATTATTTTATAATATATTAATAA-TTATT
1 ATTATTTTATAATAT-TTAAAAAGTTATT
965502 ATTATTTTATAATATTTAAAAAGTTATT
1 ATTATTTTATAATATTTAAAAAGTTATT
965530 TTAATATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
ATTATTTTATAATATTTAAAAAGTTATT
Found at i:966367 original size:22 final size:21
Alignment explanation
Indices: 966340--966381 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
966330 GATTCTTAAT
966340 TATTTAATAATAAATAT-TCAAG
1 TATTT-AT-ATAAATATATCAAG
966362 TATTTATATAAATATATCAA
1 TATTTATATAAATATATCAA
966382 TTCAAACTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 6 0.32
22 5 0.26
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (21 bp):
TATTTATATAAATATATCAAG
Found at i:968958 original size:17 final size:16
Alignment explanation
Indices: 968926--968957 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
968916 TCCTCTTAAA
968926 ATTTTATAACTTTTTT
1 ATTTTATAACTTTTTT
*
968942 ATTTTATAAATTTTTT
1 ATTTTATAACTTTTTT
968958 TTCTTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTTATAACTTTTTT
Found at i:976196 original size:27 final size:27
Alignment explanation
Indices: 976148--976209 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
976138 AGAGCTCGGA
*
976148 GTATTTTGATCAAGTTGAAGTTCATGG
1 GTATTTTGATCAAGTTGAAGTTCAGGG
* ** * *
976175 GTATTTTGGTCATTTTGGAGTTTAGGG
1 GTATTTTGATCAAGTTGAAGTTCAGGG
976202 GTATTTTG
1 GTATTTTG
976210 CTAATTTCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.19, C:0.05, G:0.29, T:0.47
Consensus pattern (27 bp):
GTATTTTGATCAAGTTGAAGTTCAGGG
Found at i:977190 original size:20 final size:20
Alignment explanation
Indices: 977165--977239 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
977155 GTCAGACCCA
977165 TTCGAGTTGACTCAAGCTGG
1 TTCGAGTTGACTCAAGCTGG
* * *
977185 TTCGAGTTGACTC-GGTTCAG
1 TTCGAGTTGACTCAAGCT-GG
*
977205 TTCGAGTTGACTCAACCTGG
1 TTCGAGTTGACTCAAGCTGG
*
977225 CTCGAGTTGACTCAA
1 TTCGAGTTGACTCAA
977240 ACCAGTTCAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.04
20 42 0.93
21 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.31
Consensus pattern (20 bp):
TTCGAGTTGACTCAAGCTGG
Found at i:977246 original size:40 final size:40
Alignment explanation
Indices: 977165--977247 Score: 112
Period size: 40 Copynumber: 2.1 Consensus size: 40
977155 GTCAGACCCA
* * ****
977165 TTCGAGTTGACTCAAGCTGGTTCGAGTTGACTCGGTTCAG
1 TTCGAGTTGACTCAACCTGGCTCGAGTTGACTCAAACCAG
977205 TTCGAGTTGACTCAACCTGGCTCGAGTTGACTCAAACCAG
1 TTCGAGTTGACTCAACCTGGCTCGAGTTGACTCAAACCAG
977245 TTC
1 TTC
977248 AAGGGTGTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.30
Consensus pattern (40 bp):
TTCGAGTTGACTCAACCTGGCTCGAGTTGACTCAAACCAG
Found at i:981105 original size:26 final size:22
Alignment explanation
Indices: 981028--981095 Score: 93
Period size: 21 Copynumber: 3.0 Consensus size: 22
981018 AAGTTTATGG
*
981028 GTATTTTGGTTATTTTGGAGTTCAA
1 GTATTTTGGTTA-TTT-CA-TTCAA
981053 GTATTTTGGTTATTTCATTCAA
1 GTATTTTGGTTATTTCATTCAA
981075 -TATTTTGGTTATTTCATTCAA
1 GTATTTTGGTTATTTCATTCAA
981096 TCCAGTATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
21 21 0.50
22 5 0.12
23 1 0.02
24 3 0.07
25 12 0.29
ACGTcount: A:0.22, C:0.07, G:0.16, T:0.54
Consensus pattern (22 bp):
GTATTTTGGTTATTTCATTCAA
Found at i:991944 original size:6 final size:6
Alignment explanation
Indices: 991933--991969 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
991923 TCGTCTCGGC
991933 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
991970 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:992272 original size:22 final size:22
Alignment explanation
Indices: 992247--992301 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
992237 TCAGGAGTTA
* *
992247 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
992269 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
992291 CGGGAGTTATA
1 CAGGAGTTATA
992302 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:997843 original size:5 final size:5
Alignment explanation
Indices: 997829--997867 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
997819 GTCCGTCCGT
* * *
997829 CTCGT CTCGG CTCGG CACGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
997868 TGGTCGTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.05, C:0.41, G:0.36, T:0.18
Consensus pattern (5 bp):
CTCGG
Found at i:997876 original size:6 final size:6
Alignment explanation
Indices: 997865--997894 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
997855 TCGGCTCGGC
*
997865 TCGTGG TCGTGG TCGTGG TCGAGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
997895 ATCAACTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.03, C:0.17, G:0.50, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:998100 original size:22 final size:22
Alignment explanation
Indices: 998075--998129 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
998065 TCAGGAGTTA
* *
998075 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
998097 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
998119 CGGGAGTTATA
1 CAGGAGTTATA
998130 ACAGCTGGAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1013250 original size:22 final size:22
Alignment explanation
Indices: 1013213--1013261 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
1013203 TTCGCAACAT
1013213 AATTT-CCAAATTCGCAACGCG
1 AATTTCCCAAATTCGCAACGCG
* *
1013234 AATTTCCCAGATTCGCAACTCG
1 AATTTCCCAAATTCGCAACGCG
1013256 AATTTC
1 AATTTC
1013262 AAAACTGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (22 bp):
AATTTCCCAAATTCGCAACGCG
Found at i:1013300 original size:42 final size:40
Alignment explanation
Indices: 1013254--1013342 Score: 108
Period size: 42 Copynumber: 2.2 Consensus size: 40
1013244 ATTCGCAACT
1013254 CGAATTTCAAAACTGAGTTGAG-AATCTGGGAAATTCGCGTTG
1 CGAATTTCAAAACTGAGTTGAGAAAT-T-GG-AATTCGCGTTG
** * *
1013296 CGAATTTGGAAACTGTGTTGCGAAATTGGAATTCGCGTTG
1 CGAATTTCAAAACTGAGTTGAGAAATTGGAATTCGCGTTG
1013336 CGAATTT
1 CGAATTT
1013343 GTTGGTTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 18 0.43
41 2 0.05
42 19 0.45
43 3 0.07
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.31
Consensus pattern (40 bp):
CGAATTTCAAAACTGAGTTGAGAAATTGGAATTCGCGTTG
Found at i:1013335 original size:20 final size:20
Alignment explanation
Indices: 1013285--1013339 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1013275 GAATCTGGGA
*
1013285 AATTCGCGTTGCGAATTTGG
1 AATTCGCGTTGCGAAATTGG
* *
1013305 AA-ACTGTGTTGCGAAATTGG
1 AATTC-GCGTTGCGAAATTGG
1013325 AATTCGCGTTGCGAA
1 AATTCGCGTTGCGAA
1013340 TTTGTTGGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (20 bp):
AATTCGCGTTGCGAAATTGG
Found at i:1016401 original size:20 final size:20
Alignment explanation
Indices: 1016376--1016423 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1016366 TGATTAAATC
1016376 ATAAAAT-ATTCATCAAA-AAA
1 ATAAAATAATT-AT-AAATAAA
1016396 ATAAAATTAATTATAAATAAA
1 ATAAAA-TAATTATAAATAAA
1016417 ATAAAAT
1 ATAAAAT
1016424 TCAATTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 10 0.40
21 12 0.48
22 3 0.12
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (20 bp):
ATAAAATAATTATAAATAAA
Found at i:1020444 original size:19 final size:18
Alignment explanation
Indices: 1020415--1020461 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
1020405 ACCGAATTAA
*
1020415 AATAA-AATAAAACATAT
1 AATAATAATAAAACAAAT
*
1020432 AATAAATAATAAAAGAAAT
1 AAT-AATAATAAAACAAAT
1020451 AATAATAATAA
1 AATAATAATAA
1020462 TATTTTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 3 0.12
18 10 0.38
19 13 0.50
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (18 bp):
AATAATAATAAAACAAAT
Found at i:1020537 original size:2 final size:2
Alignment explanation
Indices: 1020525--1020562 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1020515 ATTTTAAAAC
1020525 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1020563 TCGAAATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1020542 original size:38 final size:37
Alignment explanation
Indices: 1020455--1020540 Score: 122
Period size: 36 Copynumber: 2.4 Consensus size: 37
1020445 AGAAATAATA
*
1020455 ATAATA-ATATTTTTTCAAAAATATTTCCCAAAACTAT
1 ATAATATATATATTTTCAAAAATATTT-CCAAAACTAT
*
1020492 ATAATATATATATTTTCAAAAATATTT-TAAAACTAT
1 ATAATATATATATTTTCAAAAATATTTCCAAAACTAT
*
1020528 ATTATATATATAT
1 ATAATATATATAT
1020541 ATATATATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 20 0.44
37 6 0.13
38 19 0.42
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (37 bp):
ATAATATATATATTTTCAAAAATATTTCCAAAACTAT
Found at i:1020581 original size:57 final size:55
Alignment explanation
Indices: 1020489--1020597 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 55
1020479 TTCCCAAAAC
*
1020489 TATATAATATATATATTTTCAAAAATATTTTAAAACTATATTA-TATATATATATA
1 TATATAATATATATATATTCAAAAATATTTTAAAACTATA-TAGTATATATATATA
* *
1020544 TATATATATATATATATATTC-GAAATGTTTTCCAAAACTATATAGTATATATAT
1 TATATA-ATATATATATATTCAAAAATATTTT--AAAACTATATAGTATATATAT
1020598 TTTTTCAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
55 14 0.30
56 15 0.32
57 18 0.38
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (55 bp):
TATATAATATATATATATTCAAAAATATTTTAAAACTATATAGTATATATATATA
Found at i:1020597 original size:39 final size:39
Alignment explanation
Indices: 1020542--1020718 Score: 198
Period size: 39 Copynumber: 4.5 Consensus size: 39
1020532 TATATATATA
* * *
1020542 TATATATATATATATATATATTCGAAATGTTTTCCAAAAC
1 TATATAT-TATATATATATTTTCAAAATGTTTTCAAAAAC
* *
1020582 TATATAGTATATATATTTTTTCAAAATGTTTTCAAAAAC
1 TATATATTATATATATATTTTCAAAATGTTTTCAAAAAC
* *
1020621 TATATATTATATATATGTTTTCAAAATGTTTTCAAAAAT
1 TATATATTATATATATATTTTCAAAATGTTTTCAAAAAC
* *
1020660 TATATA-T-TATATATATTTTCAAAACCGATTTTTAAAAAAC
1 TATATATTATATATATATTTTCAAAA-TG--TTTTCAAAAAC
*
1020700 TATATGTT-TATACTATATT
1 TATATATTATATA-TATATT
1020719 AAAAAGAACT
Statistics
Matches: 119, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
37 16 0.13
38 2 0.02
39 70 0.59
40 20 0.17
41 5 0.04
42 6 0.05
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (39 bp):
TATATATTATATATATATTTTCAAAATGTTTTCAAAAAC
Found at i:1020679 original size:37 final size:38
Alignment explanation
Indices: 1020544--1020683 Score: 201
Period size: 39 Copynumber: 3.7 Consensus size: 38
1020534 TATATATATA
* * *
1020544 TATATATATATATATATATTCGAAATGTTTTCCAAAAC
1 TATATATATATATATATTTTCAAAATGTTTTCAAAAAC
*
1020582 TATATAGTATATATATTTTTTCAAAATGTTTTCAAAAAC
1 TATATA-TATATATATATTTTCAAAATGTTTTCAAAAAC
* *
1020621 TATATATTATATATATGTTTTCAAAATGTTTTCAAAAAT
1 TATATA-TATATATATATTTTCAAAATGTTTTCAAAAAC
1020660 TATATAT-TATATATATTTTCAAAA
1 TATATATATATATATATTTTCAAAA
1020684 CCGATTTTTA
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
37 16 0.17
38 7 0.08
39 70 0.75
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.46
Consensus pattern (38 bp):
TATATATATATATATATTTTCAAAATGTTTTCAAAAAC
Found at i:1025019 original size:17 final size:17
Alignment explanation
Indices: 1024997--1025035 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1024987 TGAATCAAAT
1024997 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1025014 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1025031 -AATTA
1 TAATTA
1025036 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:1028513 original size:29 final size:29
Alignment explanation
Indices: 1028471--1028551 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
1028461 TTTCATATGT
1028471 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1028499 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1028528 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
1028552 ATATCACATA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 7 0.14
29 39 0.76
30 5 0.10
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.44
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:1029078 original size:64 final size:64
Alignment explanation
Indices: 1028928--1029084 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 64
1028918 TAATGAAGGT
* * * * * * **
1028928 ATGCATCGATGAAAAACTTGTGCATCGGTGCA-TAAAATGCATTCGATGTTTTATTATTAATGGA
1 ATGCATCGATGCATACCTTATGCATCGATGCACT-AATTGCATTCGATGTTTTATTATTAAAAGA
* *
1028992 ATGCATCGATGCATGCCTTATGCTTCGATGCACTAATTGCATTCGATGTTTATATT-TTAAAAGA
1 ATGCATCGATGCATACCTTATGCATCGATGCACTAATTGCATTCGATGTTT-TATTATTAAAAGA
*
1029056 GTGCATCGATGCACTACC-TATGCATCGAT
1 ATGCATCGATGCA-TACCTTATGCATCGAT
1029085 ACAGCTTCAA
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
64 69 0.90
65 8 0.10
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCATACCTTATGCATCGATGCACTAATTGCATTCGATGTTTTATTATTAAAAGA
Found at i:1035305 original size:15 final size:15
Alignment explanation
Indices: 1035281--1035314 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1035271 CCGTAAGACC
1035281 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
1035296 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
1035311 ACTA
1 ACTA
1035315 TTATACCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:1035441 original size:29 final size:29
Alignment explanation
Indices: 1035399--1035479 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
1035389 TTTCATATGT
1035399 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1035427 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1035456 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
1035480 ATATCACATA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 7 0.14
29 39 0.76
30 5 0.10
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.44
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:1035925 original size:64 final size:64
Alignment explanation
Indices: 1035856--1036012 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 64
1035846 TAATGAAGGT
* * **
1035856 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTTGATGTTT-TATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATGTTTATATT-TTAAAAG
1035919 A
64 A
* * *
1035920 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTATATTTTAAAAGA
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATGTTTATATTTTAAAAGA
* *
1035984 GTGCATCGATGCACTACCTGTGCATCGAT
1 ATGCATCGATGCACTACTTGTGCATCGAT
1036013 ACACCTTCAA
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
63 1 0.01
64 71 0.91
65 6 0.08
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATGTTTATATTTTAAAAGA
Found at i:1040614 original size:16 final size:16
Alignment explanation
Indices: 1040593--1040623 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1040583 GGCAAACACG
*
1040593 TTTTTTATTTCATTTA
1 TTTTTTAATTCATTTA
1040609 TTTTTTAATTCATTT
1 TTTTTTAATTCATTT
1040624 TCTATTTTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTAATTCATTTA
Found at i:1044315 original size:8 final size:7
Alignment explanation
Indices: 1044295--1044346 Score: 70
Period size: 7 Copynumber: 7.3 Consensus size: 7
1044285 CTCTAAATTG
1044295 AAAA-AA
1 AAAAGAA
1044301 AAAAGAA
1 AAAAGAA
1044308 AAAGAGAA
1 AAA-AGAA
1044316 AAAAGAA
1 AAAAGAA
1044323 CAAAAGAA
1 -AAAAGAA
*
1044331 AAAAGAG
1 AAAAGAA
1044338 AAAAGAA
1 AAAAGAA
1044345 AA
1 AA
1044347 TAAGGTGGGC
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
6 4 0.10
7 23 0.56
8 14 0.34
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:1044319 original size:15 final size:15
Alignment explanation
Indices: 1044299--1044343 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
1044289 AAATTGAAAA
1044299 AAAAAAGAAAAAGAG
1 AAAAAAGAAAAAGAG
1044314 AAAAAAGAACAAA-AG
1 AAAAAAGAA-AAAGAG
1044329 AAAAAAGAGAAAAGA
1 AAAAAAGA-AAAAGA
1044344 AAATAAGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 22 0.81
16 5 0.19
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAGAG
Found at i:1045675 original size:110 final size:107
Alignment explanation
Indices: 1045467--1045697 Score: 259
Period size: 110 Copynumber: 2.1 Consensus size: 107
1045457 ATTTCGGAGC
* * * * * * *
1045467 CAATTTCAGCTTCACGGTGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTTACAACGAAT
1 CAATTTCAACTTCACAGCGAAGAATATTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAG
* *
1045532 GGGCGACTAGTTGTCAACAAACAACTTCTCAGTTTCATTCAGAG-T
66 GGGCGACTAGCTGTCAACAAACAACTTCCCAG-TTC--T-AGAGAT
* * * *
1045577 CAATTTCAACTTCACAGCGAATAATATTAGACTCGAGACAGCACAAGCTCAACTTCACAGCGAAG
1 CAATTTCAACTTCACAGCGAAGAATATTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAG
* * * *
1045642 GGGCGGCTGGCTGTCAACAAATAATTTCCCAGTTCTAGAGAT
66 GGGCGACTAGCTGTCAACAAACAACTTCCCAGTTCTAGAGAT
1045684 -AATTTCAACTTCAC
1 CAATTTCAACTTCAC
1045698 GACGGAGGAT
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
106 18 0.17
107 2 0.02
109 3 0.03
110 80 0.78
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (107 bp):
CAATTTCAACTTCACAGCGAAGAATATTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAG
GGGCGACTAGCTGTCAACAAACAACTTCCCAGTTCTAGAGAT
Found at i:1046477 original size:24 final size:24
Alignment explanation
Indices: 1046445--1046519 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 24
1046435 TACTCGTTTA
1046445 ATTATTATTTTATATATATACATT
1 ATTATTATTTTATATATATACATT
* * *
1046469 ATTATTATTTTAACACATATA-TTT
1 ATTATTATTTT-ATATATATACATT
1046493 ATTTATTTATTTTATAT-T-TACATT
1 A-TTA-TTATTTTATATATATACATT
1046517 ATT
1 ATT
1046520 TCAGGCCCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
23 4 0.10
24 18 0.44
25 12 0.29
26 7 0.17
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTATTATTTTATATATATACATT
Found at i:1047758 original size:15 final size:15
Alignment explanation
Indices: 1047723--1047758 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1047713 TTTATTCATC
*
1047723 TTATTGTTATTTCCT
1 TTATTTTTATTTCCT
1047738 TTATTTTTATTTCCT
1 TTATTTTTATTTCCT
1047753 TTATTT
1 TTATTT
1047759 ATTTATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.11, G:0.03, T:0.72
Consensus pattern (15 bp):
TTATTTTTATTTCCT
Found at i:1060107 original size:9 final size:8
Alignment explanation
Indices: 1060093--1060137 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 8
1060083 TACCGATTAT
1060093 AAAAATGAA
1 AAAAAT-AA
1060102 AAAAATAA
1 AAAAATAA
1060110 CAAAAATAA
1 -AAAAATAA
*
1060119 AAAATAAAA
1 AAAA-ATAA
1060128 AAAAATAA
1 AAAAATAA
1060136 AA
1 AA
1060138 TTAAAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 11 0.34
9 21 0.66
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.11
Consensus pattern (8 bp):
AAAAATAA
Found at i:1060122 original size:16 final size:17
Alignment explanation
Indices: 1060101--1060137 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1060091 ATAAAAATGA
*
1060101 AAAAAAT-AACAAAAAT
1 AAAAAATAAAAAAAAAT
1060117 AAAAAATAAAAAAAAAT
1 AAAAAATAAAAAAAAAT
1060134 AAAA
1 AAAA
1060138 TTAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.86, C:0.03, G:0.00, T:0.11
Consensus pattern (17 bp):
AAAAAATAAAAAAAAAT
Found at i:1062185 original size:15 final size:15
Alignment explanation
Indices: 1062167--1062201 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1062157 AACATTCTCA
*
1062167 ATAATCTTATTCCTT
1 ATAATCTTATTCCTG
1062182 ATAATCTTATTCCTG
1 ATAATCTTATTCCTG
1062197 ATAAT
1 ATAAT
1062202 TTACATTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.03, T:0.49
Consensus pattern (15 bp):
ATAATCTTATTCCTG
Found at i:1062756 original size:60 final size:59
Alignment explanation
Indices: 1062692--1062832 Score: 160
Period size: 59 Copynumber: 2.4 Consensus size: 59
1062682 TACATATTTT
** *
1062692 GATGAAACCGAAATATTTAAAAATTTGGGAATCAATTTAGAACG-AGTGTCATAATTTAGG
1 GATGAAATTGAAATATTTAAAAATTTAGG-ATCAATTTAGAACGAAG-GTCATAATTTAGG
* * * * * **
1062752 GATGAAATTGGAAGATTTAAAAGTTTAGGATCAATTTAGAATGAAGGTTATGGTTTAGG
1 GATGAAATTGAAATATTTAAAAATTTAGGATCAATTTAGAACGAAGGTCATAATTTAGG
1062811 GATGAAATTGAAAT-TTTAAAAA
1 GATGAAATTGAAATATTTAAAAA
1062833 GTTAAGGACT
Statistics
Matches: 67, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
58 7 0.10
59 35 0.52
60 25 0.37
ACGTcount: A:0.42, C:0.04, G:0.22, T:0.32
Consensus pattern (59 bp):
GATGAAATTGAAATATTTAAAAATTTAGGATCAATTTAGAACGAAGGTCATAATTTAGG
Found at i:1063056 original size:17 final size:19
Alignment explanation
Indices: 1063020--1063056 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1063010 CATTCAAAAC
*
1063020 ATTATTTTTCTTTCTAGAA
1 ATTATATTTCTTTCTAGAA
1063039 ATTATATTT-TTT-TAGAA
1 ATTATATTTCTTTCTAGAA
1063056 A
1 A
1063057 AATACCTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 3 0.18
19 8 0.47
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57
Consensus pattern (19 bp):
ATTATATTTCTTTCTAGAA
Found at i:1066564 original size:33 final size:33
Alignment explanation
Indices: 1066498--1066618 Score: 205
Period size: 33 Copynumber: 3.8 Consensus size: 33
1066488 TCCGGAACCC
*
1066498 CCTGCCCCAATTAGAGCCAGTCCT---CCACCT
1 CCTGCCCCCATTAGAGCCAGTCCTCCACCACCT
1066528 CCTGCCCCCATTAGAGCCAGTCCTCCACCACCT
1 CCTGCCCCCATTAGAGCCAGTCCTCCACCACCT
1066561 CCTGCCCCCATTAGAGCCAGTCCTCCACCACCT
1 CCTGCCCCCATTAGAGCCAGTCCTCCACCACCT
1066594 CCTG-CCCCATTAGAGCCAGTCCTCC
1 CCTGCCCCCATTAGAGCCAGTCCTCC
1066619 TGCGCCACCT
Statistics
Matches: 87, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
30 23 0.26
32 21 0.24
33 43 0.49
ACGTcount: A:0.18, C:0.50, G:0.13, T:0.19
Consensus pattern (33 bp):
CCTGCCCCCATTAGAGCCAGTCCTCCACCACCT
Found at i:1066584 original size:63 final size:63
Alignment explanation
Indices: 1066498--1066618 Score: 199
Period size: 63 Copynumber: 1.9 Consensus size: 63
1066488 TCCGGAACCC
1066498 CCTGCCCCAATTAGAGCCAGTCCT-CCACCTCCTGCCCCCATTAGAGCCAGTCCTCCACCACCT
1 CCTGCCCCAATTAGAGCCAGTCCTCCCACCTCCTG-CCCCATTAGAGCCAGTCCTCCACCACCT
*
1066561 CCTGCCCCCATTAGAGCCAGTCCTCCACCACCTCCTGCCCCATTAGAGCCAGTCCTCC
1 CCTGCCCCAATTAGAGCCAGTCCT-C-CCACCTCCTGCCCCATTAGAGCCAGTCCTCC
1066619 TGCGCCACCT
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
63 23 0.43
65 21 0.39
66 10 0.19
ACGTcount: A:0.18, C:0.50, G:0.13, T:0.19
Consensus pattern (63 bp):
CCTGCCCCAATTAGAGCCAGTCCTCCCACCTCCTGCCCCATTAGAGCCAGTCCTCCACCACCT
Found at i:1077101 original size:22 final size:22
Alignment explanation
Indices: 1077070--1077136 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 22
1077060 AGTCTATAAA
*
1077070 TTTAATATTTTATTAATTTAATT
1 TTTAA-ATTTTATTAATTTAATC
1077093 TTTAAATTTTATTAATTAAAATTAATC
1 TTTAAATTTTATTAA-T----TTAATC
1077120 TTTAAATTTTATTAATT
1 TTTAAATTTTATTAATT
1077137 AAAATTAATC
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
22 11 0.29
23 6 0.16
26 1 0.03
27 20 0.53
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTAAATTTTATTAATTTAATC
Found at i:1077105 original size:27 final size:27
Alignment explanation
Indices: 1077087--1077156 Score: 131
Period size: 27 Copynumber: 2.6 Consensus size: 27
1077077 TTTTATTAAT
*
1077087 TTAATTTTTAAATTTTATTAATTAAAA
1 TTAATCTTTAAATTTTATTAATTAAAA
1077114 TTAATCTTTAAATTTTATTAATTAAAA
1 TTAATCTTTAAATTTTATTAATTAAAA
1077141 TTAATCTTTAAATTTT
1 TTAATCTTTAAATTTT
1077157 TGCAGACTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (27 bp):
TTAATCTTTAAATTTTATTAATTAAAA
Found at i:1079905 original size:17 final size:17
Alignment explanation
Indices: 1079864--1079907 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1079854 ATATATAGTC
1079864 ATAAAATA-AAAAATGT
1 ATAAAATATAAAAATGT
*
1079880 ATCAAATATATAAAATG-
1 ATAAAATATA-AAAATGT
1079897 ATAAAATATAA
1 ATAAAATATAA
1079908 TATTATACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 8 0.33
17 10 0.42
18 6 0.25
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (17 bp):
ATAAAATATAAAAATGT
Found at i:1094137 original size:6 final size:6
Alignment explanation
Indices: 1094137--1094164 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1094127 ATATAATTAT
1094137 ATTAAA ATTAAA ATTAAA ATTAAA ATTA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTA
1094165 TATATAAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
ATTAAA
Found at i:1096358 original size:15 final size:15
Alignment explanation
Indices: 1096334--1096375 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1096324 GTATTATTAA
*
1096334 ATTAATTTATAAAAC
1 ATTAAATTATAAAAC
*
1096349 ATTAAATTAT-AAAT
1 ATTAAATTATAAAAC
1096363 ATTAAATATATAA
1 ATTAAAT-TATAA
1096376 TTATAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 10 0.43
15 12 0.52
16 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTAAATTATAAAAC
Found at i:1098692 original size:4 final size:4
Alignment explanation
Indices: 1098683--1098713 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1098673 CCCTTGTCTG
1098683 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
1098714 TATATGAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:1100044 original size:2 final size:2
Alignment explanation
Indices: 1100037--1100061 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1100027 AAAAAGGAAC
1100037 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1100062 GAATTATCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1103585 original size:26 final size:26
Alignment explanation
Indices: 1103567--1103623 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
1103557 TTAAAACCCA
*
1103567 GAAAGTTTCTTTCTAATTAAAAAAAT
1 GAAAGTTTCTTTCGAATTAAAAAAAT
*
1103593 GAAAGTTTCTTTCGAATCAAAAAAAT
1 GAAAGTTTCTTTCGAATTAAAAAAAT
1103619 AGAAA
1 -GAAA
1103624 AAAGTAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 24 0.86
27 4 0.14
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.32
Consensus pattern (26 bp):
GAAAGTTTCTTTCGAATTAAAAAAAT
Found at i:1104435 original size:19 final size:19
Alignment explanation
Indices: 1104411--1104457 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1104401 GATTTTCGAA
1104411 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
** *
1104430 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAAT
1104448 TTCGCAACAC
1 TTCGCAACAC
1104458 AAATGTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:1105365 original size:24 final size:24
Alignment explanation
Indices: 1105336--1105391 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
1105326 GTGAGTACTA
**
1105336 GTCAATATTCAAAATTTGATCTTG
1 GTCAATACCCAAAATTTGATCTTG
** *
1105360 GTCAATACCCGGACTTTGATCTTG
1 GTCAATACCCAAAATTTGATCTTG
1105384 GTCAATAC
1 GTCAATAC
1105392 TCGGATTTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (24 bp):
GTCAATACCCAAAATTTGATCTTG
Found at i:1105396 original size:24 final size:24
Alignment explanation
Indices: 1105350--1105403 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1105340 ATATTCAAAA
1105350 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1105374 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1105398 TTTGAT
1 TTTGAT
1105404 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1106389 original size:21 final size:21
Alignment explanation
Indices: 1106365--1106404 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1106355 GCGTAGAATT
*
1106365 TGTCCCGGAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
*
1106386 TGTCTCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
1106405 TAACACATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:1107095 original size:2 final size:2
Alignment explanation
Indices: 1107088--1107149 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1107078 CTACACAATC
1107088 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1107130 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1107150 GCTATCAGTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1107278 original size:24 final size:21
Alignment explanation
Indices: 1107225--1107283 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 21
1107215 TTTCCCATTG
*
1107225 AAGTGCATCGGTGCATTCTAC
1 AAGTGCATCGATGCATTCTAC
1107246 -AGTGCATCGATGCATTCTTTAAC
1 AAGTGCATCGATGCATTC--T-AC
1107269 AAGTGCATCGATGCA
1 AAGTGCATCGATGCA
1107284 CTACCATGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 2 0.06
24 14 0.42
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (21 bp):
AAGTGCATCGATGCATTCTAC
Found at i:1107791 original size:21 final size:21
Alignment explanation
Indices: 1107767--1107865 Score: 171
Period size: 21 Copynumber: 4.7 Consensus size: 21
1107757 CCTTTTGTGT
*
1107767 TTTAAGCTTATATAAGTTTTC
1 TTTAAGCTTATATAAGCTTTC
* *
1107788 TTTAAACTTATATAAGTTTTC
1 TTTAAGCTTATATAAGCTTTC
1107809 TTTAAGCTTATATAAGCTTTC
1 TTTAAGCTTATATAAGCTTTC
1107830 TTTAAGCTTATATAAGCTTTC
1 TTTAAGCTTATATAAGCTTTC
1107851 TTTAAGCTTATATAA
1 TTTAAGCTTATATAA
1107866 CACTCAAAGA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 75 1.00
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.49
Consensus pattern (21 bp):
TTTAAGCTTATATAAGCTTTC
Found at i:1107837 original size:11 final size:11
Alignment explanation
Indices: 1107800--1107859 Score: 61
Period size: 11 Copynumber: 5.6 Consensus size: 11
1107790 TAAACTTATA
*
1107800 TAAGTTTTCTT
1 TAAGCTTTCTT
* *
1107811 TAAGC-TTATA
1 TAAGCTTTCTT
1107821 TAAGCTTTCTT
1 TAAGCTTTCTT
* *
1107832 TAAGC-TTATA
1 TAAGCTTTCTT
1107842 TAAGCTTTCTT
1 TAAGCTTTCTT
1107853 TAAGCTT
1 TAAGCTT
1107860 ATATAACACT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
10 16 0.42
11 22 0.58
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.50
Consensus pattern (11 bp):
TAAGCTTTCTT
Found at i:1114403 original size:18 final size:17
Alignment explanation
Indices: 1114380--1114414 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
1114370 AAGCAAAAGG
1114380 AAATCAAAATCGCAATCA
1 AAATCAAAATC-CAATCA
1114398 AAATCAAAATCCAATCA
1 AAATCAAAATCCAATCA
1114415 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.57, C:0.23, G:0.03, T:0.17
Consensus pattern (17 bp):
AAATCAAAATCCAATCA
Found at i:1116352 original size:21 final size:21
Alignment explanation
Indices: 1116328--1116404 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
1116318 GTGAATCGGG
*
1116328 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
1116349 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* **
1116370 CTCTTGAATGAT-AGGAGGCAC
1 CTCTTGAACGATGA-GAGGGGC
1116391 CTCTTGAACGATGA
1 CTCTTGAACGATGA
1116405 TAGGTGCATC
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 44 0.98
22 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.34, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:1119051 original size:20 final size:19
Alignment explanation
Indices: 1119026--1119095 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 19
1119016 TAAACGCGCT
1119026 TTGCGAATTTAACTTTCGCG
1 TTGCGAATTT-ACTTTCGCG
*
1119046 TTGCGAATTTGAC-TTCTGTG
1 TTGCGAATTT-ACTTTC-GCG
1119066 TTGCG-ATTTACATATTCGCG
1 TTGCGAATTTAC-T-TTCGCG
1119086 TTGCGAATTT
1 TTGCGAATTT
1119096 GGAAACTGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
18 2 0.05
19 7 0.17
20 26 0.62
21 7 0.17
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (19 bp):
TTGCGAATTTACTTTCGCG
Found at i:1119248 original size:15 final size:15
Alignment explanation
Indices: 1119225--1119254 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1119215 CTCATATAAA
*
1119225 TATCTTTTATAATTT
1 TATCGTTTATAATTT
1119240 TATCGTTTATAATTT
1 TATCGTTTATAATTT
1119255 ACGTTTTGTT
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:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (15 bp):
TATCGTTTATAATTT
Found at i:1127096 original size:29 final size:29
Alignment explanation
Indices: 1127060--1127156 Score: 77
Period size: 29 Copynumber: 3.3 Consensus size: 29
1127050 ATATAACTTT
*
1127060 TATTTTAAATTGATACTTAAACTTTTTCA
1 TATTTTAAATTAATACTTAAACTTTTTCA
* * * * ** *
1127089 TATTTTAATTTTATTCTTAAAGTATGACTCT
1 TATTTTAAATTAATACTTAAACT-T-TTTCA
* **
1127120 TATTTTAAATTAATCCTTAAACTTTTGAA
1 TATTTTAAATTAATACTTAAACTTTTTCA
1127149 TATTTTAA
1 TATTTTAA
1127157 TTTTATCACT
Statistics
Matches: 50, Mismatches: 16, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
29 27 0.54
30 2 0.04
31 21 0.42
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (29 bp):
TATTTTAAATTAATACTTAAACTTTTTCA
Found at i:1127127 original size:60 final size:60
Alignment explanation
Indices: 1127059--1127210 Score: 175
Period size: 60 Copynumber: 2.6 Consensus size: 60
1127049 AATATAACTT
* ** * *
1127059 TTATTTTAAATTGATACTTAAACTTTTTCATATTTTAATTTTATTC-TTAAAGTATGACTC
1 TTATTTTAAATTAATACTTAAACTTTTGAATATTTTAATTTTA-TCACTAAACTATGACTC
*
1127119 TTATTTTAAATTAATCCTTAAACTTTTGAATATTTTAATTTTATCACTAAACTATGACTC
1 TTATTTTAAATTAATACTTAAACTTTTGAATATTTTAATTTTATCACTAAACTATGACTC
* * * **
1127179 -T-TTCTAAATTAGTCCCCAAACTTTTGAATATT
1 TTATTTTAAATTAATACTTAAACTTTTGAATATT
1127211 CCAAGTTCAT
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
58 27 0.33
59 3 0.04
60 51 0.63
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.49
Consensus pattern (60 bp):
TTATTTTAAATTAATACTTAAACTTTTGAATATTTTAATTTTATCACTAAACTATGACTC
Found at i:1127227 original size:58 final size:60
Alignment explanation
Indices: 1127106--1127227 Score: 140
Period size: 58 Copynumber: 2.1 Consensus size: 60
1127096 ATTTTATTCT
* * ** ** * *
1127106 TAAAGTATGACTCTTATTTTAAATTAATCCTTAAACTTTTGAATATTTTAATTTTATCAC
1 TAAACTATGACTCTTATTCTAAATTAATCCCCAAACTTTTGAATATTCCAAGTTCATCAC
* *
1127166 TAAACTATGACTC-T-TTCTAAATTAGTCCCCAAACTTTTGAATATTCCAAGTTCATCCC
1 TAAACTATGACTCTTATTCTAAATTAATCCCCAAACTTTTGAATATTCCAAGTTCATCAC
1127224 TAAA
1 TAAA
1127228 TTCATCCAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
58 39 0.75
59 1 0.02
60 12 0.23
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (60 bp):
TAAACTATGACTCTTATTCTAAATTAATCCCCAAACTTTTGAATATTCCAAGTTCATCAC
Found at i:1127428 original size:61 final size:59
Alignment explanation
Indices: 1127352--1127607 Score: 232
Period size: 60 Copynumber: 4.3 Consensus size: 59
1127342 GTATATACAT
* **
1127352 ATAGTTTG-GGATGAAATTGAAATGTTCAAAAAGTTTGGGGATTAATTTAAAAGGAAGGTC
1 ATAGTTTGAGGATGAAACTGAAACATTC-AAAAGTTTGGGGATTAATTTAAAAGGAA-GTC
* ** * * *
1127412 ATAGTTTGAGGATGAAACTGAAACATTCAAAATTTTAAGGACTAATTTAGAATGATAGTC
1 ATAGTTTGAGGATGAAACTGAAACATTCAAAAGTTTGGGGATTAATTTAAAAGGA-AGTC
* * * *
1127472 ATAATTT-AGGAATGAAA-TTAGAATATTTAAAAGTTTGGGGATTAATTTAAAAGGAATGTC
1 ATAGTTTGAGG-ATGAAACTGA-AACATTCAAAAGTTTGGGGATTAATTTAAAAGGAA-GTC
* * ** * * *
1127532 ATAGTTTGGGGATGAAACTGAAACATTCAAAATTTTAAGGACTAATTTAGAATGATAGTC
1 ATAGTTTGAGGATGAAACTGAAACATTCAAAAGTTTGGGGATTAATTTAAAAGGA-AGTC
*
1127592 ATAATTT-AGGATGAAA
1 ATAGTTTGAGGATGAAA
1127608 TTAGAATATT
Statistics
Matches: 156, Mismatches: 32, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
59 14 0.09
60 120 0.77
61 22 0.14
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.32
Consensus pattern (59 bp):
ATAGTTTGAGGATGAAACTGAAACATTCAAAAGTTTGGGGATTAATTTAAAAGGAAGTC
Found at i:1127593 original size:120 final size:119
Alignment explanation
Indices: 1127380--1127631 Score: 468
Period size: 120 Copynumber: 2.1 Consensus size: 119
1127370 GAAATGTTCA
1127380 AAAAGTTTGGGGATTAATTTAAAAGGAAGGTCATAGTTTGAGGATGAAACTGAAACATTCAAAAT
1 AAAAGTTTGGGGATTAATTTAAAAGGAAGGTCATAGTTTGAGGATGAAACTGAAACATTCAAAAT
1127445 TTTAAGGACTAATTTAGAATGATAGTCATAATTTAGGAATGAAATTAGAATATTT
66 TTTAAGGACTAATTTAGAATGATAGTCATAATTTAGG-ATGAAATTAGAATATTT
* *
1127500 AAAAGTTTGGGGATTAATTTAAAAGGAATGTCATAGTTTGGGGATGAAACTGAAACATTCAAAAT
1 AAAAGTTTGGGGATTAATTTAAAAGGAAGGTCATAGTTTGAGGATGAAACTGAAACATTCAAAAT
1127565 TTTAAGGACTAATTTAGAATGATAGTCATAATTTAGGATGAAATTAGAATATTT
66 TTTAAGGACTAATTTAGAATGATAGTCATAATTTAGGATGAAATTAGAATATTT
*
1127619 AAAAGTTTAGGGA
1 AAAAGTTTGGGGA
1127632 CCGAATTAAA
Statistics
Matches: 129, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
119 29 0.22
120 100 0.78
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.33
Consensus pattern (119 bp):
AAAAGTTTGGGGATTAATTTAAAAGGAAGGTCATAGTTTGAGGATGAAACTGAAACATTCAAAAT
TTTAAGGACTAATTTAGAATGATAGTCATAATTTAGGATGAAATTAGAATATTT
Found at i:1127652 original size:59 final size:59
Alignment explanation
Indices: 1127356--1127662 Score: 198
Period size: 60 Copynumber: 5.1 Consensus size: 59
1127346 ATACATATAG
* * * * *
1127356 TTTG-GGATGAAATT-GAA-ATGTTCAAAAAGTTTGGGGATTAATTTAAAAGGAAGGTCATAG
1 TTTGAGGATGAAATTAGAATAT-TT--AAAAGTTTAGGGACTAATTTAAAA-TAAAGTCATAA
* * * * * * *
1127416 TTTGAGGATGAAACT-GAAACATTCAAAATTTTAAGGACTAATTTAGAATGATAGTCATAA
1 TTTGAGGATGAAATTAG-AATATTTAAAAGTTTAGGGACTAATTTAAAAT-AAAGTCATAA
* * * * *
1127476 TTT-AGGAATGAAATTAGAATATTTAAAAGTTTGGGGATTAATTTAAAAGGAATGTCATAG
1 TTTGAGG-ATGAAATTAGAATATTTAAAAGTTTAGGGACTAATTTAAAA-TAAAGTCATAA
* * * * * * * *
1127536 TTTGGGGATGAAACT-GAAACATTCAAAATTTTAAGGACTAATTTAGAATGATAGTCATAA
1 TTTGAGGATGAAATTAG-AATATTTAAAAGTTTAGGGACTAATTTAAAAT-AAAGTCATAA
* * *
1127596 TTT-AGGATGAAATTAGAATATTTAAAAGTTTAGGGACCGAA-TTAAAATAAGGGTCATAC
1 TTTGAGGATGAAATTAGAATATTTAAAAGTTTAGGGA-CTAATTTAAAATAA-AGTCATAA
1127655 TTTGAGGA
1 TTTGAGGA
1127663 CATGTGATGC
Statistics
Matches: 186, Mismatches: 47, Indels: 28
0.71 0.18 0.11
Matches are distributed among these distances:
58 1 0.01
59 44 0.24
60 123 0.66
61 13 0.07
62 3 0.02
63 2 0.01
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (59 bp):
TTTGAGGATGAAATTAGAATATTTAAAAGTTTAGGGACTAATTTAAAATAAAGTCATAA
Found at i:1129396 original size:3 final size:3
Alignment explanation
Indices: 1129390--1129428 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1129380 GTCCCATTCG
1129390 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1129429 ATTAAGTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1131522 original size:131 final size:131
Alignment explanation
Indices: 1131352--1131716 Score: 392
Period size: 131 Copynumber: 2.8 Consensus size: 131
1131342 CGACAATGAG
*** * * ** *
1131352 AATAGTAATATC-CTTTCATTTCGGTCGGAGTAATAAATGACTAATTTAAGGCA-TAAGATGTCA
1 AATAGTAATATCTCTTT-ATTTAAATTGGAGTAATAAATGATTGTTTTAATGCACTAA-ATGTCA
* * * * ** * *
1131415 TTTATTCTCGATTGAAAATAATTTGATATTGTCGTTTTCTCTCGAATTAATATCGATTTTTTAGA
64 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCGAACCAATATCGAATTTTAAGA
*
1131480 CGG
129 CGA
* * * * *
1131483 AATATTAATATCTCTTTATTTAAATTGGGGTAATAAATGATTGTTTTAATGCATTAAAGGTCGTT
1 AATAGTAATATCTCTTTATTTAAATTGGAGTAATAAATGATTGTTTTAATGCACTAAATGTCATT
* * * ** * * * *
1131548 TATTCTTGATTGGAAATCATTAGATGTTATTATTTTCACTTGAACCGATATTGAATTTTAAGATG
66 TATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCGAACCAATATCGAATTTTAAGACG
1131613 A
131 A
* * *
1131614 AATAGTAATATCTCTTTATTTCAATTGGAGTAATAAATGATTGTTTTAATTCACGAAATGTCATT
1 AATAGTAATATCTCTTTATTTAAATTGGAGTAATAAATGATTGTTTTAATGCACTAAATGTCATT
1131679 TATTCTCGATTGGAAATAATTAGATATTATCGTTTTCA
66 TATTCTCGATTGGAAATAATTAGATATTATCGTTTTCA
1131717 TTCTTAAAAT
Statistics
Matches: 189, Mismatches: 43, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
131 182 0.96
132 7 0.04
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.43
Consensus pattern (131 bp):
AATAGTAATATCTCTTTATTTAAATTGGAGTAATAAATGATTGTTTTAATGCACTAAATGTCATT
TATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCGAACCAATATCGAATTTTAAGACG
A
Found at i:1134529 original size:12 final size:11
Alignment explanation
Indices: 1134505--1134615 Score: 80
Period size: 12 Copynumber: 9.4 Consensus size: 11
1134495 TTCAAAGAGG
1134505 TTTTAT-TTAA
1 TTTTATATTAA
1134515 TTTTATATTATA
1 TTTTATATTA-A
*
1134527 TTTTATTTTAA
1 TTTTATATTAA
1134538 TTTTAATATTAA
1 TTTT-ATATTAA
* *
1134550 TTTTTTAATAAA
1 TTTTAT-ATTAA
**
1134562 TTAAATATTAATA
1 TTTTATATT-A-A
1134575 TTTTATATTATA
1 TTTTATATTA-A
*
1134587 TTATAGATATTAA
1 TT-T-TATATTAA
1134600 TTTTAATATTAA
1 TTTT-ATATTAA
1134612 TTTT
1 TTTT
1134616 TTAAATAAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
10 6 0.08
11 11 0.14
12 45 0.56
13 12 0.15
14 6 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (11 bp):
TTTTATATTAA
Found at i:1134568 original size:23 final size:25
Alignment explanation
Indices: 1134536--1134603 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 25
1134526 ATTTTATTTT
*
1134536 AATTTTAATATTAATTTTT-TAATA
1 AATTATAATATTAATTTTTATAATA
*
1134560 AATTA-AATATTAATATTTTATATTA
1 AATTATAATATTAAT-TTTTATAATA
*
1134585 TATTATAGATATTAATTTT
1 AATTATA-ATATTAATTTT
1134604 AATATTAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 9 0.24
24 8 0.22
25 8 0.22
26 4 0.11
27 8 0.22
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (25 bp):
AATTATAATATTAATTTTTATAATA
Found at i:1134647 original size:63 final size:61
Alignment explanation
Indices: 1134511--1134668 Score: 241
Period size: 63 Copynumber: 2.6 Consensus size: 61
1134501 GAGGTTTTAT
* *
1134511 TTAA-TTTTATATTATATT-T-TATTTTAATTTTAATATTAATTTTTTAATAAATTAAATA
1 TTAATTTTTATATTATATTATAGATATTAATTTTAATATTAATTTTTTAATAAATTAAATA
1134569 TTAATATTTTATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATA
1 TTAAT-TTTTATATTATATTATAGATATTAATTTTAATATTAATTTTTT-AATAAATTAAATA
1134632 TTAATTTTTAATATTATATTATAGATATTTAATTTTA
1 TTAATTTTT-ATATTATATTATAGATA-TTAATTTTA
1134669 TATCATATAA
Statistics
Matches: 91, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
58 4 0.04
60 14 0.15
61 1 0.01
62 28 0.31
63 35 0.38
64 9 0.10
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (61 bp):
TTAATTTTTATATTATATTATAGATATTAATTTTAATATTAATTTTTTAATAAATTAAATA
Found at i:1134664 original size:21 final size:23
Alignment explanation
Indices: 1134629--1134694 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 23
1134619 AATAAATTAA
*
1134629 ATATTAATT-TTTAATATTATAT
1 ATATAAATTATTTAATATTATAT
* *
1134651 -TATAGA-TATTTAATTTTATAT
1 ATATAAATTATTTAATATTATAT
1134672 CATATAAATTATTTATATATTAT
1 -ATATAAATTATTTA-ATATTAT
1134695 TAAATTTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
20 1 0.03
21 16 0.47
23 5 0.15
24 6 0.18
25 6 0.18
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
ATATAAATTATTTAATATTATAT
Found at i:1134701 original size:63 final size:57
Alignment explanation
Indices: 1134511--1134710 Score: 160
Period size: 63 Copynumber: 3.3 Consensus size: 57
1134501 GAGGTTTTAT
* * *
1134511 TTAA-TTTTATATTATATT-T-TATTTTAATTTTAATATTAATTTTTTAATAAATTAAATA
1 TTAATTTTTATATTATATTATAGATATTAATTTTAATATTAATTATTTAATAAA-T---TA
*
1134569 TTAATATTTTATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATA
1 TTAAT-TTTTATATTATATTATAGATATTAATTTTAATATTAATTATTT-AATAAA-T---TA
*
1134632 TTAATTTTTAATATTATATTATAGATATTTAATTTTATATCATATAAATTATTT-ATATATTA
1 TTAATTTTT-ATATTATATTATAGATA-TTAATTTTA-AT-AT-T-AATTATTTAATAAATTA
*
1134694 TTAA-ATTTATATT-TATT
1 TTAATTTTTATATTATATT
1134711 TAATTATTTT
Statistics
Matches: 126, Mismatches: 5, Indels: 21
0.83 0.03 0.14
Matches are distributed among these distances:
58 4 0.03
59 4 0.03
60 19 0.15
61 4 0.03
62 34 0.27
63 35 0.28
64 9 0.07
65 3 0.02
66 6 0.05
67 1 0.01
68 7 0.06
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (57 bp):
TTAATTTTTATATTATATTATAGATATTAATTTTAATATTAATTATTTAATAAATTA
Found at i:1134703 original size:20 final size:20
Alignment explanation
Indices: 1134658--1134709 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
1134648 TATTATAGAT
1134658 ATTTAATTTTATATCATATAA
1 ATTT-ATTTTATATCATATAA
*
1134679 A-TTATTTATATATTAT-TAA
1 ATTTATTT-TATATCATATAA
1134698 ATTTATATTTAT
1 ATTTAT-TTTAT
1134710 TTAATTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 8 0.30
20 16 0.59
21 3 0.11
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTATTTTATATCATATAA
Found at i:1134709 original size:15 final size:16
Alignment explanation
Indices: 1134682--1134715 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1134672 CATATAAATT
1134682 ATTTATATATTATTAA
1 ATTTATATATTATTAA
*
1134698 ATTTATAT-TTATTTA
1 ATTTATATATTATTAA
1134713 ATT
1 ATT
1134716 ATTTTGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTATATATTATTAA
Found at i:1134717 original size:14 final size:15
Alignment explanation
Indices: 1134682--1134732 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
1134672 CATATAAATT
*
1134682 ATTTATATATTATTAA
1 ATTTATAT-TTATTTA
1134698 ATTTATATTTATTTA
1 ATTTATATTTATTTA
1134713 A-TTAT-TTTGATTTA
1 ATTTATATTT-ATTTA
1134727 AGTTTA
1 A-TTTA
1134733 AATATAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 3 0.10
14 10 0.32
15 7 0.23
16 11 0.35
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (15 bp):
ATTTATATTTATTTA
Found at i:1136765 original size:19 final size:20
Alignment explanation
Indices: 1136741--1136781 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1136731 TATATATCCT
1136741 TATTTTTT-TATTAATTAAA
1 TATTTTTTATATTAATTAAA
* *
1136760 TATTTTTTATTTTTATTAAA
1 TATTTTTTATATTAATTAAA
1136780 TA
1 TA
1136782 AATTAAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTTTTTATATTAATTAAA
Found at i:1137530 original size:19 final size:19
Alignment explanation
Indices: 1137506--1137545 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1137496 ACATATATTC
1137506 TTGGACATGTGTAGGGATA
1 TTGGACATGTGTAGGGATA
1137525 TTGGACATGTGTAGGGATA
1 TTGGACATGTGTAGGGATA
1137544 TT
1 TT
1137546 AATGGGTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.05, G:0.35, T:0.35
Consensus pattern (19 bp):
TTGGACATGTGTAGGGATA
Found at i:1138988 original size:11 final size:13
Alignment explanation
Indices: 1138970--1139001 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
1138960 ATAATATTTA
1138970 TAAATAATT-ATT
1 TAAATAATTAATT
1138982 T-AATAATTAATT
1 TAAATAATTAATT
1138994 TAAATAAT
1 TAAATAAT
1139002 ATTATCTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 7 0.39
12 5 0.28
13 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAATAATTAATT
Found at i:1144564 original size:32 final size:32
Alignment explanation
Indices: 1144522--1144591 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
1144512 AGCCATTCGT
* * *
1144522 TTTACTACACGATTATGGAATTCCGATGTATG
1 TTTACGACACGAATACGGAATTCCGATGTATG
*
1144554 TTTACGACACGAATACGGAATTCCGTTGTATG
1 TTTACGACACGAATACGGAATTCCGATGTATG
1144586 TCTTAC
1 T-TTAC
1144592 AGGCTTAGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 29 0.88
33 4 0.12
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (32 bp):
TTTACGACACGAATACGGAATTCCGATGTATG
Found at i:1146509 original size:21 final size:21
Alignment explanation
Indices: 1146483--1146527 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1146473 GATTTCTGGG
* *
1146483 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1146504 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1146525 CAA
1 CAA
1146528 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1147209 original size:23 final size:24
Alignment explanation
Indices: 1147166--1147212 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
1147156 ATATGGCATG
*
1147166 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
1147190 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
1147213 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:1147466 original size:31 final size:31
Alignment explanation
Indices: 1147428--1147582 Score: 224
Period size: 31 Copynumber: 5.0 Consensus size: 31
1147418 AGGGTCGAGG
1147428 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1147459 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1147490 ATTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1147521 GTTTACCTATGTCCTTCGGGAC-TATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1147551 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1147582 G
1 G
1147583 GTCCTTCGGG
Statistics
Matches: 112, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
30 24 0.21
31 88 0.79
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1150743 original size:21 final size:21
Alignment explanation
Indices: 1150717--1150761 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1150707 GATTTCTGGG
* *
1150717 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1150738 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1150759 CAA
1 CAA
1150762 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1151442 original size:23 final size:24
Alignment explanation
Indices: 1151399--1151445 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
1151389 ATATGGCATG
*
1151399 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
1151423 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
1151446 CAAGTATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:1151694 original size:31 final size:31
Alignment explanation
Indices: 1151656--1151810 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
1151646 AGGGTCGAGG
1151656 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1151687 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1151718 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1151749 GTTTACCTATGTCCTTCGGGACATATGGA-T
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1151779 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1151810 G
1 G
1151811 GTCCTTCGGG
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
30 24 0.21
31 89 0.79
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1152584 original size:20 final size:21
Alignment explanation
Indices: 1152561--1152600 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1152551 TATTAAAATC
*
1152561 GTTTAATGTTTATA-TCATTG
1 GTTTAATGCTTATAGTCATTG
*
1152581 GTTTGATGCTTATAGTCATT
1 GTTTAATGCTTATAGTCATT
1152601 AGATTATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.07, G:0.17, T:0.53
Consensus pattern (21 bp):
GTTTAATGCTTATAGTCATTG
Found at i:1157642 original size:2 final size:2
Alignment explanation
Indices: 1157637--1157669 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1157627 AAAATTCCAA
1157637 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1157670 AACCGAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1161580 original size:21 final size:21
Alignment explanation
Indices: 1161554--1161598 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1161544 GATTTCTGGG
* *
1161554 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1161575 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1161596 CAA
1 CAA
1161599 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1162799 original size:22 final size:21
Alignment explanation
Indices: 1162745--1162808 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
1162735 AGTCGAGGGT
1162745 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
*
1162766 CTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACA-A
*
1162788 TTCACAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
1162809 ATTTCATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:1166944 original size:21 final size:21
Alignment explanation
Indices: 1166918--1166962 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1166908 GATTTCTGGG
* *
1166918 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1166939 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1166960 CAA
1 CAA
1166963 ACGATAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1168191 original size:22 final size:21
Alignment explanation
Indices: 1168137--1168200 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
1168127 AGTTGAGGGT
1168137 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
*
1168158 CTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACA-A
*
1168180 TTCACAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
1168201 ATTTCATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Done.