Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1634
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: 78193
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Found at i:158 original size:61 final size:59
Alignment explanation
Indices: 2--226 Score: 257
Period size: 61 Copynumber: 3.8 Consensus size: 59
1 C
* ** *
2 CTTTTAAAGCCCACATGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGATGC---C-
1 CTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTTAGTCCTCAAAGAGCAGGATGCTTTCT
*
58 C-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAATCCTCAAAGAGCAGGATGCTTTCT
1 CTTTCAAAGCCCACACAAGTTGGTGGCACTTTT--AGTCCTCAAAGAGCAGGATGCTTTCT
* *
117 CTTTGCAAAGCCCATACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCCTTT-T
1 CTTT-CAAAGCCCACACAAGTTGGTGGCA-CTTTTAGTCCTCAAAGAGCAGGATG-CTTTCT
* *
178 CTTTTCAAAGCCCACACGAGTTGGTGGCACTATTAGTCCTCAAAGAGCA
1 C-TTTCAAAGCCCACACAAGTTGGTGGCACTTTTAGTCCTCAAAGAGCA
227 AGACGCCTTT
Statistics
Matches: 146, Mismatches: 11, Indels: 20
0.82 0.06 0.11
Matches are distributed among these distances:
53 4 0.03
55 42 0.29
56 1 0.01
58 1 0.01
59 1 0.01
60 21 0.14
61 65 0.45
62 7 0.05
63 4 0.03
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (59 bp):
CTTTCAAAGCCCACACAAGTTGGTGGCACTTTTAGTCCTCAAAGAGCAGGATGCTTTCT
Found at i:303 original size:45 final size:43
Alignment explanation
Indices: 239--355 Score: 139
Period size: 45 Copynumber: 2.7 Consensus size: 43
229 ACGCCTTTTC
239 CTTTTCTCC-TTTGTCCTCAAAGAGCAGGACACACTTCATTCCCTT
1 CTTTTC-CCTTTTGTCCTCAAAGAGCAGGACACACTTCATT--CTT
* * * * *
284 CTTTTCCCTTTTGTCCTCAAAAAGCAGGACGCATTTTATTTTT
1 CTTTTCCCTTTTGTCCTCAAAGAGCAGGACACACTTCATTCTT
*
327 CTTTT-TCTTTTGTCCTCAAAGAGCAGGAC
1 CTTTTCCCTTTTGTCCTCAAAGAGCAGGAC
356 GCATTTCGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
42 22 0.34
43 7 0.11
44 2 0.03
45 33 0.52
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.39
Consensus pattern (43 bp):
CTTTTCCCTTTTGTCCTCAAAGAGCAGGACACACTTCATTCTT
Found at i:352 original size:42 final size:43
Alignment explanation
Indices: 234--505 Score: 179
Period size: 42 Copynumber: 6.6 Consensus size: 43
224 GCAAGACGCC
* *
234 TTTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACACTTCA
1 TTTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACGCATTTCA
* *
277 TTCCCTT-CTTTTC-CCTTTTGTCCTCAAAAAGCAGGACGCATTTTA
1 TT---TTCCTTTTCTCC-TTTGTCCTCAAAGAGCAGGACGCATTTCA
* * *
322 TTTTTCTTTT-TCTTTTGTCCTCAAAGAGCAGGACGCATTTCG
1 TTTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACGCATTTCA
* *
364 TTTTCCTTTTTTCCTTTGTCCTCGAAA-AGCAAGACG----T-A
1 TTTTCCTTTTCTCCTTTGTCCTC-AAAGAGCAGGACGCATTTCA
* * * *
402 CTTT--TTTTC-ACTTTGTCCTC-AAGAAGCAGGACAC-TTTCC
1 TTTTCCTTTTCTCCTTTGTCCTCAAAG-AGCAGGACGCATTTCA
* *
441 TTTT-C-TTTCTTCCTTTGTCCTCAAGGAGCAAGAC-CTATTTCA
1 TTTTCCTTTTC-TCCTTTGTCCTCAAAGAGCAGGACGC-ATTTCA
* *
483 TTCT-CTTGTCT--TTTGTCCTCAAA
1 TTTTCCTTTTCTCCTTTGTCCTCAAA
506 AAGTGGGACA
Statistics
Matches: 182, Mismatches: 26, Indels: 45
0.72 0.10 0.18
Matches are distributed among these distances:
33 2 0.01
35 17 0.09
36 4 0.02
38 4 0.02
39 8 0.04
40 12 0.07
41 17 0.09
42 48 0.26
43 30 0.16
44 5 0.03
45 33 0.18
46 2 0.01
ACGTcount: A:0.19, C:0.26, G:0.12, T:0.42
Consensus pattern (43 bp):
TTTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACGCATTTCA
Found at i:355 original size:87 final size:86
Alignment explanation
Indices: 234--399 Score: 219
Period size: 87 Copynumber: 1.9 Consensus size: 86
224 GCAAGACGCC
234 TTTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACACTTC-ATTCCCTTCTTTTCCCTTTTGT
1 TTTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACACTTCGATTCCCTT-TTTT-CC-TTTGT
*
298 CCTCAAAAAGCAGGACGCATTTTA
63 CCTCAAAAAGCAAGACGCATTTTA
* * * * * *
322 TTTTTCTTTT-TCTTTTGTCCTCAAAGAGCAGGACGCATTTCGTTTTCCTTTTTTCCTTTGTCCT
1 TTTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACACTTCGATTCCCTTTTTTCCTTTGTCCT
*
386 CGAAAAGCAAGACG
66 CAAAAAGCAAGACG
400 TACTTTTTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
85 20 0.29
86 2 0.03
87 32 0.46
88 15 0.22
ACGTcount: A:0.19, C:0.27, G:0.13, T:0.41
Consensus pattern (86 bp):
TTTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACACTTCGATTCCCTTTTTTCCTTTGTCCT
CAAAAAGCAAGACGCATTTTA
Found at i:445 original size:35 final size:33
Alignment explanation
Indices: 370--438 Score: 88
Period size: 35 Copynumber: 2.1 Consensus size: 33
360 TTCGTTTTCC
370 TTTTTTCCTTTGTCCTCGAAAAGCAAGACGTACT
1 TTTTTTCCTTTGTCCTCGAAAAGCAAGACG-ACT
*
404 TTTTTTCACTTTGTCCTC-AAGAAGCAGGAC-ACT
1 TTTTTTC-CTTTGTCCTCGAA-AAGCAAGACGACT
437 TT
1 TT
439 CCTTTTCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
33 5 0.16
34 9 0.28
35 18 0.56
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.39
Consensus pattern (33 bp):
TTTTTTCCTTTGTCCTCGAAAAGCAAGACGACT
Found at i:1157 original size:69 final size:69
Alignment explanation
Indices: 1084--1237 Score: 222
Period size: 69 Copynumber: 2.2 Consensus size: 69
1074 AAATTTCACA
*
1084 ATTGTATCGATACATTGTTCATTGTATCGATACATT-TGGGTTTTACCCAGATGTATCGATACAT
1 ATTGTATCGATACATTATTCATTGTATCGATACATTCTGGG-TTTACCCAGATGTATCGATACAT
1148 TATT-C
65 T-TTGC
* * * *
1153 ATTGTTTCAATACATTATTGATTGTATCGATACATTCTGGGTTTACCTAGATGTATCGATACATT
1 ATTGTATCGATACATTATTCATTGTATCGATACATTCTGGGTTTACCCAGATGTATCGATACATT
1218 TTGC
66 TTGC
*
1222 AATGTATCGATACATT
1 ATTGTATCGATACATT
1238 CAAGCATTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
68 2 0.03
69 69 0.92
70 4 0.05
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (69 bp):
ATTGTATCGATACATTATTCATTGTATCGATACATTCTGGGTTTACCCAGATGTATCGATACATT
TTGC
Found at i:1167 original size:20 final size:20
Alignment explanation
Indices: 1135--1188 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1125 TTTACCCAGA
*
1135 TGTATCGATACATTATTCAT
1 TGTATCAATACATTATTCAT
* *
1155 TGTTTCAATACATTATTGAT
1 TGTATCAATACATTATTCAT
*
1175 TGTATCGATACATT
1 TGTATCAATACATT
1189 CTGGGTTTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (20 bp):
TGTATCAATACATTATTCAT
Found at i:3692 original size:79 final size:78
Alignment explanation
Indices: 3590--3953 Score: 439
Period size: 78 Copynumber: 4.6 Consensus size: 78
3580 TCATTCATGT
* *
3590 TTTTATTTTCCAAAACACTAATTTTTTACAATCGGGGATACTCCAACCCCATTATTTCCAAAGGG
1 TTTTATTTT-CAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCATTATTTCC-AAGGG
3655 ATACTCCAACCCTGG
64 ATACTCCAACCCTGG
* * *
3670 CTTTATTTTCAAAACACCAATTTTTCATAATCAGGGATACTCCAACCCCATTATTTCCAAGGGGA
1 TTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCATTATTTCCAA-GGGA
* *
3735 TACTCCAACTCTAG
65 TACTCCAACCCTGG
* * * * * *
3749 TTTTA-TTTCTAAAACATCAATTTTTTACAATCGGGGATACT-CTACCCCGTTATTTCCGAGAGA
1 TTTTATTTTC-AAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCATTATTTCCAAG-GG
3812 ATACTCCAA-CCTCGG
64 ATACTCCAACCCT-GG
* * *
3827 TTTTATTTTCAAAACACCAATTTTTCATAATCGGGGATACTCCAACCTCGTTATTTCCAAGGGAT
1 TTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCATTATTTCCAAGGGAT
* *
3892 ACTCCAACCCCGA
66 ACTCCAACCCTGG
** * *
3905 TTTTA-TTTCTAAAACATTAATTTTCCACAATTGGGGATACTCCAACCCC
1 TTTTATTTTC-AAAACACCAATTTTTCACAATCGGGGATACTCCAACCCC
3954 GATTTTATTT
Statistics
Matches: 243, Mismatches: 33, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
77 7 0.03
78 114 0.47
79 114 0.47
80 8 0.03
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (78 bp):
TTTTATTTTCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCATTATTTCCAAGGGAT
ACTCCAACCCTGG
Found at i:3951 original size:51 final size:51
Alignment explanation
Indices: 3887--4053 Score: 253
Period size: 51 Copynumber: 3.3 Consensus size: 51
3877 TTATTTCCAA
*
3887 GGGATACTCCAACCCCGATTTTATTTCTAAAACATTAATTTTCCACAATTG
1 GGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACAATTG
*
3938 GGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACAATTG
1 GGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACAATTG
* * * * * *
3989 GGGATACTCTAACTCCGATTTTATTTCCAAAACATCGATTTTCCACCATCG
1 GGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACAATTG
*
4040 GGGATACTCTAACC
1 GGGATACTCCAACC
4054 TTGTTATTTC
Statistics
Matches: 106, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 106 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (51 bp):
GGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACAATTG
Found at i:3954 original size:157 final size:158
Alignment explanation
Indices: 3590--3954 Score: 515
Period size: 157 Copynumber: 2.3 Consensus size: 158
3580 TCATTCATGT
* * * *
3590 TTTTATTTTCCAAAACACTAATTTTTTACAATCGGGGATACTCCAACCCCATTATTTCCAAAGGG
1 TTTTA-TTTCTAAAACATTAATTTTTTACAATCGGGGATACTCCAACCCCGTTATTTCCAAAGGA
3655 ATACTCCAACCCTGGCTTTATTTTCAAAACACCAATTTTTCATAATCAGGGATACTCCAACCCCA
65 ATACTCCAACCCTGGCTTTATTTTCAAAACACCAATTTTTCATAATCAGGGATACTCCAACCCCA
* *
3720 TTATTTCCAAGGGGATACTCCAACTCTAG
130 TTATTTCCAAGGGGATACTCCAACCCGAG
* * *
3749 TTTTATTTCTAAAACATCAATTTTTTACAATCGGGGATACT-CTACCCCGTTATTTCC-GAGAGA
1 TTTTATTTCTAAAACATTAATTTTTTACAATCGGGGATACTCCAACCCCGTTATTTCCAAAG-GA
* * *
3812 ATACTCCAA-CCTCGGTTTTATTTTCAAAACACCAATTTTTCATAATCGGGGATACTCCAACCTC
65 ATACTCCAACCCT-GGCTTTATTTTCAAAACACCAATTTTTCATAATCAGGGATACTCCAACCCC
*
3876 GTTATTTCCAA-GGGATACTCCAACCCCGA-
129 ATTATTTCCAAGGGGATACTCCAA-CCCGAG
** *
3905 TTTTATTTCTAAAACATTAATTTTCCACAATTGGGGATACTCCAACCCCG
1 TTTTATTTCTAAAACATTAATTTTTTACAATCGGGGATACTCCAACCCCG
3955 ATTTTATTTC
Statistics
Matches: 184, Mismatches: 18, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
156 54 0.29
157 92 0.50
158 33 0.18
159 5 0.03
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (158 bp):
TTTTATTTCTAAAACATTAATTTTTTACAATCGGGGATACTCCAACCCCGTTATTTCCAAAGGAA
TACTCCAACCCTGGCTTTATTTTCAAAACACCAATTTTTCATAATCAGGGATACTCCAACCCCAT
TATTTCCAAGGGGATACTCCAACCCGAG
Found at i:4125 original size:51 final size:50
Alignment explanation
Indices: 4069--4184 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 50
4059 ATTTCCAAAT
* *
4069 GGATACTCCAATCCCGGTTTTA-TTTCTAAAACATCAATTTTCCATAATTGG
1 GGATACTCCAA-CCCGATTTTATTTTC-AAAACATCAATTTTCCATAATCGG
* *
4120 GGATACTCTAACTCCGATTTTATTTTCAAAACATCAATTTTTCATAATCGG
1 GGATACTCCAAC-CCGATTTTATTTTCAAAACATCAATTTTCCATAATCGG
4171 GGATACTCCAACCC
1 GGATACTCCAACCC
4185 CGTTATTTCA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
50 3 0.05
51 51 0.88
52 4 0.07
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.35
Consensus pattern (50 bp):
GGATACTCCAACCCGATTTTATTTTCAAAACATCAATTTTCCATAATCGG
Found at i:4139 original size:181 final size:180
Alignment explanation
Indices: 3827--4178 Score: 526
Period size: 181 Copynumber: 1.9 Consensus size: 180
3817 CCAACCTCGG
* * *
3827 TTTTATTTTCAAAACACCAATTTTTCATAATCGGGGATACTCCAACCTCGTTATTTCCAAGGGAT
1 TTTTATTTCCAAAACACCAATTTTCCACAATCGGGGATACTCCAACCTCGTTATTTCCAAGGGAT
*
3892 ACTCCAACCCCGATTTTATTTCTAAAACATTAATTTTCCACAATTGGGGATACTCCAACCCCGAT
66 ACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACAATTGGGGATACTCCAACCCCGAT
*
3957 TTTA-TTTCTAAAACATCAATTTTTCACAATTGGGGATACTCTAACTCCGA
131 TTTATTTTC-AAAACATCAATTTTTCACAATCGGGGATACTCTAACTCCGA
* * * * * *
4007 TTTTATTTCCAAAACATCGATTTTCCACCATCGGGGATACTCTAACCTTGTTATTTCCAAATGGA
1 TTTTATTTCCAAAACACCAATTTTCCACAATCGGGGATACTCCAACCTCGTTATTTCC-AAGGGA
* * * * *
4072 TACTCCAATCCCGGTTTTATTTCTAAAACATCAATTTTCCATAATTGGGGATACTCTAACTCCGA
65 TACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACAATTGGGGATACTCCAACCCCGA
*
4137 TTTTATTTTCAAAACATCAATTTTTCATAATCGGGGATACTC
130 TTTTATTTTCAAAACATCAATTTTTCACAATCGGGGATACTC
4179 CAACCCCGTT
Statistics
Matches: 153, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
180 50 0.33
181 99 0.65
182 4 0.03
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (180 bp):
TTTTATTTCCAAAACACCAATTTTCCACAATCGGGGATACTCCAACCTCGTTATTTCCAAGGGAT
ACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACAATTGGGGATACTCCAACCCCGAT
TTTATTTTCAAAACATCAATTTTTCACAATCGGGGATACTCTAACTCCGA
Found at i:4203 original size:130 final size:130
Alignment explanation
Indices: 3937--4214 Score: 405
Period size: 130 Copynumber: 2.1 Consensus size: 130
3927 TTCCACAATT
*
3937 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACAATTGGGGATACTCTAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACAATTGGGGATACTCTAAC
* * * **
4002 TCCGATTTTATTTCCAAAACATCGATTTTCCACCATCGGGGATACTCTAACCTTGTTATTTCCAA
66 TCCGATTTTATTTCCAAAACATCAATTTTCCACAATCGGGGATACTCCAACCCCGTTATTTCCAA
** * * *
4067 ATGGATACTCCAATCCCGGTTTTATTTCTAAAACATCAATTTTCCATAATTGGGGATACTCTAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACAATTGGGGATACTCTAAC
* * *
4132 TCCGATTTTATTTTCAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTT-CAT
66 TCCGATTTTATTTCCAAAACATCAATTTTCCACAATCGGGGATACTCCAACCCCGTTATTTCCA-
*
4196 C
130 A
4197 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
4215 TTATTTCTGA
Statistics
Matches: 129, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
129 2 0.02
130 127 0.98
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (130 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCCACAATTGGGGATACTCTAAC
TCCGATTTTATTTCCAAAACATCAATTTTCCACAATCGGGGATACTCCAACCCCGTTATTTCCAA
Found at i:4234 original size:28 final size:28
Alignment explanation
Indices: 4166--4221 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
4156 ATTTTTCATA
4166 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
4194 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
4222 TGAGAGGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.32, G:0.18, T:0.29
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:5617 original size:28 final size:28
Alignment explanation
Indices: 5561--5632 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
5551 GGAATAAAGC
**
5561 CGGGGTTGGAGTATCCCCTCAGAGGTAA
1 CGGGGTTGGAGTATCCCCTCAGAAATAA
*
5589 CGGGGTTGGAGTATCCCC-GATGAAATAA
1 CGGGGTTGGAGTATCCCCTCA-GAAATAA
* *
5617 CGAGGTTGAAGTATCC
1 CGGGGTTGGAGTATCC
5633 TCAATTGTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 1 0.03
28 37 0.97
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTCAGAAATAA
Found at i:5684 original size:52 final size:52
Alignment explanation
Indices: 5620--5790 Score: 184
Period size: 52 Copynumber: 3.3 Consensus size: 52
5610 GAAATAACGA
* * *
5620 GGTTGAAGTATCCTCAATTGTGAAAAATTGGTGTTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCAATTGTGAAAAATTAGTGTTTTTGAAAATAAAATCGG
* * ** * ** *
5672 AGTTGGAGTATCCCCGATTAAAGGAAAATTTTTG-TTTTAAAAATAAAATCGG
1 GGTTGGAGTATCCCCAATT-GTGAAAAATTAGTGTTTTTGAAAATAAAATCGG
* * *
5724 GGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAG-CAATAAAACCGG
1 GGTTGGAGTATCCCCAATTGT-GAAAAATTAGTGTTTTTGAAAATAAAATCGG
5776 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
5791 GATTATGAGA
Statistics
Matches: 95, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
52 83 0.87
53 12 0.13
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (52 bp):
GGTTGGAGTATCCCCAATTGTGAAAAATTAGTGTTTTTGAAAATAAAATCGG
Found at i:5949 original size:53 final size:51
Alignment explanation
Indices: 5883--6005 Score: 140
Period size: 51 Copynumber: 2.4 Consensus size: 51
5873 GATTAACGGT
** *
5883 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTAG-AAAATTACTG--TTTTGAAAATAAAATCGGA
*
5936 GTTGGAGTATCCCCGATTATAGAAAATTACTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTAGAAAATTACTGTTTTGAAAATAAAATCGGA
** * *
5987 GACGGAATATCCCTGATTG
1 GTTGGAGTATCCCCGATTG
6006 CGGAGAATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
51 32 0.53
53 27 0.45
54 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTAGAAAATTACTGTTTTGAAAATAAAATCGGA
Found at i:8380 original size:13 final size:13
Alignment explanation
Indices: 8362--8387 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8352 ACAAAGATCC
8362 ATGTATCGATACA
1 ATGTATCGATACA
8375 ATGTATCGATACA
1 ATGTATCGATACA
8388 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:8383 original size:33 final size:33
Alignment explanation
Indices: 8341--8407 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
8331 AAAATTCCCA
***
8341 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
8374 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
8407 A
1 A
8408 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:9685 original size:50 final size:52
Alignment explanation
Indices: 9623--9725 Score: 165
Period size: 53 Copynumber: 2.0 Consensus size: 52
9613 TGGTCAATGC
* *
9623 AACTAGAGAATTGATTACCTT-G-GATAGTGATATAATCACCCTTTATATGG
1 AACTAGAAAATTGATTACCTTGGAGATAGTGATATAATCACCCTTCATATGG
9673 AACTAGAAAATTGATTACCTTGGAAGATAGTGATATAATCACCCTTCATATGG
1 AACTAGAAAATTGATTACCTTGG-AGATAGTGATATAATCACCCTTCATATGG
9726 TGTAAAGGTG
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
50 20 0.42
51 1 0.02
53 27 0.56
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (52 bp):
AACTAGAAAATTGATTACCTTGGAGATAGTGATATAATCACCCTTCATATGG
Found at i:10957 original size:19 final size:19
Alignment explanation
Indices: 10921--10958 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
10911 AATTTAATTT
*
10921 AATAATAATAAATTAACAA
1 AATAATAATAAATCAACAA
10940 AATAATAA-AATATCAACAA
1 AATAATAATAA-ATCAACAA
10959 TTTAAACTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (19 bp):
AATAATAATAAATCAACAA
Found at i:11003 original size:16 final size:16
Alignment explanation
Indices: 10957--11069 Score: 75
Period size: 16 Copynumber: 6.9 Consensus size: 16
10947 AAATATCAAC
**
10957 AATTTAAACTT-GCAT
1 AATTTAAACTTAAAAT
*
10972 AAATTAAACTTGAAAAT
1 AATTTAAACTT-AAAAT
10989 AATTTAAACTTAAAAT
1 AATTTAAACTTAAAAT
* * * *
11005 TATTCGAAACTCAAAAAA
1 AATT-TAAACT-TAAAAT
* *
11023 AAATTAGACTTAAAAT
1 AATTTAAACTTAAAAT
* *
11039 AATTTAAATTTAAATT
1 AATTTAAACTTAAAAT
* *
11055 GATTTAAAATTAAAA
1 AATTTAAACTTAAAA
11070 CGATTCAAAT
Statistics
Matches: 73, Mismatches: 21, Indels: 7
0.72 0.21 0.07
Matches are distributed among these distances:
15 10 0.14
16 36 0.49
17 21 0.29
18 6 0.08
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (16 bp):
AATTTAAACTTAAAAT
Found at i:11110 original size:16 final size:15
Alignment explanation
Indices: 11032--11110 Score: 50
Period size: 16 Copynumber: 5.0 Consensus size: 15
11022 AAAATTAGAC
11032 TTAAAATAATTTAAA
1 TTAAAATAATTTAAA
* *
11047 TTTAAATTGATTTAAAA
1 -TTAAAATAATTT-AAA
** *
11064 TTAAAACGATTCAAA
1 TTAAAATAATTTAAA
* **
11079 TATAAAACAAAATAAA
1 T-TAAAATAATTTAAA
11095 TCTAAAATAATTTAAA
1 T-TAAAATAATTTAAA
11111 AATTTAATAT
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
15 4 0.08
16 41 0.85
17 3 0.06
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (15 bp):
TTAAAATAATTTAAA
Found at i:11803 original size:55 final size:55
Alignment explanation
Indices: 11719--12510 Score: 925
Period size: 55 Copynumber: 14.0 Consensus size: 55
11709 ATAAAGTGTA
* * * * *
11719 TCCTGCTTTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* **
11774 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
* *
11835 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGGGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
11889 TCCTGCTCTTTAAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
11944 TCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
11999 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * * *
12054 TCCTGCTCTTTGGGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGGG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* **
12109 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
* *
12170 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGATG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
** *
12229 T-CTCGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCT-GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
12284 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
* * *
12344 TCCCGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
* * *
12404 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACTAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
12459 TCCTGCTCTTTGAGGACCG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGG
12511 AAAAGGCATC
Statistics
Matches: 656, Mismatches: 50, Indels: 63
0.85 0.07 0.08
Matches are distributed among these distances:
53 2 0.00
54 54 0.08
55 334 0.51
56 15 0.02
58 2 0.00
59 20 0.03
60 179 0.27
61 44 0.07
64 6 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:11877 original size:115 final size:114
Alignment explanation
Indices: 11718--12533 Score: 961
Period size: 115 Copynumber: 7.1 Consensus size: 114
11708 AATAAAGTGT
* * * * *
11718 ATCCTGCTTTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
* *
11783 TTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGAAAAAGC
65 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGC
* *
11834 ATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGGTGTCCTGCTCTT
1 ATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
* *
11899 TAAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGT
66 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
* * *
11943 GTCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
* *
12008 TTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT----G-AAAGGT
65 TTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
* * * * *
12053 GTCCTGCTCTTTGGGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGGGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
* *
12118 TTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
65 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGC
* *
12169 ATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGATGT-CTC
1 ATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCT-
**
12233 GCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAG----GTG-
60 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAG-GC
* *
12284 -TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
1 ATCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCT
*
12348 GCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
60 GCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
* ** * *
12403 GTCCTGCTCTTTGAGGACTGGAAAATGCCACTAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
*
12468 TTGAGGACCG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
65 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGC
*
12518 ATCCTGCTGTTTGAGG
1 ATCCTGCTCTTTGAGG
12534 GCTAAAAAGC
Statistics
Matches: 616, Mismatches: 53, Indels: 63
0.84 0.07 0.09
Matches are distributed among these distances:
108 1 0.00
109 23 0.04
110 166 0.27
111 4 0.01
112 3 0.00
113 2 0.00
114 47 0.08
115 225 0.37
116 46 0.07
118 1 0.00
119 9 0.01
120 88 0.14
121 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (114 bp):
ATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGC
Found at i:12289 original size:175 final size:175
Alignment explanation
Indices: 11719--12533 Score: 1123
Period size: 175 Copynumber: 4.7 Consensus size: 175
11709 ATAAAGTGTA
* * * *
11719 TCCTGCTTTTTGAGGACT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGAAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
*
11783 TTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGA
65 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGA
**
11848 GGACT-GAAGGTGCCACCAACTTGGGTGGGCTTT---A-AAAGGTG
130 GGACTGGAAAATGCCACCAACTTGGGTGGGCTTTAAAAGAAAGGTG
* ** * *
11889 TCCTGCTCTTTAAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTACTCTT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
* **
11954 TGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCTGCTCTTTGAG
66 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAG
*
12013 GACTGGAAAATGCCACCAACTTGTGTGGGCTTT----GAAAGGTG
131 GACTGGAAAATGCCACCAACTTGGGTGGGCTTTAAAAGAAAGGTG
* * * * *
12054 TCCTGCTCTTTGGGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGGGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
*
12119 TGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAG
66 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAG
** *
12184 GACT-GAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGATG
131 GACTGGAAAATGCCACCAACTTGGGTGGGCTTTAAAAG-AAAGGTG
12229 T-CTCGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
1 TCCT-GCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
* * *
12293 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCCGCTCTTTGA
65 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGA
* *
12357 GGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
130 GGACTGGAAAATGCCACCAACTTGGGTGGGCTTTAAAAG-AAAGGTG
* *
12404 TCCTGCTCTTTGAGGACTGGAAAATGCCACTAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
* * *
12469 TGAGGACCG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCATCCTGCTGTTTGA
66 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAA-GAAAAAGCATCCTGCTCTTTGA
12532 GG
130 GG
12534 GCTAAAAAGC
Statistics
Matches: 575, Mismatches: 52, Indels: 31
0.87 0.08 0.05
Matches are distributed among these distances:
164 19 0.03
165 125 0.22
166 4 0.01
169 4 0.01
170 113 0.20
171 22 0.04
174 62 0.11
175 224 0.39
176 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (175 bp):
TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAG
GACTGGAAAATGCCACCAACTTGGGTGGGCTTTAAAAGAAAGGTG
Found at i:13525 original size:1 final size:1
Alignment explanation
Indices: 13521--13577 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
13511 TTATTCTCTC
* * * * * * *
13521 TTTTTCTTTGTTTTGTTTTTTTGTTTTGTTTTTTTTTCTTTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
13578 AAGAGAATGT
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.88
Consensus pattern (1 bp):
T
Found at i:13543 original size:13 final size:12
Alignment explanation
Indices: 13521--13577 Score: 71
Period size: 13 Copynumber: 4.6 Consensus size: 12
13511 TTATTCTCTC
*
13521 TTTTTCTTTGTT
1 TTTTTTTTTGTT
13533 TTGTTTTTTTGTT
1 TT-TTTTTTTGTT
13546 TTGTTTTTTT-TT
1 TT-TTTTTTTGTT
13558 CTTTTTTTTTGTT
1 -TTTTTTTTTGTT
13571 TTTTTTT
1 TTTTTTT
13578 AAGAGAATGT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
12 18 0.44
13 23 0.56
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:16567 original size:13 final size:13
Alignment explanation
Indices: 16549--16573 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16539 CATAAAGTGT
16549 TGTATCGATACAA
1 TGTATCGATACAA
16562 TGTATCGATACA
1 TGTATCGATACA
16574 TATTTTTTTG
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):
TGTATCGATACAA
Found at i:16571 original size:33 final size:33
Alignment explanation
Indices: 16529--16595 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
16519 TTCAACGATT
16529 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
16562 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
16595 T
1 T
16596 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:16654 original size:13 final size:13
Alignment explanation
Indices: 16636--16660 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16626 ATCACTTAAA
16636 TGTATCGATACAT
1 TGTATCGATACAT
16649 TGTATCGATACA
1 TGTATCGATACA
16661 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:16725 original size:52 final size:52
Alignment explanation
Indices: 16669--16797 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
16659 CACTGATCTT
*
16669 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACATTA-TAAA
1 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATTAAA
* *
16720 GTGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 -TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATTAAA
16773 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
16798 TCATATTTCG
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
52 70 0.96
53 3 0.04
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATTAAA
Found at i:26140 original size:12 final size:12
Alignment explanation
Indices: 26123--26147 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26113 AAACAAACAG
26123 ATATATAAATAA
1 ATATATAAATAA
26135 ATATATAAATAA
1 ATATATAAATAA
26147 A
1 A
26148 CACCTCAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATATATAAATAA
Found at i:30342 original size:52 final size:51
Alignment explanation
Indices: 30264--30413 Score: 237
Period size: 52 Copynumber: 2.9 Consensus size: 51
30254 CGAAATATGA
30264 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
30316 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
30368 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAT
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACAT
30414 TTGAGTAAGT
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 86 0.96
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:30491 original size:13 final size:13
Alignment explanation
Indices: 30473--30497 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30463 ACAAAAAATA
30473 TGTATCGATACAT
1 TGTATCGATACAT
30486 TGTATCGATACA
1 TGTATCGATACA
30498 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:30493 original size:32 final size:33
Alignment explanation
Indices: 30452--30517 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
30442 AGTAGCTTAA
30452 ATTGTATCGATACAA-AAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
30484 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
30517 A
1 A
30518 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Found at i:31084 original size:33 final size:33
Alignment explanation
Indices: 31047--31113 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
31037 TTCAACGATC
31047 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
31080 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
31113 T
1 T
31114 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:31085 original size:13 final size:13
Alignment explanation
Indices: 31067--31091 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31057 CATAAAATGT
31067 TGTATCGATACAA
1 TGTATCGATACAA
31080 TGTATCGATACA
1 TGTATCGATACA
31092 TATTTTTTTG
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):
TGTATCGATACAA
Found at i:31177 original size:13 final size:13
Alignment explanation
Indices: 31159--31183 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31149 ATTACTCACA
31159 TGTATCGATACAT
1 TGTATCGATACAT
31172 TGTATCGATACA
1 TGTATCGATACA
31184 CTAATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:31320 original size:52 final size:52
Alignment explanation
Indices: 31172--31309 Score: 222
Period size: 52 Copynumber: 2.7 Consensus size: 52
31162 ATCGATACAT
* ***
31172 TGTATCGATACACTAATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
31224 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
31276 TGTATCGATACACTATTAAATGTATCGATACATG
1 TGTATCGATACACTATTAAATGTATCGATACATG
31310 TAGATAAATT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 78 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (52 bp):
TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:34574 original size:21 final size:21
Alignment explanation
Indices: 34549--34591 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
34539 CATGTCAGGA
34549 GCATCTCGTCATGCAATGAAT
1 GCATCTCGTCATGCAATGAAT
34570 GCATCTCGTCATGCAATGAAT
1 GCATCTCGTCATGCAATGAAT
34591 G
1 G
34592 TCATTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (21 bp):
GCATCTCGTCATGCAATGAAT
Found at i:37820 original size:22 final size:22
Alignment explanation
Indices: 37795--37863 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
37785 ATGCTGATTC
37795 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
* * *
37817 AAGG--TGCCA-ATGTGCTGA-TTC
1 AAGGCCAGCTATAT-TG--GACTTA
37838 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
37860 AAGG
1 AAGG
37864 TGAAGGTGCC
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 12 0.35
23 5 0.15
24 2 0.06
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Found at i:37889 original size:49 final size:49
Alignment explanation
Indices: 37671--37957 Score: 311
Period size: 49 Copynumber: 5.8 Consensus size: 49
37661 GTGATAAAGA
* * * *
37671 TGCCAATATG-TCGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGG
1 TGCCAATATGCT-GATTCAAGGCCAGCTATATTGGACTTAAAGAT--G---AAGG
* * *
37725 ATGTCAATGTGCTGATTCAAGGCCAGCTACATT-GATCTTAAAGATGGAAAAGG
1 -TGCCAATATGCTGATTCAAGGCCAGCTATATTGGA-CTTAAAGAT-G--AAGG
37778 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* *
37821 TGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
*
37870 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* *
37919 TGCCAATATGGTGATTCAAGGCCAGCTATATTGGGCTTA
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
37958 GAAGGGTTGC
Statistics
Matches: 205, Mismatches: 18, Indels: 24
0.83 0.07 0.10
Matches are distributed among these distances:
43 41 0.20
48 1 0.00
49 87 0.42
52 32 0.16
53 8 0.04
54 2 0.01
55 33 0.16
56 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
Found at i:38092 original size:30 final size:29
Alignment explanation
Indices: 37963--38431 Score: 330
Period size: 30 Copynumber: 15.9 Consensus size: 29
37953 GCTTAGAAGG
* *
37963 GTTGCCACCGACTTGTGTGGGCTTTGGAAAA
1 GTTGCCACTGAC-T-TGTGGGCTTTTGAAAA
* * *
37994 GGGTGCCACTGATTTGTGGGC-TTTG-AAG
1 -GTTGCCACTGACTTGTGGGCTTTTGAAAA
*
38022 GTTGCCACTGACTTGTGGGCTTTT-AAAG
1 GTTGCCACTGACTTGTGGGCTTTTGAAAA
*
38050 GTTGCCACTGACTTGTGGGCTTTTAAAAA
1 GTTGCCACTGACTTGTGGGCTTTTGAAAA
* * *
38079 ATATGCCATTGACTTGTGGGCTTTTGAACAG
1 GT-TGCCACTGACTTGTGGGCTTTTGAA-AA
* * *
38110 GGTGCCACTAACTTGTGGGCTTTT-AAAG
1 GTTGCCACTGACTTGTGGGCTTTTGAAAA
38138 GTTGCCACTGACTTGTGGGCTTTTGAAAA
1 GTTGCCACTGACTTGTGGGCTTTTGAAAA
*
38167 ATATGCCACTGACTTGTGGGCTTTTGAAAA
1 GT-TGCCACTGACTTGTGGGCTTTTGAAAA
* *
38197 GGGTGCCACTAACTTGTGGGC---TGAAAA
1 -GTTGCCACTGACTTGTGGGCTTTTGAAAA
* * * * **
38224 GAGTGCTA-TAGAGTTGTGAGCTTACAAAAGAAAAA
1 G-TTGCCACT-GACTTGTGGGCTT----TTG-AAAA
* * * * *
38259 GAGTGCCACGGAGTTGTGGACTTTGGAAAA
1 G-TTGCCACTGACTTGTGGGCTTTTGAAAA
* * **
38289 GATGCCACCGACTTGTGGGCTTCGGAAAA
1 GTTGCCACTGACTTGTGGGCTTTTGAAAA
* * *
38318 GGGTGCCACTGATTTGTGGGC-TTTG-AAG
1 -GTTGCCACTGACTTGTGGGCTTTTGAAAA
*
38346 GTTGCCACTGACTTGTGGGCTTTCGAAAAA
1 GTTGCCACTGACTTGTGGGCTTTTG-AAAA
** *
38376 AATGCCATTGACTTGTGGGC-TTTGAAAAA
1 GTTGCCACTGACTTGTGGGCTTTTG-AAAA
** *
38405 AATGCCACTGACTTGTGGACTTTTGAA
1 GTTGCCACTGACTTGTGGGCTTTTGAA
38432 GGGTGATGAA
Statistics
Matches: 358, Mismatches: 55, Indels: 51
0.77 0.12 0.11
Matches are distributed among these distances:
26 2 0.01
27 55 0.15
28 61 0.17
29 66 0.18
30 139 0.39
31 3 0.01
32 9 0.03
34 1 0.00
35 22 0.06
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (29 bp):
GTTGCCACTGACTTGTGGGCTTTTGAAAA
Found at i:38138 original size:88 final size:87
Alignment explanation
Indices: 37997--38218 Score: 367
Period size: 88 Copynumber: 2.6 Consensus size: 87
37987 TGGAAAAGGG
* * *
37997 TGCCACTGATTTGTGGGC-TTTG-AAGGTTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTG
1 TGCCACTGACTTGTGGGCTTTTGAAAGGGTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTG
38060 ACTTGTGGGCTTTTAAAAAATA
66 ACTTGTGGGCTTTTAAAAAATA
*
38082 TGCCATTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACT
1 TGCCACTGACTTGTGGGCTTTTGAA-AGGGTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACT
*
38147 GACTTGTGGGCTTTTGAAAAATA
65 GACTTGTGGGCTTTTAAAAAATA
38170 TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCT
1 TGCCACTGACTTGTGGGCTTTTG-AAAGGGTGCCACTAACTTGTGGGCT
38219 GAAAAGAGTG
Statistics
Matches: 127, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
85 16 0.13
86 4 0.03
87 1 0.01
88 104 0.82
89 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.34
Consensus pattern (87 bp):
TGCCACTGACTTGTGGGCTTTTGAAAGGGTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTG
ACTTGTGGGCTTTTAAAAAATA
Found at i:38144 original size:58 final size:59
Alignment explanation
Indices: 37962--38428 Score: 341
Period size: 57 Copynumber: 7.9 Consensus size: 59
37952 GGCTTAGAAG
* * * *
37962 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTT-GAA
1 GGTTGCCACTGAC-T-TGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAAA
*
38021 GGTTGCCACTGACTTGTGGGCTTTT--AAAGGTTGCCACTGACTTGTGGGCTTTTAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAAA
** * * *
38078 AATATGCCATTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTT-AAA
1 GGT-TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAAA
***
38137 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTT-AAAA
* * * * * * **
38197 GGGTGCCACTAACTTGTGGGC---TGAAAAGAGTGCTA-TAGAGTTGTGAGCTTACAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACT-GACTTGTGGGCTTTTAAAA
* * * * * * * **
38253 GAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAA-GATGCCACCGACTTGTGGGCTTCGGAAA
1 G-----G-TTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTT-TTAAA
38317 A
59 A
* * * *
38318 GGGTGCCACTGATTTGTGGGC-TTTG--AAGGTTGCCACTGACTTGTGGGCTTTCGAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTT-TAAAA
*** * *** *
38375 AAATGCCATTGACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGACTTTT
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTT
38429 GAAGGGTGAT
Statistics
Matches: 326, Mismatches: 59, Indels: 47
0.75 0.14 0.11
Matches are distributed among these distances:
55 22 0.07
56 11 0.03
57 79 0.24
58 71 0.22
59 54 0.17
60 48 0.15
61 1 0.00
62 15 0.05
64 15 0.05
65 10 0.03
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (59 bp):
GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAAA
Found at i:38304 original size:29 final size:29
Alignment explanation
Indices: 38255--38427 Score: 170
Period size: 29 Copynumber: 5.9 Consensus size: 29
38245 TTACAAAAGA
* * *
38255 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACTGACTTGTGGGCTTTGG
* *
38285 AAAAGATGCCACCGACTTGTGGGCTTCGG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
38314 AAAAGGGTGCCACTGATTTGTGGGCTTT-G
1 AAAA-GATGCCACTGACTTGTGGGCTTTGG
* * *
38343 -AAGGTTGCCACTGACTTGTGGGCTTTCGA
1 AAAAGATGCCACTGACTTGTGGGCTTT-GG
* * *
38372 AAAAAATGCCATTGACTTGTGGGCTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
38401 AAAAAATGCCACTGACTTGTGGACTTT
1 AAAAGATGCCACTGACTTGTGGGCTTT
38428 TGAAGGGTGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
27 21 0.17
28 2 0.02
29 51 0.42
30 47 0.39
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.28
Consensus pattern (29 bp):
AAAAGATGCCACTGACTTGTGGGCTTTGG
Found at i:39876 original size:1 final size:1
Alignment explanation
Indices: 39872--39957 Score: 55
Period size: 1 Copynumber: 86.0 Consensus size: 1
39862 CCGGACCCCC
* * * * * * * * *
39872 TTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTGTTTTTTTTTCTTTTGTTTTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** **
39937 TCATTTTTTTCGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTT
39958 AGAGGACGCC
Statistics
Matches: 61, Mismatches: 24, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.02, C:0.03, G:0.09, T:0.85
Consensus pattern (1 bp):
T
Found at i:39900 original size:15 final size:14
Alignment explanation
Indices: 39874--39957 Score: 64
Period size: 15 Copynumber: 5.6 Consensus size: 14
39864 GGACCCCCTT
39874 TTTTGTTTTTGTTTG
1 TTTT-TTTTTGTTTG
39889 TTTTTTTATTGTTTTTG
1 TTTTTTT-TTG--TTTG
*
39906 TTTTTTTTTCTTTTG
1 TTTTTTTTT-GTTTG
39921 TTTTTTTTTTGTTT-
1 -TTTTTTTTTGTTTG
* *
39935 TTTCATTTTT-TTCG
1 TTT-TTTTTTGTTTG
39949 TTTTTTTTT
1 TTTTTTTTT
39958 AGAGGACGCC
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
13 10 0.18
14 11 0.19
15 14 0.25
16 11 0.19
17 11 0.19
ACGTcount: A:0.02, C:0.04, G:0.10, T:0.85
Consensus pattern (14 bp):
TTTTTTTTTGTTTG
Found at i:39902 original size:21 final size:20
Alignment explanation
Indices: 39872--39957 Score: 95
Period size: 21 Copynumber: 4.2 Consensus size: 20
39862 CCGGACCCCC
39872 TTTT-TTGTTTTTGTTTGTTT
1 TTTTATTGTTTTTGTTT-TTT
39892 TTTTATTGTTTTTGTTTTTT
1 TTTTATTGTTTTTGTTTTTT
* *
39912 TTTCTTTTGTTTTTTTTTTGTT
1 TTT-TATTGTTTTTGTTTT-TT
39934 TTTTCATT-TTTTTCGTTTTTT
1 TTTT-ATTGTTTTT-GTTTTTT
39955 TTT
1 TTT
39958 AGAGGACGCC
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
20 10 0.18
21 36 0.63
22 11 0.19
ACGTcount: A:0.02, C:0.03, G:0.09, T:0.85
Consensus pattern (20 bp):
TTTTATTGTTTTTGTTTTTT
Found at i:39926 original size:32 final size:32
Alignment explanation
Indices: 39879--39957 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
39869 CCCTTTTTTG
*
39879 TTTTT-GTTTGTTTTTTTATTGTTTTTGT-TTT
1 TTTTTCGTTTGTTTTTTTATTGTTTTT-TCATT
* *
39910 TTTTTCTTTTGTTTTTTTTTTGTTTTTTCATT
1 TTTTTCGTTTGTTTTTTTATTGTTTTTTCATT
39942 TTTTTCGTTT-TTTTTT
1 TTTTTCGTTTGTTTTTT
39958 AGAGGACGCC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 12 0.29
32 30 0.71
ACGTcount: A:0.03, C:0.04, G:0.09, T:0.85
Consensus pattern (32 bp):
TTTTTCGTTTGTTTTTTTATTGTTTTTTCATT
Found at i:39932 original size:43 final size:42
Alignment explanation
Indices: 39874--39957 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 42
39864 GGACCCCCTT
*
39874 TTTTGTTTTTGTTTGTTTTTTTATTGTTTTT-GTTTTTTTTTC
1 TTTTGTTTTTGTTTGTTTTTTCATT-TTTTTCGTTTTTTTTTC
*
39916 TTTTGTTTTTTTTTTGTTTTTTCATTTTTTTCGTTTTTTTTT
1 TTTTG-TTTTTGTTTGTTTTTTCATTTTTTTCGTTTTTTTTT
39958 AGAGGACGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 10 0.26
43 28 0.74
ACGTcount: A:0.02, C:0.04, G:0.10, T:0.85
Consensus pattern (42 bp):
TTTTGTTTTTGTTTGTTTTTTCATTTTTTTCGTTTTTTTTTC
Found at i:39943 original size:17 final size:15
Alignment explanation
Indices: 39872--39957 Score: 91
Period size: 16 Copynumber: 5.5 Consensus size: 15
39862 CCGGACCCCC
*
39872 TTTTTTGTTTTTGTT
1 TTTTTTTTTTTTGTT
* *
39887 TGTTTTTTTATTGTT
1 TTTTTTTTTTTTGTT
*
39902 TTTGTTTTTTTTTCTT
1 TTT-TTTTTTTTTGTT
39918 TTGTTTTTTTTTTGTT
1 TT-TTTTTTTTTTGTT
*
39934 TTTTCATTTTTTTCGTT
1 TTTT--TTTTTTTTGTT
39951 TTTTTTT
1 TTTTTTT
39958 AGAGGACGCC
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
15 19 0.32
16 25 0.42
17 15 0.25
ACGTcount: A:0.02, C:0.03, G:0.09, T:0.85
Consensus pattern (15 bp):
TTTTTTTTTTTTGTT
Found at i:39945 original size:26 final size:28
Alignment explanation
Indices: 39900--39957 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
39890 TTTTTTATTG
39900 TTTTTGTTTTTT-TTTCTTTT-GTTTTT
1 TTTTTGTTTTTTATTTCTTTTCGTTTTT
39926 TTTTTGTTTTTTCATTT-TTTTCGTTTTT
1 TTTTTGTTTTTT-ATTTCTTTTCGTTTTT
39954 TTTT
1 TTTT
39958 AGAGGACGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 12 0.41
27 4 0.14
28 13 0.45
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.86
Consensus pattern (28 bp):
TTTTTGTTTTTTATTTCTTTTCGTTTTT
Found at i:39957 original size:11 final size:10
Alignment explanation
Indices: 39872--39937 Score: 80
Period size: 10 Copynumber: 6.3 Consensus size: 10
39862 CCGGACCCCC
39872 TTTTTTGTTT
1 TTTTTTGTTT
*
39882 TTGTTTGTTT
1 TTTTTTGTTT
39892 TTTTATTGTTT
1 TTTT-TTGTTT
39903 TTGTTTT-TTT
1 TT-TTTTGTTT
39913 TTCTTTTGTTTT
1 TT-TTTTG-TTT
39925 TTTTTTGTTT
1 TTTTTTGTTT
39935 TTT
1 TTT
39938 CATTTTTTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
10 27 0.55
11 15 0.31
12 7 0.14
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.86
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:49661 original size:10 final size:10
Alignment explanation
Indices: 49646--49672 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
49636 ATGTATCAAG
49646 CAAAAACAAA
1 CAAAAACAAA
49656 CAAAAACAAA
1 CAAAAACAAA
49666 CAAAAAC
1 CAAAAAC
49673 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:53879 original size:52 final size:51
Alignment explanation
Indices: 53801--53950 Score: 237
Period size: 52 Copynumber: 2.9 Consensus size: 51
53791 CGAAATATGA
53801 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
53853 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
53905 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAT
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACAT
53951 TTGAGTAAGT
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 86 0.96
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:54026 original size:33 final size:33
Alignment explanation
Indices: 53989--54055 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
53979 AATAGCTTAA
53989 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
54022 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
54055 A
1 A
54056 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:54029 original size:13 final size:13
Alignment explanation
Indices: 54011--54035 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54001 CAAAAAAATA
54011 TGTATCGATACAT
1 TGTATCGATACAT
54024 TGTATCGATACA
1 TGTATCGATACA
54036 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:54622 original size:33 final size:33
Alignment explanation
Indices: 54585--54651 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
54575 TTCAACGATC
54585 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
54618 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
54651 T
1 T
54652 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:54623 original size:13 final size:13
Alignment explanation
Indices: 54605--54629 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54595 CATAAAATGT
54605 TGTATCGATACAA
1 TGTATCGATACAA
54618 TGTATCGATACA
1 TGTATCGATACA
54630 TATTTTTTTG
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):
TGTATCGATACAA
Found at i:54715 original size:13 final size:13
Alignment explanation
Indices: 54697--54721 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54687 ATTACTCACA
54697 TGTATCGATACAT
1 TGTATCGATACAT
54710 TGTATCGATACA
1 TGTATCGATACA
54722 CTAATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:54858 original size:52 final size:52
Alignment explanation
Indices: 54710--54847 Score: 222
Period size: 52 Copynumber: 2.7 Consensus size: 52
54700 ATCGATACAT
* ***
54710 TGTATCGATACACTAATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
54762 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
54814 TGTATCGATACACTATTAAATGTATCGATACATG
1 TGTATCGATACACTATTAAATGTATCGATACATG
54848 TAGATAAATT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 78 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (52 bp):
TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:58114 original size:21 final size:21
Alignment explanation
Indices: 58089--58131 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
58079 CATGTCAGGA
58089 GCATCTCGTCATGCAATGAAT
1 GCATCTCGTCATGCAATGAAT
58110 GCATCTCGTCATGCAATGAAT
1 GCATCTCGTCATGCAATGAAT
58131 G
1 G
58132 TCATTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (21 bp):
GCATCTCGTCATGCAATGAAT
Found at i:61315 original size:54 final size:52
Alignment explanation
Indices: 61221--61506 Score: 266
Period size: 49 Copynumber: 5.8 Consensus size: 52
61211 AGTGATAAGA
* * * * *
61221 TGCCAATATG-TCGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGG
1 TGCCAATATGCT-GATTCAAGGCCAGCTACATTGGACTTAAAGATG-G-AAAAGG
* *
61275 ATGTC-ATGTGCTGATTCAAGGCCAGCTACATT-GATCTTAAAGATGGAAAAGG
1 -TGCCAATATGCTGATTCAAGGCCAGCTACATTGGA-CTTAAAGATGGAAAAGG
*
61327 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---AAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGG
* * *
61370 TGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGT-G--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGG
*
61419 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT---AAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGG
* * *
61468 TGCCAATATGGTGATTCAAGGCCAGCTATATTGGGCTTA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
61507 GAAGGGTTGC
Statistics
Matches: 204, Mismatches: 15, Indels: 30
0.82 0.06 0.12
Matches are distributed among these distances:
43 40 0.20
44 1 0.00
46 1 0.00
49 88 0.43
51 4 0.02
52 32 0.16
53 4 0.02
54 30 0.15
55 4 0.02
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (52 bp):
TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGG
Found at i:61369 original size:22 final size:22
Alignment explanation
Indices: 61344--61412 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
61334 ATGCTGATTC
61344 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
* * *
61366 AAGG--TGCCA-ATGTGCTGA-TTC
1 AAGGCCAGCTATAT-TG--GACTTA
61387 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
61409 AAGG
1 AAGG
61413 TGAAGGTGCC
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 12 0.35
23 5 0.15
24 2 0.06
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Found at i:61438 original size:49 final size:49
Alignment explanation
Indices: 61283--61506 Score: 309
Period size: 49 Copynumber: 4.6 Consensus size: 49
61273 GGATGTCATG
*
61283 TGCTGATTCAAGGCCAGCTACATT-GATCTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGA-CTTAAAGAT-G--AAGGTGCCAATA
*
61335 TGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
*
61378 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
*
61427 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
* *
61476 TGGTGATTCAAGGCCAGCTATATTGGGCTTA
1 TGCTGATTCAAGGCCAGCTATATTGGACTTA
61507 GAAGGGTTGC
Statistics
Matches: 157, Mismatches: 8, Indels: 17
0.86 0.04 0.09
Matches are distributed among these distances:
43 41 0.26
48 1 0.01
49 87 0.55
52 26 0.17
53 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
Found at i:61641 original size:30 final size:29
Alignment explanation
Indices: 61512--61980 Score: 307
Period size: 30 Copynumber: 15.9 Consensus size: 29
61502 GCTTAGAAGG
* *
61512 GTTGCCACCGACTTGTGTGGGCTTTGGAAAA
1 GTTGCCACTGAC-T-TGTGGGCTTTTGAAAA
* * *
61543 GGGTGCCACTGATTTGTGGGC-TTTG-AAG
1 -GTTGCCACTGACTTGTGGGCTTTTGAAAA
*
61571 GTTGCCACTGACTTGTGGGCTTTT-AAAG
1 GTTGCCACTGACTTGTGGGCTTTTGAAAA
*
61599 GTTGCCACTGACTTGTGGGCTTTTAAAAA
1 GTTGCCACTGACTTGTGGGCTTTTGAAAA
* * *
61628 ATATGCCATTGACTTGTGGGCTTTTGAACAG
1 GT-TGCCACTGACTTGTGGGCTTTTGAA-AA
* * *
61659 GGTGCCACTAACTTGTGGGCTTTT-AAAG
1 GTTGCCACTGACTTGTGGGCTTTTGAAAA
61687 GTTGCCACTGACTTGTGGGCTTTTGAAAA
1 GTTGCCACTGACTTGTGGGCTTTTGAAAA
*
61716 ATATGCCACTGACTTGTGGGCTTTTGAAAA
1 GT-TGCCACTGACTTGTGGGCTTTTGAAAA
* *
61746 GGGTGCCACTAACTTGTGGGC---TGAAAA
1 -GTTGCCACTGACTTGTGGGCTTTTGAAAA
* * * * **
61773 GAGTGCTA-TAGAGTTGTGAGCTTACAAAAGAAAAA
1 G-TTGCCACT-GACTTGTGGGCTT----TTG-AAAA
* * * * *
61808 GAGTGCCACGGAGTTGTGGACTTTGGAAAA
1 G-TTGCCACTGACTTGTGGGCTTTTGAAAA
* * **
61838 GATGCCACCCCCGACTTGTGGGCTTCGGAAAA
1 GTTGCCA---CTGACTTGTGGGCTTTTGAAAA
* *
61870 GGGTGCCACTGA-TTGTGGGC-TTTG-AAG
1 -GTTGCCACTGACTTGTGGGCTTTTGAAAA
*
61897 GTTGCCACTGACTTGTGGGCTTTCGAAAA
1 GTTGCCACTGACTTGTGGGCTTTTGAAAA
** *
61926 AATGCCATTGACTTGT-GGC-TTTGAAAAA
1 GTTGCCACTGACTTGTGGGCTTTTG-AAAA
** *
61954 AATGCCACTGACTTGTGGACTTTTGAA
1 GTTGCCACTGACTTGTGGGCTTTTGAA
61981 GGGTGATGAA
Statistics
Matches: 355, Mismatches: 53, Indels: 61
0.76 0.11 0.13
Matches are distributed among these distances:
26 12 0.03
27 50 0.14
28 83 0.23
29 45 0.13
30 106 0.30
31 3 0.01
32 27 0.08
33 6 0.02
34 1 0.00
35 22 0.06
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (29 bp):
GTTGCCACTGACTTGTGGGCTTTTGAAAA
Found at i:61687 original size:88 final size:87
Alignment explanation
Indices: 61546--61767 Score: 367
Period size: 88 Copynumber: 2.6 Consensus size: 87
61536 TGGAAAAGGG
* * *
61546 TGCCACTGATTTGTGGGC-TTTG-AAGGTTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTG
1 TGCCACTGACTTGTGGGCTTTTGAAAGGGTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTG
61609 ACTTGTGGGCTTTTAAAAAATA
66 ACTTGTGGGCTTTTAAAAAATA
*
61631 TGCCATTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACT
1 TGCCACTGACTTGTGGGCTTTTGAA-AGGGTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACT
*
61696 GACTTGTGGGCTTTTGAAAAATA
65 GACTTGTGGGCTTTTAAAAAATA
61719 TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCT
1 TGCCACTGACTTGTGGGCTTTTG-AAAGGGTGCCACTAACTTGTGGGCT
61768 GAAAAGAGTG
Statistics
Matches: 127, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
85 16 0.13
86 4 0.03
87 1 0.01
88 104 0.82
89 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.34
Consensus pattern (87 bp):
TGCCACTGACTTGTGGGCTTTTGAAAGGGTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTG
ACTTGTGGGCTTTTAAAAAATA
Found at i:61693 original size:58 final size:59
Alignment explanation
Indices: 61511--61977 Score: 311
Period size: 58 Copynumber: 7.9 Consensus size: 59
61501 GGCTTAGAAG
* * * *
61511 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTT-GAA
1 GGTTGCCACTGAC-T-TGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAAA
*
61570 GGTTGCCACTGACTTGTGGGCTTTT--AAAGGTTGCCACTGACTTGTGGGCTTTTAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAAA
** * * *
61627 AATATGCCATTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTT-AAA
1 GGT-TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAAA
***
61686 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTT-AAAA
* * * * * * **
61746 GGGTGCCACTAACTTGTGGGC---TGAAAAGAGTGCTA-TAGAGTTGTGAGCTTACAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACT-GACTTGTGGGCTTTTAAAA
* * * * * * * **
61802 GAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAA-GATGCCACCCCCGACTTGTGGGCTTCGG
1 G-----G-TTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCA---CTGACTTGTGGGCTT-TT
61866 AAAA
56 AAAA
* * *
61870 GGGTGCCACTGA-TTGTGGGC-TTTG--AAGGTTGCCACTGACTTGTGGGCTTTCGAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTT-TAAAA
** * *** *
61926 -AATGCCATTGACTTGT-GGC-TTTGAAAAAAATGCCACTGACTTGTGGACTTTT
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTT
61978 GAAGGGTGAT
Statistics
Matches: 325, Mismatches: 56, Indels: 57
0.74 0.13 0.13
Matches are distributed among these distances:
55 37 0.11
56 32 0.10
57 56 0.17
58 70 0.22
59 22 0.07
60 50 0.15
61 8 0.02
62 24 0.07
63 1 0.00
64 4 0.01
65 5 0.02
67 11 0.03
68 5 0.02
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (59 bp):
GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAAA
Found at i:61904 original size:26 final size:27
Alignment explanation
Indices: 61850--61985 Score: 96
Period size: 28 Copynumber: 4.8 Consensus size: 27
61840 TGCCACCCCC
*
61850 GACTTGTGGGCTTCGGAAAAGGGTGCCACT
1 GACTTGTGGGCTT-TG--AAGGGTGCCACT
*
61880 GA-TTGTGGGCTTTGAAGGTTGCCACT
1 GACTTGTGGGCTTTGAAGGGTGCCACT
*** *
61906 GACTTGTGGGCTTTCGAAAAAATGCCATT
1 GACTTGTGGGCTTT-G-AAGGGTGCCACT
***
61935 GACTTGT-GGCTTTGAAAAAAATGCCACT
1 GACTTGTGGGCTTTG--AAGGGTGCCACT
*
61963 GACTTGTGGACTTTTGAAGGGTG
1 GACTTGTGGGC-TTTGAAGGGTG
61986 ATGAATGTCT
Statistics
Matches: 89, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
26 13 0.15
27 12 0.13
28 31 0.35
29 27 0.30
30 6 0.07
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30
Consensus pattern (27 bp):
GACTTGTGGGCTTTGAAGGGTGCCACT
Found at i:61939 original size:29 final size:29
Alignment explanation
Indices: 61850--61976 Score: 120
Period size: 29 Copynumber: 4.5 Consensus size: 29
61840 TGCCACCCCC
* ***
61850 GACTTGTGGGCTTCGGAAAAGGGTGCCACT
1 GACTTGTGGGCTT-TGAAAAAAATGCCACT
***
61880 GA-TTGTGGGCTTTG--AAGGTTGCCACT
1 GACTTGTGGGCTTTGAAAAAAATGCCACT
*
61906 GACTTGTGGGCTTTCG-AAAAAATGCCATT
1 GACTTGTGGGCTTT-GAAAAAAATGCCACT
61935 GACTTGT-GGCTTTGAAAAAAATGCCACT
1 GACTTGTGGGCTTTGAAAAAAATGCCACT
*
61963 GACTTGTGGACTTT
1 GACTTGTGGGCTTT
61977 TGAAGGGTGA
Statistics
Matches: 84, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
26 13 0.15
27 12 0.14
28 27 0.32
29 30 0.36
30 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (29 bp):
GACTTGTGGGCTTTGAAAAAAATGCCACT
Found at i:63405 original size:1 final size:1
Alignment explanation
Indices: 63401--63488 Score: 77
Period size: 1 Copynumber: 88.0 Consensus size: 1
63391 CCGGACCCCC
* * * * * * *
63401 TTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** **
63466 TTTTCATTTTTTTCGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTT
63489 AGAGGACGCC
Statistics
Matches: 67, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.02, C:0.02, G:0.08, T:0.88
Consensus pattern (1 bp):
T
Found at i:63464 original size:46 final size:46
Alignment explanation
Indices: 63401--63488 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
63391 CCGGACCCCC
*
63401 TTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTT-GTTTTTTTTTTTT
1 TTTTTTGTTTTTGTTTGTTTTTTCATT-TTTTTCGTTTTTTTTTTTT
* *
63447 TTTTTTTTTTTTTTTTGTTTTTTCATTTTTTTCGTTTTTTTT
1 TTTTTTGTTTTTGTTTGTTTTTTCATTTTTTTCGTTTTTTTT
63489 AGAGGACGCC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 5 0.13
46 33 0.87
ACGTcount: A:0.02, C:0.02, G:0.08, T:0.88
Consensus pattern (46 bp):
TTTTTTGTTTTTGTTTGTTTTTTCATTTTTTTCGTTTTTTTTTTTT
Found at i:63469 original size:21 final size:21
Alignment explanation
Indices: 63403--63488 Score: 91
Period size: 21 Copynumber: 3.9 Consensus size: 21
63393 GGACCCCCTT
*
63403 TTTTGTTTTTGTTTGTTTTTT
1 TTTTGTTTTTGTTTTTTTTTT
*
63424 TATTGTTTTTGTTTTTTTTTT
1 TTTTGTTTTTGTTTTTTTTTT
* *
63445 TTTTTTTTTTTTTTTTTTGTTT
1 TTTTGTTTTTGTTTTTTT-TTT
*
63467 TTTCATTTTTTTCGTTTTTTTT
1 TTT--TGTTTTT-GTTTTTTTT
63489 AGAGGACGCC
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
21 34 0.62
22 6 0.11
24 8 0.15
25 7 0.13
ACGTcount: A:0.02, C:0.02, G:0.08, T:0.87
Consensus pattern (21 bp):
TTTTGTTTTTGTTTTTTTTTT
Found at i:63475 original size:17 final size:15
Alignment explanation
Indices: 63401--63488 Score: 106
Period size: 17 Copynumber: 5.5 Consensus size: 15
63391 CCGGACCCCC
63401 TTTTTTGTTTTTGTTTG
1 TTTTTT-TTTTT-TTTG
63418 TTTTTTTATTGTTTTTG
1 TTTTTTT-TT-TTTTTG
63435 TTTTTTTTTTTTTT-
1 TTTTTTTTTTTTTTG
63449 TTTTTTTTTTTTTTG
1 TTTTTTTTTTTTTTG
*
63464 TTTTTTCATTTTTTTCG
1 TTTTTT--TTTTTTTTG
63481 TTTTTTTT
1 TTTTTTTT
63489 AGAGGACGCC
Statistics
Matches: 65, Mismatches: 1, Indels: 12
0.83 0.01 0.15
Matches are distributed among these distances:
14 14 0.22
15 13 0.20
16 3 0.05
17 33 0.51
18 2 0.03
ACGTcount: A:0.02, C:0.02, G:0.08, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTTTTTTG
Found at i:63476 original size:35 final size:35
Alignment explanation
Indices: 63401--63488 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 35
63391 CCGGACCCCC
* * *
63401 TTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTGTT
1 TTTTTT-TTTTTTTTTTTTTTTTTATTGTTTTTGTA
*
63437 TTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTT-TCA
1 TTTTTTTTTTTTTTTTTTTTTTTATTGTTTTTGT-A
**
63472 TTTTTTTCGTTTTTTTT
1 TTTTTTTTTTTTTTTTT
63489 AGAGGACGCC
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
34 1 0.02
35 38 0.84
36 6 0.13
ACGTcount: A:0.02, C:0.02, G:0.08, T:0.88
Consensus pattern (35 bp):
TTTTTTTTTTTTTTTTTTTTTTTATTGTTTTTGTA
Found at i:77376 original size:52 final size:52
Alignment explanation
Indices: 77298--77425 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
77288 CGAAATATGA
*
77298 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
**
77350 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
77402 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
77426 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.29
52 52 0.71
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
Found at i:77532 original size:13 final size:13
Alignment explanation
Indices: 77514--77538 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
77504 CAAAAAAATA
77514 TGTATCGATACAT
1 TGTATCGATACAT
77527 TGTATCGATACA
1 TGTATCGATACA
77539 ACACTTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:78122 original size:13 final size:13
Alignment explanation
Indices: 78104--78128 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
78094 ACATAAATGT
78104 TGTATCGATACAA
1 TGTATCGATACAA
78117 TGTATCGATACA
1 TGTATCGATACA
78129 TATTTTTTTG
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):
TGTATCGATACAA
Done.