Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 18 of 211
Found at i:5782959 original size:30 final size:29
Alignment explanation
Indices: 5782925--5783007 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 29
5782915 TATTTTTTAT
*
5782925 TAAAAATTAGAAAAAATTATAAAAAAATTA
1 TAAAAATTATAAAAAATTATAAAAAAA-TA
* * *
5782955 TAAAAATCATAAAATATTAT-AAAATATA
1 TAAAAATTATAAAAAATTATAAAAAAATA
*
5782983 TATAAATATATAAAAAATTATAAAA
1 TAAAAAT-TATAAAAAATTATAAAA
5783008 TTTTATAAAG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
28 8 0.18
29 16 0.36
30 20 0.45
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (29 bp):
TAAAAATTATAAAAAATTATAAAAAAATA
Found at i:5782976 original size:10 final size:10
Alignment explanation
Indices: 5782925--5783016 Score: 84
Period size: 10 Copynumber: 9.4 Consensus size: 10
5782915 TATTTTTTAT
5782925 TAAAA-ATTA
1 TAAAATATTA
* *
5782934 GAAAAAATTA
1 TAAAATATTA
*
5782944 TAAAAAAATTA
1 T-AAAATATTA
*
5782955 TAAAA-ATCA
1 TAAAATATTA
5782964 TAAAATATTA
1 TAAAATATTA
5782974 TAAAATA-TA
1 TAAAATATTA
5782983 TATAAATA-TA
1 TA-AAATATTA
*
5782993 TAAAAAATTA
1 TAAAATATTA
*
5783003 TAAAATTTTA
1 TAAAATATTA
5783013 TAAA
1 TAAA
5783017 GTCGTAAGAA
Statistics
Matches: 71, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
9 20 0.28
10 41 0.58
11 10 0.14
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (10 bp):
TAAAATATTA
Found at i:5783014 original size:20 final size:20
Alignment explanation
Indices: 5782925--5783016 Score: 93
Period size: 20 Copynumber: 4.7 Consensus size: 20
5782915 TATTTTTTAT
*
5782925 TAAAA-ATTAGAAAAAATTA
1 TAAAATATTATAAAAAATTA
* *
5782944 TAAAAAAATTAT-AAAAATCA
1 T-AAAATATTATAAAAAATTA
*
5782964 TAAAATATTATAAAATA-TA
1 TAAAATATTATAAAAAATTA
5782983 TATAAATA-TATAAAAAATTA
1 TA-AAATATTATAAAAAATTA
*
5783003 TAAAATTTTATAAA
1 TAAAATATTATAAA
5783017 GTCGTAAGAA
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
19 25 0.42
20 31 0.52
21 4 0.07
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (20 bp):
TAAAATATTATAAAAAATTA
Found at i:5783263 original size:21 final size:21
Alignment explanation
Indices: 5783237--5783277 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5783227 GTTAAAGGGC
5783237 CTTTTTTATGCATTTTATAAT
1 CTTTTTTATGCATTTTATAAT
**
5783258 CTTTTTTATGTTTTTTATAA
1 CTTTTTTATGCATTTTATAA
5783278 AATTTTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.07, G:0.05, T:0.66
Consensus pattern (21 bp):
CTTTTTTATGCATTTTATAAT
Found at i:5783283 original size:21 final size:21
Alignment explanation
Indices: 5783238--5783283 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5783228 TTAAAGGGCC
**
5783238 TTTTTTATGCATTTTATAATC
1 TTTTTTATGCATTTTATAAAA
**
5783259 TTTTTTATGTTTTTTATAAAA
1 TTTTTTATGCATTTTATAAAA
5783280 TTTT
1 TTTT
5783284 ATAATTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTTTTATGCATTTTATAAAA
Found at i:5783292 original size:21 final size:21
Alignment explanation
Indices: 5783268--5783308 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5783258 CTTTTTTATG
*
5783268 TTTTTTATAAAATTTTATAAT
1 TTTTTTATAAAATTTAATAAT
* *
5783289 TTTTTTCTAATATTTAATAA
1 TTTTTTATAAAATTTAATAA
5783309 AAAATAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTTTATAAAATTTAATAAT
Found at i:5783309 original size:31 final size:31
Alignment explanation
Indices: 5783248--5783310 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
5783238 TTTTTTATGC
* * *
5783248 ATTTTATAATCTTTTTTATGTTTTTTATAAA
1 ATTTTATAATCTTTTTTATATATTTAATAAA
*
5783279 ATTTTATAAT-TTTTTTCTAATATTTAATAAA
1 ATTTTATAATCTTTTTTAT-ATATTTAATAAA
5783310 A
1 A
5783311 AATAAATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (31 bp):
ATTTTATAATCTTTTTTATATATTTAATAAA
Found at i:5783663 original size:92 final size:93
Alignment explanation
Indices: 5783475--5783670 Score: 229
Period size: 93 Copynumber: 2.1 Consensus size: 93
5783465 ACTTAATTGC
* * **
5783475 TTTTTTTGAAAAAGTTTGAGGGCATTTTTGATGTATTTTGGTAATTCAAGTACTTAATTGAATGG
1 TTTTTTTGAAAAAGTTTGAGGCCATTTTTGATGTATTTTGGAAATTCAAGTACCCAATTGAATGG
***
5783540 AAAAAAAACAGGGGCTTAATTG-TTTTA
66 AAAAAAAACAGCAACTTAATTGTTTTTA
* *
5783567 TTTTTTTGAAAAAGTTTGAGAGCCTTTTTTTATGTATTTT-GAAAGTTCAAGTACCCAATTG-A-
1 TTTTTTTGAAAAAGTTTGAG-GCCATTTTTGATGTATTTTGGAAA-TTCAAGTACCCAATTGAAT
* * *
5783629 GTAAAAAAAGCAGCAACTTAATTGTCTTTTT
64 GGAAAAAAAACAGCAACTTAATTGT-TTTTA
5783660 TTTTTTTGAAA
1 TTTTTTTGAAA
5783671 TGATGCAAAA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
91 19 0.22
92 24 0.27
93 45 0.51
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (93 bp):
TTTTTTTGAAAAAGTTTGAGGCCATTTTTGATGTATTTTGGAAATTCAAGTACCCAATTGAATGG
AAAAAAAACAGCAACTTAATTGTTTTTA
Found at i:5785249 original size:14 final size:15
Alignment explanation
Indices: 5785227--5785303 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
5785217 CAATCAAACA
5785227 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
5785241 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
5785256 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
*
5785276 CCAG-AAATCCTTTT
1 CCAGAAAATCATTTT
*
5785290 ACAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
5785304 ACTGGCAATC
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
14 20 0.41
15 15 0.31
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:5785268 original size:20 final size:20
Alignment explanation
Indices: 5785243--5785282 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5785233 AATATTTTCC
*
5785243 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
5785263 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
5785283 TCCTTTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:5785290 original size:34 final size:35
Alignment explanation
Indices: 5785231--5785297 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
5785221 CAAACACCAG
*
5785231 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
5785266 AAAACATTTTCCAG-AAATCCTTTTACAGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
5785298 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:5786370 original size:12 final size:13
Alignment explanation
Indices: 5786351--5786388 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
5786341 TCGGTCAATA
5786351 ATTAGTTTTAATT
1 ATTAGTTTTAATT
* *
5786364 ATT-GTTTCATTT
1 ATTAGTTTTAATT
5786376 ATTAGTTTTAATT
1 ATTAGTTTTAATT
5786389 CTTTTTCAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.63
Consensus pattern (13 bp):
ATTAGTTTTAATT
Found at i:5786406 original size:24 final size:25
Alignment explanation
Indices: 5786345--5786407 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
5786335 TTAAATTCGG
5786345 TCAATAATTAGTTTTAATTATTGTT
1 TCAATAATTAGTTTTAATTATTGTT
* * *
5786370 TCATTTATTAGTTTTAATTCTT-TT
1 TCAATAATTAGTTTTAATTATTGTT
*
5786394 TCAATAATCAGTTT
1 TCAATAATTAGTTT
5786408 GTACTTTTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 13 0.41
25 19 0.59
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (25 bp):
TCAATAATTAGTTTTAATTATTGTT
Found at i:5796690 original size:24 final size:24
Alignment explanation
Indices: 5796639--5796801 Score: 64
Period size: 26 Copynumber: 6.6 Consensus size: 24
5796629 AGCTCATGCA
* * *
5796639 AGCCAATAACGGGTAGCTCTGAAG
1 AGCCATTAACGGGAAGCTCCGAAG
* *
5796663 AGCCATTAACGGGAAGCTCCGGAT
1 AGCCATTAACGGGAAGCTCCGAAG
* * *
5796687 AGCCATATATCAGGAAG-TTC--A-
1 AGCCAT-TAACGGGAAGCTCCGAAG
* *
5796708 AGCGAGTTATATCGGGAAGCTCCGGAG
1 AGCCA-TTA-A-CGGGAAGCTCCGAAG
* * *
5796735 ATCCATTAATCAGGAAGCTCACAAAG
1 AGCCATTAA-CGGGAAGCTC-CGAAG
* * *
5796761 AGCCTTTAATTGGGTAGCTCACGAAG
1 AGCCATTAA-CGGGAAGCTC-CGAAG
*
5796787 AGCCATATATCGGGA
1 AGCCAT-TAACGGGA
5796802 CGCTTATAAG
Statistics
Matches: 102, Mismatches: 27, Indels: 18
0.69 0.18 0.12
Matches are distributed among these distances:
21 6 0.06
22 2 0.02
23 6 0.06
24 29 0.28
25 19 0.19
26 35 0.34
27 5 0.05
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20
Consensus pattern (24 bp):
AGCCATTAACGGGAAGCTCCGAAG
Found at i:5801291 original size:48 final size:48
Alignment explanation
Indices: 5801215--5801312 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
5801205 CATTTGTTCC
* *
5801215 ACCAGAGAACATTGAGAACATTATTTCTGCTCGTGCATCACAGTATCA
1 ACCAGAGAACATTGAGAACATTACTTCTGCTCATGCATCACAGTATCA
5801263 ACCAGAGAACATTGAGAACATTACTTCTGCTCATGCATCACAGTATCA
1 ACCAGAGAACATTGAGAACATTACTTCTGCTCATGCATCACAGTATCA
5801311 AC
1 AC
5801313 GAAATCCTGC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (48 bp):
ACCAGAGAACATTGAGAACATTACTTCTGCTCATGCATCACAGTATCA
Found at i:5811714 original size:124 final size:125
Alignment explanation
Indices: 5811489--5811768 Score: 401
Period size: 124 Copynumber: 2.2 Consensus size: 125
5811479 TTATTTCGAG
** *
5811489 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATCAGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTGATACCAGGATGCTATCAGAGAAGAAATTAT
* *
5811553 GAAATCGTGCCCTCGTGGACGCCATTTCGGCATAGTTGGTCATGTCA-GAAATAATT-TTTT
65 GAAATCGCGCCCTCGTGGACGCCATTTCGGCACAGTTGGTCATGT-AGGAAATAATTATTTT
5811613 TTGACGTTTTCTGAGCAAATAGTAT-AAATCGCTGATACCAGGATGCTAT-ATGAGAAGAAATTA
1 TTGACG-TTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATCA-GAGAAGAAATTA
*
5811676 TGAAATCGCGCCCTCGTGGACGCGATTTC-GCTACAGTTGGTCATGTAGGAAATAATTATTTT
64 TGAAATCGCGCCCTCGTGGACGCCATTTCGGC-ACAGTTGGTCATGTAGGAAATAATTATTTT
* *
5811738 TTGACGTTTCTGAGCAAATAGTGTCAAATCG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCG
5811769 TGCCCTCGTG
Statistics
Matches: 142, Mismatches: 7, Indels: 13
0.88 0.04 0.08
Matches are distributed among these distances:
123 4 0.03
124 105 0.74
125 32 0.23
126 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATCAGAGAAGAAATTATG
AAATCGCGCCCTCGTGGACGCCATTTCGGCACAGTTGGTCATGTAGGAAATAATTATTTT
Found at i:5815038 original size:34 final size:32
Alignment explanation
Indices: 5815000--5815086 Score: 116
Period size: 29 Copynumber: 2.9 Consensus size: 32
5814990 GATTATCAAA
5815000 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAG
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAG
5815032 ---GGTTAGGGTTTTTAATTAAATTA-G---G
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTTAG
*
5815057 TTAGGTTAGGGTTTTTAATTTAATTAGGTT
1 TTAGGTTAGGGTTTTTAATTAAATTAGGTT
5815087 CGGCATCTGG
Statistics
Matches: 48, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
25 1 0.02
28 23 0.48
29 24 0.50
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.48
Consensus pattern (32 bp):
TTAGGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:5815098 original size:29 final size:28
Alignment explanation
Indices: 5815000--5815086 Score: 156
Period size: 28 Copynumber: 3.1 Consensus size: 28
5814990 GATTATCAAA
5815000 TTAGGTTAGGGTTTTTAATTAAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAGG
5815028 TTAGGGTTAGGGTTTTTAATTAAATTAGG
1 TTA-GGTTAGGGTTTTTAATTAAATTAGG
*
5815057 TTAGGTTAGGGTTTTTAATTTAATTAGG
1 TTAGGTTAGGGTTTTTAATTAAATTAGG
5815085 TT
1 TT
5815087 CGGCATCTGG
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
28 29 0.51
29 28 0.49
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.48
Consensus pattern (28 bp):
TTAGGTTAGGGTTTTTAATTAAATTAGG
Found at i:5817021 original size:14 final size:15
Alignment explanation
Indices: 5817004--5817037 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5816994 AATATTTATC
5817004 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
5817018 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
5817033 TAAAA
1 TAAAA
5817038 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:5817168 original size:28 final size:29
Alignment explanation
Indices: 5817135--5817192 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
5817125 TTGAAAATAT
5817135 TAAAAAT-TTTAAAATTATT-TTAAAAAAA
1 TAAAAATATTTAAAATT-TTCTTAAAAAAA
5817163 TAAAAATATTTAAAATTTTCTTAAAAAAA
1 TAAAAATATTTAAAATTTTCTTAAAAAAA
5817192 T
1 T
5817193 GAAATTGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (29 bp):
TAAAAATATTTAAAATTTTCTTAAAAAAA
Found at i:5817270 original size:21 final size:21
Alignment explanation
Indices: 5817226--5817274 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
5817216 TAATATGGAG
*
5817226 TTGAGAGATTTTTTGAAGGAAAT
1 TTGAG-GA-TTTTGGAAGGAAAT
5817249 TGTGAGGATTTTGGAAGG-AAT
1 T-TGAGGATTTTGGAAGGAAAT
5817270 TTGAG
1 TTGAG
5817275 AGTTTAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 9 0.38
23 3 0.12
24 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.37
Consensus pattern (21 bp):
TTGAGGATTTTGGAAGGAAAT
Found at i:5817301 original size:52 final size:52
Alignment explanation
Indices: 5817229--5817328 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
5817219 TATGGAGTTG
* * * *
5817229 AGAGATTTTTTGAAGGAAATTGTGAGGATTTTGGAAGGAATTTGAGAGTTTA
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTTGAGAGTTTA
*
5817281 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTTGAAGGAATTTGAGAG
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTTGAGAG
5817329 AATTTTTGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (52 bp):
AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTTGAGAGTTTA
Found at i:5817306 original size:22 final size:22
Alignment explanation
Indices: 5817281--5817349 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
5817271 TGAGAGTTTA
*
5817281 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTTGAAGGAAATTG
*
5817303 AGAGAATTTTTGAAGGAATTTG
1 AGAGAATTTTTGAAGGAAATTG
*
5817325 AGAGAATTTTTGAATGAAATTG
1 AGAGAATTTTTGAAGGAAATTG
5817347 AGA
1 AGA
5817350 TGGGATTTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.32
Consensus pattern (22 bp):
AGAGAATTTTTGAAGGAAATTG
Found at i:5823748 original size:13 final size:13
Alignment explanation
Indices: 5823730--5823754 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5823720 AATAGTAAAA
5823730 TATATTTAAATTT
1 TATATTTAAATTT
5823743 TATATTTAAATT
1 TATATTTAAATT
5823755 ATAATAATAT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATTTAAATTT
Found at i:5827844 original size:46 final size:46
Alignment explanation
Indices: 5827766--5827956 Score: 332
Period size: 46 Copynumber: 4.2 Consensus size: 46
5827756 CTTGTCCCTA
*
5827766 ATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTGTCACTTG
1 ATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTCACTTG
5827811 ATCAGATAAGAT-TAGCTAAGGCTACCACTTATCACTTTCTCACTTG
1 ATCAGATAAG-TGTAGCTAAGGCTACCACTTATCACTTTCTCACTTG
5827857 ATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTCACTTG
1 ATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTCACTTG
* *
5827903 ATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTCCTCACTTG
1 ATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTCACTTG
5827949 ATCAGATA
1 ATCAGATA
5827957 CGTATAGCCA
Statistics
Matches: 140, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
45 16 0.11
46 124 0.89
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (46 bp):
ATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTCACTTG
Found at i:5832369 original size:50 final size:51
Alignment explanation
Indices: 5832268--5832372 Score: 176
Period size: 51 Copynumber: 2.1 Consensus size: 51
5832258 AATTGTCAAA
*
5832268 AATTTAAAATTTCCATTTAATCCCTTTAAGATCTTTAATTATATCAGTTTT
1 AATTGAAAATTTCCATTTAATCCCTTTAAGATCTTTAATTATATCAGTTTT
* *
5832319 AATTGAAAATTTTCATTTAATCTCTTTAA-ATCTTTAATTATATCAGTTTT
1 AATTGAAAATTTCCATTTAATCCCTTTAAGATCTTTAATTATATCAGTTTT
5832369 AATT
1 AATT
5832373 AGAATAATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
50 25 0.49
51 26 0.51
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.50
Consensus pattern (51 bp):
AATTGAAAATTTCCATTTAATCCCTTTAAGATCTTTAATTATATCAGTTTT
Found at i:5833370 original size:91 final size:91
Alignment explanation
Indices: 5833215--5833466 Score: 344
Period size: 91 Copynumber: 2.8 Consensus size: 91
5833205 TGATACATCG
* * * * * *
5833215 ATTGATAGTTCAAGTACCACATTGAACATTTTCCAAGTATAAGTACCACGTTGGGCAATTTATGA
1 ATTGATAGTTCAAGTACCACATTGGACATTTTCAAAGTACAAGTACCACATTGGACATTTTATGA
* **
5833280 AAGTACATGTGTCAAATAAGACACAA
66 AAGTACAGGTACCAAATAAGACACAA
* * *
5833306 ATTGATAGTTCAAGTATCACATTGGACATTTTCAAAGTAC-AGATATCACATTAGACATTTTATG
1 ATTGATAGTTCAAGTACCACATTGGACATTTTCAAAGTACAAG-TACCACATTGGACATTTTATG
*
5833370 AAAGTACAGGTACCAAATAATACACAA
65 AAAGTACAGGTACCAAATAAGACACAA
* * *
5833397 ATTAATAGTTCAAGTACCACGTTAGACATTTTCAAAGTACAAGTACCACATTGGACATTTTATGA
1 ATTGATAGTTCAAGTACCACATTGGACATTTTCAAAGTACAAGTACCACATTGGACATTTTATGA
5833462 AAGTA
66 AAGTA
5833467 TAAGTATCAA
Statistics
Matches: 140, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
90 2 0.01
91 136 0.97
92 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.30
Consensus pattern (91 bp):
ATTGATAGTTCAAGTACCACATTGGACATTTTCAAAGTACAAGTACCACATTGGACATTTTATGA
AAGTACAGGTACCAAATAAGACACAA
Found at i:5833472 original size:31 final size:29
Alignment explanation
Indices: 5833316--5833457 Score: 108
Period size: 29 Copynumber: 4.8 Consensus size: 29
5833306 ATTGATAGTT
* *
5833316 CAAGTATCACATTGGACATTTTCAAAGTA
1 CAAGTACCACATTAGACATTTTCAAAGTA
* *
5833345 C-AGATATCACATTAGACATTTTATGAAAGTA
1 CAAG-TACCACATTAGACA-TTT-TCAAAGTA
* * * ** *
5833376 CAGGTACCAAATAATACACAAATT-AATAGTT
1 CAAGTACCACAT--TAGACATTTTCAA-AGTA
*
5833407 CAAGTACCACGTTAGACATTTTCAAAGTA
1 CAAGTACCACATTAGACATTTTCAAAGTA
*
5833436 CAAGTACCACATTGGACATTTT
1 CAAGTACCACATTAGACATTTT
5833458 ATGAAAGTAT
Statistics
Matches: 87, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
28 2 0.02
29 44 0.51
30 7 0.08
31 27 0.31
32 2 0.02
33 5 0.06
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.30
Consensus pattern (29 bp):
CAAGTACCACATTAGACATTTTCAAAGTA
Found at i:5840146 original size:21 final size:21
Alignment explanation
Indices: 5840105--5840148 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5840095 TTTTTGTACT
* * *
5840105 TTTTAATAATTTTTAATATAA
1 TTTTAAAAATTTTAAAAATAA
5840126 TTTTAAAAATTTTAAAAATAA
1 TTTTAAAAATTTTAAAAATAA
5840147 TT
1 TT
5840149 AATTGCACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTAAAAATTTTAAAAATAA
Found at i:5843772 original size:3 final size:3
Alignment explanation
Indices: 5843764--5843789 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5843754 TGCAAAAACA
5843764 AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AG
5843790 AAGAATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:5847861 original size:14 final size:14
Alignment explanation
Indices: 5847842--5847875 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5847832 AAATAAAGGG
*
5847842 CTTTTTCTTTTTTT
1 CTTTTTCTTTATTT
5847856 CTTTTTCTTTATTT
1 CTTTTTCTTTATTT
*
5847870 ATTTTT
1 CTTTTT
5847876 AACCTTTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (14 bp):
CTTTTTCTTTATTT
Found at i:5857350 original size:53 final size:53
Alignment explanation
Indices: 5857285--5857392 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 53
5857275 TATTCCTCTG
* *
5857285 AAAGCTTGGAAGCAGGAATAAGGCCCCCTTAACAGAAATTGCAAAACTTTCCC
1 AAAGCTTAGAAGCAGGAATAAGGCCCCCTCAACAGAAATTGCAAAACTTTCCC
*
5857338 AAAGCTTAGAAGCAGGAATAAGGCCCCCTCACCAGAAATTGCAAAACTTTCCC
1 AAAGCTTAGAAGCAGGAATAAGGCCCCCTCAACAGAAATTGCAAAACTTTCCC
5857391 AA
1 AA
5857393 CTATAGTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.18
Consensus pattern (53 bp):
AAAGCTTAGAAGCAGGAATAAGGCCCCCTCAACAGAAATTGCAAAACTTTCCC
Found at i:5862358 original size:20 final size:20
Alignment explanation
Indices: 5862335--5862492 Score: 128
Period size: 20 Copynumber: 8.0 Consensus size: 20
5862325 AGAATGAGAG
5862335 GGAAAGGAGAAGAAAGAAAA
1 GGAAAGGAGAAGAAAGAAAA
* *
5862355 GGAAAGGAGAGGGAAG-AAA
1 GGAAAGGAGAAGAAAGAAAA
* *
5862374 -GAAA-AAGAATGAAAAAAAA
1 GGAAAGGAGAA-GAAAGAAAA
*
5862393 GGAAAGGAGAAGAAAAAAGAA
1 GGAAAGGAGAAGAAAGAA-AA
* * *
5862414 AGAAA-AAGAAGGAAAGAACA
1 GGAAAGGAGAA-GAAAGAAAA
*
5862434 GGAAAGGAGAAGAAAAAAAA
1 GGAAAGGAGAAGAAAGAAAA
* * *
5862454 AGAAAGAAGAAG-AAGAAGA
1 GGAAAGGAGAAGAAAGAAAA
* *
5862473 GGGAAGGAAAAGAAAGAAAA
1 GGAAAGGAGAAGAAAGAAAA
5862493 AAAGGTAATT
Statistics
Matches: 106, Mismatches: 24, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
17 3 0.03
18 7 0.07
19 19 0.18
20 57 0.54
21 20 0.19
ACGTcount: A:0.67, C:0.01, G:0.32, T:0.01
Consensus pattern (20 bp):
GGAAAGGAGAAGAAAGAAAA
Found at i:5862413 original size:31 final size:30
Alignment explanation
Indices: 5862367--5862467 Score: 105
Period size: 31 Copynumber: 3.3 Consensus size: 30
5862357 AAAGGAGAGG
5862367 GAAGAA-AGAAAAAGAATGAAAAAAAAGGAAA
1 GAAGAAGA-AAAAAGAA-GAAAAAAAAGGAAA
* *
5862398 GGAGAAGAAAAAAGAAAGAAAAAGAAGGAAA
1 GAAGAAGAAAAAAG-AAGAAAAAAAAGGAAA
* * ** *
5862429 GAACAGGAAAGGAGAAGAAAAAAAAAGAAA
1 GAAGAAGAAAAAAGAAGAAAAAAAAGGAAA
5862459 GAAGAAGAA
1 GAAGAAGAA
5862468 GAAGAGGGAA
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
30 21 0.37
31 33 0.58
32 3 0.05
ACGTcount: A:0.71, C:0.01, G:0.27, T:0.01
Consensus pattern (30 bp):
GAAGAAGAAAAAAGAAGAAAAAAAAGGAAA
Found at i:5862422 original size:41 final size:41
Alignment explanation
Indices: 5862368--5862465 Score: 153
Period size: 41 Copynumber: 2.4 Consensus size: 41
5862358 AAGGAGAGGG
*
5862368 AAGAAAGAAAAAGAATGAAAAAAAAGGAAAGGAGAAGAAAA
1 AAGAAAGAAAAAGAAGGAAAAAAAAGGAAAGGAGAAGAAAA
* *
5862409 AAGAAAGAAAAAGAAGGAAAGAACAGGAAAGGAGAAGAAAA
1 AAGAAAGAAAAAGAAGGAAAAAAAAGGAAAGGAGAAGAAAA
5862450 AA-AAAGAAAGAAGAAG
1 AAGAAAGAAA-AAGAAG
5862466 AAGAAGAGGG
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
40 7 0.13
41 46 0.87
ACGTcount: A:0.71, C:0.01, G:0.27, T:0.01
Consensus pattern (41 bp):
AAGAAAGAAAAAGAAGGAAAAAAAAGGAAAGGAGAAGAAAA
Found at i:5862481 original size:44 final size:39
Alignment explanation
Indices: 5862342--5862494 Score: 145
Period size: 41 Copynumber: 3.9 Consensus size: 39
5862332 GAGGGAAAGG
** *
5862342 AGAA-GAAAGAAAAGGAAAGGAG-AG-GGAAGAAAGAAAA
1 AGAAGGAAAG-AAAGGAAAGGAGAAGAAAAAAAAAGAAAA
* *
5862379 AGAATGAAAAAAAAGGAAAGGAGAAGAAAAAAGAAAGAAAA
1 AGAA-GGAAAGAAAGGAAAGGAGAAGAAAAAA-AAAGAAAA
5862420 AGAAGGAAAGAACAGGAAAGGAGAAGAAAAAAAAAGAAAGA
1 AGAAGGAAAGAA-AGGAAAGGAGAAGAAAAAAAAAGAAA-A
* *
5862461 AGAA-G-AAGAAGAGGGAAGGAAAAGAAAGAAAAAA
1 AGAAGGAAAGAA-AGGAAAGGAGAAGAAA-AAAAAA
5862495 AGGTAATTTT
Statistics
Matches: 98, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
37 4 0.04
38 12 0.12
39 24 0.24
40 22 0.22
41 36 0.37
ACGTcount: A:0.69, C:0.01, G:0.30, T:0.01
Consensus pattern (39 bp):
AGAAGGAAAGAAAGGAAAGGAGAAGAAAAAAAAAGAAAA
Found at i:5862493 original size:10 final size:10
Alignment explanation
Indices: 5862368--5862493 Score: 76
Period size: 10 Copynumber: 12.2 Consensus size: 10
5862358 AAGGAGAGGG
5862368 AAGAAAGAAA
1 AAGAAAGAAA
*
5862378 AAGAATGAAA
1 AAGAAAGAAA
*
5862388 AA-AAAGGAA
1 AAGAAAGAAA
*
5862397 AGGAGAAGAAAA
1 AAGA-AAG-AAA
5862409 AAGAAAGAAA
1 AAGAAAGAAA
*
5862419 AAGAAGGAAAGA
1 AAGAAAG-AA-A
* *
5862431 ACAGGAAAGGAG
1 A-A-GAAAGAAA
*
5862443 AAGAAAAAAA
1 AAGAAAGAAA
*
5862453 AAGAAAGAAG
1 AAGAAAGAAA
*
5862463 AAG-AAGAAG
1 AAGAAAGAAA
* * *
5862472 AGGGAAGGAA
1 AAGAAAGAAA
5862482 AAGAAAGAAA
1 AAGAAAGAAA
5862492 AA
1 AA
5862494 AAGGTAATTT
Statistics
Matches: 87, Mismatches: 21, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
9 14 0.16
10 50 0.57
11 9 0.10
12 8 0.09
13 2 0.02
14 4 0.05
ACGTcount: A:0.71, C:0.01, G:0.28, T:0.01
Consensus pattern (10 bp):
AAGAAAGAAA
Found at i:5862495 original size:44 final size:44
Alignment explanation
Indices: 5862368--5862495 Score: 133
Period size: 44 Copynumber: 3.0 Consensus size: 44
5862358 AAGGAGAGGG
* * * *
5862368 AAGAAAGAAAAAGAATGAAAAAAAAGG-AAAG-G-AGAAGAAAA
1 AAGAAAGAAAAAGAAGGAAAGAACAGGAAAAGAGAAGAAAAAAA
*
5862409 AAGAAAGAAAAAGAAGGAAAGAACAGGAAAGGAGAAGAAAAAAA
1 AAGAAAGAAAAAGAAGGAAAGAACAGGAAAAGAGAAGAAAAAAA
* *
5862453 AAGAAAGAAGAAGAA-GAAGAGGGA-AGGAAAAGA-AAGAAAAAAA
1 AAGAAAGAAAAAGAAGGAA-A-GAACAGGAAAAGAGAAGAAAAAAA
5862496 GGTAATTTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
41 24 0.32
42 3 0.04
43 14 0.19
44 31 0.42
45 2 0.03
ACGTcount: A:0.71, C:0.01, G:0.27, T:0.01
Consensus pattern (44 bp):
AAGAAAGAAAAAGAAGGAAAGAACAGGAAAAGAGAAGAAAAAAA
Found at i:5863400 original size:316 final size:317
Alignment explanation
Indices: 5862825--5864036 Score: 1681
Period size: 316 Copynumber: 3.9 Consensus size: 317
5862815 AAAATGGTAT
* * *
5862825 ATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATAA
1 ATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAA
* *
5862890 AATTAAAAATTATGGTATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCG
66 AATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCG
5862955 AAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAATACAAATATTTCAAACAA
131 AAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAATACAAATATTTCAAACAA
*
5863020 AACGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAA
196 AATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAA
*
5863085 ATTCGGGAAAATAATACGAGCAAAGGGCAAGAATAAGGATTTTTTTACACTAAATTA
261 ATTCGAGAAAATAATACGAGCAAAGGGCAAGAATAAGGATTTTTTTACACTAAATTA
5863142 ATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAA
1 ATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAA
* *
5863207 AATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAG-AAAAAATACGAATAAATGGCTG
66 AATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCG
5863271 AAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAATACAAATATTTCAAACAA
131 AAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAATACAAATATTTCAAACAA
*
5863336 AATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAATAATAAA
196 AATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAA
* *
5863401 ATTCGAGAAAATAATACGAGCAAAGGGTAAGAATAA-TAGTTTTTTTACACTAAATTA
261 ATTCGAGAAAATAATACGAGCAAAGGGCAAGAATAAGGA-TTTTTTTACACTAAATTA
* * *
5863458 ATTTAAAAATCATACTAAATTAATAAATTTCAAACATAATGTACTGAAATAATGTAAAATTATAA
1 ATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAA
* *
5863523 AATTATAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAAGGGCCG
66 AATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCG
5863588 AAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAATACAAATATTTCAAACAA
131 AAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAATACAAATATTTCAAACAA
* * * *
5863653 TATGTATTGAAATAATGTAAAATAATAAAATACGAAAATAATATATTTTTTATTTAAAGTAATAA
196 AATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATA-TTTTTATTGAAAGTAATAA
* * * *
5863718 AATTCGGGAAAATTATACGAGCAAATGGCAAGAATAAGGGTTTTTTTTTACACT-AA--A
260 AATTCGAGAAAATAATACGAGCAAAGGGCAAGAATAA-GG-ATTTTTTTACACTAAATTA
* ** * * * * *
5863775 ATTT-TAAAA-A-TTTATATT--GAAA-GT-AATA-A-AATTCA--GAAATAAT-T---TTTA-A
1 ATTTAAAAAACACACTAAATTAATAAATTTCAA-ACATAATGCACTGAAATAATGTAAAATTATA
* * *
5863824 AAATACAGAAATAAT-ATATTTTTATTGAAAGTAATAAAATTC-GAGAAAAAAATACGAACAAAT
65 AAAT-TAGAAATTATGATA-TTTT-TT-AAAGTAATAAAATGCGGAGAAAAAAATACGAACAAAT
* * * * * * * *
5863887 TGTCGAAATAAGGGTTTTTTACTAAATTTTTTTAGAAAA--AAGAAATAATTAATAC----ACTT
126 GGCCGAAGTAAGAGTCTTTTACTAAA-TTTTTTA-AAAATTCAGAAATAATGAATACAAATATTT
* * * *
5863946 CAAATATAATGTACTAAAATAATGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAG
189 CAAACAAAATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAG
*
5864011 TAATAAAATTCGAGAAAATAGTACGA
254 TAATAAAATTCGAGAAAATAATACGA
5864037 ATAAATGGCC
Statistics
Matches: 820, Mismatches: 62, Indels: 44
0.89 0.07 0.05
Matches are distributed among these distances:
299 35 0.04
300 50 0.06
302 8 0.01
303 14 0.02
304 57 0.07
305 21 0.03
306 5 0.01
307 8 0.01
309 4 0.00
310 3 0.00
311 2 0.00
312 3 0.00
314 5 0.01
315 2 0.00
316 306 0.37
317 233 0.28
318 50 0.06
319 2 0.00
320 12 0.01
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.31
Consensus pattern (317 bp):
ATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAA
AATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGGCCG
AAGTAAGAGTCTTTTACTAAATTTTTTAAAAATTCAGAAATAATGAATACAAATATTTCAAACAA
AATGTACTGAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAA
ATTCGAGAAAATAATACGAGCAAAGGGCAAGAATAAGGATTTTTTTACACTAAATTA
Found at i:5868133 original size:39 final size:37
Alignment explanation
Indices: 5868084--5868206 Score: 122
Period size: 39 Copynumber: 3.1 Consensus size: 37
5868074 ACTAACACGA
5868084 TAACAATAATAATAGTTTTATACTCAAAATAATACTAAC
1 TAACAATAATAATAGTTTT-TACT-AAAATAATACTAAC
*
5868123 TAACACTAATAATTAGTGTTTTACTAAAAATAATAACTAAC
1 TAACAATAATAA-TAGT-TTTTACT-AAAATAAT-ACTAAC
* * * *
5868164 -CACAATAATACTAGTTTTTTACTAACAATAATGCTAAG
1 TAACAATAATAATAG-TTTTTACTAA-AATAATACTAAC
5868202 TAACA
1 TAACA
5868207 TCTAAACCCT
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
38 6 0.09
39 30 0.43
40 25 0.36
41 9 0.13
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (37 bp):
TAACAATAATAATAGTTTTTACTAAAATAATACTAAC
Found at i:5874796 original size:19 final size:17
Alignment explanation
Indices: 5874753--5874795 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
5874743 TTATTATTTA
5874753 TTTA-TTTTCTTCTTTT
1 TTTATTTTTCTTCTTTT
*
5874769 TTTATTTTTCTCTCTATT
1 TTTATTTTTCT-TCTTTT
*
5874787 TTTGTTTTT
1 TTTATTTTT
5874796 TACAAAGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 6 0.26
18 13 0.57
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTATTTTTCTTCTTTT
Found at i:5881904 original size:13 final size:13
Alignment explanation
Indices: 5881886--5881915 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5881876 TCCAGCAACT
5881886 ATGAATTTATTTC
1 ATGAATTTATTTC
*
5881899 ATGAATTTATTTG
1 ATGAATTTATTTC
5881912 ATGA
1 ATGA
5881916 TTATCCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:5890833 original size:25 final size:26
Alignment explanation
Indices: 5890805--5890858 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
5890795 AAAATTAAAT
5890805 TAATATAT-AAAACTAAAAATTGTTA
1 TAATATATAAAAACTAAAAATTGTTA
* *
5890830 TAATATATAAAAATTGAAAATTGTTA
1 TAATATATAAAAACTAAAAATTGTTA
5890856 TAA
1 TAA
5890859 AATTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (26 bp):
TAATATATAAAAACTAAAAATTGTTA
Found at i:5891104 original size:22 final size:22
Alignment explanation
Indices: 5891077--5891122 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
5891067 ATAAAATTAT
*
5891077 TAAATA-TTAAAATAATATAATA
1 TAAATATTTAAAAGAA-ATAATA
5891099 TAAATATTTAAAAGAAATAATA
1 TAAATATTTAAAAGAAATAATA
5891121 TA
1 TA
5891123 GACGAGCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
TAAATATTTAAAAGAAATAATA
Found at i:5891795 original size:3 final size:3
Alignment explanation
Indices: 5891789--5891827 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
5891779 TTTTGTTGTG
*
5891789 CTT CTT CTT CGT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
5891828 TCCCTTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:5897522 original size:14 final size:14
Alignment explanation
Indices: 5897503--5897530 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5897493 AGGGTATACT
5897503 TAAATATTAAAAAA
1 TAAATATTAAAAAA
5897517 TAAATATTAAAAAA
1 TAAATATTAAAAAA
5897531 AGAAGAGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAATATTAAAAAA
Found at i:5906672 original size:13 final size:13
Alignment explanation
Indices: 5906654--5906679 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5906644 ATTTCAAATT
5906654 TTTTTAATTAATA
1 TTTTTAATTAATA
5906667 TTTTTAATTAATA
1 TTTTTAATTAATA
5906680 CATACATTAT
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:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTAATTAATA
Found at i:5906912 original size:15 final size:15
Alignment explanation
Indices: 5906892--5906920 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5906882 CTTTATATAT
5906892 AATATTTATTTTTTA
1 AATATTTATTTTTTA
5906907 AATATTTATTTTTT
1 AATATTTATTTTTT
5906921 TCACCTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
AATATTTATTTTTTA
Found at i:5910243 original size:46 final size:45
Alignment explanation
Indices: 5910176--5910455 Score: 312
Period size: 46 Copynumber: 6.6 Consensus size: 45
5910166 TTTGAGTACT
* *
5910176 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
5910222 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
5910258 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
5910304 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
5910340 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* *
5910386 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
5910431 TCTGATCAAG-G-ACAAGTGATAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTG
5910456 ATCATACGTA
Statistics
Matches: 201, Mismatches: 13, Indels: 43
0.78 0.05 0.17
Matches are distributed among these distances:
36 58 0.29
37 2 0.01
38 1 0.00
39 1 0.00
40 5 0.02
41 1 0.00
42 6 0.03
43 14 0.07
44 2 0.01
45 25 0.12
46 86 0.43
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:5910253 original size:36 final size:36
Alignment explanation
Indices: 5910212--5910366 Score: 184
Period size: 36 Copynumber: 4.0 Consensus size: 36
5910202 GGTAGCTTTA
5910212 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
5910248 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
5910293 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
5910330 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
5910366 G
1 G
5910367 TTAGCCTTAG
Statistics
Matches: 103, Mismatches: 6, Indels: 20
0.80 0.05 0.16
Matches are distributed among these distances:
36 65 0.63
37 2 0.02
40 2 0.02
42 2 0.02
45 2 0.02
46 30 0.29
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:5910313 original size:82 final size:82
Alignment explanation
Indices: 5910176--5910412 Score: 420
Period size: 82 Copynumber: 2.9 Consensus size: 82
5910166 TTTGAGTACT
*
5910176 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
5910241 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
5910258 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
5910323 GATAAGTGCTATACTTA
66 GATAAGTGCTACACTTA
* * * *
5910340 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAAGTGAGAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
5910405 GATAAGTG
66 GATAAGTG
5910413 GTAGCCTAGC
Statistics
Matches: 149, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 149 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:5912473 original size:21 final size:20
Alignment explanation
Indices: 5912445--5912483 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
5912435 TTTTTTTTTG
5912445 AATTGAGTCGAGTAAAATAA
1 AATTGAGTCGAGTAAAATAA
*
5912465 AATTCGAGTCGAGTTAAAT
1 AATT-GAGTCGAGTAAAAT
5912484 TGAATGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.28
Consensus pattern (20 bp):
AATTGAGTCGAGTAAAATAA
Found at i:5912725 original size:19 final size:17
Alignment explanation
Indices: 5912692--5912737 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 17
5912682 CTATTATTTC
*
5912692 ATATTTTTAATTTTTTT
1 ATATTTTTAATTTTTTA
5912709 ATATTCTTTATATTTTTTA
1 ATATT-TTTA-ATTTTTTA
5912728 ATATTTTTAA
1 ATATTTTTAA
5912738 AATTTATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 6 0.23
18 8 0.31
19 12 0.46
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
ATATTTTTAATTTTTTA
Found at i:5912749 original size:26 final size:26
Alignment explanation
Indices: 5912715--5912788 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
5912705 TTTTATATTC
5912715 TTTAT-ATTTTTTAATATTTTTAAAA
1 TTTATAATTTTTTAATATTTTTAAAA
** *
5912740 TTTATAATTTTTTTAA-AAATATAAAA
1 TTTATAA-TTTTTTAATATTTTTAAAA
*
5912766 TTTAGAATTTTTATAAATATTTT
1 TTTATAATTTTT-T-AATATTTT
5912789 GAATTTTAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
25 10 0.27
26 15 0.41
27 10 0.27
28 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (26 bp):
TTTATAATTTTTTAATATTTTTAAAA
Found at i:5912762 original size:17 final size:18
Alignment explanation
Indices: 5912726--5912768 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5912716 TTATATTTTT
*
5912726 TAATATTTTTAAAATTTA
1 TAATATTTTTAAAATATA
*
5912744 TAATTTTTTTAAAA-ATA
1 TAATATTTTTAAAATATA
*
5912761 TAAAATTT
1 TAATATTT
5912769 AGAATTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATATTTTTAAAATATA
Found at i:5912782 original size:18 final size:19
Alignment explanation
Indices: 5912759--5912795 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5912749 TTTTTAAAAA
5912759 TATAAA-ATTTAGAATTTT
1 TATAAATATTTAGAATTTT
*
5912777 TATAAATATTTTGAATTTT
1 TATAAATATTTAGAATTTT
5912796 AAAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:5915181 original size:167 final size:167
Alignment explanation
Indices: 5914906--5915245 Score: 486
Period size: 167 Copynumber: 2.0 Consensus size: 167
5914896 GTTGTTGAGA
* ** *
5914906 TAACATTCAATCCAGGGATGTGTTTCTTTTTCCTCTTAGAGCTTTTAGGAAAGATTTGCATGTAA
1 TAACATTCAATCCAGGGATGTGTTTCTTTTTCCTCTTAGAGCTCTTAGGAAAGATGCGAATGTAA
* ** *
5914971 AAAATCCATCTTATTTGGATGATTGTTTCCTCATTTCCATGTTTG-ATGTCTCCGACATGGACAT
66 AAAATCCATCTTATTCGGATGATCATATCCTCATTTCCATGTTTGAATGTCTCCGACATGGACAT
* *
5915035 CGGACCTATGTACTTTAGTAAGAATGTAGAGTTGGAG
131 CGGACCAATGTACTTTAGGAAGAATGTAGAGTTGGAG
* * *
5915072 TAACATTCAATCCAGGGATTTGTTTTCTTTTT-CTCTTAGTGCTCTTCGGAAAAGATGCGAATGT
1 TAACATTCAATCCAGGGATGTG-TTTCTTTTTCCTCTTAGAGCTCTTAGG-AAAGATGCGAATGT
* * *
5915136 CAGAAATTCATCTTATTCGGATGATCATATCCTCATTTCCATGTTTGAATGTCTCCGACATGGAC
64 AAAAAATCCATCTTATTCGGATGATCATATCCTCATTTCCATGTTTGAATGTCTCCGACATGGAC
**
5915201 ATCGGATGAATGTACTTTAGGAAGAATGTAGAGTTGGAG
129 ATCGGACCAATGTACTTTAGGAAGAATGTAGAGTTGGAG
5915240 TAACAT
1 TAACAT
5915246 AGATCAGTAG
Statistics
Matches: 153, Mismatches: 18, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
166 35 0.23
167 60 0.39
168 58 0.38
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (167 bp):
TAACATTCAATCCAGGGATGTGTTTCTTTTTCCTCTTAGAGCTCTTAGGAAAGATGCGAATGTAA
AAAATCCATCTTATTCGGATGATCATATCCTCATTTCCATGTTTGAATGTCTCCGACATGGACAT
CGGACCAATGTACTTTAGGAAGAATGTAGAGTTGGAG
Found at i:5916367 original size:28 final size:29
Alignment explanation
Indices: 5916319--5916373 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
5916309 TTATGATTTT
5916319 TTAAATAAATTTTAAATTTTA-TATTAGC
1 TTAAATAAATTTTAAATTTTATTATTAGC
*
5916347 TTAATTAAATTTTATAA-TTTATTATTA
1 TTAAATAAATTTTA-AATTTTATTATTA
5916374 ATCCTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (29 bp):
TTAAATAAATTTTAAATTTTATTATTAGC
Found at i:5917847 original size:109 final size:109
Alignment explanation
Indices: 5917651--5917869 Score: 375
Period size: 109 Copynumber: 2.0 Consensus size: 109
5917641 TCGACTTCAA
* * *
5917651 TGGTGTTTTTCGAATTGTTTTCTTGAGTATTCTATGACGGTTTACTCCTCTCTTCTTACCTTTGT
1 TGGTATTTTTCGAATTGTTTTCTTGAGTATTCTATGACGGCTTACTCCTCTCTTCTTACCGTTGT
*
5917716 CATATATAGGTCTTAGAATGCCCGAAAACCCTTAAAAATTACGT
66 CATATATAGGTCTTAGAATGCCCGAAAACCCCTAAAAATTACGT
* * *
5917760 TGGTATTTTTCGAATTGTTTTCTTGAGTATTCTATGATGGCTTACTCCTTTCTTCTTATCGTTGT
1 TGGTATTTTTCGAATTGTTTTCTTGAGTATTCTATGACGGCTTACTCCTCTCTTCTTACCGTTGT
5917825 CATATATAGGTCTTAGAATGCCCGAAAACCCCTAAAAATTACGT
66 CATATATAGGTCTTAGAATGCCCGAAAACCCCTAAAAATTACGT
5917869 T
1 T
5917870 TTTCTGTTGT
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
109 103 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (109 bp):
TGGTATTTTTCGAATTGTTTTCTTGAGTATTCTATGACGGCTTACTCCTCTCTTCTTACCGTTGT
CATATATAGGTCTTAGAATGCCCGAAAACCCCTAAAAATTACGT
Found at i:5917984 original size:29 final size:29
Alignment explanation
Indices: 5917927--5918002 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
5917917 ATGGCTGTGC
**
5917927 GGAAGCTCGTGTGGCTCACATTGCAGTGT
1 GGAAGCTCGTGTGGCTCACACGGCAGTGT
5917956 GGAAGC-CTGTGTGGCTCACACGGTC-GTGT
1 GGAAGCTC-GTGTGGCTCACACGG-CAGTGT
* *
5917985 GTACAGCTCATGTGGCTC
1 GGA-AGCTCGTGTGGCTC
5918003 TTGAAACTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 1 0.03
29 25 0.64
30 12 0.31
31 1 0.03
ACGTcount: A:0.16, C:0.24, G:0.34, T:0.26
Consensus pattern (29 bp):
GGAAGCTCGTGTGGCTCACACGGCAGTGT
Found at i:5918934 original size:17 final size:17
Alignment explanation
Indices: 5918914--5919346 Score: 137
Period size: 17 Copynumber: 24.5 Consensus size: 17
5918904 AACACGAGAA
*
5918914 TTTTAAAACACGAATTT
1 TTTTAAAACACGAAATT
*
5918931 TTTTAAAAAAACACGAAAGT
1 TTTT---AAAACACGAAATT
*
5918951 TTTTGAAACACGAGAATT
1 TTTTAAAACACGA-AATT
* *
5918969 TTTAAAAACACGAAAAT
1 TTTTAAAACACGAAATT
* *
5918986 TTTTGAAACACGAAAATAA
1 TTTTAAAACACG-AAAT-T
**** *
5919005 AAAAAAAACACGAAAAT
1 TTTTAAAACACGAAATT
*
5919022 CTTTAAAACAC-AACATT
1 TTTTAAAACACGAA-ATT
* *
5919039 TTTTGAAACAAGAGAA--
1 TTTTAAAACACGA-AATT
*
5919055 TTTTAAAACATAGAAA-T
1 TTTTAAAACA-CGAAATT
*
5919072 TTTTAAAACACGAAAAT
1 TTTTAAAACACGAAATT
* * * * *
5919089 TTGTGAAACACTAGAGTC
1 TTTTAAAACACGA-AATT
* *
5919107 GTTGAAAACACGAAAATT
1 TTTTAAAACACG-AAATT
* * *
5919125 TGTGAAAACACGAAAAT
1 TTTTAAAACACGAAATT
* *
5919142 TTTTGAAACATGGAAATT
1 TTTTAAAACA-CGAAATT
* * *
5919160 TCTGAAAACACGAGGA-T
1 TTTTAAAACACGA-AATT
* *
5919177 TTTCAAAATAC-AAATTT
1 TTTTAAAACACGAAA-TT
*
5919194 TTTTGAAAATACGAAAATT
1 TTTT-AAAACACG-AAATT
*
5919213 TTTAAAAACACAGAAATT
1 TTTTAAAACAC-GAAATT
* *
5919231 TTTAAAATACATG-AA-T
1 TTTTAAA-ACACGAAATT
* *
5919247 TTTTGAAACATGGGAAAATTTT
1 TTTTAAAACA--CG-AAA--TT
** *
5919269 TTTTAAAACGTGAAAAT
1 TTTTAAAACACGAAATT
* * *
5919286 TTCTGAAACACTGAAA-A
1 TTTTAAAACAC-GAAATT
*
5919303 TTTGAAAACACGAAGATT
1 TTTTAAAACACGAA-ATT
*
5919321 TTTTGAAACACGGAAATT
1 TTTTAAAACAC-GAAATT
5919339 TTTTAAAA
1 TTTTAAAA
5919347 ACACAAAAAA
Statistics
Matches: 301, Mismatches: 81, Indels: 67
0.67 0.18 0.15
Matches are distributed among these distances:
15 4 0.01
16 27 0.09
17 112 0.37
18 104 0.35
19 26 0.09
20 19 0.06
22 9 0.03
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.30
Consensus pattern (17 bp):
TTTTAAAACACGAAATT
Found at i:5918983 original size:35 final size:35
Alignment explanation
Indices: 5918937--5919250 Score: 171
Period size: 35 Copynumber: 9.0 Consensus size: 35
5918927 ATTTTTTTAA
*
5918937 AAAAACACGAAAGTTTTTGAAACACGAGAATTTTT
1 AAAAACACGAAAATTTTTGAAACACGAGAATTTTT
* ****
5918972 AAAAACACGAAAATTTTTGAAACACGAAAATAAAAA
1 AAAAACACGAAAATTTTTGAAACACGAGAAT-TTTT
* *
5919008 AAAAACACGAAAATCTTTAAAACAC-A-ACATTTTT
1 AAAAACACGAAAATTTTTGAAACACGAGA-ATTTTT
** * * * *
5919042 TGAAACAAGAGAA-TTTTAAAACA-TAGAAATTTTT
1 AAAAACACGAAAATTTTTGAAACACGAG-AATTTTT
* * * **
5919076 -AAAACACGAAAATTTGTGAAACACTAGAGTCGTT
1 AAAAACACGAAAATTTTTGAAACACGAGAATTTTT
* * *
5919110 GAAAACACGAAAATTTGTGAAAACACGAAAATTTTT
1 AAAAACACGAAAATTTTTG-AAACACGAGAATTTTT
* * * * * *
5919146 -GAAACATGGAAATTTCTGAAAACACGAGGATTTTC
1 AAAAACACGAAAATTTTTG-AAACACGAGAATTTTT
** * *
5919181 AAAATACA--AATTTTTTTGAAAATACGAAAATTTTT
1 AAAA-ACACGAAAATTTTTG-AAACACGAGAATTTTT
* *
5919216 AAAAACAC-AGAAATTTTTAAAATAC-ATGAATTTTT
1 AAAAACACGA-AAATTTTTGAAACACGA-GAATTTTT
5919251 GAAACATGGG
Statistics
Matches: 215, Mismatches: 50, Indels: 28
0.73 0.17 0.10
Matches are distributed among these distances:
33 19 0.09
34 32 0.15
35 119 0.55
36 42 0.20
37 3 0.01
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (35 bp):
AAAAACACGAAAATTTTTGAAACACGAGAATTTTT
Found at i:5919331 original size:18 final size:19
Alignment explanation
Indices: 5919303--5919350 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
5919293 ACACTGAAAA
5919303 TTTGAAAACAC-GAAGATTT
1 TTTGAAAACACGGAA-ATTT
5919322 TTTG-AAACACGGAAATTT
1 TTTGAAAACACGGAAATTT
*
5919340 TTTAAAAACAC
1 TTTGAAAACAC
5919351 AAAAAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (19 bp):
TTTGAAAACACGGAAATTT
Found at i:5919826 original size:10 final size:10
Alignment explanation
Indices: 5919799--5919859 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
5919789 TGCCTTATTT
*
5919799 ATTAAAATTA
1 ATTAAAATAA
* *
5919809 TTTGAAATAA
1 ATTAAAATAA
*
5919819 AATAAAATAGA
1 ATTAAAATA-A
*
5919830 ATTTAAATTAA
1 A-TTAAAATAA
*
5919841 ATTAAATTAA
1 ATTAAAATAA
5919851 ATTAAAATA
1 ATTAAAATA
5919860 TATAAATACA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
10 30 0.75
11 4 0.10
12 6 0.15
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (10 bp):
ATTAAAATAA
Found at i:5919840 original size:5 final size:5
Alignment explanation
Indices: 5919832--5919856 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5919822 AAAATAGAAT
5919832 TTAAA TTAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA
5919857 ATATATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:5920036 original size:15 final size:15
Alignment explanation
Indices: 5920016--5920072 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
5920006 TAAATCCCCC
5920016 TTTCTTTTCTCTTTT
1 TTTCTTTTCTCTTTT
5920031 TTTC-TTTCT-TTTT
1 TTTCTTTTCTCTTTT
* *
5920044 TTTTTCTTTCTTTTTCT
1 TTTCT-TTTCTCTTT-T
*
5920061 TTTTTTTTCTCT
1 TTTCTTTTCTCT
5920073 CTGCTGGGCC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
13 7 0.19
14 5 0.14
15 9 0.25
16 9 0.25
17 6 0.17
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTCTTTTCTCTTTT
Found at i:5920039 original size:19 final size:18
Alignment explanation
Indices: 5920015--5920066 Score: 74
Period size: 15 Copynumber: 3.0 Consensus size: 18
5920005 TTAAATCCCC
5920015 CTTTCTTTTCTCTTTTTTT
1 CTTTCTTTT-TCTTTTTTT
5920034 CTTTC--TTT-TTTTTTT
1 CTTTCTTTTTCTTTTTTT
5920049 CTTTCTTTTTCTTTTTTT
1 CTTTCTTTTTCTTTTTTT
5920067 TTCTCTCTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 5 0.17
18 7 0.23
19 5 0.17
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (18 bp):
CTTTCTTTTTCTTTTTTT
Found at i:5920057 original size:25 final size:24
Alignment explanation
Indices: 5920020--5920068 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
5920010 TCCCCCTTTC
5920020 TTTTCTCTTTTTTTCTTTCTTTTTT
1 TTTTCTCTTTTTTTCTTT-TTTTTT
5920045 TTTTCT-TTCTTTTTCTTTTTTTTT
1 TTTTCTCTT-TTTTTCTTTTTTTTT
5920069 CTCTCTGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (24 bp):
TTTTCTCTTTTTTTCTTTTTTTTT
Found at i:5920067 original size:19 final size:18
Alignment explanation
Indices: 5920015--5920067 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
5920005 TTAAATCCCC
5920015 CTTTCTTTTCTCTTTTTTT
1 CTTTCTTTTCT-TTTTTTT
5920034 CTTTC--TT-TTTTTTTT
1 CTTTCTTTTCTTTTTTTT
5920049 CTTTCTTTTTCTTTTTTTT
1 CTTTC-TTTTCTTTTTTTT
5920068 TCTCTCTGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 2 0.07
18 2 0.07
19 13 0.43
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (18 bp):
CTTTCTTTTCTTTTTTTT
Found at i:5920379 original size:11 final size:11
Alignment explanation
Indices: 5920313--5920403 Score: 73
Period size: 10 Copynumber: 8.0 Consensus size: 11
5920303 AAAAGGTAAT
5920313 TTTC-TTCTT-
1 TTTCTTTCTTC
*
5920322 TTTTTTTCTT-
1 TTTCTTTCTTC
5920332 TTTCTTTCTTC
1 TTTCTTTCTTC
5920343 TTCCTCTATTCTTC
1 TT--TCT-TTCTTC
*
5920357 TTTCCTTCTTC
1 TTTCTTTCTTC
5920368 TTTCTTTATTCTTC
1 TTTC--T-TTCTTC
5920382 TTT-TTTCTTCC
1 TTTCTTTCTT-C
5920393 TTTCTTTCTTC
1 TTTCTTTCTTC
5920404 CCCGATCAGC
Statistics
Matches: 68, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
9 3 0.04
10 19 0.28
11 18 0.26
12 8 0.12
13 3 0.04
14 17 0.25
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTCTTTCTTC
Found at i:5920395 original size:25 final size:25
Alignment explanation
Indices: 5920313--5920399 Score: 108
Period size: 25 Copynumber: 3.6 Consensus size: 25
5920303 AAAAGGTAAT
*
5920313 TTTCTTCTTT-TTTTTTCTT-TTTC
1 TTTCTTCTTTCTTTATTCTTCTTTC
* *
5920336 TTTCTTCTTCCTCTATTCTTCTTTC
1 TTTCTTCTTTCTTTATTCTTCTTTC
*
5920361 CTTCTTCTTTCTTTATTCTTCTTT-
1 TTTCTTCTTTCTTTATTCTTCTTTC
5920385 TTTCTTCCTTTCTTT
1 TTTCTT-CTTTCTTT
5920400 CTTCCCCGAT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
23 9 0.17
24 12 0.22
25 33 0.61
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTCTTCTTTCTTTATTCTTCTTTC
Found at i:5920709 original size:18 final size:18
Alignment explanation
Indices: 5920686--5920722 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5920676 CTTTTTTGCC
5920686 TAAAAAATTTGTGTTTTT
1 TAAAAAATTTGTGTTTTT
5920704 TAAAAAATTTGTGTTTTT
1 TAAAAAATTTGTGTTTTT
5920722 T
1 T
5920723 CTTTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (18 bp):
TAAAAAATTTGTGTTTTT
Found at i:5921669 original size:76 final size:74
Alignment explanation
Indices: 5921572--5922682 Score: 991
Period size: 75 Copynumber: 14.6 Consensus size: 74
5921562 GATTCGAAGT
* * * * *
5921572 TCAACTCACTTTTCAG-GTTATGAGTTGA-TCTTTAAAAAATAGAAATTGAAAAATACCTC-GGT
1 TCAACTCACTTCTC-GCATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAAATACCTCAGG-
*
5921634 ATATAGCCCACGGC
64 AT-GA-CCCA-GGC
* ** *
5921648 TCAACTCACCTCTCGCATTATGAGTTGAATGATTTTTTTTAAGA-AGAAATT-AAAAATACCTC-
1 TCAACTCACTTCTCGCATTATGAG-T---TGATTTTTTGAAAAACAGAAATTGAAAAATACCTCA
*
5921710 GGCATGCAGCTCGAGGC
62 GG-ATG-A-C-CCAGGC
* * * * ** *
5921727 TCAACTCACCTCTCGCAATATGAGTT-ATTTTTTTGAAAAACATAAATTGAAAAAAGAAAATCGG
1 TCAACTCACTTCTCGCATTATGAGTTGA-TTTTTTGAAAAACAGAAATTG-AAAAA-TACCTCAG
* *
5921791 CGTGTGACTCGAGAGC
63 -G-ATGAC-CCAG-GC
* * * * * *
5921807 -CAACTCACCTCTAGCAATATGAGTTGA-TTTTTGGAAAATAGAAATT-AAAATATACCTCAGTA
1 TCAACTCACTTCTCGCATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAA-ATACCTCAGGA
*
5921869 TGTGACCTGAGGC
65 --TGACC-CAGGC
* *
5921882 TCAACTCACTTCTCACATTATGAGTTTATCTTTTTGAAAAACAGAAATTGAAAAATACCTCAGGA
1 TCAACTCACTTCTCGCATTATGAGTTGAT-TTTTTGAAAAACAGAAATTGAAAAATACCTCAGGA
5921947 TGACCCGAGGC
65 TGACCC-AGGC
* * * * *
5921958 TCAACTCACTTCTCGCAATATTAGTTGATTTTTTTGAAAAACATAAATTG-ATAATACCTTAGGA
1 TCAACTCACTTCTCGCATTATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAAAATACCTCAGGA
5922022 TGACCCGAGGC
65 TGACCC-AGGC
* *
5922033 TCAACTCACTTCTCGCATTATGAGTTGATTTTTTTTAAAAAAACAAAAATT-AAAAATACCTCAG
1 TCAACTCACTTCTCGCATTATGAGTTGA--TTTTTT-GAAAAACAGAAATTGAAAAATACCTCAG
* *
5922097 GATGACCTGAGGT
63 GATGACC-CAGGC
* * * *
5922110 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAGAACATAGATTG-AAAATACCTCAGGA
1 TCAACTCACTTCTCGCATTATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAAAATACCTCAGGA
*
5922174 TGACCTGAGGC
65 TGACC-CAGGC
5922185 TCAACTCACTTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTG-AAAATACCTCAGGA
1 TCAACTCACTTCTCGCATTATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAAAATACCTCAGGA
5922249 TGACCCGAGGC
65 TGACCC-AGGC
* * * * * *
5922260 TTAACTTACTTTTCGCAATATGAGTTGATTTTTTTTTAAAAACATAAATTG-AAAATACCTCAGG
1 TCAACTCACTTCTCGCATTATGAGTTGA--TTTTTTGAAAAACAGAAATTGAAAAATACCTCAGG
5922324 ATGACCCGAGGC
64 ATGACCC-AGGC
*
5922336 TCAACTCACTTCTCGCATTATGAGTTGATTTTTTTTGAAAAACATAAATTG-AAAATACCTCAGG
1 TCAACTCACTTCTCGCATTATGAGTTGA--TTTTTTGAAAAACAGAAATTGAAAAATACCTCAGG
5922400 ATGACCCGAGGC
64 ATGACCC-AGGC
* * *
5922412 TCAACTCACTTCTCGTATTATAAGTTGATTTTTTTGAAAAACATAAATTG-AAAATACCTCAGGA
1 TCAACTCACTTCTCGCATTATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAAAATACCTCAGGA
* *
5922476 TGACCTGAGGT
65 TGACC-CAGGC
* * *
5922487 TCTACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAACAGAAAATGAAAAATACCTCAGGAT
1 TCAACTCACTTCTCGCATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAAATACCTCAGGAT
* *
5922552 CACCCGGGGC
66 GACCC-AGGC
* * * * * *
5922562 TTAACTTACGTCTCGCAATATGAGTTTA-TTTTTGAAAAAAAATAGAAATTGAAAAATACCTCGA
1 TCAACTCACTTCTCGCATTATGAGTTGATTTTTTG---AAAAACAGAAATTGAAAAATACCTC-A
*
5922626 CGTG-CGACCCGAGGC
62 -G-GATGACCC-AGGC
* * *
5922641 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAACA
1 TCAACTCACTTCTCGCATTATGAGTTGATTTTTTGAAAAACA
5922683 ACAAATAAAA
Statistics
Matches: 884, Mismatches: 107, Indels: 87
0.82 0.10 0.08
Matches are distributed among these distances:
74 26 0.03
75 300 0.34
76 270 0.31
77 91 0.10
78 50 0.06
79 114 0.13
80 23 0.03
81 10 0.01
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.31
Consensus pattern (74 bp):
TCAACTCACTTCTCGCATTATGAGTTGATTTTTTGAAAAACAGAAATTGAAAAATACCTCAGGAT
GACCCAGGC
Found at i:5922014 original size:75 final size:75
Alignment explanation
Indices: 5921807--5922682 Score: 1091
Period size: 75 Copynumber: 11.6 Consensus size: 75
5921797 ACTCGAGAGC
* * * * * * * *
5921807 CAACTCACCTCTAGCAATATGAGTTGA--TTTTTGGAAAATAGAAATTAAAATATACCTCAGTAT
1 CAACTCACTTCTCGCATTATGAGTTGATTTTTTTGAAAAACATAAATTGAAA-ATACCTCAGGA-
*
5921870 GTGACCTGAGGCT
64 -TGACCCGAGGCT
* * * *
5921883 CAACTCACTTCTCACATTATGAGTTTATCTTTTTGAAAAACAGAAATTGAAAAATACCTCAGGAT
1 CAACTCACTTCTCGCATTATGAGTTGATTTTTTTGAAAAACATAAATTG-AAAATACCTCAGGAT
5921948 GACCCGAGGCT
65 GACCCGAGGCT
* * * *
5921959 CAACTCACTTCTCGCAATATTAGTTGATTTTTTTGAAAAACATAAATTGATAATACCTTAGGATG
1 CAACTCACTTCTCGCATTATGAGTTGATTTTTTTGAAAAACATAAATTGAAAATACCTCAGGATG
5922024 ACCCGAGGCT
66 ACCCGAGGCT
* * *
5922034 CAACTCACTTCTCGCATTATGAGTTGATTTTTTTTAAAAAAACAAAAATTAAAAATACCTCAGGA
1 CAACTCACTTCTCGCATTATGAGTTGA-TTTTTTT-GAAAAACATAAATTGAAAATACCTCAGGA
* *
5922099 TGACCTGAGGTT
64 TGACCCGAGGCT
* * *
5922111 CAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAGAACATAGATTGAAAATACCTCAGGATG
1 CAACTCACTTCTCGCATTATGAGTTGATTTTTTTGAAAAACATAAATTGAAAATACCTCAGGATG
*
5922176 ACCTGAGGCT
66 ACCCGAGGCT
*
5922186 CAACTCACTTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGGATG
1 CAACTCACTTCTCGCATTATGAGTTGATTTTTTTGAAAAACATAAATTGAAAATACCTCAGGATG
5922251 ACCCGAGGCT
66 ACCCGAGGCT
* * * * *
5922261 TAACTTACTTTTCGCAATATGAGTTGATTTTTTTTTAAAAACATAAATTGAAAATACCTCAGGAT
1 CAACTCACTTCTCGCATTATGAGTTGA-TTTTTTTGAAAAACATAAATTGAAAATACCTCAGGAT
5922326 GACCCGAGGCT
65 GACCCGAGGCT
5922337 CAACTCACTTCTCGCATTATGAGTTGATTTTTTTTGAAAAACATAAATTGAAAATACCTCAGGAT
1 CAACTCACTTCTCGCATTATGAGTTGA-TTTTTTTGAAAAACATAAATTGAAAATACCTCAGGAT
5922402 GACCCGAGGCT
65 GACCCGAGGCT
* *
5922413 CAACTCACTTCTCGTATTATAAGTTGATTTTTTTGAAAAACATAAATTGAAAATACCTCAGGATG
1 CAACTCACTTCTCGCATTATGAGTTGATTTTTTTGAAAAACATAAATTGAAAATACCTCAGGATG
* *
5922478 ACCTGAGGTT
66 ACCCGAGGCT
* * * *
5922488 CTACTCACCTCTCGCATTATGAGTTGA-TTTTTTGAAAAACAGAAAATGAAAAATACCTCAGGAT
1 CAACTCACTTCTCGCATTATGAGTTGATTTTTTTGAAAAACATAAATTG-AAAATACCTCAGGAT
* *
5922552 CACCCGGGGCT
65 GACCCGAGGCT
* * * * * *
5922563 TAACTTACGTCTCGCAATATGAGTT--TATTTTTGAAAAAAAATAGAAATTGAAAAATACCTCGA
1 CAACTCACTTCTCGCATTATGAGTTGATTTTTTTG-AAAAACAT--AAATTG-AAAATACCTC-A
*
5922626 CGTG-CGACCCGAGGCT
61 -G-GATGACCCGAGGCT
* * *
5922642 CAACTCACCTCTCGCAATATGAGTTGA-TTTTTTAAAAAACA
1 CAACTCACTTCTCGCATTATGAGTTGATTTTTTTGAAAAACA
5922683 ACAAATAAAA
Statistics
Matches: 702, Mismatches: 82, Indels: 29
0.86 0.10 0.04
Matches are distributed among these distances:
74 25 0.04
75 294 0.42
76 232 0.33
77 76 0.11
78 28 0.04
79 41 0.06
80 6 0.01
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (75 bp):
CAACTCACTTCTCGCATTATGAGTTGATTTTTTTGAAAAACATAAATTGAAAATACCTCAGGATG
ACCCGAGGCT
Found at i:5922186 original size:227 final size:224
Alignment explanation
Indices: 5921645--5922682 Score: 1167
Period size: 227 Copynumber: 4.5 Consensus size: 224
5921635 TATAGCCCAC
** * * *
5921645 GGCTCAACTCACCTCTCGCATTATGAGTTGAATGATTTTTTTTAAGA-AGAAATTAAAAATACCT
1 GGCTCAACTCACCTCTCGCATTATGAGTTG-AT--TTTTTTGAAAAACATAAATTGAAAATACCT
* *
5921709 C-GGCATGCAGCTCGAGGCTCAACTCACCTCTCGCAATATGAGTT-ATTTTTTTGAAAAACATAA
63 CAGG-ATG-A-CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAAACATAA
* ** * * * *
5921772 ATTGAAAAAAGAAAATCGGCGTGTGACTCGAGAGC-CAACTCACCTCTAGCAATATGAGTTGA-T
125 ATTG--AAAA-TACCTCAG-G-ATGACCCGAG-GCTCAACTCACCTCTCGCAATATGAGTTGATT
* * * * *
5921835 TTTTGGAAAATAGAAATTAAAATATACCTCAGTATGTGACCTGA
184 TTTTGAAAAACAAAAATTAAAA-ATACCTCAGGA--TGACCCGA
* * * * *
5921879 GGCTCAACTCACTTCTCACATTATGAGTTTATCTTTTTGAAAAACAGAAATTGAAAAATACCTCA
1 GGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACATAAATTG-AAAATACCTCA
*
5921944 GGATGACCCGAGGCTCAACTCACTTCTCGCAATATTAGTTGATTTTTTTGAAAAACATAAATTGA
65 GGATGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAAACATAAATTGA
* * * * *
5922009 TAATACCTTAGGATGACCCGAGGCTCAACTCACTTCTCGCATTATGAGTTGATTTTTTTTAAAAA
130 AAATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTT-GAAA
*
5922074 AACAAAAATTAAAAATACCTCAGGATGACCTGA
192 AACAAAAATTAAAAATACCTCAGGATGACCCGA
* * *
5922107 GGTTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAGAACATAGATTGAAAATACCTCAG
1 GGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACATAAATTGAAAATACCTCAG
* * *
5922172 GATGACCTGAGGCTCAACTCACTTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAA
66 GATGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAAACATAAATTGAA
* * * * *
5922237 AATACCTCAGGATGACCCGAGGCTTAACTTACTTTTCGCAATATGAGTTGATTTTTTTTTAAAAA
131 AATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTGAAAAA
* *
5922302 CATAAATTGAAAATACCTCAGGATGACCCGA
194 CAAAAATTAAAAATACCTCAGGATGACCCGA
*
5922333 GGCTCAACTCACTTCTCGCATTATGAGTTGATTTTTTTTGAAAAACATAAATTGAAAATACCTCA
1 GGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTTTTGAAAAACATAAATTGAAAATACCTCA
* * *
5922398 GGATGACCCGAGGCTCAACTCACTTCTCGTATTATAAGTTGATTTTTTTGAAAAACATAAATTGA
65 GGATGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAAACATAAATTGA
* * * *
5922463 AAATACCTCAGGATGACCTGAGGTTCTACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAC
130 AAATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAC
* * *
5922528 AGAAAATGAAAAATACCTCAGGATCACCCGG
195 A-AAAATTAAAAATACCTCAGGATGACCCGA
* * * * * *
5922559 GGCTTAACTTACGTCTCGCAATATGAGTT--TATTTTTGAAAAAAAATAGAAATTGAAAAATACC
1 GGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTG-AAAAACAT--AAATTG-AAAATACC
* * *
5922622 TCGACGTG-CGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTAAAAAACA
62 TC-A-G-GATGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAAACA
5922683 ACAAATAAAA
Statistics
Matches: 703, Mismatches: 83, Indels: 42
0.85 0.10 0.05
Matches are distributed among these distances:
223 7 0.01
224 7 0.01
225 13 0.02
226 119 0.17
227 304 0.43
228 68 0.10
229 38 0.05
230 19 0.03
231 53 0.08
232 31 0.04
233 15 0.02
234 29 0.04
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (224 bp):
GGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACATAAATTGAAAATACCTCAG
GATGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAAAACATAAATTGAA
AATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACA
AAAATTAAAAATACCTCAGGATGACCCGA
Found at i:5922479 original size:302 final size:303
Alignment explanation
Indices: 5921572--5922674 Score: 1268
Period size: 302 Copynumber: 3.6 Consensus size: 303
5921562 GATTCGAAGT
* * * * *
5921572 TCAACTCACTTTTCAG-GTTATGAGTTGA--TCTTTAAAAAATAGAAATTGAAAAATACCTC-GG
1 TCAACTCACTTCTC-GCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGG
* * * * * *
5921633 TATATAGCCC-ACGGCTCAACTCACCTCTCGCATTATGAGTTGAATGATTTTTTTT-AAGA-AGA
65 -AT-GA-CCCGA-GGCTTAACTTACTTCTCGCAATATGAGTTG-AT--TTTTTTTTAAAAACAGA
* *
5921695 AATTAAAAATACCTC-GGCATGCAGCTCGAGGCTCAACTCACCTCTCGCAATATGAGTT-A-TTT
123 AATTGAAAATACCTCAGG-ATG-A-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
* ** * * * *
5921757 TTTTGAAAAACATAAATTGAAAAAAGAAAATCGGCGTGTGACTCGAGAGC-CAACTCACCTCTAG
185 TTTTGAAAAACATAAATTG--AAAA-TACCTCAG-G-ATGACCCGAG-GCTCAACTCACCTCTCG
* * * * * *
5921821 CAATATGAGTTGA--TTTTTGGAAAATAGAAATTAAAATATACCTCAGTATGTGACCTGAGGC
244 CATTATGAGTTGATTTTTTTGAAAAACATAAATTGAAA-ATACCTCAGGA--TGACCTGAGGC
* * *
5921882 TCAACTCACTTCTCACATTATGAGTTTATCTTTTTGAAAAACAGAAATTGAAAAATACCTCAGGA
1 TCAACTCACTTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGGA
* * * * * *
5921947 TGACCCGAGGCTCAACTCACTTCTCGCAATATTAGTTGA-TTTTTTTGAAAAACATAAATTGATA
66 TGACCCGAGGCTTAACTTACTTCTCGCAATATGAGTTGATTTTTTTTTAAAAACAGAAATTGAAA
* * * *
5922011 ATACCTTAGGATGACCCGAGGCTCAACTCACTTCTCGCATTATGAGTTGATTTTTTTTAAAAAAA
131 ATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTT-GAAAAA
* * * *
5922076 CAAAAATTAAAAATACCTCAGGATGACCTGAGGTTCAACTCACCTCTCGCATTATGAGTTGATTT
195 CATAAATTGAAAATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTT
* *
5922141 TTTTGAAGAACATAGATTGAAAATACCTCAGGATGACCTGAGGC
260 TTTTGAAAAACATAAATTGAAAATACCTCAGGATGACCTGAGGC
5922185 TCAACTCACTTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTG-AAAATACCTCAGGA
1 TCAACTCACTTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGGA
* *
5922249 TGACCCGAGGCTTAACTTACTTTTCGCAATATGAGTTGATTTTTTTTTAAAAACATAAATTGAAA
66 TGACCCGAGGCTTAACTTACTTCTCGCAATATGAGTTGATTTTTTTTTAAAAACAGAAATTGAAA
* *
5922314 ATACCTCAGGATGACCCGAGGCTCAACTCACTTCTCGCATTATGAGTTGATTTTTTTTGAAAAAC
131 ATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAAC
* * *
5922379 ATAAATTGAAAATACCTCAGGATGACCCGAGGCTCAACTCACTTCTCGTATTATAAGTTGATTTT
196 ATAAATTGAAAATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTT
*
5922444 TTTGAAAAACATAAATTGAAAATACCTCAGGATGACCTGAGGT
261 TTTGAAAAACATAAATTGAAAATACCTCAGGATGACCTGAGGC
* * *
5922487 TCTACTCACCTCTCGCATTATGAGTTGA-TTTTTTGAAAAACAGAAAATGAAAAATACCTCAGGA
1 TCAACTCACTTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGGA
* * * * **** *
5922551 TCACCCGGGGCTTAACTTACGTCTCGCAATATGAGTTTATTTTTGAAAAAAAATAGAAATTGAAA
66 TGACCCGAGGCTTAACTTACTTCTCGCAATATGAGTTGATTTTTTTTTAAAAACAGAAATTG-AA
*
5922616 AATACCTCGACGTG-CGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
130 AATACCTC-A-G-GATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
5922675 AAAAAACAAC
Statistics
Matches: 695, Mismatches: 78, Indels: 45
0.85 0.10 0.06
Matches are distributed among these distances:
301 20 0.03
302 244 0.35
303 149 0.21
304 33 0.05
305 54 0.08
306 60 0.09
307 9 0.01
308 24 0.03
309 15 0.02
310 53 0.08
311 2 0.00
312 30 0.04
313 2 0.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (303 bp):
TCAACTCACTTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGGA
TGACCCGAGGCTTAACTTACTTCTCGCAATATGAGTTGATTTTTTTTTAAAAACAGAAATTGAAA
ATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAAC
ATAAATTGAAAATACCTCAGGATGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTT
TTTGAAAAACATAAATTGAAAATACCTCAGGATGACCTGAGGC
Found at i:5923583 original size:17 final size:16
Alignment explanation
Indices: 5923561--5923617 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 16
5923551 TTATCTTGAT
5923561 TTTTTTGTTTGTTTTTG
1 TTTTTTGTTT-TTTTTG
* *
5923578 TTTTTTGTTTCTTTCTA
1 TTTTTTGTTT-TTTTTG
5923595 TTTTTTGTTTTTTTTG
1 TTTTTTGTTTTTTTTG
5923611 TTGTTTT
1 TT-TTTT
5923618 TAGGCATAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
16 6 0.18
17 28 0.82
ACGTcount: A:0.02, C:0.04, G:0.12, T:0.82
Consensus pattern (16 bp):
TTTTTTGTTTTTTTTG
Found at i:5927549 original size:4 final size:4
Alignment explanation
Indices: 5927540--5927564 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5927530 ATGTACATGC
5927540 AATG AATG AATG AATG AATG AATG A
1 AATG AATG AATG AATG AATG AATG A
5927565 CCAATGGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AATG
Found at i:5929179 original size:35 final size:34
Alignment explanation
Indices: 5929140--5929591 Score: 198
Period size: 35 Copynumber: 12.9 Consensus size: 34
5929130 AATTTATTTT
* *
5929140 AACACGAGAA-TTTTGAAACATGA-ATTTTTTTAAAA
1 AACACGA-AATTTTTGAAACACGAGA-ATTTTT-AAA
5929175 AACACGAAAGTTTTTGAAACACGAGAATTTTTAAA
1 AACACGAAA-TTTTTGAAACACGAGAATTTTTAAA
* ***
5929210 AACACGAAAATTTTTGAAACACGA-AAATAAAAAA
1 AACACG-AAATTTTTGAAACACGAGAATTTTTAAA
* * **
5929244 AACACGAAAATCTTTAAAACAC-A-ACATTTTTTGA
1 AACACG-AAATTTTTGAAACACGAGA-ATTTTTAAA
* *
5929278 AACACGAGAA-TTTTAAAACA-TAGAAATTTTT-AA
1 AACACGA-AATTTTTGAAACACGAG-AATTTTTAAA
* * * ** *
5929311 AACACGAAAATTTGTGAAACACTAGAGTCGTTGAA
1 AACACG-AAATTTTTGAAACACGAGAATTTTTAAA
* * *
5929346 AACACGAAAATTTGTGAAAACACGAAAATTTTT-GA
1 AACACG-AAATTTTTG-AAACACGAGAATTTTTAAA
*
5929381 AACACGGAAATTTTTGAAAACACGAGAA-TTTTCAA
1 AACAC-GAAATTTTTG-AAACACGAGAATTTTTAAA
* * * *
5929416 AATACGAATTTTTTTGAAAATACGAAAATTTTTAAA
1 AACACGAA-ATTTTTG-AAACACGAGAATTTTTAAA
* * *
5929452 AACACGGAAATTTTTAAAATAC-AGGAATTTTT-GA
1 AACAC-GAAATTTTTGAAACACGA-GAATTTTTAAA
* * * * *
5929486 AACATTGGAAAAGTTTTTTTAAA-ACGTGAAAGTTTT-GA
1 AACA--CG-AAA--TTTTTGAAACACGAG-AATTTTTAAA
* *
5929524 AACACTGGAA-TTTTGAAAACACGA-AGATTTTTGAA
1 AACAC-GAAATTTTTG-AAACACGAGA-ATTTTTAAA
*
5929559 AACACAAAAATTTTTTGAAACACGAGAATTTTT
1 AACAC-GAAA-TTTTTGAAACACGAGAATTTTT
5929592 TGAAAACATG
Statistics
Matches: 329, Mismatches: 53, Indels: 69
0.73 0.12 0.15
Matches are distributed among these distances:
33 27 0.08
34 79 0.24
35 123 0.37
36 66 0.20
37 14 0.04
38 20 0.06
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.30
Consensus pattern (34 bp):
AACACGAAATTTTTGAAACACGAGAATTTTTAAA
Found at i:5929206 original size:18 final size:18
Alignment explanation
Indices: 5929120--5929596 Score: 204
Period size: 17 Copynumber: 27.2 Consensus size: 18
5929110 GATCTGATCA
*
5929120 AAACACGAGAAATTTATTT
1 AAACACGAGAAATTT-TTG
*
5929139 TAACACGAG-AA-TTTTG
1 AAACACGAGAAATTTTTG
* ** *
5929155 AAACATGA-ATTTTTTTAAA
1 AAACACGAGAAATTTTT--G
*
5929174 AAACACGA-AAGTTTTTG
1 AAACACGAGAAATTTTTG
*
5929191 AAACACGAG-AATTTTTAA
1 AAACACGAGAAATTTTT-G
5929209 AAACACGA-AAATTTTTG
1 AAACACGAGAAATTTTTG
*****
5929226 AAACACGA-AAATAAAAA
1 AAACACGAGAAATTTTTG
* *
5929243 AAACACGA-AAATCTTTA
1 AAACACGAGAAATTTTTG
*
5929260 AAACAC-A-ACATTTTTTG
1 AAACACGAGA-AATTTTTG
*
5929277 AAACACGAG-AA-TTTTA
1 AAACACGAGAAATTTTTG
* *
5929293 AAACA-TAGAAATTTTTA
1 AAACACGAGAAATTTTTG
*
5929310 AAACACGA-AAATTTGTG
1 AAACACGAGAAATTTTTG
* * **
5929327 AAACACTAG-AGTCGTTG
1 AAACACGAGAAATTTTTG
*
5929344 AAAACACGA-AAATTTGTG
1 -AAACACGAGAAATTTTTG
5929362 AAAACACGA-AAATTTTTG
1 -AAACACGAGAAATTTTTG
5929380 AAACACG-GAAATTTTTG
1 AAACACGAGAAATTTTTG
**
5929397 AAAACACGAG-AATTTTCA
1 -AAACACGAGAAATTTTTG
* **
5929415 AAATACGA-ATTTTTTTG
1 AAACACGAGAAATTTTTG
* *
5929432 AAAATACGA-AAATTTTTAA
1 -AAACACGAGAAATTTTT-G
*
5929451 AAACACG-GAAATTTTTA
1 AAACACGAGAAATTTTTG
* *
5929468 AAATAC-AGGAATTTTTG
1 AAACACGAGAAATTTTTG
* *
5929485 AAACATTG-GAAAAGTTTTTTT
1 AAACA-CGAG-AAA--TTTTTG
* *
5929506 AAA-ACGTGAAAGTTTTG
1 AAACACGAGAAATTTTTG
5929523 AAACACTG-G-AA-TTTTG
1 AAACAC-GAGAAATTTTTG
*
5929539 AAAACACGA-AGATTTTTG
1 -AAACACGAGAAATTTTTG
*
5929557 AAAACAC-AAAAATTTTTTG
1 -AAACACGAGAAA-TTTTTG
*
5929576 AAACACGAGAATTTTTTG
1 AAACACGAGAAATTTTTG
5929594 AAA
1 AAA
5929597 ACATGATAAT
Statistics
Matches: 351, Mismatches: 68, Indels: 79
0.70 0.14 0.16
Matches are distributed among these distances:
15 2 0.01
16 27 0.08
17 153 0.44
18 121 0.34
19 38 0.11
20 2 0.01
21 8 0.02
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.30
Consensus pattern (18 bp):
AAACACGAGAAATTTTTG
Found at i:5929806 original size:14 final size:13
Alignment explanation
Indices: 5929787--5929854 Score: 58
Period size: 11 Copynumber: 5.5 Consensus size: 13
5929777 TTTTTTTTTC
5929787 TTTCTTCTTCCTCT
1 TTTCTTCTT-CTCT
5929801 TTTCTTCTT-TC-
1 TTTCTTCTTCTCT
*
5929812 CTTCTTCTT-TCT
1 TTTCTTCTTCTCT
*
5929824 TTT-TTCTTCTTT
1 TTTCTTCTTCTCT
5929836 TTTCTTCCTT-TC-
1 TTTCTT-CTTCTCT
5929848 TTTCTTC
1 TTTCTTC
5929855 CCCGATCAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
11 16 0.35
12 15 0.33
13 3 0.07
14 12 0.26
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTCTTCTTCTCT
Found at i:5929831 original size:36 final size:36
Alignment explanation
Indices: 5929783--5929854 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
5929773 TTCTTTTTTT
5929783 TTTCTTTCTTCTTCCTCTTTTCTT-CTTTCCTTCTTC
1 TTTCTTTCTTCTT-CTCTTTTCTTCCTTTCCTTCTTC
* * *
5929819 TTTCTTTTTTCTTCTTTTTTCTTCCTTTCTTTCTTC
1 TTTCTTTCTTCTTCTCTTTTCTTCCTTTCCTTCTTC
5929855 CCCGATCAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 9 0.28
36 23 0.72
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (36 bp):
TTTCTTTCTTCTTCTCTTTTCTTCCTTTCCTTCTTC
Found at i:5929846 original size:25 final size:24
Alignment explanation
Indices: 5929773--5929850 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 24
5929763 TCAAAGAAGG
*
5929773 TTCTTTTTT-TT-TTCTTTCTTCT
1 TTCTTTTTTCTTCTTTTTTCTTCT
* * *
5929795 TCCTCTTTTCTTCTTTCCTTCTTCT
1 TTCTTTTTTCTTCTTT-TTTCTTCT
5929820 TTCTTTTTTCTTCTTTTTTCTTCCT
1 TTCTTTTTTCTTCTTTTTTCTT-CT
5929845 TTCTTT
1 TTCTTT
5929851 CTTCCCCGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
22 7 0.16
23 2 0.04
24 7 0.16
25 29 0.64
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (24 bp):
TTCTTTTTTCTTCTTTTTTCTTCT
Found at i:5930880 original size:34 final size:35
Alignment explanation
Indices: 5930821--5930886 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 35
5930811 AAACACCAGG
*
5930821 AAATATTTTCCAGTAGATCATTTTACAGAAAAGTA
1 AAATATTTTCCAGTAAATCATTTTACAGAAAAGTA
* *
5930856 AAATATTTTCTAG-AAATCATTTTACGGAAAA
1 AAATATTTTCCAGTAAATCATTTTACAGAAAA
5930887 TATTTTACTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.35
Consensus pattern (35 bp):
AAATATTTTCCAGTAAATCATTTTACAGAAAAGTA
Found at i:5937485 original size:20 final size:21
Alignment explanation
Indices: 5937452--5937492 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5937442 AAGAAATTTG
*
5937452 TCTAATATGATAAAAA-ATAT
1 TCTAAAATGATAAAAATATAT
*
5937472 TCTAAAATGTTAAAAATATAT
1 TCTAAAATGATAAAAATATAT
5937493 ATGTTTGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (21 bp):
TCTAAAATGATAAAAATATAT
Found at i:5940896 original size:13 final size:13
Alignment explanation
Indices: 5940880--5940904 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5940870 CAAATATTCA
5940880 ACCCAACCCAATT
1 ACCCAACCCAATT
5940893 ACCCAACCCAAT
1 ACCCAACCCAAT
5940905 CATAAAAATT
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:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:5941015 original size:9 final size:9
Alignment explanation
Indices: 5941001--5941094 Score: 118
Period size: 9 Copynumber: 10.4 Consensus size: 9
5940991 GTAGTGATTC
5941001 AATTCGGTT
1 AATTCGGTT
*
5941010 AATTCGATT
1 AATTCGGTT
5941019 AATTCGAG-T
1 AATTCG-GTT
*
5941028 AATCCGGTT
1 AATTCGGTT
*
5941037 AATTCGGGT
1 AATTCGGTT
*
5941046 AATCCGGTT
1 AATTCGGTT
5941055 AATTCGGTT
1 AATTCGGTT
* *
5941064 AATTTGGGT
1 AATTCGGTT
5941073 AATTCGGTT
1 AATTCGGTT
5941082 AATTCGGTT
1 AATTCGGTT
5941091 AATT
1 AATT
5941095 TTTAACCAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
8 1 0.01
9 70 0.99
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:5942715 original size:111 final size:111
Alignment explanation
Indices: 5942521--5942743 Score: 446
Period size: 111 Copynumber: 2.0 Consensus size: 111
5942511 ACGAAAGGTG
5942521 TGTATTCTTTACGAAATGAATCGGGGCAAATTGTGTGTAAGTTTAAGGCCACACAGGCGCGTGGA
1 TGTATTCTTTACGAAATGAATCGGGGCAAATTGTGTGTAAGTTTAAGGCCACACAGGCGCGTGGA
5942586 CCACACAACCCCCTATGGCCATGTGCCATGCAAACCGTAATCTAGT
66 CCACACAACCCCCTATGGCCATGTGCCATGCAAACCGTAATCTAGT
5942632 TGTATTCTTTACGAAATGAATCGGGGCAAATTGTGTGTAAGTTTAAGGCCACACAGGCGCGTGGA
1 TGTATTCTTTACGAAATGAATCGGGGCAAATTGTGTGTAAGTTTAAGGCCACACAGGCGCGTGGA
5942697 CCACACAACCCCCTATGGCCATGTGCCATGCAAACCGTAATCTAGT
66 CCACACAACCCCCTATGGCCATGTGCCATGCAAACCGTAATCTAGT
5942743 T
1 T
5942744 CGTGAACCAT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 112 1.00
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (111 bp):
TGTATTCTTTACGAAATGAATCGGGGCAAATTGTGTGTAAGTTTAAGGCCACACAGGCGCGTGGA
CCACACAACCCCCTATGGCCATGTGCCATGCAAACCGTAATCTAGT
Found at i:5948508 original size:16 final size:17
Alignment explanation
Indices: 5948468--5948506 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5948458 TTCAAAATTT
5948468 AAATTTTAAAATTATAA
1 AAATTTTAAAATTATAA
*
5948485 AAAGTTTAAAA-TA-AA
1 AAATTTTAAAATTATAA
5948500 AAATTTT
1 AAATTTT
5948507 TATTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 8 0.40
16 2 0.10
17 10 0.50
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATTTTAAAATTATAA
Found at i:5956577 original size:19 final size:20
Alignment explanation
Indices: 5956553--5956592 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5956543 GTTGGTAAAT
5956553 ACATGTGTA-ATAATAATAA
1 ACATGTGTATATAATAATAA
*
5956572 ACATGTGTATTTAATAATAA
1 ACATGTGTATATAATAATAA
5956592 A
1 A
5956593 ATATGTATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (20 bp):
ACATGTGTATATAATAATAA
Found at i:5956588 original size:20 final size:20
Alignment explanation
Indices: 5956553--5956601 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
5956543 GTTGGTAAAT
*
5956553 ACATGTGTA-ATAATAATAA
1 ACATGTGTATTTAATAATAA
5956572 ACATGTGTATTTAATAATAA
1 ACATGTGTATTTAATAATAA
*
5956592 A-ATATGTATT
1 ACATGTGTATT
5956602 GCTTATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (20 bp):
ACATGTGTATTTAATAATAA
Found at i:5956599 original size:19 final size:20
Alignment explanation
Indices: 5956563--5956601 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5956553 ACATGTGTAA
*
5956563 TAATAATAAACATGTGTATT
1 TAATAATAAACATATGTATT
5956583 TAATAATAAA-ATATGTATT
1 TAATAATAAACATATGTATT
5956602 GCTTATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (20 bp):
TAATAATAAACATATGTATT
Found at i:5956738 original size:16 final size:15
Alignment explanation
Indices: 5956713--5956746 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
5956703 AAAACAGGGG
5956713 GAAAAAAGAAAGAAA
1 GAAAAAAGAAAGAAA
5956728 GAAAAAGAGAAAGAAA
1 GAAAAA-AGAAAGAAA
5956744 GAA
1 GAA
5956747 GGAGAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
GAAAAAAGAAAGAAA
Found at i:5959783 original size:33 final size:33
Alignment explanation
Indices: 5959746--5959817 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
5959736 TTGTTTAAGA
5959746 TTTAGATAAGGTTTAGGAAAAATTAAATTAGGG
1 TTTAGATAAGGTTTAGGAAAAATTAAATTAGGG
* *
5959779 TTTAGGTAGGGTTTAGGAAAAATTAAATTAGGG
1 TTTAGATAAGGTTTAGGAAAAATTAAATTAGGG
5959812 TATTAG
1 T-TTAG
5959818 GTTTTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 32 0.89
34 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.26, T:0.35
Consensus pattern (33 bp):
TTTAGATAAGGTTTAGGAAAAATTAAATTAGGG
Found at i:5959942 original size:30 final size:29
Alignment explanation
Indices: 5959871--5959954 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
5959861 TGCTTAGTAT
* *
5959871 TGTTCTGGAAAAAATAATTTTGTCAATATG
1 TGTTCT-GAAAAAATAAATTTGACAATATG
* *
5959901 AGTTCTGAAAAAATAAATTTGAC-GTAATG
1 TGTTCTGAAAAAATAAATTTGACAAT-ATG
* *
5959930 TGTTCTGAAAAAATTATTTTGACAA
1 TGTTCTGAAAAAATAAATTTGACAA
5959955 GATAATCTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
28 1 0.02
29 38 0.86
30 5 0.11
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.37
Consensus pattern (29 bp):
TGTTCTGAAAAAATAAATTTGACAATATG
Found at i:5961877 original size:31 final size:30
Alignment explanation
Indices: 5961829--5961890 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
5961819 GTGAAATTTA
**
5961829 ATCATTTTATTAAAATAATATTTTAATTAAT
1 ATCATTTTATTAAAATAA-ATAATAATTAAT
*
5961860 ATCATTTTCATT-TAATAAATAATAATTAAT
1 ATCATTTT-ATTAAAATAAATAATAATTAAT
5961890 A
1 A
5961891 GAATTGTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 11 0.41
31 13 0.48
32 3 0.11
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (30 bp):
ATCATTTTATTAAAATAAATAATAATTAAT
Found at i:5963235 original size:10 final size:9
Alignment explanation
Indices: 5963210--5963239 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
5963200 TTCCAATTTC
5963210 AATTTTTAT
1 AATTTTTAT
5963219 AATTTTTAT
1 AATTTTTAT
5963228 AATGTTTTAT
1 AAT-TTTTAT
5963238 AA
1 AA
5963240 AATTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.60
10 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (9 bp):
AATTTTTAT
Found at i:5968677 original size:18 final size:17
Alignment explanation
Indices: 5968656--5968689 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5968646 TAAAATTAAA
5968656 TATTAAATATAAATATAT
1 TATTAAATA-AAATATAT
*
5968674 TATTTAATAAAATATA
1 TATTAAATAAAATATA
5968690 ATATAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTAAATAAAATATAT
Found at i:5968708 original size:22 final size:22
Alignment explanation
Indices: 5968650--5968715 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 22
5968640 GTTATTTAAA
5968650 ATTAAATATTAAATATAAATATATT
1 ATTAAATA--AAATATAAATA-ATT
*
5968675 ATTTAATAAAATATAATATAATT
1 ATTAAATAAAATATAA-ATAATT
*
5968698 -TTAAATGAAAT-TAAATAA
1 ATTAAATAAAATATAAATAA
5968716 AATAAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.11
21 3 0.08
22 9 0.24
23 11 0.30
24 3 0.08
25 7 0.19
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
ATTAAATAAAATATAAATAATT
Found at i:5971618 original size:9 final size:8
Alignment explanation
Indices: 5971605--5971660 Score: 51
Period size: 9 Copynumber: 6.6 Consensus size: 8
5971595 GACTAGAAAT
5971605 TAAATAAA
1 TAAATAAA
5971613 TGAAATAACA
1 T-AAATAA-A
5971623 TAAATAAA
1 TAAATAAA
* *
5971631 CAATTAAA
1 TAAATAAA
5971639 TAAATCAAA
1 TAAAT-AAA
5971648 -AAATAAA
1 TAAATAAA
5971655 TTAAAT
1 -TAAAT
5971661 TGAGAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
7 3 0.08
8 15 0.38
9 19 0.49
10 2 0.05
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (8 bp):
TAAATAAA
Found at i:5971656 original size:21 final size:22
Alignment explanation
Indices: 5971605--5971660 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
5971595 GACTAGAAAT
*
5971605 TAAATAAATGAAATAACATAAA
1 TAAATAAATTAAATAACATAAA
*
5971627 TAAA-CAATTAAATAA-ATCAAA
1 TAAATAAATTAAATAACAT-AAA
5971648 -AAATAAATTAAAT
1 TAAATAAATTAAAT
5971661 TGAGAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 5 0.17
21 20 0.69
22 4 0.14
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (22 bp):
TAAATAAATTAAATAACATAAA
Found at i:5971672 original size:4 final size:4
Alignment explanation
Indices: 5971605--5971660 Score: 51
Period size: 4 Copynumber: 13.2 Consensus size: 4
5971595 GACTAGAAAT
* *
5971605 TAAA TAAA TGAAA TAACA TAAA TAAA CAAT TAAA TAAA TCAAA -AAA TAAA
1 TAAA TAAA T-AAA TAA-A TAAA TAAA TAAA TAAA TAAA T-AAA TAAA TAAA
5971655 TTAAA T
1 -TAAA T
5971661 TGAGAAATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
3 3 0.07
4 25 0.58
5 15 0.35
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:5975256 original size:8 final size:8
Alignment explanation
Indices: 5975245--5975275 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
5975235 TATATTGTTA
5975245 TATTATAT
1 TATTATAT
*
5975253 TATTATAA
1 TATTATAT
5975261 TATTATAT
1 TATTATAT
5975269 TATTATA
1 TATTATA
5975276 ATAAAACAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
TATTATAT
Found at i:5975263 original size:16 final size:16
Alignment explanation
Indices: 5975244--5975278 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5975234 GTATATTGTT
5975244 ATATTATATTATTATA
1 ATATTATATTATTATA
5975260 ATATTATATTATTATA
1 ATATTATATTATTATA
5975276 ATA
1 ATA
5975279 AAACAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATATTATATTATTATA
Found at i:5982559 original size:20 final size:19
Alignment explanation
Indices: 5982515--5982565 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
5982505 CAAAATAGTG
* *
5982515 AAAAAACAA-CAAGAAAAT
1 AAAAAAAAAGCAAAAAAAT
*
5982533 AATAAAAAAGCAAAAAAAGT
1 AAAAAAAAAGCAAAAAAA-T
5982553 AAAAAAAAAGCAA
1 AAAAAAAAAGCAA
5982566 CAAATTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 7 0.26
19 7 0.26
20 13 0.48
ACGTcount: A:0.78, C:0.08, G:0.08, T:0.06
Consensus pattern (19 bp):
AAAAAAAAAGCAAAAAAAT
Found at i:5983693 original size:16 final size:18
Alignment explanation
Indices: 5983667--5983703 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5983657 TAAATACAAA
*
5983667 TTTACTTTTAA-ATTATT
1 TTTACTTTTAATATAATT
5983684 TTTA-TTTTAATATAATT
1 TTTACTTTTAATATAATT
5983701 TTT
1 TTT
5983704 TTAATGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTACTTTTAATATAATT
Found at i:5983891 original size:19 final size:19
Alignment explanation
Indices: 5983869--5983920 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
5983859 CCATATTAAT
5983869 AATAAAATTAAAAAAAATA
1 AATAAAATTAAAAAAAATA
* *
5983888 AATAGATATT-TAAAAAATA
1 AATA-AAATTAAAAAAAATA
*
5983907 AATTTAAATTAAAA
1 AA-TAAAATTAAAA
5983921 TAGATTTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AATAAAATTAAAAAAAATA
Found at i:5983922 original size:16 final size:18
Alignment explanation
Indices: 5983901--5983937 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5983891 AGATATTTAA
5983901 AAAATA-AATTTA-AATT
1 AAAATAGAATTTATAATT
*
5983917 AAAATAGATTTTATAATT
1 AAAATAGAATTTATAATT
5983935 AAA
1 AAA
5983938 TAGTAGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
AAAATAGAATTTATAATT
Found at i:5983929 original size:17 final size:18
Alignment explanation
Indices: 5983909--5983955 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
5983899 AAAAAATAAA
*
5983909 TTTAAATTAAAATAG-AT
1 TTTAAATTAAAATAGTAG
5983926 TTTATAATT-AAATAGTAG
1 TTTA-AATTAAAATAGTAG
5983944 TTTAAA-TAAAAT
1 TTTAAATTAAAAT
5983956 TTAGAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 1 0.04
17 16 0.62
18 9 0.35
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (18 bp):
TTTAAATTAAAATAGTAG
Found at i:5986981 original size:29 final size:28
Alignment explanation
Indices: 5986919--5986983 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
5986909 AAAAACACAA
5986919 GACTAAAATTGATCAAATCAAAAAGTAG
1 GACTAAAATTGATCAAATCAAAAAGTAG
* *
5986947 GAACTAAGATTGATCAAATTAAAATA-TATG
1 G-ACTAAAATTGATCAAATCAAAA-AGTA-G
5986977 GACTAAA
1 GACTAAA
5986984 TTTATAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 1 0.03
29 27 0.87
30 3 0.10
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.25
Consensus pattern (28 bp):
GACTAAAATTGATCAAATCAAAAAGTAG
Found at i:5993616 original size:18 final size:18
Alignment explanation
Indices: 5993595--5993629 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5993585 ATTTTGTAAT
*
5993595 TAGTTTGAATTTAATTTC
1 TAGTTTAAATTTAATTTC
5993613 TAGTTTAAATTTAATTT
1 TAGTTTAAATTTAATTT
5993630 TTAAGTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.57
Consensus pattern (18 bp):
TAGTTTAAATTTAATTTC
Found at i:5994335 original size:28 final size:27
Alignment explanation
Indices: 5994277--5994336 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 27
5994267 AAAGCCTTTT
*
5994277 TTTTTTAAATTTACCGAAATGGGCCAC
1 TTTTTTAAATTTACCGAAATGGGCCAA
* *
5994304 TTTTTTAATTATTTATCGGAATGGG-CAA
1 TTTTTTAA--ATTTACCGAAATGGGCCAA
5994332 TTTTT
1 TTTTT
5994337 CGCGAAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 8 0.29
28 7 0.25
29 13 0.46
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.47
Consensus pattern (27 bp):
TTTTTTAAATTTACCGAAATGGGCCAA
Found at i:5994782 original size:125 final size:125
Alignment explanation
Indices: 5994554--5994835 Score: 435
Period size: 125 Copynumber: 2.3 Consensus size: 125
5994544 TTATTTCGAG
** *
5994554 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACTAGGATGCTATCAGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTGATACCAGGATGCTATCAGAGAAGAAATTGT
*
5994618 GAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATT-TTTT
65 GAAATCGTGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAAGAAATAATTATTTT
* *
5994678 TTGACATTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGTTAT-ATGAGAAGAAATTG
1 TTGAC-GTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATCA-GAGAAGAAATTG
*
5994742 TGAAATCGTGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAGGAAATAATTATTTT
64 TGAAATCGTGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAAGAAATAATTATTTT
* *
5994804 TTGACGTTTCTGAGCAAATAGTGTCAAATCGC
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGC
5994836 GCCCTCGTGG
Statistics
Matches: 144, Mismatches: 10, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
124 6 0.04
125 128 0.89
126 10 0.07
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATCAGAGAAGAAATTGTG
AAATCGTGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAAGAAATAATTATTTT
Found at i:5998070 original size:29 final size:29
Alignment explanation
Indices: 5998028--5998902 Score: 1014
Period size: 29 Copynumber: 30.5 Consensus size: 29
5998018 TTTTGTTAAT
* ****
5998028 GGTTAGGGTTTTTAATTAAAATGGGCTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
*
5998057 GGTTAGGGCTTTTAATTAAATTAAATTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
*
5998086 GGTTAGTGTTTTTAATTAAATTAAATTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
* *
5998115 GATTAGGATTTTTAATTAAATTAAATTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
5998144 GGTTAGGGTTTTTAATTAAATTAAATTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
*
5998173 GGTTAGTGTTTTTAATTAAATTAAATTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
5998202 GGTTAGGGTTTTTAATTAAATTAAATTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
* **
5998231 GGTTAGGGTTTTTAATTAAAATAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
*
5998260 GGTTAGGATTTTTAATTAAATTAAATTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
5998289 GGTTAGGGTTTTTAATTAAATTAAATTA-
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
* ***
5998317 GGTTAGGGTTTTTAATTAAAATGGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
*
5998346 GGTTAGGATTTTTAATTAAATTAAATTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
* *
5998375 GGTTAGAGTTTTTAATTAAAATGGGTTAAGGTTAG
1 GGTTAGGGTTTTTAATT-AAA----TTAA-ATTAG
*
5998410 GGTTTAGGGTTCTTAATTAAATTAAATTAG
1 GG-TTAGGGTTTTTAATTAAATTAAATTAG
*
5998440 GGTTAGTGTTTTTAATTAAATTAAATTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
* ***
5998469 GGTTAGGGTTTTTAATTAAAATGGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
* **
5998498 GGTTAGGGTTTTTAATTTAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
* * ***
5998527 GGTTTAGGATTTTTAATTAAAATGGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAAATTAG
*
5998557 GGTTAGGGTTTTTAATTAAATTAAGTTTA-
1 GGTTAGGGTTTTTAATTAAATTAA-ATTAG
* ***
5998586 GGTTAGGGTTTTTAATTAAAATGGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
*
5998615 GGTTAGGGTTTTTAATTAATTTAAATTA-
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
5998643 GGTTAGGG--TTT--TT-AATTAAATTA-
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
* * ***
5998666 GGTTAGGTTTTTTAATTAAAATGGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
*
5998695 GGTTAGGGTTTTTAATTAATTTAAATTA-
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
* ***
5998723 GGTTAGGGTTTTTAATTAAAATGGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
*
5998752 GGTTTGGGTTTTTAA-T---TT-AATTA-
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
*
5998775 GGTTATGGTTTTTAATTAAATTAAATTA-
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
* * * *
5998803 GGTTAAGGTTTTTAATTAAAATGAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
*
5998832 GGTTAGGGTTTTTAATTAATTTAAATTA-
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
5998860 GGTTAGGGTTTTTAATTAAATTAAATTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAG
5998889 GGTT-GGGTTTTTAA
1 GGTTAGGGTTTTTAA
5998903 ACAAATTATA
Statistics
Matches: 722, Mismatches: 99, Indels: 51
0.83 0.11 0.06
Matches are distributed among these distances:
23 29 0.04
24 6 0.01
25 4 0.01
26 3 0.00
27 4 0.01
28 131 0.18
29 478 0.66
30 37 0.05
31 4 0.01
34 4 0.01
35 9 0.01
36 13 0.02
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAAATTAG
Found at i:5998682 original size:18 final size:22
Alignment explanation
Indices: 5998635--5998797 Score: 83
Period size: 23 Copynumber: 6.4 Consensus size: 22
5998625 TTTAATTAAT
5998635 TTAAATTAGGTTAGGGTTTTTAA
1 TTAAATTAGGTTAGGGTTTTT-A
*
5998658 TTAAATTAGGTTAGGTTTTTTAA
1 TTAAATTAGGTTAGGGTTTTT-A
5998681 TTAAAATGGGTTAGGGTTAGGGTTTTTAATTAA
1 TT-AAA----TTA-GGTTAGGG-TT-T--TT-A
5998714 TTTAAATTAGGTTAGGGTTTTTAA
1 -TTAAATTAGGTTAGGGTTTTT-A
*
5998738 TTAAAATGGGTTAGGGTTTGGGTTTTTAA
1 TT-AAA----TTA-GGTTAGGGTTTTT-A
* *
5998767 TTTAATTAGGTTATGGTTTTTAA
1 TTAAATTAGGTTAGGGTTTTT-A
5998790 TTAAATTA
1 TTAAATTA
5998798 AATTAGGTTA
Statistics
Matches: 116, Mismatches: 7, Indels: 34
0.74 0.04 0.22
Matches are distributed among these distances:
23 46 0.40
24 13 0.11
26 1 0.01
27 2 0.02
28 16 0.14
29 26 0.22
30 2 0.02
31 1 0.01
33 7 0.06
34 2 0.02
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.48
Consensus pattern (22 bp):
TTAAATTAGGTTAGGGTTTTTA
Found at i:5999105 original size:21 final size:21
Alignment explanation
Indices: 5999080--5999125 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5999070 TCCTCTAGCT
*
5999080 TCCGGCGGTGGTTGTTCTTCC
1 TCCGGCGGTGATTGTTCTTCC
* * *
5999101 TCCGGTGGTGATTGTTGTTCT
1 TCCGGCGGTGATTGTTCTTCC
5999122 TCCG
1 TCCG
5999126 ATTCGACATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.24, G:0.33, T:0.41
Consensus pattern (21 bp):
TCCGGCGGTGATTGTTCTTCC
Found at i:6001070 original size:14 final size:15
Alignment explanation
Indices: 6001053--6001086 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6001043 AATAATTATC
6001053 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
6001067 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
6001082 TAAAA
1 TAAAA
6001087 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:6001247 original size:29 final size:28
Alignment explanation
Indices: 6001184--6001240 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
6001174 TTGAAAATAT
6001184 TAAAAATTTTAAAATTATTTTTAAAAAA
1 TAAAAATTTTAAAATTATTTTTAAAAAA
6001212 TAAAAATATTTAAAATT-TTCTTTAAAAAA
1 TAAAAAT-TTTAAAATTATT-TTTAAAAAA
6001241 ATGAAATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
TAAAAATTTTAAAATTATTTTTAAAAAA
Found at i:6001301 original size:22 final size:21
Alignment explanation
Indices: 6001276--6001326 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
6001266 TAATATGGAT
*
6001276 TTGAGAGATTTTTTGAAGGAAA
1 TTGAGAGA-TTTTAGAAGGAAA
*
6001298 TTGAGAGGATTTTAGAAGGAAT
1 TTGAGA-GATTTTAGAAGGAAA
6001320 TTGAGAG
1 TTGAGAG
6001327 TTTAAGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.88
23 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.33
Consensus pattern (21 bp):
TTGAGAGATTTTAGAAGGAAA
Found at i:6001349 original size:52 final size:52
Alignment explanation
Indices: 6001279--6001378 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
6001269 TATGGATTTG
* * * *
6001279 AGAGATTTTTTGAAGGAAATTGAGAGGATTTTAGAAGGAATTTGAGAGTTTA
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTAGAAGGAAATTGAGAGTTTA
*
6001331 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAG
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTAGAAGGAAATTGAGAG
6001379 AATATTTGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.30
Consensus pattern (52 bp):
AGAGAATTTTGGAAGGAAATTGAGAGAATTTTAGAAGGAAATTGAGAGTTTA
Done.