Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 97 of 150
Found at i:30517592 original size:12 final size:12
Alignment explanation
Indices: 30517575--30517606 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
30517565 AGCGGTGAAT
30517575 GGAGGAATGGGC
1 GGAGGAATGGGC
*
30517587 GGAGGAATGGGT
1 GGAGGAATGGGC
30517599 GGAGGAAT
1 GGAGGAAT
30517607 AGGGAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.03, G:0.56, T:0.12
Consensus pattern (12 bp):
GGAGGAATGGGC
Found at i:30518522 original size:42 final size:42
Alignment explanation
Indices: 30518463--30518547 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
30518453 ATCATAATTG
30518463 GATAATCCGCGATTCATGAAGGATGTCAAAAGTGAAAGTAGA
1 GATAATCCGCGATTCATGAAGGATGTCAAAAGTGAAAGTAGA
30518505 GATAATCCGCGATTCATGAAGGATGTCAAAAGTGAAAGTAGA
1 GATAATCCGCGATTCATGAAGGATGTCAAAAGTGAAAGTAGA
30518547 G
1 G
30518548 TCCGTGGAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.40, C:0.12, G:0.27, T:0.21
Consensus pattern (42 bp):
GATAATCCGCGATTCATGAAGGATGTCAAAAGTGAAAGTAGA
Found at i:30525814 original size:21 final size:21
Alignment explanation
Indices: 30525790--30525850 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 21
30525780 TACCATATGT
30525790 GAACCCTGTTTTACTACATGC
1 GAACCCTGTTTTACTACATGC
*
30525811 GAACCCTGTTATACTAATACATGC
1 GAACCCTGTT-T--TACTACATGC
* *
30525835 GGACCCTGTTATACTA
1 GAACCCTGTTTTACTA
30525851 TGTGCGAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 14 0.42
22 1 0.03
24 18 0.55
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (21 bp):
GAACCCTGTTTTACTACATGC
Found at i:30525840 original size:24 final size:24
Alignment explanation
Indices: 30525804--30525850 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
30525794 CCTGTTTTAC
30525804 TACATGCGAACCCTGTTATACTAA
1 TACATGCGAACCCTGTTATACTAA
*
30525828 TACATGCGGACCCTGTTATACTA
1 TACATGCGAACCCTGTTATACTA
30525851 TGTGCGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (24 bp):
TACATGCGAACCCTGTTATACTAA
Found at i:30525865 original size:17 final size:17
Alignment explanation
Indices: 30525843--30525875 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
30525833 GCGGACCCTG
*
30525843 TTATACTATGTGCGAAT
1 TTATACCATGTGCGAAT
30525860 TTATACCATGTGCGAA
1 TTATACCATGTGCGAA
30525876 CCTATGTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (17 bp):
TTATACCATGTGCGAAT
Found at i:30527306 original size:27 final size:26
Alignment explanation
Indices: 30527233--30527308 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 26
30527223 ACTGCACGAT
*
30527233 AAGTTGCGAACTAGTGGTTCACAGGGC
1 AAGTTGCG-ACTAGGGGTTCACAGGGC
* * * *
30527260 AAGTTGCGAATTGGGTGTTCGCAGGGT
1 AAGTTGCGACTAGGG-GTTCACAGGGC
*
30527287 AGGTTGCGAGCTAGGGGTTCAC
1 AAGTTGCGA-CTAGGGGTTCAC
30527309 CGAGTCATCT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
26 4 0.11
27 30 0.79
28 4 0.11
ACGTcount: A:0.21, C:0.16, G:0.38, T:0.25
Consensus pattern (26 bp):
AAGTTGCGACTAGGGGTTCACAGGGC
Found at i:30528309 original size:49 final size:49
Alignment explanation
Indices: 30528256--30528360 Score: 120
Period size: 49 Copynumber: 2.1 Consensus size: 49
30528246 TAGAGTCATA
* *
30528256 GGTTCAACTATAACTAGGGCTCCCAGTTGATAGTGATTATGCAATCACG
1 GGTTCAACTATAACTAGAGCTCCCAGTTGACAGTGATTATGCAATCACG
* * ** * ***
30528305 GGTTCAAGTATAACTTGAGCTCTTAGTTGACAGTGGTTATGTGGTCACG
1 GGTTCAACTATAACTAGAGCTCCCAGTTGACAGTGATTATGCAATCACG
30528354 GGTTCAA
1 GGTTCAA
30528361 GTTTCATGCC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (49 bp):
GGTTCAACTATAACTAGAGCTCCCAGTTGACAGTGATTATGCAATCACG
Found at i:30529039 original size:5 final size:5
Alignment explanation
Indices: 30529029--30529064 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
30529019 TTCTCAAAAT
*
30529029 ATATG ATATG ATATG ATATG ATATG CATATC ATATG
1 ATATG ATATG ATATG ATATG ATATG -ATATG ATATG
30529065 TTTATATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (5 bp):
ATATG
Found at i:30547303 original size:25 final size:25
Alignment explanation
Indices: 30547262--30547310 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
30547252 GCACATATAA
*
30547262 CAAACACACAAGCAAAAAAAAAAAC
1 CAAACACAAAAGCAAAAAAAAAAAC
*
30547287 CAAACACAAAAAG-AAAAATAAAAA
1 CAAACAC-AAAAGCAAAAAAAAAAA
30547311 TAACAAGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.76, C:0.18, G:0.04, T:0.02
Consensus pattern (25 bp):
CAAACACAAAAGCAAAAAAAAAAAC
Found at i:30561650 original size:2 final size:2
Alignment explanation
Indices: 30561645--30561678 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
30561635 TATATTCTTT
* *
30561645 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30561679 ATCTAATTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30567022 original size:25 final size:25
Alignment explanation
Indices: 30566971--30567023 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
30566961 TTTATTTCTC
* *
30566971 AAAAATATTTTTTTAATAAAATTTT
1 AAAAATATTTTTTGAATAAAATATT
*
30566996 AAAAATATTTTTTGACA-ATAATATT
1 AAAAATATTTTTTGA-ATAAAATATT
30567021 AAA
1 AAA
30567024 TACTTAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
AAAAATATTTTTTGAATAAAATATT
Found at i:30567117 original size:16 final size:16
Alignment explanation
Indices: 30567096--30567133 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
30567086 TTTGGTTCGC
*
30567096 TGTAATGGAATAGAGG
1 TGTAATGGAATAAAGG
30567112 TGTAATGGAATAAAGG
1 TGTAATGGAATAAAGG
*
30567128 CGTAAT
1 TGTAAT
30567134 AGTAATTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.03, G:0.32, T:0.26
Consensus pattern (16 bp):
TGTAATGGAATAAAGG
Found at i:30567191 original size:24 final size:24
Alignment explanation
Indices: 30567159--30567204 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
30567149 TGGTTGAATG
30567159 GAATGGAATAGA-GCTGTAATAGTT
1 GAATGGAAT-GATGCTGTAATAGTT
*
30567183 GAATGGAATGATGTTGTAATAG
1 GAATGGAATGATGCTGTAATAG
30567205 CATAAGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.37, C:0.02, G:0.30, T:0.30
Consensus pattern (24 bp):
GAATGGAATGATGCTGTAATAGTT
Found at i:30567360 original size:37 final size:38
Alignment explanation
Indices: 30567315--30567403 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 38
30567305 TAAATAATAA
* * *
30567315 ATAATTTAATCATATT-TTAACATATTTATTATTAAAT
1 ATAATTTAATAAAATTCTTAACATAATTATTATTAAAT
* * *
30567352 ATAATTTAATAAAATTCTTAATATAATTATTCTTATAT
1 ATAATTTAATAAAATTCTTAACATAATTATTATTAAAT
*
30567390 -TAATTTACTAAAAT
1 ATAATTTAATAAAAT
30567404 CATAATATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 27 0.61
38 17 0.39
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (38 bp):
ATAATTTAATAAAATTCTTAACATAATTATTATTAAAT
Found at i:30570183 original size:50 final size:50
Alignment explanation
Indices: 30570049--30570244 Score: 176
Period size: 50 Copynumber: 3.8 Consensus size: 50
30570039 ATTTGGGTAA
* * *
30570049 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
** * *
30570105 AGAGGTCCCATATAAGACTATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
30570155 AGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATAGGCACCGATATG
1 AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * *
30570205 AGAACTCTCATGTAAGACCATATCTAGGATATGGCATTGG
1 AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGG
30570245 TAGTACAAGA
Statistics
Matches: 117, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
50 75 0.64
53 3 0.03
55 1 0.01
56 38 0.32
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:30573488 original size:25 final size:25
Alignment explanation
Indices: 30573456--30573503 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
30573446 TTTTAATTCA
30573456 AAAACGTGCTATTAAAAGCAGACTC
1 AAAACGTGCTATTAAAAGCAGACTC
* *
30573481 AAAACGTGCTATTAGAAGTAGAC
1 AAAACGTGCTATTAAAAGCAGAC
30573504 AATATGATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.21
Consensus pattern (25 bp):
AAAACGTGCTATTAAAAGCAGACTC
Found at i:30577162 original size:30 final size:30
Alignment explanation
Indices: 30577104--30577171 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
30577094 ATAATTATAC
*
30577104 CTAAATT-TTAAAATTTAAAAAGTAAAAGAA
1 CTAAATTCTTAAAATATAAAAAGTAAAAG-A
30577134 CTAAATTCTTAAAA-ATAAAAATGT-AAAGA
1 CTAAATTCTTAAAATATAAAAA-GTAAAAGA
*
30577163 TTAAATTCT
1 CTAAATTCT
30577172 AAGTTTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 9 0.26
30 17 0.50
31 8 0.24
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (30 bp):
CTAAATTCTTAAAATATAAAAAGTAAAAGA
Found at i:30580282 original size:30 final size:30
Alignment explanation
Indices: 30580248--30580305 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
30580238 TGATTTGGGC
30580248 TTAAGGACTAAA-TTG-AACAAATGTCAAACT
1 TTAAGG-CTAAATTTGTAA-AAATGTCAAACT
*
30580278 TTAAGGGTAAATTTGTAAAAATGTCAAA
1 TTAAGGCTAAATTTGTAAAAATGTCAAA
30580306 GTGACCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 4 0.16
30 19 0.76
31 2 0.08
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.29
Consensus pattern (30 bp):
TTAAGGCTAAATTTGTAAAAATGTCAAACT
Found at i:30582250 original size:16 final size:16
Alignment explanation
Indices: 30582226--30582263 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
30582216 TTTGGTTCGC
* *
30582226 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
30582242 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
30582258 TGTAAT
1 TGTAAT
30582264 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:30582347 original size:39 final size:43
Alignment explanation
Indices: 30582242--30582351 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
30582232 GGATTAGAGG
30582242 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
30582287 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
30582327 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
30582352 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:30582556 original size:23 final size:21
Alignment explanation
Indices: 30582500--30582558 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 21
30582490 TTATTAAATA
30582500 ATATAATTTAATAAAATTCTT
1 ATATAATTTAATAAAATTCTT
*
30582521 ACT-TAATATT-A-AATATTCTT
1 A-TATAAT-TTAATAAAATTCTT
30582541 ATATGAATTTAATAAAAT
1 ATAT-AATTTAATAAAAT
30582559 CATAATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 11
0.70 0.05 0.26
Matches are distributed among these distances:
19 1 0.03
20 12 0.40
21 10 0.33
22 7 0.23
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (21 bp):
ATATAATTTAATAAAATTCTT
Found at i:30584259 original size:20 final size:20
Alignment explanation
Indices: 30584236--30584274 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
30584226 CATTGAGATT
30584236 TCGAAACATCTTGCATCAGG
1 TCGAAACATCTTGCATCAGG
30584256 TCGAAACATCTTGCATCAG
1 TCGAAACATCTTGCATCAG
30584275 AACCGAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (20 bp):
TCGAAACATCTTGCATCAGG
Found at i:30590535 original size:20 final size:20
Alignment explanation
Indices: 30590484--30590540 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
30590474 CTTTATTTTA
*
30590484 ATTAATTTATTCATTTTTTATT
1 ATTAATTTAAT-A-TTTTTATT
*
30590506 -TTATTTTTAATATTTTTATT
1 ATTA-ATTTAATATTTTTATT
30590526 ATTAATTTAAT-TTTT
1 ATTAATTTAATATTTT
30590541 ACATTCTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 4 0.13
20 14 0.47
21 7 0.23
22 5 0.17
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTAATTTAATATTTTTATT
Found at i:30594985 original size:30 final size:29
Alignment explanation
Indices: 30594911--30594986 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 29
30594901 CCATTTTTAA
30594911 AATAAACATTAAAAAATTATTTTAAAAATT
1 AATAAA-ATTAAAAAATTATTTTAAAAATT
* *
30594941 AAAAAAATAAAAAAAATTATTTTAAAAGTATT
1 AATAAAAT-TAAAAAATTATTTTAAAA--ATT
*
30594973 -TTAAAATTAAAAAA
1 AATAAAATTAAAAAA
30594987 AATAAAATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 2 0.05
30 28 0.74
31 5 0.13
32 3 0.08
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (29 bp):
AATAAAATTAAAAAATTATTTTAAAAATT
Found at i:30605126 original size:18 final size:18
Alignment explanation
Indices: 30605100--30605142 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
30605090 CTAAAAAAAT
*
30605100 AAGAAAATGACCAAACTG
1 AAGAAAATGAACAAACTG
* *
30605118 AATAAAATGAATAAACTG
1 AAGAAAATGAACAAACTG
30605136 AAGAAAA
1 AAGAAAA
30605143 ACATGGCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.63, C:0.09, G:0.14, T:0.14
Consensus pattern (18 bp):
AAGAAAATGAACAAACTG
Found at i:30605398 original size:22 final size:24
Alignment explanation
Indices: 30605362--30605407 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
30605352 CAACCAATCA
*
30605362 AATTTCAACACA-TTTCT-TCCTT
1 AATTTCAACAAATTTTCTCTCCTT
*
30605384 AATTTCCACAAATTTTCTCTCCTT
1 AATTTCAACAAATTTTCTCTCCTT
30605408 TACACCTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 5 0.25
24 5 0.25
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.46
Consensus pattern (24 bp):
AATTTCAACAAATTTTCTCTCCTT
Found at i:30606598 original size:8 final size:8
Alignment explanation
Indices: 30606585--30606618 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
30606575 CTTAACATGC
30606585 TTTCAGTT
1 TTTCAGTT
30606593 TTTCAGTT
1 TTTCAGTT
30606601 TTTCAGTT
1 TTTCAGTT
30606609 TTTCAGTT
1 TTTCAGTT
30606617 TT
1 TT
30606619 AGTGGTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.65
Consensus pattern (8 bp):
TTTCAGTT
Found at i:30609652 original size:2 final size:2
Alignment explanation
Indices: 30609647--30609672 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30609637 TATATATATA
30609647 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
30609673 AATTGAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:30610403 original size:30 final size:30
Alignment explanation
Indices: 30610367--30610428 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
30610357 TAATGCTTAC
30610367 TCAGTTTATTTCTTCGTGTTTTATAGAGGT
1 TCAGTTTATTTCTTCGTGTTTTATAGAGGT
30610397 TCAGTTTATTTCTTCGTGTTTTATAGAGGT
1 TCAGTTTATTTCTTCGTGTTTTATAGAGGT
30610427 TC
1 TC
30610429 GTTAGCTAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.16, C:0.11, G:0.19, T:0.53
Consensus pattern (30 bp):
TCAGTTTATTTCTTCGTGTTTTATAGAGGT
Found at i:30612439 original size:46 final size:46
Alignment explanation
Indices: 30612372--30612465 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
30612362 AGAATATTTA
30612372 ACTTCCAAATGAAACTATTATTTAGATTAAATACTAACATTCAAAC
1 ACTTCCAAATGAAACTATTATTTAGATTAAATACTAACATTCAAAC
30612418 ACTTCCAAATGAAACTATTATTTAGATTAAATACTAACATTCAAAC
1 ACTTCCAAATGAAACTATTATTTAGATTAAATACTAACATTCAAAC
30612464 AC
1 AC
30612466 ACATTACATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.46, C:0.18, G:0.04, T:0.32
Consensus pattern (46 bp):
ACTTCCAAATGAAACTATTATTTAGATTAAATACTAACATTCAAAC
Found at i:30616819 original size:15 final size:15
Alignment explanation
Indices: 30616799--30616829 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
30616789 GAATCAAACG
30616799 AATCTCATTGAATTA
1 AATCTCATTGAATTA
30616814 AATCTCATTGAATTA
1 AATCTCATTGAATTA
30616829 A
1 A
30616830 TACAATTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (15 bp):
AATCTCATTGAATTA
Found at i:30617173 original size:14 final size:14
Alignment explanation
Indices: 30617154--30617181 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30617144 ATTTATTTCT
30617154 TGGTTGCCGAATTG
1 TGGTTGCCGAATTG
30617168 TGGTTGCCGAATTG
1 TGGTTGCCGAATTG
30617182 GGCCTCTCTT
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:0.14, C:0.14, G:0.36, T:0.36
Consensus pattern (14 bp):
TGGTTGCCGAATTG
Found at i:30622903 original size:131 final size:131
Alignment explanation
Indices: 30622661--30622922 Score: 309
Period size: 131 Copynumber: 2.0 Consensus size: 131
30622651 TTTGTCCTCC
* * *
30622661 ATAAAACCTTAACTAGAGGAATCATTTTCTTTGTCAAAACTTTTACCTCATGATCCAAAATCTAA
1 ATAAAACCTTAACTAGAGGAATCATTTTCTTTCTCAAAAATTTTACCTCATGATCAAAAATCTAA
* * * *
30622726 ACTGACTCCTCCTCAAAAGACAAATTCTGATTTACATCGATCTCCTCAATCAAAACCACATAAGA
66 ACTGACTCCTCCTCAAAAGACAAATTCTAACTCACATCAATCTCCTCAATCAAAACCACATAAGA
30622791 T
131 T
30622792 ATAAAACCTTAACTAGAGGAATC-TTCTTCTTTCT-AAACAATTTTACCTCAT-ATTCAAAAATC
1 ATAAAACCTTAACTAGAGGAATCATT-TTCTTTCTCAAA-AATTTTACCTCATGA-TCAAAAATC
* ** * * **
30622854 TGAACTGGTTCCTCCTCAAAAGATAAATTC-AACCTCACCA-CAATTTCCTCAATCGGAACCACA
63 TAAACTGACTCCTCCTCAAAAGACAAATTCTAA-CTCA-CATCAATCTCCTCAATCAAAACCACA
*
30622917 TGAGAT
126 TAAGAT
30622923 GGACCAGATC
Statistics
Matches: 111, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
130 7 0.06
131 102 0.92
132 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.30
Consensus pattern (131 bp):
ATAAAACCTTAACTAGAGGAATCATTTTCTTTCTCAAAAATTTTACCTCATGATCAAAAATCTAA
ACTGACTCCTCCTCAAAAGACAAATTCTAACTCACATCAATCTCCTCAATCAAAACCACATAAGA
T
Found at i:30628978 original size:43 final size:44
Alignment explanation
Indices: 30628867--30628979 Score: 117
Period size: 44 Copynumber: 2.6 Consensus size: 44
30628857 TGTTATCGTG
* ** *
30628867 TAAGACCACATCTGGGACGTTGGCATCGACTTGTGACTTACGTG
1 TAAGACCACGTCTGGGACGTTGGCATCGACTTGTGACTTAAATA
* *
30628911 TAAGACC-CTGTTTGGGATAG-TGGCATCGA-TATGTGA-TTAAATA
1 TAAGACCAC-GTCTGGGA-CGTTGGCATCGACT-TGTGACTTAAATA
30628954 TAAGACCACGTCTGGGACGTTGGCAT
1 TAAGACCACGTCTGGGACGTTGGCAT
30628980 TGTACAAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
42 1 0.02
43 26 0.46
44 28 0.50
45 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (44 bp):
TAAGACCACGTCTGGGACGTTGGCATCGACTTGTGACTTAAATA
Found at i:30632574 original size:30 final size:30
Alignment explanation
Indices: 30632504--30632585 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
30632494 AGTAACCTTG
* * *
30632504 ATATAATGTTAGA-TTGTGTGAGCAATTATG
1 ATATAATGTCA-ACTTGTGTGAGCAATCATA
* *
30632534 TTATAATGTCAACTTGTGTGAGCAATCCTA
1 ATATAATGTCAACTTGTGTGAGCAATCATA
* *
30632564 ATATATTGTCATCTTGTGTGAG
1 ATATAATGTCAACTTGTGTGAG
30632586 AAACTTATTC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 1 0.02
30 42 0.98
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (30 bp):
ATATAATGTCAACTTGTGTGAGCAATCATA
Found at i:30642000 original size:3 final size:3
Alignment explanation
Indices: 30641987--30642028 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
30641977 ATTGTAAATG
30641987 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
30642029 TATTAATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:30642137 original size:31 final size:34
Alignment explanation
Indices: 30642101--30642171 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 34
30642091 ATATTCTAAA
* *
30642101 CGGGCCTATTTTTTTGCCC-AA-G-CTCATATTT
1 CGGGCCTATATTTTTACCCAAACGTCTCATATTT
30642132 CGGGCCTATATTTTTACCCAAACCGTCTCATATTT
1 CGGGCCTATATTTTTACCCAAA-CGTCTCATATTT
30642167 CGGGC
1 CGGGC
30642172 AGGCCGTCGG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 17 0.50
32 2 0.06
34 1 0.03
35 14 0.41
ACGTcount: A:0.18, C:0.28, G:0.17, T:0.37
Consensus pattern (34 bp):
CGGGCCTATATTTTTACCCAAACGTCTCATATTT
Found at i:30645000 original size:20 final size:20
Alignment explanation
Indices: 30644975--30645014 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
30644965 ACTAAATTTT
30644975 TTTAAAAT-AAAAATATAAAA
1 TTTAAAATCAAAAATA-AAAA
*
30644995 TTTAAATTCAAAAATAAAAA
1 TTTAAAATCAAAAATAAAAA
30645015 AATATAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (20 bp):
TTTAAAATCAAAAATAAAAA
Found at i:30645239 original size:20 final size:20
Alignment explanation
Indices: 30645206--30645246 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
30645196 AAAATAATAC
*
30645206 ATAAAAATTGAAAATT-TTT
1 ATAAAAATTAAAAATTATTT
30645225 ATAAAAATTAAAAAATTATTT
1 ATAAAAATT-AAAAATTATTT
30645246 A
1 A
30645247 AATTTCAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 6 0.32
21 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
ATAAAAATTAAAAATTATTT
Found at i:30651031 original size:13 final size:13
Alignment explanation
Indices: 30651013--30651037 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30651003 CCAGGCAGTG
30651013 TGAGACACACGGC
1 TGAGACACACGGC
30651026 TGAGACACACGG
1 TGAGACACACGG
30651038 TCGTGTATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.28, G:0.32, T:0.08
Consensus pattern (13 bp):
TGAGACACACGGC
Found at i:30652264 original size:235 final size:235
Alignment explanation
Indices: 30651838--30652305 Score: 828
Period size: 235 Copynumber: 2.0 Consensus size: 235
30651828 CGAACATCCG
* *
30651838 ATAATTTGTAAAGTCAAGGAAAATAACTACGTAAGCAATGAATGCTTAGTGAGCTCGTATAAACT
1 ATAATCTGTAAAGTAAAGGAAAATAACTACGTAAGCAATGAATGCTTAGTGAGCTCGTATAAACT
* *
30651903 ATAAACATAACATTTCATTTTAATAATGAAACTTTATGGGCTAATTATAAACTTATACTAATGCC
66 ATAAACATAACATTTCATTTTAATAATGAAACTTTATGGGCTAATTATAAACCTATACCAATGCC
* * *
30651968 ATGGGATTAATATATAGGAATGCATCTAAAACACACATATACCTAAACTTATACATATTTGACCA
131 ATAGGATTAATATATAAGAATGCATCTAAAACACACATATACCTAAACTTAAACATATTTGACCA
30652033 TAAGTCATCCATATATATATAAACATAACATTTAATTCTA
196 TAAGTCATCCATATATATATAAACATAACATTTAATTCTA
*
30652073 ATAATCTGTTAAGTAAAGGAAAATAACTACGTAAGCAATGAATGCTTAGTGAGCTCGTATAAACT
1 ATAATCTGTAAAGTAAAGGAAAATAACTACGTAAGCAATGAATGCTTAGTGAGCTCGTATAAACT
* *
30652138 TTAAACATAACATTTCATTTTAATAATGAAACTTTATGGGGTAATTATAAACCTATACCAATGCC
66 ATAAACATAACATTTCATTTTAATAATGAAACTTTATGGGCTAATTATAAACCTATACCAATGCC
* *
30652203 ATAGGATTAATATATAAGAGTGCATCTAAAACACATATATACCTAAACTTAAACATATTTGACCA
131 ATAGGATTAATATATAAGAATGCATCTAAAACACACATATACCTAAACTTAAACATATTTGACCA
30652268 TAAGTCATCCATATATATATAAACATAACATTTAATTC
196 TAAGTCATCCATATATATATAAACATAACATTTAATTC
30652306 ATCATTGTTA
Statistics
Matches: 221, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
235 221 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.32
Consensus pattern (235 bp):
ATAATCTGTAAAGTAAAGGAAAATAACTACGTAAGCAATGAATGCTTAGTGAGCTCGTATAAACT
ATAAACATAACATTTCATTTTAATAATGAAACTTTATGGGCTAATTATAAACCTATACCAATGCC
ATAGGATTAATATATAAGAATGCATCTAAAACACACATATACCTAAACTTAAACATATTTGACCA
TAAGTCATCCATATATATATAAACATAACATTTAATTCTA
Found at i:30654404 original size:12 final size:12
Alignment explanation
Indices: 30654387--30654414 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
30654377 TTTAAATTCA
30654387 AACTCATATCAG
1 AACTCATATCAG
30654399 AACTCATATCAG
1 AACTCATATCAG
30654411 AACT
1 AACT
30654415 TGATGCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.25, G:0.07, T:0.25
Consensus pattern (12 bp):
AACTCATATCAG
Found at i:30658403 original size:35 final size:35
Alignment explanation
Indices: 30658347--30658457 Score: 150
Period size: 35 Copynumber: 3.1 Consensus size: 35
30658337 AAACCACCCA
* *
30658347 AACACACCAGATGCTCATAAGAGCCAATCCAACTGT
1 AACACACCA-ATGCTCATAAGAGCTAATCCAACCGT
** *
30658383 AACATGCCAATGCTCATAAGAGTTAATCCAACCGT
1 AACACACCAATGCTCATAAGAGCTAATCCAACCGT
* *
30658418 AACACATCAATGCTCATAAGAGCTAATCCAACCGA
1 AACACACCAATGCTCATAAGAGCTAATCCAACCGT
30658453 AACAC
1 AACAC
30658458 GTCAAACATA
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 58 0.89
36 7 0.11
ACGTcount: A:0.41, C:0.29, G:0.13, T:0.18
Consensus pattern (35 bp):
AACACACCAATGCTCATAAGAGCTAATCCAACCGT
Found at i:30660829 original size:21 final size:19
Alignment explanation
Indices: 30660805--30660850 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
30660795 TTTGTTGGAT
30660805 TGTTTCGAACATTTTAGGGAC
1 TGTTT-GAA-ATTTTAGGGAC
* *
30660826 TGTTTTAAATTTTTGGGAC
1 TGTTTGAAATTTTAGGGAC
30660845 TGTTTG
1 TGTTTG
30660851 GTTTTGAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 15 0.68
20 2 0.09
21 5 0.23
ACGTcount: A:0.20, C:0.09, G:0.24, T:0.48
Consensus pattern (19 bp):
TGTTTGAAATTTTAGGGAC
Found at i:30664474 original size:23 final size:23
Alignment explanation
Indices: 30664430--30664474 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
30664420 TCTTATTTTG
* *
30664430 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
30664453 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
30664475 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:30664805 original size:23 final size:22
Alignment explanation
Indices: 30664765--30664815 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
30664755 TAATATATAT
*
30664765 TGTTTTATATATAGTATACGTA
1 TGTTTTATATATAGTATACATA
**
30664787 TGTTTATATATATTTTATACATA
1 TGTTT-TATATATAGTATACATA
30664810 TGTTTT
1 TGTTTT
30664816 TGTTTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.57
Consensus pattern (22 bp):
TGTTTTATATATAGTATACATA
Found at i:30665798 original size:28 final size:28
Alignment explanation
Indices: 30665758--30665816 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
30665748 AATGTCGTGC
30665758 TCTAACGCATTGGGTGTGACATTTTCTT
1 TCTAACGCATTGGGTGTGACATTTTCTT
30665786 TCTAACGCATTGGGTGTGACATTTTCTT
1 TCTAACGCATTGGGTGTGACATTTTCTT
30665814 TCT
1 TCT
30665817 CCGAAATGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (28 bp):
TCTAACGCATTGGGTGTGACATTTTCTT
Found at i:30667286 original size:404 final size:403
Alignment explanation
Indices: 30666537--30667464 Score: 1685
Period size: 404 Copynumber: 2.3 Consensus size: 403
30666527 NNNNNNNNNN
*
30666537 GGGTGAGGATCGAGGAATCTGCTGGTTTAGGTACCCTTACTTTAGAACCGAACCGCATATAGAAG
1 GGGTGAGGATCGAGGAATCTGCTGGTTTAGGTACCCTTACTTCAGAACCGAA-CGCATATAGAAG
*
30666602 ACCTTAGGAGCTCACCCTAGGTAGAGCCACTTCAAACCCCTAATGGTCACCCGAATTTCTGTCTT
65 ACCTTAGGAGCTCACCCTAGGTAGAGCCACTTCAAACCCCTAGTGGTCACCCGAATTTCTGTCTT
*
30666667 AGGTCGAAAATTTTTAAAAATTCATGAGATCCTTTTGCATTCATTATTTTCCTACTTAATTGGTC
130 AGGTCGAAAATTTTTAAAAATTCATGAGATCCTTTTGCATTCATTATTTTCCTACTTAATTGATC
30666732 TTTGCATTATACATTGCATGAGTTGAATGATTTTACCCCTCTAAGTGGGAGTGAAAAACTAGTCC
195 TTTGCATTATACATTGCATGAGTTGAATGATTTTACCCCTCTAAGTGGGAGTGAAAAACTAGTCC
*
30666797 TTCGTGAGGTTTTCACCTCCGTGTAGGATAGTGGATCGCCTTCGGGATACATCCGTACCTATGTC
260 TTCGTGAGGTTTTCACCTCCGTGCAGGATAGTGGATCGCCTTCGGGATACATCCGTACCTATGTC
30666862 TTCGTGAGATTTTCATCTCTGTGTAGCCATAGGGAAATGTATCCCCCTGAACTGAACTCGGTCTA
325 TTCGTGAGATTTTCATCTCTGTGTAGCCATAGGGAAATGTATCCCCCTGAACTGAACTCGGTCTA
30666927 TATGAGCCTATAAT
390 TATGAGCCTATAAT
* *
30666941 GGGTGAGGATCGAGGAATCTGCTGGTTTAGGTACCATTACTTCAGAACAGAACTGCATATAGAAG
1 GGGTGAGGATCGAGGAATCTGCTGGTTTAGGTACCCTTACTTCAGAACCGAAC-GCATATAGAAG
* *
30667006 ACCTTAGGAGCTCACCCTAGGTAGAGCCACTTCAAACCTCTGGTGGTCACCCGAATTTCTGTCTT
65 ACCTTAGGAGCTCACCCTAGGTAGAGCCACTTCAAACCCCTAGTGGTCACCCGAATTTCTGTCTT
* * *
30667071 AGGTCGAAAATTTTTAAAAGTTCATGAGATCCTTTTGCATTCATTATTTTCTTGCTTAATTGATC
130 AGGTCGAAAATTTTTAAAAATTCATGAGATCCTTTTGCATTCATTATTTTCCTACTTAATTGATC
* *
30667136 TTTGCGTTATACATTGCATGAGTTGAATGATTTTACCCCTCTAAGTGGGAGTGAGAAACTAGTCC
195 TTTGCATTATACATTGCATGAGTTGAATGATTTTACCCCTCTAAGTGGGAGTGAAAAACTAGTCC
30667201 TTCGTGAGGTTTTCACCTCCGTGCAGGATAGTGGATCGCCTTCGGGATACATCCGTACCTATGTC
260 TTCGTGAGGTTTTCACCTCCGTGCAGGATAGTGGATCGCCTTCGGGATACATCCGTACCTATGTC
*
30667266 TTCGTGAGATTTTTATCTCTGTGTAGCCATAGGGAAATGTATCCCCCTGAACTGAACTCGGTCTA
325 TTCGTGAGATTTTCATCTCTGTGTAGCCATAGGGAAATGTATCCCCCTGAACTGAACTCGGTCTA
30667331 TATGAGCCTATAAT
390 TATGAGCCTATAAT
* *
30667345 GGGTGAGGAGCGAGGAATCTACTGGTTTAGGTACCCTTACTTCAGAACCGAACGCATATAGAAGA
1 GGGTGAGGATCGAGGAATCTGCTGGTTTAGGTACCCTTACTTCAGAACCGAACGCATATAGAAGA
*
30667410 CCTTAGAAGCTCACCCTAGGTAGAGCCACTTCAAACCCCTAGTGGTCACCCGAAT
66 CCTTAGGAGCTCACCCTAGGTAGAGCCACTTCAAACCCCTAGTGGTCACCCGAAT
30667465 AGACGTTCTA
Statistics
Matches: 502, Mismatches: 21, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
403 65 0.13
404 437 0.87
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (403 bp):
GGGTGAGGATCGAGGAATCTGCTGGTTTAGGTACCCTTACTTCAGAACCGAACGCATATAGAAGA
CCTTAGGAGCTCACCCTAGGTAGAGCCACTTCAAACCCCTAGTGGTCACCCGAATTTCTGTCTTA
GGTCGAAAATTTTTAAAAATTCATGAGATCCTTTTGCATTCATTATTTTCCTACTTAATTGATCT
TTGCATTATACATTGCATGAGTTGAATGATTTTACCCCTCTAAGTGGGAGTGAAAAACTAGTCCT
TCGTGAGGTTTTCACCTCCGTGCAGGATAGTGGATCGCCTTCGGGATACATCCGTACCTATGTCT
TCGTGAGATTTTCATCTCTGTGTAGCCATAGGGAAATGTATCCCCCTGAACTGAACTCGGTCTAT
ATGAGCCTATAAT
Found at i:30670810 original size:14 final size:15
Alignment explanation
Indices: 30670786--30670818 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
30670776 TCCCAAGCTG
30670786 GGAAGGACCTTATGT
1 GGAAGGACCTTATGT
*
30670801 GGAA-GACCTTATTT
1 GGAAGGACCTTATGT
30670815 GGAA
1 GGAA
30670819 AAGCGTCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.27
Consensus pattern (15 bp):
GGAAGGACCTTATGT
Found at i:30672232 original size:22 final size:22
Alignment explanation
Indices: 30672204--30672246 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
30672194 TTTATTGTTC
30672204 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
30672226 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
30672247 TAGCACCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:30672420 original size:44 final size:43
Alignment explanation
Indices: 30672371--30672491 Score: 172
Period size: 44 Copynumber: 2.7 Consensus size: 43
30672361 GACCCCGGCT
30672371 CTATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGT-AAGTC
1 CTATCTCCCT-GACAGCAGTGGAATAGGTTGAAGATTGTGAA-TC
*
30672415 CTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTGAATC
1 CTATCTCCCT-GACAGCAGTGGAATAGGTTGAAGATTGTGAATC
* *
30672459 CTATCTCCCTGAGCAACAGTGGAGTAGGTTGAA
1 CTATCTCCCTGA-CAGCAGTGGAATAGGTTGAA
30672492 AATAGCTGAT
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
43 1 0.01
44 67 0.96
45 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (43 bp):
CTATCTCCCTGACAGCAGTGGAATAGGTTGAAGATTGTGAATC
Found at i:30672918 original size:44 final size:44
Alignment explanation
Indices: 30672855--30673193 Score: 259
Period size: 44 Copynumber: 7.8 Consensus size: 44
30672845 GAAGATGGCG
* *
30672855 AATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * * **
30672899 AATCTTATCTCTCTGAAGTTGTAGTGGAGCGGATTAAAATCACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-AT
* * * * *
30672943 GATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T--CG-CATTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-AT
* * * * *
30672983 AGTCTTATCTCCCTAAAGTTCCAGTGGAGCAGACT-AAG-TAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * * ****
30673025 CAAGTCTTATC-CTCCTAAAGTTGCCGT-GAGGCAGACTAAAGATGGT
1 -AA-TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGATTAAAGCCAAT
30673071 GAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* *
30673116 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-AT
* * * *
30673160 GATCTTATCTCTCTGAAGTTGCAGTAGAGTAGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
30673194 CACATCGGGT
Statistics
Matches: 237, Mismatches: 44, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
39 2 0.01
40 19 0.08
41 7 0.03
42 3 0.01
43 12 0.05
44 152 0.64
45 35 0.15
46 7 0.03
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
Found at i:30673308 original size:129 final size:129
Alignment explanation
Indices: 30673074--30673318 Score: 280
Period size: 129 Copynumber: 1.9 Consensus size: 129
30673064 AGATGGTGAA
* * * * * *
30673074 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGCAAACAATCCTATCCCCCTGAAATTACA
* * * * *
30673139 GTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCACATCGGG
66 GTGGAGCAGACTAAAACAACAAATCCTATCTCCCTGAAGTTGCAGTAGAGTAGATCACATCGGG
* *
30673203 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTCAAG-AAAGCAAGTCCTATCCCCCTGAAATTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGCAAA-CAA-TCCTATCCCCCTGAAATTA
* * * * *
30673267 CAGTGGGGTAGACTAAATA-AACAAATCCTGTCTCCCT-AAGTTGTAGTGGAGT
64 CAGTGGAGCAGACTAAA-ACAACAAATCCTATCTCCCTGAAGTTGCAGTAGAGT
30673319 GGATTAGAGT
Statistics
Matches: 95, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
128 2 0.02
129 49 0.52
130 43 0.45
131 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (129 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGCAAACAATCCTATCCCCCTGAAATTACA
GTGGAGCAGACTAAAACAACAAATCCTATCTCCCTGAAGTTGCAGTAGAGTAGATCACATCGGG
Found at i:30673317 original size:217 final size:217
Alignment explanation
Indices: 30672855--30673317 Score: 590
Period size: 217 Copynumber: 2.1 Consensus size: 217
30672845 GAAGATGGCG
* * * *
30672855 AATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGCCAATAATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTG
* * * * **
30672920 TAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATTTAG
66 CAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATCGAG
* * * * * *
30672985 TCTTATCTCCCTAAAGTTCCAGTGGAGCAGACTAAGTAATCAAGTCTTATCCTCCTAAAGTTGCC
131 TCTTATCTCCCTAAAGTTCCAGTGGAGCAGACTAAGAAAGCAAGTCCTATCCCCCTAAAGTTACA
****
30673050 GTGAGGCAGACTAAAGATGGTG
196 GTGAGGCAGACTAAAGATAACA
* *
30673072 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTG
1 AATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTG
* *
30673137 CAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCACATCGG
66 CAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCACATCGA
* * *
30673202 GTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTCAAGAAAGCAAGTCCTATCCCCCTGAAA-TT
130 GTCTTATCTCCCTAAAGTTCCAGTGGAGCAGACT-AAGAAAGCAAGTCCTATCCCCCT-AAAGTT
* * *
30673266 ACAGTGGGGTAGACTAAATA-AACA
193 ACAGTGAGGCAGACTAAAGATAACA
* *
30673290 AATCCTGTCTCCCT-AAGTTGTAGTGGAG
1 AATCCTATCTCCCTAAAGTTGCAGTGGAG
30673318 TGGATTAGAG
Statistics
Matches: 212, Mismatches: 31, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
217 118 0.56
218 55 0.26
219 36 0.17
220 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (217 bp):
AATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTG
CAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATCGAG
TCTTATCTCCCTAAAGTTCCAGTGGAGCAGACTAAGAAAGCAAGTCCTATCCCCCTAAAGTTACA
GTGAGGCAGACTAAAGATAACA
Found at i:30673366 original size:217 final size:217
Alignment explanation
Indices: 30672855--30673371 Score: 520
Period size: 217 Copynumber: 2.4 Consensus size: 217
30672845 GAAGATGGCG
* * * * * * * *
30672855 AATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGCCAATAATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTCAAATTA
* * * * * **
30672920 TAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATTTAG
66 CAGTGAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATCGAG
* * * * * *
30672985 TCTTATCTCCCTAAAGTTCCAGTGGAGCAGACTAAGTAATCAAGTCTTATCCTCCTAAAGTTGCC
131 TCTTATCTCCCTAAAGTTCCAGTGGAGCAGACTAAGAAAGCAAGTCCTATCCCCCTAAAGTTACA
****
30673050 GTGAGGCAGACTAAAGATGGTG
196 GTGAGGCAGACTAAAGATAACA
* * * *
30673072 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTCAAATTA
* * *
30673137 CAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCACATCGG
66 CAGTGAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCACATCGA
* * *
30673202 GTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTCAAGAAAGCAAGTCCTATCCCCCTGAAA-TT
130 GTCTTATCTCCCTAAAGTTCCAGTGGAGCAGACT-AAGAAAGCAAGTCCTATCCCCCT-AAAGTT
* * *
30673266 ACAGTGGGGTAGACTAAATA-AACA
193 ACAGTGAGGCAGACTAAAGATAACA
* * ** * ** * ** *
30673290 AATCCTGTCTCCCT-AAGTTGTAGTGGAGTGGATTAGAG-TGATGGATTTTATCTCTCTCAAATT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT-AATCCTATCTCCCTCAAATT
*
30673353 ACAGTTAAGCAGATTAAAA
65 ACAGTGAAGCAGATTAAAA
30673372 GTTACGAGTC
Statistics
Matches: 251, Mismatches: 45, Indels: 8
0.83 0.15 0.03
Matches are distributed among these distances:
216 2 0.01
217 155 0.62
218 55 0.22
219 36 0.14
220 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (217 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTCAAATTA
CAGTGAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATCGAG
TCTTATCTCCCTAAAGTTCCAGTGGAGCAGACTAAGAAAGCAAGTCCTATCCCCCTAAAGTTACA
GTGAGGCAGACTAAAGATAACA
Found at i:30673638 original size:17 final size:19
Alignment explanation
Indices: 30673616--30673690 Score: 73
Period size: 19 Copynumber: 3.9 Consensus size: 19
30673606 TATGGAAACA
30673616 TAATCTT-GA-AGGATATG
1 TAATCTTAGATAGGATATG
*
30673633 TAATCTTAGATATGATATG
1 TAATCTTAGATAGGATATG
* *
30673652 CAATCTTAGATATGATATATG
1 TAATCTTAGATA-G-GATATG
* *
30673673 CAATCTTAGATATGATAT
1 TAATCTTAGATAGGATAT
30673691 ATGCAATCTT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
17 7 0.15
18 2 0.04
19 22 0.46
21 17 0.35
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (19 bp):
TAATCTTAGATAGGATATG
Found at i:30673709 original size:19 final size:21
Alignment explanation
Indices: 30673628--30673703 Score: 129
Period size: 21 Copynumber: 3.7 Consensus size: 21
30673618 ATCTTGAAGG
*
30673628 ATATGTAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
30673647 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
30673668 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
30673689 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
30673704 AGATATGATT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
19 18 0.33
21 36 0.67
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:30673725 original size:23 final size:24
Alignment explanation
Indices: 30673640--30673726 Score: 93
Period size: 21 Copynumber: 4.0 Consensus size: 24
30673630 ATGTAATCTT
30673640 AGATATG--ATATGCAATCTT---
1 AGATATGATATATGCAATCTTAGA
30673659 AGATATGATATATGCAATCTT---
1 AGATATGATATATGCAATCTTAGA
30673680 AGATATGATATATGCAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
* *
30673704 AGATATGAT-TTTGTAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
30673727 GGTTTAATTT
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
19 7 0.11
21 33 0.54
23 12 0.20
24 9 0.15
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (24 bp):
AGATATGATATATGCAATCTTAGA
Found at i:30673954 original size:23 final size:23
Alignment explanation
Indices: 30673910--30673954 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
30673900 TCTTATTTTG
* *
30673910 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
30673933 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
30673955 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:30674021 original size:15 final size:15
Alignment explanation
Indices: 30674003--30674053 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
30673993 TTATTTTTAA
30674003 ATTTGTTTACATTTT
1 ATTTGTTTACATTTT
* *
30674018 ATTTGGCCTTATATTTT
1 ATTT-G-TTTACATTTT
*
30674035 -TTTATTTACATTTT
1 ATTTGTTTACATTTT
30674049 ATTTG
1 ATTTG
30674054 GCCTTATATT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
14 8 0.30
15 7 0.26
16 4 0.15
17 8 0.30
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.65
Consensus pattern (15 bp):
ATTTGTTTACATTTT
Found at i:30674033 original size:17 final size:17
Alignment explanation
Indices: 30674013--30674065 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
30674003 ATTTGTTTAC
30674013 ATTTTATTTGGCCTTAT
1 ATTTTATTTGGCCTTAT
** *
30674030 ATTTT-TTT--ATTTAC
1 ATTTTATTTGGCCTTAT
30674044 ATTTTATTTGGCCTTAT
1 ATTTTATTTGGCCTTAT
30674061 ATTTT
1 ATTTT
30674066 TTTATTTTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
14 8 0.30
15 3 0.11
16 3 0.11
17 13 0.48
ACGTcount: A:0.19, C:0.09, G:0.08, T:0.64
Consensus pattern (17 bp):
ATTTTATTTGGCCTTAT
Found at i:30674046 original size:31 final size:31
Alignment explanation
Indices: 30674008--30674072 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
30673998 TTTAAATTTG
30674008 TTTACATTTTATTTGGCCTTATATTTTTTTA
1 TTTACATTTTATTTGGCCTTATATTTTTTTA
30674039 TTTACATTTTATTTGGCCTTATATTTTTTTA
1 TTTACATTTTATTTGGCCTTATATTTTTTTA
30674070 TTT
1 TTT
30674073 TATACTCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.18, C:0.09, G:0.06, T:0.66
Consensus pattern (31 bp):
TTTACATTTTATTTGGCCTTATATTTTTTTA
Found at i:30674813 original size:25 final size:24
Alignment explanation
Indices: 30674771--30674818 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
30674761 GATACTTTAC
*
30674771 ATTTCGTTATTTTTTATGTACATTA
1 ATTTCGTTATTTTCTATG-ACATTA
30674796 ATTTCGTT-TATTTCTATGACATT
1 ATTTCGTTAT-TTTCTATGACATT
30674819 GTTGTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.23, C:0.10, G:0.08, T:0.58
Consensus pattern (24 bp):
ATTTCGTTATTTTCTATGACATTA
Found at i:30675950 original size:26 final size:25
Alignment explanation
Indices: 30675921--30675976 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
30675911 TCATTTTTTT
* * *
30675921 AATAAACATCAAAAATTTATTTTAAA
1 AATAAAAAT-AAAAAATCATTTTAAA
30675947 AATAAAAAATAAAAAATCATTTTAAA
1 AAT-AAAAATAAAAAATCATTTTAAA
30675973 AATA
1 AATA
30675977 TTTTAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 1 0.04
26 20 0.77
27 5 0.19
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.30
Consensus pattern (25 bp):
AATAAAAATAAAAAATCATTTTAAA
Found at i:30676842 original size:9 final size:9
Alignment explanation
Indices: 30676820--30676900 Score: 67
Period size: 9 Copynumber: 8.7 Consensus size: 9
30676810 ATTTATAAAA
*
30676820 ATAAAAATCA
1 ATAAAAAT-T
30676830 ATAAAAATT
1 ATAAAAATT
30676839 ATAAAAATT
1 ATAAAAATT
30676848 ATTAAAAA-T
1 A-TAAAAATT
30676857 ATAAAAAATT
1 AT-AAAAATT
* **
30676867 GTCAAATTTT
1 AT-AAAAATT
30676877 ATAAAAATT
1 ATAAAAATT
30676886 AT-AAAATAT
1 ATAAAAAT-T
30676895 ATAAAA
1 ATAAAA
30676901 TGCATCAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
8 6 0.10
9 27 0.47
10 25 0.43
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:30676844 original size:19 final size:18
Alignment explanation
Indices: 30676816--30676863 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
30676806 AAAAATTTAT
30676816 AAAA-ATAAAAATCAATA
1 AAAATATAAAAATCAATA
* *
30676833 AAAATTATAAAAATTATTA
1 AAAA-TATAAAAATCAATA
30676852 AAAATATAAAAA
1 AAAATATAAAAA
30676864 ATTGTCAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 4 0.15
18 8 0.30
19 15 0.56
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATATAAAAATCAATA
Found at i:30676892 original size:19 final size:19
Alignment explanation
Indices: 30676837--30676892 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
30676827 TCAATAAAAA
*
30676837 TTATAAAAATTATTAAAAAT
1 TTATAAAAATTA-TAAAATT
* * *
30676857 ATA-AAAAATTGTCAAATT
1 TTATAAAAATTATAAAATT
30676875 TTATAAAAATTATAAAAT
1 TTATAAAAATTATAAAAT
30676893 ATATAAAATG
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 7 0.25
19 19 0.68
20 2 0.07
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
TTATAAAAATTATAAAATT
Found at i:30677155 original size:29 final size:28
Alignment explanation
Indices: 30677095--30677184 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 28
30677085 TCTTCACATT
* * *
30677095 TTTTATAATTTTCTTA-TGACTTCATAAAA
1 TTTTATAATTTTTTTACT-ATTTC-TATAA
30677124 TTTTATAATTTTTTCTA-TATTTCTATATA
1 TTTTATAATTTTTT-TACTATTTCTATA-A
*
30677153 TTTTATAATTTTTTTACTATTTTTATAA
1 TTTTATAATTTTTTTACTATTTCTATAA
30677181 TTTT
1 TTTT
30677185 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
28 10 0.19
29 41 0.76
30 3 0.06
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (28 bp):
TTTTATAATTTTTTTACTATTTCTATAA
Found at i:30677193 original size:19 final size:20
Alignment explanation
Indices: 30677153--30677199 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
30677143 TTTCTATATA
*
30677153 TTTTATAATTTTTTTACTAT
1 TTTTATAATTTTTTTACGAT
*
30677173 TTTTATAA-TTTTTTGCGAT
1 TTTTATAATTTTTTTACGAT
30677192 TTTTATAA
1 TTTTATAA
30677200 AAAATTCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (20 bp):
TTTTATAATTTTTTTACGAT
Found at i:30677253 original size:19 final size:19
Alignment explanation
Indices: 30677211--30677265 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
30677201 AAATTCTAAT
30677211 TTTTAATATTTTTATTAAA
1 TTTTAATATTTTTATTAAA
* *
30677230 ATTTAATAGTTTTTA-TAAG
1 TTTTAATA-TTTTTATTAAA
*
30677249 TTTTATTGATTTTTATT
1 TTTTAAT-ATTTTTATT
30677266 TTTTATCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 21 0.72
20 8 0.28
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTTAATATTTTTATTAAA
Found at i:30681082 original size:40 final size:39
Alignment explanation
Indices: 30681028--30681183 Score: 224
Period size: 39 Copynumber: 3.9 Consensus size: 39
30681018 AAATATATTT
* *
30681028 ATTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
30681067 ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTTTA
1 ATTTTTTT-AATTTTAAAATATTTTTAAAATAC---TTTTTTA
* *
30681110 ATTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTTT
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
*
30681149 ATTTTTTTAATTTTAAAATATTTTAAAAATA-TTTT
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTT
30681184 AAAAATATTT
Statistics
Matches: 108, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
38 4 0.04
39 44 0.41
40 22 0.20
42 23 0.21
43 15 0.14
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (39 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
Found at i:30681092 original size:11 final size:11
Alignment explanation
Indices: 30681078--30681220 Score: 69
Period size: 11 Copynumber: 13.9 Consensus size: 11
30681068 TTTTTTTAAA
30681078 TTTTAAAATAT
1 TTTTAAAATAT
30681089 TTTTAAAATACTTT
1 TTTTAAAATA---T
**
30681103 TTTTTTAAT-T
1 TTTTAAAATAT
*
30681113 TTTT-TAA--T
1 TTTTAAAATAT
30681121 TT-TAAAATAT
1 TTTTAAAATAT
30681131 TTTTAAAATAT
1 TTTTAAAATAT
**
30681142 TTTT--TTTAT
1 TTTTAAAATAT
* *
30681151 TTTT---TTAA
1 TTTTAAAATAT
30681159 TTTTAAAATAT
1 TTTTAAAATAT
*
30681170 TTTAAAAATAT
1 TTTTAAAATAT
*
30681181 TTTAAAAATAT
1 TTTTAAAATAT
**
30681192 TTTTTTAAT-T
1 TTTTAAAATAT
30681202 TTTTAAAA-A-
1 TTTTAAAATAT
30681211 TTTTAAAATA
1 TTTTAAAATA
30681221 AAAATGGGCC
Statistics
Matches: 106, Mismatches: 14, Indels: 25
0.73 0.10 0.17
Matches are distributed among these distances:
7 1 0.01
8 12 0.11
9 18 0.17
10 16 0.15
11 51 0.48
14 8 0.08
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:30681196 original size:81 final size:81
Alignment explanation
Indices: 30681027--30681220 Score: 243
Period size: 82 Copynumber: 2.4 Consensus size: 81
30681017 TAAATATATT
* *
30681027 TATTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTAATTTTTTTAAATTTTAAAATATTTT
1 TATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAATTTTTTTAAATTTTAAAATATTTT
* ****
30681092 TAAAATACTTTTTTTT
66 AAAAATACTTTTAAAA
* *
30681108 TAATTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTTTATTTTTTT-AATTTTAAAATATTT
1 T-ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAATTTTTTTAAATTTTAAAATATTT
30681172 TAAAAATA-TTTTAAAAA
65 TAAAAATACTTTT-AAAA
30681189 TATTTTTTTAATTTTTTAAAA-A-TTTTAAAATA
1 TATTTTTTTAA--TTTTAAAATATTTTTAAAATA
30681221 AAAATGGGCC
Statistics
Matches: 100, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
80 24 0.24
81 25 0.25
82 51 0.51
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (81 bp):
TATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAATTTTTTTAAATTTTAAAATATTTT
AAAAATACTTTTAAAA
Found at i:30685241 original size:37 final size:37
Alignment explanation
Indices: 30685158--30685241 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 37
30685148 TGGTATAATG
30685158 GTAAGATTTGCTCAATTAAGTTCCATTCAATATAACA
1 GTAAGATTTGCTCAATTAAGTTCCATTCAATATAACA
* *
30685195 GTATGATTTGCTCAATTGAGCTT-CATTCAATATAACA
1 GTAAGATTTGCTCAATTAAG-TTCCATTCAATATAACA
*
30685232 GTAAAATTTG
1 GTAAGATTTG
30685242 GCTTGATAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
37 40 0.95
38 2 0.05
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (37 bp):
GTAAGATTTGCTCAATTAAGTTCCATTCAATATAACA
Found at i:30688112 original size:19 final size:19
Alignment explanation
Indices: 30688076--30688114 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
30688066 TATTATTAAT
**
30688076 ATATTTATAATTCTAATAA
1 ATATTTATAATTAAAATAA
*
30688095 ATATTTATTATTAAAATAA
1 ATATTTATAATTAAAATAA
30688114 A
1 A
30688115 ATTAAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:30688142 original size:13 final size:12
Alignment explanation
Indices: 30688122--30688164 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
30688112 AAAATTAAAA
30688122 TATTAAATAATT
1 TATTAAATAATT
30688134 TATTAAAATAAATT
1 TATT-AAAT-AATT
30688148 ATATT-AATAATT
1 -TATTAAATAATT
30688160 TATTA
1 TATTA
30688165 TATGACTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
11 4 0.15
12 8 0.30
13 7 0.26
14 4 0.15
15 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TATTAAATAATT
Found at i:30688175 original size:29 final size:27
Alignment explanation
Indices: 30688102--30688164 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 27
30688092 TAAATATTTA
30688102 TTATTAAAATAAAATTAAAATATTAAATAAT
1 TTATTAAAAT-AAATT---ATATTAAATAAT
30688133 TTATTAAAATAAATTATATT-AATAAT
1 TTATTAAAATAAATTATATTAAATAAT
30688159 TTATTA
1 TTATTA
30688165 TATGACTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 12 0.38
27 5 0.16
30 5 0.16
31 10 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TTATTAAAATAAATTATATTAAATAAT
Found at i:30688979 original size:15 final size:14
Alignment explanation
Indices: 30688949--30688982 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
30688939 ATATTCTAAT
30688949 AATAAAAAAATATA
1 AATAAAAAAATATA
*
30688963 AATAAAATAACTATA
1 AATAAAA-AAATATA
30688978 AATAA
1 AATAA
30688983 TATTATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (14 bp):
AATAAAAAAATATA
Found at i:30693155 original size:47 final size:46
Alignment explanation
Indices: 30693040--30693164 Score: 135
Period size: 46 Copynumber: 2.7 Consensus size: 46
30693030 GGCAATTTAC
* * * *
30693040 CTGCTCGACTAGTGGTTTATGCACAACGTATTTTACAGTAGTTTAT
1 CTGCTCGACCAGTGGTTTATCCACAACGTATTTTACAGGAGTTCAT
* * * *
30693086 CTGCTCAACCAGCGATTTATCCACAACGTATTTTAGTCGGGAG-TCAT
1 CTGCTCGACCAGTGGTTTATCCACAACGTATTTTA--CAGGAGTTCAT
* *
30693133 CTGCTCGACCAGTGGTTCATCCACAACATATT
1 CTGCTCGACCAGTGGTTTATCCACAACGTATT
30693165 AAGCAACATT
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
46 30 0.47
47 30 0.47
48 4 0.06
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (46 bp):
CTGCTCGACCAGTGGTTTATCCACAACGTATTTTACAGGAGTTCAT
Found at i:30693213 original size:93 final size:93
Alignment explanation
Indices: 30693116--30693347 Score: 247
Period size: 93 Copynumber: 2.5 Consensus size: 93
30693106 CCACAACGTA
* * *
30693116 TTTTAGTCGGGAG-TCATCTGCTCGACCAGTGGTTCATCCACAACATATTAAGCAACATTT-ATT
1 TTTTAGTCGGCAGTTCATCTGCACGACCAGTGGTTCATCCACAACATATT-AGC-ACATTTGATA
* ** *
30693179 TGCACCCATGGATGGTTCATCCACCAATAC
64 TACACAAAAGGATGGTTCATCCACCAATAC
* ** *
30693209 TTTTAGTCGGCAGTTTATCTGCACGACCAGTGGTTCATCCACAATGTATTAGCATATTTGATATA
1 TTTTAGTCGGCAGTTCATCTGCACGACCAGTGGTTCATCCACAACATATTAGCACATTTGATATA
30693274 CACAAAAGGATGGTTCATCCACCAATA-
66 CACAAAAGGATGGTTCATCCACCAATAC
** * *
30693301 TTCTTATTGTTAGCAGTTCATCTACAACGATCAGTGGTT-ATCCACAA
1 TT-TTA--GTCGGCAGTTCATCTGC-ACGACCAGTGGTTCATCCACAA
30693348 TGTGGTGTGA
Statistics
Matches: 117, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
92 7 0.06
93 45 0.38
94 32 0.27
95 21 0.18
96 12 0.10
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (93 bp):
TTTTAGTCGGCAGTTCATCTGCACGACCAGTGGTTCATCCACAACATATTAGCACATTTGATATA
CACAAAAGGATGGTTCATCCACCAATAC
Found at i:30711148 original size:21 final size:20
Alignment explanation
Indices: 30711124--30711162 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
30711114 TCTTTTTGAA
*
30711124 TTTTATGAGTTTATTTTATAC
1 TTTTATGA-ATTATTTTATAC
*
30711145 TTTTTTGAATTATTTTAT
1 TTTTATGAATTATTTTAT
30711163 TTTTAATATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTTATGAATTATTTTATAC
Found at i:30712687 original size:2 final size:2
Alignment explanation
Indices: 30712628--30712676 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
30712618 ACTACGAATG
30712628 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30712670 TA TA TA T
1 TA TA TA T
30712677 TTGTTATATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30712719 original size:47 final size:47
Alignment explanation
Indices: 30712668--30712793 Score: 162
Period size: 47 Copynumber: 2.7 Consensus size: 47
30712658 TATATATATA
** * *
30712668 TATATATATTTGTTATATATTGAAATGAATTAATCTATAGCTGAATG
1 TATATATATTTGTTATGCATTGAAATGAATTAAGCTATAGCCGAATG
* * ** *
30712715 TATATGTAATTGTTATGCAGAGAAATGAATTAAGCTATGGCCGAATG
1 TATATATATTTGTTATGCATTGAAATGAATTAAGCTATAGCCGAATG
*
30712762 TATATATATTTGTTATGCATTGAAATAAATTA
1 TATATATATTTGTTATGCATTGAAATGAATTA
30712794 TTTGAAATTA
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
47 65 1.00
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (47 bp):
TATATATATTTGTTATGCATTGAAATGAATTAAGCTATAGCCGAATG
Found at i:30712904 original size:47 final size:50
Alignment explanation
Indices: 30712848--30713106 Score: 129
Period size: 47 Copynumber: 5.0 Consensus size: 50
30712838 GGTATACATT
* * *
30712848 GAAATGAATTAATCTATAGCTGAATG-TATATGTA-A-TTGTTATGCAGA
1 GAAATGAATTAAACTATAGCCGAATGATATATATATATTTGTTATGCAGA
*
30712895 GAAATGAATTAAACTATGGCCGAATGCATATATATATATTTGTTATGCATTGAAA
1 GAAATGAATTAAACTATAGCCGAATG-ATATATATATATTTGTTATGCA--G--A
* * * * * * * * **
30712950 TAAATTATTTGAAATTACATAG--GTTATGGCCGAATGTATATATATATTTATTATACATT
1 GAAATGAATT-AAACT--ATAGCCG-AAT----G-ATATAT--ATATATTTGTTATGCAGA
* * *
30713009 GAAATGAATTAATCTATAGCTGAATG-TATATGTA-A-TTGTTATGCAGA
1 GAAATGAATTAAACTATAGCCGAATGATATATATATATTTGTTATGCAGA
*
30713056 GAAATGAATTAAACTATGGCCGAATGTATATATATATATATTTGTTATGCA
1 GAAATGAATTAAACTATAGCCGAATG---ATATATATATATTTGTTATGCA
30713107 TTGAAATAAA
Statistics
Matches: 154, Mismatches: 32, Indels: 46
0.66 0.14 0.20
Matches are distributed among these distances:
47 54 0.35
48 1 0.01
49 9 0.06
50 1 0.01
51 21 0.14
52 1 0.01
53 12 0.08
55 8 0.05
56 9 0.06
57 4 0.03
58 7 0.05
59 7 0.05
61 6 0.04
63 14 0.09
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (50 bp):
GAAATGAATTAAACTATAGCCGAATGATATATATATATTTGTTATGCAGA
Found at i:30713091 original size:163 final size:160
Alignment explanation
Indices: 30712666--30713155 Score: 763
Period size: 163 Copynumber: 3.0 Consensus size: 160
30712656 TATATATATA
*
30712666 TATATATATATTTGTTATATATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTTAT
1 TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTTAT
*
30712731 GCAGAGAAATGAATTAAGCTATGGCCGAATG---TATATATATTTGTTATGCATTGAAATAAATT
66 GCAGAGAAATGAATTAAACTATGGCCGAATGATATATATATATTTGTTATGCATTGAAATAAATT
** **
30712793 ATTTGAAATTACGGAGGGGGATGGCCGAATG
131 ATTTGAAATTACATA-GGCTATGGCCGAATG
**** *
30712824 TATATATATGGGGGGGTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTTA
1 TATATATAT-ATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTTA
30712889 TGCAGAGAAATGAATTAAACTATGGCCGAATGCATATATATATATTTGTTATGCATTGAAATAAA
65 TGCAGAGAAATGAATTAAACTATGGCCGAATG-ATATATATATATTTGTTATGCATTGAAATAAA
*
30712954 TTATTTGAAATTACATAGGTTATGGCCGAATG
129 TTATTTGAAATTACATAGGCTATGGCCGAATG
*
30712986 TATATATATATTTATTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTTAT
1 TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTTAT
30713051 GCAGAGAAATGAATTAAACTATGGCCGAATGTATATATATATATATTTGTTATGCATTGAAATAA
66 GCAGAGAAATGAATTAAACTATGGCCGAATG---ATATATATATATTTGTTATGCATTGAAATAA
* *
30713116 ATTATTTGAAGTTACATAAGCTATGGCCGAATG
128 ATTATTTGAAATTACATAGGCTATGGCCGAATG
30713149 TA-ATATA
1 TATATATA
30713156 GTGAATTGTT
Statistics
Matches: 304, Mismatches: 21, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
158 9 0.03
159 80 0.26
161 81 0.27
162 27 0.09
163 107 0.35
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37
Consensus pattern (160 bp):
TATATATATATTTGTTATACATTGAAATGAATTAATCTATAGCTGAATGTATATGTAATTGTTAT
GCAGAGAAATGAATTAAACTATGGCCGAATGATATATATATATTTGTTATGCATTGAAATAAATT
ATTTGAAATTACATAGGCTATGGCCGAATG
Found at i:30713289 original size:41 final size:41
Alignment explanation
Indices: 30713227--30713380 Score: 245
Period size: 41 Copynumber: 3.8 Consensus size: 41
30713217 TGTAAGTTTG
*
30713227 GGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATCA
1 GGCTCTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATCA
30713268 GGCTCTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATCA
1 GGCTCTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATCA
* *
30713309 GGCTCTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTAACG
1 GGCTCTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATCA
* * * *
30713350 GGCTTTGTGCCTAGCAGGCTTTATGCCGGTG
1 GGCTCTATGCCTAGCAGGCTCTGTGCCGGTG
30713381 TTTTATATAA
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 106 1.00
ACGTcount: A:0.18, C:0.23, G:0.31, T:0.28
Consensus pattern (41 bp):
GGCTCTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTATCA
Found at i:30720547 original size:2 final size:2
Alignment explanation
Indices: 30720510--30720536 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30720500 ACTACTAATG
30720510 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
30720537 TTGTTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30729007 original size:84 final size:83
Alignment explanation
Indices: 30728712--30729016 Score: 226
Period size: 84 Copynumber: 3.6 Consensus size: 83
30728702 GGCAAAGTTG
* * ** * * *
30728712 AGGACTGTACTCCAAGGAGACTCAAGTTCAAGCAAAGGGT-ATATGTTAATAA-CATAAATGATG
1 AGGACTGTACTCCAAGGAGACTGAAGTTC-GGCAAAAAGTAAT-TGTTGACAACCA-AAATGGTG
* *
30728775 ATAACCAAAACAGTAGAGTCA
63 ATAACAAAAACAGTAAAGTCA
* * * * * * * *
30728796 AGGAGTTTACCCCGAA-GAGACTCAAGTTCAGACGAAGAGAAATTGTTGACAACCAAAATGGTGA
1 AGGACTGTACTCC-AAGGAGACTGAAGTTC-GGCAAAAAGTAATTGTTGACAACCAAAATGGTGA
* *
30728860 TAACCAAAACGGTAAAGTCA
64 TAACAAAAACAGTAAAGTCA
* * * * *
30728880 AGGAGTGTACTCCAATGAGACTGAAATTTCGGCGAAGAGTAATTGTTGACAACCAAAATGGTGAT
1 AGGACTGTACTCCAAGGAGACTG-AAGTTCGGCAAAAAGTAATTGTTGACAACCAAAATGGTGAT
*
30728945 AACAAAAACAGTAGAA-TCG
65 AACAAAAACAGTA-AAGTCA
* * *
30728964 AGGAACT-TACTTCAAGGATACATG-AGTTCAGGCAAAAATTAATTGTTGACAAC
1 AGG-ACTGTACTCCAAGGAGAC-TGAAGTTC-GGCAAAAAGTAATTGTTGACAAC
30729017 ATAGATGATC
Statistics
Matches: 182, Mismatches: 30, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
83 6 0.03
84 159 0.87
85 17 0.09
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (83 bp):
AGGACTGTACTCCAAGGAGACTGAAGTTCGGCAAAAAGTAATTGTTGACAACCAAAATGGTGATA
ACAAAAACAGTAAAGTCA
Found at i:30729132 original size:81 final size:81
Alignment explanation
Indices: 30729058--30729394 Score: 584
Period size: 81 Copynumber: 4.2 Consensus size: 81
30729048 AGGAGTTTAG
* *
30729058 TCCAAGGAAACTTGAGTCCTGCCAAAGAAATCTTGACAACAGAAATTCTGATGATCAAAATAGTA
1 TCCAACGAAACTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTA
30729123 GAGGTGAGGACTCTGC
66 GAGGTGAGGACTCTGC
30729139 TCCAACGAAACTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTA
1 TCCAACGAAACTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTA
30729204 GAGGTGAGGACTCTGC
66 GAGGTGAGGACTCTGC
* * *
30729220 TCCAACGACACTTGAGTCCTGCCAAAGAACTCTTGACAACAGAATTTCTGATGATCGAAATAGTA
1 TCCAACGAAACTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTA
*
30729285 GAGGTGAGGACACTGC
66 GAGGTGAGGACTCTGC
* * *
30729301 TCCAACAAAACTTGAGTCCTGCCGAAGAGCTCTTGACAACAGAAATTCTGATGATCAAAATAGTA
1 TCCAACGAAACTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTA
30729366 GAGGTGAGGACTCTGC
66 GAGGTGAGGACTCTGC
*
30729382 TCCAAGGAAACTT
1 TCCAACGAAACTT
30729395 ATCTTCAGGC
Statistics
Matches: 241, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 241 1.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (81 bp):
TCCAACGAAACTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTA
GAGGTGAGGACTCTGC
Found at i:30737744 original size:103 final size:103
Alignment explanation
Indices: 30737500--30737868 Score: 623
Period size: 103 Copynumber: 3.6 Consensus size: 103
30737490 TAACCGTTAT
* *
30737500 CGGTGGATTCCGCACTTAGCAACCACCAATGAATCGGGGAATCAGCAGACAGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCAGACAGCAACCCCTTGGGG
* * *
30737565 GAATCAGCACTTAGCAACCCCC-TTCACATTTTAGATG
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* * *** *
30737602 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATTAGCATTTAGCAACCCCTCGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCAGACAGCAACCCCTTGGGG
30737667 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
30737705 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCAGACAGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCAGACAGCAACCCCTTGGGG
30737770 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
*
30737808 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCAGACAGCAACCCCTT
30737869 TATATGCAAT
Statistics
Matches: 248, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
102 79 0.32
103 169 0.68
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.19
Consensus pattern (103 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCAGACAGCAACCCCTTGGGG
GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
Found at i:30737751 original size:33 final size:33
Alignment explanation
Indices: 30737709--30737864 Score: 108
Period size: 33 Copynumber: 4.6 Consensus size: 33
30737699 AAAATACGGT
30737709 GGAATCAGCACTTAGCAACCACCAATGAATCGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
*** *
30737742 GGAATCAGCAGACAGCAACC-CC--T---TGGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
* *
30737769 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGG
1 GGAATCAGCACTTAGCAA-CCAC---CA-A--T-GAAT-CGG
30737811 TGGAATCAGCACTTAGCAACCACCAATGAATCGG
1 -GGAATCAGCACTTAGCAACCACCAATGAATCGG
**
30737845 GGAATCAGCACACAGCAACC
1 GGAATCAGCACTTAGCAACC
30737865 CCTTTATATG
Statistics
Matches: 95, Mismatches: 12, Indels: 32
0.68 0.09 0.23
Matches are distributed among these distances:
27 18 0.19
28 2 0.02
29 1 0.01
30 1 0.01
32 3 0.03
33 35 0.37
34 3 0.03
35 3 0.03
36 1 0.01
37 1 0.01
38 1 0.01
39 2 0.02
41 1 0.01
42 5 0.05
43 18 0.19
ACGTcount: A:0.35, C:0.29, G:0.21, T:0.16
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAATCGG
Found at i:30745428 original size:103 final size:103
Alignment explanation
Indices: 30745057--30745428 Score: 530
Period size: 106 Copynumber: 3.6 Consensus size: 103
30745047 TAACCGTTAT
* * *
30745057 CGGTGGATTCCGCACTTAGCAACCACCAATGAATCGGGGAATCAGCAGACAGCAACCCCTTAGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTAGGG
* *
30745122 GAATCAGCACTTAGCAACCCCC-TTCACATTTCAGATG
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAGATA
* * ** **
30745159 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATTAGCACTTAGCAACCCCTCCGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTAGGG
* * *
30745224 GAATCAGCAGTTAGCATCCCCCTTTCACATTTAACCGTTA
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAA--GATA
* * *
30745264 TCGGTGGATTCCGCACTTAGCAACCACCAATGAATCGGGGAATCAGCAGACAGCAACCCCTTAGG
1 -CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTAGG
*
30745329 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
65 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAGATA
* *
30745368 CGATGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAACAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTT
30745429 TATATGCAAT
Statistics
Matches: 234, Mismatches: 32, Indels: 7
0.86 0.12 0.03
Matches are distributed among these distances:
102 76 0.32
103 66 0.28
104 2 0.01
105 2 0.01
106 88 0.38
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (103 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTAGGG
GAATCAGCACTTAGCAACCCCCTTTCACATTTAAGATA
Found at i:30751823 original size:24 final size:24
Alignment explanation
Indices: 30751754--30751826 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 24
30751744 ATGCACATTC
* *
30751754 GTATATGAGAGTCCCTTGTGTGGGAC
1 GTATATGAGAG-CCCTT-TATGGGAT
*
30751780 GTATA--AGAGCCCTTTTTGGGAT
1 GTATATGAGAGCCCTTTATGGGAT
*
30751802 GTATATGAGAGCCCCTTATGGGAT
1 GTATATGAGAGCCCTTTATGGGAT
30751826 G
1 G
30751827 AATGGAAGTC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 11 0.27
23 5 0.12
24 20 0.49
26 5 0.12
ACGTcount: A:0.22, C:0.15, G:0.32, T:0.32
Consensus pattern (24 bp):
GTATATGAGAGCCCTTTATGGGAT
Found at i:30751908 original size:28 final size:28
Alignment explanation
Indices: 30751877--30752051 Score: 163
Period size: 28 Copynumber: 6.2 Consensus size: 28
30751867 GTTCGCTAGG
*
30751877 ACGATTTTAAACGTGGAAGTCCGTCAGA
1 ACGATCTTAAACGTGGAAGTCCGTCAGA
** *
30751905 ACGATCTTAAACGTGGAAGTTTG-CTAGG
1 ACGATCTTAAACGTGGAAGTCCGTC-AGA
* * *
30751933 ACAATCTTAAACGTGGAAGTCTGCCAGA
1 ACGATCTTAAACGTGGAAGTCCGTCAGA
** * * * *
30751961 ATAATCCTAAGCGTGGAAGTCCGCCAGG
1 ACGATCTTAAACGTGGAAGTCCGTCAGA
* * * *
30751989 ACGATCTTAAACATGGAAATTCATCAGA
1 ACGATCTTAAACGTGGAAGTCCGTCAGA
* *
30752017 ACGATCTTAAATGTGGAAGTCCGTCAGG
1 ACGATCTTAAACGTGGAAGTCCGTCAGA
30752045 ACGATCT
1 ACGATCT
30752052 AATGTGAAAG
Statistics
Matches: 117, Mismatches: 28, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
27 1 0.01
28 115 0.98
29 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (28 bp):
ACGATCTTAAACGTGGAAGTCCGTCAGA
Found at i:30751931 original size:56 final size:56
Alignment explanation
Indices: 30751862--30752051 Score: 211
Period size: 56 Copynumber: 3.4 Consensus size: 56
30751852 ACCATACACA
*
30751862 TGGAAGTTCGCTAGGACGATTTTAAACGTGGAAGTCCGTCAGAACGATCTTAAACG
1 TGGAAGTTCGCTAGGACGATCTTAAACGTGGAAGTCCGTCAGAACGATCTTAAACG
* * * * ** * *
30751918 TGGAAGTTTGCTAGGACAATCTTAAACGTGGAAGTCTGCCAGAATAATCCTAAGCG
1 TGGAAGTTCGCTAGGACGATCTTAAACGTGGAAGTCCGTCAGAACGATCTTAAACG
* * * * * * *
30751974 TGGAAGTCCGCCAGGACGATCTTAAACATGGAAATTCATCAGAACGATCTTAAATG
1 TGGAAGTTCGCTAGGACGATCTTAAACGTGGAAGTCCGTCAGAACGATCTTAAACG
*
30752030 TGGAAGTCCG-TCAGGACGATCT
1 TGGAAGTTCGCT-AGGACGATCT
30752052 AATGTGAAAG
Statistics
Matches: 108, Mismatches: 25, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
56 108 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (56 bp):
TGGAAGTTCGCTAGGACGATCTTAAACGTGGAAGTCCGTCAGAACGATCTTAAACG
Found at i:30768923 original size:18 final size:20
Alignment explanation
Indices: 30768902--30768951 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
30768892 AAAGGAAGAC
30768902 AGAAAAAGA-AATCAAAAA-
1 AGAAAAAGAGAATCAAAAAG
*
30768920 AGAAAAAGAGAATGAAAAAG
1 AGAAAAAGAGAATCAAAAAG
30768940 AGCAAAAAGAGA
1 AG-AAAAAGAGA
30768952 TTCAGAGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 8 0.29
20 2 0.07
21 9 0.32
ACGTcount: A:0.72, C:0.04, G:0.20, T:0.04
Consensus pattern (20 bp):
AGAAAAAGAGAATCAAAAAG
Found at i:30770747 original size:33 final size:34
Alignment explanation
Indices: 30770710--30770781 Score: 119
Period size: 33 Copynumber: 2.1 Consensus size: 34
30770700 GAGTTAGTTT
30770710 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
* *
30770743 ATTAATTTTAGTTCAGCTTAAATAAGTGTTAGTA
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
30770777 ATTAA
1 ATTAA
30770782 TTTGTTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 30 0.83
34 6 0.17
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (34 bp):
ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
Found at i:30778426 original size:16 final size:16
Alignment explanation
Indices: 30778405--30778435 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30778395 CGTTTATGAG
30778405 TTAGGGATTTCAGAAC
1 TTAGGGATTTCAGAAC
*
30778421 TTAGGGATTTTAGAA
1 TTAGGGATTTCAGAA
30778436 TAGGGAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (16 bp):
TTAGGGATTTCAGAAC
Found at i:30779229 original size:23 final size:23
Alignment explanation
Indices: 30779186--30779230 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
30779176 GGTTTTTGTA
*
30779186 CCCTAAAACCCGAAGCTATTAAT
1 CCCTAAAACCCGAAACTATTAAT
*
30779209 CCCTATAACCCGTAAAC-ATTAA
1 CCCTAAAACCCG-AAACTATTAA
30779231 AATTAAAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (23 bp):
CCCTAAAACCCGAAACTATTAAT
Found at i:30780962 original size:41 final size:41
Alignment explanation
Indices: 30780891--30780986 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
30780881 TTTTTACACC
* * *
30780891 AACGCCGCTATAGACCCAAGAGTTACCGGCGCTTCTCCAGG
1 AACGCCGCTATAGACCCAACAGTTACCGGCGATTCTCCAGA
* * *
30780932 AACGCCGCTATAGACCGGAACA-TTAGCGGCGATTCTCCATA
1 AACGCCGCTATAGACC-CAACAGTTACCGGCGATTCTCCAGA
*
30780973 AACGCCGCTTTAGA
1 AACGCCGCTATAGA
30780987 GCAGAGCATC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 44 0.94
42 3 0.06
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (41 bp):
AACGCCGCTATAGACCCAACAGTTACCGGCGATTCTCCAGA
Found at i:30781001 original size:41 final size:41
Alignment explanation
Indices: 30780891--30781003 Score: 102
Period size: 41 Copynumber: 2.8 Consensus size: 41
30780881 TTTTTACACC
* * * * * *
30780891 AACGCCGCTATAGACC-CAAGAGTTACCGGCGCTTCTCCAGG
1 AACGCCGCTATAGACCAGAACA-TCAGCGGCGATTCTCCAGA
* * *
30780932 AACGCCGCTATAGACCGGAACATTAGCGGCGATTCTCCATA
1 AACGCCGCTATAGACCAGAACATCAGCGGCGATTCTCCAGA
* * *
30780973 AACGCCGCTTTAGAGCAGAGCATCAGCGGCG
1 AACGCCGCTATAGACCAGAACATCAGCGGCG
30781004 GTTTATGAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 57 0.95
42 3 0.05
ACGTcount: A:0.27, C:0.31, G:0.26, T:0.17
Consensus pattern (41 bp):
AACGCCGCTATAGACCAGAACATCAGCGGCGATTCTCCAGA
Found at i:30781297 original size:114 final size:113
Alignment explanation
Indices: 30781096--30781448 Score: 544
Period size: 113 Copynumber: 3.1 Consensus size: 113
30781086 ACTTAACGCC
* * * *
30781096 AAACGCCGCTGAAGAACGGATTATTAGCGGCGTTTGGGCAAAAACCGCCACTAGTGTTCCCAAAT
1 AAACGCCGCTAAAGAACGGAGTATTAGCGGCGCTTGGGC-AAAACCGCCACTAATGTTCCCAAAT
*
30781161 ATATGAAAACGGCGTCGTTCTGTGTTACTCTATTTGCGACGCTTTTTGTA
65 ATATGAAAACGGCGTCGTTCTGTGTTACTCTA-TTGCGGCGCTTTTTGTA
*
30781211 AAACGCCGCTAAAGAATGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
1 AAACGCCGCTAAAGAACGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
* * *
30781276 TATGAAAATGGCGTCGTTCTGTGTTACTCCATTGCGGCGCTTTTTATA
66 TATGAAAACGGCGTCGTTCTGTGTTACTCTATTGCGGCGCTTTTTGTA
* * * *
30781324 AAACGCCGCTGAAGAACAGAGTTTTAGCGGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAATA
1 AAACGCCGCTAAAGAACGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
* *
30781389 TATGAAAACGGCGTCGTTCTGTGTGACTGTATTGCGGCGCTTTTTGTA
66 TATGAAAACGGCGTCGTTCTGTGTTACTCTATTGCGGCGCTTTTTGTA
*
30781437 AAACGCTGCTAA
1 AAACGCCGCTAA
30781449 TGCTTGGTTT
Statistics
Matches: 217, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
113 128 0.59
114 54 0.25
115 35 0.16
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (113 bp):
AAACGCCGCTAAAGAACGGAGTATTAGCGGCGCTTGGGCAAAACCGCCACTAATGTTCCCAAATA
TATGAAAACGGCGTCGTTCTGTGTTACTCTATTGCGGCGCTTTTTGTA
Found at i:30781566 original size:41 final size:40
Alignment explanation
Indices: 30781485--30781569 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
30781475 TGTAGCGGCA
* *
30781485 CTAATGCTCGATATTTTGCGGCGTTTTTCGTAAAATGCCG
1 CTAATGCTCGATATTTAGCGGCGTTTTTCGTAAAACGCCG
* * *
30781525 CTAATGCTCGAT-TATTAGTGGCGTTTTTTGTCCAAACGCCG
1 CTAATGCTCGATAT-TTAGCGGCGTTTTTCGT-AAAACGCCG
30781566 CTAA
1 CTAA
30781570 AAGCGCCGCT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
39 1 0.03
40 26 0.68
41 11 0.29
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (40 bp):
CTAATGCTCGATATTTAGCGGCGTTTTTCGTAAAACGCCG
Found at i:30782610 original size:16 final size:16
Alignment explanation
Indices: 30782586--30782623 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
30782576 TTTGGTTCGC
* *
30782586 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
30782602 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
30782618 TGTAAT
1 TGTAAT
30782624 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:30783817 original size:17 final size:18
Alignment explanation
Indices: 30783784--30783818 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
30783774 AATTTGTGTA
*
30783784 TTGTTTTAATCATTTTTT
1 TTGTTTTAATAATTTTTT
30783802 TTGTTTTAA-AATTTTTT
1 TTGTTTTAATAATTTTTT
30783819 ATTTAATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.20, C:0.03, G:0.06, T:0.71
Consensus pattern (18 bp):
TTGTTTTAATAATTTTTT
Found at i:30789379 original size:16 final size:16
Alignment explanation
Indices: 30789358--30789393 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
30789348 TTTGGTTCGC
30789358 TGTATTGGATTAGAAG
1 TGTATTGGATTAGAAG
*
30789374 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAAG
30789390 TGTA
1 TGTA
30789394 ATAGCAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.33, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAAG
Found at i:30789646 original size:16 final size:16
Alignment explanation
Indices: 30789609--30789650 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
30789599 TTAATCATAT
*
30789609 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
30789625 TT-AAATATATTATAA
1 TTAAAATATATTATAA
30789640 TTAAAATATAT
1 TTAAAATATAT
30789651 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:30789657 original size:14 final size:15
Alignment explanation
Indices: 30789618--30789659 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
30789608 TTTAAACATA
*
30789618 ATTATTATTAAATAT
1 ATTATAATTAAATAT
30789633 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
30789647 A-TATAATTTAATA
1 ATTATAATTAAATA
30789660 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:30789854 original size:26 final size:28
Alignment explanation
Indices: 30789825--30789885 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
30789815 TATGAATTTG
*
30789825 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
30789851 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
30789879 TAAAATT
1 TATAATT
30789886 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:30792793 original size:22 final size:24
Alignment explanation
Indices: 30792745--30792797 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
30792735 AATTTTGTGT
30792745 TATTTTTAAAATTATTAAATAATA
1 TATTTTTAAAATTATTAAATAATA
30792769 TATTTTTATAAATT-TTAAA-ATATA
1 TATTTTTA-AAATTATTAAATA-ATA
30792793 TATTT
1 TATTT
30792798 GCTAATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 1 0.04
24 21 0.78
25 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTTTTAAAATTATTAAATAATA
Found at i:30798397 original size:10 final size:9
Alignment explanation
Indices: 30798350--30798486 Score: 73
Period size: 10 Copynumber: 14.6 Consensus size: 9
30798340 ACATGTGACA
30798350 AAAAATTAT
1 AAAAATTAT
30798359 AAAAA--AT
1 AAAAATTAT
* *
30798366 AGAAATCAAT
1 AAAAAT-TAT
30798376 AAAAATTAT
1 AAAAATTAT
*
30798385 AAAAGTTATT
1 AAAAATTA-T
**
30798395 AAATTTTATT
1 AAAAATTA-T
* *
30798405 CAAAATTAGAA
1 AAAAATT--AT
*
30798416 AAAAATTGT
1 AAAAATTAT
*
30798425 AAAAAAATAT
1 -AAAAATTAT
*
30798435 AAAAATTGT
1 AAAAATTAT
30798444 AAAAATTTAT
1 AAAAA-TTAT
*
30798454 AAAAATCAT
1 AAAAATTAT
30798463 AAAAGATTAT
1 AAAA-ATTAT
30798473 -AAAATGTAT
1 AAAAAT-TAT
30798482 AAAAA
1 AAAAA
30798487 AAGCTCTTTA
Statistics
Matches: 97, Mismatches: 20, Indels: 21
0.70 0.14 0.15
Matches are distributed among these distances:
7 6 0.06
8 2 0.02
9 39 0.40
10 43 0.44
11 6 0.06
12 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:30798438 original size:19 final size:19
Alignment explanation
Indices: 30798416--30798459 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
30798406 AAAATTAGAA
30798416 AAAAATTGTAAAAAAATAT
1 AAAAATTGTAAAAAAATAT
**
30798435 AAAAATTGTAAAAATTTAT
1 AAAAATTGTAAAAAAATAT
30798454 AAAAAT
1 AAAAAT
30798460 CATAAAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
AAAAATTGTAAAAAAATAT
Found at i:30798457 original size:28 final size:30
Alignment explanation
Indices: 30798416--30798487 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 30
30798406 AAAATTAGAA
*
30798416 AAAAATTGTA-AAAAAAT-ATAAAA-ATTGT
1 AAAAATT-TATAAAAAATCATAAAAGATTAT
30798444 AAAAATTTAT-AAAAATCATAAAAGATTAT
1 AAAAATTTATAAAAAATCATAAAAGATTAT
*
30798473 -AAAATGTATAAAAAA
1 AAAAATTTATAAAAAA
30798488 AGCTCTTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 8 0.21
28 21 0.55
29 9 0.24
ACGTcount: A:0.65, C:0.01, G:0.06, T:0.28
Consensus pattern (30 bp):
AAAAATTTATAAAAAATCATAAAAGATTAT
Found at i:30798465 original size:19 final size:19
Alignment explanation
Indices: 30798432--30798476 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
30798422 TGTAAAAAAA
**
30798432 TATAAAAATTGTAAAA-ATT
1 TATAAAAATCATAAAAGA-T
30798451 TATAAAAATCATAAAAGAT
1 TATAAAAATCATAAAAGAT
30798470 TATAAAA
1 TATAAAA
30798477 TGTATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (19 bp):
TATAAAAATCATAAAAGAT
Found at i:30798669 original size:9 final size:9
Alignment explanation
Indices: 30798655--30798838 Score: 87
Period size: 9 Copynumber: 20.0 Consensus size: 9
30798645 TTTTGGAATG
30798655 ATAATTTTT
1 ATAATTTTT
30798664 ATAATTTCTT
1 ATAATTT-TT
* *
30798674 TTACGAATTTT
1 ATA--ATTTTT
*
30798685 ATATTTCTTT
1 ATAATT-TTT
*
30798695 AAAATTTTT
1 ATAATTTTT
30798704 ATAATTTTCT
1 ATAATTTT-T
30798714 -TACGA-TTTT
1 ATA--ATTTTT
*
30798723 ATAAAATTTT
1 AT-AATTTTT
*
30798733 AAAATTTTT
1 ATAATTTTT
30798742 AT-ATTTTT
1 ATAATTTTT
**
30798750 ACGATTTTT
1 ATAATTTTT
*
30798759 ATAA-ATTT
1 ATAATTTTT
30798767 -TAATTTTT
1 ATAATTTTT
30798775 -TAATTATTT
1 ATAATT-TTT
* *
30798784 ATTAAAATTTA
1 A-T-AATTTTT
*
30798795 ATATTTTTT
1 ATAATTTTT
*
30798804 ATAAATTTT
1 ATAATTTTT
30798813 ATAAATTTTT
1 AT-AATTTTT
30798823 AT--TTTTT
1 ATAATTTTT
30798830 ATAATTTTT
1 ATAATTTTT
30798839 TCCGCACGCC
Statistics
Matches: 132, Mismatches: 24, Indels: 38
0.68 0.12 0.20
Matches are distributed among these distances:
7 10 0.08
8 18 0.14
9 58 0.44
10 30 0.23
11 10 0.08
12 6 0.05
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:30798686 original size:21 final size:21
Alignment explanation
Indices: 30798660--30798726 Score: 72
Period size: 19 Copynumber: 3.4 Consensus size: 21
30798650 GAATGATAAT
30798660 TTTTATAATTTCTTTTACGAA
1 TTTTATAATTTCTTTTACGAA
*
30798681 TTTTAT-ATTTC-TTTA-AAA
1 TTTTATAATTTCTTTTACGAA
*
30798699 TTTTTATAATTT-TCTTACG-A
1 -TTTTATAATTTCTTTTACGAA
30798719 TTTTATAA
1 TTTTATAA
30798727 AATTTTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
18 2 0.05
19 18 0.46
20 13 0.33
21 6 0.15
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTTATAATTTCTTTTACGAA
Found at i:30798709 original size:27 final size:26
Alignment explanation
Indices: 30798679--30798838 Score: 105
Period size: 26 Copynumber: 5.9 Consensus size: 26
30798669 TTCTTTTACG
30798679 AATTTTATATTTCTTTAAAATTTTTAT
1 AATTTTATATTT-TTTAAAATTTTTAT
* * *
30798706 AATTTTCTTACGATTTTATAAAA-TTTTAA
1 AA--TT-TTA-TATTTTTTAAAATTTTTAT
**
30798735 AATTTT-TATATTTTTACGATTTTTAT
1 AATTTTATAT-TTTTTAAAATTTTTAT
* *
30798761 AAATTTTA-ATTTTTTAATTATTTATTAA
1 -AATTTTATATTTTTTAA-AATTT-TTAT
*
30798789 AATTTAATATTTTTTATAAA-TTTTAT
1 AATTTTATATTTTTTA-AAATTTTTAT
*
30798815 AAATTTT-TATTTTTTATAATTTTT
1 -AATTTTATATTTTTTAAAATTTTT
30798839 TCCGCACGCC
Statistics
Matches: 103, Mismatches: 16, Indels: 29
0.70 0.11 0.20
Matches are distributed among these distances:
24 2 0.02
25 8 0.08
26 29 0.28
27 29 0.28
28 12 0.12
29 10 0.10
30 9 0.09
31 4 0.04
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (26 bp):
AATTTTATATTTTTTAAAATTTTTAT
Found at i:30798734 original size:38 final size:37
Alignment explanation
Indices: 30798657--30798784 Score: 126
Period size: 38 Copynumber: 3.5 Consensus size: 37
30798647 TTGGAATGAT
**
30798657 AATTTTTATAATTTCTTTTACGAATTTTAT-ATTTCTTTAA
1 AATTTTTATAA-TT-TTTTACG-ATTTTATAAAAT-TTTAA
30798697 AATTTTTATAATTTTCTTACGATTTTATAAAATTTTAA
1 AATTTTTATAATTTT-TTACGATTTTATAAAATTTTAA
30798735 AATTTTTAT-A-TTTTTACGATTTT-TATAAATTTT--
1 AATTTTTATAATTTTTTACGATTTTATA-AAATTTTAA
*
30798768 AATTTTT-TAATTATTTA
1 AATTTTTATAATTTTTTA
30798785 TTAAAATTTA
Statistics
Matches: 80, Mismatches: 3, Indels: 16
0.81 0.03 0.16
Matches are distributed among these distances:
32 1 0.01
33 8 0.10
34 7 0.09
35 17 0.21
36 3 0.04
37 1 0.01
38 23 0.29
39 9 0.11
40 11 0.14
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (37 bp):
AATTTTTATAATTTTTTACGATTTTATAAAATTTTAA
Found at i:30798776 original size:17 final size:16
Alignment explanation
Indices: 30798719--30798774 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 16
30798709 TTTCTTACGA
30798719 TTTTATAAAATTTTAAAAT
1 TTTTAT-AAATTTT--AAT
*
30798738 TTTTAT-ATTTTTACGAT
1 TTTTATAAATTTTA--AT
30798755 TTTTATAAATTTTAAT
1 TTTTATAAATTTTAAT
30798771 TTTT
1 TTTT
30798775 TAATTATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
15 1 0.03
16 6 0.19
17 13 0.41
18 6 0.19
19 6 0.19
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTTATAAATTTTAAT
Found at i:30798839 original size:27 final size:27
Alignment explanation
Indices: 30798659--30798839 Score: 113
Period size: 27 Copynumber: 6.6 Consensus size: 27
30798649 GGAATGATAA
30798659 TTTTTATAATTTCTTT-TACGAATTTTATAT
1 TTTTTATAATTT-TTTATA--AATTTT-TAT
* * *
30798689 TTCTTTA-AAATTTTTATAATTTTCTTACG
1 TT-TTTATAATTTTTTATAAATTT-TTA-T
* **
30798718 ATTTTATAAAATTTTA-AAATTTTTAT
1 TTTTTATAATTTTTTATAAATTTTTAT
** *
30798744 ATTTTTACGA-TTTTTATAAATTTTAAT
1 -TTTTTATAATTTTTTATAAATTTTTAT
* * *
30798771 TTTTTAATTATTTATTA-AAATTTAATAT
1 TTTTT-ATAATTTTTTATAAATTT-TTAT
*
30798799 TTTTTATAA-ATTTTATAAATTTTTAT
1 TTTTTATAATTTTTTATAAATTTTTAT
30798825 TTTTTATAATTTTTT
1 TTTTTATAATTTTTT
30798840 CCGCACGCCA
Statistics
Matches: 117, Mismatches: 22, Indels: 27
0.70 0.13 0.16
Matches are distributed among these distances:
26 26 0.22
27 39 0.33
28 27 0.23
29 13 0.11
30 8 0.07
31 4 0.03
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTTTATAATTTTTTATAAATTTTTAT
Done.