Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015066.1 Kokia drynarioides strain JFW-HI SEQ_130110, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 364676
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 574 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:3999 original size:16 final size:17
Alignment explanation
Indices: 3980--4018 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3970 TTAATGACTT
*
3980 TTTTATATTTTA-AGAA
1 TTTTATATTTTATAAAA
*
3996 TTTTTTATTTTATAAAA
1 TTTTATATTTTATAAAA
4013 TTTTAT
1 TTTTAT
4019 TGATTTTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTTATATTTTATAAAA
Found at i:3999 original size:18 final size:17
Alignment explanation
Indices: 3968--4036 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 17
3958 ATTTTTTTGC
*
3968 TTTTAATGACTTTTTTAT
1 TTTTAA-GAATTTTTTAT
3986 ATTTTAAGAATTTTTTAT
1 -TTTTAAGAATTTTTTAT
4004 TTTATAA-AATTTTATTGAT
1 TTT-TAAGAATTTT-TT-AT
*
4023 TTTT-AGTATTTTTT
1 TTTTAAGAATTTTTT
4037 TTTATAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
17 12 0.27
18 21 0.48
19 11 0.25
ACGTcount: A:0.28, C:0.01, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTAAGAATTTTTTAT
Found at i:4565 original size:12 final size:12
Alignment explanation
Indices: 4547--4579 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
4537 CGTTTAAAAG
4547 CTCGTTTATTGA
1 CTCGTTTATTGA
*
4559 CTTGTTTA-TGA
1 CTCGTTTATTGA
4570 CTCGTTTATT
1 CTCGTTTATT
4580 TATTAATGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (12 bp):
CTCGTTTATTGA
Found at i:4724 original size:23 final size:23
Alignment explanation
Indices: 4660--4724 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
4650 AACATTGCTT
*
4660 GTGAATATGTTCAATTAAATGTTC
1 GTGAACATGTTCAATT-AATGTTC
* **
4684 ATGAACATGTTCGTTTAATGTTC
1 GTGAACATGTTCAATTAATGTTC
4707 GTGAACATGTTCAATTAA
1 GTGAACATGTTCAATTAA
4725 GTTAAATGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 22 0.65
24 12 0.35
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (23 bp):
GTGAACATGTTCAATTAATGTTC
Found at i:8582 original size:3 final size:3
Alignment explanation
Indices: 8574--8603 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
8564 ATCCCTCACT
8574 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
8604 GCAAAGTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17091 original size:63 final size:63
Alignment explanation
Indices: 17021--17149 Score: 152
Period size: 63 Copynumber: 2.0 Consensus size: 63
17011 ACATCATCAT
** * *
17021 CACATCACACACAATTGTTCCCTACATCAACACATACAA-CACCAATTTATTTTATACAAGCAC
1 CACATCACACACAATCATTCCCTACACCAACACA-ACAATCACCAATTTATTTCATACAAGCAC
** * * * *
17084 CACATCACATGCAATCATTCCCTGCACCAACACAACAATCACCACTTTATTTCATAGAGGCAC
1 CACATCACACACAATCATTCCCTACACCAACACAACAATCACCAATTTATTTCATACAAGCAC
17147 CAC
1 CAC
17150 TGCATGCGCA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
62 4 0.07
63 51 0.93
ACGTcount: A:0.37, C:0.34, G:0.05, T:0.23
Consensus pattern (63 bp):
CACATCACACACAATCATTCCCTACACCAACACAACAATCACCAATTTATTTCATACAAGCAC
Found at i:17161 original size:63 final size:64
Alignment explanation
Indices: 17038--17305 Score: 197
Period size: 63 Copynumber: 4.2 Consensus size: 64
17028 CACACAATTG
* * * *
17038 TTCCCTACATCAACACATACAA-CACCAATTTATTTTATACAAGCACCACATCACAT--GCAATC
1 TTCCCTGCACCAACACATACAATCACCAATTTATTTCATACAAGCACCAC-T-GCATGCGCAATC
17100 A
64 A
* * *
17101 TTCCCTGCACCAACACA-ACAATCACCACTTTATTTCATAGAGGCACCACTGCATGCGCAATCA
1 TTCCCTGCACCAACACATACAATCACCAATTTATTTCATACAAGCACCACTGCATGCGCAATCA
* *** * * * * * *
17164 TTCCTTGCATTGACACATTC-ATCACCAGTTTATTTCACACAAGCATCACAGCAAGCGCAATCA
1 TTCCCTGCACCAACACATACAATCACCAATTTATTTCATACAAGCACCACTGCATGCGCAATCA
* * * * * * ** ** * *
17227 TTCCTTGCACCGACACA-ACCATCATCGATTTTTTTTTTCACAAGCACCACAACACGCGTAATCA
1 TTCCCTGCACCAACACATACAATCACCAATTTATTTCAT-ACAAGCACCACTGCATGCGCAATCA
*
17291 TTCCATGCACCAACA
1 TTCCCTGCACCAACA
17306 ACTTCTCCAA
Statistics
Matches: 164, Mismatches: 35, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
61 3 0.02
62 6 0.04
63 120 0.73
64 35 0.21
ACGTcount: A:0.33, C:0.33, G:0.09, T:0.25
Consensus pattern (64 bp):
TTCCCTGCACCAACACATACAATCACCAATTTATTTCATACAAGCACCACTGCATGCGCAATCA
Found at i:25373 original size:21 final size:22
Alignment explanation
Indices: 25349--25392 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
25339 GTTTGAACAA
25349 TTTAA-TTT-TTTTTTTATGTTT
1 TTTAACTTTCTTTTTTTA-GTTT
25370 TTTAACTTTCTTTTTTTAGTTT
1 TTTAACTTTCTTTTTTTAGTTT
25392 T
1 T
25393 CATTCTCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 8 0.38
23 8 0.38
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.77
Consensus pattern (22 bp):
TTTAACTTTCTTTTTTTAGTTT
Found at i:26916 original size:21 final size:21
Alignment explanation
Indices: 26886--26931 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
26876 TACTTGTGAC
26886 TTCAACATTTTTTTTAAATAA
1 TTCAACATTTTTTTTAAATAA
* *
26907 TTCAATATTTTTTTTGAATAA
1 TTCAACATTTTTTTTAAATAA
26928 TTCA
1 TTCA
26932 GTCATTGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.54
Consensus pattern (21 bp):
TTCAACATTTTTTTTAAATAA
Found at i:34271 original size:27 final size:29
Alignment explanation
Indices: 34241--34296 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
34231 AATGTTAAAC
* *
34241 TTAACCATTGAATAA-TTA-ATATAAAAA
1 TTAACCATTCAACAATTTATATATAAAAA
34268 TTAACCATTCAACAATTTATATATAAAAA
1 TTAACCATTCAACAATTTATATATAAAAA
34297 AATTATCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 13 0.52
28 3 0.12
29 9 0.36
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.34
Consensus pattern (29 bp):
TTAACCATTCAACAATTTATATATAAAAA
Found at i:35650 original size:29 final size:29
Alignment explanation
Indices: 35618--35680 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
35608 TTTTTTTAGT
35618 TTTTAAGAGT-CCAAAATTTTTTTATCAAC
1 TTTTAAGA-TACCAAAATTTTTTTATCAAC
** * *
35647 TTTTAAGATACTTAATTTTTTTTTTCAAC
1 TTTTAAGATACCAAAATTTTTTTATCAAC
35676 TTTTA
1 TTTTA
35681 TCATTTTACC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 1 0.03
29 28 0.97
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.54
Consensus pattern (29 bp):
TTTTAAGATACCAAAATTTTTTTATCAAC
Found at i:37733 original size:2 final size:2
Alignment explanation
Indices: 37726--37760 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
37716 GAAAAGAGGG
37726 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
37761 GGATGGTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:48801 original size:27 final size:27
Alignment explanation
Indices: 48742--48804 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
48732 AATATGAAAG
*
48742 CGGCACCAAAGATGCCTACATGATAGG
1 CGGCACCAAAGATGCCTACATGATAGC
* * * *
48769 CGGCACCAAAGTTGTCTACTTGGTAGC
1 CGGCACCAAAGATGCCTACATGATAGC
*
48796 CTGCACCAA
1 CGGCACCAA
48805 TCCCACATTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.19
Consensus pattern (27 bp):
CGGCACCAAAGATGCCTACATGATAGC
Found at i:48894 original size:14 final size:14
Alignment explanation
Indices: 48852--48895 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
48842 TTTGACATAA
*
48852 ATAATACAAAAAAA
1 ATAATACAAAAAAT
* *
48866 ATTATACACCAAAAT
1 ATAATACA-AAAAAT
48881 ATAATACAAAAAAT
1 ATAATACAAAAAAT
48895 A
1 A
48896 AAATTAATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.20
Consensus pattern (14 bp):
ATAATACAAAAAAT
Found at i:48927 original size:2 final size:2
Alignment explanation
Indices: 48914--48945 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
48904 AACTTAAATA
*
48914 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48946 TTTAATCCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:52843 original size:31 final size:31
Alignment explanation
Indices: 52808--52867 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
52798 ATATACAAGA
* *
52808 AACTTTTATTGTAATTCAAATATATATATAT
1 AACTTTCATTGTAATTCAAATATACATATAT
* *
52839 AACTTTCATTTTAATTCAATTATACATAT
1 AACTTTCATTGTAATTCAAATATACATAT
52868 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (31 bp):
AACTTTCATTGTAATTCAAATATACATATAT
Found at i:54325 original size:18 final size:19
Alignment explanation
Indices: 54264--54327 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 19
54254 TCCGTGTTTA
*
54264 AATTTCGATTAAAATTAAATT
1 AATTT-GATT-AAATTAATTT
*
54285 AA-TTGATTAAATAAATTT
1 AATTTGATTAAATTAATTT
*
54303 AATTTTATT-AATTAATTT
1 AATTTGATTAAATTAATTT
54321 AATTTGA
1 AATTTGA
54328 CTAGAAATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
18 24 0.65
19 9 0.24
20 2 0.05
21 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (19 bp):
AATTTGATTAAATTAATTT
Found at i:54792 original size:30 final size:31
Alignment explanation
Indices: 54758--54823 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
54748 TTTATCATAT
* * *
54758 ATTTTTATAATTTTTAAAAGATTAAATTA-A
1 ATTTTTATAATTGTTAAAAGATCAAAGTACA
* *
54788 ATTTTTATTATTGTTAAGAGATCAAAGTACA
1 ATTTTTATAATTGTTAAAAGATCAAAGTACA
54819 ATTTT
1 ATTTT
54824 ACTTTTATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 24 0.80
31 6 0.20
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (31 bp):
ATTTTTATAATTGTTAAAAGATCAAAGTACA
Found at i:56367 original size:31 final size:31
Alignment explanation
Indices: 56332--56393 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
56322 AATAGCCTAG
56332 TGACTTAAATAAAAACTTTTAAATAATTCAA
1 TGACTTAAATAAAAACTTTTAAATAATTCAA
* * *
56363 TGACTTAAATGAAAACTTTTGAATAGTTCAA
1 TGACTTAAATAAAAACTTTTAAATAATTCAA
56394 GAATCAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTAAATAATTCAA
Found at i:56680 original size:25 final size:25
Alignment explanation
Indices: 56639--56690 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
56629 TTATATTAGC
*
56639 TTATTACAAATACAAATAATTGTAT
1 TTATTACAAATAAAAATAATTGTAT
56664 TTATT-CAATATAAAAATAATTGTAT
1 TTATTACAA-ATAAAAATAATTGTAT
56689 TT
1 TT
56691 CTTTTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (25 bp):
TTATTACAAATAAAAATAATTGTAT
Found at i:57755 original size:17 final size:17
Alignment explanation
Indices: 57735--57825 Score: 57
Period size: 19 Copynumber: 5.3 Consensus size: 17
57725 TTTATTATTT
57735 TAATATAAATATTAAAA
1 TAATATAAATATTAAAA
* *
57752 TAATATCAAAATTTTTAAA
1 TAATAT--AAATATTAAAA
*
57771 TAA-A-AAATTTTAATAAA
1 TAATATAAATATT-A-AAA
57788 TAA-A-AAATA-TAAAA
1 TAATATAAATATTAAAA
*
57802 AAATTATTAAATATTAAAA
1 TAA-TA-TAAATATTAAAA
57821 TAATA
1 TAATA
57826 CAATATAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
14 5 0.08
15 8 0.14
16 2 0.03
17 17 0.29
18 8 0.14
19 19 0.32
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATATAAATATTAAAA
Found at i:62031 original size:26 final size:24
Alignment explanation
Indices: 62002--62049 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
61992 AAGGAATAAA
62002 TAAATATAAGTTTTTATTTTTTTAGT
1 TAAAT-TAAG-TTTTATTTTTTTAGT
*
62028 TAAATTTAGTTTTATTTTTTTA
1 TAAATTAAGTTTTATTTTTTTA
62050 CAAAAAGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.62
25 3 0.14
26 5 0.24
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (24 bp):
TAAATTAAGTTTTATTTTTTTAGT
Found at i:62094 original size:30 final size:30
Alignment explanation
Indices: 62060--62121 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
62050 CAAAAAGTCA
* *
62060 AATTTT-ATTATTAATTTTTTAAAAATAATT
1 AATTTTGATTATTAA-TCTTTAAAAAGAATT
62090 AATTTTGATTATTAATCTTTAAAAAGAATT
1 AATTTTGATTATTAATCTTTAAAAAGAATT
62120 AA
1 AA
62122 ATAGTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (30 bp):
AATTTTGATTATTAATCTTTAAAAAGAATT
Found at i:62198 original size:19 final size:19
Alignment explanation
Indices: 62176--62219 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
62166 TATTTTATGC
**
62176 TTTTTAAAATTTTTTTGAT
1 TTTTTAAAATTTTTTAAAT
* *
62195 TTTTTTATATTTTTTAAAT
1 TTTTTAAAATTTTTTAAAT
62214 TTTTTA
1 TTTTTA
62220 TATATTTAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTTAAAATTTTTTAAAT
Found at i:62227 original size:17 final size:18
Alignment explanation
Indices: 62195--62231 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
62185 TTTTTTTGAT
*
62195 TTTTTTATATTTTTTAAA
1 TTTTTTATATTATTTAAA
62213 TTTTTTATA-TATTTAAA
1 TTTTTTATATTATTTAAA
62230 TT
1 TT
62232 GAGATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTTATATTATTTAAA
Found at i:64725 original size:38 final size:38
Alignment explanation
Indices: 64672--64779 Score: 162
Period size: 38 Copynumber: 2.8 Consensus size: 38
64662 CTATATTTGT
* *
64672 TTTTTTGTATATTTTTATTTAAAATTTGCTACACCTATA
1 TTTTTT-TATTTTTTTAATTAAAATTTGCTACACCTATA
*
64711 TTTTTTTATTTTTTTAATTAAAATTTGCTATACCTATA
1 TTTTTTTATTTTTTTAATTAAAATTTGCTACACCTATA
*
64749 TTTTTTTATTTTTTTTAATTAAAACTTGCTA
1 TTTTTTTA-TTTTTTTAATTAAAATTTGCTA
64780 AACTATCTAT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
38 37 0.58
39 27 0.42
ACGTcount: A:0.28, C:0.08, G:0.04, T:0.60
Consensus pattern (38 bp):
TTTTTTTATTTTTTTAATTAAAATTTGCTACACCTATA
Found at i:74326 original size:14 final size:14
Alignment explanation
Indices: 74309--74338 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
74299 CCAAAAACCT
74309 AAAAAAAAAAAAGA
1 AAAAAAAAAAAAGA
*
74323 AAAAAAAGAAAAGA
1 AAAAAAAAAAAAGA
74337 AA
1 AA
74339 CCATCTTCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAGA
Found at i:82631 original size:17 final size:16
Alignment explanation
Indices: 82609--82659 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
82599 ATATTTTACA
82609 TATAAAAATAAATATT
1 TATAAAAATAAATATT
*
82625 TACTAAAAATAATTATTT
1 TA-TAAAAATAAATA-TT
*
82643 TAAAAAAATAAATATT
1 TATAAAAATAAATATT
82659 T
1 T
82660 GAAATGTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 5 0.17
17 21 0.70
18 4 0.13
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
TATAAAAATAAATATT
Found at i:82929 original size:16 final size:16
Alignment explanation
Indices: 82908--82939 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
82898 ACAAAAACAC
82908 CATCATTTAACCATTT
1 CATCATTTAACCATTT
82924 CATCATTTAACCATTT
1 CATCATTTAACCATTT
82940 GACTAGAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (16 bp):
CATCATTTAACCATTT
Found at i:84553 original size:18 final size:18
Alignment explanation
Indices: 84532--84566 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
84522 AAAATTATTT
84532 AAAAATAAAAAGATAAAG
1 AAAAATAAAAAGATAAAG
*
84550 AAAAATAAAAATATAAA
1 AAAAATAAAAAGATAAA
84567 ATGGTTTTCC
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:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (18 bp):
AAAAATAAAAAGATAAAG
Found at i:85408 original size:20 final size:21
Alignment explanation
Indices: 85360--85407 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
85350 TTTACCCCCA
85360 ATTTTTTGTTTAAAAAATGAT
1 ATTTTTTGTTTAAAAAATGAT
85381 ATTTTTTGTTTAAAAAATGAT
1 ATTTTTTGTTTAAAAAATGAT
85402 ATTTTT
1 ATTTTT
85408 GGATGACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.56
Consensus pattern (21 bp):
ATTTTTTGTTTAAAAAATGAT
Found at i:88264 original size:2 final size:2
Alignment explanation
Indices: 88259--88286 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
88249 GTGTGAAAAT
88259 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
88287 GACACAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:89641 original size:2 final size:2
Alignment explanation
Indices: 89634--89667 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
89624 TAGGTCTCAT
89634 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
89668 ATCTAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:91652 original size:6 final size:6
Alignment explanation
Indices: 91641--91666 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
91631 CGGTGCACCT
91641 CCCAAC CCCAAC CCCAAC CCCAAC CC
1 CCCAAC CCCAAC CCCAAC CCCAAC CC
91667 TACTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.69, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCAAC
Found at i:91849 original size:15 final size:15
Alignment explanation
Indices: 91829--91866 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
91819 ATTAAATTAT
*
91829 TAAAAATTATAAAAT
1 TAAAAATTATAAAAA
*
91844 TTAAAATT-TAAAAA
1 TAAAAATTATAAAAA
91858 TAAAAATTA
1 TAAAAATTA
91867 ATTCAATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAAAATTATAAAAA
Found at i:92181 original size:31 final size:28
Alignment explanation
Indices: 92118--92181 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
92108 TATTTGAATT
* *
92118 AATTAATAACATTATAAAATATTAAACT
1 AATTAATAACATTATAAAATATAAAACG
*
92146 AATTAATAATATTATAAAAATATAAAAATCG
1 AATTAATAACATTAT-AAAATAT-AAAA-CG
92177 AATTA
1 AATTA
92182 TATTAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 14 0.47
29 7 0.23
30 3 0.10
31 6 0.20
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (28 bp):
AATTAATAACATTATAAAATATAAAACG
Found at i:97040 original size:8 final size:8
Alignment explanation
Indices: 97027--97056 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
97017 ATATTAAAGG
97027 TTTTTATA
1 TTTTTATA
97035 TTTTTATA
1 TTTTTATA
97043 TTTTTATA
1 TTTTTATA
97051 TTTTTA
1 TTTTTA
97057 AAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTATA
Found at i:108313 original size:6 final size:6
Alignment explanation
Indices: 108302--108329 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
108292 TTAGATCTAG
108302 TTTAAT TTTAAT TTTAAT TTTAAT TTTA
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTA
108330 TTAATTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTAAT
Found at i:110454 original size:11 final size:10
Alignment explanation
Indices: 110392--110467 Score: 63
Period size: 10 Copynumber: 7.7 Consensus size: 10
110382 TTTTATGTTA
110392 ATAAATAATTT
1 ATAAA-AATTT
110403 A-AAAAA--T
1 ATAAAAATTT
110410 ATAAAAATATT
1 ATAAAAAT-TT
110421 -TAAAATATTT
1 ATAAAA-ATTT
*
110431 -TAAAAAATT
1 ATAAAAATTT
110440 ATAAAAATTT
1 ATAAAAATTT
110450 CATAAAAATTT
1 -ATAAAAATTT
*
110461 TTAAAAA
1 ATAAAAA
110468 AAAATGAAGT
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
7 2 0.04
8 5 0.09
9 5 0.09
10 29 0.53
11 14 0.25
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (10 bp):
ATAAAAATTT
Found at i:110467 original size:21 final size:20
Alignment explanation
Indices: 110400--110467 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
110390 TAATAAATAA
* *
110400 TTTAAAAA-ATATAAAAATA
1 TTTAAAAATTTATAAAAATT
*
110419 TTTAAAATATTT-TAAAAAAT
1 TTTAAAA-ATTTATAAAAATT
*
110439 TATAAAAATTTCATAAAAATT
1 TTTAAAAATTT-ATAAAAATT
110460 TTTAAAAA
1 TTTAAAAA
110468 AAAATGAAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 11 0.28
20 13 0.33
21 15 0.38
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTAAAAATTTATAAAAATT
Found at i:110897 original size:17 final size:18
Alignment explanation
Indices: 110875--110912 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
110865 GTATAACAAA
110875 AAAATT-ATATAAATTTC
1 AAAATTAATATAAATTTC
*
110892 AAAATTACATCTAAATTTC
1 AAAATTA-ATATAAATTTC
110911 AA
1 AA
110913 TTAAATGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATTAATATAAATTTC
Found at i:112521 original size:28 final size:28
Alignment explanation
Indices: 112483--112539 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
112473 TTAATTGGTT
112483 ATTTAAATTTAA-TAATTCATGATAATTTA
1 ATTTAAATTTAATTAA-TC-TGATAATTTA
112512 ATTT-AATTTAATTTAATCTGATAATTTA
1 ATTTAAATTTAA-TTAATCTGATAATTTA
112540 TATTGATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 17 0.65
29 6 0.23
30 3 0.12
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (28 bp):
ATTTAAATTTAATTAATCTGATAATTTA
Found at i:116031 original size:23 final size:22
Alignment explanation
Indices: 115984--116031 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
115974 TAACTGCTGT
* * *
115984 TTACAGTAATTGATACAACTGC
1 TTACAGTAACTAATACAACTAC
116006 TTACAGTAACTAATTACAACTAC
1 TTACAGTAACTAA-TACAACTAC
116029 TTA
1 TTA
116032 GTAACTGCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (22 bp):
TTACAGTAACTAATACAACTAC
Found at i:116845 original size:22 final size:22
Alignment explanation
Indices: 116809--116866 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
116799 TTGATAACTG
*
116809 CTGCTTACAGCAACTGA-TACAA
1 CTGCTTAC-GTAACTGATTACAA
116831 CTGCTTACCGTAACT-ATTACAA
1 CTGCTTA-CGTAACTGATTACAA
*
116853 CTACTTA-GTAACTG
1 CTGCTTACGTAACTG
116867 CTAACTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 6 0.19
21 1 0.03
22 23 0.74
23 1 0.03
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (22 bp):
CTGCTTACGTAACTGATTACAA
Found at i:118999 original size:85 final size:88
Alignment explanation
Indices: 118823--119112 Score: 274
Period size: 85 Copynumber: 3.3 Consensus size: 88
118813 AGTTTTGGGA
** * *
118823 TAAAAATGTAATTTTTTTAGAAGTTTGGGGTAAAAAATGTGATTTTTGGAAGTTTAGGGGTAAAA
1 TAAAAATGTAATTTTTGGA-AAGTTTAGAGTAAAAAATGTGATTTTTGGAAGTTTAGGGGTAAAA
* * *
118888 TTTTAATTTTTAATAGTTTAGGGG
65 ATTTAATTTTTAAGAGTTTAGAGG
* *
118912 TAAAAATGTAATTTTTGGAAATTTTAGAGT-AAAAATGTGATTTTT-TAAGTTT-GGGGTAAAAA
1 TAAAAATGTAATTTTTGGAAAGTTTAGAGTAAAAAATGTGATTTTTGGAAGTTTAGGGGTAAAAA
* *
118974 TTTATTTTTTGAGAGTTT-GAAGG
66 TTTAATTTTTAAGAGTTTAG-AGG
* * * *
118997 TAAAAATGTAATTTTTGGAAAGTTT-GAAGGTCAAAATAT-T-A-CTTTGGAAAATTTAGGGGTC
1 TAAAAATGTAATTTTTGGAAAGTTTAG-A-GT-AAAAAATGTGATTTTTGG-AAGTTTAGGGGTA
* *
119058 AAAATGTAATTTTTGGAA-AGTTTAGGGG
62 AAAATTTAATTTTT--AAGAGTTTAGAGG
* *
119086 TTAAAATGTATTTTTTGGAAAGTTTAG
1 TAAAAATGTAATTTTTGGAAAGTTTAG
119113 GGGTCAAATA
Statistics
Matches: 166, Mismatches: 23, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
84 2 0.01
85 54 0.33
86 9 0.05
87 21 0.13
88 30 0.18
89 47 0.28
90 3 0.02
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.41
Consensus pattern (88 bp):
TAAAAATGTAATTTTTGGAAAGTTTAGAGTAAAAAATGTGATTTTTGGAAGTTTAGGGGTAAAAA
TTTAATTTTTAAGAGTTTAGAGG
Found at i:119062 original size:59 final size:59
Alignment explanation
Indices: 118999--119120 Score: 167
Period size: 59 Copynumber: 2.1 Consensus size: 59
118989 TTTGAAGGTA
118999 AAAATGTAATTTTTGGAAAGTTT-GAAGGTCAAAA-TATTACTTTGGAAAATTTAGGGGTC
1 AAAATGTAATTTTTGGAAAGTTTAG-AGGTCAAAAGTATT-CTTTGGAAAATTTAGGGGTC
* * * *
119058 AAAATGTAATTTTTGGAAAGTTTAGGGGTTAAAATGTATTTTTTGGAAAGTTTAGGGGTC
1 AAAATGTAATTTTTGGAAAGTTTAGAGGTCAAAA-GTATTCTTTGGAAAATTTAGGGGTC
119118 AAA
1 AAA
119121 TATGATATTT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
59 30 0.54
60 22 0.39
61 4 0.07
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (59 bp):
AAAATGTAATTTTTGGAAAGTTTAGAGGTCAAAAGTATTCTTTGGAAAATTTAGGGGTC
Found at i:119121 original size:29 final size:29
Alignment explanation
Indices: 118588--119121 Score: 286
Period size: 29 Copynumber: 18.3 Consensus size: 29
118578 GAATTTTCGA
* * * *
118588 GGGTAAAATGGTATTTTTTTG-ATGTTCAG
1 GGGTAAAAT-GTAATTTTTGGAAAGTTTAG
* * *
118617 GGCTAAAATGGTGACTTTTGGAAAG-TTAG
1 GGGTAAAAT-GTAATTTTTGGAAAGTTTAG
** *
118646 GGGTCAAAATACAATTTTTGGATA-TTTAG
1 GGGT-AAAATGTAATTTTTGGAAAGTTTAG
* * * *
118675 GGGTAAAATGGAAATTTTGGGAAGTTTGG
1 GGGTAAAATGTAATTTTTGGAAAGTTTAG
* * **
118704 GGGTTAAAAATGTAATTTATGGATA-TCCGAG
1 GGG-T-AAAATGTAATTTTTGGAAAGT-TTAG
*
118735 GGGTAAAATGGTAA-TTTTGG-ATG-TTAG
1 GGGTAAAAT-GTAATTTTTGGAAAGTTTAG
* * *
118762 AGGGCAAAATGTAAGTTTTGGAAAG-TT-C
1 -GGGTAAAATGTAATTTTTGGAAAGTTTAG
*
118790 GGGTCAAAAATG-AGATTTTTGG-AAGTTTTG
1 GGGT--AAAATGTA-ATTTTTGGAAAGTTTAG
* **
118820 GGATAAAAATGTAATTTTTTTAGAAGTTT-G
1 GGGT-AAAATGTAATTTTTGGA-AAGTTTAG
*
118850 GGGTAAAAAATGTGATTTTTGG-AAGTTTAG
1 GGGT--AAAATGTAATTTTTGGAAAGTTTAG
*
118880 GGGTAAAATTTTAATTTTT--AATAGTTTAG
1 GGGTAAAA-TGTAATTTTTGGAA-AGTTTAG
*
118909 GGGTAAAAATGTAATTTTTGGAAATTTTA-
1 GGGT-AAAATGTAATTTTTGGAAAGTTTAG
* * *
118938 GAGTAAAAATGTGATTTTT--TAAGTTT-G
1 GGGT-AAAATGTAATTTTTGGAAAGTTTAG
* * *
118965 GGGTAAAAAT-TTATTTTTTGAGAGTTT-G
1 GGGT-AAAATGTAATTTTTGGAAAGTTTAG
*
118993 AAGGTAAAAATGTAATTTTTGGAAAGTTT-G
1 -GGGT-AAAATGTAATTTTTGGAAAGTTTAG
* * * * *
119023 AAGGTCAAAATATTA-CTTTGGAAAATTTAG
1 -GGGT-AAAATGTAATTTTTGGAAAGTTTAG
119053 GGGTCAAAATGTAATTTTTGGAAAGTTTAG
1 GGGT-AAAATGTAATTTTTGGAAAGTTTAG
*
119083 GGGTTAAAATGTATTTTTTGGAAAGTTTAG
1 GGG-TAAAATGTAATTTTTGGAAAGTTTAG
*
119113 GGGTCAAAT
1 GGGTAAAAT
119122 ATGATATTTA
Statistics
Matches: 396, Mismatches: 73, Indels: 72
0.73 0.13 0.13
Matches are distributed among these distances:
26 7 0.02
27 23 0.06
28 43 0.11
29 175 0.44
30 107 0.27
31 41 0.10
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.38
Consensus pattern (29 bp):
GGGTAAAATGTAATTTTTGGAAAGTTTAG
Found at i:121274 original size:16 final size:16
Alignment explanation
Indices: 121200--121275 Score: 57
Period size: 16 Copynumber: 4.6 Consensus size: 16
121190 CTAAATATGG
121200 TTAT-TTTATTTTAAA
1 TTATGTTTATTTTAAA
121215 TTATGTAATTTATTTTAAA
1 TTATG---TTTATTTTAAA
* ** *
121234 TTCTGTTTATGCATAAT
1 TTATGTTTAT-TTTAAA
121251 TTAT-TTTATTTTAAA
1 TTATGTTTATTTTAAA
*
121266 TTCTGTTTAT
1 TTATGTTTAT
121276 AAAGGAGATG
Statistics
Matches: 46, Mismatches: 9, Indels: 11
0.70 0.14 0.17
Matches are distributed among these distances:
15 10 0.22
16 15 0.33
17 6 0.13
19 15 0.33
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (16 bp):
TTATGTTTATTTTAAA
Found at i:124010 original size:35 final size:35
Alignment explanation
Indices: 123964--124036 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
123954 AAAGAGATAT
123964 GGATCCTAAATGGATTATAAGCCCTACGATCGCTG
1 GGATCCTAAATGGATTATAAGCCCTACGATCGCTG
*
123999 GGATCCTAAATGGATTATAAGCCCTATGATCGCTG
1 GGATCCTAAATGGATTATAAGCCCTACGATCGCTG
124034 GGA
1 GGA
124037 CTATGCTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.26
Consensus pattern (35 bp):
GGATCCTAAATGGATTATAAGCCCTACGATCGCTG
Found at i:126268 original size:19 final size:21
Alignment explanation
Indices: 126232--126270 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
126222 CTTAAAAAAT
126232 ATATATATTTATATATTTTAG
1 ATATATATTTATATATTTTAG
*
126253 ATATAT-TTTTTA-ATTTTA
1 ATATATATTTATATATTTTA
126271 TAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
ATATATATTTATATATTTTAG
Found at i:127254 original size:3 final size:3
Alignment explanation
Indices: 127246--127294 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
127236 ATTAAACTTT
127246 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
127294 T
1 T
127295 GATGATGATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:129696 original size:30 final size:30
Alignment explanation
Indices: 129662--129718 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
129652 TTAATTAAAG
*
129662 TAAAATTATATTTTAATCATTTAAAAACGA
1 TAAAATTATAATTTAATCATTTAAAAACGA
* **
129692 TAAAATTTTAATTTAATTTTTTAAAAA
1 TAAAATTATAATTTAATCATTTAAAAA
129719 TTAAAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (30 bp):
TAAAATTATAATTTAATCATTTAAAAACGA
Found at i:134819 original size:24 final size:24
Alignment explanation
Indices: 134791--134841 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
134781 AATTTGACTC
*
134791 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
134815 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
134839 AAA
1 AAA
134842 GATTATTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:136797 original size:24 final size:24
Alignment explanation
Indices: 136763--136813 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
136753 AATTTGACTC
* *
136763 AAACAACTAAACAGAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTG
136787 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTG
136811 AAA
1 AAA
136814 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAAAGTTTAATTG
Found at i:137899 original size:26 final size:26
Alignment explanation
Indices: 137868--137918 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
137858 CTTTTTCTTA
137868 TTCTGTTGTTTCTTGTTCCACTATTG
1 TTCTGTTGTTTCTTGTTCCACTATTG
*
137894 TTCTGTTGTTTCTTGTTCTACTATT
1 TTCTGTTGTTTCTTGTTCCACTATT
137919 TCTTTTATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.08, C:0.18, G:0.14, T:0.61
Consensus pattern (26 bp):
TTCTGTTGTTTCTTGTTCCACTATTG
Found at i:138154 original size:29 final size:31
Alignment explanation
Indices: 138101--138173 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
138091 ATTAAAATTA
*
138101 TTTAATAATTTTATTATTTCAAAAA-AATAAT
1 TTTAATAATTTTATTATTTAAAAAATAAT-AT
*
138132 TTTCATAATTTTA-TA-TTAAAAAATAATAT
1 TTTAATAATTTTATTATTTAAAAAATAATAT
*
138161 TTTAATACTTTTA
1 TTTAATAATTTTA
138174 AAATCATTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 20 0.54
30 5 0.14
31 12 0.32
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (31 bp):
TTTAATAATTTTATTATTTAAAAAATAATAT
Found at i:141529 original size:15 final size:15
Alignment explanation
Indices: 141509--141541 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
141499 GTTTGATACC
141509 ATGTTAGATTCTCAT
1 ATGTTAGATTCTCAT
141524 ATGTTAGATTCTCAT
1 ATGTTAGATTCTCAT
141539 ATG
1 ATG
141542 AAGAGTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.45
Consensus pattern (15 bp):
ATGTTAGATTCTCAT
Found at i:142212 original size:18 final size:19
Alignment explanation
Indices: 142172--142213 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
142162 AAACAAATAG
* *
142172 AAATATAAATATTTATATT
1 AAATATAAAGATTTATATA
*
142191 AAATAT-AAGATTTGTATA
1 AAATATAAAGATTTATATA
142209 AAATA
1 AAATA
142214 ATATAAACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (19 bp):
AAATATAAAGATTTATATA
Found at i:144379 original size:16 final size:15
Alignment explanation
Indices: 144349--144382 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
144339 CATTATTTTA
*
144349 AAATTAAAAATATAT
1 AAATTAAAAAAATAT
144364 AAATTAATAAAAATAT
1 AAATTAA-AAAAATAT
144380 AAA
1 AAA
144383 AATAGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATTAAAAAAATAT
Found at i:144503 original size:8 final size:8
Alignment explanation
Indices: 144490--144650 Score: 55
Period size: 8 Copynumber: 19.1 Consensus size: 8
144480 TTAGTTCTTG
144490 TATATATT
1 TATATATT
144498 TATATATTTT
1 TATATA--TT
*
144508 TATACATT
1 TATATATT
*
144516 TATAAATT
1 TATATATT
*
144524 TGTAGTACTT
1 TATA-TA-TT
144534 T-TAT-TAT
1 TATATAT-T
*
144541 TAT-TTTT
1 TATATATT
*
144548 TCATATTTT
1 T-ATATATT
*
144557 TATAAATT
1 TATATATT
144565 TATATATT
1 TATATATT
144573 ATATATATT
1 -TATATATT
*
144582 TCA-AAATAT
1 T-ATATAT-T
*
144591 TATAGGCTTTT
1 TATA---TATT
144602 TATATATT
1 TATATATT
*
144610 TTTA-ATT
1 TATATATT
144617 GTATATATTT
1 -TATATA-TT
* *
144627 TTTAAATT
1 TATATATT
144635 T-TATATT
1 TATATATT
144642 TATATATT
1 TATATATT
144650 T
1 T
144651 TCAAAATAAC
Statistics
Matches: 117, Mismatches: 16, Indels: 40
0.68 0.09 0.23
Matches are distributed among these distances:
6 1 0.01
7 14 0.12
8 59 0.50
9 25 0.21
10 12 0.10
11 5 0.04
12 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (8 bp):
TATATATT
Found at i:144516 original size:18 final size:18
Alignment explanation
Indices: 144490--144547 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
144480 TTAGTTCTTG
*
144490 TATATATTTATATATTTT
1 TATACATTTATATATTTT
* *
144508 TATACATTTATAAATTTG
1 TATACATTTATATATTTT
*
144526 TAGTACTTTTATTATTATTTT
1 TA-TACATTTA-TA-TATTTT
144547 T
1 T
144548 TCATATTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 17 0.55
19 7 0.23
20 2 0.06
21 5 0.16
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
TATACATTTATATATTTT
Found at i:144639 original size:18 final size:16
Alignment explanation
Indices: 144599--144640 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
144589 ATTATAGGCT
144599 TTTTATATATTTTTAA
1 TTTTATATATTTTTAA
*
144615 TTGTATATATTTTTTAAA
1 TTTTATATA-TTTTT-AA
144633 TTTTATAT
1 TTTTATAT
144641 TTATATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 5 0.23
18 9 0.41
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTTATATATTTTTAA
Found at i:144657 original size:24 final size:24
Alignment explanation
Indices: 144609--144657 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
144599 TTTTATATAT
**
144609 TTTTAATTGTATATATTTTTTAAA
1 TTTTAATTGTATATATTTTCAAAA
144633 TTTTATATT-TATATATTTTCAAAA
1 TTTTA-ATTGTATATATTTTCAAAA
144657 T
1 T
144658 AACAAAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTTAATTGTATATATTTTCAAAA
Found at i:154023 original size:23 final size:23
Alignment explanation
Indices: 153997--154040 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
153987 AATACCATTT
153997 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
154020 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
154041 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:154033 original size:13 final size:11
Alignment explanation
Indices: 154001--154043 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
153991 CCATTTTCTA
*
154001 AATAAAATAAT
1 AATAAAATATT
154012 AAT-AAATATCT
1 AATAAAATAT-T
154023 AAGTAAAATATT
1 AA-TAAAATATT
154035 AATAAAATA
1 AATAAAATA
154044 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:154768 original size:16 final size:16
Alignment explanation
Indices: 154747--154779 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
154737 CCCCTTAAAA
154747 TTGGTTAAAAAAATTT
1 TTGGTTAAAAAAATTT
154763 TTGGTTAAAAAAATTT
1 TTGGTTAAAAAAATTT
154779 T
1 T
154780 GACCCCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (16 bp):
TTGGTTAAAAAAATTT
Found at i:154774 original size:15 final size:16
Alignment explanation
Indices: 154747--154780 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
154737 CCCCTTAAAA
*
154747 TTGGTTAAAAAAATTT
1 TTGGTTAAAAAAAATT
154763 TTGGTT-AAAAAAATT
1 TTGGTTAAAAAAAATT
154778 TTG
1 TTG
154781 ACCCCTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (16 bp):
TTGGTTAAAAAAAATT
Found at i:155525 original size:54 final size:54
Alignment explanation
Indices: 155391--155512 Score: 244
Period size: 54 Copynumber: 2.3 Consensus size: 54
155381 CACATAATTT
155391 TAAATAAACGAACATGAATAAGAATTTTGAAATTCTTAACAACAACTTCAAAAA
1 TAAATAAACGAACATGAATAAGAATTTTGAAATTCTTAACAACAACTTCAAAAA
155445 TAAATAAACGAACATGAATAAGAATTTTGAAATTCTTAACAACAACTTCAAAAA
1 TAAATAAACGAACATGAATAAGAATTTTGAAATTCTTAACAACAACTTCAAAAA
155499 TAAATAAACGAACA
1 TAAATAAACGAACA
155513 CGAACAAAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 68 1.00
ACGTcount: A:0.55, C:0.13, G:0.07, T:0.25
Consensus pattern (54 bp):
TAAATAAACGAACATGAATAAGAATTTTGAAATTCTTAACAACAACTTCAAAAA
Found at i:160633 original size:22 final size:23
Alignment explanation
Indices: 160606--160658 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
160596 TACTCCACGG
**
160606 AAAAAACAA-AAAAAATTAAAAA
1 AAAAAACAAGAAAAAAGGAAAAA
* *
160628 AAAAAATAAGAAAATAGGAAAAA
1 AAAAAACAAGAAAAAAGGAAAAA
160651 AAAAAACA
1 AAAAAACA
160659 CAATTAGAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.83, C:0.04, G:0.06, T:0.08
Consensus pattern (23 bp):
AAAAAACAAGAAAAAAGGAAAAA
Found at i:160668 original size:20 final size:18
Alignment explanation
Indices: 160605--160668 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 18
160595 TTACTCCACG
160605 GAAAAAACAAAAAAAATTA
1 GAAAAAA-AAAAAAAATTA
* *
160624 AAAAAAAAAATAAGAAAATA
1 GAAAAAAAAA-AA-AAATTA
160644 GGAAAAAAAAAAACACAATTA
1 -GAAAAAAAAAAA-A-AATTA
160665 GAAA
1 GAAA
160669 TATTAGAAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
18 3 0.08
19 8 0.22
20 12 0.33
21 13 0.36
ACGTcount: A:0.78, C:0.05, G:0.08, T:0.09
Consensus pattern (18 bp):
GAAAAAAAAAAAAAATTA
Found at i:165808 original size:2 final size:2
Alignment explanation
Indices: 165801--165838 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
165791 AAAGCAAAGC
165801 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
165839 TTACTGCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:168578 original size:21 final size:21
Alignment explanation
Indices: 168532--168592 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
168522 CAATCTGAGG
*
168532 AAAAATAGAAGAAACA-AAATT
1 AAAAATAAAAGAAA-ATAAATT
168553 AAAAATAAAAGAAAATATAATT
1 AAAAATAAAAGAAAATA-AATT
*
168575 AAAAGA-AATAGAAAATAA
1 AAAA-ATAAAAGAAAATAA
168593 GGAAGTCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.03
21 15 0.43
22 18 0.51
23 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.16
Consensus pattern (21 bp):
AAAAATAAAAGAAAATAAATT
Found at i:189590 original size:26 final size:24
Alignment explanation
Indices: 189547--189604 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
189537 AATATTTATA
*
189547 TTATATTATTTTAATATTTAATAATT
1 TTATA-TATTTTAATATTGAA-AATT
* *
189573 TTATATATTTTATTTATTGAAATTT
1 TTATATATTTTA-ATATTGAAAATT
189598 TTATATA
1 TTATATA
189605 GTCTTTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 17 0.61
26 11 0.39
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTATATATTTTAATATTGAAAATT
Found at i:202160 original size:19 final size:20
Alignment explanation
Indices: 202132--202169 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
202122 TTTATAAAGC
*
202132 AGAATGAAAAAAA-AAAATT
1 AGAATAAAAAAAATAAAATT
202151 AGAATAAAAAAAATAAAAT
1 AGAATAAAAAAAATAAAAT
202170 ATTACTTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (20 bp):
AGAATAAAAAAAATAAAATT
Found at i:203275 original size:21 final size:21
Alignment explanation
Indices: 203251--203292 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
203241 TTGATTCGAA
203251 ATAGATATGTCTCGAGACAAT
1 ATAGATATGTCTCGAGACAAT
203272 ATAGATATGTCTCGAGACAAT
1 ATAGATATGTCTCGAGACAAT
203293 GGCATACACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (21 bp):
ATAGATATGTCTCGAGACAAT
Found at i:204272 original size:2 final size:2
Alignment explanation
Indices: 204265--204290 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
204255 ATAACAAAGC
204265 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
204291 TAATTGTTCA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:204845 original size:2 final size:2
Alignment explanation
Indices: 204838--204865 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
204828 AAGATTTCAT
204838 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
204866 TATATATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:209450 original size:73 final size:73
Alignment explanation
Indices: 209361--209496 Score: 177
Period size: 73 Copynumber: 1.9 Consensus size: 73
209351 TATCTCAAAG
** *
209361 ACTTTTTCTTTTGTGACAAGT-GACTTTGTCACAAGCACCCAAAATTTTTTGTGATCAT-TTTTG
1 ACTTTTTCTTTTGTGAC-AGTCGACTTTGTCACAAAAACCCAAAATTTTTCGTGATCATCTTTTG
209424 GTCACGGGA
65 GTCACGGGA
* * * *
209433 ACTTTATTCTTTTGTGACGGTCGAGTTTGTCAGAAAAACTCAAAATTTTTCGTGATCATCTTTT
1 ACTTT-TTCTTTTGTGACAGTCGACTTTGTCACAAAAACCCAAAATTTTTCGTGATCATCTTTT
209497 TTGTCACAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
72 7 0.13
73 43 0.80
74 4 0.07
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (73 bp):
ACTTTTTCTTTTGTGACAGTCGACTTTGTCACAAAAACCCAAAATTTTTCGTGATCATCTTTTGG
TCACGGGA
Found at i:214923 original size:6 final size:6
Alignment explanation
Indices: 214912--214943 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
214902 GCTTTCATTT
214912 TGTTGA TGTTGA TGTTGA TGTTGA TGTTGA TG
1 TGTTGA TGTTGA TGTTGA TGTTGA TGTTGA TG
214944 GGTAACTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (6 bp):
TGTTGA
Found at i:219586 original size:111 final size:111
Alignment explanation
Indices: 219392--219601 Score: 269
Period size: 111 Copynumber: 1.9 Consensus size: 111
219382 TTGTAAGTTT
* *
219392 ATACTATTAATAAAACCCTTGACTAAGTTGGTGTCACGGGTTAACCAAGTACAAACTCGATCAAA
1 ATACTATTAATAAAACCCCTGACTAAGTTAGTGTCACGGGTTAACCAAGTACAAACTCGATCAAA
* *
219457 AAATTATGAAAATGTCCTTTTATAATTAAAATAATTAATGTTATTA
66 AAATTACGAAAATGTCCTTCTATAATTAAAATAATTAATGTTATTA
* * * * * * * * *
219503 ATACTATTAATAAAACCCCTGACTGATTTAGTG-CTATGGGTTAATCAGGTGCCAACTTGGTCAA
1 ATACTATTAATAAAACCCCTGACTAAGTTAGTGTC-ACGGGTTAACCAAGTACAAACTCGATCAA
* *
219567 GAAATTACGGAAATGTCCTTCTATAATTAAAATAA
65 AAAATTACGAAAATGTCCTTCTATAATTAAAATAA
219602 CTCATATTAT
Statistics
Matches: 83, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
110 1 0.01
111 82 0.99
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (111 bp):
ATACTATTAATAAAACCCCTGACTAAGTTAGTGTCACGGGTTAACCAAGTACAAACTCGATCAAA
AAATTACGAAAATGTCCTTCTATAATTAAAATAATTAATGTTATTA
Found at i:222527 original size:27 final size:27
Alignment explanation
Indices: 222473--222540 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
222463 ATTGTTTATG
* * *
222473 TAATTAAATAATATTGTACTTCGTCTAC
1 TAATTAAATAAT-CTATACTTCGCCTAC
*
222501 TAATTAAATAATCTATACTTTGCCTAC
1 TAATTAAATAATCTATACTTCGCCTAC
*
222528 TAGTTAAATAATC
1 TAATTAAATAATC
222541 AGTTCATGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 23 0.66
28 12 0.34
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (27 bp):
TAATTAAATAATCTATACTTCGCCTAC
Found at i:222847 original size:5 final size:5
Alignment explanation
Indices: 222839--222865 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
222829 TTTTAACTTA
222839 ATTCG ATTCG ATTCG ATTCG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG ATTCG AT
222866 CAAATACTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (5 bp):
ATTCG
Found at i:228411 original size:23 final size:25
Alignment explanation
Indices: 228384--228429 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
228374 CTAATTAGGG
228384 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
228407 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
228430 TGGATTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:228846 original size:15 final size:15
Alignment explanation
Indices: 228809--228847 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
228799 TTATGTGTGC
*
228809 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
228824 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
228838 TTAATTCTTG
1 TTAATTCTTG
228848 TTTGATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:232424 original size:17 final size:17
Alignment explanation
Indices: 232402--232443 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
232392 AATTAGTCTA
*
232402 TTTATTTTCATTTTCAT
1 TTTATTTTCATTTTAAT
**
232419 TTTATTTTTTTTTTAAT
1 TTTATTTTCATTTTAAT
232436 TTTATTTT
1 TTTATTTT
232444 AACTATGCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTATTTTCATTTTAAT
Found at i:232432 original size:11 final size:11
Alignment explanation
Indices: 232402--232445 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
232392 AATTAGTCTA
*
232402 TTTATTTTCAT
1 TTTATTTTAAT
*
232413 TTTCATTTTATT
1 TTT-ATTTTAAT
*
232425 TTTTTTTTAAT
1 TTTATTTTAAT
232436 TTTATTTTAA
1 TTTATTTTAA
232446 CTATGCACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTATTTTAAT
Found at i:233381 original size:12 final size:12
Alignment explanation
Indices: 233355--233431 Score: 52
Period size: 12 Copynumber: 6.4 Consensus size: 12
233345 TTTATTATTT
*
233355 AAAAAAAAAAAG
1 AAAAAAAAATAG
*
233367 AAAAAAAAATCG
1 AAAAAAAAATAG
* *
233379 AAAAGAAAATTTG
1 AAAA-AAAAATAG
233392 AAAAAAAAA-A-
1 AAAAAAAAATAG
*
233402 AAAAGAAAATTGAG
1 AAAA-AAAAAT-AG
*
233416 AAAAAAAGA-AG
1 AAAAAAAAATAG
233427 AAAAA
1 AAAAA
233432 GACAAAAATA
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
10 4 0.08
11 11 0.22
12 18 0.35
13 14 0.27
14 4 0.08
ACGTcount: A:0.79, C:0.01, G:0.12, T:0.08
Consensus pattern (12 bp):
AAAAAAAAATAG
Found at i:233395 original size:23 final size:24
Alignment explanation
Indices: 233365--233433 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
233355 AAAAAAAAAA
*
233365 AGAAAAAAAAATCGAAAAGAAAATT-
1 AGAAAAAAAAA--AAAAAGAAAATTG
*
233390 TGAAAAAAAAAAAAAAGAAAATTG
1 AGAAAAAAAAAAAAAAGAAAATTG
233414 AGAAAAAAAGAAGAAAAAGA
1 AGAAAAAAA-AA-AAAAAGA
233434 CAAAAATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
23 11 0.29
24 8 0.21
25 12 0.32
26 7 0.18
ACGTcount: A:0.75, C:0.01, G:0.14, T:0.09
Consensus pattern (24 bp):
AGAAAAAAAAAAAAAAGAAAATTG
Found at i:233430 original size:9 final size:8
Alignment explanation
Indices: 233355--233439 Score: 50
Period size: 8 Copynumber: 10.5 Consensus size: 8
233345 TTTATTATTT
233355 AAAA-AAA
1 AAAAGAAA
233362 AAAAGAAA
1 AAAAGAAA
*
233370 AAAA-AATCG
1 AAAAGAA--A
233379 AAAAGAAA
1 AAAAGAAA
***
233387 ATTTGAAA
1 AAAAGAAA
233395 AAAA-AAA
1 AAAAGAAA
233402 AAAAGAAA
1 AAAAGAAA
**
233410 ATTGAGAAA
1 A-AAAGAAA
233419 AAAAGAAGA
1 AAAAGAA-A
*
233428 AAAAGACA
1 AAAAGAAA
233436 AAAA
1 AAAA
233440 TATGTCTGAG
Statistics
Matches: 58, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
7 13 0.22
8 26 0.45
9 17 0.29
10 2 0.03
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (8 bp):
AAAAGAAA
Found at i:233430 original size:35 final size:36
Alignment explanation
Indices: 233356--233431 Score: 84
Period size: 35 Copynumber: 2.1 Consensus size: 36
233346 TTATTATTTA
***
233356 AAAAAAAAAAGAAAAAAAAATCGAAAAGAAAATTTG
1 AAAAAAAAAAGAAAAAAAAATCGAAAAGAAAAGAAG
* *
233392 AAAAAAAAAA-AAAAGAAAATTGAGAAA-AAAAGAAG
1 AAAAAAAAAAGAAAAAAAAATCGA-AAAGAAAAGAAG
233427 AAAAA
1 AAAAA
233432 GACAAAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
35 21 0.62
36 13 0.38
ACGTcount: A:0.79, C:0.01, G:0.12, T:0.08
Consensus pattern (36 bp):
AAAAAAAAAAGAAAAAAAAATCGAAAAGAAAAGAAG
Found at i:237703 original size:17 final size:17
Alignment explanation
Indices: 237681--237722 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
237671 AATTAGTCTA
*
237681 TTTATTTTCATTTTCAT
1 TTTATTTTCATTTTAAT
**
237698 TTTATTTTTTTTTTAAT
1 TTTATTTTCATTTTAAT
237715 TTTATTTT
1 TTTATTTT
237723 AACTATGCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTATTTTCATTTTAAT
Found at i:237711 original size:11 final size:11
Alignment explanation
Indices: 237681--237724 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
237671 AATTAGTCTA
*
237681 TTTATTTTCAT
1 TTTATTTTAAT
*
237692 TTTCATTTTATT
1 TTT-ATTTTAAT
*
237704 TTTTTTTTAAT
1 TTTATTTTAAT
237715 TTTATTTTAA
1 TTTATTTTAA
237725 CTATGCACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTATTTTAAT
Found at i:238660 original size:12 final size:12
Alignment explanation
Indices: 238634--238710 Score: 52
Period size: 12 Copynumber: 6.4 Consensus size: 12
238624 TTTATTATTT
*
238634 AAAAAAAAAAAG
1 AAAAAAAAATAG
*
238646 AAAAAAAAATCG
1 AAAAAAAAATAG
* *
238658 AAAAGAAAATTTG
1 AAAA-AAAAATAG
238671 AAAAAAAAA-A-
1 AAAAAAAAATAG
*
238681 AAAAGAAAATTGAG
1 AAAA-AAAAAT-AG
*
238695 AAAAAAAGA-AG
1 AAAAAAAAATAG
238706 AAAAA
1 AAAAA
238711 GACAAAAATA
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
10 4 0.08
11 11 0.22
12 18 0.35
13 14 0.27
14 4 0.08
ACGTcount: A:0.79, C:0.01, G:0.12, T:0.08
Consensus pattern (12 bp):
AAAAAAAAATAG
Found at i:238674 original size:23 final size:24
Alignment explanation
Indices: 238644--238712 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
238634 AAAAAAAAAA
*
238644 AGAAAAAAAAATCGAAAAGAAAATT-
1 AGAAAAAAAAA--AAAAAGAAAATTG
*
238669 TGAAAAAAAAAAAAAAGAAAATTG
1 AGAAAAAAAAAAAAAAGAAAATTG
238693 AGAAAAAAAGAAGAAAAAGA
1 AGAAAAAAA-AA-AAAAAGA
238713 CAAAAATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
23 11 0.29
24 8 0.21
25 12 0.32
26 7 0.18
ACGTcount: A:0.75, C:0.01, G:0.14, T:0.09
Consensus pattern (24 bp):
AGAAAAAAAAAAAAAAGAAAATTG
Found at i:238709 original size:9 final size:8
Alignment explanation
Indices: 238634--238718 Score: 50
Period size: 8 Copynumber: 10.5 Consensus size: 8
238624 TTTATTATTT
238634 AAAA-AAA
1 AAAAGAAA
238641 AAAAGAAA
1 AAAAGAAA
*
238649 AAAA-AATCG
1 AAAAGAA--A
238658 AAAAGAAA
1 AAAAGAAA
***
238666 ATTTGAAA
1 AAAAGAAA
238674 AAAA-AAA
1 AAAAGAAA
238681 AAAAGAAA
1 AAAAGAAA
**
238689 ATTGAGAAA
1 A-AAAGAAA
238698 AAAAGAAGA
1 AAAAGAA-A
*
238707 AAAAGACA
1 AAAAGAAA
238715 AAAA
1 AAAA
238719 TATGTCTGAG
Statistics
Matches: 58, Mismatches: 13, Indels: 13
0.69 0.15 0.15
Matches are distributed among these distances:
7 13 0.22
8 26 0.45
9 17 0.29
10 2 0.03
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (8 bp):
AAAAGAAA
Found at i:238709 original size:35 final size:36
Alignment explanation
Indices: 238635--238710 Score: 84
Period size: 35 Copynumber: 2.1 Consensus size: 36
238625 TTATTATTTA
***
238635 AAAAAAAAAAGAAAAAAAAATCGAAAAGAAAATTTG
1 AAAAAAAAAAGAAAAAAAAATCGAAAAGAAAAGAAG
* *
238671 AAAAAAAAAA-AAAAGAAAATTGAGAAA-AAAAGAAG
1 AAAAAAAAAAGAAAAAAAAATCGA-AAAGAAAAGAAG
238706 AAAAA
1 AAAAA
238711 GACAAAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
35 21 0.62
36 13 0.38
ACGTcount: A:0.79, C:0.01, G:0.12, T:0.08
Consensus pattern (36 bp):
AAAAAAAAAAGAAAAAAAAATCGAAAAGAAAAGAAG
Found at i:239778 original size:23 final size:25
Alignment explanation
Indices: 239752--239797 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
239742 CCAATTAGGA
239752 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
239775 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
239798 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:242387 original size:2 final size:2
Alignment explanation
Indices: 242380--242404 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
242370 TAATTTAAAA
242380 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
242405 ACTCAAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:245330 original size:22 final size:22
Alignment explanation
Indices: 245294--245335 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
245284 TAAAATTTTT
*
245294 AATTTTTAAATTTTT-TTTTAG
1 AATTTTAAAATTTTTATTTTAG
245315 AATTTTAATAATTTTTATTTT
1 AATTTTAA-AATTTTTATTTT
245336 TTATATCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
AATTTTAAAATTTTTATTTTAG
Found at i:245334 original size:28 final size:27
Alignment explanation
Indices: 245281--245337 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 27
245271 GTAAGTACTG
245281 TTTTAAAATTTTTAATTTTTAAATTTTT
1 TTTTAAAATTTTTAATTTTT-AATTTTT
*
245309 TTTTAGAATTTTAATAATTTTT-ATTTTT
1 TTTTAAAATTTT--TAATTTTTAATTTTT
245337 T
1 T
245338 ATATCTAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 18 0.69
30 8 0.31
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (27 bp):
TTTTAAAATTTTTAATTTTTAATTTTT
Found at i:245495 original size:10 final size:10
Alignment explanation
Indices: 245476--245517 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
245466 ATTTACATCA
*
245476 AAATAAATAT
1 AAATATATAT
245486 AAATATATAT
1 AAATATATAT
245496 --ATATATAT
1 AAATATATAT
*
245504 AAATATATTT
1 AAATATATAT
245514 AAAT
1 AAAT
245518 CTCAATACGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 8 0.29
10 20 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AAATATATAT
Found at i:245851 original size:17 final size:17
Alignment explanation
Indices: 245799--245851 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
245789 ATCTAATCAT
*
245799 GAAAAGAAGACAGAGAAG
1 GAAAAGAAGA-AGAGAAA
* *
245817 GAAAAGAAAAAGGGAAA
1 GAAAAGAAGAAGAGAAA
*
245834 GAAAAGAAGAAGATAAA
1 GAAAAGAAGAAGAGAAA
245851 G
1 G
245852 GAACCTTTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
17 20 0.69
18 9 0.31
ACGTcount: A:0.66, C:0.02, G:0.30, T:0.02
Consensus pattern (17 bp):
GAAAAGAAGAAGAGAAA
Found at i:247373 original size:22 final size:22
Alignment explanation
Indices: 247337--247397 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
247327 CGATCTAAGG
247337 AAAAATAAAAG-AAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
247358 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
247380 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
247398 GGAAGTCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
21 11 0.30
22 25 0.68
23 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.16
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:247388 original size:15 final size:16
Alignment explanation
Indices: 247363--247392 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
247353 GAATTAAAAA
247363 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
247379 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
247393 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:248199 original size:11 final size:11
Alignment explanation
Indices: 248183--248217 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
248173 TACAAAAAGA
248183 TAAATATAAAT
1 TAAATATAAAT
248194 TAAATATAAATT
1 TAAATATAAA-T
248206 TAAATAATAAAT
1 TAAAT-ATAAAT
248218 AATATCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 10 0.45
12 7 0.32
13 5 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TAAATATAAAT
Found at i:248218 original size:19 final size:18
Alignment explanation
Indices: 248182--248236 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 18
248172 ATACAAAAAG
*
248182 ATAAATATAAAT-TAAAT
1 ATAAATTTAAATATAAAT
248199 ATAAATTTAAATAATAAAT
1 ATAAATTTAAAT-ATAAAT
*
248218 A-ATATCTTAAATATTAAAT
1 ATAAAT-TTAAATA-TAAAT
248237 CCTAATACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 11 0.34
18 4 0.12
19 17 0.53
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAATTTAAATATAAAT
Found at i:248486 original size:24 final size:23
Alignment explanation
Indices: 248443--248487 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
248433 AGGATCATAC
248443 TCTAAAAATATATATATTTAATA
1 TCTAAAAATATATATATTTAATA
* *
248466 TCTAAAAGTATGTCATATTTAA
1 TCTAAAAATATAT-ATATTTAA
248488 GCATTATCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (23 bp):
TCTAAAAATATATATATTTAATA
Found at i:251962 original size:21 final size:18
Alignment explanation
Indices: 251912--252002 Score: 78
Period size: 18 Copynumber: 4.7 Consensus size: 18
251902 ACCACCACCA
*
251912 CCTTCTTTCTTCTCCCCG
1 CCTTCCTTCTTCTCCCCG
251930 CCTTCCTTCTTCTCCCCG
1 CCTTCCTTCTTCTCCCCG
251948 CCTCCTCCTTCCTTCTCCTCGCCG
1 CCT--TCCTT-CTTCT-C-C-CCG
*
251972 CCATT-CTTC-TCTCCACCT
1 CC-TTCCTTCTTCTCC-CCG
251990 CCTTCCTTCTTCT
1 CCTTCCTTCTTCT
252003 TGCCGCCGCC
Statistics
Matches: 61, Mismatches: 3, Indels: 17
0.75 0.04 0.21
Matches are distributed among these distances:
17 2 0.03
18 29 0.48
19 4 0.07
20 8 0.13
21 6 0.10
22 4 0.07
23 2 0.03
24 5 0.08
25 1 0.02
ACGTcount: A:0.02, C:0.53, G:0.04, T:0.41
Consensus pattern (18 bp):
CCTTCCTTCTTCTCCCCG
Found at i:252104 original size:18 final size:18
Alignment explanation
Indices: 252059--252104 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
252049 GTTATCACCG
252059 CCGGCGTCTTTCTTCTCT
1 CCGGCGTCTTTCTTCTCT
*
252077 CCGCCGTCTTTCTTCTCT
1 CCGGCGTCTTTCTTCTCT
*
252095 CCGGCATCTT
1 CCGGCGTCTT
252105 CTTTCTTAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.02, C:0.41, G:0.15, T:0.41
Consensus pattern (18 bp):
CCGGCGTCTTTCTTCTCT
Found at i:257699 original size:98 final size:97
Alignment explanation
Indices: 257531--257725 Score: 291
Period size: 98 Copynumber: 2.0 Consensus size: 97
257521 AAACCTTGAA
*
257531 AAGGGTATTCGATTATCCCGATTTAAAGAAAAGTCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCGATTATCCCGATTTAAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
* *
257596 AAACCCGAGATAAAGGAACATTGCCTCGATTT
66 AAACCCGAAATAAAAGAACATTGCCTCGATTT
* * * * *
257628 AAGGGTATTTGATTATCTCGATTTGAAGAAAAAATCGTGCCTAGTAAGTTAATGCACAAATTTTC
1 AAGGGTATTCGATTATCCCGATTTAAAG-AAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTC
* *
257693 AAAACCCGAAATAAAATAATATTGCCTCGATTT
65 AAAACCCGAAATAAAAGAACATTGCCTCGATTT
257726 TAAATATTTT
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
97 25 0.29
98 62 0.71
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.29
Consensus pattern (97 bp):
AAGGGTATTCGATTATCCCGATTTAAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
AAACCCGAAATAAAAGAACATTGCCTCGATTT
Found at i:258035 original size:29 final size:29
Alignment explanation
Indices: 258003--258246 Score: 97
Period size: 30 Copynumber: 8.2 Consensus size: 29
257993 TTTCAGAGAG
*
258003 TTTAGGGTTAAAACATAATTTTGGAAAGT
1 TTTAGGGTTAAAATATAATTTTGGAAAGT
** * * *
258032 TTTACGGGGAAAAATGTCATTTTAGGAAA-A
1 TTTA-GGGTTAAAATATAATTTT-GGAAAGT
* * * *
258062 TTCAGGGTAAAAACATTATTTTTGG-AAGT
1 TTTAGGGTTAAAATA-TAATTTTGGAAAGT
** ** * *
258091 TCGAGGGGCAAAAATGTGATTTTTTGG-AAGT
1 TTTA-GGGTTAAAATAT-A-ATTTTGGAAAGT
* *
258122 TTGAGGG-TAAAAAATAAATTTTGGAAAAG-
1 TTTAGGGTTAAAATAT-AATTTTGG-AAAGT
* *
258151 TTTAGGGTCAAAATGTAATTTTGGAAAAG-
1 TTTAGGGTTAAAATATAATTTTGG-AAAGT
* *
258180 TTTAGGGGTTAAAAATGTAATTTTGGAAAAT
1 TTTA-GGGTT-AAAATATAATTTTGGAAAGT
* * **
258211 TTTAAGTGTTAAAATATGATTTTTAAAAG-
1 TTT-AGGGTTAAAATATAATTTTGGAAAGT
258240 TTTAGGG
1 TTTAGGG
258247 GTCAAAATGC
Statistics
Matches: 164, Mismatches: 37, Indels: 29
0.71 0.16 0.13
Matches are distributed among these distances:
28 11 0.07
29 49 0.30
30 62 0.38
31 41 0.25
32 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (29 bp):
TTTAGGGTTAAAATATAATTTTGGAAAGT
Found at i:258077 original size:59 final size:57
Alignment explanation
Indices: 258006--258214 Score: 163
Period size: 60 Copynumber: 3.5 Consensus size: 57
257996 CAGAGAGTTT
* *
258006 AGGGTTAAAACATAATTTTGGAAAGTTTTACGGGGAAAAATGTCATTTTAGGAAAATTC
1 AGGGTAAAAACATAATTTTGGAAAGTTTTA-GGGGAAAAATGTAATTTT-GGAAAATTC
* ** * ** *
258065 AGGGTAAAAACATTATTTTTGG-AAGTTCGAGGGGCAAAAATGTGATTTTTTGGAAGTTTG
1 AGGGTAAAAACA-TAATTTTGGAAAGTTTTAGGGG-AAAAATGT-A-ATTTTGGAAAATTC
** *
258125 AGGGTAAAAA-ATAAATTTTGGAAAAG-TTTAGGGTCAAAATGTAATTTTGGAAAAGTTT
1 AGGGTAAAAACAT-AATTTTGG-AAAGTTTTAGGGGAAAAATGTAATTTTGGAAAA-TTC
** *
258183 AGGGGTTAAAAATGTAATTTTGGAAAATTTTA
1 A-GGG-TAAAAACATAATTTTGGAAAGTTTTA
258215 AGTGTTAAAA
Statistics
Matches: 118, Mismatches: 20, Indels: 23
0.73 0.12 0.14
Matches are distributed among these distances:
57 8 0.07
58 9 0.08
59 46 0.39
60 47 0.40
61 8 0.07
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (57 bp):
AGGGTAAAAACATAATTTTGGAAAGTTTTAGGGGAAAAATGTAATTTTGGAAAATTC
Found at i:258135 original size:31 final size:28
Alignment explanation
Indices: 258065--258147 Score: 85
Period size: 31 Copynumber: 2.8 Consensus size: 28
258055 AGGAAAATTC
258065 AGGGTAAAAACATTATTTTTGGAAGTTCG
1 AGGGTAAAAA-ATTATTTTTGGAAGTTCG
** *
258094 AGGGGCAAAAATGTGATTTTTTGGAAGTTTG
1 AGGGTAAAAAAT-T-A-TTTTTGGAAGTTCG
* *
258125 AGGGTAAAAAATAAATTTTGGAA
1 AGGGTAAAAAATTATTTTTGGAA
258148 AAGTTTAGGG
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
28 10 0.23
29 10 0.23
30 1 0.02
31 23 0.52
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.33
Consensus pattern (28 bp):
AGGGTAAAAAATTATTTTTGGAAGTTCG
Found at i:258152 original size:30 final size:29
Alignment explanation
Indices: 258118--258285 Score: 126
Period size: 29 Copynumber: 5.6 Consensus size: 29
258108 GATTTTTTGG
*
258118 AAGTTTGAGGGTAAAAAAT-AAATTTTGGAA
1 AAGTTT-AGGGT-CAAAATGAAATTTTGGAA
*
258148 AAGTTTAGGGTCAAAATGTAATTTTGGAA
1 AAGTTTAGGGTCAAAATGAAATTTTGGAA
* *
258177 AAGTTTAGGGGTTAAAAATGTAATTTTGGAA
1 AAGTTTA-GGG-TCAAAATGAAATTTTGGAA
* * * * *
258208 AATTTTAAGTGTTAAAAT-ATGATTTT-TAA
1 AAGTTT-AGGGTCAAAATGA-AATTTTGGAA
* **
258237 AAGTTTAGGGGTCAAAATGCAATTTTACAA
1 AAGTTTA-GGGTCAAAATGAAATTTTGGAA
258267 AAGTTTGAGGGTACAAAAT
1 AAGTTT-AGGGT-CAAAAT
258286 ATGATTTTTG
Statistics
Matches: 113, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
28 6 0.05
29 42 0.37
30 32 0.28
31 32 0.28
32 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (29 bp):
AAGTTTAGGGTCAAAATGAAATTTTGGAA
Found at i:258163 original size:60 final size:55
Alignment explanation
Indices: 258001--258208 Score: 152
Period size: 59 Copynumber: 3.5 Consensus size: 55
257991 GGTTTCAGAG
* * *
258001 AGTTTAGGGTTAAAACA-TAATTTTGGAAAGTTTTACGGGGAAAAATGTCATTTTAGGAA
1 AGTTTAGGG-TAAAAAATTAATTTTGGAAAG-TTTA-GGGCAAAAATGT-ATTTTTGG-A
* * * *
258060 AATTCAGGGTAAAAACATTATTTTTGG-AAGTTCGAGGGGCAAAAATGTGATTTTTTGGA
1 AGTTTAGGGTAAAAA-ATTAATTTTGGAAAGTT-TA-GGGCAAAAATGT-A-TTTTTGGA
* *
258119 AGTTTGAGGGTAAAAAATAAATTTTGGAAAAGTTTAGGGTC-AAAATGTAATTTTGGAAA
1 AGTTT-AGGGTAAAAAATTAATTTTGG-AAAGTTTAGGG-CAAAAATGTATTTTTGG--A
*
258178 AGTTTAGGGGTTAAAAATGTAATTTTGGAAA
1 AGTTTA-GGGTAAAAAAT-TAATTTTGGAAA
258209 ATTTTAAGTG
Statistics
Matches: 120, Mismatches: 17, Indels: 24
0.75 0.11 0.15
Matches are distributed among these distances:
57 6 0.05
58 9 0.08
59 66 0.55
60 34 0.28
61 5 0.04
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.34
Consensus pattern (55 bp):
AGTTTAGGGTAAAAAATTAATTTTGGAAAGTTTAGGGCAAAAATGTATTTTTGGA
Found at i:258209 original size:60 final size:60
Alignment explanation
Indices: 258138--258307 Score: 175
Period size: 60 Copynumber: 2.8 Consensus size: 60
258128 GTAAAAAATA
* *
258138 AATTTTGGAAAAGTTT-AGGGTCAAAATGTAATTTTGGAAAAGTTTAGGGGTTAAAAATGT
1 AATTTTGGAAAAGTTTAAGGGTCAAAATATAATTTTGGAAAAGTTTAGGGG-TAAAAATGC
* * * * * *
258198 AATTTTGGAAAATTTTAAGTGTTAAAATATGATTTT-TAAAAGTTTAGGGGTCAAAATGC
1 AATTTTGGAAAAGTTTAAGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGTAAAAATGC
** * * *
258257 AATTTTACAAAAGTTTGAGGGTACAAAATATGATTTTTGG-ATAGTTTAGGG
1 AATTTTGGAAAAGTTTAAGGGT-CAAAATAT-AATTTTGGAAAAGTTTAGGG
258308 ACTTTTTGGG
Statistics
Matches: 88, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
59 24 0.27
60 35 0.40
61 29 0.33
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.37
Consensus pattern (60 bp):
AATTTTGGAAAAGTTTAAGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGTAAAAATGC
Found at i:260060 original size:6 final size:6
Alignment explanation
Indices: 260049--260148 Score: 61
Period size: 6 Copynumber: 17.3 Consensus size: 6
260039 AGACATTATT
* *
260049 AATTTA AATTTA GAA--TA ATTTTA AATTTA AACTTA AA-TTA AATTTA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * * * *
260095 AATTTTTA AA--CA AATTTA AACTTA AA-ATA AATTTA AATATA AA-ATA
1 AA--TTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
260141 AATTTA AA
1 AATTTA AA
260149 AAAATGAGTT
Statistics
Matches: 74, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
4 4 0.05
5 16 0.22
6 46 0.62
7 2 0.03
8 6 0.08
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (6 bp):
AATTTA
Found at i:260075 original size:23 final size:23
Alignment explanation
Indices: 260050--260099 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
260040 GACATTATTA
* *
260050 ATTTAAATTTAGAA-TAATTTTAA
1 ATTTAAACTTA-AATTAAATTTAA
260073 ATTTAAACTTAAATTAAATTTAA
1 ATTTAAACTTAAATTAAATTTAA
260096 ATTT
1 ATTT
260100 TTAAACAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTTAAACTTAAATTAAATTTAA
Found at i:260089 original size:17 final size:17
Alignment explanation
Indices: 260070--260148 Score: 97
Period size: 17 Copynumber: 4.6 Consensus size: 17
260060 AGAATAATTT
*
260070 TAAATTTAAACTTAAAT
1 TAAATTTAAACTTAAAA
* *
260087 TAAATTTAAATTTTTAAA
1 TAAATTTAAA-CTTAAAA
*
260105 CAAATTTAAACTTAAAA
1 TAAATTTAAACTTAAAA
260122 TAAATTTAAA-TATAAAA
1 TAAATTTAAACT-TAAAA
260139 TAAATTTAAA
1 TAAATTTAAA
260149 AAAATGAGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
16 1 0.02
17 39 0.74
18 13 0.25
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:271308 original size:44 final size:46
Alignment explanation
Indices: 271219--271312 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 46
271209 GATTCGTTGT
*
271219 AATGGAATAGAGCTGTAATCAGTAATTCAGTTGTTTGATTGAATAG
1 AATGGAATAGAGCTATAATCAGTAATTCAGTTGTTTGATTGAATAG
* ** *
271265 AATGGAATAGAGCTATAAT-AGTATTTTTG-TGTTTGGTTGAATAG
1 AATGGAATAGAGCTATAATCAGTAATTCAGTTGTTTGATTGAATAG
271309 AATG
1 AATG
271313 ATGTTGTAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 18 0.42
45 7 0.16
46 18 0.42
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAGCTATAATCAGTAATTCAGTTGTTTGATTGAATAG
Done.