Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold166
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: 2719372
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 17868 characters in sequence are not A, C, G, or T
File 1 of 18
Found at i:1662 original size:10 final size:10
Alignment explanation
Indices: 1647--1673 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1637 ATGTATCAAG
1647 CAAAAACAAA
1 CAAAAACAAA
1657 CAAAAACAAA
1 CAAAAACAAA
1667 CAAAAAC
1 CAAAAAC
1674 TTAGTTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:5880 original size:52 final size:51
Alignment explanation
Indices: 5802--5950 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 51
5792 CGAAATATGA
5802 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
5854 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
** **
5906 AAATTTTTCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
5951 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:5957 original size:13 final size:13
Alignment explanation
Indices: 5939--5963 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5929 CAAAGATCAG
5939 TGTATCGATACAA
1 TGTATCGATACAA
5952 TGTATCGATACA
1 TGTATCGATACA
5964 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:6041 original size:33 final size:33
Alignment explanation
Indices: 6004--6070 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5994 AGTAGCTTAA
6004 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
6037 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
6070 A
1 A
6071 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:6044 original size:13 final size:13
Alignment explanation
Indices: 6026--6050 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6016 CAAAAAAATA
6026 TGTATCGATACAT
1 TGTATCGATACAT
6039 TGTATCGATACA
1 TGTATCGATACA
6051 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6979 original size:53 final size:53
Alignment explanation
Indices: 6916--7019 Score: 156
Period size: 53 Copynumber: 2.0 Consensus size: 53
6906 TATCCTTATT
* * *
6916 GATTACTATTAGGATTATGATTAAG-ATTGTCTTTGTTTAGTTAGGACTCTATA
1 GATTACTATTAGGATTATGATT-AGCATTGCCCTTGCTTAGTTAGGACTCTATA
*
6969 GATTACTATTAGGATTGTGATTAGCATTGCCCTTGCTTAGTTAGGACTCTA
1 GATTACTATTAGGATTATGATTAGCATTGCCCTTGCTTAGTTAGGACTCTA
7020 CAAATTTTAG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 2 0.04
53 44 0.96
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (53 bp):
GATTACTATTAGGATTATGATTAGCATTGCCCTTGCTTAGTTAGGACTCTATA
Found at i:7370 original size:22 final size:18
Alignment explanation
Indices: 7330--7367 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
7320 GCTTGGTTCT
7330 TAAAAATCAAGTGTAATC
1 TAAAAATCAAGTGTAATC
7348 TAAAAATCAAGTGTAATC
1 TAAAAATCAAGTGTAATC
7366 TA
1 TA
7368 TCTTTTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29
Consensus pattern (18 bp):
TAAAAATCAAGTGTAATC
Found at i:10233 original size:13 final size:13
Alignment explanation
Indices: 10215--10239 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10205 ACCCATCACC
10215 TAAATTCTCGAAA
1 TAAATTCTCGAAA
10228 TAAATTCTCGAA
1 TAAATTCTCGAA
10240 GGTAGATAGT
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
TAAATTCTCGAAA
Found at i:15769 original size:163 final size:163
Alignment explanation
Indices: 15509--16059 Score: 682
Period size: 168 Copynumber: 3.3 Consensus size: 163
15499 AAAAGTTCTT
* * *
15509 TCATTTTCATTAGTTTTTGAATTTTTTCCTTTAAATTTC-CTTTTTTTTCGAAATACATTA-TTT
1 TCATTTTCATGAGTTTTTGAA-TTTTTCCTTGAAATTTCGC--TTTTTTCGAAATACA-GAGTTT
* * * * *
15572 TCTACTCCGTGGATTTTTTCGAGAGGAGTTTTCTTGGTTTTCATTTTTAAAATTCATCAAACATT
62 TCTACTCTGTGGATTTTTTCGAGGGGATTTTTCTTGGTTTTAATTTTTAAAATTCATCAAACATC
15637 ATTATTTATTTCATATTAATTCAGTTTT-AAAAAAAC
127 ATTATTTATTTCATATTAATTCAGTTTTAAAAAAAAC
* *
15673 TCATTTTTATGAGTTTTTGAATTTTTCCTTGAAATTCTC-ATTTTTTCGAAATACAGAGTTTTCT
1 TCATTTTCATGAGTTTTTGAATTTTTCCTTGAAATT-TCGCTTTTTTCGAAATACAGAGTTTTCT
*
15737 GCTCTGTGGATTTGTTTCGAGGGGATTTTTCTTGGTTTTAATTTTTAAAATTCATCAAACATCAT
65 ACTCTGTGGATTT-TTTCGAGGGGATTTTTCTTGGTTTTAATTTTTAAAATTCATCAAACATCAT
15802 TATTTATTTCATATTAATTCAGTTTTTAAAAAAAAAC
129 TATTTATTTCATATTAATTCAG-TTTT-AAAAAAAAC
* * * ** *
15839 TCATTTTCATGAGGTTTTGAGTTTTTTCCTTGAAATTTC-CTTTTTTCCAAAATATGGTGTTTTC
1 TCATTTTCATGAGTTTTTGA-ATTTTTCCTTGAAATTTCGCTTTTTT-CGAAATACAGAGTTTTC
* * * *
15903 TACTCTGT-AATTTTTTTCGAGGGGTTTTTTTCTTGGTTTGTAATATTTAAAATTCATCAAACAA
64 TACTCTGTGGA-TTTTTTCGAGGGG-ATTTTTCTTGGTTT-TAATTTTTAAAATTCATCAAACAT
* *
15967 CATTATTTATTTCATATTAATTTAGTTTTAAAAAACAAAT
126 CATTATTTATTTCATATTAATTCAGTTTT-AAAAA-AAAC
* * *
16007 TCATTTTCATGAGTTTTTTATTTTTCTCCTTGAAATTCCGCTTTTTTCGAAAT
1 TCATTTTCATGAGTTTTTGAATTTT-TCCTTGAAATTTCGCTTTTTTCGAAAT
16060 GCTGTGTTTA
Statistics
Matches: 343, Mismatches: 30, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
161 1 0.00
162 32 0.09
163 83 0.24
164 25 0.07
166 45 0.13
167 66 0.19
168 84 0.24
169 7 0.02
ACGTcount: A:0.26, C:0.12, G:0.11, T:0.51
Consensus pattern (163 bp):
TCATTTTCATGAGTTTTTGAATTTTTCCTTGAAATTTCGCTTTTTTCGAAATACAGAGTTTTCTA
CTCTGTGGATTTTTTCGAGGGGATTTTTCTTGGTTTTAATTTTTAAAATTCATCAAACATCATTA
TTTATTTCATATTAATTCAGTTTTAAAAAAAAC
Found at i:15983 original size:168 final size:165
Alignment explanation
Indices: 15509--16068 Score: 718
Period size: 163 Copynumber: 3.4 Consensus size: 165
15499 AAAAGTTCTT
* * * * *
15509 TCATTTTCATTAGTTTTTGAATTTTTTCCTTTAAATTTCCTTTTTTTTCGAAATACATTATTTTC
1 TCATTTTCATGAGTTTTTG-ATTTTTTCCTTGAAATTTCC-TTTTTTCCGAAATACAGTGTTTTC
* * * * *
15574 TACTCCGTGGA-TTTTTTCGAGAGGAGTTTTCTTGGTTTTCATTTTTAAAATTCATCAAACATTA
64 TACTCTGTGGATTTTTTTCGAGGGGATTTTTCTTGGTTTTAATTTTTAAAATTCATCAAACATCA
15638 TTATTTATTTCATATTAATTCAGTTTT--AAAAAAAC
129 TTATTTATTTCATATTAATTCAGTTTTAAAAAAAAAC
* * * *
15673 TCATTTTTATGAGTTTTTGAATTTTTCCTTGAAATTCTCATTTTTT-CGAAATACAGAGTTTTCT
1 TCATTTTCATGAGTTTTTGATTTTTTCCTTGAAATT-TCCTTTTTTCCGAAATACAGTGTTTTCT
* *
15737 GCTCTGTGGATTTGTTTCGAGGGGATTTTTCTTGGTTTTAATTTTTAAAATTCATCAAACATCAT
65 ACTCTGTGGATTTTTTTCGAGGGGATTTTTCTTGGTTTTAATTTTTAAAATTCATCAAACATCAT
15802 TATTTATTTCATATTAATTCAGTTTTTAAAAAAAAAC
130 TATTTATTTCATATTAATTCAG-TTTTAAAAAAAAAC
* * **
15839 TCATTTTCATGAGGTTTTGAGTTTTTTCCTTGAAATTTCCTTTTTTCCAAAATATGGTGTTTTCT
1 TCATTTTCATGAGTTTTTGA-TTTTTTCCTTGAAATTTCCTTTTTTCCGAAATACAGTGTTTTCT
* * * *
15904 ACTCTGT-AATTTTTTTCGAGGGGTTTTTTTCTTGGTTTGTAATATTTAAAATTCATCAAACAAC
65 ACTCTGTGGATTTTTTTCGAGGGG-ATTTTTCTTGGTTT-TAATTTTTAAAATTCATCAAACATC
* *
15968 ATTATTTATTTCATATTAATTTAGTTTTAAAAAACAAAT
128 ATTATTTATTTCATATTAATTCAGTTTTAAAAAA-AAAC
* * * *
16007 TCATTTTCATGAGTTTTTTATTTTTCTCCTTGAAATTCCGCTTTTTT-CGAAATGCTGTGTTT
1 TCATTTTCATGAGTTTTTGATTTTT-TCCTTGAAATTTC-CTTTTTTCCGAAATACAGTGTTT
16069 ACCATTTCGT
Statistics
Matches: 346, Mismatches: 38, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
162 23 0.07
163 92 0.27
164 23 0.07
166 48 0.14
167 63 0.18
168 90 0.26
169 7 0.02
ACGTcount: A:0.26, C:0.12, G:0.11, T:0.51
Consensus pattern (165 bp):
TCATTTTCATGAGTTTTTGATTTTTTCCTTGAAATTTCCTTTTTTCCGAAATACAGTGTTTTCTA
CTCTGTGGATTTTTTTCGAGGGGATTTTTCTTGGTTTTAATTTTTAAAATTCATCAAACATCATT
ATTTATTTCATATTAATTCAGTTTTAAAAAAAAAC
Found at i:16083 original size:168 final size:162
Alignment explanation
Indices: 15509--16126 Score: 628
Period size: 168 Copynumber: 3.7 Consensus size: 162
15499 AAAAGTTCTT
* * * * *
15509 TCATTTTCATTAGTTTTTGAATTTTTTCCTTTAAATTTCCTTTTTTTTCGAAATACAT-TATTTT
1 TCATTTTCATGAGTTTTTG-ATTTTTTCCTTGAAA-TTCC-CTTTTTTCGAAAT-C-TGTGTTTC
* * * * *
15573 C-TACTCCGTGGA-TTTTTTCGAGAGGAGTTTTCTTGGTTTTCATTTTTAAAATTCATCAAACAT
61 CAT-CTCTGT-AATTTTTTTCGAGGGGATTTTTCTTGGTTTTAATTTTTAAAATTCATCAAACAT
*
15636 TATTATTTATTTCATATTAATTCAGTTTT--AAAAAAAC
124 CATTATTTATTTCATATTAATTCAGTTTTAAAAAAAAAC
* * * * * *
15673 TCATTTTTATGAGTTTTTGAATTTTTCCTTGAAATTCTCATTTTTTCGAAATACAGAGTTTTC-T
1 TCATTTTCATGAGTTTTTGATTTTTTCCTTGAAATTC-CCTTTTTTCGAAAT-CTGTGTTTCCAT
* *
15737 GCTCTGTGGATTTGTTTCGAGGGGATTTTTCTTGGTTTTAATTTTTAAAATTCATCAAACATCAT
64 -CTCTGT-AATTTTTTTCGAGGGGATTTTTCTTGGTTTTAATTTTTAAAATTCATCAAACATCAT
15802 TATTTATTTCATATTAATTCAGTTTTTAAAAAAAAAC
127 TATTTATTTCATATTAATTCAG-TTTTAAAAAAAAAC
* * * * *
15839 TCATTTTCATGAGGTTTTGAGTTTTTTCCTTGAAATTTCCTTTTTTCCAAAATATGGTGTTTTC-
1 TCATTTTCATGAGTTTTTGA-TTTTTTCCTTGAAATTCCCTTTTTT-CGAAATCT-GTGTTTCCA
* * *
15903 TACTCTGTAATTTTTTTCGAGGGGTTTTTTTCTTGGTTTGTAATATTTAAAATTCATCAAACAAC
63 T-CTCTGTAATTTTTTTCGAGGGG-ATTTTTCTTGGTTT-TAATTTTTAAAATTCATCAAACATC
* *
15968 ATTATTTATTTCATATTAATTTAGTTTTAAAAAACAAAT
125 ATTATTTATTTCATATTAATTCAGTTTTAAAAAA-AAAC
*
16007 TCATTTTCATGAGTTTTTTATTTTTCTCCTTGAAATTCCGCTTTTTTCGAAATGCTGTGTTTACC
1 TCATTTTCATGAGTTTTTGATTTTT-TCCTTGAAATTCC-CTTTTTTCGAAAT-CTGTGTTT-CC
* * *
16072 ATTTC-GTAA-TTTTTTCG-GGGAGA-TTTTCTTTGGTTTAAAATTTTTAAAATGCATC
62 ATCTCTGTAATTTTTTTCGAGGG-GATTTTTC-TTGGTTT-TAATTTTTAAAATTCATC
16127 TAATATTGTC
Statistics
Matches: 391, Mismatches: 44, Indels: 36
0.83 0.09 0.08
Matches are distributed among these distances:
162 31 0.08
163 85 0.22
164 21 0.05
165 5 0.01
166 72 0.18
167 71 0.18
168 94 0.24
169 11 0.03
170 1 0.00
ACGTcount: A:0.26, C:0.12, G:0.11, T:0.50
Consensus pattern (162 bp):
TCATTTTCATGAGTTTTTGATTTTTTCCTTGAAATTCCCTTTTTTCGAAATCTGTGTTTCCATCT
CTGTAATTTTTTTCGAGGGGATTTTTCTTGGTTTTAATTTTTAAAATTCATCAAACATCATTATT
TATTTCATATTAATTCAGTTTTAAAAAAAAAC
Found at i:16718 original size:11 final size:11
Alignment explanation
Indices: 16692--16731 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
16682 GCTCCTGCTG
*
16692 AGAAAAGAGAA
1 AGAAAAAAGAA
16703 A-AAAAAAGAA
1 AGAAAAAAGAA
*
16713 AGAAAAGAGAA
1 AGAAAAAAGAA
16724 AGAAAAAA
1 AGAAAAAA
16732 TAGGGAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AGAAAAAAGAA
Found at i:19846 original size:13 final size:13
Alignment explanation
Indices: 19828--19854 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19818 ACATTATGCT
19828 TTGTATCGATACA
1 TTGTATCGATACA
19841 TTGTATCGATACA
1 TTGTATCGATACA
19854 T
1 T
19855 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:19884 original size:20 final size:19
Alignment explanation
Indices: 19837--19894 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
19827 TTTGTATCGA
19837 TACATTGTATCGATACATG
1 TACATTGTATCGATACATG
*
19856 TTCATTGTATCGATACATAG
1 TACATTGTATCGATACAT-G
19876 -ACAATTGTATCGATACATG
1 TAC-ATTGTATCGATACATG
19895 AGATTGGCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 19 0.54
20 16 0.46
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (19 bp):
TACATTGTATCGATACATG
Found at i:19964 original size:33 final size:33
Alignment explanation
Indices: 19926--19990 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
19916 CCATTATTTG
*
19926 TATCGATACATGGT-ACAATGTATCGATACATTA
1 TATCGATACATGATGA-AATGTATCGATACATTA
*
19959 TATCGATACATGATGAATTGTATCGATACATT
1 TATCGATACATGATGAAATGTATCGATACATT
19991 GCCTGTAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (33 bp):
TATCGATACATGATGAAATGTATCGATACATTA
Found at i:27933 original size:21 final size:22
Alignment explanation
Indices: 27894--27967 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
27884 TTGACAAAGG
*
27894 GGGAG-AAATGCTATGATTAAGA
1 GGGAGAAAATTCT-TGATTAAGA
27916 GGGAGAAAATT-TTGATTAA-A
1 GGGAGAAAATTCTTGATTAAGA
* *
27936 GAGGAG-AAATTCTTCAATTAAGG
1 G-GGAGAAAATTCTT-GATTAAGA
27959 GGGAGAAAA
1 GGGAGAAAA
27968 ATGAAAACTT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
20 7 0.16
21 13 0.30
22 15 0.35
23 8 0.19
ACGTcount: A:0.43, C:0.04, G:0.30, T:0.23
Consensus pattern (22 bp):
GGGAGAAAATTCTTGATTAAGA
Found at i:28535 original size:19 final size:19
Alignment explanation
Indices: 28492--28560 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 19
28482 CACACCCAGA
*
28492 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
28512 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
28531 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
28551 TGTATCGATA
1 TGTATCGATA
28561 TATGAGATTG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 17 0.39
20 26 0.59
21 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:28630 original size:13 final size:13
Alignment explanation
Indices: 28609--28638 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28599 CGATACATGG
28609 TACAATGTATCGA
1 TACAATGTATCGA
*
28622 TACACTGTATCGA
1 TACAATGTATCGA
28635 TACA
1 TACA
28639 TGATGAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:28651 original size:33 final size:33
Alignment explanation
Indices: 28594--28656 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
28584 TACCACTATT
*
28594 TGTATCGATACATGGTACAATGTATCGATACAC
1 TGTATCGATACATGATACAATGTATCGATACAC
*
28627 TGTATCGATACATGATGA-ATTGTATCGATA
1 TGTATCGATACATGAT-ACAATGTATCGATA
28657 TATTGCTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (33 bp):
TGTATCGATACATGATACAATGTATCGATACAC
Found at i:29559 original size:32 final size:32
Alignment explanation
Indices: 29511--29613 Score: 93
Period size: 32 Copynumber: 3.2 Consensus size: 32
29501 ACGAGTATTG
* *
29511 GCACTCACGTGTATTTTCATTTATGAGCATTT
1 GCACTCATGTGCATTTTCATTTATGAGCATTT
* *
29543 GCACTCATGTGCATTTTTATTTCT-ATGC-TTT
1 GCACTCATGTGCATTTTCATTTATGA-GCATTT
* ** *
29574 CGCACTCATATGCATTTCTCATACATGAGCAGTT
1 -GCACTCATGTGCATTT-TCATTTATGAGCATTT
29608 GCACTC
1 GCACTC
29614 TTCAGTGTCG
Statistics
Matches: 56, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
31 4 0.07
32 37 0.66
33 12 0.21
34 3 0.05
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (32 bp):
GCACTCATGTGCATTTTCATTTATGAGCATTT
Found at i:32944 original size:20 final size:20
Alignment explanation
Indices: 32921--32972 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
32911 CAAAGCAAAT
*
32921 TGTATCGATACATCTAGGGA
1 TGTATCGATACATCTACGGA
* **
32941 TGTATCGATACATTTACTTA
1 TGTATCGATACATCTACGGA
32961 TGTATCGATACA
1 TGTATCGATACA
32973 ATTTTTGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATCTACGGA
Found at i:34954 original size:21 final size:21
Alignment explanation
Indices: 34928--34982 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 21
34918 CATAAGTAAA
**
34928 TGTATCGATACATTTATGGTT
1 TGTATCGATACATTTATCCTT
34949 TGTATCGATACA-TTATCCTT
1 TGTATCGATACATTTATCCTT
34969 TGTATCGATACATT
1 TGTATCGATACATT
34983 CTAGATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (21 bp):
TGTATCGATACATTTATCCTT
Found at i:39042 original size:19 final size:20
Alignment explanation
Indices: 39003--39047 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
38993 AGAGCATACC
**
39003 ATCGATACAATTGTCCATGT
1 ATCGATACAATTGAACATGT
39023 ATCGATACAA-TGAACATGT
1 ATCGATACAATTGAACATGT
39042 ATCGAT
1 ATCGAT
39048 GCATTGTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (20 bp):
ATCGATACAATTGAACATGT
Found at i:47681 original size:13 final size:13
Alignment explanation
Indices: 47663--47687 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47653 CAATTCATCA
47663 TGTATCGATACAT
1 TGTATCGATACAT
47676 TGTATCGATACA
1 TGTATCGATACA
47688 ATGTTCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:47685 original size:33 final size:33
Alignment explanation
Indices: 47643--47707 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
47633 TTTGAAGCAA
47643 TGTATCGATACAA--TTCATCATGTATCGATACAT
1 TGTATCGATACAATGTTC--CATGTATCGATACAT
47676 TGTATCGATACAATGTTCCATGTATCGATACA
1 TGTATCGATACAATGTTCCATGTATCGATACA
47708 AACAGTGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 27 0.90
35 3 0.10
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATGTTCCATGTATCGATACAT
Found at i:48985 original size:78 final size:74
Alignment explanation
Indices: 48889--49036 Score: 206
Period size: 75 Copynumber: 1.9 Consensus size: 74
48879 AAATTATATG
* *
48889 AAAGAAAAGTTTAAGTTTTTTTTTTTGAAAATCGAGGTTAGAGTATCCCCTTAGAGGAGTGAGGA
1 AAAGAAAAGTTTAAG---TTTTTTTTGAAAATCAAGGTTAGAGTATCCCCTCAGAGGAGTGAGGA
*
48954 TGGAGTTTTTCC
63 TGAAGTTTTTCC
* * *
48966 AAAGATAAAGTTTGAGTTTTTTTTGAAGATCAAGGTTAGAGTATCCCCTCAGAGGAGTGGGGATG
1 AAAGA-AAAGTTTAAGTTTTTTTTGAAAATCAAGGTTAGAGTATCCCCTCAGAGGAGTGAGGATG
49031 AAGTTT
65 AAGTTT
49037 CCTTCAAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
75 50 0.78
77 5 0.08
78 9 0.14
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.34
Consensus pattern (74 bp):
AAAGAAAAGTTTAAGTTTTTTTTGAAAATCAAGGTTAGAGTATCCCCTCAGAGGAGTGAGGATGA
AGTTTTTCC
Found at i:54037 original size:20 final size:19
Alignment explanation
Indices: 54008--54046 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
53998 AGGTCAAAAC
54008 CCTTAAATGTATCGATACA
1 CCTTAAATGTATCGATACA
54027 CCTTCAAATGTATCGATACA
1 CCTT-AAATGTATCGATACA
54047 TAATGCACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (19 bp):
CCTTAAATGTATCGATACA
Found at i:54205 original size:20 final size:20
Alignment explanation
Indices: 54162--54213 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
54152 CTTAACTGTT
*
54162 TGTATCGATACA-CACAAGA
1 TGTATCGATACATCACAAAA
*
54181 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
54201 TGTATCGATACAT
1 TGTATCGATACAT
54214 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.27
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:56061 original size:13 final size:13
Alignment explanation
Indices: 56043--56070 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
56033 ATACAAAGAT
56043 CAATGTATCGATA
1 CAATGTATCGATA
56056 CAATGTATCGATA
1 CAATGTATCGATA
56069 CA
1 CA
56071 TTGAATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:56067 original size:33 final size:33
Alignment explanation
Indices: 56025--56090 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
56015 AAATTCCCAG
56025 ATGTATCGATACAAAG-ATCAATGTATCGATACA
1 ATGTATCGATACAAAGAAT-AATGTATCGATACA
**
56058 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCGATACA
56091 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCGATACA
Found at i:58175 original size:20 final size:20
Alignment explanation
Indices: 58150--58204 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
58140 TTTTACCCAG
*
58150 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTATCA
* *
58170 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTATCA
58190 ATGTATCGATACATT
1 ATGTATCGATACATT
58205 CTGTCTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTATCA
Found at i:58255 original size:71 final size:71
Alignment explanation
Indices: 58139--58325 Score: 329
Period size: 71 Copynumber: 2.6 Consensus size: 71
58129 AAAAGTCATA
58139 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
58204 TCTGTC
66 TCTGTC
* * *
58210 TTTTTACCCAGATGTATCGATACATTTTTTAATATATCGATACATGTATGAATGTATCGGTACAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
58275 TCTGTC
66 TCTGTC
* *
58281 TCTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
58326 TGTGTCTTTT
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 109 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (71 bp):
TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
TCTGTC
Found at i:58267 original size:20 final size:20
Alignment explanation
Indices: 58221--58274 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
58211 TTTTACCCAG
* * *
58221 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATGTATGA
*
58241 ATATATCGATACATGTATGA
1 ATGTATCGATACATGTATGA
*
58261 ATGTATCGGTACAT
1 ATGTATCGATACAT
58275 TCTGTCTCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATGTATGA
Found at i:58299 original size:51 final size:51
Alignment explanation
Indices: 58244--58377 Score: 171
Period size: 51 Copynumber: 2.6 Consensus size: 51
58234 TTTTTTAATA
* * *
58244 TATCGATACATGTATGAATGTATCGGTACATTCTGTCTCTTTACCTAGATG
1 TATCGATACATGTATCAATGTATCGATACATTCTGTCTCTTTACCCAGATG
* * * *
58295 TATCGATACATTTTTCAATGTATCGATACATTGTGTCTTTTTACCCAGATG
1 TATCGATACATGTATCAATGTATCGATACATTCTGTCTCTTTACCCAGATG
* *
58346 TATCGATACATTGAAT-AATATATCGATACATT
1 TATCGATACA-TGTATCAATGTATCGATACATT
58378 TAGTTAAAAT
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
51 69 0.97
52 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.40
Consensus pattern (51 bp):
TATCGATACATGTATCAATGTATCGATACATTCTGTCTCTTTACCCAGATG
Found at i:59724 original size:34 final size:35
Alignment explanation
Indices: 59686--59752 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
59676 CCTTACAACA
59686 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
59720 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
59753 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:60249 original size:13 final size:13
Alignment explanation
Indices: 60231--60256 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60221 CTATTTATGA
60231 TGTATCGATACAC
1 TGTATCGATACAC
60244 TGTATCGATACAC
1 TGTATCGATACAC
60257 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:60387 original size:10 final size:10
Alignment explanation
Indices: 60368--60398 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
60358 GTATCGATAC
60368 ATGAACAGTG
1 ATGAACAGTG
*
60378 ATGAATAGTG
1 ATGAACAGTG
60388 ATGAACAGTG
1 ATGAACAGTG
60398 A
1 A
60399 AAAATGAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:60539 original size:20 final size:20
Alignment explanation
Indices: 60476--60546 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
60466 GCCAATGACC
**
60476 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* * *
60496 TGTATCGATAC-TGTGCAATT
1 TGTATCGATACATAT-TAATG
60516 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
60536 TGTATCGATAC
1 TGTATCGATAC
60547 TTTTCAGGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 2 0.05
20 38 0.93
21 1 0.02
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:60612 original size:21 final size:21
Alignment explanation
Indices: 60586--60626 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
60576 GTCAACCTTG
60586 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
60607 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
60627 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:73298 original size:1 final size:1
Alignment explanation
Indices: 73292--73389 Score: 52
Period size: 1 Copynumber: 98.0 Consensus size: 1
73282 CTTCGTACCC
* ** * * * * * * ** *
73292 AAAAAAAAACAAAAAAACCAAGAAAAAAACAAAAAAATAGAAAAACAGAAAAAACCAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
73357 AAAACAAAAAAACAAAAAAAAACAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
73390 GGGGTCTAGA
Statistics
Matches: 69, Mismatches: 28, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.84, C:0.12, G:0.03, T:0.01
Consensus pattern (1 bp):
A
Found at i:73307 original size:8 final size:8
Alignment explanation
Indices: 73294--73389 Score: 90
Period size: 8 Copynumber: 11.8 Consensus size: 8
73284 TCGTACCCAA
73294 AAAAAAAC
1 AAAAAAAC
73302 AAAAAAACC
1 AAAAAAA-C
73311 AAGAAAAAAAC
1 ---AAAAAAAC
*
73322 AAAAAAAT
1 AAAAAAAC
*
73330 AGAAAAAC
1 AAAAAAAC
73338 AGAAAAAAC
1 A-AAAAAAC
*
73347 -CAAAAAC
1 AAAAAAAC
73354 AAAAAAAC
1 AAAAAAAC
73362 AAAAAAAC
1 AAAAAAAC
73370 -AAAAAA-
1 AAAAAAAC
*
73376 AAACAAAC
1 AAAAAAAC
73384 AAAAAA
1 AAAAAA
73390 GGGGTCTAGA
Statistics
Matches: 72, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
7 17 0.24
8 40 0.56
9 7 0.10
11 1 0.01
12 7 0.10
ACGTcount: A:0.83, C:0.12, G:0.03, T:0.01
Consensus pattern (8 bp):
AAAAAAAC
Found at i:73377 original size:32 final size:30
Alignment explanation
Indices: 73294--73389 Score: 106
Period size: 32 Copynumber: 3.2 Consensus size: 30
73284 TCGTACCCAA
* *
73294 AAAAAAACAAAAAAAC--CAAGAAAAAAAC
1 AAAAAAACAAAAAAACAAAAAAAAAAAAAC
* * *
73322 AAAAAAATAGAAAAACAGAAAAAACCAAAAAC
1 AAAAAAACAAAAAAACA-AAAAAA-AAAAAAC
*
73354 AAAAAAACAAAAAAACAAAAAAAAACAAAC
1 AAAAAAACAAAAAAACAAAAAAAAAAAAAC
73384 AAAAAA
1 AAAAAA
73390 GGGGTCTAGA
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
28 14 0.25
30 11 0.20
31 9 0.16
32 21 0.38
ACGTcount: A:0.83, C:0.12, G:0.03, T:0.01
Consensus pattern (30 bp):
AAAAAAACAAAAAAACAAAAAAAAAAAAAC
Found at i:74662 original size:28 final size:29
Alignment explanation
Indices: 74636--75286 Score: 721
Period size: 28 Copynumber: 22.8 Consensus size: 29
74626 CATTCATCTC
* * *
74636 TTCAAAGCCCACAGGTTAGTGGCAT-CTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
* *
74664 TTCAAAGCCCACAAGTCAGTGGAAT-CTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
74692 TTCAAAGCCCACAAGTCAGTGGCA-CCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
* *
74720 TTCAAAGCCCACAAGTTAGTAGCAT-CCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
*
74748 TTTAAAGCCCACAAGTCAGTGGCAT-CCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
*
74776 TTCAAAGCCCACAAGTCAGTGGCATCTCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
* * *
74805 TTAAAAGACCACAAGTTAGTGGCAT-CCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
* *
74833 TTCAAAGCCCACAAATCAGTGGCAT-CTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
* *
74861 TTCAAAGCCCACAAGTCAATGGCAT-CTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
74889 TTCAAAGCCCACAAGTCAGTGGCA-CCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
* *
74917 TTCAAAGCCCACAAGTTAATGGCA-CCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
74945 TTCAAAGCCCACAAGTCAGTGGCAT-CCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
* *
74973 TTCAAAGCCCACAAGGCAGTGGCATCTC-
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
* *
75001 TTCAAAAGACCACAAGTTAGTGGCA-CCCT
1 TTC-AAAGCCCACAAGTCAGTGGCATCCCT
*
75030 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
*
75058 TTCAAAGCCTACAAGTCAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT-CCCT
*
75088 TTCAAAGCCCACACAAATCAGTGGCA-CCCT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCCT
* *
75118 TTTAAAGCCCACAATTCAGTGGCAT-CCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
* * *
75146 TTCAAAGCCTACAAGTTAATGGCA-CCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
* * * * *
75174 TTTAAAGCCCATAAGTTAGTGGTA-CCCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCCT
*
75202 TTCAAAGCCCACAAG-CTGGTGGCAT-CCT
1 TTCAAAGCCCACAAGTC-AGTGGCATCCCT
* * *
75230 TTCAAAGCCCACACAAGTCGGTGGCAACCTT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCCT
*
75261 TTCAAAGTCCACACAAGTTAGTGGCA
1 TTCAAAG-CC-CACAAGTCAGTGGCA
75287 CCTTTTTTTT
Statistics
Matches: 537, Mismatches: 66, Indels: 37
0.84 0.10 0.06
Matches are distributed among these distances:
28 413 0.77
29 50 0.09
30 33 0.06
31 28 0.05
32 13 0.02
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (29 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCCT
Found at i:74971 original size:197 final size:197
Alignment explanation
Indices: 74636--75292 Score: 886
Period size: 197 Copynumber: 3.3 Consensus size: 197
74626 CATTCATCTC
** * * *
74636 TTCAAAGCCCACAGGTTAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGAATCTTTTCAAAGCC
1 TTCAAAGCCCACAAATCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCC
* *
74701 CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTAGCATCCTTTTAAAGCCCACAAGTCA
66 CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCA
74766 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTTAAAAGACCACAAGTTAGTGGCATC
131 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTTAAAAGACCACAAGTTAGTGGCATC
74831 CT
196 CT
* *
74833 TTCAAAGCCCACAAATCAGTGGCATCTTTTCAAAGCCCACAAGTCAATGGCATCTTTTCAAAGCC
1 TTCAAAGCCCACAAATCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCC
* *
74898 CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAATGGCACCCTTTCAAAGCCCACAAGTCA
66 CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCA
* * *
74963 GTGGCATCCTTTCAAAGCCCACAAGGCAGTGGCATCTCTTCAAAAGACCACAAGTTAGTGGCACC
131 GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTTAAAAGACCACAAGTTAGTGGCATC
75028 CT
196 CT
* * *
75030 TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCTACAAGTCAGTGGCATACCCTTTCAAAG
1 TTCAAAGCCCACAAATCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAT--CTTTTCAAAG
* * *
75095 CCCACACAAATCAGTGGCACCCTTTTAAAGCCCACAA-TTCAGTGGCATCCTTTCAAAGCCTACA
64 -CC-CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTT-AGTGGCATCCTTTCAAAGCCCACA
* * * * * * * * * * * * *
75159 AGTTAATGGCACCCTTTTAAAGCCCATAAGTTAGTGGTA-CCCCTTCAAAGCCCACAAGCTGGTG
126 AGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTTAAAAGACCACAAGTTAGTG
75223 GCATCCT
191 GCATCCT
* * *
75230 TTCAAAGCCCACACAAGTCGGTGGCAACCTTTTCAAAGTCCACACAAGTTAGTGGCACCTTTT
1 TTCAAAGCCCACA-AA-TCAGTGGC-ACCTTTTCAAAG-CC-CACAAGTCAGTGGCATCTTTT
75293 TTTTAAAAAA
Statistics
Matches: 406, Mismatches: 44, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
197 234 0.58
199 9 0.02
200 41 0.10
201 84 0.21
202 7 0.02
203 16 0.04
204 2 0.00
205 13 0.03
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (197 bp):
TTCAAAGCCCACAAATCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCC
CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCA
GTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTTAAAAGACCACAAGTTAGTGGCATC
CT
Found at i:82869 original size:21 final size:21
Alignment explanation
Indices: 82845--82885 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
82835 AGAAAATAAA
* *
82845 GAATTAACTAATAAAAACAAT
1 GAATTAACAAAGAAAAACAAT
82866 GAATTAACAAAGAAAAACAA
1 GAATTAACAAAGAAAAACAA
82886 AAACTTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.66, C:0.10, G:0.07, T:0.17
Consensus pattern (21 bp):
GAATTAACAAAGAAAAACAAT
Found at i:83892 original size:19 final size:20
Alignment explanation
Indices: 83864--83914 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
83854 CAATTTAGTG
* *
83864 TGTATTGATACCAAG-AACA
1 TGTATCGATACAAAGCAACA
*
83883 TGTATCGATACAAAGCAATA
1 TGTATCGATACAAAGCAACA
83903 TGTATCGATACA
1 TGTATCGATACA
83915 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (20 bp):
TGTATCGATACAAAGCAACA
Found at i:84035 original size:20 final size:21
Alignment explanation
Indices: 84010--84053 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
84000 GATACTTTAA
84010 ATTATTTTTA-CTTGAAAAAC
1 ATTATTTTTAGCTTGAAAAAC
84030 ATTATTTTTATGCTTGAAAAAC
1 ATTATTTTTA-GCTTGAAAAAC
84052 AT
1 AT
84054 CCTTAACTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (21 bp):
ATTATTTTTAGCTTGAAAAAC
Found at i:87142 original size:19 final size:19
Alignment explanation
Indices: 87094--87136 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
87084 TTAGCTCATT
87094 ATTT-TCATCTTGCAACTC
1 ATTTCTCATCTTGCAACTC
87112 ATTTCTCATCTTGCAACTC
1 ATTTCTCATCTTGCAACTC
87131 ATTTCT
1 ATTTCT
87137 TTTCTTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.21, C:0.28, G:0.05, T:0.47
Consensus pattern (19 bp):
ATTTCTCATCTTGCAACTC
Found at i:88037 original size:13 final size:13
Alignment explanation
Indices: 88019--88044 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
88009 TACAGCAAGT
88019 ATGTATCGATACA
1 ATGTATCGATACA
88032 ATGTATCGATACA
1 ATGTATCGATACA
88045 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:90296 original size:21 final size:21
Alignment explanation
Indices: 90263--90307 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
90253 TTGCAAGTTG
*
90263 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
90285 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
90305 AAA
1 AAA
90308 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:92131 original size:15 final size:15
Alignment explanation
Indices: 92111--92141 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
92101 TAAAAATGTC
*
92111 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
92126 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
92141 C
1 C
92142 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:96807 original size:13 final size:13
Alignment explanation
Indices: 96789--96814 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
96779 TACAGCAAGT
96789 ATGTATCGATACA
1 ATGTATCGATACA
96802 ATGTATCGATACA
1 ATGTATCGATACA
96815 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:98744 original size:31 final size:30
Alignment explanation
Indices: 98686--98776 Score: 92
Period size: 32 Copynumber: 2.8 Consensus size: 30
98676 CCGTACAACA
98686 CTATCTTTCAAGGCTAAGATAGAAACCTTC
1 CTATCTTTCAAGGCTAAGATAGAAACCTTC
* *
98716 CTATCTTTTCACGAGCTAAGATAGAACCTCTCTCC
1 CTATC-TTTCAAG-GCTAAGATAGAAAC-CT-T-C
98751 CTATCTTTGTCAAAGGCTAAGATAGA
1 CTATC-TT-TC-AAGGCTAAGATAGA
98777 GCCTCTTAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
30 5 0.10
31 6 0.12
32 13 0.25
33 2 0.04
34 1 0.02
35 9 0.18
36 13 0.25
37 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (30 bp):
CTATCTTTCAAGGCTAAGATAGAAACCTTC
Found at i:98774 original size:36 final size:32
Alignment explanation
Indices: 98686--98783 Score: 110
Period size: 36 Copynumber: 3.0 Consensus size: 32
98676 CCGTACAACA
*
98686 CTATC-TTTCAAGGCTAAGATAGAAAC-CTTC
1 CTATCTTTTCAAGGCTAAGATAGAACCTCTTC
*
98716 CTATCTTTTCACGAGCTAAGATAGAACCTCTCTCC
1 CTATCTTTTCAAG-GCTAAGATAGAACCTCT-T-C
*
98751 CTATCTTTGTCAAAGGCTAAGATAGAGCCTCTT
1 CTATCTTT-TC-AAGGCTAAGATAGAACCTCTT
98784 AATCACTTAC
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
30 5 0.09
31 6 0.11
32 13 0.23
33 2 0.04
34 1 0.02
35 10 0.18
36 18 0.32
37 2 0.04
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.32
Consensus pattern (32 bp):
CTATCTTTTCAAGGCTAAGATAGAACCTCTTC
Found at i:99360 original size:38 final size:39
Alignment explanation
Indices: 99271--99363 Score: 118
Period size: 39 Copynumber: 2.4 Consensus size: 39
99261 CTATAAGTTT
* * *
99271 CATGTATCGATACAATTCAGTGTGTACGGATACAAAGGA
1 CATGTATCGATACAATTCAGTATGTACGAATACAAAGAA
* *
99310 CATGTATTGATACAATTCAGTATGTATC-AAT-CCAAGAA
1 CATGTATCGATACAATTCAGTATGTA-CGAATACAAAGAA
99348 CATGTATCGATACAAT
1 CATGTATCGATACAAT
99364 GTGTCGATAC
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
38 20 0.43
39 26 0.55
40 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (39 bp):
CATGTATCGATACAATTCAGTATGTACGAATACAAAGAA
Found at i:99515 original size:20 final size:21
Alignment explanation
Indices: 99490--99533 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
99480 GATACTTTGA
99490 ATTATTTTTA-CTTGAAAAAC
1 ATTATTTTTAGCTTGAAAAAC
99510 ATTATTTTTATGCTTGAAAAAC
1 ATTATTTTTA-GCTTGAAAAAC
99532 AT
1 AT
99534 CTATATGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (21 bp):
ATTATTTTTAGCTTGAAAAAC
Found at i:102767 original size:12 final size:14
Alignment explanation
Indices: 102738--102775 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
102728 TTCTACCTAT
*
102738 TTTCTCTATTTTTC
1 TTTCTCTCTTTTTC
102752 TTTCTC-CTTTTT-
1 TTTCTCTCTTTTTC
102764 TTTCTCTCTTTT
1 TTTCTCTCTTTT
102776 GCAGCTGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 6 0.27
13 10 0.45
14 6 0.27
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTCTCTCTTTTTC
Found at i:103579 original size:19 final size:21
Alignment explanation
Indices: 103557--103600 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 21
103547 TACAGAGTAG
*
103557 AAAATCGTA-TTTCAA-GAAA
1 AAAATCGGAGTTTCAAGGAAA
103576 AAAA--GGAGTTTCAAGGAAA
1 AAAATCGGAGTTTCAAGGAAA
103595 AAAATC
1 AAAATC
103601 AAAAACTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 6
0.74 0.04 0.22
Matches are distributed among these distances:
17 2 0.10
18 6 0.30
19 12 0.60
ACGTcount: A:0.55, C:0.09, G:0.16, T:0.20
Consensus pattern (21 bp):
AAAATCGGAGTTTCAAGGAAA
Found at i:103644 original size:165 final size:163
Alignment explanation
Indices: 103428--103858 Score: 521
Period size: 165 Copynumber: 2.6 Consensus size: 163
103418 ATTTCAAAGC
* * * * *
103428 AAAAAATCAAAAATTTATGAAAATGAATT-AATTTTTTTAAAATGAATTAATATG-AGTCAAATA
1 AAAAAATCAAAAACTCATGAAAATG-ATTGAA-TTTTTGAAAATGAATTAATATGAAAT-AAATG
* * * * * *
103491 ATGATGTTTGATGAATTTTAAAAATTGAAAATTGAGAAAAATCCCTCAAAAAAATTTACAGAGTA
63 ATAATATTTGATGAATTTTAAAAATTAAAAATTAAAAAAAACCCCTCAAAAAAATTTACAGAGTA
* *
103556 G-AAA-ATCGTATTTCAAGAAAAAAAGGAGTTTCAAGG
128 GAAAACACCATATTTC--GAAAAAAAGGAGTTTCAAGG
103592 AAAAAAATCAAAAACTCATGAAAATGATTGAATTTTTGAAAATGGAATTAATATGAAATAAATGA
1 -AAAAAATCAAAAACTCATGAAAATGATTGAATTTTTGAAAAT-GAATTAATATGAAATAAATGA
** * **
103657 TAATATTTGATGAATTTTAAAAATTAAAAACAAAAAAAAAACCCCTCGAAAAAATTTATGGAGTA
64 TAATATTTGATGAATTTTAAAAATTAAAAA-TTAAAAAAAACCCCTCAAAAAAATTTACAGAGTA
* *
103722 GAAAACACCATATTTCGAAAAAAGAGAAATTTCAAGG
128 GAAAACACCATATTTCGAAAAAA-AGGAGTTTCAAGG
* * *
103759 -AAAAATAAAAAACTCATGAAAATGAATGAATTTTTGAAAACTTAATTAATATGAAATAAATGAT
1 AAAAAATCAAAAACTCATGAAAATGATTGAATTTTTGAAAA-TGAATTAATATGAAATAAATGAT
*
103823 AATATTTGATAAATTTTAAAAATTAAAAATTAAAAA
65 AATATTTGATGAATTTTAAAAATTAAAAATTAAAAA
103859 TTAAGAAAAA
Statistics
Matches: 232, Mismatches: 26, Indels: 17
0.84 0.09 0.06
Matches are distributed among these distances:
164 18 0.08
165 155 0.67
166 37 0.16
167 14 0.06
168 8 0.03
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.29
Consensus pattern (163 bp):
AAAAAATCAAAAACTCATGAAAATGATTGAATTTTTGAAAATGAATTAATATGAAATAAATGATA
ATATTTGATGAATTTTAAAAATTAAAAATTAAAAAAAACCCCTCAAAAAAATTTACAGAGTAGAA
AACACCATATTTCGAAAAAAAGGAGTTTCAAGG
Found at i:103857 original size:6 final size:7
Alignment explanation
Indices: 103838--103862 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
103828 TTGATAAATT
103838 TTAAAAA
1 TTAAAAA
103845 TTAAAAA
1 TTAAAAA
103852 TTAAAAA
1 TTAAAAA
103859 TTAA
1 TTAA
103863 GAAAAATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
TTAAAAA
Found at i:112424 original size:96 final size:91
Alignment explanation
Indices: 112247--112425 Score: 214
Period size: 96 Copynumber: 1.9 Consensus size: 91
112237 CCTCAGAGGA
* * * **
112247 ATGGGTTGGAGTATCCCCGACGATGATAATTTAAAAAAAGATTTAAACCTTAACAAGTTTGAAAA
1 ATGGGTTAGAGTATCCCCGACGATGACAATTTAAAAAAAGATTTAAACCATAACAAGTTAAAAAA
**
112312 TGGGGTTAGAGTATCCTCTTAGAAGT
66 TAAGGTTAGAGTATCCTCTTAGAAGT
* * *
112338 ATGGGTTAGAGTATCCTCGACGATGACAATTTAAGCAAAAATAAGATTTAAATCATGACAAGTTA
1 ATGGGTTAGAGTATCCCCGACGATGACAATTT----AAAAA-AAGATTTAAACCATAACAAGTTA
*
112403 AAAAATAAGGTTGGAGTATCCTC
61 AAAAATAAGGTTAGAGTATCCTC
112426 AATGATGATA
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
91 29 0.40
95 5 0.07
96 38 0.53
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (91 bp):
ATGGGTTAGAGTATCCCCGACGATGACAATTTAAAAAAAGATTTAAACCATAACAAGTTAAAAAA
TAAGGTTAGAGTATCCTCTTAGAAGT
Found at i:112459 original size:70 final size:69
Alignment explanation
Indices: 112341--112493 Score: 198
Period size: 70 Copynumber: 2.2 Consensus size: 69
112331 TAGAAGTATG
* * *
112341 GGTTAGAGTATCCTCGACGATGACAATTTAAGCAAAAATAAGATTTAAATCATGACAAGTTAAAA
1 GGTTGGAGTATCCTCAACGATGACAATTTAAGCAAAAATAAGATTTAAATCATGACAAATTAAAA
112406 AATAA
66 AAT-A
* * * * * *
112411 GGTTGGAGTATCCTCAATGATGATAATTTAAGCAAAAATAATATTTAAATCTTGATAAATTTAAA
1 GGTTGGAGTATCCTCAACGATGACAATTTAAGCAAAAATAAGATTTAAATCATGACAAATTAAAA
112476 AATA
66 AATA
*
112480 GGATTGCAGTATCC
1 GG-TTGGAGTATCC
112494 CCTCAAAAGA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
69 3 0.04
70 69 0.96
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (69 bp):
GGTTGGAGTATCCTCAACGATGACAATTTAAGCAAAAATAAGATTTAAATCATGACAAATTAAAA
AATA
Found at i:114909 original size:52 final size:51
Alignment explanation
Indices: 114825--114993 Score: 212
Period size: 51 Copynumber: 3.3 Consensus size: 51
114815 ATTTGCCTGC
* * * * ** *
114825 ATGTATCGACATATTGAAGAATGTATTGATACATTTGGGTCAAAAACCCAAA
1 ATGTATCGATACAATGAAGAATGTGTCAATACATTTGGGTC-AAAACCCATA
* *
114877 ATGTATCGATACAATGAAGAATGTGTCAATACATTTAGGTTAAAACCCATA
1 ATGTATCGATACAATGAAGAATGTGTCAATACATTTGGGTCAAAACCCATA
* * *
114928 ATGTATCGATATAATGAAGAATGTGCCAATACATTTGGCTCAAAACCCATA
1 ATGTATCGATACAATGAAGAATGTGTCAATACATTTGGGTCAAAACCCATA
*
114979 ATGTATTGATACAAT
1 ATGTATCGATACAAT
114994 AAAAATTTGC
Statistics
Matches: 101, Mismatches: 16, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
51 68 0.67
52 33 0.33
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (51 bp):
ATGTATCGATACAATGAAGAATGTGTCAATACATTTGGGTCAAAACCCATA
Found at i:115944 original size:52 final size:52
Alignment explanation
Indices: 115854--116155 Score: 317
Period size: 52 Copynumber: 5.8 Consensus size: 52
115844 TAAGGGTGAG
* *
115854 AAGAGTGCCAATGTGCTGATTCATGGCCAGCGACATTGGACTTAAAGATGAA
1 AAGAGTGCTAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAA
* * * *
115906 AAGAATGCTAATGTGTTGATTCAAGGCCAGCGATATTGGACTTAAA-ATGAG
1 AAGAGTGCTAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAA
* * * * * * *
115957 AAGAATACTAATGTGTTGATTTAAGGCCAGCAACATTGGGCTTAAAAATGATA
1 AAGAGTGCTAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-A
* * * * *
116010 AAG-GTGCTAATATACTGATTCAAGGCCAGTGATATCGGACTTAAAGATGACA
1 AAGAGTGCTAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-A
* *
116062 AAG-GTGCCT-ATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAG
1 AAGAGTG-CTAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAA
* * * * *
116113 AAGAGT-CCAATGTTCTGATTCGAGACCAACGACATTGGACTTA
1 AAGAGTGCTAATGTGCTGATTCAAGGCCAGCGACATTGGACTTA
116156 GAAAGAGATG
Statistics
Matches: 207, Mismatches: 38, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
50 1 0.00
51 77 0.37
52 124 0.60
53 5 0.02
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (52 bp):
AAGAGTGCTAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAA
Found at i:116131 original size:103 final size:103
Alignment explanation
Indices: 115854--116133 Score: 318
Period size: 103 Copynumber: 2.7 Consensus size: 103
115844 TAAGGGTGAG
* * *
115854 AAGAGTGCCAATGTGCTGATTCATGGCCAGCGACATTGGACTTAAAGATGAAAAGAATGCTAATG
1 AAGAGTGCCTATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAAAGAGTGCTAATG
* *
115919 TGT-TGATTCAAGGCCAGCGATATTGGACTTAAAATGAG
66 T-TCTGATTCAAGGCCAGCGATATCGGACTTAAAATGAA
* * * * * * *
115957 AAGAAT-ACTAATGTGTTGATTTAAGGCCAGCAACATTGGGCTTAAAAATGATAAAG-GTGCTAA
1 AAGAGTGCCT-ATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-AAAGAGTGCTAA
* * *
116020 TATACTGATTCAAGGCCAGTGATATCGGACTTAAAGATGACA
64 TGTTCTGATTCAAGGCCAGCGATATCGGACTTAAA-ATGA-A
* * *
116062 AAG-GTGCCTATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAGAAGAGT-CCAATG
1 AAGAGTGCCTATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAAAGAGTGCTAATG
116125 TTCTGATTC
66 TTCTGATTC
116134 GAGACCAACG
Statistics
Matches: 143, Mismatches: 27, Indels: 14
0.78 0.15 0.08
Matches are distributed among these distances:
102 1 0.01
103 91 0.64
104 46 0.32
105 5 0.03
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (103 bp):
AAGAGTGCCTATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAAAGAGTGCTAATG
TTCTGATTCAAGGCCAGCGATATCGGACTTAAAATGAA
Found at i:116243 original size:31 final size:32
Alignment explanation
Indices: 116214--116551 Score: 205
Period size: 31 Copynumber: 10.7 Consensus size: 32
116204 ATTAGGCTTA
*
116214 GAAAGAGATGCCACCGACTTGTGTGGGC-TTT
1 GAAAGAGTTGCCACCGACTTGTGTGGGCTTTT
* * * * *
116245 AAAAGGGTTACCACCAATTTGTGTGGGCTTTT
1 GAAAGAGTTGCCACCGACTTGTGTGGGCTTTT
* * *
116277 GAAAAGGGTTGCCACCAACTTATGTGGGC-TTT
1 G-AAAGAGTTGCCACCGACTTGTGTGGGCTTTT
* * ** *
116309 GAGAA-TGTTGTCACTAACTTGTATGGGC-TTT
1 GA-AAGAGTTGCCACCGACTTGTGTGGGCTTTT
116340 GAGAAG-GTTGCCACCGACTTGTGTGGGC-TTT
1 GA-AAGAGTTGCCACCGACTTGTGTGGGCTTTT
* *
116371 GAAA-AGGTTGCCACCGACTTATATGGGCTTTT
1 GAAAGA-GTTGCCACCGACTTGTGTGGGCTTTT
* * * * *
116403 GAGAGGGTTTCCACTGACTTATGTGGGC-TTT
1 GAAAGAGTTGCCACCGACTTGTGTGGGCTTTT
* * ** * *
116434 AAAAGGGTTTTCATCGACTTATGTGGGCTTTT
1 GAAAGAGTTGCCACCGACTTGTGTGGGCTTTT
* * *
116466 GAAA-AGGATTGCCATCGACTTATGTAGGC-TTT
1 GAAAGA-G-TTGCCACCGACTTGTGTGGGCTTTT
* *
116498 CAGAAG-GTTCCCACCGACTTGTGTGGGC-TTT
1 GA-AAGAGTTGCCACCGACTTGTGTGGGCTTTT
* * * *
116529 GAAAAAGATGCCACAGAGTTGTG
1 GAAAGAGTTGCCACCGACTTGTG
116552 GACTTTAAAA
Statistics
Matches: 246, Mismatches: 47, Indels: 28
0.77 0.15 0.09
Matches are distributed among these distances:
30 4 0.02
31 152 0.62
32 46 0.19
33 44 0.18
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31
Consensus pattern (32 bp):
GAAAGAGTTGCCACCGACTTGTGTGGGCTTTT
Found at i:116303 original size:64 final size:64
Alignment explanation
Indices: 116222--116533 Score: 312
Period size: 64 Copynumber: 4.9 Consensus size: 64
116212 TAGAAAGAGA
* * * *
116222 TGCCACCGACTTGTGTGGGCTTT-AAAAGGGTTACCACCAATTTGTGTGGGCTTTTGAAAAGGGT
1 TGCCACCGACTTATGTGGGCTTTGAAAA-GGTTGCCACCGACTTGTGTGGGCTTTTGAAAAGGGT
* * * * ** * *
116286 TGCCACCAACTTATGTGGGCTTTGAGAATGTTGTCACTAACTTGTATGGGC-TTTGAGAA-GGT
1 TGCCACCGACTTATGTGGGCTTTGAAAAGGTTGCCACCGACTTGTGTGGGCTTTTGAAAAGGGT
* * * *
116348 TGCCACCGACTTGTGTGGGCTTTGAAAAGGTTGCCACCGACTTATATGGGCTTTTG-AGAGGGT
1 TGCCACCGACTTATGTGGGCTTTGAAAAGGTTGCCACCGACTTGTGTGGGCTTTTGAAAAGGGT
* * ** * * *
116411 TTCCACTGACTTATGTGGGCTTT-AAAAGGGTTTTCATCGACTTATGTGGGCTTTTGAAAAGGAT
1 TGCCACCGACTTATGTGGGCTTTGAAAA-GGTTGCCACCGACTTGTGTGGGCTTTTGAAAAGGGT
* * * * *
116475 TGCCATCGACTTATGTAGGCTTTCAGAAGGTTCCCACCGACTTGTGTGGGC-TTTGAAAA
1 TGCCACCGACTTATGTGGGCTTTGAAAAGGTTGCCACCGACTTGTGTGGGCTTTTGAAAA
116534 AGATGCCACA
Statistics
Matches: 204, Mismatches: 38, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
62 51 0.25
63 66 0.32
64 81 0.40
65 6 0.03
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.33
Consensus pattern (64 bp):
TGCCACCGACTTATGTGGGCTTTGAAAAGGTTGCCACCGACTTGTGTGGGCTTTTGAAAAGGGT
Found at i:116527 original size:95 final size:95
Alignment explanation
Indices: 116224--116533 Score: 358
Period size: 95 Copynumber: 3.3 Consensus size: 95
116214 GAAAGAGATG
* *
116224 CCACCGACTTGTGTGGGCTTT-AAAAGGGTTACCACCAATTTGTGTGGGCTTTTGAAAAGGGTTG
1 CCACCGACTTGTGTGGGCTTTGAAAAGGGTTACCACCGACTTGTGTGGGCTTTTGAAAA-GGTTG
* * *
116288 CCACCAACTTATGTGGGCTTTGAGAATGTTG
65 CCACCGACTTATGTGGGCTTTGAGAAGGTTC
* ** * * *
116319 TCACTAACTTGTATGGGCTTTGAGAA-GGTTGCCACCGACTTGTGTGGGC-TTTGAAAAGGTTGC
1 CCACCGACTTGTGTGGGCTTTGAAAAGGGTTACCACCGACTTGTGTGGGCTTTTGAAAAGGTTGC
* * *
116382 CACCGACTTATATGGGCTTTTGAGAGGGTTT
66 CACCGACTTATGTGGGC-TTTGAGAAGGTTC
* * ** * *
116413 CCACTGACTTATGTGGGCTTT-AAAAGGGTTTTCATCGACTTATGTGGGCTTTTGAAAAGGATTG
1 CCACCGACTTGTGTGGGCTTTGAAAAGGGTTACCACCGACTTGTGTGGGCTTTTGAAAAGG-TTG
* * *
116477 CCATCGACTTATGTAGGCTTTCAGAAGGTTC
65 CCACCGACTTATGTGGGCTTTGAGAAGGTTC
116508 CCACCGACTTGTGTGGGCTTTGAAAA
1 CCACCGACTTGTGTGGGCTTTGAAAA
116534 AGATGCCACA
Statistics
Matches: 179, Mismatches: 30, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
93 24 0.13
94 54 0.30
95 76 0.42
96 25 0.14
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.33
Consensus pattern (95 bp):
CCACCGACTTGTGTGGGCTTTGAAAAGGGTTACCACCGACTTGTGTGGGCTTTTGAAAAGGTTGC
CACCGACTTATGTGGGCTTTGAGAAGGTTC
Found at i:116569 original size:29 final size:29
Alignment explanation
Indices: 116519--117255 Score: 526
Period size: 29 Copynumber: 25.3 Consensus size: 29
116509 CACCGACTTG
* *
116519 TGTGGGCTTTGAAAA-AGATGCCACAGAGT
1 TGTGGACTTT-AAAAGAGGTGCCACAGAGT
116548 TGTGGACTTTAAAAGAGGTGCCAC-GAAGT
1 TGTGGACTTTAAAAGAGGTGCCACAG-AGT
* *
116577 TATGGATTTTAGAAA-AGGTGCC-CAAGAAGT
1 TGTGGACTTTA-AAAGAGGTGCCAC-AG-AGT
* **
116607 TGTGGACTTTAAAAG-GATGCCATGGAGT
1 TGTGGACTTTAAAAGAGGTGCCACAGAGT
* * *
116635 TGTGGACTTTAAAAAAGCTGCCACGGAGT
1 TGTGGACTTTAAAAGAGGTGCCACAGAGT
* * * *
116664 TCTGAAATTTAAAAGA--TGCCACAAAGT
1 TGTGGACTTTAAAAGAGGTGCCACAGAGT
* *
116691 TGTGGAC-TTAAAAAAGGGTGCTACAGAGT
1 TGTGGACTTTAAAAGA-GGTGCCACAGAGT
* * *
116720 TATGGACTTTAAAAG-GTTGCCATAGAG-
1 TGTGGACTTTAAAAGAGGTGCCACAGAGT
*
116747 T-TGGACTTTAAAAAAGGTGCCACAGAGT
1 TGTGGACTTTAAAAGAGGTGCCACAGAGT
* * * *
116775 TGTGGAATTTGAGAAAAAAGGTGCCACAAAAT
1 TGTGGACTTT---AAAAGAGGTGCCACAGAGT
*
116807 TGTGGACTTATAAAAGGGGTGCCACAGAGT
1 TGTGGACTT-TAAAAGAGGTGCCACAGAGT
* * *
116837 TTTGGACATTAGAAA-AGGTGCCATAGAGT
1 TGTGGACTTTA-AAAGAGGTGCCACAGAGT
* **
116866 TATGGACTTTAAAAGAGGTGCCATGGAGT
1 TGTGGACTTTAAAAGAGGTGCCACAGAGT
*
116895 TATGGACTTTAGAAA-AGGTGCCAC-GAAGT
1 TGTGGACTTTA-AAAGAGGTGCCACAG-AGT
* **
116924 TGTGGACCTTAAAAG-GGTGCCATGGAGT
1 TGTGGACTTTAAAAGAGGTGCCACAGAGT
* * * *
116952 TATGGACTTTAAAAAAAGTGCCATAGAGT
1 TGTGGACTTTAAAAGAGGTGCCACAGAGT
* * **
116981 TATGTACTTTTGGGAAG-GGTGCCACAGAGT
1 TGTGGAC-TTT-AAAAGAGGTGCCACAGAGT
* * *
117011 TGTAGACTTTAAAAAAAAGGTGCCACAAAGT
1 TGTGGACTTT--AAAAGAGGTGCCACAGAGT
* **
117042 TGTGGACTTTAAAAGGGGTATCACAGAGT
1 TGTGGACTTTAAAAGAGGTGCCACAGAGT
* *
117071 TGTGGACTTTTGAGAAG-GGTGCCACGGAGT
1 TGTGGAC-TTT-AAAAGAGGTGCCACAGAGT
** * * *
117101 TGTTCACTTTGAAAAAAAGGTGGCACAAAGT
1 TGTGGACTTT--AAAAGAGGTGCCACAGAGT
*
117132 TGTGGACTTTAAAA-AGGGTGCCACTGAGT
1 TGTGGACTTTAAAAGA-GGTGCCACAGAGT
* *
117161 TGTGGACTTTTGAAA-AGGTGCCACGGAGT
1 TGTGGAC-TTTAAAAGAGGTGCCACAGAGT
* * *
117190 TCTGGACTTTAAAAAAAGTGCCAC-GAAGT
1 TGTGGACTTTAAAAGAGGTGCCACAG-AGT
* *
117219 TATTGACTTTAAAAGAGGTGCCAC-GAAGT
1 TGTGGACTTTAAAAGAGGTGCCACAG-AGT
117248 TGTGGACT
1 TGTGGACT
117256 CTGAGAAGGG
Statistics
Matches: 566, Mismatches: 104, Indels: 76
0.76 0.14 0.10
Matches are distributed among these distances:
26 19 0.03
27 24 0.04
28 70 0.12
29 283 0.50
30 99 0.17
31 45 0.08
32 25 0.04
33 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (29 bp):
TGTGGACTTTAAAAGAGGTGCCACAGAGT
Found at i:117937 original size:32 final size:30
Alignment explanation
Indices: 117901--117959 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
117891 GAAATCAAAT
117901 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
117933 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
117960 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:118258 original size:13 final size:13
Alignment explanation
Indices: 118240--118265 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
118230 ATATTTTTTG
118240 TGTATCGATACAT
1 TGTATCGATACAT
118253 TGTATCGATACAT
1 TGTATCGATACAT
118266 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:118276 original size:32 final size:33
Alignment explanation
Indices: 118219--118283 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
118209 TACAAGCCAA
118219 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
118253 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
118284 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Found at i:118277 original size:19 final size:19
Alignment explanation
Indices: 118219--118283 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
118209 TACAAGCCAA
118219 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
118240 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
118253 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
118272 TGTATCGATACA
1 TGTATCGATACA
118284 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:118360 original size:20 final size:20
Alignment explanation
Indices: 118334--118390 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
118324 TACATCTTTT
118334 TCATGTATCGATACTTTGCAA
1 TCATGTATCGATACTTTG-AA
118355 -CATGTATCGATACTTTGAA
1 TCATGTATCGATACTTTGAA
**
118374 TTGTGTATCGATACTTT
1 TCATGTATCGATACTTT
118391 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (20 bp):
TCATGTATCGATACTTTGAA
Found at i:118985 original size:39 final size:40
Alignment explanation
Indices: 118910--118990 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 40
118900 TTTTCTTTCT
**
118910 CCCTTAACTAAAGTAATTTTAACAAATTTGTACATTCTCC
1 CCCTTAACTAAAGTAATTTTAACAAATTTACACATTCTCC
* * *
118950 CCCTTAA-TAAGGTAATTTTAGCAAATTTACGCATTCTCC
1 CCCTTAACTAAAGTAATTTTAACAAATTTACACATTCTCC
118989 CC
1 CC
118991 TTTTATTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 29 0.81
40 7 0.19
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (40 bp):
CCCTTAACTAAAGTAATTTTAACAAATTTACACATTCTCC
Found at i:119067 original size:29 final size:29
Alignment explanation
Indices: 119025--119092 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
119015 ATAAGGTAAT
119025 TTACACACATATCAAAAATTTATTTGCAC
1 TTACACACATATCAAAAATTTATTTGCAC
119054 TTACACACATATCAAAAATTTATTTGCAC
1 TTACACACATATCAAAAATTTATTTGCAC
* *
119083 ATACATACAT
1 TTACACACAT
119093 CTATTCTCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.43, C:0.21, G:0.03, T:0.34
Consensus pattern (29 bp):
TTACACACATATCAAAAATTTATTTGCAC
Found at i:120416 original size:21 final size:20
Alignment explanation
Indices: 120387--120429 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
120377 GACTAGTGTG
* *
120387 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
120408 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
120428 GG
1 GG
120430 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:120878 original size:13 final size:13
Alignment explanation
Indices: 120860--120897 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
120850 ATAATCCCCC
120860 TGTATCGATACAG
1 TGTATCGATACAG
*
120873 TGTATCGATACAT
1 TGTATCGATACAG
120886 TGTATCGATACA
1 TGTATCGATACA
120898 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:124838 original size:21 final size:21
Alignment explanation
Indices: 124809--124853 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
124799 AAGTTTTTAT
*
124809 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
124829 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
124851 TTT
1 TTT
124854 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:127092 original size:13 final size:13
Alignment explanation
Indices: 127074--127099 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
127064 ATATTTTTTG
127074 TGTATCGATACAT
1 TGTATCGATACAT
127087 TGTATCGATACAT
1 TGTATCGATACAT
127100 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:127110 original size:32 final size:33
Alignment explanation
Indices: 127053--127117 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
127043 TACAAGCCAA
127053 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
127087 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
127118 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Found at i:127111 original size:19 final size:19
Alignment explanation
Indices: 127053--127117 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
127043 TACAAGCCAA
127053 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
127074 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
127087 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
127106 TGTATCGATACA
1 TGTATCGATACA
127118 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:127194 original size:20 final size:20
Alignment explanation
Indices: 127168--127223 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
127158 TACATCTTTT
127168 TCATGTATCGATACTTTGCAA
1 TCATGTATCGATACTTTG-AA
127189 -CATGTATCGATA-TTTGAA
1 TCATGTATCGATACTTTGAA
**
127207 TTGTGTATCGATACTTT
1 TCATGTATCGATACTTT
127224 TATGGGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 2 0.06
19 14 0.45
20 15 0.48
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (20 bp):
TCATGTATCGATACTTTGAA
Found at i:133751 original size:70 final size:70
Alignment explanation
Indices: 133668--133823 Score: 258
Period size: 70 Copynumber: 2.2 Consensus size: 70
133658 TTAAAAGTAT
*
133668 GGGGTTAGAGTATCCCCGATGATGACAATTTAAGCAAAAATAAGATTTAAATCTTGACAAGTTTA
1 GGGGTTGGAGTATCCCCGATGATGACAATTTAAGCAAAAATAAGATTTAAATCTTGACAAGTTTA
133733 AAAAC
66 AAAAC
* * * * *
133738 GGGGTTGGAGTATCCTCGATGGTGATAATTTAAGCAAAAATAATATTTAAATCTTGATAAGTTTA
1 GGGGTTGGAGTATCCCCGATGATGACAATTTAAGCAAAAATAAGATTTAAATCTTGACAAGTTTA
133803 AAAAC
66 AAAAC
133808 GGGGTTGGAGTATCCC
1 GGGGTTGGAGTATCCC
133824 TTCAGAAGAA
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 79 1.00
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (70 bp):
GGGGTTGGAGTATCCCCGATGATGACAATTTAAGCAAAAATAAGATTTAAATCTTGACAAGTTTA
AAAAC
Found at i:136300 original size:51 final size:52
Alignment explanation
Indices: 136184--136322 Score: 174
Period size: 51 Copynumber: 2.7 Consensus size: 52
136174 ATTTGCCTAC
* * ** * *
136184 ATGTATCAATACATTAAAGAATGTATTAATATATTTGGGTCAAAAACCCAGA
1 ATGTATCAATACAATGAAGAATGTATCGATACATTTGGGTCAAAAACCCAAA
* *
136236 ATGTATCGATACAATGAAGAATGCTGT-GATACATTTGGGTC-AAAACCCAAA
1 ATGTATCAATACAATGAAGAATG-TATCGATACATTTGGGTCAAAAACCCAAA
*
136287 ATGTATTAATACAATGAAGAATGTATCGATACATTT
1 ATGTATCAATACAATGAAGAATGTATCGATACATTT
136323 TCATTCCAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
50 2 0.03
51 39 0.52
52 32 0.43
53 2 0.03
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (52 bp):
ATGTATCAATACAATGAAGAATGTATCGATACATTTGGGTCAAAAACCCAAA
Found at i:136425 original size:21 final size:20
Alignment explanation
Indices: 136378--136430 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
136368 TATTTCTAAC
136378 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
136398 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
136418 ATTGTATCGATAC
1 A-TGTATCGATAC
136431 TGTCGCAACG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 21 0.66
21 11 0.34
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:139823 original size:20 final size:20
Alignment explanation
Indices: 139798--139873 Score: 89
Period size: 20 Copynumber: 3.7 Consensus size: 20
139788 AAAAACCTAG
*
139798 AATGTATCGATACAATGAGA
1 AATGTATCGATACAATTAGA
*
139818 AATGTATCGATACAATTATA
1 AATGTATCGATACAATTAGA
* * *
139838 AGCATGTATCGATTCATTTAGT
1 A--ATGTATCGATACAATTAGA
139860 AATGTATCGATACA
1 AATGTATCGATACA
139874 TTTCTTGGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 31 0.66
22 16 0.34
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACAATTAGA
Found at i:139999 original size:21 final size:21
Alignment explanation
Indices: 139973--140024 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
139963 AGACCTTGTT
*
139973 TCGATAGATTCTAGAAATGTA
1 TCGATACATTCTAGAAATGTA
139994 TCGATACATTCTAGAAATGTA
1 TCGATACATTCTAGAAATGTA
*
140015 TAGATACATT
1 TCGATACATT
140025 TGAACAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (21 bp):
TCGATACATTCTAGAAATGTA
Found at i:142832 original size:87 final size:86
Alignment explanation
Indices: 142686--143082 Score: 352
Period size: 87 Copynumber: 4.5 Consensus size: 86
142676 ACGATTTTTA
* * *
142686 GGGAAACTCTATCCCCACTATTCTAAGGGGATACTCTAACAC-TATTCAAACAAAAATTCAAATT
1 GGGAAACTCTATCCCTACTATTCTAA-GGGATACTCTAAC-CTTGTTCTAACAAAAATTCAAATT
*
142750 TACTTTATGGAATTTTATCTTTG
64 TACTTCATGGAATTTTATCTTTG
* *
142773 GGGAAACTTTATCCCTACTATTCTAAGGGAATACTCAAACCTTGTTCTAACAAAAATTCAAATTT
1 GGGAAACTCTATCCCTACTATTCTAAGGG-ATACTCTAACCTTGTTCTAACAAAAATTCAAATTT
*
142838 ACTTCATGGAATTTTATCTTTA
65 ACTTCATGGAATTTTATCTTTG
* * * * * * *
142860 GGGAAACTCCATCCTTACAATTCTAAGGGATACTCTAACCTCGCTCTAACAAAAATTCACATTTT
1 GGGAAACTCTATCCCTACTATTCTAAGGGATACTCTAACCTTGTTCTAACAAAAATTCAAATTTA
* *
142925 CATTCATAGAATTTTATCCTTG
66 C-TTCATGGAATTTTATCTTTG
* * * ** *** * * * * *
142947 GGAAAATTCCATCCC-ACTCCTCCGGGGAGATTCTCCAACCCTGCTCTTAAAAAAAAATT-AAAT
1 GGGAAACTCTATCCCTACTATTCTAAGG-GATACTCTAACCTTGTTC-T-AACAAAAATTCAAA-
* *
143010 TTTCCTTCATGAAATTTTATCTTTG
62 TTTACTTCATGGAATTTTATCTTTG
* * * * *
143035 GGGAAACT-TCATCCCCATTATTCTGAAAGGATACCCTAACCTCGTTCT
1 GGGAAACTCT-ATCCCTACTATTCT-AAGGGATACTCTAACCTTGTTCT
143083 TCATAAAAAA
Statistics
Matches: 246, Mismatches: 54, Indels: 19
0.77 0.17 0.06
Matches are distributed among these distances:
86 42 0.17
87 142 0.58
88 32 0.13
89 29 0.12
90 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (86 bp):
GGGAAACTCTATCCCTACTATTCTAAGGGATACTCTAACCTTGTTCTAACAAAAATTCAAATTTA
CTTCATGGAATTTTATCTTTG
Found at i:145808 original size:13 final size:13
Alignment explanation
Indices: 145790--145816 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
145780 ACATTATGCT
145790 TTGTATCGATACA
1 TTGTATCGATACA
145803 TTGTATCGATACA
1 TTGTATCGATACA
145816 T
1 T
145817 GTTCATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:145850 original size:20 final size:19
Alignment explanation
Indices: 145802--145855 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
145792 GTATCGATAC
** *
145802 ATTGTATCGATACATGTTC
1 ATTGTATCGATACATCATA
*
145821 ATTATATCGATACATACATA
1 ATTGTATCGATACAT-CATA
145841 ATTGTATCGATACAT
1 ATTGTATCGATACAT
145856 GAAACTGGCA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (19 bp):
ATTGTATCGATACATCATA
Found at i:145910 original size:20 final size:20
Alignment explanation
Indices: 145885--145938 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
145875 CTACCACTGT
**
145885 TTGTATCGATACATGGC-ACA
1 TTGTATCGATACATAACGA-A
145905 TTGTATCGATACATAACGAA
1 TTGTATCGATACATAACGAA
145925 TTGTATCGATACAT
1 TTGTATCGATACAT
145939 TGTCCCAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATAACGAA
Found at i:147553 original size:18 final size:18
Alignment explanation
Indices: 147530--147566 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
147520 TCAATCATTA
147530 AAGATGATGAAGATAATG
1 AAGATGATGAAGATAATG
*
147548 AAGATGATGATGATAATG
1 AAGATGATGAAGATAATG
147566 A
1 A
147567 TAAAGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAGATGATGAAGATAATG
Found at i:148653 original size:13 final size:13
Alignment explanation
Indices: 148635--148659 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
148625 ATATTGCATA
148635 GTATCGATACATT
1 GTATCGATACATT
148648 GTATCGATACAT
1 GTATCGATACAT
148660 GACCAAATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:148777 original size:13 final size:13
Alignment explanation
Indices: 148759--148784 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
148749 TACACACAAG
148759 ATGTATCGATACA
1 ATGTATCGATACA
148772 ATGTATCGATACA
1 ATGTATCGATACA
148785 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:148801 original size:33 final size:32
Alignment explanation
Indices: 148741--148804 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
148731 CTTAACTGTT
*
148741 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
148773 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
148805 TTAGGCTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:154708 original size:8 final size:8
Alignment explanation
Indices: 154695--154721 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
154685 ATTTGATTAA
154695 ATTTTGTG
1 ATTTTGTG
154703 ATTTTGTG
1 ATTTTGTG
154711 ATTTTGTG
1 ATTTTGTG
154719 ATT
1 ATT
154722 GAATGAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.22, T:0.63
Consensus pattern (8 bp):
ATTTTGTG
Found at i:155300 original size:20 final size:22
Alignment explanation
Indices: 155267--155311 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
155257 TTTGCACTCA
*
155267 CCAGGTCACGACCG-GC-ACCC
1 CCAGGTCACAACCGAGCAACCC
*
155287 CCAGGTCGCAACCGAGCAACCC
1 CCAGGTCACAACCGAGCAACCC
155309 CCA
1 CCA
155312 CTTTCACAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 2 0.10
22 7 0.33
ACGTcount: A:0.24, C:0.49, G:0.22, T:0.04
Consensus pattern (22 bp):
CCAGGTCACAACCGAGCAACCC
Found at i:157321 original size:13 final size:13
Alignment explanation
Indices: 157303--157327 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
157293 ATATTGCATA
157303 GTATCGATACATT
1 GTATCGATACATT
157316 GTATCGATACAT
1 GTATCGATACAT
157328 GACCAAATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:157437 original size:19 final size:20
Alignment explanation
Indices: 157409--157457 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
157399 CTTAACTGTT
* *
157409 TGTATTGATACA-CACAAGA
1 TGTATCGATACATCACAAAA
*
157428 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
157448 TGTATCGATA
1 TGTATCGATA
157458 TATTAGGCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:160696 original size:126 final size:126
Alignment explanation
Indices: 160471--160721 Score: 475
Period size: 126 Copynumber: 2.0 Consensus size: 126
160461 TGGGACTTCA
* *
160471 AGTGAAGCGAACAAAGGACAGAATCTTCATCAATGAAGCAAAATATATAAAGGAGTTGCTCAAAA
1 AGTGAAGCAAACAAAGGACAGAATCTTCATCAATCAAGCAAAATATATAAAGGAGTTGCTCAAAA
*
160536 GGTTTCAAATGGATTAAGTCAAACCATGTGAAACACCGATGAGTATTTCAACAAAGCTTGG
66 GGTTTCAAATGGATCAAGTCAAACCATGTGAAACACCGATGAGTATTTCAACAAAGCTTGG
160597 AGTGAAGCAAACAAAGGACAGAATCTTCATCAATCAAGCAAAATATATAAAGGAGTTGCTCAAAA
1 AGTGAAGCAAACAAAGGACAGAATCTTCATCAATCAAGCAAAATATATAAAGGAGTTGCTCAAAA
160662 GGTTTCAAATGGATCAAGTCAAACCATGTGAAACACCGATGAGTATTTCAACAAAGCTTG
66 GGTTTCAAATGGATCAAGTCAAACCATGTGAAACACCGATGAGTATTTCAACAAAGCTTG
160722 AAAAGGATGA
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 122 1.00
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.22
Consensus pattern (126 bp):
AGTGAAGCAAACAAAGGACAGAATCTTCATCAATCAAGCAAAATATATAAAGGAGTTGCTCAAAA
GGTTTCAAATGGATCAAGTCAAACCATGTGAAACACCGATGAGTATTTCAACAAAGCTTGG
Found at i:161585 original size:70 final size:70
Alignment explanation
Indices: 161472--161611 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
161462 ATACTTGTTT
161472 TTTTTATTGTCTTTACCATTCCTTTACGAAAAATCTTACTTGATGACCTTATATGCTTATAATGT
1 TTTTTATTGTCTTTACCATTCCTTTACGAAAAATCTTACTTGATGACCTTATATGCTTATAATGT
161537 CAAAA
66 CAAAA
161542 TTTTTATTGTCTTTACCATTCCTTTACGAAAAATCTTACTTGATGACCTTATATGCTTATAATGT
1 TTTTTATTGTCTTTACCATTCCTTTACGAAAAATCTTACTTGATGACCTTATATGCTTATAATGT
161607 CAAAA
66 CAAAA
161612 ATAACTATTT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.44
Consensus pattern (70 bp):
TTTTTATTGTCTTTACCATTCCTTTACGAAAAATCTTACTTGATGACCTTATATGCTTATAATGT
CAAAA
Found at i:162664 original size:13 final size:13
Alignment explanation
Indices: 162646--162671 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
162636 CATTTTGGGA
162646 TGTATCGATACAT
1 TGTATCGATACAT
162659 TGTATCGATACAT
1 TGTATCGATACAT
162672 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:162668 original size:33 final size:32
Alignment explanation
Indices: 162626--162689 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
162616 TACAAGCCAA
*
162626 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
*
162659 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
162690 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:165113 original size:20 final size:21
Alignment explanation
Indices: 165083--165124 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
165073 CTGTTTTTGT
165083 TGATGATTTTG-A-TGAAAAA
1 TGATGATTTTGAAGTGAAAAA
165102 TGATGTATTTTGAAGTGAAAAA
1 TGATG-ATTTTGAAGTGAAAAA
165124 T
1 T
165125 AAGAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 6 0.30
21 1 0.05
22 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.38
Consensus pattern (21 bp):
TGATGATTTTGAAGTGAAAAA
Found at i:165274 original size:13 final size:13
Alignment explanation
Indices: 165256--165293 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
165246 ATAAACCCTT
* *
165256 TGTATCAATACAC
1 TGTATCGATACAA
165269 TGTATCGATACAA
1 TGTATCGATACAA
165282 TGTATCGATACA
1 TGTATCGATACA
165294 GAGAATGCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:165734 original size:34 final size:35
Alignment explanation
Indices: 165696--165762 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
165686 CCTTACAACA
165696 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
165730 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
165763 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:166238 original size:13 final size:13
Alignment explanation
Indices: 166220--166245 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
166210 CAATTTTTTG
166220 TGTATCGATACAT
1 TGTATCGATACAT
166233 TGTATCGATACAT
1 TGTATCGATACAT
166246 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:166310 original size:21 final size:21
Alignment explanation
Indices: 166284--166359 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
166274 CTGCCAAGAA
166284 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
166305 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
166325 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
166346 ATGTATCGATACAT
1 ATGTATCGATACAT
166360 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:166329 original size:20 final size:20
Alignment explanation
Indices: 166304--166377 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
166294 ACATCTTTTT
166304 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
166324 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
166345 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
166365 CATGTATCGATAC
1 CATGTATCGATAC
166378 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:166341 original size:41 final size:41
Alignment explanation
Indices: 166284--166377 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
166274 CTGCCAAGAA
166284 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
166325 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
166366 ATGTATCGATAC
1 ATGTATCGATAC
166378 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:169862 original size:84 final size:84
Alignment explanation
Indices: 169707--169871 Score: 201
Period size: 84 Copynumber: 2.0 Consensus size: 84
169697 CATTTTCCAC
* * * *
169707 TTGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTCTTTTTAAAAGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
169772 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* *
169791 TTGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCTA
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAAT-T-ATTCTCTA
* * *
169853 CACTTATTGATTTATTTTC
63 AACTCATTGATTTACTTTC
169872 TTCTTTGAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
82 6 0.09
83 9 0.13
84 54 0.78
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:171423 original size:34 final size:35
Alignment explanation
Indices: 171385--171451 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
171375 CCTTACAACA
171385 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
171419 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
171452 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:171926 original size:13 final size:13
Alignment explanation
Indices: 171908--171933 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
171898 ACAATTTTTG
171908 TGTATCGATACAT
1 TGTATCGATACAT
171921 TGTATCGATACAT
1 TGTATCGATACAT
171934 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:171930 original size:32 final size:32
Alignment explanation
Indices: 171889--171951 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
171879 TACAAGCCAA
**
171889 TGTATCGATACAATTTTTG-TGTATCGATACAT
1 TGTATCGATAC-ATACTTGCTGTATCGATACAT
171921 TGTATCGATACATACTTGCTGTATCGATACA
1 TGTATCGATACATACTTGCTGTATCGATACA
171952 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 5 0.18
32 23 0.82
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATACTTGCTGTATCGATACAT
Found at i:171998 original size:21 final size:21
Alignment explanation
Indices: 171972--172047 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
171962 CTGCCAAGAA
171972 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
171993 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
172013 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
172034 ATGTATCGATACAT
1 ATGTATCGATACAT
172048 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:172017 original size:20 final size:20
Alignment explanation
Indices: 171992--172065 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
171982 ACATCTTTTT
171992 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
172012 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
172033 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
172053 CATGTATCGATAC
1 CATGTATCGATAC
172066 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:172029 original size:41 final size:41
Alignment explanation
Indices: 171972--172065 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
171962 CTGCCAAGAA
171972 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
172013 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
172054 ATGTATCGATAC
1 ATGTATCGATAC
172066 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:178866 original size:13 final size:13
Alignment explanation
Indices: 178848--178887 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
178838 ACAATGTTCT
178848 TTGTATCGATACA
1 TTGTATCGATACA
178861 TTGTATCGATACA
1 TTGTATCGATACA
* * *
178874 ATGCATCAATACA
1 TTGTATCGATACA
178887 T
1 T
178888 GGGTTACTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:187110 original size:33 final size:33
Alignment explanation
Indices: 187065--187129 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
187055 TGTTACAAGC
*
187065 AATGTATCGATACAAT-TCATCATGTATCGATAT
1 AATGTATCGATACAATGT-ACCATGTATCGATAT
*
187098 AATGTATTGATACAATGTACCATGTATCGATA
1 AATGTATCGATACAATGTACCATGTATCGATA
187130 CAAACAGTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (33 bp):
AATGTATCGATACAATGTACCATGTATCGATAT
Done.