Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold509
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: 230775
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:167781 original size:21 final size:21
Alignment explanation
Indices: 167740--167782 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
167730 TCCCGTGTGA
**
167740 ATGTATCGATACAATTTTTTG
1 ATGTATCGATACAATCATTTG
167761 ATGTATCGATAC-ATGCATTTG
1 ATGTATCGATACAAT-CATTTG
167782 A
1 A
167783 AAATATAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACAATCATTTG
Found at i:167875 original size:32 final size:33
Alignment explanation
Indices: 167812--167879 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
167802 CGTTACAAGC
* *
167812 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCAATACATCTTATGGTGTATCGATA
167845 CAATGTATCAATACATACTT-T-GTGTATCGATA
1 CAATGTATCAATACAT-CTTATGGTGTATCGATA
167877 CAA
1 CAA
167880 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 14 0.44
33 16 0.50
34 2 0.06
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (33 bp):
CAATGTATCAATACATCTTATGGTGTATCGATA
Found at i:169810 original size:13 final size:13
Alignment explanation
Indices: 169792--169816 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
169782 ACTGAAGTAA
169792 TGTATCGATACAT
1 TGTATCGATACAT
169805 TGTATCGATACA
1 TGTATCGATACA
169817 ATCTGGAAAA
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:171188 original size:22 final size:22
Alignment explanation
Indices: 171163--171204 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
171153 AGATAAACAT
171163 ATTTCTCCCCCTTTATCAAAGC
1 ATTTCTCCCCCTTTATCAAAGC
* *
171185 ATTTCTCCCTCTTTGTCAAA
1 ATTTCTCCCCCTTTATCAAA
171205 TCTTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.33, G:0.05, T:0.40
Consensus pattern (22 bp):
ATTTCTCCCCCTTTATCAAAGC
Found at i:174460 original size:19 final size:19
Alignment explanation
Indices: 174436--174485 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
174426 AAACAGTAAC
174436 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
174455 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
174474 TGTATCGATACA
1 TGTATCGATACA
174486 ATGTATCGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:174540 original size:20 final size:20
Alignment explanation
Indices: 174515--174660 Score: 150
Period size: 20 Copynumber: 6.8 Consensus size: 20
174505 CTGCCAAGGA
174515 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
174535 AATGTATCGATACATTGA-TC
1 AATGTATCGATACATT-ATTC
**
174555 TTTGTATCGATACATCTGAGAATTTGACCC
1 AATGTATCGATACAT-T----A-TT----C
174585 AGATGTATCGATACATTATTC
1 A-ATGTATCGATACATTATTC
*
174606 AATGTATCGATACAATATTC
1 AATGTATCGATACATTATTC
174626 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
174646 AATGTATCGATACAT
1 AATGTATCGATACAT
174661 GCAGGCAAAA
Statistics
Matches: 107, Mismatches: 7, Indels: 24
0.78 0.05 0.17
Matches are distributed among these distances:
20 83 0.78
21 4 0.04
24 1 0.01
25 2 0.02
26 2 0.02
30 2 0.02
31 13 0.12
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (20 bp):
AATGTATCGATACATTATTC
Found at i:182328 original size:13 final size:13
Alignment explanation
Indices: 182310--182340 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
182300 ACAATTCATC
182310 ATGTATCGATACA
1 ATGTATCGATACA
182323 ATGTATCGATACA
1 ATGTATCGATACA
*
182336 TTGTA
1 ATGTA
182341 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:182328 original size:33 final size:33
Alignment explanation
Indices: 182289--182356 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
182279 CGTTACAAGT
*
182289 AATGTATCGATACAATT-CATCATGTATCGATAC
1 AATGTATCGATAC-ATTGCACCATGTATCGATAC
*
182322 AATGTATCGATACATTGTACCATGTATCGATAC
1 AATGTATCGATACATTGCACCATGTATCGATAC
182355 AA
1 AA
182357 ACAGTGGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 3 0.09
33 29 0.91
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (33 bp):
AATGTATCGATACATTGCACCATGTATCGATAC
Found at i:182411 original size:20 final size:20
Alignment explanation
Indices: 182386--182438 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
182376 TGCCAATTTC
182386 ATGTATCGATACAAAGCATA
1 ATGTATCGATACAAAGCATA
182406 ATGTATCGATACAAAGCATA
1 ATGTATCGATACAAAGCATA
182426 ATGTATCGATACA
1 ATGTATCGATACA
182439 TCTGGGGGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26
Consensus pattern (20 bp):
ATGTATCGATACAAAGCATA
Found at i:183558 original size:10 final size:10
Alignment explanation
Indices: 183543--183631 Score: 54
Period size: 10 Copynumber: 8.2 Consensus size: 10
183533 TATCGATACA
183543 GATGAATAGT
1 GATGAATAGT
183553 GATGAATAATGAT
1 GATGAAT-A-G-T
* * *
183566 ACATGAACAAT
1 -GATGAATAGT
183577 GATGAATAGT
1 GATGAATAGT
183587 GATATGTGAATAGT
1 G--A--TGAATAGT
*
183601 GATG-ACAGT
1 GATGAATAGT
*
183610 AATGAATAGT
1 GATGAATAGT
183620 GATGAATAGT
1 GATGAATAGT
183630 GA
1 GA
183632 AAAATGAGAT
Statistics
Matches: 60, Mismatches: 10, Indels: 18
0.68 0.11 0.20
Matches are distributed among these distances:
9 7 0.12
10 32 0.53
11 2 0.03
12 3 0.05
13 2 0.03
14 14 0.23
ACGTcount: A:0.43, C:0.03, G:0.26, T:0.28
Consensus pattern (10 bp):
GATGAATAGT
Found at i:183637 original size:24 final size:24
Alignment explanation
Indices: 183544--183638 Score: 83
Period size: 24 Copynumber: 4.2 Consensus size: 24
183534 ATCGATACAG
* *
183544 ATGAATAGTGATGAATAATGATAC
1 ATGAATAGTGATGAATAGTGATAA
* * *
183568 ATGAACAATGATGAATAGTGATAT
1 ATGAATAGTGATGAATAGTGATAA
* *
183592 GTGAATAGTGATG-ACA--G-T-A
1 ATGAATAGTGATGAATAGTGATAA
*
183611 ATGAATAGTGATGAATAGTGAAAA
1 ATGAATAGTGATGAATAGTGATAA
183635 ATGA
1 ATGA
183639 GATTTAGCTA
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
19 12 0.22
20 3 0.06
21 1 0.02
22 1 0.02
23 2 0.04
24 35 0.65
ACGTcount: A:0.45, C:0.03, G:0.24, T:0.27
Consensus pattern (24 bp):
ATGAATAGTGATGAATAGTGATAA
Found at i:186297 original size:19 final size:20
Alignment explanation
Indices: 186273--186325 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
186263 CACATCTAGA
**
186273 TGTATCGATACATGTTC-AT
1 TGTATCGATACATGCACAAT
186292 TGTATCGATACATGCACAAT
1 TGTATCGATACATGCACAAT
186312 TGTATCGATACATG
1 TGTATCGATACATG
186326 AAACTAGCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGCACAAT
Found at i:186393 original size:13 final size:13
Alignment explanation
Indices: 186375--186399 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
186365 CATGGCACAT
186375 TGTATCGATACAA
1 TGTATCGATACAA
186388 TGTATCGATACA
1 TGTATCGATACA
186400 TGATGAATTG
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:186399 original size:33 final size:32
Alignment explanation
Indices: 186355--186419 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
186345 TACCACTGTT
186355 TGTATCAATACATG-GCACATTGTATCGATACAA
1 TGTATCAATACATGAG-A-ATTGTATCGATACAA
*
186388 TGTATCGATACATGATGAATTGTATCGATACA
1 TGTATCAATACATGA-GAATTGTATCGATACA
186420 TTACTTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (32 bp):
TGTATCAATACATGAGAATTGTATCGATACAA
Found at i:188167 original size:18 final size:17
Alignment explanation
Indices: 188140--188173 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
188130 GGATGAGTTA
*
188140 TTAAATTTTATTATATTT
1 TTAAAATTTATT-TATTT
188158 TTAAAATTTATTTATT
1 TTAAAATTTATTTATT
188174 AAAAACTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTAAAATTTATTTATTT
Found at i:188526 original size:21 final size:23
Alignment explanation
Indices: 188500--188563 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
188490 TTATTTTAAA
188500 AATATT-AATTTTAATATT-TAT
1 AATATTAAATTTTAATATTATAT
*
188521 ATTATTAAATTATT--TATTAATAT
1 AATATTAAATT-TTAATATT-ATAT
188544 AATATTAAATTTTAATATTA
1 AATATTAAATTTTAATATTA
188564 CTAAATAGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
21 9 0.26
22 6 0.17
23 16 0.46
24 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AATATTAAATTTTAATATTATAT
Found at i:188534 original size:29 final size:28
Alignment explanation
Indices: 188464--188543 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 28
188454 CAATTGAATT
*
188464 TTATTAAATTTATTAATTTAATATTTTTA
1 TTATTAAA-TTATTAATTTAATATTTATA
*
188493 TT-TTAAAAATATTAATTTTAATATTTATA
1 TTATT-AAATTATTAA-TTTAATATTTATA
*
188522 TTATTAAATTATTTA-TTAATAT
1 TTATTAAATTATTAATTTAATAT
188544 AATATTAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
27 7 0.16
28 8 0.18
29 27 0.61
30 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TTATTAAATTATTAATTTAATATTTATA
Found at i:192494 original size:20 final size:20
Alignment explanation
Indices: 192469--192506 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
192459 GTAAAAAGAT
192469 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
192489 AGAATGTATCGATACATT
1 AGAATGTATCGATACATT
192507 CATACTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:193498 original size:2 final size:2
Alignment explanation
Indices: 193491--193527 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
193481 AGCTTTTGTT
*
193491 TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
193528 GTATTTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:198270 original size:61 final size:60
Alignment explanation
Indices: 198024--198340 Score: 382
Period size: 61 Copynumber: 5.3 Consensus size: 60
198014 CTCACCCTTT
*
198024 AGTCCTCAAAGAGCAGGACGC---C--TTTCAAAGCCCACACAAGTTGGTGGCAC-CTTC
1 AGTCCTCAAAGAGCAGGACGCTTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
** *
198078 AGTCCTCAAAGAGCAGGACGCCTTTTCCATTTCAAAGCCCACACAAATTGGTGGCACTTTTC
1 AGTCCTCAAAGAGCAGGACG-C-TTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
* * *
198140 AGTCCTCAAAGAGCAGGATGCTTTCTTTTTGTAAA-CCCACATAAGTTGGTGGCACTTTTC
1 AGTCCTCAAAGAGCAGGACGCTTTCTTTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTC
* * * *
198200 AGTCCTCAAAGAGCAGGATGCTTTCTTTTTGCAAATCCCACACTAGTTGGTGGCA-TCTTC
1 AGTCCTCAAAGAGCAGGACGCTTTCTTTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTC
* * *
198260 TAGTCCTCAAAGAGCAGGACGCCTTT-TCTTTTCAAAGACCACACGAGTTCGTGGCACTTTTC
1 -AGTCCTCAAAGAGCAGGACG-CTTTCT-TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
198322 AGTCCTCAAAGAGCAGGAC
1 AGTCCTCAAAGAGCAGGAC
198341 ACACTTCTTT
Statistics
Matches: 231, Mismatches: 18, Indels: 21
0.86 0.07 0.08
Matches are distributed among these distances:
54 20 0.09
55 1 0.00
59 1 0.00
60 68 0.29
61 107 0.46
62 34 0.15
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (60 bp):
AGTCCTCAAAGAGCAGGACGCTTTCTTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
Found at i:198370 original size:42 final size:41
Alignment explanation
Indices: 198323--198455 Score: 139
Period size: 42 Copynumber: 3.2 Consensus size: 41
198313 GCACTTTTCA
*
198323 GTCCTCAAAGAGCAGGACACACTTCTTTCCCTTTTTCACTTT
1 GTCCTCAAAGAGCAGGACACATTTCTTTCCCTTTTTC-CTTT
* **
198365 GTCCTC-AAGAAGTAGGACAC-TTTCCTTTTCTTTTTTTCCTTT
1 GTCCTCAAAG-AGCAGGACACATTT-C-TTTCCCTTTTTCCTTT
* *
198407 GTCCTCAAGGAGCAGGAC-CTATTTCATTCCCTTTTT-CTTT
1 GTCCTCAAAGAGCAGGACAC-ATTTCTTTCCCTTTTTCCTTT
198447 GTCCTCAAA
1 GTCCTCAAA
198456 AAAGTGGGAC
Statistics
Matches: 75, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
40 12 0.16
41 14 0.19
42 34 0.45
43 15 0.20
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.40
Consensus pattern (41 bp):
GTCCTCAAAGAGCAGGACACATTTCTTTCCCTTTTTCCTTT
Found at i:199120 original size:35 final size:35
Alignment explanation
Indices: 199074--199256 Score: 286
Period size: 35 Copynumber: 5.4 Consensus size: 35
199064 AAATAAAAAA
199074 CATGGAATGATGGGCATGGAATATAAAAATGAAGG
1 CATGGAATGATGGGCATGGAATATAAAAATGAAGG
**
199109 CATGGAATGATGGGCAT-GAA-ATAAAAA--AAAA
1 CATGGAATGATGGGCATGGAATATAAAAATGAAGG
*
199140 CATGGGATGATGGGCATGGAATATAAAAATGAAGG
1 CATGGAATGATGGGCATGGAATATAAAAATGAAGG
*
199175 CATGGAATGATGGGCATGGAATAAAAAAATGAAGG
1 CATGGAATGATGGGCATGGAATATAAAAATGAAGG
*
199210 CATAGAATGATGGGCATGGAATA-AAAAATGAAGG
1 CATGGAATGATGGGCATGGAATATAAAAATGAAGG
199244 CATGGAATGATGG
1 CATGGAATGATGG
199257 ATAAAAATGA
Statistics
Matches: 135, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
31 18 0.13
32 3 0.02
33 14 0.10
34 26 0.19
35 74 0.55
ACGTcount: A:0.45, C:0.06, G:0.31, T:0.19
Consensus pattern (35 bp):
CATGGAATGATGGGCATGGAATATAAAAATGAAGG
Found at i:199166 original size:66 final size:66
Alignment explanation
Indices: 199068--199256 Score: 308
Period size: 66 Copynumber: 2.8 Consensus size: 66
199058 ATCAAGAAAT
199068 AAAAAACATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCATGAAATAA
1 AAAAAACATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCATGAAATAA
199133 A
66 A
* *
199134 AAAAAACATGGGATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCATGGAATAA
1 AAAAAACATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCATGAAATAA
199199 A
66 A
*
199200 AAAATGAAGGCATAGAATGATGGGCATGGAATA-AAAAATGAAGGCATGGAATGATGG
1 AAAA--AA--CATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGG
199257 ATAAAAATGA
Statistics
Matches: 115, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
66 68 0.59
68 2 0.02
69 24 0.21
70 21 0.18
ACGTcount: A:0.47, C:0.06, G:0.30, T:0.18
Consensus pattern (66 bp):
AAAAAACATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCATGAAATAA
A
Found at i:200594 original size:79 final size:79
Alignment explanation
Indices: 200463--200812 Score: 549
Period size: 79 Copynumber: 4.4 Consensus size: 79
200453 GTTAAGTTTC
* * * *
200463 TCAATTTTTCACAATCGAGGATACTCCAATCCCGTTATTTTCGAGGGGATACTCCAACCCCAGTT
1 TCAATTTTTCATAATCGGGGATACTCTAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAGTT
*
200528 TTATCTCTAAAACA
66 TTATTTCTAAAACA
* **
200542 TCAATTTTTCATAATCGGGGATACTCTAACCCCGTTATTTTCGAGGAGATACTCCAACCCTGGTT
1 TCAATTTTTCATAATCGGGGATACTCTAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAGTT
*
200607 TTATTTCTAAAATA
66 TTATTTCTAAAACA
* * * *
200621 TTAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTACAACCCC-GAT
1 TCAATTTTTCATAATCGGGGATACTCTAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAG-T
200685 TTTATTTCTAAAACA
65 TTTATTTCTAAAACA
* *
200700 CCAATTTTTCATAATCGGGGATACTCTAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGTT
1 TCAATTTTTCATAATCGGGGATACTCTAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAGTT
200765 TTATTTCTAAAACA
66 TTATTTCTAAAACA
200779 TCAATTTTTCATAATCGGGGATACTCTAACCCCG
1 TCAATTTTTCATAATCGGGGATACTCTAACCCCG
200813 ATTTTATTTT
Statistics
Matches: 246, Mismatches: 23, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
78 1 0.00
79 244 0.99
80 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (79 bp):
TCAATTTTTCATAATCGGGGATACTCTAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAGTT
TTATTTCTAAAACA
Found at i:200804 original size:51 final size:50
Alignment explanation
Indices: 200744--200890 Score: 170
Period size: 52 Copynumber: 2.8 Consensus size: 50
200734 TTATTTCCGA
*
200744 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTT-CATAATC
1 GGGGATACTCTAACCCC-GTTTTATTTCTAAAACA-CAATTTTTCCATAATC
* * *
200795 GGGGATACTCTAACCCCGATTTTATTTTTTAGAACACCATTTTTCCATAATC
1 GGGGATACTCTAACCCCG-TTTTA-TTTCTAAAACACAATTTTTCCATAATC
* * *
200847 GGGGATACTCTAGCCCCGTTGTTATCTCTAAAATACTAATTTTT
1 GGGGATACTCTAACCCCGTT-TTATTTCTAAAACAC-AATTTTT
200891 TTTCTCGTCA
Statistics
Matches: 81, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
50 1 0.01
51 38 0.47
52 42 0.52
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.37
Consensus pattern (50 bp):
GGGGATACTCTAACCCCGTTTTATTTCTAAAACACAATTTTTCCATAATC
Found at i:207071 original size:55 final size:54
Alignment explanation
Indices: 206987--207677 Score: 686
Period size: 55 Copynumber: 12.0 Consensus size: 54
206977 GACGCATTTT
* *
206987 CCTTTTAAAGCCCACACAAGTTGGTGGCATCATTCAGTCCTCAAAGAGCAGGACG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGATG
* * *
207042 CCTTTTAAGGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGATG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTCAAAGAGCAGGATG
* *
207097 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGATG
* *
207151 CTTTCTTTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAAAGCAGGATG
1 C---C--TTTT-AAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGATG
* *
207212 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGATG
*
207266 CTTTCTTTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCGGTCCTCAAAGAGCAGGACT-
1 C---C--TTTT-AAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGA-TG
*
207327 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACT-
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTC-AGTCCTCAAAGAGCAGGA-TG
* * * *
207382 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGATCAGGACG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGATG
*
207436 CCTTTTCCATTTCAAAGCCCACACAAATTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATG
1 CC---T---TTT-AAAGCCCACACAAGTTGGTGGCAC-TTTCAGTCCTCAAAGAGCAGGATG
207498 CTTTCTTTTTGTAAA-CCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATG
1 C---C--TTT-TAAAGCCCACACAAGTTGGTGGCAC-TTTCAGTCCTCAAAGAGCAGGATG
* * * * * *
207558 CTTTCTTTTTGCAAATCCCACACTAGTTGGTGGCATCTTCCAATCCTCAAAGAGTAGGACG
1 C---C-TTTT--AAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGATG
* * *
207619 CCTTTTCTTTTCAAAGACCACACGAGTTAGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
1 -C----CTTTT-AAAGCCCACACAAGTTGGTGGCAC-TTTCAGTCCTCAAAGAGCAGGA
207678 CACACTTCTT
Statistics
Matches: 553, Mismatches: 46, Indels: 68
0.83 0.07 0.10
Matches are distributed among these distances:
54 69 0.12
55 172 0.31
56 7 0.01
57 3 0.01
58 3 0.01
59 10 0.02
60 101 0.18
61 150 0.27
62 30 0.05
63 4 0.01
64 3 0.01
65 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.26
Consensus pattern (54 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGATG
Found at i:207201 original size:115 final size:115
Alignment explanation
Indices: 206987--207677 Score: 808
Period size: 115 Copynumber: 6.0 Consensus size: 115
206977 GACGCATTTT
* * *
206987 CCTTTTAAAGCCCACACAAGTTGGTGGCATCATTCAGTCCTCAAAGAGCAGGACGC---C--TTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTT
* * *
207047 T-AAGGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGTAGGATG
65 TCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGATG
207097 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTT
* *
207162 CAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAAAGCAGGATG
66 CAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATG
207212 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTT
*
207277 CAAAGCCCACACAAGTTGGTGGCACCTTTCGGTCCTCAAAGAGCAGGACT-
66 CAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA-TG
* *
207327 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGA--C--TC--CT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-C-AGTCCTCAAAGAGCAGGATGCTTTCTTTT
* *
207385 TTCAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGATCAGGACGCCTTTT
64 TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA------TG
* *
207442 CCATTTCAAAGCCCACACAAATTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTT
1 CC-TTTCAAAGCCCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTT
*
207507 TGT-AAA-CCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATG
64 T-TCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATG
* * * * * *
207558 CTTTCTTTTTGCAAATCCCACACTAGTTGGTGGCATCTTCCAATCCTCAAAGAGTAGGACGCCTT
1 C---C--TTT-CAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGATG-CTT
* * * * *
207623 T-TCTTTTCAAAGACCACACGAGTTAGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
58 TCTTTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA
207678 CACACTTCTT
Statistics
Matches: 509, Mismatches: 36, Indels: 60
0.84 0.06 0.10
Matches are distributed among these distances:
109 43 0.08
110 57 0.11
112 3 0.01
114 9 0.02
115 181 0.36
116 67 0.13
117 1 0.00
118 3 0.01
119 1 0.00
120 8 0.02
121 66 0.13
122 69 0.14
123 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.26
Consensus pattern (115 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTT
CAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATG
Found at i:207238 original size:170 final size:170
Alignment explanation
Indices: 206956--207677 Score: 811
Period size: 170 Copynumber: 4.1 Consensus size: 170
206946 CTCTTTTAGC
* * * *
206956 CCTTCAGTCCTCAAAGAGTAGGACGCATTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCATCAT
1 CCTTCAGTCCTCAAAGAGCAGGATGC-TTTCT-CTTTTAAAGCCCACACAAGTTGGTGGCACCTT
* * * **
207020 TCAGTCCTCAAAGAGCAGGACGCCTTTTAAGGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCA
64 TCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCA
207085 AAGAGTAGGATGC-C-TTTCAAAGCCCACACAAGTTGGTGGCA
128 AAGAGTAGGATGCTCTTTTCAAAGCCCACACAAGTTGGTGGCA
*
207126 CCTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
1 CCTTCAGTCCTCAAAGAGCAGGATGCTTTCTCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTT
* *
207191 CAGTCTTCAAAAAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAA
65 CAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAA
*
207256 GAGCAGGATGCTTTCTTTTTTCAAAGCCCACACAAGTTGGTGGCA
130 GAGTAGGATGC--TC--TTTTCAAAGCCCACACAAGTTGGTGGCA
* *
207301 CCTTTCGGTCCTCAAAGAGCAGGA--C--TC-CTTTTAAAGCCCACACAAGTTGGTGGCA-CTTC
1 CC-TTCAGTCCTCAAAGAGCAGGATGCTTTCTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
207360 CTAGTCCTCAAAGAGCAGGACT-CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCA
65 C-AGTCCTCAAAGAGCAGGA-TGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCA
* * *
207424 AAGA-TCAGGACGCCTTTTCCATTTCAAAGCCCACACAAATTGGTGGCA
128 AAGAGT-AGGATG-C---T-CTTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
207472 CTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTGTAAA-CCCACACAAGTTGGTGGCACTTT
1 C-CTTCAGTCCTCAAAGAGCAGGATGCTTTCTCTTT-TAAAGCCCACACAAGTTGGTGGCACCTT
* * * *
207536 TCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTGCAAATCCCACACTAGTTGGTGGCATCTTCCAA
64 TCAGTCCTCAAAGAGCAGGATGC---C--TTT-CAAAGCCCACACAAGTTGGTGGCACCTT-CAG
* * * *
207601 TCCTCAAAGAGTAGGACGCCTTTTCTTTTCAAAGACCACACGAGTTAGTGGCA
122 TCCTCAAAGAGTAGGATG-C---TCTTTTCAAAGCCCACACAAGTTGGTGGCA
*
207654 CTTTTCAGTCCTCAAAGAGCAGGA
1 C-CTTCAGTCCTCAAAGAGCAGGA
207678 CACACTTCTT
Statistics
Matches: 484, Mismatches: 36, Indels: 52
0.85 0.06 0.09
Matches are distributed among these distances:
169 32 0.07
170 188 0.39
171 53 0.11
172 6 0.01
173 2 0.00
174 1 0.00
175 32 0.07
176 61 0.13
177 7 0.01
179 1 0.00
181 3 0.01
182 73 0.15
183 24 0.05
184 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.26
Consensus pattern (170 bp):
CCTTCAGTCCTCAAAGAGCAGGATGCTTTCTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
AGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAG
AGTAGGATGCTCTTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:207708 original size:42 final size:41
Alignment explanation
Indices: 207661--207793 Score: 130
Period size: 42 Copynumber: 3.2 Consensus size: 41
207651 GCACTTTTCA
* *
207661 GTCCTCAAAGAGCAGGACACACTTCTTTCCCTTTTTCACTTT
1 GTCCTCAAAGAGCAGGACACATTTCTTTCCATTTTTC-CTTT
* **
207703 GTCCTC-AAGAAGTAGGACAC-TTTCCTTTTCTTTTTTTCCTTT
1 GTCCTCAAAG-AGCAGGACACATTT-C-TTTCCATTTTTCCTTT
* *
207745 GTCCTCAAGGAGCAGGAC-CTATTTCATTCCATTTTT-CTTT
1 GTCCTCAAAGAGCAGGACAC-ATTTCTTTCCATTTTTCCTTT
207785 GTCCTCAAA
1 GTCCTCAAA
207794 AAAGTGGGAC
Statistics
Matches: 75, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
40 12 0.16
41 14 0.19
42 34 0.45
43 15 0.20
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (41 bp):
GTCCTCAAAGAGCAGGACACATTTCTTTCCATTTTTCCTTT
Found at i:208461 original size:35 final size:35
Alignment explanation
Indices: 208415--208596 Score: 286
Period size: 35 Copynumber: 5.4 Consensus size: 35
208405 AAATAAAAAA
208415 CATGGAATGATGGGCATGGAATATAAAAATGAAGG
1 CATGGAATGATGGGCATGGAATATAAAAATGAAGG
*
208450 CATGGAATGATGGGCAT-GAA-ATAAAAA--AA-A
1 CATGGAATGATGGGCATGGAATATAAAAATGAAGG
*
208480 CATGGGATGATGGGCATGGAATATAAAAATGAAGG
1 CATGGAATGATGGGCATGGAATATAAAAATGAAGG
*
208515 CATGGAATGATGGGCATGGAATAAAAAAATGAAGG
1 CATGGAATGATGGGCATGGAATATAAAAATGAAGG
*
208550 CATAGAATGATGGGCATGGAATA-AAAAATGAAGG
1 CATGGAATGATGGGCATGGAATATAAAAATGAAGG
208584 CATGGAATGATGG
1 CATGGAATGATGG
208597 ATAAAAATGA
Statistics
Matches: 135, Mismatches: 7, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
30 16 0.12
31 5 0.04
32 7 0.05
33 7 0.05
34 28 0.21
35 72 0.53
ACGTcount: A:0.45, C:0.06, G:0.31, T:0.19
Consensus pattern (35 bp):
CATGGAATGATGGGCATGGAATATAAAAATGAAGG
Found at i:208506 original size:65 final size:66
Alignment explanation
Indices: 208409--208596 Score: 299
Period size: 65 Copynumber: 2.8 Consensus size: 66
208399 ATCAAGAAAT
208409 AAAAAACATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCATGAAAT-A
1 AAAAAACATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCATGAAATAA
208473 A
66 A
* *
208474 AAAAAACATGGGATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCATGGAATAA
1 AAAAAACATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCATGAAATAA
208539 A
66 A
*
208540 AAAATGAAGGCATAGAATGATGGGCATGGAATA-AAAAATGAAGGCATGGAATGATGG
1 AAAA--AA--CATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGG
208597 ATAAAAATGA
Statistics
Matches: 114, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
65 61 0.54
66 6 0.05
68 2 0.02
69 24 0.21
70 21 0.18
ACGTcount: A:0.46, C:0.06, G:0.30, T:0.18
Consensus pattern (66 bp):
AAAAAACATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCATGAAATAA
A
Found at i:208624 original size:100 final size:96
Alignment explanation
Indices: 208415--208615 Score: 259
Period size: 100 Copynumber: 2.1 Consensus size: 96
208405 AAATAAAAAA
* *
208415 CATGGAATGATGGGCATGGAATATAAAAATGAAGGCATGGAATGATGGGCATGAAATAAAAAAAA
1 CATGGAATGATGGGCATGGAATAAAAAAATGAAGGCATAGAATGATGGGCATGAAATAAAAAAAA
*
208480 CATGGGATGATGGGCATGGAATATAAAAATGAAGG
66 CATGGGA-GAT-GGCATGG-A-ATAAAAATGAAAG
*
208515 CATGGAATGATGGGCATGGAATAAAAAAATGAAGGCATAGAATGATGGGCATGGAATAAAAAATG
1 CATGGAATGATGGGCATGGAATAAAAAAATGAAGGCATAGAATGATGGGCATGAAATAAAAAA--
208580 AAGGCAT-GGA-AT-G-ATGG-ATAAAAATGAAAG
64 AA--CATGGGAGATGGCATGGAATAAAAATGAAAG
208610 CATGGA
1 CATGGA
208616 CGAAAATGAA
Statistics
Matches: 93, Mismatches: 4, Indels: 13
0.85 0.04 0.12
Matches are distributed among these distances:
95 18 0.19
98 4 0.04
99 1 0.01
100 60 0.65
101 2 0.02
102 2 0.02
103 3 0.03
104 3 0.03
ACGTcount: A:0.46, C:0.06, G:0.30, T:0.18
Consensus pattern (96 bp):
CATGGAATGATGGGCATGGAATAAAAAAATGAAGGCATAGAATGATGGGCATGAAATAAAAAAAA
CATGGGAGATGGCATGGAATAAAAATGAAAG
Found at i:209899 original size:79 final size:79
Alignment explanation
Indices: 209803--210022 Score: 368
Period size: 79 Copynumber: 2.8 Consensus size: 79
209793 GTTAAGTTTC
* *
209803 TCAATTTTTCACAATCGGGGATACTCCAATCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
209868 TTATCTCTAAAACA
66 TTATCTCTAAAACA
* *
209882 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTGGTT
1 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
* *
209947 TTATTTCTAAAATA
66 TTATCTCTAAAACA
* *
209961 TTAATTTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
1 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
210023 TTATTTCCGA
Statistics
Matches: 131, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 131 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (79 bp):
TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTT
TTATCTCTAAAACA
Found at i:210009 original size:107 final size:107
Alignment explanation
Indices: 209898--210128 Score: 399
Period size: 107 Copynumber: 2.2 Consensus size: 107
209888 TTTCATAATC
* * * * *
209898 GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTGGTTTTATTTCTAAAATATT
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCTCTAAAACATC
209963 AATTTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGA
66 AATTTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGA
210005 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCTCTAAAACATC
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCTCTAAAACATC
* *
210070 AATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGA
66 AATTTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGA
210112 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
210129 AGTTTTATTT
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 117 1.00
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCTCTAAAACATC
AATTTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGA
Found at i:210016 original size:28 final size:28
Alignment explanation
Indices: 209978--210050 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
209968 TTCACAATCA
*
209978 GGGATACTCCAACCCCGTTATTTTCGAG
1 GGGATACTCCAACCCCGTTATTTCCGAG
210006 GGGATACTCCAACCCCGTTATTTCCGAG
1 GGGATACTCCAACCCCGTTATTTCCGAG
210034 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
210051 GTTTTATCTC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.23
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTTCCGAG
Found at i:210088 original size:79 final size:79
Alignment explanation
Indices: 210005--210496 Score: 806
Period size: 79 Copynumber: 6.2 Consensus size: 79
209995 TTATTTTCGA
* *
210005 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCTCTAAAACATC
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCTAAAACATC
210070 AATTTTTCATAATC
66 AATTTTTCATAATC
* * *
210084 GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCTAAAATATT
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCTAAAACATC
*
210149 AATTTTTCACAATC
66 AATTTTTCATAATC
* * **
210163 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCTAACCCCGGTTTTATTTCTAAAACGCC
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCTAAAACATC
210228 AATTTTTCATAATC
66 AATTTTTCATAATC
* *
210242 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCTAAAATATT
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCTAAAACATC
*
210307 AATTTTTCACAATC
66 AATTTTTCATAATC
* **
210321 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCTAACCCC-GATTTTATTTCTAAAACGC
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAG-TTTTATTTCTAAAACAT
210385 CAATTTTTCATAATC
65 CAATTTTTCATAATC
*
210400 GGGGATACTCCAACCCCGTTATTTCCGAGGGGGTACTCCAACCCCAGTTTTATTTCTAAAACATC
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCTAAAACATC
210465 AATTTTTCATAATC
66 AATTTTTCATAATC
*
210479 GGGGATACTCTAACCCCG
1 GGGGATACTCCAACCCCG
210497 ATTTTATTTT
Statistics
Matches: 379, Mismatches: 32, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
78 1 0.00
79 377 0.99
80 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCTAAAACATC
AATTTTTCATAATC
Found at i:210136 original size:186 final size:186
Alignment explanation
Indices: 209819--210208 Score: 726
Period size: 186 Copynumber: 2.1 Consensus size: 186
209809 TTTCACAATC
*
209819 GGGGATACTCCAATCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCTCTAAAACATC
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCTCTAAAACATC
**
209884 AATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTGGTTTT
66 AATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAGTTTT
*
209949 ATTTCTAAAATATTAATTTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGA
131 ATTTCTAAAATATTAATTTTTCACAATCAGGGATACTCCAACCCCGTTATTTCCGA
210005 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCTCTAAAACATC
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCTCTAAAACATC
210070 AATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAGTTTT
66 AATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAGTTTT
*
210135 ATTTCTAAAATATTAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGA
131 ATTTCTAAAATATTAATTTTTCACAATCAGGGATACTCCAACCCCGTTATTTCCGA
*
210191 GGGGATACTCTAACCCCG
1 GGGGATACTCCAACCCCG
210209 GTTTTATTTC
Statistics
Matches: 198, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
186 198 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (186 bp):
GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCTCTAAAACATC
AATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAGTTTT
ATTTCTAAAATATTAATTTTTCACAATCAGGGATACTCCAACCCCGTTATTTCCGA
Found at i:210276 original size:265 final size:265
Alignment explanation
Indices: 209803--210286 Score: 806
Period size: 265 Copynumber: 1.8 Consensus size: 265
209793 GTTAAGTTTC
* *
209803 TCAATTTTTCACAATCGGGGATACTCCAATCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGTT
* *
209868 TTATCTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATA
66 TTATCTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATA
* * **
209933 CTCCAACCCTGGTTTTATTTCTAAAATATTAATTTTTCACAATCAGGGATACTCCAACCCCGTTA
131 CTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCACAATCAGGGATACTCCAACCCCGTTA
*
209998 TTTTCGAGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCTCTA
196 TTTCCGAGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCTCTA
210063 AAACA
261 AAACA
* *
210068 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAGTT
1 TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGTT
* * *
210133 TTATTTCTAAAATATTAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATA
66 TTATCTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATA
* * * *
210198 CTCTAACCCCGGTTTTATTTCTAAAACGCCAATTTTTCATAATCGGGGATACTCCAACCCCGTTA
131 CTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCACAATCAGGGATACTCCAACCCCGTTA
210263 TTTCCGAGGGGATACTCCAACCCC
196 TTTCCGAGGGGATACTCCAACCCC
210287 AGTTTTATTT
Statistics
Matches: 201, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
265 201 1.00
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (265 bp):
TCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGTT
TTATCTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATA
CTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCACAATCAGGGATACTCCAACCCCGTTA
TTTCCGAGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCTCTA
AAACA
Found at i:210574 original size:52 final size:51
Alignment explanation
Indices: 210428--210574 Score: 140
Period size: 52 Copynumber: 2.9 Consensus size: 51
210418 TTATTTCCGA
* *
210428 GGGGGTACTCCAACCCC-AGTTTTATT-TCTAAAACATCAATTTTTCATAATC
1 GGGGATACTCTAACCCCGA-TTTTATTCTCTAAAACA-CAATTTTTCATAATC
* * * **
210479 GGGGATACTCTAACCCCGATTTTATTTTTTAGAACACCGTTTTTCCATAATC
1 GGGGATACTCTAACCCCGATTTTATTCTCTAAAACACAATTTTT-CATAATC
* *
210531 GGGGATACTCTAGCCCCG-TTGTTA-TCTCTAAAATACTAATTTTT
1 GGGGATACTCTAACCCCGATT-TTATTCTCTAAAACAC-AATTTTT
210575 TTCTCGTCAG
Statistics
Matches: 78, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
51 38 0.49
52 40 0.51
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (51 bp):
GGGGATACTCTAACCCCGATTTTATTCTCTAAAACACAATTTTTCATAATC
Found at i:212334 original size:17 final size:17
Alignment explanation
Indices: 212312--212344 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
212302 ACTTTAATTG
212312 TTTTCATCAAAAAACGT
1 TTTTCATCAAAAAACGT
*
212329 TTTTCATCTAAAAACG
1 TTTTCATCAAAAAACG
212345 GTAACCTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.36
Consensus pattern (17 bp):
TTTTCATCAAAAAACGT
Found at i:212408 original size:23 final size:24
Alignment explanation
Indices: 212358--212408 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
212348 ACCTTAATGA
**
212358 TGTTTCTTAATGGAAAAAAAATTT
1 TGTTTCTTAATGGAAAAAAAATAC
212382 TGTTTCTTAATGGAAAAAAAA-AC
1 TGTTTCTTAATGGAAAAAAAATAC
212405 TGTT
1 TGTT
212409 ATGTTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (24 bp):
TGTTTCTTAATGGAAAAAAAATAC
Found at i:212899 original size:24 final size:20
Alignment explanation
Indices: 212784--212888 Score: 93
Period size: 20 Copynumber: 4.8 Consensus size: 20
212774 CAACTCATAC
212784 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
* *
212804 ATGTATCGATTCATCGAAAA
1 ATGTATCGATACATTGAAAA
*
212824 ATATATCGATACATCTGAATAAAAGACAGA
1 ATGTATCGATACAT-TG------A-A-A-A
212854 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
212874 ATGTATCGATACATT
1 ATGTATCGATACATT
212889 TGGGTAAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
20 46 0.67
21 2 0.03
22 1 0.01
23 1 0.01
27 1 0.01
28 1 0.01
29 3 0.04
30 14 0.20
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:213664 original size:16 final size:16
Alignment explanation
Indices: 213643--213673 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
213633 TCTAATTTTA
213643 TTATCAACTTATAAAT
1 TTATCAACTTATAAAT
*
213659 TTATCAAGTTATAAA
1 TTATCAACTTATAAA
213674 CAAATTTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (16 bp):
TTATCAACTTATAAAT
Found at i:220758 original size:7 final size:7
Alignment explanation
Indices: 220746--220773 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
220736 TGTCTGATTT
220746 AGATTGG
1 AGATTGG
220753 AGATTGG
1 AGATTGG
220760 AGATTGG
1 AGATTGG
220767 AGATTGG
1 AGATTGG
220774 TTCCATACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.43, T:0.29
Consensus pattern (7 bp):
AGATTGG
Found at i:221690 original size:31 final size:31
Alignment explanation
Indices: 221652--221710 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
221642 AAATATAATG
221652 ATAAAATAATATAATTTTTATTTTTTTCCTT
1 ATAAAATAATATAATTTTTATTTTTTTCCTT
221683 ATAAAATAATATAATTTTTATTTTTTTC
1 ATAAAATAATATAATTTTTATTTTTTTC
221711 TCTCATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (31 bp):
ATAAAATAATATAATTTTTATTTTTTTCCTT
Found at i:226474 original size:23 final size:23
Alignment explanation
Indices: 226443--226488 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
226433 ATTCCACAGT
*
226443 TGAAACATATGTTTTGCAACAAG
1 TGAAACATATGTTATGCAACAAG
*
226466 TGAATCATATGTTATGCAACAAG
1 TGAAACATATGTTATGCAACAAG
226489 AGGGTCTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (23 bp):
TGAAACATATGTTATGCAACAAG
Found at i:230553 original size:1 final size:1
Alignment explanation
Indices: 230542--230671 Score: 224
Period size: 1 Copynumber: 130.0 Consensus size: 1
230532 ACGTATTTGT
* * * *
230542 CCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCTCCCCCCCCCTCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
230607 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
230672 AAAAAAAAGA
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 121 1.00
ACGTcount: A:0.02, C:0.97, G:0.00, T:0.02
Consensus pattern (1 bp):
C
Done.