Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2131
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: 76366
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:77 original size:19 final size:19
Alignment explanation
Indices: 43--81 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
33 ACCATGCATT
*
43 TTTTTACTATGTTCCATGCA
1 TTTTTAATATGTTCCA-GCA
63 TTTTTAATATG-TCCAGCA
1 TTTTTAATATGTTCCAGCA
81 T
1 T
82 CTCATTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 10 0.56
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (19 bp):
TTTTTAATATGTTCCAGCA
Found at i:1494 original size:98 final size:97
Alignment explanation
Indices: 1317--1531 Score: 286
Period size: 98 Copynumber: 2.2 Consensus size: 97
1307 AAATTTTTAT
* * * * *
1317 TTATCGAGGATACTCCAATCTGATTCCTCCGAGGAGATACTCTAACCTAATTTTTAAAACTTGTC
1 TTATCG-GGATACTCCAACCTGATTCCTCCAAGGAAAAACTCTAACCCAATTTTTAAAACTTGTC
* *
1382 AAGATCTGACACTTATTTTTGCCTAAATTATCA
65 AAGATCTGAAACTTATTCTTGCCTAAATTATCA
* * * **
1415 TTGTCGGGGATACTCCAACCTTATTCCTCTAAGGAAAAACTCTAACCCCTTTTTTAAAACTTGTC
1 TTATC-GGGATACTCCAACCTGATTCCTCCAAGGAAAAACTCTAACCCAATTTTTAAAACTTGTC
*
1480 AAGATTTGAAACTTATTCTTGCCTAAATTATCA
65 AAGATCTGAAACTTATTCTTGCCTAAATTATCA
*
1513 TTATCGGGACACTCCAACC
1 TTATCGGGATACTCCAACC
1532 CCATTCTTTC
Statistics
Matches: 101, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
97 13 0.13
98 87 0.86
99 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.34
Consensus pattern (97 bp):
TTATCGGGATACTCCAACCTGATTCCTCCAAGGAAAAACTCTAACCCAATTTTTAAAACTTGTCA
AGATCTGAAACTTATTCTTGCCTAAATTATCA
Found at i:1567 original size:98 final size:98
Alignment explanation
Indices: 1339--1569 Score: 261
Period size: 98 Copynumber: 2.4 Consensus size: 98
1329 CTCCAATCTG
** * * * *
1339 ATTCCTCCGAGGAGATACTCTAACCTAATTTTTAAAACTTGTCAAGATCTGACACTTATTTTTGC
1 ATTCCTCTAAGGAAATACTCTAACCTACTTTTTAAAACTTGTCAAGATCTGAAACTTATTCTTGC
* * **
1404 CTAAATTATCATTGTCGGGGATACTCCAACCTT
66 CTAAATTATCATTATCGGGGACACTCCAACCCC
* * *
1437 ATTCCTCTAAGGAAAAACTCTAACC-CCTTTTTTAAAACTTGTCAAGATTTGAAACTTATTCTTG
1 ATTCCTCTAAGGAAATACTCTAACCTAC-TTTTTAAAACTTGTCAAGATCTGAAACTTATTCTTG
1501 CCTAAATTATCATTATC-GGGACACTCCAACCCC
65 CCTAAATTATCATTATCGGGGACACTCCAACCCC
* * * *
1534 ATT-CTTTCGAGGGAATACTCTAACTCTGCTTTTTAA
1 ATTCCTCT-AAGGAAATACTCTAAC-CTACTTTTTAA
1570 TCAAAAATTA
Statistics
Matches: 111, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
96 3 0.03
97 29 0.26
98 78 0.70
99 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.35
Consensus pattern (98 bp):
ATTCCTCTAAGGAAATACTCTAACCTACTTTTTAAAACTTGTCAAGATCTGAAACTTATTCTTGC
CTAAATTATCATTATCGGGGACACTCCAACCCC
Found at i:6556 original size:9 final size:10
Alignment explanation
Indices: 6533--6563 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
6523 TTGGTGGAAG
6533 TTTTTCAAAA
1 TTTTTCAAAA
6543 TTTTTCAAAA
1 TTTTTCAAAA
*
6553 TTTTTTAAAA
1 TTTTTCAAAA
6563 T
1 T
6564 AATATCACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (10 bp):
TTTTTCAAAA
Found at i:7704 original size:13 final size:13
Alignment explanation
Indices: 7686--7711 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7676 CAATTTTTTG
7686 TGTATCGATACAT
1 TGTATCGATACAT
7699 TGTATCGATACAT
1 TGTATCGATACAT
7712 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:7796 original size:20 final size:20
Alignment explanation
Indices: 7771--7843 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
7761 CATCCTTTTT
7771 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
7791 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
7812 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
7832 ATGTATCGATAC
1 ATGTATCGATAC
7844 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:7816 original size:21 final size:21
Alignment explanation
Indices: 7750--7826 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
7740 CTGCCAAGAA
*
7750 ATGTATCGATACATCCTTTTT-
1 ATGTATCGATACAT-TTTTTTC
****
7771 ATGTATCGATACA-TTGCAAC
1 ATGTATCGATACATTTTTTTC
7791 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACATTTTTTTC
7812 ATGTATCGATACATT
1 ATGTATCGATACATT
7827 GCAACATGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.29
21 31 0.69
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTTTTTC
Found at i:7816 original size:41 final size:41
Alignment explanation
Indices: 7750--7843 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
7740 CTGCCAAGAA
7750 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
7791 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
7832 ATGTATCGATAC
1 ATGTATCGATAC
7844 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:8445 original size:48 final size:48
Alignment explanation
Indices: 8390--8485 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
8380 AATTTTACGA
8390 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
8438 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
8486 TTATCTCCCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.25, C:0.29, G:0.08, T:0.38
Consensus pattern (48 bp):
AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
Found at i:10344 original size:13 final size:13
Alignment explanation
Indices: 10326--10364 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
10316 ATAATCACCC
*
10326 TGTATCGATACAG
1 TGTATCGATACAA
10339 TGTATCGATACAA
1 TGTATCGATACAA
10352 TGTATCGATACAA
1 TGTATCGATACAA
10365 GGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:12463 original size:15 final size:15
Alignment explanation
Indices: 12443--12473 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12433 ATTTCGTTTG
*
12443 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
12458 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
12473 G
1 G
12474 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:16626 original size:21 final size:19
Alignment explanation
Indices: 16600--16676 Score: 82
Period size: 21 Copynumber: 3.8 Consensus size: 19
16590 CTGCCAAGAA
16600 ATGTATCGATACATCCTTTTT
1 ATGTATCGATACAT--TTTTT
***
16621 ATGTATCGATACATTGCAAT
1 ATGTATCGATACATT-TTTT
16641 ATGTATCGATACATTTTTTT
1 ATGTATCGATACA-TTTTTT
16661 CATGTATCGATACATT
1 -ATGTATCGATACATT
16677 GCAACATGTA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
19 1 0.02
20 17 0.36
21 29 0.62
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.44
Consensus pattern (19 bp):
ATGTATCGATACATTTTTT
Found at i:16645 original size:20 final size:20
Alignment explanation
Indices: 16620--16713 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
16610 ACATCCTTTT
16620 TATGTATCGATACATTGCAA
1 TATGTATCGATACATTGCAA
****
16640 TATGTATCGATACATTTTTT
1 TATGTATCGATACATTGCAA
16660 TCATGTATCGATACATTGCAA
1 T-ATGTATCGATACATTGCAA
* *
16681 CATGTATCGATACTTTG-AA
1 TATGTATCGATACATTGCAA
*
16700 TTGTGTATCGATAC
1 -TATGTATCGATAC
16714 TTTTAGGGGT
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 43 0.72
21 15 0.25
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
TATGTATCGATACATTGCAA
Found at i:16666 original size:41 final size:41
Alignment explanation
Indices: 16600--16693 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 41
16590 CTGCCAAGAA
*
16600 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAT
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
16641 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
16682 ATGTATCGATAC
1 ATGTATCGATAC
16694 TTTGAATTGT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
40 5 0.10
41 45 0.90
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:19875 original size:155 final size:156
Alignment explanation
Indices: 19612--19994 Score: 348
Period size: 155 Copynumber: 2.5 Consensus size: 156
19602 TTACTAGTCC
* * * * * ** * *
19612 TTTTTAAGTCCTTTAGGGGTACCGA-ATACTTTCACATTGAAA-GTAT-TCCCTGAGGGTATTTT
1 TTTTTAAGTCCTCTAGGGTTGCCGAGATACTTTTACA-TCAAAGGTATATCTATAAGGGCATTTT
* * *** * *
19674 CATAATTTTTCAAAACTGAGTCTTAGGTTATCACCGGGTTTGCTTTTATGCAGAAGGTGGGTATT
65 CATAATTTTTCAAAACCGAGTCTTAGGTTATCACCAGGTCCACTTTTATGCAGAAGGTAGATATT
* * * * *
19739 TAGGATTGGTTCA-CTCATCTCTAGTC
130 TAGAATAGGTTCATCCCATCTCTAATA
* * * * * * *
19765 TTTTTAGGTCCTTTAGGGTTGCTGAGGTACTTTTACGTCGAAGGTATA-CTTATAGGGGCATTTT
1 TTTTTAAGTCCTCTAGGGTTGCCGAGATACTTTTACATCAAAGGTATATC-TATAAGGGCATTTT
* * * **
19829 CATAATTTTTTAAAACCGAGTGC-TAGGTTATTACTAGGTCCACTTTTATGGTGAAGGTAGATAT
65 CATAATTTTTCAAAACCGAGT-CTTAGGTTATCACCAGGTCCACTTTTATGCAGAAGGTAGATAT
* *
19893 TTAGAATAGGTTCATCCCTTTTCTAATA
129 TTAGAATAGGTTCATCCCATCTCTAATA
*
19921 TTTTTAAGTTCTCTAGGGTTGCCGAGATACTTTTACATCAAAGGTATATCTATAAGGGC-TCTTT
1 TTTTTAAGTCCTCTAGGGTTGCCGAGATACTTTTACATCAAAGGTATATCTATAAGGGCAT-TTT
*
19985 TATAATTTTT
65 CATAATTTTT
19995 AGAACCAACT
Statistics
Matches: 180, Mismatches: 42, Indels: 13
0.77 0.18 0.06
Matches are distributed among these distances:
153 24 0.13
154 13 0.07
155 72 0.40
156 70 0.39
157 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.41
Consensus pattern (156 bp):
TTTTTAAGTCCTCTAGGGTTGCCGAGATACTTTTACATCAAAGGTATATCTATAAGGGCATTTTC
ATAATTTTTCAAAACCGAGTCTTAGGTTATCACCAGGTCCACTTTTATGCAGAAGGTAGATATTT
AGAATAGGTTCATCCCATCTCTAATA
Found at i:20247 original size:155 final size:155
Alignment explanation
Indices: 20026--20546 Score: 649
Period size: 155 Copynumber: 3.4 Consensus size: 155
20016 ACCGAGTCAA
* * * *
20026 GTGGGTATTTAGGATAGGTTCATCCTTTTTAT-AGTCTTTTTTAAGTCTTTTAGGGGTACCAGGA
1 GTGGGCATTTAAGATAGGTTCATCCCTTTTATGAGTC-TTTTTAAGTCCTTTAGGGGTACCAGGA
* * *
20090 TACTTTCACGTTGAAGGTATCCTTTAGAGGTATTTTCATAATTTTTGGAACTAACTCTCAGGTCA
65 TACTTTCACGTCGAAGGTATCCTTTAGAGGTATTTTCGTAATTTTTAGAACTAACTCTCAGGTCA
* *
20155 TCATCGGGTCCACTATTATATCGAAG
130 TCATCGGGTCCACTTTTATGTCGAAG
* * *
20181 GTGGGTATTTAAAATAGGTTCATCCCTTTTAT-AGTCTTTTTTAAGTCTTTTAGGGGTACC-GAG
1 GTGGGCATTTAAGATAGGTTCATCCCTTTTATGAGTC-TTTTTAAGTCCTTTAGGGGTACCAG-G
* * * * *
20244 ATACTTTCACGTCGAATGTATCCTCTCGAGGTATTTTCGTAATTTTTAGAACCAACTCTTAGGTC
64 ATACTTTCACGTCGAAGGTATCCTTTAGAGGTATTTTCGTAATTTTTAGAACTAACTCTCAGGTC
** *
20309 ATCATCGGGTCTGCTTTTATGTCAAAG
129 ATCATCGGGTCCACTTTTATGTCGAAG
* * *
20336 GTGGGCATTT-AGATAGGTTCATCCCTTTTATGAGTCTTTTTAAGTCCTTTAGGGTTGCTAGGAT
1 GTGGGCATTTAAGATAGGTTCATCCCTTTTATGAGTCTTTTTAAGTCCTTTAGGGGTACCAGGAT
* * * *
20400 ACTTTTACGTCGAAGGTATACCTTTAGGGGTATTTTGGTAATTTTTTAGAACTAACTC-CTAGTT
66 ACTTTCACGTCGAAGGTAT-CCTTTAGAGGTATTTTCGTAA-TTTTTAGAACTAACTCTC-AGGT
* * *
20464 CGTCA-CTAGGTCCTCTTTTATGTCGAAG
128 CATCATC-GGGTCCACTTTTATGTCGAAG
* *
20492 GTGGGCATTTAGGATAGGTTCATCCCTTGTATGAGTCTTTTTAAGTCCTTTAGGG
1 GTGGGCATTTAAGATAGGTTCATCCCTTTTATGAGTCTTTTTAAGTCCTTTAGGG
20547 CTGTTAGGAT
Statistics
Matches: 320, Mismatches: 38, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
154 60 0.19
155 169 0.53
156 49 0.15
157 42 0.13
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.40
Consensus pattern (155 bp):
GTGGGCATTTAAGATAGGTTCATCCCTTTTATGAGTCTTTTTAAGTCCTTTAGGGGTACCAGGAT
ACTTTCACGTCGAAGGTATCCTTTAGAGGTATTTTCGTAATTTTTAGAACTAACTCTCAGGTCAT
CATCGGGTCCACTTTTATGTCGAAG
Found at i:20599 original size:311 final size:309
Alignment explanation
Indices: 20026--20601 Score: 700
Period size: 311 Copynumber: 1.9 Consensus size: 309
20016 ACCGAGTCAA
* * *
20026 GTGGGTATTTAGGATAGGTTCATCCTTTTTATAGTCTTTTTTAAGTCTTTTAGGGGTACCAGGAT
1 GTGGGCATTTAGGATAGGTTCATCCCTTTTATAGTCTTTTTTAAGTCCTTTAGGGGTACCAGGAT
* *
20091 ACTTTCACGTTGAAGGTATCCTTTAGAGGTATTTTCATAATTTTTGGAACTAACTCTCAGGTCAT
66 ACTTTCACGTCGAAGGTATCCTTTAGAGGTATTTTCATAATTTTTAGAACTAACTCTCAGGTCAT
* * *
20156 CATCGGGTCCACTATTATATCGAAGGTGGGTATTTAAAATAGGTTCATCCCTTTTATAGTCTTTT
131 CATCAGGTCCACTATTATATCGAAGGTGGGCATTTAAAATAGGTTCATCCCTTGTATAGTCTTTT
* * * ** * **
20221 TTAAGTCTTTTAGGGGTACCGAGATACTTTCACGTCGAATGTATCCTCTCGAGGTATTTTCGTAA
196 TTAAGTCCTTTAGGGGTA-CGAGATACTTTCACATCAAAAATATCCCCTAAAGGTATTTTCGTAA
20286 TTTTTAGAACCAACTCTTAGGTCATCATCGGGTCTGCTTTTATGTCAAAG
260 TTTTTAGAACCAACTCTTAGGTCATCATCGGGTCTGCTTTTATGTCAAAG
* * *
20336 GTGGGCATTTA-GATAGGTTCATCCCTTTTATGAGTC-TTTTTAAGTCCTTTAGGGTTGCTAGGA
1 GTGGGCATTTAGGATAGGTTCATCCCTTTTAT-AGTCTTTTTTAAGTCCTTTAGGGGTACCAGGA
* * ** *
20399 TACTTTTACGTCGAAGGTATACCTTTAGGGGTATTTTGGTAATTTTTTAGAACTAACTC-CTAGT
65 TACTTTCACGTCGAAGGTAT-CCTTTAGAGGTATTTTCATAA-TTTTTAGAACTAACTCTC-AGG
* * * * **
20463 TCGTCA-CTAGGTCCTCTTTTATGTCGAAGGTGGGCATTTAGGATAGGTTCATCCCTTGTATGAG
127 TCATCATC-AGGTCCACTATTATATCGAAGGTGGGCATTTAAAATAGGTTCATCCCTTGTAT-AG
* *
20527 TC-TTTTTAAGTCCTTTAGGGCTGTTA-G-GATACTTTTACATTAAAAATATCCCCTAAAGGCT-
190 TCTTTTTTAAGTCCTTTAGGG--G-TACGAGATACTTTCACATCAAAAATATCCCCTAAAGG-TA
*
20588 TTTTTGTAATTTTT
251 TTTTCGTAATTTTT
20602 CTTGAACTTA
Statistics
Matches: 223, Mismatches: 33, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
309 60 0.27
310 34 0.15
311 120 0.54
312 6 0.03
313 1 0.00
314 2 0.01
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (309 bp):
GTGGGCATTTAGGATAGGTTCATCCCTTTTATAGTCTTTTTTAAGTCCTTTAGGGGTACCAGGAT
ACTTTCACGTCGAAGGTATCCTTTAGAGGTATTTTCATAATTTTTAGAACTAACTCTCAGGTCAT
CATCAGGTCCACTATTATATCGAAGGTGGGCATTTAAAATAGGTTCATCCCTTGTATAGTCTTTT
TTAAGTCCTTTAGGGGTACGAGATACTTTCACATCAAAAATATCCCCTAAAGGTATTTTCGTAAT
TTTTAGAACCAACTCTTAGGTCATCATCGGGTCTGCTTTTATGTCAAAG
Found at i:20609 original size:157 final size:156
Alignment explanation
Indices: 20178--20601 Score: 414
Period size: 157 Copynumber: 2.7 Consensus size: 156
20168 TATTATATCG
* * * * * * *
20178 AAGGTGGGTATTTAAAATAGGTTCATCCCTTTTAT-AGTCTTTTTTAAGTCTTTTAGGGGTAC-C
1 AAGGTGGGCATTT-AGATAGGTTCATCCCTTGTATGAGTC-TTTTTAAGTCCTTTAGGGCTGCTA
* * * ** ** * * *
20241 GAGATACTTTCACGTCGAATGTAT-CCTCTCGAGG-TATTTTCGTAA-TTTTTAGAACCAACTCT
64 G-GATACTTTTACATCAAAAATATACC-CTAAAGGCTATTTTGGTAATTTTTTAGAACTAACTCC
* * *
20303 TAGGTCATCA-TCGGGT-CTGCTTTTATGTCA
127 TAGTTCGTCACT-AGGTCCT-CTTTTATGTCA
* *
20333 AAGGTGGGCATTTAGATAGGTTCATCCCTTTTATGAGTCTTTTTAAGTCCTTTAGGGTTGCTAGG
1 AAGGTGGGCATTTAGATAGGTTCATCCCTTGTATGAGTCTTTTTAAGTCCTTTAGGGCTGCTAGG
* * ** * * * *
20398 ATACTTTTACGTCGAAGGTATACCTTTAGGGGTATTTTGGTAATTTTTTAGAACTAACTCCTAGT
66 ATACTTTTACATCAAAAATATACCCTAAAGGCTATTTTGGTAATTTTTTAGAACTAACTCCTAGT
*
20463 TCGTCACTAGGTCCTCTTTTATGTCG
131 TCGTCACTAGGTCCTCTTTTATGTCA
*
20489 AAGGTGGGCATTTAGGATAGGTTCATCCCTTGTATGAGTCTTTTTAAGTCCTTTAGGGCTGTTAG
1 AAGGTGGGCATTTA-GATAGGTTCATCCCTTGTATGAGTCTTTTTAAGTCCTTTAGGGCTGCTAG
* * *
20554 GATACTTTTACATTAAAAATATCCCCTAAAGGCT-TTTTTGTAATTTTT
65 GATACTTTTACATCAAAAATATACCCTAAAGGCTATTTTGGTAATTTTT
20602 CTTGAACTTA
Statistics
Matches: 228, Mismatches: 33, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
154 62 0.27
155 29 0.13
156 63 0.28
157 74 0.32
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (156 bp):
AAGGTGGGCATTTAGATAGGTTCATCCCTTGTATGAGTCTTTTTAAGTCCTTTAGGGCTGCTAGG
ATACTTTTACATCAAAAATATACCCTAAAGGCTATTTTGGTAATTTTTTAGAACTAACTCCTAGT
TCGTCACTAGGTCCTCTTTTATGTCA
Found at i:27754 original size:52 final size:51
Alignment explanation
Indices: 27629--27798 Score: 152
Period size: 52 Copynumber: 3.3 Consensus size: 51
27619 GCCAATGTGT
* * *
27629 TGATTCAAGGCCAGTGGCATT-AGACCTAAAAATGAC-AAGAGTGCTAATATG
1 TGATTCAAGGCCAG-GACATTGAGACTTAAAAATGACAAAG-GTACTAATATG
* * *
27680 ATGATTCAAGGCTAGTAGCATTGAG-CTTAAAAATGACAAAGGTACCT-ATGTG
1 -TGATTCAAGGCCAGGA-CATTGAGACTTAAAAATGACAAAGGTA-CTAATATG
* *
27732 CTGATTCAAGGCCAGCGACATTG-GACTTAGAAAAAGATAAAGGTACTAATATG
1 -TGATTCAAGGCCAG-GACATTGAGACTTA-AAAATGACAAAGGTACTAATATG
27785 TCGATTCAAGGCCA
1 T-GATTCAAGGCCA
27799 ACGATGTTGG
Statistics
Matches: 97, Mismatches: 12, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
51 1 0.01
52 59 0.61
53 37 0.38
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (51 bp):
TGATTCAAGGCCAGGACATTGAGACTTAAAAATGACAAAGGTACTAATATG
Found at i:27924 original size:52 final size:51
Alignment explanation
Indices: 27838--28141 Score: 134
Period size: 52 Copynumber: 5.9 Consensus size: 51
27828 AGAAGAGTTC
* * * ** * *
27838 CAATGTGCTGATTCATGGCTAGTGACATTAGACTTGTAGATGAGAAGAATAT
1 CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAAATGAGAAGAAT-G
* * * *
27890 CAATATGCTGATTCAAGGCCAGCGACTTTGGACTTAAAAATTAGAAGAATG
1 CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAAATGAGAAGAATG
** * * ** * *
27941 CTAATGTGCTGATTCAAGGCTTGCAACATT-GTGCTTAGGAATGATAAAAATG
1 C-AATGTGCTGATTCAAGGCCAGCGACATTAG-ACTTAAAAATGAGAAGAATG
* * * * * * * * *
27993 CCAATTTGTTAATTCAAGGCCAACGATATCAGACTTAAAGATGACCAAG-GTG
1 -CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAAATGA-GAAGAATG
* * * * *
28045 CCAATATGCTGATCCAAAGCCAGCGATATTGGACTTAAGAAA-GA-AA-AAGGTG
1 -CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAA-AAATGAGAAGAA--TG
* * * * *
28097 CCAATGTGATGATTCAAGGCCAACAACATTGGACTTAGAAA-GAGA
1 -CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAAATGAGA
28142 TGGTTTGACA
Statistics
Matches: 186, Mismatches: 56, Indels: 20
0.71 0.21 0.08
Matches are distributed among these distances:
50 2 0.01
51 7 0.04
52 171 0.92
53 6 0.03
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (51 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAAATGAGAAGAATG
Found at i:28308 original size:33 final size:33
Alignment explanation
Indices: 28201--28739 Score: 470
Period size: 32 Copynumber: 16.7 Consensus size: 33
28191 TATAAAGAGA
*
28201 TGCCATCGACTTGTGTGGGCTTTTG-AGAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAGAGGGT
* *
28233 TGCCACCGATTTTTGTGGGCTTTT-AAGAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAGAGGGT
* ** *
28265 TGTCGTCGACTTGTGTGGGCTTTTGAAGGGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAGAGGGT
* *
28298 TGCCACCGACTTAG-GTGGGCTTTAGAAGAGGAT
1 TGCCACCGACTT-GTGTGGGCTTTTGAAGAGGGT
* * *
28331 TGCCACCAACTTGTGTAGGCTTTAG-A-AGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAGAGGGT
* *
28362 TGCCACCGACTTCTGTGGGCTTTAG-A-AGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAGAGGGT
** * * *
28393 TGCCATTGACTTATATGGGCTTTAGAAG-GGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAGAGGGT
** * * *
28425 TGCCACTAACTTGTGTAGG-TTTAGAAAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAGAGGGT
*
28457 TGCCACCAACTTGTGTGGGC-TTTGAAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAG-AGGGT
* *
28490 TGCCATCGACTTGTGTGGGC-TTTGAAGAAGAGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAG-AGGGT
* * * * * *
28523 TACCATCAATTTGTGTGGGC-TTTGAAAATGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAGAGGGT
* * *
28555 TGCTACCAACTTGTGTGGGC-TTTAAAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAG-AGGGT
* *
28588 TGCCACCAACTTGTGTAGGC-TTTGAA-AGAGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAGAG-GGT
28620 TGCCACCGACTTGTGTGGG-TTTTAGATA-AGGGT
1 TGCCACCGACTTGTGTGGGCTTTT-GA-AGAGGGT
* * *
28653 TGCCACAGACTTGTGT-AG-ATTTGAAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAG-AGGGT
* *
28685 TGCCACCGACTTATGTGGG-TTTTGAAAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAGAGGGT
*
28717 TGCCACCAACTTGTGTGGGCTTT
1 TGCCACCGACTTGTGTGGGCTTT
28740 AGAAAAGATT
Statistics
Matches: 423, Mismatches: 66, Indels: 35
0.81 0.13 0.07
Matches are distributed among these distances:
30 1 0.00
31 64 0.15
32 186 0.44
33 168 0.40
34 4 0.01
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (33 bp):
TGCCACCGACTTGTGTGGGCTTTTGAAGAGGGT
Found at i:28319 original size:65 final size:65
Alignment explanation
Indices: 28209--28739 Score: 466
Period size: 65 Copynumber: 8.2 Consensus size: 65
28199 GATGCCATCG
* * * ** *
28209 ACTTGTGTGGGCTTTTG-AGAGGGTTGCCACCGATTTTTGTGGGCTTTTAAGAGGGTTGTCGTCG
1 ACTTGTGTGGGCTTTTGAAGAGGGTTGCCACCGACTTGTGTGGGCTTTTAAGAGGGTTGCCACCA
* * *
28273 ACTTGTGTGGGCTTTTGAAGGGGGTTGCCACCGACTTAG-GTGGGCTTTAGAAGAGGATTGCCAC
1 ACTTGTGTGGGCTTTTGAAGAGGGTTGCCACCGACTT-GTGTGGGCTTT-TAAGAGGGTTGCCAC
28337 CA
64 CA
* * * **
28339 ACTTGTGTAGGCTTTAG-A-AGGGTTGCCACCGACTTCTGTGGGC-TTT-AGAAGGGTTGCCATT
1 ACTTGTGTGGGCTTTTGAAGAGGGTTGCCACCGACTTGTGTGGGCTTTTAAG-AGGGTTGCCACC
*
28400 G
65 A
* * * ** * * *
28401 ACTTATATGGGCTTTAGAAG-GGGTTGCCACTAACTTGTGTAGG-TTTAGAAAAGGGTTGCCACC
1 ACTTGTGTGGGCTTTTGAAGAGGGTTGCCACCGACTTGTGTGGGCTTT-TAAGAGGGTTGCCACC
28464 A
65 A
* * * * *
28465 ACTTGTGTGGGC-TTTGAAGAAGGGTTGCCATCGACTTGTGTGGGCTTTGAAGAAGAGTTACCAT
1 ACTTGTGTGGGCTTTTGAAG-AGGGTTGCCACCGACTTGTGTGGGCTTTTAAG-AGGGTTGCCAC
28529 CA
64 CA
* * * * * *
28531 ATTTGTGTGGGC-TTTGAAAATGGTTGCTACCAACTTGTGTGGGCTTTAAAGAAGGGTTGCCACC
1 ACTTGTGTGGGCTTTTGAAGAGGGTTGCCACCGACTTGTGTGGGCTTTTAAG-AGGGTTGCCACC
28595 A
65 A
* *
28596 ACTTGTGTAGGC-TTTGAA-AGAGGTTGCCACCGACTTGTGTGGG-TTTTAGATAAGGGTTGCCA
1 ACTTGTGTGGGCTTTTGAAGAG-GGTTGCCACCGACTTGTGTGGGCTTTTA-A-GAGGGTTGCCA
28658 -CA
63 CCA
* * * *
28660 GACTTGTGT-AG-ATTTGAAGAAGGGTTGCCACCGACTTATGTGGG-TTTTGAAAAGGGTTGCCA
1 -ACTTGTGTGGGCTTTTGAAG-AGGGTTGCCACCGACTTGTGTGGGCTTTT-AAGAGGGTTGCCA
28722 CCA
63 CCA
28725 ACTTGTGTGGGCTTT
1 ACTTGTGTGGGCTTT
28740 AGAAAAGATT
Statistics
Matches: 380, Mismatches: 62, Indels: 48
0.78 0.13 0.10
Matches are distributed among these distances:
61 2 0.01
62 23 0.06
63 30 0.08
64 92 0.24
65 172 0.45
66 61 0.16
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (65 bp):
ACTTGTGTGGGCTTTTGAAGAGGGTTGCCACCGACTTGTGTGGGCTTTTAAGAGGGTTGCCACCA
Found at i:29787 original size:19 final size:19
Alignment explanation
Indices: 29742--29798 Score: 96
Period size: 19 Copynumber: 2.9 Consensus size: 19
29732 ACTGCCAGTT
*
29742 TCATGTATCGATACAATTG
1 TCATGTATCGATACAATGG
29761 TCCATGTATCGATACAATGG
1 T-CATGTATCGATACAATGG
29781 TCATGTATCGATACAATG
1 TCATGTATCGATACAATG
29799 TATCAATACA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 18 0.50
20 18 0.50
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (19 bp):
TCATGTATCGATACAATGG
Found at i:30455 original size:52 final size:52
Alignment explanation
Indices: 30372--30687 Score: 350
Period size: 52 Copynumber: 6.1 Consensus size: 52
30362 TCAAACTATC
* * * *
30372 TCATTTTTAAGCCTAATGTCACTAGCCTTGAATCAACACATTGGCACCCTTA
1 TCATCTTTAAGTCTAATATCACTAGCCTTGAATCAGCACATTGGCACCCTTA
* * * * * *
30424 TCATGTTTAAGTCTAATGTCACTGGCCTTGAATCAGCACAATGGCACCTTTG
1 TCATCTTTAAGTCTAATATCACTAGCCTTGAATCAGCACATTGGCACCCTTA
* * * * * *
30476 TCATCTTTAAGTTTGATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTG
1 TCATCTTTAAGTCTAATATCACTAGCCTTGAATCAGCACATTGGCACCCTTA
* * *
30528 TCATCTTTAAGTTTGATATCACTAGCCTTGAATCAGCATATTGGCA-CCTCTA
1 TCATCTTTAAGTCTAATATCACTAGCCTTGAATCAGCACATTGGCACCCT-TA
30580 TCAT-TTTAA-TCCTAATATCACTAGCCTTGAATCAGCACATTGGCACCCTTA
1 TCATCTTTAAGT-CTAATATCACTAGCCTTGAATCAGCACATTGGCACCCTTA
* * ** * * * *
30631 TCATGTTTAAGTCTAATGTCGTTGGCCTTGAATCAGCACATTAGCACTCTTC
1 TCATCTTTAAGTCTAATATCACTAGCCTTGAATCAGCACATTGGCACCCTTA
30683 TCATC
1 TCATC
30688 CTTATCATCT
Statistics
Matches: 230, Mismatches: 29, Indels: 10
0.86 0.11 0.04
Matches are distributed among these distances:
50 1 0.00
51 44 0.19
52 184 0.80
53 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (52 bp):
TCATCTTTAAGTCTAATATCACTAGCCTTGAATCAGCACATTGGCACCCTTA
Found at i:30660 original size:155 final size:156
Alignment explanation
Indices: 30390--30677 Score: 402
Period size: 155 Copynumber: 1.9 Consensus size: 156
30380 AAGCCTAATG
* *
30390 TCACTAGCCTTGAATCAACACATTGGCACCCTTATCATGTTTAAGTCTAATGTCACTGGCCTTGA
1 TCACTAGCCTTGAATCAACACATTGGCACCCTTATCATGTTTAAGTCTAATATCACTAGCCTTGA
* * * * * *
30455 ATCAGCACAATGGCACCTTTGTCATCTTTAAGTTTGATATCGCTAGCCTTGAATCAGCATATTGG
66 ATCAGCACAATGGCACCCTTATCATCTTTAAGTCTAATATCGCTAGCCTTGAATCAGCACATTAG
30520 CACCTTTGTCATCTTTAAGTTTGATA
131 CACCTTTGTCATCTTTAAGTTTGATA
* *
30546 TCACTAGCCTTGAATCAGCATATTGGCA-CCTCTATCAT-TTTAA-TCCTAATATCACTAGCCTT
1 TCACTAGCCTTGAATCAACACATTGGCACCCT-TATCATGTTTAAGT-CTAATATCACTAGCCTT
* * * * *
30608 GAATCAGCACATTGGCACCCTTATCATGTTTAAGTCTAATGTCGTTGGCCTTGAATCAGCACATT
64 GAATCAGCACAATGGCACCCTTATCATCTTTAAGTCTAATATCGCTAGCCTTGAATCAGCACATT
30673 AGCAC
129 AGCAC
30678 TCTTCTCATC
Statistics
Matches: 115, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
154 1 0.01
155 82 0.71
156 32 0.28
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.34
Consensus pattern (156 bp):
TCACTAGCCTTGAATCAACACATTGGCACCCTTATCATGTTTAAGTCTAATATCACTAGCCTTGA
ATCAGCACAATGGCACCCTTATCATCTTTAAGTCTAATATCGCTAGCCTTGAATCAGCACATTAG
CACCTTTGTCATCTTTAAGTTTGATA
Found at i:34071 original size:21 final size:21
Alignment explanation
Indices: 34042--34086 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
34032 AAGTTTTCAT
*
34042 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
34062 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
34084 TTT
1 TTT
34087 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:34692 original size:9 final size:9
Alignment explanation
Indices: 34678--34710 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
34668 TCTGAGTCAC
34678 CATCTTCAT
1 CATCTTCAT
34687 CATCTTCAT
1 CATCTTCAT
34696 CATCTTCAT
1 CATCTTCAT
*
34705 CGTCTT
1 CATCTT
34711 TGATGGTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.18, C:0.33, G:0.03, T:0.45
Consensus pattern (9 bp):
CATCTTCAT
Found at i:36328 original size:13 final size:13
Alignment explanation
Indices: 36310--36335 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36300 CAATTTTTTG
36310 TGTATCGATACAT
1 TGTATCGATACAT
36323 TGTATCGATACAT
1 TGTATCGATACAT
36336 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:39375 original size:21 final size:21
Alignment explanation
Indices: 39342--39382 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39332 CTAAGTAAAA
39342 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
39363 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
39383 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:39447 original size:20 final size:19
Alignment explanation
Indices: 39422--39492 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
39412 ATCCTGAAAA
39422 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
39442 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
39461 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
39482 GTATCGATACA
1 GTATCGATACA
39493 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:39542 original size:53 final size:53
Alignment explanation
Indices: 39462--39598 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
39452 AAATTGCATA
*
39462 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACA-AAATATGTATCGATACAGGACATTGGCAGTAGCCAAAATT
* *
39516 GTATCGATACACATAATATGTATCGATACAGGTCATTGGCAGTAGCCAAAATT
1 GTATCGATACACAAAATATGTATCGATACAGGACATTGGCAGTAGCCAAAATT
*
39569 GTATAGATACACAAAATATGTATCGATACA
1 GTATCGATACACAAAATATGTATCGATACA
39599 TTGGTAGTAG
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 65 0.83
54 13 0.17
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.27
Consensus pattern (53 bp):
GTATCGATACACAAAATATGTATCGATACAGGACATTGGCAGTAGCCAAAATT
Found at i:39585 original size:18 final size:19
Alignment explanation
Indices: 39562--39598 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
39552 TGGCAGTAGC
39562 CAAAAT-TGTATAGATACA
1 CAAAATATGTATAGATACA
*
39580 CAAAATATGTATCGATACA
1 CAAAATATGTATAGATACA
39599 TTGGTAGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.27
Consensus pattern (19 bp):
CAAAATATGTATAGATACA
Found at i:39641 original size:10 final size:10
Alignment explanation
Indices: 39622--39652 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
39612 AATCTCATTT
39622 TCACTGTTCA
1 TCACTGTTCA
*
39632 TCACTATTCA
1 TCACTGTTCA
39642 TCACTGTTCA
1 TCACTGTTCA
39652 T
1 T
39653 GTATCGATAC
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:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:41955 original size:17 final size:17
Alignment explanation
Indices: 41933--41967 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
41923 CACTTCACGA
41933 TTTTATTTCAGGTTGAT
1 TTTTATTTCAGGTTGAT
41950 TTTTATTTCAGGTTGAT
1 TTTTATTTCAGGTTGAT
41967 T
1 T
41968 CGAAGGTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.06, G:0.17, T:0.60
Consensus pattern (17 bp):
TTTTATTTCAGGTTGAT
Found at i:43981 original size:19 final size:19
Alignment explanation
Indices: 43933--43984 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
43923 CAAACCCCAA
* *
43933 AATGTATTGACACAATAAT
1 AATGTATCGATACAATAAT
43952 AATGTATCGATACAATAAT
1 AATGTATCGATACAATAAT
43971 AATGTATCGATACA
1 AATGTATCGATACA
43985 TTTGGTTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (19 bp):
AATGTATCGATACAATAAT
Found at i:44018 original size:70 final size:71
Alignment explanation
Indices: 43883--44036 Score: 172
Period size: 70 Copynumber: 2.2 Consensus size: 71
43873 ATTTAACTGG
* * * * *
43883 ATGTATTGATACATTGAAGAATTTATCAATACATTTGAGTCAAACCCCAAAATGTATTGACACAA
1 ATGTATCGATACAATGAAGAATGTATCAATACATTTGAGTCAAAACCCAAAATGTATCGACACAA
*
43948 T-AATA
66 TGAAAA
* * *
43953 ATGTATCGATACAAT-AATAATGTATCGATACATTTG-GTTCAAAAACCCAGAAA-GTATCGATA
1 ATGTATCGATACAATGAAGAATGTATCAATACATTTGAG-TC-AAAACCCA-AAATGTATCGACA
44015 CAATGAAAA
63 CAATGAAAA
44024 ATGTATCGATACA
1 ATGTATCGATACA
44037 TTTGGATCAA
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
68 1 0.01
69 20 0.28
70 31 0.44
71 19 0.27
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (71 bp):
ATGTATCGATACAATGAAGAATGTATCAATACATTTGAGTCAAAACCCAAAATGTATCGACACAA
TGAAAA
Found at i:44076 original size:50 final size:50
Alignment explanation
Indices: 43950--44089 Score: 192
Period size: 50 Copynumber: 2.8 Consensus size: 50
43940 TGACACAATA
* *
43950 ATAATGTATCGATACAATAATAATGTATCGATACATTTGGTTCAAAAACCC
1 ATAATGTATCGATACAATAAAAATGTATCGATACATTTGGATC-AAAACCC
* * *
44001 AGAAAGTATCGATACAATGAAAAATGTATCGATACATTTGGATC-AATCCC
1 ATAATGTATCGATACAAT-AAAAATGTATCGATACATTTGGATCAAAACCC
*
44051 ATAATGTATCAATACAATAAAAAATGTATCGATACATTT
1 ATAATGTATCGATACAAT-AAAAATGTATCGATACATTT
44090 TCTTTCCTAA
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
50 40 0.51
51 16 0.20
52 23 0.29
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (50 bp):
ATAATGTATCGATACAATAAAAATGTATCGATACATTTGGATCAAAACCC
Found at i:46330 original size:41 final size:41
Alignment explanation
Indices: 46285--46362 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
46275 CAAGACCTCA
*
46285 TCCATTTTCACTACTACATATAATGCCTTTTAAGAGGCTCG
1 TCCATTTTCACTACTACATATAACGCCTTTTAAGAGGCTCG
46326 TCCATTTTCACTACTACATATAACGCCTTTTAAGAGG
1 TCCATTTTCACTACTACATATAACGCCTTTTAAGAGG
46363 ATAGCCTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (41 bp):
TCCATTTTCACTACTACATATAACGCCTTTTAAGAGGCTCG
Found at i:52509 original size:13 final size:13
Alignment explanation
Indices: 52470--52510 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
52460 ATACAAAGAT
52470 CAATGTATCGATA
1 CAATGTATCGATA
*
52483 AAATGTATCGATA
1 CAATGTATCGATA
*
52496 CAATGTATCAATA
1 CAATGTATCGATA
52509 CA
1 CA
52511 TTGAGTAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:52570 original size:13 final size:13
Alignment explanation
Indices: 52548--52605 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
52538 GGCAGTAGCT
*
52548 TTGTAGCGATACA
1 TTGTATCGATACA
52561 TTGTATCGATACAAAA
1 TTGTATCGATAC---A
52577 CTTATGTATCGATACA
1 --T-TGTATCGATACA
52593 TTGTATCGATACA
1 TTGTATCGATACA
52606 ACACTTATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:52586 original size:19 final size:19
Alignment explanation
Indices: 52562--52666 Score: 105
Period size: 19 Copynumber: 5.7 Consensus size: 19
52552 AGCGATACAT
52562 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
52581 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
52594 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
** *
52613 TGTATCGATACAGTTACTGTT
1 TGTATCGATACA-AAACT-TA
*
52634 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
52653 TGTATCGATACAAA
1 TGTATCGATACAAA
52667 TTGTTGAAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
13 11 0.15
14 1 0.01
16 2 0.03
18 1 0.01
19 37 0.52
20 6 0.08
21 13 0.18
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:52595 original size:32 final size:32
Alignment explanation
Indices: 52549--52624 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
52539 GCAGTAGCTT
*
52549 TGTAGCGATACATTGTATCGATACAAAACTTA
1 TGTATCGATACATTGTATCGATACAAAACTTA
*
52581 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAAAACTTA
52613 TGTATCGATACA
1 TGTATCGATACA
52625 GTTACTGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAAAACTTA
Found at i:60140 original size:79 final size:79
Alignment explanation
Indices: 60039--60201 Score: 254
Period size: 79 Copynumber: 2.1 Consensus size: 79
60029 TATGTTTTTC
* * * **
60039 TTTCTGAGCGGACACTTTAACCCCGGTTTTATTTCTGAAATACTGATTTTCCATAATCGGGGATA
1 TTTCTGAGCGGACACTTCAACCCCGATTTTATTTCTAAAATACCAATTTTCCATAATCGGGGATA
60104 CTCCAACCCCGTTA
66 CTCCAACCCCGTTA
* * *
60118 TTTCTGAGGGGATACTTCAACCCCGATTTTATTTCTAAAATACCAATTTTCCATAATTGGGGATA
1 TTTCTGAGCGGACACTTCAACCCCGATTTTATTTCTAAAATACCAATTTTCCATAATCGGGGATA
60183 CTCCAACCCCGTTA
66 CTCCAACCCCGTTA
60197 TTTCT
1 TTTCT
60202 AAAACATTGA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.36
Consensus pattern (79 bp):
TTTCTGAGCGGACACTTCAACCCCGATTTTATTTCTAAAATACCAATTTTCCATAATCGGGGATA
CTCCAACCCCGTTA
Found at i:60215 original size:48 final size:49
Alignment explanation
Indices: 60125--60304 Score: 184
Period size: 51 Copynumber: 3.6 Consensus size: 49
60115 TTATTTCTGA
* * * * *
60125 GGGGATACTTCAACCCCGATTTTATTTCTAAAATACCAATTTTCCATAATT
1 GGGGATACTCCAACCCCG--TTTATTTCTAAAACATCGATTTTCCATAATC
* * *
60176 GGGGATACTCCAACCCCG-TTATTTCTAAAACATTGATTTTTCACAATC
1 GGGGATACTCCAACCCCGTTTATTTCTAAAACATCGATTTTCCATAATC
* *
60224 GGAGATACTCTAACCCCGGTTTTATTTCTAAAACATCGATTTTCCATAATC
1 GGGGATACTCCAACCCC-G-TTTATTTCTAAAACATCGATTTTCCATAATC
* *
60275 GGGGGGATACTCCAACCTC-ATTATTTCTAA
1 --GGGGATACTCCAACCCCGTTTATTTCTAA
60305 GGGGATACTC
Statistics
Matches: 107, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
48 38 0.36
49 1 0.01
50 10 0.09
51 44 0.41
53 14 0.13
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.34
Consensus pattern (49 bp):
GGGGATACTCCAACCCCGTTTATTTCTAAAACATCGATTTTCCATAATC
Found at i:60363 original size:180 final size:178
Alignment explanation
Indices: 60056--60380 Score: 474
Period size: 180 Copynumber: 1.8 Consensus size: 178
60046 GCGGACACTT
*
60056 TAACCCCGGTTTTATTTCTGAAATACTGATTTTCCATAATCGGGGATACTCCAACCCCGTTATTT
1 TAACCCCGGTTTTATTTCTGAAATACTGATTTTCCATAATCGGGGATACTCCAACCCCATTATTT
* * * * * **
60121 CTGAGGGGATACTTCAACCCCGATTTTATTTCTAAAATACCAATTTTCCATAATTGGGGATACTC
66 CTAAGGGGATACTCCAACCCCGATTATATTTCCAAAACACCAATTTTCCATAATCAGGGATACTC
60186 CAACCCCGTTATTTCTAAAACATTGATTTTTCACAATCGGAGATACTC
131 CAACCCCGTTATTTCTAAAACATTGATTTTTCACAATCGGAGATACTC
*
60234 TAACCCCGGTTTTATTTCT-AAA-ACATCGATTTTCCATAATCGGGGGGATACTCCAACCTCATT
1 TAACCCCGGTTTTATTTCTGAAATAC-T-GATTTTCCATAATC--GGGGATACTCCAACCCCATT
** *
60297 ATTTCTAAGGGGATACTCCAACCTTGATTATATTTCCAAAACACCGATTTTCCATAATCAGGGAT
62 ATTTCTAAGGGGATACTCCAACCCCGATTATATTTCCAAAACACCAATTTTCCATAATCAGGGAT
* *
60362 ACTCCAATCCGGTTATTTC
127 ACTCCAACCCCGTTATTTC
60381 CGAGAGGATA
Statistics
Matches: 129, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
176 2 0.02
177 4 0.03
178 33 0.26
180 90 0.70
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (178 bp):
TAACCCCGGTTTTATTTCTGAAATACTGATTTTCCATAATCGGGGATACTCCAACCCCATTATTT
CTAAGGGGATACTCCAACCCCGATTATATTTCCAAAACACCAATTTTCCATAATCAGGGATACTC
CAACCCCGTTATTTCTAAAACATTGATTTTTCACAATCGGAGATACTC
Found at i:60410 original size:79 final size:80
Alignment explanation
Indices: 60227--60443 Score: 242
Period size: 79 Copynumber: 2.7 Consensus size: 80
60217 CACAATCGGA
* * *
60227 GATACTCTAACCCCGGTTTTATTTCTAAAACATCGATTTTCCATAATCGGGGGGATACTCCAACC
1 GATACTCTAACCCCGATTTTATTTCTAAAACACCGATTTTCCATAATC-GAGGGATACTCCAACC
* *
60292 TCATTATTTCTAAGGG
65 TCATTATTTCCAAGAG
* ** * *
60308 GATACTCCAACCTTGATTATATTTCCAAAACACCGATTTTCCATAATC-AGGGATACTCCAATCC
1 GATACTCTAACCCCGATTTTATTTCTAAAACACCGATTTTCCATAATCGAGGGATACTCCAA-CC
** *
60372 -GGTTATTTCCGAGAG
65 TCATTATTTCCAAGAG
* * * *
60387 GATACTCTAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATTG-GGGATACT
1 GATACTCTAACCCCGATTTTATTTCTAAAACACCGATTTTCCATAATCGAGGGATACT
60444 TTAACCCCAG
Statistics
Matches: 112, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
79 69 0.62
80 2 0.02
81 41 0.37
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (80 bp):
GATACTCTAACCCCGATTTTATTTCTAAAACACCGATTTTCCATAATCGAGGGATACTCCAACCT
CATTATTTCCAAGAG
Found at i:60477 original size:51 final size:51
Alignment explanation
Indices: 60386--60500 Score: 126
Period size: 51 Copynumber: 2.3 Consensus size: 51
60376 ATTTCCGAGA
* *
60386 GGATACTCTAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATTGG
1 GGATACTCTAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAATCGG
* *** *
60437 GGATACTTTAACCCC-AGTTTTATTT-TCAAAACATTGATTTTCCATAATCGG
1 GGATACTCTAACCCCGA-TTTTATTTCT-AAAACACCAATTTTCCACAATCGG
*
60488 GGATACTCCAACC
1 GGATACTCTAACC
60501 TTGTTATATC
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
50 2 0.04
51 51 0.96
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.35
Consensus pattern (51 bp):
GGATACTCTAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAATCGG
Found at i:63322 original size:22 final size:22
Alignment explanation
Indices: 63294--63348 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
63284 TGGACATGTT
63294 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
63316 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
63338 AAAAATGCATG
1 AAAAATGCATG
63349 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:64299 original size:20 final size:20
Alignment explanation
Indices: 64252--64326 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
64242 AAAAAGACAT
*
64252 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
64271 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
64292 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
*
64312 AATGCATCGATACAT
1 AATGTATCGATACAT
64327 CAGGGTATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:64321 original size:40 final size:39
Alignment explanation
Indices: 64249--64326 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
64239 GGTAAAAAGA
* * *
64249 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATACATCGATACATT
* *
64288 CATACATGTATCGATATATTGAAAAATGCATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATACATCGATACAT
64327 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATACATCGATACATT
Found at i:65139 original size:29 final size:29
Alignment explanation
Indices: 64802--66070 Score: 1821
Period size: 29 Copynumber: 44.2 Consensus size: 29
64792 ACAGTGGTGA
* *
64802 TTTGAAAAGGGTTGCCATTGACTTGCATGGGC
1 TTTGAAAAGAG-TGCCACTGACTTG--TGGGC
* *
64834 TTT-AAAAGGGTGCCACTGACGTGCGTGGGC
1 TTTGAAAAGAGTGCCACTGAC-T-TGTGGGC
* * *
64864 TTTG-AAAGAATGCCACTAACTCGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
64892 TTTGAAAGGA-TGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
64920 TTTG-AAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
64948 TTTGAAAAG-GTACCACTGACTTGCGTGAGC
1 TTTGAAAAGAGTGCCACTGACTT--GTGGGC
64978 TTT-AAAAGGAGTGCCACTGACTTGTGTGAGC
1 TTTGAAAA-GAGTGCCACTGACTTGTG-G-GC
*
65009 TTT-AAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
65037 TTTG-AAAGAGTGCCACTGAATTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
65065 TTCGCAATG-GTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
65093 TTTG-AAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
65121 TTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
65150 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
65179 TTTGAAAGGACTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
65208 TTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
65236 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
65265 TTTGAAAAG-GTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
65293 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
65322 TTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
65350 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
65379 TTTG-AAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
65407 TTTGAATAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
65436 TTTGAAAAG-GTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
65464 TTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
65492 TTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
65521 TTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
65550 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
65579 TTTG-AAAGGGTGCCACTGAGTTGTCGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
65607 TTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
65635 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
65664 TTTGAAAAG-GTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
65692 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
65721 TTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
65749 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
65778 TTTG-AAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
65806 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
65835 TTTGAAAAG-GTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
65863 TTTG-AAAGGGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
65891 TTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
65920 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
65949 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
65978 TTTG-AAAGGGTGCCACTGAGTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
*
66006 TTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
66035 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAAGAGTGCCACTGACTTGTGGGC
66064 TTTGAAA
1 TTTGAAA
66071 GGGATGAACA
Statistics
Matches: 1125, Mismatches: 83, Indels: 61
0.89 0.07 0.05
Matches are distributed among these distances:
27 15 0.01
28 483 0.43
29 538 0.48
30 56 0.05
31 29 0.03
32 4 0.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (29 bp):
TTTGAAAAGAGTGCCACTGACTTGTGGGC
Found at i:65156 original size:57 final size:57
Alignment explanation
Indices: 64802--66073 Score: 1851
Period size: 57 Copynumber: 22.2 Consensus size: 57
64792 ACAGTGGTGA
* * *
64802 TTTGAAAAGGGTTGCCATTGACTTGCATGGGCTTT-AAAAGGGTGCCACTGACGTGCGTGGGC
1 TTTG-AAAGGG-TGCCACTGACTTG--TGGGCTTTGAAAAGAGTGCCACTGAC-T-TGTGGGC
** * * *
64864 TTTGAAAGAATGCCACTAACTCGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
64920 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTACCACTGACTTGCGTGAGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGC
* *
64978 TTTAAAAGGAGTGCCACTGACTTGTGTGAGCTTT-AAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTG-G-GCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* * * * *
65037 TTTGAAAGAGTGCCACTGAATTGTGGGCTTCGCAATG-GTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
*
65093 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
65150 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGACTGCCACTGACTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
65208 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
65265 TTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
65322 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
*
65379 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAATAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
65436 TTTGAAAAGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
65492 TTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
65550 TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGAGTTGTCGGC
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
65607 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
65664 TTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
65721 TTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
65778 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* * *
65835 TTTGAAAAGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGATTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
65891 TTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
65949 TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGAGTTGTGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
66006 TTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
66064 TTTGAAAGGG
1 TTTGAAAGGG
66074 ATGAACATTC
Statistics
Matches: 1103, Mismatches: 87, Indels: 45
0.89 0.07 0.04
Matches are distributed among these distances:
56 178 0.16
57 629 0.57
58 223 0.20
59 32 0.03
60 16 0.01
61 21 0.02
62 4 0.00
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.29
Consensus pattern (57 bp):
TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
Found at i:67308 original size:1 final size:1
Alignment explanation
Indices: 67297--67359 Score: 63
Period size: 1 Copynumber: 63.0 Consensus size: 1
67287 TTGTTTGCTA
* * * * * * *
67297 TTTTTTCTTTTTTTTTGTTTTTTTGTTTTGTTTTTTTTTGTGTTTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
67360 GGGTGTAAAG
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.89
Consensus pattern (1 bp):
T
Found at i:67320 original size:13 final size:13
Alignment explanation
Indices: 67297--67359 Score: 74
Period size: 13 Copynumber: 4.8 Consensus size: 13
67287 TTGTTTGCTA
*
67297 TTTTTTCTTTTT-
1 TTTTTTTTTTTTG
*
67309 TTTTGTTTTTTTG
1 TTTTTTTTTTTTG
67322 TTTTGTTTTTTTTTG
1 -TTT-TTTTTTTTTG
*
67337 TGTTTTTTTTTTG
1 TTTTTTTTTTTTG
67350 TTTTTTTTTT
1 TTTTTTTTTT
67360 GGGTGTAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
12 10 0.23
13 19 0.44
14 5 0.12
15 9 0.21
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:67325 original size:23 final size:23
Alignment explanation
Indices: 67297--67358 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
67287 TTGTTTGCTA
*
67297 TTTTTTCTTTTTTTTTGT-TTTT
1 TTTTTTGTTTTTTTTTGTGTTTT
67319 TTGTTTTGTTTTTTTTTGTGTTTT
1 TT-TTTTGTTTTTTTTTGTGTTTT
67343 TTTTTTGTTTTTTTTT
1 TTTTTTGTTTTTTTTT
67359 TGGGTGTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
22 2 0.05
23 29 0.78
24 6 0.16
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.89
Consensus pattern (23 bp):
TTTTTTGTTTTTTTTTGTGTTTT
Found at i:75790 original size:16 final size:16
Alignment explanation
Indices: 75769--75800 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
75759 GATAAAGTGT
75769 TTGAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAA
75785 TTGAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAA
75801 AAAAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
TTGAAAAAAAAAAAAA
Found at i:75837 original size:21 final size:21
Alignment explanation
Indices: 75813--75869 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
75803 AAAAAATTTA
75813 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
75834 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
75855 AATGTATCGATACAT
1 AATGTATCGATACAT
75870 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:75949 original size:19 final size:19
Alignment explanation
Indices: 75925--75992 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
75915 AATTCAACAA
75925 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
75944 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
75959 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
75976 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
75993 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:75964 original size:13 final size:13
Alignment explanation
Indices: 75946--75970 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
75936 ACATAAGTTT
75946 TGTATCGATACAA
1 TGTATCGATACAA
75959 TGTATCGATACA
1 TGTATCGATACA
75971 TAAGTATTGT
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:75968 original size:32 final size:32
Alignment explanation
Indices: 75927--75989 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
75917 TTCAACAATT
*
75927 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
75959 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
75990 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:76050 original size:13 final size:13
Alignment explanation
Indices: 76032--76057 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
76022 CATTTTTCTG
76032 TGTATCGATACAT
1 TGTATCGATACAT
76045 TGTATCGATACAT
1 TGTATCGATACAT
76058 GGATCTTTGT
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:76054 original size:33 final size:33
Alignment explanation
Indices: 76012--76078 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
76002 GCCAAGGAAA
***
76012 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
76045 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
76078 T
1 T
76079 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Done.