Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold725
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: 47247
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Found at i:7787 original size:15 final size:16
Alignment explanation
Indices: 7765--7811 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
7755 GTAGACAAAC
**
7765 AAACAAAAGTCAAAAA
1 AAACAAAAAACAAAAA
7781 AAA-AAAAAACAAAAA
1 AAACAAAAAACAAAAA
7796 AAACAAAAAAACAAAA
1 AAAC-AAAAAACAAAA
7812 GAAAGTGTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 13 0.48
16 3 0.11
17 11 0.41
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.02
Consensus pattern (16 bp):
AAACAAAAAACAAAAA
Found at i:7806 original size:17 final size:16
Alignment explanation
Indices: 7776--7811 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
7766 AACAAAAGTC
7776 AAAAAAAAAAAAAACA
1 AAAAAAAAAAAAAACA
7792 AAAAAAACAAAAAAACA
1 AAAAAAA-AAAAAAACA
7809 AAA
1 AAA
7812 GAAAGTGTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAACA
Found at i:8164 original size:8 final size:8
Alignment explanation
Indices: 8132--8166 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
8122 CCTACTCTTC
8132 ACAAAAAA
1 ACAAAAAA
8140 A-AAAAAA
1 ACAAAAAA
*
8147 AAAAAAAA
1 ACAAAAAA
8155 ACAAAAAA
1 ACAAAAAA
8163 ACAA
1 ACAA
8167 GGGGAAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (8 bp):
ACAAAAAA
Found at i:8175 original size:1 final size:1
Alignment explanation
Indices: 8134--8163 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
8124 TACTCTTCAC
*
8134 AAAAAAAAAAAAAAAAAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8164 CAAGGGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:9321 original size:27 final size:27
Alignment explanation
Indices: 9246--9314 Score: 111
Period size: 27 Copynumber: 2.5 Consensus size: 27
9236 TTTTTCTCTT
*
9246 TTCAAAGCCCACGACTCCGTGGGCACTC
1 TTCAAAGCCCACAACTCCGT-GGCACTC
*
9274 TTCAAAGCCCAGAACTCCGTGGCACTC
1 TTCAAAGCCCACAACTCCGTGGCACTC
9301 TTCAAAGCCCACAA
1 TTCAAAGCCCACAA
9315 TCTCGTGCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 20 0.53
28 18 0.47
ACGTcount: A:0.28, C:0.38, G:0.17, T:0.17
Consensus pattern (27 bp):
TTCAAAGCCCACAACTCCGTGGCACTC
Found at i:9525 original size:33 final size:32
Alignment explanation
Indices: 9368--9749 Score: 184
Period size: 35 Copynumber: 11.9 Consensus size: 32
9358 CTCTTGTTTC
*
9368 TCTT-TTCAAAGCCCACGACTCCGT-GCA-C-
1 TCTTCTTCAAAGCCCACAACTCCGTGGCACCT
9396 TC-T-TT-AAAGCCCACAACTCCGTTGGCAACCTTT
1 TCTTCTTCAAAGCCCACAACTCCG-TGGC-ACC--T
* *
9429 TCTTTTTCAAAG-CCACAA-TCTGTGGGCACCCT
1 TCTTCTTCAAAGCCCACAACTCCGT-GGCA-CCT
*
9461 TCTTCTTTTCAAAG-CCACCAACATCTGTGGCACCT
1 TCTTC--TTCAAAGCCCA-CAAC-TCCGTGGCACCT
*
9496 TCTTCTTCAAAGCCCACGACTCCGCTGGCA---
1 TCTTCTTCAAAGCCCACAACTCCG-TGGCACCT
*
9526 -C-TCTTAAAAGCCC-CAACTCCGTGGGCA-CT
1 TCTTCTTCAAAGCCCACAACTCCGT-GGCACCT
* *
9555 TTTCTCTTTCAAAGCCCACACCT-C-TGGCACCT
1 TCT-TC-TTCAAAGCCCACAACTCCGTGGCACCT
* *
9587 TCTTCTTTTCACAG-CCACAACTCTGTGGCACCT
1 TCTTC--TTCAAAGCCCACAACTCCGTGGCACCT
*
9620 TCTTCTGTTCAAAAGCCCACGACTCCGTGGCACC-
1 TCTTC--TTC-AAAGCCCACAACTCCGTGGCACCT
*
9654 TCTT-TT--AAGCCCACAACTCTGTTGGCACTCT
1 TCTTCTTCAAAGCCCACAACTCCG-TGGCAC-CT
* * * *
9685 TTTTCTCCTAAGCCCACCAACTCTGTTGGCACTCT
1 TCTTCTTCAAAGCCCA-CAACTCCG-TGGCAC-CT
* * *
9720 TTTTCCTTC-TAGCCCCCAAACTCCGTGGCA
1 TCTT-CTTCAAAGCCCAC-AACTCCGTGGCA
9750 TCTTTAAAGC
Statistics
Matches: 286, Mismatches: 26, Indels: 78
0.73 0.07 0.20
Matches are distributed among these distances:
26 16 0.06
27 15 0.05
28 28 0.10
29 8 0.03
30 2 0.01
31 18 0.06
32 23 0.08
33 46 0.16
34 46 0.16
35 68 0.24
36 11 0.04
37 5 0.02
ACGTcount: A:0.20, C:0.37, G:0.14, T:0.29
Consensus pattern (32 bp):
TCTTCTTCAAAGCCCACAACTCCGTGGCACCT
Found at i:9552 original size:27 final size:28
Alignment explanation
Indices: 9499--9554 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
9489 GGCACCTTCT
* *
9499 TCTTCAAAGCCCACGACTCCGCTGGCAC
1 TCTTAAAAGCCCACAACTCCGCTGGCAC
9527 TCTTAAAAGCCC-CAACTCCG-TGGGCAC
1 TCTTAAAAGCCCACAACTCCGCT-GGCAC
9554 T
1 T
9555 TTTCTCTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 1 0.04
27 13 0.52
28 11 0.44
ACGTcount: A:0.23, C:0.39, G:0.18, T:0.20
Consensus pattern (28 bp):
TCTTAAAAGCCCACAACTCCGCTGGCAC
Found at i:9574 original size:129 final size:123
Alignment explanation
Indices: 9368--9682 Score: 420
Period size: 128 Copynumber: 2.5 Consensus size: 123
9358 CTCTTGTTTC
9368 TCTT-TTCAAAGCCCACGACTCCGT-GCACTCTTTAAAGCCCACAACTCCGTTGGCAACCTTTTC
1 TCTTCTTCAAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTTGGC-A-CTTTTC
* * *
9431 TTTTTCAAAGCCACAATCTGTGGGCACCCTTCTTCTTTTCAAAGCCACCAACATCTGTGGCACCT
64 TCTTTCAAAGCCAC-ACCTCT-GGCA-CCTTCTTCTTTTCAAAGCCA-CAAC-TCTGTGGCACCT
* *
9496 TCTTCTTCAAAGCCCACGACTCCGCTGGCACTCTTAAAAGCCC-CAACTCCGTGGGCACTTTTCT
1 TCTTCTTCAAAGCCCACGACTCCG-TGGCACTCTTTAAAGCCCACAACTCCGTTGGCACTTTTCT
*
9560 CTTTCAAAGCCCACACCTCTGGCACCTTCTTCTTTTCACAGCCACAACTCTGTGGCACCT
65 CTTTCAAAG-CCACACCTCTGGCACCTTCTTCTTTTCAAAGCCACAACTCTGTGGCACCT
* *
9620 TCTTCTGTTCAAAAGCCCACGACTCCGTGGCACCTCTTTTAAGCCCACAACTCTGTTGGCACT
1 TCTTC--TTC-AAAGCCCACGACTCCGTGGCA-CTCTTTAAAGCCCACAACTCCGTTGGCACT
9683 CTTTTTCTCC
Statistics
Matches: 168, Mismatches: 10, Indels: 18
0.86 0.05 0.09
Matches are distributed among these distances:
124 17 0.10
125 4 0.02
126 27 0.16
127 31 0.18
128 37 0.22
129 24 0.14
130 13 0.08
131 15 0.09
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (123 bp):
TCTTCTTCAAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTTGGCACTTTTCTC
TTTCAAAGCCACACCTCTGGCACCTTCTTCTTTTCAAAGCCACAACTCTGTGGCACCT
Found at i:9594 original size:31 final size:33
Alignment explanation
Indices: 9396--9708 Score: 138
Period size: 33 Copynumber: 9.6 Consensus size: 33
9386 CTCCGTGCAC
9396 TCTTT-AAAGCCCACAACTC-CGTTGGCAACCTT-T
1 TCTTTCAAAGCCCACAACTCTC--TGGC-ACCTTCT
*
9429 TCTTTTTCAAAG-CCACAA-TCTGTGGGCACCCTTCT
1 TC--TTTCAAAGCCCACAACTCTCT-GGCA-CCTTCT
*
9464 TCTTTTCAAAG-CCACCAACATCTGTGGCACCTTCT
1 TC-TTTCAAAGCCCA-CAAC-TCTCTGGCACCTTCT
* *
9499 TC-TTCAAAGCCCACGACTCCGCTGGCA----C-
1 TCTTTCAAAGCCCACAACT-CTCTGGCACCTTCT
* *
9527 TC-TTAAAAGCCC-CAACTC-CGTGGGCA-CTTTT
1 TCTTTCAAAGCCCACAACTCTC-T-GGCACCTTCT
9558 CTCTTTCAAAGCCCAC-AC-CTCTGGCACCTTCT
1 -TCTTTCAAAGCCCACAACTCTCTGGCACCTTCT
* *
9590 TCTTTTCACAG-CCACAACTCTGTGGCACCTTCT
1 TC-TTTCAAAGCCCACAACTCTCTGGCACCTTCT
*
9623 TCTGTTCAAAAGCCCACGACTC-CGTGGCACC-TC-
1 TCT-TTC-AAAGCCCACAACTCTC-TGGCACCTTCT
* *
9656 T-TTT--AAGCCCACAACTCTGTTGGCACTCTTTT
1 TCTTTCAAAGCCCACAACTCT-CTGGCAC-CTTCT
* *
9688 TC-TCCTAAGCCCACCAACTCT
1 TCTTTCAAAGCCCA-CAACTCT
9709 GTTGGCACTC
Statistics
Matches: 223, Mismatches: 18, Indels: 76
0.70 0.06 0.24
Matches are distributed among these distances:
25 1 0.00
26 2 0.01
27 8 0.04
28 23 0.10
29 7 0.03
30 1 0.00
31 13 0.06
32 22 0.10
33 51 0.23
34 37 0.17
35 45 0.20
36 8 0.04
37 5 0.02
ACGTcount: A:0.21, C:0.36, G:0.13, T:0.29
Consensus pattern (33 bp):
TCTTTCAAAGCCCACAACTCTCTGGCACCTTCT
Found at i:9672 original size:28 final size:28
Alignment explanation
Indices: 9632--9687 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
9622 TTCTGTTCAA
*
9632 AAGCCCACGACTCCG-TGGCACCTCTTTT
1 AAGCCCACAACTCCGTTGGCA-CTCTTTT
*
9660 AAGCCCACAACTCTGTTGGCACTCTTTT
1 AAGCCCACAACTCCGTTGGCACTCTTTT
9688 TCTCCTAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.20, C:0.36, G:0.16, T:0.29
Consensus pattern (28 bp):
AAGCCCACAACTCCGTTGGCACTCTTTT
Found at i:10326 original size:51 final size:49
Alignment explanation
Indices: 10160--10437 Score: 224
Period size: 51 Copynumber: 5.7 Consensus size: 49
10150 CTGGCATGAA
* * *
10160 TCAGCATATTGGCATCTTCATTTTTAAAGTCCAA-GTAGCT-GCCTTGAC
1 TCAGCACATTGGCACCTTCATCTTT-AAGTCCAATGTAGCTGGCCTTGAC
* *
10208 T-AGCACATT-GCA-CTTCAACCTTAAGTCCAA---ACGCTGGCCTTGA-
1 TCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA-GCTGGCCTTGAC
* *
10251 TGCAGCAC-TTGGCATTTCATCATCTTTACAGTCCAATGTAGCTGGCCTTGGAC
1 T-CAGCACATTGGCA--CCTTCATCTTTA-AGTCCAATGTAGCTGGCCTT-GAC
* * *
10304 TCAG-ACATTGGCACCTTCCATC-TTAAGTCCAATATTCGCTGGCC-TGAA
1 TCAGCACATTGGCACCTT-CATCTTTAAGTCCAAT-GTAGCTGGCCTTGAC
* *
10352 TCAGCACATATTGGCATC-TCATCTTTAAGACCCAATGTAGCTGGCCCCTTGAC
1 TCAGCAC--ATTGGCACCTTCATCTTTAAG-TCCAATGTAGCTGG--CCTTGAC
10405 TCAGCACATTGGCACCTTCATCTTTAAGTCCAA
1 TCAGCACATTGGCACCTTCATCTTTAAGTCCAA
10438 ATATGCGGCC
Statistics
Matches: 185, Mismatches: 19, Indels: 49
0.73 0.08 0.19
Matches are distributed among these distances:
42 1 0.01
43 4 0.02
44 17 0.09
45 15 0.08
46 3 0.02
47 7 0.04
48 15 0.08
49 22 0.12
50 25 0.14
51 40 0.22
52 25 0.14
53 11 0.06
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (49 bp):
TCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAC
Found at i:10374 original size:100 final size:98
Alignment explanation
Indices: 10147--10439 Score: 310
Period size: 100 Copynumber: 3.0 Consensus size: 98
10137 ACCTAAGTAC
* * *
10147 TCGCTGGCATGAATCAG--CATATTGGCATCTTCATTTTTAAAGTCCAA-GTAGCT-GCCTTGAC
1 TCGCTGGCCTGAATCAGCACATATTGGCATCATCATCTTT-AAGTCCAATGTAGCTGGCCTTGAC
* *
10208 T-AGCACATT-GCA-CTTCAACCTTAAGTCCAAA
65 TCAGCACATTGGCACCTTCCATCTTAAGTCCAAA
10239 -CGCTGGCCTTG-ATGCAGCAC---TTGGCATTTCATCATCTTTACAGTCCAATGTAGCTGGCCT
1 TCGCTGGCC-TGAAT-CAGCACATATTGGCA--TCATCATCTTTA-AGTCCAATGTAGCTGGCCT
10299 TGGACTCAG-ACATTGGCACCTTCCATCTTAAGTCCAATA
61 T-GACTCAGCACATTGGCACCTTCCATCTTAAGTCCAA-A
*
10338 TTCGCTGGCCTGAATCAGCACATATTGGCATC-TCATCTTTAAGACCCAATGTAGCTGGCCCCTT
1 -TCGCTGGCCTGAATCAGCACATATTGGCATCATCATCTTTAAG-TCCAATGTAGCTGG--CCTT
10402 GACTCAGCACATTGGCACCTT-CATCTTTAAGTCCAAA
62 GACTCAGCACATTGGCACCTTCCATC-TTAAGTCCAAA
10439 T
1 T
10440 ATGCGGCCTG
Statistics
Matches: 170, Mismatches: 6, Indels: 42
0.78 0.03 0.19
Matches are distributed among these distances:
91 15 0.09
92 6 0.04
93 16 0.09
94 7 0.04
95 5 0.03
96 9 0.05
97 5 0.03
98 16 0.09
99 3 0.02
100 31 0.18
101 24 0.14
102 27 0.16
103 6 0.04
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (98 bp):
TCGCTGGCCTGAATCAGCACATATTGGCATCATCATCTTTAAGTCCAATGTAGCTGGCCTTGACT
CAGCACATTGGCACCTTCCATCTTAAGTCCAAA
Found at i:10928 original size:17 final size:17
Alignment explanation
Indices: 10906--10940 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
10896 ATTCTTCCAA
10906 AATCCTCTCCAAACTCT
1 AATCCTCTCCAAACTCT
10923 AATCCTCTCCAAACTCT
1 AATCCTCTCCAAACTCT
10940 A
1 A
10941 CACCTATCTA
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:0.31, C:0.40, G:0.00, T:0.29
Consensus pattern (17 bp):
AATCCTCTCCAAACTCT
Found at i:11492 original size:33 final size:33
Alignment explanation
Indices: 11455--11521 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
11445 TTCAACGATT
11455 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
11488 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
11521 T
1 T
11522 TTAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:11493 original size:13 final size:13
Alignment explanation
Indices: 11475--11499 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11465 CATAAAATGT
11475 TGTATCGATACAA
1 TGTATCGATACAA
11488 TGTATCGATACA
1 TGTATCGATACA
11500 TATTTTTTTG
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:11583 original size:13 final size:13
Alignment explanation
Indices: 11565--11589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11555 ATTACTCACA
11565 TGTATCGATACAT
1 TGTATCGATACAT
11578 TGTATCGATACA
1 TGTATCGATACA
11590 CTGATCTTTG
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:11726 original size:52 final size:52
Alignment explanation
Indices: 11598--11718 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
11588 CACTGATCTT
*
11598 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
11650 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
11702 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
11719 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:19858 original size:61 final size:63
Alignment explanation
Indices: 19809--20534 Score: 563
Period size: 61 Copynumber: 11.3 Consensus size: 63
19799 TTTTTTCTTT
* * *
19809 AAAGCCCACAATTCCGTGGCACCTCATCTTTAAGTCCACAACTTCGTGGCA-C--C--CTTTT-
1 AAAGCCCACAACTCCGTGGCACCTC-TCTTTAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
* * *
19867 ACAGCCCACAATTCCGTGGCACCTCATCTTTAAGCCCACAACTCCGTGGCACTCTTTTTCTCTTT
1 AAAGCCCACAACTCCGTGGCACCTC-TCTTTAAGCCCACAACTCCGTGGCAC-C-TTCT-TCTTT
19932 TC
62 TC
* ** *
19934 AAAGCCCACGACTCCGTGGCA-CTCT-TCAAAGCCCACGACTCCGTGGCA----C-TC--TTC
1 AAAGCCCACAACTCCGTGGCACCTCTCTTTAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
* *
19988 AAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT
1 AAAGCCCACAACTCCGTGGCACC----TCTCTTT-AAGCCCACAACTCCGTGGCAC-C-TTCT-T
20053 CTTTTC
58 CTTTTC
* *
20059 AAAGCCCACGACTCCGTGGCA-CTCT-TTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
1 AAAGCCCACAACTCCGTGGCACCTCTCTTTAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
* * *
20120 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTG
1 AAAGCCCACAACTCCGTGGCACC-TC-TC-TTT--AAGCCCACAACTCCGTGGCACCTTCTTCTT
20185 TTC
61 TTC
* *
20188 AAAGCCCACGACTCCGTGGCA-CTCT-TTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
1 AAAGCCCACAACTCCGTGGCACCTCTCTTTAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
* * *
20249 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTG
1 AAAGCCCACAACTCCGTGGCACC-TC-TC-TTT--AAGCCCACAACTCCGTGGCACCTTCTTCTT
20314 TTC
61 TTC
* * * * * *
20317 AAAGCCCACGACTCCGTGGCA-CTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTC-CTCC
1 AAAGCCCACAACTCCGTGGCACCTCTCTTT-AAGCCCACAACTCCGTGGCAC-CTTCTTCTTTTC
* * *
20380 TAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCA---TC--CTT
1 AAAGCCCACAACTCCGTGGCAC-C--TCT-CTT-TAAGCCCACAACTCCGTGGCACCTTCTTCTT
20440 TT-
61 TTC
* * * * * * *
20442 -AAGCCCATAACTCCGTGGCACTTTTTTCATCTTTGAGTCCATAACTCCGTGGCACCTTTTTTTT
1 AAAGCCCACAACTCCGTGGCAC----CTC-TCTTTAAGCCCACAACTCCGTGGCACCTTCTTCTT
20506 TTC
61 TTC
20509 TTTTAAAGCCCACAACTCCGTGGCAC
1 ----AAAGCCCACAACTCCGTGGCAC
20535 TCTTTTTCCC
Statistics
Matches: 546, Mismatches: 59, Indels: 112
0.76 0.08 0.16
Matches are distributed among these distances:
54 23 0.04
55 1 0.00
56 2 0.00
58 48 0.09
59 3 0.01
60 2 0.00
61 132 0.24
62 10 0.02
63 51 0.09
64 55 0.10
65 6 0.01
66 23 0.04
67 22 0.04
68 121 0.22
69 3 0.01
70 1 0.00
71 23 0.04
72 20 0.04
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.30
Consensus pattern (63 bp):
AAAGCCCACAACTCCGTGGCACCTCTCTTTAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
Found at i:19961 original size:27 final size:27
Alignment explanation
Indices: 19931--20009 Score: 149
Period size: 27 Copynumber: 2.9 Consensus size: 27
19921 TTTTTCTCTT
19931 TTCAAAGCCCACGACTCCGTGGCACTC
1 TTCAAAGCCCACGACTCCGTGGCACTC
19958 TTCAAAGCCCACGACTCCGTGGCACTC
1 TTCAAAGCCCACGACTCCGTGGCACTC
*
19985 TTCAAAGCCCACAACTCCGTGGCAC
1 TTCAAAGCCCACGACTCCGTGGCAC
20010 CTTTTTCTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.24, C:0.41, G:0.18, T:0.18
Consensus pattern (27 bp):
TTCAAAGCCCACGACTCCGTGGCACTC
Found at i:20031 original size:34 final size:33
Alignment explanation
Indices: 19774--20573 Score: 559
Period size: 34 Copynumber: 24.9 Consensus size: 33
19764 TCAAATACCT
* * * * *
19774 TTTTAACGTCCACGACTCAGTGGCA-TTTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
* **
19806 -TTTAAAGCCCACAATTCCGTGGCACC-TCATC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
* *
19837 -TTT-AAGTCCACAACTTCGTGGCACC-----C
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
* * **
19863 TTTTACAGCCCACAATTCCGTGGCACC-TCATC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
19895 -TTT-AAGCCCACAACTCCGTGGCACTCTTTTTCTC
1 TTTTAAAGCCCACAACTCCGTGGCAC-C-TTTT-TC
*
19929 TTTTCAAAGCCCACGACTCCGTGGCA-C----TC
1 TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
* *
19958 -TTCAAAGCCCACGACTCCGTGGCA-C----TC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
*
19985 -TTCAAAGCCCACAACTCCGTGGCACCTTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
20017 TGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTC
1 T-TTTAAAGCCCACAACTCCGTGGCAC-C-TTTT-TC
*
20054 TTTTCAAAGCCCACGACTCCGTGGCA-C----TC
1 TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
*
20083 -TTTAAAGCCCACAACTCCGTGGCACCTTCTTC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
* *
20115 TTTTCAAAGCCCACAACTCTGTGGCACCTTCTTC
1 TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
* *
20149 TTTTCAAAGCCCACAACTCTGTGGCACCTTCTTC
1 TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
* *
20183 TGTTCAAAGCCCACGACTCCGTGGCA-C----TC
1 T-TTTAAAGCCCACAACTCCGTGGCACCTTTTTC
*
20212 -TTTAAAGCCCACAACTCCGTGGCACCTTCTTC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
* *
20244 TTTTCAAAGCCCACAACTCTGTGGCACCTTCTTC
1 TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
* *
20278 TTTTCAAAGCCCACAACTCTGTGGCACCTTCTTC
1 TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTC
* * *
20312 TGTTCAAAGCCCACGACTCCGTGGCA-C--TCT-
1 T-TTTAAAGCCCACAACTCCGTGGCACCTTTTTC
*
20342 TTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCC
1 TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-C
** *
20377 TCCT-AAGCCCACAACTCTGTGGCACTCTTTTTCC
1 TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-C
* *
20411 TTCT-AAGCCCACAACTCCGTGGCA-----TCC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
* *
20438 TTTT-AAGCCCATAACTCCGTGGCACTTTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
* * *
20470 ATCTTT-GAGTCCATAACTCCGTGGCACCTTTTTTTTTTC
1 -T-TTTAAAGCCCACAACTCCGTGGCACC-----TTTTTC
20509 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT--C
* *
20545 TTTT-AAGTCCACAACTCCGTGGCATCTTT
1 TTTTAAAGCCCACAACTCCGTGGCACCTTT
20574 CTCCCTTCCT
Statistics
Matches: 648, Mismatches: 57, Indels: 124
0.78 0.07 0.15
Matches are distributed among these distances:
26 1 0.00
27 115 0.18
28 27 0.04
29 27 0.04
30 39 0.06
31 31 0.05
32 9 0.01
33 12 0.02
34 273 0.42
35 31 0.05
36 12 0.02
37 45 0.07
38 19 0.03
39 7 0.01
ACGTcount: A:0.20, C:0.35, G:0.14, T:0.31
Consensus pattern (33 bp):
TTTTAAAGCCCACAACTCCGTGGCACCTTTTTC
Found at i:20219 original size:95 final size:97
Alignment explanation
Indices: 19803--20439 Score: 488
Period size: 95 Copynumber: 6.6 Consensus size: 97
19793 GTGGCATTTT
* * *
19803 TTCTTT-AAAGCCCACAATTCCGTGGCACCTCATCTTT--AAGTCCACAACTTCGTGGCA-C--C
1 TTCTTTCAAAGCCCACAACTCCGTGGCACCT--TCTTTCAAAGCCCACAACTCCGTGGCACCTTC
* * *
19862 --CTTTT-ACAGCCCACAATTCCGTGGCACC-TC
64 TTCTTTTCAAAGCCCACAACTCTGTGGCACCTTC
* *
19892 ATCTTT--AAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCA
1 TTCTTTCAAAGCCCACAACTCCGTGGCAC-C----T-TC-TTTCAAAGCCCACAACTCCGTGGCA
* *
19955 ----C-TC--TTCAAAGCCCACGACTCCGTGGCA----C
59 CCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTC
*
19983 -TC-TTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTC
1 TTCTTTCAAAGCCCACAACTCCGTGGCACC---TTCT-TTCAAAGCCCACAACTCCGTGGCAC-C
* * *
20046 TTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCA----C
61 -TTCT-TCTTTTCAAAGCCCACAACTCTGTGGCACCTTC
*
20081 -TCTTT-AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCT
1 TTCTTTCAAAGCCCACAACTCCGTGGCA-C--CTTC-TTTCAAAGCCCACAACTCCGTGGCACCT
20144 TCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTC
62 TCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTC
*
20180 TTCTGTTCAAAGCCCACGACTCCGTGGCA-C-TCTTT-AAAGCCCACAACTCCGTGGCACCTTCT
1 TTCT-TTCAAAGCCCACAACTCCGTGGCACCTTCTTTCAAAGCCCACAACTCCGTGGCACCTTCT
20242 TCTTTTCAAAGCCCACAACTCTGTGGCACCTTC
65 TCTTTTCAAAGCCCACAACTCTGTGGCACCTTC
* *
20275 TTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCTTCTGTTCAAAGCCCACGACTCCGTGGCA-C
1 TTC-TTTCAAAGCCCACAACTCCGTGGCA-C--CTTCT-TTCAAAGCCCACAACTCCGTGGCACC
*
20339 -TC-T-TTTT-AAAGCCCACAACTCTGTGGCACTCTTT
61 TTCTTCTTTTCAAAGCCCACAACTCTGTGGCAC-CTTC
* * * * * *
20373 TTCCTCCTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCATCC
1 TTCTTTCAAAGCCCACAACTCCGTGGCAC-C---TTCTTTCAAAGCCCACAACTCCGTGGCA-CC
20438 TT
61 TT
20440 TTAAGCCCAT
Statistics
Matches: 469, Mismatches: 29, Indels: 89
0.80 0.05 0.15
Matches are distributed among these distances:
87 1 0.00
88 44 0.09
89 12 0.03
90 3 0.01
91 22 0.05
92 2 0.00
93 6 0.01
94 19 0.04
95 130 0.28
96 10 0.02
97 69 0.15
98 88 0.19
99 8 0.02
100 9 0.02
101 6 0.01
102 40 0.09
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (97 bp):
TTCTTTCAAAGCCCACAACTCCGTGGCACCTTCTTTCAAAGCCCACAACTCCGTGGCACCTTCTT
CTTTTCAAAGCCCACAACTCTGTGGCACCTTC
Found at i:20232 original size:129 final size:129
Alignment explanation
Indices: 19809--20439 Score: 751
Period size: 129 Copynumber: 4.9 Consensus size: 129
19799 TTTTTTCTTT
* * * * * *
19809 AAAGCCCACAATTCCGTGGCACCTCATCTTTAAGTCCACAACTTCGTGGCACC--C-T-TTT-AC
1 AAAGCCCACGACTCCGTGGCA-CTC-T-TTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTCAA
* * * *
19869 AGCCCACAATTCCGTGGCACC-TCATC-TTT--AAGCCCACAACTCCGTGGCACTCTTTTTCTCT
63 AGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCAC-C-TTCTCTCT
*
19930 TTTC
126 GTTC
* *
19934 AAAGCCCACGACTCCGTGGCACTCTTCAAAGCCCACGACTCCGTGGCA----C-TC-TTCAAAGC
1 AAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTCAAAGC
* * * *
19993 CCACAACTCCGTGGCACCTTTTTCTGTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCTCTTT
66 CCACAACTCTGTGGCACCTTCTTCT-TTTCAAAGCCCACAACTCCGTGGCAC-C-TTCTCTCTGT
20057 TC
128 TC
20059 AAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAG
1 AAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTC-TTTCAAAG
*
20124 CCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCT-TCTGTTC
65 CCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTCTCTGTTC
20188 AAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAG
1 AAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTC-TTTCAAAG
*
20253 CCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCACCTTCT-TCTGTTC
65 CCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTCTCTGTTC
* * * * *
20317 AAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCTCCTA
1 AAAGCCCACGACTCCGTGGCACTC--TTTAAAGCCCACAACTCCGTGGCAC-CTTCTTCTTTCAA
* * *
20382 AGCCCACAACTCTGTGGCACTCTTTTTC-CTTCTAAGCCCACAACTCCGTGGCATCCTT
63 AGCCCACAACTCTGTGGCAC-CTTCTTCTTTTCAAAGCCCACAACTCCGTGGCA-CCTT
20440 TTAAGCCCAT
Statistics
Matches: 460, Mismatches: 27, Indels: 31
0.89 0.05 0.06
Matches are distributed among these distances:
120 4 0.01
121 21 0.05
122 21 0.05
123 1 0.00
124 6 0.01
125 101 0.22
129 160 0.35
130 5 0.01
131 73 0.16
132 68 0.15
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (129 bp):
AAAGCCCACGACTCCGTGGCACTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCTTTCAAAGC
CCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTCTCTCTGTTC
Found at i:20468 original size:27 final size:27
Alignment explanation
Indices: 20408--20461 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
20398 GCACTCTTTT
*
20408 TCCTTCTAAGCCCACAACTCCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
*
20435 TCCTTTTAAGCCCATAACTCCGTGGCA
1 TCCTTTTAAGCCCACAACTCCGTGGCA
20462 CTTTTTTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.37, G:0.15, T:0.26
Consensus pattern (27 bp):
TCCTTTTAAGCCCACAACTCCGTGGCA
Found at i:20503 original size:95 final size:97
Alignment explanation
Indices: 19839--20541 Score: 390
Period size: 95 Copynumber: 7.3 Consensus size: 97
19829 ACCTCATCTT
* * * * *
19839 TAAGTCCACAACTTCGTGGCAC-CCTTTTACAGCCCACAATTCCGTGGCAC-C----TCATCTTT
1 TAAGCCCACAACTCCGTGGCACTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCATC-CT
* *
19898 AAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTC
65 AAGCCCACAACTCTGTGGCAC-CTTTTT-TC-CTTC
* * * *
19934 AAAGCCCACGACTCCGTGGCACT-C-TTCAAAGCCCACGACTCCGTGGCACTC---TTCA----A
1 TAAGCCCACAACTCCGTGGCACTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCATCCTA
* *
19990 AGCCCACAACTCCGTGGCACC-TTTTT-CTGTT
66 AGCCCACAACTCTGTGGCACCTTTTTTCCT-TC
*
20021 TAAAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGACTCCGTGGCACTC--T
1 T-AAGCCCACAACTCCGTGGCA--C----TC-CTTTT-AAAGCCCACAACTCCGTGGCACTCTTT
*
20084 TT-A----AAGCCCACAACTCCGTGGCACCTTCTTCTT--TTC
57 TTCATCCTAAGCCCACAACTCTGTGGCACCTT-TT-TTCCTTC
* * * *
20120 AAAGCCCACAACTCTGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCAC-CTTCTTCT
1 TAAGCCCACAACTCCGTGGCA-C-TC--CTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTC-
* * * * *
20184 GTTCAAAGCCCACGACTCCGTGGCA-C-----T-CTT-
60 ATCCTAAGCCCACAACTCTGTGGCACCTTTTTTCCTTC
* *
20214 TAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTCAAAGCCCACAACTCTGTGGCAC-CTTCTTC
1 T-AAGCCCACAACTCCGTGGCA-C-TC--CTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTC
* * * * *
20278 TTTTCAAAGCCCACAACTCTGTGGCACC-TTCTTCTGTTC
60 -ATCCTAAGCCCACAACTCTGTGGCACCTTTTTTC-CTTC
* * * * *
20317 AAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCTCCTA
1 TAAGCCCACAACTCCGTGGCACTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCATCCTA
20382 AGCCCACAACTCTGTGGCA-CTCTTTTTCCTTC
66 AGCCCACAACTCTGTGGCACCT-TTTTTCCTTC
* *
20414 TAAGCCCACAACTCCGTGGCA-TCCTTTT-AAGCCCATAACTCCGTGGCACT-TTTTTCATCTTT
1 TAAGCCCACAACTCCGTGGCACTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCATC-CT
* * * * * *
20476 GAGTCCATAACTCCGTGGCACCTTTTTTTTTTCTTT
65 AAGCCCACAACTCTGTGGCACC---TTTTTTCCTTC
*
20512 TAAAGCCCACAACTCCGTGGCACTCTTTTT
1 T-AAGCCCACAACTCCGTGGCACTCCTTTT
20542 CCCTTTTAAG
Statistics
Matches: 509, Mismatches: 51, Indels: 91
0.78 0.08 0.14
Matches are distributed among these distances:
86 1 0.00
87 1 0.00
88 20 0.04
89 4 0.01
90 2 0.00
91 21 0.04
94 35 0.07
95 170 0.33
96 15 0.03
97 69 0.14
98 90 0.18
99 25 0.05
100 12 0.02
101 4 0.01
102 40 0.08
ACGTcount: A:0.20, C:0.35, G:0.14, T:0.31
Consensus pattern (97 bp):
TAAGCCCACAACTCCGTGGCACTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCATCCTA
AGCCCACAACTCTGTGGCACCTTTTTTCCTTC
Found at i:20527 original size:72 final size:72
Alignment explanation
Indices: 20437--20573 Score: 197
Period size: 73 Copynumber: 1.9 Consensus size: 72
20427 CCGTGGCATC
* * * *
20437 CTTTTAAGCCCATAACTCCGTGGCACT-TTTTT-CATCTTTGAGTCCATAACTCCGTGGCACCTT
1 CTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCCT-TTTAAGTCCACAACTCCGTGGCACCTT
20500 TTTTTTTT
65 TTTTTTTT
*
20508 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCATCTT
1 CTTTT-AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCACCTT
20573 T
65 T
20574 CTCCCTTCCT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
71 5 0.09
72 21 0.36
73 30 0.52
74 2 0.03
ACGTcount: A:0.18, C:0.30, G:0.12, T:0.39
Consensus pattern (72 bp):
CTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCACCTTT
TTTTTTT
Found at i:20596 original size:73 final size:71
Alignment explanation
Indices: 20442--20593 Score: 173
Period size: 73 Copynumber: 2.1 Consensus size: 71
20432 GCATCCTTTT
* * * * ***
20442 AAGCCCATAACTCCGTGGCACTTTTTTCATCTTTGAGTCCATAACTCCGTGGCACCTTTTTTTTT
1 AAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTCTCCCT
*
20507 TCTTTTA
66 TC-TCTA
* *
20514 AAGCCCACAACTCCGTGGCACTCTTTTTC-CCTTTTAAGTCCACAACTCCGTGGCATCTTTCTCC
1 AAGCCCACAACTCCGTGGCACT-TTTTTCATC-TTTAAGTCCACAACTCCGTGGCACCTTTCTCC
20578 CTTC-CTA
64 CTTCTCTA
20585 AAGCCCACA
1 AAGCCCACA
20594 CAAGTCGGTG
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
71 11 0.16
72 22 0.32
73 35 0.51
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.36
Consensus pattern (71 bp):
AAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTCTCCCT
TCTCTA
Found at i:20621 original size:33 final size:35
Alignment explanation
Indices: 20578--20647 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 35
20568 ATCTTTCTCC
20578 CTTCCTAAAGCCCACACAAGTCGGTGGCAA-CCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
20612 CTTCC-AAAGCCCACACAAGTCGGTGGCAACCCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
20646 CT
1 CT
20648 AAGCCCAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 24 0.69
34 11 0.31
ACGTcount: A:0.26, C:0.37, G:0.17, T:0.20
Consensus pattern (35 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
Found at i:20711 original size:49 final size:49
Alignment explanation
Indices: 20647--21207 Score: 661
Period size: 49 Copynumber: 11.6 Consensus size: 49
20637 GCAACCCTTC
*
20647 TAAGCCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCTT
*
20696 TAAGTCCAATGTAGCTGGCCTTGAATCAGCA-CATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATC-TTGGCATCTTCATCTT
* * * *
20739 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCATCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCTT
*
20788 TAAGTCCAATATCGCTGGCCTTGAATCAGCA-CATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATC-TTGGCATCTTCATCTT
* * *
20831 TAAGTCCAATATCGCTGGCATTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCTT
* * * *
20880 TAAGTCCAATGTAGCTGGCCTTGACTCAGCA-CATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATC-TTGGCATCTTCATCTT
* * *
20929 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCTT
* * *
20978 TAAGTCCAATGTAGCTGGCCTTGACTCAGCA-CATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATC-TTGGCATCTTCATCTT
* *
21027 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCTT
* * * *
21076 TAAGACCAATGTAGCTGGCCTTGACTCAGCA-CATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATC-TTGGCATCTTCATCTT
* *
21125 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATCTTGG--CATCTT-CATCTT
* *
21177 TAAGTTCAATGTAGCTGGCCTTGAATCAGCA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCA
21208 CGTTGACATC
Statistics
Matches: 436, Mismatches: 51, Indels: 47
0.82 0.10 0.09
Matches are distributed among these distances:
43 76 0.17
45 2 0.00
47 2 0.00
48 1 0.00
49 316 0.72
51 4 0.01
52 35 0.08
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCTT
Found at i:20955 original size:98 final size:98
Alignment explanation
Indices: 20642--21208 Score: 834
Period size: 98 Copynumber: 5.9 Consensus size: 98
20632 CGGTGGCAAC
* *
20642 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATCTTGGCATCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
20707 TAGCTGGCCTTGAATCAGCACATTGG------CA
65 TAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * *
20735 CCTTTAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCATCTTCACCTTTAAGTCCAATAT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
*
20800 CGCTGGCCTTGAATCAGCACATTGG------CA
66 AGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
20827 CCTTTAAGTCCAATATCGCTGGCATTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
*
20892 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
66 AGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
20925 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
*
20990 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
66 AGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
21023 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGACCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
*
21088 AGCTGGCCTTGACTCAGCACATTGGCACCTTCA
66 AGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
21121 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTCAA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG--CATCTT-CATCTTTAAGTCCAA
21186 TGTAGCTGGCCTTGAATCAGCAC
63 TGTAGCTGGCCTTGAATCAGCAC
21209 GTTGACATCT
Statistics
Matches: 442, Mismatches: 23, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
92 165 0.37
93 4 0.01
98 233 0.53
100 5 0.01
101 35 0.08
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (98 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCACCTTCA
Found at i:21273 original size:55 final size:55
Alignment explanation
Indices: 20828--21337 Score: 351
Period size: 49 Copynumber: 9.8 Consensus size: 55
20818 ACATTGGCAC
* *
20828 CTTTAAGTCCAATATCGCTGGCATTGAATCAGCATATTGGCATC-----T-TCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCTCAT
* * * * *
20877 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-C----CT-TCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCTCAT
* *
20926 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATC------ATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCTCAT
* * * *
20975 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-C----CT-TCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCTCAT
*
21024 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATC-----T-TCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCTCAT
* * * * *
21073 CTTTAAGACCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-C----CT-TCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCTCAT
*
21122 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C-ATTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCTCAT
* * ** *
21174 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCTTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCTCAT
* * * * * *
21229 CTTCAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG---C---AT--CTTTT-T--TC-TC
21294 AT
54 AT
*
21296 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
21338 CCTTCATCAT
Statistics
Matches: 383, Mismatches: 52, Indels: 40
0.81 0.11 0.08
Matches are distributed among these distances:
48 3 0.01
49 248 0.65
50 2 0.01
52 41 0.11
53 1 0.00
54 5 0.01
55 32 0.08
58 1 0.00
61 3 0.01
63 5 0.01
64 2 0.01
66 2 0.01
67 38 0.10
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCTCAT
Found at i:21617 original size:17 final size:17
Alignment explanation
Indices: 21595--21629 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
21585 ATTCTTCCAA
21595 AATCCTCTCCAAACTCT
1 AATCCTCTCCAAACTCT
21612 AATCCTCTCCAAACTCT
1 AATCCTCTCCAAACTCT
21629 A
1 A
21630 CACCTATCTA
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:0.31, C:0.40, G:0.00, T:0.29
Consensus pattern (17 bp):
AATCCTCTCCAAACTCT
Found at i:22189 original size:33 final size:33
Alignment explanation
Indices: 22152--22218 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
22142 TTCAACGATT
22152 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
22185 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
22218 T
1 T
22219 TTAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:22190 original size:13 final size:13
Alignment explanation
Indices: 22172--22196 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22162 CATAAAATGT
22172 TGTATCGATACAA
1 TGTATCGATACAA
22185 TGTATCGATACA
1 TGTATCGATACA
22197 TATTTTTTTG
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:22410 original size:52 final size:52
Alignment explanation
Indices: 22261--22402 Score: 225
Period size: 52 Copynumber: 2.7 Consensus size: 52
22251 CATTACTCAC
*
22261 ATGTATCGATACACTGATCT--TTGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACACT-AT-TAAATGTATCGATACATGCAGGCAAATTTGCCCAG
* *
22313 ATGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAG
22365 ATGTATCGATACACTATTAAATGTATCGATACATGCAG
1 ATGTATCGATACACTATTAAATGTATCGATACATGCAG
22403 ATAAATTTTC
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 81 0.98
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
ATGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAG
Found at i:28034 original size:52 final size:52
Alignment explanation
Indices: 27956--28138 Score: 303
Period size: 52 Copynumber: 3.5 Consensus size: 52
27946 CCCGAAATAT
* *
27956 GAAAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTGTATAATGTATCGATACATCTGG
* *
28008 GAAAATTTTCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTGTATAATGTATCGATACATCTGG
* *
28060 GCAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTGTATAATGTATCGATACATCTGG
*
28112 GCAAATTTGCCTGCATGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACA
28139 AAGATCAGTG
Statistics
Matches: 125, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTGTATAATGTATCGATACATCTGG
Found at i:28165 original size:13 final size:13
Alignment explanation
Indices: 28147--28171 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28137 CAAAGATCAG
28147 TGTATCGATACAA
1 TGTATCGATACAA
28160 TGTATCGATACA
1 TGTATCGATACA
28172 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:28253 original size:13 final size:13
Alignment explanation
Indices: 28235--28259 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28225 AAAAAAAATA
28235 TGTATCGATACAT
1 TGTATCGATACAT
28248 TGTATCGATACA
1 TGTATCGATACA
28260 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:30112 original size:33 final size:33
Alignment explanation
Indices: 30074--30140 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 33
30064 GTTACAAGCT
30074 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
*
30107 ATGTATCGATGCATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
30140 A
1 A
30141 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:30209 original size:13 final size:13
Alignment explanation
Indices: 30191--30216 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30181 CAATTTGTCC
30191 ATGTATCGATACA
1 ATGTATCGATACA
30204 ATGTATCGATACA
1 ATGTATCGATACA
30217 TTATACCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:30227 original size:20 final size:20
Alignment explanation
Indices: 30199--30236 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30189 CCATGTATCG
*
30199 ATACAATGTATCGATACATT
1 ATACAATGTATCAATACATT
*
30219 ATACCATGTATCAATACA
1 ATACAATGTATCAATACA
30237 AATAGTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (20 bp):
ATACAATGTATCAATACATT
Found at i:30236 original size:33 final size:34
Alignment explanation
Indices: 30170--30237 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 34
30160 TGCCAATTTC
* *
30170 ATGTATCGATACAATTTGTCCATGTATCGATACA
1 ATGTATCGATACAATTTGACCATGTATCAATACA
30204 ATGTATCGATAC-ATTAT-ACCATGTATCAATACA
1 ATGTATCGATACAATT-TGACCATGTATCAATACA
30237 A
1 A
30238 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
33 18 0.58
34 13 0.42
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.34
Consensus pattern (34 bp):
ATGTATCGATACAATTTGACCATGTATCAATACA
Found at i:30239 original size:97 final size:97
Alignment explanation
Indices: 30074--30298 Score: 380
Period size: 97 Copynumber: 2.3 Consensus size: 97
30064 GTTACAAGCT
* * * * *
30074 ATGTATCGATAC-ATTTCTTCATGTATCGATACAATGTATCGATGCATTGTACCATGTATCGATA
1 ATGTATCGATACAATTTATCCATGTATCGATACAATGTATCGATACATTATACCATGTATCAATA
30138 CAAATAGTGATAGGGTAGCTACTGCCAATTTC
66 CAAATAGTGATAGGGTAGCTACTGCCAATTTC
*
30170 ATGTATCGATACAATTTGTCCATGTATCGATACAATGTATCGATACATTATACCATGTATCAATA
1 ATGTATCGATACAATTTATCCATGTATCGATACAATGTATCGATACATTATACCATGTATCAATA
30235 CAAATAGTGATAGGGTAGCTACTGCCAATTTC
66 CAAATAGTGATAGGGTAGCTACTGCCAATTTC
*
30267 ATGTATCGATACAATTTATCCATGTATTGATA
1 ATGTATCGATACAATTTATCCATGTATCGATA
30299 TATTAAACAT
Statistics
Matches: 121, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
96 12 0.10
97 109 0.90
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (97 bp):
ATGTATCGATACAATTTATCCATGTATCGATACAATGTATCGATACATTATACCATGTATCAATA
CAAATAGTGATAGGGTAGCTACTGCCAATTTC
Found at i:30325 original size:13 final size:13
Alignment explanation
Indices: 30307--30333 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30297 TATATTAAAC
30307 ATGTATCGATACA
1 ATGTATCGATACA
30320 ATGTATCGATACA
1 ATGTATCGATACA
30333 A
1 A
30334 GGCAGCAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:32051 original size:166 final size:163
Alignment explanation
Indices: 31696--32177 Score: 492
Period size: 165 Copynumber: 2.9 Consensus size: 163
31686 AATGTATACA
* * * ** * * *
31696 AAAAATACAAAATTCATG-AAATAAATTGAATTTTTCAAAACTAATTTAAT-TGGAGTTTAATGA
1 AAAAATAAAAAACTCATGAAAATAAA-TAAATTTTTCAAAACCGATTAAATAT-GA-TTAAATAA
* * * *
31759 CAATATTAGATGAATTTTAAAAATTTTAAACCGAGAAAAAT-CTCT--AAAAAACCTTTATGGAA
63 TAATATTTGATGAATTTTAAAAATTATAAACCAAGAAAAATCCTCTCGAAAAAA--TTTATGGAA
* * * *
31821 TAGAAAATTCAGTTTTTCAAAAATAAGGGCATTTTCAAGG
126 TAGAAAACTCA-TTTTTCGAAAAT-AGGGAAATTTCAAGG
* * * *
31861 AAAAATAAAAAACTCATGAAAATAAAT-GATTTTCTTAAAACCGATTTAATATGAATTAAATGAT
1 AAAAATAAAAAACTCATGAAAATAAATAAATTTT-TCAAAACCGATTAAATATG-ATTAAATAAT
* * * *
31925 GATATTTGATAAATTTTAAAAATTATAAACCAAGAAAAATCCTTTCGAAAAATTTTATGGAATAG
64 AATATTTGATGAATTTTAAAAATTATAAACCAAGAAAAATCCTCTCGAAAAAATTTATGGAATAG
31990 AAAACTCGATTTTTCGAAAATAGGGAAATTTCAAGG
129 AAAACTC-ATTTTTCGAAAATAGGGAAATTTCAAGG
* * * *
32026 AAAAAATGAAAAACTCATGAAAATAAGTAAATTTTTCAAAACTGATTAAATGTGATTAAATAATA
1 -AAAAATAAAAAACTCATGAAAATAAATAAATTTTTCAAAACCGATTAAATATGATTAAATAATA
* * * * *
32091 ATATTTTATGAATTTTAAAATTTATAAACTAAGAAAAATCCACCCGAAAAAATTTATGGAGA-AG
65 ATATTTGATGAATTTTAAAAATTATAAACCAAGAAAAATCCTCTCGAAAAAATTTATGGA-ATAG
*
32155 AAAACTCCATATTTCGAAAATAG
129 AAAACT-CATTTTTCGAAAATAG
32178 TTAGAATTCC
Statistics
Matches: 268, Mismatches: 37, Indels: 24
0.81 0.11 0.07
Matches are distributed among these distances:
164 5 0.02
165 169 0.63
166 83 0.31
167 6 0.02
168 5 0.02
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (163 bp):
AAAAATAAAAAACTCATGAAAATAAATAAATTTTTCAAAACCGATTAAATATGATTAAATAATAA
TATTTGATGAATTTTAAAAATTATAAACCAAGAAAAATCCTCTCGAAAAAATTTATGGAATAGAA
AACTCATTTTTCGAAAATAGGGAAATTTCAAGG
Found at i:32226 original size:165 final size:164
Alignment explanation
Indices: 31724--32262 Score: 441
Period size: 165 Copynumber: 3.3 Consensus size: 164
31714 AAATAAATTG
* * * * * * *
31724 AATTTTTCAAAACTAATTTAAT-TGGAGTTTAATGACAATATTAGATGAATTTTAAAAATTTTAA
1 AATTTTTCAAAACTGATTTAATAT-GA-TTAAATAATAATATTTGATAAATTTTAAAAATTATAA
* * * * * *
31788 ACCGAGAAAAAT---CTCTAAAAAACCTTTATGGAATAGAAAA-TTCAGTTTTTCAAAAATAAGG
64 ACCAAGAAAAATCCACCCGAAAAAA--TTTATGGAATAGAAAACTCCA-TATTTCGAAAAT-AGG
* * * * * * *
31849 GCATTTTCAAGGAAAAATAAAAAACTCATGAAAATAAAT-
125 GAAATTCCAAGAAAAAATCAAAAACGCATGAAAATAAGTA
* * * * *
31888 GATTTTCTTAAAACCGATTTAATATGAATTAAATGATGATATTTGATAAATTTTAAAAATTATAA
1 AATTTT-TCAAAACTGATTTAATATG-ATTAAATAATAATATTTGATAAATTTTAAAAATTATAA
*** * * *
31953 ACCAAGAAAAATCCTTTCGAAAAATTTTATGGAATAGAAAACTCGATTTTTCGAAAATAGGGAAA
64 ACCAAGAAAAATCCACCCGAAAAAATTTATGGAATAGAAAACTCCATATTTCGAAAATAGGGAAA
* * *
32018 TTTCAAGGAAAAAATGAAAAACTCATGAAAATAAGTA
129 TTCCAA-GAAAAAATCAAAAACGCATGAAAATAAGTA
* * * * *
32055 AATTTTTCAAAACTGATTAAATGTGATTAAATAATAATATTTTATGAATTTTAAAATTTATAAAC
1 AATTTTTCAAAACTGATTTAATATGATTAAATAATAATATTTGATAAATTTTAAAAATTATAAAC
* **
32120 TAAGAAAAATCCACCCGAAAAAATTTATGGAGA-AGAAAACTCCATATTTCGAAAATAGTTAGAA
66 CAAGAAAAATCCACCCGAAAAAATTTATGGA-ATAGAAAACTCCATATTTCGAAAATAGGGA-AA
* * *
32184 TTCCAA-AAGAAAATCAATAACGCAT-ACAATCGAAG-G
129 TTCCAAGAA-AAAATCAAAAACGCATGAAAAT--AAGTA
* **
32220 AATTTTTCAAAATTGATTTAATAAAAATTAAATAATAATATTT
1 AATTTTTCAAAACTGATTTAAT-ATGATTAAATAATAATATTT
32263 AAAGAGTTTT
Statistics
Matches: 308, Mismatches: 52, Indels: 28
0.79 0.13 0.07
Matches are distributed among these distances:
164 11 0.04
165 185 0.60
166 98 0.32
167 7 0.02
168 7 0.02
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (164 bp):
AATTTTTCAAAACTGATTTAATATGATTAAATAATAATATTTGATAAATTTTAAAAATTATAAAC
CAAGAAAAATCCACCCGAAAAAATTTATGGAATAGAAAACTCCATATTTCGAAAATAGGGAAATT
CCAAGAAAAAATCAAAAACGCATGAAAATAAGTA
Found at i:35083 original size:22 final size:22
Alignment explanation
Indices: 35025--35101 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
35015 AATGCATATT
35025 TTGTTATAGTGATATATACATA
1 TTGTTATAGTGATATATACATA
*
35047 TAGTTATAGTGATATATACATA
1 TTGTTATAGTGATATATACATA
* * * *
35069 TTGTTATAATAATATGTCCATA
1 TTGTTATAGTGATATATACATA
*
35091 TTGTTACAGTG
1 TTGTTATAGTG
35102 CTATGTACGT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.44
Consensus pattern (22 bp):
TTGTTATAGTGATATATACATA
Found at i:35594 original size:22 final size:22
Alignment explanation
Indices: 35547--35595 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
35537 AATTATTATG
** *
35547 ATATGTACATTATGTTATTATG
1 ATATGTACATTATGTTACAATC
35569 ATATGTACATGT-TGTTACAATC
1 ATATGTACAT-TATGTTACAATC
35591 ATATG
1 ATATG
35596 GAATATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (22 bp):
ATATGTACATTATGTTACAATC
Found at i:37493 original size:21 final size:21
Alignment explanation
Indices: 37467--37508 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
37457 AAACCAATTC
37467 TTCACTGAA-GAAACCAACCCT
1 TTCACT-AACGAAACCAACCCT
*
37488 TTCACTAACGAAACTAACCCT
1 TTCACTAACGAAACCAACCCT
37509 ACACAAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.38, C:0.33, G:0.07, T:0.21
Consensus pattern (21 bp):
TTCACTAACGAAACCAACCCT
Found at i:41722 original size:16 final size:16
Alignment explanation
Indices: 41697--41735 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
41687 CTCAGGGAGA
*
41697 AGAT-AGGGTGGTTGG
1 AGATAAGGGTGGCTGG
41712 AGATAAGGGTGGCTGG
1 AGATAAGGGTGGCTGG
41728 AGATAAGG
1 AGATAAGG
41736 TTTGGCAGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.28, C:0.03, G:0.49, T:0.21
Consensus pattern (16 bp):
AGATAAGGGTGGCTGG
Found at i:43067 original size:26 final size:26
Alignment explanation
Indices: 43027--43083 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 26
43017 TTTCACATAT
43027 ATTATTATATAAT-AATATA-TA-AA
1 ATTATTATATAATAAATATATTACAA
43050 ATTATTATACTTACATAAATATATTACAA
1 ATTATTATA--TA-ATAAATATATTACAA
43079 ATTAT
1 ATTAT
43084 ATAAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 9 0.32
25 2 0.07
26 2 0.07
27 6 0.21
28 2 0.07
29 7 0.25
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTATTATATAATAAATATATTACAA
Found at i:43160 original size:21 final size:20
Alignment explanation
Indices: 43122--43164 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
43112 TTATCAATAA
*
43122 ATATTATAATTACTTAAATT
1 ATATTATAATTACATAAATT
*
43142 ATATTATCTATTACATAAATT
1 ATATTAT-AATTACATAAATT
43163 AT
1 AT
43165 TATGATTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTATAATTACATAAATT
Found at i:43755 original size:24 final size:24
Alignment explanation
Indices: 43727--43785 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
43717 TTGTTAAATA
*
43727 TATTATATTTGTAGAAAAAAATTT
1 TATTATATTTGAAGAAAAAAATTT
* *
43751 TATTAATTTTTGAAGTAAAAAATTT
1 TATT-ATATTTGAAGAAAAAAATTT
43776 TATATATATT
1 TAT-TATATT
43786 ATTTTATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 4 0.14
25 24 0.83
26 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (24 bp):
TATTATATTTGAAGAAAAAAATTT
Found at i:43791 original size:14 final size:14
Alignment explanation
Indices: 43772--43812 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
43762 GAAGTAAAAA
43772 ATTTTA-TATATATT
1 ATTTTATTA-ATATT
43786 ATTTTATTAATATT
1 ATTTTATTAATATT
43800 ATTATTATTAATA
1 ATT-TTATTAATA
43813 ATAAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTTATTAATATT
Found at i:43850 original size:18 final size:19
Alignment explanation
Indices: 43804--43842 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
43794 AATATTATTA
*
43804 TTATTAATAATAAATATAT
1 TTATTAATAATAAATAAAT
43823 TTATTAATAA-AAATAAAT
1 TTATTAATAATAAATAAAT
43841 TT
1 TT
43843 GATAATAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTATTAATAATAAATAAAT
Found at i:44528 original size:21 final size:20
Alignment explanation
Indices: 44466--44529 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 20
44456 TTTATGTGTA
*
44466 ACAAATTACATAAAAACATT
1 ACAAGTTACATAAAAACATT
* * *
44486 AGCAAGTTACGTATAAATATT
1 A-CAAGTTACATAAAAACATT
*
44507 ACAGAGTTACTTAAAAACATT
1 ACA-AGTTACATAAAAACATT
44528 AC
1 AC
44530 CGCAACTATA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
20 3 0.09
21 32 0.91
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.28
Consensus pattern (20 bp):
ACAAGTTACATAAAAACATT
Found at i:44889 original size:19 final size:19
Alignment explanation
Indices: 44865--44924 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
44855 TTTTATTAAA
44865 ATATTAAAAATTTTATTTT
1 ATATTAAAAATTTTATTTT
* *
44884 ATATTAATATTTATTATTTAT
1 ATATTAAAAATT-TTATTT-T
* *
44905 ATAATAAAAATATT-TTTT
1 ATATTAAAAATTTTATTTT
44923 AT
1 AT
44925 TAATTAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 3 0.09
19 13 0.39
20 8 0.24
21 9 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTAAAAATTTTATTTT
Found at i:44892 original size:40 final size:41
Alignment explanation
Indices: 44837--44924 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 41
44827 ATTTATATAA
* *
44837 ATTTTGATATGTAATAATTT-TTATTAAAATATTAAAAATTTT
1 ATTTT-ATATGTAAT-ATTTATTATTAAAATAATAAAAATATT
* *
44879 ATTTTATAT-TAATATTTATTATTTATATAATAAAAATATT
1 ATTTTATATGTAATATTTATTATTAAAATAATAAAAATATT
44919 -TTTTAT
1 ATTTTAT
44925 TAATTAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
39 10 0.24
40 22 0.54
41 4 0.10
42 5 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (41 bp):
ATTTTATATGTAATATTTATTATTAAAATAATAAAAATATT
Found at i:45055 original size:19 final size:19
Alignment explanation
Indices: 45031--45067 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
45021 TAAATATTTT
*
45031 AATAAAAAATTATTTAAAA
1 AATAAAAAATGATTTAAAA
*
45050 AATAAAACATGATTTAAA
1 AATAAAAAATGATTTAAA
45068 TCCCTCCCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (19 bp):
AATAAAAAATGATTTAAAA
Done.