Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2300
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: 160161
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:731 original size:13 final size:13
Alignment explanation
Indices: 713--738 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
703 CAATTTTTTG
713 TGTATCGATACAT
1 TGTATCGATACAT
726 TGTATCGATACAT
1 TGTATCGATACAT
739 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:803 original size:21 final size:20
Alignment explanation
Indices: 777--853 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 20
767 CTGCCAAGAA
777 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACAT-TTTTTT
*****
798 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTTTTTT
818 ATGTATCGATACATTTTTTT
1 ATGTATCGATACATTTTTTT
838 CATGTATCGATACATT
1 -ATGTATCGATACATT
854 GCAACATGTA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTT
Found at i:823 original size:20 final size:20
Alignment explanation
Indices: 798--870 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
788 CATCTTTTTT
798 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
818 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
839 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
859 ATGTATCGATAC
1 ATGTATCGATAC
871 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:837 original size:41 final size:41
Alignment explanation
Indices: 777--870 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
767 CTGCCAAGAA
*
777 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
*
818 ATGTATCGATACATTTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
859 ATGTATCGATAC
1 ATGTATCGATAC
871 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1532 original size:33 final size:32
Alignment explanation
Indices: 1489--1551 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 32
1479 CCCGTTTATT
1489 AAAAAATCTCCCCCTTAATCAAGTAATTCAAA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCAAA
1521 AAAAAAGTCTCCCCCTTAATCAAGTAATTCA
1 AAAAAA-TCTCCCCCTTAATCAAGTAATTCA
1552 TATCAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.20
33 24 0.80
ACGTcount: A:0.44, C:0.25, G:0.05, T:0.25
Consensus pattern (32 bp):
AAAAAATCTCCCCCTTAATCAAGTAATTCAAA
Found at i:3362 original size:13 final size:13
Alignment explanation
Indices: 3344--3382 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3334 ATAATCACCC
*
3344 TGTATCGATACAG
1 TGTATCGATACAA
3357 TGTATCGATACAA
1 TGTATCGATACAA
3370 TGTATCGATACAA
1 TGTATCGATACAA
3383 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:5475 original size:15 final size:15
Alignment explanation
Indices: 5455--5485 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5445 ATTTCGTTTG
*
5455 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
5470 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
5485 G
1 G
5486 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:9563 original size:13 final size:13
Alignment explanation
Indices: 9545--9570 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9535 CAATTTTTTG
9545 TGTATCGATACAT
1 TGTATCGATACAT
9558 TGTATCGATACAT
1 TGTATCGATACAT
9571 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:9635 original size:21 final size:20
Alignment explanation
Indices: 9609--9685 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 20
9599 CTGCCAAGAA
9609 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACAT-TTTTTT
*****
9630 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTTTTTT
9650 ATGTATCGATACATTTTTTT
1 ATGTATCGATACATTTTTTT
9670 CATGTATCGATACATT
1 -ATGTATCGATACATT
9686 GCAACATGTA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTT
Found at i:9655 original size:20 final size:20
Alignment explanation
Indices: 9630--9702 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
9620 CATCTTTTTT
9630 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
9650 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
9671 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
9691 ATGTATCGATAC
1 ATGTATCGATAC
9703 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:9669 original size:41 final size:41
Alignment explanation
Indices: 9609--9702 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
9599 CTGCCAAGAA
*
9609 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
*
9650 ATGTATCGATACATTTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
9691 ATGTATCGATAC
1 ATGTATCGATAC
9703 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:13976 original size:27 final size:27
Alignment explanation
Indices: 13938--14841 Score: 1070
Period size: 27 Copynumber: 32.9 Consensus size: 27
13928 TGGCATTTCT
* *
13938 TTTTAAGTCCACAACTTCGTGGCAACC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
13965 TTTTAAGTCCACAACTCCGTGGCAACC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* ** *
13992 TTTTAAGTCCATAACTCTATGGCAACC
1 TTTTAAGTCCACAACTCCGTGGCACCC
14019 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* * *
14046 TTTTAAGTCCACAGCTCCATGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* *
14073 TTTTAAGTCCACAACTCTGTGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
14100 TTTTAAAGTCCACAACTCCATGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
*
14128 TTTTAAGTCTACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* * *
14155 TTTAAAGTCCATAACTCCGTGGCACCT
1 TTTTAAGTCCACAACTCCGTGGCACCC
* *
14182 TTTTAAGTCCACAACTCCGCGACAGCCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
*
14210 ATTTTAATTCCACAACTCCGTGGCACCC
1 -TTTTAAGTCCACAACTCCGTGGCACCC
* *
14238 TTTTAAAGTCCACAACTCCATGGCATCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
* * *
14266 TTTTAAATTCCACAACTCGGTGGCACAC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
14294 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
14321 TTTTAAGTCCACAACTCCGTGACACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
14348 TTTTAAAGTCCACAACTCTGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
** *
14376 TTTTAAAGTCTGCAACTCCGTGGCATCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
* * ** *
14404 TTTAAAGTCCATAACTCTATGACACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* * * **
14431 TTTAAAGTCCATAACTCTGTGGCATTC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
14458 TTTTAAAGTCCATAACTCCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
* *
14486 TTTCAAAGTCCACAACTCCGTGGCACAC
1 TTT-TAAGTCCACAACTCCGTGGCACCC
14514 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
* *
14542 TTTTAAGTCTACAACTTCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* *
14569 TTTTAAGTCCACAACTCTGTGGTAGCCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
14597 TTTTGAAGTCCACAACTCCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
* *
14625 TTTTAAAGTCCACAACTCTGTGGTACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
14653 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
14680 TTTTAAGTCCACAACTCCGTGGCAGCCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
*
14708 TTTTTAAGTCCACAAGTCCGTGGCACCC
1 -TTTTAAGTCCACAACTCCGTGGCACCC
* * * *
14736 TTTTAAGTCCACAAGTCAGTGGCATCA
1 TTTTAAGTCCACAACTCCGTGGCACCC
* * * ** * *
14763 TTTCAAAGCCCACAAGTCAATGGCATCA
1 TTT-TAAGTCCACAACTCCGTGGCACCC
* *
14791 TTTTAAGTCCACAACTCTGTGGTACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* * *
14818 TTTTAAGCCCACAAGTCAGTGGCA
1 TTTTAAGTCCACAACTCCGTGGCA
14842 TCATTTCAAA
Statistics
Matches: 762, Mismatches: 102, Indels: 26
0.86 0.11 0.03
Matches are distributed among these distances:
27 434 0.57
28 266 0.35
29 62 0.08
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCGTGGCACCC
Found at i:14117 original size:28 final size:28
Alignment explanation
Indices: 13936--15197 Score: 1050
Period size: 28 Copynumber: 45.6 Consensus size: 28
13926 AATGGCATTT
* * *
13936 CTTTTTAAGTCCACAACTTCGTGGCAAC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
13964 CTTTT-AAGTCCACAACTCCGTGGCAAC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* ** *
13991 CTTTT-AAGTCCATAACTCTATGGCAAC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
14018 CTTTT-AAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
14045 CTTTT-AAGTCCACAGCTCCATGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
14072 CTTTT-AAGTCCACAACTCTGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
14099 CTTTTAAAGTCCACAACTCCATGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
14127 CTTTT-AAGTCTACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
14154 C-TTTAAAGTCCATAACTCCGTGGCA-C
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
14180 CTTTTTAAGTCCACAACTCCGCGACAGCC
1 CTTTTAAAGTCCACAACTCCGTGGCA-CC
*
14209 CATTTT-AATTCCACAACTCCGTGGCACC
1 C-TTTTAAAGTCCACAACTCCGTGGCACC
* *
14237 CTTTTAAAGTCCACAACTCCATGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
14265 CTTTTAAATTCCACAACTCGGTGGCACA
1 CTTTTAAAGTCCACAACTCCGTGGCACC
14293 CTTTT-AAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
14320 CTTTT-AAGTCCACAACTCCGTGACACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
14347 CTTTTAAAGTCCACAACTCTGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
** *
14375 CTTTTAAAGTCTGCAACTCCGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* ** *
14403 C-TTTAAAGTCCATAACTCTATGACACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * **
14430 C-TTTAAAGTCCATAACTCTGTGGCATT
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
14457 CTTTTAAAGTCCATAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
14485 CTTTCAAAGTCCACAACTCCGTGGCACA
1 CTTTTAAAGTCCACAACTCCGTGGCACC
14513 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
14541 CTTTT-AAGTCTACAACTTCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
14568 CTTTT-AAGTCCACAACTCTGTGGTAGCC
1 CTTTTAAAGTCCACAACTCCGTGGCA-CC
*
14596 CTTTTGAAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
14624 CTTTTAAAGTCCACAACTCTGTGGTACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
14652 CTTTT-AAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
14679 CTTTT-AAGTCCACAACTCCGTGGCAGCC
1 CTTTTAAAGTCCACAACTCCGTGGCA-CC
* *
14707 CTTTTTAAGTCCACAAGTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
14735 CTTTT-AAGTCCACAAGTCAGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * * ** *
14762 ATTTCAAAGCCCACAAGTCAATGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
14790 ATTTT-AAGTCCACAACTCTGTGGTACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * *
14817 CTTTT-AAGCCCACAAGTCAGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * * ** *
14844 ATTTCAAAGCCCACAAGTTAGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * * *
14872 ATTTCAAAG-CTCACAAGTCAGTGGCATC
1 CTTTTAAAGTC-CACAACTCCGTGGCACC
* *
14900 CTTTTCAAAGCCCACGAA-TCAGTGGCACC
1 CTTTT-AAAGTCCAC-AACTCCGTGGCACC
* ** * ** *
14929 CTTTCAAAACCCACAAGTTAGTGGCA-T
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
14956 CTTTTCCAAG-CTCACAAGTCAGTGGCA-C
1 CTTTT-AAAGTC-CACAACTCCGTGGCACC
* * * * *
14984 CTTTTCATAGACCACAAGTCAGTGGCATC
1 CTTTT-AAAGTCCACAACTCCGTGGCACC
* * * ** *
15013 CTTTCAAAGCCCACAAGTTAGTGGCA-T
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * * *
15040 CTCTTCAAAGCCCACAAGTCAGTGGCATC
1 CT-TTTAAAGTCCACAACTCCGTGGCACC
* * * * *
15069 ATTTTAAAGCCCACAAGTCAGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* **
15097 CTTTTCAAAGCCCACGAA-TCAATGGCACC
1 CTTTT-AAAGTCCAC-AACTCCGTGGCACC
* * * * **
15126 CTTTCATAGCCCACAAATTAGTGGCA-C
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * * *
15153 CTTTTCAAAGCCCACGAGTCAGTGGCATC
1 CTTTT-AAAGTCCACAACTCCGTGGCACC
* *
15182 CTTTCAAAGCCCACAA
1 CTTTTAAAGTCCACAA
15198 GTCAATGGCA
Statistics
Matches: 1064, Mismatches: 139, Indels: 62
0.84 0.11 0.05
Matches are distributed among these distances:
26 5 0.00
27 443 0.42
28 496 0.47
29 111 0.10
30 9 0.01
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.27
Consensus pattern (28 bp):
CTTTTAAAGTCCACAACTCCGTGGCACC
Found at i:14151 original size:82 final size:82
Alignment explanation
Indices: 13936--14859 Score: 1084
Period size: 82 Copynumber: 11.2 Consensus size: 82
13926 AATGGCATTT
* * * *
13936 CTTTTTAAGTCCACAACTTCGTGGCAACCTTTTAAGTCCACAACTCCGTGGCAACCTTTTAAGTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* ** *
14001 CATAACTCTATGGCAAC
66 CACAACTCCGTGGCATC
* * *
14018 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAGCTCCATGGCATCCTTTTAAGTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
14082 CACAACTCTGTGGCATC
66 CACAACTCCGTGGCATC
* * *
14099 CTTTTAAAGTCCACAACTCCATGGCACCCTTTTAAGTCTACAACTCCGTGGCACCCTTTAAAGTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
14164 CATAACTCCGTGGCA-C
66 CACAACTCCGTGGCATC
* * * *
14180 CTTTTTAAGTCCACAACTCCGCGACAGCCCATTTTAATTCCACAACTCCGTGGCACCCTTTTAAA
1 CTTTTAAAGTCCACAACTCCGTGGCA-CCC-TTTTAAGTCCACAACTCCGTGGCACCCTTTT-AA
*
14245 GTCCACAACTCCATGGCATC
63 GTCCACAACTCCGTGGCATC
* * *
14265 CTTTTAAATTCCACAACTCGGTGGCACACTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* *
14330 CACAACTCCGTGACACC
66 CACAACTCCGTGGCATC
* ** * *
14347 CTTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCTGCAACTCCGTGGCATCCTTTAAAGT
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGT
* ** *
14412 CCATAACTCTATGACA-C
65 CCACAACTCCGTGGCATC
* * * ** * *
14429 CCTTTAAAGTCCATAACTCTGTGGCATTCTTTTAAAGTCCATAACTCCGTGGCACCCTTTCAAAG
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTT-TAAG
14494 TCCACAACTCCGTGGCA-C
64 TCCACAACTCCGTGGCATC
* *
14512 ACTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCTACAACTTCGTGGCACCCTTTTAAGT
1 -CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
* * *
14577 CCACAACTCTGTGGTAGCC
65 CCACAACTCCGTGGCA-TC
* * *
14596 CTTTTGAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGTACCCTTTTAAGT
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGT
*
14661 CCACAACTCCGTGGCACC
65 CCACAACTCCGTGGCATC
*
14679 CTTTT-AAGTCCACAACTCCGTGGCAGCCCTTTTTAAGTCCACAAGTCCGTGGCACCCTTTTAAG
1 CTTTTAAAGTCCACAACTCCGTGGCA-CCC-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAG
* *
14743 TCCACAAGTCAGTGGCATC
64 TCCACAACTCCGTGGCATC
* * * * ** * * * * *
14762 ATTTCAAAGCCCACAAGTCAATGGCATCATTTTAAGTCCACAACTCTGTGGTACCCTTTTAAGCC
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* *
14827 CACAAGTCAGTGGCATC
66 CACAACTCCGTGGCATC
* * *
14844 ATTTCAAAGCCCACAA
1 CTTTTAAAGTCCACAA
14860 GTTAGTGGCA
Statistics
Matches: 735, Mismatches: 93, Indels: 28
0.86 0.11 0.03
Matches are distributed among these distances:
81 96 0.13
82 279 0.38
83 228 0.31
84 110 0.15
85 22 0.03
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28
Consensus pattern (82 bp):
CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
CACAACTCCGTGGCATC
Found at i:14360 original size:138 final size:137
Alignment explanation
Indices: 13936--14841 Score: 1102
Period size: 138 Copynumber: 6.6 Consensus size: 137
13926 AATGGCATTT
* * * *
13936 CTTTTTAAGTCCACAACTTCGTGGCAACCTTTT-AAGTCCACAACTCCGTGGCAACCTTTTAAGT
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGT
* ** * * *
14000 CCATAACTCTATGGCAACCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAGCTCCA
66 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCG
*
14065 TGGCATC
131 TGGCACC
* * *
14072 CTTTT-AAGTCCACAACTCTGTGGCATCCTTTTAAAGTCCACAACTCCATGGCACCCTTTTAAGT
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGT
* * * *
14136 CTACAACTCCGTGGCACCCTTTAAAGTCCATAACTCCGTGGCACCTTTTTAAGTCCACAACTCCG
66 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCG
* *
14201 CGACAGCC
131 TGGCA-CC
* * *
14209 CATTTT-AATTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCATGGCATCCTTTTAAA
1 C-TTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AA
* * *
14273 TTCCACAACTCGGTGGCACACTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTC
64 GTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTC
*
14338 CGTGACACC
129 CGTGGCACC
* ** * *
14347 CTTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCTGCAACTCCGTGGCATCCTTTAAAGT
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGT
* ** * * * * ** *
14412 CCATAACTCTATGACACCCTTTAAAGTCCATAACTCTGTGGCATTCTTTTAAAGTCCATAACTCC
66 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCC
14477 GTGGCACC
130 GTGGCACC
* *
14485 CTTTCAAAGTCCACAACTCCGTGGCACACTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGT
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGT
* * * *
14550 CTACAACTTCGTGGCACCCTTTTAAGTCCACAACTCTGTGGTAGCCCTTTTGAAGTCCACAACTC
66 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTT-AAGTCCACAACTC
14615 CGTGGCACC
129 CGTGGCACC
* *
14624 CTTTTAAAGTCCACAACTCTGTGGTACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGT
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGT
* *
14688 CCACAACTCCGTGGCAGCCCTTTTTAAGTCCACAAGTCCGTGGCACCCTTTTAAGTCCACAAGTC
66 CCACAACTCCGTGGCA-CCC-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTC
* *
14753 AGTGGCATC
129 CGTGGCACC
* * * * ** * * * * *
14762 ATTTCAAAGCCCACAAGTCAATGGCATCATTTT-AAGTCCACAACTCTGTGGTACCCTTTTAAGC
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGT
* *
14826 CCACAAGTCAGTGGCA
66 CCACAACTCCGTGGCA
14842 TCATTTCAAA
Statistics
Matches: 666, Mismatches: 95, Indels: 16
0.86 0.12 0.02
Matches are distributed among these distances:
135 24 0.04
136 92 0.14
137 49 0.07
138 349 0.52
139 131 0.20
140 21 0.03
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (137 bp):
CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGT
CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCG
TGGCACC
Found at i:15086 original size:197 final size:196
Alignment explanation
Indices: 14727--15293 Score: 741
Period size: 197 Copynumber: 2.9 Consensus size: 196
14717 CCACAAGTCC
* * * * * *
14727 GTGGCACCCTTT-TAAGTCCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTCAATGGCATCA
1 GTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCC
* * * * * * *
14791 TTTT-AAGTCCACAACTCTGTGGTACCCTTTTAAGCCCACAAGTCAGTGGCATCAT-TTCAAAGC
66 TTTTCAAGACCACAAGTCAGTGGCATCCTTTAAAGCCCACAAGTTAGTGGCATC-TCTTCAAAGC
* * *
14854 CCACAAGTTAGTGGCATCATTTCAAAGCTCACAAGTCAGTGGCATCCTTTTCAAAGCCCACGAAT
130 CCACAAGTCAGTGGCATCATTTTAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACGAAT
14919 CA
195 CA
* * *
14921 GTGGCACCCTTTCAAAACCCACAAGTTAGTGGCATCTTTTCCAAGCTCACAAGTCAGTGGCA-CC
1 GTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCC
14985 TTTTCATAGACCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCTCTTCAAAG
66 TTTTCA-AGACCACAAGTCAGTGGCATCCTTT-AAAGCCCACAAGTTAGTGGCATCTCTTCAAAG
15050 CCCACAAGTCAGTGGCATCATTTTAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACGAA
129 CCCACAAGTCAGTGGCATCATTTTAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACGAA
15115 TCA
194 TCA
* * * * *
15118 ATGGCACCCTTTCATAGCCCACAAATTAGTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCATCC
1 GTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCC
* *
15183 -TTTCAAAGCCCACAAGTCAATGGCATCTCTTTAAAGCCCACAAGTTAGTGGCATC-CTTCCAAA
66 TTTTC-AAGACCACAAGTCAGTGGCATC-CTTTAAAGCCCACAAGTTAGTGGCATCTCTT-CAAA
* * * * *
15246 GCCTACGAGTCAGTGGCATCCTTTTAAGGCCTACACAAGTCGGTGGCA
128 GCCCACAAGTCAGTGGCATCATTTTAAAGCC--CACAAGTCAGTGGCA
15294 ACTTTCTCTA
Statistics
Matches: 328, Mismatches: 34, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
194 17 0.05
195 42 0.13
196 24 0.07
197 224 0.68
198 7 0.02
199 14 0.04
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (196 bp):
GTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCC
TTTTCAAGACCACAAGTCAGTGGCATCCTTTAAAGCCCACAAGTTAGTGGCATCTCTTCAAAGCC
CACAAGTCAGTGGCATCATTTTAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACGAATC
A
Found at i:15233 original size:56 final size:56
Alignment explanation
Indices: 14606--15293 Score: 549
Period size: 56 Copynumber: 12.3 Consensus size: 56
14596 CTTTTGAAGT
* * * * * * * * * * *
14606 CCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGGTA-CCCTTTTAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTTAAAGC
* * * * * * * * * * *
14661 CCACAACTCCGTGGCACCCTTT-TAAGTCCACAACTCCGTGGCAGCCCTTTTTAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTC-TTTAAAGC
* * * * *
14717 CCACAAGTCCGTGGCACCCTTT-TAAGTCCACAAGTCAGTGGCATCAT-TTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATC-TCTTTAAAGC
* * * * * * * * *
14772 CCACAAGTCAATGGCATCATTT-TAAGTCCACAACTCTGTGGTA-CCCTTTTAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTTAAAGC
* * *
14826 CCACAAGTCAGTGGCATCATTTCAAAGCCCACAAGTTAGTGGCATCAT-TTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATC-TCTTTAAAGC
* * *
14882 TCACAAGTCAGTGGCATCCTTTTCAAAGCCCACGAA-TCAGTGGCA-CCCTTTCAAAAC
1 CCACAAGTCAGTGGCATCC-TTTCAAAGCCCAC-AAGTCAGTGGCATCTCTTT-AAAGC
* * * * * * *
14939 CCACAAGTTAGTGGCATCTTTTCCAAGCTCACAAGTCAGTGGCACCT-TTTCATAGA
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTT-AAAGC
* *
14995 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCTCTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTTAAAGC
* *
15051 CCACAAGTCAGTGGCATCATTTTAAAGCCCACAAGTCAGTGGCATC-CTTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTC-TTT-AAAGC
* * * * * *
15108 CCACGAA-TCAATGGCACCCTTTCATAGCCCACAAATTAGTGGCACCT-TTTCAAAGC
1 CCAC-AAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTT-AAAGC
* *
15164 CCACGAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCTCTTTAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTTAAAGC
* * * * *
15220 CCACAAGTTAGTGGCATCCTTCCAAAGCCTACGAGTCAGTGGCATC-CTTTTAAGGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTC-TTTAAAGC
*
15276 CTACACAAGTCGGTGGCA
1 C--CACAAGTCAGTGGCA
15294 ACTTTCTCTA
Statistics
Matches: 526, Mismatches: 84, Indels: 43
0.81 0.13 0.07
Matches are distributed among these distances:
54 46 0.09
55 86 0.16
56 290 0.55
57 87 0.17
58 17 0.03
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (56 bp):
CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCTCTTTAAAGC
Found at i:16182 original size:20 final size:20
Alignment explanation
Indices: 16157--16255 Score: 99
Period size: 20 Copynumber: 4.8 Consensus size: 20
16147 TTTTTACCTA
* *
16157 AATGTATCAATACATTTTTC
1 AATGTATCGATACATTCTTC
* *** *
16177 AATGTATCGATATATGGATG
1 AATGTATCGATACATTCTTC
16197 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
*
16217 AATGTATCGATACATTCTACCC
1 AATGTATCGATACATTCT--TC
16239 AGATGTATCGATACATT
1 A-ATGTATCGATACATT
16256 GTAGTTAAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 47 0.73
22 2 0.03
23 15 0.23
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.37
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:17114 original size:22 final size:22
Alignment explanation
Indices: 17089--17143 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
17079 ACGCCTTTGA
17089 CCATGCATTTTTTTCCTATGTT
1 CCATGCATTTTTTTCCTATGTT
17111 CCATGCATTTTTTTCCTATGTT
1 CCATGCATTTTTTTCCTATGTT
17133 CCATGCATTTT
1 CCATGCATTTT
17144 AACATGTCCA
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:0.15, C:0.24, G:0.09, T:0.53
Consensus pattern (22 bp):
CCATGCATTTTTTTCCTATGTT
Found at i:21214 original size:20 final size:19
Alignment explanation
Indices: 21189--21226 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
21179 TAATAAATTT
21189 AATAATAAAGTAAAAATAAG
1 AATAAT-AAGTAAAAATAAG
*
21209 AATAATAATTAAAAATAA
1 AATAATAAGTAAAAATAA
21227 ATAAGAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (19 bp):
AATAATAAGTAAAAATAAG
Found at i:21489 original size:24 final size:24
Alignment explanation
Indices: 21462--21582 Score: 147
Period size: 24 Copynumber: 5.1 Consensus size: 24
21452 AATATAAGTC
*
21462 AAATATAAATAAAAAATTATTATA
1 AAATATAAAGAAAAAATTATTATA
* * *
21486 AAATATAAAGAAATAATTGTTATC
1 AAATATAAAGAAAAAATTATTATA
* *
21510 AAATATAAATAAACAATTATTATA
1 AAATATAAAGAAAAAATTATTATA
** *
21534 AAATAT-AA-AAATGATTGTTATA
1 AAATATAAAGAAAAAATTATTATA
21556 AAATATAAAGAAAAAATTATTATA
1 AAATATAAAGAAAAAATTATTATA
21580 AAA
1 AAA
21583 ATTCCAATCT
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
22 17 0.21
23 4 0.05
24 60 0.74
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (24 bp):
AAATATAAAGAAAAAATTATTATA
Found at i:21574 original size:46 final size:48
Alignment explanation
Indices: 21462--21582 Score: 192
Period size: 46 Copynumber: 2.6 Consensus size: 48
21452 AATATAAGTC
*
21462 AAATATAAATAAAAAATTATTATAAAATATAAAGAAATAATTGTTATC
1 AAATATAAATAAAAAATTATTATAAAATATAAAGAAATAATTGTTATA
* *
21510 AAATATAAATAAACAATTATTATAAAATAT-AA-AAATGATTGTTATA
1 AAATATAAATAAAAAATTATTATAAAATATAAAGAAATAATTGTTATA
*
21556 AAATATAAAGAAAAAATTATTATAAAA
1 AAATATAAATAAAAAATTATTATAAAA
21583 ATTCCAATCT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
46 37 0.54
47 2 0.03
48 29 0.43
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (48 bp):
AAATATAAATAAAAAATTATTATAAAATATAAAGAAATAATTGTTATA
Found at i:27388 original size:4 final size:4
Alignment explanation
Indices: 27379--27405 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
27369 ATCAAATCAA
27379 TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAA
27406 AAAGTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:28553 original size:3 final size:3
Alignment explanation
Indices: 28545--28584 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
28535 TCCATGGACA
*
28545 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTT CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
28585 GTGGGAATTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
CTC
Found at i:30222 original size:8 final size:8
Alignment explanation
Indices: 30209--30244 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
30199 CGGGGACCGC
30209 TTTTCTTT
1 TTTTCTTT
30217 TTTTCTTT
1 TTTTCTTT
30225 TTTTCTTT
1 TTTTCTTT
30233 TTTT-TTT
1 TTTTCTTT
30240 TTTTC
1 TTTTC
30245 ATTATCTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTCTTT
Found at i:32357 original size:33 final size:33
Alignment explanation
Indices: 32320--32382 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
32310 TTAAAAATAC
32320 ATTTTATTATTTAAAAT-ATATTAATATATTAAA
1 ATTTTATT-TTTAAAATAATATTAATATATTAAA
* * *
32353 ATTTTATTTTTATATTAATATTTATATATT
1 ATTTTATTTTTAAAATAATATTAATATATT
32383 TTATTATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 6 0.23
33 20 0.77
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (33 bp):
ATTTTATTTTTAAAATAATATTAATATATTAAA
Found at i:32366 original size:27 final size:27
Alignment explanation
Indices: 32336--32387 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
32326 TTATTTAAAA
32336 TATATTAATATATTA-AAATTTTATTTT
1 TATATTAATAT-TTATAAATTTTATTTT
*
32363 TATATTAATATTTATATATTTTATT
1 TATATTAATATTTATAAATTTTATT
32388 ATTAAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TATATTAATATTTATAAATTTTATTTT
Found at i:32387 original size:19 final size:19
Alignment explanation
Indices: 32344--32388 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
32334 AATATATTAA
*
32344 TATATTAAAATTTTATTTT
1 TATATTAAAATTTTATATT
*
32363 TATATTAATATTTATATATT
1 TATATTAAAATTT-TATATT
32383 T-TATTA
1 TATATTA
32389 TTAAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATATTAAAATTTTATATT
Found at i:32587 original size:19 final size:17
Alignment explanation
Indices: 32559--32601 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
32549 AGTAATTGAA
32559 ATATAATATTTTTTAATTT
1 ATATAATA-TTTTT-ATTT
*
32578 ATATATTATTTTTATTT
1 ATATAATATTTTTATTT
32595 ATATAAT
1 ATATAAT
32602 TACATTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 10 0.45
18 5 0.23
19 7 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATATAATATTTTTATTT
Found at i:33866 original size:15 final size:15
Alignment explanation
Indices: 33832--33869 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
33822 TAGGATTAAA
33832 AAAATTTATAAATATT
1 AAAATTT-TAAATATT
*
33848 -AAATTTTAAATTTT
1 AAAATTTTAAATATT
33862 AAAATTTT
1 AAAATTTT
33870 TTAAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAAATTTTAAATATT
Found at i:35518 original size:2 final size:2
Alignment explanation
Indices: 35511--35551 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
35501 ATATTACATT
35511 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35552 GTAAACACAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36457 original size:20 final size:19
Alignment explanation
Indices: 36423--36465 Score: 52
Period size: 22 Copynumber: 2.2 Consensus size: 19
36413 TAAATTAGTT
36423 AAAAATTTTAAAAATATTATAA
1 AAAAATTTT-AAAAT-TT-TAA
36445 AAAAATTTT-AAATTTTAA
1 AAAAATTTTAAAATTTTAA
36463 AAA
1 AAA
36466 TGAATGAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.29
19 2 0.10
20 4 0.19
22 9 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTTTAAAATTTTAA
Found at i:36857 original size:23 final size:22
Alignment explanation
Indices: 36829--36872 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
36819 CGCCCTTAAT
36829 TTTAAATTTATTT-TAATAATTTA
1 TTTAAATTT-TTTATAA-AATTTA
36852 TTTAAATTTTTTATAAAATTT
1 TTTAAATTTTTTATAAAATTT
36873 TTAATTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTAAATTTTTTATAAAATTTA
Found at i:37731 original size:12 final size:12
Alignment explanation
Indices: 37714--37752 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
37704 ATAAAATAAT
*
37714 AATGGCAATGGC
1 AATGGCAATGGA
37726 AATGGCAATGGA
1 AATGGCAATGGA
**
37738 AATGAAAATGGA
1 AATGGCAATGGA
37750 AAT
1 AAT
37753 TGAAATGCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.28, T:0.18
Consensus pattern (12 bp):
AATGGCAATGGA
Found at i:40534 original size:13 final size:13
Alignment explanation
Indices: 40516--40541 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40506 TACACAAAGT
40516 ATGTATCGATACA
1 ATGTATCGATACA
40529 ATGTATCGATACA
1 ATGTATCGATACA
40542 CAAAAAAATT
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:40560 original size:34 final size:32
Alignment explanation
Indices: 40498--40562 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
40488 TAGCCAAACT
**
40498 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
40530 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
40563 TTGATTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:44638 original size:15 final size:15
Alignment explanation
Indices: 44618--44648 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
44608 TAAAAATGTC
*
44618 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
44633 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
44648 C
1 C
44649 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:46747 original size:13 final size:13
Alignment explanation
Indices: 46729--46766 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
46719 CATTTTTCTT
*
46729 TGTATCGATATAA
1 TGTATCGATACAA
*
46742 TGTATCGATACAC
1 TGTATCGATACAA
46755 TGTATCGATACA
1 TGTATCGATACA
46767 GGGGGATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:46902 original size:21 final size:22
Alignment explanation
Indices: 46878--46918 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
46868 AAATCTTTTG
46878 CAAAATACTT-GTTTTTCATTT
1 CAAAATACTTCGTTTTTCATTT
*
46899 CAAATTACTTCGTTTTTCAT
1 CAAAATACTTCGTTTTTCAT
46919 CAAAACCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (22 bp):
CAAAATACTTCGTTTTTCATTT
Found at i:46921 original size:20 final size:20
Alignment explanation
Indices: 46878--46923 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
46868 AAATCTTTTG
46878 CAAAATACTTGTTTTTCATTT
1 CAAAATACTTGTTTTTCA-TT
*
46899 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCATT
46919 CAAAA
1 CAAAA
46924 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCATT
Found at i:49341 original size:13 final size:13
Alignment explanation
Indices: 49323--49348 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49313 TACACAAAGT
49323 ATGTATCGATACA
1 ATGTATCGATACA
49336 ATGTATCGATACA
1 ATGTATCGATACA
49349 CAAAAAAATT
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:49367 original size:34 final size:32
Alignment explanation
Indices: 49305--49369 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
49295 TAGCCAAACT
**
49305 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
49337 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
49370 TTGGTTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:51482 original size:33 final size:35
Alignment explanation
Indices: 51444--51517 Score: 93
Period size: 33 Copynumber: 2.2 Consensus size: 35
51434 AAAATTAAAC
51444 AAAAATAATTAA-TATTTTAA-A-TATA-TTAAAAT
1 AAAAATAATTAATTA-TTTAATATTATATTTAAAAT
*
51476 ATAAAATATTTAATTATTTAATATTATATTTAAAAT
1 A-AAAATAATTAATTATTTAATATTATATTTAAAAT
51512 AAAAAT
1 AAAAAT
51518 TTAACATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
32 1 0.03
33 15 0.42
34 3 0.08
35 9 0.25
36 8 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (35 bp):
AAAAATAATTAATTATTTAATATTATATTTAAAAT
Found at i:51531 original size:14 final size:14
Alignment explanation
Indices: 51445--51537 Score: 62
Period size: 14 Copynumber: 6.3 Consensus size: 14
51435 AAATTAAACA
51445 AAAATAATTAATATTTT
1 AAAAT-ATTAA-A-TTT
*
51462 AAATATATTAAAATAT
1 AAA-ATATT-AAATTT
*
51478 AAAATATTTAATTAT
1 AAAATATTAAATT-T
** *
51493 TTAATATTATATTT
1 AAAATATTAAATTT
*
51507 AAAATA-AAAATTT
1 AAAATATTAAATTT
*
51520 AACATATTAAATTT
1 AAAATATTAAATTT
51534 AAAA
1 AAAA
51538 ATAATAATAT
Statistics
Matches: 58, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
13 10 0.17
14 17 0.29
15 15 0.26
16 5 0.09
17 7 0.12
18 4 0.07
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAATATTAAATTT
Found at i:51571 original size:36 final size:38
Alignment explanation
Indices: 51518--51607 Score: 102
Period size: 38 Copynumber: 2.4 Consensus size: 38
51508 AAATAAAAAT
51518 TTAACATATTA-A-ATTT-AAAAATAATA-A-TATCATAA
1 TTAA-ATATTATATATTTAAAAAATAATATATTAT-ATAA
*
51553 TTAAATATTATATATTTAAAAAATAATATATTATATAT
1 TTAAATATTATATATTTAAAAAATAATATATTATATAA
51591 TATAAATATT-TATATTT
1 T-TAAATATTATATATTT
51608 TATATATAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
34 6 0.12
35 5 0.10
36 4 0.08
37 10 0.21
38 12 0.25
39 11 0.23
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (38 bp):
TTAAATATTATATATTTAAAAAATAATATATTATATAA
Found at i:51584 original size:23 final size:24
Alignment explanation
Indices: 51557--51614 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
51547 TCATAATTAA
51557 ATATTATATATT-TAAAAAATAAT
1 ATATTATATATTATAAAAAATAAT
* * *
51580 ATATTATATATTATAAATATTTAT
1 ATATTATATATTATAAAAAATAAT
*
51604 ATTTTATATAT
1 ATATTATATAT
51615 AAAAATATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 12 0.40
24 18 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATATTATATATTATAAAAAATAAT
Found at i:51603 original size:17 final size:18
Alignment explanation
Indices: 51577--51611 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
51567 TTTAAAAAAT
51577 AATATATTATATATTATA
1 AATATATTATATATTATA
*
51595 AATAT-TTATATTTTATA
1 AATATATTATATATTATA
51612 TATAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATATATTATATATTATA
Found at i:54373 original size:12 final size:12
Alignment explanation
Indices: 54356--54380 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54346 AATAATCATC
54356 ATAATGACAAGT
1 ATAATGACAAGT
54368 ATAATGACAAGT
1 ATAATGACAAGT
54380 A
1 A
54381 AAAGAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (12 bp):
ATAATGACAAGT
Found at i:56082 original size:23 final size:24
Alignment explanation
Indices: 56034--56083 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 24
56024 TATTTTTTTA
* *
56034 TTTTTTAAAACAAATAAAGATCAT
1 TTTTTTAAAACAAATAAACATAAT
*
56058 TTTTTTAAAA-AAA-AAACATAAA
1 TTTTTTAAAACAAATAAACATAAT
56080 TTTT
1 TTTT
56084 GAACTTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 10 0.43
23 3 0.13
24 10 0.43
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (24 bp):
TTTTTTAAAACAAATAAACATAAT
Found at i:56585 original size:35 final size:35
Alignment explanation
Indices: 56539--56613 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
56529 AAAAATGAAC
56539 GTGGCAAAGTGGTTAGTGGTTGTTTTCCATTATGG
1 GTGGCAAAGTGGTTAGTGGTTGTTTTCCATTATGG
56574 GTGGCAAAGTGGTTAGTGGTTGTTTTCCATTATGG
1 GTGGCAAAGTGGTTAGTGGTTGTTTTCCATTATGG
56609 GTGGC
1 GTGGC
56614 CTGGGATTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.16, C:0.09, G:0.36, T:0.39
Consensus pattern (35 bp):
GTGGCAAAGTGGTTAGTGGTTGTTTTCCATTATGG
Found at i:56669 original size:17 final size:17
Alignment explanation
Indices: 56647--56682 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
56637 CATTTCATAT
* *
56647 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTCTTTCTTC
56664 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
56681 TT
1 TT
56683 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:57642 original size:17 final size:17
Alignment explanation
Indices: 57622--57668 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
57612 ATTTTCTTAG
57622 TATTATAATTAATATAT
1 TATTATAATTAATATAT
57639 TATTAT--TT-ATA-AT
1 TATTATAATTAATATAT
*
57652 T-TTATAACTAATATAT
1 TATTATAATTAATATAT
57668 T
1 T
57669 GATGAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 9
0.71 0.03 0.26
Matches are distributed among these distances:
12 4 0.16
13 3 0.12
14 4 0.16
15 5 0.20
16 3 0.12
17 6 0.24
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTATAATTAATATAT
Found at i:60207 original size:56 final size:56
Alignment explanation
Indices: 60140--60253 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
60130 ACTTACCAAT
60140 CATTTTTAACATAAAAGATTTATGGGAAGTAAATATAATTCTTAGCATTAGGATTA
1 CATTTTTAACATAAAAGATTTATGGGAAGTAAATATAATTCTTAGCATTAGGATTA
60196 CATTTTTAACATAAAAGATTTATGGGAAGTAAATATAATTCTTAGCATTAGGATTA
1 CATTTTTAACATAAAAGATTTATGGGAAGTAAATATAATTCTTAGCATTAGGATTA
60252 CA
1 CA
60254 AGGACTTCAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (56 bp):
CATTTTTAACATAAAAGATTTATGGGAAGTAAATATAATTCTTAGCATTAGGATTA
Found at i:61637 original size:13 final size:13
Alignment explanation
Indices: 61619--61643 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61609 ACAATAAACA
61619 TGTATCGATACAC
1 TGTATCGATACAC
61632 TGTATCGATACA
1 TGTATCGATACA
61644 AAGCATAATG
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:63125 original size:13 final size:13
Alignment explanation
Indices: 63107--63131 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63097 ATTACTCACA
63107 TGTATCGATACAT
1 TGTATCGATACAT
63120 TGTATCGATACA
1 TGTATCGATACA
63132 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:63268 original size:52 final size:52
Alignment explanation
Indices: 63140--63259 Score: 222
Period size: 52 Copynumber: 2.3 Consensus size: 52
63130 CACTGATCTT
*
63140 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
63192 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
63244 TGTATCGATACATGCA
1 TGTATCGATACATGCA
63260 AATAAATTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:71530 original size:14 final size:14
Alignment explanation
Indices: 71511--71539 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
71501 GTGTGGCCAC
71511 GTTTATGGCATAAT
1 GTTTATGGCATAAT
71525 GTTTATGGCATAAT
1 GTTTATGGCATAAT
71539 G
1 G
71540 AACACGTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (14 bp):
GTTTATGGCATAAT
Found at i:71913 original size:15 final size:15
Alignment explanation
Indices: 71881--71931 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
71871 GAGAGTTTCC
*
71881 TTTTCTATTTCGACAA
1 TTTTCT-TTTCAACAA
*
71897 TTTTCTTTTCAAGAA
1 TTTTCTTTTCAACAA
*
71912 TTTTATTTTCAACAAA
1 TTTTCTTTTCAAC-AA
71928 TTTT
1 TTTT
71932 GATTTATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 18 0.60
16 12 0.40
ACGTcount: A:0.27, C:0.14, G:0.04, T:0.55
Consensus pattern (15 bp):
TTTTCTTTTCAACAA
Found at i:74006 original size:13 final size:13
Alignment explanation
Indices: 73988--74018 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
73978 ACTTTTCACT
73988 ATGTATCGATACA
1 ATGTATCGATACA
74001 ATGTATCGATACA
1 ATGTATCGATACA
74014 ATGTA
1 ATGTA
74019 CCATGTATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:74109 original size:19 final size:20
Alignment explanation
Indices: 74085--74135 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
74075 CAATTGAGTG
*
74085 TGTATCGATACAATG-A-ACA
1 TGTATCGATACAAAGCATA-A
74104 TGTATCGATACAAAGCATAA
1 TGTATCGATACAAAGCATAA
74124 TGTATCGATACA
1 TGTATCGATACA
74136 TCTGGATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 14 0.48
20 14 0.48
21 1 0.03
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (20 bp):
TGTATCGATACAAAGCATAA
Found at i:76269 original size:43 final size:42
Alignment explanation
Indices: 76208--76292 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 42
76198 GATAAAGCTA
* *
76208 TTCAATTAATTGAAAATATTTTTATAATAAGAAATTGAAATTC
1 TTCAATTAATTGAAAATATTTATATAACAAG-AATTGAAATTC
*
76251 TTCAATTAATTGATAATATTTATATAACAAGAATTGAAATTC
1 TTCAATTAATTGAAAATATTTATATAACAAGAATTGAAATTC
76293 ATAATATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 11 0.28
43 28 0.72
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (42 bp):
TTCAATTAATTGAAAATATTTATATAACAAGAATTGAAATTC
Found at i:77692 original size:57 final size:57
Alignment explanation
Indices: 77625--77741 Score: 216
Period size: 57 Copynumber: 2.1 Consensus size: 57
77615 TCCTTTGCTC
77625 TTGGAAGTGTTGGAAAAACTTATTTATAGCTTGAGATTGAATTATGATTATTAGAAA
1 TTGGAAGTGTTGGAAAAACTTATTTATAGCTTGAGATTGAATTATGATTATTAGAAA
* *
77682 TTGGAAGTGTTGGAAAAACTTATTTATGGCTTGAGATTGAGTTATGATTATTAGAAA
1 TTGGAAGTGTTGGAAAAACTTATTTATAGCTTGAGATTGAATTATGATTATTAGAAA
77739 TTG
1 TTG
77742 ATTAAGATGG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.34, C:0.03, G:0.23, T:0.39
Consensus pattern (57 bp):
TTGGAAGTGTTGGAAAAACTTATTTATAGCTTGAGATTGAATTATGATTATTAGAAA
Found at i:78720 original size:21 final size:21
Alignment explanation
Indices: 78696--78739 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
78686 AGTTTGGCTA
*
78696 AACCTTAAATAATTGAGGTTC
1 AACCTCAAATAATTGAGGTTC
* *
78717 AACCTCAATTATTTGAGGTTC
1 AACCTCAAATAATTGAGGTTC
78738 AA
1 AA
78740 ATAAAATAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (21 bp):
AACCTCAAATAATTGAGGTTC
Found at i:80961 original size:31 final size:31
Alignment explanation
Indices: 80925--80991 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
80915 ACGGAAATAT
*
80925 TTAAACCCAATGAAATTTGCATGAGATAAGG
1 TTAAACCCAATGAAATTTGCATGAGATAACG
80956 TTAAACCCAATGAAATTTGCATGAGATAACG
1 TTAAACCCAATGAAATTTGCATGAGATAACG
80987 TTAAA
1 TTAAA
80992 TATGCACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.27
Consensus pattern (31 bp):
TTAAACCCAATGAAATTTGCATGAGATAACG
Found at i:82571 original size:40 final size:39
Alignment explanation
Indices: 82523--82619 Score: 115
Period size: 40 Copynumber: 2.5 Consensus size: 39
82513 TTGATTATAG
*
82523 GAGCTTTTAATTTTAAAGTTGTAGACCCTCTAAATT-GCAA
1 GAGCTTTTAATTTTAAAGTTATAGACCCTC-AAATTAG-AA
* * * * *
82563 GAGCTTTTAATTTTGAAGTTATGGAGCCTCCAATTAGAG
1 GAGCTTTTAATTTTAAAGTTATAGACCCTCAAATTAGAA
82602 GAGCTTTTAATTTTAAAG
1 GAGCTTTTAATTTTAAAG
82620 CTATGAAACC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
39 22 0.45
40 27 0.55
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (39 bp):
GAGCTTTTAATTTTAAAGTTATAGACCCTCAAATTAGAA
Found at i:82642 original size:39 final size:38
Alignment explanation
Indices: 82521--82658 Score: 127
Period size: 39 Copynumber: 3.6 Consensus size: 38
82511 CTTTGATTAT
* *
82521 AGGAGCTTTTAATTTTAAAGT-TGTAGACCCTCTAAATTGC
1 AGGAGCTTTTAATTTTAAAGTATG-A-AACCTCT-AATTGG
* * * * * *
82561 AAGAGCTTTTAATTTTGAAGTTATGGAGCCTCCAATTAG
1 AGGAGCTTTTAATTTTAAAG-TATGAAACCTCTAATTGG
82600 AGGAGCTTTTAATTTTAAAGCTATGAAACCTCTAATTGG
1 AGGAGCTTTTAATTTTAAAG-TATGAAACCTCTAATTGG
**
82639 AGGATATTTTAA-TTTAAAGT
1 AGGAGCTTTTAATTTTAAAGT
82659 TGTCAAGACT
Statistics
Matches: 80, Mismatches: 16, Indels: 7
0.78 0.16 0.07
Matches are distributed among these distances:
37 1 0.01
38 7 0.09
39 46 0.57
40 23 0.29
41 1 0.01
42 2 0.03
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.38
Consensus pattern (38 bp):
AGGAGCTTTTAATTTTAAAGTATGAAACCTCTAATTGG
Found at i:82820 original size:39 final size:38
Alignment explanation
Indices: 82723--82836 Score: 99
Period size: 39 Copynumber: 2.9 Consensus size: 38
82713 TAAAGGAATT
** * * *
82723 TTTAATTTTAAAATTGTATAGC-CTATTATTAGAGGAGCT
1 TTTAATTTTAAAATTGTGGAGCTCTA--ATGAGAAGAGCA
*
82762 TTTAATTTTAATGAA--GTGGAGCATCTGATGAGAAGAGCA
1 TTTAATTTTAA--AATTGTGGAGC-TCTAATGAGAAGAGCA
82801 TTTAATTTTAAAATTGTGGAGGCTCTAATGAGAAGA
1 TTTAATTTTAAAATTGTGGA-GCTCTAATGAGAAGA
82837 TTTTTTTTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
37 2 0.03
39 53 0.87
40 2 0.03
41 4 0.07
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.37
Consensus pattern (38 bp):
TTTAATTTTAAAATTGTGGAGCTCTAATGAGAAGAGCA
Found at i:84498 original size:14 final size:13
Alignment explanation
Indices: 84466--84495 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
84456 CATTTTAAGG
84466 AAAAGAGGAAAAA
1 AAAAGAGGAAAAA
84479 AAAAGAGGAAAAA
1 AAAAGAGGAAAAA
84492 AAAA
1 AAAA
84496 AGAAATTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAGAGGAAAAA
Found at i:91772 original size:2 final size:2
Alignment explanation
Indices: 91765--91791 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
91755 AAACACCATA
91765 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
91792 AGTGAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:94975 original size:12 final size:11
Alignment explanation
Indices: 94953--95024 Score: 53
Period size: 12 Copynumber: 6.5 Consensus size: 11
94943 AGAGAAAGAA
*
94953 GAGAGAGGAGG
1 GAGATAGGAGG
94964 GATGATAGGAGG
1 GA-GATAGGAGG
*
94976 AGAGACAGGA--
1 -GAGATAGGAGG
*
94986 GAGATAGTA--
1 GAGATAGGAGG
94995 GAGATAGGAGG
1 GAGATAGGAGG
95006 GATGATAGGAGG
1 GA-GATAGGAGG
95018 AGAGATA
1 -GAGATA
95025 ATAGAGAGAG
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
9 15 0.30
11 4 0.08
12 27 0.54
13 4 0.08
ACGTcount: A:0.40, C:0.01, G:0.47, T:0.11
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:95004 original size:42 final size:42
Alignment explanation
Indices: 94943--95022 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
94933 TAGCCCTCAA
94943 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* * *
94985 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGA
1 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGA
95023 TAATAGAGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.44, C:0.01, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:95019 original size:33 final size:33
Alignment explanation
Indices: 94982--95052 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
94972 GAGGAGAGAC
* * *
94982 AGGAGAGATAGTAGAGATAGGAGGGATGATAGG
1 AGGAGAGATAATAGAGAGAGGAGGGATGACAGG
95015 AGGAGAGATAATAGAGAGAGGAGGGATGACAGG
1 AGGAGAGATAATAGAGAGAGGAGGGATGACAGG
95048 AGGAG
1 AGGAG
95053 GAGAGAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.41, C:0.01, G:0.46, T:0.11
Consensus pattern (33 bp):
AGGAGAGATAATAGAGAGAGGAGGGATGACAGG
Found at i:95031 original size:42 final size:42
Alignment explanation
Indices: 94943--95031 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
94933 TAGCCCTCAA
*
94943 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAAG
* * * * *
94985 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATAAT
1 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAAG
95027 AGAGA
1 AGAGA
95032 GAGGAGGGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.45, C:0.01, G:0.44, T:0.10
Consensus pattern (42 bp):
AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAAG
Found at i:100359 original size:25 final size:25
Alignment explanation
Indices: 100308--100368 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
100298 ATTTATATTT
*
100308 AATAAATATTTAAACATAAATATAA
1 AATAAATATTTAAACATAAATAAAA
* *
100333 AATATAATTTTTAAA-ATACATAAAAA
1 AATA-AATATTTAAACATAAAT-AAAA
100359 AATTAAATAT
1 AA-TAAATAT
100369 ATTTGTTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 9 0.31
26 18 0.62
27 2 0.07
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (25 bp):
AATAAATATTTAAACATAAATAAAA
Found at i:101241 original size:15 final size:15
Alignment explanation
Indices: 101199--101248 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
101189 AGAAAAATAT
* *
101199 TAAATTTTTAAAGAT
1 TAAATTTTTAAAAAA
101214 TAAATTTTT-AAAAA
1 TAAATTTTTAAAAAA
*
101228 TATATTTTTAAAAAA
1 TAAATTTTTAAAAAA
101243 TAAATT
1 TAAATT
101249 AAAAAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
TAAATTTTTAAAAAA
Found at i:103049 original size:17 final size:17
Alignment explanation
Indices: 103027--103078 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
103017 TTTTATGATT
*
103027 ATAAAAATATAAATATA
1 ATAAAATTATAAATATA
* *
103044 ATAAAATTATTAGTATA
1 ATAAAATTATAAATATA
* *
103061 TTAAAATTTTAAATATA
1 ATAAAATTATAAATATA
103078 A
1 A
103079 ATTTAATATA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
ATAAAATTATAAATATA
Found at i:104499 original size:18 final size:18
Alignment explanation
Indices: 104476--104510 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
104466 AAAAAAATAT
104476 AATTTATA-ATTATATTAA
1 AATTTATATATTA-ATTAA
104494 AATTTATATATTAATTA
1 AATTTATATATTAATTA
104511 TTGATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTTATATATTAATTAA
Found at i:104505 original size:14 final size:14
Alignment explanation
Indices: 104486--104532 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
104476 AATTTATAAT
104486 TATATTAAAATTTA
1 TATATTAAAATTTA
* *
104500 TATATTAATTATTGA
1 TATATTAA-AATTTA
*
104515 TATATTAAATTTTA
1 TATATTAAAATTTA
104529 TATA
1 TATA
104533 AAAATAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (14 bp):
TATATTAAAATTTA
Found at i:110462 original size:50 final size:50
Alignment explanation
Indices: 110338--110542 Score: 286
Period size: 50 Copynumber: 4.1 Consensus size: 50
110328 AGTTGCTTAG
* *
110338 AGTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAA-AAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGCGAAGAAT
* * * *
110387 AGTCAACAACTGCGACCACTTCTCTCGATTGTCAAAGGTTGGCGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGCGAAGAAT
* * *
110437 AGTCAATAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGACGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGCGAAGAAT
* * * *
110487 AGTCAACAATTACGGCCATCGCTCTCGATTGTCAAAGGTTAGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGCGAAGAAT
110537 AGTCAA
1 AGTCAA
110543 ATCACTTTGT
Statistics
Matches: 135, Mismatches: 20, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
49 40 0.30
50 95 0.70
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (50 bp):
AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGCGAAGAAT
Found at i:113085 original size:20 final size:20
Alignment explanation
Indices: 113057--113131 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
113047 TTTTACCCTG
113057 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
113077 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
113097 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
113117 ATGTATCGATACATT
1 ATGTATCGATACATT
113132 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:113124 original size:40 final size:39
Alignment explanation
Indices: 113057--113134 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
113047 TTTTACCCTG
* *
113057 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
113097 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
113135 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:118483 original size:50 final size:50
Alignment explanation
Indices: 118424--118728 Score: 418
Period size: 50 Copynumber: 6.1 Consensus size: 50
118414 AGTTGCTTAA
* * *
118424 AGTCAACAATTACGACCACCTCTCTCTATTGTCAAAGTTTGGTGAAGAAT
1 AGTCAACAATTATGACCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
*
118474 AGTCAACAATTATGACCACCTCTCTTGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGACCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* *
118524 AGTCAACAATTAT-AGCCATCTCTCTCGATTGTCAAAAGTTGGTGAAGAAT
1 AGTCAACAATTATGA-CCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* ** *
118574 AGCCAACAATTATGGTCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAAT
1 AGTCAACAATTATGACCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
** * *
118624 AGTCAACAATTATGGTCACCT-TCTTGATTGTCAAAGGTTGGTGAATAAT
1 AGTCAACAATTATGACCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * *
118673 AG-CTAATAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTC-AACAATTATGACCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
118723 AGTCAA
1 AGTCAA
118729 ATCACTTTGC
Statistics
Matches: 230, Mismatches: 20, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
48 1 0.00
49 42 0.18
50 186 0.81
51 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (50 bp):
AGTCAACAATTATGACCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
Found at i:118717 original size:149 final size:150
Alignment explanation
Indices: 118440--118724 Score: 450
Period size: 149 Copynumber: 1.9 Consensus size: 150
118430 CAATTACGAC
*
118440 CACCTCTCTCTATTGTCAAAGTTTGGTGAAGAATAGTCAACAATTATGACCACCTCTCTTGATTG
1 CACCTCTCTCGATTGTCAAAGTTTGGTGAAGAATAGTCAACAATTATGACCACCTCTCTTGATTG
* *
118505 TCAAAGGTTGGTGAAGAATAGTCAACAATTATAGCCATCTCTCTCGATTGTCAAAAGTTGGTGAA
66 TCAAAGGTTGGTGAAGAATAGTCAACAATTACAGCCACCTCTCTCGATTGTCAAAAGTTGGTGAA
118570 GAATAGCCAACAATTATGGT
131 GAATAGCCAACAATTATGGT
**
118590 CACCTCTCTCGATTGTCAAAAG-TTGGTGAAGAATAGTCAACAATTATGGTCACCT-TCTTGATT
1 CACCTCTCTCGATTGTC-AAAGTTTGGTGAAGAATAGTCAACAATTATGACCACCTCTCTTGATT
* * * *
118653 GTCAAAGGTTGGTGAATAATAG-CTAATAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTG
65 GTCAAAGGTTGGTGAAGAATAGTC-AACAATTACAGCCACCTCTCTCGATTGTCAAAAGTTGGTG
118717 AAGAATAG
129 AAGAATAG
118725 TCAAATCACT
Statistics
Matches: 124, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
148 1 0.01
149 72 0.58
150 47 0.38
151 4 0.03
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (150 bp):
CACCTCTCTCGATTGTCAAAGTTTGGTGAAGAATAGTCAACAATTATGACCACCTCTCTTGATTG
TCAAAGGTTGGTGAAGAATAGTCAACAATTACAGCCACCTCTCTCGATTGTCAAAAGTTGGTGAA
GAATAGCCAACAATTATGGT
Found at i:120375 original size:50 final size:50
Alignment explanation
Indices: 120295--120598 Score: 376
Period size: 50 Copynumber: 6.1 Consensus size: 50
120285 ATATTTAGAA
* * *
120295 TCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGTGAACAATAG
1 TCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
* *
120345 TTAAAAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
1 TCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
* * * * *
120395 GCAACAATTGCGGCCACCTCTCTCGATTGTAAAAGGTTAGTGAAAAATAG
1 TCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
* ** *
120445 -CTAACAATTACGGTCACCTCTCTCGATTGTCAAAATTTGGTGAAAAATAG
1 TC-AACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
** * * *
120495 TCAACAATTATAGTCACCTCTCTCGATTGTTAAAGGTTGGTAAAGAATAG
1 TCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
* * * * *
120545 TCAATAATTACGACCACTTCTCTCTATTGTCAACGGTTGGTGAAGAATAG
1 TCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
120595 TCAA
1 TCAA
120599 ATCACTTTGC
Statistics
Matches: 217, Mismatches: 35, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
49 1 0.00
50 215 0.99
51 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (50 bp):
TCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
Found at i:126000 original size:2 final size:2
Alignment explanation
Indices: 125995--126041 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
125985 TGTGTGTGTG
125995 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
126037 TA TA T
1 TA TA T
126042 GAAACTTCTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:128217 original size:13 final size:13
Alignment explanation
Indices: 128176--128224 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
128166 CCGTTACAAG
128176 CAATGTATCGATA
1 CAATGTATCGATA
128189 CAAT-T-TC-AT-
1 CAATGTATCGATA
128198 C-ATGTATCGATA
1 CAATGTATCGATA
128210 CAATGTATCGATA
1 CAATGTATCGATA
128223 CA
1 CA
128225 TTGTCCTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 2 0.06
9 2 0.06
10 4 0.13
11 4 0.13
12 2 0.06
13 17 0.55
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:128217 original size:34 final size:33
Alignment explanation
Indices: 128176--128245 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
128166 CCGTTACAAG
128176 CAATGTATCGATACAATT-TCATCATGTATCGATA
1 CAATGTATCGATAC-ATTGTCAT-ATGTATCGATA
* *
128210 CAATGTATCGATACATTGTCCTATGTATTGATA
1 CAATGTATCGATACATTGTCATATGTATCGATA
128243 CAA
1 CAA
128246 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 16 0.48
34 17 0.52
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (33 bp):
CAATGTATCGATACATTGTCATATGTATCGATA
Found at i:128312 original size:13 final size:13
Alignment explanation
Indices: 128294--128320 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
128284 TACAATGGGC
128294 ATGTATCGATACA
1 ATGTATCGATACA
128307 ATGTATCGATACA
1 ATGTATCGATACA
128320 A
1 A
128321 AGCATAATGT
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:130786 original size:13 final size:13
Alignment explanation
Indices: 130768--130796 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
130758 AAATAGTACC
130768 CAATGTATCGATA
1 CAATGTATCGATA
130781 CAATGTATCGATA
1 CAATGTATCGATA
130794 CAA
1 CAA
130797 GGAATGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:134743 original size:21 final size:21
Alignment explanation
Indices: 134710--134749 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
134700 CTACAAGTTT
* *
134710 TTATTTCTCTTAGCTAATTCA
1 TTATTTCTATTAGCCAATTCA
*
134731 TTATTTTTATTAGCCAATT
1 TTATTTCTATTAGCCAATT
134750 ATTTAATATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.15, G:0.05, T:0.55
Consensus pattern (21 bp):
TTATTTCTATTAGCCAATTCA
Found at i:137056 original size:63 final size:63
Alignment explanation
Indices: 136957--137095 Score: 224
Period size: 63 Copynumber: 2.2 Consensus size: 63
136947 TATCGATATA
* * *
136957 ATGTATAGATACATTGTCCCATGTATCGATACAAACAGTGGTAGGGTAGCTATTACCAATCTT
1 ATGTATCGATACATTGTCCCATGTATCGATACAAACAGTGGTAGGGTAGCTACTACCAATCTC
* * *
137020 ATGTATCGATACATTGTCCCATGTATTGATACAAACAGTGGTAGGGTAGTTACTGCCAATCTC
1 ATGTATCGATACATTGTCCCATGTATCGATACAAACAGTGGTAGGGTAGCTACTACCAATCTC
137083 ATGTATCGATACA
1 ATGTATCGATACA
137096 ATGTATCGAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 70 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (63 bp):
ATGTATCGATACATTGTCCCATGTATCGATACAAACAGTGGTAGGGTAGCTACTACCAATCTC
Found at i:137101 original size:13 final size:13
Alignment explanation
Indices: 137083--137109 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
137073 TGCCAATCTC
137083 ATGTATCGATACA
1 ATGTATCGATACA
137096 ATGTATCGATACA
1 ATGTATCGATACA
137109 A
1 A
137110 AGCATAATGT
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:138699 original size:20 final size:19
Alignment explanation
Indices: 138656--138706 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
138646 TAATTCAGTG
* *
138656 TGTATCGATACCAGGAACA
1 TGTATCGATACAAGCAACA
*
138675 TGTATCGATACTAAGCAATA
1 TGTATCGATAC-AAGCAACA
138695 TGTATCGATACA
1 TGTATCGATACA
138707 TCTAGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (19 bp):
TGTATCGATACAAGCAACA
Found at i:148601 original size:22 final size:22
Alignment explanation
Indices: 148567--148610 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
148557 ATATCTCTAA
*
148567 TTTGATTTCATAAAT-TTAATT
1 TTTGATTTAATAAATCTTAATT
*
148588 TTTGTATTTAATAATTCTTAATT
1 TTTG-ATTTAATAAATCTTAATT
148611 GAACTAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (22 bp):
TTTGATTTAATAAATCTTAATT
Found at i:148651 original size:53 final size:52
Alignment explanation
Indices: 148587--148716 Score: 147
Period size: 53 Copynumber: 2.4 Consensus size: 52
148577 TAAATTTAAT
* *
148587 TTTTGTATTTAATAATTCTTAATTGAACTAATTCAATTAAATCTTTCATA-T-TAC
1 TTTT-TATTTAATAAATCAT-ATTGAA-T-ATTCAATTAAATCTTTCATATTATAC
* * *
148641 TTTTTATTTAATTAAATCATATTTAATTTTTAATTAAATCTTTCATATTATAC
1 TTTTTATTTAA-TAAATCATATTGAATATTCAATTAAATCTTTCATATTATAC
148694 TTTTTATTTAATTAAATCATATT
1 TTTTTATTTAA-TAAATCATATT
148717 TAATTAAATC
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
51 18 0.26
52 2 0.03
53 38 0.56
54 10 0.15
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (52 bp):
TTTTTATTTAATAAATCATATTGAATATTCAATTAAATCTTTCATATTATAC
Found at i:148679 original size:51 final size:53
Alignment explanation
Indices: 148621--148721 Score: 188
Period size: 53 Copynumber: 1.9 Consensus size: 53
148611 GAACTAATTC
148621 AATTAAATCTTTCATA-T-TACTTTTTATTTAATTAAATCATATTTAATTTTT
1 AATTAAATCTTTCATATTATACTTTTTATTTAATTAAATCATATTTAATTTTT
148672 AATTAAATCTTTCATATTATACTTTTTATTTAATTAAATCATATTTAATT
1 AATTAAATCTTTCATATTATACTTTTTATTTAATTAAATCATATTTAATT
148722 AAATCCTAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
51 16 0.33
52 1 0.02
53 31 0.65
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (53 bp):
AATTAAATCTTTCATATTATACTTTTTATTTAATTAAATCATATTTAATTTTT
Found at i:148713 original size:27 final size:26
Alignment explanation
Indices: 148632--148718 Score: 104
Period size: 26 Copynumber: 3.3 Consensus size: 26
148622 ATTAAATCTT
148632 TCATA-TTACTTTTTATTTAATTAAA
1 TCATATTTACTTTTTATTTAATTAAA
* * * ***
148657 TCATATTTAATTTTTAATTAAATCTT
1 TCATATTTACTTTTTATTTAATTAAA
148683 TCATATTATACTTTTTATTTAATTAAA
1 TCATATT-TACTTTTTATTTAATTAAA
148710 TCATATTTA
1 TCATATTTA
148719 ATTAAATCCT
Statistics
Matches: 48, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
25 5 0.10
26 23 0.48
27 20 0.42
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (26 bp):
TCATATTTACTTTTTATTTAATTAAA
Found at i:148718 original size:15 final size:15
Alignment explanation
Indices: 148698--148726 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
148688 TTATACTTTT
148698 TATTTAATTAAATCA
1 TATTTAATTAAATCA
148713 TATTTAATTAAATC
1 TATTTAATTAAATC
148727 CTAGATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTTAATTAAATCA
Found at i:153285 original size:16 final size:17
Alignment explanation
Indices: 153266--153300 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
153256 CAAAATTCTC
153266 AAAAGAG-AAAAAGAAA
1 AAAAGAGAAAAAAGAAA
*
153282 AAAAGGGAAAAAAGAAA
1 AAAAGAGAAAAAAGAAA
153299 AA
1 AA
153301 TTAGGTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAAGAGAAAAAAGAAA
Found at i:154360 original size:20 final size:21
Alignment explanation
Indices: 154308--154361 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
154298 TTCATTATTA
* *
154308 TATTTTAA-ATTAATATATTT
1 TATTTTAATATTTATATAATT
*
154328 TATTTTATTTATTTATATAATT
1 TATTTTA-ATATTTATATAATT
154350 T-TTTTAATATTT
1 TATTTTAATATTT
154362 TTTAAATTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 12 0.43
21 5 0.18
22 11 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTTTAATATTTATATAATT
Found at i:155720 original size:15 final size:16
Alignment explanation
Indices: 155700--155732 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
155690 GTTTTCCTTC
155700 TTATAATATAAT-ATA
1 TTATAATATAATAATA
155715 TTATAATATAATAATA
1 TTATAATATAATAATA
155731 TT
1 TT
155733 CCCTAAAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATAATATAATAATA
Found at i:156687 original size:16 final size:16
Alignment explanation
Indices: 156666--156696 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
156656 GATAAATCAC
156666 TAAGATTTATATTTTA
1 TAAGATTTATATTTTA
*
156682 TAAGATTTTTATTTT
1 TAAGATTTATATTTT
156697 TTATTAGTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (16 bp):
TAAGATTTATATTTTA
Found at i:158453 original size:20 final size:20
Alignment explanation
Indices: 158424--158499 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
158414 TTTTTACCTA
158424 GATGTATCGATACATTTTTC
1 GATGTATCGATACATTTTTC
* * *
158444 GATATATCGATACATGTAT-
1 GATGTATCGATACATTTTTC
* *
158463 GAATGTATCGATATATTCTTC
1 G-ATGTATCGATACATTTTTC
*
158484 AATGTATCGATACATT
1 GATGTATCGATACATT
158500 ATATCTTTTT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 1 0.02
20 43 0.98
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (20 bp):
GATGTATCGATACATTTTTC
Found at i:158532 original size:21 final size:21
Alignment explanation
Indices: 158508--158570 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
158498 TTATATCTTT
158508 TTACCTAGATGTATCGATACA
1 TTACCTAGATGTATCGATACA
158529 TTACCTAGATGTATCGATACA
1 TTACCTAGATGTATCGATACA
*
158550 TTGA-ATA-ATGTATCGATACA
1 TT-ACCTAGATGTATCGATACA
158570 T
1 T
158571 CTAGTTAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
20 14 0.35
21 25 0.62
22 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (21 bp):
TTACCTAGATGTATCGATACA
Done.